Add pio_reader Fortran unit tests (#403)

Tag name (required for release branches):
Originator(s): @mwaxmonsky @nusbaume

Description (include the issue title, and the keyword ['closes',
'fixes', 'resolves'] followed by the issue number):

This PR introduces pFUnit Fortran unit tests for the `pio_reader`
implementation of the `ccpp_io_reader` abstract class that is used in
CAM-SIMA, which should now run automatically with any PR to CAM-SIMA as
part of the Fortran unit tests Github Action.

Note that although several tests are added by this PR, the code coverage
is not complete, as several of the edge cases require specialized NetCDF
files that will need to be created. Github issue #404 can be used to
keep track of this.

Describe any changes made to build system:

A       src/physics/utils/CMakeLists.txt
M       test/unit/fortran/CMakeLists.txt
A       test/unit/fortran/ccpp_framework_stub/CMakeLists.txt
A       test/unit/fortran/cmake/FindNetCDF.cmake
A       test/unit/fortran/cmake/FindPIO.cmake
A       test/unit/fortran/mock_routines/CMakeLists.txt
A       test/unit/fortran/src/pio_reader/CMakeLists.tx
- Add files needed to build the pio_reader unit tests and their
dependencies using CMake.

Describe any changes made to the namelist: N/A

List any changes to the defaults for the input datasets (e.g. boundary
datasets): N/A

List all files eliminated and why: N/A

List all files added and what they do:

A       test/unit/fortran/ccpp_framework_stub/ccpp_kinds.F90
A       test/unit/fortran/mock_routines/cam_pio_utils.F90
A       test/unit/fortran/src/pio_reader/test_pio_reader.pf
  - Add pio_reader unit tests (and associated dependencies).

List all existing files that have been modified, and describe the
changes:
(Helpful git command: `git diff --name-status
development...<your_branch_name>`)

M       .github/workflows/fortran_unit_tests.yml
  - Add pio_reader unit tests to Github Action worfklow.

M       .gitignore
  - Have git ignore all compiled Fortran files (".o" and ".mod").

M       src/physics/utils/pio_reader.F90
- Fix bugs and remove un-needed host model dependencies found during
testing.

M       src/utils/cam_pio_utils.F90
- Add optional "errcode" variable that can be used during testing (and
to ensure that pio_reader doesn't kill the host model).

If there are new failures (compared to the
`test/existing-test-failures.txt` file),
have them OK'd by the gatekeeper, note them here, and add them to the
file.
If there are baseline differences, include the test and the reason for
the
diff. What is the nature of the change? Roundoff?

derecho/intel/aux_sima:  ALL PASS

derecho/gnu/aux_sima:  ALL PASS

If this changes climate describe any run(s) done to evaluate the new
climate in enough detail that it(they) could be reproduced:

CAM-SIMA date used for the baseline comparison tests if different than
latest:

---------

Co-authored-by: Michael Waxmonsky <mwaxmonsky@ucar.edu>

Author: nusbaume

.github/workflows/fortran_unit_tests.yml

@@ -23,6 +23,10 @@ jobs:
       CXX: g++-${{ matrix.version }}
       FC: gfortran-${{ matrix.version }}
     steps:
+      - name: install dependencies
+        run: |
+          sudo apt install -y libnetcdff-dev libnetcdf-mpi-dev libopenmpi-dev openmpi-bin doxygen
+
       - name: Checkout cam-sima
         uses: actions/checkout@v4
 
@@ -34,16 +38,45 @@ jobs:
           cd build
           make install
 
+      - name: Build PIO
+        run: |
+          git clone --depth 1 --branch pio2_6_6 https://github.com/NCAR/ParallelIO.git
+          cd ParallelIO
+          FC=$(which mpif90) \
+          CC=$(which mpicc) \
+          cmake -S./ -B./build \
+            -DCMAKE_INSTALL_PREFIX=./install \
+            -DPIO_ENABLE_TIMING=OFF \
+            -DWITH_PNETCDF=OFF \
+            -DCMAKE_PREFIX_PATH="/usr/lib/x86_64-linux-gnu/cmake/netCDF" \
+            -DNetCDF_Fortran_LIBRARY="/usr/lib/x86_64-linux-gnu/libnetcdff.a" \
+            -DNetCDF_C_LIBRARY="/usr/lib/x86_64-linux-gnu/libnetcdf.so" \
+            -DCMAKE_EXE_LINKER_FLAGS="-lmpi -Wl,--no-as-needed"
+          cd build
+          make
+          make install
+
+      - name: Checkout atmospheric_physics
+        run: |
+          bin/git-fleximod update ncar-physics ccpp-framework share
+
       - name: Build cam-sima
         run: |
+          PIO_ROOT=$GITHUB_WORKSPACE/ParallelIO/install/ \
           cmake \
-            -DCMAKE_PREFIX_PATH=$GITHUB_WORKSPACE/pFUnit/build/installed \
+            -DCMAKE_PREFIX_PATH="$GITHUB_WORKSPACE/pFUnit/build/installed;/usr/lib/x86_64-linux-gnu/cmake/netCDF;/usr/lib/x86_64-linux-gnu/" \
             -DCAM_SIMA_ENABLE_CODE_COVERAGE=ON \
+            -DCAM_SIMA_ENABLE_IO_TESTS=ON \
+            -DCAM_SIMA_ENABLE_TESTS=ON \
             -B./build \
             -S./test/unit/fortran
           cd build
           make
 
+      - name: Checkout datafiles for file IO reader tests
+        run: |
+          git clone https://github.com/earth-system-radiation/rrtmgp-data.git
+
       - name: Run fortran unit tests
         run: |
           cd build && ctest -V --output-on-failure --output-junit test_results.xml

.gitignore

@@ -2,13 +2,18 @@
 *.pyc
 buildnmlc
 
+# Ignore compiled Fortran
+*.mod
+*.o
+
 # Ignore test output
 test/include/*.mod
 test/include/*.o
 test/unit/python/tmp
 test/system/*.log
 test/system/cime-tests.o*
 test_driver_*.sh
+build/
 
 # Ignore editor temporaries and backups
 *.swp

src/physics/utils/CMakeLists.txt

@@ -0,0 +1,21 @@
+set(IO_READER_SOURCE pio_reader.F90
+	             pio_reader_sub.F90
+		     ${CMAKE_CURRENT_SOURCE_DIR}/../ncar_ccpp/phys_utils/ccpp_io_reader.F90
+		     ${CMAKE_CURRENT_SOURCE_DIR}/../../../share/src/shr_kind_mod.F90)
+
+# io_reader is not integrated into the CMake build of any top level
+# project yet and this CMake is for testing purposes only.
+# Making a change to this project's CMake will not impact the build of
+# a parent project at this time.
+add_library(io_reader ${IO_READER_SOURCE})
+target_link_libraries(io_reader PUBLIC
+                      MPI::MPI_Fortran
+                      MPI::MPI_C
+                      NetCDF::NetCDF_C
+                      NetCDF::NetCDF_Fortran
+                      PIO::PIO_Fortran
+                      PIO::PIO_C
+                      cam_pio_utils
+                      ccpp_framework)
+target_include_directories(io_reader PRIVATE ${CMAKE_BINARY_DIR}/ccpp_framework_stub
+                                             ${CMAKE_BINARY_DIR}/mock_routines)