add selmaprotbas to list of optional models (#107)

* add selmaprotbas to list of optional models * try fixing aocc by using python rather than python3 * install python after aocc * aocc: show python executable path * debug aocc * debug aocc * add aocc 5.0; debug aocc * debug aocc * debug aocc * debug aocc * debug aocc * debug aocc * debug aocc * clean-up * type correction * suppress aocc/flang warning * disable aocc-5-0 testing (buggy) * reduce unnecessary differences with master * drop special treatment of horizontal_shape
fabm-model · Jan 25, 2025 · 948c8c7 · 948c8c7
1 parent 2178e41
commit 948c8c7
Show file tree

Hide file tree

Showing 3 changed files with 19 additions and 12 deletions.
diff --git a/.github/workflows/fabm.yml b/.github/workflows/fabm.yml
@@ -48,9 +48,9 @@ jobs:
         with:
           submodules: recursive
       - name: Run all test cases with host emulators
-        run: python3 util/developers/run_all_testcases.py harness --show_logs --compiler gfortran-${{ matrix.version }} ${{ matrix.cmake_args }}
+        run: python util/developers/run_all_testcases.py harness --show_logs --compiler gfortran-${{ matrix.version }} ${{ matrix.cmake_args }}
       - name: Run all test cases with pyfabm
-        run: python3 util/developers/run_all_testcases.py pyfabm --show_logs --compiler gfortran-${{ matrix.version }} ${{ matrix.cmake_args }}
+        run: python util/developers/run_all_testcases.py pyfabm --show_logs --compiler gfortran-${{ matrix.version }} ${{ matrix.cmake_args }}
   ifort:
     # for available versions, see https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/intel-oneapi-compilers/package.py
     if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository
@@ -87,11 +87,11 @@ jobs:
       - name: Run all test cases with host emulators
         run: |
           source ${HOME}/intel/setvars.sh
-          python3 util/developers/run_all_testcases.py harness --show_logs --compiler ifort
+          python util/developers/run_all_testcases.py harness --show_logs --compiler ifort
       - name: Run all test cases with pyfabm
         run: |
           source ${HOME}/intel/setvars.sh
-          python3 util/developers/run_all_testcases.py pyfabm --show_logs --compiler ifort
+          python util/developers/run_all_testcases.py pyfabm --show_logs --compiler ifort
         env:
           FFLAGS: ${{ env.FFLAGS }} -fp-model precise -fp-model source
   ifx:
@@ -132,13 +132,13 @@ jobs:
       - name: Run all test cases with host emulators
         run: |
           source ${HOME}/intel/setvars.sh
-          python3 util/developers/run_all_testcases.py harness --show_logs --compiler ifx
+          python util/developers/run_all_testcases.py harness --show_logs --compiler ifx
         env:
           FFLAGS: ${{ matrix.fflags }}
       - name: Run all test cases with pyfabm
         run: |
           source ${HOME}/intel/setvars.sh
-          python3 util/developers/run_all_testcases.py pyfabm --show_logs --compiler ifx
+          python util/developers/run_all_testcases.py pyfabm --show_logs --compiler ifx
         env:
           FFLAGS: ${{ matrix.fflags }} -fp-model=precise
   nvfortran:
@@ -187,9 +187,9 @@ jobs:
         with:
           submodules: recursive
       - name: Run all test cases with host emulators
-        run: python3 util/developers/run_all_testcases.py harness --show_logs --compiler /home/runner/nvhpc/Linux_x86_64/${{ matrix.version }}/compilers/bin/pgfortran
+        run: python util/developers/run_all_testcases.py harness --show_logs --compiler /home/runner/nvhpc/Linux_x86_64/${{ matrix.version }}/compilers/bin/pgfortran
       - name: Run all test cases with pyfabm
-        run: python3 util/developers/run_all_testcases.py pyfabm --show_logs --compiler /home/runner/nvhpc/Linux_x86_64/${{ matrix.version }}/compilers/bin/pgfortran
+        run: python util/developers/run_all_testcases.py pyfabm --show_logs --compiler /home/runner/nvhpc/Linux_x86_64/${{ matrix.version }}/compilers/bin/pgfortran
   aocc:
     # for available versions, see https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/aocc/package.py
     if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository
@@ -205,6 +205,8 @@ jobs:
           #   url_dir: https://download.amd.com/developer/eula/aocc/aocc-4-1
           - version: "4.2.0" # released 2024-02-27 (LLVM 16.0.3)
             url_dir: https://download.amd.com/developer/eula/aocc/aocc-4-2
+          # - version: "5.0.0" # released 2024-10-10 (LLVM 17.0.6)
+          #   url_dir: https://download.amd.com/developer/eula/aocc/aocc-5-0
       fail-fast: false
     runs-on: ubuntu-latest
     steps:
@@ -227,12 +229,16 @@ jobs:
           submodules: recursive
       - name: Run all test cases with host emulators
         run: |
+          OLD_LD_LIBRARY_PATH=$LD_LIBRARY_PATH
           source /home/runner/setenv_AOCC.sh
-          python3 util/developers/run_all_testcases.py harness --show_logs --compiler flang
+          export LD_LIBRARY_PATH=$OLD_LD_LIBRARY_PATH:$LD_LIBRARY_PATH
+          python util/developers/run_all_testcases.py harness --show_logs --compiler flang
       - name: Run all test cases with pyfabm
         run: |
+          OLD_LD_LIBRARY_PATH=$LD_LIBRARY_PATH
           source /home/runner/setenv_AOCC.sh
-          python3 util/developers/run_all_testcases.py pyfabm --show_logs --compiler flang ${{ matrix.pyfabm_cmake_args }}
+          export LD_LIBRARY_PATH=$OLD_LD_LIBRARY_PATH:$LD_LIBRARY_PATH
+          python util/developers/run_all_testcases.py pyfabm --show_logs --compiler flang ${{ matrix.pyfabm_cmake_args }}
   flang-new:
     if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository
     strategy:

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -21,11 +21,12 @@ set(DEFAULT_INSTITUTES
     pisces       # Pelagic Interactions Scheme for Carbon and Ecosystem Studies, https://doi.org/10.5194/gmd-8-2465-2015
     pml          # Plymouth Marine Laboratory, United Kingdom
     selma        # Simple EcoLogical Model for the Aquatic - PROGNOS
+    selmaprotbas # Adaptation of SELMA as described in https://doi.org/10.1002/lno.12040
     su           # Swansea University, United Kingdom
     uhh          # University of Hamburg, Germany
 )
 
-set(OPTIONAL_INSTITUTES ersem mops pclake pisces ihamocc ogs)
+set(OPTIONAL_INSTITUTES ersem mops pclake pisces ihamocc ogs selmaprotbas)
 
 if(CMAKE_CURRENT_LIST_DIR STREQUAL CMAKE_SOURCE_DIR)
   message(FATAL_ERROR "Please point cmake to the top-level directory with FABM source code, not to its src subdirectory.")

diff --git a/src/builtin/depth_mapping.F90 b/src/builtin/depth_mapping.F90
@@ -167,7 +167,7 @@ subroutine vertical_depth_range_do(self, _ARGUMENTS_DO_)
       class (type_vertical_depth_range), intent(in) :: self
       _DECLARE_ARGUMENTS_DO_
 
-      real :: z_center, h, z_top, z_bottom, h_overlap
+      real(rk) :: z_center, h, z_top, z_bottom, h_overlap
 
       _LOOP_BEGIN_
          _GET_(self%id_z, z_center)