From: Nicholas M Glykos (glykos_at_mbg.duth.gr)
Date: Wed Feb 15 2012 - 03:22:43 CST
> And for a small number of nodes, Gigabit is very sufficient, whereas GPU
> nodes would already need expensive Infiniband or 10Gbit/s-Ethernet.
Even with old CPUs (quad-core Q6600), loaded with consumer GPUs (GTX 460,
one card per node) and with simple gigabit, you can have useful speedups
for small (tiny) number of nodes and large-ish systems (say, 100K atoms).
To put this in numbers using the ApoA1 benchmark (measurements in ns/day):
Nodes/Cores/GPUs With CUDA Without CUDA Times faster with CUDA
1 / 4 / 1 1.11 0.22 5.04
2 / 8 / 2 1.79 0.42 4.25
4 / 16 / 4 2.27 0.77 2.94
Although the parallel scaling with CUDA (at ~68% with four nodes) is far
from ideal, for small (tiny) research groups which can relax the big
cluster rules, this may still be a useful toy-cluster. Having said than,
you can substitute the whole lot discussed above (4 nodes + LAN) with a
single (cheap) node based on an AMD 8-core FX-8150 plus one GTX 570 card
which for the same benchmark delivers 2.33 ns/day.
-- Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
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