On Jun 8, 2010, at 3:06 PM, Jeff Squyres wrote: > 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. > Hi,
this can be checked by looking at the Gromacs output file md.log. The second line should read something like Host: <somename> pid: <somepid> nodeid: 0 nnodes: 4 Lauren, you will want to ensure that nnodes is 4 in your case, and not 1. You can also easily test that without any input file by typing mpirun -np 4 mdrun -h and then should see NNODES=4, MYRANK=1, HOSTNAME=<...> NNODES=4, MYRANK=2, HOSTNAME=<...> NNODES=4, MYRANK=3, HOSTNAME=<...> NNODES=4, MYRANK=4, HOSTNAME=<...> ... Carsten > > 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/ > > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
