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October 10, 2024 09:53
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Logfiles for GitLab pipeline https://bbpgitlab.epfl.ch/hpc/sim/neurodamus/-/pipelines/235315 (:no_entry:) running on GitHub PR BlueBrain/neurodamus#175.
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| [0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1728553011:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1728553011:resolve_secrets [0Ksection_start:1728553011: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-executor445115808, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 235315, build ref , job ID 1459834 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1459834, 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_J1459834_PROD_P2354_CP0_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 2568930 | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1459834_PROD_P2354_CP0_C2 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1459834 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1459834 --ntasks=1 --jobid=2568930 --cpus-per-task=6 --mem=30750M | |
| section_end:1728553013:prepare_executor [0Ksection_start:1728553013:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i7n20 via bbpv1.epfl.ch... | |
| section_end:1728553018:prepare_script [0Ksection_start:1728553018: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/J1459834/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out 533687c1 as weji/actions_improve...[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:1728553030:get_sources [0Ksection_start:1728553030: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/J1459834/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:1728553052: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 62.1 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 176.3 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 220.0 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/13d/996adcd792e7c/tox-4.21.2-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 237.5 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/47f/8c22fd27c27e2/distlib-0.3.9-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-0.3.9 filelock-3.16.1 packaging-24.1 platformdirs-4.3.6 pluggy-1.5.0 pyproject-api-1.8.0 tox-4.21.2 virtualenv-20.26.6 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1728553154: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:1728553154: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/J1459834/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/J1459834/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/J1459834/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/J1459834/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.6.1.dev69.tar.gz | |
| docs: freeze> python -m pip freeze --all | |
| docs: alabaster==0.7.16,babel==2.16.0,certifi==2024.8.30,charset-normalizer==3.4.0,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==3.0.1,neurodamus @ file:///gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459834/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.6.1.dev69.tar.gz#sha256=c5febcbdbadae5ce70a40593ed84f704e22a7a37a4142382307de0962492b91b,numpy==2.1.2,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/J1459834/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| docs: OK (240.66=setup[218.29]+cmd[22.37] seconds) | |
| congratulations :) (242.40 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1728553400:section_tox [0K | |
| section_end:1728553400:step_script [0Ksection_start:1728553400: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=146786 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=1459834 responseStatus[0;m=201 Created token[0;m=glcbt-64 | |
| section_end:1728553403:upload_artifacts_on_success [0Ksection_start:1728553403: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:1728553404: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 yyi8s2pK, system ID: r_j5AS6h5XNfdt[0;m | |
| [0K[36;1mResolving secrets[0;m[0;m | |
| section_start:1728553011: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:1728553011:prepare_executor [0Ksection_start:1728553011: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-yyi8s2pk-project-2354-concurrent-0-c7up2w8h to be running, status is Pending | |
| Waiting for pod gitlab-runners/runner-yyi8s2pk-project-2354-concurrent-0-c7up2w8h to be running, status is Pending | |
| ContainersNotReady: "containers with unready status: [build helper]" | |
| ContainersNotReady: "containers with unready status: [build helper]" | |
| Running on runner-yyi8s2pk-project-2354-concurrent-0-c7up2w8h via cs-gitlab-runners-gitlab-runner-c4db7d7cd-g7hlg... | |
| section_end:1728553020:prepare_script [0Ksection_start:1728553020: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 533687c1 as detached HEAD (ref is weji/actions_improve)...[0;m | |
| [32;1mUpdating/initializing submodules recursively with git depth set to 100...[0;m | |
| [32;1mUpdated submodules[0;m | |
| section_end:1728553029:get_sources [0Ksection_start:1728553029: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:1728553029:step_script [0Ksection_start:1728553029: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=1459840 responseStatus[0;m=201 Created token[0;m=glcbt-64 | |
| section_end:1728553032:upload_artifacts_on_success [0Ksection_start:1728553032:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| section_end:1728553032: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:1728553014:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1728553014:resolve_secrets [0Ksection_start:1728553014: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-executor413380871, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 235315, build ref , job ID 1459837 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1459837, 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_J1459837_PROD_P2354_CP3_C9 | |
| 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 2568933 | |
| job state: PD | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1459837_PROD_P2354_CP3_C9 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1459837 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1459837 --ntasks=1 --jobid=2568933 --cpus-per-task=6 --mem=30750M | |
| section_end:1728553016:prepare_executor [0Ksection_start:1728553016:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i4n16 via bbpv1.epfl.ch... | |
| section_end:1728553017:prepare_script [0Ksection_start:1728553017: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/J1459837/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out 533687c1 as weji/actions_improve...[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:1728553021:get_sources [0Ksection_start:1728553021: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/J1459837/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:1728553043: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 243.3 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 215.3 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/13d/996adcd792e7c/tox-4.21.2-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 236.5 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/47f/8c22fd27c27e2/distlib-0.3.9-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/J1459837/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-0.3.9 filelock-3.16.1 packaging-24.1 platformdirs-4.3.6 pluggy-1.5.0 pyproject-api-1.8.0 tox-4.21.2 virtualenv-20.26.6 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1728553060: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:1728553060: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/J1459837/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/J1459837/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/J1459837/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/J1459837/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.6.1.dev69.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/J1459837/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/J1459837/hpc/sim/neurodamus/.tox/bbp-model/bin/python | |
| cachedir: .tox/bbp-model/.pytest_cache | |
| rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459837/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_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 SKIPPED | |
| 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/J1459837/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 ============================== | |
| 34.37s call tests/integration-e2e/test_cli_opts.py::test_cli_lb_mode | |
| 28.34s call tests/integration-e2e/test_loadbalance.py::test_loadbal_integration | |
| 23.64s call tests/integration-e2e/test_loadbalance.py::test_multisplit | |
| 23.61s call tests/integration-e2e/test_loadbalance.py::test_load_balance_integrated | |
| (1 durations < 15s hidden. Use -vv to show these durations.) | |
| ============= 27 passed, 2 skipped, 1 warning in 185.45s (0:03:05) ============= | |
| .pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459837/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| bbp-model: OK (225.63=setup[39.71]+cmd[0.04,185.89] seconds) | |
| congratulations :) (225.84 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1728553287:section_tox [0K | |
| section_end:1728553287:step_script [0Ksection_start:1728553287: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:1728553287: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:1728553013:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1728553013:resolve_secrets [0Ksection_start:1728553013: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-executor4218124028, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 235315, build ref , job ID 1459836 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1459836, 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_J1459836_PROD_P2354_CP2_C8 | |
| 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 2568932 | |
| job state: PD | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1459836_PROD_P2354_CP2_C8 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1459836 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1459836 --ntasks=1 --jobid=2568932 --cpus-per-task=6 --mem=30750M | |
| section_end:1728553015:prepare_executor [0Ksection_start:1728553015:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i4n16 via bbpv1.epfl.ch... | |
| section_end:1728553020:prepare_script [0Ksection_start:1728553020: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/J1459836/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out 533687c1 as weji/actions_improve...[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:1728553024:get_sources [0Ksection_start:1728553024: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/J1459836/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:1728553043: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 238.0 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 223.4 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/13d/996adcd792e7c/tox-4.21.2-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 241.9 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/47f/8c22fd27c27e2/distlib-0.3.9-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-0.3.9 filelock-3.16.1 packaging-24.1 platformdirs-4.3.6 pluggy-1.5.0 pyproject-api-1.8.0 tox-4.21.2 virtualenv-20.26.6 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1728553060: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:1728553060: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/J1459836/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/J1459836/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/J1459836/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/J1459836/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.6.1.dev69.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/J1459836/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.6.1.dev69.tar.gz#sha256=c5febcbdbadae5ce70a40593ed84f704e22a7a37a4142382307de0962492b91b,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/J1459836/hpc/sim/neurodamus/neurodamus/data | |
| + CORE_DIR=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459836/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/J1459836/hpc/sim/neurodamus/neurodamus/data/mod/ALU.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459836/hpc/sim/neurodamus/neurodamus/data/mod/CoreNEURONArtificialCell.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459836/hpc/sim/neurodamus/neurodamus/data/mod/netstim_inhpoisson.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459836/hpc/sim/neurodamus/neurodamus/data/mod/SonataReportHelper.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459836/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/J1459836/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/J1459836/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 DetAMPANMDA.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459836/hpc/sim/neurodamus/x86_64/DetAMPANMDA.c | |
| Translating ALU.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459836/hpc/sim/neurodamus/x86_64/ALU.c | |
| Translating CoreNEURONArtificialCell.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459836/hpc/sim/neurodamus/x86_64/CoreNEURONArtificialCell.c | |
| Warning: next_delay_weight undefined. (declared within VERBATIM?) | |
| Warning: next_delay_t undefined. (declared within VERBATIM?) | |
| Thread Safe | |
| Thread Safe | |
| Thread Safe | |
| -> [32mNMODL[0m ../mods.tmp/DetGABAAB.mod | |
| -> [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/J1459836/hpc/sim/neurodamus/x86_64/DetGABAAB.c | |
| Translating gap.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459836/hpc/sim/neurodamus/x86_64/gap.c | |
| Thread Safe | |
| Translating GluSynapse.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459836/hpc/sim/neurodamus/x86_64/GluSynapse.c | |
| Warning: next_delay_weight undefined. (declared within VERBATIM?) | |
| Warning: next_delay_t undefined. (declared within VERBATIM?) | |
| Thread Safe | |
| Warning: next_delay_weight undefined. (declared within VERBATIM?) | |
| Warning: next_delay_t undefined. (declared within VERBATIM?) | |
| -> [32mNMODL[0m ../mods.tmp/netstim_inhpoisson.mod | |
| -> [32mNMODL[0m ../mods.tmp/ProbAMPANMDA_EMS.mod | |
| Thread Safe | |
| -> [32mNMODL[0m ../mods.tmp/ProbGABAAB_EMS.mod | |
| Translating netstim_inhpoisson.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459836/hpc/sim/neurodamus/x86_64/netstim_inhpoisson.c | |
| Translating ProbAMPANMDA_EMS.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459836/hpc/sim/neurodamus/x86_64/ProbAMPANMDA_EMS.c | |
| Warning: POST_RESTORE_RESTART_FLAG 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 | |
| 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?) | |
| Translating ProbGABAAB_EMS.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459836/hpc/sim/neurodamus/x86_64/ProbGABAAB_EMS.c | |
| Thread Safe | |
| -> [32mNMODL[0m ../mods.tmp/SonataReportHelper.mod | |
| 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 | |
| -> [32mNMODL[0m ../mods.tmp/SonataReports.mod | |
| -> [32mNMODL[0m ../mods.tmp/TTXDynamicsSwitch.mod | |
| Translating SonataReports.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459836/hpc/sim/neurodamus/x86_64/SonataReports.c | |
| Translating SonataReportHelper.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459836/hpc/sim/neurodamus/x86_64/SonataReportHelper.c | |
| Thread Safe | |
| Thread Safe | |
| Translating TTXDynamicsSwitch.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459836/hpc/sim/neurodamus/x86_64/TTXDynamicsSwitch.c | |
| -> [32mNMODL[0m ../mods.tmp/VecStim.mod | |
| Thread Safe | |
| -> [32mCompiling[0m ALU.c | |
| -> [32mCompiling[0m CoreNEURONArtificialCell.c | |
| Translating VecStim.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459836/hpc/sim/neurodamus/x86_64/VecStim.c | |
| Thread Safe | |
| -> [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/J1459836/hpc/sim/neurodamus/neurodamus/data/hoc/Cell.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459836/hpc/sim/neurodamus/neurodamus/data/hoc/ConnectionUtils.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459836/hpc/sim/neurodamus/neurodamus/data/hoc/defvar.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459836/hpc/sim/neurodamus/neurodamus/data/hoc/fileUtils.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459836/hpc/sim/neurodamus/neurodamus/data/hoc/Map.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459836/hpc/sim/neurodamus/neurodamus/data/hoc/MorphIO.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459836/hpc/sim/neurodamus/neurodamus/data/hoc/neurodamus.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459836/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/J1459836/hpc/sim/neurodamus/neurodamus/data | |
| + ls -l | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459836/hpc/sim/neurodamus/neurodamus/data | |
| total 80 | |
| -rw-rw----+ 1 bbpcihpcsim bbp 578 Oct 10 11:37 authors.txt | |
| drwxrwx---+ 3 bbpcihpcsim bbp 4096 Oct 10 11:37 _benchmarks | |
| -rw-rw----+ 1 bbpcihpcsim bbp 29097 Oct 10 11:37 CHANGES.rst | |
| drwxrwx---+ 2 bbpcihpcsim bbp 4096 Oct 10 11:37 ci | |
| drwxrwx---+ 7 bbpcihpcsim bbp 4096 Oct 10 11:38 _common | |
| -rw-rw----+ 1 bbpcihpcsim bbp 6240 Oct 10 11:37 CONTRIBUTING.md | |
| drwxrwx---+ 2 bbpcihpcsim bbp 4096 Oct 10 11:37 docker | |
| drwxrwx---+ 5 bbpcihpcsim bbp 4096 Oct 10 11:37 docs | |
| drwxrwx---+ 2 bbpcihpcsim bbp 4096 Oct 10 11:37 examples | |
| drwxrwx---+ 2 bbpcihpcsim bbp 4096 Oct 10 11:38 _lib | |
| -rw-rw----+ 1 bbpcihpcsim bbp 11358 Oct 10 11:37 LICENSE.txt | |
| drwxrwx---+ 3 bbpcihpcsim bbp 4096 Oct 10 11:37 local_config | |
| drwxrwx---+ 2 bbpcihpcsim bbp 4096 Oct 10 11:38 mods.tmp | |
| drwxrwx---+ 6 bbpcihpcsim bbp 4096 Oct 10 11:37 neurodamus | |
| -rw-rw----+ 1 bbpcihpcsim bbp 1355 Oct 10 11:37 pyproject.toml | |
| -rw-rw----+ 1 bbpcihpcsim bbp 4598 Oct 10 11:37 README.rst | |
| -rw-rw----+ 1 bbpcihpcsim bbp 52 Oct 10 11:37 requirements_docs.txt | |
| + ls -l _lib | |
| -rw-rw----+ 1 bbpcihpcsim bbp 37 Oct 10 11:37 requirements.txt | |
| drwxrwx---+ 9 bbpcihpcsim bbp 4096 Oct 10 11:37 tests | |
| -rw-rw----+ 1 bbpcihpcsim bbp 1422 Oct 10 11:37 tox.ini | |
| drwxrwx---+ 5 bbpcihpcsim bbp 4096 Oct 10 11:37 venv | |
| drwxrwx---+ 3 bbpcihpcsim bbp 4096 Oct 10 11:38 x86_64 | |
| total 6 | |
| -rw-rw----+ 1 bbpcihpcsim bbp 2470 Oct 10 11:38 AMPANMDAHelper.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 15774 Oct 10 11:38 Cell.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 1064 Oct 10 11:38 ConnectionUtils.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 998 Oct 10 11:38 defvar.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 1173 Oct 10 11:38 DetAMPANMDAHelper.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 1636 Oct 10 11:38 DetGABAABHelper.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 1971 Oct 10 11:38 fileUtils.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 3294 Oct 10 11:38 GABAABHelper.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 3736 Oct 10 11:38 GluSynapseHelper.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 4633 Oct 10 11:38 GluSynapseLegacyHelper.hoc | |
| -rwxrwx---+ 1 bbpcihpcsim bbp 274824 Oct 10 11:38 libnrnmech.so | |
| -rw-rw----+ 1 bbpcihpcsim bbp 10723 Oct 10 11:38 Map.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 976 Oct 10 11:38 MorphIO.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 371 Oct 10 11:38 neurodamus.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 2610 Oct 10 11:38 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/J1459836/hpc/sim/neurodamus/.tox/integration/bin/python | |
| cachedir: .tox/integration/.pytest_cache | |
| rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459836/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/J1459836/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 3.01s ========================= | |
| .pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459836/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| integration: OK (48.74=setup[42.57]+cmd[2.83,3.34] seconds) | |
| congratulations :) (48.88 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1728553109:section_tox [0K | |
| section_end:1728553110:step_script [0Ksection_start:1728553110: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:1728553110: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:1728553016:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1728553016:resolve_secrets [0Ksection_start:1728553016: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-executor670601599, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 235315, build ref , job ID 1459839 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1459839, 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_J1459839_PROD_P2354_CP5_C11 | |
| 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 2568935 | |
| 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_J1459839_PROD_P2354_CP5_C11 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1459839 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1459839 --ntasks=1 --jobid=2568935 --cpus-per-task=6 --mem=30750M | |
| section_end:1728553019:prepare_executor [0Ksection_start:1728553019:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i4n16 via bbpv1.epfl.ch... | |
| section_end:1728553023:prepare_script [0Ksection_start:1728553023: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/J1459839/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out 533687c1 as weji/actions_improve...[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:1728553027:get_sources [0Ksection_start:1728553027: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/J1459839/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:1728553049: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 66.2 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 227.2 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 211.2 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/13d/996adcd792e7c/tox-4.21.2-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 243.7 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/47f/8c22fd27c27e2/distlib-0.3.9-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/J1459839/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-0.3.9 filelock-3.16.1 packaging-24.1 platformdirs-4.3.6 pluggy-1.5.0 pyproject-api-1.8.0 tox-4.21.2 virtualenv-20.26.6 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1728553068: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:1728553068: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/J1459839/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/J1459839/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/J1459839/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/J1459839/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.6.1.dev69.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/J1459839/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/J1459839/hpc/sim/neurodamus/.tox/bbp-model/bin/python | |
| cachedir: .tox/bbp-model/.pytest_cache | |
| rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459839/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 ============================== | |
| 111.84s call tests/scientific-ngv/test_ngv.py::test_vasccouplingB_radii | |
| (2 durations < 15s hidden. Use -vv to show these durations.) | |
| ======================== 1 passed in 112.05s (0:01:52) ========================= | |
| .pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459839/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| bbp-model: OK (147.05=setup[34.52]+cmd[0.04,112.49] seconds) | |
| congratulations :) (147.17 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1728553215:section_tox [0K | |
| section_end:1728553215:step_script [0Ksection_start:1728553215: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:1728553216: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:1728553015:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1728553015:resolve_secrets [0Ksection_start:1728553015: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-executor818831440, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 235315, build ref , job ID 1459838 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1459838, 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_J1459838_PROD_P2354_CP4_C10 | |
| 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 2568934 | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1459838_PROD_P2354_CP4_C10 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1459838 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1459838 --ntasks=1 --jobid=2568934 --cpus-per-task=6 --mem=30750M | |
| section_end:1728553016:prepare_executor [0Ksection_start:1728553016:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i4n16 via bbpv1.epfl.ch... | |
| section_end:1728553017:prepare_script [0Ksection_start:1728553017: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/J1459838/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out 533687c1 as weji/actions_improve...[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:1728553021:get_sources [0Ksection_start:1728553021: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 $EXTRA_MODULES[0;m | |
| Loaded module intel-oneapi-compilers from unstable | |
| Loaded module neurodamus-neocortex from unstable | |
| [32;1m$ 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/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/J1459838/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:1728553045: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 ./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 243.8 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 214.8 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/13d/996adcd792e7c/tox-4.21.2-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 246.8 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/47f/8c22fd27c27e2/distlib-0.3.9-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/J1459838/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-0.3.9 filelock-3.16.1 packaging-24.1 platformdirs-4.3.6 pluggy-1.5.0 pyproject-api-1.8.0 tox-4.21.2 virtualenv-20.26.6 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1728553064: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:1728553064: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/J1459838/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/J1459838/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/J1459838/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/J1459838/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.6.1.dev69.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/J1459838/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/J1459838/hpc/sim/neurodamus/.tox/bbp-model/bin/python | |
| cachedir: .tox/bbp-model/.pytest_cache | |
| rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459838/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 PASSED | |
| tests/scientific/test_synapses.py::test_synapses_params PASSED | |
| tests/scientific/test_synapses.py::test__constrained_hill PASSED | |
| tests/scientific/test_synapses.py::test_no_edge_creation PASSED | |
| =============================== warnings summary =============================== | |
| neurodamus/core/configuration.py:162 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459838/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 ============================== | |
| 18.71s call tests/scientific/test_sonata_properties.py::test_input_resistance | |
| 18.70s call tests/scientific/test_sonata_properties.py::test_input_resistance_2 | |
| (3 durations < 15s hidden. Use -vv to show these durations.) | |
| ============= 28 passed, 1 skipped, 1 warning in 111.46s (0:01:51) ============= | |
| .pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459838/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| bbp-model: OK (149.52=setup[37.46]+cmd[0.09,111.96] seconds) | |
| congratulations :) (149.64 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1728553214:section_tox [0K | |
| section_end:1728553214:step_script [0Ksection_start:1728553214: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:1728553215: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:1728553012:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1728553012:resolve_secrets [0Ksection_start:1728553012: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-executor1607021017, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 235315, build ref , job ID 1459835 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1459835, 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_J1459835_PROD_P2354_CP1_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 2568931 | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1459835_PROD_P2354_CP1_C7 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1459835 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1459835 --ntasks=1 --jobid=2568931 --cpus-per-task=6 --mem=30750M | |
| section_end:1728553014:prepare_executor [0Ksection_start:1728553014:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i4n16 via bbpv1.epfl.ch... | |
| section_end:1728553016:prepare_script [0Ksection_start:1728553016: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/J1459835/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out 533687c1 as weji/actions_improve...[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:1728553020:get_sources [0Ksection_start:1728553020: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/J1459835/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:1728553039: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 87.9 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 226.4 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/13d/996adcd792e7c/tox-4.21.2-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 208.5 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/47f/8c22fd27c27e2/distlib-0.3.9-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-0.3.9 filelock-3.16.1 packaging-24.1 platformdirs-4.3.6 pluggy-1.5.0 pyproject-api-1.8.0 tox-4.21.2 virtualenv-20.26.6 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1728553057: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:1728553057: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 7.68 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/J1459835/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/J1459835/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/J1459835/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/J1459835/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.6.1.dev69.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/J1459835/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.6.1.dev69.tar.gz#sha256=c5febcbdbadae5ce70a40593ed84f704e22a7a37a4142382307de0962492b91b,numpy==2.1.2,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/J1459835/hpc/sim/neurodamus/.tox/unit/bin/python | |
| cachedir: .tox/unit/.pytest_cache | |
| rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459835/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/J1459835/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 1.02s ========================= | |
| .pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1459835/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| flake8: OK (7.68=setup[6.26]+cmd[1.42] seconds) | |
| unit: OK (38.75=setup[37.24]+cmd[1.51] seconds) | |
| congratulations :) (46.54 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1728553104:section_tox [0K | |
| section_end:1728553104:step_script [0Ksection_start:1728553104: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:1728553105:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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