Low cost tip: Ask your cluster administrator if it is possible apply channel bonding to the Gigabit interfaces. You need two network switches for that to be efficient (a cut-through switch may also help). It increases network bandwidth by 70%. It also helps to use Cat6 cables.
You may try this MPICH compilation: ./configure --with-device=ch3:nemesis --enable-fast --disable-cxx --enable-error-checking=no CFLAGS=-O3 FFLAGS=-O3 There is patch to run PME faster over ethernet... maybe that paper from Dr. Carsten that Dr. Christian suggested. High cost tip: Migrate to Infiniband. Anyone tried GotoBLAS ? Does it work well with GMX ? On 10/9/07, Christian Burisch <[EMAIL PROTECTED]> wrote: > Berk Hess schrieb: > > Hi all, > > > So this is 4 cores sharing one ethernet connection? > > perhaps the two Gigabit NICs were bundled somehow. But I guess this > doesn't work out-of-the-box&plug'n'play. And latency and not bandwidth > may be limiting in this case. > > > With such a setup you will never get good scaling. > > You need something like an Infiniband network. > > Or check: > > Carsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo > W. Schmitt, Bert L. de Groot and Helmut Grubmuller: Speeding up parallel > GROMACS on high-latency networks J. Comp. Chem 28 pp. 2075-2084 (2007) > > Haven't tried it yet but sounds good! > > Regards > > Christian > > -- > Dr. Christian Burisch > Lehrstuhl für Biophysik > PG Theoretische Biophysik > Ruhr-Universität Bochum > D-44780 Bochum > Raum ND04/67 > Fon: +49 234 32 28363 > Fax: +49 234 32 14626 > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php