[gmx-users] Gromacs 4 with mpi interface

Manik Mayur manik.mayur at gmail.com
Thu Dec 18 16:53:57 CET 2008

I am not sure that mdrun_mpi or for that matter mdrun with options -np 2
-multi 1 (I have a core 2 duo machine) is actually running the process
parallely, as the estimated time for completion for a simulation is the same
as without.

I have built open-mpi library, so do I have to make some changes at its
configuration level(even if I am using single machine with multiple core
processor)? Like adding localhost and the no. of nodes. If yes, then can
anybody help me with that.

Also, for the information, mdrum_mpi or mdrun with relevant options shows
NNODES=1. why?


On Thu, Dec 18, 2008 at 1:24 PM, Jussi Lehtola <jussi.lehtola at helsinki.fi>wrote:

> On Thu, 2008-12-18 at 01:03 +0530, Chitrita Dutta Roy wrote:
> > Can anyone give me a detailed notes on how to install gromacs 4 with
> > mpi feature..I am using Intel Q9300 and fedora 10.It's very urgent as
> > i am new to using gromacs plz give me as detailed note as possible..
> Just install using yum:
> # yum -y install gromacs gromacs-mpi
> Due to some clashing names, all binaries have been renamed to start with
> g_, i.e. mdrun is g_mdrun and so on. Everything is compiled both in
> single and double precision, and MPI binaries are available of mdrun
> (and once the Makefiles are updated I'll put in also the MPI enabled
> analysis tools).
> Example:
> g_mdrun         single precision
> g_mdrun_d       double precision
> g_mdrun_mpi     single precision MPI
> g_mdrun_mpi_d   double precision MPI
> --
> ------------------------------------------------------
> Jussi Lehtola, FM, Tohtorikoulutettava
> Fysiikan laitos, Helsingin Yliopisto
> jussi.lehtola at helsinki.fi, p. 191 50632
> ------------------------------------------------------
> Mr. Jussi Lehtola, M. Sc., Doctoral Student
> Department of Physics, University of Helsinki, Finland
> jussi.lehtola at helsinki.fi
> ------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20081218/ee8d581c/attachment.html>

More information about the gromacs.org_gmx-users mailing list