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

[Mark Abraham]

On Wed, Oct 22, 2014 at 4:08 AM, Vinson Leung <lwhvinson1990 at gmail.com>
wrote:

> 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 :(
>

What were your performance observations on another MPI program? I'll bet
the OpenMPI back end is not configured suitably for your hardware.

Mark

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?
> Thanks
>
> VIncent
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