[gmx-users] Re: scaling issues in GROMACS
spoel at xray.bmc.uu.se
Wed Oct 15 19:53:00 CEST 2003
On Wed, 2003-10-15 at 21:33, David wrote:
> On Wed, 2003-10-15 at 19:19, Dean Johnson wrote:
> > Hello,
> > I've been trying to get GROMACS running on a 16 dual xeon 1.7/1.8
> > cluster, with gigE, and I'm running into some problems. It isn't seeming
> > to load-balance very well and cpu utilization for 1 process per cpu is
> > on the order of 10-20%. It seems to stay at about that level from 8 cpus
> > on. Is this consistent with expectations? If not, any idea of what the
> > problem may be? I'm using latest of everything, including mpich.
Oh by the way, if you are running an old Linux kernel you may want to
turn off hyperthreading in the bios. Furthermore you'd want to use the
shared memory between processors for more performance.
David van der Spoel, PhD, Assist. 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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