Update CIME to ESMCI cime5.8.7-2

cime/config/cesm/config_grids.xml

@@ -926,11 +926,11 @@
       <mask>gx3v7</mask>
     </model_grid>
 
-    <model_grid alias="ne16pg3_ne16pg3_mg37" not_compset="_POP|_CLM">
+    <model_grid alias="ne16pg3_ne16pg3_mg17" not_compset="_POP|_CLM">
       <grid name="atm">ne16np4.pg3</grid>
       <grid name="lnd">ne16np4.pg3</grid>
       <grid name="ocnice">ne16np4.pg3</grid>
-      <mask>gx3v7</mask>
+      <mask>gx1v7</mask>
     </model_grid>
 
     <model_grid alias="ne30pg3_ne30pg3_mg17" not_compset="_POP">

cime/scripts/lib/CIME/XML/compilers.py

@@ -24,16 +24,16 @@ def __init__(self, machobj, infile=None, compiler=None, mpilib=None, files=None,
             if files is None:
                 files = Files()
             infile = files.get_value("COMPILERS_SPEC_FILE")
-            schema = files.get_schema("COMPILERS_SPEC_FILE")
+        schema = files.get_schema("COMPILERS_SPEC_FILE")
 
         GenericXML.__init__(self, infile, schema)
-        self._machobj = machobj
         if version is not None:
             # this is used in scripts_regression_tests to force version 2, it should not be used otherwise
             self._version = version
         else:
             self._version = self.get_version()
 
+        self._machobj = machobj
         self.machine  = machobj.get_machine_name()
         self.os = machobj.get_value("OS")
         if compiler is None:
@@ -52,7 +52,7 @@ def __init__(self, machobj, infile=None, compiler=None, mpilib=None, files=None,
         #This could cause problems if node matchs are repeated when only one is expected
         infile = os.path.join(os.environ.get("HOME"),".cime","config_compilers.xml")
         if os.path.exists(infile):
-            GenericXML.read(self, infile)
+            GenericXML.read(self, infile, schema=schema)
 
         if self.compiler is not None:
             self.set_compiler(compiler)

cime/scripts/lib/CIME/case/case.py

@@ -1021,6 +1021,7 @@ def configure(self, compset_name, grid_name, machine_name=None,
         # we don't want to resolve variables until we need them
         if output_root is None:
             output_root = self.get_value("CIME_OUTPUT_ROOT")
+        output_root = os.path.abspath(output_root)
         self.set_value("CIME_OUTPUT_ROOT", output_root)
         if non_local:
             self.set_value("EXEROOT", os.path.join(output_root, self.get_value("CASE"), "bld"))

cime/scripts/lib/CIME/get_timing.py

@@ -484,7 +484,7 @@ def _getTiming(self, inst=0):
             for k in self.case.get_values("COMP_CLASSES"):
                 m = self.models[k]
                 self.write("    {} Run Time:  {:10.3f} seconds   {:10.3f} seconds/mday   {:10.2f} myears/wday \n".format(k, m.tmax, m.tmax/adays, m.tmaxr))
-                self.write("    CPL COMM Time: {:10.3f} seconds   {:10.3f} seconds/mday   {:10.2f} myears/wday \n".format(xmax, xmax/adays, xmaxr))
+            self.write("    CPL COMM Time: {:10.3f} seconds   {:10.3f} seconds/mday   {:10.2f} myears/wday \n".format(xmax, xmax/adays, xmaxr))
 
             pstrlen = 25
             hoffset = 1

cime/src/drivers/mct/cime_config/config_component_cesm.xml

@@ -226,10 +226,13 @@
       <value compset="_DATM%COPYALL_NPS">72</value>
       <value compset="_DATM.*_CLM">48</value>
       <value compset="_DATM.*_DICE.*_POP2">4</value>
+      <value compset="_DATM.*_DICE.*_MOM6">24</value>
       <value compset="_DATM.*_SLND.*_CICE.*_POP2">24</value>
+      <value compset="_DATM.*_SLND.*_CICE.*_MOM6">24</value>
       <value compset="_DATM.*_CICE.*_DOCN">24</value>
       <value compset="_DATM.*_DOCN%US20">24</value>
       <value compset="_DATM%CPLHIST.+POP\d">48</value>
+      <value compset="_DATM%CPLHIST.+MOM\d">48</value>
       <value compset="_MPAS">1</value>
       <value compset=".+" grid="a%0.23x0.31">96</value>
       <value compset=".+" grid="a%ne60np4">96</value>
@@ -252,7 +255,9 @@
       <value compset=".+" grid="1x1_vancou">24</value>
       <value compset="_DLND.*_CISM\d">1</value>
       <value compset="_DATM.*_DICE.*_POP2.*_WW3">4</value>
+      <value compset="_DATM.*_DICE.*_MOM6.*_WW3">4</value>
       <value compset="_DATM.*_DICE.*_POP2.*_DWAV">4</value>
+      <value compset="_DATM.*_DICE.*_MOM6.*_DWAV">4</value>
     </values>
     <group>run_coupling</group>
     <file>env_run.xml</file>
@@ -292,6 +297,7 @@
     <default_value>$ATM_NCPL</default_value>
     <values match="last">
       <value compset="_POP2">1</value>
+      <value compset="_MOM6">24</value>
       <value compset="_POP2" grid="oi%tx0.1v2">4</value>
       <value compset="_POP2" grid="oi%gx1v6">24</value>
       <value compset="_POP2" grid="oi%gx1v7">24</value>
@@ -316,6 +322,7 @@
       <value compset="_DLND.*_CISM\d">1</value>
       <value compset="_SGLC">$ATM_NCPL</value>
       <value compset="_XGLC">$ATM_NCPL</value>
+      <value compset="_MOM6">1</value>
     </values>
     <group>run_coupling</group>
     <file>env_run.xml</file>
@@ -348,9 +355,11 @@
     <default_value>8</default_value>
     <values match="last">
       <value compset="_DATM.*_POP2.*_DROF">$ATM_NCPL</value>
+      <value compset="_DATM.*_MOM6.*_DROF">$ATM_NCPL</value>
       <value compset="_DATM.*_DOCN%SOM">$ATM_NCPL</value>
       <value compset="_DATM.*_SLND.*_DICE.*_DOCN">$ATM_NCPL</value>
       <value compset="_DATM%CPLHIST.+POP\d">8</value>
+      <value compset="_DATM%CPLHIST.+MOM\d">8</value>
       <value compset="_XATM.*_XLND.*_XICE.*_XOCN">$ATM_NCPL</value>
       <value compset="_DLND.*_CISM\d">1</value>
       <value compset="_SROF">$ATM_NCPL</value>
@@ -433,6 +442,7 @@
     <values match="last">
       <value compset="_DATM.*_DOCN%SOM"			>CESM1_MOD</value>
       <value compset="_POP2"				>CESM1_MOD</value>
+      <value compset="_MOM6"				>RASM_OPTION1</value>
       <value compset="_POP2" grid="oi%gx1v6"		>RASM_OPTION1</value>
       <value compset="_POP2" grid="oi%gx1v7"		>RASM_OPTION1</value>
       <value compset="_DATM%NYF.*_SLND.*_DICE.*_DOCN"	>CESM1_MOD</value>

cime/src/externals/pio2/.travis.yml

@@ -40,15 +40,14 @@ env:
     - LDFLAGS='-L/usr/lib'
 
 script:
-  - ls -l /usr/include
   - autoreconf -i
-  - export CFLAGS='-std=c99  -fsanitize=address -fno-omit-frame-pointer'
+  - export CFLAGS='-std=c99  -fsanitize=address -fno-omit-frame-pointer -Werror'
   - export FFLAGS='-fsanitize=address -fno-omit-frame-pointer'
-  - export FCFLAGS='-fsanitize=address -fno-omit-frame-pointer'
+  - export FCFLAGS='-fsanitize=address -fno-omit-frame-pointer -Werror'
   - export DISTCHECK_CONFIGURE_FLAGS='--enable-fortran'
   - ./configure --enable-fortran --enable-developer-docs
-  - make
   - make -j distcheck
+  - make -j distclean
   - rm -rf build
   - mkdir build
   - cd build

cime/src/externals/pio2/configure.ac

@@ -21,6 +21,7 @@ AC_SUBST([VERSION_PATCH], [4])
 AC_CONFIG_MACRO_DIR([m4])
 
 # Libtool initialisation.
+LD=ld # Required for MPE to work.
 LT_INIT
 
 # Find and learn about the C compiler.
@@ -52,22 +53,6 @@ if test "x$enable_logging" = xyes; then
    AC_DEFINE([PIO_ENABLE_LOGGING], 1, [If true, turn on logging.])
 fi
 
-# Does the user want to use MPE library?
-AC_MSG_CHECKING([whether use of MPE library is enabled])
-AC_ARG_ENABLE([mpe],
-              [AS_HELP_STRING([--enable-mpe],
-                              [enable use of MPE library for timing and diagnostic info (may negatively impact performance).])])
-test "x$enable_mpe" = xyes || enable_mpe=no
-AC_MSG_RESULT([$enable_mpe])
-if test "x$enable_mpe" = xyes; then
-   AC_SEARCH_LIBS([MPE_Log_get_event_number], [mpe], [HAVE_LIBMPE=yes], [HAVE_LIBMPE=no], [-lpthread -lm])
-   AC_CHECK_HEADERS([mpe.h], [HAVE_MPE=yes], [HAVE_MPE=no])
-   if test "x$HAVE_LIBMPE" = xno -o "x$HAVE_MPE" = xno; then
-      AC_MSG_ERROR([MPE not found but --enable-mpe used.])
-   fi
-   AC_DEFINE([USE_MPE], 1, [If true, use MPE timing library.])
-fi
-
 # Does the user want to enable timing?
 AC_MSG_CHECKING([whether GPTL timing library is used])
 AC_ARG_ENABLE([timing],
@@ -104,6 +89,32 @@ test "x$enable_fortran" = xyes || enable_fortran=no
 AC_MSG_RESULT([$enable_fortran])
 AM_CONDITIONAL(BUILD_FORTRAN, [test "x$enable_fortran" = xyes])
 
+# Does the user want to use MPE library?
+AC_MSG_CHECKING([whether use of MPE library is enabled])
+AC_ARG_ENABLE([mpe],
+              [AS_HELP_STRING([--enable-mpe],
+                              [enable use of MPE library for timing and diagnostic info (may negatively impact performance).])])
+test "x$enable_mpe" = xyes || enable_mpe=no
+AC_MSG_RESULT([$enable_mpe])
+if test "x$enable_mpe" = xyes; then
+
+   AC_SEARCH_LIBS([pthread_setspecific], [pthread], [], [], [])
+   dnl AC_SEARCH_LIBS([MPE_Log_get_event_number], [mpe], [HAVE_LIBMPE=yes], [HAVE_LIBMPE=no], [])
+   dnl AC_SEARCH_LIBS([MPE_Init_mpi_core], [lmpe], [HAVE_LIBLMPE=yes], [HAVE_LIBLMPE=no], [])
+   AC_CHECK_HEADERS([mpe.h], [HAVE_MPE=yes], [HAVE_MPE=no])
+   dnl if test "x$HAVE_LIBMPE" != xyes; then
+   dnl    AC_MSG_ERROR([-lmpe not found but --enable-mpe used.])
+   dnl fi
+   dnl if test "x$HAVE_LIBLMPE" != xyes; then
+   dnl    AC_MSG_ERROR([-llmpe not found but --enable-mpe used.])
+   dnl fi
+   if test $enable_fortran = yes; then
+      AC_MSG_ERROR([MPE not implemented in Fortran tests and examples. Build without --enable-fortran])
+   fi
+   AC_DEFINE([USE_MPE], 1, [If true, use MPE timing library.])
+
+fi
+
 # Does the user want to disable pnetcdf?
 AC_MSG_CHECKING([whether pnetcdf is to be used])
 AC_ARG_ENABLE([pnetcdf],
@@ -150,9 +161,9 @@ if test "x$enable_docs" = xyes; then
    fi
    AC_SUBST([FORTRAN_SRC_FILES], ["../src/flib/piodarray.f90  ../src/flib/pio.F90  ../src/flib/pio_kinds.F90  ../src/flib/piolib_mod.f90  ../src/flib/pionfatt_mod_2.f90  ../src/flib/pio_nf.F90  ../src/flib/pionfget_mod_2.f90  ../src/flib/pionfput_mod.f90  ../src/flib/pio_support.F90  ../src/flib/pio_types.F90"])
    if test "x$enable_developer_docs" = xyes; then
-      AC_SUBST([C_SRC_FILES], ["../src/clib"])
+      AC_SUBST([C_SRC_FILES], ["../src/clib ../src/ncint"])
    else
-      AC_SUBST([C_SRC_FILES], ["../src/clib/pio_nc.c ../src/clib/pio_nc4.c ../src/clib/pio_darray.c ../src/clib/pio_get_nc.c ../src/clib/pio_put_nc.c ../src/clib/pioc_support.c ../src/clib/pioc.c ../src/clib/pio_file.c ../src/clib/pio.h ../src/clib/pio_get_vard.c ../src/clib/pio_put_vard.c"])
+      AC_SUBST([C_SRC_FILES], ["../src/clib/pio_nc.c ../src/clib/pio_nc4.c ../src/clib/pio_darray.c ../src/clib/pio_get_nc.c ../src/clib/pio_put_nc.c ../src/clib/pioc_support.c ../src/clib/pioc.c ../src/clib/pio_file.c ../src/clib/pio.h ../src/clib/pio_get_vard.c ../src/clib/pio_put_vard.c ../src/ncint/ncint_pio.c ../src/ncint/nc_put_vard.c ../src/ncint/nc_get_vard.c"])
    fi
    AC_CONFIG_FILES([doc/Doxyfile])
 fi
@@ -251,6 +262,30 @@ if test "x$enable_timing" = xyes; then
 fi
 AM_CONDITIONAL([HAVE_PAPI], [test "x$have_papi" = xyes])
 
+# Does the user want to build netcdf-c integration layer?
+AC_MSG_CHECKING([whether netcdf-c integration layer should be build])
+AC_ARG_ENABLE([netcdf-integration],
+              [AS_HELP_STRING([--enable-netcdf-integration],
+                              [enable building of netCDF C API integration.])])
+test "x$enable_netcdf_integration" = xyes || enable_netcdf_integration=no
+AC_MSG_RESULT([$enable_netcdf_integration])
+if test "x$enable_netcdf_integration" = xyes -a "x$enable_timing" = xyes; then
+   AC_MSG_ERROR([Cannot use GPTL timing library with netCDF interation.])
+fi
+if test "x$enable_netcdf_integration" = xyes -a "x$have_netcdf_par" = xno; then
+   AC_MSG_ERROR([Cannot use netCDF integration unless netCDF library was built for parallel I/O.])
+fi
+# These are needed by ncdispatch.h. Only build with HDF5 parallel
+# versions of netCDF. */
+if test "x$enable_netcdf_integration" = xyes; then
+  AC_DEFINE([HDF5_PARALLEL],[1],[Does HDF5 library provide parallel access])
+  AC_DEFINE([USE_NETCDF4],[1],[Does HDF5 library provide parallel access])
+  AC_DEFINE([NETCDF_INTEGRATION],[1],[Are we building with netCDF integration])
+fi
+
+AM_CONDITIONAL(BUILD_NCINT, [test "x$enable_netcdf_integration" = xyes])
+AM_CONDITIONAL(NETCDF_INTEGRATION, [test "x$enable_netcdf_integration" = xyes])
+
 AC_CONFIG_FILES([tests/general/pio_tutil.F90:tests/general/util/pio_tutil.F90])
 
 AC_CONFIG_LINKS([tests/unit/input.nl:tests/unit/input.nl])
@@ -262,10 +297,13 @@ AC_CONFIG_HEADERS([config.h])
 AC_OUTPUT(Makefile
           src/Makefile
           src/clib/Makefile
+          src/ncint/Makefile
           src/flib/Makefile
           src/gptl/Makefile
           tests/Makefile
           tests/cunit/Makefile
+          tests/ncint/Makefile
+          tests/fncint/Makefile
           tests/unit/Makefile
           tests/general/Makefile
           tests/general/util/Makefile
@@ -275,4 +313,5 @@ AC_OUTPUT(Makefile
           doc/images/Makefile
           examples/Makefile
           examples/c/Makefile
+          examples/f03/Makefile
           scripts/Makefile)

cime/src/externals/pio2/doc/source/netcdf_integration.txt

@@ -0,0 +1,22 @@
+/** @page netcdf_integration NetCDF API Integration
+
+The netCDF integration feature allows existing netCDF codes, in C or
+Fortran, to be easily converted to use PIO.
+
+# Building and Using PIO with NetCDF Integration
+
+In order to use netCDF integration:
+
+* The PIO configure must use the option --enable-netcdf-integration.
+
+* The latest master of the netcdf-c library must be built and used,
+and the PIO build must include the netcdf-c/include directory in its
+CPPFLAGS, in order to find internal netCDF header files needed for
+netCDF integration. (The netcdf-c library is being modified to export
+publically everything needed, so future releases of netcdf-c will no
+longer require this.)
+
+Once PIO is build for netCDF integration, it provides the nc_* and
+nf_* functions required to fully integrate PIO and netCDF.
+
+*/

cime/src/externals/pio2/doc/source/users_guide.txt

@@ -12,6 +12,7 @@ releases.
  - @ref decomp
  - @ref error
  - @ref examp
+ - @ref netcdf_integration
  - @ref faq
  - @ref api
  - @ref c_api

cime/src/externals/pio2/examples/Makefile.am

@@ -2,5 +2,8 @@
 
 # Ed Hartnett
 
-SUBDIRS = c
+if BUILD_FORTRAN
+F03 = f03
+endif # BUILD_FORTRAN
 
+SUBDIRS = c ${F03}

cime/src/externals/pio2/examples/c/Makefile.am

@@ -4,7 +4,7 @@
 # Ed Hartnett 5/7/18
 
 # Link to our assembled library.
-AM_LDFLAGS = ${top_builddir}/src/clib/libpio.la
+LDADD = ${top_builddir}/src/clib/libpioc.la
 AM_CPPFLAGS = -I$(top_srcdir)/src/clib
 
 # Build the tests for make check.
@@ -19,4 +19,4 @@ endif # RUN_TESTS
 EXTRA_DIST = run_tests.sh
 
 # Clean up files produced during testing.
-CLEANFILES = *.nc *.log
+CLEANFILES = *.nc *.log *.clog2 *.slog2

cime/src/externals/pio2/examples/c/darray_async.c

@@ -71,31 +71,6 @@ int dim_len[NDIM3] = {NC_UNLIMITED, DIM_LEN_X, DIM_LEN_Y};
 /* Names of dimensions. */
 char dim_name[NDIM3][PIO_MAX_NAME + 1] = {"unlimted", "x", "y"};
 
-/* Handle MPI errors. This should only be used with MPI library
- * function calls. */
-#define MPIERR(e) do {                                                  \
-	MPI_Error_string(e, err_buffer, &resultlen);			\
-	printf("MPI error, line %d, file %s: %s\n", __LINE__, __FILE__, err_buffer); \
-	MPI_Finalize();							\
-	return 2;							\
-    } while (0)
-
-/* Handle non-MPI errors by finalizing the MPI library and exiting
- * with an exit code. */
-#define ERR(e) do {				\
-	MPI_Finalize();				\
-	return e;				\
-    } while (0)
-
-/* Global err buffer for MPI. When there is an MPI error, this buffer
- * is used to store the error message that is associated with the MPI
- * error. */
-char err_buffer[MPI_MAX_ERROR_STRING];
-
-/* This is the length of the most recent MPI error message, stored
- * int the global error string. */
-int resultlen;
-
 /* @brief Check the output file.
  *
  *  Use netCDF to check that the output is as expected.