Bioperl: Memory leak in BLAST modules

[Steve Chervitz]

Lincoln,

I've been grappling with the memory leak for a while and have a new
version of Blast.pm that includes a fix for memory leaks when parsing
streams of reports. This is version 0.063 which you can get from:

http://genome-www.stanford.edu/perlOOP/bioperl/lib/Bio/Tools/Blast.pm

Memory use is still an issue, particularly if you are parsing huge
reports (on the order of 1 Mb or more) and not imposing significance
criteria. If you can include even a minimal cutoff (i.e., -signif =>
0.01), that should improve memory usage compared to using no cutoff. 

Also, when creating individual Blast objects, it's a good idea to
explicitly destroy them when you're done processing each one
($blast_obj->destroy). Using a single $blast_obj variable and
re-assigning it should accomplish the same thing (but calling
destroy() makes me feel better ;). 

If you (or others) have additional ideas for how to improve memory
usage, I'd be happy to hear them. Do you know of a good memory
management tool for Perl that can show reference counts etc. during
the course of an execution?

I haven't bundled the new version of Blast.pm into a distribution
package yet since there are other changes I want to include. But look
for it soon. 

Steve 
___________________________________________________
Steve A. Chervitz               Neomorphic Software  
sac@neomorphic.com              2612b 8th Street
http://www.neomorphic.com       Berkeley, CA 94710 


Lincoln Stein writes:
 > Does anyone know of a memory leak in the Bio::Tools::Blast module?
 > I've got a script that creates and destroys several thousands of these 
 > objects and it is definitely leaking.  I don't want spend time
 > debugging the thing if there's a known problem.
 > 
 > Lincoln
 > 
 > -- 
 > ========================================================================
 > Lincoln D. Stein                           Cold Spring Harbor Laboratory
 > lstein@cshl.org			                  Cold Spring Harbor, NY
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