Apache Spark method not found sun.nio.ch.DirectBuffer.cleaner()Lsun/misc/Cleaner;

Question

I encounter this problem while running an automated data processing script in spark-shell. First couple of iterations work fine, but it always sooner or later bumps into this error. I googled this issue but haven't found an exact match. Other similar issues are outside of spark context. I guess it may have something to do with JVM version, but I cannot figure out how to solve the problem.

I used 2 machines within a spark standalone cluster.

Machine No.1 Java Information:

java 10.0.2 2018-07-17
Java(TM) SE Runtime Environment 18.3 (build 10.0.2+13)
Java HotSpot(TM) 64-Bit Server VM 18.3 (build 10.0.2+13, mixed mode)

Machine No.2 Java Information:

openjdk 10.0.2 2018-07-17
OpenJDK Runtime Environment (build 10.0.2+13-Ubuntu-1ubuntu0.18.04.4)
OpenJDK 64-Bit Server VM (build 10.0.2+13-Ubuntu-1ubuntu0.18.04.4, mixed mode)

Error Information:

WARN  TaskSetManager:66 - Lost task 3.0 in stage 28.0 (TID 1368, 169.254.115.145, executor 1): 
java.lang.NoSuchMethodError: sun.nio.ch.DirectBuffer.cleaner()Lsun/misc/Cleaner;
        at org.apache.spark.storage.StorageUtils$.cleanDirectBuffer(StorageUtils.scala:212)
        at org.apache.spark.storage.StorageUtils$.dispose(StorageUtils.scala:207)
        at org.apache.spark.storage.StorageUtils.dispose(StorageUtils.scala)
        at org.apache.spark.io.NioBufferedFileInputStream.close(NioBufferedFileInputStream.java:130)
        at java.base/java.io.FilterInputStream.close(FilterInputStream.java:180)
        at org.apache.spark.io.ReadAheadInputStream.close(ReadAheadInputStream.java:400)
        at org.apache.spark.util.collection.unsafe.sort.UnsafeSorterSpillReader.close(UnsafeSorterSpillReader.java:152)
        at org.apache.spark.util.collection.unsafe.sort.UnsafeSorterSpillReader.loadNext(UnsafeSorterSpillReader.java:124)
        at org.apache.spark.util.collection.unsafe.sort.UnsafeExternalSorter$SpillableIterator.loadNext(UnsafeExternalSorter.java:590)
        at org.apache.spark.sql.execution.UnsafeKVExternalSorter$KVSorterIterator.next(UnsafeKVExternalSorter.java:287)
        at org.apache.spark.sql.execution.aggregate.SortBasedAggregator$$anon$1.findNextSortedGroup(ObjectAggregationIterator.scala:276)
        at org.apache.spark.sql.execution.aggregate.SortBasedAggregator$$anon$1.hasNext(ObjectAggregationIterator.scala:247)
        at org.apache.spark.sql.execution.aggregate.ObjectAggregationIterator.hasNext(ObjectAggregationIterator.scala:81)
        at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
        at org.apache.spark.shuffle.sort.BypassMergeSortShuffleWriter.write(BypassMergeSortShuffleWriter.java:148)
        at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:99)
        at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:55)
        at org.apache.spark.scheduler.Task.run(Task.scala:121)
        at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:402)
        at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
        at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:408)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1135)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
        at java.base/java.lang.Thread.run(Thread.java:844)

Answer 1

I managed to solve the problem by setting JAVA_HOME for spark to a java8 JDK. It is a quite new issue but has been spotted by the developers of spark, see here https://github.com/apache/spark/pull/22993/files/7f58ae61262d7c2f2d70c24d051c63e8830d5062.

The latest pre-compiled spark provided by the official site was released on Nov 2 and this pull request happened later. Hopefully later release would avoid this issue with java of newer version.