Merge branch 'main' into refactoring_bugfix_cavity

.github/inactive_workflows/fesom2_icepack.yml

@@ -21,14 +21,13 @@ jobs:
 
     - name: prepeare FESOM2_icepack
       run: |
-        sed -i 's/USE_ICEPACK OFF/USE_ICEPACK ON/g' CMakeLists.txt
         cd ./src/icepack_drivers/
         ./download_icepack.sh
         cd ../../
     
     - name: Compile model
       run: |
-        bash -l configure.sh ubuntu
+        bash -l configure.sh ubuntu -DUSE_ICEPACK=ON
     
     - name: Create global test run with ICEPACK
       run: |

.github/workflows/fesom2.1.yml

@@ -12,24 +12,49 @@ jobs:
     # Containers must run in Linux based operating systems
     runs-on: ubuntu-latest
     # Docker Hub image that `container-job` executes in
-    container: koldunovn/fesom2_test:refactoring2
+    container: ghcr.io/fesom/fesom2_docker:fesom2_test_refactoring-master
 
     # Service containers to run with `gfortran_ubuntu`
     steps:
     # NK: this changes working directory to fesom2
     - uses: actions/checkout@v2
-
+
+    - name: Git safe directory
+      run: |
+        git config --global --add safe.directory ${PWD}
+
     - name: Compile model (binary)
       run: |
-        bash -l configure.sh ubuntu
+        ./configure.sh ubuntu
 
-    - name: Compile model (library)
+    - name: Compile model (ifs_interface)
       run: |
-        bash ./test/ifs_interface/configure_lib.sh -l
+        export BUILD_DIR=$PWD/build.ifs_interface
+        ./configure.sh ubuntu -DENABLE_IFS_INTERFACE=ON -DCMAKE_INSTALL_PREFIX=$PWD/install.ifs_interface
 
-    - name: Library exists
+    - name: Test downstream from install-dir
       run: |
-        bash ./test/ifs_interface/check_exist.sh
+        export fesom_ROOT=${PWD}
+        rm -rf test_downstream/build
+        cmake -S test_downstream -B test_downstream/build -DASSERT_HAVE_IFS_INTERFACE=OFF -DASSERT_FESOM_DIR=${fesom_ROOT}
+        cmake --build test_downstream/build
+        test_downstream/build/main
+
+    - name: Test downstream from ifs_interface build-dir
+      run: |
+        export fesom_ROOT=$PWD/build.ifs_interface
+        rm -rf test_downstream/build
+        cmake -S test_downstream -B test_downstream/build -DASSERT_HAVE_IFS_INTERFACE=ON -DASSERT_FESOM_DIR=${fesom_ROOT}
+        cmake --build test_downstream/build
+        test_downstream/build/main
+
+    - name: Test downstream from ifs_interface install-dir
+      run: |
+        export fesom_ROOT=$PWD/install.ifs_interface
+        rm -rf test_downstream/build
+        cmake -S test_downstream -B test_downstream/build -DASSERT_HAVE_IFS_INTERFACE=ON -DASSERT_FESOM_DIR=${fesom_ROOT}
+        cmake --build test_downstream/build
+        test_downstream/build/main
 
     - name: Create global test run
       run: |
@@ -44,6 +69,12 @@ jobs:
       run: |
         cd work_pi
         fcheck .
+    - name: Check UGRID Compliance
+      run: |
+        pip install ugrid-checks xarray
+        # Needed to combine the mesh diag and output
+        python3 -c "import xarray as xr; ds1 = xr.open_dataset('./test/output_pi/sst.fesom.1948.nc'); ds2 = xr.open_dataset('./test/output_pi/fesom.mesh.diag.nc'); xr.merge([ds1, ds2]).to_netcdf('./test/output_pi/merged_ugrid_check.nc')"
+        ugrid-checker ./test/output_pi/merged_ugrid_check.nc
 
     - name: Check restarts
       run: |

.github/workflows/fesom2_openmp.yml

@@ -12,22 +12,20 @@ jobs:
     # Containers must run in Linux based operating systems
     runs-on: ubuntu-latest
     # Docker Hub image that `container-job` executes in
-    container: koldunovn/fesom2_test:refactoring2
+    container: ghcr.io/fesom/fesom2_docker:fesom2_test_refactoring-nightly
 
     # Service containers to run with `gfortran_ubuntu`
     steps:
     # NK: this changes working directory to fesom2
     - uses: actions/checkout@v2
 
-    - name: switch OpenMP ON
+    - name: Git safe directory
       run: |
-        cd ./src/
-        sed -i 's/with OpenMP\" OFF/with OpenMP\" ON/g' CMakeLists.txt
-        cd ../
+        git config --global --add safe.directory ${PWD}
 
     - name: Compile model
       run: |
-        bash -l configure.sh ubuntu
+        bash -l configure.sh ubuntu -DENABLE_OPENMP=ON
     
     - name: Create global test run with 4 OpenMP threads
       run: |

.github/workflows/lumi-sync.yaml

@@ -0,0 +1,28 @@
+name: Run CICD on Lumi (using .gitlab-ci.yml)
+
+on: 
+  push:
+    branches:
+      - refactoring
+      - lumi_gpu_evatali
+
+jobs:
+  gitlabsync:
+    runs-on: ubuntu-latest
+    steps:
+      - name: "Check out code"
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: "Gitlab mirror and CI"
+        uses: "tiggi/gitlab-mirror-and-ci-action@tiggi/fixes"
+        with:
+          args: "https://gitlab.com/lumi-cicd/fesom2.git"
+        env:
+          FOLLOW_TAGS: "true"
+          FORCE_PUSH: "true"
+          GITLAB_HOSTNAME: "gitlab.com"
+          GITLAB_USERNAME: "tiggi"
+          GITLAB_PASSWORD: ${{ secrets.GITLAB_PASSWORD }}
+          GITLAB_PROJECT_ID: "51374059"
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -1,5 +1,7 @@
 /build
 /build.lib
+/work
+/lib64
 *.o
 *.mod
 *.x
@@ -12,3 +14,4 @@ lib/*.so
 /work_*
 Makefile.in
 mesh_part/build
+test/output_pi 

.gitlab-ci.yml

@@ -0,0 +1,12 @@
+fesom-job:
+  stage: build
+  variables:
+    SCHEDULER_PARAMETERS: "-N 1 -n 56 --mem=32G -p dev-g -t 00:30:00 -A project_462000376"
+  tags:
+    - lumi
+#  artifacts:
+#    paths:
+#      - fesom_build.log
+  script:
+    - echo "building fesom branch"
+    - bash -l configure.sh lumi

.readthedocs.yaml

@@ -0,0 +1,35 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.9"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+   install:
+   - requirements: docs/requirements.txt

CMakeLists.txt

@@ -1,23 +1,37 @@
-cmake_minimum_required(VERSION 3.9)
+cmake_minimum_required(VERSION 3.16)
 
 # set default build type cache entry (do so before project(...) is called, which would create this cache entry on its own)
 if(NOT CMAKE_BUILD_TYPE)
-	message(STATUS "setting default build type: Release")
-	set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: None(CMAKE_CXX_FLAGS or CMAKE_C_FLAGS used) Debug Release RelWithDebInfo MinSizeRel.")
+  message(STATUS "setting default build type: Release")
+  set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: None(CMAKE_CXX_FLAGS or CMAKE_C_FLAGS used) Debug Release RelWithDebInfo MinSizeRel.")
 endif()
 
 project(FESOM2.0)
 
-set(CMAKE_VERBOSE_MAKEFILE ON)
-
-option(BUILD_SHARED_LIBS "Build using shared libraries" OFF) # cmake-internal switch to toggle if library targets are being build as STATIC or SHARED, see https://cmake.org/cmake/help/latest/guide/tutorial/Selecting%20Static%20or%20Shared%20Libraries.html
+set(BUILD_SHARED_LIBS ON CACHE BOOL "Default to using shared libs")
 set(TOPLEVEL_DIR ${CMAKE_CURRENT_LIST_DIR})
 set(FESOM_COUPLED OFF CACHE BOOL "compile fesom standalone or with oasis support (i.e. coupled)")
 set(OIFS_COUPLED OFF CACHE BOOL "compile fesom coupled to OpenIFS. (Also needs FESOM_COUPLED to work)")
 set(CRAY OFF CACHE BOOL "compile with cray ftn")
 set(USE_ICEPACK OFF CACHE BOOL "compile fesom with the Iceapck modules for sea ice column physics.")
 set(OPENMP_REPRODUCIBLE OFF CACHE BOOL "serialize OpenMP loops that are critical for reproducible results")
-
-#set(VERBOSE OFF CACHE BOOL "toggle debug output")
+set(RECOM_COUPLED OFF CACHE BOOL "compile fesom including biogeochemistry, REcoM3")
+set(CISO_COUPLED OFF CACHE BOOL "compile ciso coupled to REcoM3. RECOM_COUPLED has to be active")
+set(USE_MULTIO OFF CACHE BOOL "Use MULTIO for IO, either grib or binary for now. This also means path to MULTIO installation has to provided using env MULTIO_INSTALL_PATH='..' and multio configuration yamls must be present to run the model with MULTIO")
+set(OASIS_WITH_YAC OFF CACHE BOOL "Useing a version of OASIS compiled with YAC instead of SCRIP for interpolation?")
+set(ASYNC_ICEBERGS ON CACHE BOOL "compile fesom with or without support for asynchronous iceberg computations")
+set(VERBOSE OFF CACHE BOOL "toggle debug output")
 #add_subdirectory(oasis3-mct/lib/psmile)
 add_subdirectory(src)
+
+foreach( _file fesom-config.cmake fesom-config-version.cmake fesom-targets.cmake )
+  execute_process( COMMAND ${CMAKE_COMMAND} -E create_symlink ${PROJECT_BINARY_DIR}/src/${_file} ${PROJECT_BINARY_DIR}/${_file}  )
+endforeach()
+
+# Define ${PROJECT_NAME}_DIR in PARENT_SCOPE so that a `find_package( <this-project> )` in a bundle
+# will easily find the project without requiring a `HINT <this-project>_BINARY_DIR` argument
+if( NOT CMAKE_SOURCE_DIR STREQUAL PROJECT_SOURCE_DIR )
+    # Guard needed because PARENT_SCOPE cannot be used in top-level CMake project
+
+    set( fesom_DIR ${fesom_DIR} PARENT_SCOPE )
+endif()

README.md

@@ -29,12 +29,3 @@ References
 * **[Version with ICEPACK sea ice thermodynamics]** Zampieri, Lorenzo, Frank Kauker, Jörg Fröhle, Hiroshi Sumata, Elizabeth C. Hunke, and Helge Goessling. Impact of Sea-Ice Model Complexity on the Performance of an Unstructured-Mesh Sea-ice/ocean Model Under Different Atmospheric Forcings. Washington: American Geophysical Union, 2020. https://dx.doi.org/10.1002/essoar.10505308.1.
 
 * **[Version coupled with OpenIFS atmosphere]** Streffing, J., Sidorenko, D., Semmler, T., Zampieri, L., Scholz, P., Andrés-Martínez, M., et al ( 2022). AWI-CM3 coupled climate model: description and evaluation experiments for a prototype post-CMIP6 model. Geoscientific Model Development, 15. https://doi.org/10.5194/gmd-15-6399-2022
-
-Documentation for FESOM2
-************************
-
-Here lives FESOM2 documentation
-
-Rendered version: https://fesom2.readthedocs.io/en/latest/
-
-

cmake/FindMULTIO.cmake

@@ -0,0 +1,50 @@
+# FindMULTIO.cmake
+
+include(FindPackageHandleStandardArgs)
+
+# Use the environment variable as a hint
+set(MULTIO_HINT_PATH $ENV{MULTIO_INSTALL_PATH})
+
+# Try to find the library
+find_library(MULTIO_FAPI_LIBRARY
+    NAMES multio-fapi # Adjust this if the library name is different
+    HINTS ${MULTIO_HINT_PATH}/lib
+)
+
+# Try to find the dependency library
+find_library(MULTIO_API_LIBRARY
+    NAMES multio-api
+    HINTS ${MULTIO_HINT_PATH}/lib
+)
+
+# Try to find the dependency library
+find_library(MULTIO_LIBRARY
+    NAMES multio
+    HINTS ${MULTIO_HINT_PATH}/lib
+)
+
+# Try to find the Fortran module path
+find_path(MULTIO_MODULE_PATH
+    NAMES multio_api.mod # Replace <module_name> with an actual module name you expect to find
+    HINTS ${MULTIO_HINT_PATH}/module ${MULTIO_HINT_PATH}/multio/module
+)
+
+
+# Aggregate the libraries for easier linking
+set(MULTIO_LIBRARIES ${MULTIO_FAPI_LIBRARY} ${MULTIO_API_LIBRARY} ${MULTIO_LIBRARY})
+
+
+# Handle the results
+find_package_handle_standard_args(MULTIO 
+    REQUIRED_VARS MULTIO_LIBRARIES MULTIO_MODULE_PATH
+    FOUND_VAR MULTIO_FOUND
+)
+
+# If found, set the MULTIO_LIBRARIES and MULTIO_INCLUDE_DIRS variables for easy use
+if(MULTIO_FOUND)
+    set(MULTIO_INCLUDE_DIRS ${MULTIO_MODULE_PATH})
+endif()
+
+# Mark variables as advanced
+mark_as_advanced(MULTIO_LIBRARY MULTIO_MODULE_PATH)
+