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bbpbuildbot/GitLab logs for bluebrain-nmodl#1098 Secret

Created November 21, 2023 16:32
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Logfiles for GitLab pipeline https://bbpgitlab.epfl.ch/hpc/nmodl/-/pipelines/172206 (:white_check_mark:) running on GitHub PR BlueBrain/nmodl#1098.
Raw
build-intel.txt
Running with gitlab-runner 15.5.0 (0d4137b8)
 on BB5 map runner pnPo3yJy
section_start:1700582489:resolve_secrets Resolving secrets
section_end:1700582489:resolve_secrets section_start:1700582489: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-executor4076039880, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name nmodl
Pipeline ID 172206, build ref , job ID 1029080
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P172206, 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_J1029080_PROD_P30_CP4_C13
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 1904708
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1029080_PROD_P30_CP4_C13 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P172206 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P172206 --ntasks=1 --jobid=1904708 --cpus-per-task=6 --mem=30750M
section_end:1700582490:prepare_executor section_start:1700582490:prepare_script Preparing environment
Using git from spack modules
Running on r1i4n8 via bbpv1.epfl.ch...
section_end:1700582495:prepare_script section_start:1700582495: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:1700582495:get_sources section_start:1700582495:restore_cache Restoring cache
Using git from spack modules
Checking cache for build:intel-2-non_protected...
Runtime platform  arch=amd64 os=linux pid=147054 revision=58ba2b95 version=14.2.0
cache.zip is up to date 
Successfully extracted cache
section_end:1700582501:restore_cache section_start:1700582501:download_artifacts Downloading artifacts
Using git from spack modules
Downloading artifacts for spack_setup (1029079)...
Runtime platform  arch=amd64 os=linux pid=147773 revision=58ba2b95 version=14.2.0
Downloading artifacts from coordinator... ok  id=1029079 responseStatus=200 OK token=64_HEs6T
section_end:1700582502:download_artifacts section_start:1700582502: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/P172206/J1029080/spack-config/config.yaml:2 build_stage:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029080/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029080/spack-build
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029080/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029080/spack-source-cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/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/P172206/J1029079/spack/etc/spack/defaults/config.yaml:18 extensions:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:18 - $spack/bluebrain/spack-scripting
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/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/P172206/J1029079/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/P172206/J1029079/spack/etc/spack/defaults/config.yaml:37 template_dirs:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:37 - $spack/share/spack/templates
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:38 # Directory where licenses should be located
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:41 license_dir: $spack/etc/spack/licenses
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:76 test_stage: $user_cache_path/test
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:89 misc_cache: $user_cache_path/cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:95 connect_timeout: 10
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:100 verify_ssl: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:108 suppress_gpg_warnings: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:114 install_missing_compilers: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:119 checksum: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:124 deprecated: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:129 dirty: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:137 build_language: C
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:146 locks: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:151 url_fetch_method: urllib
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:180 concretizer: clingo
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:187 db_lock_timeout: 600
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:195 package_lock_timeout: null
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:200 shared_linking:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:205 type: rpath
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:211 bind: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:216 allow_sgid: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:221 terminal_title: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/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/P172206/J1029080/spack-config/concretizer.yaml:2 reuse: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/concretizer.yaml:22 targets:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/concretizer.yaml:26 granularity: microarchitectures
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/concretizer.yaml:30 host_compatible: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/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/P172206/J1029080_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/P172206
$ 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/bbpcihpcproj12/1904708/ccache
Primary config: /nvme/bbpcihpcproj12/1904708/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: Tue Nov 21 17:01:56 2023
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 (85.27 %)
Files: 1523
$ fi
$ module load unstable git ${SPACK_EXTRA_MODULES}
$ spack ${SPACK_EXTRA_FLAGS} spec -Il ${SPACK_FULL_SPEC}
Input spec
--------------------------------
- nmodl%oneapi+python
Concretized
--------------------------------
- 5iqrurm 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
==> Warning: Expected user 904556 to own /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206, but it is owned by 0
==> bison@3.8.2 : has external module in ['bison/3.8.2']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/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/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/nlohmann-json-3.9.1-ee7ugz
[+] /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-tomli-2.0.1-ksqdpf
[+] /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-pybind11-2.10.1-pi3gda
[+] /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-markupsafe-2.1.1-d4uhr4
[+] /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-pyyaml-6.0-d4xzk5
[+] /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-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-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-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
[+] /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-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-5iqrurmyweoqpqa52uwp4je6fg3d54sq
==> No binary for nmodl-develop-5iqrurmyweoqpqa52uwp4je6fg3d54sq 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-5iqrurmyweoqpqa52uwp4je6fg3d54sq
Fetch: 1m 54.34s. Build: 3m 41.36s. Total: 5m 35.70s.
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/software/install_oneapi-2022.2.1-skylake/nmodl-develop-5iqrur
$ 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 5iqrurmyweoqpqa52uwp4je6fg3d54sq
$ 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/bbpcihpcproj12/1904708/ccache
Primary config: /nvme/bbpcihpcproj12/1904708/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: Tue Nov 21 17:10:28 2023
Hits: 132 / 138 (95.65 %)
Direct: 23 / 138 (16.67 %)
Preprocessed: 109 / 115 (94.78 %)
Misses: 6
Direct: 115
Preprocessed: 6
Uncacheable: 174
Primary storage:
Hits: 155 / 276 (56.16 %)
Misses: 121
Cache size (GB): 0.44 / 0.51 (85.30 %)
Files: 1535
Uncacheable:
Called for linking: 174
$ 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:1700583029:step_script section_start:1700583029: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=163299 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:1700583048:archive_cache section_start:1700583048:upload_artifacts_on_success Uploading artifacts for successful job
Using git from spack modules
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=163520 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=1029080 responseStatus=201 Created token=64_HEs6T
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=163548 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
Uploading artifacts as "junit" to coordinator... ok id=1029080 responseStatus=201 Created token=64_HEs6T
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=163623 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=1029080 responseStatus=201 Created token=64_HEs6T
section_end:1700583049:upload_artifacts_on_success section_start:1700583049:cleanup_file_variables Cleaning up project directory and file based variables
Using git from spack modules
section_end:1700583050:cleanup_file_variables Job succeeded
Raw
build-nvhpc.txt
Running with gitlab-runner 15.5.0 (0d4137b8)
 on BB5 map runner pnPo3yJy
section_start:1700582490:resolve_secrets Resolving secrets
section_end:1700582490:resolve_secrets section_start:1700582490: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-executor3643506889, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name nmodl
Pipeline ID 172206, build ref , job ID 1029081
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P172206, 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_J1029081_PROD_P30_CP5_C20
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 1904710
job state: PD
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1029081_PROD_P30_CP5_C20 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P172206 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P172206 --ntasks=1 --jobid=1904710 --cpus-per-task=6 --mem=30750M
section_end:1700582493:prepare_executor section_start:1700582493:prepare_script Preparing environment
Using git from spack modules
Running on r1i4n8 via bbpv1.epfl.ch...
section_end:1700582502:prepare_script section_start:1700582502: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:1700582503:get_sources section_start:1700582503:restore_cache Restoring cache
Using git from spack modules
Checking cache for build:nvhpc-2-non_protected...
Runtime platform  arch=amd64 os=linux pid=148504 revision=58ba2b95 version=14.2.0
cache.zip is up to date 
Successfully extracted cache
section_end:1700582508:restore_cache section_start:1700582508:download_artifacts Downloading artifacts
Using git from spack modules
Downloading artifacts for spack_setup (1029079)...
Runtime platform  arch=amd64 os=linux pid=149127 revision=58ba2b95 version=14.2.0
Downloading artifacts from coordinator... ok  id=1029079 responseStatus=200 OK token=64_Cze53
section_end:1700582509:download_artifacts section_start:1700582509: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/P172206/J1029081/spack-config/config.yaml:2 build_stage:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029081/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029081/spack-build
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029081/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029081/spack-source-cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/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/P172206/J1029079/spack/etc/spack/defaults/config.yaml:18 extensions:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:18 - $spack/bluebrain/spack-scripting
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/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/P172206/J1029079/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/P172206/J1029079/spack/etc/spack/defaults/config.yaml:37 template_dirs:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:37 - $spack/share/spack/templates
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:38 # Directory where licenses should be located
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:41 license_dir: $spack/etc/spack/licenses
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:76 test_stage: $user_cache_path/test
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:89 misc_cache: $user_cache_path/cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:95 connect_timeout: 10
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:100 verify_ssl: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:108 suppress_gpg_warnings: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:114 install_missing_compilers: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:119 checksum: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:124 deprecated: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:129 dirty: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:137 build_language: C
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:146 locks: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:151 url_fetch_method: urllib
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:180 concretizer: clingo
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:187 db_lock_timeout: 600
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:195 package_lock_timeout: null
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:200 shared_linking:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:205 type: rpath
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:211 bind: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:216 allow_sgid: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/config.yaml:221 terminal_title: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/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/P172206/J1029081/spack-config/concretizer.yaml:2 reuse: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/concretizer.yaml:22 targets:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/concretizer.yaml:26 granularity: microarchitectures
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/spack/etc/spack/defaults/concretizer.yaml:30 host_compatible: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029079/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/P172206/J1029081_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/P172206
$ 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/bbpcihpcproj12/1904710/ccache
Primary config: /nvme/bbpcihpcproj12/1904710/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: Tue Nov 21 17:02:03 2023
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): 0.46 / 0.51 (90.53 %)
Files: 1771
$ 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
--------------------------------
- ig5xxxq 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/fmt-9.1.0-t7yyhx
[+] /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/cli11-2.1.1-u27b4t
[+] /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/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-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-cython-0.29.32-bjojgf
[+] /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-markupsafe-2.1.1-d4uhr4
[+] /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-pybind11-2.10.1-pi3gda
[+] /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-pyyaml-6.0-d4xzk5
[+] /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-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-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
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-py-1.11.0-a53pqv
==> Warning: Expected user 904556 to own /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206, 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-ig5xxxqcms4p7raynztlf4ikjbovtifr
==> No binary for nmodl-develop-ig5xxxqcms4p7raynztlf4ikjbovtifr 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-ig5xxxqcms4p7raynztlf4ikjbovtifr
Fetch: 1m 45.54s. Build: 3m 51.87s. Total: 5m 37.41s.
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/software/install_nvhpc-23.1-skylake/nmodl-develop-ig5xxx
$ 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 ig5xxxqcms4p7raynztlf4ikjbovtifr
$ 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/bbpcihpcproj12/1904710/ccache
Primary config: /nvme/bbpcihpcproj12/1904710/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: Tue Nov 21 17:10:25 2023
Hits: 132 / 135 (97.78 %)
Direct: 23 / 135 (17.04 %)
Preprocessed: 109 / 112 (97.32 %)
Misses: 3
Direct: 112
Preprocessed: 3
Uncacheable: 22
Primary storage:
Hits: 155 / 270 (57.41 %)
Misses: 115
Cache size (GB): 0.46 / 0.51 (90.54 %)
Files: 1777
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:1700583026:step_script section_start:1700583026: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=163221 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:1700583047:archive_cache section_start:1700583047:upload_artifacts_on_success Uploading artifacts for successful job
Using git from spack modules
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=163399 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=1029081 responseStatus=201 Created token=64_Cze53
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=163421 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
Uploading artifacts as "junit" to coordinator... ok id=1029081 responseStatus=201 Created token=64_Cze53
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=163455 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=1029081 responseStatus=201 Created token=64_Cze53
section_end:1700583048:upload_artifacts_on_success section_start:1700583048:cleanup_file_variables Cleaning up project directory and file based variables
Using git from spack modules
section_end:1700583049:cleanup_file_variables Job succeeded
Raw
spack-setup.txt
Running with gitlab-runner 15.5.0 (0d4137b8)
 on BB5 map runner pnPo3yJy
section_start:1700582171:resolve_secrets Resolving secrets
section_end:1700582171:resolve_secrets section_start:1700582171: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-executor2810196587, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name nmodl
Pipeline ID 172206, build ref , job ID 1029079
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P172206, 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_J1029079_PROD_P30_CP4_C13
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 1904675
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1029079_PROD_P30_CP4_C13 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P172206 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P172206 --ntasks=1 --jobid=1904675 --cpus-per-task=6 --mem=30750M
section_end:1700582172:prepare_executor section_start:1700582172:prepare_script Preparing environment
Using git from spack modules
Running on r1i4n8 via bbpv1.epfl.ch...
section_end:1700582177:prepare_script section_start:1700582177: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:1700582178:get_sources section_start:1700582178: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/P172206/J1029079
$ if [[ -z "${SPACK_BRANCH}" && ( -n "${SPACK_COMMIT}" || -n "${SPACK_TAG}" ) ]]; then
$ echo Checking out the ${SPACK_BRANCH} of Spack...
Checking out the develop of Spack...
$ module load unstable git
$ git clone -c feature.manyFiles=true --depth 1 --single-branch --branch ${SPACK_BRANCH} ${SPACK_URL} spack
Cloning into 'spack'...
Updating files: 14% (1475/10340) Updating files: 15% (1551/10340) Updating files: 16% (1655/10340) Updating files: 17% (1758/10340) Updating files: 18% (1862/10340) Updating files: 19% (1965/10340) Updating files: 19% (2048/10340) Updating files: 20% (2068/10340) Updating files: 21% (2172/10340) Updating files: 22% (2275/10340) Updating files: 23% (2379/10340) Updating files: 24% (2482/10340) Updating files: 24% (2528/10340) Updating files: 25% (2585/10340) Updating files: 26% (2689/10340) Updating files: 27% (2792/10340) Updating files: 28% (2896/10340) Updating files: 28% (2971/10340) Updating files: 29% (2999/10340) Updating files: 30% (3102/10340) Updating files: 31% (3206/10340) Updating files: 32% (3309/10340) Updating files: 32% (3398/10340) Updating files: 33% (3413/10340) Updating files: 34% (3516/10340) Updating files: 35% (3619/10340) Updating files: 36% (3723/10340) Updating files: 36% (3781/10340) Updating files: 37% (3826/10340) Updating files: 38% (3930/10340) Updating files: 39% (4033/10340) Updating files: 40% (4136/10340) Updating files: 41% (4240/10340) Updating files: 41% (4306/10340) Updating files: 42% (4343/10340) Updating files: 43% (4447/10340) Updating files: 44% (4550/10340) Updating files: 45% (4653/10340) Updating files: 46% (4757/10340) Updating files: 47% (4860/10340) Updating files: 47% (4909/10340) Updating files: 48% (4964/10340) Updating files: 49% (5067/10340) Updating files: 50% (5170/10340) Updating files: 51% (5274/10340) Updating files: 51% (5374/10340) Updating files: 52% (5377/10340) Updating files: 53% (5481/10340) Updating files: 54% (5584/10340) Updating files: 55% (5687/10340) Updating files: 55% (5778/10340) Updating files: 56% (5791/10340) Updating files: 57% (5894/10340) Updating files: 58% (5998/10340) Updating files: 59% (6101/10340) Updating files: 59% (6146/10340) Updating files: 60% (6204/10340) Updating files: 61% (6308/10340) Updating files: 62% (6411/10340) Updating files: 62% (6474/10340) Updating files: 63% (6515/10340) Updating files: 64% (6618/10340) Updating files: 65% (6721/10340) Updating files: 66% (6825/10340) Updating files: 66% (6895/10340) Updating files: 67% (6928/10340) Updating files: 68% (7032/10340) Updating files: 69% (7135/10340) Updating files: 70% (7238/10340) Updating files: 71% (7342/10340) Updating files: 71% (7400/10340) Updating files: 72% (7445/10340) Updating files: 73% (7549/10340) Updating files: 74% (7652/10340) Updating files: 75% (7755/10340) Updating files: 75% (7838/10340) Updating files: 76% (7859/10340) Updating files: 77% (7962/10340) Updating files: 78% (8066/10340) Updating files: 79% (8169/10340) Updating files: 80% (8272/10340) Updating files: 80% (8310/10340) Updating files: 81% (8376/10340) Updating files: 82% (8479/10340) Updating files: 83% (8583/10340) Updating files: 84% (8686/10340) Updating files: 84% (8696/10340) Updating files: 85% (8789/10340) Updating files: 86% (8893/10340) Updating files: 87% (8996/10340) Updating files: 88% (9100/10340) Updating files: 88% (9105/10340) Updating files: 89% (9203/10340) Updating files: 90% (9306/10340) Updating files: 91% (9410/10340) Updating files: 92% (9513/10340) Updating files: 92% (9533/10340) Updating files: 93% (9617/10340) Updating files: 94% (9720/10340) Updating files: 95% (9823/10340) Updating files: 96% (9927/10340) Updating files: 96% (9966/10340) Updating files: 97% (10030/10340) Updating files: 98% (10134/10340) Updating files: 99% (10237/10340) Updating files: 100% (10340/10340) Updating files: 100% (10340/10340), done.
$ export SPACK_ROOT=${PWD}/spack
$ export SPACK_RESOLVED_COMMIT=$(cd "${SPACK_ROOT}" && git rev-parse HEAD)
$ export SPACK_USER_CACHE_PATH="${CI_BUILDS_DIR}"
$ export SPACK_SYSTEM_CONFIG_PATH="/gpfs/bbp.cscs.ch/ssd/apps/bsd/${SPACK_DEPLOYMENT_SUFFIX}/config"
$ echo "SPACK_ROOT=${SPACK_ROOT}" >> spack_clone_variables.env
$ echo "SPACK_RESOLVED_COMMIT=${SPACK_RESOLVED_COMMIT}" >> spack_clone_variables.env
$ echo "SPACK_USER_CACHE_PATH=${SPACK_USER_CACHE_PATH}" >> spack_clone_variables.env
$ echo "SPACK_SYSTEM_CONFIG_PATH=${SPACK_SYSTEM_CONFIG_PATH}" >> spack_clone_variables.env
$ . ${SPACK_ROOT}/share/spack/setup-env.sh
$ export XDG_CONFIG_HOME=${CI_BUILDS_DIR}/J${CI_JOB_ID}_local_config
$ echo "Configuring git to use CI_JOB_TOKEN to access git@bbpgitlab.epfl.ch (${XDG_CONFIG_HOME})"
Configuring git to use CI_JOB_TOKEN to access git@bbpgitlab.epfl.ch (/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P172206/J1029079_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=cornu/at_most_one_derivative_block NMODL_COMMIT=2438b34cba75fa3cba90f10074e2226545c76201 SPACK_RESOLVED_COMMIT=b055dcdcaa4d1c3fb2933770f0184821ab7d3fb9 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=cornu/at_most_one_derivative_block
==> SPACK_RESOLVED: ignoring SPACK_RESOLVED_COMMIT=b055dcdcaa4d1c3fb2933770f0184821ab7d3fb9
==> 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 bc5ed0576598fa30c30607620473ce1effb7f2e1
==> libsonata-report: resolved branch master to b95d1c8633282c6bd5358d2511777d399b8c447f
==> nmodl@develop: remove branch/commit/tag
==> nmodl@develop: use commit="2438b34cba75fa3cba90f10074e2226545c76201"
==> nmodl@develop: add preferred=True
==> neuron@develop: remove branch/commit/tag
==> neuron@develop: use commit="bc5ed0576598fa30c30607620473ce1effb7f2e1"
==> neuron@develop: add preferred=True
==> libsonata-report@develop: remove branch/commit/tag
==> libsonata-report@develop: use commit="b95d1c8633282c6bd5358d2511777d399b8c447f"
==> 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 6e7fe956..6b63c942 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='b95d1c8633282c6bd5358d2511777d399b8c447f', submodules=False, get_full_repo=True) # old: branch="master"
version("1.2.1", tag="1.2.1", submodules=False)
version("1.2", tag="1.2", submodules=False)
version("1.1.1", tag="1.1.1", submodules=False)
diff --git a/bluebrain/repo-bluebrain/packages/nmodl/package.py b/bluebrain/repo-bluebrain/packages/nmodl/package.py
index eaf08b46..0fd8cec9 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='2438b34cba75fa3cba90f10074e2226545c76201', 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 e0298eaf..b4a5afcd 100644
--- a/bluebrain/repo-patches/packages/neuron/package.py
+++ b/bluebrain/repo-patches/packages/neuron/package.py
@@ -31,7 +31,7 @@ class Neuron(CMakePackage):
# Patch for recent CMake versions that don't identify NVHPC as PGI
patch("patch-v800-cmake-nvhpc.patch", when="@8.0.0%nvhpc^cmake@3.20:")
- version("develop", branch="master")
+ version('develop', preferred=True, commit='bc5ed0576598fa30c30607620473ce1effb7f2e1') # old: branch="master"
version("9.0.a13", commit="3bbdd8da")
version("9.0.a12", commit="6004512f")
version("9.0.a11", commit="b38dd11b")
$ cat commit-mapping.env
NMODL_COMMIT=2438b34cba75fa3cba90f10074e2226545c76201
NEURON_COMMIT=bc5ed0576598fa30c30607620473ce1effb7f2e1
LIBSONATA_REPORT_COMMIT=b95d1c8633282c6bd5358d2511777d399b8c447f
$ 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:1700582482:step_script section_start:1700582482:upload_artifacts_on_success Uploading artifacts for successful job
Using git from spack modules
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=145708 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=1029079 responseStatus=201 Created token=64_MwLS8
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=145743 revision=58ba2b95 version=14.2.0
spack_clone_variables.env: found 1 matching files and directories
Uploading artifacts as "dotenv" to coordinator... ok id=1029079 responseStatus=201 Created token=64_MwLS8
section_end:1700582484:upload_artifacts_on_success section_start:1700582484:cleanup_file_variables Cleaning up project directory and file based variables
Using git from spack modules
section_end:1700582485:cleanup_file_variables Job succeeded
Raw
test-intel.txt
Running with gitlab-runner 15.5.0 (0d4137b8)
 on BB5 map runner pnPo3yJy
section_start:1700583062:resolve_secrets Resolving secrets
section_end:1700583062:resolve_secrets section_start:1700583062: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-executor4213070078, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name nmodl
Pipeline ID 172206, build ref , job ID 1029082
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P172206, 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_J1029082_PROD_P30_CP0_C2
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 1904761
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=1 --mem=30750M --job-name=GL_J1029082_PROD_P30_CP0_C2 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P172206 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P172206 --ntasks=1 --jobid=1904761 --cpus-per-task=1 --mem=30750M
section_end:1700583063:prepare_executor section_start:1700583063:prepare_script Preparing environment
Using git from spack modules
Running on r1i7n22 via bbpv1.epfl.ch...
section_end:1700583066:prepare_script section_start:1700583066: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:1700583067:get_sources section_start:1700583067:download_artifacts Downloading artifacts
Using git from spack modules
Downloading artifacts for build:intel (1029080)...
Runtime platform  arch=amd64 os=linux pid=271520 revision=58ba2b95 version=14.2.0
Downloading artifacts from coordinator... ok  id=1029080 responseStatus=200 OK token=64_b_G5j
section_end:1700583068:download_artifacts section_start:1700583068: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: r1i4n8
Build name: Linux-icpx
Create new tag: 20231121-1612 - Experimental
Test project /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029080/spack-build/spack-stage-nmodl-develop-5iqrurmyweoqpqa52uwp4je6fg3d54sq/spack-build-5iqrurm
Start 1: testcodegen/Scenario: unusual / failing mod files
1/109 Test #1: testcodegen/Scenario: unusual / failing mod files ................................................... Passed 0.06 sec
Start 2: testcodegen/Scenario: Check global variable setup
2/109 Test #2: testcodegen/Scenario: Check global variable setup ................................................... Passed 0.04 sec
Start 3: testcodegen/Scenario: C codegen utility functions
3/109 Test #3: testcodegen/Scenario: C codegen utility functions ................................................... Passed 0.04 sec
Start 4: testcodegen/Scenario: Check instance variable definition order
4/109 Test #4: testcodegen/Scenario: Check instance variable definition order ...................................... Passed 0.04 sec
Start 5: testcodegen/Scenario: Check parameter constness with VERBATIM block
5/109 Test #5: testcodegen/Scenario: Check parameter constness with VERBATIM block ................................. Passed 0.04 sec
Start 6: testcodegen/Scenario: Check NEURON globals are added to the instance struct on demand
6/109 Test #6: testcodegen/Scenario: Check NEURON globals are added to the instance struct on demand ............... Passed 0.04 sec
Start 7: testcodegen/Scenario: Check code generation for TABLE statements
7/109 Test #7: testcodegen/Scenario: Check code generation for TABLE statements .................................... Passed 0.04 sec
Start 8: testcodegen/Scenario: Check that BEFORE/AFTER block are well generated
8/109 Test #8: testcodegen/Scenario: Check that BEFORE/AFTER block are well generated .............................. Passed 0.04 sec
Start 9: testcodegen/Scenario: Check CONSTANT variables are added to global variable structure
9/109 Test #9: testcodegen/Scenario: Check CONSTANT variables are added to global variable structure ............... Passed 0.04 sec
Start 10: testcodegen/Scenario: Check code generation for FUNCTION_TABLE block
10/109 Test #10: testcodegen/Scenario: Check code generation for FUNCTION_TABLE block ................................ Passed 0.04 sec
Start 11: testcodegen/Scenario: Check that loops are well generated
11/109 Test #11: testcodegen/Scenario: Check that loops are well generated ........................................... Passed 0.04 sec
Start 12: testcodegen/Scenario: Check that top verbatim blocks are well generated
12/109 Test #12: testcodegen/Scenario: Check that top verbatim blocks are well generated ............................. Passed 0.04 sec
Start 13: testcodegen/Scenario: Check that codegen generate event functions well
13/109 Test #13: testcodegen/Scenario: Check that codegen generate event functions well .............................. Passed 0.04 sec
Start 14: testcodegen/Scenario: Some tests on derivimplicit
14/109 Test #14: testcodegen/Scenario: Some tests on derivimplicit ................................................... Passed 0.04 sec
Start 15: testcodegen/Scenario: Some tests on euler solver
15/109 Test #15: testcodegen/Scenario: Some tests on euler solver .................................................... Passed 0.04 sec
Start 16: testcodegen/Scenario: Check codegen for MUTEX and PROTECT
16/109 Test #16: testcodegen/Scenario: Check codegen for MUTEX and PROTECT ........................................... Passed 0.04 sec
Start 17: testcodegen/Scenario: Array STATE variable
17/109 Test #17: testcodegen/Scenario: Array STATE variable .......................................................... Passed 0.04 sec
Start 18: testcodegen/Scenario: Adding a variable for a table inside a function
18/109 Test #18: testcodegen/Scenario: Adding a variable for a table inside a function ............................... Passed 0.04 sec
Start 19: testcodegen/Scenario: Uncompatible constructs should failed
19/109 Test #19: testcodegen/Scenario: Uncompatible constructs should failed ......................................... Passed 0.04 sec
Start 20: testmodtoken/NMODL Lexer returning valid ModToken object
20/109 Test #20: testmodtoken/NMODL Lexer returning valid ModToken object ............................................ Passed 0.01 sec
Start 21: testmodtoken/Addition of two ModToken objects
21/109 Test #21: testmodtoken/Addition of two ModToken objects ....................................................... Passed 0.01 sec
Start 22: testlexer/NMODL Lexer returning valid token types
22/109 Test #22: testlexer/NMODL Lexer returning valid token types ................................................... Passed 0.01 sec
Start 23: testparser/Scenario: NMODL can accept CR as return char for one line comment
23/109 Test #23: testparser/Scenario: NMODL can accept CR as return char for one line comment ........................ Passed 0.02 sec
Start 24: testparser/Scenario: NMODL can define macros using DEFINE keyword
24/109 Test #24: testparser/Scenario: NMODL can define macros using DEFINE keyword ................................... Passed 0.02 sec
Start 25: testparser/Scenario: Macros can be used anywhere in the mod file
25/109 Test #25: testparser/Scenario: Macros can be used anywhere in the mod file .................................... Passed 0.01 sec
Start 26: testparser/Scenario: NMODL parser accepts empty unit specification
26/109 Test #26: testparser/Scenario: NMODL parser accepts empty unit specification .................................. Passed 0.01 sec
Start 27: testparser/Scenario: NMODL parser running number of valid NMODL constructs
27/109 Test #27: testparser/Scenario: NMODL parser running number of valid NMODL constructs .......................... Passed 0.04 sec
Start 28: testparser/Scenario: NMODL parser running number of invalid NMODL constructs
28/109 Test #28: testparser/Scenario: NMODL parser running number of invalid NMODL constructs ........................ Passed 0.02 sec
Start 29: testparser/Scenario: Check that the parser doesn't crash when passing invalid INCLUDE constructs
29/109 Test #29: testparser/Scenario: Check that the parser doesn't crash when passing invalid INCLUDE constructs .... Passed 0.02 sec
Start 30: testparser/Scenario: NEURON block can add CURIE information
30/109 Test #30: testparser/Scenario: NEURON block can add CURIE information ......................................... Passed 0.01 sec
Start 31: testparser/Scenario: Check parents in valid NMODL constructs
31/109 Test #31: testparser/Scenario: Check parents in valid NMODL constructs ........................................ Passed 0.26 sec
Start 32: testparser/Scenario: Legacy differential equation solver
32/109 Test #32: testparser/Scenario: Legacy differential equation solver ............................................ Passed 0.02 sec
Start 33: testparser/Scenario: Check if a NEURON block is parsed with correct location info in its token
33/109 Test #33: testparser/Scenario: Check if a NEURON block is parsed with correct location info in its token ...... Passed 0.01 sec
Start 34: testvisitor/Scenario: AfterCVodeToCnexpVisitor changes after_cvode solver method to cnexp
34/109 Test #34: testvisitor/Scenario: AfterCVodeToCnexpVisitor changes after_cvode solver method to cnexp ........... Passed 0.05 sec
Start 35: testvisitor/Scenario: Perform constant folder on NMODL constructs
35/109 Test #35: testvisitor/Scenario: Perform constant folder on NMODL constructs ................................... Passed 0.04 sec
Start 36: testvisitor/Scenario: Perform DefUse analysis on NMODL constructs
36/109 Test #36: testvisitor/Scenario: Perform DefUse analysis on NMODL constructs ................................... Passed 0.05 sec
Start 37: testvisitor/Scenario: GLOBAL to RANGE variable transformer
37/109 Test #37: testvisitor/Scenario: GLOBAL to RANGE variable transformer .......................................... Passed 0.04 sec
Start 38: testvisitor/Scenario: Check insertion of implicit arguments
38/109 Test #38: testvisitor/Scenario: Check insertion of implicit arguments ......................................... Passed 0.04 sec
Start 39: testvisitor/Scenario: Inlining of external procedure calls
39/109 Test #39: testvisitor/Scenario: Inlining of external procedure calls .......................................... Passed 0.04 sec
Start 40: testvisitor/Scenario: Inlining of function call as argument in external function
40/109 Test #40: testvisitor/Scenario: Inlining of function call as argument in external function .................... Passed 0.04 sec
Start 41: testvisitor/Scenario: Inlining of simple, one level procedure call
41/109 Test #41: testvisitor/Scenario: Inlining of simple, one level procedure call .................................. Passed 0.04 sec
Start 42: testvisitor/Scenario: Inlining of nested procedure call
42/109 Test #42: testvisitor/Scenario: Inlining of nested procedure call ............................................. Passed 0.04 sec
Start 43: testvisitor/Scenario: Inline function call in procedure
43/109 Test #43: testvisitor/Scenario: Inline function call in procedure ............................................. Passed 0.04 sec
Start 44: testvisitor/Scenario: Inling function call within conditional statement
44/109 Test #44: testvisitor/Scenario: Inling function call within conditional statement ............................. Passed 0.04 sec
Start 45: testvisitor/Scenario: Inline multiple function calls in same statement
45/109 Test #45: testvisitor/Scenario: Inline multiple function calls in same statement .............................. Passed 0.04 sec
Start 46: testvisitor/Scenario: Inline nested function calls withing arguments
46/109 Test #46: testvisitor/Scenario: Inline nested function calls withing arguments ................................ Passed 0.04 sec
Start 47: testvisitor/Scenario: Inline function call in non-binary expression
47/109 Test #47: testvisitor/Scenario: Inline function call in non-binary expression ................................. Passed 0.04 sec
Start 48: testvisitor/Scenario: Inline function call as standalone expression
48/109 Test #48: testvisitor/Scenario: Inline function call as standalone expression ................................. Passed 0.04 sec
Start 49: testvisitor/Scenario: Inline procedure call as standalone statement as well as part of expression
49/109 Test #49: testvisitor/Scenario: Inline procedure call as standalone statement as well as part of expression ... Passed 0.04 sec
Start 50: testvisitor/Scenario: Inlining pass handles local-global name conflict
50/109 Test #50: testvisitor/Scenario: Inlining pass handles local-global name conflict .............................. Passed 0.04 sec
Start 51: testvisitor/Scenario: Trying to inline a function with VERBATIM block
51/109 Test #51: testvisitor/Scenario: Trying to inline a function with VERBATIM block ............................... Passed 0.04 sec
Start 52: testvisitor/Convert NMODL to AST to JSON form using JSONVisitor
52/109 Test #52: testvisitor/Convert NMODL to AST to JSON form using JSONVisitor ..................................... Passed 0.04 sec
Start 53: testvisitor/Scenario: Convert KINETIC to DERIVATIVE using KineticBlock visitor
53/109 Test #53: testvisitor/Scenario: Convert KINETIC to DERIVATIVE using KineticBlock visitor ...................... Passed 0.05 sec
Start 54: testvisitor/Scenario: Localizer test with single global block
54/109 Test #54: testvisitor/Scenario: Localizer test with single global block ....................................... Passed 0.04 sec
Start 55: testvisitor/Scenario: Localizer test with use of verbatim block
55/109 Test #55: testvisitor/Scenario: Localizer test with use of verbatim block ..................................... Passed 0.04 sec
Start 56: testvisitor/Scenario: Localizer test with multiple global blocks
56/109 Test #56: testvisitor/Scenario: Localizer test with multiple global blocks .................................... Passed 0.04 sec
Start 57: testvisitor/Scenario: LocalVarRenameVisitor works with InlineVisitor
57/109 Test #57: testvisitor/Scenario: LocalVarRenameVisitor works with InlineVisitor ................................ Passed 0.04 sec
Start 58: testvisitor/Scenario: LOCAL to ASSIGNED variable transformer
58/109 Test #58: testvisitor/Scenario: LOCAL to ASSIGNED variable transformer ........................................ Passed 0.04 sec
Start 59: testvisitor/Scenario: Searching for ast nodes using AstLookupVisitor
59/109 Test #59: testvisitor/Scenario: Searching for ast nodes using AstLookupVisitor ................................ Passed 0.04 sec
Start 60: testvisitor/Scenario: Perform loop unrolling of FROM construct
60/109 Test #60: testvisitor/Scenario: Perform loop unrolling of FROM construct ...................................... Passed 0.04 sec
Start 61: testvisitor/Scenario: Running visitor passes multiple times
61/109 Test #61: testvisitor/Scenario: Running visitor passes multiple times ......................................... Passed 0.04 sec
Start 62: testvisitor/Scenario: Sympy specific AST to NMODL conversion
62/109 Test #62: testvisitor/Scenario: Sympy specific AST to NMODL conversion ........................................ Passed 0.04 sec
Start 63: testvisitor/Scenario: NeuronSolveVisitor visitor solves different ODE types
63/109 Test #63: testvisitor/Scenario: NeuronSolveVisitor visitor solves different ODE types ......................... Passed 0.04 sec
Start 64: testvisitor/Scenario: Convert AST back to NMODL form
64/109 Test #64: testvisitor/Scenario: Convert AST back to NMODL form ................................................ Passed 0.09 sec
Start 65: testvisitor/Scenario: Symbol table generation with Perf stat visitor
65/109 Test #65: testvisitor/Scenario: Symbol table generation with Perf stat visitor ................................ Passed 0.04 sec
Start 66: testvisitor/Scenario: Renaming any variable in mod file with RenameVisitor
66/109 Test #66: testvisitor/Scenario: Renaming any variable in mod file with RenameVisitor .......................... Passed 0.04 sec
Start 67: testvisitor/Scenario: Renaming with presence of local and global variables in same block
67/109 Test #67: testvisitor/Scenario: Renaming with presence of local and global variables in same block ............ Passed 0.04 sec
Start 68: testvisitor/Scenario: Renaming in the absence of global blocks
68/109 Test #68: testvisitor/Scenario: Renaming in the absence of global blocks ...................................... Passed 0.04 sec
Start 69: testvisitor/Scenario: Variable renaming in nested blocks
69/109 Test #69: testvisitor/Scenario: Variable renaming in nested blocks ............................................ Passed 0.04 sec
Start 70: testvisitor/Scenario: Renaming in presence of local variable in verbatim block
70/109 Test #70: testvisitor/Scenario: Renaming in presence of local variable in verbatim block ...................... Passed 0.04 sec
Start 71: testvisitor/Scenario: TABLE stmt
71/109 Test #71: testvisitor/Scenario: TABLE stmt .................................................................... Passed 0.04 sec
Start 72: testvisitor/Scenario: Destructor block
72/109 Test #72: testvisitor/Scenario: Destructor block .............................................................. Passed 0.04 sec
Start 73: testvisitor/Scenario: Ion variable in CONSTANT block
73/109 Test #73: testvisitor/Scenario: Ion variable in CONSTANT block ................................................ Passed 0.04 sec
Start 74: testvisitor/Scenario: INDEPENDENT block
74/109 Test #74: testvisitor/Scenario: INDEPENDENT block ............................................................. Passed 0.04 sec
Start 75: testvisitor/Scenario: FUNCTION_TABLE block
75/109 Test #75: testvisitor/Scenario: FUNCTION_TABLE block .......................................................... Passed 0.04 sec
Start 76: testvisitor/Scenario: At most one DERIVATIVE block
76/109 Test #76: testvisitor/Scenario: At most one DERIVATIVE block .................................................. Passed 0.04 sec
Start 77: testvisitor/Solve ODEs using legacy NeuronSolveVisitor
77/109 Test #77: testvisitor/Solve ODEs using legacy NeuronSolveVisitor .............................................. Passed 0.04 sec
Start 78: testvisitor/Scenario: Solving ODEs with STEADYSTATE solve method
78/109 Test #78: testvisitor/Scenario: Solving ODEs with STEADYSTATE solve method .................................... Passed 0.04 sec
Start 79: testvisitor/Scenario: Addition of CONDUCTANCE using SympyConductance visitor
79/109 Test #79: testvisitor/Scenario: Addition of CONDUCTANCE using SympyConductance visitor ........................ Passed 55.43 sec
Start 80: testvisitor/Scenario: Check compare_blocks in sympy unit tests
80/109 Test #80: testvisitor/Scenario: Check compare_blocks in sympy unit tests ...................................... Passed 0.85 sec
Start 81: testvisitor/Scenario: Check local vars name-clash prevention
81/109 Test #81: testvisitor/Scenario: Check local vars name-clash prevention ........................................ Passed 0.98 sec
Start 82: testvisitor/Scenario: Solve ODEs with cnexp or euler method using SympySolverVisitor
82/109 Test #82: testvisitor/Scenario: Solve ODEs with cnexp or euler method using SympySolverVisitor ................ Passed 8.85 sec
Start 83: testvisitor/Scenario: Solve ODEs with derivimplicit method using SympySolverVisitor
83/109 Test #83: testvisitor/Scenario: Solve ODEs with derivimplicit method using SympySolverVisitor ................. Passed 2.67 sec
Start 84: testvisitor/Scenario: LINEAR solve block (SympySolver Visitor)
84/109 Test #84: testvisitor/Scenario: LINEAR solve block (SympySolver Visitor) ...................................... Passed 2.04 sec
Start 85: testvisitor/Scenario: Solve NONLINEAR block using SympySolver Visitor
85/109 Test #85: testvisitor/Scenario: Solve NONLINEAR block using SympySolver Visitor ............................... Passed 0.97 sec
Start 86: testvisitor/Scenario: Solve KINETIC block using SympySolver Visitor
86/109 Test #86: testvisitor/Scenario: Solve KINETIC block using SympySolver Visitor ................................. Passed 1.10 sec
Start 87: testvisitor/Scenario: Code generation for EigenNewtonSolver
87/109 Test #87: testvisitor/Scenario: Code generation for EigenNewtonSolver ......................................... Passed 1.03 sec
Start 88: testvisitor/Scenario: Parse UNITS block of mod files using Units Visitor
88/109 Test #88: testvisitor/Scenario: Parse UNITS block of mod files using Units Visitor ............................ Passed 0.05 sec
Start 89: testvisitor/Scenario: Searching for variable name using VarUsageVisitor
89/109 Test #89: testvisitor/Scenario: Searching for variable name using VarUsageVisitor ............................. Passed 0.04 sec
Start 90: testvisitor/Parse VERBATIM block using Verbatim Visitor
90/109 Test #90: testvisitor/Parse VERBATIM block using Verbatim Visitor ............................................. Passed 0.04 sec
Start 91: testvisitor/Scenario: Get node name with index TestVisitor
91/109 Test #91: testvisitor/Scenario: Get node name with index TestVisitor .......................................... Passed 0.04 sec
Start 92: testprinter/JSON printer converting object to string form
92/109 Test #92: testprinter/JSON printer converting object to string form ........................................... Passed 0.01 sec
Start 93: testsymtab/Scenario: Symbol properties can be added and converted to string
93/109 Test #93: testsymtab/Scenario: Symbol properties can be added and converted to string ......................... Passed 0.01 sec
Start 94: testsymtab/Scenario: Multiple properties can be added to Symbol
94/109 Test #94: testsymtab/Scenario: Multiple properties can be added to Symbol ..................................... Passed 0.01 sec
Start 95: testsymtab/Scenario: Symbol table allows operations like insert, lookup
95/109 Test #95: testsymtab/Scenario: Symbol table allows operations like insert, lookup ............................. Passed 0.01 sec
Start 96: testsymtab/Scenario: Global symbol table (ModelSymbol) allows scope based operations
96/109 Test #96: testsymtab/Scenario: Global symbol table (ModelSymbol) allows scope based operations ................ Passed 0.01 sec
Start 97: testsymtab/Scenario: Symbol class allows manipulation
97/109 Test #97: testsymtab/Scenario: Symbol class allows manipulation ............................................... Passed 0.01 sec
Start 98: testnewton/Scenario: Non-linear system to solve with Newton Numerical Diff Solver
98/109 Test #98: testnewton/Scenario: Non-linear system to solve with Newton Numerical Diff Solver ................... Passed 0.01 sec
Start 99: testnewton/Scenario: Non-linear system to solve with Newton Solver
99/109 Test #99: testnewton/Scenario: Non-linear system to solve with Newton Solver .................................. Passed 0.01 sec
Start 100: testcrout/Scenario: Compare Crout solver with Eigen
100/109 Test #100: testcrout/Scenario: Compare Crout solver with Eigen ................................................. Passed 0.30 sec
Start 101: testunitlexer/Unit Lexer tests for valid tokens
101/109 Test #101: testunitlexer/Unit Lexer tests for valid tokens ..................................................... Passed 0.01 sec
Start 102: testunitparser/Scenario: Unit parser accepting valid units definition
102/109 Test #102: testunitparser/Scenario: Unit parser accepting valid units definition ............................... Passed 0.02 sec
Start 103: testunitparser/Scenario: Unit parser accepting dependent/nested units definition
103/109 Test #103: testunitparser/Scenario: Unit parser accepting dependent/nested units definition .................... Passed 0.01 sec
Start 104: Ode
104/109 Test #104: Ode ................................................................................................. Passed 2.23 sec
Start 105: Pybind
105/109 Test #105: Pybind .............................................................................................. Passed 0.61 sec
Start 106: cabpump.mod
106/109 Test #106: cabpump.mod ......................................................................................... Passed 0.07 sec
Start 107: ican.mod
107/109 Test #107: ican.mod ............................................................................................ Passed 0.04 sec
Start 108: test_functor.mod
108/109 Test #108: test_functor.mod .................................................................................... Passed 0.04 sec
Start 109: watch_test.mod
109/109 Test #109: watch_test.mod ...................................................................................... Passed 0.05 sec
100% tests passed, 0 tests failed out of 109
Total Test time (real) = 80.82 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:1700583201:step_script section_start:1700583201:upload_artifacts_on_success Uploading artifacts for successful job
Using git from spack modules
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=273759 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=1029082 responseStatus=201 Created token=64_b_G5j
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=273775 revision=58ba2b95 version=14.2.0
ctest.xml: found 1 matching files and directories 
Uploading artifacts as "junit" to coordinator... ok id=1029082 responseStatus=201 Created token=64_b_G5j
section_end:1700583202:upload_artifacts_on_success section_start:1700583202:cleanup_file_variables Cleaning up project directory and file based variables
Using git from spack modules
section_end:1700583203:cleanup_file_variables Job succeeded
Raw
test-nvhpc.txt
Running with gitlab-runner 15.5.0 (0d4137b8)
 on BB5 map runner pnPo3yJy
section_start:1700583062:resolve_secrets Resolving secrets
section_end:1700583062:resolve_secrets section_start:1700583062: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-executor1727409773, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name nmodl
Pipeline ID 172206, build ref , job ID 1029083
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P172206, 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_J1029083_PROD_P30_CP1_C4
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 1904762
job state: PD
job state: PD
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=1 --mem=30750M --job-name=GL_J1029083_PROD_P30_CP1_C4 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P172206 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P172206 --ntasks=1 --jobid=1904762 --cpus-per-task=1 --mem=30750M
section_end:1700583066:prepare_executor section_start:1700583066:prepare_script Preparing environment
Using git from spack modules
Running on r1i7n31 via bbpv1.epfl.ch...
section_end:1700583070:prepare_script section_start:1700583070: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:1700583070:get_sources section_start:1700583070:download_artifacts Downloading artifacts
Using git from spack modules
Downloading artifacts for build:nvhpc (1029081)...
Runtime platform  arch=amd64 os=linux pid=48740 revision=58ba2b95 version=14.2.0
Downloading artifacts from coordinator... ok  id=1029081 responseStatus=200 OK token=64_W6cmx
section_end:1700583071:download_artifacts section_start:1700583071: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: r1i4n8
Build name: Linux-nvc++
Create new tag: 20231121-1611 - Experimental
Test project /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P172206/J1029081/spack-build/spack-stage-nmodl-develop-ig5xxxqcms4p7raynztlf4ikjbovtifr/spack-build-ig5xxxq
Start 1: testcodegen/Scenario: unusual / failing mod files
1/109 Test #1: testcodegen/Scenario: unusual / failing mod files ................................................... Passed 0.08 sec
Start 2: testcodegen/Scenario: Check global variable setup
2/109 Test #2: testcodegen/Scenario: Check global variable setup ................................................... Passed 0.04 sec
Start 3: testcodegen/Scenario: C codegen utility functions
3/109 Test #3: testcodegen/Scenario: C codegen utility functions ................................................... Passed 0.04 sec
Start 4: testcodegen/Scenario: Check instance variable definition order
4/109 Test #4: testcodegen/Scenario: Check instance variable definition order ...................................... Passed 0.04 sec
Start 5: testcodegen/Scenario: Check parameter constness with VERBATIM block
5/109 Test #5: testcodegen/Scenario: Check parameter constness with VERBATIM block ................................. Passed 0.04 sec
Start 6: testcodegen/Scenario: Check NEURON globals are added to the instance struct on demand
6/109 Test #6: testcodegen/Scenario: Check NEURON globals are added to the instance struct on demand ............... Passed 0.04 sec
Start 7: testcodegen/Scenario: Check code generation for TABLE statements
7/109 Test #7: testcodegen/Scenario: Check code generation for TABLE statements .................................... Passed 0.04 sec
Start 8: testcodegen/Scenario: Check that BEFORE/AFTER block are well generated
8/109 Test #8: testcodegen/Scenario: Check that BEFORE/AFTER block are well generated .............................. Passed 0.04 sec
Start 9: testcodegen/Scenario: Check CONSTANT variables are added to global variable structure
9/109 Test #9: testcodegen/Scenario: Check CONSTANT variables are added to global variable structure ............... Passed 0.04 sec
Start 10: testcodegen/Scenario: Check code generation for FUNCTION_TABLE block
10/109 Test #10: testcodegen/Scenario: Check code generation for FUNCTION_TABLE block ................................ Passed 0.04 sec
Start 11: testcodegen/Scenario: Check that loops are well generated
11/109 Test #11: testcodegen/Scenario: Check that loops are well generated ........................................... Passed 0.04 sec
Start 12: testcodegen/Scenario: Check that top verbatim blocks are well generated
12/109 Test #12: testcodegen/Scenario: Check that top verbatim blocks are well generated ............................. Passed 0.04 sec
Start 13: testcodegen/Scenario: Check that codegen generate event functions well
13/109 Test #13: testcodegen/Scenario: Check that codegen generate event functions well .............................. Passed 0.04 sec
Start 14: testcodegen/Scenario: Some tests on derivimplicit
14/109 Test #14: testcodegen/Scenario: Some tests on derivimplicit ................................................... Passed 0.04 sec
Start 15: testcodegen/Scenario: Some tests on euler solver
15/109 Test #15: testcodegen/Scenario: Some tests on euler solver .................................................... Passed 0.04 sec
Start 16: testcodegen/Scenario: Check codegen for MUTEX and PROTECT
16/109 Test #16: testcodegen/Scenario: Check codegen for MUTEX and PROTECT ........................................... Passed 0.04 sec
Start 17: testcodegen/Scenario: Array STATE variable
17/109 Test #17: testcodegen/Scenario: Array STATE variable .......................................................... Passed 0.04 sec
Start 18: testcodegen/Scenario: Adding a variable for a table inside a function
18/109 Test #18: testcodegen/Scenario: Adding a variable for a table inside a function ............................... Passed 0.04 sec
Start 19: testcodegen/Scenario: Uncompatible constructs should failed
19/109 Test #19: testcodegen/Scenario: Uncompatible constructs should failed ......................................... Passed 0.04 sec
Start 20: testmodtoken/NMODL Lexer returning valid ModToken object
20/109 Test #20: testmodtoken/NMODL Lexer returning valid ModToken object ............................................ Passed 0.01 sec
Start 21: testmodtoken/Addition of two ModToken objects
21/109 Test #21: testmodtoken/Addition of two ModToken objects ....................................................... Passed 0.01 sec
Start 22: testlexer/NMODL Lexer returning valid token types
22/109 Test #22: testlexer/NMODL Lexer returning valid token types ................................................... Passed 0.01 sec
Start 23: testparser/Scenario: NMODL can accept CR as return char for one line comment
23/109 Test #23: testparser/Scenario: NMODL can accept CR as return char for one line comment ........................ Passed 0.02 sec
Start 24: testparser/Scenario: NMODL can define macros using DEFINE keyword
24/109 Test #24: testparser/Scenario: NMODL can define macros using DEFINE keyword ................................... Passed 0.02 sec
Start 25: testparser/Scenario: Macros can be used anywhere in the mod file
25/109 Test #25: testparser/Scenario: Macros can be used anywhere in the mod file .................................... Passed 0.02 sec
Start 26: testparser/Scenario: NMODL parser accepts empty unit specification
26/109 Test #26: testparser/Scenario: NMODL parser accepts empty unit specification .................................. Passed 0.02 sec
Start 27: testparser/Scenario: NMODL parser running number of valid NMODL constructs
27/109 Test #27: testparser/Scenario: NMODL parser running number of valid NMODL constructs .......................... Passed 0.05 sec
Start 28: testparser/Scenario: NMODL parser running number of invalid NMODL constructs
28/109 Test #28: testparser/Scenario: NMODL parser running number of invalid NMODL constructs ........................ Passed 0.02 sec
Start 29: testparser/Scenario: Check that the parser doesn't crash when passing invalid INCLUDE constructs
29/109 Test #29: testparser/Scenario: Check that the parser doesn't crash when passing invalid INCLUDE constructs .... Passed 0.02 sec
Start 30: testparser/Scenario: NEURON block can add CURIE information
30/109 Test #30: testparser/Scenario: NEURON block can add CURIE information ......................................... Passed 0.02 sec
Start 31: testparser/Scenario: Check parents in valid NMODL constructs
31/109 Test #31: testparser/Scenario: Check parents in valid NMODL constructs ........................................ Passed 0.29 sec
Start 32: testparser/Scenario: Legacy differential equation solver
32/109 Test #32: testparser/Scenario: Legacy differential equation solver ............................................ Passed 0.02 sec
Start 33: testparser/Scenario: Check if a NEURON block is parsed with correct location info in its token
33/109 Test #33: testparser/Scenario: Check if a NEURON block is parsed with correct location info in its token ...... Passed 0.02 sec
Start 34: testvisitor/Scenario: AfterCVodeToCnexpVisitor changes after_cvode solver method to cnexp
34/109 Test #34: testvisitor/Scenario: AfterCVodeToCnexpVisitor changes after_cvode solver method to cnexp ........... Passed 0.06 sec
Start 35: testvisitor/Scenario: Perform constant folder on NMODL constructs
35/109 Test #35: testvisitor/Scenario: Perform constant folder on NMODL constructs ................................... Passed 0.04 sec
Start 36: testvisitor/Scenario: Perform DefUse analysis on NMODL constructs
36/109 Test #36: testvisitor/Scenario: Perform DefUse analysis on NMODL constructs ................................... Passed 0.05 sec
Start 37: testvisitor/Scenario: GLOBAL to RANGE variable transformer
37/109 Test #37: testvisitor/Scenario: GLOBAL to RANGE variable transformer .......................................... Passed 0.04 sec
Start 38: testvisitor/Scenario: Check insertion of implicit arguments
38/109 Test #38: testvisitor/Scenario: Check insertion of implicit arguments ......................................... Passed 0.04 sec
Start 39: testvisitor/Scenario: Inlining of external procedure calls
39/109 Test #39: testvisitor/Scenario: Inlining of external procedure calls .......................................... Passed 0.04 sec
Start 40: testvisitor/Scenario: Inlining of function call as argument in external function
40/109 Test #40: testvisitor/Scenario: Inlining of function call as argument in external function .................... Passed 0.04 sec
Start 41: testvisitor/Scenario: Inlining of simple, one level procedure call
41/109 Test #41: testvisitor/Scenario: Inlining of simple, one level procedure call .................................. Passed 0.04 sec
Start 42: testvisitor/Scenario: Inlining of nested procedure call
42/109 Test #42: testvisitor/Scenario: Inlining of nested procedure call ............................................. Passed 0.04 sec
Start 43: testvisitor/Scenario: Inline function call in procedure
43/109 Test #43: testvisitor/Scenario: Inline function call in procedure ............................................. Passed 0.04 sec
Start 44: testvisitor/Scenario: Inling function call within conditional statement
44/109 Test #44: testvisitor/Scenario: Inling function call within conditional statement ............................. Passed 0.04 sec
Start 45: testvisitor/Scenario: Inline multiple function calls in same statement
45/109 Test #45: testvisitor/Scenario: Inline multiple function calls in same statement .............................. Passed 0.04 sec
Start 46: testvisitor/Scenario: Inline nested function calls withing arguments
46/109 Test #46: testvisitor/Scenario: Inline nested function calls withing arguments ................................ Passed 0.04 sec
Start 47: testvisitor/Scenario: Inline function call in non-binary expression
47/109 Test #47: testvisitor/Scenario: Inline function call in non-binary expression ................................. Passed 0.04 sec
Start 48: testvisitor/Scenario: Inline function call as standalone expression
48/109 Test #48: testvisitor/Scenario: Inline function call as standalone expression ................................. Passed 0.04 sec
Start 49: testvisitor/Scenario: Inline procedure call as standalone statement as well as part of expression
49/109 Test #49: testvisitor/Scenario: Inline procedure call as standalone statement as well as part of expression ... Passed 0.04 sec
Start 50: testvisitor/Scenario: Inlining pass handles local-global name conflict
50/109 Test #50: testvisitor/Scenario: Inlining pass handles local-global name conflict .............................. Passed 0.04 sec
Start 51: testvisitor/Scenario: Trying to inline a function with VERBATIM block
51/109 Test #51: testvisitor/Scenario: Trying to inline a function with VERBATIM block ............................... Passed 0.04 sec
Start 52: testvisitor/Convert NMODL to AST to JSON form using JSONVisitor
52/109 Test #52: testvisitor/Convert NMODL to AST to JSON form using JSONVisitor ..................................... Passed 0.04 sec
Start 53: testvisitor/Scenario: Convert KINETIC to DERIVATIVE using KineticBlock visitor
53/109 Test #53: testvisitor/Scenario: Convert KINETIC to DERIVATIVE using KineticBlock visitor ...................... Passed 0.06 sec
Start 54: testvisitor/Scenario: Localizer test with single global block
54/109 Test #54: testvisitor/Scenario: Localizer test with single global block ....................................... Passed 0.04 sec
Start 55: testvisitor/Scenario: Localizer test with use of verbatim block
55/109 Test #55: testvisitor/Scenario: Localizer test with use of verbatim block ..................................... Passed 0.04 sec
Start 56: testvisitor/Scenario: Localizer test with multiple global blocks
56/109 Test #56: testvisitor/Scenario: Localizer test with multiple global blocks .................................... Passed 0.04 sec
Start 57: testvisitor/Scenario: LocalVarRenameVisitor works with InlineVisitor
57/109 Test #57: testvisitor/Scenario: LocalVarRenameVisitor works with InlineVisitor ................................ Passed 0.04 sec
Start 58: testvisitor/Scenario: LOCAL to ASSIGNED variable transformer
58/109 Test #58: testvisitor/Scenario: LOCAL to ASSIGNED variable transformer ........................................ Passed 0.04 sec
Start 59: testvisitor/Scenario: Searching for ast nodes using AstLookupVisitor
59/109 Test #59: testvisitor/Scenario: Searching for ast nodes using AstLookupVisitor ................................ Passed 0.04 sec
Start 60: testvisitor/Scenario: Perform loop unrolling of FROM construct
60/109 Test #60: testvisitor/Scenario: Perform loop unrolling of FROM construct ...................................... Passed 0.04 sec
Start 61: testvisitor/Scenario: Running visitor passes multiple times
61/109 Test #61: testvisitor/Scenario: Running visitor passes multiple times ......................................... Passed 0.04 sec
Start 62: testvisitor/Scenario: Sympy specific AST to NMODL conversion
62/109 Test #62: testvisitor/Scenario: Sympy specific AST to NMODL conversion ........................................ Passed 0.04 sec
Start 63: testvisitor/Scenario: NeuronSolveVisitor visitor solves different ODE types
63/109 Test #63: testvisitor/Scenario: NeuronSolveVisitor visitor solves different ODE types ......................... Passed 0.04 sec
Start 64: testvisitor/Scenario: Convert AST back to NMODL form
64/109 Test #64: testvisitor/Scenario: Convert AST back to NMODL form ................................................ Passed 0.13 sec
Start 65: testvisitor/Scenario: Symbol table generation with Perf stat visitor
65/109 Test #65: testvisitor/Scenario: Symbol table generation with Perf stat visitor ................................ Passed 0.04 sec
Start 66: testvisitor/Scenario: Renaming any variable in mod file with RenameVisitor
66/109 Test #66: testvisitor/Scenario: Renaming any variable in mod file with RenameVisitor .......................... Passed 0.04 sec
Start 67: testvisitor/Scenario: Renaming with presence of local and global variables in same block
67/109 Test #67: testvisitor/Scenario: Renaming with presence of local and global variables in same block ............ Passed 0.04 sec
Start 68: testvisitor/Scenario: Renaming in the absence of global blocks
68/109 Test #68: testvisitor/Scenario: Renaming in the absence of global blocks ...................................... Passed 0.04 sec
Start 69: testvisitor/Scenario: Variable renaming in nested blocks
69/109 Test #69: testvisitor/Scenario: Variable renaming in nested blocks ............................................ Passed 0.04 sec
Start 70: testvisitor/Scenario: Renaming in presence of local variable in verbatim block
70/109 Test #70: testvisitor/Scenario: Renaming in presence of local variable in verbatim block ...................... Passed 0.04 sec
Start 71: testvisitor/Scenario: TABLE stmt
71/109 Test #71: testvisitor/Scenario: TABLE stmt .................................................................... Passed 0.04 sec
Start 72: testvisitor/Scenario: Destructor block
72/109 Test #72: testvisitor/Scenario: Destructor block .............................................................. Passed 0.04 sec
Start 73: testvisitor/Scenario: Ion variable in CONSTANT block
73/109 Test #73: testvisitor/Scenario: Ion variable in CONSTANT block ................................................ Passed 0.04 sec
Start 74: testvisitor/Scenario: INDEPENDENT block
74/109 Test #74: testvisitor/Scenario: INDEPENDENT block ............................................................. Passed 0.04 sec
Start 75: testvisitor/Scenario: FUNCTION_TABLE block
75/109 Test #75: testvisitor/Scenario: FUNCTION_TABLE block .......................................................... Passed 0.04 sec
Start 76: testvisitor/Scenario: At most one DERIVATIVE block
76/109 Test #76: testvisitor/Scenario: At most one DERIVATIVE block .................................................. Passed 0.04 sec
Start 77: testvisitor/Solve ODEs using legacy NeuronSolveVisitor
77/109 Test #77: testvisitor/Solve ODEs using legacy NeuronSolveVisitor .............................................. Passed 0.04 sec
Start 78: testvisitor/Scenario: Solving ODEs with STEADYSTATE solve method
78/109 Test #78: testvisitor/Scenario: Solving ODEs with STEADYSTATE solve method .................................... Passed 0.04 sec
Start 79: testvisitor/Scenario: Addition of CONDUCTANCE using SympyConductance visitor
79/109 Test #79: testvisitor/Scenario: Addition of CONDUCTANCE using SympyConductance visitor ........................ Passed 55.36 sec
Start 80: testvisitor/Scenario: Check compare_blocks in sympy unit tests
80/109 Test #80: testvisitor/Scenario: Check compare_blocks in sympy unit tests ...................................... Passed 0.85 sec
Start 81: testvisitor/Scenario: Check local vars name-clash prevention
81/109 Test #81: testvisitor/Scenario: Check local vars name-clash prevention ........................................ Passed 1.00 sec
Start 82: testvisitor/Scenario: Solve ODEs with cnexp or euler method using SympySolverVisitor
82/109 Test #82: testvisitor/Scenario: Solve ODEs with cnexp or euler method using SympySolverVisitor ................ Passed 8.83 sec
Start 83: testvisitor/Scenario: Solve ODEs with derivimplicit method using SympySolverVisitor
83/109 Test #83: testvisitor/Scenario: Solve ODEs with derivimplicit method using SympySolverVisitor ................. Passed 2.66 sec
Start 84: testvisitor/Scenario: LINEAR solve block (SympySolver Visitor)
84/109 Test #84: testvisitor/Scenario: LINEAR solve block (SympySolver Visitor) ...................................... Passed 2.03 sec
Start 85: testvisitor/Scenario: Solve NONLINEAR block using SympySolver Visitor
85/109 Test #85: testvisitor/Scenario: Solve NONLINEAR block using SympySolver Visitor ............................... Passed 0.98 sec
Start 86: testvisitor/Scenario: Solve KINETIC block using SympySolver Visitor
86/109 Test #86: testvisitor/Scenario: Solve KINETIC block using SympySolver Visitor ................................. Passed 1.11 sec
Start 87: testvisitor/Scenario: Code generation for EigenNewtonSolver
87/109 Test #87: testvisitor/Scenario: Code generation for EigenNewtonSolver ......................................... Passed 1.05 sec
Start 88: testvisitor/Scenario: Parse UNITS block of mod files using Units Visitor
88/109 Test #88: testvisitor/Scenario: Parse UNITS block of mod files using Units Visitor ............................ Passed 0.05 sec
Start 89: testvisitor/Scenario: Searching for variable name using VarUsageVisitor
89/109 Test #89: testvisitor/Scenario: Searching for variable name using VarUsageVisitor ............................. Passed 0.04 sec
Start 90: testvisitor/Parse VERBATIM block using Verbatim Visitor
90/109 Test #90: testvisitor/Parse VERBATIM block using Verbatim Visitor ............................................. Passed 0.04 sec
Start 91: testvisitor/Scenario: Get node name with index TestVisitor
91/109 Test #91: testvisitor/Scenario: Get node name with index TestVisitor .......................................... Passed 0.04 sec
Start 92: testprinter/JSON printer converting object to string form
92/109 Test #92: testprinter/JSON printer converting object to string form ........................................... Passed 0.01 sec
Start 93: testsymtab/Scenario: Symbol properties can be added and converted to string
93/109 Test #93: testsymtab/Scenario: Symbol properties can be added and converted to string ......................... Passed 0.01 sec
Start 94: testsymtab/Scenario: Multiple properties can be added to Symbol
94/109 Test #94: testsymtab/Scenario: Multiple properties can be added to Symbol ..................................... Passed 0.01 sec
Start 95: testsymtab/Scenario: Symbol table allows operations like insert, lookup
95/109 Test #95: testsymtab/Scenario: Symbol table allows operations like insert, lookup ............................. Passed 0.01 sec
Start 96: testsymtab/Scenario: Global symbol table (ModelSymbol) allows scope based operations
96/109 Test #96: testsymtab/Scenario: Global symbol table (ModelSymbol) allows scope based operations ................ Passed 0.01 sec
Start 97: testsymtab/Scenario: Symbol class allows manipulation
97/109 Test #97: testsymtab/Scenario: Symbol class allows manipulation ............................................... Passed 0.01 sec
Start 98: testnewton/Scenario: Non-linear system to solve with Newton Numerical Diff Solver
98/109 Test #98: testnewton/Scenario: Non-linear system to solve with Newton Numerical Diff Solver ................... Passed 0.01 sec
Start 99: testnewton/Scenario: Non-linear system to solve with Newton Solver
99/109 Test #99: testnewton/Scenario: Non-linear system to solve with Newton Solver .................................. Passed 0.01 sec
Start 100: testcrout/Scenario: Compare Crout solver with Eigen
100/109 Test #100: testcrout/Scenario: Compare Crout solver with Eigen ................................................. Passed 0.29 sec
Start 101: testunitlexer/Unit Lexer tests for valid tokens
101/109 Test #101: testunitlexer/Unit Lexer tests for valid tokens ..................................................... Passed 0.01 sec
Start 102: testunitparser/Scenario: Unit parser accepting valid units definition
102/109 Test #102: testunitparser/Scenario: Unit parser accepting valid units definition ............................... Passed 0.02 sec
Start 103: testunitparser/Scenario: Unit parser accepting dependent/nested units definition
103/109 Test #103: testunitparser/Scenario: Unit parser accepting dependent/nested units definition .................... Passed 0.01 sec
Start 104: Ode
104/109 Test #104: Ode ................................................................................................. Passed 2.30 sec
Start 105: Pybind
105/109 Test #105: Pybind .............................................................................................. Passed 0.63 sec
Start 106: cabpump.mod
106/109 Test #106: cabpump.mod ......................................................................................... Passed 0.07 sec
Start 107: ican.mod
107/109 Test #107: ican.mod ............................................................................................ Passed 0.05 sec
Start 108: test_functor.mod
108/109 Test #108: test_functor.mod .................................................................................... Passed 0.07 sec
Start 109: watch_test.mod
109/109 Test #109: watch_test.mod ...................................................................................... Passed 0.05 sec
100% tests passed, 0 tests failed out of 109
Total Test time (real) = 81.13 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:1700583201:step_script section_start:1700583201:upload_artifacts_on_success Uploading artifacts for successful job
Using git from spack modules
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=49645 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=1029083 responseStatus=201 Created token=64_W6cmx
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=49659 revision=58ba2b95 version=14.2.0
ctest.xml: found 1 matching files and directories 
Uploading artifacts as "junit" to coordinator... ok id=1029083 responseStatus=201 Created token=64_W6cmx
section_end:1700583202:upload_artifacts_on_success section_start:1700583202:cleanup_file_variables Cleaning up project directory and file based variables
Using git from spack modules
section_end:1700583203:cleanup_file_variables Job succeeded
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