[gmx-users] Re: intel or gcc for opteron

[Myunggi Yi]

Thank you for the answer.

I compiled gmx with gcc and gnu onpempi.

I have seen very good performance with 16 cpus (about 12,000 atoms).

+++++++++++++++++++++++++++++++++++
               (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:     50.828     19.920     14.648      1.638
Total Scaling: 95% of max performance
+++++++++++++++++++++++++++++++++++

Now I just submit a job with 32 cpus (about 48,000 atoms).
It looks very very slow.


Would you recommend the optimal numer of cpus?




On Nov 24, 2007 10:53 AM, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Myunggi Yi wrote:
> > Sorry. Here is more information.
> >
> >
> > GNU C/C++     3.4.6
> > Intel C/C++   10.0.026
> > and
> > OpenMPI GNU   1.2.4
> > OpenMPI Intel         1.2.4
>
> Everything will probably be easier with the gcc compiler, and the
> performance difference is negligible for gromacs.
>
> >
> >
> >
> > On Nov 24, 2007 10:31 AM, Myunggi Yi <myunggi at gmail.com> wrote:
> >> Dear gromacs users,
> >>
> >> I'm a beginner.
> >> I'm trying to compile gromacs 3.3.1 or 3.3.2 on the following linux
> >> cluster (centOS).
> >> Dual, Dual-Core 2220 2.8 GHz Opterons, 2 GB RAM per core, 64-bit.
> >> I will use 16 to 32 (64) cpus for the parallel simulations.
> >>
> >> I tested mpich2, but there is a problem with infiniband communications.
> >>
> >> I have intel and GNU compilers and openMPI.
> >>
> >> Which option will give me the best performance?
> >>
> >> Have a nice weekend.
> >>
> >>
> >> --
> >> Best wishes,
> >>
> >> MYUNGGI YI
> >> ==================================
> >> KLB 419
> >> Institute of Molecular Biophysics
> >> Florida State University
> >> Tallahassee, FL 32306
> >>
> >> Office: (850) 645-1334
> >> http://www.scs.fsu.edu/~myunggi
> >>
> >
> >
> >
>
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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-- 
Best wishes,

MYUNGGI YI
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi