Merge branch 'master' into lnd2glc_bilinear

Merging in latest version of master for the sake of testing the integration
ESMCI · May 25, 2017 · 6d8cda5 · 6d8cda5
2 parents bb9b17a + 2deb949
commit 6d8cda5
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diff --git a/ChangeLog b/ChangeLog
diff --git a/config/acme/machines/config_machines.xml b/config/acme/machines/config_machines.xml
@@ -630,7 +630,6 @@
 <machine MACH="anlworkstation">
     <DESC>Linux workstation for ANL</DESC>
     <NODENAME_REGEX>compute.*mcs.anl.gov</NODENAME_REGEX>
-    <PROXY></PROXY>
     <TESTS>acme_developer</TESTS>
     <OS>LINUX</OS>
     <COMPILERS>gnu</COMPILERS>

diff --git a/config/acme/machines/template.case.test b/config/acme/machines/template.case.test
@@ -1,14 +1,10 @@
 #!/usr/bin/env python
-
-# Batch system directives
 {{ batchdirectives }}
-
 """
 This is the system test submit script for CIME. This should only ever be called
 by case.submit when on batch system. This script only exists as a way of providing
 batch directives. Use case.submit from the command line to run your case.
 """
-
 import os, sys
 os.chdir( '{{ caseroot }}')
 
@@ -50,12 +46,15 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
     parser.add_argument("--caseroot",
                         help="Case directory to build")
 
+    parser.add_argument("--reset", action="store_true",
+                        help="Reset the case to its original state as defined by config_tests.xml")
+
     args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     if args.caseroot is not None:
         os.chdir(args.caseroot)
 
-    return args.caseroot, args.testname
+    return args.caseroot, args.testname, args.reset
 
 ###############################################################################
 def _main_func(description):
@@ -64,9 +63,9 @@ def _main_func(description):
         test_results = doctest.testmod(verbose=True)
         sys.exit(1 if test_results.failed > 0 else 0)
 
-    caseroot, testname = parse_command_line(sys.argv, description)
+    caseroot, testname, reset = parse_command_line(sys.argv, description)
     with Case(caseroot, read_only=False) as case:
-        success = case_test(case, testname)
+        success = case_test(case, testname, reset)
 
     sys.exit(0 if success else 1)
 

diff --git a/config/cesm/config_grids.xml b/config/cesm/config_grids.xml
@@ -8,11 +8,11 @@
     =========================================
     The notation for the grid longname is
         a%name_l%name_oi%name_r%name_m%mask_g%name_w%name
-    where     
+    where
         a% => atm, l% => lnd, oi% => ocn/ice, r% => river, m% => mask, g% => glc, w% => wav
 
     Supported out of the box grid configurations are given via alias specification in
-    the file "config_grids.xml". Each grid alias can also be associated  with the 
+    the file "config_grids.xml". Each grid alias can also be associated  with the
     following optional attributes
 
     compset       (Regular expression for compset matches that are required for this grid)
@@ -35,12 +35,15 @@
       <grid name="rof"    compset="MOSART">r05</grid>
       <grid name="rof"    compset="DROF"  >rx1</grid>
       <grid name="rof"    compset="DROF%CPLHIST">r05</grid>
+      <grid name="rof"    compset="XROF"  >r05</grid>
       <grid name="glc"	  compset="SGLC"  >null</grid>
       <grid name="glc"	  compset="CISM1" >gland5UM</grid>
       <grid name="glc"	  compset="CISM2" >gland4</grid>
+      <grid name="glc"    compset="XGLC"  >gland4</grid>
       <grid name="wav"	  compset="SWAV"  >null</grid>
       <grid name="wav"	  compset="DWAV"  >ww3a</grid>
       <grid name="wav"	  compset="WW3"	  >ww3a</grid>
+      <grid name="wav"    compset="XWAV"  >ww3a</grid>
     </model_grid_defaults>
 
     <model_grid alias="g16_g16" compset="DATM.+DROF">
@@ -586,7 +589,7 @@
       <grid name="ocnice">10x15</grid>
       <mask>usgs</mask>
     </model_grid>
-    
+
     <model_grid alias="f10_f10_musgs" not_compset="_POP">
       <grid name="atm">10x15</grid>
       <grid name="lnd">10x15</grid>
@@ -971,6 +974,8 @@
       <nx>144</nx>  <ny>96</ny>
       <file grid="atm|lnd" mask="gx1v6">domain.lnd.fv1.9x2.5_gx1v6.090206.nc</file>
       <file grid="ocnice"  mask="gx1v6">domain.ocn.1.9x2.5_gx1v6_090403.nc</file>
+      <file grid="atm|lnd" mask="gx1v7">domain.lnd.fv1.9x2.5_gx1v7.170518.nc</file>
+      <file grid="ocnice"  mask="gx1v7">domain.ocn.fv1.9x2.5_gx1v7.170518.nc</file>
       <file grid="ocnice"  mask="null">domain.aqua.fv1.9x2.5.nc</file>
       <desc>1.9x2.5 is FV 2-deg grid:</desc>
     </domain>
@@ -1089,8 +1094,8 @@
 
     <domain name="gx1v7">
       <nx>320</nx>  <ny>384</ny>
-      <file grid="atm|lnd">$DIN_LOC_ROOT/share/domains/domain.ocn.gx1v7.151020.nc</file>
-      <file grid="ocnice">$DIN_LOC_ROOT/share/domains/domain.ocn.gx1v7.151020.nc</file>
+      <file grid="atm|lnd">$DIN_LOC_ROOT/share/domains/domain.ocn.gx1v7.151008.nc</file>
+      <file grid="ocnice">$DIN_LOC_ROOT/share/domains/domain.ocn.gx1v7.151008.nc</file>
       <desc>gx1v7 is displaced Greenland pole 1-deg grid with Caspian as a land feature:</desc>
     </domain>
 
@@ -1154,7 +1159,7 @@
     </domain>
 
     <domain name="gland4">
-      <nx>376</nx> <ny>701</ny>
+      <nx>416</nx> <ny>704</ny>
       <desc>4-km Greenland grid, for use with the glissade dycore</desc>
     </domain>
 
@@ -1264,6 +1269,13 @@
       <map name="OCN2ATM_FMAPNAME">cpl/gridmaps/gx1v6/map_gx1v6_TO_fv1.9x2.5_aave.130322.nc</map>
       <map name="OCN2ATM_SMAPNAME">cpl/gridmaps/gx1v6/map_gx1v6_TO_fv1.9x2.5_aave.130322.nc</map>
     </gridmap>
+    <gridmap atm_grid="1.9x2.5" ocn_grid="gx1v7">
+      <map name="ATM2OCN_FMAPNAME">cpl/gridmaps/fv1.9x2.5/map_fv1.9x2.5_TO_gx1v7_aave.170518.nc</map>
+      <map name="ATM2OCN_SMAPNAME">cpl/gridmaps/fv1.9x2.5/map_fv1.9x2.5_TO_gx1v7_blin.170518.nc</map>
+      <map name="ATM2OCN_VMAPNAME">cpl/gridmaps/fv1.9x2.5/map_fv1.9x2.5_TO_gx1v7_patc.170518.nc</map>
+      <map name="OCN2ATM_FMAPNAME">cpl/gridmaps/gx1v7/map_gx1v7_TO_fv1.9x2.5_aave.170518.nc</map>
+      <map name="OCN2ATM_SMAPNAME">cpl/gridmaps/gx1v7/map_gx1v7_TO_fv1.9x2.5_aave.170518.nc</map>
+    </gridmap>
     <gridmap atm_grid="1.9x2.5" ocn_grid="tx1v1">
       <map name="ATM2OCN_FMAPNAME">cpl/cpl6/map_fv1.9x2.5_to_tx1v1_aave_da_090710.nc</map>
       <map name="ATM2OCN_SMAPNAME">cpl/cpl6/map_fv1.9x2.5_to_tx1v1_bilin_da_090710.nc</map>
@@ -1476,6 +1488,12 @@
       <map name="ICE2WAV_SMAPNAME">cpl/gridmaps/gx1v7/map_gx1v7_TO_ww3a_splice_170214.nc</map>
     </gridmap>
 
+    <gridmap ocn_grid="tx1v1" wav_grid="ww3a">
+      <map name="WAV2OCN_SMAPNAME">cpl/gridmaps/ww3a/map_ww3a_TO_tx1v1_blin.170523.nc</map>
+      <map name="OCN2WAV_SMAPNAME">cpl/gridmaps/tx1v1/map_tx1v1_TO_ww3a_blin.170523.nc</map>
+      <map name="ICE2WAV_SMAPNAME">cpl/gridmaps/tx1v1/map_tx1v1_TO_ww3a_blin.170523.nc</map>
+    </gridmap>
+
     <gridmap atm_grid="48x96" wav_grid="ww3a">
       <map name="ATM2WAV_SMAPNAME">cpl/gridmaps/T31/map_T31_TO_ww3a_bilin_131104.nc</map>
     </gridmap>
@@ -1655,17 +1673,6 @@
       <map name="ROF2OCN_ICE_RMAPNAME">cpl/cpl6/map_r01_to_gx1v6_120711.nc</map>
     </gridmap>
 
-    <!--- river flooding variables -->
-
-    <gridmap lnd_grid="1.9x2.5" rof_grid="r05" ocn_grid="gx1v6" >
-      <map name="XROF_FLOOD_MODE">ACTIVE</map>
-    </gridmap>
-
-    <gridmap lnd_grid="1.9x2.5" rof_grid="r05" ocn_grid="gx1v7" >
-      <map name="XROF_FLOOD_MODE">ACTIVE</map>
-    </gridmap>
-
-
     <!-- ======================================================== -->
     <!-- gridS: lnd to glc and glc to lnd mapping                 -->
     <!--                                                          -->

diff --git a/config/cesm/machines/config_machines.xml b/config/cesm/machines/config_machines.xml
@@ -216,7 +216,7 @@
 	<arg name="anum_tasks"> -np $TOTALPES</arg>
 	<arg name="labelstdout">-p "%g:"</arg>
 	<!-- the omplace argument needs to be last -->
-	<arg name="zthreadplacement"> omplace </arg>
+	<arg name="zthreadplacement"> omplace -tm open64 </arg>
       </arguments>
     </mpirun>
     <mpirun mpilib="default" unit_testing="true">
@@ -259,7 +259,7 @@
 	<command name="load">gnu/6.3.0</command>
       </modules>
       <modules>
-	<command name="load">mpt/2.15</command>
+	<command name="load">mpt/2.15f</command>
 	<command name="load">ncarcompilers/0.3.5</command>
       </modules>
       <modules mpilib="mpi-serial">
@@ -878,7 +878,7 @@
 	<command name="load">  tool/parallel-netcdf/1.7.0/intel/mvapich2  </command>
       </modules>
       <modules compiler="pgi">
-	<command name="load">compiler/pgi/15.1</command>
+	<command name="load">compiler/pgi/17.04</command>
       </modules>
       <modules  compiler="pgi" mpilib="mvapich2">
 	  <command name="load">  tool/parallel-netcdf/1.6.1/pgi/mvapich2  </command>

diff --git a/config/cesm/machines/template.case.test b/config/cesm/machines/template.case.test
@@ -46,12 +46,15 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
     parser.add_argument("--caseroot",
                         help="Case directory to build")
 
+    parser.add_argument("--reset", action="store_true",
+                        help="Reset the case to its original state as defined by config_tests.xml")
+
     args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     if args.caseroot is not None:
         os.chdir(args.caseroot)
 
-    return args.caseroot, args.testname
+    return args.caseroot, args.testname, args.reset
 
 ###############################################################################
 def _main_func(description):
@@ -60,9 +63,9 @@ def _main_func(description):
         test_results = doctest.testmod(verbose=True)
         sys.exit(1 if test_results.failed > 0 else 0)
 
-    caseroot, testname = parse_command_line(sys.argv, description)
+    caseroot, testname, reset = parse_command_line(sys.argv, description)
     with Case(caseroot, read_only=False) as case:
-        success = case_test(case, testname)
+        success = case_test(case, testname, reset)
 
     sys.exit(0 if success else 1)
 

diff --git a/config/xml_schemas/config_compsets.xsd b/config/xml_schemas/config_compsets.xsd
@@ -11,7 +11,6 @@
   <xs:element name="alias" type="xs:NCName"/>
   <xs:element name="lname" type="xs:string"/>
   <xs:element name="science_support"/>
-  <xs:element name="user_mods" type="xs:string"/>
 
   <!-- complex elements -->
 
@@ -33,9 +32,7 @@
         <xs:element ref="alias"/>
         <xs:element ref="lname"/>
 	<xs:element ref="science_support" minOccurs="0" maxOccurs="unbounded"/>
-	<xs:element ref="user_mods" minOccurs="0" maxOccurs="1"/>
       </xs:sequence>
-      <xs:attribute ref="grid"/>
     </xs:complexType>
   </xs:element>
 
@@ -68,8 +65,8 @@
   <xs:element name="value">
     <xs:complexType>
       <xs:simpleContent>
-        <xs:extension base="xs:NMTOKEN">
-          <xs:attribute ref="compset" use="required"/>
+        <xs:extension base="xs:string">
+          <xs:attribute ref="compset"/>
           <xs:attribute ref="grid"/>
         </xs:extension>
       </xs:simpleContent>

diff --git a/config/xml_schemas/env_mach_specific.xsd b/config/xml_schemas/env_mach_specific.xsd
@@ -23,9 +23,9 @@
       <xs:sequence>
         <xs:element ref="header"/>
         <xs:element ref="module_system"/>
-        <xs:element maxOccurs="unbounded" ref="environment_variables"/>
-        <xs:element maxOccurs="unbounded" ref="mpirun"/>
-        <xs:element maxOccurs="unbounded" ref="entry"/>
+        <xs:element minOccurs="0" maxOccurs="unbounded" ref="environment_variables"/>
+        <xs:element minOccurs="0" maxOccurs="unbounded" ref="mpirun"/>
+        <xs:element minOccurs="0" maxOccurs="unbounded" ref="entry"/>
       </xs:sequence>
       <xs:attribute ref="id" use="required"/>
       <xs:attribute ref="version" use="required"/>
@@ -35,9 +35,9 @@
   <xs:element name="module_system">
     <xs:complexType>
       <xs:sequence>
-        <xs:element maxOccurs="unbounded" ref="init_path"/>
-        <xs:element maxOccurs="unbounded" ref="cmd_path"/>
-        <xs:element maxOccurs="unbounded" ref="modules"/>
+        <xs:element minOccurs="0" maxOccurs="unbounded" ref="init_path"/>
+        <xs:element minOccurs="0" maxOccurs="unbounded" ref="cmd_path"/>
+        <xs:element minOccurs="0" maxOccurs="unbounded" ref="modules"/>
       </xs:sequence>
       <xs:attribute name="type" use="required" type="xs:NCName"/>
     </xs:complexType>

diff --git a/scripts/Tools/xmlconvertors/config_pes_converter.py b/scripts/Tools/xmlconvertors/config_pes_converter.py
@@ -1,7 +1,8 @@
 #!/usr/bin/env python
 """
-config_pes_converter.py -- convert (or verify) config_pesfrom CIME2 format
-    to CIME5
+config_pes_converter.py -- convert (or verify) config_pes elements from CIME2
+format to CIME5. This tool will compare the two versions and suggest updates to
+the CIME5 file.
 
 The location of these files are needed by the script:
     CIME2: cime/machines-acme/config_pes.xml
@@ -25,14 +26,15 @@ def parse_command_line(args):
     CIME.utils.setup_standard_logging_options(parser)
 
     # Set command line options
-    parser.add_argument("-cime2file", "--cime2file", help="location of config_grid.xml file in CIME2 repository")
-    parser.add_argument("-cime5file", "--cime5file", help="location of config_grids.xml file in CIME5 repository")
+    parser.add_argument("-cime2file", "--cime2file",
+                        help="location of config_grid.xml file in CIME2 format",
+                        required=True)
+    parser.add_argument("-cime5file", "--cime5file",
+                        help="location of config_grids.xml file in CIME5 format",
+                        required=True)
 
-    CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
-
-    if args.cime2file is None or args.cime5file is None:
-        parser.print_help()
-        exit()
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args,
+                                                                     parser)
 
     return args.cime2file, args.cime5file
 
@@ -176,18 +178,23 @@ class PesTree(grid_xml_converter.DataTree):
     def __init__(self, xmlfilename):
         # original xml file has bad comments
         import re, StringIO
-        with open(xmlfilename,'r') as xmlfile:
-            t1 = xmlfile.read()
-            t2 = re.sub(r'(?<=<!--)([ -]+)',
-                        lambda x: x.group(0).replace('-',' '), t1)
-            t3 = re.sub(r'([ -]+)(?=-->)',
-                        lambda x: x.group(0).replace('-',' '), t2)
-            tempxml = StringIO.StringIO(t3)
-            super(PesTree, self).__init__(tempxml)
-            tempxml.close()
+        if os.access(xmlfilename, os.R_OK):
+            with open(xmlfilename, 'r') as xmlfile:
+                t1 = xmlfile.read()
+                t2 = re.sub(r'(?<=<!--)([ -]+)',
+                            lambda x: x.group(0).replace('-', ' '), t1)
+                t3 = re.sub(r'([ -]+)(?=-->)',
+                            lambda x: x.group(0).replace('-', ' '), t2)
+                tempxml = StringIO.StringIO(t3)
+                super(PesTree, self).__init__(tempxml)
+                tempxml.close()
 
+        else:
+            super(PesTree, self).__init__(xmlfilename)
 
     def populate(self):
+        if self.root is None:
+            return
         xmlnodes = self.root.findall('grid')
         nodeclass = Cime5PesNode
 
@@ -256,7 +263,7 @@ def diff_tree(atree, btree):
     LOGGER.info("Number of wrong nodes: %d" % len(fixlist))
     LOGGER.info("Number of missing nodes: %d" % len(addlist))
     for miss in addlist:
-        LOGGER.info(miss[0].keyvalue())
+        LOGGER.debug(miss[0].keyvalue())
     LOGGER.info("Number of duplicate nodes: %d" % len(duplist))
     for dup in duplist:
         LOGGER.info(dup)