Merge pull request #5 from NOAA-GFDL/dev/gfdl

Sync dev/gfdl with NOAA-GFDL version of repository

.gitlab-ci.yml

@@ -8,7 +8,7 @@ stages:
 # Merges MOM6 with dev/gfdl. Changes directory to test directory, if it exists.
 before_script:
   - MOM6_SRC=$CI_PROJECT_DIR
-  - CACHE_DIR=/lustre/f1/oar.gfdl.ogrp-account/runner/cache/
+  - echo Cache directory set to ${CACHE_DIR:=/lustre/f2/scratch/oar.gfdl.ogrp-account/runner/cache/}
   - git pull --no-edit https://github.com/NOAA-GFDL/MOM6.git dev/gfdl && git submodule init && git submodule update
   - pwd ; ls
 
@@ -34,10 +34,12 @@ setup:
     - git clone https://github.com/adcroft/MRS.git MRS
     # Update MOM6-examples and submodules
     - (cd MOM6-examples && git checkout . && git checkout dev/gfdl && git pull && git submodule init && git submodule update)
+    - (cd MOM6-examples/src/MOM6 && git submodule update)
     - test -d MOM6-examples/src/LM3 || make -f MRS/Makefile.clone clone_gfdl -s
     - make -f MRS/Makefile.clone MOM6-examples/.datasets -s
     #- (cd MOM6-examples/src/mkmf && git pull https://github.com/adcroft/mkmf.git add_coverage_mode)
     - env > gitlab_session.log
+    # Cache everything under tests to unpack for each subsequent stage
     - cd ../ ; time tar zcf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz tests
 
 # Compiles
@@ -114,8 +116,9 @@ run:
     - time tar zxf $CACHE_DIR/build-pgi-repro-$CI_PIPELINE_ID.tgz
     # time tar zxf $CACHE_DIR/build-gnu-debug-$CI_PIPELINE_ID.tgz
     - echo "make -f MRS/Makefile.tests all -B" > job.sh
-    - msub -l partition=c4,nodes=29,walltime=00:29:00,qos=norm -q debug -S /bin/tcsh -j oe -A gfdl_o -z -o log.$CI_PIPELINE_ID -N mom6_regression -K job.sh
+    - msub -l partition=c4,nodes=29,walltime=00:31:00,qos=norm -q debug -S /bin/tcsh -j oe -A gfdl_o -z -o log.$CI_PIPELINE_ID -N mom6_regression -K job.sh
     - cat log.$CI_PIPELINE_ID
+    - test -f restart_results_gnu.tar.gz
     - time tar zvcf $CACHE_DIR/results-$CI_PIPELINE_ID.tgz *.tar.gz
 
 # Tests
@@ -218,6 +221,16 @@ gnu:restart:
     - time tar zxf $CACHE_DIR/results-$CI_PIPELINE_ID.tgz
     - make -f MRS/Makefile.tests gnu_check_restarts
 
+gnu:params:
+  stage: tests
+  tags:
+    - ncrc4
+  script:
+    - time tar zxf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz && cd tests
+    - time tar zxf $CACHE_DIR/results-$CI_PIPELINE_ID.tgz
+    - make -f MRS/Makefile.tests params_gnu_symmetric
+  allow_failure: true
+
 cleanup:
   stage: cleanup
   tags:

.travis.yml

@@ -4,14 +4,13 @@
 # This is a not a c-language project but we use the same environment.
 language: c
 dist: trusty
-sudo: false
 
 addons:
   apt:
     sources:
     - ubuntu-toolchain-r-test
     packages:
-    - tcsh pkg-config netcdf-bin libnetcdf-dev openmpi-bin libopenmpi-dev gfortran
+    - tcsh pkg-config netcdf-bin libnetcdf-dev mpich2 libmpich2-dev gfortran
 
 # For saving time...
 cache:

config_src/coupled_driver/coupler_util.F90

@@ -1,9 +1,9 @@
+!> Provides a couple of interfaces to allow more transparent and
+!! robust extraction of the various fields in the coupler types.
 module coupler_util
 
 ! This file is part of MOM6. See LICENSE.md for the license.
 
-!   This code provides a couple of interfaces to allow more transparent and
-! robust extraction of the various fields in the coupler types.
 use MOM_error_handler, only : MOM_error, FATAL, WARNING
 use coupler_types_mod, only : coupler_2d_bc_type, ind_flux, ind_alpha
 use coupler_types_mod, only : ind_csurf
@@ -15,24 +15,20 @@ module coupler_util
 
 contains
 
+!> Extract an array of values in a coupler bc type
 subroutine extract_coupler_values(BC_struc, BC_index, BC_element, array_out, &
                                   is, ie, js, je, conversion)
-  type(coupler_2d_bc_type), intent(in)  :: BC_struc
-  integer,                  intent(in)  :: BC_index, BC_element
-  real, dimension(:,:),     intent(out) :: array_out
-  integer,        optional, intent(in)  :: is, ie, js, je
-  real,           optional, intent(in)  :: conversion
-! Arguments: BC_struc - The type from which the data is being extracted.
-!  (in)      BC_index - The boundary condition number being extracted.
-!  (in)      BC_element - The element of the boundary condition being extracted.
-!            This could be ind_csurf, ind_alpha, ind_flux or ind_deposition.
-!  (out)     array_out - The array being filled with the input values.
-!  (in, opt) is, ie, js, je - The i- and j- limits of array_out to be filled.
-!            These must match the size of the corresponding value array or an
-!            error message is issued.
-!  (in, opt) conversion - A number that every element is multiplied by, to
-!                         permit sign convention or unit conversion.
-
+  type(coupler_2d_bc_type), intent(in)  :: BC_struc !< The type from which the data is being extracted.
+  integer,                  intent(in)  :: BC_index !< The boundary condition number being extracted.
+  integer,                  intent(in)  :: BC_element !< The element of the boundary condition being extracted.
+  real, dimension(:,:),     intent(out) :: array_out !< The array being filled with the input values.
+  integer,        optional, intent(in)  :: is !< Start i-index
+  integer,        optional, intent(in)  :: ie !< End i-index
+  integer,        optional, intent(in)  :: js !< Start j-index
+  integer,        optional, intent(in)  :: je !< End j-index
+  real,           optional, intent(in)  :: conversion !< A number that every element is multiplied by, to
+                                           !! permit sign convention or unit conversion.
+  ! Local variables
   real, pointer, dimension(:,:) :: Array_in
   real :: conv
   integer :: i, j, is0, ie0, js0, je0, i_offset, j_offset
@@ -78,24 +74,21 @@ subroutine extract_coupler_values(BC_struc, BC_index, BC_element, array_out, &
 
 end subroutine extract_coupler_values
 
+!> Set an array of values in a coupler bc type
 subroutine set_coupler_values(array_in, BC_struc, BC_index, BC_element, &
                               is, ie, js, je, conversion)
-  real, dimension(:,:),     intent(in)    :: array_in
-  type(coupler_2d_bc_type), intent(inout) :: BC_struc
-  integer,                  intent(in)    :: BC_index, BC_element
-  integer,        optional, intent(in)    :: is, ie, js, je
-  real,           optional, intent(in)    :: conversion
-! Arguments: array_in - The array containing the values to load into the BC.
-!  (out)     BC_struc - The type into which the data is being loaded.
-!  (in)      BC_index - The boundary condition number being extracted.
-!  (in)      BC_element - The element of the boundary condition being extracted.
-!            This could be ind_csurf, ind_alpha, ind_flux or ind_deposition.
-!  (in, opt) is, ie, js, je - The i- and j- limits of array_out to be filled.
-!            These must match the size of the corresponding value array or an
-!            error message is issued.
-!  (in, opt) conversion - A number that every element is multiplied by, to
-!                         permit sign convention or unit conversion.
-
+  real, dimension(:,:),     intent(in)    :: array_in !< The array containing the values to load into the BC.
+  type(coupler_2d_bc_type), intent(inout) :: BC_struc !< The type from which the data is being extracted.
+  integer,                  intent(in)    :: BC_index !< The boundary condition number being extracted.
+  integer,                  intent(in)    :: BC_element !< The element of the boundary condition being extracted.
+                                             !! This could be ind_csurf, ind_alpha, ind_flux or ind_deposition.
+  integer,        optional, intent(in)    :: is !< Start i-index
+  integer,        optional, intent(in)    :: ie !< End i-index
+  integer,        optional, intent(in)    :: js !< Start j-index
+  integer,        optional, intent(in)    :: je !< End j-index
+  real,           optional, intent(in)    :: conversion !< A number that every element is multiplied by, to
+                                             !! permit sign convention or unit conversion.
+  ! Local variables
   real, pointer, dimension(:,:) :: Array_out
   real :: conv
   integer :: i, j, is0, ie0, js0, je0, i_offset, j_offset