[gmx-users] GROMACS 4.6v - Myrinet2000

[Justin Lemkul]

On Mon, Apr 8, 2013 at 2:28 AM, Hrachya Astsatryan <hrach at sci.am> wrote:

> Dear all,
>
> We have installed the latest version of Gromacs (version 4.6) on our
> cluster by the following step:
>
>  * cmake .. -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/**backup/sicnas/gromacs
>    -DGMX_BUILD_OWN_FFTW=ON -DGMX_PREFER_STATIC_LIBS=ON
>
>
With this command, you're building Gromacs' internal FFT rather than using
FFTW. Your performance will be much better if you use FFTW. See the
installation instructions for more information.

-Justin


> The interconnection of the cluster is Myrinet2000 and the driver is MX
> (and mpich 1.3.1).
>
> The job scripts (see below) and different simulations show that there is
> no adequate performance (usually it should be 2-3 time more).
>
> Could you, pls. help us to overcome the problem in order to get better
> performance?
>
> With regards,
> Hrach
>
> #PBS -l nodes=8:ppn=2
> ##PBS -l walltime=360:00
> #PBS -q armcluster
> #PBS -e 33mM_16_new.err
> #PBS -o 33mM_16_new.log
> ## Specify the shell to be bash
> #PBS -S /bin/bash
>
> export LD_LIBRARY_PATH=$LD_LIBRARY_**PATH:/backup/sicnas/gromacs/**
> lib:/opt/mpi/lib
>
> /opt/mpi/bin/mpirun -machinefile /backup/sicnas/npt101/machine -np 16
> /backup/sicnas/gromacs/bin/**mdrun_mpi -s /backup/sicnas/npt101/topol.**tpr
> -v
>
>
>
>
>
> --
> Hrachya Astsatryan
> Head of HPC Laboratory,
> Institute for Informatics and Automation Problems,
> National Academy of Sciences of the Republic of Armenia
> 1, P. Sevak str., Yerevan 0014, Armenia
> t: 374 10 284780
> f: 374 10 285812
> e: hrach at sci.am
> skype: tighra
> --
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>



-- 

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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