slight changes to job running structure on maunaloa

da/platform/maunaloa.py

@@ -14,14 +14,63 @@ import os
 import logging
 import subprocess
 
-from da.baseclasses.platform import PlatForm
+from da.baseclasses.platform import PlatForm, std_joboptions
 
 class MaunaloaPlatForm(PlatForm):
     def __init__(self):
 
-        self.Identifier     = 'WUR maunaloa'    # the identifier gives the platform name
+        self.Identifier     = 'WU maunaloa'    # the identifier gives the platform name
         self.Version        = '1.0'     # the platform version used
 
+    def GetJobTemplate(self,joboptions={},block=False):
+        """ 
+        Returns the job template for a given computing system, and fill it with options from the dictionary provided as argument.
+        The job template should return the preamble of a job that can be submitted to a queue on your platform, 
+        examples of popular queuing systems are:
+            - SGE
+            - MOAB
+            - XGrid
+            -
+
+        A list of job options can be passed through a dictionary, which are then filled in on the proper line,
+        an example is for instance passing the dictionary {'account':'co2'} which will be placed 
+        after the ``-A`` flag in a ``qsub`` environment.
+
+        An extra option ``block`` has been added that allows the job template to be configured to block the current
+        job until the submitted job in this template has been completed fully.
+        """
+
+        template = """## \n"""+ \
+                   """## This is a set of dummy names, to be replaced by values from the dictionary \n"""+ \
+                   """## Please make your own platform specific template with your own keys and place it in a subfolder of the da package.\n """+ \
+                   """## \n"""+ \
+                   """ \n"""+ \
+                   """#$ jobname \n"""+ \
+                   """#$ jobaccount \n"""+ \
+                   """#$ jobnodes \n"""+ \
+                   """#$ jobtime \n"""+ \
+                   """#$ jobshell \n"""+ \
+                   """\n"""+ \
+                   """source /usr/local/Modules/3.2.8/init/sh\n"""+ \
+                   """module load python\n"""+ \
+                   """\n"""
+
+        if 'depends' in joboptions:
+            template += """#$ -hold_jid depends \n"""
+
+        # First replace from passed dictionary
+        for k,v in joboptions.iteritems():
+            while k in template:
+                template = template.replace(k,v)
+
+        # Fill remaining values with std_options
+        for k,v in std_joboptions.iteritems():
+            while k in template:
+                template = template.replace(k,v)
+
+        return template
+
+
         msg1  = 'Platform initialized: %s'%self.Identifier      ; logging.info(msg1)
         #msg2  = '%s version: %s'%(self.Identifier,self.Version) ; logging.info(msg2)
 

da/tools/initexit.py

@@ -644,8 +644,8 @@ class CycleControl(dict):
             # Template and commands for job
             jobparams               = {'jobname':sys.argv[0][2:],'jobtime':'01:30:00'}
             template                = DaPlatForm.GetJobTemplate(jobparams)
-            template                += '\ncd %s\n'% self['dir.da_submit'] 
-            template                += '%s rc=%s %s >& %s' % (sys.argv[0],self['da.restart.fname'],join(self.opts,''),logfile,) 
+            execcommand             = os.path.join(self['dir.da_submit'],sys.argv[0]) 
+            template                += 'python %s rc=%s %s >& %s' % (execcommand,self['da.restart.fname'],join(self.opts,''),logfile,) 
 
             # write and submit 
 

das.jb

@@ -3,6 +3,7 @@
 #$ nserial 1 
 #$ 01:30:00 
 #$ /bin/sh 
- 
+
  echo "All output piped to file das.out"
-/opt/local/bin/python2.6 das.py rc=da.rc $1  >& das.out
+ module load python
+ python das.py rc=da.rc $1  >& das.out