Update CIME to ESMCI cime5.8.2-3

cime/README.md

@@ -38,3 +38,7 @@ of NSF's Division of Atmospheric and Geospace Sciences.
 # License
 
 CIME is free software made available under the BSD License. For details see the LICENSE file.
+
+# Digital Object Identifier
+
+DOI:[10.5065/WE0D-9K91](http://dx.doi.org/10.5065/WE0D-9K91)

cime/config/cesm/config_grids.xml

@@ -1412,6 +1412,7 @@
       <file grid="ocnice"  mask="tx0.1v2">$DIN_LOC_ROOT/share/domains/domain.ocn.tx0.1v2.161014.nc</file>
       <file grid="atm|lnd" mask="tx0.1v3">$DIN_LOC_ROOT/share/domains/domain.lnd.TL319_tx0.1v3.170730.nc</file>
       <file grid="ocnice"  mask="tx0.1v3">$DIN_LOC_ROOT/share/domains/domain.ocn.tx0.1v3.170730.nc</file>
+      <mesh driver="nuopc">$DIN_LOC_ROOT/share/meshes/TL319_151007_ESMFmesh.nc</mesh>
       <desc>TL319 grid for JRA55</desc>
     </domain>
 
@@ -1528,6 +1529,7 @@
 
     <domain name="JRA025">
       <nx>1440</nx> <ny>720</ny>
+      <mesh driver="nuopc">$DIN_LOC_ROOT/share/meshes/JRA025m.170209_ESMFmesh.nc</mesh>
       <!-- TODO (mvertens, 2018-12-02): create a domain file for this  -->
       <desc>JRA is 0.25 degree runoff grid for use with JRA-55 runoff data</desc>
     </domain>

cime/config/cesm/machines/config_compilers.xml

@@ -503,6 +503,38 @@ using a fortran linker.
   <TRILINOS_PATH MPILIB="mpich2">$ENV{TRILINOS_PATH}</TRILINOS_PATH>
 </compiler>
 
+<compiler MACH="athena">
+  <CPPDEFS>
+    <!-- these flags enable nano timers -->
+    <append MODEL="gptl"> -DHAVE_NANOTIME -DBIT64 -DHAVE_VPRINTF -DHAVE_BACKTRACE -DHAVE_SLASHPROC -DHAVE_COMM_F2C -DHAVE_TIMES -DHAVE_GETTIMEOFDAY </append>
+  </CPPDEFS>
+  <NETCDF_PATH>$ENV{NETCDF}</NETCDF_PATH>
+  <PIO_FILESYSTEM_HINTS>gpfs</PIO_FILESYSTEM_HINTS>
+  <PNETCDF_PATH>$ENV{PNETCDF}</PNETCDF_PATH>
+  <AR>xiar</AR>
+  <ARFLAGS>
+    <base>cru</base>
+  </ARFLAGS>
+</compiler>
+
+<compiler MACH="athena" COMPILER="intel">
+  <CFLAGS>
+    <append>  -xHost </append>
+  </CFLAGS>
+  <CPPDEFS>
+    <append> -DINTEL_MKL -DHAVE_SSE2 </append>
+  </CPPDEFS>
+  <FFLAGS>
+    <append>  -xHost </append>
+  </FFLAGS>
+  <MPICXX MPILIB="mpich2">mpiicpc</MPICXX>
+  <MPICC MPILIB="mpich2">mpiicc</MPICC>
+  <MPIFC MPILIB="mpich2">mpiifort</MPIFC>
+  <SCC>icc</SCC>
+  <SFC>ifort</SFC>
+  <TRILINOS_PATH MPILIB="mpich2">$ENV{TRILINOS_PATH}</TRILINOS_PATH>
+</compiler>
+
 <compiler MACH="bluewaters">
   <CPPDEFS>
     <append MODEL="gptl"> -DHAVE_PAPI </append>
@@ -590,8 +622,8 @@ using a fortran linker.
   </CMAKE_OPTS>
   <PFUNIT_PATH MPILIB="mpi-serial" compile_threaded="FALSE">$ENV{CESMDATAROOT}/tools/pFUnit/pFUnit3.2.8_cheyenne_Intel17.0.1_noMPI_noOpenMP</PFUNIT_PATH>
   <PFUNIT_PATH MPILIB="mpt" compile_threaded="TRUE">$ENV{CESMDATAROOT}/tools/pFUnit/pFUnit3.2.8_cheyenne_Intel17.0.1_MPI_openMP</PFUNIT_PATH>
-  <!-- Bug in the intel/17.0.1 compiler requires this, remove this line when compiler is updated -->
-  <HAS_F2008_CONTIGUOUS>FALSE</HAS_F2008_CONTIGUOUS>
+  <!-- SET to FALSE for intel 17 and 18 TRUE otherwise -->
+  <HAS_F2008_CONTIGUOUS>TRUE</HAS_F2008_CONTIGUOUS>
 </compiler>
 
 <compiler MACH="cheyenne" COMPILER="pgi">
@@ -1071,7 +1103,7 @@ using a fortran linker.
   <SLIBS>
     <append>-L$ENV{NETCDF}/lib -lnetcdff -lnetcdf</append>
   </SLIBS>
-  <ESMF_LIBDIR>/home6/fvitt/esmf_7_0_0/esmf/lib/libO/Linux.intel.64.mpi.default</ESMF_LIBDIR>
+  <ESMF_LIBDIR>/home6/fvitt/esmf_7_1_0r/esmf/lib/libO/Linux.intel.64.mpi.default</ESMF_LIBDIR>
 </compiler>
 
 <compiler MACH="pleiades-has">
@@ -1085,7 +1117,7 @@ using a fortran linker.
   <SLIBS>
     <append>-L$ENV{NETCDF}/lib -lnetcdff -lnetcdf</append>
   </SLIBS>
-  <ESMF_LIBDIR>/home6/fvitt/esmf_7_0_0/esmf/lib/libO/Linux.intel.64.mpi.default</ESMF_LIBDIR>
+  <ESMF_LIBDIR>/home6/fvitt/esmf_7_1_0r/esmf/lib/libO/Linux.intel.64.mpi.default</ESMF_LIBDIR>
 </compiler>
 
 <compiler MACH="pleiades-ivy">
@@ -1099,7 +1131,7 @@ using a fortran linker.
   <SLIBS>
     <append>-L$ENV{NETCDF}/lib -lnetcdff -lnetcdf</append>
   </SLIBS>
-  <ESMF_LIBDIR>/home6/fvitt/esmf_7_0_0/esmf/lib/libO/Linux.intel.64.mpi.default</ESMF_LIBDIR>
+  <ESMF_LIBDIR>/home6/fvitt/esmf_7_1_0r/esmf/lib/libO/Linux.intel.64.mpi.default</ESMF_LIBDIR>
 </compiler>
 
 <compiler MACH="pleiades-san">
@@ -1113,7 +1145,7 @@ using a fortran linker.
   <SLIBS>
     <append>-L$ENV{NETCDF}/lib -lnetcdff -lnetcdf</append>
   </SLIBS>
-  <ESMF_LIBDIR>/home6/fvitt/esmf_7_0_0/esmf/lib/libO/Linux.intel.64.mpi.default</ESMF_LIBDIR>
+  <ESMF_LIBDIR>/home6/fvitt/esmf_7_1_0r/esmf/lib/libO/Linux.intel.64.mpi.default</ESMF_LIBDIR>
 </compiler>
 
 <compiler MACH="sandiatoss3" COMPILER="intel">

cime/config/cesm/machines/config_machines.xml

@@ -1930,7 +1930,7 @@ This allows using a different mpirun command to launch unit tests
 	<command name="purge"/>
 	<command name="load">nas</command>
 	<command name="load">pkgsrc</command>
-	<command name="load">comp-intel/2016.2.181</command>
+	<command name="load">comp-intel/2018.3.222</command>
 	<command name="load">mpi-sgi/mpt.2.15r20</command>
 	<command name="load">szip/2.1.1</command>
 	<command name="load">hdf4/4.2.12</command>
@@ -1984,7 +1984,7 @@ This allows using a different mpirun command to launch unit tests
 	<command name="purge"/>
 	<command name="load">nas</command>
 	<command name="load">pkgsrc</command>
-	<command name="load">comp-intel/2016.2.181</command>
+	<command name="load">comp-intel/2018.3.222</command>
 	<command name="load">mpi-sgi/mpt.2.15r20</command>
 	<command name="load">szip/2.1.1</command>
 	<command name="load">hdf4/4.2.12</command>
@@ -2038,7 +2038,7 @@ This allows using a different mpirun command to launch unit tests
 	<command name="purge"/>
 	<command name="load">nas</command>
 	<command name="load">pkgsrc</command>
-	<command name="load">comp-intel/2016.2.181</command>
+	<command name="load">comp-intel/2018.3.222</command>
 	<command name="load">mpi-sgi/mpt.2.15r20</command>
 	<command name="load">szip/2.1.1</command>
 	<command name="load">hdf4/4.2.12</command>
@@ -2092,7 +2092,7 @@ This allows using a different mpirun command to launch unit tests
 	<command name="purge"/>
 	<command name="load">nas</command>
 	<command name="load">pkgsrc</command>
-	<command name="load">comp-intel/2016.2.181</command>
+	<command name="load">comp-intel/2018.3.222</command>
 	<command name="load">mpi-sgi/mpt.2.15r20</command>
 	<command name="load">szip/2.1.1</command>
 	<command name="load">hdf4/4.2.12</command>
@@ -2238,7 +2238,7 @@ This allows using a different mpirun command to launch unit tests
     <CIME_OUTPUT_ROOT>$ENV{SCRATCH}</CIME_OUTPUT_ROOT>
     <DIN_LOC_ROOT>/work/02503/edwardsj/CESM/inputdata</DIN_LOC_ROOT>
     <DIN_LOC_ROOT_CLMFORC>/work/02503/edwardsj/CESM/inputdata/lmwg</DIN_LOC_ROOT_CLMFORC>
-    <DOUT_S_ROOT>$WORK/archive/$CASE</DOUT_S_ROOT>
+    <DOUT_S_ROOT>$ENV{WORK}/archive/$CASE</DOUT_S_ROOT>
     <BASELINE_ROOT>/work/02503/edwardsj/CESM/cesm_baselines</BASELINE_ROOT>
     <CCSM_CPRNC>/work/02503/edwardsj/CESM/cime/tools/cprnc/cprnc</CCSM_CPRNC>
     <GMAKE_J>4</GMAKE_J>
@@ -2276,13 +2276,13 @@ This allows using a different mpirun command to launch unit tests
       </modules>
       <modules mpilib="mvapich2">
         <command name="load">mvapich2/2.3b</command>
-        <command name="load">pnetcdf/1.8.1</command>
+        <command name="load">pnetcdf/1.11.0</command>
         <command name="load">parallel-netcdf/4.3.3.1</command>
       </modules>
       <modules mpilib="impi">
         <command name="rm">mvapich2</command>
         <command name="load">impi/18.0.2</command>
-        <command name="load">pnetcdf/1.8.1</command>
+        <command name="load">pnetcdf/1.11.0</command>
         <command name="load">parallel-netcdf/4.3.3.1</command>
       </modules>
       <modules mpilib="mpi-serial">
@@ -2318,7 +2318,7 @@ This allows using a different mpirun command to launch unit tests
     <CIME_OUTPUT_ROOT>$ENV{SCRATCH}</CIME_OUTPUT_ROOT>
     <DIN_LOC_ROOT>/work/02503/edwardsj/CESM/inputdata</DIN_LOC_ROOT>
     <DIN_LOC_ROOT_CLMFORC>/work/02503/edwardsj/CESM/inputdata/lmwg</DIN_LOC_ROOT_CLMFORC>
-    <DOUT_S_ROOT>$WORK/archive/$CASE</DOUT_S_ROOT>
+    <DOUT_S_ROOT>$ENV{WORK}/archive/$CASE</DOUT_S_ROOT>
     <BASELINE_ROOT>/work/02503/edwardsj/CESM/cesm_baselines</BASELINE_ROOT>
     <CCSM_CPRNC>/work/02503/edwardsj/CESM/cime/tools/cprnc/cprnc</CCSM_CPRNC>
     <GMAKE_J>4</GMAKE_J>
@@ -2350,13 +2350,13 @@ This allows using a different mpirun command to launch unit tests
       </modules>
       <modules mpilib="mvapich2">
         <command name="load">mvapich2/2.3b</command>
-        <command name="load">pnetcdf/1.8.1</command>
+        <command name="load">pnetcdf/1.11.0</command>
         <command name="load">parallel-netcdf/4.3.3.1</command>
       </modules>
       <modules mpilib="impi">
         <command name="rm">mvapich2</command>
         <command name="load">impi/17.0.3</command>
-        <command name="load">pnetcdf/1.8.1</command>
+        <command name="load">pnetcdf/1.11.0</command>
         <command name="load">parallel-netcdf/4.3.3.1</command>
       </modules>
       <modules mpilib="mpi-serial">

cime/config/cesm/machines/config_pio.xml

@@ -25,12 +25,13 @@
     </values>
   </entry>
 
+  <!--
   <entry id="PIO_VERSION">
     <values>
       <value mach="stampede2-skx">1</value>
     </values>
   </entry>
-
+  -->
 
   <!--- uncomment and fill in relevant sections
   <entry id="PIO_ROOT">
@@ -57,7 +58,9 @@
 
   <entry id="PIO_REARRANGER">
     <values>
-      <value>$PIO_VERSION</value>
+      <!-- Note: problem not using box rearranger with nuopc caps -->
+      <!-- <value>$PIO_VERSION</value> -->
+      <value>1</value>
     </values>
   </entry>
 

cime/config/e3sm/machines/config_machines.xml

@@ -218,6 +218,7 @@
     <CCSM_CPRNC>/project/projectdirs/acme/tools/cprnc.cori/cprnc</CCSM_CPRNC>
     <GMAKE_J>8</GMAKE_J>
     <TESTS>e3sm_developer</TESTS>
+    <NTEST_PARALLEL_JOBS>4</NTEST_PARALLEL_JOBS>
     <BATCH_SYSTEM>nersc_slurm</BATCH_SYSTEM>
     <SUPPORTED_BY>e3sm</SUPPORTED_BY>
     <MAX_TASKS_PER_NODE>32</MAX_TASKS_PER_NODE>
@@ -356,6 +357,7 @@
     <CCSM_CPRNC>/project/projectdirs/acme/tools/cprnc.cori/cprnc</CCSM_CPRNC>
     <GMAKE_J>8</GMAKE_J>
     <TESTS>e3sm_developer</TESTS>
+    <NTEST_PARALLEL_JOBS>4</NTEST_PARALLEL_JOBS>
     <BATCH_SYSTEM>nersc_slurm</BATCH_SYSTEM>
     <SUPPORTED_BY>e3sm</SUPPORTED_BY>
     <MAX_TASKS_PER_NODE>128</MAX_TASKS_PER_NODE>
@@ -1040,6 +1042,7 @@
     <CCSM_CPRNC>/home/ccsm-data/tools/cprnc</CCSM_CPRNC>
     <GMAKE_J>4</GMAKE_J>
     <TESTS>e3sm_integration</TESTS>
+    <NTEST_PARALLEL_JOBS>4</NTEST_PARALLEL_JOBS>
     <BATCH_SYSTEM>pbs</BATCH_SYSTEM>
     <SUPPORTED_BY>acme</SUPPORTED_BY>
     <MAX_TASKS_PER_NODE>16</MAX_TASKS_PER_NODE>
@@ -1143,6 +1146,7 @@
     <CCSM_CPRNC>/lcrc/group/acme/tools/cprnc/cprnc</CCSM_CPRNC>
     <GMAKE_J>8</GMAKE_J>
     <TESTS>e3sm_integration</TESTS>
+    <NTEST_PARALLEL_JOBS>4</NTEST_PARALLEL_JOBS>
     <BATCH_SYSTEM>slurm</BATCH_SYSTEM>
     <SUPPORTED_BY>E3SM</SUPPORTED_BY>
     <MAX_TASKS_PER_NODE>36</MAX_TASKS_PER_NODE>
@@ -1257,6 +1261,7 @@
     <CCSM_CPRNC>/lcrc/group/acme/tools/cprnc/cprnc</CCSM_CPRNC>
     <GMAKE_J>8</GMAKE_J>
     <TESTS>e3sm_integration</TESTS>
+    <NTEST_PARALLEL_JOBS>4</NTEST_PARALLEL_JOBS>
     <BATCH_SYSTEM>slurm</BATCH_SYSTEM>
     <SUPPORTED_BY>E3SM</SUPPORTED_BY>
     <MAX_TASKS_PER_NODE>36</MAX_TASKS_PER_NODE>
@@ -1576,6 +1581,7 @@
     <CCSM_CPRNC>/projects/ccsm/acme/tools/cprnc/cprnc</CCSM_CPRNC>
     <GMAKE_J>8</GMAKE_J>
     <TESTS>e3sm_developer</TESTS>
+    <NTEST_PARALLEL_JOBS>4</NTEST_PARALLEL_JOBS>
     <BATCH_SYSTEM>cobalt_theta</BATCH_SYSTEM>
     <SUPPORTED_BY>E3SM</SUPPORTED_BY>
     <MAX_TASKS_PER_NODE>128</MAX_TASKS_PER_NODE>
@@ -2187,6 +2193,7 @@
     <CCSM_CPRNC>/lustre/atlas1/cli900/world-shared/cesm/tools/cprnc/cprnc.titan</CCSM_CPRNC>
     <GMAKE_J>8</GMAKE_J>
     <TESTS>e3sm_developer</TESTS>
+    <NTEST_PARALLEL_JOBS>4</NTEST_PARALLEL_JOBS>
     <BATCH_SYSTEM>pbs</BATCH_SYSTEM>
     <ALLOCATE_SPARE_NODES>TRUE</ALLOCATE_SPARE_NODES>
     <SUPPORTED_BY>E3SM</SUPPORTED_BY>
@@ -3075,6 +3082,7 @@
     <CCSM_CPRNC>/gpfs/alpine/cli115/world-shared/e3sm/tools/cprnc.summit/cprnc</CCSM_CPRNC>
     <GMAKE_J>32</GMAKE_J>
     <TESTS>e3sm_developer</TESTS>
+    <NTEST_PARALLEL_JOBS>4</NTEST_PARALLEL_JOBS>
     <BATCH_SYSTEM>lsf</BATCH_SYSTEM>
     <SUPPORTED_BY>e3sm</SUPPORTED_BY>
     <MAX_TASKS_PER_NODE>84</MAX_TASKS_PER_NODE>

cime/config/xml_schemas/config_machines.xsd

@@ -46,6 +46,7 @@
   <xs:element name="GMAKE" type="xs:string"/>
   <xs:element name="GMAKE_J" type="xs:integer"/>
   <xs:element name="TESTS" type="xs:string"/>
+  <xs:element name="NTEST_PARALLEL_JOBS" type="xs:integer"/>
   <xs:element name="BATCH_SYSTEM" type="xs:NCName"/>
   <xs:element name="ALLOCATE_SPARE_NODES" type="upperBoolean"/>
   <xs:element name="SUPPORTED_BY" type="xs:string"/>
@@ -140,6 +141,8 @@
         <xs:element ref="GMAKE_J" minOccurs="0" maxOccurs="1"/>
         <!-- TESTS: (acme only) list of tests to run on this machine -->
         <xs:element ref="TESTS" minOccurs="0" maxOccurs="1"/>
+        <!-- NTEST_PARALLEL_JOBS: number of parallel jobs create_test will launch -->
+        <xs:element ref="NTEST_PARALLEL_JOBS" minOccurs="0" maxOccurs="1"/>
         <!-- BATCH_SYSTEM: batch system used on this machine (none is okay) -->
         <xs:element ref="BATCH_SYSTEM" minOccurs="1" maxOccurs="1"/>
         <!-- ALLOCATE_SPARE_NODES: allocate spare nodes when job is launched default False-->

cime/doc/source/users_guide/compsets.rst

@@ -55,7 +55,7 @@ A compset longname has this form::
 
 Supported values for each element of the longname::
 
-  TIME = model time period (e.g. 1850, 2000, 20TR, RCP8...)
+  TIME = model time period (e.g. 1850, 2000, 20TR, SSP585...)
 
   CIME supports the following values for ATM,LND,ICE,OCN,ROF,GLC,WAV and ESP.
   ATM  = [DATM, SATM, XATM]

cime/doc/source/users_guide/create-a-case.rst

@@ -187,3 +187,26 @@ CIME locks your ``$CASEROOT`` files according to the following rules:
 - Variables in **env_run.xml**, **env_batch.xml** and **env_archive.xml** are never locked, and most can be changed at any time.
 
 - There are some exceptions in the **env_batch.xml** file.
+
+===================================
+Adding a --user-mods-dir argument to **create_newcase**
+===================================
+
+A user may want to customize a target case with a combination of
+``user_nl_xxx`` file modifications and/or ``SourceMods`` for some
+components and/or **xmlchange** commands. As an example, the user
+might want to carry out a series of experiments based on a common set
+of changes to the namelists, source code and/or case xml settings.
+Rather than make these changes each time a new experimental
+``CASEROOT`` is generated, the user can create a directory on local
+disk with a set of changes that will be applied to each case.
+
+As an example, the directory could contain the following files: ::
+
+  > user_nl_cpl
+  > shell_commands  (this would contain ./xmlchange commands)
+  > SourceMods/src.cam/dyncomp.F90
+
+When the user calls **create_newcase** with the ``--user-mods-dir`` pointing to the
+full pathname of the directory containing these changes, then the ``CASEROOT`` will be
+created with these changes applied.

cime/scripts/Tools/archive_metadata

@@ -454,8 +454,6 @@ def get_pp_status(case_dict):
     # get xconform status
     case_dict['xconform_path'] = ''
     case_dict['xconform_path'] = get_pp_path(pp_dir, 'xconform')
-    if (len(case_dict['xconform_path']) > 2):
-        case_dict['xconform_path'] = os.path.join(case_dict['xconform_path'], str(case_dict['case_id']))
     case_dict['xconform_status'] = 'Unknown'
     case_dict['xconform_size'] = get_disk_usage(case_dict['xconform_path'])
     case_dict['xconform_dates'] = case_dict['timeseries_dates']

cime/scripts/create_test

@@ -158,6 +158,9 @@ def parse_command_line(args, description):
         parser.add_argument("--xml-testlist",
                             help="Use this testlist to lookup tests.The default is specified in config_files.xml")
 
+        parser.add_argument("--xml-driver", choices=('mct', 'nuopc', 'moab'),
+                            help="Override driver specified in tests and use this one.")
+
         parser.add_argument("testargs", nargs="*",
                             help="Tests to run. Testname form is TEST.GRID.COMPSET[.MACHINE_COMPILER]")
 
@@ -389,9 +392,9 @@ def parse_command_line(args, description):
                    "At least one of --xml-machine, --xml-testlist, "
                    "--xml-compiler, --xml-category or a valid test name must be provided.")
 
-            test_data = get_tests_from_xml(args.xml_machine, args.xml_category,
-                                           args.xml_compiler, args.xml_testlist,
-                                           machine_name, args.compiler)
+            test_data = get_tests_from_xml(xml_machine=args.xml_machine, xml_category=args.xml_category,
+                                           xml_compiler=args.xml_compiler, xml_testlist=args.xml_testlist,
+                                           machine=machine_name, compiler=args.compiler, driver=args.xml_driver)
             test_names = [item["name"] for item in test_data]
             for test_datum in test_data:
                 test_extra_data[test_datum["name"]] = test_datum

cime/scripts/lib/CIME/SystemTests/seq.py

@@ -32,7 +32,7 @@ def _case_two_setup(self):
                 self._case.set_value("ROOTPE_{}".format(comp), 0)
         else:
             totalpes = self._case.get_value("TOTALPES")
-            newntasks = max(1, totalpes/len(comp_classes))
+            newntasks = max(1, totalpes//len(comp_classes))
             rootpe = newntasks
 
             for comp in comp_classes: