Why CPU Usage is low when I run ibverbs-smp-cuda version NAMD

From: Bin He (binhe_at_hustunique.com)
Date: Sat Nov 08 2014 - 01:24:32 CST

Hi everyone,

I am a fresh man to NAMD.

The Desc of our clusters:
cpu:E5-2670(8cores)
memory:32GB
socket:2
network:IB
GPU:k20m*2
CUDA:6.5
workload:* f1atpase(numsteps2000)*

When I run the multicores-namd version, the cpu usage is about 100% and GPU
usage is about 50%;

*CMD:./namd2 +p16 +devices 0,1 ../workload/f1atpase/f1atpase.namd*

cpu time is about 88s.

When I run the ibverbs-smp-cuda version, the cpu usage is about just 40%us
and 30 % sy. GPU usage is about 50%.

*CMD:/home/gpuusr/binhe/namd/NAMD_2.10b1_Linux-x86_64-ibverbs-smp-CUDA/charmrun
++p 60 ++ppn 15 ++nodelist nodelist ++scalable-start ++verbose
/home/gpuusr/binhe/namd/NAMD_2.10b1_Linux-x86_64-ibverbs-smp-CUDA/namd2
+devices 0,1 /home/gpuusr/binhe/namd/workload/f1atpase/f1atpase.namd*

cpu time is about 37s.

when I try to use setcpuaffinity, the result is worst.

So what is wrong with my operation?

Thanks

------------------------
Best Regards!
Bin He
Member of IT
Unique Studio

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