#248 memory leaks in tide-search

[William S Noble]

I ran tide-search in peptide-centric mode under valgrind (compiled with debug mode) and found lots of memory leaks. The full experiment is here:

/net/noble/vol1/home/noble/proj/crux-projects/2011dia/results/bill/2015-02-25memory-bug/small

I am attaching the script I used to run the test as well as the stderr output that details which blocks were lost from which lines of code.

[William S Noble]

FWIW, these memory leaks do not seem to be related to the peptide-centric option. I re-ran the same search in spectrum-centric mode and got basically the same results. See attached and the directory

/net/noble/vol1/home/noble/proj/crux-projects/2011dia/results/bill/2015-02-25memory-bug/spectrum-centric

[Kaipo]

Most of those look like they are from the Google Protocol Buffers, which are harmless according to Google:

Also notice the call to ShutdownProtobufLibrary() at the end of the program. All this does is delete any global objects that were allocated by the Protocol Buffer library. This is unnecessary for most programs, since the process is just going to exit anyway and the OS will take care of reclaiming all of its memory.

The peptide centric search does have one additional leak, which looks like it could be problematic. I attached a patch but I'm not sure if it fixes the issue or not.

[William S Noble]

Ok, if you are satisfied that we shouldn't worry about this, you can
resolve this issue.
On Mar 3, 2015 1:09 PM, "Kaipo" kaipot@users.sf.net wrote:

Most of those look like they are from the Google Protocol Buffers, which
are harmless according to Google:

Also notice the call to ShutdownProtobufLibrary() at the end of the
program. All this does is delete any global objects that were allocated by
the Protocol Buffer library. This is unnecessary for most programs, since
the process is just going to exit anyway and the OS will take care of
reclaiming all of its memory.
The peptide centric search does have one additional leak, which looks like
it could be problematic. I attached a patch but I'm not sure if it fixes
the issue or not.

Attachment: leaks.diff (19.1 kB; text/x-patch)

• [issues:#248] http://sourceforge.net/p/cruxtoolkit/issues/248 memory
  leaks in tide-search*

Status: open
Milestone: post v2.0
Labels: High priority
Created: Thu Feb 26, 2015 04:56 PM UTC by William S Noble
Last Updated: Fri Feb 27, 2015 02:15 AM UTC
Owner: Kaipo

I ran tide-search in peptide-centric mode under valgrind (compiled with
debug mode) and found lots of memory leaks. The full experiment is here:

/net/noble/vol1/home/noble/proj/crux-projects/2011dia/results/bill/2015-02-25memory-bug/small

I am attaching the script I used to run the test as well as the stderr
output that details which blocks were lost from which lines of code.

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