Merge branch 'hotfix-v7.1'

This merge addresses several issues in the MPAS-Atmosphere model and
initialization, and it corrects several minor compilation issues.

MPAS-Atmosphere:
----------------

* In calculating moist air density in the real-data initialization case, virtual
  temperature, rather than temperature, should be used.

* An out-of-bounds array access in the GWDO scheme when running with multiple
  OpenMP threads has been corrected.

* A check has been added in the init_atmosphere core to ensure that the
  intermediate file interval and the 'surface' stream output interval are
  consistent.

* A non-standard BOZ-literal constant has been corrected in the
  module_ra_cam_support.F file. The non-standard constant lead to build
  failures, particularly with newer versions of the GNU compilers.

General software:
-----------------

* The logic to add PIO libraries to the definition of LIBS in the top-level
  Makefile has been updated to accommodate newer versions (approx. 2.5.2 or
  later) of the PIO library; without the fix to the Makefile, builds would
  fail with the message

  Checking for a usable PIO library...
  ************ ERROR ************
  Failed to compile a PIO test program
  Please ensure the PIO environment variable is set to the PIO installation directory
  ************ ERROR ************

* Various options for the 'gfortran' build target have been cleaned up.

* Occasional parallel build failures related to a race condition in the ezxml
  library compilation have been addressed.

Makefile

@@ -1,4 +1,4 @@
-MODEL_FORMULATION = 
+MODEL_FORMULATION =
 
 
 dummy:
@@ -219,14 +219,14 @@ gfortran:
 	"CC_SERIAL = gcc" \
 	"CXX_SERIAL = g++" \
 	"FFLAGS_PROMOTION = -fdefault-real-8 -fdefault-double-8" \
-	"FFLAGS_OPT = -O3 -m64 -ffree-line-length-none -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 -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" \
+	"FFLAGS_OPT = -O3 -ffree-line-length-none -fconvert=big-endian -ffree-form" \
+	"CFLAGS_OPT = -O3" \
+	"CXXFLAGS_OPT = -O3" \
+	"LDFLAGS_OPT = -O3" \
+	"FFLAGS_DEBUG = -g -ffree-line-length-none -fconvert=big-endian -ffree-form -fcheck=all -fbacktrace -ffpe-trap=invalid,zero,overflow" \
+	"CFLAGS_DEBUG = -g" \
+	"CXXFLAGS_DEBUG = -g" \
+	"LDFLAGS_DEBUG = -g" \
 	"FFLAGS_OMP = -fopenmp" \
 	"CFLAGS_OMP = -fopenmp" \
 	"CORE = $(CORE)" \
@@ -421,9 +421,9 @@ llvm:
 	"OPENMP = $(OPENMP)" \
 	"CPPFLAGS = $(MODEL_FORMULATION) -D_MPI" )
 
-CPPINCLUDES = 
-FCINCLUDES = 
-LIBS = 
+CPPINCLUDES =
+FCINCLUDES =
+LIBS =
 
 #
 # If user has indicated a PIO2 library, define USE_PIO2 pre-processor macro
@@ -458,9 +458,15 @@ endif
 # Depending on PIO version, libraries may be libpio.a, or libpiof.a and libpioc.a
 # Keep open the possibility of shared libraries in future with, e.g., .so suffix
 #
+# Check if libpio.* exists and link -lpio if so, but we make an exception for
+# libpio.settings (a file added in PIO2), which is not a library to link
 ifneq ($(wildcard $(PIO_LIB)/libpio\.*), )
-	LIBS += -lpio
+	# Makefiles don't support "and" operators so we have nested "if" instead
+	ifneq "$(wildcard $(PIO_LIB)/libpio\.*)" "$(PIO_LIB)/libpio.settings"
+		LIBS += -lpio
+	endif
 endif
+
 ifneq ($(wildcard $(PIO_LIB)/libpiof\.*), )
 	LIBS += -lpiof
 endif

README.md

@@ -1,4 +1,4 @@
-MPAS-v7.0
+MPAS-v7.1
 ====
 
 The Model for Prediction Across Scales (MPAS) is a collaborative project for

src/core_atmosphere/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="atmosphere" core_abbrev="atm" version="7.0">
+<registry model="mpas" core="atmosphere" core_abbrev="atm" version="7.1">
 
 <!-- **************************************************************************************** -->
 <!-- ************************************** Dimensions ************************************** -->
@@ -1352,10 +1352,10 @@
                      description="weights for cell-centered second derivative, normal to edge, for transport scheme"/>
 
                 <var name="adv_coefs" type="real" dimensions="FIFTEEN nEdges" units="unitless"
-                     description="Weighting coefficents used for reconstructing cell-based foelds at edges"/>
+                     description="Weighting coefficients used for reconstructing cell-based fields at edges"/>
 
                 <var name="adv_coefs_3rd" type="real" dimensions="FIFTEEN nEdges" units="unitless"
-                     description="Weighting coefficents used for reconstructing cell-based foelds at edges"/>
+                     description="Weighting coefficients used for reconstructing cell-based fields at edges"/>
 
                 <var name="advCellsForEdge" type="integer" dimensions="FIFTEEN nEdges" units="-"
                      description="Cells used to reconstruct a cell-based field at an edge"/>
@@ -3009,7 +3009,7 @@
                      description="terrain height"/>
 
                 <var name="albedo12m" type="real" dimensions="nMonths nCells" units="unitless"
-                     description="monthly-mean climatological aurface albedo"/>
+                     description="monthly-mean climatological surface albedo"/>
 
                 <var name="greenfrac" type="real" dimensions="nMonths nCells" units="unitless"
                      description="monthly-mean climatological greeness fraction"/>

src/core_atmosphere/physics/physics_wrf/module_bl_gwdo.F

@@ -365,7 +365,7 @@ subroutine gwdo2d(dudt, dvdt, dtaux2d, dtauy2d,                             &
    dxy4p(its:ite,3) = dxy4(its:ite,4)
    dxy4p(its:ite,4) = dxy4(its:ite,3)
 !
-   cleff(its:ite) = dxmeter
+   cleff(its:ite) = dxmeter(its:ite)
 !
 ! initialize arrays                                                 
 !                                                                       

src/core_atmosphere/physics/physics_wrf/module_ra_cam_support.F

@@ -8,7 +8,7 @@ MODULE module_ra_cam_support
   implicit none
       integer, parameter :: r8 = 8
       real(r8), parameter:: inf = 1.e20 ! CAM sets this differently in infnan.F90
-      integer, parameter:: bigint = O'17777777777'           ! largest possible 32-bit integer 
+      integer, parameter:: bigint = int(O'17777777777')      ! largest possible 32-bit integer 
 
       integer :: ixcldliq 
       integer :: ixcldice

src/core_init_atmosphere/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="init_atmosphere" core_abbrev="init_atm" version="7.0">
+<registry model="mpas" core="init_atmosphere" core_abbrev="init_atm" version="7.1">
 
 <!-- **************************************************************************************** -->
 <!-- ************************************** Dimensions ************************************** -->

src/core_init_atmosphere/mpas_init_atm_cases.F

@@ -74,7 +74,7 @@ subroutine init_atm_setup_case(domain, stream_manager)
       character(len=StrKIND), pointer :: xtime
 
       type (MPAS_Time_type)  :: curr_time, stop_time
-      type (MPAS_TimeInterval_type)  :: clock_interval, lbc_stream_interval
+      type (MPAS_TimeInterval_type)  :: clock_interval, lbc_stream_interval, surface_stream_interval
       character(len=StrKIND) :: timeString
 
       integer, pointer :: nCells
@@ -264,6 +264,21 @@ subroutine init_atm_setup_case(domain, stream_manager)
       else if (config_init_case == 8 ) then
 
          call mpas_log_write('real-data surface (SST) update test case ')
+
+         !
+         ! Check that config_fg_interval matches the output_interval of the surface stream
+         !
+         clock_interval = mpas_get_clock_timestep(domain % clock, ierr=ierr)
+         surface_stream_interval = MPAS_stream_mgr_get_stream_interval(stream_manager, 'surface', MPAS_STREAM_OUTPUT, ierr)
+         if (clock_interval /= surface_stream_interval) then
+            call mpas_log_write('****************************************************************',       messageType=MPAS_LOG_ERR)
+            call mpas_log_write('The intermediate SST file interval specified by ''config_fg_interval''', messageType=MPAS_LOG_ERR)
+            call mpas_log_write('does not match the output_interval for the ''surface'' stream.',         messageType=MPAS_LOG_ERR)
+            call mpas_log_write('Please correct the namelist.init_atmosphere and/or',                     messageType=MPAS_LOG_ERR)
+            call mpas_log_write('streams.init_atmosphere files.',                                         messageType=MPAS_LOG_ERR)
+            call mpas_log_write('****************************************************************',       messageType=MPAS_LOG_CRIT)
+         end if
+
          block_ptr => domain % blocklist
          do while (associated(block_ptr))
             call mpas_pool_get_subpool(block_ptr % structs, 'mesh', mesh)
@@ -4758,7 +4773,8 @@ subroutine init_atm_case_gfs(block, mesh, nCells, nEdges, nVertLevels, fg, state
             t(k,iCell) = t(k,iCell) * (p0 / pressure(k,iCell)) ** (rgas / cp)
 
             ! RHO_ZZ
-            rho_zz(k,iCell) = pressure(k,iCell) / rgas / (p(k,iCell) * t(k,iCell))
+            rho_zz(k,iCell) = pressure(k,iCell) / rgas / (p(k,iCell) * t(k,iCell) &
+                              * (1.0 + (rvord - 1.0) * scalars(index_qv,k,iCell)))
             rho_zz(k,iCell) = rho_zz(k,iCell) / (1.0 + scalars(index_qv,k,iCell))
          end do
       end do

src/core_landice/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="landice" core_abbrev="li" version="7.0">
+<registry model="mpas" core="landice" core_abbrev="li" version="7.1">
 
 
 <!-- ======================================================================= -->

src/core_ocean/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="ocean" core_abbrev="ocn" version="7.0">
+<registry model="mpas" core="ocean" core_abbrev="ocn" version="7.1">
 
 	<dims>
 		<dim name="nCells" units="unitless"

src/core_seaice/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="seaice" core_abbrev="seaice" version="7.0">
+<registry model="mpas" core="seaice" core_abbrev="seaice" version="7.1">
 
 	<dims>
 		<dim name="nCells"

src/core_sw/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="sw" core_abbrev="sw" version="7.0">
+<registry model="mpas" core="sw" core_abbrev="sw" version="7.1">
 	<dims>
 		<dim name="nCells"/>
 		<dim name="nEdges"/>

src/core_test/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="test" core_abbrev="test" version="7.0">
+<registry model="mpas" core="test" core_abbrev="test" version="7.1">
 	<dims>
 		<dim name="nCells"/>
 		<dim name="nEdges"/>

src/external/Makefile

@@ -6,7 +6,7 @@ esmf_time:
 	( cd esmf_time_f90; $(MAKE) FC="$(FC) $(FFLAGS)" CPP="$(CPP)" CPPFLAGS="$(CPPFLAGS) -DHIDE_MPI" GEN_F90=$(GEN_F90) )
 
 ezxml-lib:
-	( cd ezxml; $(MAKE) )
+	( cd ezxml; $(MAKE) OBJFILE="ezxml.o" )
 
 clean:
 	( cd esmf_time_f90; $(MAKE) clean )

src/external/ezxml/Makefile

@@ -1,14 +1,5 @@
-.SUFFIXES: .c .o
-
-OBJS = ezxml.o
-
-all: clean
-	$(MAKE) -j 1 library
-
-library: $(OBJS)
+$(OBJFILE): ezxml.c
+	$(CC) $(CFLAGS) $(CPPFLAGS) -c $< -o $(OBJFILE)
 
 clean:
 	$(RM) *.o *.i
-
-.c.o:
-	$(CC) $(CFLAGS) $(CPPFLAGS) -c $<

src/tools/input_gen/Makefile

@@ -4,14 +4,14 @@ EZXML_PATH= ../../external/ezxml
 
 NL_OBJS = namelist_gen.o test_functions.o
 ST_OBJS = streams_gen.o test_functions.o
-XML_OBJS = $(EZXML_PATH)/ezxml.o
+XML_OBJS = $(EZXML_PATH)/ezxml_tools.o
 
 all: ezxml
 	($(MAKE) -j 1 namelist_gen CPPFLAGS="$(CPPFLAGS)" CPPINCLUDES="$(CPPINCLUDES)")
 	($(MAKE) -j 1 streams_gen CPPFLAGS="$(CPPFLAGS)" CPPINCLUDES="$(CPPINCLUDES)")
 
 ezxml:
-	(cd $(EZXML_PATH); $(MAKE) CFLAGS="$(CFLAGS) $(TOOL_TARGET_ARCH)")
+	(cd $(EZXML_PATH); $(MAKE) CFLAGS="$(CFLAGS) $(TOOL_TARGET_ARCH)" OBJFILE="ezxml_tools.o")
 
 namelist_gen: ezxml $(NL_OBJS) $(XML_OBJS)
 	$(CC) $(CPPFLAGS) $(CFLAGS) -I$(EZXML_PATH) -o $@ $(NL_OBJS) $(XML_OBJS)

src/tools/registry/Makefile

@@ -9,10 +9,10 @@ all: ezxml
 	($(MAKE) parse CPPFLAGS="$(CPPFLAGS)" CPPINCLUDES="$(CPPINCLUDES)")
 
 ezxml:
-	(cd $(EZXML_PATH); $(MAKE) CFLAGS="$(CFLAGS) $(TOOL_TARGET_ARCH)")
+	(cd $(EZXML_PATH); $(MAKE) CFLAGS="$(CFLAGS) $(TOOL_TARGET_ARCH)" OBJFILE="ezxml_tools.o")
 
 parse: $(OBJS)
-	$(CC) $(CPPFLAGS) $(CFLAGS) $(EZXML_PATH)/ezxml.o  -I$(EZXML_PATH) -o $@ $(OBJS)
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(EZXML_PATH)/ezxml_tools.o -I$(EZXML_PATH) -o $@ $(OBJS)
 
 parse.o: