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

[Tom]

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
>
> ==================================================
>
>
>