Arkansas High Performace Computing Center [hpcwiki]

Several versions of the http://www.gromacs.org molecular dynamics program are installed. The most complete and latest is version 2023.2. Only the single precision version is installed at this time. The various computers are compared with the GMX50 water benchmark. As shown, the GPU version is much faster. Because of poor scaling over multiple GPUs, Gromacs is not approved for multiple GPU public-use servers. These results reflect four separate installations that are autoselected by the module at runtime. Multiple node runs are not yet tested and will require a machinefile and possibly -genv as shown in mpi. These versions are compiled with OpenMP but OMP_NUM_THREADS>1 on CPU-only nodes did not improve results.

Node Type                     GPU       NS/day  partition

32-core dual Intel 6130       none       2.645  comp
32-core dual Intel 6130       1xV100    16.242  gpu
64-core dual AMD 7543         none       7.057  acomp
64-core dual AMD 7543         1xA100    24.775  agpu

With $NC=32 or 64 physical cores:
CPU:

module load intel/23.0.0 python/intel-3.7.7 impi/21.8.0 mkl/22.1.0 gromacs/2023.2
OMP_NUM_THREADS=1 mpirun -np $NC gmx_mpi mdrun -resethway -npme 0 -notunepme -noconfout -nsteps 1000 -v -s  bench.tpr

Single GPU:

nvidia-smi -c 0  #shared mode#
module load gcc/11.2.1 cuda/12.1 impi/19.0.9 python/intel-3.7.7 gromacs/2023.2
OMP_NUM_THREADS=$NC gmx_mpi mdrun -nb gpu -resethway -npme 0 -notunepme -noconfout -nsteps 1000 -v -s  bench.tpr