[Bioclusters] Fwd: pre-configured clusters

Robert Myers bioclusters@bioinformatics.org
Thu, 29 Jan 2004 20:04:52 -0500

Jeffrey B. Layton wrote:

> Robert Myers wrote:
>> "The SGI Altix 350 is priced starting at $12,199. A 4-processor 
>> configuration carries at a list price of $21,599, or $5,400 per 
>> processor. " 
> I will agree/disagree. It depends upon your application(s). Some will
> run faster on the Altix, some won't. Test your application on both
> and then do the price/performance.
> Personally, if you need a single-system image machine and you know
> you are not going to grow the machine, then the 350 is a great deal.
> Otherwise, look at clusters. I think the Xserve deserves a second look
> as does the IBM 970 (same thing really). Also look at the Xeon
> nodes and the Opteron nodes. I think the Opterons are especially
> promising.

The directly comparable Xserver 455 from IBM lists for at least twice as 
much per processor, not counting added cost if you want infiniband-type 
performance for more than one box.  That is not to say that Xeon or 
Opteron boxes in the Xserver series might not be a better buy for some 
applications.  If you're consdering IBM, be sure to have a quote on a 
350 to show to the IBM salesman.  At a minimum, you will probably get a 
better price.

>> The Apple cluster comes standard with gigabit ethernet: an acceptable 
>> interconnect only for a limited number of problems. The SGI uses 
>> proprietary Numa-Link, which is at least competitive with Infiniband, 
>> a much faster and much more expensive solution than gigabit ethernet, 
>> but the Altix 350 looks like a really good buy, especially if you're 
>> looking for a pre-packaged solution. 
> I don't see anything wrong with GigE at all. Again, it depends upon
> your application. If you need a highbandwidth low latency interconnect
> then something like IB, Myrinet, Quadrics, or Dolphin are the way to go.
> If you need single system image, then NUMAflex is the way to go
> (just a small correction - the SGI website and literatures refers to 
> it as
> NUMAflex, not NUMA-Link). 

As you can tell, the amyloid plaque is already showing its effects, so 
there is not a moment to lose.

> Believe it or not, my main application
> scales very well with Fast Ethernet (over 90% scaling for at least 300
> processors). It's not a Bio application, but some bio apps aren't even
> really parallel apps at all - just HUGE amounts of serial processing with
> varying data sets. 

Agreed that not everything needs a low latency, high-bandwidth 
interconnect.  For those who do, and who want a pre-packaged solution, 
the Altix 350 just happens to be what appears to be an exceptional buy 
at the moment, as compared to other prepackaged low-latency, 
high-bandwidth solutions currently on the market.

> Oh, another thing about NUMAflex, it's not the same across their
> product line. While I can't confirm this, I was told that the Altix
> 350 had a ring type connection for NUMAflex. The larger and more
> expensive machines had a fat-tree type connection for NUMAflex.
> If you're going this route, be sure to ask (and be sure to test!). 

Altix 3700 has a very expensive two-plane, fat tree switched NUMAflex 
network.  The Altix 350, which scales up to 16 processors under a single 
system image, uses a ring NUMAflex network as does the Altix 3300.  From 
usenet posts made by someone associated with SGI, I infer that the boxes 
have pairs of Itania sitting on a standard Intel processor bus sharing a 
memory controller.  An eight processor configuration involves at most 
three NUMAflex hops, from the ASCII-art diagram he posted.  No one has 
ever said so officially, but I am sure you can cluster the single-image 
clusters, but to do that you have to start buying stuff like router 
bricks.  The 350 is likely to be most attractive to people who want 
relatively uniform access to large datasets in memory with a relatively 
modest number of processors.