Merge branch 'release-v4.0'

This merge introduces v4.0 of all MPAS models.

* release-v4.0: (198 commits)
  Fix an issue realted to core_run failing for the ocean model
  Move computation of invAreaCell field above first call to atm_compute_solve_diagnostics()
  Remove unused &io namelist options from init_atmosphere and atmosphere Registry.xml files
  Don't abort if errors occur when computing the MSLP diagnostic
  Update the code version to 4.0 in the physics table checkout script
  Change name of default physics suite from 'wrf' to 'mesoscale_reference'
  Add missing code for 2nd and 4th order vertical advection of 'u'
  Only write 'restart_timestamp' file from MPI rank 0
  Set default surface update interval to 86400 s during initialization
  Process input streams individually and write a message to the log for each stream that is read
  Recompute longitude grid increment for Gaussian input data
  Set any negative soil moisture values to 0.001
  Correctly detect non-isobaric data in real-data initialization
  Fix two LANDSEA masking errors for real-data cases
  Avoid writing initial diagnostics output file on restart runs
  Fix intent for output arguments in interface for xml_stream_get_attributes()
  Remove tab characters from shared infrastructure code
  Remove tab characters from Fortran code in init_atmosphere and atmosphere cores
  * In ./physics_wrf/module_ra_rrtmg_lw.F, in subroutine taugb7, corrected line number 6145
  Update version number to 4.0
  ...

.gitignore

@@ -18,7 +18,6 @@ src/operators/*.f90
 
 # Executables
 *_model
-src/registry/parse
 
 # NetCDF Files
 *.nc
@@ -54,3 +53,5 @@ stream_list.*
 # Intermediate files that may be produced by Intel compilers
 *.i
 *.i90
+
+src/core_*/inc

Makefile

@@ -8,13 +8,17 @@ xlf:
 	( $(MAKE) all \
 	"FC_PARALLEL = mpxlf90" \
 	"CC_PARALLEL = mpcc" \
+	"CXX_PARALLEL = mpixlcxx" \
 	"FC_SERIAL = xlf90" \
 	"CC_SERIAL = xlc" \
+	"CXX_SERIAL = xlcxx" \
 	"FFLAGS_OPT = -O3 -qrealsize=8" \
 	"CFLAGS_OPT = -O3" \
+	"CXXFLAGS_OPT = -O3" \
 	"LDFLAGS_OPT = -O3" \
 	"FFLAGS_DEBUG = -O0 -g -C -qrealsize=8" \
 	"CFLAGS_DEBUG = -O0 -g" \
+	"CXXFLAGS_DEBUG = -O0 -g" \
 	"LDFLAGS_DEBUG = -O0 -g" \
 	"CORE = $(CORE)" \
 	"DEBUG = $(DEBUG)" \
@@ -25,10 +29,13 @@ ftn:
 	( $(MAKE) all \
 	"FC_PARALLEL = ftn" \
 	"CC_PARALLEL = cc" \
+	"CXX_PARALLEL = CC" \
 	"FC_SERIAL = ftn" \
 	"CC_SERIAL = cc" \
+	"CXX_SERIAL = CC" \
 	"FFLAGS_OPT = -i4 -r8 -gopt -O2 -Mvect=nosse -Kieee -convert big_endian" \
 	"CFLAGS_OPT = -fast" \
+	"CXXFLAGS_OPT = -fast" \
 	"LDFLAGS_OPT = " \
 	"CORE = $(CORE)" \
 	"DEBUG = $(DEBUG)" \
@@ -53,13 +60,17 @@ pgi:
 	( $(MAKE) all \
 	"FC_PARALLEL = mpif90" \
 	"CC_PARALLEL = mpicc" \
+	"CXX_PARALLEL = mpicxx" \
 	"FC_SERIAL = pgf90" \
 	"CC_SERIAL = pgcc" \
+	"CXX_SERIAL = pgc++" \
 	"FFLAGS_OPT = -r8 -O3 -byteswapio -Mfree" \
 	"CFLAGS_OPT = -O3" \
+	"CXXFLAGS_OPT = -O3" \
 	"LDFLAGS_OPT = -O3" \
 	"FFLAGS_DEBUG = -r8 -O0 -g -Mbounds -Mchkptr -byteswapio -Mfree -Ktrap=divz,fp,inv,ovf -traceback" \
 	"CFLAGS_DEBUG = -O0 -g -traceback" \
+	"CXXFLAGS_DEBUG = -O0 -g -traceback" \
 	"LDFLAGS_DEBUG = -O0 -g -Mbounds -Mchkptr -Ktrap=divz,fp,inv,ovf -traceback" \
 	"CORE = $(CORE)" \
 	"DEBUG = $(DEBUG)" \
@@ -70,10 +81,13 @@ pgi-nersc:
 	( $(MAKE) all \
 	"FC_PARALLEL = ftn" \
 	"CC_PARALLEL = cc" \
+	"CXX_PARALLEL = CC" \
 	"FC_SERIAL = ftn" \
 	"CC_SERIAL = cc" \
+	"CXX_SERIAL = CC" \
 	"FFLAGS_OPT = -r8 -O3 -byteswapio -Mfree" \
 	"CFLAGS_OPT = -O3" \
+	"CXXFLAGS_OPT = -O3" \
 	"LDFLAGS_OPT = -O3" \
 	"CORE = $(CORE)" \
 	"DEBUG = $(DEBUG)" \
@@ -84,10 +98,13 @@ pgi-llnl:
 	( $(MAKE) all \
 	"FC_PARALLEL = mpipgf90" \
 	"CC_PARALLEL = pgcc" \
+	"CXX_PARALLEL = mpipgcxx" \
 	"FC_SERIAL = pgf90" \
 	"CC_SERIAL = pgcc" \
+	"CXX_SERIAL = pgc++" \
 	"FFLAGS_OPT = -i4 -r8 -g -O2 -byteswapio" \
 	"CFLAGS_OPT = -fast" \
+	"CXXFLAGS_OPT = -fast" \
 	"LDFLAGS_OPT = " \
 	"CORE = $(CORE)" \
 	"DEBUG = $(DEBUG)" \
@@ -98,13 +115,17 @@ ifort:
 	( $(MAKE) all \
 	"FC_PARALLEL = mpif90" \
 	"CC_PARALLEL = mpicc" \
+	"CXX_PARALLEL = mpicxx" \
 	"FC_SERIAL = ifort" \
 	"CC_SERIAL = icc" \
+	"CXX_SERIAL = icpc" \
 	"FFLAGS_OPT = -real-size 64 -O3 -convert big_endian -FR" \
 	"CFLAGS_OPT = -O3" \
+	"CXXFLAGS_OPT = -O3" \
 	"LDFLAGS_OPT = -O3" \
 	"FFLAGS_DEBUG = -real-size 64 -g -convert big_endian -FR -CU -CB -check all -fpe0 -traceback" \
 	"CFLAGS_DEBUG = -g -fpe0 -traceback" \
+	"CXXFLAGS_DEBUG = -g -fpe0 -traceback" \
 	"LDFLAGS_DEBUG = -g -fpe0 -traceback" \
 	"CORE = $(CORE)" \
 	"DEBUG = $(DEBUG)" \
@@ -115,13 +136,17 @@ ifort-gcc:
 	( $(MAKE) all \
 	"FC_PARALLEL = mpif90" \
 	"CC_PARALLEL = mpicc" \
+	"CXX_PARALLEL = mpicxx" \
 	"FC_SERIAL = ifort" \
 	"CC_SERIAL = gcc" \
+	"CXX_SERIAL = g++" \
 	"FFLAGS_OPT = -real-size 64 -O3 -convert big_endian -FR" \
 	"CFLAGS_OPT = -O3" \
+	"CXXFLAGS_OPT = -O3" \
 	"LDFLAGS_OPT = -O3" \
 	"FFLAGS_DEBUG = -real-size 64 -g -convert big_endian -FR -CU -CB -check all -fpe0 -traceback" \
 	"CFLAGS_DEBUG = -g" \
+	"CXXFLAGS_DEBUG = -g" \
 	"LDFLAGS_DEBUG = -g -fpe0 -traceback" \
 	"CORE = $(CORE)" \
 	"DEBUG = $(DEBUG)" \
@@ -132,30 +157,17 @@ gfortran:
 	( $(MAKE) all \
 	"FC_PARALLEL = mpif90" \
 	"CC_PARALLEL = mpicc" \
+	"CXX_PARALLEL = mpicxx" \
 	"FC_SERIAL = gfortran" \
 	"CC_SERIAL = gcc" \
+	"CXX_SERIAL = g++" \
 	"FFLAGS_OPT = -O3 -m64 -ffree-line-length-none -fdefault-real-8 -fdefault-double-8 -fconvert=big-endian -ffree-form" \
 	"CFLAGS_OPT = -O3 -m64" \
+	"CXXFLAGS_OPT = -O3 -m64" \
 	"LDFLAGS_OPT = -O3 -m64" \
 	"FFLAGS_DEBUG = -g -m64 -ffree-line-length-none -fdefault-real-8 -fdefault-double-8 -fconvert=big-endian -ffree-form -fbounds-check -fbacktrace -ffpe-trap=invalid,zero,overflow" \
 	"CFLAGS_DEBUG = -g -m64" \
-	"LDFLAGS_DEBUG = -g -m64" \
-	"CORE = $(CORE)" \
-	"DEBUG = $(DEBUG)" \
-	"USE_PAPI = $(USE_PAPI)" \
-	"CPPFLAGS = $(MODEL_FORMULATION) -D_MPI -DUNDERSCORE" )
-
-gfortran-openmpi:
-	( $(MAKE) all \
-	"FC_PARALLEL = openmpif90" \
-	"CC_PARALLEL = openmpicc" \
-	"FC_SERIAL = gfortran" \
-	"CC_SERIAL = gcc" \
-	"FFLAGS_OPT = -O3 -m64 -ffree-line-length-none -fdefault-real-8 -fdefault-double-8 -fconvert=big-endian -ffree-form" \
-	"CFLAGS_OPT = -O3 -m64" \
-	"LDFLAGS_OPT = -O3 -m64" \
-	"FFLAGS_DEBUG = -g -m64 -ffree-line-length-none -fdefault-real-8 -fdefault-double-8 -fconvert=big-endian -ffree-form -fbounds-check -fbacktrace -ffpe-trap=invalid,zero,overflow" \
-	"CFLAGS_DEBUG = -g -m64" \
+	"CXXFLAGS_DEBUG = -O3 -m64" \
 	"LDFLAGS_DEBUG = -g -m64" \
 	"CORE = $(CORE)" \
 	"DEBUG = $(DEBUG)" \
@@ -166,10 +178,13 @@ g95:
 	( $(MAKE) all \
 	"FC_PARALLEL = mpif90" \
 	"CC_PARALLEL = mpicc" \
+	"CXX_PARALLEL = mpicxx" \
 	"FC_SERIAL = g95" \
 	"CC_SERIAL = gcc" \
+	"CXX_SERIAL = g++" \
 	"FFLAGS_OPT = -O3 -ffree-line-length-huge -r8 -fendian=big" \
 	"CFLAGS_OPT = -O3" \
+	"CXXFLAGS_OPT = -O3" \
 	"LDFLAGS_OPT = -O3" \
 	"CORE = $(CORE)" \
 	"DEBUG = $(DEBUG)" \
@@ -180,10 +195,13 @@ pathscale-nersc:
 	( $(MAKE) all \
 	"FC_PARALLEL = ftn" \
 	"CC_PARALLEL = cc" \
+	"CXX_PARALLEL = CC" \
 	"FC_SERIAL = ftn" \
 	"CC_SERIAL = cc" \
+	"CXX_SERIAL = CC" \
 	"FFLAGS_OPT = -r8 -O3 -freeform -extend-source" \
 	"CFLAGS_OPT = -O3" \
+	"CXXFLAGS_OPT = -O3" \
 	"LDFLAGS_OPT = -O3" \
 	"CORE = $(CORE)" \
 	"DEBUG = $(DEBUG)" \
@@ -194,24 +212,52 @@ cray-nersc:
 	( $(MAKE) all \
 	"FC_PARALLEL = ftn" \
 	"CC_PARALLEL = cc" \
+	"CXX_PARALLEL = CC" \
 	"FC_SERIAL = ftn" \
 	"CC_SERIAL = cc" \
+	"CXX_SERIAL = CC" \
 	"FFLAGS_OPT = -default64 -O3 -f free" \
 	"CFLAGS_OPT = -O3" \
+	"CXXFLAGS_OPT = -O3" \
 	"LDFLAGS_OPT = -O3" \
 	"CORE = $(CORE)" \
 	"DEBUG = $(DEBUG)" \
 	"USE_PAPI = $(USE_PAPI)" \
 	"CPPFLAGS = $(MODEL_FORMULATION) -D_MPI -DUNDERSCORE" )
 
+gnu-nersc:
+	( $(MAKE) all \
+	"FC_PARALLEL = ftn" \
+	"CC_PARALLEL = cc" \
+	"CXX_PARALLEL = CC" \
+	"FC_SERIAL = ftn" \
+	"CC_SERIAL = cc" \
+	"CXX_SERIAL = CC" \
+	"FFLAGS_OPT = -O3 -m64 -ffree-line-length-none -fdefault-real-8 -fdefault-double-8 -fconvert=big-endian -ffree-form" \
+	"CFLAGS_OPT = -O3 -m64" \
+	"CXXFLAGS_OPT = -O3 -m64" \
+	"LDFLAGS_OPT = -O3 -m64" \
+	"FFLAGS_DEBUG = -g -m64 -ffree-line-length-none -fdefault-real-8 -fdefault-double-8 -fconvert=big-endian -ffree-form" \
+	"CFLAGS_DEBUG = -g -m64" \
+	"CXXFLAGS_DEBUG = -g -m64" \
+	"LDFLAGS_DEBUG = -g -m64" \
+	"CORE = $(CORE)" \
+	"DEBUG = $(DEBUG)" \
+	"SERIAL = $(SERIAL)" \
+	"USE_PAPI = $(USE_PAPI)" \
+	"CPPFLAGS = $(MODEL_FORMULATION) -DUNDERSCORE -D_MPI $(FILE_OFFSET) $(ZOLTAN_DEFINE)" )
+
 intel-nersc:
 	( $(MAKE) all \
 	"FC_PARALLEL = ftn" \
 	"CC_PARALLEL = cc" \
+	"CXX_PARALLEL = CC" \
 	"FC_SERIAL = ftn" \
 	"CC_SERIAL = cc" \
+	"CXX_SERIAL = CC" \
 	"FFLAGS_OPT = -real-size 64 -O3 -convert big_endian -FR" \
 	"CFLAGS_OPT = -O3" \
+	"CXXFLAGS_OPT = -O3" \
 	"LDFLAGS_OPT = -O3" \
 	"CORE = $(CORE)" \
 	"DEBUG = $(DEBUG)" \
@@ -222,13 +268,17 @@ bluegene:
 	( $(MAKE) all \
 	"FC_PARALLEL = mpixlf95_r" \
 	"CC_PARALLEL = mpixlc_r" \
+	"CXX_PARALLEL = mpixlcxx_r" \
 	"FC_SERIAL = bgxlf95_r" \
 	"CC_SERIAL = bgxlc_r" \
+	"CXX_SERIAL = bgxlc++_r" \
 	"FFLAGS_OPT = -O2 -g -qrealsize=8" \
 	"CFLAGS_OPT = -O2 -g" \
+	"CXXFLAGS_OPT = -O2 -g" \
 	"LDFLAGS_OPT = -O2 -g" \
 	"FFLAGS_DEBUG = -O0 -g -C -qinitalloc -qinitauto -qrealsize=8" \
 	"CFLAGS_DEBUG = -O0 -g" \
+	"CXXFLAGS_DEBUG = -O0 -g" \
 	"LDFLAGS_DEBUG = -O0 -g" \
 	"CORE = $(CORE)" \
 	"DEBUG = $(DEBUG)" \
@@ -295,11 +345,13 @@ ifeq "$(DEBUG)" "true"
 ifndef FFLAGS_DEBUG
 	FFLAGS=$(FFLAGS_OPT)
 	CFLAGS=$(CFLAGS_OPT)
+	CXXFLAGS=$(CXXFLAGS_OPT)
 	LDFLAGS=$(LDFLAGS_OPT)
 	DEBUG_MESSAGE="Debug flags are not defined for this compile group. Defaulting to Optimized flags"
 else # FFLAGS_DEBUG IF
 	FFLAGS=$(FFLAGS_DEBUG)
 	CFLAGS=$(CFLAGS_DEBUG)
+	CXXFLAGS=$(CXXFLAGS_DEBUG)
 	LDFLAGS=$(LDFLAGS_DEBUG)
 	override CPPFLAGS += -DMPAS_DEBUG
 	DEBUG_MESSAGE="Debugging is on."
@@ -308,12 +360,14 @@ endif # FFLAGS_DEBUG IF
 else # DEBUG IF
 	FFLAGS=$(FFLAGS_OPT)
 	CFLAGS=$(CFLAGS_OPT)
+	CXXFLAGS=$(CXXFLAGS_OPT)
 	LDFLAGS=$(LDFLAGS_OPT)
 	DEBUG_MESSAGE="Debugging is off."
 endif # DEBUG IF
 
 FC=$(FC_PARALLEL)
 CC=$(CC_PARALLEL)
+CXX=$(CXX_PARALLEL)
 SFC=$(FC_SERIAL)
 SCC=$(CC_SERIAL)
 PARALLEL_MESSAGE="Parallel version is on."
@@ -428,12 +482,14 @@ mpas_main:
 ifeq "$(AUTOCLEAN)" "true"
 	$(RM) .mpas_core_*
 endif
-	cd src; $(MAKE) -j1 FC="$(FC)" \
+	cd src; $(MAKE) FC="$(FC)" \
                  CC="$(CC)" \
+                 CXX="$(CXX)" \
                  SFC="$(SFC)" \
                  SCC="$(SCC)" \
                  LINKER="$(LINKER)" \
                  CFLAGS="$(CFLAGS)" \
+                 CXXFLAGS="$(CXXFLAGS)" \
                  FFLAGS="$(FFLAGS)" \
                  LDFLAGS="$(LDFLAGS)" \
                  RM="$(RM)" \
@@ -450,11 +506,7 @@ endif
 
 	@echo "$(EXE_NAME)" > .mpas_core_$(CORE)
 	if [ -e src/$(EXE_NAME) ]; then mv src/$(EXE_NAME) .; fi
-	if [ -e src/inc/namelist.$(NAMELIST_SUFFIX).defaults ]; then mv src/inc/namelist.$(NAMELIST_SUFFIX).defaults .; fi
-	if [ ! -e namelist.$(NAMELIST_SUFFIX) ]; then cp namelist.$(NAMELIST_SUFFIX).defaults namelist.$(NAMELIST_SUFFIX); fi
-	if [ -e src/inc/streams.$(NAMELIST_SUFFIX).defaults ]; then mv src/inc/streams.$(NAMELIST_SUFFIX).defaults .; fi
-	if [ ! -e streams.$(NAMELIST_SUFFIX) ]; then cp streams.$(NAMELIST_SUFFIX).defaults streams.$(NAMELIST_SUFFIX); fi
-	for f in `find src/inc -name "stream_list.*"`; do mv $$f .; done
+	( cd src/core_$(CORE); $(MAKE) ROOT_DIR="$(PWD)" post_build )
 	@echo "*******************************************************************************"
 	@echo $(DEBUG_MESSAGE)
 	@echo $(PARALLEL_MESSAGE)
@@ -464,8 +516,6 @@ ifeq "$(AUTOCLEAN)" "true"
 	@echo $(AUTOCLEAN_MESSAGE)
 endif
 	@echo $(GEN_F90_MESSAGE)
-	@echo $(NAMELIST_MESSAGE)
-	@echo $(STREAM_MESSAGE)
 	@echo "*******************************************************************************"
 clean:
 	cd src; $(MAKE) clean RM="$(RM)" CORE="$(CORE)"

README.md

@@ -1,4 +1,4 @@
-MPAS-v3.3
+MPAS-v4.0
 ====
 
 The Model for Prediction Across Scales (MPAS) is a collaborative project for