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
