AMBER Archive (2006)

Subject: Re: AMBER: Middlebury College Cluster and Amber 8

From: David A. Case (
Date: Fri Aug 11 2006 - 13:30:46 CDT

On Fri, Aug 11, 2006, Lubans, Peter S wrote:
> When I run mpdboot and specify that mpd should use either two processors on
> the local machine or one processor on each of two nodes (and set
> DO_PARALLEL="/opt/mpich2/mpich2-pgi-64/bin/mpiexec -n 2"), the parallel
> testing passes. However, if I tell the mpd system to use more than two
> processors (four on the headnode, two processors on each of two nodes, four
> processors on each of two nodes, etc) and set DO_PARALLEL to use the same
> number of processors, then one of the sander tests quits by calling
> MPI_Abort and complains that there must be more residues than processors.

This is not a problem...some test cases are small ones and cannot run on
large numbers of processors. As Bob Duke pointed out, there are other tests
available that will work on large numbers of processors.

> I tried to alleviate the situation by setting DO_PARALLEL to run more
> processes than the number of processors specified when I run mpdboot.

Sounds like a bad idea to me, and I am not surprised that you found problems
with this. I'm not sure how a program could exit gracefully from this
situation. For now, avoid requesting more processes than are specified
with mpdboot.

...good luck...dac

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