Does getz have a memory leak

John Peden johnp at worf.molbiol.ox.ac.uk
Thu Aug 28 07:20:30 EST 1997


Hi,

Problem on Digital UNIX 4.0 and SRS

I have been having trouble with a memory leak in getz for several months, the leak was present in SRS4 and is still
present in SRS5.05. The problem occurs when multiple sequence entries are read from disk and written to standard 
output. Memory is allocated to hold each sequence when it is read, but the memory is not released after the 
sequence has been written to the standard out. This process repeats until memory is exhausted. 

I have checked for memory leaks in getz using PURIFY, and cannot find any. I have also checked the getz /SRS 
code, and while memory is being allocated for each sequence object via EntryOpen(), it is apparently being 
correctly released by a EntryClose() call, on an entry by entry basis.

I am therefore confused where this problem is occurring and whether this is a SRS or Digital UNIX or
compiler specific problem and would appreciate confirmation that the problem does or does not occur on 
other systems/setups.

A typical getz query:

getz -sf fasta -f  "id des seq"  "[libs={genbank embl}-sl#45:] ! ([libs-org:escherichia coli]  |  [libs-org:metazoa])" 


After the query is processed and the first sequence is outputted, my memory usage is approximately 34Mb. 
However on my system memory usage continues to grow until it hits either the soft or hard memory limit
(the hard limit is 600 Mb). 

John

Oxfrord University Molecular Biology Data Centre.




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