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

[Berk Hess]

> Date: Mon, 3 Nov 2008 10:33:41 -0500
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] gromacs-4: statring in parallel on solaris 8
> 
> 
> 
> 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.

The mdrun flag has been removed from mdrun a long time ago,
it was already gone in 3.3 (but mdrun does not check for incorrect
command line options).

> 
> > 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.

The is no multi-threading in 4.0.

Berk


> 
> -Justin
> 
> 
> > 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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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