From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Nov 10 2014 - 00:53:15 CST
What you observe might be expectable as the CUDA code of NAMD is officially tuned for the multicore version. BUT, do you actually notice any performance difference regarding time/step?
Norman Geist.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Bin He
Gesendet: Samstag, 8. November 2014 08:25
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: Why CPU Usage is low when I run ibverbs-smp-cuda version NAMD
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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