Taub submitter for QWalk

	modified:   QWalkRunner.py

Author: bbusemeyer

QWalkRunner.py

@@ -80,8 +80,62 @@ def run(self,qwinps,qwouts,jobname=None):
          "#PBS -o %s \n"%jobout +\
          self.prefix+"\n" +\
          "cd ${PBS_O_WORKDIR}\n" +\
-         "cp %s INPUT\n"%(qwinp) +\
-         "mpirun -np %i %s %s \n"%(np_tot,self.exe,qwinp) +\
+         "mpirun -np %i %s %s > %s \n"%(np_tot,self.exe,qwinp,qwinp+'.out') +\
+         self.postfix
+      qsubfile=qwinp+".qsub"
+      with open(qsubfile,'w') as f:
+        f.write(qsub)
+      result = sub.check_output("qsub %s"%(qsubfile),shell=True)
+      self.queueid.append(result.decode().split()[0].split('.')[0])
+      print("Submitted as %s"%self.queueid)
+      
+####################################################
+
+class QWalkRunnerTaub:
+  _name_='QWalkRunnerPBS'
+  def __init__(self,exe='~/bin/qwalk',
+                    queue='batch',
+                    walltime='12:00:00',
+                    jobname=os.getcwd().split('/')[-1]+'_qwalk',
+                    prefix="",#for example, load modules
+                    postfix="",#for any clean-up.
+                    np=1,nn=1
+                    ):
+    self.exe=exe
+    self.np=np
+    self.nn=nn
+    self.jobname=jobname
+    self.queue=queue
+    self.walltime=walltime
+    self.prefix=prefix
+    self.postfix=postfix
+    self.queueid=[]
+
+  #-------------------------------------
+  def check_status(self):
+    return submitter.check_PBS_stati(self.queueid)
+  #-------------------------------------
+
+  def run(self,qwinps,qwouts,jobname=None):
+    if jobname is None:
+      jobname=self.jobname
+    #Just supporting one run for the moment
+    qwinp=qwinps[0]
+    qwout=qwouts[0]
+    for qwinp,qwout in zip(qwinps,qwouts):
+      jobout=qwinp+".jobout"
+      np_tot=self.np*self.nn
+    
+      qsub="#PBS -q %s \n"%self.queue +\
+         "#PBS -l nodes=%i:ppn=%i\n"%(self.nn,self.np) +\
+         "#PBS -l walltime=%s\n"%self.walltime +\
+         "#PBS -j oe \n" +\
+         "#PBS -N %s \n"%jobname +\
+         "#PBS -o %s \n"%jobout +\
+         self.prefix+"\n" +\
+         "cd ${PBS_O_WORKDIR}\n" +\
+         "module load openmpi/1.4-gcc+ifort" +\
+         "mpirun -np %i %s %s > %s \n"%(np_tot,self.exe,qwinp,qwinp+'.out') +\
          self.postfix
       qsubfile=qwinp+".qsub"
       with open(qsubfile,'w') as f: