From: Bin He (binhe_at_hustunique.com)
Date: Mon Nov 10 2014 - 13:51:15 CST
1. Using the servers mentioned above, I got the result:
multicores-CUDAGPUCORETIME
41664s
ibverbs-smp-cudaGPUCORENODETIME2 per node12 per node2572 per node12 per node
437
when running ibverbs-smp-cuda, the cpu usr usage is less than 50%, and sys
usage is about 30%.
The cpu usage is too ugly. *What I want to do is to find the reason why the
cpu usage is so strange*.
2. If I want to get the best performance with cuda, what parameters in the
config file I can modify?
------------------------
Best Regards!
Bin He
Member of IT
Unique Studio
Room 811,Building LiangSheng,1037 Luoyu Road, Wuhan 430074,P.R. China
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Email:binhe_at_hustunique.com
Email:binhe22_at_gmail.com
2014-11-10 14:53 GMT+08:00 Norman Geist <norman.geist_at_uni-greifswald.de>:
> 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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