Merge pull request #1494 from jedwards4b/pesfile_usage

Pesfile usage

Previously the user was only allowed to specify a file in the config_pes.xml format in the --pesfile argument to create_newcase. This change allows the user to specify a file in either the config_pes.xml or the env_mach_pes.xml format. Also add a test for this feature

Test suite: scripts_regression_tests.py
Test baseline:
Test namelist changes:
Test status: bit for bit

Fixes

User interface changes?: --pesfile argument in create_newcase

Code review:

scripts/create_newcase

@@ -76,7 +76,8 @@ OR
     parser.add_argument("--pesfile",
                         help="Only used and required for --user-compset argument."
                         "Full pathname of the pes specification file"
-                        "This argument is required if --user-compset is True")
+                        "This argument is required if --user-compset is True"
+                        "The file can follow either the config_pes.xml or the env_mach_pes.xml format")
 
     parser.add_argument("--user-grid", action="store_true",
                         help="If set, then the -grid argument is treated as a user specified grid."

scripts/lib/CIME/XML/env_mach_pes.py

@@ -34,7 +34,7 @@ def get_max_thread_count(self, comp_classes):
         ''' Find the maximum number of openmp threads for any component in the case '''
         max_threads = 1
         for comp in comp_classes:
-            threads = self.get_value("NTHRDS_%s"%comp)
+            threads = self.get_value("NTHRDS",attribute={"component":comp})
             expect(threads is not None, "Error no thread count found for component class %s"%comp)
             if threads > max_threads:
                 max_threads = threads
@@ -44,6 +44,7 @@ def get_cost_pes(self, totaltasks, max_thread_count, machine=None):
         """
         figure out the value of COST_PES which is the pe value used to estimate model cost
         """
+        expect(totaltasks > 0,"totaltasks > 0 expected totaltasks = %s"%totaltasks)
         pespn = self.get_value("PES_PER_NODE")
         num_nodes, spare_nodes = self.get_total_nodes(totaltasks, max_thread_count)
         num_nodes += spare_nodes
@@ -57,14 +58,15 @@ def get_cost_pes(self, totaltasks, max_thread_count, machine=None):
     def get_total_tasks(self, comp_classes):
         total_tasks = 0
         for comp in comp_classes:
-            ntasks = self.get_value("NTASKS_%s"%comp)
-            rootpe = self.get_value("ROOTPE_%s"%comp)
-            pstrid = self.get_value("PSTRID_%s"%comp)
+            ntasks = self.get_value("NTASKS", attribute={"component":comp})
+            rootpe = self.get_value("ROOTPE", attribute={"component":comp})
+            pstrid = self.get_value("PSTRID", attribute={"component":comp})
             tt = rootpe + (ntasks - 1) * pstrid + 1
             total_tasks = max(tt, total_tasks)
         return total_tasks
 
     def get_tasks_per_node(self, total_tasks, max_thread_count):
+        expect(total_tasks > 0,"totaltasks > 0 expected totaltasks = %s"%total_tasks)
         tasks_per_node = min(self.get_value("MAX_TASKS_PER_NODE")/ max_thread_count,
                              self.get_value("PES_PER_NODE"), total_tasks)
         return tasks_per_node

scripts/lib/CIME/XML/generic_xml.py

@@ -295,4 +295,7 @@ def get_raw_record(self, root=None):
         return xmlstr
 
     def get_id(self):
-        return self.root.get("id")
+        xmlid = self.root.get("id")
+        if xmlid is not None:
+            return xmlid
+        return self.root.tag

scripts/lib/CIME/case.py

@@ -415,6 +415,9 @@ def _set_compset_and_pesfile(self, compset_name, files, user_compset=False, pesf
         components = files.get_components("COMPSETS_SPEC_FILE")
         logger.debug(" Possible components for COMPSETS_SPEC_FILE are %s" % components)
 
+        if pesfile is not None:
+            self._pesfile = pesfile
+
         # Loop through all of the files listed in COMPSETS_SPEC_FILE and find the file
         # that has a match for either the alias or the longname in that order
         for component in components:
@@ -426,9 +429,11 @@ def _set_compset_and_pesfile(self, compset_name, files, user_compset=False, pesf
             if (os.path.isfile(compsets_filename)):
                 compsets = Compsets(compsets_filename)
                 match, compset_alias, science_support, self._user_mods = compsets.get_compset_match(name=compset_name)
-                pesfile = files.get_value("PES_SPEC_FILE"     , {"component":component})
                 if match is not None:
-                    self._pesfile = pesfile
+                    if pesfile is None:
+                        self._pesfile = files.get_value("PES_SPEC_FILE"     , {"component":component})
+                        self.set_lookup_value("PES_SPEC_FILE"      ,
+                                              files.get_value("PES_SPEC_FILE"     , {"component":component}, resolved=False))
                     self._compsetsfile = compsets_filename
                     self._compsetname = match
                     tests_filename    = files.get_value("TESTS_SPEC_FILE"   , {"component":component}, resolved=False)
@@ -439,8 +444,6 @@ def _set_compset_and_pesfile(self, compset_name, files, user_compset=False, pesf
                     self.set_lookup_value("TESTS_SPEC_FILE"    , tests_filename)
                     self.set_lookup_value("TESTS_MODS_DIR"     , tests_mods_dir)
                     self.set_lookup_value("USER_MODS_DIR"      , user_mods_dir)
-                    self.set_lookup_value("PES_SPEC_FILE"      ,
-                                   files.get_value("PES_SPEC_FILE"     , {"component":component}, resolved=False))
                     compset_info = "Compset longname is %s"%(match)
                     if self._user_mods is not None:
                         compset_info += " with user_mods directory %s"%(self._user_mods)
@@ -453,7 +456,7 @@ def _set_compset_and_pesfile(self, compset_name, files, user_compset=False, pesf
             #Do not error out for user_compset
             logger.warn("Could not find a compset match for either alias or longname in %s" %(compset_name))
             self._compsetname = compset_name
-            self._pesfile = pesfile
+            logger.info("Pes     specification file is %s" %(pesfile))
             self.set_lookup_value("PES_SPEC_FILE", pesfile)
         else:
             expect(False,
@@ -552,95 +555,21 @@ def _get_component_config_data(self, files):
             if result is not None:
                 del self.lookups[key]
 
-    def configure(self, compset_name, grid_name, machine_name=None,
-                  project=None, pecount=None, compiler=None, mpilib=None,
-                  user_compset=False, pesfile=None,
-                  user_grid=False, gridfile=None, ninst=1, test=False,
-                  walltime=None, queue=None, output_root=None, run_unsupported=False, answer=None,
-                  input_dir=None):
-
-        #--------------------------------------------
-        # compset, pesfile, and compset components
-        #--------------------------------------------
-        files = Files()
-        compset_alias, science_support = self._set_compset_and_pesfile(compset_name, files, user_compset=user_compset, pesfile=pesfile)
-
-        self._components = self.get_compset_components()
-        #FIXME - if --user-compset is True then need to determine that
-        #all of the compset settings are valid
-
-        #--------------------------------------------
-        # grid
-        #--------------------------------------------
-        if user_grid is True and gridfile is not None:
-            self.set_value("GRIDS_SPEC_FILE", gridfile)
-        grids = Grids(gridfile)
-
-        gridinfo = grids.get_grid_info(name=grid_name, compset=self._compsetname)
-
-        self._gridname = gridinfo["GRID"]
-        for key,value in gridinfo.items():
-            logger.debug("Set grid %s %s"%(key,value))
-            self.set_lookup_value(key,value)
-
-        #--------------------------------------------
-        # component config data
-        #--------------------------------------------
-        self._get_component_config_data(files)
-
-        self.get_compset_var_settings()
-
-        #--------------------------------------------
-        # machine
-        #--------------------------------------------
-        # set machine values in env_xxx files
-        machobj = Machines(machine=machine_name)
-        probed_machine = machobj.probe_machine_name()
-        machine_name = machobj.get_machine_name()
-        self.set_value("MACH", machine_name)
-        if probed_machine != machine_name and probed_machine is not None:
-            logger.warning("WARNING: User-selected machine '%s' does not match probed machine '%s'" % (machine_name, probed_machine))
-        else:
-            logger.info("Machine is %s" % machine_name)
-
-        nodenames = machobj.get_node_names()
-        nodenames =  [x for x in nodenames if
-                      '_system' not in x and '_variables' not in x and 'mpirun' not in x and\
-                      'COMPILER' not in x and 'MPILIB' not in x]
-
-        for nodename in nodenames:
-            value = machobj.get_value(nodename, resolved=False)
-            type_str = self.get_type_info(nodename)
-            if type_str is not None:
-                logger.debug("machine nodname %s value %s"%(nodename, value))
-                self.set_value(nodename, convert_to_type(value, type_str, nodename))
-
-        if compiler is None:
-            compiler = machobj.get_default_compiler()
-        else:
-            expect(machobj.is_valid_compiler(compiler),
-                   "compiler %s is not supported on machine %s" %(compiler, machine_name))
-
-        self.set_value("COMPILER",compiler)
-
-        if mpilib is None:
-            mpilib = machobj.get_default_MPIlib({"compiler":compiler})
-        else:
-            expect(machobj.is_valid_MPIlib(mpilib, {"compiler":compiler}),
-                   "MPIlib %s is not supported on machine %s" %(mpilib, machine_name))
-        self.set_value("MPILIB",mpilib)
-
-        machdir = machobj.get_machines_dir()
-        self.set_value("MACHDIR", machdir)
-
-        # Create env_mach_specific settings from machine info.
-        env_mach_specific_obj = self.get_env("mach_specific")
-        env_mach_specific_obj.populate(machobj)
-        self.schedule_rewrite(env_mach_specific_obj)
-
+    def _setup_mach_pes(self, pecount, ninst, machine_name, mpilib):
         #--------------------------------------------
         # pe layout
         #--------------------------------------------
+        mach_pes_obj = None
+        # self._pesfile may already be env_mach_pes.xml if so we can just return
+        gfile = GenericXML(infile=self._pesfile)
+        ftype = gfile.get_id()
+        expect(ftype == "env_mach_pes.xml" or ftype == "config_pes", " Do not recognize %s as a valid CIME pes file %s"%(self._pesfile, ftype))
+        if ftype == "env_mach_pes.xml":
+            new_mach_pes_obj = EnvMachPes(infile=self._pesfile, components=self._components)
+            self.update_env(new_mach_pes_obj, "mach_pes")
+            return new_mach_pes_obj.get_value("TOTALPES")
+        pesobj = Pes(self._pesfile)
+
         match1 = re.match('(.+)x([0-9]+)', "" if pecount is None else pecount)
         match2 = re.match('([0-9]+)', "" if pecount is None else pecount)
 
@@ -649,8 +578,6 @@ def configure(self, compset_name, grid_name, machine_name=None,
         pes_rootpe = {}
         other      = {}
 
-        pesobj = Pes(self._pesfile)
-
         force_tasks = None
         force_thrds = None
 
@@ -703,13 +630,13 @@ def configure(self, compset_name, grid_name, machine_name=None,
             mach_pes_obj.set_value(nthrds_str, nthrds)
             mach_pes_obj.set_value(rootpe_str, rootpe)
 
-        maxval = 1
+        pesize = 1
         pes_per_node = self.get_value("PES_PER_NODE")
         for val in totaltasks:
             if val < 0:
                 val = -1*val*pes_per_node
-            if val > maxval:
-                maxval = val
+            if val > pesize:
+                pesize = val
 
         # Make sure that every component has been accounted for
         # set, nthrds and ntasks to 1 otherwise. Also set the ninst values here.
@@ -730,6 +657,97 @@ def configure(self, compset_name, grid_name, machine_name=None,
             if compclass not in pes_nthrds.keys():
                 mach_pes_obj.set_value(compclass,1)
 
+        return pesize
+
+
+    def configure(self, compset_name, grid_name, machine_name=None,
+                  project=None, pecount=None, compiler=None, mpilib=None,
+                  user_compset=False, pesfile=None,
+                  user_grid=False, gridfile=None, ninst=1, test=False,
+                  walltime=None, queue=None, output_root=None, run_unsupported=False, answer=None,
+                  input_dir=None):
+
+        #--------------------------------------------
+        # compset, pesfile, and compset components
+        #--------------------------------------------
+        files = Files()
+        compset_alias, science_support = self._set_compset_and_pesfile(compset_name, files, user_compset=user_compset, pesfile=pesfile)
+
+        self._components = self.get_compset_components()
+        #FIXME - if --user-compset is True then need to determine that
+        #all of the compset settings are valid
+
+        #--------------------------------------------
+        # grid
+        #--------------------------------------------
+        if user_grid is True and gridfile is not None:
+            self.set_value("GRIDS_SPEC_FILE", gridfile)
+        grids = Grids(gridfile)
+
+        gridinfo = grids.get_grid_info(name=grid_name, compset=self._compsetname)
+
+        self._gridname = gridinfo["GRID"]
+        for key,value in gridinfo.items():
+            logger.debug("Set grid %s %s"%(key,value))
+            self.set_lookup_value(key,value)
+
+        #--------------------------------------------
+        # component config data
+        #--------------------------------------------
+        self._get_component_config_data(files)
+
+        self.get_compset_var_settings()
+
+        #--------------------------------------------
+        # machine
+        #--------------------------------------------
+        # set machine values in env_xxx files
+        machobj = Machines(machine=machine_name)
+        probed_machine = machobj.probe_machine_name()
+        machine_name = machobj.get_machine_name()
+        self.set_value("MACH", machine_name)
+        if probed_machine != machine_name and probed_machine is not None:
+            logger.warning("WARNING: User-selected machine '%s' does not match probed machine '%s'" % (machine_name, probed_machine))
+        else:
+            logger.info("Machine is %s" % machine_name)
+
+        nodenames = machobj.get_node_names()
+        nodenames =  [x for x in nodenames if
+                      '_system' not in x and '_variables' not in x and 'mpirun' not in x and\
+                      'COMPILER' not in x and 'MPILIB' not in x]
+
+        for nodename in nodenames:
+            value = machobj.get_value(nodename, resolved=False)
+            type_str = self.get_type_info(nodename)
+            if type_str is not None:
+                logger.debug("machine nodname %s value %s"%(nodename, value))
+                self.set_value(nodename, convert_to_type(value, type_str, nodename))
+
+        if compiler is None:
+            compiler = machobj.get_default_compiler()
+        else:
+            expect(machobj.is_valid_compiler(compiler),
+                   "compiler %s is not supported on machine %s" %(compiler, machine_name))
+
+        self.set_value("COMPILER",compiler)
+
+        if mpilib is None:
+            mpilib = machobj.get_default_MPIlib({"compiler":compiler})
+        else:
+            expect(machobj.is_valid_MPIlib(mpilib, {"compiler":compiler}),
+                   "MPIlib %s is not supported on machine %s" %(mpilib, machine_name))
+        self.set_value("MPILIB",mpilib)
+
+        machdir = machobj.get_machines_dir()
+        self.set_value("MACHDIR", machdir)
+
+        # Create env_mach_specific settings from machine info.
+        env_mach_specific_obj = self.get_env("mach_specific")
+        env_mach_specific_obj.populate(machobj)
+        self.schedule_rewrite(env_mach_specific_obj)
+
+        pesize = self._setup_mach_pes(pecount, ninst, machine_name, mpilib)
+
         #--------------------------------------------
         # batch system
         #--------------------------------------------
@@ -741,7 +759,7 @@ def configure(self, compset_name, grid_name, machine_name=None,
 
         env_batch.set_batch_system(batch, batch_system_type=batch_system_type)
         env_batch.create_job_groups(bjobs)
-        env_batch.set_job_defaults(bjobs, pesize=maxval, walltime=walltime, force_queue=queue, allow_walltime_override=test)
+        env_batch.set_job_defaults(bjobs, pesize=pesize, walltime=walltime, force_queue=queue, allow_walltime_override=test)
         self.schedule_rewrite(env_batch)
 
         #--------------------------------------------
@@ -1246,3 +1264,21 @@ def set_file(self, xmlfile):
                     break
 
         self._files = self._env_entryid_files + self._env_generic_files
+
+    def update_env(self, new_object, env_file):
+        """
+        Replace a case env object file
+        """
+        old_object = self.get_env(env_file)
+        new_object.filename = old_object.filename
+        if old_object in self._env_entryid_files:
+            self._env_entryid_files.remove(old_object)
+            self._env_entryid_files.append(new_object)
+        elif old_object in self._env_generic_files:
+            self._env_generic_files.remove(old_object)
+            self._env_generic_files.append(new_object)
+        if old_object in self._env_files_that_need_rewrite:
+            self._env_files_that_need_rewrite.remove(old_object)
+        self._files.remove(old_object)
+        self._files.append(new_object)
+        self.schedule_rewrite(new_object)