I'm trying to run a (py)Spark job on EMR that will process a large amount of data. Currently my job is failing with the following error message:
Reason: Container killed by YARN for exceeding memory limits.
5.5 GB of 5.5 GB physical memory used.
Consider boosting spark.yarn.executor.memoryOverhead.
So I google'd how to do this, and found that I should pass along the spark.yarn.executor.memoryOverhead
parameter with the --conf flag. I'm doing it this way:
aws emr add-steps\
--cluster-id %s\
--profile EMR\
--region us-west-2\
--steps Name=Spark,Jar=command-runner.jar,\
Args=[\
/usr/lib/spark/bin/spark-submit,\
--deploy-mode,client,\
/home/hadoop/%s,\
--executor-memory,100g,\
--num-executors,3,\
--total-executor-cores,1,\
--conf,'spark.python.worker.memory=1200m',\
--conf,'spark.yarn.executor.memoryOverhead=15300',\
],ActionOnFailure=CONTINUE" % (cluster_id,script_name)\
But when I rerun the job it keeps giving me the same error message, with the 5.5 GB of 5.5 GB physical memory used
, which implies that my memory did not increase.. any hints on what I am doing wrong?
EDIT
Here are details on how I initially create the cluster:
aws emr create-cluster\
--name "Spark"\
--release-label emr-4.7.0\
--applications Name=Spark\
--bootstrap-action Path=s3://emr-code-matgreen/bootstraps/install_python_modules.sh\
--ec2-attributes KeyName=EMR2,InstanceProfile=EMR_EC2_DefaultRole\
--log-uri s3://emr-logs-zerex\
--instance-type r3.xlarge\
--instance-count 4\
--profile EMR\
--service-role EMR_DefaultRole\
--region us-west-2'
Thanks.
After a couple of hours I found the solution to this problem. When creating the cluster, I needed to pass on the following flag as a parameter:
--configurations file://./sparkConfig.json\
With the JSON file containing:
[
{
"Classification": "spark-defaults",
"Properties": {
"spark.executor.memory": "10G"
}
}
]
This allows me to increase the memoryOverhead in the next step by using the parameter I initially posted.