Very Helpful, Thanks Ben and Aron!
Jonathan
On Fri, Mar 1, 2013 at 1:05 AM, Benjamin D Madej <bmadej.ucsd.edu> wrote:
> Right, the single-GPU pmemd.cuda is currently not limited by PCI-E
> bandwidth.
>
> Ben
> ________________________________________
> From: Benjamin D Madej [bmadej.ucsd.edu]
> Sent: Thursday, February 28, 2013 10:00 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] PCI-E 2.0 vs 3.0 (AMD vs INTEL?)
>
> Hi Jonathan,
>
> The biggest impact will be in multi-GPU simulations. PCI-E 3.0 is used for
> inter-GPU communication and is the current bottleneck there. The multi-GPU
> pmemd.cuda scaling is currently limited by PCI-E bandwidth.
>
> Actually, currently the most efficient (i.e. GB of trajectory data per
> day) way to run simulations on systems with multiple GPUs is to run one job
> per GPU. In our group, we use this approach and run multiple simulations of
> each system we're studying.
>
> In those machines, we've mainly used PCI-E 2.0 with AMD CPUs and
> motherboards. See
> http://ambermd.org/gpus/recommended_hardware.htm#hardware
> With our current usage strategy, the main reason we've chosen AMD is that
> they're currently a lot cheaper than Intel right now and the CPU is not
> heavily used in GPU-accelerated pmemd.cuda. The DIY system with 2 GPUs has
> served us well and we get full performance out of each GPU.
>
> Ben Madej
> Walker Molecular Dynamics Lab
>
> ________________________________________
> From: Jonathan Gough [jonathan.d.gough.gmail.com]
> Sent: Thursday, February 28, 2013 6:53 PM
> To: AMBER Mailing List
> Subject: [AMBER] PCI-E 2.0 vs 3.0 (AMD vs INTEL?)
>
> While doing some window shopping I noticed that the current AMD chipset
> doesn't support PCI-E 3.0 x16 while Intel does. Muy understanding is this
> would/does have an impact on the communication speed between the GPU and
> the MOBO, but would that (or does anyone know if it does) have an effect on
> the overall simulation speed (GPU-intercommunication)?
>
> Apparently ASUS recently launched a MOBO that has an onboard chip to
> compensate or cover the distance(?) such that 3.0 bandwidth is possible.
> That being said I wonder if and how that might interfere with calculations.
>
> any thoughts?
> JOnathan
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 01 2013 - 04:30:02 PST
