Merge pull request #102 from climbfuji/update_gsl_develop_from_develo…

…p_20210921

Update gsl/develop from develop 2021/09/21

CICE-interface/cice_files.cmake

@@ -22,6 +22,7 @@ list(APPEND cice_shared_files
   CICE/cicecore/cicedynB/analysis/ice_history_mechred.F90
   CICE/cicecore/cicedynB/analysis/ice_history_pond.F90
   CICE/cicecore/cicedynB/analysis/ice_history_shared.F90
+  CICE/cicecore/cicedynB/analysis/ice_history_snow.F90
 
   #Dynamics List:
   CICE/cicecore/cicedynB/dynamics/ice_dyn_eap.F90
@@ -74,6 +75,7 @@ list(APPEND icepack_files
   CICE/icepack/columnphysics/icepack_orbital.F90
   CICE/icepack/columnphysics/icepack_parameters.F90
   CICE/icepack/columnphysics/icepack_shortwave.F90
+  CICE/icepack/columnphysics/icepack_snow.F90
   CICE/icepack/columnphysics/icepack_therm_0layer.F90
   CICE/icepack/columnphysics/icepack_therm_bl99.F90
   CICE/icepack/columnphysics/icepack_therm_itd.F90

CMEPS-interface/CMakeLists.txt

@@ -1,6 +1,9 @@
 # CMEPS compiler flags
 if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
   set(CMAKE_Fortran_FLAGS "-g -fbacktrace -ffree-line-length-none")
+  if(${CMAKE_Fortran_COMPILER_VERSION} VERSION_GREATER_EQUAL 10)
+    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fallow-argument-mismatch -fallow-invalid-boz")
+  endif()
   set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS}")
   set(CMAKE_Fortran_FLAGS_RELEASE "-O2")
   set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -fcheck=bounds -ffpe-trap=invalid,zero,overflow,underflow" )

MOM6-interface/mom6_files.cmake

@@ -206,6 +206,7 @@ list(APPEND mom6_src_files
   MOM6/src/tracer/oil_tracer.F90
   MOM6/src/tracer/pseudo_salt_tracer.F90
   MOM6/src/tracer/tracer_example.F90
+  MOM6/src/tracer/MOM_CFC_cap.F90
 
   MOM6/src/user/BFB_initialization.F90
   MOM6/src/user/BFB_surface_forcing.F90

doc/UsersGuide/source/AutomatedTesting.rst

@@ -0,0 +1,136 @@
+.. _AutomatedTesting:
+
+*****************
+Automated Testing
+*****************
+
+The UFS Weather Model repository on GitHub employs two types of automated testing.
+One is the CI/CD on cloud and the other is the AutoRT on NOAA R&D platforms.
+Both are application level tests, and utilize the regression testing framework
+discussed in :numref:`Section %s <UsingRegressionTest>`.
+
+=====
+CI/CD
+=====
+
+The following summarizes the CI/CD used in the UFS Weather Model:
+
+* GitHub Actions (GHA), a GitHub-hosted continuous integration service is used.
+* Build jobs are done on GHA-provided virtual machines.
+* Test jobs are performed on Amazon cloud using a number of EC2 instances.
+* Builds and tests are carried out using a Docker container.
+* Docker container has prerequisite libraries installed via the hpc-stack.
+* Input data needed to run tests are stored as a separate Docker container.
+
+
+When a developer makes a pull request (PR) to the UFS Weather Model repository, and a code
+manager subsequently adds the `run-ci` label, the CI/CD workflow is triggerd:
+
+#. A check is performed to make sure the UFS Weather Model and its first level
+   subcomponents are up to date with the top of develop branch.
+
+#. If the check is successful, build jobs are started on GHA-provided virtual machines
+   by downloading the hpc-stack Docker container stored in Docker Hub.
+
+#. Once all build jobs are successful, the created executable files are stored as
+   artifacts in GHA.
+
+#. A number of AWS EC2 instances are started.
+
+#. Test jobs are started on Amazon cloud by downloading the hpc-stack Docker container,
+   the executable file from the build job, and the input-data Docker container.
+
+#. When all tests are finished, EC2 instances are stopped. Test results are reported
+   on GitHub.
+
+
+The GHA-related yaml scripts are located in the ``.github/workflows/`` directory.
+``build_test.yml`` is the main workflow file, and ``aux.yml`` is an auxiliary
+file responsible for checking the up-to-dateness of the PR branch, and starting
+and stopping the EC2 instances. Other CI-related scrips are located in the ``tests/ci/``
+directory. ``ci.sh`` is the main script that invokes Docker build and run. ``Dockerfile``
+is used to build UFS Weather Model. Other shell and python scripts help with various
+tasks such as checking the up-to-dateness of the PR branch (``repo_check.sh``),
+checking the status of EC2 instances (``check_status.py``), and configuring the test cases
+to carry out in the CI/CD workflow (``setup.py`` and ``ci.test``).
+
+
+=======
+Auto RT
+=======
+
+The Automated Regression Testing (AutoRT) system:
+
+* Automates the process of regression testing on NOAA HPC platforms.
+
+* Written in python.
+
+* Contains the following files:
+
+.. table:: *Files for Automated Regression Testing (AutoRT) system*
+
+   +-------------------+-----------------------------------------------------+
+   | **File Name**     | **Description**                                     |
+   +===================+=====================================================+
+   |  start_rt_auto.sh | Verifies HPC name, sets the python paths            |
+   +-------------------+-----------------------------------------------------+
+   |  rt_auto.py       | Python interface between the HPC and the github API |
+   +-------------------+-----------------------------------------------------+
+   |  jobs/bl.py       | Functions for the baseline job                      |
+   +-------------------+-----------------------------------------------------+
+   |  jobs/rt.py       | Functions for the regression test job               |
+   +-------------------+-----------------------------------------------------+
+
+~~~~~~~~~~~~~~~
+AutoRT Workflow
+~~~~~~~~~~~~~~~
+* Cron-job on supported HPC systems runs start_rt_auto.sh bash script every
+  15 minutes.
+
+  * This script verifies the HPC name, and sets the python paths. Runs
+    rt_auto.py.
+
+* rt_auto.py: Uses the Github API (Through pyGitHub)
+
+  * Checks the pull requests to ufs-community/ufs-weather-model for
+    labels specific to the HPC name. If no match to HPC name, exits.
+    (i.e. hera-intel-RT or cheyenne-gnu-BL)
+
+  * If the HPC name matches the label in ufs-weather-model pull
+    request, the label provides the HPC with the compiler and job to run on
+    the machine.
+
+    * For example the label gaea-intel-BL will be recognized by the HPC
+      machine 'Gaea', set the RT_COMPILER variable to 'intel' and run the
+      baseline creation script (bl.py).
+
+  * Creates a Job class that contains all information from the machine
+    that the job will need to run. That is sent into the jobs/rt[bl].py script.
+
+* rt.py: Sets directories for storage, gets repo information, runs RT,
+  post processes.
+
+.. code-block:: python3
+
+    def run(job_obj):
+        logger = logging.getLogger('RT/RUN')
+        workdir = set_directories(job_obj)
+        branch, pr_repo_loc, repo_dir_str = clone_pr_repo(job_obj, workdir)
+        run_regression_test(job_obj, pr_repo_loc)
+        post_process(job_obj, pr_repo_loc, repo_dir_str, branch)
+
+* bl.py: (similar to rt.py) Adds functionality to create baselines before
+  running regression testing.
+
+.. code-block:: python3
+  :emphasize-lines: 5,6,7
+
+    def run(job_obj):
+        logger = logging.getLogger('BL/RUN')
+        workdir, rtbldir, blstore = set_directories(job_obj)
+        pr_repo_loc, repo_dir_str = clone_pr_repo(job_obj, workdir)
+        bldate = get_bl_date(job_obj, pr_repo_loc)
+        bldir = f'{blstore}/develop-{bldate}/{job_obj.compiler.upper()}'
+        bldirbool = check_for_bl_dir(bldir, job_obj)
+        run_regression_test(job_obj, pr_repo_loc)
+        post_process(job_obj, pr_repo_loc, repo_dir_str, rtbldir, bldir)

doc/UsersGuide/source/index.rst

@@ -14,6 +14,7 @@ Welcome to the UFS Weather Model User's Guide
    CodeOverview
    BuildingAndRunning
    InputsOutputs
+   AutomatedTesting
    FAQ
    Acronyms
    Glossary

modulefiles/ufs_cheyenne.gnu

@@ -15,8 +15,8 @@ module load mpt/2.22
 module load ncarcompilers/0.5.0
 module unload netcdf
 
-module use /glade/p/ral/jntp/GMTB/tools/hpc-stack-v1.1.0/modulefiles/stack
-module load hpc/1.1.0
+module use /glade/p/ral/jntp/GMTB/tools/hpc-stack-v1.2.0/modulefiles/stack
+module load hpc/1.2.0
 module load hpc-gnu/10.1.0
 module load hpc-mpt/2.22
 

modulefiles/ufs_cheyenne.gnu_debug

@@ -15,8 +15,8 @@ module load mpt/2.22
 module load ncarcompilers/0.5.0
 module unload netcdf
 
-module use /glade/p/ral/jntp/GMTB/tools/hpc-stack-v1.1.0/modulefiles/stack
-module load hpc/1.1.0
+module use /glade/p/ral/jntp/GMTB/tools/hpc-stack-v1.2.0/modulefiles/stack
+module load hpc/1.2.0
 module load hpc-gnu/10.1.0
 module load hpc-mpt/2.22
 

modulefiles/ufs_cheyenne.intel

@@ -15,8 +15,8 @@ module load mpt/2.22
 module load ncarcompilers/0.5.0
 module unload netcdf
 
-module use /glade/p/ral/jntp/GMTB/tools/hpc-stack-v1.1.0/modulefiles/stack
-module load hpc/1.1.0
+module use /glade/p/ral/jntp/GMTB/tools/hpc-stack-v1.2.0/modulefiles/stack
+module load hpc/1.2.0
 module load hpc-intel/2021.2
 module load hpc-mpt/2.22
 

modulefiles/ufs_cheyenne.intel_debug

@@ -15,8 +15,8 @@ module load mpt/2.22
 module load ncarcompilers/0.5.0
 module unload netcdf
 
-module use /glade/p/ral/jntp/GMTB/tools/hpc-stack-v1.1.0/modulefiles/stack
-module load hpc/1.1.0
+module use /glade/p/ral/jntp/GMTB/tools/hpc-stack-v1.2.0/modulefiles/stack
+module load hpc/1.2.0
 module load hpc-intel/2021.2
 module load hpc-mpt/2.22
 

modulefiles/ufs_common

@@ -7,8 +7,8 @@ module load png/1.6.35
 module load hdf5/1.10.6
 module load netcdf/4.7.4
 module load pio/2.5.2
-module load esmf/8_1_1
-module load fms/2020.04.03
+module load esmf/8_2_0_beta_snapshot_14
+module load fms/2021.03
 
 module load bacio/2.4.1
 module load crtm/2.3.0
@@ -17,8 +17,8 @@ module load g2tmpl/1.10.0
 module load ip/3.3.3
 module load sp/2.3.3
 module load w3nco/2.4.1
-module load upp/10.0.8
+module load upp/10.0.9
 
-module load gftl-shared/v1.3.0
-module load yafyaml/v0.5.1
-module load mapl/v2.7.3
+#module load gftl-shared/v1.3.0
+#module load yafyaml/v0.5.1
+#module load mapl/v2.7.3-esmf820bs14

modulefiles/ufs_common_debug

@@ -7,8 +7,8 @@ module load png/1.6.35
 module load hdf5/1.10.6
 module load netcdf/4.7.4
 module load pio/2.5.2
-module load esmf/8_1_1-debug
-module load fms/2020.04.03
+module load esmf/8_2_0_beta_snapshot_14-debug
+module load fms/2021.03
 
 module load bacio/2.4.1
 module load crtm/2.3.0
@@ -17,8 +17,8 @@ module load g2tmpl/1.10.0
 module load ip/3.3.3
 module load sp/2.3.3
 module load w3nco/2.4.1
-module load upp/10.0.8
+module load upp/10.0.9
 
-module load gftl-shared/v1.3.0
-module load yafyaml/v0.5.1
-module load mapl/v2.7.3
+#module load gftl-shared/v1.3.0
+#module load yafyaml/v0.5.1
+#module load mapl/v2.7.3-esmf820bs14

modulefiles/ufs_hera.gnu

@@ -23,6 +23,9 @@ module load hpc-mpich/3.3.2
 
 module load ufs_common
 
+module unload fms
+module load fms/2021.03-avx
+
 setenv CC mpicc
 setenv CXX mpicxx
 setenv FC mpif90

modulefiles/ufs_hera.intel

@@ -23,6 +23,12 @@ module load hpc-impi/2018.0.4
 
 module load ufs_common
 
+module unload fms
+module load fms/2021.03-avx
+module load gftl-shared/v1.3.0
+module load yafyaml/v0.5.1
+module load mapl/v2.7.3-esmf820bs14
+
 setenv CC mpiicc
 setenv CXX mpiicpc
 setenv FC mpiifort

modulefiles/ufs_hera.intel_debug

@@ -23,6 +23,10 @@ module load hpc-impi/2018.0.4
 
 module load ufs_common_debug
 
+module load gftl-shared/v1.3.0
+module load yafyaml/v0.5.1
+module load mapl/v2.7.3-esmf820bs14
+
 setenv CC mpiicc
 setenv CXX mpiicpc
 setenv FC mpiifort

modulefiles/ufs_wcoss_cray

@@ -53,7 +53,7 @@ module load gfsio/1.4.1
 module load sfcio/1.4.1
 module load sigio/2.3.2
 
-module load upp/10.0.8
+module load upp/10.0.9
 
 ## WCOSS Cray execution prereqs:
 module load rca
@@ -64,7 +64,7 @@ module load udreg
 module load ugni
 
 module load esmf/811
-module load fms/2020.04.03
+module load fms/2021.03
 
 module swap pmi pmi/5.0.11
 

modulefiles/ufs_wcoss_cray_debug

@@ -53,7 +53,7 @@ module load gfsio/1.4.1
 module load sfcio/1.4.1
 module load sigio/2.3.2
 
-module load upp/10.0.8
+module load upp/10.0.9
 
 ## WCOSS Cray execution prereqs:
 module load rca
@@ -64,7 +64,7 @@ module load udreg
 module load ugni
 
 module load esmf/811-debug
-module load fms/2020.04.03
+module load fms/2021.03
 
 module swap pmi pmi/5.0.11