I missed the whole discussion... too busy working on other stuff. Something to add: 1) Make sure you benchmark YOUR code Some CPUs show very nice benchmark scores, but they just fail to run your code efficiently. I think most vendors offer at least remote access to their testdrive machines. 2) Also, make sure you are comparing apples of the same class: If you are planning to go for PBSPro, make sure you also try out the commercial version of SGE. But nevertheless, ask on the Torque/PBS and the SGE mailing lists before making up your mind. The problem with clustering software is that your can't mix/match PBS/SGE/LSF or Condor... If you go with PBSPro and later, you decide that SGE is better, the $$ you spent on PBSPro will be lost :( Rayson --- Gary Van Domselaar <gary at www.bioinformatics.org> wrote: > I wanted to express my gratitude for all the valuable contributions > to my > query about how to best advise on the purchase of a computing system > for > EST/cDNA assembly and clustering. The question raised a lot of very > interesting discussion and opinions, including some offline > discussion. > That I can get such high quality advice from the top experts in the > field > sp quickly and for free, well it simply blows my mind--huzzah for the > bioclusters list! > > Here is how I interpreted the advice. Hopefully I didnt misinterpret > it > too badly. > > 1. Don't put the cart before the horse. Identify the expertise > available > to you and the workflow you intend to implement and use that to guide > your > hardware purchasing decisions. This keeps you from looking like a > grade > 'A' dunce when the critical application you need to run is not > compatible > with the system on which you just spent 120 000 dollars. It also > allows > you to focus more on the science and less on the IT. > > 2. If you have a specific application, build your system around that > > application. Generic clustering systems may not meet your specific > needs > and can cause lots of grief when you try to hack it to do your > specific > task. > > 3. Assembly and clustering require lots of memory to run efficiently, > so > 64-bit SMP systems with lots of RAM are preferred. > > > Anyways thanks again to all who contributed. > > Regards, > > g. > > > > > > On Fri, 25 Feb 2005, Gary Van Domselaar wrote: > > > > > 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 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 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. > > > > 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 > > > > _______________________________________________ > Bioclusters maillist - Bioclusters at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bioclusters > __________________________________ Celebrate Yahoo!'s 10th Birthday! Yahoo! Netrospective: 100 Moments of the Web http://birthday.yahoo.com/netrospective/