On Wed, 2014-03-05 at 21:46 -0700, Ahmed Ayoub wrote:
> Hi Jason,
>
> Thanks for you answer.
> 1) The script runs in serial from the command line (MMPBSA.py) but the
> MMPBSA.py.MPI does not run in parallel.
And the results you get for 1 or 2 frames seem reasonable?
My best guess is that at _some_ point you are trying to use more CPUs
than you have frames to analyze. It would help to know what input file
you are trying to use.
What happens if you try fewer processors? Keep in mind if you are doing
normal mode calculations and reducing the number of frames analyzed via
normal modes (using the variables nmstartframe, nmendframe, etc.) then
you cannot use more processors than normal mode frames you're
analyzing...
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Mar 06 2014 - 05:00:02 PST
