Re: [AMBER] Running Amber 11 simulations using pmemd.cuda.MPI

From: Gould, Ian R <>
Date: Tue, 5 Jul 2011 15:21:41 +0000

Hi David,

You say Fermi cards, do you mean Tesla or GTX's?


On 05/07/2011 15:57, "Baker D.J." <> wrote:

>We recently installed Amber 11 on our RHELS computational cluster. I
>build Amber 11 for both CPUs and GPUs. We have 15 computes nodes each
>with 2 Fermi GPUs installed. All these GPU nodes have QDR Mellanox
>Infiniband cards installed. One of the users and I can successfully run
>Amber simulations using pmemd.cuda.MPI over 2 GPUs (that is locally on
>one of the compute nodes) - the speed up isn't bad. On the other hand
>I've so far failed to run a simulation using multiple nodes (let's say
>over 4 GPUs). In this case, the calculation appears to hang, and I see
>very little output - apart from the GPUs being detected and general set
>up, etc, etc. I've been working with a couple of the Amber PME benchmarks.
>Could anyone please advise us. I've already noted that we have a fairly
>top notch IB network - the Qlogic switch and Mellanox cards are all QDR.
>I build pmemd.cuda.MPI with the Intel compilers, cuda 3.1, and OpenMPI
>1.3.3. Could it be that I should employ another flavor of MPI or that
>OpenMPI needs to be configured in a particular way?
>Any tips or thoughts would be appreciated, please.
>Best regards - David.
>AMBER mailing list

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Received on Tue Jul 05 2011 - 08:30:03 PDT
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