Merge pull request #47 from bertinia/master

NCAR · Dec 11, 2016 · 2bf3031 · 2bf3031
2 parents 6625ef7 + d94aabe
commit 2bf3031
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Showing 10 changed files with 170 additions and 102 deletions.
diff --git a/Config/config_postprocess.xml b/Config/config_postprocess.xml
@@ -53,55 +53,55 @@
 
       <entry id="ATM_GRID"
 	     type="string"
-	     valid_values=""  
+	     valid_values="0.9x1.25"  
 	     value="inherit"
 	     group="case_info"
 	     desc="Atmosphere model grid"
 	     ></entry> 
 
       <entry id="ICE_GRID"
 	     type="string"
-	     valid_values=""  
+	     valid_values="gx1v6" 
 	     value="inherit"
 	     group="case_info"
 	     desc="Sea-Ice model grid"
 	     ></entry> 
 
       <entry id="ICE_NX"
 	     type="string"
-	     valid_values=""  
+	     valid_values="320"  
 	     value="inherit"
 	     group="case_info"
 	     desc="Sea-Ice model grid NX - default 320 for 1-degree ocean grid"
 	     ></entry> 
 
       <entry id="ICE_NY"
 	     type="string"
-	     valid_values=""  
+	     valid_values="384"
 	     value="inherit"
 	     group="case_info"
 	     desc="Sea-Ice model grid NY - default 384 for 1-degree ocean grid"
 	     ></entry> 
 
       <entry id="LND_GRID"
 	     type="string"
-	     valid_values=""  
+	     valid_values="0.9x1.25"
 	     value="inherit"
 	     group="case_info"
 	     desc="Land model grid"
 	     ></entry> 
 
       <entry id="OCN_GRID"
 	     type="string"
-	     valid_values=""  
+	     valid_values="gx1v6"   
 	     value="inherit"
 	     group="case_info"
 	     desc="Ocean model grid"
 	     ></entry> 
 
       <entry id="CESM_TAG"
 	     type="string"
-	     valid_values=""  
+	     valid_values="cesm2_0_beta05"  
 	     value="inherit"
 	     group="case_info"
 	     desc="CESM tag used to create this case"
@@ -215,23 +215,23 @@
 
       <entry id="GLOBAL_WEBHOST"
 	     type="char"
-	     valid_values=""
+	     valid_values="http://some-remote-host"
 	     value=""
 	     group="web_options"
 	     desc="Remote web host machine to serve HTML pages and diagnostics plots."
 	     ></entry>
 
       <entry id="GLOBAL_WEBLOGIN"
 	     type="char"
-	     valid_values=""
+	     valid_values="remote-username"
 	     value=""
 	     group="web_options"
 	     desc="Remote web host login name which can be used with ssh keys. If ssh key is not setup, then will prompt for login on remote web host machine."
 	     ></entry>
 
       <entry id="GLOBAL_REMOTE_WEBDIR"
 	     type="char"
-	     valid_values=""
+	     valid_values="/path/to/diags/$CASE/"
 	     value=""
 	     group="web_options"
 	     desc="Remote machine path to diagnostics directory."

diff --git a/Machines/machine_postprocess.xml b/Machines/machine_postprocess.xml
@@ -34,26 +34,26 @@
     </modules>
     <components>
       <component name="atm">
-	<averages_pes queue="regular" pes_per_node="15" wallclock="00:30">128</averages_pes>
-	<diagnostics_pes queue="geyser" pes_per_node="8" wallclock="02:00">16</diagnostics_pes>
+	<averages_pes queue="geyser" pes_per_node="4" wallclock="2:00">16</averages_pes>
+	<diagnostics_pes queue="geyser" pes_per_node="4" wallclock="02:00">16</diagnostics_pes>
 	<regrid_pes queue="geyser" pes_per_node="2" wallclock="02:00">6</regrid_pes>
 	<obs_root>/glade/p/cesm/amwg/amwg_data</obs_root>
       </component>
       <component name="ice">
-	<averages_pes queue="regular" pes_per_node="15" wallclock="00:30">128</averages_pes>
+	<averages_pes queue="geyser" pes_per_node="4" wallclock="02:00">16</averages_pes>
 	<diagnostics_pes queue="geyser" pes_per_node="2" wallclock="01:00">4</diagnostics_pes>
 	<obs_root>/glade/p/cesm/pcwg/ice/data</obs_root>
       </component>
       <component name="lnd">
-	<averages_pes queue="regular" pes_per_node="15" wallclock="02:00">128</averages_pes>
+	<averages_pes queue="geyser" pes_per_node="4" wallclock="02:00">16</averages_pes>
 	<diagnostics_pes queue="geyser" pes_per_node="4" wallclock="02:00">12</diagnostics_pes>
 	<regrid_pes queue="geyser" pes_per_node="2" wallclock="02:00">6</regrid_pes>
 	<obs_root>/glade/p/cesm/lmwg/diag/lnd_diag_data</obs_root>
       </component>
       <component name="ocn">
-	<averages_pes queue="regular" pes_per_node="15" wallclock="00:30">128</averages_pes>
+	<averages_pes queue="geyser" pes_per_node="4" wallclock="02:00">16</averages_pes>
 	<diagnostics_pes queue="geyser" pes_per_node="4" wallclock="02:00">16</diagnostics_pes>
-	<obs_root>/glade/p/cesm</obs_root>
+	<obs_root>/glade/p/cesm/</obs_root>
       </component>
     </components>
   </machine>

diff --git a/Templates/env_diags.tmpl b/Templates/env_diags.tmpl
@@ -23,7 +23,8 @@
 <!-- {{ comment }} -->
 <!-- ======================================================================= -->
        {% for xml in v %}
-<!-- {{ xml._desc }} -->
+<!-- ** Description:  {{ xml._desc }} -->
+<!-- ** Valid Values: {{ xml._valid_values }} -->
 <entry id="{{ xml._id }}" value="{{ xml._value }}" />
        {% endfor %}
     {% endif %}

diff --git a/Templates/env_postprocess.tmpl b/Templates/env_postprocess.tmpl
@@ -22,7 +22,7 @@
 <!-- {{ comment }} -->
 <!-- ======================================================================= -->
        {% for xml in v %}
-<!-- {{ xml._desc }} -->
+<!-- ** Description: {{ xml._desc }} --> 
 <entry id="{{ xml._id }}" value="{{ xml._value }}" />
        {% endfor %}
     {% endif %}

diff --git a/cesm_utils/cesm_utils/create_postprocess b/cesm_utils/cesm_utils/create_postprocess
@@ -94,10 +94,11 @@ import jinja2
 # define a class to be used for the xml entry, id, desc values
 # -------------------------------------------------------------------------------
 class XmlEntry(object):
-    def __init__(self, id, value, desc):
+    def __init__(self, id, value, desc, valid_values):
         self._id = id
         self._value = value
         self._desc = desc
+        self._valid_values = valid_values
 
     def id(self):
         return self._id
@@ -108,6 +109,9 @@ class XmlEntry(object):
     def desc(self):
         return self._desc
 
+    def valid_values(self):
+        return self._valid_values
+
 # -------------------------------------------------------------------------------
 # commandline_options - parse any command line options
 # -------------------------------------------------------------------------------
@@ -204,9 +208,11 @@ def create_env_file(envDict, configFile, tmplFile, envFile, obs_root, comp, stan
         for entry_tag in group_tag.findall('entry'):
             # check if the value needs to be inherited from the envDict
             if entry_tag.get('value') == 'inherit':
-                xml_list.append(XmlEntry(entry_tag.get('id'), envDict[entry_tag.get('id')], entry_tag.get('desc')))
+                xml_list.append(XmlEntry(entry_tag.get('id'), envDict[entry_tag.get('id')], 
+                                         entry_tag.get('desc'), entry_tag.get('valid_values')))
             else:
-                xml_list.append(XmlEntry(entry_tag.get('id'), entry_tag.get('value'), entry_tag.get('desc')))
+                xml_list.append(XmlEntry(entry_tag.get('id'), entry_tag.get('value'), 
+                                         entry_tag.get('desc'), entry_tag.get('valid_values')))
 
         group_dict = { 'order' : order, 'name' : name, 'comment' : comment, 'xml_list' : xml_list }
         group_list.append(group_dict)
@@ -217,9 +223,8 @@ def create_env_file(envDict, configFile, tmplFile, envFile, obs_root, comp, stan
     xml_list = list()
     if obs_root:
         if len(obs_root) > 0:
-            xml_obs = XmlEntry('{0}DIAG_DIAGOBSROOT'.format(comp.upper()), 
-                               obs_root, 
-                               'Machine dependent diagnostics observation files root path')
+            xml_obs = XmlEntry('{0}DIAG_DIAGOBSROOT'.format(comp.upper()), obs_root, 
+                               'Machine dependent diagnostics observation files root path', '')
             xml_list.append(xml_obs)
 
     # the xml_list now contains a list of XmlEntry classes that can be written to the template
@@ -562,7 +567,8 @@ def main(options):
         config_file = '{0}/diagnostics/diagnostics/{1}/Config/config_diags_{1}.xml'.format(envDict['POSTPROCESS_PATH'], comp)
         tmpl_file = 'env_diags.tmpl'
         env_file = '{0}/env_diags_{1}.xml'.format(envDict['PP_CASE_PATH'], comp)
-        create_env_file(envDict, config_file, tmpl_file, env_file, machine['{0}_obs_root'.format(comp)], comp, standalone)
+        create_env_file(envDict, config_file, tmpl_file, env_file, machine['{0}_obs_root'.format(comp)], 
+                        comp, standalone)
 
     # define the template files for the batch scripts
     batch_tmpl = 'batch_{0}.tmpl'.format(envDict['MACH'])
@@ -575,39 +581,47 @@ def main(options):
 
     create_batch(envDict['POSTPROCESS_PATH'], machine['timeseries_pes'], batch_tmpl, run_tmpl, postProcessCmd, 
                  machine['mpi_command'], outFile, processName, machine['project'], machine['pythonpath'], 
-                 envDict['PP_CASE_PATH'], machine['reset_modules'], machine['modules'], machine['timeseries_queue'], 
-                 machine['timeseries_ppn'], machine['timeseries_wallclock'], options, standalone)
+                 envDict['PP_CASE_PATH'], machine['reset_modules'], machine['modules'], 
+                 machine['timeseries_queue'], machine['timeseries_ppn'], machine['timeseries_wallclock'], 
+                 options, standalone)
 
     # generate the diagnostics batch submit scripts from template files
     for comp in compList:
         # generate the averages batch submit script
         postProcessCmd = '{0}_avg_generator.py'.format(comp)
         processName = '{0}_averages'.format(comp)
         outFile = '{0}/{1}'.format(envDict['PP_CASE_PATH'], processName)
-        create_batch(envDict['POSTPROCESS_PATH'], machine['{0}_averages_pes'.format(comp)], batch_tmpl, run_tmpl, postProcessCmd, 
-                     machine['mpi_command'], outFile, processName, machine['project'], machine['pythonpath'], 
-                     envDict['PP_CASE_PATH'], machine['reset_modules'], machine['modules'], machine['{0}_averages_queue'.format(comp)], 
-                     machine['{0}_averages_ppn'.format(comp)], machine['{0}_averages_wallclock'.format(comp)], options, standalone)
+        create_batch(envDict['POSTPROCESS_PATH'], machine['{0}_averages_pes'.format(comp)], batch_tmpl, 
+                     run_tmpl, postProcessCmd, machine['mpi_command'], outFile, processName, 
+                     machine['project'], machine['pythonpath'], envDict['PP_CASE_PATH'], 
+                     machine['reset_modules'], machine['modules'], machine['{0}_averages_queue'.format(comp)], 
+                     machine['{0}_averages_ppn'.format(comp)], machine['{0}_averages_wallclock'.format(comp)],
+                     options, standalone)
 
         # generate the diagnostics batch submit script
         postProcessCmd = '{0}_diags_generator.py'.format(comp)
         processName = '{0}_diagnostics'.format(comp)
         outFile = '{0}/{1}'.format(envDict['PP_CASE_PATH'], processName)
-        create_batch(envDict['POSTPROCESS_PATH'], machine['{0}_diagnostics_pes'.format(comp)], batch_tmpl, run_tmpl, postProcessCmd, 
-                     machine['mpi_command'], outFile, processName, machine['project'], machine['pythonpath'], 
-                     envDict['PP_CASE_PATH'],  machine['reset_modules'], machine['modules'], machine['{0}_diagnostics_queue'.format(comp)],
-                     machine['{0}_diagnostics_ppn'.format(comp)], machine['{0}_diagnostics_wallclock'.format(comp)], options, standalone)
+        create_batch(envDict['POSTPROCESS_PATH'], machine['{0}_diagnostics_pes'.format(comp)], batch_tmpl, 
+                     run_tmpl, postProcessCmd, machine['mpi_command'], outFile, processName, 
+                     machine['project'], machine['pythonpath'], envDict['PP_CASE_PATH'],  
+                     machine['reset_modules'], machine['modules'], 
+                     machine['{0}_diagnostics_queue'.format(comp)],
+                     machine['{0}_diagnostics_ppn'.format(comp)], 
+                     machine['{0}_diagnostics_wallclock'.format(comp)], options, standalone)
 
     # generate the regrid batch submit scripts from template files
     for comp in regridList:
         # generate the regrid batch submit script
         postProcessCmd = '{0}_regrid_generator.py'.format(comp)
         processName = '{0}_regrid'.format(comp)
         outFile = '{0}/{1}'.format(envDict['PP_CASE_PATH'], processName)
-        create_batch(envDict['POSTPROCESS_PATH'], machine['{0}_regrid_pes'.format(comp)], batch_tmpl, run_tmpl, postProcessCmd, 
-                     machine['mpi_command'], outFile, processName, machine['project'], machine['pythonpath'], 
-                     envDict['PP_CASE_PATH'],  machine['reset_modules'], machine['modules'], machine['{0}_regrid_queue'.format(comp)], 
-                     machine['{0}_regrid_ppn'.format(comp)], machine['{0}_regrid_wallclock'.format(comp)], options, standalone)
+        create_batch(envDict['POSTPROCESS_PATH'], machine['{0}_regrid_pes'.format(comp)], batch_tmpl, 
+                     run_tmpl, postProcessCmd, machine['mpi_command'], outFile, processName, 
+                     machine['project'], machine['pythonpath'], envDict['PP_CASE_PATH'],  
+                     machine['reset_modules'], machine['modules'], machine['{0}_regrid_queue'.format(comp)], 
+                     machine['{0}_regrid_ppn'.format(comp)], machine['{0}_regrid_wallclock'.format(comp)], 
+                     options, standalone)
 
     # copy some tools to the PP_CASE_PATH
     files_to_copy = ['copy_html', 'pp_config', 'create_env_script', 'env_file.xsd']

diff --git a/diagnostics/diagnostics/ice/Config/config_diags_ice.xml b/diagnostics/diagnostics/ice/Config/config_diags_ice.xml
@@ -45,6 +45,16 @@
          desc="Controls whether to generate model vs. model diagnostics"
          ></entry>
 
+  <entry id="ICEDIAG_netcdf_format"
+         type="string"
+         valid_values="netcdf, netcdf4, netcdf4c, netcdfLarge"
+         value="netcdf"
+         group="global"
+         desc="Output NetCDF file format - either 'netcdf4c' (netcdf4 compressed (lev=1)), 
+'netcdf4' (netcdf classic), 'netcdf' (netcdf3 classic), or netcdfLarge for high-resolution data sets. DEFAULT = 'netcdf'. 
+Applies to both model and control cases."
+         ></entry>
+
   <entry id="ICEDIAG_CLEANUP_FILES"
          type="logical"
          valid_values="True/False"