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submit_analysis_job.py
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import configparser
import argparse
import boto3
import utility
import sys
from collections import OrderedDict
global job_configuration, cluster_id, spark_extra_config
job_configuration = "analysis_job.config"
cluster_id = ""
spark_extra_config = [("spark.memory.fraction", "0.9"),
("spark.python.profile", "true"),
("spark.python.worker.reuse", "false"),
("spark.yarn.executor.memoryOverhead", "4096"),
("spark.driver.maxResultSize", "0"),
("spark.executor.extraJavaOptions",
"-Dlog4j.configuration=file:///etc/spark/conf/log4j.properties "
"-XX:+UseConcMarkSweepGC -XX:CMSInitiatingOccupancyFraction=30 "
"-XX:MaxHeapFreeRatio=50 -XX:+CMSClassUnloadingEnabled "
"-XX:MaxPermSize=512M -XX:OnOutOfMemoryError='kill -9 %%p'"
" -XX:+HeapDumpOnOutOfMemoryError -XX:HeapDumpPath=/app/oom_dump_`date`.hprof")]
def check_configuration(config):
if not utility.check_config(config, "job_config", ["name", "action_on_failure", "analysis_script",
"analysis_script_s3_location", "upload_analysis_script"]):
return False
if not utility.check_upload_config(config["job_config"], "upload_analysis_script", "analysis_script",
"analysis_script_local_location", "analysis_script_s3_location"):
return False
if not utility.check_config(config, "spark_config", ["driver_memory", "executor_memory"]):
return False
if not utility.check_config(config, "script_arguments", ["input_location", "output_location", "annotation_file",
"region", "strand_specificity", "aligner_tool",
"counter_tool"]):
return False
if not utility.check_s3_region(config["script_arguments"]["region"]):
return False
return True
def calculate_num_executor(cluster_id, executor_memory):
global spark_extra_config
memory_overhead = 512
for conf in spark_extra_config:
if conf[0] == "spark.yarn.executor.memoryOverhead":
memory_overhead = int(conf[1])
memory_per_executor = int(executor_memory.strip("g")) + memory_overhead/1024
total_mem, total_cpu = utility.get_cluster_mem_cpu(cluster_id)
if total_mem < 0 or total_cpu < 0:
num_executors = -1 # dry run
else:
num_executors = int(total_mem/memory_per_executor)
return num_executors
def build_command(config):
global cluster_id
job_arguments = OrderedDict()
job_arguments["JobFlowId"] = cluster_id
step_arguments = OrderedDict()
step_arguments['Name'] = config["job_config"]["name"]
step_arguments["ActionOnFailure"] = config["job_config"]["action_on_failure"]
hadoop_arguments = OrderedDict()
hadoop_arguments["Jar"] = "command-runner.jar"
command_args = ["spark-submit",
"--deploy-mode", "cluster"]
for config_name, config_value in spark_extra_config:
command_args.append("--conf")
command_args.append("{}={}".format(config_name, config_value))
for spark_conf in config["spark_config"]:
command_args.append("--" + spark_conf.replace("_", "-"))
command_args.append(config["spark_config"][spark_conf])
command_args.append(config["job_config"]["analysis_script_s3_location"].rstrip("/") + "/" +
config["job_config"]["analysis_script"])
command_args.append("-i")
command_args.append(config["script_arguments"]["input_location"])
command_args.append("-o")
command_args.append(config["script_arguments"]["output_location"])
command_args.append("-a")
command_args.append(config["script_arguments"]["annotation_file"])
command_args.append("-ss")
command_args.append(config["script_arguments"]["strand_specificity"].upper())
command_args.append("-at={}".format(config["script_arguments"]["aligner_tool"]))
command_args.append("-ct={}".format(config["script_arguments"]["counter_tool"]))
if "run_picard" in config["script_arguments"] and config["script_arguments"]["run_picard"].lower() == "true":
command_args.append("--run_picard")
if "aligner_extra_args" in config["script_arguments"] and \
config["script_arguments"]["aligner_extra_args"].strip() != "":
command_args.append('-s={}'.format(config["script_arguments"]["aligner_extra_args"]))
if "counter_extra_args" in config["script_arguments"] and \
config["script_arguments"]["counter_extra_args"].strip() != "":
command_args.append('-c={}'.format(config["script_arguments"]["counter_extra_args"]))
if "picard_extra_args" in config["script_arguments"] and \
config["script_arguments"]["picard_extra_args"].strip() != "":
command_args.append('-p={}'.format(config["script_arguments"]["picard_extra_args"]))
command_args.append("-r")
command_args.append(config["script_arguments"]["region"])
hadoop_arguments['Args'] = command_args
step_arguments["HadoopJarStep"] = hadoop_arguments
job_arguments["Steps"] = [step_arguments]
return job_arguments
if __name__ == "__main__":
parser = argparse.ArgumentParser(description='Job submission script for spark-based RNA-seq Quantification')
parser.add_argument('--config', '-c', action="store", dest="job_config", help="Job configuration file")
parser.add_argument('--cluster-id', '-id', action="store", dest="cluster_id", help="Cluster ID for submission")
parser.add_argument('--dry-run', '-d', action="store_true", dest="dry_run",
help="Produce the configurations for the job flow to be submitted")
parser_result = parser.parse_args()
if parser_result.job_config is not None and parser_result.job_config.strip() != "":
job_configuration = parser_result.job_config.strip()
config = configparser.ConfigParser()
config.optionxform = str
config.read(job_configuration)
if parser_result.cluster_id is None or parser_result.cluster_id.strip() == "":
cluster_id = utility.get_cluster_id(parser_result.dry_run)
else:
cluster_id = parser_result.cluster_id.strip()
if cluster_id != "" and check_configuration(config):
if config["job_config"].get("upload_analysis_script", "False") == "True":
utility.upload_files_to_s3([(config["job_config"]["analysis_script"],
config["job_config"]["analysis_script_local_location"],
config["job_config"]["analysis_script_s3_location"])], parser_result.dry_run)
num_executors = calculate_num_executor(cluster_id, config["spark_config"]["executor_memory"])
if num_executors < 0:
config["spark_config"]["num_executors"] = "None"
else:
config["spark_config"]["num_executors"] = str(num_executors)
config["spark_config"]["executor_cores"] = "1"
job_argument = build_command(config)
if not parser_result.dry_run:
emr_client = boto3.client("emr")
# warn user before removing any output
out = config["script_arguments"]["output_location"]
# find out which output dirs, if any, exist
dirs_to_remove = utility.check_s3_path_exists([out])
# create a list of the names of the directories to remove
if dirs_to_remove:
response = input("About to remove any existing output directories." +
"\n\n\t{}\n\nProceed? [y/n]: ".format(
'\n\n\t'.join(dirs_to_remove)))
while response not in ['y', 'n']:
response = input('Proceed? [y/n]: ')
if response == 'n':
print("Program Terminated. Modify config file to change " +
"output directories.")
sys.exit(0)
# remove the output directories
if not utility.remove_s3_files(dirs_to_remove):
print("Program terminated")
sys.exit(1)
job_submission = emr_client.add_job_flow_steps(**job_argument)
print("Submitted job to cluster {}. Job id is {}".format(cluster_id, job_submission["StepIds"][0]))
else:
print(job_argument)