On Sat, Feb 14, 2009 at 10:13 AM, Nicholas M Glykos <gly...@mbg.duth.gr>wrote:
> > Hi Tiago, > > > <snip> > > I tried with Gromacs ... > </snip> > > Concerning your MD tests, would it be worthwhile to check also NAMD's > parallel efficiency ? Based on past experience, I would suggest that you > try both the UDP- & TCP-based versions (don't forget to use the +giga and > possibly the +atm flags). Also, keep in mind that parallel efficiency > varies greatly with problem size (for example, you should expect very > different results from, say, a 1,500 atom peptide system, as compared with > a 100,000 atoms large protein system). I will try NAMD like you say. Can you give me a usual performance test you have, to which I can compare to? Gromacs tests I've been able to scale better are the ones with 100k+ atoms. > > > > > From what I could also digg around, it seems that some switches have too > > much latency and hamper any kind of proper performance from GbE. Were > this > > my case, any benchmarks I could use to test that theory out? > > We have been using NetPipe (http://www.scl.ameslab.gov/netpipe/) to > measure latency, but the experts on this list will probably tell you more > about the subjest that you'd ever wished to know ;-) > > Ok, thanks! Much appreciated. Best regards, Tiago Marques > Nicholas > > -- > > > Dr Nicholas M. Glykos, Department of Molecular > Biology and Genetics, Democritus University of Thrace, > University Campus, 68100 Alexandroupolis, Greece, Fax +302551030620 > Tel ++302551030620 (77620), http://www.mbg.duth.gr/~glykos/ > > >
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