I committed a fix for this hang to trunk.
Karl
On Mon, May 13, 2019 at 11:40 AM Karl Wright <daddy...@gmail.com> wrote:
> 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
>> >>>>
>> >>>
>> >>>
>>
>>
