SimTK: FEATURE: [#1315] Memory is not freed after parsing a PDB file

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Date:
2010-08-18 16:54

Priority:
3

State:
Closed

Submitted by:
Teague Sterling (teague)

Assigned to:
Teague Sterling (teague)

Summary:
Memory is not freed after parsing a PDB file

Detailed description
Featurize does not release it's atom or protein objects from memory after parsing a point file. This results huge memory usage in point files spanning multiple of PDBs as all atoms are retained in (and lost from) memory. The memory usage can be high enough to cause the system to crash from memory allocation failures resulting in no results being produced. Recommended fix: Aggressive and comprehensive freeing of memory once it is no longer in use as well as profiling to search for possible leaks.
Featurize does not release it's atom or protein objects from memory after parsing a point file. This results huge memory usage in point files spanning multiple of PDBs as all atoms are retained in (and lost from) memory. The memory usage can be high enough to cause the system to crash from memory allocation failures resulting in no results being produced. Recommended fix: Aggressive and comprehensive freeing of memory once it is no longer in use as well as profiling to search for possible leaks.

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Date: 2010-10-18 23:24 Sender: Teague Sterling Revisions 771 and 775 fix a lot of outstanding memory issues in featurize. In negative smoke tests, memory loss has dropped from approx 190MB to around 10KB. A lot of this "loss" is coming from static function variables that are dynamically allocated, resulting in memory never being explicitly freed, but that does not ever really grow with respect to runtime. Marking this bug closed, but further minor patches may follow.
Date: 2010-09-23 02:23 Sender: Teague Sterling Revision 740 should address some of these issues. Further testing need to make sure it handles a good majority of related leaks.

Field	Old Value	Date	By
status_id	Open	2010-10-18 23:24	teague
close_date	2010-10-18 23:24	2010-10-18 23:24	teague
resolution_id	100	2010-08-18 16:54	teague
assigned_to	none	2010-08-18 16:54	teague

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