Update Phonopy and Phono3py installations #803
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| # This is testing the python versions *other than* the | |
| # one in the QUIP Docker, which is 3.7.10 at the time | |
| # of writing this. Coverage is disabled. | |
| name: Python Package and tests | |
| # on all push actions AND can be triggered manually as well | |
| on: | |
| workflow_dispatch: | |
| pull_request: | |
| jobs: | |
| build-and-test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [ "3.9" ] | |
| max-parallel: 5 | |
| env: | |
| coverage-on-version: "3.9" | |
| use-mpi: True | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up python ${{ matrix.python-version }} via conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| - name: Check python version | |
| run: | | |
| which python3 | |
| python3 --version | |
| - name: Install dependencies from pip | |
| run: python3 -m pip install wheel setuptools "numpy<2" scipy click matplotlib pyyaml spglib rdkit flake8 pytest pytest-cov requests | |
| - name: Install latest ASE from gitlab | |
| run: | | |
| python3 -m pip install ase | |
| echo -n "ASE VERSION " | |
| python3 -c "import ase; print(ase.__file__, ase.__version__)" | |
| - name: Install intel-oneapi-mkl for phono3py | |
| run: | | |
| # based on | |
| # https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl-download.html?operatingsystem=linux&distributions=aptpackagemanager | |
| # download the key to system keyring | |
| wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB | gpg --dearmor | sudo tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null | |
| # add signed entry to apt sources and configure the APT client to use Intel repository: | |
| echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list | |
| sudo apt update | |
| sudo apt install intel-oneapi-mkl | |
| sudo apt install intel-oneapi-mkl-devel | |
| - name: Install phono3py from source | |
| run: | | |
| # find mklvars | |
| for pkg in $( apt list --installed | fgrep "installed" | fgrep "mkl" | sed "s#/.*##" ); do | |
| if dpkg -L $pkg | egrep -q 'vars.sh$'; then | |
| mklvars=$( dpkg -L $pkg | egrep 'vars.sh$' ) | |
| break | |
| fi | |
| done | |
| if [ -z $mklvars ]; then | |
| echo 'Failed to find *vars.sh in any pkg named *mkl*' | |
| exit 1 | |
| fi | |
| source $mklvars intel64 | |
| git clone https://github.com/phonopy/phonopy | |
| cd phonopy | |
| sed -i -e sed -e 's/\(requires.*"numpy\)"/\1<2"/' pyproject.toml | |
| cat pyproject.toml | |
| python3 -m pip install -e . -vvv | |
| cd .. | |
| git clone https://github.com/phonopy/phono3py | |
| cd phono3py | |
| sed -i -e sed -e 's/\(requires.*"numpy\)"/\1<2"/' pyproject.toml | |
| python3 -m pip install -e . -vvv | |
| python3 -m pip install -e . -vvv | |
| cd .. | |
| - name: Install Quippy from PyPI | |
| run: python3 -m pip install quippy-ase | |
| - name: Install xTB (before things that need pandas like MACE and wfl, since it will break pandas-numpy compatibility by downgrading numpy) | |
| run: | | |
| conda install -c conda-forge xtb-python | |
| python3 -m pip install typing-extensions | |
| # install pandas now to encourage compatible numpy version after conda regressed it | |
| python3 -m pip install pandas | |
| - name: MACE | |
| run: | | |
| echo "search for torch version" | |
| set +o pipefail | |
| torch_version=$( python3 -m pip install torch== 2>&1 | fgrep 'from versions' | sed -e 's/.* //' -e 's/)//' ) | |
| echo "found torch version $torch_version, installing cpu-only variant" | |
| python3 -m pip install torch==${torch_version}+cpu -f https://download.pytorch.org/whl/torch_stable.html | |
| echo "installing mace" | |
| python3 -m pip install git+https://github.com/ACEsuit/mace.git@main | |
| python3 -c "import mace; print(mace.__file__)" | |
| - name: Julia and ace fit | |
| run: | | |
| python3 -m pip install threadpoolctl | |
| wget https://julialang-s3.julialang.org/bin/linux/x64/1.8/julia-1.8.1-linux-x86_64.tar.gz | |
| tar xzf julia-1.8.1-linux-x86_64.tar.gz | |
| # note that this hardwires a particular compatible ACE1pack version | |
| echo 'using Pkg; pkg"registry add https://github.com/JuliaRegistries/General"; pkg"registry add https://github.com/JuliaMolSim/MolSim.git"; pkg"add [email protected], ACE1, JuLIP, IPFitting, ASE"' > ace1pack_install.jl | |
| ${PWD}/julia-1.8.1/bin/julia ace1pack_install.jl | |
| - name: Install wfl (expyre and universalSOAP are dependencies) | |
| run: python3 -m pip install . | |
| - name: Install Quantum Espresso | |
| run: | | |
| sudo apt-get install --no-install-recommends quantum-espresso | |
| - name: Install MOPAC | |
| run: | | |
| wget https://github.com/openmopac/mopac/releases/download/v22.0.6/mopac-22.0.6-linux.tar.gz | |
| tar -xzvf mopac-22.0.6-linux.tar.gz | |
| - name: add mopac to path | |
| run: echo $GITHUB_WORKSPACE/mopac-22.0.6-linux/bin >> $GITHUB_PATH | |
| - name: Install buildcell | |
| run: | | |
| sudo apt-get install gfortran | |
| wget https://www.mtg.msm.cam.ac.uk/system/files/documents/airss-0.9.1.tgz | |
| tar xzf airss-0.9.1.tgz | |
| cd airss-0.9.1 | |
| make buildcell | |
| mkdir -p $HOME/bin | |
| cp src/buildcell/src/buildcell $HOME/bin/ | |
| cd .. | |
| - name: Add buildcell to system path | |
| run: | | |
| echo $HOME/bin >> $GITHUB_PATH | |
| - name: Install MPI dependencies | |
| if: env.use-mpi | |
| run: | | |
| # this can eaily be turned off if needed | |
| conda install -c conda-forge mpi4py openmpi pytest-mpi | |
| python3 -m pip install mpipool | |
| - name: Install and configure slurm and ExPyRe | |
| run: | | |
| sudo apt-get install -u slurm-wlm mailutils | |
| echo "SLURM apt-get done, doing local configuration" | |
| host_s=$( hostname -s ) | |
| if [ -f /etc/slurm/slurm.conf ]; then sudo mv /etc/slurm/slurm.conf /etc/slurm/slurm.conf.orig; fi | |
| sudo bash -c 'gzip -cd /usr/share/doc/slurmd/examples/slurm.conf.simple.gz > /etc/slurm/slurm.conf' | |
| # sudo sed -E -i -e "s/^\s*ClusterName\s*=.*/ClusterName=github_expyre_test/" /etc/slurm/slurm.conf | |
| sudo bash -c 'sed -E -i -e "s/^\s*SlurmctldHost\s*=.*/SlurmctldHost=_HOST_/" /etc/slurm/slurm.conf' | |
| # sudo sed -E -i -e "s/^\s*DefaultStorageHost\s*=.*/DefaultStorageHost=none" /etc/slurm/slurm.conf | |
| sudo bash -c 'echo "NodeName=_HOST_ CPUs=2 Weight=1 Sockets=1 CoresPerSocket=2 ThreadsPerCore=1 RealMemory=1000" >> /etc/slurm/slurm.conf' | |
| sudo bash -c 'echo "PartitionName=standard Default=YES AllocNodes=_HOST_ Nodes=ALL State=UP" >> /etc/slurm/slurm.conf' | |
| sudo sed -i -e "s/_HOST_/$host_s/g" /etc/slurm/slurm.conf | |
| sudo mkdir -p /var/log/slurm | |
| sudo mkdir -p /var/spool/slurmd | |
| sudo service slurmd start | |
| sudo service slurmctld start | |
| sleep 5 | |
| echo "sinfo -s --long" | |
| sinfo -s --long | |
| mkdir $HOME/.expyre | |
| cp .github/workflows_assets/config.json $HOME/.expyre | |
| - name: Set up pw.x for running in wfl | |
| run: | | |
| echo "which pw.x" | |
| which pw.x | |
| ls -l /usr/bin/pw.x | |
| export PYTEST_WFL_ASE_ESPRESSO_COMMAND=pw.x | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 wfl/ --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. | |
| flake8 wfl/ --count --exit-zero --max-complexity=20 --max-line-length=140 --ignore=E127,E128 --statistics | |
| - name: Test with pytest - plain | |
| if: env.coverage-on-version != matrix.python-version | |
| run: | | |
| rm -rf $HOME/pytest_plain | |
| mkdir $HOME/pytest_plain | |
| # | |
| export EXPYRE_PYTEST_SYSTEMS=github | |
| export WFL_PYTEST_BUILDCELL=$HOME/bin/buildcell | |
| export WFL_NUM_PYTHON_SUBPROCESSES=2 | |
| export OMP_NUM_THREADS=1 | |
| export WFL_JULIA_COMMAND=${PWD}/julia-1.8.1/bin/julia | |
| pytest --runremote --basetemp $HOME/pytest_plain -rxXs | |
| - name: Test with pytest - coverage | |
| if: env.coverage-on-version == matrix.python-version | |
| run: | | |
| echo "BOB pre actual pytest" | |
| which python3 | |
| python3 -m pip list | grep numpy | |
| python3 -c "import numpy; print(numpy.__file__, numpy.__version__)" | |
| rm -rf $HOME/pytest_cov | |
| mkdir $HOME/pytest_cov | |
| # | |
| export EXPYRE_PYTEST_SYSTEMS=github | |
| export WFL_PYTEST_BUILDCELL=$HOME/bin/buildcell | |
| export WFL_NUM_PYTHON_SUBPROCESSES=2 | |
| export OMP_NUM_THREADS=1 | |
| export WFL_JULIA_COMMAND=${PWD}/julia-1.8.1/bin/julia | |
| pytest -v --cov=wfl --cov-report term --cov-report html --cov-config=tests/.coveragerc --cov-report term-missing --cov-report term:skip-covered --runremote --basetemp $HOME/pytest_cov -rxXs | |
| # # DEBUGGING | |
| # - name: Setup tmate session | |
| # if: failure() | |
| # uses: mxschmitt/action-tmate@v3 | |
| # timeout-minutes: 15 | |
| - name: MPI tests -- plain | |
| if: ${{ env.use-mpi && env.coverage-on-version != matrix.python-version}} | |
| run: | | |
| # envvar and test run - No coverage | |
| export WFL_MPIPOOL=2 | |
| export WFL_NUM_PYTHON_SUBPROCESSES=2 | |
| export OMP_NUM_THREADS=1 | |
| mpirun -n 2 pytest --with-mpi -k mpi | |
| - name: MPI tests -- coverage | |
| if: ${{ env.use-mpi && env.coverage-on-version == matrix.python-version}} | |
| run: | | |
| # envvar and coverage Appended to the previous | |
| export WFL_MPIPOOL=2 | |
| export WFL_NUM_PYTHON_SUBPROCESSES=2 | |
| export OMP_NUM_THREADS=1 | |
| export WFL_JULIA_COMMAND=${PWD}/julia-1.8.1/bin/julia | |
| mpirun -n 2 pytest --cov=wfl --cov-report term --cov-config=tests/.coveragerc --cov-report term-missing --cov-report term:skip-covered --with-mpi -k mpi --cov-append | |
| - name: 'Upload Coverage Data' | |
| uses: actions/upload-artifact@v2 | |
| if: env.coverage-on-version == matrix.python-version | |
| with: | |
| name: coverage-html-${{ matrix.python-version }} | |
| path: coverage-html/ | |
| retention-days: 7 |