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

[Seaclear Theory]

Thanks for your help very much.

Best,

Ocean

On 12/21/06, Yang Ye <leafyoung81-group at yahoo.com> wrote:
>
> normally we use following commands when compiling gromacs
> ./configure ... --program_suffix=_mpi --enable-mpi ...
>
> So we will have mdrun_mpi in the end.
>
> The usage of mdrun_mpi is the same as mdrun but -np, -replex and other
> switches are activated.
>
> That statement on the user manual is to clarify that you don't need
> MPI-enabled mdrun to run on a multiprocessor machine. But if you want to
> tap the capability of the multiprocessor machine, you need to use MPI
> and use mdrun_mpi
>
> Regards,
> Yang Ye
>
> On 12/21/2006 4:20 PM, Seaclear Theory wrote:
> >
> >
> > On 12/20/06, *Mark Abraham* <Mark.Abraham at anu.edu.au
> > <mailto:Mark.Abraham at anu.edu.au>> wrote:
> >
> >     Seaclear Theory wrote:
> >     >
> >     >
> >     > On 12/20/06, *Mark Abraham* <Mark.Abraham at anu.edu.au
> >     <mailto:Mark.Abraham at anu.edu.au>
> >     > <mailto:Mark.Abraham at anu.edu.au
> >     <mailto:Mark.Abraham at anu.edu.au>>> wrote:
> >     >
> >     >     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.
> >     >
> >     >     So which part of the manual section entitled "Running GROMACS
> in
> >     >     parallel" doesn't work?
> >     >
> >     >
> >     > What I want is to  run  gromacs  on a signle  machine with
> multiple
> >     > processors.
> >     >
> >     > In "A.5 Running GROMACS in parallel"
> >     > "If you have a single machine with multiple processors you don't
> >     have to
> >     > use the mpirun command,
> >     > but you can do with an extra option to mdrun:
> >     > % mdrun -np 8 -s topol -v -N 8
> >     > In this example MPI reads the first option from the command
> >     line. Since
> >     > mdrun also wants to
> >     > know the number of processes you have to type it twice."
> >
> >     So what does it say? Should you be using mdrun_mpi? How about using
> a
> >     mpirun command anyway...
> >
> >     If you want meaningful feedback you need to describe your setup
> >     thoroughly, say what you've tried and why that didn't work and why
> >     the
> >     error messages didn't help you. Otherwise, you need to pay someone
> >     for a
> >     support contract :-) I'll help solve problems, but I won't help if
> you
> >     don't give the impression you're helping yourself too!
> >
> >     Mark
> >
> >
> > I do not understand  why you are so upset. Are you the author of the
> > user manual :-)  Any way, let's go back for the issue, not person.
> >
> > The user manual said that "you don't have to use the mpirun command"
> > if you want to run gromacs on a single machine with multiple
> > processors. How should I understand this? By the way, the manual (
> > v.3.3) and the reference does not have information about "mdrun_mpi".
> > Thanks.
> >
> > Ocean
> >
> >     _______________________________________________
> >     gmx-users mailing list    gmx-users at gromacs.org
> >     <mailto:gmx-users at gromacs.org>
> >     http://www.gromacs.org/mailman/listinfo/gmx-users
> >     <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
> >     <mailto:gmx-users-request at gromacs.org>.
> >     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > 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
>
>
> _______________________________________________
> 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/20061221/6e659909/attachment.html>