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bbpbuildbot/GitLab logs for neuronsimulator-nrn#2909 Secret

Created June 11, 2024 15:07
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Logfiles for GitLab pipeline https://bbpgitlab.epfl.ch/hpc/cellular/nrn/-/pipelines/216288 (:no_entry:) running on GitHub PR neuronsimulator/nrn#2909.
Raw
build-neuron-nmodl-intel-legacy.txt
Running with gitlab-runner 15.5.0 (0d4137b8)
 on BB5 map runner pnPo3yJy
section_start:1718117531:resolve_secrets Resolving secrets
section_end:1718117531:resolve_secrets section_start:1718117531: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-executor921467487, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name nrn
Pipeline ID 216288, build ref , job ID 1315417
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P216288, 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_J1315417_PROD_P2160_CP0_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 2246817
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=2 --cpus-per-task=8 --mem=160G --job-name=GL_J1315417_PROD_P2160_CP0_C4 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P216288 --time=2:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P216288 --ntasks=2 --jobid=2246817 --cpus-per-task=8 --mem=160G
section_end:1718117533:prepare_executor section_start:1718117533:prepare_script Preparing environment
Using git from spack modules
Running on r1i7n20 via bbpv1.epfl.ch...
section_end:1718117544:prepare_script section_start:1718117544: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:1718117545:get_sources section_start:1718117545: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=27380 revision=58ba2b95 version=14.2.0
cache.zip is up to date 
Successfully extracted cache
section_end:1718117551:restore_cache section_start:1718117551:download_artifacts Downloading artifacts
Using git from spack modules
Downloading artifacts for build:nmodl (1315416)...
Runtime platform  arch=amd64 os=linux pid=27487 revision=58ba2b95 version=14.2.0
Downloading artifacts from coordinator... ok  id=1315416 responseStatus=200 OK token=glcbt-64
section_end:1718117552:download_artifacts section_start:1718117552: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/P216288/J1315417/spack-config/config.yaml:2 build_stage:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315417/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315417/spack-build
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315417/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315417/spack-source-cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/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/P216288/J1315414/spack/etc/spack/defaults/config.yaml:18 extensions:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:19 - $spack/bluebrain/spack-scripting
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:37 template_dirs:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:38 - $spack/share/spack/templates
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:41 license_dir: $spack/etc/spack/licenses
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:81 test_stage: $user_cache_path/test
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:94 misc_cache: $user_cache_path/cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:100 connect_timeout: 10
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:105 verify_ssl: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:113 suppress_gpg_warnings: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:119 install_missing_compilers: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:124 checksum: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:129 deprecated: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:134 dirty: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:142 build_language: C
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:151 locks: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:156 url_fetch_method: urllib
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:185 concretizer: clingo
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:192 db_lock_timeout: 60
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:200 package_lock_timeout: null
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:205 shared_linking:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:210 type: rpath
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:216 bind: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:221 allow_sgid: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:227 install_status: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:231 binary_index_ttl: 600
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:233 flags:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:235 keep_werror: none
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:240 aliases:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:241 concretise: concretize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:242 containerise: containerize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/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/P216288/J1315417/spack-config/concretizer.yaml:2 reuse: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:23 targets:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:28 granularity: microarchitectures
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:32 host_compatible: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:38 unify: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:40 duplicates:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/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/P216288/J1315417_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 ^/pis5gl5kpxkhvpyg2ej73radyh56itvx
$ 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/P216288
$ 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/bbpcihpcproj12/2246817/ccache
Config file: /nvme/bbpcihpcproj12/2246817/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: Tue Jun 11 16:52:37 2024
Local storage:
Cache size (GB): 0.45 / 0.51 (88.31%)
Files: 10009
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
- ^/pis5gl5kpxkhvpyg2ej73radyh56itvx
Concretized
--------------------------------
- 5doyqyr neuron@git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9=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
[+] pis5gl5 ^nmodl@git.c5ecfea39cbd53ffcc248b1dcf732c1e0ae1ffc4=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/P216288, 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/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/libyaml-0.2.5-bzl4xc
[+] /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/pkgconf-1.9.5-e533uu
[+] /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-pybind11-2.11.1-tabj2m
[+] /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-markupsafe-2.1.3-r3ehtm
[+] /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-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-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/py-packaging-23.1-uqml2t
==> Installing libsonata-report-git.5602aadfa710d6766ce23cd151a1855190271bd8=develop-fz3oxtcl57lk2z5alhm3jvnsf6bsoiul [41/49]
==> 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: 2.07s. Cmake: 5.14s. Build: 1.53s. Install: 0.11s. Post-install: 0.10s. Total: 9.11s
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/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/gettext-0.22.3-nbi5w5
[+] /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-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-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/P216288/software/install_gcc-12.3.0-skylake/nmodl-git.c5ecfea39cbd53ffcc248b1dcf732c1e0ae1ffc4_develop-pis5gl
==> Installing neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9=develop-5doyqyrjsxjlhn5kjo5pxrln2gyo4ru3 [49/49]
==> No binary for neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9=develop-5doyqyrjsxjlhn5kjo5pxrln2gyo4ru3 found: installing from source
==> No patches needed for neuron
==> neuron: Executing phase: 'cmake'
==> neuron: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
'make' '-j8'
73 errors found in build log:
2757 [ 35%] Built target coreneuron-for-tests
2758 cd /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1
315417/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc
862039da2e2a4ce9_develop-5doyqyrjsxjlhn5kjo5pxrln2gyo4ru3/spack-bu
ild-5doyqyr/bin && /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage
_externals/install_gcc-12.3.0-skylake/cmake-3.27.7-slyoes/bin/cmak
e -E env NMODLHOME= /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpc
proj12/P216288/J1315417/spack-build/spack-stage-neuron-git.e2a6b6e
811fb9749543b72cc862039da2e2a4ce9_develop-5doyqyrjsxjlhn5kjo5pxrln
2gyo4ru3/spack-build-5doyqyr/bin/nrnivmodl-core -b STATIC -m /gpfs
/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/software/i
nstall_gcc-12.3.0-skylake/nmodl-git.c5ecfea39cbd53ffcc248b1dcf732c
1e0ae1ffc4_develop-pis5gl/bin/nmodl -n internal -p 4 .
2759 WARNING: No mod files found in '/gpfs/bbp.cscs.ch/ssd/gitlab_map_j
obs/bbpcihpcproj12/P216288/J1315417/spack-build/spack-stage-neuron
-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-5doyqyrjsxjl
hn5kjo5pxrln2gyo4ru3/spack-build-5doyqyr/bin', compiling default o
nes only!
2760 [INFO] Running: make -j4 -f /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/
bbpcihpcproj12/P216288/J1315417/spack-build/spack-stage-neuron-git
.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-5doyqyrjsxjlhn5k
jo5pxrln2gyo4ru3/spack-build-5doyqyr/share/coreneuron/nrnivmodl_co
re_makefile ROOT=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcpro
j12/P216288/J1315417/spack-build/spack-stage-neuron-git.e2a6b6e811
fb9749543b72cc862039da2e2a4ce9_develop-5doyqyrjsxjlhn5kjo5pxrln2gy
o4ru3/spack-build-5doyqyr MECHLIB_SUFFIX=internal NMODL_BINARY=/gp
fs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/software
/install_gcc-12.3.0-skylake/nmodl-git.c5ecfea39cbd53ffcc248b1dcf73
2c1e0ae1ffc4_develop-pis5gl/bin/nmodl MODS_PATH=x86_64/corenrn/mod
2c BUILD_TYPE=STATIC NRN_PRCELLSTATE=0
2761 make[3]: Entering directory '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs
/bbpcihpcproj12/P216288/J1315417/spack-build/spack-stage-neuron-gi
t.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-5doyqyrjsxjlhn5
kjo5pxrln2gyo4ru3/spack-build-5doyqyr/bin'
2762 make[3]: warning: -j4 forced in submake: resetting jobserver mode.
>> 2763 make[3]: xcrun: No such file or directory
2764 Default NMODL flags:
>> 2765 diff: x86_64/corenrn/mod2c/_mod_func.cpp: No such file or director
y
2766 [NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shado
ws <extern_neuron_var> definition in NMODL_GLOBAL
2767 [NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shado
ws <extern_neuron_var> definition in NMODL_GLOBAL
2768 [NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shado
ws <extern_neuron_var> definition in NMODL_GLOBAL
2769 [NMODL] [warning] :: CVode solver of icur in 64.20-30 replaced wit
h cnexp solver
2770 make[2]: Leaving directory '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/
bbpcihpcproj12/P216288/J1315417/spack-build/spack-stage-neuron-git
.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-5doyqyrjsxjlhn5k
jo5pxrln2gyo4ru3/spack-build-5doyqyr'
2771 [ 35%] Built target nrnpython
...
3364 [ 44%] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/n
rnoc/intfire1.cpp.o
3365 cd /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1
315417/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc
862039da2e2a4ce9_develop-5doyqyrjsxjlhn5kjo5pxrln2gyo4ru3/spack-bu
ild-5doyqyr/src/nrniv && /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbp
cihpcproj12/P216288/J1315414/spack/lib/spack/env/oneapi/icpx -DCOR
ENRN_BUILD=0 -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX=1 -DMPI_NO_CPPBIN
D=1 -DNRN_AVOID_ABSOLUTE_PATHS -DNRN_ENABLE_THREADS -DOMPI_SKIP_MP
ICXX=1 -DUSE_PYTHON -Dnrniv_lib_EXPORTS -I/gpfs/bbp.cscs.ch/ssd/gi
tlab_map_jobs/bbpcihpcproj12/P216288/J1315417/spack-build/spack-st
age-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-5d
oyqyrjsxjlhn5kjo5pxrln2gyo4ru3/spack-build-5doyqyr/include -I/gpfs
/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315417/s
pack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da
2e2a4ce9_develop-5doyqyrjsxjlhn5kjo5pxrln2gyo4ru3/spack-src/src/iv
oc -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/
J1315417/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72
cc862039da2e2a4ce9_develop-5doyqyrjsxjlhn5kjo5pxrln2gyo4ru3/spack-
src/src/nrncvode -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcp
roj12/P216288/J1315417/spack-build/spack-stage-neuron-git.e2a6b6e8
11fb9749543b72cc862039da2e2a4ce9_develop-5doyqyrjsxjlhn5kjo5pxrln2
gyo4ru3/spack-src/src/nrniv -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_job
s/bbpcihpcproj12/P216288/J1315417/spack-build/spack-stage-neuron-g
it.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-5doyqyrjsxjlhn
5kjo5pxrln2gyo4ru3/spack-src/src/nrnoc -I/gpfs/bbp.cscs.ch/ssd/git
lab_map_jobs/bbpcihpcproj12/P216288/J1315417/spack-build/spack-sta
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all_gcc-12.3.0-skylake/python-3.11.6-bj4i6m/include/python3.11 -is
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3368 [ 44%] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/n
rnoc/intfire4.cpp.o
3369 cd /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1
315417/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc
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cihpcproj12/P216288/J1315414/spack/lib/spack/env/oneapi/icpx -DCOR
ENRN_BUILD=0 -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX=1 -DMPI_NO_CPPBIN
D=1 -DNRN_AVOID_ABSOLUTE_PATHS -DNRN_ENABLE_THREADS -DOMPI_SKIP_MP
ICXX=1 -DUSE_PYTHON -Dnrniv_lib_EXPORTS -I/gpfs/bbp.cscs.ch/ssd/gi
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spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039d
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ge-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-5do
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7/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc86203
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pcproj12/P216288/J1315417/spack-build/spack-stage-neuron-git.e2a6b
6e811fb9749543b72cc862039da2e2a4ce9_develop-5doyqyrjsxjlhn5kjo5pxr
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sd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315417/spack-build/spa
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s -I/gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/inst
all_gcc-12.3.0-skylake/python-3.11.6-bj4i6m/include/python3.11 -is
ystem /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288
/J1315417/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b7
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-src/external/eigen -march=skylake -mtune=skylake -fopenmp-simd -g
-O1 -fp-model precise -std=c++17 -fPIC -pthread -MD -MT src/nrni
v/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire4.cpp.o -MF CMakeFiles/
nrniv_lib.dir/__/nrnoc/intfire4.cpp.o.d -o CMakeFiles/nrniv_lib.di
r/__/nrnoc/intfire4.cpp.o -c /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs
/bbpcihpcproj12/P216288/J1315417/spack-build/spack-stage-neuron-gi
t.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-5doyqyrjsxjlhn5
kjo5pxrln2gyo4ru3/spack-build-5doyqyr/src/nrnoc/intfire4.cpp
>> 3370 ../nrnoc/apcount.cpp:346:28: error: use of undeclared identifier '
_gth'; did you mean '_nt'?
3371 double* _globals = _thread[_gth].get<double*>(); // 4
3372 ^~~~
3373 _nt
3374 ../nrnoc/apcount.cpp:337:79: note: '_nt' declared here
3375 static void nrn_init(_nrn_model_sorted_token const& _sorted_token,
NrnThread* _nt, Memb_list* _ml_arg, int _type){
3376
^
>> 3377 ../nrnoc/apcount.cpp:346:27: error: array subscript is not an inte
ger
3378 double* _globals = _thread[_gth].get<double*>(); // 4
3379 ^~~~~
>> 3380 ../nrnoc/apcount.cpp:372:28: error: use of undeclared identifier '
_gth'; did you mean '_nt'?
3381 double* _globals = _thread[_gth].get<double*>(); // 5
3382 ^~~~
3383 _nt
3384 ../nrnoc/apcount.cpp:361:78: note: '_nt' declared here
3385 static void nrn_cur(_nrn_model_sorted_token const& _sorted_token,
NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3386
^
>> 3387 ../nrnoc/apcount.cpp:372:27: error: array subscript is not an inte
ger
3388 double* _globals = _thread[_gth].get<double*>(); // 5
3389 ^~~~~
>> 3390 ../nrnoc/apcount.cpp:391:28: error: use of undeclared identifier '
_gth'; did you mean '_nt'?
3391 double* _globals = _thread[_gth].get<double*>(); // 6
3392 ^~~~
3393 _nt
3394 ../nrnoc/apcount.cpp:381:80: note: '_nt' declared here
3395 static void nrn_jacob(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3396
^
>> 3397 ../nrnoc/apcount.cpp:391:27: error: array subscript is not an inte
ger
3398 double* _globals = _thread[_gth].get<double*>(); // 6
3399 ^~~~~
>> 3400 ../nrnoc/apcount.cpp:408:28: error: use of undeclared identifier '
_gth'; did you mean '_nt'?
3401 double* _globals = _thread[_gth].get<double*>();// 7
3402 ^~~~
3403 _nt
3404 ../nrnoc/apcount.cpp:399:80: note: '_nt' declared here
3405 static void nrn_state(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3406
^
>> 3407 ../nrnoc/apcount.cpp:408:27: error: array subscript is not an inte
ger
3408 double* _globals = _thread[_gth].get<double*>();// 7
3409 ^~~~~
3410 8 errors generated.
>> 3411 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2511:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/apcount.cpp.o] Error 1
3412 make[2]: *** Waiting for unfinished jobs....
>> 3413 ../nrnoc/exp2syn.cpp:358:28: error: use of undeclared identifier '
_gth'; did you mean '_nt'?
3414 double* _globals{_thread[_gth].get<double*>()};
3415 ^~~~
3416 _nt
3417 ../nrnoc/exp2syn.cpp:349:80: note: '_nt' declared here
3418 static void _ode_spec(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3419
^
>> 3420 ../nrnoc/exp2syn.cpp:358:27: error: array subscript is not an inte
ger
3421 double* _globals{_thread[_gth].get<double*>()};
3422 ^~~~~
>> 3423 ../nrnoc/exp2syn.cpp:390:28: error: use of undeclared identifier '
_gth'; did you mean '_nt'?
3424 double* _globals{_thread[_gth].get<double*>()};
3425 ^~~~
3426 _nt
3427 ../nrnoc/exp2syn.cpp:381:82: note: '_nt' declared here
3428 static void _ode_matsol(_nrn_model_sorted_token const& _sorted_tok
en, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3429
^
>> 3430 ../nrnoc/exp2syn.cpp:390:27: error: array subscript is not an inte
ger
3431 double* _globals{_thread[_gth].get<double*>()};
3432 ^~~~~
>> 3433 ../nrnoc/exp2syn.cpp:429:28: error: use of undeclared identifier '
_gth'; did you mean '_nt'?
3434 double* _globals = _thread[_gth].get<double*>(); // 4
3435 ^~~~
3436 _nt
3437 ../nrnoc/exp2syn.cpp:420:79: note: '_nt' declared here
3438 static void nrn_init(_nrn_model_sorted_token const& _sorted_token,
NrnThread* _nt, Memb_list* _ml_arg, int _type){
3439
^
>> 3440 ../nrnoc/exp2syn.cpp:429:27: error: array subscript is not an inte
ger
3441 double* _globals = _thread[_gth].get<double*>(); // 4
3442 ^~~~~
>> 3443 ../nrnoc/exp2syn.cpp:461:28: error: use of undeclared identifier '
_gth'; did you mean '_nt'?
3444 double* _globals = _thread[_gth].get<double*>(); // 5
3445 ^~~~
3446 _nt
3447 ../nrnoc/exp2syn.cpp:450:78: note: '_nt' declared here
3448 static void nrn_cur(_nrn_model_sorted_token const& _sorted_token,
NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3449
^
>> 3450 ../nrnoc/exp2syn.cpp:461:27: error: array subscript is not an inte
ger
3451 double* _globals = _thread[_gth].get<double*>(); // 5
3452 ^~~~~
>> 3453 ../nrnoc/exp2syn.cpp:487:28: error: use of undeclared identifier '
_gth'; did you mean '_nt'?
3454 double* _globals = _thread[_gth].get<double*>(); // 6
3455 ^~~~
3456 _nt
3457 ../nrnoc/exp2syn.cpp:477:80: note: '_nt' declared here
3458 static void nrn_jacob(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3459
^
>> 3460 ../nrnoc/exp2syn.cpp:487:27: error: array subscript is not an inte
ger
3461 double* _globals = _thread[_gth].get<double*>(); // 6
3462 ^~~~~
>> 3463 ../nrnoc/exp2syn.cpp:504:28: error: use of undeclared identifier '
_gth'; did you mean '_nt'?
3464 double* _globals = _thread[_gth].get<double*>();// 7
3465 ^~~~
3466 _nt
3467 ../nrnoc/exp2syn.cpp:495:80: note: '_nt' declared here
3468 static void nrn_state(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3469
^
>> 3470 ../nrnoc/exp2syn.cpp:504:27: error: array subscript is not an inte
ger
3471 double* _globals = _thread[_gth].get<double*>();// 7
3472 ^~~~~
3473 12 errors generated.
>> 3474 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2525:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/exp2syn.cpp.o] Error 1
>> 3475 ../nrnoc/expsyn.cpp:321:28: error: use of undeclared identifier '_
gth'; did you mean '_nt'?
3476 double* _globals{_thread[_gth].get<double*>()};
3477 ^~~~
3478 _nt
3479 ../nrnoc/expsyn.cpp:312:80: note: '_nt' declared here
3480 static void _ode_spec(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3481
^
>> 3482 ../nrnoc/expsyn.cpp:321:27: error: array subscript is not an integ
er
3483 double* _globals{_thread[_gth].get<double*>()};
3484 ^~~~~
>> 3485 ../nrnoc/expsyn.cpp:353:28: error: use of undeclared identifier '_
gth'; did you mean '_nt'?
3486 double* _globals{_thread[_gth].get<double*>()};
3487 ^~~~
3488 _nt
3489 ../nrnoc/expsyn.cpp:344:82: note: '_nt' declared here
3490 static void _ode_matsol(_nrn_model_sorted_token const& _sorted_tok
en, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3491
^
>> 3492 ../nrnoc/expsyn.cpp:353:27: error: array subscript is not an integ
er
3493 double* _globals{_thread[_gth].get<double*>()};
3494 ^~~~~
>> 3495 ../nrnoc/expsyn.cpp:380:28: error: use of undeclared identifier '_
gth'; did you mean '_nt'?
3496 double* _globals = _thread[_gth].get<double*>(); // 4
3497 ^~~~
3498 _nt
3499 ../nrnoc/expsyn.cpp:371:79: note: '_nt' declared here
3500 static void nrn_init(_nrn_model_sorted_token const& _sorted_token,
NrnThread* _nt, Memb_list* _ml_arg, int _type){
3501
^
>> 3502 ../nrnoc/expsyn.cpp:380:27: error: array subscript is not an integ
er
3503 double* _globals = _thread[_gth].get<double*>(); // 4
3504 ^~~~~
>> 3505 ../nrnoc/expsyn.cpp:411:28: error: use of undeclared identifier '_
gth'; did you mean '_nt'?
3506 double* _globals = _thread[_gth].get<double*>(); // 5
3507 ^~~~
3508 _nt
3509 ../nrnoc/expsyn.cpp:400:78: note: '_nt' declared here
3510 static void nrn_cur(_nrn_model_sorted_token const& _sorted_token,
NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3511
^
>> 3512 ../nrnoc/expsyn.cpp:411:27: error: array subscript is not an integ
er
3513 double* _globals = _thread[_gth].get<double*>(); // 5
3514 ^~~~~
>> 3515 ../nrnoc/expsyn.cpp:437:28: error: use of undeclared identifier '_
gth'; did you mean '_nt'?
3516 double* _globals = _thread[_gth].get<double*>(); // 6
3517 ^~~~
3518 _nt
3519 ../nrnoc/expsyn.cpp:427:80: note: '_nt' declared here
3520 static void nrn_jacob(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3521
^
>> 3522 ../nrnoc/expsyn.cpp:437:27: error: array subscript is not an integ
er
3523 double* _globals = _thread[_gth].get<double*>(); // 6
3524 ^~~~~
>> 3525 ../nrnoc/expsyn.cpp:454:28: error: use of undeclared identifier '_
gth'; did you mean '_nt'?
3526 double* _globals = _thread[_gth].get<double*>();// 7
3527 ^~~~
3528 _nt
3529 ../nrnoc/expsyn.cpp:445:80: note: '_nt' declared here
3530 static void nrn_state(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3531
^
>> 3532 ../nrnoc/expsyn.cpp:454:27: error: array subscript is not an integ
er
3533 double* _globals = _thread[_gth].get<double*>();// 7
3534 ^~~~~
3535 12 errors generated.
>> 3536 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2539:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/expsyn.cpp.o] Error 1
>> 3537 ../nrnoc/intfire1.cpp:333:28: error: use of undeclared identifier
'_gth'; did you mean '_nt'?
3538 double* _globals = _thread[_gth].get<double*>(); // 4
3539 ^~~~
3540 _nt
3541 ../nrnoc/intfire1.cpp:324:79: note: '_nt' declared here
3542 static void nrn_init(_nrn_model_sorted_token const& _sorted_token,
NrnThread* _nt, Memb_list* _ml_arg, int _type){
3543
^
>> 3544 ../nrnoc/intfire1.cpp:333:27: error: array subscript is not an int
eger
3545 double* _globals = _thread[_gth].get<double*>(); // 4
3546 ^~~~~
>> 3547 ../nrnoc/intfire1.cpp:356:28: error: use of undeclared identifier
'_gth'; did you mean '_nt'?
3548 double* _globals = _thread[_gth].get<double*>();// 7
3549 ^~~~
3550 _nt
3551 ../nrnoc/intfire1.cpp:347:80: note: '_nt' declared here
3552 static void nrn_state(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3553
^
>> 3554 ../nrnoc/intfire1.cpp:356:27: error: array subscript is not an int
eger
3555 double* _globals = _thread[_gth].get<double*>();// 7
3556 ^~~~~
3557 4 errors generated.
>> 3558 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2581:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire1.cpp.o] Error
1
>> 3559 ../nrnoc/hh.cpp:511:28: error: use of undeclared identifier '_gth'
; did you mean '_nt'?
3560 double* _globals{_thread[_gth].get<double*>()};
3561 ^~~~
3562 _nt
3563 ../nrnoc/hh.cpp:502:80: note: '_nt' declared here
3564 static void _ode_spec(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3565
^
>> 3566 ../nrnoc/hh.cpp:511:27: error: array subscript is not an integer
3567 double* _globals{_thread[_gth].get<double*>()};
3568 ^~~~~
>> 3569 ../nrnoc/hh.cpp:545:28: error: use of undeclared identifier '_gth'
; did you mean '_nt'?
3570 double* _globals{_thread[_gth].get<double*>()};
3571 ^~~~
3572 _nt
3573 ../nrnoc/hh.cpp:536:82: note: '_nt' declared here
3574 static void _ode_matsol(_nrn_model_sorted_token const& _sorted_tok
en, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3575
^
>> 3576 ../nrnoc/hh.cpp:545:27: error: array subscript is not an integer
3577 double* _globals{_thread[_gth].get<double*>()};
3578 ^~~~~
>> 3579 ../nrnoc/hh.cpp:579:28: error: use of undeclared identifier '_gth'
; did you mean '_nt'?
3580 double* _globals = _thread[_gth].get<double*>(); // 4
3581 ^~~~
3582 _nt
3583 ../nrnoc/hh.cpp:570:79: note: '_nt' declared here
3584 static void nrn_init(_nrn_model_sorted_token const& _sorted_token,
NrnThread* _nt, Memb_list* _ml_arg, int _type){
3585
^
>> 3586 ../nrnoc/hh.cpp:579:27: error: array subscript is not an integer
3587 double* _globals = _thread[_gth].get<double*>(); // 4
3588 ^~~~~
>> 3589 ../nrnoc/hh.cpp:617:28: error: use of undeclared identifier '_gth'
; did you mean '_nt'?
3590 double* _globals = _thread[_gth].get<double*>(); // 5
3591 ^~~~
3592 _nt
3593 ../nrnoc/hh.cpp:606:78: note: '_nt' declared here
3594 static void nrn_cur(_nrn_model_sorted_token const& _sorted_token,
NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3595
^
>> 3596 ../nrnoc/hh.cpp:617:27: error: array subscript is not an integer
3597 double* _globals = _thread[_gth].get<double*>(); // 5
3598 ^~~~~
>> 3599 ../nrnoc/hh.cpp:651:28: error: use of undeclared identifier '_gth'
; did you mean '_nt'?
3600 double* _globals = _thread[_gth].get<double*>(); // 6
3601 ^~~~
3602 _nt
3603 ../nrnoc/hh.cpp:641:80: note: '_nt' declared here
3604 static void nrn_jacob(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3605
^
>> 3606 ../nrnoc/hh.cpp:651:27: error: array subscript is not an integer
3607 double* _globals = _thread[_gth].get<double*>(); // 6
3608 ^~~~~
>> 3609 ../nrnoc/hh.cpp:668:28: error: use of undeclared identifier '_gth'
; did you mean '_nt'?
3610 double* _globals = _thread[_gth].get<double*>();// 7
3611 ^~~~
3612 _nt
3613 ../nrnoc/hh.cpp:659:80: note: '_nt' declared here
3614 static void nrn_state(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3615
^
>> 3616 ../nrnoc/hh.cpp:668:27: error: array subscript is not an integer
3617 double* _globals = _thread[_gth].get<double*>();// 7
3618 ^~~~~
3619 12 errors generated.
>> 3620 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2567:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/hh.cpp.o] Error 1
>> 3621 ../nrnoc/intfire2.cpp:344:63: error: use of undeclared identifier
'_globals'
3622 artcell_net_send ( _tqitem, _args, _pnt, t + firetime ( _thr
eadargscomma_ ib , _libf , 0.0 ) , 1.0 ) ;
3623 ^
3624 ../nrnoc/intfire2.cpp:48:55: note: expanded from macro '_threadarg
scomma_'
3625 #define _threadargscomma_ _ml, _iml, _ppvar, _thread, _globals, _n
t,
3626 ^
>> 3627 ../nrnoc/intfire2.cpp:354:53: error: use of undeclared identifier
'_globals'
3628 artcell_net_move ( _tqitem, _pnt, firetime ( _threadargscom
ma_ ib , _libf , m ) + t ) ;
3629 ^
3630 ../nrnoc/intfire2.cpp:48:55: note: expanded from macro '_threadarg
scomma_'
3631 #define _threadargscomma_ _ml, _iml, _ppvar, _thread, _globals, _n
t,
3632 ^
>> 3633 ../nrnoc/intfire2.cpp:497:28: error: use of undeclared identifier
'_gth'; did you mean '_nt'?
3634 double* _globals = _thread[_gth].get<double*>(); // 4
3635 ^~~~
3636 _nt
3637 ../nrnoc/intfire2.cpp:488:79: note: '_nt' declared here
3638 static void nrn_init(_nrn_model_sorted_token const& _sorted_token,
NrnThread* _nt, Memb_list* _ml_arg, int _type){
3639
^
>> 3640 ../nrnoc/intfire2.cpp:497:27: error: array subscript is not an int
eger
3641 double* _globals = _thread[_gth].get<double*>(); // 4
3642 ^~~~~
>> 3643 ../nrnoc/intfire2.cpp:520:28: error: use of undeclared identifier
'_gth'; did you mean '_nt'?
3644 double* _globals = _thread[_gth].get<double*>();// 7
3645 ^~~~
3646 _nt
3647 ../nrnoc/intfire2.cpp:511:80: note: '_nt' declared here
3648 static void nrn_state(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3649
^
>> 3650 ../nrnoc/intfire2.cpp:520:27: error: array subscript is not an int
eger
3651 double* _globals = _thread[_gth].get<double*>();// 7
3652 ^~~~~
3653 6 errors generated.
>> 3654 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2595:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire2.cpp.o] Error
1
>> 3655 ../nrnoc/intfire4.cpp:764:16: error: use of undeclared identifier
'_globals'
3656 newstates ( _threadargscomma_ t - t0 ) ;
3657 ^
3658 ../nrnoc/intfire4.cpp:52:55: note: expanded from macro '_threadarg
scomma_'
3659 #define _threadargscomma_ _ml, _iml, _ppvar, _thread, _globals, _n
t,
3660 ^
>> 3661 ../nrnoc/intfire4.cpp:765:13: error: use of undeclared identifier
'_globals'
3662 update ( _threadargs_ ) ;
3663 ^
3664 ../nrnoc/intfire4.cpp:55:50: note: expanded from macro '_threadarg
s_'
3665 #define _threadargs_ _ml, _iml, _ppvar, _thread, _globals, _nt
3666 ^
>> 3667 ../nrnoc/intfire4.cpp:772:68: error: use of undeclared identifier
'_globals'
3668 artcell_net_send ( _tqitem, _args, _pnt, t + firetimebound (
_threadargs_ ) , 1.0 ) ;
3669
^
3670 ../nrnoc/intfire4.cpp:55:50: note: expanded from macro '_threadarg
s_'
3671 #define _threadargs_ _ml, _iml, _ppvar, _thread, _globals, _nt
3672 ^
>> 3673 ../nrnoc/intfire4.cpp:783:56: error: use of undeclared identifier
'_globals'
3674 artcell_net_move ( _tqitem, _pnt, firetimebound ( _threadargs
_ ) + t ) ;
3675 ^
3676 ../nrnoc/intfire4.cpp:55:50: note: expanded from macro '_threadarg
s_'
3677 #define _threadargs_ _ml, _iml, _ppvar, _thread, _globals, _nt
3678 ^
>> 3679 ../nrnoc/intfire4.cpp:848:28: error: use of undeclared identifier
'_gth'; did you mean '_nt'?
3680 double* _globals = _thread[_gth].get<double*>(); // 4
3681 ^~~~
3682 _nt
3683 ../nrnoc/intfire4.cpp:839:79: note: '_nt' declared here
3684 static void nrn_init(_nrn_model_sorted_token const& _sorted_token,
NrnThread* _nt, Memb_list* _ml_arg, int _type){
3685
^
>> 3686 ../nrnoc/intfire4.cpp:848:27: error: array subscript is not an int
eger
3687 double* _globals = _thread[_gth].get<double*>(); // 4
3688 ^~~~~
>> 3689 ../nrnoc/intfire4.cpp:871:28: error: use of undeclared identifier
'_gth'; did you mean '_nt'?
3690 double* _globals = _thread[_gth].get<double*>();// 7
3691 ^~~~
3692 _nt
3693 ../nrnoc/intfire4.cpp:862:80: note: '_nt' declared here
3694 static void nrn_state(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3695
^
>> 3696 ../nrnoc/intfire4.cpp:871:27: error: array subscript is not an int
eger
3697 double* _globals = _thread[_gth].get<double*>();// 7
3698 ^~~~~
3699 8 errors generated.
>> 3700 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2609:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire4.cpp.o] Error
1
3701 make[2]: Leaving directory '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/
bbpcihpcproj12/P216288/J1315417/spack-build/spack-stage-neuron-git
.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-5doyqyrjsxjlhn5k
jo5pxrln2gyo4ru3/spack-build-5doyqyr'
>> 3702 make[1]: *** [CMakeFiles/Makefile2:2691: src/nrniv/CMakeFiles/nrni
v_lib.dir/all] Error 2
3703 make[1]: Leaving directory '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/
bbpcihpcproj12/P216288/J1315417/spack-build/spack-stage-neuron-git
.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-5doyqyrjsxjlhn5k
jo5pxrln2gyo4ru3/spack-build-5doyqyr'
>> 3704 make: *** [Makefile:169: all] Error 2
See build log for details:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315417/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-5doyqyrjsxjlhn5kjo5pxrln2gyo4ru3/spack-build-out.txt
$ set +o pipefail
$ chmod -R g+rX "${SPACK_BUILD}"
$ if [[ ${install_failed} == 1 ]]; then exit 1; fi
srun: error: r1i7n20: task 0: Exited with exit code 1
section_end:1718117892:step_script section_start:1718117892:upload_artifacts_on_failure Uploading artifacts for failed job
Using git from spack modules
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=35997 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=1315417 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=36043 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
Uploading artifacts as "junit" to coordinator... ok id=1315417 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=36086 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=1315417 responseStatus=201 Created token=glcbt-64
section_end:1718117894:upload_artifacts_on_failure section_start:1718117894:cleanup_file_variables Cleaning up project directory and file based variables
Using git from spack modules
section_end:1718117896:cleanup_file_variables ERROR: Job failed: exit status 1

Raw
build-neuron-nmodl-intel-shared.txt
Running with gitlab-runner 15.5.0 (0d4137b8)
 on BB5 map runner pnPo3yJy
section_start:1718117531:resolve_secrets Resolving secrets
section_end:1718117531:resolve_secrets section_start:1718117531: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-executor559721933, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name nrn
Pipeline ID 216288, build ref , job ID 1315418
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P216288, 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_J1315418_PROD_P2160_CP1_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 2246818
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_J1315418_PROD_P2160_CP1_C7 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P216288 --time=2:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P216288 --ntasks=2 --jobid=2246818 --cpus-per-task=8 --mem=160G
section_end:1718117535:prepare_executor section_start:1718117535:prepare_script Preparing environment
Using git from spack modules
Running on r1i6n12 via bbpv1.epfl.ch...
section_end:1718117544:prepare_script section_start:1718117544: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:1718117545:get_sources section_start:1718117545: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=62001 revision=58ba2b95 version=14.2.0
cache.zip is up to date 
Successfully extracted cache
section_end:1718117551:restore_cache section_start:1718117551:download_artifacts Downloading artifacts
Using git from spack modules
Downloading artifacts for build:nmodl (1315416)...
Runtime platform  arch=amd64 os=linux pid=62110 revision=58ba2b95 version=14.2.0
Downloading artifacts from coordinator... ok  id=1315416 responseStatus=200 OK token=glcbt-64
section_end:1718117553:download_artifacts section_start:1718117553: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/P216288/J1315418/spack-config/config.yaml:2 build_stage:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315418/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315418/spack-build
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315418/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315418/spack-source-cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/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/P216288/J1315414/spack/etc/spack/defaults/config.yaml:18 extensions:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:19 - $spack/bluebrain/spack-scripting
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:37 template_dirs:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:38 - $spack/share/spack/templates
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:41 license_dir: $spack/etc/spack/licenses
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:81 test_stage: $user_cache_path/test
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:94 misc_cache: $user_cache_path/cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:100 connect_timeout: 10
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:105 verify_ssl: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:113 suppress_gpg_warnings: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:119 install_missing_compilers: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:124 checksum: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:129 deprecated: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:134 dirty: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:142 build_language: C
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:151 locks: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:156 url_fetch_method: urllib
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:185 concretizer: clingo
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:192 db_lock_timeout: 60
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:200 package_lock_timeout: null
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:205 shared_linking:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:210 type: rpath
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:216 bind: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:221 allow_sgid: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:227 install_status: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:231 binary_index_ttl: 600
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:233 flags:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:235 keep_werror: none
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:240 aliases:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:241 concretise: concretize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:242 containerise: containerize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/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/P216288/J1315418/spack-config/concretizer.yaml:2 reuse: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:23 targets:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:28 granularity: microarchitectures
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:32 host_compatible: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:38 unify: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:40 duplicates:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/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/P216288/J1315418_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 ^/pis5gl5kpxkhvpyg2ej73radyh56itvx
$ 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/P216288
$ 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/bbpcihpcproj12/2246818/ccache
Config file: /nvme/bbpcihpcproj12/2246818/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: Tue Jun 11 16:52:38 2024
Local storage:
Cache size (GB): 0.47 / 0.51 (91.20%)
Files: 10032
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
- ^/pis5gl5kpxkhvpyg2ej73radyh56itvx
Concretized
--------------------------------
- 3l6td4q neuron@git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9=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
[+] pis5gl5 ^nmodl@git.c5ecfea39cbd53ffcc248b1dcf732c1e0ae1ffc4=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/P216288, 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/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/pkgconf-1.9.5-e533uu
[+] /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/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/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-pybind11-2.11.1-tabj2m
[+] /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-mpmath-1.2.1-4fflyi
[+] /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-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-pip-23.1.2-77ku3v
[+] /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/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-pyyaml-5.4.1-2inh3r
[+] /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-numpy-1.26.1-elr5pn
[+] /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/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-cov-4.0.0-z5nf6n
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/software/install_gcc-12.3.0-skylake/nmodl-git.c5ecfea39cbd53ffcc248b1dcf732c1e0ae1ffc4_develop-pis5gl
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/software/install_oneapi-2023.2.0-skylake/libsonata-report-git.5602aadfa710d6766ce23cd151a1855190271bd8_develop-fz3oxt
==> Installing neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9=develop-3l6td4q3vuabsx5dwdtk7snu7mxieviz [49/49]
==> No binary for neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9=develop-3l6td4q3vuabsx5dwdtk7snu7mxieviz found: installing from source
==> No patches needed for neuron
==> neuron: Executing phase: 'cmake'
==> neuron: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
'make' '-j8'
73 errors found in build log:
2764 [ 34%] Built target coreneuron-for-tests
2765 cd /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1
315418/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc
862039da2e2a4ce9_develop-3l6td4q3vuabsx5dwdtk7snu7mxieviz/spack-bu
ild-3l6td4q/bin && /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage
_externals/install_gcc-12.3.0-skylake/cmake-3.27.7-slyoes/bin/cmak
e -E env NMODLHOME= /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpc
proj12/P216288/J1315418/spack-build/spack-stage-neuron-git.e2a6b6e
811fb9749543b72cc862039da2e2a4ce9_develop-3l6td4q3vuabsx5dwdtk7snu
7mxieviz/spack-build-3l6td4q/bin/nrnivmodl-core -b SHARED -m /gpfs
/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/software/i
nstall_gcc-12.3.0-skylake/nmodl-git.c5ecfea39cbd53ffcc248b1dcf732c
1e0ae1ffc4_develop-pis5gl/bin/nmodl -n internal -p 4 .
2766 WARNING: No mod files found in '/gpfs/bbp.cscs.ch/ssd/gitlab_map_j
obs/bbpcihpcproj12/P216288/J1315418/spack-build/spack-stage-neuron
-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-3l6td4q3vuab
sx5dwdtk7snu7mxieviz/spack-build-3l6td4q/bin', compiling default o
nes only!
2767 [INFO] Running: make -j4 -f /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/
bbpcihpcproj12/P216288/J1315418/spack-build/spack-stage-neuron-git
.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-3l6td4q3vuabsx5d
wdtk7snu7mxieviz/spack-build-3l6td4q/share/coreneuron/nrnivmodl_co
re_makefile ROOT=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcpro
j12/P216288/J1315418/spack-build/spack-stage-neuron-git.e2a6b6e811
fb9749543b72cc862039da2e2a4ce9_develop-3l6td4q3vuabsx5dwdtk7snu7mx
ieviz/spack-build-3l6td4q MECHLIB_SUFFIX=internal NMODL_BINARY=/gp
fs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/software
/install_gcc-12.3.0-skylake/nmodl-git.c5ecfea39cbd53ffcc248b1dcf73
2c1e0ae1ffc4_develop-pis5gl/bin/nmodl MODS_PATH=x86_64/corenrn/mod
2c BUILD_TYPE=SHARED NRN_PRCELLSTATE=0
2768 make[3]: Entering directory '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs
/bbpcihpcproj12/P216288/J1315418/spack-build/spack-stage-neuron-gi
t.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-3l6td4q3vuabsx5
dwdtk7snu7mxieviz/spack-build-3l6td4q/bin'
2769 make[3]: warning: -j4 forced in submake: resetting jobserver mode.
>> 2770 make[3]: xcrun: No such file or directory
2771 Default NMODL flags:
>> 2772 diff: x86_64/corenrn/mod2c/_mod_func.cpp: No such file or director
y
2773 [NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shado
ws <extern_neuron_var> definition in NMODL_GLOBAL
2774 [NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shado
ws <extern_neuron_var> definition in NMODL_GLOBAL
2775 [NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shado
ws <extern_neuron_var> definition in NMODL_GLOBAL
2776 [NMODL] [warning] :: CVode solver of icur in 64.20-30 replaced wit
h cnexp solver
2777 x86_64/corenrn/mod2c/netstim.cpp:487:13: warning: loop not vectori
zed: the optimizer was unable to perform the requested transformat
ion; the transformation might be disabled or specified as part of
an unsupported transformation ordering [-Wpass-failed=transform-wa
rning]
2778 #pragma omp simd
...
3371 [ 43%] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/n
rnoc/intfire1.cpp.o
3372 cd /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1
315418/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc
862039da2e2a4ce9_develop-3l6td4q3vuabsx5dwdtk7snu7mxieviz/spack-bu
ild-3l6td4q/src/nrniv && /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbp
cihpcproj12/P216288/J1315414/spack/lib/spack/env/oneapi/icpx -DCOR
ENRN_BUILD=0 -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX=1 -DMPI_NO_CPPBIN
D=1 -DNRN_AVOID_ABSOLUTE_PATHS -DNRN_ENABLE_THREADS -DOMPI_SKIP_MP
ICXX=1 -DUSE_PYTHON -Dnrniv_lib_EXPORTS -I/gpfs/bbp.cscs.ch/ssd/gi
tlab_map_jobs/bbpcihpcproj12/P216288/J1315418/spack-build/spack-st
age-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-3l
6td4q3vuabsx5dwdtk7snu7mxieviz/spack-build-3l6td4q/include -I/gpfs
/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315418/s
pack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da
2e2a4ce9_develop-3l6td4q3vuabsx5dwdtk7snu7mxieviz/spack-src/src/iv
oc -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/
J1315418/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72
cc862039da2e2a4ce9_develop-3l6td4q3vuabsx5dwdtk7snu7mxieviz/spack-
src/src/nrncvode -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcp
roj12/P216288/J1315418/spack-build/spack-stage-neuron-git.e2a6b6e8
11fb9749543b72cc862039da2e2a4ce9_develop-3l6td4q3vuabsx5dwdtk7snu7
mxieviz/spack-src/src/nrniv -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_job
s/bbpcihpcproj12/P216288/J1315418/spack-build/spack-stage-neuron-g
it.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-3l6td4q3vuabsx
5dwdtk7snu7mxieviz/spack-src/src/nrnoc -I/gpfs/bbp.cscs.ch/ssd/git
lab_map_jobs/bbpcihpcproj12/P216288/J1315418/spack-build/spack-sta
ge-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-3l6
td4q3vuabsx5dwdtk7snu7mxieviz/spack-src/src/oc -I/gpfs/bbp.cscs.ch
/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315418/spack-build/s
pack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_dev
elop-3l6td4q3vuabsx5dwdtk7snu7mxieviz/spack-build-3l6td4q -I/gpfs/
bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315418/sp
ack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2
e2a4ce9_develop-3l6td4q3vuabsx5dwdtk7snu7mxieviz/spack-build-3l6td
4q/src/nrncvode -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcpr
oj12/P216288/J1315418/spack-build/spack-stage-neuron-git.e2a6b6e81
1fb9749543b72cc862039da2e2a4ce9_develop-3l6td4q3vuabsx5dwdtk7snu7m
xieviz/spack-build-3l6td4q/src/nrnoc -I/gpfs/bbp.cscs.ch/ssd/gitla
b_map_jobs/bbpcihpcproj12/P216288/J1315418/spack-build/spack-stage
-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-3l6td
4q3vuabsx5dwdtk7snu7mxieviz/spack-build-3l6td4q/src/nrnpython -I/g
pfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J131541
8/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc86203
9da2e2a4ce9_develop-3l6td4q3vuabsx5dwdtk7snu7mxieviz/spack-build-3
l6td4q/src/oc -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj
12/P216288/J1315418/spack-build/spack-stage-neuron-git.e2a6b6e811f
b9749543b72cc862039da2e2a4ce9_develop-3l6td4q3vuabsx5dwdtk7snu7mxi
eviz/spack-build-3l6td4q/src/parallel -I/gpfs/bbp.cscs.ch/ssd/gitl
ab_map_jobs/bbpcihpcproj12/P216288/J1315418/spack-build/spack-stag
e-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-3l6t
d4q3vuabsx5dwdtk7snu7mxieviz/spack-build-3l6td4q/src/sundials -I/g
pfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J131541
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s -I/gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/inst
all_gcc-12.3.0-skylake/python-3.11.6-bj4i6m/include/python3.11 -is
ystem /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288
/J1315418/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b7
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r/__/nrnoc/intfire2.cpp.o -c /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs
/bbpcihpcproj12/P216288/J1315418/spack-build/spack-stage-neuron-gi
t.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-3l6td4q3vuabsx5
dwdtk7snu7mxieviz/spack-build-3l6td4q/src/nrnoc/intfire2.cpp
3375 [ 43%] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/n
rnoc/intfire4.cpp.o
3376 cd /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1
315418/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc
862039da2e2a4ce9_develop-3l6td4q3vuabsx5dwdtk7snu7mxieviz/spack-bu
ild-3l6td4q/src/nrniv && /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbp
cihpcproj12/P216288/J1315414/spack/lib/spack/env/oneapi/icpx -DCOR
ENRN_BUILD=0 -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX=1 -DMPI_NO_CPPBIN
D=1 -DNRN_AVOID_ABSOLUTE_PATHS -DNRN_ENABLE_THREADS -DOMPI_SKIP_MP
ICXX=1 -DUSE_PYTHON -Dnrniv_lib_EXPORTS -I/gpfs/bbp.cscs.ch/ssd/gi
tlab_map_jobs/bbpcihpcproj12/P216288/J1315418/spack-build/spack-st
age-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-3l
6td4q3vuabsx5dwdtk7snu7mxieviz/spack-build-3l6td4q/include -I/gpfs
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pack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da
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J1315418/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72
cc862039da2e2a4ce9_develop-3l6td4q3vuabsx5dwdtk7snu7mxieviz/spack-
src/src/nrncvode -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcp
roj12/P216288/J1315418/spack-build/spack-stage-neuron-git.e2a6b6e8
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lab_map_jobs/bbpcihpcproj12/P216288/J1315418/spack-build/spack-sta
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elop-3l6td4q3vuabsx5dwdtk7snu7mxieviz/spack-build-3l6td4q -I/gpfs/
bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315418/sp
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rc/src/parallel -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcpr
oj12/P216288/J1315418/spack-build/spack-stage-neuron-git.e2a6b6e81
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e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-3l6td4q3vuabsx5dw
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on-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-3l6td4q3vu
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gitlab_map_jobs/bbpcihpcproj12/P216288/J1315418/spack-build/spack-
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s/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315418/
spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039d
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ieviz/spack-src/src/nrnpython/../nrnoc -I/gpfs/bbp.cscs.ch/ssd/git
lab_map_jobs/bbpcihpcproj12/P216288/J1315418/spack-build/spack-sta
ge-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-3l6
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pfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J131541
8/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc86203
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/nrnpython/../nrniv -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcih
pcproj12/P216288/J1315418/spack-build/spack-stage-neuron-git.e2a6b
6e811fb9749543b72cc862039da2e2a4ce9_develop-3l6td4q3vuabsx5dwdtk7s
nu7mxieviz/spack-src/src/nrnpython/../nrnmpi -I/gpfs/bbp.cscs.ch/s
sd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315418/spack-build/spa
ck-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_devel
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s -I/gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/inst
all_gcc-12.3.0-skylake/python-3.11.6-bj4i6m/include/python3.11 -is
ystem /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288
/J1315418/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b7
2cc862039da2e2a4ce9_develop-3l6td4q3vuabsx5dwdtk7snu7mxieviz/spack
-src/external/eigen -march=skylake -mtune=skylake -fopenmp-simd -g
-O1 -fp-model precise -std=c++17 -fPIC -pthread -MD -MT src/nrni
v/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire4.cpp.o -MF CMakeFiles/
nrniv_lib.dir/__/nrnoc/intfire4.cpp.o.d -o CMakeFiles/nrniv_lib.di
r/__/nrnoc/intfire4.cpp.o -c /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs
/bbpcihpcproj12/P216288/J1315418/spack-build/spack-stage-neuron-gi
t.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-3l6td4q3vuabsx5
dwdtk7snu7mxieviz/spack-build-3l6td4q/src/nrnoc/intfire4.cpp
>> 3377 ../nrnoc/apcount.cpp:346:28: error: use of undeclared identifier '
_gth'; did you mean '_nt'?
3378 double* _globals = _thread[_gth].get<double*>(); // 4
3379 ^~~~
3380 _nt
3381 ../nrnoc/apcount.cpp:337:79: note: '_nt' declared here
3382 static void nrn_init(_nrn_model_sorted_token const& _sorted_token,
NrnThread* _nt, Memb_list* _ml_arg, int _type){
3383
^
>> 3384 ../nrnoc/apcount.cpp:346:27: error: array subscript is not an inte
ger
3385 double* _globals = _thread[_gth].get<double*>(); // 4
3386 ^~~~~
>> 3387 ../nrnoc/apcount.cpp:372:28: error: use of undeclared identifier '
_gth'; did you mean '_nt'?
3388 double* _globals = _thread[_gth].get<double*>(); // 5
3389 ^~~~
3390 _nt
3391 ../nrnoc/apcount.cpp:361:78: note: '_nt' declared here
3392 static void nrn_cur(_nrn_model_sorted_token const& _sorted_token,
NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3393
^
>> 3394 ../nrnoc/apcount.cpp:372:27: error: array subscript is not an inte
ger
3395 double* _globals = _thread[_gth].get<double*>(); // 5
3396 ^~~~~
>> 3397 ../nrnoc/apcount.cpp:391:28: error: use of undeclared identifier '
_gth'; did you mean '_nt'?
3398 double* _globals = _thread[_gth].get<double*>(); // 6
3399 ^~~~
3400 _nt
3401 ../nrnoc/apcount.cpp:381:80: note: '_nt' declared here
3402 static void nrn_jacob(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3403
^
>> 3404 ../nrnoc/apcount.cpp:391:27: error: array subscript is not an inte
ger
3405 double* _globals = _thread[_gth].get<double*>(); // 6
3406 ^~~~~
>> 3407 ../nrnoc/apcount.cpp:408:28: error: use of undeclared identifier '
_gth'; did you mean '_nt'?
3408 double* _globals = _thread[_gth].get<double*>();// 7
3409 ^~~~
3410 _nt
3411 ../nrnoc/apcount.cpp:399:80: note: '_nt' declared here
3412 static void nrn_state(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3413
^
>> 3414 ../nrnoc/apcount.cpp:408:27: error: array subscript is not an inte
ger
3415 double* _globals = _thread[_gth].get<double*>();// 7
3416 ^~~~~
3417 8 errors generated.
>> 3418 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2511:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/apcount.cpp.o] Error 1
3419 make[2]: *** Waiting for unfinished jobs....
>> 3420 ../nrnoc/exp2syn.cpp:358:28: error: use of undeclared identifier '
_gth'; did you mean '_nt'?
3421 double* _globals{_thread[_gth].get<double*>()};
3422 ^~~~
3423 _nt
3424 ../nrnoc/exp2syn.cpp:349:80: note: '_nt' declared here
3425 static void _ode_spec(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3426
^
>> 3427 ../nrnoc/exp2syn.cpp:358:27: error: array subscript is not an inte
ger
3428 double* _globals{_thread[_gth].get<double*>()};
3429 ^~~~~
>> 3430 ../nrnoc/exp2syn.cpp:390:28: error: use of undeclared identifier '
_gth'; did you mean '_nt'?
3431 double* _globals{_thread[_gth].get<double*>()};
3432 ^~~~
3433 _nt
3434 ../nrnoc/exp2syn.cpp:381:82: note: '_nt' declared here
3435 static void _ode_matsol(_nrn_model_sorted_token const& _sorted_tok
en, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3436
^
>> 3437 ../nrnoc/exp2syn.cpp:390:27: error: array subscript is not an inte
ger
3438 double* _globals{_thread[_gth].get<double*>()};
3439 ^~~~~
>> 3440 ../nrnoc/exp2syn.cpp:429:28: error: use of undeclared identifier '
_gth'; did you mean '_nt'?
3441 double* _globals = _thread[_gth].get<double*>(); // 4
3442 ^~~~
3443 _nt
3444 ../nrnoc/exp2syn.cpp:420:79: note: '_nt' declared here
3445 static void nrn_init(_nrn_model_sorted_token const& _sorted_token,
NrnThread* _nt, Memb_list* _ml_arg, int _type){
3446
^
>> 3447 ../nrnoc/exp2syn.cpp:429:27: error: array subscript is not an inte
ger
3448 double* _globals = _thread[_gth].get<double*>(); // 4
3449 ^~~~~
>> 3450 ../nrnoc/exp2syn.cpp:461:28: error: use of undeclared identifier '
_gth'; did you mean '_nt'?
3451 double* _globals = _thread[_gth].get<double*>(); // 5
3452 ^~~~
3453 _nt
3454 ../nrnoc/exp2syn.cpp:450:78: note: '_nt' declared here
3455 static void nrn_cur(_nrn_model_sorted_token const& _sorted_token,
NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3456
^
>> 3457 ../nrnoc/exp2syn.cpp:461:27: error: array subscript is not an inte
ger
3458 double* _globals = _thread[_gth].get<double*>(); // 5
3459 ^~~~~
>> 3460 ../nrnoc/exp2syn.cpp:487:28: error: use of undeclared identifier '
_gth'; did you mean '_nt'?
3461 double* _globals = _thread[_gth].get<double*>(); // 6
3462 ^~~~
3463 _nt
3464 ../nrnoc/exp2syn.cpp:477:80: note: '_nt' declared here
3465 static void nrn_jacob(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3466
^
>> 3467 ../nrnoc/exp2syn.cpp:487:27: error: array subscript is not an inte
ger
3468 double* _globals = _thread[_gth].get<double*>(); // 6
3469 ^~~~~
>> 3470 ../nrnoc/exp2syn.cpp:504:28: error: use of undeclared identifier '
_gth'; did you mean '_nt'?
3471 double* _globals = _thread[_gth].get<double*>();// 7
3472 ^~~~
3473 _nt
3474 ../nrnoc/exp2syn.cpp:495:80: note: '_nt' declared here
3475 static void nrn_state(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3476
^
>> 3477 ../nrnoc/exp2syn.cpp:504:27: error: array subscript is not an inte
ger
3478 double* _globals = _thread[_gth].get<double*>();// 7
3479 ^~~~~
3480 12 errors generated.
>> 3481 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2525:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/exp2syn.cpp.o] Error 1
>> 3482 ../nrnoc/expsyn.cpp:321:28: error: use of undeclared identifier '_
gth'; did you mean '_nt'?
3483 double* _globals{_thread[_gth].get<double*>()};
3484 ^~~~
3485 _nt
3486 ../nrnoc/expsyn.cpp:312:80: note: '_nt' declared here
3487 static void _ode_spec(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3488
^
>> 3489 ../nrnoc/expsyn.cpp:321:27: error: array subscript is not an integ
er
3490 double* _globals{_thread[_gth].get<double*>()};
3491 ^~~~~
>> 3492 ../nrnoc/expsyn.cpp:353:28: error: use of undeclared identifier '_
gth'; did you mean '_nt'?
3493 double* _globals{_thread[_gth].get<double*>()};
3494 ^~~~
3495 _nt
3496 ../nrnoc/expsyn.cpp:344:82: note: '_nt' declared here
3497 static void _ode_matsol(_nrn_model_sorted_token const& _sorted_tok
en, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3498
^
>> 3499 ../nrnoc/expsyn.cpp:353:27: error: array subscript is not an integ
er
3500 double* _globals{_thread[_gth].get<double*>()};
3501 ^~~~~
>> 3502 ../nrnoc/expsyn.cpp:380:28: error: use of undeclared identifier '_
gth'; did you mean '_nt'?
3503 double* _globals = _thread[_gth].get<double*>(); // 4
3504 ^~~~
3505 _nt
3506 ../nrnoc/expsyn.cpp:371:79: note: '_nt' declared here
3507 static void nrn_init(_nrn_model_sorted_token const& _sorted_token,
NrnThread* _nt, Memb_list* _ml_arg, int _type){
3508
^
>> 3509 ../nrnoc/expsyn.cpp:380:27: error: array subscript is not an integ
er
3510 double* _globals = _thread[_gth].get<double*>(); // 4
3511 ^~~~~
>> 3512 ../nrnoc/expsyn.cpp:411:28: error: use of undeclared identifier '_
gth'; did you mean '_nt'?
3513 double* _globals = _thread[_gth].get<double*>(); // 5
3514 ^~~~
3515 _nt
3516 ../nrnoc/expsyn.cpp:400:78: note: '_nt' declared here
3517 static void nrn_cur(_nrn_model_sorted_token const& _sorted_token,
NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3518
^
>> 3519 ../nrnoc/expsyn.cpp:411:27: error: array subscript is not an integ
er
3520 double* _globals = _thread[_gth].get<double*>(); // 5
3521 ^~~~~
>> 3522 ../nrnoc/expsyn.cpp:437:28: error: use of undeclared identifier '_
gth'; did you mean '_nt'?
3523 double* _globals = _thread[_gth].get<double*>(); // 6
3524 ^~~~
3525 _nt
3526 ../nrnoc/expsyn.cpp:427:80: note: '_nt' declared here
3527 static void nrn_jacob(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3528
^
>> 3529 ../nrnoc/expsyn.cpp:437:27: error: array subscript is not an integ
er
3530 double* _globals = _thread[_gth].get<double*>(); // 6
3531 ^~~~~
>> 3532 ../nrnoc/expsyn.cpp:454:28: error: use of undeclared identifier '_
gth'; did you mean '_nt'?
3533 double* _globals = _thread[_gth].get<double*>();// 7
3534 ^~~~
3535 _nt
3536 ../nrnoc/expsyn.cpp:445:80: note: '_nt' declared here
3537 static void nrn_state(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3538
^
>> 3539 ../nrnoc/expsyn.cpp:454:27: error: array subscript is not an integ
er
3540 double* _globals = _thread[_gth].get<double*>();// 7
3541 ^~~~~
3542 12 errors generated.
>> 3543 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2539:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/expsyn.cpp.o] Error 1
>> 3544 ../nrnoc/hh.cpp:511:28: error: use of undeclared identifier '_gth'
; did you mean '_nt'?
3545 double* _globals{_thread[_gth].get<double*>()};
3546 ^~~~
3547 _nt
3548 ../nrnoc/hh.cpp:502:80: note: '_nt' declared here
3549 static void _ode_spec(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3550
^
>> 3551 ../nrnoc/hh.cpp:511:27: error: array subscript is not an integer
3552 double* _globals{_thread[_gth].get<double*>()};
3553 ^~~~~
>> 3554 ../nrnoc/hh.cpp:545:28: error: use of undeclared identifier '_gth'
; did you mean '_nt'?
3555 double* _globals{_thread[_gth].get<double*>()};
3556 ^~~~
3557 _nt
3558 ../nrnoc/hh.cpp:536:82: note: '_nt' declared here
3559 static void _ode_matsol(_nrn_model_sorted_token const& _sorted_tok
en, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3560
^
>> 3561 ../nrnoc/hh.cpp:545:27: error: array subscript is not an integer
3562 double* _globals{_thread[_gth].get<double*>()};
3563 ^~~~~
>> 3564 ../nrnoc/hh.cpp:579:28: error: use of undeclared identifier '_gth'
; did you mean '_nt'?
3565 double* _globals = _thread[_gth].get<double*>(); // 4
3566 ^~~~
3567 _nt
3568 ../nrnoc/hh.cpp:570:79: note: '_nt' declared here
3569 static void nrn_init(_nrn_model_sorted_token const& _sorted_token,
NrnThread* _nt, Memb_list* _ml_arg, int _type){
3570
^
>> 3571 ../nrnoc/hh.cpp:579:27: error: array subscript is not an integer
3572 double* _globals = _thread[_gth].get<double*>(); // 4
3573 ^~~~~
>> 3574 ../nrnoc/hh.cpp:617:28: error: use of undeclared identifier '_gth'
; did you mean '_nt'?
3575 double* _globals = _thread[_gth].get<double*>(); // 5
3576 ^~~~
3577 _nt
3578 ../nrnoc/hh.cpp:606:78: note: '_nt' declared here
3579 static void nrn_cur(_nrn_model_sorted_token const& _sorted_token,
NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3580
^
>> 3581 ../nrnoc/hh.cpp:617:27: error: array subscript is not an integer
3582 double* _globals = _thread[_gth].get<double*>(); // 5
3583 ^~~~~
>> 3584 ../nrnoc/hh.cpp:651:28: error: use of undeclared identifier '_gth'
; did you mean '_nt'?
3585 double* _globals = _thread[_gth].get<double*>(); // 6
3586 ^~~~
3587 _nt
3588 ../nrnoc/hh.cpp:641:80: note: '_nt' declared here
3589 static void nrn_jacob(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3590
^
>> 3591 ../nrnoc/hh.cpp:651:27: error: array subscript is not an integer
3592 double* _globals = _thread[_gth].get<double*>(); // 6
3593 ^~~~~
>> 3594 ../nrnoc/hh.cpp:668:28: error: use of undeclared identifier '_gth'
; did you mean '_nt'?
3595 double* _globals = _thread[_gth].get<double*>();// 7
3596 ^~~~
3597 _nt
3598 ../nrnoc/hh.cpp:659:80: note: '_nt' declared here
3599 static void nrn_state(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3600
^
>> 3601 ../nrnoc/hh.cpp:668:27: error: array subscript is not an integer
3602 double* _globals = _thread[_gth].get<double*>();// 7
3603 ^~~~~
3604 12 errors generated.
>> 3605 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2567:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/hh.cpp.o] Error 1
>> 3606 ../nrnoc/intfire1.cpp:333:28: error: use of undeclared identifier
'_gth'; did you mean '_nt'?
3607 double* _globals = _thread[_gth].get<double*>(); // 4
3608 ^~~~
3609 _nt
3610 ../nrnoc/intfire1.cpp:324:79: note: '_nt' declared here
3611 static void nrn_init(_nrn_model_sorted_token const& _sorted_token,
NrnThread* _nt, Memb_list* _ml_arg, int _type){
3612
^
>> 3613 ../nrnoc/intfire1.cpp:333:27: error: array subscript is not an int
eger
3614 double* _globals = _thread[_gth].get<double*>(); // 4
3615 ^~~~~
>> 3616 ../nrnoc/intfire1.cpp:356:28: error: use of undeclared identifier
'_gth'; did you mean '_nt'?
3617 double* _globals = _thread[_gth].get<double*>();// 7
3618 ^~~~
3619 _nt
3620 ../nrnoc/intfire1.cpp:347:80: note: '_nt' declared here
3621 static void nrn_state(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3622
^
>> 3623 ../nrnoc/intfire1.cpp:356:27: error: array subscript is not an int
eger
3624 double* _globals = _thread[_gth].get<double*>();// 7
3625 ^~~~~
3626 4 errors generated.
>> 3627 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2581:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire1.cpp.o] Error
1
>> 3628 ../nrnoc/intfire2.cpp:344:63: error: use of undeclared identifier
'_globals'
3629 artcell_net_send ( _tqitem, _args, _pnt, t + firetime ( _thr
eadargscomma_ ib , _libf , 0.0 ) , 1.0 ) ;
3630 ^
3631 ../nrnoc/intfire2.cpp:48:55: note: expanded from macro '_threadarg
scomma_'
3632 #define _threadargscomma_ _ml, _iml, _ppvar, _thread, _globals, _n
t,
3633 ^
>> 3634 ../nrnoc/intfire2.cpp:354:53: error: use of undeclared identifier
'_globals'
3635 artcell_net_move ( _tqitem, _pnt, firetime ( _threadargscom
ma_ ib , _libf , m ) + t ) ;
3636 ^
3637 ../nrnoc/intfire2.cpp:48:55: note: expanded from macro '_threadarg
scomma_'
3638 #define _threadargscomma_ _ml, _iml, _ppvar, _thread, _globals, _n
t,
3639 ^
>> 3640 ../nrnoc/intfire2.cpp:497:28: error: use of undeclared identifier
'_gth'; did you mean '_nt'?
3641 double* _globals = _thread[_gth].get<double*>(); // 4
3642 ^~~~
3643 _nt
3644 ../nrnoc/intfire2.cpp:488:79: note: '_nt' declared here
3645 static void nrn_init(_nrn_model_sorted_token const& _sorted_token,
NrnThread* _nt, Memb_list* _ml_arg, int _type){
3646
^
>> 3647 ../nrnoc/intfire2.cpp:497:27: error: array subscript is not an int
eger
3648 double* _globals = _thread[_gth].get<double*>(); // 4
3649 ^~~~~
>> 3650 ../nrnoc/intfire2.cpp:520:28: error: use of undeclared identifier
'_gth'; did you mean '_nt'?
3651 double* _globals = _thread[_gth].get<double*>();// 7
3652 ^~~~
3653 _nt
3654 ../nrnoc/intfire2.cpp:511:80: note: '_nt' declared here
3655 static void nrn_state(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3656
^
>> 3657 ../nrnoc/intfire2.cpp:520:27: error: array subscript is not an int
eger
3658 double* _globals = _thread[_gth].get<double*>();// 7
3659 ^~~~~
3660 6 errors generated.
>> 3661 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2595:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire2.cpp.o] Error
1
>> 3662 ../nrnoc/intfire4.cpp:764:16: error: use of undeclared identifier
'_globals'
3663 newstates ( _threadargscomma_ t - t0 ) ;
3664 ^
3665 ../nrnoc/intfire4.cpp:52:55: note: expanded from macro '_threadarg
scomma_'
3666 #define _threadargscomma_ _ml, _iml, _ppvar, _thread, _globals, _n
t,
3667 ^
>> 3668 ../nrnoc/intfire4.cpp:765:13: error: use of undeclared identifier
'_globals'
3669 update ( _threadargs_ ) ;
3670 ^
3671 ../nrnoc/intfire4.cpp:55:50: note: expanded from macro '_threadarg
s_'
3672 #define _threadargs_ _ml, _iml, _ppvar, _thread, _globals, _nt
3673 ^
>> 3674 ../nrnoc/intfire4.cpp:772:68: error: use of undeclared identifier
'_globals'
3675 artcell_net_send ( _tqitem, _args, _pnt, t + firetimebound (
_threadargs_ ) , 1.0 ) ;
3676
^
3677 ../nrnoc/intfire4.cpp:55:50: note: expanded from macro '_threadarg
s_'
3678 #define _threadargs_ _ml, _iml, _ppvar, _thread, _globals, _nt
3679 ^
>> 3680 ../nrnoc/intfire4.cpp:783:56: error: use of undeclared identifier
'_globals'
3681 artcell_net_move ( _tqitem, _pnt, firetimebound ( _threadargs
_ ) + t ) ;
3682 ^
3683 ../nrnoc/intfire4.cpp:55:50: note: expanded from macro '_threadarg
s_'
3684 #define _threadargs_ _ml, _iml, _ppvar, _thread, _globals, _nt
3685 ^
>> 3686 ../nrnoc/intfire4.cpp:848:28: error: use of undeclared identifier
'_gth'; did you mean '_nt'?
3687 double* _globals = _thread[_gth].get<double*>(); // 4
3688 ^~~~
3689 _nt
3690 ../nrnoc/intfire4.cpp:839:79: note: '_nt' declared here
3691 static void nrn_init(_nrn_model_sorted_token const& _sorted_token,
NrnThread* _nt, Memb_list* _ml_arg, int _type){
3692
^
>> 3693 ../nrnoc/intfire4.cpp:848:27: error: array subscript is not an int
eger
3694 double* _globals = _thread[_gth].get<double*>(); // 4
3695 ^~~~~
>> 3696 ../nrnoc/intfire4.cpp:871:28: error: use of undeclared identifier
'_gth'; did you mean '_nt'?
3697 double* _globals = _thread[_gth].get<double*>();// 7
3698 ^~~~
3699 _nt
3700 ../nrnoc/intfire4.cpp:862:80: note: '_nt' declared here
3701 static void nrn_state(_nrn_model_sorted_token const& _sorted_token
, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
3702
^
>> 3703 ../nrnoc/intfire4.cpp:871:27: error: array subscript is not an int
eger
3704 double* _globals = _thread[_gth].get<double*>();// 7
3705 ^~~~~
3706 8 errors generated.
>> 3707 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2609:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire4.cpp.o] Error
1
3708 make[2]: Leaving directory '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/
bbpcihpcproj12/P216288/J1315418/spack-build/spack-stage-neuron-git
.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-3l6td4q3vuabsx5d
wdtk7snu7mxieviz/spack-build-3l6td4q'
>> 3709 make[1]: *** [CMakeFiles/Makefile2:2699: src/nrniv/CMakeFiles/nrni
v_lib.dir/all] Error 2
3710 make[1]: Leaving directory '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/
bbpcihpcproj12/P216288/J1315418/spack-build/spack-stage-neuron-git
.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-3l6td4q3vuabsx5d
wdtk7snu7mxieviz/spack-build-3l6td4q'
>> 3711 make: *** [Makefile:169: all] Error 2
See build log for details:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315418/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-3l6td4q3vuabsx5dwdtk7snu7mxieviz/spack-build-out.txt
$ set +o pipefail
$ chmod -R g+rX "${SPACK_BUILD}"
$ if [[ ${install_failed} == 1 ]]; then exit 1; fi
srun: error: r1i6n12: task 0: Exited with exit code 1
section_end:1718117910:step_script section_start:1718117910:upload_artifacts_on_failure Uploading artifacts for failed job
Using git from spack modules
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=70246 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=1315418 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=70285 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
Uploading artifacts as "junit" to coordinator... ok id=1315418 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=70327 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=1315418 responseStatus=201 Created token=glcbt-64
section_end:1718117912:upload_artifacts_on_failure section_start:1718117912:cleanup_file_variables Cleaning up project directory and file based variables
Using git from spack modules
section_end:1718117913:cleanup_file_variables ERROR: Job failed: exit status 1

Raw
build-neuron-nmodl-nvhpc-acc-legacy.txt
Running with gitlab-runner 15.5.0 (0d4137b8)
 on BB5 map runner pnPo3yJy
section_start:1718117532:resolve_secrets Resolving secrets
section_end:1718117532:resolve_secrets section_start:1718117532: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-executor3589325974, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name nrn
Pipeline ID 216288, build ref , job ID 1315419
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P216288, 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_J1315419_PROD_P2160_CP2_C8
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 2246819
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_J1315419_PROD_P2160_CP2_C8 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P216288 --time=2:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P216288 --ntasks=2 --jobid=2246819 --cpus-per-task=8 --mem=160G
section_end:1718117536:prepare_executor section_start:1718117536:prepare_script Preparing environment
Using git from spack modules
Running on r1i6n15 via bbpv1.epfl.ch...
section_end:1718117544:prepare_script section_start:1718117544: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:1718117545:get_sources section_start:1718117545: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=80656 revision=58ba2b95 version=14.2.0
cache.zip is up to date 
Successfully extracted cache
section_end:1718117551:restore_cache section_start:1718117551:download_artifacts Downloading artifacts
Using git from spack modules
Downloading artifacts for build:nmodl (1315416)...
Runtime platform  arch=amd64 os=linux pid=80760 revision=58ba2b95 version=14.2.0
Downloading artifacts from coordinator... ok  id=1315416 responseStatus=200 OK token=glcbt-64
section_end:1718117552:download_artifacts section_start:1718117552: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/P216288/J1315419/spack-config/config.yaml:2 build_stage:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315419/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315419/spack-build
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315419/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315419/spack-source-cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/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/P216288/J1315414/spack/etc/spack/defaults/config.yaml:18 extensions:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:19 - $spack/bluebrain/spack-scripting
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:37 template_dirs:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:38 - $spack/share/spack/templates
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:41 license_dir: $spack/etc/spack/licenses
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:81 test_stage: $user_cache_path/test
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:94 misc_cache: $user_cache_path/cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:100 connect_timeout: 10
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:105 verify_ssl: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:113 suppress_gpg_warnings: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:119 install_missing_compilers: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:124 checksum: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:129 deprecated: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:134 dirty: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:142 build_language: C
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:151 locks: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:156 url_fetch_method: urllib
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:185 concretizer: clingo
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:192 db_lock_timeout: 60
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:200 package_lock_timeout: null
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:205 shared_linking:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:210 type: rpath
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:216 bind: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:221 allow_sgid: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:227 install_status: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:231 binary_index_ttl: 600
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:233 flags:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:235 keep_werror: none
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:240 aliases:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:241 concretise: concretize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:242 containerise: containerize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/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/P216288/J1315419/spack-config/concretizer.yaml:2 reuse: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:23 targets:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:28 granularity: microarchitectures
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:32 host_compatible: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:38 unify: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:40 duplicates:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/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/P216288/J1315419_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 ^/pis5gl5kpxkhvpyg2ej73radyh56itvx
$ 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/P216288
$ 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/bbpcihpcproj12/2246819/ccache
Config file: /nvme/bbpcihpcproj12/2246819/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: Tue Jun 11 16:52:37 2024
Local storage:
Cache size (GB): 0.45 / 0.51 (87.43%)
Files: 9802
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
- ^/pis5gl5kpxkhvpyg2ej73radyh56itvx
Concretized
--------------------------------
- t2jmm4v neuron@git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9=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
[+] pis5gl5 ^nmodl@git.c5ecfea39cbd53ffcc248b1dcf732c1e0ae1ffc4=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/P216288, 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/catch2-3.4.0-pywly2
[+] /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/pkgconf-1.9.5-e533uu
[+] /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/pigz-2.7-dwjcgu
[+] /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/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-markupsafe-2.1.3-r3ehtm
[+] /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-pluggy-1.0.0-6su7kv
[+] /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-mpi4py-3.1.4-x733hw
[+] /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-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/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/hdf5-1.14.3-5o77ye
[+] /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-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-az6cwiduk3774jmb44p477xjr6dtnm4g [44/50]
==> 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: 2.13s. Cmake: 4.13s. Build: 1.27s. Install: 0.10s. Post-install: 0.11s. Total: 7.92s
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/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-pytest-7.3.2-lrf2u3
[+] /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/P216288/software/install_gcc-12.3.0-skylake/nmodl-git.c5ecfea39cbd53ffcc248b1dcf732c1e0ae1ffc4_develop-pis5gl
==> Installing neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9=develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt [50/50]
==> No binary for neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9=develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt found: installing from source
==> No patches needed for neuron
==> neuron: Executing phase: 'cmake'
==> neuron: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
'make' '-j8'
98 errors found in build log:
2875 [ 29%] Running nrnivmodl-core with internal mod files
2876 cd /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1
315419/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc
862039da2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-bu
ild-t2jmm4v/bin && /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage
_externals/install_gcc-12.3.0-skylake/cmake-3.27.7-slyoes/bin/cmak
e -E env NMODLHOME= /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpc
proj12/P216288/J1315419/spack-build/spack-stage-neuron-git.e2a6b6e
811fb9749543b72cc862039da2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo
6pc6lbdt/spack-build-t2jmm4v/bin/nrnivmodl-core -b STATIC -m /gpfs
/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/software/i
nstall_gcc-12.3.0-skylake/nmodl-git.c5ecfea39cbd53ffcc248b1dcf732c
1e0ae1ffc4_develop-pis5gl/bin/nmodl -n internal -p 4 .
2877 WARNING: No mod files found in '/gpfs/bbp.cscs.ch/ssd/gitlab_map_j
obs/bbpcihpcproj12/P216288/J1315419/spack-build/spack-stage-neuron
-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t2jmm4vlh7ja
6jtfjua3hnwo6pc6lbdt/spack-build-t2jmm4v/bin', compiling default o
nes only!
2878 [INFO] Running: make -j4 -f /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/
bbpcihpcproj12/P216288/J1315419/spack-build/spack-stage-neuron-git
.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t2jmm4vlh7ja6jtf
jua3hnwo6pc6lbdt/spack-build-t2jmm4v/share/coreneuron/nrnivmodl_co
re_makefile ROOT=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcpro
j12/P216288/J1315419/spack-build/spack-stage-neuron-git.e2a6b6e811
fb9749543b72cc862039da2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc
6lbdt/spack-build-t2jmm4v MECHLIB_SUFFIX=internal NMODL_BINARY=/gp
fs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/software
/install_gcc-12.3.0-skylake/nmodl-git.c5ecfea39cbd53ffcc248b1dcf73
2c1e0ae1ffc4_develop-pis5gl/bin/nmodl MODS_PATH=x86_64/corenrn/mod
2c BUILD_TYPE=STATIC NRN_PRCELLSTATE=0
2879 make[3]: Entering directory '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs
/bbpcihpcproj12/P216288/J1315419/spack-build/spack-stage-neuron-gi
t.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t2jmm4vlh7ja6jt
fjua3hnwo6pc6lbdt/spack-build-t2jmm4v/bin'
2880 make[3]: warning: -j4 forced in submake: resetting jobserver mode.
>> 2881 make[3]: xcrun: No such file or directory
2882 Default NMODL flags:
>> 2883 diff: x86_64/corenrn/mod2c/_mod_func.cpp: No such file or director
y
2884 [NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shado
ws <extern_neuron_var> definition in NMODL_GLOBAL
2885 [NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shado
ws <extern_neuron_var> definition in NMODL_GLOBAL
2886 [NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shado
ws <extern_neuron_var> definition in NMODL_GLOBAL
2887 [NMODL] [warning] :: CVode solver of icur in 64.20-30 replaced wit
h cnexp solver
2888 "../../../spack-src/external/eigen/Eigen/src/Core/arch/AVX/PacketM
ath.h", line 984: warning: integer conversion resulted in a change
of sign [integer_sign_change]
2889 const __m128i sign_mask = _mm_set1_epi16(static_cast<numext::u
int16_t>(0x8000));
...
3491 [ 36%] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/n
rnoc/intfire1.cpp.o
3492 cd /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1
315419/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc
862039da2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-bu
ild-t2jmm4v/src/nrniv && /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbp
cihpcproj12/P216288/J1315414/spack/lib/spack/env/nvhpc/nvc++ -DCOR
ENRN_BUILD=0 -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX=1 -DMPI_NO_CPPBIN
D=1 -DNRN_AVOID_ABSOLUTE_PATHS -DNRN_ENABLE_THREADS -DOMPI_SKIP_MP
ICXX=1 -DUSE_PYTHON -Dnrniv_lib_EXPORTS -I/gpfs/bbp.cscs.ch/ssd/gi
tlab_map_jobs/bbpcihpcproj12/P216288/J1315419/spack-build/spack-st
age-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t2
jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-build-t2jmm4v/include -I/gpfs
/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315419/s
pack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da
2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-src/src/iv
oc -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/
J1315419/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72
cc862039da2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-
src/src/nrncvode -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcp
roj12/P216288/J1315419/spack-build/spack-stage-neuron-git.e2a6b6e8
11fb9749543b72cc862039da2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6
pc6lbdt/spack-src/src/nrniv -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_job
s/bbpcihpcproj12/P216288/J1315419/spack-build/spack-stage-neuron-g
it.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t2jmm4vlh7ja6j
tfjua3hnwo6pc6lbdt/spack-src/src/nrnoc -I/gpfs/bbp.cscs.ch/ssd/git
lab_map_jobs/bbpcihpcproj12/P216288/J1315419/spack-build/spack-sta
ge-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t2j
mm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-src/src/oc -I/gpfs/bbp.cscs.ch
/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315419/spack-build/s
pack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_dev
elop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-build-t2jmm4v -I/gpfs/
bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315419/sp
ack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2
e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-build-t2jmm
4v/src/nrncvode -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcpr
oj12/P216288/J1315419/spack-build/spack-stage-neuron-git.e2a6b6e81
1fb9749543b72cc862039da2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6p
c6lbdt/spack-build-t2jmm4v/src/nrnoc -I/gpfs/bbp.cscs.ch/ssd/gitla
b_map_jobs/bbpcihpcproj12/P216288/J1315419/spack-build/spack-stage
-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t2jmm
4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-build-t2jmm4v/src/nrnpython -I/g
pfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J131541
9/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc86203
9da2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-build-t
2jmm4v/src/oc -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj
12/P216288/J1315419/spack-build/spack-stage-neuron-git.e2a6b6e811f
b9749543b72cc862039da2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6
lbdt/spack-build-t2jmm4v/src/parallel -I/gpfs/bbp.cscs.ch/ssd/gitl
ab_map_jobs/bbpcihpcproj12/P216288/J1315419/spack-build/spack-stag
e-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t2jm
m4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-build-t2jmm4v/src/sundials -I/g
pfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J131541
9/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc86203
9da2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-build-t
2jmm4v/src/sundials/shared -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs
/bbpcihpcproj12/P216288/J1315419/spack-build/spack-stage-neuron-gi
t.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t2jmm4vlh7ja6jt
fjua3hnwo6pc6lbdt/spack-src/src -I/gpfs/bbp.cscs.ch/ssd/gitlab_map
_jobs/bbpcihpcproj12/P216288/J1315419/spack-build/spack-stage-neur
on-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t2jmm4vlh7
ja6jtfjua3hnwo6pc6lbdt/spack-src/src/gnu -I/gpfs/bbp.cscs.ch/ssd/g
itlab_map_jobs/bbpcihpcproj12/P216288/J1315419/spack-build/spack-s
tage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t
2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-src/src/nrnmpi -I/gpfs/bbp.c
scs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315419/spack-b
uild/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4c
e9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-src/src/nrnpytho
n -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J
1315419/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72c
c862039da2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-s
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2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-build-t2jmm4
v/src/nrnoc/intfire2.cpp
3495 [ 36%] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/n
rnoc/intfire4.cpp.o
3496 cd /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1
315419/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc
862039da2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-bu
ild-t2jmm4v/src/nrniv && /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbp
cihpcproj12/P216288/J1315414/spack/lib/spack/env/nvhpc/nvc++ -DCOR
ENRN_BUILD=0 -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX=1 -DMPI_NO_CPPBIN
D=1 -DNRN_AVOID_ABSOLUTE_PATHS -DNRN_ENABLE_THREADS -DOMPI_SKIP_MP
ICXX=1 -DUSE_PYTHON -Dnrniv_lib_EXPORTS -I/gpfs/bbp.cscs.ch/ssd/gi
tlab_map_jobs/bbpcihpcproj12/P216288/J1315419/spack-build/spack-st
age-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t2
jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-build-t2jmm4v/include -I/gpfs
/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315419/s
pack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da
2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-src/src/iv
oc -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/
J1315419/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72
cc862039da2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-
src/src/nrncvode -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcp
roj12/P216288/J1315419/spack-build/spack-stage-neuron-git.e2a6b6e8
11fb9749543b72cc862039da2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6
pc6lbdt/spack-src/src/nrniv -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_job
s/bbpcihpcproj12/P216288/J1315419/spack-build/spack-stage-neuron-g
it.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t2jmm4vlh7ja6j
tfjua3hnwo6pc6lbdt/spack-src/src/nrnoc -I/gpfs/bbp.cscs.ch/ssd/git
lab_map_jobs/bbpcihpcproj12/P216288/J1315419/spack-build/spack-sta
ge-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t2j
mm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-src/src/oc -I/gpfs/bbp.cscs.ch
/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315419/spack-build/s
pack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_dev
elop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-build-t2jmm4v -I/gpfs/
bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315419/sp
ack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2
e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-build-t2jmm
4v/src/nrncvode -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcpr
oj12/P216288/J1315419/spack-build/spack-stage-neuron-git.e2a6b6e81
1fb9749543b72cc862039da2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6p
c6lbdt/spack-build-t2jmm4v/src/nrnoc -I/gpfs/bbp.cscs.ch/ssd/gitla
b_map_jobs/bbpcihpcproj12/P216288/J1315419/spack-build/spack-stage
-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t2jmm
4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-build-t2jmm4v/src/nrnpython -I/g
pfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J131541
9/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc86203
9da2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-build-t
2jmm4v/src/oc -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj
12/P216288/J1315419/spack-build/spack-stage-neuron-git.e2a6b6e811f
b9749543b72cc862039da2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6
lbdt/spack-build-t2jmm4v/src/parallel -I/gpfs/bbp.cscs.ch/ssd/gitl
ab_map_jobs/bbpcihpcproj12/P216288/J1315419/spack-build/spack-stag
e-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t2jm
m4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-build-t2jmm4v/src/sundials -I/g
pfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J131541
9/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc86203
9da2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-build-t
2jmm4v/src/sundials/shared -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs
/bbpcihpcproj12/P216288/J1315419/spack-build/spack-stage-neuron-gi
t.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t2jmm4vlh7ja6jt
fjua3hnwo6pc6lbdt/spack-src/src -I/gpfs/bbp.cscs.ch/ssd/gitlab_map
_jobs/bbpcihpcproj12/P216288/J1315419/spack-build/spack-stage-neur
on-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t2jmm4vlh7
ja6jtfjua3hnwo6pc6lbdt/spack-src/src/gnu -I/gpfs/bbp.cscs.ch/ssd/g
itlab_map_jobs/bbpcihpcproj12/P216288/J1315419/spack-build/spack-s
tage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t
2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-src/src/nrnmpi -I/gpfs/bbp.c
scs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315419/spack-b
uild/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4c
e9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-src/src/nrnpytho
n -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J
1315419/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72c
c862039da2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-s
rc/src/parallel -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcpr
oj12/P216288/J1315419/spack-build/spack-stage-neuron-git.e2a6b6e81
1fb9749543b72cc862039da2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6p
c6lbdt/spack-src/src/scopmath -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_j
obs/bbpcihpcproj12/P216288/J1315419/spack-build/spack-stage-neuron
-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t2jmm4vlh7ja
6jtfjua3hnwo6pc6lbdt/spack-src/src/sparse -I/gpfs/bbp.cscs.ch/ssd/
gitlab_map_jobs/bbpcihpcproj12/P216288/J1315419/spack-build/spack-
stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-
t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-src/src/sparse13 -I/gpfs/bb
p.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315419/spac
k-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2
a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-src/src/sundi
als -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288
/J1315419/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b7
2cc862039da2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack
-src/src/sundials/cvodes -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/b
bpcihpcproj12/P216288/J1315419/spack-build/spack-stage-neuron-git.
e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t2jmm4vlh7ja6jtfj
ua3hnwo6pc6lbdt/spack-src/src/sundials/ida -I/gpfs/bbp.cscs.ch/ssd
/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315419/spack-build/spack
-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop
-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-src/src/sundials/shared -I
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315
419/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862
039da2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-build
-t2jmm4v/src/nrniv/oc_generated -I/gpfs/bbp.cscs.ch/ssd/apps/bsd/2
024-02-01/stage_externals/install_gcc-12.3.0-skylake/hpe-mpi-2.27.
p1.hmpt-6rr256/include -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbp
cihpcproj12/P216288/J1315419/spack-build/spack-stage-neuron-git.e2
a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua
3hnwo6pc6lbdt/spack-src/src/ivos -I/gpfs/bbp.cscs.ch/ssd/gitlab_ma
p_jobs/bbpcihpcproj12/P216288/J1315419/spack-build/spack-stage-neu
ron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t2jmm4vlh
7ja6jtfjua3hnwo6pc6lbdt/spack-src/src/nrnpython/.. -I/gpfs/bbp.csc
s.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315419/spack-bui
ld/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9
_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-src/src/nrnpython/
../oc -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P2162
88/J1315419/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543
b72cc862039da2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spa
ck-src/src/nrnpython/../nrnoc -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_j
obs/bbpcihpcproj12/P216288/J1315419/spack-build/spack-stage-neuron
-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t2jmm4vlh7ja
6jtfjua3hnwo6pc6lbdt/spack-src/src/nrnpython/../ivoc -I/gpfs/bbp.c
scs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315419/spack-b
uild/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4c
e9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-src/src/nrnpytho
n/../nrniv -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/
P216288/J1315419/spack-build/spack-stage-neuron-git.e2a6b6e811fb97
49543b72cc862039da2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbd
t/spack-src/src/nrnpython/../nrnmpi -I/gpfs/bbp.cscs.ch/ssd/gitlab
_map_jobs/bbpcihpcproj12/P216288/J1315419/spack-build/spack-stage-
neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t2jmm4
vlh7ja6jtfjua3hnwo6pc6lbdt/spack-src/src/nrnpython/../ivos -I/gpfs
/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-1
2.3.0-skylake/python-3.11.6-bj4i6m/include/python3.11 -isystem /gp
fs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315419
/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039
da2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-src/exte
rnal/eigen -tp haswell -g -O1 -fno-omit-frame-pointer --c++17 -fP
IC --diag_suppress=1,47,111,128,170,174,177,186,541,550,816,2465 -
noswitcherror -MD -MT src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/
intfire4.cpp.o -MF CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire4.cpp.
o.d -o CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire4.cpp.o -c /gpfs/b
bp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315419/spa
ck-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e
2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-build-t2jmm4
v/src/nrnoc/intfire4.cpp
>> 3497 "../nrnoc/exp2syn.cpp", line 358: error: identifier "_gth" is unde
fined
3498 double* _globals{_thread[_gth].get<double*>()};
3499 ^
3500
>> 3501 "../nrnoc/exp2syn.cpp", line 358: error: type name is not allowed
3502 double* _globals{_thread[_gth].get<double*>()};
3503 ^
3504
>> 3505 "../nrnoc/exp2syn.cpp", line 358: error: expected an expression
3506 double* _globals{_thread[_gth].get<double*>()};
3507 ^
3508
>> 3509 "../nrnoc/exp2syn.cpp", line 390: error: identifier "_gth" is unde
fined
3510 double* _globals{_thread[_gth].get<double*>()};
3511 ^
3512
>> 3513 "../nrnoc/exp2syn.cpp", line 390: error: type name is not allowed
3514 double* _globals{_thread[_gth].get<double*>()};
3515 ^
3516
>> 3517 "../nrnoc/exp2syn.cpp", line 390: error: expected an expression
3518 double* _globals{_thread[_gth].get<double*>()};
3519 ^
3520
>> 3521 "../nrnoc/exp2syn.cpp", line 429: error: identifier "_gth" is unde
fined
3522 double* _globals = _thread[_gth].get<double*>(); // 4
3523 ^
3524
>> 3525 "../nrnoc/exp2syn.cpp", line 429: error: type name is not allowed
3526 double* _globals = _thread[_gth].get<double*>(); // 4
3527 ^
3528
>> 3529 "../nrnoc/exp2syn.cpp", line 429: error: expected an expression
3530 double* _globals = _thread[_gth].get<double*>(); // 4
3531 ^
3532
>> 3533 "../nrnoc/exp2syn.cpp", line 461: error: identifier "_gth" is unde
fined
3534 double* _globals = _thread[_gth].get<double*>(); // 5
3535 ^
3536
>> 3537 "../nrnoc/exp2syn.cpp", line 461: error: type name is not allowed
3538 double* _globals = _thread[_gth].get<double*>(); // 5
3539 ^
3540
>> 3541 "../nrnoc/exp2syn.cpp", line 461: error: expected an expression
3542 double* _globals = _thread[_gth].get<double*>(); // 5
3543 ^
3544
>> 3545 "../nrnoc/exp2syn.cpp", line 487: error: identifier "_gth" is unde
fined
3546 double* _globals = _thread[_gth].get<double*>(); // 6
3547 ^
3548
>> 3549 "../nrnoc/exp2syn.cpp", line 487: error: type name is not allowed
3550 double* _globals = _thread[_gth].get<double*>(); // 6
3551 ^
3552
>> 3553 "../nrnoc/exp2syn.cpp", line 487: error: expected an expression
3554 double* _globals = _thread[_gth].get<double*>(); // 6
3555 ^
3556
>> 3557 "../nrnoc/exp2syn.cpp", line 504: error: identifier "_gth" is unde
fined
3558 double* _globals = _thread[_gth].get<double*>();// 7
3559 ^
3560
>> 3561 "../nrnoc/exp2syn.cpp", line 504: error: type name is not allowed
3562 double* _globals = _thread[_gth].get<double*>();// 7
3563 ^
3564
>> 3565 "../nrnoc/exp2syn.cpp", line 504: error: expected an expression
3566 double* _globals = _thread[_gth].get<double*>();// 7
3567 ^
3568
3569 18 errors detected in the compilation of "../nrnoc/exp2syn.cpp".
>> 3570 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2514:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/exp2syn.cpp.o] Error 2
3571 make[2]: *** Waiting for unfinished jobs....
>> 3572 "../nrnoc/apcount.cpp", line 346: error: identifier "_gth" is unde
fined
3573 double* _globals = _thread[_gth].get<double*>(); // 4
3574 ^
3575
>> 3576 "../nrnoc/apcount.cpp", line 346: error: type name is not allowed
3577 double* _globals = _thread[_gth].get<double*>(); // 4
3578 ^
3579
>> 3580 "../nrnoc/apcount.cpp", line 346: error: expected an expression
3581 double* _globals = _thread[_gth].get<double*>(); // 4
3582 ^
3583
>> 3584 "../nrnoc/apcount.cpp", line 372: error: identifier "_gth" is unde
fined
3585 double* _globals = _thread[_gth].get<double*>(); // 5
3586 ^
3587
>> 3588 "../nrnoc/apcount.cpp", line 372: error: type name is not allowed
3589 double* _globals = _thread[_gth].get<double*>(); // 5
3590 ^
3591
>> 3592 "../nrnoc/apcount.cpp", line 372: error: expected an expression
3593 double* _globals = _thread[_gth].get<double*>(); // 5
3594 ^
3595
>> 3596 "../nrnoc/apcount.cpp", line 391: error: identifier "_gth" is unde
fined
3597 double* _globals = _thread[_gth].get<double*>(); // 6
3598 ^
3599
>> 3600 "../nrnoc/apcount.cpp", line 391: error: type name is not allowed
3601 double* _globals = _thread[_gth].get<double*>(); // 6
3602 ^
3603
>> 3604 "../nrnoc/apcount.cpp", line 391: error: expected an expression
3605 double* _globals = _thread[_gth].get<double*>(); // 6
3606 ^
3607
>> 3608 "../nrnoc/apcount.cpp", line 408: error: identifier "_gth" is unde
fined
3609 double* _globals = _thread[_gth].get<double*>();// 7
3610 ^
3611
>> 3612 "../nrnoc/apcount.cpp", line 408: error: type name is not allowed
3613 double* _globals = _thread[_gth].get<double*>();// 7
3614 ^
3615
>> 3616 "../nrnoc/apcount.cpp", line 408: error: expected an expression
3617 double* _globals = _thread[_gth].get<double*>();// 7
3618 ^
3619
3620 12 errors detected in the compilation of "../nrnoc/apcount.cpp".
>> 3621 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2500:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/apcount.cpp.o] Error 2
>> 3622 "../nrnoc/expsyn.cpp", line 321: error: identifier "_gth" is undef
ined
3623 double* _globals{_thread[_gth].get<double*>()};
3624 ^
3625
>> 3626 "../nrnoc/expsyn.cpp", line 321: error: type name is not allowed
3627 double* _globals{_thread[_gth].get<double*>()};
3628 ^
3629
>> 3630 "../nrnoc/expsyn.cpp", line 321: error: expected an expression
3631 double* _globals{_thread[_gth].get<double*>()};
3632 ^
3633
>> 3634 "../nrnoc/expsyn.cpp", line 353: error: identifier "_gth" is undef
ined
3635 double* _globals{_thread[_gth].get<double*>()};
3636 ^
3637
>> 3638 "../nrnoc/expsyn.cpp", line 353: error: type name is not allowed
3639 double* _globals{_thread[_gth].get<double*>()};
3640 ^
3641
>> 3642 "../nrnoc/expsyn.cpp", line 353: error: expected an expression
3643 double* _globals{_thread[_gth].get<double*>()};
3644 ^
3645
>> 3646 "../nrnoc/expsyn.cpp", line 380: error: identifier "_gth" is undef
ined
3647 double* _globals = _thread[_gth].get<double*>(); // 4
3648 ^
3649
>> 3650 "../nrnoc/expsyn.cpp", line 380: error: type name is not allowed
3651 double* _globals = _thread[_gth].get<double*>(); // 4
3652 ^
3653
>> 3654 "../nrnoc/expsyn.cpp", line 380: error: expected an expression
3655 double* _globals = _thread[_gth].get<double*>(); // 4
3656 ^
3657
>> 3658 "../nrnoc/expsyn.cpp", line 411: error: identifier "_gth" is undef
ined
3659 double* _globals = _thread[_gth].get<double*>(); // 5
3660 ^
3661
>> 3662 "../nrnoc/expsyn.cpp", line 411: error: type name is not allowed
3663 double* _globals = _thread[_gth].get<double*>(); // 5
3664 ^
3665
>> 3666 "../nrnoc/expsyn.cpp", line 411: error: expected an expression
3667 double* _globals = _thread[_gth].get<double*>(); // 5
3668 ^
3669
>> 3670 "../nrnoc/expsyn.cpp", line 437: error: identifier "_gth" is undef
ined
3671 double* _globals = _thread[_gth].get<double*>(); // 6
3672 ^
3673
>> 3674 "../nrnoc/expsyn.cpp", line 437: error: type name is not allowed
3675 double* _globals = _thread[_gth].get<double*>(); // 6
3676 ^
3677
>> 3678 "../nrnoc/expsyn.cpp", line 437: error: expected an expression
3679 double* _globals = _thread[_gth].get<double*>(); // 6
3680 ^
3681
>> 3682 "../nrnoc/expsyn.cpp", line 454: error: identifier "_gth" is undef
ined
3683 double* _globals = _thread[_gth].get<double*>();// 7
3684 ^
3685
>> 3686 "../nrnoc/expsyn.cpp", line 454: error: type name is not allowed
3687 double* _globals = _thread[_gth].get<double*>();// 7
3688 ^
3689
>> 3690 "../nrnoc/expsyn.cpp", line 454: error: expected an expression
3691 double* _globals = _thread[_gth].get<double*>();// 7
3692 ^
3693
3694 18 errors detected in the compilation of "../nrnoc/expsyn.cpp".
>> 3695 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2528:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/expsyn.cpp.o] Error 2
>> 3696 "../nrnoc/hh.cpp", line 511: error: identifier "_gth" is undefined
3697 double* _globals{_thread[_gth].get<double*>()};
3698 ^
3699
>> 3700 "../nrnoc/hh.cpp", line 511: error: type name is not allowed
3701 double* _globals{_thread[_gth].get<double*>()};
3702 ^
3703
>> 3704 "../nrnoc/hh.cpp", line 511: error: expected an expression
3705 double* _globals{_thread[_gth].get<double*>()};
3706 ^
3707
>> 3708 "../nrnoc/hh.cpp", line 545: error: identifier "_gth" is undefined
3709 double* _globals{_thread[_gth].get<double*>()};
3710 ^
3711
>> 3712 "../nrnoc/hh.cpp", line 545: error: type name is not allowed
3713 double* _globals{_thread[_gth].get<double*>()};
3714 ^
3715
>> 3716 "../nrnoc/hh.cpp", line 545: error: expected an expression
3717 double* _globals{_thread[_gth].get<double*>()};
3718 ^
3719
>> 3720 "../nrnoc/hh.cpp", line 579: error: identifier "_gth" is undefined
3721 double* _globals = _thread[_gth].get<double*>(); // 4
3722 ^
3723
>> 3724 "../nrnoc/hh.cpp", line 579: error: type name is not allowed
3725 double* _globals = _thread[_gth].get<double*>(); // 4
3726 ^
3727
>> 3728 "../nrnoc/hh.cpp", line 579: error: expected an expression
3729 double* _globals = _thread[_gth].get<double*>(); // 4
3730 ^
3731
>> 3732 "../nrnoc/hh.cpp", line 617: error: identifier "_gth" is undefined
3733 double* _globals = _thread[_gth].get<double*>(); // 5
3734 ^
3735
>> 3736 "../nrnoc/hh.cpp", line 617: error: type name is not allowed
3737 double* _globals = _thread[_gth].get<double*>(); // 5
3738 ^
3739
>> 3740 "../nrnoc/hh.cpp", line 617: error: expected an expression
3741 double* _globals = _thread[_gth].get<double*>(); // 5
3742 ^
3743
>> 3744 "../nrnoc/hh.cpp", line 651: error: identifier "_gth" is undefined
3745 double* _globals = _thread[_gth].get<double*>(); // 6
3746 ^
3747
>> 3748 "../nrnoc/hh.cpp", line 651: error: type name is not allowed
3749 double* _globals = _thread[_gth].get<double*>(); // 6
3750 ^
3751
>> 3752 "../nrnoc/hh.cpp", line 651: error: expected an expression
3753 double* _globals = _thread[_gth].get<double*>(); // 6
3754 ^
3755
>> 3756 "../nrnoc/hh.cpp", line 668: error: identifier "_gth" is undefined
3757 double* _globals = _thread[_gth].get<double*>();// 7
3758 ^
3759
>> 3760 "../nrnoc/hh.cpp", line 668: error: type name is not allowed
3761 double* _globals = _thread[_gth].get<double*>();// 7
3762 ^
3763
>> 3764 "../nrnoc/hh.cpp", line 668: error: expected an expression
3765 double* _globals = _thread[_gth].get<double*>();// 7
3766 ^
3767
3768 18 errors detected in the compilation of "../nrnoc/hh.cpp".
>> 3769 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2556:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/hh.cpp.o] Error 2
>> 3770 "../nrnoc/intfire1.cpp", line 333: error: identifier "_gth" is und
efined
3771 double* _globals = _thread[_gth].get<double*>(); // 4
3772 ^
3773
>> 3774 "../nrnoc/intfire1.cpp", line 333: error: type name is not allowed
3775 double* _globals = _thread[_gth].get<double*>(); // 4
3776 ^
3777
>> 3778 "../nrnoc/intfire1.cpp", line 333: error: expected an expression
3779 double* _globals = _thread[_gth].get<double*>(); // 4
3780 ^
3781
>> 3782 "../nrnoc/intfire1.cpp", line 356: error: identifier "_gth" is und
efined
3783 double* _globals = _thread[_gth].get<double*>();// 7
3784 ^
3785
>> 3786 "../nrnoc/intfire1.cpp", line 356: error: type name is not allowed
3787 double* _globals = _thread[_gth].get<double*>();// 7
3788 ^
3789
>> 3790 "../nrnoc/intfire1.cpp", line 356: error: expected an expression
3791 double* _globals = _thread[_gth].get<double*>();// 7
3792 ^
3793
3794 6 errors detected in the compilation of "../nrnoc/intfire1.cpp".
>> 3795 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2570:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire1.cpp.o] Error
2
>> 3796 "../nrnoc/intfire2.cpp", line 344: error: identifier "_globals" is
undefined
3797 artcell_net_send ( _tqitem, _args, _pnt, t + firetime ( _t
hreadargscomma_ ib , _libf , 0.0 ) , 1.0 ) ;
3798 ^
3799
>> 3800 "../nrnoc/intfire2.cpp", line 354: error: identifier "_globals" is
undefined
3801 artcell_net_move ( _tqitem, _pnt, firetime ( _threadargsc
omma_ ib , _libf , m ) + t ) ;
3802 ^
3803
>> 3804 "../nrnoc/intfire2.cpp", line 497: error: identifier "_gth" is und
efined
3805 double* _globals = _thread[_gth].get<double*>(); // 4
3806 ^
3807
>> 3808 "../nrnoc/intfire2.cpp", line 497: error: type name is not allowed
3809 double* _globals = _thread[_gth].get<double*>(); // 4
3810 ^
3811
>> 3812 "../nrnoc/intfire2.cpp", line 497: error: expected an expression
3813 double* _globals = _thread[_gth].get<double*>(); // 4
3814 ^
3815
>> 3816 "../nrnoc/intfire2.cpp", line 520: error: identifier "_gth" is und
efined
3817 double* _globals = _thread[_gth].get<double*>();// 7
3818 ^
3819
>> 3820 "../nrnoc/intfire2.cpp", line 520: error: type name is not allowed
3821 double* _globals = _thread[_gth].get<double*>();// 7
3822 ^
3823
>> 3824 "../nrnoc/intfire2.cpp", line 520: error: expected an expression
3825 double* _globals = _thread[_gth].get<double*>();// 7
3826 ^
3827
3828 8 errors detected in the compilation of "../nrnoc/intfire2.cpp".
>> 3829 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2584:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire2.cpp.o] Error
2
>> 3830 "../nrnoc/intfire4.cpp", line 764: error: identifier "_globals" is
undefined
3831 newstates ( _threadargscomma_ t - t0 ) ;
3832 ^
3833
>> 3834 "../nrnoc/intfire4.cpp", line 848: error: identifier "_gth" is und
efined
3835 double* _globals = _thread[_gth].get<double*>(); // 4
3836 ^
3837
>> 3838 "../nrnoc/intfire4.cpp", line 848: error: type name is not allowed
3839 double* _globals = _thread[_gth].get<double*>(); // 4
3840 ^
3841
>> 3842 "../nrnoc/intfire4.cpp", line 848: error: expected an expression
3843 double* _globals = _thread[_gth].get<double*>(); // 4
3844 ^
3845
>> 3846 "../nrnoc/intfire4.cpp", line 871: error: identifier "_gth" is und
efined
3847 double* _globals = _thread[_gth].get<double*>();// 7
3848 ^
3849
>> 3850 "../nrnoc/intfire4.cpp", line 871: error: type name is not allowed
3851 double* _globals = _thread[_gth].get<double*>();// 7
3852 ^
3853
>> 3854 "../nrnoc/intfire4.cpp", line 871: error: expected an expression
3855 double* _globals = _thread[_gth].get<double*>();// 7
3856 ^
3857
3858 7 errors detected in the compilation of "../nrnoc/intfire4.cpp".
>> 3859 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2598:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire4.cpp.o] Error
2
3860 make[2]: Leaving directory '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/
bbpcihpcproj12/P216288/J1315419/spack-build/spack-stage-neuron-git
.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t2jmm4vlh7ja6jtf
jua3hnwo6pc6lbdt/spack-build-t2jmm4v'
>> 3861 make[1]: *** [CMakeFiles/Makefile2:2920: src/nrniv/CMakeFiles/nrni
v_lib.dir/all] Error 2
3862 make[1]: Leaving directory '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/
bbpcihpcproj12/P216288/J1315419/spack-build/spack-stage-neuron-git
.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t2jmm4vlh7ja6jtf
jua3hnwo6pc6lbdt/spack-build-t2jmm4v'
>> 3863 make: *** [Makefile:169: all] Error 2
See build log for details:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315419/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-t2jmm4vlh7ja6jtfjua3hnwo6pc6lbdt/spack-build-out.txt
$ set +o pipefail
$ chmod -R g+rX "${SPACK_BUILD}"
$ if [[ ${install_failed} == 1 ]]; then exit 1; fi
srun: error: r1i6n15: task 0: Exited with exit code 1
section_end:1718118171:step_script section_start:1718118171:upload_artifacts_on_failure Uploading artifacts for failed job
Using git from spack modules
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=89858 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=1315419 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=89896 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
Uploading artifacts as "junit" to coordinator... ok id=1315419 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=89937 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=1315419 responseStatus=201 Created token=glcbt-64
section_end:1718118173:upload_artifacts_on_failure section_start:1718118173:cleanup_file_variables Cleaning up project directory and file based variables
Using git from spack modules
section_end:1718118175:cleanup_file_variables ERROR: Job failed: exit status 1

Raw
build-neuron-nmodl-nvhpc-acc-shared.txt
Running with gitlab-runner 15.5.0 (0d4137b8)
 on BB5 map runner pnPo3yJy
section_start:1718117532:resolve_secrets Resolving secrets
section_end:1718117532:resolve_secrets section_start:1718117532: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-executor4285087646, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name nrn
Pipeline ID 216288, build ref , job ID 1315420
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P216288, 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_J1315420_PROD_P2160_CP3_C9
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 2246820
job state: PD
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=2 --cpus-per-task=8 --mem=160G --job-name=GL_J1315420_PROD_P2160_CP3_C9 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P216288 --time=2:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P216288 --ntasks=2 --jobid=2246820 --cpus-per-task=8 --mem=160G
section_end:1718117535:prepare_executor section_start:1718117535:prepare_script Preparing environment
Using git from spack modules
Running on r1i6n17 via bbpv1.epfl.ch...
section_end:1718117544:prepare_script section_start:1718117544: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:1718117545:get_sources section_start:1718117545: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=130273 revision=58ba2b95 version=14.2.0
cache.zip is up to date 
Successfully extracted cache
section_end:1718117551:restore_cache section_start:1718117551:download_artifacts Downloading artifacts
Using git from spack modules
Downloading artifacts for build:nmodl (1315416)...
Runtime platform  arch=amd64 os=linux pid=130381 revision=58ba2b95 version=14.2.0
Downloading artifacts from coordinator... ok  id=1315416 responseStatus=200 OK token=glcbt-64
section_end:1718117552:download_artifacts section_start:1718117552: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/P216288/J1315420/spack-config/config.yaml:2 build_stage:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-source-cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/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/P216288/J1315414/spack/etc/spack/defaults/config.yaml:18 extensions:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:19 - $spack/bluebrain/spack-scripting
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:37 template_dirs:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:38 - $spack/share/spack/templates
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:41 license_dir: $spack/etc/spack/licenses
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:81 test_stage: $user_cache_path/test
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:94 misc_cache: $user_cache_path/cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:100 connect_timeout: 10
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:105 verify_ssl: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:113 suppress_gpg_warnings: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:119 install_missing_compilers: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:124 checksum: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:129 deprecated: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:134 dirty: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:142 build_language: C
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:151 locks: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:156 url_fetch_method: urllib
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:185 concretizer: clingo
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:192 db_lock_timeout: 60
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:200 package_lock_timeout: null
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:205 shared_linking:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:210 type: rpath
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:216 bind: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:221 allow_sgid: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:227 install_status: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:231 binary_index_ttl: 600
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:233 flags:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:235 keep_werror: none
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:240 aliases:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:241 concretise: concretize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:242 containerise: containerize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/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/P216288/J1315420/spack-config/concretizer.yaml:2 reuse: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:23 targets:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:28 granularity: microarchitectures
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:32 host_compatible: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:38 unify: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:40 duplicates:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/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/P216288/J1315420_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 ^/pis5gl5kpxkhvpyg2ej73radyh56itvx
$ 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/P216288
$ 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/bbpcihpcproj12/2246820/ccache
Config file: /nvme/bbpcihpcproj12/2246820/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: Tue Jun 11 16:52:37 2024
Local storage:
Cache size (GB): 0.46 / 0.51 (90.21%)
Files: 9876
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
- ^/pis5gl5kpxkhvpyg2ej73radyh56itvx
Concretized
--------------------------------
- feyazz7 neuron@git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9=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
[+] pis5gl5 ^nmodl@git.c5ecfea39cbd53ffcc248b1dcf732c1e0ae1ffc4=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/P216288, 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/readline-8.2-pdugg7
[+] /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/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/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/cli11-2.3.2-ud3ech
[+] /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-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-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-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/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/libxml2-2.10.3-oh2g4i
[+] /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-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-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-pyyaml-5.4.1-2inh3r
[+] /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/gettext-0.22.3-nbi5w5
[+] /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-7.3.2-lrf2u3
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/software/install_gcc-12.3.0-skylake/nmodl-git.c5ecfea39cbd53ffcc248b1dcf732c1e0ae1ffc4_develop-pis5gl
[+] /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/P216288/software/install_nvhpc-23.1-skylake/libsonata-report-git.5602aadfa710d6766ce23cd151a1855190271bd8_develop-az6cwi
==> Installing neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9=develop-feyazz75k3pwq642nptcoja6bhwenqvf [50/50]
==> No binary for neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9=develop-feyazz75k3pwq642nptcoja6bhwenqvf found: installing from source
==> No patches needed for neuron
==> neuron: Executing phase: 'cmake'
==> neuron: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
'make' '-j8'
98 errors found in build log:
2878 [ 26%] Running nrnivmodl-core with internal mod files
2879 cd /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1
315420/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc
862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-bu
ild-feyazz7/bin && /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage
_externals/install_gcc-12.3.0-skylake/cmake-3.27.7-slyoes/bin/cmak
e -E env NMODLHOME= /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpc
proj12/P216288/J1315420/spack-build/spack-stage-neuron-git.e2a6b6e
811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6
bhwenqvf/spack-build-feyazz7/bin/nrnivmodl-core -b SHARED -m /gpfs
/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/software/i
nstall_gcc-12.3.0-skylake/nmodl-git.c5ecfea39cbd53ffcc248b1dcf732c
1e0ae1ffc4_develop-pis5gl/bin/nmodl -n internal -p 4 .
2880 WARNING: No mod files found in '/gpfs/bbp.cscs.ch/ssd/gitlab_map_j
obs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage-neuron
-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pw
q642nptcoja6bhwenqvf/spack-build-feyazz7/bin', compiling default o
nes only!
2881 [INFO] Running: make -j4 -f /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/
bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage-neuron-git
.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642
nptcoja6bhwenqvf/spack-build-feyazz7/share/coreneuron/nrnivmodl_co
re_makefile ROOT=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcpro
j12/P216288/J1315420/spack-build/spack-stage-neuron-git.e2a6b6e811
fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhw
enqvf/spack-build-feyazz7 MECHLIB_SUFFIX=internal NMODL_BINARY=/gp
fs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/software
/install_gcc-12.3.0-skylake/nmodl-git.c5ecfea39cbd53ffcc248b1dcf73
2c1e0ae1ffc4_develop-pis5gl/bin/nmodl MODS_PATH=x86_64/corenrn/mod
2c BUILD_TYPE=SHARED NRN_PRCELLSTATE=0
2882 make[3]: Entering directory '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs
/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage-neuron-gi
t.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq64
2nptcoja6bhwenqvf/spack-build-feyazz7/bin'
2883 make[3]: warning: -j4 forced in submake: resetting jobserver mode.
>> 2884 make[3]: xcrun: No such file or directory
2885 Default NMODL flags:
>> 2886 diff: x86_64/corenrn/mod2c/_mod_func.cpp: No such file or director
y
2887 [NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shado
ws <extern_neuron_var> definition in NMODL_GLOBAL
2888 [NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shado
ws <extern_neuron_var> definition in NMODL_GLOBAL
2889 [NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shado
ws <extern_neuron_var> definition in NMODL_GLOBAL
2890 [NMODL] [warning] :: CVode solver of icur in 64.20-30 replaced wit
h cnexp solver
2891 "../../../spack-src/external/eigen/Eigen/src/Core/arch/AVX/PacketM
ath.h", line 984: warning: integer conversion resulted in a change
of sign [integer_sign_change]
2892 const __m128i sign_mask = _mm_set1_epi16(static_cast<numext::u
int16_t>(0x8000));
...
3496 [ 34%] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/n
rnoc/intfire1.cpp.o
3497 cd /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1
315420/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc
862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-bu
ild-feyazz7/src/nrniv && /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbp
cihpcproj12/P216288/J1315414/spack/lib/spack/env/nvhpc/nvc++ -DCOR
ENRN_BUILD=0 -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX=1 -DMPI_NO_CPPBIN
D=1 -DNRN_AVOID_ABSOLUTE_PATHS -DNRN_ENABLE_THREADS -DOMPI_SKIP_MP
ICXX=1 -DUSE_PYTHON -Dnrniv_lib_EXPORTS -I/gpfs/bbp.cscs.ch/ssd/gi
tlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-st
age-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fe
yazz75k3pwq642nptcoja6bhwenqvf/spack-build-feyazz7/include -I/gpfs
/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/s
pack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da
2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-src/src/iv
oc -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/
J1315420/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72
cc862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-
src/src/nrncvode -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcp
roj12/P216288/J1315420/spack-build/spack-stage-neuron-git.e2a6b6e8
11fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6b
hwenqvf/spack-src/src/nrniv -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_job
s/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage-neuron-g
it.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq6
42nptcoja6bhwenqvf/spack-src/src/nrnoc -I/gpfs/bbp.cscs.ch/ssd/git
lab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-sta
ge-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fey
azz75k3pwq642nptcoja6bhwenqvf/spack-src/src/oc -I/gpfs/bbp.cscs.ch
/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/s
pack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_dev
elop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-build-feyazz7 -I/gpfs/
bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/sp
ack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2
e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-build-feyaz
z7/src/nrncvode -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcpr
oj12/P216288/J1315420/spack-build/spack-stage-neuron-git.e2a6b6e81
1fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bh
wenqvf/spack-build-feyazz7/src/nrnoc -I/gpfs/bbp.cscs.ch/ssd/gitla
b_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage
-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyaz
z75k3pwq642nptcoja6bhwenqvf/spack-build-feyazz7/src/nrnpython -I/g
pfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J131542
0/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc86203
9da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-build-f
eyazz7/src/oc -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj
12/P216288/J1315420/spack-build/spack-stage-neuron-git.e2a6b6e811f
b9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwe
nqvf/spack-build-feyazz7/src/parallel -I/gpfs/bbp.cscs.ch/ssd/gitl
ab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stag
e-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feya
zz75k3pwq642nptcoja6bhwenqvf/spack-build-feyazz7/src/sundials -I/g
pfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J131542
0/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc86203
9da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-build-f
eyazz7/src/sundials/shared -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs
/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage-neuron-gi
t.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq64
2nptcoja6bhwenqvf/spack-src/src -I/gpfs/bbp.cscs.ch/ssd/gitlab_map
_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage-neur
on-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3
pwq642nptcoja6bhwenqvf/spack-src/src/gnu -I/gpfs/bbp.cscs.ch/ssd/g
itlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-s
tage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-f
eyazz75k3pwq642nptcoja6bhwenqvf/spack-src/src/nrnmpi -I/gpfs/bbp.c
scs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-b
uild/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4c
e9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-src/src/nrnpytho
n -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J
1315420/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72c
c862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-s
rc/src/parallel -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcpr
oj12/P216288/J1315420/spack-build/spack-stage-neuron-git.e2a6b6e81
1fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bh
wenqvf/spack-src/src/scopmath -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_j
obs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage-neuron
-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pw
q642nptcoja6bhwenqvf/spack-src/src/sparse -I/gpfs/bbp.cscs.ch/ssd/
gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-
stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-
feyazz75k3pwq642nptcoja6bhwenqvf/spack-src/src/sparse13 -I/gpfs/bb
p.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spac
k-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2
a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-src/src/sundi
als -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288
/J1315420/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b7
2cc862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack
-src/src/sundials/cvodes -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/b
bpcihpcproj12/P216288/J1315420/spack-build/spack-stage-neuron-git.
e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642n
ptcoja6bhwenqvf/spack-src/src/sundials/ida -I/gpfs/bbp.cscs.ch/ssd
/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack
-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop
-feyazz75k3pwq642nptcoja6bhwenqvf/spack-src/src/sundials/shared -I
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315
420/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862
039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-build
-feyazz7/src/nrniv/oc_generated -I/gpfs/bbp.cscs.ch/ssd/apps/bsd/2
024-02-01/stage_externals/install_gcc-12.3.0-skylake/hpe-mpi-2.27.
p1.hmpt-6rr256/include -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbp
cihpcproj12/P216288/J1315420/spack-build/spack-stage-neuron-git.e2
a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642npt
coja6bhwenqvf/spack-src/src/ivos -I/gpfs/bbp.cscs.ch/ssd/gitlab_ma
p_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage-neu
ron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k
3pwq642nptcoja6bhwenqvf/spack-src/src/nrnpython/.. -I/gpfs/bbp.csc
s.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-bui
ld/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9
_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-src/src/nrnpython/
../oc -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P2162
88/J1315420/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543
b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spa
ck-src/src/nrnpython/../nrnoc -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_j
obs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage-neuron
-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pw
q642nptcoja6bhwenqvf/spack-src/src/nrnpython/../ivoc -I/gpfs/bbp.c
scs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-b
uild/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4c
e9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-src/src/nrnpytho
n/../nrniv -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/
P216288/J1315420/spack-build/spack-stage-neuron-git.e2a6b6e811fb97
49543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqv
f/spack-src/src/nrnpython/../nrnmpi -I/gpfs/bbp.cscs.ch/ssd/gitlab
_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage-
neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz
75k3pwq642nptcoja6bhwenqvf/spack-src/src/nrnpython/../ivos -I/gpfs
/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-1
2.3.0-skylake/python-3.11.6-bj4i6m/include/python3.11 -isystem /gp
fs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420
/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039
da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-src/exte
rnal/eigen -tp haswell -g -O1 -fno-omit-frame-pointer --c++17 -fP
IC --diag_suppress=1,47,111,128,170,174,177,186,541,550,816,2465 -
noswitcherror -MD -MT src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/
intfire1.cpp.o -MF CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire1.cpp.
o.d -o CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire1.cpp.o -c /gpfs/b
bp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spa
ck-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e
2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-build-feyazz
7/src/nrnoc/intfire1.cpp
3498 [ 35%] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/n
rnoc/intfire2.cpp.o
3499 cd /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1
315420/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc
862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-bu
ild-feyazz7/src/nrniv && /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbp
cihpcproj12/P216288/J1315414/spack/lib/spack/env/nvhpc/nvc++ -DCOR
ENRN_BUILD=0 -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX=1 -DMPI_NO_CPPBIN
D=1 -DNRN_AVOID_ABSOLUTE_PATHS -DNRN_ENABLE_THREADS -DOMPI_SKIP_MP
ICXX=1 -DUSE_PYTHON -Dnrniv_lib_EXPORTS -I/gpfs/bbp.cscs.ch/ssd/gi
tlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-st
age-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fe
yazz75k3pwq642nptcoja6bhwenqvf/spack-build-feyazz7/include -I/gpfs
/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/s
pack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da
2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-src/src/iv
oc -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/
J1315420/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72
cc862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-
src/src/nrncvode -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcp
roj12/P216288/J1315420/spack-build/spack-stage-neuron-git.e2a6b6e8
11fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6b
hwenqvf/spack-src/src/nrniv -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_job
s/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage-neuron-g
it.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq6
42nptcoja6bhwenqvf/spack-src/src/nrnoc -I/gpfs/bbp.cscs.ch/ssd/git
lab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-sta
ge-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fey
azz75k3pwq642nptcoja6bhwenqvf/spack-src/src/oc -I/gpfs/bbp.cscs.ch
/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/s
pack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_dev
elop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-build-feyazz7 -I/gpfs/
bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/sp
ack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2
e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-build-feyaz
z7/src/nrncvode -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcpr
oj12/P216288/J1315420/spack-build/spack-stage-neuron-git.e2a6b6e81
1fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bh
wenqvf/spack-build-feyazz7/src/nrnoc -I/gpfs/bbp.cscs.ch/ssd/gitla
b_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage
-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyaz
z75k3pwq642nptcoja6bhwenqvf/spack-build-feyazz7/src/nrnpython -I/g
pfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J131542
0/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc86203
9da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-build-f
eyazz7/src/oc -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj
12/P216288/J1315420/spack-build/spack-stage-neuron-git.e2a6b6e811f
b9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwe
nqvf/spack-build-feyazz7/src/parallel -I/gpfs/bbp.cscs.ch/ssd/gitl
ab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stag
e-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feya
zz75k3pwq642nptcoja6bhwenqvf/spack-build-feyazz7/src/sundials -I/g
pfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J131542
0/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc86203
9da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-build-f
eyazz7/src/sundials/shared -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs
/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage-neuron-gi
t.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq64
2nptcoja6bhwenqvf/spack-src/src -I/gpfs/bbp.cscs.ch/ssd/gitlab_map
_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage-neur
on-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3
pwq642nptcoja6bhwenqvf/spack-src/src/gnu -I/gpfs/bbp.cscs.ch/ssd/g
itlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-s
tage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-f
eyazz75k3pwq642nptcoja6bhwenqvf/spack-src/src/nrnmpi -I/gpfs/bbp.c
scs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-b
uild/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4c
e9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-src/src/nrnpytho
n -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J
1315420/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72c
c862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-s
rc/src/parallel -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcpr
oj12/P216288/J1315420/spack-build/spack-stage-neuron-git.e2a6b6e81
1fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bh
wenqvf/spack-src/src/scopmath -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_j
obs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage-neuron
-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pw
q642nptcoja6bhwenqvf/spack-src/src/sparse -I/gpfs/bbp.cscs.ch/ssd/
gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-
stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-
feyazz75k3pwq642nptcoja6bhwenqvf/spack-src/src/sparse13 -I/gpfs/bb
p.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spac
k-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2
a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-src/src/sundi
als -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288
/J1315420/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b7
2cc862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack
-src/src/sundials/cvodes -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/b
bpcihpcproj12/P216288/J1315420/spack-build/spack-stage-neuron-git.
e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642n
ptcoja6bhwenqvf/spack-src/src/sundials/ida -I/gpfs/bbp.cscs.ch/ssd
/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack
-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop
-feyazz75k3pwq642nptcoja6bhwenqvf/spack-src/src/sundials/shared -I
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315
420/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862
039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-build
-feyazz7/src/nrniv/oc_generated -I/gpfs/bbp.cscs.ch/ssd/apps/bsd/2
024-02-01/stage_externals/install_gcc-12.3.0-skylake/hpe-mpi-2.27.
p1.hmpt-6rr256/include -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbp
cihpcproj12/P216288/J1315420/spack-build/spack-stage-neuron-git.e2
a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642npt
coja6bhwenqvf/spack-src/src/ivos -I/gpfs/bbp.cscs.ch/ssd/gitlab_ma
p_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage-neu
ron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k
3pwq642nptcoja6bhwenqvf/spack-src/src/nrnpython/.. -I/gpfs/bbp.csc
s.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-bui
ld/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9
_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-src/src/nrnpython/
../oc -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P2162
88/J1315420/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543
b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spa
ck-src/src/nrnpython/../nrnoc -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_j
obs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage-neuron
-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pw
q642nptcoja6bhwenqvf/spack-src/src/nrnpython/../ivoc -I/gpfs/bbp.c
scs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-b
uild/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4c
e9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-src/src/nrnpytho
n/../nrniv -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/
P216288/J1315420/spack-build/spack-stage-neuron-git.e2a6b6e811fb97
49543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqv
f/spack-src/src/nrnpython/../nrnmpi -I/gpfs/bbp.cscs.ch/ssd/gitlab
_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage-
neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz
75k3pwq642nptcoja6bhwenqvf/spack-src/src/nrnpython/../ivos -I/gpfs
/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-1
2.3.0-skylake/python-3.11.6-bj4i6m/include/python3.11 -isystem /gp
fs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420
/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039
da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-src/exte
rnal/eigen -tp haswell -g -O1 -fno-omit-frame-pointer --c++17 -fP
IC --diag_suppress=1,47,111,128,170,174,177,186,541,550,816,2465 -
noswitcherror -MD -MT src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/
intfire2.cpp.o -MF CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire2.cpp.
o.d -o CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire2.cpp.o -c /gpfs/b
bp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spa
ck-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e
2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-build-feyazz
7/src/nrnoc/intfire2.cpp
3500 [ 35%] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/n
rnoc/intfire4.cpp.o
3501 cd /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1
315420/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc
862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-bu
ild-feyazz7/src/nrniv && /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbp
cihpcproj12/P216288/J1315414/spack/lib/spack/env/nvhpc/nvc++ -DCOR
ENRN_BUILD=0 -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX=1 -DMPI_NO_CPPBIN
D=1 -DNRN_AVOID_ABSOLUTE_PATHS -DNRN_ENABLE_THREADS -DOMPI_SKIP_MP
ICXX=1 -DUSE_PYTHON -Dnrniv_lib_EXPORTS -I/gpfs/bbp.cscs.ch/ssd/gi
tlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-st
age-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fe
yazz75k3pwq642nptcoja6bhwenqvf/spack-build-feyazz7/include -I/gpfs
/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/s
pack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da
2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-src/src/iv
oc -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/
J1315420/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72
cc862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-
src/src/nrncvode -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcp
roj12/P216288/J1315420/spack-build/spack-stage-neuron-git.e2a6b6e8
11fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6b
hwenqvf/spack-src/src/nrniv -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_job
s/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage-neuron-g
it.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq6
42nptcoja6bhwenqvf/spack-src/src/nrnoc -I/gpfs/bbp.cscs.ch/ssd/git
lab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-sta
ge-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fey
azz75k3pwq642nptcoja6bhwenqvf/spack-src/src/oc -I/gpfs/bbp.cscs.ch
/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/s
pack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_dev
elop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-build-feyazz7 -I/gpfs/
bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/sp
ack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2
e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-build-feyaz
z7/src/nrncvode -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcpr
oj12/P216288/J1315420/spack-build/spack-stage-neuron-git.e2a6b6e81
1fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bh
wenqvf/spack-build-feyazz7/src/nrnoc -I/gpfs/bbp.cscs.ch/ssd/gitla
b_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage
-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyaz
z75k3pwq642nptcoja6bhwenqvf/spack-build-feyazz7/src/nrnpython -I/g
pfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J131542
0/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc86203
9da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-build-f
eyazz7/src/oc -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj
12/P216288/J1315420/spack-build/spack-stage-neuron-git.e2a6b6e811f
b9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwe
nqvf/spack-build-feyazz7/src/parallel -I/gpfs/bbp.cscs.ch/ssd/gitl
ab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stag
e-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feya
zz75k3pwq642nptcoja6bhwenqvf/spack-build-feyazz7/src/sundials -I/g
pfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J131542
0/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc86203
9da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-build-f
eyazz7/src/sundials/shared -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs
/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage-neuron-gi
t.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq64
2nptcoja6bhwenqvf/spack-src/src -I/gpfs/bbp.cscs.ch/ssd/gitlab_map
_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage-neur
on-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3
pwq642nptcoja6bhwenqvf/spack-src/src/gnu -I/gpfs/bbp.cscs.ch/ssd/g
itlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-s
tage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-f
eyazz75k3pwq642nptcoja6bhwenqvf/spack-src/src/nrnmpi -I/gpfs/bbp.c
scs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-b
uild/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4c
e9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-src/src/nrnpytho
n -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J
1315420/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72c
c862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-s
rc/src/parallel -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcpr
oj12/P216288/J1315420/spack-build/spack-stage-neuron-git.e2a6b6e81
1fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bh
wenqvf/spack-src/src/scopmath -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_j
obs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage-neuron
-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pw
q642nptcoja6bhwenqvf/spack-src/src/sparse -I/gpfs/bbp.cscs.ch/ssd/
gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-
stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-
feyazz75k3pwq642nptcoja6bhwenqvf/spack-src/src/sparse13 -I/gpfs/bb
p.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spac
k-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2
a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-src/src/sundi
als -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288
/J1315420/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b7
2cc862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack
-src/src/sundials/cvodes -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/b
bpcihpcproj12/P216288/J1315420/spack-build/spack-stage-neuron-git.
e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642n
ptcoja6bhwenqvf/spack-src/src/sundials/ida -I/gpfs/bbp.cscs.ch/ssd
/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack
-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop
-feyazz75k3pwq642nptcoja6bhwenqvf/spack-src/src/sundials/shared -I
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315
420/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862
039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-build
-feyazz7/src/nrniv/oc_generated -I/gpfs/bbp.cscs.ch/ssd/apps/bsd/2
024-02-01/stage_externals/install_gcc-12.3.0-skylake/hpe-mpi-2.27.
p1.hmpt-6rr256/include -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbp
cihpcproj12/P216288/J1315420/spack-build/spack-stage-neuron-git.e2
a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642npt
coja6bhwenqvf/spack-src/src/ivos -I/gpfs/bbp.cscs.ch/ssd/gitlab_ma
p_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage-neu
ron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k
3pwq642nptcoja6bhwenqvf/spack-src/src/nrnpython/.. -I/gpfs/bbp.csc
s.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-bui
ld/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9
_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-src/src/nrnpython/
../oc -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P2162
88/J1315420/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543
b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spa
ck-src/src/nrnpython/../nrnoc -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_j
obs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage-neuron
-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pw
q642nptcoja6bhwenqvf/spack-src/src/nrnpython/../ivoc -I/gpfs/bbp.c
scs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-b
uild/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4c
e9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-src/src/nrnpytho
n/../nrniv -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/
P216288/J1315420/spack-build/spack-stage-neuron-git.e2a6b6e811fb97
49543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqv
f/spack-src/src/nrnpython/../nrnmpi -I/gpfs/bbp.cscs.ch/ssd/gitlab
_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage-
neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz
75k3pwq642nptcoja6bhwenqvf/spack-src/src/nrnpython/../ivos -I/gpfs
/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-1
2.3.0-skylake/python-3.11.6-bj4i6m/include/python3.11 -isystem /gp
fs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420
/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039
da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-src/exte
rnal/eigen -tp haswell -g -O1 -fno-omit-frame-pointer --c++17 -fP
IC --diag_suppress=1,47,111,128,170,174,177,186,541,550,816,2465 -
noswitcherror -MD -MT src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/
intfire4.cpp.o -MF CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire4.cpp.
o.d -o CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire4.cpp.o -c /gpfs/b
bp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spa
ck-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e
2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-build-feyazz
7/src/nrnoc/intfire4.cpp
>> 3502 "../nrnoc/exp2syn.cpp", line 358: error: identifier "_gth" is unde
fined
3503 double* _globals{_thread[_gth].get<double*>()};
3504 ^
3505
>> 3506 "../nrnoc/exp2syn.cpp", line 358: error: type name is not allowed
3507 double* _globals{_thread[_gth].get<double*>()};
3508 ^
3509
>> 3510 "../nrnoc/exp2syn.cpp", line 358: error: expected an expression
3511 double* _globals{_thread[_gth].get<double*>()};
3512 ^
3513
>> 3514 "../nrnoc/exp2syn.cpp", line 390: error: identifier "_gth" is unde
fined
3515 double* _globals{_thread[_gth].get<double*>()};
3516 ^
3517
>> 3518 "../nrnoc/exp2syn.cpp", line 390: error: type name is not allowed
3519 double* _globals{_thread[_gth].get<double*>()};
3520 ^
3521
>> 3522 "../nrnoc/exp2syn.cpp", line 390: error: expected an expression
3523 double* _globals{_thread[_gth].get<double*>()};
3524 ^
3525
>> 3526 "../nrnoc/exp2syn.cpp", line 429: error: identifier "_gth" is unde
fined
3527 double* _globals = _thread[_gth].get<double*>(); // 4
3528 ^
3529
>> 3530 "../nrnoc/exp2syn.cpp", line 429: error: type name is not allowed
3531 double* _globals = _thread[_gth].get<double*>(); // 4
3532 ^
3533
>> 3534 "../nrnoc/exp2syn.cpp", line 429: error: expected an expression
3535 double* _globals = _thread[_gth].get<double*>(); // 4
3536 ^
3537
>> 3538 "../nrnoc/exp2syn.cpp", line 461: error: identifier "_gth" is unde
fined
3539 double* _globals = _thread[_gth].get<double*>(); // 5
3540 ^
3541
>> 3542 "../nrnoc/exp2syn.cpp", line 461: error: type name is not allowed
3543 double* _globals = _thread[_gth].get<double*>(); // 5
3544 ^
3545
>> 3546 "../nrnoc/exp2syn.cpp", line 461: error: expected an expression
3547 double* _globals = _thread[_gth].get<double*>(); // 5
3548 ^
3549
>> 3550 "../nrnoc/exp2syn.cpp", line 487: error: identifier "_gth" is unde
fined
3551 double* _globals = _thread[_gth].get<double*>(); // 6
3552 ^
3553
>> 3554 "../nrnoc/exp2syn.cpp", line 487: error: type name is not allowed
3555 double* _globals = _thread[_gth].get<double*>(); // 6
3556 ^
3557
>> 3558 "../nrnoc/exp2syn.cpp", line 487: error: expected an expression
3559 double* _globals = _thread[_gth].get<double*>(); // 6
3560 ^
3561
>> 3562 "../nrnoc/exp2syn.cpp", line 504: error: identifier "_gth" is unde
fined
3563 double* _globals = _thread[_gth].get<double*>();// 7
3564 ^
3565
>> 3566 "../nrnoc/exp2syn.cpp", line 504: error: type name is not allowed
3567 double* _globals = _thread[_gth].get<double*>();// 7
3568 ^
3569
>> 3570 "../nrnoc/exp2syn.cpp", line 504: error: expected an expression
3571 double* _globals = _thread[_gth].get<double*>();// 7
3572 ^
3573
3574 18 errors detected in the compilation of "../nrnoc/exp2syn.cpp".
>> 3575 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2514:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/exp2syn.cpp.o] Error 2
3576 make[2]: *** Waiting for unfinished jobs....
>> 3577 "../nrnoc/apcount.cpp", line 346: error: identifier "_gth" is unde
fined
3578 double* _globals = _thread[_gth].get<double*>(); // 4
3579 ^
3580
>> 3581 "../nrnoc/apcount.cpp", line 346: error: type name is not allowed
3582 double* _globals = _thread[_gth].get<double*>(); // 4
3583 ^
3584
>> 3585 "../nrnoc/apcount.cpp", line 346: error: expected an expression
3586 double* _globals = _thread[_gth].get<double*>(); // 4
3587 ^
3588
>> 3589 "../nrnoc/apcount.cpp", line 372: error: identifier "_gth" is unde
fined
3590 double* _globals = _thread[_gth].get<double*>(); // 5
3591 ^
3592
>> 3593 "../nrnoc/apcount.cpp", line 372: error: type name is not allowed
3594 double* _globals = _thread[_gth].get<double*>(); // 5
3595 ^
3596
>> 3597 "../nrnoc/apcount.cpp", line 372: error: expected an expression
3598 double* _globals = _thread[_gth].get<double*>(); // 5
3599 ^
3600
>> 3601 "../nrnoc/apcount.cpp", line 391: error: identifier "_gth" is unde
fined
3602 double* _globals = _thread[_gth].get<double*>(); // 6
3603 ^
3604
>> 3605 "../nrnoc/apcount.cpp", line 391: error: type name is not allowed
3606 double* _globals = _thread[_gth].get<double*>(); // 6
3607 ^
3608
>> 3609 "../nrnoc/apcount.cpp", line 391: error: expected an expression
3610 double* _globals = _thread[_gth].get<double*>(); // 6
3611 ^
3612
>> 3613 "../nrnoc/apcount.cpp", line 408: error: identifier "_gth" is unde
fined
3614 double* _globals = _thread[_gth].get<double*>();// 7
3615 ^
3616
>> 3617 "../nrnoc/apcount.cpp", line 408: error: type name is not allowed
3618 double* _globals = _thread[_gth].get<double*>();// 7
3619 ^
3620
>> 3621 "../nrnoc/apcount.cpp", line 408: error: expected an expression
3622 double* _globals = _thread[_gth].get<double*>();// 7
3623 ^
3624
3625 12 errors detected in the compilation of "../nrnoc/apcount.cpp".
>> 3626 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2500:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/apcount.cpp.o] Error 2
>> 3627 "../nrnoc/expsyn.cpp", line 321: error: identifier "_gth" is undef
ined
3628 double* _globals{_thread[_gth].get<double*>()};
3629 ^
3630
>> 3631 "../nrnoc/expsyn.cpp", line 321: error: type name is not allowed
3632 double* _globals{_thread[_gth].get<double*>()};
3633 ^
3634
>> 3635 "../nrnoc/expsyn.cpp", line 321: error: expected an expression
3636 double* _globals{_thread[_gth].get<double*>()};
3637 ^
3638
>> 3639 "../nrnoc/expsyn.cpp", line 353: error: identifier "_gth" is undef
ined
3640 double* _globals{_thread[_gth].get<double*>()};
3641 ^
3642
>> 3643 "../nrnoc/expsyn.cpp", line 353: error: type name is not allowed
3644 double* _globals{_thread[_gth].get<double*>()};
3645 ^
3646
>> 3647 "../nrnoc/expsyn.cpp", line 353: error: expected an expression
3648 double* _globals{_thread[_gth].get<double*>()};
3649 ^
3650
>> 3651 "../nrnoc/expsyn.cpp", line 380: error: identifier "_gth" is undef
ined
3652 double* _globals = _thread[_gth].get<double*>(); // 4
3653 ^
3654
>> 3655 "../nrnoc/expsyn.cpp", line 380: error: type name is not allowed
3656 double* _globals = _thread[_gth].get<double*>(); // 4
3657 ^
3658
>> 3659 "../nrnoc/expsyn.cpp", line 380: error: expected an expression
3660 double* _globals = _thread[_gth].get<double*>(); // 4
3661 ^
3662
>> 3663 "../nrnoc/expsyn.cpp", line 411: error: identifier "_gth" is undef
ined
3664 double* _globals = _thread[_gth].get<double*>(); // 5
3665 ^
3666
>> 3667 "../nrnoc/expsyn.cpp", line 411: error: type name is not allowed
3668 double* _globals = _thread[_gth].get<double*>(); // 5
3669 ^
3670
>> 3671 "../nrnoc/expsyn.cpp", line 411: error: expected an expression
3672 double* _globals = _thread[_gth].get<double*>(); // 5
3673 ^
3674
>> 3675 "../nrnoc/expsyn.cpp", line 437: error: identifier "_gth" is undef
ined
3676 double* _globals = _thread[_gth].get<double*>(); // 6
3677 ^
3678
>> 3679 "../nrnoc/expsyn.cpp", line 437: error: type name is not allowed
3680 double* _globals = _thread[_gth].get<double*>(); // 6
3681 ^
3682
>> 3683 "../nrnoc/expsyn.cpp", line 437: error: expected an expression
3684 double* _globals = _thread[_gth].get<double*>(); // 6
3685 ^
3686
>> 3687 "../nrnoc/expsyn.cpp", line 454: error: identifier "_gth" is undef
ined
3688 double* _globals = _thread[_gth].get<double*>();// 7
3689 ^
3690
>> 3691 "../nrnoc/expsyn.cpp", line 454: error: type name is not allowed
3692 double* _globals = _thread[_gth].get<double*>();// 7
3693 ^
3694
>> 3695 "../nrnoc/expsyn.cpp", line 454: error: expected an expression
3696 double* _globals = _thread[_gth].get<double*>();// 7
3697 ^
3698
3699 18 errors detected in the compilation of "../nrnoc/expsyn.cpp".
>> 3700 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2528:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/expsyn.cpp.o] Error 2
>> 3701 "../nrnoc/hh.cpp", line 511: error: identifier "_gth" is undefined
3702 double* _globals{_thread[_gth].get<double*>()};
3703 ^
3704
>> 3705 "../nrnoc/hh.cpp", line 511: error: type name is not allowed
3706 double* _globals{_thread[_gth].get<double*>()};
3707 ^
3708
>> 3709 "../nrnoc/hh.cpp", line 511: error: expected an expression
3710 double* _globals{_thread[_gth].get<double*>()};
3711 ^
3712
>> 3713 "../nrnoc/hh.cpp", line 545: error: identifier "_gth" is undefined
3714 double* _globals{_thread[_gth].get<double*>()};
3715 ^
3716
>> 3717 "../nrnoc/hh.cpp", line 545: error: type name is not allowed
3718 double* _globals{_thread[_gth].get<double*>()};
3719 ^
3720
>> 3721 "../nrnoc/hh.cpp", line 545: error: expected an expression
3722 double* _globals{_thread[_gth].get<double*>()};
3723 ^
3724
>> 3725 "../nrnoc/hh.cpp", line 579: error: identifier "_gth" is undefined
3726 double* _globals = _thread[_gth].get<double*>(); // 4
3727 ^
3728
>> 3729 "../nrnoc/hh.cpp", line 579: error: type name is not allowed
3730 double* _globals = _thread[_gth].get<double*>(); // 4
3731 ^
3732
>> 3733 "../nrnoc/hh.cpp", line 579: error: expected an expression
3734 double* _globals = _thread[_gth].get<double*>(); // 4
3735 ^
3736
>> 3737 "../nrnoc/hh.cpp", line 617: error: identifier "_gth" is undefined
3738 double* _globals = _thread[_gth].get<double*>(); // 5
3739 ^
3740
>> 3741 "../nrnoc/hh.cpp", line 617: error: type name is not allowed
3742 double* _globals = _thread[_gth].get<double*>(); // 5
3743 ^
3744
>> 3745 "../nrnoc/hh.cpp", line 617: error: expected an expression
3746 double* _globals = _thread[_gth].get<double*>(); // 5
3747 ^
3748
>> 3749 "../nrnoc/hh.cpp", line 651: error: identifier "_gth" is undefined
3750 double* _globals = _thread[_gth].get<double*>(); // 6
3751 ^
3752
>> 3753 "../nrnoc/hh.cpp", line 651: error: type name is not allowed
3754 double* _globals = _thread[_gth].get<double*>(); // 6
3755 ^
3756
>> 3757 "../nrnoc/hh.cpp", line 651: error: expected an expression
3758 double* _globals = _thread[_gth].get<double*>(); // 6
3759 ^
3760
>> 3761 "../nrnoc/hh.cpp", line 668: error: identifier "_gth" is undefined
3762 double* _globals = _thread[_gth].get<double*>();// 7
3763 ^
3764
>> 3765 "../nrnoc/hh.cpp", line 668: error: type name is not allowed
3766 double* _globals = _thread[_gth].get<double*>();// 7
3767 ^
3768
>> 3769 "../nrnoc/hh.cpp", line 668: error: expected an expression
3770 double* _globals = _thread[_gth].get<double*>();// 7
3771 ^
3772
3773 18 errors detected in the compilation of "../nrnoc/hh.cpp".
>> 3774 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2556:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/hh.cpp.o] Error 2
>> 3775 "../nrnoc/intfire1.cpp", line 333: error: identifier "_gth" is und
efined
3776 double* _globals = _thread[_gth].get<double*>(); // 4
3777 ^
3778
>> 3779 "../nrnoc/intfire1.cpp", line 333: error: type name is not allowed
3780 double* _globals = _thread[_gth].get<double*>(); // 4
3781 ^
3782
>> 3783 "../nrnoc/intfire1.cpp", line 333: error: expected an expression
3784 double* _globals = _thread[_gth].get<double*>(); // 4
3785 ^
3786
>> 3787 "../nrnoc/intfire1.cpp", line 356: error: identifier "_gth" is und
efined
3788 double* _globals = _thread[_gth].get<double*>();// 7
3789 ^
3790
>> 3791 "../nrnoc/intfire1.cpp", line 356: error: type name is not allowed
3792 double* _globals = _thread[_gth].get<double*>();// 7
3793 ^
3794
>> 3795 "../nrnoc/intfire1.cpp", line 356: error: expected an expression
3796 double* _globals = _thread[_gth].get<double*>();// 7
3797 ^
3798
3799 6 errors detected in the compilation of "../nrnoc/intfire1.cpp".
>> 3800 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2570:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire1.cpp.o] Error
2
>> 3801 "../nrnoc/intfire2.cpp", line 344: error: identifier "_globals" is
undefined
3802 artcell_net_send ( _tqitem, _args, _pnt, t + firetime ( _t
hreadargscomma_ ib , _libf , 0.0 ) , 1.0 ) ;
3803 ^
3804
>> 3805 "../nrnoc/intfire2.cpp", line 354: error: identifier "_globals" is
undefined
3806 artcell_net_move ( _tqitem, _pnt, firetime ( _threadargsc
omma_ ib , _libf , m ) + t ) ;
3807 ^
3808
>> 3809 "../nrnoc/intfire2.cpp", line 497: error: identifier "_gth" is und
efined
3810 double* _globals = _thread[_gth].get<double*>(); // 4
3811 ^
3812
>> 3813 "../nrnoc/intfire2.cpp", line 497: error: type name is not allowed
3814 double* _globals = _thread[_gth].get<double*>(); // 4
3815 ^
3816
>> 3817 "../nrnoc/intfire2.cpp", line 497: error: expected an expression
3818 double* _globals = _thread[_gth].get<double*>(); // 4
3819 ^
3820
>> 3821 "../nrnoc/intfire2.cpp", line 520: error: identifier "_gth" is und
efined
3822 double* _globals = _thread[_gth].get<double*>();// 7
3823 ^
3824
>> 3825 "../nrnoc/intfire2.cpp", line 520: error: type name is not allowed
3826 double* _globals = _thread[_gth].get<double*>();// 7
3827 ^
3828
>> 3829 "../nrnoc/intfire2.cpp", line 520: error: expected an expression
3830 double* _globals = _thread[_gth].get<double*>();// 7
3831 ^
3832
3833 8 errors detected in the compilation of "../nrnoc/intfire2.cpp".
>> 3834 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2584:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire2.cpp.o] Error
2
>> 3835 "../nrnoc/intfire4.cpp", line 764: error: identifier "_globals" is
undefined
3836 newstates ( _threadargscomma_ t - t0 ) ;
3837 ^
3838
>> 3839 "../nrnoc/intfire4.cpp", line 848: error: identifier "_gth" is und
efined
3840 double* _globals = _thread[_gth].get<double*>(); // 4
3841 ^
3842
>> 3843 "../nrnoc/intfire4.cpp", line 848: error: type name is not allowed
3844 double* _globals = _thread[_gth].get<double*>(); // 4
3845 ^
3846
>> 3847 "../nrnoc/intfire4.cpp", line 848: error: expected an expression
3848 double* _globals = _thread[_gth].get<double*>(); // 4
3849 ^
3850
>> 3851 "../nrnoc/intfire4.cpp", line 871: error: identifier "_gth" is und
efined
3852 double* _globals = _thread[_gth].get<double*>();// 7
3853 ^
3854
>> 3855 "../nrnoc/intfire4.cpp", line 871: error: type name is not allowed
3856 double* _globals = _thread[_gth].get<double*>();// 7
3857 ^
3858
>> 3859 "../nrnoc/intfire4.cpp", line 871: error: expected an expression
3860 double* _globals = _thread[_gth].get<double*>();// 7
3861 ^
3862
3863 7 errors detected in the compilation of "../nrnoc/intfire4.cpp".
>> 3864 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2598:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire4.cpp.o] Error
2
3865 make[2]: Leaving directory '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/
bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage-neuron-git
.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642
nptcoja6bhwenqvf/spack-build-feyazz7'
>> 3866 make[1]: *** [CMakeFiles/Makefile2:2932: src/nrniv/CMakeFiles/nrni
v_lib.dir/all] Error 2
3867 make[1]: Leaving directory '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/
bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage-neuron-git
.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642
nptcoja6bhwenqvf/spack-build-feyazz7'
>> 3868 make: *** [Makefile:169: all] Error 2
See build log for details:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315420/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-feyazz75k3pwq642nptcoja6bhwenqvf/spack-build-out.txt
$ set +o pipefail
$ chmod -R g+rX "${SPACK_BUILD}"
$ if [[ ${install_failed} == 1 ]]; then exit 1; fi
srun: error: r1i6n17: task 0: Exited with exit code 1
section_end:1718118170:step_script section_start:1718118170:upload_artifacts_on_failure Uploading artifacts for failed job
Using git from spack modules
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=139228 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=1315420 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=139265 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
Uploading artifacts as "junit" to coordinator... ok id=1315420 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=139306 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=1315420 responseStatus=201 Created token=glcbt-64
section_end:1718118172:upload_artifacts_on_failure section_start:1718118172:cleanup_file_variables Cleaning up project directory and file based variables
Using git from spack modules
section_end:1718118173:cleanup_file_variables ERROR: Job failed: exit status 1

Raw
build-neuron-nmodl-nvhpc-omp-legacy.txt
Running with gitlab-runner 15.5.0 (0d4137b8)
 on BB5 map runner pnPo3yJy
section_start:1718117533:resolve_secrets Resolving secrets
section_end:1718117533:resolve_secrets section_start:1718117533: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-executor2282554699, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name nrn
Pipeline ID 216288, build ref , job ID 1315421
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P216288, 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_J1315421_PROD_P2160_CP4_C10
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 2246821
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=2 --cpus-per-task=8 --mem=160G --job-name=GL_J1315421_PROD_P2160_CP4_C10 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P216288 --time=2:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P216288 --ntasks=2 --jobid=2246821 --cpus-per-task=8 --mem=160G
section_end:1718117535:prepare_executor section_start:1718117535:prepare_script Preparing environment
Using git from spack modules
Running on r1i6n21 via bbpv1.epfl.ch...
section_end:1718117544:prepare_script section_start:1718117544: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:1718117545:get_sources section_start:1718117545: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=188012 revision=58ba2b95 version=14.2.0
cache.zip is up to date 
Successfully extracted cache
section_end:1718117551:restore_cache section_start:1718117551:download_artifacts Downloading artifacts
Using git from spack modules
Downloading artifacts for build:nmodl (1315416)...
Runtime platform  arch=amd64 os=linux pid=188153 revision=58ba2b95 version=14.2.0
Downloading artifacts from coordinator... ok  id=1315416 responseStatus=200 OK token=glcbt-64
section_end:1718117552:download_artifacts section_start:1718117552: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/P216288/J1315421/spack-config/config.yaml:2 build_stage:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315421/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315421/spack-build
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315421/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315421/spack-source-cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/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/P216288/J1315414/spack/etc/spack/defaults/config.yaml:18 extensions:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:19 - $spack/bluebrain/spack-scripting
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:37 template_dirs:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:38 - $spack/share/spack/templates
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:41 license_dir: $spack/etc/spack/licenses
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:81 test_stage: $user_cache_path/test
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:94 misc_cache: $user_cache_path/cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:100 connect_timeout: 10
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:105 verify_ssl: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:113 suppress_gpg_warnings: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:119 install_missing_compilers: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:124 checksum: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:129 deprecated: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:134 dirty: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:142 build_language: C
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:151 locks: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:156 url_fetch_method: urllib
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:185 concretizer: clingo
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:192 db_lock_timeout: 60
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:200 package_lock_timeout: null
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:205 shared_linking:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:210 type: rpath
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:216 bind: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:221 allow_sgid: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:227 install_status: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:231 binary_index_ttl: 600
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:233 flags:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:235 keep_werror: none
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:240 aliases:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:241 concretise: concretize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:242 containerise: containerize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/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/P216288/J1315421/spack-config/concretizer.yaml:2 reuse: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:23 targets:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:28 granularity: microarchitectures
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:32 host_compatible: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:38 unify: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:40 duplicates:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/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/P216288/J1315421_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 ^/pis5gl5kpxkhvpyg2ej73radyh56itvx
$ 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/P216288
$ 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/bbpcihpcproj12/2246821/ccache
Config file: /nvme/bbpcihpcproj12/2246821/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: Tue Jun 11 16:52:37 2024
Local storage:
Cache size (GB): 0.47 / 0.51 (91.58%)
Files: 10609
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
- ^/pis5gl5kpxkhvpyg2ej73radyh56itvx
- ^caliper+cuda cuda_arch=70
Concretized
--------------------------------
- fmolayf neuron@git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9=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
[+] pis5gl5 ^nmodl@git.c5ecfea39cbd53ffcc248b1dcf732c1e0ae1ffc4=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/P216288, 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/catch2-3.4.0-pywly2
[+] /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/hdf5-1.14.3-5o77ye
[+] /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/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/papi-6.0.0.1-vol6np
[+] /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/binutils-2.41-tj3mv5
[+] /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/fmt-10.1.1-evtttr
[+] /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-markupsafe-2.1.3-r3ehtm
[+] /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-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-setuptools-68.0.0-p3xbqx
[+] /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-pybind11-2.11.1-tabj2m
[+] /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-pytest-7.3.2-lrf2u3
[+] /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-mpmath-1.2.1-4fflyi
[+] /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-cov-4.0.0-z5nf6n
[+] /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/elfutils-0.189-a46bi6
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/software/install_gcc-12.3.0-skylake/nmodl-git.c5ecfea39cbd53ffcc248b1dcf732c1e0ae1ffc4_develop-pis5gl
==> 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: 2.82s. Cmake: 9.29s. Build: 7.62s. Install: 1.00s. Post-install: 0.18s. Total: 21.22s
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/software/install_gcc-12.3.0-skylake/caliper-2.11.0-vjj3tp
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/software/install_nvhpc-23.1-skylake/libsonata-report-git.5602aadfa710d6766ce23cd151a1855190271bd8_develop-az6cwi
==> Installing neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9=develop-fmolayfdcgpm7kk2y64ajnykaw4oarhb [55/55]
==> No binary for neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9=develop-fmolayfdcgpm7kk2y64ajnykaw4oarhb found: installing from source
==> No patches needed for neuron
==> neuron: Executing phase: 'cmake'
==> neuron: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
'make' '-j8'
98 errors found in build log:
2878 [ 29%] Running nrnivmodl-core with internal mod files
2879 cd /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1
315421/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc
862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack-bu
ild-fmolayf/bin && /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage
_externals/install_gcc-12.3.0-skylake/cmake-3.27.7-slyoes/bin/cmak
e -E env NMODLHOME= /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpc
proj12/P216288/J1315421/spack-build/spack-stage-neuron-git.e2a6b6e
811fb9749543b72cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnyk
aw4oarhb/spack-build-fmolayf/bin/nrnivmodl-core -b STATIC -m /gpfs
/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/software/i
nstall_gcc-12.3.0-skylake/nmodl-git.c5ecfea39cbd53ffcc248b1dcf732c
1e0ae1ffc4_develop-pis5gl/bin/nmodl -n internal -p 4 .
2880 WARNING: No mod files found in '/gpfs/bbp.cscs.ch/ssd/gitlab_map_j
obs/bbpcihpcproj12/P216288/J1315421/spack-build/spack-stage-neuron
-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fmolayfdcgpm
7kk2y64ajnykaw4oarhb/spack-build-fmolayf/bin', compiling default o
nes only!
2881 [INFO] Running: make -j4 -f /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/
bbpcihpcproj12/P216288/J1315421/spack-build/spack-stage-neuron-git
.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2
y64ajnykaw4oarhb/spack-build-fmolayf/share/coreneuron/nrnivmodl_co
re_makefile ROOT=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcpro
j12/P216288/J1315421/spack-build/spack-stage-neuron-git.e2a6b6e811
fb9749543b72cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4
oarhb/spack-build-fmolayf MECHLIB_SUFFIX=internal NMODL_BINARY=/gp
fs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/software
/install_gcc-12.3.0-skylake/nmodl-git.c5ecfea39cbd53ffcc248b1dcf73
2c1e0ae1ffc4_develop-pis5gl/bin/nmodl MODS_PATH=x86_64/corenrn/mod
2c BUILD_TYPE=STATIC NRN_PRCELLSTATE=0
2882 make[3]: Entering directory '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs
/bbpcihpcproj12/P216288/J1315421/spack-build/spack-stage-neuron-gi
t.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk
2y64ajnykaw4oarhb/spack-build-fmolayf/bin'
2883 make[3]: warning: -j4 forced in submake: resetting jobserver mode.
>> 2884 make[3]: xcrun: No such file or directory
2885 Default NMODL flags:
>> 2886 diff: x86_64/corenrn/mod2c/_mod_func.cpp: No such file or director
y
2887 [NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shado
ws <extern_neuron_var> definition in NMODL_GLOBAL
2888 [NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shado
ws <extern_neuron_var> definition in NMODL_GLOBAL
2889 [NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shado
ws <extern_neuron_var> definition in NMODL_GLOBAL
2890 [NMODL] [warning] :: CVode solver of icur in 64.20-30 replaced wit
h cnexp solver
2891 "../../../spack-src/external/eigen/Eigen/src/Core/arch/AVX/PacketM
ath.h", line 984: warning: integer conversion resulted in a change
of sign [integer_sign_change]
2892 const __m128i sign_mask = _mm_set1_epi16(static_cast<numext::u
int16_t>(0x8000));
...
3494 [ 36%] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/n
rnoc/intfire1.cpp.o
3495 cd /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1
315421/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc
862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack-bu
ild-fmolayf/src/nrniv && /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbp
cihpcproj12/P216288/J1315414/spack/lib/spack/env/nvhpc/nvc++ -DCOR
ENRN_BUILD=0 -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX=1 -DMPI_NO_CPPBIN
D=1 -DNRN_AVOID_ABSOLUTE_PATHS -DNRN_CALIPER -DNRN_ENABLE_THREADS
-DNRN_PROFILING -DOMPI_SKIP_MPICXX=1 -DUSE_PYTHON -Dnrniv_lib_EXPO
RTS -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288
/J1315421/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b7
2cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack
-build-fmolayf/include -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbp
cihpcproj12/P216288/J1315421/spack-build/spack-stage-neuron-git.e2
a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64
ajnykaw4oarhb/spack-src/src/ivoc -I/gpfs/bbp.cscs.ch/ssd/gitlab_ma
p_jobs/bbpcihpcproj12/P216288/J1315421/spack-build/spack-stage-neu
ron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fmolayfdc
gpm7kk2y64ajnykaw4oarhb/spack-src/src/nrncvode -I/gpfs/bbp.cscs.ch
/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315421/spack-build/s
pack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_dev
elop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack-src/src/nrniv -I/gpfs/
bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315421/sp
ack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2
e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack-src/src/nrn
oc -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/
J1315421/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72
cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack-
src/src/oc -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/
P216288/J1315421/spack-build/spack-stage-neuron-git.e2a6b6e811fb97
49543b72cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4oarh
b/spack-build-fmolayf -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpc
ihpcproj12/P216288/J1315421/spack-build/spack-stage-neuron-git.e2a
6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64a
jnykaw4oarhb/spack-build-fmolayf/src/nrncvode -I/gpfs/bbp.cscs.ch/
ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315421/spack-build/sp
ack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_deve
lop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack-build-fmolayf/src/nrnoc
-I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1
315421/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc
862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack-bu
ild-fmolayf/src/nrnpython -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/
bbpcihpcproj12/P216288/J1315421/spack-build/spack-stage-neuron-git
.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2
y64ajnykaw4oarhb/spack-build-fmolayf/src/oc -I/gpfs/bbp.cscs.ch/ss
d/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315421/spack-build/spac
k-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develo
p-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack-build-fmolayf/src/paralle
l -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J
1315421/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72c
c862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack-b
uild-fmolayf/src/sundials -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/
bbpcihpcproj12/P216288/J1315421/spack-build/spack-stage-neuron-git
.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2
y64ajnykaw4oarhb/spack-build-fmolayf/src/sundials/shared -I/gpfs/b
bp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315421/spa
ck-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e
2a4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack-src/src -I/g
pfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J131542
1/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc86203
9da2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack-src/src
/gnu -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P21628
8/J1315421/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b
72cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spac
k-src/src/nrnmpi -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcp
roj12/P216288/J1315421/spack-build/spack-stage-neuron-git.e2a6b6e8
11fb9749543b72cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnyka
w4oarhb/spack-src/src/nrnpython -I/gpfs/bbp.cscs.ch/ssd/gitlab_map
_jobs/bbpcihpcproj12/P216288/J1315421/spack-build/spack-stage-neur
on-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fmolayfdcg
pm7kk2y64ajnykaw4oarhb/spack-src/src/parallel -I/gpfs/bbp.cscs.ch/
ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315421/spack-build/sp
ack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_deve
lop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack-src/src/scopmath -I/gpf
s/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315421/
spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039d
a2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack-src/src/s
parse -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P2162
88/J1315421/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543
b72cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spa
ck-src/src/sparse13 -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcih
pcproj12/P216288/J1315421/spack-build/spack-stage-neuron-git.e2a6b
6e811fb9749543b72cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajn
ykaw4oarhb/spack-src/src/sundials -I/gpfs/bbp.cscs.ch/ssd/gitlab_m
ap_jobs/bbpcihpcproj12/P216288/J1315421/spack-build/spack-stage-ne
uron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fmolayfd
cgpm7kk2y64ajnykaw4oarhb/spack-src/src/sundials/cvodes -I/gpfs/bbp
.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315421/spack
-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a
4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack-src/src/sundia
ls/ida -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216
288/J1315421/spack-build/spack-stage-neuron-git.e2a6b6e811fb974954
3b72cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/sp
ack-src/src/sundials/shared -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_job
s/bbpcihpcproj12/P216288/J1315421/spack-build/spack-stage-neuron-g
it.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fmolayfdcgpm7k
k2y64ajnykaw4oarhb/spack-build-fmolayf/src/nrniv/oc_generated -I/g
pfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gc
c-12.3.0-skylake/hpe-mpi-2.27.p1.hmpt-6rr256/include -I/gpfs/bbp.c
scs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315421/spack-b
uild/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4c
e9_develop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack-src/src/ivos -I/
gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J13154
21/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc8620
39da2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack-src/sr
c/nrnpython/.. -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcpro
j12/P216288/J1315421/spack-build/spack-stage-neuron-git.e2a6b6e811
fb9749543b72cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4
oarhb/spack-src/src/nrnpython/../oc -I/gpfs/bbp.cscs.ch/ssd/gitlab
_map_jobs/bbpcihpcproj12/P216288/J1315421/spack-build/spack-stage-
neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fmolay
fdcgpm7kk2y64ajnykaw4oarhb/spack-src/src/nrnpython/../nrnoc -I/gpf
s/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315421/
spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039d
a2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack-src/src/n
rnpython/../ivoc -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcp
roj12/P216288/J1315421/spack-build/spack-stage-neuron-git.e2a6b6e8
11fb9749543b72cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnyka
w4oarhb/spack-src/src/nrnpython/../nrniv -I/gpfs/bbp.cscs.ch/ssd/g
itlab_map_jobs/bbpcihpcproj12/P216288/J1315421/spack-build/spack-s
tage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-f
molayfdcgpm7kk2y64ajnykaw4oarhb/spack-src/src/nrnpython/../nrnmpi
-I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J13
15421/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc8
62039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack-src
/src/nrnpython/../ivos -I/gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01
/stage_externals/install_gcc-12.3.0-skylake/python-3.11.6-bj4i6m/i
nclude/python3.11 -isystem /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/b
bpcihpcproj12/P216288/software/install_gcc-12.3.0-skylake/caliper-
2.11.0-vjj3tp/include -isystem /gpfs/bbp.cscs.ch/ssd/gitlab_map_jo
bs/bbpcihpcproj12/P216288/J1315421/spack-build/spack-stage-neuron-
git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fmolayfdcgpm7
kk2y64ajnykaw4oarhb/spack-src/external/eigen -tp haswell -g -O1 -f
no-omit-frame-pointer --c++17 -fPIC --diag_suppress=1,47,111,128,
170,174,177,186,541,550,816,2465 -noswitcherror -MD -MT src/nrniv/
CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire1.cpp.o -MF CMakeFiles/nr
niv_lib.dir/__/nrnoc/intfire1.cpp.o.d -o CMakeFiles/nrniv_lib.dir/
__/nrnoc/intfire1.cpp.o -c /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/b
bpcihpcproj12/P216288/J1315421/spack-build/spack-stage-neuron-git.
e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y
64ajnykaw4oarhb/spack-build-fmolayf/src/nrnoc/intfire1.cpp
3496 [ 36%] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/n
rnoc/intfire2.cpp.o
3497 cd /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1
315421/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc
862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack-bu
ild-fmolayf/src/nrniv && /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbp
cihpcproj12/P216288/J1315414/spack/lib/spack/env/nvhpc/nvc++ -DCOR
ENRN_BUILD=0 -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX=1 -DMPI_NO_CPPBIN
D=1 -DNRN_AVOID_ABSOLUTE_PATHS -DNRN_CALIPER -DNRN_ENABLE_THREADS
-DNRN_PROFILING -DOMPI_SKIP_MPICXX=1 -DUSE_PYTHON -Dnrniv_lib_EXPO
RTS -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288
/J1315421/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b7
2cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack
-build-fmolayf/include -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbp
cihpcproj12/P216288/J1315421/spack-build/spack-stage-neuron-git.e2
a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64
ajnykaw4oarhb/spack-src/src/ivoc -I/gpfs/bbp.cscs.ch/ssd/gitlab_ma
p_jobs/bbpcihpcproj12/P216288/J1315421/spack-build/spack-stage-neu
ron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fmolayfdc
gpm7kk2y64ajnykaw4oarhb/spack-src/src/nrncvode -I/gpfs/bbp.cscs.ch
/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315421/spack-build/s
pack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_dev
elop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack-src/src/nrniv -I/gpfs/
bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315421/sp
ack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2
e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack-src/src/nrn
oc -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/
J1315421/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72
cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack-
src/src/oc -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/
P216288/J1315421/spack-build/spack-stage-neuron-git.e2a6b6e811fb97
49543b72cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4oarh
b/spack-build-fmolayf -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpc
ihpcproj12/P216288/J1315421/spack-build/spack-stage-neuron-git.e2a
6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64a
jnykaw4oarhb/spack-build-fmolayf/src/nrncvode -I/gpfs/bbp.cscs.ch/
ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315421/spack-build/sp
ack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_deve
lop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack-build-fmolayf/src/nrnoc
-I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1
315421/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc
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fdcgpm7kk2y64ajnykaw4oarhb/spack-src/src/nrnpython/../nrnoc -I/gpf
s/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315421/
spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039d
a2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack-src/src/n
rnpython/../ivoc -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcp
roj12/P216288/J1315421/spack-build/spack-stage-neuron-git.e2a6b6e8
11fb9749543b72cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnyka
w4oarhb/spack-src/src/nrnpython/../nrniv -I/gpfs/bbp.cscs.ch/ssd/g
itlab_map_jobs/bbpcihpcproj12/P216288/J1315421/spack-build/spack-s
tage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-f
molayfdcgpm7kk2y64ajnykaw4oarhb/spack-src/src/nrnpython/../nrnmpi
-I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J13
15421/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc8
62039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack-src
/src/nrnpython/../ivos -I/gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01
/stage_externals/install_gcc-12.3.0-skylake/python-3.11.6-bj4i6m/i
nclude/python3.11 -isystem /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/b
bpcihpcproj12/P216288/software/install_gcc-12.3.0-skylake/caliper-
2.11.0-vjj3tp/include -isystem /gpfs/bbp.cscs.ch/ssd/gitlab_map_jo
bs/bbpcihpcproj12/P216288/J1315421/spack-build/spack-stage-neuron-
git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fmolayfdcgpm7
kk2y64ajnykaw4oarhb/spack-src/external/eigen -tp haswell -g -O1 -f
no-omit-frame-pointer --c++17 -fPIC --diag_suppress=1,47,111,128,
170,174,177,186,541,550,816,2465 -noswitcherror -MD -MT src/nrniv/
CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire4.cpp.o -MF CMakeFiles/nr
niv_lib.dir/__/nrnoc/intfire4.cpp.o.d -o CMakeFiles/nrniv_lib.dir/
__/nrnoc/intfire4.cpp.o -c /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/b
bpcihpcproj12/P216288/J1315421/spack-build/spack-stage-neuron-git.
e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y
64ajnykaw4oarhb/spack-build-fmolayf/src/nrnoc/intfire4.cpp
>> 3500 "../nrnoc/apcount.cpp", line 346: error: identifier "_gth" is unde
fined
3501 double* _globals = _thread[_gth].get<double*>(); // 4
3502 ^
3503
>> 3504 "../nrnoc/apcount.cpp", line 346: error: type name is not allowed
3505 double* _globals = _thread[_gth].get<double*>(); // 4
3506 ^
3507
>> 3508 "../nrnoc/apcount.cpp", line 346: error: expected an expression
3509 double* _globals = _thread[_gth].get<double*>(); // 4
3510 ^
3511
>> 3512 "../nrnoc/apcount.cpp", line 372: error: identifier "_gth" is unde
fined
3513 double* _globals = _thread[_gth].get<double*>(); // 5
3514 ^
3515
>> 3516 "../nrnoc/apcount.cpp", line 372: error: type name is not allowed
3517 double* _globals = _thread[_gth].get<double*>(); // 5
3518 ^
3519
>> 3520 "../nrnoc/apcount.cpp", line 372: error: expected an expression
3521 double* _globals = _thread[_gth].get<double*>(); // 5
3522 ^
3523
>> 3524 "../nrnoc/apcount.cpp", line 391: error: identifier "_gth" is unde
fined
3525 double* _globals = _thread[_gth].get<double*>(); // 6
3526 ^
3527
>> 3528 "../nrnoc/apcount.cpp", line 391: error: type name is not allowed
3529 double* _globals = _thread[_gth].get<double*>(); // 6
3530 ^
3531
>> 3532 "../nrnoc/apcount.cpp", line 391: error: expected an expression
3533 double* _globals = _thread[_gth].get<double*>(); // 6
3534 ^
3535
>> 3536 "../nrnoc/apcount.cpp", line 408: error: identifier "_gth" is unde
fined
3537 double* _globals = _thread[_gth].get<double*>();// 7
3538 ^
3539
>> 3540 "../nrnoc/apcount.cpp", line 408: error: type name is not allowed
3541 double* _globals = _thread[_gth].get<double*>();// 7
3542 ^
3543
>> 3544 "../nrnoc/apcount.cpp", line 408: error: expected an expression
3545 double* _globals = _thread[_gth].get<double*>();// 7
3546 ^
3547
3548 12 errors detected in the compilation of "../nrnoc/apcount.cpp".
>> 3549 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2500:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/apcount.cpp.o] Error 2
3550 make[2]: *** Waiting for unfinished jobs....
>> 3551 "../nrnoc/exp2syn.cpp", line 358: error: identifier "_gth" is unde
fined
3552 double* _globals{_thread[_gth].get<double*>()};
3553 ^
3554
>> 3555 "../nrnoc/exp2syn.cpp", line 358: error: type name is not allowed
3556 double* _globals{_thread[_gth].get<double*>()};
3557 ^
3558
>> 3559 "../nrnoc/exp2syn.cpp", line 358: error: expected an expression
3560 double* _globals{_thread[_gth].get<double*>()};
3561 ^
3562
>> 3563 "../nrnoc/exp2syn.cpp", line 390: error: identifier "_gth" is unde
fined
3564 double* _globals{_thread[_gth].get<double*>()};
3565 ^
3566
>> 3567 "../nrnoc/exp2syn.cpp", line 390: error: type name is not allowed
3568 double* _globals{_thread[_gth].get<double*>()};
3569 ^
3570
>> 3571 "../nrnoc/exp2syn.cpp", line 390: error: expected an expression
3572 double* _globals{_thread[_gth].get<double*>()};
3573 ^
3574
>> 3575 "../nrnoc/exp2syn.cpp", line 429: error: identifier "_gth" is unde
fined
3576 double* _globals = _thread[_gth].get<double*>(); // 4
3577 ^
3578
>> 3579 "../nrnoc/exp2syn.cpp", line 429: error: type name is not allowed
3580 double* _globals = _thread[_gth].get<double*>(); // 4
3581 ^
3582
>> 3583 "../nrnoc/exp2syn.cpp", line 429: error: expected an expression
3584 double* _globals = _thread[_gth].get<double*>(); // 4
3585 ^
3586
>> 3587 "../nrnoc/exp2syn.cpp", line 461: error: identifier "_gth" is unde
fined
3588 double* _globals = _thread[_gth].get<double*>(); // 5
3589 ^
3590
>> 3591 "../nrnoc/exp2syn.cpp", line 461: error: type name is not allowed
3592 double* _globals = _thread[_gth].get<double*>(); // 5
3593 ^
3594
>> 3595 "../nrnoc/exp2syn.cpp", line 461: error: expected an expression
3596 double* _globals = _thread[_gth].get<double*>(); // 5
3597 ^
3598
>> 3599 "../nrnoc/exp2syn.cpp", line 487: error: identifier "_gth" is unde
fined
3600 double* _globals = _thread[_gth].get<double*>(); // 6
3601 ^
3602
>> 3603 "../nrnoc/exp2syn.cpp", line 487: error: type name is not allowed
3604 double* _globals = _thread[_gth].get<double*>(); // 6
3605 ^
3606
>> 3607 "../nrnoc/exp2syn.cpp", line 487: error: expected an expression
3608 double* _globals = _thread[_gth].get<double*>(); // 6
3609 ^
3610
>> 3611 "../nrnoc/exp2syn.cpp", line 504: error: identifier "_gth" is unde
fined
3612 double* _globals = _thread[_gth].get<double*>();// 7
3613 ^
3614
>> 3615 "../nrnoc/exp2syn.cpp", line 504: error: type name is not allowed
3616 double* _globals = _thread[_gth].get<double*>();// 7
3617 ^
3618
>> 3619 "../nrnoc/exp2syn.cpp", line 504: error: expected an expression
3620 double* _globals = _thread[_gth].get<double*>();// 7
3621 ^
3622
3623 18 errors detected in the compilation of "../nrnoc/exp2syn.cpp".
>> 3624 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2514:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/exp2syn.cpp.o] Error 2
>> 3625 "../nrnoc/expsyn.cpp", line 321: error: identifier "_gth" is undef
ined
3626 double* _globals{_thread[_gth].get<double*>()};
3627 ^
3628
>> 3629 "../nrnoc/expsyn.cpp", line 321: error: type name is not allowed
3630 double* _globals{_thread[_gth].get<double*>()};
3631 ^
3632
>> 3633 "../nrnoc/expsyn.cpp", line 321: error: expected an expression
3634 double* _globals{_thread[_gth].get<double*>()};
3635 ^
3636
>> 3637 "../nrnoc/expsyn.cpp", line 353: error: identifier "_gth" is undef
ined
3638 double* _globals{_thread[_gth].get<double*>()};
3639 ^
3640
>> 3641 "../nrnoc/expsyn.cpp", line 353: error: type name is not allowed
3642 double* _globals{_thread[_gth].get<double*>()};
3643 ^
3644
>> 3645 "../nrnoc/expsyn.cpp", line 353: error: expected an expression
3646 double* _globals{_thread[_gth].get<double*>()};
3647 ^
3648
>> 3649 "../nrnoc/expsyn.cpp", line 380: error: identifier "_gth" is undef
ined
3650 double* _globals = _thread[_gth].get<double*>(); // 4
3651 ^
3652
>> 3653 "../nrnoc/expsyn.cpp", line 380: error: type name is not allowed
3654 double* _globals = _thread[_gth].get<double*>(); // 4
3655 ^
3656
>> 3657 "../nrnoc/expsyn.cpp", line 380: error: expected an expression
3658 double* _globals = _thread[_gth].get<double*>(); // 4
3659 ^
3660
>> 3661 "../nrnoc/expsyn.cpp", line 411: error: identifier "_gth" is undef
ined
3662 double* _globals = _thread[_gth].get<double*>(); // 5
3663 ^
3664
>> 3665 "../nrnoc/expsyn.cpp", line 411: error: type name is not allowed
3666 double* _globals = _thread[_gth].get<double*>(); // 5
3667 ^
3668
>> 3669 "../nrnoc/expsyn.cpp", line 411: error: expected an expression
3670 double* _globals = _thread[_gth].get<double*>(); // 5
3671 ^
3672
>> 3673 "../nrnoc/expsyn.cpp", line 437: error: identifier "_gth" is undef
ined
3674 double* _globals = _thread[_gth].get<double*>(); // 6
3675 ^
3676
>> 3677 "../nrnoc/expsyn.cpp", line 437: error: type name is not allowed
3678 double* _globals = _thread[_gth].get<double*>(); // 6
3679 ^
3680
>> 3681 "../nrnoc/expsyn.cpp", line 437: error: expected an expression
3682 double* _globals = _thread[_gth].get<double*>(); // 6
3683 ^
3684
>> 3685 "../nrnoc/expsyn.cpp", line 454: error: identifier "_gth" is undef
ined
3686 double* _globals = _thread[_gth].get<double*>();// 7
3687 ^
3688
>> 3689 "../nrnoc/expsyn.cpp", line 454: error: type name is not allowed
3690 double* _globals = _thread[_gth].get<double*>();// 7
3691 ^
3692
>> 3693 "../nrnoc/expsyn.cpp", line 454: error: expected an expression
3694 double* _globals = _thread[_gth].get<double*>();// 7
3695 ^
3696
3697 18 errors detected in the compilation of "../nrnoc/expsyn.cpp".
>> 3698 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2528:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/expsyn.cpp.o] Error 2
>> 3699 "../nrnoc/hh.cpp", line 511: error: identifier "_gth" is undefined
3700 double* _globals{_thread[_gth].get<double*>()};
3701 ^
3702
>> 3703 "../nrnoc/hh.cpp", line 511: error: type name is not allowed
3704 double* _globals{_thread[_gth].get<double*>()};
3705 ^
3706
>> 3707 "../nrnoc/hh.cpp", line 511: error: expected an expression
3708 double* _globals{_thread[_gth].get<double*>()};
3709 ^
3710
>> 3711 "../nrnoc/hh.cpp", line 545: error: identifier "_gth" is undefined
3712 double* _globals{_thread[_gth].get<double*>()};
3713 ^
3714
>> 3715 "../nrnoc/hh.cpp", line 545: error: type name is not allowed
3716 double* _globals{_thread[_gth].get<double*>()};
3717 ^
3718
>> 3719 "../nrnoc/hh.cpp", line 545: error: expected an expression
3720 double* _globals{_thread[_gth].get<double*>()};
3721 ^
3722
>> 3723 "../nrnoc/hh.cpp", line 579: error: identifier "_gth" is undefined
3724 double* _globals = _thread[_gth].get<double*>(); // 4
3725 ^
3726
>> 3727 "../nrnoc/hh.cpp", line 579: error: type name is not allowed
3728 double* _globals = _thread[_gth].get<double*>(); // 4
3729 ^
3730
>> 3731 "../nrnoc/hh.cpp", line 579: error: expected an expression
3732 double* _globals = _thread[_gth].get<double*>(); // 4
3733 ^
3734
>> 3735 "../nrnoc/hh.cpp", line 617: error: identifier "_gth" is undefined
3736 double* _globals = _thread[_gth].get<double*>(); // 5
3737 ^
3738
>> 3739 "../nrnoc/hh.cpp", line 617: error: type name is not allowed
3740 double* _globals = _thread[_gth].get<double*>(); // 5
3741 ^
3742
>> 3743 "../nrnoc/hh.cpp", line 617: error: expected an expression
3744 double* _globals = _thread[_gth].get<double*>(); // 5
3745 ^
3746
>> 3747 "../nrnoc/hh.cpp", line 651: error: identifier "_gth" is undefined
3748 double* _globals = _thread[_gth].get<double*>(); // 6
3749 ^
3750
>> 3751 "../nrnoc/hh.cpp", line 651: error: type name is not allowed
3752 double* _globals = _thread[_gth].get<double*>(); // 6
3753 ^
3754
>> 3755 "../nrnoc/hh.cpp", line 651: error: expected an expression
3756 double* _globals = _thread[_gth].get<double*>(); // 6
3757 ^
3758
>> 3759 "../nrnoc/hh.cpp", line 668: error: identifier "_gth" is undefined
3760 double* _globals = _thread[_gth].get<double*>();// 7
3761 ^
3762
>> 3763 "../nrnoc/hh.cpp", line 668: error: type name is not allowed
3764 double* _globals = _thread[_gth].get<double*>();// 7
3765 ^
3766
>> 3767 "../nrnoc/hh.cpp", line 668: error: expected an expression
3768 double* _globals = _thread[_gth].get<double*>();// 7
3769 ^
3770
3771 18 errors detected in the compilation of "../nrnoc/hh.cpp".
>> 3772 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2556:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/hh.cpp.o] Error 2
>> 3773 "../nrnoc/intfire1.cpp", line 333: error: identifier "_gth" is und
efined
3774 double* _globals = _thread[_gth].get<double*>(); // 4
3775 ^
3776
>> 3777 "../nrnoc/intfire1.cpp", line 333: error: type name is not allowed
3778 double* _globals = _thread[_gth].get<double*>(); // 4
3779 ^
3780
>> 3781 "../nrnoc/intfire1.cpp", line 333: error: expected an expression
3782 double* _globals = _thread[_gth].get<double*>(); // 4
3783 ^
3784
>> 3785 "../nrnoc/intfire1.cpp", line 356: error: identifier "_gth" is und
efined
3786 double* _globals = _thread[_gth].get<double*>();// 7
3787 ^
3788
>> 3789 "../nrnoc/intfire1.cpp", line 356: error: type name is not allowed
3790 double* _globals = _thread[_gth].get<double*>();// 7
3791 ^
3792
>> 3793 "../nrnoc/intfire1.cpp", line 356: error: expected an expression
3794 double* _globals = _thread[_gth].get<double*>();// 7
3795 ^
3796
3797 6 errors detected in the compilation of "../nrnoc/intfire1.cpp".
>> 3798 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2570:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire1.cpp.o] Error
2
>> 3799 "../nrnoc/intfire2.cpp", line 344: error: identifier "_globals" is
undefined
3800 artcell_net_send ( _tqitem, _args, _pnt, t + firetime ( _t
hreadargscomma_ ib , _libf , 0.0 ) , 1.0 ) ;
3801 ^
3802
>> 3803 "../nrnoc/intfire2.cpp", line 354: error: identifier "_globals" is
undefined
3804 artcell_net_move ( _tqitem, _pnt, firetime ( _threadargsc
omma_ ib , _libf , m ) + t ) ;
3805 ^
3806
>> 3807 "../nrnoc/intfire2.cpp", line 497: error: identifier "_gth" is und
efined
3808 double* _globals = _thread[_gth].get<double*>(); // 4
3809 ^
3810
>> 3811 "../nrnoc/intfire2.cpp", line 497: error: type name is not allowed
3812 double* _globals = _thread[_gth].get<double*>(); // 4
3813 ^
3814
>> 3815 "../nrnoc/intfire2.cpp", line 497: error: expected an expression
3816 double* _globals = _thread[_gth].get<double*>(); // 4
3817 ^
3818
>> 3819 "../nrnoc/intfire2.cpp", line 520: error: identifier "_gth" is und
efined
3820 double* _globals = _thread[_gth].get<double*>();// 7
3821 ^
3822
>> 3823 "../nrnoc/intfire2.cpp", line 520: error: type name is not allowed
3824 double* _globals = _thread[_gth].get<double*>();// 7
3825 ^
3826
>> 3827 "../nrnoc/intfire2.cpp", line 520: error: expected an expression
3828 double* _globals = _thread[_gth].get<double*>();// 7
3829 ^
3830
3831 8 errors detected in the compilation of "../nrnoc/intfire2.cpp".
>> 3832 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2584:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire2.cpp.o] Error
2
>> 3833 "../nrnoc/intfire4.cpp", line 764: error: identifier "_globals" is
undefined
3834 newstates ( _threadargscomma_ t - t0 ) ;
3835 ^
3836
>> 3837 "../nrnoc/intfire4.cpp", line 848: error: identifier "_gth" is und
efined
3838 double* _globals = _thread[_gth].get<double*>(); // 4
3839 ^
3840
>> 3841 "../nrnoc/intfire4.cpp", line 848: error: type name is not allowed
3842 double* _globals = _thread[_gth].get<double*>(); // 4
3843 ^
3844
>> 3845 "../nrnoc/intfire4.cpp", line 848: error: expected an expression
3846 double* _globals = _thread[_gth].get<double*>(); // 4
3847 ^
3848
>> 3849 "../nrnoc/intfire4.cpp", line 871: error: identifier "_gth" is und
efined
3850 double* _globals = _thread[_gth].get<double*>();// 7
3851 ^
3852
>> 3853 "../nrnoc/intfire4.cpp", line 871: error: type name is not allowed
3854 double* _globals = _thread[_gth].get<double*>();// 7
3855 ^
3856
>> 3857 "../nrnoc/intfire4.cpp", line 871: error: expected an expression
3858 double* _globals = _thread[_gth].get<double*>();// 7
3859 ^
3860
3861 7 errors detected in the compilation of "../nrnoc/intfire4.cpp".
>> 3862 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2598:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire4.cpp.o] Error
2
3863 make[2]: Leaving directory '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/
bbpcihpcproj12/P216288/J1315421/spack-build/spack-stage-neuron-git
.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2
y64ajnykaw4oarhb/spack-build-fmolayf'
>> 3864 make[1]: *** [CMakeFiles/Makefile2:2920: src/nrniv/CMakeFiles/nrni
v_lib.dir/all] Error 2
3865 make[1]: Leaving directory '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/
bbpcihpcproj12/P216288/J1315421/spack-build/spack-stage-neuron-git
.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2
y64ajnykaw4oarhb/spack-build-fmolayf'
>> 3866 make: *** [Makefile:169: all] Error 2
See build log for details:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315421/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-fmolayfdcgpm7kk2y64ajnykaw4oarhb/spack-build-out.txt
$ set +o pipefail
$ chmod -R g+rX "${SPACK_BUILD}"
$ if [[ ${install_failed} == 1 ]]; then exit 1; fi
srun: error: r1i6n21: task 0: Exited with exit code 1
section_end:1718118255:step_script section_start:1718118255:upload_artifacts_on_failure Uploading artifacts for failed job
Using git from spack modules
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=198316 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=1315421 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=198356 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
Uploading artifacts as "junit" to coordinator... ok id=1315421 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=198397 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=1315421 responseStatus=201 Created token=glcbt-64
section_end:1718118258:upload_artifacts_on_failure section_start:1718118258:cleanup_file_variables Cleaning up project directory and file based variables
Using git from spack modules
section_end:1718118259:cleanup_file_variables ERROR: Job failed: exit status 1

Raw
build-neuron-nmodl-nvhpc-omp.txt
Running with gitlab-runner 15.5.0 (0d4137b8)
 on BB5 map runner pnPo3yJy
section_start:1718117534:resolve_secrets Resolving secrets
section_end:1718117534:resolve_secrets section_start:1718117534: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-executor2157987749, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name nrn
Pipeline ID 216288, build ref , job ID 1315422
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P216288, 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_J1315422_PROD_P2160_CP5_C11
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 2246822
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=2 --cpus-per-task=8 --mem=160G --job-name=GL_J1315422_PROD_P2160_CP5_C11 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P216288 --time=2:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P216288 --ntasks=2 --jobid=2246822 --cpus-per-task=8 --mem=160G
section_end:1718117536:prepare_executor section_start:1718117536:prepare_script Preparing environment
Using git from spack modules
Running on r1i6n20 via bbpv1.epfl.ch...
section_end:1718117544:prepare_script section_start:1718117544: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:1718117545:get_sources section_start:1718117545: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=230395 revision=58ba2b95 version=14.2.0
cache.zip is up to date 
Successfully extracted cache
section_end:1718117551:restore_cache section_start:1718117551:download_artifacts Downloading artifacts
Using git from spack modules
Downloading artifacts for build:nmodl (1315416)...
Runtime platform  arch=amd64 os=linux pid=230503 revision=58ba2b95 version=14.2.0
Downloading artifacts from coordinator... ok  id=1315416 responseStatus=200 OK token=glcbt-64
section_end:1718117552:download_artifacts section_start:1718117552: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/P216288/J1315422/spack-config/config.yaml:2 build_stage:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315422/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315422/spack-build
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315422/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315422/spack-source-cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/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/P216288/J1315414/spack/etc/spack/defaults/config.yaml:18 extensions:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:19 - $spack/bluebrain/spack-scripting
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:37 template_dirs:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:38 - $spack/share/spack/templates
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:41 license_dir: $spack/etc/spack/licenses
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:81 test_stage: $user_cache_path/test
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:94 misc_cache: $user_cache_path/cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:100 connect_timeout: 10
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:105 verify_ssl: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:113 suppress_gpg_warnings: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:119 install_missing_compilers: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:124 checksum: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:129 deprecated: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:134 dirty: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:142 build_language: C
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:151 locks: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:156 url_fetch_method: urllib
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:185 concretizer: clingo
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:192 db_lock_timeout: 60
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:200 package_lock_timeout: null
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:205 shared_linking:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:210 type: rpath
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:216 bind: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:221 allow_sgid: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:227 install_status: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:231 binary_index_ttl: 600
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:233 flags:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:235 keep_werror: none
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:240 aliases:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:241 concretise: concretize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:242 containerise: containerize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/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/P216288/J1315422/spack-config/concretizer.yaml:2 reuse: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:23 targets:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:28 granularity: microarchitectures
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:32 host_compatible: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:38 unify: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:40 duplicates:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/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/P216288/J1315422_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 ^/pis5gl5kpxkhvpyg2ej73radyh56itvx
$ 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/P216288
$ 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/bbpcihpcproj12/2246822/ccache
Config file: /nvme/bbpcihpcproj12/2246822/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: Tue Jun 11 16:52:38 2024
Local storage:
Cache size (GB): 0.46 / 0.51 (90.54%)
Files: 10025
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
- ^/pis5gl5kpxkhvpyg2ej73radyh56itvx
- ^caliper+cuda cuda_arch=70
Concretized
--------------------------------
- g3mlwqa neuron@git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9=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
[+] pis5gl5 ^nmodl@git.c5ecfea39cbd53ffcc248b1dcf732c1e0ae1ffc4=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/P216288, 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/hdf5-1.14.3-5o77ye
[+] /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/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/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/cli11-2.3.2-ud3ech
[+] /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/pigz-2.7-dwjcgu
[+] /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/binutils-2.41-tj3mv5
[+] /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/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-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-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-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-pluggy-1.0.0-6su7kv
[+] /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-pybind11-2.11.1-tabj2m
[+] /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-7.3.2-lrf2u3
[+] /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/gitlab_map_jobs/bbpcihpcproj12/P216288/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-pytest-cov-4.0.0-z5nf6n
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/software/install_gcc-12.3.0-skylake/nmodl-git.c5ecfea39cbd53ffcc248b1dcf732c1e0ae1ffc4_develop-pis5gl
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/software/install_gcc-12.3.0-skylake/caliper-2.11.0-vjj3tp
==> Installing neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9=develop-g3mlwqaims3h3es5innhsuvbibqkcdsf [55/55]
==> No binary for neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9=develop-g3mlwqaims3h3es5innhsuvbibqkcdsf found: installing from source
==> No patches needed for neuron
==> neuron: Executing phase: 'cmake'
==> neuron: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
'make' '-j8'
98 errors found in build log:
2878 [ 29%] Running nrnivmodl-core with internal mod files
2879 cd /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1
315422/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc
862039da2e2a4ce9_develop-g3mlwqaims3h3es5innhsuvbibqkcdsf/spack-bu
ild-g3mlwqa/bin && /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage
_externals/install_gcc-12.3.0-skylake/cmake-3.27.7-slyoes/bin/cmak
e -E env NMODLHOME= /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpc
proj12/P216288/J1315422/spack-build/spack-stage-neuron-git.e2a6b6e
811fb9749543b72cc862039da2e2a4ce9_develop-g3mlwqaims3h3es5innhsuvb
ibqkcdsf/spack-build-g3mlwqa/bin/nrnivmodl-core -b STATIC -m /gpfs
/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/software/i
nstall_gcc-12.3.0-skylake/nmodl-git.c5ecfea39cbd53ffcc248b1dcf732c
1e0ae1ffc4_develop-pis5gl/bin/nmodl -n internal -p 4 .
2880 WARNING: No mod files found in '/gpfs/bbp.cscs.ch/ssd/gitlab_map_j
obs/bbpcihpcproj12/P216288/J1315422/spack-build/spack-stage-neuron
-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-g3mlwqaims3h
3es5innhsuvbibqkcdsf/spack-build-g3mlwqa/bin', compiling default o
nes only!
2881 [INFO] Running: make -j4 -f /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/
bbpcihpcproj12/P216288/J1315422/spack-build/spack-stage-neuron-git
.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-g3mlwqaims3h3es5
innhsuvbibqkcdsf/spack-build-g3mlwqa/share/coreneuron/nrnivmodl_co
re_makefile ROOT=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcpro
j12/P216288/J1315422/spack-build/spack-stage-neuron-git.e2a6b6e811
fb9749543b72cc862039da2e2a4ce9_develop-g3mlwqaims3h3es5innhsuvbibq
kcdsf/spack-build-g3mlwqa MECHLIB_SUFFIX=internal NMODL_BINARY=/gp
fs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/software
/install_gcc-12.3.0-skylake/nmodl-git.c5ecfea39cbd53ffcc248b1dcf73
2c1e0ae1ffc4_develop-pis5gl/bin/nmodl MODS_PATH=x86_64/corenrn/mod
2c BUILD_TYPE=STATIC NRN_PRCELLSTATE=0
2882 make[3]: Entering directory '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs
/bbpcihpcproj12/P216288/J1315422/spack-build/spack-stage-neuron-gi
t.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-g3mlwqaims3h3es
5innhsuvbibqkcdsf/spack-build-g3mlwqa/bin'
2883 make[3]: warning: -j4 forced in submake: resetting jobserver mode.
>> 2884 make[3]: xcrun: No such file or directory
2885 Default NMODL flags:
>> 2886 diff: x86_64/corenrn/mod2c/_mod_func.cpp: No such file or director
y
2887 [NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shado
ws <extern_neuron_var> definition in NMODL_GLOBAL
2888 [NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shado
ws <extern_neuron_var> definition in NMODL_GLOBAL
2889 [NMODL] [warning] :: SYMTAB :: t [Argument] in init_sequence shado
ws <extern_neuron_var> definition in NMODL_GLOBAL
2890 [NMODL] [warning] :: CVode solver of icur in 64.20-30 replaced wit
h cnexp solver
2891 "../../../spack-src/external/eigen/Eigen/src/Core/arch/AVX/PacketM
ath.h", line 984: warning: integer conversion resulted in a change
of sign [integer_sign_change]
2892 const __m128i sign_mask = _mm_set1_epi16(static_cast<numext::u
int16_t>(0x8000));
...
3494 [ 36%] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/n
rnoc/intfire1.cpp.o
3495 cd /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1
315422/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc
862039da2e2a4ce9_develop-g3mlwqaims3h3es5innhsuvbibqkcdsf/spack-bu
ild-g3mlwqa/src/nrniv && /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbp
cihpcproj12/P216288/J1315414/spack/lib/spack/env/nvhpc/nvc++ -DCOR
ENRN_BUILD=0 -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX=1 -DMPI_NO_CPPBIN
D=1 -DNRN_AVOID_ABSOLUTE_PATHS -DNRN_CALIPER -DNRN_ENABLE_THREADS
-DNRN_PROFILING -DOMPI_SKIP_MPICXX=1 -DUSE_PYTHON -Dnrniv_lib_EXPO
RTS -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288
/J1315422/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b7
2cc862039da2e2a4ce9_develop-g3mlwqaims3h3es5innhsuvbibqkcdsf/spack
-build-g3mlwqa/include -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbp
cihpcproj12/P216288/J1315422/spack-build/spack-stage-neuron-git.e2
a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-g3mlwqaims3h3es5inn
hsuvbibqkcdsf/spack-src/src/ivoc -I/gpfs/bbp.cscs.ch/ssd/gitlab_ma
p_jobs/bbpcihpcproj12/P216288/J1315422/spack-build/spack-stage-neu
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288/J1315422/spack-build/spack-stage-neuron-git.e2a6b6e811fb974954
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3498 [ 36%] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/n
rnoc/intfire4.cpp.o
3499 cd /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1
315422/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc
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cihpcproj12/P216288/J1315414/spack/lib/spack/env/nvhpc/nvc++ -DCOR
ENRN_BUILD=0 -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX=1 -DMPI_NO_CPPBIN
D=1 -DNRN_AVOID_ABSOLUTE_PATHS -DNRN_CALIPER -DNRN_ENABLE_THREADS
-DNRN_PROFILING -DOMPI_SKIP_MPICXX=1 -DUSE_PYTHON -Dnrniv_lib_EXPO
RTS -I/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288
/J1315422/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b7
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/stage_externals/install_gcc-12.3.0-skylake/python-3.11.6-bj4i6m/i
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2.11.0-vjj3tp/include -isystem /gpfs/bbp.cscs.ch/ssd/gitlab_map_jo
bs/bbpcihpcproj12/P216288/J1315422/spack-build/spack-stage-neuron-
git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-g3mlwqaims3h3
es5innhsuvbibqkcdsf/spack-src/external/eigen -tp haswell -g -O1 -f
no-omit-frame-pointer --c++17 -fPIC --diag_suppress=1,47,111,128,
170,174,177,186,541,550,816,2465 -noswitcherror -MD -MT src/nrniv/
CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire4.cpp.o -MF CMakeFiles/nr
niv_lib.dir/__/nrnoc/intfire4.cpp.o.d -o CMakeFiles/nrniv_lib.dir/
__/nrnoc/intfire4.cpp.o -c /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/b
bpcihpcproj12/P216288/J1315422/spack-build/spack-stage-neuron-git.
e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-g3mlwqaims3h3es5i
nnhsuvbibqkcdsf/spack-build-g3mlwqa/src/nrnoc/intfire4.cpp
>> 3500 "../nrnoc/apcount.cpp", line 346: error: identifier "_gth" is unde
fined
3501 double* _globals = _thread[_gth].get<double*>(); // 4
3502 ^
3503
>> 3504 "../nrnoc/apcount.cpp", line 346: error: type name is not allowed
3505 double* _globals = _thread[_gth].get<double*>(); // 4
3506 ^
3507
>> 3508 "../nrnoc/apcount.cpp", line 346: error: expected an expression
3509 double* _globals = _thread[_gth].get<double*>(); // 4
3510 ^
3511
>> 3512 "../nrnoc/apcount.cpp", line 372: error: identifier "_gth" is unde
fined
3513 double* _globals = _thread[_gth].get<double*>(); // 5
3514 ^
3515
>> 3516 "../nrnoc/apcount.cpp", line 372: error: type name is not allowed
3517 double* _globals = _thread[_gth].get<double*>(); // 5
3518 ^
3519
>> 3520 "../nrnoc/apcount.cpp", line 372: error: expected an expression
3521 double* _globals = _thread[_gth].get<double*>(); // 5
3522 ^
3523
>> 3524 "../nrnoc/apcount.cpp", line 391: error: identifier "_gth" is unde
fined
3525 double* _globals = _thread[_gth].get<double*>(); // 6
3526 ^
3527
>> 3528 "../nrnoc/apcount.cpp", line 391: error: type name is not allowed
3529 double* _globals = _thread[_gth].get<double*>(); // 6
3530 ^
3531
>> 3532 "../nrnoc/apcount.cpp", line 391: error: expected an expression
3533 double* _globals = _thread[_gth].get<double*>(); // 6
3534 ^
3535
>> 3536 "../nrnoc/apcount.cpp", line 408: error: identifier "_gth" is unde
fined
3537 double* _globals = _thread[_gth].get<double*>();// 7
3538 ^
3539
>> 3540 "../nrnoc/apcount.cpp", line 408: error: type name is not allowed
3541 double* _globals = _thread[_gth].get<double*>();// 7
3542 ^
3543
>> 3544 "../nrnoc/apcount.cpp", line 408: error: expected an expression
3545 double* _globals = _thread[_gth].get<double*>();// 7
3546 ^
3547
3548 12 errors detected in the compilation of "../nrnoc/apcount.cpp".
>> 3549 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2500:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/apcount.cpp.o] Error 2
3550 make[2]: *** Waiting for unfinished jobs....
>> 3551 "../nrnoc/exp2syn.cpp", line 358: error: identifier "_gth" is unde
fined
3552 double* _globals{_thread[_gth].get<double*>()};
3553 ^
3554
>> 3555 "../nrnoc/exp2syn.cpp", line 358: error: type name is not allowed
3556 double* _globals{_thread[_gth].get<double*>()};
3557 ^
3558
>> 3559 "../nrnoc/exp2syn.cpp", line 358: error: expected an expression
3560 double* _globals{_thread[_gth].get<double*>()};
3561 ^
3562
>> 3563 "../nrnoc/exp2syn.cpp", line 390: error: identifier "_gth" is unde
fined
3564 double* _globals{_thread[_gth].get<double*>()};
3565 ^
3566
>> 3567 "../nrnoc/exp2syn.cpp", line 390: error: type name is not allowed
3568 double* _globals{_thread[_gth].get<double*>()};
3569 ^
3570
>> 3571 "../nrnoc/exp2syn.cpp", line 390: error: expected an expression
3572 double* _globals{_thread[_gth].get<double*>()};
3573 ^
3574
>> 3575 "../nrnoc/exp2syn.cpp", line 429: error: identifier "_gth" is unde
fined
3576 double* _globals = _thread[_gth].get<double*>(); // 4
3577 ^
3578
>> 3579 "../nrnoc/exp2syn.cpp", line 429: error: type name is not allowed
3580 double* _globals = _thread[_gth].get<double*>(); // 4
3581 ^
3582
>> 3583 "../nrnoc/exp2syn.cpp", line 429: error: expected an expression
3584 double* _globals = _thread[_gth].get<double*>(); // 4
3585 ^
3586
>> 3587 "../nrnoc/exp2syn.cpp", line 461: error: identifier "_gth" is unde
fined
3588 double* _globals = _thread[_gth].get<double*>(); // 5
3589 ^
3590
>> 3591 "../nrnoc/exp2syn.cpp", line 461: error: type name is not allowed
3592 double* _globals = _thread[_gth].get<double*>(); // 5
3593 ^
3594
>> 3595 "../nrnoc/exp2syn.cpp", line 461: error: expected an expression
3596 double* _globals = _thread[_gth].get<double*>(); // 5
3597 ^
3598
>> 3599 "../nrnoc/exp2syn.cpp", line 487: error: identifier "_gth" is unde
fined
3600 double* _globals = _thread[_gth].get<double*>(); // 6
3601 ^
3602
>> 3603 "../nrnoc/exp2syn.cpp", line 487: error: type name is not allowed
3604 double* _globals = _thread[_gth].get<double*>(); // 6
3605 ^
3606
>> 3607 "../nrnoc/exp2syn.cpp", line 487: error: expected an expression
3608 double* _globals = _thread[_gth].get<double*>(); // 6
3609 ^
3610
>> 3611 "../nrnoc/exp2syn.cpp", line 504: error: identifier "_gth" is unde
fined
3612 double* _globals = _thread[_gth].get<double*>();// 7
3613 ^
3614
>> 3615 "../nrnoc/exp2syn.cpp", line 504: error: type name is not allowed
3616 double* _globals = _thread[_gth].get<double*>();// 7
3617 ^
3618
>> 3619 "../nrnoc/exp2syn.cpp", line 504: error: expected an expression
3620 double* _globals = _thread[_gth].get<double*>();// 7
3621 ^
3622
3623 18 errors detected in the compilation of "../nrnoc/exp2syn.cpp".
>> 3624 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2514:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/exp2syn.cpp.o] Error 2
>> 3625 "../nrnoc/expsyn.cpp", line 321: error: identifier "_gth" is undef
ined
3626 double* _globals{_thread[_gth].get<double*>()};
3627 ^
3628
>> 3629 "../nrnoc/expsyn.cpp", line 321: error: type name is not allowed
3630 double* _globals{_thread[_gth].get<double*>()};
3631 ^
3632
>> 3633 "../nrnoc/expsyn.cpp", line 321: error: expected an expression
3634 double* _globals{_thread[_gth].get<double*>()};
3635 ^
3636
>> 3637 "../nrnoc/expsyn.cpp", line 353: error: identifier "_gth" is undef
ined
3638 double* _globals{_thread[_gth].get<double*>()};
3639 ^
3640
>> 3641 "../nrnoc/expsyn.cpp", line 353: error: type name is not allowed
3642 double* _globals{_thread[_gth].get<double*>()};
3643 ^
3644
>> 3645 "../nrnoc/expsyn.cpp", line 353: error: expected an expression
3646 double* _globals{_thread[_gth].get<double*>()};
3647 ^
3648
>> 3649 "../nrnoc/expsyn.cpp", line 380: error: identifier "_gth" is undef
ined
3650 double* _globals = _thread[_gth].get<double*>(); // 4
3651 ^
3652
>> 3653 "../nrnoc/expsyn.cpp", line 380: error: type name is not allowed
3654 double* _globals = _thread[_gth].get<double*>(); // 4
3655 ^
3656
>> 3657 "../nrnoc/expsyn.cpp", line 380: error: expected an expression
3658 double* _globals = _thread[_gth].get<double*>(); // 4
3659 ^
3660
>> 3661 "../nrnoc/expsyn.cpp", line 411: error: identifier "_gth" is undef
ined
3662 double* _globals = _thread[_gth].get<double*>(); // 5
3663 ^
3664
>> 3665 "../nrnoc/expsyn.cpp", line 411: error: type name is not allowed
3666 double* _globals = _thread[_gth].get<double*>(); // 5
3667 ^
3668
>> 3669 "../nrnoc/expsyn.cpp", line 411: error: expected an expression
3670 double* _globals = _thread[_gth].get<double*>(); // 5
3671 ^
3672
>> 3673 "../nrnoc/expsyn.cpp", line 437: error: identifier "_gth" is undef
ined
3674 double* _globals = _thread[_gth].get<double*>(); // 6
3675 ^
3676
>> 3677 "../nrnoc/expsyn.cpp", line 437: error: type name is not allowed
3678 double* _globals = _thread[_gth].get<double*>(); // 6
3679 ^
3680
>> 3681 "../nrnoc/expsyn.cpp", line 437: error: expected an expression
3682 double* _globals = _thread[_gth].get<double*>(); // 6
3683 ^
3684
>> 3685 "../nrnoc/expsyn.cpp", line 454: error: identifier "_gth" is undef
ined
3686 double* _globals = _thread[_gth].get<double*>();// 7
3687 ^
3688
>> 3689 "../nrnoc/expsyn.cpp", line 454: error: type name is not allowed
3690 double* _globals = _thread[_gth].get<double*>();// 7
3691 ^
3692
>> 3693 "../nrnoc/expsyn.cpp", line 454: error: expected an expression
3694 double* _globals = _thread[_gth].get<double*>();// 7
3695 ^
3696
3697 18 errors detected in the compilation of "../nrnoc/expsyn.cpp".
>> 3698 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2528:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/expsyn.cpp.o] Error 2
>> 3699 "../nrnoc/hh.cpp", line 511: error: identifier "_gth" is undefined
3700 double* _globals{_thread[_gth].get<double*>()};
3701 ^
3702
>> 3703 "../nrnoc/hh.cpp", line 511: error: type name is not allowed
3704 double* _globals{_thread[_gth].get<double*>()};
3705 ^
3706
>> 3707 "../nrnoc/hh.cpp", line 511: error: expected an expression
3708 double* _globals{_thread[_gth].get<double*>()};
3709 ^
3710
>> 3711 "../nrnoc/hh.cpp", line 545: error: identifier "_gth" is undefined
3712 double* _globals{_thread[_gth].get<double*>()};
3713 ^
3714
>> 3715 "../nrnoc/hh.cpp", line 545: error: type name is not allowed
3716 double* _globals{_thread[_gth].get<double*>()};
3717 ^
3718
>> 3719 "../nrnoc/hh.cpp", line 545: error: expected an expression
3720 double* _globals{_thread[_gth].get<double*>()};
3721 ^
3722
>> 3723 "../nrnoc/hh.cpp", line 579: error: identifier "_gth" is undefined
3724 double* _globals = _thread[_gth].get<double*>(); // 4
3725 ^
3726
>> 3727 "../nrnoc/hh.cpp", line 579: error: type name is not allowed
3728 double* _globals = _thread[_gth].get<double*>(); // 4
3729 ^
3730
>> 3731 "../nrnoc/hh.cpp", line 579: error: expected an expression
3732 double* _globals = _thread[_gth].get<double*>(); // 4
3733 ^
3734
>> 3735 "../nrnoc/hh.cpp", line 617: error: identifier "_gth" is undefined
3736 double* _globals = _thread[_gth].get<double*>(); // 5
3737 ^
3738
>> 3739 "../nrnoc/hh.cpp", line 617: error: type name is not allowed
3740 double* _globals = _thread[_gth].get<double*>(); // 5
3741 ^
3742
>> 3743 "../nrnoc/hh.cpp", line 617: error: expected an expression
3744 double* _globals = _thread[_gth].get<double*>(); // 5
3745 ^
3746
>> 3747 "../nrnoc/hh.cpp", line 651: error: identifier "_gth" is undefined
3748 double* _globals = _thread[_gth].get<double*>(); // 6
3749 ^
3750
>> 3751 "../nrnoc/hh.cpp", line 651: error: type name is not allowed
3752 double* _globals = _thread[_gth].get<double*>(); // 6
3753 ^
3754
>> 3755 "../nrnoc/hh.cpp", line 651: error: expected an expression
3756 double* _globals = _thread[_gth].get<double*>(); // 6
3757 ^
3758
>> 3759 "../nrnoc/hh.cpp", line 668: error: identifier "_gth" is undefined
3760 double* _globals = _thread[_gth].get<double*>();// 7
3761 ^
3762
>> 3763 "../nrnoc/hh.cpp", line 668: error: type name is not allowed
3764 double* _globals = _thread[_gth].get<double*>();// 7
3765 ^
3766
>> 3767 "../nrnoc/hh.cpp", line 668: error: expected an expression
3768 double* _globals = _thread[_gth].get<double*>();// 7
3769 ^
3770
3771 18 errors detected in the compilation of "../nrnoc/hh.cpp".
>> 3772 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2556:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/hh.cpp.o] Error 2
>> 3773 "../nrnoc/intfire1.cpp", line 333: error: identifier "_gth" is und
efined
3774 double* _globals = _thread[_gth].get<double*>(); // 4
3775 ^
3776
>> 3777 "../nrnoc/intfire1.cpp", line 333: error: type name is not allowed
3778 double* _globals = _thread[_gth].get<double*>(); // 4
3779 ^
3780
>> 3781 "../nrnoc/intfire1.cpp", line 333: error: expected an expression
3782 double* _globals = _thread[_gth].get<double*>(); // 4
3783 ^
3784
>> 3785 "../nrnoc/intfire1.cpp", line 356: error: identifier "_gth" is und
efined
3786 double* _globals = _thread[_gth].get<double*>();// 7
3787 ^
3788
>> 3789 "../nrnoc/intfire1.cpp", line 356: error: type name is not allowed
3790 double* _globals = _thread[_gth].get<double*>();// 7
3791 ^
3792
>> 3793 "../nrnoc/intfire1.cpp", line 356: error: expected an expression
3794 double* _globals = _thread[_gth].get<double*>();// 7
3795 ^
3796
3797 6 errors detected in the compilation of "../nrnoc/intfire1.cpp".
>> 3798 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2570:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire1.cpp.o] Error
2
>> 3799 "../nrnoc/intfire2.cpp", line 344: error: identifier "_globals" is
undefined
3800 artcell_net_send ( _tqitem, _args, _pnt, t + firetime ( _t
hreadargscomma_ ib , _libf , 0.0 ) , 1.0 ) ;
3801 ^
3802
>> 3803 "../nrnoc/intfire2.cpp", line 354: error: identifier "_globals" is
undefined
3804 artcell_net_move ( _tqitem, _pnt, firetime ( _threadargsc
omma_ ib , _libf , m ) + t ) ;
3805 ^
3806
>> 3807 "../nrnoc/intfire2.cpp", line 497: error: identifier "_gth" is und
efined
3808 double* _globals = _thread[_gth].get<double*>(); // 4
3809 ^
3810
>> 3811 "../nrnoc/intfire2.cpp", line 497: error: type name is not allowed
3812 double* _globals = _thread[_gth].get<double*>(); // 4
3813 ^
3814
>> 3815 "../nrnoc/intfire2.cpp", line 497: error: expected an expression
3816 double* _globals = _thread[_gth].get<double*>(); // 4
3817 ^
3818
>> 3819 "../nrnoc/intfire2.cpp", line 520: error: identifier "_gth" is und
efined
3820 double* _globals = _thread[_gth].get<double*>();// 7
3821 ^
3822
>> 3823 "../nrnoc/intfire2.cpp", line 520: error: type name is not allowed
3824 double* _globals = _thread[_gth].get<double*>();// 7
3825 ^
3826
>> 3827 "../nrnoc/intfire2.cpp", line 520: error: expected an expression
3828 double* _globals = _thread[_gth].get<double*>();// 7
3829 ^
3830
3831 8 errors detected in the compilation of "../nrnoc/intfire2.cpp".
>> 3832 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2584:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire2.cpp.o] Error
2
>> 3833 "../nrnoc/intfire4.cpp", line 764: error: identifier "_globals" is
undefined
3834 newstates ( _threadargscomma_ t - t0 ) ;
3835 ^
3836
>> 3837 "../nrnoc/intfire4.cpp", line 848: error: identifier "_gth" is und
efined
3838 double* _globals = _thread[_gth].get<double*>(); // 4
3839 ^
3840
>> 3841 "../nrnoc/intfire4.cpp", line 848: error: type name is not allowed
3842 double* _globals = _thread[_gth].get<double*>(); // 4
3843 ^
3844
>> 3845 "../nrnoc/intfire4.cpp", line 848: error: expected an expression
3846 double* _globals = _thread[_gth].get<double*>(); // 4
3847 ^
3848
>> 3849 "../nrnoc/intfire4.cpp", line 871: error: identifier "_gth" is und
efined
3850 double* _globals = _thread[_gth].get<double*>();// 7
3851 ^
3852
>> 3853 "../nrnoc/intfire4.cpp", line 871: error: type name is not allowed
3854 double* _globals = _thread[_gth].get<double*>();// 7
3855 ^
3856
>> 3857 "../nrnoc/intfire4.cpp", line 871: error: expected an expression
3858 double* _globals = _thread[_gth].get<double*>();// 7
3859 ^
3860
3861 7 errors detected in the compilation of "../nrnoc/intfire4.cpp".
>> 3862 make[2]: *** [src/nrniv/CMakeFiles/nrniv_lib.dir/build.make:2598:
src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire4.cpp.o] Error
2
3863 make[2]: Leaving directory '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/
bbpcihpcproj12/P216288/J1315422/spack-build/spack-stage-neuron-git
.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-g3mlwqaims3h3es5
innhsuvbibqkcdsf/spack-build-g3mlwqa'
>> 3864 make[1]: *** [CMakeFiles/Makefile2:2920: src/nrniv/CMakeFiles/nrni
v_lib.dir/all] Error 2
3865 make[1]: Leaving directory '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/
bbpcihpcproj12/P216288/J1315422/spack-build/spack-stage-neuron-git
.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-g3mlwqaims3h3es5
innhsuvbibqkcdsf/spack-build-g3mlwqa'
>> 3866 make: *** [Makefile:169: all] Error 2
See build log for details:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315422/spack-build/spack-stage-neuron-git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9_develop-g3mlwqaims3h3es5innhsuvbibqkcdsf/spack-build-out.txt
$ set +o pipefail
$ chmod -R g+rX "${SPACK_BUILD}"
$ if [[ ${install_failed} == 1 ]]; then exit 1; fi
srun: error: r1i6n20: task 0: Exited with exit code 1
section_end:1718118259:step_script section_start:1718118259:upload_artifacts_on_failure Uploading artifacts for failed job
Using git from spack modules
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=239633 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=1315422 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=239674 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
Uploading artifacts as "junit" to coordinator... ok id=1315422 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=239723 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=1315422 responseStatus=201 Created token=glcbt-64
section_end:1718118261:upload_artifacts_on_failure section_start:1718118261:cleanup_file_variables Cleaning up project directory and file based variables
Using git from spack modules
section_end:1718118262:cleanup_file_variables ERROR: Job failed: exit status 1

Raw
build-nmodl.txt
Running with gitlab-runner 15.5.0 (0d4137b8)
 on BB5 map runner pnPo3yJy
section_start:1718117222:resolve_secrets Resolving secrets
section_end:1718117222:resolve_secrets section_start:1718117222: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-executor486668653, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name nrn
Pipeline ID 216288, build ref , job ID 1315416
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P216288, 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_J1315416_PROD_P2160_CP0_C4
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 2246810
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=2 --cpus-per-task=8 --mem=160G --job-name=GL_J1315416_PROD_P2160_CP0_C4 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P216288 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P216288 --ntasks=2 --jobid=2246810 --cpus-per-task=8 --mem=160G
section_end:1718117224:prepare_executor section_start:1718117224:prepare_script Preparing environment
Using git from spack modules
Running on r1i7n20 via bbpv1.epfl.ch...
section_end:1718117227:prepare_script section_start:1718117227: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:1718117229:get_sources section_start:1718117229:restore_cache Restoring cache
Using git from spack modules
Checking cache for build:nmodl-1-non_protected...
Runtime platform  arch=amd64 os=linux pid=23808 revision=58ba2b95 version=14.2.0
cache.zip is up to date 
Successfully extracted cache
section_end:1718117234:restore_cache section_start:1718117234:download_artifacts Downloading artifacts
Using git from spack modules
Downloading artifacts for spack_setup (1315414)...
Runtime platform  arch=amd64 os=linux pid=23943 revision=58ba2b95 version=14.2.0
Downloading artifacts from coordinator... ok  id=1315414 responseStatus=200 OK token=glcbt-64
section_end:1718117236:download_artifacts section_start:1718117236: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/P216288/J1315416/spack-config/config.yaml:2 build_stage:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315416/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315416/spack-build
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315416/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315416/spack-source-cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/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/P216288/J1315414/spack/etc/spack/defaults/config.yaml:18 extensions:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:19 - $spack/bluebrain/spack-scripting
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:37 template_dirs:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:38 - $spack/share/spack/templates
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:41 license_dir: $spack/etc/spack/licenses
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:81 test_stage: $user_cache_path/test
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:94 misc_cache: $user_cache_path/cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:100 connect_timeout: 10
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:105 verify_ssl: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:113 suppress_gpg_warnings: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:119 install_missing_compilers: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:124 checksum: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:129 deprecated: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:134 dirty: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:142 build_language: C
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:151 locks: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:156 url_fetch_method: urllib
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:185 concretizer: clingo
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:192 db_lock_timeout: 60
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:200 package_lock_timeout: null
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:205 shared_linking:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:210 type: rpath
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:216 bind: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:221 allow_sgid: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:227 install_status: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:231 binary_index_ttl: 600
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:233 flags:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:235 keep_werror: none
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:240 aliases:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:241 concretise: concretize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/config.yaml:242 containerise: containerize
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/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/P216288/J1315416/spack-config/concretizer.yaml:2 reuse: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:23 targets:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:28 granularity: microarchitectures
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:32 host_compatible: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:38 unify: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/spack/etc/spack/defaults/concretizer.yaml:40 duplicates:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414/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/P216288/J1315416_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/P216288
$ 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/bbpcihpcproj12/2246810/ccache
Config file: /nvme/bbpcihpcproj12/2246810/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: Tue Jun 11 16:47:20 2024
Local storage:
Cache size (GB): 0.45 / 0.51 (87.04%)
Files: 5013
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
--------------------------------
- pis5gl5 nmodl@git.c5ecfea39cbd53ffcc248b1dcf732c1e0ae1ffc4=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/P216288, 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-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-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-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.c5ecfea39cbd53ffcc248b1dcf732c1e0ae1ffc4=develop-pis5gl5kpxkhvpyg2ej73radyh56itvx [19/19]
==> No binary for nmodl-git.c5ecfea39cbd53ffcc248b1dcf732c1e0ae1ffc4=develop-pis5gl5kpxkhvpyg2ej73radyh56itvx 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.c5ecfea39cbd53ffcc248b1dcf732c1e0ae1ffc4=develop-pis5gl5kpxkhvpyg2ej73radyh56itvx
Stage: 41.57s. Cmake: 2.64s. Build: 1m 27.57s. Install: 1.44s. Post-install: 0.36s. Total: 2m 13.83s
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/software/install_gcc-12.3.0-skylake/nmodl-git.c5ecfea39cbd53ffcc248b1dcf732c1e0ae1ffc4_develop-pis5gl
$ 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 pis5gl5kpxkhvpyg2ej73radyh56itvx
$ 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/bbpcihpcproj12/2246810/ccache
Config file: /nvme/bbpcihpcproj12/2246810/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: Tue Jun 11 16:51:41 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 (87.05%)
Files: 5017
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:1718117502:step_script section_start:1718117502: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=26409 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:1718117524:archive_cache section_start:1718117524:upload_artifacts_on_success Uploading artifacts for successful job
Using git from spack modules
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=26537 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=1315416 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=26576 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
Uploading artifacts as "junit" to coordinator... ok id=1315416 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=26618 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=1315416 responseStatus=201 Created token=glcbt-64
section_end:1718117527:upload_artifacts_on_success section_start:1718117527:cleanup_file_variables Cleaning up project directory and file based variables
Using git from spack modules
section_end:1718117528:cleanup_file_variables Job succeeded
Raw
mac-m1-cmake-build-cmake-on-off-off-address.txt
Running with gitlab-runner 15.4.0 (43b2dc3d)
 on macos-arm64 vGzz-bdp
section_start:1718117114:resolve_secrets Resolving secrets
section_end:1718117114:resolve_secrets section_start:1718117114:prepare_executor Preparing the "shell" executor
Using Shell executor...
section_end:1718117114:prepare_executor section_start:1718117114:prepare_script Preparing environment
Running on bbpmacglr01.bbp.epfl.ch...
section_end:1718117114:prepare_script section_start:1718117114: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/P216288/J1315413/hpc/cellular/nrn/.git/
Created fresh repository.
Checking out e2a6b6e8 as cornu/use_globals...
Skipping Git submodules setup
section_end:1718117116:get_sources section_start:1718117116: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=69544 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:1718117116:restore_cache section_start:1718117116: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/tmp3s14dwpu
Processing /private/var/folders/dm/mrnbn5ld56v61w1_hpbmskfw0000gp/T/tmp3s14dwpu/setuptools-68.2.2-py3-none-any.whl
Processing /private/var/folders/dm/mrnbn5ld56v61w1_hpbmskfw0000gp/T/tmp3s14dwpu/pip-23.3.1-py3-none-any.whl
Installing collected packages: setuptools, pip
Successfully installed pip-23.3.1 setuptools-68.2.2
$ 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)
Collecting setuptools_scm (from -r nrn_requirements.txt (line 3))
Using cached setuptools_scm-8.1.0-py3-none-any.whl.metadata (6.6 kB)
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)
Collecting ipython (from -r nrn_requirements.txt (line 8))
Using cached ipython-8.25.0-py3-none-any.whl.metadata (4.9 kB)
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)
Collecting packaging (from -r nrn_requirements.txt (line 10))
Using cached packaging-24.1-py3-none-any.whl.metadata (3.2 kB)
Collecting pytest<=8.1.1 (from -r nrn_requirements.txt (line 11))
Using cached pytest-8.1.1-py3-none-any.whl.metadata (7.6 kB)
Collecting pytest-cov (from -r nrn_requirements.txt (line 12))
Using cached pytest_cov-5.0.0-py3-none-any.whl.metadata (27 kB)
Collecting mpi4py (from -r nrn_requirements.txt (line 13))
Using cached mpi4py-3.1.6-cp310-cp310-macosx_12_0_arm64.whl
Collecting numpy (from -r nrn_requirements.txt (line 14))
Using cached numpy-1.26.4-cp310-cp310-macosx_11_0_arm64.whl.metadata (61 kB)
Collecting find_libpython (from -r nrn_requirements.txt (line 15))
Using cached find_libpython-0.4.0-py3-none-any.whl.metadata (2.8 kB)
Collecting tomli>=1 (from setuptools_scm->-r nrn_requirements.txt (line 3))
Using cached tomli-2.0.1-py3-none-any.whl.metadata (8.9 kB)
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)
Collecting python-dateutil>=2.7 (from matplotlib->-r nrn_requirements.txt (line 5))
Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting Jinja2>=2.9 (from bokeh<3->-r nrn_requirements.txt (line 7))
Using cached jinja2-3.1.4-py3-none-any.whl.metadata (2.6 kB)
Collecting PyYAML>=3.10 (from bokeh<3->-r nrn_requirements.txt (line 7))
Using cached PyYAML-6.0.1-cp310-cp310-macosx_11_0_arm64.whl.metadata (2.1 kB)
Collecting tornado>=5.1 (from bokeh<3->-r nrn_requirements.txt (line 7))
Using cached tornado-6.4.1-cp38-abi3-macosx_10_9_universal2.whl.metadata (2.5 kB)
Collecting typing-extensions>=3.10.0 (from bokeh<3->-r nrn_requirements.txt (line 7))
Using cached typing_extensions-4.12.2-py3-none-any.whl.metadata (3.0 kB)
Collecting decorator (from ipython->-r nrn_requirements.txt (line 8))
Using cached decorator-5.1.1-py3-none-any.whl.metadata (4.0 kB)
Collecting jedi>=0.16 (from ipython->-r nrn_requirements.txt (line 8))
Using cached jedi-0.19.1-py2.py3-none-any.whl.metadata (22 kB)
Collecting matplotlib-inline (from ipython->-r nrn_requirements.txt (line 8))
Using cached matplotlib_inline-0.1.7-py3-none-any.whl.metadata (3.9 kB)
Collecting prompt-toolkit<3.1.0,>=3.0.41 (from ipython->-r nrn_requirements.txt (line 8))
Using cached prompt_toolkit-3.0.47-py3-none-any.whl.metadata (6.4 kB)
Collecting pygments>=2.4.0 (from ipython->-r nrn_requirements.txt (line 8))
Using cached pygments-2.18.0-py3-none-any.whl.metadata (2.5 kB)
Collecting stack-data (from ipython->-r nrn_requirements.txt (line 8))
Using cached stack_data-0.6.3-py3-none-any.whl.metadata (18 kB)
Collecting traitlets>=5.13.0 (from ipython->-r nrn_requirements.txt (line 8))
Using cached traitlets-5.14.3-py3-none-any.whl.metadata (10 kB)
Collecting exceptiongroup (from ipython->-r nrn_requirements.txt (line 8))
Using cached exceptiongroup-1.2.1-py3-none-any.whl.metadata (6.6 kB)
Collecting pexpect>4.3 (from ipython->-r nrn_requirements.txt (line 8))
Using cached pexpect-4.9.0-py2.py3-none-any.whl.metadata (2.5 kB)
Collecting iniconfig (from pytest<=8.1.1->-r nrn_requirements.txt (line 11))
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 nrn_requirements.txt (line 11))
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 nrn_requirements.txt (line 12))
Using cached coverage-7.5.3-cp310-cp310-macosx_11_0_arm64.whl.metadata (8.2 kB)
Collecting parso<0.9.0,>=0.8.3 (from jedi>=0.16->ipython->-r nrn_requirements.txt (line 8))
Using cached parso-0.8.4-py2.py3-none-any.whl.metadata (7.7 kB)
Collecting MarkupSafe>=2.0 (from Jinja2>=2.9->bokeh<3->-r nrn_requirements.txt (line 7))
Using cached MarkupSafe-2.1.5-cp310-cp310-macosx_10_9_universal2.whl.metadata (3.0 kB)
Collecting ptyprocess>=0.5 (from pexpect>4.3->ipython->-r nrn_requirements.txt (line 8))
Using cached ptyprocess-0.7.0-py2.py3-none-any.whl.metadata (1.3 kB)
Collecting wcwidth (from prompt-toolkit<3.1.0,>=3.0.41->ipython->-r nrn_requirements.txt (line 8))
Using cached wcwidth-0.2.13-py2.py3-none-any.whl.metadata (14 kB)
Collecting six>=1.5 (from python-dateutil>=2.7->matplotlib->-r nrn_requirements.txt (line 5))
Using cached six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB)
Collecting executing>=1.2.0 (from stack-data->ipython->-r nrn_requirements.txt (line 8))
Using cached executing-2.0.1-py2.py3-none-any.whl.metadata (9.0 kB)
Collecting asttokens>=2.1.0 (from stack-data->ipython->-r nrn_requirements.txt (line 8))
Using cached asttokens-2.4.1-py2.py3-none-any.whl.metadata (5.2 kB)
Collecting pure-eval (from stack-data->ipython->-r nrn_requirements.txt (line 8))
Using cached pure_eval-0.2.2-py3-none-any.whl.metadata (6.2 kB)
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 setuptools_scm-8.1.0-py3-none-any.whl (43 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 ipython-8.25.0-py3-none-any.whl (817 kB)
Using cached Cython-0.29.37-py2.py3-none-any.whl (989 kB)
Using cached packaging-24.1-py3-none-any.whl (53 kB)
Using cached pytest-8.1.1-py3-none-any.whl (337 kB)
Using cached pytest_cov-5.0.0-py3-none-any.whl (21 kB)
Using cached numpy-1.26.4-cp310-cp310-macosx_11_0_arm64.whl (14.0 MB)
Using cached find_libpython-0.4.0-py3-none-any.whl (8.7 kB)
Using cached contourpy-1.2.1-cp310-cp310-macosx_11_0_arm64.whl (244 kB)
Using cached coverage-7.5.3-cp310-cp310-macosx_11_0_arm64.whl (204 kB)
Using cached cycler-0.12.1-py3-none-any.whl (8.3 kB)
Using cached exceptiongroup-1.2.1-py3-none-any.whl (16 kB)
Using cached fonttools-4.53.0-cp310-cp310-macosx_11_0_arm64.whl (2.2 MB)
Using cached jedi-0.19.1-py2.py3-none-any.whl (1.6 MB)
Using cached jinja2-3.1.4-py3-none-any.whl (133 kB)
Using cached kiwisolver-1.4.5-cp310-cp310-macosx_11_0_arm64.whl (66 kB)
Using cached pexpect-4.9.0-py2.py3-none-any.whl (63 kB)
Using cached pillow-10.3.0-cp310-cp310-macosx_11_0_arm64.whl (3.4 MB)
Using cached pluggy-1.5.0-py3-none-any.whl (20 kB)
Using cached prompt_toolkit-3.0.47-py3-none-any.whl (386 kB)
Using cached pygments-2.18.0-py3-none-any.whl (1.2 MB)
Using cached pyparsing-3.1.2-py3-none-any.whl (103 kB)
Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
Using cached PyYAML-6.0.1-cp310-cp310-macosx_11_0_arm64.whl (169 kB)
Using cached tomli-2.0.1-py3-none-any.whl (12 kB)
Using cached tornado-6.4.1-cp38-abi3-macosx_10_9_universal2.whl (435 kB)
Using cached traitlets-5.14.3-py3-none-any.whl (85 kB)
Using cached typing_extensions-4.12.2-py3-none-any.whl (37 kB)
Using cached decorator-5.1.1-py3-none-any.whl (9.1 kB)
Using cached distro-1.9.0-py3-none-any.whl (20 kB)
Using cached iniconfig-2.0.0-py3-none-any.whl (5.9 kB)
Using cached matplotlib_inline-0.1.7-py3-none-any.whl (9.9 kB)
Using cached stack_data-0.6.3-py3-none-any.whl (24 kB)
Using cached asttokens-2.4.1-py2.py3-none-any.whl (27 kB)
Using cached executing-2.0.1-py2.py3-none-any.whl (24 kB)
Using cached MarkupSafe-2.1.5-cp310-cp310-macosx_10_9_universal2.whl (18 kB)
Using cached parso-0.8.4-py2.py3-none-any.whl (103 kB)
Using cached ptyprocess-0.7.0-py2.py3-none-any.whl (13 kB)
Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
Using cached pure_eval-0.2.2-py3-none-any.whl (11 kB)
Using cached wcwidth-0.2.13-py2.py3-none-any.whl (34 kB)
Installing collected packages: wcwidth, pure-eval, ptyprocess, find_libpython, wheel, typing-extensions, traitlets, tornado, tomli, six, setuptools, PyYAML, pyparsing, pygments, prompt-toolkit, pluggy, pip, pillow, pexpect, parso, packaging, numpy, mpi4py, MarkupSafe, kiwisolver, iniconfig, fonttools, executing, exceptiongroup, distro, decorator, cython, cycler, coverage, setuptools_scm, scikit-build, python-dateutil, pytest, matplotlib-inline, Jinja2, jedi, contourpy, asttokens, stack-data, pytest-cov, matplotlib, bokeh, ipython
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
Successfully installed Jinja2-3.1.4 MarkupSafe-2.1.5 PyYAML-6.0.1 asttokens-2.4.1 bokeh-2.4.3 contourpy-1.2.1 coverage-7.5.3 cycler-0.12.1 cython-0.29.37 decorator-5.1.1 distro-1.9.0 exceptiongroup-1.2.1 executing-2.0.1 find_libpython-0.4.0 fonttools-4.53.0 iniconfig-2.0.0 ipython-8.25.0 jedi-0.19.1 kiwisolver-1.4.5 matplotlib-3.9.0 matplotlib-inline-0.1.7 mpi4py-3.1.6 numpy-1.26.4 packaging-24.1 parso-0.8.4 pexpect-4.9.0 pillow-10.3.0 pip-24.0 pluggy-1.5.0 prompt-toolkit-3.0.47 ptyprocess-0.7.0 pure-eval-0.2.2 pygments-2.18.0 pyparsing-3.1.2 pytest-8.1.1 pytest-cov-5.0.0 python-dateutil-2.9.0.post0 scikit-build-0.17.6 setuptools-70.0.0 setuptools_scm-8.1.0 six-1.16.0 stack-data-0.6.3 tomli-2.0.1 tornado-6.4.1 traitlets-5.14.3 typing-extensions-4.12.2 wcwidth-0.2.13 wheel-0.43.0
$ 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/P216288/J1315413/hpc/cellular/nrn/external/nmodl'...
From https://github.com/BlueBrain/nmodl
* branch 70553cc4d9092aafed42aa49ac4e730830af1124 -> FETCH_HEAD
Submodule path 'external/nmodl': checked out '70553cc4d9092aafed42aa49ac4e730830af1124'
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'
Submodule 'test/usecases/references' (https://github.com/BlueBrain/nmodl-references.git) registered for path 'external/nmodl/test/usecases/references'
Cloning into '/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/external/nmodl/cmake/hpc-coding-conventions'...
Cloning into '/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/external/nmodl/ext/backward'...
Cloning into '/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/external/nmodl/ext/catch2'...
Cloning into '/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/external/nmodl/ext/cli11'...
Cloning into '/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/external/nmodl/ext/eigen'...
Cloning into '/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/external/nmodl/ext/fmt'...
Cloning into '/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/external/nmodl/ext/json'...
Cloning into '/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/external/nmodl/ext/pybind11'...
Cloning into '/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/external/nmodl/ext/spdlog'...
Cloning into '/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/external/nmodl/test/usecases/references'...
Submodule path 'external/nmodl/cmake/hpc-coding-conventions': checked out '8f8115597817365c5c4fa39e217b3ab0b3640cb2'
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 8a099e44b3d5f85b20f05828d919d2332a8de841 -> FETCH_HEAD
Submodule path 'external/nmodl/ext/pybind11': checked out '8a099e44b3d5f85b20f05828d919d2332a8de841'
From https://github.com/gabime/spdlog
* branch 7c02e204c92545f869e2f04edaab1f19fe8b19fd -> FETCH_HEAD
Submodule path 'external/nmodl/ext/spdlog': checked out '7c02e204c92545f869e2f04edaab1f19fe8b19fd'
From https://github.com/BlueBrain/nmodl-references
* branch c9f0aaa9270e9a49598c5424ad03eaa48a7eec47 -> FETCH_HEAD
Submodule path 'external/nmodl/test/usecases/references': checked out 'c9f0aaa9270e9a49598c5424ad03eaa48a7eec47'
$ 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-0.9.5-py3-none-any.whl.metadata (19 kB)
Requirement already satisfied: setuptools-scm>=8.0 in ./venv/lib/python3.10/site-packages (from -r external/nmodl/requirements.txt (line 3)) (8.1.0)
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Requirement already satisfied: PyYAML>=3.13 in ./venv/lib/python3.10/site-packages (from -r external/nmodl/requirements.txt (line 5)) (6.0.1)
Requirement already satisfied: find_libpython in ./venv/lib/python3.10/site-packages (from -r external/nmodl/requirements.txt (line 7)) (0.4.0)
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)
Requirement already satisfied: pytest<=8.1.1 in ./venv/lib/python3.10/site-packages (from -r external/nmodl/requirements.txt (line 12)) (8.1.1)
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Requirement already satisfied: numpy in ./venv/lib/python3.10/site-packages (from -r external/nmodl/requirements.txt (line 14)) (1.26.4)
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)
Requirement already satisfied: exceptiongroup>=1.0 in ./venv/lib/python3.10/site-packages (from scikit-build-core->-r external/nmodl/requirements.txt (line 2)) (1.2.1)
Requirement already satisfied: packaging>=21.3 in ./venv/lib/python3.10/site-packages (from scikit-build-core->-r external/nmodl/requirements.txt (line 2)) (24.1)
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)
Requirement already satisfied: tomli>=1.2.2 in ./venv/lib/python3.10/site-packages (from scikit-build-core->-r external/nmodl/requirements.txt (line 2)) (2.0.1)
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Requirement already satisfied: MarkupSafe>=2.0 in ./venv/lib/python3.10/site-packages (from Jinja2>=2.9.3->-r external/nmodl/requirements.txt (line 4)) (2.1.5)
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)
Requirement already satisfied: iniconfig in ./venv/lib/python3.10/site-packages (from pytest<=8.1.1->-r external/nmodl/requirements.txt (line 12)) (2.0.0)
Requirement already satisfied: pluggy<2.0,>=1.4 in ./venv/lib/python3.10/site-packages (from pytest<=8.1.1->-r external/nmodl/requirements.txt (line 12)) (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 external/nmodl/requirements.txt (line 13)) (7.5.3)
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)
Requirement already satisfied: python-dateutil>=2.8.2 in ./venv/lib/python3.10/site-packages (from jupyter-client->-r external/nmodl/requirements.txt (line 16)) (2.9.0.post0)
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)
Requirement already satisfied: tornado>=6.2 in ./venv/lib/python3.10/site-packages (from jupyter-client->-r external/nmodl/requirements.txt (line 16)) (6.4.1)
Requirement already satisfied: traitlets>=5.3 in ./venv/lib/python3.10/site-packages (from jupyter-client->-r external/nmodl/requirements.txt (line 16)) (5.14.3)
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))
Using cached nbformat-5.10.4-py3-none-any.whl.metadata (3.6 kB)
Collecting pandocfilters>=1.4.1 (from nbconvert->-r external/nmodl/requirements.txt (line 20))
Using cached pandocfilters-1.5.1-py2.py3-none-any.whl.metadata (9.0 kB)
Requirement already satisfied: pygments>=2.4.1 in ./venv/lib/python3.10/site-packages (from nbconvert->-r external/nmodl/requirements.txt (line 20)) (2.18.0)
Collecting tinycss2 (from nbconvert->-r external/nmodl/requirements.txt (line 20))
Using cached tinycss2-1.3.0-py3-none-any.whl.metadata (3.0 kB)
Collecting sphinxcontrib-devhelp (from sphinx<6->-r external/nmodl/requirements.txt (line 24))
Using cached sphinxcontrib_devhelp-1.0.6-py3-none-any.whl.metadata (2.3 kB)
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))
Using cached Babel-2.15.0-py3-none-any.whl.metadata (1.5 kB)
Collecting alabaster<0.8,>=0.7 (from sphinx<6->-r external/nmodl/requirements.txt (line 24))
Using cached alabaster-0.7.16-py3-none-any.whl.metadata (2.9 kB)
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))
Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
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)
Requirement already satisfied: six>=1.9.0 in ./venv/lib/python3.10/site-packages (from bleach!=5.0.0->nbconvert->-r external/nmodl/requirements.txt (line 20)) (1.16.0)
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-2.19.1-py3-none-any.whl.metadata (2.1 kB)
Collecting jsonschema>=2.6 (from nbformat>=5.7->nbconvert->-r external/nmodl/requirements.txt (line 20))
Using cached jsonschema-4.22.0-py3-none-any.whl.metadata (8.2 kB)
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 urllib3-2.2.1-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 soupsieve>1.2 (from beautifulsoup4->nbconvert->-r external/nmodl/requirements.txt (line 20))
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Collecting appnope (from ipykernel->jupyter->-r external/nmodl/requirements.txt (line 17))
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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))
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Collecting nest-asyncio (from ipykernel->jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached nest_asyncio-1.6.0-py3-none-any.whl.metadata (2.8 kB)
Collecting psutil (from ipykernel->jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached psutil-5.9.8-cp38-abi3-macosx_11_0_arm64.whl.metadata (21 kB)
Collecting widgetsnbextension~=4.0.11 (from ipywidgets->jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached widgetsnbextension-4.0.11-py3-none-any.whl.metadata (1.6 kB)
Collecting jupyterlab-widgets~=3.0.11 (from ipywidgets->jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached jupyterlab_widgets-3.0.11-py3-none-any.whl.metadata (4.1 kB)
Requirement already satisfied: prompt-toolkit>=3.0.30 in ./venv/lib/python3.10/site-packages (from jupyter-console->jupyter->-r external/nmodl/requirements.txt (line 17)) (3.0.47)
Collecting jupyter-server<3,>=2.4.0 (from notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
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Collecting jupyterlab-server<3,>=2.27.1 (from notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
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Collecting jupyterlab<4.3,>=4.2.0 (from notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
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Collecting notebook-shim<0.3,>=0.2 (from notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
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Collecting qtpy>=2.4.0 (from qtconsole->jupyter->-r external/nmodl/requirements.txt (line 17))
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Collecting attrs>=22.2.0 (from jsonschema>=2.6->nbformat>=5.7->nbconvert->-r external/nmodl/requirements.txt (line 20))
Using cached attrs-23.2.0-py3-none-any.whl.metadata (9.5 kB)
Collecting jsonschema-specifications>=2023.03.6 (from jsonschema>=2.6->nbformat>=5.7->nbconvert->-r external/nmodl/requirements.txt (line 20))
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Collecting referencing>=0.28.4 (from jsonschema>=2.6->nbformat>=5.7->nbconvert->-r external/nmodl/requirements.txt (line 20))
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Collecting rpds-py>=0.7.1 (from jsonschema>=2.6->nbformat>=5.7->nbconvert->-r external/nmodl/requirements.txt (line 20))
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Collecting anyio>=3.1.0 (from jupyter-server<3,>=2.4.0->notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
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Collecting send2trash>=1.8.2 (from jupyter-server<3,>=2.4.0->notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
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Collecting terminado>=0.8.3 (from jupyter-server<3,>=2.4.0->notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached terminado-0.18.1-py3-none-any.whl.metadata (5.8 kB)
Collecting websocket-client>=1.7 (from jupyter-server<3,>=2.4.0->notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached websocket_client-1.8.0-py3-none-any.whl.metadata (8.0 kB)
Collecting async-lru>=1.0.0 (from jupyterlab<4.3,>=4.2.0->notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached async_lru-2.0.4-py3-none-any.whl.metadata (4.5 kB)
Collecting httpx>=0.25.0 (from jupyterlab<4.3,>=4.2.0->notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached httpx-0.27.0-py3-none-any.whl.metadata (7.2 kB)
Collecting jupyter-lsp>=2.0.0 (from jupyterlab<4.3,>=4.2.0->notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
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Collecting json5>=0.9.0 (from jupyterlab-server<3,>=2.27.1->notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
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Collecting sniffio>=1.1 (from anyio>=3.1.0->jupyter-server<3,>=2.4.0->notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached sniffio-1.3.1-py3-none-any.whl.metadata (3.9 kB)
Collecting argon2-cffi-bindings (from argon2-cffi>=21.1->jupyter-server<3,>=2.4.0->notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached argon2_cffi_bindings-21.2.0-cp38-abi3-macosx_10_9_universal2.whl.metadata (6.7 kB)
Collecting httpcore==1.* (from httpx>=0.25.0->jupyterlab<4.3,>=4.2.0->notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached httpcore-1.0.5-py3-none-any.whl.metadata (20 kB)
Collecting h11<0.15,>=0.13 (from httpcore==1.*->httpx>=0.25.0->jupyterlab<4.3,>=4.2.0->notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached h11-0.14.0-py3-none-any.whl.metadata (8.2 kB)
Requirement already satisfied: parso<0.9.0,>=0.8.3 in ./venv/lib/python3.10/site-packages (from jedi>=0.16->ipython>=7.23.1->ipykernel->jupyter->-r external/nmodl/requirements.txt (line 17)) (0.8.4)
Collecting python-json-logger>=2.0.4 (from jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached python_json_logger-2.0.7-py3-none-any.whl.metadata (6.5 kB)
Collecting rfc3339-validator (from jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached rfc3339_validator-0.1.4-py2.py3-none-any.whl.metadata (1.5 kB)
Collecting rfc3986-validator>=0.1.1 (from jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached rfc3986_validator-0.1.1-py2.py3-none-any.whl.metadata (1.7 kB)
Requirement already satisfied: ptyprocess>=0.5 in ./venv/lib/python3.10/site-packages (from pexpect>4.3->ipython>=7.23.1->ipykernel->jupyter->-r external/nmodl/requirements.txt (line 17)) (0.7.0)
Requirement already satisfied: executing>=1.2.0 in ./venv/lib/python3.10/site-packages (from stack-data->ipython>=7.23.1->ipykernel->jupyter->-r external/nmodl/requirements.txt (line 17)) (2.0.1)
Requirement already satisfied: asttokens>=2.1.0 in ./venv/lib/python3.10/site-packages (from stack-data->ipython>=7.23.1->ipykernel->jupyter->-r external/nmodl/requirements.txt (line 17)) (2.4.1)
Requirement already satisfied: pure-eval in ./venv/lib/python3.10/site-packages (from stack-data->ipython>=7.23.1->ipykernel->jupyter->-r external/nmodl/requirements.txt (line 17)) (0.2.2)
Collecting fqdn (from jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached fqdn-1.5.1-py3-none-any.whl.metadata (1.4 kB)
Collecting isoduration (from jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached isoduration-20.11.0-py3-none-any.whl.metadata (5.7 kB)
Collecting jsonpointer>1.13 (from jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached jsonpointer-3.0.0-py2.py3-none-any.whl.metadata (2.3 kB)
Collecting uri-template (from jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached uri_template-1.3.0-py3-none-any.whl.metadata (8.8 kB)
Collecting webcolors>=1.11 (from jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached webcolors-24.6.0-py3-none-any.whl.metadata (2.6 kB)
Collecting cffi>=1.0.1 (from argon2-cffi-bindings->argon2-cffi>=21.1->jupyter-server<3,>=2.4.0->notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached cffi-1.16.0-cp310-cp310-macosx_11_0_arm64.whl.metadata (1.5 kB)
Collecting pycparser (from cffi>=1.0.1->argon2-cffi-bindings->argon2-cffi>=21.1->jupyter-server<3,>=2.4.0->notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached pycparser-2.22-py3-none-any.whl.metadata (943 bytes)
Collecting arrow>=0.15.0 (from isoduration->jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached arrow-1.3.0-py3-none-any.whl.metadata (7.5 kB)
Collecting types-python-dateutil>=2.8.10 (from arrow>=0.15.0->isoduration->jsonschema[format-nongpl]>=4.18.0->jupyter-events>=0.9.0->jupyter-server<3,>=2.4.0->notebook->jupyter->-r external/nmodl/requirements.txt (line 17))
Using cached types_python_dateutil-2.9.0.20240316-py3-none-any.whl.metadata (1.8 kB)
Using cached scikit_build_core-0.9.5-py3-none-any.whl (152 kB)
Using cached sympy-1.12.1-py3-none-any.whl (5.7 MB)
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Installing collected packages: webencodings, snowballstemmer, mpmath, mistune, fastjsonschema, widgetsnbextension, websocket-client, webcolors, urllib3, uri-template, types-python-dateutil, tinycss2, terminado, sympy, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, sniffio, send2trash, rpds-py, rfc3986-validator, rfc3339-validator, qtpy, pyzmq, python-json-logger, pycparser, psutil, prometheus-client, platformdirs, pathspec, pandocfilters, overrides, nest-asyncio, mdurl, jupyterlab-widgets, jupyterlab-pygments, jsonpointer, json5, imagesize, idna, h11, fqdn, docutils, defusedxml, debugpy, comm, charset-normalizer, certifi, bleach, babel, attrs, async-lru, appnope, alabaster, scikit-build-core, requests, referencing, markdown-it-py, jupyter-server-terminals, jupyter-core, httpcore, cffi, beautifulsoup4, arrow, anyio, sphinx, mdit-py-plugins, jupyter-client, jsonschema-specifications, isoduration, httpx, argon2-cffi-bindings, sphinxcontrib-jquery, myst_parser, jsonschema, ipywidgets, ipykernel, argon2-cffi, sphinx-rtd-theme, qtconsole, nbformat, jupyter-console, nbclient, jupyter-events, nbconvert, nbsphinx, jupyter-server, notebook-shim, jupyterlab-server, jupyter-lsp, jupyterlab, notebook, jupyter
Successfully installed 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 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 debugpy-1.8.1 defusedxml-0.7.1 docutils-0.19 fastjsonschema-2.19.1 fqdn-1.5.1 h11-0.14.0 httpcore-1.0.5 httpx-0.27.0 idna-3.7 imagesize-1.4.1 ipykernel-6.29.4 ipywidgets-8.1.3 isoduration-20.11.0 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 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 overrides-7.7.0 pandocfilters-1.5.1 pathspec-0.12.1 platformdirs-4.2.2 prometheus-client-0.20.0 psutil-5.9.8 pycparser-2.22 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-0.9.5 send2trash-1.8.3 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 sympy-1.12.1 terminado-0.18.1 tinycss2-1.3.0 types-python-dateutil-2.9.0.20240316 uri-template-1.3.0 urllib3-2.2.1 webcolors-24.6.0 webencodings-0.5.1 websocket-client-1.8.0 widgetsnbextension-4.0.11
$ 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/P216288/J1315413/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/P216288/J1315413/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/P216288/J1315413/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/P216288/J1315413/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/P216288/J1315413/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/P216288/J1315413/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/P216288/J1315413/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/P216288/J1315413/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/P216288/J1315413/hpc/cellular/nrn/external/nmodl/ext/json/include/
-- 3rd party project: using pybind11 from "ext/pybind11"
-- pybind11 v2.11.1
CMake Warning (dev) at external/nmodl/ext/pybind11/tools/FindPythonLibsNew.cmake:98 (find_package):
Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
are removed. Run "cmake --help-policy CMP0148" for policy details. Use
the cmake_policy command to set the policy and suppress this warning.
Call Stack (most recent call first):
external/nmodl/ext/pybind11/tools/pybind11Tools.cmake:50 (find_package)
external/nmodl/ext/pybind11/tools/pybind11Common.cmake:188 (include)
external/nmodl/ext/pybind11/CMakeLists.txt:210 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Found PythonInterp: /Users/gitlab-runner/builds/2/P216288/J1315413/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
CMake Warning (dev) at external/nmodl/ext/spdlog/CMakeLists.txt:91 (option):
Policy CMP0077 is not set: option() honors normal variables. Run "cmake
--help-policy CMP0077" for policy details. Use the cmake_policy command to
set the policy and suppress this warning.
For compatibility with older versions of CMake, option is clearing the
normal variable 'SPDLOG_FMT_EXTERNAL'.
This warning is for project developers. Use -Wno-dev to suppress it.
-- Build type: Custom
-- CHECKING FOR PYTHON
CMake Warning (dev) at external/nmodl/CMakeLists.txt:173 (find_package):
Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
are removed. Run "cmake --help-policy CMP0148" for policy details. Use
the cmake_policy command to set the policy and suppress this warning.
This warning is for project developers. Use -Wno-dev to suppress it.
-- Found PythonInterp: /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/venv/bin/python (found suitable version "3.10.13", minimum required is "3.8")
--
-- Configured NMODL 0.0 (70553cc 2024-05-01 23:16:44 +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/P216288/J1315413/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/P216288/J1315413/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/P216288/J1315413/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/P216288/J1315413/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/P216288/J1315413/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/P216288/J1315413/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/P216288/J1315413/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/P216288/J1315413/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/P216288/J1315413/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 (24.5s)
-- Generating done (0.1s)
-- Build files have been written to: /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build
$ ccache -z
Statistics zeroed
$ ccache -vs 2>/dev/null
Cache directory: /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/ccache
Config file: /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/ccache/ccache.conf
System config file: /opt/homebrew/Cellar/ccache/4.9/etc/ccache.conf
Stats updated: Tue Jun 11 16:46:29 2024
Local storage:
Cache size (GiB): 0.0 / 5.0 ( 0.00%)
Files: 0
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/demo.ses
[3/1930] Generating share/nrn/demo/dend3/syn3.hoc
[4/1930] Generating share/nrn/demo/d3init.hoc
[5/1930] Generating share/nrn/demo/dend3/control.hoc
[6/1930] Generating share/nrn/demo/demo.hoc
[7/1930] Generating share/nrn/demo/dend3.ses
[8/1930] Generating share/nrn/demo/dend3/dend3.nrn
[9/1930] Generating share/nrn/demo/dynchan.ses
[10/1930] Generating share/nrn/demo/dynclamp.ses
[11/1930] Generating share/nrn/demo/hh.ses
[12/1930] Generating share/nrn/demo/dynclamp.hoc
[13/1930] Generating share/nrn/demo/hh.hoc
[14/1930] Generating share/nrn/demo/nomodel.hoc
[15/1930] Generating share/nrn/demo/pyramid.ses
[16/1930] Generating share/nrn/demo/pyramid.nrn
[17/1930] Generating share/nrn/demo/release.hoc
[18/1930] Update hh.mod for CoreNEURON compatibility
[19/1930] Generating share/nrn/demo/reconst.hoc
[20/1930] Generating share/nrn/demo/release.ses
[21/1930] Generating share/nrn/demo/release/cachan1.mod
[22/1930] Generating share/nrn/demo/release/camchan.mod
[23/1930] Generating share/nrn/demo/release/cabpump.mod
[24/1930] Generating share/nrn/demo/release/capump.mod
[25/1930] Generating share/nrn/demo/release/invlfire.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/release.mod
[29/1930] Generating share/nrn/demo/release/nachan.mod
[30/1930] Generating share/nrn/demo/singhh.hoc
[31/1930] Generating share/nrn/demo/singhh.ses
[32/1930] Generating share/nrn/demo/sync/cell.hoc
[33/1930] Generating share/nrn/demo/singhhchan.hoc
[34/1930] Generating share/nrn/demo/sync/init.hoc
[35/1930] Generating share/nrn/demo/sync/spkplot.hoc
[36/1930] Generating share/nrn/demo/sync/demosync.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/hoc/atoltool.hoc
[43/1930] Generating share/nrn/lib/auditscripts/notes
[44/1930] Generating share/nrn/lib/auditscripts/retrieve.sh
[45/1930] Generating share/nrn/lib/auditscripts/saveaudit
[46/1930] Generating share/nrn/lib/cleanup
[47/1930] Generating share/nrn/lib/helpdict
[48/1930] Generating share/nrn/lib/hoc/attshape.hoc
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| ^~~~~~~~~~~~~~~~~~~~~~~~
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56 | %define parser_class_name {DiffeqParser}
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| %define api.parser.class {DiffeqParser}
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| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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[569/1930] Building CXX object src/nrniv/CMakeFiles/nocmodl.dir/__/nmodl/simultan.cpp.o
[570/1930] Building CXX object src/nrniv/CMakeFiles/nocmodl.dir/__/nmodl/parsact.cpp.o
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[572/1930] Building CXX object src/nrniv/CMakeFiles/nocmodl.dir/__/nmodl/solve.cpp.o
[573/1930] Building CXX object src/nrniv/CMakeFiles/nocmodl.dir/__/nmodl/version.cpp.o
[574/1930] Building CXX object src/nrniv/CMakeFiles/nocmodl.dir/__/nmodl/symbol.cpp.o
[575/1930] Generating ../../share/nrn/nrnmain.cpp
[576/1930] Generating ../../include/nrnmpiuse.h
[577/1930] Generating ../../include/nrncvode/nrnneosm.h
[578/1930] Generating ../../include/nrnconf.h
[579/1930] Generating ../oc/hocusr.h
[580/1930] cd /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrniv && true
[581/1930] Building CXX object src/nrnpython/CMakeFiles/rxdmath.dir/rxdmath.cpp.o
[582/1930] Building CXX object src/nrniv/CMakeFiles/nocmodl.dir/nocmodl_generated/lex.cpp.o
[583/1930] Linking CXX shared library lib/librxdmath.dylib
ld: warning: -undefined dynamic_lookup may not work with chained fixups
[584/1930] Building CXX object src/nrniv/CMakeFiles/nocmodl.dir/nocmodl_generated/diffeq.cpp.o
[585/1930] Building CXX object src/nrniv/CMakeFiles/nocmodl.dir/nocmodl_generated/parse1.cpp.o
[586/1930] Building CXX object src/nrniv/CMakeFiles/nocmodl.dir/__/nmodl/nocpout.cpp.o
[587/1930] Building CXX object external/nmodl/src/pybind/CMakeFiles/pyembed.dir/pyembed.cpp.o
[588/1930] Building CXX object external/nmodl/src/utils/CMakeFiles/util.dir/logger.cpp.o
[589/1930] Building CXX object external/nmodl/src/pybind/CMakeFiles/pywrapper.dir/wrapper.cpp.o
[590/1930] Linking CXX static library lib/libutil.a
[591/1930] Linking CXX static library lib/libpywrapper.a
[592/1930] -- NMODL : GENERATING NMODL LEXER WITH FLEX! --
../../../../../external/nmodl/src/lexer/nmodl.ll:503: warning, -s option given but default rule can be matched
[593/1930] -- NMODL : GENERATING VERBATIM LEXER WITH FLEX! --
[594/1930] -- NMODL : GENERATING DIFFERENTIAL EQUATION LEXER WITH FLEX! --
../../../../../external/nmodl/src/lexer/diffeq.ll:100: warning, -s option given but default rule can be matched
[595/1930] -- NMODL : GENERATING C(11) LEXER WITH FLEX! --
[596/1930] -- NMODL : GENERATING UNIT LEXER WITH FLEX! --
../../../../../external/nmodl/src/lexer/unit.ll:171: warning, -s option given but default rule can be matched
[597/1930] Linking CXX static library lib/libpyembed.a
[598/1930] Building CXX object src/nrnpython/CMakeFiles/nrnpython.dir/nrnpython.cpp.o
[599/1930] Building CXX object src/nrnpython/CMakeFiles/nrnpython.dir/nrnpy_p2h.cpp.o
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[602/1930] Building CXX object src/nrnpython/CMakeFiles/nrnpython.dir/rxd_extracellular.cpp.o
[603/1930] Building CXX object src/nrnpython/CMakeFiles/nrnpython.dir/nrnpy_nrn.cpp.o
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[606/1930] Building CXX object src/nrnpython/CMakeFiles/nrnpython.dir/rxd.cpp.o
[607/1930] Building CXX object external/nmodl/src/codegen/CMakeFiles/codegen.dir/codegen_info.cpp.o
[608/1930] Building CXX object src/nrniv/CMakeFiles/nocmodl.dir/__/nmodl/modl.cpp.o
[609/1930] Building CXX object external/nmodl/src/lexer/CMakeFiles/lexer.dir/modtoken.cpp.o
[610/1930] Building CXX object external/nmodl/src/codegen/CMakeFiles/codegen.dir/codegen_utils.cpp.o
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[612/1930] Building CXX object external/nmodl/src/lexer/CMakeFiles/lexer.dir/verbatim_lexer.cpp.o
[613/1930] Building CXX object external/nmodl/src/codegen/CMakeFiles/codegen.dir/codegen_helper_visitor.cpp.o
[614/1930] Building CXX object external/nmodl/src/lexer/CMakeFiles/lexer.dir/diffeq_base_lexer.cpp.o
[615/1930] Building CXX object external/nmodl/src/lexer/CMakeFiles/lexer.dir/nmodl_utils.cpp.o
[616/1930] Building CXX object external/nmodl/src/codegen/CMakeFiles/codegen.dir/codegen_compatibility_visitor.cpp.o
[617/1930] Building CXX object external/nmodl/src/lexer/CMakeFiles/lexer.dir/c11_base_lexer.cpp.o
[618/1930] Building CXX object external/nmodl/src/lexer/CMakeFiles/lexer.dir/unit_base_lexer.cpp.o
[619/1930] Building CXX object external/nmodl/src/lexer/CMakeFiles/lexer.dir/__/parser/diffeq_driver.cpp.o
[620/1930] Building CXX object external/nmodl/src/lexer/CMakeFiles/lexer.dir/nmodl_base_lexer.cpp.o
[621/1930] Building CXX object external/nmodl/src/lexer/CMakeFiles/lexer.dir/__/parser/diffeq_context.cpp.o
[622/1930] Building CXX object external/nmodl/src/codegen/CMakeFiles/codegen.dir/codegen_neuron_cpp_visitor.cpp.o
[623/1930] Building CXX object external/nmodl/src/lexer/CMakeFiles/lexer.dir/__/parser/verbatim_parser.cpp.o
[624/1930] Building CXX object external/nmodl/src/lexer/CMakeFiles/lexer.dir/__/parser/c11_driver.cpp.o
[625/1930] Building CXX object external/nmodl/src/lexer/CMakeFiles/lexer.dir/__/parser/unit_driver.cpp.o
[626/1930] Building CXX object external/nmodl/src/codegen/CMakeFiles/codegen.dir/codegen_cpp_visitor.cpp.o
[627/1930] Building CXX object external/nmodl/src/lexer/CMakeFiles/lexer.dir/__/parser/c/c11_parser.cpp.o
[628/1930] Building CXX object external/nmodl/src/lexer/CMakeFiles/lexer.dir/__/parser/diffeq/diffeq_parser.cpp.o
[629/1930] Building CXX object external/nmodl/src/lexer/CMakeFiles/lexer.dir/__/parser/unit/unit_parser.cpp.o
[630/1930] Building CXX object external/nmodl/src/symtab/CMakeFiles/symtab.dir/symbol_properties.cpp.o
[631/1930] Building CXX object external/nmodl/src/codegen/CMakeFiles/codegen.dir/codegen_coreneuron_cpp_visitor.cpp.o
[632/1930] Building CXX object external/nmodl/src/lexer/CMakeFiles/lexer.dir/__/units/units.cpp.o
[633/1930] Building CXX object external/nmodl/src/lexer/CMakeFiles/lexer.dir/__/parser/nmodl_driver.cpp.o
[634/1930] Building CXX object external/nmodl/src/symtab/CMakeFiles/symtab.dir/symbol_table.cpp.o
[635/1930] Building CXX object external/nmodl/src/symtab/CMakeFiles/symtab.dir/symbol.cpp.o
[636/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/function_callpath_visitor.cpp.o
[637/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/global_var_visitor.cpp.o
[638/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/indexedname_visitor.cpp.o
[639/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/implicit_argument_visitor.cpp.o
[640/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/after_cvode_to_cnexp_visitor.cpp.o
[641/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/constant_folder_visitor.cpp.o
[642/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/index_remover.cpp.o
[643/1930] Building CXX object external/nmodl/src/lexer/CMakeFiles/lexer.dir/__/parser/nmodl/nmodl_parser.cpp.o
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[645/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/defuse_analyze_visitor.cpp.o
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[647/1930] Building CXX object external/nmodl/src/CMakeFiles/nmodl.dir/main.cpp.o
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[649/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/solve_block_visitor.cpp.o
[650/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/loop_unroll_visitor.cpp.o
[651/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/neuron_solve_visitor.cpp.o
[652/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/localize_visitor.cpp.o
[653/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/inline_visitor.cpp.o
[654/1930] Building CXX object external/nmodl/src/lexer/CMakeFiles/lexer.dir/__/ast/ast.cpp.o
[655/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/semantic_analysis_visitor.cpp.o
[656/1930] Linking CXX static library lib/liblexer.a
[657/1930] Linking CXX static library lib/libsymtab.a
[658/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/var_usage_visitor.cpp.o
[659/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/kinetic_block_visitor.cpp.o
[660/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/rename_visitor.cpp.o
[661/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/verbatim_visitor.cpp.o
[662/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/units_visitor.cpp.o
[663/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/ast_visitor.cpp.o
[664/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/steadystate_visitor.cpp.o
[665/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/lookup_visitor.cpp.o
[666/1930] Linking CXX executable bin/nocmodl
[667/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/json_visitor.cpp.o
[668/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/verbatim_var_rename_visitor.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/rxd_llgramarea.cpp.o
[671/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/benchmark/catch_chronometer.cpp.o
[672/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/visitor_utils.cpp.o
[673/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/nmodl_visitor.cpp.o
[674/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/benchmark/detail/catch_benchmark_function.cpp.o
[675/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/sympy_replace_solutions_visitor.cpp.o
[676/1930] Building CXX object src/nrnpython/CMakeFiles/nrnpython.dir/rxd_intracellular.cpp.o
[677/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/sympy_conductance_visitor.cpp.o
[678/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/benchmark/detail/catch_analyse.cpp.o
[679/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/generators/catch_generator_exception.cpp.o
[680/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/checkparent_visitor.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] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/generators/catch_generators.cpp.o
[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_random.cpp.o
[685/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_automake.cpp.o
[686/1930] Building CXX object src/nrnpython/CMakeFiles/nrnpython.dir/rxd_vol.cpp.o
[687/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_common_base.cpp.o
[688/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_compact.cpp.o
[689/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_event_listener.cpp.o
[690/1930] Building CXX object external/nmodl/src/visitors/CMakeFiles/visitor.dir/symtab_visitor.cpp.o
[691/1930] Generating ../nrnoc/exp2syn.cpp
Translating /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/exp2syn.mod into /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/exp2syn.cpp
Thread Safe
[692/1930] Generating ../nrnoc/apcount.cpp
Translating /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/apcount.mod into /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/apcount.cpp
Thread Safe
[693/1930] Generating ../nrnoc/expsyn.cpp
Translating /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/expsyn.mod into /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/expsyn.cpp
Thread Safe
[694/1930] Generating ../nrnoc/feature.cpp
Translating /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/feature.mod into /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/feature.cpp
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[695/1930] Generating ../nrnoc/intfire1.cpp
Translating /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/intfire1.mod into /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/intfire1.cpp
Thread Safe
[696/1930] Generating ../nrnoc/hh.cpp
Translating /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/hh.mod into /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/hh.cpp
Thread Safe
[697/1930] Generating ../nrnoc/intfire2.cpp
Translating /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/intfire2.mod into /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/intfire2.cpp
Thread Safe
[698/1930] Generating ../nrnoc/intfire4.cpp
Translating /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/intfire4.mod into /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/intfire4.cpp
Thread Safe
[699/1930] Generating ../nrnoc/netstim.cpp
Translating /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/netstim.mod into /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/netstim.cpp
Thread Safe
[700/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_console.cpp.o
[701/1930] Generating ../nrnoc/oclmp.cpp
Translating /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/oclmp.mod into /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/oclmp.cpp
Thread Safe
[702/1930] Generating ../nrnoc/passive.cpp
Translating /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/passive.mod into /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/passive.cpp
Thread Safe
[703/1930] Generating ../nrnoc/pattern.cpp
Translating /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/pattern.mod into /Users/gitlab-runner/builds/2/P216288/J1315413/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
[704/1930] Generating ../nrnoc/ppmark.cpp
Translating /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/ppmark.mod into /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/ppmark.cpp
Thread Safe
[705/1930] Generating ../nrnoc/stim.cpp
Translating /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/stim.mod into /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/stim.cpp
Thread Safe
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Translating /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/syn.mod into /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/syn.cpp
Thread Safe
[707/1930] Generating ../nrnoc/vclmp.cpp
Translating /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/vclmp.mod into /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/vclmp.cpp
Notice: VERBATIM blocks are not thread safe
Notice: LINEAR is not thread safe.
[708/1930] Generating ../nrnoc/svclmp.cpp
Translating /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/svclmp.mod into /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc/svclmp.cpp
Thread Safe
[709/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_cumulative_base.cpp.o
[710/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_helpers.cpp.o
[711/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/axis.cpp.o
[712/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/apwindow.cpp.o
[713/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_registrars.cpp.o
[714/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_streaming_base.cpp.o
[715/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/bndedval.cpp.o
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[717/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/cbwidget.cpp.o
[718/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/epsprint.cpp.o
[719/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/checkpnt.cpp.o
[720/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_multi.cpp.o
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[722/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/gifimage.cpp.o
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[724/1930] Building CXX object external/catch2/src/CMakeFiles/Catch2.dir/catch2/reporters/catch_reporter_junit.cpp.o
[725/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/graphvec.cpp.o
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[730/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/hocmark.cpp.o
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[733/1930] Linking CXX executable bin/nmodl
[734/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/idraw.cpp.o
[735/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/graph.cpp.o
[736/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/mlinedit.cpp.o
[737/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/ivocmain.cpp.o
[738/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/mymath.cpp.o
/Users/gitlab-runner/builds/2/P216288/J1315413/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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WARNING: No mod files found in '/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/bin', compiling default ones only!
[INFO] Running: make -j4 -f /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/share/coreneuron/nrnivmodl_core_makefile ROOT=/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build MECHLIB_SUFFIX=internal NMODL_BINARY=/Users/gitlab-runner/builds/2/P216288/J1315413/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
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/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/oc/hoc.cpp:2:14: warning: '#pragma FENV_ACCESS' is not supported on this target - ignored [-Wignored-pragmas]
#pragma STDC FENV_ACCESS ON
^
1 warning generated.
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/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/oc/math.cpp:2:14: warning: '#pragma FENV_ACCESS' is not supported on this target - ignored [-Wignored-pragmas]
#pragma STDC FENV_ACCESS ON
^
1 warning generated.
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[888/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/apcount.cpp.o
FAILED: src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/apcount.cpp.o
ccache /usr/bin/g++ -DCORENRN_BUILD=0 -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX=1 -DMPI_NO_CPPBIND=1 -DNRN_ASAN_ENABLED -DNRN_ENABLE_THREADS -DOMPI_SKIP_MPICXX=1 -DUSE_PYTHON -Dnrniv_lib_EXPORTS -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/include -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/ivoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrncvode -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrniv -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/oc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrncvode -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnpython -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/oc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/parallel -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/sundials -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/sundials/shared -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/gnu -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnmpi -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/parallel -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/scopmath -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sparse -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sparse13 -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sundials -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sundials/cvodes -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sundials/ida -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sundials/shared -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrniv/oc_generated -I/opt/homebrew/Cellar/open-mpi/5.0.1/include -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/ivos -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/.. -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../oc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../nrnoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../ivoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../nrniv -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../nrnmpi -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../ivos -I/opt/homebrew/opt/python@3.10/Frameworks/Python.framework/Versions/3.10/include/python3.10 -isystem /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/external/eigen -O1 -g -openmp-simd -std=c++17 -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -fPIC -fno-omit-frame-pointer -shared-libsan -fsanitize=address -fsanitize-address-use-after-scope -MD -MT src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/apcount.cpp.o -MF src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/apcount.cpp.o.d -o src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/apcount.cpp.o -c /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/apcount.cpp
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/apcount.cpp:346:28: error: use of undeclared identifier '_gth'; did you mean '_nt'?
double* _globals = _thread[_gth].get<double*>(); // 4
^~~~
_nt
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/apcount.cpp:337:79: note: '_nt' declared here
static void nrn_init(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type){
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/apcount.cpp:346:27: error: array subscript is not an integer
double* _globals = _thread[_gth].get<double*>(); // 4
^~~~~
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/apcount.cpp:372:28: error: use of undeclared identifier '_gth'; did you mean '_nt'?
double* _globals = _thread[_gth].get<double*>(); // 5
^~~~
_nt
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/apcount.cpp:361:78: note: '_nt' declared here
static void nrn_cur(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/apcount.cpp:372:27: error: array subscript is not an integer
double* _globals = _thread[_gth].get<double*>(); // 5
^~~~~
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/apcount.cpp:391:28: error: use of undeclared identifier '_gth'; did you mean '_nt'?
double* _globals = _thread[_gth].get<double*>(); // 6
^~~~
_nt
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/apcount.cpp:381:80: note: '_nt' declared here
static void nrn_jacob(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/apcount.cpp:391:27: error: array subscript is not an integer
double* _globals = _thread[_gth].get<double*>(); // 6
^~~~~
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/apcount.cpp:408:28: error: use of undeclared identifier '_gth'; did you mean '_nt'?
double* _globals = _thread[_gth].get<double*>();// 7
^~~~
_nt
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/apcount.cpp:399:80: note: '_nt' declared here
static void nrn_state(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/apcount.cpp:408:27: error: array subscript is not an integer
double* _globals = _thread[_gth].get<double*>();// 7
^~~~~
8 errors generated.
[889/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/exp2syn.cpp.o
FAILED: src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/exp2syn.cpp.o
ccache /usr/bin/g++ -DCORENRN_BUILD=0 -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX=1 -DMPI_NO_CPPBIND=1 -DNRN_ASAN_ENABLED -DNRN_ENABLE_THREADS -DOMPI_SKIP_MPICXX=1 -DUSE_PYTHON -Dnrniv_lib_EXPORTS -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/include -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/ivoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrncvode -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrniv -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/oc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrncvode -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnpython -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/oc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/parallel -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/sundials -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/sundials/shared -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/gnu -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnmpi -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/parallel -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/scopmath -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sparse -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sparse13 -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sundials -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sundials/cvodes -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sundials/ida -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sundials/shared -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrniv/oc_generated -I/opt/homebrew/Cellar/open-mpi/5.0.1/include -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/ivos -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/.. -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../oc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../nrnoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../ivoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../nrniv -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../nrnmpi -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../ivos -I/opt/homebrew/opt/python@3.10/Frameworks/Python.framework/Versions/3.10/include/python3.10 -isystem /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/external/eigen -O1 -g -openmp-simd -std=c++17 -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -fPIC -fno-omit-frame-pointer -shared-libsan -fsanitize=address -fsanitize-address-use-after-scope -MD -MT src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/exp2syn.cpp.o -MF src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/exp2syn.cpp.o.d -o src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/exp2syn.cpp.o -c /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/exp2syn.cpp
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/exp2syn.cpp:358:28: error: use of undeclared identifier '_gth'; did you mean '_nt'?
double* _globals{_thread[_gth].get<double*>()};
^~~~
_nt
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/exp2syn.cpp:349:80: note: '_nt' declared here
static void _ode_spec(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/exp2syn.cpp:358:27: error: array subscript is not an integer
double* _globals{_thread[_gth].get<double*>()};
^~~~~
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/exp2syn.cpp:390:28: error: use of undeclared identifier '_gth'; did you mean '_nt'?
double* _globals{_thread[_gth].get<double*>()};
^~~~
_nt
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/exp2syn.cpp:381:82: note: '_nt' declared here
static void _ode_matsol(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/exp2syn.cpp:390:27: error: array subscript is not an integer
double* _globals{_thread[_gth].get<double*>()};
^~~~~
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/exp2syn.cpp:429:28: error: use of undeclared identifier '_gth'; did you mean '_nt'?
double* _globals = _thread[_gth].get<double*>(); // 4
^~~~
_nt
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/exp2syn.cpp:420:79: note: '_nt' declared here
static void nrn_init(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type){
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/exp2syn.cpp:429:27: error: array subscript is not an integer
double* _globals = _thread[_gth].get<double*>(); // 4
^~~~~
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/exp2syn.cpp:461:28: error: use of undeclared identifier '_gth'; did you mean '_nt'?
double* _globals = _thread[_gth].get<double*>(); // 5
^~~~
_nt
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/exp2syn.cpp:450:78: note: '_nt' declared here
static void nrn_cur(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/exp2syn.cpp:461:27: error: array subscript is not an integer
double* _globals = _thread[_gth].get<double*>(); // 5
^~~~~
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/exp2syn.cpp:487:28: error: use of undeclared identifier '_gth'; did you mean '_nt'?
double* _globals = _thread[_gth].get<double*>(); // 6
^~~~
_nt
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/exp2syn.cpp:477:80: note: '_nt' declared here
static void nrn_jacob(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/exp2syn.cpp:487:27: error: array subscript is not an integer
double* _globals = _thread[_gth].get<double*>(); // 6
^~~~~
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/exp2syn.cpp:504:28: error: use of undeclared identifier '_gth'; did you mean '_nt'?
double* _globals = _thread[_gth].get<double*>();// 7
^~~~
_nt
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/exp2syn.cpp:495:80: note: '_nt' declared here
static void nrn_state(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/exp2syn.cpp:504:27: error: array subscript is not an integer
double* _globals = _thread[_gth].get<double*>();// 7
^~~~~
12 errors generated.
[890/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/oc_generated/parse.cpp.o
[891/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/expsyn.cpp.o
FAILED: src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/expsyn.cpp.o
ccache /usr/bin/g++ -DCORENRN_BUILD=0 -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX=1 -DMPI_NO_CPPBIND=1 -DNRN_ASAN_ENABLED -DNRN_ENABLE_THREADS -DOMPI_SKIP_MPICXX=1 -DUSE_PYTHON -Dnrniv_lib_EXPORTS -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/include -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/ivoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrncvode -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrniv -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/oc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrncvode -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnpython -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/oc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/parallel -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/sundials -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/sundials/shared -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/gnu -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnmpi -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/parallel -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/scopmath -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sparse -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sparse13 -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sundials -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sundials/cvodes -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sundials/ida -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sundials/shared -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrniv/oc_generated -I/opt/homebrew/Cellar/open-mpi/5.0.1/include -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/ivos -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/.. -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../oc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../nrnoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../ivoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../nrniv -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../nrnmpi -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../ivos -I/opt/homebrew/opt/python@3.10/Frameworks/Python.framework/Versions/3.10/include/python3.10 -isystem /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/external/eigen -O1 -g -openmp-simd -std=c++17 -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -fPIC -fno-omit-frame-pointer -shared-libsan -fsanitize=address -fsanitize-address-use-after-scope -MD -MT src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/expsyn.cpp.o -MF src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/expsyn.cpp.o.d -o src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/expsyn.cpp.o -c /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/expsyn.cpp
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/expsyn.cpp:321:28: error: use of undeclared identifier '_gth'; did you mean '_nt'?
double* _globals{_thread[_gth].get<double*>()};
^~~~
_nt
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/expsyn.cpp:312:80: note: '_nt' declared here
static void _ode_spec(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/expsyn.cpp:321:27: error: array subscript is not an integer
double* _globals{_thread[_gth].get<double*>()};
^~~~~
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/expsyn.cpp:353:28: error: use of undeclared identifier '_gth'; did you mean '_nt'?
double* _globals{_thread[_gth].get<double*>()};
^~~~
_nt
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/expsyn.cpp:344:82: note: '_nt' declared here
static void _ode_matsol(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/expsyn.cpp:353:27: error: array subscript is not an integer
double* _globals{_thread[_gth].get<double*>()};
^~~~~
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/expsyn.cpp:380:28: error: use of undeclared identifier '_gth'; did you mean '_nt'?
double* _globals = _thread[_gth].get<double*>(); // 4
^~~~
_nt
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/expsyn.cpp:371:79: note: '_nt' declared here
static void nrn_init(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type){
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/expsyn.cpp:380:27: error: array subscript is not an integer
double* _globals = _thread[_gth].get<double*>(); // 4
^~~~~
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/expsyn.cpp:411:28: error: use of undeclared identifier '_gth'; did you mean '_nt'?
double* _globals = _thread[_gth].get<double*>(); // 5
^~~~
_nt
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/expsyn.cpp:400:78: note: '_nt' declared here
static void nrn_cur(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/expsyn.cpp:411:27: error: array subscript is not an integer
double* _globals = _thread[_gth].get<double*>(); // 5
^~~~~
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/expsyn.cpp:437:28: error: use of undeclared identifier '_gth'; did you mean '_nt'?
double* _globals = _thread[_gth].get<double*>(); // 6
^~~~
_nt
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/expsyn.cpp:427:80: note: '_nt' declared here
static void nrn_jacob(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/expsyn.cpp:437:27: error: array subscript is not an integer
double* _globals = _thread[_gth].get<double*>(); // 6
^~~~~
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/expsyn.cpp:454:28: error: use of undeclared identifier '_gth'; did you mean '_nt'?
double* _globals = _thread[_gth].get<double*>();// 7
^~~~
_nt
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/expsyn.cpp:445:80: note: '_nt' declared here
static void nrn_state(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/expsyn.cpp:454:27: error: array subscript is not an integer
double* _globals = _thread[_gth].get<double*>();// 7
^~~~~
12 errors generated.
[892/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/feature.cpp.o
[893/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/oc/code.cpp.o
[894/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/hh.cpp.o
FAILED: src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/hh.cpp.o
ccache /usr/bin/g++ -DCORENRN_BUILD=0 -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX=1 -DMPI_NO_CPPBIND=1 -DNRN_ASAN_ENABLED -DNRN_ENABLE_THREADS -DOMPI_SKIP_MPICXX=1 -DUSE_PYTHON -Dnrniv_lib_EXPORTS -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/include -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/ivoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrncvode -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrniv -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/oc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrncvode -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnpython -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/oc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/parallel -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/sundials -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/sundials/shared -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/gnu -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnmpi -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/parallel -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/scopmath -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sparse -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sparse13 -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sundials -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sundials/cvodes -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sundials/ida -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sundials/shared -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrniv/oc_generated -I/opt/homebrew/Cellar/open-mpi/5.0.1/include -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/ivos -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/.. -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../oc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../nrnoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../ivoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../nrniv -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../nrnmpi -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../ivos -I/opt/homebrew/opt/python@3.10/Frameworks/Python.framework/Versions/3.10/include/python3.10 -isystem /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/external/eigen -O1 -g -openmp-simd -std=c++17 -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -fPIC -fno-omit-frame-pointer -shared-libsan -fsanitize=address -fsanitize-address-use-after-scope -MD -MT src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/hh.cpp.o -MF src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/hh.cpp.o.d -o src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/hh.cpp.o -c /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/hh.cpp
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/hh.cpp:511:28: error: use of undeclared identifier '_gth'; did you mean '_nt'?
double* _globals{_thread[_gth].get<double*>()};
^~~~
_nt
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/hh.cpp:502:80: note: '_nt' declared here
static void _ode_spec(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/hh.cpp:511:27: error: array subscript is not an integer
double* _globals{_thread[_gth].get<double*>()};
^~~~~
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/hh.cpp:545:28: error: use of undeclared identifier '_gth'; did you mean '_nt'?
double* _globals{_thread[_gth].get<double*>()};
^~~~
_nt
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/hh.cpp:536:82: note: '_nt' declared here
static void _ode_matsol(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/hh.cpp:545:27: error: array subscript is not an integer
double* _globals{_thread[_gth].get<double*>()};
^~~~~
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/hh.cpp:579:28: error: use of undeclared identifier '_gth'; did you mean '_nt'?
double* _globals = _thread[_gth].get<double*>(); // 4
^~~~
_nt
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/hh.cpp:570:79: note: '_nt' declared here
static void nrn_init(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type){
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/hh.cpp:579:27: error: array subscript is not an integer
double* _globals = _thread[_gth].get<double*>(); // 4
^~~~~
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/hh.cpp:617:28: error: use of undeclared identifier '_gth'; did you mean '_nt'?
double* _globals = _thread[_gth].get<double*>(); // 5
^~~~
_nt
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/hh.cpp:606:78: note: '_nt' declared here
static void nrn_cur(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/hh.cpp:617:27: error: array subscript is not an integer
double* _globals = _thread[_gth].get<double*>(); // 5
^~~~~
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/hh.cpp:651:28: error: use of undeclared identifier '_gth'; did you mean '_nt'?
double* _globals = _thread[_gth].get<double*>(); // 6
^~~~
_nt
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/hh.cpp:641:80: note: '_nt' declared here
static void nrn_jacob(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/hh.cpp:651:27: error: array subscript is not an integer
double* _globals = _thread[_gth].get<double*>(); // 6
^~~~~
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/hh.cpp:668:28: error: use of undeclared identifier '_gth'; did you mean '_nt'?
double* _globals = _thread[_gth].get<double*>();// 7
^~~~
_nt
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/hh.cpp:659:80: note: '_nt' declared here
static void nrn_state(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/hh.cpp:668:27: error: array subscript is not an integer
double* _globals = _thread[_gth].get<double*>();// 7
^~~~~
12 errors generated.
[895/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire1.cpp.o
FAILED: src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire1.cpp.o
ccache /usr/bin/g++ -DCORENRN_BUILD=0 -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX=1 -DMPI_NO_CPPBIND=1 -DNRN_ASAN_ENABLED -DNRN_ENABLE_THREADS -DOMPI_SKIP_MPICXX=1 -DUSE_PYTHON -Dnrniv_lib_EXPORTS -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/include -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/ivoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrncvode -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrniv -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/oc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrncvode -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnpython -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/oc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/parallel -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/sundials -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/sundials/shared -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/gnu -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnmpi -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/parallel -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/scopmath -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sparse -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sparse13 -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sundials -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sundials/cvodes -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sundials/ida -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sundials/shared -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrniv/oc_generated -I/opt/homebrew/Cellar/open-mpi/5.0.1/include -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/ivos -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/.. -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../oc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../nrnoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../ivoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../nrniv -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../nrnmpi -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../ivos -I/opt/homebrew/opt/python@3.10/Frameworks/Python.framework/Versions/3.10/include/python3.10 -isystem /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/external/eigen -O1 -g -openmp-simd -std=c++17 -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -fPIC -fno-omit-frame-pointer -shared-libsan -fsanitize=address -fsanitize-address-use-after-scope -MD -MT src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire1.cpp.o -MF src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire1.cpp.o.d -o src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire1.cpp.o -c /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/intfire1.cpp
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/intfire1.cpp:333:28: error: use of undeclared identifier '_gth'; did you mean '_nt'?
double* _globals = _thread[_gth].get<double*>(); // 4
^~~~
_nt
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/intfire1.cpp:324:79: note: '_nt' declared here
static void nrn_init(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type){
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/intfire1.cpp:333:27: error: array subscript is not an integer
double* _globals = _thread[_gth].get<double*>(); // 4
^~~~~
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/intfire1.cpp:356:28: error: use of undeclared identifier '_gth'; did you mean '_nt'?
double* _globals = _thread[_gth].get<double*>();// 7
^~~~
_nt
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/intfire1.cpp:347:80: note: '_nt' declared here
static void nrn_state(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/intfire1.cpp:356:27: error: array subscript is not an integer
double* _globals = _thread[_gth].get<double*>();// 7
^~~~~
4 errors generated.
[896/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire2.cpp.o
FAILED: src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire2.cpp.o
ccache /usr/bin/g++ -DCORENRN_BUILD=0 -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX=1 -DMPI_NO_CPPBIND=1 -DNRN_ASAN_ENABLED -DNRN_ENABLE_THREADS -DOMPI_SKIP_MPICXX=1 -DUSE_PYTHON -Dnrniv_lib_EXPORTS -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/include -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/ivoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrncvode -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrniv -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/oc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrncvode -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnpython -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/oc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/parallel -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/sundials -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/sundials/shared -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/gnu -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnmpi -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/parallel -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/scopmath -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sparse -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sparse13 -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sundials -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sundials/cvodes -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sundials/ida -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/sundials/shared -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrniv/oc_generated -I/opt/homebrew/Cellar/open-mpi/5.0.1/include -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/ivos -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/.. -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../oc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../nrnoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../ivoc -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../nrniv -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../nrnmpi -I/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/src/nrnpython/../ivos -I/opt/homebrew/opt/python@3.10/Frameworks/Python.framework/Versions/3.10/include/python3.10 -isystem /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/external/eigen -O1 -g -openmp-simd -std=c++17 -arch arm64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk -fPIC -fno-omit-frame-pointer -shared-libsan -fsanitize=address -fsanitize-address-use-after-scope -MD -MT src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire2.cpp.o -MF src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire2.cpp.o.d -o src/nrniv/CMakeFiles/nrniv_lib.dir/__/nrnoc/intfire2.cpp.o -c /Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/intfire2.cpp
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/intfire2.cpp:344:63: error: use of undeclared identifier '_globals'
artcell_net_send ( _tqitem, _args, _pnt, t + firetime ( _threadargscomma_ ib , _libf , 0.0 ) , 1.0 ) ;
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/intfire2.cpp:48:55: note: expanded from macro '_threadargscomma_'
#define _threadargscomma_ _ml, _iml, _ppvar, _thread, _globals, _nt,
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/intfire2.cpp:354:53: error: use of undeclared identifier '_globals'
artcell_net_move ( _tqitem, _pnt, firetime ( _threadargscomma_ ib , _libf , m ) + t ) ;
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/intfire2.cpp:48:55: note: expanded from macro '_threadargscomma_'
#define _threadargscomma_ _ml, _iml, _ppvar, _thread, _globals, _nt,
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/intfire2.cpp:497:28: error: use of undeclared identifier '_gth'; did you mean '_nt'?
double* _globals = _thread[_gth].get<double*>(); // 4
^~~~
_nt
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/intfire2.cpp:488:79: note: '_nt' declared here
static void nrn_init(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type){
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/intfire2.cpp:497:27: error: array subscript is not an integer
double* _globals = _thread[_gth].get<double*>(); // 4
^~~~~
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/intfire2.cpp:520:28: error: use of undeclared identifier '_gth'; did you mean '_nt'?
double* _globals = _thread[_gth].get<double*>();// 7
^~~~
_nt
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/intfire2.cpp:511:80: note: '_nt' declared here
static void nrn_state(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
^
/Users/gitlab-runner/builds/2/P216288/J1315413/hpc/cellular/nrn/build/src/nrnoc/intfire2.cpp:520:27: error: array subscript is not an integer
double* _globals = _thread[_gth].get<double*>();// 7
^~~~~
6 errors generated.
[897/1930] Building CXX object src/nrniv/CMakeFiles/nrniv_lib.dir/__/ivoc/ocmatrix.cpp.o
ninja: build stopped: subcommand failed.
section_end:1718117273:step_script section_start:1718117273:cleanup_file_variables Cleaning up project directory and file based variables
section_end:1718117273:cleanup_file_variables ERROR: Job failed: exit status 1

Raw
spack-setup.txt
Running with gitlab-runner 15.5.0 (0d4137b8)
 on BB5 map runner pnPo3yJy
section_start:1718117114:resolve_secrets Resolving secrets
section_end:1718117114:resolve_secrets section_start:1718117114: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-executor2702824377, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name nrn
Pipeline ID 216288, build ref , job ID 1315414
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P216288, optional exclusive flag , optional cpus per task flag --cpus-per-task=6, optional qos flag , optional reservation flag
A slurm job will be created with name GL_J1315414_PROD_P2160_CP1_C4
Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 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 2246807
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1315414_PROD_P2160_CP1_C4 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P216288 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P216288 --ntasks=1 --jobid=2246807 --cpus-per-task=6 --mem=30750M
section_end:1718117115:prepare_executor section_start:1718117115:prepare_script Preparing environment
Using git from spack modules
Running on r1i7n20 via bbpv1.epfl.ch...
section_end:1718117118:prepare_script section_start:1718117118: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:1718117120:get_sources section_start:1718117120: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
$ if [[ -n "${SPACK_ENV_FILE_URL}" && "${PARSE_GITHUB_PR_DESCRIPTIONS,,}" == "true" ]]; then
$ cat > parse_description.py << END_SCRIPT # collapsed multi-line command
$ cat parse_description.py
import os
import re
import requests
pr_info = requests.get("https://api.github.com/repos/{}/pulls/{}".format(
os.environ['CI_EXTERNAL_PULL_REQUEST_TARGET_REPOSITORY'],
os.environ['CI_EXTERNAL_PULL_REQUEST_IID']),
headers={'Accept': 'application/vnd.github.v3+json'})
pr_body = pr_info.json()["body"]
# match something like NEURON_BRANCH=foo/bar
# special case for SPACK_DEPLOYMENT_SUFFIX=foo/bar
pat = re.compile('^([A-Z0-9_]+)_([A-Z]+)=([A-Z0-9\-\_\/\+\.]+)$', re.IGNORECASE)
def parse_term(m):
ref_type = m.group(2).lower()
is_deployment_suffix = ref_type == 'suffix' and m.group(1).lower() == 'spack_deployment'
if ref_type not in {'branch', 'tag', 'ref'} and not is_deployment_suffix: return
print(m.group(1).upper() + '_' + ref_type.upper() + '=' + m.group(3))
if pr_body is not None:
for pr_body_line in pr_body.splitlines():
if not pr_body_line.startswith('CI_BRANCHES:'): continue
for config_term in pr_body_line[12:].split(','):
pat.sub(parse_term, config_term)
$ (module load unstable python-dev; python parse_description.py) > input_variables.env
$ else
$ cat input_variables.env
$ for var_to_unset in $(sed 's/^\(.*\?\)_\(BRANCH\|COMMIT\|TAG\)=.*$/\1_BRANCH\n\1_COMMIT\n\1_TAG/' input_variables.env); do # collapsed multi-line command
$ set -o allexport
$ . input_variables.env
$ set +o allexport
$ unset MODULEPATH
$ . /gpfs/bbp.cscs.ch/ssd/apps/bsd/${SPACK_DEPLOYMENT_SUFFIX}/config/modules.sh
$ echo "MODULEPATH=${MODULEPATH}" > spack_clone_variables.env
$ echo Preparing to clone Spack into ${PWD}
Preparing to clone Spack into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P216288/J1315414
$ if [[ -z "${SPACK_BRANCH}" && ( -n "${SPACK_COMMIT}" || -n "${SPACK_TAG}" ) ]]; then
$ echo Checking out the ${SPACK_BRANCH} of Spack...
Checking out the develop of Spack...
$ module load unstable git
$ git clone -c feature.manyFiles=true --depth 1 --single-branch --branch ${SPACK_BRANCH} ${SPACK_URL} spack
Cloning into 'spack'...
Updating files: 19% (2163/11305) Updating files: 20% (2261/11305) Updating files: 21% (2375/11305) Updating files: 22% (2488/11305) Updating files: 23% (2601/11305) Updating files: 24% (2714/11305) Updating files: 25% (2827/11305) Updating files: 26% (2940/11305) Updating files: 27% (3053/11305) Updating files: 28% (3166/11305) Updating files: 29% (3279/11305) Updating files: 30% (3392/11305) Updating files: 31% (3505/11305) Updating files: 32% (3618/11305) Updating files: 33% (3731/11305) Updating files: 34% (3844/11305) Updating files: 35% (3957/11305) Updating files: 36% (4070/11305) Updating files: 37% (4183/11305) Updating files: 38% (4296/11305) Updating files: 39% (4409/11305) Updating files: 40% (4522/11305) Updating files: 41% (4636/11305) Updating files: 41% (4662/11305) Updating files: 42% (4749/11305) Updating files: 43% (4862/11305) Updating files: 44% (4975/11305) Updating files: 45% (5088/11305) Updating files: 46% (5201/11305) Updating files: 47% (5314/11305) Updating files: 47% (5387/11305) Updating files: 48% (5427/11305) Updating files: 49% (5540/11305) Updating files: 50% (5653/11305) Updating files: 51% (5766/11305) Updating files: 52% (5879/11305) Updating files: 53% (5992/11305) Updating files: 54% (6105/11305) Updating files: 55% (6218/11305) Updating files: 55% (6242/11305) Updating files: 56% (6331/11305) Updating files: 57% (6444/11305) Updating files: 58% (6557/11305) Updating files: 59% (6670/11305) Updating files: 60% (6783/11305) Updating files: 61% (6897/11305) Updating files: 62% (7010/11305) Updating files: 63% (7123/11305) Updating files: 64% (7236/11305) Updating files: 65% (7349/11305) Updating files: 66% (7462/11305) Updating files: 67% (7575/11305) Updating files: 68% (7688/11305) Updating files: 69% (7801/11305) Updating files: 70% (7914/11305) Updating files: 71% (8027/11305) Updating files: 72% (8140/11305) Updating files: 73% (8253/11305) Updating files: 74% (8366/11305) Updating files: 75% (8479/11305) Updating files: 76% (8592/11305) Updating files: 77% (8705/11305) Updating files: 77% (8737/11305) Updating files: 78% (8818/11305) Updating files: 79% (8931/11305) Updating files: 80% (9044/11305) Updating files: 81% (9158/11305) Updating files: 82% (9271/11305) Updating files: 83% (9384/11305) Updating files: 84% (9497/11305) Updating files: 85% (9610/11305) Updating files: 86% (9723/11305) Updating files: 87% (9836/11305) Updating files: 88% (9949/11305) Updating files: 88% (9980/11305) Updating files: 89% (10062/11305) Updating files: 90% (10175/11305) Updating files: 91% (10288/11305) Updating files: 92% (10401/11305) Updating files: 93% (10514/11305) Updating files: 94% (10627/11305) Updating files: 95% (10740/11305) Updating files: 96% (10853/11305) Updating files: 97% (10966/11305) Updating files: 98% (11079/11305) Updating files: 99% (11192/11305) Updating files: 100% (11305/11305) Updating files: 100% (11305/11305), done.
$ export SPACK_ROOT=${PWD}/spack
$ export SPACK_RESOLVED_COMMIT=$(cd "${SPACK_ROOT}" && git rev-parse HEAD)
$ export SPACK_USER_CACHE_PATH="${CI_BUILDS_DIR}"
$ export SPACK_SYSTEM_CONFIG_PATH="/gpfs/bbp.cscs.ch/ssd/apps/bsd/${SPACK_DEPLOYMENT_SUFFIX}/config"
$ echo "SPACK_ROOT=${SPACK_ROOT}" >> spack_clone_variables.env
$ echo "SPACK_RESOLVED_COMMIT=${SPACK_RESOLVED_COMMIT}" >> spack_clone_variables.env
$ echo "SPACK_USER_CACHE_PATH=${SPACK_USER_CACHE_PATH}" >> spack_clone_variables.env
$ echo "SPACK_SYSTEM_CONFIG_PATH=${SPACK_SYSTEM_CONFIG_PATH}" >> spack_clone_variables.env
$ . ${SPACK_ROOT}/share/spack/setup-env.sh
$ 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/P216288/J1315414_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/
$ env -0 | sed -nz '/^CUSTOM_ENV_/d;/^[^=]\+_\(BRANCH\|COMMIT\|TAG\)=.\+/p' | xargs -0t spack ${SPACK_EXTRA_FLAGS} configure-pipeline --ignore-packages CI_BUILD CI_COMMIT CI_DEFAULT GITLAB_PIPELINES SPACK SPACK_RESOLVED ${SPACK_SETUP_IGNORE_PACKAGE_VARIABLES} --write-commit-file=commit-mapping.env
spack configure-pipeline --ignore-packages CI_BUILD CI_COMMIT CI_DEFAULT GITLAB_PIPELINES SPACK SPACK_RESOLVED BLUECONFIGS --write-commit-file=commit-mapping.env CI_COMMIT_BRANCH=cornu/use_globals SPACK_RESOLVED_COMMIT=4b0a0d188d95af4428f193a1997e4333a2e8e1cf GITLAB_PIPELINES_BRANCH=main NEURON_COMMIT=e2a6b6e811fb9749543b72cc862039da2e2a4ce9 NMODL_BRANCH=master LIBSONATA_REPORT_BRANCH=master SPACK_BRANCH=develop CI_DEFAULT_BRANCH=master BLUECONFIGS_BRANCH=main
==> CI_COMMIT: ignoring CI_COMMIT_BRANCH=cornu/use_globals
==> SPACK_RESOLVED: ignoring SPACK_RESOLVED_COMMIT=4b0a0d188d95af4428f193a1997e4333a2e8e1cf
==> GITLAB_PIPELINES: ignoring GITLAB_PIPELINES_BRANCH=main
==> SPACK: ignoring SPACK_BRANCH=develop
==> CI_DEFAULT: ignoring CI_DEFAULT_BRANCH=master
==> BLUECONFIGS: ignoring BLUECONFIGS_BRANCH=main
==> nmodl: resolved branch master to c5ecfea39cbd53ffcc248b1dcf732c1e0ae1ffc4
==> libsonata-report: resolved branch master to 5602aadfa710d6766ce23cd151a1855190271bd8
==> adding config: packages:neuron:require: '@git.e2a6b6e811fb9749543b72cc862039da2e2a4ce9=develop'
==> adding config: packages:nmodl:require: '@git.c5ecfea39cbd53ffcc248b1dcf732c1e0ae1ffc4=develop'
==> adding config: packages:libsonata-report:require: '@git.5602aadfa710d6766ce23cd151a1855190271bd8=develop'
$ (cd "${SPACK_ROOT}" && git diff)
$ cat commit-mapping.env
NEURON_COMMIT=e2a6b6e811fb9749543b72cc862039da2e2a4ce9
NMODL_COMMIT=c5ecfea39cbd53ffcc248b1dcf732c1e0ae1ffc4
LIBSONATA_REPORT_COMMIT=5602aadfa710d6766ce23cd151a1855190271bd8
$ echo "SPACK_BRANCH=${SPACK_BRANCH}" >> commit-mapping.env
$ echo "SPACK_DEPLOYMENT_SUFFIX=${SPACK_DEPLOYMENT_SUFFIX}" >> commit-mapping.env
$ cat commit-mapping.env >> spack_clone_variables.env
$ spack ${SPACK_EXTRA_FLAGS} spec -IL ninja
==> Warning: Expected user 904556 to own /nvme/bbpcihpcproj12, but it is owned by 0
==> Fetching https://mirror.spack.io/bootstrap/github-actions/v0.5/build_cache/linux-centos7-x86_64-gcc-10.2.1-patchelf-0.18.0-afv7arjarb7nzmlh7c5slkfxykybuqce.spec.json
==> Fetching https://mirror.spack.io/bootstrap/github-actions/v0.5/build_cache/linux-centos7-x86_64/gcc-10.2.1/patchelf-0.18.0/linux-centos7-x86_64-gcc-10.2.1-patchelf-0.18.0-afv7arjarb7nzmlh7c5slkfxykybuqce.spack
==> Installing "patchelf@=0.18.0%gcc@=10.2.1 ldflags="-static-libstdc++ -static-libgcc" build_system=autotools arch=linux-centos7-x86_64" from a buildcache
==> Fetching https://mirror.spack.io/bootstrap/github-actions/v0.5/build_cache/linux-centos7-x86_64-gcc-10.2.1-clingo-bootstrap-spack-t4yf34cuvquqp5xd66zybmcfyhwbdlsf.spec.json
==> Fetching https://mirror.spack.io/bootstrap/github-actions/v0.5/build_cache/linux-centos7-x86_64/gcc-10.2.1/clingo-bootstrap-spack/linux-centos7-x86_64-gcc-10.2.1-clingo-bootstrap-spack-t4yf34cuvquqp5xd66zybmcfyhwbdlsf.spack
==> Installing "clingo-bootstrap@=spack%gcc@=10.2.1~docs+ipo+optimized+python+static_libstdcpp build_system=cmake build_type=Release generator=make patches=bebb819,ec99431 arch=linux-centos7-x86_64" from a buildcache
Input spec
--------------------------------
- ninja
Concretized
--------------------------------
[e] omn6mm4a3zsbpbkptvdwxs6kkrh6yafw ninja@1.11.1%gcc@12.3.0+re2c build_system=generic arch=linux-rhel7-skylake
$ echo "SPACK_SETUP_COMMIT_MAPPING_URL=${CI_API_V4_URL}/projects/${CI_PROJECT_ID}/jobs/${CI_JOB_ID}/artifacts/commit-mapping.env" >> spack_clone_variables.env
$ spack ${SPACK_EXTRA_FLAGS} config --scope site add "config:ccache:true"
$ echo "SPACK_USE_CCACHE=true" >> spack_clone_variables.env
$ echo "BLUECONFIGS_BRANCH=${BLUECONFIGS_BRANCH}" >> commit-mapping.env
$ echo "BLUECONFIGS_BRANCH=${BLUECONFIGS_BRANCH}" >> spack_clone_variables.env
section_end:1718117216:step_script section_start:1718117216:upload_artifacts_on_success Uploading artifacts for successful job
Using git from spack modules
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=22857 revision=58ba2b95 version=14.2.0
commit-mapping.env: found 1 matching files and directories
input_variables.env: found 1 matching files and directories
spack_clone_variables.env: found 1 matching files and directories
Uploading artifacts as "archive" to coordinator... ok id=1315414 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=22880 revision=58ba2b95 version=14.2.0
spack_clone_variables.env: found 1 matching files and directories
Uploading artifacts as "dotenv" to coordinator... ok id=1315414 responseStatus=201 Created token=glcbt-64
section_end:1718117218:upload_artifacts_on_success section_start:1718117218:cleanup_file_variables Cleaning up project directory and file based variables
Using git from spack modules
section_end:1718117219:cleanup_file_variables Job succeeded
Raw
test-neuron-nmodl-intel-legacy.txt
Log was not fetched because job had status: skipped
Raw
test-neuron-nmodl-intel-shared.txt
Log was not fetched because job had status: skipped
Raw
test-neuron-nmodl-nvhpc-acc-legacy.txt
Log was not fetched because job had status: skipped
Raw
test-neuron-nmodl-nvhpc-acc-shared.txt
Log was not fetched because job had status: skipped
Raw
test-neuron-nmodl-nvhpc-omp-legacy.txt
Log was not fetched because job had status: skipped
Raw
test-neuron-nmodl-nvhpc-omp.txt
Log was not fetched because job had status: skipped
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