Autoconf netCDF flag update

.gitignore

@@ -4,19 +4,7 @@
 html
 
 
-# Build output
-*.o
-*.mod
-MOM6
-build/
-_build/
-deps/
-MOM6.tags
-bib*.aux
-citelist.doc*
-
-
-# Autoconf
+# Autoconf output
 aclocal.m4
 autom4te.cache/
 config.log

ac/configure.ac

@@ -83,25 +83,56 @@ AX_FC_CHECK_MODULE([mpi],
 
 # netCDF configuration
 
-# NOTE: `nf-config --flibs` combines library paths (-L) and libraries (-l),
-#   even though these ought to be separated in the invocation of `ld`.
-#
-# We use `sed` to strip the -l and pass the -L to LDFLAGS, and rely on autoconf
-#   to configure the -l flags.
-AC_PROG_SED
-
-AC_PATH_PROG([NF_CONFIG], [nf-config])
-AS_IF([test -n "$NF_CONFIG"],
-  [CPPFLAGS="$CPPFLAGS $($NF_CONFIG --fflags)"
-  FCFLAGS="$FCFLAGS $($NF_CONFIG --fflags)"
-  LDFLAGS="$LDFLAGS $($NF_CONFIG --flibs | $SED -e 's/-l[[^ 	]]*//g')"],
-  [AC_MSG_ERROR([Could not find nf-config.])])
-
-AX_FC_CHECK_MODULE([netcdf],
-  [], [AC_MSG_ERROR([Could not find netcdf module.])])
-AX_FC_CHECK_LIB([netcdff], [nf_create], [netcdf],
-  [], [AC_MSG_ERROR([Could not link netcdff library.])]
-)
+# Search for the Fortran netCDF module, fallback to nf-config.
+AX_FC_CHECK_MODULE([netcdf], [], [
+  AS_UNSET([ax_fc_cv_mod_netcdf])
+  AC_PATH_PROG([NF_CONFIG], [nf-config])
+  AS_IF([test -n "$NF_CONFIG"], [
+    AC_SUBST([FCFLAGS], ["$FCFLAGS -I$($NF_CONFIG --includedir)"])
+    ], [AC_MSG_ERROR([Could not find nf-config.])]
+  )
+  AX_FC_CHECK_MODULE([netcdf], [], [
+    AC_MSG_ERROR([Could not find netcdf module.])
+  ])
+])
+
+# FMS may invoke netCDF C calls, so we link to libnetcdf.
+AC_LANG_PUSH([C])
+AC_CHECK_LIB([netcdf], [nc_create], [], [
+  AS_UNSET([ac_cv_lib_netcdf_nc_create])
+  AC_PATH_PROG([NC_CONFIG], [nc-config])
+  AS_IF([test -n "$NC_CONFIG"], [
+    AC_SUBST([LDFLAGS],
+      ["$LDFLAGS -L$($NC_CONFIG --libdir)"]
+    )
+    ], [AC_MSG_ERROR([Could not find nc-config.])]
+  )
+  AC_CHECK_LIB([netcdf], [nc_create], [], [
+    AC_MSG_ERROR([Could not find libnetcdf.])
+  ])
+])
+AC_LANG_POP([C])
+
+# NOTE: We test for nf_create, rather than nf90_create, because AX_FC_CHECK_LIB
+#   is currently not yet able to properly probe inside modules.
+#   Testing of the nf90_* functions will require a macro update.
+# NOTE: nf-config does not have a --libdir flag, so we use --prefix and assume
+#   that libraries are in the $prefix/lib directory.
+
+# Link to Fortran netCDF library, netcdff
+AX_FC_CHECK_LIB([netcdff], [nf_create], [], [], [
+  AS_UNSET([ax_fc_cv_lib_netcdff_nf_create])
+  AC_PATH_PROG([NF_CONFIG], [nf-config])
+  AS_IF([test -n "$NF_CONFIG"], [
+    AC_SUBST([LDFLAGS],
+      ["$LDFLAGS -L$($NF_CONFIG --prefix)/lib"]
+    )
+    ], [AC_MSG_ERROR([Could not find nf-config.])]
+  )
+  AX_FC_CHECK_LIB([netcdff], [nf_create], [], [], [
+    AC_MSG_ERROR([Could not find libnetcdff.])
+  ])
+])
 
 
 # Force 8-byte reals

ac/deps/Makefile

@@ -13,7 +13,7 @@ MKMF_COMMIT ?= master
 
 # FMS framework
 FMS_URL ?= https://github.com/NOAA-GFDL/FMS.git
-FMS_COMMIT ?= 2019.01.03
+FMS_COMMIT ?= 2020.04
 
 
 # List of source files to link this Makefile's dependencies to model Makefiles

ac/deps/configure.fms.ac

@@ -15,6 +15,7 @@ AC_PROG_CC
 AX_MPI
 CC=$MPICC
 
+
 # FMS configuration
 
 # Linux and macOS have a gettid system call, but it is not implemented in older
@@ -74,25 +75,38 @@ AC_DEFINE([use_libMPI])
 
 # netCDF configuration
 
-# NOTE: `nf-config --flibs` combines library paths (-L) and libraries (-l),
-#   even though these ought to be separated in the invocation of `ld`.
-#
-# We use `sed` to strip the -l and pass the -L to LDFLAGS, and rely on autoconf
-#   to configure the -l flags.
-AC_PROG_SED
-
-AC_PATH_PROG([NF_CONFIG], [nf-config])
-AS_IF([test -n "$NF_CONFIG"],
-  [CPPFLAGS="$CPPFLAGS $($NF_CONFIG --fflags)"
-  FCFLAGS="$FCFLAGS $($NF_CONFIG --fflags)"
-  LDFLAGS="$LDFLAGS $($NF_CONFIG --flibs | $SED -e 's/-l[[^ 	]]*//g')"],
-  [AC_MSG_ERROR([Could not find nf-config.])])
-
-AX_FC_CHECK_MODULE([netcdf],
-  [], [AC_MSG_ERROR([Could not find netcdf module.])])
-AX_FC_CHECK_LIB([netcdff], [nf_create], [netcdf],
-  [], [AC_MSG_ERROR([Could not link netcdff library.])]
-)
+# Check for netcdf.h header function declarations.
+# If unavailable, then try to invoke nc-create.
+AC_LANG_PUSH([C])
+AC_CHECK_HEADERS([netcdf.h], [], [
+  AS_UNSET([ac_cv_header_netcdf_h])
+  AC_PATH_PROG([NC_CONFIG], [nc-config])
+  AS_IF([test -n "$NC_CONFIG"], [
+      AC_SUBST([CPPFLAGS], ["$CPPFLAGS -I$($NC_CONFIG --includedir)"])
+    ],
+    [AC_MSG_ERROR([Could not find nc-config.])]
+  )
+  AC_CHECK_HEADERS([netcdf.h], [], [
+    AC_MSG_ERROR([Could not find netcdf.h])
+  ])
+])
+AC_LANG_POP([C])
+
+# Search for the Fortran netCDF module, fallback to nf-config.
+AX_FC_CHECK_MODULE([netcdf], [], [
+  AS_UNSET([ax_fc_cv_mod_netcdf])
+  AC_PATH_PROG([NF_CONFIG], [nf-config])
+  AS_IF([test -n "$NF_CONFIG"], [
+      AC_SUBST([FCFLAGS], ["$FCFLAGS -I$($NF_CONFIG --includedir)"])
+    ],
+    [AC_MSG_ERROR([Could not find nf-config.])]
+  )
+  AX_FC_CHECK_MODULE([netcdf], [], [
+    AC_MSG_ERROR([Could not find netcdf module.])
+  ])
+])
+
+# FMS requires this macro to signal netCDF support.
 AC_DEFINE([use_netCDF])
 
 

ac/m4/ax_fc_check_lib.m4

@@ -18,7 +18,7 @@ dnl    library with different -L flags, or perhaps other ld configurations.
 dnl
 dnl Results are cached in the ax_fc_cv_lib_LIBRARY_FUNCTION variable.
 dnl
-AC_DEFUN([AX_FC_CHECK_LIB],[dnl
+AC_DEFUN([AX_FC_CHECK_LIB],[
   AS_VAR_PUSHDEF([ax_fc_Lib], [ax_fc_cv_lib_$1_$2])
   m4_ifval([$6],
     [ax_fc_lib_msg_LDFLAGS=" with $6"],
@@ -29,14 +29,15 @@ AC_DEFUN([AX_FC_CHECK_LIB],[dnl
     LDFLAGS="$6 $LDFLAGS"
     ax_fc_check_lib_save_LIBS=$LIBS
     LIBS="-l$1 $7 $LIBS"
-    AS_IF([test -n $3],
+    AS_IF([test -n "$3"],
       [ax_fc_use_mod="use $3"],
       [ax_fc_use_mod=""])
-    AC_LINK_IFELSE([
-        AC_LANG_PROGRAM([], [dnl
+    AC_LINK_IFELSE([dnl
+dnl Begin 7-column code block
+AC_LANG_PROGRAM([], [dnl
         $ax_fc_use_mod
-        call $2]dnl
-        )
+        call $2])dnl
+dnl End code block
       ],
       [AS_VAR_SET([ax_fc_Lib], [yes])],
       [AS_VAR_SET([ax_fc_Lib], [no])]

docs/.gitignore

@@ -4,8 +4,15 @@ doxygen.log
 APIs
 MOM6.tags
 details/tutorial
+
+
 # Ignore sphinx-build output
 _build
 api
 src
 xml
+
+
+# Citation output
+bib*.aux
+citelist.doc*