Tuesday, 20 September 2011

Are BIG RAM servers popular?

I know for sure

BGI has them :(

ucdavis has one :(

Titus Brown recommends 512 Gb or even 1 Tb (shudder)

Jerm makes a case for owning one here http://jermdemo.blogspot.com/2011/06/big-ass-servers-and-myths-of-clusters.html

Nick Loman is already doing market research on buying one,

More importantly seqanswers wiki suggests that you shld own one for de novo assembly ;)

Do you own one? how often does it get used?
More MPI or memory efficient de Brujin assemblers are being pushed out now ... is throwing more ram at the problem really something that is still required?

Hmmm I don't have access to one but my limited experience with a 256 Gb ram machine for a de novo assembly of a fish transcriptome didn't give me the contigs that I wanted. (it ran out of memory midway :( )


  1. Uppsala university has a 2 Tb RAM cluster that we are using for de novo assembly: http://www.uppmax.uu.se/systems/halvan

    Yes, it gets used!

  2. jap, velvet and oasis is ran often on halvan... :)


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