[Bioclusters] Newbies

Joe Landman bioclusters@bioinformatics.org
11 May 2002 22:46:19 -0400

On Sat, 2002-05-11 at 22:38, Ron Chen wrote:

> 3. Network
> 100 Mbps may be the best, in terms of cost-effetive.
> But if you run parallel BLAST, then you may consider
> high-speed, low latency like Myrinet.

Parallel BLAST (on Linux clusters) does not generally require such a
network.  There may be valid other reasons to have a low latency high
bandwidth network.

Parallel BLAST is generally done either using the built in pthreads
support, or via coarse grain job segmentation.  The pthreads mechanism
depends upon the machines SMP ability and OS support for pthreads. 
Pthreaded programs generally do not make use of low latency
interconnects unless some attempt is made to add support for MPI or
other mechanism.  The coarse grained mechanisms depend upon a
segmentation operation, and then a data distribution.  This distribution
tends to be quite small (though not always).