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Some test cases to start with can be found at ftp://ftp.gromacs.org/pub/benchmarks/gmxbench-3.0.tar.gz.

Table of Contents

Build and Install Gromacs

Download the source code

Code Block
wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020.2.tar.gz

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Note: if you get hwloc error, comment out the following lines from the following file: /src/gromacs/hardware/hardwaretopology.cpp.

Code Block
//#        if GMX_HWLOC_API_VERSION < 0x00020000
//#            error "HWLOC library major version set during configuration is 1, but currently using version 2 headers"
//#        endif

Check the install directory for the file mdrun_mpi

Code Block
$ ls ../install/
bin  include  lib64  share
$ ls ../install/bin    
gmx-completion-mdrun_mpi.bash  mdrun_mpi

Build Gromacs with GPU support

Code Block
tar xfz gromacs-2020.2.tar.gz
cd gromacs-2020.2
module load intel/2019.5.281
module load mkl/2019.5.281
module load gcc/8.4.0
module load cmake/3.13.4
module load hpcx/2.6.0
module load cuda/10.1
mkdir build 
mkdir install 
cd build
cmake .. -DGMX_FFT_LIBRARY=mkl -DMKL_LIBRARIES=-mkl \
        -DMKL_INCLUDE_DIR=$MKLROOT/include \
        -DGMX_SIMD=AVX2_256 \
        -DGMX_MPI=ON \
        -DGMX_GPU=ON \
        -DGMX_BUILD_MDRUN_ONLY=on \
        -DBUILD_SHARED_LIBS=on \
        -DCMAKE_INSTALL_PREFIX=<install path>../install \        
        -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx
make -j 16 install

Run Gromacs

To run Gromacs with CPU only using stmv case

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