I just met the previously discussed (see
http://archive.ambermd.org/201101/0301.html and
http://archive.ambermd.org/201101/0391.html ) NaN error. My system is a dual opteron with GTX 590, applying all the bugfixes 17 for Amber11, and bugfixes 13, 14, 15 (bugfixes all) for AmberTools1.5.
I'm using gcc 4.5, and cuda toolkit 3.2, on OpenSUSE 11.4 x64.
The system is organic solvent with ~40,000 atoms. Using ntp=1, ntb=2, ntt=1. Running with pmemd.MPI eliminates the error. Changing the GPU also eliminates the error (CUDA_VISIBLE_DEVICES).
I suspect this is a memory error on the particular GPU, and sure enough, rebooting the system solved the problem. My question is, is it really memory error or is it some known issue with GTX5XX?
--Farid
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Received on Sat Aug 27 2011 - 13:30:02 PDT
