Hi Ian,

The database size seems way too big for this crawl size.  I've not seen this problem before but I suspect that whatever is causing the bloat is also causing HSQLDB to fail.

Can you give me further details about what repository connections you are using?  It is possible that there's a heretofore unknown pathological case you are running into during the crawl.  Are there any custom connectors involved?

If we rule out a bug of some kind, then the next thing to do would be to go to a real database, e.g. PostgreSQL.

Karl


On Wed, Mar 16, 2016 at 11:04 AM, Ian Zapczynski <Ian.Zapczynski@veritablelp.com> wrote:
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