[Bioclusters] Re: Recommendations for building a cluster

Ahmed Moustafa ahmed at pobox.com
Fri Oct 19 18:23:00 EDT 2007

Thank you so much Chris!

By "genome-wide", it is more like performing the same task (e.g. blast, 
clustalw and phyml) for every single gene in a genome. But because a 
single task could include +200 sequences to align or to build a 
phylogeny, it takes a significant amount of time and memory to process a 
single gene. So by using, for example, mpiblast and raxmlmpi, it could 
be possible to distribute these tasks over a cluster and finish an 
analysis in a reasonable time.

I have googled and found these options Dell PowerEdge SC1435 
Sun Fire X2100 M2 (http://www.sun.com/servers/entry/x2100/) and Mac 
Cluster (http://www.apple.com/science/solutions/workgroupcluster.html), 
do you have an experience with any of these options?

Thanks again!


On 10/19/2007 9:16 AM, Ahmed Moustafa wrote:
> Hello!
> What would be your recommendations for building a cluster of ~20-30 
> machines with a budget of about $50K?
> I think more medium power machines would provide higher throughput 
> than fewer super power machines, especially, while performing 
> genome-wide analyses.
> What would you recommend for hardware brands and specs and OS?
> Thanks in advance! 

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