From: Atanu Maity (atanuchem48_at_gmail.com)
Date: Thu Nov 17 2016 - 01:27:04 CST
We are not getting expected benchmark for the acceleration of NAMD2.11
simulation speed using Multiple CPUs and GPU.
The configuration of the CPU processor is "Intel(R) Xeon(R) CPU E5-2650 v3
@ 2.30GHz" and we are using NVIDIA Tesla K40c GPU card.
The benchmark time of the simulation of a system containing ~1,70,000 atom
is as follows
No. of CPU ns/day (CPU) ns/day (CPU+K40c)
32 2.244 2.087
16 2.760 3.002
8 2.591 2.582
4 1.984 2.051
2 1.141 1.145
1 0.591 0.590
The NAMD version is 'NAMD_2.11_Linux-x86_64-multicore-CUDA' and the command
line is as follows -
charmrun +p32 namd2 +idlepoll input.namd > output.log
Can anyone please explain or suggest the probable reasons why we are not
getting the acceleration using GPU ?
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