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https://issues.apache.org/jira/browse/HIVE-14258?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15383159#comment-15383159
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zhihai xu commented on HIVE-14258:
----------------------------------
Thanks [~jxiang] for review and committing the patch!
> Reduce task timed out because CommonJoinOperator.genUniqueJoinObject took too
> long to finish without reporting progress
> -----------------------------------------------------------------------------------------------------------------------
>
> Key: HIVE-14258
> URL: https://issues.apache.org/jira/browse/HIVE-14258
> Project: Hive
> Issue Type: Bug
> Components: Query Processor
> Affects Versions: 2.1.0
> Reporter: zhihai xu
> Assignee: zhihai xu
> Fix For: 2.1.0
>
> Attachments: HIVE-14258.patch
>
>
> Reduce task timed out because CommonJoinOperator.genUniqueJoinObject took too
> long to finish without reporting progress.
> This timeout happened when reducer.close() is called in ReduceTask.java.
> CommonJoinOperator.genUniqueJoinObject() called by reducer.close() will loop
> over every row in the AbstractRowContainer. This can take a long time if
> there are a large number or rows, and during this time, it does not report
> progress. If this runs for long enough more than "mapreduce.task.timeout",
> ApplicationMaster will kill the task for failing to report progress.
> we configured "mapreduce.task.timeout" as 10 minutes. I captured the stack
> trace in the 10 minutes before AM killed the reduce task at 2016-07-15
> 07:19:11.
> The following three stack traces can prove it:
> at 2016-07-15 07:09:42:
> {code}
> "main" prio=10 tid=0x00007f90ec017000 nid=0xd193 runnable [0x00007f90f62e5000]
> java.lang.Thread.State: RUNNABLE
> at java.io.FileInputStream.readBytes(Native Method)
> at java.io.FileInputStream.read(FileInputStream.java:272)
> at
> org.apache.hadoop.fs.RawLocalFileSystem$LocalFSFileInputStream.read(RawLocalFileSystem.java:154)
> at java.io.BufferedInputStream.fill(BufferedInputStream.java:235)
> at java.io.BufferedInputStream.read1(BufferedInputStream.java:275)
> at java.io.BufferedInputStream.read(BufferedInputStream.java:334)
> - locked <0x00000007deecefb0> (a
> org.apache.hadoop.fs.BufferedFSInputStream)
> at java.io.DataInputStream.read(DataInputStream.java:149)
> at
> org.apache.hadoop.fs.FSInputChecker.readFully(FSInputChecker.java:436)
> at
> org.apache.hadoop.fs.ChecksumFileSystem$ChecksumFSInputChecker.readChunk(ChecksumFileSystem.java:252)
> at
> org.apache.hadoop.fs.FSInputChecker.readChecksumChunk(FSInputChecker.java:276)
> at org.apache.hadoop.fs.FSInputChecker.fill(FSInputChecker.java:214)
> at org.apache.hadoop.fs.FSInputChecker.read1(FSInputChecker.java:232)
> at org.apache.hadoop.fs.FSInputChecker.read(FSInputChecker.java:196)
> - locked <0x00000007deecb978> (a
> org.apache.hadoop.fs.ChecksumFileSystem$ChecksumFSInputChecker)
> at java.io.DataInputStream.readFully(DataInputStream.java:195)
> at
> org.apache.hadoop.io.DataOutputBuffer$Buffer.write(DataOutputBuffer.java:70)
> at
> org.apache.hadoop.io.DataOutputBuffer.write(DataOutputBuffer.java:120)
> at
> org.apache.hadoop.io.SequenceFile$Reader.next(SequenceFile.java:2359)
> - locked <0x00000007deec8f70> (a
> org.apache.hadoop.io.SequenceFile$Reader)
> at
> org.apache.hadoop.io.SequenceFile$Reader.next(SequenceFile.java:2491)
> - locked <0x00000007deec8f70> (a
> org.apache.hadoop.io.SequenceFile$Reader)
> at
> org.apache.hadoop.mapred.SequenceFileRecordReader.next(SequenceFileRecordReader.java:82)
> - locked <0x00000007deec82f0> (a
> org.apache.hadoop.mapred.SequenceFileRecordReader)
> at
> org.apache.hadoop.hive.ql.exec.persistence.RowContainer.nextBlock(RowContainer.java:360)
> at
> org.apache.hadoop.hive.ql.exec.persistence.RowContainer.next(RowContainer.java:267)
> at
> org.apache.hadoop.hive.ql.exec.persistence.RowContainer.next(RowContainer.java:74)
> at
> org.apache.hadoop.hive.ql.exec.CommonJoinOperator.genUniqueJoinObject(CommonJoinOperator.java:644)
> at
> org.apache.hadoop.hive.ql.exec.CommonJoinOperator.checkAndGenObject(CommonJoinOperator.java:750)
> at
> org.apache.hadoop.hive.ql.exec.JoinOperator.endGroup(JoinOperator.java:256)
> at
> org.apache.hadoop.hive.ql.exec.mr.ExecReducer.close(ExecReducer.java:284)
> at
> org.apache.hadoop.mapred.ReduceTask.runOldReducer(ReduceTask.java:453)
> at org.apache.hadoop.mapred.ReduceTask.run(ReduceTask.java:392)
> at org.apache.hadoop.mapred.YarnChild$2.run(YarnChild.java:163)
> at java.security.AccessController.doPrivileged(Native Method)
> at javax.security.auth.Subject.doAs(Subject.java:415)
> at
> org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1671)
> {code}
> at 2016-07-15 07:15:35
> {code}
> "main" prio=10 tid=0x00007f90ec017000 nid=0xd193 runnable [0x00007f90f62e5000]
> java.lang.Thread.State: RUNNABLE
> at java.util.zip.CRC32.updateBytes(Native Method)
> at java.util.zip.CRC32.update(CRC32.java:65)
> at
> org.apache.hadoop.fs.FSInputChecker.verifySums(FSInputChecker.java:316)
> at
> org.apache.hadoop.fs.FSInputChecker.readChecksumChunk(FSInputChecker.java:279)
> at org.apache.hadoop.fs.FSInputChecker.fill(FSInputChecker.java:214)
> at org.apache.hadoop.fs.FSInputChecker.read1(FSInputChecker.java:232)
> at org.apache.hadoop.fs.FSInputChecker.read(FSInputChecker.java:196)
> - locked <0x00000007d68db510> (a
> org.apache.hadoop.fs.ChecksumFileSystem$ChecksumFSInputChecker)
> at java.io.DataInputStream.readFully(DataInputStream.java:195)
> at
> org.apache.hadoop.io.DataOutputBuffer$Buffer.write(DataOutputBuffer.java:70)
> at
> org.apache.hadoop.io.DataOutputBuffer.write(DataOutputBuffer.java:120)
> at
> org.apache.hadoop.io.SequenceFile$Reader.next(SequenceFile.java:2359)
> - locked <0x00000007d68d8b68> (a
> org.apache.hadoop.io.SequenceFile$Reader)
> at
> org.apache.hadoop.io.SequenceFile$Reader.next(SequenceFile.java:2491)
> - locked <0x00000007d68d8b68> (a
> org.apache.hadoop.io.SequenceFile$Reader)
> at
> org.apache.hadoop.mapred.SequenceFileRecordReader.next(SequenceFileRecordReader.java:82)
> - locked <0x00000007d68d7f08> (a
> org.apache.hadoop.mapred.SequenceFileRecordReader)
> at
> org.apache.hadoop.hive.ql.exec.persistence.RowContainer.nextBlock(RowContainer.java:360)
> at
> org.apache.hadoop.hive.ql.exec.persistence.RowContainer.next(RowContainer.java:267)
> at
> org.apache.hadoop.hive.ql.exec.persistence.RowContainer.next(RowContainer.java:74)
> at
> org.apache.hadoop.hive.ql.exec.CommonJoinOperator.genUniqueJoinObject(CommonJoinOperator.java:644)
> at
> org.apache.hadoop.hive.ql.exec.CommonJoinOperator.checkAndGenObject(CommonJoinOperator.java:750)
> at
> org.apache.hadoop.hive.ql.exec.JoinOperator.endGroup(JoinOperator.java:256)
> at
> org.apache.hadoop.hive.ql.exec.mr.ExecReducer.close(ExecReducer.java:284)
> at
> org.apache.hadoop.mapred.ReduceTask.runOldReducer(ReduceTask.java:453)
> at org.apache.hadoop.mapred.ReduceTask.run(ReduceTask.java:392)
> at org.apache.hadoop.mapred.YarnChild$2.run(YarnChild.java:163)
> at java.security.AccessController.doPrivileged(Native Method)
> at javax.security.auth.Subject.doAs(Subject.java:415)
> at
> org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1671)
> at org.apache.hadoop.mapred.YarnChild.main(YarnChild.java:158)
> {code}
> at 2016-07-15 07:19:10
> {code}
> "main" prio=10 tid=0x00007f90ec017000 nid=0xd193 runnable [0x00007f90f62e5000]
> java.lang.Thread.State: RUNNABLE
> at java.io.FileInputStream.readBytes(Native Method)
> at java.io.FileInputStream.read(FileInputStream.java:272)
> at
> org.apache.hadoop.fs.RawLocalFileSystem$LocalFSFileInputStream.read(RawLocalFileSystem.java:154)
> at java.io.BufferedInputStream.fill(BufferedInputStream.java:235)
> at java.io.BufferedInputStream.read1(BufferedInputStream.java:275)
> at java.io.BufferedInputStream.read(BufferedInputStream.java:334)
> - locked <0x00000007df731218> (a
> org.apache.hadoop.fs.BufferedFSInputStream)
> at java.io.DataInputStream.read(DataInputStream.java:149)
> at
> org.apache.hadoop.fs.FSInputChecker.readFully(FSInputChecker.java:436)
> at
> org.apache.hadoop.fs.ChecksumFileSystem$ChecksumFSInputChecker.readChunk(ChecksumFileSystem.java:252)
> at
> org.apache.hadoop.fs.FSInputChecker.readChecksumChunk(FSInputChecker.java:276)
> at org.apache.hadoop.fs.FSInputChecker.fill(FSInputChecker.java:214)
> at org.apache.hadoop.fs.FSInputChecker.read1(FSInputChecker.java:232)
> at org.apache.hadoop.fs.FSInputChecker.read(FSInputChecker.java:196)
> - locked <0x00000007df72dc20> (a
> org.apache.hadoop.fs.ChecksumFileSystem$ChecksumFSInputChecker)
> at java.io.DataInputStream.readFully(DataInputStream.java:195)
> at
> org.apache.hadoop.io.DataOutputBuffer$Buffer.write(DataOutputBuffer.java:70)
> at
> org.apache.hadoop.io.DataOutputBuffer.write(DataOutputBuffer.java:120)
> at
> org.apache.hadoop.io.SequenceFile$Reader.next(SequenceFile.java:2359)
> - locked <0x00000007df72b278> (a
> org.apache.hadoop.io.SequenceFile$Reader)
> at
> org.apache.hadoop.io.SequenceFile$Reader.next(SequenceFile.java:2491)
> - locked <0x00000007df72b278> (a
> org.apache.hadoop.io.SequenceFile$Reader)
> at
> org.apache.hadoop.mapred.SequenceFileRecordReader.next(SequenceFileRecordReader.java:82)
> - locked <0x00000007df72a618> (a
> org.apache.hadoop.mapred.SequenceFileRecordReader)
> at
> org.apache.hadoop.hive.ql.exec.persistence.RowContainer.nextBlock(RowContainer.java:360)
> at
> org.apache.hadoop.hive.ql.exec.persistence.RowContainer.nextBlock(RowContainer.java:373)
> at
> org.apache.hadoop.hive.ql.exec.persistence.RowContainer.next(RowContainer.java:267)
> at
> org.apache.hadoop.hive.ql.exec.persistence.RowContainer.next(RowContainer.java:74)
> at
> org.apache.hadoop.hive.ql.exec.CommonJoinOperator.genUniqueJoinObject(CommonJoinOperator.java:644)
> at
> org.apache.hadoop.hive.ql.exec.CommonJoinOperator.checkAndGenObject(CommonJoinOperator.java:750)
> at
> org.apache.hadoop.hive.ql.exec.JoinOperator.endGroup(JoinOperator.java:256)
> at
> org.apache.hadoop.hive.ql.exec.mr.ExecReducer.close(ExecReducer.java:284)
> at
> org.apache.hadoop.mapred.ReduceTask.runOldReducer(ReduceTask.java:453)
> at org.apache.hadoop.mapred.ReduceTask.run(ReduceTask.java:392)
> at org.apache.hadoop.mapred.YarnChild$2.run(YarnChild.java:163)
> at java.security.AccessController.doPrivileged(Native Method)
> at javax.security.auth.Subject.doAs(Subject.java:415)
> at
> org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1671)
> at org.apache.hadoop.mapred.YarnChild.main(YarnChild.java:158)
> {code}
> You can see all three stack traces show
> CommonJoinOperator.genUniqueJoinObject was called by ExecReducer.close.
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