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sgeCoat.py
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Sun, Jul 7, 09:15

sgeCoat.py
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#!/usr/bin/env python
from BlackDynamite import *
import os,stat
import subprocess
import re
import socket
import shlex
admissible_params = {"walltime":str,"email":str,"nproc":int,"sge_option":[str],"module":[str]}
#default_params = {"walltime":"00:05:00"}
help = {"walltime":"Specify the wall time for the runs",
"email":"Specify the email to notify",
"nproc":"Force the number of processors and update the run",
"sge_option":"Allow to provide additional SGE options",
"module":"List of module to load"}
def launch(run,params):
_exec = run.getExecFile()
if ("walltime" not in params):
raise Exception("walltime not set for this job {0}".format(run.id))
head = \
"""#!/bin/bash
#$ -S /bin/sh
#$ -cwd
#$ -j y
#$ -notify
#$ -l walltime={0}
""".format(params["walltime"])
if ("email" in params):
head += "#$ -m eas -M {0}\n".format(params["email"])
sge_head_name = "#$ -N " + "run" + str(run.id) + "-" + run["run_name"] + "\n"
sge_head_name = sge_head_name.replace(":","_")
head += sge_head_name
run["state"] = "SGE submit"
if ("nproc" in params):
run["nproc"] = params["nproc"]
nproc = run["nproc"]
if (nproc % 12 == 0 and nproc % 8 == 0):
head += "#$ -pe orte* " + str(nproc) + "\n"
elif (nproc % 12 == 0):
head += "#$ -pe orte12 " + str(nproc) + "\n"
elif (nproc % 8 == 0):
head += "#$ -pe orte8 " + str(nproc) + "\n"
if ("sge_option" in params):
for i in params["sge_option"]:
head += "#$ {0}\n".format(i)
if ("module" in params):
for i in params["module"]:
head += "module load {0}\n".format(i)
run.update()
head += """
export BLACKDYNAMITE_HOST=__BLACKDYNAMITE__dbhost__
export BLACKDYNAMITE_SCHEMA=__BLACKDYNAMITE__study__
export BLACKDYNAMITE_STUDY=__BLACKDYNAMITE__study__
export BLACKDYNAMITE_RUN_ID=__BLACKDYNAMITE__run_id__
export BLACKDYNAMITE_USER=""" + params["user"] + """
on_kill()
{
updateRuns.py --updates \"state = SGE killed\" --truerun
exit 0
}
on_stop()
{
updateRuns.py --updates \"state = SGE stopped\" --truerun
exit 0
}
# Execute function on_die() receiving TERM signal
#
trap on_stop SIGUSR1
trap on_kill SIGUSR2
"""
_exec["file"] = run.replaceBlackDynamiteVariables(head) + _exec["file"]
f = open(_exec["filename"], 'w')
f.write(_exec["file"])
f.close()
# os.chmod(_exec["filename"], stat.S_IRWXU)
print ("execute qsub ./" + _exec["filename"])
print ("in dir ")
subprocess.call("pwd")
if (params["truerun"] == True):
ret = subprocess.call("qsub " + _exec["filename"],shell=True)

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