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

[Justin Lemkul]

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

==================================================