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Scripts for running Apache Spark on HPC infrastructure

Introduction

This repo offers a set of scripts that simplify running Apache Spark clusters on HPC infrastructure with a PBS job scheduler.

Installation and configuration

Download/clone the repo and customize the userConfiguration.template.sh and submit.template.pbs files following the instructions provided in each file. Save the edited userConfiguration.template.sh as userConfiguration.sh (and if desired save submit.template.pbs as submit.pbs). Then submit the PBS script to the job scheduler on your cluster.

If working with sensitive data, users may wish to ensure that all writes to disk (i.e. intermediate and final data, log and temp files, etc.) are made in a permissible directory as defined in their DUA/DMP.

Users may wish to customize config-spark.sh to ensure that the Spark cluster configuration is matched well to the resources allocated to the job and job's computational needs.

Script work-spark.sh

Script work-spark.sh submits user's job to the spark cluster. Users have the option of passing the following variables as arguments to their work script $MY_SPARK_JOBSCRIPT:

  • $MY_SPARK_DATASET
  • $MDB_MASTER_NODE
  • $MDB_NODES
  • $MDB_USER_CREDENTIALS
  • $MDB_BACKEND_CREDENTIALS
  • $MDB_DATABASE_NAME

If specified, these variables, additional details for which are provided in userConfiguration.template.sh, are passed to the work script in the order in which they appear above.

Integration with MariaDB

Integration with MariaDB is provided via variables in userConfiguration.template.sh that begin with MDB and variable SPARK_CLASS_PATH.

If users choose to pass all relevant db information to their work script as arguments, they should use:

  • All MDB_* variables, in the case of running a distributed MariaDB instance
  • Variables MDB_CONF_DIR, MDB_MASTER_NODE, MDB_USER_CREDENTIALS and MDB_DATABASE_NAME, in the case of running a non-distributed MariaDB instance.

Variable SPARK_CLASS_PATH has to point to the location of the MariaDB Java Connector.

Repo sparkDBUtilities contains utilities that facilitate pushing Spark RDD's to MariaDB distributed instances. These utilities can be called from within a work script written in either Python or R.