[AMBER] parallel MMPBSA: no of cores versus no of frames analyzed

From: Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
Date: Mon, 01 Oct 2012 18:10:47 +0200

Dear AMBERs,

We are experiencing some issues with the parallel version of MMPBSA. We
use AMBER 12 on AMD Opterons (with 12 or 48 cores/node).
In a test with 9 frames to process, we noticed that the parallel MMPBSA
does not run on 12 cores (it hangs at the cpptraj step with no error).
We actually realized that it runs on a number of cores equal or lower
than the number of frames to analyze.

 From this test, we suspect that the number of frames to analyze has to
be a multiple of the number of cores to be used in the parallel MMPBSA run.

We could not find documentation regarding this issue so I would like to
confirm whether this is a known issue of the parallel MMPBSA.

Thank you for any clarifications on this issue,

Best wishes

Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
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Received on Mon Oct 01 2012 - 09:30:03 PDT
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