July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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Chapter 12: Hardware and Software Optimizations
One obvious improvement is to employ faster networking. Doing so increases the
cost of each compute node a little and significantly increases the cost of network
switches because gigabit network switches are still quite expensive. However, it is
possible to use a hybrid solution in which the database server is connected to a
hybrid network switch via a gigabit line and the compute nodes are connected to the
switch via the more common 100-Mb interface. This is much cheaper than using
gigabit everywhere, and, because exceeding 12.5 MBps is rare, it doesn’t hinder per-
formance too much.
When building file servers, people often neglect to put in enough RAM. For BLAST
database servers, though, you really want as much RAM as possible. Caching applies
on the file-server end, too, and if several computers request data from the file server,
it’s much better if it can be served from memory rather than from disk. If you’re
thinking of using autonomous network attached servers as a BLAST database server,
think again. Most don’t have gigabit networking or enough RAM.
Local databases
Keeping local copies of your BLAST databases on each node of the cluster will make
access to the data very fast. Most hard disks can read data at 20 to 30 MB per sec- ...
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I'm always learning. So when I got on to O'Reilly, I was like a kid in a candy store. There are playlists. There are answers. There's on-demand training. It's worth its weight in gold, in terms of what it allows me to do.