[Bioclusters] Need some advice on a cluster for EST/cDNA assembly, clustering

[Elia Stupka]

> There's always the option of a mixed architecture cluster; buy lots of 
> cheap 32-bit boxes for the vast majority of compute tasks which can 
> run in a 4GB address space, and then spend the money saved to buy one 
> or two large and much more expensive machines to handle the very large 
> memory tasks.

This is exactly the option we have been taking. I think the only 
difference is that we really cannot afford lots of money on the second 
part, (i.e. to address more than 4GB of space) and my message was 
related to cheap options to overcome this issue.

> really quite affordable [ as Itanic machines go ], and if you want a 
> 64GB machine with, say, 4 CPUs, they're only mildly expensive  :-)

He he, Tim, I am afraid "mildly" is still a scary figure for most labs 
;) But they are interesting, I admit my ignorance, I thought the SGIs 
were not running linux, now I realized they do, that changes things...

> The main issue with several types of machine in the same cluster is of 
> course that the users then have to specify their requirements to the 
> DRM so that it schedules to the right kind of machine.  And I don't 
> know about you guys, but ours are notoriously bad at estimating what 
> their jobs' requirements actually are.

I know exactly what you mean, luckily we are small enough groups to 
manage these issues usually, most of the times it really involves 
talking to the single person to find out what they are planning to do 
and why they plan to use a certain hardware. Incredibly often things 
that could be run in small parallel jobs on a cluster are run as one 
silly job on an SMP...

Elia


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