Re: NAMD 2.9 with CUDA runs

From: Chris Harrison (
Date: Fri Aug 31 2012 - 13:14:02 CDT


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.


Ashley Chew <> writes:
> Date: Fri, 31 Aug 2012 17:02:48 +0800
> From: Ashley Chew <>
> To: "" <>
> 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
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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       Voice: 773-570-6078               Fax:   217-244-6078

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