[Bioclusters] anyone using ensembl pipeline with gridengine?

Chris Dagdigian bioclusters@bioinformatics.org
Thu, 19 Sep 2002 13:51:02 -0400

Hi folks,

Just got back from an amazing swing through Singapore where I got to 
see some existing bioclusters and read the many tenders that are 
outstanding for new/future systems. Singapore has jumped on the grid 
computing bandwagon in a big way but they are being smart about it -- 
people are actually buying and testing all sorts of different clusters, 
interconnects and storage systems (hi Lai Loong Fong!) now for the 
express purpose of making sure stuff actually interoperates when 
"biogrids" turn from useless vendor-hyped vaporware into something real 
& useful.

Many of the future clusters planned are going to use Platform LSF 
mostly because one of the application requirements is being able to run 
the ensembl annotation pipeline (ensembl has a dependency on LSF for 
bulk computation). One of the most common questions asked was "can we 
run ensembl without LSF?"

I remember this question being asked in the past and also hearing that 
the Fugu-sg.org folks were going to do a SGE port of ensembl. I think 
this never happened because Platform came out with low academic per-CPU 
pricing and it turned out to be just easier and simpler to use ensmbl 
as-is with LSF underneath.

Has this changed? Anyone using ensembl with gridengine? Is there 
interest in trying to do this?

I'll summarize any responses and if I don't hear from anyone on this 
list I'll go pester the ensembl-dev mailing list.