python - 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>

3. 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}.
   ".
   --> 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

Answer 1

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.

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