How to improve the GPU utility in NAMD

From: 王军 (
Date: Tue Dec 25 2012 - 02:35:06 CST


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.


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