[GE users] ncbi blast on SGE

foisysdiploide sylvain.foisy at diploide.net
Tue May 25 14:07:43 BST 2010


Hi,

Blast and SGE: looks can be deceiving... Ok, here goes my experience on this
topic:

- Blast coming straight from the NCBI is not MPI aware but is multi-thread.
So on a single node, you can specify blast to use more than one core. The
flag for blast is -a <int>, where int is the number of cores you want to
use.

- If you want to do MPI with blast, your only recourse is to use (as
prefiously suggested) mpiblast:

 http://www.mpiblast.org/

- Performance wise, blast is bound how much RAM you have and by the I/O from
your storage for accessing the sequence databases. Even with
parallelization, accessing the dbs becomes the bottleneck.

Personnaly, I have often found that mpiblast is one layer of complexity to
much for simple clusters with minimal support (my case). In addition, most
blast runs are quite speedy by themselves and from experience, writing the
report is always the the longest part and to the best of my knowledge, this
is not parallized by mpiblast.



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