[AMBER] Good cluster configuration for running PMEMD.MPI?

From: Juan Carlos Muñoz García <juan.munioz.iiq.csic.es>
Date: Mon, 16 Apr 2012 15:19:56 +0200 (CEST)


I'd like to ask you for your advise regarding a good/fast cluster for
running PMEMD.MPI of AMBER. Our group has the possibility of adquiring a
computer cluster with the following configuration:

- 4 Processors Opteron Interlagos 16 Cores/each 6276 at 2,3 GHz, 8 Mb
cache L2 and 16 Mb cache L3, and 4 Hipertransport vers. 3 channels of 6,4
- Dual circuit board H8QGI+-F 3 SATA Hot Swap, VGA MATROX G200.
- 16Mb, 2x PCI-e 2.0 x16, 2 PCI-e x8, 2 network cards 1000 (Gigabit) IPMI
2.0 (KVM over LAN).
- Memory: 128 GB DDR3/1600 ECC.

According to what I've read in AMBER benchmarks site, it seems it's better
to use a higher number of processors/node but with a lower number of cores
per node.
In any case, could you please tell me if, with the configuration above
indicated, is it expected to get good averages ns/day rates for MD
simulations (specially of ligand-protein complexes) in explicit water?

I apologize if this is not the type of question you expect to be sent to
the AMBER reflector, but your commentaries would be of great help.


Juan Carlos Munoz Garcia.
Glycosystems laboratory, IIQ (CSIC), Spain.

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Received on Mon Apr 16 2012 - 06:30:05 PDT
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