[Beowulf] GPU Beowulf Clusters

Jon Forrest jlforrest at berkeley.edu
Sat Jan 30 13:24:09 EST 2010


On 1/30/2010 4:31 AM, Micha Feigin wrote:

> It is recommended BTW, that you have at least the same amount of system memory
> as GPU memory, so with tesla it is 4GB per GPU.

I'm not going to get Teslas, for several reasons:

1) This is a proof of concept cluster. Spending $1200
per graphics card means that the GPUs alone, assuming
2 GPUs, would cost as much as a whole node with
2 consumer-grade cards. (See below)

2) We know that the Fermi cards are coming out
soon. If we were going to spend big bucks
on GPUs, we'd wait for them. But, our funding
runs out before the Fermis will be available.
This is too bad but there's nothing I can do
about it.

See below for comments regarding CPUs and cores.

> You use dedicated systems. Either one 1u pizza box for the CPU and a matched 1u
> tesla s1070 pizza box which has 4 tesla GPUs

Since my first post I've learned about the Supermicro boxes
that have space for two GPUs
(http://www.supermicro.com/products/system/1U/6016/SYS-6016GT-TF.cfm?GPU=) .
This looks like a good way to go for a proof-of-concept cluster. Plus,
since we have to pay $10/U/month at the Data Center, it's a good
way to use space.

The GPU that looks the most promising is the GeForce GTX275.
(http://www.evga.com/products/moreInfo.asp?pn=017-P3-1175-AR)
It has 1792MB of RAM and is only ~$300. I realize that there
are better cards but for this proof-of-concept cluster we
want to get the best bang for the buck. Later, after we've
ported our programs, and have some experience optimizing them,
then we'll consider something better, probably using whatever
the best Fermi-based card is.

The research group that will be purchasing this cluster does
molecular dynamics simulations that usually take 24 hours or more
to complete using quad-core Xeons. We hope to bring down this
time substantially.

> It doesn't have a swap in/swap out mechanism, so the way it may time share is
> by alternating kernels as long as there is enough memory. Shouldn't be done for
> HPC (same with CPU by the way due to numa/l2 cache and context switching
> issues).

Right. So this means 4 cores should be good enough for 2 GPUs.
I wish somebody made a motherboard that would allow 6-core
AMD Istanbuls, but they don't. Putting 2 4-cores CPUs on the
motherboard might not be worth the cost. I'm not sure.

> The processes will be sharing the pci bus though for communications so you may
> prefer to setup the system as 1 job per machine or at least a round robin
> scheduler.

This is another reason not to go crazy with lots of cores.
They'll be sitting idle most of the time, unless I also
create queues for normal non-GPU jobs.

> Take note that the s1070 is ~6k$ so you are talking at most two to three
> machines here with your budget.

Ha, ha!! ~$6K should get me two compute nodes, complete
with graphics cards.

I appreciate everyone's comments, and I welcome more.

Cordially,
-- 
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
jlforrest at berkeley.edu

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