Hello Ying,
We have a machine of this type where the GPU is a GTX-580. To demonstrate the much larger efficiency of using a GPU compared to CPU multiprocessing with amber, I asked my students to compare both methods for the protein 1AO6. Using the GTX-580 you could get about 12 ns/day for an explicit water simulation with TIP3P waters in an 8 A octahedral box using ff99SB, and the SPDP model in Amber 12. Using 12 CPU cores the performance was a factor of 100 slower. Thus, even if you use all 64 cores, the CPU performance is unuseable.
I built this machine for teaching computational chemistry methods - you need many CPU processors to give many students a chance to go simultaneous computations with g09, and other packages that don't parallelize well. But for doing MD, it is much better to have even a cheap GTX-560 card in many PC's to have many students work at the same time.
Hope that helps somewhat.
Cheers,
Sergio
SFSU
-----Original Message-----
From: sun [mailto:sun.ntnu.edu.tw]
Sent: Wednesday, May 08, 2013 9:40 AM
To: amber.ambermd.org
Subject: [AMBER] pmemd performance on AMD 16cores x 4 (total 64 CPU cores) + 1 GPU
Hi,
does anyone have experience on the machine of this configuration? and benchmarks?
Thanks very much.
Ying-chieh
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Received on Wed May 08 2013 - 12:30:02 PDT
