Merge branch 'dev/gfdl' into salt_flux_unit_fix

.github/workflows/documentation-and-style.yml

@@ -18,11 +18,11 @@ jobs:
       continue-on-error: true
 
     - name: Install packages used when generating documentation
-      run: >
-        sudo apt-get install
-        python3-sphinx python3-lxml perl
-        texlive-binaries texlive-base bibtool tex-common texlive-bibtex-extra
-        graphviz
+      run: |
+        sudo apt-get update
+        sudo apt-get install python3-sphinx python3-lxml perl
+        sudo apt-get install texlive-binaries texlive-base bibtool tex-common texlive-bibtex-extra
+        sudo apt-get install graphviz
 
     - name: Build doxygen HTML
       run: |

ac/configure.ac

@@ -82,12 +82,20 @@ AX_FC_CHECK_MODULE([mpi],
 
 
 # netCDF configuration
-AC_PATH_PROG([NC_CONFIG], [nc-config])
-AS_IF([test -n "$NC_CONFIG"],
-  [CPPFLAGS="$CPPFLAGS -I$($NC_CONFIG --includedir)"
-  FCFLAGS="$FCFLAGS -I$($NC_CONFIG --includedir)"
-  LDFLAGS="$LDFLAGS -L$($NC_CONFIG --libdir)"],
-  [AC_MSG_ERROR([Could not find nc-config.])])
+
+# 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.])])

ac/deps/configure.fms.ac

@@ -73,12 +73,20 @@ AC_DEFINE([use_libMPI])
 
 
 # netCDF configuration
-AC_PATH_PROG([NC_CONFIG], [nc-config])
-AS_IF([test -n "$NC_CONFIG"],
-  [CPPFLAGS="$CPPFLAGS -I$($NC_CONFIG --includedir)"
-  FCFLAGS="$FCFLAGS -I$($NC_CONFIG --includedir)"
-  LDFLAGS="$LDFLAGS -L$($NC_CONFIG --libdir)"],
-  [AC_MSG_ERROR([Could not find nc-config.])])
+
+# 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.])])

src/diagnostics/MOM_diagnostics.F90

@@ -2225,6 +2225,7 @@ subroutine set_dependent_diagnostics(MIS, ADp, CDp, G, CS)
   if (associated(CS%KE_dia)) then
     call safe_alloc_ptr(ADp%du_dt_dia,IsdB,IedB,jsd,jed,nz)
     call safe_alloc_ptr(ADp%dv_dt_dia,isd,ied,JsdB,JedB,nz)
+    call safe_alloc_ptr(CDp%diapyc_vel,isd,ied,jsd,jed,nz+1)
   endif
 
   if (associated(CS%uhGM_Rlay)) call safe_alloc_ptr(CDp%uhGM,IsdB,IedB,jsd,jed,nz)