Sorry for the missing information.
Well, I use only one node with four processors. When I say stop I means
that the out file is no longer updated (with tail -f command), even the
sander.MPI continue to appear in "top" command and no error message was
showed at all. I try use 3 processors and the same thing happened. I just
do not try 2 processors. As I said when I use only one processor (with
sander), the work finish well.
Regards!
2013/9/25 Jason Swails <jason.swails.gmail.com>
> On Wed, Sep 25, 2013 at 1:12 PM, Moacyr Comar <mcomjr.gmail.com> wrote:
>
> > Dear Amber users,
> >
> > I trying run a minimization of 20000 steps using sander.MPI but it failed
> > every time. I use CentOS 6.4, Amber 11 and AmberTools 1.5, When I use the
> > serial mode, the work finish well. However, in the parallel mode the
> > min.out stop at different step every time, that is, in the first try it
> > stop at 3100, in the second, 6300, in the third with a different value. I
> > use openmpi 1.6.5.
> >
>
> What do you mean by 'stop'? Does it stop and crash with an error message?
> Does it just stop producing output and hang forever? How many CPUs did
> you try using? Did you try using fewer? Are you using just 1 node?
> Multiple nodes? If you were using multiple nodes, does it start working
> if you reduce the number of processors to only use 1 node?
>
> We need as much information as possible to help.
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Prof. Dr. Moacyr Comar Junior
Universidade Federal de São João del Rei
Campus Centro-Oeste
Divinópolis - MG
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Received on Wed Sep 25 2013 - 11:30:02 PDT
