Arkansas High Performace Computing Center [hpcwiki]

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.

=== Gromacs 2023.2/2023.3===

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 bare water benchmark [[https://ftp.gromacs.org/pub/benchmarks/]] . As shown below, the GPU version is much faster. Because of poor scaling over multiple GPUs, Gromacs is not approved on 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|mpi]]. These versions are compiled with OpenMP but OMP\_NUM\_THREADS>1 on CPU-only nodes did not improve results. ``gromacs/2023.3`` may also be selected in both CPU and GPU.  Performance appears similar. CPU version with gcc or GPU version with icx have not been compiled
  
<code>

Node Type                     GPU       NS/day  partition

32-core dual Intel 6130       none       3.021  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:

sudo nvidia-smi -c 0  #set 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
</code>

Arkansas High Performace Computing Center [hpcwiki]

User Tools

Site Tools

Page Tools