[gmx-users] MPI runs on a local computer

Xu, Jianqing xuj at MedImmune.com
Thu Sep 19 14:48:51 CEST 2013

Dear all,

I am learning the parallelization issues from the instructions on Gromacs website. I guess I got a rough understanding of MPI, thread-MPI, OpenMP. But I hope to get some advice about a correct way to run jobs.

Say I have a local desktop having 16 cores. If I just want to run jobs on one computer or a single node (but multiple cores), I understand that I don't have to install and use OpenMPI, as Gromacs has its own thread-MPI included already and it should be good enough to run jobs on one machine. However, for some reasons, OpenMPI has already been installed on my machine, and I compiled Gromacs with it by using the flag: "-DGMX_MPI=ON". My questions are:

1.       Can I still use this executable (mdrun_mpi, built with OpenMPI library) to run multi-core jobs on my local desktop? Or the default Thread-MPI is actually a better option for a single computer or single node (but multi-cores) for whatever reasons?

2.       Assuming I can still use this executable, let's say I want to use half of the cores (8 cores) on my machine to run a job,

mpirun -np 8 mdrun_mpi -v -deffnm md

a). Since I am not using all the cores, do I still need to "lock" the physical cores to use for better performance? Something like "-nt" for Thread-MPI? Or it is not necessary?

b). For running jobs on a local desktop, or single node having ...  say 16 cores, or even 64 cores, should I turn off the "separate PME nodes" (-npme 0)? Or it is better to leave as is?

3.       If I want to run two different projects on my local desktop, say one project takes 8 cores, the other takes 4 cores (assuming I have enough memory), I just submit the jobs twice on my desktop:

nohup mpirun -np 8 mdrun_mpi -v -deffnm md1 >& log1&

nohup mpirun -np 4 mdrun_mpi -v -deffnm md2 >& log2 &

Will this be acceptable ? Will two jobs be competing the resource and eventually affect the performance?

Sorry for so many detailed questions, but your help on this will be highly appreciated!

Thanks a lot,


To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.

More information about the gromacs.org_gmx-users mailing list