Zeppelin/Spark: org.apache.spark.SparkException: Cannot run program "/usr/bin/": error=13, no permission

Question

I try to get a basic regression run with Zeppelin 0.7.2 and Spark 2.1.1 on Debian 9. Both zeppelin are "installed" in /usr/local/ that means /usr/local/zeppelin/ and /usr/local/spark. Zeppelin also knows the correct SPARK_HOME. First I load the data:

%spark.pyspark
from sqlalchemy import create_engine #sql query
import pandas as pd #sql query
from pyspark import SparkContext #Spark DataFrame
from pyspark.sql import SQLContext #Spark DataFrame

# database connection and sql query
pdf = pd.read_sql("select col1, col2, col3 from table", create_engine('mysql+mysqldb://user:pass@host:3306/db').connect())

print(pdf.size) # size of pandas dataFrame

# convert pandas dataFrame into spark dataFrame
sdf = SQLContext(SparkContext.getOrCreate()).createDataFrame(pdf)

sdf.printSchema()# what does the spark dataFrame look like?

Fine, it works and I get the output with 46977 row and three cols:

46977
root
 |-- col1: double (nullable = true)
 |-- col2: double (nullable = true)
 |-- col3: date (nullable = true)

Ok, now I want to do the regression:

%spark.pyspark
# do a linear regression with sparks ml libs
# https://community.intersystems.com/post/machine-learning-spark-and-cach%C3%A9
from pyspark.ml.regression import LinearRegression
from pyspark.ml.feature import VectorAssembler

# choose several inputCols and transform the "Features" column(s) into the correct vector format
vectorAssembler = VectorAssembler(inputCols=["col1"], outputCol="features")
data=vectorAssembler.transform(sdf)
print(data)

# Split the data into 70% training and 30% test sets.
trainingData,testData = data.randomSplit([0.7, 0.3], 0.0)
print(trainingData)

# Configure the model.
lr = LinearRegression().setFeaturesCol("features").setLabelCol("col2").setMaxIter(10)

## Train the model using the training data.
lrm = lr.fit(trainingData)

## Run the test data through the model and display its predictions for PetalLength.
#predictions = lrm.transform(testData)
#predictions.show()

But while doing lr.fit(trainingData), I get errors in the console (and log files of zeppelin). The errors seems to be while starting spark: Cannot run program "/usr/bin/": error=13, Keine Berechtigung. I wonder what should to be started in /usr/bin/ since I only use the path /usr/local/.

Traceback (most recent call last):
  File "/tmp/zeppelin_pyspark-4001144784380663394.py", line 367, in <module>
    raise Exception(traceback.format_exc())
Exception: Traceback (most recent call last):
  File "/tmp/zeppelin_pyspark-4001144784380663394.py", line 360, in <module>
    exec(code, _zcUserQueryNameSpace)
  File "<stdin>", line 9, in <module>
  File "/usr/local/spark/python/pyspark/ml/base.py", line 64, in fit
    return self._fit(dataset)
  File "/usr/local/spark/python/pyspark/ml/wrapper.py", line 236, in _fit
    java_model = self._fit_java(dataset)
  File "/usr/local/spark/python/pyspark/ml/wrapper.py", line 233, in _fit_java
    return self._java_obj.fit(dataset._jdf)
  File "/usr/local/spark/python/lib/py4j-0.10.4-src.zip/py4j/java_gateway.py", line 1133, in __call__
    answer, self.gateway_client, self.target_id, self.name)
  File "/usr/local/spark/python/pyspark/sql/utils.py", line 63, in deco
    return f(*a, **kw)
  File "/usr/local/spark/python/lib/py4j-0.10.4-src.zip/py4j/protocol.py", line 319, in get_return_value
    format(target_id, ".", name), value)
Py4JJavaError: An error occurred while calling o70.fit.
: 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, localhost, executor driver): **java.io.IOException: Cannot run program "/usr/bin/": error=13, Keine Berechtigung**
    at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)
    at org.apache.spark.api.python.PythonWorkerFactory.startDaemon(PythonWorkerFactory.scala:163)
    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)

Answer 1

It was a configuration error in Zeppelins conf/zeppelin-env.sh. There, I had the following line uncommented that caused the error and I now commented the line and it works:

#export PYSPARK_PYTHON=/usr/bin/   # path to the python command. must be the same path on the driver(Zeppelin) and all workers.

So the problem was that the path to PYSPARK_PYTHON was not set correctly, now it uses the default python binary. I found the solution by looking for the string /usr/bin/ by doing grep -R "/usr/bin/" in the Zeppelin base directory and checked the files.