Logfiles for GitLab pipeline https://bbpgitlab.epfl.ch/hpc/sim/neurodamus/-/pipelines/143266 (:no_entry:) running on GitHub PR BlueBrain/neurodamus#21.

build-package.txt

Log was not fetched because job had status: skipped

docs.txt

Running with gitlab-runner 15.5.0 (0d4137b8)
  on BB5 map runner pnPo3yJy
section_start:1691669745:resolve_secrets
Resolving secrets
section_end:1691669745:resolve_secrets
section_start:1691669745:prepare_executor
Preparing the "custom" executor
Using Custom executor with driver BB5 PROD runner v0.0.3...
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user 
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor4063056336, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name neurodamus
Pipeline ID 143266, build ref , job ID 841816
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J841816, 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_J841816_PROD_P2354_CP0_C2
Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcsim partition=prod qos= reservation=
Not executing the chown -R
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx]
Submitted batch job 1659094
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_J841816_PROD_P2354_CP0_C2 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J841816 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J841816 --ntasks=1 --jobid=1659094 --cpus-per-task=6 --mem=30750M     
section_end:1691669748:prepare_executor
section_start:1691669748:prepare_script
Preparing environment
Using git from spack modules
Running on r1i7n31 via bbpv1.epfl.ch...
section_end:1691669754:prepare_script
section_start:1691669754:get_sources
Getting source from Git repository
Using git from spack modules
$ 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 '*'
Fetching changes with git depth set to 20...
Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841816/hpc/sim/neurodamus/.git/
Created fresh repository.
Checking out 73653388 as 1uc/free-deleted-stable-identifiers...
Skipping object checkout, Git LFS is not installed.

Updating/initializing submodules recursively with git depth set to 20...
section_end:1691669757:get_sources
section_start:1691669757:step_script
Executing "step_script" stage of the job script
WARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426
Using git from spack modules
$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi
$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }
$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }
$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }
$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }
$ module purge
$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')
$ module load archive/2020-12 python/3.7.4
$ module unload archive/2020-12
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.7.4
$ module load archive/2021-12 python/3.8.3
$ module unload archive/2021-12
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.8.3
$ module load archive/2023-02 python/3.9.7
$ module unload archive/2023-02
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.9.7
$ module load unstable python
$ module unload unstable
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.10.8
$ load-modules() { # collapsed multi-line command
$ load-modules $SYSTEM_MODULES
Loaded module git from unstable
Loaded module cmake from unstable
Loaded module graphviz from unstable
$ load-modules $EXTRA_MODULES
$ module list -t
Currently Loaded Modulefiles:
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/external-libraries/2020-12/tcl/linux-rhel7-x86_64/python/3.7.4
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/externals/2021-12/tcl/linux-rhel7-x86_64/python/3.8.3
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-02/externals/linux-rhel7-skylake/python/3.9.7
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-08/externals/linux-rhel7-skylake/python/3.10.8
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-08/externals/linux-rhel7-skylake/git/2.38.1
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-08/externals/linux-rhel7-skylake/cmake/3.24.3
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-08/externals/linux-rhel7-skylake/graphviz/2.49.0
$ export XDG_CONFIG_HOME=${PWD}/local_config
$ print_var XDG_CONFIG_HOME
XDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841816/hpc/sim/neurodamus/local_config
$ mkdir -p "${XDG_CONFIG_HOME}/git"
$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command
$ cat "${XDG_CONFIG_HOME}/git/config"
[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:
$ section_start section_venv[collapsed=true] "Setting up the virtual env"
section_start:1691669759:section_venv[collapsed=true]
Setting up the virtual env
$ cd "${PYTHON_PROJECT_DIR}"
$ CI_VENV="$(pwd)/venv"
$ rm -rf "$CI_VENV"
$ python -mvenv "$CI_VENV"
$ source "$CI_VENV/bin/activate"
$ python -mpip install --upgrade pip setuptools wheel
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
Requirement already satisfied: pip in ./venv/lib/python3.10/site-packages (22.2.2)
Collecting pip
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/7cc/f472345f20d35/pip-23.2.1-py3-none-any.whl (2.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 73.6 MB/s eta 0:00:00
Requirement already satisfied: setuptools in ./venv/lib/python3.10/site-packages (63.2.0)
Collecting setuptools
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/11e/52c67415a381d/setuptools-68.0.0-py3-none-any.whl (804 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 804.0/804.0 kB 244.0 MB/s eta 0:00:00
Collecting wheel
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/473/219bd4cbedc62/wheel-0.41.1-py3-none-any.whl (64 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 64.8/64.8 kB 224.5 MB/s eta 0:00:00
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 63.2.0
    Uninstalling setuptools-63.2.0:
      Successfully uninstalled setuptools-63.2.0
  Attempting uninstall: pip
    Found existing installation: pip 22.2.2
    Uninstalling pip-22.2.2:
      Successfully uninstalled pip-22.2.2
Successfully installed pip-23.2.1 setuptools-68.0.0 wheel-0.41.1
$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
Collecting tox
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/793/99a3d4641d1fd/tox-4.7.0-py3-none-any.whl (152 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 152.4/152.4 kB 17.0 MB/s eta 0:00:00
Collecting cachetools>=5.3.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/95e/f631eeaea14ba/cachetools-5.3.1-py3-none-any.whl (9.3 kB)
Collecting chardet>=5.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 199.4/199.4 kB 24.4 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>=3.12.2 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/cbb/791cdea2a72f2/filelock-3.12.2-py3-none-any.whl (10 kB)
Collecting packaging>=23.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/994/793af429502c4/packaging-23.1-py3-none-any.whl (48 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.9/48.9 kB 205.3 MB/s eta 0:00:00
Collecting platformdirs>=3.9.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/d7c/24979f292f916/platformdirs-3.10.0-py3-none-any.whl (17 kB)
Collecting pluggy>=1.2 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/c2f/d55a7d7a3863c/pluggy-1.2.0-py3-none-any.whl (17 kB)
Collecting pyproject-api>=1.5.3 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/14c/f09828670c7b0/pyproject_api-1.5.3-py3-none-any.whl (12 kB)
Collecting tomli>=2.0.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/939/de3e7a6161af0/tomli-2.0.1-py3-none-any.whl (12 kB)
Collecting virtualenv>=20.24.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/43a/3052be3608054/virtualenv-20.24.2-py3-none-any.whl (3.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.0/3.0 MB 42.5 MB/s eta 0:00:00
Collecting distlib<1,>=0.3.7 (from virtualenv>=20.24.1->tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2e2/4928bc811348f/distlib-0.3.7-py2.py3-none-any.whl (468 kB)
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Installing collected packages: distlib, tomli, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox
Successfully installed cachetools-5.3.1 chardet-5.2.0 colorama-0.4.6 distlib-0.3.7 filelock-3.12.2 packaging-23.1 platformdirs-3.10.0 pluggy-1.2.0 pyproject-api-1.5.3 tomli-2.0.1 tox-4.7.0 virtualenv-20.24.2
$ section_end section_venv
section_end:1691669774:section_venv

$ print_var PRE_BUILD_COMMAND
PRE_BUILD_COMMAND=
$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi
$ section_start section_tox "Running Tox"
section_start:1691669774:section_tox
Running Tox
$ python -mtox $TOX_OPTIONS
docs: install_deps> python -I -m pip install sphinx-bluebrain-theme 'sphinx<5.1.0'
.pkg: install_requires> python -I -m pip install 'setuptools>=40.8.0' wheel
.pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841816/hpc/sim/neurodamus/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
.pkg: get_requires_for_build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841816/hpc/sim/neurodamus/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
.pkg: get_requires_for_build_editable> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841816/hpc/sim/neurodamus/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
.pkg: install_requires_for_build_editable> python -I -m pip install wheel
.pkg: freeze> python -m pip freeze --all
.pkg: pip==23.2.1,setuptools==68.0.0,wheel==0.41.0
.pkg: build_editable> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841816/hpc/sim/neurodamus/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
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/J841816/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-2.16.0.dev5-0.editable-py2.py3-none-any.whl
docs: freeze> python -m pip freeze --all
docs: alabaster==0.7.13,Babel==2.12.1,certifi==2023.7.22,charset-normalizer==3.2.0,docopt==0.6.2,docutils==0.18.1,h5py==3.9.0,idna==3.4,imagesize==1.4.1,Jinja2==3.0.3,libsonata==0.1.22,MarkupSafe==2.1.3,neurodamus==2.16.0.dev5,numpy==1.25.2,packaging==23.1,pip==23.2.1,psutil==5.9.5,Pygments==2.16.1,requests==2.31.0,setuptools==68.0.0,snowballstemmer==2.2.0,Sphinx==5.0.2,sphinx-bluebrain-theme==0.4.2,sphinxcontrib-applehelp==1.0.6,sphinxcontrib-devhelp==1.0.4,sphinxcontrib-htmlhelp==2.0.3,sphinxcontrib-jsmath==1.0.1,sphinxcontrib-qthelp==1.0.5,sphinxcontrib-serializinghtml==1.1.7,urllib3==2.0.4,wheel==0.41.0
docs: commands[0]> sphinx-build 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 17 source files that are out of date
updating environment: [new config] 17 added, 0 changed, 0 removed
reading sources... [  5%] api/modules
reading sources... [ 11%] api/neurodamus
reading sources... [ 17%] api/neurodamus.core
reading sources... [ 23%] api/neurodamus.io
reading sources... [ 29%] api/neurodamus.utils
reading sources... [ 35%] api/subpackages/core
reading sources... [ 41%] api/subpackages/io
reading sources... [ 47%] api/subpackages/top
reading sources... [ 52%] api/subpackages/utils
reading sources... [ 58%] architecture
reading sources... [ 64%] changes
reading sources... [ 70%] development
reading sources... [ 76%] examples
reading sources... [ 82%] index
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... [ 17%] api/neurodamus.core
writing output... [ 23%] api/neurodamus.io
writing output... [ 29%] api/neurodamus.utils
writing output... [ 35%] api/subpackages/core
writing output... [ 41%] api/subpackages/io
writing output... [ 47%] api/subpackages/top
writing output... [ 52%] api/subpackages/utils
writing output... [ 58%] architecture
writing output... [ 64%] changes
writing output... [ 70%] development
writing output... [ 76%] examples
writing output... [ 82%] index
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... [ 12%] img/neurodamus-prev-concept.png
copying images... [ 25%] img/neurodamus-prev-arch.png
copying images... [ 37%] img/neurodamus-arch.png
copying images... [ 50%] img/cell-hierarchy.png
copying images... [ 62%] img/multi-population-concept.png
copying images... [ 75%] img/cell-managers.png
copying images... [ 87%] img/conn-managers.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/J841816/hpc/sim/neurodamus/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
  docs: OK (38.73=setup[29.76]+cmd[8.97] seconds)
  congratulations :) (39.07 seconds)
$ section_end section_tox
section_end:1691669813:section_tox

section_end:1691669813:step_script
section_start:1691669813:upload_artifacts_on_success
Uploading artifacts for successful job
Using git from spack modules
Uploading artifacts...
Runtime platform                                    arch=amd64 os=linux pid=59865 revision=58ba2b95 version=14.2.0
docs/_build: found 192 matching files and directories 
Uploading artifacts as "archive" to coordinator... ok  id=841816 responseStatus=201 Created token=64_qwsCx
section_end:1691669814:upload_artifacts_on_success
section_start:1691669814:cleanup_file_variables
Cleaning up project directory and file based variables
Using git from spack modules
section_end:1691669815:cleanup_file_variables
Job succeeded

GitLab logs for bluebrain-neurodamus#21

!

publish-docs.txt

Log was not fetched because job had status: skipped

publish-package.txt

Log was not fetched because job had status: skipped

py38-full-spack.txt

Running with gitlab-runner 15.5.0 (0d4137b8)
  on BB5 map runner pnPo3yJy
section_start:1691669747:resolve_secrets
Resolving secrets
section_end:1691669747:resolve_secrets
section_start:1691669747:prepare_executor
Preparing the "custom" executor
Using Custom executor with driver BB5 PROD runner v0.0.3...
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user 
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor811545853, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name neurodamus
Pipeline ID 143266, build ref , job ID 841818
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J841818, 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_J841818_PROD_P2354_CP2_C4
Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcsim partition=prod qos= reservation=
Not executing the chown -R
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx]
Submitted batch job 1659096
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M    --job-name=GL_J841818_PROD_P2354_CP2_C4 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J841818 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J841818 --ntasks=1 --jobid=1659096 --cpus-per-task=6 --mem=30750M     
section_end:1691669748:prepare_executor
section_start:1691669748:prepare_script
Preparing environment
Using git from spack modules
Running on r1i7n31 via bbpv1.epfl.ch...
section_end:1691669754:prepare_script
section_start:1691669754:get_sources
Getting source from Git repository
Using git from spack modules
$ 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 '*'
Fetching changes with git depth set to 20...
Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841818/hpc/sim/neurodamus/.git/
Created fresh repository.
Checking out 73653388 as 1uc/free-deleted-stable-identifiers...
Skipping object checkout, Git LFS is not installed.

Updating/initializing submodules recursively with git depth set to 20...
section_end:1691669758:get_sources
section_start:1691669758:step_script
Executing "step_script" stage of the job script
WARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426
Using git from spack modules
$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi
$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }
$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }
$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }
$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }
$ module purge
$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')
$ module load archive/2020-12 python/3.7.4
$ module unload archive/2020-12
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.7.4
$ module load archive/2021-12 python/3.8.3
$ module unload archive/2021-12
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.8.3
$ module load archive/2023-02 python/3.9.7
$ module unload archive/2023-02
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.9.7
$ module load unstable python
$ module unload unstable
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.10.8
$ load-modules() { # collapsed multi-line command
$ load-modules $SYSTEM_MODULES
Loaded module git from unstable
Loaded module cmake from unstable
Loaded module graphviz from unstable
$ load-modules $EXTRA_MODULES
unstable(9):ERROR:105: Unable to locate a modulefile for 'py-psutil'
Loaded module py-psutil from unstable
Loaded module intel-oneapi-compilers from unstable
Autoloading python/3.10.8
Autoloading intel-oneapi-mkl/2021.4.0
Autoloading hpe-mpi/2.25.hmpt
Loaded module py-bluepy from unstable
Autoloading python/3.10.8
Autoloading intel-oneapi-mkl/2021.4.0
Autoloading hpe-mpi/2.25.hmpt
Loaded module neurodamus-neocortex from unstable
Autoloading python/3.10.8
Autoloading intel-oneapi-mkl/2021.4.0
Autoloading hpe-mpi/2.25.hmpt
Loaded module py-neurodamus from unstable
$ module list -t
Currently Loaded Modulefiles:
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/external-libraries/2020-12/tcl/linux-rhel7-x86_64/python/3.7.4
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/externals/2021-12/tcl/linux-rhel7-x86_64/python/3.8.3
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-02/externals/linux-rhel7-skylake/python/3.9.7
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-08/externals/linux-rhel7-skylake/python/3.10.8
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-08/externals/linux-rhel7-skylake/git/2.38.1
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-08/externals/linux-rhel7-skylake/cmake/3.24.3
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-08/externals/linux-rhel7-skylake/graphviz/2.49.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-08/compilers/linux-rhel7-haswell/intel-oneapi-compilers/2022.2.1
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-08/externals/linux-rhel7-skylake/intel-oneapi-mkl/2021.4.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-08/externals/linux-rhel7-skylake/hpe-mpi/2.25.hmpt
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-08/applications/linux-rhel7-skylake/py-bluepy/2.5.1
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-08/applications/linux-rhel7-skylake/neurodamus-neocortex/1.12-2.16.0-2.8.0
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-08/applications/linux-rhel7-skylake/py-neurodamus/2.16.0
$ export XDG_CONFIG_HOME=${PWD}/local_config
$ print_var XDG_CONFIG_HOME
XDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841818/hpc/sim/neurodamus/local_config
$ mkdir -p "${XDG_CONFIG_HOME}/git"
$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command
$ cat "${XDG_CONFIG_HOME}/git/config"
[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:
$ section_start section_venv[collapsed=true] "Setting up the virtual env"
section_start:1691669760:section_venv[collapsed=true]
Setting up the virtual env
$ cd "${PYTHON_PROJECT_DIR}"
$ CI_VENV="$(pwd)/venv"
$ rm -rf "$CI_VENV"
$ python -mvenv "$CI_VENV"
$ source "$CI_VENV/bin/activate"
$ python -mpip install --upgrade pip setuptools wheel
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
Requirement already satisfied: pip in ./venv/lib/python3.10/site-packages (22.2.2)
Collecting pip
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/7cc/f472345f20d35/pip-23.2.1-py3-none-any.whl (2.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 72.8 MB/s eta 0:00:00
Requirement already satisfied: setuptools in /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-setuptools-63.0.0-c6hdpv/lib/python3.10/site-packages (63.0.0)
Collecting setuptools
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/11e/52c67415a381d/setuptools-68.0.0-py3-none-any.whl (804 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 804.0/804.0 kB 165.6 MB/s eta 0:00:00
Collecting wheel
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/473/219bd4cbedc62/wheel-0.41.1-py3-none-any.whl (64 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 64.8/64.8 kB 232.1 MB/s eta 0:00:00
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 63.0.0
    Not uninstalling setuptools at /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-setuptools-63.0.0-c6hdpv/lib/python3.10/site-packages, outside environment /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841818/hpc/sim/neurodamus/venv
    Can't uninstall 'setuptools'. No files were found to uninstall.
  Attempting uninstall: pip
    Found existing installation: pip 22.2.2
    Uninstalling pip-22.2.2:
      Successfully uninstalled pip-22.2.2
Successfully installed pip-23.2.1 setuptools-68.0.0 wheel-0.41.1
$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
Collecting tox
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/793/99a3d4641d1fd/tox-4.7.0-py3-none-any.whl (152 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 152.4/152.4 kB 11.3 MB/s eta 0:00:00
Collecting cachetools>=5.3.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/95e/f631eeaea14ba/cachetools-5.3.1-py3-none-any.whl (9.3 kB)
Collecting chardet>=5.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 199.4/199.4 kB 40.5 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>=3.12.2 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/cbb/791cdea2a72f2/filelock-3.12.2-py3-none-any.whl (10 kB)
Collecting packaging>=23.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/994/793af429502c4/packaging-23.1-py3-none-any.whl (48 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.9/48.9 kB 200.7 MB/s eta 0:00:00
Collecting platformdirs>=3.9.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/d7c/24979f292f916/platformdirs-3.10.0-py3-none-any.whl (17 kB)
Collecting pluggy>=1.2 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/c2f/d55a7d7a3863c/pluggy-1.2.0-py3-none-any.whl (17 kB)
Collecting pyproject-api>=1.5.3 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/14c/f09828670c7b0/pyproject_api-1.5.3-py3-none-any.whl (12 kB)
Collecting tomli>=2.0.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/939/de3e7a6161af0/tomli-2.0.1-py3-none-any.whl (12 kB)
Collecting virtualenv>=20.24.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/43a/3052be3608054/virtualenv-20.24.2-py3-none-any.whl (3.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.0/3.0 MB 155.8 MB/s eta 0:00:00
Collecting distlib<1,>=0.3.7 (from virtualenv>=20.24.1->tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2e2/4928bc811348f/distlib-0.3.7-py2.py3-none-any.whl (468 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 468.9/468.9 kB 257.2 MB/s eta 0:00:00
Installing collected packages: distlib, tomli, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox
  Attempting uninstall: packaging
    Found existing installation: packaging 21.3
    Not uninstalling packaging at /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-packaging-21.3-ugynn7/lib/python3.10/site-packages, outside environment /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841818/hpc/sim/neurodamus/venv
    Can't uninstall 'packaging'. No files were found to uninstall.
Successfully installed cachetools-5.3.1 chardet-5.2.0 colorama-0.4.6 distlib-0.3.7 filelock-3.12.2 packaging-23.1 platformdirs-3.10.0 pluggy-1.2.0 pyproject-api-1.5.3 tomli-2.0.1 tox-4.7.0 virtualenv-20.24.2
$ section_end section_venv
section_end:1691669779:section_venv

$ print_var PRE_BUILD_COMMAND
PRE_BUILD_COMMAND=
$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi
$ section_start section_tox "Running Tox"
section_start:1691669779:section_tox
Running Tox
$ python -mtox $TOX_OPTIONS
bb5: install_deps> python -I -m pip install pytest pytest-cov pytest-forked pytest-xdist
.pkg: install_requires> python -I -m pip install 'setuptools>=40.8.0' wheel
.pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841818/hpc/sim/neurodamus/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
.pkg: get_requires_for_build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841818/hpc/sim/neurodamus/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
.pkg: get_requires_for_build_wheel> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841818/hpc/sim/neurodamus/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
.pkg: install_requires_for_build_wheel> python -I -m pip install wheel
.pkg: get_requires_for_build_editable> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841818/hpc/sim/neurodamus/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
.pkg: install_requires_for_build_editable> python -I -m pip install wheel
.pkg: freeze> python -m pip freeze --all
.pkg: pip==23.2.1,setuptools==68.0.0,wheel==0.41.0
.pkg: build_wheel> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841818/hpc/sim/neurodamus/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
.pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841818/hpc/sim/neurodamus/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
bb5: install_package_deps> python -I -m pip install docopt h5py libsonata psutil
bb5: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841818/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-2.16.0.dev5.tar.gz
bb5: freeze> python -m pip freeze --all
bb5: asttokens @ file:///nvme/bbpcihpcdeploy/1277566/spack-stage/spack-stage-py-asttokens-2.0.8-pwkxr5biginj2nhemauznk3hxm2ievqf/spack-src,backcall @ file:///nvme/bbpcihpcdeploy/1277510/spack-stage/spack-stage-py-backcall-0.2.0-tqc25xkppzf3yrghv2be57m74rolp5lw/spack-src,bluepy @ file:///nvme/bbpcihpcdeploy/1650361/spack-stage/spack-stage-py-bluepy-2.5.1-e44df2hu7fblz4hp7idtjrapy6o66y4y/spack-src,bluepy-configfile @ file:///nvme/bbpcihpcdeploy/1353049/spack-stage/spack-stage-py-bluepy-configfile-0.1.20-55bfeorpwrhihcm6toytm2uozcbf7hi3/spack-src,bluepyopt @ file:///nvme/bbpcihpcdeploy/1650361/spack-stage/spack-stage-py-bluepyopt-1.13.86-xaaxt6px7gz4bvraeykowj5j4tswbuob/spack-src,Bottleneck @ file:///gpfs/bbp.cscs.ch/ssd/slurmTmpFS/bbpcihpcdeploy/1645509/spack-stage/spack-stage-py-bottleneck-1.3.5-nbtnkqkzw4r5grmy2ha2xyriyik6gdmf/spack-src,cached-property @ file:///nvme/bbpcihpcdeploy/1277510/spack-stage/spack-stage-py-cached-property-1.5.2-nhmtalhtweotcmxejfe4wk5vrpzv77fk/spack-src,certifi @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-certifi-2022.9.14-tle7w753dtmfpfghsgadu7g6gtixtxxi/spack-src,cffi @ file:///nvme/bbpcihpcdeploy/1277566/spack-stage/spack-stage-py-cffi-1.15.0-ablzzy7oxan3ujlomr2toxzqdoxdvbds/spack-src,charset-normalizer @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-charset-normalizer-2.0.12-citf2jcejsiumzwu2ar5qkaxkio2byhr/spack-src,click @ file:///nvme/bbpcihpcdeploy/1277510/spack-stage/spack-stage-py-click-8.1.3-hogerxyr7gzbwys3ryq5wpsjvk4jihxp/spack-src,cloudpickle @ file:///nvme/bbpcihpcdeploy/1277566/spack-stage/spack-stage-py-cloudpickle-2.2.0-6o5ynlv5hmcrddueod6p2z2zisvockyp/spack-src,contourpy @ file:///nvme/bbpcihpcdeploy/1334696/spack-stage/spack-stage-py-contourpy-1.0.5-wzxdnvh2maqacj2xzlfvuxsi6v7ybycv/spack-src,coverage==7.2.7,cycler @ file:///nvme/bbpcihpcdeploy/1277510/spack-stage/spack-stage-py-cycler-0.11.0-4keh3r62hagsaf7l5jdp5tbp4tepkhas/spack-src,dask @ file:///nvme/bbpcihpcdeploy/1650292/spack-stage/spack-stage-py-dask-2022.10.2-mkzjnsmx7ymxpktdzdbbl6t56hu64s2q/spack-src,deap @ file:///nvme/bbpcihpcdeploy/1299870/spack-stage/spack-stage-py-deap-1.3.3-fybuhnaovu7p6hbaspnyluibhjeoybgz/spack-src,debugpy @ file:///nvme/bbpcihpcdeploy/1277566/spack-stage/spack-stage-py-debugpy-1.6.3-ax7yed36ijwhklwtslbjgneayq7qdjup/spack-src,decorator @ file:///nvme/bbpcihpcdeploy/1277566/spack-stage/spack-stage-py-decorator-5.1.1-mnqdmw6k5h5aqnq2cs7henfbin3tqqtr/spack-src,deprecation @ file:///nvme/bbpcihpcdeploy/1277566/spack-stage/spack-stage-py-deprecation-2.1.0-jug3e4tdfyrfhb2rp2ijjix3ncd5hkpk/spack-src,distributed @ file:///nvme/bbpcihpcdeploy/1650292/spack-stage/spack-stage-py-distributed-2022.10.2-txwxfxznv5q2x42mptxs2e3huglblic2/spack-src,docopt @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-docopt-0.6.2-u7r3e4y6uhhphn7jhq2tdqsw3w3nxspx/spack-src,efel @ file:///nvme/bbpcihpcdeploy/1277579/spack-stage/spack-stage-py-efel-4.0.4-uyoweppu5g72i2qk2gtvw7awchqcixh7/spack-src,entrypoints @ file:///nvme/bbpcihpcdeploy/1277510/spack-stage/spack-stage-py-entrypoints-0.4-ge4oa44x6n2vn7w2733oasksq2cuf7rs/spack-src,exceptiongroup==1.1.2,execnet==2.0.2,executing @ file:///nvme/bbpcihpcdeploy/1277566/spack-stage/spack-stage-py-executing-1.1.0-wvokdujsvyidrlmqwq4di7v3jbpxuefu/spack-src,fonttools @ file:///nvme/bbpcihpcdeploy/1334696/spack-stage/spack-stage-py-fonttools-4.37.3-ufovmgzagmjigaobnv56vt5pg46jilqz/spack-src,fsspec @ file:///gpfs/bbp.cscs.ch/ssd/slurmTmpFS/bbpcihpcdeploy/1645623/spack-stage/spack-stage-py-fsspec-2023.1.0-6qrv5vkggqyxcqrses4y5x3hm2zg3fwk/spack-src,future @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-future-0.18.2-6kugxu6r36gg6xbzvn6a6zilqq2sxeb7/spack-src,gevent @ file:///nvme/bbpcihpcdeploy/1277566/spack-stage/spack-stage-py-gevent-1.5.0-lri7laxr5n3zzinowqyjjqrorwcmjmv7/spack-src,greenlet @ file:///nvme/bbpcihpcdeploy/1277566/spack-stage/spack-stage-py-greenlet-1.1.3-mithmgfnxaq2akff5aavhcngxrmy3c7q/spack-src,h5py @ file:///nvme/bbpcihpcdeploy/1643940/spack-stage/spack-stage-py-h5py-3.8.0-zl4guqckp5gp7iprj3f45nnnifabkgwm/spack-src,idna @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-idna-3.4-sr3ijepdcc3v4yfghjk6xkxdo4bxqc4e/spack-src,iniconfig==2.0.0,ipykernel @ file:///nvme/bbpcihpcdeploy/1650361/spack-stage/spack-stage-py-ipykernel-6.16.0-fawelkl3fjiwfd4o47htpw7bawrjym7b/spack-src,ipyparallel @ file:///nvme/bbpcihpcdeploy/1650361/spack-stage/spack-stage-py-ipyparallel-8.4.1-ayieqzfr7bsnqywdek53bzy22ueppqyh/spack-src,ipython @ file:///nvme/bbpcihpcdeploy/1277566/spack-stage/spack-stage-py-ipython-8.5.0-bjmsnk3cjhifw2ddyf4f44mfaha4hyf3/spack-src,jedi @ file:///nvme/bbpcihpcdeploy/1277566/spack-stage/spack-stage-py-jedi-0.18.1-ojm24nkxorklt4pyccsge4clpa3elc5r/spack-src,Jinja2 @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-jinja2-3.1.2-3s7iuckjkeads6k7ixulnxdxhllimnri/spack-src,jupyter-client @ file:///gpfs/bbp.cscs.ch/ssd/slurmTmpFS/bbpcihpcdeploy/1645756/spack-stage/spack-stage-py-jupyter-client-7.1.2-s22hr5ehe7ed6w3geedvfnxchmphf6cs/spack-src,jupyter_core @ file:///nvme/bbpcihpcdeploy/1277566/spack-stage/spack-stage-py-jupyter-core-4.11.1-ziq4ybwtnq5uuduhztv4pbztcjpx5rwr/spack-src,kiwisolver @ file:///nvme/bbpcihpcdeploy/1334696/spack-stage/spack-stage-py-kiwisolver-1.3.2-3ar7vsmntznfptqt2752xfrssn6fte4b/spack-src,libsonata @ file:///nvme/bbpcihpcdeploy/1643940/spack-stage/spack-stage-py-libsonata-0.1.22-hzbch63pxbxsaepmtx557gx6gok524by/spack-src,locket @ file:///gpfs/bbp.cscs.ch/ssd/slurmTmpFS/bbpcihpcdeploy/1645623/spack-stage/spack-stage-py-locket-1.0.0-3rbk7nyipew7jebyjnzkhvc3g3njaral/spack-src,MarkupSafe @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-markupsafe-2.1.1-d4uhr4fhwx7whrqrt6ofdfr2w4hoxr36/spack-src,matplotlib @ file:///nvme/bbpcihpcdeploy/1334696/spack-stage/spack-stage-py-matplotlib-3.6.2-svgi5rf5ixxdo75ng6ch4clu4hx5cmyw/spack-src,matplotlib-inline @ file:///nvme/bbpcihpcdeploy/1277566/spack-stage/spack-stage-py-matplotlib-inline-0.1.3-z6ia6xf7rwp7jql6iydlfg3x6zqebhql/spack-src,more-itertools @ file:///nvme/bbpcihpcdeploy/1277510/spack-stage/spack-stage-py-more-itertools-8.14.0-5c3pblhkegdko5mrtlbifx3pnp6a6mie/spack-src,morph-tool @ file:///nvme/bbpcihpcdeploy/1650361/spack-stage/spack-stage-py-morph-tool-2.9.0-r3e6uphseh6zj7klmvrv5bvnami62lgh/spack-src,MorphIO @ file:///nvme/bbpcihpcdeploy/1643940/spack-stage/spack-stage-py-morphio-3.3.6-pkmv4tgebucjyz2embcovqtpfok2c5zb/spack-src,mpi4py @ file:///nvme/bbpcihpcdeploy/1643940/spack-stage/spack-stage-py-mpi4py-3.1.4-glx4cfnu5cionch2hbeyzns5ol3vexp7/spack-src,mpmath @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-mpmath-1.2.1-7rza5j7b6be2regpqtm3lqgkjc6wkgur/spack-src,msgpack @ file:///nvme/bbpcihpcdeploy/1277566/spack-stage/spack-stage-py-msgpack-1.0.4-kajohx426vgpsvugqy7cwzxld3vmzai7/spack-src,MVDTool @ file:///nvme/bbpcihpcdeploy/1643940/spack-stage/spack-stage-py-mvdtool-2.4.9-sy5ow4k7afte4hf2t6wgso7afama57il/spack-src,nest-asyncio @ file:///nvme/bbpcihpcdeploy/1277566/spack-stage/spack-stage-py-nest-asyncio-1.5.5-3plbvyajxsrmpsmkltt3qpvz2hurom2b/spack-src,neurodamus==2.16.0.dev5,neurom @ file:///nvme/bbpcihpcdeploy/1650361/spack-stage/spack-stage-py-neurom-3.2.2-pc3mehsjjof5kcxrr5qkmkymoceatic5/spack-src,nptyping @ file:///nvme/bbpcihpcdeploy/1277510/spack-stage/spack-stage-py-nptyping-2.4.1-cpkdqlddwjxddbh73fvoc7h2qysqaz47/spack-src,numexpr @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-numexpr-2.8.3-nk3nggbgzt4frjfma5y34mktwd7y6nkb/spack-src,numpy @ file:///nvme/bbpcihpcdeploy/1334696/spack-stage/spack-stage-py-numpy-1.22.4-ly6cmfc3te7agzn6gzifal4ufdj3bixb/spack-src,packaging @ file:///nvme/bbpcihpcdeploy/1334696/spack-stage/spack-stage-py-packaging-21.3-ugynn7hp3af6db6k3j4d7m5qktfiav5g/spack-src,pandas @ file:///nvme/bbpcihpcdeploy/1650292/spack-stage/spack-stage-py-pandas-1.5.1-jnbitoiy55zcvoxhnfspzol3hduzx3sc/spack-src,parso @ file:///nvme/bbpcihpcdeploy/1277566/spack-stage/spack-stage-py-parso-0.8.3-e4caarkwn25qtxtnghpbzqhoqndphqod/spack-src,partd @ file:///gpfs/bbp.cscs.ch/ssd/slurmTmpFS/bbpcihpcdeploy/1645623/spack-stage/spack-stage-py-partd-1.4.0-czz4lsecwbsrsthfmjonpgxwrpnxyhtw/spack-src,Pebble @ file:///nvme/bbpcihpcdeploy/1307794/spack-stage/spack-stage-py-pebble-5.0.3-q6ie3baimff5kazyzym5fdbsu2qfjpww/spack-src,pexpect @ file:///nvme/bbpcihpcdeploy/1277566/spack-stage/spack-stage-py-pexpect-4.8.0-zkkywrmhqaxpbx56sigw4mtr6cng7xze/spack-src,pickleshare @ file:///nvme/bbpcihpcdeploy/1277566/spack-stage/spack-stage-py-pickleshare-0.7.5-gsisd2qxbvigfo3rxkhwepdmqutjljrx/spack-src,Pillow @ file:///nvme/bbpcihpcdeploy/1334696/spack-stage/spack-stage-py-pillow-9.2.0-bu6x5asg3kf6vaefgaziwdvuepfbjlx5/spack-src,pip==23.2.1,plotly @ file:///nvme/bbpcihpcdeploy/1277579/spack-stage/spack-stage-py-plotly-5.2.2-xilb37irjmwaq5opqdgrwugs3etelr26/spack-src,pluggy==1.2.0,prompt-toolkit @ file:///nvme/bbpcihpcdeploy/1277566/spack-stage/spack-stage-py-prompt-toolkit-3.0.31-g7b4iospq2di75dmoviluobcqqybnkhw/spack-src,psutil @ file:///nvme/bbpcihpcdeploy/1650292/spack-stage/spack-stage-py-psutil-5.9.5-sthlvjx6auwvuxb6q3lmccthkch2gzqo/spack-src,ptyprocess @ file:///nvme/bbpcihpcdeploy/1277510/spack-stage/spack-stage-py-ptyprocess-0.7.0-ckcjrhiro5t3bo3rlhqkyutisxbsnih2/spack-src,pure-eval @ file:///nvme/bbpcihpcdeploy/1277566/spack-stage/spack-stage-py-pure-eval-0.2.2-rd2u3o33kznpxz7hubnp3axtg2sdhgpe/spack-src,py==1.11.0,pycparser @ file:///nvme/bbpcihpcdeploy/1277566/spack-stage/spack-stage-py-pycparser-2.21-yvgp57q6pfokgxov3vxvt2gzhqbz22yh/spack-src,Pygments @ file:///nvme/bbpcihpcdeploy/1277566/spack-stage/spack-stage-py-pygments-2.13.0-fxzeet7wsb4h7jovylyc7ammfo5vztef/spack-src,pynrrd @ file:///nvme/bbpcihpcdeploy/1277510/spack-stage/spack-stage-py-pynrrd-1.0.0-clsbpkngakkns2nytgnu6avpcvces5dt/spack-src,pyparsing @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-pyparsing-3.0.9-4ld7fkigcpkytqnavpn63xk2sysacq4e/spack-src,pytest==7.4.0,pytest-cov==4.1.0,pytest-forked==1.6.0,pytest-xdist==3.3.1,python-dateutil @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-python-dateutil-2.8.2-sfiwbpa6wvmhpw2o5tfqkqz6d3sfyapv/spack-src,pytz @ file:///nvme/bbpcihpcdeploy/1650292/spack-stage/spack-stage-py-pytz-2023.3-il5b4xzfcjzfw4yly4w3pmjzqe5ixgtv/spack-src,PyYAML @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-pyyaml-6.0-d4xzk5tnn4irdwh3qxoa6ttihne35b4l/spack-src,pyzmq @ file:///nvme/bbpcihpcdeploy/1343732/spack-stage/spack-stage-py-pyzmq-24.0.1-jckbdzilfor3blslypb7ry4ahqsfh7w7/spack-src,requests @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-requests-2.28.1-g7ea4mu3bbm6nxguq6dckafo5pb3mn5e/spack-src,scipy @ file:///nvme/bbpcihpcdeploy/1307435/spack-stage/spack-stage-py-scipy-1.10.0-hhwv3ka77tvxq36oflay5j4f4lz4naf7/spack-src/dist/scipy-1.10.0-cp310-cp310-linux_x86_64.whl,setuptools @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-setuptools-63.0.0-c6hdpvjjddmcm3xf5begyfpkjkzj2oke/spack-src/setuptools-63.0.0-py3-none-any.whl,six @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-six-1.16.0-4jvgkuyxgnqwcwvoniqpkoqu3j75psbo/spack-src,sortedcontainers @ file:///nvme/bbpcihpcdeploy/1277566/spack-stage/spack-stage-py-sortedcontainers-2.1.0-ysycvpibokqibyqlw4jctjh3wllmq2si/spack-src,stack-data @ file:///nvme/bbpcihpcdeploy/1277566/spack-stage/spack-stage-py-stack-data-0.5.0-fsikahpvfal75cnmhnwfyt5b5lig7s3z/spack-src,sympy @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-sympy-1.11.1-d5vf2aue7esyoaqk4gyuk4zw6lbfgllg/spack-src,tblib @ file:///nvme/bbpcihpcdeploy/1277566/spack-stage/spack-stage-py-tblib-1.6.0-d6mqnz43fyuqefhmcppgw3ydk3defugg/spack-src,tenacity @ file:///nvme/bbpcihpcdeploy/1277579/spack-stage/spack-stage-py-tenacity-8.0.1-f5kfg7ls7afaixmktozi57h5lqclgjbk/spack-src,tomli==2.0.1,toolz @ file:///nvme/bbpcihpcdeploy/1345255/spack-stage/spack-stage-py-toolz-0.12.0-tngnvec2n4x3zb6s7mfd2hwe4u4dfmjc/spack-src,tornado @ file:///gpfs/bbp.cscs.ch/ssd/slurmTmpFS/bbpcihpcdeploy/1645744/spack-stage/spack-stage-py-tornado-6.1-6tq7dy2rpy22tpxkqjznmwpzwbzdsu67/spack-src,tqdm @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-tqdm-4.64.1-qzllp2hywiblf6kqwleyr7c6reywhnoy/spack-src,traitlets @ file:///nvme/bbpcihpcdeploy/1277566/spack-stage/spack-stage-py-traitlets-5.3.0-bfpog7hugqbcjxqsckr3bjgx57h5qg4g/spack-src,typing_extensions @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-typing-extensions-4.3.0-ihcuyoxmcsrvpttgeschthry3s2dz6zl/spack-src,typish @ file:///nvme/bbpcihpcdeploy/1277510/spack-stage/spack-stage-py-typish-1.9.3-nvun3f3dpr6miltealsxtbij3utomlsg/spack-src,urllib3 @ file:///nvme/bbpcihpcdeploy/1277276/spack-stage/spack-stage-py-urllib3-1.26.12-w57ocychxkvwq2yd4gukzjsr7kolxl5l/spack-src,voxcell @ file:///nvme/bbpcihpcdeploy/1650361/spack-stage/spack-stage-py-voxcell-3.1.5-zxvialullj5glm2imoa3j7pdqumhctz4/spack-src,wcwidth @ file:///nvme/bbpcihpcdeploy/1277566/spack-stage/spack-stage-py-wcwidth-0.2.5-wrxexzu3tc5pgbirwyg6c37typjbtwaa/spack-src,wheel==0.41.0,xmltodict @ file:///nvme/bbpcihpcdeploy/1277579/spack-stage/spack-stage-py-xmltodict-0.12.0-tdkuh6b22klzyihbsurstyhsu2pl3nyy/spack-src,zict @ 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bb5: commands[0]> /usr/bin/echo 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bb5: commands[1]> /usr/bin/echo /gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_oneapi-2022.2.1-skylake/neurodamus-neocortex-1.12-2.16.0-2.8.0-dfz2ii/lib/hoc:/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841818/hpc/sim/neurodamus/core/hoc
/gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_oneapi-2022.2.1-skylake/neurodamus-neocortex-1.12-2.16.0-2.8.0-dfz2ii/lib/hoc:/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841818/hpc/sim/neurodamus/core/hoc
bb5: commands[2]> pytest -s -x -n2 --forked --cov=neurodamus
============================= test session starts ==============================
platform linux -- Python 3.10.8, pytest-7.4.0, pluggy-1.2.0 -- /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841818/hpc/sim/neurodamus/.tox/bb5/bin/python
cachedir: .tox/bb5/.pytest_cache
rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841818/hpc/sim/neurodamus
configfile: setup.cfg
plugins: xdist-3.3.1, forked-1.6.0, cov-4.1.0
created: 2/2 workers
2 workers [137 items]

scheduling tests via LoadScheduling

tests/test_blueconfig_parser.py::test_blueconfig_parser 
tests/test_conn_manager.py::test_population_get_create_conn 
[gw0] PASSED tests/test_blueconfig_parser.py::test_blueconfig_parser 
[gw1] PASSED tests/test_conn_manager.py::test_population_get_create_conn 
tests/test_conn_manager.py::test_population_all_conns 
tests/test_blueconfig_parser.py::test_blueconfig_err_no_close 
[gw1] PASSED tests/test_conn_manager.py::test_population_all_conns 
tests/test_conn_manager.py::test_population_get_connections[test_input0-expected0] 
[gw0] PASSED tests/test_blueconfig_parser.py::test_blueconfig_err_no_close 
tests/test_blueconfig_parser.py::test_blueconfig_commented_section 
[gw1] PASSED tests/test_conn_manager.py::test_population_get_connections[test_input0-expected0] 
tests/test_conn_manager.py::test_population_get_connections[test_input1-expected1] 
[gw0] PASSED tests/test_blueconfig_parser.py::test_blueconfig_commented_section 
tests/test_blueconfig_parser.py::test_blueconfig_err_single_token 
[gw1] PASSED tests/test_conn_manager.py::test_population_get_connections[test_input1-expected1] 
tests/test_conn_manager.py::test_population_get_connections[test_input2-expected2] 
[gw0] PASSED tests/test_blueconfig_parser.py::test_blueconfig_err_single_token 
tests/test_blueconfig_parser.py::test_require_run 
[gw1] PASSED tests/test_conn_manager.py::test_population_get_connections[test_input2-expected2] 
tests/test_conn_manager.py::test_population_get_connections[test_input3-expected3] 
[gw0] PASSED tests/test_blueconfig_parser.py::test_require_run 
tests/test_cell.py::test_load_cell[C060114A7.asc] 
[gw1] PASSED tests/test_conn_manager.py::test_population_get_connections[test_input3-expected3] 
tests/test_conn_manager.py::test_population_get_connections[test_input4-expected4] 
[gw1] PASSED tests/test_conn_manager.py::test_population_get_connections[test_input4-expected4] 
tests/test_conn_manager.py::test_population_get_connections[test_input5-expected5] 
[gw1] PASSED tests/test_conn_manager.py::test_population_get_connections[test_input5-expected5] 
tests/test_conn_manager.py::test_population_get_connections[test_input6-expected6] 
[gw1] PASSED tests/test_conn_manager.py::test_population_get_connections[test_input6-expected6] 
tests/test_conn_manager.py::test_population_get_connections[test_input7-expected7] 
[gw1] PASSED tests/test_conn_manager.py::test_population_get_connections[test_input7-expected7] 
tests/test_conn_manager.py::test_population_get_connections[test_input8-expected8] 
[gw1] PASSED tests/test_conn_manager.py::test_population_get_connections[test_input8-expected8] 
tests/test_conn_manager.py::test_population_get_connections[test_input9-expected9] 
[gw1] PASSED tests/test_conn_manager.py::test_population_get_connections[test_input9-expected9] 
tests/test_conn_manager.py::test_population_get_connections[test_input10-expected10] 
[gw1] PASSED tests/test_conn_manager.py::test_population_get_connections[test_input10-expected10] 
tests/test_conn_manager.py::test_population_delete 
[gw1] PASSED tests/test_conn_manager.py::test_population_delete 
tests/test_conn_manager.py::test_population_delete_group[test_input0-expected0] 
[gw1] PASSED tests/test_conn_manager.py::test_population_delete_group[test_input0-expected0] 
tests/test_conn_manager.py::test_population_delete_group[test_input1-expected1] 
[gw1] PASSED tests/test_conn_manager.py::test_population_delete_group[test_input1-expected1] 
tests/test_conn_manager.py::test_population_delete_group[test_input2-expected2] 
[gw1] PASSED tests/test_conn_manager.py::test_population_delete_group[test_input2-expected2] 
tests/test_conn_manager.py::test_population_delete_group[test_input3-expected3] 
[gw0] PASSED tests/test_cell.py::test_load_cell[C060114A7.asc] 
tests/test_cell.py::test_load_cell[C060114A7.h5] 
[gw1] PASSED tests/test_conn_manager.py::test_population_delete_group[test_input3-expected3] 
tests/test_conn_manager.py::test_population_delete_group[test_input4-expected4] 
[gw1] PASSED tests/test_conn_manager.py::test_population_delete_group[test_input4-expected4] 
tests/test_conn_manager.py::test_population_delete_group[test_input5-expected5] 
[gw1] PASSED tests/test_conn_manager.py::test_population_delete_group[test_input5-expected5] 
tests/test_conn_manager.py::test_population_delete_group[test_input6-expected6] 
[gw1] PASSED tests/test_conn_manager.py::test_population_delete_group[test_input6-expected6] 
tests/test_conn_manager.py::test_population_delete_group[test_input7-expected7] 
[gw1] PASSED tests/test_conn_manager.py::test_population_delete_group[test_input7-expected7] 
tests/test_conn_manager.py::test_population_delete_group[test_input8-expected8] 
[gw1] PASSED tests/test_conn_manager.py::test_population_delete_group[test_input8-expected8] 
tests/test_conn_manager.py::test_population_delete_group[test_input9-expected9] 
[gw0] PASSED tests/test_cell.py::test_load_cell[C060114A7.h5] 
tests/test_cell.py::test_load_cell[merged_container.h5/C060114A7.h5] 
[gw1] PASSED tests/test_conn_manager.py::test_population_delete_group[test_input9-expected9] 
tests/test_conn_manager.py::test_population_delete_group[test_input10-expected10] 
[gw1] PASSED tests/test_conn_manager.py::test_population_delete_group[test_input10-expected10] 
tests/test_conn_manager.py::test_population_ids_match 
[gw1] PASSED tests/test_conn_manager.py::test_population_ids_match 
tests/test_connection.py::test_add_synapses 
[gw0] PASSED tests/test_cell.py::test_load_cell[merged_container.h5/C060114A7.h5] 
tests/test_cell.py::test_morphio_read 
[gw0] PASSED tests/test_cell.py::test_morphio_read 
tests/test_cell.py::test_create_cell 
[gw0] PASSED tests/test_cell.py::test_create_cell 
tests/test_cell.py::test_create_cell_2 
[gw1] PASSED tests/test_connection.py::test_add_synapses 
tests/test_coords.py::test_coord_mapping1 
[gw0] PASSED tests/test_cell.py::test_create_cell_2 
tests/test_cell.py::test_create_cell_3 
[gw1] PASSED tests/test_coords.py::test_coord_mapping1 
tests/test_coords.py::test_coord_mapping2 
[gw1] PASSED tests/test_coords.py::test_coord_mapping2 
tests/test_dry_run.py::test_dry_run_distribution 
[gw1] PASSED tests/test_dry_run.py::test_dry_run_distribution 
tests/test_dry_run.py::test_retrieve_unique_metypes 
[gw0] PASSED tests/test_cell.py::test_create_cell_3 
tests/test_cell.py::test_basic_system 
[gw1] PASSED tests/test_dry_run.py::test_retrieve_unique_metypes 
tests/test_lfp.py::test_load_lfp_config 
[gw1] PASSED tests/test_lfp.py::test_load_lfp_config 
tests/test_lfp.py::test_read_lfp_factors 
[gw0] PASSED tests/test_cell.py::test_basic_system 
tests/test_cli_opts.py::test_save_restore_cli 
[gw1] PASSED tests/test_lfp.py::test_read_lfp_factors 
tests/test_lfp.py::test_number_electrodes 
[gw1] PASSED tests/test_lfp.py::test_number_electrodes 
tests/test_loadbalance.py::test_loadbal_no_cx 
[gw1] PASSED tests/test_loadbalance.py::test_loadbal_no_cx 
tests/test_loadbalance.py::test_loadbal_subtarget 
[gw1] PASSED tests/test_loadbalance.py::test_loadbal_subtarget 
tests/test_loadbalance.py::test_load_balance_integrated 
[gw1] PASSED tests/test_loadbalance.py::test_load_balance_integrated 
tests/test_loadbalance.py::test_multisplit 
[gw0] FAILED tests/test_cli_opts.py::test_save_restore_cli 

=================================== FAILURES ===================================
____________________________ test_save_restore_cli _____________________________
[gw0] linux -- Python 3.10.8 /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841818/hpc/sim/neurodamus/.tox/bb5/bin/python
@pytest.mark.slow
    @pytest.mark.skipif(
        not os.environ.get("NEURODAMUS_NEOCORTEX_ROOT"),
        reason="Test requires loading a neocortex model to run")
    def test_save_restore_cli():
        with open(SIM_DIR / CONFIG_FILE_MINI, "r") as f:
            sim_config_data = json.load(f)
    
        for simulator in ("NEURON", "CORENEURON"):
            test_folder = tempfile.TemporaryDirectory("cli-test-" + simulator)  # auto removed
            test_folder_path = Path(test_folder.name)
            # Copy non-modified files
            for f in ("node_sets.json", "circuit_config.json", "input.dat"):
                shutil.copy(SIM_DIR / f, test_folder_path)
    
            for action, tstop in (("save", 100), ("restore", 200)):
                sim_config_data["target_simulator"] = simulator
                sim_config_data["run"]["tstop"] = tstop
                sim_config_data["output"]["output_dir"] = str(test_folder_path / ("output-" + action))
    
                with open(test_folder_path / CONFIG_FILE_MINI, "w") as f:
                    json.dump(sim_config_data, f, indent=2)
    
                # Checkpoints inside the output good tradition w CoreNeuron
                checkpoint_dir = test_folder_path / "output-save" / "checkpoint"
    
                command = ["neurodamus", test_folder_path / CONFIG_FILE_MINI,
                            "--" + action, checkpoint_dir]
                # Save-Restore raises exception when using NEURON
                if simulator == "NEURON":
                    with pytest.raises(subprocess.CalledProcessError):
                        subprocess.run(command, check=True)
                else:
>                   subprocess.run(command, check=True)

tests/test_cli_opts.py:47: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

input = None, capture_output = False, timeout = None, check = True
popenargs = (['neurodamus', PosixPath('/nvme/bbpcihpcsim/1659096/tmpwnjtenztcli-test-CORENEURON/simulation_config_mini.json'), '--save', PosixPath('/nvme/bbpcihpcsim/1659096/tmpwnjtenztcli-test-CORENEURON/output-save/checkpoint')],)
kwargs = {}
process = <Popen: returncode: 80 args: ['neurodamus', PosixPath('/nvme/bbpcihpcsim/165...>
stdout = None, stderr = None, retcode = 80

    def run(*popenargs,
            input=None, capture_output=False, timeout=None, check=False, **kwargs):
        """Run command with arguments and return a CompletedProcess instance.
    
        The returned instance will have attributes args, returncode, stdout and
        stderr. By default, stdout and stderr are not captured, and those attributes
        will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
        or pass capture_output=True to capture both.
    
        If check is True and the exit code was non-zero, it raises a
        CalledProcessError. The CalledProcessError object will have the return code
        in the returncode attribute, and output & stderr attributes if those streams
        were captured.
    
        If timeout is given, and the process takes too long, a TimeoutExpired
        exception will be raised.
    
        There is an optional argument "input", allowing you to
        pass bytes or a string to the subprocess's stdin.  If you use this argument
        you may not also use the Popen constructor's "stdin" argument, as
        it will be used internally.
    
        By default, all communication is in bytes, and therefore any "input" should
        be bytes, and the stdout and stderr will be bytes. If in text mode, any
        "input" should be a string, and stdout and stderr will be strings decoded
        according to locale encoding, or by "encoding" if set. Text mode is
        triggered by setting any of text, encoding, errors or universal_newlines.
    
        The other arguments are the same as for the Popen constructor.
        """
        if input is not None:
            if kwargs.get('stdin') is not None:
                raise ValueError('stdin and input arguments may not both be used.')
            kwargs['stdin'] = PIPE
    
        if capture_output:
            if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
                raise ValueError('stdout and stderr arguments may not be used '
                                 'with capture_output.')
            kwargs['stdout'] = PIPE
            kwargs['stderr'] = PIPE
    
        with Popen(*popenargs, **kwargs) as process:
            try:
                stdout, stderr = process.communicate(input, timeout=timeout)
            except TimeoutExpired as exc:
                process.kill()
                if _mswindows:
                    # Windows accumulates the output in a single blocking
                    # read() call run on child threads, with the timeout
                    # being done in a join() on those threads.  communicate()
                    # _after_ kill() is required to collect that and add it
                    # to the exception.
                    exc.stdout, exc.stderr = process.communicate()
                else:
                    # POSIX _communicate already populated the output so
                    # far into the TimeoutExpired exception.
                    process.wait()
                raise
            except:  # Including KeyboardInterrupt, communicate handled that.
                process.kill()
                # We don't call process.wait() as .__exit__ does that for us.
                raise
            retcode = process.poll()
            if check and retcode:
>               raise CalledProcessError(retcode, process.args,
                                         output=stdout, stderr=stderr)
E               subprocess.CalledProcessError: Command '['neurodamus', PosixPath('/nvme/bbpcihpcsim/1659096/tmpwnjtenztcli-test-CORENEURON/simulation_config_mini.json'), '--save', PosixPath('/nvme/bbpcihpcsim/1659096/tmpwnjtenztcli-test-CORENEURON/output-save/checkpoint')]' returned non-zero exit status 80.

../../../../../../apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/python-3.10.8-rvn6l5/lib/python3.10/subprocess.py:526: CalledProcessError
=============================== warnings summary ===============================
.tox/bb5/lib/python3.10/site-packages/xdist/plugin.py:252
.tox/bb5/lib/python3.10/site-packages/xdist/plugin.py:252
.tox/bb5/lib/python3.10/site-packages/xdist/plugin.py:252
  /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841818/hpc/sim/neurodamus/.tox/bb5/lib/python3.10/site-packages/xdist/plugin.py:252: DeprecationWarning: The --rsyncdir command line argument and rsyncdirs config variable are deprecated.
  The rsync feature will be removed in pytest-xdist 4.0.
    config.issue_config_time_warning(warning, 2)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html

------------------------------ coverage ------------------------------
Name                                    Stmts   Miss Branch BrPart  Cover
-------------------------------------------------------------------------
neurodamus/__init__.py                     11     11      0      0     0%
neurodamus/cell_distributor.py            645    318    222     39    52%
neurodamus/commands.py                    108    108     36      0     0%
neurodamus/connection.py                  429    314    160     20    26%
neurodamus/connection_manager.py          592    344    272     43    41%
neurodamus/core/__init__.py                 9      9      0      0     0%
neurodamus/core/_engine.py                 57     48     18      4    20%
neurodamus/core/_mpi.py                    57     40     12      2    30%
neurodamus/core/_neurodamus.py             71     34     18      7    54%
neurodamus/core/_neuron.py                168     88     36      8    50%
neurodamus/core/_shmutils.py               57     57      8      0     0%
neurodamus/core/_utils.py                  52     45      8      3    17%
neurodamus/core/cell.py                   219    127     56     13    45%
neurodamus/core/configuration.py          782    509    299     66    35%
neurodamus/core/mechanisms.py              39     32      8      2    23%
neurodamus/core/nodeset.py                241    158     98     15    32%
neurodamus/core/random.py                  59     59     16      0     0%
neurodamus/core/stimuli.py                261    227     40      2    12%
neurodamus/core/synapses.py                60     60     16      0     0%
neurodamus/gap_junction.py                 75     75     18      0     0%
neurodamus/hocify.py                       56     56     14      0     0%
neurodamus/io/__init__.py                   0      0      0      0   100%
neurodamus/io/cell_readers.py             272    171    118     17    34%
neurodamus/io/config_parser.py             70     16     36      5    80%
neurodamus/io/sonata_config.py            223     84    110     15    64%
neurodamus/io/synapse_reader.py           279    190    100     23    33%
neurodamus/managers.py                     50     50     20      0     0%
neurodamus/metype.py                      222    141     36      5    34%
neurodamus/modification_manager.py         94     94     43      0     0%
neurodamus/morphio_wrapper.py             168     37     40      4    77%
neurodamus/neuromodulation_manager.py      73     73     28      0     0%
neurodamus/ngv.py                         304    304     84      0     0%
neurodamus/node.py                       1194   1049    514     25    11%
neurodamus/replay.py                       80     80     24      0     0%
neurodamus/stimulus_manager.py            423    423    178      0     0%
neurodamus/target_manager.py              440    341    150     22    23%
neurodamus/utils/__init__.py                2      2      0      0     0%
neurodamus/utils/compat.py                100     88     22      2    13%
neurodamus/utils/logging.py                78     36     20      9    54%
neurodamus/utils/memory.py                 44     44      6      0     0%
neurodamus/utils/multimap.py               96     96     28      0     0%
neurodamus/utils/progressbar.py           100     49     28      8    52%
neurodamus/utils/pyutils.py               111     80     44      4    32%
neurodamus/utils/timeit.py                101     73     24      4    26%
-------------------------------------------------------------------------
TOTAL                                    8572   6240   3008    367    27%

=========================== short test summary info ============================
FAILED tests/test_cli_opts.py::test_save_restore_cli
!!!!!!!!!!!!!!!!!!!!!!!!!! stopping after 1 failures !!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!! xdist.dsession.Interrupted: stopping after 1 failures !!!!!!!!!!!!!
============= 1 failed, 50 passed, 3 warnings in 83.58s (0:01:23) ==============
bb5: exit 2 (84.75 seconds) /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841818/hpc/sim/neurodamus> pytest -s -x -n2 --forked --cov=neurodamus pid=59323
.pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841818/hpc/sim/neurodamus/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
  bb5: FAIL code 2 (109.94=setup[25.18]+cmd[0.01,0.00,84.75] seconds)
  evaluation failed :( (111.06 seconds)
srun: error: r1i7n31: task 0: Exited with exit code 1
section_end:1691669892:step_script
section_start:1691669892:cleanup_file_variables
Cleaning up project directory and file based variables
Using git from spack modules
section_end:1691669893:cleanup_file_variables
ERROR: Job failed: exit status 1


python3-base.txt

Running with gitlab-runner 15.5.0 (0d4137b8)
  on BB5 map runner pnPo3yJy
section_start:1691669747:resolve_secrets
Resolving secrets
section_end:1691669747:resolve_secrets
section_start:1691669747:prepare_executor
Preparing the "custom" executor
Using Custom executor with driver BB5 PROD runner v0.0.3...
BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user 
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor559057351, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name neurodamus
Pipeline ID 143266, build ref , job ID 841817
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J841817, 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_J841817_PROD_P2354_CP1_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 1659095
job state: PD
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M    --job-name=GL_J841817_PROD_P2354_CP1_C3 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J841817 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J841817 --ntasks=1 --jobid=1659095 --cpus-per-task=6 --mem=30750M     
section_end:1691669749:prepare_executor
section_start:1691669749:prepare_script
Preparing environment
Using git from spack modules
Running on r1i7n31 via bbpv1.epfl.ch...
section_end:1691669750:prepare_script
section_start:1691669750:get_sources
Getting source from Git repository
Using git from spack modules
$ 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 '*'
Fetching changes with git depth set to 20...
Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/.git/
Created fresh repository.
Checking out 73653388 as 1uc/free-deleted-stable-identifiers...
Skipping object checkout, Git LFS is not installed.

Updating/initializing submodules recursively with git depth set to 20...
section_end:1691669753:get_sources
section_start:1691669753:step_script
Executing "step_script" stage of the job script
WARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426
Using git from spack modules
$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi
$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }
$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }
$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }
$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }
$ module purge
$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')
$ module load archive/2020-12 python/3.7.4
$ module unload archive/2020-12
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.7.4
$ module load archive/2021-12 python/3.8.3
$ module unload archive/2021-12
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.8.3
$ module load archive/2023-02 python/3.9.7
$ module unload archive/2023-02
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.9.7
$ module load unstable python
$ module unload unstable
$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH
$ echo "Loaded $(python -V)"
Loaded Python 3.10.8
$ load-modules() { # collapsed multi-line command
$ load-modules $SYSTEM_MODULES
Loaded module git from unstable
Loaded module cmake from unstable
Loaded module graphviz from unstable
$ load-modules $EXTRA_MODULES
$ module list -t
Currently Loaded Modulefiles:
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/external-libraries/2020-12/tcl/linux-rhel7-x86_64/python/3.7.4
/gpfs/bbp.cscs.ch/ssd/apps/hpc/jenkins/modules/externals/2021-12/tcl/linux-rhel7-x86_64/python/3.8.3
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-02/externals/linux-rhel7-skylake/python/3.9.7
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-08/externals/linux-rhel7-skylake/python/3.10.8
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-08/externals/linux-rhel7-skylake/git/2.38.1
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-08/externals/linux-rhel7-skylake/cmake/3.24.3
/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2023-08/externals/linux-rhel7-skylake/graphviz/2.49.0
$ export XDG_CONFIG_HOME=${PWD}/local_config
$ print_var XDG_CONFIG_HOME
XDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/local_config
$ mkdir -p "${XDG_CONFIG_HOME}/git"
$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command
$ cat "${XDG_CONFIG_HOME}/git/config"
[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:
$ section_start section_venv[collapsed=true] "Setting up the virtual env"
section_start:1691669755:section_venv[collapsed=true]
Setting up the virtual env
$ cd "${PYTHON_PROJECT_DIR}"
$ CI_VENV="$(pwd)/venv"
$ rm -rf "$CI_VENV"
$ python -mvenv "$CI_VENV"
$ source "$CI_VENV/bin/activate"
$ python -mpip install --upgrade pip setuptools wheel
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
Requirement already satisfied: pip in ./venv/lib/python3.10/site-packages (22.2.2)
Collecting pip
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/7cc/f472345f20d35/pip-23.2.1-py3-none-any.whl (2.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 74.6 MB/s eta 0:00:00
Requirement already satisfied: setuptools in ./venv/lib/python3.10/site-packages (63.2.0)
Collecting setuptools
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/11e/52c67415a381d/setuptools-68.0.0-py3-none-any.whl (804 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 804.0/804.0 kB 260.9 MB/s eta 0:00:00
Collecting wheel
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/473/219bd4cbedc62/wheel-0.41.1-py3-none-any.whl (64 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 64.8/64.8 kB 225.4 MB/s eta 0:00:00
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 63.2.0
    Uninstalling setuptools-63.2.0:
      Successfully uninstalled setuptools-63.2.0
  Attempting uninstall: pip
    Found existing installation: pip 22.2.2
    Uninstalling pip-22.2.2:
      Successfully uninstalled pip-22.2.2
Successfully installed pip-23.2.1 setuptools-68.0.0 wheel-0.41.1
$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi
Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple
Collecting tox
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/793/99a3d4641d1fd/tox-4.7.0-py3-none-any.whl (152 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 152.4/152.4 kB 18.0 MB/s eta 0:00:00
Collecting cachetools>=5.3.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/95e/f631eeaea14ba/cachetools-5.3.1-py3-none-any.whl (9.3 kB)
Collecting chardet>=5.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 199.4/199.4 kB 45.4 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>=3.12.2 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/cbb/791cdea2a72f2/filelock-3.12.2-py3-none-any.whl (10 kB)
Collecting packaging>=23.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/994/793af429502c4/packaging-23.1-py3-none-any.whl (48 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.9/48.9 kB 204.4 MB/s eta 0:00:00
Collecting platformdirs>=3.9.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/d7c/24979f292f916/platformdirs-3.10.0-py3-none-any.whl (17 kB)
Collecting pluggy>=1.2 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/c2f/d55a7d7a3863c/pluggy-1.2.0-py3-none-any.whl (17 kB)
Collecting pyproject-api>=1.5.3 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/14c/f09828670c7b0/pyproject_api-1.5.3-py3-none-any.whl (12 kB)
Collecting tomli>=2.0.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/939/de3e7a6161af0/tomli-2.0.1-py3-none-any.whl (12 kB)
Collecting virtualenv>=20.24.1 (from tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/43a/3052be3608054/virtualenv-20.24.2-py3-none-any.whl (3.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.0/3.0 MB 150.8 MB/s eta 0:00:00
Collecting distlib<1,>=0.3.7 (from virtualenv>=20.24.1->tox)
  Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2e2/4928bc811348f/distlib-0.3.7-py2.py3-none-any.whl (468 kB)
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Installing collected packages: distlib, tomli, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox
Successfully installed cachetools-5.3.1 chardet-5.2.0 colorama-0.4.6 distlib-0.3.7 filelock-3.12.2 packaging-23.1 platformdirs-3.10.0 pluggy-1.2.0 pyproject-api-1.5.3 tomli-2.0.1 tox-4.7.0 virtualenv-20.24.2
$ section_end section_venv
section_end:1691669771:section_venv

$ print_var PRE_BUILD_COMMAND
PRE_BUILD_COMMAND=
$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi
$ section_start section_tox "Running Tox"
section_start:1691669771:section_tox
Running Tox
$ python -mtox $TOX_OPTIONS
flake8: install_deps> python -I -m pip install flake8
flake8: freeze> python -m pip freeze --all
flake8: flake8==6.1.0,mccabe==0.7.0,pip==23.2.1,pycodestyle==2.11.0,pyflakes==3.1.0,setuptools==68.0.0,wheel==0.41.0
flake8: commands[0]> flake8
flake8: OK ✔ in 5.49 seconds
py3: install_deps> python -I -m pip install morphio NEURON pytest pytest-forked scipy
.pkg: install_requires> python -I -m pip install 'setuptools>=40.8.0' wheel
.pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
.pkg: get_requires_for_build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
.pkg: get_requires_for_build_wheel> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
.pkg: install_requires_for_build_wheel> python -I -m pip install wheel
.pkg: get_requires_for_build_editable> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
.pkg: install_requires_for_build_editable> python -I -m pip install wheel
.pkg: freeze> python -m pip freeze --all
.pkg: pip==23.2.1,setuptools==68.0.0,wheel==0.41.0
.pkg: build_wheel> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
.pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
py3: install_package_deps> python -I -m pip install docopt h5py libsonata psutil
py3: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-2.16.0.dev5.tar.gz
py3: freeze> python -m pip freeze --all
py3: docopt==0.6.2,exceptiongroup==1.1.2,h5py==3.9.0,iniconfig==2.0.0,libsonata==0.1.22,MorphIO==3.3.6,neurodamus @ file:///gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-2.16.0.dev5.tar.gz#sha256=432b27f685411998836b75180b236141b3b4ce2156ee9c07533ae69988b9d18f,NEURON==8.2.2,numpy==1.25.2,packaging==23.1,pip==23.2.1,pluggy==1.2.0,psutil==5.9.5,py==1.11.0,pytest==7.4.0,pytest-forked==1.6.0,scipy==1.11.1,setuptools==68.0.0,tomli==2.0.1,wheel==0.41.0
py3: commands[0]> ci/build_ndcore.sh /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core
+ CORE_DIR=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core
+ '[' -d _lib ']'
+ COMMON_DIR=_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/J841817/hpc/sim/neurodamus/core/mod/ALU.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/mod/CoreConfig.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/mod/HDF5reader.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/mod/lookupTableV2.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/mod/netstim_inhpoisson.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/mod/SonataReportHelper.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/mod/SonataReports.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/mod/SpikeWriter.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/mod/SynapseReader.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/mod/VecStim.mod mods.tmp
+ cp -f _common/mod/DetAMPANMDA.mod _common/mod/DetGABAAB.mod _common/mod/gap.mod _common/mod/GluSynapse.mod _common/mod/netstim_inhpoisson.mod _common/mod/ProbAMPANMDA_EMS.mod _common/mod/ProbGABAAB_EMS.mod _common/mod/TTXDynamicsSwitch.mod _common/mod/VecStim.mod mods.tmp
+ nrnivmodl -incflags '-DDISABLE_REPORTINGLIB -DDISABLE_HDF5 -DDISABLE_MPI' mods.tmp
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/.tox/py3/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/J841817/hpc/sim/neurodamus
Mod files: "mods.tmp/mods.tmp/ALU.mod" "mods.tmp/mods.tmp/CoreConfig.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/lookupTableV2.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/SpikeWriter.mod" "mods.tmp/mods.tmp/SynapseReader.mod" "mods.tmp/mods.tmp/TTXDynamicsSwitch.mod" "mods.tmp/mods.tmp/VecStim.mod"

Creating 'x86_64' directory for .o files.

 -> Compiling mod_func.cpp
 -> NMODL ../mods.tmp/ALU.mod
 -> NMODL ../mods.tmp/CoreConfig.mod
 -> NMODL ../mods.tmp/DetAMPANMDA.mod
Translating CoreConfig.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/x86_64/CoreConfig.c
Translating ALU.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/x86_64/ALU.c
Translating DetAMPANMDA.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/x86_64/DetAMPANMDA.c
Thread Safe
Thread Safe
Warning: next_delay_weight undefined. (declared within VERBATIM?)
Warning: next_delay_t undefined. (declared within VERBATIM?)
Thread Safe
 -> NMODL ../mods.tmp/DetGABAAB.mod
 -> NMODL ../mods.tmp/gap.mod
 -> NMODL ../mods.tmp/GluSynapse.mod
Translating DetGABAAB.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/x86_64/DetGABAAB.c
Translating gap.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/x86_64/gap.c
Warning: next_delay_weight undefined. (declared within VERBATIM?)
Warning: next_delay_t undefined. (declared within VERBATIM?)
Thread Safe
Translating GluSynapse.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/x86_64/GluSynapse.c
Thread Safe
 -> NMODL ../mods.tmp/HDF5reader.mod
Warning: next_delay_weight undefined. (declared within VERBATIM?)
Warning: next_delay_t undefined. (declared within VERBATIM?)
 -> NMODL ../mods.tmp/lookupTableV2.mod
Thread Safe
 -> NMODL ../mods.tmp/netstim_inhpoisson.mod
Translating HDF5reader.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/x86_64/HDF5reader.c
Notice: Use of POINTER is not thread safe.
Translating lookupTableV2.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/x86_64/lookupTableV2.c
Notice: VERBATIM blocks are not thread safe
Notice: Use of POINTER is not thread safe.
Notice: VERBATIM blocks are not thread safe
Notice: ARTIFICIAL_CELL is a synonym for POINT_PROCESS which hints that it
only affects and is affected by discrete events. As such it is not
located in a section and is not associated with an integrator
Notice: 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 netstim_inhpoisson.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/x86_64/netstim_inhpoisson.c
Warning: POST_RESTORE_RESTART_FLAG undefined. (declared within VERBATIM?)
 -> NMODL ../mods.tmp/ProbAMPANMDA_EMS.mod
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
 -> NMODL ../mods.tmp/ProbGABAAB_EMS.mod
 -> NMODL ../mods.tmp/SonataReportHelper.mod
Translating ProbAMPANMDA_EMS.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/x86_64/ProbAMPANMDA_EMS.c
Notice: This mechanism cannot be used with CVODE
Notice: A_AMPA discontinuity adjustment not available.
Notice: B_AMPA discontinuity adjustment not available.
Notice: A_NMDA discontinuity adjustment not available.
Notice: B_NMDA discontinuity adjustment not available.
Warning: dt undefined. (declared within VERBATIM?)
Warning: next_delay_weight undefined. (declared within VERBATIM?)
Warning: next_delay_t undefined. (declared within VERBATIM?)
Translating ProbGABAAB_EMS.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/x86_64/ProbGABAAB_EMS.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?)
Translating SonataReportHelper.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/x86_64/SonataReportHelper.c
Thread Safe
Thread Safe
 -> NMODL ../mods.tmp/SonataReports.mod
 -> NMODL ../mods.tmp/SpikeWriter.mod
 -> NMODL ../mods.tmp/SynapseReader.mod
Translating SonataReports.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/x86_64/SonataReports.c
Thread Safe
Translating SpikeWriter.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/x86_64/SpikeWriter.c
Notice: VERBATIM blocks are not 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
 -> NMODL ../mods.tmp/TTXDynamicsSwitch.mod
 -> NMODL ../mods.tmp/VecStim.mod
Translating SynapseReader.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/x86_64/SynapseReader.c
Thread Safe
Translating TTXDynamicsSwitch.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/x86_64/TTXDynamicsSwitch.c
Translating VecStim.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/x86_64/VecStim.c
 -> Compiling ALU.c
Thread Safe
Thread Safe
 -> Compiling CoreConfig.c
 -> Compiling DetAMPANMDA.c
 -> Compiling DetGABAAB.c
 -> Compiling gap.c
 -> Compiling GluSynapse.c
 -> Compiling HDF5reader.c
 -> Compiling lookupTableV2.c
 -> Compiling netstim_inhpoisson.c
 -> Compiling ProbAMPANMDA_EMS.c
 -> Compiling ProbGABAAB_EMS.c
 -> Compiling SonataReportHelper.c
 -> Compiling SonataReports.c
 -> Compiling SpikeWriter.c
 -> Compiling SynapseReader.c
 -> Compiling TTXDynamicsSwitch.c
 -> Compiling VecStim.c
 => LINKING shared library ./libnrnmech.so
 => LINKING 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/J841817/hpc/sim/neurodamus/core/hoc/Cell.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/hoc/CompartmentMapping.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/hoc/ConfigParser.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/hoc/ConnectionUtils.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/hoc/defvar.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/hoc/ElectrodeManager.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/hoc/EStim.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/hoc/fileUtils.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/hoc/Map.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/hoc/MorphIO.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/hoc/neurodamus.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/hoc/Report.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/hoc/RNGSettings.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/hoc/SerializedSections.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/hoc/ShowProgress.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/hoc/SimSettings.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/hoc/StimulusManager.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/hoc/Target.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/hoc/TargetManager.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/hoc/TargetParser.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/hoc/TDistFunc.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/hoc/TPointList.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/hoc/TStim.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/core/hoc/TType.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/
py3: commands[1]> python setup.py test
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/.tox/py3/lib/python3.10/site-packages/setuptools/__init__.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!

        ********************************************************************************
        Requirements should be satisfied by a PEP 517 installer.
        If you are using pip, you can try `pip install --use-pep517`.
        ********************************************************************************

!!
  dist.fetch_build_eggs(dist.setup_requires)
running pytest
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/.tox/py3/lib/python3.10/site-packages/setuptools/command/test.py:194: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!

        ********************************************************************************
        Requirements should be satisfied by a PEP 517 installer.
        If you are using pip, you can try `pip install --use-pep517`.
        ********************************************************************************

!!
  ir_d = dist.fetch_build_eggs(dist.install_requires)
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/.tox/py3/lib/python3.10/site-packages/setuptools/command/test.py:195: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!

        ********************************************************************************
        Requirements should be satisfied by a PEP 517 installer.
        If you are using pip, you can try `pip install --use-pep517`.
        ********************************************************************************

!!
  tr_d = dist.fetch_build_eggs(dist.tests_require or [])
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/.tox/py3/lib/python3.10/site-packages/setuptools/command/test.py:196: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!

        ********************************************************************************
        Requirements should be satisfied by a PEP 517 installer.
        If you are using pip, you can try `pip install --use-pep517`.
        ********************************************************************************

!!
  er_d = dist.fetch_build_eggs(
running egg_info
writing neurodamus.egg-info/PKG-INFO
writing dependency_links to neurodamus.egg-info/dependency_links.txt
writing entry points to neurodamus.egg-info/entry_points.txt
writing requirements to neurodamus.egg-info/requires.txt
writing top-level names to neurodamus.egg-info/top_level.txt
reading manifest file 'neurodamus.egg-info/SOURCES.txt'
adding license file 'LICENSE.txt'
writing manifest file 'neurodamus.egg-info/SOURCES.txt'
running build_ext
============================= test session starts ==============================
platform linux -- Python 3.10.8, pytest-7.4.0, pluggy-1.2.0 -- /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/.tox/py3/bin/python
cachedir: .tox/py3/.pytest_cache
rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus
configfile: setup.cfg
plugins: forked-1.6.0
collecting ... collected 137 items

tests/test_blueconfig_parser.py::test_blueconfig_parser PASSED           [  0%]
tests/test_blueconfig_parser.py::test_blueconfig_err_no_close PASSED     [  1%]
tests/test_blueconfig_parser.py::test_blueconfig_commented_section PASSED [  2%]
tests/test_blueconfig_parser.py::test_blueconfig_err_single_token PASSED [  2%]
tests/test_blueconfig_parser.py::test_require_run PASSED                 [  3%]
tests/test_cell.py::test_load_cell[C060114A7.asc] PASSED                 [  4%]
tests/test_cell.py::test_load_cell[C060114A7.h5] PASSED                  [  5%]
tests/test_cell.py::test_load_cell[merged_container.h5/C060114A7.h5] PASSED [  5%]
tests/test_cell.py::test_morphio_read PASSED                             [  6%]
tests/test_cell.py::test_create_cell PASSED                              [  7%]
tests/test_cell.py::test_create_cell_2 PASSED                            [  8%]
tests/test_cell.py::test_create_cell_3 PASSED                            [  8%]
tests/test_cell.py::test_basic_system PASSED                             [  9%]
tests/test_cli_opts.py::test_save_restore_cli SKIPPED (Test requires...) [ 10%]
tests/test_cli_opts.py::test_cli_prcellgid SKIPPED (Test requires lo...) [ 10%]
tests/test_conn_manager.py::test_population_get PASSED                   [ 11%]
tests/test_conn_manager.py::test_population_store_order PASSED           [ 12%]
tests/test_conn_manager.py::test_population_get_create_conn PASSED       [ 13%]
tests/test_conn_manager.py::test_population_all_conns PASSED             [ 13%]
tests/test_conn_manager.py::test_population_get_connections[test_input0-expected0] PASSED [ 14%]
tests/test_conn_manager.py::test_population_get_connections[test_input1-expected1] PASSED [ 15%]
tests/test_conn_manager.py::test_population_get_connections[test_input2-expected2] PASSED [ 16%]
tests/test_conn_manager.py::test_population_get_connections[test_input3-expected3] PASSED [ 16%]
tests/test_conn_manager.py::test_population_get_connections[test_input4-expected4] PASSED [ 17%]
tests/test_conn_manager.py::test_population_get_connections[test_input5-expected5] PASSED [ 18%]
tests/test_conn_manager.py::test_population_get_connections[test_input6-expected6] PASSED [ 18%]
tests/test_conn_manager.py::test_population_get_connections[test_input7-expected7] PASSED [ 19%]
tests/test_conn_manager.py::test_population_get_connections[test_input8-expected8] PASSED [ 20%]
tests/test_conn_manager.py::test_population_get_connections[test_input9-expected9] PASSED [ 21%]
tests/test_conn_manager.py::test_population_get_connections[test_input10-expected10] PASSED [ 21%]
tests/test_conn_manager.py::test_population_delete PASSED                [ 22%]
tests/test_conn_manager.py::test_population_delete_group[test_input0-expected0] PASSED [ 23%]
tests/test_conn_manager.py::test_population_delete_group[test_input1-expected1] PASSED [ 24%]
tests/test_conn_manager.py::test_population_delete_group[test_input2-expected2] PASSED [ 24%]
tests/test_conn_manager.py::test_population_delete_group[test_input3-expected3] PASSED [ 25%]
tests/test_conn_manager.py::test_population_delete_group[test_input4-expected4] PASSED [ 26%]
tests/test_conn_manager.py::test_population_delete_group[test_input5-expected5] PASSED [ 27%]
tests/test_conn_manager.py::test_population_delete_group[test_input6-expected6] PASSED [ 27%]
tests/test_conn_manager.py::test_population_delete_group[test_input7-expected7] PASSED [ 28%]
tests/test_conn_manager.py::test_population_delete_group[test_input8-expected8] PASSED [ 29%]
tests/test_conn_manager.py::test_population_delete_group[test_input9-expected9] PASSED [ 29%]
tests/test_conn_manager.py::test_population_delete_group[test_input10-expected10] PASSED [ 30%]
tests/test_conn_manager.py::test_population_ids_match PASSED             [ 31%]
tests/test_connection.py::test_add_synapses SKIPPED (Test requires l...) [ 32%]
tests/test_coords.py::test_coord_mapping1 PASSED                         [ 32%]
tests/test_coords.py::test_coord_mapping2 PASSED                         [ 33%]
tests/test_dry_run.py::test_dry_run_distribution PASSED                  [ 34%]
tests/test_dry_run.py::test_retrieve_unique_metypes PASSED               [ 35%]
tests/test_lfp.py::test_load_lfp_config PASSED                           [ 35%]
tests/test_lfp.py::test_read_lfp_factors PASSED                          [ 36%]
tests/test_lfp.py::test_number_electrodes PASSED                         [ 37%]
tests/test_loadbalance.py::test_loadbal_no_cx PASSED                     [ 37%]
tests/test_loadbalance.py::test_loadbal_subtarget PASSED                 [ 38%]
tests/test_loadbalance.py::test_load_balance_integrated SKIPPED (Tes...) [ 39%]
tests/test_loadbalance.py::test_multisplit SKIPPED (Test requires lo...) [ 40%]
tests/test_loadbalance.py::test_loadbal_integration SKIPPED (Test re...) [ 40%]
tests/test_modification.py::test_TTX_modification SKIPPED (Test requ...) [ 41%]
tests/test_modification.py::test_ConfigureAllSections_modification SKIPPED [ 42%]
tests/test_multicycle_runs.py::test_nodeset_target_generate_subtargets SKIPPED [ 43%]
tests/test_multicycle_runs.py::test_hoc_target_generate_subtargets PASSED [ 43%]
tests/test_multicycle_runs.py::test_v5_sonata_multisteps SKIPPED (Te...) [ 44%]
tests/test_multicycle_runs.py::test_usecase3_sonata_multisteps SKIPPED   [ 45%]
tests/test_neuromodulation.py::test_neuromodulation_sims_neuron SKIPPED  [ 45%]
tests/test_neuromodulation.py::test_neuromodulation_sims_coreneuron SKIPPED [ 46%]
tests/test_neuron.py::test_base_h PASSED                                 [ 47%]
tests/test_ngv.py::test_vasccouplingB_radii SKIPPED (Test requires l...) [ 48%]
tests/test_nodeset.py::test_NodeSet_base PASSED                          [ 48%]
tests/test_nodeset.py::test_NodeSet_add PASSED                           [ 49%]
tests/test_nodeset.py::test_ranges_overlap[ranges10-ranges20-expected0] PASSED [ 50%]
tests/test_nodeset.py::test_ranges_overlap[ranges11-ranges21-expected1] PASSED [ 51%]
tests/test_nodeset.py::test_ranges_overlap[ranges12-ranges22-expected2] PASSED [ 51%]
tests/test_nodeset.py::test_ranges_overlap[ranges13-ranges23-expected3] PASSED [ 52%]
tests/test_nodeset.py::test_ranges_overlap[ranges14-ranges24-expected4] PASSED [ 53%]
tests/test_nodeset.py::test_ranges_overlap[ranges15-ranges25-expected5] PASSED [ 54%]
tests/test_nodeset.py::test_ranges_overlap[ranges16-ranges26-expected6] PASSED [ 54%]
tests/test_nodeset.py::test_ranges_vec_overlap[ranges10-vec0-expected0] PASSED [ 55%]
tests/test_nodeset.py::test_ranges_vec_overlap[ranges11-vec1-expected1] PASSED [ 56%]
tests/test_nodeset.py::test_ranges_vec_overlap[ranges12-vec2-expected2] PASSED [ 56%]
tests/test_nodeset.py::test_ranges_vec_overlap[ranges13-vec3-expected3] PASSED [ 57%]
tests/test_nodeset.py::test_ranges_vec_overlap[ranges14-vec4-expected4] PASSED [ 58%]
tests/test_patched_delays.py::test_eager_caching SKIPPED (Test requi...) [ 59%]
tests/test_plugin.py::test_run_acell_circuit FAILED                      [ 59%]
tests/test_pyutils.py::test_map_1 PASSED                                 [ 60%]
tests/test_pyutils.py::test_map_other_data PASSED                        [ 61%]
tests/test_pyutils.py::test_map_duplicates PASSED                        [ 62%]
tests/test_pyutils.py::test_map_duplicates_struct PASSED                 [ 62%]
tests/test_pyutils.py::test_badly_formed PASSED                          [ 63%]
tests/test_pyutils.py::test_merge PASSED                                 [ 64%]
tests/test_pyutils.py::test_merge_grouped PASSED                         [ 64%]
tests/test_pyutils.py::test_flatten_grouped PASSED                       [ 65%]
tests/test_replay_manager.py::test_replay_manager_sonata PASSED          [ 66%]
tests/test_simulation.py::test_quick_v6 SKIPPED (Simulation tests re...) [ 67%]
tests/test_simulation.py::test_simulation_sonata_config SKIPPED (Tes...) [ 67%]
tests/test_simulation.py::test_v5_sonata_config SKIPPED (Test requir...) [ 68%]
tests/test_simulation.py::test_v5_gap_junction SKIPPED (Test require...) [ 69%]
tests/test_sonata_config.py::test_parse_base PASSED                      [ 70%]
tests/test_sonata_config.py::test_SimConfig_from_sonata PASSED           [ 70%]
tests/test_sonata_config.py::test_parse_seeds PASSED                     [ 71%]
tests/test_sonata_config.py::test_parse_modifications PASSED             [ 72%]
tests/test_sonata_config.py::test_parse_connections PASSED               [ 72%]
tests/test_sonata_output.py::test_sonata_logfile SKIPPED (Test requi...) [ 73%]
tests/test_sonata_output.py::test_throw_spike_sort_order PASSED          [ 74%]
tests/test_sonata_properties.py::test_input_resistance SKIPPED (Test...) [ 75%]
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tests/test_stimuli.py::TestStimuli::test_flat_segment PASSED             [ 76%]
tests/test_stimuli.py::TestStimuli::test_pulse PASSED                    [ 77%]
tests/test_stimuli.py::TestStimuli::test_pulse_diff_base[-1] PASSED      [ 78%]
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tests/test_stimuli.py::TestStimuli::test_pulse_diff_base[1.5] PASSED     [ 79%]
tests/test_stimuli.py::TestStimuli::test_two_pulses PASSED               [ 80%]
tests/test_stimuli.py::TestStimuli::test_ramp PASSED                     [ 81%]
tests/test_stimuli.py::TestStimuli::test_delay_ramp PASSED               [ 81%]
tests/test_stimuli.py::TestStimuli::test_train PASSED                    [ 82%]
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tests/test_stimuli.py::TestStimuli::test_ornstein_uhlenbeck PASSED       [ 86%]
tests/test_stimuli.py::TestStimuli::test_stacked PASSED                  [ 87%]
tests/test_synapse_reader.py::test_gapjunction_synreaderNRN SKIPPED      [ 88%]
tests/test_synapse_reader.py::test_gapjunction_sonata_reader SKIPPED     [ 89%]
tests/test_synapses.py::test_synapses_params SKIPPED (Test requires ...) [ 89%]
tests/test_synapses.py::test__constrained_hill PASSED                    [ 90%]
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tests/test_target_intersection.py::test_targetspec_overlap_name PASSED   [ 91%]
tests/test_target_intersection.py::test_populations_disjoint PASSED      [ 92%]
tests/test_target_intersection.py::test_targetspec_overlap PASSED        [ 93%]
tests/test_target_intersection.py::test_hoc_target_intersect PASSED      [ 94%]
tests/test_target_intersection.py::test_nodeset_target_intersect PASSED  [ 94%]
tests/test_target_intersection.py::test_nodeset_gids PASSED              [ 95%]
tests/scientific/test_multipop.py::test_multipop_simple[extra_config0] SKIPPED [ 96%]
tests/scientific/test_multipop.py::test_multipop_full_conn[extra_config0] SKIPPED [ 97%]
tests/scientific/test_projections.py::test_projections SKIPPED (Test...) [ 97%]
tests/scientific/test_replay.py::test_replay_sim SKIPPED (Test requi...) [ 98%]
tests/scientific/test_replay.py::test_replay_sonata_spikes SKIPPED (...) [ 99%]
tests/scientific/test_spont_minis.py::test_spont_minis SKIPPED (Test...) [100%]

=================================== FAILURES ===================================
____________________________ test_run_acell_circuit ____________________________

    def test_run_acell_circuit():
        simdir = SIM_DIR / "acell_engine"
        env = os.environ.copy()
        env['NEURODAMUS_PYTHON'] = "."
        env['PYTHONPATH'] += ":" + os.path.dirname(__file__)
        env['NEURODAMUS_PLUGIN'] = os.path.splitext(os.path.basename(__file__))[0]
>       subprocess.run(
            ["bash", "tests/test_simulation.bash", str(simdir), "BlueConfig", ""],
            env=env,
            check=True,
        )

tests/test_plugin.py:141: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

input = None, capture_output = False, timeout = None, check = True
popenargs = (['bash', 'tests/test_simulation.bash', '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/tests/simulations/acell_engine', 'BlueConfig', ''],)
kwargs = {'env': {'HOC_LIBRARY_PATH': '_lib', 'HOME': '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J841817', 'HTTPS_PROXY': 'http://bbpproxy.epfl.ch:80', 'HTTP_PROXY': 'http://bbpproxy.epfl.ch:80', ...}}
process = <Popen: returncode: 1 args: ['bash', 'tests/test_simulation.bash', '/gpfs/bb...>
stdout = None, stderr = None, retcode = 1

    def run(*popenargs,
            input=None, capture_output=False, timeout=None, check=False, **kwargs):
        """Run command with arguments and return a CompletedProcess instance.
    
        The returned instance will have attributes args, returncode, stdout and
        stderr. By default, stdout and stderr are not captured, and those attributes
        will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
        or pass capture_output=True to capture both.
    
        If check is True and the exit code was non-zero, it raises a
        CalledProcessError. The CalledProcessError object will have the return code
        in the returncode attribute, and output & stderr attributes if those streams
        were captured.
    
        If timeout is given, and the process takes too long, a TimeoutExpired
        exception will be raised.
    
        There is an optional argument "input", allowing you to
        pass bytes or a string to the subprocess's stdin.  If you use this argument
        you may not also use the Popen constructor's "stdin" argument, as
        it will be used internally.
    
        By default, all communication is in bytes, and therefore any "input" should
        be bytes, and the stdout and stderr will be bytes. If in text mode, any
        "input" should be a string, and stdout and stderr will be strings decoded
        according to locale encoding, or by "encoding" if set. Text mode is
        triggered by setting any of text, encoding, errors or universal_newlines.
    
        The other arguments are the same as for the Popen constructor.
        """
        if input is not None:
            if kwargs.get('stdin') is not None:
                raise ValueError('stdin and input arguments may not both be used.')
            kwargs['stdin'] = PIPE
    
        if capture_output:
            if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
                raise ValueError('stdout and stderr arguments may not be used '
                                 'with capture_output.')
            kwargs['stdout'] = PIPE
            kwargs['stderr'] = PIPE
    
        with Popen(*popenargs, **kwargs) as process:
            try:
                stdout, stderr = process.communicate(input, timeout=timeout)
            except TimeoutExpired as exc:
                process.kill()
                if _mswindows:
                    # Windows accumulates the output in a single blocking
                    # read() call run on child threads, with the timeout
                    # being done in a join() on those threads.  communicate()
                    # _after_ kill() is required to collect that and add it
                    # to the exception.
                    exc.stdout, exc.stderr = process.communicate()
                else:
                    # POSIX _communicate already populated the output so
                    # far into the TimeoutExpired exception.
                    process.wait()
                raise
            except:  # Including KeyboardInterrupt, communicate handled that.
                process.kill()
                # We don't call process.wait() as .__exit__ does that for us.
                raise
            retcode = process.poll()
            if check and retcode:
>               raise CalledProcessError(retcode, process.args,
                                         output=stdout, stderr=stderr)
E               subprocess.CalledProcessError: Command '['bash', 'tests/test_simulation.bash', '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/tests/simulations/acell_engine', 'BlueConfig', '']' returned non-zero exit status 1.

../../../../../../apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/python-3.10.8-rvn6l5/lib/python3.10/subprocess.py:526: CalledProcessError
----------------------------- Captured stdout call -----------------------------
[STEP] Initializing Neurodamus... Logfile: pydamus_2023-08-10_14h16.log
[INFO]  => Neurodamus Mod & Hoc lib loaded.
[INFO] Checking for plugins...
[INFO]  * Registering Engine ACell (test_plugin.ACellEngine)
[INFO]  => Engines Available: ['Base', 'NGV', 'METype', 'ACell']
[INFO]   : Connections Types: ['NeuroGlial', 'GlioVascular', None, 'Synaptic', 'GapJunction', 'NeuroModulation']
[STEP] Setting up Neurodamus configuration
[INFO] Initializing Simulation Configuration and Validation
[WARNING] Setting CurrentDir to '.' is discouraged and shall never be used in production jobs.
[INFO] Checking simulation requirements
[INFO] Initializing hoc config objects
[INFO] User-defined RNG base seed 719775.0
[CRITICAL] (rank 0) Unhandled Exception. Terminating...
Traceback (most recent call last):
  File "/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/neurodamus/commands.py", line 75, in neurodamus
    Neurodamus(config_file, True, log_level, **options).run()
  File "/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/neurodamus/node.py", line 1685, in __init__
    self._instantiate_simulation()
  File "/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/neurodamus/node.py", line 1774, in _instantiate_simulation
    print_mem_usage()
  File "/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/neurodamus/utils/memory.py", line 77, in print_mem_usage
    MPI.pc.print_memory_stats()
AttributeError: 'hoc.HocObject' object has no attribute 'print_memory_stats'
No MorphologyType in BlueConfig, default to legacy 'asc'. MorphologyPath becomes: False/ascii 
Taking Simulator mode from BlueConfig
SimulatorMode set to 'NEURON'
As of Oct 2020 Neurodamus uses Random123 as default
RNGMode set to 1  [COMPATIBILITY=0, RANDOM123=1, UPMCELLRAN4=2]
----------------------------- Captured stderr call -----------------------------
+ SIMDIR=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/tests/simulations/acell_engine
+ CONFIG_FILE=BlueConfig
+ mpi_launcher=
+ neurodamus /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/tests/simulations/acell_engine/BlueConfig --verbose
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/x86_64/special: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
Warning: no DISPLAY environment variable.
--No graphics will be displayed.
NEURON -- VERSION 8.2.2 HEAD (93d41fafd) 2022-12-15
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2022
See http://neuron.yale.edu/neuron/credits

Additional mechanisms from files
 "mods.tmp/ALU.mod" "mods.tmp/CoreConfig.mod" "mods.tmp/DetAMPANMDA.mod" "mods.tmp/DetGABAAB.mod" "mods.tmp/gap.mod" "mods.tmp/GluSynapse.mod" "mods.tmp/HDF5reader.mod" "mods.tmp/lookupTableV2.mod" "mods.tmp/netstim_inhpoisson.mod" "mods.tmp/ProbAMPANMDA_EMS.mod" "mods.tmp/ProbGABAAB_EMS.mod" "mods.tmp/SonataReportHelper.mod" "mods.tmp/SonataReports.mod" "mods.tmp/SpikeWriter.mod" "mods.tmp/SynapseReader.mod" "mods.tmp/TTXDynamicsSwitch.mod" "mods.tmp/VecStim.mod"
Traceback (most recent call last):
  File "/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/neurodamus/commands.py", line 75, in neurodamus
    Neurodamus(config_file, True, log_level, **options).run()
  File "/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/neurodamus/node.py", line 1685, in __init__
    self._instantiate_simulation()
  File "/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/neurodamus/node.py", line 1774, in _instantiate_simulation
    print_mem_usage()
  File "/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/neurodamus/utils/memory.py", line 77, in print_mem_usage
    MPI.pc.print_memory_stats()
AttributeError: 'hoc.HocObject' object has no attribute 'print_memory_stats'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "./init.py", line 36, in <module>
    h.quit(main())
  File "./init.py", line 31, in main
    return commands.neurodamus(args)
  File "/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/neurodamus/commands.py", line 83, in neurodamus
    show_exception_abort("Unhandled Exception. Terminating...", sys.exc_info())
  File "/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/neurodamus/commands.py", line 165, in show_exception_abort
    _mpi_abort()  # abort all ranks which have waited. Seems to help avoiding MPT stack
  File "/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/neurodamus/commands.py", line 195, in _mpi_abort
    c_api.MPI_Abort(0)
  File "/gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/python-3.10.8-rvn6l5/lib/python3.10/ctypes/__init__.py", line 387, in __getattr__
    func = self.__getitem__(name)
  File "/gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/python-3.10.8-rvn6l5/lib/python3.10/ctypes/__init__.py", line 392, in __getitem__
    func = self._FuncPtr((name_or_ordinal, self))
AttributeError: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/x86_64/special: undefined symbol: MPI_Abort
=========================== short test summary info ============================
FAILED tests/test_plugin.py::test_run_acell_circuit - subprocess.CalledProces...
================== 1 failed, 104 passed, 32 skipped in 6.11s ===================
py3: exit 1 (7.67 seconds) /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus> python setup.py test pid=59374
.pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J841817/hpc/sim/neurodamus/venv/lib/python3.10/site-packages/pyproject_api/_backend.py True setuptools.build_meta __legacy__
  flake8: OK (5.49=setup[3.96]+cmd[1.52] seconds)
  py3: FAIL code 1 (37.34=setup[26.33]+cmd[3.33,7.67] seconds)
  evaluation failed :( (43.18 seconds)
srun: error: r1i7n31: task 0: Exited with exit code 1
section_end:1691669815:step_script
section_start:1691669815:cleanup_file_variables
Cleaning up project directory and file based variables
Using git from spack modules
section_end:1691669816:cleanup_file_variables
ERROR: Job failed: exit status 1


set-alt-branches.txt

Running with gitlab-runner 16.0.2 (85586bd1)
  on kubernetes UyS3rsx9, system ID: r_DKDlByjIUN4Z
section_start:1691669746:resolve_secrets
Resolving secrets
section_end:1691669746:resolve_secrets
section_start:1691669746:prepare_executor
Preparing the "kubernetes" executor
Using Kubernetes namespace: gitlab-runners
Using Kubernetes executor with image quay.io/pypa/manylinux2014_x86_64 ...
Using attach strategy to execute scripts...
section_end:1691669746:prepare_executor
section_start:1691669746:prepare_script
Preparing environment
Waiting for pod gitlab-runners/runner-uys3rsx9-project-2354-concurrent-0hl2h7 to be running, status is Pending
Waiting for pod gitlab-runners/runner-uys3rsx9-project-2354-concurrent-0hl2h7 to be running, status is Pending
	ContainersNotReady: "containers with unready status: [build helper]"
	ContainersNotReady: "containers with unready status: [build helper]"
Running on runner-uys3rsx9-project-2354-concurrent-0hl2h7 via cs-gitlab-runners-gitlab-runner-77449f5787-4jx2j...

section_end:1691669755:prepare_script
section_start:1691669755:get_sources
Getting source from Git repository
Fetching changes with git depth set to 20...
Initialized empty Git repository in /builds/hpc/sim/neurodamus/.git/
Created fresh repository.
Checking out 73653388 as detached HEAD (ref is 1uc/free-deleted-stable-identifiers)...

Updating/initializing submodules recursively with git depth set to 20...

section_end:1691669760:get_sources
section_start:1691669760:step_script
Executing "step_script" stage of the job script
$ grep '^[[:alnum:]_]*_BRANCH=' <<< "$CI_COMMIT_MESSAGE" > branch_variables.env || touch branch_variables.env
$ . branch_variables.env
$ echo "BLUECONFIGS_PIPELINE_BRANCH=$BLUECONFIGS_BRANCH" >> branch_variables.env
$ cat branch_variables.env
BLUECONFIGS_PIPELINE_BRANCH=main

section_end:1691669761:step_script
section_start:1691669761:upload_artifacts_on_success
Uploading artifacts for successful job
Uploading artifacts...
branch_variables.env: found 1 matching artifact files and directories 
Uploading artifacts as "dotenv" to coordinator... 201 Created  id=841819 responseStatus=201 Created token=64_xymyb

section_end:1691669763:upload_artifacts_on_success
section_start:1691669763:cleanup_file_variables
Cleaning up project directory and file based variables

section_end:1691669763:cleanup_file_variables
Job succeeded