Re: [AMBER] cpptraj.MPI running in 'ensemble' mode.

From: Jason Swails <>
Date: Sat, 9 Aug 2014 14:55:14 -0400

On Sat, Aug 9, 2014 at 2:28 PM, Jonathan Gough <>

> 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

You can try that and see if it speeds up your analyses.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Sat Aug 09 2014 - 12:00:03 PDT
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