Merge branch 'refactoring' into mzapponi_refactoring

.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 }}

.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

@@ -17,6 +17,8 @@ set(OIFS_COUPLED OFF CACHE BOOL "compile fesom coupled to OpenIFS. (Also needs F
 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(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(VERBOSE OFF CACHE BOOL "toggle debug output")
 #add_subdirectory(oasis3-mct/lib/psmile)

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)
+

cmake/FindNETCDF.cmake

@@ -13,9 +13,13 @@ if(CMAKE_Fortran_COMPILER_LOADED)
 	if(HAVE_Fortran_NETCDF)
 		set(NETCDF_Fortran_INCLUDE_DIRECTORIES "")
 		set(NETCDF_Fortran_LIBRARIES "")
+		set(NETCDF_Fortran_FOUND 1)
 	else()
-		find_path(NETCDF_Fortran_INCLUDE_DIRECTORIES netcdf.inc HINTS $ENV{NETCDF_DIR}/include ENV NETCDF_Fortran_INCLUDE_DIRECTORIES)
+		find_path(NETCDF_Fortran_INCLUDE_DIRECTORIES netcdf.inc HINTS $ENV{NETCDF_ROOT}/include $ENV{NETCDF_DIR}/include $ENV{NETCDF4_DIR}/include ENV NETCDF_Fortran_INCLUDE_DIRECTORIES)
 		find_library(NETCDF_Fortran_LIBRARIES netcdff HINTS ${NETCDF_Fortran_INCLUDE_DIRECTORIES}/../lib)
+		if( NETCDF_Fortran_INCLUDE_DIRECTORIES AND NETCDF_Fortran_LIBRARIES )
+			set(NETCDF_Fortran_FOUND 1)
+		endif()
 	endif()	
 endif()
 
@@ -27,14 +31,18 @@ if(CMAKE_C_COMPILER_LOADED OR CMAKE_CXX_COMPILER_LOADED)
 	if(HAVE_C_NETCDF)
 		set(NETCDF_C_INCLUDE_DIRECTORIES "")
 		set(NETCDF_C_LIBRARIES "")
+		set(NETCDF_C_FOUND 1)
 	else()
-		find_path(NETCDF_C_INCLUDE_DIRECTORIES netcdf.h HINTS $ENV{NETCDF_DIR}/include ENV NETCDF_C_INCLUDE_DIRECTORIES)
+		find_path(NETCDF_C_INCLUDE_DIRECTORIES netcdf.h HINTS $ENV{NETCDF_ROOT}/include $ENV{NETCDF_DIR}/include $ENV{NETCDF4_DIR}/include ENV NETCDF_C_INCLUDE_DIRECTORIES)
 		find_library(NETCDF_C_LIBRARIES netcdf HINTS ${NETCDF_C_INCLUDE_DIRECTORIES}/../lib)
+		if( NETCDF_C_INCLUDE_DIRECTORIES AND NETCDF_C_LIBRARIES )
+			set(NETCDF_C_FOUND 1)
+		endif()
 	endif()
 endif()
 
 if(CMAKE_CXX_COMPILER_LOADED)
-	find_path(NETCDF_CXX_INCLUDE_DIRECTORIES netcdf HINTS $ENV{NETCDF_DIR}/include ENV NETCDF_CXX_INCLUDE_DIRECTORIES)
+	find_path(NETCDF_CXX_INCLUDE_DIRECTORIES netcdf HINTS $ENV{NETCDF_ROOT}/include $ENV{NETCDF_DIR}/include $ENV{NETCDF4_DIR} ENV NETCDF_CXX_INCLUDE_DIRECTORIES)
 	# the cray toolchain (e.g. hlrn) disables dynamic linking by default. to enable it at build time do e.g. "CRAYPE_LINK_TYPE=dynamic make".	
 	find_library(NETCDF_CXX_LIBRARIES NAMES netcdf_c++4 netcdf-cxx4 HINTS ${NETCDF_CXX_INCLUDE_DIRECTORIES}/../lib)
 	if(NETCDF_CXX_INCLUDE_DIRECTORIES AND NETCDF_C_INCLUDE_DIRECTORIES)
@@ -43,4 +51,21 @@ if(CMAKE_CXX_COMPILER_LOADED)
 	if(NETCDF_CXX_LIBRARIES AND NETCDF_C_LIBRARIES)
 		list(APPEND NETCDF_CXX_LIBRARIES ${NETCDF_C_LIBRARIES})
 	endif()
-endif()
+	if( NETCDF_CXX_INCLUDE_DIRECTORIES AND NETCDF_CXX_LIBRARIES )
+		set(NETCDF_CXX_FOUND 1)
+	endif()
+endif()
+
+if(NOT ${CMAKE_FIND_PACKAGE_NAME}_FIND_COMPONENTS)
+  set(${CMAKE_FIND_PACKAGE_NAME}_FIND_COMPONENTS C)
+endif()
+
+unset({CMAKE_FIND_PACKAGE_NAME}_REQUIRED_VARS)
+foreach(COMP C CXX Fortran)
+  if("${COMP}" IN_LIST ${CMAKE_FIND_PACKAGE_NAME}_FIND_COMPONENTS) 
+    list(APPEND ${CMAKE_FIND_PACKAGE_NAME}_REQUIRED_VARS NETCDF_${COMP}_FOUND)
+  endif()
+endforeach()
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(${CMAKE_FIND_PACKAGE_NAME} HANDLE_COMPONENTS REQUIRED_VARS ${CMAKE_FIND_PACKAGE_NAME}_REQUIRED_VARS)
+

cmake/FindOASISYAC.cmake

@@ -0,0 +1,19 @@
+find_path(OASIS_Fortran_INCLUDE_DIRECTORIES mod_oasis.mod HINTS ${TOPLEVEL_DIR}/../oasis/build/lib/psmile)
+find_library(OASIS_Fortran_LIBRARIES psmile HINTS ${TOPLEVEL_DIR}/../oasis/build/lib/psmile)
+
+find_path(MCT_Fortran_INCLUDE_DIRECTORIES mct_mod.mod HINTS ${TOPLEVEL_DIR}/../oasis/build/lib/psmile/mct)
+find_library(MCT_Fortran_LIBRARIES mct HINTS ${TOPLEVEL_DIR}/../oasis/build/lib/psmile/mct)
+
+find_path(MPEU_Fortran_INCLUDE_DIRECTORIES m_mpout.mod HINTS ${TOPLEVEL_DIR}/../oasis/build/lib/psmile/mct)
+find_library(MPEU_Fortran_LIBRARIES mpeu HINTS ${TOPLEVEL_DIR}/../oasis/build/lib/psmile/mct)
+
+find_path(SCRIP_Fortran_INCLUDE_DIRECTORIES remap_bicubic_reduced.mod HINTS ${TOPLEVEL_DIR}/../oasis/build/lib/psmile/scrip)
+find_library(SCRIP_Fortran_LIBRARIES scrip HINTS ${TOPLEVEL_DIR}/../oasis/build/lib/psmile/scrip)
+
+find_path(YAC_Fortran_INCLUDE_DIRECTORIES mo_yac_utils.mod HINTS ${TOPLEVEL_DIR}/../oasis/lib/yac/include)
+find_library(YACUTILS_Fortran_LIBRARIES yac_utils HINTS ${TOPLEVEL_DIR}/../oasis/lib/yac/lib)
+find_library(YACCORE_Fortran_LIBRARIES yac_core HINTS ${TOPLEVEL_DIR}/../oasis/lib/yac/lib)
+
+find_path(YAXT_Fortran_INCLUDE_DIRECTORIES yaxt.mod HINTS ${TOPLEVEL_DIR}/../oasis/lib/yaxt/include)
+find_library(YAXT_Fortran_LIBRARIES yaxt HINTS ${TOPLEVEL_DIR}/../oasis/lib/yaxt/lib)
+find_library(YAXTC_Fortran_LIBRARIES yaxt_c HINTS ${TOPLEVEL_DIR}/../oasis/lib/yaxt/lib)

config/namelist.cvmix

@@ -26,7 +26,9 @@ idemix_mu0         = 0.33333333 ! dissipation parameter (dimensionless)
 idemix_sforcusage  = 0.2
 idemix_n_hor_iwe_prop_iter = 5  ! iterations for contribution from horiz. wave propagation
 idemix_surforc_file = '/work/ollie/clidyn/forcing/IDEMIX/fourier_smooth_2005_cfsr_inert_rgrid.nc'
+idemix_surforc_vname= 'var706'
 idemix_botforc_file = '/work/ollie/clidyn/forcing/IDEMIX/tidal_energy_gx1v6_20090205_rgrid.nc'
+idemix_botforc_vname= 'wave_dissipation'
 /
 
 ! namelist for PP