· Aug 3, 2018 4m read

The way to launch Jupyter Notebook + Apache Spark + InterSystems IRIS

Hi all. Today we are going to install Jupyter Notebook and connect it to Apache Spark and InterSystems IRIS.

Note: I have done the following on Ubuntu 18.04,  Python 3.6.5.


If you are looking for well-known, widely-spread and mainly popular among Python users notebook instead of Apache Zeppelin, you should choose Jupyter notebook. Jupyter notebook is a very powerful and great data science tool. it has a big community and a lot of additional software and integrations. Jupyter notebook allows you to create and share documents that contain live code, equations, visualizations and narrative text. Uses include data cleaning and transformation, numerical simulation, statistical modeling, data visualization, machine learning, and much more. And most importantly, it is a big community that will help you solve the problems you face.

Check requirements

If something doesn't work, look at the "Possible problems and solutions" paragraph in the bottom.

First of all, ensure that you have Java 8 (java -version returns "1.8.x"). Next, download apache spark and unzip it. After, run the following in the terminal:

pip3 install jupyter

pip3 install toree

jupyter toree install --spark_home=/path_to_spark/spark-2.3.1-bin-hadoop2.7 --interpreters=PySpark --user

Now, open the terminal and run vim ~/.bashrc . Paste in the bottom the following code (this is environment variables):

 export JAVA_HOME=/usr/lib/jvm/installed java 8
 export PATH="$PATH:$JAVA_HOME/bin"
 export SPARK_HOME=/path to spark/spark-2.3.1-bin-hadoop2.7
 export PATH="$PATH:$SPARK_HOME/bin"

And run source ~/.bashrc.

Check that it works

Now, let us launch Jupyter notebook. Run pyspark in the terminal.

Open in your browser the returned URL.  Should be something like the image below:

Click on new, choose Python 3, paste the following code into a paragraph:

import sys

Your output should look like this:

Stop jupyter using ctrl-c in the terminal.

Note: To add custom jars just move desired jars into $SPARK_HOME/jars.

So, we want to work with intersystems-jdbc and intersystems-spark (we will also need a jpmml library). Let us copy required jars into spark. Run the following in the terminal:

sudo cp /path to intersystems iris/dev/java/lib/JDK18/intersystems-jdbc-3.0.0.jar /path to spark/spark-2.3.1-bin-hadoop2.7/jars

sudo cp /path to intersystems iris/dev/java/lib/JDK18/intersystems-spark-1.0.0.jar /path to spark/spark-2.3.1-bin-hadoop2.7/jars

sudo cp /path to jpmml/jpmml-sparkml-executable-version.jar /path to spark/spark-2.3.1-bin-hadoop2.7/jars

Ensure that is works. Run pyspark in the terminal again and run the following code (from the previous article):

from import Vectors
from import VectorAssembler
from import KMeans
from import Pipeline
from import RFormula
from pyspark2pmml import PMMLBuilder"com.intersystems.spark").\
option("url", "IRIS://localhost:51773/NAMESPACE").option("user", "dev").\
option("password", "123").\
option("dbtable", "DataMining.IrisDataset").load() # load iris dataset

(trainingData, testData) = dataFrame.randomSplit([0.7, 0.3]) # split the data into two sets
assembler = VectorAssembler(inputCols = ["PetalLength", "PetalWidth", "SepalLength", "SepalWidth"], outputCol="features") # add a new column with features

kmeans = KMeans().setK(3).setSeed(2000) # clustering algorithm that we use

pipeline = Pipeline(stages=[assembler, kmeans]) # First, passed data will run against assembler and after will run against kmeans.
modelKMeans = # pass training data

pmmlBuilder = PMMLBuilder(sc, dataFrame, modelKMeans)
pmmlBuilder.buildFile("KMeans.pmml") # create pmml model

My output:

The output file is a jpmml kmeans model. Everything works!

Possible problems and solutions

  • command not found: 'jupyter':
  1. vim ~/bashrc;
  2. add in the bottom export PATH="$PATH:~/.local/bin";
  3. in terminal source ~/.bashrc.
  4. If it doesn't help, reinstall pip3 and jupyter.
  • env: 'jupyter': No such file or directory:
  1. In ~/.bashrc export PYSPARK_DRIVER_PYTHON=/home/.../.local/bin/jupyter.
  • TypeError: 'JavaPackage' object is not callable:
  1. Check that the required .jar file in /.../spark-2.3.1-bin-hadoop2.7/jars;
  2. Restart notebook.
  • Java gateway process exited before sending the driver its port number:
  1. Your Java version should be 8 (probably works with Java 6/7 too, but I didn't check it);
  2. echo $JAVA_HOME should return to you Java 8 version. If not, change the path in ~/.bashrc;
  3. Paste sudo update-alternatives --config java in the terminal and choose a proper java version;
  4. Paste sudo update-alternatives --config javac in the terminal and choose a proper java version.
  • PermissionError: [Errno 13] Permission denied: '/usr/local/share/jupyter'
  1. Add --user at the end of your command in the terminal
  • Error executing Jupyter command 'toree': [Errno 2] No such file or directory
  1. Run the command without sudo.
  • A specific error may appear if you use system variables like PYSPARK_SUBMIT_ARGS and other spark/pyspark variables or because of /.../spark-2.3.1-bin-hadoop2.7/conf/ changes.
  1. Delete these variables and check


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