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: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]] > Sent: Friday, March 01, 2002 2:26 PM > To: [EMAIL PROTECTED] > 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 > > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
