Unable to run analytics using GraphFrames and PySpark on Jupyter Notebook

Question

I've been trying to install GraphFrames on my environment. I am using Jupyter Notebook and I've successfully installed Spark. In order to install GraphFrames, I did !pip install graphframes directly from my notebook, which ran successfully. Then, I downloaded the graphframes jar from graphframes package, version 0.8.2-spark3.2-s_2.12 and I put it inside my spark-3.2.1-bin-hadoop3.2/jars/ directory. My Spark version is 3.2.1.

The thing is, I can import graphframes inside my notebook and create a GraphFrame object without any error, but the moment I run inDegrees or any other computation, I get an error. By looking at the jupyter terminal I could see that the jar loads correctly, but when my jobs run, I end up getting Python was not found. Run without arguments. I want to specify that PySpark works just fine when I'm not using graphframes.

I don't know if that will help to identify the problem, but when I type python in my cmd, it uses the version 3.9.2 which I installed a while ago. I just checked the python version inside my notebook and it tells me 3.9.7. Is there any way this might conflict?

Here's my script:

from pyspark.sql import SparkSession
from graphframes import *

spark = SparkSession.builder.appName("Gene graph processing")\
        .config("spark.jars.packages", "graphframes:graphframes:0.8.2-spark3.2-s_2.12") \
        .master("local[*]").getOrCreate()

vertices = spark.createDataFrame([('1', 'Carter', 'Derrick', 50), 
                                  ('2', 'May', 'Derrick', 26),
                                 ('3', 'Mills', 'Jeff', 80),
                                  ('4', 'Hood', 'Robert', 65),
                                  ('5', 'Banks', 'Mike', 93),
                                 ('98', 'Berg', 'Tim', 28),
                                 ('99', 'Page', 'Allan', 16)],
                                 ['id', 'name', 'firstname', 'age'])
edges = spark.createDataFrame([('1', '2', 'friend'), 
                               ('2', '1', 'friend'),
                              ('3', '1', 'friend'),
                              ('1', '3', 'friend'),
                               ('2', '3', 'follows'),
                               ('3', '4', 'friend'),
                               ('4', '3', 'friend'),
                               ('5', '3', 'friend'),
                               ('3', '5', 'friend'),
                               ('4', '5', 'follows'),
                              ('98', '99', 'friend'),
                              ('99', '98', 'friend')],
                              ['src', 'dst', 'type'])
g = GraphFrame(vertices, edges)
g.inDegrees.show()

And here's my error when I run the inDegrees:

Py4JJavaError: An error occurred while calling o69.showString.
: org.apache.spark.SparkException: Job aborted due to stage failure: Task 3 in stage 0.0 failed 1 times, most recent failure: Lost task 3.0 in stage 0.0 (TID 3) (LAPTOP-B2L5S698 executor driver): org.apache.spark.SparkException: Python worker failed to connect back.
    at org.apache.spark.api.python.PythonWorkerFactory.createSimpleWorker(PythonWorkerFactory.scala:188)
    at org.apache.spark.api.python.PythonWorkerFactory.create(PythonWorkerFactory.scala:108)
    at org.apache.spark.SparkEnv.createPythonWorker(SparkEnv.scala:121)
    at org.apache.spark.api.python.BasePythonRunner.compute(PythonRunner.scala:162)
    at org.apache.spark.api.python.PythonRDD.compute(PythonRDD.scala:65)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:373)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:337)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:373)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:337)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:373)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:337)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:373)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:337)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:373)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:337)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:373)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:337)
    at org.apache.spark.shuffle.ShuffleWriteProcessor.write(ShuffleWriteProcessor.scala:59)
    at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:99)
    at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:52)
    at org.apache.spark.scheduler.Task.run(Task.scala:131)
    at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:506)
    at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1462)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:509)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:750)
Caused by: java.net.SocketTimeoutException: Accept timed out
    at java.net.DualStackPlainSocketImpl.waitForNewConnection(Native Method)
    at java.net.DualStackPlainSocketImpl.socketAccept(DualStackPlainSocketImpl.java:131)
    at java.net.AbstractPlainSocketImpl.accept(AbstractPlainSocketImpl.java:535)
    at java.net.PlainSocketImpl.accept(PlainSocketImpl.java:189)
    at java.net.ServerSocket.implAccept(ServerSocket.java:545)
    at java.net.ServerSocket.accept(ServerSocket.java:513)
    at org.apache.spark.api.python.PythonWorkerFactory.createSimpleWorker(PythonWorkerFactory.scala:175)
    ... 31 more

Driver stacktrace:
    at org.apache.spark.scheduler.DAGScheduler.failJobAndIndependentStages(DAGScheduler.scala:2454)
    at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$2(DAGScheduler.scala:2403)
    at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$2$adapted(DAGScheduler.scala:2402)
    at scala.collection.mutable.ResizableArray.foreach(ResizableArray.scala:62)
    at scala.collection.mutable.ResizableArray.foreach$(ResizableArray.scala:55)
    at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:49)
    at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:2402)
    at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$1(DAGScheduler.scala:1160)
    at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$1$adapted(DAGScheduler.scala:1160)
    at scala.Option.foreach(Option.scala:407)
    at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:1160)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2642)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2584)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2573)
    at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
Caused by: org.apache.spark.SparkException: Python worker failed to connect back.
    at org.apache.spark.api.python.PythonWorkerFactory.createSimpleWorker(PythonWorkerFactory.scala:188)
    at org.apache.spark.api.python.PythonWorkerFactory.create(PythonWorkerFactory.scala:108)
    at org.apache.spark.SparkEnv.createPythonWorker(SparkEnv.scala:121)
    at org.apache.spark.api.python.BasePythonRunner.compute(PythonRunner.scala:162)
    at org.apache.spark.api.python.PythonRDD.compute(PythonRDD.scala:65)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:373)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:337)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:373)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:337)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:373)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:337)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:373)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:337)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:373)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:337)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:373)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:337)
    at org.apache.spark.shuffle.ShuffleWriteProcessor.write(ShuffleWriteProcessor.scala:59)
    at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:99)
    at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:52)
    at org.apache.spark.scheduler.Task.run(Task.scala:131)
    at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:506)
    at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1462)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:509)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:750)
Caused by: java.net.SocketTimeoutException: Accept timed out
    at java.net.DualStackPlainSocketImpl.waitForNewConnection(Native Method)
    at java.net.DualStackPlainSocketImpl.socketAccept(DualStackPlainSocketImpl.java:131)
    at java.net.AbstractPlainSocketImpl.accept(AbstractPlainSocketImpl.java:535)
    at java.net.PlainSocketImpl.accept(PlainSocketImpl.java:189)
    at java.net.ServerSocket.implAccept(ServerSocket.java:545)
    at java.net.ServerSocket.accept(ServerSocket.java:513)
    at org.apache.spark.api.python.PythonWorkerFactory.createSimpleWorker(PythonWorkerFactory.scala:175)
    ... 31 more

mamonu · Accepted Answer · 2022-03-10 23:20:45Z

0

you probably need to define your PYSPARK_PYTHON environment variable

can you try this

import os
from pyspark.sql import SparkSession
os.environ['PYSPARK_PYTHON'] = "where_your_python_is_if_you_do_which_python"

and then create your sparkSession object as you do above

spark = SparkSession.builder.appName("Gene graph processing")\
.config("spark.jars.packages", "graphframes:graphframes:0.8.2-spark3.2-s_2.12") \
.master("local[*]").getOrCreate()

answered Mar 10, 2022 at 23:20

mamonu

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