Re: [AMBER] cluster configuration help

From: Sangeetha B <>
Date: Sun, 11 Mar 2012 20:41:30 +0530

Dear Sir,

Thanks for your kind reply and suggestions. I am sorry for sending the same
question many times. Since I had a deadline to meet and I did not get any
suggestions for three days, I had to resend the question.

Thank you,
B. Sangeetha
On Sat, Mar 10, 2012 at 11:54 PM, Thomas Cheatham <> wrote:
> Please try to avoid sending the same question multiple times to the
> reflector.
> > I have been running simulations using Amber 11 on a GPU Tesla C2050
> > since a year. I would be running simulations with systems as large as
> > 1,00,000 atoms.
> Fantastic.  Given this experience, you already know the relative
> performance of GPUs and also presumably the clusters you have access to.
> Given this knowledge, you should be able to answer these questions
> yourself.  If not, I would suggest looking at the benchmarks on the AMBER
> WWW page.  You should at least verify that what you were seeing (on your
> GPUs / clusters) in the 1,00,000 atom simulations is consistent with what
> is reported on the AMBER page.
> > 1. If I set up a cluster with the following configurations, what would
> > be the performance for a parallel run using Sander?
> Use your experience and also look at the AMBER benchmarks.  Performance
> will depend on how you utilize the resources.
> > 2. How many jobs can I run in parallel at a time without affecting the
> > performance?
> This depends on how you run your job.  The description of the resources
> you provide is confusing.  As I read it, the configutation is:
> 1 master node.  12-core, 3 TB RAID.  Infiniband.
> 2 compute nodes.  Each 12-core.  Infiniband.
> So, you have one front-end node, and a back-end with two 12-core nodes (or
> 24 processors total).  This will likely be ~1/2 the performance of one of
> the GPUs you were running on previously.  On this setup, you could likely
> run two 12 processor jobs or one 24 processor job.  If I had this setup, I
> would runit as three nodes rather than dedicating a front-end/master.
> If you are only buying three nodes, look at buying two and adding GPU
> cards to each.  If it was a typo on the number of nodes, and you are
> actually buying 10's to 100's of nodes, look at the balanced cost of GPUs
> vs. cores.  In my experience with the current GPUs, they match ~48-60
> cores.
> --tec3
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Received on Sun Mar 11 2012 - 08:30:03 PDT
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