Re: [AMBER] NaN error in .rst files

From: peker milas <>
Date: Tue, 25 Jan 2011 08:28:06 -0500

Thank you so much for all those responses.

Dear Ross, I was sick yesterday, so i could start another run just
couple minutes ago. This time i am using iwrap=1 and I will let you
know about the results. Thank you for your advice and pointing me to
the right direction.

Dear Jason, I had a brief knowledge about this flag/option. Now, i
believe i deeply learned about it. I also got the reason of this NaN
issue. Thank you for all those explanations about the problem. I am
really enlightened.

Dear, Filip, about my card, although i recently ordered a new cooler
(zalman vf3000f), i couldn't plug it in. A geometry optimization
program is currently running side by side with amber, so i need to
wait for the end of those calculations. But, to be honest, this card
gets hotter than 80 C, based on observation it can reach up to 90 C. I
am not sure if this will cause a problem in future. Anyway i will
definitely use this new python based software for monitoring it. I
also want to thank you for this great advice.

Thank you again and i will let you know about the results...
All the best


On Tue, Jan 25, 2011 at 3:25 AM, filip fratev <> wrote:
> Hi Peker,
> I use GTX470 card too and as I reported previously there were no problems till now after bugfix12. After bugfix12 has been released I performed more that 100ns simulations including several restarts. What kind of OC you are using?
> About the heat issue..
> Probably most of you know these options, but I will share them again:
> You can be able to run the graphical interface of nvidia-settings (nvidia-settings X Server Display Configuration) that allows you to follow the temperature levels. Just type: nvidia-settings. This package comes with Nvidia drivers and should be included in your system too. There are many programs that show the CPU and GPU temps and should also be included in your Linux distribution (if it is Linux). †The last what I saw is python based software written just few days ago, which is very helpful because it shows graphically almost everything about your card (memory usage, temperature and so on, thus you donít need to use nvidia-smi anymore:
> 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 you use the default speed for Amber calculations I can not imagine what is your temperatureÖand this really can be problem. Unfortunately, Nvidia continue to irritate the people and donít 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 section: †Option "Coolbits" "5" and than restart and type nvidia-settings and you should see that your fan control is enabled and can control your fan speed.
> Hope that helps,
> Filip
> --- On Tue, 1/25/11, peker milas <> wrote:
>> From: peker milas <>
>> Subject: [AMBER] NaN error in .rst files
>> To: "AMBER Mailing List" <>
>> Date: Tuesday, January 25, 2011, 12:42 AM
>> Dear Amber coders/users
>> We had a discussion about this problem couple days ago.
>> Briefly at
>> some point of simulations pmemd.cuda creates NaN s in the
>> restart
>> files. Then the next step of simulation messes up. This is
>> sort of a
>> problem which happens in totally random way. As some users
>> already
>> pointed out, part of it can be related with heating problem
>> because
>> GTX 470/480 cards were not designed for this kind of
>> intense
>> calculations.† Although i totally agree with this, i
>> couldn't find an
>> easy way of observing this behavior. In fact there is only
>> nvidia-smi
>> command which shows me the current state of the card (like
>> its
>> temperature, etc...). So i really want to go little bit
>> deep with this
>> problem and i would like to know if anybody knows a good
>> indicator for
>> checking cards behavior in detail. It can be a command or
>> any sort
>> additional package/program for monitoring it.
>> Any help will be appreciated
>> regards
>> peker milas
>> _______________________________________________
>> AMBER mailing list
> _______________________________________________
> AMBER mailing list

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Received on Tue Jan 25 2011 - 05:30:04 PST
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