Merge branch 'dev/gfdl' into ice_shelf_travis_upgrade

.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.])])

config_src/solo_driver/MOM_driver.F90

@@ -261,7 +261,7 @@ program MOM_main
 !$  call omp_set_num_threads(ocean_nthreads)
 !$OMP PARALLEL
 !$  write(6,*) "ocean_solo OMPthreading ", fms_affinity_get(), omp_get_thread_num(), omp_get_num_threads()
-!$  call flush(6)
+!$  flush(6)
 !$OMP END PARALLEL
 
   ! Read ocean_solo restart, which can override settings from the namelist.

src/core/MOM_forcing_type.F90

@@ -1875,17 +1875,16 @@ subroutine register_forcing_type_diags(Time, diag, US, use_temperature, handles,
 
   handles%id_total_saltflux = register_scalar_field('ocean_model',          &
       'total_salt_flux', Time, diag,                                        &
-      long_name='Area integrated surface salt flux', units='kg',            &
+      long_name='Area integrated surface salt flux', units='kg s-1',        &
       cmor_field_name='total_sfdsi',                                        &
-      cmor_units='kg s-1',                                                  &
       cmor_standard_name='downward_sea_ice_basal_salt_flux_area_integrated',&
       cmor_long_name='Downward Sea Ice Basal Salt Flux Area Integrated')
 
   handles%id_total_saltFluxIn = register_scalar_field('ocean_model', 'total_salt_Flux_In', &
-      Time, diag, long_name='Area integrated surface salt flux at surface from coupler', units='kg')
+      Time, diag, long_name='Area integrated surface salt flux at surface from coupler', units='kg s-1')
 
   handles%id_total_saltFluxAdded = register_scalar_field('ocean_model', 'total_salt_Flux_Added', &
-      Time, diag, long_name='Area integrated surface salt flux due to restoring or flux adjustment', units='kg')
+      Time, diag, long_name='Area integrated surface salt flux due to restoring or flux adjustment', units='kg s-1')
 
 
 end subroutine register_forcing_type_diags

src/diagnostics/MOM_PointAccel.F90

@@ -390,7 +390,7 @@ subroutine write_u_accel(I, j, um, hin, ADp, CDp, dt_in_T, G, GV, US, CS, vel_rp
 
     write(file,'(2/)')
 
-    call flush(file)
+    flush(file)
   endif
 
 end subroutine write_u_accel
@@ -722,7 +722,7 @@ subroutine write_v_accel(i, J, vm, hin, ADp, CDp, dt_in_T, G, GV, US, CS, vel_rp
 
     write(file,'(2/)')
 
-    call flush(file)
+    flush(file)
   endif
 
 end subroutine write_v_accel

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)