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
>>>>
>>>
>>>
