Re: [AMBER] NaN error in .rst files

From: Ross Walker <>
Date: Tue, 25 Jan 2011 07:10:44 -0800

Hi Peker and others,

> your temperature…and this really can be problem. Unfortunately, Nvidia
> continue to irritate the people and don’t provide overcklock possibility for
> Fermi (even in the new beta drivers 270.13), but fortunately there is a fan
> control option. You just need to write in your Xorg file, just below device

I think I have said this already but I will say it again. Please please please (pretty please?) do NOT overclock any of your graphics cards, GTX or Tesla if you want to run AMBER (or any other simulations for that matter). Gaining yourself a few % speedup is not worth it given you just end up wasting everybody's time trying to trackdown bugs that do not exist. This also applies to buying manufacturer overclocked versions of GTX cards. The reason you overclock graphics cards so much is that when running graphics they are much more fault tolerant than CPUs. For example read and write errors in the memory only translate to the odd graphical glitch which likely goes unnoticed. During a MD calculation, however, this can be disastrous.

People do not overclock clusters and supercomputers for a reason and you should NOT overclock your GPU for the same reason. Certainly as a reviewer of manuscripts I would not accept one for publication if the calculations had been done on overclocked GPU hardware since that would throw doubt on the entire set of simulations.

> Probably you know that the default GTX470 fan speed is ONLY 40%. I run my,
> during Amber calculations, with fan speed between 75-80% in order to keep
> the temperature up to 70C, but some times it reach the level of 80C. Thus if

With regards to the fan speed my recommendation is that you should set ALL fans, both the GPU and case / CPU fans to 100% (you can often set CPU and case fans to performance mode in the bios to achieve this) if you are running calculations on a machine. It will also benefit from an air conditioned room or office.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| | |
| Tel: +1 858 822 0854 | EMail:- |

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Received on Tue Jan 25 2011 - 07:30:02 PST
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