2008/11/11 Justin A. Lemkul <[EMAIL PROTECTED]> > > > 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?
Everybody thanks for your usefull suggestions.. What do you mean by % imbalance reported in log file. I don't know how to assign the specific load to PME, but I can see that around 37% of the computation is being used by PME. I am not assigning PME nodes separately. I have no idea of dynamic load balancing and how to use it ? Looking forward for answers... With Thanks, Vivek > > > 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 >> > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > 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 >
_______________________________________________ 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