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

[Myunggi Yi]

I have tested with 8, 16, 24 and 32 cpus.
Only parallel with 8 and 16 cpus works, and the other cases (24 and
32) are even much slower than 8 cpus' case.

Any idea about this?


On Nov 24, 2007 11:42 AM, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Myunggi Yi wrote:
> > 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?
> No. You have to test for yourself (as you are doing right now).
> It is very dependent on simulation size, network etc.
>
> >
> >
> >
> >
> > 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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> >>
> >
> >
> >
>
>
> --
> 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
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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