[Biojava-dev] memory leak

[mark.schreiber at group.novartis.com]

Following a tip off from Rainer I have discovered that there is a memory 
leak in BioJava caused by calling subList() or subStr() on 
SimpleSymbolLists

The simple routine below will run for a long time but if left it will 
eventually cause an out of memory error.

  public void run() throws Exception{
    SymbolList sl = 
DNATools.createDNA("acgctcgagctcgagctagcgactacgagcgctgcag");
    while(true){
      SymbolList sl2 = sl.subList(1,12);
    }
  }


I ran this through a profiller and found the following:

> 99% of the CPUs time is taken up calling SimpleSymbolList.finalize(), 
all of this is due to a call to AbstractChangeable.removeChangeListener(). 
All the calls to finalize() are to be expected as the variable sl2 gets 
garbage collected a lot but the burden of the removeChangeListener is 
unexpected. 99% in finalize() is pretty bad when I would have thought the 
sublist operations would have been more expensive.

Overtime the stack becomes overloaded with tens of thousands of 
WeakReference instances that are apparently not that weak as the GC is not 
touching them.

99.72% of these WeakReferences are being generated by calls to 
ChangeSupport.addChangeListener() They are being stored in a HashMap that 
is taking a bit of a punishing!

It would seem that the change support mechanism somewhere has a memory 
leak and is not releasing references from the HashMap. It is also placing 
a very heavy burden on the CPU.

My java is 1.4.2 and biojava from CVS

Can anyone think of what might be going wrong?

- Mark

Mark Schreiber
Principal Scientist (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com

phone +65 6722 2973
fax  +65 6722 2910