During your installation, if you use --program-suffix=_mpi, so the mdrun_mpi will work. I suggest you to check the nodes of the cluster, probably try pbsnodes, on a master node no job may be run. Note that I do not know much about your information, so the (guessing) suggestion maybe not fit for your problems, just cause I once confused about why mine 4cpus barely used before too.
Best, lina ________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Carsten Kutzner [ckut...@gwdg.de] Sent: Thursday, July 08, 2010 4:04 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mpi run Hi Mahmoud, for anyone to be able to help you, you need to provide a lot more information, at least: - which mpi library are you using? - how did you compile and/or install Gromacs? - what commands do you use to run mdrun and what was the output of it? Best, Carsten On Jul 8, 2010, at 9:41 AM, nanogroup wrote: Dear GMX Users, I have a PC with 4 CPU, but the Gromacs only use one CPU. the command of mpiru works on linux; however, the command of mdrun_mpi does not work. Would you please help me how to set up the mdrun_mpi in Gromacs 4.0.4 Many thanks, Mahmoud -- gmx-users mailing list gmx-users@gromacs.org<mailto:gmx-users@gromacs.org> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
