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October 2, 2024 11:32
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Logfiles for GitLab pipeline https://bbpgitlab.epfl.ch/hpc/sim/neurodamus/-/pipelines/234614 (:no_entry:) running on GitHub PR BlueBrain/neurodamus#198.
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| [0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1727866693:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1727866693:resolve_secrets [0Ksection_start:1727866693:prepare_executor [0K[0K[36;1mPreparing the "custom" executor[0;m[0;m | |
| [0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m | |
| 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-executor3485099017, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 234614, build ref , job ID 1453485 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1453485, 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_J1453485_PROD_P2354_CP0_C1 | |
| Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcsim 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 2557982 | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1453485_PROD_P2354_CP0_C1 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1453485 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1453485 --ntasks=1 --jobid=2557982 --cpus-per-task=6 --mem=30750M | |
| section_end:1727866694:prepare_executor [0Ksection_start:1727866694:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i6n14 via bbpv1.epfl.ch... | |
| section_end:1727866697:prepare_script [0Ksection_start:1727866697:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
| Using git from spack modules | |
| [32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m | |
| [32;1mFetching changes with git depth set to 100...[0;m | |
| Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453485/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out 5f3fdcfc as leite/fix-iterate-conns-intersect...[0;m | |
| Skipping object checkout, Git LFS is not installed. | |
| [32;1mUpdating/initializing submodules recursively with git depth set to 100...[0;m | |
| section_end:1727866701:get_sources [0Ksection_start:1727866701:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
| [0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m | |
| Using git from spack modules | |
| [32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m | |
| [32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m | |
| [32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m | |
| [32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m | |
| [32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m | |
| [32;1m$ module purge[0;m | |
| [32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m | |
| [32;1m$ module load unstable python/3.12.0[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.12.0 | |
| [32;1m$ module load unstable python/3.8.18[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.8.18 | |
| [32;1m$ module load unstable python/3.9.18[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.9.18 | |
| [32;1m$ module load unstable python/3.10.13[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.10.13 | |
| [32;1m$ module load unstable python/3.11.6[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.11.6 | |
| [32;1m$ load-modules() { # collapsed multi-line command[0;m | |
| [32;1m$ load-modules $SYSTEM_MODULES[0;m | |
| Loaded module git from unstable | |
| Loaded module cmake from unstable | |
| Loaded module graphviz from unstable | |
| [32;1m$ load-modules $EXTRA_MODULES[0;m | |
| [32;1m$ module list -t[0;m | |
| Currently Loaded Modulefiles: | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.12.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.8.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.9.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.10.13 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.11.6 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/git/2.42.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/cmake/3.27.7 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/graphviz/8.0.5 | |
| [32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
| [32;1m$ print_var XDG_CONFIG_HOME[0;m | |
| [36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453485/hpc/sim/neurodamus/local_config[0m | |
| [32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m | |
| [32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m | |
| [32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
| [url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
| insteadOf = https://bbpgitlab.epfl.ch/ | |
| insteadOf = ssh://git@bbpgitlab.epfl.ch/ | |
| insteadOf = git@bbpgitlab.epfl.ch: | |
| [32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m | |
| [0Ksection_start:1727866721:section_venv[collapsed=true] [0KSetting up the virtual env | |
| [32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
| [32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
| [32;1m$ rm -rf "$CI_VENV"[0;m | |
| [32;1m$ python -mvenv "$CI_VENV"[0;m | |
| [32;1m$ source "$CI_VENV/bin/activate"[0;m | |
| [32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Requirement already satisfied: pip in ./venv/lib/python3.11/site-packages (23.2.1) | |
| Collecting pip | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2cd/581cf58ab7fcf/pip-24.2-py3-none-any.whl (1.8 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.8/1.8 MB 66.5 MB/s eta 0:00:00 | |
| Requirement already satisfied: setuptools in ./venv/lib/python3.11/site-packages (65.5.0) | |
| Collecting setuptools | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/35a/b7fd3bcd95e6b/setuptools-75.1.0-py3-none-any.whl (1.2 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.2/1.2 MB 216.2 MB/s eta 0:00:00 | |
| Collecting wheel | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/237/6a90c98cc337d/wheel-0.44.0-py3-none-any.whl (67 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 67.1/67.1 kB 227.0 MB/s eta 0:00:00 | |
| Installing collected packages: wheel, setuptools, pip | |
| Attempting uninstall: setuptools | |
| Found existing installation: setuptools 65.5.0 | |
| Uninstalling setuptools-65.5.0: | |
| Successfully uninstalled setuptools-65.5.0 | |
| Attempting uninstall: pip | |
| Found existing installation: pip 23.2.1 | |
| Uninstalling pip-23.2.1: | |
| Successfully uninstalled pip-23.2.1 | |
| Successfully installed pip-24.2 setuptools-75.1.0 wheel-0.44.0 | |
| [32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Collecting tox | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/693/ac51378255d34/tox-4.21.0-py3-none-any.whl (165 kB) | |
| Collecting cachetools>=5.5 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/021/34e8439cdc2ff/cachetools-5.5.0-py3-none-any.whl (9.5 kB) | |
| Collecting chardet>=5.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB) | |
| Collecting colorama>=0.4.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB) | |
| Collecting filelock>=3.16.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/208/2e5703d51fbf9/filelock-3.16.1-py3-none-any.whl (16 kB) | |
| Collecting packaging>=24.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/5b8/f2217dbdbd2f7/packaging-24.1-py3-none-any.whl (53 kB) | |
| Collecting platformdirs>=4.3.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/73e/575e1408ab810/platformdirs-4.3.6-py3-none-any.whl (18 kB) | |
| Collecting pluggy>=1.5 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/44e/1ad92c8ca002d/pluggy-1.5.0-py3-none-any.whl (20 kB) | |
| Collecting pyproject-api>=1.8 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/3d7/d347a047afe79/pyproject_api-1.8.0-py3-none-any.whl (13 kB) | |
| Collecting virtualenv>=20.26.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/734/5cc5b25405607/virtualenv-20.26.6-py3-none-any.whl (6.0 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 6.0/6.0 MB 237.4 MB/s eta 0:00:00 | |
| Collecting distlib<1,>=0.3.7 (from virtualenv>=20.26.6->tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/034/db59a0b96f8ca/distlib-0.3.8-py2.py3-none-any.whl (468 kB) | |
| Installing collected packages: distlib, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
| Successfully installed cachetools-5.5.0 chardet-5.2.0 colorama-0.4.6 distlib-0.3.8 filelock-3.16.1 packaging-24.1 platformdirs-4.3.6 pluggy-1.5.0 pyproject-api-1.8.0 tox-4.21.0 virtualenv-20.26.6 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1727866739:section_venv [0K | |
| [32;1m$ print_var PRE_BUILD_COMMAND[0;m | |
| [36mPRE_BUILD_COMMAND=[0m | |
| [32;1m$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi[0;m | |
| [32;1m$ section_start section_tox "Running Tox"[0;m | |
| [0Ksection_start:1727866739:section_tox [0KRunning Tox | |
| [32;1m$ python -mtox $TOX_OPTIONS[0;m | |
| docs: install_deps> python -I -m pip install sphinx-bluebrain-theme 'sphinx<5.1.0' | |
| .pkg: install_requires> python -I -m pip install hatch-vcs hatchling | |
| .pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453485/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| .pkg: get_requires_for_build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453485/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| .pkg: freeze> python -m pip freeze --all | |
| .pkg: hatch-vcs==0.4.0,hatchling==1.25.0,packaging==24.1,pathspec==0.12.1,pip==24.2,pluggy==1.5.0,setuptools==75.1.0,setuptools-scm==8.1.0,trove-classifiers==2024.9.12,wheel==0.44.0 | |
| .pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453485/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| docs: install_package_deps> python -I -m pip install docopt h5py libsonata psutil | |
| docs: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453485/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.6.1.dev7.tar.gz | |
| docs: freeze> python -m pip freeze --all | |
| docs: alabaster==0.7.16,babel==2.16.0,certifi==2024.8.30,charset-normalizer==3.3.2,docopt==0.6.2,docutils==0.18.1,h5py==3.12.1,idna==3.10,imagesize==1.4.1,Jinja2==3.1.4,libsonata==0.1.28,MarkupSafe==2.1.5,neurodamus @ file:///gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453485/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.6.1.dev7.tar.gz#sha256=99c562df7bb7e9093d77d4e15af7afbba51a11b943125f4464240d5227ad3869,numpy==2.1.1,packaging==24.1,pip==24.2,psutil==6.0.0,Pygments==2.18.0,requests==2.32.3,setuptools==75.1.0,snowballstemmer==2.2.0,Sphinx==5.0.2,sphinx-bluebrain-theme==0.4.4,sphinxcontrib-applehelp==2.0.0,sphinxcontrib-devhelp==2.0.0,sphinxcontrib-htmlhelp==2.1.0,sphinxcontrib-jsmath==1.0.1,sphinxcontrib-qthelp==2.0.0,sphinxcontrib-serializinghtml==2.0.0,urllib3==2.2.3,wheel==0.44.0 | |
| docs: commands[0]> sphinx-build -T -W docs docs/_build | |
| Running Sphinx v5.0.2 | |
| making output directory... done | |
| building [mo]: targets for 0 po files that are out of date | |
| building [html]: targets for 18 source files that are out of date | |
| updating environment: [new config] 18 added, 0 changed, 0 removed | |
| reading sources... [ 5%] api/modules | |
| reading sources... [ 11%] api/neurodamus | |
| reading sources... [ 16%] api/neurodamus.core | |
| reading sources... [ 22%] api/neurodamus.io | |
| reading sources... [ 27%] api/neurodamus.utils | |
| reading sources... [ 33%] api/subpackages/core | |
| reading sources... [ 38%] api/subpackages/io | |
| reading sources... [ 44%] api/subpackages/top | |
| reading sources... [ 50%] api/subpackages/utils | |
| reading sources... [ 55%] architecture | |
| reading sources... [ 61%] changes | |
| reading sources... [ 66%] development | |
| reading sources... [ 72%] examples | |
| reading sources... [ 77%] index | |
| reading sources... [ 83%] online-lfp | |
| reading sources... [ 88%] overview | |
| reading sources... [ 94%] sonata-faq | |
| reading sources... [100%] sonata-simulation | |
| looking for now-outdated files... none found | |
| pickling environment... done | |
| checking consistency... done | |
| preparing documents... done | |
| writing output... [ 5%] api/modules | |
| writing output... [ 11%] api/neurodamus | |
| writing output... [ 16%] api/neurodamus.core | |
| writing output... [ 22%] api/neurodamus.io | |
| writing output... [ 27%] api/neurodamus.utils | |
| writing output... [ 33%] api/subpackages/core | |
| writing output... [ 38%] api/subpackages/io | |
| writing output... [ 44%] api/subpackages/top | |
| writing output... [ 50%] api/subpackages/utils | |
| writing output... [ 55%] architecture | |
| writing output... [ 61%] changes | |
| writing output... [ 66%] development | |
| writing output... [ 72%] examples | |
| writing output... [ 77%] index | |
| writing output... [ 83%] online-lfp | |
| writing output... [ 88%] overview | |
| writing output... [ 94%] sonata-faq | |
| writing output... [100%] sonata-simulation | |
| generating indices... genindex py-modindex done | |
| writing additional pages... search done | |
| copying images... [ 10%] img/neurodamus-prev-concept.png | |
| copying images... [ 20%] img/neurodamus-prev-arch.png | |
| copying images... [ 30%] img/neurodamus-arch.png | |
| copying images... [ 40%] img/cell-hierarchy.png | |
| copying images... [ 50%] img/multi-population-concept.png | |
| copying images... [ 60%] img/cell-managers.png | |
| copying images... [ 70%] img/conn-managers.png | |
| copying images... [ 80%] img/neurodamus_dry_run.png | |
| copying images... [ 90%] img/neurodamus_banner_230701.png | |
| copying images... [100%] img/sonata.png | |
| copying static files... done | |
| copying extra files... done | |
| dumping search index in English (code: en)... done | |
| dumping object inventory... done | |
| build succeeded. | |
| The HTML pages are in docs/_build. | |
| .pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453485/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| docs: OK (59.34=setup[50.07]+cmd[9.27] seconds) | |
| congratulations :) (59.53 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1727866799:section_tox [0K | |
| section_end:1727866799:step_script [0Ksection_start:1727866799:upload_artifacts_on_success [0K[0K[36;1mUploading artifacts for successful job[0;m[0;m | |
| Using git from spack modules | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=134001 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| docs/_build: found 197 matching files and directories[0;m | |
| Uploading artifacts as "archive" to coordinator... ok[0;m id[0;m=1453485 responseStatus[0;m=201 Created token[0;m=glcbt-64 | |
| section_end:1727866801:upload_artifacts_on_success [0Ksection_start:1727866801:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| Using git from spack modules | |
| section_end:1727866802:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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| ! |
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| Log was not fetched because job had status: skipped |
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| Log was not fetched because job had status: skipped |
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| [0KRunning with gitlab-runner 16.11.1 (535ced5f)[0;m | |
| [0K on kubernetes xwY3Anqz, system ID: r_j5AS6h5XNfdt[0;m | |
| [0K[36;1mResolving secrets[0;m[0;m | |
| section_start:1727866695:prepare_executor [0K[0K[36;1mPreparing the "kubernetes" executor[0;m[0;m | |
| [0KUsing Kubernetes namespace: gitlab-runners[0;m | |
| [0KUsing Kubernetes executor with image quay.io/pypa/manylinux2014_x86_64 ...[0;m | |
| [0KUsing attach strategy to execute scripts...[0;m | |
| section_end:1727866695:prepare_executor [0Ksection_start:1727866695:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| [0KUsing FF_USE_POD_ACTIVE_DEADLINE_SECONDS, the Pod activeDeadlineSeconds will be set to the job timeout: 1h0m0s...[0;m | |
| Waiting for pod gitlab-runners/runner-xwy3anqz-project-2354-concurrent-0-bi4tqevr to be running, status is Pending | |
| Running on runner-xwy3anqz-project-2354-concurrent-0-bi4tqevr via cs-gitlab-runners-gitlab-runner-c4db7d7cd-g7hlg... | |
| section_end:1727866701:prepare_script [0Ksection_start:1727866701:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
| [32;1mFetching changes with git depth set to 100...[0;m | |
| Initialized empty Git repository in /builds/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out 5f3fdcfc as detached HEAD (ref is leite/fix-iterate-conns-intersect)...[0;m | |
| [32;1mUpdating/initializing submodules recursively with git depth set to 100...[0;m | |
| [32;1mUpdated submodules[0;m | |
| section_end:1727866708:get_sources [0Ksection_start:1727866708:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
| [32;1m$ grep '^[[:alnum:]_]*_BRANCH=' <<< "$CI_COMMIT_MESSAGE" > branch_variables.env || touch branch_variables.env[0;m | |
| [32;1m$ . branch_variables.env[0;m | |
| [32;1m$ echo "BLUECONFIGS_PIPELINE_BRANCH=$BLUECONFIGS_BRANCH" >> branch_variables.env[0;m | |
| [32;1m$ cat branch_variables.env[0;m | |
| BLUECONFIGS_PIPELINE_BRANCH=main | |
| section_end:1727866708:step_script [0Ksection_start:1727866708:upload_artifacts_on_success [0K[0K[36;1mUploading artifacts for successful job[0;m[0;m | |
| [32;1mUploading artifacts...[0;m | |
| branch_variables.env: found 1 matching artifact files and directories[0;m | |
| Uploading artifacts as "dotenv" to coordinator... 201 Created[0;m id[0;m=1453491 responseStatus[0;m=201 Created token[0;m=glcbt-64 | |
| section_end:1727866710:upload_artifacts_on_success [0Ksection_start:1727866710:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| section_end:1727866711:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| [0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1727866695:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1727866695:resolve_secrets [0Ksection_start:1727866695:prepare_executor [0K[0K[36;1mPreparing the "custom" executor[0;m[0;m | |
| [0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m | |
| 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-executor2976607881, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 234614, build ref , job ID 1453488 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1453488, 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_J1453488_PROD_P2354_CP4_C5 | |
| Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcsim 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 2557985 | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1453488_PROD_P2354_CP4_C5 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1453488 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1453488 --ntasks=1 --jobid=2557985 --cpus-per-task=6 --mem=30750M | |
| section_end:1727866697:prepare_executor [0Ksection_start:1727866697:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i6n14 via bbpv1.epfl.ch... | |
| section_end:1727866698:prepare_script [0Ksection_start:1727866698:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
| Using git from spack modules | |
| [32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m | |
| [32;1mFetching changes with git depth set to 100...[0;m | |
| Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453488/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out 5f3fdcfc as leite/fix-iterate-conns-intersect...[0;m | |
| Skipping object checkout, Git LFS is not installed. | |
| [32;1mUpdating/initializing submodules recursively with git depth set to 100...[0;m | |
| section_end:1727866703:get_sources [0Ksection_start:1727866703:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
| [0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m | |
| Using git from spack modules | |
| [32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m | |
| [32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m | |
| [32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m | |
| [32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m | |
| [32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m | |
| [32;1m$ module purge[0;m | |
| [32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m | |
| [32;1m$ module load unstable python/3.12.0[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.12.0 | |
| [32;1m$ module load unstable python/3.8.18[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.8.18 | |
| [32;1m$ module load unstable python/3.9.18[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.9.18 | |
| [32;1m$ module load unstable python/3.10.13[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.10.13 | |
| [32;1m$ module load unstable python/3.11.6[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.11.6 | |
| [32;1m$ load-modules() { # collapsed multi-line command[0;m | |
| [32;1m$ load-modules $SYSTEM_MODULES[0;m | |
| Loaded module git from unstable | |
| Loaded module cmake from unstable | |
| Loaded module graphviz from unstable | |
| [32;1m$ load-modules $EXTRA_MODULES[0;m | |
| Loaded module neurodamus-neocortex from unstable | |
| [32;1m$ module list -t[0;m | |
| Currently Loaded Modulefiles: | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.12.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.8.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.9.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.10.13 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.11.6 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/git/2.42.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/cmake/3.27.7 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/graphviz/8.0.5 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/intel-oneapi-mkl/2023.2.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/hpe-mpi/2.27.p1.hmpt | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/applications/linux-rhel7-skylake/neurodamus-neocortex/2.4.1 | |
| [32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
| [32;1m$ print_var XDG_CONFIG_HOME[0;m | |
| [36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453488/hpc/sim/neurodamus/local_config[0m | |
| [32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m | |
| [32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m | |
| [32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
| [url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
| insteadOf = https://bbpgitlab.epfl.ch/ | |
| insteadOf = ssh://git@bbpgitlab.epfl.ch/ | |
| insteadOf = git@bbpgitlab.epfl.ch: | |
| [32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m | |
| [0Ksection_start:1727866724:section_venv[collapsed=true] [0KSetting up the virtual env | |
| [32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
| [32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
| [32;1m$ rm -rf "$CI_VENV"[0;m | |
| [32;1m$ python -mvenv "$CI_VENV"[0;m | |
| [32;1m$ source "$CI_VENV/bin/activate"[0;m | |
| [32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Requirement already satisfied: pip in ./venv/lib/python3.11/site-packages (23.2.1) | |
| Collecting pip | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2cd/581cf58ab7fcf/pip-24.2-py3-none-any.whl (1.8 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.8/1.8 MB 65.9 MB/s eta 0:00:00 | |
| Requirement already satisfied: setuptools in ./venv/lib/python3.11/site-packages (65.5.0) | |
| Collecting setuptools | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/35a/b7fd3bcd95e6b/setuptools-75.1.0-py3-none-any.whl (1.2 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.2/1.2 MB 254.5 MB/s eta 0:00:00 | |
| Collecting wheel | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/237/6a90c98cc337d/wheel-0.44.0-py3-none-any.whl (67 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 67.1/67.1 kB 217.8 MB/s eta 0:00:00 | |
| Installing collected packages: wheel, setuptools, pip | |
| Attempting uninstall: setuptools | |
| Found existing installation: setuptools 65.5.0 | |
| Uninstalling setuptools-65.5.0: | |
| Successfully uninstalled setuptools-65.5.0 | |
| Attempting uninstall: pip | |
| Found existing installation: pip 23.2.1 | |
| Uninstalling pip-23.2.1: | |
| Successfully uninstalled pip-23.2.1 | |
| Successfully installed pip-24.2 setuptools-75.1.0 wheel-0.44.0 | |
| [32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Collecting tox | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/693/ac51378255d34/tox-4.21.0-py3-none-any.whl (165 kB) | |
| Collecting cachetools>=5.5 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/021/34e8439cdc2ff/cachetools-5.5.0-py3-none-any.whl (9.5 kB) | |
| Collecting chardet>=5.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB) | |
| Collecting colorama>=0.4.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB) | |
| Collecting filelock>=3.16.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/208/2e5703d51fbf9/filelock-3.16.1-py3-none-any.whl (16 kB) | |
| Collecting packaging>=24.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/5b8/f2217dbdbd2f7/packaging-24.1-py3-none-any.whl (53 kB) | |
| Collecting platformdirs>=4.3.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/73e/575e1408ab810/platformdirs-4.3.6-py3-none-any.whl (18 kB) | |
| Collecting pluggy>=1.5 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/44e/1ad92c8ca002d/pluggy-1.5.0-py3-none-any.whl (20 kB) | |
| Collecting pyproject-api>=1.8 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/3d7/d347a047afe79/pyproject_api-1.8.0-py3-none-any.whl (13 kB) | |
| Collecting virtualenv>=20.26.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/734/5cc5b25405607/virtualenv-20.26.6-py3-none-any.whl (6.0 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 6.0/6.0 MB 173.6 MB/s eta 0:00:00 | |
| Collecting distlib<1,>=0.3.7 (from virtualenv>=20.26.6->tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/034/db59a0b96f8ca/distlib-0.3.8-py2.py3-none-any.whl (468 kB) | |
| Installing collected packages: distlib, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
| Attempting uninstall: packaging | |
| Found existing installation: packaging 23.1 | |
| Not uninstalling packaging at /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-packaging-23.1-uqml2t/lib/python3.11/site-packages, outside environment /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453488/hpc/sim/neurodamus/venv | |
| Can't uninstall 'packaging'. No files were found to uninstall. | |
| Successfully installed cachetools-5.5.0 chardet-5.2.0 colorama-0.4.6 distlib-0.3.8 filelock-3.16.1 packaging-24.1 platformdirs-4.3.6 pluggy-1.5.0 pyproject-api-1.8.0 tox-4.21.0 virtualenv-20.26.6 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1727866748:section_venv [0K | |
| [32;1m$ print_var PRE_BUILD_COMMAND[0;m | |
| [36mPRE_BUILD_COMMAND=[0m | |
| [32;1m$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi[0;m | |
| [32;1m$ section_start section_tox "Running Tox"[0;m | |
| [0Ksection_start:1727866748:section_tox [0KRunning Tox | |
| [32;1m$ python -mtox $TOX_OPTIONS[0;m | |
| bbp-model: install_deps> python -I -m pip install -r tests/requirements.txt | |
| .pkg: install_requires> python -I -m pip install hatch-vcs hatchling | |
| .pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453488/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| .pkg: get_requires_for_build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453488/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| .pkg: freeze> python -m pip freeze --all | |
| .pkg: hatch-vcs==0.4.0,hatchling==1.25.0,packaging==24.1,pathspec==0.12.1,pip==24.2,pluggy==1.5.0,setuptools==75.1.0,setuptools-scm==8.1.0,trove-classifiers==2024.9.12,wheel==0.44.0 | |
| .pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453488/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| bbp-model: install_package_deps> python -I -m pip install docopt h5py libsonata psutil | |
| bbp-model: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453488/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.6.1.dev7.tar.gz | |
| bbp-model: freeze> python -m pip freeze --all | |
| bbp-model: docopt @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-docopt-0.6.2-noukz4jts6de5g3xamvap6n4mh7mmcsy/spack-src,find-libpython @ file:///nvme/[MASKED]/2058794/spack-stage/spack-stage-py-find-libpython-0.3.1-5dylncaukuijf2r5t5lrj2s2y2kth2bh/spack-src,h5py @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-h5py-3.8.0-5woxna6nieu5jokc2tdxsfmolza6724e/spack-src,iniconfig==2.0.0,Jinja2 @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-jinja2-3.1.2-7validyciqteluvu43co5k7perpr2baq/spack-src,libsonata @ file:///nvme/[MASKED]/2371376/spack-stage/spack-stage-py-libsonata-0.1.28-jsuf4xxzlybtxiqfdwyqxyxf4c6svcva/spack-src,MarkupSafe @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-markupsafe-2.1.3-r3ehtmw6pkktralavqtazezwbkbsivnt/spack-src,MorphIO @ file:///nvme/[MASKED]/2246265/spack-stage/spack-stage-py-morphio-3.3.6-xap3flagvbfvuospv22jpkdw65c2ypln/spack-src,mpi4py @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-mpi4py-3.1.4-x733hwb2he3bpi423fnogkrw4w33wehe/spack-src,mpmath @ file:///nvme/[MASKED]/2246265/spack-stage/spack-stage-py-mpmath-1.2.1-4fflyibqfjfxrjhnx3jr7bhpt2tpcqn2/spack-src,neurodamus @ file:///nvme/[MASKED]/2379226/spack-stage/spack-stage-py-neurodamus-3.6.0-27enlnafey5xfe6ek7hhy7uozlbps45a/spack-src,numpy @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-numpy-1.26.1-elr5pntecdmhfynrjk3actlxb4go2bua/spack-src,packaging @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-packaging-23.1-uqml2togm4tkpdvzr37r5dnsrpnd76j2/spack-src,pip==24.2,pluggy==1.5.0,psutil @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-psutil-5.9.5-wieplgkaapfkhmzgrsesk5s3h46l3rx4/spack-src,py==1.11.0,pybind11 @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pybind11-2.11.0-7rjfjlzjfm5suub2ks5ttsby2mhqlcfl/spack-src,pytest==7.4.0,pytest-forked==1.6.0,PyYAML @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pyyaml-6.0-c3eqkahwrcjjvgo2irs4ocswyrgh2p64/spack-src,scipy @ file:///nvme/[MASKED]/2045970/spack-stage/spack-stage-py-scipy-1.11.3-dhxei7gha3wm6mobqp3urw6k4ovd7blx/spack-src,setuptools==75.1.0,sympy @ file:///nvme/[MASKED]/2246265/spack-stage/spack-stage-py-sympy-1.11.1-t5tovexvy2goo63j3w6dlqmcnv4yqrqd/spack-src,wheel==0.44.0 | |
| bbp-model: commands[0]> python -c 'import os; print(os.environ.get('"'"'HOC_LIBRARY_PATH'"'"', '"'"''"'"'))' | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453488/hpc/sim/neurodamus/core/hoc:/gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_oneapi-2023.2.0-skylake/neurodamus-models-2.4.1-kjfywd/share/neurodamus_neocortex/hoc | |
| bbp-model: commands[1]> pytest -s -x --forked --durations=5 --durations-min=15 tests/integration-e2e | |
| ============================= test session starts ============================== | |
| platform linux -- Python 3.11.6, pytest-7.4.0, pluggy-1.5.0 -- /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453488/hpc/sim/neurodamus/.tox/bbp-model/bin/python | |
| cachedir: .tox/bbp-model/.pytest_cache | |
| rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453488/hpc/sim/neurodamus | |
| configfile: pyproject.toml | |
| plugins: forked-1.6.0 | |
| collecting ... collected 29 items | |
| tests/integration-e2e/test_cli_opts.py::test_save_restore_cli PASSED | |
| tests/integration-e2e/test_cli_opts.py::test_cli_prcellgid PASSED | |
| tests/integration-e2e/test_cli_opts.py::test_cli_disable_reports PASSED | |
| tests/integration-e2e/test_cli_opts.py::test_cli_keep_build PASSED | |
| tests/integration-e2e/test_cli_opts.py::test_cli_build_model PASSED | |
| tests/integration-e2e/test_cli_opts.py::test_cli_shm_transfer PASSED | |
| tests/integration-e2e/test_cli_opts.py::test_cli_lb_mode PASSED | |
| tests/integration-e2e/test_cli_opts.py::test_cli_output_path PASSED | |
| tests/integration-e2e/test_connection.py::test_add_synapses PASSED | |
| tests/integration-e2e/test_connection.py::test_config_error PASSED | |
| tests/integration-e2e/test_coreneuron_directmode.py::test_coreneuron_no_write_model PASSED | |
| tests/integration-e2e/test_crashmode.py::test_crash_test_cell_loading PASSED | |
| tests/integration-e2e/test_dry_run_workflow.py::test_dry_run_workflow PASSED | |
| tests/integration-e2e/test_dry_run_workflow.py::test_memory_load_balance_workflow PASSED | |
| tests/integration-e2e/test_dry_run_workflow.py::test_dry_run_workflow_multi PASSED | |
| tests/integration-e2e/test_dry_run_workflow.py::test_dynamic_distribute PASSED | |
| tests/integration-e2e/test_error_handling.py::test_handling_neuron_exceptions PASSED | |
| tests/integration-e2e/test_loadbalance.py::test_loadbal_no_cx PASSED | |
| tests/integration-e2e/test_loadbalance.py::test_loadbal_subtarget PASSED | |
| tests/integration-e2e/test_loadbalance.py::test_load_balance_integrated PASSED | |
| tests/integration-e2e/test_loadbalance.py::test_multisplit PASSED | |
| tests/integration-e2e/test_loadbalance.py::test_loadbal_integration PASSED | |
| tests/integration-e2e/test_multicycle_runs.py::test_nodeset_target_generate_subtargets PASSED | |
| tests/integration-e2e/test_multicycle_runs.py::test_v5_sonata_multisteps PASSED | |
| tests/integration-e2e/test_multicycle_runs.py::test_usecase3_sonata_multisteps PASSED | |
| tests/integration-e2e/test_plugin.py::test_run_acell_circuit SKIPPED | |
| tests/integration-e2e/test_reports.py::test_report_config_error PASSED | |
| tests/integration-e2e/test_reports.py::test_report_disabled PASSED | |
| tests/integration-e2e/test_reports.py::test_v5_sonata_reports PASSED | |
| =============================== warnings summary =============================== | |
| neurodamus/core/configuration.py:162 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453488/hpc/sim/neurodamus/neurodamus/core/configuration.py:162: DeprecationWarning: In 3.13 classes created inside an enum will not become a member. Use the `member` decorator to keep the current behavior. | |
| class AutoBalanceModeParams: | |
| -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html | |
| ============================= slowest 5 durations ============================== | |
| 91.19s call tests/integration-e2e/test_crashmode.py::test_crash_test_cell_loading | |
| 35.13s call tests/integration-e2e/test_cli_opts.py::test_cli_lb_mode | |
| 28.73s call tests/integration-e2e/test_loadbalance.py::test_load_balance_integrated | |
| 28.39s call tests/integration-e2e/test_loadbalance.py::test_loadbal_integration | |
| 28.19s call tests/integration-e2e/test_loadbalance.py::test_multisplit | |
| ============= 28 passed, 1 skipped, 1 warning in 338.44s (0:05:38) ============= | |
| .pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453488/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| bbp-model: OK (379.46=setup[40.12]+cmd[0.07,339.27] seconds) | |
| congratulations :) (379.63 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1727867128:section_tox [0K | |
| section_end:1727867129:step_script [0Ksection_start:1727867129:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| Using git from spack modules | |
| section_end:1727867129:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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| [0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1727866695:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1727866695:resolve_secrets [0Ksection_start:1727866695:prepare_executor [0K[0K[36;1mPreparing the "custom" executor[0;m[0;m | |
| [0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m | |
| 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-executor3047576784, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 234614, build ref , job ID 1453487 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1453487, 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_J1453487_PROD_P2354_CP2_C4 | |
| Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcsim 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 2557984 | |
| job state: PD | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1453487_PROD_P2354_CP2_C4 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1453487 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1453487 --ntasks=1 --jobid=2557984 --cpus-per-task=6 --mem=30750M | |
| section_end:1727866697:prepare_executor [0Ksection_start:1727866697:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i6n14 via bbpv1.epfl.ch... | |
| section_end:1727866704:prepare_script [0Ksection_start:1727866704:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
| Using git from spack modules | |
| [32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m | |
| [32;1mFetching changes with git depth set to 100...[0;m | |
| Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out 5f3fdcfc as leite/fix-iterate-conns-intersect...[0;m | |
| Skipping object checkout, Git LFS is not installed. | |
| [32;1mUpdating/initializing submodules recursively with git depth set to 100...[0;m | |
| section_end:1727866708:get_sources [0Ksection_start:1727866708:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
| [0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m | |
| Using git from spack modules | |
| [32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m | |
| [32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m | |
| [32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m | |
| [32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m | |
| [32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m | |
| [32;1m$ module purge[0;m | |
| [32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m | |
| [32;1m$ module load unstable python/3.12.0[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.12.0 | |
| [32;1m$ module load unstable python/3.8.18[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.8.18 | |
| [32;1m$ module load unstable python/3.9.18[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.9.18 | |
| [32;1m$ module load unstable python/3.10.13[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.10.13 | |
| [32;1m$ module load unstable python/3.11.6[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.11.6 | |
| [32;1m$ load-modules() { # collapsed multi-line command[0;m | |
| [32;1m$ load-modules $SYSTEM_MODULES[0;m | |
| Loaded module git from unstable | |
| Loaded module cmake from unstable | |
| Loaded module graphviz from unstable | |
| [32;1m$ load-modules $EXTRA_MODULES[0;m | |
| [32;1m$ module list -t[0;m | |
| Currently Loaded Modulefiles: | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.12.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.8.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.9.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.10.13 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.11.6 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/git/2.42.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/cmake/3.27.7 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/graphviz/8.0.5 | |
| [32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
| [32;1m$ print_var XDG_CONFIG_HOME[0;m | |
| [36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/local_config[0m | |
| [32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m | |
| [32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m | |
| [32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
| [url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
| insteadOf = https://bbpgitlab.epfl.ch/ | |
| insteadOf = ssh://git@bbpgitlab.epfl.ch/ | |
| insteadOf = git@bbpgitlab.epfl.ch: | |
| [32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m | |
| [0Ksection_start:1727866727:section_venv[collapsed=true] [0KSetting up the virtual env | |
| [32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
| [32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
| [32;1m$ rm -rf "$CI_VENV"[0;m | |
| [32;1m$ python -mvenv "$CI_VENV"[0;m | |
| [32;1m$ source "$CI_VENV/bin/activate"[0;m | |
| [32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Requirement already satisfied: pip in ./venv/lib/python3.11/site-packages (23.2.1) | |
| Collecting pip | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2cd/581cf58ab7fcf/pip-24.2-py3-none-any.whl (1.8 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.8/1.8 MB 67.3 MB/s eta 0:00:00 | |
| Requirement already satisfied: setuptools in ./venv/lib/python3.11/site-packages (65.5.0) | |
| Collecting setuptools | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/35a/b7fd3bcd95e6b/setuptools-75.1.0-py3-none-any.whl (1.2 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.2/1.2 MB 250.6 MB/s eta 0:00:00 | |
| Collecting wheel | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/237/6a90c98cc337d/wheel-0.44.0-py3-none-any.whl (67 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 67.1/67.1 kB 218.8 MB/s eta 0:00:00 | |
| Installing collected packages: wheel, setuptools, pip | |
| Attempting uninstall: setuptools | |
| Found existing installation: setuptools 65.5.0 | |
| Uninstalling setuptools-65.5.0: | |
| Successfully uninstalled setuptools-65.5.0 | |
| Attempting uninstall: pip | |
| Found existing installation: pip 23.2.1 | |
| Uninstalling pip-23.2.1: | |
| Successfully uninstalled pip-23.2.1 | |
| Successfully installed pip-24.2 setuptools-75.1.0 wheel-0.44.0 | |
| [32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Collecting tox | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/693/ac51378255d34/tox-4.21.0-py3-none-any.whl (165 kB) | |
| Collecting cachetools>=5.5 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/021/34e8439cdc2ff/cachetools-5.5.0-py3-none-any.whl (9.5 kB) | |
| Collecting chardet>=5.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB) | |
| Collecting colorama>=0.4.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB) | |
| Collecting filelock>=3.16.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/208/2e5703d51fbf9/filelock-3.16.1-py3-none-any.whl (16 kB) | |
| Collecting packaging>=24.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/5b8/f2217dbdbd2f7/packaging-24.1-py3-none-any.whl (53 kB) | |
| Collecting platformdirs>=4.3.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/73e/575e1408ab810/platformdirs-4.3.6-py3-none-any.whl (18 kB) | |
| Collecting pluggy>=1.5 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/44e/1ad92c8ca002d/pluggy-1.5.0-py3-none-any.whl (20 kB) | |
| Collecting pyproject-api>=1.8 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/3d7/d347a047afe79/pyproject_api-1.8.0-py3-none-any.whl (13 kB) | |
| Collecting virtualenv>=20.26.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/734/5cc5b25405607/virtualenv-20.26.6-py3-none-any.whl (6.0 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 6.0/6.0 MB 202.2 MB/s eta 0:00:00 | |
| Collecting distlib<1,>=0.3.7 (from virtualenv>=20.26.6->tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/034/db59a0b96f8ca/distlib-0.3.8-py2.py3-none-any.whl (468 kB) | |
| Installing collected packages: distlib, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
| Successfully installed cachetools-5.5.0 chardet-5.2.0 colorama-0.4.6 distlib-0.3.8 filelock-3.16.1 packaging-24.1 platformdirs-4.3.6 pluggy-1.5.0 pyproject-api-1.8.0 tox-4.21.0 virtualenv-20.26.6 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1727866753:section_venv [0K | |
| [32;1m$ print_var PRE_BUILD_COMMAND[0;m | |
| [36mPRE_BUILD_COMMAND=[0m | |
| [32;1m$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi[0;m | |
| [32;1m$ section_start section_tox "Running Tox"[0;m | |
| [0Ksection_start:1727866753:section_tox [0KRunning Tox | |
| [32;1m$ python -mtox $TOX_OPTIONS[0;m | |
| integration: install_deps> python -I -m pip install morphio NEURON -r tests/requirements.txt | |
| .pkg: install_requires> python -I -m pip install hatch-vcs hatchling | |
| .pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| .pkg: get_requires_for_build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| .pkg: freeze> python -m pip freeze --all | |
| .pkg: hatch-vcs==0.4.0,hatchling==1.25.0,packaging==24.1,pathspec==0.12.1,pip==24.2,pluggy==1.5.0,setuptools==75.1.0,setuptools-scm==8.1.0,trove-classifiers==2024.9.12,wheel==0.44.0 | |
| .pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| integration: install_package_deps> python -I -m pip install docopt h5py libsonata psutil | |
| integration: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.6.1.dev7.tar.gz | |
| integration: freeze> python -m pip freeze --all | |
| integration: docopt==0.6.2,find_libpython==0.4.0,h5py==3.12.1,iniconfig==2.0.0,libsonata==0.1.28,morphio==3.3.9,neurodamus @ file:///gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.6.1.dev7.tar.gz#sha256=99c562df7bb7e9093d77d4e15af7afbba51a11b943125f4464240d5227ad3869,NEURON==8.2.6,numpy==1.26.4,packaging==24.1,pip==24.2,pluggy==1.5.0,psutil==6.0.0,py==1.11.0,pytest==7.4.0,pytest-forked==1.6.0,scipy==1.14.1,setuptools==75.1.0,wheel==0.44.0 | |
| integration: commands[0]> ci/build_ndcore.sh /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/neurodamus/data | |
| + CORE_DIR=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/neurodamus/data | |
| + '[' -d _lib ']' | |
| + COMMON_DIR=_common | |
| + '[' -d _common ']' | |
| + git clone git@bbpgitlab.epfl.ch:hpc/sim/models/common.git _common --depth=1 | |
| Cloning into '_common'... | |
| + MOD_BUILD_DIR=mods.tmp | |
| + mkdir -p mods.tmp | |
| + cp -f /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/neurodamus/data/mod/ALU.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/neurodamus/data/mod/CoreNEURONArtificialCell.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/neurodamus/data/mod/netstim_inhpoisson.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/neurodamus/data/mod/SonataReportHelper.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/neurodamus/data/mod/SonataReports.mod mods.tmp | |
| + cp -f _common/mod/DetAMPANMDA.mod _common/mod/DetGABAAB.mod _common/mod/gap.mod _common/mod/GluSynapse.mod _common/mod/netstim_inhpoisson.mod _common/mod/ProbAMPANMDA_EMS.mod _common/mod/ProbGABAAB_EMS.mod _common/mod/TTXDynamicsSwitch.mod _common/mod/VecStim.mod mods.tmp | |
| + nrnivmodl -incflags '-DDISABLE_REPORTINGLIB -DDISABLE_HDF5 -DDISABLE_MPI' mods.tmp | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/.tox/integration/bin/nrnivmodl:10: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html | |
| from pkg_resources import working_set | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus | |
| Mod files: "mods.tmp/mods.tmp/ALU.mod" "mods.tmp/mods.tmp/CoreNEURONArtificialCell.mod" "mods.tmp/mods.tmp/DetAMPANMDA.mod" "mods.tmp/mods.tmp/DetGABAAB.mod" "mods.tmp/mods.tmp/gap.mod" "mods.tmp/mods.tmp/GluSynapse.mod" "mods.tmp/mods.tmp/netstim_inhpoisson.mod" "mods.tmp/mods.tmp/ProbAMPANMDA_EMS.mod" "mods.tmp/mods.tmp/ProbGABAAB_EMS.mod" "mods.tmp/mods.tmp/SonataReportHelper.mod" "mods.tmp/mods.tmp/SonataReports.mod" "mods.tmp/mods.tmp/TTXDynamicsSwitch.mod" "mods.tmp/mods.tmp/VecStim.mod" | |
| Creating 'x86_64' directory for .o files. | |
| -> [32mCompiling[0m mod_func.cpp | |
| -> [32mNMODL[0m ../mods.tmp/CoreNEURONArtificialCell.mod | |
| -> [32mNMODL[0m ../mods.tmp/ALU.mod | |
| -> [32mNMODL[0m ../mods.tmp/DetAMPANMDA.mod | |
| Translating ALU.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/x86_64/ALU.c | |
| Thread Safe | |
| Translating CoreNEURONArtificialCell.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/x86_64/CoreNEURONArtificialCell.c | |
| Thread Safe | |
| Translating DetAMPANMDA.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/x86_64/DetAMPANMDA.c | |
| -> [32mNMODL[0m ../mods.tmp/DetGABAAB.mod | |
| Warning: next_delay_weight undefined. (declared within VERBATIM?) | |
| Warning: next_delay_t undefined. (declared within VERBATIM?) | |
| Thread Safe | |
| -> [32mNMODL[0m ../mods.tmp/gap.mod | |
| -> [32mNMODL[0m ../mods.tmp/GluSynapse.mod | |
| Translating DetGABAAB.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/x86_64/DetGABAAB.c | |
| Translating gap.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/x86_64/gap.c | |
| Warning: next_delay_weight undefined. (declared within VERBATIM?) | |
| Warning: next_delay_t undefined. (declared within VERBATIM?) | |
| Thread Safe | |
| Thread Safe | |
| -> [32mNMODL[0m ../mods.tmp/netstim_inhpoisson.mod | |
| -> [32mNMODL[0m ../mods.tmp/ProbAMPANMDA_EMS.mod | |
| Translating GluSynapse.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/x86_64/GluSynapse.c | |
| Translating netstim_inhpoisson.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/x86_64/netstim_inhpoisson.c | |
| Warning: POST_RESTORE_RESTART_FLAG undefined. (declared within VERBATIM?) | |
| Warning: next_delay_weight undefined. (declared within VERBATIM?) | |
| Warning: next_delay_t undefined. (declared within VERBATIM?) | |
| Thread Safe | |
| Notice: ARTIFICIAL_CELL is a synonym for POINT_PROCESS which hints that it | |
| only affects and is affected by discrete events. As such it is not | |
| located in a section and is not associated with an integrator | |
| Thread Safe | |
| -> [32mNMODL[0m ../mods.tmp/ProbGABAAB_EMS.mod | |
| Translating ProbAMPANMDA_EMS.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/x86_64/ProbAMPANMDA_EMS.c | |
| -> [32mNMODL[0m ../mods.tmp/SonataReportHelper.mod | |
| Notice: This mechanism cannot be used with CVODE | |
| Notice: A_AMPA discontinuity adjustment not available. | |
| Notice: B_AMPA discontinuity adjustment not available. | |
| Notice: A_NMDA discontinuity adjustment not available. | |
| Notice: B_NMDA discontinuity adjustment not available. | |
| Warning: dt undefined. (declared within VERBATIM?) | |
| Warning: next_delay_weight undefined. (declared within VERBATIM?) | |
| Warning: next_delay_t undefined. (declared within VERBATIM?) | |
| Thread Safe | |
| -> [32mNMODL[0m ../mods.tmp/SonataReports.mod | |
| Translating ProbGABAAB_EMS.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/x86_64/ProbGABAAB_EMS.c | |
| Translating SonataReportHelper.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/x86_64/SonataReportHelper.c | |
| Notice: This mechanism cannot be used with CVODE | |
| Notice: A_GABAA discontinuity adjustment not available. | |
| Notice: B_GABAA discontinuity adjustment not available. | |
| Notice: A_GABAB discontinuity adjustment not available. | |
| Notice: B_GABAB discontinuity adjustment not available. | |
| Warning: dt undefined. (declared within VERBATIM?) | |
| Warning: next_delay_weight undefined. (declared within VERBATIM?) | |
| Warning: next_delay_t undefined. (declared within VERBATIM?) | |
| Thread Safe | |
| Thread Safe | |
| -> [32mNMODL[0m ../mods.tmp/TTXDynamicsSwitch.mod | |
| -> [32mNMODL[0m ../mods.tmp/VecStim.mod | |
| Translating SonataReports.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/x86_64/SonataReports.c | |
| Thread Safe | |
| -> [32mCompiling[0m ALU.c | |
| Translating TTXDynamicsSwitch.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/x86_64/TTXDynamicsSwitch.c | |
| Thread Safe | |
| Translating VecStim.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/x86_64/VecStim.c | |
| Thread Safe | |
| -> [32mCompiling[0m CoreNEURONArtificialCell.c | |
| -> [32mCompiling[0m DetAMPANMDA.c | |
| -> [32mCompiling[0m DetGABAAB.c | |
| -> [32mCompiling[0m gap.c | |
| -> [32mCompiling[0m GluSynapse.c | |
| -> [32mCompiling[0m netstim_inhpoisson.c | |
| -> [32mCompiling[0m ProbAMPANMDA_EMS.c | |
| -> [32mCompiling[0m ProbGABAAB_EMS.c | |
| -> [32mCompiling[0m SonataReportHelper.c | |
| -> [32mCompiling[0m SonataReports.c | |
| -> [32mCompiling[0m TTXDynamicsSwitch.c | |
| -> [32mCompiling[0m VecStim.c | |
| => [32mLINKING[0m shared library ./libnrnmech.so | |
| => [32mLINKING[0m executable ./special LDFLAGS are: -pthread | |
| Successfully created x86_64/special | |
| + '[' '!' -f x86_64/special ']' | |
| + mkdir -p _lib | |
| + cp -f x86_64/libnrnmech.so _lib/ | |
| + cp -f /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/neurodamus/data/hoc/Cell.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/neurodamus/data/hoc/ConnectionUtils.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/neurodamus/data/hoc/defvar.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/neurodamus/data/hoc/fileUtils.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/neurodamus/data/hoc/Map.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/neurodamus/data/hoc/MorphIO.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/neurodamus/data/hoc/neurodamus.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/neurodamus/data/hoc/RNGSettings.hoc _lib/ | |
| + cp -f _common/hoc/AMPANMDAHelper.hoc _common/hoc/DetAMPANMDAHelper.hoc _common/hoc/DetGABAABHelper.hoc _common/hoc/GABAABHelper.hoc _common/hoc/GluSynapseHelper.hoc _common/hoc/GluSynapseLegacyHelper.hoc _lib/ | |
| + echo /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/neurodamus/data | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/neurodamus/data | |
| + ls -l | |
| total 80 | |
| -rw-rw----+ 1 bbpcihpcsim bbp 578 Oct 2 12:58 authors.txt | |
| drwxrwx---+ 3 bbpcihpcsim bbp 4096 Oct 2 12:58 _benchmarks | |
| -rw-rw----+ 1 bbpcihpcsim bbp 29097 Oct 2 12:58 CHANGES.rst | |
| drwxrwx---+ 2 bbpcihpcsim bbp 4096 Oct 2 12:58 ci | |
| drwxrwx---+ 7 bbpcihpcsim bbp 4096 Oct 2 12:59 _common | |
| -rw-rw----+ 1 bbpcihpcsim bbp 6240 Oct 2 12:58 CONTRIBUTING.md | |
| drwxrwx---+ 2 bbpcihpcsim bbp 4096 Oct 2 12:58 docker | |
| drwxrwx---+ 5 bbpcihpcsim bbp 4096 Oct 2 12:58 docs | |
| drwxrwx---+ 2 bbpcihpcsim bbp 4096 Oct 2 12:58 examples | |
| drwxrwx---+ 2 bbpcihpcsim bbp 4096 Oct 2 12:59 _lib | |
| -rw-rw----+ 1 bbpcihpcsim bbp 11358 Oct 2 12:58 LICENSE.txt | |
| drwxrwx---+ 3 bbpcihpcsim bbp 4096 Oct 2 12:58 local_config | |
| drwxrwx---+ 2 bbpcihpcsim bbp 4096 Oct 2 12:59 mods.tmp | |
| drwxrwx---+ 6 bbpcihpcsim bbp 4096 Oct 2 12:58 neurodamus | |
| -rw-rw----+ 1 bbpcihpcsim bbp 1355 Oct 2 12:58 pyproject.toml | |
| -rw-rw----+ 1 bbpcihpcsim bbp 4598 Oct 2 12:58 README.rst | |
| + ls -l _lib | |
| -rw-rw----+ 1 bbpcihpcsim bbp 52 Oct 2 12:58 requirements_docs.txt | |
| -rw-rw----+ 1 bbpcihpcsim bbp 37 Oct 2 12:58 requirements.txt | |
| drwxrwx---+ 10 bbpcihpcsim bbp 4096 Oct 2 12:58 tests | |
| -rw-rw----+ 1 bbpcihpcsim bbp 1422 Oct 2 12:58 tox.ini | |
| drwxrwx---+ 5 bbpcihpcsim bbp 4096 Oct 2 12:58 venv | |
| drwxrwx---+ 3 bbpcihpcsim bbp 4096 Oct 2 12:59 x86_64 | |
| total 6 | |
| -rw-rw----+ 1 bbpcihpcsim bbp 2470 Oct 2 12:59 AMPANMDAHelper.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 15774 Oct 2 12:59 Cell.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 1064 Oct 2 12:59 ConnectionUtils.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 998 Oct 2 12:59 defvar.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 1173 Oct 2 12:59 DetAMPANMDAHelper.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 1636 Oct 2 12:59 DetGABAABHelper.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 1971 Oct 2 12:59 fileUtils.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 3294 Oct 2 12:59 GABAABHelper.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 3736 Oct 2 12:59 GluSynapseHelper.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 4633 Oct 2 12:59 GluSynapseLegacyHelper.hoc | |
| -rwxrwx---+ 1 bbpcihpcsim bbp 274824 Oct 2 12:59 libnrnmech.so | |
| -rw-rw----+ 1 bbpcihpcsim bbp 10723 Oct 2 12:59 Map.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 976 Oct 2 12:59 MorphIO.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 371 Oct 2 12:59 neurodamus.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 2610 Oct 2 12:59 RNGSettings.hoc | |
| integration: commands[1]> pytest -x --forked tests/integration | |
| ============================= test session starts ============================== | |
| platform linux -- Python 3.11.6, pytest-7.4.0, pluggy-1.5.0 -- /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/.tox/integration/bin/python | |
| cachedir: .tox/integration/.pytest_cache | |
| rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus | |
| configfile: pyproject.toml | |
| plugins: forked-1.6.0 | |
| collecting ... collected 24 items | |
| tests/integration/test_cell.py::test_load_cell[C060114A7.asc] PASSED [ 4%] | |
| tests/integration/test_cell.py::test_load_cell[C060114A7.h5] PASSED [ 8%] | |
| tests/integration/test_cell.py::test_load_cell[merged_container.h5/C060114A7.h5] PASSED [ 12%] | |
| tests/integration/test_cell.py::test_morphio_read PASSED [ 16%] | |
| tests/integration/test_cell.py::test_create_cell PASSED [ 20%] | |
| tests/integration/test_cell.py::test_create_cell_2 PASSED [ 25%] | |
| tests/integration/test_cell.py::test_create_cell_3 PASSED [ 29%] | |
| tests/integration/test_cell.py::test_basic_system PASSED [ 33%] | |
| tests/integration/test_neuron.py::test_base_h PASSED [ 37%] | |
| tests/integration/test_sonata_config.py::test_parse_base PASSED [ 41%] | |
| tests/integration/test_sonata_config.py::test_SimConfig_from_sonata PASSED [ 45%] | |
| tests/integration/test_sonata_config.py::test_parse_seeds PASSED [ 50%] | |
| tests/integration/test_sonata_config.py::test_parse_modifications PASSED [ 54%] | |
| tests/integration/test_sonata_config.py::test_parse_connections PASSED [ 58%] | |
| tests/integration/test_sonata_config.py::test_parse_inputs PASSED [ 62%] | |
| tests/integration/test_sonata_output.py::test_sonata_logfile PASSED [ 66%] | |
| tests/integration/test_sonata_output.py::test_throw_spike_sort_order PASSED [ 70%] | |
| tests/integration/test_stimulus2.py::TestStimuli::test_sin PASSED [ 75%] | |
| tests/integration/test_stimulus2.py::TestStimuli::test_sin_long PASSED [ 79%] | |
| tests/integration/test_stimulus2.py::TestStimuli::test_add_pulses PASSED [ 83%] | |
| tests/integration/test_stimulus2.py::TestStimuli::test_noise PASSED [ 87%] | |
| tests/integration/test_stimulus2.py::TestStimuli::test_shot_noise PASSED [ 91%] | |
| tests/integration/test_stimulus2.py::TestStimuli::test_ornstein_uhlenbeck PASSED [ 95%] | |
| tests/integration/test_stimulus2.py::TestStimuli::test_stacked PASSED [100%] | |
| =============================== warnings summary =============================== | |
| .tox/integration/lib/python3.11/site-packages/neurodamus/core/configuration.py:162 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/.tox/integration/lib/python3.11/site-packages/neurodamus/core/configuration.py:162: DeprecationWarning: In 3.13 classes created inside an enum will not become a member. Use the `member` decorator to keep the current behavior. | |
| class AutoBalanceModeParams: | |
| -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html | |
| ======================== 24 passed, 1 warning in 3.05s ========================= | |
| .pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453487/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| integration: OK (47.49=setup[41.02]+cmd[3.05,3.42] seconds) | |
| congratulations :) (47.70 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1727866801:section_tox [0K | |
| section_end:1727866801:step_script [0Ksection_start:1727866801:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| Using git from spack modules | |
| section_end:1727866802:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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| [0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1727866696:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1727866696:resolve_secrets [0Ksection_start:1727866696:prepare_executor [0K[0K[36;1mPreparing the "custom" executor[0;m[0;m | |
| [0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m | |
| 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-executor1397054797, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 234614, build ref , job ID 1453490 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1453490, 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_J1453490_PROD_P2354_CP6_C7 | |
| Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcsim 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 2557987 | |
| job state: PD | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1453490_PROD_P2354_CP6_C7 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1453490 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1453490 --ntasks=1 --jobid=2557987 --cpus-per-task=6 --mem=30750M | |
| section_end:1727866699:prepare_executor [0Ksection_start:1727866699:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i6n14 via bbpv1.epfl.ch... | |
| section_end:1727866700:prepare_script [0Ksection_start:1727866700:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
| Using git from spack modules | |
| [32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m | |
| [32;1mFetching changes with git depth set to 100...[0;m | |
| Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453490/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out 5f3fdcfc as leite/fix-iterate-conns-intersect...[0;m | |
| Skipping object checkout, Git LFS is not installed. | |
| [32;1mUpdating/initializing submodules recursively with git depth set to 100...[0;m | |
| section_end:1727866705:get_sources [0Ksection_start:1727866705:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
| [0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m | |
| Using git from spack modules | |
| [32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m | |
| [32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m | |
| [32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m | |
| [32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m | |
| [32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m | |
| [32;1m$ module purge[0;m | |
| [32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m | |
| [32;1m$ module load unstable python/3.12.0[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.12.0 | |
| [32;1m$ module load unstable python/3.8.18[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.8.18 | |
| [32;1m$ module load unstable python/3.9.18[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.9.18 | |
| [32;1m$ module load unstable python/3.10.13[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.10.13 | |
| [32;1m$ module load unstable python/3.11.6[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.11.6 | |
| [32;1m$ load-modules() { # collapsed multi-line command[0;m | |
| [32;1m$ load-modules $SYSTEM_MODULES[0;m | |
| Loaded module git from unstable | |
| Loaded module cmake from unstable | |
| Loaded module graphviz from unstable | |
| [32;1m$ load-modules $EXTRA_MODULES[0;m | |
| Loaded module neurodamus-neocortex-multiscale from unstable | |
| [32;1m$ module list -t[0;m | |
| Currently Loaded Modulefiles: | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.12.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.8.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.9.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.10.13 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.11.6 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/git/2.42.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/cmake/3.27.7 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/graphviz/8.0.5 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/intel-oneapi-mkl/2023.2.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/hpe-mpi/2.27.p1.hmpt | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/applications/linux-rhel7-skylake/neurodamus-neocortex-multiscale/2.4.1 | |
| [32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
| [32;1m$ print_var XDG_CONFIG_HOME[0;m | |
| [36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453490/hpc/sim/neurodamus/local_config[0m | |
| [32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m | |
| [32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m | |
| [32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
| [url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
| insteadOf = https://bbpgitlab.epfl.ch/ | |
| insteadOf = ssh://git@bbpgitlab.epfl.ch/ | |
| insteadOf = git@bbpgitlab.epfl.ch: | |
| [32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m | |
| [0Ksection_start:1727866726:section_venv[collapsed=true] [0KSetting up the virtual env | |
| [32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
| [32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
| [32;1m$ rm -rf "$CI_VENV"[0;m | |
| [32;1m$ python -mvenv "$CI_VENV"[0;m | |
| [32;1m$ source "$CI_VENV/bin/activate"[0;m | |
| [32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Requirement already satisfied: pip in ./venv/lib/python3.11/site-packages (23.2.1) | |
| Collecting pip | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2cd/581cf58ab7fcf/pip-24.2-py3-none-any.whl (1.8 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.8/1.8 MB 65.8 MB/s eta 0:00:00 | |
| Requirement already satisfied: setuptools in ./venv/lib/python3.11/site-packages (65.5.0) | |
| Collecting setuptools | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/35a/b7fd3bcd95e6b/setuptools-75.1.0-py3-none-any.whl (1.2 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.2/1.2 MB 234.6 MB/s eta 0:00:00 | |
| Collecting wheel | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/237/6a90c98cc337d/wheel-0.44.0-py3-none-any.whl (67 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 67.1/67.1 kB 219.6 MB/s eta 0:00:00 | |
| Installing collected packages: wheel, setuptools, pip | |
| Attempting uninstall: setuptools | |
| Found existing installation: setuptools 65.5.0 | |
| Uninstalling setuptools-65.5.0: | |
| Successfully uninstalled setuptools-65.5.0 | |
| Attempting uninstall: pip | |
| Found existing installation: pip 23.2.1 | |
| Uninstalling pip-23.2.1: | |
| Successfully uninstalled pip-23.2.1 | |
| Successfully installed pip-24.2 setuptools-75.1.0 wheel-0.44.0 | |
| [32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Collecting tox | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/693/ac51378255d34/tox-4.21.0-py3-none-any.whl (165 kB) | |
| Collecting cachetools>=5.5 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/021/34e8439cdc2ff/cachetools-5.5.0-py3-none-any.whl (9.5 kB) | |
| Collecting chardet>=5.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB) | |
| Collecting colorama>=0.4.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB) | |
| Collecting filelock>=3.16.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/208/2e5703d51fbf9/filelock-3.16.1-py3-none-any.whl (16 kB) | |
| Collecting packaging>=24.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/5b8/f2217dbdbd2f7/packaging-24.1-py3-none-any.whl (53 kB) | |
| Collecting platformdirs>=4.3.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/73e/575e1408ab810/platformdirs-4.3.6-py3-none-any.whl (18 kB) | |
| Collecting pluggy>=1.5 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/44e/1ad92c8ca002d/pluggy-1.5.0-py3-none-any.whl (20 kB) | |
| Collecting pyproject-api>=1.8 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/3d7/d347a047afe79/pyproject_api-1.8.0-py3-none-any.whl (13 kB) | |
| Collecting virtualenv>=20.26.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/734/5cc5b25405607/virtualenv-20.26.6-py3-none-any.whl (6.0 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 6.0/6.0 MB 171.9 MB/s eta 0:00:00 | |
| Collecting distlib<1,>=0.3.7 (from virtualenv>=20.26.6->tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/034/db59a0b96f8ca/distlib-0.3.8-py2.py3-none-any.whl (468 kB) | |
| Installing collected packages: distlib, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
| Attempting uninstall: packaging | |
| Found existing installation: packaging 23.1 | |
| Not uninstalling packaging at /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-packaging-23.1-uqml2t/lib/python3.11/site-packages, outside environment /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453490/hpc/sim/neurodamus/venv | |
| Can't uninstall 'packaging'. No files were found to uninstall. | |
| Successfully installed cachetools-5.5.0 chardet-5.2.0 colorama-0.4.6 distlib-0.3.8 filelock-3.16.1 packaging-24.1 platformdirs-4.3.6 pluggy-1.5.0 pyproject-api-1.8.0 tox-4.21.0 virtualenv-20.26.6 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1727866753:section_venv [0K | |
| [32;1m$ print_var PRE_BUILD_COMMAND[0;m | |
| [36mPRE_BUILD_COMMAND=[0m | |
| [32;1m$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi[0;m | |
| [32;1m$ section_start section_tox "Running Tox"[0;m | |
| [0Ksection_start:1727866753:section_tox [0KRunning Tox | |
| [32;1m$ python -mtox $TOX_OPTIONS[0;m | |
| bbp-model: install_deps> python -I -m pip install -r tests/requirements.txt | |
| .pkg: install_requires> python -I -m pip install hatch-vcs hatchling | |
| .pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453490/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| .pkg: get_requires_for_build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453490/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| .pkg: freeze> python -m pip freeze --all | |
| .pkg: hatch-vcs==0.4.0,hatchling==1.25.0,packaging==24.1,pathspec==0.12.1,pip==24.2,pluggy==1.5.0,setuptools==75.1.0,setuptools-scm==8.1.0,trove-classifiers==2024.9.12,wheel==0.44.0 | |
| .pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453490/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| bbp-model: install_package_deps> python -I -m pip install docopt h5py libsonata psutil | |
| bbp-model: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453490/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.6.1.dev7.tar.gz | |
| bbp-model: freeze> python -m pip freeze --all | |
| bbp-model: docopt @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-docopt-0.6.2-noukz4jts6de5g3xamvap6n4mh7mmcsy/spack-src,h5py @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-h5py-3.8.0-5woxna6nieu5jokc2tdxsfmolza6724e/spack-src,iniconfig==2.0.0,libsonata @ file:///nvme/[MASKED]/2371376/spack-stage/spack-stage-py-libsonata-0.1.28-jsuf4xxzlybtxiqfdwyqxyxf4c6svcva/spack-src,MorphIO @ file:///nvme/[MASKED]/2246265/spack-stage/spack-stage-py-morphio-3.3.6-xap3flagvbfvuospv22jpkdw65c2ypln/spack-src,mpi4py @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-mpi4py-3.1.4-x733hwb2he3bpi423fnogkrw4w33wehe/spack-src,neurodamus @ file:///nvme/[MASKED]/2379226/spack-stage/spack-stage-py-neurodamus-3.6.0-27enlnafey5xfe6ek7hhy7uozlbps45a/spack-src,numpy @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-numpy-1.26.1-elr5pntecdmhfynrjk3actlxb4go2bua/spack-src,packaging @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-packaging-23.1-uqml2togm4tkpdvzr37r5dnsrpnd76j2/spack-src,pip==24.2,pluggy==1.5.0,psutil @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-psutil-5.9.5-wieplgkaapfkhmzgrsesk5s3h46l3rx4/spack-src,py==1.11.0,pytest==7.4.0,pytest-forked==1.6.0,scipy @ file:///nvme/[MASKED]/2045970/spack-stage/spack-stage-py-scipy-1.11.3-dhxei7gha3wm6mobqp3urw6k4ovd7blx/spack-src,setuptools==75.1.0,wheel==0.44.0 | |
| bbp-model: commands[0]> python -c 'import os; print(os.environ.get('"'"'HOC_LIBRARY_PATH'"'"', '"'"''"'"'))' | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453490/hpc/sim/neurodamus/core/hoc:/gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_oneapi-2023.2.0-skylake/neurodamus-models-2.4.1-dkbxgo/share/neurodamus_neocortex/hoc | |
| bbp-model: commands[1]> pytest -s -x --forked --durations=5 --durations-min=15 tests/scientific-ngv | |
| ============================= test session starts ============================== | |
| platform linux -- Python 3.11.6, pytest-7.4.0, pluggy-1.5.0 -- /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453490/hpc/sim/neurodamus/.tox/bbp-model/bin/python | |
| cachedir: .tox/bbp-model/.pytest_cache | |
| rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453490/hpc/sim/neurodamus | |
| configfile: pyproject.toml | |
| plugins: forked-1.6.0 | |
| collecting ... collected 1 item | |
| tests/scientific-ngv/test_ngv.py::test_vasccouplingB_radii PASSED | |
| ============================= slowest 5 durations ============================== | |
| 125.67s call tests/scientific-ngv/test_ngv.py::test_vasccouplingB_radii | |
| (2 durations < 15s hidden. Use -vv to show these durations.) | |
| ======================== 1 passed in 125.90s (0:02:05) ========================= | |
| .pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453490/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| bbp-model: OK (167.54=setup[41.16]+cmd[0.04,126.34] seconds) | |
| congratulations :) (167.77 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1727866922:section_tox [0K | |
| section_end:1727866922:step_script [0Ksection_start:1727866922:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| Using git from spack modules | |
| section_end:1727866922:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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| [0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1727866696:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1727866696:resolve_secrets [0Ksection_start:1727866696:prepare_executor [0K[0K[36;1mPreparing the "custom" executor[0;m[0;m | |
| [0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m | |
| 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-executor3945048280, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 234614, build ref , job ID 1453489 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1453489, 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_J1453489_PROD_P2354_CP5_C6 | |
| Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcsim 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 2557986 | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1453489_PROD_P2354_CP5_C6 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1453489 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1453489 --ntasks=1 --jobid=2557986 --cpus-per-task=6 --mem=30750M | |
| section_end:1727866697:prepare_executor [0Ksection_start:1727866697:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i6n14 via bbpv1.epfl.ch... | |
| section_end:1727866698:prepare_script [0Ksection_start:1727866698:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
| Using git from spack modules | |
| [32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m | |
| [32;1mFetching changes with git depth set to 100...[0;m | |
| Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453489/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out 5f3fdcfc as leite/fix-iterate-conns-intersect...[0;m | |
| Skipping object checkout, Git LFS is not installed. | |
| [32;1mUpdating/initializing submodules recursively with git depth set to 100...[0;m | |
| section_end:1727866702:get_sources [0Ksection_start:1727866702:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
| [0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m | |
| Using git from spack modules | |
| [32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m | |
| [32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m | |
| [32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m | |
| [32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m | |
| [32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m | |
| [32;1m$ module purge[0;m | |
| [32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m | |
| [32;1m$ module load unstable python/3.12.0[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.12.0 | |
| [32;1m$ module load unstable python/3.8.18[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.8.18 | |
| [32;1m$ module load unstable python/3.9.18[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.9.18 | |
| [32;1m$ module load unstable python/3.10.13[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.10.13 | |
| [32;1m$ module load unstable python/3.11.6[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.11.6 | |
| [32;1m$ load-modules() { # collapsed multi-line command[0;m | |
| [32;1m$ load-modules $SYSTEM_MODULES[0;m | |
| Loaded module git from unstable | |
| Loaded module cmake from unstable | |
| Loaded module graphviz from unstable | |
| [32;1m$ load-modules $EXTRA_MODULES[0;m | |
| Loaded module intel-oneapi-compilers from unstable | |
| Loaded module py-bluepysnap from unstable | |
| Loaded module neurodamus-neocortex from unstable | |
| [32;1m$ module list -t[0;m | |
| Currently Loaded Modulefiles: | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.12.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.8.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.9.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.10.13 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.11.6 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/git/2.42.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/cmake/3.27.7 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/graphviz/8.0.5 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/compilers/linux-rhel7-haswell/intel-oneapi-compilers/2023.2.1 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/intel-oneapi-mkl/2023.2.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/hpe-mpi/2.27.p1.hmpt | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/applications/linux-rhel7-skylake/py-bluepysnap/3.0.1 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/applications/linux-rhel7-skylake/neurodamus-neocortex/2.4.1 | |
| [32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
| [32;1m$ print_var XDG_CONFIG_HOME[0;m | |
| [36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453489/hpc/sim/neurodamus/local_config[0m | |
| [32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m | |
| [32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m | |
| [32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
| [url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
| insteadOf = https://bbpgitlab.epfl.ch/ | |
| insteadOf = ssh://git@bbpgitlab.epfl.ch/ | |
| insteadOf = git@bbpgitlab.epfl.ch: | |
| [32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m | |
| [0Ksection_start:1727866728:section_venv[collapsed=true] [0KSetting up the virtual env | |
| [32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
| [32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
| [32;1m$ rm -rf "$CI_VENV"[0;m | |
| [32;1m$ python -mvenv "$CI_VENV"[0;m | |
| [32;1m$ source "$CI_VENV/bin/activate"[0;m | |
| [32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Requirement already satisfied: pip in ./venv/lib/python3.11/site-packages (23.2.1) | |
| Collecting pip | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2cd/581cf58ab7fcf/pip-24.2-py3-none-any.whl (1.8 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.8/1.8 MB 66.1 MB/s eta 0:00:00 | |
| Requirement already satisfied: setuptools in /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-setuptools-68.0.0-p3xbqx/lib/python3.11/site-packages (68.0.0) | |
| Collecting setuptools | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/35a/b7fd3bcd95e6b/setuptools-75.1.0-py3-none-any.whl (1.2 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.2/1.2 MB 238.6 MB/s eta 0:00:00 | |
| Collecting wheel | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/237/6a90c98cc337d/wheel-0.44.0-py3-none-any.whl (67 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 67.1/67.1 kB 216.7 MB/s eta 0:00:00 | |
| Installing collected packages: wheel, setuptools, pip | |
| Attempting uninstall: setuptools | |
| Found existing installation: setuptools 68.0.0 | |
| Not uninstalling setuptools at /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-setuptools-68.0.0-p3xbqx/lib/python3.11/site-packages, outside environment /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453489/hpc/sim/neurodamus/venv | |
| Can't uninstall 'setuptools'. No files were found to uninstall. | |
| Attempting uninstall: pip | |
| Found existing installation: pip 23.2.1 | |
| Uninstalling pip-23.2.1: | |
| Successfully uninstalled pip-23.2.1 | |
| Successfully installed pip-24.2 setuptools-75.1.0 wheel-0.44.0 | |
| [32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Collecting tox | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/693/ac51378255d34/tox-4.21.0-py3-none-any.whl (165 kB) | |
| Collecting cachetools>=5.5 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/021/34e8439cdc2ff/cachetools-5.5.0-py3-none-any.whl (9.5 kB) | |
| Collecting chardet>=5.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB) | |
| Collecting colorama>=0.4.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB) | |
| Collecting filelock>=3.16.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/208/2e5703d51fbf9/filelock-3.16.1-py3-none-any.whl (16 kB) | |
| Collecting packaging>=24.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/5b8/f2217dbdbd2f7/packaging-24.1-py3-none-any.whl (53 kB) | |
| Collecting platformdirs>=4.3.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/73e/575e1408ab810/platformdirs-4.3.6-py3-none-any.whl (18 kB) | |
| Collecting pluggy>=1.5 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/44e/1ad92c8ca002d/pluggy-1.5.0-py3-none-any.whl (20 kB) | |
| Collecting pyproject-api>=1.8 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/3d7/d347a047afe79/pyproject_api-1.8.0-py3-none-any.whl (13 kB) | |
| Collecting virtualenv>=20.26.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/734/5cc5b25405607/virtualenv-20.26.6-py3-none-any.whl (6.0 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 6.0/6.0 MB 189.6 MB/s eta 0:00:00 | |
| Collecting distlib<1,>=0.3.7 (from virtualenv>=20.26.6->tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/034/db59a0b96f8ca/distlib-0.3.8-py2.py3-none-any.whl (468 kB) | |
| Installing collected packages: distlib, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
| Attempting uninstall: packaging | |
| Found existing installation: packaging 23.1 | |
| Not uninstalling packaging at /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-packaging-23.1-uqml2t/lib/python3.11/site-packages, outside environment /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453489/hpc/sim/neurodamus/venv | |
| Can't uninstall 'packaging'. No files were found to uninstall. | |
| Successfully installed cachetools-5.5.0 chardet-5.2.0 colorama-0.4.6 distlib-0.3.8 filelock-3.16.1 packaging-24.1 platformdirs-4.3.6 pluggy-1.5.0 pyproject-api-1.8.0 tox-4.21.0 virtualenv-20.26.6 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1727866754:section_venv [0K | |
| [32;1m$ print_var PRE_BUILD_COMMAND[0;m | |
| [36mPRE_BUILD_COMMAND=[0m | |
| [32;1m$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi[0;m | |
| [32;1m$ section_start section_tox "Running Tox"[0;m | |
| [0Ksection_start:1727866754:section_tox [0KRunning Tox | |
| [32;1m$ python -mtox $TOX_OPTIONS[0;m | |
| bbp-model: install_deps> python -I -m pip install -r tests/requirements.txt | |
| .pkg: install_requires> python -I -m pip install hatch-vcs hatchling | |
| .pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453489/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| .pkg: get_requires_for_build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453489/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| .pkg: freeze> python -m pip freeze --all | |
| .pkg: hatch-vcs==0.4.0,hatchling==1.25.0,packaging==24.1,pathspec==0.12.1,pip==24.2,pluggy==1.5.0,setuptools==75.1.0,setuptools-scm==8.1.0,trove-classifiers==2024.9.12,wheel==0.44.0 | |
| .pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453489/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| bbp-model: install_package_deps> python -I -m pip install docopt h5py libsonata psutil | |
| bbp-model: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453489/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.6.1.dev7.tar.gz | |
| bbp-model: freeze> python -m pip freeze --all | |
| bbp-model: attrs @ file:///nvme/[MASKED]/2246473/spack-stage/spack-stage-py-attrs-23.1.0-ezrhok2cuu3airbxanfm2gapncxqee32/spack-src,bluepysnap @ file:///nvme/[MASKED]/2371225/spack-stage/spack-stage-py-bluepysnap-3.0.1-tiuwbhrnefyyippdanvb2hefwuylvtfo/spack-src,Bottleneck @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-bottleneck-1.3.7-reskjku2fhby75ljzxdozjw2l3w7ywov/spack-src,cached-property @ file:///nvme/[MASKED]/1998173/spack-stage/spack-stage-py-cached-property-1.5.2-4ra43fkav4led5iceclzwqkgfbqpigp2/spack-src,click @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-click-8.1.7-uppfa4dbkn3thlvfus7yusscvyx6jcbl/spack-src,contourpy @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-contourpy-1.0.7-zjyhvvw5jf6zl6ymi4izavk7qifgt74g/spack-src,cycler @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-cycler-0.11.0-rjj5clifiqnwny3vechb5v66hvaiy76y/spack-src,deprecation @ file:///nvme/[MASKED]/1998173/spack-stage/spack-stage-py-deprecation-2.1.0-qqtamvzujmbchjj24k5drbi753ovygnv/spack-src,docopt @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-docopt-0.6.2-noukz4jts6de5g3xamvap6n4mh7mmcsy/spack-src,find-libpython @ file:///nvme/[MASKED]/2058794/spack-stage/spack-stage-py-find-libpython-0.3.1-5dylncaukuijf2r5t5lrj2s2y2kth2bh/spack-src,fonttools @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-fonttools-4.39.4-z2lufuxxznv35oq32lldyarzx26e5k4o/spack-src,h5py @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-h5py-3.8.0-5woxna6nieu5jokc2tdxsfmolza6724e/spack-src,importlib-resources @ file:///nvme/[MASKED]/2246473/spack-stage/spack-stage-py-importlib-resources-5.12.0-w2x4piqet2l4fc2mbky5qx3cdqp6nqmo/spack-src,iniconfig==2.0.0,Jinja2 @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-jinja2-3.1.2-7validyciqteluvu43co5k7perpr2baq/spack-src,jsonschema @ file:///nvme/[MASKED]/2246473/spack-stage/spack-stage-py-jsonschema-4.17.3-umwrreft5lo3vo3l2rtpblavb4drgykn/spack-src,kiwisolver @ file:///nvme/[MASKED]/2246473/spack-stage/spack-stage-py-kiwisolver-1.4.5-r3ayx65netwojt5s3ncfcg3ofdmv6wws/spack-src,libsonata @ file:///nvme/[MASKED]/2371376/spack-stage/spack-stage-py-libsonata-0.1.28-jsuf4xxzlybtxiqfdwyqxyxf4c6svcva/spack-src,MarkupSafe @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-markupsafe-2.1.3-r3ehtmw6pkktralavqtazezwbkbsivnt/spack-src,matplotlib @ file:///nvme/[MASKED]/2246473/spack-stage/spack-stage-py-matplotlib-3.8.1-xi6eafz2tryv35tt57nrkzqqhkvl25rh/spack-src,more-itertools @ file:///nvme/[MASKED]/1998173/spack-stage/spack-stage-py-more-itertools-9.1.0-j5cqgsrmywy3254zni76f3rd3xza4ond/spack-src,morph-tool @ file:///nvme/[MASKED]/2246797/spack-stage/spack-stage-py-morph-tool-2.9.1-cflsl6yofwtousvmskdvuol3wp6arhjg/spack-src,MorphIO @ file:///nvme/[MASKED]/2246265/spack-stage/spack-stage-py-morphio-3.3.6-xap3flagvbfvuospv22jpkdw65c2ypln/spack-src,mpi4py @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-mpi4py-3.1.4-x733hwb2he3bpi423fnogkrw4w33wehe/spack-src,mpmath @ file:///nvme/[MASKED]/2246265/spack-stage/spack-stage-py-mpmath-1.2.1-4fflyibqfjfxrjhnx3jr7bhpt2tpcqn2/spack-src,neurodamus @ file:///nvme/[MASKED]/2379226/spack-stage/spack-stage-py-neurodamus-3.6.0-27enlnafey5xfe6ek7hhy7uozlbps45a/spack-src,neurom @ file:///nvme/[MASKED]/2246797/spack-stage/spack-stage-py-neurom-3.2.4-5vi6ybrglq5zfzwqu3cjtoy2eoogosbt/spack-src,numexpr @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-numexpr-2.8.4-wu4xk2pywd64hyhoqfr57fzxfbzuuj2y/spack-src,numpy @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-numpy-1.26.1-elr5pntecdmhfynrjk3actlxb4go2bua/spack-src,numpy-quaternion @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-numpy-quaternion-2021.11.4.15.26.3-n3ap27fwuc6c7emgakpydtlt7yvk7nhi/spack-src,packaging @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-packaging-23.1-uqml2togm4tkpdvzr37r5dnsrpnd76j2/spack-src,pandas @ file:///nvme/[MASKED]/2246473/spack-stage/spack-stage-py-pandas-1.5.3-ehpg6zdjazwirtecfrigm3uv43s7g7jm/spack-src,Pillow @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pillow-10.0.0-ygox4axk4dznocekteux3ecwkyfjndzk/spack-src,pip==24.2,pluggy==1.5.0,psutil @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-psutil-5.9.5-wieplgkaapfkhmzgrsesk5s3h46l3rx4/spack-src,py==1.11.0,pybind11 @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pybind11-2.11.0-7rjfjlzjfm5suub2ks5ttsby2mhqlcfl/spack-src,pyparsing @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pyparsing-3.0.9-v3agjtpvgnpemnowjrjcowiw2ksk4xke/spack-src,pyrsistent @ file:///nvme/[MASKED]/1998173/spack-stage/spack-stage-py-pyrsistent-0.19.3-lzzxq7szeqnnyawu4d363tyqva3jui2v/spack-src,pytest==7.4.0,pytest-forked==1.6.0,python-dateutil @ file:///nvme/[MASKED]/2246473/spack-stage/spack-stage-py-python-dateutil-2.8.2-gevcbam356jgwsvvdwcuei4j2tnlncvg/spack-src,pytz @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pytz-2023.3-nr5mf4btvdphj755hbmkq57as5rmwtun/spack-src,PyYAML @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pyyaml-6.0-c3eqkahwrcjjvgo2irs4ocswyrgh2p64/spack-src,scipy @ file:///nvme/[MASKED]/2045970/spack-stage/spack-stage-py-scipy-1.11.3-dhxei7gha3wm6mobqp3urw6k4ovd7blx/spack-src,setuptools @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-setuptools-68.0.0-p3xbqxjqvq45co6xoirlfe5ydwive63k/spack-src/setuptools-68.0.0-py3-none-any.whl#sha256=11e52c67415a381d10d6b462ced9cfb97066179f0e871399e006c4ab101fc85f,six @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-six-1.16.0-brkaopna2ofwxv7qsutpldwizeauixze/spack-src,spatial-index @ file:///nvme/[MASKED]/2371225/spack-stage/spack-stage-spatial-index-2.1.0-n2umqxc5nx44vbdv3jd2gfaswcg4qpyk/spack-src,sympy @ file:///nvme/[MASKED]/2246265/spack-stage/spack-stage-py-sympy-1.11.1-t5tovexvy2goo63j3w6dlqmcnv4yqrqd/spack-src,tqdm @ file:///nvme/[MASKED]/2246473/spack-stage/spack-stage-py-tqdm-4.66.1-yg4xktewd2ufy7xeic3ooh64musayu4c/spack-src,wheel==0.44.0,xmltodict @ file:///nvme/[MASKED]/1998173/spack-stage/spack-stage-py-xmltodict-0.12.0-wgpjtfuvtu6cuzobkx5tatwjzfobtx6x/spack-src | |
| bbp-model: commands[0]> python -c 'import os; print(os.environ.get('"'"'HOC_LIBRARY_PATH'"'"', '"'"''"'"'))' | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453489/hpc/sim/neurodamus/core/hoc:/gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_oneapi-2023.2.0-skylake/neurodamus-models-2.4.1-kjfywd/share/neurodamus_neocortex/hoc | |
| bbp-model: commands[1]> pytest -s -x --forked --durations=5 --durations-min=15 tests/scientific | |
| ============================= test session starts ============================== | |
| platform linux -- Python 3.11.6, pytest-7.4.0, pluggy-1.5.0 -- /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453489/hpc/sim/neurodamus/.tox/bbp-model/bin/python | |
| cachedir: .tox/bbp-model/.pytest_cache | |
| rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453489/hpc/sim/neurodamus | |
| configfile: pyproject.toml | |
| plugins: forked-1.6.0 | |
| collecting ... collected 29 items | |
| tests/scientific/test_current_injection.py::test_current_conductance_injection[current_clamp] PASSED | |
| tests/scientific/test_current_injection.py::test_current_conductance_injection[conductance] PASSED | |
| tests/scientific/test_lfp.py::test_load_lfp_config PASSED | |
| tests/scientific/test_lfp.py::test_read_lfp_factors PASSED | |
| tests/scientific/test_lfp.py::test_number_electrodes PASSED | |
| tests/scientific/test_lfp.py::test_v5_sonata_lfp PASSED | |
| tests/scientific/test_modification.py::test_TTX_modification PASSED | |
| tests/scientific/test_modification.py::test_ConfigureAllSections_modification PASSED | |
| tests/scientific/test_multipop.py::test_multipop_simple[extra_config0] PASSED | |
| tests/scientific/test_multipop.py::test_multipop_full_conn[extra_config0] PASSED | |
| tests/scientific/test_neuromodulation.py::test_neuromodulation_sims_neuron PASSED | |
| tests/scientific/test_neuromodulation.py::test_neuromodulation_sims_coreneuron PASSED | |
| tests/scientific/test_patched_delays.py::test_eager_caching PASSED | |
| tests/scientific/test_projections.py::test_synapse_delay_override[sonata_config_file0] PASSED | |
| tests/scientific/test_projections.py::test_synapse_delay_override[sonata_config_file1] PASSED | |
| tests/scientific/test_projections.py::test_synapse_delay_override[sonata_config_file2] PASSED | |
| tests/scientific/test_projections.py::test_synapse_delay_override[sonata_config_file3] PASSED | |
| tests/scientific/test_replay.py::test_replay_sim PASSED | |
| tests/scientific/test_replay.py::test_many_replay_sim PASSED | |
| tests/scientific/test_replay.py::test_replay_sonata_spikes PASSED | |
| tests/scientific/test_simulation.py::test_simulation_sonata_config SKIPPED | |
| tests/scientific/test_simulation.py::test_v5_sonata_config PASSED | |
| tests/scientific/test_simulation.py::test_v5_gap_junction PASSED | |
| tests/scientific/test_sonata_properties.py::test_input_resistance PASSED | |
| tests/scientific/test_sonata_properties.py::test_input_resistance_2 PASSED | |
| tests/scientific/test_spont_minis.py::test_spont_minis FAILED | |
| =================================== FAILURES =================================== | |
| _______________________________ test_spont_minis _______________________________ | |
| sonata_config_file = <tempfile._TemporaryFileWrapper object at 0x2aaac1d3ab50> | |
| def test_spont_minis(sonata_config_file): | |
| from neurodamus.connection_manager import Nd, SynapseRuleManager | |
| from neurodamus import Neurodamus | |
| from neurodamus.core.configuration import Feature | |
| > nd = Neurodamus( | |
| sonata_config_file.name, | |
| restrict_node_populations=["NodeA"], | |
| restrict_features=[Feature.SpontMinis], # Enable Feature.SynConfigure to see events | |
| restrict_connectivity=1, # base restriction, no projections | |
| disable_reports=True, | |
| cleanup_atexit=False, | |
| # logging_level=3, | |
| ) | |
| tests/scientific/test_spont_minis.py:39: | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| neurodamus/node.py:1628: in __init__ | |
| self._instantiate_simulation() | |
| neurodamus/node.py:1726: in _instantiate_simulation | |
| self._build_model() | |
| neurodamus/node.py:1646: in _build_model | |
| self.create_synapses() | |
| neurodamus/core/_utils.py:37: in mpi_ok_wrapper | |
| res = f(*args, **kw) | |
| ../../../../../../apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/python-3.11.6-bj4i6m/lib/python3.11/contextlib.py:81: in inner | |
| return func(*args, **kwds) | |
| neurodamus/node.py:528: in create_synapses | |
| self._create_synapse_manager(SynManagerCls, circuit, target_manager, **manager_kwa) | |
| neurodamus/node.py:580: in _create_synapse_manager | |
| self._load_connections(conf, manager) # load internal connections right away | |
| neurodamus/node.py:601: in _load_connections | |
| conn_manager.create_connections() | |
| neurodamus/connection_manager.py:491: in create_connections | |
| self.connect_group(conn_src, conn_dst, synapse_id, mod_override) | |
| neurodamus/connection_manager.py:580: in connect_group | |
| for sgid, tgid, syns_params, extra_params, offset in \ | |
| neurodamus/connection_manager.py:654: in _iterate_conn_params | |
| gids = target_gids(gids) | |
| neurodamus/connection_manager.py:651: in target_gids | |
| gids = numpy.intersect1d(gids, dst_target.get_raw_gids()) | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| self = <neurodamus.target_manager.NodesetTarget object at 0x2aaac1578e90> | |
| def get_raw_gids(self): | |
| """ Retrieve the raw gids of the nodeset target """ | |
| if not self.nodesets: | |
| logging.warning("Nodeset '%s' can't be materialized. No node populations", self.name) | |
| return [] | |
| if len(self.nodesets) > 1: | |
| > raise TargetError("Can not get raw gids for Nodeset target with multiple populations.") | |
| E neurodamus.target_manager.TargetError: Can not get raw gids for Nodeset target with multiple populations. | |
| neurodamus/target_manager.py:475: TargetError | |
| =============================== warnings summary =============================== | |
| neurodamus/core/configuration.py:162 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453489/hpc/sim/neurodamus/neurodamus/core/configuration.py:162: DeprecationWarning: In 3.13 classes created inside an enum will not become a member. Use the `member` decorator to keep the current behavior. | |
| class AutoBalanceModeParams: | |
| -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html | |
| ============================= slowest 5 durations ============================== | |
| 32.35s call tests/scientific/test_sonata_properties.py::test_input_resistance | |
| 31.53s call tests/scientific/test_sonata_properties.py::test_input_resistance_2 | |
| 20.04s call tests/scientific/test_simulation.py::test_v5_sonata_config | |
| (2 durations < 15s hidden. Use -vv to show these durations.) | |
| =========================== short test summary info ============================ | |
| FAILED tests/scientific/test_spont_minis.py::test_spont_minis | |
| !!!!!!!!!!!!!!!!!!!!!!!!!! stopping after 1 failures !!!!!!!!!!!!!!!!!!!!!!!!!!! | |
| ======== 1 failed, 24 passed, 1 skipped, 1 warning in 153.57s (0:02:33) ======== | |
| bbp-model: exit 1 (154.20 seconds) /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453489/hpc/sim/neurodamus> pytest -s -x --forked --durations=5 --durations-min=15 tests/scientific pid=133488 | |
| .pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453489/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| bbp-model: FAIL code 1 (195.72=setup[41.46]+cmd[0.06,154.20] seconds) | |
| evaluation failed :( (195.92 seconds) | |
| srun: error: r1i6n14: task 0: Exited with exit code 1 | |
| section_end:1727866951:step_script [0Ksection_start:1727866951:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| Using git from spack modules | |
| section_end:1727866952:cleanup_file_variables [0K[31;1mERROR: Job failed: exit status 1 | |
| [0;m |
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| [0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1727866694:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1727866694:resolve_secrets [0Ksection_start:1727866694:prepare_executor [0K[0K[36;1mPreparing the "custom" executor[0;m[0;m | |
| [0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m | |
| 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-executor3317258710, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 234614, build ref , job ID 1453486 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1453486, 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_J1453486_PROD_P2354_CP1_C2 | |
| Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcsim 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 2557983 | |
| job state: PD | |
| job state: PD | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1453486_PROD_P2354_CP1_C2 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1453486 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1453486 --ntasks=1 --jobid=2557983 --cpus-per-task=6 --mem=30750M | |
| section_end:1727866697:prepare_executor [0Ksection_start:1727866697:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i6n14 via bbpv1.epfl.ch... | |
| section_end:1727866703:prepare_script [0Ksection_start:1727866703:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
| Using git from spack modules | |
| [32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m | |
| [32;1mFetching changes with git depth set to 100...[0;m | |
| Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453486/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out 5f3fdcfc as leite/fix-iterate-conns-intersect...[0;m | |
| Skipping object checkout, Git LFS is not installed. | |
| [32;1mUpdating/initializing submodules recursively with git depth set to 100...[0;m | |
| section_end:1727866708:get_sources [0Ksection_start:1727866708:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
| [0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m | |
| Using git from spack modules | |
| [32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m | |
| [32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m | |
| [32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m | |
| [32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m | |
| [32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m | |
| [32;1m$ module purge[0;m | |
| [32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m | |
| [32;1m$ module load unstable python/3.12.0[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.12.0 | |
| [32;1m$ module load unstable python/3.8.18[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.8.18 | |
| [32;1m$ module load unstable python/3.9.18[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.9.18 | |
| [32;1m$ module load unstable python/3.10.13[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.10.13 | |
| [32;1m$ module load unstable python/3.11.6[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.11.6 | |
| [32;1m$ load-modules() { # collapsed multi-line command[0;m | |
| [32;1m$ load-modules $SYSTEM_MODULES[0;m | |
| Loaded module git from unstable | |
| Loaded module cmake from unstable | |
| Loaded module graphviz from unstable | |
| [32;1m$ load-modules $EXTRA_MODULES[0;m | |
| [32;1m$ module list -t[0;m | |
| Currently Loaded Modulefiles: | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.12.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.8.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.9.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.10.13 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.11.6 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/git/2.42.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/cmake/3.27.7 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/graphviz/8.0.5 | |
| [32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
| [32;1m$ print_var XDG_CONFIG_HOME[0;m | |
| [36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453486/hpc/sim/neurodamus/local_config[0m | |
| [32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m | |
| [32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m | |
| [32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
| [url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
| insteadOf = https://bbpgitlab.epfl.ch/ | |
| insteadOf = ssh://git@bbpgitlab.epfl.ch/ | |
| insteadOf = git@bbpgitlab.epfl.ch: | |
| [32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m | |
| [0Ksection_start:1727866727:section_venv[collapsed=true] [0KSetting up the virtual env | |
| [32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
| [32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
| [32;1m$ rm -rf "$CI_VENV"[0;m | |
| [32;1m$ python -mvenv "$CI_VENV"[0;m | |
| [32;1m$ source "$CI_VENV/bin/activate"[0;m | |
| [32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Requirement already satisfied: pip in ./venv/lib/python3.11/site-packages (23.2.1) | |
| Collecting pip | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2cd/581cf58ab7fcf/pip-24.2-py3-none-any.whl (1.8 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.8/1.8 MB 67.1 MB/s eta 0:00:00 | |
| Requirement already satisfied: setuptools in ./venv/lib/python3.11/site-packages (65.5.0) | |
| Collecting setuptools | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/35a/b7fd3bcd95e6b/setuptools-75.1.0-py3-none-any.whl (1.2 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.2/1.2 MB 253.7 MB/s eta 0:00:00 | |
| Collecting wheel | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/237/6a90c98cc337d/wheel-0.44.0-py3-none-any.whl (67 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 67.1/67.1 kB 220.8 MB/s eta 0:00:00 | |
| Installing collected packages: wheel, setuptools, pip | |
| Attempting uninstall: setuptools | |
| Found existing installation: setuptools 65.5.0 | |
| Uninstalling setuptools-65.5.0: | |
| Successfully uninstalled setuptools-65.5.0 | |
| Attempting uninstall: pip | |
| Found existing installation: pip 23.2.1 | |
| Uninstalling pip-23.2.1: | |
| Successfully uninstalled pip-23.2.1 | |
| Successfully installed pip-24.2 setuptools-75.1.0 wheel-0.44.0 | |
| [32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Collecting tox | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/693/ac51378255d34/tox-4.21.0-py3-none-any.whl (165 kB) | |
| Collecting cachetools>=5.5 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/021/34e8439cdc2ff/cachetools-5.5.0-py3-none-any.whl (9.5 kB) | |
| Collecting chardet>=5.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB) | |
| Collecting colorama>=0.4.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB) | |
| Collecting filelock>=3.16.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/208/2e5703d51fbf9/filelock-3.16.1-py3-none-any.whl (16 kB) | |
| Collecting packaging>=24.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/5b8/f2217dbdbd2f7/packaging-24.1-py3-none-any.whl (53 kB) | |
| Collecting platformdirs>=4.3.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/73e/575e1408ab810/platformdirs-4.3.6-py3-none-any.whl (18 kB) | |
| Collecting pluggy>=1.5 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/44e/1ad92c8ca002d/pluggy-1.5.0-py3-none-any.whl (20 kB) | |
| Collecting pyproject-api>=1.8 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/3d7/d347a047afe79/pyproject_api-1.8.0-py3-none-any.whl (13 kB) | |
| Collecting virtualenv>=20.26.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/734/5cc5b25405607/virtualenv-20.26.6-py3-none-any.whl (6.0 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 6.0/6.0 MB 148.3 MB/s eta 0:00:00 | |
| Collecting distlib<1,>=0.3.7 (from virtualenv>=20.26.6->tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/034/db59a0b96f8ca/distlib-0.3.8-py2.py3-none-any.whl (468 kB) | |
| Installing collected packages: distlib, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
| Successfully installed cachetools-5.5.0 chardet-5.2.0 colorama-0.4.6 distlib-0.3.8 filelock-3.16.1 packaging-24.1 platformdirs-4.3.6 pluggy-1.5.0 pyproject-api-1.8.0 tox-4.21.0 virtualenv-20.26.6 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1727866750:section_venv [0K | |
| [32;1m$ print_var PRE_BUILD_COMMAND[0;m | |
| [36mPRE_BUILD_COMMAND=[0m | |
| [32;1m$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi[0;m | |
| [32;1m$ section_start section_tox "Running Tox"[0;m | |
| [0Ksection_start:1727866750:section_tox [0KRunning Tox | |
| [32;1m$ python -mtox $TOX_OPTIONS[0;m | |
| flake8: install_deps> python -I -m pip install flake8-pyproject | |
| flake8: freeze> python -m pip freeze --all | |
| flake8: flake8==7.1.1,Flake8-pyproject==1.2.3,mccabe==0.7.0,pip==24.2,pycodestyle==2.12.1,pyflakes==3.2.0,setuptools==75.1.0,wheel==0.44.0 | |
| flake8: commands[0]> flake8 | |
| flake8: OK â in 9.1 seconds | |
| unit: install_deps> python -I -m pip install -r tests/requirements.txt | |
| .pkg: install_requires> python -I -m pip install hatch-vcs hatchling | |
| .pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453486/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| .pkg: get_requires_for_build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453486/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| .pkg: freeze> python -m pip freeze --all | |
| .pkg: hatch-vcs==0.4.0,hatchling==1.25.0,packaging==24.1,pathspec==0.12.1,pip==24.2,pluggy==1.5.0,setuptools==75.1.0,setuptools-scm==8.1.0,trove-classifiers==2024.9.12,wheel==0.44.0 | |
| .pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453486/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| unit: install_package_deps> python -I -m pip install docopt h5py libsonata psutil | |
| unit: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453486/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.6.1.dev7.tar.gz | |
| unit: freeze> python -m pip freeze --all | |
| unit: docopt==0.6.2,h5py==3.12.1,iniconfig==2.0.0,libsonata==0.1.28,neurodamus @ file:///gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453486/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.6.1.dev7.tar.gz#sha256=99c562df7bb7e9093d77d4e15af7afbba51a11b943125f4464240d5227ad3869,numpy==2.1.1,packaging==24.1,pip==24.2,pluggy==1.5.0,psutil==6.0.0,py==1.11.0,pytest==7.4.0,pytest-forked==1.6.0,scipy==1.14.1,setuptools==75.1.0,wheel==0.44.0 | |
| unit: commands[0]> pytest tests/unit | |
| ============================= test session starts ============================== | |
| platform linux -- Python 3.11.6, pytest-7.4.0, pluggy-1.5.0 -- /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453486/hpc/sim/neurodamus/.tox/unit/bin/python | |
| cachedir: .tox/unit/.pytest_cache | |
| rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453486/hpc/sim/neurodamus | |
| configfile: pyproject.toml | |
| plugins: forked-1.6.0 | |
| collecting ... collected 82 items | |
| tests/unit/test_conn_manager.py::test_population_get PASSED [ 1%] | |
| tests/unit/test_conn_manager.py::test_population_store_order PASSED [ 2%] | |
| tests/unit/test_conn_manager.py::test_population_get_create_conn PASSED [ 3%] | |
| tests/unit/test_conn_manager.py::test_population_all_conns PASSED [ 4%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input0-expected0] PASSED [ 6%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input1-expected1] PASSED [ 7%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input2-expected2] PASSED [ 8%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input3-expected3] PASSED [ 9%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input4-expected4] PASSED [ 10%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input5-expected5] PASSED [ 12%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input6-expected6] PASSED [ 13%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input7-expected7] PASSED [ 14%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input8-expected8] PASSED [ 15%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input9-expected9] PASSED [ 17%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input10-expected10] PASSED [ 18%] | |
| tests/unit/test_conn_manager.py::test_population_delete PASSED [ 19%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input0-expected0] PASSED [ 20%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input1-expected1] PASSED [ 21%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input2-expected2] PASSED [ 23%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input3-expected3] PASSED [ 24%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input4-expected4] PASSED [ 25%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input5-expected5] PASSED [ 26%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input6-expected6] PASSED [ 28%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input7-expected7] PASSED [ 29%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input8-expected8] PASSED [ 30%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input9-expected9] PASSED [ 31%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input10-expected10] PASSED [ 32%] | |
| tests/unit/test_conn_manager.py::test_population_ids_match PASSED [ 34%] | |
| tests/unit/test_coords.py::test_coord_mapping1 PASSED [ 35%] | |
| tests/unit/test_coords.py::test_coord_mapping2 PASSED [ 36%] | |
| tests/unit/test_core_config.py::test_write_report_config PASSED [ 37%] | |
| tests/unit/test_core_config.py::test_write_sim_config PASSED [ 39%] | |
| tests/unit/test_dry_run.py::test_dry_run_distribution PASSED [ 40%] | |
| tests/unit/test_dry_run.py::test_retrieve_unique_metypes PASSED [ 41%] | |
| tests/unit/test_init_py_config.py::test_init_empty PASSED [ 42%] | |
| tests/unit/test_init_py_config.py::test_init_non_positional PASSED [ 43%] | |
| tests/unit/test_init_py_config.py::test_init_config_only PASSED [ 45%] | |
| tests/unit/test_init_py_config.py::test_init_pass_options PASSED [ 46%] | |
| tests/unit/test_init_py_config.py::test_init_first_args PASSED [ 47%] | |
| tests/unit/test_init_py_config.py::test_init_early_config_file PASSED [ 48%] | |
| tests/unit/test_nodeset.py::test_NodeSet_base PASSED [ 50%] | |
| tests/unit/test_nodeset.py::test_NodeSet_add PASSED [ 51%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges10-ranges20-expected0] PASSED [ 52%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges11-ranges21-expected1] PASSED [ 53%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges12-ranges22-expected2] PASSED [ 54%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges13-ranges23-expected3] PASSED [ 56%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges14-ranges24-expected4] PASSED [ 57%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges15-ranges25-expected5] PASSED [ 58%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges16-ranges26-expected6] PASSED [ 59%] | |
| tests/unit/test_nodeset.py::test_ranges_vec_overlap[ranges10-vec0-expected0] PASSED [ 60%] | |
| tests/unit/test_nodeset.py::test_ranges_vec_overlap[ranges11-vec1-expected1] PASSED [ 62%] | |
| tests/unit/test_nodeset.py::test_ranges_vec_overlap[ranges12-vec2-expected2] PASSED [ 63%] | |
| tests/unit/test_nodeset.py::test_ranges_vec_overlap[ranges13-vec3-expected3] PASSED [ 64%] | |
| tests/unit/test_nodeset.py::test_ranges_vec_overlap[ranges14-vec4-expected4] PASSED [ 65%] | |
| tests/unit/test_nodeset.py::test_read_nodesets_from_file PASSED [ 67%] | |
| tests/unit/test_nodeset_target.py::test_get_local_gids PASSED [ 68%] | |
| tests/unit/test_pyutils.py::test_map_1 PASSED [ 69%] | |
| tests/unit/test_pyutils.py::test_map_other_data PASSED [ 70%] | |
| tests/unit/test_pyutils.py::test_map_duplicates PASSED [ 71%] | |
| tests/unit/test_pyutils.py::test_map_duplicates_struct PASSED [ 73%] | |
| tests/unit/test_pyutils.py::test_badly_formed PASSED [ 74%] | |
| tests/unit/test_pyutils.py::test_merge PASSED [ 75%] | |
| tests/unit/test_pyutils.py::test_merge_grouped PASSED [ 76%] | |
| tests/unit/test_pyutils.py::test_flatten_grouped PASSED [ 78%] | |
| tests/unit/test_replay_manager.py::test_replay_manager_sonata PASSED [ 79%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_flat_segment PASSED [ 80%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_pulse PASSED [ 81%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_pulse_diff_base[-1] PASSED [ 82%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_pulse_diff_base[0] PASSED [ 84%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_pulse_diff_base[1.5] PASSED [ 85%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_two_pulses PASSED [ 86%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_ramp PASSED [ 87%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_delay_ramp PASSED [ 89%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_train PASSED [ 90%] | |
| tests/unit/test_synapse_reader.py::test_gapjunction_sonata_reader PASSED [ 91%] | |
| tests/unit/test_synapse_reader.py::test_syn_read_counts PASSED [ 92%] | |
| tests/unit/test_synapse_reader.py::test_conn_manager_syn_stats PASSED [ 93%] | |
| tests/unit/test_target_intersection.py::test_targetspec_overlap_name PASSED [ 95%] | |
| tests/unit/test_target_intersection.py::test_populations_disjoint PASSED [ 96%] | |
| tests/unit/test_target_intersection.py::test_targetspec_overlap PASSED [ 97%] | |
| tests/unit/test_target_intersection.py::test_nodeset_target_intersect PASSED [ 98%] | |
| tests/unit/test_target_intersection.py::test_nodeset_gids PASSED [100%] | |
| =============================== warnings summary =============================== | |
| .tox/unit/lib/python3.11/site-packages/neurodamus/core/configuration.py:162 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453486/hpc/sim/neurodamus/.tox/unit/lib/python3.11/site-packages/neurodamus/core/configuration.py:162: DeprecationWarning: In 3.13 classes created inside an enum will not become a member. Use the `member` decorator to keep the current behavior. | |
| class AutoBalanceModeParams: | |
| -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html | |
| ======================== 82 passed, 1 warning in 1.26s ========================= | |
| .pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1453486/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| flake8: OK (9.10=setup[7.47]+cmd[1.63] seconds) | |
| unit: OK (37.24=setup[35.39]+cmd[1.85] seconds) | |
| congratulations :) (46.51 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1727866797:section_tox [0K | |
| section_end:1727866797:step_script [0Ksection_start:1727866797:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| Using git from spack modules | |
| section_end:1727866798:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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