[gmx-users] Dppc Benchmark

[Andrea Carotti]

I've run:
grompp -f -c  -p -po -shuffle -sort -np 4 -o
and then
mpirun -np 4
/home/Application/gromacs3.2.1/i686-pc-linux-gnu/bin/mdrun -s -x -c
conf_wat.gro -g -e -np 4 >& log.log &

----- Original Message ----- 
From: "David" <spoel at xray.bmc.uu.se>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Friday, June 18, 2004 4:35 PM
Subject: Re: [gmx-users] Dppc Benchmark


> On Fri, 2004-06-18 at 13:22, Andrea Carotti wrote:
> > Hi all.
> >     I' ve the same problem: same hardware and bad performance..but I've
> > MPICH 1.2.5.2, Fedora Core2, gromacs 3.2.1.
> > (I've used the howto:
> > http://www.gromacs.org/documentation/howtos/mpich_howto.html)
> > There is a solution also for me? ...like a flag in the compilation of
mpich
> > that i've missed....
> same question then, have you used grompp -shuffle ?
> > TNX in advance
> > Andrea
> >
> >
> > ----- 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.
> > > >
> > > > _______________________________________________
> > > > gmx-users mailing list
> > > > gmx-users at gromacs.org
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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://xray.bmc.uu.se/~spoel
> > >
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > >
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> >
> >
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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://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
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