[gmx-users] help with poor performance on gromacs on Cray linux

[Mark Abraham]

That thread referred to the Cray compilers (these machines ship several),
but whether that is relevant we don't know. Showing the top and bottom .log
file chunks is absolutely critical if you want performance feedback.

Mark
On Jun 26, 2014 10:55 PM, "Tom" <dnaafm at gmail.com> wrote:

> Justin,
>
> I compared the peromance (the time spent for mdrun) using md.log files for
> the same simulatin run on Cary Linux and any other Linux system.
>
> I agree different hardware can have different performance.
> But these tests were run on the supper computer clusters with very good
> reputations of performance. The one on Cray is very slow.
>
> I am the first time to run gmc on Cray linux. I am doubting if there is any
> wrong for my installation.
>
> From the previous dissusion, gmx looks to have performance problem
> on Cray linux:
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-May/081473.html
>
> I am also wondering if the newest version solved this issue.
>
> Thanks!
>
> Thom
>
>
> >
> > Message: 2
> > Date: Mon, 23 Jun 2014 08:17:55 -0400
> > From: Justin Lemkul <jalemkul at vt.edu>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] help with poor performance on gromacs on Cray
> >         linux
> > Message-ID: <53A81AF3.7090401 at vt.edu>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> >
> >
> > On 6/23/14, 1:12 AM, Tom wrote:
> > > Dear Gromacs Developers and Experts:
> > >
> > > I noticed that the performance of gromacs on Cray linux clusters is
> only
> > > 36.7% of the normal.
> > >
> >
> > Normal what?  Another run on the same system?  You can't directly compare
> > different clusters with different hardware.
> >
> > >
> > > The following is the detail about the installation
> > > --------------------------
> > > CC=gcc FC=ifort F77=ifort CXX=icpc
> > > CMAKE_PREFIX_PATH=/opt/cray/modulefiles/cray-mpich/6.3.0
> > > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=OFF -DGMX_MPI=ON
> > > -DBUILD_SHARED_LIBS=off -DCMAKE_SKIP_RPATH=ON
> > > -DCMAKE_INSTALL_PREFIX=~/App/GROMACS
> > > make F77=gfortran
> > > make install
> > > ----------------------
> > >
> > > This is the bash_profile:
> > > ---------------------
> > > module swap PrgEnv-pgi PrgEnv-gnu
> > > module load cmake
> > > export PATH=/home/test/App/GROMACS/bin:$PATH
> > > -------------------------
> > >
> > > Is there any suggestion for my installation to improve the efficiency?
> > >
> >
> > More important is the output of the .log file from the simulation.  It
> > will tell
> > you where mdrun spent all its time.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 601
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> >
> >
> >
> --
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