[Biojava-l] A Simple Genbank Parser Runs Out of Memory

[Muratet, Michael]

Larry

I forget what the default memory allocation is for the jvm, but there is an
argument -Xmx that will allow you to increase the heap size. Maybe that will
fix the problem.

Mike

> -----Original Message-----
> From: cantey.lg@pg.com [mailto:cantey.lg@pg.com]
> Sent: Friday, March 01, 2002 2:26 PM
> To: biojava-l@biojava.org
> Subject: [Biojava-l] A Simple Genbank Parser Runs Out of Memory
> 
> 
> I created a simple parser based on the Genbank demo, to test 
> a proof of concept.
> I ran it on a large Genbank source file ( contains over 
> 160,000 "sequences").
> The program  processed 34,170 sequences then crashed with the
> java.lang.OutOfMemoryError .   I ran this on an NT with 768mb 
> ram, using the
> 1.2.2 JVM.
> 
> The interesting thing about this is that I was able watch the 
> size of the JVM.
> For the first 34,169 sequences it reached a steady state at 
> about 14 mb with
> normal expansion and contraction.  Then it processed a 
> sequence and the JVM size
> jumped up to 85 mb and crashed.  This scenario was exactly 
> reproducible.  To
> make sure it wasn't a data issue,  I took 5 sequences before 
> and after the
> "crashing" sequence and put them in a separate file.  I was 
> able to process this
> file with no interesting problems.
> 
> The net result was that I was able to "solve" this problem by 
> pre-allocating a
> larger JVM.  However, I am concerned when I see an expansion 
> of the JVM by 70 mb
> when it does a simple parse of a sequence.
> 
> Are any of you aware of perhaps garbage collecting problems 
> in jdk 1.2.2 ?
> 
> Any other ideas?
> 
> Thanks and Best Regards,
> Larry Cantey
> 
> 
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