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Genomic analysis using Glow on EMR Serverless

Some customers may want to use Glow to work with genomic data.

This is an example of how to package Glow dependencies and run a job on EMR Serverless using 1000 Genomes data.

Getting Started

First, we'll need to build a virtualenv that we can upload to S3. Similar to our base example, we'll use a Dockerfile to do this.

In addition, we're also going to create an uber-jar directly from the Glow project.

  • In this directory, run the following command and it will build the Dockerfile and export pyspark_glow.tar.gz and glow-spark3-assembly-1.1.2-SNAPSHOT.jar to your local filesystem.
# Enable BuildKit backend
DOCKER_BUILDKIT=1 docker build --output ./dependencies .
  • Now copy those files to S3.
export S3_BUCKET=<YOUR_S3_BUCKET_NAME>
aws s3 sync ./dependencies/ s3://${S3_BUCKET}/artifacts/pyspark/glow/
  • And this demo code
aws s3 cp glow_demo.py s3://${S3_BUCKET}/code/pyspark/

Submitting a new job

Make sure to follow the EMR Serverless getting started guide to spin up your Spark application.

  • Define your EMR Serverless app ID and job role and submit the job.

Unfortunately, in preview EMR Serverless does not have outbound internet access. So we can't use the --packages option. Instead, we'll provide an --archives option for our PySpark virtualenv and --jars to our Glow uberjar on S3.

export APPLICATION_ID=<EMR_SERVERLESS_APPLICATION_ID>
export JOB_ROLE_ARN=<EMR_SERVERLESS_IAM_ROLE>

aws emr-serverless start-job-run \
    --application-id $APPLICATION_ID \
    --execution-role-arn $JOB_ROLE_ARN \
    --job-driver '{
        "sparkSubmit": {
            "entryPoint": "s3://'${S3_BUCKET}'/code/pyspark/glow_demo.py",
            "entryPointArguments": ["pyspark_glow.tar.gz"],
            "sparkSubmitParameters": "--conf spark.hadoop.io.compression.codecs=io.projectglow.sql.util.BGZFCodec --conf spark.driver.cores=1 --conf spark.driver.memory=2g --conf spark.executor.cores=3 --conf spark.executor.memory=4g --conf spark.executor.instances=20 --archives=s3://'${S3_BUCKET}'/artifacts/pyspark/glow/pyspark_glow.tar.gz --jars s3://'${S3_BUCKET}'/artifacts/pyspark/glow/glow-spark3-assembly-1.1.2-SNAPSHOT.jar"
        }
    }' \
    --configuration-overrides '{
        "monitoringConfiguration": {
            "s3MonitoringConfiguration": {
                "logUri": "s3://'${S3_BUCKET}'/logs/"
            }
        }
    }'
  • Set your job run ID and get the status of the job.
export JOB_RUN_ID=001234567890

aws emr-serverless get-job-run \
    --application-id $APPLICATION_ID \
    --job-run-id $JOB_RUN_ID
  • View the logs while the job is running.
aws s3 cp s3://${S3_BUCKET}/logs/applications/${APPLICATION_ID}/jobs/${JOB_RUN_ID}/SPARK_DRIVER/stdout.gz - | gunzip

Alternatives

One other alternative I came up with while researching this is using a temp image to fetch your dependencies.

It uses an EMR on EKS image, so you'll need to authenticate before building.

# Enable BuildKit backend
DOCKER_BUILDKIT=1 docker build -f Dockerfile.jars . --output jars

This will export ~100 jars to your local filesystem, which you can upload to S3 and specificy via the --jars variable as a comma-delimited list.