Re: [AMBER] Parallel pmemd.cuda: any preliminary cross-node tests?

From: Scott Le Grand <>
Date: Sat, 31 Jul 2010 10:12:29 -0700

I'd definitely go for QDR between nodes.

What's up in the air ATM is whether it's best to spread the C2050s across as many nodes as possible or whether 2 or 4 C2050s per node is the optimum configuration.

-----Original Message-----
From: Ross Walker []
Sent: Thursday, July 29, 2010 19:09
To: 'AMBER Mailing List'
Subject: Re: [AMBER] Parallel pmemd.cuda: any preliminary cross-node tests?

Hi Sasha,

> The question is primarily for Ross and Scott.
> Have you been able to implement any parallel code for pmemd.cuda? If
> so,
> how does it look in multiple node situations and how much bandwidth is
> needed to keep all cards fully utilized?

I am putting together a patch and testing things. We are hoping to have a
release, a provisional beta one at least shortly. In the meantime
performance is generally better running across IB with 1 card per node. Our
best guess is that you need a 'minimum' of QDR IB to be able to keep the
cards fully utilized. I don't have a complete range of numbers for you
though due to not having enough variations of hardware to test on. Some
'provisional' numbers for C2050's at 1 per node with QDR IB are:


2 x E5462 = 5.94 ns/day
1 x C2050 = 20.70 ns/day
2 x C2050 = 29.8 ns/day
4 x C2050 = 41.14 ns/day
8 x C2050 = 48.97 ns/day

Cf. NICS Kraken XT4 using 192 cores at 1 core per node = 192 nodes (768
cores effectively) = 46.01 ns/day.
> I wonder whether DDR infiniband would be sufficient to maintain
> performance across several nodes or is this the case for QDR. If you
> haven't tested it yet, what's your best guess at this point?

Unfortunately I think it will be suck it and see - I haven't had enough
variations to actually know. Scott may have tested on a DDR machine. It
might work okay for 2 nodes, 1 GPU each but beyond that my best guess is
that QDR is needed.

All the best

|\oss Walker

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

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Received on Sat Jul 31 2010 - 10:30:04 PDT
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