I know nothing about Gromacs, but you might want to ensure that your Gromacs was compiled with Open MPI. A common symptom of "mpirun -np 4 my_mpi_application" running 4 1-process MPI jobs (instead of 1 4-process MPI job) is that you compiled my_mpi_application with one MPI implementation, but then used the mpirun from a different MPI implementation.
On Jun 8, 2010, at 8:59 AM, lauren wrote: > > The version of Gromacs is 4.0.7. > This is the first time that I using Gromacs, then excuse me if I'm nonsense. > > Wich part of md.log output should I post? > after or before the input description? > > thanks for all, > and sorry > > De: Carsten Kutzner <ckut...@gwdg.de> > Para: Open MPI Users <us...@open-mpi.org> > Enviadas: Domingo, 6 de Junho de 2010 9:51:26 > Assunto: Re: [OMPI users] Gromacs run in parallel > > Hi, > > which version of Gromacs is this? Could you post the first lines of > the md.log output file? > > Carsten > > > On Jun 5, 2010, at 10:23 PM, lauren wrote: > >> sorry my english.. >> >> I want to know how can I run Gromancs in parallel! >> Because when I used >> >> mdrun & >> mpiexec -np 4 mdrun_mpi -v -deffnm em >> >> to run the minimization in 4 cores > all cores make the same job, again! >> They don't run together. >> I want all in parallel make the job faster. >> >> >> what could be wrong? >> >> thank's a lot! >> >> >> >> _______________________________________________ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users > > > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users -- Jeff Squyres jsquy...@cisco.com For corporate legal information go to: http://www.cisco.com/web/about/doing_business/legal/cri/
