Qsub.py

#!/usr/bin/env python
#$ -cwd
#$ -j y
#$ -V

## Copyright (c) 2015 Ryan Koesterer GNU General Public License v3
##
##    This program is free software: you can redistribute it and/or modify
##    it under the terms of the GNU General Public License as published by
##    the Free Software Foundation, either version 3 of the License, or
##    (at your option) any later version.
##
##    This program is distributed in the hope that it will be useful,
##    but WITHOUT ANY WARRANTY; without even the implied warranty of
##    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
##    GNU General Public License for more details.
##
##    You should have received a copy of the GNU General Public License
##    along with this program.  If not, see <http://www.gnu.org/licenses/>.

import os
import pwd
import psutil
import resource
import sys
from time import strftime, localtime, time, gmtime

sys.stdout = os.fdopen(sys.stdout.fileno(), 'w')

def main(argv):

	start_time = (localtime(), time())
	env_vars = os.environ.copy()
	local=False
	user_name=pwd.getpwuid(os.getuid()).pw_name
	if argv[1].split('(')[0] in ["RunSnv","RunSnvgroup","RunMeta","RunMerge","RunTools"] and 'SGE_TASK_ID' in env_vars:
		if env_vars['SGE_TASK_ID'] not in ['None','undefined']:
			with open(argv[2]) as f:
				joblist = [line.rstrip() for line in f]
			job = joblist[int(env_vars['SGE_TASK_ID'])-1]
			argv[1] = argv[1].replace("UGA_JOB_ID",job)
			argv[3] = argv[3].replace("UGA_JOB_ID",job)
			argv[1] = argv[1].replace("UGA_JOB_RANGE",str(int((100 * ((int(job)-1) // 100) + 1))) + "-" + str(int((100 * ((int(job)-1) // 100) + 100))))
			argv[3] = argv[3].replace("UGA_JOB_RANGE",str(int((100 * ((int(job)-1) // 100) + 1))) + "-" + str(int((100 * ((int(job)-1) // 100) + 100))))
			try:
				lf = open(argv[3],'w')
			except(IOError, OSError):
				return
			sys.stdout = lf
			sys.stderr = lf

	if not 'REQNAME' in list(env_vars.keys()):
		local=True
		env_vars['REQNAME'] = env_vars['HOSTNAME'] + '_' + strftime('%Y_%m_%d_%H_%M_%S', start_time[0]) if 'HOSTNAME' in list(env_vars.keys()) else strftime('%Y_%m_%d_%H_%M_%S', start_time[0])
	if not 'JOB_ID' in list(env_vars.keys()):
		env_vars['JOB_ID'] = '1'
	if not 'SGE_TASK_ID' in list(env_vars.keys()):
		env_vars['SGE_TASK_ID'] = 'None'

	from uga.__version__ import version

	print("uga v" + version)
	print("start time: " + strftime("%Y-%m-%d %H:%M:%S", start_time[0]))
	if 'SGE_CLUSTER_NAME' in list(env_vars.keys()):
		print("sge cluster: " + env_vars['SGE_CLUSTER_NAME'])
	if 'HOST' in list(env_vars.keys()):
		print("host: " + env_vars['HOST'])
	if 'Queue' in list(env_vars.keys()):
		print("queue: " + env_vars['QUEUE'])
	if 'HOSTNAME' in list(env_vars.keys()):
		print("compute node: " + env_vars['HOSTNAME'])
	if 'PWD' in list(env_vars.keys()):
		print("current directory: " + env_vars['PWD'])
	print("user name: " + user_name)
	if 'JOB_ID' in list(env_vars.keys()):
		print("job id: " + env_vars['JOB_ID'])
	if 'REQNAME' in list(env_vars.keys()):
		print("job name: " + env_vars['REQNAME'])
	if 'SGE_TASK_ID' in list(env_vars.keys()):
		print("task index number: " + env_vars['SGE_TASK_ID'])
	if 'SGE_STDOUT_PATH' in list(env_vars.keys()):
		print("sge log file: " + env_vars['SGE_STDOUT_PATH'])

	if argv[1].split('(')[0] == "RunSnv":
		from uga.RunSnv import RunSnv
	if argv[1].split('(')[0] == "RunSnvgroup":
		from uga.RunSnvgroup import RunSnvgroup
	if argv[1].split('(')[0] == "RunMeta":
		from uga.RunMeta import RunMeta
	if argv[1].split('(')[0] == "RunMerge":
		from uga.RunMerge import RunMerge
	if argv[1].split('(')[0] == "RunSnvplot":
		from uga.RunSnvplot import RunSnvplot
	if argv[1].split('(')[0] == "RunSnvgroupplot":
		from uga.RunSnvgroupplot import RunSnvgroupplot
	if argv[1].split('(')[0] == "RunFilter":
		from uga.RunFilter import RunFilter
	if argv[1].split('(')[0] == "RunTools":
		from uga.RunTools import RunTools

	print("")
	print("command entered: " + argv[1])
	r = eval(argv[1])
	if r == 0:
		end_time = (localtime(), time())
		process = psutil.Process(os.getpid())
		mem=resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/1000.0
		mem_children=resource.getrusage(resource.RUSAGE_CHILDREN).ru_maxrss/1000.0
		print('finish time: ' + strftime("%Y-%m-%d %H:%M:%S", end_time[0]))
		print('time elapsed: ' + strftime('%H:%M:%S', gmtime(end_time[1] - start_time[1])))
		print('max memory used by main process: ' + str('%.2f' % mem) + ' MB')
		print('max memory used by any subprocess: ' + str('%.2f' % mem_children) + ' MB')

if __name__ == "__main__":
	main(sys.argv)