[gmx-users] gromacs-4: statring in parallel on solaris 8

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 3 16:33:41 CET 2008

DimitryASuplatov wrote:
> Hello,
> I have installed gromacs-4 on Solaris 8 with mpi support.
> I was very disappointed by the lack of -np option in grompp and mdrun.

The -np option is absent in grompp, as it is no longer necessary.  The -np flag 
is indeed present for mdrun, however.

> After reading the manual and the site I came to a conclusion that now we
> do not need to specify number of nodes via gromacs status file but
> instead use mpirun option only.
> Executing (for gromacs benchmarking set)
> grompp
> mpirun c0-5 mdrun_mpi -v
> starts six threads on six processors though output speed is the same as
> for a single-node run. No errors, no warnings.

I didn't think threading was supported yet, maybe I'm wrong.  But you can 
definitely use -np 6 with mdrun_mpi.


> So, am I doing wrong with gromacs parallelization or is this the problem
> of the Solaris MPI?
> Thank you.
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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