[FLINK-11783] Deadlock during Join operation

• Type: Bug
• Status: Open
• Priority: Not a Priority
• Resolution: Unresolved
• Affects Version/s: 1.7.2
• Component/s: API / DataSet
• Labels: auto-deprioritized-major auto-deprioritized-minor
• Assignee: Unassigned
• Reporter: Julien Nioche
• Created: 28/Feb/19 11:49
• Updated: 28/Nov/21 22:38

Description

I am running a filtering job on a large dataset with Flink running in distributed mode. Most tasks in the Join operation have completed a while ago and only the tasks from a particular TaskManager are still running. These tasks make progress but extremely slowly.

When logging onto the machine running this TM I can see that all threads are TIMED_WAITING .

Could there be a synchronization problem?

See attachment for a screenshot of the Flink UI and the stack below.

 

$ jstack 9183 | grep -A 15 "DataSetFilterJob"

"CHAIN Join (Join at with(JoinOperator.java:543)) -> Map (Map at <init>(DataSetFilterJob.java:67)) (66/150)" #155 prio=5 os_prio=0 tid=0x00007faa5c01c000 nid=0x248c waiting on condition [0x00007fa9d15d5000]
{{ java.lang.Thread.State: TIMED_WAITING (parking)}}
{{ at sun.misc.Unsafe.park(Native Method)}}
{{ - parking to wait for <0x00000007bfa89578> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)}}
{{ at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)}}
{{ at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2078)}}
{{ at java.util.concurrent.LinkedBlockingQueue.poll(LinkedBlockingQueue.java:467)}}
{{ at org.apache.flink.runtime.io.disk.iomanager.AsynchronousBlockReader.getNextReturnedBlock(AsynchronousBlockReader.java:98)}}
{{ at org.apache.flink.runtime.io.disk.iomanager.AsynchronousBlockReader.getNextReturnedBlock(AsynchronousBlockReader.java:43)}}
{{ at org.apache.flink.runtime.io.disk.iomanager.ChannelReaderInputView.nextSegment(ChannelReaderInputView.java:228)}}
{{ at org.apache.flink.runtime.memory.AbstractPagedInputView.advance(AbstractPagedInputView.java:158)}}
{{ at org.apache.flink.runtime.memory.AbstractPagedInputView.readByte(AbstractPagedInputView.java:271)}}
{{ at org.apache.flink.runtime.memory.AbstractPagedInputView.readUnsignedByte(AbstractPagedInputView.java:278)}}
{{ at org.apache.flink.types.StringValue.readString(StringValue.java:746)}}
{{ at org.apache.flink.api.common.typeutils.base.StringSerializer.deserialize(StringSerializer.java:75)}}
{{ at org.apache.flink.api.common.typeutils.base.StringSerializer.deserialize(StringSerializer.java:80)}}
--
"CHAIN Join (Join at with(JoinOperator.java:543)) -> Map (Map at <init>(DataSetFilterJob.java:67)) (65/150)" #154 prio=5 os_prio=0 tid=0x00007faa5c01b000 nid=0x248b waiting on condition [0x00007fa9d14d4000]
{{ java.lang.Thread.State: TIMED_WAITING (parking)}}
{{ at sun.misc.Unsafe.park(Native Method)}}
{{ - parking to wait for <0x00000007b8e0eb50> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)}}
{{ at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)}}
{{ at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2078)}}
{{ at java.util.concurrent.LinkedBlockingQueue.poll(LinkedBlockingQueue.java:467)}}
{{ at org.apache.flink.runtime.io.disk.iomanager.AsynchronousBlockReader.getNextReturnedBlock(AsynchronousBlockReader.java:98)}}
{{ at org.apache.flink.runtime.io.disk.iomanager.AsynchronousBlockReader.getNextReturnedBlock(AsynchronousBlockReader.java:43)}}
{{ at org.apache.flink.runtime.io.disk.iomanager.ChannelReaderInputView.nextSegment(ChannelReaderInputView.java:228)}}
{{ at org.apache.flink.runtime.memory.AbstractPagedInputView.advance(AbstractPagedInputView.java:158)}}
{{ at org.apache.flink.runtime.memory.AbstractPagedInputView.readByte(AbstractPagedInputView.java:271)}}
{{ at org.apache.flink.runtime.memory.AbstractPagedInputView.readUnsignedByte(AbstractPagedInputView.java:278)}}
{{ at org.apache.flink.types.StringValue.readString(StringValue.java:746)}}
{{ at org.apache.flink.api.common.typeutils.base.StringSerializer.deserialize(StringSerializer.java:75)}}
{{ at org.apache.flink.api.common.typeutils.base.StringSerializer.deserialize(StringSerializer.java:80)}}
--
"CHAIN Join (Join at with(JoinOperator.java:543)) -> Map (Map at <init>(DataSetFilterJob.java:67)) (68/150)" #153 prio=5 os_prio=0 tid=0x00007faa5c019800 nid=0x248a waiting on condition [0x00007fa981df6000]
{{ java.lang.Thread.State: TIMED_WAITING (parking)}}
{{ at sun.misc.Unsafe.park(Native Method)}}
{{ - parking to wait for <0x0000000774903a00> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)}}
{{ at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)}}
{{ at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2078)}}
{{ at java.util.concurrent.LinkedBlockingQueue.poll(LinkedBlockingQueue.java:467)}}
{{ at org.apache.flink.runtime.io.disk.iomanager.AsynchronousBlockReader.getNextReturnedBlock(AsynchronousBlockReader.java:98)}}
{{ at org.apache.flink.runtime.io.disk.iomanager.AsynchronousBlockReader.getNextReturnedBlock(AsynchronousBlockReader.java:43)}}
{{ at org.apache.flink.runtime.io.disk.iomanager.HeaderlessChannelReaderInputView.nextSegment(HeaderlessChannelReaderInputView.java:90)}}
{{ at org.apache.flink.runtime.memory.AbstractPagedInputView.advance(AbstractPagedInputView.java:158)}}
{{ at org.apache.flink.runtime.memory.AbstractPagedInputView.readByte(AbstractPagedInputView.java:271)}}
{{ at org.apache.flink.runtime.memory.AbstractPagedInputView.readUnsignedByte(AbstractPagedInputView.java:278)}}
{{ at org.apache.flink.types.StringValue.readString(StringValue.java:769)}}
{{ at org.apache.flink.api.common.typeutils.base.StringSerializer.deserialize(StringSerializer.java:75)}}
{{ at org.apache.flink.api.common.typeutils.base.StringSerializer.deserialize(StringSerializer.java:80)}}
--
"CHAIN Join (Join at with(JoinOperator.java:543)) -> Map (Map at <init>(DataSetFilterJob.java:67)) (67/150)" #152 prio=5 os_prio=0 tid=0x00007faa5c018800 nid=0x2489 waiting on condition [0x00007fa98c194000]
{{ java.lang.Thread.State: TIMED_WAITING (parking)}}
{{ at sun.misc.Unsafe.park(Native Method)}}
{{ - parking to wait for <0x00000007b08a0508> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)}}
{{ at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)}}
{{ at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2078)}}
{{ at java.util.concurrent.LinkedBlockingQueue.poll(LinkedBlockingQueue.java:467)}}
{{ at org.apache.flink.runtime.io.disk.iomanager.AsynchronousBlockReader.getNextReturnedBlock(AsynchronousBlockReader.java:98)}}
{{ at org.apache.flink.runtime.io.disk.iomanager.AsynchronousBlockReader.getNextReturnedBlock(AsynchronousBlockReader.java:43)}}
{{ at org.apache.flink.runtime.io.disk.iomanager.ChannelReaderInputView.nextSegment(ChannelReaderInputView.java:228)}}
{{ at org.apache.flink.runtime.memory.AbstractPagedInputView.advance(AbstractPagedInputView.java:158)}}
{{ at org.apache.flink.runtime.memory.AbstractPagedInputView.readByte(AbstractPagedInputView.java:271)}}
{{ at org.apache.flink.runtime.memory.AbstractPagedInputView.readUnsignedByte(AbstractPagedInputView.java:278)}}
{{ at org.apache.flink.types.StringValue.readString(StringValue.java:746)}}
{{ at org.apache.flink.api.common.typeutils.base.StringSerializer.deserialize(StringSerializer.java:75)}}
{{ at org.apache.flink.api.common.typeutils.base.StringSerializer.deserialize(StringSerializer.java:80)}}
--
"CHAIN Join (Join at with(JoinOperator.java:543)) -> Map (Map at <init>(DataSetFilterJob.java:67)) (62/150)" #151 prio=5 os_prio=0 tid=0x00007faa5c017800 nid=0x2488 in Object.wait() [0x00007fa98c295000]
{{ java.lang.Thread.State: TIMED_WAITING (on object monitor)}}
{{ at java.lang.Object.wait(Native Method)}}
{{ at org.apache.flink.runtime.io.disk.iomanager.AsynchronousFileIOChannel.close(AsynchronousFileIOChannel.java:127)}}
{{ - locked <0x00000007ab60d660> (a java.lang.Object)}}
{{ at org.apache.flink.runtime.io.disk.iomanager.AsynchronousFileIOChannel.closeAndDelete(AsynchronousFileIOChannel.java:159)}}
{{ at org.apache.flink.runtime.operators.hash.MutableHashTable.buildTableFromSpilledPartition(MutableHashTable.java:877)}}
{{ at org.apache.flink.runtime.operators.hash.MutableHashTable.prepareNextPartition(MutableHashTable.java:631)}}
{{ at org.apache.flink.runtime.operators.hash.MutableHashTable.nextRecord(MutableHashTable.java:666)}}
{{ at org.apache.flink.runtime.operators.hash.NonReusingBuildFirstHashJoinIterator.callWithNextKey(NonReusingBuildFirstHashJoinIterator.java:116)}}
{{ at org.apache.flink.runtime.operators.JoinDriver.run(JoinDriver.java:221)}}
{{ at org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:503)}}
{{ at org.apache.flink.runtime.operators.BatchTask.invoke(BatchTask.java:368)}}
{{ at org.apache.flink.runtime.taskmanager.Task.run(Task.java:704)}}
{{ at java.lang.Thread.run(Thread.java:748)}}"CHAIN Join (Join at with(JoinOperator.java:543)) -> Map (Map at <init>(DataSetFilterJob.java:67)) (64/150)" #150 prio=5 os_prio=0 tid=0x00007faa5c016800 nid=0x2487 in Object.wait() [0x00007fa981ef7000]
{{ java.lang.Thread.State: TIMED_WAITING (on object monitor)}}
{{ at java.lang.Object.wait(Native Method)}}
{{ at org.apache.flink.runtime.io.disk.iomanager.AsynchronousFileIOChannel.close(AsynchronousFileIOChannel.java:127)}}
{{ - locked <0x00000007ab60d650> (a java.lang.Object)}}
{{ at org.apache.flink.runtime.io.disk.iomanager.AsynchronousFileIOChannel.closeAndDelete(AsynchronousFileIOChannel.java:159)}}
{{ at org.apache.flink.runtime.operators.hash.MutableHashTable.buildTableFromSpilledPartition(MutableHashTable.java:877)}}
{{ at org.apache.flink.runtime.operators.hash.MutableHashTable.prepareNextPartition(MutableHashTable.java:631)}}
{{ at org.apache.flink.runtime.operators.hash.MutableHashTable.nextRecord(MutableHashTable.java:666)}}
{{ at org.apache.flink.runtime.operators.hash.NonReusingBuildFirstHashJoinIterator.callWithNextKey(NonReusingBuildFirstHashJoinIterator.java:116)}}
{{ at org.apache.flink.runtime.operators.JoinDriver.run(JoinDriver.java:221)}}
{{ at org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:503)}}
{{ at org.apache.flink.runtime.operators.BatchTask.invoke(BatchTask.java:368)}}
{{ at org.apache.flink.runtime.taskmanager.Task.run(Task.java:704)}}
{{ at java.lang.Thread.run(Thread.java:748)}}"CHAIN Join (Join at with(JoinOperator.java:543)) -> Map (Map at <init>(DataSetFilterJob.java:67)) (63/150)" #149 prio=5 os_prio=0 tid=0x00007faa5c015800 nid=0x2486 waiting on condition [0x00007fa9d0fcf000]
{{ java.lang.Thread.State: TIMED_WAITING (parking)}}
{{ at sun.misc.Unsafe.park(Native Method)}}
{{ - parking to wait for <0x000000077439ea00> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)}}
{{ at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)}}
{{ at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2078)}}
{{ at java.util.concurrent.LinkedBlockingQueue.poll(LinkedBlockingQueue.java:467)}}
{{ at org.apache.flink.runtime.io.disk.iomanager.AsynchronousBlockReader.getNextReturnedBlock(AsynchronousBlockReader.java:98)}}
{{ at org.apache.flink.runtime.io.disk.iomanager.AsynchronousBlockReader.getNextReturnedBlock(AsynchronousBlockReader.java:43)}}
{{ at org.apache.flink.runtime.io.disk.iomanager.HeaderlessChannelReaderInputView.nextSegment(HeaderlessChannelReaderInputView.java:90)}}
{{ at org.apache.flink.runtime.memory.AbstractPagedInputView.advance(AbstractPagedInputView.java:158)}}
{{ at org.apache.flink.runtime.memory.AbstractPagedInputView.readByte(AbstractPagedInputView.java:271)}}
{{ at org.apache.flink.runtime.memory.AbstractPagedInputView.readUnsignedByte(AbstractPagedInputView.java:278)}}
{{ at org.apache.flink.types.StringValue.readString(StringValue.java:769)}}
{{ at org.apache.flink.api.common.typeutils.base.StringSerializer.deserialize(StringSerializer.java:75)}}
{{ at org.apache.flink.api.common.typeutils.base.StringSerializer.deserialize(StringSerializer.java:80)}}
--
"CHAIN Join (Join at with(JoinOperator.java:543)) -> Map (Map at <init>(DataSetFilterJob.java:67)) (61/150)" #148 prio=5 os_prio=0 tid=0x00007faa5c014800 nid=0x2485 in Object.wait() [0x00007fa9d2cf1000]
{{ java.lang.Thread.State: TIMED_WAITING (on object monitor)}}
{{ at java.lang.Object.wait(Native Method)}}
{{ at org.apache.flink.runtime.io.disk.iomanager.AsynchronousFileIOChannel.close(AsynchronousFileIOChannel.java:127)}}
{{ - locked <0x00000007ab60d640> (a java.lang.Object)}}
{{ at org.apache.flink.runtime.io.disk.iomanager.AsynchronousFileIOChannel.closeAndDelete(AsynchronousFileIOChannel.java:159)}}
{{ at org.apache.flink.runtime.operators.hash.MutableHashTable.buildTableFromSpilledPartition(MutableHashTable.java:877)}}
{{ at org.apache.flink.runtime.operators.hash.MutableHashTable.prepareNextPartition(MutableHashTable.java:631)}}
{{ at org.apache.flink.runtime.operators.hash.MutableHashTable.nextRecord(MutableHashTable.java:666)}}
{{ at org.apache.flink.runtime.operators.hash.NonReusingBuildFirstHashJoinIterator.callWithNextKey(NonReusingBuildFirstHashJoinIterator.java:116)}}
{{ at org.apache.flink.runtime.operators.JoinDriver.run(JoinDriver.java:221)}}
{{ at org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:503)}}
{{ at org.apache.flink.runtime.operators.BatchTask.invoke(BatchTask.java:368)}}
{{ at org.apache.flink.runtime.taskmanager.Task.run(Task.java:704)}}
{{ at java.lang.Thread.run(Thread.java:748)}}