The code now compiles itself on a clean start, and then proceeds with the rest...

The code now compiles itself on a clean start, and then proceeds with the rest of CTDAS. The name of the tm5 rcfile is modified
to reflect the new name and location (something like ${rundir}/tm5-tm5-ctdas-base.x). This file will be read, modified, and rewritten
in each sample step of CTDAS. This file already contains a proper submit.command key which can be used to submit TM5 runs automatically, he script then handles the details of the queue system etcetera.

To Do:

- modify the Run() routines to use submit_tm5 (Ivar)
- modify the PrepareRun() routine to make sure all needed keys are replaced in the tm5.rc file
    - such as the submit.option : -s !!!
- test for multiple cycles
- test with a restart option to check logic of compiling

da/tm5/observationoperator.py

@@ -103,12 +103,30 @@ class TM5ObservationOperator(ObservationOperator):
             tm5compiledir  = self.tm_settings[self.rundirkey]
             dummy          = CreateDirs(tm5compiledir)
 
-            self.RcFileName = self.WriteRc()
+            rcfilename      = os.path.join(tm5compiledir,'tm5_setup_init.rc')
+            dummy           = self.WriteRc(rcfilename)
+            self.RcFileName = rcfilename
 
             # Compile TM5 in the new directory, but only if this is a fresh start
 
             self.CompileTM5()
 
+        # Replace the rc filename for TM5 with the newly created one in the new run directory
+
+        workingcopytm5rc = os.path.join(self.tm_settings['rundir'], self.tm_settings['install.rc'] )
+
+        self.RcFileName  = workingcopytm5rc
+
+        msg              = 'Working copy of the tm5.rc file is in place (%s) '%workingcopytm5rc ; logging.debug(msg)
+
+        # And also replace the path to the ObservationOperator in the DaCycle object so we can work from the TM5 copy from here on
+
+        self.DaCycle['obs.operator.rc'] = workingcopytm5rc
+        self.DaCycle['dir.exec.tm5']    = self.tm_settings[self.rundirkey]
+
+        msg              = '...and set as the da.obsoperator.rc value in this DaCycle '; logging.debug(msg)
+
+
         return 0
 
     def CompileTM5(self):
@@ -154,10 +172,9 @@ class TM5ObservationOperator(ObservationOperator):
         """ 
         Prepare a forward model TM5 run, this consists of:
 
-          - reading the TM5 rc-file, 
+          - reading the working copy TM5 rc-file, 
           - validating it, 
           - modifying the values,
-          - Creating a tm5_runtime.rc file
           - Removing the existing tm5.ok file if present
     
         """
@@ -169,15 +186,6 @@ class TM5ObservationOperator(ObservationOperator):
         dummy               = self.ValidateRc()         # validate the contents
 
 
-# Create a link from TM5 to the rundirectory of the das system
-
-        sourcedir           = self.tm_settings[self.rundirkey]
-        targetdir           = os.path.join(self.DaCycle['dir.exec'],'tm5')
-        dummy               = CreateLinks(sourcedir,targetdir)
-        self.outputdir      = self.tm_settings[self.outputdirkey]
-
-        self.DaCycle['dir.exec.tm5'] = targetdir
-
 # Write a modified TM5 model rc-file in which run/break times are defined by our da system
 
         NewItems = {
@@ -199,10 +207,7 @@ class TM5ObservationOperator(ObservationOperator):
 
         self.ModifyRC(NewItems)
 
-        newrcfile = self.WriteRc()
-
-        #self.WriteRunRc() No longer needed with pycasso !
-
+        dummy = self.WriteRc(self.RcFileName)
 
         return 0
 
@@ -324,19 +329,17 @@ class TM5ObservationOperator(ObservationOperator):
                 logging.debug('Added new tm5 rc-item %s ' % k)
 
 
-    def WriteRc(self):
+    def WriteRc(self,tm5rcfilename):
         """ 
         Write the rc-file settings to a tm5.rc file in the rundir
         """
         import da.tools.rc as rc
 
-        tm5rcfilename   = os.path.join(self.tm_settings[self.rundirkey],'tm5_ctdas_setup.rc')
-
         dummy           = rc.write(tm5rcfilename,self.tm_settings)
 
         msg             = "Modified rc file for TM5 written (%s)" % tm5rcfilename      ;logging.debug(msg)
 
-        return tm5rcfilename
+        return None
 
     def WriteRunRc(self):
         """