Hi Karl, Thank you for your mail. I installed an ootb MCF 2.13 to have a clean installation. I launched the File-based multiprocess example and I did the previous tests I mentioned. I managed to see the error that you told me about :
agents process ran out of memory - shutting down java.lang.OutOfMemoryError: Java heap space at com.mysql.jdbc.Buffer.ensureCapacity(Buffer.java:155) at com.mysql.jdbc.Buffer.writeBytesNoNull(Buffer.java:513) at com.mysql.jdbc.MysqlIO.readRemainingMultiPackets(MysqlIO.java:3116) at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2971) at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2871) at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3414) at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:910) at com.mysql.jdbc.MysqlIO.nextRow(MysqlIO.java:1405) at com.mysql.jdbc.MysqlIO.readSingleRowSet(MysqlIO.java:2816) at com.mysql.jdbc.MysqlIO.getResultSet(MysqlIO.java:467) at com.mysql.jdbc.MysqlIO.readResultsForQueryOrUpdate(MysqlIO.java:2510) at com.mysql.jdbc.MysqlIO.readAllResults(MysqlIO.java:1746) at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2135) at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2542) at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1734) at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:1885) at org.apache.manifoldcf.jdbc.JDBCConnection$PreparedStatementQueryThread.run(JDBCConnection.java:1392) But the mcf-agent process is still active, it was not shut down. I did a new thread dump, I obtained this : Full thread dump OpenJDK 64-Bit Server VM (25.212-b01 mixed mode): "Shutdown thread" #8 prio=5 os_prio=0 tid=0x00007f8ccc014000 nid=0x436a in Object.wait() [0x00007f8c2a9e8000] java.lang.Thread.State: TIMED_WAITING (on object monitor) at java.lang.Object.wait(Native Method) at org.apache.manifoldcf.core.system.ManifoldCF.sleep(ManifoldCF.java:1248) - locked <0x00000000e0930708> (a java.lang.Integer) at org.apache.manifoldcf.crawler.system.CrawlerAgent.stopSystem(CrawlerAgent.java:617) at org.apache.manifoldcf.crawler.system.CrawlerAgent.stopAgent(CrawlerAgent.java:249) at org.apache.manifoldcf.agents.system.AgentsDaemon.stopAgents(AgentsDaemon.java:168) - locked <0x00000000eab32808> (a java.util.HashMap) at org.apache.manifoldcf.agents.system.AgentsDaemon$AgentsShutdownHook.doCleanup(AgentsDaemon.java:395) at org.apache.manifoldcf.core.system.ManifoldCF.cleanUpEnvironment(ManifoldCF.java:1540) - locked <0x00000000eab24af8> (a java.util.ArrayList) - locked <0x00000000eab24ca0> (a java.lang.Integer) at org.apache.manifoldcf.core.system.ManifoldCF$ShutdownThread.run(ManifoldCF.java:1718) "MySQL Statement Cancellation Timer" #2567 daemon prio=5 os_prio=0 tid=0x00007f8c84061800 nid=0x4090 in Object.wait() [0x00007f8c2aeed000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:502) at java.util.TimerThread.mainLoop(Timer.java:526) - locked <0x00000000ebe79d20> (a java.util.TaskQueue) at java.util.TimerThread.run(Timer.java:505) "Connection pool reaper" #2565 daemon prio=5 os_prio=0 tid=0x00007f8cf809d000 nid=0x408e waiting on condition [0x00007f8c2aceb000] java.lang.Thread.State: TIMED_WAITING (sleeping) at java.lang.Thread.sleep(Native Method) at org.apache.manifoldcf.core.jdbcpool.ConnectionPoolManager$ConnectionCloserThread.run(ConnectionPoolManager.java:152) "Worker thread '0'" #66 daemon prio=5 os_prio=0 tid=0x00007f8cfc209800 nid=0x35d8 in Object.wait() [0x00007f8d0c6f4000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) at java.lang.Thread.join(Thread.java:1252) - locked <0x00000000eab24b28> (a org.apache.manifoldcf.core.system.ManifoldCF$ShutdownThread) at java.lang.Thread.join(Thread.java:1326) at java.lang.ApplicationShutdownHooks.runHooks(ApplicationShutdownHooks.java:107) at java.lang.ApplicationShutdownHooks$1.run(ApplicationShutdownHooks.java:46) at java.lang.Shutdown.runHooks(Shutdown.java:123) at java.lang.Shutdown.sequence(Shutdown.java:167) at java.lang.Shutdown.exit(Shutdown.java:212) - locked <0x00000000eaae4150> (a java.lang.Class for java.lang.Shutdown) at java.lang.Runtime.exit(Runtime.java:109) at java.lang.System.exit(System.java:971) at org.apache.manifoldcf.crawler.system.WorkerThread.run(WorkerThread.java:851) "Connection pool reaper" #13 daemon prio=5 os_prio=0 tid=0x00007f8cfc04b000 nid=0x35a0 waiting on condition [0x00007f8d2c47b000] java.lang.Thread.State: TIMED_WAITING (sleeping) at java.lang.Thread.sleep(Native Method) at org.apache.manifoldcf.core.jdbcpool.ConnectionPoolManager$ConnectionCloserThread.run(ConnectionPoolManager.java:152) "Service Thread" #7 daemon prio=9 os_prio=0 tid=0x00007f8d3c0b6000 nid=0x359c runnable [0x0000000000000000] java.lang.Thread.State: RUNNABLE "C1 CompilerThread1" #6 daemon prio=9 os_prio=0 tid=0x00007f8d3c0b3000 nid=0x359b waiting on condition [0x0000000000000000] java.lang.Thread.State: RUNNABLE "C2 CompilerThread0" #5 daemon prio=9 os_prio=0 tid=0x00007f8d3c0b0800 nid=0x359a waiting on condition [0x0000000000000000] java.lang.Thread.State: RUNNABLE "Signal Dispatcher" #4 daemon prio=9 os_prio=0 tid=0x00007f8d3c0af000 nid=0x3599 waiting on condition [0x0000000000000000] java.lang.Thread.State: RUNNABLE "Finalizer" #3 daemon prio=8 os_prio=0 tid=0x00007f8d3c07b800 nid=0x3598 in Object.wait() [0x00007f8d410d3000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:144) - locked <0x00000000eaaf2038> (a java.lang.ref.ReferenceQueue$Lock) at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:165) at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:216) "Reference Handler" #2 daemon prio=10 os_prio=0 tid=0x00007f8d3c079000 nid=0x3597 in Object.wait() [0x00007f8d411d4000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) at java.lang.Object.wait(Object.java:502) at java.lang.ref.Reference.tryHandlePending(Reference.java:191) - locked <0x00000000eaaf21f0> (a java.lang.ref.Reference$Lock) at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:153) "main" #1 prio=5 os_prio=0 tid=0x00007f8d3c00b800 nid=0x3595 in Object.wait() [0x00007f8d45902000] java.lang.Thread.State: TIMED_WAITING (on object monitor) at java.lang.Object.wait(Native Method) at org.apache.manifoldcf.core.system.ManifoldCF.sleep(ManifoldCF.java:1248) - locked <0x00000000e26ec910> (a java.lang.Integer) at org.apache.manifoldcf.agents.system.AgentsDaemon.runAgents(AgentsDaemon.java:115) at org.apache.manifoldcf.agents.AgentRun.doExecute(AgentRun.java:64) at org.apache.manifoldcf.agents.BaseAgentsInitializationCommand.execute(BaseAgentsInitializationCommand.java:37) at org.apache.manifoldcf.agents.AgentRun.main(AgentRun.java:93) "VM Thread" os_prio=0 tid=0x00007f8d3c06f800 nid=0x3596 runnable "VM Periodic Task Thread" os_prio=0 tid=0x00007f8d3c0b9000 nid=0x359d waiting on condition JNI global references: 13 Heap def new generation total 157248K, used 39902K [0x00000000e0000000, 0x00000000eaaa0000, 0x00000000eaaa0000) eden space 139776K, 28% used [0x00000000e0000000, 0x00000000e26f7a80, 0x00000000e8880000) from space 17472K, 0% used [0x00000000e9990000, 0x00000000e9990000, 0x00000000eaaa0000) to space 17472K, 0% used [0x00000000e8880000, 0x00000000e8880000, 0x00000000e9990000) tenured generation total 349568K, used 173322K [0x00000000eaaa0000, 0x0000000100000000, 0x0000000100000000) the space 349568K, 49% used [0x00000000eaaa0000, 0x00000000f53e2ac8, 0x00000000f53e2c00, 0x0000000100000000) Metaspace used 16548K, capacity 16750K, committed 17024K, reserved 1064960K class space used 1806K, capacity 1891K, committed 1920K, reserved 1048576K Best regards, Olivier > Le 7 mai 2019 à 13:02, Karl Wright <daddy...@gmail.com> a écrit : > > The thread dump is not helpful. I see no traces for any threads that > identify code from MCF at all. That's new and has nothing to do with MCF; > it's probably a new Java "feature". > > The OutOfMemoryException should, I've confirmed, be rethrown. The Worker > Thread code does in fact catch the exception and terminate the process: > >>>>>>> > catch (OutOfMemoryError e) > { > System.err.println("agents process ran out of memory - shutting > down"); > e.printStackTrace(System.err); > System.exit(-200); > } > <<<<<< > > So that is what you should see happening. > > Are you providing the complete stack trace from your out-of-memory > exception? That would help confirm the picture. It had to have been > printed from somewhere; it goes to standard error, whatever that is. > > Karl > > > On Tue, May 7, 2019 at 6:42 AM Karl Wright <daddy...@gmail.com> wrote: > >> Hi Olivier, >> >> Any out-of-memory exception that makes it to the top level should cause >> the agents process to shut itself down. >> >> The reason for this is simple: in a multithread environment, with lots of >> third-party jars, an out-of-memory in one thread is usually indicative of >> an out-of-memory in other threads as well, and we cannot count on that >> third-party software being rigorous about letting an OutOfMemoryException >> be thrown to the top level. So we tend to get corrupted results that are >> hard to recover from. >> >> In this case, the exception is being thrown within the JDBCConnector, so >> it ought to rethrow the OutOfMemoryException. Let me confirm that is what >> the code indicates. >> >> Karl >> >> >> On Tue, May 7, 2019 at 6:14 AM Olivier Tavard < >> olivier.tav...@francelabs.com> wrote: >> >>> Hi Karl, >>> >>> Thank you for your help. >>> Indeed I found a OoM error in the logs of the MCF-agent process : >>> java.lang.OutOfMemoryError: Java heap space >>> at com.mysql.jdbc.Buffer.<init>(Buffer.java:58) >>> at com.mysql.jdbc.MysqlIO.nextRow(MysqlIO.java:1441) >>> at com.mysql.jdbc.MysqlIO.readSingleRowSet(MysqlIO.java:2816) >>> at com.mysql.jdbc.MysqlIO.getResultSet(MysqlIO.java:467) >>> at >>> com.mysql.jdbc.MysqlIO.readResultsForQueryOrUpdate(MysqlIO.java:2510) >>> at com.mysql.jdbc.MysqlIO.readAllResults(MysqlIO.java:1746) >>> at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2135) >>> at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2542) >>> at >>> com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1734) >>> at >>> com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:1885) >>> at >>> org.apache.manifoldcf.jdbc.JDBCConnection$PreparedStatementQueryThread.run(JDBCConnection.java:1392) >>> >>> >>> But the MCF process agent was not killed, it is still active. Why is the >>> process still active in this case ? Since we know that we can get an OOM, >>> couldn't we find an elegant way to notify users of this problem from the >>> MCF admin UI, rather than just having the process endlessly active ? >>> >>> As for the OOM, the work around we decided to use is to increase the >>> values of xms and xmx java memory in options.env.unix. >>> I also attached the thread dump to this mail. >>> >>> Thanks, >>> Best regards, >>> >>> Olivier >>> >>> Le 6 mai 2019 à 12:55, Karl Wright <daddy...@gmail.com> a écrit : >>> >>> It sounds like there might be an out-of-memory situation, although if >>> that is the case I would expect that the MCF agents process would just shut >>> itself down. >>> >>> If the process is hung, it should be easy to get a thread dump. That >>> would be the first step. >>> >>> Some thoughts as to what might be happening: there might be an >>> out-of-memory condition that is being silently eaten somewhere. MCF relies >>> on its connectors to use streams rather than load documents into memory, >>> BUT we're at the mercy of the JDBC drivers and Tika. So another experiment >>> would be to try to crawl your documents without the tika extractor (just >>> send them to the null output connector) and see if that succeeds. If it >>> does, then maybe try the external Tika Service connector instead and see >>> what happens then. >>> >>> Karl >>> >>> >>> On Mon, May 6, 2019 at 5:56 AM Olivier Tavard < >>> olivier.tav...@francelabs.com> wrote: >>> >>>> Hi MCF community, >>>> >>>> We have some issues with the JDBC connector to index database with large >>>> LONGBLOB into it : I mean files more than 100 MB. >>>> To reproduce the issue, I created a simple database on MySQL 5.7 with >>>> only one table into it with 2 columns : id (int) and data (longblob). >>>> There are 8 records in the table : two records with very small files : >>>> less than 5 KB and 6 records with a large file of 192 MB. >>>> >>>> If I include in my crawl only one big BLOB, the crawl is successful. >>>> seeding query : SELECT id AS $(IDCOLUMN) FROM data WHERE id =6 >>>> >>>> But if I include more than 2 of these (with a WHERE IN condition or if >>>> select all the records of the table) the job stays in running condition but >>>> no document is processed : >>>> seeding query : SELECT id AS $(IDCOLUMN) FROM data WHERE id IN (6,7) >>>> >>>> >>>> >>>> There is no message in the logs (even with debug mode activated). >>>> The tests were done in a Docker cluster on dedicated servers (4 cores, >>>> 32 GB RAM each). >>>> Regarding MCF, the version is 2.12. The MCF agent has 1GB of RAM (xmx >>>> and xmx) the internal database is PostgreSQL 10.1 and we use Zookeeper >>>> based synchronization. >>>> We have a dump of the database here : >>>> https://www.datafari.com/files/mcftest.tar.gz >>>> >>>> In other cases, we also encounter this error : >>>> Error: Unexpected jobqueue status - record id 1555190422690, expecting >>>> active status, saw 0 >>>> >>>> Any ideas of what the problem could be ? or at least why there is >>>> nothing in the debug log you think ? >>>> >>>> Thank you, >>>> Best regards, >>>> >>>> Olivier >>>> >>> >>>