{ai,bio}[foss/2024a] AlphaFold3 v3.0.0, jax-triton v0.2.0, jaxtyping v0.2.36, dm-tree v0.1.8 w/ CUDA 12.6.0 DRAFT! #39283
Workflow file for this run
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| name: easyconfigs unit tests | |
| on: [push, pull_request] | |
| permissions: | |
| contents: read # to fetch code (actions/checkout) | |
| concurrency: | |
| group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}} | |
| cancel-in-progress: true | |
| jobs: | |
| test-suite: | |
| runs-on: ubuntu-20.04 | |
| strategy: | |
| matrix: | |
| python: [3.6, '3.11'] | |
| modules_tool: [Lmod-7.8.22, Lmod-8.6.8] | |
| module_syntax: [Lua, Tcl] | |
| # exclude some configurations: only test Tcl module syntax with Lmod 8.x and Python 3.6 | |
| exclude: | |
| - modules_tool: Lmod-7.8.22 | |
| module_syntax: Tcl | |
| fail-fast: false | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 # Required for git merge-base to work | |
| - name: Cache source files in /tmp/sources | |
| id: cache-sources | |
| uses: actions/cache@v2 | |
| with: | |
| path: /tmp/sources | |
| key: eb-sourcepath | |
| - name: set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{matrix.python}} | |
| architecture: x64 | |
| - name: install OS & Python packages | |
| run: | | |
| # disable apt-get update, we don't really need it, | |
| # and it does more harm than good (it's fairly expensive, and it results in flaky test runs) | |
| # sudo apt-get update | |
| # for modules tool | |
| sudo apt-get install lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev | |
| # fix for lua-posix packaging issue, see https://bugs.launchpad.net/ubuntu/+source/lua-posix/+bug/1752082 | |
| # needed for Ubuntu 18.04, but not for Ubuntu 20.04, so skipping symlinking if posix.so already exists | |
| if [ ! -e /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so ] ; then | |
| sudo ln -s /usr/lib/x86_64-linux-gnu/lua/5.2/posix_c.so /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so | |
| fi | |
| # for testing OpenMPI-system*eb we need to have Open MPI installed | |
| sudo apt-get install libopenmpi-dev openmpi-bin | |
| # required for test_dep_graph | |
| pip install pep8 python-graph-core python-graph-dot | |
| - name: install EasyBuild framework | |
| run: | | |
| cd $HOME | |
| # first determine which branch of easybuild-framework repo to install | |
| BRANCH=develop | |
| if [ "x$GITHUB_BASE_REF" = 'xmain' ]; then BRANCH=main; fi | |
| if [ "x$GITHUB_BASE_REF" = 'x4.x' ]; then BRANCH=4.x; fi | |
| echo "Using easybuild-framework branch $BRANCH (\$GITHUB_BASE_REF $GITHUB_BASE_REF)" | |
| git clone -b $BRANCH --depth 10 --single-branch https://github.com/easybuilders/easybuild-framework.git | |
| cd easybuild-framework; git log -n 1; cd - | |
| pip install $PWD/easybuild-framework | |
| git clone -b $BRANCH --depth 10 --single-branch https://github.com/easybuilders/easybuild-easyblocks.git | |
| cd easybuild-easyblocks; git log -n 1; cd - | |
| pip install $PWD/easybuild-easyblocks | |
| - name: install modules tool | |
| run: | | |
| cd $HOME | |
| # use install_eb_dep.sh script provided with easybuild-framework | |
| export INSTALL_DEP=$(which install_eb_dep.sh) | |
| echo "Found install_eb_dep.sh script: $INSTALL_DEP" | |
| # install modules tool | |
| source $INSTALL_DEP ${{matrix.modules_tool}} $HOME | |
| # changes in environment are not passed to other steps, so need to create files... | |
| echo $MOD_INIT > mod_init | |
| echo $PATH > path | |
| if [ ! -z $MODULESHOME ]; then echo $MODULESHOME > moduleshome; fi | |
| - name: run test suite | |
| env: | |
| EB_VERBOSE: 1 | |
| EASYBUILD_MODULE_SYNTAX: ${{matrix.module_syntax}} | |
| run: | | |
| # pull in target so we can diff against it to obtain list of touched files | |
| if [ "x$GITHUB_BASE_REF" != 'xmain' ]; then git fetch -v origin ${GITHUB_BASE_REF}:${GITHUB_BASE_REF}; fi | |
| # initialize environment for modules tool | |
| if [ -f $HOME/moduleshome ]; then export MODULESHOME=$(cat $HOME/moduleshome); fi | |
| source $(cat $HOME/mod_init); type module | |
| # make sure 'eb' is available via $PATH, and that $PYTHONPATH is set (some tests expect that); | |
| # also pick up changes to $PATH set by sourcing $MOD_INIT | |
| WORKDIR=$GITHUB_WORKSPACE/easybuild-easyconfigs | |
| export PATH=$WORKDIR/test/bin:$(cat $HOME/path) | |
| export PYTHONPATH=$WORKDIR | |
| # tell EasyBuild which modules tool is available | |
| if [[ ${{matrix.modules_tool}} =~ ^modules-tcl- ]]; then | |
| export EASYBUILD_MODULES_TOOL=EnvironmentModulesTcl | |
| elif [[ ${{matrix.modules_tool}} =~ ^modules-3 ]]; then | |
| export EASYBUILD_MODULES_TOOL=EnvironmentModulesC | |
| elif [[ ${{matrix.modules_tool}} =~ ^modules-4 ]]; then | |
| export EASYBUILD_MODULES_TOOL=EnvironmentModules | |
| else | |
| export EASYBUILD_MODULES_TOOL=Lmod | |
| fi | |
| eb --version | |
| eb --show-config | |
| # gather some useful info on test system | |
| eb --show-system-info | |
| # run test suite | |
| # if tests failed, print error message that is picked up by boegelbot to determine end of test output | |
| python -O -m test.easyconfigs.suite || (echo "ERROR: Not all tests were successful" && exit 1) | |
| unset PYTHONPATH | |
| # install easyconfigs via distribution package | |
| python setup.py sdist > /dev/null | |
| ls dist | |
| pip install dist/easybuild-easyconfigs*tar.gz > /dev/null | |
| # robot-paths value should not be empty, but have an entry that includes easybuild/easyconfigs subdir | |
| echo "eb --show-config" | |
| eb --show-config | tee eb_show_config.out | |
| grep "^robot-paths .*/easybuild/easyconfigs" eb_show_config.out | |
| # check whether some specific easyconfig files are found | |
| echo "eb --search 'TensorFlow-1.14.*.eb'" | |
| eb --search 'TensorFlow-1.14.*.eb' | tee eb_search_TF.out | |
| grep '/TensorFlow-1.14.0-foss-2019a-Python-3.7.2.eb$' eb_search_TF.out | |
| echo "eb --search '^foss-2019b.eb'" | |
| eb --search '^foss-2019b.eb' | tee eb_search_foss.out | |
| grep '/foss-2019b.eb$' eb_search_foss.out | |
| # try installing M4 with system toolchain (requires ConfigureMake easyblock + easyconfig) | |
| # use /tmp/sources because that has cached downloads (see cache step above) | |
| eb --prefix /tmp/$USER/$GITHUB_SHA --sourcepath /tmp/sources M4-1.4.18.eb | |
| test-sdist: | |
| runs-on: ubuntu-20.04 | |
| strategy: | |
| matrix: | |
| python: [3.6, '3.11'] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{matrix.python}} | |
| - name: Create source distribution | |
| run: python setup.py sdist | |
| - name: Inspect files included in source distribution | |
| working-directory: dist | |
| run: | | |
| tar xfz easybuild-easyconfigs*tar.gz | |
| cd easybuild-easyconfigs-*/ | |
| # .git folder should not be there in source tarball | |
| dot_git_files=$(find . -name .git) | |
| if [ -n "$dot_git_files" ]; then | |
| echo "Found .git folders in source tarball: $dot_git_files" && false | |
| else | |
| echo "No .git folders found in source tarball: OK" | |
| fi |