On Nov 10, 2012, at 10:32 AM, Sasha Perkins <slperks49.gmail.com> wrote:
> Jason,
>
> Thanks for the prompt reply. I agree with you that the cut off is very
> large. The only reason I'm using that cut off is because in the literature,
> that is the typical cut off for my type of system and so I tried that
> first.
>
> The latest bugfix for Amber12 we have is 26.
Amber 12 does not have that many bug fixes. What is the output of
./patch_amber.py --patch-level
?
>
> I am using the Penn State Lion-GA cluster with only one GPU for now
> using pmemd.cuda_SPFP.MPI. The Lion-GA cluster GPUs I believe are Nvidia
> Tesla M2090. Should I be using a different command if I'm only running in
> one GPU? Or simply use more GPUs?
Use pmemd.cuda_SPFP for only a single GPU.
As Adrian said, though, try the CPU version of Amber12 first to isolate the problem to GPUs.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Nov 10 2012 - 08:30:02 PST
