Bioperl: Memory leak in BLAST modules

[Lincoln Stein]

Unfortunately it's still leaking, although maybe not quite so fast.  I
don't think I'm going to be able to complete my analysis task at this
rate.

Are there any cycles in the object references that Blast.pm generates?

Lincoln

Steve Chervitz writes:
 > 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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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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