Gromacs Challenge

Owned by Ophir Maor
Last updated: Jun 08, 2020 by David Jaekyu Cho
3 min read

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions many groups are also using it for research on non-biological systems.

Some test cases to start with can be found here:

ftp://ftp.gromacs.org/pub/benchmarks/gmxbench-3.0.tar.gz

You can use any Gromacs version, more details to come.

For more information about Gromacs, refer to Gromacs docs at http://manual.gromacs.org/documentation/current/index.html.

 

In ISC20 Competition we will use two input files:

  • stmv

  • lignocellulose

Both are available to download via the teams box account and have to be run with -nsteps 100000.

Running Gromacs

To build Gromacs 2020.2 with CPU only

wget http://ftp.gromacs.org/pub/gromacs/gromacs-2020.2.tar.gz tar xfz gromacs-2020.2.tar.gz cd gromacs-2020.2 # <load compilers and MPI> mkdir build cd build cmake .. -DGMX_FFT_LIBRARY=mkl -DMKL_LIBRARIES=-mkl -DMKL_INCLUDE_DIR=$MKLROOT/include \ -DGMX_SIMD=AVX2_256 \ -DGMX_MPI=ON \ -DGMX_BUILD_MDRUN_ONLY=on \ -DBUILD_SHARED_LIBS=on \ -DCMAKE_INSTALL_PREFIX=<install path> \ -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx make -j 16 install

To build with GPU support

cmake .. -DGMX_FFT_LIBRARY=mkl -DMKL_LIBRARIES=-mkl -DMKL_INCLUDE_DIR=$MKLROOT/include \ -DGMX_SIMD=AVX2_256 \ -DGMX_MPI=ON \ -DGMX_GPU=ON \ -DGMX_BUILD_MDRUN_ONLY=on \ -DBUILD_SHARED_LIBS=on \ -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx \ -DCMAKE_INSTALL_PREFIX=$BASE/install-$MPI make -j 16 install

To run Gromacs with CPU only

mpirun <mpi flags> mdrun_mpi -v -s <inp> -nsteps 100000 -noconfout

To run Gromacs with GPU

Sample output:

Submission:

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