[gmx-users] it is very slowly to run gromacs with OpenMPI

Vinson Leung lwhvinson1990 at gmail.com
Wed Oct 22 04:08:20 CEST 2014

Hi all. I rencently I try different MPI library to run gromacs and find
that unlike Intel MPI and MPICH (which is normally can reach nearly 100%
CPU utilization ), it only can reach 20% CPU utilization when  using
OpenMPI. It seriously contradict the offical Performance checklist (
http://www.gromacs.org/Documentation/Performance_checklist) which claims
that OpenMPI usually has good performance and causes little trouble :(

And I also got some message when I run with OpenMPI:

[cn3:28072] 9 more processes have sent help message
help-opal-shmem-mmap.txt / mmap on nfs
[cn3:28072] Set MCA parameter "orte_base_help_aggregate" to 0 to see all
help / error messages

Any idea?


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