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

[Joe Landman]

Hi Gary:


---------- Original Message -----------
From: Gary Van Domselaar <gary at www.bioinformatics.org>
To: bioclusters at bioinformatics.org
Sent: Fri, 25 Feb 2005 14:26:04 -0500 (EST)
Subject: [Bioclusters] Need some advice on a cluster for EST/cDNA assembly,
clustering

> Hey Gang,
> 
> I've been called in at the last moment to "consult" on the purchase of 
> a cluster for a sequencing project.  Admittedly, I know nothing about life
> science clusters, despite having been subscribed to this list from its
> inception.  I am not making any money on this consulting, just helping 
> out a neighbouring academic lab.  So what I know at this point is that 
> they have about $Cdn 200K to spend.  They hae already talked to Sun, 
> and Sun is offering them a "sweetheart" deal for (something) at about 
> $120k.  My only exposure is to a G4/G5 cluseter from BioTeam.  I am 

Its all about the support and expertise they have onsite.  If they have linux
backgrounds and experts, the Sun is an easy choice.  If they have an Apple
background, the Apple is an easy choice.  

> impressed with it andit works really well for my purposes, and Im 
> guessing it would work well for theirs too.  I'm guessing a linux 
> cluster would perfrom nicely too. The lab currently does not have a 

There is lots of hype about performance, and little "real" data.  Generally the
best thing to do is to test their apps, the way they want to run them.  Avoid
"benchmarks" that try to play "fair".  Run the apps the way they were intended.

> bioinforatician, but I thnik they have money for one.  I'll probably 
> just end up pointing them to Glen, Joe , and Chris, but any advice,
>  suggestions, and pointers to where I can get a little more 
> familiarity, well shucks, that would really be swell.

Focus on Linux for Sun.  Late model Opterons are hard to beat performance wise
on informatics apps (from my testing), so if they are performance bound, the Sun
might be a better choice (IMO).  The other issue is whether or not their
software is up and operating correctly on OSX.  Lots of software compiles, but
as I found using some chemistry apps, not all of it works they way you expect
with the IBM xlf compiler (GAMESS issues, PMEMD and AMBER issues, ...).  Always
run the sanity checks to make sure it works correctly.  I didn't have a chance
to try gcc/g77 with the Apple I had, so I am not sure if it would have made a
difference.

The other big issue is the 64 bit issue.  What is the status of OSX as a 64 bit
OS, and can the tools see more than 4 GB of ram?  This is not an issue under
x86_64 linux, and I presume it will not be under Yellow dog linux, though I
would find it strange that people might buy an apple to run something other than
OSX.  I never had time to answer these questions, and they may or may not be
relevant for the work.

Joe



> 
> Decidedly,
> 
> g.
> --
> Gary Van Domselaar, PhD.
> Postdoctoral Fellow, Computing Science
> and Biological Sciences
> University of Alberta
> Edmonton, AB, Canada
> Phone: 780-492-5969
> 
> Assistant Director, Bioinformatics.Org
> gary at bioinformatics.org
> 
> _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters
------- End of Original Message -------