[gmx-users] mdrun in parallel

[Tsjerk Wassenaar]

Hi Alessandro,

With gromacs versions <4 you have to generate the .tpr file with
grompp using the flag -np 16 to be able to run on 16 processors.
But why not upgrade to gromacs 4.02 and get much better scaling?

Cheers,

Tsjerk

On Fri, Nov 21, 2008 at 12:06 PM,  <Alessandro.Maiorana at roma2.infn.it> wrote:
> Hi All,
>
> I'd need an help to run GROMACS 3.3.3 in parallel. I'm running mdrun in
> parallel using the command:
>
> mpirun -machinefile /storage1/home/rgr/machines_16 -np 16
> /storage2/rgr/software/gromacs/bin/mdrun_d -s min0.tpr -g min0.log -e
> min0.edr -o min0.trr -x min0.xtc -c min0.gro
>
> but the following error appear:
>
> Program mdrun_d, VERSION 3.3.3
> Source code file: init.c, line: 69
>
> Fatal error:
> run input file min0.tpr was made for 1 nodes,
>             while mdrun_d expected it to be for 16 nodes.
>
> Many thanks and regard
> Alessandro
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623