Fixed conflicts with upstream dev/gfdl

.gitlab-ci.yml

@@ -0,0 +1,138 @@
+stages:
+  - merge
+  - setup
+  - builds
+  - run
+  - tests
+
+# Moves to re-used workspace
+before_script:
+  - MOM6_SRC=$CI_PROJECT_DIR
+  - WORKSPACE=`pwd | sed 's:/[0-9]/:/:'`
+  - git pull --no-edit https://github.com/NOAA-GFDL/MOM6.git dev/gfdl
+  - test -d $WORKSPACE/tests && cd $WORKSPACE/tests
+
+# Merge
+merge:
+  stage: merge
+  tags:
+    - ncrc3
+  script:
+    - cd $CI_PROJECT_DIR
+    - git pull --no-edit https://github.com/NOAA-GFDL/MOM6.git dev/gfdl
+
+# Clones regression repo, if necessary, pulls latest of everything, and sets up working space
+setup:
+  stage: setup
+  tags:
+    - ncrc3
+  script:
+    - mkdir -p $WORKSPACE && cd $WORKSPACE
+    - ln -sf $MOM6_SRC/{config_src,src,pkg} .
+    - test -d tests || (git clone --recursive http://gitlab.gfdl.noaa.gov/ogrp/Gaea_c3-stats-MOM6-examples.git tests)
+    - cd tests
+    - git checkout dev/gfdl
+    - git checkout . && git pull
+    - git status
+    - bash Gitlab/before_script.sh
+    - (cd MOM6-examples/src/mkmf && git pull https://github.com/adcroft/mkmf.git add_coverage_mode)
+
+# Compiles
+gnu:repro:
+  stage: builds
+  tags:
+    - ncrc3
+  script:
+    - make -f Gitlab/Makefile.build MOM6_SRC=../ build_gnu -s -j
+    - make -f Gitlab/Makefile.build MOM6_SRC=../ static_gnu -s -j #coverage_gnu
+
+intel:repro:
+  stage: builds
+  tags:
+    - ncrc3
+  script:
+    - make -f Gitlab/Makefile.build MOM6_SRC=../ build_intel -s -j
+
+pgi:repro:
+  stage: builds
+  tags:
+    - ncrc3
+  script:
+    - make -f Gitlab/Makefile.build MOM6_SRC=../ build_pgi -s -j
+
+gnu:debug:
+  stage: builds
+  tags:
+    - ncrc3
+  script:
+    - make -f Gitlab/Makefile.build MOM6_SRC=../ debug_gnu -s -j
+
+# Runs
+run:
+  stage: run
+  tags:
+    - ncrc3
+  script:
+    - rm MOM6-examples/*.tar
+    - bash Gitlab/run_stage.sh
+
+# Tests
+gnu:regressions:
+  stage: tests
+  tags:
+    - ncrc3
+  script:
+    - cd regressions && git checkout .
+    - md5sum `find . -name ocean.stats.gnu` > all_gnu.md5 && find . -name ocean.stats.gnu -exec rm {} \;
+    - echo "Regression results for non-symmetric gnu executables"
+    - tar xf ../MOM6-examples/non_symmetric_gnu.tar && md5sum -c all_gnu.md5 && rm all_gnu.md5
+
+intel:regressions:
+  stage: tests
+  tags:
+    - ncrc3
+  script:
+    - cd regressions && git checkout .
+    - md5sum `find . -name ocean.stats.intel` > all_intel.md5 && find . -name ocean.stats.intel -exec rm {} \;
+    - echo "Regression results for non-symmetric intel executables"
+    - tar xf ../MOM6-examples/non_symmetric_intel.tar && md5sum -c all_intel.md5 && rm all_intel.md5
+
+pgi:regressions:
+  stage: tests
+  tags:
+    - ncrc3
+  script:
+    - cd regressions && git checkout .
+    - md5sum `find . -name ocean.stats.pgi` > all_pgi.md5 && find . -name ocean.stats.pgi -exec rm {} \;
+    - echo "Regression results for non-symmetric pgi executables"
+    - tar xf ../MOM6-examples/non_symmetric_pgi.tar && md5sum -c all_pgi.md5 && rm all_pgi.md5
+
+gnu:symmetric:
+  stage: tests
+  tags:
+    - ncrc3
+  script:
+    - mkdir -p _gnu && cd _gnu
+    - tar xf ../MOM6-examples/non_symmetric_gnu.tar && md5sum `find . -name ocean.stats.gnu` > all_gnu.md5 && find . -name ocean.stats.gnu -exec rm {} \;
+    - echo "Regression results for symmetric executables"
+    - tar xf ../MOM6-examples/symmetric_gnu.tar && md5sum -c all_gnu.md5 && rm all_gnu.md5
+
+intel:symmetric:
+  stage: tests
+  tags:
+    - ncrc3
+  script:
+    - mkdir -p _intel && cd _intel
+    - tar xf ../MOM6-examples/non_symmetric_intel.tar && md5sum `find . -name ocean.stats.intel` > all_intel.md5 && find . -name ocean.stats.intel -exec rm {} \;
+    - echo "Regression results for symmetric executables"
+    - tar xf ../MOM6-examples/symmetric_intel.tar && md5sum -c all_intel.md5 && rm all_intel.md5
+
+pgi:symmetric:
+  stage: tests
+  tags:
+    - ncrc3
+  script:
+    - mkdir -p _pgi && cd _pgi
+    - tar xf ../MOM6-examples/non_symmetric_pgi.tar && md5sum `find . -name ocean.stats.pgi` > all_pgi.md5 && find . -name ocean.stats.pgi -exec rm {} \;
+    - echo "Regression results for symmetric executables"
+    - tar xf ../MOM6-examples/symmetric_pgi.tar && md5sum -c all_pgi.md5 && rm all_pgi.md5

config_src/ice_solo_driver/MOM_surface_forcing.F90

@@ -715,7 +715,8 @@ subroutine buoyancy_forcing_from_files(state, fluxes, day, dt, G, CS)
   type(surface),         intent(inout) :: state
   type(forcing),         intent(inout) :: fluxes
   type(time_type),       intent(in)    :: day
-  real,                  intent(in)    :: dt
+  real,                  intent(in)    :: dt   !< The amount of time over which
+                                               !! the fluxes apply, in s
   type(ocean_grid_type), intent(inout) :: G    !< The ocean's grid structure
   type(surface_forcing_CS), pointer    :: CS
 
@@ -918,7 +919,8 @@ subroutine buoyancy_forcing_zero(state, fluxes, day, dt, G, CS)
   type(surface),         intent(inout) :: state
   type(forcing),         intent(inout) :: fluxes
   type(time_type),       intent(in)    :: day
-  real,                  intent(in)    :: dt
+  real,                  intent(in)    :: dt   !< The amount of time over which
+                                               !! the fluxes apply, in s
   type(ocean_grid_type), intent(in)    :: G    !< The ocean's grid structure
   type(surface_forcing_CS), pointer    :: CS
 
@@ -975,7 +977,8 @@ subroutine buoyancy_forcing_linear(state, fluxes, day, dt, G, CS)
   type(surface),         intent(inout) :: state
   type(forcing),         intent(inout) :: fluxes
   type(time_type),       intent(in)    :: day
-  real,                  intent(in)    :: dt
+  real,                  intent(in)    :: dt   !< The amount of time over which
+                                               !! the fluxes apply, in s
   type(ocean_grid_type), intent(in)    :: G    !< The ocean's grid structure
   type(surface_forcing_CS), pointer    :: CS
 

config_src/ice_solo_driver/user_surface_forcing.F90

@@ -166,7 +166,8 @@ subroutine USER_buoyancy_forcing(state, fluxes, day, dt, G, CS)
   type(surface),                 intent(inout) :: state
   type(forcing),                 intent(inout) :: fluxes
   type(time_type),               intent(in)    :: day
-  real,                          intent(in)    :: dt
+  real,                          intent(in)    :: dt   !< The amount of time over which
+                                               !! the fluxes apply, in s
   type(ocean_grid_type),         intent(in)    :: G    !< The ocean's grid structure
   type(user_surface_forcing_CS), pointer       :: CS
 

config_src/solo_driver/MESO_surface_forcing.F90

@@ -178,7 +178,8 @@ subroutine MESO_buoyancy_forcing(state, fluxes, day, dt, G, CS)
   type(surface),                 intent(inout) :: state
   type(forcing),                 intent(inout) :: fluxes
   type(time_type),               intent(in)    :: day
-  real,                          intent(in)    :: dt
+  real,                          intent(in)    :: dt   !< The amount of time over which
+                                                       !! the fluxes apply, in s
   type(ocean_grid_type),         intent(in)    :: G    !< The ocean's grid structure
   type(MESO_surface_forcing_CS), pointer       :: CS
 

config_src/solo_driver/MOM_surface_forcing.F90

@@ -831,7 +831,8 @@ subroutine buoyancy_forcing_from_files(state, fluxes, day, dt, G, CS)
   type(surface),         intent(inout) :: state
   type(forcing),         intent(inout) :: fluxes
   type(time_type),       intent(in)    :: day
-  real,                  intent(in)    :: dt
+  real,                  intent(in)    :: dt   !< The amount of time over which
+                                               !! the fluxes apply, in s
   type(ocean_grid_type), intent(inout) :: G    !< The ocean's grid structure
   type(surface_forcing_CS), pointer    :: CS
 
@@ -1119,7 +1120,8 @@ subroutine buoyancy_forcing_from_data_override(state, fluxes, day, dt, G, CS)
   type(surface),         intent(inout) :: state
   type(forcing),         intent(inout) :: fluxes
   type(time_type),       intent(in)    :: day
-  real,                  intent(in)    :: dt
+  real,                  intent(in)    :: dt   !< The amount of time over which
+                                               !! the fluxes apply, in s
   type(ocean_grid_type), intent(inout) :: G    !< The ocean's grid structure
   type(surface_forcing_CS), pointer    :: CS
 
@@ -1295,7 +1297,8 @@ subroutine buoyancy_forcing_zero(state, fluxes, day, dt, G, CS)
   type(surface),         intent(inout) :: state
   type(forcing),         intent(inout) :: fluxes
   type(time_type),       intent(in)    :: day
-  real,                  intent(in)    :: dt
+  real,                  intent(in)    :: dt   !< The amount of time over which
+                                               !! the fluxes apply, in s
   type(ocean_grid_type), intent(in)    :: G    !< The ocean's grid structure
   type(surface_forcing_CS), pointer    :: CS
 
@@ -1347,7 +1350,8 @@ subroutine buoyancy_forcing_const(state, fluxes, day, dt, G, CS)
   type(surface),         intent(inout) :: state
   type(forcing),         intent(inout) :: fluxes
   type(time_type),       intent(in)    :: day
-  real,                  intent(in)    :: dt
+  real,                  intent(in)    :: dt   !< The amount of time over which
+                                               !! the fluxes apply, in s
   type(ocean_grid_type), intent(in)    :: G    !< The ocean's grid structure
   type(surface_forcing_CS), pointer    :: CS
 
@@ -1398,7 +1402,8 @@ subroutine buoyancy_forcing_linear(state, fluxes, day, dt, G, CS)
   type(surface),         intent(inout) :: state
   type(forcing),         intent(inout) :: fluxes
   type(time_type),       intent(in)    :: day
-  real,                  intent(in)    :: dt
+  real,                  intent(in)    :: dt   !< The amount of time over which
+                                               !! the fluxes apply, in s
   type(ocean_grid_type), intent(in)    :: G    !< The ocean's grid structure
   type(surface_forcing_CS), pointer    :: CS
 

config_src/solo_driver/user_surface_forcing.F90

@@ -166,7 +166,8 @@ subroutine USER_buoyancy_forcing(state, fluxes, day, dt, G, CS)
   type(surface),                 intent(inout) :: state
   type(forcing),                 intent(inout) :: fluxes
   type(time_type),               intent(in)    :: day
-  real,                          intent(in)    :: dt
+  real,                          intent(in)    :: dt   !< The amount of time over which
+                                                       !! the fluxes apply, in s
   type(ocean_grid_type),         intent(in)    :: G    !< The ocean's grid structure
   type(user_surface_forcing_CS), pointer       :: CS
 

src/ALE/MOM_regridding.F90

@@ -1421,7 +1421,7 @@ subroutine build_grid_adaptive(G, GV, h, tv, dzInterface, remapCS, CS)
   type(ocean_grid_type),                       intent(in)    :: G    !< The ocean's grid structure
   type(verticalGrid_type),                     intent(in)    :: GV   !< The ocean's vertical grid structure
   real, dimension(SZI_(G),SZJ_(G),SZK_(GV)),   intent(in)    :: h    !< Layer thicknesses, in H (usually m or kg m-2)
-  type(thermo_var_ptrs),                       intent(in)    :: tv
+  type(thermo_var_ptrs),                       intent(in)    :: tv   !< A structure pointing to various thermodynamic variables
   real, dimension(SZI_(G),SZJ_(G),SZK_(GV)+1), intent(inout) :: dzInterface
   type(remapping_CS),                          intent(in)    :: remapCS
   type(regridding_CS),                         intent(in)    :: CS
@@ -1737,7 +1737,7 @@ subroutine convective_adjustment(G, GV, h, tv)
   type(ocean_grid_type), intent(in)                  :: G    !< The ocean's grid structure
   type(verticalGrid_type), intent(in)                :: GV   !< The ocean's vertical grid structure
   real, dimension(SZI_(G),SZJ_(G),SZK_(GV)), intent(inout) :: h    !< Layer thicknesses, in H (usually m or kg m-2)
-  type(thermo_var_ptrs), intent(inout)               :: tv
+  type(thermo_var_ptrs), intent(inout)               :: tv   !< A structure pointing to various thermodynamic variables
 
   ! Local variables
   integer   :: i, j, k
@@ -1834,6 +1834,8 @@ subroutine initCoord(CS, coord_mode)
   select case (coordinateMode(coord_mode))
   case (REGRIDDING_ZSTAR)
     call init_coord_zlike(CS%zlike_CS, CS%nk, CS%coordinateResolution)
+  case (REGRIDDING_SIGMA_SHELF_ZSTAR)
+    call init_coord_zlike(CS%zlike_CS, CS%nk, CS%coordinateResolution)
   case (REGRIDDING_SIGMA)
     call init_coord_sigma(CS%sigma_CS, CS%nk, CS%coordinateResolution)
   case (REGRIDDING_RHO)
@@ -2098,6 +2100,8 @@ subroutine set_regrid_params( CS, boundary_extrapolation, min_thickness, old_gri
   select case (CS%regridding_scheme)
   case (REGRIDDING_ZSTAR)
     if (present(min_thickness)) call set_zlike_params(CS%zlike_CS, min_thickness=min_thickness)
+  case (REGRIDDING_SIGMA_SHELF_ZSTAR)
+    if (present(min_thickness)) call set_zlike_params(CS%zlike_CS, min_thickness=min_thickness)
   case (REGRIDDING_SIGMA)
     if (present(min_thickness)) call set_sigma_params(CS%sigma_CS, min_thickness=min_thickness)
   case (REGRIDDING_RHO)

src/ALE/coord_adapt.F90

@@ -92,7 +92,7 @@ subroutine build_adapt_column(CS, G, GV, tv, i, j, zInt, tInt, sInt, h, zNext)
   type(adapt_CS),                              intent(in)    :: CS
   type(ocean_grid_type),                       intent(in)    :: G    !< The ocean's grid structure
   type(verticalGrid_type),                     intent(in)    :: GV   !< The ocean's vertical grid structure
-  type(thermo_var_ptrs),                       intent(in)    :: tv
+  type(thermo_var_ptrs),                       intent(in)    :: tv   !< A structure pointing to various thermodynamic variables
   integer,                                     intent(in)    :: i, j
   real, dimension(SZI_(G),SZJ_(G),SZK_(GV)+1), intent(in)    :: zInt, tInt, sInt
   real, dimension(SZI_(G),SZJ_(G),SZK_(GV)),   intent(in)    :: h    !< Layer thicknesses, in H (usually m or kg m-2)