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From Maximilian Bode <maximilian.b...@tngtech.com>
Subject Re: JDBCInputFormat GC overhead limit exceeded error
Date Wed, 20 Jan 2016 17:03:14 GMT
Hi Stephan,

thanks for your fast answer. Just setting the Flink-managed memory to a low value would not
have worked for us, as we need joins etc. in the same job.

After investigating the JDBCInputFormat, we found the line 
statement = dbConn.createStatement(ResultSet.TYPE_SCROLL_INSENSITIVE, ResultSet.CONCUR_READ_ONLY);
to be the culprit; to be more exact, the scrollable result set. When replaced with TYPE_FORWARD_ONLY,
some changes have to be made to nextRecord() and reachedEnd(), but this does the job without
memory leak.

Another change that might be useful (as far as performance is concerned) is disabling autocommits
and letting users decide the fetchSize (somewhat in parallel to batchInterval in JDBCOutputFormat).

Maximilian Bode * Junior Consultant * maximilian.bode@tngtech.com * 0176 1000 75 50
TNG Technology Consulting GmbH, Betastr. 13a, 85774 Unterföhring
Geschäftsführer: Henrik Klagges, Christoph Stock, Dr. Robert Dahlke
Sitz: Unterföhring * Amtsgericht München * HRB 135082

> Am 19.01.2016 um 21:26 schrieb Stephan Ewen <sewen@apache.org>:
> Hi!
> This kind of error (GC overhead exceeded) usually means that the system is reaching a
state where it has very many still living objects and frees little memory during each collection.
As a consequence, it is basically busy with only garbage collection.
> Your job probably has about 500-600 MB or free memory, the rest is at that memory size
reserved for JVM overhead and Flink's worker memory.
> Now, since your job actually does not keep any objects or rows around, this should be
plenty. I can only suspect that the Oracle JDBC driver is very memory hungry, thus pushing
the system to the limit. (I found this, for example 
> What you can do:
>  For this kind of job, you can simply tell Flink to not reserve as much memory, by using
the option "taskmanager.memory.size=1". If the JDBC driver has no leak, but is simply super
hungry, this should solve it.
> Greetings,
> Stephan
> I also found these resources concerning Oracle JDBC memory:
>  - http://stackoverflow.com/questions/2876895/oracle-t4cpreparedstatement-memory-leaks
(bottom answer)
>  - https://community.oracle.com/thread/2220078?tstart=0 <https://community.oracle.com/thread/2220078?tstart=0>
> On Tue, Jan 19, 2016 at 5:44 PM, Maximilian Bode <maximilian.bode@tngtech.com <mailto:maximilian.bode@tngtech.com>>
> Hi Robert,
> I am using 0.10.1.
>> Am 19.01.2016 um 17:42 schrieb Robert Metzger <rmetzger@apache.org <mailto:rmetzger@apache.org>>:
>> Hi Max,
>> which version of Flink are you using?
>> On Tue, Jan 19, 2016 at 5:35 PM, Maximilian Bode <maximilian.bode@tngtech.com
<mailto:maximilian.bode@tngtech.com>> wrote:
>> Hi everyone,
>> I am facing a problem using the JDBCInputFormat which occurred in a larger Flink
job. As a minimal example I can reproduce it when just writing data into a csv after having
read it from a database, i.e.
>> DataSet<Tuple1<String>> existingData = env.createInput(
>> 	JDBCInputFormat.buildJDBCInputFormat()
>> 		.setDrivername("oracle.jdbc.driver.OracleDriver")
>> 		.setUsername(…)
>> 		.setPassword(…)
>> 		.setDBUrl(…)
>> 		.setQuery("select DATA from TABLENAME")
>> 		.finish(),
>> 	new TupleTypeInfo<>(Tuple1.class, BasicTypeInfo.STRING_TYPE_INFO));
>> existingData.writeAsCsv(…);
>> where DATA is a column containing strings of length ~25 characters and TABLENAME
contains 20 million rows.
>> After starting the job on a YARN cluster (using -tm 3072 and leaving the other memory
settings at default values), Flink happily goes along at first but then fails after something
like three million records have been sent by the JDBCInputFormat. The Exception reads "The
slot in which the task was executed has been released. Probably loss of TaskManager …".
The local taskmanager.log in the affected container reads
>> "java.lang.OutOfMemoryError: GC overhead limit exceeded
>>         at java.util.Collections$UnmodifiableCollection.iterator(Collections.java:1063)
>>         at org.jboss.netty.channel.socket.nio.NioClientBoss.processConnectTimeout(NioClientBoss.java:119)
>>         at org.jboss.netty.channel.socket.nio.NioClientBoss.process(NioClientBoss.java:83)
>>         at org.jboss.netty.channel.socket.nio.AbstractNioSelector.run(AbstractNioSelector.java:312)
>>         at org.jboss.netty.channel.socket.nio.NioClientBoss.run(NioClientBoss.java:42)
>>         at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
>>         at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
>>         at java.lang.Thread.run(Thread.java:744)"
>> Any ideas what is going wrong here?
>> Cheers,
>> Max
>> — 
>> Maximilian Bode * Junior Consultant * maximilian.bode@tngtech.com <mailto:maximilian.bode@tngtech.com>
>> TNG Technology Consulting GmbH, Betastr. 13a, 85774 Unterföhring
>> Geschäftsführer: Henrik Klagges, Christoph Stock, Dr. Robert Dahlke
>> Sitz: Unterföhring * Amtsgericht München * HRB 135082

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