Hi Ross,
Thanks a lot for your reply.
I did want to run a single job in parallel across multiple nodes in a
cluster.
I am waiting for the patch. :)
~mayank
On Tue, Aug 24, 2010 at 1:34 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Mayank,
>
> > I would like to know whether it is possible to run AMBER on a cluster
> > where
> > each node has one GPU. If yes, what are the things that I have to
> > differently?
>
> It depends on what you want to actually run. Right now you can run
> individual jobs on individual nodes using 1 GPU per node. You would just
> need to craft your scripts correctly to submit these jobs to the queue.
>
> If you mean can you run a single job in parallel across multiple nodes in a
> cluster the answer is, right now, no. However, I plan to release a patch,
> within a month, against AMBER 11 that will allow you to use multiple GPUs
> for a single run. These can be within a single node or across multiple
> nodes
> and it will use MPI v2.0. Speedup across 4 to 8 GPUs is anticipated
> depending on the system size and job parameters.
>
> Note you will need a VERY good interconnect between nodes. The minimum is
> probably QDR Infiniband in PCI-E 8x slots, better would be QDR IB or dual
> rail QDR IB in PCI-E 16x slots. With DDR or SDR IB the scaling will
> probably
> be limited to 2 or 3 nodes at most although I don't have definitive numbers
> right now.
>
> So, stay tuned.
>
> 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 |
> ---------------------------------------------------------
>
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--
Mayank Daga | SyNeRGy Laboratory | Dept. of Computer Science
Virginia Tech | http://synergy.cs.vt.edu | http://www.cs.vt.edu
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Received on Tue Aug 24 2010 - 11:00:04 PDT
