Merge pull request #967 from jedwards4b/pio_namelist_fix

Pio namelist fix

cime_config/cesm/machines/config_compilers.xml

@@ -978,7 +978,9 @@ using a fortran linker.
   <FFLAGS>
     <append> -vec-report </append>
   </FFLAGS>
-
+  <CMAKE_OPTS>
+    <append DEBUG="TRUE"> -DPIO_ENABLE_LOGGING=ON </append>
+  </CMAKE_OPTS>
 </compiler>
 
 <compiler MACH="yellowstone" COMPILER="gnu">

cime_config/cesm/machines/config_machines.xml

@@ -956,6 +956,7 @@
     </module_system>
     <environment_variables>
       <env name="OMP_STACKSIZE">256M</env>
+      <env name="MPI_TYPE_DEPTH">16</env>
     </environment_variables>
   </machine>
 

share/csm_share/shr/shr_pio_mod.F90

@@ -531,7 +531,7 @@ subroutine shr_pio_read_component_namelist(nlfilename, Comm, pio_stride, pio_roo
        if(pio_root == -99) pio_root = pio_default_root
        if(pio_rearranger == -99) pio_rearranger = pio_default_rearranger
        if(pio_numiotasks == -99) then
-          pio_numiotasks = min(pio_default_numiotasks,npes/pio_stride)
+          pio_numiotasks = npes/pio_stride
        endif
     endif
 

utils/python/CIME/case.py

@@ -799,6 +799,7 @@ def _set_pio_xml(self):
         compset = self.get_value("COMPSET")
         mpilib = self.get_value("MPILIB")
         defaults = pioobj.get_defaults(grid=grid,compset=compset,mach=mach,compiler=compiler, mpilib=mpilib)
+
         for vid, value in defaults.items():
             self.set_value(vid,value)
 

utils/python/CIME/case_run.py

@@ -177,9 +177,9 @@ def resubmit_check(case):
         submit(case, job=job, resubmit=True)
 
 ###############################################################################
-def do_data_assimilation(da_script, cycle, data_assimilation_cycles, lid):
+def do_data_assimilation(da_script, caseroot, cycle, lid):
 ###############################################################################
-    cmd = da_script + " 1> da.log.%s %d %d 2>&1" %(lid, cycle, data_assimilation_cycles)
+    cmd = da_script + " 1> da.log.%s %d %d 2>&1" %(lid, caseroot, cycle)
     logger.debug("running %s" %da_script)
     run_cmd_no_fail(cmd)
     # disposeLog(case, 'da', lid)  THIS IS UNDEFINED!
@@ -218,7 +218,7 @@ def case_run(case):
             get_timing(case, lid)     # Run the getTiming script
 
         if data_assimilation:
-            do_data_assimilation(data_assimilation_script, cycle, data_assimilation_cycles, lid)
+            do_data_assimilation(data_assimilation_script, case.get_value("CASEROOT"), cycle, lid)
 
         save_postrun_provenance(case)
 

utils/python/CIME/case_setup.py

@@ -188,16 +188,11 @@ def _case_setup_impl(case, caseroot, clean=False, test_mode=False, reset=False):
 
             expect(not (case.get_value("BUILD_THREADED")  and compiler == "nag"),
                    "it is not possible to run with OpenMP if using the NAG Fortran compiler")
-
-
             cost_pes = env_mach_pes.get_cost_pes(pestot, thread_count, machine=case.get_value("MACH"))
             case.set_value("COST_PES", cost_pes)
 
-            # create batch file
+            # create batch files
             logger.info("Creating batch script case.run")
-
-            # Use BatchFactory to get the appropriate instance of a BatchMaker,
-            # use it to create our batch scripts
             env_batch = case.get_env("batch")
             num_nodes = env_mach_pes.get_total_nodes(pestot, thread_count)
             tasks_per_node = env_mach_pes.get_tasks_per_node(pestot, thread_count)
@@ -212,6 +207,17 @@ def _case_setup_impl(case, caseroot, clean=False, test_mode=False, reset=False):
                 elif job != "case.test":
                     logger.info("Writing %s script from input template %s" % (job, input_batch_script))
                     env_batch.make_batch_script(input_batch_script, job, case, pestot, tasks_per_node, num_nodes, thread_count)
+            # Make sure pio settings are consistant
+            for comp in models:
+                pio_stride = case.get_value("PIO_STRIDE_%s"%comp)
+                pio_numtasks = case.get_value("PIO_NUMTASKS_%s"%comp)
+                ntasks = case.get_value("NTASKS_%s"%comp)
+                if pio_stride < 0 or pio_stride > ntasks:
+                    pio_stride = min(ntasks, tasks_per_node)
+                    case.set_value("PIO_STRIDE_%s"%comp, pio_stride)
+                if pio_numtasks < 0 or pio_numtasks > ntasks:
+                    pio_numtasks = max(1, ntasks//pio_stride)
+                    case.set_value("PIO_NUMTASKS_%s"%comp, pio_numtasks)
 
             # Make a copy of env_mach_pes.xml in order to be able
             # to check that it does not change once case.setup is invoked

utils/python/CIME/preview_namelists.py

@@ -72,27 +72,34 @@ def create_namelists(case):
         else:
             compname = case.get_value("COMP_%s" % model_str.upper())
         cmd = os.path.join(config_dir, "buildnml")
-        logger.info("   Calling %s buildnml"%compname)
+        do_run_cmd = False
         try:
-            mod = imp.load_source("buildnml", cmd)
-            mod.buildnml(case, caseroot, compname)
-
-        except SyntaxError as detail:
             with open(cmd, 'r') as f:
                 first_line = f.readline()
+            if "python" in first_line:    
+                logger.info("   Calling %s buildnml"%compname)
+                mod = imp.load_source("buildnml", cmd)
+                mod.buildnml(case, caseroot, compname)
+            else:
+                raise SyntaxError
+        except SyntaxError as detail:
             if 'python' in first_line:
                 expect(False, detail)
             else:
-                run_cmd_no_fail("%s %s" % (cmd, caseroot), verbose=False)
+                do_run_cmd = True
         except AttributeError:
-            run_cmd_no_fail("%s %s" % (cmd, caseroot), verbose=False)
+            do_run_cmd = True
         except:
             raise
 
+        if do_run_cmd:
+            logger.info("   Running %s buildnml"%compname)
+            case.flush()
+            run_cmd_no_fail("%s %s" % (cmd, caseroot), verbose=False)
+            # refresh case xml object from file
+            case.read_xml()            
     logger.info("Finished creating component namelists")
 
-    # refresh case xml object from file
-    case.read_xml()
 
     # Save namelists to docdir
     if (not os.path.isdir(docdir)):