Re: [AMBER] Problems with sander.MPI

From: Jason Swails <>
Date: Wed, 25 Sep 2013 13:18:52 -0400

On Wed, Sep 25, 2013 at 1:12 PM, Moacyr Comar <> 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 M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Sep 25 2013 - 10:30:03 PDT
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