Re: How to improve the GPU utility in NAMD

From: Thomas Evangelidis (
Date: Tue Dec 25 2012 - 04:33:56 CST

According to your command line you utilize only the second GPU. Try using:

namd2 +idlepoll +p6 +devices 0,1,2,3 md_run.conf &> md_run.log


On 25 December 2012 10:35, 鐜嬪啗 <> wrote:

> Hello,
> NAMD users, I'm a beginner of NAMD. I run my simulation on a Linux
> Workstation which has 4 GTX680 GPU card, but whatever I do, the GPU utility
> of my process which is never greater than 45%. Compared with amber12
> pmemd.cuda, which can always stay at 99%, NAMD is too low. I think this is
> the reason why amber12 is obviously faster than NAMD by GPU. This problem
> makes me puzzled. Is there anyone who knows what's wrong with it? My NAMD
> version is 2.9b for CUDA, the CUDA driver version is 310.19, my OS is
> CentOS6.3, and my command for running NAMD is: namd2 +idlepoll +p6 +devices
> 1 md_run.conf &> md_run.log. Any help will be appreciated, thanks in
> advance.
> Jun

Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens


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