[
https://issues.apache.org/jira/browse/SPARK-18289?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
]
KaiXu updated SPARK-18289:
--------------------------
Environment:
CentOS7.2 kernel: 3.10.0-327.el7.x86_64
Hadoop2.7.1
Spark2.0.0 release version
Hive2.1 with patch HIVE-14029 (https://issues.apache.org/jira/browse/HIVE-14029)
Intel(R) Xeon(R) CPU E5-2699 v4 @ 2.20GHz
384GB memory
was:
CentOS7.2 kernel: 3.10.0-327.el7.x86_64
Hadoop2.7.1
Spark2.0.0 release version
Hive2.1 with patch HIVE-14029 (https://issues.apache.org/jira/browse/HIVE-14029)
Intel(R) Xeon(R) CPU E5-2699 v4 @ 2.20GHz
384GB memory
> spark.util.collection.ExternalSorter leak memory when task force spilling
> in-memory map to disk
> ------------------------------------------------------------------------------------------------
>
> Key: SPARK-18289
> URL: https://issues.apache.org/jira/browse/SPARK-18289
> Project: Spark
> Issue Type: Bug
> Components: Scheduler, Shuffle, Spark Core
> Affects Versions: 2.0.0
> Environment: CentOS7.2 kernel: 3.10.0-327.el7.x86_64
> Hadoop2.7.1
> Spark2.0.0 release version
> Hive2.1 with patch HIVE-14029
> (https://issues.apache.org/jira/browse/HIVE-14029)
> Intel(R) Xeon(R) CPU E5-2699 v4 @ 2.20GHz
> 384GB memory
> Reporter: KaiXu
> Labels: hive, spark2.0.0
>
> We use BigBench to test the performance of Hive on Spark2.0 on Intel(R)
> Xeon(R) CPU E5-2699 v4(1 master + 4 worker) with 3TB scale factor, we found 4
> tasks failed when running q30. When checking in executor's log, we found it
> has memory leak when task force spilling in-memory map to disk.
> notable configuration parameters:
> spark.master=yarn
> spark.deploy.mode=cluster
> spark.driver.memory=4g;
> spark.executor.cores=7;
> spark.executor.memory=22g;
> spark.yarn.executor.memoryOverhead=8192;
> spark.executor.instances=50;
> spark.storage.memoryFraction=0.01;
> spark.memory.useLegacyMode=true;
> spark.executor.extraJavaOptions=-XX:+UseParallelOldGC -XX:NewRatio=1
> -XX:SurvivorRatio=1 -XX:ParallelGCThreads=4;
> executor's log:
> 16/11/05 18:12:32 INFO exec.CommonJoinOperator: table 0 has 2000 rows for
> join key [973089]
> 16/11/05 18:12:32 INFO exec.CommonJoinOperator: table 0 has 4000 rows for
> join key [973089]
> 16/11/05 18:12:32 INFO exec.CommonJoinOperator: table 0 has 8000 rows for
> join key [973089]
> 16/11/05 18:12:32 INFO exec.CommonJoinOperator: table 0 has 16000 rows for
> join key [973089]
> 16/11/05 18:12:32 INFO exec.CommonJoinOperator: table 0 has 1000 rows for
> join key [972962]
> 16/11/05 18:12:32 INFO exec.CommonJoinOperator: table 0 has 2000 rows for
> join key [972962]
> 16/11/05 18:12:32 INFO exec.CommonJoinOperator: table 0 has 4000 rows for
> join key [972962]
> 16/11/05 18:12:32 INFO exec.CommonJoinOperator: table 0 has 8000 rows for
> join key [972962]
> 16/11/05 18:12:32 INFO exec.CommonJoinOperator: table 0 has 16000 rows for
> join key [972962]
> 16/11/05 18:12:32 INFO spark.SparkRecordHandler: processed 1051034 rows: used
> memory = 10801674800
> 16/11/05 18:12:32 INFO exec.JoinOperator: SKEWJOINFOLLOWUPJOBS:0,
> 16/11/05 18:12:32 INFO exec.ReduceSinkOperator: RS[9]: records written -
> 1050990
> 16/11/05 18:12:32 INFO exec.ReduceSinkOperator:
> RECORDS_OUT_INTERMEDIATE:1050990,
> 16/11/05 18:12:32 INFO collection.ExternalSorter: Task 6856 force spilling
> in-memory map to disk and it will release 347.0 MB memory
> 16/11/05 18:12:32 WARN memory.TaskMemoryManager: leak 347.0 MB memory from
> org.apache.spark.util.collection.ExternalSorter@1bf0a514
> 16/11/05 18:12:32 ERROR executor.Executor: Exception in task 5978.0 in stage
> 1.0 (TID 6856)
> java.lang.NullPointerException
> at
> org.apache.spark.util.collection.ExternalSorter$SpillReader.cleanup(ExternalSorter.scala:625)
> at
> org.apache.spark.util.collection.ExternalSorter$SpillReader.nextBatchStream(ExternalSorter.scala:540)
> at
> org.apache.spark.util.collection.ExternalSorter$SpillReader.<init>(ExternalSorter.scala:508)
> at
> org.apache.spark.util.collection.ExternalSorter$SpillableIterator.spill(ExternalSorter.scala:814)
> at
> org.apache.spark.util.collection.ExternalSorter.forceSpill(ExternalSorter.scala:254)
> at org.apache.spark.util.collection.Spillable.spill(Spillable.scala:111)
> at
> org.apache.spark.memory.TaskMemoryManager.acquireExecutionMemory(TaskMemoryManager.java:150)
> at
> org.apache.spark.memory.TaskMemoryManager.allocatePage(TaskMemoryManager.java:245)
> at
> org.apache.spark.memory.MemoryConsumer.allocateArray(MemoryConsumer.java:92)
> at
> org.apache.spark.shuffle.sort.ShuffleExternalSorter.growPointerArrayIfNecessary(ShuffleExternalSorter.java:333)
> at
> org.apache.spark.shuffle.sort.ShuffleExternalSorter.insertRecord(ShuffleExternalSorter.java:384)
> at
> org.apache.spark.shuffle.sort.UnsafeShuffleWriter.insertRecordIntoSorter(UnsafeShuffleWriter.java:235)
> at
> org.apache.spark.shuffle.sort.UnsafeShuffleWriter.write(UnsafeShuffleWriter.java:162)
> at
> org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:79)
> at
> org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:47)
> at org.apache.spark.scheduler.Task.run(Task.scala:85)
> at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
> at java.lang.Thread.run(Thread.java:745)
> 16/11/05 18:12:32 INFO executor.CoarseGrainedExecutorBackend: Got assigned
> task 7173
> 16/11/05 18:12:32 INFO executor.Executor: Running task 6294.0 in stage 1.0
> (TID 7173)
> 16/11/05 18:12:32 INFO storage.ShuffleBlockFetcherIterator: Getting 878
> non-empty blocks out of 878 blocks
> 16/11/05 18:12:32 INFO storage.ShuffleBlockFetcherIterator: Started 46 remote
> fetches in 17 ms
> 16/11/05 18:12:39 INFO executor.Executor: Finished task 6095.0 in stage 1.0
> (TID 6973). 3681 bytes result sent to driver
> 16/11/05 18:12:39 INFO executor.CoarseGrainedExecutorBackend: Got assigned
> task 7418
> 16/11/05 18:12:39 INFO executor.Executor: Running task 6538.0 in stage 1.0
> (TID 7418)
> 16/11/05 18:12:39 INFO storage.ShuffleBlockFetcherIterator: Getting 878
> non-empty blocks out of 878 blocks
> 16/11/05 18:12:39 INFO storage.ShuffleBlockFetcherIterator: Started 46 remote
> fetches in 10 ms
> 16/11/05 18:12:39 INFO executor.Executor: Finished task 6010.0 in stage 1.0
> (TID 6888). 3681 bytes result sent to driver
> 16/11/05 18:12:39 INFO executor.CoarseGrainedExecutorBackend: Got assigned
> task 7421
> 16/11/05 18:12:39 INFO executor.Executor: Running task 6541.0 in stage 1.0
> (TID 7421)
> 16/11/05 18:12:39 INFO storage.ShuffleBlockFetcherIterator: Getting 878
> non-empty blocks out of 878 blocks
> 16/11/05 18:12:39 INFO storage.ShuffleBlockFetcherIterator: Started 46 remote
> fetches in 10 ms
> 16/11/05 18:12:40 INFO executor.Executor: Finished task 6160.0 in stage 1.0
> (TID 7038). 3681 bytes result sent to driver
> 16/11/05 18:12:40 INFO executor.CoarseGrainedExecutorBackend: Got assigned
> task 7424
> 16/11/05 18:12:40 INFO executor.Executor: Running task 6544.0 in stage 1.0
> (TID 7424)
> 16/11/05 18:12:40 INFO storage.ShuffleBlockFetcherIterator: Getting 878
> non-empty blocks out of 878 blocks
> 16/11/05 18:12:40 INFO storage.ShuffleBlockFetcherIterator: Started 46 remote
> fetches in 16 ms
> 16/11/05 18:12:40 INFO spark.SparkRecordHandler: maximum memory = 19685441536
> 16/11/05 18:12:40 INFO spark.SparkRecordHandler: conf classpath =
> [file:/mnt/disk6/yarn/nm/usercache/root/appcache/application_1478318297544_0031/container_1478318297544_0031_01_000022/__app__.jar,
>
> file:/mnt/disk6/yarn/nm/usercache/root/appcache/application_1478318297544_0031/container_1478318297544_0031_01_000022/__app__.jar,
>
> file:/mnt/disk6/yarn/nm/usercache/root/appcache/application_1478318297544_0031/container_1478318297544_0031_01_000022/./bigbenchqueriesmr.jar,
>
> file:/mnt/disk6/yarn/nm/usercache/root/appcache/application_1478318297544_0031/container_1478318297544_0031_01_000022/./hive-exec-2.2.0-SNAPSHOT.jar]
> 16/11/05 18:12:40 INFO spark.SparkRecordHandler: thread classpath =
> [file:/mnt/disk6/yarn/nm/usercache/root/appcache/application_1478318297544_0031/container_1478318297544_0031_01_000022/__app__.jar,
>
> file:/mnt/disk6/yarn/nm/usercache/root/appcache/application_1478318297544_0031/container_1478318297544_0031_01_000022/__app__.jar,
>
> file:/mnt/disk6/yarn/nm/usercache/root/appcache/application_1478318297544_0031/container_1478318297544_0031_01_000022/./bigbenchqueriesmr.jar,
>
> file:/mnt/disk6/yarn/nm/usercache/root/appcache/application_1478318297544_0031/container_1478318297544_0031_01_000022/./hive-exec-2.2.0-SNAPSHOT.jar]
> 16/11/05 18:12:40 INFO exec.Utilities: PLAN PATH =
> hdfs://eurus-master:8020/tmp/hive/root/6d511c4f-2750-49c3-894b-f5e78d1095c4/hive_2016-11-05_18-01-42_902_5968983454776048389-1/-mr-10002/b2c01f90-f0d1-43bb-bb80-f0e3a874c390/reduce.xml
> 16/11/05 18:12:40 INFO exec.SerializationUtilities: Deserializing ReduceWork
> using kryo
> 16/11/05 18:12:40 INFO exec.Utilities: Deserialized plan (via FILE) - name:
> Reducer 2 size: 3.91KB
> 16/11/05 18:21:02 INFO exec.CommonJoinOperator: table 0 has 8000 rows for
> join key [802585]
> 16/11/05 18:21:02 INFO exec.CommonJoinOperator: table 0 has 16000 rows for
> join key [802585]
> 16/11/05 18:21:02 INFO exec.CommonJoinOperator: table 0 has 1000 rows for
> join key [825039]
> 16/11/05 18:21:02 INFO exec.CommonJoinOperator: table 0 has 2000 rows for
> join key [825039]
> 16/11/05 18:21:02 INFO exec.CommonJoinOperator: table 0 has 4000 rows for
> join key [825039]
> 16/11/05 18:21:02 INFO exec.CommonJoinOperator: table 0 has 8000 rows for
> join key [825039]
> 16/11/05 18:21:02 INFO exec.CommonJoinOperator: table 0 has 16000 rows for
> join key [825039]
> 16/11/05 18:21:02 INFO collection.ExternalSorter: Task 16349 force spilling
> in-memory map to disk and it will release 360.5 MB memory
> 16/11/05 18:21:02 WARN memory.TaskMemoryManager: leak 360.5 MB memory from
> org.apache.spark.util.collection.ExternalSorter@5879fd17
> 16/11/05 18:21:02 ERROR executor.Executor: Exception in task 15468.0 in stage
> 1.0 (TID 16349)
> java.lang.NullPointerException
> at
> org.apache.spark.util.collection.ExternalSorter$SpillReader.cleanup(ExternalSorter.scala:625)
> at
> org.apache.spark.util.collection.ExternalSorter$SpillReader.nextBatchStream(ExternalSorter.scala:540)
> at
> org.apache.spark.util.collection.ExternalSorter$SpillReader.<init>(ExternalSorter.scala:508)
> at
> org.apache.spark.util.collection.ExternalSorter$SpillableIterator.spill(ExternalSorter.scala:814)
> at
> org.apache.spark.util.collection.ExternalSorter.forceSpill(ExternalSorter.scala:254)
> at org.apache.spark.util.collection.Spillable.spill(Spillable.scala:111)
> at
> org.apache.spark.memory.TaskMemoryManager.acquireExecutionMemory(TaskMemoryManager.java:150)
> at
> org.apache.spark.memory.TaskMemoryManager.allocatePage(TaskMemoryManager.java:245)
> at
> org.apache.spark.memory.MemoryConsumer.allocateArray(MemoryConsumer.java:92)
> at
> org.apache.spark.shuffle.sort.ShuffleExternalSorter.growPointerArrayIfNecessary(ShuffleExternalSorter.java:333)
> at
> org.apache.spark.shuffle.sort.ShuffleExternalSorter.insertRecord(ShuffleExternalSorter.java:384)
> at
> org.apache.spark.shuffle.sort.UnsafeShuffleWriter.insertRecordIntoSorter(UnsafeShuffleWriter.java:235)
> at
> org.apache.spark.shuffle.sort.UnsafeShuffleWriter.write(UnsafeShuffleWriter.java:162)
> at
> org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:79)
> at
> org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:47)
> at org.apache.spark.scheduler.Task.run(Task.scala:85)
> at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
> at java.lang.Thread.run(Thread.java:745)
> 16/11/05 18:21:02 INFO executor.CoarseGrainedExecutorBackend: Got assigned
> task 16611
> 16/11/05 18:21:02 INFO executor.Executor: Running task 15730.0 in stage 1.0
> (TID 16611)
> 16/11/05 18:21:02 INFO exec.CommonJoinOperator: table 0 has 1000 rows for
> join key [667774]
> 16/11/05 18:21:02 INFO exec.CommonJoinOperator: table 0 has 2000 rows for
> join key [667774]
> 16/11/05 18:21:02 INFO exec.CommonJoinOperator: table 0 has 4000 rows for
> join key [667774]
> 16/11/05 18:21:02 INFO exec.CommonJoinOperator: table 0 has 8000 rows for
> join key [667774]
> 16/11/05 18:21:02 INFO storage.ShuffleBlockFetcherIterator: Getting 877
> non-empty blocks out of 878 blocks
> 16/11/05 18:21:02 INFO exec.CommonJoinOperator: table 0 has 16000 rows for
> join key [667774]
> 16/11/05 18:21:02 INFO storage.ShuffleBlockFetcherIterator: Started 46 remote
> fetches in 9 ms
> 16/11/05 18:21:02 INFO exec.CommonJoinOperator: table 0 has 1000 rows for
> join key [825073]
> 16/11/05 18:21:02 INFO exec.CommonJoinOperator: table 0 has 2000 rows for
> join key [825073]
> 16/11/05 18:21:02 INFO exec.CommonJoinOperator: table 0 has 4000 rows for
> join key [825073]
> 16/11/05 18:21:02 INFO exec.CommonJoinOperator: table 0 has 8000 rows for
> join key [825073]
> 16/11/05 18:21:02 INFO exec.CommonJoinOperator: table 0 has 16000 rows for
> join key [825073]
> 16/11/05 18:21:02 INFO exec.CommonJoinOperator: table 0 has 1000 rows for
> join key [847527]
> 16/11/05 18:21:02 INFO exec.CommonJoinOperator: table 0 has 2000 rows for
> join key [847527]
> 16/11/05 18:12:22 INFO exec.CommonJoinOperator: table 0 has 1000 rows for
> join key [972725]
> 16/11/05 18:12:22 INFO exec.CommonJoinOperator: table 0 has 2000 rows for
> join key [972725]
> 16/11/05 18:12:22 INFO exec.CommonJoinOperator: table 0 has 4000 rows for
> join key [972725]
> 16/11/05 18:12:22 INFO exec.CommonJoinOperator: table 0 has 8000 rows for
> join key [972725]
> 16/11/05 18:12:22 INFO exec.CommonJoinOperator: table 0 has 16000 rows for
> join key [972725]
> 16/11/05 18:12:22 INFO collection.ExternalSorter: Task 6619 force spilling
> in-memory map to disk and it will release 357.9 MB memory
> 16/11/05 18:12:22 WARN memory.TaskMemoryManager: leak 357.9 MB memory from
> org.apache.spark.util.collection.ExternalSorter@71b91fb4
> 16/11/05 18:12:22 ERROR executor.Executor: Exception in task 5741.0 in stage
> 1.0 (TID 6619)
> java.lang.NullPointerException
> at
> org.apache.spark.util.collection.ExternalSorter$SpillReader.cleanup(ExternalSorter.scala:625)
> at
> org.apache.spark.util.collection.ExternalSorter$SpillReader.nextBatchStream(ExternalSorter.scala:540)
> at
> org.apache.spark.util.collection.ExternalSorter$SpillReader.<init>(ExternalSorter.scala:508)
> at
> org.apache.spark.util.collection.ExternalSorter$SpillableIterator.spill(ExternalSorter.scala:814)
> at
> org.apache.spark.util.collection.ExternalSorter.forceSpill(ExternalSorter.scala:254)
> at org.apache.spark.util.collection.Spillable.spill(Spillable.scala:111)
> at
> org.apache.spark.memory.TaskMemoryManager.acquireExecutionMemory(TaskMemoryManager.java:150)
> at
> org.apache.spark.memory.TaskMemoryManager.allocatePage(TaskMemoryManager.java:245)
> at
> org.apache.spark.memory.MemoryConsumer.allocateArray(MemoryConsumer.java:92)
> at
> org.apache.spark.shuffle.sort.ShuffleExternalSorter.growPointerArrayIfNecessary(ShuffleExternalSorter.java:333)
> at
> org.apache.spark.shuffle.sort.ShuffleExternalSorter.insertRecord(ShuffleExternalSorter.java:384)
> at
> org.apache.spark.shuffle.sort.UnsafeShuffleWriter.insertRecordIntoSorter(UnsafeShuffleWriter.java:235)
> at
> org.apache.spark.shuffle.sort.UnsafeShuffleWriter.write(UnsafeShuffleWriter.java:162)
> at
> org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:79)
> at
> org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:47)
> at org.apache.spark.scheduler.Task.run(Task.scala:85)
> at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
> at java.lang.Thread.run(Thread.java:745)
> 16/11/05 18:12:22 INFO executor.CoarseGrainedExecutorBackend: Got assigned
> task 7053
> 16/11/05 18:12:22 INFO executor.Executor: Running task 6175.0 in stage 1.0
> (TID 7053)
> 16/11/05 18:12:22 INFO storage.ShuffleBlockFetcherIterator: Getting 878
> non-empty blocks out of 878 blocks
> 16/11/05 18:12:22 INFO storage.ShuffleBlockFetcherIterator: Started 46 remote
> fetches in 7 ms
> 16/11/05 18:12:25 INFO spark.SparkRecordHandler: maximum memory = 19685441536
> 16/11/05 18:12:25 INFO spark.SparkRecordHandler: conf classpath =
> [file:/mnt/disk1/yarn/nm/usercache/root/appcache/application_1478318297544_0031/container_1478318297544_0031_01_000030/__app__.jar,
>
> file:/mnt/disk1/yarn/nm/usercache/root/appcache/application_1478318297544_0031/container_1478318297544_0031_01_000030/__app__.jar,
>
> file:/mnt/disk1/yarn/nm/usercache/root/appcache/application_1478318297544_0031/container_1478318297544_0031_01_000030/./bigbenchqueriesmr.jar,
>
> file:/mnt/disk1/yarn/nm/usercache/root/appcache/application_1478318297544_0031/container_1478318297544_0031_01_000030/./hive-exec-2.2.0-SNAPSHOT.jar]
> 16/11/05 18:12:25 INFO spark.SparkRecordHandler: thread classpath =
> [file:/mnt/disk1/yarn/nm/usercache/root/appcache/application_1478318297544_0031/container_1478318297544_0031_01_000030/__app__.jar,
>
> file:/mnt/disk1/yarn/nm/usercache/root/appcache/application_1478318297544_0031/container_1478318297544_0031_01_000030/__app__.jar,
>
> file:/mnt/disk1/yarn/nm/usercache/root/appcache/application_1478318297544_0031/container_1478318297544_0031_01_000030/./bigbenchqueriesmr.jar,
>
> file:/mnt/disk1/yarn/nm/usercache/root/appcache/application_1478318297544_0031/container_1478318297544_0031_01_000030/./hive-exec-2.2.0-SNAPSHOT.jar]
> 16/11/05 18:12:25 INFO exec.Utilities: PLAN PATH =
> hdfs://eurus-master:8020/tmp/hive/root/6d511c4f-2750-49c3-894b-f5e78d1095c4/hive_2016-11-05_18-01-42_902_5968983454776048389-1/-mr-10002/b2c01f90-f0d1-43bb-bb80-f0e3a874c390/reduce.xml
> 16/11/05 18:12:25 INFO exec.SerializationUtilities: Deserializing ReduceWork
> using kryo
> 16/11/05 18:12:25 INFO exec.Utilities: Deserialized plan (via FILE) - name:
> Reducer 2 size: 3.91KB
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