E3SM-Project · rljacob · Mar 15, 2017 · Mar 7, 2017 · Mar 7, 2017 · Feb 13, 2017
diff --git a/cime/.gitignore b/cime/.gitignore
@@ -1,5 +1,6 @@
 # Ignore python bytecode files
 *.pyc
+buildnmlc
 
 # Ignore emacs backup files
 *~
diff --git a/cime/CMakeLists.txt b/cime/CMakeLists.txt
@@ -1,14 +1,17 @@
 cmake_minimum_required(VERSION 2.8)
 include(ExternalProject)
+set(CIME_ROOT "${CMAKE_CURRENT_SOURCE_DIR}")
 
 project(cime_tests Fortran C)
 
-list(APPEND CMAKE_MODULE_PATH ${CESM_CMAKE_MODULE_DIRECTORY})
-include(CESM_utils)
-find_package(NETCDF)
-include_directories(${NETCDF_INCLUDE_DIRS})
+# We rely on pio for cmake utilities like findnetcdf.cmake, so that we don't
+# need to duplicate this cmake code
+list(APPEND CMAKE_MODULE_PATH "${CIME_ROOT}/externals/pio2/cmake")
 
-set(CIME_ROOT "${CMAKE_CURRENT_SOURCE_DIR}")
+list(APPEND CMAKE_MODULE_PATH ${CIME_CMAKE_MODULE_DIRECTORY})
+include(CIME_utils)
+find_package(NetCDF COMPONENTS C Fortran)
+include_directories(${NetCDF_C_INCLUDE_DIRS} ${NetCDF_Fortran_INCLUDE_DIRS})
 
 # TODO: Some of the below should be done in the relevant directories, not in
 # this top level CMakeLists.
@@ -22,8 +25,8 @@ ExternalProject_add(mct_project
   PREFIX ${CMAKE_CURRENT_BINARY_DIR}
   SOURCE_DIR ${MCT_ROOT}
   BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR}/mct
-  CONFIGURE_COMMAND ${MCT_ROOT}/configure --enable-debugging --prefix=${CMAKE_CURRENT_BINARY_DIR}
-  BUILD_COMMAND make SRCDIR=${MCT_ROOT}
+  CONFIGURE_COMMAND ${MCT_ROOT}/configure --enable-debugging --prefix=${CMAKE_CURRENT_BINARY_DIR} CFLAGS=${CFLAGS} FCFLAGS=${FFLAGS} SRCDIR=${MCT_ROOT} DEBUG="-g"
+  BUILD_COMMAND $(MAKE)
   # Leave things in <BINARY_DIR> rather than "installing", because we have
   # no need to move things around inside of the CMake binary directory.
   INSTALL_COMMAND :

diff --git a/cime/ChangeLog b/cime/ChangeLog
diff --git a/cime/ChangeLog_template b/cime/ChangeLog_template
@@ -11,7 +11,9 @@ Brief Summary:
 
 User interface changes: 
 
-Modified files: git diff --name-status
+PR summary: git log --oneline --first-parent [previous_tag]..master 
+
+Modified files: git diff --name-status [previous_tag]
 
 ======================================================================
 
diff --git a/cime/README.unit_testing b/cime/README.unit_testing
@@ -1,6 +1,16 @@
 # To run all CIME unit tests on caldera, run the following command:
 # (Note that this must be done from an interactive caldera session, not from yellowstone)
-tools/unit_testing/run_tests.py --test-spec-dir=. --compiler=intel --mpilib=mpich2 --mpirun-command=mpirun.lsf --cmake-args=-DPAPI_LIB=/glade/apps/opt/papi/5.3.0/intel/12.1.5/lib64
+# Note also that this requires module load all-python-libs
+#
+# The creation of a temporary directory ensures that you are doing a completely
+# clean build of the unit tests. (The use of the --clean flag to run_tests.py
+# cleans most, but not all of the files created by the unit test build.) For
+# rerunning the tests after an incremental change, you can instead use an
+# existing build directory.
+#
+# We would encourage you to port these tests to other platforms.
+# The test requires an install of pFunit available from
+# https://sourceforge.net/projects/pfunit/
+#
 
-# The inclusion of PAPI_LIB is needed above since config_compilers includes:
-#   <ADD_SLIBS> -Wl,-rpath ${PAPI_LIB} -L${PAPI_LIB} -lpapi</ADD_SLIBS>
+tools/unit_testing/run_tests.py --test-spec-dir=. --compiler=intel --mpilib=mpich2 --use-openmp --mpirun-command=mpirun.lsf --build-dir `mktemp -d --tmpdir=. unit_tests.XXXXXXXX`
diff --git a/cime/cime_config/acme/allactive/testmods_dirs/cam/outfrq9s/shell_commands b/cime/cime_config/acme/allactive/testmods_dirs/cam/outfrq9s/shell_commands
@@ -0,0 +1,5 @@
+if [ `./xmlquery MACH -value` = "melvin" ]; then
+    ./xmlchange PIO_TYPENAME=netcdf
+fi
+
+./xmlchange ROF_NCPL=48
diff --git a/cime/cime_config/acme/config_archive.xml b/cime/cime_config/acme/config_archive.xml
@@ -1,4 +1,4 @@
-<components>
+<components version="2.0">
 
   <comp_archive_spec compname="cam" compclass="atm">
     <rest_file_extension>\.[ri]\..*</rest_file_extension>
@@ -11,15 +11,6 @@
     </rpointer>
   </comp_archive_spec>
 
-  <comp_archive_spec compname="datm" compclass="atm">
-    <rest_file_extension>\.r\..*</rest_file_extension>
-    <rest_history_varname>unset</rest_history_varname>
-    <rpointer>
-      <rpointer_file>rpointer$NINST_STRING.atm</rpointer_file>
-      <rpointer_content >$CASE.datm$NINST_STRING.r.$DATENAME.nc,$CASE.datm$NINST_STRING.rs1.$DATENAME.bin</rpointer_content>
-    </rpointer>
-  </comp_archive_spec>
-
   <comp_archive_spec compname="clm" compclass="lnd">
     <rest_file_extension>\.[ri]\..*</rest_file_extension>
     <rest_file_extension>\.rh.*</rest_file_extension>
@@ -31,15 +22,6 @@
     </rpointer>
   </comp_archive_spec>
 
-  <comp_archive_spec compname="dlnd" compclass="lnd">
-    <rest_file_extension>\.r.*</rest_file_extension>
-    <rest_history_varname>unset</rest_history_varname>
-    <rpointer>
-      <rpointer_file>rpointer$NINST_STRING.lnd</rpointer_file>
-      <rpointer_content >$CASE.dlnd$NINST_STRING.r.$DATENAME.nc,$CASE.dlnd$NINST_STRING.rs1.$DATENAME.bin</rpointer_content>
-    </rpointer>
-  </comp_archive_spec>
-
   <comp_archive_spec compname="rtm" compclass="rof">
     <rest_file_extension>\.r.*</rest_file_extension>
     <hist_file_extension>\.h.*.nc$</hist_file_extension>
@@ -60,15 +42,6 @@
     </rpointer>
   </comp_archive_spec>
 
-  <comp_archive_spec compname="drof" compclass="rof">
-    <rest_file_extension>\.r.*</rest_file_extension>
-    <rest_history_varname>unset</rest_history_varname>
-    <rpointer>
-      <rpointer_file>rpointer$NINST_STRING.rof</rpointer_file>
-      <rpointer_content>$CASE.drof$NINST_STRING.r.$DATENAME.nc,$CASE.drof$NINST_STRING.rs1.$DATENAME.bin</rpointer_content>
-    </rpointer>
-  </comp_archive_spec>
-
   <comp_archive_spec compname="cice" compclass="ice">
     <rest_file_extension>\.[ri].*</rest_file_extension>
     <hist_file_extension>\.h.*.nc$</hist_file_extension>
@@ -88,15 +61,6 @@
     </rpointer>
   </comp_archive_spec>
 
-  <comp_archive_spec compname="dice" compclass="ice">
-    <rest_file_extension>\.r.*</rest_file_extension>
-    <rest_history_varname>unset</rest_history_varname>
-    <rpointer>
-      <rpointer_file>rpointer$NINST_STRING.ice</rpointer_file>
-      <rpointer_content>$CASE.dice$NINST_STRING.r.$DATENAME.nc,$CASE.dice$NINST_STRING.rs1.$DATENAME.bin</rpointer_content>
-    </rpointer>
-  </comp_archive_spec>
-
   <comp_archive_spec compname="pop" compclass="ocn">
     <rest_file_extension>\.r.*</rest_file_extension>
     <hist_file_extension>\.h.*.nc$|\.d[dovt]\.</hist_file_extension>
@@ -120,18 +84,10 @@
     </rpointer>
   </comp_archive_spec>
 
-  <comp_archive_spec compname="docn" compclass="ocn">
-    <rest_file_extension>\.r.*</rest_file_extension>
-    <rest_history_varname>unset</rest_history_varname>
-    <rpointer>
-      <rpointer_file>rpointer$NINST_STRING.ocn</rpointer_file>
-      <rpointer_content>$CASE.docn$NINST_STRING.r.$DATENAME.nc,$CASE.docn$NINST_STRING.rs1.$DATENAME.bin</rpointer_content>
-    </rpointer>
-  </comp_archive_spec>
-
   <comp_archive_spec compname="cism" compclass="glc">
     <rest_file_extension>\.[ri]\..*</rest_file_extension>
-    <hist_file_extension>\.h.*.nc$</hist_file_extension>
+    <hist_file_extension>\.h\..*\.nc$</hist_file_extension>
+    <hist_file_extension>\.initial_hist\..*\.nc$</hist_file_extension>
     <rest_history_varname>unset</rest_history_varname>
     <rpointer>
       <rpointer_file>rpointer$NINST_STRING.glc</rpointer_file>
@@ -158,35 +114,18 @@
     </rpointer>
   </comp_archive_spec>
 
-  <comp_archive_spec compname="dwav" compclass="wav">
-    <rest_file_extension>\.r.*</rest_file_extension>
-    <rest_history_varname>unset</rest_history_varname>
-    <rpointer>
-      <rpointer_file>rpointer$NINST_STRING.wav</rpointer_file>
-      <rpointer_content >$CASE.dwav$NINST_STRING.r.$DATENAME.nc,$CASE.dwav$NINST_STRING.rs1.$DATENAME.bin</rpointer_content>
-    </rpointer>
-  </comp_archive_spec>
-
-  <comp_archive_spec compname="dart" compclass="esp">
+  <comp_archive_spec compclass="esp" compname="dart">
     <rest_file_extension>inflate_restart.*</rest_file_extension>
-    <hist_file_extension>True_State.*</hist_file_extension>
-    <hist_file_extension>Prior_Diag.*</hist_file_extension>
-    <hist_file_extension>Posterior_Diag.*</hist_file_extension>
-    <hist_file_extension>obs_seq.*</hist_file_extension>
+    <hist_file_extension>\.True_State.*</hist_file_extension>
+    <hist_file_extension>\.Prior_Diag.*</hist_file_extension>
+    <hist_file_extension>\.Posterior_Diag.*</hist_file_extension>
+    <hist_file_extension>\..+\.posterior*</hist_file_extension>
+    <hist_file_extension>\..+\.prior*</hist_file_extension>
+    <hist_file_extension>\..+$_obs_seq.*</hist_file_extension>
     <rest_history_varname>unset</rest_history_varname>
     <rpointer>
       <rpointer_file>rpointer.unset</rpointer_file>
-      <rpointer_content >unset</rpointer_content>
-    </rpointer>
-  </comp_archive_spec>
-
-  <comp_archive_spec compname="cpl" compclass="cpl">
-    <rest_file_extension>\.r\..*</rest_file_extension>
-    <hist_file_extension>\.h.*.nc$</hist_file_extension>
-    <rest_history_varname>unset</rest_history_varname>
-    <rpointer>
-      <rpointer_file>rpointer.cpl</rpointer_file>
-      <rpointer_content >$CASE.cpl.r.$DATENAME.nc</rpointer_content>
+      <rpointer_content>unset</rpointer_content>
     </rpointer>
   </comp_archive_spec>
 

diff --git a/cime/cime_config/acme/config_files.xml b/cime/cime_config/acme/config_files.xml
@@ -2,7 +2,7 @@
 
 <?xml-stylesheet type="text/xsl" href="definitions_variables.xsl" ?>
 
-<files>
+<entry_id version="2.0">
 
   <entry id="MODEL">
     <type>char</type>
@@ -24,6 +24,15 @@
     <desc>contains both header and group information for all the case env_*.xml files </desc>
   </entry>
 
+  <entry id="BATCH_SPEC_FILE">
+    <type>char</type>
+    <default_value>$CIMEROOT/cime_config/$MODEL/machines/config_batch.xml</default_value>
+    <group>case_last</group>
+    <file>env_case.xml</file>
+    <desc>file containing batch system details for target system  (for documentation only - DO NOT EDIT)</desc>
+    <schema>$CIMEROOT/cime_config/xml_schemas/config_batch.xsd</schema>
+  </entry>
+
   <entry id="GRIDS_SPEC_FILE">
     <type>char</type>
     <default_value>$CIMEROOT/cime_config/$MODEL/config_grids.xml</default_value>
@@ -38,6 +47,7 @@
     <group>case_last</group>
     <file>env_case.xml</file>
     <desc>file containing compiler specifications for target model primary component (for documentation only - DO NOT EDIT)</desc>
+    <schema>$CIMEROOT/cime_config/xml_schemas/config_compilers_v2.xsd</schema>
   </entry>
 
   <entry id="MACHINES_SPEC_FILE">
@@ -48,14 +58,6 @@
     <desc>file containing machine specifications for target model primary component (for documentation only - DO NOT EDIT)</desc>
   </entry>
 
-  <entry id="BUILD_SPEC_FILE">
-    <type>char</type>
-    <default_value>$CIMEROOT/cime_config/$MODEL/machines/config_build.xml</default_value>
-    <group>case_last</group>
-    <file>env_case.xml</file>
-    <desc>file containing build specifications for target model primary component (for documentation only - DO NOT EDIT)</desc>
-  </entry>
-
   <entry id="PIO_SPEC_FILE">
     <type>char</type>
     <default_value>$CIMEROOT/cime_config/$MODEL/machines/config_pio.xml</default_value>
@@ -95,6 +97,7 @@
     <group>case_last</group>
     <file>env_case.xml</file>
     <desc>file containing specification of all compsets for primary component (for documentation only - DO NOT EDIT)</desc>
+    <schema>$CIMEROOT/cime_config/xml_schemas/config_compsets.xsd</schema>
   </entry>
 
   <entry id="PES_SPEC_FILE">
@@ -115,6 +118,35 @@
     <group>case_last</group>
     <file>env_case.xml</file>
     <desc>file containing specification of all pe-layouts for primary component (for documentation only - DO NOT EDIT)</desc>
+    <schema>$CIMEROOT/cime_config/xml_schemas/config_pes.xsd</schema>
+  </entry>
+
+  <entry id="ARCHIVE_SPEC_FILE">
+    <type>char</type>
+    <values>
+      <value>$CIMEROOT/cime_config/acme/config_archive.xml</value>
+      <value component="cpl"      >$CIMEROOT/driver_cpl/cime_config/config_archive.xml</value>
+      <!-- data model components -->
+      <value component="drof">$CIMEROOT/components/data_comps/drof/cime_config/config_archive.xml</value>
+      <value component="datm">$CIMEROOT/components/data_comps/datm/cime_config/config_archive.xml</value>
+      <value component="dice">$CIMEROOT/components/data_comps/dice/cime_config/config_archive.xml</value>
+      <value component="dlnd">$CIMEROOT/components/data_comps/dlnd/cime_config/config_archive.xml</value>
+      <value component="docn">$CIMEROOT/components/data_comps/docn/cime_config/config_archive.xml</value>
+      <value component="dwav">$CIMEROOT/components/data_comps/dwav/cime_config/config_archive.xml</value>
+      <!-- external model components -->
+      <value component="cam"      >$SRCROOT/components/cam/cime_config/config_archive.xml</value>
+      <value component="cism"     >$SRCROOT/components/cism/cime_config/config_archive.xml</value>
+      <value component="clm"      >$SRCROOT/components/clm/cime_config/config_archive.xml</value>
+      <value component="cice"     >$SRCROOT/components/cice/cime_config/config_archive.xml</value>
+      <value component="pop"      >$SRCROOT/components/pop/cime_config/config_archive.xml</value>
+      <value component="mpaso"    >$SRCROOT/components/mpas-o/cime_config/config_archive.xml</value>
+      <value component="mpasli"   >$SRCROOT/components/mpasli/cime_config/config_archive.xml</value>
+      <value component="mpascice" >$SRCROOT/components/mpas-cice/cime_config/config_archive.xml</value>
+    </values>
+    <group>case_last</group>
+    <file>env_case.xml</file>
+    <desc>file containing specification of archive files for each component (for documentation only - DO NOT EDIT)</desc>
+    <schema>$CIMEROOT/cime_config/xml_schemas/config_archive.xsd</schema>
   </entry>
 
   <entry id="SYSTEM_TESTS_DIR">
@@ -189,18 +221,65 @@
     <desc>directory containing user modifications for primary components (for documentation only - DO NOT EDIT)</desc>
   </entry>
 
+  <entry id="NAMELIST_DEFINITION_FILE">
+    <type>char</type>
+    <default_value>unset</default_value>
+    <values>
+      <value component="modelio"      >$CIMEROOT/driver_cpl/cime_config/namelist_definition_modelio.xml</value>
+      <value component="drv_flds"      >$CIMEROOT/driver_cpl/bld/namelist_files/namelist_definition_drv_flds.xml</value>
+      <value component="drv"      >$CIMEROOT/driver_cpl/cime_config/namelist_definition_drv.xml</value>
+      <!-- data model components -->
+      <value component="drof">$CIMEROOT/components/data_comps/drof/cime_config/namelist_definition_drof.xml</value>
+      <value component="datm">$CIMEROOT/components/data_comps/datm/cime_config/namelist_definition_datm.xml</value>
+      <value component="dice">$CIMEROOT/components/data_comps/dice/cime_config/namelist_definition_dice.xml</value>
+      <value component="dlnd">$CIMEROOT/components/data_comps/dlnd/cime_config/namelist_definition_dlnd.xml</value>
+      <value component="docn">$CIMEROOT/components/data_comps/docn/cime_config/namelist_definition_docn.xml</value>
+      <value component="dwav">$CIMEROOT/components/data_comps/dwav/cime_config/namelist_definition_dwav.xml</value>
+      <!-- external model components -->
+      <!--  TODO
+      <value component="cam"      >$SRCROOT/components/cam/bld/namelist_files/namelist_definition.xml</value>
+      <value component="cism"     >$SRCROOT/components/cism/bld/namelist_files/namelist_definition_cism.xml</value>
+      <value component="cice"     >$SRCROOT/components/cice/cime_config/namelist_definition_cice.xml</value>
+      <value component="clm"      >$SRCROOT/components/clm/bld/namelist_files/namelist_definition_clm4_5.xml</value>
+      <value component="clm"      >$SRCROOT/components/clm/bld/namelist_files/namelist_definition_clm4_0.xml</value>
+      <value component="pop"      >$SRCROOT/components/pop/bld/namelist_files/namelist_definition_pop.xml</value>
+      -->
+    </values>
+    <group>case_last</group>
+    <file>env_case.xml</file>
+    <desc>file containing namelist_definitions for all components </desc>
+    <schema>$CIMEROOT/cime_config/xml_schemas/entry_id_namelist.xsd</schema>
+  </entry>
+
+  <entry id="LTARCHIVE_SPEC_FILE">
+    <type>char</type>
+    <default_value>$CIMEROOT/cime_config/$MODEL/machines/config_lt_archive.xml</default_value>
+    <group>case_last</group>
+    <file>env_case.xml</file>
+    <desc>file containing all lt archive configuration variables (for documentation only - DO NOT EDIT)</desc>
+  </entry>
+
   <!-- =============================================================== -->
   <!-- File names for all component specific configuration variables -->
   <!-- =============================================================== -->
 
-  <entry id="CONFIG_DRV_FILE">
+  <entry id="CONFIG_CPL_FILE">
     <type>char</type>
     <default_value>$CIMEROOT/driver_cpl/cime_config/config_component.xml</default_value>
     <group>case_last</group>
     <file>env_case.xml</file>
     <desc>file containing all non-component specific case configuration variables (for documentation only - DO NOT EDIT)</desc>
   </entry>
 
+  <entry id="CONFIG_CPL_FILE_MODEL_SPECIFIC">
+    <type>char</type>
+    <default_value>$CIMEROOT/driver_cpl/cime_config/config_component_$MODEL.xml</default_value>
+    <group>case_last</group>
+    <file>env_case.xml</file>
+    <desc>file containing all component specific driver configuration variables (for documentation only - DO NOT EDIT)</desc>
+    <schema>$CIMEROOT/cime_config/xml_schemas/entry_id.xsd</schema>
+  </entry>
+
   <entry id="CONFIG_ATM_FILE">
     <type>char</type>
     <default_value>unset</default_value>
@@ -312,11 +391,12 @@
     <default_value>$CIMEROOT/components/stub_comps/sesp/cime_config/config_component.xml</default_value>
     <values>
       <value component="sesp">$CIMEROOT/components/stub_comps/sesp/cime_config/config_component.xml</value>
+      <value component="desp">$CIMEROOT/components/data_comps/desp/cime_config/config_component.xml</value>
     </values>
     <group>case_last</group>
     <file>env_case.xml</file>
     <desc>file containing specification of component specific definitions and values(for documentation only - DO NOT EDIT)</desc>
   </entry>
 
-</files>
+</entry_id>