PySpark in iPython notebook raises Py4JJavaError when using count() and first()

Question:

I am using PySpark(v.2.1.0) in iPython notebook (python v.3.6) over virtualenv in my Mac(Sierra 10.12.3 Beta).

1.I launched iPython notebook by shooting this in Terminal –

 PYSPARK_PYTHON=python3 PYSPARK_DRIVER_PYTHON=ipython PYSPARK_DRIVER_PYTHON_OPTS="notebook" /Applications/spark-2.1.0-bin-hadoop2.7/bin/pyspark

2.Loaded my file to Spark Context and ensured its loaded-

>>>lines = sc.textFile("/Users/PanchusMac/Dropbox/Learn_py/Virtual_Env/pyspark/README.md") 

>>>for i in lines.collect(): 
    print(i)

And it worked fine and printed the result over my console as shown:

# Apache Spark

Spark is a fast and general cluster computing system for Big Data. It provides
high-level APIs in Scala, Java, Python, and R, and an optimized engine that
supports general computation graphs for data analysis. It also supports a
rich set of higher-level tools including Spark SQL for SQL and DataFrames,
MLlib for machine learning, GraphX for graph processing,
and Spark Streaming for stream processing.

<http://spark.apache.org/>


## Online Documentation

You can find the latest Spark documentation, including a programming
guide, on the [project web page](http://spark.apache.org/documentation.html).
This README file only contains basic setup instructions. 

Also checked the sc –

>>>print(sc)

<pyspark.context.SparkContext object at 0x101ce4cc0>
  1. Now when I am trying to execute lines.count() or lines.first() functions over my RDD, I ended up with following error –


    Py4JJavaError                             Traceback (most recent call last)
    <ipython-input-33-44aeefde846d> in <module>()
    ----> 1 lines.count()
    
    /Applications/spark-2.1.0-bin-hadoop2.7/python/pyspark/rdd.py in count(self)
       1039         3
       1040         """
    -> 1041         return self.mapPartitions(lambda i: [sum(1 for _ in i)]).sum()
       1042 
       1043     def stats(self):
    
    /Applications/spark-2.1.0-bin-hadoop2.7/python/pyspark/rdd.py in sum(self)
       1030         6.0
       1031         """
    -> 1032         return self.mapPartitions(lambda x: [sum(x)]).fold(0, operator.add)
       1033 
       1034     def count(self):
    
    /Applications/spark-2.1.0-bin-hadoop2.7/python/pyspark/rdd.py in fold(self, zeroValue, op)
        904         # zeroValue provided to each partition is unique from the one provided
        905         # to the final reduce call
    --> 906         vals = self.mapPartitions(func).collect()
        907         return reduce(op, vals, zeroValue)
        908 
    
    /Applications/spark-2.1.0-bin-hadoop2.7/python/pyspark/rdd.py in collect(self)
        807         """
        808         with SCCallSiteSync(self.context) as css:
    --> 809             port = self.ctx._jvm.PythonRDD.collectAndServe(self._jrdd.rdd())
        810         return list(_load_from_socket(port, self._jrdd_deserializer))
        811 
    
    /Applications/spark-2.1.0-bin-hadoop2.7/python/lib/py4j-0.10.4-src.zip/py4j/java_gateway.py in __call__(self, *args)
       1131         answer = self.gateway_client.send_command(command)
       1132         return_value = get_return_value(
    -> 1133             answer, self.gateway_client, self.target_id, self.name)
       1134 
       1135         for temp_arg in temp_args:
    
    /Applications/spark-2.1.0-bin-hadoop2.7/python/pyspark/sql/utils.py in deco(*a, **kw)
         61     def deco(*a, **kw):
         62         try:
    ---> 63             return f(*a, **kw)
         64         except py4j.protocol.Py4JJavaError as e:
         65             s = e.java_exception.toString()
    
    /Applications/spark-2.1.0-bin-hadoop2.7/python/lib/py4j-0.10.4-src.zip/py4j/protocol.py in get_return_value(answer, gateway_client, target_id, name)
        317                 raise Py4JJavaError(
        318                     "An error occurred while calling {0}{1}{2}.n".
    --> 319                     format(target_id, ".", name), value)
        320             else:
        321                 raise Py4JError(
    
    Py4JJavaError: An error occurred while calling z:org.apache.spark.api.python.PythonRDD.collectAndServe.
    : org.apache.spark.SparkException: Job aborted due to stage failure: Task 1 in stage 14.0 failed 1 times, most recent failure: Lost task 1.0 in stage 14.0 (TID 22, localhost, executor driver): org.apache.spark.SparkException: 
    Error from python worker:
      Traceback (most recent call last):
        File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/runpy.py", line 183, in _run_module_as_main
          mod_name, mod_spec, code = _get_module_details(mod_name, _Error)
        File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/runpy.py", line 109, in _get_module_details
          __import__(pkg_name)
        File "<frozen importlib._bootstrap>", line 961, in _find_and_load
        File "<frozen importlib._bootstrap>", line 950, in _find_and_load_unlocked
        File "<frozen importlib._bootstrap>", line 646, in _load_unlocked
        File "<frozen importlib._bootstrap>", line 616, in _load_backward_compatible
        File "/Applications/spark-2.1.0-bin-hadoop2.7/python/lib/pyspark.zip/pyspark/__init__.py", line 44, in <module>
        File "<frozen importlib._bootstrap>", line 961, in _find_and_load
        File "<frozen importlib._bootstrap>", line 950, in _find_and_load_unlocked
        File "<frozen importlib._bootstrap>", line 646, in _load_unlocked
        File "<frozen importlib._bootstrap>", line 616, in _load_backward_compatible
        File "/Applications/spark-2.1.0-bin-hadoop2.7/python/lib/pyspark.zip/pyspark/context.py", line 36, in <module>
        File "<frozen importlib._bootstrap>", line 961, in _find_and_load
        File "<frozen importlib._bootstrap>", line 950, in _find_and_load_unlocked
        File "<frozen importlib._bootstrap>", line 646, in _load_unlocked
        File "<frozen importlib._bootstrap>", line 616, in _load_backward_compatible
        File "/Applications/spark-2.1.0-bin-hadoop2.7/python/lib/pyspark.zip/pyspark/java_gateway.py", line 25, in <module>
        File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/platform.py", line 886, in <module>
          "system node release version machine processor")
        File "/Applications/spark-2.1.0-bin-hadoop2.7/python/lib/pyspark.zip/pyspark/serializers.py", line 393, in namedtuple
      TypeError: namedtuple() missing 3 required keyword-only arguments: 'verbose', 'rename', and 'module'
    PYTHONPATH was:
      /Applications/spark-2.1.0-bin-hadoop2.7/python/lib/pyspark.zip:/Applications/spark-2.1.0-bin-hadoop2.7/python/lib/py4j-0.10.4-src.zip:/Applications/spark-2.1.0-bin-hadoop2.7/jars/spark-core_2.11-2.1.0.jar:/Applications/spark-2.1.0-bin-hadoop2.7/python/lib/py4j-0.10.4-src.zip:/Applications/spark-2.1.0-bin-hadoop2.7/python/:
    java.io.EOFException
        at java.io.DataInputStream.readInt(DataInputStream.java:392)
        at org.apache.spark.api.python.PythonWorkerFactory.startDaemon(PythonWorkerFactory.scala:166)
        at org.apache.spark.api.python.PythonWorkerFactory.createThroughDaemon(PythonWorkerFactory.scala:89)
        at org.apache.spark.api.python.PythonWorkerFactory.create(PythonWorkerFactory.scala:65)
        at org.apache.spark.SparkEnv.createPythonWorker(SparkEnv.scala:116)
        at org.apache.spark.api.python.PythonRunner.compute(PythonRDD.scala:128)
        at org.apache.spark.api.python.PythonRDD.compute(PythonRDD.scala:63)
        at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
        at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
        at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
        at org.apache.spark.scheduler.Task.run(Task.scala:99)
        at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:282)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:745)
    
    Driver stacktrace:
        at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1435)
        at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1423)
        at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1422)
        at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
        at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
        at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1422)
        at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:802)
        at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:802)
        at scala.Option.foreach(Option.scala:257)
        at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:802)
        at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1650)
        at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1605)
        at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1594)
        at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
        at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:628)
        at org.apache.spark.SparkContext.runJob(SparkContext.scala:1918)
        at org.apache.spark.SparkContext.runJob(SparkContext.scala:1931)
        at org.apache.spark.SparkContext.runJob(SparkContext.scala:1944)
        at org.apache.spark.SparkContext.runJob(SparkContext.scala:1958)
        at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:935)
        at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
        at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
        at org.apache.spark.rdd.RDD.withScope(RDD.scala:362)
        at org.apache.spark.rdd.RDD.collect(RDD.scala:934)
        at org.apache.spark.api.python.PythonRDD$.collectAndServe(PythonRDD.scala:453)
        at org.apache.spark.api.python.PythonRDD.collectAndServe(PythonRDD.scala)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:497)
        at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
        at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
        at py4j.Gateway.invoke(Gateway.java:280)
        at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
        at py4j.commands.CallCommand.execute(CallCommand.java:79)
        at py4j.GatewayConnection.run(GatewayConnection.java:214)
        at java.lang.Thread.run(Thread.java:745)
    Caused by: org.apache.spark.SparkException: 
    Error from python worker:
      Traceback (most recent call last):
        File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/runpy.py", line 183, in _run_module_as_main
          mod_name, mod_spec, code = _get_module_details(mod_name, _Error)
        File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/runpy.py", line 109, in _get_module_details
          __import__(pkg_name)
        File "<frozen importlib._bootstrap>", line 961, in _find_and_load
        File "<frozen importlib._bootstrap>", line 950, in _find_and_load_unlocked
        File "<frozen importlib._bootstrap>", line 646, in _load_unlocked
        File "<frozen importlib._bootstrap>", line 616, in _load_backward_compatible
        File "/Applications/spark-2.1.0-bin-hadoop2.7/python/lib/pyspark.zip/pyspark/__init__.py", line 44, in <module>
        File "<frozen importlib._bootstrap>", line 961, in _find_and_load
        File "<frozen importlib._bootstrap>", line 950, in _find_and_load_unlocked
        File "<frozen importlib._bootstrap>", line 646, in _load_unlocked
        File "<frozen importlib._bootstrap>", line 616, in _load_backward_compatible
        File "/Applications/spark-2.1.0-bin-hadoop2.7/python/lib/pyspark.zip/pyspark/context.py", line 36, in <module>
        File "<frozen importlib._bootstrap>", line 961, in _find_and_load
        File "<frozen importlib._bootstrap>", line 950, in _find_and_load_unlocked
        File "<frozen importlib._bootstrap>", line 646, in _load_unlocked
        File "<frozen importlib._bootstrap>", line 616, in _load_backward_compatible
        File "/Applications/spark-2.1.0-bin-hadoop2.7/python/lib/pyspark.zip/pyspark/java_gateway.py", line 25, in <module>
        File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/platform.py", line 886, in <module>
          "system node release version machine processor")
        File "/Applications/spark-2.1.0-bin-hadoop2.7/python/lib/pyspark.zip/pyspark/serializers.py", line 393, in namedtuple
      TypeError: namedtuple() missing 3 required keyword-only arguments: 'verbose', 'rename', and 'module'
    PYTHONPATH was:
      /Applications/spark-2.1.0-bin-hadoop2.7/python/lib/pyspark.zip:/Applications/spark-2.1.0-bin-hadoop2.7/python/lib/py4j-0.10.4-src.zip:/Applications/spark-2.1.0-bin-hadoop2.7/jars/spark-core_2.11-2.1.0.jar:/Applications/spark-2.1.0-bin-hadoop2.7/python/lib/py4j-0.10.4-src.zip:/Applications/spark-2.1.0-bin-hadoop2.7/python/:
    java.io.EOFException
        at java.io.DataInputStream.readInt(DataInputStream.java:392)
        at org.apache.spark.api.python.PythonWorkerFactory.startDaemon(PythonWorkerFactory.scala:166)
        at org.apache.spark.api.python.PythonWorkerFactory.createThroughDaemon(PythonWorkerFactory.scala:89)
        at org.apache.spark.api.python.PythonWorkerFactory.create(PythonWorkerFactory.scala:65)
        at org.apache.spark.SparkEnv.createPythonWorker(SparkEnv.scala:116)
        at org.apache.spark.api.python.PythonRunner.compute(PythonRDD.scala:128)
        at org.apache.spark.api.python.PythonRDD.compute(PythonRDD.scala:63)
        at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
        at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
        at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
        at org.apache.spark.scheduler.Task.run(Task.scala:99)
        at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:282)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        ... 1 more
    

Could someone explain me where does it went wrong ?
Note: When I performed the same operations in my Mac Terminal, they worked just as expected.

Asked By: Panchu

||

Answers:

Pyspark 2.1.0 is not compatible with python 3.6, see https://issues.apache.org/jira/browse/SPARK-19019.

You need to use earlier python version or you can try building master or 2.1 branch from github and it should work.

Answered By: Mariusz

Yeah I had the same problem long time ago in Pyspark in Anaconda I tried several ways to rectify this finally I found on my own by installing Java for anaconda separately afterwards there is no Py4jerror.

conda install -c cyclus java-jdk

https://anaconda.org/cyclus/java-jdk

Answered By: Raja Rajan

If you are using Anaconda, try to install java-jdk for Anaconda:

conda install -c cyclus java-jdk
Answered By: Tung Nguyen

I’m not in Anaconda, I use Pyspark manual installation (without pip!). I had this issue until I put on my notebook :

os.environ['PYSPARK_DRIVER_PYTHON_OPTS']= "notebook"
os.environ['PYSPARK_DRIVER_PYTHON'] = sys.executable
os.environ['PYSPARK_PYTHON'] = sys.executable
Answered By: Alexander Walsh