[gmx-users] (no) superlinear Scaling on Opterons

[David van der Spoel]

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
> 
> 
> 
> 
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-- 
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.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se