Thanks -- this shows a classic deadlock occurring, where the System.exit()
call effectively blocks the thread that does it from exiting, and thus
blocks the system from shutting down. This is a change of behavior in the
JVM; not sure when it happened, but this didn't happen before. But it
easily addressed.
Karl
On Mon, May 13, 2019 at 10:58 AM Olivier Tavard <
olivier.tav...@francelabs.com> wrote:
> 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
> >>>>
> >>>
> >>>
>
>
