Blast Configuration Notes
Use the Sun Studio 11 compiler with the following flags
-fast -xO4 -xtarget=ultraT1 -xarch=generic64
There is a huge performance advantage to caching the database in memory. Set the following parameters in /etc/system
set ufs:freebehind=0
set segmap_percent=80
segmap_percent should be based on your amount of memory in the system and the size of
the databases (make sure they fit in RAM)
You can do a dry run or just copy the databases to /dev/null to cache them in RAM.
Depending on the amount of memory on your box you may not be able to cache all of the BLAST databases. In this case you may want to group the BLAST runs: all the queries accessing a specific database will run one after the other (or in parallel).
Make sure you use the latest version of BLAST, I believe it's 2.2.13.
This version has a new algorithm, apparently 2-3x faster than the previous one.
