[gmx-users] parallel problem

Bert de Groot bgroot at gwdg.de
Fri Mar 1 15:11:38 CET 2002

David van der Spoel wrote:
> On Fri, 1 Mar 2002, Yuguang Mu wrote:
> >I do use
> > mpirun -c 2 mdrun -np 2  -s mini
> >But the problem is the same :
> >
> >Back Off! I just backed up mini.log to #mini.log#
> >Reading file mini.tpr, VERSION 3.0.5 (single precision)
> >Reading file mini.tpr, VERSION 3.0.5 (single precision)
> >Fatal error: run input file mini.tpr was made for 2 nodes,
> >             while mdrun expected it to be for 1 nodes.
> >[0] MPI Abort by user Aborting program !
> >[0] Aborting program!
> >    p4_error: latest msg from perror: No such file or directory
> Hm, apparently you are using MPICH. I don't know whether we have a MPICH
> expert in the audience?
> We've had some reports about MPICH before, but hitherto it has ended
> mostly in people moving to LAM...

mpich should work just as well. When you use the p4 device, you should specify
a configuration file that tells MPICH on which hosts it should run. When you've
compiled with the shared memory device enabled, it looks on the local host
by default, if such a file is not specified. It's all written in the manual!


Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de

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