[gmx-users] Dppc Benchmark

[David]

On Fri, 2004-06-18 at 16:43, Andrea Carotti wrote:
> 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 &

and what does the performance look like for 1,2,4 processors?
Are they SMP or single CPU nodes?
> 
> ----- 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
> > > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > > Please don't post (un)subscribe requests to the list. Use the
> > > > > www interface or send it to gmx-users-request at gromacs.org.
> > > > -- 
> > > > 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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> > > >
> > >
> > >
> > > _______________________________________________
> > > gmx-users mailing list
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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
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
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> 
> 
> _______________________________________________
> gmx-users mailing list
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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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