Hi,
On Sat, Aug 9, 2014 at 12:55 PM, Jason Swails <jason.swails.gmail.com> wrote:
> "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.
Just to expand upon this a bit: the primary use of 'ensemble' is to
process/analyze REMD sims, but you could potentially use it to process
any ensemble of trajectories; just supply the 'nosort' keyword to
'ensemble' as you would with HREMD sims where no sorting is required.
It will still process everything in parallel, although the total # of
frames processed will be limited to whatever the shortest trajectory
in the ensemble is. Be advised this is advanced usage however, so
caveat emptor.
-Dan
>
> 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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
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Received on Sat Aug 09 2014 - 16:00:02 PDT
