[HADOOP-17201] Spark job with s3acommitter stuck at the last stage

• Type: Bug
• Status: Open
• Priority: Major
• Resolution: Unresolved
• Affects Version/s: 3.2.1
• Component/s: fs/s3
• Labels: pull-request-available

Environment

we are on spark 2.4.5/hadoop 3.2.1 with s3a committer.
spark.hadoop.fs.s3a.committer.magic.enabled: 'true'
spark.hadoop.fs.s3a.committer.name: magic

• Assignee: Unassigned
• Reporter: Dyno
• Created: 10/Aug/20 21:12
• Updated: 10/Jan/22 12:55

Description

usually our spark job took 1 hour or 2 to finish, occasionally it runs for more than 3 hour and then we know it's stuck and usually the executor has stack like this

{{
"Executor task launch worker for task 78620" #265 daemon prio=5 os_prio=0 tid=0x00007f73e0005000 nid=0x12d waiting on condition [0x00007f74cb291000]
java.lang.Thread.State: TIMED_WAITING (sleeping)
at java.lang.Thread.sleep(Native Method)
at org.apache.hadoop.fs.s3a.Invoker.retryUntranslated(Invoker.java:349)
at org.apache.hadoop.fs.s3a.Invoker.retryUntranslated(Invoker.java:285)
at org.apache.hadoop.fs.s3a.S3AFileSystem.deleteObjects(S3AFileSystem.java:1457)
at org.apache.hadoop.fs.s3a.S3AFileSystem.removeKeys(S3AFileSystem.java:1717)
at org.apache.hadoop.fs.s3a.S3AFileSystem.deleteUnnecessaryFakeDirectories(S3AFileSystem.java:2785)
at org.apache.hadoop.fs.s3a.S3AFileSystem.finishedWrite(S3AFileSystem.java:2751)
at org.apache.hadoop.fs.s3a.WriteOperationHelper.lambda$finalizeMultipartUpload$1(WriteOperationHelper.java:238)
at org.apache.hadoop.fs.s3a.WriteOperationHelper$$Lambda$210/1059071691.execute(Unknown Source)
at org.apache.hadoop.fs.s3a.Invoker.once(Invoker.java:109)
at org.apache.hadoop.fs.s3a.Invoker.lambda$retry$3(Invoker.java:265)
at org.apache.hadoop.fs.s3a.Invoker$$Lambda$23/586859139.execute(Unknown Source)
at org.apache.hadoop.fs.s3a.Invoker.retryUntranslated(Invoker.java:322)
at org.apache.hadoop.fs.s3a.Invoker.retry(Invoker.java:261)
at org.apache.hadoop.fs.s3a.WriteOperationHelper.finalizeMultipartUpload(WriteOperationHelper.java:226)
at org.apache.hadoop.fs.s3a.WriteOperationHelper.completeMPUwithRetries(WriteOperationHelper.java:271)
at org.apache.hadoop.fs.s3a.S3ABlockOutputStream$MultiPartUpload.complete(S3ABlockOutputStream.java:660)
at org.apache.hadoop.fs.s3a.S3ABlockOutputStream$MultiPartUpload.access$200(S3ABlockOutputStream.java:521)
at org.apache.hadoop.fs.s3a.S3ABlockOutputStream.close(S3ABlockOutputStream.java:385)
at org.apache.hadoop.fs.FSDataOutputStream$PositionCache.close(FSDataOutputStream.java:72)
at org.apache.hadoop.fs.FSDataOutputStream.close(FSDataOutputStream.java:101)
at org.apache.parquet.hadoop.util.HadoopPositionOutputStream.close(HadoopPositionOutputStream.java:64)
at org.apache.parquet.hadoop.ParquetFileWriter.end(ParquetFileWriter.java:685)
at org.apache.parquet.hadoop.InternalParquetRecordWriter.close(InternalParquetRecordWriter.java:122)
at org.apache.parquet.hadoop.ParquetRecordWriter.close(ParquetRecordWriter.java:165)
at org.apache.spark.sql.execution.datasources.parquet.ParquetOutputWriter.close(ParquetOutputWriter.scala:42)
at org.apache.spark.sql.execution.datasources.FileFormatDataWriter.releaseResources(FileFormatDataWriter.scala:57)
at org.apache.spark.sql.execution.datasources.FileFormatDataWriter.commit(FileFormatDataWriter.scala:74)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask$3.apply(FileFormatWriter.scala:247)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask$3.apply(FileFormatWriter.scala:242)
at org.apache.spark.util.Utils$.tryWithSafeFinallyAndFailureCallbacks(Utils.scala:1394)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$.org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask(FileFormatWriter.scala:248)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply(FileFormatWriter.scala:170)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply(FileFormatWriter.scala:169)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
at org.apache.spark.scheduler.Task.run(Task.scala:123)
at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

Locked ownable synchronizers:

• <0x00000003a57332e0> (a java.util.concurrent.ThreadPoolExecutor$Worker)

}}
captured jstack on the stuck executors in case it's useful.

Issue Links

• relates to: HADOOP-17063 S3A deleteObjects hanging/retrying forever
• links to: GitHub Pull Request #2402