Hi All, one thing I forgot to mention I am getting here around 6 ns/day...for a protein of size around 2600 atoms..
With Thanks, Vivek 2008/11/11 vivek sharma <[EMAIL PROTECTED]> > 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. > > With Thanks, > Vivek > > 2008/11/11 Martin Höfling <[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 >> 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 >> > >
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