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Spark on Elastic MapReduce

Takes this article on running Spark on Elastic MapReduce and explores making it a usable workflow for ad hoc Spark programmes.

See SparkEMRBootstrap also for similar work.

Notes

0.7-SNAPSHOT Version of Spark

The version of Spark deployed in the bootstrap used in the article above is a 0.7-SNAPSHOT. This is awkward for dependency management and anyway, Spark has moved on to 0.7.2.

The build-spark-0.7.2-hadoop103.sh script here builds a replacement binary tarball for the one used in the article. This build is of the most recent Spark and made against the version of Hadoop current in Elastic MapReduce, i.e. 1.0.3.

You can find a copy of this tarball here. This is the tarball used by install-spark-0.7.2-bootstrap.sh.

If you are inclined to paranoia, build your own spark-0.7.2-hadoop103.tgz and replace the wget in install-spark-0.7.2-bootstrap.sh.

Scala 2.9.3 Required for Spark 0.7.2

The bootstrap script here also bumps the version of Scala.

Spark Environment Properties Files

Even with an installed and functional Spark cluster on Elastic MapReduce, it is still difficult to create the necessary SparkContext objects in code or correctly access HDFS.

Spark is sensitive to whether IP address or DNS names are using in cluster connection URLs. This requires a DNS lookup, etc. Similarly, HDFS must be referenced in paths using the full http://host:port/path syntax.

In addition, the AWS access key and secret key are extracted from the on instance Hadoop configuration and made available so that S3 input/output can be made convenient with helper methods.

All these properties are placed at /home/hadoop/spark.properties.

HDFS Permissions

Spark sometimes creates files in HDFS owned by the root user. This is a problem because the superuser in HDFS on Elastic MapReduce is actually the user named hadoop. So you may encounter problems where a directory is owned by the hadoop user running the job and preventing root owned files from being created.

One way around this is to create an Elastic MapReduce cluster with a HDFS that does not use permissions. This is unlikely to be an issue with short lived Elastic Map Reduce clusters but you may want to consider an alternative if you have a large persistent cluster.

To disable HDFS permissions, launch the cluster with a configure-hadoop bootstrap and pass --hdfs-key-value dfs.permissions=false as arguments.

--bootstrap-action s3://elasticmapreduce/bootstrap-actions/configure-hadoop
--args "--hdfs-key-value,dfs.permissions=false"

S3 Filesystem

Using S3 for input/output works if you use s3n:// prefixes. The necessary access and secret keys are set from those taken from the Hadoop configuration.

If your input paths are S3 directories, you also need to add path filters to your input locations to ignore the base directory files in S3. See here for a discussion of the problem.

See S3AwareSparkContext.textFile for an example of how to set this up assuming specified paths are directories and not files. File paths work without modification.

Running Spark Jars

Fatjar Spark applications must be copied up and run from the cluster explicitly. There is no corresponding feature to initiating Jar Steps in the Elastic MapReduce API.

This is somewhat difficult to implement as a Jar Step because the Hadoop 1.0.3 RunJar isolates the fatjar in a different classloader from the Hadoop classes. This is a problem because Spark needs certain package default acccesses to some Hadoop internals and achieves this by creating classes in the same Hadoop namespaces. This does not work when the classes are in separate classloaders.

It is relatively easy to include a run script instead, however, that can be run using the script runner jar pattern already in Elastic MapReduce. S3Cmd and the previously sneaked AWS key values are used to download the fatjar from S3 so it is functionally as transparent as the jar step would have been.

Yet Unresolved

The Spark cluster boots and runs jobs but refinements are needed to make it convenient for general use.

Use S3 Filesystem with Streaming

Similar to SparkApp.s3nText, some code is required to add the right path filters to ignore directory S3 files which cause problems.

Working example needed.

Underutilisation?

One worker per worker node may not be using the full resources of the Elastic MapReduce cluster.

Examples

First build spark-assembly-1-SNAPSHOT.jar in example/target/scala-2.9.3 using:

cd example
./sbt assembly

Upload install-spark-0.7.2-bootstrap.sh to S3 where you can access it from the cluster you are creating.

Start a Test Cluster

Create an Elastic MapReduce cluster with a key for ssh/scp access. You should add two bootstrap actions:

  • Action s3://elasticmapreduce/bootstrap-actions/configure-hadoop with arguments --hdfs-key-value dfs.permissions=false. These arguments may need to be comma delimited or formatted per the technique you use to create the cluster.
  • Action: S3 path to the install-spark-0.7.2-bootstrap.sh you uploaded. No arguments.

A cluster like this can be created in eu-west1 using TestSparkEMRCluster:

java -cp target/scala-2.9.3/spark-assembly-1-SNAPSHOT.jar \
  org.boringtechiestuff.spark.TestSparkEMRCluster \
  <aws-access-key> <aws-secret-key> <ssh-key-pair> \
  <log-uri> <s3-path-to-spark-bootstrap>

Wait.

When the cluster has booted and completed installation, ssh on:

ssh -i <pem-file> hadoop@<master-public-dns>

Check your cluster is all there using:

lynx http://localhost:8080

You should expect one worker per worker node you specified in cluster construction.

Now, scp up the example fatjar spark-assembly-1-SNAPSHOT.jar and the example/dev/sample.json data file to /home/hadoop/ on the master node.

scp -i <pem-file> example/target/scala-2.9.3/spark-assembly-1-SNAPSHOT.jar hadoop@<master-public-dns>:/home/hadoop/
scp -i <pem-file> example/dev/sample.json hadoop@<master-public-dns>:/home/hadoop/

Connect to the master and edit /home/hadoop/spark.properties and ensure the spark.library property is present and set:

spark.library=/home/hadoop/spark-assembly-1-SNAPSHOT.jar

This is necessary while we test the applications directly on the cluster without launching using the run-spark.sh script which takes care of setting this property value correctly.

HDFS Batch Example

From the master run the following to insert the data file into HDFS:

hadoop fs -mkdir /input
hadoop fs -put /home/hadoop/sample.json /input

Now, run the fatjar with path arguments in HDFS.

java -cp /home/hadoop/spark-assembly-1-SNAPSHOT.jar \
  org.boringtechiestuff.spark.TweetWordCount /input /output

When this completes, you can inspect the output using:

hadoop fs -ls /output
hadoop fs -text /output/part*

S3 Batch Example

The SparkContext objects produced are S3 aware for certain operations, and in particular they are S3 aware for the example above.

Upload sample.json to an S3 location, and run:

java -cp /home/hadoop/spark-assembly-1-SNAPSHOT.jar \
  org.boringtechiestuff.spark.TweetWordCount \
  s3n://<input-bucket>/<input-path> \
  s3n://<output-bucket>/<output-path>

Note that s3n:// prefixes are required. The input path has to be an S3 directory. Using the full path of sample.json will not work.

HDFS Streaming Example

Spark also provides a streaming mode.

As in the batch example, run the fatjar but using the streaming code instead:

java -cp /home/hadoop/spark-assembly-1-SNAPSHOT.jar \
  org.boringtechiestuff.spark.StreamingTweetWordCount /input /output

Whenever any files are placed in HDFS under /input they will be picked up by Spark Streaming and processed with output in HDFS under output by timestamp.

In another console:

hadoop fs -put /home/hadoop/sample.json /input/sample2.json
hadoop fs -put /home/hadoop/sample.json /input/sample3.json
hadoop fs -put /home/hadoop/sample.json /input/sample4.json
hadoop fs -lsr /output

And look for nonempty part files.

TBD: S3 Streaming Example

Remote Invocation Example

Upload the assembled fatjar and run-spark.sh to a location in S3. Then locally you can start a test cluster and run a Spark task on it remotely using:

java -cp example/target/scala-2.9.3/spark-assembly-1-SNAPSHOT.jar \
  org.boringtechiestuff.spark.TestSparkEMRJarStep \
  <aws-access-key> \
  <aws-secret-key> \
  <ec2-key-pair-name> \
  <s3-log-directory> \
  <s3-path-to-install-spark-0.7.2-bootstrap.sh> \
  <s3-path-to-run-spark.sh> \
  <s3-path-to-run-spark-assembly-1-SNAPSHOT.jar> \
  <s3n-input-path> <s3n-output-path>

Note, the input and output paths must be S3N paths, not S3 paths.

The test cluster has to be manually terminated. It can easily be set up to automatically terminate on task completion, just in test we may be interested in examining the cluster post completion.

TBD Remote Streaming Invocation Example