Is there a way to tell how many threads cpptraj.OMP is using?
On Fri, Jan 9, 2015 at 2:10 PM, Jonathan Gough <jonathan.d.gough.gmail.com>
wrote:
> 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
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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
>> (801) 585-6208 (Fax)
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Fri Jan 09 2015 - 12:00:03 PST
