Interesting ... What was the file causing the problem?. If it represented a very large sequence then it would require a large memory allocation while it was being processed. If the required allocation was larger than the memory available to the JVM them garbage collection wouldn't help it.
Mark Mark Schreiber Bioinformatics AgResearch Invermay PO Box 50034 Mosgiel New Zealand PH: +64 3 489 9175 -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]] Sent: Saturday, 2 March 2002 9:26 a.m. 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 ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
