From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Nov 06 2012 - 14:46:02 CST
One additional thing that complicates things for Sandy Bridge processors is
the Turbo Boost. You had equal speed between 4 cores and 7 cores, so
things were not going so well. Many people have dealt with this problem
for benchmarking purposes, and posted different solutions online to disable
it. (Ajasja: how are your scalings without GPU?)
In any case, the main problem is most often the limited bandwidth between
CPU and GPU, like Ajasja and Aron already said. The motherboard that
you're planning to use is a good choice, the one you're currently making
tests on may not be: what is it?. Also not knowing which Opterons you had
nor the PCI-e bus speed, the comparison you made with the ThinkPad is not
That said, I don't think it's worth going beyond 1 CPU for every GPU.
First, it will be hard to find suitable motherboards. Second and most
important, 12-16 CPU cores plus 2 GPUs all exchanging data on the same bus
will probably already clog up the PCI-e bus. I agree with Ajasja that
hyperthreading may be useless, and actually harmful if you're sharing the
bandwidth (that would be 24-32 CPU cores... again all sharing the same bus).
On which CPU, I would vote for less cores but higher clock (e.g. Xeon 2640
or 2667), if you're planning to use them with a GPU.
On Tue, Nov 6, 2012 at 2:01 PM, Michael Purdy <mdp3w_at_virginia.edu> wrote:
> Hello, I am running NAMD simulations (multicore-CUDA) on a ThinkPad with
> dual Core i7-2760QM CPUs and a Quadro 2000M running Debian. For a 150k atom
> system I get performance like this:
> Benchmark time: 4 CPUs 0.287062 s/step 1.66124 days/ns 387.641 MB memory
> Benchmark time: 7 CPUs 0.289229 s/step 1.67378 days/ns 428.574 MB memory
> Things are going well so we purchased a GTX-690 which we installed in a
> workstation with two dual core Opterons, which is evidently far short of
> the CPU cores we need to get the most of the 2 GPUs and 3072 cuda cores.
> Performance was just slightly better than the ThinkPad:
> Benchmark time: 4 CPUs ~0.2 s/step ~1.4 days/ns
> We would like to build a new workstation to get the most out of the
> GTX-690 and I'd like to know how many CPU cores we need. I'm considering
> two Core i7-3930k (6-core/12-thread) or two Xeon E5-2650
> (8-core/16-thread). Will either of these be a good match for the GTX-690 or
> will I still be short running short on CPUs? The current plans is to build
> this on an Asus Z9PE-D8 WS board.
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