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Created June 17, 2024 21:32
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Logfiles for GitLab pipeline https://bbpgitlab.epfl.ch/hpc/cellular/nrn/-/pipelines/217482 (:white_check_mark:) running on GitHub PR neuronsimulator/nrn#2909.
Running with gitlab-runner 15.5.0 (0d4137b8)
 on BB5 map runner pnPo3yJy
section_start:1718655568:resolve_secrets Resolving secrets
section_end:1718655568:resolve_secrets section_start:1718655568:prepare_executor Preparing the "custom" executor
Using Custom executor with driver BB5 PROD runner v0.0.3...
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor3004598397, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name nrn
Pipeline ID 217482, build ref , job ID 1322442
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482, optional exclusive flag , optional cpus per task flag --cpus-per-task=8, optional qos flag , optional reservation flag
A slurm job will be created with name GL_J1322442_PROD_P2160_CP0_C1
Job parameters: memory=160G, cpus_per_task=8, duration=2:00:00, constraint=cpu ntasks=2 account=proj9998 user=bbpcihpcproj12 partition=prod qos= reservation=
Not executing the chown -R
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx]
Submitted batch job 2255978
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=2 --cpus-per-task=8 --mem=160G --job-name=GL_J1322442_PROD_P2160_CP0_C1 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482 --time=2:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482 --ntasks=2 --jobid=2255978 --cpus-per-task=8 --mem=160G
section_end:1718655569:prepare_executor section_start:1718655569:prepare_script Preparing environment
Using git from spack modules
Running on r1i7n21 via bbpv1.epfl.ch...
section_end:1718655573:prepare_script section_start:1718655573:get_sources Getting source from Git repository
Using git from spack modules
Skipping Git repository setup
Skipping Git checkout
Skipping Git submodules setup
section_end:1718655574:get_sources section_start:1718655574:restore_cache Restoring cache
Using git from spack modules
Checking cache for build:neuron:nmodl:intel:legacy-1-non_protected...
Runtime platform  arch=amd64 os=linux pid=149512 revision=58ba2b95 version=14.2.0
cache.zip is up to date 
Successfully extracted cache
section_end:1718655580:restore_cache section_start:1718655580:download_artifacts Downloading artifacts
Using git from spack modules
Downloading artifacts for build:nmodl (1322441)...
Runtime platform  arch=amd64 os=linux pid=149627 revision=58ba2b95 version=14.2.0
Downloading artifacts from coordinator... ok  id=1322441 responseStatus=200 OK token=glcbt-64
section_end:1718655581:download_artifacts section_start:1718655581:step_script Executing "step_script" stage of the job script
WARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426
Using git from spack modules
$ SPACK_BUILD="${PWD}/spack-build"
$ env -0 | sort -z | xargs -0 -L 1 echo > initial_environment.env
$ . ${SPACK_ROOT}/share/spack/setup-env.sh
$ export SPACK_USER_CONFIG_PATH=${PWD}/spack-config
$ mkdir ${SPACK_USER_CONFIG_PATH}
$ cat > ${SPACK_USER_CONFIG_PATH}/config.yaml << END_SCRIPT # collapsed multi-line command
$ spack ${SPACK_EXTRA_FLAGS} config add concretizer:reuse:false
$ spack ${SPACK_EXTRA_FLAGS} config blame config
--- config:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322442/spack-config/config.yaml:2 build_stage:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322442/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322442/spack-build
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322442/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322442/spack-source-cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/config.yaml:2 ccache: True
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:2 install_tree:
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:3 root: $user_cache_path/software
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:4 projections:
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:5 all: install_{compiler.name}-{compiler.version}-{target}/{name}-{version}-{hash:6}
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:7 environments_root: $user_cache_path/environments
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:9 build_jobs: 8
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:18 extensions:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:19 - $spack/bluebrain/spack-scripting
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:37 template_dirs:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:38 - $spack/share/spack/templates
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:41 license_dir: $spack/etc/spack/licenses
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:81 test_stage: $user_cache_path/test
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:94 misc_cache: $user_cache_path/cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:100 connect_timeout: 10
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:105 verify_ssl: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:113 suppress_gpg_warnings: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:119 install_missing_compilers: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:124 checksum: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:129 deprecated: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:134 dirty: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:142 build_language: C
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:151 locks: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:156 url_fetch_method: urllib
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:185 concretizer: clingo
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:192 db_lock_timeout: 60
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:200 package_lock_timeout: null
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:205 shared_linking:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:210 type: rpath
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:216 bind: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:221 allow_sgid: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:227 install_status: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:231 binary_index_ttl: 600
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:233 flags:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:235 keep_werror: none
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:240 aliases:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:241 concretise: concretize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:242 containerise: containerize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:243 rm: remove
_builtin debug: False
$ spack ${SPACK_EXTRA_FLAGS} config blame concretizer
--- concretizer:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322442/spack-config/concretizer.yaml:2 reuse: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:23 targets:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:28 granularity: microarchitectures
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:32 host_compatible: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:38 unify: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:40 duplicates:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:44 strategy: minimal
$ export XDG_CONFIG_HOME=${CI_BUILDS_DIR}/J${CI_JOB_ID}_local_config
$ echo "Configuring git to use CI_JOB_TOKEN to access git@bbpgitlab.epfl.ch (${XDG_CONFIG_HOME})"
Configuring git to use CI_JOB_TOKEN to access git@bbpgitlab.epfl.ch (/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482/J1322442_local_config)
$ mkdir -p "${XDG_CONFIG_HOME}/git"
$ echo -e "[url \"https://gitlab-ci-token:${CI_JOB_TOKEN}@bbpgitlab.epfl.ch/\"]\n insteadOf = git@bbpgitlab.epfl.ch:" > "${XDG_CONFIG_HOME}/git/config"
$ echo -e "[url \"https://gitlab-ci-token:${CI_JOB_TOKEN}@bbpgitlab.epfl.ch/\"]\n insteadOf = ssh://git@bbpgitlab.epfl.ch/" >> "${XDG_CONFIG_HOME}/git/config"
$ cat "${XDG_CONFIG_HOME}/git/config"
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
insteadOf = git@bbpgitlab.epfl.ch:
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
insteadOf = ssh://git@bbpgitlab.epfl.ch/
$ SPACK_FULL_SPEC="${SPACK_PACKAGE}${SPACK_PACKAGE_COMPILER:+%}${SPACK_PACKAGE_COMPILER} ${SPACK_PACKAGE_SPEC} ${SPACK_PACKAGE_DEPENDENCIES} ${SPACK_PACKAGE_DEPENDENCY_ON_PREVIOUS_JOB}"
$ echo "Preparing to install ${SPACK_FULL_SPEC}"
Preparing to install neuron%oneapi ~rx3d~caliper~gpu+coreneuron~legacy-unit~openmp~shared~sympy+tests build_type=FastDebug model_tests=channel-benchmark,olfactory,tqperf-heavy ^/53hy2ex7xntc24cnbuojh6rrc3l2auap
$ if [ ${SPACK_USE_CCACHE+x} ]; then
$ module load unstable ccache
$ export CCACHE_BASEDIR=$(realpath -P ${CI_BUILDS_DIR})
$ echo CCACHE_BASEDIR=${CCACHE_BASEDIR}
CCACHE_BASEDIR=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482
$ export CCACHE_MAXSIZE=512M
$ export CCACHE_DIR="${TMPDIR}/ccache"
$ mkdir -p ${CCACHE_DIR}
$ if [ -f ${CI_PROJECT_DIR}/ccache.tar ]; then
$ tar -C "${CCACHE_DIR}" -xf "${CI_PROJECT_DIR}/ccache.tar"
$ fi
$ ccache --zero-stats
Statistics zeroed
$ ccache --show-stats --verbose
Cache directory: /nvme/bbpcihpcproj12/2255978/ccache
Config file: /nvme/bbpcihpcproj12/2255978/ccache/ccache.conf
System config file: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/ccache-4.7.4-eompz5/etc/ccache.conf
Stats updated: Mon Jun 17 22:19:46 2024
Local storage:
Cache size (GB): 0.47 / 0.51 (91.81%)
Files: 10902
Hits: 0
Misses: 0
Reads: 0
Writes: 0
$ fi
$ module load unstable git ${SPACK_EXTRA_MODULES}
$ spack ${SPACK_EXTRA_FLAGS} spec -Il ${SPACK_FULL_SPEC}
Input spec
--------------------------------
- neuron%oneapi~caliper+coreneuron~gpu~legacy-unit~openmp~rx3d~shared~sympy+tests build_type=FastDebug model_tests=channel-benchmark,olfactory,tqperf-heavy
- ^/53hy2ex7xntc24cnbuojh6rrc3l2auap
Concretized
--------------------------------
- dynwhp6 neuron@git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662=develop%oneapi@2023.2.0~backtrace~caliper+coreneuron~gpu~interviews~ipo~legacy-unit+mpi~openmp~prcellstate+python+report~rx3d~shared~sympy~sympyopt+tests build_system=cmake build_type=FastDebug generator=make model_tests=channel-benchmark,olfactory,tqperf-heavy sanitizers=None arch=linux-rhel7-skylake
[^] tj3mv5i ^binutils@2.41%gcc@12.3.0+gas+gold~gprofng~headers~interwork+ld~libiberty~lto~nls~pgo+plugins build_system=autotools compress_debug_sections=zlib libs=shared,static arch=linux-rhel7-skylake
[^] 7jd6loj ^diffutils@3.9%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[^] e533uuv ^pkgconf@1.9.5%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[^] z7jpg7s ^zlib-ng@2.1.4%gcc@12.3.0+compat+opt build_system=autotools arch=linux-rhel7-skylake
[^] aivjoo2 ^zstd@1.5.5%gcc@12.3.0+programs build_system=makefile compression=none libs=shared,static arch=linux-rhel7-skylake
[e] yn5fbwg ^bison@3.8.2%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[e] rd65pst ^boost@1.83.0%gcc@12.3.0~atomic~chrono~clanglibcpp~container~context~contract~coroutine~date_time~debug~exception~fiber+filesystem~graph~graph_parallel~icu~iostreams~json~locale~log~math~mpi+multithreaded~nowide~numpy+pic~program_options~python~random~regex+serialization+shared~signals~singlethreaded~stacktrace~system~taggedlayout+test~thread~timer~type_erasure~versionedlayout~wave build_system=generic cxxstd=98 patches=a440f96 visibility=hidden arch=linux-rhel7-skylake
[e] b5zzpr3 ^cmake@3.27.7%gcc@12.3.0~doc+ncurses+ownlibs build_system=generic build_type=Release arch=linux-rhel7-skylake
[e] 77vzaxs ^flex@2.6.3%gcc@12.3.0+lex~nls build_system=autotools arch=linux-rhel7-skylake
[^] nbi5w5c ^gettext@0.22.3%gcc@12.3.0+bzip2+curses+git~libunistring+libxml2+pic+shared+tar+xz build_system=autotools arch=linux-rhel7-skylake
[^] vdqwmgi ^bzip2@1.0.8%gcc@12.3.0~debug~pic+shared build_system=generic arch=linux-rhel7-skylake
[^] nv4xh4v ^libiconv@1.17%gcc@12.3.0 build_system=autotools libs=shared,static arch=linux-rhel7-skylake
[^] oh2g4in ^libxml2@2.10.3%gcc@12.3.0+pic~python+shared build_system=autotools arch=linux-rhel7-skylake
[^] zz4acmm ^tar@1.34%gcc@12.3.0 build_system=autotools zip=pigz arch=linux-rhel7-skylake
[^] dwjcguu ^pigz@2.7%gcc@12.3.0 build_system=makefile arch=linux-rhel7-skylake
[^] wwn5enj ^xz@5.4.1%gcc@12.3.0~pic build_system=autotools libs=shared,static arch=linux-rhel7-skylake
[^] swjylul ^gmake@4.4.1%gcc@12.3.0~guile build_system=generic arch=linux-rhel7-skylake
[e] h6t3hgb ^hpe-mpi@2.27.p1.hmpt%gcc@12.3.0 build_system=generic arch=linux-rhel7-skylake
- fz3oxtc ^libsonata-report@git.5602aadfa710d6766ce23cd151a1855190271bd8=develop%oneapi@2023.2.0~ipo+mpi build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] 5o77yem ^hdf5@1.14.3%gcc@12.3.0+cxx~fortran+hl~ipo~java~map+mpi+shared~szip~threadsafe+tools api=default build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] ihotvbs ^spdlog@1.12.0%gcc@12.3.0+fmt_external~ipo+shared build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] 6kdbhvi ^ncurses@6.4%gcc@12.3.0~symlinks+termlib abi=none build_system=autotools arch=linux-rhel7-skylake
[e] omn6mm4 ^ninja@1.11.1%gcc@12.3.0+re2c build_system=generic arch=linux-rhel7-skylake
[+] 53hy2ex ^nmodl@git.5ff221d045c92389b4cab5ee159d46770aa12665=develop%gcc@12.3.0~ipo~legacy-unit~llvm~llvm_cuda~python~tests build_system=cmake build_type=Release generator=ninja arch=linux-rhel7-skylake
[^] pywly2v ^catch2@3.4.0%gcc@12.3.0~ipo+pic~shared build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] ud3echq ^cli11@2.3.2%gcc@12.3.0~ipo build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] evtttrh ^fmt@10.1.1%gcc@12.3.0~ipo+pic~shared build_system=cmake build_type=Release cxxstd=11 generator=make arch=linux-rhel7-skylake
[^] teske2k ^nlohmann-json@3.9.1%gcc@12.3.0~ipo+multiple_headers build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] 5dylnca ^py-find-libpython@0.3.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 7validy ^py-jinja2@3.1.2%gcc@12.3.0~i18n build_system=python_pip arch=linux-rhel7-skylake
[^] r3ehtmw ^py-markupsafe@2.1.3%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] tabj2mo ^py-pybind11@2.11.1%gcc@12.3.0~ipo build_system=cmake build_type=Release generator=ninja arch=linux-rhel7-skylake
[^] 2inh3rt ^py-pyyaml@5.4.1%gcc@12.3.0+libyaml build_system=python_pip arch=linux-rhel7-skylake
[^] bzl4xcz ^libyaml@0.2.5%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[^] x733hwb ^py-mpi4py@3.1.4%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] m3dslef ^py-cython@0.29.36%gcc@12.3.0 build_system=python_pip patches=c4369ad arch=linux-rhel7-skylake
[^] aj3rk42 ^py-wheel@0.41.2%gcc@12.3.0 build_system=generic arch=linux-rhel7-skylake
[^] elr5pnt ^py-numpy@1.26.1%gcc@12.3.0 build_system=python_pip patches=873745d arch=linux-rhel7-skylake
[e] w2ldcy2 ^intel-oneapi-mkl@2023.2.0%gcc@12.3.0~cluster+envmods~ilp64+shared build_system=generic mpi_family=none threads=none arch=linux-rhel7-skylake
[^] 3y7uuwr ^py-pyproject-metadata@0.7.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] uqml2to ^py-packaging@23.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] h6f6feu ^py-flit-core@3.9.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 77ku3vv ^py-pip@23.1.2%gcc@12.3.0 build_system=generic arch=linux-rhel7-skylake
[^] lrf2u3h ^py-pytest@7.3.2%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] mvxx6gh ^py-iniconfig@2.0.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] cbpzath ^py-hatch-vcs@0.3.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 2o7gdvi ^py-hatchling@1.21.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 6domhtg ^py-editables@0.3%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] edobf76 ^py-pathspec@0.11.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] a6ialdh ^py-trove-classifiers@2023.8.7%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] jurd5ga ^py-calver@2022.6.26%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 6su7kvx ^py-pluggy@1.0.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] sokbfzv ^py-setuptools-scm@8.0.4%gcc@12.3.0+toml build_system=python_pip arch=linux-rhel7-skylake
[e] 2sazdxk ^git@2.42.0%gcc@12.3.0+man+nls+perl+subtree~svn~tcltk build_system=autotools arch=linux-rhel7-skylake
[^] xwl5l6q ^py-tomli@2.0.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 275jtek ^py-typing-extensions@4.8.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] z5nf6n2 ^py-pytest-cov@4.0.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] wuxetkw ^py-coverage@7.2.6%gcc@12.3.0+toml build_system=python_pip arch=linux-rhel7-skylake
[^] p3xbqxj ^py-setuptools@68.0.0%gcc@12.3.0 build_system=generic arch=linux-rhel7-skylake
[^] t5tovex ^py-sympy@1.11.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 4fflyib ^py-mpmath@1.2.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[e] 5wl76vp ^python@3.11.6%gcc@12.3.0+bz2+crypt+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tkinter+uuid+zlib build_system=generic patches=13fa8bf,b0615b2,ebdca64,f2fd060 arch=linux-rhel7-skylake
[^] pdugg7r ^readline@8.2%gcc@12.3.0 build_system=autotools patches=bbf97f1 arch=linux-rhel7-skylake
$ set -o pipefail
$ (spack ${SPACK_EXTRA_FLAGS} install --overwrite -y -j${SLURM_CPUS_PER_TASK} --log-format=junit --log-file=${CI_PROJECT_DIR}/install.xml --keep-stage ${SPACK_FULL_SPEC} | tee log) || install_failed=1
==> Warning: Expected user 904556 to own /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482, but it is owned by 0
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/zlib-ng-2.1.4-z7jpg7
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/zstd-1.5.5-aivjoo
==> bison@3.8.2 : has external module in ['bison/3.8.2']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/bison-3.8.2-qcx3sg (external bison-3.8.2-yn5fbwgteilgqg6b62shkhkjg3hlwmrq)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/boost-1.83.0-2quv7w (external boost-1.83.0-rd65pstwb56uftszduzg7lsiq4za4lnn)
==> cmake@3.27.7 : has external module in ['cmake/3.27.7']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/cmake-3.27.7-slyoes (external cmake-3.27.7-b5zzpr3mwm7jxv6bvvrs6zpeg62cfhbu)
==> flex@2.6.3 : has external module in ['flex/2.6.3']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/flex-2.6.3-edx4lf (external flex-2.6.3-77vzaxsa3g7wr3omktr4skpetx5ds4pt)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/bzip2-1.0.8-vdqwmg
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/libiconv-1.17-nv4xh4
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/xz-5.4.1-wwn5en
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/ncurses-6.4-6kdbhv
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/gmake-4.4.1-swjylu
==> hpe-mpi@2.27.p1.hmpt : has external module in ['hpe-mpi/2.27.p1.hmpt']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/hpe-mpi-2.27.p1.hmpt-6rr256 (external hpe-mpi-2.27.p1.hmpt-h6t3hgbguhacajbyzlp43xpawsnreb3m)
==> ninja@1.11.1 : has external module in ['ninja/1.11.1']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/ninja-1.11.1-nxtlgo (external ninja-1.11.1-omn6mm4a3zsbpbkptvdwxs6kkrh6yafw)
==> python@3.11.6 : has external module in ['python/3.11.6']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/python-3.11.6-bj4i6m (external python-3.11.6-5wl76vphfvpcapfaipipf7xn2xylnc4o)
==> intel-oneapi-mkl@2023.2.0 : has external module in ['intel-oneapi-mkl/2023.2.0']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/intel-oneapi-mkl-2023.2.0-twl2n4 (external intel-oneapi-mkl-2023.2.0-w2ldcy2y2urm3uaa7omu3w7nhwsqt433)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/readline-8.2-pdugg7
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/catch2-3.4.0-pywly2
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/libyaml-0.2.5-bzl4xc
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/libxml2-2.10.3-oh2g4i
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/pigz-2.7-dwjcgu
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/nlohmann-json-3.9.1-teske2
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/cli11-2.3.2-ud3ech
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/fmt-10.1.1-evtttr
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/pkgconf-1.9.5-e533uu
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-packaging-23.1-uqml2t
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pybind11-2.11.1-tabj2m
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-mpmath-1.2.1-4fflyi
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pip-23.1.2-77ku3v
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/tar-1.34-zz4acm
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/spdlog-1.12.0-ihotvb
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/hdf5-1.14.3-5o77ye
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/binutils-2.41-tj3mv5
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-numpy-1.26.1-elr5pn
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pyyaml-5.4.1-2inh3r
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-iniconfig-2.0.0-mvxx6g
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pluggy-1.0.0-6su7kv
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-coverage-7.2.6-wuxetk
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-mpi4py-3.1.4-x733hw
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-find-libpython-0.3.1-5dylnc
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-markupsafe-2.1.3-r3ehtm
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-setuptools-68.0.0-p3xbqx
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/gettext-0.22.3-nbi5w5
==> Installing libsonata-report-git.5602aadfa710d6766ce23cd151a1855190271bd8=develop-fz3oxtcl57lk2z5alhm3jvnsf6bsoiul [43/49]
==> No binary for libsonata-report-git.5602aadfa710d6766ce23cd151a1855190271bd8=develop-fz3oxtcl57lk2z5alhm3jvnsf6bsoiul found: installing from source
==> No patches needed for libsonata-report
==> libsonata-report: Executing phase: 'cmake'
==> libsonata-report: Executing phase: 'build'
==> libsonata-report: Executing phase: 'install'
==> libsonata-report: Successfully installed libsonata-report-git.5602aadfa710d6766ce23cd151a1855190271bd8=develop-fz3oxtcl57lk2z5alhm3jvnsf6bsoiul
Stage: 2.59s. Cmake: 5.13s. Build: 1.58s. Install: 0.11s. Post-install: 0.10s. Total: 9.79s
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/software/install_oneapi-2023.2.0-skylake/libsonata-report-git.5602aadfa710d6766ce23cd151a1855190271bd8_develop-fz3oxt
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-jinja2-3.1.2-7valid
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pytest-7.3.2-lrf2u3
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-sympy-1.11.1-t5tove
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pytest-cov-4.0.0-z5nf6n
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/software/install_gcc-12.3.0-skylake/nmodl-git.5ff221d045c92389b4cab5ee159d46770aa12665_develop-53hy2e
==> Installing neuron-git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662=develop-dynwhp6ge4j2e6zugw7osbjvpivrimqx [49/49]
==> No binary for neuron-git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662=develop-dynwhp6ge4j2e6zugw7osbjvpivrimqx found: installing from source
==> No patches needed for neuron
==> neuron: Executing phase: 'cmake'
==> neuron: Executing phase: 'build'
==> neuron: Executing phase: 'install'
==> neuron: Successfully installed neuron-git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662=develop-dynwhp6ge4j2e6zugw7osbjvpivrimqx
Stage: 21.11s. Cmake: 1m 3.46s. Build: 9m 54.44s. Install: 32.89s. Post-install: 0.59s. Total: 11m 53.08s
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/software/install_oneapi-2023.2.0-skylake/neuron-git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662_develop-dynwhp
$ set +o pipefail
$ chmod -R g+rX "${SPACK_BUILD}"
$ if [[ ${install_failed} == 1 ]]; then exit 1; fi
$ SPACK_INSTALLED_HASH=$(spack ${SPACK_EXTRA_FLAGS} find --format "{hash}" /$(sed -ne '${s/.*-//;p}' log))
$ echo "Determined the installed hash to be ${SPACK_INSTALLED_HASH}"
Determined the installed hash to be dynwhp6ge4j2e6zugw7osbjvpivrimqx
$ SPACK_STAGE_DIR=$(spack location -s "${SPACK_FULL_SPEC}")
$ SPACK_BUILD_DIR=$(spack location -b "${SPACK_FULL_SPEC}")
$ SPACK_SOURCE_DIR=${SPACK_STAGE_DIR}/spack-src
$ if [ ${SPACK_USE_CCACHE+x} ]; then
$ ccache --cleanup
$ ccache --show-stats --verbose
Cache directory: /nvme/bbpcihpcproj12/2255978/ccache
Config file: /nvme/bbpcihpcproj12/2255978/ccache/ccache.conf
System config file: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/ccache-4.7.4-eompz5/etc/ccache.conf
Stats updated: Mon Jun 17 22:34:32 2024
Cacheable calls: 1022 / 1200 (85.17%)
Hits: 728 / 1022 (71.23%)
Direct: 371 / 728 (50.96%)
Preprocessed: 357 / 728 (49.04%)
Misses: 294 / 1022 (28.77%)
Uncacheable calls: 178 / 1200 (14.83%)
Autoconf compile/link: 5 / 178 ( 2.81%)
Called for linking: 147 / 178 (82.58%)
Called for preprocessing: 1 / 178 ( 0.56%)
Compilation failed: 2 / 178 ( 1.12%)
No input file: 23 / 178 (12.92%)
Successful lookups:
Direct: 371 / 1024 (36.23%)
Preprocessed: 357 / 653 (54.67%)
Local storage:
Cache size (GB): 0.45 / 0.51 (88.12%)
Files: 9983
Cleanups: 10
Hits: 728 / 1024 (71.09%)
Misses: 296 / 1024 (28.91%)
Reads: 2048
Writes: 869
$ tar -C "${CCACHE_DIR}" -cf "${CI_PROJECT_DIR}/ccache.tar" .
$ fi
$ touch ${SPACK_STAGE_DIR}/spack-configure-args.txt
$ cp ${SPACK_STAGE_DIR}/spack-{build-env,build-out,configure-args}.txt ${CI_PROJECT_DIR}/
$ echo "SPACK_BUILD_DIR=${SPACK_BUILD_DIR}" > ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_FULL_SPEC=${SPACK_FULL_SPEC}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_SOURCE_DIR=${SPACK_SOURCE_DIR}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_INSTALLED_HASH=${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ SPACK_PACKAGE_SLUGIFY=$(echo -n ${SPACK_PACKAGE} | tr -c '[:alnum:]' '_' | tr '[:lower:]' '[:upper:]')
$ echo "${SPACK_PACKAGE_SLUGIFY}_INSTALLED_HASH=${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_PACKAGE_DEPENDENCY_ON_PREVIOUS_JOB=^/${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ num_failures=$(module load unstable python-dev; python -c "from lxml import etree; xml = etree.parse('${CI_PROJECT_DIR}/install.xml'); print(sum(1 for _ in xml.getroot().iter('failure')) + sum(1 for _ in xml.getroot().iter('error')))")
$ if [[ ${num_failures} > 0 ]]; then exit ${num_failures}; fi
section_end:1718656473:step_script section_start:1718656473:archive_cache Saving cache for successful job
Using git from spack modules
Creating cache build:neuron:nmodl:intel:legacy-1-non_protected...
Runtime platform  arch=amd64 os=linux pid=176524 revision=58ba2b95 version=14.2.0
ccache.tar: found 1 matching files and directories
Uploading cache.zip to https://bbpobjectstorage.epfl.ch/gitlab-runners-cache/project/2160/build%3Aneuron%3Anmodl%3Aintel%3Alegacy-1-non_protected
Created cache
section_end:1718656495:archive_cache section_start:1718656495:upload_artifacts_on_success Uploading artifacts for successful job
Using git from spack modules
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=176656 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
spack_build_info.env: found 1 matching files and directories
spack_clone_variables.env: found 1 matching files and directories
initial_environment.env: found 1 matching files and directories
spack-build-env.txt: found 1 matching files and directories
spack-build-out.txt: found 1 matching files and directories
spack-configure-args.txt: found 1 matching files and directories
Uploading artifacts as "archive" to coordinator... ok id=1322442 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=176697 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
Uploading artifacts as "junit" to coordinator... ok id=1322442 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=176737 revision=58ba2b95 version=14.2.0
spack_build_info.env: found 1 matching files and directories
spack_clone_variables.env: found 1 matching files and directories
Uploading artifacts as "dotenv" to coordinator... ok id=1322442 responseStatus=201 Created token=glcbt-64
section_end:1718656497:upload_artifacts_on_success section_start:1718656497:cleanup_file_variables Cleaning up project directory and file based variables
Using git from spack modules
section_end:1718656498:cleanup_file_variables Job succeeded
Running with gitlab-runner 15.5.0 (0d4137b8)
 on BB5 map runner pnPo3yJy
section_start:1718655568:resolve_secrets Resolving secrets
section_end:1718655568:resolve_secrets section_start:1718655568:prepare_executor Preparing the "custom" executor
Using Custom executor with driver BB5 PROD runner v0.0.3...
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor2464794414, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name nrn
Pipeline ID 217482, build ref , job ID 1322443
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482, optional exclusive flag , optional cpus per task flag --cpus-per-task=8, optional qos flag , optional reservation flag
A slurm job will be created with name GL_J1322443_PROD_P2160_CP1_C2
Job parameters: memory=160G, cpus_per_task=8, duration=2:00:00, constraint=cpu ntasks=2 account=proj9998 user=bbpcihpcproj12 partition=prod qos= reservation=
Not executing the chown -R
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx]
Submitted batch job 2255979
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=2 --cpus-per-task=8 --mem=160G --job-name=GL_J1322443_PROD_P2160_CP1_C2 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482 --time=2:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482 --ntasks=2 --jobid=2255979 --cpus-per-task=8 --mem=160G
section_end:1718655570:prepare_executor section_start:1718655570:prepare_script Preparing environment
Using git from spack modules
Running on r1i5n12 via bbpv1.epfl.ch...
section_end:1718655573:prepare_script section_start:1718655573:get_sources Getting source from Git repository
Using git from spack modules
Skipping Git repository setup
Skipping Git checkout
Skipping Git submodules setup
section_end:1718655574:get_sources section_start:1718655574:restore_cache Restoring cache
Using git from spack modules
Checking cache for build:neuron:nmodl:intel:shared-1-non_protected...
Runtime platform  arch=amd64 os=linux pid=110165 revision=58ba2b95 version=14.2.0
cache.zip is up to date 
Successfully extracted cache
section_end:1718655580:restore_cache section_start:1718655580:download_artifacts Downloading artifacts
Using git from spack modules
Downloading artifacts for build:nmodl (1322441)...
Runtime platform  arch=amd64 os=linux pid=110276 revision=58ba2b95 version=14.2.0
Downloading artifacts from coordinator... ok  id=1322441 responseStatus=200 OK token=glcbt-64
section_end:1718655581:download_artifacts section_start:1718655581:step_script Executing "step_script" stage of the job script
WARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426
Using git from spack modules
$ SPACK_BUILD="${PWD}/spack-build"
$ env -0 | sort -z | xargs -0 -L 1 echo > initial_environment.env
$ . ${SPACK_ROOT}/share/spack/setup-env.sh
$ export SPACK_USER_CONFIG_PATH=${PWD}/spack-config
$ mkdir ${SPACK_USER_CONFIG_PATH}
$ cat > ${SPACK_USER_CONFIG_PATH}/config.yaml << END_SCRIPT # collapsed multi-line command
$ spack ${SPACK_EXTRA_FLAGS} config add concretizer:reuse:false
$ spack ${SPACK_EXTRA_FLAGS} config blame config
--- config:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322443/spack-config/config.yaml:2 build_stage:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322443/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322443/spack-build
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322443/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322443/spack-source-cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/config.yaml:2 ccache: True
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:2 install_tree:
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:3 root: $user_cache_path/software
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:4 projections:
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:5 all: install_{compiler.name}-{compiler.version}-{target}/{name}-{version}-{hash:6}
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:7 environments_root: $user_cache_path/environments
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:9 build_jobs: 8
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:18 extensions:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:19 - $spack/bluebrain/spack-scripting
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:37 template_dirs:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:38 - $spack/share/spack/templates
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:41 license_dir: $spack/etc/spack/licenses
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:81 test_stage: $user_cache_path/test
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:94 misc_cache: $user_cache_path/cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:100 connect_timeout: 10
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:105 verify_ssl: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:113 suppress_gpg_warnings: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:119 install_missing_compilers: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:124 checksum: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:129 deprecated: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:134 dirty: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:142 build_language: C
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:151 locks: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:156 url_fetch_method: urllib
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:185 concretizer: clingo
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:192 db_lock_timeout: 60
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:200 package_lock_timeout: null
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:205 shared_linking:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:210 type: rpath
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:216 bind: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:221 allow_sgid: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:227 install_status: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:231 binary_index_ttl: 600
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:233 flags:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:235 keep_werror: none
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:240 aliases:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:241 concretise: concretize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:242 containerise: containerize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:243 rm: remove
_builtin debug: False
$ spack ${SPACK_EXTRA_FLAGS} config blame concretizer
--- concretizer:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322443/spack-config/concretizer.yaml:2 reuse: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:23 targets:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:28 granularity: microarchitectures
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:32 host_compatible: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:38 unify: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:40 duplicates:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:44 strategy: minimal
$ export XDG_CONFIG_HOME=${CI_BUILDS_DIR}/J${CI_JOB_ID}_local_config
$ echo "Configuring git to use CI_JOB_TOKEN to access git@bbpgitlab.epfl.ch (${XDG_CONFIG_HOME})"
Configuring git to use CI_JOB_TOKEN to access git@bbpgitlab.epfl.ch (/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482/J1322443_local_config)
$ mkdir -p "${XDG_CONFIG_HOME}/git"
$ echo -e "[url \"https://gitlab-ci-token:${CI_JOB_TOKEN}@bbpgitlab.epfl.ch/\"]\n insteadOf = git@bbpgitlab.epfl.ch:" > "${XDG_CONFIG_HOME}/git/config"
$ echo -e "[url \"https://gitlab-ci-token:${CI_JOB_TOKEN}@bbpgitlab.epfl.ch/\"]\n insteadOf = ssh://git@bbpgitlab.epfl.ch/" >> "${XDG_CONFIG_HOME}/git/config"
$ cat "${XDG_CONFIG_HOME}/git/config"
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
insteadOf = git@bbpgitlab.epfl.ch:
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
insteadOf = ssh://git@bbpgitlab.epfl.ch/
$ SPACK_FULL_SPEC="${SPACK_PACKAGE}${SPACK_PACKAGE_COMPILER:+%}${SPACK_PACKAGE_COMPILER} ${SPACK_PACKAGE_SPEC} ${SPACK_PACKAGE_DEPENDENCIES} ${SPACK_PACKAGE_DEPENDENCY_ON_PREVIOUS_JOB}"
$ echo "Preparing to install ${SPACK_FULL_SPEC}"
Preparing to install neuron%oneapi ~rx3d~caliper~gpu+coreneuron~legacy-unit~openmp+shared+sympy+tests build_type=FastDebug model_tests=channel-benchmark,olfactory,tqperf-heavy ^/53hy2ex7xntc24cnbuojh6rrc3l2auap
$ if [ ${SPACK_USE_CCACHE+x} ]; then
$ module load unstable ccache
$ export CCACHE_BASEDIR=$(realpath -P ${CI_BUILDS_DIR})
$ echo CCACHE_BASEDIR=${CCACHE_BASEDIR}
CCACHE_BASEDIR=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482
$ export CCACHE_MAXSIZE=512M
$ export CCACHE_DIR="${TMPDIR}/ccache"
$ mkdir -p ${CCACHE_DIR}
$ if [ -f ${CI_PROJECT_DIR}/ccache.tar ]; then
$ tar -C "${CCACHE_DIR}" -xf "${CI_PROJECT_DIR}/ccache.tar"
$ fi
$ ccache --zero-stats
Statistics zeroed
$ ccache --show-stats --verbose
Cache directory: /nvme/bbpcihpcproj12/2255979/ccache
Config file: /nvme/bbpcihpcproj12/2255979/ccache/ccache.conf
System config file: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/ccache-4.7.4-eompz5/etc/ccache.conf
Stats updated: Mon Jun 17 22:19:48 2024
Local storage:
Cache size (GB): 0.46 / 0.51 (90.79%)
Files: 10426
Hits: 0
Misses: 0
Reads: 0
Writes: 0
$ fi
$ module load unstable git ${SPACK_EXTRA_MODULES}
$ spack ${SPACK_EXTRA_FLAGS} spec -Il ${SPACK_FULL_SPEC}
Input spec
--------------------------------
- neuron%oneapi~caliper+coreneuron~gpu~legacy-unit~openmp~rx3d+shared+sympy+tests build_type=FastDebug model_tests=channel-benchmark,olfactory,tqperf-heavy
- ^/53hy2ex7xntc24cnbuojh6rrc3l2auap
Concretized
--------------------------------
- q2yq6bu neuron@git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662=develop%oneapi@2023.2.0~backtrace~caliper+coreneuron~gpu~interviews~ipo~legacy-unit+mpi~openmp~prcellstate+python+report~rx3d+shared+sympy~sympyopt+tests build_system=cmake build_type=FastDebug generator=make model_tests=channel-benchmark,olfactory,tqperf-heavy sanitizers=None arch=linux-rhel7-skylake
[^] tj3mv5i ^binutils@2.41%gcc@12.3.0+gas+gold~gprofng~headers~interwork+ld~libiberty~lto~nls~pgo+plugins build_system=autotools compress_debug_sections=zlib libs=shared,static arch=linux-rhel7-skylake
[^] 7jd6loj ^diffutils@3.9%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[^] e533uuv ^pkgconf@1.9.5%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[^] z7jpg7s ^zlib-ng@2.1.4%gcc@12.3.0+compat+opt build_system=autotools arch=linux-rhel7-skylake
[^] aivjoo2 ^zstd@1.5.5%gcc@12.3.0+programs build_system=makefile compression=none libs=shared,static arch=linux-rhel7-skylake
[e] yn5fbwg ^bison@3.8.2%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[e] rd65pst ^boost@1.83.0%gcc@12.3.0~atomic~chrono~clanglibcpp~container~context~contract~coroutine~date_time~debug~exception~fiber+filesystem~graph~graph_parallel~icu~iostreams~json~locale~log~math~mpi+multithreaded~nowide~numpy+pic~program_options~python~random~regex+serialization+shared~signals~singlethreaded~stacktrace~system~taggedlayout+test~thread~timer~type_erasure~versionedlayout~wave build_system=generic cxxstd=98 patches=a440f96 visibility=hidden arch=linux-rhel7-skylake
[e] b5zzpr3 ^cmake@3.27.7%gcc@12.3.0~doc+ncurses+ownlibs build_system=generic build_type=Release arch=linux-rhel7-skylake
[e] 77vzaxs ^flex@2.6.3%gcc@12.3.0+lex~nls build_system=autotools arch=linux-rhel7-skylake
[^] nbi5w5c ^gettext@0.22.3%gcc@12.3.0+bzip2+curses+git~libunistring+libxml2+pic+shared+tar+xz build_system=autotools arch=linux-rhel7-skylake
[^] vdqwmgi ^bzip2@1.0.8%gcc@12.3.0~debug~pic+shared build_system=generic arch=linux-rhel7-skylake
[^] nv4xh4v ^libiconv@1.17%gcc@12.3.0 build_system=autotools libs=shared,static arch=linux-rhel7-skylake
[^] oh2g4in ^libxml2@2.10.3%gcc@12.3.0+pic~python+shared build_system=autotools arch=linux-rhel7-skylake
[^] zz4acmm ^tar@1.34%gcc@12.3.0 build_system=autotools zip=pigz arch=linux-rhel7-skylake
[^] dwjcguu ^pigz@2.7%gcc@12.3.0 build_system=makefile arch=linux-rhel7-skylake
[^] wwn5enj ^xz@5.4.1%gcc@12.3.0~pic build_system=autotools libs=shared,static arch=linux-rhel7-skylake
[^] swjylul ^gmake@4.4.1%gcc@12.3.0~guile build_system=generic arch=linux-rhel7-skylake
[e] h6t3hgb ^hpe-mpi@2.27.p1.hmpt%gcc@12.3.0 build_system=generic arch=linux-rhel7-skylake
- fz3oxtc ^libsonata-report@git.5602aadfa710d6766ce23cd151a1855190271bd8=develop%oneapi@2023.2.0~ipo+mpi build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] 5o77yem ^hdf5@1.14.3%gcc@12.3.0+cxx~fortran+hl~ipo~java~map+mpi+shared~szip~threadsafe+tools api=default build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] ihotvbs ^spdlog@1.12.0%gcc@12.3.0+fmt_external~ipo+shared build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] 6kdbhvi ^ncurses@6.4%gcc@12.3.0~symlinks+termlib abi=none build_system=autotools arch=linux-rhel7-skylake
[e] omn6mm4 ^ninja@1.11.1%gcc@12.3.0+re2c build_system=generic arch=linux-rhel7-skylake
[+] 53hy2ex ^nmodl@git.5ff221d045c92389b4cab5ee159d46770aa12665=develop%gcc@12.3.0~ipo~legacy-unit~llvm~llvm_cuda~python~tests build_system=cmake build_type=Release generator=ninja arch=linux-rhel7-skylake
[^] pywly2v ^catch2@3.4.0%gcc@12.3.0~ipo+pic~shared build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] ud3echq ^cli11@2.3.2%gcc@12.3.0~ipo build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] evtttrh ^fmt@10.1.1%gcc@12.3.0~ipo+pic~shared build_system=cmake build_type=Release cxxstd=11 generator=make arch=linux-rhel7-skylake
[^] teske2k ^nlohmann-json@3.9.1%gcc@12.3.0~ipo+multiple_headers build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] 5dylnca ^py-find-libpython@0.3.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 7validy ^py-jinja2@3.1.2%gcc@12.3.0~i18n build_system=python_pip arch=linux-rhel7-skylake
[^] r3ehtmw ^py-markupsafe@2.1.3%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] tabj2mo ^py-pybind11@2.11.1%gcc@12.3.0~ipo build_system=cmake build_type=Release generator=ninja arch=linux-rhel7-skylake
[^] 2inh3rt ^py-pyyaml@5.4.1%gcc@12.3.0+libyaml build_system=python_pip arch=linux-rhel7-skylake
[^] bzl4xcz ^libyaml@0.2.5%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[^] x733hwb ^py-mpi4py@3.1.4%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] m3dslef ^py-cython@0.29.36%gcc@12.3.0 build_system=python_pip patches=c4369ad arch=linux-rhel7-skylake
[^] aj3rk42 ^py-wheel@0.41.2%gcc@12.3.0 build_system=generic arch=linux-rhel7-skylake
[^] elr5pnt ^py-numpy@1.26.1%gcc@12.3.0 build_system=python_pip patches=873745d arch=linux-rhel7-skylake
[e] w2ldcy2 ^intel-oneapi-mkl@2023.2.0%gcc@12.3.0~cluster+envmods~ilp64+shared build_system=generic mpi_family=none threads=none arch=linux-rhel7-skylake
[^] 3y7uuwr ^py-pyproject-metadata@0.7.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] uqml2to ^py-packaging@23.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] h6f6feu ^py-flit-core@3.9.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 77ku3vv ^py-pip@23.1.2%gcc@12.3.0 build_system=generic arch=linux-rhel7-skylake
[^] lrf2u3h ^py-pytest@7.3.2%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] mvxx6gh ^py-iniconfig@2.0.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] cbpzath ^py-hatch-vcs@0.3.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 2o7gdvi ^py-hatchling@1.21.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 6domhtg ^py-editables@0.3%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] edobf76 ^py-pathspec@0.11.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] a6ialdh ^py-trove-classifiers@2023.8.7%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] jurd5ga ^py-calver@2022.6.26%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 6su7kvx ^py-pluggy@1.0.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] sokbfzv ^py-setuptools-scm@8.0.4%gcc@12.3.0+toml build_system=python_pip arch=linux-rhel7-skylake
[e] 2sazdxk ^git@2.42.0%gcc@12.3.0+man+nls+perl+subtree~svn~tcltk build_system=autotools arch=linux-rhel7-skylake
[^] xwl5l6q ^py-tomli@2.0.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 275jtek ^py-typing-extensions@4.8.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] z5nf6n2 ^py-pytest-cov@4.0.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] wuxetkw ^py-coverage@7.2.6%gcc@12.3.0+toml build_system=python_pip arch=linux-rhel7-skylake
[^] p3xbqxj ^py-setuptools@68.0.0%gcc@12.3.0 build_system=generic arch=linux-rhel7-skylake
[^] t5tovex ^py-sympy@1.11.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 4fflyib ^py-mpmath@1.2.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[e] 5wl76vp ^python@3.11.6%gcc@12.3.0+bz2+crypt+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tkinter+uuid+zlib build_system=generic patches=13fa8bf,b0615b2,ebdca64,f2fd060 arch=linux-rhel7-skylake
[^] pdugg7r ^readline@8.2%gcc@12.3.0 build_system=autotools patches=bbf97f1 arch=linux-rhel7-skylake
$ set -o pipefail
$ (spack ${SPACK_EXTRA_FLAGS} install --overwrite -y -j${SLURM_CPUS_PER_TASK} --log-format=junit --log-file=${CI_PROJECT_DIR}/install.xml --keep-stage ${SPACK_FULL_SPEC} | tee log) || install_failed=1
==> Warning: Expected user 904556 to own /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482, but it is owned by 0
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/zlib-ng-2.1.4-z7jpg7
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/zstd-1.5.5-aivjoo
==> bison@3.8.2 : has external module in ['bison/3.8.2']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/bison-3.8.2-qcx3sg (external bison-3.8.2-yn5fbwgteilgqg6b62shkhkjg3hlwmrq)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/boost-1.83.0-2quv7w (external boost-1.83.0-rd65pstwb56uftszduzg7lsiq4za4lnn)
==> cmake@3.27.7 : has external module in ['cmake/3.27.7']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/cmake-3.27.7-slyoes (external cmake-3.27.7-b5zzpr3mwm7jxv6bvvrs6zpeg62cfhbu)
==> flex@2.6.3 : has external module in ['flex/2.6.3']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/flex-2.6.3-edx4lf (external flex-2.6.3-77vzaxsa3g7wr3omktr4skpetx5ds4pt)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/bzip2-1.0.8-vdqwmg
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/libiconv-1.17-nv4xh4
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/xz-5.4.1-wwn5en
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/ncurses-6.4-6kdbhv
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/gmake-4.4.1-swjylu
==> hpe-mpi@2.27.p1.hmpt : has external module in ['hpe-mpi/2.27.p1.hmpt']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/hpe-mpi-2.27.p1.hmpt-6rr256 (external hpe-mpi-2.27.p1.hmpt-h6t3hgbguhacajbyzlp43xpawsnreb3m)
==> ninja@1.11.1 : has external module in ['ninja/1.11.1']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/ninja-1.11.1-nxtlgo (external ninja-1.11.1-omn6mm4a3zsbpbkptvdwxs6kkrh6yafw)
==> python@3.11.6 : has external module in ['python/3.11.6']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/python-3.11.6-bj4i6m (external python-3.11.6-5wl76vphfvpcapfaipipf7xn2xylnc4o)
==> intel-oneapi-mkl@2023.2.0 : has external module in ['intel-oneapi-mkl/2023.2.0']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/intel-oneapi-mkl-2023.2.0-twl2n4 (external intel-oneapi-mkl-2023.2.0-w2ldcy2y2urm3uaa7omu3w7nhwsqt433)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/libyaml-0.2.5-bzl4xc
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/nlohmann-json-3.9.1-teske2
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/readline-8.2-pdugg7
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/fmt-10.1.1-evtttr
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/pkgconf-1.9.5-e533uu
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/cli11-2.3.2-ud3ech
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/pigz-2.7-dwjcgu
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/catch2-3.4.0-pywly2
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-iniconfig-2.0.0-mvxx6g
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-packaging-23.1-uqml2t
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pluggy-1.0.0-6su7kv
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pybind11-2.11.1-tabj2m
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-coverage-7.2.6-wuxetk
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pip-23.1.2-77ku3v
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/spdlog-1.12.0-ihotvb
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/hdf5-1.14.3-5o77ye
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/libxml2-2.10.3-oh2g4i
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/binutils-2.41-tj3mv5
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/tar-1.34-zz4acm
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-mpi4py-3.1.4-x733hw
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pyyaml-5.4.1-2inh3r
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-setuptools-68.0.0-p3xbqx
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-numpy-1.26.1-elr5pn
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/gettext-0.22.3-nbi5w5
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-markupsafe-2.1.3-r3ehtm
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-mpmath-1.2.1-4fflyi
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pytest-7.3.2-lrf2u3
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-find-libpython-0.3.1-5dylnc
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/software/install_oneapi-2023.2.0-skylake/libsonata-report-git.5602aadfa710d6766ce23cd151a1855190271bd8_develop-fz3oxt
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-jinja2-3.1.2-7valid
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-sympy-1.11.1-t5tove
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pytest-cov-4.0.0-z5nf6n
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/software/install_gcc-12.3.0-skylake/nmodl-git.5ff221d045c92389b4cab5ee159d46770aa12665_develop-53hy2e
==> Installing neuron-git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662=develop-q2yq6buqp6gpgpidmz23qxvdenjjjqng [49/49]
==> No binary for neuron-git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662=develop-q2yq6buqp6gpgpidmz23qxvdenjjjqng found: installing from source
==> No patches needed for neuron
==> neuron: Executing phase: 'cmake'
==> neuron: Executing phase: 'build'
==> neuron: Executing phase: 'install'
==> neuron: Successfully installed neuron-git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662=develop-q2yq6buqp6gpgpidmz23qxvdenjjjqng
Stage: 20.18s. Cmake: 1m 3.48s. Build: 10m 10.19s. Install: 33.55s. Post-install: 0.59s. Total: 12m 8.62s
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/software/install_oneapi-2023.2.0-skylake/neuron-git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662_develop-q2yq6b
$ set +o pipefail
$ chmod -R g+rX "${SPACK_BUILD}"
$ if [[ ${install_failed} == 1 ]]; then exit 1; fi
$ SPACK_INSTALLED_HASH=$(spack ${SPACK_EXTRA_FLAGS} find --format "{hash}" /$(sed -ne '${s/.*-//;p}' log))
$ echo "Determined the installed hash to be ${SPACK_INSTALLED_HASH}"
Determined the installed hash to be q2yq6buqp6gpgpidmz23qxvdenjjjqng
$ SPACK_STAGE_DIR=$(spack location -s "${SPACK_FULL_SPEC}")
$ SPACK_BUILD_DIR=$(spack location -b "${SPACK_FULL_SPEC}")
$ SPACK_SOURCE_DIR=${SPACK_STAGE_DIR}/spack-src
$ if [ ${SPACK_USE_CCACHE+x} ]; then
$ ccache --cleanup
$ ccache --show-stats --verbose
Cache directory: /nvme/bbpcihpcproj12/2255979/ccache
Config file: /nvme/bbpcihpcproj12/2255979/ccache/ccache.conf
System config file: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/ccache-4.7.4-eompz5/etc/ccache.conf
Stats updated: Mon Jun 17 22:35:06 2024
Cacheable calls: 1000 / 1166 (85.76%)
Hits: 707 / 1000 (70.70%)
Direct: 349 / 707 (49.36%)
Preprocessed: 358 / 707 (50.64%)
Misses: 293 / 1000 (29.30%)
Uncacheable calls: 166 / 1166 (14.24%)
Autoconf compile/link: 5 / 166 ( 3.01%)
Called for linking: 146 / 166 (87.95%)
Called for preprocessing: 1 / 166 ( 0.60%)
Compilation failed: 2 / 166 ( 1.20%)
No input file: 12 / 166 ( 7.23%)
Successful lookups:
Direct: 349 / 1002 (34.83%)
Preprocessed: 358 / 653 (54.82%)
Local storage:
Cache size (GB): 0.46 / 0.51 (89.78%)
Files: 9828
Cleanups: 8
Hits: 707 / 1002 (70.56%)
Misses: 295 / 1002 (29.44%)
Reads: 2004
Writes: 868
$ tar -C "${CCACHE_DIR}" -cf "${CI_PROJECT_DIR}/ccache.tar" .
$ fi
$ touch ${SPACK_STAGE_DIR}/spack-configure-args.txt
$ cp ${SPACK_STAGE_DIR}/spack-{build-env,build-out,configure-args}.txt ${CI_PROJECT_DIR}/
$ echo "SPACK_BUILD_DIR=${SPACK_BUILD_DIR}" > ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_FULL_SPEC=${SPACK_FULL_SPEC}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_SOURCE_DIR=${SPACK_SOURCE_DIR}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_INSTALLED_HASH=${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ SPACK_PACKAGE_SLUGIFY=$(echo -n ${SPACK_PACKAGE} | tr -c '[:alnum:]' '_' | tr '[:lower:]' '[:upper:]')
$ echo "${SPACK_PACKAGE_SLUGIFY}_INSTALLED_HASH=${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_PACKAGE_DEPENDENCY_ON_PREVIOUS_JOB=^/${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ num_failures=$(module load unstable python-dev; python -c "from lxml import etree; xml = etree.parse('${CI_PROJECT_DIR}/install.xml'); print(sum(1 for _ in xml.getroot().iter('failure')) + sum(1 for _ in xml.getroot().iter('error')))")
$ if [[ ${num_failures} > 0 ]]; then exit ${num_failures}; fi
section_end:1718656508:step_script section_start:1718656508:archive_cache Saving cache for successful job
Using git from spack modules
Creating cache build:neuron:nmodl:intel:shared-1-non_protected...
Runtime platform  arch=amd64 os=linux pid=134157 revision=58ba2b95 version=14.2.0
ccache.tar: found 1 matching files and directories
Uploading cache.zip to https://bbpobjectstorage.epfl.ch/gitlab-runners-cache/project/2160/build%3Aneuron%3Anmodl%3Aintel%3Ashared-1-non_protected
Created cache
section_end:1718656531:archive_cache section_start:1718656531:upload_artifacts_on_success Uploading artifacts for successful job
Using git from spack modules
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=134309 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
spack_build_info.env: found 1 matching files and directories
spack_clone_variables.env: found 1 matching files and directories
initial_environment.env: found 1 matching files and directories
spack-build-env.txt: found 1 matching files and directories
spack-build-out.txt: found 1 matching files and directories
spack-configure-args.txt: found 1 matching files and directories
Uploading artifacts as "archive" to coordinator... ok id=1322443 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=134351 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
Uploading artifacts as "junit" to coordinator... ok id=1322443 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=134390 revision=58ba2b95 version=14.2.0
spack_build_info.env: found 1 matching files and directories
spack_clone_variables.env: found 1 matching files and directories
Uploading artifacts as "dotenv" to coordinator... ok id=1322443 responseStatus=201 Created token=glcbt-64
section_end:1718656533:upload_artifacts_on_success section_start:1718656533:cleanup_file_variables Cleaning up project directory and file based variables
Using git from spack modules
section_end:1718656534:cleanup_file_variables Job succeeded
Running with gitlab-runner 15.5.0 (0d4137b8)
 on BB5 map runner pnPo3yJy
section_start:1718655569:resolve_secrets Resolving secrets
section_end:1718655569:resolve_secrets section_start:1718655569:prepare_executor Preparing the "custom" executor
Using Custom executor with driver BB5 PROD runner v0.0.3...
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor1678946064, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name nrn
Pipeline ID 217482, build ref , job ID 1322444
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482, optional exclusive flag , optional cpus per task flag --cpus-per-task=8, optional qos flag , optional reservation flag
A slurm job will be created with name GL_J1322444_PROD_P2160_CP2_C4
Job parameters: memory=160G, cpus_per_task=8, duration=2:00:00, constraint=cpu ntasks=2 account=proj9998 user=bbpcihpcproj12 partition=prod qos= reservation=
Not executing the chown -R
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx]
Submitted batch job 2255980
job state: PD
job state: PD
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=2 --cpus-per-task=8 --mem=160G --job-name=GL_J1322444_PROD_P2160_CP2_C4 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482 --time=2:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482 --ntasks=2 --jobid=2255980 --cpus-per-task=8 --mem=160G
section_end:1718655572:prepare_executor section_start:1718655572:prepare_script Preparing environment
Using git from spack modules
Running on r3i5n31 via bbpv1.epfl.ch...
section_end:1718655575:prepare_script section_start:1718655575:get_sources Getting source from Git repository
Using git from spack modules
Skipping Git repository setup
Skipping Git checkout
Skipping Git submodules setup
section_end:1718655577:get_sources section_start:1718655577:restore_cache Restoring cache
Using git from spack modules
Checking cache for build:neuron:nmodl:nvhpc:acc:legacy-1-non_protected...
Runtime platform  arch=amd64 os=linux pid=123382 revision=58ba2b95 version=14.2.0
cache.zip is up to date 
Successfully extracted cache
section_end:1718655583:restore_cache section_start:1718655583:download_artifacts Downloading artifacts
Using git from spack modules
Downloading artifacts for build:nmodl (1322441)...
Runtime platform  arch=amd64 os=linux pid=123590 revision=58ba2b95 version=14.2.0
Downloading artifacts from coordinator... ok  id=1322441 responseStatus=200 OK token=glcbt-64
section_end:1718655584:download_artifacts section_start:1718655584:step_script Executing "step_script" stage of the job script
WARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426
Using git from spack modules
$ SPACK_BUILD="${PWD}/spack-build"
$ env -0 | sort -z | xargs -0 -L 1 echo > initial_environment.env
$ . ${SPACK_ROOT}/share/spack/setup-env.sh
$ export SPACK_USER_CONFIG_PATH=${PWD}/spack-config
$ mkdir ${SPACK_USER_CONFIG_PATH}
$ cat > ${SPACK_USER_CONFIG_PATH}/config.yaml << END_SCRIPT # collapsed multi-line command
$ spack ${SPACK_EXTRA_FLAGS} config add concretizer:reuse:false
$ spack ${SPACK_EXTRA_FLAGS} config blame config
--- config:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322444/spack-config/config.yaml:2 build_stage:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322444/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322444/spack-build
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322444/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322444/spack-source-cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/config.yaml:2 ccache: True
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:2 install_tree:
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:3 root: $user_cache_path/software
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:4 projections:
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:5 all: install_{compiler.name}-{compiler.version}-{target}/{name}-{version}-{hash:6}
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:7 environments_root: $user_cache_path/environments
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:9 build_jobs: 8
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:18 extensions:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:19 - $spack/bluebrain/spack-scripting
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:37 template_dirs:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:38 - $spack/share/spack/templates
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:41 license_dir: $spack/etc/spack/licenses
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:81 test_stage: $user_cache_path/test
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:94 misc_cache: $user_cache_path/cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:100 connect_timeout: 10
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:105 verify_ssl: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:113 suppress_gpg_warnings: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:119 install_missing_compilers: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:124 checksum: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:129 deprecated: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:134 dirty: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:142 build_language: C
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:151 locks: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:156 url_fetch_method: urllib
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:185 concretizer: clingo
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:192 db_lock_timeout: 60
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:200 package_lock_timeout: null
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:205 shared_linking:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:210 type: rpath
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:216 bind: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:221 allow_sgid: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:227 install_status: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:231 binary_index_ttl: 600
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:233 flags:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:235 keep_werror: none
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:240 aliases:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:241 concretise: concretize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:242 containerise: containerize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:243 rm: remove
_builtin debug: False
$ spack ${SPACK_EXTRA_FLAGS} config blame concretizer
--- concretizer:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322444/spack-config/concretizer.yaml:2 reuse: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:23 targets:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:28 granularity: microarchitectures
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:32 host_compatible: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:38 unify: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:40 duplicates:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:44 strategy: minimal
$ export XDG_CONFIG_HOME=${CI_BUILDS_DIR}/J${CI_JOB_ID}_local_config
$ echo "Configuring git to use CI_JOB_TOKEN to access git@bbpgitlab.epfl.ch (${XDG_CONFIG_HOME})"
Configuring git to use CI_JOB_TOKEN to access git@bbpgitlab.epfl.ch (/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482/J1322444_local_config)
$ mkdir -p "${XDG_CONFIG_HOME}/git"
$ echo -e "[url \"https://gitlab-ci-token:${CI_JOB_TOKEN}@bbpgitlab.epfl.ch/\"]\n insteadOf = git@bbpgitlab.epfl.ch:" > "${XDG_CONFIG_HOME}/git/config"
$ echo -e "[url \"https://gitlab-ci-token:${CI_JOB_TOKEN}@bbpgitlab.epfl.ch/\"]\n insteadOf = ssh://git@bbpgitlab.epfl.ch/" >> "${XDG_CONFIG_HOME}/git/config"
$ cat "${XDG_CONFIG_HOME}/git/config"
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
insteadOf = git@bbpgitlab.epfl.ch:
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
insteadOf = ssh://git@bbpgitlab.epfl.ch/
$ SPACK_FULL_SPEC="${SPACK_PACKAGE}${SPACK_PACKAGE_COMPILER:+%}${SPACK_PACKAGE_COMPILER} ${SPACK_PACKAGE_SPEC} ${SPACK_PACKAGE_DEPENDENCIES} ${SPACK_PACKAGE_DEPENDENCY_ON_PREVIOUS_JOB}"
$ echo "Preparing to install ${SPACK_FULL_SPEC}"
Preparing to install neuron%nvhpc ~rx3d~caliper+gpu+coreneuron~legacy-unit~openmp~shared~sympy+tests~unified build_type=FastDebug model_tests=channel-benchmark,olfactory,tqperf-heavy ^/53hy2ex7xntc24cnbuojh6rrc3l2auap
$ if [ ${SPACK_USE_CCACHE+x} ]; then
$ module load unstable ccache
$ export CCACHE_BASEDIR=$(realpath -P ${CI_BUILDS_DIR})
$ echo CCACHE_BASEDIR=${CCACHE_BASEDIR}
CCACHE_BASEDIR=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482
$ export CCACHE_MAXSIZE=512M
$ export CCACHE_DIR="${TMPDIR}/ccache"
$ mkdir -p ${CCACHE_DIR}
$ if [ -f ${CI_PROJECT_DIR}/ccache.tar ]; then
$ tar -C "${CCACHE_DIR}" -xf "${CI_PROJECT_DIR}/ccache.tar"
$ fi
$ ccache --zero-stats
Statistics zeroed
$ ccache --show-stats --verbose
Cache directory: /gpfs/bbp.cscs.ch/ssd/slurmTmpFS/bbpcihpcproj12/2255980/ccache
Config file: /gpfs/bbp.cscs.ch/ssd/slurmTmpFS/bbpcihpcproj12/2255980/ccache/ccache.conf
System config file: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/ccache-4.7.4-eompz5/etc/ccache.conf
Stats updated: Mon Jun 17 22:19:56 2024
Local storage:
Cache size (GB): 0.47 / 0.51 (92.26%)
Files: 10722
Hits: 0
Misses: 0
Reads: 0
Writes: 0
$ fi
$ module load unstable git ${SPACK_EXTRA_MODULES}
$ spack ${SPACK_EXTRA_FLAGS} spec -Il ${SPACK_FULL_SPEC}
Input spec
--------------------------------
- neuron%nvhpc~caliper+coreneuron+gpu~legacy-unit~openmp~rx3d~shared~sympy+tests~unified build_type=FastDebug model_tests=channel-benchmark,olfactory,tqperf-heavy
- ^/53hy2ex7xntc24cnbuojh6rrc3l2auap
Concretized
--------------------------------
- drodya6 neuron@git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662=develop%nvhpc@23.1~backtrace~caliper+coreneuron+gpu~interviews~ipo~legacy-unit+mpi~openmp~prcellstate+python+report~rx3d~shared~sympy~sympyopt+tests~unified build_system=cmake build_type=FastDebug generator=make model_tests=channel-benchmark,olfactory,tqperf-heavy sanitizers=None arch=linux-rhel7-skylake
[^] tj3mv5i ^binutils@2.41%gcc@12.3.0+gas+gold~gprofng~headers~interwork+ld~libiberty~lto~nls~pgo+plugins build_system=autotools compress_debug_sections=zlib libs=shared,static arch=linux-rhel7-skylake
[^] 7jd6loj ^diffutils@3.9%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[^] e533uuv ^pkgconf@1.9.5%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[^] z7jpg7s ^zlib-ng@2.1.4%gcc@12.3.0+compat+opt build_system=autotools arch=linux-rhel7-skylake
[^] aivjoo2 ^zstd@1.5.5%gcc@12.3.0+programs build_system=makefile compression=none libs=shared,static arch=linux-rhel7-skylake
[e] yn5fbwg ^bison@3.8.2%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[e] rd65pst ^boost@1.83.0%gcc@12.3.0~atomic~chrono~clanglibcpp~container~context~contract~coroutine~date_time~debug~exception~fiber+filesystem~graph~graph_parallel~icu~iostreams~json~locale~log~math~mpi+multithreaded~nowide~numpy+pic~program_options~python~random~regex+serialization+shared~signals~singlethreaded~stacktrace~system~taggedlayout+test~thread~timer~type_erasure~versionedlayout~wave build_system=generic cxxstd=98 patches=a440f96 visibility=hidden arch=linux-rhel7-skylake
[e] b5zzpr3 ^cmake@3.27.7%gcc@12.3.0~doc+ncurses+ownlibs build_system=generic build_type=Release arch=linux-rhel7-skylake
[e] 3fsjp3m ^cuda@12.0.0%gcc@12.3.0~allow-unsupported-compilers~dev build_system=generic arch=linux-rhel7-skylake
[e] 77vzaxs ^flex@2.6.3%gcc@12.3.0+lex~nls build_system=autotools arch=linux-rhel7-skylake
[^] nbi5w5c ^gettext@0.22.3%gcc@12.3.0+bzip2+curses+git~libunistring+libxml2+pic+shared+tar+xz build_system=autotools arch=linux-rhel7-skylake
[^] vdqwmgi ^bzip2@1.0.8%gcc@12.3.0~debug~pic+shared build_system=generic arch=linux-rhel7-skylake
[^] nv4xh4v ^libiconv@1.17%gcc@12.3.0 build_system=autotools libs=shared,static arch=linux-rhel7-skylake
[^] oh2g4in ^libxml2@2.10.3%gcc@12.3.0+pic~python+shared build_system=autotools arch=linux-rhel7-skylake
[^] zz4acmm ^tar@1.34%gcc@12.3.0 build_system=autotools zip=pigz arch=linux-rhel7-skylake
[^] dwjcguu ^pigz@2.7%gcc@12.3.0 build_system=makefile arch=linux-rhel7-skylake
[^] wwn5enj ^xz@5.4.1%gcc@12.3.0~pic build_system=autotools libs=shared,static arch=linux-rhel7-skylake
[^] swjylul ^gmake@4.4.1%gcc@12.3.0~guile build_system=generic arch=linux-rhel7-skylake
[e] h6t3hgb ^hpe-mpi@2.27.p1.hmpt%gcc@12.3.0 build_system=generic arch=linux-rhel7-skylake
- az6cwid ^libsonata-report@git.5602aadfa710d6766ce23cd151a1855190271bd8=develop%nvhpc@23.1~ipo+mpi build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] 5o77yem ^hdf5@1.14.3%gcc@12.3.0+cxx~fortran+hl~ipo~java~map+mpi+shared~szip~threadsafe+tools api=default build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] ihotvbs ^spdlog@1.12.0%gcc@12.3.0+fmt_external~ipo+shared build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] 6kdbhvi ^ncurses@6.4%gcc@12.3.0~symlinks+termlib abi=none build_system=autotools arch=linux-rhel7-skylake
[e] omn6mm4 ^ninja@1.11.1%gcc@12.3.0+re2c build_system=generic arch=linux-rhel7-skylake
[+] 53hy2ex ^nmodl@git.5ff221d045c92389b4cab5ee159d46770aa12665=develop%gcc@12.3.0~ipo~legacy-unit~llvm~llvm_cuda~python~tests build_system=cmake build_type=Release generator=ninja arch=linux-rhel7-skylake
[^] pywly2v ^catch2@3.4.0%gcc@12.3.0~ipo+pic~shared build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] ud3echq ^cli11@2.3.2%gcc@12.3.0~ipo build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] evtttrh ^fmt@10.1.1%gcc@12.3.0~ipo+pic~shared build_system=cmake build_type=Release cxxstd=11 generator=make arch=linux-rhel7-skylake
[^] teske2k ^nlohmann-json@3.9.1%gcc@12.3.0~ipo+multiple_headers build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] 5dylnca ^py-find-libpython@0.3.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 7validy ^py-jinja2@3.1.2%gcc@12.3.0~i18n build_system=python_pip arch=linux-rhel7-skylake
[^] r3ehtmw ^py-markupsafe@2.1.3%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] tabj2mo ^py-pybind11@2.11.1%gcc@12.3.0~ipo build_system=cmake build_type=Release generator=ninja arch=linux-rhel7-skylake
[^] 2inh3rt ^py-pyyaml@5.4.1%gcc@12.3.0+libyaml build_system=python_pip arch=linux-rhel7-skylake
[^] bzl4xcz ^libyaml@0.2.5%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[^] x733hwb ^py-mpi4py@3.1.4%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] m3dslef ^py-cython@0.29.36%gcc@12.3.0 build_system=python_pip patches=c4369ad arch=linux-rhel7-skylake
[^] aj3rk42 ^py-wheel@0.41.2%gcc@12.3.0 build_system=generic arch=linux-rhel7-skylake
[^] elr5pnt ^py-numpy@1.26.1%gcc@12.3.0 build_system=python_pip patches=873745d arch=linux-rhel7-skylake
[e] w2ldcy2 ^intel-oneapi-mkl@2023.2.0%gcc@12.3.0~cluster+envmods~ilp64+shared build_system=generic mpi_family=none threads=none arch=linux-rhel7-skylake
[^] 3y7uuwr ^py-pyproject-metadata@0.7.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] uqml2to ^py-packaging@23.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] h6f6feu ^py-flit-core@3.9.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 77ku3vv ^py-pip@23.1.2%gcc@12.3.0 build_system=generic arch=linux-rhel7-skylake
[^] lrf2u3h ^py-pytest@7.3.2%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] mvxx6gh ^py-iniconfig@2.0.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] cbpzath ^py-hatch-vcs@0.3.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 2o7gdvi ^py-hatchling@1.21.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 6domhtg ^py-editables@0.3%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] edobf76 ^py-pathspec@0.11.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] a6ialdh ^py-trove-classifiers@2023.8.7%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] jurd5ga ^py-calver@2022.6.26%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 6su7kvx ^py-pluggy@1.0.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] sokbfzv ^py-setuptools-scm@8.0.4%gcc@12.3.0+toml build_system=python_pip arch=linux-rhel7-skylake
[e] 2sazdxk ^git@2.42.0%gcc@12.3.0+man+nls+perl+subtree~svn~tcltk build_system=autotools arch=linux-rhel7-skylake
[^] xwl5l6q ^py-tomli@2.0.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 275jtek ^py-typing-extensions@4.8.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] z5nf6n2 ^py-pytest-cov@4.0.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] wuxetkw ^py-coverage@7.2.6%gcc@12.3.0+toml build_system=python_pip arch=linux-rhel7-skylake
[^] p3xbqxj ^py-setuptools@68.0.0%gcc@12.3.0 build_system=generic arch=linux-rhel7-skylake
[^] t5tovex ^py-sympy@1.11.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 4fflyib ^py-mpmath@1.2.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[e] 5wl76vp ^python@3.11.6%gcc@12.3.0+bz2+crypt+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tkinter+uuid+zlib build_system=generic patches=13fa8bf,b0615b2,ebdca64,f2fd060 arch=linux-rhel7-skylake
[^] pdugg7r ^readline@8.2%gcc@12.3.0 build_system=autotools patches=bbf97f1 arch=linux-rhel7-skylake
$ set -o pipefail
$ (spack ${SPACK_EXTRA_FLAGS} install --overwrite -y -j${SLURM_CPUS_PER_TASK} --log-format=junit --log-file=${CI_PROJECT_DIR}/install.xml --keep-stage ${SPACK_FULL_SPEC} | tee log) || install_failed=1
==> Warning: Expected user 904556 to own /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482, but it is owned by 0
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/zlib-ng-2.1.4-z7jpg7
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/zstd-1.5.5-aivjoo
==> bison@3.8.2 : has external module in ['bison/3.8.2']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/bison-3.8.2-qcx3sg (external bison-3.8.2-yn5fbwgteilgqg6b62shkhkjg3hlwmrq)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/boost-1.83.0-2quv7w (external boost-1.83.0-rd65pstwb56uftszduzg7lsiq4za4lnn)
==> cmake@3.27.7 : has external module in ['cmake/3.27.7']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/cmake-3.27.7-slyoes (external cmake-3.27.7-b5zzpr3mwm7jxv6bvvrs6zpeg62cfhbu)
==> cuda@12.0.0 : has external module in ['cuda/12.0.0']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/cuda-12.0.0-ucajzb (external cuda-12.0.0-3fsjp3mjnqnrrtfa6vspkddejnyei5sa)
==> flex@2.6.3 : has external module in ['flex/2.6.3']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/flex-2.6.3-edx4lf (external flex-2.6.3-77vzaxsa3g7wr3omktr4skpetx5ds4pt)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/bzip2-1.0.8-vdqwmg
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/libiconv-1.17-nv4xh4
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/xz-5.4.1-wwn5en
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/ncurses-6.4-6kdbhv
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/gmake-4.4.1-swjylu
==> hpe-mpi@2.27.p1.hmpt : has external module in ['hpe-mpi/2.27.p1.hmpt']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/hpe-mpi-2.27.p1.hmpt-6rr256 (external hpe-mpi-2.27.p1.hmpt-h6t3hgbguhacajbyzlp43xpawsnreb3m)
==> ninja@1.11.1 : has external module in ['ninja/1.11.1']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/ninja-1.11.1-nxtlgo (external ninja-1.11.1-omn6mm4a3zsbpbkptvdwxs6kkrh6yafw)
==> python@3.11.6 : has external module in ['python/3.11.6']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/python-3.11.6-bj4i6m (external python-3.11.6-5wl76vphfvpcapfaipipf7xn2xylnc4o)
==> intel-oneapi-mkl@2023.2.0 : has external module in ['intel-oneapi-mkl/2023.2.0']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/intel-oneapi-mkl-2023.2.0-twl2n4 (external intel-oneapi-mkl-2023.2.0-w2ldcy2y2urm3uaa7omu3w7nhwsqt433)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/libyaml-0.2.5-bzl4xc
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/fmt-10.1.1-evtttr
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/pigz-2.7-dwjcgu
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/pkgconf-1.9.5-e533uu
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/cli11-2.3.2-ud3ech
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/nlohmann-json-3.9.1-teske2
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/readline-8.2-pdugg7
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/catch2-3.4.0-pywly2
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-coverage-7.2.6-wuxetk
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-iniconfig-2.0.0-mvxx6g
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pip-23.1.2-77ku3v
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/spdlog-1.12.0-ihotvb
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/tar-1.34-zz4acm
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/libxml2-2.10.3-oh2g4i
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/hdf5-1.14.3-5o77ye
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/binutils-2.41-tj3mv5
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-markupsafe-2.1.3-r3ehtm
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pluggy-1.0.0-6su7kv
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-numpy-1.26.1-elr5pn
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-mpmath-1.2.1-4fflyi
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-setuptools-68.0.0-p3xbqx
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-packaging-23.1-uqml2t
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/gettext-0.22.3-nbi5w5
==> Installing libsonata-report-git.5602aadfa710d6766ce23cd151a1855190271bd8=develop-az6cwiduk3774jmb44p477xjr6dtnm4g [40/50]
==> No binary for libsonata-report-git.5602aadfa710d6766ce23cd151a1855190271bd8=develop-az6cwiduk3774jmb44p477xjr6dtnm4g found: installing from source
==> No patches needed for libsonata-report
==> libsonata-report: Executing phase: 'cmake'
==> libsonata-report: Executing phase: 'build'
==> libsonata-report: Executing phase: 'install'
==> libsonata-report: Successfully installed libsonata-report-git.5602aadfa710d6766ce23cd151a1855190271bd8=develop-az6cwiduk3774jmb44p477xjr6dtnm4g
Stage: 2.79s. Cmake: 3.66s. Build: 1.15s. Install: 0.08s. Post-install: 0.10s. Total: 7.94s
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/software/install_nvhpc-23.1-skylake/libsonata-report-git.5602aadfa710d6766ce23cd151a1855190271bd8_develop-az6cwi
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-jinja2-3.1.2-7valid
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pyyaml-5.4.1-2inh3r
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-sympy-1.11.1-t5tove
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-find-libpython-0.3.1-5dylnc
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-mpi4py-3.1.4-x733hw
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pybind11-2.11.1-tabj2m
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pytest-7.3.2-lrf2u3
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/software/install_gcc-12.3.0-skylake/nmodl-git.5ff221d045c92389b4cab5ee159d46770aa12665_develop-53hy2e
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pytest-cov-4.0.0-z5nf6n
==> Installing neuron-git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662=develop-drodya6odybnvasdqqrsac2xoga5jhtt [50/50]
==> No binary for neuron-git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662=develop-drodya6odybnvasdqqrsac2xoga5jhtt found: installing from source
==> No patches needed for neuron
==> neuron: Executing phase: 'cmake'
==> neuron: Executing phase: 'build'
==> neuron: Executing phase: 'install'
==> neuron: Successfully installed neuron-git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662=develop-drodya6odybnvasdqqrsac2xoga5jhtt
Stage: 22.68s. Cmake: 1m 42.14s. Build: 39m 53.05s. Install: 1m 10.81s. Post-install: 0.58s. Total: 43m 9.93s
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/software/install_nvhpc-23.1-skylake/neuron-git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662_develop-drodya
$ set +o pipefail
$ chmod -R g+rX "${SPACK_BUILD}"
$ if [[ ${install_failed} == 1 ]]; then exit 1; fi
$ SPACK_INSTALLED_HASH=$(spack ${SPACK_EXTRA_FLAGS} find --format "{hash}" /$(sed -ne '${s/.*-//;p}' log))
$ echo "Determined the installed hash to be ${SPACK_INSTALLED_HASH}"
Determined the installed hash to be drodya6odybnvasdqqrsac2xoga5jhtt
$ SPACK_STAGE_DIR=$(spack location -s "${SPACK_FULL_SPEC}")
$ SPACK_BUILD_DIR=$(spack location -b "${SPACK_FULL_SPEC}")
$ SPACK_SOURCE_DIR=${SPACK_STAGE_DIR}/spack-src
$ if [ ${SPACK_USE_CCACHE+x} ]; then
$ ccache --cleanup
$ ccache --show-stats --verbose
Cache directory: /gpfs/bbp.cscs.ch/ssd/slurmTmpFS/bbpcihpcproj12/2255980/ccache
Config file: /gpfs/bbp.cscs.ch/ssd/slurmTmpFS/bbpcihpcproj12/2255980/ccache/ccache.conf
System config file: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/ccache-4.7.4-eompz5/etc/ccache.conf
Stats updated: Mon Jun 17 23:06:33 2024
Cacheable calls: 1018 / 1174 (86.71%)
Hits: 724 / 1018 (71.12%)
Direct: 367 / 724 (50.69%)
Preprocessed: 357 / 724 (49.31%)
Misses: 294 / 1018 (28.88%)
Uncacheable calls: 156 / 1174 (13.29%)
Autoconf compile/link: 5 / 156 ( 3.21%)
Called for linking: 130 / 156 (83.33%)
Called for preprocessing: 2 / 156 ( 1.28%)
Compilation failed: 2 / 156 ( 1.28%)
No input file: 16 / 156 (10.26%)
Preprocessing failed: 1 / 156 ( 0.64%)
Successful lookups:
Direct: 367 / 1021 (35.95%)
Preprocessed: 357 / 653 (54.67%)
Local storage:
Cache size (GB): 0.50 / 0.51 (98.38%)
Files: 11214
Cleanups: 7
Hits: 724 / 1020 (70.98%)
Misses: 296 / 1020 (29.02%)
Reads: 2041
Writes: 869
$ tar -C "${CCACHE_DIR}" -cf "${CI_PROJECT_DIR}/ccache.tar" .
$ fi
$ touch ${SPACK_STAGE_DIR}/spack-configure-args.txt
$ cp ${SPACK_STAGE_DIR}/spack-{build-env,build-out,configure-args}.txt ${CI_PROJECT_DIR}/
$ echo "SPACK_BUILD_DIR=${SPACK_BUILD_DIR}" > ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_FULL_SPEC=${SPACK_FULL_SPEC}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_SOURCE_DIR=${SPACK_SOURCE_DIR}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_INSTALLED_HASH=${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ SPACK_PACKAGE_SLUGIFY=$(echo -n ${SPACK_PACKAGE} | tr -c '[:alnum:]' '_' | tr '[:lower:]' '[:upper:]')
$ echo "${SPACK_PACKAGE_SLUGIFY}_INSTALLED_HASH=${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_PACKAGE_DEPENDENCY_ON_PREVIOUS_JOB=^/${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ num_failures=$(module load unstable python-dev; python -c "from lxml import etree; xml = etree.parse('${CI_PROJECT_DIR}/install.xml'); print(sum(1 for _ in xml.getroot().iter('failure')) + sum(1 for _ in xml.getroot().iter('error')))")
$ if [[ ${num_failures} > 0 ]]; then exit ${num_failures}; fi
section_end:1718658401:step_script section_start:1718658401:archive_cache Saving cache for successful job
Using git from spack modules
Creating cache build:neuron:nmodl:nvhpc:acc:legacy-1-non_protected...
Runtime platform  arch=amd64 os=linux pid=180861 revision=58ba2b95 version=14.2.0
ccache.tar: found 1 matching files and directories
Uploading cache.zip to https://bbpobjectstorage.epfl.ch/gitlab-runners-cache/project/2160/build%3Aneuron%3Anmodl%3Anvhpc%3Aacc%3Alegacy-1-non_protected
Created cache
section_end:1718658424:archive_cache section_start:1718658424:upload_artifacts_on_success Uploading artifacts for successful job
Using git from spack modules
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=181120 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
spack_build_info.env: found 1 matching files and directories
spack_clone_variables.env: found 1 matching files and directories
initial_environment.env: found 1 matching files and directories
spack-build-env.txt: found 1 matching files and directories
spack-build-out.txt: found 1 matching files and directories
spack-configure-args.txt: found 1 matching files and directories
Uploading artifacts as "archive" to coordinator... ok id=1322444 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=181202 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
Uploading artifacts as "junit" to coordinator... ok id=1322444 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=181249 revision=58ba2b95 version=14.2.0
spack_build_info.env: found 1 matching files and directories
spack_clone_variables.env: found 1 matching files and directories
Uploading artifacts as "dotenv" to coordinator... ok id=1322444 responseStatus=201 Created token=glcbt-64
section_end:1718658426:upload_artifacts_on_success section_start:1718658426:cleanup_file_variables Cleaning up project directory and file based variables
Using git from spack modules
section_end:1718658427:cleanup_file_variables Job succeeded
Running with gitlab-runner 15.5.0 (0d4137b8)
 on BB5 map runner pnPo3yJy
section_start:1718655569:resolve_secrets Resolving secrets
section_end:1718655569:resolve_secrets section_start:1718655569:prepare_executor Preparing the "custom" executor
Using Custom executor with driver BB5 PROD runner v0.0.3...
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor3955483139, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name nrn
Pipeline ID 217482, build ref , job ID 1322445
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482, optional exclusive flag , optional cpus per task flag --cpus-per-task=8, optional qos flag , optional reservation flag
A slurm job will be created with name GL_J1322445_PROD_P2160_CP3_C5
Job parameters: memory=160G, cpus_per_task=8, duration=2:00:00, constraint=cpu ntasks=2 account=proj9998 user=bbpcihpcproj12 partition=prod qos= reservation=
Not executing the chown -R
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx]
Submitted batch job 2255981
job state: PD
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=2 --cpus-per-task=8 --mem=160G --job-name=GL_J1322445_PROD_P2160_CP3_C5 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482 --time=2:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482 --ntasks=2 --jobid=2255981 --cpus-per-task=8 --mem=160G
section_end:1718655572:prepare_executor section_start:1718655572:prepare_script Preparing environment
Using git from spack modules
Running on r3i5n31 via bbpv1.epfl.ch...
section_end:1718655575:prepare_script section_start:1718655575:get_sources Getting source from Git repository
Using git from spack modules
Skipping Git repository setup
Skipping Git checkout
Skipping Git submodules setup
section_end:1718655576:get_sources section_start:1718655576:restore_cache Restoring cache
Using git from spack modules
Checking cache for build:neuron:nmodl:nvhpc:acc:shared-1-non_protected...
Runtime platform  arch=amd64 os=linux pid=123289 revision=58ba2b95 version=14.2.0
cache.zip is up to date 
Successfully extracted cache
section_end:1718655582:restore_cache section_start:1718655582:download_artifacts Downloading artifacts
Using git from spack modules
Downloading artifacts for build:nmodl (1322441)...
Runtime platform  arch=amd64 os=linux pid=123493 revision=58ba2b95 version=14.2.0
Downloading artifacts from coordinator... ok  id=1322441 responseStatus=200 OK token=glcbt-64
section_end:1718655583:download_artifacts section_start:1718655583:step_script Executing "step_script" stage of the job script
WARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426
Using git from spack modules
$ SPACK_BUILD="${PWD}/spack-build"
$ env -0 | sort -z | xargs -0 -L 1 echo > initial_environment.env
$ . ${SPACK_ROOT}/share/spack/setup-env.sh
$ export SPACK_USER_CONFIG_PATH=${PWD}/spack-config
$ mkdir ${SPACK_USER_CONFIG_PATH}
$ cat > ${SPACK_USER_CONFIG_PATH}/config.yaml << END_SCRIPT # collapsed multi-line command
$ spack ${SPACK_EXTRA_FLAGS} config add concretizer:reuse:false
$ spack ${SPACK_EXTRA_FLAGS} config blame config
--- config:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322445/spack-config/config.yaml:2 build_stage:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322445/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322445/spack-build
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322445/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322445/spack-source-cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/config.yaml:2 ccache: True
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:2 install_tree:
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:3 root: $user_cache_path/software
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:4 projections:
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:5 all: install_{compiler.name}-{compiler.version}-{target}/{name}-{version}-{hash:6}
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:7 environments_root: $user_cache_path/environments
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:9 build_jobs: 8
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:18 extensions:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:19 - $spack/bluebrain/spack-scripting
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:37 template_dirs:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:38 - $spack/share/spack/templates
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:41 license_dir: $spack/etc/spack/licenses
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:81 test_stage: $user_cache_path/test
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:94 misc_cache: $user_cache_path/cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:100 connect_timeout: 10
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:105 verify_ssl: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:113 suppress_gpg_warnings: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:119 install_missing_compilers: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:124 checksum: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:129 deprecated: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:134 dirty: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:142 build_language: C
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:151 locks: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:156 url_fetch_method: urllib
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:185 concretizer: clingo
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:192 db_lock_timeout: 60
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:200 package_lock_timeout: null
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:205 shared_linking:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:210 type: rpath
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:216 bind: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:221 allow_sgid: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:227 install_status: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:231 binary_index_ttl: 600
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:233 flags:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:235 keep_werror: none
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:240 aliases:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:241 concretise: concretize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:242 containerise: containerize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:243 rm: remove
_builtin debug: False
$ spack ${SPACK_EXTRA_FLAGS} config blame concretizer
--- concretizer:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322445/spack-config/concretizer.yaml:2 reuse: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:23 targets:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:28 granularity: microarchitectures
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:32 host_compatible: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:38 unify: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:40 duplicates:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:44 strategy: minimal
$ export XDG_CONFIG_HOME=${CI_BUILDS_DIR}/J${CI_JOB_ID}_local_config
$ echo "Configuring git to use CI_JOB_TOKEN to access git@bbpgitlab.epfl.ch (${XDG_CONFIG_HOME})"
Configuring git to use CI_JOB_TOKEN to access git@bbpgitlab.epfl.ch (/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482/J1322445_local_config)
$ mkdir -p "${XDG_CONFIG_HOME}/git"
$ echo -e "[url \"https://gitlab-ci-token:${CI_JOB_TOKEN}@bbpgitlab.epfl.ch/\"]\n insteadOf = git@bbpgitlab.epfl.ch:" > "${XDG_CONFIG_HOME}/git/config"
$ echo -e "[url \"https://gitlab-ci-token:${CI_JOB_TOKEN}@bbpgitlab.epfl.ch/\"]\n insteadOf = ssh://git@bbpgitlab.epfl.ch/" >> "${XDG_CONFIG_HOME}/git/config"
$ cat "${XDG_CONFIG_HOME}/git/config"
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
insteadOf = git@bbpgitlab.epfl.ch:
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
insteadOf = ssh://git@bbpgitlab.epfl.ch/
$ SPACK_FULL_SPEC="${SPACK_PACKAGE}${SPACK_PACKAGE_COMPILER:+%}${SPACK_PACKAGE_COMPILER} ${SPACK_PACKAGE_SPEC} ${SPACK_PACKAGE_DEPENDENCIES} ${SPACK_PACKAGE_DEPENDENCY_ON_PREVIOUS_JOB}"
$ echo "Preparing to install ${SPACK_FULL_SPEC}"
Preparing to install neuron%nvhpc ~rx3d~caliper+gpu+coreneuron~legacy-unit~openmp+shared+sympy+tests~unified build_type=FastDebug model_tests=channel-benchmark,olfactory,tqperf-heavy ^/53hy2ex7xntc24cnbuojh6rrc3l2auap
$ if [ ${SPACK_USE_CCACHE+x} ]; then
$ module load unstable ccache
$ export CCACHE_BASEDIR=$(realpath -P ${CI_BUILDS_DIR})
$ echo CCACHE_BASEDIR=${CCACHE_BASEDIR}
CCACHE_BASEDIR=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482
$ export CCACHE_MAXSIZE=512M
$ export CCACHE_DIR="${TMPDIR}/ccache"
$ mkdir -p ${CCACHE_DIR}
$ if [ -f ${CI_PROJECT_DIR}/ccache.tar ]; then
$ tar -C "${CCACHE_DIR}" -xf "${CI_PROJECT_DIR}/ccache.tar"
$ fi
$ ccache --zero-stats
Statistics zeroed
$ ccache --show-stats --verbose
Cache directory: /gpfs/bbp.cscs.ch/ssd/slurmTmpFS/bbpcihpcproj12/2255981/ccache
Config file: /gpfs/bbp.cscs.ch/ssd/slurmTmpFS/bbpcihpcproj12/2255981/ccache/ccache.conf
System config file: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/ccache-4.7.4-eompz5/etc/ccache.conf
Stats updated: Mon Jun 17 22:19:55 2024
Local storage:
Cache size (GB): 0.48 / 0.51 (94.06%)
Files: 10543
Hits: 0
Misses: 0
Reads: 0
Writes: 0
$ fi
$ module load unstable git ${SPACK_EXTRA_MODULES}
$ spack ${SPACK_EXTRA_FLAGS} spec -Il ${SPACK_FULL_SPEC}
Input spec
--------------------------------
- neuron%nvhpc~caliper+coreneuron+gpu~legacy-unit~openmp~rx3d+shared+sympy+tests~unified build_type=FastDebug model_tests=channel-benchmark,olfactory,tqperf-heavy
- ^/53hy2ex7xntc24cnbuojh6rrc3l2auap
Concretized
--------------------------------
- bysapcg neuron@git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662=develop%nvhpc@23.1~backtrace~caliper+coreneuron+gpu~interviews~ipo~legacy-unit+mpi~openmp~prcellstate+python+report~rx3d+shared+sympy~sympyopt+tests~unified build_system=cmake build_type=FastDebug generator=make model_tests=channel-benchmark,olfactory,tqperf-heavy sanitizers=None arch=linux-rhel7-skylake
[^] tj3mv5i ^binutils@2.41%gcc@12.3.0+gas+gold~gprofng~headers~interwork+ld~libiberty~lto~nls~pgo+plugins build_system=autotools compress_debug_sections=zlib libs=shared,static arch=linux-rhel7-skylake
[^] 7jd6loj ^diffutils@3.9%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[^] e533uuv ^pkgconf@1.9.5%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[^] z7jpg7s ^zlib-ng@2.1.4%gcc@12.3.0+compat+opt build_system=autotools arch=linux-rhel7-skylake
[^] aivjoo2 ^zstd@1.5.5%gcc@12.3.0+programs build_system=makefile compression=none libs=shared,static arch=linux-rhel7-skylake
[e] yn5fbwg ^bison@3.8.2%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[e] rd65pst ^boost@1.83.0%gcc@12.3.0~atomic~chrono~clanglibcpp~container~context~contract~coroutine~date_time~debug~exception~fiber+filesystem~graph~graph_parallel~icu~iostreams~json~locale~log~math~mpi+multithreaded~nowide~numpy+pic~program_options~python~random~regex+serialization+shared~signals~singlethreaded~stacktrace~system~taggedlayout+test~thread~timer~type_erasure~versionedlayout~wave build_system=generic cxxstd=98 patches=a440f96 visibility=hidden arch=linux-rhel7-skylake
[e] b5zzpr3 ^cmake@3.27.7%gcc@12.3.0~doc+ncurses+ownlibs build_system=generic build_type=Release arch=linux-rhel7-skylake
[e] 3fsjp3m ^cuda@12.0.0%gcc@12.3.0~allow-unsupported-compilers~dev build_system=generic arch=linux-rhel7-skylake
[e] 77vzaxs ^flex@2.6.3%gcc@12.3.0+lex~nls build_system=autotools arch=linux-rhel7-skylake
[^] nbi5w5c ^gettext@0.22.3%gcc@12.3.0+bzip2+curses+git~libunistring+libxml2+pic+shared+tar+xz build_system=autotools arch=linux-rhel7-skylake
[^] vdqwmgi ^bzip2@1.0.8%gcc@12.3.0~debug~pic+shared build_system=generic arch=linux-rhel7-skylake
[^] nv4xh4v ^libiconv@1.17%gcc@12.3.0 build_system=autotools libs=shared,static arch=linux-rhel7-skylake
[^] oh2g4in ^libxml2@2.10.3%gcc@12.3.0+pic~python+shared build_system=autotools arch=linux-rhel7-skylake
[^] zz4acmm ^tar@1.34%gcc@12.3.0 build_system=autotools zip=pigz arch=linux-rhel7-skylake
[^] dwjcguu ^pigz@2.7%gcc@12.3.0 build_system=makefile arch=linux-rhel7-skylake
[^] wwn5enj ^xz@5.4.1%gcc@12.3.0~pic build_system=autotools libs=shared,static arch=linux-rhel7-skylake
[^] swjylul ^gmake@4.4.1%gcc@12.3.0~guile build_system=generic arch=linux-rhel7-skylake
[e] h6t3hgb ^hpe-mpi@2.27.p1.hmpt%gcc@12.3.0 build_system=generic arch=linux-rhel7-skylake
- az6cwid ^libsonata-report@git.5602aadfa710d6766ce23cd151a1855190271bd8=develop%nvhpc@23.1~ipo+mpi build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] 5o77yem ^hdf5@1.14.3%gcc@12.3.0+cxx~fortran+hl~ipo~java~map+mpi+shared~szip~threadsafe+tools api=default build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] ihotvbs ^spdlog@1.12.0%gcc@12.3.0+fmt_external~ipo+shared build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] 6kdbhvi ^ncurses@6.4%gcc@12.3.0~symlinks+termlib abi=none build_system=autotools arch=linux-rhel7-skylake
[e] omn6mm4 ^ninja@1.11.1%gcc@12.3.0+re2c build_system=generic arch=linux-rhel7-skylake
[+] 53hy2ex ^nmodl@git.5ff221d045c92389b4cab5ee159d46770aa12665=develop%gcc@12.3.0~ipo~legacy-unit~llvm~llvm_cuda~python~tests build_system=cmake build_type=Release generator=ninja arch=linux-rhel7-skylake
[^] pywly2v ^catch2@3.4.0%gcc@12.3.0~ipo+pic~shared build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] ud3echq ^cli11@2.3.2%gcc@12.3.0~ipo build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] evtttrh ^fmt@10.1.1%gcc@12.3.0~ipo+pic~shared build_system=cmake build_type=Release cxxstd=11 generator=make arch=linux-rhel7-skylake
[^] teske2k ^nlohmann-json@3.9.1%gcc@12.3.0~ipo+multiple_headers build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] 5dylnca ^py-find-libpython@0.3.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 7validy ^py-jinja2@3.1.2%gcc@12.3.0~i18n build_system=python_pip arch=linux-rhel7-skylake
[^] r3ehtmw ^py-markupsafe@2.1.3%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] tabj2mo ^py-pybind11@2.11.1%gcc@12.3.0~ipo build_system=cmake build_type=Release generator=ninja arch=linux-rhel7-skylake
[^] 2inh3rt ^py-pyyaml@5.4.1%gcc@12.3.0+libyaml build_system=python_pip arch=linux-rhel7-skylake
[^] bzl4xcz ^libyaml@0.2.5%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[^] x733hwb ^py-mpi4py@3.1.4%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] m3dslef ^py-cython@0.29.36%gcc@12.3.0 build_system=python_pip patches=c4369ad arch=linux-rhel7-skylake
[^] aj3rk42 ^py-wheel@0.41.2%gcc@12.3.0 build_system=generic arch=linux-rhel7-skylake
[^] elr5pnt ^py-numpy@1.26.1%gcc@12.3.0 build_system=python_pip patches=873745d arch=linux-rhel7-skylake
[e] w2ldcy2 ^intel-oneapi-mkl@2023.2.0%gcc@12.3.0~cluster+envmods~ilp64+shared build_system=generic mpi_family=none threads=none arch=linux-rhel7-skylake
[^] 3y7uuwr ^py-pyproject-metadata@0.7.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] uqml2to ^py-packaging@23.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] h6f6feu ^py-flit-core@3.9.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 77ku3vv ^py-pip@23.1.2%gcc@12.3.0 build_system=generic arch=linux-rhel7-skylake
[^] lrf2u3h ^py-pytest@7.3.2%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] mvxx6gh ^py-iniconfig@2.0.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] cbpzath ^py-hatch-vcs@0.3.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 2o7gdvi ^py-hatchling@1.21.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 6domhtg ^py-editables@0.3%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] edobf76 ^py-pathspec@0.11.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] a6ialdh ^py-trove-classifiers@2023.8.7%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] jurd5ga ^py-calver@2022.6.26%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 6su7kvx ^py-pluggy@1.0.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] sokbfzv ^py-setuptools-scm@8.0.4%gcc@12.3.0+toml build_system=python_pip arch=linux-rhel7-skylake
[e] 2sazdxk ^git@2.42.0%gcc@12.3.0+man+nls+perl+subtree~svn~tcltk build_system=autotools arch=linux-rhel7-skylake
[^] xwl5l6q ^py-tomli@2.0.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 275jtek ^py-typing-extensions@4.8.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] z5nf6n2 ^py-pytest-cov@4.0.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] wuxetkw ^py-coverage@7.2.6%gcc@12.3.0+toml build_system=python_pip arch=linux-rhel7-skylake
[^] p3xbqxj ^py-setuptools@68.0.0%gcc@12.3.0 build_system=generic arch=linux-rhel7-skylake
[^] t5tovex ^py-sympy@1.11.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 4fflyib ^py-mpmath@1.2.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[e] 5wl76vp ^python@3.11.6%gcc@12.3.0+bz2+crypt+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tkinter+uuid+zlib build_system=generic patches=13fa8bf,b0615b2,ebdca64,f2fd060 arch=linux-rhel7-skylake
[^] pdugg7r ^readline@8.2%gcc@12.3.0 build_system=autotools patches=bbf97f1 arch=linux-rhel7-skylake
$ set -o pipefail
$ (spack ${SPACK_EXTRA_FLAGS} install --overwrite -y -j${SLURM_CPUS_PER_TASK} --log-format=junit --log-file=${CI_PROJECT_DIR}/install.xml --keep-stage ${SPACK_FULL_SPEC} | tee log) || install_failed=1
==> Warning: Expected user 904556 to own /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482, but it is owned by 0
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/zlib-ng-2.1.4-z7jpg7
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/zstd-1.5.5-aivjoo
==> bison@3.8.2 : has external module in ['bison/3.8.2']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/bison-3.8.2-qcx3sg (external bison-3.8.2-yn5fbwgteilgqg6b62shkhkjg3hlwmrq)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/boost-1.83.0-2quv7w (external boost-1.83.0-rd65pstwb56uftszduzg7lsiq4za4lnn)
==> cmake@3.27.7 : has external module in ['cmake/3.27.7']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/cmake-3.27.7-slyoes (external cmake-3.27.7-b5zzpr3mwm7jxv6bvvrs6zpeg62cfhbu)
==> cuda@12.0.0 : has external module in ['cuda/12.0.0']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/cuda-12.0.0-ucajzb (external cuda-12.0.0-3fsjp3mjnqnrrtfa6vspkddejnyei5sa)
==> flex@2.6.3 : has external module in ['flex/2.6.3']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/flex-2.6.3-edx4lf (external flex-2.6.3-77vzaxsa3g7wr3omktr4skpetx5ds4pt)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/bzip2-1.0.8-vdqwmg
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/libiconv-1.17-nv4xh4
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/xz-5.4.1-wwn5en
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/ncurses-6.4-6kdbhv
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/gmake-4.4.1-swjylu
==> hpe-mpi@2.27.p1.hmpt : has external module in ['hpe-mpi/2.27.p1.hmpt']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/hpe-mpi-2.27.p1.hmpt-6rr256 (external hpe-mpi-2.27.p1.hmpt-h6t3hgbguhacajbyzlp43xpawsnreb3m)
==> ninja@1.11.1 : has external module in ['ninja/1.11.1']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/ninja-1.11.1-nxtlgo (external ninja-1.11.1-omn6mm4a3zsbpbkptvdwxs6kkrh6yafw)
==> python@3.11.6 : has external module in ['python/3.11.6']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/python-3.11.6-bj4i6m (external python-3.11.6-5wl76vphfvpcapfaipipf7xn2xylnc4o)
==> intel-oneapi-mkl@2023.2.0 : has external module in ['intel-oneapi-mkl/2023.2.0']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/intel-oneapi-mkl-2023.2.0-twl2n4 (external intel-oneapi-mkl-2023.2.0-w2ldcy2y2urm3uaa7omu3w7nhwsqt433)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/libxml2-2.10.3-oh2g4i
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/libyaml-0.2.5-bzl4xc
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/binutils-2.41-tj3mv5
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/nlohmann-json-3.9.1-teske2
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/fmt-10.1.1-evtttr
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/cli11-2.3.2-ud3ech
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/readline-8.2-pdugg7
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/pigz-2.7-dwjcgu
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/pkgconf-1.9.5-e533uu
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/catch2-3.4.0-pywly2
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pybind11-2.11.1-tabj2m
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-mpi4py-3.1.4-x733hw
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-markupsafe-2.1.3-r3ehtm
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pip-23.1.2-77ku3v
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/spdlog-1.12.0-ihotvb
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/tar-1.34-zz4acm
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/hdf5-1.14.3-5o77ye
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-jinja2-3.1.2-7valid
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-packaging-23.1-uqml2t
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pluggy-1.0.0-6su7kv
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-numpy-1.26.1-elr5pn
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-coverage-7.2.6-wuxetk
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-setuptools-68.0.0-p3xbqx
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-iniconfig-2.0.0-mvxx6g
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/gettext-0.22.3-nbi5w5
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pyyaml-5.4.1-2inh3r
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-mpmath-1.2.1-4fflyi
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-find-libpython-0.3.1-5dylnc
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pytest-7.3.2-lrf2u3
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-sympy-1.11.1-t5tove
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pytest-cov-4.0.0-z5nf6n
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/software/install_gcc-12.3.0-skylake/nmodl-git.5ff221d045c92389b4cab5ee159d46770aa12665_develop-53hy2e
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/software/install_nvhpc-23.1-skylake/libsonata-report-git.5602aadfa710d6766ce23cd151a1855190271bd8_develop-az6cwi
==> Installing neuron-git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662=develop-bysapcgth5mqs2hl5lox4l6ry55fbxbb [50/50]
==> No binary for neuron-git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662=develop-bysapcgth5mqs2hl5lox4l6ry55fbxbb found: installing from source
==> No patches needed for neuron
==> neuron: Executing phase: 'cmake'
==> neuron: Executing phase: 'build'
==> neuron: Executing phase: 'install'
==> neuron: Successfully installed neuron-git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662=develop-bysapcgth5mqs2hl5lox4l6ry55fbxbb
Stage: 20.70s. Cmake: 1m 5.69s. Build: 40m 29.00s. Install: 1m 14.05s. Post-install: 0.59s. Total: 43m 10.50s
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/software/install_nvhpc-23.1-skylake/neuron-git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662_develop-bysapc
$ set +o pipefail
$ chmod -R g+rX "${SPACK_BUILD}"
$ if [[ ${install_failed} == 1 ]]; then exit 1; fi
$ SPACK_INSTALLED_HASH=$(spack ${SPACK_EXTRA_FLAGS} find --format "{hash}" /$(sed -ne '${s/.*-//;p}' log))
$ echo "Determined the installed hash to be ${SPACK_INSTALLED_HASH}"
Determined the installed hash to be bysapcgth5mqs2hl5lox4l6ry55fbxbb
$ SPACK_STAGE_DIR=$(spack location -s "${SPACK_FULL_SPEC}")
$ SPACK_BUILD_DIR=$(spack location -b "${SPACK_FULL_SPEC}")
$ SPACK_SOURCE_DIR=${SPACK_STAGE_DIR}/spack-src
$ if [ ${SPACK_USE_CCACHE+x} ]; then
$ ccache --cleanup
$ ccache --show-stats --verbose
Cache directory: /gpfs/bbp.cscs.ch/ssd/slurmTmpFS/bbpcihpcproj12/2255981/ccache
Config file: /gpfs/bbp.cscs.ch/ssd/slurmTmpFS/bbpcihpcproj12/2255981/ccache/ccache.conf
System config file: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/ccache-4.7.4-eompz5/etc/ccache.conf
Stats updated: Mon Jun 17 23:06:33 2024
Cacheable calls: 998 / 1152 (86.63%)
Hits: 705 / 998 (70.64%)
Direct: 347 / 705 (49.22%)
Preprocessed: 358 / 705 (50.78%)
Misses: 293 / 998 (29.36%)
Uncacheable calls: 154 / 1152 (13.37%)
Autoconf compile/link: 5 / 154 ( 3.25%)
Called for linking: 136 / 154 (88.31%)
Called for preprocessing: 2 / 154 ( 1.30%)
Compilation failed: 2 / 154 ( 1.30%)
No input file: 8 / 154 ( 5.19%)
Preprocessing failed: 1 / 154 ( 0.65%)
Successful lookups:
Direct: 347 / 1001 (34.67%)
Preprocessed: 358 / 653 (54.82%)
Local storage:
Cache size (GB): 0.50 / 0.51 (98.49%)
Files: 10866
Cleanups: 11
Hits: 705 / 1000 (70.50%)
Misses: 295 / 1000 (29.50%)
Reads: 2001
Writes: 868
$ tar -C "${CCACHE_DIR}" -cf "${CI_PROJECT_DIR}/ccache.tar" .
$ fi
$ touch ${SPACK_STAGE_DIR}/spack-configure-args.txt
$ cp ${SPACK_STAGE_DIR}/spack-{build-env,build-out,configure-args}.txt ${CI_PROJECT_DIR}/
$ echo "SPACK_BUILD_DIR=${SPACK_BUILD_DIR}" > ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_FULL_SPEC=${SPACK_FULL_SPEC}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_SOURCE_DIR=${SPACK_SOURCE_DIR}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_INSTALLED_HASH=${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ SPACK_PACKAGE_SLUGIFY=$(echo -n ${SPACK_PACKAGE} | tr -c '[:alnum:]' '_' | tr '[:lower:]' '[:upper:]')
$ echo "${SPACK_PACKAGE_SLUGIFY}_INSTALLED_HASH=${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_PACKAGE_DEPENDENCY_ON_PREVIOUS_JOB=^/${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ num_failures=$(module load unstable python-dev; python -c "from lxml import etree; xml = etree.parse('${CI_PROJECT_DIR}/install.xml'); print(sum(1 for _ in xml.getroot().iter('failure')) + sum(1 for _ in xml.getroot().iter('error')))")
$ if [[ ${num_failures} > 0 ]]; then exit ${num_failures}; fi
section_end:1718658401:step_script section_start:1718658401:archive_cache Saving cache for successful job
Using git from spack modules
Creating cache build:neuron:nmodl:nvhpc:acc:shared-1-non_protected...
Runtime platform  arch=amd64 os=linux pid=180791 revision=58ba2b95 version=14.2.0
ccache.tar: found 1 matching files and directories
Uploading cache.zip to https://bbpobjectstorage.epfl.ch/gitlab-runners-cache/project/2160/build%3Aneuron%3Anmodl%3Anvhpc%3Aacc%3Ashared-1-non_protected
Created cache
section_end:1718658423:archive_cache section_start:1718658423:upload_artifacts_on_success Uploading artifacts for successful job
Using git from spack modules
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=181001 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
spack_build_info.env: found 1 matching files and directories
spack_clone_variables.env: found 1 matching files and directories
initial_environment.env: found 1 matching files and directories
spack-build-env.txt: found 1 matching files and directories
spack-build-out.txt: found 1 matching files and directories
spack-configure-args.txt: found 1 matching files and directories
Uploading artifacts as "archive" to coordinator... ok id=1322445 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=181051 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
Uploading artifacts as "junit" to coordinator... ok id=1322445 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=181161 revision=58ba2b95 version=14.2.0
spack_build_info.env: found 1 matching files and directories
spack_clone_variables.env: found 1 matching files and directories
Uploading artifacts as "dotenv" to coordinator... ok id=1322445 responseStatus=201 Created token=glcbt-64
section_end:1718658425:upload_artifacts_on_success section_start:1718658425:cleanup_file_variables Cleaning up project directory and file based variables
Using git from spack modules
section_end:1718658426:cleanup_file_variables Job succeeded
Running with gitlab-runner 15.5.0 (0d4137b8)
 on BB5 map runner pnPo3yJy
section_start:1718655570:resolve_secrets Resolving secrets
section_end:1718655570:resolve_secrets section_start:1718655570:prepare_executor Preparing the "custom" executor
Using Custom executor with driver BB5 PROD runner v0.0.3...
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor476828288, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name nrn
Pipeline ID 217482, build ref , job ID 1322446
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482, optional exclusive flag , optional cpus per task flag --cpus-per-task=8, optional qos flag , optional reservation flag
A slurm job will be created with name GL_J1322446_PROD_P2160_CP4_C6
Job parameters: memory=160G, cpus_per_task=8, duration=2:00:00, constraint=cpu ntasks=2 account=proj9998 user=bbpcihpcproj12 partition=prod qos= reservation=
Not executing the chown -R
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx]
Submitted batch job 2255982
job state: PD
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=2 --cpus-per-task=8 --mem=160G --job-name=GL_J1322446_PROD_P2160_CP4_C6 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482 --time=2:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482 --ntasks=2 --jobid=2255982 --cpus-per-task=8 --mem=160G
section_end:1718655573:prepare_executor section_start:1718655573:prepare_script Preparing environment
Using git from spack modules
Running on r3i5n32 via bbpv1.epfl.ch...
section_end:1718655576:prepare_script section_start:1718655576:get_sources Getting source from Git repository
Using git from spack modules
Skipping Git repository setup
Skipping Git checkout
Skipping Git submodules setup
section_end:1718655577:get_sources section_start:1718655577:restore_cache Restoring cache
Using git from spack modules
Checking cache for build:neuron:nmodl:nvhpc:omp:legacy-1-non_protected...
Runtime platform  arch=amd64 os=linux pid=308503 revision=58ba2b95 version=14.2.0
cache.zip is up to date 
Successfully extracted cache
section_end:1718655582:restore_cache section_start:1718655582:download_artifacts Downloading artifacts
Using git from spack modules
Downloading artifacts for build:nmodl (1322441)...
Runtime platform  arch=amd64 os=linux pid=308690 revision=58ba2b95 version=14.2.0
Downloading artifacts from coordinator... ok  id=1322441 responseStatus=200 OK token=glcbt-64
section_end:1718655584:download_artifacts section_start:1718655584:step_script Executing "step_script" stage of the job script
WARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426
Using git from spack modules
$ SPACK_BUILD="${PWD}/spack-build"
$ env -0 | sort -z | xargs -0 -L 1 echo > initial_environment.env
$ . ${SPACK_ROOT}/share/spack/setup-env.sh
$ export SPACK_USER_CONFIG_PATH=${PWD}/spack-config
$ mkdir ${SPACK_USER_CONFIG_PATH}
$ cat > ${SPACK_USER_CONFIG_PATH}/config.yaml << END_SCRIPT # collapsed multi-line command
$ spack ${SPACK_EXTRA_FLAGS} config add concretizer:reuse:false
$ spack ${SPACK_EXTRA_FLAGS} config blame config
--- config:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322446/spack-config/config.yaml:2 build_stage:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322446/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322446/spack-build
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322446/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322446/spack-source-cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/config.yaml:2 ccache: True
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:2 install_tree:
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:3 root: $user_cache_path/software
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:4 projections:
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:5 all: install_{compiler.name}-{compiler.version}-{target}/{name}-{version}-{hash:6}
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:7 environments_root: $user_cache_path/environments
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:9 build_jobs: 8
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:18 extensions:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:19 - $spack/bluebrain/spack-scripting
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:37 template_dirs:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:38 - $spack/share/spack/templates
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:41 license_dir: $spack/etc/spack/licenses
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:81 test_stage: $user_cache_path/test
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:94 misc_cache: $user_cache_path/cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:100 connect_timeout: 10
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:105 verify_ssl: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:113 suppress_gpg_warnings: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:119 install_missing_compilers: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:124 checksum: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:129 deprecated: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:134 dirty: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:142 build_language: C
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:151 locks: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:156 url_fetch_method: urllib
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:185 concretizer: clingo
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:192 db_lock_timeout: 60
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:200 package_lock_timeout: null
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:205 shared_linking:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:210 type: rpath
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:216 bind: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:221 allow_sgid: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:227 install_status: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:231 binary_index_ttl: 600
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:233 flags:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:235 keep_werror: none
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:240 aliases:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:241 concretise: concretize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:242 containerise: containerize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:243 rm: remove
_builtin debug: False
$ spack ${SPACK_EXTRA_FLAGS} config blame concretizer
--- concretizer:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322446/spack-config/concretizer.yaml:2 reuse: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:23 targets:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:28 granularity: microarchitectures
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:32 host_compatible: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:38 unify: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:40 duplicates:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:44 strategy: minimal
$ export XDG_CONFIG_HOME=${CI_BUILDS_DIR}/J${CI_JOB_ID}_local_config
$ echo "Configuring git to use CI_JOB_TOKEN to access git@bbpgitlab.epfl.ch (${XDG_CONFIG_HOME})"
Configuring git to use CI_JOB_TOKEN to access git@bbpgitlab.epfl.ch (/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482/J1322446_local_config)
$ mkdir -p "${XDG_CONFIG_HOME}/git"
$ echo -e "[url \"https://gitlab-ci-token:${CI_JOB_TOKEN}@bbpgitlab.epfl.ch/\"]\n insteadOf = git@bbpgitlab.epfl.ch:" > "${XDG_CONFIG_HOME}/git/config"
$ echo -e "[url \"https://gitlab-ci-token:${CI_JOB_TOKEN}@bbpgitlab.epfl.ch/\"]\n insteadOf = ssh://git@bbpgitlab.epfl.ch/" >> "${XDG_CONFIG_HOME}/git/config"
$ cat "${XDG_CONFIG_HOME}/git/config"
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
insteadOf = git@bbpgitlab.epfl.ch:
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
insteadOf = ssh://git@bbpgitlab.epfl.ch/
$ SPACK_FULL_SPEC="${SPACK_PACKAGE}${SPACK_PACKAGE_COMPILER:+%}${SPACK_PACKAGE_COMPILER} ${SPACK_PACKAGE_SPEC} ${SPACK_PACKAGE_DEPENDENCIES} ${SPACK_PACKAGE_DEPENDENCY_ON_PREVIOUS_JOB}"
$ echo "Preparing to install ${SPACK_FULL_SPEC}"
Preparing to install neuron%nvhpc ~rx3d+caliper+gpu+coreneuron~legacy-unit+openmp~shared~sympy+tests~unified build_type=FastDebug model_tests=channel-benchmark,olfactory,tqperf-heavy ^caliper+cuda cuda_arch=70 ^/53hy2ex7xntc24cnbuojh6rrc3l2auap
$ if [ ${SPACK_USE_CCACHE+x} ]; then
$ module load unstable ccache
$ export CCACHE_BASEDIR=$(realpath -P ${CI_BUILDS_DIR})
$ echo CCACHE_BASEDIR=${CCACHE_BASEDIR}
CCACHE_BASEDIR=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482
$ export CCACHE_MAXSIZE=512M
$ export CCACHE_DIR="${TMPDIR}/ccache"
$ mkdir -p ${CCACHE_DIR}
$ if [ -f ${CI_PROJECT_DIR}/ccache.tar ]; then
$ tar -C "${CCACHE_DIR}" -xf "${CI_PROJECT_DIR}/ccache.tar"
$ fi
$ ccache --zero-stats
Statistics zeroed
$ ccache --show-stats --verbose
Cache directory: /gpfs/bbp.cscs.ch/ssd/slurmTmpFS/bbpcihpcproj12/2255982/ccache
Config file: /gpfs/bbp.cscs.ch/ssd/slurmTmpFS/bbpcihpcproj12/2255982/ccache/ccache.conf
System config file: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/ccache-4.7.4-eompz5/etc/ccache.conf
Stats updated: Mon Jun 17 22:19:58 2024
Local storage:
Cache size (GB): 0.48 / 0.51 (93.38%)
Files: 11118
Hits: 0
Misses: 0
Reads: 0
Writes: 0
$ fi
$ module load unstable git ${SPACK_EXTRA_MODULES}
$ spack ${SPACK_EXTRA_FLAGS} spec -Il ${SPACK_FULL_SPEC}
Input spec
--------------------------------
- neuron%nvhpc+caliper+coreneuron+gpu~legacy-unit+openmp~rx3d~shared~sympy+tests~unified build_type=FastDebug model_tests=channel-benchmark,olfactory,tqperf-heavy
- ^/53hy2ex7xntc24cnbuojh6rrc3l2auap
- ^caliper+cuda cuda_arch=70
Concretized
--------------------------------
- dm5tz6c neuron@git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662=develop%nvhpc@23.1~backtrace+caliper+coreneuron+gpu~interviews~ipo~legacy-unit+mpi+openmp~prcellstate+python+report~rx3d~shared~sympy~sympyopt+tests~unified build_system=cmake build_type=FastDebug generator=make model_tests=channel-benchmark,olfactory,tqperf-heavy sanitizers=None arch=linux-rhel7-skylake
[^] tj3mv5i ^binutils@2.41%gcc@12.3.0+gas+gold~gprofng~headers~interwork+ld~libiberty~lto~nls~pgo+plugins build_system=autotools compress_debug_sections=zlib libs=shared,static arch=linux-rhel7-skylake
[^] 7jd6loj ^diffutils@3.9%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[^] e533uuv ^pkgconf@1.9.5%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[^] z7jpg7s ^zlib-ng@2.1.4%gcc@12.3.0+compat+opt build_system=autotools arch=linux-rhel7-skylake
[^] aivjoo2 ^zstd@1.5.5%gcc@12.3.0+programs build_system=makefile compression=none libs=shared,static arch=linux-rhel7-skylake
[e] yn5fbwg ^bison@3.8.2%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[e] rd65pst ^boost@1.83.0%gcc@12.3.0~atomic~chrono~clanglibcpp~container~context~contract~coroutine~date_time~debug~exception~fiber+filesystem~graph~graph_parallel~icu~iostreams~json~locale~log~math~mpi+multithreaded~nowide~numpy+pic~program_options~python~random~regex+serialization+shared~signals~singlethreaded~stacktrace~system~taggedlayout+test~thread~timer~type_erasure~versionedlayout~wave build_system=generic cxxstd=98 patches=a440f96 visibility=hidden arch=linux-rhel7-skylake
- vjj3tpl ^caliper@2.11.0%gcc@12.3.0+adiak+cuda~fortran+gotcha~ipo+kokkos+libdw~libpfm+libunwind+mpi+papi~rocm+sampler+shared~sosflow~tests~variorum~vtune build_system=cmake build_type=Release cuda_arch=70 generator=make arch=linux-rhel7-skylake
[^] hficqq7 ^adiak@0.4.0%gcc@12.3.0~ipo+mpi+shared build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] a46bi6u ^elfutils@0.189%gcc@12.3.0~debuginfod+exeprefix+nls build_system=autotools arch=linux-rhel7-skylake
[^] wtcpudz ^m4@1.4.19%gcc@12.3.0+sigsegv build_system=autotools patches=9dc5fbd,bfdffa7 arch=linux-rhel7-skylake
[^] rytdxw5 ^libsigsegv@2.14%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[^] 7xnekxr ^libunwind@1.6.2%gcc@12.3.0~block_signals~conservative_checks~cxx_exceptions~debug~debug_frame+docs~pic+tests+weak_backtrace~xz~zlib build_system=autotools components=none libs=shared,static arch=linux-rhel7-skylake
[^] vol6npp ^papi@6.0.0.1%gcc@12.3.0~cuda~debug+example~infiniband~lmsensors~nvml~powercap~rapl~rocm~rocm_smi~sde+shared~static_tools build_system=autotools arch=linux-rhel7-skylake
[e] b5zzpr3 ^cmake@3.27.7%gcc@12.3.0~doc+ncurses+ownlibs build_system=generic build_type=Release arch=linux-rhel7-skylake
[e] 3fsjp3m ^cuda@12.0.0%gcc@12.3.0~allow-unsupported-compilers~dev build_system=generic arch=linux-rhel7-skylake
[e] 77vzaxs ^flex@2.6.3%gcc@12.3.0+lex~nls build_system=autotools arch=linux-rhel7-skylake
[^] nbi5w5c ^gettext@0.22.3%gcc@12.3.0+bzip2+curses+git~libunistring+libxml2+pic+shared+tar+xz build_system=autotools arch=linux-rhel7-skylake
[^] vdqwmgi ^bzip2@1.0.8%gcc@12.3.0~debug~pic+shared build_system=generic arch=linux-rhel7-skylake
[^] nv4xh4v ^libiconv@1.17%gcc@12.3.0 build_system=autotools libs=shared,static arch=linux-rhel7-skylake
[^] oh2g4in ^libxml2@2.10.3%gcc@12.3.0+pic~python+shared build_system=autotools arch=linux-rhel7-skylake
[^] zz4acmm ^tar@1.34%gcc@12.3.0 build_system=autotools zip=pigz arch=linux-rhel7-skylake
[^] dwjcguu ^pigz@2.7%gcc@12.3.0 build_system=makefile arch=linux-rhel7-skylake
[^] wwn5enj ^xz@5.4.1%gcc@12.3.0~pic build_system=autotools libs=shared,static arch=linux-rhel7-skylake
[^] swjylul ^gmake@4.4.1%gcc@12.3.0~guile build_system=generic arch=linux-rhel7-skylake
[e] h6t3hgb ^hpe-mpi@2.27.p1.hmpt%gcc@12.3.0 build_system=generic arch=linux-rhel7-skylake
- az6cwid ^libsonata-report@git.5602aadfa710d6766ce23cd151a1855190271bd8=develop%nvhpc@23.1~ipo+mpi build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] 5o77yem ^hdf5@1.14.3%gcc@12.3.0+cxx~fortran+hl~ipo~java~map+mpi+shared~szip~threadsafe+tools api=default build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] ihotvbs ^spdlog@1.12.0%gcc@12.3.0+fmt_external~ipo+shared build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] 6kdbhvi ^ncurses@6.4%gcc@12.3.0~symlinks+termlib abi=none build_system=autotools arch=linux-rhel7-skylake
[e] omn6mm4 ^ninja@1.11.1%gcc@12.3.0+re2c build_system=generic arch=linux-rhel7-skylake
[+] 53hy2ex ^nmodl@git.5ff221d045c92389b4cab5ee159d46770aa12665=develop%gcc@12.3.0~ipo~legacy-unit~llvm~llvm_cuda~python~tests build_system=cmake build_type=Release generator=ninja arch=linux-rhel7-skylake
[^] pywly2v ^catch2@3.4.0%gcc@12.3.0~ipo+pic~shared build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] ud3echq ^cli11@2.3.2%gcc@12.3.0~ipo build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] evtttrh ^fmt@10.1.1%gcc@12.3.0~ipo+pic~shared build_system=cmake build_type=Release cxxstd=11 generator=make arch=linux-rhel7-skylake
[^] teske2k ^nlohmann-json@3.9.1%gcc@12.3.0~ipo+multiple_headers build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] 5dylnca ^py-find-libpython@0.3.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 7validy ^py-jinja2@3.1.2%gcc@12.3.0~i18n build_system=python_pip arch=linux-rhel7-skylake
[^] r3ehtmw ^py-markupsafe@2.1.3%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] tabj2mo ^py-pybind11@2.11.1%gcc@12.3.0~ipo build_system=cmake build_type=Release generator=ninja arch=linux-rhel7-skylake
[^] 2inh3rt ^py-pyyaml@5.4.1%gcc@12.3.0+libyaml build_system=python_pip arch=linux-rhel7-skylake
[^] bzl4xcz ^libyaml@0.2.5%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[^] x733hwb ^py-mpi4py@3.1.4%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] m3dslef ^py-cython@0.29.36%gcc@12.3.0 build_system=python_pip patches=c4369ad arch=linux-rhel7-skylake
[^] aj3rk42 ^py-wheel@0.41.2%gcc@12.3.0 build_system=generic arch=linux-rhel7-skylake
[^] elr5pnt ^py-numpy@1.26.1%gcc@12.3.0 build_system=python_pip patches=873745d arch=linux-rhel7-skylake
[e] w2ldcy2 ^intel-oneapi-mkl@2023.2.0%gcc@12.3.0~cluster+envmods~ilp64+shared build_system=generic mpi_family=none threads=none arch=linux-rhel7-skylake
[^] 3y7uuwr ^py-pyproject-metadata@0.7.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] uqml2to ^py-packaging@23.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] h6f6feu ^py-flit-core@3.9.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 77ku3vv ^py-pip@23.1.2%gcc@12.3.0 build_system=generic arch=linux-rhel7-skylake
[^] lrf2u3h ^py-pytest@7.3.2%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] mvxx6gh ^py-iniconfig@2.0.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] cbpzath ^py-hatch-vcs@0.3.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 2o7gdvi ^py-hatchling@1.21.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 6domhtg ^py-editables@0.3%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] edobf76 ^py-pathspec@0.11.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] a6ialdh ^py-trove-classifiers@2023.8.7%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] jurd5ga ^py-calver@2022.6.26%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 6su7kvx ^py-pluggy@1.0.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] sokbfzv ^py-setuptools-scm@8.0.4%gcc@12.3.0+toml build_system=python_pip arch=linux-rhel7-skylake
[e] 2sazdxk ^git@2.42.0%gcc@12.3.0+man+nls+perl+subtree~svn~tcltk build_system=autotools arch=linux-rhel7-skylake
[^] xwl5l6q ^py-tomli@2.0.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 275jtek ^py-typing-extensions@4.8.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] z5nf6n2 ^py-pytest-cov@4.0.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] wuxetkw ^py-coverage@7.2.6%gcc@12.3.0+toml build_system=python_pip arch=linux-rhel7-skylake
[^] p3xbqxj ^py-setuptools@68.0.0%gcc@12.3.0 build_system=generic arch=linux-rhel7-skylake
[^] t5tovex ^py-sympy@1.11.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 4fflyib ^py-mpmath@1.2.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[e] 5wl76vp ^python@3.11.6%gcc@12.3.0+bz2+crypt+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tkinter+uuid+zlib build_system=generic patches=13fa8bf,b0615b2,ebdca64,f2fd060 arch=linux-rhel7-skylake
[^] pdugg7r ^readline@8.2%gcc@12.3.0 build_system=autotools patches=bbf97f1 arch=linux-rhel7-skylake
$ set -o pipefail
$ (spack ${SPACK_EXTRA_FLAGS} install --overwrite -y -j${SLURM_CPUS_PER_TASK} --log-format=junit --log-file=${CI_PROJECT_DIR}/install.xml --keep-stage ${SPACK_FULL_SPEC} | tee log) || install_failed=1
==> Warning: Expected user 904556 to own /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482, but it is owned by 0
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/zlib-ng-2.1.4-z7jpg7
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/zstd-1.5.5-aivjoo
==> bison@3.8.2 : has external module in ['bison/3.8.2']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/bison-3.8.2-qcx3sg (external bison-3.8.2-yn5fbwgteilgqg6b62shkhkjg3hlwmrq)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/boost-1.83.0-2quv7w (external boost-1.83.0-rd65pstwb56uftszduzg7lsiq4za4lnn)
==> hpe-mpi@2.27.p1.hmpt : has external module in ['hpe-mpi/2.27.p1.hmpt']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/hpe-mpi-2.27.p1.hmpt-6rr256 (external hpe-mpi-2.27.p1.hmpt-h6t3hgbguhacajbyzlp43xpawsnreb3m)
==> cmake@3.27.7 : has external module in ['cmake/3.27.7']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/cmake-3.27.7-slyoes (external cmake-3.27.7-b5zzpr3mwm7jxv6bvvrs6zpeg62cfhbu)
==> cuda@12.0.0 : has external module in ['cuda/12.0.0']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/cuda-12.0.0-ucajzb (external cuda-12.0.0-3fsjp3mjnqnrrtfa6vspkddejnyei5sa)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/bzip2-1.0.8-vdqwmg
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/libiconv-1.17-nv4xh4
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/xz-5.4.1-wwn5en
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/ncurses-6.4-6kdbhv
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/pkgconf-1.9.5-e533uu
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/gmake-4.4.1-swjylu
==> python@3.11.6 : has external module in ['python/3.11.6']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/python-3.11.6-bj4i6m (external python-3.11.6-5wl76vphfvpcapfaipipf7xn2xylnc4o)
==> flex@2.6.3 : has external module in ['flex/2.6.3']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/flex-2.6.3-edx4lf (external flex-2.6.3-77vzaxsa3g7wr3omktr4skpetx5ds4pt)
==> ninja@1.11.1 : has external module in ['ninja/1.11.1']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/ninja-1.11.1-nxtlgo (external ninja-1.11.1-omn6mm4a3zsbpbkptvdwxs6kkrh6yafw)
==> intel-oneapi-mkl@2023.2.0 : has external module in ['intel-oneapi-mkl/2023.2.0']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/intel-oneapi-mkl-2023.2.0-twl2n4 (external intel-oneapi-mkl-2023.2.0-w2ldcy2y2urm3uaa7omu3w7nhwsqt433)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/cli11-2.3.2-ud3ech
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/nlohmann-json-3.9.1-teske2
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/libyaml-0.2.5-bzl4xc
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/pigz-2.7-dwjcgu
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/catch2-3.4.0-pywly2
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/fmt-10.1.1-evtttr
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/libxml2-2.10.3-oh2g4i
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/libunwind-1.6.2-7xnekx
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/hdf5-1.14.3-5o77ye
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/binutils-2.41-tj3mv5
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/adiak-0.4.0-hficqq
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/papi-6.0.0.1-vol6np
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/readline-8.2-pdugg7
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-packaging-23.1-uqml2t
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-iniconfig-2.0.0-mvxx6g
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-find-libpython-0.3.1-5dylnc
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-mpi4py-3.1.4-x733hw
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-markupsafe-2.1.3-r3ehtm
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-mpmath-1.2.1-4fflyi
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-coverage-7.2.6-wuxetk
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pip-23.1.2-77ku3v
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/tar-1.34-zz4acm
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/spdlog-1.12.0-ihotvb
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-numpy-1.26.1-elr5pn
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pyyaml-5.4.1-2inh3r
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pybind11-2.11.1-tabj2m
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-sympy-1.11.1-t5tove
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-jinja2-3.1.2-7valid
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pluggy-1.0.0-6su7kv
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-setuptools-68.0.0-p3xbqx
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/gettext-0.22.3-nbi5w5
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/software/install_gcc-12.3.0-skylake/nmodl-git.5ff221d045c92389b4cab5ee159d46770aa12665_develop-53hy2e
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pytest-7.3.2-lrf2u3
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/elfutils-0.189-a46bi6
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pytest-cov-4.0.0-z5nf6n
==> Installing caliper-2.11.0-vjj3tplvh6es4rqhqhzfqqelewsp44m2 [54/55]
==> No binary for caliper-2.11.0-vjj3tplvh6es4rqhqhzfqqelewsp44m2 found: installing from source
==> Fetching https://github.com/LLNL/Caliper/archive/v2.11.0.tar.gz
==> No patches needed for caliper
==> caliper: Executing phase: 'cmake'
==> caliper: Executing phase: 'build'
==> caliper: Executing phase: 'install'
==> caliper: Successfully installed caliper-2.11.0-vjj3tplvh6es4rqhqhzfqqelewsp44m2
Stage: 2.74s. Cmake: 7.64s. Build: 6.89s. Install: 0.96s. Post-install: 0.15s. Total: 18.70s
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/software/install_gcc-12.3.0-skylake/caliper-2.11.0-vjj3tp
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/software/install_nvhpc-23.1-skylake/libsonata-report-git.5602aadfa710d6766ce23cd151a1855190271bd8_develop-az6cwi
==> Installing neuron-git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662=develop-dm5tz6cwujvm5slx7rwxfuw2rpitwr7f [55/55]
==> No binary for neuron-git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662=develop-dm5tz6cwujvm5slx7rwxfuw2rpitwr7f found: installing from source
==> No patches needed for neuron
==> neuron: Executing phase: 'cmake'
==> neuron: Executing phase: 'build'
==> neuron: Executing phase: 'install'
==> neuron: Successfully installed neuron-git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662=develop-dm5tz6cwujvm5slx7rwxfuw2rpitwr7f
Stage: 22.45s. Cmake: 1m 10.41s. Build: 43m 59.04s. Install: 1m 29.20s. Post-install: 0.64s. Total: 47m 2.67s
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/software/install_nvhpc-23.1-skylake/neuron-git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662_develop-dm5tz6
$ set +o pipefail
$ chmod -R g+rX "${SPACK_BUILD}"
$ if [[ ${install_failed} == 1 ]]; then exit 1; fi
$ SPACK_INSTALLED_HASH=$(spack ${SPACK_EXTRA_FLAGS} find --format "{hash}" /$(sed -ne '${s/.*-//;p}' log))
$ echo "Determined the installed hash to be ${SPACK_INSTALLED_HASH}"
Determined the installed hash to be dm5tz6cwujvm5slx7rwxfuw2rpitwr7f
$ SPACK_STAGE_DIR=$(spack location -s "${SPACK_FULL_SPEC}")
$ SPACK_BUILD_DIR=$(spack location -b "${SPACK_FULL_SPEC}")
$ SPACK_SOURCE_DIR=${SPACK_STAGE_DIR}/spack-src
$ if [ ${SPACK_USE_CCACHE+x} ]; then
$ ccache --cleanup
$ ccache --show-stats --verbose
Cache directory: /gpfs/bbp.cscs.ch/ssd/slurmTmpFS/bbpcihpcproj12/2255982/ccache
Config file: /gpfs/bbp.cscs.ch/ssd/slurmTmpFS/bbpcihpcproj12/2255982/ccache/ccache.conf
System config file: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/ccache-4.7.4-eompz5/etc/ccache.conf
Stats updated: Mon Jun 17 23:10:50 2024
Cacheable calls: 1161 / 1331 (87.23%)
Hits: 862 / 1161 (74.25%)
Direct: 502 / 862 (58.24%)
Preprocessed: 360 / 862 (41.76%)
Misses: 299 / 1161 (25.75%)
Uncacheable calls: 170 / 1331 (12.77%)
Autoconf compile/link: 5 / 170 ( 2.94%)
Called for linking: 136 / 170 (80.00%)
Called for preprocessing: 4 / 170 ( 2.35%)
Compilation failed: 2 / 170 ( 1.18%)
No input file: 22 / 170 (12.94%)
Preprocessing failed: 1 / 170 ( 0.59%)
Successful lookups:
Direct: 502 / 1160 (43.28%)
Preprocessed: 360 / 657 (54.79%)
Local storage:
Cache size (GB): 0.50 / 0.51 (97.98%)
Files: 11448
Cleanups: 10
Hits: 862 / 1159 (74.37%)
Misses: 297 / 1159 (25.63%)
Reads: 2318
Writes: 873
$ tar -C "${CCACHE_DIR}" -cf "${CI_PROJECT_DIR}/ccache.tar" .
$ fi
$ touch ${SPACK_STAGE_DIR}/spack-configure-args.txt
$ cp ${SPACK_STAGE_DIR}/spack-{build-env,build-out,configure-args}.txt ${CI_PROJECT_DIR}/
$ echo "SPACK_BUILD_DIR=${SPACK_BUILD_DIR}" > ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_FULL_SPEC=${SPACK_FULL_SPEC}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_SOURCE_DIR=${SPACK_SOURCE_DIR}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_INSTALLED_HASH=${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ SPACK_PACKAGE_SLUGIFY=$(echo -n ${SPACK_PACKAGE} | tr -c '[:alnum:]' '_' | tr '[:lower:]' '[:upper:]')
$ echo "${SPACK_PACKAGE_SLUGIFY}_INSTALLED_HASH=${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_PACKAGE_DEPENDENCY_ON_PREVIOUS_JOB=^/${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ num_failures=$(module load unstable python-dev; python -c "from lxml import etree; xml = etree.parse('${CI_PROJECT_DIR}/install.xml'); print(sum(1 for _ in xml.getroot().iter('failure')) + sum(1 for _ in xml.getroot().iter('error')))")
$ if [[ ${num_failures} > 0 ]]; then exit ${num_failures}; fi
section_end:1718658658:step_script section_start:1718658658:archive_cache Saving cache for successful job
Using git from spack modules
Creating cache build:neuron:nmodl:nvhpc:omp:legacy-1-non_protected...
Runtime platform  arch=amd64 os=linux pid=55721 revision=58ba2b95 version=14.2.0
ccache.tar: found 1 matching files and directories
Uploading cache.zip to https://bbpobjectstorage.epfl.ch/gitlab-runners-cache/project/2160/build%3Aneuron%3Anmodl%3Anvhpc%3Aomp%3Alegacy-1-non_protected
Created cache
section_end:1718658681:archive_cache section_start:1718658681:upload_artifacts_on_success Uploading artifacts for successful job
Using git from spack modules
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=55908 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
spack_build_info.env: found 1 matching files and directories
spack_clone_variables.env: found 1 matching files and directories
initial_environment.env: found 1 matching files and directories
spack-build-env.txt: found 1 matching files and directories
spack-build-out.txt: found 1 matching files and directories
spack-configure-args.txt: found 1 matching files and directories
Uploading artifacts as "archive" to coordinator... ok id=1322446 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=55948 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
Uploading artifacts as "junit" to coordinator... ok id=1322446 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=55992 revision=58ba2b95 version=14.2.0
spack_build_info.env: found 1 matching files and directories
spack_clone_variables.env: found 1 matching files and directories
Uploading artifacts as "dotenv" to coordinator... ok id=1322446 responseStatus=201 Created token=glcbt-64
section_end:1718658683:upload_artifacts_on_success section_start:1718658683:cleanup_file_variables Cleaning up project directory and file based variables
Using git from spack modules
section_end:1718658684:cleanup_file_variables Job succeeded
Running with gitlab-runner 15.5.0 (0d4137b8)
 on BB5 map runner pnPo3yJy
section_start:1718655570:resolve_secrets Resolving secrets
section_end:1718655570:resolve_secrets section_start:1718655570:prepare_executor Preparing the "custom" executor
Using Custom executor with driver BB5 PROD runner v0.0.3...
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor3736059455, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name nrn
Pipeline ID 217482, build ref , job ID 1322447
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482, optional exclusive flag , optional cpus per task flag --cpus-per-task=8, optional qos flag , optional reservation flag
A slurm job will be created with name GL_J1322447_PROD_P2160_CP5_C7
Job parameters: memory=160G, cpus_per_task=8, duration=2:00:00, constraint=cpu ntasks=2 account=proj9998 user=bbpcihpcproj12 partition=prod qos= reservation=
Not executing the chown -R
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx]
Submitted batch job 2255983
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=2 --cpus-per-task=8 --mem=160G --job-name=GL_J1322447_PROD_P2160_CP5_C7 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482 --time=2:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482 --ntasks=2 --jobid=2255983 --cpus-per-task=8 --mem=160G
section_end:1718655572:prepare_executor section_start:1718655572:prepare_script Preparing environment
Using git from spack modules
Running on r3i5n32 via bbpv1.epfl.ch...
section_end:1718655577:prepare_script section_start:1718655577:get_sources Getting source from Git repository
Using git from spack modules
Skipping Git repository setup
Skipping Git checkout
Skipping Git submodules setup
section_end:1718655578:get_sources section_start:1718655578:restore_cache Restoring cache
Using git from spack modules
Checking cache for build:neuron:nmodl:nvhpc:omp-1-non_protected...
Runtime platform  arch=amd64 os=linux pid=308582 revision=58ba2b95 version=14.2.0
cache.zip is up to date 
Successfully extracted cache
section_end:1718655583:restore_cache section_start:1718655583:download_artifacts Downloading artifacts
Using git from spack modules
Downloading artifacts for build:nmodl (1322441)...
Runtime platform  arch=amd64 os=linux pid=308778 revision=58ba2b95 version=14.2.0
Downloading artifacts from coordinator... ok  id=1322441 responseStatus=200 OK token=glcbt-64
section_end:1718655585:download_artifacts section_start:1718655585:step_script Executing "step_script" stage of the job script
WARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426
Using git from spack modules
$ SPACK_BUILD="${PWD}/spack-build"
$ env -0 | sort -z | xargs -0 -L 1 echo > initial_environment.env
$ . ${SPACK_ROOT}/share/spack/setup-env.sh
$ export SPACK_USER_CONFIG_PATH=${PWD}/spack-config
$ mkdir ${SPACK_USER_CONFIG_PATH}
$ cat > ${SPACK_USER_CONFIG_PATH}/config.yaml << END_SCRIPT # collapsed multi-line command
$ spack ${SPACK_EXTRA_FLAGS} config add concretizer:reuse:false
$ spack ${SPACK_EXTRA_FLAGS} config blame config
--- config:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322447/spack-config/config.yaml:2 build_stage:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322447/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322447/spack-build
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322447/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322447/spack-source-cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/config.yaml:2 ccache: True
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:2 install_tree:
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:3 root: $user_cache_path/software
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:4 projections:
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:5 all: install_{compiler.name}-{compiler.version}-{target}/{name}-{version}-{hash:6}
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:7 environments_root: $user_cache_path/environments
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:9 build_jobs: 8
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:18 extensions:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:19 - $spack/bluebrain/spack-scripting
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:37 template_dirs:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:38 - $spack/share/spack/templates
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:41 license_dir: $spack/etc/spack/licenses
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:81 test_stage: $user_cache_path/test
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:94 misc_cache: $user_cache_path/cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:100 connect_timeout: 10
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:105 verify_ssl: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:113 suppress_gpg_warnings: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:119 install_missing_compilers: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:124 checksum: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:129 deprecated: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:134 dirty: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:142 build_language: C
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:151 locks: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:156 url_fetch_method: urllib
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:185 concretizer: clingo
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:192 db_lock_timeout: 60
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:200 package_lock_timeout: null
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:205 shared_linking:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:210 type: rpath
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:216 bind: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:221 allow_sgid: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:227 install_status: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:231 binary_index_ttl: 600
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:233 flags:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:235 keep_werror: none
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:240 aliases:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:241 concretise: concretize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:242 containerise: containerize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:243 rm: remove
_builtin debug: False
$ spack ${SPACK_EXTRA_FLAGS} config blame concretizer
--- concretizer:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322447/spack-config/concretizer.yaml:2 reuse: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:23 targets:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:28 granularity: microarchitectures
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:32 host_compatible: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:38 unify: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:40 duplicates:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:44 strategy: minimal
$ export XDG_CONFIG_HOME=${CI_BUILDS_DIR}/J${CI_JOB_ID}_local_config
$ echo "Configuring git to use CI_JOB_TOKEN to access git@bbpgitlab.epfl.ch (${XDG_CONFIG_HOME})"
Configuring git to use CI_JOB_TOKEN to access git@bbpgitlab.epfl.ch (/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482/J1322447_local_config)
$ mkdir -p "${XDG_CONFIG_HOME}/git"
$ echo -e "[url \"https://gitlab-ci-token:${CI_JOB_TOKEN}@bbpgitlab.epfl.ch/\"]\n insteadOf = git@bbpgitlab.epfl.ch:" > "${XDG_CONFIG_HOME}/git/config"
$ echo -e "[url \"https://gitlab-ci-token:${CI_JOB_TOKEN}@bbpgitlab.epfl.ch/\"]\n insteadOf = ssh://git@bbpgitlab.epfl.ch/" >> "${XDG_CONFIG_HOME}/git/config"
$ cat "${XDG_CONFIG_HOME}/git/config"
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
insteadOf = git@bbpgitlab.epfl.ch:
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
insteadOf = ssh://git@bbpgitlab.epfl.ch/
$ SPACK_FULL_SPEC="${SPACK_PACKAGE}${SPACK_PACKAGE_COMPILER:+%}${SPACK_PACKAGE_COMPILER} ${SPACK_PACKAGE_SPEC} ${SPACK_PACKAGE_DEPENDENCIES} ${SPACK_PACKAGE_DEPENDENCY_ON_PREVIOUS_JOB}"
$ echo "Preparing to install ${SPACK_FULL_SPEC}"
Preparing to install neuron%nvhpc ~rx3d+caliper+gpu+coreneuron~legacy-unit+openmp~shared+sympy+tests~unified build_type=FastDebug model_tests=channel-benchmark,olfactory,tqperf-heavy ^caliper+cuda cuda_arch=70 ^/53hy2ex7xntc24cnbuojh6rrc3l2auap
$ if [ ${SPACK_USE_CCACHE+x} ]; then
$ module load unstable ccache
$ export CCACHE_BASEDIR=$(realpath -P ${CI_BUILDS_DIR})
$ echo CCACHE_BASEDIR=${CCACHE_BASEDIR}
CCACHE_BASEDIR=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482
$ export CCACHE_MAXSIZE=512M
$ export CCACHE_DIR="${TMPDIR}/ccache"
$ mkdir -p ${CCACHE_DIR}
$ if [ -f ${CI_PROJECT_DIR}/ccache.tar ]; then
$ tar -C "${CCACHE_DIR}" -xf "${CI_PROJECT_DIR}/ccache.tar"
$ fi
$ ccache --zero-stats
Statistics zeroed
$ ccache --show-stats --verbose
Cache directory: /gpfs/bbp.cscs.ch/ssd/slurmTmpFS/bbpcihpcproj12/2255983/ccache
Config file: /gpfs/bbp.cscs.ch/ssd/slurmTmpFS/bbpcihpcproj12/2255983/ccache/ccache.conf
System config file: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/ccache-4.7.4-eompz5/etc/ccache.conf
Stats updated: Mon Jun 17 22:19:59 2024
Local storage:
Cache size (GB): 0.48 / 0.51 (93.80%)
Files: 10723
Hits: 0
Misses: 0
Reads: 0
Writes: 0
$ fi
$ module load unstable git ${SPACK_EXTRA_MODULES}
$ spack ${SPACK_EXTRA_FLAGS} spec -Il ${SPACK_FULL_SPEC}
Input spec
--------------------------------
- neuron%nvhpc+caliper+coreneuron+gpu~legacy-unit+openmp~rx3d~shared+sympy+tests~unified build_type=FastDebug model_tests=channel-benchmark,olfactory,tqperf-heavy
- ^/53hy2ex7xntc24cnbuojh6rrc3l2auap
- ^caliper+cuda cuda_arch=70
Concretized
--------------------------------
- aixdwqm neuron@git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662=develop%nvhpc@23.1~backtrace+caliper+coreneuron+gpu~interviews~ipo~legacy-unit+mpi+openmp~prcellstate+python+report~rx3d~shared+sympy~sympyopt+tests~unified build_system=cmake build_type=FastDebug generator=make model_tests=channel-benchmark,olfactory,tqperf-heavy sanitizers=None arch=linux-rhel7-skylake
[^] tj3mv5i ^binutils@2.41%gcc@12.3.0+gas+gold~gprofng~headers~interwork+ld~libiberty~lto~nls~pgo+plugins build_system=autotools compress_debug_sections=zlib libs=shared,static arch=linux-rhel7-skylake
[^] 7jd6loj ^diffutils@3.9%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[^] e533uuv ^pkgconf@1.9.5%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[^] z7jpg7s ^zlib-ng@2.1.4%gcc@12.3.0+compat+opt build_system=autotools arch=linux-rhel7-skylake
[^] aivjoo2 ^zstd@1.5.5%gcc@12.3.0+programs build_system=makefile compression=none libs=shared,static arch=linux-rhel7-skylake
[e] yn5fbwg ^bison@3.8.2%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[e] rd65pst ^boost@1.83.0%gcc@12.3.0~atomic~chrono~clanglibcpp~container~context~contract~coroutine~date_time~debug~exception~fiber+filesystem~graph~graph_parallel~icu~iostreams~json~locale~log~math~mpi+multithreaded~nowide~numpy+pic~program_options~python~random~regex+serialization+shared~signals~singlethreaded~stacktrace~system~taggedlayout+test~thread~timer~type_erasure~versionedlayout~wave build_system=generic cxxstd=98 patches=a440f96 visibility=hidden arch=linux-rhel7-skylake
- vjj3tpl ^caliper@2.11.0%gcc@12.3.0+adiak+cuda~fortran+gotcha~ipo+kokkos+libdw~libpfm+libunwind+mpi+papi~rocm+sampler+shared~sosflow~tests~variorum~vtune build_system=cmake build_type=Release cuda_arch=70 generator=make arch=linux-rhel7-skylake
[^] hficqq7 ^adiak@0.4.0%gcc@12.3.0~ipo+mpi+shared build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] a46bi6u ^elfutils@0.189%gcc@12.3.0~debuginfod+exeprefix+nls build_system=autotools arch=linux-rhel7-skylake
[^] wtcpudz ^m4@1.4.19%gcc@12.3.0+sigsegv build_system=autotools patches=9dc5fbd,bfdffa7 arch=linux-rhel7-skylake
[^] rytdxw5 ^libsigsegv@2.14%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[^] 7xnekxr ^libunwind@1.6.2%gcc@12.3.0~block_signals~conservative_checks~cxx_exceptions~debug~debug_frame+docs~pic+tests+weak_backtrace~xz~zlib build_system=autotools components=none libs=shared,static arch=linux-rhel7-skylake
[^] vol6npp ^papi@6.0.0.1%gcc@12.3.0~cuda~debug+example~infiniband~lmsensors~nvml~powercap~rapl~rocm~rocm_smi~sde+shared~static_tools build_system=autotools arch=linux-rhel7-skylake
[e] b5zzpr3 ^cmake@3.27.7%gcc@12.3.0~doc+ncurses+ownlibs build_system=generic build_type=Release arch=linux-rhel7-skylake
[e] 3fsjp3m ^cuda@12.0.0%gcc@12.3.0~allow-unsupported-compilers~dev build_system=generic arch=linux-rhel7-skylake
[e] 77vzaxs ^flex@2.6.3%gcc@12.3.0+lex~nls build_system=autotools arch=linux-rhel7-skylake
[^] nbi5w5c ^gettext@0.22.3%gcc@12.3.0+bzip2+curses+git~libunistring+libxml2+pic+shared+tar+xz build_system=autotools arch=linux-rhel7-skylake
[^] vdqwmgi ^bzip2@1.0.8%gcc@12.3.0~debug~pic+shared build_system=generic arch=linux-rhel7-skylake
[^] nv4xh4v ^libiconv@1.17%gcc@12.3.0 build_system=autotools libs=shared,static arch=linux-rhel7-skylake
[^] oh2g4in ^libxml2@2.10.3%gcc@12.3.0+pic~python+shared build_system=autotools arch=linux-rhel7-skylake
[^] zz4acmm ^tar@1.34%gcc@12.3.0 build_system=autotools zip=pigz arch=linux-rhel7-skylake
[^] dwjcguu ^pigz@2.7%gcc@12.3.0 build_system=makefile arch=linux-rhel7-skylake
[^] wwn5enj ^xz@5.4.1%gcc@12.3.0~pic build_system=autotools libs=shared,static arch=linux-rhel7-skylake
[^] swjylul ^gmake@4.4.1%gcc@12.3.0~guile build_system=generic arch=linux-rhel7-skylake
[e] h6t3hgb ^hpe-mpi@2.27.p1.hmpt%gcc@12.3.0 build_system=generic arch=linux-rhel7-skylake
- az6cwid ^libsonata-report@git.5602aadfa710d6766ce23cd151a1855190271bd8=develop%nvhpc@23.1~ipo+mpi build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] 5o77yem ^hdf5@1.14.3%gcc@12.3.0+cxx~fortran+hl~ipo~java~map+mpi+shared~szip~threadsafe+tools api=default build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] ihotvbs ^spdlog@1.12.0%gcc@12.3.0+fmt_external~ipo+shared build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] 6kdbhvi ^ncurses@6.4%gcc@12.3.0~symlinks+termlib abi=none build_system=autotools arch=linux-rhel7-skylake
[e] omn6mm4 ^ninja@1.11.1%gcc@12.3.0+re2c build_system=generic arch=linux-rhel7-skylake
[+] 53hy2ex ^nmodl@git.5ff221d045c92389b4cab5ee159d46770aa12665=develop%gcc@12.3.0~ipo~legacy-unit~llvm~llvm_cuda~python~tests build_system=cmake build_type=Release generator=ninja arch=linux-rhel7-skylake
[^] pywly2v ^catch2@3.4.0%gcc@12.3.0~ipo+pic~shared build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] ud3echq ^cli11@2.3.2%gcc@12.3.0~ipo build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] evtttrh ^fmt@10.1.1%gcc@12.3.0~ipo+pic~shared build_system=cmake build_type=Release cxxstd=11 generator=make arch=linux-rhel7-skylake
[^] teske2k ^nlohmann-json@3.9.1%gcc@12.3.0~ipo+multiple_headers build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] 5dylnca ^py-find-libpython@0.3.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 7validy ^py-jinja2@3.1.2%gcc@12.3.0~i18n build_system=python_pip arch=linux-rhel7-skylake
[^] r3ehtmw ^py-markupsafe@2.1.3%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] tabj2mo ^py-pybind11@2.11.1%gcc@12.3.0~ipo build_system=cmake build_type=Release generator=ninja arch=linux-rhel7-skylake
[^] 2inh3rt ^py-pyyaml@5.4.1%gcc@12.3.0+libyaml build_system=python_pip arch=linux-rhel7-skylake
[^] bzl4xcz ^libyaml@0.2.5%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[^] x733hwb ^py-mpi4py@3.1.4%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] m3dslef ^py-cython@0.29.36%gcc@12.3.0 build_system=python_pip patches=c4369ad arch=linux-rhel7-skylake
[^] aj3rk42 ^py-wheel@0.41.2%gcc@12.3.0 build_system=generic arch=linux-rhel7-skylake
[^] elr5pnt ^py-numpy@1.26.1%gcc@12.3.0 build_system=python_pip patches=873745d arch=linux-rhel7-skylake
[e] w2ldcy2 ^intel-oneapi-mkl@2023.2.0%gcc@12.3.0~cluster+envmods~ilp64+shared build_system=generic mpi_family=none threads=none arch=linux-rhel7-skylake
[^] 3y7uuwr ^py-pyproject-metadata@0.7.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] uqml2to ^py-packaging@23.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] h6f6feu ^py-flit-core@3.9.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 77ku3vv ^py-pip@23.1.2%gcc@12.3.0 build_system=generic arch=linux-rhel7-skylake
[^] lrf2u3h ^py-pytest@7.3.2%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] mvxx6gh ^py-iniconfig@2.0.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] cbpzath ^py-hatch-vcs@0.3.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 2o7gdvi ^py-hatchling@1.21.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 6domhtg ^py-editables@0.3%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] edobf76 ^py-pathspec@0.11.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] a6ialdh ^py-trove-classifiers@2023.8.7%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] jurd5ga ^py-calver@2022.6.26%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 6su7kvx ^py-pluggy@1.0.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] sokbfzv ^py-setuptools-scm@8.0.4%gcc@12.3.0+toml build_system=python_pip arch=linux-rhel7-skylake
[e] 2sazdxk ^git@2.42.0%gcc@12.3.0+man+nls+perl+subtree~svn~tcltk build_system=autotools arch=linux-rhel7-skylake
[^] xwl5l6q ^py-tomli@2.0.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 275jtek ^py-typing-extensions@4.8.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] z5nf6n2 ^py-pytest-cov@4.0.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] wuxetkw ^py-coverage@7.2.6%gcc@12.3.0+toml build_system=python_pip arch=linux-rhel7-skylake
[^] p3xbqxj ^py-setuptools@68.0.0%gcc@12.3.0 build_system=generic arch=linux-rhel7-skylake
[^] t5tovex ^py-sympy@1.11.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 4fflyib ^py-mpmath@1.2.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[e] 5wl76vp ^python@3.11.6%gcc@12.3.0+bz2+crypt+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tkinter+uuid+zlib build_system=generic patches=13fa8bf,b0615b2,ebdca64,f2fd060 arch=linux-rhel7-skylake
[^] pdugg7r ^readline@8.2%gcc@12.3.0 build_system=autotools patches=bbf97f1 arch=linux-rhel7-skylake
$ set -o pipefail
$ (spack ${SPACK_EXTRA_FLAGS} install --overwrite -y -j${SLURM_CPUS_PER_TASK} --log-format=junit --log-file=${CI_PROJECT_DIR}/install.xml --keep-stage ${SPACK_FULL_SPEC} | tee log) || install_failed=1
==> Warning: Expected user 904556 to own /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482, but it is owned by 0
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/zlib-ng-2.1.4-z7jpg7
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/zstd-1.5.5-aivjoo
==> bison@3.8.2 : has external module in ['bison/3.8.2']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/bison-3.8.2-qcx3sg (external bison-3.8.2-yn5fbwgteilgqg6b62shkhkjg3hlwmrq)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/boost-1.83.0-2quv7w (external boost-1.83.0-rd65pstwb56uftszduzg7lsiq4za4lnn)
==> hpe-mpi@2.27.p1.hmpt : has external module in ['hpe-mpi/2.27.p1.hmpt']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/hpe-mpi-2.27.p1.hmpt-6rr256 (external hpe-mpi-2.27.p1.hmpt-h6t3hgbguhacajbyzlp43xpawsnreb3m)
==> cmake@3.27.7 : has external module in ['cmake/3.27.7']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/cmake-3.27.7-slyoes (external cmake-3.27.7-b5zzpr3mwm7jxv6bvvrs6zpeg62cfhbu)
==> cuda@12.0.0 : has external module in ['cuda/12.0.0']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/cuda-12.0.0-ucajzb (external cuda-12.0.0-3fsjp3mjnqnrrtfa6vspkddejnyei5sa)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/bzip2-1.0.8-vdqwmg
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/libiconv-1.17-nv4xh4
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/xz-5.4.1-wwn5en
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/ncurses-6.4-6kdbhv
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/pkgconf-1.9.5-e533uu
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/gmake-4.4.1-swjylu
==> python@3.11.6 : has external module in ['python/3.11.6']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/python-3.11.6-bj4i6m (external python-3.11.6-5wl76vphfvpcapfaipipf7xn2xylnc4o)
==> flex@2.6.3 : has external module in ['flex/2.6.3']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/flex-2.6.3-edx4lf (external flex-2.6.3-77vzaxsa3g7wr3omktr4skpetx5ds4pt)
==> ninja@1.11.1 : has external module in ['ninja/1.11.1']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/ninja-1.11.1-nxtlgo (external ninja-1.11.1-omn6mm4a3zsbpbkptvdwxs6kkrh6yafw)
==> intel-oneapi-mkl@2023.2.0 : has external module in ['intel-oneapi-mkl/2023.2.0']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/intel-oneapi-mkl-2023.2.0-twl2n4 (external intel-oneapi-mkl-2023.2.0-w2ldcy2y2urm3uaa7omu3w7nhwsqt433)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/libyaml-0.2.5-bzl4xc
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/adiak-0.4.0-hficqq
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/papi-6.0.0.1-vol6np
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/nlohmann-json-3.9.1-teske2
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/libunwind-1.6.2-7xnekx
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/fmt-10.1.1-evtttr
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/binutils-2.41-tj3mv5
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/hdf5-1.14.3-5o77ye
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/catch2-3.4.0-pywly2
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/libxml2-2.10.3-oh2g4i
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/readline-8.2-pdugg7
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/cli11-2.3.2-ud3ech
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/pigz-2.7-dwjcgu
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-mpmath-1.2.1-4fflyi
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-find-libpython-0.3.1-5dylnc
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-markupsafe-2.1.3-r3ehtm
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-coverage-7.2.6-wuxetk
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-mpi4py-3.1.4-x733hw
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-iniconfig-2.0.0-mvxx6g
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-setuptools-68.0.0-p3xbqx
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-packaging-23.1-uqml2t
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pip-23.1.2-77ku3v
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/spdlog-1.12.0-ihotvb
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/tar-1.34-zz4acm
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pyyaml-5.4.1-2inh3r
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-jinja2-3.1.2-7valid
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pluggy-1.0.0-6su7kv
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-sympy-1.11.1-t5tove
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-numpy-1.26.1-elr5pn
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pybind11-2.11.1-tabj2m
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/gettext-0.22.3-nbi5w5
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pytest-7.3.2-lrf2u3
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/software/install_gcc-12.3.0-skylake/nmodl-git.5ff221d045c92389b4cab5ee159d46770aa12665_develop-53hy2e
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/elfutils-0.189-a46bi6
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pytest-cov-4.0.0-z5nf6n
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/software/install_nvhpc-23.1-skylake/libsonata-report-git.5602aadfa710d6766ce23cd151a1855190271bd8_develop-az6cwi
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/software/install_gcc-12.3.0-skylake/caliper-2.11.0-vjj3tp
==> Installing neuron-git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662=develop-aixdwqmfjcgbmkqb7roplsqios35ogub [55/55]
==> No binary for neuron-git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662=develop-aixdwqmfjcgbmkqb7roplsqios35ogub found: installing from source
==> No patches needed for neuron
==> neuron: Executing phase: 'cmake'
==> neuron: Executing phase: 'build'
==> neuron: Executing phase: 'install'
==> neuron: Successfully installed neuron-git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662=develop-aixdwqmfjcgbmkqb7roplsqios35ogub
Stage: 21.83s. Cmake: 1m 11.03s. Build: 44m 18.80s. Install: 1m 9.78s. Post-install: 0.64s. Total: 47m 2.67s
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/software/install_nvhpc-23.1-skylake/neuron-git.1d48abc57bc5f4e2d668aff620267f0e5ac0e662_develop-aixdwq
$ set +o pipefail
$ chmod -R g+rX "${SPACK_BUILD}"
$ if [[ ${install_failed} == 1 ]]; then exit 1; fi
$ SPACK_INSTALLED_HASH=$(spack ${SPACK_EXTRA_FLAGS} find --format "{hash}" /$(sed -ne '${s/.*-//;p}' log))
$ echo "Determined the installed hash to be ${SPACK_INSTALLED_HASH}"
Determined the installed hash to be aixdwqmfjcgbmkqb7roplsqios35ogub
$ SPACK_STAGE_DIR=$(spack location -s "${SPACK_FULL_SPEC}")
$ SPACK_BUILD_DIR=$(spack location -b "${SPACK_FULL_SPEC}")
$ SPACK_SOURCE_DIR=${SPACK_STAGE_DIR}/spack-src
$ if [ ${SPACK_USE_CCACHE+x} ]; then
$ ccache --cleanup
$ ccache --show-stats --verbose
Cache directory: /gpfs/bbp.cscs.ch/ssd/slurmTmpFS/bbpcihpcproj12/2255983/ccache
Config file: /gpfs/bbp.cscs.ch/ssd/slurmTmpFS/bbpcihpcproj12/2255983/ccache/ccache.conf
System config file: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/ccache-4.7.4-eompz5/etc/ccache.conf
Stats updated: Mon Jun 17 23:10:50 2024
Cacheable calls: 1004 / 1143 (87.84%)
Hits: 707 / 1004 (70.42%)
Direct: 349 / 707 (49.36%)
Preprocessed: 358 / 707 (50.64%)
Misses: 297 / 1004 (29.58%)
Uncacheable calls: 139 / 1143 (12.16%)
Autoconf compile/link: 5 / 139 ( 3.60%)
Called for linking: 121 / 139 (87.05%)
Called for preprocessing: 2 / 139 ( 1.44%)
Compilation failed: 2 / 139 ( 1.44%)
No input file: 8 / 139 ( 5.76%)
Preprocessing failed: 1 / 139 ( 0.72%)
Successful lookups:
Direct: 349 / 1003 (34.80%)
Preprocessed: 358 / 653 (54.82%)
Local storage:
Cache size (GB): 0.50 / 0.51 (98.24%)
Files: 10987
Cleanups: 9
Hits: 707 / 1002 (70.56%)
Misses: 295 / 1002 (29.44%)
Reads: 2005
Writes: 868
$ tar -C "${CCACHE_DIR}" -cf "${CI_PROJECT_DIR}/ccache.tar" .
$ fi
$ touch ${SPACK_STAGE_DIR}/spack-configure-args.txt
$ cp ${SPACK_STAGE_DIR}/spack-{build-env,build-out,configure-args}.txt ${CI_PROJECT_DIR}/
$ echo "SPACK_BUILD_DIR=${SPACK_BUILD_DIR}" > ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_FULL_SPEC=${SPACK_FULL_SPEC}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_SOURCE_DIR=${SPACK_SOURCE_DIR}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_INSTALLED_HASH=${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ SPACK_PACKAGE_SLUGIFY=$(echo -n ${SPACK_PACKAGE} | tr -c '[:alnum:]' '_' | tr '[:lower:]' '[:upper:]')
$ echo "${SPACK_PACKAGE_SLUGIFY}_INSTALLED_HASH=${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_PACKAGE_DEPENDENCY_ON_PREVIOUS_JOB=^/${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ num_failures=$(module load unstable python-dev; python -c "from lxml import etree; xml = etree.parse('${CI_PROJECT_DIR}/install.xml'); print(sum(1 for _ in xml.getroot().iter('failure')) + sum(1 for _ in xml.getroot().iter('error')))")
$ if [[ ${num_failures} > 0 ]]; then exit ${num_failures}; fi
section_end:1718658658:step_script section_start:1718658658:archive_cache Saving cache for successful job
Using git from spack modules
Creating cache build:neuron:nmodl:nvhpc:omp-1-non_protected...
Runtime platform  arch=amd64 os=linux pid=55763 revision=58ba2b95 version=14.2.0
ccache.tar: found 1 matching files and directories
Uploading cache.zip to https://bbpobjectstorage.epfl.ch/gitlab-runners-cache/project/2160/build%3Aneuron%3Anmodl%3Anvhpc%3Aomp-1-non_protected
Created cache
section_end:1718658682:archive_cache section_start:1718658682:upload_artifacts_on_success Uploading artifacts for successful job
Using git from spack modules
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=56074 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
spack_build_info.env: found 1 matching files and directories
spack_clone_variables.env: found 1 matching files and directories
initial_environment.env: found 1 matching files and directories
spack-build-env.txt: found 1 matching files and directories
spack-build-out.txt: found 1 matching files and directories
spack-configure-args.txt: found 1 matching files and directories
Uploading artifacts as "archive" to coordinator... ok id=1322447 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=56125 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
Uploading artifacts as "junit" to coordinator... ok id=1322447 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=56169 revision=58ba2b95 version=14.2.0
spack_build_info.env: found 1 matching files and directories
spack_clone_variables.env: found 1 matching files and directories
Uploading artifacts as "dotenv" to coordinator... ok id=1322447 responseStatus=201 Created token=glcbt-64
section_end:1718658684:upload_artifacts_on_success section_start:1718658684:cleanup_file_variables Cleaning up project directory and file based variables
Using git from spack modules
section_end:1718658685:cleanup_file_variables Job succeeded
Running with gitlab-runner 15.5.0 (0d4137b8)
 on BB5 map runner pnPo3yJy
section_start:1718655241:resolve_secrets Resolving secrets
section_end:1718655241:resolve_secrets section_start:1718655241:prepare_executor Preparing the "custom" executor
Using Custom executor with driver BB5 PROD runner v0.0.3...
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor1796204821, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name nrn
Pipeline ID 217482, build ref , job ID 1322441
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482, optional exclusive flag , optional cpus per task flag --cpus-per-task=8, optional qos flag , optional reservation flag
A slurm job will be created with name GL_J1322441_PROD_P2160_CP0_C2
Job parameters: memory=160G, cpus_per_task=8, duration=1:00:00, constraint=cpu ntasks=2 account=proj9998 user=bbpcihpcproj12 partition=prod qos= reservation=
Not executing the chown -R
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx]
Submitted batch job 2255954
job state: PD
job state: PD
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=2 --cpus-per-task=8 --mem=160G --job-name=GL_J1322441_PROD_P2160_CP0_C2 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482 --ntasks=2 --jobid=2255954 --cpus-per-task=8 --mem=160G
section_end:1718655244:prepare_executor section_start:1718655244:prepare_script Preparing environment
Using git from spack modules
Running on r1i7n21 via bbpv1.epfl.ch...
section_end:1718655248:prepare_script section_start:1718655248:get_sources Getting source from Git repository
Using git from spack modules
Skipping Git repository setup
Skipping Git checkout
Skipping Git submodules setup
section_end:1718655249:get_sources section_start:1718655249:restore_cache Restoring cache
Using git from spack modules
Checking cache for build:nmodl-1-non_protected...
Runtime platform  arch=amd64 os=linux pid=144720 revision=58ba2b95 version=14.2.0
cache.zip is up to date 
Successfully extracted cache
section_end:1718655254:restore_cache section_start:1718655254:download_artifacts Downloading artifacts
Using git from spack modules
Downloading artifacts for spack_setup (1322439)...
Runtime platform  arch=amd64 os=linux pid=144865 revision=58ba2b95 version=14.2.0
Downloading artifacts from coordinator... ok  id=1322439 responseStatus=200 OK token=glcbt-64
section_end:1718655256:download_artifacts section_start:1718655256:step_script Executing "step_script" stage of the job script
WARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426
Using git from spack modules
$ SPACK_BUILD="${PWD}/spack-build"
$ env -0 | sort -z | xargs -0 -L 1 echo > initial_environment.env
$ . ${SPACK_ROOT}/share/spack/setup-env.sh
$ export SPACK_USER_CONFIG_PATH=${PWD}/spack-config
$ mkdir ${SPACK_USER_CONFIG_PATH}
$ cat > ${SPACK_USER_CONFIG_PATH}/config.yaml << END_SCRIPT # collapsed multi-line command
$ spack ${SPACK_EXTRA_FLAGS} config add concretizer:reuse:false
$ spack ${SPACK_EXTRA_FLAGS} config blame config
--- config:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322441/spack-config/config.yaml:2 build_stage:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322441/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322441/spack-build
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322441/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322441/spack-source-cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/config.yaml:2 ccache: True
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:2 install_tree:
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:3 root: $user_cache_path/software
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:4 projections:
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:5 all: install_{compiler.name}-{compiler.version}-{target}/{name}-{version}-{hash:6}
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:7 environments_root: $user_cache_path/environments
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:9 build_jobs: 8
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:18 extensions:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:19 - $spack/bluebrain/spack-scripting
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:37 template_dirs:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:38 - $spack/share/spack/templates
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:41 license_dir: $spack/etc/spack/licenses
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:81 test_stage: $user_cache_path/test
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:94 misc_cache: $user_cache_path/cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:100 connect_timeout: 10
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:105 verify_ssl: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:113 suppress_gpg_warnings: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:119 install_missing_compilers: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:124 checksum: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:129 deprecated: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:134 dirty: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:142 build_language: C
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:151 locks: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:156 url_fetch_method: urllib
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:185 concretizer: clingo
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:192 db_lock_timeout: 60
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:200 package_lock_timeout: null
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:205 shared_linking:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:210 type: rpath
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:216 bind: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:221 allow_sgid: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:227 install_status: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:231 binary_index_ttl: 600
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:233 flags:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:235 keep_werror: none
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:240 aliases:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:241 concretise: concretize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:242 containerise: containerize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/config.yaml:243 rm: remove
_builtin debug: False
$ spack ${SPACK_EXTRA_FLAGS} config blame concretizer
--- concretizer:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322441/spack-config/concretizer.yaml:2 reuse: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:23 targets:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:28 granularity: microarchitectures
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:32 host_compatible: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:38 unify: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:40 duplicates:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/J1322439/spack/etc/spack/defaults/concretizer.yaml:44 strategy: minimal
$ export XDG_CONFIG_HOME=${CI_BUILDS_DIR}/J${CI_JOB_ID}_local_config
$ echo "Configuring git to use CI_JOB_TOKEN to access git@bbpgitlab.epfl.ch (${XDG_CONFIG_HOME})"
Configuring git to use CI_JOB_TOKEN to access git@bbpgitlab.epfl.ch (/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P217482/J1322441_local_config)
$ mkdir -p "${XDG_CONFIG_HOME}/git"
$ echo -e "[url \"https://gitlab-ci-token:${CI_JOB_TOKEN}@bbpgitlab.epfl.ch/\"]\n insteadOf = git@bbpgitlab.epfl.ch:" > "${XDG_CONFIG_HOME}/git/config"
$ echo -e "[url \"https://gitlab-ci-token:${CI_JOB_TOKEN}@bbpgitlab.epfl.ch/\"]\n insteadOf = ssh://git@bbpgitlab.epfl.ch/" >> "${XDG_CONFIG_HOME}/git/config"
$ cat "${XDG_CONFIG_HOME}/git/config"
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
insteadOf = git@bbpgitlab.epfl.ch:
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
insteadOf = ssh://git@bbpgitlab.epfl.ch/
$ SPACK_FULL_SPEC="${SPACK_PACKAGE}${SPACK_PACKAGE_COMPILER:+%}${SPACK_PACKAGE_COMPILER} ${SPACK_PACKAGE_SPEC} ${SPACK_PACKAGE_DEPENDENCIES} ${SPACK_PACKAGE_DEPENDENCY_ON_PREVIOUS_JOB}"
$ echo "Preparing to install ${SPACK_FULL_SPEC}"
Preparing to install nmodl%gcc ~legacy-unit
$ if [ ${SPACK_USE_CCACHE+x} ]; then
$ module load unstable ccache
$ export CCACHE_BASEDIR=$(realpath -P ${CI_BUILDS_DIR})
$ echo CCACHE_BASEDIR=${CCACHE_BASEDIR}
CCACHE_BASEDIR=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482
$ export CCACHE_MAXSIZE=512M
$ export CCACHE_DIR="${TMPDIR}/ccache"
$ mkdir -p ${CCACHE_DIR}
$ if [ -f ${CI_PROJECT_DIR}/ccache.tar ]; then
$ tar -C "${CCACHE_DIR}" -xf "${CI_PROJECT_DIR}/ccache.tar"
$ fi
$ ccache --zero-stats
Statistics zeroed
$ ccache --show-stats --verbose
Cache directory: /nvme/bbpcihpcproj12/2255954/ccache
Config file: /nvme/bbpcihpcproj12/2255954/ccache/ccache.conf
System config file: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/ccache-4.7.4-eompz5/etc/ccache.conf
Stats updated: Mon Jun 17 22:14:21 2024
Local storage:
Cache size (GB): 0.45 / 0.51 (87.22%)
Files: 5151
Hits: 0
Misses: 0
Reads: 0
Writes: 0
$ fi
$ module load unstable git ${SPACK_EXTRA_MODULES}
$ spack ${SPACK_EXTRA_FLAGS} spec -Il ${SPACK_FULL_SPEC}
Input spec
--------------------------------
- nmodl%gcc~legacy-unit
Concretized
--------------------------------
- 53hy2ex nmodl@git.5ff221d045c92389b4cab5ee159d46770aa12665=develop%gcc@12.3.0~ipo~legacy-unit~llvm~llvm_cuda~python~tests build_system=cmake build_type=Release generator=ninja arch=linux-rhel7-skylake
[e] yn5fbwg ^bison@3.8.2%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[^] pywly2v ^catch2@3.4.0%gcc@12.3.0~ipo+pic~shared build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] swjylul ^gmake@4.4.1%gcc@12.3.0~guile build_system=generic arch=linux-rhel7-skylake
[^] ud3echq ^cli11@2.3.2%gcc@12.3.0~ipo build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[e] b5zzpr3 ^cmake@3.27.7%gcc@12.3.0~doc+ncurses+ownlibs build_system=generic build_type=Release arch=linux-rhel7-skylake
[e] 77vzaxs ^flex@2.6.3%gcc@12.3.0+lex~nls build_system=autotools arch=linux-rhel7-skylake
[^] evtttrh ^fmt@10.1.1%gcc@12.3.0~ipo+pic~shared build_system=cmake build_type=Release cxxstd=11 generator=make arch=linux-rhel7-skylake
[e] omn6mm4 ^ninja@1.11.1%gcc@12.3.0+re2c build_system=generic arch=linux-rhel7-skylake
[^] teske2k ^nlohmann-json@3.9.1%gcc@12.3.0~ipo+multiple_headers build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
[^] 5dylnca ^py-find-libpython@0.3.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 77ku3vv ^py-pip@23.1.2%gcc@12.3.0 build_system=generic arch=linux-rhel7-skylake
[^] p3xbqxj ^py-setuptools@68.0.0%gcc@12.3.0 build_system=generic arch=linux-rhel7-skylake
[^] aj3rk42 ^py-wheel@0.41.2%gcc@12.3.0 build_system=generic arch=linux-rhel7-skylake
[^] 7validy ^py-jinja2@3.1.2%gcc@12.3.0~i18n build_system=python_pip arch=linux-rhel7-skylake
[^] r3ehtmw ^py-markupsafe@2.1.3%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] tabj2mo ^py-pybind11@2.11.1%gcc@12.3.0~ipo build_system=cmake build_type=Release generator=ninja arch=linux-rhel7-skylake
[^] 2inh3rt ^py-pyyaml@5.4.1%gcc@12.3.0+libyaml build_system=python_pip arch=linux-rhel7-skylake
[^] bzl4xcz ^libyaml@0.2.5%gcc@12.3.0 build_system=autotools arch=linux-rhel7-skylake
[^] t5tovex ^py-sympy@1.11.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 4fflyib ^py-mpmath@1.2.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] sokbfzv ^py-setuptools-scm@8.0.4%gcc@12.3.0+toml build_system=python_pip arch=linux-rhel7-skylake
[e] 2sazdxk ^git@2.42.0%gcc@12.3.0+man+nls+perl+subtree~svn~tcltk build_system=autotools arch=linux-rhel7-skylake
[^] uqml2to ^py-packaging@23.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] h6f6feu ^py-flit-core@3.9.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] xwl5l6q ^py-tomli@2.0.1%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 275jtek ^py-typing-extensions@4.8.0%gcc@12.3.0 build_system=python_pip arch=linux-rhel7-skylake
[e] 5wl76vp ^python@3.11.6%gcc@12.3.0+bz2+crypt+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tkinter+uuid+zlib build_system=generic patches=13fa8bf,b0615b2,ebdca64,f2fd060 arch=linux-rhel7-skylake
[^] ihotvbs ^spdlog@1.12.0%gcc@12.3.0+fmt_external~ipo+shared build_system=cmake build_type=Release generator=make arch=linux-rhel7-skylake
$ set -o pipefail
$ (spack ${SPACK_EXTRA_FLAGS} install --overwrite -y -j${SLURM_CPUS_PER_TASK} --log-format=junit --log-file=${CI_PROJECT_DIR}/install.xml --keep-stage ${SPACK_FULL_SPEC} | tee log) || install_failed=1
==> Warning: Expected user 904556 to own /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482, but it is owned by 0
==> bison@3.8.2 : has external module in ['bison/3.8.2']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/bison-3.8.2-qcx3sg (external bison-3.8.2-yn5fbwgteilgqg6b62shkhkjg3hlwmrq)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/catch2-3.4.0-pywly2
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/cli11-2.3.2-ud3ech
==> cmake@3.27.7 : has external module in ['cmake/3.27.7']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/cmake-3.27.7-slyoes (external cmake-3.27.7-b5zzpr3mwm7jxv6bvvrs6zpeg62cfhbu)
==> flex@2.6.3 : has external module in ['flex/2.6.3']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/flex-2.6.3-edx4lf (external flex-2.6.3-77vzaxsa3g7wr3omktr4skpetx5ds4pt)
==> ninja@1.11.1 : has external module in ['ninja/1.11.1']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/ninja-1.11.1-nxtlgo (external ninja-1.11.1-omn6mm4a3zsbpbkptvdwxs6kkrh6yafw)
==> python@3.11.6 : has external module in ['python/3.11.6']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/python-3.11.6-bj4i6m (external python-3.11.6-5wl76vphfvpcapfaipipf7xn2xylnc4o)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/libyaml-0.2.5-bzl4xc
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/nlohmann-json-3.9.1-teske2
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/fmt-10.1.1-evtttr
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pybind11-2.11.1-tabj2m
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-find-libpython-0.3.1-5dylnc
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-markupsafe-2.1.3-r3ehtm
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-mpmath-1.2.1-4fflyi
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-pyyaml-5.4.1-2inh3r
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/spdlog-1.12.0-ihotvb
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-jinja2-3.1.2-7valid
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-sympy-1.11.1-t5tove
==> Installing nmodl-git.5ff221d045c92389b4cab5ee159d46770aa12665=develop-53hy2ex7xntc24cnbuojh6rrc3l2auap [19/19]
==> No binary for nmodl-git.5ff221d045c92389b4cab5ee159d46770aa12665=develop-53hy2ex7xntc24cnbuojh6rrc3l2auap found: installing from source
==> No patches needed for nmodl
==> nmodl: Executing phase: 'cmake'
==> nmodl: Executing phase: 'build'
==> nmodl: Executing phase: 'install'
==> nmodl: Successfully installed nmodl-git.5ff221d045c92389b4cab5ee159d46770aa12665=develop-53hy2ex7xntc24cnbuojh6rrc3l2auap
Stage: 46.88s. Cmake: 2.59s. Build: 1m 29.57s. Install: 1.37s. Post-install: 0.34s. Total: 2m 21.01s
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P217482/software/install_gcc-12.3.0-skylake/nmodl-git.5ff221d045c92389b4cab5ee159d46770aa12665_develop-53hy2e
$ set +o pipefail
$ chmod -R g+rX "${SPACK_BUILD}"
$ if [[ ${install_failed} == 1 ]]; then exit 1; fi
$ SPACK_INSTALLED_HASH=$(spack ${SPACK_EXTRA_FLAGS} find --format "{hash}" /$(sed -ne '${s/.*-//;p}' log))
$ echo "Determined the installed hash to be ${SPACK_INSTALLED_HASH}"
Determined the installed hash to be 53hy2ex7xntc24cnbuojh6rrc3l2auap
$ SPACK_STAGE_DIR=$(spack location -s "${SPACK_FULL_SPEC}")
$ SPACK_BUILD_DIR=$(spack location -b "${SPACK_FULL_SPEC}")
$ SPACK_SOURCE_DIR=${SPACK_STAGE_DIR}/spack-src
$ if [ ${SPACK_USE_CCACHE+x} ]; then
$ ccache --cleanup
$ ccache --show-stats --verbose
Cache directory: /nvme/bbpcihpcproj12/2255954/ccache
Config file: /nvme/bbpcihpcproj12/2255954/ccache/ccache.conf
System config file: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/ccache-4.7.4-eompz5/etc/ccache.conf
Stats updated: Mon Jun 17 22:18:50 2024
Cacheable calls: 138 / 165 (83.64%)
Hits: 136 / 138 (98.55%)
Direct: 28 / 136 (20.59%)
Preprocessed: 108 / 136 (79.41%)
Misses: 2 / 138 ( 1.45%)
Uncacheable calls: 27 / 165 (16.36%)
Called for linking: 24 / 27 (88.89%)
No input file: 3 / 27 (11.11%)
Successful lookups:
Direct: 28 / 138 (20.29%)
Preprocessed: 108 / 110 (98.18%)
Local storage:
Cache size (GB): 0.45 / 0.51 (87.23%)
Files: 5155
Hits: 136 / 138 (98.55%)
Misses: 2 / 138 ( 1.45%)
Reads: 276
Writes: 4
$ tar -C "${CCACHE_DIR}" -cf "${CI_PROJECT_DIR}/ccache.tar" .
$ fi
$ touch ${SPACK_STAGE_DIR}/spack-configure-args.txt
$ cp ${SPACK_STAGE_DIR}/spack-{build-env,build-out,configure-args}.txt ${CI_PROJECT_DIR}/
$ echo "SPACK_BUILD_DIR=${SPACK_BUILD_DIR}" > ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_FULL_SPEC=${SPACK_FULL_SPEC}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_SOURCE_DIR=${SPACK_SOURCE_DIR}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_INSTALLED_HASH=${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ SPACK_PACKAGE_SLUGIFY=$(echo -n ${SPACK_PACKAGE} | tr -c '[:alnum:]' '_' | tr '[:lower:]' '[:upper:]')
$ echo "${SPACK_PACKAGE_SLUGIFY}_INSTALLED_HASH=${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_PACKAGE_DEPENDENCY_ON_PREVIOUS_JOB=^/${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ num_failures=$(module load unstable python-dev; python -c "from lxml import etree; xml = etree.parse('${CI_PROJECT_DIR}/install.xml'); print(sum(1 for _ in xml.getroot().iter('failure')) + sum(1 for _ in xml.getroot().iter('error')))")
$ if [[ ${num_failures} > 0 ]]; then exit ${num_failures}; fi
section_end:1718655532:step_script section_start:1718655532:archive_cache Saving cache for successful job
Using git from spack modules
Creating cache build:nmodl-1-non_protected...
Runtime platform  arch=amd64 os=linux pid=148537 revision=58ba2b95 version=14.2.0
ccache.tar: found 1 matching files and directories
Uploading cache.zip to https://bbpobjectstorage.epfl.ch/gitlab-runners-cache/project/2160/build%3Anmodl-1-non_protected
Created cache
section_end:1718655554:archive_cache section_start:1718655554:upload_artifacts_on_success Uploading artifacts for successful job
Using git from spack modules
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=148706 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
spack_build_info.env: found 1 matching files and directories
spack_clone_variables.env: found 1 matching files and directories
initial_environment.env: found 1 matching files and directories
spack-build-env.txt: found 1 matching files and directories
spack-build-out.txt: found 1 matching files and directories
spack-configure-args.txt: found 1 matching files and directories
Uploading artifacts as "archive" to coordinator... ok id=1322441 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=148741 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
Uploading artifacts as "junit" to coordinator... ok id=1322441 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=148784 revision=58ba2b95 version=14.2.0
spack_build_info.env: found 1 matching files and directories
spack_clone_variables.env: found 1 matching files and directories
Uploading artifacts as "dotenv" to coordinator... ok id=1322441 responseStatus=201 Created token=glcbt-64
section_end:1718655563:upload_artifacts_on_success section_start:1718655563:cleanup_file_variables Cleaning up project directory and file based variables
Using git from spack modules
section_end:1718655564:cleanup_file_variables Job succeeded
This file has been truncated, but you can view the full file.
Running with gitlab-runner 15.4.0 (43b2dc3d)
 on macos-arm64 vGzz-bdp
section_start:1718655134:resolve_secrets Resolving secrets
section_end:1718655134:resolve_secrets section_start:1718655134:prepare_executor Preparing the "shell" executor
Using Shell executor...
section_end:1718655134:prepare_executor section_start:1718655134:prepare_script Preparing environment
Running on bbpmacglr01.bbp.epfl.ch...
section_end:1718655134:prepare_script section_start:1718655134:get_sources Getting source from Git repository
Fetching changes with git depth set to 20...
Initialized empty Git repository in /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/.git/
Created fresh repository.
Checking out 1d48abc5 as cornu/use_globals...
Skipping Git submodules setup
section_end:1718655136:get_sources section_start:1718655136:restore_cache Restoring cache
Checking cache for mac_m1_cmake_build: [cmake, ON, OFF, OFF, address]-cornu/use_globals-1-non_protected...
Runtime platform  arch=arm64 os=darwin pid=26792 revision=43b2dc3d version=15.4.0
No URL provided, cache will not be downloaded from shared cache server. Instead a local version of cache will be extracted.
Successfully extracted cache
section_end:1718655139:restore_cache section_start:1718655139:step_script Executing "step_script" stage of the job script
$ cat > resolve_shim.py << END_SCRIPT # collapsed multi-line command
$ real_python=$(python3 resolve_shim.py)
$ echo "python3=$(command -v python3) is really ${real_python}"
python3=/opt/homebrew/bin/python3 is really /opt/homebrew/Cellar/python@3.10/3.10.13_1/Frameworks/Python.framework/Versions/3.10/Resources/Python.app/Contents/MacOS/Python
$ PYTHONEXECUTABLE=${real_python} ${real_python} -mvenv venv
$ venv/bin/python3 -m ensurepip --upgrade --default-pip
Looking in links: /var/folders/dm/mrnbn5ld56v61w1_hpbmskfw0000gp/T/tmphcau2etk
Processing /private/var/folders/dm/mrnbn5ld56v61w1_hpbmskfw0000gp/T/tmphcau2etk/setuptools-68.2.2-py3-none-any.whl
Processing /private/var/folders/dm/mrnbn5ld56v61w1_hpbmskfw0000gp/T/tmphcau2etk/pip-23.3.1-py3-none-any.whl
Installing collected packages: setuptools, pip
Successfully installed pip-23.3.1 setuptools-68.2.2
$ git submodule update --init --recursive --force --depth 1 -- external/nmodl
Submodule 'external/nmodl' (https://github.com/BlueBrain/nmodl) registered for path 'external/nmodl'
Cloning into '/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/external/nmodl'...
From https://github.com/BlueBrain/nmodl
* branch c5ecfea39cbd53ffcc248b1dcf732c1e0ae1ffc4 -> FETCH_HEAD
Submodule path 'external/nmodl': checked out 'c5ecfea39cbd53ffcc248b1dcf732c1e0ae1ffc4'
Submodule 'cmake/hpc-coding-conventions' (https://github.com/BlueBrain/hpc-coding-conventions.git) registered for path 'external/nmodl/cmake/hpc-coding-conventions'
Submodule 'ext/backward' (https://github.com/bombela/backward-cpp.git) registered for path 'external/nmodl/ext/backward'
Submodule 'ext/catch2' (https://github.com/catchorg/Catch2.git) registered for path 'external/nmodl/ext/catch2'
Submodule 'ext/cli11' (https://github.com/CLIUtils/CLI11.git) registered for path 'external/nmodl/ext/cli11'
Submodule 'ext/eigen' (https://gitlab.com/libeigen/eigen.git) registered for path 'external/nmodl/ext/eigen'
Submodule 'ext/fmt' (https://github.com/fmtlib/fmt.git) registered for path 'external/nmodl/ext/fmt'
Submodule 'ext/json' (https://github.com/nlohmann/json.git) registered for path 'external/nmodl/ext/json'
Submodule 'ext/pybind11' (https://github.com/pybind/pybind11.git) registered for path 'external/nmodl/ext/pybind11'
Submodule 'ext/spdlog' (https://github.com/gabime/spdlog) registered for path 'external/nmodl/ext/spdlog'
Cloning into '/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/external/nmodl/cmake/hpc-coding-conventions'...
Cloning into '/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/external/nmodl/ext/backward'...
Cloning into '/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/external/nmodl/ext/catch2'...
Cloning into '/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/external/nmodl/ext/cli11'...
Cloning into '/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/external/nmodl/ext/eigen'...
Cloning into '/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/external/nmodl/ext/fmt'...
Cloning into '/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/external/nmodl/ext/json'...
Cloning into '/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/external/nmodl/ext/pybind11'...
Cloning into '/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/external/nmodl/ext/spdlog'...
From https://github.com/BlueBrain/hpc-coding-conventions
* branch f8f8d69a66c23978d1c9c5dce62de79466f26e5d -> FETCH_HEAD
Submodule path 'external/nmodl/cmake/hpc-coding-conventions': checked out 'f8f8d69a66c23978d1c9c5dce62de79466f26e5d'
Submodule path 'external/nmodl/ext/backward': checked out '51f0700452cf71c57d43c2d028277b24cde32502'
From https://github.com/catchorg/Catch2
* branch 8ac8190e494a381072c89f5e161b92a08d98b37b -> FETCH_HEAD
Submodule path 'external/nmodl/ext/catch2': checked out '8ac8190e494a381072c89f5e161b92a08d98b37b'
From https://github.com/CLIUtils/CLI11
* branch f4d0731cebb123ff0ace712c099dffbcd2c58e5a -> FETCH_HEAD
Submodule path 'external/nmodl/ext/cli11': checked out 'f4d0731cebb123ff0ace712c099dffbcd2c58e5a'
From https://gitlab.com/libeigen/eigen
* branch 3147391d946bb4b6c68edd901f2add6ac1f31f8c -> FETCH_HEAD
Submodule path 'external/nmodl/ext/eigen': checked out '3147391d946bb4b6c68edd901f2add6ac1f31f8c'
From https://github.com/fmtlib/fmt
* branch e69e5f977d458f2650bb346dadf2ad30c5320281 -> FETCH_HEAD
Submodule path 'external/nmodl/ext/fmt': checked out 'e69e5f977d458f2650bb346dadf2ad30c5320281'
From https://github.com/nlohmann/json
* branch 9cca280a4d0ccf0c08f47a99aa71d1b0e52f8d03 -> FETCH_HEAD
Submodule path 'external/nmodl/ext/json': checked out '9cca280a4d0ccf0c08f47a99aa71d1b0e52f8d03'
From https://github.com/pybind/pybind11
* branch 3e9dfa2866941655c56877882565e7577de6fc7b -> FETCH_HEAD
Submodule path 'external/nmodl/ext/pybind11': checked out '3e9dfa2866941655c56877882565e7577de6fc7b'
From https://github.com/gabime/spdlog
* branch 7c02e204c92545f869e2f04edaab1f19fe8b19fd -> FETCH_HEAD
Submodule path 'external/nmodl/ext/spdlog': checked out '7c02e204c92545f869e2f04edaab1f19fe8b19fd'
$ venv/bin/pip install --upgrade -r external/nmodl/requirements.txt
Ignoring importlib-metadata: markers 'python_version < "3.9"' don't match your environment
Ignoring importlib-resources: markers 'python_version < "3.9"' don't match your environment
Collecting scikit-build-core (from -r external/nmodl/requirements.txt (line 2))
Using cached scikit_build_core-0.9.6-py3-none-any.whl.metadata (19 kB)
Collecting setuptools-scm>=8.0 (from -r external/nmodl/requirements.txt (line 3))
Using cached setuptools_scm-8.1.0-py3-none-any.whl.metadata (6.6 kB)
Collecting Jinja2>=2.9.3 (from -r external/nmodl/requirements.txt (line 4))
Using cached jinja2-3.1.4-py3-none-any.whl.metadata (2.6 kB)
Collecting PyYAML>=3.13 (from -r external/nmodl/requirements.txt (line 5))
Using cached PyYAML-6.0.1-cp310-cp310-macosx_11_0_arm64.whl.metadata (2.1 kB)
Collecting find_libpython (from -r external/nmodl/requirements.txt (line 7))
Using cached find_libpython-0.4.0-py3-none-any.whl.metadata (2.8 kB)
Collecting sympy>=1.3 (from -r external/nmodl/requirements.txt (line 8))
Using cached sympy-1.12.1-py3-none-any.whl.metadata (12 kB)
Collecting pytest<=8.1.1 (from -r external/nmodl/requirements.txt (line 12))
Using cached pytest-8.1.1-py3-none-any.whl.metadata (7.6 kB)
Collecting pytest-cov (from -r external/nmodl/requirements.txt (line 13))
Using cached pytest_cov-5.0.0-py3-none-any.whl.metadata (27 kB)
Collecting numpy (from -r external/nmodl/requirements.txt (line 14))
Using cached numpy-2.0.0-cp310-cp310-macosx_11_0_arm64.whl.metadata (114 kB)
Collecting jupyter-client (from -r external/nmodl/requirements.txt (line 16))
Using cached jupyter_client-8.6.2-py3-none-any.whl.metadata (8.3 kB)
Collecting jupyter (from -r external/nmodl/requirements.txt (line 17))
Using cached jupyter-1.0.0-py2.py3-none-any.whl.metadata (995 bytes)
Collecting myst_parser<2.0.0 (from -r external/nmodl/requirements.txt (line 18))
Using cached myst_parser-1.0.0-py3-none-any.whl.metadata (5.5 kB)
Collecting mistune<3 (from -r external/nmodl/requirements.txt (line 19))
Using cached mistune-2.0.5-py2.py3-none-any.whl.metadata (1.5 kB)
Collecting nbconvert (from -r external/nmodl/requirements.txt (line 20))
Using cached nbconvert-7.16.4-py3-none-any.whl.metadata (8.5 kB)
Collecting nbsphinx>=0.3.2 (from -r external/nmodl/requirements.txt (line 21))
Using cached nbsphinx-0.9.4-py3-none-any.whl.metadata (2.1 kB)
Collecting sphinxcontrib-applehelp<1.0.3 (from -r external/nmodl/requirements.txt (line 22))
Using cached sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl.metadata (1.4 kB)
Collecting sphinxcontrib-htmlhelp<=2.0.0 (from -r external/nmodl/requirements.txt (line 23))
Using cached sphinxcontrib_htmlhelp-2.0.0-py2.py3-none-any.whl.metadata (1.6 kB)
Collecting sphinx<6 (from -r external/nmodl/requirements.txt (line 24))
Using cached sphinx-5.3.0-py3-none-any.whl.metadata (6.4 kB)
Collecting sphinx-rtd-theme (from -r external/nmodl/requirements.txt (line 25))
Using cached sphinx_rtd_theme-2.0.0-py2.py3-none-any.whl.metadata (4.4 kB)
Collecting docutils<0.20 (from -r external/nmodl/requirements.txt (line 26))
Using cached docutils-0.19-py3-none-any.whl.metadata (2.7 kB)
Collecting exceptiongroup>=1.0 (from scikit-build-core->-r external/nmodl/requirements.txt (line 2))
Using cached exceptiongroup-1.2.1-py3-none-any.whl.metadata (6.6 kB)
Collecting packaging>=21.3 (from scikit-build-core->-r external/nmodl/requirements.txt (line 2))
Using cached packaging-24.1-py3-none-any.whl.metadata (3.2 kB)
Collecting pathspec>=0.10.1 (from scikit-build-core->-r external/nmodl/requirements.txt (line 2))
Using cached pathspec-0.12.1-py3-none-any.whl.metadata (21 kB)
Collecting tomli>=1.2.2 (from scikit-build-core->-r external/nmodl/requirements.txt (line 2))
Using cached tomli-2.0.1-py3-none-any.whl.metadata (8.9 kB)
Requirement already satisfied: setuptools in ./venv/lib/python3.10/site-packages (from setuptools-scm>=8.0->-r external/nmodl/requirements.txt (line 3)) (68.2.2)
Collecting MarkupSafe>=2.0 (from Jinja2>=2.9.3->-r external/nmodl/requirements.txt (line 4))
Using cached MarkupSafe-2.1.5-cp310-cp310-macosx_10_9_universal2.whl.metadata (3.0 kB)
Collecting mpmath<1.4.0,>=1.1.0 (from sympy>=1.3->-r external/nmodl/requirements.txt (line 8))
Using cached mpmath-1.3.0-py3-none-any.whl.metadata (8.6 kB)
Collecting iniconfig (from pytest<=8.1.1->-r external/nmodl/requirements.txt (line 12))
Using cached iniconfig-2.0.0-py3-none-any.whl.metadata (2.6 kB)
Collecting pluggy<2.0,>=1.4 (from pytest<=8.1.1->-r external/nmodl/requirements.txt (line 12))
Using cached pluggy-1.5.0-py3-none-any.whl.metadata (4.8 kB)
Collecting coverage>=5.2.1 (from coverage[toml]>=5.2.1->pytest-cov->-r external/nmodl/requirements.txt (line 13))
Using cached coverage-7.5.3-cp310-cp310-macosx_11_0_arm64.whl.metadata (8.2 kB)
Collecting jupyter-core!=5.0.*,>=4.12 (from jupyter-client->-r external/nmodl/requirements.txt (line 16))
Using cached jupyter_core-5.7.2-py3-none-any.whl.metadata (3.4 kB)
Collecting python-dateutil>=2.8.2 (from jupyter-client->-r external/nmodl/requirements.txt (line 16))
Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting pyzmq>=23.0 (from jupyter-client->-r external/nmodl/requirements.txt (line 16))
Using cached pyzmq-26.0.3-cp310-cp310-macosx_10_15_universal2.whl.metadata (6.1 kB)
Collecting tornado>=6.2 (from jupyter-client->-r external/nmodl/requirements.txt (line 16))
Using cached tornado-6.4.1-cp38-abi3-macosx_10_9_universal2.whl.metadata (2.5 kB)
Collecting traitlets>=5.3 (from jupyter-client->-r external/nmodl/requirements.txt (line 16))
Using cached traitlets-5.14.3-py3-none-any.whl.metadata (10 kB)
Collecting notebook (from jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached notebook-7.2.1-py3-none-any.whl.metadata (10 kB)
Collecting qtconsole (from jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached qtconsole-5.5.2-py3-none-any.whl.metadata (5.1 kB)
Collecting jupyter-console (from jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached jupyter_console-6.6.3-py3-none-any.whl.metadata (5.8 kB)
Collecting ipykernel (from jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached ipykernel-6.29.4-py3-none-any.whl.metadata (6.3 kB)
Collecting ipywidgets (from jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached ipywidgets-8.1.3-py3-none-any.whl.metadata (2.4 kB)
Collecting markdown-it-py<3.0.0,>=1.0.0 (from myst_parser<2.0.0->-r external/nmodl/requirements.txt (line 18))
Using cached markdown_it_py-2.2.0-py3-none-any.whl.metadata (6.8 kB)
Collecting mdit-py-plugins~=0.3.4 (from myst_parser<2.0.0->-r external/nmodl/requirements.txt (line 18))
Using cached mdit_py_plugins-0.3.5-py3-none-any.whl.metadata (2.8 kB)
Collecting beautifulsoup4 (from nbconvert->-r external/nmodl/requirements.txt (line 20))
Using cached beautifulsoup4-4.12.3-py3-none-any.whl.metadata (3.8 kB)
Collecting bleach!=5.0.0 (from nbconvert->-r external/nmodl/requirements.txt (line 20))
Using cached bleach-6.1.0-py3-none-any.whl.metadata (30 kB)
Collecting defusedxml (from nbconvert->-r external/nmodl/requirements.txt (line 20))
Using cached defusedxml-0.7.1-py2.py3-none-any.whl.metadata (32 kB)
Collecting jupyterlab-pygments (from nbconvert->-r external/nmodl/requirements.txt (line 20))
Using cached jupyterlab_pygments-0.3.0-py3-none-any.whl.metadata (4.4 kB)
Collecting nbclient>=0.5.0 (from nbconvert->-r external/nmodl/requirements.txt (line 20))
Using cached nbclient-0.10.0-py3-none-any.whl.metadata (7.8 kB)
Collecting nbformat>=5.7 (from nbconvert->-r external/nmodl/requirements.txt (line 20))
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Collecting pandocfilters>=1.4.1 (from nbconvert->-r external/nmodl/requirements.txt (line 20))
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Collecting pygments>=2.4.1 (from nbconvert->-r external/nmodl/requirements.txt (line 20))
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Collecting tinycss2 (from nbconvert->-r external/nmodl/requirements.txt (line 20))
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Collecting sphinxcontrib-devhelp (from sphinx<6->-r external/nmodl/requirements.txt (line 24))
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Collecting sphinxcontrib-jsmath (from sphinx<6->-r external/nmodl/requirements.txt (line 24))
Using cached sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl.metadata (1.4 kB)
Collecting sphinxcontrib-serializinghtml>=1.1.5 (from sphinx<6->-r external/nmodl/requirements.txt (line 24))
Using cached sphinxcontrib_serializinghtml-1.1.10-py3-none-any.whl.metadata (2.4 kB)
Collecting sphinxcontrib-qthelp (from sphinx<6->-r external/nmodl/requirements.txt (line 24))
Using cached sphinxcontrib_qthelp-1.0.7-py3-none-any.whl.metadata (2.2 kB)
Collecting snowballstemmer>=2.0 (from sphinx<6->-r external/nmodl/requirements.txt (line 24))
Using cached snowballstemmer-2.2.0-py2.py3-none-any.whl.metadata (6.5 kB)
Collecting babel>=2.9 (from sphinx<6->-r external/nmodl/requirements.txt (line 24))
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Collecting alabaster<0.8,>=0.7 (from sphinx<6->-r external/nmodl/requirements.txt (line 24))
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Collecting imagesize>=1.3 (from sphinx<6->-r external/nmodl/requirements.txt (line 24))
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Collecting requests>=2.5.0 (from sphinx<6->-r external/nmodl/requirements.txt (line 24))
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Collecting sphinxcontrib-jquery<5,>=4 (from sphinx-rtd-theme->-r external/nmodl/requirements.txt (line 25))
Using cached sphinxcontrib_jquery-4.1-py2.py3-none-any.whl.metadata (2.6 kB)
Collecting six>=1.9.0 (from bleach!=5.0.0->nbconvert->-r external/nmodl/requirements.txt (line 20))
Using cached six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB)
Collecting webencodings (from bleach!=5.0.0->nbconvert->-r external/nmodl/requirements.txt (line 20))
Using cached webencodings-0.5.1-py2.py3-none-any.whl.metadata (2.1 kB)
Collecting platformdirs>=2.5 (from jupyter-core!=5.0.*,>=4.12->jupyter-client->-r external/nmodl/requirements.txt (line 16))
Using cached platformdirs-4.2.2-py3-none-any.whl.metadata (11 kB)
Collecting mdurl~=0.1 (from markdown-it-py<3.0.0,>=1.0.0->myst_parser<2.0.0->-r external/nmodl/requirements.txt (line 18))
Using cached mdurl-0.1.2-py3-none-any.whl.metadata (1.6 kB)
Collecting fastjsonschema>=2.15 (from nbformat>=5.7->nbconvert->-r external/nmodl/requirements.txt (line 20))
Using cached fastjsonschema-2.20.0-py3-none-any.whl.metadata (2.1 kB)
Collecting jsonschema>=2.6 (from nbformat>=5.7->nbconvert->-r external/nmodl/requirements.txt (line 20))
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Collecting charset-normalizer<4,>=2 (from requests>=2.5.0->sphinx<6->-r external/nmodl/requirements.txt (line 24))
Using cached charset_normalizer-3.3.2-cp310-cp310-macosx_11_0_arm64.whl.metadata (33 kB)
Collecting idna<4,>=2.5 (from requests>=2.5.0->sphinx<6->-r external/nmodl/requirements.txt (line 24))
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Collecting urllib3<3,>=1.21.1 (from requests>=2.5.0->sphinx<6->-r external/nmodl/requirements.txt (line 24))
Using cached urllib3-2.2.2-py3-none-any.whl.metadata (6.4 kB)
Collecting certifi>=2017.4.17 (from requests>=2.5.0->sphinx<6->-r external/nmodl/requirements.txt (line 24))
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Collecting comm>=0.1.1 (from ipykernel->jupyter->-r external/nmodl/requirements.txt (line 17))
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Collecting debugpy>=1.6.5 (from ipykernel->jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached debugpy-1.8.1-py2.py3-none-any.whl.metadata (1.1 kB)
Collecting ipython>=7.23.1 (from ipykernel->jupyter->-r external/nmodl/requirements.txt (line 17))
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Collecting matplotlib-inline>=0.1 (from ipykernel->jupyter->-r external/nmodl/requirements.txt (line 17))
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Collecting nest-asyncio (from ipykernel->jupyter->-r external/nmodl/requirements.txt (line 17))
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Using cached argon2_cffi_bindings-21.2.0-cp38-abi3-macosx_10_9_universal2.whl (53 kB)
Using cached pure_eval-0.2.2-py3-none-any.whl (11 kB)
Using cached rfc3339_validator-0.1.4-py2.py3-none-any.whl (3.5 kB)
Using cached cffi-1.16.0-cp310-cp310-macosx_11_0_arm64.whl (176 kB)
Using cached h11-0.14.0-py3-none-any.whl (58 kB)
Using cached jsonpointer-3.0.0-py2.py3-none-any.whl (7.6 kB)
Using cached webcolors-24.6.0-py3-none-any.whl (14 kB)
Using cached fqdn-1.5.1-py3-none-any.whl (9.1 kB)
Using cached isoduration-20.11.0-py3-none-any.whl (11 kB)
Using cached uri_template-1.3.0-py3-none-any.whl (11 kB)
Using cached arrow-1.3.0-py3-none-any.whl (66 kB)
Using cached pycparser-2.22-py3-none-any.whl (117 kB)
Using cached types_python_dateutil-2.9.0.20240316-py3-none-any.whl (9.7 kB)
Installing collected packages: webencodings, wcwidth, snowballstemmer, pure-eval, ptyprocess, mpmath, mistune, find_libpython, fastjsonschema, widgetsnbextension, websocket-client, webcolors, urllib3, uri-template, typing-extensions, types-python-dateutil, traitlets, tornado, tomli, tinycss2, sympy, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, sniffio, six, send2trash, rpds-py, rfc3986-validator, pyzmq, PyYAML, python-json-logger, pygments, pycparser, psutil, prompt-toolkit, prometheus-client, pluggy, platformdirs, pexpect, pathspec, parso, pandocfilters, packaging, overrides, numpy, nest-asyncio, mdurl, MarkupSafe, jupyterlab-widgets, jupyterlab-pygments, jsonpointer, json5, iniconfig, imagesize, idna, h11, fqdn, executing, exceptiongroup, docutils, defusedxml, decorator, debugpy, coverage, charset-normalizer, certifi, babel, attrs, appnope, alabaster, terminado, setuptools-scm, scikit-build-core, rfc3339-validator, requests, referencing, qtpy, python-dateutil, pytest, matplotlib-inline, markdown-it-py, jupyter-core, Jinja2, jedi, httpcore, comm, cffi, bleach, beautifulsoup4, async-lru, asttokens, anyio, stack-data, sphinx, pytest-cov, mdit-py-plugins, jupyter-server-terminals, jupyter-client, jsonschema-specifications, httpx, arrow, argon2-cffi-bindings, sphinxcontrib-jquery, myst_parser, jsonschema, isoduration, ipython, argon2-cffi, sphinx-rtd-theme, nbformat, ipywidgets, ipykernel, qtconsole, nbclient, jupyter-events, jupyter-console, nbconvert, nbsphinx, jupyter-server, notebook-shim, jupyterlab-server, jupyter-lsp, jupyterlab, notebook, jupyter
Successfully installed Jinja2-3.1.4 MarkupSafe-2.1.5 PyYAML-6.0.1 alabaster-0.7.16 anyio-4.4.0 appnope-0.1.4 argon2-cffi-23.1.0 argon2-cffi-bindings-21.2.0 arrow-1.3.0 asttokens-2.4.1 async-lru-2.0.4 attrs-23.2.0 babel-2.15.0 beautifulsoup4-4.12.3 bleach-6.1.0 certifi-2024.6.2 cffi-1.16.0 charset-normalizer-3.3.2 comm-0.2.2 coverage-7.5.3 debugpy-1.8.1 decorator-5.1.1 defusedxml-0.7.1 docutils-0.19 exceptiongroup-1.2.1 executing-2.0.1 fastjsonschema-2.20.0 find_libpython-0.4.0 fqdn-1.5.1 h11-0.14.0 httpcore-1.0.5 httpx-0.27.0 idna-3.7 imagesize-1.4.1 iniconfig-2.0.0 ipykernel-6.29.4 ipython-8.25.0 ipywidgets-8.1.3 isoduration-20.11.0 jedi-0.19.1 json5-0.9.25 jsonpointer-3.0.0 jsonschema-4.22.0 jsonschema-specifications-2023.12.1 jupyter-1.0.0 jupyter-client-8.6.2 jupyter-console-6.6.3 jupyter-core-5.7.2 jupyter-events-0.10.0 jupyter-lsp-2.2.5 jupyter-server-2.14.1 jupyter-server-terminals-0.5.3 jupyterlab-4.2.2 jupyterlab-pygments-0.3.0 jupyterlab-server-2.27.2 jupyterlab-widgets-3.0.11 markdown-it-py-2.2.0 matplotlib-inline-0.1.7 mdit-py-plugins-0.3.5 mdurl-0.1.2 mistune-2.0.5 mpmath-1.3.0 myst_parser-1.0.0 nbclient-0.10.0 nbconvert-7.16.4 nbformat-5.10.4 nbsphinx-0.9.4 nest-asyncio-1.6.0 notebook-7.2.1 notebook-shim-0.2.4 numpy-2.0.0 overrides-7.7.0 packaging-24.1 pandocfilters-1.5.1 parso-0.8.4 pathspec-0.12.1 pexpect-4.9.0 platformdirs-4.2.2 pluggy-1.5.0 prometheus-client-0.20.0 prompt-toolkit-3.0.47 psutil-5.9.8 ptyprocess-0.7.0 pure-eval-0.2.2 pycparser-2.22 pygments-2.18.0 pytest-8.1.1 pytest-cov-5.0.0 python-dateutil-2.9.0.post0 python-json-logger-2.0.7 pyzmq-26.0.3 qtconsole-5.5.2 qtpy-2.4.1 referencing-0.35.1 requests-2.32.3 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 rpds-py-0.18.1 scikit-build-core-0.9.6 send2trash-1.8.3 setuptools-scm-8.1.0 six-1.16.0 sniffio-1.3.1 snowballstemmer-2.2.0 soupsieve-2.5 sphinx-5.3.0 sphinx-rtd-theme-2.0.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.6 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jquery-4.1 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.7 sphinxcontrib-serializinghtml-1.1.10 stack-data-0.6.3 sympy-1.12.1 terminado-0.18.1 tinycss2-1.3.0 tomli-2.0.1 tornado-6.4.1 traitlets-5.14.3 types-python-dateutil-2.9.0.20240316 typing-extensions-4.12.2 uri-template-1.3.0 urllib3-2.2.2 wcwidth-0.2.13 webcolors-24.6.0 webencodings-0.5.1 websocket-client-1.8.0 widgetsnbextension-4.0.11
[notice] A new release of pip is available: 23.3.1 -> 24.0
[notice] To update, run: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/venv/bin/python3 -m pip install --upgrade pip
$ venv/bin/pip install --upgrade pip -r nrn_requirements.txt
Requirement already satisfied: pip in ./venv/lib/python3.10/site-packages (23.3.1)
Collecting pip
Using cached pip-24.0-py3-none-any.whl.metadata (3.6 kB)
Collecting wheel (from -r nrn_requirements.txt (line 1))
Using cached wheel-0.43.0-py3-none-any.whl.metadata (2.2 kB)
Requirement already satisfied: setuptools in ./venv/lib/python3.10/site-packages (from -r nrn_requirements.txt (line 2)) (68.2.2)
Collecting setuptools (from -r nrn_requirements.txt (line 2))
Using cached setuptools-70.0.0-py3-none-any.whl.metadata (5.9 kB)
Requirement already satisfied: setuptools_scm in ./venv/lib/python3.10/site-packages (from -r nrn_requirements.txt (line 3)) (8.1.0)
Collecting scikit-build (from -r nrn_requirements.txt (line 4))
Using cached scikit_build-0.17.6-py3-none-any.whl.metadata (14 kB)
Collecting matplotlib (from -r nrn_requirements.txt (line 5))
Using cached matplotlib-3.9.0-cp310-cp310-macosx_11_0_arm64.whl.metadata (11 kB)
Collecting bokeh<3 (from -r nrn_requirements.txt (line 7))
Using cached bokeh-2.4.3-py3-none-any.whl.metadata (14 kB)
Requirement already satisfied: ipython in ./venv/lib/python3.10/site-packages (from -r nrn_requirements.txt (line 8)) (8.25.0)
Collecting cython<3 (from -r nrn_requirements.txt (line 9))
Using cached Cython-0.29.37-py2.py3-none-any.whl.metadata (3.1 kB)
Requirement already satisfied: packaging in ./venv/lib/python3.10/site-packages (from -r nrn_requirements.txt (line 10)) (24.1)
Requirement already satisfied: pytest<=8.1.1 in ./venv/lib/python3.10/site-packages (from -r nrn_requirements.txt (line 11)) (8.1.1)
Requirement already satisfied: pytest-cov in ./venv/lib/python3.10/site-packages (from -r nrn_requirements.txt (line 12)) (5.0.0)
Collecting mpi4py (from -r nrn_requirements.txt (line 13))
Using cached mpi4py-3.1.6-cp310-cp310-macosx_12_0_arm64.whl
Collecting numpy<2 (from -r nrn_requirements.txt (line 14))
Using cached numpy-1.26.4-cp310-cp310-macosx_11_0_arm64.whl.metadata (61 kB)
Requirement already satisfied: find_libpython in ./venv/lib/python3.10/site-packages (from -r nrn_requirements.txt (line 15)) (0.4.0)
Requirement already satisfied: tomli>=1 in ./venv/lib/python3.10/site-packages (from setuptools_scm->-r nrn_requirements.txt (line 3)) (2.0.1)
Collecting distro (from scikit-build->-r nrn_requirements.txt (line 4))
Using cached distro-1.9.0-py3-none-any.whl.metadata (6.8 kB)
Collecting contourpy>=1.0.1 (from matplotlib->-r nrn_requirements.txt (line 5))
Using cached contourpy-1.2.1-cp310-cp310-macosx_11_0_arm64.whl.metadata (5.8 kB)
Collecting cycler>=0.10 (from matplotlib->-r nrn_requirements.txt (line 5))
Using cached cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
Collecting fonttools>=4.22.0 (from matplotlib->-r nrn_requirements.txt (line 5))
Using cached fonttools-4.53.0-cp310-cp310-macosx_11_0_arm64.whl.metadata (162 kB)
Collecting kiwisolver>=1.3.1 (from matplotlib->-r nrn_requirements.txt (line 5))
Using cached kiwisolver-1.4.5-cp310-cp310-macosx_11_0_arm64.whl.metadata (6.4 kB)
Collecting pillow>=8 (from matplotlib->-r nrn_requirements.txt (line 5))
Using cached pillow-10.3.0-cp310-cp310-macosx_11_0_arm64.whl.metadata (9.2 kB)
Collecting pyparsing>=2.3.1 (from matplotlib->-r nrn_requirements.txt (line 5))
Using cached pyparsing-3.1.2-py3-none-any.whl.metadata (5.1 kB)
Requirement already satisfied: python-dateutil>=2.7 in ./venv/lib/python3.10/site-packages (from matplotlib->-r nrn_requirements.txt (line 5)) (2.9.0.post0)
Requirement already satisfied: Jinja2>=2.9 in ./venv/lib/python3.10/site-packages (from bokeh<3->-r nrn_requirements.txt (line 7)) (3.1.4)
Requirement already satisfied: PyYAML>=3.10 in ./venv/lib/python3.10/site-packages (from bokeh<3->-r nrn_requirements.txt (line 7)) (6.0.1)
Requirement already satisfied: tornado>=5.1 in ./venv/lib/python3.10/site-packages (from bokeh<3->-r nrn_requirements.txt (line 7)) (6.4.1)
Requirement already satisfied: typing-extensions>=3.10.0 in ./venv/lib/python3.10/site-packages (from bokeh<3->-r nrn_requirements.txt (line 7)) (4.12.2)
Requirement already satisfied: decorator in ./venv/lib/python3.10/site-packages (from ipython->-r nrn_requirements.txt (line 8)) (5.1.1)
Requirement already satisfied: jedi>=0.16 in ./venv/lib/python3.10/site-packages (from ipython->-r nrn_requirements.txt (line 8)) (0.19.1)
Requirement already satisfied: matplotlib-inline in ./venv/lib/python3.10/site-packages (from ipython->-r nrn_requirements.txt (line 8)) (0.1.7)
Requirement already satisfied: prompt-toolkit<3.1.0,>=3.0.41 in ./venv/lib/python3.10/site-packages (from ipython->-r nrn_requirements.txt (line 8)) (3.0.47)
Requirement already satisfied: pygments>=2.4.0 in ./venv/lib/python3.10/site-packages (from ipython->-r nrn_requirements.txt (line 8)) (2.18.0)
Requirement already satisfied: stack-data in ./venv/lib/python3.10/site-packages (from ipython->-r nrn_requirements.txt (line 8)) (0.6.3)
Requirement already satisfied: traitlets>=5.13.0 in ./venv/lib/python3.10/site-packages (from ipython->-r nrn_requirements.txt (line 8)) (5.14.3)
Requirement already satisfied: exceptiongroup in ./venv/lib/python3.10/site-packages (from ipython->-r nrn_requirements.txt (line 8)) (1.2.1)
Requirement already satisfied: pexpect>4.3 in ./venv/lib/python3.10/site-packages (from ipython->-r nrn_requirements.txt (line 8)) (4.9.0)
Requirement already satisfied: iniconfig in ./venv/lib/python3.10/site-packages (from pytest<=8.1.1->-r nrn_requirements.txt (line 11)) (2.0.0)
Requirement already satisfied: pluggy<2.0,>=1.4 in ./venv/lib/python3.10/site-packages (from pytest<=8.1.1->-r nrn_requirements.txt (line 11)) (1.5.0)
Requirement already satisfied: coverage>=5.2.1 in ./venv/lib/python3.10/site-packages (from coverage[toml]>=5.2.1->pytest-cov->-r nrn_requirements.txt (line 12)) (7.5.3)
Requirement already satisfied: parso<0.9.0,>=0.8.3 in ./venv/lib/python3.10/site-packages (from jedi>=0.16->ipython->-r nrn_requirements.txt (line 8)) (0.8.4)
Requirement already satisfied: MarkupSafe>=2.0 in ./venv/lib/python3.10/site-packages (from Jinja2>=2.9->bokeh<3->-r nrn_requirements.txt (line 7)) (2.1.5)
Requirement already satisfied: ptyprocess>=0.5 in ./venv/lib/python3.10/site-packages (from pexpect>4.3->ipython->-r nrn_requirements.txt (line 8)) (0.7.0)
Requirement already satisfied: wcwidth in ./venv/lib/python3.10/site-packages (from prompt-toolkit<3.1.0,>=3.0.41->ipython->-r nrn_requirements.txt (line 8)) (0.2.13)
Requirement already satisfied: six>=1.5 in ./venv/lib/python3.10/site-packages (from python-dateutil>=2.7->matplotlib->-r nrn_requirements.txt (line 5)) (1.16.0)
Requirement already satisfied: executing>=1.2.0 in ./venv/lib/python3.10/site-packages (from stack-data->ipython->-r nrn_requirements.txt (line 8)) (2.0.1)
Requirement already satisfied: asttokens>=2.1.0 in ./venv/lib/python3.10/site-packages (from stack-data->ipython->-r nrn_requirements.txt (line 8)) (2.4.1)
Requirement already satisfied: pure-eval in ./venv/lib/python3.10/site-packages (from stack-data->ipython->-r nrn_requirements.txt (line 8)) (0.2.2)
Using cached pip-24.0-py3-none-any.whl (2.1 MB)
Using cached wheel-0.43.0-py3-none-any.whl (65 kB)
Using cached setuptools-70.0.0-py3-none-any.whl (863 kB)
Using cached scikit_build-0.17.6-py3-none-any.whl (84 kB)
Using cached matplotlib-3.9.0-cp310-cp310-macosx_11_0_arm64.whl (7.8 MB)
Using cached bokeh-2.4.3-py3-none-any.whl (18.5 MB)
Using cached Cython-0.29.37-py2.py3-none-any.whl (989 kB)
Using cached numpy-1.26.4-cp310-cp310-macosx_11_0_arm64.whl (14.0 MB)
Using cached contourpy-1.2.1-cp310-cp310-macosx_11_0_arm64.whl (244 kB)
Using cached cycler-0.12.1-py3-none-any.whl (8.3 kB)
Using cached fonttools-4.53.0-cp310-cp310-macosx_11_0_arm64.whl (2.2 MB)
Using cached kiwisolver-1.4.5-cp310-cp310-macosx_11_0_arm64.whl (66 kB)
Using cached pillow-10.3.0-cp310-cp310-macosx_11_0_arm64.whl (3.4 MB)
Using cached pyparsing-3.1.2-py3-none-any.whl (103 kB)
Using cached distro-1.9.0-py3-none-any.whl (20 kB)
Installing collected packages: wheel, setuptools, pyparsing, pip, pillow, numpy, mpi4py, kiwisolver, fonttools, distro, cython, cycler, scikit-build, contourpy, bokeh, matplotlib
Attempting uninstall: setuptools
Found existing installation: setuptools 68.2.2
Uninstalling setuptools-68.2.2:
Successfully uninstalled setuptools-68.2.2
Attempting uninstall: pip
Found existing installation: pip 23.3.1
Uninstalling pip-23.3.1:
Successfully uninstalled pip-23.3.1
Attempting uninstall: numpy
Found existing installation: numpy 2.0.0
Uninstalling numpy-2.0.0:
Successfully uninstalled numpy-2.0.0
Successfully installed bokeh-2.4.3 contourpy-1.2.1 cycler-0.12.1 cython-0.29.37 distro-1.9.0 fonttools-4.53.0 kiwisolver-1.4.5 matplotlib-3.9.0 mpi4py-3.1.6 numpy-1.26.4 pillow-10.3.0 pip-24.0 pyparsing-3.1.2 scikit-build-0.17.6 setuptools-70.0.0 wheel-0.43.0
$ source ./venv/bin/activate
$ export PYTHON=${PWD}/venv/bin/python
$ ${PYTHON} --version
Python 3.10.13
$ ${PYTHON} -c "import os,matplotlib; f = open(os.path.join(os.path.dirname(matplotlib.__file__), \"mpl-data/matplotlibrc\"),\"a\"); f.write(\"backend: TkAgg\");f.close();"
$ export CXX=${CXX:-g++}
$ export CC=${CC:-gcc}
$ brew install flex bison
Warning: flex 2.6.4_2 is already installed and up-to-date.
To reinstall 2.6.4_2, run:
brew reinstall flex
Warning: bison 3.8.2 is already installed and up-to-date.
To reinstall 3.8.2, run:
brew reinstall bison
$ export PATH="/opt/homebrew/opt/flex/bin:/opt/homebrew/opt/bison/bin:$PATH"
$ export INSTALL_DIR=$(pwd)/install
$ echo $LANG
$ echo $LC_ALL
$ export PYTHONPATH=$(${PYTHON} -c "import site; print(\":\".join(site.getsitepackages()))")
$ ${PYTHON} -c 'import os,sys; os.set_blocking(sys.stdout.fileno(), True)'
$ cmake_args=(-G Ninja)
$ if [[ -n "${sanitizer}" ]]; then
$ cmake_args+=(-DCMAKE_BUILD_TYPE=Custom -DCMAKE_C_FLAGS="-O1 -g" -DCMAKE_CXX_FLAGS="-O1 -g" -DNRN_SANITIZERS=$(echo ${sanitizer} | sed -e 's/-/,/g'))
$ fi
$ cmake_args+=(-DCMAKE_C_COMPILER="${CC}" -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER="${CXX}" -DCMAKE_CXX_COMPILER_LAUNCHER=ccache -DCMAKE_INSTALL_PREFIX="${INSTALL_DIR}" -DNRN_ENABLE_TESTS=ON -DNRN_ENABLE_PERFORMANCE_TESTS=OFF -DNRN_ENABLE_CORENEURON=${cmake_coreneuron} -DNRN_ENABLE_INTERVIEWS=${cmake_interviews} -DNRN_ENABLE_RX3D=${cmake_rx3d})
$ cmake_args+=(-DPYTHON_EXECUTABLE="${PYTHON}")
$ mkdir build && cd build
$ echo "Building with ${cmake_args[@]}"
Building with -G Ninja -DCMAKE_BUILD_TYPE=Custom -DCMAKE_C_FLAGS=-O1 -g -DCMAKE_CXX_FLAGS=-O1 -g -DNRN_SANITIZERS=address -DCMAKE_C_COMPILER=gcc -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER=g++ -DCMAKE_CXX_COMPILER_LAUNCHER=ccache -DCMAKE_INSTALL_PREFIX=/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install -DNRN_ENABLE_TESTS=ON -DNRN_ENABLE_PERFORMANCE_TESTS=OFF -DNRN_ENABLE_CORENEURON=ON -DNRN_ENABLE_INTERVIEWS=OFF -DNRN_ENABLE_RX3D=OFF -DPYTHON_EXECUTABLE=/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/venv/bin/python
$ cmake .. "${cmake_args[@]}"
-- The C compiler identification is AppleClang 14.0.0.14000029
-- The CXX compiler identification is AppleClang 14.0.0.14000029
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- git describe failed (stdout: '', stderr: 'fatal: No names found, cannot describe anything.', code: 128), skipping the version check
-- Sub-module : missing external/coding-conventions : running git submodule update --init
Submodule 'external/coding-conventions' (https://github.com/BlueBrain/hpc-coding-conventions.git) registered for path 'external/coding-conventions'
Cloning into '/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/external/coding-conventions'...
Submodule path 'external/coding-conventions': checked out '3d157f9c8ea94d196a825aaa7f523265e360dc4b'
-- Fetching git submodule external/Random123: running git submodule update --init;--recursive;--depth;1 -- external/Random123
Submodule 'external/Random123' (https://github.com/BlueBrain/Random123.git) registered for path 'external/Random123'
Cloning into '/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/external/Random123'...
From https://github.com/BlueBrain/Random123
* branch b5cb15614e8f3eb0ff316bdc50c300ddd32fa3c1 -> FETCH_HEAD
Submodule path 'external/Random123': checked out 'b5cb15614e8f3eb0ff316bdc50c300ddd32fa3c1'
-- 3rd party project: using Random123 from "external/Random123"
-- Fetching git submodule external/eigen: running git submodule update --init;--recursive;--depth;1 -- external/eigen
Submodule 'external/eigen' (https://gitlab.com/libeigen/eigen.git) registered for path 'external/eigen'
Cloning into '/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/external/eigen'...
From https://gitlab.com/libeigen/eigen
* branch 3147391d946bb4b6c68edd901f2add6ac1f31f8c -> FETCH_HEAD
Submodule path 'external/eigen': checked out '3147391d946bb4b6c68edd901f2add6ac1f31f8c'
-- 3rd party project: using eigen from "external/eigen"
-- Enabling sanitizers: address
-- Sanitizer runtime library: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/14.0.0/lib/darwin/libclang_rt.asan_osx_dynamic.dylib
-- Checking if /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/venv/bin/python is a working python
-- Found BISON: /opt/homebrew/opt/bison/bin/bison (found version "3.8.2")
-- Found FLEX: /opt/homebrew/opt/flex/bin/flex (found suitable version "2.6.4", minimum required is "2.6")
-- Found Readline: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include
-- Found MPI_C: /opt/homebrew/Cellar/open-mpi/5.0.1/lib/libmpi.dylib (found version "3.1")
-- Found MPI_CXX: /opt/homebrew/Cellar/open-mpi/5.0.1/lib/libmpi.dylib (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Fetching git submodule external/CLI11: running git submodule update --init;--recursive;--depth;1 -- external/CLI11
Submodule 'external/CLI11' (https://github.com/CLIUtils/CLI11.git) registered for path 'external/CLI11'
Cloning into '/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/external/CLI11'...
From https://github.com/CLIUtils/CLI11
* branch 291c58789c031208f08f4f261a858b5b7083e8e2 -> FETCH_HEAD
Submodule path 'external/CLI11': checked out '291c58789c031208f08f4f261a858b5b7083e8e2'
-- 3rd party project: using CLI11 from "external/CLI11"
CMake Deprecation Warning at external/CLI11/CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
-- Building CoreNEURON
-- Found Git: /usr/bin/git (found version "2.37.0 (Apple Git-136)")
-- Found Perl: /usr/bin/perl (found version "5.30.3")
-- Could NOT find nmodl (missing: nmodl_BINARY nmodl_INCLUDE nmodl_PYTHONPATH)
-- Sub-project : using nmodl from from /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/external/nmodl
-- CHECKING FOR FLEX/BISON
-- Found BISON: /opt/homebrew/opt/bison/bin/bison (found suitable version "3.8.2", minimum required is "3.0")
-- Adding Flex include path as : /opt/homebrew/opt/flex/include/
-- NMODL_TEST_FORMATTING: OFF
-- NMODL_GIT_HOOKS: OFF
-- NMODL_GIT_COMMIT_HOOKS:
-- NMODL_GIT_PUSH_HOOKS: courtesy-msg
-- NMODL_STATIC_ANALYSIS: OFF
-- NMODL_TEST_STATIC_ANALYSIS: OFF
-- 3rd party project: using eigen from "ext/eigen"
-- 3rd party project: using fmt from "ext/fmt"
-- Version: 10.2.1
-- Build type: Custom
-- 3rd party project: using json from "ext/json"
-- Using the multi-header code from /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/external/nmodl/ext/json/include/
-- 3rd party project: using pybind11 from "ext/pybind11"
-- pybind11 v2.12.0
-- Found PythonInterp: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/venv/bin/python (found suitable version "3.10.13", minimum required is "3.6")
-- Found PythonLibs: /opt/homebrew/opt/python@3.10/Frameworks/Python.framework/Versions/3.10/lib/libpython3.10.dylib
-- 3rd party project: using spdlog from "ext/spdlog"
-- Build spdlog: 1.13.0
-- Build type: Custom
-- CHECKING FOR PYTHON
-- Found Python: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/venv/bin/python3.10 (found suitable version "3.10.13", minimum required is "3.8") found components: Interpreter
CMake Warning (dev) at external/nmodl/src/pybind/CMakeLists.txt:27 (configure_file):
configure_file called with unknown argument(s):
@ONLY@
This warning is for project developers. Use -Wno-dev to suppress it.
--
-- Configured NMODL 0.0 (c5ecfea 2024-06-10 16:25:23 +0200)
--
-- You can now build NMODL using:
-- cmake --build . --parallel 8 [--target TARGET]
-- You might want to adjust the number of parallel build jobs for your system.
-- Some non-default targets you might want to build:
-- --------------------+--------------------------------------------------------
-- Target | Description
-- --------------------+--------------------------------------------------------
-- test | Run unit tests
-- install | Will install NMODL to: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install
-- --------------------+--------------------------------------------------------
-- Build option | Status
-- --------------------+--------------------------------------------------------
-- CXX COMPILER | /usr/bin/g++
-- COMPILE FLAGS | -O1 -g -openmp-simd
-- Build Type | Custom
-- Python Bindings | OFF
-- Flex | /opt/homebrew/opt/flex/bin/flex
-- Bison | /opt/homebrew/opt/bison/bin/bison
-- Python | /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/venv/bin/python
-- Linked against | ON
-- --------------------+--------------------------------------------------------
-- See documentation : https://github.com/BlueBrain/nmodl/
-- --------------------+--------------------------------------------------------
--
--
-- CoreNEURON is enabled with following build configuration:
-- --------------------+--------------------------------------------------------
-- Build option | Status
-- --------------------+--------------------------------------------------------
-- CXX COMPILER | /usr/bin/g++
-- COMPILE FLAGS | -O1 -g -openmp-simd -std=c++17 -DCORENEURON_BUILD -DCORENRN_BUILD=1 -DEIGEN_DONT_PARALLELIZE -DNRNMPI=1 -DLAYOUT=0 -DDISABLE_HOC_EXP -DENABLE_SPLAYTREE_QUEUING -fno-omit-frame-pointer -shared-libsan -fsanitize=address -fsanitize-address-use-after-scope
-- Build Type | SHARED
-- MPI | ON
-- DYNAMIC | OFF
-- INC | /opt/homebrew/Cellar/open-mpi/5.0.1/include
-- OpenMP | ON
-- NMODL PATH | /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/bin/nmodl
-- NMODL FLAGS |
-- GPU Support | OFF
-- Auto Timeout | ON
-- Wrap exp() | OFF
-- SplayTree Queue | ON
-- NetReceive Buffer | ON
-- Caliper | OFF
-- Likwid | OFF
-- Unit Tests | ON
-- Reporting | OFF
-- --------------------+--------------------------------------------------------
--
Extracting link flags from target 'nrngnu', beware that this can be fragile. Got:
Extracting link flags from target 'sparse13', beware that this can be fragile. Got:
Generating link flags from name 'nrnpython', beware that this can be fragile. Got: -lnrnpython
Extracting link flags from target 'Threads::Threads', beware that this can be fragile. Got: -lnrnpython
Generating link flags from path /opt/homebrew/Cellar/open-mpi/5.0.1/lib/libmpi.dylib Got: /opt/homebrew/Cellar/open-mpi/5.0.1/lib/libmpi.dylib -Wl,-rpath,/opt/homebrew/Cellar/open-mpi/5.0.1/lib
-- Sub-module : missing /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/external/catch2 : running git submodule update --init
Submodule 'external/catch2' (https://github.com/catchorg/Catch2.git) registered for path 'external/catch2'
Cloning into '/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/external/catch2'...
Submodule path 'external/catch2': checked out '8ac8190e494a381072c89f5e161b92a08d98b37b'
-- Found Python module 'pytest' with version(s): 8.1.1
-- Found Python module 'pytest_cov' with version(s): 5.0.0
-- Fetching git submodule test/rxd/testdata: running git submodule update --init;--recursive;--depth;1 -- test/rxd/testdata
Submodule 'test/rxd/testdata' (https://github.com/neuronsimulator/rxdtestdata) registered for path 'test/rxd/testdata'
Cloning into '/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/test/rxd/testdata'...
From https://github.com/neuronsimulator/rxdtestdata
* branch 30c76babbbc2cff005fd3f6f649c8b81da41ee58 -> FETCH_HEAD
Submodule path 'test/rxd/testdata': checked out '30c76babbbc2cff005fd3f6f649c8b81da41ee58'
-- 3rd party project: using rxd/testdata from "test/rxd/testdata"
-- Found Python module 'mpi4py' with version(s): 3.1.6
-- Disabling coreneuron_modtests::fornetcon_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::direct_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::direct_hoc_gpu: gpu not enabled
-- Disabling coreneuron_modtests::spikes_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::spikes_file_mode_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::fast_imem_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::datareturn_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::test_units_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::test_netmove_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::test_pointer_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::test_watchrange_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::test_psolve_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::test_ba_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::test_nmodlrandom_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::test_nmodlrandom_syntax_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::test_natrans_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::array_variable_transfer_run_mode_0_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::array_variable_transfer_run_mode_1_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::array_variable_transfer_run_mode_2_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::array_variable_transfer_file_mode_py_gpu: gpu not enabled
-- Found Python module 'mpi4py' with version(s): 3.1.6
-- Disabling coreneuron_modtests::spikes_mpi_file_mode_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::test_subworlds_py_gpu: gpu not enabled
-- Disabling nmodl_tests_coreneuron::test_table_coreneuron_gpu: gpu not enabled
-- Disabling nmodl_tests_coreneuron::test_disc_coreneuron_gpu: gpu not enabled
-- Disabling nmodl_tests_coreneuron::test_function_table_coreneuron_gpu: gpu not enabled
-- Disabling nmodl_tests_coreneuron::test_kinetic_coreneuron_gpu: gpu not enabled
-- Disabling reduced_dentate::coreneuron_gpu: gpu not enabled
-- Disabling external_ringtest::coreneuron_gpu_mpi_offline_saverestore: gpu not enabled
-- Disabling external_ringtest::coreneuron_gpu_mpi: gpu not enabled
-- Disabling external_ringtest::coreneuron_gpu_mpi_python: gpu not enabled
-- Disabling external_ringtest::coreneuron_gpu_mpi_offline: gpu not enabled
-- Disabling external_ringtest::coreneuron_gpu_mpi_threads: gpu not enabled
-- Disabling external_ringtest::coreneuron_gpu_mpi_threads_python: gpu not enabled
-- Disabling testcorenrn_bbcore::coreneuron_gpu_online: gpu not enabled
-- Disabling testcorenrn_bbcore::coreneuron_gpu_online_psolve_alternate: gpu not enabled
-- Disabling testcorenrn_bbcore::coreneuron_gpu_offline: gpu not enabled
-- Disabling testcorenrn_conc::coreneuron_gpu_online: gpu not enabled
-- Disabling testcorenrn_conc::coreneuron_gpu_online_psolve_alternate: gpu not enabled
-- Disabling testcorenrn_conc::coreneuron_gpu_offline: gpu not enabled
-- Disabling testcorenrn_deriv::coreneuron_gpu_online: gpu not enabled
-- Disabling testcorenrn_deriv::coreneuron_gpu_online_psolve_alternate: gpu not enabled
-- Disabling testcorenrn_deriv::coreneuron_gpu_offline: gpu not enabled
-- Disabling testcorenrn_gf::coreneuron_gpu_online: gpu not enabled
-- Disabling testcorenrn_gf::coreneuron_gpu_online_psolve_alternate: gpu not enabled
-- Disabling testcorenrn_gf::coreneuron_gpu_offline: gpu not enabled
-- Disabling testcorenrn_kin::coreneuron_gpu_online: gpu not enabled
-- Disabling testcorenrn_kin::coreneuron_gpu_online_psolve_alternate: gpu not enabled
-- Disabling testcorenrn_kin::coreneuron_gpu_offline: gpu not enabled
-- Disabling testcorenrn_patstim::coreneuron_gpu_offline_saverestore: gpu not enabled
-- Disabling testcorenrn_patstim::coreneuron_gpu_offline: gpu not enabled
-- Disabling testcorenrn_vecplay::coreneuron_gpu_online: gpu not enabled
-- Disabling testcorenrn_vecplay::coreneuron_gpu_online_psolve_alternate: gpu not enabled
-- Disabling testcorenrn_vecplay::coreneuron_gpu_offline: gpu not enabled
-- Disabling testcorenrn_vecevent::coreneuron_gpu_online: gpu not enabled
-- Disabling testcorenrn_vecevent::coreneuron_gpu_online_psolve_alternate: gpu not enabled
-- Disabling testcorenrn_vecevent::coreneuron_gpu_offline: gpu not enabled
-- Disabling testcorenrn_watch::coreneuron_gpu_online: gpu not enabled
-- Disabling testcorenrn_watch::coreneuron_gpu_online_psolve_alternate: gpu not enabled
-- Disabling testcorenrn_watch::coreneuron_gpu_offline: gpu not enabled
-- Found OpenSSL: /opt/homebrew/Cellar/openssl@3/3.2.0_1/lib/libcrypto.dylib (found version "3.2.0")
--
-- Configured NEURON 9.0.0
--
-- You can now build NEURON using:
-- cmake --build . --parallel 8 [--target TARGET]
-- You might want to adjust the number of parallel build jobs for your system.
-- Some non-default targets you might want to build:
-- --------------+--------------------------------------------------------------
-- Target | Description
-- --------------+--------------------------------------------------------------
-- install | Will install NEURON to: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install
-- | Change the install location of NEURON using:
-- | cmake <src_path> -DCMAKE_INSTALL_PREFIX=<install_path>
-- docs | Build full docs. Calls targets: doxygen, notebooks, sphinx, notebooks-clean
-- uninstall | Removes files installed by make install (todo)
-- --------------+--------------------------------------------------------------
-- Build option | Status
-- --------------+--------------------------------------------------------------
-- C COMPILER | /usr/bin/gcc
-- CXX COMPILER | /usr/bin/g++
-- BUILD_TYPE | Custom (allowed: Custom;Debug;Release;RelWithDebInfo;Fast;FastDebug)
-- COMPILE FLAGS | -O1 -g -openmp-simd -fno-omit-frame-pointer -shared-libsan -fsanitize=address -fsanitize-address-use-after-scope -O1 -g -openmp-simd
-- Shared | ON
-- MPI | ON
-- DYNAMIC | OFF
-- INC | /opt/homebrew/Cellar/open-mpi/5.0.1/include
-- LIB | /opt/homebrew/Cellar/open-mpi/5.0.1/lib/libmpi.dylib
-- Python | ON
-- DYNAMIC | OFF
-- MODULE | ON
-- python3.10 (default)
-- EXE | /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/venv/bin/python
-- INC | /opt/homebrew/opt/python@3.10/Frameworks/Python.framework/Versions/3.10/include/python3.10
-- LIB | /opt/homebrew/opt/python@3.10/Frameworks/Python.framework/Versions/3.10/lib/libpython3.10.dylib
-- Readline | /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/lib/libreadline.tbd
-- Curses | /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/lib/libcurses.tbd;/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/lib/libform.tbd
-- RX3D | OFF
-- Interviews | OFF
-- CoreNEURON | ON
-- PATH | /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/coreneuron
-- LINK FLAGS | -lcorenrnmech -Wl,-rpath,/opt/homebrew/Cellar/open-mpi/5.0.1/lib /opt/homebrew/Cellar/open-mpi/5.0.1/lib/libmpi.dylib
-- Tests | ON
-- --------------+--------------------------------------------------------------
-- See documentation : https://www.neuron.yale.edu/neuron/
-- --------------+--------------------------------------------------------------
--
-- Configuring done (24.3s)
-- Generating done (0.2s)
-- Build files have been written to: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build
$ ccache -z
Statistics zeroed
$ ccache -vs 2>/dev/null
Cache directory: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/ccache
Config file: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/ccache/ccache.conf
System config file: /opt/homebrew/Cellar/ccache/4.9/etc/ccache.conf
Stats updated: Mon Jun 17 22:13:31 2024
Local storage:
Cache size (GiB): 0.2 / 5.0 ( 4.34%)
Files: 2368
Hits: 0
Misses: 0
Reads: 0
Writes: 0
$ cmake --build . --parallel
[0/2] Re-checking globbed directories...
[1/1930] Generating share/nrn/demo/cycle.hoc
[2/1930] Generating share/nrn/demo/d3init.hoc
[3/1930] Generating share/nrn/demo/demo.ses
[4/1930] Generating share/nrn/demo/dend3/control.hoc
[5/1930] Generating share/nrn/demo/demo.hoc
[6/1930] Generating share/nrn/demo/dend3.ses
[7/1930] Generating share/nrn/demo/dend3/dend3.nrn
[8/1930] Generating share/nrn/demo/dend3/syn3.hoc
[9/1930] Generating share/nrn/demo/dynclamp.hoc
[10/1930] Generating share/nrn/demo/dynchan.ses
[11/1930] Generating share/nrn/demo/dynclamp.ses
[12/1930] Generating share/nrn/demo/hh.hoc
[13/1930] Update hh.mod for CoreNEURON compatibility
[14/1930] Generating share/nrn/demo/hh.ses
[15/1930] Generating share/nrn/demo/pyramid.nrn
[16/1930] Generating share/nrn/demo/nomodel.hoc
[17/1930] Generating share/nrn/demo/pyramid.ses
[18/1930] Generating share/nrn/demo/release.hoc
[19/1930] Generating share/nrn/demo/reconst.hoc
[20/1930] Generating share/nrn/demo/release.ses
[21/1930] Generating share/nrn/demo/release/cabpump.mod
[22/1930] Generating share/nrn/demo/release/cachan1.mod
[23/1930] Generating share/nrn/demo/release/capump.mod
[24/1930] Generating share/nrn/demo/release/invlfire.mod
[25/1930] Generating share/nrn/demo/release/camchan.mod
[26/1930] Generating share/nrn/demo/release/nacaex.mod
[27/1930] Generating share/nrn/demo/release/khhchan.mod
[28/1930] Generating share/nrn/demo/release/nachan.mod
[29/1930] Generating share/nrn/demo/singhh.ses
[30/1930] Generating share/nrn/demo/release/release.mod
[31/1930] Generating share/nrn/demo/singhh.hoc
[32/1930] Generating share/nrn/demo/singhhchan.hoc
[33/1930] Generating share/nrn/demo/sync/cell.hoc
[34/1930] Generating share/nrn/demo/sync/spkplot.hoc
[35/1930] Generating share/nrn/demo/sync/demosync.hoc
[36/1930] Generating share/nrn/demo/sync/init.hoc
[37/1930] Generating share/nrn/demo/sync/start.ses
[38/1930] Generating share/nrn/demo/testca.hoc
[39/1930] Generating share/nrn/demo/sync/synchronize.hoc
[40/1930] Generating share/nrn/lib/auditscripts/gettarname
[41/1930] Generating share/nrn/lib/auditscripts/hocaudit.sh
[42/1930] Generating share/nrn/lib/auditscripts/notes
[43/1930] Generating share/nrn/lib/cleanup
[44/1930] Generating share/nrn/lib/auditscripts/retrieve.sh
[45/1930] Generating share/nrn/lib/helpdict
[46/1930] Generating share/nrn/lib/auditscripts/saveaudit
[47/1930] Generating share/nrn/lib/hoc/binfo.hoc
[48/1930] Generating share/nrn/lib/hoc/attshape.hoc
[49/1930] Generating share/nrn/lib/hoc/atoltool.hoc
[50/1930] Generating share/nrn/lib/hoc/celbild.hoc
[51/1930] Generating share/nrn/lib/hoc/celbild/celbild1.hoc
[52/1930] Generating share/nrn/lib/hoc/celbild/celmang.hoc
[53/1930] Generating share/nrn/lib/hoc/celbild/celgeom.hoc
[54/1930] Generating share/nrn/lib/hoc/celbild/celmemb.hoc
[55/1930] Generating share/nrn/lib/hoc/celbild/celset.hoc
[56/1930] Generating share/nrn/lib/hoc/chanbild.hoc
[57/1930] Generating share/nrn/lib/hoc/celbild/celtopol.hoc
[58/1930] Generating share/nrn/lib/hoc/celbild/inhomofn.hoc
[59/1930] Generating share/nrn/lib/hoc/chanbild/chanbild1.hoc
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[72/1930] Generating share/nrn/lib/hoc/chanbild/properties.hoc
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[74/1930] Generating share/nrn/lib/hoc/funfit.hoc
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[80/1930] Generating share/nrn/lib/hoc/import3d/import3d_gui.hoc
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[83/1930] Generating share/nrn/lib/hoc/import3d/read_morphml.hoc
[84/1930] Generating share/nrn/lib/hoc/import3d/import3d_sec.hoc
[85/1930] Generating share/nrn/lib/hoc/import3d/read_nlcda.hoc
[86/1930] Generating share/nrn/lib/hoc/import3d/read_nts.hoc
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[88/1930] Generating share/nrn/lib/hoc/import3d/read_nlcda3.hoc
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[90/1930] Generating share/nrn/lib/hoc/lincir/elmbase.hoc
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[99/1930] Generating share/nrn/lib/hoc/mkcurve.hoc
[100/1930] Generating share/nrn/lib/hoc/modlunit.hoc
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[109/1930] Generating share/nrn/lib/hoc/mulfit/eoneprim.hoc
[110/1930] Generating share/nrn/lib/hoc/mulfit/eonerun.hoc
[111/1930] Generating share/nrn/lib/hoc/mulfit/eonefunc.hoc
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[476/1930] Building CXX object src/coreneuron/CMakeFiles/coreneuron-core.dir/utils/randoms/nrnran123.cpp.o
[477/1930] -- NMODL : GENERATING AST CLASSES WITH PYTHON GENERATOR! --
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[479/1930] Building CXX object external/nmodl/ext/spdlog/CMakeFiles/spdlog.dir/src/cfg.cpp.o
[480/1930] Building CXX object external/nmodl/src/printer/CMakeFiles/printer.dir/nmodl_printer.cpp.o
[481/1930] -- NMODL : GENERATING VERBATIM PARSER WITH BISON! --
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29 | %name-prefix "Verbatim_"
| ^~~~~~~~~~~~~~~~~~~~~~~~
| %define api.prefix {Verbatim_}
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In file included from /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/external/nmodl/src/printer/code_printer.cpp:8:
In file included from /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/external/nmodl/src/printer/code_printer.hpp:17:
In file included from /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/external/nmodl/ext/fmt/include/fmt/format.h:41:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/memory:682:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__memory/shared_ptr.h:25:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__memory/unique_ptr.h:57:5: warning: delete called on 'nmodl::utils::Blame' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor]
delete __ptr;
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__memory/unique_ptr.h:318:7: note: in instantiation of member function 'std::default_delete<nmodl::utils::Blame>::operator()' requested here
__ptr_.second()(__tmp);
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__memory/unique_ptr.h:272:19: note: in instantiation of member function 'std::unique_ptr<nmodl::utils::Blame>::reset' requested here
~unique_ptr() { reset(); }
^
/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/external/nmodl/src/printer/code_printer.cpp:115:26: note: in instantiation of member function 'std::unique_ptr<nmodl::utils::Blame>::~unique_ptr' requested here
auto blame_printer = utils::make_blame(blame_line);
^
1 warning generated.
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../../../../../external/nmodl/src/parser/diffeq.yy:56.1-40: warning: deprecated directive: '%define parser_class_name {DiffeqParser}', use '%define api.parser.class {DiffeqParser}' [-Wdeprecated]
56 | %define parser_class_name {DiffeqParser}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| %define api.parser.class {DiffeqParser}
../../../../../external/nmodl/src/parser/diffeq.yy: warning: 2 shift/reduce conflicts [-Wconflicts-sr]
../../../../../external/nmodl/src/parser/diffeq.yy: note: rerun with option '-Wcounterexamples' to generate conflict counterexamples
../../../../../external/nmodl/src/parser/diffeq.yy: warning: fix-its can be applied. Rerun with option '--update'. [-Wother]
[486/1930] -- NMODL : GENERATING UNIT PARSER WITH BISON! --
../../../../../external/nmodl/src/parser/unit.yy:49.1-38: warning: deprecated directive: '%define parser_class_name {UnitParser}', use '%define api.parser.class {UnitParser}' [-Wdeprecated]
49 | %define parser_class_name {UnitParser}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| %define api.parser.class {UnitParser}
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../../../../../external/nmodl/src/parser/c11.yy:52.1-35: warning: deprecated directive: '%define parser_class_name {CParser}', use '%define api.parser.class {CParser}' [-Wdeprecated]
52 | %define parser_class_name {CParser}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| %define api.parser.class {CParser}
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[504/1930] -- NMODL : GENERATING NMODL_CORE PARSER WITH BISON! --
../../../../../external/nmodl/src/parser/nmodl.yy:64.1-39: warning: deprecated directive: '%define parser_class_name {NmodlParser}', use '%define api.parser.class {NmodlParser}' [-Wdeprecated]
64 | %define parser_class_name {NmodlParser}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| %define api.parser.class {NmodlParser}
../../../../../external/nmodl/src/parser/nmodl.yy: warning: 3 shift/reduce conflicts [-Wconflicts-sr]
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[528/1930] Building CXX object src/gnu/CMakeFiles/nrngnu.dir/RndInt.cpp.o
[529/1930] [FLEX][modlunitlexer] Building scanner with flex 2.6.4
[530/1930] Building CXX object src/gnu/CMakeFiles/nrngnu.dir/RNG.cpp.o
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[533/1930] [BISON][nocmodlparser] Building parser with bison 3.8.2
../src/nmodl/diffeq.ypp: warning: 5 shift/reduce conflicts [-Wconflicts-sr]
../src/nmodl/diffeq.ypp: note: rerun with option '-Wcounterexamples' to generate conflict counterexamples
[534/1930] [FLEX][nocmodllexer] Building scanner with flex 2.6.4
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[536/1930] [BISON][modlunitparser] Building parser with bison 3.8.2
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[538/1930] [BISON][ocparser] Building parser with bison 3.8.2
../src/oc/parse.ypp: warning: 108 shift/reduce conflicts [-Wconflicts-sr]
../src/oc/parse.ypp: note: rerun with option '-Wcounterexamples' to generate conflict counterexamples
[539/1930] [BISON][nocmodlparser] Building parser with bison 3.8.2
../src/nmodl/parse1.ypp: warning: 3 shift/reduce conflicts [-Wconflicts-sr]
../src/nmodl/parse1.ypp: note: rerun with option '-Wcounterexamples' to generate conflict counterexamples
[540/1930] Building CXX object external/nmodl/src/printer/CMakeFiles/printer.dir/json_printer.cpp.o
[541/1930] Building CXX object src/nrniv/CMakeFiles/modlunit.dir/__/modlunit/declare.cpp.o
[542/1930] Building CXX object src/nrniv/CMakeFiles/modlunit.dir/__/modlunit/init.cpp.o
[543/1930] Building CXX object src/nrniv/CMakeFiles/modlunit.dir/__/modlunit/consist.cpp.o
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[545/1930] Building CXX object src/nrniv/CMakeFiles/modlunit.dir/__/modlunit/list.cpp.o
[546/1930] cd /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/src/nrnoc && /opt/homebrew/Cellar/cmake/3.28.1/bin/cmake -E env PROJECT_VERSION=9.0.0 bash /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/git2nrnversion_h.sh /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn > nrnversion.h.tmp && /opt/homebrew/Cellar/cmake/3.28.1/bin/cmake -E copy_if_different nrnversion.h.tmp nrnversion.h
fatal: No names found, cannot describe anything.
[547/1930] Building CXX object src/nrniv/CMakeFiles/modlunit.dir/__/modlunit/nrnunit.cpp.o
[548/1930] Building CXX object src/nrniv/CMakeFiles/modlunit.dir/__/modlunit/passn.cpp.o
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[551/1930] Building CXX object src/coreneuron/CMakeFiles/coreneuron-core.dir/apps/corenrn_parameters.cpp.o
[552/1930] Building CXX object src/nrniv/CMakeFiles/modlunit.dir/__/modlunit/version.cpp.o
[553/1930] Building CXX object src/nrniv/CMakeFiles/modlunit.dir/__/modlunit/units1.cpp.o
[554/1930] Building CXX object src/nrniv/CMakeFiles/modlunit.dir/modlunit_generated/lex.cpp.o
[555/1930] Building CXX object src/nrniv/CMakeFiles/modlunit.dir/__/modlunit/symbol.cpp.o
[556/1930] Building CXX object src/nrniv/CMakeFiles/modlunit.dir/modlunit_generated/parse1.cpp.o
[557/1930] Building CXX object external/nmodl/src/pybind/CMakeFiles/pyembed.dir/pyembed.cpp.o
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[560/1930] Linking CXX static library lib/libcoreneuron-core.a
[561/1930] Building CXX object external/nmodl/src/utils/CMakeFiles/util.dir/logger.cpp.o
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[563/1930] Building CXX object src/nrniv/CMakeFiles/nocmodl.dir/__/nmodl/discrete.cpp.o
[564/1930] Linking CXX static library lib/libutil.a
[565/1930] Building CXX object src/nrniv/CMakeFiles/nocmodl.dir/__/nmodl/deriv.cpp.o
[566/1930] -- NMODL : GENERATING VERBATIM LEXER WITH FLEX! --
[567/1930] -- NMODL : GENERATING NMODL LEXER WITH FLEX! --
../../../../../external/nmodl/src/lexer/nmodl.ll:503: warning, -s option given but default rule can be matched
[568/1930] -- NMODL : GENERATING DIFFERENTIAL EQUATION LEXER WITH FLEX! --
../../../../../external/nmodl/src/lexer/diffeq.ll:100: warning, -s option given but default rule can be matched
[569/1930] Building CXX object src/nrniv/CMakeFiles/nocmodl.dir/__/nmodl/list.cpp.o
[570/1930] -- NMODL : GENERATING C(11) LEXER WITH FLEX! --
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[572/1930] Building CXX object src/nrniv/CMakeFiles/nocmodl.dir/__/nmodl/kinetic.cpp.o
[573/1930] -- NMODL : GENERATING UNIT LEXER WITH FLEX! --
../../../../../external/nmodl/src/lexer/unit.ll:171: warning, -s option given but default rule can be matched
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[575/1930] Building CXX object src/nrniv/CMakeFiles/nocmodl.dir/__/nmodl/io.cpp.o
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[579/1930] Building CXX object src/nrniv/CMakeFiles/nocmodl.dir/__/nmodl/parsact.cpp.o
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[581/1930] Building CXX object src/nrniv/CMakeFiles/nocmodl.dir/__/nmodl/nocpout.cpp.o
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[602/1930] Building CXX object external/nmodl/src/codegen/CMakeFiles/codegen.dir/codegen_neuron_cpp_visitor.cpp.o
[603/1930] Building CXX object external/nmodl/src/lexer/CMakeFiles/lexer.dir/__/parser/diffeq/diffeq_parser.cpp.o
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[605/1930] Building CXX object external/nmodl/src/lexer/CMakeFiles/lexer.dir/__/parser/c/c11_parser.cpp.o
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[614/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/function_callpath_visitor.cpp.o
[615/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/global_var_visitor.cpp.o
[616/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/constant_folder_visitor.cpp.o
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[620/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/defuse_analyze_visitor.cpp.o
[621/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/index_remover.cpp.o
[622/1930] Building CXX object external/nmodl/src/lexer/CMakeFiles/lexer.dir/__/parser/nmodl/nmodl_parser.cpp.o
[623/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/local_var_rename_visitor.cpp.o
[624/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/localize_visitor.cpp.o
[625/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/loop_unroll_visitor.cpp.o
[626/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/perf_visitor.cpp.o
[627/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/neuron_solve_visitor.cpp.o
[628/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/inline_visitor.cpp.o
[629/1930] Building CXX object external/nmodl/src/CMakeFiles/nmodl.dir/main.cpp.o
[630/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/kinetic_block_visitor.cpp.o
[631/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/semantic_analysis_visitor.cpp.o
[632/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/rename_visitor.cpp.o
[633/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/solve_block_visitor.cpp.o
[634/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/var_usage_visitor.cpp.o
[635/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/units_visitor.cpp.o
[636/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/verbatim_visitor.cpp.o
[637/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/steadystate_visitor.cpp.o
[638/1930] Building CXX object external/nmodl/src/lexer/CMakeFiles/lexer.dir/__/ast/ast.cpp.o
[639/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/verbatim_var_rename_visitor.cpp.o
[640/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/ast_visitor.cpp.o
[641/1930] Linking CXX static library lib/liblexer.a
[642/1930] Linking CXX static library lib/libsymtab.a
[643/1930] Linking CXX static library lib/libpywrapper.a
[644/1930] Building CXX object src/nrniv/CMakeFiles/nocmodl.dir/__/nmodl/solve.cpp.o
[645/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/sympy_replace_solutions_visitor.cpp.o
[646/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/sympy_conductance_visitor.cpp.o
[647/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/checkparent_visitor.cpp.o
[648/1930] Building CXX object src/nrniv/CMakeFiles/nocmodl.dir/__/modlunit/units.cpp.o
[649/1930] Building CXX object src/nrniv/CMakeFiles/nocmodl.dir/__/nmodl/version.cpp.o
[650/1930] Building CXX object src/nrniv/CMakeFiles/nocmodl.dir/__/nmodl/symbol.cpp.o
[651/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/lookup_visitor.cpp.o
[652/1930] Generating ../../share/nrn/nrnmain.cpp
[653/1930] Generating ../../include/nrnmpiuse.h
[654/1930] Generating ../../include/nrncvode/nrnneosm.h
[655/1930] Generating ../oc/hocusr.h
[656/1930] cd /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/src/nrniv && true
[657/1930] Generating ../../include/nrnconf.h
[658/1930] Building CXX object src/nrnpython/CMakeFiles/rxdmath.dir/rxdmath.cpp.o
[659/1930] Linking CXX shared library lib/librxdmath.dylib
ld: warning: -undefined dynamic_lookup may not work with chained fixups
[660/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/json_visitor.cpp.o
[661/1930] Building CXX object src/nrniv/CMakeFiles/nocmodl.dir/nocmodl_generated/lex.cpp.o
[662/1930] Building CXX object src/nrniv/CMakeFiles/nocmodl.dir/nocmodl_generated/diffeq.cpp.o
[663/1930] Building CXX object src/nrniv/CMakeFiles/nocmodl.dir/nocmodl_generated/parse1.cpp.o
[664/1930] Linking CXX executable bin/nocmodl
[665/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/visitor_utils.cpp.o
[666/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/nmodl_visitor.cpp.o
[667/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/sympy_solver_visitor.cpp.o
[668/1930] Building CXX object src/nrnpython/CMakeFiles/nrnpython.dir/nrnpython.cpp.o
[669/1930] Building CXX object src/nrnpython/CMakeFiles/nrnpython.dir/rxd_marching_cubes.cpp.o
[670/1930] Building CXX object src/nrnpython/CMakeFiles/nrnpython.dir/nrnpy_p2h.cpp.o
[671/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/symtab_visitor.cpp.o
[672/1930] Building CXX object src/nrnpython/CMakeFiles/nrnpython.dir/rxd_llgramarea.cpp.o
[673/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/benchmark/catch_chronometer.cpp.o
[674/1930] Building CXX object src/nrnpython/CMakeFiles/nrnpython.dir/grids.cpp.o
[675/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/benchmark/detail/catch_benchmark_function.cpp.o
[676/1930] Linking CXX static library lib/libvisitor.a
[677/1930] Linking CXX static library lib/libcodegen.a
[678/1930] Building CXX object src/nrnpython/CMakeFiles/nrnpython.dir/rxd_intracellular.cpp.o
[679/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/benchmark/detail/catch_analyse.cpp.o
[680/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/generators/catch_generator_exception.cpp.o
[681/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/benchmark/detail/catch_run_for_at_least.cpp.o
[682/1930] Linking CXX executable bin/nmodl
[683/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/benchmark/detail/catch_stats.cpp.o
[684/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/generators/catch_generators.cpp.o
[685/1930] Building CXX object src/nrnpython/CMakeFiles/nrnpython.dir/rxd_vol.cpp.o
[686/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/generators/catch_generators_random.cpp.o
[687/1930] Building CXX object src/nrnpython/CMakeFiles/nrnpython.dir/nrnpy_nrn.cpp.o
[688/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_automake.cpp.o
[689/1930] Building CXX object src/nrnpython/CMakeFiles/nrnpython.dir/rxd_extracellular.cpp.o
[690/1930] Building CXX object src/nrnpython/CMakeFiles/nrnpython.dir/nrnpy_hoc.cpp.o
[691/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_common_base.cpp.o
[692/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_event_listener.cpp.o
[693/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_compact.cpp.o
[694/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_registrars.cpp.o
[695/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_cumulative_base.cpp.o
[696/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_console.cpp.o
[697/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_helpers.cpp.o
[698/1930] Building CXX object src/nrnpython/CMakeFiles/nrnpython.dir/rxd.cpp.o
[699/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_junit.cpp.o
[700/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_multi.cpp.o
[701/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_streaming_base.cpp.o
[702/1930] Generating ../nrnoc/exp2syn.cpp
Translating /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/exp2syn.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/exp2syn.cpp
Thread Safe
[703/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_json.cpp.o
[704/1930] Generating ../nrnoc/expsyn.cpp
Translating /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/expsyn.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/expsyn.cpp
Thread Safe
[705/1930] Generating ../nrnoc/apcount.cpp
Translating /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/apcount.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/apcount.cpp
Thread Safe
[706/1930] Generating ../nrnoc/feature.cpp
Translating /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/feature.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/feature.cpp
Notice: VERBATIM blocks are not thread safe
[707/1930] Generating ../nrnoc/hh.cpp
Translating /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/hh.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/hh.cpp
Thread Safe
[708/1930] Generating ../nrnoc/intfire1.cpp
Translating /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/intfire1.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/intfire1.cpp
Thread Safe
[709/1930] Generating ../nrnoc/intfire2.cpp
Translating /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/intfire2.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/intfire2.cpp
Thread Safe
[710/1930] Generating ../nrnoc/intfire4.cpp
Translating /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/intfire4.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/intfire4.cpp
Thread Safe
[711/1930] Generating ../nrnoc/netstim.cpp
Translating /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/netstim.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/netstim.cpp
Thread Safe
[712/1930] Generating ../nrnoc/oclmp.cpp
Translating /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/oclmp.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/oclmp.cpp
Thread Safe
[713/1930] Generating ../nrnoc/passive.cpp
Translating /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/passive.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/passive.cpp
Thread Safe
[714/1930] Generating ../nrnoc/ppmark.cpp
Translating /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/ppmark.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/ppmark.cpp
Thread Safe
[715/1930] Generating ../nrnoc/pattern.cpp
Translating /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/pattern.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/pattern.cpp
Thread Safe
Notice: ARTIFICIAL_CELL is a synonym for POINT_PROCESS which hints that it
only affects and is affected by discrete events. As such it is not
located in a section and is not associated with an integrator
[716/1930] Generating ../nrnoc/stim.cpp
Translating /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/stim.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/stim.cpp
Thread Safe
[717/1930] Generating ../nrnoc/syn.cpp
Translating /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/syn.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/syn.cpp
Thread Safe
[718/1930] Generating ../nrnoc/svclmp.cpp
Translating /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/svclmp.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/svclmp.cpp
Thread Safe
[719/1930] Generating ../nrnoc/vclmp.cpp
Translating /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/vclmp.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/nrnoc/vclmp.cpp
Notice: VERBATIM blocks are not thread safe
Notice: LINEAR is not thread safe.
[720/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_sonarqube.cpp.o
[721/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_tap.cpp.o
[722/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_teamcity.cpp.o
[723/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_xml.cpp.o
[724/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/apwindow.cpp.o
[725/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/interfaces/catch_interfaces_capture.cpp.o
[726/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/axis.cpp.o
[727/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/interfaces/catch_interfaces_config.cpp.o
[728/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/bndedval.cpp.o
[729/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/interfaces/catch_interfaces_generatortracker.cpp.o
[730/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/interfaces/catch_interfaces_exception.cpp.o
[731/1930] Running nrnivmodl-core with internal mod files
WARNING: No mod files found in '/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/bin', compiling default ones only!
[INFO] Running: make -j4 -f /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/coreneuron/nrnivmodl_core_makefile ROOT=/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build MECHLIB_SUFFIX=internal NMODL_BINARY=/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/bin/nmodl MODS_PATH=arm64/corenrn/mod2c BUILD_TYPE=SHARED NRN_PRCELLSTATE=0
Default NMODL flags:
diff: arm64/corenrn/mod2c/_mod_func.cpp: No such file or directory
[NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shadows <extern_neuron_var> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shadows <extern_neuron_var> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shadows <extern_neuron_var> definition in NMODL_GLOBAL
[NMODL] [warning] :: CVode solver of icur in 64.20-30 replaced with cnexp solver
ld: warning: -undefined dynamic_lookup may not work with chained fixups
=> Binary creating arm64/special-core
[INFO] MOD files built successfully for CoreNEURON
[732/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/cbwidget.cpp.o
[733/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/epsprint.cpp.o
[734/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/gifimage.cpp.o
[735/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/checkpnt.cpp.o
[736/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/graphvec.cpp.o
[737/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/grmanip.cpp.o
[738/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/graph.cpp.o
[739/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/fourier.cpp.o
[740/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/grglyph.cpp.o
[741/1930] Building CXX object test/coreneuron/unit/cmdline_interface/CMakeFiles/cmd_interface_test_bin.dir/test_cmdline_interface.cpp.o
[742/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/hocmark.cpp.o
[743/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/idraw.cpp.o
[744/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/htlist.cpp.o
[745/1930] Building CXX object test/coreneuron/unit/random/CMakeFiles/random_test_bin.dir/test_random.cpp.o
[746/1930] Building CXX object test/coreneuron/unit/interleave_info/CMakeFiles/interleave_info_bin.dir/check_constructors.cpp.o
[747/1930] Building CXX object test/coreneuron/unit/alignment/CMakeFiles/alignment_test_bin.dir/alignment.cpp.o
[748/1930] Building CXX object test/coreneuron/unit/queueing/CMakeFiles/queuing_test_bin.dir/test_queueing.cpp.o
[749/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/mlinedit.cpp.o
[750/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/ivocmain.cpp.o
[751/1930] Building CXX object test/coreneuron/unit/lfp/CMakeFiles/lfp_test_bin.dir/lfp.cpp.o
[752/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/mymath.cpp.o
/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/ivoc/mymath.cpp:2:14: warning: '#pragma FENV_ACCESS' is not supported on this target - ignored [-Wignored-pragmas]
#pragma STDC FENV_ACCESS ON
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[1155/1930] Generating nrniv_pydef_python_check_sys_base_prefix/dump_sys_attr.py
[1156/1930] Building CXX object test/api/CMakeFiles/netcon_cpp.dir/netcon.cpp.o
[1157/1930] Generating nrniv_pydef_nrnpython_check_sys_base_prefix/check_sys_attr.hoc
[1158/1930] Generating nrniv_pydef_python_check_sys_base_exec_prefix/check_sys_attr.py
[1159/1930] Generating nrniv_pydef_nrnpython_check_sys_base_prefix/dump_sys_attr.py
[1160/1930] Generating nrniv_pydef_python_check_sys_base_exec_prefix/dump_sys_attr.py
[1161/1930] Generating nrniv_pydef_python_check_sys_stderr.encoding/check_sys_attr.py
[1162/1930] Generating nrniv_pydef_nrnpython_check_sys_base_exec_prefix/check_sys_attr.hoc
[1163/1930] Generating nrniv_pydef_nrnpython_check_sys_base_exec_prefix/dump_sys_attr.py
[1164/1930] Building CXX object test/api/CMakeFiles/hh_sim_cpp.dir/hh_sim.cpp.o
[1165/1930] Generating nrniv_pydef_nrnpython_check_sys_stderr.encoding/dump_sys_attr.py
[1166/1930] Generating nrniv_pydef_python_check_sys_stderr.encoding/dump_sys_attr.py
[1167/1930] Generating nrniv_pydef_nrnpython_check_sys_stderr.encoding/check_sys_attr.hoc
[1168/1930] Generating nrniv_pydef_python_check_sys_stdin.encoding/check_sys_attr.py
[1169/1930] Generating nrniv_pydef_nrnpython_check_sys_stdin.encoding/check_sys_attr.hoc
[1170/1930] Generating nrniv_pydef_python_check_sys_stdin.encoding/dump_sys_attr.py
[1171/1930] Generating nrniv_pydef_nrnpython_check_sys_stdin.encoding/dump_sys_attr.py
[1172/1930] Generating nrniv_pydef_python_check_sys_stdout.encoding/check_sys_attr.py
[1173/1930] Generating nrniv_pydef_python_check_sys_stdout.encoding/dump_sys_attr.py
[1174/1930] Generating nrniv_pydef_nrnpython_check_sys_stdout.encoding/check_sys_attr.hoc
[1175/1930] Generating nrniv_pydef_nrnpython_check_sys_stdout.encoding/dump_sys_attr.py
[1176/1930] Generating ../../compare_test_results.py
[1177/1930] Generating ../tests/ringtest/reference_data/spk1.100ms.std.ref
[1178/1930] Generating ../tests/testcorenrn/reference/out_bbcore.spk
[1179/1930] Building CXX object test/api/CMakeFiles/vclamp_cpp.dir/vclamp.cpp.o
[1180/1930] Generating ../tests/testcorenrn/reference/out_conc.spk
[1181/1930] Generating ../tests/testcorenrn/reference/out_deriv.spk
[1182/1930] Generating ../tests/testcorenrn/reference/out_gf.spk
[1183/1930] Generating ../tests/testcorenrn/reference/out_kin.spk
[1184/1930] Generating ../tests/testcorenrn/reference/out_vecplay.spk
[1185/1930] Generating ../tests/testcorenrn/reference/out_patstim.spk
[1186/1930] Generating ../tests/testcorenrn/reference/out_netstimdirect.spk
[1187/1930] Generating ../tests/testcorenrn/reference/out_vecevent.spk
[1188/1930] Generating ../tests/testcorenrn/reference/out_watch.spk
[1189/1930] Building CXX object test/CMakeFiles/testneuron.dir/unit_tests/container/mechanism.cpp.o
[1190/1930] Building CXX object test/CMakeFiles/nrn-benchmarks.dir/benchmarks/threads/test_multicore.cpp.o
[1191/1930] Building CXX object test/CMakeFiles/testneuron.dir/unit_tests/container/container.cpp.o
[1192/1930] Building CXX object test/CMakeFiles/testneuron.dir/unit_tests/container/node.cpp.o
[1193/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/ocmatrix.cpp.o
[1194/1930] Linking CXX shared library lib/libnrniv.dylib
ld: warning: -undefined dynamic_lookup may not work with chained fixups
[1195/1930] Generating inithoc.cpp
[1196/1930] Generating nrnivmodl/c448d279dd3b91940d228c42e4a7c280bafe100b4e840f9c938be979cceb8fe0/gap.mod
[1197/1930] Generating nrnivmodl/c448d279dd3b91940d228c42e4a7c280bafe100b4e840f9c938be979cceb8fe0/unitstest.mod
[1198/1930] Generating nrnivmodl/c448d279dd3b91940d228c42e4a7c280bafe100b4e840f9c938be979cceb8fe0/follower.mod
[1199/1930] Generating nrnivmodl/c448d279dd3b91940d228c42e4a7c280bafe100b4e840f9c938be979cceb8fe0/name_clashes.mod
[1200/1930] Generating nrnivmodl/8b70050800897334ac3dcf9bccbec23ce253950bb3247c96e6ab2f9c53f6288c/mcna.mod
[1201/1930] Generating nrnivmodl/c448d279dd3b91940d228c42e4a7c280bafe100b4e840f9c938be979cceb8fe0/version_macros.mod
[1202/1930] Generating nrnivmodl/7378b0d1010df9fb9d314452ba3c6ac85ab5bcd507940792ff794d6831e1b453/opaque_token.mod
[1203/1930] Generating nrnivmodl/7378b0d1010df9fb9d314452ba3c6ac85ab5bcd507940792ff794d6831e1b453/ptr.mod
[1204/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/argpass.mod
[1205/1930] Generating nrnivmodl/fb5fb42ddab2ff650e8e4e789eb94701174e41ce7edaa51ad58d4fd93f798b51/ppxsrc.mod
[1206/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/cabpump.mod
[1207/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/cachan.mod
[1208/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/cacum.mod
[1209/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/cacur.mod
[1210/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/cadif.mod
[1211/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/cadifusl.mod
[1212/1930] Linking CXX executable bin/nrniv
[1213/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/cagk.mod
[1214/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/cagkftab.mod
[1215/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/capmp.mod
[1216/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/expsynspine.mod
[1217/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/fh.mod
[1218/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/fit1.mod
[1219/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/gap.mod
[1220/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/hh1.mod
[1221/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/hhvect.mod
[1222/1930] Linking CXX executable bin/test/nrn-benchmarks
[1223/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/inatest.mod
[1224/1930] Linking CXX executable bin/test/testneuron
[1225/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/ionleak.mod
[1226/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/nacum.mod
[1227/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/nacur.mod
[1228/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/nadifl.mod
[1229/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/nonlin.mod
[1230/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/order.mod
[1231/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/obj_ex.mod
[1232/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/passiv.mod
[1233/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/standard.inc
[1234/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/rchan.mod
[1235/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/stim1.mod
[1236/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/str.mod
[1237/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/synpre.mod
[1238/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/syn1.mod
[1239/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/trivial.mod
[1240/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/tstdarray.mod
[1241/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/tstextrn.mod
[1242/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/tstpnt1.mod
[1243/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/tstpnt2.mod
[1244/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/tstvec.mod
[1245/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/vclmp1.mod
[1246/1930] Generating nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/vlag.mod
[1247/1930] Generating nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad/atest.mod
[1248/1930] Generating nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad/rand.mod
[1249/1930] Generating nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad/rand_art.mod
[1250/1930] Generating nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad/rand_pp.mod
[1251/1930] Generating nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad/sdata.inc
[1252/1930] Generating nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad/sdata.mod
[1253/1930] Generating nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad/sdata_pp.mod
[1254/1930] Generating nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad/sdata_ppts.mod
[1255/1930] Generating nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad/sdata_ts.mod
[1256/1930] Generating nrnivmodl/5b499c48b620b3f996279dafe88ff900a32797c8807f2acc88ebe24f2d04a100/gap.mod
[1257/1930] Generating nrnivmodl/5b499c48b620b3f996279dafe88ff900a32797c8807f2acc88ebe24f2d04a100/follower.mod
[1258/1930] Generating nrnivmodl/5b499c48b620b3f996279dafe88ff900a32797c8807f2acc88ebe24f2d04a100/name_clashes.mod
[1259/1930] Generating nrnivmodl/5b499c48b620b3f996279dafe88ff900a32797c8807f2acc88ebe24f2d04a100/unitstest.mod
[1260/1930] Generating nrnivmodl/5b499c48b620b3f996279dafe88ff900a32797c8807f2acc88ebe24f2d04a100/version_macros.mod
[1261/1930] Generating nrnivmodl/ae2c9b73c9a624bce358af1b0042b70ba7c70ce86d0fb0bf97de8ac420156de5/cadif.mod
[1262/1930] Generating nrnivmodl/ae2c9b73c9a624bce358af1b0042b70ba7c70ce86d0fb0bf97de8ac420156de5/disc.mod
[1263/1930] Generating nrnivmodl/ae2c9b73c9a624bce358af1b0042b70ba7c70ce86d0fb0bf97de8ac420156de5/fornetcon.mod
[1264/1930] Generating nrnivmodl/ae2c9b73c9a624bce358af1b0042b70ba7c70ce86d0fb0bf97de8ac420156de5/hhwatch.mod
[1265/1930] Generating nrnivmodl/ae2c9b73c9a624bce358af1b0042b70ba7c70ce86d0fb0bf97de8ac420156de5/k3st.mod
[1266/1930] Generating nrnivmodl/ae2c9b73c9a624bce358af1b0042b70ba7c70ce86d0fb0bf97de8ac420156de5/table.mod
[1267/1930] Generating nrnivmodl/ae2c9b73c9a624bce358af1b0042b70ba7c70ce86d0fb0bf97de8ac420156de5/variabletypes.mod
[1268/1930] Running utility command for hoc_module
INFO:root:setup.py called with:setup.py build --cmake-build-dir /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build --disable-rx3d --without-nrnpython --build-lib=/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python build_ext --define=NRN_ASAN_ENABLED,USE_PYTHON,NRN_ENABLE_THREADS,CORENRN_BUILD=0
INFO:root:Setting SDKROOT=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk
WARNING:root:You are building a wheel with a Python built for macOS >=12.0.0. Your wheel won't run on older versions, consider using an official Python build from python.org
WARNING:root:Setting MACOSX_DEPLOYMENT_TARGET=12.0
INFO:root:Extension common compile flags defaultdict(<class 'list'>, {'library_dirs': ['/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib'], 'libraries': ['nrniv'], 'language': 'c++'})
INFO:root:RX3D is DISABLED
/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/venv/lib/python3.10/site-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!
********************************************************************************
Requirements should be satisfied by a PEP 517 installer.
If you are using pip, you can try `pip install --use-pep517`.
********************************************************************************
!!
dist.fetch_build_eggs(dist.setup_requires)
WARNING setuptools_scm.pyproject_reading toml section missing 'pyproject.toml does not contain a tool.setuptools_scm section'
Traceback (most recent call last):
File "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/venv/lib/python3.10/site-packages/setuptools_scm/_integration/pyproject_reading.py", line 36, in read_pyproject
section = defn.get("tool", {})[tool_name]
KeyError: 'setuptools_scm'
/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/venv/lib/python3.10/site-packages/setuptools_scm/git.py:167: UserWarning: "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn" is shallow and may cause errors
warnings.warn(f'"{wd.path}" is shallow and may cause errors')
INFO:root:running build
INFO:root:running build_py
INFO:root:copying share/lib/python/neuron/hclass3.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron
INFO:root:copying share/lib/python/neuron/expect_hocerr.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron
INFO:root:copying share/lib/python/neuron/psection.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron
INFO:root:copying share/lib/python/neuron/config.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron
INFO:root:copying share/lib/python/neuron/units.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron
INFO:root:copying share/lib/python/neuron/sections.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron
INFO:root:copying share/lib/python/neuron/__init__.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron
INFO:root:copying share/lib/python/neuron/coreneuron.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron
INFO:root:copying share/lib/python/neuron/doc.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron
INFO:root:copying share/lib/python/neuron/gui.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron
INFO:root:copying share/lib/python/neuron/nonvint_block_supervisor.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron
INFO:root:creating /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/neuroml
INFO:root:copying share/lib/python/neuron/neuroml/metadata.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/neuroml
INFO:root:copying share/lib/python/neuron/neuroml/morphml.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/neuroml
INFO:root:copying share/lib/python/neuron/neuroml/xml2nrn.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/neuroml
INFO:root:copying share/lib/python/neuron/neuroml/__init__.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/neuroml
INFO:root:copying share/lib/python/neuron/neuroml/neuroml.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/neuroml
INFO:root:copying share/lib/python/neuron/neuroml/rdxml.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/neuroml
INFO:root:copying share/lib/python/neuron/neuroml/biophysics.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/neuroml
INFO:root:creating /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/tests
INFO:root:copying share/lib/python/neuron/tests/_subclass.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/tests
INFO:root:copying share/lib/python/neuron/tests/test_all.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/tests
INFO:root:copying share/lib/python/neuron/tests/__init__.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/tests
INFO:root:copying share/lib/python/neuron/tests/test_neuron.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/tests
INFO:root:copying share/lib/python/neuron/tests/test_vector.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/tests
INFO:root:copying share/lib/python/neuron/tests/test_rxd.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/tests
INFO:root:creating /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/tests/utils
INFO:root:copying share/lib/python/neuron/tests/utils/coreneuron_available.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/tests/utils
INFO:root:copying share/lib/python/neuron/tests/utils/__init__.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/tests/utils
INFO:root:copying share/lib/python/neuron/tests/utils/strtobool.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/tests/utils
INFO:root:copying share/lib/python/neuron/tests/utils/capture_stdout.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/tests/utils
INFO:root:copying share/lib/python/neuron/tests/utils/checkresult.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/tests/utils
INFO:root:creating /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/rxdException.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/options.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/plugins.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/rxdsection.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/species.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/rxdmath.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/rate.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/region.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/multiCompartmentReaction.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/constants.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/dimension3.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/__init__.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/section1d.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/export.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/initializer.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/rangevar.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/geometry.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/rxd.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/generalizedReaction.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/nodelist.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/node.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/gui.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/reaction.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:creating /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/crxd
INFO:root:copying share/lib/python/neuron/crxd/__init__.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/crxd
INFO:root:creating /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/gui2
INFO:root:copying share/lib/python/neuron/gui2/setup_threejs.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/gui2
INFO:root:copying share/lib/python/neuron/gui2/config.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/gui2
INFO:root:copying share/lib/python/neuron/gui2/__init__.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/gui2
INFO:root:copying share/lib/python/neuron/gui2/rangevar.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/gui2
INFO:root:copying share/lib/python/neuron/gui2/plotshape.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/gui2
INFO:root:copying share/lib/python/neuron/gui2/utilities.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/gui2
INFO:root:running build_ext
INFO:root:==> Building Python extensions
INFO:root:building 'neuron.hoc' extension
INFO:root:/usr/bin/gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -fno-omit-frame-pointer -shared-libsan -fsanitize=address -fsanitize-address-use-after-scope -DNRN_ASAN_ENABLED=1 -DUSE_PYTHON=1 -DNRN_ENABLE_THREADS=1 -DCORENRN_BUILD=0=1 -Isrc -Isrc/oc -Isrc/nrnpython -Isrc/nrnmpi -I/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/src -I/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/src/oc -I/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/src/nrnpython -I/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/src/nrnmpi -I/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/venv/include -I/opt/homebrew/opt/python@3.10/Frameworks/Python.framework/Versions/3.10/include/python3.10 -c src/nrnpython/inithoc.cpp -o /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/src/nrnpython/inithoc.o -fno-omit-frame-pointer -shared-libsan -fsanitize=address -fsanitize-address-use-after-scope -std=c++17
INFO:root:/usr/bin/g++ -bundle -undefined dynamic_lookup -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -fno-omit-frame-pointer -shared-libsan -fsanitize=address -fsanitize-address-use-after-scope -Wl,-rpath,/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/14.0.0/lib/darwin -fno-omit-frame-pointer -shared-libsan -fsanitize=address -fsanitize-address-use-after-scope /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/src/nrnpython/inithoc.o -L/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib -lnrniv -o /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/hoc.cpython-310-darwin.so -fno-omit-frame-pointer -shared-libsan -fsanitize=address -fsanitize-address-use-after-scope -Wl,-rpath,/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/14.0.0/lib/darwin -Wl,-rpath,@loader_path/../../
ld: warning: -undefined dynamic_lookup may not work with chained fixups
INFO:root:running build_scripts
INFO:root:creating build/scripts-3.10
INFO:root:copying and adjusting share/lib/python/scripts/nrniv -> build/scripts-3.10
INFO:root:copying and adjusting share/lib/python/scripts/nrngui -> build/scripts-3.10
INFO:root:copying and adjusting share/lib/python/scripts/nmodl -> build/scripts-3.10
INFO:root:copying and adjusting share/lib/python/scripts/nrniv-core -> build/scripts-3.10
INFO:root:copying and adjusting share/lib/python/scripts/nrnpyenv.sh -> build/scripts-3.10
INFO:root:copying and adjusting share/lib/python/scripts/nrnivmodl-core -> build/scripts-3.10
INFO:root:copying and adjusting share/lib/python/scripts/neurondemo -> build/scripts-3.10
INFO:root:copying and adjusting share/lib/python/scripts/nrnivmodl -> build/scripts-3.10
INFO:root:copying and adjusting share/lib/python/scripts/modlunit -> build/scripts-3.10
INFO:root:copying and adjusting share/lib/python/scripts/idraw -> build/scripts-3.10
INFO:root:copying and adjusting share/lib/python/scripts/sortspike -> build/scripts-3.10
INFO:root:copying and adjusting share/lib/python/scripts/mkthreadsafe -> build/scripts-3.10
INFO:root:changing mode of build/scripts-3.10/nrniv from 644 to 755
INFO:root:changing mode of build/scripts-3.10/nrngui from 644 to 755
INFO:root:changing mode of build/scripts-3.10/nmodl from 644 to 755
INFO:root:changing mode of build/scripts-3.10/nrniv-core from 644 to 755
INFO:root:changing mode of build/scripts-3.10/nrnpyenv.sh from 644 to 755
INFO:root:changing mode of build/scripts-3.10/nrnivmodl-core from 644 to 755
INFO:root:changing mode of build/scripts-3.10/neurondemo from 644 to 755
INFO:root:changing mode of build/scripts-3.10/nrnivmodl from 644 to 755
INFO:root:changing mode of build/scripts-3.10/modlunit from 644 to 755
INFO:root:changing mode of build/scripts-3.10/idraw from 644 to 755
INFO:root:changing mode of build/scripts-3.10/sortspike from 644 to 755
INFO:root:changing mode of build/scripts-3.10/mkthreadsafe from 644 to 755
[1269/1930] Generating nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/axial.inc
[1270/1930] Generating nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/axial.mod
[1271/1930] Generating nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/axial_pp.mod
[1272/1930] Generating nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/bacur.mod
[1273/1930] Generating nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/banocur.mod
[1274/1930] Generating nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/fornetcon.mod
[1275/1930] Generating nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/green.mod
[1276/1930] Generating nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/invlfire.mod
[1277/1930] Generating nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/natrans.mod
[1278/1930] Generating nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/netmove.mod
[1279/1930] Generating nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/noisychan.mod
[1280/1930] Generating nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/red.mod
[1281/1930] Generating nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/sample.mod
[1282/1930] Generating nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/unitstest.mod
[1283/1930] Generating nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/version_macros.mod
[1284/1930] Generating nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/watchrange.mod
[1285/1930] Generating nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/watchrange2.mod
[1286/1930] Building special[-core] for test group datahandle
/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/7378b0d1010df9fb9d314452ba3c6ac85ab5bcd507940792ff794d6831e1b453
cfiles =
Mod files: "./opaque_token.mod" "./ptr.mod"
MODOBJS= ./opaque_token.o ./ptr.o
-> NMODL .././opaque_token.mod
-> Compiling mod_func.cpp
-> NMODL .././ptr.mod
Translating ptr.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/7378b0d1010df9fb9d314452ba3c6ac85ab5bcd507940792ff794d6831e1b453/arm64/ptr.cpp
Notice: Use of POINTER is not thread safe.
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/7378b0d1010df9fb9d314452ba3c6ac85ab5bcd507940792ff794d6831e1b453/arm64/ptr.cpp
Translating opaque_token.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/7378b0d1010df9fb9d314452ba3c6ac85ab5bcd507940792ff794d6831e1b453/arm64/opaque_token.cpp
Notice: VERBATIM blocks are not thread safe
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/7378b0d1010df9fb9d314452ba3c6ac85ab5bcd507940792ff794d6831e1b453/arm64/opaque_token.cpp
=> LINKING shared library "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/7378b0d1010df9fb9d314452ba3c6ac85ab5bcd507940792ff794d6831e1b453/arm64/./libnrnmech.dylib"
ld: warning: -undefined dynamic_lookup may not work with chained fixups
=> LINKING executable "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/7378b0d1010df9fb9d314452ba3c6ac85ab5bcd507940792ff794d6831e1b453/arm64/./special" LDFLAGS are:
Successfully created arm64/special
[1287/1930] Generating datahandle/datahandle_tests/test/datahandle/test_1.py
[1288/1930] Generating datahandle/datahandle_tests/test/datahandle/test_token.py
[1289/1930] Linking CXX executable bin/test/hh_sim_cpp
[1290/1930] Linking CXX executable bin/test/netcon_cpp
[1291/1930] Linking CXX executable bin/test/sections_c
[1292/1930] Linking CXX executable bin/test/vclamp_cpp
[1293/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/Aradi_Ca.mod
[1294/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/Aradi_CadepK.mod
[1295/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/Aradi_KA.mod
[1296/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/Aradi_KDRf.mod
[1297/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/Aradi_KDRs.mod
[1298/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/Aradi_Na.mod
[1299/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/CaBK.mod
[1300/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/DGC_M.mod
[1301/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/DGC_UK.mod
[1302/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/DGC_sAHP.mod
[1303/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/Gfluct3.mod
[1304/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/LcaMig.mod
[1305/1930] Building special[-core] for test group coverage_tests
/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/fb5fb42ddab2ff650e8e4e789eb94701174e41ce7edaa51ad58d4fd93f798b51
cfiles =
Mod files: "./ppxsrc.mod"
MODOBJS= ./ppxsrc.o
-> Compiling mod_func.cpp
-> NMODL .././ppxsrc.mod
Translating ppxsrc.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/fb5fb42ddab2ff650e8e4e789eb94701174e41ce7edaa51ad58d4fd93f798b51/arm64/ppxsrc.cpp
Thread Safe
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/fb5fb42ddab2ff650e8e4e789eb94701174e41ce7edaa51ad58d4fd93f798b51/arm64/ppxsrc.cpp
=> LINKING shared library "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/fb5fb42ddab2ff650e8e4e789eb94701174e41ce7edaa51ad58d4fd93f798b51/arm64/./libnrnmech.dylib"
ld: warning: -undefined dynamic_lookup may not work with chained fixups
=> LINKING executable "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/fb5fb42ddab2ff650e8e4e789eb94701174e41ce7edaa51ad58d4fd93f798b51/arm64/./special" LDFLAGS are:
Successfully created arm64/special
[1306/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/SH_KIn.mod
[1307/1930] Generating coverage_tests/cover_tests/test/cover/test_netcvode.py
[1308/1930] Generating coverage_tests/cover_tests/test/cover/test_netcvode.json
[1309/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/SH_na8st.mod
[1310/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/bgka.mod
[1311/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/ccanl.mod
[1312/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/ggap.mod
[1313/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/gskch.mod
[1314/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/holdingi.mod
[1315/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/hyperde3.mod
[1316/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/ichan2.mod
[1317/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/iconc_Ca.mod
[1318/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/kcaPR.mod
[1319/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/na3n.mod
[1320/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/nca.mod
[1321/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/spines.mod
[1322/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/tca.mod
[1323/1930] Generating ../../nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/vecevent.mod
[1324/1930] Generating ../../nrnivmodl/a9c54b18e4b54351cb4fd3e79067cafa02da4514b4383a54de8ff121657615ff/halfgap.mod
[1325/1930] Building special[-core] for test group pytest
/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/8b70050800897334ac3dcf9bccbec23ce253950bb3247c96e6ab2f9c53f6288c
cfiles =
Mod files: "./mcna.mod"
MODOBJS= ./mcna.o
-> NMODL .././mcna.mod
-> Compiling mod_func.cpp
Translating mcna.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/8b70050800897334ac3dcf9bccbec23ce253950bb3247c96e6ab2f9c53f6288c/arm64/mcna.cpp
Thread Safe
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/8b70050800897334ac3dcf9bccbec23ce253950bb3247c96e6ab2f9c53f6288c/arm64/mcna.cpp
=> LINKING shared library "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/8b70050800897334ac3dcf9bccbec23ce253950bb3247c96e6ab2f9c53f6288c/arm64/./libnrnmech.dylib"
ld: warning: -undefined dynamic_lookup may not work with chained fixups
=> LINKING executable "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/8b70050800897334ac3dcf9bccbec23ce253950bb3247c96e6ab2f9c53f6288c/arm64/./special" LDFLAGS are:
Successfully created arm64/special
[1326/1930] Generating pytest/basic_tests_py3.10/test/pytest/test_nrntest_thread.json
[1327/1930] Generating pytest/basic_tests_py3.10/test/pytest/test_nrntest_thread.py
[1328/1930] Generating ../../nrnivmodl/bbd7c82eee28b931214a8172bb776ba66c406a6620c807381c850fedcdd74295/halfgap.mod
[1329/1930] Building special[-core] for test group parallel
/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/5b499c48b620b3f996279dafe88ff900a32797c8807f2acc88ebe24f2d04a100
cfiles =
Mod files: "./follower.mod" "./gap.mod" "./name_clashes.mod" "./unitstest.mod" "./version_macros.mod"
MODOBJS= ./follower.o ./gap.o ./name_clashes.o ./unitstest.o ./version_macros.o
-> Compiling mod_func.cpp
-> NMODL .././follower.mod
-> NMODL .././gap.mod
-> NMODL .././name_clashes.mod
Translating name_clashes.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/5b499c48b620b3f996279dafe88ff900a32797c8807f2acc88ebe24f2d04a100/arm64/name_clashes.cpp
Thread Safe
-> NMODL .././unitstest.mod
Translating gap.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/5b499c48b620b3f996279dafe88ff900a32797c8807f2acc88ebe24f2d04a100/arm64/gap.cpp
Thread Safe
-> NMODL .././version_macros.mod
Translating follower.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/5b499c48b620b3f996279dafe88ff900a32797c8807f2acc88ebe24f2d04a100/arm64/follower.cpp
Thread Safe
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/5b499c48b620b3f996279dafe88ff900a32797c8807f2acc88ebe24f2d04a100/arm64/follower.cpp
Translating version_macros.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/5b499c48b620b3f996279dafe88ff900a32797c8807f2acc88ebe24f2d04a100/arm64/version_macros.cpp
Thread Safe
Translating unitstest.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/5b499c48b620b3f996279dafe88ff900a32797c8807f2acc88ebe24f2d04a100/arm64/unitstest.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/5b499c48b620b3f996279dafe88ff900a32797c8807f2acc88ebe24f2d04a100/arm64/gap.cpp
Thread Safe
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/5b499c48b620b3f996279dafe88ff900a32797c8807f2acc88ebe24f2d04a100/arm64/name_clashes.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/5b499c48b620b3f996279dafe88ff900a32797c8807f2acc88ebe24f2d04a100/arm64/unitstest.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/5b499c48b620b3f996279dafe88ff900a32797c8807f2acc88ebe24f2d04a100/arm64/version_macros.cpp
=> LINKING shared library "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/5b499c48b620b3f996279dafe88ff900a32797c8807f2acc88ebe24f2d04a100/arm64/./libnrnmech.dylib"
ld: warning: -undefined dynamic_lookup may not work with chained fixups
=> LINKING executable "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/5b499c48b620b3f996279dafe88ff900a32797c8807f2acc88ebe24f2d04a100/arm64/./special" LDFLAGS are:
Successfully created arm64/special
[1330/1930] Generating parallel/subworld/test/parallel_tests/test_subworld.py
[1331/1930] Generating parallel/partrans/test/pytest_coreneuron/test_partrans.py
[1332/1930] Generating parallel/netpar/test/pytest_coreneuron/test_hoc_po.py
[1333/1930] Generating parallel/netpar/test/pytest_coreneuron/test_netpar.py
[1334/1930] Generating parallel/bas/test/parallel_tests/test_bas.py
[1335/1930] Generating parallel/nrntest_fast/test/pytest_coreneuron/run_pytest.py
[1336/1930] Generating parallel/nrntest_fast/test/pytest_coreneuron/test_nrntest_fast.json
[1337/1930] Generating parallel/nrntest_fast/test/pytest_coreneuron/test_nrntest_fast.py
[1338/1930] Generating ../../nrnivmodl/b62f97c7d3f6d905c774d64e10128b3300792f8f757b926b965c058a4d6ee876/Gfluct3.mod
[1339/1930] Generating ../../nrnivmodl/b62f97c7d3f6d905c774d64e10128b3300792f8f757b926b965c058a4d6ee876/hhderiv.mod
[1340/1930] Generating ../../nrnivmodl/b62f97c7d3f6d905c774d64e10128b3300792f8f757b926b965c058a4d6ee876/hhkin.mod
[1341/1930] Generating ../../nrnivmodl/b62f97c7d3f6d905c774d64e10128b3300792f8f757b926b965c058a4d6ee876/hhwatch.mod
[1342/1930] Generating ../../nrnivmodl/b62f97c7d3f6d905c774d64e10128b3300792f8f757b926b965c058a4d6ee876/nacum.mod
[1343/1930] Generating ../../nrnivmodl/b62f97c7d3f6d905c774d64e10128b3300792f8f757b926b965c058a4d6ee876/vecevent.mod
[1344/1930] Building special[-core] for test group nmodl_tests
/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/ae2c9b73c9a624bce358af1b0042b70ba7c70ce86d0fb0bf97de8ac420156de5
cfiles =
Mod files: "./cadif.mod" "./disc.mod" "./fornetcon.mod" "./hhwatch.mod" "./k3st.mod" "./table.mod" "./variabletypes.mod"
MODOBJS= ./cadif.o ./disc.o ./fornetcon.o ./hhwatch.o ./k3st.o ./table.o ./variabletypes.o
-> Compiling mod_func.cpp
-> NMODL .././cadif.mod
-> NMODL .././disc.mod
-> NMODL .././fornetcon.mod
Translating disc.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/ae2c9b73c9a624bce358af1b0042b70ba7c70ce86d0fb0bf97de8ac420156de5/arm64/disc.cpp
Notice: DISCRETE is not thread safe.
Notice: This mechanism cannot be used with CVODE
-> NMODL .././hhwatch.mod
Translating cadif.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/ae2c9b73c9a624bce358af1b0042b70ba7c70ce86d0fb0bf97de8ac420156de5/arm64/cadif.cpp
Thread Safe
Translating fornetcon.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/ae2c9b73c9a624bce358af1b0042b70ba7c70ce86d0fb0bf97de8ac420156de5/arm64/fornetcon.cpp
-> NMODL .././k3st.mod
Thread Safe
-> NMODL .././table.mod
Translating k3st.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/ae2c9b73c9a624bce358af1b0042b70ba7c70ce86d0fb0bf97de8ac420156de5/arm64/k3st.cpp
NEURON's CVode method ignores conservation
Thread Safe
-> NMODL .././variabletypes.mod
Translating hhwatch.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/ae2c9b73c9a624bce358af1b0042b70ba7c70ce86d0fb0bf97de8ac420156de5/arm64/hhwatch.cpp
Thread Safe
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/ae2c9b73c9a624bce358af1b0042b70ba7c70ce86d0fb0bf97de8ac420156de5/arm64/cadif.cpp
Translating table.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/ae2c9b73c9a624bce358af1b0042b70ba7c70ce86d0fb0bf97de8ac420156de5/arm64/table.cpp
Thread Safe
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/ae2c9b73c9a624bce358af1b0042b70ba7c70ce86d0fb0bf97de8ac420156de5/arm64/disc.cpp
Translating variabletypes.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/ae2c9b73c9a624bce358af1b0042b70ba7c70ce86d0fb0bf97de8ac420156de5/arm64/variabletypes.cpp
Thread Safe
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/ae2c9b73c9a624bce358af1b0042b70ba7c70ce86d0fb0bf97de8ac420156de5/arm64/fornetcon.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/ae2c9b73c9a624bce358af1b0042b70ba7c70ce86d0fb0bf97de8ac420156de5/arm64/hhwatch.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/ae2c9b73c9a624bce358af1b0042b70ba7c70ce86d0fb0bf97de8ac420156de5/arm64/k3st.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/ae2c9b73c9a624bce358af1b0042b70ba7c70ce86d0fb0bf97de8ac420156de5/arm64/table.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/ae2c9b73c9a624bce358af1b0042b70ba7c70ce86d0fb0bf97de8ac420156de5/arm64/variabletypes.cpp
=> LINKING shared library "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/ae2c9b73c9a624bce358af1b0042b70ba7c70ce86d0fb0bf97de8ac420156de5/arm64/./libnrnmech.dylib"
ld: warning: -undefined dynamic_lookup may not work with chained fixups
=> LINKING executable "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/ae2c9b73c9a624bce358af1b0042b70ba7c70ce86d0fb0bf97de8ac420156de5/arm64/./special" LDFLAGS are:
Successfully created arm64/special
[1345/1930] Generating nmodl_tests/test_table/test/nmodl/test_table.py
[1346/1930] Generating nmodl_tests/test_disc/test/nmodl/test_disc.py
[1347/1930] Generating nmodl_tests/test_function_table/test/nmodl/test_function_table.py
[1348/1930] Generating nmodl_tests/test_kinetic/test/nmodl/test_kinetic.py
[1349/1930] Generating nmodl_tests/test_random/test/nmodl/test_random.py
[1350/1930] Generating nmodl_tests/test_path_spaces/test/nmodl/Project Path Space/test.mod
[1351/1930] Generating nmodl_tests/test_path_spaces/test/nmodl/Project Path Space/test.py
[1352/1930] Generating nmodl_tests_coreneuron/test_table_coreneuron_cpu/test/nmodl/test_table.py
[1353/1930] Generating nmodl_tests_coreneuron/test_disc_coreneuron_cpu/test/nmodl/test_disc.py
[1354/1930] Generating nmodl_tests_coreneuron/test_function_table_coreneuron_cpu/test/nmodl/test_function_table.py
[1355/1930] Generating nmodl_tests_coreneuron/test_kinetic_coreneuron_cpu/test/nmodl/test_kinetic.py
[1356/1930] Generating ../../nrnivmodl/358a2005c5c0c89444ba4a268056fedbea5728b0d3948c6488fe911d6bafc951/invlfire.mod
[1357/1930] Generating ../../nrnivmodl/358a2005c5c0c89444ba4a268056fedbea5728b0d3948c6488fe911d6bafc951/invlfiresha.mod
[1358/1930] Generating ../../nrnivmodl/358a2005c5c0c89444ba4a268056fedbea5728b0d3948c6488fe911d6bafc951/invlfirestats.mod
[1359/1930] Building special[-core] for test group hoctests
/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad
cfiles =
Mod files: "./atest.mod" "./rand.mod" "./rand_art.mod" "./rand_pp.mod" "./sdata.mod" "./sdata_pp.mod" "./sdata_ppts.mod" "./sdata_ts.mod"
MODOBJS= ./atest.o ./rand.o ./rand_art.o ./rand_pp.o ./sdata.o ./sdata_pp.o ./sdata_ppts.o ./sdata_ts.o
-> Compiling mod_func.cpp
-> NMODL .././atest.mod
-> NMODL .././rand_art.mod
-> NMODL .././rand.mod
Translating atest.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad/arm64/atest.cpp
Thread Safe
-> NMODL .././rand_pp.mod
Translating rand_art.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad/arm64/rand_art.cpp
Thread Safe
-> NMODL .././sdata.mod
Translating rand.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad/arm64/rand.cpp
Thread Safe
-> NMODL .././sdata_pp.mod
Translating sdata_pp.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad/arm64/sdata_pp.cpp
INCLUDEing sdata.inc
Notice: Use of POINTER is not thread safe.
Notice: VERBATIM blocks are not thread safe
Translating rand_pp.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad/arm64/rand_pp.cpp
Thread Safe
-> NMODL .././sdata_ppts.mod
-> NMODL .././sdata_ts.mod
Translating sdata.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad/arm64/sdata.cpp
INCLUDEing sdata.inc
Notice: Use of POINTER is not thread safe.
Notice: VERBATIM blocks are not thread safe
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad/arm64/atest.cpp
Translating sdata_ppts.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad/arm64/sdata_ppts.cpp
INCLUDEing sdata.inc
Thread Safe
Translating sdata_ts.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad/arm64/sdata_ts.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad/arm64/rand.cpp
INCLUDEing sdata.inc
Thread Safe
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad/arm64/rand_art.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad/arm64/rand_pp.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad/arm64/sdata.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad/arm64/sdata_pp.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad/arm64/sdata_ppts.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad/arm64/sdata_ts.cpp
=> LINKING shared library "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad/arm64/./libnrnmech.dylib"
ld: warning: -undefined dynamic_lookup may not work with chained fixups
=> LINKING executable "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/39368a3f2faa5c7f6c1a704095364be6ec3af30bbfc8f85c1eef2176aae784ad/arm64/./special" LDFLAGS are:
Successfully created arm64/special
[1360/1930] Generating hoctests/test_loadbal_hoc/expect_err.hoc
[1361/1930] Generating hoctests/test_loadbal_hoc/tests/test_loadbal.hoc
[1362/1930] Generating hoctests/test_random_hoc/expect_err.hoc
[1363/1930] Generating hoctests/test_random_hoc/tests/test_random.hoc
[1364/1930] Generating hoctests/test_random_hoc/tests/test_random.json
[1365/1930] Generating hoctests/perf1_hoc/expect_err.hoc
[1366/1930] Generating hoctests/perf1_hoc/vardimtests/perf1.hoc
[1367/1930] Generating hoctests/test1_hoc/expect_err.hoc
[1368/1930] Generating hoctests/test1_hoc/vardimtests/test1.hoc
[1369/1930] Generating hoctests/test2_hoc/expect_err.hoc
[1370/1930] Generating hoctests/test2_hoc/vardimtests/test2.hoc
[1371/1930] Generating hoctests/test3_hoc/expect_err.hoc
[1372/1930] Generating hoctests/test3_hoc/vardimtests/test3.hoc
[1373/1930] Generating hoctests/test4_hoc/expect_err.hoc
[1374/1930] Generating hoctests/test4_hoc/vardimtests/test4.hoc
[1375/1930] Generating hoctests/test5_hoc/expect_err.hoc
[1376/1930] Generating hoctests/test5_hoc/vardimtests/test5.hoc
[1377/1930] Generating hoctests/test6_hoc/expect_err.hoc
[1378/1930] Generating hoctests/test6_hoc/vardimtests/test6.hoc
[1379/1930] Generating hoctests/test7_hoc/expect_err.hoc
[1380/1930] Generating hoctests/test7_hoc/vardimtests/test7.hoc
[1381/1930] Generating hoctests/test8_hoc/expect_err.hoc
[1382/1930] Generating hoctests/test8_hoc/vardimtests/test8.hoc
[1383/1930] Generating hoctests/test9_hoc/expect_err.hoc
[1384/1930] Generating hoctests/test9_hoc/vardimtests/test9.hoc
[1385/1930] Generating hoctests/test_bbss_py/tests/test_bbss.py
[1386/1930] Generating hoctests/test_cvinterp_py/tests/test_cvinterp.py
[1387/1930] Generating hoctests/test_hocGUI2_py/tests/test_hocGUI2.py
[1388/1930] Generating hoctests/test_hocmech_py/tests/test_hocmech.py
[1389/1930] Generating hoctests/test_kschan_py/tests/test_kschan.json
[1390/1930] Generating hoctests/test_kschan_py/tests/test_kschan.py
[1391/1930] Generating hoctests/test_legacy_setpointer_py/tests/test_legacy_setpointer.py
[1392/1930] Generating hoctests/test_mechfunc_py/tests/test_mechfunc.py
[1393/1930] Generating hoctests/test_mechstd_py/tests/test_mechstd.py
[1394/1930] Generating hoctests/test_mode_py/tests/test_mode.py
[1395/1930] Generating hoctests/test_neurondemo_py/tests/test_neurondemo.json
[1396/1930] Generating hoctests/test_neurondemo_py/tests/test_neurondemo.py
[1397/1930] Generating hoctests/test_nrniv-launch_py/tests/test_nrniv-launch.py
[1398/1930] Generating hoctests/test_optim_node_order_py/tests/test_optim_node_order.json
[1399/1930] Generating hoctests/test_optim_node_order_py/tests/test_optim_node_order.py
[1400/1930] Generating hoctests/test_random_py/tests/test_random.json
[1401/1930] Generating hoctests/test_random_py/tests/test_random.py
[1402/1930] Generating hoctests/test_setdata_py/tests/test_setdata.py
[1403/1930] Generating hoctests/test_shape_py/tests/test_shape.py
[1404/1930] Generating hoctests/test_thread_partition_py/tests/test_thread_partition.py
[1405/1930] Generating hoctests/test1_py/vardimtests/test1.py
[1406/1930] Generating hoctests/test2_py/vardimtests/test2.py
[1407/1930] Generating hoctests/test9_py/vardimtests/test9.py
[1408/1930] Building special[-core] for test group external_ringtest_nrn
/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/bbd7c82eee28b931214a8172bb776ba66c406a6620c807381c850fedcdd74295
cfiles =
Mod files: "./halfgap.mod"
MODOBJS= ./halfgap.o
-> Compiling mod_func.cpp
-> NMODL .././halfgap.mod
Translating halfgap.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/bbd7c82eee28b931214a8172bb776ba66c406a6620c807381c850fedcdd74295/arm64/halfgap.cpp
Thread Safe
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/bbd7c82eee28b931214a8172bb776ba66c406a6620c807381c850fedcdd74295/arm64/halfgap.cpp
=> LINKING shared library "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/bbd7c82eee28b931214a8172bb776ba66c406a6620c807381c850fedcdd74295/arm64/./libnrnmech.dylib"
ld: warning: -undefined dynamic_lookup may not work with chained fixups
=> LINKING executable "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/bbd7c82eee28b931214a8172bb776ba66c406a6620c807381c850fedcdd74295/arm64/./special" LDFLAGS are:
Successfully created arm64/special
[1409/1930] Generating ../../external_ringtest_nrn/optim_node_order/args.py
[1410/1930] Generating ../../external_ringtest_nrn/optim_node_order/cell.hoc
[1411/1930] Generating ../../external_ringtest_nrn/optim_node_order/celluniform.hoc
[1412/1930] Generating ../../external_ringtest_nrn/optim_node_order/commonutils.py
[1413/1930] Generating ../../external_ringtest_nrn/optim_node_order/ranparm.py
[1414/1930] Generating ../../external_ringtest_nrn/optim_node_order/ring.py
[1415/1930] Generating ../../external_ringtest_nrn/optim_node_order/ringtest.py
[1416/1930] Generating ../../external_ringtest_nrn/optim_node_order/ringuniform.py
[1417/1930] Generating ../../external_ringtest_nrn/optim_node_order/settings.py
[1418/1930] Generating ../../external_ringtest_nrn/optim_node_order/test_optimize_node_order.py
[1419/1930] Generating share/nrn/demo/release/arm64/special, share/nrn/demo/release/arm64/libnrnmech.dylib
/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/nrn/demo/release
cfiles =
Mod files: "cabpump.mod" "cachan1.mod" "camchan.mod" "capump.mod" "invlfire.mod" "khhchan.mod" "nacaex.mod" "nachan.mod" "release.mod"
MODOBJS= ./cabpump.o ./cachan1.o ./camchan.o ./capump.o ./invlfire.o ./khhchan.o ./nacaex.o ./nachan.o ./release.o
-> Compiling mod_func.cpp
-> NMODL ../cabpump.mod
-> NMODL ../cachan1.mod
-> NMODL ../camchan.mod
Translating camchan.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/nrn/demo/release/arm64/camchan.cpp
Thread Safe
-> NMODL ../capump.mod
Translating cabpump.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/nrn/demo/release/arm64/cabpump.cpp
Translating cachan1.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/nrn/demo/release/arm64/cachan1.cpp
Thread Safe
-> NMODL ../invlfire.mod
Notice: Assignment to the GLOBAL variable, "vol", is not thread safe
-> NMODL ../khhchan.mod
Translating invlfire.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/nrn/demo/release/arm64/invlfire.cpp
Thread Safe
Translating capump.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/nrn/demo/release/arm64/capump.cpp
Thread Safe
-> NMODL ../nacaex.mod
-> NMODL ../nachan.mod
Translating khhchan.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/nrn/demo/release/arm64/khhchan.cpp
Thread Safe
-> NMODL ../release.mod
Translating nachan.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/nrn/demo/release/arm64/nachan.cpp
Thread Safe
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/nrn/demo/release/arm64/cabpump.cpp
Translating nacaex.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/nrn/demo/release/arm64/nacaex.cpp
Thread Safe
Translating release.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/nrn/demo/release/arm64/release.cpp
Thread Safe
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/nrn/demo/release/arm64/cachan1.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/nrn/demo/release/arm64/camchan.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/nrn/demo/release/arm64/capump.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/nrn/demo/release/arm64/invlfire.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/nrn/demo/release/arm64/khhchan.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/nrn/demo/release/arm64/nacaex.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/nrn/demo/release/arm64/nachan.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/nrn/demo/release/arm64/release.cpp
=> LINKING shared library "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/nrn/demo/release/arm64/./libnrnmech.dylib"
ld: warning: -undefined dynamic_lookup may not work with chained fixups
=> LINKING executable "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/nrn/demo/release/arm64/./special" LDFLAGS are:
Successfully created arm64/special
[1420/1930] Building special[-core] for test group pytest_coreneuron
/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c448d279dd3b91940d228c42e4a7c280bafe100b4e840f9c938be979cceb8fe0
cfiles =
Mod files: "./follower.mod" "./gap.mod" "./name_clashes.mod" "./unitstest.mod" "./version_macros.mod"
MODOBJS= ./follower.o ./gap.o ./name_clashes.o ./unitstest.o ./version_macros.o
[INFO] Running: make -j4 -f /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/coreneuron/nrnivmodl_core_makefile ROOT=/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build MODS_PATH=arm64/corenrn/mod2c BUILD_TYPE=SHARED NRN_PRCELLSTATE=0
Default NMODL flags:
diff: arm64/corenrn/mod2c/_mod_func.cpp: No such file or directory
[NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shadows <extern_neuron_var> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shadows <extern_neuron_var> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shadows <extern_neuron_var> definition in NMODL_GLOBAL
[NMODL] [warning] :: CVode solver of icur in 64.20-30 replaced with cnexp solver
ld: warning: -undefined dynamic_lookup may not work with chained fixups
=> Binary creating arm64/special-core
[INFO] MOD files built successfully for CoreNEURON
-> Compiling mod_func.cpp
-> NMODL .././follower.mod
-> NMODL .././gap.mod
-> NMODL .././name_clashes.mod
Translating gap.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c448d279dd3b91940d228c42e4a7c280bafe100b4e840f9c938be979cceb8fe0/arm64/gap.cpp
Thread Safe
-> NMODL .././unitstest.mod
Translating follower.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c448d279dd3b91940d228c42e4a7c280bafe100b4e840f9c938be979cceb8fe0/arm64/follower.cpp
Thread Safe
-> NMODL .././version_macros.mod
Translating name_clashes.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c448d279dd3b91940d228c42e4a7c280bafe100b4e840f9c938be979cceb8fe0/arm64/name_clashes.cpp
Thread Safe
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c448d279dd3b91940d228c42e4a7c280bafe100b4e840f9c938be979cceb8fe0/arm64/follower.cpp
Translating unitstest.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c448d279dd3b91940d228c42e4a7c280bafe100b4e840f9c938be979cceb8fe0/arm64/unitstest.cpp
Thread Safe
Translating version_macros.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c448d279dd3b91940d228c42e4a7c280bafe100b4e840f9c938be979cceb8fe0/arm64/version_macros.cpp
Thread Safe
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c448d279dd3b91940d228c42e4a7c280bafe100b4e840f9c938be979cceb8fe0/arm64/gap.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c448d279dd3b91940d228c42e4a7c280bafe100b4e840f9c938be979cceb8fe0/arm64/name_clashes.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c448d279dd3b91940d228c42e4a7c280bafe100b4e840f9c938be979cceb8fe0/arm64/unitstest.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c448d279dd3b91940d228c42e4a7c280bafe100b4e840f9c938be979cceb8fe0/arm64/version_macros.cpp
=> LINKING shared library "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c448d279dd3b91940d228c42e4a7c280bafe100b4e840f9c938be979cceb8fe0/arm64/./libnrnmech.dylib"
ld: warning: -undefined dynamic_lookup may not work with chained fixups
=> LINKING executable "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c448d279dd3b91940d228c42e4a7c280bafe100b4e840f9c938be979cceb8fe0/arm64/./special" LDFLAGS are:
Successfully created arm64/special
[1421/1930] Generating pytest_coreneuron/basic_tests_py3.10/test/pytest_coreneuron/test_a_neuronoptions.py
[1422/1930] Generating pytest_coreneuron/basic_tests_py3.10/test/pytest_coreneuron/gui_pycallobject.py
[1423/1930] Generating pytest_coreneuron/basic_tests_py3.10/test/pytest_coreneuron/run_pytest.py
[1424/1930] Generating pytest_coreneuron/basic_tests_py3.10/test/pytest_coreneuron/test_basic.py
[1425/1930] Generating pytest_coreneuron/basic_tests_py3.10/test/pytest_coreneuron/test_bbss.py
[1426/1930] Generating pytest_coreneuron/basic_tests_py3.10/test/pytest_coreneuron/test_coreneuron_configuration.py
[1427/1930] Generating pytest_coreneuron/basic_tests_py3.10/test/pytest_coreneuron/test_fast_imem.py
[1428/1930] Generating pytest_coreneuron/basic_tests_py3.10/test/pytest_coreneuron/test_hoc_po.py
[1429/1930] Generating pytest_coreneuron/basic_tests_py3.10/test/pytest_coreneuron/test_imem.py
[1430/1930] Generating pytest_coreneuron/basic_tests_py3.10/test/pytest_coreneuron/test_inheritance.py
[1431/1930] Generating pytest_coreneuron/basic_tests_py3.10/test/pytest_coreneuron/test_loadbal.py
[1432/1930] Generating pytest_coreneuron/basic_tests_py3.10/test/pytest_coreneuron/test_memory_usage.py
[1433/1930] Generating pytest_coreneuron/basic_tests_py3.10/test/pytest_coreneuron/test_multigid.py
[1434/1930] Generating pytest_coreneuron/basic_tests_py3.10/test/pytest_coreneuron/test_netpar.py
[1435/1930] Generating pytest_coreneuron/basic_tests_py3.10/test/pytest_coreneuron/test_nlayer.py
[1436/1930] Generating pytest_coreneuron/basic_tests_py3.10/test/pytest_coreneuron/test_nrnste.py
[1437/1930] Generating pytest_coreneuron/basic_tests_py3.10/test/pytest_coreneuron/test_nrntest_fast.json
[1438/1930] Generating pytest_coreneuron/basic_tests_py3.10/test/pytest_coreneuron/test_nrntest_fast.py
[1439/1930] Generating pytest_coreneuron/basic_tests_py3.10/test/pytest_coreneuron/test_partrans.py
[1440/1930] Generating pytest_coreneuron/basic_tests_py3.10/test/pytest_coreneuron/test_py2nrnstring.py
[1441/1930] Generating pytest_coreneuron/basic_tests_py3.10/test/pytest_coreneuron/test_pycallobject.py
[1442/1930] Generating pytest_coreneuron/basic_tests_py3.10/test/pytest_coreneuron/test_pyobj.py
[1443/1930] Generating pytest_coreneuron/basic_tests_py3.10/test/pytest_coreneuron/test_swc.py
[1444/1930] Generating pytest_coreneuron/basic_tests_py3.10/test/pytest_coreneuron/test_template_err.py
[1445/1930] Generating pytest_coreneuron/basic_tests_py3.10/test/pytest_coreneuron/test_vector_api.py
[1446/1930] Generating pytest_coreneuron/basic_tests_py3.10/test/pytest_coreneuron/test_version_macros.py
[1447/1930] Generating pytest_coreneuron/basic_tests_py3.10/test/pytest_coreneuron/test_zptrlist.py
[1448/1930] Building special[-core] for test group external_ringtest
/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/a9c54b18e4b54351cb4fd3e79067cafa02da4514b4383a54de8ff121657615ff
cfiles =
Mod files: "./halfgap.mod"
MODOBJS= ./halfgap.o
[INFO] Running: make -j4 -f /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/coreneuron/nrnivmodl_core_makefile ROOT=/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build MODS_PATH=arm64/corenrn/mod2c BUILD_TYPE=SHARED NRN_PRCELLSTATE=0
Default NMODL flags:
diff: arm64/corenrn/mod2c/_mod_func.cpp: No such file or directory
[NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shadows <extern_neuron_var> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shadows <extern_neuron_var> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shadows <extern_neuron_var> definition in NMODL_GLOBAL
[NMODL] [warning] :: CVode solver of icur in 64.20-30 replaced with cnexp solver
ld: warning: -undefined dynamic_lookup may not work with chained fixups
=> Binary creating arm64/special-core
[INFO] MOD files built successfully for CoreNEURON
-> Compiling mod_func.cpp
-> NMODL .././halfgap.mod
Translating halfgap.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/a9c54b18e4b54351cb4fd3e79067cafa02da4514b4383a54de8ff121657615ff/arm64/halfgap.cpp
Thread Safe
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/a9c54b18e4b54351cb4fd3e79067cafa02da4514b4383a54de8ff121657615ff/arm64/halfgap.cpp
=> LINKING shared library "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/a9c54b18e4b54351cb4fd3e79067cafa02da4514b4383a54de8ff121657615ff/arm64/./libnrnmech.dylib"
ld: warning: -undefined dynamic_lookup may not work with chained fixups
=> LINKING executable "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/a9c54b18e4b54351cb4fd3e79067cafa02da4514b4383a54de8ff121657615ff/arm64/./special" LDFLAGS are:
Successfully created arm64/special
[1449/1930] Generating ../../external_ringtest/neuron/cell.hoc
[1450/1930] Generating ../../external_ringtest/neuron/commonutils.py
[1451/1930] Generating ../../external_ringtest/neuron/args.py
[1452/1930] Generating ../../external_ringtest/neuron/celluniform.hoc
[1453/1930] Generating ../../external_ringtest/neuron/ranparm.py
[1454/1930] Generating ../../external_ringtest/neuron/ring.py
[1455/1930] Generating ../../external_ringtest/neuron/ringtest.py
[1456/1930] Generating ../../external_ringtest/neuron/settings.py
[1457/1930] Generating ../../external_ringtest/neuron/ringuniform.py
[1458/1930] Generating ../../external_ringtest/neuron/test_optimize_node_order.py
[1459/1930] Generating ../../external_ringtest/neuron_mpi/args.py
[1460/1930] Generating ../../external_ringtest/neuron_mpi/cell.hoc
[1461/1930] Generating ../../external_ringtest/neuron_mpi/celluniform.hoc
[1462/1930] Generating ../../external_ringtest/neuron_mpi/commonutils.py
[1463/1930] Generating ../../external_ringtest/neuron_mpi/ring.py
[1464/1930] Generating ../../external_ringtest/neuron_mpi/ranparm.py
[1465/1930] Generating ../../external_ringtest/neuron_mpi/ringtest.py
[1466/1930] Generating ../../external_ringtest/neuron_mpi/ringuniform.py
[1467/1930] Generating ../../external_ringtest/neuron_mpi/settings.py
[1468/1930] Generating ../../external_ringtest/neuron_mpi/test_optimize_node_order.py
[1469/1930] Generating ../../external_ringtest/neuron_mpi_python/args.py
[1470/1930] Generating ../../external_ringtest/neuron_mpi_python/cell.hoc
[1471/1930] Generating ../../external_ringtest/neuron_mpi_python/celluniform.hoc
[1472/1930] Generating ../../external_ringtest/neuron_mpi_python/commonutils.py
[1473/1930] Generating ../../external_ringtest/neuron_mpi_python/ranparm.py
[1474/1930] Generating ../../external_ringtest/neuron_mpi_python/ring.py
[1475/1930] Generating ../../external_ringtest/neuron_mpi_python/ringtest.py
[1476/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_offline_saverestore/args.py
[1477/1930] Generating ../../external_ringtest/neuron_mpi_python/ringuniform.py
[1478/1930] Generating ../../external_ringtest/neuron_mpi_python/settings.py
[1479/1930] Generating ../../external_ringtest/neuron_mpi_python/test_optimize_node_order.py
[1480/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_offline_saverestore/cell.hoc
[1481/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_offline_saverestore/ranparm.py
[1482/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_offline_saverestore/celluniform.hoc
[1483/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_offline_saverestore/commonutils.py
[1484/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_offline_saverestore/ring.py
[1485/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_offline_saverestore/ringuniform.py
[1486/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_offline_saverestore/ringtest.py
[1487/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi/args.py
[1488/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_offline_saverestore/test_optimize_node_order.py
[1489/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_offline_saverestore/settings.py
[1490/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi/cell.hoc
[1491/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi/celluniform.hoc
[1492/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi/commonutils.py
[1493/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi/ring.py
[1494/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi/ranparm.py
[1495/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi/ringtest.py
[1496/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi/ringuniform.py
[1497/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi/settings.py
[1498/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_python/args.py
[1499/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi/test_optimize_node_order.py
[1500/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_python/cell.hoc
[1501/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_python/celluniform.hoc
[1502/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_python/ranparm.py
[1503/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_python/commonutils.py
[1504/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_python/ring.py
[1505/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_python/ringtest.py
[1506/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_python/ringuniform.py
[1507/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_python/settings.py
[1508/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_python/test_optimize_node_order.py
[1509/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_offline/args.py
[1510/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_offline/celluniform.hoc
[1511/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_offline/cell.hoc
[1512/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_offline/commonutils.py
[1513/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_offline/ranparm.py
[1514/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_offline/ring.py
[1515/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_offline/ringtest.py
[1516/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_offline/ringuniform.py
[1517/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_offline/settings.py
[1518/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_offline/test_optimize_node_order.py
[1519/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_threads/args.py
[1520/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_threads/cell.hoc
[1521/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_threads/celluniform.hoc
[1522/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_threads/ringtest.py
[1523/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_threads/commonutils.py
[1524/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_threads/ring.py
[1525/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_threads/ranparm.py
[1526/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_threads/ringuniform.py
[1527/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_threads/settings.py
[1528/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_threads/test_optimize_node_order.py
[1529/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_threads_python/args.py
[1530/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_threads_python/cell.hoc
[1531/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_threads_python/celluniform.hoc
[1532/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_threads_python/commonutils.py
[1533/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_threads_python/ranparm.py
[1534/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_threads_python/ring.py
[1535/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_threads_python/ringtest.py
[1536/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_threads_python/ringuniform.py
[1537/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_threads_python/settings.py
[1538/1930] Generating ../../external_ringtest/coreneuron_mpi_registermapping_directmode/args.py
[1539/1930] Generating ../../external_ringtest/coreneuron_cpu_mpi_threads_python/test_optimize_node_order.py
[1540/1930] Generating ../../external_ringtest/coreneuron_mpi_registermapping_directmode/cell.hoc
[1541/1930] Generating ../../external_ringtest/coreneuron_mpi_registermapping_directmode/celluniform.hoc
[1542/1930] Generating ../../external_ringtest/coreneuron_mpi_registermapping_directmode/commonutils.py
[1543/1930] Generating ../../external_ringtest/coreneuron_mpi_registermapping_directmode/ring.py
[1544/1930] Generating ../../external_ringtest/coreneuron_mpi_registermapping_directmode/ranparm.py
[1545/1930] Generating ../../external_ringtest/coreneuron_mpi_registermapping_directmode/ringtest.py
[1546/1930] Generating ../../external_ringtest/coreneuron_mpi_registermapping_directmode/ringuniform.py
[1547/1930] Generating ../../external_ringtest/coreneuron_mpi_registermapping_directmode/settings.py
[1548/1930] Generating ../../external_ringtest/coreneuron_mpi_registermapping_directmode/test_optimize_node_order.py
[1549/1930] Generating ../../external_ringtest/coreneuron_mpi_registermapping_filemode/cell.hoc
[1550/1930] Generating ../../external_ringtest/coreneuron_mpi_registermapping_filemode/args.py
[1551/1930] Generating ../../external_ringtest/coreneuron_mpi_registermapping_filemode/celluniform.hoc
[1552/1930] Generating ../../external_ringtest/coreneuron_mpi_registermapping_filemode/ranparm.py
[1553/1930] Generating ../../external_ringtest/coreneuron_mpi_registermapping_filemode/ringtest.py
[1554/1930] Generating ../../external_ringtest/coreneuron_mpi_registermapping_filemode/commonutils.py
[1555/1930] Generating ../../external_ringtest/coreneuron_mpi_registermapping_filemode/ring.py
[1556/1930] Generating ../../external_ringtest/coreneuron_mpi_registermapping_filemode/ringuniform.py
[1557/1930] Generating ../../external_ringtest/coreneuron_mpi_registermapping_filemode/settings.py
[1558/1930] Generating ../../external_ringtest/coreneuron_mpi_registermapping_filemode/test_optimize_node_order.py
[1559/1930] Building special[-core] for test group tqperf
/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/358a2005c5c0c89444ba4a268056fedbea5728b0d3948c6488fe911d6bafc951
cfiles =
Mod files: "./invlfire.mod" "./invlfiresha.mod" "./invlfirestats.mod"
MODOBJS= ./invlfire.o ./invlfiresha.o ./invlfirestats.o
[INFO] Running: make -j4 -f /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/coreneuron/nrnivmodl_core_makefile ROOT=/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build INCFLAGS=-I/opt/homebrew/Cellar/openssl@3/3.2.0_1/include LINKFLAGS=/opt/homebrew/Cellar/openssl@3/3.2.0_1/lib/libcrypto.dylib MODS_PATH=arm64/corenrn/mod2c BUILD_TYPE=SHARED NRN_PRCELLSTATE=0
Default NMODL flags:
diff: arm64/corenrn/mod2c/_mod_func.cpp: No such file or directory
[NMODL] [warning] :: Can not inline function call to specify_invl
[NMODL] [warning] :: Can not inline function call to specify_invl
[NMODL] [warning] :: Can not inline function call to specify_invl
[NMODL] [warning] :: Can not inline function call to specify_invl
[NMODL] [warning] :: Can not inline function call to specify_invl
[NMODL] [warning] :: Can not inline function call to specify_invl
[NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shadows <extern_neuron_var> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shadows <extern_neuron_var> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shadows <extern_neuron_var> definition in NMODL_GLOBAL
[NMODL] [warning] :: CVode solver of icur in 64.20-30 replaced with cnexp solver
arm64/corenrn/mod2c/invlfiresha.cpp:313:16: warning: 'SHA1_Init' is deprecated [-Wdeprecated-declarations]
int status = SHA1_Init((SHA_CTX*)(*ctx));
^
/opt/homebrew/Cellar/openssl@3/3.2.0_1/include/openssl/sha.h:49:1: note: 'SHA1_Init' has been explicitly marked deprecated here
OSSL_DEPRECATEDIN_3_0 int SHA1_Init(SHA_CTX *c);
^
/opt/homebrew/Cellar/openssl@3/3.2.0_1/include/openssl/macros.h:194:49: note: expanded from macro 'OSSL_DEPRECATEDIN_3_0'
# define OSSL_DEPRECATEDIN_3_0 OSSL_DEPRECATED(3.0)
^
/opt/homebrew/Cellar/openssl@3/3.2.0_1/include/openssl/macros.h:62:52: note: expanded from macro 'OSSL_DEPRECATED'
# define OSSL_DEPRECATED(since) __attribute__((deprecated))
^
arm64/corenrn/mod2c/invlfiresha.cpp:318:16: warning: 'SHA1_Update' is deprecated [-Wdeprecated-declarations]
int status = SHA1_Update((SHA_CTX*)ctx, data, len);
^
/opt/homebrew/Cellar/openssl@3/3.2.0_1/include/openssl/sha.h:50:1: note: 'SHA1_Update' has been explicitly marked deprecated here
OSSL_DEPRECATEDIN_3_0 int SHA1_Update(SHA_CTX *c, const void *data, size_t len);
^
/opt/homebrew/Cellar/openssl@3/3.2.0_1/include/openssl/macros.h:194:49: note: expanded from macro 'OSSL_DEPRECATEDIN_3_0'
# define OSSL_DEPRECATEDIN_3_0 OSSL_DEPRECATED(3.0)
^
/opt/homebrew/Cellar/openssl@3/3.2.0_1/include/openssl/macros.h:62:52: note: expanded from macro 'OSSL_DEPRECATED'
# define OSSL_DEPRECATED(since) __attribute__((deprecated))
^
arm64/corenrn/mod2c/invlfiresha.cpp:329:16: warning: 'SHA1_Final' is deprecated [-Wdeprecated-declarations]
int status = SHA1_Final(u.md, (SHA_CTX*)ctx);
^
/opt/homebrew/Cellar/openssl@3/3.2.0_1/include/openssl/sha.h:51:1: note: 'SHA1_Final' has been explicitly marked deprecated here
OSSL_DEPRECATEDIN_3_0 int SHA1_Final(unsigned char *md, SHA_CTX *c);
^
/opt/homebrew/Cellar/openssl@3/3.2.0_1/include/openssl/macros.h:194:49: note: expanded from macro 'OSSL_DEPRECATEDIN_3_0'
# define OSSL_DEPRECATEDIN_3_0 OSSL_DEPRECATED(3.0)
^
/opt/homebrew/Cellar/openssl@3/3.2.0_1/include/openssl/macros.h:62:52: note: expanded from macro 'OSSL_DEPRECATED'
# define OSSL_DEPRECATED(since) __attribute__((deprecated))
^
3 warnings generated.
ld: warning: -undefined dynamic_lookup may not work with chained fixups
=> Binary creating arm64/special-core
[INFO] MOD files built successfully for CoreNEURON
-> Compiling mod_func.cpp
-> NMODL .././invlfire.mod
-> NMODL .././invlfiresha.mod
-> NMODL .././invlfirestats.mod
Translating invlfirestats.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/358a2005c5c0c89444ba4a268056fedbea5728b0d3948c6488fe911d6bafc951/arm64/invlfirestats.cpp
Translating invlfire.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/358a2005c5c0c89444ba4a268056fedbea5728b0d3948c6488fe911d6bafc951/arm64/invlfire.cpp
Thread Safe
Notice: ARTIFICIAL_CELL is a synonym for POINT_PROCESS which hints that it
only affects and is affected by discrete events. As such it is not
located in a section and is not associated with an integrator
Translating invlfiresha.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/358a2005c5c0c89444ba4a268056fedbea5728b0d3948c6488fe911d6bafc951/arm64/invlfiresha.cpp
Thread Safe
Notice: ARTIFICIAL_CELL is a synonym for POINT_PROCESS which hints that it
only affects and is affected by discrete events. As such it is not
located in a section and is not associated with an integrator
Thread Safe
Notice: ARTIFICIAL_CELL is a synonym for POINT_PROCESS which hints that it
only affects and is affected by discrete events. As such it is not
located in a section and is not associated with an integrator
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/358a2005c5c0c89444ba4a268056fedbea5728b0d3948c6488fe911d6bafc951/arm64/invlfirestats.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/358a2005c5c0c89444ba4a268056fedbea5728b0d3948c6488fe911d6bafc951/arm64/invlfire.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/358a2005c5c0c89444ba4a268056fedbea5728b0d3948c6488fe911d6bafc951/arm64/invlfiresha.cpp
/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/358a2005c5c0c89444ba4a268056fedbea5728b0d3948c6488fe911d6bafc951/arm64/invlfiresha.cpp:371:16: warning: 'SHA1_Init' is deprecated [-Wdeprecated-declarations]
int status = SHA1_Init((SHA_CTX*)(*ctx));
^
/opt/homebrew/Cellar/openssl@3/3.2.0_1/include/openssl/sha.h:49:1: note: 'SHA1_Init' has been explicitly marked deprecated here
OSSL_DEPRECATEDIN_3_0 int SHA1_Init(SHA_CTX *c);
^
/opt/homebrew/Cellar/openssl@3/3.2.0_1/include/openssl/macros.h:194:49: note: expanded from macro 'OSSL_DEPRECATEDIN_3_0'
# define OSSL_DEPRECATEDIN_3_0 OSSL_DEPRECATED(3.0)
^
/opt/homebrew/Cellar/openssl@3/3.2.0_1/include/openssl/macros.h:62:52: note: expanded from macro 'OSSL_DEPRECATED'
# define OSSL_DEPRECATED(since) __attribute__((deprecated))
^
/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/358a2005c5c0c89444ba4a268056fedbea5728b0d3948c6488fe911d6bafc951/arm64/invlfiresha.cpp:376:16: warning: 'SHA1_Update' is deprecated [-Wdeprecated-declarations]
int status = SHA1_Update((SHA_CTX*)ctx, data, len);
^
/opt/homebrew/Cellar/openssl@3/3.2.0_1/include/openssl/sha.h:50:1: note: 'SHA1_Update' has been explicitly marked deprecated here
OSSL_DEPRECATEDIN_3_0 int SHA1_Update(SHA_CTX *c, const void *data, size_t len);
^
/opt/homebrew/Cellar/openssl@3/3.2.0_1/include/openssl/macros.h:194:49: note: expanded from macro 'OSSL_DEPRECATEDIN_3_0'
# define OSSL_DEPRECATEDIN_3_0 OSSL_DEPRECATED(3.0)
^
/opt/homebrew/Cellar/openssl@3/3.2.0_1/include/openssl/macros.h:62:52: note: expanded from macro 'OSSL_DEPRECATED'
# define OSSL_DEPRECATED(since) __attribute__((deprecated))
^
/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/358a2005c5c0c89444ba4a268056fedbea5728b0d3948c6488fe911d6bafc951/arm64/invlfiresha.cpp:387:16: warning: 'SHA1_Final' is deprecated [-Wdeprecated-declarations]
int status = SHA1_Final(u.md, (SHA_CTX*)ctx);
^
/opt/homebrew/Cellar/openssl@3/3.2.0_1/include/openssl/sha.h:51:1: note: 'SHA1_Final' has been explicitly marked deprecated here
OSSL_DEPRECATEDIN_3_0 int SHA1_Final(unsigned char *md, SHA_CTX *c);
^
/opt/homebrew/Cellar/openssl@3/3.2.0_1/include/openssl/macros.h:194:49: note: expanded from macro 'OSSL_DEPRECATEDIN_3_0'
# define OSSL_DEPRECATEDIN_3_0 OSSL_DEPRECATED(3.0)
^
/opt/homebrew/Cellar/openssl@3/3.2.0_1/include/openssl/macros.h:62:52: note: expanded from macro 'OSSL_DEPRECATED'
# define OSSL_DEPRECATED(since) __attribute__((deprecated))
^
3 warnings generated.
=> LINKING shared library "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/358a2005c5c0c89444ba4a268056fedbea5728b0d3948c6488fe911d6bafc951/arm64/./libnrnmech.dylib"
ld: warning: -undefined dynamic_lookup may not work with chained fixups
=> LINKING executable "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/358a2005c5c0c89444ba4a268056fedbea5728b0d3948c6488fe911d6bafc951/arm64/./special" LDFLAGS are: /opt/homebrew/Cellar/openssl@3/3.2.0_1/lib/libcrypto.dylib
Successfully created arm64/special
[1560/1930] Generating ../../tqperf/coreneuron_special/mosinit.hoc
[1561/1930] Generating ../../tqperf/coreneuron_special/net.hoc
[1562/1930] Generating ../../tqperf/coreneuron_special/extracell.hoc
[1563/1930] Generating ../../tqperf/coreneuron_special/init.hoc
[1564/1930] Generating ../../tqperf/coreneuron_special/invl.hoc
[1565/1930] Generating ../../tqperf/coreneuron_special/movie.hoc
[1566/1930] Generating ../../tqperf/coreneuron_special/param.hoc
[1567/1930] Generating ../../tqperf/coreneuron_special/run.hoc
[1568/1930] Generating ../../tqperf/coreneuron_special/run128.hoc
[1569/1930] Generating ../../tqperf/coreneuron_special/perfrun.hoc
[1570/1930] Generating ../../tqperf/coreneuron_special/randist.hoc
[1571/1930] Generating ../../tqperf/coreneuron_special/pltq.hoc
[1572/1930] Generating ../../tqperf/coreneuron_special/spkplt.hoc
[1573/1930] Generating ../../tqperf/coreneuron_special/table.hoc
[1574/1930] Generating ../../tqperf/coreneuron_special/test1.py
[1575/1930] Generating ../../tqperf/coreneuron_special/runs.hoc
[1576/1930] Generating ../../tqperf/coreneuron_special/tperf.hoc
[1577/1930] Generating ../../tqperf/coreneuron_special/tperfnew.hoc
[1578/1930] Generating ../../tqperf/coreneuron_special/spike2file.hoc
[1579/1930] Generating ../../tqperf/coreneuron_python/invl.hoc
[1580/1930] Generating ../../tqperf/coreneuron_python/movie.hoc
[1581/1930] Generating ../../tqperf/coreneuron_python/extracell.hoc
[1582/1930] Generating ../../tqperf/coreneuron_python/init.hoc
[1583/1930] Generating ../../tqperf/coreneuron_python/mosinit.hoc
[1584/1930] Generating ../../tqperf/coreneuron_python/net.hoc
[1585/1930] Generating ../../tqperf/coreneuron_python/pltq.hoc
[1586/1930] Generating ../../tqperf/coreneuron_python/param.hoc
[1587/1930] Generating ../../tqperf/coreneuron_python/perfrun.hoc
[1588/1930] Generating ../../tqperf/coreneuron_python/run.hoc
[1589/1930] Generating ../../tqperf/coreneuron_python/randist.hoc
[1590/1930] Generating ../../tqperf/coreneuron_python/run128.hoc
[1591/1930] Generating ../../tqperf/coreneuron_python/table.hoc
[1592/1930] Generating ../../tqperf/coreneuron_python/runs.hoc
[1593/1930] Generating ../../tqperf/coreneuron_python/spike2file.hoc
[1594/1930] Generating ../../tqperf/coreneuron_python/spkplt.hoc
[1595/1930] Generating ../../tqperf/coreneuron_python/test1.py
[1596/1930] Generating ../../tqperf/coreneuron_python/tperfnew.hoc
[1597/1930] Generating ../../tqperf/coreneuron_python/tperf.hoc
[1598/1930] Building special[-core] for test group testcorenrn_bbcore
/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/b62f97c7d3f6d905c774d64e10128b3300792f8f757b926b965c058a4d6ee876
cfiles =
Mod files: "./Gfluct3.mod" "./hhderiv.mod" "./hhkin.mod" "./hhwatch.mod" "./nacum.mod" "./vecevent.mod"
MODOBJS= ./Gfluct3.o ./hhderiv.o ./hhkin.o ./hhwatch.o ./nacum.o ./vecevent.o
[INFO] Running: make -j4 -f /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/coreneuron/nrnivmodl_core_makefile ROOT=/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build MODS_PATH=arm64/corenrn/mod2c BUILD_TYPE=SHARED NRN_PRCELLSTATE=0
Default NMODL flags:
diff: arm64/corenrn/mod2c/_mod_func.cpp: No such file or directory
[NMODL] [warning] :: Can not inline function call to mynormrand
[NMODL] [warning] :: Can not inline function call to mynormrand
[NMODL] [warning] :: Can not inline function call to mynormrand
[NMODL] [warning] :: Can not inline function call to mynormrand
[NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shadows <extern_neuron_var> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shadows <extern_neuron_var> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shadows <extern_neuron_var> definition in NMODL_GLOBAL
[NMODL] [warning] :: CVode solver of icur in 64.20-30 replaced with cnexp solver
ld: warning: -undefined dynamic_lookup may not work with chained fixups
=> Binary creating arm64/special-core
[INFO] MOD files built successfully for CoreNEURON
-> NMODL .././Gfluct3.mod
-> NMODL .././hhderiv.mod
-> NMODL .././hhkin.mod
-> Compiling mod_func.cpp
Translating Gfluct3.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/b62f97c7d3f6d905c774d64e10128b3300792f8f757b926b965c058a4d6ee876/arm64/Gfluct3.cpp
Translating hhderiv.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/b62f97c7d3f6d905c774d64e10128b3300792f8f757b926b965c058a4d6ee876/arm64/hhderiv.cpp
Translating hhkin.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/b62f97c7d3f6d905c774d64e10128b3300792f8f757b926b965c058a4d6ee876/arm64/hhkin.cpp
Thread Safe
Thread Safe
-> NMODL .././hhwatch.mod
-> NMODL .././nacum.mod
Thread Safe
-> NMODL .././vecevent.mod
Translating hhwatch.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/b62f97c7d3f6d905c774d64e10128b3300792f8f757b926b965c058a4d6ee876/arm64/hhwatch.cpp
Thread Safe
Translating nacum.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/b62f97c7d3f6d905c774d64e10128b3300792f8f757b926b965c058a4d6ee876/arm64/nacum.cpp
Thread Safe
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/b62f97c7d3f6d905c774d64e10128b3300792f8f757b926b965c058a4d6ee876/arm64/Gfluct3.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/b62f97c7d3f6d905c774d64e10128b3300792f8f757b926b965c058a4d6ee876/arm64/hhderiv.cpp
Translating vecevent.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/b62f97c7d3f6d905c774d64e10128b3300792f8f757b926b965c058a4d6ee876/arm64/vecevent.cpp
Thread Safe
Notice: ARTIFICIAL_CELL is a synonym for POINT_PROCESS which hints that it
only affects and is affected by discrete events. As such it is not
located in a section and is not associated with an integrator
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/b62f97c7d3f6d905c774d64e10128b3300792f8f757b926b965c058a4d6ee876/arm64/hhkin.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/b62f97c7d3f6d905c774d64e10128b3300792f8f757b926b965c058a4d6ee876/arm64/hhwatch.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/b62f97c7d3f6d905c774d64e10128b3300792f8f757b926b965c058a4d6ee876/arm64/nacum.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/b62f97c7d3f6d905c774d64e10128b3300792f8f757b926b965c058a4d6ee876/arm64/vecevent.cpp
=> LINKING shared library "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/b62f97c7d3f6d905c774d64e10128b3300792f8f757b926b965c058a4d6ee876/arm64/./libnrnmech.dylib"
ld: warning: -undefined dynamic_lookup may not work with chained fixups
=> LINKING executable "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/b62f97c7d3f6d905c774d64e10128b3300792f8f757b926b965c058a4d6ee876/arm64/./special" LDFLAGS are:
Successfully created arm64/special
[1599/1930] Generating ../../testcorenrn_bbcore/neuron/common.hoc
[1600/1930] Generating ../../testcorenrn_bbcore/neuron/defvar.hoc
[1601/1930] Generating ../../testcorenrn_bbcore/neuron/testbbcore.hoc
[1602/1930] Generating ../../testcorenrn_bbcore/coreneuron_cpu_online/common.hoc
[1603/1930] Generating ../../testcorenrn_bbcore/coreneuron_cpu_online/testbbcore.hoc
[1604/1930] Generating ../../testcorenrn_bbcore/coreneuron_cpu_online/defvar.hoc
[1605/1930] Generating ../../testcorenrn_bbcore/coreneuron_cpu_online_psolve_alternate/common.hoc
[1606/1930] Generating ../../testcorenrn_bbcore/coreneuron_cpu_online_psolve_alternate/defvar.hoc
[1607/1930] Generating ../../testcorenrn_bbcore/coreneuron_cpu_online_psolve_alternate/testbbcore.hoc
[1608/1930] Generating ../../testcorenrn_bbcore/coreneuron_cpu_offline/common.hoc
[1609/1930] Generating ../../testcorenrn_bbcore/coreneuron_cpu_offline/defvar.hoc
[1610/1930] Generating ../../testcorenrn_bbcore/coreneuron_cpu_offline/testbbcore.hoc
[1611/1930] Generating ../../testcorenrn_conc/neuron/defvar.hoc
[1612/1930] Generating ../../testcorenrn_conc/neuron/common.hoc
[1613/1930] Generating ../../testcorenrn_conc/neuron/testconc.hoc
[1614/1930] Generating ../../testcorenrn_conc/coreneuron_cpu_online/testconc.hoc
[1615/1930] Generating ../../testcorenrn_conc/coreneuron_cpu_online/common.hoc
[1616/1930] Generating ../../testcorenrn_conc/coreneuron_cpu_online/defvar.hoc
[1617/1930] Generating ../../testcorenrn_conc/coreneuron_cpu_online_psolve_alternate/common.hoc
[1618/1930] Generating ../../testcorenrn_conc/coreneuron_cpu_online_psolve_alternate/defvar.hoc
[1619/1930] Generating ../../testcorenrn_conc/coreneuron_cpu_offline/common.hoc
[1620/1930] Generating ../../testcorenrn_conc/coreneuron_cpu_online_psolve_alternate/testconc.hoc
[1621/1930] Generating ../../testcorenrn_conc/coreneuron_cpu_offline/defvar.hoc
[1622/1930] Generating ../../testcorenrn_deriv/neuron/common.hoc
[1623/1930] Generating ../../testcorenrn_deriv/coreneuron_cpu_online/common.hoc
[1624/1930] Generating ../../testcorenrn_conc/coreneuron_cpu_offline/testconc.hoc
[1625/1930] Generating ../../testcorenrn_deriv/neuron/testderiv.hoc
[1626/1930] Generating ../../testcorenrn_deriv/coreneuron_cpu_online/defvar.hoc
[1627/1930] Generating ../../testcorenrn_deriv/neuron/defvar.hoc
[1628/1930] Generating ../../testcorenrn_deriv/coreneuron_cpu_online/testderiv.hoc
[1629/1930] Generating ../../testcorenrn_deriv/coreneuron_cpu_online_psolve_alternate/common.hoc
[1630/1930] Generating ../../testcorenrn_deriv/coreneuron_cpu_offline/common.hoc
[1631/1930] Generating ../../testcorenrn_deriv/coreneuron_cpu_online_psolve_alternate/defvar.hoc
[1632/1930] Generating ../../testcorenrn_deriv/coreneuron_cpu_online_psolve_alternate/testderiv.hoc
[1633/1930] Generating ../../testcorenrn_deriv/coreneuron_cpu_offline/testderiv.hoc
[1634/1930] Generating ../../testcorenrn_deriv/coreneuron_cpu_offline/defvar.hoc
[1635/1930] Generating ../../testcorenrn_gf/coreneuron_cpu_online/common.hoc
[1636/1930] Generating ../../testcorenrn_gf/neuron/common.hoc
[1637/1930] Generating ../../testcorenrn_gf/neuron/testgf.hoc
[1638/1930] Generating ../../testcorenrn_gf/neuron/defvar.hoc
[1639/1930] Generating ../../testcorenrn_gf/coreneuron_cpu_online/defvar.hoc
[1640/1930] Generating ../../testcorenrn_gf/coreneuron_cpu_online/testgf.hoc
[1641/1930] Generating ../../testcorenrn_gf/coreneuron_cpu_online_psolve_alternate/defvar.hoc
[1642/1930] Generating ../../testcorenrn_gf/coreneuron_cpu_offline/common.hoc
[1643/1930] Generating ../../testcorenrn_gf/coreneuron_cpu_online_psolve_alternate/common.hoc
[1644/1930] Generating ../../testcorenrn_gf/coreneuron_cpu_offline/defvar.hoc
[1645/1930] Generating ../../testcorenrn_gf/coreneuron_cpu_online_psolve_alternate/testgf.hoc
[1646/1930] Generating ../../testcorenrn_gf/coreneuron_cpu_offline/testgf.hoc
[1647/1930] Generating ../../testcorenrn_kin/neuron/common.hoc
[1648/1930] Generating ../../testcorenrn_kin/coreneuron_cpu_online/common.hoc
[1649/1930] Generating ../../testcorenrn_kin/neuron/defvar.hoc
[1650/1930] Generating ../../testcorenrn_kin/coreneuron_cpu_online/defvar.hoc
[1651/1930] Generating ../../testcorenrn_kin/neuron/testkin.hoc
[1652/1930] Generating ../../testcorenrn_kin/coreneuron_cpu_online/testkin.hoc
[1653/1930] Generating ../../testcorenrn_kin/coreneuron_cpu_online_psolve_alternate/common.hoc
[1654/1930] Generating ../../testcorenrn_kin/coreneuron_cpu_offline/testkin.hoc
[1655/1930] Generating ../../testcorenrn_kin/coreneuron_cpu_online_psolve_alternate/testkin.hoc
[1656/1930] Generating ../../testcorenrn_kin/coreneuron_cpu_online_psolve_alternate/defvar.hoc
[1657/1930] Generating ../../testcorenrn_kin/coreneuron_cpu_offline/defvar.hoc
[1658/1930] Generating ../../testcorenrn_kin/coreneuron_cpu_offline/common.hoc
[1659/1930] Generating ../../testcorenrn_patstim/neuron/common.hoc
[1660/1930] Generating ../../testcorenrn_patstim/neuron/defvar.hoc
[1661/1930] Generating ../../testcorenrn_patstim/neuron/testpatstim.hoc
[1662/1930] Generating ../../testcorenrn_patstim/coreneuron_cpu_offline_saverestore/testpatstim.hoc
[1663/1930] Generating ../../testcorenrn_patstim/coreneuron_cpu_offline/common.hoc
[1664/1930] Generating ../../testcorenrn_patstim/coreneuron_cpu_offline_saverestore/common.hoc
[1665/1930] Generating ../../testcorenrn_patstim/coreneuron_cpu_offline_saverestore/defvar.hoc
[1666/1930] Generating ../../testcorenrn_vecplay/coreneuron_cpu_online/common.hoc
[1667/1930] Generating ../../testcorenrn_vecplay/neuron/common.hoc
[1668/1930] Generating ../../testcorenrn_patstim/coreneuron_cpu_offline/defvar.hoc
[1669/1930] Generating ../../testcorenrn_patstim/coreneuron_cpu_offline/testpatstim.hoc
[1670/1930] Generating ../../testcorenrn_vecplay/neuron/defvar.hoc
[1671/1930] Generating ../../testcorenrn_vecplay/neuron/testvecplay.hoc
[1672/1930] Generating ../../testcorenrn_vecplay/coreneuron_cpu_online/defvar.hoc
[1673/1930] Generating ../../testcorenrn_vecplay/coreneuron_cpu_online/testvecplay.hoc
[1674/1930] Generating ../../testcorenrn_vecplay/coreneuron_cpu_online_psolve_alternate/defvar.hoc
[1675/1930] Generating ../../testcorenrn_vecplay/coreneuron_cpu_online_psolve_alternate/common.hoc
[1676/1930] Generating ../../testcorenrn_vecplay/coreneuron_cpu_online_psolve_alternate/testvecplay.hoc
[1677/1930] Generating ../../testcorenrn_vecevent/neuron/common.hoc
[1678/1930] Generating ../../testcorenrn_vecplay/coreneuron_cpu_offline/common.hoc
[1679/1930] Generating ../../testcorenrn_vecplay/coreneuron_cpu_offline/testvecplay.hoc
[1680/1930] Generating ../../testcorenrn_vecevent/neuron/defvar.hoc
[1681/1930] Generating ../../testcorenrn_vecplay/coreneuron_cpu_offline/defvar.hoc
[1682/1930] Generating ../../testcorenrn_vecevent/neuron/testvecevent.hoc
[1683/1930] Generating ../../testcorenrn_vecevent/coreneuron_cpu_online/common.hoc
[1684/1930] Generating ../../testcorenrn_vecevent/coreneuron_cpu_online/defvar.hoc
[1685/1930] Generating ../../testcorenrn_vecevent/coreneuron_cpu_online_psolve_alternate/common.hoc
[1686/1930] Generating ../../testcorenrn_vecevent/coreneuron_cpu_online_psolve_alternate/defvar.hoc
[1687/1930] Generating ../../testcorenrn_vecevent/coreneuron_cpu_online/testvecevent.hoc
[1688/1930] Generating ../../testcorenrn_vecevent/coreneuron_cpu_online_psolve_alternate/testvecevent.hoc
[1689/1930] Generating ../../testcorenrn_vecevent/coreneuron_cpu_offline/defvar.hoc
[1690/1930] Generating ../../testcorenrn_vecevent/coreneuron_cpu_offline/common.hoc
[1691/1930] Generating ../../testcorenrn_vecevent/coreneuron_cpu_offline/testvecevent.hoc
[1692/1930] Generating ../../testcorenrn_watch/neuron/common.hoc
[1693/1930] Generating ../../testcorenrn_watch/neuron/testwatch.hoc
[1694/1930] Generating ../../testcorenrn_watch/neuron/defvar.hoc
[1695/1930] Generating ../../testcorenrn_watch/coreneuron_cpu_online/common.hoc
[1696/1930] Generating ../../testcorenrn_watch/coreneuron_cpu_online/testwatch.hoc
[1697/1930] Generating ../../testcorenrn_watch/coreneuron_cpu_online/defvar.hoc
[1698/1930] Generating ../../testcorenrn_watch/coreneuron_cpu_online_psolve_alternate/defvar.hoc
[1699/1930] Generating ../../testcorenrn_watch/coreneuron_cpu_online_psolve_alternate/common.hoc
[1700/1930] Generating ../../testcorenrn_watch/coreneuron_cpu_offline/common.hoc
[1701/1930] Generating ../../testcorenrn_watch/coreneuron_cpu_offline/defvar.hoc
[1702/1930] Generating ../../testcorenrn_watch/coreneuron_cpu_offline/testwatch.hoc
[1703/1930] Generating ../../testcorenrn_watch/coreneuron_cpu_online_psolve_alternate/testwatch.hoc
[1704/1930] Generating ../../testcorenrn_netstimdirect/direct_netstimdirect/common.hoc
[1705/1930] Generating ../../testcorenrn_netstimdirect/direct_netstimdirect/defvar.hoc
[1706/1930] Generating ../../testcorenrn_netstimdirect/direct_netstimdirect_psolve_alternate/defvar.hoc
[1707/1930] Generating ../../testcorenrn_netstimdirect/direct_netstimdirect/testnetstimdirect.hoc
[1708/1930] Generating ../../testcorenrn_netstimdirect/direct_netstimdirect_psolve_alternate/common.hoc
[1709/1930] Generating ../../testcorenrn_netstimdirect/direct_netstimdirect_psolve_alternate/testnetstimdirect.hoc
[1710/1930] Building special[-core] for test group coreneuron_modtests
/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7
cfiles =
Mod files: "./axial.mod" "./axial_pp.mod" "./bacur.mod" "./banocur.mod" "./fornetcon.mod" "./green.mod" "./invlfire.mod" "./natrans.mod" "./netmove.mod" "./noisychan.mod" "./red.mod" "./sample.mod" "./unitstest.mod" "./version_macros.mod" "./watchrange.mod" "./watchrange2.mod"
MODOBJS= ./axial.o ./axial_pp.o ./bacur.o ./banocur.o ./fornetcon.o ./green.o ./invlfire.o ./natrans.o ./netmove.o ./noisychan.o ./red.o ./sample.o ./unitstest.o ./version_macros.o ./watchrange.o ./watchrange2.o
[INFO] Running: make -j4 -f /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/coreneuron/nrnivmodl_core_makefile ROOT=/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build MODS_PATH=arm64/corenrn/mod2c BUILD_TYPE=SHARED NRN_PRCELLSTATE=0
Default NMODL flags:
diff: arm64/corenrn/mod2c/_mod_func.cpp: No such file or directory
[NMODL] [warning] :: SYMTAB :: w [Argument] in ForNetcon shadows <argument> definition in NetReceiveBlock
[NMODL] [warning] :: SYMTAB :: w [Argument] in ForNetcon shadows <argument> definition in NetReceiveBlock
[NMODL] [warning] :: SYMTAB :: w [Argument] in ForNetcon shadows <argument> definition in NetReceiveBlock
[NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shadows <extern_neuron_var> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shadows <extern_neuron_var> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shadows <extern_neuron_var> definition in NMODL_GLOBAL
[NMODL] [warning] :: CVode solver of icur in 64.20-30 replaced with cnexp solver
ld: warning: -undefined dynamic_lookup may not work with chained fixups
=> Binary creating arm64/special-core
[INFO] MOD files built successfully for CoreNEURON
-> Compiling mod_func.cpp
-> NMODL .././axial.mod
-> NMODL .././axial_pp.mod
-> NMODL .././bacur.mod
Translating axial.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/axial.cpp
INCLUDEing axial.inc
Translating bacur.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/bacur.cpp
Thread Safe
Translating axial_pp.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/axial_pp.cpp
INCLUDEing axial.inc
Thread Safe
Thread Safe
-> NMODL .././banocur.mod
-> NMODL .././fornetcon.mod
-> NMODL .././green.mod
Translating fornetcon.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/fornetcon.cpp
Thread Safe
Translating green.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/green.cpp
Warning: dt undefined. (declared within VERBATIM?)
-> NMODL .././invlfire.mod
Translating banocur.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/banocur.cpp
Notice: This mechanism cannot be used with CVODE
Thread Safe
Thread Safe
-> NMODL .././natrans.mod
-> NMODL .././netmove.mod
Translating invlfire.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/invlfire.cpp
Thread Safe
-> NMODL .././noisychan.mod
Translating netmove.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/netmove.cpp
Thread Safe
Translating natrans.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/natrans.cpp
-> NMODL .././red.mod
Thread Safe
-> NMODL .././sample.mod
Translating noisychan.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/noisychan.cpp
Thread Safe
Translating red.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/red.cpp
Thread Safe
-> NMODL .././unitstest.mod
-> NMODL .././version_macros.mod
Translating sample.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/sample.cpp
Thread Safe
-> NMODL .././watchrange.mod
Translating version_macros.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/version_macros.cpp
Thread Safe
Translating unitstest.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/unitstest.cpp
Thread Safe
-> NMODL .././watchrange2.mod
Translating watchrange.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/watchrange.cpp
Thread Safe
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/axial.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/axial_pp.cpp
Translating watchrange2.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/watchrange2.cpp
Thread Safe
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/bacur.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/banocur.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/fornetcon.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/green.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/invlfire.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/natrans.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/netmove.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/noisychan.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/red.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/sample.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/unitstest.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/version_macros.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/watchrange.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/watchrange2.cpp
=> LINKING shared library "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/./libnrnmech.dylib"
ld: warning: -undefined dynamic_lookup may not work with chained fixups
=> LINKING executable "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/c35d2f235e0f3860fbecadf05ec8c2b6901bba2525195c69836276a4b5d88ca7/arm64/./special" LDFLAGS are:
Successfully created arm64/special
[1711/1930] Generating coreneuron_modtests/version_macros/test/pytest_coreneuron/test_version_macros.py
[1712/1930] Generating coreneuron_modtests/inputpresyn_py/test/coreneuron/test_inputpresyn.py
[1713/1930] Generating coreneuron_modtests/fornetcon_py_cpu/test/coreneuron/test_fornetcon.py
[1714/1930] Generating coreneuron_modtests/direct_py_cpu/test/coreneuron/test_direct.py
[1715/1930] Generating coreneuron_modtests/direct_hoc_cpu/test/coreneuron/test_direct.hoc
[1716/1930] Generating coreneuron_modtests/spikes_py_cpu/test/coreneuron/test_spikes.py
[1717/1930] Generating coreneuron_modtests/test_units_py_cpu/test/coreneuron/test_units.py
[1718/1930] Generating coreneuron_modtests/datareturn_py_cpu/test/coreneuron/test_datareturn.py
[1719/1930] Generating coreneuron_modtests/spikes_file_mode_py_cpu/test/coreneuron/test_spikes.py
[1720/1930] Generating coreneuron_modtests/test_pointer_py_cpu/test/coreneuron/test_pointer.py
[1721/1930] Generating coreneuron_modtests/fast_imem_py_cpu/test/pytest_coreneuron/test_fast_imem.py
[1722/1930] Generating coreneuron_modtests/test_psolve_py_cpu/test/coreneuron/test_psolve.py
[1723/1930] Generating coreneuron_modtests/test_netmove_py_cpu/test/coreneuron/test_netmove.py
[1724/1930] Generating coreneuron_modtests/test_watchrange_py_cpu/test/coreneuron/test_watchrange.py
[1725/1930] Generating coreneuron_modtests/test_nmodlrandom_py_cpu/test/coreneuron/test_nmodlrandom.py
[1726/1930] Generating coreneuron_modtests/test_ba_py_cpu/test/coreneuron/test_ba.py
[1727/1930] Generating coreneuron_modtests/test_nmodlrandom_syntax_py_cpu/test/coreneuron/test_nmodlrandom_syntax.py
[1728/1930] Generating coreneuron_modtests/test_natrans_py_cpu/test/gjtests/test_natrans.py
[1729/1930] Generating coreneuron_modtests/array_variable_transfer_run_mode_0_py_cpu/test/coreneuron/test_array_variables_transfer.py
[1730/1930] Generating coreneuron_modtests/array_variable_transfer_run_mode_1_py_cpu/test/coreneuron/test_array_variables_transfer.py
[1731/1930] Generating coreneuron_modtests/array_variable_transfer_file_mode_py_cpu/test/coreneuron/test_array_variables_transfer.py
[1732/1930] Generating coreneuron_modtests/array_variable_transfer_run_mode_2_py_cpu/test/coreneuron/test_array_variables_transfer.py
[1733/1930] Generating coreneuron_modtests/spikes_mpi_file_mode_py_cpu/test/coreneuron/test_spikes.py
[1734/1930] Generating coreneuron_modtests/test_subworlds_py_cpu/test/coreneuron/test_subworlds.py
[1735/1930] Building special[-core] for test group example_nmodl
/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2
cfiles =
Mod files: "./argpass.mod" "./cabpump.mod" "./cachan.mod" "./cacum.mod" "./cacur.mod" "./cadif.mod" "./cadifusl.mod" "./cagk.mod" "./cagkftab.mod" "./capmp.mod" "./expsynspine.mod" "./fh.mod" "./fit1.mod" "./gap.mod" "./hh1.mod" "./hhvect.mod" "./inatest.mod" "./ionleak.mod" "./nacum.mod" "./nacur.mod" "./nadifl.mod" "./nonlin.mod" "./obj_ex.mod" "./order.mod" "./passiv.mod" "./rchan.mod" "./stim1.mod" "./str.mod" "./syn1.mod" "./synpre.mod" "./trivial.mod" "./tstdarray.mod" "./tstextrn.mod" "./tstpnt1.mod" "./tstpnt2.mod" "./tstvec.mod" "./vclmp1.mod" "./vlag.mod"
MODOBJS= ./argpass.o ./cabpump.o ./cachan.o ./cacum.o ./cacur.o ./cadif.o ./cadifusl.o ./cagk.o ./cagkftab.o ./capmp.o ./expsynspine.o ./fh.o ./fit1.o ./gap.o ./hh1.o ./hhvect.o ./inatest.o ./ionleak.o ./nacum.o ./nacur.o ./nadifl.o ./nonlin.o ./obj_ex.o ./order.o ./passiv.o ./rchan.o ./stim1.o ./str.o ./syn1.o ./synpre.o ./trivial.o ./tstdarray.o ./tstextrn.o ./tstpnt1.o ./tstpnt2.o ./tstvec.o ./vclmp1.o ./vlag.o
-> Compiling mod_func.cpp
-> NMODL .././argpass.mod
-> NMODL .././cabpump.mod
-> NMODL .././cachan.mod
Translating cabpump.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/cabpump.cpp
Notice: Assignment to the GLOBAL variable, "vol", is not thread safe
-> NMODL .././cacum.mod
Translating argpass.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/argpass.cpp
Notice: VERBATIM blocks are not thread safe
Translating cachan.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/cachan.cpp
-> NMODL .././cacur.mod
Thread Safe
-> NMODL .././cadif.mod
Translating cacum.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/cacum.cpp
Thread Safe
-> NMODL .././cadifusl.mod
Translating cacur.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/cacur.cpp
Thread Safe
Translating cadif.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/cadif.cpp
Thread Safe
-> NMODL .././cagk.mod
-> NMODL .././cagkftab.mod
Translating cadifusl.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/cadifusl.cpp
Translating cagkftab.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/cagkftab.cpp
Notice: Assignment to the GLOBAL variable, "vol", is not thread safe
Translating cagk.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/cagk.cpp
Thread Safe
Thread Safe
-> NMODL .././capmp.mod
-> NMODL .././expsynspine.mod
-> NMODL .././fh.mod
Translating expsynspine.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/expsynspine.cpp
Notice: LINEAR is not thread safe.
-> NMODL .././fit1.mod
Translating capmp.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/capmp.cpp
NEURON's CVode method ignores conservation
Translating fh.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/fh.cpp
Thread Safe
INCLUDEing standard.inc
Notice: Assignment to the GLOBAL variable, "inf", is not thread safe
Notice: Assignment to the GLOBAL variable, "tau", is not thread safe
-> NMODL .././gap.mod
-> NMODL .././hh1.mod
Translating fit1.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/fit1.cpp
Notice: VERBATIM blocks are not thread safe
-> NMODL .././hhvect.mod
Translating hh1.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/hh1.cpp
Notice: This mechanism cannot be used with CVODE
Notice: Assignment to the GLOBAL variable, "hexp", is not thread safe
Notice: Assignment to the GLOBAL variable, "hinf", is not thread safe
Notice: Assignment to the GLOBAL variable, "mexp", is not thread safe
Notice: Assignment to the GLOBAL variable, "minf", is not thread safe
Notice: Assignment to the GLOBAL variable, "nexp", is not thread safe
Notice: Assignment to the GLOBAL variable, "ninf", is not thread safe
Warning: Default 6.3 of PARAMETER celsius will be ignored and set by NEURON.
Warning: Default -77.5 of PARAMETER ek will be ignored and set by NEURON.
Warning: Default 50 of PARAMETER ena will be ignored and set by NEURON.
Translating gap.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/gap.cpp
Notice: Use of POINTER is not thread safe.
-> NMODL .././inatest.mod
-> NMODL .././ionleak.mod
Translating hhvect.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/hhvect.cpp
Notice: This mechanism cannot be used with CVODE
Thread Safe
Warning: Default 6.3 of PARAMETER celsius will be ignored and set by NEURON.
Warning: Default -77.5 of PARAMETER ek will be ignored and set by NEURON.
Warning: Default 50 of PARAMETER ena will be ignored and set by NEURON.
-> NMODL .././nacum.mod
Translating inatest.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/inatest.cpp
Thread Safe
-> NMODL .././nacur.mod
Translating ionleak.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/ionleak.cpp
Thread Safe
-> NMODL .././nadifl.mod
Translating nacur.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/nacur.cpp
Thread Safe
-> NMODL .././nonlin.mod
Translating nadifl.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/nadifl.cpp
Thread Safe
-> NMODL .././obj_ex.mod
Translating nacum.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/nacum.cpp
Thread Safe
-> NMODL .././order.mod
Translating obj_ex.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/obj_ex.cpp
Thread Safe
Translating nonlin.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/nonlin.cpp
Notice: NONLINEAR is not thread safe.
Notice: ARTIFICIAL_CELL is a synonym for POINT_PROCESS which hints that it
only affects and is affected by discrete events. As such it is not
located in a section and is not associated with an integrator
-> NMODL .././passiv.mod
-> NMODL .././rchan.mod
Translating order.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/order.cpp
Thread Safe
-> NMODL .././stim1.mod
Translating passiv.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/passiv.cpp
Thread Safe
-> NMODL .././str.mod
Translating rchan.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/rchan.cpp
Notice: normrand is not thread safe
Notice: This mechanism cannot be used with CVODE
-> NMODL .././syn1.mod
Translating str.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/str.cpp
Notice: VERBATIM blocks are not thread safe
-> NMODL .././synpre.mod
Translating stim1.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/stim1.cpp
Thread Safe
-> NMODL .././trivial.mod
-> NMODL .././tstdarray.mod
Translating synpre.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/synpre.cpp
Notice: Use of POINTER is not thread safe.
Notice: VERBATIM blocks are not thread safe
Notice: This mechanism cannot be used with CVODE
-> NMODL .././tstextrn.mod
Translating trivial.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/trivial.cpp
-> NMODL .././tstpnt1.mod
Translating syn1.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/syn1.cpp
Thread Safe
Translating tstdarray.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/tstdarray.cpp
Thread Safe
-> NMODL .././tstpnt2.mod
-> NMODL .././tstvec.mod
Translating tstpnt2.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/tstpnt2.cpp
Notice: Use of POINTER is not thread safe.
Translating tstvec.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/tstvec.cpp
Notice: VERBATIM blocks are not thread safe
-> NMODL .././vclmp1.mod
-> NMODL .././vlag.mod
Translating tstextrn.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/tstextrn.cpp
Notice: Use of EXTERNAL is not thread safe.
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/argpass.cpp
Translating tstpnt1.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/tstpnt1.cpp
Notice: Use of POINTER is not thread safe.
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/cabpump.cpp
Translating vlag.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/vlag.cpp
Thread Safe
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/cachan.cpp
Translating vclmp1.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/vclmp1.cpp
Notice: VERBATIM blocks are not thread safe
Notice: This mechanism cannot be used with CVODE
Notice: LINEAR is not thread safe.
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/cacum.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/cacur.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/cadif.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/cadifusl.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/cagk.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/cagkftab.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/capmp.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/expsynspine.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/fh.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/fit1.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/gap.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/hh1.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/hhvect.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/inatest.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/ionleak.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/nacum.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/nacur.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/nadifl.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/nonlin.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/obj_ex.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/order.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/passiv.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/rchan.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/stim1.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/str.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/syn1.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/synpre.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/trivial.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/tstdarray.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/tstextrn.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/tstpnt1.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/tstpnt2.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/tstvec.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/vclmp1.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/vlag.cpp
=> LINKING shared library "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/./libnrnmech.dylib"
ld: warning: -undefined dynamic_lookup may not work with chained fixups
=> LINKING executable "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/263a5c542e063ee6760ce51af8be262e1c89db6e16b2211fb308c533e45334f2/arm64/./special" LDFLAGS are:
Successfully created arm64/special
[1736/1930] Generating example_nmodl/ca_ap_hoc/ca_ap.hoc
[1737/1930] Generating example_nmodl/cachan_hoc/cachan.hoc
[1738/1930] Generating example_nmodl/cabpump_hoc/cabpump.hoc
[1739/1930] Generating example_nmodl/cadif_hoc/cadif.hoc
[1740/1930] Generating example_nmodl/cadifusl2_hoc/cadifusl2.hoc
[1741/1930] Generating example_nmodl/cadifusl_hoc/cadifusl.hoc
[1742/1930] Generating example_nmodl/cadifusl1_hoc/cadifusl1.hoc
[1743/1930] Generating example_nmodl/capmp_hoc/capmp.hoc
[1744/1930] Generating example_nmodl/cadif_hoc/cadif.ses
[1745/1930] Generating example_nmodl/cagk_hoc/cagk.hoc
[1746/1930] Generating example_nmodl/cv_hoc/cv.hoc
[1747/1930] Generating example_nmodl/fh_hoc/fh.hoc
[1748/1930] Generating example_nmodl/fit1_hoc/fit1.hoc
[1749/1930] Generating example_nmodl/gap_hoc/gap.hoc
[1750/1930] Generating example_nmodl/hh1_hoc/hh1.hoc
[1751/1930] Generating example_nmodl/hhvect_hoc/hhvect.hoc
[1752/1930] Generating example_nmodl/nacum_hoc/nacum.hoc
[1753/1930] Generating example_nmodl/nadifl1_hoc/nadifl1.hoc
[1754/1930] Generating example_nmodl/nadifl1_hoc/nadifl1.ses
[1755/1930] Generating example_nmodl/nadifl2_hoc/nadifl2.hoc
[1756/1930] Generating example_nmodl/nadifl2_hoc/nadifl2.ses
[1757/1930] Generating example_nmodl/nadifl3_hoc/nadifl3.ses
[1758/1930] Generating example_nmodl/obj_ex_hoc/obj_ex.hoc
[1759/1930] Generating example_nmodl/nadifl3_hoc/nadifl3.hoc
[1760/1930] Generating example_nmodl/nadifl4_hoc/nadifl4.hoc
[1761/1930] Generating example_nmodl/nadifl4_hoc/nadifl4.ses
[1762/1930] Generating example_nmodl/order_hoc/order.hoc
[1763/1930] Generating example_nmodl/stim1_hoc/stim1.hoc
[1764/1930] Generating example_nmodl/passiv_hoc/passiv.hoc
[1765/1930] Generating example_nmodl/syn1_hoc/syn1.hoc
[1766/1930] Generating example_nmodl/synpre_hoc/synpre.hoc
[1767/1930] Generating example_nmodl/tstpnt1_hoc/tstpnt1.hoc
[1768/1930] Generating example_nmodl/tstpnt2_hoc/tstpnt2.hoc
[1769/1930] Generating example_nmodl/expsynspine_py/expsynspine.ses
[1770/1930] Generating example_nmodl/tstextrn_hoc/tstextrn.hoc
[1771/1930] Generating example_nmodl/cagkftab_py/cagkftab.py
[1772/1930] Generating example_nmodl/tstpnt2_py/tstpnt2.py
[1773/1930] Generating example_nmodl/expsynspine_py/expsynspine.py
[1774/1930] Generating example_nmodl/tstvec_hoc/tstvec.hoc
[1775/1930] Generating example_nmodl/nonlin_py/nonlin.py
[1776/1930] Generating example_nmodl/tstpnt1_py/tstpnt1.py
[1777/1930] Generating example_nmodl/vlag_py/vlag.py
[1778/1930] Building special[-core] for test group reduced_dentate
/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead
cfiles =
Mod files: "./Aradi_Ca.mod" "./Aradi_CadepK.mod" "./Aradi_KA.mod" "./Aradi_KDRf.mod" "./Aradi_KDRs.mod" "./Aradi_Na.mod" "./CaBK.mod" "./DGC_M.mod" "./DGC_UK.mod" "./DGC_sAHP.mod" "./Gfluct3.mod" "./LcaMig.mod" "./SH_KIn.mod" "./SH_na8st.mod" "./bgka.mod" "./ccanl.mod" "./ggap.mod" "./gskch.mod" "./holdingi.mod" "./hyperde3.mod" "./ichan2.mod" "./iconc_Ca.mod" "./kcaPR.mod" "./na3n.mod" "./nca.mod" "./spines.mod" "./tca.mod" "./vecevent.mod"
MODOBJS= ./Aradi_Ca.o ./Aradi_CadepK.o ./Aradi_KA.o ./Aradi_KDRf.o ./Aradi_KDRs.o ./Aradi_Na.o ./CaBK.o ./DGC_M.o ./DGC_UK.o ./DGC_sAHP.o ./Gfluct3.o ./LcaMig.o ./SH_KIn.o ./SH_na8st.o ./bgka.o ./ccanl.o ./ggap.o ./gskch.o ./holdingi.o ./hyperde3.o ./ichan2.o ./iconc_Ca.o ./kcaPR.o ./na3n.o ./nca.o ./spines.o ./tca.o ./vecevent.o
[INFO] Running: make -j4 -f /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/share/coreneuron/nrnivmodl_core_makefile ROOT=/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build MODS_PATH=arm64/corenrn/mod2c BUILD_TYPE=SHARED NRN_PRCELLSTATE=0
Default NMODL flags:
diff: arm64/corenrn/mod2c/_mod_func.cpp: No such file or directory
[NMODL] [warning] :: SYMTAB :: k [Argument] in exp1 shadows <ion> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: k [Argument] in exp1 shadows <ion> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: k [Argument] in exp1 shadows <ion> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: k [Argument] in exp1 shadows <ion> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: k [Argument] in exp1 shadows <ion> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: k [Argument] in exp1 shadows <ion> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: cai [Argument] in h2 shadows <assigned_definition read_ion> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: celsius [Argument] in KTF shadows <assigned_definition extern_neuron_var> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: cai [Argument] in h2 shadows <assigned_definition read_ion> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: celsius [Argument] in KTF shadows <assigned_definition extern_neuron_var> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: cai [Argument] in h2 shadows <assigned_definition read_ion> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: celsius [Argument] in KTF shadows <assigned_definition extern_neuron_var> definition in NMODL_GLOBAL
[NMODL] [warning] :: Can not inline function call to mynormrand
[NMODL] [warning] :: Can not inline function call to mynormrand
[NMODL] [warning] :: Can not inline function call to mynormrand
[NMODL] [warning] :: Can not inline function call to mynormrand
[NMODL] [warning] :: SYMTAB :: cai [Argument] in rate shadows <assigned_definition> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: cai [Argument] in rate shadows <assigned_definition> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: cai [Argument] in rate shadows <assigned_definition> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shadows <extern_neuron_var> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shadows <extern_neuron_var> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shadows <extern_neuron_var> definition in NMODL_GLOBAL
[NMODL] [warning] :: CVode solver of icur in 64.20-30 replaced with cnexp solver
[NMODL] [warning] :: SYMTAB :: celsius [Argument] in KTF shadows <assigned_definition extern_neuron_var> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: celsius [Argument] in KTF shadows <assigned_definition extern_neuron_var> definition in NMODL_GLOBAL
[NMODL] [warning] :: SYMTAB :: celsius [Argument] in KTF shadows <assigned_definition extern_neuron_var> definition in NMODL_GLOBAL
ld: warning: -undefined dynamic_lookup may not work with chained fixups
=> Binary creating arm64/special-core
[INFO] MOD files built successfully for CoreNEURON
-> Compiling mod_func.cpp
-> NMODL .././Aradi_Ca.mod
-> NMODL .././Aradi_CadepK.mod
-> NMODL .././Aradi_KA.mod
Translating Aradi_KA.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/Aradi_KA.cpp
Translating Aradi_CadepK.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/Aradi_CadepK.cpp
Thread Safe
Thread Safe
Translating Aradi_Ca.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/Aradi_Ca.cpp
Thread Safe
-> NMODL .././Aradi_KDRf.mod
-> NMODL .././Aradi_KDRs.mod
-> NMODL .././Aradi_Na.mod
Translating Aradi_KDRf.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/Aradi_KDRf.cpp
Thread Safe
Translating Aradi_KDRs.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/Aradi_KDRs.cpp
Thread Safe
Translating Aradi_Na.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/Aradi_Na.cpp
Thread Safe
-> NMODL .././CaBK.mod
-> NMODL .././DGC_M.mod
-> NMODL .././DGC_UK.mod
Translating DGC_M.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/DGC_M.cpp
Translating CaBK.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/CaBK.cpp
Thread Safe
Thread Safe
Translating DGC_UK.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/DGC_UK.cpp
Thread Safe
-> NMODL .././DGC_sAHP.mod
-> NMODL .././Gfluct3.mod
-> NMODL .././LcaMig.mod
Translating DGC_sAHP.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/DGC_sAHP.cpp
Translating Gfluct3.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/Gfluct3.cpp
Thread Safe
Thread Safe
-> NMODL .././SH_KIn.mod
-> NMODL .././SH_na8st.mod
Translating LcaMig.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/LcaMig.cpp
Thread Safe
-> NMODL .././bgka.mod
Translating SH_KIn.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/SH_KIn.cpp
Thread Safe
Translating SH_na8st.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/SH_na8st.cpp
NEURON's CVode method ignores conservation
Thread Safe
-> NMODL .././ccanl.mod
-> NMODL .././ggap.mod
Translating bgka.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/bgka.cpp
Thread Safe
-> NMODL .././gskch.mod
Translating ccanl.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/ccanl.cpp
Thread Safe
-> NMODL .././holdingi.mod
Translating ggap.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/ggap.cpp
Thread Safe
-> NMODL .././hyperde3.mod
-> NMODL .././ichan2.mod
Translating gskch.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/gskch.cpp
Thread Safe
Translating holdingi.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/holdingi.cpp
Thread Safe
-> NMODL .././iconc_Ca.mod
Translating ichan2.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/ichan2.cpp
Translating hyperde3.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/hyperde3.cpp
Thread Safe
Thread Safe
-> NMODL .././kcaPR.mod
-> NMODL .././na3n.mod
-> NMODL .././nca.mod
Translating iconc_Ca.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/iconc_Ca.cpp
Thread Safe
-> NMODL .././spines.mod
Translating na3n.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/na3n.cpp
Thread Safe
Translating nca.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/nca.cpp
Thread Safe
Translating kcaPR.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/kcaPR.cpp
Thread Safe
-> NMODL .././tca.mod
-> NMODL .././vecevent.mod
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/Aradi_Ca.cpp
Translating spines.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/spines.cpp
Thread Safe
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/Aradi_CadepK.cpp
Translating tca.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/tca.cpp
Thread Safe
Translating vecevent.mod into /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/vecevent.cpp
Thread Safe
Notice: ARTIFICIAL_CELL is a synonym for POINT_PROCESS which hints that it
only affects and is affected by discrete events. As such it is not
located in a section and is not associated with an integrator
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/Aradi_KA.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/Aradi_KDRf.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/Aradi_KDRs.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/Aradi_Na.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/CaBK.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/DGC_M.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/DGC_UK.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/DGC_sAHP.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/Gfluct3.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/LcaMig.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/SH_KIn.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/SH_na8st.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/bgka.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/ccanl.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/ggap.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/gskch.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/holdingi.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/hyperde3.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/ichan2.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/iconc_Ca.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/kcaPR.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/na3n.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/nca.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/spines.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/tca.cpp
-> Compiling /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/vecevent.cpp
=> LINKING shared library "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/./libnrnmech.dylib"
ld: warning: -undefined dynamic_lookup may not work with chained fixups
=> LINKING executable "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/test/nrnivmodl/53c432f7080fe7b786e16536f2d17f96d387425d200c645a6b4cec93b5edfead/arm64/./special" LDFLAGS are:
Successfully created arm64/special
[1779/1930] Generating ../../reduced_dentate/neuron/dat/DGC_dendrite_topology.dat
[1780/1930] Generating ../../reduced_dentate/neuron/commonutils.py
[1781/1930] Generating ../../reduced_dentate/neuron/dat/DGC_spine_density.dat
[1782/1930] Generating ../../reduced_dentate/neuron/datasets/Control/AACstim.dat
[1783/1930] Generating ../../reduced_dentate/neuron/dat/DGC_dendrite_points.dat
[1784/1930] Generating ../../reduced_dentate/neuron/dat/axon_st8.dat
[1785/1930] Generating ../../reduced_dentate/neuron/datasets/Control/AACtoMC.dat
[1786/1930] Generating ../../reduced_dentate/neuron/dat/soma_st8.dat
[1787/1930] Generating ../../reduced_dentate/neuron/datasets/Control/AAC.dat
[1788/1930] Generating ../../reduced_dentate/neuron/datasets/Control/AACtoGC.dat
[1789/1930] Generating ../../reduced_dentate/neuron/datasets/Control/BC.dat
[1790/1930] Generating ../../reduced_dentate/neuron/datasets/Control/BCstim.dat
[1791/1930] Generating ../../reduced_dentate/neuron/datasets/Control/BCtoBC.dat
[1792/1930] Generating ../../reduced_dentate/neuron/datasets/Control/BCtoMC.dat
[1793/1930] Generating ../../reduced_dentate/neuron/datasets/Control/GCtoAAC.dat
[1794/1930] Generating ../../reduced_dentate/neuron/datasets/Control/GCstim.dat
[1795/1930] Generating ../../reduced_dentate/neuron/datasets/Control/BCtoGC.dat
[1796/1930] Generating ../../reduced_dentate/neuron/datasets/Control/GC.dat
[1797/1930] Generating ../../reduced_dentate/neuron/datasets/Control/GCtoBC.dat
[1798/1930] Generating ../../reduced_dentate/neuron/datasets/Control/HCtoGC.dat
[1799/1930] Generating ../../reduced_dentate/neuron/datasets/Control/GCtoMC.dat
[1800/1930] Generating ../../reduced_dentate/neuron/datasets/Control/HC.dat
[1801/1930] Generating ../../reduced_dentate/neuron/datasets/Control/HCtoMC.dat
[1802/1930] Generating ../../reduced_dentate/neuron/datasets/Control/HCstim.dat
[1803/1930] Generating ../../reduced_dentate/neuron/datasets/Control/HCtoHC.dat
[1804/1930] Generating ../../reduced_dentate/neuron/datasets/Control/HCtoNGFC.dat
[1805/1930] Generating ../../reduced_dentate/neuron/datasets/Control/MC.dat
[1806/1930] Generating ../../reduced_dentate/neuron/datasets/Control/MCtoAAC.dat
[1807/1930] Generating ../../reduced_dentate/neuron/datasets/Control/MCstim.dat
[1808/1930] Generating ../../reduced_dentate/neuron/datasets/Control/MCtoMC.dat
[1809/1930] Generating ../../reduced_dentate/neuron/datasets/Control/MCtoGC.dat
[1810/1930] Generating ../../reduced_dentate/neuron/datasets/Control/MCtoHC.dat
[1811/1930] Generating ../../reduced_dentate/neuron/datasets/Control/MCtoBC.dat
[1812/1930] Generating ../../reduced_dentate/neuron/datasets/Control/MPP.dat
[1813/1930] Generating ../../reduced_dentate/neuron/datasets/Control/NGFCstim.dat
[1814/1930] Generating ../../reduced_dentate/neuron/datasets/Control/MPP/MPPspiketrain.dat
[1815/1930] Generating ../../reduced_dentate/neuron/datasets/Control/MPPtoGC.dat
[1816/1930] Generating ../../reduced_dentate/neuron/datasets/Control/NGFC.dat
[1817/1930] Generating ../../reduced_dentate/neuron/datasets/Control/NGFCtoAAC.dat
[1818/1930] Generating ../../reduced_dentate/neuron/datasets/Control/NGFCtoBC.dat
[1819/1930] Generating ../../reduced_dentate/neuron/datasets/Control/NGFCtoNGFC.dat
[1820/1930] Generating ../../reduced_dentate/neuron/datasets/Control/celltypes.dat
[1821/1930] Generating ../../reduced_dentate/neuron/datasets/Control/NGFCtoGC.dat
[1822/1930] Generating ../../reduced_dentate/neuron/datasets/Control/gapjunctions.dat
[1823/1930] Generating ../../reduced_dentate/neuron/datasets/Control/gjBCtoBC.dat
[1824/1930] Generating ../../reduced_dentate/neuron/datasets/Control/connectivity.dat
[1825/1930] Generating ../../reduced_dentate/neuron/datasets/Control/gjHCtoHC.dat
[1826/1930] Generating ../../reduced_dentate/neuron/datasets/Control/gjNGFCtoNGFC.dat
[1827/1930] Generating ../../reduced_dentate/neuron/datasets/Control/stim.dat
[1828/1930] Generating ../../reduced_dentate/neuron/datasets/Control/syncomp.dat
[1829/1930] Generating ../../reduced_dentate/neuron/datasets/Control/syndecay.dat
[1830/1930] Generating ../../reduced_dentate/neuron/datasets/Control/synrise.dat
[1831/1930] Generating ../../reduced_dentate/neuron/datasets/Control/syndend.dat
[1832/1930] Generating ../../reduced_dentate/neuron/lib.hoc
[1833/1930] Generating ../../reduced_dentate/neuron/parameters/Control.hoc
[1834/1930] Generating ../../reduced_dentate/neuron/run.hoc
[1835/1930] Generating ../../reduced_dentate/neuron/datasets/Control/synerev.dat
[1836/1930] Generating ../../reduced_dentate/neuron/datasets/Control/synweight.dat
[1837/1930] Generating ../../reduced_dentate/neuron/main.hoc
[1838/1930] Generating ../../reduced_dentate/neuron/templates/BasketCell.hoc
[1839/1930] Generating ../../reduced_dentate/neuron/templates/AxoAxonicCell.hoc
[1840/1930] Generating ../../reduced_dentate/neuron/templates/DGC.hoc
[1841/1930] Generating ../../reduced_dentate/neuron/templates/DGC_Morphology_from_file_na8st.hoc
[1842/1930] Generating ../../reduced_dentate/neuron/templates/DGC_Biophysics_passive_na8st.hoc
[1843/1930] Generating ../../reduced_dentate/neuron/templates/HICAPCell.hoc
[1844/1930] Generating ../../reduced_dentate/neuron/templates/DGC_Parameters_passive_na8st.hoc
[1845/1930] Generating ../../reduced_dentate/neuron/templates/DGC_Synapses.hoc
[1846/1930] Generating ../../reduced_dentate/neuron/templates/Dict.hoc
[1847/1930] Generating ../../reduced_dentate/neuron/templates/HIPPCell.hoc
[1848/1930] Generating ../../reduced_dentate/neuron/templates/MPPCell.hoc
[1849/1930] Generating ../../reduced_dentate/neuron/templates/MossyCell.hoc
[1850/1930] Generating ../../reduced_dentate/neuron/templates/NGFCell.hoc
[1851/1930] Generating ../../reduced_dentate/neuron/templates/StimCell.hoc
[1852/1930] Generating ../../reduced_dentate/neuron/templates/defvar.hoc
[1853/1930] Generating ../../reduced_dentate/neuron/templates/Value.hoc
[1854/1930] Generating ../../reduced_dentate/neuron/templates/ranstream.hoc
[1855/1930] Generating ../../reduced_dentate/coreneuron_cpu/commonutils.py
[1856/1930] Generating ../../reduced_dentate/coreneuron_cpu/dat/DGC_dendrite_topology.dat
[1857/1930] Generating ../../reduced_dentate/coreneuron_cpu/dat/DGC_spine_density.dat
[1858/1930] Generating ../../reduced_dentate/coreneuron_cpu/dat/DGC_dendrite_points.dat
[1859/1930] Generating ../../reduced_dentate/coreneuron_cpu/dat/axon_st8.dat
[1860/1930] Generating ../../reduced_dentate/coreneuron_cpu/dat/soma_st8.dat
[1861/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/AAC.dat
[1862/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/AACstim.dat
[1863/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/AACtoGC.dat
[1864/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/BC.dat
[1865/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/AACtoMC.dat
[1866/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/BCstim.dat
[1867/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/GC.dat
[1868/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/BCtoBC.dat
[1869/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/BCtoGC.dat
[1870/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/BCtoMC.dat
[1871/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/GCstim.dat
[1872/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/GCtoBC.dat
[1873/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/GCtoAAC.dat
[1874/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/HC.dat
[1875/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/GCtoMC.dat
[1876/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/HCtoGC.dat
[1877/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/HCstim.dat
[1878/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/HCtoHC.dat
[1879/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/HCtoMC.dat
[1880/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/MCstim.dat
[1881/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/MC.dat
[1882/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/MCtoBC.dat
[1883/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/MCtoGC.dat
[1884/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/MCtoAAC.dat
[1885/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/HCtoNGFC.dat
[1886/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/MPP.dat
[1887/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/MPPtoGC.dat
[1888/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/MCtoHC.dat
[1889/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/MCtoMC.dat
[1890/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/NGFC.dat
[1891/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/MPP/MPPspiketrain.dat
[1892/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/NGFCtoBC.dat
[1893/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/NGFCtoAAC.dat
[1894/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/NGFCstim.dat
[1895/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/NGFCtoGC.dat
[1896/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/connectivity.dat
[1897/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/celltypes.dat
[1898/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/gjBCtoBC.dat
[1899/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/NGFCtoNGFC.dat
[1900/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/gapjunctions.dat
[1901/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/stim.dat
[1902/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/gjNGFCtoNGFC.dat
[1903/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/syndecay.dat
[1904/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/gjHCtoHC.dat
[1905/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/syndend.dat
[1906/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/syncomp.dat
[1907/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/synerev.dat
[1908/1930] Generating ../../reduced_dentate/coreneuron_cpu/lib.hoc
[1909/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/synrise.dat
[1910/1930] Generating ../../reduced_dentate/coreneuron_cpu/run.hoc
[1911/1930] Generating ../../reduced_dentate/coreneuron_cpu/templates/BasketCell.hoc
[1912/1930] Generating ../../reduced_dentate/coreneuron_cpu/datasets/Control/synweight.dat
[1913/1930] Generating ../../reduced_dentate/coreneuron_cpu/main.hoc
[1914/1930] Generating ../../reduced_dentate/coreneuron_cpu/parameters/Control.hoc
[1915/1930] Generating ../../reduced_dentate/coreneuron_cpu/templates/AxoAxonicCell.hoc
[1916/1930] Generating ../../reduced_dentate/coreneuron_cpu/templates/DGC.hoc
[1917/1930] Generating ../../reduced_dentate/coreneuron_cpu/templates/DGC_Biophysics_passive_na8st.hoc
[1918/1930] Generating ../../reduced_dentate/coreneuron_cpu/templates/DGC_Morphology_from_file_na8st.hoc
[1919/1930] Generating ../../reduced_dentate/coreneuron_cpu/templates/HICAPCell.hoc
[1920/1930] Generating ../../reduced_dentate/coreneuron_cpu/templates/DGC_Parameters_passive_na8st.hoc
[1921/1930] Generating ../../reduced_dentate/coreneuron_cpu/templates/DGC_Synapses.hoc
[1922/1930] Generating ../../reduced_dentate/coreneuron_cpu/templates/HIPPCell.hoc
[1923/1930] Generating ../../reduced_dentate/coreneuron_cpu/templates/Dict.hoc
[1924/1930] Generating ../../reduced_dentate/coreneuron_cpu/templates/MPPCell.hoc
[1925/1930] Generating ../../reduced_dentate/coreneuron_cpu/templates/StimCell.hoc
[1926/1930] Generating ../../reduced_dentate/coreneuron_cpu/templates/NGFCell.hoc
[1927/1930] Generating ../../reduced_dentate/coreneuron_cpu/templates/Value.hoc
[1928/1930] Generating ../../reduced_dentate/coreneuron_cpu/templates/MossyCell.hoc
[1929/1930] Generating ../../reduced_dentate/coreneuron_cpu/templates/ranstream.hoc
[1930/1930] Generating ../../reduced_dentate/coreneuron_cpu/templates/defvar.hoc
$ ccache -vs 2>/dev/null
Cache directory: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/ccache
Config file: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/ccache/ccache.conf
System config file: /opt/homebrew/Cellar/ccache/4.9/etc/ccache.conf
Stats updated: Mon Jun 17 22:15:05 2024
Cacheable calls: 626 / 626 (100.0%)
Hits: 2 / 626 ( 0.32%)
Direct: 1 / 2 (50.00%)
Preprocessed: 1 / 2 (50.00%)
Misses: 624 / 626 (99.68%)
Successful lookups:
Direct: 1 / 626 ( 0.16%)
Preprocessed: 1 / 625 ( 0.16%)
Local storage:
Cache size (GiB): 0.3 / 5.0 ( 6.51%)
Files: 3552
Hits: 2 / 626 ( 0.32%)
Misses: 624 / 626 (99.68%)
Reads: 1252
Writes: 1184
$ echo $'[install]\nprefix='>src/nrnpython/setup.cfg
$ cat src/nrnpython/setup.cfg
[install]
prefix=
$ ctest --output-on-failure
Test project /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build
Start 241: external_ringtest::coreneuron_cpu_mpi_offline::preparation
Start 251: testcorenrn_bbcore::coreneuron_cpu_offline::preparation
1/304 Test #251: testcorenrn_bbcore::coreneuron_cpu_offline::preparation .................. Passed 1.53 sec
Start 257: testcorenrn_conc::coreneuron_cpu_offline::preparation
2/304 Test #257: testcorenrn_conc::coreneuron_cpu_offline::preparation .................... Passed 0.23 sec
Start 263: testcorenrn_deriv::coreneuron_cpu_offline::preparation
3/304 Test #263: testcorenrn_deriv::coreneuron_cpu_offline::preparation ................... Passed 0.23 sec
Start 275: testcorenrn_kin::coreneuron_cpu_offline::preparation
4/304 Test #241: external_ringtest::coreneuron_cpu_mpi_offline::preparation ............... Passed 2.06 sec
Start 269: testcorenrn_gf::coreneuron_cpu_offline::preparation
5/304 Test #275: testcorenrn_kin::coreneuron_cpu_offline::preparation ..................... Passed 0.23 sec
Start 159: pyinit::nrniv_py3.10_python_check_sys_path::preparation
6/304 Test #159: pyinit::nrniv_py3.10_python_check_sys_path::preparation .................. Passed 0.02 sec
Start 161: pyinit::nrniv_py3.10_nrnpython_check_sys_path::preparation
7/304 Test #161: pyinit::nrniv_py3.10_nrnpython_check_sys_path::preparation ............... Passed 0.02 sec
Start 163: pyinit::nrniv_py3.10_python_check_sys_prefix::preparation
8/304 Test #163: pyinit::nrniv_py3.10_python_check_sys_prefix::preparation ................ Passed 0.02 sec
Start 165: pyinit::nrniv_py3.10_nrnpython_check_sys_prefix::preparation
9/304 Test #269: testcorenrn_gf::coreneuron_cpu_offline::preparation ...................... Passed 0.25 sec
Start 280: testcorenrn_patstim::coreneuron_cpu_offline::preparation
10/304 Test #165: pyinit::nrniv_py3.10_nrnpython_check_sys_prefix::preparation ............. Passed 0.02 sec
Start 167: pyinit::nrniv_py3.10_python_check_sys_exec_prefix::preparation
11/304 Test #167: pyinit::nrniv_py3.10_python_check_sys_exec_prefix::preparation ........... Passed 0.02 sec
Start 169: pyinit::nrniv_py3.10_nrnpython_check_sys_exec_prefix::preparation
12/304 Test #169: pyinit::nrniv_py3.10_nrnpython_check_sys_exec_prefix::preparation ........ Passed 0.02 sec
Start 171: pyinit::nrniv_py3.10_python_check_sys_base_prefix::preparation
13/304 Test #171: pyinit::nrniv_py3.10_python_check_sys_base_prefix::preparation ........... Passed 0.02 sec
Start 173: pyinit::nrniv_py3.10_nrnpython_check_sys_base_prefix::preparation
14/304 Test #173: pyinit::nrniv_py3.10_nrnpython_check_sys_base_prefix::preparation ........ Passed 0.02 sec
Start 175: pyinit::nrniv_py3.10_python_check_sys_base_exec_prefix::preparation
15/304 Test #175: pyinit::nrniv_py3.10_python_check_sys_base_exec_prefix::preparation ...... Passed 0.02 sec
Start 177: pyinit::nrniv_py3.10_nrnpython_check_sys_base_exec_prefix::preparation
16/304 Test #177: pyinit::nrniv_py3.10_nrnpython_check_sys_base_exec_prefix::preparation ... Passed 0.02 sec
Start 179: pyinit::nrniv_py3.10_python_check_sys_stderr.encoding::preparation
17/304 Test #179: pyinit::nrniv_py3.10_python_check_sys_stderr.encoding::preparation ....... Passed 0.02 sec
Start 181: pyinit::nrniv_py3.10_nrnpython_check_sys_stderr.encoding::preparation
18/304 Test #181: pyinit::nrniv_py3.10_nrnpython_check_sys_stderr.encoding::preparation .... Passed 0.02 sec
Start 183: pyinit::nrniv_py3.10_python_check_sys_stdin.encoding::preparation
19/304 Test #183: pyinit::nrniv_py3.10_python_check_sys_stdin.encoding::preparation ........ Passed 0.02 sec
Start 185: pyinit::nrniv_py3.10_nrnpython_check_sys_stdin.encoding::preparation
20/304 Test #185: pyinit::nrniv_py3.10_nrnpython_check_sys_stdin.encoding::preparation ..... Passed 0.02 sec
Start 187: pyinit::nrniv_py3.10_python_check_sys_stdout.encoding::preparation
21/304 Test #187: pyinit::nrniv_py3.10_python_check_sys_stdout.encoding::preparation ....... Passed 0.02 sec
Start 189: pyinit::nrniv_py3.10_nrnpython_check_sys_stdout.encoding::preparation
22/304 Test #189: pyinit::nrniv_py3.10_nrnpython_check_sys_stdout.encoding::preparation .... Passed 0.02 sec
Start 195: pyinit::nrniv_pydef_python_check_sys_path::preparation
23/304 Test #280: testcorenrn_patstim::coreneuron_cpu_offline::preparation ................. Passed 0.28 sec
Start 286: testcorenrn_vecplay::coreneuron_cpu_offline::preparation
24/304 Test #195: pyinit::nrniv_pydef_python_check_sys_path::preparation ................... Passed 0.02 sec
Start 197: pyinit::nrniv_pydef_nrnpython_check_sys_path::preparation
25/304 Test #197: pyinit::nrniv_pydef_nrnpython_check_sys_path::preparation ................ Passed 0.02 sec
Start 199: pyinit::nrniv_pydef_python_check_sys_prefix::preparation
26/304 Test #199: pyinit::nrniv_pydef_python_check_sys_prefix::preparation ................. Passed 0.02 sec
Start 201: pyinit::nrniv_pydef_nrnpython_check_sys_prefix::preparation
27/304 Test #201: pyinit::nrniv_pydef_nrnpython_check_sys_prefix::preparation .............. Passed 0.02 sec
Start 203: pyinit::nrniv_pydef_python_check_sys_exec_prefix::preparation
28/304 Test #203: pyinit::nrniv_pydef_python_check_sys_exec_prefix::preparation ............ Passed 0.02 sec
Start 205: pyinit::nrniv_pydef_nrnpython_check_sys_exec_prefix::preparation
29/304 Test #205: pyinit::nrniv_pydef_nrnpython_check_sys_exec_prefix::preparation ......... Passed 0.02 sec
Start 207: pyinit::nrniv_pydef_python_check_sys_base_prefix::preparation
30/304 Test #207: pyinit::nrniv_pydef_python_check_sys_base_prefix::preparation ............ Passed 0.02 sec
Start 209: pyinit::nrniv_pydef_nrnpython_check_sys_base_prefix::preparation
31/304 Test #209: pyinit::nrniv_pydef_nrnpython_check_sys_base_prefix::preparation ......... Passed 0.02 sec
Start 211: pyinit::nrniv_pydef_python_check_sys_base_exec_prefix::preparation
32/304 Test #211: pyinit::nrniv_pydef_python_check_sys_base_exec_prefix::preparation ....... Passed 0.02 sec
Start 213: pyinit::nrniv_pydef_nrnpython_check_sys_base_exec_prefix::preparation
33/304 Test #213: pyinit::nrniv_pydef_nrnpython_check_sys_base_exec_prefix::preparation .... Passed 0.02 sec
Start 215: pyinit::nrniv_pydef_python_check_sys_stderr.encoding::preparation
34/304 Test #215: pyinit::nrniv_pydef_python_check_sys_stderr.encoding::preparation ........ Passed 0.02 sec
Start 217: pyinit::nrniv_pydef_nrnpython_check_sys_stderr.encoding::preparation
35/304 Test #286: testcorenrn_vecplay::coreneuron_cpu_offline::preparation ................. Passed 0.24 sec
Start 298: testcorenrn_watch::coreneuron_cpu_offline::preparation
36/304 Test #217: pyinit::nrniv_pydef_nrnpython_check_sys_stderr.encoding::preparation ..... Passed 0.02 sec
Start 219: pyinit::nrniv_pydef_python_check_sys_stdin.encoding::preparation
37/304 Test #219: pyinit::nrniv_pydef_python_check_sys_stdin.encoding::preparation ......... Passed 0.02 sec
Start 221: pyinit::nrniv_pydef_nrnpython_check_sys_stdin.encoding::preparation
38/304 Test #221: pyinit::nrniv_pydef_nrnpython_check_sys_stdin.encoding::preparation ...... Passed 0.02 sec
Start 223: pyinit::nrniv_pydef_python_check_sys_stdout.encoding::preparation
39/304 Test #223: pyinit::nrniv_pydef_python_check_sys_stdout.encoding::preparation ........ Passed 0.02 sec
Start 225: pyinit::nrniv_pydef_nrnpython_check_sys_stdout.encoding::preparation
40/304 Test #225: pyinit::nrniv_pydef_nrnpython_check_sys_stdout.encoding::preparation ..... Passed 0.02 sec
Start 233: external_ringtest::neuron
41/304 Test #298: testcorenrn_watch::coreneuron_cpu_offline::preparation ................... Passed 0.23 sec
Start 234: external_ringtest::neuron_mpi
42/304 Test #234: external_ringtest::neuron_mpi ............................................ Passed 8.54 sec
Start 235: external_ringtest::neuron_mpi_python
43/304 Test #233: external_ringtest::neuron ................................................ Passed 16.32 sec
Start 247: testcorenrn_bbcore::neuron
44/304 Test #247: testcorenrn_bbcore::neuron ............................................... Passed 0.24 sec
Start 248: testcorenrn_bbcore::coreneuron_cpu_online
45/304 Test #248: testcorenrn_bbcore::coreneuron_cpu_online ................................ Passed 0.51 sec
Start 249: testcorenrn_bbcore::coreneuron_cpu_online_psolve_alternate
46/304 Test #235: external_ringtest::neuron_mpi_python ..................................... Passed 8.89 sec
Start 237: external_ringtest::coreneuron_cpu_mpi_offline_saverestore
47/304 Test #249: testcorenrn_bbcore::coreneuron_cpu_online_psolve_alternate ............... Passed 0.59 sec
Start 250: testcorenrn_bbcore::coreneuron_cpu_offline
48/304 Test #250: testcorenrn_bbcore::coreneuron_cpu_offline ............................... Passed 0.30 sec
Start 253: testcorenrn_conc::neuron
49/304 Test #253: testcorenrn_conc::neuron ................................................. Passed 0.28 sec
Start 254: testcorenrn_conc::coreneuron_cpu_online
50/304 Test #254: testcorenrn_conc::coreneuron_cpu_online .................................. Passed 0.50 sec
Start 255: testcorenrn_conc::coreneuron_cpu_online_psolve_alternate
51/304 Test #255: testcorenrn_conc::coreneuron_cpu_online_psolve_alternate ................. Passed 0.56 sec
Start 256: testcorenrn_conc::coreneuron_cpu_offline
52/304 Test #256: testcorenrn_conc::coreneuron_cpu_offline ................................. Passed 0.17 sec
Start 259: testcorenrn_deriv::neuron
53/304 Test #237: external_ringtest::coreneuron_cpu_mpi_offline_saverestore ................ Passed 2.03 sec
Start 238: external_ringtest::coreneuron_cpu_mpi
54/304 Test #259: testcorenrn_deriv::neuron ................................................ Passed 0.26 sec
Start 260: testcorenrn_deriv::coreneuron_cpu_online
55/304 Test #260: testcorenrn_deriv::coreneuron_cpu_online ................................. Passed 0.52 sec
Start 261: testcorenrn_deriv::coreneuron_cpu_online_psolve_alternate
56/304 Test #261: testcorenrn_deriv::coreneuron_cpu_online_psolve_alternate ................ Passed 0.54 sec
Start 262: testcorenrn_deriv::coreneuron_cpu_offline
57/304 Test #238: external_ringtest::coreneuron_cpu_mpi .................................... Passed 1.33 sec
Start 239: external_ringtest::coreneuron_cpu_mpi_python
58/304 Test #262: testcorenrn_deriv::coreneuron_cpu_offline ................................ Passed 0.19 sec
Start 271: testcorenrn_kin::neuron
59/304 Test #271: testcorenrn_kin::neuron .................................................. Passed 0.32 sec
Start 272: testcorenrn_kin::coreneuron_cpu_online
60/304 Test #272: testcorenrn_kin::coreneuron_cpu_online ................................... Passed 0.62 sec
Start 273: testcorenrn_kin::coreneuron_cpu_online_psolve_alternate
61/304 Test #273: testcorenrn_kin::coreneuron_cpu_online_psolve_alternate .................. Passed 0.54 sec
Start 274: testcorenrn_kin::coreneuron_cpu_offline
62/304 Test #239: external_ringtest::coreneuron_cpu_mpi_python ............................. Passed 1.62 sec
Start 240: external_ringtest::coreneuron_cpu_mpi_offline
63/304 Test #274: testcorenrn_kin::coreneuron_cpu_offline .................................. Passed 0.19 sec
Start 1: cmd_interface_test
64/304 Test #1: cmd_interface_test ....................................................... Passed 0.46 sec
Start 2: interleave_info_constructor_test
65/304 Test #2: interleave_info_constructor_test ......................................... Passed 0.22 sec
Start 3: alignment_test
66/304 Test #240: external_ringtest::coreneuron_cpu_mpi_offline ............................ Passed 0.81 sec
Start 244: external_ringtest::coreneuron_mpi_registermapping_directmode
67/304 Test #3: alignment_test ........................................................... Passed 0.23 sec
Start 4: queuing_test
68/304 Test #4: queuing_test ............................................................. Passed 0.28 sec
Start 5: test-solver
69/304 Test #5: test-solver .............................................................. Passed 0.32 sec
Start 6: random_test
70/304 Test #6: random_test .............................................................. Passed 0.24 sec
Start 7: lfp_test
71/304 Test #7: lfp_test ................................................................. Passed 0.28 sec
Start 8: unit_tests::testneuron
72/304 Test #8: unit_tests::testneuron ................................................... Passed 0.29 sec
Start 9: unit_tests::testneuron_soa_erase_calls_terminate
73/304 Test #244: external_ringtest::coreneuron_mpi_registermapping_directmode ............. Passed 1.63 sec
Start 245: external_ringtest::coreneuron_mpi_registermapping_filemode
74/304 Test #9: unit_tests::testneuron_soa_erase_calls_terminate ......................... Passed 0.10 sec
Start 10: ringtest
75/304 Test #10: ringtest ................................................................. Passed 0.83 sec
Start 11: connect_dend
76/304 Test #11: connect_dend ............................................................. Passed 0.16 sec
Start 12: mpi_init::nrniv_mpiopt
77/304 Test #12: mpi_init::nrniv_mpiopt ................................................... Passed 0.18 sec
Start 13: mpi_init::nrniv_nrnmpi_init
78/304 Test #13: mpi_init::nrniv_nrnmpi_init .............................................. Passed 0.18 sec
Start 14: mpi_init::python_nrnmpi_init
79/304 Test #245: external_ringtest::coreneuron_mpi_registermapping_filemode ............... Passed 1.73 sec
Start 265: testcorenrn_gf::neuron
80/304 Test #14: mpi_init::python_nrnmpi_init ............................................. Passed 0.62 sec
Start 15: mpi_init::python_mpienv
81/304 Test #15: mpi_init::python_mpienv .................................................. Passed 0.58 sec
Start 16: mpi_init::nrniv_mpiexec_mpiopt
82/304 Test #16: mpi_init::nrniv_mpiexec_mpiopt ........................................... Passed 0.17 sec
Start 17: mpi_init::nrniv_mpiexec_nrnmpi_init
83/304 Test #17: mpi_init::nrniv_mpiexec_nrnmpi_init ...................................... Passed 0.18 sec
Start 18: mpi_init::python_mpiexec_nrnmpi_init
84/304 Test #18: mpi_init::python_mpiexec_nrnmpi_init ..................................... Passed 0.66 sec
Start 19: mpi_init::python_mpiexec_mpienv
85/304 Test #265: testcorenrn_gf::neuron ................................................... Passed 2.50 sec
Start 266: testcorenrn_gf::coreneuron_cpu_online
86/304 Test #19: mpi_init::python_mpiexec_mpienv .......................................... Passed 0.64 sec
Start 20: unit_tests::python_unit_tests
87/304 Test #266: testcorenrn_gf::coreneuron_cpu_online .................................... Passed 0.79 sec
Start 267: testcorenrn_gf::coreneuron_cpu_online_psolve_alternate
88/304 Test #20: unit_tests::python_unit_tests ............................................ Passed 0.88 sec
Start 21: pytest::basic_tests_py3.10
89/304 Test #21: pytest::basic_tests_py3.10 ............................................... Passed 0.89 sec
Start 22: pytest_coreneuron::basic_tests_py3.10
90/304 Test #267: testcorenrn_gf::coreneuron_cpu_online_psolve_alternate ................... Passed 2.19 sec
Start 268: testcorenrn_gf::coreneuron_cpu_offline
91/304 Test #268: testcorenrn_gf::coreneuron_cpu_offline ................................... Passed 0.31 sec
Start 277: testcorenrn_patstim::neuron
92/304 Test #277: testcorenrn_patstim::neuron .............................................. Passed 0.48 sec
Start 278: testcorenrn_patstim::coreneuron_cpu_offline_saverestore
93/304 Test #278: testcorenrn_patstim::coreneuron_cpu_offline_saverestore .................. Passed 0.63 sec
Start 279: testcorenrn_patstim::coreneuron_cpu_offline
94/304 Test #279: testcorenrn_patstim::coreneuron_cpu_offline .............................. Passed 0.19 sec
Start 282: testcorenrn_vecplay::neuron
95/304 Test #282: testcorenrn_vecplay::neuron .............................................. Passed 0.29 sec
Start 283: testcorenrn_vecplay::coreneuron_cpu_online
96/304 Test #283: testcorenrn_vecplay::coreneuron_cpu_online ............................... Passed 0.55 sec
Start 284: testcorenrn_vecplay::coreneuron_cpu_online_psolve_alternate
97/304 Test #284: testcorenrn_vecplay::coreneuron_cpu_online_psolve_alternate .............. Passed 0.64 sec
Start 285: testcorenrn_vecplay::coreneuron_cpu_offline
98/304 Test #285: testcorenrn_vecplay::coreneuron_cpu_offline .............................. Passed 0.20 sec
Start 294: testcorenrn_watch::neuron
99/304 Test #22: pytest_coreneuron::basic_tests_py3.10 .................................... Passed 4.55 sec
Start 23: datahandle::datahandle_tests
100/304 Test #294: testcorenrn_watch::neuron ................................................ Passed 0.38 sec
Start 295: testcorenrn_watch::coreneuron_cpu_online
101/304 Test #23: datahandle::datahandle_tests ............................................. Passed 0.77 sec
Start 24: coverage_tests::cover_tests
102/304 Test #295: testcorenrn_watch::coreneuron_cpu_online ................................. Passed 0.68 sec
Start 296: testcorenrn_watch::coreneuron_cpu_online_psolve_alternate
103/304 Test #24: coverage_tests::cover_tests .............................................. Passed 0.99 sec
Start 25: example_nmodl::ca_ap_hoc
104/304 Test #296: testcorenrn_watch::coreneuron_cpu_online_psolve_alternate ................ Passed 0.87 sec
Start 297: testcorenrn_watch::coreneuron_cpu_offline
105/304 Test #297: testcorenrn_watch::coreneuron_cpu_offline ................................ Passed 0.19 sec
Start 300: testcorenrn_netstimdirect::direct_netstimdirect
106/304 Test #25: example_nmodl::ca_ap_hoc ................................................. Passed 0.42 sec
Start 26: example_nmodl::cabpump_hoc
107/304 Test #26: example_nmodl::cabpump_hoc ............................................... Passed 0.40 sec
Start 27: example_nmodl::cachan_hoc
108/304 Test #27: example_nmodl::cachan_hoc ................................................ Passed 0.17 sec
Start 28: example_nmodl::cadif_hoc
109/304 Test #300: testcorenrn_netstimdirect::direct_netstimdirect .......................... Passed 0.78 sec
Start 301: testcorenrn_netstimdirect::direct_netstimdirect_psolve_alternate
110/304 Test #28: example_nmodl::cadif_hoc ................................................. Passed 0.18 sec
Start 29: example_nmodl::cadifusl_hoc
111/304 Test #29: example_nmodl::cadifusl_hoc .............................................. Passed 0.39 sec
Start 30: example_nmodl::cadifusl1_hoc
112/304 Test #30: example_nmodl::cadifusl1_hoc ............................................. Passed 0.33 sec
Start 31: example_nmodl::cadifusl2_hoc
113/304 Test #301: testcorenrn_netstimdirect::direct_netstimdirect_psolve_alternate ......... Passed 0.85 sec
Start 32: example_nmodl::cagk_hoc
Start 33: example_nmodl::capmp_hoc
114/304 Test #32: example_nmodl::cagk_hoc .................................................. Passed 0.15 sec
Start 34: example_nmodl::cv_hoc
115/304 Test #31: example_nmodl::cadifusl2_hoc ............................................. Passed 0.17 sec
Start 35: example_nmodl::fh_hoc
116/304 Test #33: example_nmodl::capmp_hoc ................................................. Passed 0.26 sec
Start 36: example_nmodl::fit1_hoc
117/304 Test #34: example_nmodl::cv_hoc .................................................... Passed 0.14 sec
Start 37: example_nmodl::gap_hoc
118/304 Test #35: example_nmodl::fh_hoc .................................................... Passed 0.14 sec
Start 38: example_nmodl::hh1_hoc
119/304 Test #36: example_nmodl::fit1_hoc .................................................. Passed 0.14 sec
Start 39: example_nmodl::hhvect_hoc
120/304 Test #37: example_nmodl::gap_hoc ................................................... Passed 0.15 sec
Start 40: example_nmodl::nacum_hoc
121/304 Test #38: example_nmodl::hh1_hoc ................................................... Passed 0.14 sec
Start 41: example_nmodl::nadifl1_hoc
122/304 Test #39: example_nmodl::hhvect_hoc ................................................ Passed 0.15 sec
Start 42: example_nmodl::nadifl2_hoc
123/304 Test #40: example_nmodl::nacum_hoc ................................................. Passed 0.14 sec
Start 43: example_nmodl::nadifl3_hoc
124/304 Test #41: example_nmodl::nadifl1_hoc ............................................... Passed 0.16 sec
Start 44: example_nmodl::nadifl4_hoc
125/304 Test #42: example_nmodl::nadifl2_hoc ............................................... Passed 0.18 sec
Start 45: example_nmodl::obj_ex_hoc
126/304 Test #43: example_nmodl::nadifl3_hoc ............................................... Passed 0.17 sec
Start 46: example_nmodl::order_hoc
127/304 Test #44: example_nmodl::nadifl4_hoc ............................................... Passed 0.17 sec
Start 47: example_nmodl::passiv_hoc
128/304 Test #45: example_nmodl::obj_ex_hoc ................................................ Passed 0.14 sec
Start 48: example_nmodl::stim1_hoc
129/304 Test #46: example_nmodl::order_hoc ................................................. Passed 0.17 sec
Start 49: example_nmodl::syn1_hoc
130/304 Test #47: example_nmodl::passiv_hoc ................................................ Passed 0.14 sec
Start 50: example_nmodl::synpre_hoc
131/304 Test #48: example_nmodl::stim1_hoc ................................................. Passed 0.15 sec
Start 51: example_nmodl::tstextrn_hoc
132/304 Test #49: example_nmodl::syn1_hoc .................................................. Passed 0.15 sec
Start 52: example_nmodl::tstpnt1_hoc
133/304 Test #50: example_nmodl::synpre_hoc ................................................ Passed 0.21 sec
Start 53: example_nmodl::tstpnt2_hoc
134/304 Test #51: example_nmodl::tstextrn_hoc .............................................. Passed 0.14 sec
Start 54: example_nmodl::tstvec_hoc
135/304 Test #52: example_nmodl::tstpnt1_hoc ............................................... Passed 0.14 sec
Start 55: example_nmodl::cagkftab_py
136/304 Test #53: example_nmodl::tstpnt2_hoc ............................................... Passed 0.14 sec
Start 56: example_nmodl::expsynspine_py
137/304 Test #54: example_nmodl::tstvec_hoc ................................................ Passed 0.15 sec
Start 57: example_nmodl::nonlin_py
138/304 Test #56: example_nmodl::expsynspine_py ............................................ Passed 0.77 sec
Start 58: example_nmodl::tstpnt1_py
139/304 Test #58: example_nmodl::tstpnt1_py ................................................ Passed 0.52 sec
Start 59: example_nmodl::tstpnt2_py
140/304 Test #59: example_nmodl::tstpnt2_py ................................................ Passed 0.51 sec
Start 60: example_nmodl::vlag_py
141/304 Test #60: example_nmodl::vlag_py ................................................... Passed 0.56 sec
Start 61: hoctests::test_loadbal_hoc
142/304 Test #57: example_nmodl::nonlin_py ................................................. Passed 2.73 sec
Start 62: hoctests::test_random_hoc
143/304 Test #61: hoctests::test_loadbal_hoc ............................................... Passed 0.43 sec
Start 63: hoctests::perf1_hoc
144/304 Test #62: hoctests::test_random_hoc ................................................ Passed 0.14 sec
Start 64: hoctests::test1_hoc
145/304 Test #64: hoctests::test1_hoc ...................................................... Passed 0.36 sec
Start 65: hoctests::test2_hoc
146/304 Test #65: hoctests::test2_hoc ...................................................... Passed 0.21 sec
Start 66: hoctests::test3_hoc
147/304 Test #66: hoctests::test3_hoc ...................................................... Passed 0.16 sec
Start 67: hoctests::test4_hoc
148/304 Test #67: hoctests::test4_hoc ...................................................... Passed 0.13 sec
Start 68: hoctests::test5_hoc
149/304 Test #68: hoctests::test5_hoc ...................................................... Passed 0.13 sec
Start 69: hoctests::test6_hoc
150/304 Test #69: hoctests::test6_hoc ...................................................... Passed 0.13 sec
Start 70: hoctests::test7_hoc
151/304 Test #70: hoctests::test7_hoc ...................................................... Passed 0.13 sec
Start 71: hoctests::test8_hoc
152/304 Test #63: hoctests::perf1_hoc ...................................................... Passed 1.48 sec
Start 72: hoctests::test9_hoc
153/304 Test #71: hoctests::test8_hoc ...................................................... Passed 0.13 sec
Start 73: hoctests::test_bbss_py
154/304 Test #55: example_nmodl::cagkftab_py ............................................... Passed 4.42 sec
Start 74: hoctests::test_cvinterp_py
155/304 Test #72: hoctests::test9_hoc ...................................................... Passed 0.14 sec
Start 75: hoctests::test_hocGUI2_py
156/304 Test #74: hoctests::test_cvinterp_py ............................................... Passed 0.69 sec
Start 76: hoctests::test_hocmech_py
157/304 Test #73: hoctests::test_bbss_py ................................................... Passed 0.83 sec
Start 77: hoctests::test_kschan_py
158/304 Test #75: hoctests::test_hocGUI2_py ................................................ Passed 0.77 sec
Start 78: hoctests::test_legacy_setpointer_py
159/304 Test #76: hoctests::test_hocmech_py ................................................ Passed 0.87 sec
Start 79: hoctests::test_mechfunc_py
160/304 Test #78: hoctests::test_legacy_setpointer_py ...................................... Passed 0.75 sec
Start 80: hoctests::test_mechstd_py
161/304 Test #77: hoctests::test_kschan_py ................................................. Passed 0.93 sec
Start 81: hoctests::test_mode_py
162/304 Test #79: hoctests::test_mechfunc_py ............................................... Passed 0.78 sec
Start 82: hoctests::test_neurondemo_py
163/304 Test #80: hoctests::test_mechstd_py ................................................ Passed 0.83 sec
Start 83: hoctests::test_nrniv-launch_py
164/304 Test #81: hoctests::test_mode_py ................................................... Passed 0.79 sec
Start 84: hoctests::test_optim_node_order_py
165/304 Test #83: hoctests::test_nrniv-launch_py ........................................... Passed 0.42 sec
Start 85: hoctests::test_random_py
166/304 Test #82: hoctests::test_neurondemo_py ............................................. Passed 0.68 sec
Start 86: hoctests::test_setdata_py
167/304 Test #84: hoctests::test_optim_node_order_py ....................................... Passed 1.09 sec
Start 87: hoctests::test_shape_py
168/304 Test #85: hoctests::test_random_py ................................................. Passed 0.82 sec
Start 88: hoctests::test_thread_partition_py
169/304 Test #86: hoctests::test_setdata_py ................................................ Passed 0.70 sec
Start 89: hoctests::test1_py
170/304 Test #87: hoctests::test_shape_py .................................................. Passed 0.84 sec
Start 90: hoctests::test2_py
171/304 Test #89: hoctests::test1_py ....................................................... Passed 0.81 sec
Start 91: hoctests::test9_py
172/304 Test #88: hoctests::test_thread_partition_py ....................................... Passed 0.98 sec
Start 97: coreneuron_standalone::test_nrn_corenrn_standalone
173/304 Test #90: hoctests::test2_py ....................................................... Passed 0.68 sec
Start 98: nmodl_tests::test_table
174/304 Test #91: hoctests::test9_py ....................................................... Passed 0.86 sec
Start 99: nmodl_tests::test_disc
175/304 Test #97: coreneuron_standalone::test_nrn_corenrn_standalone ....................... Passed 1.31 sec
Start 100: nmodl_tests::test_function_table
176/304 Test #98: nmodl_tests::test_table .................................................. Passed 1.14 sec
Start 101: nmodl_tests::test_kinetic
177/304 Test #99: nmodl_tests::test_disc ................................................... Passed 0.88 sec
Start 102: nmodl_tests::test_random
178/304 Test #100: nmodl_tests::test_function_table ......................................... Passed 1.07 sec
Start 103: nmodl_tests::test_path_spaces
179/304 Test #101: nmodl_tests::test_kinetic ................................................ Passed 1.13 sec
Start 104: coreneuron_modtests::version_macros
180/304 Test #102: nmodl_tests::test_random ................................................. Passed 1.15 sec
Start 106: coreneuron_modtests::fornetcon_py_cpu
181/304 Test #103: nmodl_tests::test_path_spaces ............................................ Passed 1.00 sec
Start 107: coreneuron_modtests::direct_py_cpu
182/304 Test #104: coreneuron_modtests::version_macros ...................................... Passed 1.19 sec
Start 108: coreneuron_modtests::direct_hoc_cpu
183/304 Test #106: coreneuron_modtests::fornetcon_py_cpu .................................... Passed 1.20 sec
Start 109: coreneuron_modtests::spikes_py_cpu
184/304 Test #107: coreneuron_modtests::direct_py_cpu ....................................... Passed 1.04 sec
Start 110: coreneuron_modtests::spikes_file_mode_py_cpu
185/304 Test #108: coreneuron_modtests::direct_hoc_cpu ...................................... Passed 0.78 sec
Start 111: coreneuron_modtests::fast_imem_py_cpu
186/304 Test #109: coreneuron_modtests::spikes_py_cpu ....................................... Passed 1.35 sec
Start 112: coreneuron_modtests::datareturn_py_cpu
187/304 Test #110: coreneuron_modtests::spikes_file_mode_py_cpu ............................. Passed 1.15 sec
Start 113: coreneuron_modtests::test_units_py_cpu
188/304 Test #111: coreneuron_modtests::fast_imem_py_cpu .................................... Passed 1.62 sec
Start 114: coreneuron_modtests::test_netmove_py_cpu
189/304 Test #113: coreneuron_modtests::test_units_py_cpu ................................... Passed 0.88 sec
Start 115: coreneuron_modtests::test_pointer_py_cpu
190/304 Test #112: coreneuron_modtests::datareturn_py_cpu ................................... Passed 1.54 sec
Start 116: coreneuron_modtests::test_watchrange_py_cpu
191/304 Test #116: coreneuron_modtests::test_watchrange_py_cpu .............................. Passed 0.89 sec
Start 117: coreneuron_modtests::test_psolve_py_cpu
192/304 Test #114: coreneuron_modtests::test_netmove_py_cpu ................................. Passed 1.51 sec
Start 118: coreneuron_modtests::test_ba_py_cpu
193/304 Test #118: coreneuron_modtests::test_ba_py_cpu ...................................... Passed 0.81 sec
Start 119: coreneuron_modtests::test_nmodlrandom_py_cpu
194/304 Test #117: coreneuron_modtests::test_psolve_py_cpu .................................. Passed 0.97 sec
Start 120: coreneuron_modtests::test_nmodlrandom_syntax_py_cpu
195/304 Test #115: coreneuron_modtests::test_pointer_py_cpu ................................. Passed 3.34 sec
Start 121: coreneuron_modtests::test_natrans_py_cpu
196/304 Test #119: coreneuron_modtests::test_nmodlrandom_py_cpu ............................. Passed 1.36 sec
Start 122: coreneuron_modtests::array_variable_transfer_run_mode_0_py_cpu
197/304 Test #121: coreneuron_modtests::test_natrans_py_cpu ................................. Passed 0.99 sec
Start 123: coreneuron_modtests::array_variable_transfer_run_mode_1_py_cpu
198/304 Test #122: coreneuron_modtests::array_variable_transfer_run_mode_0_py_cpu ........... Passed 1.04 sec
Start 124: coreneuron_modtests::array_variable_transfer_run_mode_2_py_cpu
199/304 Test #123: coreneuron_modtests::array_variable_transfer_run_mode_1_py_cpu ........... Passed 1.09 sec
Start 125: coreneuron_modtests::array_variable_transfer_file_mode_py_cpu
200/304 Test #124: coreneuron_modtests::array_variable_transfer_run_mode_2_py_cpu ........... Passed 1.10 sec
Start 128: nmodl_tests_coreneuron::test_table_coreneuron_cpu
201/304 Test #120: coreneuron_modtests::test_nmodlrandom_syntax_py_cpu ...................... Passed 3.58 sec
Start 129: nmodl_tests_coreneuron::test_disc_coreneuron_cpu
202/304 Test #125: coreneuron_modtests::array_variable_transfer_file_mode_py_cpu ............ Passed 1.22 sec
Start 130: nmodl_tests_coreneuron::test_function_table_coreneuron_cpu
203/304 Test #128: nmodl_tests_coreneuron::test_table_coreneuron_cpu ........................ Passed 1.10 sec
Start 131: nmodl_tests_coreneuron::test_kinetic_coreneuron_cpu
204/304 Test #129: nmodl_tests_coreneuron::test_disc_coreneuron_cpu ......................... Passed 0.99 sec
Start 132: modlunit_unitstest
205/304 Test #132: modlunit_unitstest ....................................................... Passed 0.22 sec
Start 133: modlunit_hh
206/304 Test #133: modlunit_hh .............................................................. Passed 0.09 sec
Start 134: modlunit_stim
207/304 Test #134: modlunit_stim ............................................................ Passed 0.10 sec
Start 135: modlunit_pattern
208/304 Test #135: modlunit_pattern ......................................................... Passed 0.12 sec
Start 136: modlunit_rand
209/304 Test #136: modlunit_rand ............................................................ Passed 0.10 sec
Start 137: api::hh_sim_cpp
210/304 Test #130: nmodl_tests_coreneuron::test_function_table_coreneuron_cpu ............... Passed 0.98 sec
Start 138: api::netcon_cpp
211/304 Test #131: nmodl_tests_coreneuron::test_kinetic_coreneuron_cpu ...................... Passed 0.91 sec
Start 139: api::sections_c
212/304 Test #137: api::hh_sim_cpp .......................................................... Passed 0.25 sec
Start 140: api::vclamp_cpp
213/304 Test #139: api::sections_c .......................................................... Passed 0.25 sec
Start 141: pyinit::nrniv_script.py
214/304 Test #138: api::netcon_cpp .......................................................... Passed 0.38 sec
Start 142: pyinit::nrniv_script.py_error
215/304 Test #141: pyinit::nrniv_script.py .................................................. Passed 0.13 sec
Start 143: pyinit::nrniv_two_scripts.py
216/304 Test #140: api::vclamp_cpp .......................................................... Passed 0.35 sec
Start 144: pyinit::nrniv_two_scripts.py_error_check_code
217/304 Test #142: pyinit::nrniv_script.py_error ............................................ Passed 0.12 sec
Start 145: pyinit::nrniv_two_scripts.py_error_check_output
218/304 Test #143: pyinit::nrniv_two_scripts.py ............................................. Passed 0.13 sec
Start 146: pyinit::nrniv_python_command
219/304 Test #144: pyinit::nrniv_two_scripts.py_error_check_code ............................ Passed 0.12 sec
Start 147: pyinit::nrniv_python_command_error
220/304 Test #145: pyinit::nrniv_two_scripts.py_error_check_output .......................... Passed 0.12 sec
Start 148: pyinit::nrniv_python_script.py
221/304 Test #146: pyinit::nrniv_python_command ............................................. Passed 0.13 sec
Start 149: pyinit::nrniv_python_script.py_error
222/304 Test #147: pyinit::nrniv_python_command_error ....................................... Passed 0.13 sec
Start 150: pyinit::nrniv_python_command_twice
223/304 Test #148: pyinit::nrniv_python_script.py ........................................... Passed 0.13 sec
Start 151: pyinit::nrniv_python_script.py_twice
224/304 Test #149: pyinit::nrniv_python_script.py_error ..................................... Passed 0.13 sec
Start 152: pyinit::nrniv_python_command_args
225/304 Test #150: pyinit::nrniv_python_command_twice ....................................... Passed 0.13 sec
Start 153: pyinit::nrniv_python_script.py_args
226/304 Test #151: pyinit::nrniv_python_script.py_twice ..................................... Passed 0.12 sec
Start 154: pyinit::nrniv_nopython_PythonObject
227/304 Test #154: pyinit::nrniv_nopython_PythonObject ...................................... Passed 0.11 sec
Start 155: pyinit::nrniv_nopython_PythonObject_pyexe
228/304 Test #153: pyinit::nrniv_python_script.py_args ...................................... Passed 0.13 sec
Start 156: pyinit::nrniv_nopython_PythonObject_pyenv
229/304 Test #152: pyinit::nrniv_python_command_args ........................................ Passed 0.13 sec
Start 157: pyinit::nrniv_py3.10_python_command_version_check
230/304 Test #155: pyinit::nrniv_nopython_PythonObject_pyexe ................................ Passed 0.11 sec
Start 158: pyinit::nrniv_py3.10_python_check_sys_path
231/304 Test #156: pyinit::nrniv_nopython_PythonObject_pyenv ................................ Passed 0.11 sec
Start 160: pyinit::nrniv_py3.10_nrnpython_check_sys_path
232/304 Test #157: pyinit::nrniv_py3.10_python_command_version_check ........................ Passed 0.13 sec
Start 162: pyinit::nrniv_py3.10_python_check_sys_prefix
233/304 Test #158: pyinit::nrniv_py3.10_python_check_sys_path ............................... Passed 0.14 sec
Start 164: pyinit::nrniv_py3.10_nrnpython_check_sys_prefix
234/304 Test #160: pyinit::nrniv_py3.10_nrnpython_check_sys_path ............................ Passed 0.13 sec
Start 166: pyinit::nrniv_py3.10_python_check_sys_exec_prefix
235/304 Test #162: pyinit::nrniv_py3.10_python_check_sys_prefix ............................. Passed 0.13 sec
Start 168: pyinit::nrniv_py3.10_nrnpython_check_sys_exec_prefix
236/304 Test #164: pyinit::nrniv_py3.10_nrnpython_check_sys_prefix .......................... Passed 0.13 sec
Start 170: pyinit::nrniv_py3.10_python_check_sys_base_prefix
237/304 Test #166: pyinit::nrniv_py3.10_python_check_sys_exec_prefix ........................ Passed 0.13 sec
Start 172: pyinit::nrniv_py3.10_nrnpython_check_sys_base_prefix
238/304 Test #168: pyinit::nrniv_py3.10_nrnpython_check_sys_exec_prefix ..................... Passed 0.13 sec
Start 174: pyinit::nrniv_py3.10_python_check_sys_base_exec_prefix
239/304 Test #170: pyinit::nrniv_py3.10_python_check_sys_base_prefix ........................ Passed 0.13 sec
Start 176: pyinit::nrniv_py3.10_nrnpython_check_sys_base_exec_prefix
240/304 Test #172: pyinit::nrniv_py3.10_nrnpython_check_sys_base_prefix ..................... Passed 0.13 sec
Start 178: pyinit::nrniv_py3.10_python_check_sys_stderr.encoding
241/304 Test #174: pyinit::nrniv_py3.10_python_check_sys_base_exec_prefix ................... Passed 0.13 sec
Start 180: pyinit::nrniv_py3.10_nrnpython_check_sys_stderr.encoding
242/304 Test #176: pyinit::nrniv_py3.10_nrnpython_check_sys_base_exec_prefix ................ Passed 0.13 sec
Start 182: pyinit::nrniv_py3.10_python_check_sys_stdin.encoding
243/304 Test #178: pyinit::nrniv_py3.10_python_check_sys_stderr.encoding .................... Passed 0.13 sec
Start 184: pyinit::nrniv_py3.10_nrnpython_check_sys_stdin.encoding
244/304 Test #180: pyinit::nrniv_py3.10_nrnpython_check_sys_stderr.encoding ................. Passed 0.13 sec
Start 186: pyinit::nrniv_py3.10_python_check_sys_stdout.encoding
245/304 Test #182: pyinit::nrniv_py3.10_python_check_sys_stdin.encoding ..................... Passed 0.13 sec
Start 188: pyinit::nrniv_py3.10_nrnpython_check_sys_stdout.encoding
246/304 Test #184: pyinit::nrniv_py3.10_nrnpython_check_sys_stdin.encoding .................. Passed 0.13 sec
Start 190: pyinit::nrniv_py3.10_python_command_import_neuron
247/304 Test #186: pyinit::nrniv_py3.10_python_check_sys_stdout.encoding .................... Passed 0.13 sec
Start 191: pyinit::py3.10_command_import_neuron
248/304 Test #188: pyinit::nrniv_py3.10_nrnpython_check_sys_stdout.encoding ................. Passed 0.13 sec
Start 192: pyinit::nrniv_py3.10_hoc_command_nrnpython
249/304 Test #192: pyinit::nrniv_py3.10_hoc_command_nrnpython ............................... Passed 0.31 sec
Start 193: pyinit::nrniv_pydef_python_command_version_check
250/304 Test #193: pyinit::nrniv_pydef_python_command_version_check ......................... Passed 0.15 sec
Start 194: pyinit::nrniv_pydef_python_check_sys_path
251/304 Test #191: pyinit::py3.10_command_import_neuron ..................................... Passed 0.64 sec
Start 196: pyinit::nrniv_pydef_nrnpython_check_sys_path
252/304 Test #190: pyinit::nrniv_py3.10_python_command_import_neuron ........................ Passed 0.67 sec
Start 198: pyinit::nrniv_pydef_python_check_sys_prefix
253/304 Test #194: pyinit::nrniv_pydef_python_check_sys_path ................................ Passed 0.14 sec
Start 200: pyinit::nrniv_pydef_nrnpython_check_sys_prefix
254/304 Test #196: pyinit::nrniv_pydef_nrnpython_check_sys_path ............................. Passed 0.14 sec
Start 202: pyinit::nrniv_pydef_python_check_sys_exec_prefix
255/304 Test #198: pyinit::nrniv_pydef_python_check_sys_prefix .............................. Passed 0.14 sec
Start 204: pyinit::nrniv_pydef_nrnpython_check_sys_exec_prefix
256/304 Test #200: pyinit::nrniv_pydef_nrnpython_check_sys_prefix ........................... Passed 0.14 sec
Start 206: pyinit::nrniv_pydef_python_check_sys_base_prefix
257/304 Test #202: pyinit::nrniv_pydef_python_check_sys_exec_prefix ......................... Passed 0.14 sec
Start 208: pyinit::nrniv_pydef_nrnpython_check_sys_base_prefix
258/304 Test #204: pyinit::nrniv_pydef_nrnpython_check_sys_exec_prefix ...................... Passed 0.13 sec
Start 210: pyinit::nrniv_pydef_python_check_sys_base_exec_prefix
259/304 Test #206: pyinit::nrniv_pydef_python_check_sys_base_prefix ......................... Passed 0.14 sec
Start 212: pyinit::nrniv_pydef_nrnpython_check_sys_base_exec_prefix
260/304 Test #208: pyinit::nrniv_pydef_nrnpython_check_sys_base_prefix ...................... Passed 0.14 sec
Start 214: pyinit::nrniv_pydef_python_check_sys_stderr.encoding
261/304 Test #210: pyinit::nrniv_pydef_python_check_sys_base_exec_prefix .................... Passed 0.13 sec
Start 216: pyinit::nrniv_pydef_nrnpython_check_sys_stderr.encoding
262/304 Test #212: pyinit::nrniv_pydef_nrnpython_check_sys_base_exec_prefix ................. Passed 0.14 sec
Start 218: pyinit::nrniv_pydef_python_check_sys_stdin.encoding
263/304 Test #214: pyinit::nrniv_pydef_python_check_sys_stderr.encoding ..................... Passed 0.14 sec
Start 220: pyinit::nrniv_pydef_nrnpython_check_sys_stdin.encoding
264/304 Test #216: pyinit::nrniv_pydef_nrnpython_check_sys_stderr.encoding .................. Passed 0.14 sec
Start 222: pyinit::nrniv_pydef_python_check_sys_stdout.encoding
265/304 Test #218: pyinit::nrniv_pydef_python_check_sys_stdin.encoding ...................... Passed 0.14 sec
Start 224: pyinit::nrniv_pydef_nrnpython_check_sys_stdout.encoding
266/304 Test #220: pyinit::nrniv_pydef_nrnpython_check_sys_stdin.encoding ................... Passed 0.14 sec
Start 226: pyinit::nrniv_pydef_python_command_import_neuron
267/304 Test #222: pyinit::nrniv_pydef_python_check_sys_stdout.encoding ..................... Passed 0.13 sec
Start 227: pyinit::pydef_command_import_neuron
268/304 Test #224: pyinit::nrniv_pydef_nrnpython_check_sys_stdout.encoding .................. Passed 0.14 sec
Start 228: pyinit::nrniv_pydef_hoc_command_nrnpython
269/304 Test #228: pyinit::nrniv_pydef_hoc_command_nrnpython ................................ Passed 0.28 sec
Start 229: external_nrntest
270/304 Test #226: pyinit::nrniv_pydef_python_command_import_neuron ......................... Passed 0.62 sec
Start 236: external_ringtest_nrn::optim_node_order
271/304 Test #227: pyinit::pydef_command_import_neuron ...................................... Passed 0.62 sec
Start 252: testcorenrn_bbcore::compare_results
272/304 Test #252: testcorenrn_bbcore::compare_results ...................................... Passed 0.18 sec
Start 258: testcorenrn_conc::compare_results
273/304 Test #258: testcorenrn_conc::compare_results ........................................ Passed 0.02 sec
Start 264: testcorenrn_deriv::compare_results
274/304 Test #264: testcorenrn_deriv::compare_results ....................................... Passed 0.02 sec
Start 270: testcorenrn_gf::compare_results
275/304 Test #270: testcorenrn_gf::compare_results .......................................... Passed 0.02 sec
Start 276: testcorenrn_kin::compare_results
276/304 Test #276: testcorenrn_kin::compare_results ......................................... Passed 0.02 sec
Start 281: testcorenrn_patstim::compare_results
277/304 Test #281: testcorenrn_patstim::compare_results ..................................... Passed 0.02 sec
Start 287: testcorenrn_vecplay::compare_results
278/304 Test #287: testcorenrn_vecplay::compare_results ..................................... Passed 0.02 sec
Start 299: testcorenrn_watch::compare_results
279/304 Test #299: testcorenrn_watch::compare_results ....................................... Passed 0.02 sec
Start 302: testcorenrn_netstimdirect::compare_results
280/304 Test #302: testcorenrn_netstimdirect::compare_results ............................... Passed 0.02 sec
281/304 Test #236: external_ringtest_nrn::optim_node_order .................................. Passed 25.06 sec
Start 93: parallel::partrans
282/304 Test #93: parallel::partrans ....................................................... Passed 0.87 sec
Start 94: parallel::netpar
283/304 Test #94: parallel::netpar ......................................................... Passed 0.75 sec
Start 95: parallel::bas
284/304 Test #95: parallel::bas ............................................................ Passed 2.20 sec
Start 96: parallel::nrntest_fast
285/304 Test #96: parallel::nrntest_fast ................................................... Passed 1.19 sec
Start 105: coreneuron_modtests::inputpresyn_py
286/304 Test #105: coreneuron_modtests::inputpresyn_py ...................................... Passed 0.94 sec
Start 126: coreneuron_modtests::spikes_mpi_file_mode_py_cpu
287/304 Test #126: coreneuron_modtests::spikes_mpi_file_mode_py_cpu ......................... Passed 0.98 sec
Start 303: tqperf::coreneuron_special
288/304 Test #303: tqperf::coreneuron_special ............................................... Passed 2.46 sec
Start 304: tqperf::coreneuron_python
289/304 Test #304: tqperf::coreneuron_python ................................................ Passed 2.60 sec
290/304 Test #229: external_nrntest ......................................................... Passed 45.98 sec
Start 292: testcorenrn_vecevent::coreneuron_cpu_offline::preparation
291/304 Test #292: testcorenrn_vecevent::coreneuron_cpu_offline::preparation ................ Passed 0.24 sec
Start 230: reduced_dentate::neuron
292/304 Test #230: reduced_dentate::neuron .................................................. Passed 39.20 sec
Start 231: reduced_dentate::coreneuron_cpu
293/304 Test #231: reduced_dentate::coreneuron_cpu .......................................... Passed 31.98 sec
Start 242: external_ringtest::coreneuron_cpu_mpi_threads
294/304 Test #242: external_ringtest::coreneuron_cpu_mpi_threads ............................ Passed 1.35 sec
Start 243: external_ringtest::coreneuron_cpu_mpi_threads_python
295/304 Test #243: external_ringtest::coreneuron_cpu_mpi_threads_python ..................... Passed 1.39 sec
Start 288: testcorenrn_vecevent::neuron
296/304 Test #288: testcorenrn_vecevent::neuron ............................................. Passed 0.25 sec
Start 289: testcorenrn_vecevent::coreneuron_cpu_online
297/304 Test #289: testcorenrn_vecevent::coreneuron_cpu_online .............................. Passed 0.58 sec
Start 290: testcorenrn_vecevent::coreneuron_cpu_online_psolve_alternate
298/304 Test #290: testcorenrn_vecevent::coreneuron_cpu_online_psolve_alternate ............. Passed 0.63 sec
Start 291: testcorenrn_vecevent::coreneuron_cpu_offline
299/304 Test #291: testcorenrn_vecevent::coreneuron_cpu_offline ............................. Passed 0.21 sec
Start 92: parallel::subworld
300/304 Test #92: parallel::subworld ....................................................... Passed 1.15 sec
Start 127: coreneuron_modtests::test_subworlds_py_cpu
301/304 Test #127: coreneuron_modtests::test_subworlds_py_cpu ............................... Passed 1.34 sec
Start 232: reduced_dentate::compare_results
Start 246: external_ringtest::compare_results
Start 293: testcorenrn_vecevent::compare_results
302/304 Test #232: reduced_dentate::compare_results ......................................... Passed 0.02 sec
303/304 Test #293: testcorenrn_vecevent::compare_results .................................... Passed 0.02 sec
304/304 Test #246: external_ringtest::compare_results ....................................... Passed 0.03 sec
100% tests passed, 0 tests failed out of 304
Total Test time (real) = 194.33 sec
$ cmake --build . --target install
[0/2] Re-checking globbed directories...
[1/2] Re-running CMake...
-- git describe failed (stdout: '', stderr: 'fatal: No names found, cannot describe anything.', code: 128), skipping the version check
-- 3rd party project: using Random123 from "external/Random123"
-- 3rd party project: using eigen from "external/eigen"
-- Enabling sanitizers: address
-- Sanitizer runtime library: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/14.0.0/lib/darwin/libclang_rt.asan_osx_dynamic.dylib
-- Checking if /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/venv/bin/python is a working python
-- Found BISON: /opt/homebrew/opt/bison/bin/bison (found version "3.8.2")
-- 3rd party project: using CLI11 from "external/CLI11"
CMake Deprecation Warning at external/CLI11/CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
-- Building CoreNEURON
-- Could NOT find nmodl (missing: nmodl_BINARY nmodl_INCLUDE nmodl_PYTHONPATH)
-- Sub-project : using nmodl from from /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/external/nmodl
-- CHECKING FOR FLEX/BISON
-- Found BISON: /opt/homebrew/opt/bison/bin/bison (found suitable version "3.8.2", minimum required is "3.0")
-- Adding Flex include path as : /opt/homebrew/opt/flex/include/
-- NMODL_TEST_FORMATTING: OFF
-- NMODL_GIT_HOOKS: OFF
-- NMODL_GIT_COMMIT_HOOKS:
-- NMODL_GIT_PUSH_HOOKS: courtesy-msg
-- NMODL_STATIC_ANALYSIS: OFF
-- NMODL_TEST_STATIC_ANALYSIS: OFF
-- 3rd party project: using eigen from "ext/eigen"
-- 3rd party project: using fmt from "ext/fmt"
-- Version: 10.2.1
-- Build type: Custom
-- 3rd party project: using json from "ext/json"
-- Using the multi-header code from /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/external/nmodl/ext/json/include/
-- 3rd party project: using pybind11 from "ext/pybind11"
-- pybind11 v2.12.0
-- 3rd party project: using spdlog from "ext/spdlog"
-- Build spdlog: 1.13.0
-- Build type: Custom
-- CHECKING FOR PYTHON
CMake Warning (dev) at external/nmodl/src/pybind/CMakeLists.txt:27 (configure_file):
configure_file called with unknown argument(s):
@ONLY@
This warning is for project developers. Use -Wno-dev to suppress it.
--
-- Configured NMODL 0.0 (c5ecfea 2024-06-10 16:25:23 +0200)
--
-- You can now build NMODL using:
-- cmake --build . --parallel 8 [--target TARGET]
-- You might want to adjust the number of parallel build jobs for your system.
-- Some non-default targets you might want to build:
-- --------------------+--------------------------------------------------------
-- Target | Description
-- --------------------+--------------------------------------------------------
-- test | Run unit tests
-- install | Will install NMODL to: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install
-- --------------------+--------------------------------------------------------
-- Build option | Status
-- --------------------+--------------------------------------------------------
-- CXX COMPILER | /usr/bin/g++
-- COMPILE FLAGS | -O1 -g -openmp-simd
-- Build Type | Custom
-- Python Bindings | OFF
-- Flex | /opt/homebrew/opt/flex/bin/flex
-- Bison | /opt/homebrew/opt/bison/bin/bison
-- Python | /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/venv/bin/python
-- Linked against | ON
-- --------------------+--------------------------------------------------------
-- See documentation : https://github.com/BlueBrain/nmodl/
-- --------------------+--------------------------------------------------------
--
--
-- CoreNEURON is enabled with following build configuration:
-- --------------------+--------------------------------------------------------
-- Build option | Status
-- --------------------+--------------------------------------------------------
-- CXX COMPILER | /usr/bin/g++
-- COMPILE FLAGS | -O1 -g -openmp-simd -std=c++17 -DCORENEURON_BUILD -DCORENRN_BUILD=1 -DEIGEN_DONT_PARALLELIZE -DNRNMPI=1 -DLAYOUT=0 -DDISABLE_HOC_EXP -DENABLE_SPLAYTREE_QUEUING -fno-omit-frame-pointer -shared-libsan -fsanitize=address -fsanitize-address-use-after-scope
-- Build Type | SHARED
-- MPI | ON
-- DYNAMIC | OFF
-- INC | /opt/homebrew/Cellar/open-mpi/5.0.1/include
-- OpenMP | ON
-- NMODL PATH | /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/bin/nmodl
-- NMODL FLAGS |
-- GPU Support | OFF
-- Auto Timeout | ON
-- Wrap exp() | OFF
-- SplayTree Queue | ON
-- NetReceive Buffer | ON
-- Caliper | OFF
-- Likwid | OFF
-- Unit Tests | ON
-- Reporting | OFF
-- --------------------+--------------------------------------------------------
--
Extracting link flags from target 'nrngnu', beware that this can be fragile. Got:
Extracting link flags from target 'sparse13', beware that this can be fragile. Got:
Generating link flags from name 'nrnpython', beware that this can be fragile. Got: -lnrnpython
Extracting link flags from target 'Threads::Threads', beware that this can be fragile. Got: -lnrnpython
Generating link flags from path /opt/homebrew/Cellar/open-mpi/5.0.1/lib/libmpi.dylib Got: /opt/homebrew/Cellar/open-mpi/5.0.1/lib/libmpi.dylib -Wl,-rpath,/opt/homebrew/Cellar/open-mpi/5.0.1/lib
-- Sub-project : using catch2 from from /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/external/catch2
-- Found Python module 'pytest' with version(s): 8.1.1
-- Found Python module 'pytest_cov' with version(s): 5.0.0
-- 3rd party project: using rxd/testdata from "test/rxd/testdata"
-- Found Python module 'mpi4py' with version(s): 3.1.6
-- Disabling coreneuron_modtests::fornetcon_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::direct_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::direct_hoc_gpu: gpu not enabled
-- Disabling coreneuron_modtests::spikes_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::spikes_file_mode_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::fast_imem_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::datareturn_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::test_units_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::test_netmove_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::test_pointer_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::test_watchrange_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::test_psolve_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::test_ba_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::test_nmodlrandom_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::test_nmodlrandom_syntax_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::test_natrans_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::array_variable_transfer_run_mode_0_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::array_variable_transfer_run_mode_1_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::array_variable_transfer_run_mode_2_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::array_variable_transfer_file_mode_py_gpu: gpu not enabled
-- Found Python module 'mpi4py' with version(s): 3.1.6
-- Disabling coreneuron_modtests::spikes_mpi_file_mode_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::test_subworlds_py_gpu: gpu not enabled
-- Disabling nmodl_tests_coreneuron::test_table_coreneuron_gpu: gpu not enabled
-- Disabling nmodl_tests_coreneuron::test_disc_coreneuron_gpu: gpu not enabled
-- Disabling nmodl_tests_coreneuron::test_function_table_coreneuron_gpu: gpu not enabled
-- Disabling nmodl_tests_coreneuron::test_kinetic_coreneuron_gpu: gpu not enabled
-- Disabling reduced_dentate::coreneuron_gpu: gpu not enabled
-- Disabling external_ringtest::coreneuron_gpu_mpi_offline_saverestore: gpu not enabled
-- Disabling external_ringtest::coreneuron_gpu_mpi: gpu not enabled
-- Disabling external_ringtest::coreneuron_gpu_mpi_python: gpu not enabled
-- Disabling external_ringtest::coreneuron_gpu_mpi_offline: gpu not enabled
-- Disabling external_ringtest::coreneuron_gpu_mpi_threads: gpu not enabled
-- Disabling external_ringtest::coreneuron_gpu_mpi_threads_python: gpu not enabled
-- Disabling testcorenrn_bbcore::coreneuron_gpu_online: gpu not enabled
-- Disabling testcorenrn_bbcore::coreneuron_gpu_online_psolve_alternate: gpu not enabled
-- Disabling testcorenrn_bbcore::coreneuron_gpu_offline: gpu not enabled
-- Disabling testcorenrn_conc::coreneuron_gpu_online: gpu not enabled
-- Disabling testcorenrn_conc::coreneuron_gpu_online_psolve_alternate: gpu not enabled
-- Disabling testcorenrn_conc::coreneuron_gpu_offline: gpu not enabled
-- Disabling testcorenrn_deriv::coreneuron_gpu_online: gpu not enabled
-- Disabling testcorenrn_deriv::coreneuron_gpu_online_psolve_alternate: gpu not enabled
-- Disabling testcorenrn_deriv::coreneuron_gpu_offline: gpu not enabled
-- Disabling testcorenrn_gf::coreneuron_gpu_online: gpu not enabled
-- Disabling testcorenrn_gf::coreneuron_gpu_online_psolve_alternate: gpu not enabled
-- Disabling testcorenrn_gf::coreneuron_gpu_offline: gpu not enabled
-- Disabling testcorenrn_kin::coreneuron_gpu_online: gpu not enabled
-- Disabling testcorenrn_kin::coreneuron_gpu_online_psolve_alternate: gpu not enabled
-- Disabling testcorenrn_kin::coreneuron_gpu_offline: gpu not enabled
-- Disabling testcorenrn_patstim::coreneuron_gpu_offline_saverestore: gpu not enabled
-- Disabling testcorenrn_patstim::coreneuron_gpu_offline: gpu not enabled
-- Disabling testcorenrn_vecplay::coreneuron_gpu_online: gpu not enabled
-- Disabling testcorenrn_vecplay::coreneuron_gpu_online_psolve_alternate: gpu not enabled
-- Disabling testcorenrn_vecplay::coreneuron_gpu_offline: gpu not enabled
-- Disabling testcorenrn_vecevent::coreneuron_gpu_online: gpu not enabled
-- Disabling testcorenrn_vecevent::coreneuron_gpu_online_psolve_alternate: gpu not enabled
-- Disabling testcorenrn_vecevent::coreneuron_gpu_offline: gpu not enabled
-- Disabling testcorenrn_watch::coreneuron_gpu_online: gpu not enabled
-- Disabling testcorenrn_watch::coreneuron_gpu_online_psolve_alternate: gpu not enabled
-- Disabling testcorenrn_watch::coreneuron_gpu_offline: gpu not enabled
--
-- Configured NEURON 9.0.0
--
-- You can now build NEURON using:
-- cmake --build . --parallel 8 [--target TARGET]
-- You might want to adjust the number of parallel build jobs for your system.
-- Some non-default targets you might want to build:
-- --------------+--------------------------------------------------------------
-- Target | Description
-- --------------+--------------------------------------------------------------
-- install | Will install NEURON to: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install
-- | Change the install location of NEURON using:
-- | cmake <src_path> -DCMAKE_INSTALL_PREFIX=<install_path>
-- docs | Build full docs. Calls targets: doxygen, notebooks, sphinx, notebooks-clean
-- uninstall | Removes files installed by make install (todo)
-- --------------+--------------------------------------------------------------
-- Build option | Status
-- --------------+--------------------------------------------------------------
-- C COMPILER | /usr/bin/gcc
-- CXX COMPILER | /usr/bin/g++
-- BUILD_TYPE | Custom (allowed: Custom;Debug;Release;RelWithDebInfo;Fast;FastDebug)
-- COMPILE FLAGS | -O1 -g -openmp-simd -fno-omit-frame-pointer -shared-libsan -fsanitize=address -fsanitize-address-use-after-scope -O1 -g -openmp-simd
-- Shared | ON
-- MPI | ON
-- DYNAMIC | OFF
-- INC | /opt/homebrew/Cellar/open-mpi/5.0.1/include
-- LIB | /opt/homebrew/Cellar/open-mpi/5.0.1/lib/libmpi.dylib
-- Python | ON
-- DYNAMIC | OFF
-- MODULE | ON
-- python3.10 (default)
-- EXE | /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/venv/bin/python
-- INC | /opt/homebrew/opt/python@3.10/Frameworks/Python.framework/Versions/3.10/include/python3.10
-- LIB | /opt/homebrew/opt/python@3.10/Frameworks/Python.framework/Versions/3.10/lib/libpython3.10.dylib
-- Readline | /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/lib/libreadline.tbd
-- Curses | /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/lib/libcurses.tbd;/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/lib/libform.tbd
-- RX3D | OFF
-- Interviews | OFF
-- CoreNEURON | ON
-- PATH | /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/src/coreneuron
-- LINK FLAGS | -lcorenrnmech -Wl,-rpath,/opt/homebrew/Cellar/open-mpi/5.0.1/lib /opt/homebrew/Cellar/open-mpi/5.0.1/lib/libmpi.dylib
-- Tests | ON
-- --------------+--------------------------------------------------------------
-- See documentation : https://www.neuron.yale.edu/neuron/
-- --------------+--------------------------------------------------------------
--
-- Configuring done (3.3s)
-- Generating done (0.2s)
-- Build files have been written to: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build
[0/2] Re-checking globbed directories...
[1/6] Update hh.mod for CoreNEURON compatibility
[2/6] Generating help_data.dat
[3/6] cd /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/src/nrnoc && /opt/homebrew/Cellar/cmake/3.28.1/bin/cmake -E env PROJECT_VERSION=9.0.0 bash /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/git2nrnversion_h.sh /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn > nrnversion.h.tmp && /opt/homebrew/Cellar/cmake/3.28.1/bin/cmake -E copy_if_different nrnversion.h.tmp nrnversion.h
fatal: No names found, cannot describe anything.
[4/6] cd /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/src/nrniv && true
[5/6] Running utility command for hoc_module
INFO:root:setup.py called with:setup.py build --cmake-build-dir /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build --disable-rx3d --without-nrnpython --build-lib=/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python build_ext --define=NRN_ASAN_ENABLED,USE_PYTHON,NRN_ENABLE_THREADS,CORENRN_BUILD=0
INFO:root:Setting SDKROOT=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk
WARNING:root:You are building a wheel with a Python built for macOS >=12.0.0. Your wheel won't run on older versions, consider using an official Python build from python.org
WARNING:root:Setting MACOSX_DEPLOYMENT_TARGET=12.0
INFO:root:Extension common compile flags defaultdict(<class 'list'>, {'library_dirs': ['/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib'], 'libraries': ['nrniv'], 'language': 'c++'})
INFO:root:RX3D is DISABLED
/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/venv/lib/python3.10/site-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!
********************************************************************************
Requirements should be satisfied by a PEP 517 installer.
If you are using pip, you can try `pip install --use-pep517`.
********************************************************************************
!!
dist.fetch_build_eggs(dist.setup_requires)
WARNING setuptools_scm.pyproject_reading toml section missing 'pyproject.toml does not contain a tool.setuptools_scm section'
Traceback (most recent call last):
File "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/venv/lib/python3.10/site-packages/setuptools_scm/_integration/pyproject_reading.py", line 36, in read_pyproject
section = defn.get("tool", {})[tool_name]
KeyError: 'setuptools_scm'
/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/venv/lib/python3.10/site-packages/setuptools_scm/git.py:167: UserWarning: "/Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn" is shallow and may cause errors
warnings.warn(f'"{wd.path}" is shallow and may cause errors')
INFO:root:running build
INFO:root:running build_py
INFO:root:copying share/lib/python/neuron/hclass3.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron
INFO:root:copying share/lib/python/neuron/expect_hocerr.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron
INFO:root:copying share/lib/python/neuron/psection.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron
INFO:root:copying share/lib/python/neuron/config.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron
INFO:root:copying share/lib/python/neuron/units.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron
INFO:root:copying share/lib/python/neuron/sections.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron
INFO:root:copying share/lib/python/neuron/__init__.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron
INFO:root:copying share/lib/python/neuron/coreneuron.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron
INFO:root:copying share/lib/python/neuron/doc.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron
INFO:root:copying share/lib/python/neuron/gui.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron
INFO:root:copying share/lib/python/neuron/nonvint_block_supervisor.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron
INFO:root:copying share/lib/python/neuron/neuroml/metadata.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/neuroml
INFO:root:copying share/lib/python/neuron/neuroml/morphml.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/neuroml
INFO:root:copying share/lib/python/neuron/neuroml/xml2nrn.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/neuroml
INFO:root:copying share/lib/python/neuron/neuroml/__init__.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/neuroml
INFO:root:copying share/lib/python/neuron/neuroml/neuroml.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/neuroml
INFO:root:copying share/lib/python/neuron/neuroml/rdxml.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/neuroml
INFO:root:copying share/lib/python/neuron/neuroml/biophysics.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/neuroml
INFO:root:copying share/lib/python/neuron/tests/_subclass.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/tests
INFO:root:copying share/lib/python/neuron/tests/test_all.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/tests
INFO:root:copying share/lib/python/neuron/tests/__init__.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/tests
INFO:root:copying share/lib/python/neuron/tests/test_neuron.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/tests
INFO:root:copying share/lib/python/neuron/tests/test_vector.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/tests
INFO:root:copying share/lib/python/neuron/tests/test_rxd.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/tests
INFO:root:copying share/lib/python/neuron/tests/utils/coreneuron_available.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/tests/utils
INFO:root:copying share/lib/python/neuron/tests/utils/__init__.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/tests/utils
INFO:root:copying share/lib/python/neuron/tests/utils/strtobool.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/tests/utils
INFO:root:copying share/lib/python/neuron/tests/utils/capture_stdout.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/tests/utils
INFO:root:copying share/lib/python/neuron/tests/utils/checkresult.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/tests/utils
INFO:root:copying share/lib/python/neuron/rxd/rxdException.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/options.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/plugins.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/rxdsection.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/species.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/rxdmath.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/rate.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/region.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/multiCompartmentReaction.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/constants.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/dimension3.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/__init__.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/section1d.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/export.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/initializer.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/rangevar.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/geometry.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/rxd.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/generalizedReaction.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/nodelist.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/node.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/gui.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/rxd/reaction.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/rxd
INFO:root:copying share/lib/python/neuron/crxd/__init__.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/crxd
INFO:root:copying share/lib/python/neuron/gui2/setup_threejs.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/gui2
INFO:root:copying share/lib/python/neuron/gui2/config.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/gui2
INFO:root:copying share/lib/python/neuron/gui2/__init__.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/gui2
INFO:root:copying share/lib/python/neuron/gui2/rangevar.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/gui2
INFO:root:copying share/lib/python/neuron/gui2/plotshape.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/gui2
INFO:root:copying share/lib/python/neuron/gui2/utilities.py -> /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/build/lib/python/neuron/gui2
INFO:root:running build_ext
INFO:root:==> Building Python extensions
INFO:root:running build_scripts
[5/6] Install the project...
-- Install configuration: "Custom"
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/bin/nrn-enable-sanitizer
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/libsymtab.a
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/librxdmath.dylib
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/libnrniv.dylib
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/libnrngnu.a
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/libvisitor.a
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/hclass3.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/hoc.cpython-310-darwin.so
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/expect_hocerr.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/psection.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/neuroml
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/neuroml/metadata.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/neuroml/morphml.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/neuroml/xml2nrn.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/neuroml/__init__.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/neuroml/neuroml.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/neuroml/rdxml.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/neuroml/biophysics.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/config.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/units.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/sections.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/rxd
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/rxd/rxdException.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/rxd/options.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/rxd/plugins.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/rxd/rxdsection.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/rxd/species.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/rxd/rxdmath.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/rxd/rate.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/rxd/region.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/rxd/multiCompartmentReaction.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/rxd/constants.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/rxd/dimension3.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/rxd/__init__.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/rxd/section1d.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/rxd/export.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/rxd/initializer.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/rxd/rangevar.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/rxd/geometry.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/rxd/rxd.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/rxd/generalizedReaction.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/rxd/nodelist.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/rxd/node.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/rxd/gui.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/rxd/reaction.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/tests
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/tests/_subclass.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/tests/test_all.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/tests/__init__.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/tests/utils
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/tests/utils/coreneuron_available.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/tests/utils/__init__.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/tests/utils/strtobool.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/tests/utils/capture_stdout.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/tests/utils/checkresult.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/tests/test_neuron.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/tests/test_vector.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/tests/test_rxd.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/__init__.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/_config_params.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/coreneuron.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/doc.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/gui2
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/gui2/setup_threejs.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/gui2/config.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/gui2/__init__.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/gui2/rangevar.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/gui2/plotshape.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/gui2/utilities.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/crxd
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/crxd/__init__.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/help_data.dat
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/gui.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron/nonvint_block_supervisor.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/libspdlog.a
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/libfmt.a
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/nmodl
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/nmodl/dsl.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/nmodl/symtab.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/nmodl/ext
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/nmodl/ext/example
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/nmodl/ext/example/passive.mod
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/nmodl/ext/example/expsyn.mod
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/nmodl/ext/example/exp2syn.mod
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/nmodl/ext/example/hh.mod
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/nmodl/ext/viz
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-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/nmodl/ext/viz/css
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-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/nmodl/ext/viz/js
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/nmodl/ext/viz/js/d3.min.js
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/nmodl/ext/viz/js/tree.js
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/nmodl/__init__.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/nmodl/_binwrapper.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/nmodl/visitor.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/nmodl/ast.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/nmodl/ode.py
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/libpywrapper.a
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/liblexer.a
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/libCatch2.a
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/libsparse13.a
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/libpyembed.a
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/libcoreneuron-core.a
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/libcodegen.a
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/libutil.a
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/libCatch2Main.a
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/crout_thread.hpp
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/neuron
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/neuron/cache
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/neuron/cache/mechanism_range.hpp
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-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/mpi/lib
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/mpi/lib/nrnmpi.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/mpi/nrnmpiuse.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/config
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/config/config.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/config/version_macros.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/config/neuron_version.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/coreneuron.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/network
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/network/multisend.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/network/have2want.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/network/netpar.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/network/tnode.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/network/netcon.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/network/partrans.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/network/tqueue.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/network/netcvode.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/io
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/io/nrn2core_direct.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/io/mech_report.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/io/core2nrn_data_return.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/io/prcellstate.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/io/nrn_setup.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/io/output_spikes.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/io/lfp.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/io/setup_fornetcon.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/io/nrn_checkpoint.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/io/user_params.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/io/nrnsection_mapping.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/io/nrn_filehandler.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/io/mem_layout_util.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/io/phase1.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/io/phase3.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/io/reports
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/io/reports/report_event.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/io/reports/report_handler.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/io/reports/sonata_report_handler.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/io/reports/nrnreport.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/io/phase2.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/utils
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/utils/vrecitem.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/utils/utils_cuda.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/utils/nrnmutdec.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/utils/string_utils.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/utils/nrn_assert.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/utils/nrnoc_aux.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/utils/progressbar
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/utils/progressbar/progressbar.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/utils/memory_utils.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/utils/profile
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/utils/profile/profiler_interface.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/utils/lpt.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/utils/offload.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/utils/memory.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/utils/units.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/utils/utils.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/utils/randoms
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/utils/randoms/nrnran123.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/utils/nrn_stats.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/utils/ivocvect.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/nrnoc
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/nrnoc/md2redef.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/nrnoc/md1redef.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/membrane_definitions.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/sim
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/sim/multicore.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/sim/fast_imem.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/sim/scopmath
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/sim/scopmath/crout_thread.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/sim/scopmath/errcodes.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/sim/scopmath/newton_struct.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/sim/scopmath/newton_thread.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/sim/scopmath/ssimplic_thread.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/sim/scopmath/sparse_thread.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/apps
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/apps/corenrn_parameters.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/permute
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/permute/node_permute.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/permute/cellorder.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include//coreneuron/permute/data_layout.hpp
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/share/coreneuron/mod_func.c.pl
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/share/coreneuron/enginemech.cpp
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/bin/nmodl
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/bin/nrniv-core
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/share/coreneuron/coreneuron.cpp
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/libcorenrnmech_internal.dylib
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/crout_thread.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/neuron
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/neuron/cache
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/neuron/cache/mechanism_range.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/neuron/container
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/neuron/container/non_owning_soa_identifier.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/neuron/container/data_handle.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/neuron/container/generic_data_handle.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/neuron/model_data_fwd.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/nrnrandom.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/hocassrt.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/multicore.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/nrnconf.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/wrap_sprintf.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/simeq.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/ocmisc.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/multisplit.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/oc_ansi.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/hoclist.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/membfunc.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/neuronapi.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/nrnmpidec.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/nrnversionmacros.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/scoplib.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/sparse.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/membdef.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/neuron.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/newton_struct.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/newton
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/newton/newton.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/nrncvode
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/nrncvode/nrnneosm.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/bbsavestate.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/nmodlmutex.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/euler_thread.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/hocdec.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/md2redef.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/hocgetsym.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/euler.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/cabvars.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/options.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/nrnmpi.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/nrnran123.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/CholmodSupport
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/StdVector
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/StdDeque
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/Core
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/SparseLU
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/OrderingMethods
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/QtAlignedMalloc
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/Householder
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/PardisoSupport
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/SparseCore
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/Jacobi
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/Dense
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/SPQRSupport
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/QR
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/Eigen
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/SparseQR
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/SVD
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/Cholesky
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/UmfPackSupport
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/IterativeLinearSolvers
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/LU
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/Sparse
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/Geometry
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/SuperLUSupport
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/StdList
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/MetisSupport
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/SparseCholesky
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/Eigenvalues
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/PaStiXSupport
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/CholmodSupport
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/CholmodSupport/CholmodSupport.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/misc
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/misc/blas.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/misc/lapacke.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/misc/Kernel.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/misc/RealSvd2x2.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/misc/Image.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/misc/lapack.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/misc/lapacke_mangling.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/Reverse.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/ConditionEstimator.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/PermutationMatrix.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/Assign.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/MathFunctionsImpl.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/CwiseUnaryOp.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/DiagonalMatrix.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/StlIterators.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/VectorBlock.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/ReturnByValue.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/Solve.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/products
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/products/SelfadjointRank2Update.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/products/GeneralBlockPanelKernel.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/products/GeneralMatrixMatrixTriangular_BLAS.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/products/GeneralMatrixMatrix_BLAS.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/products/GeneralMatrixVector_BLAS.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/products/GeneralMatrixMatrix.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/products/Parallelizer.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/products/GeneralMatrixMatrixTriangular.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/products/TriangularMatrixVector.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/products/SelfadjointMatrixVector.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/products/TriangularSolverMatrix.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/products/GeneralMatrixVector.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/products/SelfadjointProduct.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/products/TriangularMatrixVector_BLAS.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/products/TriangularMatrixMatrix_BLAS.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/products/SelfadjointMatrixVector_BLAS.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/products/TriangularSolverMatrix_BLAS.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/products/SelfadjointMatrixMatrix_BLAS.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/products/TriangularSolverVector.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/products/TriangularMatrixMatrix.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/products/SelfadjointMatrixMatrix.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/ArithmeticSequence.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/Product.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/util
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/util/NonMPL2.h
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-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/util/BlasUtil.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/util/StaticAssert.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/util/Constants.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/util/XprHelper.h
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-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/util/Macros.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/util/DisableStupidWarnings.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/util/SymbolicIndex.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/util/ForwardDeclarations.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/util/Memory.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/util/Meta.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/util/ConfigureVectorization.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/util/IntegralConstant.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/util/ReenableStupidWarnings.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/util/IndexedViewHelper.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/MatrixBase.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/Stride.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/Map.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/ForceAlignedAccess.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/MathFunctions.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/functors
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/functors/UnaryFunctors.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/functors/TernaryFunctors.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/functors/AssignmentFunctors.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/functors/BinaryFunctors.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/functors/StlFunctors.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/functors/NullaryFunctors.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/SelfCwiseBinaryOp.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/BandMatrix.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/Inverse.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/Assign_MKL.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/Swap.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/ProductEvaluators.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/MapBase.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/Matrix.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/EigenBase.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/StableNorm.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/GenericPacketMath.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/CwiseBinaryOp.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/Visitor.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/DenseStorage.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/DiagonalProduct.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/CwiseUnaryView.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/NoAlias.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/DenseCoeffsBase.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/PartialReduxEvaluator.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/IndexedView.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/Fuzzy.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/TriangularMatrix.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/IO.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/SSE
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/SSE/PacketMath.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/SSE/MathFunctions.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/SSE/TypeCasting.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/SSE/Complex.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/GPU
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/GPU/PacketMath.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/GPU/MathFunctions.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/GPU/TypeCasting.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/MSA
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/MSA/PacketMath.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/MSA/MathFunctions.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/MSA/Complex.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/CUDA
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/CUDA/Complex.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/ZVector
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/ZVector/PacketMath.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/ZVector/MathFunctions.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/ZVector/Complex.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/Default
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/Default/Half.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/Default/Settings.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/Default/TypeCasting.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/Default/BFloat16.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/Default/GenericPacketMathFunctionsFwd.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/Default/GenericPacketMathFunctions.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/Default/ConjHelper.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/AVX512
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/AVX512/PacketMath.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/AVX512/MathFunctions.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/AVX512/TypeCasting.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/AVX512/Complex.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/SVE
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/SVE/PacketMath.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/SVE/MathFunctions.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/SVE/TypeCasting.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/HIP
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/HIP/hcc
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/HIP/hcc/math_constants.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/AVX
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/AVX/PacketMath.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/AVX/MathFunctions.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/AVX/TypeCasting.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/AVX/Complex.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/SYCL
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/SYCL/PacketMath.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/SYCL/MathFunctions.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/SYCL/SyclMemoryModel.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/SYCL/InteropHeaders.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/SYCL/TypeCasting.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/NEON
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/NEON/GeneralBlockPanelKernel.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/NEON/PacketMath.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/NEON/MathFunctions.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/NEON/TypeCasting.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/NEON/Complex.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/AltiVec
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/AltiVec/PacketMath.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/AltiVec/MathFunctions.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/AltiVec/MatrixProduct.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/AltiVec/MatrixProductMMA.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/AltiVec/MatrixProductCommon.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/AltiVec/Complex.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/Array.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/SolverBase.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/AssignEvaluator.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/Replicate.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/CoreIterators.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/ArrayBase.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/Block.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/Dot.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/PlainObjectBase.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/SelfAdjointView.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/GeneralProduct.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/SolveTriangular.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/CoreEvaluators.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/CwiseNullaryOp.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/VectorwiseOp.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/ArrayWrapper.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/BooleanRedux.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/Transpositions.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/NestByValue.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/Ref.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/Reshaped.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/Transpose.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/Redux.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/NumTraits.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/CommaInitializer.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/GlobalFunctions.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/Random.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/Diagonal.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/DenseBase.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/CwiseTernaryOp.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/Select.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseLU
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseLU/SparseLU_Utils.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseLU/SparseLU_kernel_bmod.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseLU/SparseLU_column_bmod.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseLU/SparseLU_gemm_kernel.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseLU/SparseLU.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseLU/SparseLU_column_dfs.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseLU/SparseLU_panel_dfs.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseLU/SparseLU_relax_snode.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseLU/SparseLU_panel_bmod.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseLU/SparseLU_Structs.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseLU/SparseLU_pruneL.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseLU/SparseLU_Memory.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseLU/SparseLU_pivotL.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseLU/SparseLUImpl.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/OrderingMethods
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/OrderingMethods/Ordering.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/OrderingMethods/Eigen_Colamd.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/OrderingMethods/Amd.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/plugins
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/plugins/ArrayCwiseUnaryOps.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/plugins/CommonCwiseUnaryOps.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/plugins/BlockMethods.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/plugins/ArrayCwiseBinaryOps.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/plugins/MatrixCwiseBinaryOps.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/plugins/IndexedViewMethods.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/plugins/CommonCwiseBinaryOps.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/plugins/ReshapedMethods.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/plugins/MatrixCwiseUnaryOps.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Householder
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Householder/HouseholderSequence.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Householder/Householder.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Householder/BlockHouseholder.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/PardisoSupport
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/PardisoSupport/PardisoSupport.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/SparseSelfAdjointView.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/SparseMatrix.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/CompressedStorage.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/SparseCwiseBinaryOp.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/SparseView.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/SparseColEtree.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/SparseMatrixBase.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/SparseDiagonalProduct.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/SparseTriangularView.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/SparseAssign.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/SparsePermutation.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/SparseCwiseUnaryOp.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/SparseMap.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/SparseDenseProduct.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/SparseRef.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/SparseFuzzy.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/MappedSparseMatrix.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/SparseSparseProductWithPruning.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/SparseSolverBase.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/SparseBlock.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/TriangularSolver.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/SparseVector.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/SparseCompressedBase.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/SparseTranspose.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/SparseProduct.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/AmbiVector.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/SparseRedux.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/SparseUtil.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCore/SparseDot.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Jacobi
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Jacobi/Jacobi.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SPQRSupport
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/QR
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/QR/FullPivHouseholderQR.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/QR/HouseholderQR.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/QR/CompleteOrthogonalDecomposition.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/QR/ColPivHouseholderQR.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/QR/HouseholderQR_LAPACKE.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseQR
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseQR/SparseQR.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SVD
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SVD/JacobiSVD_LAPACKE.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SVD/SVDBase.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SVD/JacobiSVD.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SVD/BDCSVD.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SVD/UpperBidiagonalization.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Cholesky
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Cholesky/LLT_LAPACKE.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Cholesky/LDLT.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Cholesky/LLT.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/UmfPackSupport
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/UmfPackSupport/UmfPackSupport.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/IterativeLinearSolvers
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/LU
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/LU/PartialPivLU_LAPACKE.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/LU/InverseImpl.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/LU/Determinant.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/LU/arch
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/LU/arch/InverseSize4.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/LU/PartialPivLU.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/LU/FullPivLU.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Geometry
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Geometry/AngleAxis.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Geometry/RotationBase.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Geometry/EulerAngles.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Geometry/Hyperplane.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Geometry/Homogeneous.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Geometry/AlignedBox.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Geometry/Quaternion.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Geometry/Umeyama.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Geometry/Translation.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Geometry/Scaling.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Geometry/OrthoMethods.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Geometry/Rotation2D.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Geometry/arch
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Geometry/arch/Geometry_SIMD.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Geometry/Transform.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Geometry/ParametrizedLine.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SuperLUSupport
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SuperLUSupport/SuperLUSupport.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/MetisSupport
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/MetisSupport/MetisSupport.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/StlSupport
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/StlSupport/StdList.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/StlSupport/StdDeque.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/StlSupport/details.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/StlSupport/StdVector.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCholesky
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/SparseCholesky/SimplicialCholesky.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Eigenvalues
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Eigenvalues/EigenSolver.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Eigenvalues/RealSchur.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Eigenvalues/Tridiagonalization.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Eigenvalues/HessenbergDecomposition.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Eigenvalues/ComplexEigenSolver.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Eigenvalues/ComplexSchur.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Eigenvalues/RealQZ.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/PaStiXSupport
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/PaStiXSupport/PaStiXSupport.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/KLUSupport
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/KLUSupport/KLUSupport.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/KLUSupport
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/nrnapi.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/nrncvode.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/nrnsemanticversion.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/spmatrix.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/ocfunc.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/section_fwd.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/row_view.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/hoc_membf.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/backtrace_utils.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/nrnisaac.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/parse_with_deps.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/newton_thread.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/nrnredef.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/dimplic.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/hoc.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/newton.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/crout.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/nrnmpiuse.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/md1redef.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/nrniv_mf.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/memory.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/nrn_ansi.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/deflate.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/errcodes.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/nrniv
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/nrniv/profiler_interface.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/nrniv/nrniv_decl.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/engine.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/nrnconf.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/gpu
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/gpu/nrn_acc_manager.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/mechanism
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/mechanism/membfunc.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/mechanism/register_mech.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/mechanism/mechanism.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/mechanism/mech_mapping.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/mechanism/eion.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/mechanism/mech
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/mechanism/mech/mod2c_core_thread.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/mechanism/mech/cfile
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/mechanism/mech/cfile/cabvars.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/mpi
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/mpi/core
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/mpi/core/nrnmpi.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/mpi/nrnmpidec.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/mpi/nrnmpi.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/mpi/lib
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/mpi/lib/nrnmpi.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/mpi/nrnmpiuse.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/config
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/config/config.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/config/version_macros.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/config/neuron_version.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/coreneuron.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/network
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/network/multisend.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/network/have2want.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/network/netpar.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/network/tnode.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/network/netcon.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/network/partrans.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/network/tqueue.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/network/netcvode.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/io
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/io/nrn2core_direct.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/io/mech_report.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/io/core2nrn_data_return.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/io/prcellstate.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/io/nrn_setup.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/io/output_spikes.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/io/lfp.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/io/setup_fornetcon.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/io/nrn_checkpoint.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/io/user_params.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/io/nrnsection_mapping.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/io/nrn_filehandler.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/io/mem_layout_util.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/io/phase1.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/io/phase3.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/io/reports
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/io/reports/report_event.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/io/reports/report_handler.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/io/reports/sonata_report_handler.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/io/reports/nrnreport.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/io/phase2.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/utils
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-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/utils/utils_cuda.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/utils/nrnmutdec.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/utils/string_utils.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/utils/nrn_assert.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/utils/nrnoc_aux.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/utils/progressbar
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-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/utils/memory_utils.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/utils/profile
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-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/utils/lpt.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/utils/offload.hpp
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-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/utils/units.hpp
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-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/utils/nrn_stats.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/utils/ivocvect.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/nrnoc
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-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/sim/fast_imem.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/sim/scopmath
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-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/sim/scopmath/errcodes.h
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-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/sim/scopmath/newton_thread.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/sim/scopmath/ssimplic_thread.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/sim/scopmath/sparse_thread.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/apps
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/apps/corenrn_parameters.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/permute
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/permute/node_permute.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/permute/cellorder.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/coreneuron/permute/data_layout.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/nrnassrt.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/spconfig.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/runge.hpp
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/nrnoc_ml.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/mech_api.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/mcran4.h
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-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/hocparse.h
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-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Random123
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-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/treeset.h
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/share/modfile
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-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/share/coreneuron/nrnivmodl_core_makefile
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/bin/nrnivmodl-core
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/bin/nrniv
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-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/bin/nrngui
-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/bin/neurondemo
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-- Installing: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/bin/set_nrnpyenv.sh
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/librxdmath.dylib
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-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/lib/python/neuron
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-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/products
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-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/TriangularMatrix.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/IO.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/SSE
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/SSE/PacketMath.h
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-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/SSE/Complex.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/GPU
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/GPU/PacketMath.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/GPU/MathFunctions.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/GPU/TypeCasting.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/MSA
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/MSA/PacketMath.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/MSA/MathFunctions.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/MSA/Complex.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/CUDA
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/CUDA/Complex.h
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/ZVector
-- Up-to-date: /Users/gitlab-runner/builds/2/P217482/J1322438/hpc/cellular/nrn/install/include/Eigen/src/Core/arch/ZVector/PacketMath.h
-- Up-to-date: /Users/gitlab-runn
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