Re: [AMBER] NaN error in .rst files

From: peker milas <>
Date: Tue, 25 Jan 2011 10:28:26 -0500

Hi again Ross,

I should say that we specifically bought this card for being not
overclocked. Also we definitely didn't overclock it. In fact we were
very careful about this issue. Actually that is why we just ordered a
new cooling system for it. I really don't have much idea about the
architecture of those cards. I also don't know while Filip's card can
only go up to 80 C and ours can go easily 90 C. There is only one idea
in my mind related with this. It is simply like that. We have 2
nehalem cpu packs (total 16 logical cores) in the same box that we
have GPU in. If those CPU s can increase the ambient temperature they
are able to quickly increase the GPU temperature too. One quick
observation which supports this idea is when the GPU is idle, i read
45 C as its temperature. That is all i can figured out. As i already
told it is definitely not overclocked.

thanks again for advices

On Tue, Jan 25, 2011 at 10:10 AM, Ross Walker <> wrote:
> 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
> Ross
> /\
> \/
> |\oss Walker
> ---------------------------------------------------------
> |             Assistant Research Professor              |
> |            San Diego Supercomputer Center             |
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> |         Dept. of Chemistry and Biochemistry           |
> |          University of California San Diego           |
> |                     NVIDIA Fellow                     |
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Received on Tue Jan 25 2011 - 07:30:03 PST
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