AMBER Archive (2007)

Subject: Re: AMBER: OpenMPI on MacBook Pro -- problems

From: Mike Summers (summers_at_hhmi.umbc.edu)
Date: Fri Mar 02 2007 - 14:36:07 CST

David,

make test-parallel worked fine on a different MacBook in the lab, so I must
have something setup wrong on my laptop. I'll get back to you later after
I have a chance to sort this out.

Mike

On Fri, Mar 02, 2007 at 09:36:28AM -0800, David A. Case wrote:
> 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).
>
> Mike:
>
> 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
> simulations.
>
> 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
> parameter.]
>
>
> ...good luck...dave
>
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-- 

*********************************
Michael F. Summers
Department of Chemistry and Biochemistry
  and Howard Hughes Medical Institute
University of Maryland Baltimore County
1000 Hilltop Circle 
Baltimore, MD 21250

Phone: (410)-455-2527  
FAX:   (410)-455-1174
Email: summers_at_hhmi.umbc.edu
Web:   www.hhmi.umbc.edu
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