Add unit testing

.github/pull_request_template.md

@@ -35,3 +35,8 @@ Do PRs in upstream repositories need to be merged first?
 If so add the "waiting for other repos" label and list the upstream PRs
 - waiting on noaa-emc/nems/pull/<pr_number>
 - waiting on noaa-emc/fv3atm/pull/<pr_number>
+
+# Requirements before merging
+- [ ] All new code in this PR is tested by at least one unit test
+- [ ] All new code in this PR includes Doxygen documentation
+- [ ] All new code in this PR does not add new compilation warnings (check CI output)

.github/workflows/GCC.yml

@@ -26,9 +26,19 @@ jobs:
 
     steps:
 
-    - name: install-doxygen
+    # Only do Doxygen and gcovr build for one job
+    - name: decide-doc-gcovr-build
       run: |
-        sudo apt-get install doxygen graphviz
+        if [[ "${{ matrix.cmake_opts }}" == "-D32BIT=ON" && "${{ matrix.gcc_ver }}" == 11 && "${{ matrix.mpi }}" == mpich ]]; then
+          echo 'devbuild=ON' | tee -a ${GITHUB_ENV}
+          echo 'gcov_cmake="-DCMAKE_Fortran_FLAGS=-fprofile-abs-path -fprofile-arcs -ftest-coverage -O0"' | tee -a ${GITHUB_ENV}
+        else
+          echo 'devbuild=OFF' | tee -a ${GITHUB_ENV}
+        fi
+
+    - name: apt-install
+      run: |
+        sudo apt-get install gcovr doxygen graphviz
 
     - name: checkout-fv3atm
       uses: actions/checkout@v3
@@ -58,6 +68,14 @@ jobs:
         spack config add "packages:mpi:require:'${{ matrix.mpi }}'"
         spack concretize |& tee ${SPACK_ENV}/log.concretize
         spack install -j2 --fail-fast
+        echo "spackrc=$?" >> ${GITHUB_ENV}
+
+    - name: cache-save
+      uses: actions/cache/save@v3
+      if: ${{ (env.spackrc) == 0 }}
+      with:
+        path: ${{ github.workspace }}/spack-develop
+        key: spack-${{ hashFiles('fv3atm/ci/spack.yaml') }}-gcc11-2
 
     - name: build-fv3atm
       run: |
@@ -67,23 +85,44 @@ jobs:
         cd ${GITHUB_WORKSPACE}/fv3atm
         git clone https://github.com/NOAA-EMC/CMakeModules
         git clone --recurse-submodules https://github.com/NOAA-PSL/stochastic_physics stochastic_physics_repo
-        mkdir ${GITHUB_WORKSPACE}/build
         sed -i 's/doc /upp_doc /' upp/docs/CMakeLists.txt
-        cd ${GITHUB_WORKSPACE}/build
-        cmake ${GITHUB_WORKSPACE}/fv3atm -DBUILD_TESTING=ON ${{ matrix.cmake_opts }} -DENABLE_DOCS=ON
+        mkdir ${GITHUB_WORKSPACE}/fv3atm/build
+        cd ${GITHUB_WORKSPACE}/fv3atm/build
+        cmake ${GITHUB_WORKSPACE}/fv3atm -DBUILD_TESTING=ON ${{ matrix.cmake_opts }} -DENABLE_DOCS=${{ env.devbuild }} ${{ env.gcov_cmake }}
         make -j2
         ls -l /home/runner/work/fv3atm/fv3atm/fv3atm/io
 
-    - uses: actions/upload-artifact@v3
+    - name: run-tests
+      run: |
+        cd $GITHUB_WORKSPACE/fv3atm/build
+        ctest -j2 --output-on-failure --rerun-failed
+
+    - name: get-test-coverage
+      if: ${{ env.devbuild == 'ON' }}
+      run: |
+        f=${GITHUB_WORKSPACE}/fv3atm
+        cd $f/build
+        gcovr -r .. -v --html-details --exclude ${f}/tests --exclude $f/stochastic_physics_repo --exclude $f/build/ccpp --exclude $f/ccpp/physics --exclude $f/ccpp/framework --exclude $f/atmos_cubed_sphere  --exclude CMakeFiles --print-summary -o test-coverage.html
+
+    - name: upload-test-coverage
+      uses: actions/upload-artifact@v4
+      if: ${{ env.devbuild == 'ON' }}
+      with:
+        name: test-coverage-fv3atm-${{ github.sha }}
+        path: |
+              ${{ github.workspace }}/fv3atm/build/*.html 
+              ${{ github.workspace }}/fv3atm/build/*.css
+
+    - uses: actions/upload-artifact@v4
+      if: ${{ env.devbuild == 'ON' }}
       with:
         name: docs
         path: |
-          build/docs/html
+          ${{ github.workspace }}/fv3atm/build/docs/html
 
     - name: debug-artifacts
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:
         name: ccpp_prebuild_logs
-        path: ${{ github.workspace }}/build/ccpp/ccpp_prebuild.*
-
+        path: ${{ github.workspace }}/fv3atm/build/ccpp/ccpp_prebuild.*

CMakeLists.txt

@@ -154,6 +154,11 @@ if(OPENMP)
   target_link_libraries(fv3atm PUBLIC OpenMP::OpenMP_Fortran)
 endif()
 
+if(BUILD_TESTING)
+  include(CTest)
+  add_subdirectory(tests)
+endif()
+
 ###############################################################################
 ### Install
 ###############################################################################

ci/CMakeLists.txt

@@ -64,6 +64,7 @@ endif()
 find_package(bacio 2.4.0 REQUIRED)
 find_package(sp 2.3.3 REQUIRED)
 find_package(w3emc 2.9.2 REQUIRED)
+find_package(PIO REQUIRED)
 
 find_package(Python 3.6 REQUIRED COMPONENTS Interpreter)
 

tests/CMakeLists.txt

@@ -0,0 +1,29 @@
+# This file sets up CTest unit tests for fv3atm.
+#
+# Alex Richert, Jan 2024
+
+# Stage test data
+execute_process(COMMAND cmake -E create_symlink
+  "${CMAKE_CURRENT_SOURCE_DIR}/data"
+  "${CMAKE_CURRENT_BINARY_DIR}/data"
+  )
+
+function(add_fv3atm_mpi_test TESTNAME)
+  add_executable(${TESTNAME} ${TESTNAME}.F90)
+  target_link_libraries(${TESTNAME} PRIVATE fv3atm MPI::MPI_Fortran PIO::PIO_Fortran)
+  add_test(${TESTNAME} ${MPIEXEC_EXECUTABLE} -n 2 ${CMAKE_CURRENT_BINARY_DIR}/${TESTNAME})
+endfunction()
+
+function(add_fv3atm_serial_test TESTNAME)
+  add_executable(${TESTNAME} ${TESTNAME}.F90)
+  target_link_libraries(${TESTNAME} PRIVATE fv3atm)
+  add_test(${TESTNAME} ${CMAKE_CURRENT_BINARY_DIR}/${TESTNAME})
+endfunction()
+
+#foreach(testname test_write_netcdf)
+#  add_fv3atm_mpi_test(${testname})
+#endforeach()
+
+foreach(testname test_fv3_io_def test_post_nems_routines)
+  add_fv3atm_serial_test(${testname})
+endforeach()

tests/data/post_namelist.nml

@@ -0,0 +1,20 @@
+&model_inputs
+  modelname = "DMMY"
+  submodelname = "SUBM"
+/
+&nampgb
+  kpo = 5
+  kth = 7
+  kpv = 9
+  po = 0.5 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
+  th = 1.0 2.0 3.0 4.0 5.0 6.0 7.0
+  pv = 11. 12. 13. 14. 15. 16. 17. 18. 19.
+  hyb_sigp = F
+  d3d_on = T
+  gocart_on = T
+  popascal = T
+  rdaod = T
+  nasa_on = T
+  gccpp_on = T
+  d2d_chem = T
+/

tests/data/post_namelist_empty.nml

@@ -0,0 +1,4 @@
+&model_inputs
+/
+&nampgb
+/

tests/test_fv3_io_def.F90

@@ -0,0 +1,130 @@
+! This program provides a unit test to verify that the variables in
+! module_fv3_io_def.F90 are accessible.
+! Alex Richert, 11 Jan 2024
+
+program test_fv3_io_def
+
+  use module_fv3_io_def
+
+  implicit none
+
+  num_pes_fcst = 2
+  if (num_pes_fcst .ne. 2) stop 1
+  wrttasks_per_group = 4
+  if (wrttasks_per_group .ne. 4) stop 2
+  write_groups = 8
+  if (write_groups .ne. 8) stop 3
+  n_group = 16
+  if (n_group .ne. 16) stop 4
+  num_files = 32
+  if (num_files .ne. 32) stop 5
+  nbdlphys = 64
+  if (nbdlphys .ne. 64) stop 6
+  iau_offset = 128
+  if (iau_offset .ne. 128) stop 7
+
+  lflname_fulltime = .true.
+  if (.not. lflname_fulltime) stop 8
+  time_unlimited = .true.
+  if (.not. time_unlimited) stop 9
+
+  allocate(filename_base(1))
+  filename_base(1)="abc"
+  if (trim(filename_base(1)).ne."abc") stop 10
+  allocate(output_file(1))
+  output_file(1)="def"
+  if (trim(output_file(1)).ne."def") stop 11
+
+  allocate(lead_wrttask(10))
+  lead_wrttask = 42
+  if (any(lead_wrttask(1:10).ne.42)) stop 12
+  allocate(last_wrttask(12))
+  last_wrttask = 43
+  if (any(last_wrttask(1:12).ne.43)) stop 13
+
+  allocate(output_grid(2))
+  output_grid(1) = "ABC"
+  output_grid(2) = "DEF"
+  if (trim(output_grid(1)).ne."ABC") stop 14
+  if (trim(output_grid(2)).ne."DEF") stop 15
+
+  allocate(imo(6))
+  imo(1:6) = 17
+  if (any(imo.ne.17)) stop 16
+  allocate(jmo(6))
+  jmo(1:6) = 18
+  if (any(jmo.ne.18)) stop 17
+
+  allocate(cen_lon(8))
+  cen_lon(1:8) = 2.1
+  if(any(cen_lon.ne.2.1)) stop 18
+  allocate(cen_lat(8))
+  cen_lat(1:8) = 3.2
+  if(any(cen_lat.ne.3.2)) stop 19
+
+  allocate(lon1(10))
+  lon1(1:10) = 4.3
+  if(any(lon1.ne.4.3)) stop 20
+  allocate(lat1(10))
+  lat1(1:10) = 5.4
+  if(any(lat1.ne.5.4)) stop 21
+
+  allocate(lon2(12))
+  lon2(1:12) = 6.5
+  if(any(lon2.ne.6.5)) stop 22
+  allocate(lat2(12))
+  lat2(1:12) = 7.6
+  if(any(lat2.ne.7.6)) stop 23
+
+  allocate(dlon(15))
+  dlon(1:15) = 8.7
+  if(any(dlon.ne.8.7)) stop 24
+  allocate(dlat(15))
+  dlat(1:15) = 9.8
+  if(any(dlat.ne.9.8)) stop 25
+
+  allocate(stdlat1(18))
+  stdlat1(1:18) = 10.9
+  if(any(stdlat1.ne.10.9)) stop 26
+  allocate(stdlat2(18))
+  stdlat2(1:18) = 11.0
+  if(any(stdlat2.ne.11.0)) stop 27
+
+  allocate(dx(20))
+  dx(1:20) = 12.1
+  if(any(dx.ne.12.1)) stop 28
+  allocate(dy(20))
+  dy(1:20) = 13.2
+  if(any(dy.ne.13.2)) stop 29
+
+  allocate(ideflate(25))
+  ideflate(1:25) = 123
+  if(any(ideflate.ne.123)) stop 30
+  allocate(quantize_nsd(25))
+  quantize_nsd(1:25) = 123
+  if(any(quantize_nsd.ne.123)) stop 31
+  allocate(zstandard_level(25))
+  zstandard_level(1:25) = 123
+  if(any(zstandard_level.ne.123)) stop 32
+
+  allocate(quantize_mode(5))
+  quantize_mode(1:5) = "xyz"
+  if(.not.trim(quantize_mode(5)).eq."xyz") stop 33
+
+  allocate(ichunk2d(30))
+  ichunk2d(1:30) = 50
+  if(any(ichunk2d.ne.50)) stop 34
+  allocate(jchunk2d(30))
+  jchunk2d(1:30) = 51
+  if(any(jchunk2d.ne.51)) stop 35
+  allocate(ichunk3d(30))
+  ichunk3d(1:30) = 52
+  if(any(ichunk3d.ne.52)) stop 36
+  allocate(jchunk3d(30))
+  jchunk3d(1:30) = 53
+  if(any(jchunk3d.ne.53)) stop 37
+  allocate(kchunk3d(30))
+  kchunk3d(1:30) = 54
+  if(any(kchunk3d.ne.54)) stop 38
+
+end program test_fv3_io_def

tests/test_post_nems_routines.F90

@@ -0,0 +1,55 @@
+! This program provides unit testing for the subroutines in io/post_nems_routines.F90
+!
+! Alex Richert, 11 Jan 2024
+program test_post_nems_routines
+
+  use ctlblk_mod, only : komax,hyb_sigp,d3d_on,gocart_on, &
+   rdaod,nasa_on,gccpp_on,d2d_chem,modelname,submodelname, lsm
+
+  implicit none
+
+  character (len=*), parameter :: post_namelist_empty="data/post_namelist_empty.nml"
+  character (len=*), parameter :: post_namelist="data/post_namelist.nml"
+  integer :: kpo,kth,kpv
+  real(4),dimension(komax) :: po,th,pv
+  logical :: popascal
+  real, parameter :: tini=tiny(1.0)
+
+  ! Verify default settings by using empty nml file
+  call read_postnmlt(kpo,kth,kpv,po,th,pv,trim(post_namelist_empty))
+  if (kpo.ne.0) stop 1
+  if (kth.ne.6) stop 2
+  if (kpv.ne.8) stop 3
+  if (any(po.ne.0.0)) stop 4
+  if (any(abs(th(1:6)-(/310.,320.,350.,450.,550.,650./)).gt.tini)) stop 5
+  if (any(abs(pv(1:8)-(/0.5,-0.5,1.0,-1.0,1.5,-1.5,2.0,-2.0/)).gt.tini)) stop 6
+  if (.not.hyb_sigp) stop 7
+  if (d3d_on) stop 8
+  if (gocart_on) stop 9
+  if (lsm.ne.46) stop 10 ! 'lsm' is determined by 'popascal'
+  if (rdaod) stop 11
+  if (nasa_on) stop 12
+  if (gccpp_on) stop 13
+  if (d2d_chem) stop 14
+
+  ! Now use fully populated nml file
+  call read_postnmlt(kpo,kth,kpv,po,th,pv,trim(post_namelist))
+  if (kpo.ne.5) stop 101
+  if (kth.ne.7) stop 102
+  if (kpv.ne.9) stop 103
+  if (po(1).ne.0.5) stop 104
+  if (any(po(2:komax).ne.1.0)) stop 104
+  if (any(abs(th(1:7)-(/1.,2.,3.,4.,5.,6.,7./)).gt.tini)) stop 105
+  if (any(abs(pv(1:9)-(/11.,12.,13.,14.,15.,16.,17.,18.,19./)).gt.tini)) stop 106
+  if (hyb_sigp) stop 107
+  if (.not.d3d_on) stop 108
+  if (.not.gocart_on) stop 109
+  if (lsm.ne.5) stop 110 ! 'lsm' is determined by 'popascal'
+  if (.not.rdaod) stop 111
+  if (.not.nasa_on) stop 112
+  if (.not.gccpp_on) stop 113
+  if (.not.d2d_chem) stop 114
+  if (trim(modelname).ne."DMMY") stop 115
+  if (trim(submodelname).ne."SUBM") stop 116
+
+end program test_post_nems_routines