Re: [AMBER] NaN error in .rst files

From: peker milas <pekermilas.gmail.com>
Date: Tue, 25 Jan 2011 14:30:53 -0800

Hello again,

I made 3 consecutive runs (500ps each) with iwrap=1 but unfortunately
the last one created an .rst file with full of NaN s in it.
That is being said, only remaining candidate is temperature. I will
try to fix it according to your examples and advices. I will let you
know about results.

all the best
peker

On Tue, Jan 25, 2011 at 10:09 AM, filip fratev <filipfratev.yahoo.com> wrote:
> Hi Ross,
> Thank you for the detailed explanation! I was surprised about the factory overclock but I am not an expert. Do you think that 3GB version of GTX580 will produce any problems?
> I never did GPU overclock under Linux. However I think it is sometime helpful just for testing propose, anyway..
>
> My personal opinion is that 100% fan speed on GTX470 produce very very high noise, and it will be helpful someone to share some experience and define the temperature level that is “safety” for CUDA calculations.  Probably I did not understand well the point about differences in the GTX470 temperatures. I thought that the problem is just the fan control. To be clear I will share my data:
>
> 100% fan speed –max 65C
> 80% -70% fan speed –max 73C-80C
> 40% fan speed – 90C+
>
> For me 75%-80% it is ok regarding to the noise level.
>
> All the best,
> Filip
>
>
>
> --- On Tue, 1/25/11, Ross Walker <ross.rosswalker.co.uk> wrote:
>
>> From: Ross Walker <ross.rosswalker.co.uk>
>> Subject: Re: [AMBER] NaN error in .rst files
>> To: "'AMBER Mailing List'" <amber.ambermd.org>
>> Date: Tuesday, January 25, 2011, 5:10 PM
>> 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
>>    |
>> |
>>    Adjunct Assistant Professor
>>            |
>> |         Dept. of Chemistry
>> and Biochemistry
>>    |
>> |          University of
>> California San Diego
>>    |
>> |
>>      NVIDIA Fellow
>>
>>    |
>> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk
>> |
>> ---------------------------------------------------------
>>
>> Note: Electronic Mail is not secure, has no guarantee of
>> delivery, may not be read every day, and should not be used
>> for urgent or sensitive issues.
>>
>>
>>
>>
>>
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Received on Tue Jan 25 2011 - 15:00:02 PST
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