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From Tamara Bobic <tamara.bo...@scai.fraunhofer.de>
Subject OutOfMemoryError
Date Tue, 18 Oct 2011 16:21:32 GMT
Hi all,

I am using Lucene to query Medline abstracts and as a result I get around 3 million hits.
Each of the hits is processed and information from a certain field is used.

After certain number of hits, somewhere around 1 million (not always the same number) I get
OutOfMemory exception that looks like this:

Exception in thread "main" java.lang.OutOfMemoryError
	at java.util.zip.Inflater.inflateBytes(Native Method)
	at java.util.zip.Inflater.inflate(Inflater.java:221)
	at java.util.zip.Inflater.inflate(Inflater.java:238)
	at org.apache.lucene.document.CompressionTools.decompress(CompressionTools.java:108)
	at org.apache.lucene.index.FieldsReader.uncompress(FieldsReader.java:609)
	at org.apache.lucene.index.FieldsReader.addField(FieldsReader.java:385)
	at org.apache.lucene.index.FieldsReader.doc(FieldsReader.java:231)
	at org.apache.lucene.index.SegmentReader.document(SegmentReader.java:1013)
	at org.apache.lucene.index.DirectoryReader.document(DirectoryReader.java:520)
	at org.apache.lucene.index.FilterIndexReader.document(FilterIndexReader.java:149)
	at org.apache.lucene.index.IndexReader.document(IndexReader.java:947)
	at org.apache.lucene.search.IndexSearcher.doc(IndexSearcher.java:152)
	at org.apache.lucene.search.MultiSearcher.doc(MultiSearcher.java:156)
	at org.apache.lucene.search.Hits.doc(Hits.java:180)
	at de.fhg.scai.bio.tamara.corpusBuilding.LuceneCmdLineInterface.queryMedline(LuceneCmdLineInterface.java:178)
	at de.fhg.scai.bio.tamara.corpusBuilding.LuceneCmdLineInterface.main(LuceneCmdLineInterface.java:152)


this line which causes problems is:
String docText = hits.doc(j).getField("DOCUMENT").stringValue() ; 

I am using java 1.6 and I tried solving this issue with different garbage collectors (-XX:+UseParallelGC
and -XX:+UseParallelOldGC) but it didn't help.

Does anyone have any idea how to solve this problem?

There is also an official bug report:
http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6293787

Help is much appreciated. :)

Best regards,
Tamara Bobic

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