Re: [AMBER] Cluster considerations

From: peker milas <>
Date: Fri, 18 Feb 2011 19:29:18 -0800

Hi Brent and Ross,

I am sorry for my late response but i was terribly sick last week.
This GPU cluster idea is related with the need of pushing the
simulation to higher time scales. I really want to simulate my system
upto a microsecond. Unfortunately, it looks like we will not be able
to start building it right away. You may probably guess that there are
always funding issues.

On the other hand we needed to have some information about the
hardware. So, thank you so much Ross for enlightening us about
hardware. Also, thank you so much Brent for letting us know about the
other possible ways of simulation, and sharing your ideas.


On Fri, Feb 11, 2011 at 8:12 PM, Ross Walker <> wrote:
> Hi Peker,
>> We are considering putting together a small GPU cluster for running
>> AMBER simulations of some larger biomolecules (~100k atoms).
>> Naturally, there are many decisions to be made and not a whole lot of
>> documentation describing what works. Our budget is <$10k, so our first
>> inclination is to buy four Intel i5s boxes, each with two GPUs
>> connected over Gigabit Ethernet. Have people had good experiences with
>> this sort of setup? In particular,
>> 1) Has anyone had experience using GPUs in an MPI configuration over
>> gigabit ethernet? Is Gigabit Ethernet capable of delivering the
>> bandwidth/latency to keep the cards busy?
> The gigabit Ethernet will be fine for mounting a file system, say over NFS.
> For MPI communication, to run simulations in parallel it will be completely
> useless. For GPU runs in parallel across nodes you need QDR Infiniband as a
> minimum. However, you'd be able to run in parallel within a node over one or
> more GPUs.
>> 2) In the event that gigabit ethernet is insufficient, we have
>> considered purchasing an Infiniband interconnect. This, of course,
> Only if you want to run across multiple nodes. If you have multiple jobs you
> could always just run them on individual nodes which should be fine.
>> would require 3x16 PCIe lanes, which no consumer motherboard I have
>> seen provides. It seems like the most common configuration is one x16
> See:
> Works well with 4 GPUs in one box. All 4 lanes are X16. If you want the
> specs for a complete machine here's an option:
>> slot with two x8 slots. This brings us to the question, how much does
>> AMBER rely on GPU-CPU data transfers? Would running two GPUs with 8
>> lanes each substantially reduce performance? Is there a way we could
>> disable 8 lanes of our current setup for benchmarking purposes?
> Running in parallel across multiple GPUs will be poor if you only have them
> in x8 slots. It should not affect single GPU runs too much. Maybe 10% or so.
> However, for running a single calculation across multiple GPUs then you need
> them all in x16 slots.
> 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                     |
> | | |
> | Tel: +1 858 822 0854 | EMail:-  |
> ---------------------------------------------------------
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Fri Feb 18 2011 - 19:30:04 PST
Custom Search