(DEPRECATED) Apache Flink User Mailing List archive.

RE: Left join with unbalanced dataset

Posted by LINZ, Arnaud on
URL: http://deprecated-apache-flink-user-mailing-list-archive.369.s1.nabble.com/Left-join-with-unbalanced-dataset-tp4572p4600.html

Thanks,

I’m using the official 0.10 release. I will try to use the 0.10 snapshot.

 

FYI, setting the heap cut-off ratio to 0.5 lead to the following error :

 

12:20:17,313 INFO  org.apache.flink.yarn.YarnJobManager                          - Status of job c55216ab9383fd14e1d287a69a6e0f7e (KUBERA-GEO-BRUT2SEGMENT) changed to FAILING.

java.lang.Exception: The data preparation for task 'CHAIN GroupReduce (GroupReduce at calculeMinArea(TransfoStage2StageOnTaz.java:153)) -> Map (Key Extractor 1)' , caused an error: Error obtaining the sorted input: Thread 'SortMerger Reading Thread' terminated due to an exception: java.lang.OutOfMemoryError: Direct buffer memory

         at org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:465)

         at org.apache.flink.runtime.operators.BatchTask.invoke(BatchTask.java:354)

         at org.apache.flink.runtime.taskmanager.Task.run(Task.java:584)

         at java.lang.Thread.run(Thread.java:744)

Caused by: java.lang.RuntimeException: Error obtaining the sorted input: Thread 'SortMerger Reading Thread' terminated due to an exception: java.lang.OutOfMemoryError: Direct buffer memory

         at org.apache.flink.runtime.operators.sort.UnilateralSortMerger.getIterator(UnilateralSortMerger.java:619)

         at org.apache.flink.runtime.operators.BatchTask.getInput(BatchTask.java:1089)

         at org.apache.flink.runtime.operators.GroupReduceDriver.prepare(GroupReduceDriver.java:94)

         at org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:459)

         ... 3 more

Caused by: java.io.IOException: Thread 'SortMerger Reading Thread' terminated due to an exception: java.lang.OutOfMemoryError: Direct buffer memory

         at org.apache.flink.runtime.operators.sort.UnilateralSortMerger$ThreadBase.run(UnilateralSortMerger.java:800)

Caused by: org.apache.flink.runtime.io.network.netty.exception.LocalTransportException: java.lang.OutOfMemoryError: Direct buffer memory

         at org.apache.flink.runtime.io.network.netty.PartitionRequestClientHandler.exceptionCaught(PartitionRequestClientHandler.java:153)

         at io.netty.channel.AbstractChannelHandlerContext.invokeExceptionCaught(AbstractChannelHandlerContext.java:246)

         at io.netty.channel.AbstractChannelHandlerContext.fireExceptionCaught(AbstractChannelHandlerContext.java:224)

         at io.netty.channel.ChannelInboundHandlerAdapter.exceptionCaught(ChannelInboundHandlerAdapter.java:131)

         at io.netty.channel.AbstractChannelHandlerContext.invokeExceptionCaught(AbstractChannelHandlerContext.java:246)

         at io.netty.channel.AbstractChannelHandlerContext.fireExceptionCaught(AbstractChannelHandlerContext.java:224)

         at io.netty.channel.ChannelInboundHandlerAdapter.exceptionCaught(ChannelInboundHandlerAdapter.java:131)

         at io.netty.channel.AbstractChannelHandlerContext.invokeExceptionCaught(AbstractChannelHandlerContext.java:246)

         at io.netty.channel.AbstractChannelHandlerContext.notifyHandlerException(AbstractChannelHandlerContext.java:737)

         at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:310)

         at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:294)

         at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:846)

         at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:131)

         at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:511)

         at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:468)

         at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:382)

         at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:354)

         at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:112)

         at java.lang.Thread.run(Thread.java:744)

Caused by: io.netty.handler.codec.DecoderException: java.lang.OutOfMemoryError: Direct buffer memory

         at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:234)

         at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:308)

         ... 9 more

Caused by: java.lang.OutOfMemoryError: Direct buffer memory

         at java.nio.Bits.reserveMemory(Bits.java:658)

         at java.nio.DirectByteBuffer.<init>(DirectByteBuffer.java:123)

         at java.nio.ByteBuffer.allocateDirect(ByteBuffer.java:306)

         at io.netty.buffer.PoolArena$DirectArena.newUnpooledChunk(PoolArena.java:651)

         at io.netty.buffer.PoolArena.allocateHuge(PoolArena.java:237)

         at io.netty.buffer.PoolArena.allocate(PoolArena.java:215)

         at io.netty.buffer.PoolArena.reallocate(PoolArena.java:358)

         at io.netty.buffer.PooledByteBuf.capacity(PooledByteBuf.java:111)

         at io.netty.buffer.AbstractByteBuf.ensureWritable(AbstractByteBuf.java:251)

         at io.netty.buffer.AbstractByteBuf.writeBytes(AbstractByteBuf.java:849)

         at io.netty.buffer.AbstractByteBuf.writeBytes(AbstractByteBuf.java:841)

         at io.netty.buffer.AbstractByteBuf.writeBytes(AbstractByteBuf.java:831)

         at io.netty.handler.codec.ByteToMessageDecoder$1.cumulate(ByteToMessageDecoder.java:92)

         at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:228)

 

 

De : [hidden email] [mailto:[hidden email]] De la part de Stephan Ewen
Envoyé : mardi 2 février 2016 11:30
À : [hidden email]
Objet : Re: Left join with unbalanced dataset

 

Hi Arnaud!

 

Which version of Flink are you using? In 0.10.1, the Netty library version that we use has changed behavior, and allocates a lot of off-heap memory. Would be my guess that this is the cause. In 1.0-SNAPSHOT, that should be fixed, also on 0.10-SNAPSHOT.

 

If that turns out to be the cause, the good news is that we started discussing a 0.10.2 maintenance release that should also have a fix for that.

 

Greetings,

Stephan

 

 

On Tue, Feb 2, 2016 at 11:12 AM, LINZ, Arnaud <[hidden email]> wrote:

Hi,

 

Changing for a outer join did not change the error ; nor balancing the join with another dataset ; nor dividing parallelism level by 2 ; nor increasing memory by 2.

Heap size & thread number is OK under JvisualVM.  So the problem is elsewhere.

 

Do Flink uses off-heap memory ? How can I monitor it ?

 

Thanks,

Arnaud

 

10:58:53,384 INFO  org.apache.flink.yarn.YarnJobManager                          - Status of job 8b2ea62e16b82ccc2242bb5549d434a5 (KUBERA-GEO-BRUT2SEGMENT) changed to FAILING.

java.lang.Exception: The data preparation for task 'CHAIN GroupReduce (GroupReduce at process(TransfoStage2StageOnTaz.java:106)) -> Map (Map at writeExternalTable(HiveHCatDAO.java:206))' , caused an error: Error obtaining the sorted input: Thread 'SortMerger spilling thread' terminated due to an exception: java.io.IOException: I/O channel already closed. Could not fulfill: [hidden email]

          at org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:465)

          at org.apache.flink.runtime.operators.BatchTask.invoke(BatchTask.java:354)

          at org.apache.flink.runtime.taskmanager.Task.run(Task.java:584)

          at java.lang.Thread.run(Thread.java:744)

Caused by: java.lang.RuntimeException: Error obtaining the sorted input: Thread 'SortMerger spilling thread' terminated due to an exception: java.io.IOException: I/O channel already closed. Could not fulfill: [hidden email]

          at org.apache.flink.runtime.operators.sort.UnilateralSortMerger.getIterator(UnilateralSortMerger.java:619)

          at org.apache.flink.runtime.operators.BatchTask.getInput(BatchTask.java:1089)

          at org.apache.flink.runtime.operators.GroupReduceDriver.prepare(GroupReduceDriver.java:94)

          at org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:459)

          ... 3 more

Caused by: java.io.IOException: Thread 'SortMerger spilling thread' terminated due to an exception: java.io.IOException: I/O channel already closed. Could not fulfill: [hidden email]

          at org.apache.flink.runtime.operators.sort.UnilateralSortMerger$ThreadBase.run(UnilateralSortMerger.java:800)

Caused by: com.esotericsoftware.kryo.KryoException: java.io.IOException: I/O channel already closed. Could not fulfill: [hidden email]

          at com.esotericsoftware.kryo.io.Output.flush(Output.java:165)

          at org.apache.flink.api.java.typeutils.runtime.kryo.KryoSerializer.serialize(KryoSerializer.java:194)

          at org.apache.flink.api.java.typeutils.runtime.kryo.KryoSerializer.copy(KryoSerializer.java:247)

          at org.apache.flink.api.java.typeutils.runtime.TupleSerializerBase.copy(TupleSerializerBase.java:73)

          at org.apache.flink.api.java.typeutils.runtime.TupleSerializerBase.copy(TupleSerializerBase.java:73)

          at org.apache.flink.api.java.typeutils.runtime.TupleSerializerBase.copy(TupleSerializerBase.java:73)

          at org.apache.flink.runtime.operators.sort.NormalizedKeySorter.writeToOutput(NormalizedKeySorter.java:499)

          at org.apache.flink.runtime.operators.sort.UnilateralSortMerger$SpillingThread.go(UnilateralSortMerger.java:1344)

          at org.apache.flink.runtime.operators.sort.UnilateralSortMerger$ThreadBase.run(UnilateralSortMerger.java:796)

Caused by: java.io.IOException: I/O channel already closed. Could not fulfill: [hidden email]

          at org.apache.flink.runtime.io.disk.iomanager.AsynchronousFileIOChannel.addRequest(AsynchronousFileIOChannel.java:249)

          at org.apache.flink.runtime.io.disk.iomanager.AsynchronousBlockWriterWithCallback.writeBlock(AsynchronousBlockWriterWithCallback.java:54)

          at org.apache.flink.runtime.io.disk.iomanager.AsynchronousBlockWriterWithCallback.writeBlock(AsynchronousBlockWriterWithCallback.java:29)

          at org.apache.flink.runtime.io.disk.iomanager.ChannelWriterOutputView.writeSegment(ChannelWriterOutputView.java:217)

          at org.apache.flink.runtime.io.disk.iomanager.ChannelWriterOutputView.nextSegment(ChannelWriterOutputView.java:203)

          at org.apache.flink.runtime.memory.AbstractPagedOutputView.advance(AbstractPagedOutputView.java:140)

          at org.apache.flink.runtime.memory.AbstractPagedOutputView.write(AbstractPagedOutputView.java:201)

          at org.apache.flink.api.java.typeutils.runtime.DataOutputViewStream.write(DataOutputViewStream.java:39)

          at com.esotericsoftware.kryo.io.Output.flush(Output.java:163)

 

(…)

10:58:54,423 WARN  akka.remote.ReliableDeliverySupervisor                        - Association with remote system [akka.tcp://flink@172.21.125.13:40286] has failed, address is now gated for [5000] ms. Reason is: [Disassociated].
10:58:54,470 INFO  org.apache.flink.yarn.YarnJobManager                          - Container container_e11_1453202008841_2794_01_000025 is completed with diagnostics: Container [pid=14331,containerID=container_e11_1453202008841_2794_01_000025] is running beyond physical memory limits. Current usage: 8.0 GB of 8 GB physical memory used; 9.1 GB of 16.8 GB virtual memory used. Killing container.
Dump of the process-tree for container_e11_1453202008841_2794_01_000025 :
          |- PID PPID PGRPID SESSID CMD_NAME USER_MODE_TIME(MILLIS) SYSTEM_TIME(MILLIS) VMEM_USAGE(BYTES) RSSMEM_USAGE(PAGES) FULL_CMD_LINE
          |- 14331 14329 14331 14331 (bash) 0 0 108646400 308 /bin/bash -c /usr/java/default/bin/java -Xms5376m -Xmx5376m -XX:MaxDirectMemorySize=5376m  -Dlog.file=/data/3/hadoop/yarn/log/application_1453202008841_2794/container_e11_1453202008841_2794_01_000025/taskmanager.log -Dlogback.configurationFile=file:logback.xml -Dlog4j.configuration=file:log4j.properties org.apache.flink.yarn.YarnTaskManagerRunner --configDir . 1> /data/3/hadoop/yarn/log/application_1453202008841_2794/container_e11_1453202008841_2794_01_000025/taskmanager.out 2> /data/3/hadoop/yarn/log/application_1453202008841_2794/container_e11_1453202008841_2794_01_000025/taskmanager.err --streamingMode batch 
          |- 14348 14331 14331 14331 (java) 565583 11395 9636184064 2108473 /usr/java/default/bin/java -Xms5376m -Xmx5376m -XX:MaxDirectMemorySize=5376m -Dlog.file=/data/3/hadoop/yarn/log/application_1453202008841_2794/container_e11_1453202008841_2794_01_000025/taskmanager.log -Dlogback.configurationFile=file:logback.xml -Dlog4j.configuration=file:log4j.properties org.apache.flink.yarn.YarnTaskManagerRunner --configDir . --streamingMode batch 
 
Container killed on request. Exit code is 143
Container exited with a non-zero exit code 143
 
10:58:54,471 INFO  org.apache.flink.yarn.YarnJobManager         

 

 

 

De : LINZ, Arnaud
Envoyé : lundi 1 février 2016 09:40
À : [hidden email]
Objet : RE: Left join with unbalanced dataset

 

Hi,

Thanks, I can’t believe I missed the outer join operators… Will try them and will keep you informed.

I use the “official” 0.10 release from the maven repo. The off-heap memory I use is the one HDFS I/O uses (codec, DFSOutputstream threads…), but I don’t have many open files at once, and doubling the amount of memory did not solve the problem.

Arnaud

 

 

De : [hidden email] [[hidden email]] De la part de Stephan Ewen
Envoyé : dimanche 31 janvier 2016 20:57
À : [hidden email]
Objet : Re: Left join with unbalanced dataset

 

Hi!

 

YARN killing the application seems strange. The memory use that YARN sees should not change even when one node gets a lot or data.

 

Can you share what version of Flink (plus commit hash) you are using and whether you use off-heap memory or not?

 

Thanks,

Stephan

 

 

On Sun, Jan 31, 2016 at 10:47 AM, Till Rohrmann <[hidden email]> wrote:

Hi Arnaud,

 

the unmatched elements of A will only end up on the same worker node if they all share the same key. Otherwise, they will be evenly spread out across your cluster. However, I would also recommend you to use Flink's leftOuterJoin.

 

Cheers,

Till

 

On Sun, Jan 31, 2016 at 5:27 AM, Chiwan Park <[hidden email]> wrote:

Hi Arnaud,

To join two datasets, the community recommends using join operation rather than cogroup operation. For left join, you can use leftOuterJoin method. Flink’s optimizer decides distributed join execution strategy using some statistics of the datasets such as size of the dataset. Additionally, you can set join hint to help optimizer decide the strategy.

In transformations section [1] of Flink documentation, you can find about outer join operation in detail.

I hope this helps.

[1]: https://ci.apache.org/projects/flink/flink-docs-release-0.10/apis/programming_guide.html#transformations

Regards,
Chiwan Park

> On Jan 30, 2016, at 6:43 PM, LINZ, Arnaud <[hidden email]> wrote:
>
> Hello,
>
> I have a very big dataset A to left join with a dataset B that is half its size. That is to say, half of A records will be matched with one record of B, and the other half with null values.
>
> I used a CoGroup for that, but my batch fails because yarn kills the container due to memory problems.
>
> I guess that’s because one worker will get half of A dataset (the unmatched ones), and that’s too much for a single JVM
>
> Am I right in my diagnostic ? Is there a better way to left join unbalanced datasets ?
>
> Best regards,
>
> Arnaud
>
>
>

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