Hi David,
Ok, that rules the first idea I had out. I assume that you've run standard
pmemd.MPI the non cuda version across the infiniband?
Cheers
Ian
On 05/07/2011 16:26, "Baker D.J." <D.J.Baker.soton.ac.uk> wrote:
>Hello,
>
>Yes, sorry, I do mean Tesla cards. Each compute node has two Tesla M2050
>GPUs installed.
>
>Best regards -- David.
>
>-----Original Message-----
>From: Gould, Ian R [mailto:i.gould.imperial.ac.uk]
>Sent: Tuesday, July 05, 2011 4:22 PM
>To: AMBER Mailing List
>Subject: Re: [AMBER] Running Amber 11 simulations using pmemd.cuda.MPI
>
>Hi David,
>
>You say Fermi cards, do you mean Tesla or GTX's?
>
>Cheers
>Ian
>
>
>On 05/07/2011 15:57, "Baker D.J." <D.J.Baker.soton.ac.uk> wrote:
>
>>Hello,
>>
>>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
>>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 Tue Jul 05 2011 - 09:00:04 PDT
