Update Phonopy and Phono3py installations #813
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
| # 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 | |
| PIP_CONSTRAINT: pip_constraint.txt | |
| 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: | | |
| echo "numpy<2" >> $PIP_CONSTRAINT | |
| python3 -m pip install wheel setuptools numpy scipy click matplotlib pyyaml spglib rdkit flake8 pytest pytest-cov requests | |
| - name: Install latest ASE from pypi | |
| run: | | |
| echo PIP_CONSTRAINT $PIP_CONSTRAINT | |
| 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 $pkg | egrep -q 'env/vars.sh$'; then | |
| mklvars=$( dpkg -L $pkg | egrep 'env/vars.sh$' ) | |
| break | |
| fi | |
| done | |
| if [ $( echo $mklvars | wc -w ) != 2 ]; then | |
| echo "wrong number of mkl setvars.sh '$mklvars'" 1>&2 | |
| exit 1 | |
| fi | |
| source $mklvars intel64 | |
| export PIP_CONSTRAINT=$PWD/$PIP_CONSTRAINT | |
| git clone https://github.com/phonopy/phonopy | |
| cd phonopy | |
| echo python3 -m pip install -e . -vvv | |
| python3 -m pip install -e . -vvv | |
| cd .. | |
| git clone https://github.com/phonopy/phono3py | |
| cd phono3py | |
| python3 -m pip install -e . -vvv | |
| cd .. | |
| - name: Install Quippy from PyPI | |
| run: python3 -m pip install quippy-ase | |
| - name: Install xTB (before things that need pandas like MACE and wfl, since it will break pandas-numpy compatibility by downgrading numpy) | |
| run: | | |
| conda install -c conda-forge xtb-python | |
| python3 -m pip install typing-extensions | |
| # install pandas now to encourage compatible numpy version after conda regressed it | |
| python3 -m pip install pandas | |
| - name: MACE | |
| run: | | |
| echo "search for torch version" | |
| set +o pipefail | |
| torch_version=$( 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: | | |
| 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 |