Update usage.rst #108
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| name: GH Actions CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| - develop | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| namd-tests: | |
| if: github.repository == 'Becksteinlab/imdclient' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Build information | |
| run: | | |
| uname -a | |
| df -h | |
| ulimit -a | |
| # More info on options: https://github.com/conda-incubator/setup-miniconda | |
| - name: Install conda dependencies | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: "3.12" | |
| environment-file: devtools/conda-envs/test_env.yaml | |
| add-pip-as-python-dependency: true | |
| channels: conda-forge, defaults | |
| activate-environment: imdreader-integration-test | |
| auto-update-conda: true | |
| auto-activate-base: false | |
| show-channel-urls: true | |
| miniconda-version: latest | |
| - name: Install MDAnalysis version | |
| uses: MDAnalysis/install-mdanalysis@main | |
| with: | |
| version: "2.7.0" | |
| install-tests: true | |
| installer: conda | |
| shell: bash -l {0} | |
| - name: Install package | |
| run: | | |
| python --version | |
| python -m pip install . --no-deps | |
| - name: Python information | |
| run: | | |
| which python | |
| which pip | |
| pip list | |
| conda info | |
| conda list | |
| - name: Clone namd fork | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: amruthesht/namd-3.0 | |
| ref: IMDv3-dev | |
| path: namd | |
| - name: Build namd | |
| run: | | |
| cd namd | |
| tar xf charm-8.0.0.tar | |
| cd charm-8.0.0 | |
| ./build charm++ multicore-linux-x86_64 --with-production | |
| cd multicore-linux-x86_64/tests/charm++/megatest | |
| make | |
| cd ../../../../.. | |
| wget https://www.fftw.org/fftw-2.1.5.tar.gz | |
| tar xzf fftw-2.1.5.tar.gz | |
| cd fftw-2.1.5 | |
| ./configure --enable-float --enable-type-prefix --enable-static | |
| make | |
| sudo make install | |
| cd .. | |
| wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.6.13-linux-x86_64-threaded.tar.gz | |
| tar xzf tcl8.6.13-linux-x86_64-threaded.tar.gz | |
| mv tcl8.6.13-linux-x86_64-threaded tcl-threaded | |
| ./config Linux-x86_64-g++.simple --charm-arch multicore-linux-x86_64 --fftw-prefix "/usr/local" | |
| cd Linux-x86_64-g++.simple | |
| make | |
| sudo ln -s $PWD/namd3 /usr/local/bin/namd3 | |
| - name: Run namd tests | |
| run: | | |
| pytest -n auto -v --color=yes imdclient/tests/test_namd.py |