July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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Chapter 12: Hardware and Software Optimizations
Multiprocessor Computers
One way to speed up BLAST is to employ multiprocessor computers. BLAST is a
multithreaded application and can utilize the additional processors. Adding addi-
tional processors to a computer is sometimes cheaper than purchasing multiple
machines because you don’t have to duplicate all the other components. That said,
once outside the commodity computer market, prices rise steeply, and a computer
with 32 CPUs is likely to cost you much more than 16 dual-CPU computers. The
improvement with multiple processors isn’t completely linear, and it depends on the
type of search.
If you want a single BLAST job to complete quickly, it’s best to use as many CPUs as
possible. On NCBI-BLAST, you can increase the number of processors with the -a
option, and on WU-BLAST you use the -cpus option (see Chapters 13 and 14 for
more information). However, for best aggregate performance, it is better to use only
1 CPU for each BLAST job and load up the machine with as many jobs as there are
processors. If you are searching multiple databases, you may need a lot of RAM if
you wish to keep them all cached.
Operating Systems and Compilers
Even on the same hardware, BLAST may run faster under different operating sys-
tems. Due to the complex ...
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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.