ahhhhhh
my bad. I just realized that OpenMP and MPI are different and not
interchangeable (synonymous-different programs that do the same thing).
compiling using -openmp now...
sorry.
On Fri, Jan 9, 2015 at 1:40 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> As stated in the Amber 14 manual (section "28.2.7 MPI Parallelization
> for 'ensemble'"), the MPI version of cpptraj is *only* supposed to be
> used with the 'ensemble' command (so e.g. on trajectories from a REMD
> simulation), wherein every member of the ensemble is assigned to a
> single MPI thread. Therefore, unless you are using the 'ensemble'
> command you will get zero benefit from using cpptraj.MPI (as you have
> seen). Section "28.2.6 OpenMP Parallelization" has a list of all
> actions and analyses that currently benefit from OpenMP, including
> 2drms and cluster (pair-wise distances calculation and sieved frame
> restore only).
>
> Also note that by default OpenMP will use all available threads, and
> depending on the action (and various other factors) this may not be
> optimal. If the OpenMP version seems slow for some reason you may need
> to restrict the number of threads via the OMP_NUM_THREADS environment
> variable. In such cases it is recommended that you run some short (~ 1
> min in length or so) tests to find what the optimal number of threads
> will be.
>
> -Dan
>
>
> On Fri, Jan 9, 2015 at 11:30 AM, Jonathan Gough
> <jonathan.d.gough.gmail.com> wrote:
> > Just a quick question,
> >
> > I observed that running either cluster or rms2d using cpptraj.MPI
> (compiled
> > with mpich2) was MUCH slower (orders of magnitude) than just using the
> > serial version.
> >
> > Is this an artifact of mpich2? are things faster with OpenMP?
> >
> > the trajectory is ~32GB, 432 residues, ~600,000 frames.
> >
> > I have run it on different machines (48cpu 132GB RAM vs. 8cpu 64GB RAM)
> and
> > gotten similar time lag results.
> >
> > any insight would be appreciated.
> >
> > Thanks,
> > Jonathan
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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
> (801) 585-6208 (Fax)
>
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Received on Fri Jan 09 2015 - 11:30:04 PST
