[gmx-users] gromacs 5.1.2 MPI performance

Stephen Chan hcsinfo.2009 at googlemail.com
Thu Sep 8 13:09:10 CEST 2016


I am compiling an MPI version of gromacs 5.1.2 on a computer cluster. 
The compilation seems ok. However, when running MPI jobs, I got some issues:

1) mpirun -n 112 gmx_mpi grompp -f 0.mdp -o 0.tpr -n -c input.pdb
Certainly using 112 cores for a simple task doesn't make sense. The 
problem is the ouput 0.tpr was overwritten for ~ 16 times. Is it a sign 
that my gromacs hasn't enabled MPI?

2) Next, I got domain decomposition error (again...!) when running:
mpirun -n 112 gmx_mpi mdrun -s 0.tpr -x 1.xtc -g 1.log -v -c 1.gro >& 1.info
The issue resolved if i only used 8 cores. But the speed drops to 10+ 
ns/day which is far from ideal. I'm expecting ~100ns/day with 112 cores. 
Is there any other ways to boost the speed?

It would be nice if someone can give me some hints.


More information about the gromacs.org_gmx-users mailing list