Very Helpful.
FWIW - I already have a small cluster of i7's for QM, so it's helpful to
know that I can just drop in GPU's to run MD. The
first machines I received as donations were intel, so I have just built new
intel machines going forward to maintain consistency.
Thanks!
JOnathan
On Fri, Sep 21, 2012 at 1:22 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Dear Jonathan,
>
>
> >ON a slightly related note:
> >
> >When running gpu calculations, has anyone looked at or have an idea of the
> >effect that the CPU speed has? For example -- if you were to compare
> >machines that were identical (same motherboard, hard drive, RAM, and a
> >680X) but had different CPU's would you see a performance bump/drop or is
> >it still a level playing field? Can you get by with an i3 or i5 instead
> >of
> >a top end i7? (could be another way to save $ if your building on a
> >budget)
> >
> >any thoughts or insight?
>
> For AMBER the CPU speed will have no impact on single GPU calculations.
> You just need at least 1 core per physical GPU. Thus just buy the lowest
> bin cheapest CPUs you can. We tend to go with the AMD processors since
> they are dirt cheap compared with Intel. I tend to get slightly higher
> clock speeds and the 8 core versions of these since that only adds a few
> tens of dollars and means the machine has some grunt for running CPU
> calculations as well if one wants to do that. If you go with Intel top bin
> parts can costs 10x or more lower bin parts sometimes.
>
> For multi-GPU runs (i.e. pmemd.cuda.MPI) then the front side bus speed can
> make a difference and so going for the ultra top end chips can help but it
> is on the order of 10% or so for a massive increase in price so that
> really doesn't help much either.
>
> The spec I have on my shopping list page:
>
> http://www.rosswalker.co.uk/current_amber_gpu_spec.htm
>
> Is pretty much optimized in terms of price / performance for GPU
> calculations. Don't expect to run multi GTX680 runs with this setup but it
> will scream for 2 independent runs and is not too shabby for CPU runs
> either. You can get cheaper by getting a lower spec power supply, 2GB
> GTX680 cards etc but then you start cutting into the bone.
>
> Hope this helps.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
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>
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Received on Fri Sep 21 2012 - 11:00:02 PDT
