general fixes to the daemon (#39)

submit/calibJobHandlerCondor.py

@@ -9,7 +9,7 @@
 
 # def checkNjobsCondor(noDaemon=True):
 # checkJobs = subprocess.Popen(['condor_q'], stdout=subprocess.PIPE, shell=True);
-# datalines = (checkJobs.communicate()[0]).splitlines()
+# datalines = (checkJobs.communicate()[0].decode()).splitlines()
 # nRetjobs = 0
 # for l in datalines:
 # if all(x in l for x in ["jobs", "completed", "removed"]):
@@ -34,11 +34,10 @@ def checkNjobsCondor(grepArg="ecalpro"):
  # 0 jobs; 0 completed, 0 removed, 0 idle, 0 running, 0 held, 0 suspended
 
  checkJobs = subprocess.Popen(['condor_q'], stdout=subprocess.PIPE, shell=True);
- tmp = str(checkJobs.communicate()[0])
+ tmp = str(checkJobs.communicate()[0].decode())
  if all(x in tmp for x in ["OWNER", "BATCH_NAME", "SUBMITTED", "jobs", "completed", "removed"]): # a very dumb check, I know
  checkJobs = subprocess.Popen(['condor_q -af JobBatchName| grep {gr} | wc -l'.format(gr=grepArg)], stdout=subprocess.PIPE, shell=True);
- nRetjobs = checkJobs.communicate()[0]
- # check nRetjobs is not a null string, but a number (either 0 or something else)
+ nRetjobs = checkJobs.communicate()[0].decode()
  if len(nRetjobs) and nRetjobs != "\n" and nRetjobs.replace('\n','').isdigit():
  return int(nRetjobs)
  else:
@@ -173,7 +172,7 @@ def writeCondorSubmitBase(condor_file="", dummy_exec_name="", logdir="", jobBatc
  print(">>> Running --> " + submit_s)
  # actually submitting filling tasks
  submitJobs = subprocess.Popen([submit_s], stdout=subprocess.PIPE, shell=True);
- output = submitJobs.communicate()
+ output = submitJobs.communicate()[0].decode()
  print("Out: " + str(output))
 
  time.sleep(15) 
@@ -189,7 +188,7 @@ def writeCondorSubmitBase(condor_file="", dummy_exec_name="", logdir="", jobBatc
  nFilljobs = checkNjobsCondor("ecalpro_Fill")
  print("I still see {n} jobs for Fill part".format(n=nFilljobs))
  checkJobs2 = subprocess.Popen(['rm -rf ' + pwd + '/core.*'], stdout=subprocess.PIPE, shell=True);
- datalines2 = (checkJobs2.communicate()[0]).splitlines()
+ datalines2 = (checkJobs2.communicate()[0].decode()).splitlines()
  nCheck += 1
  if nCheck * sleeptime > 43200: 
  renewTokenAFS(daemonLocal=options.daemonLocal, infile=options.tokenFile) 
@@ -261,7 +260,7 @@ def writeCondorSubmitBase(condor_file="", dummy_exec_name="", logdir="", jobBatc
  Ntpsubmit_s = "condor_submit {cfn}".format(cfn=condor_file_name)
  # actually submitting recovery tasks
  subJobs = subprocess.Popen([Ntpsubmit_s], stdout=subprocess.PIPE, shell=True);
- outJobs = subJobs.communicate()
+ outJobs = subJobs.communicate().decode()
  print(outJobs)
 
  time.sleep(30)
@@ -278,7 +277,7 @@ def writeCondorSubmitBase(condor_file="", dummy_exec_name="", logdir="", jobBatc
  nFilljobs = checkNjobsCondor("ecalpro_Fill_recovery")
  print("I still see {n} jobs for Fill_recovery part ({nr})".format(n=nFilljobs,nr=NtpRecoveryAttempt))
  checkJobs2 = subprocess.Popen(['rm -rf ' + pwd + '/core.*'], stdout=subprocess.PIPE, shell=True);
- datalines2 = (checkJobs2.communicate()[0]).splitlines()
+ datalines2 = (checkJobs2.communicate()[0].decode()).splitlines()
  nCheck += 1
  if nCheck * sleeptime > 43200: 
  renewTokenAFS(daemonLocal=options.daemonLocal, infile=options.tokenFile) 
@@ -323,20 +322,13 @@ def writeCondorSubmitBase(condor_file="", dummy_exec_name="", logdir="", jobBatc
  #BUT we do that only if you are working on batch
  Grepcommand = "grep -i list " + Hadd_src_n + " | grep -v echo | grep -v bash | awk '{print $2}'"
  myGrep = subprocess.Popen([Grepcommand], stdout=subprocess.PIPE, shell=True )
- FoutGrep = myGrep.communicate()
- # FoutGrep is something like the following
- # ('/afs_path_to_dirName/src/hadd/hadd_iter_XXX_step_YYY.list`\n', None)
- # we want to keep /afs_path_to_dirName/src/hadd/hadd_iter_XXX_step_YYY.list
- # removing (' and `\n', None)
- FoutGrep_2 = str(FoutGrep)[3:]
- FoutGrep_2 = str(FoutGrep_2)[:-11]
- #print('Checking ' + str(FoutGrep_2))
+ FoutGrep = myGrep.communicate()[0].decode().replace("'","")[:-2]
  #Chech The size for each line
- f = open( str(FoutGrep_2) )
+ f = open(FoutGrep)
  lines = f.readlines()
  f.close()
  # create backup of original list of files
- fbckp = open( FoutGrep_2.replace(".list","_backup.list"), "w")
+ fbckp = open( FoutGrep.replace(".list","_backup.list"), "w")
  for l in lines:
  fbckp.write(l)
  fbckp.close()
@@ -369,16 +361,16 @@ def writeCondorSubmitBase(condor_file="", dummy_exec_name="", logdir="", jobBatc
 
  #moving the .list to the correct one
  if( len(newlines) ):
- prunedfile = FoutGrep_2.replace(".list","_pruned.list")
+ prunedfile = FoutGrep.replace(".list","_pruned.list")
  fprun = open(prunedfile,"w")
  for l in newlines:
  fprun.write(l)
  fprun.close()
- MoveComm = "cp " + prunedfile + " " + str(FoutGrep_2)
+ MoveComm = "cp " + prunedfile + " " + str(FoutGrep)
  MoveC = subprocess.Popen([MoveComm], stdout=subprocess.PIPE, shell=True);
- mvOut = MoveC.communicate()
- #print "Some files were removed in " + str(FoutGrep_2)
- #print "Copied " + prunedfile + " into " + str(FoutGrep_2)
+ mvOut = MoveC.communicate()[0].decode()
+ #print "Some files were removed in " + str(FoutGrep)
+ #print "Copied " + prunedfile + " into " + str(FoutGrep)
 
  #End of the check, sending the job
  print("Preparing job to hadd files in list number " + str(nHadds) + "/" + str(Nlist - 1)) #nHadds goes from 0 to Nlist -1
@@ -387,7 +379,7 @@ def writeCondorSubmitBase(condor_file="", dummy_exec_name="", logdir="", jobBatc
  Hsubmit_s = "condor_submit {cfn}".format(cfn=condor_file_name)
  print(">>> Running --> " + Hsubmit_s)
  subJobs = subprocess.Popen([Hsubmit_s], stdout=subprocess.PIPE, shell=True);
- outJobs = subJobs.communicate()
+ outJobs = subJobs.communicate()[0].decode()
 
  print(str(outJobs))
  time.sleep(15)
@@ -401,7 +393,7 @@ def writeCondorSubmitBase(condor_file="", dummy_exec_name="", logdir="", jobBatc
  nHaddjobs = checkNjobsCondor("ecalpro_Hadd")
  print("I still see {n} jobs for Hadd part".format(n=nHaddjobs))
  #checkJobs2 = subprocess.Popen(['rm -rf ' + pwd + '/core.*'], stdout=subprocess.PIPE, shell=True);
- #datalines2 = (checkJobs2.communicate()[0]).splitlines()
+ #datalines2 = (checkJobs2.communicate()[0].decode()).splitlines()
  print('Done with various hadd')
 
  # Check if all the hadds are there and files are not empty
@@ -470,7 +462,7 @@ def writeCondorSubmitBase(condor_file="", dummy_exec_name="", logdir="", jobBatc
  print(">>> Running --> " + Hsubmit_s)
  # actually submitting recovery tasks
  subJobs = subprocess.Popen([Hsubmit_s], stdout=subprocess.PIPE, shell=True);
- outJobs = subJobs.communicate()
+ outJobs = subJobs.communicate()[0].decode()
  print(outJobs)
 
  time.sleep(15)
@@ -521,7 +513,7 @@ def writeCondorSubmitBase(condor_file="", dummy_exec_name="", logdir="", jobBatc
  FHsubmit_s = "condor_submit {cfn}".format(cfn=condor_file_name)
  print(">>> Running --> " + FHsubmit_s)
  FsubJobs = subprocess.Popen([FHsubmit_s], stdout=subprocess.PIPE, shell=True);
- FoutJobs = FsubJobs.communicate()
+ FoutJobs = FsubJobs.communicate()[0].decode()
  print(FoutJobs)
  time.sleep(5)
 
@@ -559,7 +551,7 @@ def writeCondorSubmitBase(condor_file="", dummy_exec_name="", logdir="", jobBatc
  Fitsubmit_s = "{src}".format(src=srcFold_n)
  print(">>> Running --> " + Fitsubmit_s) 
  FsubJobs = subprocess.Popen([Fitsubmit_s], stdout=subprocess.PIPE, shell=True);
- FoutJobs = FsubJobs.communicate() # do I really need to communicate to stdout?
+ FoutJobs = FsubJobs.communicate()[0].decode() # do I really need to communicate to stdout?
  print(FoutJobs) 
  #os.system(Fitsubmit_s) 
 
@@ -619,7 +611,7 @@ def writeCondorSubmitBase(condor_file="", dummy_exec_name="", logdir="", jobBatc
  Fitsubmit_s = "condor_submit {cfn}".format(cfn=condor_file_name)
  print(">>> Running --> " + Fitsubmit_s)
  FsubJobs = subprocess.Popen([Fitsubmit_s], stdout=subprocess.PIPE, shell=True);
- FoutJobs = FsubJobs.communicate()
+ FoutJobs = FsubJobs.communicate()[0].decode()
  print(FoutJobs)
  time.sleep(5)
 
@@ -672,7 +664,7 @@ def writeCondorSubmitBase(condor_file="", dummy_exec_name="", logdir="", jobBatc
  Fitsubmit_s = "condor_submit {cfn}".format(cfn=condor_file_name)
  print(">>> Running --> " + Fitsubmit_s)
  FsubJobs = subprocess.Popen([Fitsubmit_s], stdout=subprocess.PIPE, shell=True);
- FoutJobs = FsubJobs.communicate()
+ FoutJobs = FsubJobs.communicate()[0].decode()
  print(FoutJobs)
  time.sleep(5)
 
@@ -923,7 +915,7 @@ def writeCondorSubmitBase(condor_file="", dummy_exec_name="", logdir="", jobBatc
  # print "############################"
  # cmdEosLs = 'ls ' + eosPath + '/' + dirname + '/iter_' + str(iters) + "/"
  # eosFileList = subprocess.Popen([cmdEosLs], stdout=subprocess.PIPE, shell=True);
- # print eosFileList.communicate()
+ # print eosFileList.communicate()[0].decode()
  # print "############################"
 
  print("Going to merge the following files ...")