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bbpbuildbot/GitLab logs for bluebrain-nmodl#1137 Secret

Created January 11, 2024 10:18
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Logfiles for GitLab pipeline https://bbpgitlab.epfl.ch/hpc/nmodl/-/pipelines/184894 (:white_check_mark:) running on GitHub PR BlueBrain/nmodl#1137.
Raw
build-intel.txt
Running with gitlab-runner 15.5.0 (0d4137b8)
 on BB5 map runner pnPo3yJy
section_start:1704966532:resolve_secrets Resolving secrets
section_end:1704966532:resolve_secrets section_start:1704966532: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-executor979699841, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name nmodl
Pipeline ID 184894, build ref , job ID 1111512
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P184894, 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_J1111512_PROD_P30_CP0_C11
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 1970460
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1111512_PROD_P30_CP0_C11 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P184894 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P184894 --ntasks=1 --jobid=1970460 --cpus-per-task=6 --mem=30750M
section_end:1704966541:prepare_executor section_start:1704966541:prepare_script Preparing environment
Using git from spack modules
Running on r1i7n20 via bbpv1.epfl.ch...
section_end:1704966549:prepare_script section_start:1704966549: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:1704966549:get_sources section_start:1704966549:restore_cache Restoring cache
Using git from spack modules
Checking cache for build:intel-2-non_protected...
Runtime platform  arch=amd64 os=linux pid=256696 revision=58ba2b95 version=14.2.0
cache.zip is up to date 
Successfully extracted cache
section_end:1704966555:restore_cache section_start:1704966555:download_artifacts Downloading artifacts
Using git from spack modules
Downloading artifacts for spack_setup (1111511)...
Runtime platform  arch=amd64 os=linux pid=257008 revision=58ba2b95 version=14.2.0
Downloading artifacts from coordinator... ok  id=1111511 responseStatus=200 OK token=64_bGtq5
section_end:1704966556:download_artifacts section_start:1704966556: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/P184894/J1111512/spack-config/config.yaml:2 build_stage:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111512/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111512/spack-build
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111512/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111512/spack-source-cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/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/P184894/J1111511/spack/etc/spack/defaults/config.yaml:18 extensions:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:18 - $spack/bluebrain/spack-scripting
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:19 # This is the path to the root of the Spack install tree.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:19 # You can use $spack here to refer to the root of the spack instance.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:37 template_dirs:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:37 - $spack/share/spack/templates
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:38 # Directory where licenses should be located
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:41 license_dir: $spack/etc/spack/licenses
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:76 test_stage: $user_cache_path/test
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:89 misc_cache: $user_cache_path/cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:95 connect_timeout: 10
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:100 verify_ssl: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:108 suppress_gpg_warnings: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:114 install_missing_compilers: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:119 checksum: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:124 deprecated: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:129 dirty: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:137 build_language: C
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:146 locks: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:151 url_fetch_method: urllib
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:180 concretizer: clingo
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:187 db_lock_timeout: 600
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:195 package_lock_timeout: null
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:200 shared_linking:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:205 type: rpath
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:211 bind: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:216 allow_sgid: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:221 terminal_title: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:225 binary_index_ttl: 600
_builtin debug: False
$ spack ${SPACK_EXTRA_FLAGS} config blame concretizer
--- concretizer:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111512/spack-config/concretizer.yaml:2 reuse: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/concretizer.yaml:22 targets:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/concretizer.yaml:26 granularity: microarchitectures
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/concretizer.yaml:30 host_compatible: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/concretizer.yaml:36 unify: True
$ 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/P184894/J1111512_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%oneapi +python
$ 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/P184894
$ 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
Summary:
Cache directory: /nvme/bbpcihpcproj12/1970460/ccache
Primary config: /nvme/bbpcihpcproj12/1970460/ccache/ccache.conf
Secondary config: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/ccache-4.6.1-q2jyor/etc/ccache.conf
Stats updated: Thu Jan 11 10:49:24 2024
Hits: 0 / 0
Direct: 0 / 0
Preprocessed: 0 / 0
Misses: 0
Direct: 0
Preprocessed: 0
Primary storage:
Hits: 0 / 0
Misses: 0
Cache size (GB): 0.44 / 0.51 (85.21 %)
Files: 1562
$ fi
$ module load unstable git ${SPACK_EXTRA_MODULES}
$ spack ${SPACK_EXTRA_FLAGS} spec -Il ${SPACK_FULL_SPEC}
Input spec
--------------------------------
- nmodl%oneapi+python
Concretized
--------------------------------
- ez7jxlj nmodl@develop%oneapi@2022.2.1~ipo~legacy-unit~llvm~llvm_cuda+python build_system=cmake build_type=RelWithDebInfo arch=linux-rhel7-skylake
[^] sgwmsqz ^bison@3.8.2%gcc@12.2.0 build_system=autotools arch=linux-rhel7-skylake
[^] 7v6k26x ^catch2@3.0.1%gcc@12.2.0~ipo build_system=cmake build_type=RelWithDebInfo arch=linux-rhel7-skylake
[^] u27b4to ^cli11@2.1.1%gcc@12.2.0~ipo build_system=cmake build_type=RelWithDebInfo arch=linux-rhel7-skylake
[^] vb7bdpg ^cmake@3.24.3%gcc@12.2.0~doc+ncurses+ownlibs~qt build_system=generic build_type=Release arch=linux-rhel7-skylake
[^] bbjadbi ^flex@2.6.3%gcc@12.2.0+lex~nls build_system=autotools arch=linux-rhel7-skylake
[^] t7yyhxk ^fmt@9.1.0%gcc@12.2.0~ipo+pic~shared build_system=cmake build_type=RelWithDebInfo cxxstd=11 patches=08fb707 arch=linux-rhel7-skylake
[^] zk4skox ^ninja@1.11.1%gcc@12.2.0 build_system=generic arch=linux-rhel7-skylake
[^] ee7ugzv ^nlohmann-json@3.9.1%gcc@12.2.0~ipo+multiple_headers build_system=cmake build_type=RelWithDebInfo arch=linux-rhel7-skylake
[^] 3s7iuck ^py-jinja2@3.1.2%gcc@12.2.0~i18n build_system=python_pip arch=linux-rhel7-skylake
[^] d4uhr4f ^py-markupsafe@2.1.1%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 3wgk4cb ^py-pip@22.2.2%gcc@12.2.0 build_system=generic arch=linux-rhel7-skylake
[^] c6hdpvj ^py-setuptools@63.0.0%gcc@12.2.0 build_system=generic arch=linux-rhel7-skylake
[^] ffmy45c ^py-wheel@0.37.1%gcc@12.2.0 build_system=generic arch=linux-rhel7-skylake
[^] pi3gdaj ^py-pybind11@2.10.1%gcc@12.2.0~ipo build_system=cmake build_type=RelWithDebInfo arch=linux-rhel7-skylake
[^] uucrzmi ^py-pytest@7.1.3%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] axib53z ^py-attrs@22.1.0%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] s5xlzyb ^py-iniconfig@1.1.1%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] ugynn7h ^py-packaging@21.3%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 4ld7fki ^py-pyparsing@3.0.9%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] d7dkmvv ^py-flit-core@3.7.1%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 2zoh6fg ^py-pluggy@1.0.0%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] a53pqvu ^py-py@1.11.0%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 6tqbi2i ^py-setuptools-scm@7.0.5%gcc@12.2.0+toml build_system=python_pip arch=linux-rhel7-skylake
[^] c564cvo ^py-typing-extensions@4.8.0%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] ksqdpfx ^py-tomli@2.0.1%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] d4xzk5t ^py-pyyaml@6.0%gcc@12.2.0+libyaml build_system=python_pip arch=linux-rhel7-skylake
[^] skgytub ^libyaml@0.2.5%gcc@12.2.0 build_system=autotools arch=linux-rhel7-skylake
[^] bjojgfi ^py-cython@0.29.32%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] oumzlg3 ^py-sympy@1.11.1%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] yqakowj ^py-mpmath@1.2.1%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] c2xj4m2 ^python@3.10.8%gcc@12.2.0+bz2+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tix~tkinter~ucs4+uuid+zlib build_system=generic patches=0d98e93,7d40923,f2fd060 arch=linux-rhel7-skylake
[^] xfi3vdr ^spdlog@1.10.0%gcc@12.2.0+fmt_external~ipo+shared build_system=cmake build_type=RelWithDebInfo 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
==> bison@3.8.2 : has external module in ['bison/3.8.2']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/bison-3.8.2-4q6ji4 (external bison-3.8.2-sgwmsqzphphzby2busuinegoak6lb3id)
==> cmake@3.24.3 : has external module in ['cmake/3.24.3']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/cmake-3.24.3-4blf3d (external cmake-3.24.3-vb7bdpgsupe5e2klkhkqos6vje2u4pns)
==> flex@2.6.3 : has external module in ['flex/2.6.3']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/flex-2.6.3-2jtkry (external flex-2.6.3-bbjadbirwaev3yr2guiy2u55ast426li)
==> ninja@1.11.1 : has external module in ['ninja/1.11.1']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/ninja-1.11.1-o5qggc (external ninja-1.11.1-zk4skoxmkt7do2mk5lgnesas7ol3hhgg)
==> python@3.10.8 : has external module in ['python/3.10.8']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/python-3.10.8-rvn6l5 (external python-3.10.8-c2xj4m2nyz6efq4m7arw3lneeqoz4z5m)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/libyaml-0.2.5-skgytu
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/nlohmann-json-3.9.1-ee7ugz
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/catch2-3.0.1-7v6k26
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/fmt-9.1.0-t7yyhx
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/cli11-2.1.1-u27b4t
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-pip-22.2.2-3wgk4c
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/spdlog-1.10.0-xfi3vd
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-wheel-0.37.1-ffmy45
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-setuptools-63.0.0-c6hdpv
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-tomli-2.0.1-ksqdpf
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-flit-core-3.7.1-d7dkmv
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-attrs-22.1.0-axib53
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-markupsafe-2.1.1-d4uhr4
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-iniconfig-1.1.1-s5xlzy
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-cython-0.29.32-bjojgf
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-pybind11-2.10.1-pi3gda
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-typing-extensions-4.8.0-c564cv
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-pyparsing-3.0.9-4ld7fk
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-jinja2-3.1.2-3s7iuc
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-pyyaml-6.0-d4xzk5
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-packaging-21.3-ugynn7
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-setuptools-scm-7.0.5-6tqbi2
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-py-1.11.0-a53pqv
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-pluggy-1.0.0-2zoh6f
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-mpmath-1.2.1-yqakow
==> Warning: Expected user 904556 to own /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894, but it is owned by 0
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-pytest-7.1.3-uucrzm
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-sympy-1.11.1-oumzlg
==> Installing nmodl-develop-ez7jxljmgsodr6pwt6gpsnv2zez7ure6
==> No binary for nmodl-develop-ez7jxljmgsodr6pwt6gpsnv2zez7ure6 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-develop-ez7jxljmgsodr6pwt6gpsnv2zez7ure6
Fetch: 1m 44.99s. Build: 3m 56.58s. Total: 5m 41.57s.
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/software/install_oneapi-2022.2.1-skylake/nmodl-develop-ez7jxl
$ 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 ez7jxljmgsodr6pwt6gpsnv2zez7ure6
$ SPACK_STAGE_DIR=${SPACK_BUILD}/spack-stage-${SPACK_PACKAGE}-develop-${SPACK_INSTALLED_HASH}
$ SPACK_BUILD_DIR=${SPACK_STAGE_DIR}/spack-build-${SPACK_INSTALLED_HASH:0:7}
$ SPACK_SOURCE_DIR=${SPACK_STAGE_DIR}/spack-src
$ if [ ${SPACK_USE_CCACHE+x} ]; then
$ ccache --cleanup
$ ccache --show-stats --verbose
Summary:
Cache directory: /nvme/bbpcihpcproj12/1970460/ccache
Primary config: /nvme/bbpcihpcproj12/1970460/ccache/ccache.conf
Secondary config: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/ccache-4.6.1-q2jyor/etc/ccache.conf
Stats updated: Thu Jan 11 10:57:11 2024
Hits: 134 / 141 (95.04 %)
Direct: 23 / 141 (16.31 %)
Preprocessed: 111 / 118 (94.07 %)
Misses: 7
Direct: 118
Preprocessed: 7
Uncacheable: 178
Primary storage:
Hits: 157 / 282 (55.67 %)
Misses: 125
Cache size (GB): 0.44 / 0.51 (85.33 %)
Files: 1575
Uncacheable:
Called for linking: 178
$ 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')))")
Autoloading python/3.10.8
Autoloading intel-oneapi-mkl/2021.4.0
Autoloading hpe-mpi/2.25.hmpt
$ if [[ ${num_failures} > 0 ]]; then exit ${num_failures}; fi
section_end:1704967033:step_script section_start:1704967033:archive_cache Saving cache for successful job
Using git from spack modules
Creating cache build:intel-2-non_protected...
Runtime platform  arch=amd64 os=linux pid=275324 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/30/build%3Aintel-2-non_protected
Created cache
section_end:1704967053:archive_cache section_start:1704967053:upload_artifacts_on_success Uploading artifacts for successful job
Using git from spack modules
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=275576 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=1111512 responseStatus=201 Created token=64_bGtq5
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=275596 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
Uploading artifacts as "junit" to coordinator... ok id=1111512 responseStatus=201 Created token=64_bGtq5
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=275617 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=1111512 responseStatus=201 Created token=64_bGtq5
section_end:1704967054:upload_artifacts_on_success section_start:1704967054:cleanup_file_variables Cleaning up project directory and file based variables
Using git from spack modules
section_end:1704967055:cleanup_file_variables Job succeeded
Raw
build-nvhpc.txt
Running with gitlab-runner 15.5.0 (0d4137b8)
 on BB5 map runner pnPo3yJy
section_start:1704966533:resolve_secrets Resolving secrets
section_end:1704966533:resolve_secrets section_start:1704966533: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-executor1740081075, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name nmodl
Pipeline ID 184894, build ref , job ID 1111513
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P184894, 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_J1111513_PROD_P30_CP3_C21
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 1970461
job state: PD
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1111513_PROD_P30_CP3_C21 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P184894 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P184894 --ntasks=1 --jobid=1970461 --cpus-per-task=6 --mem=30750M
section_end:1704966543:prepare_executor section_start:1704966543:prepare_script Preparing environment
Using git from spack modules
Running on r1i7n30 via bbpv1.epfl.ch...
section_end:1704966547:prepare_script section_start:1704966547: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:1704966548:get_sources section_start:1704966548:restore_cache Restoring cache
Using git from spack modules
Checking cache for build:nvhpc-2-non_protected...
Runtime platform  arch=amd64 os=linux pid=96620 revision=58ba2b95 version=14.2.0
cache.zip is up to date 
Successfully extracted cache
section_end:1704966554:restore_cache section_start:1704966554:download_artifacts Downloading artifacts
Using git from spack modules
Downloading artifacts for spack_setup (1111511)...
Runtime platform  arch=amd64 os=linux pid=96692 revision=58ba2b95 version=14.2.0
Downloading artifacts from coordinator... ok  id=1111511 responseStatus=200 OK token=64_WiUSe
section_end:1704966555:download_artifacts section_start:1704966555: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/P184894/J1111513/spack-config/config.yaml:2 build_stage:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111513/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111513/spack-build
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111513/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111513/spack-source-cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/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/P184894/J1111511/spack/etc/spack/defaults/config.yaml:18 extensions:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:18 - $spack/bluebrain/spack-scripting
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:19 # This is the path to the root of the Spack install tree.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:19 # You can use $spack here to refer to the root of the spack instance.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:37 template_dirs:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:37 - $spack/share/spack/templates
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:38 # Directory where licenses should be located
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:41 license_dir: $spack/etc/spack/licenses
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:76 test_stage: $user_cache_path/test
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:89 misc_cache: $user_cache_path/cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:95 connect_timeout: 10
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:100 verify_ssl: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:108 suppress_gpg_warnings: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:114 install_missing_compilers: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:119 checksum: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:124 deprecated: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:129 dirty: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:137 build_language: C
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:146 locks: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:151 url_fetch_method: urllib
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:180 concretizer: clingo
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:187 db_lock_timeout: 600
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:195 package_lock_timeout: null
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:200 shared_linking:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:205 type: rpath
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:211 bind: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:216 allow_sgid: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:221 terminal_title: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/config.yaml:225 binary_index_ttl: 600
_builtin debug: False
$ spack ${SPACK_EXTRA_FLAGS} config blame concretizer
--- concretizer:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111513/spack-config/concretizer.yaml:2 reuse: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/concretizer.yaml:22 targets:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/concretizer.yaml:26 granularity: microarchitectures
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/concretizer.yaml:30 host_compatible: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111511/spack/etc/spack/defaults/concretizer.yaml:36 unify: True
$ 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/P184894/J1111513_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%nvhpc +python ^bison%gcc^flex%gcc^py-jinja2%gcc^py-sympy%gcc^py-pyyaml%gcc
$ 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/P184894
$ 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
Summary:
Cache directory: /nvme/bbpcihpcproj12/1970461/ccache
Primary config: /nvme/bbpcihpcproj12/1970461/ccache/ccache.conf
Secondary config: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/ccache-4.6.1-q2jyor/etc/ccache.conf
Stats updated: Thu Jan 11 10:49:19 2024
Hits: 0 / 0
Direct: 0 / 0
Preprocessed: 0 / 0
Misses: 0
Direct: 0
Preprocessed: 0
Primary storage:
Hits: 0 / 0
Misses: 0
Cache size (GB): 0.47 / 0.51 (91.13 %)
Files: 1867
$ fi
$ module load unstable git ${SPACK_EXTRA_MODULES}
$ spack ${SPACK_EXTRA_FLAGS} spec -Il ${SPACK_FULL_SPEC}
Input spec
--------------------------------
- nmodl%nvhpc+python
- ^bison%gcc
- ^flex%gcc
- ^py-jinja2%gcc
- ^py-pyyaml%gcc
- ^py-sympy%gcc
Concretized
--------------------------------
- qtnmqhf nmodl@develop%nvhpc@23.1~ipo~legacy-unit~llvm~llvm_cuda+python build_system=cmake build_type=RelWithDebInfo arch=linux-rhel7-skylake
[^] sgwmsqz ^bison@3.8.2%gcc@12.2.0 build_system=autotools arch=linux-rhel7-skylake
[^] 7v6k26x ^catch2@3.0.1%gcc@12.2.0~ipo build_system=cmake build_type=RelWithDebInfo arch=linux-rhel7-skylake
[^] u27b4to ^cli11@2.1.1%gcc@12.2.0~ipo build_system=cmake build_type=RelWithDebInfo arch=linux-rhel7-skylake
[^] vb7bdpg ^cmake@3.24.3%gcc@12.2.0~doc+ncurses+ownlibs~qt build_system=generic build_type=Release arch=linux-rhel7-skylake
[^] bbjadbi ^flex@2.6.3%gcc@12.2.0+lex~nls build_system=autotools arch=linux-rhel7-skylake
[^] t7yyhxk ^fmt@9.1.0%gcc@12.2.0~ipo+pic~shared build_system=cmake build_type=RelWithDebInfo cxxstd=11 patches=08fb707 arch=linux-rhel7-skylake
[^] zk4skox ^ninja@1.11.1%gcc@12.2.0 build_system=generic arch=linux-rhel7-skylake
[^] ee7ugzv ^nlohmann-json@3.9.1%gcc@12.2.0~ipo+multiple_headers build_system=cmake build_type=RelWithDebInfo arch=linux-rhel7-skylake
[^] 3s7iuck ^py-jinja2@3.1.2%gcc@12.2.0~i18n build_system=python_pip arch=linux-rhel7-skylake
[^] d4uhr4f ^py-markupsafe@2.1.1%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 3wgk4cb ^py-pip@22.2.2%gcc@12.2.0 build_system=generic arch=linux-rhel7-skylake
[^] c6hdpvj ^py-setuptools@63.0.0%gcc@12.2.0 build_system=generic arch=linux-rhel7-skylake
[^] ffmy45c ^py-wheel@0.37.1%gcc@12.2.0 build_system=generic arch=linux-rhel7-skylake
[^] pi3gdaj ^py-pybind11@2.10.1%gcc@12.2.0~ipo build_system=cmake build_type=RelWithDebInfo arch=linux-rhel7-skylake
[^] uucrzmi ^py-pytest@7.1.3%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] axib53z ^py-attrs@22.1.0%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] s5xlzyb ^py-iniconfig@1.1.1%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] ugynn7h ^py-packaging@21.3%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 4ld7fki ^py-pyparsing@3.0.9%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] d7dkmvv ^py-flit-core@3.7.1%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 2zoh6fg ^py-pluggy@1.0.0%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] a53pqvu ^py-py@1.11.0%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] 6tqbi2i ^py-setuptools-scm@7.0.5%gcc@12.2.0+toml build_system=python_pip arch=linux-rhel7-skylake
[^] c564cvo ^py-typing-extensions@4.8.0%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] ksqdpfx ^py-tomli@2.0.1%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] d4xzk5t ^py-pyyaml@6.0%gcc@12.2.0+libyaml build_system=python_pip arch=linux-rhel7-skylake
[^] skgytub ^libyaml@0.2.5%gcc@12.2.0 build_system=autotools arch=linux-rhel7-skylake
[^] bjojgfi ^py-cython@0.29.32%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] oumzlg3 ^py-sympy@1.11.1%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] yqakowj ^py-mpmath@1.2.1%gcc@12.2.0 build_system=python_pip arch=linux-rhel7-skylake
[^] c2xj4m2 ^python@3.10.8%gcc@12.2.0+bz2+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tix~tkinter~ucs4+uuid+zlib build_system=generic patches=0d98e93,7d40923,f2fd060 arch=linux-rhel7-skylake
[^] xfi3vdr ^spdlog@1.10.0%gcc@12.2.0+fmt_external~ipo+shared build_system=cmake build_type=RelWithDebInfo 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
==> bison@3.8.2 : has external module in ['bison/3.8.2']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/bison-3.8.2-4q6ji4 (external bison-3.8.2-sgwmsqzphphzby2busuinegoak6lb3id)
==> cmake@3.24.3 : has external module in ['cmake/3.24.3']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/cmake-3.24.3-4blf3d (external cmake-3.24.3-vb7bdpgsupe5e2klkhkqos6vje2u4pns)
==> flex@2.6.3 : has external module in ['flex/2.6.3']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/flex-2.6.3-2jtkry (external flex-2.6.3-bbjadbirwaev3yr2guiy2u55ast426li)
==> ninja@1.11.1 : has external module in ['ninja/1.11.1']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/ninja-1.11.1-o5qggc (external ninja-1.11.1-zk4skoxmkt7do2mk5lgnesas7ol3hhgg)
==> python@3.10.8 : has external module in ['python/3.10.8']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/python-3.10.8-rvn6l5 (external python-3.10.8-c2xj4m2nyz6efq4m7arw3lneeqoz4z5m)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/libyaml-0.2.5-skgytu
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/nlohmann-json-3.9.1-ee7ugz
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/fmt-9.1.0-t7yyhx
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/catch2-3.0.1-7v6k26
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/cli11-2.1.1-u27b4t
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-pip-22.2.2-3wgk4c
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/spdlog-1.10.0-xfi3vd
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-setuptools-63.0.0-c6hdpv
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-wheel-0.37.1-ffmy45
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-markupsafe-2.1.1-d4uhr4
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-iniconfig-1.1.1-s5xlzy
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-tomli-2.0.1-ksqdpf
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-cython-0.29.32-bjojgf
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-attrs-22.1.0-axib53
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-flit-core-3.7.1-d7dkmv
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-pybind11-2.10.1-pi3gda
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-jinja2-3.1.2-3s7iuc
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-pyyaml-6.0-d4xzk5
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-pyparsing-3.0.9-4ld7fk
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-typing-extensions-4.8.0-c564cv
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-packaging-21.3-ugynn7
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-setuptools-scm-7.0.5-6tqbi2
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-py-1.11.0-a53pqv
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-mpmath-1.2.1-yqakow
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-pluggy-1.0.0-2zoh6f
==> Warning: Expected user 904556 to own /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894, but it is owned by 0
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-sympy-1.11.1-oumzlg
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-pytest-7.1.3-uucrzm
==> Installing nmodl-develop-qtnmqhfx65jfeom3wxbcbj7i3dwxxuxg
==> No binary for nmodl-develop-qtnmqhfx65jfeom3wxbcbj7i3dwxxuxg 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-develop-qtnmqhfx65jfeom3wxbcbj7i3dwxxuxg
Fetch: 1m 14.02s. Build: 2m 37.14s. Total: 3m 51.16s.
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/software/install_nvhpc-23.1-skylake/nmodl-develop-qtnmqh
$ 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 qtnmqhfx65jfeom3wxbcbj7i3dwxxuxg
$ SPACK_STAGE_DIR=${SPACK_BUILD}/spack-stage-${SPACK_PACKAGE}-develop-${SPACK_INSTALLED_HASH}
$ SPACK_BUILD_DIR=${SPACK_STAGE_DIR}/spack-build-${SPACK_INSTALLED_HASH:0:7}
$ SPACK_SOURCE_DIR=${SPACK_STAGE_DIR}/spack-src
$ if [ ${SPACK_USE_CCACHE+x} ]; then
$ ccache --cleanup
$ ccache --show-stats --verbose
Summary:
Cache directory: /nvme/bbpcihpcproj12/1970461/ccache
Primary config: /nvme/bbpcihpcproj12/1970461/ccache/ccache.conf
Secondary config: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/ccache-4.6.1-q2jyor/etc/ccache.conf
Stats updated: Thu Jan 11 10:55:07 2024
Hits: 134 / 138 (97.10 %)
Direct: 23 / 138 (16.67 %)
Preprocessed: 111 / 115 (96.52 %)
Misses: 4
Direct: 115
Preprocessed: 4
Uncacheable: 22
Primary storage:
Hits: 157 / 276 (56.88 %)
Misses: 119
Cache size (GB): 0.47 / 0.51 (91.23 %)
Files: 1874
Uncacheable:
Called for linking: 22
$ 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')))")
Autoloading python/3.10.8
Autoloading intel-oneapi-mkl/2021.4.0
Autoloading hpe-mpi/2.25.hmpt
$ if [[ ${num_failures} > 0 ]]; then exit ${num_failures}; fi
section_end:1704966908:step_script section_start:1704966908:archive_cache Saving cache for successful job
Using git from spack modules
Creating cache build:nvhpc-2-non_protected...
Runtime platform  arch=amd64 os=linux pid=110073 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/30/build%3Anvhpc-2-non_protected
Created cache
section_end:1704966929:archive_cache section_start:1704966929:upload_artifacts_on_success Uploading artifacts for successful job
Using git from spack modules
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=110615 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=1111513 responseStatus=201 Created token=64_WiUSe
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=110639 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
Uploading artifacts as "junit" to coordinator... ok id=1111513 responseStatus=201 Created token=64_WiUSe
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=110662 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=1111513 responseStatus=201 Created token=64_WiUSe
section_end:1704966932:upload_artifacts_on_success section_start:1704966932:cleanup_file_variables Cleaning up project directory and file based variables
Using git from spack modules
section_end:1704966933:cleanup_file_variables Job succeeded
Raw
spack-setup.txt
Running with gitlab-runner 15.5.0 (0d4137b8)
 on BB5 map runner pnPo3yJy
section_start:1704966193:resolve_secrets Resolving secrets
section_end:1704966193:resolve_secrets section_start:1704966193: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-executor1863661444, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name nmodl
Pipeline ID 184894, build ref , job ID 1111511
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P184894, 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_J1111511_PROD_P30_CP6_C11
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 1970442
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1111511_PROD_P30_CP6_C11 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P184894 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P184894 --ntasks=1 --jobid=1970442 --cpus-per-task=6 --mem=30750M
section_end:1704966195:prepare_executor section_start:1704966195:prepare_script Preparing environment
Using git from spack modules
Running on r1i6n18 via bbpv1.epfl.ch...
section_end:1704966200:prepare_script section_start:1704966200: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:1704966201:get_sources section_start:1704966201: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
Autoloading python/3.10.8
Autoloading intel-oneapi-mkl/2021.4.0
Autoloading hpe-mpi/2.25.hmpt
$ 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/P184894/J1111511
$ 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} ${SPACK_URL} spack
Cloning into 'spack'...
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$ 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/P184894/J1111511_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 CVF BLUECONFIGS --write-commit-file=commit-mapping.env CI_COMMIT_BRANCH=1uc/move-global-related-code NMODL_COMMIT=f92d2ee02ceee3d22af7bcaea5751f3f0cc38cfe SPACK_RESOLVED_COMMIT=2a59d6093084d5175dabd2e32ad30db858299fc2 NEURON_BRANCH=master LIBSONATA_REPORT_BRANCH=master SPACK_BRANCH=develop CI_DEFAULT_BRANCH=master CVF_BRANCH=main BLUECONFIGS_BRANCH=main
==> CI_COMMIT: ignoring CI_COMMIT_BRANCH=1uc/move-global-related-code
==> SPACK_RESOLVED: ignoring SPACK_RESOLVED_COMMIT=2a59d6093084d5175dabd2e32ad30db858299fc2
==> SPACK: ignoring SPACK_BRANCH=develop
==> CI_DEFAULT: ignoring CI_DEFAULT_BRANCH=master
==> CVF: ignoring CVF_BRANCH=main
==> BLUECONFIGS: ignoring BLUECONFIGS_BRANCH=main
==> neuron: resolved branch master to 67f6bedcfc172ea5545af3731c2b636cfd04e922
==> libsonata-report: resolved branch master to ab8958769a65c7ddea10ba6b318252653cce86c2
==> nmodl@develop: remove branch/commit/tag
==> nmodl@develop: use commit="f92d2ee02ceee3d22af7bcaea5751f3f0cc38cfe"
==> nmodl@develop: add preferred=True
==> neuron@develop: remove branch/commit/tag
==> neuron@develop: use commit="67f6bedcfc172ea5545af3731c2b636cfd04e922"
==> neuron@develop: add preferred=True
==> libsonata-report@develop: remove branch/commit/tag
==> libsonata-report@develop: use commit="ab8958769a65c7ddea10ba6b318252653cce86c2"
==> libsonata-report@develop: add preferred=True
$ (cd "${SPACK_ROOT}" && git diff)
diff --git a/bluebrain/repo-bluebrain/packages/libsonata-report/package.py b/bluebrain/repo-bluebrain/packages/libsonata-report/package.py
index 6944ddee..add5c47a 100644
--- a/bluebrain/repo-bluebrain/packages/libsonata-report/package.py
+++ b/bluebrain/repo-bluebrain/packages/libsonata-report/package.py
@@ -17,7 +17,7 @@ class LibsonataReport(CMakePackage):
homepage = "https://github.com/BlueBrain/libsonatareport"
git = "https://github.com/BlueBrain/libsonatareport.git"
- version("develop", branch="master", submodules=False, get_full_repo=True)
+ version('develop', preferred=True, commit='ab8958769a65c7ddea10ba6b318252653cce86c2', submodules=False, get_full_repo=True) # old: branch="master"
version("1.2.2", tag="1.2.2", submodules=False)
version("1.2.1", tag="1.2.1", submodules=False)
version("1.2", tag="1.2", submodules=False)
diff --git a/bluebrain/repo-bluebrain/packages/nmodl/package.py b/bluebrain/repo-bluebrain/packages/nmodl/package.py
index eaf08b46..763a0eca 100644
--- a/bluebrain/repo-bluebrain/packages/nmodl/package.py
+++ b/bluebrain/repo-bluebrain/packages/nmodl/package.py
@@ -13,7 +13,7 @@ class Nmodl(CMakePackage):
url = "https://github.com/BlueBrain/nmodl.git"
git = "https://github.com/BlueBrain/nmodl.git"
- version("develop", branch="master", submodules=True)
+ version('develop', preferred=True, commit='f92d2ee02ceee3d22af7bcaea5751f3f0cc38cfe', submodules=True) # old: branch="master"
version("llvm", branch="llvm", submodules=True)
version("0.7.a2", commit="6f6db3b6f25e066db46d8a5fc85a1697363b995c")
version("0.7.a1", commit="2ce4a2b91dfcfe6356b6a5003c4e99b8711564ee")
diff --git a/bluebrain/repo-patches/packages/neuron/package.py b/bluebrain/repo-patches/packages/neuron/package.py
index 9591c7c9..9945fa53 100644
--- a/bluebrain/repo-patches/packages/neuron/package.py
+++ b/bluebrain/repo-patches/packages/neuron/package.py
@@ -13,7 +13,7 @@ class Neuron(BuiltinNeuron):
__doc__ = BuiltinNeuron.__doc__
# BBP specific version
- version("develop", branch="master")
+ version('develop', preferred=True, commit='67f6bedcfc172ea5545af3731c2b636cfd04e922') # old: branch="master"
version("9.0.a14", commit="bd9426d9")
version("9.0.a13", commit="3bbdd8da")
version("9.0.a5", commit="522c866")
$ cat commit-mapping.env
NMODL_COMMIT=f92d2ee02ceee3d22af7bcaea5751f3f0cc38cfe
NEURON_COMMIT=67f6bedcfc172ea5545af3731c2b636cfd04e922
LIBSONATA_REPORT_COMMIT=ab8958769a65c7ddea10ba6b318252653cce86c2
$ 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
==> Bootstrapping clingo from pre-built binaries
==> Fetching https://mirror.spack.io/bootstrap/github-actions/v0.4/build_cache/linux-centos7-x86_64-gcc-10.2.1-clingo-bootstrap-spack-prqkzynv2nwko5mktitebgkeumuxkveu.spec.json
==> Fetching https://mirror.spack.io/bootstrap/github-actions/v0.4/build_cache/linux-centos7-x86_64/gcc-10.2.1/clingo-bootstrap-spack/linux-centos7-x86_64-gcc-10.2.1-clingo-bootstrap-spack-prqkzynv2nwko5mktitebgkeumuxkveu.spack
==> Installing "clingo-bootstrap@spack%gcc@10.2.1~docs~ipo+python+static_libstdcpp build_type=Release arch=linux-centos7-x86_64" from a buildcache
Input spec
--------------------------------
- ninja
Concretized
--------------------------------
[^] zk4skoxmkt7do2mk5lgnesas7ol3hhgg ninja@1.11.1%gcc@12.2.0 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 "CVF_BRANCH=${CVF_BRANCH}" >> spack_clone_variables.env
$ echo "BLUECONFIGS_BRANCH=${BLUECONFIGS_BRANCH}" >> spack_clone_variables.env
section_end:1704966526:step_script section_start:1704966526:upload_artifacts_on_success Uploading artifacts for successful job
Using git from spack modules
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=100343 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=1111511 responseStatus=201 Created token=64_d5nsc
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=100367 revision=58ba2b95 version=14.2.0
spack_clone_variables.env: found 1 matching files and directories
Uploading artifacts as "dotenv" to coordinator... ok id=1111511 responseStatus=201 Created token=64_d5nsc
section_end:1704966528:upload_artifacts_on_success section_start:1704966528:cleanup_file_variables Cleaning up project directory and file based variables
Using git from spack modules
section_end:1704966529:cleanup_file_variables Job succeeded
Raw
test-intel.txt
Running with gitlab-runner 15.5.0 (0d4137b8)
 on BB5 map runner pnPo3yJy
section_start:1704967057:resolve_secrets Resolving secrets
section_end:1704967057:resolve_secrets section_start:1704967057: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-executor2234114111, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name nmodl
Pipeline ID 184894, build ref , job ID 1111514
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P184894, optional exclusive flag , optional cpus per task flag --cpus-per-task=1, optional qos flag , optional reservation flag
A slurm job will be created with name GL_J1111514_PROD_P30_CP0_C5
Job parameters: memory=30750M, cpus_per_task=1, 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 1970486
job state: PD
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=1 --mem=30750M --job-name=GL_J1111514_PROD_P30_CP0_C5 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P184894 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P184894 --ntasks=1 --jobid=1970486 --cpus-per-task=1 --mem=30750M
section_end:1704967060:prepare_executor section_start:1704967060:prepare_script Preparing environment
Using git from spack modules
Running on r1i7n20 via bbpv1.epfl.ch...
section_end:1704967064:prepare_script section_start:1704967064: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:1704967065:get_sources section_start:1704967065:download_artifacts Downloading artifacts
Using git from spack modules
Downloading artifacts for build:intel (1111512)...
Runtime platform  arch=amd64 os=linux pid=276652 revision=58ba2b95 version=14.2.0
Downloading artifacts from coordinator... ok  id=1111512 responseStatus=200 OK token=64_kYh-L
section_end:1704967066:download_artifacts section_start:1704967066: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
$ env -0 | sort -z | xargs -0 -L 1 echo > initial_environment.env
$ export CTEST_PARALLEL_LEVEL=${SLURM_TASKS_PER_NODE}
$ . ${SPACK_ROOT}/share/spack/setup-env.sh
$ cd ${SPACK_BUILD_DIR}
$ export BOOST_TEST_COLOR_OUTPUT=no
$ i_am_a_failure=0
$ spack ${SPACK_EXTRA_FLAGS} build-env ${SPACK_FULL_SPEC} -- ctest --no-tests=error --output-on-failure -T Test || i_am_a_failure=1
Site: r1i7n20
Build name: Linux-icpx
Create new tag: 20240111-0958 - Experimental
Test project /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111512/spack-build/spack-stage-nmodl-develop-ez7jxljmgsodr6pwt6gpsnv2zez7ure6/spack-build-ez7jxlj
Start 1: testcodegen/Scenario: unusual / failing mod files
1/110 Test #1: testcodegen/Scenario: unusual / failing mod files ................................................... Passed 0.54 sec
Start 2: testcodegen/Scenario: Check global variable setup
2/110 Test #2: testcodegen/Scenario: Check global variable setup ................................................... Passed 0.55 sec
Start 3: testcodegen/Scenario: C codegen utility functions
3/110 Test #3: testcodegen/Scenario: C codegen utility functions ................................................... Passed 0.57 sec
Start 4: testcodegen/Scenario: Check instance variable definition order
4/110 Test #4: testcodegen/Scenario: Check instance variable definition order ...................................... Passed 0.56 sec
Start 5: testcodegen/Scenario: Check parameter constness with VERBATIM block
5/110 Test #5: testcodegen/Scenario: Check parameter constness with VERBATIM block ................................. Passed 0.59 sec
Start 6: testcodegen/Scenario: Check NEURON globals are added to the instance struct on demand
6/110 Test #6: testcodegen/Scenario: Check NEURON globals are added to the instance struct on demand ............... Passed 0.55 sec
Start 7: testcodegen/Scenario: Check code generation for TABLE statements
7/110 Test #7: testcodegen/Scenario: Check code generation for TABLE statements .................................... Passed 0.50 sec
Start 8: testcodegen/Scenario: Check that BEFORE/AFTER block are well generated
8/110 Test #8: testcodegen/Scenario: Check that BEFORE/AFTER block are well generated .............................. Passed 0.55 sec
Start 9: testcodegen/Scenario: Check CONSTANT variables are added to global variable structure
9/110 Test #9: testcodegen/Scenario: Check CONSTANT variables are added to global variable structure ............... Passed 0.57 sec
Start 10: testcodegen/Scenario: Check code generation for FUNCTION_TABLE block
10/110 Test #10: testcodegen/Scenario: Check code generation for FUNCTION_TABLE block ................................ Passed 0.59 sec
Start 11: testcodegen/Scenario: Check that loops are well generated
11/110 Test #11: testcodegen/Scenario: Check that loops are well generated ........................................... Passed 0.60 sec
Start 12: testcodegen/Scenario: Check that top verbatim blocks are well generated
12/110 Test #12: testcodegen/Scenario: Check that top verbatim blocks are well generated ............................. Passed 0.58 sec
Start 13: testcodegen/Scenario: Check that codegen generate event functions well
13/110 Test #13: testcodegen/Scenario: Check that codegen generate event functions well .............................. Passed 0.62 sec
Start 14: testcodegen/Scenario: Some tests on derivimplicit
14/110 Test #14: testcodegen/Scenario: Some tests on derivimplicit ................................................... Passed 0.57 sec
Start 15: testcodegen/Scenario: Some tests on euler solver
15/110 Test #15: testcodegen/Scenario: Some tests on euler solver .................................................... Passed 0.53 sec
Start 16: testcodegen/Scenario: Check codegen for MUTEX and PROTECT
16/110 Test #16: testcodegen/Scenario: Check codegen for MUTEX and PROTECT ........................................... Passed 0.54 sec
Start 17: testcodegen/Scenario: Array STATE variable
17/110 Test #17: testcodegen/Scenario: Array STATE variable .......................................................... Passed 0.56 sec
Start 18: testcodegen/Scenario: Check NEURON codegen for simple MOD file
18/110 Test #18: testcodegen/Scenario: Check NEURON codegen for simple MOD file ...................................... Passed 0.61 sec
Start 19: testcodegen/Scenario: Adding a variable for a table inside a function
19/110 Test #19: testcodegen/Scenario: Adding a variable for a table inside a function ............................... Passed 0.58 sec
Start 20: testcodegen/Scenario: Uncompatible constructs should failed
20/110 Test #20: testcodegen/Scenario: Uncompatible constructs should failed ......................................... Passed 0.57 sec
Start 21: testmodtoken/NMODL Lexer returning valid ModToken object
21/110 Test #21: testmodtoken/NMODL Lexer returning valid ModToken object ............................................ Passed 0.16 sec
Start 22: testmodtoken/Addition of two ModToken objects
22/110 Test #22: testmodtoken/Addition of two ModToken objects ....................................................... Passed 0.16 sec
Start 23: testlexer/NMODL Lexer returning valid token types
23/110 Test #23: testlexer/NMODL Lexer returning valid token types ................................................... Passed 0.15 sec
Start 24: testparser/Scenario: NMODL can accept CR as return char for one line comment
24/110 Test #24: testparser/Scenario: NMODL can accept CR as return char for one line comment ........................ Passed 0.33 sec
Start 25: testparser/Scenario: NMODL can define macros using DEFINE keyword
25/110 Test #25: testparser/Scenario: NMODL can define macros using DEFINE keyword ................................... Passed 0.33 sec
Start 26: testparser/Scenario: Macros can be used anywhere in the mod file
26/110 Test #26: testparser/Scenario: Macros can be used anywhere in the mod file .................................... Passed 0.31 sec
Start 27: testparser/Scenario: NMODL parser accepts empty unit specification
27/110 Test #27: testparser/Scenario: NMODL parser accepts empty unit specification .................................. Passed 0.32 sec
Start 28: testparser/Scenario: NMODL parser running number of valid NMODL constructs
28/110 Test #28: testparser/Scenario: NMODL parser running number of valid NMODL constructs .......................... Passed 0.42 sec
Start 29: testparser/Scenario: NMODL parser running number of invalid NMODL constructs
29/110 Test #29: testparser/Scenario: NMODL parser running number of invalid NMODL constructs ........................ Passed 0.28 sec
Start 30: testparser/Scenario: Check that the parser doesn't crash when passing invalid INCLUDE constructs
30/110 Test #30: testparser/Scenario: Check that the parser doesn't crash when passing invalid INCLUDE constructs .... Passed 0.32 sec
Start 31: testparser/Scenario: NEURON block can add CURIE information
31/110 Test #31: testparser/Scenario: NEURON block can add CURIE information ......................................... Passed 0.30 sec
Start 32: testparser/Scenario: Check parents in valid NMODL constructs
32/110 Test #32: testparser/Scenario: Check parents in valid NMODL constructs ........................................ Passed 0.68 sec
Start 33: testparser/Scenario: Legacy differential equation solver
33/110 Test #33: testparser/Scenario: Legacy differential equation solver ............................................ Passed 0.30 sec
Start 34: testparser/Scenario: Check if a NEURON block is parsed with correct location info in its token
34/110 Test #34: testparser/Scenario: Check if a NEURON block is parsed with correct location info in its token ...... Passed 0.29 sec
Start 35: testvisitor/Scenario: AfterCVodeToCnexpVisitor changes after_cvode solver method to cnexp
35/110 Test #35: testvisitor/Scenario: AfterCVodeToCnexpVisitor changes after_cvode solver method to cnexp ........... Passed 0.55 sec
Start 36: testvisitor/Scenario: Perform constant folder on NMODL constructs
36/110 Test #36: testvisitor/Scenario: Perform constant folder on NMODL constructs ................................... Passed 0.56 sec
Start 37: testvisitor/Scenario: Perform DefUse analysis on NMODL constructs
37/110 Test #37: testvisitor/Scenario: Perform DefUse analysis on NMODL constructs ................................... Passed 0.56 sec
Start 38: testvisitor/Scenario: GLOBAL to RANGE variable transformer
38/110 Test #38: testvisitor/Scenario: GLOBAL to RANGE variable transformer .......................................... Passed 0.57 sec
Start 39: testvisitor/Scenario: Check insertion of implicit arguments
39/110 Test #39: testvisitor/Scenario: Check insertion of implicit arguments ......................................... Passed 0.56 sec
Start 40: testvisitor/Scenario: Inlining of external procedure calls
40/110 Test #40: testvisitor/Scenario: Inlining of external procedure calls .......................................... Passed 0.56 sec
Start 41: testvisitor/Scenario: Inlining of function call as argument in external function
41/110 Test #41: testvisitor/Scenario: Inlining of function call as argument in external function .................... Passed 0.57 sec
Start 42: testvisitor/Scenario: Inlining of simple, one level procedure call
42/110 Test #42: testvisitor/Scenario: Inlining of simple, one level procedure call .................................. Passed 0.59 sec
Start 43: testvisitor/Scenario: Inlining of nested procedure call
43/110 Test #43: testvisitor/Scenario: Inlining of nested procedure call ............................................. Passed 0.60 sec
Start 44: testvisitor/Scenario: Inline function call in procedure
44/110 Test #44: testvisitor/Scenario: Inline function call in procedure ............................................. Passed 0.56 sec
Start 45: testvisitor/Scenario: Inling function call within conditional statement
45/110 Test #45: testvisitor/Scenario: Inling function call within conditional statement ............................. Passed 0.55 sec
Start 46: testvisitor/Scenario: Inline multiple function calls in same statement
46/110 Test #46: testvisitor/Scenario: Inline multiple function calls in same statement .............................. Passed 0.51 sec
Start 47: testvisitor/Scenario: Inline nested function calls withing arguments
47/110 Test #47: testvisitor/Scenario: Inline nested function calls withing arguments ................................ Passed 0.56 sec
Start 48: testvisitor/Scenario: Inline function call in non-binary expression
48/110 Test #48: testvisitor/Scenario: Inline function call in non-binary expression ................................. Passed 0.58 sec
Start 49: testvisitor/Scenario: Inline function call as standalone expression
49/110 Test #49: testvisitor/Scenario: Inline function call as standalone expression ................................. Passed 0.57 sec
Start 50: testvisitor/Scenario: Inline procedure call as standalone statement as well as part of expression
50/110 Test #50: testvisitor/Scenario: Inline procedure call as standalone statement as well as part of expression ... Passed 0.58 sec
Start 51: testvisitor/Scenario: Inlining pass handles local-global name conflict
51/110 Test #51: testvisitor/Scenario: Inlining pass handles local-global name conflict .............................. Passed 0.64 sec
Start 52: testvisitor/Scenario: Trying to inline a function with VERBATIM block
52/110 Test #52: testvisitor/Scenario: Trying to inline a function with VERBATIM block ............................... Passed 0.64 sec
Start 53: testvisitor/Convert NMODL to AST to JSON form using JSONVisitor
53/110 Test #53: testvisitor/Convert NMODL to AST to JSON form using JSONVisitor ..................................... Passed 0.62 sec
Start 54: testvisitor/Scenario: Convert KINETIC to DERIVATIVE using KineticBlock visitor
54/110 Test #54: testvisitor/Scenario: Convert KINETIC to DERIVATIVE using KineticBlock visitor ...................... Passed 0.59 sec
Start 55: testvisitor/Scenario: Localizer test with single global block
55/110 Test #55: testvisitor/Scenario: Localizer test with single global block ....................................... Passed 0.65 sec
Start 56: testvisitor/Scenario: Localizer test with use of verbatim block
56/110 Test #56: testvisitor/Scenario: Localizer test with use of verbatim block ..................................... Passed 0.63 sec
Start 57: testvisitor/Scenario: Localizer test with multiple global blocks
57/110 Test #57: testvisitor/Scenario: Localizer test with multiple global blocks .................................... Passed 0.62 sec
Start 58: testvisitor/Scenario: LocalVarRenameVisitor works with InlineVisitor
58/110 Test #58: testvisitor/Scenario: LocalVarRenameVisitor works with InlineVisitor ................................ Passed 0.63 sec
Start 59: testvisitor/Scenario: LOCAL to ASSIGNED variable transformer
59/110 Test #59: testvisitor/Scenario: LOCAL to ASSIGNED variable transformer ........................................ Passed 0.59 sec
Start 60: testvisitor/Scenario: Searching for ast nodes using AstLookupVisitor
60/110 Test #60: testvisitor/Scenario: Searching for ast nodes using AstLookupVisitor ................................ Passed 0.61 sec
Start 61: testvisitor/Scenario: Perform loop unrolling of FROM construct
61/110 Test #61: testvisitor/Scenario: Perform loop unrolling of FROM construct ...................................... Passed 0.57 sec
Start 62: testvisitor/Scenario: Running visitor passes multiple times
62/110 Test #62: testvisitor/Scenario: Running visitor passes multiple times ......................................... Passed 0.63 sec
Start 63: testvisitor/Scenario: Sympy specific AST to NMODL conversion
63/110 Test #63: testvisitor/Scenario: Sympy specific AST to NMODL conversion ........................................ Passed 0.61 sec
Start 64: testvisitor/Scenario: NeuronSolveVisitor visitor solves different ODE types
64/110 Test #64: testvisitor/Scenario: NeuronSolveVisitor visitor solves different ODE types ......................... Passed 0.59 sec
Start 65: testvisitor/Scenario: Convert AST back to NMODL form
65/110 Test #65: testvisitor/Scenario: Convert AST back to NMODL form ................................................ Passed 0.70 sec
Start 66: testvisitor/Scenario: Symbol table generation with Perf stat visitor
66/110 Test #66: testvisitor/Scenario: Symbol table generation with Perf stat visitor ................................ Passed 0.57 sec
Start 67: testvisitor/Scenario: Renaming any variable in mod file with RenameVisitor
67/110 Test #67: testvisitor/Scenario: Renaming any variable in mod file with RenameVisitor .......................... Passed 0.63 sec
Start 68: testvisitor/Scenario: Renaming with presence of local and global variables in same block
68/110 Test #68: testvisitor/Scenario: Renaming with presence of local and global variables in same block ............ Passed 0.63 sec
Start 69: testvisitor/Scenario: Renaming in the absence of global blocks
69/110 Test #69: testvisitor/Scenario: Renaming in the absence of global blocks ...................................... Passed 0.63 sec
Start 70: testvisitor/Scenario: Variable renaming in nested blocks
70/110 Test #70: testvisitor/Scenario: Variable renaming in nested blocks ............................................ Passed 0.62 sec
Start 71: testvisitor/Scenario: Renaming in presence of local variable in verbatim block
71/110 Test #71: testvisitor/Scenario: Renaming in presence of local variable in verbatim block ...................... Passed 0.58 sec
Start 72: testvisitor/Scenario: TABLE stmt
72/110 Test #72: testvisitor/Scenario: TABLE stmt .................................................................... Passed 0.55 sec
Start 73: testvisitor/Scenario: Destructor block
73/110 Test #73: testvisitor/Scenario: Destructor block .............................................................. Passed 0.53 sec
Start 74: testvisitor/Scenario: Ion variable in CONSTANT block
74/110 Test #74: testvisitor/Scenario: Ion variable in CONSTANT block ................................................ Passed 0.62 sec
Start 75: testvisitor/Scenario: INDEPENDENT block
75/110 Test #75: testvisitor/Scenario: INDEPENDENT block ............................................................. Passed 0.60 sec
Start 76: testvisitor/Scenario: FUNCTION_TABLE block
76/110 Test #76: testvisitor/Scenario: FUNCTION_TABLE block .......................................................... Passed 0.63 sec
Start 77: testvisitor/Scenario: At most one DERIVATIVE block
77/110 Test #77: testvisitor/Scenario: At most one DERIVATIVE block .................................................. Passed 0.62 sec
Start 78: testvisitor/Solve ODEs using legacy NeuronSolveVisitor
78/110 Test #78: testvisitor/Solve ODEs using legacy NeuronSolveVisitor .............................................. Passed 0.60 sec
Start 79: testvisitor/Scenario: Solving ODEs with STEADYSTATE solve method
79/110 Test #79: testvisitor/Scenario: Solving ODEs with STEADYSTATE solve method .................................... Passed 0.63 sec
Start 80: testvisitor/Scenario: Addition of CONDUCTANCE using SympyConductance visitor
80/110 Test #80: testvisitor/Scenario: Addition of CONDUCTANCE using SympyConductance visitor ........................ Passed 59.55 sec
Start 81: testvisitor/Scenario: Check compare_blocks in sympy unit tests
81/110 Test #81: testvisitor/Scenario: Check compare_blocks in sympy unit tests ...................................... Passed 4.84 sec
Start 82: testvisitor/Scenario: Check local vars name-clash prevention
82/110 Test #82: testvisitor/Scenario: Check local vars name-clash prevention ........................................ Passed 5.04 sec
Start 83: testvisitor/Scenario: Solve ODEs with cnexp or euler method using SympySolverVisitor
83/110 Test #83: testvisitor/Scenario: Solve ODEs with cnexp or euler method using SympySolverVisitor ................ Passed 13.26 sec
Start 84: testvisitor/Scenario: Solve ODEs with derivimplicit method using SympySolverVisitor
84/110 Test #84: testvisitor/Scenario: Solve ODEs with derivimplicit method using SympySolverVisitor ................. Passed 7.05 sec
Start 85: testvisitor/Scenario: LINEAR solve block (SympySolver Visitor)
85/110 Test #85: testvisitor/Scenario: LINEAR solve block (SympySolver Visitor) ...................................... Passed 6.10 sec
Start 86: testvisitor/Scenario: Solve NONLINEAR block using SympySolver Visitor
86/110 Test #86: testvisitor/Scenario: Solve NONLINEAR block using SympySolver Visitor ............................... Passed 5.10 sec
Start 87: testvisitor/Scenario: Solve KINETIC block using SympySolver Visitor
87/110 Test #87: testvisitor/Scenario: Solve KINETIC block using SympySolver Visitor ................................. Passed 5.19 sec
Start 88: testvisitor/Scenario: Code generation for EigenNewtonSolver
88/110 Test #88: testvisitor/Scenario: Code generation for EigenNewtonSolver ......................................... Passed 5.36 sec
Start 89: testvisitor/Scenario: Parse UNITS block of mod files using Units Visitor
89/110 Test #89: testvisitor/Scenario: Parse UNITS block of mod files using Units Visitor ............................ Passed 0.64 sec
Start 90: testvisitor/Scenario: Searching for variable name using VarUsageVisitor
90/110 Test #90: testvisitor/Scenario: Searching for variable name using VarUsageVisitor ............................. Passed 0.62 sec
Start 91: testvisitor/Parse VERBATIM block using Verbatim Visitor
91/110 Test #91: testvisitor/Parse VERBATIM block using Verbatim Visitor ............................................. Passed 0.66 sec
Start 92: testvisitor/Scenario: Get node name with index TestVisitor
92/110 Test #92: testvisitor/Scenario: Get node name with index TestVisitor .......................................... Passed 0.67 sec
Start 93: testprinter/JSON printer converting object to string form
93/110 Test #93: testprinter/JSON printer converting object to string form ........................................... Passed 0.15 sec
Start 94: testsymtab/Scenario: Symbol properties can be added and converted to string
94/110 Test #94: testsymtab/Scenario: Symbol properties can be added and converted to string ......................... Passed 0.13 sec
Start 95: testsymtab/Scenario: Multiple properties can be added to Symbol
95/110 Test #95: testsymtab/Scenario: Multiple properties can be added to Symbol ..................................... Passed 0.14 sec
Start 96: testsymtab/Scenario: Symbol table allows operations like insert, lookup
96/110 Test #96: testsymtab/Scenario: Symbol table allows operations like insert, lookup ............................. Passed 0.13 sec
Start 97: testsymtab/Scenario: Global symbol table (ModelSymbol) allows scope based operations
97/110 Test #97: testsymtab/Scenario: Global symbol table (ModelSymbol) allows scope based operations ................ Passed 0.14 sec
Start 98: testsymtab/Scenario: Symbol class allows manipulation
98/110 Test #98: testsymtab/Scenario: Symbol class allows manipulation ............................................... Passed 0.14 sec
Start 99: testnewton/Scenario: Non-linear system to solve with Newton Numerical Diff Solver
99/110 Test #99: testnewton/Scenario: Non-linear system to solve with Newton Numerical Diff Solver ................... Passed 0.13 sec
Start 100: testnewton/Scenario: Non-linear system to solve with Newton Solver
100/110 Test #100: testnewton/Scenario: Non-linear system to solve with Newton Solver .................................. Passed 0.14 sec
Start 101: testcrout/Scenario: Compare Crout solver with Eigen
101/110 Test #101: testcrout/Scenario: Compare Crout solver with Eigen ................................................. Passed 0.44 sec
Start 102: testunitlexer/Unit Lexer tests for valid tokens
102/110 Test #102: testunitlexer/Unit Lexer tests for valid tokens ..................................................... Passed 0.17 sec
Start 103: testunitparser/Scenario: Unit parser accepting valid units definition
103/110 Test #103: testunitparser/Scenario: Unit parser accepting valid units definition ............................... Passed 0.18 sec
Start 104: testunitparser/Scenario: Unit parser accepting dependent/nested units definition
104/110 Test #104: testunitparser/Scenario: Unit parser accepting dependent/nested units definition .................... Passed 0.17 sec
Start 105: Ode
105/110 Test #105: Ode ................................................................................................. Passed 7.61 sec
Start 106: Pybind
106/110 Test #106: Pybind .............................................................................................. Passed 4.03 sec
Start 107: cabpump.mod
107/110 Test #107: cabpump.mod ......................................................................................... Passed 0.45 sec
Start 108: ican.mod
108/110 Test #108: ican.mod ............................................................................................ Passed 0.41 sec
Start 109: test_functor.mod
109/110 Test #109: test_functor.mod .................................................................................... Passed 0.36 sec
Start 110: watch_test.mod
110/110 Test #110: watch_test.mod ...................................................................................... Passed 0.32 sec
100% tests passed, 0 tests failed out of 110
Total Test time (real) = 172.33 sec
$ cp -r Testing/ ${CI_PROJECT_DIR}/
$ module load unstable unit-test-translator
Autoloading python/3.10.8
$ cmake2junit > ${CI_PROJECT_DIR}/ctest.xml
$ exit ${i_am_a_failure}
section_end:1704967312:step_script section_start:1704967312:upload_artifacts_on_success Uploading artifacts for successful job
Using git from spack modules
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=282071 revision=58ba2b95 version=14.2.0
initial_environment.env: found 1 matching files and directories
Testing/: found 7 matching files and directories 
Uploading artifacts as "archive" to coordinator... ok id=1111514 responseStatus=201 Created token=64_kYh-L
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=282096 revision=58ba2b95 version=14.2.0
ctest.xml: found 1 matching files and directories 
Uploading artifacts as "junit" to coordinator... ok id=1111514 responseStatus=201 Created token=64_kYh-L
section_end:1704967314:upload_artifacts_on_success section_start:1704967314:cleanup_file_variables Cleaning up project directory and file based variables
Using git from spack modules
section_end:1704967315:cleanup_file_variables Job succeeded
Raw
test-nvhpc.txt
Running with gitlab-runner 15.5.0 (0d4137b8)
 on BB5 map runner pnPo3yJy
section_start:1704966937:resolve_secrets Resolving secrets
section_end:1704966937:resolve_secrets section_start:1704966937: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-executor2521975028, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name nmodl
Pipeline ID 184894, build ref , job ID 1111515
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P184894, optional exclusive flag , optional cpus per task flag --cpus-per-task=1, optional qos flag , optional reservation flag
A slurm job will be created with name GL_J1111515_PROD_P30_CP3_C15
Job parameters: memory=30750M, cpus_per_task=1, 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 1970477
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=1 --mem=30750M --job-name=GL_J1111515_PROD_P30_CP3_C15 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P184894 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P184894 --ntasks=1 --jobid=1970477 --cpus-per-task=1 --mem=30750M
section_end:1704966939:prepare_executor section_start:1704966939:prepare_script Preparing environment
Using git from spack modules
Running on r1i7n30 via bbpv1.epfl.ch...
section_end:1704966943:prepare_script section_start:1704966943: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:1704966944:get_sources section_start:1704966944:download_artifacts Downloading artifacts
Using git from spack modules
Downloading artifacts for build:nvhpc (1111513)...
Runtime platform  arch=amd64 os=linux pid=111347 revision=58ba2b95 version=14.2.0
Downloading artifacts from coordinator... ok  id=1111513 responseStatus=200 OK token=64_KW32L
section_end:1704966945:download_artifacts section_start:1704966945: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
$ env -0 | sort -z | xargs -0 -L 1 echo > initial_environment.env
$ export CTEST_PARALLEL_LEVEL=${SLURM_TASKS_PER_NODE}
$ . ${SPACK_ROOT}/share/spack/setup-env.sh
$ cd ${SPACK_BUILD_DIR}
$ export BOOST_TEST_COLOR_OUTPUT=no
$ i_am_a_failure=0
$ spack ${SPACK_EXTRA_FLAGS} build-env ${SPACK_FULL_SPEC} -- ctest --no-tests=error --output-on-failure -T Test || i_am_a_failure=1
Site: r1i7n30
Build name: Linux-nvc++
Create new tag: 20240111-0956 - Experimental
Test project /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P184894/J1111513/spack-build/spack-stage-nmodl-develop-qtnmqhfx65jfeom3wxbcbj7i3dwxxuxg/spack-build-qtnmqhf
Start 1: testcodegen/Scenario: unusual / failing mod files
1/110 Test #1: testcodegen/Scenario: unusual / failing mod files ................................................... Passed 0.06 sec
Start 2: testcodegen/Scenario: Check global variable setup
2/110 Test #2: testcodegen/Scenario: Check global variable setup ................................................... Passed 0.05 sec
Start 3: testcodegen/Scenario: C codegen utility functions
3/110 Test #3: testcodegen/Scenario: C codegen utility functions ................................................... Passed 0.06 sec
Start 4: testcodegen/Scenario: Check instance variable definition order
4/110 Test #4: testcodegen/Scenario: Check instance variable definition order ...................................... Passed 0.05 sec
Start 5: testcodegen/Scenario: Check parameter constness with VERBATIM block
5/110 Test #5: testcodegen/Scenario: Check parameter constness with VERBATIM block ................................. Passed 0.05 sec
Start 6: testcodegen/Scenario: Check NEURON globals are added to the instance struct on demand
6/110 Test #6: testcodegen/Scenario: Check NEURON globals are added to the instance struct on demand ............... Passed 0.05 sec
Start 7: testcodegen/Scenario: Check code generation for TABLE statements
7/110 Test #7: testcodegen/Scenario: Check code generation for TABLE statements .................................... Passed 0.05 sec
Start 8: testcodegen/Scenario: Check that BEFORE/AFTER block are well generated
8/110 Test #8: testcodegen/Scenario: Check that BEFORE/AFTER block are well generated .............................. Passed 0.05 sec
Start 9: testcodegen/Scenario: Check CONSTANT variables are added to global variable structure
9/110 Test #9: testcodegen/Scenario: Check CONSTANT variables are added to global variable structure ............... Passed 0.06 sec
Start 10: testcodegen/Scenario: Check code generation for FUNCTION_TABLE block
10/110 Test #10: testcodegen/Scenario: Check code generation for FUNCTION_TABLE block ................................ Passed 0.05 sec
Start 11: testcodegen/Scenario: Check that loops are well generated
11/110 Test #11: testcodegen/Scenario: Check that loops are well generated ........................................... Passed 0.05 sec
Start 12: testcodegen/Scenario: Check that top verbatim blocks are well generated
12/110 Test #12: testcodegen/Scenario: Check that top verbatim blocks are well generated ............................. Passed 0.05 sec
Start 13: testcodegen/Scenario: Check that codegen generate event functions well
13/110 Test #13: testcodegen/Scenario: Check that codegen generate event functions well .............................. Passed 0.06 sec
Start 14: testcodegen/Scenario: Some tests on derivimplicit
14/110 Test #14: testcodegen/Scenario: Some tests on derivimplicit ................................................... Passed 0.05 sec
Start 15: testcodegen/Scenario: Some tests on euler solver
15/110 Test #15: testcodegen/Scenario: Some tests on euler solver .................................................... Passed 0.07 sec
Start 16: testcodegen/Scenario: Check codegen for MUTEX and PROTECT
16/110 Test #16: testcodegen/Scenario: Check codegen for MUTEX and PROTECT ........................................... Passed 0.06 sec
Start 17: testcodegen/Scenario: Array STATE variable
17/110 Test #17: testcodegen/Scenario: Array STATE variable .......................................................... Passed 0.06 sec
Start 18: testcodegen/Scenario: Check NEURON codegen for simple MOD file
18/110 Test #18: testcodegen/Scenario: Check NEURON codegen for simple MOD file ...................................... Passed 0.06 sec
Start 19: testcodegen/Scenario: Adding a variable for a table inside a function
19/110 Test #19: testcodegen/Scenario: Adding a variable for a table inside a function ............................... Passed 0.05 sec
Start 20: testcodegen/Scenario: Uncompatible constructs should failed
20/110 Test #20: testcodegen/Scenario: Uncompatible constructs should failed ......................................... Passed 0.07 sec
Start 21: testmodtoken/NMODL Lexer returning valid ModToken object
21/110 Test #21: testmodtoken/NMODL Lexer returning valid ModToken object ............................................ Passed 0.02 sec
Start 22: testmodtoken/Addition of two ModToken objects
22/110 Test #22: testmodtoken/Addition of two ModToken objects ....................................................... Passed 0.01 sec
Start 23: testlexer/NMODL Lexer returning valid token types
23/110 Test #23: testlexer/NMODL Lexer returning valid token types ................................................... Passed 0.02 sec
Start 24: testparser/Scenario: NMODL can accept CR as return char for one line comment
24/110 Test #24: testparser/Scenario: NMODL can accept CR as return char for one line comment ........................ Passed 0.02 sec
Start 25: testparser/Scenario: NMODL can define macros using DEFINE keyword
25/110 Test #25: testparser/Scenario: NMODL can define macros using DEFINE keyword ................................... Passed 0.02 sec
Start 26: testparser/Scenario: Macros can be used anywhere in the mod file
26/110 Test #26: testparser/Scenario: Macros can be used anywhere in the mod file .................................... Passed 0.02 sec
Start 27: testparser/Scenario: NMODL parser accepts empty unit specification
27/110 Test #27: testparser/Scenario: NMODL parser accepts empty unit specification .................................. Passed 0.02 sec
Start 28: testparser/Scenario: NMODL parser running number of valid NMODL constructs
28/110 Test #28: testparser/Scenario: NMODL parser running number of valid NMODL constructs .......................... Passed 0.05 sec
Start 29: testparser/Scenario: NMODL parser running number of invalid NMODL constructs
29/110 Test #29: testparser/Scenario: NMODL parser running number of invalid NMODL constructs ........................ Passed 0.03 sec
Start 30: testparser/Scenario: Check that the parser doesn't crash when passing invalid INCLUDE constructs
30/110 Test #30: testparser/Scenario: Check that the parser doesn't crash when passing invalid INCLUDE constructs .... Passed 0.02 sec
Start 31: testparser/Scenario: NEURON block can add CURIE information
31/110 Test #31: testparser/Scenario: NEURON block can add CURIE information ......................................... Passed 0.02 sec
Start 32: testparser/Scenario: Check parents in valid NMODL constructs
32/110 Test #32: testparser/Scenario: Check parents in valid NMODL constructs ........................................ Passed 0.31 sec
Start 33: testparser/Scenario: Legacy differential equation solver
33/110 Test #33: testparser/Scenario: Legacy differential equation solver ............................................ Passed 0.03 sec
Start 34: testparser/Scenario: Check if a NEURON block is parsed with correct location info in its token
34/110 Test #34: testparser/Scenario: Check if a NEURON block is parsed with correct location info in its token ...... Passed 0.02 sec
Start 35: testvisitor/Scenario: AfterCVodeToCnexpVisitor changes after_cvode solver method to cnexp
35/110 Test #35: testvisitor/Scenario: AfterCVodeToCnexpVisitor changes after_cvode solver method to cnexp ........... Passed 0.06 sec
Start 36: testvisitor/Scenario: Perform constant folder on NMODL constructs
36/110 Test #36: testvisitor/Scenario: Perform constant folder on NMODL constructs ................................... Passed 0.05 sec
Start 37: testvisitor/Scenario: Perform DefUse analysis on NMODL constructs
37/110 Test #37: testvisitor/Scenario: Perform DefUse analysis on NMODL constructs ................................... Passed 0.06 sec
Start 38: testvisitor/Scenario: GLOBAL to RANGE variable transformer
38/110 Test #38: testvisitor/Scenario: GLOBAL to RANGE variable transformer .......................................... Passed 0.05 sec
Start 39: testvisitor/Scenario: Check insertion of implicit arguments
39/110 Test #39: testvisitor/Scenario: Check insertion of implicit arguments ......................................... Passed 0.05 sec
Start 40: testvisitor/Scenario: Inlining of external procedure calls
40/110 Test #40: testvisitor/Scenario: Inlining of external procedure calls .......................................... Passed 0.06 sec
Start 41: testvisitor/Scenario: Inlining of function call as argument in external function
41/110 Test #41: testvisitor/Scenario: Inlining of function call as argument in external function .................... Passed 0.05 sec
Start 42: testvisitor/Scenario: Inlining of simple, one level procedure call
42/110 Test #42: testvisitor/Scenario: Inlining of simple, one level procedure call .................................. Passed 0.06 sec
Start 43: testvisitor/Scenario: Inlining of nested procedure call
43/110 Test #43: testvisitor/Scenario: Inlining of nested procedure call ............................................. Passed 0.05 sec
Start 44: testvisitor/Scenario: Inline function call in procedure
44/110 Test #44: testvisitor/Scenario: Inline function call in procedure ............................................. Passed 0.06 sec
Start 45: testvisitor/Scenario: Inling function call within conditional statement
45/110 Test #45: testvisitor/Scenario: Inling function call within conditional statement ............................. Passed 0.05 sec
Start 46: testvisitor/Scenario: Inline multiple function calls in same statement
46/110 Test #46: testvisitor/Scenario: Inline multiple function calls in same statement .............................. Passed 0.05 sec
Start 47: testvisitor/Scenario: Inline nested function calls withing arguments
47/110 Test #47: testvisitor/Scenario: Inline nested function calls withing arguments ................................ Passed 0.05 sec
Start 48: testvisitor/Scenario: Inline function call in non-binary expression
48/110 Test #48: testvisitor/Scenario: Inline function call in non-binary expression ................................. Passed 0.05 sec
Start 49: testvisitor/Scenario: Inline function call as standalone expression
49/110 Test #49: testvisitor/Scenario: Inline function call as standalone expression ................................. Passed 0.05 sec
Start 50: testvisitor/Scenario: Inline procedure call as standalone statement as well as part of expression
50/110 Test #50: testvisitor/Scenario: Inline procedure call as standalone statement as well as part of expression ... Passed 0.05 sec
Start 51: testvisitor/Scenario: Inlining pass handles local-global name conflict
51/110 Test #51: testvisitor/Scenario: Inlining pass handles local-global name conflict .............................. Passed 0.05 sec
Start 52: testvisitor/Scenario: Trying to inline a function with VERBATIM block
52/110 Test #52: testvisitor/Scenario: Trying to inline a function with VERBATIM block ............................... Passed 0.06 sec
Start 53: testvisitor/Convert NMODL to AST to JSON form using JSONVisitor
53/110 Test #53: testvisitor/Convert NMODL to AST to JSON form using JSONVisitor ..................................... Passed 0.05 sec
Start 54: testvisitor/Scenario: Convert KINETIC to DERIVATIVE using KineticBlock visitor
54/110 Test #54: testvisitor/Scenario: Convert KINETIC to DERIVATIVE using KineticBlock visitor ...................... Passed 0.06 sec
Start 55: testvisitor/Scenario: Localizer test with single global block
55/110 Test #55: testvisitor/Scenario: Localizer test with single global block ....................................... Passed 0.05 sec
Start 56: testvisitor/Scenario: Localizer test with use of verbatim block
56/110 Test #56: testvisitor/Scenario: Localizer test with use of verbatim block ..................................... Passed 0.05 sec
Start 57: testvisitor/Scenario: Localizer test with multiple global blocks
57/110 Test #57: testvisitor/Scenario: Localizer test with multiple global blocks .................................... Passed 0.05 sec
Start 58: testvisitor/Scenario: LocalVarRenameVisitor works with InlineVisitor
58/110 Test #58: testvisitor/Scenario: LocalVarRenameVisitor works with InlineVisitor ................................ Passed 0.05 sec
Start 59: testvisitor/Scenario: LOCAL to ASSIGNED variable transformer
59/110 Test #59: testvisitor/Scenario: LOCAL to ASSIGNED variable transformer ........................................ Passed 0.05 sec
Start 60: testvisitor/Scenario: Searching for ast nodes using AstLookupVisitor
60/110 Test #60: testvisitor/Scenario: Searching for ast nodes using AstLookupVisitor ................................ Passed 0.05 sec
Start 61: testvisitor/Scenario: Perform loop unrolling of FROM construct
61/110 Test #61: testvisitor/Scenario: Perform loop unrolling of FROM construct ...................................... Passed 0.05 sec
Start 62: testvisitor/Scenario: Running visitor passes multiple times
62/110 Test #62: testvisitor/Scenario: Running visitor passes multiple times ......................................... Passed 0.05 sec
Start 63: testvisitor/Scenario: Sympy specific AST to NMODL conversion
63/110 Test #63: testvisitor/Scenario: Sympy specific AST to NMODL conversion ........................................ Passed 0.05 sec
Start 64: testvisitor/Scenario: NeuronSolveVisitor visitor solves different ODE types
64/110 Test #64: testvisitor/Scenario: NeuronSolveVisitor visitor solves different ODE types ......................... Passed 0.05 sec
Start 65: testvisitor/Scenario: Convert AST back to NMODL form
65/110 Test #65: testvisitor/Scenario: Convert AST back to NMODL form ................................................ Passed 0.10 sec
Start 66: testvisitor/Scenario: Symbol table generation with Perf stat visitor
66/110 Test #66: testvisitor/Scenario: Symbol table generation with Perf stat visitor ................................ Passed 0.06 sec
Start 67: testvisitor/Scenario: Renaming any variable in mod file with RenameVisitor
67/110 Test #67: testvisitor/Scenario: Renaming any variable in mod file with RenameVisitor .......................... Passed 0.05 sec
Start 68: testvisitor/Scenario: Renaming with presence of local and global variables in same block
68/110 Test #68: testvisitor/Scenario: Renaming with presence of local and global variables in same block ............ Passed 0.05 sec
Start 69: testvisitor/Scenario: Renaming in the absence of global blocks
69/110 Test #69: testvisitor/Scenario: Renaming in the absence of global blocks ...................................... Passed 0.05 sec
Start 70: testvisitor/Scenario: Variable renaming in nested blocks
70/110 Test #70: testvisitor/Scenario: Variable renaming in nested blocks ............................................ Passed 0.05 sec
Start 71: testvisitor/Scenario: Renaming in presence of local variable in verbatim block
71/110 Test #71: testvisitor/Scenario: Renaming in presence of local variable in verbatim block ...................... Passed 0.05 sec
Start 72: testvisitor/Scenario: TABLE stmt
72/110 Test #72: testvisitor/Scenario: TABLE stmt .................................................................... Passed 0.05 sec
Start 73: testvisitor/Scenario: Destructor block
73/110 Test #73: testvisitor/Scenario: Destructor block .............................................................. Passed 0.05 sec
Start 74: testvisitor/Scenario: Ion variable in CONSTANT block
74/110 Test #74: testvisitor/Scenario: Ion variable in CONSTANT block ................................................ Passed 0.05 sec
Start 75: testvisitor/Scenario: INDEPENDENT block
75/110 Test #75: testvisitor/Scenario: INDEPENDENT block ............................................................. Passed 0.05 sec
Start 76: testvisitor/Scenario: FUNCTION_TABLE block
76/110 Test #76: testvisitor/Scenario: FUNCTION_TABLE block .......................................................... Passed 0.05 sec
Start 77: testvisitor/Scenario: At most one DERIVATIVE block
77/110 Test #77: testvisitor/Scenario: At most one DERIVATIVE block .................................................. Passed 0.05 sec
Start 78: testvisitor/Solve ODEs using legacy NeuronSolveVisitor
78/110 Test #78: testvisitor/Solve ODEs using legacy NeuronSolveVisitor .............................................. Passed 0.07 sec
Start 79: testvisitor/Scenario: Solving ODEs with STEADYSTATE solve method
79/110 Test #79: testvisitor/Scenario: Solving ODEs with STEADYSTATE solve method .................................... Passed 0.07 sec
Start 80: testvisitor/Scenario: Addition of CONDUCTANCE using SympyConductance visitor
80/110 Test #80: testvisitor/Scenario: Addition of CONDUCTANCE using SympyConductance visitor ........................ Passed 56.32 sec
Start 81: testvisitor/Scenario: Check compare_blocks in sympy unit tests
81/110 Test #81: testvisitor/Scenario: Check compare_blocks in sympy unit tests ...................................... Passed 0.95 sec
Start 82: testvisitor/Scenario: Check local vars name-clash prevention
82/110 Test #82: testvisitor/Scenario: Check local vars name-clash prevention ........................................ Passed 1.08 sec
Start 83: testvisitor/Scenario: Solve ODEs with cnexp or euler method using SympySolverVisitor
83/110 Test #83: testvisitor/Scenario: Solve ODEs with cnexp or euler method using SympySolverVisitor ................ Passed 9.13 sec
Start 84: testvisitor/Scenario: Solve ODEs with derivimplicit method using SympySolverVisitor
84/110 Test #84: testvisitor/Scenario: Solve ODEs with derivimplicit method using SympySolverVisitor ................. Passed 2.74 sec
Start 85: testvisitor/Scenario: LINEAR solve block (SympySolver Visitor)
85/110 Test #85: testvisitor/Scenario: LINEAR solve block (SympySolver Visitor) ...................................... Passed 2.09 sec
Start 86: testvisitor/Scenario: Solve NONLINEAR block using SympySolver Visitor
86/110 Test #86: testvisitor/Scenario: Solve NONLINEAR block using SympySolver Visitor ............................... Passed 1.15 sec
Start 87: testvisitor/Scenario: Solve KINETIC block using SympySolver Visitor
87/110 Test #87: testvisitor/Scenario: Solve KINETIC block using SympySolver Visitor ................................. Passed 1.19 sec
Start 88: testvisitor/Scenario: Code generation for EigenNewtonSolver
88/110 Test #88: testvisitor/Scenario: Code generation for EigenNewtonSolver ......................................... Passed 1.32 sec
Start 89: testvisitor/Scenario: Parse UNITS block of mod files using Units Visitor
89/110 Test #89: testvisitor/Scenario: Parse UNITS block of mod files using Units Visitor ............................ Passed 0.06 sec
Start 90: testvisitor/Scenario: Searching for variable name using VarUsageVisitor
90/110 Test #90: testvisitor/Scenario: Searching for variable name using VarUsageVisitor ............................. Passed 0.05 sec
Start 91: testvisitor/Parse VERBATIM block using Verbatim Visitor
91/110 Test #91: testvisitor/Parse VERBATIM block using Verbatim Visitor ............................................. Passed 0.08 sec
Start 92: testvisitor/Scenario: Get node name with index TestVisitor
92/110 Test #92: testvisitor/Scenario: Get node name with index TestVisitor .......................................... Passed 0.05 sec
Start 93: testprinter/JSON printer converting object to string form
93/110 Test #93: testprinter/JSON printer converting object to string form ........................................... Passed 0.01 sec
Start 94: testsymtab/Scenario: Symbol properties can be added and converted to string
94/110 Test #94: testsymtab/Scenario: Symbol properties can be added and converted to string ......................... Passed 0.01 sec
Start 95: testsymtab/Scenario: Multiple properties can be added to Symbol
95/110 Test #95: testsymtab/Scenario: Multiple properties can be added to Symbol ..................................... Passed 0.01 sec
Start 96: testsymtab/Scenario: Symbol table allows operations like insert, lookup
96/110 Test #96: testsymtab/Scenario: Symbol table allows operations like insert, lookup ............................. Passed 0.01 sec
Start 97: testsymtab/Scenario: Global symbol table (ModelSymbol) allows scope based operations
97/110 Test #97: testsymtab/Scenario: Global symbol table (ModelSymbol) allows scope based operations ................ Passed 0.01 sec
Start 98: testsymtab/Scenario: Symbol class allows manipulation
98/110 Test #98: testsymtab/Scenario: Symbol class allows manipulation ............................................... Passed 0.02 sec
Start 99: testnewton/Scenario: Non-linear system to solve with Newton Numerical Diff Solver
99/110 Test #99: testnewton/Scenario: Non-linear system to solve with Newton Numerical Diff Solver ................... Passed 0.02 sec
Start 100: testnewton/Scenario: Non-linear system to solve with Newton Solver
100/110 Test #100: testnewton/Scenario: Non-linear system to solve with Newton Solver .................................. Passed 0.01 sec
Start 101: testcrout/Scenario: Compare Crout solver with Eigen
101/110 Test #101: testcrout/Scenario: Compare Crout solver with Eigen ................................................. Passed 0.29 sec
Start 102: testunitlexer/Unit Lexer tests for valid tokens
102/110 Test #102: testunitlexer/Unit Lexer tests for valid tokens ..................................................... Passed 0.01 sec
Start 103: testunitparser/Scenario: Unit parser accepting valid units definition
103/110 Test #103: testunitparser/Scenario: Unit parser accepting valid units definition ............................... Passed 0.02 sec
Start 104: testunitparser/Scenario: Unit parser accepting dependent/nested units definition
104/110 Test #104: testunitparser/Scenario: Unit parser accepting dependent/nested units definition .................... Passed 0.01 sec
Start 105: Ode
105/110 Test #105: Ode ................................................................................................. Passed 2.19 sec
Start 106: Pybind
106/110 Test #106: Pybind .............................................................................................. Passed 0.58 sec
Start 107: cabpump.mod
107/110 Test #107: cabpump.mod ......................................................................................... Passed 0.07 sec
Start 108: ican.mod
108/110 Test #108: ican.mod ............................................................................................ Passed 0.05 sec
Start 109: test_functor.mod
109/110 Test #109: test_functor.mod .................................................................................... Passed 0.05 sec
Start 110: watch_test.mod
110/110 Test #110: watch_test.mod ...................................................................................... Passed 0.05 sec
100% tests passed, 0 tests failed out of 110
Total Test time (real) = 83.93 sec
$ cp -r Testing/ ${CI_PROJECT_DIR}/
$ module load unstable unit-test-translator
Autoloading python/3.10.8
$ cmake2junit > ${CI_PROJECT_DIR}/ctest.xml
$ exit ${i_am_a_failure}
section_end:1704967085:step_script section_start:1704967085:upload_artifacts_on_success Uploading artifacts for successful job
Using git from spack modules
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=116615 revision=58ba2b95 version=14.2.0
initial_environment.env: found 1 matching files and directories
Testing/: found 7 matching files and directories 
Uploading artifacts as "archive" to coordinator... ok id=1111515 responseStatus=201 Created token=64_KW32L
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=116640 revision=58ba2b95 version=14.2.0
ctest.xml: found 1 matching files and directories 
Uploading artifacts as "junit" to coordinator... ok id=1111515 responseStatus=201 Created token=64_KW32L
section_end:1704967086:upload_artifacts_on_success section_start:1704967086:cleanup_file_variables Cleaning up project directory and file based variables
Using git from spack modules
section_end:1704967087:cleanup_file_variables Job succeeded
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