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From "Ian Zapczynski" <Ian.Zapczyn...@veritablelp.com>
Subject org.hsqldb.HsqlException: java.lang.NegativeArraySizeException
Date Wed, 16 Mar 2016 15:04:45 GMT
Hello,
 
We've had ManifoldCF 2.0.1 working well with SOLR for months on Windows 2012 using the single
process model.   We recently just noticed that new documents are not getting ingested, even
after restarting the job, the server, etc.   What I see in the logs are first a bunch of 500
errors coming out of SOLR as a result of ManifoldCF trying to index .tif files that are found
in the directory structure being indexed.   After that (not sure if related or not), I see
a bunch of these errors:
 
FATAL 2016-03-15 16:01:48,801 (Thread-1387745) - C:\apache-manifoldcf-2.0.1\example\.\./dbname.data
getFromFile failed 33337202
org.hsqldb.HsqlException: java.lang.NegativeArraySizeException
 at org.hsqldb.error.Error.error(Unknown Source)
 at org.hsqldb.persist.DataFileCache.getFromFile(Unknown Source)
 at org.hsqldb.persist.DataFileCache.get(Unknown Source)
 at org.hsqldb.persist.RowStoreAVLDisk.get(Unknown Source)
 at org.hsqldb.index.NodeAVLDisk.findNode(Unknown Source)
 at org.hsqldb.index.NodeAVLDisk.getRight(Unknown Source)
 at org.hsqldb.index.IndexAVL.next(Unknown Source)
 at org.hsqldb.index.IndexAVL.next(Unknown Source)
 at org.hsqldb.index.IndexAVL$IndexRowIterator.getNextRow(Unknown Source)
 at org.hsqldb.RangeVariable$RangeIteratorMain.findNext(Unknown Source)
 at org.hsqldb.RangeVariable$RangeIteratorMain.next(Unknown Source)
 at org.hsqldb.QuerySpecification.buildResult(Unknown Source)
 at org.hsqldb.QuerySpecification.getSingleResult(Unknown Source)
 at org.hsqldb.QuerySpecification.getResult(Unknown Source)
 at org.hsqldb.StatementQuery.getResult(Unknown Source)
 at org.hsqldb.StatementDMQL.execute(Unknown Source)
 at org.hsqldb.Session.executeCompiledStatement(Unknown Source)
 at org.hsqldb.Session.execute(Unknown Source)
 at org.hsqldb.jdbc.JDBCPreparedStatement.fetchResult(Unknown Source)
 at org.hsqldb.jdbc.JDBCPreparedStatement.executeQuery(Unknown Source)
 at org.apache.manifoldcf.core.database.Database.execute(Database.java:889)
 at org.apache.manifoldcf.core.database.Database$ExecuteQueryThread.run(Database.java:683)
Caused by: java.lang.NegativeArraySizeException
 at org.hsqldb.lib.StringConverter.readUTF(Unknown Source)
 at org.hsqldb.rowio.RowInputBinary.readString(Unknown Source)
 at org.hsqldb.rowio.RowInputBinary.readChar(Unknown Source)
 at org.hsqldb.rowio.RowInputBase.readData(Unknown Source)
 at org.hsqldb.rowio.RowInputBinary.readData(Unknown Source)
 at org.hsqldb.rowio.RowInputBase.readData(Unknown Source)
 at org.hsqldb.rowio.RowInputBinary.readData(Unknown Source)
 at org.hsqldb.rowio.RowInputBinaryDecode.readData(Unknown Source)
 at org.hsqldb.RowAVLDisk.<init>(Unknown Source)
 at org.hsqldb.persist.RowStoreAVLDisk.get(Unknown Source)
 ... 21 more
ERROR 2016-03-15 16:01:48,911 (Stuffer thread) - Stuffer thread aborting and restarting due
to database connection reset: Database exception: SQLException doing query (S1000): java.lang.NegativeArraySizeException
org.apache.manifoldcf.core.interfaces.ManifoldCFException: Database exception: SQLException
doing query (S1000): java.lang.NegativeArraySizeException
 at org.apache.manifoldcf.core.database.Database$ExecuteQueryThread.finishUp(Database.java:702)
 at org.apache.manifoldcf.core.database.Database.executeViaThread(Database.java:728)
 at org.apache.manifoldcf.core.database.Database.executeUncachedQuery(Database.java:771)
 at org.apache.manifoldcf.core.database.Database$QueryCacheExecutor.create(Database.java:1444)
 at org.apache.manifoldcf.core.cachemanager.CacheManager.findObjectsAndExecute(CacheManager.java:146)
 at org.apache.manifoldcf.core.database.Database.executeQuery(Database.java:191)
 at org.apache.manifoldcf.core.database.DBInterfaceHSQLDB.performQuery(DBInterfaceHSQLDB.java:916)
 at org.apache.manifoldcf.core.database.BaseTable.performQuery(BaseTable.java:221)
 at org.apache.manifoldcf.agents.incrementalingest.IncrementalIngester.getPipelineDocumentIngestDataChunk(IncrementalIngester.java:1783)
 at org.apache.manifoldcf.agents.incrementalingest.IncrementalIngester.getPipelineDocumentIngestDataMultiple(IncrementalIngester.java:1748)
 at org.apache.manifoldcf.agents.incrementalingest.IncrementalIngester.getPipelineDocumentIngestDataMultiple(IncrementalIngester.java:1703)
 at org.apache.manifoldcf.crawler.system.StufferThread.run(StufferThread.java:254)
Caused by: java.sql.SQLException: java.lang.NegativeArraySizeException
 at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source)
 at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source)
 at org.hsqldb.jdbc.JDBCPreparedStatement.fetchResult(Unknown Source)
 at org.hsqldb.jdbc.JDBCPreparedStatement.executeQuery(Unknown Source)
 at org.apache.manifoldcf.core.database.Database.execute(Database.java:889)
 at org.apache.manifoldcf.core.database.Database$ExecuteQueryThread.run(Database.java:683)
Caused by: org.hsqldb.HsqlException: java.lang.NegativeArraySizeException
 
After these errors occur, the job just seems to hang and not process any further documents
or log anything more in the manifoldcf.log.   So I see the error is coming out of the HyperSQL
database, but I don't know why.   There is sufficient disk space.   Now the database file
is 33 Gb (larger than I'd expect for our ~110,000 documents), but I haven't seen any evidence
that we're hitting a limit on file size.   I'm afraid I'm not sure where to go from here to
further nail down the problem.
 
As always, any and all help is much appreciated.
 
Thanks,
 
-Ian

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