[gmx-users] Dppc Benchmark
and.carotti at farmchim.uniba.it
Fri Jun 18 13:22:46 CEST 2004
I' ve the same problem: same hardware and bad performance..but I've
MPICH 184.108.40.206, Fedora Core2, gromacs 3.2.1.
(I've used the howto:
There is a solution also for me? ...like a flag in the compilation of mpich
that i've missed....
TNX in advance
----- Original Message -----
From: "David" <spoel at xray.bmc.uu.se>
To: "Seonah Kim" <kim at qtp.ufl.edu>; "Discussion list for GROMACS users"
<gmx-users at gromacs.org>
Sent: Friday, June 18, 2004 10:43 AM
Subject: Re: [gmx-users] Dppc Benchmark
> On Thu, 2004-06-17 at 23:23, Seonah Kim wrote:
> > Dear all,
> > We are testing our linux cluster now, using gromacs 3.2.1, with the dppc
> > benchmark.
> > We have dual Xeon 2.88 Ghz, 1 GB memory per box. We run RedHat 9.0, and
> > use LAM. 512 Mb L2 cache as far as I can tell.
> > We see 135 ps/day for a single processor, but only 250 for two.
> > This is not the superscaling reported in the gromacs web site.
> > The two processor run really works in the same box, using the 2 procs,
> > we checked, so it is not the network. We read/write only at the
> > beggining and end, so it is not the disk.
> > Can anyone help us ? Is this a LAM issue ?
> You may need to recompile using some flags for LAM (short message size
> or something like that and set it to 512 kb).
> Did you run grompp -shuffle?
> > Thanks !!!
> > a.
> > _______________________________________________
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> 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://xray.bmc.uu.se/~spoel
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