From: Peter Jones (pm-jones_at_bigpond.com)
Date: Fri Aug 31 2012 - 21:41:25 CDT
Hi,
I am the researcher having problems running NAMD2.9 with CUDA. I'm finding that for all of a number of completely different and independent systems (protein and water with 50K to 200K atoms), the simulations crash after 320K steps with errors concerning rattle constraints and atoms moving too fast. This occurs directly after writing the dcd trajectory at 325K steps, the trajectory being written every 5K steps. These simulations all run normally on other machines, although I do not have access to another gpu-accelerated machine for that comparison. I can run the simulations by checkpointing and ending at 320K steps and then resubmitting the job automatically via pbs. These simulations have run this way for over 100M steps without problems, and the trajectories all appear normal.
Regards,
Peter Jones
On 01/09/2012, at 4:14 AM, Chris Harrison wrote:
> Ashley,
>
> How reproducible is the error and does it occur on other GPU boards? I
> ask b/c if you have a system where it occurs reproducibly at ~320K steps
> or very close to that we would ask you to send us the inputs so we can
> use it to track down the problem.
>
> Best,
> Chris
>
>
>
> Ashley Chew <ashley.chew_at_uwa.edu.au> writes:
>> Date: Fri, 31 Aug 2012 17:02:48 +0800
>> From: Ashley Chew <ashley.chew_at_uwa.edu.au>
>> To: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
>> Subject: namd-l: NAMD 2.9 with CUDA runs
>>
>> Hi this is my first post in regards to NAMD
>>
>> I was wondering if anyone in the community was having problems with NAMD built with CUDA (Using a single Tesla M2075 6gb, node has 72GB of Ram) once it passes a certain point (In his case pass 320k steps)
>>
>> In our case one of the researcher notice the errors returned in the output are common internal errors to do with unstable simulations but if they checkpoint and stop the runs prior to 320K steps, and then restart from the restart files internally generated by NAMD, the restarted simulation runs past the previous crash point.
>>
>> I have even rebuilt the NAMD from CVS 20120828 build with fftw3 (which works) but it pretty much did the same things once it passes a certain point.
>>
>> Ashley Chew
>> HPC System Administrator
>> iVEC_at_UWA (MBDP: M024)
>> The University of Western Australia
>> 35 Stirling Highway
>> CRAWLEY WA 6009
>>
>> E: ashley.chew_at_uwa.edu.au<mailto:ashley.chew_at_uwa.edu.au>
>> P: +61 8 6488 8742
>> F: +61 8 6488 1015
>>
>>
>> CRICOS Provider Code: 00126G
>>
>> [cid:image003.png_at_01CD879A.72D35BE0]
>>
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>
>
>
>
> Best,
> Chris
>
>
> --
> Chris Harrison, Ph.D.
> NIH Center for Macromolecular Modeling and Bioinformatics
> Theoretical and Computational Biophysics Group
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>
> http://www.ks.uiuc.edu/Research/namd Voice: 773-570-6078
> http://www.ks.uiuc.edu/~char Fax: 217-244-6078
>
>
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