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condor_submit.py
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#! /usr/bin/env python2
import time
import sys
import os
import subprocess
import cPickle
import shutil
from collections import defaultdict
import multiprocessing
import logging
import glob
import re
import datetime
import traceback
log = logging.getLogger(__name__)
log.addHandler(logging.NullHandler())
def submitWorker(job):
job.submit()
return job
def runWorker(job):
job.runLocal()
return job
def resubmitWorker(job):
job.resubmit()
return job
def killWorker(job):
job.kill()
return job
class Task:
"""This is a collection of jobs"""
def __init__(self,sample,run_folder):
self.run_folder=run_folder
self.sample=sample
self.frontendstatus="None"
self.starttime=datetime.datetime.now()
self.endtime=datetime.datetime.now()
self.allcondorlogs=glob.glob(os.path.join(self.run_folder,self.sample)+"/condor*.log")
self.condorlog=self.allcondorlogs[0]
self.id =int(self.condorlog.split("_")[-1].split(".")[0])
self.condorfile=os.path.join(self.run_folder,self.sample,"condor.jdl")
self.jobs=[]
self.njobs=len(glob.glob(os.path.join(run_folder,sample)+"/run_*.sh"))
for i in range(self.njobs):
self.jobs.append(Job(i,self))
self.resubmitted=False
self.resubmitted_ids=[]
for ilog in self.allcondorlogs:
self.resubmitted_ids.append(int(ilog.split("_")[-1].split(".")[0]))
def status(self,condor_output):
condor_output=condor_output.split("\n")
this_job_status=filter(lambda x: sum(["%d"%iid in x for iid in self.resubmitted_ids])>0 ,condor_output)
staus_translate={
"H":"HOLD",
"R":"RUNNING",
"I":"IDLE",
"C":"COMPLETED",
"X":"REMOVED",
"S":"SUSPENDED",
">":"FINISHING",
"<":"STARTING",
}
self.jobs=[]
for i in range(self.njobs):
self.jobs.append(Job(i,self))
#ID OWNER SUBMITTED RUN_TIME ST PRI SIZE CMD
#270462.18 kpadeken 10/2 09:30 0+02:57:19 R 0 976.6 wrapper.sh /uscms_
#270470.80 kpadeken 10/2 09:30 0+02:55:39 R 0 976.6 wrapper.sh /uscms_
#270470.112 kpadeken 10/2 09:30 0+02:55:30 R 0 976.6 wrapper.sh /uscms_
for stati in this_job_status:
tmp=stati.split()
if len(tmp)>7:
comb_id,user,date_subm,time_subm,run_time,status,priority,size_job =tmp[:8]
task_id=int(comb_id.split(".")[0])
job_id=int(comb_id.split(".")[-1])
submitted_time=datetime.datetime(*time.strptime("%d "%(time.localtime().tm_year)+date_subm+" "+time_subm, "%Y %m/%d %H:%M")[:6])
days=run_time.split("+")[0]
rest=run_time.split("+")[1]
hour,minute,sec=rest.split(":")
runtime=datetime.timedelta(days=int(days),hours=int(hour),minutes=int(minute),seconds=int(sec))
try:
status=staus_translate[status]
except:
log.info(status)
log.info(stati)
#unchanged id
if(task_id==self.id):
self.jobs[job_id].update(status,"None",submitted_time,runtime)
else:
for ijob in self.jobs:
if ijob.id==job_id and ijob.task_id==task_id:
self.jobs[ijob.orig_id].update(status,"None",submitted_time,runtime)
for i in range(self.njobs):
#log.info(self.jobs[i].status)
if self.jobs[i].status=="None" or self.jobs[i].status=="COMPLETED" :
output_status="Done OK"
total_runtime=datetime.timedelta(0)
if(os.path.getsize(self.jobs[i].errorfile)>0):
output_status="Error"
start_time=None
end_time=None
for ilog in self.allcondorlogs:
if "%d"%(self.jobs[i].task_id) not in ilog:
continue
condor_log=open(ilog)
condor_log=condor_log.read()
condor_log=condor_log.split("\n")
this_task=filter(lambda x: "%d"%self.jobs[i].task_id in x,condor_log)
for line in this_task:
#345964.004
if "Job executing on host" in line and "%s.%03d"%(self.jobs[i].task_id,self.jobs[i].id) in line:
tmp=line.split()
start_time=time.strptime("%d "%(time.localtime().tm_year)+tmp[2]+" "+tmp[3], "%Y %m/%d %H:%M:%S")
elif "Job terminated" in line and "%s.%03d"%(self.jobs[i].task_id,self.jobs[i].id) in line:
tmp=line.split()
end_time=time.strptime("%d "%(time.localtime().tm_year)+tmp[2]+" "+tmp[3], "%Y %m/%d %H:%M:%S")
break
if start_time is not None and end_time is not None:
self.jobs[i].starttime=datetime.datetime(*start_time[:6])
self.jobs[i].runtime=datetime.datetime(*end_time[:6])-datetime.datetime(*start_time[:6])
self.jobs[i].endtime=datetime.datetime(*end_time[:6])
self.jobs[i].frontendstatus=output_status
if output_status=="Error":
self.jobs[i].status="FAILED"
else:
self.jobs[i].status="COMPLETED"
overall_state = "Done OK"
for i in range(self.njobs):
tmp_state = self.jobs[i].frontendstatus
if tmp_state == "REMOVED":
overall_state = "ERROR"
break
if tmp_state == "IDLE":
overall_state = "IDLE"
break
if tmp_state == "Error":
overall_state = "FAILED"
break
if tmp_state != "COMPLETED":
overall_state = "RUNNING"
if tmp_state == "Done OK":
overall_state = "Done OK"
self.frontendstatus = overall_state
def jobStatusNumbers(self):
jobStatusNumbers=defaultdict(int)
good, bad = 0, 0
for job in self.jobs:
if job.status!=job.frontendstatus:
jobStatusNumbers[job.status]+=1
jobStatusNumbers[job.frontendstatus]+=1
else:
jobStatusNumbers[job.status]+=1
if job.status in ["ABORTED", "FAILED","ERROR"]:
bad += 1
if job.frontendstatus == "Done OK":
good += 1
jobStatusNumbers["total"]=len(self.jobs)
jobStatusNumbers["good"] = good
jobStatusNumbers["bad"] = bad
return jobStatusNumbers
def resubmit(self,tasklist):
if(len(tasklist)==0):
return
if self.resubmitted:
log.info("task already resubmitted, close and redo again")
return
condor_jdl_file=open(self.condorfile)
condor_jdl_resubmit_file=open(self.condorfile.replace(".jdl","_resubmit.jdl"),"w")
log.debug(self.condorfile.replace(".jdl","_resubmit.jdl"))
removed_line=False
for line in condor_jdl_file:
if "arguments" in line:
failedTask=False
for itask in tasklist:
if "_%d.sh"%itask in line:
failedTask=True
if failedTask:
condor_jdl_resubmit_file.write(line)
else:
removed_line=True
elif not removed_line:
condor_jdl_resubmit_file.write(line)
else:
removed_line=False
condor_jdl_file.close()
condor_jdl_resubmit_file.close()
cwd=os.getcwd()
os.chdir(os.path.join(self.run_folder,self.sample))
command="condor_submit condor_resubmit.jdl"
log.debug(command)
subprocess.call(command, shell=True)
os.chdir(cwd)
self.allcondorlogs=glob.glob(os.path.join(self.run_folder,self.sample)+"/condor*.log")
self.resubmitted_ids=[]
for ilog in self.allcondorlogs:
self.resubmitted_ids.append(int(ilog.split("_")[-1].split(".")[0]))
for i,itask in enumerate(tasklist):
self.jobs[itask].update_resubmit(i,self.resubmitted_ids[-1],self)
self.resubmitted=True
def kill(self,tasklist):
condor_jdl_file=open(self.condorfile)
condor_jdl_resubmit_file=open(self.condorfile.replace(".jdl","_resubmit.jdl"),"w")
removed_line=False
for itask in tasklist:
command="condor_rm %d.%d"%(self.id,itask)
log.debug(command)
subprocess.call(command, shell=True)
def run_time(self):
runtime=datetime.timedelta(0)
now=datetime.datetime.now()
for ijob in self.jobs:
if (ijob.starttime-now)>runtime:
runtime=ijob.starttime-now
if ijob.runtime > runtime:
runtime=ijob.runtime
return runtime
class Job:
"""This is represents one actual process on condor"""
def __init__(self,_id,task):
self.status="None"
self.frontendstatus="None"
self.id = _id
self.orig_id= _id
self.task_id=task.id
self.starttime=datetime.datetime.now()
self.runtime=datetime.timedelta(0)
self.endtime=None
self.errorfile=os.path.join(task.run_folder,task.sample,"err.%d_%d"%(self.id,self.task_id))
self.outfile=os.path.join(task.run_folder,task.sample,"out.%d_%d"%(self.id,self.task_id))
self.resubmitted=False
if os.path.exists(os.path.join(task.run_folder,task.sample,"resubmitted.txt")):
resubmissionFile=open(os.path.join(task.run_folder,task.sample,"resubmitted.txt"),"r")
for line in resubmissionFile:
if "%d %d ->"%(self.id,task.id) in line:
update=line.split("->")[-1].strip().split(" ")
self.task_id=int(update[0])
self.id=int(update[1])
self.resubmitted=True
resubmissionFile.close()
def update(self,_status="None",_frontendstatus="None",_starttime=datetime.datetime.now(),_runtime=datetime.timedelta(0),_endtime=None):
self.status=_status
self.frontendstatus=_frontendstatus
self.starttime=_starttime
self.runtime=_runtime
self.endtime=_endtime
def update_resubmit(self,job_id,condor_id,task):
shutil.move(self.errorfile,self.errorfile+"_resub")
shutil.move(self.outfile,self.outfile+"_resub")
resubmissionFile=open(os.path.join(task.run_folder,task.sample,"resubmitted.txt"),"w+")
resubmissionFile.write("%d %d -> %d %d\n"%(task.id,self.id,job_id,condor_id))
resubmissionFile.close()
log.info("try to link: ",self.errorfile)
log.info(glob.glob(os.path.join(task.run_folder,task.sample)+"\err.*"))
self.resubmitted=True
os.symlink(os.path.abspath(os.path.join(task.run_folder,task.sample,"err.%d_%d"%(job_id,condor_id))),os.path.abspath(self.errorfile))
os.symlink(os.path.abspath(os.path.join(task.run_folder,task.sample,"out.%d_%d"%(job_id,condor_id))),os.path.abspath(self.outfile))
class ProxyError( Exception ):
pass
def timeLeftVomsProxy():
log.debug('Check time left of VomsProxy')
"""Return the time left for the proxy."""
proc = subprocess.Popen( ['voms-proxy-info', '-timeleft' ], stdout=subprocess.PIPE, stderr=subprocess.STDOUT )
output = proc.communicate()[0]
log.debug('Check time left of VomsProxy [Done]')
if proc.returncode != 0:
return False
else:
return int( output )
def checkVomsProxy( time=86400 ):
"""Returns True if the proxy is valid longer than time, False otherwise."""
timeleft = timeLeftVomsProxy()
return timeleft > time
def renewVomsProxy( voms='cms', passphrase=None ):
"""Make a new proxy with a lifetime of one week."""
if passphrase:
p = subprocess.Popen(['voms-proxy-init', '--voms', voms, '--valid', '192:00'], stdout=subprocess.PIPE, stdin=subprocess.PIPE, stderr=subprocess.STDOUT)
stdout = p.communicate(input=passphrase+'\n')[0]
retcode = p.returncode
if not retcode == 0:
raise ProxyError( 'Proxy initialization command failed: '+stdout )
else:
retcode = subprocess.call( ['voms-proxy-init', '--voms', voms, '--valid', '192:00'] )
if not retcode == 0:
raise ProxyError( 'Proxy initialization command failed.')
def checkAndRenewVomsProxy( time=604800, voms='cms', passphrase=None ):
log.debug('Check and renew VomsProxy')
"""Check if the proxy is valid longer than time and renew if needed."""
if not checkVomsProxy( time ):
renewVomsProxy(passphrase=passphrase)
if not checkVomsProxy( time ):
raise ProxyError( 'Proxy still not valid long enough!' )
log.debug('Check and renew VomsProxy [Done]')