[Bioperl-l] Memory Leak in Bio::SearchIO

[Chris Fields]

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Clarke, Wayne
> Sent: Tuesday, May 16, 2006 4:25 PM
> To: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Memory Leak in Bio::SearchIO
> 
> 
> Thanks Chris,
> 
> I did forget to mention however that I did parse one single report and
> found no problems, it finished fast and with no noticeable memory usage.
> I will consider getting my SA to update bioperl from CVS as a precaution
> but he has already stated he prefers to wait for the release of v1.5.

Um, you can tell him the last release was v.1.5.1 (last October).  It's
considered a developer release but is pretty stable; well, except for that
whole SearchIO quibble, and that's not our fault.

You could also install a local version in case he doesn't budge; see here:

http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_I
N_A_PERSONAL_MODULE_AREA

Chris

> Even a single job of 10000 will finish but the problem is that I am
> trying to loop through many jobs of 10000 and it seems to be additive
> for reasons I can not determine. During testing I noticed that the RSS
> on top decreased around 80% MEM usage, but then the shared mem
> increased. I am wondering if this is due to the perl garbage collector
> freeing up memory but keeping it in its pool for use, if so that is fine
> as long as the it does not then want to reach into swapped mem.
> 
> Thanks again, Wayne
> ...