How to make Pyspark script running on Amazon EMR to recognize boto3 module? It says module not found

Question

Spark version 2.4.5

I have files that need to be processed in an S3 bucket. (s3a://tobeprocessed)

I have a pyspark application that reads files from the S3 bucket and writes output to another S3 bucket (s3://processed).

I intend to run this as a step function in my emr cluster.

I used to following command from my terminal to add a step to my cluster.

aws emr add-steps --cluster-id j-xxxxxx --steps Name=etlapp,Jar=command-runner.jar,Args=[spark-submit,--deploy-mode,cluster,--master,yarn,--conf,spark.yarn.submit.waitAppCompletion=true,s3://bucketname/spark_app.py,s3://bucketname/configuration_file.cfg],ActionOnFailure=CONTINUE

I got an error message like this

STDERR

20/03/10 19:50:46 INFO RMProxy: Connecting to ResourceManager at ip-172-31-27-34.ec2.internal/172.31.27.34:8032
20/03/10 19:50:47 INFO Client: Requesting a new application from cluster with 2 NodeManagers
20/03/10 19:50:47 INFO Client: Verifying our application has not requested more than the maximum memory capability of the cluster (12288 MB per container)
20/03/10 19:50:47 INFO Client: Will allocate AM container, with 2432 MB memory including 384 MB overhead
20/03/10 19:50:47 INFO Client: Setting up container launch context for our AM
20/03/10 19:50:47 INFO Client: Setting up the launch environment for our AM container
20/03/10 19:50:47 INFO Client: Preparing resources for our AM container
20/03/10 19:50:47 WARN Client: Neither spark.yarn.jars nor spark.yarn.archive is set, falling back to uploading libraries under SPARK_HOME.
20/03/10 19:50:49 INFO Client: Uploading resource file:/mnt/tmp/spark-4c4ea7ac-b2bb-4a61-929d-c371d87417ff/__spark_libs__2224504543987850085.zip -> hdfs://ip-172-31-27-34.ec2.internal:8020/user/hadoop/.sparkStaging/application_1583867709817_0003/__spark_libs__2224504543987850085.zip
20/03/10 19:50:50 INFO ClientConfigurationFactory: Set initial getObject socket timeout to 2000 ms.
20/03/10 19:50:50 INFO Client: Uploading resource s3://imdbetlapp/complete_etl.py -> hdfs://ip-172-31-27-34.ec2.internal:8020/user/hadoop/.sparkStaging/application_1583867709817_0003/complete_etl.py
20/03/10 19:50:51 INFO S3NativeFileSystem: Opening 's3://imdbetlapp/complete_etl.py' for reading
20/03/10 19:50:51 INFO Client: Uploading resource file:/usr/lib/spark/python/lib/pyspark.zip -> hdfs://ip-172-31-27-34.ec2.internal:8020/user/hadoop/.sparkStaging/application_1583867709817_0003/pyspark.zip
20/03/10 19:50:51 INFO Client: Uploading resource file:/usr/lib/spark/python/lib/py4j-0.10.7-src.zip -> hdfs://ip-172-31-27-34.ec2.internal:8020/user/hadoop/.sparkStaging/application_1583867709817_0003/py4j-0.10.7-src.zip
20/03/10 19:50:52 INFO Client: Uploading resource file:/mnt/tmp/spark-4c4ea7ac-b2bb-4a61-929d-c371d87417ff/__spark_conf__476112427502500805.zip -> hdfs://ip-172-31-27-34.ec2.internal:8020/user/hadoop/.sparkStaging/application_1583867709817_0003/__spark_conf__.zip
20/03/10 19:50:52 INFO SecurityManager: Changing view acls to: hadoop
20/03/10 19:50:52 INFO SecurityManager: Changing modify acls to: hadoop
20/03/10 19:50:52 INFO SecurityManager: Changing view acls groups to: 
20/03/10 19:50:52 INFO SecurityManager: Changing modify acls groups to: 
20/03/10 19:50:52 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users  with view permissions: Set(hadoop); groups with view permissions: Set(); users  with modify permissions: Set(hadoop); groups with modify permissions: Set()
20/03/10 19:50:53 INFO Client: Submitting application application_1583867709817_0003 to ResourceManager
20/03/10 19:50:53 INFO YarnClientImpl: Submitted application application_1583867709817_0003
20/03/10 19:50:54 INFO Client: Application report for application_1583867709817_0003 (state: ACCEPTED)
20/03/10 19:50:54 INFO Client: 
     client token: N/A
     diagnostics: AM container is launched, waiting for AM container to Register with RM
     ApplicationMaster host: N/A
     ApplicationMaster RPC port: -1
     queue: default
     start time: 1583869853550
     final status: UNDEFINED
     tracking URL: http://ip-172-31-27-34.ec2.internal:20888/proxy/application_1583867709817_0003/
     user: hadoop
20/03/10 19:50:55 INFO Client: Application report for application_1583867709817_0003 (state: ACCEPTED)
20/03/10 19:50:56 INFO Client: Application report for application_1583867709817_0003 (state: ACCEPTED)
20/03/10 19:50:57 INFO Client: Application report for application_1583867709817_0003 (state: ACCEPTED)
20/03/10 19:50:58 INFO Client: Application report for application_1583867709817_0003 (state: ACCEPTED)
20/03/10 19:50:59 INFO Client: Application report for application_1583867709817_0003 (state: ACCEPTED)
20/03/10 19:51:00 INFO Client: Application report for application_1583867709817_0003 (state: ACCEPTED)
20/03/10 19:51:01 INFO Client: Application report for application_1583867709817_0003 (state: ACCEPTED)
20/03/10 19:51:02 INFO Client: Application report for application_1583867709817_0003 (state: FAILED)
20/03/10 19:51:02 INFO Client: 
     client token: N/A
     diagnostics: Application application_1583867709817_0003 failed 2 times due to AM Container for appattempt_1583867709817_0003_000002 exited with  exitCode: 13
Failing this attempt.Diagnostics: Exception from container-launch.
Container id: container_1583867709817_0003_02_000001
Exit code: 13
Stack trace: ExitCodeException exitCode=13: 
    at org.apache.hadoop.util.Shell.runCommand(Shell.java:972)
    at org.apache.hadoop.util.Shell.run(Shell.java:869)
    at org.apache.hadoop.util.Shell$ShellCommandExecutor.execute(Shell.java:1170)
    at org.apache.hadoop.yarn.server.nodemanager.DefaultContainerExecutor.launchContainer(DefaultContainerExecutor.java:235)
    at org.apache.hadoop.yarn.server.nodemanager.containermanager.launcher.ContainerLaunch.call(ContainerLaunch.java:299)
    at org.apache.hadoop.yarn.server.nodemanager.containermanager.launcher.ContainerLaunch.call(ContainerLaunch.java:83)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)


Container exited with a non-zero exit code 13
For more detailed output, check the application tracking page: http://ip-172-31-27-34.ec2.internal:8088/cluster/app/application_1583867709817_0003 Then click on links to logs of each attempt.
. Failing the application.
     ApplicationMaster host: N/A
     ApplicationMaster RPC port: -1
     queue: default
     start time: 1583869853550
     final status: FAILED
     tracking URL: http://ip-172-31-27-34.ec2.internal:8088/cluster/app/application_1583867709817_0003
     user: hadoop
20/03/10 19:51:02 ERROR Client: Application diagnostics message: Application application_1583867709817_0003 failed 2 times due to AM Container for appattempt_1583867709817_0003_000002 exited with  exitCode: 13
Failing this attempt.Diagnostics: Exception from container-launch.
Container id: container_1583867709817_0003_02_000001
Exit code: 13
Stack trace: ExitCodeException exitCode=13: 
    at org.apache.hadoop.util.Shell.runCommand(Shell.java:972)
    at org.apache.hadoop.util.Shell.run(Shell.java:869)
    at org.apache.hadoop.util.Shell$ShellCommandExecutor.execute(Shell.java:1170)
    at org.apache.hadoop.yarn.server.nodemanager.DefaultContainerExecutor.launchContainer(DefaultContainerExecutor.java:235)
    at org.apache.hadoop.yarn.server.nodemanager.containermanager.launcher.ContainerLaunch.call(ContainerLaunch.java:299)
    at org.apache.hadoop.yarn.server.nodemanager.containermanager.launcher.ContainerLaunch.call(ContainerLaunch.java:83)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)


Container exited with a non-zero exit code 13
For more detailed output, check the application tracking page: http://ip-172-31-27-34.ec2.internal:8088/cluster/app/application_1583867709817_0003 Then click on links to logs of each attempt.
. Failing the application.
Exception in thread "main" org.apache.spark.SparkException: Application application_1583867709817_0003 finished with failed status
    at org.apache.spark.deploy.yarn.Client.run(Client.scala:1149)
    at org.apache.spark.deploy.yarn.YarnClusterApplication.start(Client.scala:1526)
    at org.apache.spark.deploy.SparkSubmit.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:853)
    at org.apache.spark.deploy.SparkSubmit.doRunMain$1(SparkSubmit.scala:161)
    at org.apache.spark.deploy.SparkSubmit.submit(SparkSubmit.scala:184)
    at org.apache.spark.deploy.SparkSubmit.doSubmit(SparkSubmit.scala:86)
    at org.apache.spark.deploy.SparkSubmit$$anon$2.doSubmit(SparkSubmit.scala:928)
    at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:937)
    at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
20/03/10 19:51:02 INFO ShutdownHookManager: Shutdown hook called
20/03/10 19:51:02 INFO ShutdownHookManager: Deleting directory /mnt/tmp/spark-4c4ea7ac-b2bb-4a61-929d-c371d87417ff
20/03/10 19:51:02 INFO ShutdownHookManager: Deleting directory /mnt/tmp/spark-a72b6dba-91bb-46b0-b2c3-893ac3b8581f
Command exiting with ret '1'

When I dug through the container logs, I found the script spitting out an error as follows

boto3 module not found

I ran a bootstrap script that installs boto3 using pip.

I even logged in to the master node and found that boto3 was installed using the command pip list

Answer 1

You have to use a bootstrap script that installs boto3 but you have to be very specific about the version of python being used.

sudo pip-3.6 install boto3

Answer 2

On the console homepage, where you click on Create Cluster, a page appears. On the top, there is an option to "go to advanced options". There you will find the option to "Auto terminate" on "After last step completes"