Re: [AMBER] How to choose between implicit and explicit solvent

From: Ross Walker <>
Date: Mon, 9 Nov 2015 13:09:37 -0800

> On Nov 9, 2015, at 12:43 PM, Josh Berryman <> wrote:
> "I would like to get some inputs from somebody with some experience with
> drugs and MD."
> Big mistake. Might be OK just looking at the simulations, but don't get
> high and start messing around with an expensive shared supercomputer.


> Of course you could get a personal GPU in which case you are hurting noone,
> 5 million atoms should fit on a Tesla K40, a K80 is twice as big although
> it hasn't made it onto the "supported cards" list here:
> . I'd be tempted to have a go at
> that myself, it sounds like a fun calculation. Off-topic: a K80 looks like
> it is just two K40s in a box, does anyone know if you can use it OK as a
> single card?

Huh? - From that page:

Hardware Version 3.0 / 3.5 (Kepler I / Kepler II)
        • Tesla K20/K20X/K40/K80

Says K80 there and benchmarks are on the GPU benchmark page for K80. A K80 is essentially two K40s on the same card hooked together with PCI-E switch and then down clocked a little to fit within the 300W power envelope of a PCI-E card. They work very well although cost a LOT! - Titan-X or 980TI is probably more cost effective and has 12GB so can handle bigger simulations than K40 or K80 if that is a concern.

The K80 will appear to the OS as two distinctly different GPUs. So having 4 in a box is actually just like having 8 GPUs in a box. On a single K80 you can run 2 x 1 GPU jobs or 1 x 2 GPU job - dealers choice.

All the best

|\oss Walker

| Associate Research Professor |
| San Diego Supercomputer Center |
| Adjunct Associate Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
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| Tel: +1 858 822 0854 | EMail:- |

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Received on Mon Nov 09 2015 - 13:30:03 PST
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