AMBER Archive (2009)

Subject: RE: [AMBER] Amber on GPU

From: Ross Walker (
Date: Mon Apr 06 2009 - 20:14:07 CDT

Hi Sasha,

>Considering the emerging interest in GPU-based computational
>applications, what do you think about efforts to port MD code to GPU
>hardware? Are there any inherent limitations? Considering that accuracy
>should be a higher priority than speed, are there any serious issues
>with GPUs?

There are of course issues although I'm not sure that the scientific impact
of these issues has been carefully studied yet so I'm not sure anyone
actually definitively knows the answer to this. I would suggest that the
biggest issue right now is a psychological one in the mind of some people
implementing such things. With any accelerator or complex hardware there are
always some parts of the problem that map better than others and right now
the pressure to show that 'my code is faster than your code on a GPU' could
lead some people to make algorithmic shortcuts that are somewhat
questionable. Thus right now I would tread lightly when it comes to GPU
implementations and demand internal consistency against 'trusted' cpu

>Finally, if GPUs look like a reasonable platform to pursue, are there
>any plans for of Amber code?
>Since the advertised hardware acceleration sounds very tempting, it
>would be interesting to know your opinion.

I have been discussing this with Vijay Pande and various people at NVIDIA
and we are looking at ways of possibly hooking in their openMM GPU MD suite
into AMBER. This is subject to the constraints that we can get it to support
the same sort of functionality as PMEMD and more importantly pass all the
test cases in the same fashion that PMEMD vs Sander does. Once there is
something more concrete I'll let you know.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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