bbpbuildbot/GitLab logs for bluebrain-neurodamus#173 Secret

## build-package.txt
Log was not fetched because job had status: skipped

## docs.txt
[0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m
[0K  on BB5 map runner pnPo3yJy[0;m
section_start:1716990332:resolve_secrets
[0K[0K[36;1mResolving secrets[0;m[0;m
section_end:1716990332:resolve_secrets
[0Ksection_start:1716990332: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-executor2223943766, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name neurodamus
Pipeline ID 213527, build ref , job ID 1297954
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1297954, 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_J1297954_PROD_P2354_CP0_C3
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 2220028
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M    --job-name=GL_J1297954_PROD_P2354_CP0_C3 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1297954 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1297954 --ntasks=1 --jobid=2220028 --cpus-per-task=6 --mem=30750M
section_end:1716990334:prepare_executor
[0Ksection_start:1716990334:prepare_script
[0K[0K[36;1mPreparing environment[0;m[0;m
Using git from spack modules
Running on r1i4n32 via bbpv1.epfl.ch...
section_end:1716990346:prepare_script
[0Ksection_start:1716990346: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/J1297954/hpc/sim/neurodamus/.git/
[32;1mCreated fresh repository.[0;m
[32;1mChecking out 8fa643ed as weji/replay_coreneuron...[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:1716990350:get_sources
[0Ksection_start:1716990350: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/J1297954/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:1716990352: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 66.3 MB/s eta 0:00:00
Requirement already satisfied: setuptools in ./venv/lib/python3.11/site-packages (65.5.0)
Collecting setuptools
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/54f/aa7f2e8d2d11b/setuptools-70.0.0-py3-none-any.whl (863 kB)
     âââââââââââââââââââââââââââââââââââââ 863.4/863.4 kB 247.9 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 224.3 MB/s eta 0:00:00
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 65.5.0
    Uninstalling setuptools-65.5.0:
      Successfully uninstalled setuptools-65.5.0
  Attempting uninstall: pip
    Found existing installation: pip 23.2.1
    Uninstalling pip-23.2.1:
      Successfully uninstalled pip-23.2.1
Successfully installed pip-24.0 setuptools-70.0.0 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 20.1 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 38.8 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 199.3 MB/s eta 0:00:00
Collecting platformdirs>=4.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2d7/a1657e36a80ea/platformdirs-4.2.2-py3-none-any.whl (18 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/a62/4db5e94f01ad9/virtualenv-20.26.2-py3-none-any.whl (3.9 MB)
     ââââââââââââââââââââââââââââââââââââââââ 3.9/3.9 MB 45.0 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)
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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-4.2.2 pluggy-1.5.0 pyproject-api-1.6.1 tox-4.15.0 virtualenv-20.26.2
[32;1m$ section_end section_venv[0;m
[0Ksection_end:1716990366: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:1716990366: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/J1297954/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/J1297954/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==2024.5.22,wheel==0.43.0
.pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297954/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/J1297954/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.3.1.dev3.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/J1297954/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.3.1.dev3.tar.gz#sha256=7f6c290d09d8a0f428926f0ba2260b681a4a64371ce96f26101c0e80d62ec143,numpy==1.26.4,packaging==24.0,pip==24.0,psutil==5.9.8,Pygments==2.18.0,requests==2.32.2,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/J1297954/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build
  docs: OK (46.02=setup[38.35]+cmd[7.67] seconds)
  congratulations :) (46.14 seconds)
[32;1m$ section_end section_tox[0;m
[0Ksection_end:1716990413:section_tox
[0K
section_end:1716990413:step_script
[0Ksection_start:1716990413: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=223178 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=1297954 responseStatus[0;m=201 Created token[0;m=glcbt-64
section_end:1716990415:upload_artifacts_on_success
[0Ksection_start:1716990415: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:1716990417:cleanup_file_variables
[0K[32;1mJob succeeded[0;m

## GitLab logs for bluebrain-neurodamus#173
!

## publish-docs.txt
Log was not fetched because job had status: skipped

## publish-package.txt
Log was not fetched because job had status: skipped

## set-alt-branches.txt
[0KRunning with gitlab-runner 16.10.0 (81ab07f6)[0;m
[0K  on kubernetes 57R9wbgA, system ID: r_04euBIqrn4Pl[0;m
section_start:1716990332:resolve_secrets
[0K[0K[36;1mResolving secrets[0;m[0;m
section_end:1716990332:resolve_secrets
[0Ksection_start:1716990332: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:1716990332:prepare_executor
[0Ksection_start:1716990332: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-57r9wbga-project-2354-concurrent-0-j851wpdf to be running, status is Pending
Running on runner-57r9wbga-project-2354-concurrent-0-j851wpdf via cs-gitlab-runners-gitlab-runner-8488ffdb8c-khrmj...

section_end:1716990338:prepare_script
[0Ksection_start:1716990338: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 8fa643ed as detached HEAD (ref is weji/replay_coreneuron)...[0;m

[32;1mUpdating/initializing submodules recursively with git depth set to 100...[0;m
[32;1mUpdated submodules[0;m

section_end:1716990345:get_sources
[0Ksection_start:1716990345: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
NEURODAMUS_MODELS_BRANCH=weji/GluSynapse
BLUECONFIGS_PIPELINE_BRANCH=main

section_end:1716990346:step_script
[0Ksection_start:1716990346: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=1297960 responseStatus[0;m=201 Created token[0;m=glcbt-64

section_end:1716990348:upload_artifacts_on_success
[0Ksection_start:1716990348:cleanup_file_variables
[0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m

section_end:1716990348:cleanup_file_variables
[0K[32;1mJob succeeded[0;m

## test-integration-e2e.txt
[0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m
[0K  on BB5 map runner pnPo3yJy[0;m
section_start:1716990334:resolve_secrets
[0K[0K[36;1mResolving secrets[0;m[0;m
section_end:1716990334:resolve_secrets
[0Ksection_start:1716990334: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-executor3984248272, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name neurodamus
Pipeline ID 213527, build ref , job ID 1297957
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1297957, 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_J1297957_PROD_P2354_CP3_C6
Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcsim partition=prod qos= reservation=
Not executing the chown -R
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx]
Submitted batch job 2220031
job state: PD
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M    --job-name=GL_J1297957_PROD_P2354_CP3_C6 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1297957 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1297957 --ntasks=1 --jobid=2220031 --cpus-per-task=6 --mem=30750M
section_end:1716990337:prepare_executor
[0Ksection_start:1716990337:prepare_script
[0K[0K[36;1mPreparing environment[0;m[0;m
Using git from spack modules
Running on r1i7n30 via bbpv1.epfl.ch...
section_end:1716990342:prepare_script
[0Ksection_start:1716990342: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/J1297957/hpc/sim/neurodamus/.git/
[32;1mCreated fresh repository.[0;m
[32;1mChecking out 8fa643ed as weji/replay_coreneuron...[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:1716990355:get_sources
[0Ksection_start:1716990355: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/J1297957/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:1716990358: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 75.4 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/54f/aa7f2e8d2d11b/setuptools-70.0.0-py3-none-any.whl (863 kB)
     âââââââââââââââââââââââââââââââââââââ 863.4/863.4 kB 253.0 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 191.8 MB/s eta 0:00:00
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 65.5.0
    Uninstalling setuptools-65.5.0:
      Successfully uninstalled setuptools-65.5.0
  Attempting uninstall: pip
    Found existing installation: pip 23.2.1
    Uninstalling pip-23.2.1:
      Successfully uninstalled pip-23.2.1
Successfully installed pip-24.0 setuptools-70.0.0 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 18.7 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 53.7 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 218.5 MB/s eta 0:00:00
Collecting platformdirs>=4.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2d7/a1657e36a80ea/platformdirs-4.2.2-py3-none-any.whl (18 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/a62/4db5e94f01ad9/virtualenv-20.26.2-py3-none-any.whl (3.9 MB)
     ââââââââââââââââââââââââââââââââââââââââ 3.9/3.9 MB 179.7 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 278.5 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/J1297957/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-4.2.2 pluggy-1.5.0 pyproject-api-1.6.1 tox-4.15.0 virtualenv-20.26.2
[32;1m$ section_end section_venv[0;m
[0Ksection_end:1716990382: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:1716990382: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/J1297957/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/J1297957/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==2024.5.22,wheel==0.43.0
.pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297957/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/J1297957/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.3.1.dev3.tar.gz
bbp-model: freeze> python -m pip freeze --all
bbp-model: docopt @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-docopt-0.6.2-noukz4jts6de5g3xamvap6n4mh7mmcsy/spack-src,find-libpython @ file:///nvme/[MASKED]/2058794/spack-stage/spack-stage-py-find-libpython-0.3.1-5dylncaukuijf2r5t5lrj2s2y2kth2bh/spack-src,h5py @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-h5py-3.8.0-5woxna6nieu5jokc2tdxsfmolza6724e/spack-src,iniconfig==2.0.0,Jinja2 @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-jinja2-3.1.2-7validyciqteluvu43co5k7perpr2baq/spack-src,libsonata @ file:///nvme/[MASKED]/2168638/spack-stage/spack-stage-py-libsonata-0.1.26-yrmo7gqoak7endw3yiwgzbrvsxvikl53/spack-src,MarkupSafe @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-markupsafe-2.1.3-r3ehtmw6pkktralavqtazezwbkbsivnt/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,mpmath @ file:///nvme/[MASKED]/1999465/spack-stage/spack-stage-py-mpmath-1.2.1-quibu6o2qmwwkidntnfpa4ws3jfzckww/spack-src,neurodamus @ file:///nvme/[MASKED]/2209659/spack-stage/spack-stage-py-neurodamus-3.3.0-hxzpsm7mqgfnuxuj2nddox4ocgfxwudt/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,pybind11 @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pybind11-2.11.0-7rjfjlzjfm5suub2ks5ttsby2mhqlcfl/spack-src,pytest==7.4.0,pytest-forked==1.6.0,PyYAML @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pyyaml-6.0-c3eqkahwrcjjvgo2irs4ocswyrgh2p64/spack-src,scipy @ file:///nvme/[MASKED]/2045970/spack-stage/spack-stage-py-scipy-1.11.3-dhxei7gha3wm6mobqp3urw6k4ovd7blx/spack-src,setuptools==69.5.1,sympy @ file:///nvme/[MASKED]/1999465/spack-stage/spack-stage-py-sympy-1.11.1-dw56njg6spnrvf5w7qtjq7fwxmbj7kfb/spack-src,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/J1297957/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-exzmzh/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/J1297957/hpc/sim/neurodamus/.tox/bbp-model/bin/python
cachedir: .tox/bbp-model/.pytest_cache
rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297957/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:159
  /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297957/hpc/sim/neurodamus/neurodamus/core/configuration.py:159: 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 ==============================
35.20s call     tests/integration-e2e/test_cli_opts.py::test_cli_lb_mode
28.46s call     tests/integration-e2e/test_loadbalance.py::test_load_balance_integrated
28.26s call     tests/integration-e2e/test_loadbalance.py::test_loadbal_integration
28.01s call     tests/integration-e2e/test_loadbalance.py::test_multisplit
20.02s call     tests/integration-e2e/test_reports.py::test_v5_sonata_reports
============= 25 passed, 1 skipped, 1 warning in 222.91s (0:03:42) =============
.pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297957/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build
  bbp-model: OK (250.04=setup[26.70]+cmd[0.03,223.31] seconds)
  congratulations :) (250.16 seconds)
[32;1m$ section_end section_tox[0;m
[0Ksection_end:1716990633:section_tox
[0K
section_end:1716990633:step_script
[0Ksection_start:1716990633: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:1716990634:cleanup_file_variables
[0K[32;1mJob succeeded[0;m

## test-integration.txt
[0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m
[0K  on BB5 map runner pnPo3yJy[0;m
section_start:1716990333:resolve_secrets
[0K[0K[36;1mResolving secrets[0;m[0;m
section_end:1716990333:resolve_secrets
[0Ksection_start:1716990333: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-executor433655648, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name neurodamus
Pipeline ID 213527, build ref , job ID 1297956
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1297956, 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_J1297956_PROD_P2354_CP2_C5
Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcsim partition=prod qos= reservation=
Not executing the chown -R
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx]
Submitted batch job 2220030
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_J1297956_PROD_P2354_CP2_C5 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1297956 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1297956 --ntasks=1 --jobid=2220030 --cpus-per-task=6 --mem=30750M
section_end:1716990337:prepare_executor
[0Ksection_start:1716990337:prepare_script
[0K[0K[36;1mPreparing environment[0;m[0;m
Using git from spack modules
Running on r1i4n32 via bbpv1.epfl.ch...
section_end:1716990339:prepare_script
[0Ksection_start:1716990339: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/J1297956/hpc/sim/neurodamus/.git/
[32;1mCreated fresh repository.[0;m
[32;1mChecking out 8fa643ed as weji/replay_coreneuron...[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:1716990343:get_sources
[0Ksection_start:1716990343: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/J1297956/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:1716990345: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 82.4 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/54f/aa7f2e8d2d11b/setuptools-70.0.0-py3-none-any.whl (863 kB)
     âââââââââââââââââââââââââââââââââââââ 863.4/863.4 kB 270.7 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 219.2 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-70.0.0 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 18.8 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 51.5 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 227.3 MB/s eta 0:00:00
Collecting platformdirs>=4.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2d7/a1657e36a80ea/platformdirs-4.2.2-py3-none-any.whl (18 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/a62/4db5e94f01ad9/virtualenv-20.26.2-py3-none-any.whl (3.9 MB)
     ââââââââââââââââââââââââââââââââââââââââ 3.9/3.9 MB 164.0 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 274.1 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-4.2.2 pluggy-1.5.0 pyproject-api-1.6.1 tox-4.15.0 virtualenv-20.26.2
[32;1m$ section_end section_venv[0;m
[0Ksection_end:1716990361: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:1716990361: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/J1297956/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/J1297956/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==2024.5.22,wheel==0.43.0
.pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/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/J1297956/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.3.1.dev3.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/J1297956/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.3.1.dev3.tar.gz#sha256=7f6c290d09d8a0f428926f0ba2260b681a4a64371ce96f26101c0e80d62ec143,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==1.13.1,setuptools==69.5.1,wheel==0.43.0
integration: commands[0]> ci/build_ndcore.sh /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/hpc/sim/neurodamus/neurodamus/data
+ CORE_DIR=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/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/J1297956/hpc/sim/neurodamus/neurodamus/data/mod/ALU.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/hpc/sim/neurodamus/neurodamus/data/mod/CoreNEURONArtificialCell.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/hpc/sim/neurodamus/neurodamus/data/mod/HDF5reader.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/hpc/sim/neurodamus/neurodamus/data/mod/netstim_inhpoisson.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/hpc/sim/neurodamus/neurodamus/data/mod/SonataReportHelper.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/hpc/sim/neurodamus/neurodamus/data/mod/SonataReports.mod mods.tmp
+ cp -f _common/mod/DetAMPANMDA.mod _common/mod/DetGABAAB.mod _common/mod/gap.mod _common/mod/GluSynapse.mod _common/mod/netstim_inhpoisson.mod _common/mod/ProbAMPANMDA_EMS.mod _common/mod/ProbGABAAB_EMS.mod _common/mod/TTXDynamicsSwitch.mod _common/mod/VecStim.mod mods.tmp
+ nrnivmodl -incflags '-DDISABLE_REPORTINGLIB -DDISABLE_HDF5 -DDISABLE_MPI' mods.tmp
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/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/J1297956/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 DetAMPANMDA.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/hpc/sim/neurodamus/x86_64/DetAMPANMDA.c
Translating CoreNEURONArtificialCell.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/hpc/sim/neurodamus/x86_64/CoreNEURONArtificialCell.c
Translating ALU.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/hpc/sim/neurodamus/x86_64/ALU.c
Thread Safe
Warning: next_delay_weight undefined. (declared within VERBATIM?)
Warning: next_delay_t undefined. (declared within VERBATIM?)
Thread Safe
Thread Safe
 -> [32mNMODL[0m ../mods.tmp/gap.mod
 -> [32mNMODL[0m ../mods.tmp/DetGABAAB.mod
 -> [32mNMODL[0m ../mods.tmp/GluSynapse.mod
Translating gap.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/hpc/sim/neurodamus/x86_64/gap.c
Translating DetGABAAB.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/hpc/sim/neurodamus/x86_64/DetGABAAB.c
Translating GluSynapse.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/hpc/sim/neurodamus/x86_64/GluSynapse.c
Thread Safe
Warning: next_delay_weight undefined. (declared within VERBATIM?)
Warning: next_delay_t undefined. (declared within VERBATIM?)
Thread Safe
 -> [32mNMODL[0m ../mods.tmp/HDF5reader.mod
Warning: next_delay_weight undefined. (declared within VERBATIM?)
Warning: next_delay_t undefined. (declared within VERBATIM?)
 -> [32mNMODL[0m ../mods.tmp/netstim_inhpoisson.mod
Thread Safe
 -> [32mNMODL[0m ../mods.tmp/ProbAMPANMDA_EMS.mod
Translating HDF5reader.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/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/J1297956/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
Translating ProbAMPANMDA_EMS.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/hpc/sim/neurodamus/x86_64/ProbAMPANMDA_EMS.c
 -> [32mNMODL[0m ../mods.tmp/ProbGABAAB_EMS.mod
 -> [32mNMODL[0m ../mods.tmp/SonataReportHelper.mod
Notice: This mechanism cannot be used with CVODE
Notice: A_AMPA discontinuity adjustment not available.
Notice: B_AMPA discontinuity adjustment not available.
Notice: A_NMDA discontinuity adjustment not available.
Notice: B_NMDA discontinuity adjustment not available.
Warning: dt undefined. (declared within VERBATIM?)
Warning: next_delay_weight undefined. (declared within VERBATIM?)
Warning: next_delay_t undefined. (declared within VERBATIM?)
Thread Safe
 -> [32mNMODL[0m ../mods.tmp/SonataReports.mod
Translating ProbGABAAB_EMS.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/hpc/sim/neurodamus/x86_64/ProbGABAAB_EMS.c
Translating SonataReportHelper.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/hpc/sim/neurodamus/x86_64/SonataReportHelper.c
Thread Safe
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
Translating SonataReports.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/hpc/sim/neurodamus/x86_64/SonataReports.c
 -> [32mNMODL[0m ../mods.tmp/TTXDynamicsSwitch.mod
Thread Safe
 -> [32mNMODL[0m ../mods.tmp/VecStim.mod
 -> [32mCompiling[0m ALU.c
Translating TTXDynamicsSwitch.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/hpc/sim/neurodamus/x86_64/TTXDynamicsSwitch.c
Thread Safe
Translating VecStim.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/hpc/sim/neurodamus/x86_64/VecStim.c
Thread Safe
 -> [32mCompiling[0m CoreNEURONArtificialCell.c
 -> [32mCompiling[0m DetAMPANMDA.c
 -> [32mCompiling[0m DetGABAAB.c
 -> [32mCompiling[0m gap.c
 -> [32mCompiling[0m GluSynapse.c
 -> [32mCompiling[0m 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/J1297956/hpc/sim/neurodamus/neurodamus/data/hoc/Cell.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/hpc/sim/neurodamus/neurodamus/data/hoc/ConnectionUtils.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/hpc/sim/neurodamus/neurodamus/data/hoc/defvar.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/hpc/sim/neurodamus/neurodamus/data/hoc/fileUtils.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/hpc/sim/neurodamus/neurodamus/data/hoc/Map.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/hpc/sim/neurodamus/neurodamus/data/hoc/MorphIO.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/hpc/sim/neurodamus/neurodamus/data/hoc/neurodamus.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/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/J1297956/hpc/sim/neurodamus/neurodamus/data
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/hpc/sim/neurodamus/neurodamus/data
+ ls -l
total 80
-rw-rw----+  1 bbpcihpcsim bbp   561 May 29 15:45 authors.txt
drwxrwx---+  3 bbpcihpcsim bbp  4096 May 29 15:45 _benchmarks
-rw-rw----+  1 bbpcihpcsim bbp 27945 May 29 15:45 CHANGES.rst
drwxrwx---+  2 bbpcihpcsim bbp  4096 May 29 15:45 ci
drwxrwx---+  7 bbpcihpcsim bbp  4096 May 29 15:46 _common
-rw-rw----+  1 bbpcihpcsim bbp  6240 May 29 15:45 CONTRIBUTING.md
drwxrwx---+  2 bbpcihpcsim bbp  4096 May 29 15:45 docker
drwxrwx---+  5 bbpcihpcsim bbp  4096 May 29 15:45 docs
drwxrwx---+  2 bbpcihpcsim bbp  4096 May 29 15:45 examples
drwxrwx---+  2 bbpcihpcsim bbp  4096 May 29 15:46 _lib
-rw-rw----+  1 bbpcihpcsim bbp 11358 May 29 15:45 LICENSE.txt
drwxrwx---+  3 bbpcihpcsim bbp  4096 May 29 15:45 local_config
drwxrwx---+  2 bbpcihpcsim bbp  4096 May 29 15:46 mods.tmp
drwxrwx---+  6 bbpcihpcsim bbp  4096 May 29 15:45 neurodamus
-rw-rw----+  1 bbpcihpcsim bbp  1347 May 29 15:45 pyproject.toml
-rw-rw----+  1 bbpcihpcsim bbp  4598 May 29 15:45 README.rst
+ ls -l _lib
-rw-rw----+  1 bbpcihpcsim bbp    52 May 29 15:45 requirements_docs.txt
-rw-rw----+  1 bbpcihpcsim bbp    28 May 29 15:45 requirements.txt
drwxrwx---+ 10 bbpcihpcsim bbp  4096 May 29 15:45 tests
-rw-rw----+  1 bbpcihpcsim bbp  1422 May 29 15:45 tox.ini
drwxrwx---+  5 bbpcihpcsim bbp  4096 May 29 15:45 venv
drwxrwx---+  3 bbpcihpcsim bbp  4096 May 29 15:46 x86_64
total 6
-rw-rw----+ 1 bbpcihpcsim bbp   2470 May 29 15:46 AMPANMDAHelper.hoc
-rw-rw----+ 1 bbpcihpcsim bbp  15774 May 29 15:46 Cell.hoc
-rw-rw----+ 1 bbpcihpcsim bbp   1064 May 29 15:46 ConnectionUtils.hoc
-rw-rw----+ 1 bbpcihpcsim bbp    998 May 29 15:46 defvar.hoc
-rw-rw----+ 1 bbpcihpcsim bbp   1173 May 29 15:46 DetAMPANMDAHelper.hoc
-rw-rw----+ 1 bbpcihpcsim bbp   1636 May 29 15:46 DetGABAABHelper.hoc
-rw-rw----+ 1 bbpcihpcsim bbp   1971 May 29 15:46 fileUtils.hoc
-rw-rw----+ 1 bbpcihpcsim bbp   3294 May 29 15:46 GABAABHelper.hoc
-rw-rw----+ 1 bbpcihpcsim bbp   3736 May 29 15:46 GluSynapseHelper.hoc
-rw-rw----+ 1 bbpcihpcsim bbp   4633 May 29 15:46 GluSynapseLegacyHelper.hoc
-rwxrwx---+ 1 bbpcihpcsim bbp 334552 May 29 15:46 libnrnmech.so
-rw-rw----+ 1 bbpcihpcsim bbp  10723 May 29 15:46 Map.hoc
-rw-rw----+ 1 bbpcihpcsim bbp    976 May 29 15:46 MorphIO.hoc
-rw-rw----+ 1 bbpcihpcsim bbp    371 May 29 15:46 neurodamus.hoc
-rw-rw----+ 1 bbpcihpcsim bbp   2610 May 29 15:46 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/J1297956/hpc/sim/neurodamus/.tox/integration/bin/python
cachedir: .tox/integration/.pytest_cache
rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/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:159
  /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/hpc/sim/neurodamus/.tox/integration/lib/python3.11/site-packages/neurodamus/core/configuration.py:159: 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 2.99s =========================
.pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297956/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build
  integration: OK (37.01=setup[30.58]+cmd[3.11,3.32] seconds)
  congratulations :) (37.13 seconds)
[32;1m$ section_end section_tox[0;m
[0Ksection_end:1716990398:section_tox
[0K
section_end:1716990398:step_script
[0Ksection_start:1716990398: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:1716990400:cleanup_file_variables
[0K[32;1mJob succeeded[0;m

## test-scientific-ngv.txt
[0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m
[0K  on BB5 map runner pnPo3yJy[0;m
section_start:1716990335:resolve_secrets
[0K[0K[36;1mResolving secrets[0;m[0;m
section_end:1716990335:resolve_secrets
[0Ksection_start:1716990335: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-executor2093800468, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name neurodamus
Pipeline ID 213527, build ref , job ID 1297959
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1297959, 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_J1297959_PROD_P2354_CP5_C8
Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcsim partition=prod qos= reservation=
Not executing the chown -R
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx]
Submitted batch job 2220033
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M    --job-name=GL_J1297959_PROD_P2354_CP5_C8 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1297959 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1297959 --ntasks=1 --jobid=2220033 --cpus-per-task=6 --mem=30750M
section_end:1716990337:prepare_executor
[0Ksection_start:1716990337:prepare_script
[0K[0K[36;1mPreparing environment[0;m[0;m
Using git from spack modules
Running on r1i7n21 via bbpv1.epfl.ch...
section_end:1716990350:prepare_script
[0Ksection_start:1716990350: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/J1297959/hpc/sim/neurodamus/.git/
[32;1mCreated fresh repository.[0;m
[32;1mChecking out 8fa643ed as weji/replay_coreneuron...[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:1716990355:get_sources
[0Ksection_start:1716990355: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/J1297959/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:1716990357: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 75.1 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/54f/aa7f2e8d2d11b/setuptools-70.0.0-py3-none-any.whl (863 kB)
     âââââââââââââââââââââââââââââââââââââ 863.4/863.4 kB 259.8 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 208.0 MB/s eta 0:00:00
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 65.5.0
    Uninstalling setuptools-65.5.0:
      Successfully uninstalled setuptools-65.5.0
  Attempting uninstall: pip
    Found existing installation: pip 23.2.1
    Uninstalling pip-23.2.1:
      Successfully uninstalled pip-23.2.1
Successfully installed pip-24.0 setuptools-70.0.0 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 19.6 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 54.1 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 201.4 MB/s eta 0:00:00
Collecting platformdirs>=4.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2d7/a1657e36a80ea/platformdirs-4.2.2-py3-none-any.whl (18 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/a62/4db5e94f01ad9/virtualenv-20.26.2-py3-none-any.whl (3.9 MB)
     ââââââââââââââââââââââââââââââââââââââââ 3.9/3.9 MB 187.5 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 257.4 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/J1297959/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-4.2.2 pluggy-1.5.0 pyproject-api-1.6.1 tox-4.15.0 virtualenv-20.26.2
[32;1m$ section_end section_venv[0;m
[0Ksection_end:1716990372: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:1716990372: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/J1297959/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/J1297959/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==2024.5.22,wheel==0.43.0
.pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297959/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/J1297959/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.3.1.dev3.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]/2209659/spack-stage/spack-stage-py-neurodamus-3.3.0-hxzpsm7mqgfnuxuj2nddox4ocgfxwudt/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/J1297959/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-2.1.0-43aim3/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/J1297959/hpc/sim/neurodamus/.tox/bbp-model/bin/python
cachedir: .tox/bbp-model/.pytest_cache
rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297959/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 ==============================
58.79s call     tests/scientific-ngv/test_ngv.py::test_vasccouplingB_radii

(2 durations < 15s hidden.  Use -vv to show these durations.)
============================== 1 passed in 59.21s ==============================
.pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297959/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build
  bbp-model: OK (87.89=setup[28.23]+cmd[0.03,59.63] seconds)
  congratulations :) (88.02 seconds)
[32;1m$ section_end section_tox[0;m
[0Ksection_end:1716990460:section_tox
[0K
section_end:1716990460:step_script
[0Ksection_start:1716990460: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:1716990461:cleanup_file_variables
[0K[32;1mJob succeeded[0;m

## test-scientific.txt
[0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m
[0K  on BB5 map runner pnPo3yJy[0;m
section_start:1716990335:resolve_secrets
[0K[0K[36;1mResolving secrets[0;m[0;m
section_end:1716990335:resolve_secrets
[0Ksection_start:1716990335: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-executor579628255, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name neurodamus
Pipeline ID 213527, build ref , job ID 1297958
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1297958, 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_J1297958_PROD_P2354_CP4_C7
Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcsim partition=prod qos= reservation=
Not executing the chown -R
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx]
Submitted batch job 2220032
job state: PD
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M    --job-name=GL_J1297958_PROD_P2354_CP4_C7 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1297958 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1297958 --ntasks=1 --jobid=2220032 --cpus-per-task=6 --mem=30750M
section_end:1716990338:prepare_executor
[0Ksection_start:1716990338:prepare_script
[0K[0K[36;1mPreparing environment[0;m[0;m
Using git from spack modules
Running on r1i7n21 via bbpv1.epfl.ch...
section_end:1716990350:prepare_script
[0Ksection_start:1716990350: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/J1297958/hpc/sim/neurodamus/.git/
[32;1mCreated fresh repository.[0;m
[32;1mChecking out 8fa643ed as weji/replay_coreneuron...[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:1716990355:get_sources
[0Ksection_start:1716990355: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/J1297958/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:1716990357: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 73.3 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/54f/aa7f2e8d2d11b/setuptools-70.0.0-py3-none-any.whl (863 kB)
     âââââââââââââââââââââââââââââââââââââ 863.4/863.4 kB 260.7 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 201.7 MB/s eta 0:00:00
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 68.0.0
    Not uninstalling setuptools at /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-setuptools-68.0.0-p3xbqx/lib/python3.11/site-packages, outside environment /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297958/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-70.0.0 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 15.7 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 56.6 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 194.7 MB/s eta 0:00:00
Collecting platformdirs>=4.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2d7/a1657e36a80ea/platformdirs-4.2.2-py3-none-any.whl (18 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/a62/4db5e94f01ad9/virtualenv-20.26.2-py3-none-any.whl (3.9 MB)
     ââââââââââââââââââââââââââââââââââââââââ 3.9/3.9 MB 177.6 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 263.5 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/J1297958/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-4.2.2 pluggy-1.5.0 pyproject-api-1.6.1 tox-4.15.0 virtualenv-20.26.2
[32;1m$ section_end section_venv[0;m
[0Ksection_end:1716990375: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:1716990375: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/J1297958/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/J1297958/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==2024.5.22,wheel==0.43.0
.pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297958/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/J1297958/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.3.1.dev3.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,find-libpython @ file:///nvme/[MASKED]/2058794/spack-stage/spack-stage-py-find-libpython-0.3.1-5dylncaukuijf2r5t5lrj2s2y2kth2bh/spack-src,fonttools @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-fonttools-4.39.4-z2lufuxxznv35oq32lldyarzx26e5k4o/spack-src,h5py @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-h5py-3.8.0-5woxna6nieu5jokc2tdxsfmolza6724e/spack-src,importlib-resources @ file:///nvme/[MASKED]/1999508/spack-stage/spack-stage-py-importlib-resources-5.12.0-tzns2fbqmiwlczz6jt4pxr3ycakrqvc7/spack-src,iniconfig==2.0.0,Jinja2 @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-jinja2-3.1.2-7validyciqteluvu43co5k7perpr2baq/spack-src,jsonschema @ file:///nvme/[MASKED]/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,MarkupSafe @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-markupsafe-2.1.3-r3ehtmw6pkktralavqtazezwbkbsivnt/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,mpmath @ file:///nvme/[MASKED]/1999465/spack-stage/spack-stage-py-mpmath-1.2.1-quibu6o2qmwwkidntnfpa4ws3jfzckww/spack-src,neurodamus @ file:///nvme/[MASKED]/2209659/spack-stage/spack-stage-py-neurodamus-3.3.0-hxzpsm7mqgfnuxuj2nddox4ocgfxwudt/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,pybind11 @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pybind11-2.11.0-7rjfjlzjfm5suub2ks5ttsby2mhqlcfl/spack-src,pyparsing @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pyparsing-3.0.9-v3agjtpvgnpemnowjrjcowiw2ksk4xke/spack-src,pyrsistent @ file:///nvme/[MASKED]/1998173/spack-stage/spack-stage-py-pyrsistent-0.19.3-lzzxq7szeqnnyawu4d363tyqva3jui2v/spack-src,pytest==7.4.0,pytest-forked==1.6.0,python-dateutil @ file:///nvme/[MASKED]/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,sympy @ file:///nvme/[MASKED]/1999465/spack-stage/spack-stage-py-sympy-1.11.1-dw56njg6spnrvf5w7qtjq7fwxmbj7kfb/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/J1297958/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-exzmzh/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/J1297958/hpc/sim/neurodamus/.tox/bbp-model/bin/python
cachedir: .tox/bbp-model/.pytest_cache
rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297958/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 FAILED

=================================== FAILURES ===================================
_____________________ test_neuromodulation_sims_coreneuron _____________________
def test_neuromodulation_sims_coreneuron():
        from neurodamus import Neurodamus
        from neurodamus.replay import SpikeManager

        config_file = str(SIM_DIR / "simulation_config.json")
        os.chdir(SIM_DIR)
        nd = Neurodamus(config_file, disable_reports=True, simulator="CORENEURON",
                        output_path="output_coreneuron")
        nd.run()

        # compare spikes with refs
        spike_dat = Path(nd._run_conf.get("OutputRoot"))/nd._run_conf.get("SpikesFile")
        obtained_timestamps, obtained_spike_gids = SpikeManager._read_spikes_sonata(spike_dat, "All")
        spike_gids = np.array([1, 2, 2])  # 1-based
        timestamps = np.array([1.55, 2.025, 13.525])
        npt.assert_allclose(spike_gids, obtained_spike_gids)
>       npt.assert_allclose(timestamps, obtained_timestamps)

/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297958/hpc/sim/neurodamus/tests/scientific/test_neuromodulation.py:43:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

args = (<function assert_allclose.<locals>.compare at 0x2aaac1e07ce0>, array([ 1.55 ,  2.025, 13.525]), array([ 1.55 ,  2.025, 13.625]))
kwds = {'equal_nan': True, 'err_msg': '', 'header': 'Not equal to tolerance rtol=1e-07, atol=0', 'verbose': True}

    @wraps(func)
    def inner(*args, **kwds):
        with self._recreate_cm():
>           return func(*args, **kwds)
E           AssertionError:
E           Not equal to tolerance rtol=1e-07, atol=0
E
E           Mismatched elements: 1 / 3 (33.3%)
E           Max absolute difference: 0.1
E           Max relative difference: 0.00733945
E            x: array([ 1.55 ,  2.025, 13.525])
E            y: array([ 1.55 ,  2.025, 13.625])

/gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_externals/install_gcc-12.3.0-skylake/python-3.11.6-bj4i6m/lib/python3.11/contextlib.py:81: AssertionError
=============================== warnings summary ===============================
neurodamus/core/configuration.py:159
  /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297958/hpc/sim/neurodamus/neurodamus/core/configuration.py:159: 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_neuromodulation.py::test_neuromodulation_sims_coreneuron
!!!!!!!!!!!!!!!!!!!!!!!!!! stopping after 1 failures !!!!!!!!!!!!!!!!!!!!!!!!!!!
=================== 1 failed, 11 passed, 1 warning in 41.77s ===================
bbp-model: exit 1 (42.32 seconds) /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297958/hpc/sim/neurodamus> pytest -s -x --forked --durations=5 --durations-min=15 tests/scientific pid=216210
.pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297958/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build
  bbp-model: FAIL code 1 (72.41=setup[30.04]+cmd[0.05,42.32] seconds)
  evaluation failed :( (72.57 seconds)
srun: error: r1i7n21: task 0: Exited with exit code 1
section_end:1716990448:step_script
[0Ksection_start:1716990448: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:1716990449:cleanup_file_variables
[0K[31;1mERROR: Job failed: exit status 1
[0;m

## test-unit.txt
[0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m
[0K  on BB5 map runner pnPo3yJy[0;m
section_start:1716990333:resolve_secrets
[0K[0K[36;1mResolving secrets[0;m[0;m
section_end:1716990333:resolve_secrets
[0Ksection_start:1716990333: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-executor3397131191, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name neurodamus
Pipeline ID 213527, build ref , job ID 1297955
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1297955, 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_J1297955_PROD_P2354_CP1_C4
Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcsim partition=prod qos= reservation=
Not executing the chown -R
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx]
Submitted batch job 2220029
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M    --job-name=GL_J1297955_PROD_P2354_CP1_C4 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1297955 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1297955 --ntasks=1 --jobid=2220029 --cpus-per-task=6 --mem=30750M
section_end:1716990335:prepare_executor
[0Ksection_start:1716990335:prepare_script
[0K[0K[36;1mPreparing environment[0;m[0;m
Using git from spack modules
Running on r1i4n32 via bbpv1.epfl.ch...
section_end:1716990346:prepare_script
[0Ksection_start:1716990346: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/J1297955/hpc/sim/neurodamus/.git/
[32;1mCreated fresh repository.[0;m
[32;1mChecking out 8fa643ed as weji/replay_coreneuron...[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:1716990351:get_sources
[0Ksection_start:1716990351: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/J1297955/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:1716990353: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 73.2 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/54f/aa7f2e8d2d11b/setuptools-70.0.0-py3-none-any.whl (863 kB)
     âââââââââââââââââââââââââââââââââââââ 863.4/863.4 kB 262.9 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 217.3 MB/s eta 0:00:00
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 65.5.0
    Uninstalling setuptools-65.5.0:
      Successfully uninstalled setuptools-65.5.0
  Attempting uninstall: pip
    Found existing installation: pip 23.2.1
    Uninstalling pip-23.2.1:
      Successfully uninstalled pip-23.2.1
Successfully installed pip-24.0 setuptools-70.0.0 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 18.6 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 53.8 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 221.6 MB/s eta 0:00:00
Collecting platformdirs>=4.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2d7/a1657e36a80ea/platformdirs-4.2.2-py3-none-any.whl (18 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/a62/4db5e94f01ad9/virtualenv-20.26.2-py3-none-any.whl (3.9 MB)
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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 210.7 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-4.2.2 pluggy-1.5.0 pyproject-api-1.6.1 tox-4.15.0 virtualenv-20.26.2
[32;1m$ section_end section_venv[0;m
[0Ksection_end:1716990367: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:1716990367: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 5.88 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/J1297955/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/J1297955/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==2024.5.22,wheel==0.43.0
.pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297955/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/J1297955/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.3.1.dev3.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/J1297955/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.3.1.dev3.tar.gz#sha256=7f6c290d09d8a0f428926f0ba2260b681a4a64371ce96f26101c0e80d62ec143,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==1.13.1,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/J1297955/hpc/sim/neurodamus/.tox/unit/bin/python
cachedir: .tox/unit/.pytest_cache
rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297955/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:159
  /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297955/hpc/sim/neurodamus/.tox/unit/lib/python3.11/site-packages/neurodamus/core/configuration.py:159: 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 0.81s =========================
.pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297955/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build
  flake8: OK (5.88=setup[4.65]+cmd[1.23] seconds)
  unit: OK (28.29=setup[27.09]+cmd[1.20] seconds)
  congratulations :) (34.32 seconds)
[32;1m$ section_end section_tox[0;m
[0Ksection_end:1716990401:section_tox
[0K
section_end:1716990401:step_script
[0Ksection_start:1716990401: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:1716990403:cleanup_file_variables
[0K[32;1mJob succeeded[0;m
	[0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m
	[0K on BB5 map runner pnPo3yJy[0;m
	section_start:1716990332:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m
	section_end:1716990332:resolve_secrets [0Ksection_start:1716990332: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-executor2223943766, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
	Runner ID 29, project root hpc, project name neurodamus
	Pipeline ID 213527, build ref , job ID 1297954
	Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1297954, 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_J1297954_PROD_P2354_CP0_C3
	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 2220028
	job state: R
	sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1297954_PROD_P2354_CP0_C3 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1297954 --time=1:00:00 --wrap="sleep infinity"
	srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1297954 --ntasks=1 --jobid=2220028 --cpus-per-task=6 --mem=30750M
	section_end:1716990334:prepare_executor [0Ksection_start:1716990334:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m
	Using git from spack modules
	Running on r1i4n32 via bbpv1.epfl.ch...
	section_end:1716990346:prepare_script [0Ksection_start:1716990346: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/J1297954/hpc/sim/neurodamus/.git/
	[32;1mCreated fresh repository.[0;m
	[32;1mChecking out 8fa643ed as weji/replay_coreneuron...[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:1716990350:get_sources [0Ksection_start:1716990350: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/J1297954/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:1716990352: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 66.3 MB/s eta 0:00:00
	Requirement already satisfied: setuptools in ./venv/lib/python3.11/site-packages (65.5.0)
	Collecting setuptools
	Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/54f/aa7f2e8d2d11b/setuptools-70.0.0-py3-none-any.whl (863 kB)
	âââââââââââââââââââââââââââââââââââââ 863.4/863.4 kB 247.9 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 224.3 MB/s eta 0:00:00
	Installing collected packages: wheel, setuptools, pip
	Attempting uninstall: setuptools
	Found existing installation: setuptools 65.5.0
	Uninstalling setuptools-65.5.0:
	Successfully uninstalled setuptools-65.5.0
	Attempting uninstall: pip
	Found existing installation: pip 23.2.1
	Uninstalling pip-23.2.1:
	Successfully uninstalled pip-23.2.1
	Successfully installed pip-24.0 setuptools-70.0.0 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 20.1 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 38.8 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 199.3 MB/s eta 0:00:00
	Collecting platformdirs>=4.1 (from tox)
	Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2d7/a1657e36a80ea/platformdirs-4.2.2-py3-none-any.whl (18 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/a62/4db5e94f01ad9/virtualenv-20.26.2-py3-none-any.whl (3.9 MB)
	ââââââââââââââââââââââââââââââââââââââââ 3.9/3.9 MB 45.0 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)
	ââââââââââââââââââââââââââââââââââââââ 468.9/468.9 kB 90.5 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-4.2.2 pluggy-1.5.0 pyproject-api-1.6.1 tox-4.15.0 virtualenv-20.26.2
	[32;1m$ section_end section_venv[0;m
	[0Ksection_end:1716990366: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:1716990366: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/J1297954/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/J1297954/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==2024.5.22,wheel==0.43.0
	.pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297954/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/J1297954/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.3.1.dev3.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/J1297954/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.3.1.dev3.tar.gz#sha256=7f6c290d09d8a0f428926f0ba2260b681a4a64371ce96f26101c0e80d62ec143,numpy==1.26.4,packaging==24.0,pip==24.0,psutil==5.9.8,Pygments==2.18.0,requests==2.32.2,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/J1297954/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build
	docs: OK (46.02=setup[38.35]+cmd[7.67] seconds)
	congratulations :) (46.14 seconds)
	[32;1m$ section_end section_tox[0;m
	[0Ksection_end:1716990413:section_tox [0K
	section_end:1716990413:step_script [0Ksection_start:1716990413: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=223178 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=1297954 responseStatus[0;m=201 Created token[0;m=glcbt-64
	section_end:1716990415:upload_artifacts_on_success [0Ksection_start:1716990415: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:1716990417:cleanup_file_variables [0K[32;1mJob succeeded[0;m
	[0KRunning with gitlab-runner 16.10.0 (81ab07f6)[0;m
	[0K on kubernetes 57R9wbgA, system ID: r_04euBIqrn4Pl[0;m
	section_start:1716990332:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m
	section_end:1716990332:resolve_secrets [0Ksection_start:1716990332: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:1716990332:prepare_executor [0Ksection_start:1716990332: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-57r9wbga-project-2354-concurrent-0-j851wpdf to be running, status is Pending
	Running on runner-57r9wbga-project-2354-concurrent-0-j851wpdf via cs-gitlab-runners-gitlab-runner-8488ffdb8c-khrmj...

	section_end:1716990338:prepare_script [0Ksection_start:1716990338: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 8fa643ed as detached HEAD (ref is weji/replay_coreneuron)...[0;m

	[32;1mUpdating/initializing submodules recursively with git depth set to 100...[0;m
	[32;1mUpdated submodules[0;m

	section_end:1716990345:get_sources [0Ksection_start:1716990345: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
	NEURODAMUS_MODELS_BRANCH=weji/GluSynapse
	BLUECONFIGS_PIPELINE_BRANCH=main

	section_end:1716990346:step_script [0Ksection_start:1716990346: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=1297960 responseStatus[0;m=201 Created token[0;m=glcbt-64

	section_end:1716990348:upload_artifacts_on_success [0Ksection_start:1716990348:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m

	section_end:1716990348:cleanup_file_variables [0K[32;1mJob succeeded[0;m
	[0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m
	[0K on BB5 map runner pnPo3yJy[0;m
	section_start:1716990334:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m
	section_end:1716990334:resolve_secrets [0Ksection_start:1716990334: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-executor3984248272, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
	Runner ID 29, project root hpc, project name neurodamus
	Pipeline ID 213527, build ref , job ID 1297957
	Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1297957, 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_J1297957_PROD_P2354_CP3_C6
	Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcsim partition=prod qos= reservation=
	Not executing the chown -R
	sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS
	sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl\|clx]
	Submitted batch job 2220031
	job state: PD
	job state: R
	sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1297957_PROD_P2354_CP3_C6 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1297957 --time=1:00:00 --wrap="sleep infinity"
	srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1297957 --ntasks=1 --jobid=2220031 --cpus-per-task=6 --mem=30750M
	section_end:1716990337:prepare_executor [0Ksection_start:1716990337:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m
	Using git from spack modules
	Running on r1i7n30 via bbpv1.epfl.ch...
	section_end:1716990342:prepare_script [0Ksection_start:1716990342: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/J1297957/hpc/sim/neurodamus/.git/
	[32;1mCreated fresh repository.[0;m
	[32;1mChecking out 8fa643ed as weji/replay_coreneuron...[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:1716990355:get_sources [0Ksection_start:1716990355: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/J1297957/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:1716990358: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 75.4 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/54f/aa7f2e8d2d11b/setuptools-70.0.0-py3-none-any.whl (863 kB)
	âââââââââââââââââââââââââââââââââââââ 863.4/863.4 kB 253.0 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 191.8 MB/s eta 0:00:00
	Installing collected packages: wheel, setuptools, pip
	Attempting uninstall: setuptools
	Found existing installation: setuptools 65.5.0
	Uninstalling setuptools-65.5.0:
	Successfully uninstalled setuptools-65.5.0
	Attempting uninstall: pip
	Found existing installation: pip 23.2.1
	Uninstalling pip-23.2.1:
	Successfully uninstalled pip-23.2.1
	Successfully installed pip-24.0 setuptools-70.0.0 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 18.7 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 53.7 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 218.5 MB/s eta 0:00:00
	Collecting platformdirs>=4.1 (from tox)
	Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2d7/a1657e36a80ea/platformdirs-4.2.2-py3-none-any.whl (18 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/a62/4db5e94f01ad9/virtualenv-20.26.2-py3-none-any.whl (3.9 MB)
	ââââââââââââââââââââââââââââââââââââââââ 3.9/3.9 MB 179.7 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 278.5 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/J1297957/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-4.2.2 pluggy-1.5.0 pyproject-api-1.6.1 tox-4.15.0 virtualenv-20.26.2
	[32;1m$ section_end section_venv[0;m
	[0Ksection_end:1716990382: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:1716990382: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/J1297957/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/J1297957/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==2024.5.22,wheel==0.43.0
	.pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297957/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/J1297957/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.3.1.dev3.tar.gz
	bbp-model: freeze> python -m pip freeze --all
	bbp-model: docopt @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-docopt-0.6.2-noukz4jts6de5g3xamvap6n4mh7mmcsy/spack-src,find-libpython @ file:///nvme/[MASKED]/2058794/spack-stage/spack-stage-py-find-libpython-0.3.1-5dylncaukuijf2r5t5lrj2s2y2kth2bh/spack-src,h5py @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-h5py-3.8.0-5woxna6nieu5jokc2tdxsfmolza6724e/spack-src,iniconfig==2.0.0,Jinja2 @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-jinja2-3.1.2-7validyciqteluvu43co5k7perpr2baq/spack-src,libsonata @ file:///nvme/[MASKED]/2168638/spack-stage/spack-stage-py-libsonata-0.1.26-yrmo7gqoak7endw3yiwgzbrvsxvikl53/spack-src,MarkupSafe @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-markupsafe-2.1.3-r3ehtmw6pkktralavqtazezwbkbsivnt/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,mpmath @ file:///nvme/[MASKED]/1999465/spack-stage/spack-stage-py-mpmath-1.2.1-quibu6o2qmwwkidntnfpa4ws3jfzckww/spack-src,neurodamus @ file:///nvme/[MASKED]/2209659/spack-stage/spack-stage-py-neurodamus-3.3.0-hxzpsm7mqgfnuxuj2nddox4ocgfxwudt/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,pybind11 @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pybind11-2.11.0-7rjfjlzjfm5suub2ks5ttsby2mhqlcfl/spack-src,pytest==7.4.0,pytest-forked==1.6.0,PyYAML @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pyyaml-6.0-c3eqkahwrcjjvgo2irs4ocswyrgh2p64/spack-src,scipy @ file:///nvme/[MASKED]/2045970/spack-stage/spack-stage-py-scipy-1.11.3-dhxei7gha3wm6mobqp3urw6k4ovd7blx/spack-src,setuptools==69.5.1,sympy @ file:///nvme/[MASKED]/1999465/spack-stage/spack-stage-py-sympy-1.11.1-dw56njg6spnrvf5w7qtjq7fwxmbj7kfb/spack-src,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/J1297957/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-exzmzh/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/J1297957/hpc/sim/neurodamus/.tox/bbp-model/bin/python
	cachedir: .tox/bbp-model/.pytest_cache
	rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297957/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:159
	/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297957/hpc/sim/neurodamus/neurodamus/core/configuration.py:159: 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 ==============================
	35.20s call tests/integration-e2e/test_cli_opts.py::test_cli_lb_mode
	28.46s call tests/integration-e2e/test_loadbalance.py::test_load_balance_integrated
	28.26s call tests/integration-e2e/test_loadbalance.py::test_loadbal_integration
	28.01s call tests/integration-e2e/test_loadbalance.py::test_multisplit
	20.02s call tests/integration-e2e/test_reports.py::test_v5_sonata_reports
	============= 25 passed, 1 skipped, 1 warning in 222.91s (0:03:42) =============
	.pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297957/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build
	bbp-model: OK (250.04=setup[26.70]+cmd[0.03,223.31] seconds)
	congratulations :) (250.16 seconds)
	[32;1m$ section_end section_tox[0;m
	[0Ksection_end:1716990633:section_tox [0K
	section_end:1716990633:step_script [0Ksection_start:1716990633: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:1716990634:cleanup_file_variables [0K[32;1mJob succeeded[0;m
	[0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m
	[0K on BB5 map runner pnPo3yJy[0;m
	section_start:1716990335:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m
	section_end:1716990335:resolve_secrets [0Ksection_start:1716990335: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-executor2093800468, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
	Runner ID 29, project root hpc, project name neurodamus
	Pipeline ID 213527, build ref , job ID 1297959
	Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1297959, 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_J1297959_PROD_P2354_CP5_C8
	Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcsim partition=prod qos= reservation=
	Not executing the chown -R
	sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS
	sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl\|clx]
	Submitted batch job 2220033
	job state: R
	sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1297959_PROD_P2354_CP5_C8 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1297959 --time=1:00:00 --wrap="sleep infinity"
	srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1297959 --ntasks=1 --jobid=2220033 --cpus-per-task=6 --mem=30750M
	section_end:1716990337:prepare_executor [0Ksection_start:1716990337:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m
	Using git from spack modules
	Running on r1i7n21 via bbpv1.epfl.ch...
	section_end:1716990350:prepare_script [0Ksection_start:1716990350: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/J1297959/hpc/sim/neurodamus/.git/
	[32;1mCreated fresh repository.[0;m
	[32;1mChecking out 8fa643ed as weji/replay_coreneuron...[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:1716990355:get_sources [0Ksection_start:1716990355: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/J1297959/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:1716990357: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 75.1 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/54f/aa7f2e8d2d11b/setuptools-70.0.0-py3-none-any.whl (863 kB)
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	Collecting wheel
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	âââââââââââââââââââââââââââââââââââââââ 65.8/65.8 kB 208.0 MB/s eta 0:00:00
	Installing collected packages: wheel, setuptools, pip
	Attempting uninstall: setuptools
	Found existing installation: setuptools 65.5.0
	Uninstalling setuptools-65.5.0:
	Successfully uninstalled setuptools-65.5.0
	Attempting uninstall: pip
	Found existing installation: pip 23.2.1
	Uninstalling pip-23.2.1:
	Successfully uninstalled pip-23.2.1
	Successfully installed pip-24.0 setuptools-70.0.0 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)
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	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)
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	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)
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	Collecting packaging>=23.2 (from tox)
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	Collecting platformdirs>=4.1 (from tox)
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	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)
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	Collecting virtualenv>=20.25 (from tox)
	Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/a62/4db5e94f01ad9/virtualenv-20.26.2-py3-none-any.whl (3.9 MB)
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	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)
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	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/J1297959/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-4.2.2 pluggy-1.5.0 pyproject-api-1.6.1 tox-4.15.0 virtualenv-20.26.2
	[32;1m$ section_end section_venv[0;m
	[0Ksection_end:1716990372: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:1716990372: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/J1297959/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/J1297959/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==2024.5.22,wheel==0.43.0
	.pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297959/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/J1297959/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.3.1.dev3.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]/2209659/spack-stage/spack-stage-py-neurodamus-3.3.0-hxzpsm7mqgfnuxuj2nddox4ocgfxwudt/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/J1297959/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-2.1.0-43aim3/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/J1297959/hpc/sim/neurodamus/.tox/bbp-model/bin/python
	cachedir: .tox/bbp-model/.pytest_cache
	rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297959/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 ==============================
	58.79s call tests/scientific-ngv/test_ngv.py::test_vasccouplingB_radii

	(2 durations < 15s hidden. Use -vv to show these durations.)
	============================== 1 passed in 59.21s ==============================
	.pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1297959/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build
	bbp-model: OK (87.89=setup[28.23]+cmd[0.03,59.63] seconds)
	congratulations :) (88.02 seconds)
	[32;1m$ section_end section_tox[0;m
	[0Ksection_end:1716990460:section_tox [0K
	section_end:1716990460:step_script [0Ksection_start:1716990460: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:1716990461:cleanup_file_variables [0K[32;1mJob succeeded[0;m