[gmx-users] Dppc Benchmark
spoel at xray.bmc.uu.se
Fri Jun 18 10:43:17 CEST 2004
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
> 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 !!!
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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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