Re: [AMBER-Developers] incompatible processor requirements in parallel tests

From: Jason Swails <>
Date: Thu, 18 Feb 2010 15:59:30 -0500

On Thu, Feb 18, 2010 at 3:39 PM, Volodymyr Babin <> wrote:
> On Thu, February 18, 2010 15:17, Jason Swails wrote:
>> On Thu, Feb 18, 2010 at 3:07 PM, Volodymyr Babin <> wrote:
>>>> I checked in the new rules to Makefile.  People can feel free to
>>>> remove it if they think it's pointless.  But I agree with Lachele that
>>>> there should probably be some documentation about it (at least some
>>>> blurb in the README).
>>> The rules are very convenient indeed. Another option (less flexible,
>>> but potentially more automatic) would be to set -np inside the Makefile
>>> sh$ export DO_PARALLEL='command -np AMBER_NTHREADS'
>> The problem with this is that not all MPIs use the same flag to
>> represent the number of threads.  For instance, mpiexec for many MPIs
>> uses -n instead.  -c is another common option.
> But this is exactly what I was trying to illustrate: it could be
> either DO_PARALLEL='mpirun -n AMBER_NTHREADS' or
> 'mpiexec -c AMBER_NTHREADS' -- in both cases AMBER_NTHREADS would
> be substituted by the actual number later. This is not the "right"
> way (there is probably more than one anyway) -- just another possibility.

Ah, I see. I'd be interested to see how this would be implemented.
Probably setting AMBER_NTHREADS in each Run file, and DO_PARALLEL="cmd
-arg $AMBER_NTHREADS"? I think this is a good idea, especially if
results change slightly using different numbers of processors (which
I've seen a little doing tests with different numbers of processors).

All the best,

> Best,
> Volodymyr
> _______________________________________________
> AMBER-Developers mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER-Developers mailing list
Received on Thu Feb 18 2010 - 13:30:02 PST
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