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[Exist-open] Exception while undoing transactions; is the database corrupted?
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From: Raviv M-G <ra...@gm...> - 2011-04-22 15:16:30
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Hi all, While renaming collections in the Java Admin Client, the process crashed. Now I can't seem to get eXist to start up again. I've pasted the exist.log output below. Any advice? I'm using eXist 1.4.1 rev14247 on RHL 5.1. Thanks, Raviv 2011-04-22 11:07:09,153 [main] INFO (Configuration.java [<init>]:266) - Reading configuration from file /n/nobackup1/freeman_lab/Patents/eXist/conf.xml 2011-04-22 11:07:09,410 [main] WARN (XQueryContext.java [lookupModuleClass]:2901) - Module http://exist-db.org/xquery/httpclient could not be initialized due to a missing dependancy (NoClassDefFoundError): org/apache/commons/httpclient/URIException 2011-04-22 11:07:09,421 [main] INFO (eXistURLStreamHandlerFactory.java [init]:53) - Succesfully registered eXistURLStreamHandlerFactory. 2011-04-22 11:07:09,423 [main] INFO (Configuration.java [configureValidation]:1228) - Add catalog uri file:/n/nobackup1/freeman_lab/Patents/eXist/webapp//WEB-INF/catalog.xml 2011-04-22 11:07:09,425 [main] INFO (GrammarPool.java [<init>]:53) - Initializing GrammarPool. 2011-04-22 11:07:09,428 [main] INFO (BrokerPool.java [<init>]:583) - database instance 'exist' will have between 1 and 20 brokers 2011-04-22 11:07:09,428 [main] INFO (BrokerPool.java [<init>]:590) - database instance 'exist' will be synchronized every 120,000 ms 2011-04-22 11:07:09,428 [main] INFO (BrokerPool.java [<init>]:597) - database instance 'exist' will wait 120,000 ms during shutdown 2011-04-22 11:07:09,429 [main] INFO (BrokerPool.java [<init>]:603) - database instance 'exist' is enabled for transactions : true 2011-04-22 11:07:09,540 [main] INFO (FileLock.java [message]:276) - File lock last access timestamp: Apr 22, 2011 /n/home08/ravivmg/freeman_lab/Patents/eXist/webapp/WEB-INF/data/dbx_dir.lck 2011-04-22 11:07:09,541 [main] INFO (FileLock.java [message]:276) - Found a stale lockfile. Trying to remove it: /n/home08/ravivmg/freeman_lab/Patents/eXist/webapp/WEB-INF/data/dbx_dir.lck 2011-04-22 11:07:09,541 [main] INFO (FileLock.java [release]:175) - Deleting lock file: /n/home08/ravivmg/freeman_lab/Patents/eXist/webapp/WEB-INF/data/dbx_dir.lck 2011-04-22 11:07:09,554 [main] INFO (DefaultCacheManager.java [<init>]:141) - Cache settings: 49,152k; totalPages: 12,288; maxCacheSize: 11,059 2011-04-22 11:07:09,572 [main] INFO (XQueryPool.java [<init>]:112) - QueryPool: size = 128; maxStackSize = 5; timeout = 120,000; timeoutCheckInterval = 30,000 2011-04-22 11:07:09,593 [main] INFO (FileLock.java [message]:276) - File lock last access timestamp: Apr 22, 2011 /n/home08/ravivmg/freeman_lab/Patents/eXist/webapp/WEB-INF/data/journal.lck 2011-04-22 11:07:09,593 [main] INFO (FileLock.java [message]:276) - Found a stale lockfile. Trying to remove it: /n/home08/ravivmg/freeman_lab/Patents/eXist/webapp/WEB-INF/data/journal.lck 2011-04-22 11:07:09,593 [main] INFO (FileLock.java [release]:175) - Deleting lock file: /n/home08/ravivmg/freeman_lab/Patents/eXist/webapp/WEB-INF/data/journal.lck 2011-04-22 11:07:09,654 [main] INFO (IndexManager.java [<init>]:89) - Registered index org.exist.indexing.ngram.NGramIndex as ngram-index 2011-04-22 11:07:09,741 [main] INFO (IndexManager.java [<init>]:89) - Registered index org.exist.indexing.lucene.LuceneIndex as lucene-index 2011-04-22 11:07:09,747 [main] INFO (IndexManager.java [<init>]:89) - Registered index org.exist.fulltext.FTIndex as ft-legacy-index 2011-04-22 11:07:09,949 [main] INFO (RecoveryManager.java [recover]:109) - Scanning journal... 2011-04-22 11:07:28,667 [main] INFO (RecoveryManager.java [recover]:144) - Dirty transactions: 4 2011-04-22 11:07:28,667 [main] INFO (RecoveryManager.java [doRecovery]:186) - Running recovery ... 2011-04-22 11:07:28,667 [main] INFO (RecoveryManager.java [doRecovery]:195) - First pass: redoing 4 transactions... 2011-04-22 11:09:09,662 [main] INFO (RecoveryManager.java [doRecovery]:228) - Redo processed 1 out of 4 transactions. 2011-04-22 11:09:09,662 [main] INFO (RecoveryManager.java [doRecovery]:233) - Second pass: undoing dirty transactions. Uncommitted transactions: 3 2011-04-22 11:09:48,027 [main] WARN (RecoveryManager.java [doRecovery]:262) - Exception caught while undoing dirty transactions. Remaining transactions to be undone: 3 java.lang.NullPointerException at org.exist.storage.index.BFile$SinglePage.setOffset(BFile.java:2640) at org.exist.storage.index.BFile.storeValueHelper(BFile.java:1347) at org.exist.storage.index.BFile.undoRemoveValue(BFile.java:1103) at org.exist.storage.index.RemoveValueLoggable.undo(RemoveValueLoggable.java:96) at org.exist.storage.recovery.RecoveryManager.doRecovery(RecoveryManager.java:257) at org.exist.storage.recovery.RecoveryManager.recover(RecoveryManager.java:154) at org.exist.storage.txn.TransactionManager.runRecovery(TransactionManager.java:130) at org.exist.storage.BrokerPool.initialize(BrokerPool.java:791) at org.exist.storage.BrokerPool.<init>(BrokerPool.java:655) at org.exist.storage.BrokerPool.configure(BrokerPool.java:214) at org.exist.xmldb.DatabaseImpl.configure(DatabaseImpl.java:100) at org.exist.xmldb.DatabaseImpl.getLocalCollection(DatabaseImpl.java:175) at org.exist.xmldb.DatabaseImpl.getCollection(DatabaseImpl.java:155) at org.exist.xmldb.DatabaseImpl.getCollection(DatabaseImpl.java:150) at org.xmldb.api.DatabaseManager.getCollection(Unknown Source) at org.exist.client.InteractiveClient.connect(InteractiveClient.java:282) at org.exist.client.InteractiveClient.connectToDatabase(InteractiveClient.java:2289) at org.exist.client.InteractiveClient.run(InteractiveClient.java:2375) at org.exist.client.InteractiveClient.main(InteractiveClient.java:261) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.exist.start.Main.invokeMain(Main.java:128) at org.exist.start.Main.run(Main.java:407) at org.exist.start.Main.main(Main.java:59) 2011-04-22 11:09:48,028 [main] WARN (RecoveryManager.java [doRecovery]:265) - Log entry that caused the exception: [305, 36290035] org.exist.storage.index.RemoveValueLoggable [BFile] - remove value with tid 12 from page 83838 2011-04-22 11:09:48,065 [main] INFO (NativeBroker.java [sync]:3220) - Memory: 505,088K total; 1,820,480K max; 73,510K free 2011-04-22 11:09:48,065 [main] INFO (BTree.java [printStatistics]:2356) - dom.dbx INDEX Buffers occupation : 100% (2458 out of 2458) Cache efficiency : 99% 2011-04-22 11:09:48,066 [main] INFO (DOMFile.java [printStatistics]:1434) - dom.dbx DATA Buffers occupation : 100% (256 out of 256) Cache efficiency : 0% 2011-04-22 11:09:48,066 [main] INFO (BTree.java [printStatistics]:2356) - collections.dbx INDEX Buffers occupation : 100% (64 out of 64) Cache efficiency : 99% 2011-04-22 11:09:48,066 [main] INFO (BFile.java [printStatistics]:427) - collections.dbx DATA Buffers occupation : 0% (0 out of 64) Cache efficiency : 91% 2011-04-22 11:09:48,066 [main] INFO (BTree.java [printStatistics]:2356) - elements.dbx INDEX Buffers occupation : 0% (0 out of 64) Cache efficiency : N/A 2011-04-22 11:09:48,067 [main] INFO (BFile.java [printStatistics]:427) - elements.dbx DATA Buffers occupation : 0% (0 out of 64) Cache efficiency : N/A 2011-04-22 11:09:48,067 [main] INFO (BTree.java [printStatistics]:2356) - values.dbx INDEX Buffers occupation : 0% (0 out of 64) Cache efficiency : N/A 2011-04-22 11:09:48,067 [main] INFO (BFile.java [printStatistics]:427) - values.dbx DATA Buffers occupation : 0% (0 out of 64) Cache efficiency : N/A 2011-04-22 11:09:48,067 [main] ERROR (BrokerPool.java [configure]:236) - Unable to initialialize database instance 'exist': Recovery aborted org.exist.storage.journal.LogException: Recovery aborted at org.exist.storage.recovery.RecoveryManager.doRecovery(RecoveryManager.java:266) at org.exist.storage.recovery.RecoveryManager.recover(RecoveryManager.java:154) at org.exist.storage.txn.TransactionManager.runRecovery(TransactionManager.java:130) at org.exist.storage.BrokerPool.initialize(BrokerPool.java:791) at org.exist.storage.BrokerPool.<init>(BrokerPool.java:655) at org.exist.storage.BrokerPool.configure(BrokerPool.java:214) at org.exist.xmldb.DatabaseImpl.configure(DatabaseImpl.java:100) at org.exist.xmldb.DatabaseImpl.getLocalCollection(DatabaseImpl.java:175) at org.exist.xmldb.DatabaseImpl.getCollection(DatabaseImpl.java:155) at org.exist.xmldb.DatabaseImpl.getCollection(DatabaseImpl.java:150) at org.xmldb.api.DatabaseManager.getCollection(Unknown Source) at org.exist.client.InteractiveClient.connect(InteractiveClient.java:282) at org.exist.client.InteractiveClient.connectToDatabase(InteractiveClient.java:2289) at org.exist.client.InteractiveClient.run(InteractiveClient.java:2375) at org.exist.client.InteractiveClient.main(InteractiveClient.java:261) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.exist.start.Main.invokeMain(Main.java:128) at org.exist.start.Main.run(Main.java:407) at org.exist.start.Main.main(Main.java:59) |