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October 24, 2024 14:30
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Logfiles for GitLab pipeline https://bbpgitlab.epfl.ch/hpc/sim/neurodamus/-/pipelines/236741 (:white_check_mark:) running on GitHub PR BlueBrain/neurodamus#206.
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| [0KRunning with gitlab-runner 16.11.1 (535ced5f)[0;m | |
| [0K on kubernetes -ypBJ96G, system ID: r_j5AS6h5XNfdt[0;m | |
| [0K[36;1mResolving secrets[0;m[0;m | |
| section_start:1729780118:prepare_executor [0K[0K[36;1mPreparing the "kubernetes" executor[0;m[0;m | |
| [0KUsing Kubernetes namespace: gitlab-runners[0;m | |
| [0KUsing Kubernetes executor with image quay.io/pypa/manylinux2014_x86_64 ...[0;m | |
| [0KUsing attach strategy to execute scripts...[0;m | |
| section_end:1729780118:prepare_executor [0Ksection_start:1729780118:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| [0KUsing FF_USE_POD_ACTIVE_DEADLINE_SECONDS, the Pod activeDeadlineSeconds will be set to the job timeout: 1h0m0s...[0;m | |
| Waiting for pod gitlab-runners/runner--ypbj96g-project-2354-concurrent-0-pvcm5ls6 to be running, status is Pending | |
| Running on runner--ypbj96g-project-2354-concurrent-0-pvcm5ls6 via cs-gitlab-runners-gitlab-runner-c4db7d7cd-g7hlg... | |
| section_end:1729780123:prepare_script [0Ksection_start:1729780123:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
| [32;1mFetching changes with git depth set to 100...[0;m | |
| Initialized empty Git repository in /builds/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out 05a30124 as detached HEAD (ref is leite/corenrn-rebalancer)...[0;m | |
| [32;1mUpdating/initializing submodules recursively with git depth set to 100...[0;m | |
| [32;1mUpdated submodules[0;m | |
| section_end:1729780131:get_sources [0Ksection_start:1729780131:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
| [32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m | |
| [32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m | |
| [32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m | |
| [32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m | |
| [32;1m$ PYTHON_ROOT=/opt/python/cp311-cp311[0;m | |
| [32;1m$ export PATH=$PYTHON_ROOT/bin:$PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.11.10 | |
| [32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m | |
| [0Ksection_start:1729780131:section_venv[collapsed=true] [0KSetting up the virtual env | |
| [32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
| [32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
| [32;1m$ rm -rf "$CI_VENV"[0;m | |
| [32;1m$ python -mvenv "$CI_VENV"[0;m | |
| [32;1m$ source "$CI_VENV/bin/activate"[0;m | |
| [32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Requirement already satisfied: pip in ./venv/lib/python3.11/site-packages (24.0) | |
| Collecting pip | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2cd/581cf58ab7fcf/pip-24.2-py3-none-any.whl (1.8 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.8/1.8 MB 129.0 MB/s eta 0:00:00 | |
| Requirement already satisfied: setuptools in ./venv/lib/python3.11/site-packages (65.5.0) | |
| Collecting setuptools | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/a7f/cb66f68b4d9e8/setuptools-75.2.0-py3-none-any.whl (1.2 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.2/1.2 MB 122.5 MB/s eta 0:00:00 | |
| Collecting wheel | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/237/6a90c98cc337d/wheel-0.44.0-py3-none-any.whl (67 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 67.1/67.1 kB 116.4 MB/s eta 0:00:00 | |
| Installing collected packages: wheel, setuptools, pip | |
| Attempting uninstall: setuptools | |
| Found existing installation: setuptools 65.5.0 | |
| Uninstalling setuptools-65.5.0: | |
| Successfully uninstalled setuptools-65.5.0 | |
| Attempting uninstall: pip | |
| Found existing installation: pip 24.0 | |
| Uninstalling pip-24.0: | |
| Successfully uninstalled pip-24.0 | |
| Successfully installed pip-24.2 setuptools-75.2.0 wheel-0.44.0 | |
| [32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Collecting build | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/1d6/1c0887fa860c0/build-1.2.2.post1-py3-none-any.whl (22 kB) | |
| Collecting twine | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/215/dbe7b4b94c2c5/twine-5.1.1-py3-none-any.whl (38 kB) | |
| Collecting packaging>=19.1 (from build) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/5b8/f2217dbdbd2f7/packaging-24.1-py3-none-any.whl (53 kB) | |
| Collecting pyproject_hooks (from build) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/9e5/c6bfa8dcc3009/pyproject_hooks-1.2.0-py3-none-any.whl (10 kB) | |
| Collecting pkginfo>=1.8.1 (from twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/9ec/518eefccd159d/pkginfo-1.11.2-py3-none-any.whl (31 kB) | |
| Collecting readme-renderer>=35.0 (from twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2fb/ca89b81a08526/readme_renderer-44.0-py3-none-any.whl (13 kB) | |
| Collecting requests>=2.20 (from twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/707/61cfe03c773ce/requests-2.32.3-py3-none-any.whl (64 kB) | |
| Collecting requests-toolbelt!=0.9.0,>=0.8.0 (from twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/ccc/fdd665f0a24fc/requests_toolbelt-1.0.0-py2.py3-none-any.whl (54 kB) | |
| Collecting urllib3>=1.26.0 (from twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/ca8/99ca043dcb1ba/urllib3-2.2.3-py3-none-any.whl (126 kB) | |
| Collecting importlib-metadata>=3.6 (from twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/45e/54197d28b7a7f/importlib_metadata-8.5.0-py3-none-any.whl (26 kB) | |
| Collecting keyring>=15.1 (from twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/542/6f817cf7f6f00/keyring-25.4.1-py3-none-any.whl (38 kB) | |
| Collecting rfc3986>=1.4.0 (from twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/50b/1502b60e289cb/rfc3986-2.0.0-py2.py3-none-any.whl (31 kB) | |
| Collecting rich>=12.0.0 (from twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/983/6f5096eb2172c/rich-13.9.3-py3-none-any.whl (242 kB) | |
| Collecting pkginfo>=1.8.1 (from twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/889/a6da2ed7ffc58/pkginfo-1.10.0-py3-none-any.whl (30 kB) | |
| Collecting zipp>=3.20 (from importlib-metadata>=3.6->twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/a81/7ac80d6cf4b23/zipp-3.20.2-py3-none-any.whl (9.2 kB) | |
| Collecting jaraco.classes (from keyring>=15.1->twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/f66/2826b6bed8cac/jaraco.classes-3.4.0-py3-none-any.whl (6.8 kB) | |
| Collecting jaraco.functools (from keyring>=15.1->twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/ad1/59f13428bc4ac/jaraco.functools-4.1.0-py3-none-any.whl (10 kB) | |
| Collecting jaraco.context (from keyring>=15.1->twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/f79/7fc481b490edb/jaraco.context-6.0.1-py3-none-any.whl (6.8 kB) | |
| Collecting SecretStorage>=3.2 (from keyring>=15.1->twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/f35/6e6628222568e/SecretStorage-3.3.3-py3-none-any.whl (15 kB) | |
| Collecting jeepney>=0.4.2 (from keyring>=15.1->twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/c0a/454ad016ca575/jeepney-0.8.0-py3-none-any.whl (48 kB) | |
| Collecting nh3>=0.2.14 (from readme-renderer>=35.0->twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/de3/ceed6e6619548/nh3-0.2.18-cp37-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (769 kB) | |
| âââââââââââââââââââââââââââââââââââââ 769.2/769.2 kB 169.9 MB/s eta 0:00:00 | |
| Collecting docutils>=0.21.2 (from readme-renderer>=35.0->twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/daf/ca5b9e384f0e4/docutils-0.21.2-py3-none-any.whl (587 kB) | |
| âââââââââââââââââââââââââââââââââââââ 587.4/587.4 kB 192.1 MB/s eta 0:00:00 | |
| Collecting Pygments>=2.5.1 (from readme-renderer>=35.0->twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/b8e/6aca0523f3ab7/pygments-2.18.0-py3-none-any.whl (1.2 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.2/1.2 MB 247.4 MB/s eta 0:00:00 | |
| Collecting charset-normalizer<4,>=2 (from requests>=2.20->twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/371/0a9751938947e/charset_normalizer-3.4.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (142 kB) | |
| Collecting idna<4,>=2.5 (from requests>=2.20->twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/946/d195a0d259cbb/idna-3.10-py3-none-any.whl (70 kB) | |
| Collecting certifi>=2017.4.17 (from requests>=2.20->twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/922/820b53db7a725/certifi-2024.8.30-py3-none-any.whl (167 kB) | |
| Collecting markdown-it-py>=2.2.0 (from rich>=12.0.0->twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/355/216845c60bd96/markdown_it_py-3.0.0-py3-none-any.whl (87 kB) | |
| Collecting mdurl~=0.1 (from markdown-it-py>=2.2.0->rich>=12.0.0->twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/840/08a41e51615a4/mdurl-0.1.2-py3-none-any.whl (10.0 kB) | |
| Collecting cryptography>=2.0 (from SecretStorage>=3.2->keyring>=15.1->twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/0f9/96e7268af6259/cryptography-43.0.3-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.0 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 4.0/4.0 MB 248.6 MB/s eta 0:00:00 | |
| Collecting more-itertools (from jaraco.classes->keyring>=15.1->twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/037/b0d3203ce90cc/more_itertools-10.5.0-py3-none-any.whl (60 kB) | |
| Collecting backports.tarfile (from jaraco.context->keyring>=15.1->twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/77e/284d754527b01/backports.tarfile-1.2.0-py3-none-any.whl (30 kB) | |
| Collecting cffi>=1.12 (from cryptography>=2.0->SecretStorage>=3.2->keyring>=15.1->twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/610/faea79c43e44c/cffi-1.17.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (467 kB) | |
| Collecting pycparser (from cffi>=1.12->cryptography>=2.0->SecretStorage>=3.2->keyring>=15.1->twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/c37/02b6d3dd8c7ab/pycparser-2.22-py3-none-any.whl (117 kB) | |
| Installing collected packages: nh3, zipp, urllib3, rfc3986, pyproject_hooks, Pygments, pycparser, pkginfo, packaging, more-itertools, mdurl, jeepney, idna, docutils, charset-normalizer, certifi, backports.tarfile, requests, readme-renderer, markdown-it-py, jaraco.functools, jaraco.context, jaraco.classes, importlib-metadata, cffi, build, rich, requests-toolbelt, cryptography, SecretStorage, keyring, twine | |
| Successfully installed Pygments-2.18.0 SecretStorage-3.3.3 backports.tarfile-1.2.0 build-1.2.2.post1 certifi-2024.8.30 cffi-1.17.1 charset-normalizer-3.4.0 cryptography-43.0.3 docutils-0.21.2 idna-3.10 importlib-metadata-8.5.0 jaraco.classes-3.4.0 jaraco.context-6.0.1 jaraco.functools-4.1.0 jeepney-0.8.0 keyring-25.4.1 markdown-it-py-3.0.0 mdurl-0.1.2 more-itertools-10.5.0 nh3-0.2.18 packaging-24.1 pkginfo-1.10.0 pycparser-2.22 pyproject_hooks-1.2.0 readme-renderer-44.0 requests-2.32.3 requests-toolbelt-1.0.0 rfc3986-2.0.0 rich-13.9.3 twine-5.1.1 urllib3-2.2.3 zipp-3.20.2 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1729780159:section_venv [0K | |
| [32;1m$ rm -Rf build dist *.egg-info[0;m | |
| [32;1m$ python -m build --sdist[0;m | |
| * Creating isolated environment: venv+pip... | |
| * Installing packages in isolated environment: | |
| - hatch-vcs | |
| - hatchling | |
| * Getting build dependencies for sdist... | |
| * Building sdist... | |
| /tmp/build-env-zrjor6b1/lib/python3.11/site-packages/setuptools_scm/git.py:167: UserWarning: "/builds/hpc/sim/neurodamus" is shallow and may cause errors | |
| warnings.warn(f'"{wd.path}" is shallow and may cause errors') | |
| Successfully built neurodamus-3.6.1.dev17.tar.gz | |
| [32;1m$ twine check dist/*[0;m | |
| Checking dist/neurodamus-3.6.1.dev17.tar.gz: [32mPASSED[0m | |
| section_end:1729780164:step_script [0Ksection_start:1729780164:upload_artifacts_on_success [0K[0K[36;1mUploading artifacts for successful job[0;m[0;m | |
| [32;1mUploading artifacts...[0;m | |
| ./dist/*.tar.gz: found 1 matching artifact files and directories[0;m | |
| Uploading artifacts as "archive" to coordinator... 201 Created[0;m id[0;m=1467940 responseStatus[0;m=201 Created token[0;m=glcbt-64 | |
| section_end:1729780166:upload_artifacts_on_success [0Ksection_start:1729780166:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| section_end:1729780167:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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| [0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1729779532:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1729779532:resolve_secrets [0Ksection_start:1729779532:prepare_executor [0K[0K[36;1mPreparing the "custom" executor[0;m[0;m | |
| [0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m | |
| BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user | |
| TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor2918167727, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 236741, build ref , job ID 1467932 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1467932, 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_J1467932_PROD_P2354_CP0_C6 | |
| Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcsim partition=prod qos= reservation= | |
| Not executing the chown -R | |
| sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS | |
| sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx] | |
| Submitted batch job 2601911 | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1467932_PROD_P2354_CP0_C6 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1467932 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1467932 --ntasks=1 --jobid=2601911 --cpus-per-task=6 --mem=30750M | |
| section_end:1729779533:prepare_executor [0Ksection_start:1729779533:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i5n2 via bbpv1.epfl.ch... | |
| section_end:1729779537:prepare_script [0Ksection_start:1729779537:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
| Using git from spack modules | |
| [32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m | |
| [32;1mFetching changes with git depth set to 100...[0;m | |
| Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467932/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out 05a30124 as leite/corenrn-rebalancer...[0;m | |
| Skipping object checkout, Git LFS is not installed. | |
| [32;1mUpdating/initializing submodules recursively with git depth set to 100...[0;m | |
| section_end:1729779552:get_sources [0Ksection_start:1729779552:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
| [0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m | |
| Using git from spack modules | |
| [32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m | |
| [32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m | |
| [32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m | |
| [32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m | |
| [32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m | |
| [32;1m$ module purge[0;m | |
| [32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m | |
| [32;1m$ module load unstable python/3.12.0[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.12.0 | |
| [32;1m$ module load unstable python/3.8.18[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.8.18 | |
| [32;1m$ module load unstable python/3.9.18[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.9.18 | |
| [32;1m$ module load unstable python/3.10.13[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.10.13 | |
| [32;1m$ module load unstable python/3.11.6[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.11.6 | |
| [32;1m$ load-modules() { # collapsed multi-line command[0;m | |
| [32;1m$ load-modules $SYSTEM_MODULES[0;m | |
| Loaded module git from unstable | |
| Loaded module cmake from unstable | |
| Loaded module graphviz from unstable | |
| [32;1m$ load-modules $EXTRA_MODULES[0;m | |
| [32;1m$ module list -t[0;m | |
| Currently Loaded Modulefiles: | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.12.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.8.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.9.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.10.13 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.11.6 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/git/2.42.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/cmake/3.27.7 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/graphviz/8.0.5 | |
| [32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
| [32;1m$ print_var XDG_CONFIG_HOME[0;m | |
| [36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467932/hpc/sim/neurodamus/local_config[0m | |
| [32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m | |
| [32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m | |
| [32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
| [url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
| insteadOf = https://bbpgitlab.epfl.ch/ | |
| insteadOf = ssh://git@bbpgitlab.epfl.ch/ | |
| insteadOf = git@bbpgitlab.epfl.ch: | |
| [32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m | |
| [0Ksection_start:1729779573:section_venv[collapsed=true] [0KSetting up the virtual env | |
| [32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
| [32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
| [32;1m$ rm -rf "$CI_VENV"[0;m | |
| [32;1m$ python -mvenv "$CI_VENV"[0;m | |
| [32;1m$ source "$CI_VENV/bin/activate"[0;m | |
| [32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Requirement already satisfied: pip in ./venv/lib/python3.11/site-packages (23.2.1) | |
| Collecting pip | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2cd/581cf58ab7fcf/pip-24.2-py3-none-any.whl (1.8 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.8/1.8 MB 60.7 MB/s eta 0:00:00 | |
| Requirement already satisfied: setuptools in ./venv/lib/python3.11/site-packages (65.5.0) | |
| Collecting setuptools | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/a7f/cb66f68b4d9e8/setuptools-75.2.0-py3-none-any.whl (1.2 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.2/1.2 MB 190.6 MB/s eta 0:00:00 | |
| Collecting wheel | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/237/6a90c98cc337d/wheel-0.44.0-py3-none-any.whl (67 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 67.1/67.1 kB 221.5 MB/s eta 0:00:00 | |
| Installing collected packages: wheel, setuptools, pip | |
| Attempting uninstall: setuptools | |
| Found existing installation: setuptools 65.5.0 | |
| Uninstalling setuptools-65.5.0: | |
| Successfully uninstalled setuptools-65.5.0 | |
| Attempting uninstall: pip | |
| Found existing installation: pip 23.2.1 | |
| Uninstalling pip-23.2.1: | |
| Successfully uninstalled pip-23.2.1 | |
| Successfully installed pip-24.2 setuptools-75.2.0 wheel-0.44.0 | |
| [32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Collecting tox | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/452/bc32bb031f228/tox-4.23.2-py3-none-any.whl (166 kB) | |
| Collecting cachetools>=5.5 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/021/34e8439cdc2ff/cachetools-5.5.0-py3-none-any.whl (9.5 kB) | |
| Collecting chardet>=5.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB) | |
| Collecting colorama>=0.4.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB) | |
| Collecting filelock>=3.16.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/208/2e5703d51fbf9/filelock-3.16.1-py3-none-any.whl (16 kB) | |
| Collecting packaging>=24.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/5b8/f2217dbdbd2f7/packaging-24.1-py3-none-any.whl (53 kB) | |
| Collecting platformdirs>=4.3.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/73e/575e1408ab810/platformdirs-4.3.6-py3-none-any.whl (18 kB) | |
| Collecting pluggy>=1.5 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/44e/1ad92c8ca002d/pluggy-1.5.0-py3-none-any.whl (20 kB) | |
| Collecting pyproject-api>=1.8 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/3d7/d347a047afe79/pyproject_api-1.8.0-py3-none-any.whl (13 kB) | |
| Collecting virtualenv>=20.26.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/44a/72c29cceb0ee0/virtualenv-20.27.0-py3-none-any.whl (3.1 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 3.1/3.1 MB 156.9 MB/s eta 0:00:00 | |
| Collecting distlib<1,>=0.3.7 (from virtualenv>=20.26.6->tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/47f/8c22fd27c27e2/distlib-0.3.9-py2.py3-none-any.whl (468 kB) | |
| Installing collected packages: distlib, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
| Successfully installed cachetools-5.5.0 chardet-5.2.0 colorama-0.4.6 distlib-0.3.9 filelock-3.16.1 packaging-24.1 platformdirs-4.3.6 pluggy-1.5.0 pyproject-api-1.8.0 tox-4.23.2 virtualenv-20.27.0 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1729779659:section_venv [0K | |
| [32;1m$ print_var PRE_BUILD_COMMAND[0;m | |
| [36mPRE_BUILD_COMMAND=[0m | |
| [32;1m$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi[0;m | |
| [32;1m$ section_start section_tox "Running Tox"[0;m | |
| [0Ksection_start:1729779659:section_tox [0KRunning Tox | |
| [32;1m$ python -mtox $TOX_OPTIONS[0;m | |
| docs: install_deps> python -I -m pip install sphinx-bluebrain-theme 'sphinx<5.1.0' | |
| .pkg: install_requires> python -I -m pip install hatch-vcs hatchling | |
| .pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467932/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| .pkg: get_requires_for_build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467932/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| .pkg: freeze> python -m pip freeze --all | |
| .pkg: hatch-vcs==0.4.0,hatchling==1.25.0,packaging==24.1,pathspec==0.12.1,pip==24.2,pluggy==1.5.0,setuptools==75.2.0,setuptools-scm==8.1.0,trove-classifiers==2024.10.21.16,wheel==0.44.0 | |
| .pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467932/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| docs: install_package_deps> python -I -m pip install docopt h5py libsonata psutil | |
| docs: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467932/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.6.1.dev17.tar.gz | |
| docs: freeze> python -m pip freeze --all | |
| docs: alabaster==0.7.16,babel==2.16.0,certifi==2024.8.30,charset-normalizer==3.4.0,docopt==0.6.2,docutils==0.18.1,h5py==3.12.1,idna==3.10,imagesize==1.4.1,Jinja2==3.1.4,libsonata==0.1.29,MarkupSafe==3.0.2,neurodamus @ file:///gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467932/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.6.1.dev17.tar.gz#sha256=a7d49bca41a60ba7db928207533e4867a4b4839782739dac62a2c775a798bf67,numpy==2.1.2,packaging==24.1,pip==24.2,psutil==6.1.0,Pygments==2.18.0,requests==2.32.3,setuptools==75.2.0,snowballstemmer==2.2.0,Sphinx==5.0.2,sphinx-bluebrain-theme==0.4.4,sphinxcontrib-applehelp==2.0.0,sphinxcontrib-devhelp==2.0.0,sphinxcontrib-htmlhelp==2.1.0,sphinxcontrib-jsmath==1.0.1,sphinxcontrib-qthelp==2.0.0,sphinxcontrib-serializinghtml==2.0.0,urllib3==2.2.3,wheel==0.44.0 | |
| docs: commands[0]> sphinx-build -T -W docs docs/_build | |
| Running Sphinx v5.0.2 | |
| making output directory... done | |
| building [mo]: targets for 0 po files that are out of date | |
| building [html]: targets for 18 source files that are out of date | |
| updating environment: [new config] 18 added, 0 changed, 0 removed | |
| reading sources... [ 5%] api/modules | |
| reading sources... [ 11%] api/neurodamus | |
| reading sources... [ 16%] api/neurodamus.core | |
| reading sources... [ 22%] api/neurodamus.io | |
| reading sources... [ 27%] api/neurodamus.utils | |
| reading sources... [ 33%] api/subpackages/core | |
| reading sources... [ 38%] api/subpackages/io | |
| reading sources... [ 44%] api/subpackages/top | |
| reading sources... [ 50%] api/subpackages/utils | |
| reading sources... [ 55%] architecture | |
| reading sources... [ 61%] changes | |
| reading sources... [ 66%] development | |
| reading sources... [ 72%] examples | |
| reading sources... [ 77%] index | |
| reading sources... [ 83%] online-lfp | |
| reading sources... [ 88%] overview | |
| reading sources... [ 94%] sonata-faq | |
| reading sources... [100%] sonata-simulation | |
| looking for now-outdated files... none found | |
| pickling environment... done | |
| checking consistency... done | |
| preparing documents... done | |
| writing output... [ 5%] api/modules | |
| writing output... [ 11%] api/neurodamus | |
| writing output... [ 16%] api/neurodamus.core | |
| writing output... [ 22%] api/neurodamus.io | |
| writing output... [ 27%] api/neurodamus.utils | |
| writing output... [ 33%] api/subpackages/core | |
| writing output... [ 38%] api/subpackages/io | |
| writing output... [ 44%] api/subpackages/top | |
| writing output... [ 50%] api/subpackages/utils | |
| writing output... [ 55%] architecture | |
| writing output... [ 61%] changes | |
| writing output... [ 66%] development | |
| writing output... [ 72%] examples | |
| writing output... [ 77%] index | |
| writing output... [ 83%] online-lfp | |
| writing output... [ 88%] overview | |
| writing output... [ 94%] sonata-faq | |
| writing output... [100%] sonata-simulation | |
| generating indices... genindex py-modindex done | |
| writing additional pages... search done | |
| copying images... [ 10%] img/neurodamus-prev-concept.png | |
| copying images... [ 20%] img/neurodamus-prev-arch.png | |
| copying images... [ 30%] img/neurodamus-arch.png | |
| copying images... [ 40%] img/cell-hierarchy.png | |
| copying images... [ 50%] img/multi-population-concept.png | |
| copying images... [ 60%] img/cell-managers.png | |
| copying images... [ 70%] img/conn-managers.png | |
| copying images... [ 80%] img/neurodamus_dry_run.png | |
| copying images... [ 90%] img/neurodamus_banner_230701.png | |
| copying images... [100%] img/sonata.png | |
| copying static files... done | |
| copying extra files... done | |
| dumping search index in English (code: en)... done | |
| dumping object inventory... done | |
| build succeeded. | |
| The HTML pages are in docs/_build. | |
| .pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467932/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| docs: OK (183.30=setup[164.10]+cmd[19.20] seconds) | |
| congratulations :) (184.95 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1729779846:section_tox [0K | |
| section_end:1729779846:step_script [0Ksection_start:1729779847:upload_artifacts_on_success [0K[0K[36;1mUploading artifacts for successful job[0;m[0;m | |
| Using git from spack modules | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=121313 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| docs/_build: found 197 matching files and directories[0;m | |
| Uploading artifacts as "archive" to coordinator... ok[0;m id[0;m=1467932 responseStatus[0;m=201 Created token[0;m=glcbt-64 | |
| section_end:1729779849:upload_artifacts_on_success [0Ksection_start:1729779849:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| Using git from spack modules | |
| section_end:1729779849:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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| ! |
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| No log output from job with status: manual |
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| No log output from job with status: manual |
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| [0KRunning with gitlab-runner 16.11.1 (535ced5f)[0;m | |
| [0K on kubernetes -ypBJ96G, system ID: r_j5AS6h5XNfdt[0;m | |
| [0K[36;1mResolving secrets[0;m[0;m | |
| section_start:1729779532:prepare_executor [0K[0K[36;1mPreparing the "kubernetes" executor[0;m[0;m | |
| [0KUsing Kubernetes namespace: gitlab-runners[0;m | |
| [0KUsing Kubernetes executor with image quay.io/pypa/manylinux2014_x86_64 ...[0;m | |
| [0KUsing attach strategy to execute scripts...[0;m | |
| section_end:1729779532:prepare_executor [0Ksection_start:1729779532:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| [0KUsing FF_USE_POD_ACTIVE_DEADLINE_SECONDS, the Pod activeDeadlineSeconds will be set to the job timeout: 1h0m0s...[0;m | |
| Waiting for pod gitlab-runners/runner--ypbj96g-project-2354-concurrent-0-a14pwgzc to be running, status is Pending | |
| Running on runner--ypbj96g-project-2354-concurrent-0-a14pwgzc via cs-gitlab-runners-gitlab-runner-c4db7d7cd-g7hlg... | |
| section_end:1729779538:prepare_script [0Ksection_start:1729779538:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
| [32;1mFetching changes with git depth set to 100...[0;m | |
| Initialized empty Git repository in /builds/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out 05a30124 as detached HEAD (ref is leite/corenrn-rebalancer)...[0;m | |
| [32;1mUpdating/initializing submodules recursively with git depth set to 100...[0;m | |
| [32;1mUpdated submodules[0;m | |
| section_end:1729779546:get_sources [0Ksection_start:1729779546:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
| [32;1m$ grep '^[[:alnum:]_]*_BRANCH=' <<< "$CI_COMMIT_MESSAGE" > branch_variables.env || touch branch_variables.env[0;m | |
| [32;1m$ . branch_variables.env[0;m | |
| [32;1m$ echo "BLUECONFIGS_PIPELINE_BRANCH=$BLUECONFIGS_BRANCH" >> branch_variables.env[0;m | |
| [32;1m$ cat branch_variables.env[0;m | |
| BLUECONFIGS_PIPELINE_BRANCH=main | |
| section_end:1729779546:step_script [0Ksection_start:1729779546:upload_artifacts_on_success [0K[0K[36;1mUploading artifacts for successful job[0;m[0;m | |
| [32;1mUploading artifacts...[0;m | |
| branch_variables.env: found 1 matching artifact files and directories[0;m | |
| Uploading artifacts as "dotenv" to coordinator... 201 Created[0;m id[0;m=1467938 responseStatus[0;m=201 Created token[0;m=glcbt-64 | |
| section_end:1729779548:upload_artifacts_on_success [0Ksection_start:1729779548:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| section_end:1729779549:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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| [0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1729779534:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1729779534:resolve_secrets [0Ksection_start:1729779534:prepare_executor [0K[0K[36;1mPreparing the "custom" executor[0;m[0;m | |
| [0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m | |
| BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user | |
| TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor2134595896, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 236741, build ref , job ID 1467935 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1467935, 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_J1467935_PROD_P2354_CP3_C9 | |
| Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcsim partition=prod qos= reservation= | |
| Not executing the chown -R | |
| sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS | |
| sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx] | |
| Submitted batch job 2601914 | |
| job state: PD | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1467935_PROD_P2354_CP3_C9 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1467935 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1467935 --ntasks=1 --jobid=2601914 --cpus-per-task=6 --mem=30750M | |
| section_end:1729779536:prepare_executor [0Ksection_start:1729779536:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i5n5 via bbpv1.epfl.ch... | |
| section_end:1729779541:prepare_script [0Ksection_start:1729779541:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
| Using git from spack modules | |
| [32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m | |
| [32;1mFetching changes with git depth set to 100...[0;m | |
| Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467935/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out 05a30124 as leite/corenrn-rebalancer...[0;m | |
| Skipping object checkout, Git LFS is not installed. | |
| [32;1mUpdating/initializing submodules recursively with git depth set to 100...[0;m | |
| section_end:1729779545:get_sources [0Ksection_start:1729779545:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
| [0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m | |
| Using git from spack modules | |
| [32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m | |
| [32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m | |
| [32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m | |
| [32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m | |
| [32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m | |
| [32;1m$ module purge[0;m | |
| [32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m | |
| [32;1m$ module load unstable python/3.12.0[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.12.0 | |
| [32;1m$ module load unstable python/3.8.18[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.8.18 | |
| [32;1m$ module load unstable python/3.9.18[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.9.18 | |
| [32;1m$ module load unstable python/3.10.13[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.10.13 | |
| [32;1m$ module load unstable python/3.11.6[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.11.6 | |
| [32;1m$ load-modules() { # collapsed multi-line command[0;m | |
| [32;1m$ load-modules $SYSTEM_MODULES[0;m | |
| Loaded module git from unstable | |
| Loaded module cmake from unstable | |
| Loaded module graphviz from unstable | |
| [32;1m$ load-modules $EXTRA_MODULES[0;m | |
| Loaded module neurodamus-neocortex from unstable | |
| [32;1m$ module list -t[0;m | |
| Currently Loaded Modulefiles: | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.12.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.8.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.9.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.10.13 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.11.6 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/git/2.42.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/cmake/3.27.7 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/graphviz/8.0.5 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/intel-oneapi-mkl/2023.2.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/hpe-mpi/2.27.p1.hmpt | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/applications/linux-rhel7-skylake/neurodamus-neocortex/2.4.1 | |
| [32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
| [32;1m$ print_var XDG_CONFIG_HOME[0;m | |
| [36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467935/hpc/sim/neurodamus/local_config[0m | |
| [32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m | |
| [32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m | |
| [32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
| [url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
| insteadOf = https://bbpgitlab.epfl.ch/ | |
| insteadOf = ssh://git@bbpgitlab.epfl.ch/ | |
| insteadOf = git@bbpgitlab.epfl.ch: | |
| [32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m | |
| [0Ksection_start:1729779568:section_venv[collapsed=true] [0KSetting up the virtual env | |
| [32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
| [32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
| [32;1m$ rm -rf "$CI_VENV"[0;m | |
| [32;1m$ python -mvenv "$CI_VENV"[0;m | |
| [32;1m$ source "$CI_VENV/bin/activate"[0;m | |
| [32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Requirement already satisfied: pip in ./venv/lib/python3.11/site-packages (23.2.1) | |
| Collecting pip | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2cd/581cf58ab7fcf/pip-24.2-py3-none-any.whl (1.8 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.8/1.8 MB 61.1 MB/s eta 0:00:00 | |
| Requirement already satisfied: setuptools in ./venv/lib/python3.11/site-packages (65.5.0) | |
| Collecting setuptools | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/a7f/cb66f68b4d9e8/setuptools-75.2.0-py3-none-any.whl (1.2 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.2/1.2 MB 123.3 MB/s eta 0:00:00 | |
| Collecting wheel | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/237/6a90c98cc337d/wheel-0.44.0-py3-none-any.whl (67 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 67.1/67.1 kB 229.2 MB/s eta 0:00:00 | |
| Installing collected packages: wheel, setuptools, pip | |
| Attempting uninstall: setuptools | |
| Found existing installation: setuptools 65.5.0 | |
| Uninstalling setuptools-65.5.0: | |
| Successfully uninstalled setuptools-65.5.0 | |
| Attempting uninstall: pip | |
| Found existing installation: pip 23.2.1 | |
| Uninstalling pip-23.2.1: | |
| Successfully uninstalled pip-23.2.1 | |
| Successfully installed pip-24.2 setuptools-75.2.0 wheel-0.44.0 | |
| [32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Collecting tox | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/452/bc32bb031f228/tox-4.23.2-py3-none-any.whl (166 kB) | |
| Collecting cachetools>=5.5 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/021/34e8439cdc2ff/cachetools-5.5.0-py3-none-any.whl (9.5 kB) | |
| Collecting chardet>=5.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB) | |
| Collecting colorama>=0.4.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB) | |
| Collecting filelock>=3.16.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/208/2e5703d51fbf9/filelock-3.16.1-py3-none-any.whl (16 kB) | |
| Collecting packaging>=24.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/5b8/f2217dbdbd2f7/packaging-24.1-py3-none-any.whl (53 kB) | |
| Collecting platformdirs>=4.3.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/73e/575e1408ab810/platformdirs-4.3.6-py3-none-any.whl (18 kB) | |
| Collecting pluggy>=1.5 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/44e/1ad92c8ca002d/pluggy-1.5.0-py3-none-any.whl (20 kB) | |
| Collecting pyproject-api>=1.8 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/3d7/d347a047afe79/pyproject_api-1.8.0-py3-none-any.whl (13 kB) | |
| Collecting virtualenv>=20.26.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/44a/72c29cceb0ee0/virtualenv-20.27.0-py3-none-any.whl (3.1 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 3.1/3.1 MB 168.2 MB/s eta 0:00:00 | |
| Collecting distlib<1,>=0.3.7 (from virtualenv>=20.26.6->tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/47f/8c22fd27c27e2/distlib-0.3.9-py2.py3-none-any.whl (468 kB) | |
| Installing collected packages: distlib, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
| Attempting uninstall: packaging | |
| Found existing installation: packaging 23.1 | |
| Not uninstalling packaging at /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-packaging-23.1-uqml2t/lib/python3.11/site-packages, outside environment /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467935/hpc/sim/neurodamus/venv | |
| Can't uninstall 'packaging'. No files were found to uninstall. | |
| Successfully installed cachetools-5.5.0 chardet-5.2.0 colorama-0.4.6 distlib-0.3.9 filelock-3.16.1 packaging-24.1 platformdirs-4.3.6 pluggy-1.5.0 pyproject-api-1.8.0 tox-4.23.2 virtualenv-20.27.0 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1729779644:section_venv [0K | |
| [32;1m$ print_var PRE_BUILD_COMMAND[0;m | |
| [36mPRE_BUILD_COMMAND=[0m | |
| [32;1m$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi[0;m | |
| [32;1m$ section_start section_tox "Running Tox"[0;m | |
| [0Ksection_start:1729779644:section_tox [0KRunning Tox | |
| [32;1m$ python -mtox $TOX_OPTIONS[0;m | |
| bbp-model: install_deps> python -I -m pip install -r tests/requirements.txt | |
| .pkg: install_requires> python -I -m pip install hatch-vcs hatchling | |
| .pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467935/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| .pkg: get_requires_for_build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467935/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| .pkg: freeze> python -m pip freeze --all | |
| .pkg: hatch-vcs==0.4.0,hatchling==1.25.0,packaging==24.1,pathspec==0.12.1,pip==24.2,pluggy==1.5.0,setuptools==75.2.0,setuptools-scm==8.1.0,trove-classifiers==2024.10.21.16,wheel==0.44.0 | |
| .pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467935/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| bbp-model: install_package_deps> python -I -m pip install docopt h5py libsonata psutil | |
| bbp-model: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467935/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.6.1.dev17.tar.gz | |
| bbp-model: freeze> python -m pip freeze --all | |
| bbp-model: docopt @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-docopt-0.6.2-noukz4jts6de5g3xamvap6n4mh7mmcsy/spack-src,find-libpython @ file:///nvme/[MASKED]/2058794/spack-stage/spack-stage-py-find-libpython-0.3.1-5dylncaukuijf2r5t5lrj2s2y2kth2bh/spack-src,h5py @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-h5py-3.8.0-5woxna6nieu5jokc2tdxsfmolza6724e/spack-src,iniconfig==2.0.0,Jinja2 @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-jinja2-3.1.2-7validyciqteluvu43co5k7perpr2baq/spack-src,libsonata @ file:///nvme/[MASKED]/2371376/spack-stage/spack-stage-py-libsonata-0.1.28-jsuf4xxzlybtxiqfdwyqxyxf4c6svcva/spack-src,MarkupSafe @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-markupsafe-2.1.3-r3ehtmw6pkktralavqtazezwbkbsivnt/spack-src,MorphIO @ file:///nvme/[MASKED]/2246265/spack-stage/spack-stage-py-morphio-3.3.6-xap3flagvbfvuospv22jpkdw65c2ypln/spack-src,mpi4py @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-mpi4py-3.1.4-x733hwb2he3bpi423fnogkrw4w33wehe/spack-src,mpmath @ file:///nvme/[MASKED]/2246265/spack-stage/spack-stage-py-mpmath-1.2.1-4fflyibqfjfxrjhnx3jr7bhpt2tpcqn2/spack-src,neurodamus @ file:///nvme/[MASKED]/2379226/spack-stage/spack-stage-py-neurodamus-3.6.0-27enlnafey5xfe6ek7hhy7uozlbps45a/spack-src,numpy @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-numpy-1.26.1-elr5pntecdmhfynrjk3actlxb4go2bua/spack-src,packaging @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-packaging-23.1-uqml2togm4tkpdvzr37r5dnsrpnd76j2/spack-src,pip==24.2,pluggy==1.5.0,psutil @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-psutil-5.9.5-wieplgkaapfkhmzgrsesk5s3h46l3rx4/spack-src,py==1.11.0,pybind11 @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pybind11-2.11.0-7rjfjlzjfm5suub2ks5ttsby2mhqlcfl/spack-src,pytest==7.4.0,pytest-forked==1.6.0,PyYAML @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pyyaml-6.0-c3eqkahwrcjjvgo2irs4ocswyrgh2p64/spack-src,scipy @ file:///nvme/[MASKED]/2045970/spack-stage/spack-stage-py-scipy-1.11.3-dhxei7gha3wm6mobqp3urw6k4ovd7blx/spack-src,setuptools==75.2.0,sympy @ file:///nvme/[MASKED]/2246265/spack-stage/spack-stage-py-sympy-1.11.1-t5tovexvy2goo63j3w6dlqmcnv4yqrqd/spack-src,wheel==0.44.0 | |
| bbp-model: commands[0]> python -c 'import os; print(os.environ.get('"'"'HOC_LIBRARY_PATH'"'"', '"'"''"'"'))' | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467935/hpc/sim/neurodamus/core/hoc:/gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_oneapi-2023.2.0-skylake/neurodamus-models-2.4.1-kjfywd/share/neurodamus_neocortex/hoc | |
| bbp-model: commands[1]> pytest -s -x --forked --durations=5 --durations-min=15 tests/integration-e2e | |
| ============================= test session starts ============================== | |
| platform linux -- Python 3.11.6, pytest-7.4.0, pluggy-1.5.0 -- /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467935/hpc/sim/neurodamus/.tox/bbp-model/bin/python | |
| cachedir: .tox/bbp-model/.pytest_cache | |
| rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467935/hpc/sim/neurodamus | |
| configfile: pyproject.toml | |
| plugins: forked-1.6.0 | |
| collecting ... collected 28 items | |
| tests/integration-e2e/test_cli_opts.py::test_save_restore_cli PASSED | |
| tests/integration-e2e/test_cli_opts.py::test_cli_prcellgid PASSED | |
| tests/integration-e2e/test_cli_opts.py::test_cli_disable_reports PASSED | |
| tests/integration-e2e/test_cli_opts.py::test_cli_keep_build PASSED | |
| tests/integration-e2e/test_cli_opts.py::test_cli_build_model PASSED | |
| tests/integration-e2e/test_cli_opts.py::test_cli_shm_transfer PASSED | |
| tests/integration-e2e/test_cli_opts.py::test_cli_lb_mode PASSED | |
| tests/integration-e2e/test_cli_opts.py::test_cli_output_path PASSED | |
| tests/integration-e2e/test_connection.py::test_add_synapses PASSED | |
| tests/integration-e2e/test_connection.py::test_config_error PASSED | |
| tests/integration-e2e/test_coreneuron_directmode.py::test_coreneuron_no_write_model PASSED | |
| tests/integration-e2e/test_crashmode.py::test_crash_test_loading PASSED | |
| tests/integration-e2e/test_dry_run_workflow.py::test_dry_run_workflow[neurodamus_instance0] PASSED | |
| tests/integration-e2e/test_dry_run_workflow.py::test_dynamic_distribute[neurodamus_instance0] PASSED | |
| tests/integration-e2e/test_dry_run_workflow.py::test_distribute_cells_multi_pop_multi_cycle PASSED | |
| tests/integration-e2e/test_error_handling.py::test_handling_neuron_exceptions PASSED | |
| tests/integration-e2e/test_loadbalance.py::test_loadbal_no_cx PASSED | |
| tests/integration-e2e/test_loadbalance.py::test_loadbal_subtarget PASSED | |
| tests/integration-e2e/test_loadbalance.py::test_load_balance_integrated PASSED | |
| tests/integration-e2e/test_loadbalance.py::test_multisplit PASSED | |
| tests/integration-e2e/test_loadbalance.py::test_loadbal_integration PASSED | |
| tests/integration-e2e/test_multicycle_runs.py::test_nodeset_target_generate_subtargets PASSED | |
| tests/integration-e2e/test_multicycle_runs.py::test_v5_sonata_multisteps PASSED | |
| tests/integration-e2e/test_multicycle_runs.py::test_usecase3_sonata_multisteps PASSED | |
| tests/integration-e2e/test_plugin.py::test_run_acell_circuit SKIPPED | |
| tests/integration-e2e/test_reports.py::test_report_config_error PASSED | |
| tests/integration-e2e/test_reports.py::test_report_disabled PASSED | |
| tests/integration-e2e/test_reports.py::test_v5_sonata_reports PASSED | |
| =============================== warnings summary =============================== | |
| neurodamus/core/configuration.py:162 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467935/hpc/sim/neurodamus/neurodamus/core/configuration.py:162: DeprecationWarning: In 3.13 classes created inside an enum will not become a member. Use the `member` decorator to keep the current behavior. | |
| class AutoBalanceModeParams: | |
| -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html | |
| ============================= slowest 5 durations ============================== | |
| 43.73s call tests/integration-e2e/test_cli_opts.py::test_cli_lb_mode | |
| 42.44s call tests/integration-e2e/test_crashmode.py::test_crash_test_loading | |
| 29.37s call tests/integration-e2e/test_loadbalance.py::test_load_balance_integrated | |
| 29.29s call tests/integration-e2e/test_loadbalance.py::test_multisplit | |
| 29.25s call tests/integration-e2e/test_loadbalance.py::test_loadbal_integration | |
| ============= 27 passed, 1 skipped, 1 warning in 345.34s (0:05:45) ============= | |
| .pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467935/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| bbp-model: OK (466.90=setup[119.06]+cmd[0.26,347.59] seconds) | |
| congratulations :) (468.02 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1729780114:section_tox [0K | |
| section_end:1729780115:step_script [0Ksection_start:1729780115:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| Using git from spack modules | |
| section_end:1729780115:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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| [0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1729779533:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1729779533:resolve_secrets [0Ksection_start:1729779533:prepare_executor [0K[0K[36;1mPreparing the "custom" executor[0;m[0;m | |
| [0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m | |
| BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user | |
| TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor181787392, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 236741, build ref , job ID 1467934 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1467934, 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_J1467934_PROD_P2354_CP2_C8 | |
| Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcsim partition=prod qos= reservation= | |
| Not executing the chown -R | |
| sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS | |
| sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx] | |
| Submitted batch job 2601913 | |
| 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_J1467934_PROD_P2354_CP2_C8 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1467934 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1467934 --ntasks=1 --jobid=2601913 --cpus-per-task=6 --mem=30750M | |
| section_end:1729779536:prepare_executor [0Ksection_start:1729779536:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i5n16 via bbpv1.epfl.ch... | |
| section_end:1729779539:prepare_script [0Ksection_start:1729779539:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
| Using git from spack modules | |
| [32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m | |
| [32;1mFetching changes with git depth set to 100...[0;m | |
| Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out 05a30124 as leite/corenrn-rebalancer...[0;m | |
| Skipping object checkout, Git LFS is not installed. | |
| [32;1mUpdating/initializing submodules recursively with git depth set to 100...[0;m | |
| section_end:1729779543:get_sources [0Ksection_start:1729779543:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
| [0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m | |
| Using git from spack modules | |
| [32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m | |
| [32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m | |
| [32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m | |
| [32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m | |
| [32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m | |
| [32;1m$ module purge[0;m | |
| [32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m | |
| [32;1m$ module load unstable python/3.12.0[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.12.0 | |
| [32;1m$ module load unstable python/3.8.18[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.8.18 | |
| [32;1m$ module load unstable python/3.9.18[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.9.18 | |
| [32;1m$ module load unstable python/3.10.13[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.10.13 | |
| [32;1m$ module load unstable python/3.11.6[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.11.6 | |
| [32;1m$ load-modules() { # collapsed multi-line command[0;m | |
| [32;1m$ load-modules $SYSTEM_MODULES[0;m | |
| Loaded module git from unstable | |
| Loaded module cmake from unstable | |
| Loaded module graphviz from unstable | |
| [32;1m$ load-modules $EXTRA_MODULES[0;m | |
| [32;1m$ module list -t[0;m | |
| Currently Loaded Modulefiles: | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.12.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.8.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.9.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.10.13 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.11.6 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/git/2.42.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/cmake/3.27.7 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/graphviz/8.0.5 | |
| [32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
| [32;1m$ print_var XDG_CONFIG_HOME[0;m | |
| [36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/local_config[0m | |
| [32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m | |
| [32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m | |
| [32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
| [url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
| insteadOf = https://bbpgitlab.epfl.ch/ | |
| insteadOf = ssh://git@bbpgitlab.epfl.ch/ | |
| insteadOf = git@bbpgitlab.epfl.ch: | |
| [32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m | |
| [0Ksection_start:1729779562:section_venv[collapsed=true] [0KSetting up the virtual env | |
| [32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
| [32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
| [32;1m$ rm -rf "$CI_VENV"[0;m | |
| [32;1m$ python -mvenv "$CI_VENV"[0;m | |
| [32;1m$ source "$CI_VENV/bin/activate"[0;m | |
| [32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Requirement already satisfied: pip in ./venv/lib/python3.11/site-packages (23.2.1) | |
| Collecting pip | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2cd/581cf58ab7fcf/pip-24.2-py3-none-any.whl (1.8 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.8/1.8 MB 64.4 MB/s eta 0:00:00 | |
| Requirement already satisfied: setuptools in ./venv/lib/python3.11/site-packages (65.5.0) | |
| Collecting setuptools | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/a7f/cb66f68b4d9e8/setuptools-75.2.0-py3-none-any.whl (1.2 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.2/1.2 MB 87.3 MB/s eta 0:00:00 | |
| Collecting wheel | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/237/6a90c98cc337d/wheel-0.44.0-py3-none-any.whl (67 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 67.1/67.1 kB 212.5 MB/s eta 0:00:00 | |
| Installing collected packages: wheel, setuptools, pip | |
| Attempting uninstall: setuptools | |
| Found existing installation: setuptools 65.5.0 | |
| Uninstalling setuptools-65.5.0: | |
| Successfully uninstalled setuptools-65.5.0 | |
| Attempting uninstall: pip | |
| Found existing installation: pip 23.2.1 | |
| Uninstalling pip-23.2.1: | |
| Successfully uninstalled pip-23.2.1 | |
| Successfully installed pip-24.2 setuptools-75.2.0 wheel-0.44.0 | |
| [32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Collecting tox | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/452/bc32bb031f228/tox-4.23.2-py3-none-any.whl (166 kB) | |
| Collecting cachetools>=5.5 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/021/34e8439cdc2ff/cachetools-5.5.0-py3-none-any.whl (9.5 kB) | |
| Collecting chardet>=5.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB) | |
| Collecting colorama>=0.4.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB) | |
| Collecting filelock>=3.16.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/208/2e5703d51fbf9/filelock-3.16.1-py3-none-any.whl (16 kB) | |
| Collecting packaging>=24.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/5b8/f2217dbdbd2f7/packaging-24.1-py3-none-any.whl (53 kB) | |
| Collecting platformdirs>=4.3.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/73e/575e1408ab810/platformdirs-4.3.6-py3-none-any.whl (18 kB) | |
| Collecting pluggy>=1.5 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/44e/1ad92c8ca002d/pluggy-1.5.0-py3-none-any.whl (20 kB) | |
| Collecting pyproject-api>=1.8 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/3d7/d347a047afe79/pyproject_api-1.8.0-py3-none-any.whl (13 kB) | |
| Collecting virtualenv>=20.26.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/44a/72c29cceb0ee0/virtualenv-20.27.0-py3-none-any.whl (3.1 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 3.1/3.1 MB 196.0 MB/s eta 0:00:00 | |
| Collecting distlib<1,>=0.3.7 (from virtualenv>=20.26.6->tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/47f/8c22fd27c27e2/distlib-0.3.9-py2.py3-none-any.whl (468 kB) | |
| Installing collected packages: distlib, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
| Successfully installed cachetools-5.5.0 chardet-5.2.0 colorama-0.4.6 distlib-0.3.9 filelock-3.16.1 packaging-24.1 platformdirs-4.3.6 pluggy-1.5.0 pyproject-api-1.8.0 tox-4.23.2 virtualenv-20.27.0 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1729779578:section_venv [0K | |
| [32;1m$ print_var PRE_BUILD_COMMAND[0;m | |
| [36mPRE_BUILD_COMMAND=[0m | |
| [32;1m$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi[0;m | |
| [32;1m$ section_start section_tox "Running Tox"[0;m | |
| [0Ksection_start:1729779578:section_tox [0KRunning Tox | |
| [32;1m$ python -mtox $TOX_OPTIONS[0;m | |
| integration: install_deps> python -I -m pip install morphio NEURON -r tests/requirements.txt | |
| .pkg: install_requires> python -I -m pip install hatch-vcs hatchling | |
| .pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| .pkg: get_requires_for_build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| .pkg: freeze> python -m pip freeze --all | |
| .pkg: hatch-vcs==0.4.0,hatchling==1.25.0,packaging==24.1,pathspec==0.12.1,pip==24.2,pluggy==1.5.0,setuptools==75.2.0,setuptools-scm==8.1.0,trove-classifiers==2024.10.21.16,wheel==0.44.0 | |
| .pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| integration: install_package_deps> python -I -m pip install docopt h5py libsonata psutil | |
| integration: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.6.1.dev17.tar.gz | |
| integration: freeze> python -m pip freeze --all | |
| integration: docopt==0.6.2,find_libpython==0.4.0,h5py==3.12.1,iniconfig==2.0.0,libsonata==0.1.29,morphio==3.4.0,neurodamus @ file:///gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.6.1.dev17.tar.gz#sha256=a7d49bca41a60ba7db928207533e4867a4b4839782739dac62a2c775a798bf67,NEURON==8.2.6,numpy==1.26.4,packaging==24.1,pip==24.2,pluggy==1.5.0,psutil==6.1.0,py==1.11.0,pytest==7.4.0,pytest-forked==1.6.0,scipy==1.14.1,setuptools==75.2.0,wheel==0.44.0 | |
| integration: commands[0]> ci/build_ndcore.sh /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/neurodamus/data | |
| + CORE_DIR=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/neurodamus/data | |
| + '[' -d _lib ']' | |
| + COMMON_DIR=_common | |
| + '[' -d _common ']' | |
| + git clone git@bbpgitlab.epfl.ch:hpc/sim/models/common.git _common --depth=1 | |
| Cloning into '_common'... | |
| + MOD_BUILD_DIR=mods.tmp | |
| + mkdir -p mods.tmp | |
| + cp -f /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/neurodamus/data/mod/ALU.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/neurodamus/data/mod/CoreNEURONArtificialCell.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/neurodamus/data/mod/netstim_inhpoisson.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/neurodamus/data/mod/SonataReportHelper.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/neurodamus/data/mod/SonataReports.mod mods.tmp | |
| + cp -f _common/mod/DetAMPANMDA.mod _common/mod/DetGABAAB.mod _common/mod/gap.mod _common/mod/GluSynapse.mod _common/mod/netstim_inhpoisson.mod _common/mod/ProbAMPANMDA_EMS.mod _common/mod/ProbGABAAB_EMS.mod _common/mod/TTXDynamicsSwitch.mod _common/mod/VecStim.mod mods.tmp | |
| + nrnivmodl -incflags '-DDISABLE_REPORTINGLIB -DDISABLE_HDF5 -DDISABLE_MPI' mods.tmp | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/.tox/integration/bin/nrnivmodl:10: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html | |
| from pkg_resources import working_set | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus | |
| Mod files: "mods.tmp/mods.tmp/ALU.mod" "mods.tmp/mods.tmp/CoreNEURONArtificialCell.mod" "mods.tmp/mods.tmp/DetAMPANMDA.mod" "mods.tmp/mods.tmp/DetGABAAB.mod" "mods.tmp/mods.tmp/gap.mod" "mods.tmp/mods.tmp/GluSynapse.mod" "mods.tmp/mods.tmp/netstim_inhpoisson.mod" "mods.tmp/mods.tmp/ProbAMPANMDA_EMS.mod" "mods.tmp/mods.tmp/ProbGABAAB_EMS.mod" "mods.tmp/mods.tmp/SonataReportHelper.mod" "mods.tmp/mods.tmp/SonataReports.mod" "mods.tmp/mods.tmp/TTXDynamicsSwitch.mod" "mods.tmp/mods.tmp/VecStim.mod" | |
| Creating 'x86_64' directory for .o files. | |
| -> [32mCompiling[0m mod_func.cpp | |
| -> [32mNMODL[0m ../mods.tmp/CoreNEURONArtificialCell.mod | |
| -> [32mNMODL[0m ../mods.tmp/ALU.mod | |
| -> [32mNMODL[0m ../mods.tmp/DetAMPANMDA.mod | |
| Translating CoreNEURONArtificialCell.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/x86_64/CoreNEURONArtificialCell.c | |
| Translating ALU.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/x86_64/ALU.c | |
| Translating DetAMPANMDA.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/x86_64/DetAMPANMDA.c | |
| Thread Safe | |
| Warning: next_delay_weight undefined. (declared within VERBATIM?) | |
| Warning: next_delay_t undefined. (declared within VERBATIM?) | |
| Thread Safe | |
| Thread Safe | |
| -> [32mNMODL[0m ../mods.tmp/DetGABAAB.mod | |
| -> [32mNMODL[0m ../mods.tmp/gap.mod | |
| -> [32mNMODL[0m ../mods.tmp/GluSynapse.mod | |
| Translating DetGABAAB.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/x86_64/DetGABAAB.c | |
| Translating gap.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/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/J1467934/hpc/sim/neurodamus/x86_64/GluSynapse.c | |
| Thread Safe | |
| Warning: next_delay_weight undefined. (declared within VERBATIM?) | |
| Warning: next_delay_t undefined. (declared within VERBATIM?) | |
| -> [32mNMODL[0m ../mods.tmp/netstim_inhpoisson.mod | |
| -> [32mNMODL[0m ../mods.tmp/ProbAMPANMDA_EMS.mod | |
| Thread Safe | |
| -> [32mNMODL[0m ../mods.tmp/ProbGABAAB_EMS.mod | |
| Translating netstim_inhpoisson.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/x86_64/netstim_inhpoisson.c | |
| Warning: POST_RESTORE_RESTART_FLAG undefined. (declared within VERBATIM?) | |
| Translating ProbAMPANMDA_EMS.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/x86_64/ProbAMPANMDA_EMS.c | |
| Thread Safe | |
| Notice: ARTIFICIAL_CELL is a synonym for POINT_PROCESS which hints that it | |
| only affects and is affected by discrete events. As such it is not | |
| located in a section and is not associated with an integrator | |
| Notice: This mechanism cannot be used with CVODE | |
| Notice: A_AMPA discontinuity adjustment not available. | |
| Notice: B_AMPA discontinuity adjustment not available. | |
| Notice: A_NMDA discontinuity adjustment not available. | |
| Notice: B_NMDA discontinuity adjustment not available. | |
| Warning: dt undefined. (declared within VERBATIM?) | |
| Warning: next_delay_weight undefined. (declared within VERBATIM?) | |
| Warning: next_delay_t undefined. (declared within VERBATIM?) | |
| Translating ProbGABAAB_EMS.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/x86_64/ProbGABAAB_EMS.c | |
| Thread Safe | |
| -> [32mNMODL[0m ../mods.tmp/SonataReportHelper.mod | |
| Notice: This mechanism cannot be used with CVODE | |
| Notice: A_GABAA discontinuity adjustment not available. | |
| Notice: B_GABAA discontinuity adjustment not available. | |
| Notice: A_GABAB discontinuity adjustment not available. | |
| Notice: B_GABAB discontinuity adjustment not available. | |
| Warning: dt undefined. (declared within VERBATIM?) | |
| Warning: next_delay_weight undefined. (declared within VERBATIM?) | |
| Warning: next_delay_t undefined. (declared within VERBATIM?) | |
| -> [32mNMODL[0m ../mods.tmp/SonataReports.mod | |
| Thread Safe | |
| Translating SonataReportHelper.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/x86_64/SonataReportHelper.c | |
| -> [32mNMODL[0m ../mods.tmp/TTXDynamicsSwitch.mod | |
| Thread Safe | |
| Translating SonataReports.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/x86_64/SonataReports.c | |
| Thread Safe | |
| -> [32mNMODL[0m ../mods.tmp/VecStim.mod | |
| Translating TTXDynamicsSwitch.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/x86_64/TTXDynamicsSwitch.c | |
| -> [32mCompiling[0m ALU.c | |
| Thread Safe | |
| Translating VecStim.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/x86_64/VecStim.c | |
| -> [32mCompiling[0m CoreNEURONArtificialCell.c | |
| Thread Safe | |
| -> [32mCompiling[0m DetAMPANMDA.c | |
| -> [32mCompiling[0m DetGABAAB.c | |
| -> [32mCompiling[0m gap.c | |
| -> [32mCompiling[0m GluSynapse.c | |
| -> [32mCompiling[0m netstim_inhpoisson.c | |
| -> [32mCompiling[0m ProbAMPANMDA_EMS.c | |
| -> [32mCompiling[0m ProbGABAAB_EMS.c | |
| -> [32mCompiling[0m SonataReportHelper.c | |
| -> [32mCompiling[0m SonataReports.c | |
| -> [32mCompiling[0m TTXDynamicsSwitch.c | |
| -> [32mCompiling[0m VecStim.c | |
| => [32mLINKING[0m shared library ./libnrnmech.so | |
| => [32mLINKING[0m executable ./special LDFLAGS are: -pthread | |
| Successfully created x86_64/special | |
| + '[' '!' -f x86_64/special ']' | |
| + mkdir -p _lib | |
| + cp -f x86_64/libnrnmech.so _lib/ | |
| + cp -f /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/neurodamus/data/hoc/Cell.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/neurodamus/data/hoc/ConnectionUtils.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/neurodamus/data/hoc/defvar.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/neurodamus/data/hoc/fileUtils.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/neurodamus/data/hoc/Map.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/neurodamus/data/hoc/MorphIO.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/neurodamus/data/hoc/neurodamus.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/neurodamus/data/hoc/RNGSettings.hoc _lib/ | |
| + cp -f _common/hoc/AMPANMDAHelper.hoc _common/hoc/DetAMPANMDAHelper.hoc _common/hoc/DetGABAABHelper.hoc _common/hoc/GABAABHelper.hoc _common/hoc/GluSynapseHelper.hoc _common/hoc/GluSynapseLegacyHelper.hoc _lib/ | |
| + echo /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/neurodamus/data | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/neurodamus/data | |
| + ls -l | |
| total 81 | |
| -rw-rw----+ 1 bbpcihpcsim bbp 578 Oct 24 16:19 authors.txt | |
| drwxrwx---+ 3 bbpcihpcsim bbp 4096 Oct 24 16:19 _benchmarks | |
| -rw-rw----+ 1 bbpcihpcsim bbp 29097 Oct 24 16:19 CHANGES.rst | |
| drwxrwx---+ 2 bbpcihpcsim bbp 4096 Oct 24 16:19 ci | |
| drwxrwx---+ 7 bbpcihpcsim bbp 4096 Oct 24 16:20 _common | |
| -rw-rw----+ 1 bbpcihpcsim bbp 6240 Oct 24 16:19 CONTRIBUTING.md | |
| drwxrwx---+ 2 bbpcihpcsim bbp 4096 Oct 24 16:19 docker | |
| drwxrwx---+ 5 bbpcihpcsim bbp 4096 Oct 24 16:19 docs | |
| drwxrwx---+ 2 bbpcihpcsim bbp 4096 Oct 24 16:19 examples | |
| drwxrwx---+ 2 bbpcihpcsim bbp 4096 Oct 24 16:20 _lib | |
| -rw-rw----+ 1 bbpcihpcsim bbp 11358 Oct 24 16:19 LICENSE.txt | |
| drwxrwx---+ 3 bbpcihpcsim bbp 4096 Oct 24 16:19 local_config | |
| drwxrwx---+ 2 bbpcihpcsim bbp 4096 Oct 24 16:20 mods.tmp | |
| drwxrwx---+ 6 bbpcihpcsim bbp 4096 Oct 24 16:19 neurodamus | |
| -rw-rw----+ 1 bbpcihpcsim bbp 1355 Oct 24 16:19 pyproject.toml | |
| -rw-rw----+ 1 bbpcihpcsim bbp 4598 Oct 24 16:19 README.rst | |
| -rw-rw----+ 1 bbpcihpcsim bbp 52 Oct 24 16:19 requirements_docs.txt | |
| -rw-rw----+ 1 bbpcihpcsim bbp 37 Oct 24 16:19 requirements.txt | |
| drwxrwx---+ 10 bbpcihpcsim bbp 4096 Oct 24 16:19 tests | |
| drwxrwx---+ 2 bbpcihpcsim bbp 4096 Oct 24 16:19 tools | |
| -rw-rw----+ 1 bbpcihpcsim bbp 1422 Oct 24 16:19 tox.ini | |
| drwxrwx---+ 5 bbpcihpcsim bbp 4096 Oct 24 16:19 venv | |
| drwxrwx---+ 3 bbpcihpcsim bbp 4096 Oct 24 16:20 x86_64 | |
| + ls -l _lib | |
| total 6 | |
| -rw-rw----+ 1 bbpcihpcsim bbp 2470 Oct 24 16:20 AMPANMDAHelper.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 15774 Oct 24 16:20 Cell.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 1064 Oct 24 16:20 ConnectionUtils.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 998 Oct 24 16:20 defvar.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 1173 Oct 24 16:20 DetAMPANMDAHelper.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 1636 Oct 24 16:20 DetGABAABHelper.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 1971 Oct 24 16:20 fileUtils.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 3294 Oct 24 16:20 GABAABHelper.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 3736 Oct 24 16:20 GluSynapseHelper.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 4633 Oct 24 16:20 GluSynapseLegacyHelper.hoc | |
| -rwxrwx---+ 1 bbpcihpcsim bbp 274824 Oct 24 16:20 libnrnmech.so | |
| -rw-rw----+ 1 bbpcihpcsim bbp 10723 Oct 24 16:20 Map.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 976 Oct 24 16:20 MorphIO.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 371 Oct 24 16:20 neurodamus.hoc | |
| -rw-rw----+ 1 bbpcihpcsim bbp 2610 Oct 24 16:20 RNGSettings.hoc | |
| integration: commands[1]> pytest -x --forked tests/integration | |
| ============================= test session starts ============================== | |
| platform linux -- Python 3.11.6, pytest-7.4.0, pluggy-1.5.0 -- /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/.tox/integration/bin/python | |
| cachedir: .tox/integration/.pytest_cache | |
| rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus | |
| configfile: pyproject.toml | |
| plugins: forked-1.6.0 | |
| collecting ... collected 24 items | |
| tests/integration/test_cell.py::test_load_cell[C060114A7.asc] PASSED [ 4%] | |
| tests/integration/test_cell.py::test_load_cell[C060114A7.h5] PASSED [ 8%] | |
| tests/integration/test_cell.py::test_load_cell[merged_container.h5/C060114A7.h5] PASSED [ 12%] | |
| tests/integration/test_cell.py::test_morphio_read PASSED [ 16%] | |
| tests/integration/test_cell.py::test_create_cell PASSED [ 20%] | |
| tests/integration/test_cell.py::test_create_cell_2 PASSED [ 25%] | |
| tests/integration/test_cell.py::test_create_cell_3 PASSED [ 29%] | |
| tests/integration/test_cell.py::test_basic_system PASSED [ 33%] | |
| tests/integration/test_neuron.py::test_base_h PASSED [ 37%] | |
| tests/integration/test_sonata_config.py::test_parse_base PASSED [ 41%] | |
| tests/integration/test_sonata_config.py::test_SimConfig_from_sonata PASSED [ 45%] | |
| tests/integration/test_sonata_config.py::test_parse_seeds PASSED [ 50%] | |
| tests/integration/test_sonata_config.py::test_parse_modifications PASSED [ 54%] | |
| tests/integration/test_sonata_config.py::test_parse_connections PASSED [ 58%] | |
| tests/integration/test_sonata_config.py::test_parse_inputs PASSED [ 62%] | |
| tests/integration/test_sonata_output.py::test_sonata_logfile PASSED [ 66%] | |
| tests/integration/test_sonata_output.py::test_throw_spike_sort_order PASSED [ 70%] | |
| tests/integration/test_stimulus2.py::TestStimuli::test_sin PASSED [ 75%] | |
| tests/integration/test_stimulus2.py::TestStimuli::test_sin_long PASSED [ 79%] | |
| tests/integration/test_stimulus2.py::TestStimuli::test_add_pulses PASSED [ 83%] | |
| tests/integration/test_stimulus2.py::TestStimuli::test_noise PASSED [ 87%] | |
| tests/integration/test_stimulus2.py::TestStimuli::test_shot_noise PASSED [ 91%] | |
| tests/integration/test_stimulus2.py::TestStimuli::test_ornstein_uhlenbeck PASSED [ 95%] | |
| tests/integration/test_stimulus2.py::TestStimuli::test_stacked PASSED [100%] | |
| =============================== warnings summary =============================== | |
| .tox/integration/lib/python3.11/site-packages/neurodamus/core/configuration.py:162 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/.tox/integration/lib/python3.11/site-packages/neurodamus/core/configuration.py:162: DeprecationWarning: In 3.13 classes created inside an enum will not become a member. Use the `member` decorator to keep the current behavior. | |
| class AutoBalanceModeParams: | |
| -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html | |
| ======================== 24 passed, 1 warning in 3.28s ========================= | |
| .pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467934/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| integration: OK (52.00=setup[41.54]+cmd[6.29,4.17] seconds) | |
| congratulations :) (52.11 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1729779631:section_tox [0K | |
| section_end:1729779631:step_script [0Ksection_start:1729779631:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| Using git from spack modules | |
| section_end:1729779632:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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| [0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1729779536:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1729779536:resolve_secrets [0Ksection_start:1729779536:prepare_executor [0K[0K[36;1mPreparing the "custom" executor[0;m[0;m | |
| [0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m | |
| BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user | |
| TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor2557697651, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 236741, build ref , job ID 1467937 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1467937, 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_J1467937_PROD_P2354_CP5_C11 | |
| Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcsim partition=prod qos= reservation= | |
| Not executing the chown -R | |
| sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS | |
| sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx] | |
| Submitted batch job 2601916 | |
| 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_J1467937_PROD_P2354_CP5_C11 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1467937 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1467937 --ntasks=1 --jobid=2601916 --cpus-per-task=6 --mem=30750M | |
| section_end:1729779539:prepare_executor [0Ksection_start:1729779539:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i5n5 via bbpv1.epfl.ch... | |
| section_end:1729779540:prepare_script [0Ksection_start:1729779540:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
| Using git from spack modules | |
| [32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m | |
| [32;1mFetching changes with git depth set to 100...[0;m | |
| Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467937/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out 05a30124 as leite/corenrn-rebalancer...[0;m | |
| Skipping object checkout, Git LFS is not installed. | |
| [32;1mUpdating/initializing submodules recursively with git depth set to 100...[0;m | |
| section_end:1729779545:get_sources [0Ksection_start:1729779545:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
| [0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m | |
| Using git from spack modules | |
| [32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m | |
| [32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m | |
| [32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m | |
| [32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m | |
| [32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m | |
| [32;1m$ module purge[0;m | |
| [32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m | |
| [32;1m$ module load unstable python/3.12.0[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.12.0 | |
| [32;1m$ module load unstable python/3.8.18[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.8.18 | |
| [32;1m$ module load unstable python/3.9.18[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.9.18 | |
| [32;1m$ module load unstable python/3.10.13[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.10.13 | |
| [32;1m$ module load unstable python/3.11.6[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.11.6 | |
| [32;1m$ load-modules() { # collapsed multi-line command[0;m | |
| [32;1m$ load-modules $SYSTEM_MODULES[0;m | |
| Loaded module git from unstable | |
| Loaded module cmake from unstable | |
| Loaded module graphviz from unstable | |
| [32;1m$ load-modules $EXTRA_MODULES[0;m | |
| Loaded module neurodamus-neocortex-multiscale from unstable | |
| [32;1m$ module list -t[0;m | |
| Currently Loaded Modulefiles: | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.12.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.8.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.9.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.10.13 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.11.6 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/git/2.42.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/cmake/3.27.7 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/graphviz/8.0.5 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/intel-oneapi-mkl/2023.2.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/hpe-mpi/2.27.p1.hmpt | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/applications/linux-rhel7-skylake/neurodamus-neocortex-multiscale/2.4.1 | |
| [32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
| [32;1m$ print_var XDG_CONFIG_HOME[0;m | |
| [36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467937/hpc/sim/neurodamus/local_config[0m | |
| [32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m | |
| [32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m | |
| [32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
| [url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
| insteadOf = https://bbpgitlab.epfl.ch/ | |
| insteadOf = ssh://git@bbpgitlab.epfl.ch/ | |
| insteadOf = git@bbpgitlab.epfl.ch: | |
| [32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m | |
| [0Ksection_start:1729779567:section_venv[collapsed=true] [0KSetting up the virtual env | |
| [32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
| [32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
| [32;1m$ rm -rf "$CI_VENV"[0;m | |
| [32;1m$ python -mvenv "$CI_VENV"[0;m | |
| [32;1m$ source "$CI_VENV/bin/activate"[0;m | |
| [32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Requirement already satisfied: pip in ./venv/lib/python3.11/site-packages (23.2.1) | |
| Collecting pip | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2cd/581cf58ab7fcf/pip-24.2-py3-none-any.whl (1.8 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.8/1.8 MB 63.7 MB/s eta 0:00:00 | |
| Requirement already satisfied: setuptools in ./venv/lib/python3.11/site-packages (65.5.0) | |
| Collecting setuptools | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/a7f/cb66f68b4d9e8/setuptools-75.2.0-py3-none-any.whl (1.2 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.2/1.2 MB 151.8 MB/s eta 0:00:00 | |
| Collecting wheel | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/237/6a90c98cc337d/wheel-0.44.0-py3-none-any.whl (67 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 67.1/67.1 kB 220.2 MB/s eta 0:00:00 | |
| Installing collected packages: wheel, setuptools, pip | |
| Attempting uninstall: setuptools | |
| Found existing installation: setuptools 65.5.0 | |
| Uninstalling setuptools-65.5.0: | |
| Successfully uninstalled setuptools-65.5.0 | |
| Attempting uninstall: pip | |
| Found existing installation: pip 23.2.1 | |
| Uninstalling pip-23.2.1: | |
| Successfully uninstalled pip-23.2.1 | |
| Successfully installed pip-24.2 setuptools-75.2.0 wheel-0.44.0 | |
| [32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Collecting tox | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/452/bc32bb031f228/tox-4.23.2-py3-none-any.whl (166 kB) | |
| Collecting cachetools>=5.5 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/021/34e8439cdc2ff/cachetools-5.5.0-py3-none-any.whl (9.5 kB) | |
| Collecting chardet>=5.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB) | |
| Collecting colorama>=0.4.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB) | |
| Collecting filelock>=3.16.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/208/2e5703d51fbf9/filelock-3.16.1-py3-none-any.whl (16 kB) | |
| Collecting packaging>=24.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/5b8/f2217dbdbd2f7/packaging-24.1-py3-none-any.whl (53 kB) | |
| Collecting platformdirs>=4.3.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/73e/575e1408ab810/platformdirs-4.3.6-py3-none-any.whl (18 kB) | |
| Collecting pluggy>=1.5 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/44e/1ad92c8ca002d/pluggy-1.5.0-py3-none-any.whl (20 kB) | |
| Collecting pyproject-api>=1.8 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/3d7/d347a047afe79/pyproject_api-1.8.0-py3-none-any.whl (13 kB) | |
| Collecting virtualenv>=20.26.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/44a/72c29cceb0ee0/virtualenv-20.27.0-py3-none-any.whl (3.1 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 3.1/3.1 MB 183.4 MB/s eta 0:00:00 | |
| Collecting distlib<1,>=0.3.7 (from virtualenv>=20.26.6->tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/47f/8c22fd27c27e2/distlib-0.3.9-py2.py3-none-any.whl (468 kB) | |
| Installing collected packages: distlib, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
| Attempting uninstall: packaging | |
| Found existing installation: packaging 23.1 | |
| Not uninstalling packaging at /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-packaging-23.1-uqml2t/lib/python3.11/site-packages, outside environment /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467937/hpc/sim/neurodamus/venv | |
| Can't uninstall 'packaging'. No files were found to uninstall. | |
| Successfully installed cachetools-5.5.0 chardet-5.2.0 colorama-0.4.6 distlib-0.3.9 filelock-3.16.1 packaging-24.1 platformdirs-4.3.6 pluggy-1.5.0 pyproject-api-1.8.0 tox-4.23.2 virtualenv-20.27.0 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1729779637:section_venv [0K | |
| [32;1m$ print_var PRE_BUILD_COMMAND[0;m | |
| [36mPRE_BUILD_COMMAND=[0m | |
| [32;1m$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi[0;m | |
| [32;1m$ section_start section_tox "Running Tox"[0;m | |
| [0Ksection_start:1729779637:section_tox [0KRunning Tox | |
| [32;1m$ python -mtox $TOX_OPTIONS[0;m | |
| bbp-model: install_deps> python -I -m pip install -r tests/requirements.txt | |
| .pkg: install_requires> python -I -m pip install hatch-vcs hatchling | |
| .pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467937/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| .pkg: get_requires_for_build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467937/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| .pkg: freeze> python -m pip freeze --all | |
| .pkg: hatch-vcs==0.4.0,hatchling==1.25.0,packaging==24.1,pathspec==0.12.1,pip==24.2,pluggy==1.5.0,setuptools==75.2.0,setuptools-scm==8.1.0,trove-classifiers==2024.10.21.16,wheel==0.44.0 | |
| .pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467937/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| bbp-model: install_package_deps> python -I -m pip install docopt h5py libsonata psutil | |
| bbp-model: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467937/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.6.1.dev17.tar.gz | |
| bbp-model: freeze> python -m pip freeze --all | |
| bbp-model: docopt @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-docopt-0.6.2-noukz4jts6de5g3xamvap6n4mh7mmcsy/spack-src,h5py @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-h5py-3.8.0-5woxna6nieu5jokc2tdxsfmolza6724e/spack-src,iniconfig==2.0.0,libsonata @ file:///nvme/[MASKED]/2371376/spack-stage/spack-stage-py-libsonata-0.1.28-jsuf4xxzlybtxiqfdwyqxyxf4c6svcva/spack-src,MorphIO @ file:///nvme/[MASKED]/2246265/spack-stage/spack-stage-py-morphio-3.3.6-xap3flagvbfvuospv22jpkdw65c2ypln/spack-src,mpi4py @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-mpi4py-3.1.4-x733hwb2he3bpi423fnogkrw4w33wehe/spack-src,neurodamus @ file:///nvme/[MASKED]/2379226/spack-stage/spack-stage-py-neurodamus-3.6.0-27enlnafey5xfe6ek7hhy7uozlbps45a/spack-src,numpy @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-numpy-1.26.1-elr5pntecdmhfynrjk3actlxb4go2bua/spack-src,packaging @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-packaging-23.1-uqml2togm4tkpdvzr37r5dnsrpnd76j2/spack-src,pip==24.2,pluggy==1.5.0,psutil @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-psutil-5.9.5-wieplgkaapfkhmzgrsesk5s3h46l3rx4/spack-src,py==1.11.0,pytest==7.4.0,pytest-forked==1.6.0,scipy @ file:///nvme/[MASKED]/2045970/spack-stage/spack-stage-py-scipy-1.11.3-dhxei7gha3wm6mobqp3urw6k4ovd7blx/spack-src,setuptools==75.2.0,wheel==0.44.0 | |
| bbp-model: commands[0]> python -c 'import os; print(os.environ.get('"'"'HOC_LIBRARY_PATH'"'"', '"'"''"'"'))' | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467937/hpc/sim/neurodamus/core/hoc:/gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_oneapi-2023.2.0-skylake/neurodamus-models-2.4.1-dkbxgo/share/neurodamus_neocortex/hoc | |
| bbp-model: commands[1]> pytest -s -x --forked --durations=5 --durations-min=15 tests/scientific-ngv | |
| ============================= test session starts ============================== | |
| platform linux -- Python 3.11.6, pytest-7.4.0, pluggy-1.5.0 -- /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467937/hpc/sim/neurodamus/.tox/bbp-model/bin/python | |
| cachedir: .tox/bbp-model/.pytest_cache | |
| rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467937/hpc/sim/neurodamus | |
| configfile: pyproject.toml | |
| plugins: forked-1.6.0 | |
| collecting ... collected 1 item | |
| tests/scientific-ngv/test_ngv.py::test_vasccouplingB_radii PASSED | |
| ============================= slowest 5 durations ============================== | |
| 124.35s call tests/scientific-ngv/test_ngv.py::test_vasccouplingB_radii | |
| (2 durations < 15s hidden. Use -vv to show these durations.) | |
| ======================== 1 passed in 125.33s (0:02:05) ========================= | |
| .pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467937/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| bbp-model: OK (250.66=setup[123.07]+cmd[0.24,127.34] seconds) | |
| congratulations :) (252.64 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1729779892:section_tox [0K | |
| section_end:1729779892:step_script [0Ksection_start:1729779892:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| Using git from spack modules | |
| section_end:1729779893:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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| [0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1729779535:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1729779535:resolve_secrets [0Ksection_start:1729779535:prepare_executor [0K[0K[36;1mPreparing the "custom" executor[0;m[0;m | |
| [0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m | |
| BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user | |
| TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor3305210649, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 236741, build ref , job ID 1467936 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1467936, 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_J1467936_PROD_P2354_CP4_C10 | |
| Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcsim partition=prod qos= reservation= | |
| Not executing the chown -R | |
| sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS | |
| sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx] | |
| Submitted batch job 2601915 | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1467936_PROD_P2354_CP4_C10 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1467936 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1467936 --ntasks=1 --jobid=2601915 --cpus-per-task=6 --mem=30750M | |
| section_end:1729779536:prepare_executor [0Ksection_start:1729779536:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i5n5 via bbpv1.epfl.ch... | |
| section_end:1729779542:prepare_script [0Ksection_start:1729779542:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
| Using git from spack modules | |
| [32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m | |
| [32;1mFetching changes with git depth set to 100...[0;m | |
| Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467936/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out 05a30124 as leite/corenrn-rebalancer...[0;m | |
| Skipping object checkout, Git LFS is not installed. | |
| [32;1mUpdating/initializing submodules recursively with git depth set to 100...[0;m | |
| section_end:1729779546:get_sources [0Ksection_start:1729779546:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
| [0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m | |
| Using git from spack modules | |
| [32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m | |
| [32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m | |
| [32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m | |
| [32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m | |
| [32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m | |
| [32;1m$ module purge[0;m | |
| [32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m | |
| [32;1m$ module load unstable python/3.12.0[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.12.0 | |
| [32;1m$ module load unstable python/3.8.18[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.8.18 | |
| [32;1m$ module load unstable python/3.9.18[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.9.18 | |
| [32;1m$ module load unstable python/3.10.13[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.10.13 | |
| [32;1m$ module load unstable python/3.11.6[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.11.6 | |
| [32;1m$ load-modules() { # collapsed multi-line command[0;m | |
| [32;1m$ load-modules $SYSTEM_MODULES[0;m | |
| Loaded module git from unstable | |
| Loaded module cmake from unstable | |
| Loaded module graphviz from unstable | |
| [32;1m$ load-modules $EXTRA_MODULES[0;m | |
| Loaded module intel-oneapi-compilers from unstable | |
| Loaded module py-bluepysnap from unstable | |
| Loaded module neurodamus-neocortex from unstable | |
| [32;1m$ module list -t[0;m | |
| Currently Loaded Modulefiles: | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.12.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.8.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.9.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.10.13 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.11.6 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/git/2.42.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/cmake/3.27.7 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/graphviz/8.0.5 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/compilers/linux-rhel7-haswell/intel-oneapi-compilers/2023.2.1 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/intel-oneapi-mkl/2023.2.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/hpe-mpi/2.27.p1.hmpt | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/applications/linux-rhel7-skylake/py-bluepysnap/3.0.1 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/applications/linux-rhel7-skylake/neurodamus-neocortex/2.4.1 | |
| [32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
| [32;1m$ print_var XDG_CONFIG_HOME[0;m | |
| [36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467936/hpc/sim/neurodamus/local_config[0m | |
| [32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m | |
| [32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m | |
| [32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
| [url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
| insteadOf = https://bbpgitlab.epfl.ch/ | |
| insteadOf = ssh://git@bbpgitlab.epfl.ch/ | |
| insteadOf = git@bbpgitlab.epfl.ch: | |
| [32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m | |
| [0Ksection_start:1729779574:section_venv[collapsed=true] [0KSetting up the virtual env | |
| [32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
| [32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
| [32;1m$ rm -rf "$CI_VENV"[0;m | |
| [32;1m$ python -mvenv "$CI_VENV"[0;m | |
| [32;1m$ source "$CI_VENV/bin/activate"[0;m | |
| [32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Requirement already satisfied: pip in ./venv/lib/python3.11/site-packages (23.2.1) | |
| Collecting pip | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2cd/581cf58ab7fcf/pip-24.2-py3-none-any.whl (1.8 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.8/1.8 MB 63.4 MB/s eta 0:00:00 | |
| Requirement already satisfied: setuptools in /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-setuptools-68.0.0-p3xbqx/lib/python3.11/site-packages (68.0.0) | |
| Collecting setuptools | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/a7f/cb66f68b4d9e8/setuptools-75.2.0-py3-none-any.whl (1.2 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.2/1.2 MB 54.1 MB/s eta 0:00:00 | |
| Collecting wheel | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/237/6a90c98cc337d/wheel-0.44.0-py3-none-any.whl (67 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 67.1/67.1 kB 213.0 MB/s eta 0:00:00 | |
| Installing collected packages: wheel, setuptools, pip | |
| Attempting uninstall: setuptools | |
| Found existing installation: setuptools 68.0.0 | |
| Not uninstalling setuptools at /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-setuptools-68.0.0-p3xbqx/lib/python3.11/site-packages, outside environment /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467936/hpc/sim/neurodamus/venv | |
| Can't uninstall 'setuptools'. No files were found to uninstall. | |
| Attempting uninstall: pip | |
| Found existing installation: pip 23.2.1 | |
| Uninstalling pip-23.2.1: | |
| Successfully uninstalled pip-23.2.1 | |
| Successfully installed pip-24.2 setuptools-65.5.0 wheel-0.44.0 | |
| [32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Collecting tox | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/452/bc32bb031f228/tox-4.23.2-py3-none-any.whl (166 kB) | |
| Collecting cachetools>=5.5 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/021/34e8439cdc2ff/cachetools-5.5.0-py3-none-any.whl (9.5 kB) | |
| Collecting chardet>=5.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB) | |
| Collecting colorama>=0.4.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB) | |
| Collecting filelock>=3.16.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/208/2e5703d51fbf9/filelock-3.16.1-py3-none-any.whl (16 kB) | |
| Collecting packaging>=24.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/5b8/f2217dbdbd2f7/packaging-24.1-py3-none-any.whl (53 kB) | |
| Collecting platformdirs>=4.3.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/73e/575e1408ab810/platformdirs-4.3.6-py3-none-any.whl (18 kB) | |
| Collecting pluggy>=1.5 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/44e/1ad92c8ca002d/pluggy-1.5.0-py3-none-any.whl (20 kB) | |
| Collecting pyproject-api>=1.8 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/3d7/d347a047afe79/pyproject_api-1.8.0-py3-none-any.whl (13 kB) | |
| Collecting virtualenv>=20.26.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/44a/72c29cceb0ee0/virtualenv-20.27.0-py3-none-any.whl (3.1 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 3.1/3.1 MB 166.4 MB/s eta 0:00:00 | |
| Collecting distlib<1,>=0.3.7 (from virtualenv>=20.26.6->tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/47f/8c22fd27c27e2/distlib-0.3.9-py2.py3-none-any.whl (468 kB) | |
| Installing collected packages: distlib, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
| Attempting uninstall: packaging | |
| Found existing installation: packaging 23.1 | |
| Not uninstalling packaging at /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-packaging-23.1-uqml2t/lib/python3.11/site-packages, outside environment /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467936/hpc/sim/neurodamus/venv | |
| Can't uninstall 'packaging'. No files were found to uninstall. | |
| Successfully installed cachetools-5.5.0 chardet-5.2.0 colorama-0.4.6 distlib-0.3.9 filelock-3.16.1 packaging-24.1 platformdirs-4.3.6 pluggy-1.5.0 pyproject-api-1.8.0 tox-4.23.2 virtualenv-20.27.0 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1729779658:section_venv [0K | |
| [32;1m$ print_var PRE_BUILD_COMMAND[0;m | |
| [36mPRE_BUILD_COMMAND=[0m | |
| [32;1m$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi[0;m | |
| [32;1m$ section_start section_tox "Running Tox"[0;m | |
| [0Ksection_start:1729779658:section_tox [0KRunning Tox | |
| [32;1m$ python -mtox $TOX_OPTIONS[0;m | |
| bbp-model: install_deps> python -I -m pip install -r tests/requirements.txt | |
| .pkg: install_requires> python -I -m pip install hatch-vcs hatchling | |
| .pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467936/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| .pkg: get_requires_for_build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467936/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| .pkg: freeze> python -m pip freeze --all | |
| .pkg: hatch-vcs==0.4.0,hatchling==1.25.0,packaging==24.1,pathspec==0.12.1,pip==24.2,pluggy==1.5.0,setuptools==75.2.0,setuptools-scm==8.1.0,trove-classifiers==2024.10.21.16,wheel==0.44.0 | |
| .pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467936/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| bbp-model: install_package_deps> python -I -m pip install docopt h5py libsonata psutil | |
| bbp-model: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467936/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.6.1.dev17.tar.gz | |
| bbp-model: freeze> python -m pip freeze --all | |
| bbp-model: attrs @ file:///nvme/[MASKED]/2246265/spack-stage/spack-stage-py-attrs-23.1.0-vboa6fdag3yd4y3ogikbfun4jbmiptsw/spack-src,bluepysnap @ file:///nvme/[MASKED]/2572043/spack-stage/spack-stage-py-bluepysnap-3.0.1-baxgrs3kooeyjf5fa2wbemzm7p5usa6v/spack-src,Bottleneck @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-bottleneck-1.3.7-reskjku2fhby75ljzxdozjw2l3w7ywov/spack-src,brain-indexer @ file:///nvme/[MASKED]/2572043/spack-stage/spack-stage-py-brain-indexer-3.0.0-lvspdgrmngj7zyyzddiz6qs63yqtuuce/spack-src,cached-property @ file:///nvme/[MASKED]/1998173/spack-stage/spack-stage-py-cached-property-1.5.2-4ra43fkav4led5iceclzwqkgfbqpigp2/spack-src,click @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-click-8.1.7-uppfa4dbkn3thlvfus7yusscvyx6jcbl/spack-src,contourpy @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-contourpy-1.0.7-zjyhvvw5jf6zl6ymi4izavk7qifgt74g/spack-src,cycler @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-cycler-0.11.0-rjj5clifiqnwny3vechb5v66hvaiy76y/spack-src,deprecation @ file:///nvme/[MASKED]/1998173/spack-stage/spack-stage-py-deprecation-2.1.0-qqtamvzujmbchjj24k5drbi753ovygnv/spack-src,docopt @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-docopt-0.6.2-noukz4jts6de5g3xamvap6n4mh7mmcsy/spack-src,docopt-ng @ file:///nvme/[MASKED]/2246265/spack-stage/spack-stage-py-docopt-ng-0.9.0-dmzzljykzploydvsjvjrwnbg6jm2mxht/spack-src,find-libpython @ file:///nvme/[MASKED]/2058794/spack-stage/spack-stage-py-find-libpython-0.3.1-5dylncaukuijf2r5t5lrj2s2y2kth2bh/spack-src,fonttools @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-fonttools-4.39.4-z2lufuxxznv35oq32lldyarzx26e5k4o/spack-src,h5py @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-h5py-3.8.0-5woxna6nieu5jokc2tdxsfmolza6724e/spack-src,importlib-resources @ file:///nvme/[MASKED]/2430307/spack-stage/spack-stage-py-importlib-resources-5.12.0-hsw22m3vzcbe2j542ohp2dvibczkgjde/spack-src,iniconfig==2.0.0,Jinja2 @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-jinja2-3.1.2-7validyciqteluvu43co5k7perpr2baq/spack-src,jsonschema @ file:///nvme/[MASKED]/2246265/spack-stage/spack-stage-py-jsonschema-4.17.3-3rp6hm5bn66ufu63mxqg4de2spphwdwp/spack-src,kiwisolver @ file:///nvme/[MASKED]/2246265/spack-stage/spack-stage-py-kiwisolver-1.4.5-3d4lqrdrunib5u5xxipwmcm3j5m26pox/spack-src,libsonata @ file:///nvme/[MASKED]/2371376/spack-stage/spack-stage-py-libsonata-0.1.28-jsuf4xxzlybtxiqfdwyqxyxf4c6svcva/spack-src,MarkupSafe @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-markupsafe-2.1.3-r3ehtmw6pkktralavqtazezwbkbsivnt/spack-src,matplotlib @ file:///nvme/[MASKED]/2246265/spack-stage/spack-stage-py-matplotlib-3.8.1-bmj72as3i3rad6lxvfczfebkk3n3wgk2/spack-src,more-itertools @ file:///nvme/[MASKED]/1998173/spack-stage/spack-stage-py-more-itertools-9.1.0-j5cqgsrmywy3254zni76f3rd3xza4ond/spack-src,morph-tool @ file:///nvme/[MASKED]/2430307/spack-stage/spack-stage-py-morph-tool-2.9.1-3oulyivmww6xdiu42orfaapq4ftqahxi/spack-src,MorphIO @ file:///nvme/[MASKED]/2246265/spack-stage/spack-stage-py-morphio-3.3.6-xap3flagvbfvuospv22jpkdw65c2ypln/spack-src,mpi4py @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-mpi4py-3.1.4-x733hwb2he3bpi423fnogkrw4w33wehe/spack-src,mpmath @ file:///nvme/[MASKED]/2246265/spack-stage/spack-stage-py-mpmath-1.2.1-4fflyibqfjfxrjhnx3jr7bhpt2tpcqn2/spack-src,neurodamus @ file:///nvme/[MASKED]/2379226/spack-stage/spack-stage-py-neurodamus-3.6.0-27enlnafey5xfe6ek7hhy7uozlbps45a/spack-src,neurom @ file:///nvme/[MASKED]/2430307/spack-stage/spack-stage-py-neurom-3.2.4-xvzvf6weitv72lultecrfvau7uu6oaqk/spack-src,numexpr @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-numexpr-2.8.4-wu4xk2pywd64hyhoqfr57fzxfbzuuj2y/spack-src,numpy @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-numpy-1.26.1-elr5pntecdmhfynrjk3actlxb4go2bua/spack-src,numpy-quaternion @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-numpy-quaternion-2021.11.4.15.26.3-n3ap27fwuc6c7emgakpydtlt7yvk7nhi/spack-src,packaging @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-packaging-23.1-uqml2togm4tkpdvzr37r5dnsrpnd76j2/spack-src,pandas @ file:///nvme/[MASKED]/2246265/spack-stage/spack-stage-py-pandas-1.5.3-utuy7ahauxsvfrn5zqx3g5jvo3efdt2a/spack-src,Pillow @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pillow-10.0.0-ygox4axk4dznocekteux3ecwkyfjndzk/spack-src,pip==24.2,pluggy==1.5.0,psutil @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-psutil-5.9.5-wieplgkaapfkhmzgrsesk5s3h46l3rx4/spack-src,py==1.11.0,pybind11 @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pybind11-2.11.0-7rjfjlzjfm5suub2ks5ttsby2mhqlcfl/spack-src,pyparsing @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pyparsing-3.0.9-v3agjtpvgnpemnowjrjcowiw2ksk4xke/spack-src,pyrsistent @ file:///nvme/[MASKED]/1998173/spack-stage/spack-stage-py-pyrsistent-0.19.3-lzzxq7szeqnnyawu4d363tyqva3jui2v/spack-src,pytest==7.4.0,pytest-forked==1.6.0,python-dateutil @ file:///nvme/[MASKED]/2246265/spack-stage/spack-stage-py-python-dateutil-2.8.2-fcc6z5e5gvfd7gee352zpq6smosax3yk/spack-src,pytz @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pytz-2023.3-nr5mf4btvdphj755hbmkq57as5rmwtun/spack-src,PyYAML @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pyyaml-6.0-c3eqkahwrcjjvgo2irs4ocswyrgh2p64/spack-src,scipy @ file:///nvme/[MASKED]/2045970/spack-stage/spack-stage-py-scipy-1.11.3-dhxei7gha3wm6mobqp3urw6k4ovd7blx/spack-src,setuptools @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-setuptools-68.0.0-p3xbqxjqvq45co6xoirlfe5ydwive63k/spack-src/setuptools-68.0.0-py3-none-any.whl#sha256=11e52c67415a381d10d6b462ced9cfb97066179f0e871399e006c4ab101fc85f,six @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-six-1.16.0-brkaopna2ofwxv7qsutpldwizeauixze/spack-src,sympy @ file:///nvme/[MASKED]/2246265/spack-stage/spack-stage-py-sympy-1.11.1-t5tovexvy2goo63j3w6dlqmcnv4yqrqd/spack-src,tqdm @ file:///nvme/[MASKED]/2246265/spack-stage/spack-stage-py-tqdm-4.66.1-x2yeryg6h3ldae5dbm6c6wx5soxwk6b4/spack-src,wheel==0.44.0,xmltodict @ file:///nvme/[MASKED]/1998173/spack-stage/spack-stage-py-xmltodict-0.12.0-wgpjtfuvtu6cuzobkx5tatwjzfobtx6x/spack-src | |
| bbp-model: commands[0]> python -c 'import os; print(os.environ.get('"'"'HOC_LIBRARY_PATH'"'"', '"'"''"'"'))' | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467936/hpc/sim/neurodamus/core/hoc:/gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_oneapi-2023.2.0-skylake/neurodamus-models-2.4.1-kjfywd/share/neurodamus_neocortex/hoc | |
| bbp-model: commands[1]> pytest -s -x --forked --durations=5 --durations-min=15 tests/scientific | |
| ============================= test session starts ============================== | |
| platform linux -- Python 3.11.6, pytest-7.4.0, pluggy-1.5.0 -- /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467936/hpc/sim/neurodamus/.tox/bbp-model/bin/python | |
| cachedir: .tox/bbp-model/.pytest_cache | |
| rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467936/hpc/sim/neurodamus | |
| configfile: pyproject.toml | |
| plugins: forked-1.6.0 | |
| collecting ... collected 29 items | |
| tests/scientific/test_current_injection.py::test_current_conductance_injection[current_clamp] PASSED | |
| tests/scientific/test_current_injection.py::test_current_conductance_injection[conductance] PASSED | |
| tests/scientific/test_lfp.py::test_load_lfp_config PASSED | |
| tests/scientific/test_lfp.py::test_read_lfp_factors PASSED | |
| tests/scientific/test_lfp.py::test_number_electrodes PASSED | |
| tests/scientific/test_lfp.py::test_v5_sonata_lfp PASSED | |
| tests/scientific/test_modification.py::test_TTX_modification PASSED | |
| tests/scientific/test_modification.py::test_ConfigureAllSections_modification PASSED | |
| tests/scientific/test_multipop.py::test_multipop_simple[extra_config0] PASSED | |
| tests/scientific/test_multipop.py::test_multipop_full_conn[extra_config0] PASSED | |
| tests/scientific/test_neuromodulation.py::test_neuromodulation_sims_neuron PASSED | |
| tests/scientific/test_neuromodulation.py::test_neuromodulation_sims_coreneuron PASSED | |
| tests/scientific/test_patched_delays.py::test_eager_caching PASSED | |
| tests/scientific/test_projections.py::test_synapse_delay_override[sonata_config_file0] PASSED | |
| tests/scientific/test_projections.py::test_synapse_delay_override[sonata_config_file1] PASSED | |
| tests/scientific/test_projections.py::test_synapse_delay_override[sonata_config_file2] PASSED | |
| tests/scientific/test_projections.py::test_synapse_delay_override[sonata_config_file3] PASSED | |
| tests/scientific/test_replay.py::test_replay_sim PASSED | |
| tests/scientific/test_replay.py::test_many_replay_sim PASSED | |
| tests/scientific/test_replay.py::test_replay_sonata_spikes PASSED | |
| tests/scientific/test_simulation.py::test_simulation_sonata_config SKIPPED | |
| tests/scientific/test_simulation.py::test_v5_sonata_config PASSED | |
| tests/scientific/test_simulation.py::test_v5_gap_junction PASSED | |
| tests/scientific/test_sonata_properties.py::test_input_resistance PASSED | |
| tests/scientific/test_sonata_properties.py::test_input_resistance_2 PASSED | |
| tests/scientific/test_spont_minis.py::test_spont_minis PASSED | |
| tests/scientific/test_synapses.py::test_synapses_params PASSED | |
| tests/scientific/test_synapses.py::test__constrained_hill PASSED | |
| tests/scientific/test_synapses.py::test_no_edge_creation PASSED | |
| =============================== warnings summary =============================== | |
| neurodamus/core/configuration.py:162 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467936/hpc/sim/neurodamus/neurodamus/core/configuration.py:162: DeprecationWarning: In 3.13 classes created inside an enum will not become a member. Use the `member` decorator to keep the current behavior. | |
| class AutoBalanceModeParams: | |
| -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html | |
| ============================= slowest 5 durations ============================== | |
| 34.14s call tests/scientific/test_sonata_properties.py::test_input_resistance | |
| 31.66s call tests/scientific/test_sonata_properties.py::test_input_resistance_2 | |
| 23.63s call tests/scientific/test_current_injection.py::test_current_conductance_injection[current_clamp] | |
| 22.55s call tests/scientific/test_current_injection.py::test_current_conductance_injection[conductance] | |
| 21.10s call tests/scientific/test_simulation.py::test_v5_sonata_config | |
| ============= 28 passed, 1 skipped, 1 warning in 214.07s (0:03:34) ============= | |
| .pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467936/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| bbp-model: OK (350.27=setup[131.83]+cmd[0.40,218.04] seconds) | |
| congratulations :) (351.79 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1729780013:section_tox [0K | |
| section_end:1729780013:step_script [0Ksection_start:1729780013:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| Using git from spack modules | |
| section_end:1729780013:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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| [0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1729779532:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1729779532:resolve_secrets [0Ksection_start:1729779532:prepare_executor [0K[0K[36;1mPreparing the "custom" executor[0;m[0;m | |
| [0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m | |
| BB5 PROD runner running on bbpv1.epfl.ch, version 15.5.0, user | |
| TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor2964034606, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 236741, build ref , job ID 1467933 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1467933, 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_J1467933_PROD_P2354_CP1_C7 | |
| Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcsim partition=prod qos= reservation= | |
| Not executing the chown -R | |
| sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS | |
| sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx] | |
| Submitted batch job 2601912 | |
| 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_J1467933_PROD_P2354_CP1_C7 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1467933 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1467933 --ntasks=1 --jobid=2601912 --cpus-per-task=6 --mem=30750M | |
| section_end:1729779536:prepare_executor [0Ksection_start:1729779536:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i5n3 via bbpv1.epfl.ch... | |
| section_end:1729779540:prepare_script [0Ksection_start:1729779540:get_sources [0K[0K[36;1mGetting source from Git repository[0;m[0;m | |
| Using git from spack modules | |
| [32;1m$ git config --global http.proxy http://bbpproxy.epfl.ch:80/; git config --global https.proxy http://bbpproxy.epfl.ch:80/; git config --global --add safe.directory '*'[0;m | |
| [32;1mFetching changes with git depth set to 100...[0;m | |
| Initialized empty Git repository in /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467933/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out 05a30124 as leite/corenrn-rebalancer...[0;m | |
| Skipping object checkout, Git LFS is not installed. | |
| [32;1mUpdating/initializing submodules recursively with git depth set to 100...[0;m | |
| section_end:1729779555:get_sources [0Ksection_start:1729779555:step_script [0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m | |
| [0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m | |
| Using git from spack modules | |
| [32;1m$ if [[ -z $TOXENV ]]; then echo 'Please set the $TOXENV variable'; exit 1; fi[0;m | |
| [32;1m$ section_start() { echo -e "\e[0Ksection_start:`date +%s`:$1\r\e[0K$2"; }[0;m | |
| [32;1m$ section_end() { echo -e "\e[0Ksection_end:`date +%s`:$1\r\e[0K"; }[0;m | |
| [32;1m$ print_var() { for i in $*; do echo -e "${TXT_CYAN}${i}=${!i}${TXT_CLEAR}"; done }[0;m | |
| [32;1m$ set_and_print() { eval "$1=\"$2\""; print_var "$1"; }[0;m | |
| [32;1m$ module purge[0;m | |
| [32;1m$ unset $(env|awk -F= '/^(PMI|SLURM)_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')[0;m | |
| [32;1m$ module load unstable python/3.12.0[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.12.0 | |
| [32;1m$ module load unstable python/3.8.18[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.8.18 | |
| [32;1m$ module load unstable python/3.9.18[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.9.18 | |
| [32;1m$ module load unstable python/3.10.13[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.10.13 | |
| [32;1m$ module load unstable python/3.11.6[0;m | |
| [32;1m$ module unload unstable[0;m | |
| [32;1m$ unset CPATH PKG_CONFIG_PATH CMAKE_PREFIX_PATH[0;m | |
| [32;1m$ echo "Loaded $(python -V)"[0;m | |
| Loaded Python 3.11.6 | |
| [32;1m$ load-modules() { # collapsed multi-line command[0;m | |
| [32;1m$ load-modules $SYSTEM_MODULES[0;m | |
| Loaded module git from unstable | |
| Loaded module cmake from unstable | |
| Loaded module graphviz from unstable | |
| [32;1m$ load-modules $EXTRA_MODULES[0;m | |
| [32;1m$ module list -t[0;m | |
| Currently Loaded Modulefiles: | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.12.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.8.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.9.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.10.13 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/python/3.11.6 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/git/2.42.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/cmake/3.27.7 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-10/externals/linux-rhel7-skylake/graphviz/8.0.5 | |
| [32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
| [32;1m$ print_var XDG_CONFIG_HOME[0;m | |
| [36mXDG_CONFIG_HOME=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467933/hpc/sim/neurodamus/local_config[0m | |
| [32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m | |
| [32;1m$ cat > "${XDG_CONFIG_HOME}/git/config" << END_SCRIPT # collapsed multi-line command[0;m | |
| [32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
| [url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
| insteadOf = https://bbpgitlab.epfl.ch/ | |
| insteadOf = ssh://git@bbpgitlab.epfl.ch/ | |
| insteadOf = git@bbpgitlab.epfl.ch: | |
| [32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m | |
| [0Ksection_start:1729779576:section_venv[collapsed=true] [0KSetting up the virtual env | |
| [32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
| [32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
| [32;1m$ rm -rf "$CI_VENV"[0;m | |
| [32;1m$ python -mvenv "$CI_VENV"[0;m | |
| [32;1m$ source "$CI_VENV/bin/activate"[0;m | |
| [32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Requirement already satisfied: pip in ./venv/lib/python3.11/site-packages (23.2.1) | |
| Collecting pip | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2cd/581cf58ab7fcf/pip-24.2-py3-none-any.whl (1.8 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.8/1.8 MB 67.4 MB/s eta 0:00:00 | |
| Requirement already satisfied: setuptools in ./venv/lib/python3.11/site-packages (65.5.0) | |
| Collecting setuptools | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/a7f/cb66f68b4d9e8/setuptools-75.2.0-py3-none-any.whl (1.2 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.2/1.2 MB 209.7 MB/s eta 0:00:00 | |
| Collecting wheel | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/237/6a90c98cc337d/wheel-0.44.0-py3-none-any.whl (67 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 67.1/67.1 kB 223.3 MB/s eta 0:00:00 | |
| Installing collected packages: wheel, setuptools, pip | |
| Attempting uninstall: setuptools | |
| Found existing installation: setuptools 65.5.0 | |
| Uninstalling setuptools-65.5.0: | |
| Successfully uninstalled setuptools-65.5.0 | |
| Attempting uninstall: pip | |
| Found existing installation: pip 23.2.1 | |
| Uninstalling pip-23.2.1: | |
| Successfully uninstalled pip-23.2.1 | |
| Successfully installed pip-24.2 setuptools-75.2.0 wheel-0.44.0 | |
| [32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Collecting tox | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/452/bc32bb031f228/tox-4.23.2-py3-none-any.whl (166 kB) | |
| Collecting cachetools>=5.5 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/021/34e8439cdc2ff/cachetools-5.5.0-py3-none-any.whl (9.5 kB) | |
| Collecting chardet>=5.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB) | |
| Collecting colorama>=0.4.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB) | |
| Collecting filelock>=3.16.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/208/2e5703d51fbf9/filelock-3.16.1-py3-none-any.whl (16 kB) | |
| Collecting packaging>=24.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/5b8/f2217dbdbd2f7/packaging-24.1-py3-none-any.whl (53 kB) | |
| Collecting platformdirs>=4.3.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/73e/575e1408ab810/platformdirs-4.3.6-py3-none-any.whl (18 kB) | |
| Collecting pluggy>=1.5 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/44e/1ad92c8ca002d/pluggy-1.5.0-py3-none-any.whl (20 kB) | |
| Collecting pyproject-api>=1.8 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/3d7/d347a047afe79/pyproject_api-1.8.0-py3-none-any.whl (13 kB) | |
| Collecting virtualenv>=20.26.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/44a/72c29cceb0ee0/virtualenv-20.27.0-py3-none-any.whl (3.1 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 3.1/3.1 MB 163.6 MB/s eta 0:00:00 | |
| Collecting distlib<1,>=0.3.7 (from virtualenv>=20.26.6->tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/47f/8c22fd27c27e2/distlib-0.3.9-py2.py3-none-any.whl (468 kB) | |
| Installing collected packages: distlib, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
| Successfully installed cachetools-5.5.0 chardet-5.2.0 colorama-0.4.6 distlib-0.3.9 filelock-3.16.1 packaging-24.1 platformdirs-4.3.6 pluggy-1.5.0 pyproject-api-1.8.0 tox-4.23.2 virtualenv-20.27.0 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1729779639:section_venv [0K | |
| [32;1m$ print_var PRE_BUILD_COMMAND[0;m | |
| [36mPRE_BUILD_COMMAND=[0m | |
| [32;1m$ if [[ -n $PRE_BUILD_COMMAND ]]; then eval "$PRE_BUILD_COMMAND"; fi[0;m | |
| [32;1m$ section_start section_tox "Running Tox"[0;m | |
| [0Ksection_start:1729779639:section_tox [0KRunning Tox | |
| [32;1m$ python -mtox $TOX_OPTIONS[0;m | |
| flake8: install_deps> python -I -m pip install flake8-pyproject | |
| flake8: freeze> python -m pip freeze --all | |
| flake8: flake8==7.1.1,Flake8-pyproject==1.2.3,mccabe==0.7.0,pip==24.2,pycodestyle==2.12.1,pyflakes==3.2.0,setuptools==75.2.0,wheel==0.44.0 | |
| flake8: commands[0]> flake8 | |
| flake8: OK â in 30.28 seconds | |
| unit: install_deps> python -I -m pip install -r tests/requirements.txt | |
| .pkg: install_requires> python -I -m pip install hatch-vcs hatchling | |
| .pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467933/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| .pkg: get_requires_for_build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467933/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| .pkg: freeze> python -m pip freeze --all | |
| .pkg: hatch-vcs==0.4.0,hatchling==1.25.0,packaging==24.1,pathspec==0.12.1,pip==24.2,pluggy==1.5.0,setuptools==75.2.0,setuptools-scm==8.1.0,trove-classifiers==2024.10.21.16,wheel==0.44.0 | |
| .pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467933/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| unit: install_package_deps> python -I -m pip install docopt h5py libsonata psutil | |
| unit: install_package> python -I -m pip install --force-reinstall --no-deps /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467933/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.6.1.dev17.tar.gz | |
| unit: freeze> python -m pip freeze --all | |
| unit: docopt==0.6.2,h5py==3.12.1,iniconfig==2.0.0,libsonata==0.1.29,neurodamus @ file:///gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467933/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.6.1.dev17.tar.gz#sha256=a7d49bca41a60ba7db928207533e4867a4b4839782739dac62a2c775a798bf67,numpy==2.1.2,packaging==24.1,pip==24.2,pluggy==1.5.0,psutil==6.1.0,py==1.11.0,pytest==7.4.0,pytest-forked==1.6.0,scipy==1.14.1,setuptools==75.2.0,wheel==0.44.0 | |
| unit: commands[0]> pytest tests/unit | |
| ============================= test session starts ============================== | |
| platform linux -- Python 3.11.6, pytest-7.4.0, pluggy-1.5.0 -- /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467933/hpc/sim/neurodamus/.tox/unit/bin/python | |
| cachedir: .tox/unit/.pytest_cache | |
| rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467933/hpc/sim/neurodamus | |
| configfile: pyproject.toml | |
| plugins: forked-1.6.0 | |
| collecting ... collected 82 items | |
| tests/unit/test_conn_manager.py::test_population_get PASSED [ 1%] | |
| tests/unit/test_conn_manager.py::test_population_store_order PASSED [ 2%] | |
| tests/unit/test_conn_manager.py::test_population_get_create_conn PASSED [ 3%] | |
| tests/unit/test_conn_manager.py::test_population_all_conns PASSED [ 4%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input0-expected0] PASSED [ 6%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input1-expected1] PASSED [ 7%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input2-expected2] PASSED [ 8%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input3-expected3] PASSED [ 9%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input4-expected4] PASSED [ 10%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input5-expected5] PASSED [ 12%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input6-expected6] PASSED [ 13%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input7-expected7] PASSED [ 14%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input8-expected8] PASSED [ 15%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input9-expected9] PASSED [ 17%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input10-expected10] PASSED [ 18%] | |
| tests/unit/test_conn_manager.py::test_population_delete PASSED [ 19%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input0-expected0] PASSED [ 20%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input1-expected1] PASSED [ 21%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input2-expected2] PASSED [ 23%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input3-expected3] PASSED [ 24%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input4-expected4] PASSED [ 25%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input5-expected5] PASSED [ 26%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input6-expected6] PASSED [ 28%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input7-expected7] PASSED [ 29%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input8-expected8] PASSED [ 30%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input9-expected9] PASSED [ 31%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input10-expected10] PASSED [ 32%] | |
| tests/unit/test_conn_manager.py::test_population_ids_match PASSED [ 34%] | |
| tests/unit/test_coords.py::test_coord_mapping1 PASSED [ 35%] | |
| tests/unit/test_coords.py::test_coord_mapping2 PASSED [ 36%] | |
| tests/unit/test_core_config.py::test_write_report_config PASSED [ 37%] | |
| tests/unit/test_core_config.py::test_write_sim_config PASSED [ 39%] | |
| tests/unit/test_dry_run.py::test_dry_run_distribution PASSED [ 40%] | |
| tests/unit/test_dry_run.py::test_retrieve_unique_metypes PASSED [ 41%] | |
| tests/unit/test_init_py_config.py::test_init_empty PASSED [ 42%] | |
| tests/unit/test_init_py_config.py::test_init_non_positional PASSED [ 43%] | |
| tests/unit/test_init_py_config.py::test_init_config_only PASSED [ 45%] | |
| tests/unit/test_init_py_config.py::test_init_pass_options PASSED [ 46%] | |
| tests/unit/test_init_py_config.py::test_init_first_args PASSED [ 47%] | |
| tests/unit/test_init_py_config.py::test_init_early_config_file PASSED [ 48%] | |
| tests/unit/test_nodeset.py::test_NodeSet_base PASSED [ 50%] | |
| tests/unit/test_nodeset.py::test_NodeSet_add PASSED [ 51%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges10-ranges20-expected0] PASSED [ 52%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges11-ranges21-expected1] PASSED [ 53%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges12-ranges22-expected2] PASSED [ 54%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges13-ranges23-expected3] PASSED [ 56%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges14-ranges24-expected4] PASSED [ 57%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges15-ranges25-expected5] PASSED [ 58%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges16-ranges26-expected6] PASSED [ 59%] | |
| tests/unit/test_nodeset.py::test_ranges_vec_overlap[ranges10-vec0-expected0] PASSED [ 60%] | |
| tests/unit/test_nodeset.py::test_ranges_vec_overlap[ranges11-vec1-expected1] PASSED [ 62%] | |
| tests/unit/test_nodeset.py::test_ranges_vec_overlap[ranges12-vec2-expected2] PASSED [ 63%] | |
| tests/unit/test_nodeset.py::test_ranges_vec_overlap[ranges13-vec3-expected3] PASSED [ 64%] | |
| tests/unit/test_nodeset.py::test_ranges_vec_overlap[ranges14-vec4-expected4] PASSED [ 65%] | |
| tests/unit/test_nodeset.py::test_read_nodesets_from_file PASSED [ 67%] | |
| tests/unit/test_nodeset_target.py::test_get_local_gids PASSED [ 68%] | |
| tests/unit/test_pyutils.py::test_map_1 PASSED [ 69%] | |
| tests/unit/test_pyutils.py::test_map_other_data PASSED [ 70%] | |
| tests/unit/test_pyutils.py::test_map_duplicates PASSED [ 71%] | |
| tests/unit/test_pyutils.py::test_map_duplicates_struct PASSED [ 73%] | |
| tests/unit/test_pyutils.py::test_badly_formed PASSED [ 74%] | |
| tests/unit/test_pyutils.py::test_merge PASSED [ 75%] | |
| tests/unit/test_pyutils.py::test_merge_grouped PASSED [ 76%] | |
| tests/unit/test_pyutils.py::test_flatten_grouped PASSED [ 78%] | |
| tests/unit/test_replay_manager.py::test_replay_manager_sonata PASSED [ 79%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_flat_segment PASSED [ 80%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_pulse PASSED [ 81%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_pulse_diff_base[-1] PASSED [ 82%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_pulse_diff_base[0] PASSED [ 84%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_pulse_diff_base[1.5] PASSED [ 85%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_two_pulses PASSED [ 86%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_ramp PASSED [ 87%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_delay_ramp PASSED [ 89%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_train PASSED [ 90%] | |
| tests/unit/test_synapse_reader.py::test_gapjunction_sonata_reader PASSED [ 91%] | |
| tests/unit/test_synapse_reader.py::test_syn_read_counts PASSED [ 92%] | |
| tests/unit/test_synapse_reader.py::test_conn_manager_syn_stats PASSED [ 93%] | |
| tests/unit/test_target_intersection.py::test_targetspec_overlap_name PASSED [ 95%] | |
| tests/unit/test_target_intersection.py::test_populations_disjoint PASSED [ 96%] | |
| tests/unit/test_target_intersection.py::test_targetspec_overlap PASSED [ 97%] | |
| tests/unit/test_target_intersection.py::test_nodeset_target_intersect PASSED [ 98%] | |
| tests/unit/test_target_intersection.py::test_nodeset_gids PASSED [100%] | |
| =============================== warnings summary =============================== | |
| .tox/unit/lib/python3.11/site-packages/neurodamus/core/configuration.py:162 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467933/hpc/sim/neurodamus/.tox/unit/lib/python3.11/site-packages/neurodamus/core/configuration.py:162: DeprecationWarning: In 3.13 classes created inside an enum will not become a member. Use the `member` decorator to keep the current behavior. | |
| class AutoBalanceModeParams: | |
| -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html | |
| ======================== 82 passed, 1 warning in 3.95s ========================= | |
| .pkg: _exit> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1467933/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True hatchling.build | |
| flake8: OK (30.28=setup[27.93]+cmd[2.35] seconds) | |
| unit: OK (130.30=setup[124.05]+cmd[6.26] seconds) | |
| congratulations :) (161.70 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1729779802:section_tox [0K | |
| section_end:1729779802:step_script [0Ksection_start:1729779802:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| Using git from spack modules | |
| section_end:1729779803:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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