GROMACS

GROMACS

GROMACS Benchmark Information

GROMACS benchPEP benchmark from Dept. of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, https://www.mpinat.mpg.de/grubmueller/bench

Performance is measured in the ns/day output given by the GROMACS .log files.

Results

• Performance analysis script
• Calculation:
  • OpenFabrics
  • UCX

Compiling GROMACS 2021.5

These instructions are for compiling GROMACS 2021.5 on ARCHER2 using the GCC compilers with OpenMP threading.

Extract the source code and prepare the environment.

Unpack the source

tar -xvf gromacs-2021.5.tar.gz

Then load the modules and set up the CPE 21.09 environment:

module load cpe/21.09
module swap PrgEnv-cray PrgEnv-gnu
module load cmake/3.21.3
export LD_LIBRARY_PATH=$CRAY_LD_LIBRARY_PATH:$LD_LIBRARY_PATH

If you wish to profile with CrayPat-lite, you will need to perform load the following modules instead:

module load cpe/21.09
module swap PrgEnv-cray PrgEnv-gnu
module load cmake/3.21.3
module load perftools-base
module load perftools-lite
export LD_LIBRARY_PATH=$CRAY_LD_LIBRARY_PATH:$LD_LIBRARY_PATH

Finally, set the following environment variables:

export CC=cc
export CXX=CC
export GROMACS_PREFIX=/path/to/install/location

where you should choose GROMACS_PREFIX to be the location you want to install the software to.

Configure, build and install

Move into the new GROMACS source code directory you just extracted, and create a build directory. Then move inside that.

cd gromacs-2021.5
mkdir build
cd build

Configure the CMake build:

cmake .. -DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_GPU=OFF -DGMX_X11=OFF -DGMX_DOUBLE=OFF -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_INSTALL_PREFIX=$GROMACS_PREFIX

Finally, build GROMACS and then install it to $GROMACS_PREFIX.

make -j 8
make install

This will produce the gmx_mpi executable in $GROMACS_PREFIX/bin to be used for the benchmarks.