Merge branch 'hotfix-v8.2.1'

This merge addresses several issues in the MPAS-Atmosphere model and in the MPAS
infrastructure. Specific changes in this merge include:

* Improved detection of an 'mpi_f08' module (PR #1202), as well as improved
  detection of netCDF and PnetCDF library paths (PR #1203), in the top-level
  Makefile.

* The addition of a missing dependency in the physics Makefile to correct
  parallel build issues (PR #1204).

* Fixes to the CMake build files used by MPAS-JEDI (PR #1205).

* Fixes to double-precision builds of MPAS-Atmosphere (PR #1207, PR #1208).

* Correction of the calculation of height AGL used in the computation of 1-km
  radar reflectivity fields (PR #1213).

* Correction of an issue that prevented the MYNN PBL scheme from being used
  without also using the Thompson aerosol-aware microphysics (PR #1215).

* Fixes to allow MPAS-Atmosphere to be built without physics (i.e., dynamics-
  only builds) (PR #1221).

* Various code cleanup and minor corrections (PR #1206, PR #1212, PR #1224,
  PR #1226).

Makefile

@@ -737,10 +737,10 @@ else # Not using PIO, using SMIOL
 endif
 
 ifneq "$(NETCDF)" ""
-ifneq ($(wildcard $(NETCDF)/lib), )
+ifneq ($(wildcard $(NETCDF)/lib/libnetcdf.*), )
 	NETCDFLIBLOC = lib
 endif
-ifneq ($(wildcard $(NETCDF)/lib64), )
+ifneq ($(wildcard $(NETCDF)/lib64/libnetcdf.*), )
 	NETCDFLIBLOC = lib64
 endif
 	CPPINCLUDES += -I$(NETCDF)/include
@@ -761,10 +761,10 @@ endif
 
 
 ifneq "$(PNETCDF)" ""
-ifneq ($(wildcard $(PNETCDF)/lib), )
+ifneq ($(wildcard $(PNETCDF)/lib/libpnetcdf.*), )
 	PNETCDFLIBLOC = lib
 endif
-ifneq ($(wildcard $(PNETCDF)/lib64), )
+ifneq ($(wildcard $(PNETCDF)/lib64/libpnetcdf.*), )
 	PNETCDFLIBLOC = lib64
 endif
 	CPPINCLUDES += -I$(PNETCDF)/include
@@ -1352,9 +1352,10 @@ mpi_f08_test:
 	$(info Checking for mpi_f08 support...)
 	$(eval MPAS_MPI_F08 := $(shell $\
 		printf "program main\n$\
-		        &   use mpi_f08, only : MPI_Init, MPI_Comm\n$\
+		        &   use mpi_f08, only : MPI_Init, MPI_Comm, MPI_INTEGER, MPI_Datatype\n$\
 		        &   integer :: ierr\n$\
 		        &   type (MPI_Comm) :: comm\n$\
+		        &   type (MPI_Datatype), parameter :: MPI_INTEGERKIND = MPI_INTEGER\n$\
 		        &   call MPI_Init(ierr)\n$\
 		        end program main\n" | sed 's/&/ /' > mpi_f08.f90; $\
 		$\

README.md

@@ -1,4 +1,4 @@
-MPAS-v8.2.0
+MPAS-v8.2.1
 ====
 
 The Model for Prediction Across Scales (MPAS) is a collaborative project for

cmake/Functions/MPAS_Functions.cmake

@@ -29,6 +29,33 @@ function(get_mpas_version mpas_version)
     set(${mpas_version} ${CMAKE_MATCH_1} PARENT_SCOPE)
 endfunction()
 
+##
+# get_git_version( <git_version> )
+# Extracts the current Git version of the project.
+# <git_version> will contain the Git version string.
+# Example usage:
+# get_git_version(GIT_VERSION)
+# message("Git Version: ${GIT_VERSION}")
+##
+
+
+function(get_git_version git_version)
+    execute_process(
+            COMMAND git describe --tags --always
+            WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+            RESULT_VARIABLE RESULT
+            OUTPUT_VARIABLE GIT_VERSION
+            OUTPUT_STRIP_TRAILING_WHITESPACE
+    )
+
+    if(NOT RESULT EQUAL 0)
+        message(WARNING "Failed to get Git version!")
+    endif()
+    set(${git_version} ${GIT_VERSION} PARENT_SCOPE
+    )
+endfunction()
+
+
 ##
 # mpas_fortran_target( <target-name> )
 #
@@ -162,15 +189,20 @@ function(mpas_core_target)
     file(MAKE_DIRECTORY ${CORE_DATADIR})
 
     #Process registry and generate includes, namelists, and streams
-    if(${ARG_CORE} STREQUAL "atmosphere" AND ${DO_PHYSICS})
-            set(CPP_EXTRA_FLAGS ${CPP_EXTRA_FLAGS} -DDO_PHYSICS)
+    get_git_version(git_version)
+    string(TOUPPER ${ARG_CORE} ARG_CORE_UPPER)
+    set(CPP_EXTRA_FLAGS ${CPP_EXTRA_FLAGS} -DCORE_${ARG_CORE_UPPER} -DMPAS_NAMELIST_SUFFIX=${ARG_CORE} -DMPAS_EXE_NAME=mpas_${ARG_CORE} -DMPAS_GIT_VERSION=${git_version} -DMPAS_BUILD_TARGET=${CMAKE_Fortran_COMPILER_ID})
+    message("CPP_EXTRA_FLAGS: ${CPP_EXTRA_FLAGS}")
+    if (${DO_PHYSICS})
+        set(CPP_EXTRA_FLAGS ${CPP_EXTRA_FLAGS} -DDO_PHYSICS)
     endif()
-    add_custom_command(OUTPUT Registry_processed.xml
+
+add_custom_command(OUTPUT Registry_processed.xml
             COMMAND ${CPP_EXECUTABLE} -E -P ${CPP_EXTRA_FLAGS} ${CMAKE_CURRENT_SOURCE_DIR}/Registry.xml > Registry_processed.xml
             COMMENT "CORE ${ARG_CORE}: Pre-Process Registry"
             DEPENDS Registry.xml)
     add_custom_command(OUTPUT ${ARG_INCLUDES}
-            COMMAND mpas_parse_${ARG_CORE} Registry_processed.xml
+            COMMAND mpas_parse_${ARG_CORE} Registry_processed.xml ${CPP_EXTRA_FLAGS}
             COMMENT "CORE ${ARG_CORE}: Parse Registry"
             DEPENDS mpas_parse_${ARG_CORE} Registry_processed.xml)
     add_custom_command(OUTPUT namelist.${ARG_CORE}