Laurens created SPARK-34680:
-------------------------------
Summary: Spark hangs when out of diskspace
Key: SPARK-34680
URL: https://issues.apache.org/jira/browse/SPARK-34680
Project: Spark
Issue Type: Bug
Components: PySpark
Affects Versions: 3.1.1, 3.0.1
Environment: Running Spark and Pyspark 3.1.1. with Hadoop 3.2.2 and
Koalas 1.6.0.
Some environment variables:
|Java Home|/usr/lib/jvm/java-11-openjdk-11.0.3.7-0.el7_6.x86_64|
|Java Version|11.0.3 (Oracle Corporation)|
|Scala Version|version 2.12.10|
Reporter: Laurens
Parsing a workflow using Koalas, I noticed a stage is hanging for 8 hours
already. I checked the logs and the last output is:
{code:java}
21/03/09 13:50:31 ERROR TaskMemoryManager: error while calling spill() on
org.apache.spark.shuffle.sort.ShuffleExternalSorter@4127a515
java.io.IOException: No space left on device
at java.base/java.io.FileOutputStream.writeBytes(Native Method)
at java.base/java.io.FileOutputStream.write(FileOutputStream.java:354)
at
org.apache.spark.storage.TimeTrackingOutputStream.write(TimeTrackingOutputStream.java:59)
at
java.base/java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:81)
at java.base/java.io.BufferedOutputStream.write(BufferedOutputStream.java:127)
at
net.jpountz.lz4.LZ4BlockOutputStream.flushBufferedData(LZ4BlockOutputStream.java:223)
at net.jpountz.lz4.LZ4BlockOutputStream.write(LZ4BlockOutputStream.java:176)
at
org.apache.spark.storage.DiskBlockObjectWriter.write(DiskBlockObjectWriter.scala:260)
at
org.apache.spark.shuffle.sort.ShuffleExternalSorter.writeSortedFile(ShuffleExternalSorter.java:218)
at
org.apache.spark.shuffle.sort.ShuffleExternalSorter.spill(ShuffleExternalSorter.java:276)
at
org.apache.spark.memory.TaskMemoryManager.acquireExecutionMemory(TaskMemoryManager.java:208)
at
org.apache.spark.memory.TaskMemoryManager.allocatePage(TaskMemoryManager.java:289)
at org.apache.spark.memory.MemoryConsumer.allocatePage(MemoryConsumer.java:116)
at
org.apache.spark.shuffle.sort.ShuffleExternalSorter.acquireNewPageIfNecessary(ShuffleExternalSorter.java:385)
at
org.apache.spark.shuffle.sort.ShuffleExternalSorter.insertRecord(ShuffleExternalSorter.java:409)
at
org.apache.spark.shuffle.sort.UnsafeShuffleWriter.insertRecordIntoSorter(UnsafeShuffleWriter.java:249)
at
org.apache.spark.shuffle.sort.UnsafeShuffleWriter.write(UnsafeShuffleWriter.java:178)
at
org.apache.spark.shuffle.ShuffleWriteProcessor.write(ShuffleWriteProcessor.scala:59)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:99)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:52)
at org.apache.spark.scheduler.Task.run(Task.scala:131)
at
org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:497)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1439)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:500)
at
java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at
java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:834)
Suppressed: java.io.IOException: No space left on device
at java.base/java.io.FileOutputStream.writeBytes(Native Method)
at java.base/java.io.FileOutputStream.write(FileOutputStream.java:354)
at
org.apache.spark.storage.TimeTrackingOutputStream.write(TimeTrackingOutputStream.java:59)
at
java.base/java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:81)
at java.base/java.io.BufferedOutputStream.flush(BufferedOutputStream.java:142)
at net.jpountz.lz4.LZ4BlockOutputStream.flush(LZ4BlockOutputStream.java:243)
at
org.apache.spark.serializer.DummySerializerInstance$1.flush(DummySerializerInstance.java:50)
at
org.apache.spark.storage.DiskBlockObjectWriter.commitAndGet(DiskBlockObjectWriter.scala:173)
at
org.apache.spark.storage.DiskBlockObjectWriter.$anonfun$close$1(DiskBlockObjectWriter.scala:156)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1439)
at
org.apache.spark.storage.DiskBlockObjectWriter.close(DiskBlockObjectWriter.scala:158)
at
org.apache.spark.shuffle.sort.ShuffleExternalSorter.writeSortedFile(ShuffleExternalSorter.java:226)
... 18 more
Suppressed: java.io.IOException: No space left on device
at java.base/java.io.FileOutputStream.writeBytes(Native Method)
at java.base/java.io.FileOutputStream.write(FileOutputStream.java:354)
at
org.apache.spark.storage.TimeTrackingOutputStream.write(TimeTrackingOutputStream.java:59)
at
java.base/java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:81)
at java.base/java.io.BufferedOutputStream.flush(BufferedOutputStream.java:142)
at java.base/java.io.FilterOutputStream.close(FilterOutputStream.java:182)
at
org.apache.spark.storage.DiskBlockObjectWriter$ManualCloseBufferedOutputStream$1.org$apache$spark$storage$DiskBlockObjectWriter$ManualCloseOutputStream$$super$close(DiskBlockObjectWriter.scala:108)
at
org.apache.spark.storage.DiskBlockObjectWriter$ManualCloseOutputStream.manualClose(DiskBlockObjectWriter.scala:65)
at
org.apache.spark.storage.DiskBlockObjectWriter$ManualCloseOutputStream.manualClose$(DiskBlockObjectWriter.scala:64)
at
org.apache.spark.storage.DiskBlockObjectWriter$ManualCloseBufferedOutputStream$1.manualClose(DiskBlockObjectWriter.scala:108)
at
org.apache.spark.storage.DiskBlockObjectWriter.$anonfun$closeResources$1(DiskBlockObjectWriter.scala:135)
at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1439)
at
org.apache.spark.storage.DiskBlockObjectWriter.closeResources(DiskBlockObjectWriter.scala:136)
at
org.apache.spark.storage.DiskBlockObjectWriter.$anonfun$close$2(DiskBlockObjectWriter.scala:158)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1448)
... 20 more
21/03/09 13:50:31 INFO TaskMemoryManager: Memory used in task 1255
21/03/09 13:50:31 INFO TaskMemoryManager: Acquired by
HybridRowQueue(org.apache.spark.memory.TaskMemoryManager@394bad48,/local/anonymized/spark/spark-4b70492b-8f2e-4108-b6a0-6ed423a98bd9/executor-b88a6782-4592-45c0-a484-73a2f642cb3e/spark-c20b49eb-83d4-4145-b07a-fe6fddef7ffe,7,org.apache.spark.serializer.SerializerManager@59dd92e8):
105.5 MiB
21/03/09 13:50:31 INFO TaskMemoryManager: Acquired by
org.apache.spark.shuffle.sort.ShuffleExternalSorter@4127a515: 14.4 GiB
21/03/09 13:50:31 INFO TaskMemoryManager: Acquired by
org.apache.spark.util.collection.unsafe.sort.UnsafeExternalSorter@34a4b163:
15.1 GiB
21/03/09 13:50:31 INFO TaskMemoryManager: 67108864 bytes of memory were used by
task 1255 but are not associated with specific consumers
21/03/09 13:50:31 INFO TaskMemoryManager: 31853114929 bytes of memory are used
for execution and 526799 bytes of memory are used for storage{code}
Local time is 21/03/09 21:33:00, so it appears the worker is stuck and the
stage is not terminating unsuccessfully.
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