GROMACS
GROMACS is a versatile package to perform molecular dynamics. More information can be found here
Available containers
| Name | sha256 | mpi | labels | descripion |
|---|---|---|---|---|
| Singularity.gromacs-2021.3-intel-2021a.localimage.sif | 203ef1e9ee79b289b3091dad5208d2da7c550dcb0370a5ed2bbbaf4c26d86ae3 | IntelMPI 2021a | pmi2 | benchmark |
| Singularity.gromacs-2022-foss-2021b.localimage.sif | f42b5345ce2ca84abb728c378145ab0490f24a274980ba7299e4d3d4a4d42dfb | OpenMPI 4.1.2 | pmix | benchmark |
| Singularity.gromacs-2022-foss-2021b-CUDA-11.4.1.localimage.sif | 8da37e4c191edb53e1a1e49334d3b06c87f4ae7ec052b7617034f75a1c4a9177 | OpenMPI 4.1.2 | pmix |
Running the container
Example invocation of GROMACS benchmark
# Note: $PLCR is base path of container repository
export I_MPI_PMI_LIBRARY=$PLCR/local/pmi2/libpmi2.so
cd $TMPDIR
wget https://ftp.gromacs.org/pub/benchmarks/water_GMX50_bare.tar.gz
tar xzf water_GMX50_bare.tar.gz
cp water-cut1.0_GMX50_bare/3072/* .
srun --mpi=pmi2 --cpu-bind=cores singularity -s run -B $I_MPI_PMI_LIBRARY -B $PWD:/host_pwd --pwd /host_pwd $PLCR/images/$CONT gmx_mpi grompp -f pme.mdp -o bench.tpr
srun --mpi=pmi2 --cpu-bind=cores singularity -s run -B $I_MPI_PMI_LIBRARY -B $PWD:/host_pwd --pwd /host_pwd $PLCR/images/$CONT gmx_mpi mdrun -resethway -npme 0 -notunepme -noconfout -nsteps 1000 -v -s bench.tpr