A page on the wiki with further information and hints would be nice. Topic: "improving performance with GMX4" or "Pimp my GMX4" ;-)
The beta manualpage of mdrun (version4) is not very comprehensible/user friendly in my eyes. - Christian On Tue, 2008-11-11 at 09:12 -0500, Justin A. Lemkul wrote: > > vivek sharma wrote: > > HI MArtin, > > I am using here the infiniband having speed more than 10 gbps..Can you > > suggest some option to scale better in this case. > > > > What % imbalance is being reported in the log file? What fraction of the > load > is being assigned to PME, from grompp? How many processors are you assigning > to > the PME calculation? Are you using dynamic load balancing? > > All of these factors affect performance. > > -Justin > > > With Thanks, > > Vivek > > > > 2008/11/11 Martin Höfling <[EMAIL PROTECTED] > > <mailto:[EMAIL PROTECTED]>> > > > > Am Dienstag 11 November 2008 12:06:06 schrieb vivek sharma: > > > > > > > I have also tried scaling gromacs for a number of nodes ....but > > was not > > > able to optimize it beyond 20 processor..on 20 nodes i.e. 1 > > processor per > > > > As mentioned before, performance strongly depends on the type of > > interconnect > > you're using between your processes. Shared Memory, Ethernet, > > Infiniband, > > NumaLink, whatever... > > > > I assume you're using ethernet (100/1000 MBit?), you can tune here > > to some > > extend as described in: > > > > Kutzner, C.; Spoel, D. V. D.; Fechner, M.; Lindahl, E.; Schmitt, U. > > W.; Groot, > > B. L. D. & Grubmüller, H. Speeding up parallel GROMACS on high-latency > > networks Journal of Computational Chemistry, 2007 > > > > ...but be aware that principal limitations of ethernet remain. To > > come around > > this, you might consider to invest in the interconnect. If you can > > come out > > with <16 cores, shared memory nodes will give you the "biggest bang > > for the > > buck". > > > > Best > > Martin > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > <mailto: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] > > <mailto:[EMAIL PROTECTED]>. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 > -- M. Sc. Christian Seifert Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] Web: http://www.bph.rub.de _______________________________________________ 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
