All posts by John Ohle

Run Common Data Science Packages on Anaconda and Oozie with Amazon EMR

Post Syndicated from John Ohle original https://aws.amazon.com/blogs/big-data/run-common-data-science-packages-on-anaconda-and-oozie-with-amazon-emr/

In the world of data science, users must often sacrifice cluster set-up time to allow for complex usability scenarios. Amazon EMR allows data scientists to spin up complex cluster configurations easily, and to be up and running with complex queries in a matter of minutes.

Data scientists often use scheduling applications such as Oozie to run jobs overnight. However, Oozie can be difficult to configure when you are trying to use popular Python packages (such as “pandas,” “numpy,” and “statsmodels”), which are not included by default.

One such popular platform that contains these types of packages (and more) is Anaconda. This post focuses on setting up an Anaconda platform on EMR, with an intent to use its packages with Oozie. I describe how to run jobs using a popular open source scheduler like Oozie.

Walkthrough

For this post, you walk through the following tasks:

  • Create an EMR cluster.
  • Download Anaconda on your master node.
  • Configure Oozie.
  • Test the steps.

Create an EMR cluster

Spin up an Amazon EMR cluster using the console or the AWS CLI. Use the latest release, and include Apache Hadoop, Apache Spark, Apache Hive, and Oozie.

To create a three-node cluster in the us-east-1 region, issue an AWS CLI command such as the following. This command must be typed as one line, as shown below. It is shown here separated for readability purposes only.

aws emr create-cluster \ 
--release-label emr-5.7.0 \ 
 --name '<YOUR-CLUSTER-NAME>' \
 --applications Name=Hadoop Name=Oozie Name=Spark Name=Hive \ 
 --ec2-attributes '{"KeyName":"<YOUR-KEY-PAIR>","SubnetId":"<YOUR-SUBNET-ID>","EmrManagedSlaveSecurityGroup":"<YOUR-EMR-SLAVE-SECURITY-GROUP>","EmrManagedMasterSecurityGroup":"<YOUR-EMR-MASTER-SECURITY-GROUP>"}' \ 
 --use-default-roles \ 
 --instance-groups '[{"InstanceCount":1,"InstanceGroupType":"MASTER","InstanceType":"<YOUR-INSTANCE-TYPE>","Name":"Master - 1"},{"InstanceCount":<YOUR-CORE-INSTANCE-COUNT>,"InstanceGroupType":"CORE","InstanceType":"<YOUR-INSTANCE-TYPE>","Name":"Core - 2"}]'

One-line version for reference:

aws emr create-cluster --release-label emr-5.7.0 --name '<YOUR-CLUSTER-NAME>' --applications Name=Hadoop Name=Oozie Name=Spark Name=Hive --ec2-attributes '{"KeyName":"<YOUR-KEY-PAIR>","SubnetId":"<YOUR-SUBNET-ID>","EmrManagedSlaveSecurityGroup":"<YOUR-EMR-SLAVE-SECURITY-GROUP>","EmrManagedMasterSecurityGroup":"<YOUR-EMR-MASTER-SECURITY-GROUP>"}' --use-default-roles --instance-groups '[{"InstanceCount":1,"InstanceGroupType":"MASTER","InstanceType":"<YOUR-INSTANCE-TYPE>","Name":"Master - 1"},{"InstanceCount":<YOUR-CORE-INSTANCE-COUNT>,"InstanceGroupType":"CORE","InstanceType":"<YOUR-INSTANCE-TYPE>","Name":"Core - 2"}]'

Download Anaconda

SSH into your EMR master node instance and download the official Anaconda installer:

wget https://repo.continuum.io/archive/Anaconda2-4.4.0-Linux-x86_64.sh

At the time of publication, Anaconda 4.4 is the most current version available. For the download link location for the latest Python 2.7 version (Python 3.6 may encounter issues), see https://www.continuum.io/downloads.  Open the context (right-click) menu for the Python 2.7 download link, choose Copy Link Location, and use this value in the previous wget command.

This post used the Anaconda 4.4 installation. If you have a later version, it is shown in the downloaded filename:  “anaconda2-<version number>-Linux-x86_64.sh”.

Run this downloaded script and follow the on-screen installer prompts.

chmod u+x Anaconda2-4.4.0-Linux-x86_64.sh
./Anaconda2-4.4.0-Linux-x86_64.sh

For an installation directory, select somewhere with enough space on your cluster, such as “/mnt/anaconda/”.

The process should take approximately 1–2 minutes to install. When prompted if you “wish the installer to prepend the Anaconda2 install location”, select the default option of [no].

After you are done, export the PATH to include this new Anaconda installation:

export PATH=/mnt/anaconda/bin:$PATH

Zip up the Anaconda installation:

cd /mnt/anaconda/
zip -r anaconda.zip .

The zip process may take 4–5 minutes to complete.

(Optional) Upload this anaconda.zip file to your S3 bucket for easier inclusion into future EMR clusters. This removes the need to repeat the previous steps for future EMR clusters.

Configure Oozie

Next, you configure Oozie to use Pyspark and the Anaconda platform.

Get the location of your Oozie sharelibupdate folder. Issue the following command and take note of the “sharelibDirNew” value:

oozie admin -sharelibupdate

For this post, this value is “hdfs://ip-192-168-4-200.us-east-1.compute.internal:8020/user/oozie/share/lib/lib_20170616133136”.

Pass in the required Pyspark files into Oozies sharelibupdate location. The following files are required for Oozie to be able to run Pyspark commands:

  • pyspark.zip
  • py4j-0.10.4-src.zip

These are located on the EMR master instance in the location “/usr/lib/spark/python/lib/”, and must be put into the Oozie sharelib spark directory. This location is the value of the sharelibDirNew parameter value (shown above) with “/spark/” appended, that is, “hdfs://ip-192-168-4-200.us-east-1.compute.internal:8020/user/oozie/share/lib/lib_20170616133136/spark/”.

To do this, issue the following commands:

hdfs dfs -put /usr/lib/spark/python/lib/py4j-0.10.4-src.zip hdfs://ip-192-168-4-200.us-east-1.compute.internal:8020/user/oozie/share/lib/lib_20170616133136/spark/
hdfs dfs -put /usr/lib/spark/python/lib/pyspark.zip hdfs://ip-192-168-4-200.us-east-1.compute.internal:8020/user/oozie/share/lib/lib_20170616133136/spark/

After you’re done, Oozie can use Pyspark in its processes.

Pass the anaconda.zip file into HDFS as follows:

hdfs dfs -put /mnt/anaconda/anaconda.zip /tmp/myLocation/anaconda.zip

(Optional) Verify that it was transferred successfully with the following command:

hdfs dfs -ls /tmp/myLocation/

On your master node, execute the following command:

export PYSPARK_PYTHON=/mnt/anaconda/bin/python

Set the PYSPARK_PYTHON environment variable on the executor nodes. Put the following configurations in your “spark-opts” values in your Oozie workflow.xml file:

–conf spark.executorEnv.PYSPARK_PYTHON=./anaconda_remote/bin/python
–conf spark.yarn.appMasterEnv.PYSPARK_PYTHON=./anaconda_remote/bin/python

This is referenced from the Oozie job in the following line in your workflow.xml file, also included as part of your “spark-opts”:

--archives hdfs:///tmp/myLocation/anaconda.zip#anaconda_remote

Your Oozie workflow.xml file should now look something like the following:

<workflow-app name="spark-wf" xmlns="uri:oozie:workflow:0.5">
<start to="start_spark" />
<action name="start_spark">
    <spark xmlns="uri:oozie:spark-action:0.1">
        <job-tracker>${jobTracker}</job-tracker>
        <name-node>${nameNode}</name-node>
        <prepare>
            <delete path="/tmp/test/spark_oozie_test_out3"/>
        </prepare>
        <master>yarn-cluster</master>
        <mode>cluster</mode>
        <name>SparkJob</name>
        <class>clear</class>
        <jar>hdfs:///user/oozie/apps/myPysparkProgram.py</jar>
        <spark-opts>--queue default
            --conf spark.ui.view.acls=*
            --executor-memory 2G --num-executors 2 --executor-cores 2 --driver-memory 3g
            --conf spark.executorEnv.PYSPARK_PYTHON=./anaconda_remote/bin/python
            --conf spark.yarn.appMasterEnv.PYSPARK_PYTHON=./anaconda_remote/bin/python
            --archives hdfs:///tmp/myLocation/anaconda.zip#anaconda_remote
        </spark-opts>
    </spark>
    <ok to="end"/>
    <error to="kill"/>
</action>
        <kill name="kill">
                <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
        </kill>
        <end name="end"/>
</workflow-app>

Test steps

To test this out, you can use the following job.properties and myPysparkProgram.py file, along with the following steps:

job.properties

masterNode ip-xxx-xxx-xxx-xxx.us-east-1.compute.internal
nameNode hdfs://${masterNode}:8020
jobTracker ${masterNode}:8032
master yarn
mode cluster
queueName default
oozie.libpath ${nameNode}/user/oozie/share/lib
oozie.use.system.libpath true
oozie.wf.application.path ${nameNode}/user/oozie/apps/

Note: You can get your master node IP address (denoted as “ip-xxx-xxx-xxx-xxx” here) from the value for the sharelibDirNew parameter noted earlier.

myPysparkProgram.py

from pyspark import SparkContext, SparkConf
import numpy
import sys

conf = SparkConf().setAppName('myPysparkProgram')
sc = SparkContext(conf=conf)

rdd = sc.textFile("/user/hadoop/input.txt")

x = numpy.sum([3,4,5]) #total = 12

rdd = rdd.map(lambda line: line + str(x))
rdd.saveAsTextFile("/user/hadoop/output")

Put the “myPysparkProgram.py” into the location mentioned between the “<jar>xxxxx</jar>” tags in your workflow.xml. In this example, the location is “hdfs:///user/oozie/apps/”. Use the following command to move the “myPysparkProgram.py” file to the correct location:

hdfs dfs -put myPysparkProgram.py /user/oozie/apps/

Put the above workflow.xml file into the “/user/oozie/apps/” location in hdfs:

hdfs dfs –put workflow.xml /user/oozie/apps/

Note: The job.properties file is run locally from the EMR master node.

Create a sample input.txt file with some data in it. For example:

input.txt

This is a sentence.
So is this. 
This is also a sentence.

Put this file into hdfs:

hdfs dfs -put input.txt /user/hadoop/

Execute the job in Oozie with the following command. This creates an Oozie job ID.

oozie job -config job.properties -run

You can check the Oozie job state with the command:

oozie job -info <Oozie job ID>

  1. When the job is successfully finished, the results are located at:
/user/hadoop/output/part-00000
/user/hadoop/output/part-00001

  1. Run the following commands to view the output:
hdfs dfs -cat /user/hadoop/output/part-00000
hdfs dfs -cat /user/hadoop/output/part-00001

The output will be:

This is a sentence. 12
So is this 12
This is also a sentence 12

Summary

The myPysparkProgram.py has successfully imported the numpy library from the Anaconda platform and has produced some output with it. If you tried to run this using standard Python, you’d encounter the following error:

Now when your Python job runs in Oozie, any imported packages that are implicitly imported by your Pyspark script are imported into your job within Oozie directly from the Anaconda platform. Simple!

If you have questions or suggestions, please leave a comment below.


Additional Reading

Learn how to use Apache Oozie workflows to automate Apache Spark jobs on Amazon EMR.

 


About the Author

John Ohle is an AWS BigData Cloud Support Engineer II for the BigData team in Dublin. He works to provide advice and solutions to our customers on their Big Data projects and workflows on AWS. In his spare time, he likes to play music, learn, develop tools and write documentation to further help others – both colleagues and customers alike.