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March 12, 2024 12:12
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Logfiles for GitLab pipeline https://bbpgitlab.epfl.ch/hpc/sim/neurodamus/-/pipelines/199941 (:white_check_mark:) running on GitHub PR BlueBrain/neurodamus#138.
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| [0KRunning with gitlab-runner 16.8.1 (a6097117)[0;m | |
| [0K on kubernetes Me7zLFRu, system ID: r_WxT1lHy8HIG7[0;m | |
| section_start:1710245441:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1710245441:resolve_secrets [0Ksection_start:1710245441: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:1710245441:prepare_executor [0Ksection_start:1710245441: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-me7zlfru-project-2354-concurrent-0-9m51x8ik to be running, status is Pending | |
| Waiting for pod gitlab-runners/runner-me7zlfru-project-2354-concurrent-0-9m51x8ik to be running, status is Pending | |
| ContainersNotReady: "containers with unready status: [build helper]" | |
| ContainersNotReady: "containers with unready status: [build helper]" | |
| Running on runner-me7zlfru-project-2354-concurrent-0-9m51x8ik via cs-gitlab-runners-gitlab-runner-557b4c775c-8nsmw... | |
| section_end:1710245449:prepare_script [0Ksection_start:1710245449: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 48df6b9b as detached HEAD (ref is weji/ChangeLog)...[0;m | |
| [32;1mUpdating/initializing submodules recursively with git depth set to 100...[0;m | |
| [32;1mUpdated submodules[0;m | |
| section_end:1710245457:get_sources [0Ksection_start:1710245457: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 $(python -V)"[0;m | |
| Loaded Python 3.11.8 | |
| [32;1m$ section_start section_venv[collapsed=true] "Setting up the virtual env"[0;m | |
| [0Ksection_start:1710245457: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) | |
| 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/02f/a291a0471b3a1/setuptools-69.1.1-py3-none-any.whl (819 kB) | |
| âââââââââââââââââââââââââââââââââââââ 819.3/819.3 kB 126.9 MB/s eta 0:00:00 | |
| Collecting wheel | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/55c/570405f142630/wheel-0.43.0-py3-none-any.whl (65 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 65.8/65.8 kB 109.7 MB/s eta 0:00:00 | |
| Installing collected packages: wheel, setuptools | |
| Attempting uninstall: setuptools | |
| Found existing installation: setuptools 65.5.0 | |
| Uninstalling setuptools-65.5.0: | |
| Successfully uninstalled setuptools-65.5.0 | |
| Successfully installed setuptools-69.1.1 wheel-0.43.0 | |
| [32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Collecting build | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/8ed/0851ee76e6e38/build-1.1.1-py3-none-any.whl (19 kB) | |
| Collecting twine | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/a26/2933de0b484c5/twine-5.0.0-py3-none-any.whl (37 kB) | |
| Collecting packaging>=19.0 (from build) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2dd/fb553fdf02fb7/packaging-24.0-py3-none-any.whl (53 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 53.5/53.5 kB 100.5 MB/s eta 0:00:00 | |
| Collecting pyproject_hooks (from build) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/283/c11acd6b928d2/pyproject_hooks-1.0.0-py3-none-any.whl (9.3 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 readme-renderer>=35.0 (from twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/19d/b308d86ecd60e/readme_renderer-43.0-py3-none-any.whl (13 kB) | |
| Collecting requests>=2.20 (from twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/58c/d2187c01e70e6/requests-2.31.0-py3-none-any.whl (62 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 62.6/62.6 kB 107.0 MB/s eta 0:00:00 | |
| 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) | |
| âââââââââââââââââââââââââââââââââââââââ 54.5/54.5 kB 126.4 MB/s eta 0:00:00 | |
| Collecting urllib3>=1.26.0 (from twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/450/b20ec296a4670/urllib3-2.2.1-py3-none-any.whl (121 kB) | |
| âââââââââââââââââââââââââââââââââââââ 121.1/121.1 kB 126.4 MB/s eta 0:00:00 | |
| Collecting importlib-metadata>=3.6 (from twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/f4b/c4c0c070c490a/importlib_metadata-7.0.2-py3-none-any.whl (24 kB) | |
| Collecting keyring>=15.1 (from twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/df3/8a4d7419a6a60/keyring-24.3.1-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/4ed/bae314f59eb48/rich-13.7.1-py3-none-any.whl (240 kB) | |
| âââââââââââââââââââââââââââââââââââââ 240.7/240.7 kB 136.1 MB/s eta 0:00:00 | |
| Collecting zipp>=0.5 (from importlib-metadata>=3.6->twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/0e9/23e726174922d/zipp-3.17.0-py3-none-any.whl (7.4 kB) | |
| Collecting jaraco.classes (from keyring>=15.1->twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/86b/534de565381f6/jaraco.classes-3.3.1-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) | |
| âââââââââââââââââââââââââââââââââââââââ 48.4/48.4 kB 120.4 MB/s eta 0:00:00 | |
| Collecting nh3>=0.2.14 (from readme-renderer>=35.0->twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/606/84857cfa8fdbb/nh3-0.2.15-cp37-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.7 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.7/1.7 MB 138.1 MB/s eta 0:00:00 | |
| Collecting docutils>=0.13.1 (from readme-renderer>=35.0->twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/96f/387a2c5562db4/docutils-0.20.1-py3-none-any.whl (572 kB) | |
| âââââââââââââââââââââââââââââââââââââ 572.7/572.7 kB 142.1 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/b27/c2826c47d0f32/pygments-2.17.2-py3-none-any.whl (1.2 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 1.2/1.2 MB 143.6 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/753/f10e867343b45/charset_normalizer-3.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (140 kB) | |
| âââââââââââââââââââââââââââââââââââââ 140.3/140.3 kB 137.1 MB/s eta 0:00:00 | |
| Collecting idna<4,>=2.5 (from requests>=2.20->twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/c05/567e9c24a6b9f/idna-3.6-py3-none-any.whl (61 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 61.6/61.6 kB 107.4 MB/s eta 0:00:00 | |
| Collecting certifi>=2017.4.17 (from requests>=2.20->twine) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/dc3/83c07b76109f3/certifi-2024.2.2-py3-none-any.whl (163 kB) | |
| âââââââââââââââââââââââââââââââââââââ 163.8/163.8 kB 123.3 MB/s eta 0:00:00 | |
| 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) | |
| âââââââââââââââââââââââââââââââââââââââ 87.5/87.5 kB 122.9 MB/s eta 0:00:00 | |
| 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/7cd/e5f38e614f55e/cryptography-42.0.5-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.6 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 4.6/4.6 MB 137.0 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/686/b06abe565edfa/more_itertools-10.2.0-py3-none-any.whl (57 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 57.0/57.0 kB 124.1 MB/s eta 0:00:00 | |
| 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/7b7/8010e7b97fef4/cffi-1.16.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (464 kB) | |
| âââââââââââââââââââââââââââââââââââââ 464.8/464.8 kB 146.3 MB/s eta 0:00:00 | |
| 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/8ee/45429555515e1/pycparser-2.21-py2.py3-none-any.whl (118 kB) | |
| âââââââââââââââââââââââââââââââââââââ 118.7/118.7 kB 134.9 MB/s eta 0:00:00 | |
| Installing collected packages: nh3, zipp, urllib3, rfc3986, pyproject_hooks, Pygments, pycparser, pkginfo, packaging, more-itertools, mdurl, jeepney, idna, docutils, charset-normalizer, certifi, requests, readme-renderer, markdown-it-py, jaraco.classes, importlib-metadata, cffi, build, rich, requests-toolbelt, cryptography, SecretStorage, keyring, twine | |
| Successfully installed Pygments-2.17.2 SecretStorage-3.3.3 build-1.1.1 certifi-2024.2.2 cffi-1.16.0 charset-normalizer-3.3.2 cryptography-42.0.5 docutils-0.20.1 idna-3.6 importlib-metadata-7.0.2 jaraco.classes-3.3.1 jeepney-0.8.0 keyring-24.3.1 markdown-it-py-3.0.0 mdurl-0.1.2 more-itertools-10.2.0 nh3-0.2.15 packaging-24.0 pkginfo-1.10.0 pycparser-2.21 pyproject_hooks-1.0.0 readme-renderer-43.0 requests-2.31.0 requests-toolbelt-1.0.0 rfc3986-2.0.0 rich-13.7.1 twine-5.0.0 urllib3-2.2.1 zipp-3.17.0 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1710245480:section_venv [0K | |
| [32;1m$ rm -Rf build dist *.egg-info[0;m | |
| [32;1m$ python -m build --sdist[0;m | |
| * Creating venv isolated environment... | |
| * Installing packages in isolated environment... (setuptools, setuptools_scm, wheel) | |
| * Getting build dependencies for sdist... | |
| /tmp/build-env-f0_qc8mc/lib/python3.11/site-packages/setuptools_scm/git.py:163: UserWarning: "/builds/hpc/sim/neurodamus" is shallow and may cause errors | |
| warnings.warn(f'"{wd.path}" is shallow and may cause errors') | |
| running egg_info | |
| creating neurodamus.egg-info | |
| writing neurodamus.egg-info/PKG-INFO | |
| writing dependency_links to neurodamus.egg-info/dependency_links.txt | |
| writing entry points to neurodamus.egg-info/entry_points.txt | |
| writing requirements to neurodamus.egg-info/requires.txt | |
| writing top-level names to neurodamus.egg-info/top_level.txt | |
| writing manifest file 'neurodamus.egg-info/SOURCES.txt' | |
| reading manifest template 'MANIFEST.in' | |
| adding license file 'LICENSE.txt' | |
| writing manifest file 'neurodamus.egg-info/SOURCES.txt' | |
| * Building sdist... | |
| /tmp/build-env-f0_qc8mc/lib/python3.11/site-packages/setuptools_scm/git.py:163: UserWarning: "/builds/hpc/sim/neurodamus" is shallow and may cause errors | |
| warnings.warn(f'"{wd.path}" is shallow and may cause errors') | |
| running sdist | |
| running egg_info | |
| writing neurodamus.egg-info/PKG-INFO | |
| writing dependency_links to neurodamus.egg-info/dependency_links.txt | |
| writing entry points to neurodamus.egg-info/entry_points.txt | |
| writing requirements to neurodamus.egg-info/requires.txt | |
| writing top-level names to neurodamus.egg-info/top_level.txt | |
| reading manifest template 'MANIFEST.in' | |
| adding license file 'LICENSE.txt' | |
| writing manifest file 'neurodamus.egg-info/SOURCES.txt' | |
| running check | |
| creating neurodamus-3.0.1.dev18 | |
| creating neurodamus-3.0.1.dev18/.github | |
| creating neurodamus-3.0.1.dev18/.github/workflows | |
| creating neurodamus-3.0.1.dev18/_benchmarks | |
| creating neurodamus-3.0.1.dev18/_benchmarks/opti_configure_0.2.2 | |
| creating neurodamus-3.0.1.dev18/ci | |
| creating neurodamus-3.0.1.dev18/core | |
| creating neurodamus-3.0.1.dev18/core/hoc | |
| creating neurodamus-3.0.1.dev18/core/mod | |
| creating neurodamus-3.0.1.dev18/docker | |
| creating neurodamus-3.0.1.dev18/examples | |
| creating neurodamus-3.0.1.dev18/neurodamus | |
| creating neurodamus-3.0.1.dev18/neurodamus.egg-info | |
| creating neurodamus-3.0.1.dev18/neurodamus/core | |
| creating neurodamus-3.0.1.dev18/neurodamus/io | |
| creating neurodamus-3.0.1.dev18/neurodamus/utils | |
| creating neurodamus-3.0.1.dev18/venv | |
| creating neurodamus-3.0.1.dev18/venv/bin | |
| copying files to neurodamus-3.0.1.dev18... | |
| copying .coveragerc -> neurodamus-3.0.1.dev18 | |
| copying .gitattributes -> neurodamus-3.0.1.dev18 | |
| copying .gitignore -> neurodamus-3.0.1.dev18 | |
| copying .gitlab-ci.yml -> neurodamus-3.0.1.dev18 | |
| copying .gitmodules -> neurodamus-3.0.1.dev18 | |
| copying .pre-commit-config.yaml -> neurodamus-3.0.1.dev18 | |
| copying .readthedocs.yml -> neurodamus-3.0.1.dev18 | |
| copying CHANGES.rst -> neurodamus-3.0.1.dev18 | |
| copying CONTRIBUTING.md -> neurodamus-3.0.1.dev18 | |
| copying LICENSE.txt -> neurodamus-3.0.1.dev18 | |
| copying MANIFEST.in -> neurodamus-3.0.1.dev18 | |
| copying README.rst -> neurodamus-3.0.1.dev18 | |
| copying _debug.py -> neurodamus-3.0.1.dev18 | |
| copying authors.txt -> neurodamus-3.0.1.dev18 | |
| copying init.py -> neurodamus-3.0.1.dev18 | |
| copying pyproject.toml -> neurodamus-3.0.1.dev18 | |
| copying requirements.txt -> neurodamus-3.0.1.dev18 | |
| copying requirements_docs.txt -> neurodamus-3.0.1.dev18 | |
| copying tox.ini -> neurodamus-3.0.1.dev18 | |
| copying .github/pull_request_template.md -> neurodamus-3.0.1.dev18/.github | |
| copying .github/workflows/publish_wheels.yml -> neurodamus-3.0.1.dev18/.github/workflows | |
| copying .github/workflows/simulation_test.yml -> neurodamus-3.0.1.dev18/.github/workflows | |
| copying _benchmarks/init.py -> neurodamus-3.0.1.dev18/_benchmarks | |
| copying _benchmarks/out.lprof -> neurodamus-3.0.1.dev18/_benchmarks | |
| copying _benchmarks/pydamus.png -> neurodamus-3.0.1.dev18/_benchmarks | |
| copying _benchmarks/synstats.py -> neurodamus-3.0.1.dev18/_benchmarks | |
| copying _benchmarks/timeit.py -> neurodamus-3.0.1.dev18/_benchmarks | |
| copying _benchmarks/opti_configure_0.2.2/line_stats.0.txt -> neurodamus-3.0.1.dev18/_benchmarks/opti_configure_0.2.2 | |
| copying _benchmarks/opti_configure_0.2.2/line_stats.txt -> neurodamus-3.0.1.dev18/_benchmarks/opti_configure_0.2.2 | |
| copying ci/build_ndcore.sh -> neurodamus-3.0.1.dev18/ci | |
| copying core/hoc/Cell.hoc -> neurodamus-3.0.1.dev18/core/hoc | |
| copying core/hoc/ConnectionUtils.hoc -> neurodamus-3.0.1.dev18/core/hoc | |
| copying core/hoc/Map.hoc -> neurodamus-3.0.1.dev18/core/hoc | |
| copying core/hoc/MorphIO.hoc -> neurodamus-3.0.1.dev18/core/hoc | |
| copying core/hoc/RNGSettings.hoc -> neurodamus-3.0.1.dev18/core/hoc | |
| copying core/hoc/Report.hoc -> neurodamus-3.0.1.dev18/core/hoc | |
| copying core/hoc/TPointList.hoc -> neurodamus-3.0.1.dev18/core/hoc | |
| copying core/hoc/TType.hoc -> neurodamus-3.0.1.dev18/core/hoc | |
| copying core/hoc/defvar.hoc -> neurodamus-3.0.1.dev18/core/hoc | |
| copying core/hoc/fileUtils.hoc -> neurodamus-3.0.1.dev18/core/hoc | |
| copying core/hoc/neurodamus.hoc -> neurodamus-3.0.1.dev18/core/hoc | |
| copying core/mod/ALU.mod -> neurodamus-3.0.1.dev18/core/mod | |
| copying core/mod/CoreNEURONArtificialCell.mod -> neurodamus-3.0.1.dev18/core/mod | |
| copying core/mod/HDF5reader.mod -> neurodamus-3.0.1.dev18/core/mod | |
| copying core/mod/SonataReportHelper.mod -> neurodamus-3.0.1.dev18/core/mod | |
| copying core/mod/SonataReports.mod -> neurodamus-3.0.1.dev18/core/mod | |
| copying core/mod/VecStim.mod -> neurodamus-3.0.1.dev18/core/mod | |
| copying core/mod/coreneuron_modlist.txt -> neurodamus-3.0.1.dev18/core/mod | |
| copying core/mod/netstim_inhpoisson.mod -> neurodamus-3.0.1.dev18/core/mod | |
| copying docker/Dockerfile -> neurodamus-3.0.1.dev18/docker | |
| copying docker/README.md -> neurodamus-3.0.1.dev18/docker | |
| copying docker/build_neurodamus.sh -> neurodamus-3.0.1.dev18/docker | |
| copying examples/composed_signal.py -> neurodamus-3.0.1.dev18/examples | |
| copying examples/create_cell.py -> neurodamus-3.0.1.dev18/examples | |
| copying examples/neuron_first_steps.py -> neurodamus-3.0.1.dev18/examples | |
| copying examples/neuron_tut1.py -> neurodamus-3.0.1.dev18/examples | |
| copying examples/neuron_tut2.py -> neurodamus-3.0.1.dev18/examples | |
| copying examples/test_neurodamus.py -> neurodamus-3.0.1.dev18/examples | |
| copying neurodamus/__init__.py -> neurodamus-3.0.1.dev18/neurodamus | |
| copying neurodamus/cell_distributor.py -> neurodamus-3.0.1.dev18/neurodamus | |
| copying neurodamus/commands.py -> neurodamus-3.0.1.dev18/neurodamus | |
| copying neurodamus/connection.py -> neurodamus-3.0.1.dev18/neurodamus | |
| copying neurodamus/connection_manager.py -> neurodamus-3.0.1.dev18/neurodamus | |
| copying neurodamus/gap_junction.py -> neurodamus-3.0.1.dev18/neurodamus | |
| copying neurodamus/hocify.py -> neurodamus-3.0.1.dev18/neurodamus | |
| copying neurodamus/lfp_manager.py -> neurodamus-3.0.1.dev18/neurodamus | |
| copying neurodamus/metype.py -> neurodamus-3.0.1.dev18/neurodamus | |
| copying neurodamus/modification_manager.py -> neurodamus-3.0.1.dev18/neurodamus | |
| copying neurodamus/morphio_wrapper.py -> neurodamus-3.0.1.dev18/neurodamus | |
| copying neurodamus/neuromodulation_manager.py -> neurodamus-3.0.1.dev18/neurodamus | |
| copying neurodamus/ngv.py -> neurodamus-3.0.1.dev18/neurodamus | |
| copying neurodamus/node.py -> neurodamus-3.0.1.dev18/neurodamus | |
| copying neurodamus/replay.py -> neurodamus-3.0.1.dev18/neurodamus | |
| copying neurodamus/stimulus_manager.py -> neurodamus-3.0.1.dev18/neurodamus | |
| copying neurodamus/target_manager.py -> neurodamus-3.0.1.dev18/neurodamus | |
| copying neurodamus.egg-info/PKG-INFO -> neurodamus-3.0.1.dev18/neurodamus.egg-info | |
| copying neurodamus.egg-info/SOURCES.txt -> neurodamus-3.0.1.dev18/neurodamus.egg-info | |
| copying neurodamus.egg-info/dependency_links.txt -> neurodamus-3.0.1.dev18/neurodamus.egg-info | |
| copying neurodamus.egg-info/entry_points.txt -> neurodamus-3.0.1.dev18/neurodamus.egg-info | |
| copying neurodamus.egg-info/requires.txt -> neurodamus-3.0.1.dev18/neurodamus.egg-info | |
| copying neurodamus.egg-info/top_level.txt -> neurodamus-3.0.1.dev18/neurodamus.egg-info | |
| copying neurodamus/core/__init__.py -> neurodamus-3.0.1.dev18/neurodamus/core | |
| copying neurodamus/core/_engine.py -> neurodamus-3.0.1.dev18/neurodamus/core | |
| copying neurodamus/core/_mpi.py -> neurodamus-3.0.1.dev18/neurodamus/core | |
| copying neurodamus/core/_neurodamus.py -> neurodamus-3.0.1.dev18/neurodamus/core | |
| copying neurodamus/core/_neuron.py -> neurodamus-3.0.1.dev18/neurodamus/core | |
| copying neurodamus/core/_shmutils.py -> neurodamus-3.0.1.dev18/neurodamus/core | |
| copying neurodamus/core/_utils.py -> neurodamus-3.0.1.dev18/neurodamus/core | |
| copying neurodamus/core/cell.py -> neurodamus-3.0.1.dev18/neurodamus/core | |
| copying neurodamus/core/configuration.py -> neurodamus-3.0.1.dev18/neurodamus/core | |
| copying neurodamus/core/coreneuron_configuration.py -> neurodamus-3.0.1.dev18/neurodamus/core | |
| copying neurodamus/core/mechanisms.py -> neurodamus-3.0.1.dev18/neurodamus/core | |
| copying neurodamus/core/nodeset.py -> neurodamus-3.0.1.dev18/neurodamus/core | |
| copying neurodamus/core/random.py -> neurodamus-3.0.1.dev18/neurodamus/core | |
| copying neurodamus/core/stimuli.py -> neurodamus-3.0.1.dev18/neurodamus/core | |
| copying neurodamus/core/synapses.py -> neurodamus-3.0.1.dev18/neurodamus/core | |
| copying neurodamus/io/__init__.py -> neurodamus-3.0.1.dev18/neurodamus/io | |
| copying neurodamus/io/cell_readers.py -> neurodamus-3.0.1.dev18/neurodamus/io | |
| copying neurodamus/io/sonata_config.py -> neurodamus-3.0.1.dev18/neurodamus/io | |
| copying neurodamus/io/synapse_reader.py -> neurodamus-3.0.1.dev18/neurodamus/io | |
| copying neurodamus/utils/__init__.py -> neurodamus-3.0.1.dev18/neurodamus/utils | |
| copying neurodamus/utils/cli.py -> neurodamus-3.0.1.dev18/neurodamus/utils | |
| copying neurodamus/utils/compat.py -> neurodamus-3.0.1.dev18/neurodamus/utils | |
| copying neurodamus/utils/logging.py -> neurodamus-3.0.1.dev18/neurodamus/utils | |
| copying neurodamus/utils/memory.py -> neurodamus-3.0.1.dev18/neurodamus/utils | |
| copying neurodamus/utils/multimap.py -> neurodamus-3.0.1.dev18/neurodamus/utils | |
| copying neurodamus/utils/progressbar.py -> neurodamus-3.0.1.dev18/neurodamus/utils | |
| copying neurodamus/utils/pyutils.py -> neurodamus-3.0.1.dev18/neurodamus/utils | |
| copying neurodamus/utils/timeit.py -> neurodamus-3.0.1.dev18/neurodamus/utils | |
| copying venv/bin/rst2html.py -> neurodamus-3.0.1.dev18/venv/bin | |
| copying venv/bin/rst2html4.py -> neurodamus-3.0.1.dev18/venv/bin | |
| copying venv/bin/rst2html5.py -> neurodamus-3.0.1.dev18/venv/bin | |
| copying venv/bin/rst2latex.py -> neurodamus-3.0.1.dev18/venv/bin | |
| copying venv/bin/rst2man.py -> neurodamus-3.0.1.dev18/venv/bin | |
| copying venv/bin/rst2odt.py -> neurodamus-3.0.1.dev18/venv/bin | |
| copying venv/bin/rst2odt_prepstyles.py -> neurodamus-3.0.1.dev18/venv/bin | |
| copying venv/bin/rst2pseudoxml.py -> neurodamus-3.0.1.dev18/venv/bin | |
| copying venv/bin/rst2s5.py -> neurodamus-3.0.1.dev18/venv/bin | |
| copying venv/bin/rst2xetex.py -> neurodamus-3.0.1.dev18/venv/bin | |
| copying venv/bin/rst2xml.py -> neurodamus-3.0.1.dev18/venv/bin | |
| copying venv/bin/rstpep2html.py -> neurodamus-3.0.1.dev18/venv/bin | |
| copying neurodamus.egg-info/SOURCES.txt -> neurodamus-3.0.1.dev18/neurodamus.egg-info | |
| Writing neurodamus-3.0.1.dev18/setup.cfg | |
| Creating tar archive | |
| removing 'neurodamus-3.0.1.dev18' (and everything under it) | |
| Successfully built neurodamus-3.0.1.dev18.tar.gz | |
| [32;1m$ twine check dist/*[0;m | |
| Checking dist/neurodamus-3.0.1.dev18.tar.gz: [32mPASSED[0m | |
| section_end:1710245487:step_script [0Ksection_start:1710245487: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=1205849 responseStatus[0;m=201 Created token[0;m=64_Wype9 | |
| section_end:1710245489:upload_artifacts_on_success [0Ksection_start:1710245489:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| section_end:1710245489: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:1710244396:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1710244396:resolve_secrets [0Ksection_start:1710244396: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-executor2689240563, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 199941, build ref , job ID 1205841 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1205841, 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_J1205841_PROD_P2354_CP0_C1 | |
| 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 2080742 | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1205841_PROD_P2354_CP0_C1 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1205841 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1205841 --ntasks=1 --jobid=2080742 --cpus-per-task=6 --mem=30750M | |
| section_end:1710244397:prepare_executor [0Ksection_start:1710244397:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i6n22 via bbpv1.epfl.ch... | |
| section_end:1710244409:prepare_script [0Ksection_start:1710244409: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/J1205841/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out 48df6b9b as weji/ChangeLog...[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:1710244417:get_sources [0Ksection_start:1710244417: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/2024-03/externals/linux-rhel7-skylake/python/3.12.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.8.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.9.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.10.13 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.11.6 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/git/2.42.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/cmake/3.27.7 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/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/J1205841/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:1710244422:section_venv[collapsed=true] [0KSetting up the virtual env | |
| [32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
| [32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
| [32;1m$ rm -rf "$CI_VENV"[0;m | |
| [32;1m$ python -mvenv "$CI_VENV"[0;m | |
| [32;1m$ source "$CI_VENV/bin/activate"[0;m | |
| [32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Requirement already satisfied: pip in ./venv/lib/python3.11/site-packages (23.2.1) | |
| Collecting pip | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/ba0/d021a166865d2/pip-24.0-py3-none-any.whl (2.1 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 2.1/2.1 MB 73.4 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/02f/a291a0471b3a1/setuptools-69.1.1-py3-none-any.whl (819 kB) | |
| âââââââââââââââââââââââââââââââââââââ 819.3/819.3 kB 223.2 MB/s eta 0:00:00 | |
| Collecting wheel | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/55c/570405f142630/wheel-0.43.0-py3-none-any.whl (65 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 65.8/65.8 kB 199.9 MB/s eta 0:00:00 | |
| Installing collected packages: wheel, setuptools, pip | |
| Attempting uninstall: setuptools | |
| Found existing installation: setuptools 65.5.0 | |
| Uninstalling setuptools-65.5.0: | |
| Successfully uninstalled setuptools-65.5.0 | |
| Attempting uninstall: pip | |
| Found existing installation: pip 23.2.1 | |
| Uninstalling pip-23.2.1: | |
| Successfully uninstalled pip-23.2.1 | |
| Successfully installed pip-24.0 setuptools-69.1.1 wheel-0.43.0 | |
| [32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Collecting tox | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/b03/754b6ee6dadc7/tox-4.14.1-py3-none-any.whl (155 kB) | |
| ââââââââââââââââââââââââââââââââââââââ 155.3/155.3 kB 19.5 MB/s eta 0:00:00 | |
| Collecting cachetools>=5.3.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/0ab/ad1021d3f8325/cachetools-5.3.3-py3-none-any.whl (9.3 kB) | |
| Collecting chardet>=5.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB) | |
| ââââââââââââââââââââââââââââââââââââââ 199.4/199.4 kB 59.9 MB/s eta 0:00:00 | |
| Collecting colorama>=0.4.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB) | |
| Collecting filelock>=3.13.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/57d/bda9b35157b05/filelock-3.13.1-py3-none-any.whl (11 kB) | |
| Collecting packaging>=23.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2dd/fb553fdf02fb7/packaging-24.0-py3-none-any.whl (53 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 53.5/53.5 kB 215.1 MB/s eta 0:00:00 | |
| Collecting platformdirs>=4.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/061/4df2a2f37e1a6/platformdirs-4.2.0-py3-none-any.whl (17 kB) | |
| Collecting pluggy>=1.3 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/7db/9f7b503d67d1c/pluggy-1.4.0-py3-none-any.whl (20 kB) | |
| Collecting pyproject-api>=1.6.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4c0/116d60476b078/pyproject_api-1.6.1-py3-none-any.whl (12 kB) | |
| Collecting virtualenv>=20.25 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/961/c026ac520bac5/virtualenv-20.25.1-py3-none-any.whl (3.8 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 3.8/3.8 MB 106.8 MB/s eta 0:00:00 | |
| Collecting distlib<1,>=0.3.7 (from virtualenv>=20.25->tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/034/db59a0b96f8ca/distlib-0.3.8-py2.py3-none-any.whl (468 kB) | |
| âââââââââââââââââââââââââââââââââââââ 468.9/468.9 kB 202.5 MB/s eta 0:00:00 | |
| Installing collected packages: distlib, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
| Successfully installed cachetools-5.3.3 chardet-5.2.0 colorama-0.4.6 distlib-0.3.8 filelock-3.13.1 packaging-24.0 platformdirs-4.2.0 pluggy-1.4.0 pyproject-api-1.6.1 tox-4.14.1 virtualenv-20.25.1 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1710244439: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:1710244439: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 setuptools setuptools_scm wheel | |
| .pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205841/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True setuptools.build_meta | |
| .pkg: get_requires_for_build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205841/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True setuptools.build_meta | |
| .pkg: freeze> python -m pip freeze --all | |
| .pkg: packaging==24.0,pip==24.0,setuptools==69.1.0,setuptools-scm==8.0.4,typing_extensions==4.10.0,wheel==0.42.0 | |
| .pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205841/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True setuptools.build_meta | |
| 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/J1205841/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.0.1.dev18.tar.gz | |
| docs: freeze> python -m pip freeze --all | |
| docs: alabaster==0.7.16,Babel==2.14.0,certifi==2024.2.2,charset-normalizer==3.3.2,docopt==0.6.2,docutils==0.18.1,h5py==3.10.0,idna==3.6,imagesize==1.4.1,Jinja2==3.1.3,libsonata==0.1.25,MarkupSafe==2.1.5,neurodamus==3.0.1.dev18,numpy==1.26.4,packaging==24.0,pip==24.0,psutil==5.9.8,Pygments==2.17.2,requests==2.31.0,setuptools==69.1.0,snowballstemmer==2.2.0,Sphinx==5.0.2,sphinx-bluebrain-theme==0.4.4,sphinxcontrib-applehelp==1.0.8,sphinxcontrib-devhelp==1.0.6,sphinxcontrib-htmlhelp==2.0.5,sphinxcontrib-jsmath==1.0.1,sphinxcontrib-qthelp==1.0.7,sphinxcontrib-serializinghtml==1.1.10,urllib3==2.2.1,wheel==0.42.0 | |
| 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. | |
| docs: OK (49.71=setup[41.74]+cmd[7.98] seconds) | |
| congratulations :) (49.82 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1710244489:section_tox [0K | |
| section_end:1710244489:step_script [0Ksection_start:1710244489: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=5897 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=1205841 responseStatus[0;m=201 Created token[0;m=64_4Eaye | |
| section_end:1710244492:upload_artifacts_on_success [0Ksection_start:1710244492: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:1710244493: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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Learn more about bidirectional Unicode characters
| [0KRunning with gitlab-runner 16.8.1 (a6097117)[0;m | |
| [0K on kubernetes Me7zLFRu, system ID: r_WxT1lHy8HIG7[0;m | |
| section_start:1710244397:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1710244397:resolve_secrets [0Ksection_start:1710244397: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:1710244397:prepare_executor [0Ksection_start:1710244397: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-me7zlfru-project-2354-concurrent-0-us02pym7 to be running, status is Pending | |
| Running on runner-me7zlfru-project-2354-concurrent-0-us02pym7 via cs-gitlab-runners-gitlab-runner-557b4c775c-8nsmw... | |
| section_end:1710244402:prepare_script [0Ksection_start:1710244402: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 48df6b9b as detached HEAD (ref is weji/ChangeLog)...[0;m | |
| [32;1mUpdating/initializing submodules recursively with git depth set to 100...[0;m | |
| [32;1mUpdated submodules[0;m | |
| section_end:1710244409:get_sources [0Ksection_start:1710244409: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:1710244410:step_script [0Ksection_start:1710244410: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=1205847 responseStatus[0;m=201 Created token[0;m=64_Yi9PM | |
| section_end:1710244412:upload_artifacts_on_success [0Ksection_start:1710244412:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| section_end:1710244412:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| [0KRunning with gitlab-runner 15.5.0 (0d4137b8)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1710244397:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1710244397:resolve_secrets [0Ksection_start:1710244397: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-executor3958570974, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 199941, build ref , job ID 1205844 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1205844, 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_J1205844_PROD_P2354_CP3_C4 | |
| Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcsim partition=prod qos= reservation= | |
| Not executing the chown -R | |
| sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS | |
| sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx] | |
| Submitted batch job 2080745 | |
| 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_J1205844_PROD_P2354_CP3_C4 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1205844 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1205844 --ntasks=1 --jobid=2080745 --cpus-per-task=6 --mem=30750M | |
| section_end:1710244401:prepare_executor [0Ksection_start:1710244401:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i4n1 via bbpv1.epfl.ch... | |
| section_end:1710244408:prepare_script [0Ksection_start:1710244408: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/J1205844/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out 48df6b9b as weji/ChangeLog...[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:1710244471:get_sources [0Ksection_start:1710244471: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/2024-03/externals/linux-rhel7-skylake/python/3.12.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.8.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.9.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.10.13 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.11.6 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/git/2.42.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/cmake/3.27.7 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/graphviz/8.0.5 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/intel-oneapi-mkl/2023.2.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/hpe-mpi/2.27.p1.hmpt | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/applications/linux-rhel7-skylake/neurodamus-neocortex/1.15-3.0.0-2.8.1 | |
| [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/J1205844/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:1710244480:section_venv[collapsed=true] [0KSetting up the virtual env | |
| [32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
| [32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
| [32;1m$ rm -rf "$CI_VENV"[0;m | |
| [32;1m$ python -mvenv "$CI_VENV"[0;m | |
| [32;1m$ source "$CI_VENV/bin/activate"[0;m | |
| [32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Requirement already satisfied: pip in ./venv/lib/python3.11/site-packages (23.2.1) | |
| Collecting pip | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/ba0/d021a166865d2/pip-24.0-py3-none-any.whl (2.1 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 2.1/2.1 MB 68.9 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/02f/a291a0471b3a1/setuptools-69.1.1-py3-none-any.whl (819 kB) | |
| ââââââââââââââââââââââââââââââââââââââ 819.3/819.3 kB 42.2 MB/s eta 0:00:00 | |
| Collecting wheel | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/55c/570405f142630/wheel-0.43.0-py3-none-any.whl (65 kB) | |
| ââââââââââââââââââââââââââââââââââââââââ 65.8/65.8 kB 12.1 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/J1205844/hpc/sim/neurodamus/venv | |
| Can't uninstall 'setuptools'. No files were found to uninstall. | |
| Attempting uninstall: pip | |
| Found existing installation: pip 23.2.1 | |
| Uninstalling pip-23.2.1: | |
| Successfully uninstalled pip-23.2.1 | |
| Successfully installed pip-24.0 setuptools-65.5.0 wheel-0.43.0 | |
| [32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Collecting tox | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/b03/754b6ee6dadc7/tox-4.14.1-py3-none-any.whl (155 kB) | |
| ââââââââââââââââââââââââââââââââââââââ 155.3/155.3 kB 15.9 MB/s eta 0:00:00 | |
| Collecting cachetools>=5.3.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/0ab/ad1021d3f8325/cachetools-5.3.3-py3-none-any.whl (9.3 kB) | |
| Collecting chardet>=5.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB) | |
| ââââââââââââââââââââââââââââââââââââââ 199.4/199.4 kB 14.1 MB/s eta 0:00:00 | |
| Collecting colorama>=0.4.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB) | |
| Collecting filelock>=3.13.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/57d/bda9b35157b05/filelock-3.13.1-py3-none-any.whl (11 kB) | |
| Collecting packaging>=23.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2dd/fb553fdf02fb7/packaging-24.0-py3-none-any.whl (53 kB) | |
| ââââââââââââââââââââââââââââââââââââââââ 53.5/53.5 kB 9.7 MB/s eta 0:00:00 | |
| Collecting platformdirs>=4.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/061/4df2a2f37e1a6/platformdirs-4.2.0-py3-none-any.whl (17 kB) | |
| Collecting pluggy>=1.3 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/7db/9f7b503d67d1c/pluggy-1.4.0-py3-none-any.whl (20 kB) | |
| Collecting pyproject-api>=1.6.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4c0/116d60476b078/pyproject_api-1.6.1-py3-none-any.whl (12 kB) | |
| Collecting virtualenv>=20.25 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/961/c026ac520bac5/virtualenv-20.25.1-py3-none-any.whl (3.8 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 3.8/3.8 MB 105.3 MB/s eta 0:00:00 | |
| Collecting distlib<1,>=0.3.7 (from virtualenv>=20.25->tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/034/db59a0b96f8ca/distlib-0.3.8-py2.py3-none-any.whl (468 kB) | |
| ââââââââââââââââââââââââââââââââââââââ 468.9/468.9 kB 36.7 MB/s eta 0:00:00 | |
| Installing collected packages: distlib, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
| Attempting uninstall: packaging | |
| Found existing installation: packaging 23.1 | |
| Not uninstalling packaging at /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-packaging-23.1-uqml2t/lib/python3.11/site-packages, outside environment /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205844/hpc/sim/neurodamus/venv | |
| Can't uninstall 'packaging'. No files were found to uninstall. | |
| Successfully installed cachetools-5.3.3 chardet-5.2.0 colorama-0.4.6 distlib-0.3.8 filelock-3.13.1 packaging-24.0 platformdirs-4.2.0 pluggy-1.4.0 pyproject-api-1.6.1 tox-4.14.1 virtualenv-20.25.1 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1710244720: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:1710244721: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 setuptools setuptools_scm wheel | |
| .pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205844/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True setuptools.build_meta | |
| .pkg: get_requires_for_build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205844/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True setuptools.build_meta | |
| .pkg: freeze> python -m pip freeze --all | |
| .pkg: packaging==24.0,pip==24.0,setuptools==69.1.0,setuptools-scm==8.0.4,typing_extensions==4.10.0,wheel==0.42.0 | |
| .pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205844/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True setuptools.build_meta | |
| 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/J1205844/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.0.1.dev18.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]/1999465/spack-stage/spack-stage-py-libsonata-0.1.25-ize5sebjka4rjtetqhgtcyqqq3qkbpui/spack-src,MorphIO @ file:///nvme/[MASKED]/1999465/spack-stage/spack-stage-py-morphio-3.3.6-ldbyc4finxjpb2srmufv63ymssplqotw/spack-src,mpi4py @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-mpi4py-3.1.4-x733hwb2he3bpi423fnogkrw4w33wehe/spack-src,MVDTool @ file:///nvme/[MASKED]/1999465/spack-stage/spack-stage-py-mvdtool-2.4.9-m44q3n5mmnqpfl52d7nvzru4w6chzm6a/spack-src,neurodamus==3.0.1.dev18,numpy @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-numpy-1.26.1-elr5pntecdmhfynrjk3actlxb4go2bua/spack-src,packaging @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-packaging-23.1-uqml2togm4tkpdvzr37r5dnsrpnd76j2/spack-src,pip==24.0,pluggy==1.4.0,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 @ 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,wheel==0.42.0 | |
| bbp-model: commands[0]> python -c 'import os; print(os.environ.get('"'"'HOC_LIBRARY_PATH'"'"', '"'"''"'"'))' | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205844/hpc/sim/neurodamus/core/hoc:/gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_oneapi-2023.2.0-skylake/neurodamus-neocortex-1.15-3.0.0-2.8.1-e55rfj/lib/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-1.4.0 -- /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205844/hpc/sim/neurodamus/.tox/bbp-model/bin/python | |
| cachedir: .tox/bbp-model/.pytest_cache | |
| rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205844/hpc/sim/neurodamus | |
| configfile: pyproject.toml | |
| plugins: forked-1.6.0 | |
| collecting ... collected 23 items | |
| tests/integration-e2e/test_cli_opts.py::test_save_restore_cli PASSED | |
| tests/integration-e2e/test_cli_opts.py::test_cli_prcellgid PASSED | |
| tests/integration-e2e/test_cli_opts.py::test_cli_disable_reports PASSED | |
| tests/integration-e2e/test_cli_opts.py::test_cli_keep_build PASSED | |
| tests/integration-e2e/test_cli_opts.py::test_cli_build_model PASSED | |
| tests/integration-e2e/test_cli_opts.py::test_cli_shm_transfer PASSED | |
| tests/integration-e2e/test_cli_opts.py::test_cli_lb_mode PASSED | |
| tests/integration-e2e/test_cli_opts.py::test_cli_output_path PASSED | |
| tests/integration-e2e/test_connection.py::test_add_synapses PASSED | |
| tests/integration-e2e/test_connection.py::test_config_error PASSED | |
| tests/integration-e2e/test_dry_run_workflow.py::test_dry_run_workflow PASSED | |
| tests/integration-e2e/test_dry_run_workflow.py::test_memory_load_balance_workflow PASSED | |
| tests/integration-e2e/test_error_handling.py::test_handling_neuron_exceptions PASSED | |
| tests/integration-e2e/test_loadbalance.py::test_loadbal_no_cx PASSED | |
| tests/integration-e2e/test_loadbalance.py::test_loadbal_subtarget PASSED | |
| tests/integration-e2e/test_loadbalance.py::test_load_balance_integrated PASSED | |
| tests/integration-e2e/test_loadbalance.py::test_multisplit PASSED | |
| tests/integration-e2e/test_loadbalance.py::test_loadbal_integration PASSED | |
| tests/integration-e2e/test_multicycle_runs.py::test_nodeset_target_generate_subtargets PASSED | |
| tests/integration-e2e/test_multicycle_runs.py::test_v5_sonata_multisteps PASSED | |
| tests/integration-e2e/test_multicycle_runs.py::test_usecase3_sonata_multisteps PASSED | |
| tests/integration-e2e/test_plugin.py::test_run_acell_circuit SKIPPED | |
| tests/integration-e2e/test_synapse_reader.py::test_gapjunction_sonata_reader PASSED | |
| =============================== warnings summary =============================== | |
| neurodamus/core/configuration.py:161 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205844/hpc/sim/neurodamus/neurodamus/core/configuration.py:161: DeprecationWarning: In 3.13 classes created inside an enum will not become a member. Use the `member` decorator to keep the current behavior. | |
| class AutoBalanceModeParams: | |
| -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html | |
| ============================= slowest 5 durations ============================== | |
| 55.92s call tests/integration-e2e/test_cli_opts.py::test_cli_lb_mode | |
| 52.06s call tests/integration-e2e/test_cli_opts.py::test_save_restore_cli | |
| 37.63s call tests/integration-e2e/test_cli_opts.py::test_cli_build_model | |
| 34.42s call tests/integration-e2e/test_loadbalance.py::test_load_balance_integrated | |
| 33.83s call tests/integration-e2e/test_loadbalance.py::test_multisplit | |
| ============= 22 passed, 1 skipped, 1 warning in 357.80s (0:05:57) ============= | |
| bbp-model: OK (702.90=setup[338.46]+cmd[0.62,363.82] seconds) | |
| congratulations :) (706.74 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1710245436:section_tox [0K | |
| section_end:1710245437:step_script [0Ksection_start:1710245437: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:1710245437: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:1710244397:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1710244397:resolve_secrets [0Ksection_start:1710244397: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-executor3981838060, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 199941, build ref , job ID 1205843 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1205843, 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_J1205843_PROD_P2354_CP2_C3 | |
| Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcsim partition=prod qos= reservation= | |
| Not executing the chown -R | |
| sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS | |
| sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx] | |
| Submitted batch job 2080744 | |
| 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_J1205843_PROD_P2354_CP2_C3 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1205843 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1205843 --ntasks=1 --jobid=2080744 --cpus-per-task=6 --mem=30750M | |
| section_end:1710244400:prepare_executor [0Ksection_start:1710244400:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i6n22 via bbpv1.epfl.ch... | |
| section_end:1710244409:prepare_script [0Ksection_start:1710244409: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/J1205843/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out 48df6b9b as weji/ChangeLog...[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:1710244416:get_sources [0Ksection_start:1710244416: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/2024-03/externals/linux-rhel7-skylake/python/3.12.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.8.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.9.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.10.13 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.11.6 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/git/2.42.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/cmake/3.27.7 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/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/J1205843/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:1710244422:section_venv[collapsed=true] [0KSetting up the virtual env | |
| [32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
| [32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
| [32;1m$ rm -rf "$CI_VENV"[0;m | |
| [32;1m$ python -mvenv "$CI_VENV"[0;m | |
| [32;1m$ source "$CI_VENV/bin/activate"[0;m | |
| [32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Requirement already satisfied: pip in ./venv/lib/python3.11/site-packages (23.2.1) | |
| Collecting pip | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/ba0/d021a166865d2/pip-24.0-py3-none-any.whl (2.1 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 2.1/2.1 MB 75.3 MB/s eta 0:00:00 | |
| Requirement already satisfied: setuptools in ./venv/lib/python3.11/site-packages (65.5.0) | |
| Collecting setuptools | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/02f/a291a0471b3a1/setuptools-69.1.1-py3-none-any.whl (819 kB) | |
| âââââââââââââââââââââââââââââââââââââ 819.3/819.3 kB 280.2 MB/s eta 0:00:00 | |
| Collecting wheel | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/55c/570405f142630/wheel-0.43.0-py3-none-any.whl (65 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 65.8/65.8 kB 225.9 MB/s eta 0:00:00 | |
| Installing collected packages: wheel, setuptools, pip | |
| Attempting uninstall: setuptools | |
| Found existing installation: setuptools 65.5.0 | |
| Uninstalling setuptools-65.5.0: | |
| Successfully uninstalled setuptools-65.5.0 | |
| Attempting uninstall: pip | |
| Found existing installation: pip 23.2.1 | |
| Uninstalling pip-23.2.1: | |
| Successfully uninstalled pip-23.2.1 | |
| Successfully installed pip-24.0 setuptools-69.1.1 wheel-0.43.0 | |
| [32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Collecting tox | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/b03/754b6ee6dadc7/tox-4.14.1-py3-none-any.whl (155 kB) | |
| ââââââââââââââââââââââââââââââââââââââ 155.3/155.3 kB 12.2 MB/s eta 0:00:00 | |
| Collecting cachetools>=5.3.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/0ab/ad1021d3f8325/cachetools-5.3.3-py3-none-any.whl (9.3 kB) | |
| Collecting chardet>=5.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB) | |
| ââââââââââââââââââââââââââââââââââââââ 199.4/199.4 kB 51.5 MB/s eta 0:00:00 | |
| Collecting colorama>=0.4.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB) | |
| Collecting filelock>=3.13.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/57d/bda9b35157b05/filelock-3.13.1-py3-none-any.whl (11 kB) | |
| Collecting packaging>=23.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2dd/fb553fdf02fb7/packaging-24.0-py3-none-any.whl (53 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 53.5/53.5 kB 238.2 MB/s eta 0:00:00 | |
| Collecting platformdirs>=4.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/061/4df2a2f37e1a6/platformdirs-4.2.0-py3-none-any.whl (17 kB) | |
| Collecting pluggy>=1.3 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/7db/9f7b503d67d1c/pluggy-1.4.0-py3-none-any.whl (20 kB) | |
| Collecting pyproject-api>=1.6.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4c0/116d60476b078/pyproject_api-1.6.1-py3-none-any.whl (12 kB) | |
| Collecting virtualenv>=20.25 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/961/c026ac520bac5/virtualenv-20.25.1-py3-none-any.whl (3.8 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 3.8/3.8 MB 123.7 MB/s eta 0:00:00 | |
| Collecting distlib<1,>=0.3.7 (from virtualenv>=20.25->tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/034/db59a0b96f8ca/distlib-0.3.8-py2.py3-none-any.whl (468 kB) | |
| âââââââââââââââââââââââââââââââââââââ 468.9/468.9 kB 277.1 MB/s eta 0:00:00 | |
| Installing collected packages: distlib, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
| Successfully installed cachetools-5.3.3 chardet-5.2.0 colorama-0.4.6 distlib-0.3.8 filelock-3.13.1 packaging-24.0 platformdirs-4.2.0 pluggy-1.4.0 pyproject-api-1.6.1 tox-4.14.1 virtualenv-20.25.1 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1710244439: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:1710244439: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 setuptools setuptools_scm wheel | |
| .pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True setuptools.build_meta | |
| .pkg: get_requires_for_build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True setuptools.build_meta | |
| .pkg: freeze> python -m pip freeze --all | |
| .pkg: packaging==24.0,pip==24.0,setuptools==69.1.0,setuptools-scm==8.0.4,typing_extensions==4.10.0,wheel==0.42.0 | |
| .pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True setuptools.build_meta | |
| 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/J1205843/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.0.1.dev18.tar.gz | |
| integration: freeze> python -m pip freeze --all | |
| integration: docopt==0.6.2,find-libpython==0.3.1,h5py==3.10.0,iniconfig==2.0.0,libsonata==0.1.25,MorphIO==3.3.7,neurodamus @ file:///gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.0.1.dev18.tar.gz#sha256=b82ee2df5132e086f241c73aa3fe2785ef9eb853100e5fd8391be9921183e1f5,NEURON==8.2.4,numpy==1.26.4,packaging==24.0,pip==24.0,pluggy==1.4.0,psutil==5.9.8,py==1.11.0,pytest==7.4.0,pytest-forked==1.6.0,scipy==1.12.0,setuptools==69.1.0,wheel==0.42.0 | |
| integration: commands[0]> ci/build_ndcore.sh /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/core | |
| + CORE_DIR=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/core | |
| + '[' -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/J1205843/hpc/sim/neurodamus/core/mod/ALU.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/core/mod/CoreNEURONArtificialCell.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/core/mod/HDF5reader.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/core/mod/netstim_inhpoisson.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/core/mod/SonataReportHelper.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/core/mod/SonataReports.mod /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/core/mod/VecStim.mod mods.tmp | |
| + cp -f _common/mod/DetAMPANMDA.mod _common/mod/DetGABAAB.mod _common/mod/gap.mod _common/mod/GluSynapse.mod _common/mod/netstim_inhpoisson.mod _common/mod/ProbAMPANMDA_EMS.mod _common/mod/ProbGABAAB_EMS.mod _common/mod/TTXDynamicsSwitch.mod _common/mod/VecStim.mod mods.tmp | |
| + nrnivmodl -incflags '-DDISABLE_REPORTINGLIB -DDISABLE_HDF5 -DDISABLE_MPI' mods.tmp | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/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/J1205843/hpc/sim/neurodamus | |
| Mod files: "mods.tmp/mods.tmp/ALU.mod" "mods.tmp/mods.tmp/CoreNEURONArtificialCell.mod" "mods.tmp/mods.tmp/DetAMPANMDA.mod" "mods.tmp/mods.tmp/DetGABAAB.mod" "mods.tmp/mods.tmp/gap.mod" "mods.tmp/mods.tmp/GluSynapse.mod" "mods.tmp/mods.tmp/HDF5reader.mod" "mods.tmp/mods.tmp/netstim_inhpoisson.mod" "mods.tmp/mods.tmp/ProbAMPANMDA_EMS.mod" "mods.tmp/mods.tmp/ProbGABAAB_EMS.mod" "mods.tmp/mods.tmp/SonataReportHelper.mod" "mods.tmp/mods.tmp/SonataReports.mod" "mods.tmp/mods.tmp/TTXDynamicsSwitch.mod" "mods.tmp/mods.tmp/VecStim.mod" | |
| Creating 'x86_64' directory for .o files. | |
| -> [32mCompiling[0m mod_func.cpp | |
| -> [32mNMODL[0m ../mods.tmp/ALU.mod | |
| -> [32mNMODL[0m ../mods.tmp/CoreNEURONArtificialCell.mod | |
| -> [32mNMODL[0m ../mods.tmp/DetAMPANMDA.mod | |
| Translating ALU.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/x86_64/ALU.c | |
| Thread Safe | |
| Translating CoreNEURONArtificialCell.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/x86_64/CoreNEURONArtificialCell.c | |
| Thread Safe | |
| Translating DetAMPANMDA.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/x86_64/DetAMPANMDA.c | |
| Warning: next_delay_weight undefined. (declared within VERBATIM?) | |
| Warning: next_delay_t undefined. (declared within VERBATIM?) | |
| Thread Safe | |
| -> [32mNMODL[0m ../mods.tmp/DetGABAAB.mod | |
| -> [32mNMODL[0m ../mods.tmp/gap.mod | |
| -> [32mNMODL[0m ../mods.tmp/GluSynapse.mod | |
| Translating DetGABAAB.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/x86_64/DetGABAAB.c | |
| Warning: next_delay_weight undefined. (declared within VERBATIM?) | |
| Warning: next_delay_t undefined. (declared within VERBATIM?) | |
| Thread Safe | |
| Translating gap.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/x86_64/gap.c | |
| Thread Safe | |
| Translating GluSynapse.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/x86_64/GluSynapse.c | |
| Warning: next_delay_weight undefined. (declared within VERBATIM?) | |
| Warning: next_delay_t undefined. (declared within VERBATIM?) | |
| Thread Safe | |
| -> [32mNMODL[0m ../mods.tmp/HDF5reader.mod | |
| -> [32mNMODL[0m ../mods.tmp/netstim_inhpoisson.mod | |
| -> [32mNMODL[0m ../mods.tmp/ProbAMPANMDA_EMS.mod | |
| Translating HDF5reader.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/x86_64/HDF5reader.c | |
| Translating netstim_inhpoisson.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/x86_64/netstim_inhpoisson.c | |
| Notice: Use of POINTER is not thread safe. | |
| Translating ProbAMPANMDA_EMS.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/x86_64/ProbAMPANMDA_EMS.c | |
| Notice: VERBATIM blocks are not thread safe | |
| Warning: POST_RESTORE_RESTART_FLAG undefined. (declared within VERBATIM?) | |
| Thread Safe | |
| Notice: ARTIFICIAL_CELL is a synonym for POINT_PROCESS which hints that it | |
| only affects and is affected by discrete events. As such it is not | |
| located in a section and is not associated with an integrator | |
| Notice: This mechanism cannot be used with CVODE | |
| Notice: A_AMPA discontinuity adjustment not available. | |
| Notice: B_AMPA discontinuity adjustment not available. | |
| Notice: A_NMDA discontinuity adjustment not available. | |
| Notice: B_NMDA discontinuity adjustment not available. | |
| Warning: dt undefined. (declared within VERBATIM?) | |
| Warning: next_delay_weight undefined. (declared within VERBATIM?) | |
| Warning: next_delay_t undefined. (declared within VERBATIM?) | |
| Notice: ARTIFICIAL_CELL is a synonym for POINT_PROCESS which hints that it | |
| only affects and is affected by discrete events. As such it is not | |
| located in a section and is not associated with an integrator | |
| Thread Safe | |
| -> [32mNMODL[0m ../mods.tmp/ProbGABAAB_EMS.mod | |
| -> [32mNMODL[0m ../mods.tmp/SonataReportHelper.mod | |
| -> [32mNMODL[0m ../mods.tmp/SonataReports.mod | |
| Translating ProbGABAAB_EMS.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/x86_64/ProbGABAAB_EMS.c | |
| Notice: This mechanism cannot be used with CVODE | |
| Notice: A_GABAA discontinuity adjustment not available. | |
| Notice: B_GABAA discontinuity adjustment not available. | |
| Notice: A_GABAB discontinuity adjustment not available. | |
| Notice: B_GABAB discontinuity adjustment not available. | |
| Warning: dt undefined. (declared within VERBATIM?) | |
| Warning: next_delay_weight undefined. (declared within VERBATIM?) | |
| Warning: next_delay_t undefined. (declared within VERBATIM?) | |
| Thread Safe | |
| Translating SonataReportHelper.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/x86_64/SonataReportHelper.c | |
| Thread Safe | |
| Translating SonataReports.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/x86_64/SonataReports.c | |
| Thread Safe | |
| -> [32mNMODL[0m ../mods.tmp/TTXDynamicsSwitch.mod | |
| -> [32mNMODL[0m ../mods.tmp/VecStim.mod | |
| -> [32mCompiling[0m ALU.c | |
| -> [32mCompiling[0m CoreNEURONArtificialCell.c | |
| Translating TTXDynamicsSwitch.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/x86_64/TTXDynamicsSwitch.c | |
| Thread Safe | |
| Translating VecStim.mod into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/x86_64/VecStim.c | |
| Thread Safe | |
| -> [32mCompiling[0m DetAMPANMDA.c | |
| -> [32mCompiling[0m DetGABAAB.c | |
| -> [32mCompiling[0m gap.c | |
| -> [32mCompiling[0m GluSynapse.c | |
| -> [32mCompiling[0m HDF5reader.c | |
| -> [32mCompiling[0m netstim_inhpoisson.c | |
| -> [32mCompiling[0m ProbAMPANMDA_EMS.c | |
| -> [32mCompiling[0m ProbGABAAB_EMS.c | |
| -> [32mCompiling[0m SonataReportHelper.c | |
| -> [32mCompiling[0m SonataReports.c | |
| -> [32mCompiling[0m TTXDynamicsSwitch.c | |
| -> [32mCompiling[0m VecStim.c | |
| => [32mLINKING[0m shared library ./libnrnmech.so | |
| => [32mLINKING[0m executable ./special LDFLAGS are: -pthread | |
| Successfully created x86_64/special | |
| + '[' '!' -f x86_64/special ']' | |
| + mkdir -p _lib | |
| + cp -f x86_64/libnrnmech.so _lib/ | |
| + cp -f /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/core/hoc/Cell.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/core/hoc/ConnectionUtils.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/core/hoc/defvar.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/core/hoc/fileUtils.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/core/hoc/Map.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/core/hoc/MorphIO.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/core/hoc/neurodamus.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/core/hoc/Report.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/core/hoc/RNGSettings.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/core/hoc/TPointList.hoc /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/core/hoc/TType.hoc _lib/ | |
| + cp -f _common/hoc/AMPANMDAHelper.hoc _common/hoc/DetAMPANMDAHelper.hoc _common/hoc/DetGABAABHelper.hoc _common/hoc/GABAABHelper.hoc _common/hoc/GluSynapseHelper.hoc _common/hoc/GluSynapseLegacyHelper.hoc _lib/ | |
| integration: commands[1]> pytest -x --forked tests/integration | |
| ============================= test session starts ============================== | |
| platform linux -- Python 3.11.6, pytest-7.4.0, pluggy-1.4.0 -- /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/.tox/integration/bin/python | |
| cachedir: .tox/integration/.pytest_cache | |
| rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus | |
| configfile: pyproject.toml | |
| plugins: forked-1.6.0 | |
| collecting ... collected 24 items | |
| tests/integration/test_cell.py::test_load_cell[C060114A7.asc] PASSED [ 4%] | |
| tests/integration/test_cell.py::test_load_cell[C060114A7.h5] PASSED [ 8%] | |
| tests/integration/test_cell.py::test_load_cell[merged_container.h5/C060114A7.h5] PASSED [ 12%] | |
| tests/integration/test_cell.py::test_morphio_read PASSED [ 16%] | |
| tests/integration/test_cell.py::test_create_cell PASSED [ 20%] | |
| tests/integration/test_cell.py::test_create_cell_2 PASSED [ 25%] | |
| tests/integration/test_cell.py::test_create_cell_3 PASSED [ 29%] | |
| tests/integration/test_cell.py::test_basic_system PASSED [ 33%] | |
| tests/integration/test_neuron.py::test_base_h PASSED [ 37%] | |
| tests/integration/test_sonata_config.py::test_parse_base PASSED [ 41%] | |
| tests/integration/test_sonata_config.py::test_SimConfig_from_sonata PASSED [ 45%] | |
| tests/integration/test_sonata_config.py::test_parse_seeds PASSED [ 50%] | |
| tests/integration/test_sonata_config.py::test_parse_modifications PASSED [ 54%] | |
| tests/integration/test_sonata_config.py::test_parse_connections PASSED [ 58%] | |
| tests/integration/test_sonata_config.py::test_parse_inputs PASSED [ 62%] | |
| tests/integration/test_sonata_output.py::test_sonata_logfile PASSED [ 66%] | |
| tests/integration/test_sonata_output.py::test_throw_spike_sort_order PASSED [ 70%] | |
| tests/integration/test_stimulus2.py::TestStimuli::test_sin PASSED [ 75%] | |
| tests/integration/test_stimulus2.py::TestStimuli::test_sin_long PASSED [ 79%] | |
| tests/integration/test_stimulus2.py::TestStimuli::test_add_pulses PASSED [ 83%] | |
| tests/integration/test_stimulus2.py::TestStimuli::test_noise PASSED [ 87%] | |
| tests/integration/test_stimulus2.py::TestStimuli::test_shot_noise PASSED [ 91%] | |
| tests/integration/test_stimulus2.py::TestStimuli::test_ornstein_uhlenbeck PASSED [ 95%] | |
| tests/integration/test_stimulus2.py::TestStimuli::test_stacked PASSED [100%] | |
| =============================== warnings summary =============================== | |
| .tox/integration/lib/python3.11/site-packages/neurodamus/core/configuration.py:161 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205843/hpc/sim/neurodamus/.tox/integration/lib/python3.11/site-packages/neurodamus/core/configuration.py:161: DeprecationWarning: In 3.13 classes created inside an enum will not become a member. Use the `member` decorator to keep the current behavior. | |
| class AutoBalanceModeParams: | |
| -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html | |
| ======================== 24 passed, 1 warning in 3.32s ========================= | |
| integration: OK (45.01=setup[34.78]+cmd[6.56,3.66] seconds) | |
| congratulations :) (45.12 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1710244484:section_tox [0K | |
| section_end:1710244484:step_script [0Ksection_start:1710244484: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:1710244486: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:1710244398:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1710244398:resolve_secrets [0Ksection_start:1710244398: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-executor3605328704, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 199941, build ref , job ID 1205846 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1205846, 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_J1205846_PROD_P2354_CP5_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 2080747 | |
| job state: PD | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1205846_PROD_P2354_CP5_C9 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1205846 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1205846 --ntasks=1 --jobid=2080747 --cpus-per-task=6 --mem=30750M | |
| section_end:1710244401:prepare_executor [0Ksection_start:1710244401:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i4n1 via bbpv1.epfl.ch... | |
| section_end:1710244403:prepare_script [0Ksection_start:1710244403: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/J1205846/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out 48df6b9b as weji/ChangeLog...[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:1710244466:get_sources [0Ksection_start:1710244466: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/2024-03/externals/linux-rhel7-skylake/python/3.12.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.8.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.9.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.10.13 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.11.6 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/git/2.42.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/cmake/3.27.7 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/graphviz/8.0.5 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/intel-oneapi-mkl/2023.2.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/hpe-mpi/2.27.p1.hmpt | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/applications/linux-rhel7-skylake/neurodamus-neocortex-multiscale/1.15-3.0.0-2.8.1 | |
| [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/J1205846/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:1710244475:section_venv[collapsed=true] [0KSetting up the virtual env | |
| [32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
| [32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
| [32;1m$ rm -rf "$CI_VENV"[0;m | |
| [32;1m$ python -mvenv "$CI_VENV"[0;m | |
| [32;1m$ source "$CI_VENV/bin/activate"[0;m | |
| [32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Requirement already satisfied: pip in ./venv/lib/python3.11/site-packages (23.2.1) | |
| Collecting pip | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/ba0/d021a166865d2/pip-24.0-py3-none-any.whl (2.1 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 2.1/2.1 MB 74.3 MB/s eta 0:00:00 | |
| Requirement already satisfied: setuptools in /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-setuptools-68.0.0-p3xbqx/lib/python3.11/site-packages (68.0.0) | |
| Collecting setuptools | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/02f/a291a0471b3a1/setuptools-69.1.1-py3-none-any.whl (819 kB) | |
| ââââââââââââââââââââââââââââââââââââââ 819.3/819.3 kB 41.5 MB/s eta 0:00:00 | |
| Collecting wheel | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/55c/570405f142630/wheel-0.43.0-py3-none-any.whl (65 kB) | |
| ââââââââââââââââââââââââââââââââââââââââ 65.8/65.8 kB 12.2 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/J1205846/hpc/sim/neurodamus/venv | |
| Can't uninstall 'setuptools'. No files were found to uninstall. | |
| Attempting uninstall: pip | |
| Found existing installation: pip 23.2.1 | |
| Uninstalling pip-23.2.1: | |
| Successfully uninstalled pip-23.2.1 | |
| Successfully installed pip-24.0 setuptools-65.5.0 wheel-0.43.0 | |
| [32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Collecting tox | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/b03/754b6ee6dadc7/tox-4.14.1-py3-none-any.whl (155 kB) | |
| ââââââââââââââââââââââââââââââââââââââ 155.3/155.3 kB 15.8 MB/s eta 0:00:00 | |
| Collecting cachetools>=5.3.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/0ab/ad1021d3f8325/cachetools-5.3.3-py3-none-any.whl (9.3 kB) | |
| Collecting chardet>=5.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB) | |
| ââââââââââââââââââââââââââââââââââââââ 199.4/199.4 kB 20.3 MB/s eta 0:00:00 | |
| Collecting colorama>=0.4.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB) | |
| Collecting filelock>=3.13.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/57d/bda9b35157b05/filelock-3.13.1-py3-none-any.whl (11 kB) | |
| Collecting packaging>=23.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2dd/fb553fdf02fb7/packaging-24.0-py3-none-any.whl (53 kB) | |
| ââââââââââââââââââââââââââââââââââââââââ 53.5/53.5 kB 9.7 MB/s eta 0:00:00 | |
| Collecting platformdirs>=4.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/061/4df2a2f37e1a6/platformdirs-4.2.0-py3-none-any.whl (17 kB) | |
| Collecting pluggy>=1.3 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/7db/9f7b503d67d1c/pluggy-1.4.0-py3-none-any.whl (20 kB) | |
| Collecting pyproject-api>=1.6.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4c0/116d60476b078/pyproject_api-1.6.1-py3-none-any.whl (12 kB) | |
| Collecting virtualenv>=20.25 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/961/c026ac520bac5/virtualenv-20.25.1-py3-none-any.whl (3.8 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 3.8/3.8 MB 105.8 MB/s eta 0:00:00 | |
| Collecting distlib<1,>=0.3.7 (from virtualenv>=20.25->tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/034/db59a0b96f8ca/distlib-0.3.8-py2.py3-none-any.whl (468 kB) | |
| ââââââââââââââââââââââââââââââââââââââ 468.9/468.9 kB 37.8 MB/s eta 0:00:00 | |
| Installing collected packages: distlib, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
| Attempting uninstall: packaging | |
| Found existing installation: packaging 23.1 | |
| Not uninstalling packaging at /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-packaging-23.1-uqml2t/lib/python3.11/site-packages, outside environment /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205846/hpc/sim/neurodamus/venv | |
| Can't uninstall 'packaging'. No files were found to uninstall. | |
| Successfully installed cachetools-5.3.3 chardet-5.2.0 colorama-0.4.6 distlib-0.3.8 filelock-3.13.1 packaging-24.0 platformdirs-4.2.0 pluggy-1.4.0 pyproject-api-1.6.1 tox-4.14.1 virtualenv-20.25.1 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1710244726: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:1710244726: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 setuptools setuptools_scm wheel | |
| .pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205846/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True setuptools.build_meta | |
| .pkg: get_requires_for_build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205846/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True setuptools.build_meta | |
| .pkg: freeze> python -m pip freeze --all | |
| .pkg: packaging==24.0,pip==24.0,setuptools==69.1.0,setuptools-scm==8.0.4,typing_extensions==4.10.0,wheel==0.42.0 | |
| .pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205846/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True setuptools.build_meta | |
| 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/J1205846/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.0.1.dev18.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]/1999465/spack-stage/spack-stage-py-libsonata-0.1.25-ize5sebjka4rjtetqhgtcyqqq3qkbpui/spack-src,MorphIO @ file:///nvme/[MASKED]/1999465/spack-stage/spack-stage-py-morphio-3.3.6-ldbyc4finxjpb2srmufv63ymssplqotw/spack-src,mpi4py @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-mpi4py-3.1.4-x733hwb2he3bpi423fnogkrw4w33wehe/spack-src,MVDTool @ file:///nvme/[MASKED]/1999465/spack-stage/spack-stage-py-mvdtool-2.4.9-m44q3n5mmnqpfl52d7nvzru4w6chzm6a/spack-src,neurodamus==3.0.1.dev18,numpy @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-numpy-1.26.1-elr5pntecdmhfynrjk3actlxb4go2bua/spack-src,packaging @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-packaging-23.1-uqml2togm4tkpdvzr37r5dnsrpnd76j2/spack-src,pip==24.0,pluggy==1.4.0,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 @ 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,wheel==0.42.0 | |
| bbp-model: commands[0]> python -c 'import os; print(os.environ.get('"'"'HOC_LIBRARY_PATH'"'"', '"'"''"'"'))' | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205846/hpc/sim/neurodamus/core/hoc:/gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_oneapi-2023.2.0-skylake/neurodamus-neocortex-1.15-3.0.0-2.8.1-qktybo/lib/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-1.4.0 -- /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205846/hpc/sim/neurodamus/.tox/bbp-model/bin/python | |
| cachedir: .tox/bbp-model/.pytest_cache | |
| rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205846/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 ============================== | |
| 52.36s call tests/scientific-ngv/test_ngv.py::test_vasccouplingB_radii | |
| (2 durations < 15s hidden. Use -vv to show these durations.) | |
| ============================== 1 passed in 54.08s ============================== | |
| bbp-model: OK (407.37=setup[347.73]+cmd[0.57,59.07] seconds) | |
| congratulations :) (411.16 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1710245146:section_tox [0K | |
| section_end:1710245146:step_script [0Ksection_start:1710245146: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:1710245147: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:1710244398:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1710244398:resolve_secrets [0Ksection_start:1710244398: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-executor1615996264, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 199941, build ref , job ID 1205845 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1205845, 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_J1205845_PROD_P2354_CP4_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 2080746 | |
| job state: PD | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1205845_PROD_P2354_CP4_C6 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1205845 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1205845 --ntasks=1 --jobid=2080746 --cpus-per-task=6 --mem=30750M | |
| section_end:1710244400:prepare_executor [0Ksection_start:1710244400:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i4n1 via bbpv1.epfl.ch... | |
| section_end:1710244408:prepare_script [0Ksection_start:1710244408: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/J1205845/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out 48df6b9b as weji/ChangeLog...[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:1710244471:get_sources [0Ksection_start:1710244471: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/2024-03/externals/linux-rhel7-skylake/python/3.12.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.8.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.9.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.10.13 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.11.6 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/git/2.42.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/cmake/3.27.7 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/graphviz/8.0.5 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/compilers/linux-rhel7-haswell/intel-oneapi-compilers/2023.2.1 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/intel-oneapi-mkl/2023.2.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/hpe-mpi/2.27.p1.hmpt | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/applications/linux-rhel7-skylake/py-bluepysnap/2.0.2 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/applications/linux-rhel7-skylake/neurodamus-neocortex/1.15-3.0.0-2.8.1 | |
| [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/J1205845/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:1710244487:section_venv[collapsed=true] [0KSetting up the virtual env | |
| [32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
| [32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
| [32;1m$ rm -rf "$CI_VENV"[0;m | |
| [32;1m$ python -mvenv "$CI_VENV"[0;m | |
| [32;1m$ source "$CI_VENV/bin/activate"[0;m | |
| [32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Requirement already satisfied: pip in ./venv/lib/python3.11/site-packages (23.2.1) | |
| Collecting pip | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/ba0/d021a166865d2/pip-24.0-py3-none-any.whl (2.1 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 2.1/2.1 MB 69.4 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/02f/a291a0471b3a1/setuptools-69.1.1-py3-none-any.whl (819 kB) | |
| ââââââââââââââââââââââââââââââââââââââ 819.3/819.3 kB 35.7 MB/s eta 0:00:00 | |
| Collecting wheel | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/55c/570405f142630/wheel-0.43.0-py3-none-any.whl (65 kB) | |
| ââââââââââââââââââââââââââââââââââââââââ 65.8/65.8 kB 12.2 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/J1205845/hpc/sim/neurodamus/venv | |
| Can't uninstall 'setuptools'. No files were found to uninstall. | |
| Attempting uninstall: pip | |
| Found existing installation: pip 23.2.1 | |
| Uninstalling pip-23.2.1: | |
| Successfully uninstalled pip-23.2.1 | |
| Successfully installed pip-24.0 setuptools-65.5.0 wheel-0.43.0 | |
| [32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Collecting tox | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/b03/754b6ee6dadc7/tox-4.14.1-py3-none-any.whl (155 kB) | |
| ââââââââââââââââââââââââââââââââââââââ 155.3/155.3 kB 15.7 MB/s eta 0:00:00 | |
| Collecting cachetools>=5.3.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/0ab/ad1021d3f8325/cachetools-5.3.3-py3-none-any.whl (9.3 kB) | |
| Collecting chardet>=5.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB) | |
| ââââââââââââââââââââââââââââââââââââââ 199.4/199.4 kB 14.2 MB/s eta 0:00:00 | |
| Collecting colorama>=0.4.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB) | |
| Collecting filelock>=3.13.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/57d/bda9b35157b05/filelock-3.13.1-py3-none-any.whl (11 kB) | |
| Collecting packaging>=23.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2dd/fb553fdf02fb7/packaging-24.0-py3-none-any.whl (53 kB) | |
| ââââââââââââââââââââââââââââââââââââââââ 53.5/53.5 kB 9.6 MB/s eta 0:00:00 | |
| Collecting platformdirs>=4.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/061/4df2a2f37e1a6/platformdirs-4.2.0-py3-none-any.whl (17 kB) | |
| Collecting pluggy>=1.3 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/7db/9f7b503d67d1c/pluggy-1.4.0-py3-none-any.whl (20 kB) | |
| Collecting pyproject-api>=1.6.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4c0/116d60476b078/pyproject_api-1.6.1-py3-none-any.whl (12 kB) | |
| Collecting virtualenv>=20.25 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/961/c026ac520bac5/virtualenv-20.25.1-py3-none-any.whl (3.8 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 3.8/3.8 MB 104.6 MB/s eta 0:00:00 | |
| Collecting distlib<1,>=0.3.7 (from virtualenv>=20.25->tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/034/db59a0b96f8ca/distlib-0.3.8-py2.py3-none-any.whl (468 kB) | |
| ââââââââââââââââââââââââââââââââââââââ 468.9/468.9 kB 25.7 MB/s eta 0:00:00 | |
| Installing collected packages: distlib, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
| Attempting uninstall: packaging | |
| Found existing installation: packaging 23.1 | |
| Not uninstalling packaging at /gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_gcc-12.3.0-skylake/py-packaging-23.1-uqml2t/lib/python3.11/site-packages, outside environment /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205845/hpc/sim/neurodamus/venv | |
| Can't uninstall 'packaging'. No files were found to uninstall. | |
| Successfully installed cachetools-5.3.3 chardet-5.2.0 colorama-0.4.6 distlib-0.3.8 filelock-3.13.1 packaging-24.0 platformdirs-4.2.0 pluggy-1.4.0 pyproject-api-1.6.1 tox-4.14.1 virtualenv-20.25.1 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1710244813: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:1710244813: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 setuptools setuptools_scm wheel | |
| .pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205845/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True setuptools.build_meta | |
| .pkg: get_requires_for_build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205845/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True setuptools.build_meta | |
| .pkg: freeze> python -m pip freeze --all | |
| .pkg: packaging==24.0,pip==24.0,setuptools==69.1.0,setuptools-scm==8.0.4,typing_extensions==4.10.0,wheel==0.42.0 | |
| .pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205845/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True setuptools.build_meta | |
| 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/J1205845/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.0.1.dev18.tar.gz | |
| bbp-model: freeze> python -m pip freeze --all | |
| bbp-model: attrs @ file:///nvme/[MASKED]/1999496/spack-stage/spack-stage-py-attrs-23.1.0-m43qi5v5os6yetyyxglmqeqtd7g776s7/spack-src,bluepysnap @ file:///nvme/[MASKED]/2046135/spack-stage/spack-stage-py-bluepysnap-2.0.2-d557wdugo3bzmnzqsz2bk2w65tztpr3i/spack-src,Bottleneck @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-bottleneck-1.3.7-reskjku2fhby75ljzxdozjw2l3w7ywov/spack-src,cached-property @ file:///nvme/[MASKED]/1998173/spack-stage/spack-stage-py-cached-property-1.5.2-4ra43fkav4led5iceclzwqkgfbqpigp2/spack-src,click @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-click-8.1.7-uppfa4dbkn3thlvfus7yusscvyx6jcbl/spack-src,contourpy @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-contourpy-1.0.7-zjyhvvw5jf6zl6ymi4izavk7qifgt74g/spack-src,cycler @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-cycler-0.11.0-rjj5clifiqnwny3vechb5v66hvaiy76y/spack-src,deprecation @ file:///nvme/[MASKED]/1998173/spack-stage/spack-stage-py-deprecation-2.1.0-qqtamvzujmbchjj24k5drbi753ovygnv/spack-src,docopt @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-docopt-0.6.2-noukz4jts6de5g3xamvap6n4mh7mmcsy/spack-src,fonttools @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-fonttools-4.39.4-z2lufuxxznv35oq32lldyarzx26e5k4o/spack-src,h5py @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-h5py-3.8.0-5woxna6nieu5jokc2tdxsfmolza6724e/spack-src,importlib-resources @ file:///nvme/[MASKED]/1999508/spack-stage/spack-stage-py-importlib-resources-5.12.0-tzns2fbqmiwlczz6jt4pxr3ycakrqvc7/spack-src,iniconfig==2.0.0,jsonschema @ file:///nvme/[MASKED]/1999496/spack-stage/spack-stage-py-jsonschema-4.17.3-bxp3bkjqpvyzgwf7sk2iew7kukpm7hib/spack-src,kiwisolver @ file:///nvme/[MASKED]/1999465/spack-stage/spack-stage-py-kiwisolver-1.4.5-eh2wcdfnihumaea4n2zlqf2speb7qh4z/spack-src,libsonata @ file:///nvme/[MASKED]/1999465/spack-stage/spack-stage-py-libsonata-0.1.25-ize5sebjka4rjtetqhgtcyqqq3qkbpui/spack-src,matplotlib @ file:///nvme/[MASKED]/1999465/spack-stage/spack-stage-py-matplotlib-3.8.1-gdsdw2ni2jkl4h5ctu7d3uc7zkukcgbt/spack-src,more-itertools @ file:///nvme/[MASKED]/1998173/spack-stage/spack-stage-py-more-itertools-9.1.0-j5cqgsrmywy3254zni76f3rd3xza4ond/spack-src,morph-tool @ file:///nvme/[MASKED]/2046135/spack-stage/spack-stage-py-morph-tool-2.9.1-fsdk5ta6k6og5iij4ut63w5qmmyr4var/spack-src,MorphIO @ file:///nvme/[MASKED]/1999465/spack-stage/spack-stage-py-morphio-3.3.6-ldbyc4finxjpb2srmufv63ymssplqotw/spack-src,mpi4py @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-mpi4py-3.1.4-x733hwb2he3bpi423fnogkrw4w33wehe/spack-src,MVDTool @ file:///nvme/[MASKED]/1999465/spack-stage/spack-stage-py-mvdtool-2.4.9-m44q3n5mmnqpfl52d7nvzru4w6chzm6a/spack-src,neurodamus==3.0.1.dev18,neurom @ file:///nvme/[MASKED]/2046135/spack-stage/spack-stage-py-neurom-3.2.4-6wbrfox5pcxfxt53aoo2tgl3aja26wwd/spack-src,numexpr @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-numexpr-2.8.4-wu4xk2pywd64hyhoqfr57fzxfbzuuj2y/spack-src,numpy @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-numpy-1.26.1-elr5pntecdmhfynrjk3actlxb4go2bua/spack-src,numpy-quaternion @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-numpy-quaternion-2021.11.4.15.26.3-n3ap27fwuc6c7emgakpydtlt7yvk7nhi/spack-src,packaging @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-packaging-23.1-uqml2togm4tkpdvzr37r5dnsrpnd76j2/spack-src,pandas @ file:///nvme/[MASKED]/1999465/spack-stage/spack-stage-py-pandas-1.5.3-zd4wiyt5mnihf5stkktnaatq7mb4xlqd/spack-src,Pillow @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pillow-10.0.0-ygox4axk4dznocekteux3ecwkyfjndzk/spack-src,pip==24.0,pluggy==1.4.0,psutil @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-psutil-5.9.5-wieplgkaapfkhmzgrsesk5s3h46l3rx4/spack-src,py==1.11.0,pyparsing @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pyparsing-3.0.9-v3agjtpvgnpemnowjrjcowiw2ksk4xke/spack-src,pyrsistent @ file:///nvme/[MASKED]/1998173/spack-stage/spack-stage-py-pyrsistent-0.19.3-lzzxq7szeqnnyawu4d363tyqva3jui2v/spack-src,pytest==7.4.0,pytest-forked==1.6.0,python-dateutil @ file:///nvme/[MASKED]/1999465/spack-stage/spack-stage-py-python-dateutil-2.8.2-deg2kve3zwqhool34wn4tgxk2shs543p/spack-src,pytz @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pytz-2023.3-nr5mf4btvdphj755hbmkq57as5rmwtun/spack-src,PyYAML @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-pyyaml-6.0-c3eqkahwrcjjvgo2irs4ocswyrgh2p64/spack-src,scipy @ file:///nvme/[MASKED]/2045970/spack-stage/spack-stage-py-scipy-1.11.3-dhxei7gha3wm6mobqp3urw6k4ovd7blx/spack-src,setuptools @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-setuptools-68.0.0-p3xbqxjqvq45co6xoirlfe5ydwive63k/spack-src/setuptools-68.0.0-py3-none-any.whl#sha256=11e52c67415a381d10d6b462ced9cfb97066179f0e871399e006c4ab101fc85f,six @ file:///nvme/[MASKED]/1997818/spack-stage/spack-stage-py-six-1.16.0-brkaopna2ofwxv7qsutpldwizeauixze/spack-src,spatial-index @ file:///nvme/[MASKED]/1999508/spack-stage/spack-stage-spatial-index-2.1.0-bqtjnwanv62gxruectalykhxx3iqdjwl/spack-src,tqdm @ file:///nvme/[MASKED]/1999465/spack-stage/spack-stage-py-tqdm-4.66.1-hskcxsqsus2dj2llmtici7mfycwmrmku/spack-src,wheel==0.42.0,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/J1205845/hpc/sim/neurodamus/core/hoc:/gpfs/bbp.cscs.ch/ssd/apps/bsd/2024-02-01/stage_applications/install_oneapi-2023.2.0-skylake/neurodamus-neocortex-1.15-3.0.0-2.8.1-e55rfj/lib/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-1.4.0 -- /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205845/hpc/sim/neurodamus/.tox/bbp-model/bin/python | |
| cachedir: .tox/bbp-model/.pytest_cache | |
| rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205845/hpc/sim/neurodamus | |
| configfile: pyproject.toml | |
| plugins: forked-1.6.0 | |
| collecting ... collected 27 items | |
| 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:161 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205845/hpc/sim/neurodamus/neurodamus/core/configuration.py:161: DeprecationWarning: In 3.13 classes created inside an enum will not become a member. Use the `member` decorator to keep the current behavior. | |
| class AutoBalanceModeParams: | |
| -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html | |
| ============================= slowest 5 durations ============================== | |
| 34.97s call tests/scientific/test_sonata_properties.py::test_input_resistance | |
| 32.97s call tests/scientific/test_sonata_properties.py::test_input_resistance_2 | |
| 21.38s call tests/scientific/test_simulation.py::test_v5_sonata_config | |
| (2 durations < 15s hidden. Use -vv to show these durations.) | |
| ============= 26 passed, 1 skipped, 1 warning in 182.86s (0:03:02) ============= | |
| bbp-model: OK (527.52=setup[337.27]+cmd[0.78,189.47] seconds) | |
| congratulations :) (532.86 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1710245362:section_tox [0K | |
| section_end:1710245362:step_script [0Ksection_start:1710245362: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:1710245363: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:1710244396:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1710244396:resolve_secrets [0Ksection_start:1710244396: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-executor919069554, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"] | |
| Runner ID 29, project root hpc, project name neurodamus | |
| Pipeline ID 199941, build ref , job ID 1205842 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1205842, 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_J1205842_PROD_P2354_CP1_C2 | |
| Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcsim partition=prod qos= reservation= | |
| Not executing the chown -R | |
| sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS | |
| sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx] | |
| Submitted batch job 2080743 | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J1205842_PROD_P2354_CP1_C2 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1205842 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcsim/J1205842 --ntasks=1 --jobid=2080743 --cpus-per-task=6 --mem=30750M | |
| section_end:1710244398:prepare_executor [0Ksection_start:1710244398:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Using git from spack modules | |
| Running on r1i6n22 via bbpv1.epfl.ch... | |
| section_end:1710244409:prepare_script [0Ksection_start:1710244409: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/J1205842/hpc/sim/neurodamus/.git/ | |
| [32;1mCreated fresh repository.[0;m | |
| [32;1mChecking out 48df6b9b as weji/ChangeLog...[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:1710244417:get_sources [0Ksection_start:1710244417: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/2024-03/externals/linux-rhel7-skylake/python/3.12.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.8.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.9.18 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.10.13 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/python/3.11.6 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/git/2.42.0 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/externals/linux-rhel7-skylake/cmake/3.27.7 | |
| /gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/2024-03/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/J1205842/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:1710244422:section_venv[collapsed=true] [0KSetting up the virtual env | |
| [32;1m$ cd "${PYTHON_PROJECT_DIR}"[0;m | |
| [32;1m$ CI_VENV="$(pwd)/venv"[0;m | |
| [32;1m$ rm -rf "$CI_VENV"[0;m | |
| [32;1m$ python -mvenv "$CI_VENV"[0;m | |
| [32;1m$ source "$CI_VENV/bin/activate"[0;m | |
| [32;1m$ python -mpip install --upgrade pip setuptools wheel[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Requirement already satisfied: pip in ./venv/lib/python3.11/site-packages (23.2.1) | |
| Collecting pip | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/ba0/d021a166865d2/pip-24.0-py3-none-any.whl (2.1 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 2.1/2.1 MB 76.7 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/02f/a291a0471b3a1/setuptools-69.1.1-py3-none-any.whl (819 kB) | |
| âââââââââââââââââââââââââââââââââââââ 819.3/819.3 kB 280.8 MB/s eta 0:00:00 | |
| Collecting wheel | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/55c/570405f142630/wheel-0.43.0-py3-none-any.whl (65 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 65.8/65.8 kB 228.0 MB/s eta 0:00:00 | |
| Installing collected packages: wheel, setuptools, pip | |
| Attempting uninstall: setuptools | |
| Found existing installation: setuptools 65.5.0 | |
| Uninstalling setuptools-65.5.0: | |
| Successfully uninstalled setuptools-65.5.0 | |
| Attempting uninstall: pip | |
| Found existing installation: pip 23.2.1 | |
| Uninstalling pip-23.2.1: | |
| Successfully uninstalled pip-23.2.1 | |
| Successfully installed pip-24.0 setuptools-69.1.1 wheel-0.43.0 | |
| [32;1m$ if [[ -n $PIP_PACKAGES ]]; then python -mpip install --upgrade $PIP_PACKAGES; fi[0;m | |
| Looking in indexes: https://bbpteam.epfl.ch/repository/devpi/simple | |
| Collecting tox | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/b03/754b6ee6dadc7/tox-4.14.1-py3-none-any.whl (155 kB) | |
| ââââââââââââââââââââââââââââââââââââââ 155.3/155.3 kB 16.2 MB/s eta 0:00:00 | |
| Collecting cachetools>=5.3.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/0ab/ad1021d3f8325/cachetools-5.3.3-py3-none-any.whl (9.3 kB) | |
| Collecting chardet>=5.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/e1c/f59446890a001/chardet-5.2.0-py3-none-any.whl (199 kB) | |
| ââââââââââââââââââââââââââââââââââââââ 199.4/199.4 kB 51.7 MB/s eta 0:00:00 | |
| Collecting colorama>=0.4.6 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4f1/d9991f5acc0ca/colorama-0.4.6-py2.py3-none-any.whl (25 kB) | |
| Collecting filelock>=3.13.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/57d/bda9b35157b05/filelock-3.13.1-py3-none-any.whl (11 kB) | |
| Collecting packaging>=23.2 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/2dd/fb553fdf02fb7/packaging-24.0-py3-none-any.whl (53 kB) | |
| âââââââââââââââââââââââââââââââââââââââ 53.5/53.5 kB 222.5 MB/s eta 0:00:00 | |
| Collecting platformdirs>=4.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/061/4df2a2f37e1a6/platformdirs-4.2.0-py3-none-any.whl (17 kB) | |
| Collecting pluggy>=1.3 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/7db/9f7b503d67d1c/pluggy-1.4.0-py3-none-any.whl (20 kB) | |
| Collecting pyproject-api>=1.6.1 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/4c0/116d60476b078/pyproject_api-1.6.1-py3-none-any.whl (12 kB) | |
| Collecting virtualenv>=20.25 (from tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/961/c026ac520bac5/virtualenv-20.25.1-py3-none-any.whl (3.8 MB) | |
| ââââââââââââââââââââââââââââââââââââââââ 3.8/3.8 MB 124.9 MB/s eta 0:00:00 | |
| Collecting distlib<1,>=0.3.7 (from virtualenv>=20.25->tox) | |
| Downloading https://bbpteam.epfl.ch/repository/devpi/root/pypi/%2Bf/034/db59a0b96f8ca/distlib-0.3.8-py2.py3-none-any.whl (468 kB) | |
| âââââââââââââââââââââââââââââââââââââ 468.9/468.9 kB 285.3 MB/s eta 0:00:00 | |
| Installing collected packages: distlib, pluggy, platformdirs, packaging, filelock, colorama, chardet, cachetools, virtualenv, pyproject-api, tox | |
| Successfully installed cachetools-5.3.3 chardet-5.2.0 colorama-0.4.6 distlib-0.3.8 filelock-3.13.1 packaging-24.0 platformdirs-4.2.0 pluggy-1.4.0 pyproject-api-1.6.1 tox-4.14.1 virtualenv-20.25.1 | |
| [32;1m$ section_end section_venv[0;m | |
| [0Ksection_end:1710244439: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:1710244439:section_tox [0KRunning Tox | |
| [32;1m$ python -mtox $TOX_OPTIONS[0;m | |
| flake8: install_deps> python -I -m pip install flake8-pyproject | |
| flake8: freeze> python -m pip freeze --all | |
| flake8: flake8==7.0.0,Flake8-pyproject==1.2.3,mccabe==0.7.0,pip==24.0,pycodestyle==2.11.1,pyflakes==3.2.0,setuptools==69.1.0,wheel==0.42.0 | |
| flake8: commands[0]> flake8 | |
| flake8: OK â in 6.76 seconds | |
| unit: install_deps> python -I -m pip install -r tests/requirements.txt | |
| .pkg: install_requires> python -I -m pip install setuptools setuptools_scm wheel | |
| .pkg: _optional_hooks> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205842/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True setuptools.build_meta | |
| .pkg: get_requires_for_build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205842/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True setuptools.build_meta | |
| .pkg: freeze> python -m pip freeze --all | |
| .pkg: packaging==24.0,pip==24.0,setuptools==69.1.0,setuptools-scm==8.0.4,typing_extensions==4.10.0,wheel==0.42.0 | |
| .pkg: build_sdist> python /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205842/hpc/sim/neurodamus/venv/lib/python3.11/site-packages/pyproject_api/_backend.py True setuptools.build_meta | |
| 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/J1205842/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.0.1.dev18.tar.gz | |
| unit: freeze> python -m pip freeze --all | |
| unit: docopt==0.6.2,h5py==3.10.0,iniconfig==2.0.0,libsonata==0.1.25,neurodamus @ file:///gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205842/hpc/sim/neurodamus/.tox/.tmp/package/1/neurodamus-3.0.1.dev18.tar.gz#sha256=0d401ff7a03a8aad9e4e2b65f3d6640e4c468b35e6a61b35cd1269e8abf9462b,numpy==1.26.4,packaging==24.0,pip==24.0,pluggy==1.4.0,psutil==5.9.8,py==1.11.0,pytest==7.4.0,pytest-forked==1.6.0,scipy==1.12.0,setuptools==69.1.0,wheel==0.42.0 | |
| unit: commands[0]> pytest tests/unit | |
| ============================= test session starts ============================== | |
| platform linux -- Python 3.11.6, pytest-7.4.0, pluggy-1.4.0 -- /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205842/hpc/sim/neurodamus/.tox/unit/bin/python | |
| cachedir: .tox/unit/.pytest_cache | |
| rootdir: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205842/hpc/sim/neurodamus | |
| configfile: pyproject.toml | |
| plugins: forked-1.6.0 | |
| collecting ... collected 79 items | |
| tests/unit/test_conn_manager.py::test_population_get PASSED [ 1%] | |
| tests/unit/test_conn_manager.py::test_population_store_order PASSED [ 2%] | |
| tests/unit/test_conn_manager.py::test_population_get_create_conn PASSED [ 3%] | |
| tests/unit/test_conn_manager.py::test_population_all_conns PASSED [ 5%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input0-expected0] PASSED [ 6%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input1-expected1] PASSED [ 7%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input2-expected2] PASSED [ 8%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input3-expected3] PASSED [ 10%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input4-expected4] PASSED [ 11%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input5-expected5] PASSED [ 12%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input6-expected6] PASSED [ 13%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input7-expected7] PASSED [ 15%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input8-expected8] PASSED [ 16%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input9-expected9] PASSED [ 17%] | |
| tests/unit/test_conn_manager.py::test_population_get_connections[test_input10-expected10] PASSED [ 18%] | |
| tests/unit/test_conn_manager.py::test_population_delete PASSED [ 20%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input0-expected0] PASSED [ 21%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input1-expected1] PASSED [ 22%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input2-expected2] PASSED [ 24%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input3-expected3] PASSED [ 25%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input4-expected4] PASSED [ 26%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input5-expected5] PASSED [ 27%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input6-expected6] PASSED [ 29%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input7-expected7] PASSED [ 30%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input8-expected8] PASSED [ 31%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input9-expected9] PASSED [ 32%] | |
| tests/unit/test_conn_manager.py::test_population_delete_group[test_input10-expected10] PASSED [ 34%] | |
| tests/unit/test_conn_manager.py::test_population_ids_match PASSED [ 35%] | |
| tests/unit/test_coords.py::test_coord_mapping1 PASSED [ 36%] | |
| tests/unit/test_coords.py::test_coord_mapping2 PASSED [ 37%] | |
| tests/unit/test_core_config.py::test_write_report_config PASSED [ 39%] | |
| tests/unit/test_core_config.py::test_write_sim_config PASSED [ 40%] | |
| tests/unit/test_dry_run.py::test_dry_run_distribution PASSED [ 41%] | |
| tests/unit/test_dry_run.py::test_retrieve_unique_metypes PASSED [ 43%] | |
| tests/unit/test_init_py_config.py::test_init_empty PASSED [ 44%] | |
| tests/unit/test_init_py_config.py::test_init_non_positional PASSED [ 45%] | |
| tests/unit/test_init_py_config.py::test_init_config_only PASSED [ 46%] | |
| tests/unit/test_init_py_config.py::test_init_pass_options PASSED [ 48%] | |
| tests/unit/test_init_py_config.py::test_init_first_args PASSED [ 49%] | |
| tests/unit/test_init_py_config.py::test_init_early_config_file PASSED [ 50%] | |
| tests/unit/test_nodeset.py::test_NodeSet_base PASSED [ 51%] | |
| tests/unit/test_nodeset.py::test_NodeSet_add PASSED [ 53%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges10-ranges20-expected0] PASSED [ 54%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges11-ranges21-expected1] PASSED [ 55%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges12-ranges22-expected2] PASSED [ 56%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges13-ranges23-expected3] PASSED [ 58%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges14-ranges24-expected4] PASSED [ 59%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges15-ranges25-expected5] PASSED [ 60%] | |
| tests/unit/test_nodeset.py::test_ranges_overlap[ranges16-ranges26-expected6] PASSED [ 62%] | |
| tests/unit/test_nodeset.py::test_ranges_vec_overlap[ranges10-vec0-expected0] PASSED [ 63%] | |
| tests/unit/test_nodeset.py::test_ranges_vec_overlap[ranges11-vec1-expected1] PASSED [ 64%] | |
| tests/unit/test_nodeset.py::test_ranges_vec_overlap[ranges12-vec2-expected2] PASSED [ 65%] | |
| tests/unit/test_nodeset.py::test_ranges_vec_overlap[ranges13-vec3-expected3] PASSED [ 67%] | |
| tests/unit/test_nodeset.py::test_ranges_vec_overlap[ranges14-vec4-expected4] PASSED [ 68%] | |
| tests/unit/test_nodeset.py::test_read_nodesets_from_file PASSED [ 69%] | |
| tests/unit/test_nodeset_target.py::test_get_local_gids PASSED [ 70%] | |
| tests/unit/test_pyutils.py::test_map_1 PASSED [ 72%] | |
| tests/unit/test_pyutils.py::test_map_other_data PASSED [ 73%] | |
| tests/unit/test_pyutils.py::test_map_duplicates PASSED [ 74%] | |
| tests/unit/test_pyutils.py::test_map_duplicates_struct PASSED [ 75%] | |
| tests/unit/test_pyutils.py::test_badly_formed PASSED [ 77%] | |
| tests/unit/test_pyutils.py::test_merge PASSED [ 78%] | |
| tests/unit/test_pyutils.py::test_merge_grouped PASSED [ 79%] | |
| tests/unit/test_pyutils.py::test_flatten_grouped PASSED [ 81%] | |
| tests/unit/test_replay_manager.py::test_replay_manager_sonata PASSED [ 82%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_flat_segment PASSED [ 83%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_pulse PASSED [ 84%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_pulse_diff_base[-1] PASSED [ 86%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_pulse_diff_base[0] PASSED [ 87%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_pulse_diff_base[1.5] PASSED [ 88%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_two_pulses PASSED [ 89%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_ramp PASSED [ 91%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_delay_ramp PASSED [ 92%] | |
| tests/unit/test_stimuli.py::TestStimuli::test_train PASSED [ 93%] | |
| tests/unit/test_target_intersection.py::test_targetspec_overlap_name PASSED [ 94%] | |
| tests/unit/test_target_intersection.py::test_populations_disjoint PASSED [ 96%] | |
| tests/unit/test_target_intersection.py::test_targetspec_overlap PASSED [ 97%] | |
| tests/unit/test_target_intersection.py::test_nodeset_target_intersect PASSED [ 98%] | |
| tests/unit/test_target_intersection.py::test_nodeset_gids PASSED [100%] | |
| =============================== warnings summary =============================== | |
| .tox/unit/lib/python3.11/site-packages/neurodamus/core/configuration.py:161 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcsim/J1205842/hpc/sim/neurodamus/.tox/unit/lib/python3.11/site-packages/neurodamus/core/configuration.py:161: DeprecationWarning: In 3.13 classes created inside an enum will not become a member. Use the `member` decorator to keep the current behavior. | |
| class AutoBalanceModeParams: | |
| -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html | |
| ======================== 79 passed, 1 warning in 0.87s ========================= | |
| flake8: OK (6.76=setup[5.51]+cmd[1.26] seconds) | |
| unit: OK (33.34=setup[32.05]+cmd[1.29] seconds) | |
| congratulations :) (40.22 seconds) | |
| [32;1m$ section_end section_tox[0;m | |
| [0Ksection_end:1710244479:section_tox [0K | |
| section_end:1710244479:step_script [0Ksection_start:1710244479: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:1710244481:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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