[gmx-users] Suggestions for Gromacs Perfomance

[Dinesh Mali]

​Dear gmx users,

I
​ have been performing some benchmarks as given taken from following URL,
​
​​
​
​
​
​
​
​
​
​
​
​
​
​
​
​
​
​
​
​
​
​
http://www.gromacs.org/GPU_acceleration
​​

​The expected performance values is taken from the graph
​s​
.
​This cluster
 has a two nodes, of which one has two Nvidia K20 gpus.
I have follo
​​
wed the performance checklist given in following URL,
http://www.
​​
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
​​
Kindly provide inputs to improve the performance
​ with gpus​
.
​Also, if possible please suggest
simulation
with reported performance
​​
​
​
simulation for
​
performing benchmarks
 for both CPU & GPU.  ​
​
​​
​​​
​​
​Regards,
Dinesh Mali