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

From: Vlad Cojocaru <>
Date: Mon, 01 Oct 2012 18:39:06 +0200


Thanks. This confirms our conclusion.
We found no problems on any number of cores that is lower or equal to
the number of frames to process.


On 10/01/2012 06:32 PM, Jason Swails wrote:
> On Mon, Oct 1, 2012 at 12:10 PM, Vlad Cojocaru <
>> wrote:
>> 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.
> does not support using more processors than you have frames,
> since it splits the workload by frame. Even though you could potentially
> scale past nframes by assigning the complex and receptor of the same frames
> to different cores (and this is before trying to call parallel external
> programs), the gain for such an approach was not worth the cost of
> programming.
> does handle non-multiple core counts, although it does so
> naively. For a 10-frame analysis, for instance, 5 cores will run 2 frames
> on each core. 6 cores will run 2 frames on 4 of the cores and just 1 frame
> on the other 2 (so you see virtually no speed-up relative to 5 cores).
> Similarly with 9 cores, 1 frame will be run on each of 9 cores, and 2
> frames will be run on the first core (so again, no speedup from 5 cores).
> However, it should work.
> 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,
> Does stall in parallel when the number of cores is 9 or
> fewer? Or is it only when nproc>nframes?
> Thanks!
> Jason

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]
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Received on Mon Oct 01 2012 - 10:00:03 PDT
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