Merge branch 'master' into develop

This merge introduces fixes from the v5.2 release for building with PIO 2.x,
and it connects the v5.2 tag to future commits on develop.

* master:
  Check for GPTL library when building with PIO2
  For PIO2, set 'pio_mode' to zero when creating netCDF-4 files
  Obtain MPI_COMM_SELF from mpas_dmpar in MPAS_stream_mgr_block_write
  Export MPI_COMM_SELF from mpas_dmpar module
  Fix MPAS fillvalue usage when using PIO2
  Update version number to v5.2

Makefile

@@ -404,6 +404,9 @@ ifeq "$(USE_PIO2)" "true"
 	CPPINCLUDES = -DUSE_PIO2 -I$(PIO)/include
 	FCINCLUDES = -DUSE_PIO2 -I$(PIO)/include
 	LIBS = -L$(PIO)/lib -lpiof -lpioc
+ifneq ($(wildcard $(PIO)/lib/libgptl.a), ) # Check for GPTL library for PIO2
+	LIBS += -lgptl
+endif
 else
 	CPPINCLUDES = -I$(PIO)/include
 	FCINCLUDES = -I$(PIO)/include
@@ -414,6 +417,9 @@ ifeq "$(USE_PIO2)" "true"
 	CPPINCLUDES = -DUSE_PIO2 -I$(PIO)/include
 	FCINCLUDES = -DUSE_PIO2 -I$(PIO)/include
 	LIBS = -L$(PIO) -lpiof -lpioc
+ifneq ($(wildcard $(PIO)/libgptl.a), ) # Check for GPTL library for PIO2
+	LIBS += -lgptl
+endif
 else
 	CPPINCLUDES = -I$(PIO)
 	FCINCLUDES = -I$(PIO)

README.md

@@ -1,4 +1,4 @@
-MPAS-v5.1
+MPAS-v5.2
 ====
 
 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="5.1">
+<registry model="mpas" core="atmosphere" core_abbrev="atm" version="5.2">
 
 <!-- **************************************************************************************** -->
 <!-- ************************************** Dimensions ************************************** -->

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="5.1">
+<registry model="mpas" core="init_atmosphere" core_abbrev="init_atm" version="5.2">
 
 <!-- **************************************************************************************** -->
 <!-- ************************************** Dimensions ************************************** -->

src/core_landice/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="landice" core_abbrev="li" version="5.1">
+<registry model="mpas" core="landice" core_abbrev="li" version="5.2">
 
 
 <!-- ======================================================================= -->

src/core_ocean/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="ocean" core_abbrev="ocn" version="5.1">
+<registry model="mpas" core="ocean" core_abbrev="ocn" version="5.2">
 
 	<dims>
 		<dim name="nCells" units="unitless"

src/core_sw/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="sw" core_abbrev="sw" version="5.1">
+<registry model="mpas" core="sw" core_abbrev="sw" version="5.2">
 	<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="5.1">
+<registry model="mpas" core="test" core_abbrev="test" version="5.2">
 	<dims>
 		<dim name="nCells"/>
 		<dim name="nEdges"/>

src/framework/mpas_dmpar.F

@@ -57,6 +57,12 @@ module mpas_dmpar
    integer, parameter, public :: IO_NODE = 0
    integer, parameter, public :: BUFSIZE = 6000
 
+#ifdef _MPI
+   public :: MPI_COMM_SELF
+#else
+   integer, parameter, public :: MPI_COMM_SELF = 0
+#endif
+
    public :: mpas_dmpar_init
    public :: mpas_dmpar_finalize
    public :: mpas_dmpar_abort

src/framework/mpas_io.F

@@ -281,7 +281,11 @@ type (MPAS_IO_Handle_type) function MPAS_io_open(filename, mode, ioformat, ioCon
             pio_mode = PIO_64BIT_OFFSET
          else if (ioformat == MPAS_IO_NETCDF4) then
             pio_iotype = PIO_iotype_netcdf4p
+#ifdef USE_PIO2
+            pio_mode = 0
+#else
             pio_mode = PIO_64BIT_OFFSET
+#endif
          end if
       end if
 

src/framework/mpas_stream_manager.F

@@ -2678,6 +2678,8 @@ end subroutine MPAS_stream_mgr_write !}}}
     !-----------------------------------------------------------------------
     subroutine MPAS_stream_mgr_block_write(manager, writeBlock, streamID, timeLevel, mgLevel, forceWriteNow, writeTime, ierr) !{{{
 
+        use mpas_dmpar, only : MPI_COMM_SELF
+
         implicit none
 
         type (MPAS_streamManager_type), intent(inout) :: manager