Gromacs Challenge
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=$MKLROOT/include \
-DGMX_SIMD=AVX2_256 \
-DGMX_MPI=ON \
-DGMX_BUILD_MDRUN_ONLY=on \
-DBUILD_SHARED_LIBS=on \
-DCMAKE_INSTALL_PREFIX=<install path> \
-DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx
make -j 16 installTo build with GPU support
cmake .. -DGMX_FFT_LIBRARY=mkl -DMKL_LIBRARIES=-mkl -DMKL_INCLUDE_DIR=$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 installTo run Gromacs with CPU only
mpirun <mpi flags> mdrun_mpi -v -s <inp> -nsteps 100000 -noconfoutTo run Gromacs with GPU
Sample output:
Submission: