[Bioclusters] FPGA in bioinformatics clusters (again?)

Farul Mohd. Ghazali farul at aldrix.net
Sat Jan 14 00:07:48 EST 2006

This has been an interesting and very eye opening discussion for me.

Joe, I'm aware of SGI's woes. I was using SGI RASC as an example since
I don't have much experience in hardware accelerators in general aside
from a brief fling with Paracel 5 years ago. I do like their
interconnect and SSI technology but their long term viability isn't

In general my only concern is whether or not it makes sense to get a
hardware accelerator. The cluster in question is in the late planning
stages today and isn't large (hundreds of CPUs max). Man power wise,
there are some programmers in the group but there are very few
postdocs actually doing advanced algorithms that will truly take
advantage of the FPGA accelerator. I've been asked to see if the
accelerators can be used with general purpose apps first and for
custom algorithms when the group needs it.

TIA again

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