[gmx-users] Suggestions for Gromacs Perfomance

Dinesh Mali dmali085 at gmail.com
Wed Aug 6 12:03:18 CEST 2014


​Dear gmx users,

I
​ have been performing some benchmarks as given taken from following URL,
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http://www.gromacs.org/GPU_acceleration
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​The expected performance values is taken from the graph
​s​
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​This cluster
 has a two nodes, of which one has two Nvidia K20 gpus.
I have follo
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wed the performance checklist given in following URL,
http://www.
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gromacs.org/Documentation/Performance_checklist
<http://www.gromacs.org/Documentation/Performance_checklist>

I am using fftw-3.3.4 with sse2 SIMD instructions and using cuda-5.5.

The results are as follows:

Gromacs Version 4.6.5 GCC Version 4.4.6

System CPU/GPU used  performance(ns/day) expected(ns/day)
RNASE 2 CPU (Cores 16, nopm 1) 63.815 80
RNASE 1CPU(8cores)+1GPU
(-gpu_id 00000000) 50.647 95
ADH 4 CPU on 2 on each node
(32 Cores) 15.115 15


Gromacs Version 5.0.0 GCC Version 4.7.2

System CPU/GPU used  performance(ns/day) expected(ns/day)
RNASE 2 CPU (Cores 16, nopm 1)    66.698 80
RNASE 1CPU(8cores)+1GPU
(-np 8 -gpu_id 00000000) 47.763 95
ADH 4 CPU on 2 on each node
(32 Cores) 14.142 15
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Kindly provide inputs to improve the performance
​ with gpus​
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​Also, if possible please suggest
simulation
with reported performance
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simulation for
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performing benchmarks
 for both CPU & GPU.  ​
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​Regards,
Dinesh Mali


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