Add uninitialised variables check to CI build (#361)

* Add uninitialised variables check to CI build * Make optional preprocessor labels into comments * gotm-4.0: Changed parameter to single precision to match call. * Fixed some double ifdef defined preprocessor directives * Removed all preprocessor comment like labels * Undefine preprocessor types before reusing * Fix formatting and update do/enddo in icarus.F90 * Rewrote deprecated arithmetic if statement for 20.04 compatibility * Make init checks depend on setting DEBUG in build * Only run debug compilation with non-atmosphere configs
mom-ocean · Feb 10, 2022 · b68f137 · b68f137
1 parent b74873b
commit b68f137
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Showing 43 changed files with 167 additions and 120 deletions.
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -88,7 +88,16 @@ jobs:
         LIBACCESSOM2_ROOT: ${{ env.libaccessom2_dir }}
       run: |
         env
-        ./MOM_compile.csh --type ${{ matrix.TYPE }} --platform github --use_netcdf4
+        case "${{ matrix.TYPE }}" in
+          CM2M|ICCM|ESM2M)
+            debug=""
+          ;;
+          *)
+            debug="--debug"
+          ;;
+        esac
+        echo ./MOM_compile.csh $debug --type ${{ matrix.TYPE }} --platform github --use_netcdf4
+        ./MOM_compile.csh $debug --type ${{ matrix.TYPE }} --platform github --use_netcdf4
 
     # ----------
     # Test MOM-solo only currently
@@ -97,6 +106,7 @@ jobs:
       uses: actions/checkout@v2
       with: 
           repository: mom-ocean/MOM5-examples
+          ref: master
           path: MOM5-examples
 
     - name: Run bowl1 cold start

diff --git a/bin/mkmf.template.github b/bin/mkmf.template.github
@@ -41,7 +41,11 @@ FPPFLAGS := $(INCLUDE)
 
 CFLAGS := -D__IFC -O2 -no-pie $(shell nc-config --cflags) -I/usr/include/openmpi $(INCLUDE)
 
-FFLAGS := -O2 -no-pie -fcray-pointer -fdefault-real-8 -ffree-line-length-none -fno-range-check $(shell nf-config --fflags)
+FFLAGS := -O -g -no-pie -fcray-pointer -fdefault-real-8 -ffree-line-length-none -fno-range-check $(shell nf-config --fflags)
+
+ifdef DEBUG
+  FFLAGS := $(FFLAGS) -Wuninitialized -Wno-maybe-uninitialized -fcheck=bounds -Werror
+endif
 
 LDFLAGS += -no-pie $(LIBS)
 

diff --git a/exp/MOM_compile.csh b/exp/MOM_compile.csh
@@ -59,6 +59,8 @@ if ( $help ) then
     echo
     echo "--platform   followed by the platform name that has a corresponding environ file in the ../bin dir, default is gfortran"
     echo
+    echo "--debug      make a debugging build"
+    echo
     echo "--use_netcdf4  use NetCDF4, the default is NetCDF4. Warning: many of the standard experiments don't work with NetCDF4."
     echo
     echo "--no_environ  do not source platform specific environment. Allows customising/overriding default environment"

diff --git a/src/atmos_fv_dynamics/model/dyn_core.F90 b/src/atmos_fv_dynamics/model/dyn_core.F90
@@ -13,7 +13,7 @@ module dyn_core
 
 #ifdef MARS_GCM
    use fv_pack,      only: p_ref, fv_sponge_damp, fv_sponge_lev
-#endif MARS_GCM
+#endif
 
 
    use pft_module,   only: pft2d
@@ -249,7 +249,7 @@ subroutine cd_core(im,  jm,  km,   nq,  nx, jfirst, jlast,      &
             allocate( fc(im,jsfc:jnfc) )
 #else
             allocate( fc(jsfc:jnfc) )
-#endif 
+#endif
 
 
 #ifndef USE_LIMA
@@ -322,7 +322,7 @@ subroutine cd_core(im,  jm,  km,   nq,  nx, jfirst, jlast,      &
         call get_eta_level(km, p_ref, pfull, phalf, 0.01) 
 #else
         call get_eta_level(km, 1.E5, pfull, phalf, 0.01) 
-#endif MARS_GCM 
+#endif
 
 
         do k=1,km
@@ -891,7 +891,7 @@ subroutine geop_d(ptop, pe, delp, pk, wz, hs, pt, im, jm, km,  &
       real dp
 #ifndef MARS_GCM
       parameter (dpmin = 0.02)              ! unit: pascal
-#endif 
+#endif
       integer :: ixjs, ixje
 
 
@@ -1034,7 +1034,7 @@ subroutine geopk(ptop, pe, delp, pk, wz, hs, pt, im, jm, km,  &
 #else
 !    rjw    Note that dpmin was 0.02 in the memphis code  
    parameter (dpmin = 0.1)              ! unit: pascal
-#endif MARS_GCM
+#endif
 
    call fv_print_chksums( 'Entering  geopk' )
    call fv_array_check( LOC(hs) )

diff --git a/src/atmos_fv_dynamics/model/fv_arrays.F90 b/src/atmos_fv_dynamics/model/fv_arrays.F90
@@ -87,14 +87,14 @@ module fv_arrays_mod
 #ifdef MARS_GCM
    real, allocatable :: delp_dt(:,:,:)
    real, allocatable :: mars_sfc_budg(:,:,:)
-#endif MARS_GCM
+#endif
 
 !! declarations from fv_pack.F90.1D2D
 #ifdef MARS_GCM
   integer, parameter :: NUMPTRS=28
 #else
   integer, parameter :: NUMPTRS=26
-#endif MARS_GCM
+#endif
 
   integer(POINTER_KIND) :: ptrArray(NUMPTRS) !this array contains addresses to all the variables to be shared
                               !between physics and dynamics.
@@ -163,7 +163,7 @@ module fv_arrays_mod
             ptr_u_srf, ptr_v_srf, ptr_u_dt, ptr_v_dt, ptr_t_dt, ptr_q_dt
 #   ifdef MARS_GCM
   public ::  ptr_delp_dt, ptr_mars_sfc_budg
-#   endif MARS_GCM
+#   endif
 
 #else
 !arrays themselves are public
@@ -173,9 +173,9 @@ module fv_arrays_mod
             u_srf, v_srf, u_dt, v_dt, t_dt, q_dt
 #   ifdef MARS_GCM
   public ::  delp_dt, mars_sfc_budg
-#   endif MARS_GCM
+#   endif
 
-#endif use_shared_pointers
+#endif
 
 contains
 
@@ -311,7 +311,7 @@ subroutine fv_arrays_init( nx, ny, nz, nt, shalo, nhalo, ighost, domain )
 #ifdef MARS_GCM
         allocate( delp_dt(isg:ieg, js:je, nz) )
         allocate( mars_sfc_budg(isg:ieg, js:je, 5) )
-#endif MARS_GCM
+#endif
     end if
     isp = isg; iep = ieg
     jsp = js; jep = je
@@ -347,7 +347,7 @@ subroutine fv_arrays_init( nx, ny, nz, nt, shalo, nhalo, ighost, domain )
 #ifdef MARS_GCM
     ptr_delp_dt = LOC(delp_dt)
     ptr_mars_sfc_budg = LOC(mars_sfc_budg)
-#endif MARS_GCM
+#endif
 !the array ptrArray is now filled by equivalence()
     ptrArray( 1) = ptr_u
     ptrArray( 2) = ptr_v
@@ -378,7 +378,7 @@ subroutine fv_arrays_init( nx, ny, nz, nt, shalo, nhalo, ighost, domain )
 #ifdef MARS_GCM
     ptrArray(27) = ptr_delp_dt
     ptrArray(28) = ptr_mars_sfc_budg
-#endif MARS_GCM
+#endif
     endif
     call mpp_pset_broadcast_ptr( pset, ptrArray )
     ptr_u = ptrArray( 1)
@@ -410,7 +410,7 @@ subroutine fv_arrays_init( nx, ny, nz, nt, shalo, nhalo, ighost, domain )
 #ifdef MARS_GCM
     ptr_delp_dt = ptrArray(27)
     ptr_mars_sfc_budg = ptrArray(28)
-#endif MARS_GCM
+#endif
 !isp,... index limits when you divide the computational domain by npex
     isp = is
     iep = ie
@@ -556,7 +556,7 @@ subroutine fv_print_chksums(caller)
          delp_dt(isg:ieg,js:je,:) )
     call mpp_pset_print_chksum( pset, trim(caller)//' mars_sfc_budg=', &
          mars_sfc_budg(isg:ieg,js:je,:) )
-#endif MARS_GCM
+#endif
     call mpp_pset_print_stack_chksum(pset, caller)
 #endif
     return
@@ -599,7 +599,7 @@ subroutine fv_arrays_exit
 #ifdef MARS_GCM
         deallocate ( delp_dt )
         deallocate ( mars_sfc_budg )
-#endif MARS_GCM
+#endif
 
 
     end if

diff --git a/src/atmos_fv_dynamics/model/fv_arrays.h b/src/atmos_fv_dynamics/model/fv_arrays.h
@@ -17,7 +17,7 @@
   use fv_arrays_mod, only: is,ie,js,je, isd,ied,jsd,jed, isg,ieg,jsg,jeg
 #  ifdef MARS_GCM
   use fv_arrays_mod, only: ptr_delp_dt, ptr_mars_sfc_budg
-#  endif MARS_GCM
+#  endif
 
 #else
 !get arrays from fv_arrays_mod
@@ -28,9 +28,9 @@
 
 #  ifdef MARS_GCM
   use fv_arrays_mod, only: delp_dt, mars_sfc_budg
-#  endif MARS_GCM
+#  endif
 
-#endif  use_shared_pointers
+#endif
 
   implicit none
 
diff --git a/src/atmos_fv_dynamics/model/fv_dynamics.F90 b/src/atmos_fv_dynamics/model/fv_dynamics.F90
@@ -446,11 +446,11 @@ subroutine fv_dynamics(im,   jm,    km,    jfirst, jlast,     &
 
 #if !defined (SW_DYN)                                                                 
       call mp_send4d_ns(im, jm, km, 1, jfirst, jlast, 1, km, ng_d, ng_d, pt)      
-#endif                                                                                
+#endif
       call mp_send4d_ns(im, jm, km, 1, jfirst, jlast, 1, km, ng_d, ng_d, delpf)   
 #if !defined (SW_DYN)                                                                 
       call mp_recv4d_ns(im, jm, km, 1, jfirst, jlast, 1, km, ng_d, ng_d, pt)      
-#endif                                                                                
+#endif
       call mp_recv4d_ns(im, jm, km, 1, jfirst, jlast, 1, km, ng_d, ng_d, delpf)   
       call fv_array_sync()
 #endif

diff --git a/src/atmos_fv_dynamics/model/fv_pack.F90 b/src/atmos_fv_dynamics/model/fv_pack.F90
@@ -186,7 +186,7 @@ module fv_pack
                          tra_step, dyn_step, dry_mass, print_freq,  icase,    &
 #ifdef MARS_GCM
                         p_ref, fv_sponge_lev, fv_sponge_damp,                      &
-#endif MARS_GCM 
+#endif
                          layout, fv_pset_stack
 #else
    namelist /fv_core_nml/nlon,      mlat,     nlev,                           &
@@ -201,7 +201,7 @@ module fv_pack
                          use_tendency, do_ch4_chem,  pft_phys, age_tracer,    &
 #ifdef MARS_GCM
                          p_ref, fv_sponge_lev, fv_sponge_damp,                      &
-#endif MARS_GCM 
+#endif
                          print_freq,  icase, layout
 
 #endif
@@ -422,7 +422,7 @@ subroutine fv_init(ndt)
        endif !}
 #endif
 
-#endif 
+#endif
 
        call tm_register_tracers (MODEL_ATMOS, ncnst, nt_prog, pnats, num_family)
        if(mpp_pe() == mpp_root_pe()) then
@@ -592,7 +592,7 @@ subroutine fv_init(ndt)
 
 #ifdef MARS_GCM
           cp_vir = 0.0
-#endif 
+#endif
 
 !--------------------------------------------
 ! Set up horizontal grid geometrical factors:
@@ -1400,7 +1400,7 @@ subroutine drymadj( im,  jm,  km,  jfirst,  jlast,  ng, &
                 enddo
              enddo
          endif
-#endif MARS_GCM
+#endif
 
 1000  continue
       call fv_array_sync() !probably needed before gmean

diff --git a/src/atmos_fv_dynamics/model/fv_point.inc b/src/atmos_fv_dynamics/model/fv_point.inc
@@ -30,7 +30,7 @@
 #ifdef MARS_GCM
   real :: delp_dt(isg:ieg, js:je, nlev)
   real :: mars_sfc_budg(isg:ieg, js:je, 5)
-#endif MARS_GCM
+#endif
   pointer( p_u, u )
   pointer( p_v, v )
   pointer( p_delp, delp )
@@ -60,7 +60,7 @@
 #ifdef MARS_GCM
   pointer( p_delp_dt, delp_dt )
   pointer( p_mars_sfc_budg, mars_sfc_budg )
-#endif MARS_GCM
+#endif
 !point all the shared pointers
   p_u = ptr_u
   p_v = ptr_v
@@ -91,6 +91,6 @@
 #ifdef MARS_GCM
   p_delp_dt = ptr_delp_dt
   p_mars_sfc_budg = ptr_mars_sfc_budg
-#endif MARS_GCM
+#endif
 
-#endif  use_shared_pointers
+#endif
diff --git a/src/atmos_fv_dynamics/model/update_fv_phys.F90 b/src/atmos_fv_dynamics/model/update_fv_phys.F90
@@ -147,7 +147,7 @@ subroutine update_fv_phys ( dt, nq, full_phys, nudge, Time )
            enddo
 
        endif
-#endif 
+#endif
 
 ! Average tendencies for scalars at poles (make it single-valued)
 ! This is necessary because the the physics/land/ocean use different grid
@@ -160,7 +160,7 @@ subroutine update_fv_phys ( dt, nq, full_phys, nudge, Time )
 #ifdef MARS_GCM
 !!!!       call polavg( delp_dt(1,beglat,k), nlon, mlat, beglat, endlat)
 !!!!       This is carried out in fv_phys.F90
-#endif MARS_GCM
+#endif
 
        if ( use_tendency ) then
            do j=beglat,endlat
@@ -234,7 +234,7 @@ subroutine update_fv_phys ( dt, nq, full_phys, nudge, Time )
               enddo
 !      endif
            enddo
-#endif 
+#endif
        endif
 
     enddo         ! -----------------------k-loop------------------
@@ -358,7 +358,7 @@ subroutine update_fv_phys ( dt, nq, full_phys, nudge, Time )
     endif
     call fv_array_sync()
     u_ghosted = .false.
-#endif  SPMD 
+#endif
     call fv_print_chksums( 'Exiting update_fv_phys' )
   end subroutine update_fv_phys
 

diff --git a/src/atmos_fv_dynamics/tools/fv_diagnostics.F90 b/src/atmos_fv_dynamics/tools/fv_diagnostics.F90
@@ -22,7 +22,7 @@ module fv_diagnostics
 #ifdef MARS_GCM
  use fv_pack,       only:   p_ref
  use fv_phys_mod,   only:   mars_mass_budget
-#endif MARS_GCM
+#endif
 
 ! --- tracer manager ---
  use tracer_manager_mod, only : get_tracer_names, get_number_tracers
@@ -91,7 +91,7 @@ subroutine fv_diag_init(axes, Time)
     trange = (/  50.,  350. /)  ! temperature
 #else
     trange = (/  100.,  350. /)  ! temperature
-#endif 
+#endif
     arange = (/    0.,   20. /)  ! age-of-air
     slprange = (/800.,  1200./)  ! sea-level-pressure
 
@@ -104,7 +104,7 @@ subroutine fv_diag_init(axes, Time)
     call get_eta_level(nlev, p_ref, pfull, phalf, 0.01) 
 #else
     call get_eta_level(nlev, 1.E5, pfull, phalf, 0.01) 
-#endif 
+#endif
 
     id_lonb=diag_axis_init('lonb', lonb, 'degrees_E', 'x', 'longitude edges', &
          set_name=mod_name , Domain2=fv_domain )
@@ -236,7 +236,7 @@ subroutine fv_diag_init(axes, Time)
         enddo
 ! for higher tracer number we take the default missing values from FMS
         do i = nt_phys+1, ncnst
-#endif MARS_GCM
+#endif
            call get_tracer_names ( MODEL_ATMOS, i, tname, tlongname, tunits )
            id_tracer(i) = register_diag_field ( mod_name, trim(tname),  &
                 axes(1:3), Time, trim(tlongname),           &
@@ -278,7 +278,7 @@ subroutine fv_diag_init(axes, Time)
              endif
            endif
         enddo
-#endif 
+#endif
 !-------
 
     endif !}
@@ -475,7 +475,7 @@ subroutine fv_diag( Time, im, jm, km, jfirst, jlast, nq, zvir, dt_atmos, hs_phys
              call drymadj(im, jm, km, jfirst, jlast, ng_d, .true., kappa,   &
                           ptop,  ps, delp, pe, pk, peln, pkz, nq,           &
                           q, .false.)  
-#endif MARS_GCM
+#endif
              call pmaxmin('U', ua, qmin, qmax, im*(jlast-jfirst+1), km, 1.)
              call pmaxmin('V', va, qmin, qmax, im*(jlast-jfirst+1), km, 1.)
     endif
@@ -595,7 +595,7 @@ subroutine fv_diag( Time, im, jm, km, jfirst, jlast, nq, zvir, dt_atmos, hs_phys
          if(qmin < 50.) call error_mesg('fv_diagnostics:','too cold', FATAL)
 #else
          if(qmin < 100.) call error_mesg('fv_diagnostics:','too cold', FATAL)
-#endif 
+#endif
       endif
 
     endif
@@ -776,7 +776,7 @@ subroutine fv_diag( Time, im, jm, km, jfirst, jlast, nq, zvir, dt_atmos, hs_phys
             endif
           endif
         enddo
-#endif 
+#endif
 !-------
 
 ! Check tracer mass. Unit: