Yes, there are motherboards out there like that. And I suspect specific recommendations will come in the near future. That said, it's hard to get one's hands on such things on demand. But I can say across the board, the better the bandwidth both within the motherboard and between nodes the better the overall performance. MPI pmemd.cuda is entirely bandwidth-bound.
-----Original Message-----
From: Thomas Zeiser [mailto:thomas.zeiser.rrze.uni-erlangen.de]
Sent: Sunday, August 01, 2010 00:32
To: AMBER Mailing List
Subject: Re: [AMBER] Parallel pmemd.cuda: any preliminary cross-node tests?
On Sat, Jul 31, 2010 at 10:12:29AM -0700, Scott Le Grand wrote:
> 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.
for QDR to work at full speed you need PCIe2.0 8x (not only
mechanically but also electrically). Are there any boards which have
four 16x slots and additionally more than only 4x electrically?
At least in the typical Intel-based boards you have two 16x and one
4x slot when there is one chipset on the mainboard; or four 16x and
(several) 4x slots (4x electrically although their mechanics width
is 8x) if there are two chipsets.
Thus, with these boards, the maximum feasable is full DDR speed
using a DDR-IB card supporting 5.0 GT/s; (slightly cheaper DDR
cards with 2.5 GT/s only operate with an effective speed similar to
SDR ...)
--
Dr.-Ing. Thomas Zeiser, HPC Services
Friedrich-Alexander-Universitaet Erlangen-Nuernberg
Regionales Rechenzentrum Erlangen (RRZE)
Martensstrasse 1, 91058 Erlangen, Germany
http://www.rrze.uni-erlangen.de/hpc/
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Received on Mon Aug 02 2010 - 10:30:05 PDT
