[gmx-users] run gromacs on a single machine with mutiple CPUs

Seaclear Theory oceanclear at gmail.com
Thu Dec 21 08:41:13 CET 2006

Thanks for the guideline. I installed the lam/mpi 7.0.6 and compile the
gromance with "--enable-mpi" option.
When I run mdrun, I got message that lamboot is not start. Then I start the
lamboot and try to run mdrun witn "-np 4 -v N 4" (gromacs user guide
example). However, the gromacs still run on single CPU. It does not take the
advantage of other three CPUs on the server. Do I miss anything? Or I
misunderstand the parallel computing/MPI concept? Thanks.



On 12/20/06, Erik Lindahl <lindahl at cbr.su.se> wrote:
> Hi,
> On Dec 21, 2006, at 3:12 AM, Seaclear Theory wrote:
> > Hi! All,
> >
> > I have a linux server with 4 CPUs. How can I run gromacs on all CPUs?
> > The gromacs manual has very limit information. And it does not works.
> > I installed Lam/mpi and compile gromacs with mpi. Thanks lot!
> >
> The problem is that there is no standard for how you start MPI
> programs - that is entirely up to the MPI implementation.
> Essentially, add "-np 4" to grompp to get a parallel input file, boot
> your "virtual" parallel computer with "lamboot <hostfile>", and then
> start a parallel run as "mpirun -np 4 mdrun <normal args>".
> Most MPI libraries use mpirun is some form, but they differ in how
> you specify the machines to run on.
> Cheers,
> Erik
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> 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/20061220/beaf64ca/attachment.html>

More information about the gromacs.org_gmx-users mailing list