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May 13, 2024 15:45
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Logfiles for GitLab pipeline https://bbpgitlab.epfl.ch/hpc/sim/neurodamus/-/pipelines/210758 (:no_entry:) running on GitHub PR BlueBrain/neurodamus#166.
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| [0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1715614536:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1715614536:resolve_secrets [0Ksection_start:1715614536: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-executor1915015745, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 210758, build ref , job ID 1278737 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1278737, 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_J1278737_PROD_P2354_CP0_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 2178911 | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1278737_PROD_P2354_CP0_C10 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1278737 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1278737 --ntasks=1 --jobid=2178911 --cpus-per-task=6 --mem=30750M | |
| section_end:1715614538:prepare_executor [0Ksection_start:1715614538:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i7n31 via bbpv1.epfl.ch... | |
| section_end:1715614542:prepare_script [0Ksection_start:1715614542: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/J1278737/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out bb40a954 as weji/cache-neuron...[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:1715614565:get_sources [0Ksection_start:1715614565: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/2024-05/externals/linux-rhel7-skylake/python/3.12.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/python/3.8.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/python/3.9.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/python/3.10.13 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/python/3.11.6 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/git/2.42.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/cmake/3.27.7 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/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/J1278737/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:1715614568: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/ba0/d021a166865d2/pip-24.0-py3-none-any.whl (2.1 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 2.1/2.1 MB 76.1 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/c63/6ac361bc47580/setuptools-69.5.1-py3-none-any.whl (894 kB) | |
| âââââââââââââââââââââââââââââââââââââ 894.6/894.6 kB 266.1 MB/s eta 0:00:00 | |
| Collecting wheel | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/55c/570405f142630/wheel-0.43.0-py3-none-any.whl (65 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 65.8/65.8 kB 227.6 MB/s eta 0:00:00 | |
| Installing collected packages: wheel, setuptools, pip | |
| Attempting uninstall: setuptools | |
| Found existing installation: setuptools 65.5.0 | |
| Uninstalling setuptools-65.5.0: | |
| Successfully uninstalled setuptools-65.5.0 | |
| Attempting uninstall: pip | |
| Found existing installation: pip 23.2.1 | |
| Uninstalling pip-23.2.1: | |
| Successfully uninstalled pip-23.2.1 | |
| Successfully installed pip-24.0 setuptools-69.5.1 wheel-0.43.0 | |
| [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/300/055f335d855b2/tox-4.15.0-py3-none-any.whl (155 kB) | |
| ââââââââââââââââââââââââââââââââââââââ 155.7/155.7 kB 12.1 MB/s eta 0:00:00 | |
| Collecting cachetools>=5.3.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/0ab/ad1021d3f8325/cachetools-5.3.3-py3-none-any.whl (9.3 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) | |
| ââââââââââââââââââââââââââââââââââââââ 199.4/199.4 kB 56.3 MB/s eta 0:00:00 | |
| 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>=3.13.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/433/39835842f110c/filelock-3.14.0-py3-none-any.whl (12 kB) | |
| Collecting packaging>=23.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2dd/fb553fdf02fb7/packaging-24.0-py3-none-any.whl (53 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 53.5/53.5 kB 212.0 MB/s eta 0:00:00 | |
| Collecting platformdirs>=4.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/17d/5a1161b3fd67b/platformdirs-4.2.1-py3-none-any.whl (17 kB) | |
| Collecting pluggy>=1.3 (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>=1.6.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4c0/116d60476b078/pyproject_api-1.6.1-py3-none-any.whl (12 kB) | |
| Collecting virtualenv>=20.25 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/7aa/9982a728ae589/virtualenv-20.26.1-py3-none-any.whl (3.9 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 3.9/3.9 MB 199.2 MB/s eta 0:00:00 | |
| Collecting distlib<1,>=0.3.7 (from virtualenv>=20.25->tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/034/db59a0b96f8ca/distlib-0.3.8-py2.py3-none-any.whl (468 kB) | |
| âââââââââââââââââââââââââââââââââââââ 468.9/468.9 kB 277.7 MB/s eta 0:00:00 | |
| Installing collected packages: distlib, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
| Successfully installed cachetools-5.3.3 chardet-5.2.0 colorama-0.4.6 distlib-0.3.8 filelock-3.14.0 packaging-24.0 platformdirs-4.2.1 pluggy-1.5.0 pyproject-api-1.6.1 tox-4.15.0 virtualenv-20.26.1 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1715614631: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:1715614631: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/J1278737/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/J1278737/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==1.24.2,packaging==24.0,pathspec==0.12.1,pip==24.0,pluggy==1.5.0,setuptools==69.5.1,setuptools-scm==8.1.0,trove-classifiers==2024.4.10,wheel==0.43.0 | |
| .pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278737/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/J1278737/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.2.2.dev24.tar.gz | |
| docs: freeze> python -m pip freeze --all | |
| docs: alabaster==0.7.16,Babel==2.15.0,certifi==2024.2.2,charset-normalizer==3.3.2,docopt==0.6.2,docutils==0.18.1,h5py==3.11.0,idna==3.7,imagesize==1.4.1,Jinja2==3.1.4,libsonata==0.1.26,MarkupSafe==2.1.5,neurodamus @ file:///gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278737/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.2.2.dev24.tar.gz#sha256=d8ed36bad447d6675412a12089fae4a42b5319ef49366ec5f679007807efeec2,numpy==1.26.4,packaging==24.0,pip==24.0,psutil==5.9.8,Pygments==2.18.0,requests==2.31.0,setuptools==69.5.1,snowballstemmer==2.2.0,Sphinx==5.0.2,sphinx-bluebrain-theme==0.4.4,sphinxcontrib-applehelp==1.0.8,sphinxcontrib-devhelp==1.0.6,sphinxcontrib-htmlhelp==2.0.5,sphinxcontrib-jsmath==1.0.1,sphinxcontrib-qthelp==1.0.7,sphinxcontrib-serializinghtml==1.1.10,urllib3==2.2.1,wheel==0.43.0 | |
| 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/J1278737/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| docs: OK (236.20=setup[215.77]+cmd[20.42] seconds) | |
| congratulations :) (237.08 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1715614870:section_tox [0K | |
| section_end:1715614870:step_script [0Ksection_start:1715614870: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=91653 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=1278737 responseStatus[0;m=201 Created token[0;m=glcbt-64 | |
| section_end:1715614872:upload_artifacts_on_success [0Ksection_start:1715614872: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:1715614873: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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Learn more about bidirectional Unicode characters
| [0KRunning with gitlab-runner 16.10.0 (81ab07f6)[0;m | |
| [0K on kubernetes z_hx4W-s, system ID: r_04euBIqrn4Pl[0;m | |
| section_start:1715614537:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1715614537:resolve_secrets [0Ksection_start:1715614537: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:1715614537:prepare_executor [0Ksection_start:1715614537: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-zhx4w-s-project-2354-concurrent-0-ama5kjqm to be running, status is Pending | |
| Running on runner-zhx4w-s-project-2354-concurrent-0-ama5kjqm via cs-gitlab-runners-gitlab-runner-8488ffdb8c-khrmj... | |
| section_end:1715614542:prepare_script [0Ksection_start:1715614542: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 bb40a954 as detached HEAD (ref is weji/cache-neuron)...[0;m | |
| [32;1mUpdating/initializing submodules recursively with git depth set to 100...[0;m | |
| [32;1mUpdated submodules[0;m | |
| section_end:1715614549:get_sources [0Ksection_start:1715614549: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:1715614549:step_script [0Ksection_start:1715614549: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=1278743 responseStatus[0;m=201 Created token[0;m=glcbt-64 | |
| section_end:1715614551:upload_artifacts_on_success [0Ksection_start:1715614551:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| section_end:1715614552: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.
Learn more about bidirectional Unicode characters
| [0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1715614538:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1715614538:resolve_secrets [0Ksection_start:1715614538: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-executor467354653, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 210758, build ref , job ID 1278740 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1278740, 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_J1278740_PROD_P2354_CP3_C27 | |
| 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 2178914 | |
| 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_J1278740_PROD_P2354_CP3_C27 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1278740 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1278740 --ntasks=1 --jobid=2178914 --cpus-per-task=6 --mem=30750M | |
| section_end:1715614541:prepare_executor [0Ksection_start:1715614541:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i5n2 via bbpv1.epfl.ch... | |
| section_end:1715614550:prepare_script [0Ksection_start:1715614550: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/J1278740/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out bb40a954 as weji/cache-neuron...[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:1715614571:get_sources [0Ksection_start:1715614571: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/2024-05/externals/linux-rhel7-skylake/python/3.12.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/python/3.8.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/python/3.9.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/python/3.10.13 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/python/3.11.6 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/git/2.42.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/cmake/3.27.7 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/graphviz/8.0.5 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/intel-oneapi-mkl/2023.2.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/hpe-mpi/2.27.p1.hmpt | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/applications/linux-rhel7-skylake/neurodamus-neocortex/2.1.0 | |
| [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/J1278740/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:1715614594: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/ba0/d021a166865d2/pip-24.0-py3-none-any.whl (2.1 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 2.1/2.1 MB 73.8 MB/s eta 0:00:00 | |
| Requirement already satisfied: setuptools in ./venv/lib/python3.11/site-packages (65.5.0) | |
| Collecting setuptools | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/c63/6ac361bc47580/setuptools-69.5.1-py3-none-any.whl (894 kB) | |
| âââââââââââââââââââââââââââââââââââââ 894.6/894.6 kB 110.4 MB/s eta 0:00:00 | |
| Collecting wheel | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/55c/570405f142630/wheel-0.43.0-py3-none-any.whl (65 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 65.8/65.8 kB 213.1 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-24.0 setuptools-69.5.1 wheel-0.43.0 | |
| [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/300/055f335d855b2/tox-4.15.0-py3-none-any.whl (155 kB) | |
| ââââââââââââââââââââââââââââââââââââââ 155.7/155.7 kB 15.9 MB/s eta 0:00:00 | |
| Collecting cachetools>=5.3.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/0ab/ad1021d3f8325/cachetools-5.3.3-py3-none-any.whl (9.3 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) | |
| ââââââââââââââââââââââââââââââââââââââ 199.4/199.4 kB 22.7 MB/s eta 0:00:00 | |
| 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>=3.13.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/433/39835842f110c/filelock-3.14.0-py3-none-any.whl (12 kB) | |
| Collecting packaging>=23.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2dd/fb553fdf02fb7/packaging-24.0-py3-none-any.whl (53 kB) | |
| ââââââââââââââââââââââââââââââââââââââââ 53.5/53.5 kB 13.4 MB/s eta 0:00:00 | |
| Collecting platformdirs>=4.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/17d/5a1161b3fd67b/platformdirs-4.2.1-py3-none-any.whl (17 kB) | |
| Collecting pluggy>=1.3 (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>=1.6.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4c0/116d60476b078/pyproject_api-1.6.1-py3-none-any.whl (12 kB) | |
| Collecting virtualenv>=20.25 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/7aa/9982a728ae589/virtualenv-20.26.1-py3-none-any.whl (3.9 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 3.9/3.9 MB 105.2 MB/s eta 0:00:00 | |
| Collecting distlib<1,>=0.3.7 (from virtualenv>=20.25->tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/034/db59a0b96f8ca/distlib-0.3.8-py2.py3-none-any.whl (468 kB) | |
| âââââââââââââââââââââââââââââââââââââ 468.9/468.9 kB 234.6 MB/s eta 0:00:00 | |
| 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/J1278740/hpc/sim/neurodamus/venv | |
| Can't uninstall 'packaging'. No files were found to uninstall. | |
| Successfully installed cachetools-5.3.3 chardet-5.2.0 colorama-0.4.6 distlib-0.3.8 filelock-3.14.0 packaging-24.0 platformdirs-4.2.1 pluggy-1.5.0 pyproject-api-1.6.1 tox-4.15.0 virtualenv-20.26.1 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1715614674: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:1715614674: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/J1278740/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/J1278740/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==1.24.2,packaging==24.0,pathspec==0.12.1,pip==24.0,pluggy==1.5.0,setuptools==69.5.1,setuptools-scm==8.1.0,trove-classifiers==2024.4.10,wheel==0.43.0 | |
| .pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278740/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/J1278740/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.2.2.dev24.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]/2168638/spack-stage/spack-stage-py-libsonata-0.1.26-yrmo7gqoak7endw3yiwgzbrvsxvikl53/spack-src,MorphIO @ file:///nvme/[MASKED]/1999465/spack-stage/spack-stage-py-morphio-3.3.6-ldbyc4finxjpb2srmufv63ymssplqotw/spack-src,mpi4py @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-mpi4py-3.1.4-x733hwb2he3bpi423fnogkrw4w33wehe/spack-src,neurodamus @ file:///nvme/[MASKED]/2168638/spack-stage/spack-stage-py-neurodamus-3.2.1-5ljhk7zjlfzillmcauyrwohjzo55uc54/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==24.0,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==69.5.1,wheel==0.43.0 | |
| bbp-model: commands[0]> python -c 'import os; print(os.environ.get('"'"'HOC_LIBRARY_PATH'"'"', '"'"''"'"'))' | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278740/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-2.1.0-nefgvo/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/J1278740/hpc/sim/neurodamus/.tox/bbp-model/bin/python | |
| cachedir: .tox/bbp-model/.pytest_cache | |
| rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278740/hpc/sim/neurodamus | |
| configfile: pyproject.toml | |
| plugins: forked-1.6.0 | |
| collecting ... collected 26 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_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_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 | |
| tests/integration-e2e/test_synapse_reader.py::test_gapjunction_sonata_reader PASSED | |
| =============================== warnings summary =============================== | |
| neurodamus/core/configuration.py:161 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278740/hpc/sim/neurodamus/neurodamus/core/configuration.py:161: 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 ============================== | |
| 45.29s call tests/integration-e2e/test_cli_opts.py::test_cli_lb_mode | |
| 37.77s call tests/integration-e2e/test_loadbalance.py::test_load_balance_integrated | |
| 35.69s call tests/integration-e2e/test_loadbalance.py::test_loadbal_integration | |
| 35.60s call tests/integration-e2e/test_loadbalance.py::test_multisplit | |
| 23.18s call tests/integration-e2e/test_reports.py::test_v5_sonata_reports | |
| ============= 25 passed, 1 skipped, 1 warning in 279.58s (0:04:39) ============= | |
| .pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278740/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| bbp-model: OK (390.17=setup[110.00]+cmd[0.06,280.11] seconds) | |
| congratulations :) (391.27 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1715615068:section_tox [0K | |
| section_end:1715615068:step_script [0Ksection_start:1715615068: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:1715615069: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:1715614537:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1715614537:resolve_secrets [0Ksection_start:1715614537: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-executor1561902610, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 210758, build ref , job ID 1278739 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1278739, 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_J1278739_PROD_P2354_CP2_C21 | |
| 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 2178913 | |
| 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_J1278739_PROD_P2354_CP2_C21 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1278739 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1278739 --ntasks=1 --jobid=2178913 --cpus-per-task=6 --mem=30750M | |
| section_end:1715614541:prepare_executor [0Ksection_start:1715614541:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i5n2 via bbpv1.epfl.ch... | |
| section_end:1715614552:prepare_script [0Ksection_start:1715614552: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/J1278739/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out bb40a954 as weji/cache-neuron...[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:1715614571:get_sources [0Ksection_start:1715614571: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/2024-05/externals/linux-rhel7-skylake/python/3.12.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/python/3.8.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/python/3.9.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/python/3.10.13 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/python/3.11.6 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/git/2.42.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/cmake/3.27.7 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/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/J1278739/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:1715614591: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/ba0/d021a166865d2/pip-24.0-py3-none-any.whl (2.1 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 2.1/2.1 MB 76.2 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/c63/6ac361bc47580/setuptools-69.5.1-py3-none-any.whl (894 kB) | |
| âââââââââââââââââââââââââââââââââââââ 894.6/894.6 kB 187.0 MB/s eta 0:00:00 | |
| Collecting wheel | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/55c/570405f142630/wheel-0.43.0-py3-none-any.whl (65 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 65.8/65.8 kB 207.2 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-24.0 setuptools-69.5.1 wheel-0.43.0 | |
| [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/300/055f335d855b2/tox-4.15.0-py3-none-any.whl (155 kB) | |
| ââââââââââââââââââââââââââââââââââââââ 155.7/155.7 kB 12.2 MB/s eta 0:00:00 | |
| Collecting cachetools>=5.3.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/0ab/ad1021d3f8325/cachetools-5.3.3-py3-none-any.whl (9.3 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) | |
| ââââââââââââââââââââââââââââââââââââââ 199.4/199.4 kB 55.7 MB/s eta 0:00:00 | |
| 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>=3.13.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/433/39835842f110c/filelock-3.14.0-py3-none-any.whl (12 kB) | |
| Collecting packaging>=23.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2dd/fb553fdf02fb7/packaging-24.0-py3-none-any.whl (53 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 53.5/53.5 kB 216.2 MB/s eta 0:00:00 | |
| Collecting platformdirs>=4.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/17d/5a1161b3fd67b/platformdirs-4.2.1-py3-none-any.whl (17 kB) | |
| Collecting pluggy>=1.3 (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>=1.6.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4c0/116d60476b078/pyproject_api-1.6.1-py3-none-any.whl (12 kB) | |
| Collecting virtualenv>=20.25 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/7aa/9982a728ae589/virtualenv-20.26.1-py3-none-any.whl (3.9 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 3.9/3.9 MB 178.7 MB/s eta 0:00:00 | |
| Collecting distlib<1,>=0.3.7 (from virtualenv>=20.25->tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/034/db59a0b96f8ca/distlib-0.3.8-py2.py3-none-any.whl (468 kB) | |
| âââââââââââââââââââââââââââââââââââââ 468.9/468.9 kB 262.3 MB/s eta 0:00:00 | |
| Installing collected packages: distlib, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
| Successfully installed cachetools-5.3.3 chardet-5.2.0 colorama-0.4.6 distlib-0.3.8 filelock-3.14.0 packaging-24.0 platformdirs-4.2.1 pluggy-1.5.0 pyproject-api-1.6.1 tox-4.15.0 virtualenv-20.26.1 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1715614655: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:1715614655: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/J1278739/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/J1278739/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==1.24.2,packaging==24.0,pathspec==0.12.1,pip==24.0,pluggy==1.5.0,setuptools==69.5.1,setuptools-scm==8.1.0,trove-classifiers==2024.4.10,wheel==0.43.0 | |
| .pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/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/J1278739/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.2.2.dev24.tar.gz | |
| integration: freeze> python -m pip freeze --all | |
| integration: docopt==0.6.2,find_libpython==0.4.0,h5py==3.11.0,iniconfig==2.0.0,libsonata==0.1.26,morphio==3.3.9,neurodamus @ file:///gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.2.2.dev24.tar.gz#sha256=d8ed36bad447d6675412a12089fae4a42b5319ef49366ec5f679007807efeec2,NEURON==8.2.4,numpy==1.26.4,packaging==24.0,pip==24.0,pluggy==1.5.0,psutil==5.9.8,py==1.11.0,pytest==7.4.0,pytest-forked==1.6.0,scipy==1.13.0,setuptools==69.5.1,wheel==0.43.0 | |
| integration: commands[0]> ci/build_ndcore.sh /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/neurodamus/data | |
| + CORE_DIR=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/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/J1278739/hpc/sim/neurodamus/neurodamus/data/mod/ALU.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/neurodamus/data/mod/CoreNEURONArtificialCell.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/neurodamus/data/mod/HDF5reader.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/neurodamus/data/mod/netstim_inhpoisson.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/neurodamus/data/mod/SonataReportHelper.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/neurodamus/data/mod/SonataReports.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/neurodamus/data/mod/VecStim.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/J1278739/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/J1278739/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/HDF5reader.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/ALU.mod | |
| -> [32mNMODL[0m ../mods.tmp/CoreNEURONArtificialCell.mod | |
| -> [32mNMODL[0m ../mods.tmp/DetAMPANMDA.mod | |
| Translating CoreNEURONArtificialCell.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/x86_64/CoreNEURONArtificialCell.c | |
| Translating ALU.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/x86_64/ALU.c | |
| Translating DetAMPANMDA.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/x86_64/DetAMPANMDA.c | |
| Thread Safe | |
| Thread Safe | |
| Warning: next_delay_weight undefined. (declared within VERBATIM?) | |
| Warning: next_delay_t undefined. (declared within VERBATIM?) | |
| 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/J1278739/hpc/sim/neurodamus/x86_64/DetGABAAB.c | |
| Translating gap.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/x86_64/gap.c | |
| Thread Safe | |
| Warning: next_delay_weight undefined. (declared within VERBATIM?) | |
| Warning: next_delay_t undefined. (declared within VERBATIM?) | |
| Thread Safe | |
| Translating GluSynapse.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/x86_64/GluSynapse.c | |
| -> [32mNMODL[0m ../mods.tmp/HDF5reader.mod | |
| -> [32mNMODL[0m ../mods.tmp/netstim_inhpoisson.mod | |
| Warning: next_delay_weight undefined. (declared within VERBATIM?) | |
| Warning: next_delay_t undefined. (declared within VERBATIM?) | |
| Thread Safe | |
| -> [32mNMODL[0m ../mods.tmp/ProbAMPANMDA_EMS.mod | |
| Translating HDF5reader.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/x86_64/HDF5reader.c | |
| Notice: Use of POINTER is not thread safe. | |
| Notice: VERBATIM blocks are not thread safe | |
| Translating netstim_inhpoisson.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/x86_64/netstim_inhpoisson.c | |
| Warning: POST_RESTORE_RESTART_FLAG undefined. (declared within VERBATIM?) | |
| Notice: ARTIFICIAL_CELL is a synonym for POINT_PROCESS which hints that it | |
| only affects and is affected by discrete events. As such it is not | |
| located in a section and is not associated with an integrator | |
| Thread Safe | |
| 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 | |
| -> [32mNMODL[0m ../mods.tmp/ProbGABAAB_EMS.mod | |
| -> [32mNMODL[0m ../mods.tmp/SonataReportHelper.mod | |
| Translating ProbAMPANMDA_EMS.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/x86_64/ProbAMPANMDA_EMS.c | |
| Notice: This mechanism cannot be used with CVODE | |
| Notice: A_AMPA discontinuity adjustment not available. | |
| Notice: B_AMPA discontinuity adjustment not available. | |
| Notice: A_NMDA discontinuity adjustment not available. | |
| Notice: B_NMDA discontinuity adjustment not available. | |
| Warning: dt undefined. (declared within VERBATIM?) | |
| Warning: next_delay_weight undefined. (declared within VERBATIM?) | |
| Warning: next_delay_t undefined. (declared within VERBATIM?) | |
| Thread Safe | |
| -> [32mNMODL[0m ../mods.tmp/SonataReports.mod | |
| Translating ProbGABAAB_EMS.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/x86_64/ProbGABAAB_EMS.c | |
| Translating SonataReportHelper.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/x86_64/SonataReportHelper.c | |
| Notice: This mechanism cannot be used with CVODE | |
| Notice: A_GABAA discontinuity adjustment not available. | |
| Notice: B_GABAA discontinuity adjustment not available. | |
| Notice: A_GABAB discontinuity adjustment not available. | |
| Notice: B_GABAB discontinuity adjustment not available. | |
| Warning: dt undefined. (declared within VERBATIM?) | |
| Warning: next_delay_weight undefined. (declared within VERBATIM?) | |
| Warning: next_delay_t undefined. (declared within VERBATIM?) | |
| Thread Safe | |
| Thread Safe | |
| -> [32mNMODL[0m ../mods.tmp/TTXDynamicsSwitch.mod | |
| -> [32mNMODL[0m ../mods.tmp/VecStim.mod | |
| Translating SonataReports.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/x86_64/SonataReports.c | |
| Thread Safe | |
| -> [32mCompiling[0m ALU.c | |
| Translating VecStim.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/x86_64/VecStim.c | |
| Translating TTXDynamicsSwitch.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/x86_64/TTXDynamicsSwitch.c | |
| Thread Safe | |
| Thread Safe | |
| -> [32mCompiling[0m CoreNEURONArtificialCell.c | |
| -> [32mCompiling[0m DetAMPANMDA.c | |
| -> [32mCompiling[0m DetGABAAB.c | |
| -> [32mCompiling[0m gap.c | |
| -> [32mCompiling[0m GluSynapse.c | |
| -> [32mCompiling[0m HDF5reader.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/J1278739/hpc/sim/neurodamus/neurodamus/data/hoc/Cell.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/neurodamus/data/hoc/ConnectionUtils.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/neurodamus/data/hoc/defvar.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/neurodamus/data/hoc/fileUtils.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/neurodamus/data/hoc/Map.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/neurodamus/data/hoc/MorphIO.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/neurodamus/data/hoc/neurodamus.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/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/J1278739/hpc/sim/neurodamus/neurodamus/data | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/neurodamus/data | |
| + ls -l | |
| total 80 | |
| -rw-rw----+ 1 bbpcihpcsim bbp 561 May 13 17:35 authors.txt | |
| drwxrwx---+ 3 bbpcihpcsim bbp 4096 May 13 17:35 _benchmarks | |
| -rw-rw----+ 1 bbpcihpcsim bbp 27245 May 13 17:35 CHANGES.rst | |
| drwxrwx---+ 2 bbpcihpcsim bbp 4096 May 13 17:35 ci | |
| drwxrwx---+ 7 bbpcihpcsim bbp 4096 May 13 17:39 _common | |
| -rw-rw----+ 1 bbpcihpcsim bbp 6240 May 13 17:35 CONTRIBUTING.md | |
| drwxrwx---+ 2 bbpcihpcsim bbp 4096 May 13 17:35 docker | |
| drwxrwx---+ 5 bbpcihpcsim bbp 4096 May 13 17:35 docs | |
| drwxrwx---+ 2 bbpcihpcsim bbp 4096 May 13 17:35 examples | |
| drwxrwx---+ 2 bbpcihpcsim bbp 4096 May 13 17:39 _lib | |
| -rw-rw----+ 1 bbpcihpcsim bbp 11358 May 13 17:35 LICENSE.txt | |
| drwxrwx---+ 3 bbpcihpcsim bbp 4096 May 13 17:36 local_config | |
| drwxrwx---+ 2 bbpcihpcsim bbp 4096 May 13 17:39 mods.tmp | |
| drwxrwx---+ 6 bbpcihpcsim bbp 4096 May 13 17:35 neurodamus | |
| -rw-rw----+ 1 bbpcihpcsim bbp 1347 May 13 17:35 pyproject.toml | |
| -rw-rw----+ 1 bbpcihpcsim bbp 4598 May 13 17:35 README.rst | |
| -rw-rw----+ 1 bbpcihpcsim bbp 52 May 13 17:35 requirements_docs.txt | |
| -rw-rw----+ 1 bbpcihpcsim bbp 28 May 13 17:35 requirements.txt | |
| drwxrwx---+ 10 bbpcihpcsim bbp 4096 May 13 17:35 tests | |
| -rw-rw----+ 1 bbpcihpcsim bbp 1422 May 13 17:35 tox.ini | |
| drwxrwx---+ 5 bbpcihpcsim bbp 4096 May 13 17:36 venv | |
| drwxrwx---+ 3 bbpcihpcsim bbp 4096 May 13 17:39 x86_64 | |
| + ls -l _lib | |
| total 5 | |
| -rw-rw----+ 1 bbpcihpcsim bbp 2470 May 13 17:39 AMPANMDAHelper.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 15774 May 13 17:39 Cell.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 1064 May 13 17:39 ConnectionUtils.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 998 May 13 17:39 defvar.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 1173 May 13 17:39 DetAMPANMDAHelper.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 1636 May 13 17:39 DetGABAABHelper.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 1971 May 13 17:39 fileUtils.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 3294 May 13 17:39 GABAABHelper.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 3736 May 13 17:39 GluSynapseHelper.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 4633 May 13 17:39 GluSynapseLegacyHelper.hoc | |
| -rwxrwx---+ 1 bbpcihpcsim bbp 334552 May 13 17:39 libnrnmech.so | |
| -rw-rw----+ 1 bbpcihpcsim bbp 10723 May 13 17:39 Map.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 976 May 13 17:39 MorphIO.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 371 May 13 17:39 neurodamus.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 6805 May 13 17:39 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/J1278739/hpc/sim/neurodamus/.tox/integration/bin/python | |
| cachedir: .tox/integration/.pytest_cache | |
| rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/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:161 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/.tox/integration/lib/python3.11/site-packages/neurodamus/core/configuration.py:161: 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 3.99s ========================= | |
| .pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278739/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| integration: OK (130.87=setup[120.24]+cmd[5.88,4.76] seconds) | |
| congratulations :) (131.80 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1715614788:section_tox [0K | |
| section_end:1715614788:step_script [0Ksection_start:1715614788: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:1715614789: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:1715614539:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1715614539:resolve_secrets [0Ksection_start:1715614539: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-executor681914844, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 210758, build ref , job ID 1278742 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1278742, 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_J1278742_PROD_P2354_CP5_C35 | |
| 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 2178916 | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1278742_PROD_P2354_CP5_C35 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1278742 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1278742 --ntasks=1 --jobid=2178916 --cpus-per-task=6 --mem=30750M | |
| section_end:1715614540:prepare_executor [0Ksection_start:1715614540:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i5n2 via bbpv1.epfl.ch... | |
| section_end:1715614550:prepare_script [0Ksection_start:1715614550: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/J1278742/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out bb40a954 as weji/cache-neuron...[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:1715614571:get_sources [0Ksection_start:1715614571: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/2024-05/externals/linux-rhel7-skylake/python/3.12.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/python/3.8.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/python/3.9.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/python/3.10.13 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/python/3.11.6 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/git/2.42.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/cmake/3.27.7 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/graphviz/8.0.5 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/intel-oneapi-mkl/2023.2.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/hpe-mpi/2.27.p1.hmpt | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/applications/linux-rhel7-skylake/neurodamus-neocortex-multiscale/2.1.0 | |
| [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/J1278742/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:1715614594: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/ba0/d021a166865d2/pip-24.0-py3-none-any.whl (2.1 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 2.1/2.1 MB 75.8 MB/s eta 0:00:00 | |
| Requirement already satisfied: setuptools in ./venv/lib/python3.11/site-packages (65.5.0) | |
| Collecting setuptools | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/c63/6ac361bc47580/setuptools-69.5.1-py3-none-any.whl (894 kB) | |
| âââââââââââââââââââââââââââââââââââââ 894.6/894.6 kB 107.3 MB/s eta 0:00:00 | |
| Collecting wheel | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/55c/570405f142630/wheel-0.43.0-py3-none-any.whl (65 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 65.8/65.8 kB 210.1 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-24.0 setuptools-69.5.1 wheel-0.43.0 | |
| [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/300/055f335d855b2/tox-4.15.0-py3-none-any.whl (155 kB) | |
| ââââââââââââââââââââââââââââââââââââââ 155.7/155.7 kB 15.7 MB/s eta 0:00:00 | |
| Collecting cachetools>=5.3.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/0ab/ad1021d3f8325/cachetools-5.3.3-py3-none-any.whl (9.3 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) | |
| ââââââââââââââââââââââââââââââââââââââ 199.4/199.4 kB 23.3 MB/s eta 0:00:00 | |
| 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>=3.13.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/433/39835842f110c/filelock-3.14.0-py3-none-any.whl (12 kB) | |
| Collecting packaging>=23.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2dd/fb553fdf02fb7/packaging-24.0-py3-none-any.whl (53 kB) | |
| ââââââââââââââââââââââââââââââââââââââââ 53.5/53.5 kB 11.9 MB/s eta 0:00:00 | |
| Collecting platformdirs>=4.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/17d/5a1161b3fd67b/platformdirs-4.2.1-py3-none-any.whl (17 kB) | |
| Collecting pluggy>=1.3 (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>=1.6.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4c0/116d60476b078/pyproject_api-1.6.1-py3-none-any.whl (12 kB) | |
| Collecting virtualenv>=20.25 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/7aa/9982a728ae589/virtualenv-20.26.1-py3-none-any.whl (3.9 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 3.9/3.9 MB 110.5 MB/s eta 0:00:00 | |
| Collecting distlib<1,>=0.3.7 (from virtualenv>=20.25->tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/034/db59a0b96f8ca/distlib-0.3.8-py2.py3-none-any.whl (468 kB) | |
| âââââââââââââââââââââââââââââââââââââ 468.9/468.9 kB 271.0 MB/s eta 0:00:00 | |
| 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/J1278742/hpc/sim/neurodamus/venv | |
| Can't uninstall 'packaging'. No files were found to uninstall. | |
| Successfully installed cachetools-5.3.3 chardet-5.2.0 colorama-0.4.6 distlib-0.3.8 filelock-3.14.0 packaging-24.0 platformdirs-4.2.1 pluggy-1.5.0 pyproject-api-1.6.1 tox-4.15.0 virtualenv-20.26.1 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1715614668: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:1715614668: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/J1278742/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/J1278742/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==1.24.2,packaging==24.0,pathspec==0.12.1,pip==24.0,pluggy==1.5.0,setuptools==69.5.1,setuptools-scm==8.1.0,trove-classifiers==2024.4.10,wheel==0.43.0 | |
| .pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278742/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/J1278742/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.2.2.dev24.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]/2168638/spack-stage/spack-stage-py-libsonata-0.1.26-yrmo7gqoak7endw3yiwgzbrvsxvikl53/spack-src,MorphIO @ file:///nvme/[MASKED]/1999465/spack-stage/spack-stage-py-morphio-3.3.6-ldbyc4finxjpb2srmufv63ymssplqotw/spack-src,mpi4py @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-mpi4py-3.1.4-x733hwb2he3bpi423fnogkrw4w33wehe/spack-src,neurodamus @ file:///nvme/[MASKED]/2168638/spack-stage/spack-stage-py-neurodamus-3.2.1-5ljhk7zjlfzillmcauyrwohjzo55uc54/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==24.0,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==69.5.1,wheel==0.43.0 | |
| bbp-model: commands[0]> python -c 'import os; print(os.environ.get('"'"'HOC_LIBRARY_PATH'"'"', '"'"''"'"'))' | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278742/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-2.1.0-rierx4/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/J1278742/hpc/sim/neurodamus/.tox/bbp-model/bin/python | |
| cachedir: .tox/bbp-model/.pytest_cache | |
| rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278742/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 ============================== | |
| 51.61s call tests/scientific-ngv/test_ngv.py::test_vasccouplingB_radii | |
| (2 durations < 15s hidden. Use -vv to show these durations.) | |
| ============================== 1 passed in 52.08s ============================== | |
| .pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278742/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| bbp-model: OK (165.41=setup[112.67]+cmd[0.10,52.64] seconds) | |
| congratulations :) (166.47 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1715614837:section_tox [0K | |
| section_end:1715614837:step_script [0Ksection_start:1715614837: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:1715614838: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:1715614538:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1715614538:resolve_secrets [0Ksection_start:1715614538: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-executor3942915226, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 210758, build ref , job ID 1278741 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1278741, 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_J1278741_PROD_P2354_CP4_C34 | |
| 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 2178915 | |
| job state: PD | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1278741_PROD_P2354_CP4_C34 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1278741 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1278741 --ntasks=1 --jobid=2178915 --cpus-per-task=6 --mem=30750M | |
| section_end:1715614541:prepare_executor [0Ksection_start:1715614541:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i5n2 via bbpv1.epfl.ch... | |
| section_end:1715614552:prepare_script [0Ksection_start:1715614552: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/J1278741/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out bb40a954 as weji/cache-neuron...[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:1715614572:get_sources [0Ksection_start:1715614572:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
| [0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m | |
| Using git from spack modules | |
| [32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m | |
| [32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m | |
| [32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m | |
| [32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m | |
| [32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m | |
| [32;1m$ module purge[0;m | |
| [32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m | |
| [32;1m$ module load unstable python/3.12.0[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.12.0 | |
| [32;1m$ module load unstable python/3.8.18[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.8.18 | |
| [32;1m$ module load unstable python/3.9.18[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.9.18 | |
| [32;1m$ module load unstable python/3.10.13[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.10.13 | |
| [32;1m$ module load unstable python/3.11.6[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.11.6 | |
| [32;1m$ load-modules() { # collapsed multi-line command[0;m | |
| [32;1m$ load-modules $SYSTEM_MODULES[0;m | |
| Loaded module git from unstable | |
| Loaded module cmake from unstable | |
| Loaded module graphviz from unstable | |
| [32;1m$ load-modules $EXTRA_MODULES[0;m | |
| Loaded module intel-oneapi-compilers from unstable | |
| Loaded module py-bluepysnap from unstable | |
| Loaded module neurodamus-neocortex from unstable | |
| [32;1m$ module list -t[0;m | |
| Currently Loaded Modulefiles: | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/python/3.12.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/python/3.8.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/python/3.9.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/python/3.10.13 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/python/3.11.6 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/git/2.42.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/cmake/3.27.7 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/graphviz/8.0.5 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/compilers/linux-rhel7-haswell/intel-oneapi-compilers/2023.2.1 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/intel-oneapi-mkl/2023.2.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/hpe-mpi/2.27.p1.hmpt | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/applications/linux-rhel7-skylake/py-bluepysnap/3.0.1 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/applications/linux-rhel7-skylake/neurodamus-neocortex/2.1.0 | |
| [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/J1278741/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:1715614601: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/ba0/d021a166865d2/pip-24.0-py3-none-any.whl (2.1 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 2.1/2.1 MB 69.5 MB/s eta 0:00:00 | |
| Requirement already satisfied: setuptools in /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-setuptools-68.0.0-p3xbqx/lib/python3.11/site-packages (68.0.0) | |
| Collecting setuptools | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/c63/6ac361bc47580/setuptools-69.5.1-py3-none-any.whl (894 kB) | |
| ââââââââââââââââââââââââââââââââââââââ 894.6/894.6 kB 48.3 MB/s eta 0:00:00 | |
| Collecting wheel | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/55c/570405f142630/wheel-0.43.0-py3-none-any.whl (65 kB) | |
| ââââââââââââââââââââââââââââââââââââââââ 65.8/65.8 kB 15.6 MB/s eta 0:00:00 | |
| Installing collected packages: wheel, setuptools, pip | |
| Attempting uninstall: setuptools | |
| Found existing installation: setuptools 68.0.0 | |
| Not uninstalling setuptools at /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-setuptools-68.0.0-p3xbqx/lib/python3.11/site-packages, outside environment /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278741/hpc/sim/neurodamus/venv | |
| Can't uninstall 'setuptools'. No files were found to uninstall. | |
| Attempting uninstall: pip | |
| Found existing installation: pip 23.2.1 | |
| Uninstalling pip-23.2.1: | |
| Successfully uninstalled pip-23.2.1 | |
| Successfully installed pip-24.0 setuptools-65.5.0 wheel-0.43.0 | |
| [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/300/055f335d855b2/tox-4.15.0-py3-none-any.whl (155 kB) | |
| ââââââââââââââââââââââââââââââââââââââ 155.7/155.7 kB 15.3 MB/s eta 0:00:00 | |
| Collecting cachetools>=5.3.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/0ab/ad1021d3f8325/cachetools-5.3.3-py3-none-any.whl (9.3 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) | |
| ââââââââââââââââââââââââââââââââââââââ 199.4/199.4 kB 19.7 MB/s eta 0:00:00 | |
| 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>=3.13.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/433/39835842f110c/filelock-3.14.0-py3-none-any.whl (12 kB) | |
| Collecting packaging>=23.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2dd/fb553fdf02fb7/packaging-24.0-py3-none-any.whl (53 kB) | |
| ââââââââââââââââââââââââââââââââââââââââ 53.5/53.5 kB 9.4 MB/s eta 0:00:00 | |
| Collecting platformdirs>=4.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/17d/5a1161b3fd67b/platformdirs-4.2.1-py3-none-any.whl (17 kB) | |
| Collecting pluggy>=1.3 (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>=1.6.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4c0/116d60476b078/pyproject_api-1.6.1-py3-none-any.whl (12 kB) | |
| Collecting virtualenv>=20.25 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/7aa/9982a728ae589/virtualenv-20.26.1-py3-none-any.whl (3.9 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 3.9/3.9 MB 109.7 MB/s eta 0:00:00 | |
| Collecting distlib<1,>=0.3.7 (from virtualenv>=20.25->tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/034/db59a0b96f8ca/distlib-0.3.8-py2.py3-none-any.whl (468 kB) | |
| âââââââââââââââââââââââââââââââââââââ 468.9/468.9 kB 103.4 MB/s eta 0:00:00 | |
| 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/J1278741/hpc/sim/neurodamus/venv | |
| Can't uninstall 'packaging'. No files were found to uninstall. | |
| Successfully installed cachetools-5.3.3 chardet-5.2.0 colorama-0.4.6 distlib-0.3.8 filelock-3.14.0 packaging-24.0 platformdirs-4.2.1 pluggy-1.5.0 pyproject-api-1.6.1 tox-4.15.0 virtualenv-20.26.1 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1715614700: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:1715614700: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/J1278741/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/J1278741/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==1.24.2,packaging==24.0,pathspec==0.12.1,pip==24.0,pluggy==1.5.0,setuptools==69.5.1,setuptools-scm==8.1.0,trove-classifiers==2024.4.10,wheel==0.43.0 | |
| .pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278741/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/J1278741/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.2.2.dev24.tar.gz | |
| bbp-model: freeze> python -m pip freeze --all | |
| bbp-model: attrs @ file:///nvme/[MASKED]/2168638/spack-stage/spack-stage-py-attrs-23.1.0-r6enfrrneplexqngww6mv4idfupw2vjm/spack-src,bluepysnap @ file:///nvme/[MASKED]/2168890/spack-stage/spack-stage-py-bluepysnap-3.0.1-ozqs7cfcm443vowqbfidzb55bormynsm/spack-src,Bottleneck @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-bottleneck-1.3.7-reskjku2fhby75ljzxdozjw2l3w7ywov/spack-src,cached-property @ file:///nvme/[MASKED]/1998173/spack-stage/spack-stage-py-cached-property-1.5.2-4ra43fkav4led5iceclzwqkgfbqpigp2/spack-src,click @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-click-8.1.7-uppfa4dbkn3thlvfus7yusscvyx6jcbl/spack-src,contourpy @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-contourpy-1.0.7-zjyhvvw5jf6zl6ymi4izavk7qifgt74g/spack-src,cycler @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-cycler-0.11.0-rjj5clifiqnwny3vechb5v66hvaiy76y/spack-src,deprecation @ file:///nvme/[MASKED]/1998173/spack-stage/spack-stage-py-deprecation-2.1.0-qqtamvzujmbchjj24k5drbi753ovygnv/spack-src,docopt @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-docopt-0.6.2-noukz4jts6de5g3xamvap6n4mh7mmcsy/spack-src,fonttools @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-fonttools-4.39.4-z2lufuxxznv35oq32lldyarzx26e5k4o/spack-src,h5py @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-h5py-3.8.0-5woxna6nieu5jokc2tdxsfmolza6724e/spack-src,importlib-resources @ file:///nvme/[MASKED]/1999508/spack-stage/spack-stage-py-importlib-resources-5.12.0-tzns2fbqmiwlczz6jt4pxr3ycakrqvc7/spack-src,iniconfig==2.0.0,jsonschema @ file:///nvme/[MASKED]/2168638/spack-stage/spack-stage-py-jsonschema-4.17.3-3shrbhzoj6gpic4vgrekm4rspnxodadr/spack-src,kiwisolver @ file:///nvme/[MASKED]/1999465/spack-stage/spack-stage-py-kiwisolver-1.4.5-eh2wcdfnihumaea4n2zlqf2speb7qh4z/spack-src,libsonata @ file:///nvme/[MASKED]/2168638/spack-stage/spack-stage-py-libsonata-0.1.26-yrmo7gqoak7endw3yiwgzbrvsxvikl53/spack-src,matplotlib @ file:///nvme/[MASKED]/1999465/spack-stage/spack-stage-py-matplotlib-3.8.1-gdsdw2ni2jkl4h5ctu7d3uc7zkukcgbt/spack-src,more-itertools @ file:///nvme/[MASKED]/1998173/spack-stage/spack-stage-py-more-itertools-9.1.0-j5cqgsrmywy3254zni76f3rd3xza4ond/spack-src,morph-tool @ file:///nvme/[MASKED]/2046135/spack-stage/spack-stage-py-morph-tool-2.9.1-fsdk5ta6k6og5iij4ut63w5qmmyr4var/spack-src,MorphIO @ file:///nvme/[MASKED]/1999465/spack-stage/spack-stage-py-morphio-3.3.6-ldbyc4finxjpb2srmufv63ymssplqotw/spack-src,mpi4py @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-mpi4py-3.1.4-x733hwb2he3bpi423fnogkrw4w33wehe/spack-src,neurodamus @ file:///nvme/[MASKED]/2168638/spack-stage/spack-stage-py-neurodamus-3.2.1-5ljhk7zjlfzillmcauyrwohjzo55uc54/spack-src,neurom @ file:///nvme/[MASKED]/2046135/spack-stage/spack-stage-py-neurom-3.2.4-6wbrfox5pcxfxt53aoo2tgl3aja26wwd/spack-src,numexpr @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-numexpr-2.8.4-wu4xk2pywd64hyhoqfr57fzxfbzuuj2y/spack-src,numpy @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-numpy-1.26.1-elr5pntecdmhfynrjk3actlxb4go2bua/spack-src,numpy-quaternion @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-numpy-quaternion-2021.11.4.15.26.3-n3ap27fwuc6c7emgakpydtlt7yvk7nhi/spack-src,packaging @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-packaging-23.1-uqml2togm4tkpdvzr37r5dnsrpnd76j2/spack-src,pandas @ file:///nvme/[MASKED]/1999465/spack-stage/spack-stage-py-pandas-1.5.3-zd4wiyt5mnihf5stkktnaatq7mb4xlqd/spack-src,Pillow @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pillow-10.0.0-ygox4axk4dznocekteux3ecwkyfjndzk/spack-src,pip==24.0,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,pyparsing @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pyparsing-3.0.9-v3agjtpvgnpemnowjrjcowiw2ksk4xke/spack-src,pyrsistent @ file:///nvme/[MASKED]/1998173/spack-stage/spack-stage-py-pyrsistent-0.19.3-lzzxq7szeqnnyawu4d363tyqva3jui2v/spack-src,pytest==7.4.0,pytest-forked==1.6.0,python-dateutil @ file:///nvme/[MASKED]/1999465/spack-stage/spack-stage-py-python-dateutil-2.8.2-deg2kve3zwqhool34wn4tgxk2shs543p/spack-src,pytz @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pytz-2023.3-nr5mf4btvdphj755hbmkq57as5rmwtun/spack-src,PyYAML @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pyyaml-6.0-c3eqkahwrcjjvgo2irs4ocswyrgh2p64/spack-src,scipy @ file:///nvme/[MASKED]/2045970/spack-stage/spack-stage-py-scipy-1.11.3-dhxei7gha3wm6mobqp3urw6k4ovd7blx/spack-src,setuptools @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-setuptools-68.0.0-p3xbqxjqvq45co6xoirlfe5ydwive63k/spack-src/setuptools-68.0.0-py3-none-any.whl#sha256=11e52c67415a381d10d6b462ced9cfb97066179f0e871399e006c4ab101fc85f,six @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-six-1.16.0-brkaopna2ofwxv7qsutpldwizeauixze/spack-src,spatial-index @ file:///nvme/[MASKED]/2168890/spack-stage/spack-stage-spatial-index-2.1.0-byctkc5hq75da2ynvncealalqilduszn/spack-src,tqdm @ file:///nvme/[MASKED]/1999465/spack-stage/spack-stage-py-tqdm-4.66.1-hskcxsqsus2dj2llmtici7mfycwmrmku/spack-src,wheel==0.43.0,xmltodict @ file:///nvme/[MASKED]/1998173/spack-stage/spack-stage-py-xmltodict-0.12.0-wgpjtfuvtu6cuzobkx5tatwjzfobtx6x/spack-src | |
| bbp-model: commands[0]> python -c 'import os; print(os.environ.get('"'"'HOC_LIBRARY_PATH'"'"', '"'"''"'"'))' | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278741/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-2.1.0-nefgvo/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/J1278741/hpc/sim/neurodamus/.tox/bbp-model/bin/python | |
| cachedir: .tox/bbp-model/.pytest_cache | |
| rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278741/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 FAILED | |
| =================================== FAILURES =================================== | |
| ______________________________ test_eager_caching ______________________________ | |
| self = <neurodamus.metype.Cell_V6 object at 0x2aaac1de8310>, gid = 3587718 | |
| etype_path = '/gpfs/bbp.cscs.ch/project/proj83/singlecell/release_2020-07-31/hoc' | |
| emodel = 'cSTUT_L6NGC' | |
| morpho_path = '/gpfs/bbp.cscs.ch/project/proj83/morphologies/fixed_ais_L23PC_20201210/ascii' | |
| meinfos_v6 = <neurodamus.metype.METypeItem object at 0x2aaac1de8040> | |
| detailed_axon = False | |
| def _instantiate_cell(self, gid, etype_path, emodel, morpho_path, meinfos_v6, detailed_axon): | |
| """Instantiates a SSCx v6 cell | |
| """ | |
| Nd.load_hoc(ospath.join(etype_path, emodel)) | |
| EModel = getattr(Nd, emodel) | |
| morpho_file = meinfos_v6.morph_name + "." + self.morpho_extension | |
| keep_axon = detailed_axon and self.KEEP_AXON_FLAG | |
| add_params = meinfos_v6.add_params or (keep_axon,) # Keep axon incompatible with add_params | |
| logging.debug("Loading Gid %d: emodel: %s, Morphology: %s", gid, emodel, morpho_file) | |
| try: | |
| # For this step, do not call mpi_abort in neuron and let neurodamus handle and abort, | |
| # NB: Do not re-raise as ConfigurationError, neurodamus doesn't call mpi_abort so hangs | |
| old_flag = Nd.pc.mpiabort_on_error(0) | |
| > self._cellref = EModel(gid, morpho_path, morpho_file, *add_params) | |
| E RuntimeError: hocobj_call error: hoc_execerror: /gpfs/bbp.cscs.ch/project/proj83/morphologies/fixed_ais_L23PC_20201210/ascii/rp110711_C3_idA_-_Scale_x1.000_y1.025_z1.000_-_Clone_1.asc :file is not open | |
| neurodamus/metype.py:165: RuntimeError | |
| The above exception was the direct cause of the following exception: | |
| @pytest.mark.slow | |
| def test_eager_caching(): | |
| """ | |
| A test of the impact of eager caching of synaptic parameters. BBPBGLIB-813 | |
| """ | |
| from neurodamus.core import NeurodamusCore as Nd | |
| # create Node from config | |
| GlobalConfig.verbosity = LogLevel.VERBOSE | |
| n = Node(str(CONFIG_FILE)) | |
| # append Connection blocks programmatically | |
| # plasticity | |
| CONN_plast = {"Source": "pre_L5_PCs", | |
| "Destination": "post_L5_PC", | |
| "ModOverride": "GluSynapse", | |
| "Weight": 1.0} | |
| SimConfig.connections["plasticity"] = CONN_plast | |
| # init_I_E | |
| CONN_i2e = {"Source": "pre_L5_BCs", | |
| "Destination": "post_L5_PC", | |
| "Weight": 1.0 | |
| } | |
| SimConfig.connections["init_I_E"] = CONN_i2e | |
| assert len(SimConfig.connections) == 2 | |
| # setup sim | |
| n.load_targets() | |
| > n.create_cells() | |
| tests/scientific/test_patched_delays.py:40: | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| neurodamus/core/_utils.py:37: in mpi_ok_wrapper | |
| res = f(*args, **kw) | |
| ../../../../../../apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/python-3.11.6-bj4i6m/lib/python3.11/contextlib.py:81: in inner | |
| return func(*args, **kwds) | |
| neurodamus/node.py:482: in create_cells | |
| cell_manager.finalize() | |
| neurodamus/cell_distributor.py:272: in finalize | |
| self._instantiate_cells(**opts) | |
| neurodamus/cell_distributor.py:567: in _instantiate_cells | |
| super()._instantiate_cells(CellType, **opts) | |
| neurodamus/core/_utils.py:37: in mpi_ok_wrapper | |
| res = f(*args, **kw) | |
| neurodamus/cell_distributor.py:292: in _instantiate_cells | |
| cell = CellType(gid, cell_info, self._circuit_conf) | |
| neurodamus/metype.py:149: in __init__ | |
| super().__init__(gid, mepath, meinfo.emodel_tpl, morpho_path, meinfo, detailed_axon) | |
| neurodamus/metype.py:75: in __init__ | |
| self._instantiate_cell(gid, etype_path, emodel, morpho_path, meinfos, detailed_axon) | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| self = <neurodamus.metype.Cell_V6 object at 0x2aaac1de8310>, gid = 3587718 | |
| etype_path = '/gpfs/bbp.cscs.ch/project/proj83/singlecell/release_2020-07-31/hoc' | |
| emodel = 'cSTUT_L6NGC' | |
| morpho_path = '/gpfs/bbp.cscs.ch/project/proj83/morphologies/fixed_ais_L23PC_20201210/ascii' | |
| meinfos_v6 = <neurodamus.metype.METypeItem object at 0x2aaac1de8040> | |
| detailed_axon = False | |
| def _instantiate_cell(self, gid, etype_path, emodel, morpho_path, meinfos_v6, detailed_axon): | |
| """Instantiates a SSCx v6 cell | |
| """ | |
| Nd.load_hoc(ospath.join(etype_path, emodel)) | |
| EModel = getattr(Nd, emodel) | |
| morpho_file = meinfos_v6.morph_name + "." + self.morpho_extension | |
| keep_axon = detailed_axon and self.KEEP_AXON_FLAG | |
| add_params = meinfos_v6.add_params or (keep_axon,) # Keep axon incompatible with add_params | |
| logging.debug("Loading Gid %d: emodel: %s, Morphology: %s", gid, emodel, morpho_file) | |
| try: | |
| # For this step, do not call mpi_abort in neuron and let neurodamus handle and abort, | |
| # NB: Do not re-raise as ConfigurationError, neurodamus doesn't call mpi_abort so hangs | |
| old_flag = Nd.pc.mpiabort_on_error(0) | |
| self._cellref = EModel(gid, morpho_path, morpho_file, *add_params) | |
| Nd.pc.mpiabort_on_error(old_flag) | |
| except Exception as e: | |
| > raise RuntimeError("Error from NEURON when loading Gid %d: emodel: %s, Morphology: %s" | |
| ": %s" % (gid, emodel, morpho_file, str(e))) from e | |
| E RuntimeError: Error from NEURON when loading Gid 3587718: emodel: cSTUT_L6NGC, Morphology: rp110711_C3_idA_-_Scale_x1.000_y1.025_z1.000_-_Clone_1.asc: hocobj_call error: hoc_execerror: /gpfs/bbp.cscs.ch/project/proj83/morphologies/fixed_ais_L23PC_20201210/ascii/rp110711_C3_idA_-_Scale_x1.000_y1.025_z1.000_-_Clone_1.asc :file is not open | |
| neurodamus/metype.py:168: RuntimeError | |
| =============================== warnings summary =============================== | |
| neurodamus/core/configuration.py:161 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278741/hpc/sim/neurodamus/neurodamus/core/configuration.py:161: 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 ============================== | |
| (5 durations < 15s hidden. Use -vv to show these durations.) | |
| =========================== short test summary info ============================ | |
| FAILED tests/scientific/test_patched_delays.py::test_eager_caching | |
| !!!!!!!!!!!!!!!!!!!!!!!!!! stopping after 1 failures !!!!!!!!!!!!!!!!!!!!!!!!!!! | |
| =================== 1 failed, 12 passed, 1 warning in 46.91s =================== | |
| bbp-model: exit 1 (47.83 seconds) /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278741/hpc/sim/neurodamus> pytest -s -x --forked --durations=5 --durations-min=15 tests/scientific pid=114662 | |
| .pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278741/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| bbp-model: FAIL code 1 (138.02=setup[90.08]+cmd[0.11,47.83] seconds) | |
| evaluation failed :( (139.69 seconds) | |
| srun: error: r1i5n2: task 0: Exited with exit code 1 | |
| section_end:1715614845:step_script [0Ksection_start:1715614845: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:1715614846:cleanup_file_variables [0K[31;1mERROR: Job failed: exit status 1 | |
| [0;m |
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| [0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1715614537:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1715614537:resolve_secrets [0Ksection_start:1715614537: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-executor2454812673, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 210758, build ref , job ID 1278738 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1278738, 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_J1278738_PROD_P2354_CP1_C18 | |
| 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 2178912 | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1278738_PROD_P2354_CP1_C18 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1278738 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1278738 --ntasks=1 --jobid=2178912 --cpus-per-task=6 --mem=30750M | |
| section_end:1715614538:prepare_executor [0Ksection_start:1715614538:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i7n31 via bbpv1.epfl.ch... | |
| section_end:1715614539:prepare_script [0Ksection_start:1715614539: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/J1278738/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out bb40a954 as weji/cache-neuron...[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:1715614563:get_sources [0Ksection_start:1715614563: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/2024-05/externals/linux-rhel7-skylake/python/3.12.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/python/3.8.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/python/3.9.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/python/3.10.13 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/python/3.11.6 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/git/2.42.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/externals/linux-rhel7-skylake/cmake/3.27.7 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-05/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/J1278738/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:1715614566: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/ba0/d021a166865d2/pip-24.0-py3-none-any.whl (2.1 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 2.1/2.1 MB 74.8 MB/s eta 0:00:00 | |
| Requirement already satisfied: setuptools in ./venv/lib/python3.11/site-packages (65.5.0) | |
| Collecting setuptools | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/c63/6ac361bc47580/setuptools-69.5.1-py3-none-any.whl (894 kB) | |
| âââââââââââââââââââââââââââââââââââââ 894.6/894.6 kB 260.3 MB/s eta 0:00:00 | |
| Collecting wheel | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/55c/570405f142630/wheel-0.43.0-py3-none-any.whl (65 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 65.8/65.8 kB 215.4 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-24.0 setuptools-69.5.1 wheel-0.43.0 | |
| [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/300/055f335d855b2/tox-4.15.0-py3-none-any.whl (155 kB) | |
| ââââââââââââââââââââââââââââââââââââââ 155.7/155.7 kB 12.0 MB/s eta 0:00:00 | |
| Collecting cachetools>=5.3.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/0ab/ad1021d3f8325/cachetools-5.3.3-py3-none-any.whl (9.3 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) | |
| ââââââââââââââââââââââââââââââââââââââ 199.4/199.4 kB 53.9 MB/s eta 0:00:00 | |
| 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>=3.13.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/433/39835842f110c/filelock-3.14.0-py3-none-any.whl (12 kB) | |
| Collecting packaging>=23.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2dd/fb553fdf02fb7/packaging-24.0-py3-none-any.whl (53 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 53.5/53.5 kB 224.8 MB/s eta 0:00:00 | |
| Collecting platformdirs>=4.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/17d/5a1161b3fd67b/platformdirs-4.2.1-py3-none-any.whl (17 kB) | |
| Collecting pluggy>=1.3 (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>=1.6.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4c0/116d60476b078/pyproject_api-1.6.1-py3-none-any.whl (12 kB) | |
| Collecting virtualenv>=20.25 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/7aa/9982a728ae589/virtualenv-20.26.1-py3-none-any.whl (3.9 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 3.9/3.9 MB 181.1 MB/s eta 0:00:00 | |
| Collecting distlib<1,>=0.3.7 (from virtualenv>=20.25->tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/034/db59a0b96f8ca/distlib-0.3.8-py2.py3-none-any.whl (468 kB) | |
| âââââââââââââââââââââââââââââââââââââ 468.9/468.9 kB 264.9 MB/s eta 0:00:00 | |
| Installing collected packages: distlib, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
| Successfully installed cachetools-5.3.3 chardet-5.2.0 colorama-0.4.6 distlib-0.3.8 filelock-3.14.0 packaging-24.0 platformdirs-4.2.1 pluggy-1.5.0 pyproject-api-1.6.1 tox-4.15.0 virtualenv-20.26.1 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1715614622: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:1715614622: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==7.0.0,Flake8-pyproject==1.2.3,mccabe==0.7.0,pip==24.0,pycodestyle==2.11.1,pyflakes==3.2.0,setuptools==69.5.1,wheel==0.43.0 | |
| flake8: commands[0]> flake8 | |
| flake8: OK â in 24.97 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/J1278738/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/J1278738/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==1.24.2,packaging==24.0,pathspec==0.12.1,pip==24.0,pluggy==1.5.0,setuptools==69.5.1,setuptools-scm==8.1.0,trove-classifiers==2024.4.10,wheel==0.43.0 | |
| .pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278738/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/J1278738/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.2.2.dev24.tar.gz | |
| unit: freeze> python -m pip freeze --all | |
| unit: docopt==0.6.2,h5py==3.11.0,iniconfig==2.0.0,libsonata==0.1.26,neurodamus @ file:///gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278738/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.2.2.dev24.tar.gz#sha256=d8ed36bad447d6675412a12089fae4a42b5319ef49366ec5f679007807efeec2,numpy==1.26.4,packaging==24.0,pip==24.0,pluggy==1.5.0,psutil==5.9.8,py==1.11.0,pytest==7.4.0,pytest-forked==1.6.0,scipy==1.13.0,setuptools==69.5.1,wheel==0.43.0 | |
| 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/J1278738/hpc/sim/neurodamus/.tox/unit/bin/python | |
| cachedir: .tox/unit/.pytest_cache | |
| rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278738/hpc/sim/neurodamus | |
| configfile: pyproject.toml | |
| plugins: forked-1.6.0 | |
| collecting ... collected 79 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 [ 5%] | |
| 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 [ 10%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input4-expected4] PASSED [ 11%] | |
| 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 [ 15%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input8-expected8] PASSED [ 16%] | |
| 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 [ 20%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input0-expected0] PASSED [ 21%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input1-expected1] PASSED [ 22%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input2-expected2] PASSED [ 24%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input3-expected3] PASSED [ 25%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input4-expected4] PASSED [ 26%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input5-expected5] PASSED [ 27%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input6-expected6] PASSED [ 29%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input7-expected7] PASSED [ 30%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input8-expected8] PASSED [ 31%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input9-expected9] PASSED [ 32%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input10-expected10] PASSED [ 34%] | |
| tests/unit/test_conn_manager.py::test_population_ids_match PASSED [ 35%] | |
| tests/unit/test_coords.py::test_coord_mapping1 PASSED [ 36%] | |
| tests/unit/test_coords.py::test_coord_mapping2 PASSED [ 37%] | |
| tests/unit/test_core_config.py::test_write_report_config PASSED [ 39%] | |
| tests/unit/test_core_config.py::test_write_sim_config PASSED [ 40%] | |
| tests/unit/test_dry_run.py::test_dry_run_distribution PASSED [ 41%] | |
| tests/unit/test_dry_run.py::test_retrieve_unique_metypes PASSED [ 43%] | |
| tests/unit/test_init_py_config.py::test_init_empty PASSED [ 44%] | |
| tests/unit/test_init_py_config.py::test_init_non_positional PASSED [ 45%] | |
| tests/unit/test_init_py_config.py::test_init_config_only PASSED [ 46%] | |
| tests/unit/test_init_py_config.py::test_init_pass_options PASSED [ 48%] | |
| tests/unit/test_init_py_config.py::test_init_first_args PASSED [ 49%] | |
| tests/unit/test_init_py_config.py::test_init_early_config_file PASSED [ 50%] | |
| tests/unit/test_nodeset.py::test_NodeSet_base PASSED [ 51%] | |
| tests/unit/test_nodeset.py::test_NodeSet_add PASSED [ 53%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges10-ranges20-expected0] PASSED [ 54%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges11-ranges21-expected1] PASSED [ 55%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges12-ranges22-expected2] PASSED [ 56%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges13-ranges23-expected3] PASSED [ 58%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges14-ranges24-expected4] PASSED [ 59%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges15-ranges25-expected5] PASSED [ 60%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges16-ranges26-expected6] PASSED [ 62%] | |
| tests/unit/test_nodeset.py::test_ranges_vec_overlap[ranges10-vec0-expected0] PASSED [ 63%] | |
| tests/unit/test_nodeset.py::test_ranges_vec_overlap[ranges11-vec1-expected1] PASSED [ 64%] | |
| tests/unit/test_nodeset.py::test_ranges_vec_overlap[ranges12-vec2-expected2] PASSED [ 65%] | |
| tests/unit/test_nodeset.py::test_ranges_vec_overlap[ranges13-vec3-expected3] PASSED [ 67%] | |
| tests/unit/test_nodeset.py::test_ranges_vec_overlap[ranges14-vec4-expected4] PASSED [ 68%] | |
| tests/unit/test_nodeset.py::test_read_nodesets_from_file PASSED [ 69%] | |
| tests/unit/test_nodeset_target.py::test_get_local_gids PASSED [ 70%] | |
| tests/unit/test_pyutils.py::test_map_1 PASSED [ 72%] | |
| tests/unit/test_pyutils.py::test_map_other_data PASSED [ 73%] | |
| tests/unit/test_pyutils.py::test_map_duplicates PASSED [ 74%] | |
| tests/unit/test_pyutils.py::test_map_duplicates_struct PASSED [ 75%] | |
| tests/unit/test_pyutils.py::test_badly_formed PASSED [ 77%] | |
| tests/unit/test_pyutils.py::test_merge PASSED [ 78%] | |
| tests/unit/test_pyutils.py::test_merge_grouped PASSED [ 79%] | |
| tests/unit/test_pyutils.py::test_flatten_grouped PASSED [ 81%] | |
| tests/unit/test_replay_manager.py::test_replay_manager_sonata PASSED [ 82%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_flat_segment PASSED [ 83%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_pulse PASSED [ 84%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_pulse_diff_base[-1] PASSED [ 86%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_pulse_diff_base[0] PASSED [ 87%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_pulse_diff_base[1.5] PASSED [ 88%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_two_pulses PASSED [ 89%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_ramp PASSED [ 91%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_delay_ramp PASSED [ 92%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_train PASSED [ 93%] | |
| tests/unit/test_target_intersection.py::test_targetspec_overlap_name PASSED [ 94%] | |
| 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:161 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278738/hpc/sim/neurodamus/.tox/unit/lib/python3.11/site-packages/neurodamus/core/configuration.py:161: 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 | |
| ======================== 79 passed, 1 warning in 4.03s ========================= | |
| .pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1278738/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| flake8: OK (24.97=setup[22.21]+cmd[2.76] seconds) | |
| unit: OK (167.35=setup[160.78]+cmd[6.57] seconds) | |
| congratulations :) (193.10 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1715614816:section_tox [0K | |
| section_end:1715614816:step_script [0Ksection_start:1715614816: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:1715614817:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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