Hello Ross,
Many thanks for your prompt reply.
Regards
Anu
On Fri, Feb 26, 2016 at 10:36 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Anu,
>
> Think of this as a standard Disclaimer rather than a flat out warning.
> Essentially the CPU code has been around for many years and has been widely
> tested. The GPU code on the other hand is very new.
>
> The key here is that if you see strange behavior from the GPU code - by
> strange I means simulations crashing etc - try it with the CPU code and see
> if the problem persists. If it does not then write to the AMBER list with
> details of what you are trying to simulate. The GPU code is now heavily
> used - upwards of 400 citations and I would guess something like 80% of
> AMBER PMEMD simulations are now likely with GPUs. So you shouldn't need to
> worry. Just be aware that if you are simulating some kind of exotic system
> - as opposed to regular proteins, DNA, RNA and standard organic ligands -
> the GPU code may give results that don't make sense. It may crash with
> limited error messages or give give some other result that you cannot
> rationalize / understand. In this case don't just blindly go down that path
> trying to make conclusions - consider that it could be coming from a bug in
> the code.
>
> As with everything in science you should always be devising ways to test
> your hypothesis in multiple independent ways from different directions. If
> two different approaches lead to the same conclusion that adds more weight
> to that conclusion.
>
> I hope that helps. I'll tone down this message for the next release of
> AMBER since the GPU is much more widely used now. (Being in the US I am
> obligated to state however that there is still no warranty implied or
> otherwise or any other guarantee that it is for any purpose however).
>
> All the best
> Ross
>
> > On Feb 26, 2016, at 3:28 AM, anu chandra <anu80125.gmail.com> wrote:
> >
> > Dear Amber users,
> >
> > I have recently started using pmemd.cuda.MPI (Amber 14) for carrying out
> MD
> > simulations. I have noticed in the .out file that a caution message has
> > appeared about the CUDA version of PMEMD. It says...
> >
> > CAUTION: The CUDA code is currently experimental.
> > You use it at your own risk. Be sure to
> > check ALL results carefully.
> >
> >
> > I just wonder how should I make sure the iterations are going fine?.
> > Precisely, what all results I should check to make sure the simulation
> goes
> > on the right direction?
> >
> >
> > Many thanks in advance
> >
> > Anu
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Mon Feb 29 2016 - 07:00:05 PST
