Re: [gmx-users] No scale up beyond 4 processors for 240000 atom system
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 listgmx-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 listgmx-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
Re: [gmx-users] No scale up beyond 4 processors for 240000 atom system
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 listgmx-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
RE: [gmx-users] No scale up beyond 4 processors for 240000 atom system
From: "maria goranovic" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] No scale up beyond 4 processors for 24 atom system Date: Tue, 9 Oct 2007 12:09:50 +0200 Hello, I was wondering what the scale up was with GROMACS 3.3.1 on 8 or 16 processors. Here are my benchmarks: Hardware: Dell PowerEdge 2950, 2x 2,66Ghz Intel Woodcrest CPUs, 8 GB Ram, 2x Gigabit Ethernet GROMACS 3.3.1: 24 atoms, PME, 1.0 nm real cutoff processors ns/day 1 0.141 2 0.253 4 0.409 8 0.232 16 0.107 Do I need to recompile with some other options ? Or is this the best I can get ? Will another type of network improve performance ? It seems communication is the rate limiting step for 8 or 16 cores ? Thank you for the help, -Maria So this is 4 cores sharing one ethernet connection? With such a setup you will never get good scaling. You need something like an Infiniband network. Gromacs 4.0 will give a big improvement, but I don't know how much. Berk. _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-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
[gmx-users] No scale up beyond 4 processors for 240000 atom system
Hello, I was wondering what the scale up was with GROMACS 3.3.1 on 8 or 16 processors. Here are my benchmarks: Hardware: Dell PowerEdge 2950, 2x 2,66Ghz Intel Woodcrest CPUs, 8 GB Ram, 2x Gigabit Ethernet GROMACS 3.3.1: 24 atoms, PME, 1.0 nm real cutoff processors ns/day 1 0.141 2 0.253 4 0.409 8 0.232 16 0.107 Do I need to recompile with some other options ? Or is this the best I can get ? Will another type of network improve performance ? It seems communication is the rate limiting step for 8 or 16 cores ? Thank you for the help, -Maria -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-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
