[gmx-users] GROMACS 4.6v - Myrinet2000

[Szilárd Páll]

On Mon, Apr 8, 2013 at 1:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 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.
>

No, the GMX_BUILD_OWN_FFTW option will simply tell the build system to
download FFTW 3.3(.3?), build it, and link it statically against mdrun. I'm
just realizing that the naming of the option allows it to be confused with
GROMACS' built-in (=own) fftpack (which is typically at 2-3x+ slower).

Unfortunately, the install guide refers to the option as
-DGMX_BUILD_OWN_FFTW=ON which means that even Google can't find it.

http://www.gromacs.org/Documentation/Installation_Instructions#3.4.1._FFTW

Cheers,
--
Szilard


>
> -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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