[gmx-users] Procedure for running Gromacs in Parallel??

Vivek Raut vraut at CLEMSON.EDU
Wed Nov 19 20:11:01 CET 2003


I am trying to run one gromacs simulation in parallel. I have already done 
that on a single node, following the standard procedure & it worked fine. I 
now want to run the same simulation simultaneously on multiple processors ( 
I believe thats what is meant by running a job in parallel) so see the 
difference in speed & as well as accuracy  by comparing the two results.

I was going through the previous mails on users list... which confused me 
even more. Some mails say that "I have to run mdrun 'under' mpirun." I 
didn't find any command such as mpirun in gromacs. Some mentioned that we 
have to use "np= node numbers  & then -shuffle -sort in grompp command", 
and then run the "mdrun under mpirun".  It is still not clear to me what is 
exactly meant by that. I didnt imagine that running a parallel job can be 
so confusing!!!

Could anyone explain in detail, what commands exactly I need to use to make 
the simulation run in parallel, say on 10 nodes?

Also, how to check your node performance??... I want to see how the nodes 
perform after I start the parallel jobs. Which command should I use for this??

I appreciate your help in clearing my confusion.

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