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Subject: [OMPI users] Res: Res: Gromacs run in parallel
From: lauren (owenlany_at_[hidden])
Date: 2010-06-08 11:50:00


I saw Host: <somename> pid: <somepid> nodeid: 0 nnodes: 1 really it`s running in 1 node and All of you really undestood my problem, thanks But how can I fix it. How can I run 1 job in 4 nodes...? I really need help, I took a look in my files and erase all the errors and the implementations seem corect. From the beginning, please. `case all tutorials only explain the same thing that look right. And thanks very much for this help! ________________________________ De: Jeff Squyres <jsquyres_at_[hidden]> Para: Open MPI Users <users_at_[hidden]> Enviadas: Terça-feira, 8 de Junho de 2010 10:30:03 Assunto: Re: [OMPI users] Res: Gromacs run in parallel No, I'm sorry -- I wasn't clear. What I meant was, that if you run: mpirun -np 4 my_mpi_application 1. If you see a single, 4-process MPI job (regardless of how many nodes/servers it's spread across), then all is good. This is what you want. 2. But if you're seeing 4 independent 1-process MPI jobs (again, regardless of how many nodes/servers they are spread across), it's possible that you compiled your application with MPI implementation X and then used the "mpirun" from MPI implementation Y. You will need X==Y to make it work properly -- i.e., to see case #1, above. I mention this because your first post mentioned that you're seeing the same job run 4 times. This implied to me that you are running into case #2. If I misunderstood your problem, then ignore me and forgive the noise. On Jun 8, 2010, at 9:20 AM, Carsten Kutzner wrote: > 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 <ckutzne_at_[hidden]> > >> Para: Open MPI Users <users_at_[hidden]> > >> 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 > >>> users_at_[hidden] > >>> http://www.open-mpi.org/mailman/listinfo.cgi/users > >> > >> > >> > >> _______________________________________________ > >> users mailing list > >> users_at_[hidden] > >> http://www.open-mpi.org/mailman/listinfo.cgi/users > > > > > > -- > > Jeff Squyres > > jsquyres_at_[hidden] > > For corporate legal information go to: > > http://www.cisco.com/web/about/doing_business/legal/cri/ > > > > > > _______________________________________________ > > users mailing list > > users_at_[hidden] > > 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 > > > > > > _______________________________________________ > users mailing list > users_at_[hidden] > http://www.open-mpi.org/mailman/listinfo.cgi/users > -- Jeff Squyres jsquyres_at_[hidden] For corporate legal information go to: http://www.cisco.com/web/about/doing_business/legal/cri/ _______________________________________________ users mailing list users_at_[hidden] http://www.open-mpi.org/mailman/listinfo.cgi/users