On Sat, Aug 9, 2014 at 2:28 PM, Jonathan Gough <jonathan.d.gough.gmail.com>
wrote:
> Dear All,
>
> Is there any documentation on what it means to run cpptraj in parallel? I
> got the error that it can only be run in ensemble mode. The Amber14.pdf
> only has the following:
>
> "Note that currently this version requires that each thread be assigned to
> a single member of the ensemble, i.e. the number of threads must equal the
> ensemble size."
>
> I can't seem to locate a AmberTools14.pdf.
>
It's all in the same manual now.
Best i can gather from the above is that you have to have the number of
> trajectories = to the number of MPI threads, is that correct?
>
Not quite.
> serial works fine, but would love to get things moving faster. Any insight
> would be appreciated.
>
"ensemble" is only for analyzing REMD simulations. If you're not using
REMD simulations, you should not be using ensemble. The number of threads
must be == to the number of replicas you are running.
MPI is fine for this task because each thread can take a different
temperature and run the analyses on that one replica. For analyzing a
single trajectory, though, MPI parallelization is not necessarily the best
way to go. As a result, Dan used OpenMP to parallelize cpptraj
calculations. The manual should have some details about which actions are
OMP-parallelized as well as information about how to compile OpenMP
programs.
You can try that and see if it speeds up your analyses.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Aug 09 2014 - 12:00:03 PDT
