Jens Krueger wrote: > Hello, > > there have been multiple reports on the list of superlinear scaling on > AMD Opterons of the 200 series. > > We have recently purchased a small cluster with the following > configuration for each compute node: > - 2x Opteron 2218 (4 cores per node) > - 2 GB RAM > - Supermicro H8DM8 mainboard > - Mellanox PCI-E x8 Infiniband (running with OFED-1.2 and mvapich2) > - Rockscluster 4.3 > - Gromacs-3.3.1
try grompp -shuffle > > > For the DPPC benchmark we achieve the following numbers: > > cores ns/day speedup > > 01 0.289 1.00 > 02 0.487 1.69 > 04 0.768 2.66 > 08 1.330 4.60 > 12 1.776 6.15 > 16 2.137 7.39 > 20 2.550 8.82 > > > Compared to the benchmark section > (http://www.gromacs.org/content/view/25/38/) and other published data > (e.g. http://biowulf.nih.gov/apps/gromacs/bench-3.3.1.html) the > performance drops to soon when using more cpu's. In fact we are far away > from superlinear scaling and the performance on 20 cores is only half as > good as on the biowulf cluster. > We systematically checked the hardware and tried different compiler and > MPI, all giving no or only minor improvement. > > Has anybody hands on an Opteron cluster with cpu's from the 2000 series? > It would be of immense value for us to get reference data from a similar > machine. > > > Thanks, > > Jens > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se _______________________________________________ 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