replacing getoutput function for slurm jobs

runOPAL/runOPAL.py

@@ -17,8 +17,9 @@ from runoptpilot import Runoptpilot
 from opaldict import OpalDict
 
 def getNearestRestartStep(restart_pos,fn):
-#    print 'pos= ',restart_pos,' fn= ',fn
-    #res = commands.getoutput('H5getStep ' + str(restart_pos) + "  " + fn);
+    print('pos= ',restart_pos,' fn= ',fn)
+    res = subprocess.check_output('H5getStep ' + str(restart_pos) + "  " + fn);
+    
     return int(res.split("=")[2])
 
 def getBaseName():
@@ -87,7 +88,7 @@ def traverseRanges(list, opaldict, args):
                 if args[10]:
                     print("... finished!\n")
                 else:
-                    print("SGE-ID= ",qid,'\n')
+                    print("SGE-ID= {}\n".format(qid))
             else:
                 traverseRanges(tail, opaldict, args)
             curval = curval + step
@@ -179,14 +180,14 @@ def main(argv):
         if doNobatch:
             print("... finished!\n")
         else:
-            print("SGE-ID= ",qid,'\n')
+            print("SGE-ID= {}\n".format(qid)) 
     elif not opaldict.hasRanges():
         sim = Simulation(opaldict)
         qid = sim.run(N, baseFileName, restart_step, inputfilePath, tmplFile, oinpFile, restart_file, doTest, doKeep, doNobatch, info, queue, hypert)
         if doNobatch:
             print( "... finished!\n")
         else:
-            print( "SGE-ID= ",qid,'\n')
+            print( "SGE-ID= {}\n".format(qid))
     else:
         ranges = opaldict.Range()
 

runOPAL/simulation.py

@@ -112,8 +112,8 @@ class Simulation:
 
         if not doNobatch:
             #hostname = commands.getoutput("hostname")
-            hostname = subprocess.check_output('hostname')
-            print("On host ",hostname.strip())
+            hostname = (subprocess.check_output('hostname').decode('utf-8')).strip()
+            print("On host {}".format(hostname))
 
             if os.getenv("SGE_TIME"):
                 print( "You use deprecated environment variable SGE_TIME. Please use in the future TIME")
@@ -134,7 +134,7 @@ class Simulation:
                     queue = os.getenv("SGE_QUEUE", "prime_bd.q")
 
             # Merlin5
-            if (hostname.startswith(b"merlin-l")):
+            if (hostname.startswith("merlin-l")):
                 batchsys  = 'SLURM'
                 runfile   = 'run.merlin5'
                 time      = os.getenv("SLURM_TIME", "24:00:00")
@@ -143,27 +143,27 @@ class Simulation:
                 self.WriteMerlin5(opalexe, oinpFile, CORES, time, ram, info, runfile, partition)
 
             # ANL blues.lcrc.anl.gov
-            elif (hostname.startswith(b"blogin")):
+            elif (hostname.startswith("blogin")):
                 batchsys = 'PBS'
                 runfile  = 'run.blues'
                 self.WritePBSBlues(opalexe, oinpFile, CORES, time, ram, info, queue)
 
-            elif (hostname.startswith(b"bebop") or hostname.startswith(b"bdw") or hostname.startswith(b"knl")):
+            elif (hostname.startswith("bebop") or hostname.startswith("bdw") or hostname.startswith("knl")):
                 batchsys = 'SLURM'
                 runfile  = 'run.bebop'
                 self.WriteBebop(opalexe, oinpFile, CORES, time, ram, info, runfile, queue, hypert)
 
-            elif (hostname.startswith(b"cori")):
+            elif (hostname.startswith("cori")):
                 batchsys = 'SLURM'
                 runfile  = 'run.cori'
                 self.WriteCori(opalexe, oinpFile, CORES, time, ram, info, runfile)
 
-            elif (hostname.startswith(b"edison")):
+            elif (hostname.startswith("edison")):
                 batchsys = 'SLURM'
                 runfile  = 'run.edison'
                 self.WriteEdison(opalexe, oinpFile, CORES, time, ram, info, runfile)
 
-            elif (hostname.startswith(b"daint")):
+            elif (hostname.startswith("daint")):
                 batchsys = 'SLURM'
                 runfile  = 'run.daint'
                 time = os.getenv("SLURM_TIME", "24:00:00")
@@ -171,7 +171,7 @@ class Simulation:
                 partition = os.getenv("SLURM_PARTITION", "normal")
                 self.WritePizDaint(opalexe, oinpFile, CORES, time, ram, info, runfile, partition)
 
-            elif (hostname.startswith(b"eofe")):
+            elif (hostname.startswith("eofe")):
                 batchsys = 'SLURM'
                 runfile = 'run.engaging'
                 time = os.getenv("SLURM_TIME", "24:00:00")
@@ -191,17 +191,17 @@ class Simulation:
         if doNobatch:
             print( 'Done with setup of the OPAL simulation and executing the job on ' + str(CORES) + ' cores...\n\n\n')
             ofn, fileExtension = os.path.splitext(oinpFile)
-            print( 'STD output is written to ' + ofn + '.out')
+            print( 'STD output is written to {}.out'.format(ofn))
             execommand = 'mpirun -np ' + str(CORES)  + ' ' + opalexe + ' ' + oinpFile + '  2>&1 | tee ' + ofn + '.out'
-            qid = commands.getoutput(execommand)
+            qid = subprocess.check_output(execommand)
             os.chdir('..')
             return -1
         else:
             qid = ""
  
             if batchsys == 'SLURM':
-                qid = commands.getoutput('sbatch ' + runfile + ' | awk \'{print $3}\' ')
-                print( 'Done with setup of the OPAL simulation and submitting the job with ', CORES, ' cores \n\n\n')
+                qid = subprocess.call(['sbatch', runfile, '|', 'awk','\'{print $3}\''])
+                print( 'Done with setup of the OPAL simulation and submitting the job with {} cores \n\n\n'.format(CORES))
 
             elif batchsys == 'PBS':
                 print( 'Done with setup of the OPAL simulation, please submit the job yourself')