Re: AMBER: OpenMPI on MacBook Pro -- problems

From: David A. Case <>
Date: Fri, 2 Mar 2007 09:36:28 -0800

On Fri, Mar 02, 2007, Mike Summers wrote:

> I'm having a strange problem using Amber9 with OpenMPI-1.1.4 on a MacBook Pro

> I have no problem running in MPI mode on our linux cluster, which has only 1G
> memory per node (compared to 2 G on the MacBook).


Just to be sure: are you saying that the *same* job fails on the Mac but runs
correctly on the Linux cluster? And does this job work OK in serial but not
in parallel?

Does the Mac version pass the test suite in parallel?

How many atoms are in your system?

[On a more general note, your system looks pretty dangerous (and may be
related to the error message you got). You are running at
constant pressure, but starting with irest=0. This is dangerous unless you
actually have equilibrated coordinates -- the general rule is to equilibrate
at constant volume, then use a restart to switch to constant pressure. Also,
the job plans to cool the system down to 0K at the end; this probably won't
work with constant pressure, since the calculation of pressure is very
unstable at low temperature. For this and other reasons, simulated annealing
runs that cool down to 0K generally don't work well for explicit solvent

Another wild guess: You file names are things like "capwat...". Do you want
to just solvate part of the system? If so, set ntb=0 and use the fcap

...good luck...dave

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Received on Sun Mar 04 2007 - 06:07:56 PST
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