PySAGES installation notes

# PySAGES installation notes Collections of recipes for installing [PySAGES](https://github.com/SSAGESLabs/PySAGES) ### Installation of HOOMD and PySAGES using a conda environment in a PC *Requirements:* - A git installation - A conda installation (consider using [miniforge](https://github.com/conda-forge/miniforge) instead of miniconda) - CUDA (optional) if you have a Nvidia GPU *Steps:* 1. Create new conda environment ```sh conda activate pysages ``` 2. Activate your conda environment ```sh conda activate pysages ``` 3. Install hoomd ```sh conda install -c conda-forge hoomd ``` or if you have a GPU ```sh conda install -c conda-forge hoomd=*=*gpu* ``` 5. Get and build hoomd-dlext ```sh git clone https://github.com/SSAGESLabs/hoomd-dlext cd hoomd-dlext ./build.sh ``` ### Gotchas ### Installation of HOOMD and PySAGES on midway2 *Load required modules* ```sh module load python/anaconda-2021.05 module load gcc/10.2.0 cmake/3.15 cuda/11.2 eigen/3.3 ``` *Steps* 1. Create a conda environment ```sh conda create -n pysages ``` ```sh source activate pysages ``` 2. Install HOOMD required libraries ```sh conda install -c conda-forge pybind11 ``` ```sh conda install python=3.8 #[Downgrade for numba. If pybind11 installs python=3.10; numba installation may fail.] ``` 3. Download HOOMD source ```sh curl -O https://glotzerlab.engin.umich.edu/Downloads/hoomd/hoomd-v2.9.7.tar.gz tar -zxvf hoomd-v2.9.7.tar.gz cd hoomd-v2.9.7.tar.gz mkdir build cd build ``` 4. Install HOOMD ```sh PYTHON_EXECUTABLE=$(which python3) HOOMD_ROOT=$(${PYTHON_EXECUTABLE} -c 'import site; print(site.getsitepackages()[0])')` cmake ../ \ -DCMAKE_INSTALL_PREFIX=$HOOMD_ROOT \ -DCOPY_HEADERS=ON \ -DENABLE_CUDA=ON \ -DCMAKE_C_COMPILER=/software/gcc-10.2.0-el7-x86_64/bin/gcc\ -DCMAKE_CXX_COMPILER=/software/gcc-10.2.0-el7-x86_64/bin/g++ make -j 10 # On an interactive GPU node. make install ``` 5. Install HOOMD-dlext [currently minimum version is 3.16 (can be installed using source code or conda environment easily); midway2 max version is 3.15] ```sh git clone https://github.com/SSAGESLabs/hoomd-dlext source build.sh # Edit cuda path to cuda/11.2 on midway2 ``` 6. Install other required libraries and JAX ```sh conda install numpy numba ``` ```sh conda install -c conda-forge cupy ``` ```sh conda install gsd matplotlib ``` ```sh pip install --upgrade "jax[cuda11_pip]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html ``` 6. Install PySAGES ```sh git clone pysages cd to pysages pip install . ``` ### Installation of OpenMM and PySAGES using a conda environment on a Mac *Requirements:* - A git installation - A conda installation *Steps:* 1. Create new conda environment ```sh conda create -n pysages python=3 ``` 2. Activate your conda environment ```sh conda activate pysages ``` 3. Install OpenMM ```sh conda install -c conda-forge openmm ``` 4. Install other required libraries and JAX ```sh conda install -c conda-forge clang_osx-64 conda install -c conda-forge clangxx_osx-64 conda install -c conda-forge swig conda install -c conda-forge plum-dispatch conda install -c fastai fastcore conda install -c conda-forge numba pip install jax pip install jaxlib pip install --upgrade jaxlib ``` 5. Install openmm-dlext ```sh git clone https://github.com/pabloferz/openmm-dlext cd openmm-dlext cmake -S . -B build cmake --build build --target install ``` 6. Install PySAGES ```sh git clone https://github.com/SSAGESLabs/PySAGES.git cd PySAGES pip install . ``` ### Installation of OpenMM and PySAGES on midway2 *Load required modules* ```sh module load python/intel-2020.up1 module load gcc/10.2.0 cuda/11.2 ``` *Steps* 1. Create a conda environment ```sh conda create -n pysages-openmm ``` ```sh source activate pysages-openmm ``` 2. Install OpenMM using conda ```sh conda install -c omnia openmm ``` 3. Install jaxlib and jax cuda with pip ```sh pip install jaxlib ``` ```sh pip install --upgrade "jax[cuda11_pip]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html ``` 3. Download and install cmake/3.16 (may take few min) ```sh wget https://cmake.org/files/v3.16/cmake-3.16.0.tar.gz tar -zxvf cmake-3.16.0.tar.gz mkdir installed-files cmakeLocation=$(pwd) ./configure --prefix=$cmakeLocation/installed-files make install ``` 4. Install OpenMM-dlext [currently minimum version is 3.16] ```sh git clone https://github.com/SSAGESLabs/openmm-dlext.git $cmakeLocation/installed-files/bin/cmake -S . -B build $cmakeLocation/installed-files/bin/cmake --build build --target install ``` 5. Install PySAGES ```sh git clone pysages cd to pysages pip install . ``` 6. If it doesn't work, upgrade python (if prompted, upgrade openmm), then rerun jaxlib ```sh conda install python=3.9.10 ``` ```sh pip install --upgrade "jax[cuda11_pip]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html ``` 7. Re-install openmm-dlext. ```sh cd openmm-dlext rm -f -r build $cmakeLocation/installed-files/bin/cmake -S . -B build $cmakeLocation/installed-files/bin/cmake --build build --target install ``` 8. Re-install PySAGES ```sh cd pysages pip install . ``` 9. install cupy ```sh conda install cupy ``` ### Installation of PySAGES on midway3 Summary of [this discussion](https://github.com/SSAGESLabs/PySAGES/discussions/96) and [this discussion](https://github.com/SSAGESLabs/PySAGES/issues/316). 1. Load the modules: ``` module load pysages ``` 2. Then, if you want to use your own version of PySAGES, that environment can be cloned an modified with the following: ``` conda create --clone pysages-0.4.0 --name mypysages # clone the env conda activate mypysages cd PySAGES # move to your local version of github.com/SSAGESLabs/PySAGES pip install -e . # run inside pysages directory to get latest dev in editable mode pip install --upgrade jaxlib ``` 3. Then you are ready to submit PySAGES jobs. **NOTE.** In case you encounter a [`No GPU/TPU found, falling back to CPU` error](https://github.com/SSAGESLabs/PySAGES/discussions/96) upgrading both `jax` and `jaxlib` by using the following command ([see here for details](https://github.com/SSAGESLabs/PySAGES/discussions/96#discussioncomment-2841226)) should solve that: ``` pip install --upgrade pip ### OLDER (seems not to work anymore) ### # Installs the wheel compatible with Cuda 11.4+ and cudnn 8.2+ (deprecated). ### pip install "jax[cuda11_cudnn82]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html # CUDA 11 installation (this works as of 2023-08-01) # Note: wheels only available on linux. pip install --upgrade "jax[cuda11_pip]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html ```

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