Re: [AMBER] CUDA MPI issues

From: Biplab Ghosh <>
Date: Thu, 26 May 2016 23:42:18 +0530

Dear Dr. Ross Walker,

Thank you very much for keeping my hope alive. I will try to execute your
tomorrow and will post you the updates.

With regards

On Thursday 26 May 2016, Ross Walker <> wrote:

> Hi Biplab,
> No worries... So I took a look at the motherboard manual here:
> If you look at page 10 of that manual it has a block diagram for how the
> motherboard is wired.
> Note it shows two PCI-E x16 slots (1 and 3) connected to the left CPU and
> a PCI-E x16 slot and two PCI-E x8 slots connected to the right CPU (slots
> 5,4 and 2). Right now you likely have one GPU in slot 5 and one in slot 1
> or 3. This configuration will run 2 x pmemd.cuda jobs fine but if you want
> a single job to span 2 gpus then you can't do this (and get performance)
> unless they are on the same CPU. Thus you would need to remove the GPU from
> PCI-E slot 5 and plug it into whichever of slot 1 or 3 is available. Of
> course this assumes that there is physical room in the case to do this -
> and you might need to move any cards in the other slots (network etc) if
> they are present. Looking at the motherboard picture page 3:
> It looks like there could be an issue with using slot 1 for a double wide
> card since it may foul with the cabling connected to the pins on the edge
> of the motherboard. If there isn't room then this would explain why they
> used slot-3 and slot-5.
> So, if you are comfortable moving GPUs around you could try this yourself
> and see if there is room but you might want to inquire with the vendor if
> it can be supported and if they can help do it.
> Ultimately this was not a very good choice of motherboard for optimum GPU
> computing - I certainly wouldn't have picked this one. If you plan on
> getting more machines let me know and I'll make sure you get optimum
> designs.
> All the best
> Ross
> --
> Sent from my iPad

Sent from my iPad

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Received on Thu May 26 2016 - 11:30:03 PDT
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