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 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 -- Dr. Jens Krueger Institute of Biophotonics School of Biomedical Science and Engineering National Yang-Ming University 155, Li-Non St., Sec. 2 Taipei, 112, Taiwan (R.O.C.) mobile: 0921452940 http://www.ym.edu.tw/~wfischer
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