Introduction

Spark-on-HPC dynamically provisions Apache Spark clusters and run spark jobs on an HPC under its traditional resource manager. Currently, PBS, OAR or Torque on a linux cluster are supported.

Features

• Run under PBS or OAR resource limit, i.e. number of nodes, number of cores, memory and walltime
• Multiple spark jobs (master port is selected randomly for each job) for any user
• Only master and workers of the same job are allowed to connect together by a shared secret.

Requirements

• Linux (should work with most distributions)
• Apache Spark 1.3.0+

Installation

• Download and unpack Spark package into SPARK_HOME directory
• Download and unzip the Spark-on-HPC package. Change directory to SPARK_ON_HPC root directory

#cd $SPARK_ON_HPC

• Copy scripts into $SPARK_HOME/sbin

#cp pbs/spark-sbin/* $SPARK_HOME/sbin

or

#cp oar/spark-sbin/* $SPARK_HOME/sbin

Usage

Root permission is NOT required.

• Once installed, create a job directory.

#cd $HOME
#mkdir test
#cd test

PBS

• Copy an example job script inside the package. There are two examples in the package. One is for single node script. The other is for multiple node script.

#cp $SPARK_ON_HPC/examples/test_spark_multi/spark_multi.sh test_spark_job.sh

• Make change to the script. Usually, the directives, shell variables and spark-submit arguments are changed. Set directives. For a PBS example, request 5 nodes (1 master + 4 workers), each with 2 cores and 1gb memory allocated, and queue "test".

#PBS -l nodes=5:ppn=2
#PBS -l vmem=1gb
#PBS -q test

• In job script, set SPARK_HOME to where the spark package is installed, and SPARK_JOB_DIR to the directory where the configuration and log files will be created. Note that the PBS_O_WORKDIR is the location where qsub command is executed.

export SPARK_HOME=$HOME/spark-1.4.1-bin-1.2.1
export SPARK_JOB_DIR=$PBS_O_WORKDIR

• In job script, change the spark-submit arguments. For example, running JavaSparkPi 10 tasks

SPARK_HOME/bin/spark-submit --master $SPARK_URL --class org.apache.spark.examples.JavaSparkPi $SPARK_HOME/lib/spark-examples-1.4.1-hadoop1.2.1.jar 10 > $PBS_O_WORKDIR/pi.txt

• Submit a job

#qsub test_spark_job.sh

The directory conf, logs, and work will be created in SPARK_JOB_DIR during the execution of spark. Examine them if necessary in addition to the normal job stdout and stderr files.

OAR

# create a job folder
mkdir jobs
# copy an example submission script
cp spark-on-oar/oar/spark-multi.sh jobs/
# Edit the $SPARK_HOME env variable in spark-multi.sh to point to your spark folder
# then submit with oarsub, e.g.:
oarsub -l nodes=2/cpu=1/core=1,walltime=0:20 -n sparkPi spark-multi.sh

By default spark-multi.sh submits a SparkPi job with parameter 10. You should replace this line with your own submissions. Spark will write all the logs in your jobs folder.

How to run spark-on-hpc manually for testing purpose

Set environment variables SPARK_JOB_DIR, SPARK_HOME, and PBS_NODEFILE.