Dear Amber users,
I compared scalability of classical explicit-solvent MD implemented in
AMBER on GPU and CPU. You can see the resulting plot by the dropbox link
below (different colors correspond to four proteins of different size):
https://www.dropbox.com/s/zmjspl1p5ajso5s/Acceleration_EN.png?dl=0
As you can see from this plot, the optimal acceleration of the MD is
achieved on 4 nodes; however, on GPUs we can see minor increase in
productivity even on 6-8 nodes, while on CPUs the performance degrades to
zero on the same number of nodes.
My Question is: can you explain the performance degradation on large number
of CPU nodes given the stable performance on the same number of GPU nodes?
Thank you for your time,
Dmitry
Technical details:
- Amber 14 (pmemd.cuda.MPI, pmemd.MPI)
- intel15.0.3, openmpi2.1.1-icc, mkl11.1.3, cuda6.5
- 1 Node = Intel Haswell-EP E5-2697v3, 2.6 GHz (14 cores); NVidia Tesla
K40M; 64 GB; Infiniband FDR; Infiniband FDR; Gigabit Ethernet
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Received on Wed Jun 13 2018 - 03:00:02 PDT
