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). > 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 ;-) 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/ _______________________________________________ Beowulf mailing list, Beowulf@beowulf.org To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf
