OpenMM Installation on Summit

openmm-summit.md

OpenMM

• Installation

  1. Download the package from GitHub

     git clone https://github.com/pandegroup/openmm.git 

  2. Load Anaconda module and create your own conda environment

  • python 2: . /sw/summit/python/2.7/anaconda2/5.3.0/etc/profile.d/conda.sh
  • python 3: . /sw/summit/python/3.7/anaconda3/5.3.0/etc/profile.d/conda.sh

  3. Install the dependencies, swig, numpy and cython

     • conda install swig numpy cython
     • (swig version 3+)

  4. Module load necessary packages

     • module load cmake
     • module load gcc/7.4.0
     • module load cuda/9.1.85

  5. Compile the code using cmake (version >= 3.12.0)

     cd openmm
     
     mkdir -p build_openmm
     
     cd build_openmm
     
     >>>Summit
     cmake .. -DCUDA_HOST_COMPILER=/sw/summit/gcc/7.4.0/bin/gcc -DCUDA_SDK_ROOT_DIR=/sw/summit/cuda/9.1.85/samples -DCUDA_TOOLKIT_ROOT_DIR=/sw/summit/cuda/9.1.85/ -DCMAKE_CXX_COMPILER=/sw/summit/gcc/7.4.0/bin/g++ -DCMAKE_C_COMPILER=/sw/summit/gcc/7.4.0/bin/gcc -DCMAKE_INSTALL_PREFIX=${openmm_install_path} 

     Set the variable CMAKE_INSTALL_PREFIX to the location where you want to install OpenMM

  6. Build the package

     make -j 40 
     
     make install 
     
     make PythonInstall

  7. Test the installation

     python -m simtk.testInstallation 
     make test

• Known issues

  1. A lower version (6.4.0) of gcc may result in no module found: simtk.
  2. A higher version gcc/8.1.0 may result in large/wrong Median difference from CPU platform from python -m simtk.testInstallation.

Credit goes to @hengma1001