Docker-stacks: java.lang.UnsupportedOperationException using pandas in Spark

[angelcervera]

What docker image you are using?
jupyter/all-spark-notebook

What complete docker command do you run to launch the container (omitting sensitive values)?
docker run -d -p 8888:8888 jupyter/all-spark-notebook

What steps do you take once the container is running to reproduce the issue?

1. Visit http://localhost:8888 with the token
2. Create a new spylon-kernel notebook.

3. Copy and paste the example from Spark documentation:

   %%python
   from pyspark.sql.functions import pandas_udf
   df = spark.createDataFrame([(1, 21), (2, 30)], ("id", "age"))
   def filter_func(iterator):
       for pdf in iterator:
           yield pdf[pdf.id == 1]
   
   df.mapInPandas(filter_func, df.schema).show()
   

4. Enjoy the exception:

Traceback (most recent call last):
  File "python cell", line 7, in <module>
  File "/usr/local/spark/python/pyspark/sql/dataframe.py", line 440, in show
    print(self._jdf.showString(n, 20, vertical))
  File "/usr/local/spark/python/lib/py4j-0.10.9-src.zip/py4j/java_gateway.py", line 1304, in __call__
    return_value = get_return_value(
  File "/usr/local/spark/python/pyspark/sql/utils.py", line 128, in deco
    return f(*a, **kw)
  File "/usr/local/spark/python/lib/py4j-0.10.9-src.zip/py4j/protocol.py", line 326, in get_return_value
    raise Py4JJavaError(
Py4JJavaError: An error occurred while calling o135.showString.
: org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 0.0 failed 1 times, most recent failure: Lost task 0.0 in stage 0.0 (TID 0, a9b99f9c2052, executor driver): java.lang.UnsupportedOperationException: sun.misc.Unsafe or java.nio.DirectByteBuffer.<init>(long, int) not available
    at io.netty.util.internal.PlatformDependent.directBuffer(PlatformDependent.java:490)
    at io.netty.buffer.NettyArrowBuf.getDirectBuffer(NettyArrowBuf.java:243)
    at io.netty.buffer.NettyArrowBuf.nioBuffer(NettyArrowBuf.java:233)
    at io.netty.buffer.ArrowBuf.nioBuffer(ArrowBuf.java:245)
    at org.apache.arrow.vector.ipc.message.ArrowRecordBatch.computeBodyLength(ArrowRecordBatch.java:222)
    at org.apache.arrow.vector.ipc.message.MessageSerializer.serialize(MessageSerializer.java:240)
    at org.apache.arrow.vector.ipc.ArrowWriter.writeRecordBatch(ArrowWriter.java:132)
    at org.apache.arrow.vector.ipc.ArrowWriter.writeBatch(ArrowWriter.java:120)
    at org.apache.spark.sql.execution.python.ArrowPythonRunner$$anon$1.$anonfun$writeIteratorToStream$1(ArrowPythonRunner.scala:94)
    at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23)
    at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
    at org.apache.spark.sql.execution.python.ArrowPythonRunner$$anon$1.writeIteratorToStream(ArrowPythonRunner.scala:101)
    at org.apache.spark.api.python.BasePythonRunner$WriterThread.$anonfun$run$1(PythonRunner.scala:383)
    at org.apache.spark.util.Utils$.logUncaughtExceptions(Utils.scala:1932)
    at org.apache.spark.api.python.BasePythonRunner$WriterThread.run(PythonRunner.scala:218)

Driver stacktrace:
    at org.apache.spark.scheduler.DAGScheduler.failJobAndIndependentStages(DAGScheduler.scala:2059)
    at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$2(DAGScheduler.scala:2008)
    at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$2$adapted(DAGScheduler.scala:2007)
    at scala.collection.mutable.ResizableArray.foreach(ResizableArray.scala:62)
    at scala.collection.mutable.ResizableArray.foreach$(ResizableArray.scala:55)
    at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:49)
    at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:2007)
    at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$1(DAGScheduler.scala:973)
    at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$1$adapted(DAGScheduler.scala:973)
    at scala.Option.foreach(Option.scala:407)
    at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:973)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2239)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2188)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2177)
    at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
    at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:775)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2099)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2120)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2139)
    at org.apache.spark.sql.execution.SparkPlan.executeTake(SparkPlan.scala:467)
    at org.apache.spark.sql.execution.SparkPlan.executeTake(SparkPlan.scala:420)
    at org.apache.spark.sql.execution.CollectLimitExec.executeCollect(limit.scala:47)
    at org.apache.spark.sql.Dataset.collectFromPlan(Dataset.scala:3627)
    at org.apache.spark.sql.Dataset.$anonfun$head$1(Dataset.scala:2697)
    at org.apache.spark.sql.Dataset.$anonfun$withAction$1(Dataset.scala:3618)
    at org.apache.spark.sql.execution.SQLExecution$.$anonfun$withNewExecutionId$5(SQLExecution.scala:100)
    at org.apache.spark.sql.execution.SQLExecution$.withSQLConfPropagated(SQLExecution.scala:160)
    at org.apache.spark.sql.execution.SQLExecution$.$anonfun$withNewExecutionId$1(SQLExecution.scala:87)
    at org.apache.spark.sql.SparkSession.withActive(SparkSession.scala:764)
    at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:64)
    at org.apache.spark.sql.Dataset.withAction(Dataset.scala:3616)
    at org.apache.spark.sql.Dataset.head(Dataset.scala:2697)
    at org.apache.spark.sql.Dataset.take(Dataset.scala:2904)
    at org.apache.spark.sql.Dataset.getRows(Dataset.scala:300)
    at org.apache.spark.sql.Dataset.showString(Dataset.scala:337)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
    at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
    at py4j.Gateway.invoke(Gateway.java:282)
    at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
    at py4j.commands.CallCommand.execute(CallCommand.java:79)
    at py4j.GatewayConnection.run(GatewayConnection.java:238)
    at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: java.lang.UnsupportedOperationException: sun.misc.Unsafe or java.nio.DirectByteBuffer.<init>(long, int) not available
    at io.netty.util.internal.PlatformDependent.directBuffer(PlatformDependent.java:490)
    at io.netty.buffer.NettyArrowBuf.getDirectBuffer(NettyArrowBuf.java:243)
    at io.netty.buffer.NettyArrowBuf.nioBuffer(NettyArrowBuf.java:233)
    at io.netty.buffer.ArrowBuf.nioBuffer(ArrowBuf.java:245)
    at org.apache.arrow.vector.ipc.message.ArrowRecordBatch.computeBodyLength(ArrowRecordBatch.java:222)
    at org.apache.arrow.vector.ipc.message.MessageSerializer.serialize(MessageSerializer.java:240)
    at org.apache.arrow.vector.ipc.ArrowWriter.writeRecordBatch(ArrowWriter.java:132)
    at org.apache.arrow.vector.ipc.ArrowWriter.writeBatch(ArrowWriter.java:120)
    at org.apache.spark.sql.execution.python.ArrowPythonRunner$$anon$1.$anonfun$writeIteratorToStream$1(ArrowPythonRunner.scala:94)
    at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23)
    at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
    at org.apache.spark.sql.execution.python.ArrowPythonRunner$$anon$1.writeIteratorToStream(ArrowPythonRunner.scala:101)
    at org.apache.spark.api.python.BasePythonRunner$WriterThread.$anonfun$run$1(PythonRunner.scala:383)
    at org.apache.spark.util.Utils$.logUncaughtExceptions(Utils.scala:1932)
    at org.apache.spark.api.python.BasePythonRunner$WriterThread.run(PythonRunner.scala:218)

What do you expect to happen?

+---+---+
| id|age|
+---+---+
|  1| 21|
+---+---+

What actually happens?

There is know limitation with pySpark (more precise with Arrow) and Java11 and there are few option to fix it. Downgrade to Java8 or patch the configuration adding -Dio.netty.tryReflectionSetAccessible=true property.

Reference
From the Spark documentation

For Java 11, -Dio.netty.tryReflectionSetAccessible=true is required additionally for Apache Arrow library. This prevents java.lang.UnsupportedOperationException: sun.misc.Unsafe or java.nio.DirectByteBuffer.(long, int) not available when Apache Arrow uses Netty internally.

[romainx]

Hello @angelcervera,

Thanks for reporting this issue.

Not sure we want to downgrade to Java 8. So if you want to draft a PR to implement the -Dio.netty.tryReflectionSetAccessible=true solution, go for it. In this case, it would be interesting to add a test case for that based on this example.

https://github.com/jupyter/docker-stacks/blob/332db3db9ebb51167ef6b21cf261022bd0fc4eae/pyspark-notebook/test/test_spark.py

Many thanks.

[Bidek56]

Please add these config options to resolve the issue:

conf.set("spark.sql.legacy.setCommandRejectsSparkCoreConfs","false") conf.set("spark.driver.extraJavaOptions", "-Dio.netty.tryReflectionSetAccessible=true") conf.set("spark.executor.extraJavaOptions", "-Dio.netty.tryReflectionSetAccessible=true")

I am going to try upgrading JRE to see if this issue is fixed in the newer versions, but last time I have tried, Spark would not work with anything higher than JRE 11, which is very old these days.

[angelcervera]

Hi Derek.
If you want, I can work on it, but no time until weekend.
If it's ok for you, I can create a PR.

Regards

On Tue 29 Sep 2020, 15:28 Darek, [e-mail] wrote:

Please add these config options to resolve the issue:

conf.set("spark.sql.legacy.setCommandRejectsSparkCoreConfs","false")
conf.set("spark.driver.extraJavaOptions",
"-Dio.netty.tryReflectionSetAccessible=true")
conf.set("spark.executor.extraJavaOptions",
"-Dio.netty.tryReflectionSetAccessible=true")

I am going to try upgrading JRE to see if this issue is fixed in the newer
versions, but last time I have tried, Spark would not work with anything
higher than JRE 11, which is very old these days.

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[Bidek56]

I just tried upgrading Open JDK to 14, Spark work OK but this error still exists.
Not sure if it's worth upgrading JDK to 14 since it's not a LTS and it does not fixes this issue.
We may have to wait until JDK 14.0.2 or 15 to be available.

[Bidek56]

I may do a PR for JDK 14 anyway hoping that it fixes this issue.

[romainx]

Hello, just submitted the PR #1198 to fix it.
Please let me know if it's OK for you.
Best.