From: Atanu Maity (atanuchem48_at_gmail.com)
Date: Thu Nov 17 2016 - 01:27:04 CST
Dear experts,
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 ?
With regards
Atanu Maity
Bioinformatics Center
Bose Institute
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