FESOM · JanStreffing · Sep 8, 2025 · Sep 5, 2025 · Sep 5, 2025 · Sep 5, 2025
diff --git a/.github/workflows/ecbundle_release.yml b/.github/workflows/ecbundle_release.yml
@@ -145,7 +145,6 @@ jobs:
           cmake \
             -DCMAKE_BUILD_TYPE=${{ github.event.inputs.build_type || 'Release' }} \
             -DBUILD_TESTING=ON \
-            -DENABLE_INTEGRATION_TESTS=ON \
             -DENABLE_MPI_TESTS=ON \
             -DTEST_TIMEOUT=${{ github.event.inputs.test_timeout || '600' }} \
             -DCMAKE_C_COMPILER=gcc \

diff --git a/.github/workflows/fesom2_ctest_runner.yml b/.github/workflows/fesom2_ctest_runner.yml
@@ -1,5 +1,10 @@
 name: FESOM2 CTest Framework (Native Runner)
 
+# This workflow tests FESOM2 core functionality using local meshes only.
+# It skips remote mesh tests to avoid external dependencies in CI.
+# For full testing including remote meshes, run locally with:
+# ./configure.sh ubuntu -DBUILD_TESTING=ON -DBUILD_MESHDIAG=ON -DBUILD_MESHPARTITIONER=ON
+
 # Controls when the action will run
 on:
   # Triggers the workflow on push or pull request events
@@ -128,7 +133,8 @@ jobs:
           cmake \
             -DCMAKE_BUILD_TYPE=${{ github.event.inputs.build_type || 'Release' }} \
             -DBUILD_TESTING=ON \
-            -DENABLE_INTEGRATION_TESTS=ON \
+            -DBUILD_MESHDIAG=ON \
+            -DBUILD_MESHPARTITIONER=ON \
             -DENABLE_MPI_TESTS=ON \
             -DTEST_TIMEOUT=${{ github.event.inputs.test_timeout || '600' }} \
             -DCMAKE_C_COMPILER=gcc \
@@ -154,7 +160,7 @@ jobs:
 
           echo "Build completed successfully"
 
-          # Verify executable exists
+          # Verify executables exist
           if [ -f "bin/fesom.x" ]; then
             echo "✅ FESOM2 executable created successfully"
             ls -la bin/fesom.x
@@ -163,6 +169,20 @@ jobs:
             find . -name "fesom.x" -type f || echo "No fesom.x found anywhere"
             exit 1
           fi
+
+          if [ -f "bin/fesom_meshdiag" ]; then
+            echo "✅ FESOM2 meshdiag executable created successfully"
+            ls -la bin/fesom_meshdiag
+          else
+            echo "⚠️ FESOM2 meshdiag executable not found"
+          fi
+
+          if [ -f "bin/fesom_meshpart" ]; then
+            echo "✅ FESOM2 mesh partitioner executable created successfully" 
+            ls -la bin/fesom_meshpart
+          else
+            echo "⚠️ FESOM2 mesh partitioner executable not found"
+          fi
 
       - name: List available tests
         run: |
@@ -205,14 +225,15 @@ jobs:
             echo "Running tests matching pattern: $TEST_PATTERN"
             ctest $CTEST_ARGS -R "$TEST_PATTERN"
           else
-            echo "Running selected integration tests:"
-            echo "- integration_full_run_mpi2"
-            echo "- integration_full_run_mpi8" 
+            echo "Running core integration tests:"
+            echo "- integration_pi_mpi2"
+            echo "- integration_pi_mpi8" 
             echo "- integration_pi_cavity_mpi2"
-            echo "- integration_test_data_check"
+            echo "- integration_meshdiag_pi_mpi2"
+            echo "- meshpartitioner_partition_local_pi_mesh_4"
 
-            # Run only the specified tests using regex pattern
-            ctest $CTEST_ARGS -R "(integration_full_run_mpi2|integration_full_run_mpi8|integration_pi_cavity_mpi2|integration_test_data_check)"
+            # Run only the core local tests (skip remote tests in CI to avoid external dependencies)
+            ctest $CTEST_ARGS -R "(integration_pi_mpi2|integration_pi_mpi8|integration_pi_cavity_mpi2|integration_meshdiag_pi_mpi2|meshpartitioner_partition_local_pi_mesh_4)"
           fi
 
           # Capture exit code

diff --git a/cmake/FesomTesting.cmake b/cmake/FesomTesting.cmake
@@ -85,9 +85,9 @@ function(update_namelist_config_with_options NAMELIST_IN NAMELIST_OUT STEP_PER_D
     # Set logfile output frequency
     string(REGEX REPLACE "logfile_outfreq=[0-9]+" "logfile_outfreq=${LOGFILE_OUTFREQ}" CONTENT "${CONTENT}")
     # Force rotation for test geometry
-    string(REGEX REPLACE "force_rotation=.[a-zA-Z]." "force_rotation=${FORCE_ROTATION}" CONTENT "${CONTENT}")
+    string(REGEX REPLACE "force_rotation=\\.[a-zA-Z]+\\." "force_rotation=${FORCE_ROTATION}" CONTENT "${CONTENT}")
     # Set cavity usage
-    string(REGEX REPLACE "use_cavity=.[a-zA-Z]." "use_cavity=${USE_CAVITY}" CONTENT "${CONTENT}")
+    string(REGEX REPLACE "use_cavity=\\.[a-zA-Z]+\\." "use_cavity=${USE_CAVITY}" CONTENT "${CONTENT}")
 
     file(WRITE "${NAMELIST_OUT}" "${CONTENT}")
 endfunction()
@@ -482,10 +482,15 @@ endfunction()
 
 # Function to add a FESOM meshdiag test with custom options
 function(add_fesom_meshdiag_test_with_options TEST_NAME MESH_NAME RUNID)
-    set(oneValueArgs NP TIMEOUT)
+    set(oneValueArgs NP TIMEOUT PREFIX)
     set(multiValueArgs COMMAND_ARGS)
     cmake_parse_arguments(FESOM_TEST "" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
 
+    # Apply prefix if provided
+    if(FESOM_TEST_PREFIX)
+        set(TEST_NAME "${FESOM_TEST_PREFIX}_${TEST_NAME}")
+    endif()
+
     # Set defaults (meshdiag requires MPI, minimum 2 processes)
     if(NOT DEFINED FESOM_TEST_NP)
         set(FESOM_TEST_NP 2)
@@ -566,3 +571,187 @@ function(add_fesom_meshdiag_test_with_options TEST_NAME MESH_NAME RUNID)
 
     message(STATUS "Added FESOM meshdiag test: ${TEST_NAME} with mesh: ${MESH_NAME}, runid: ${RUNID}")
 endfunction()
+
+#===============================================================================
+# Generic Mesh Pipeline Functions
+#===============================================================================
+
+# Function to add mesh download fixture
+function(add_mesh_download_fixture MESH_NAME)
+    # Parse optional prefix argument
+    set(oneValueArgs PREFIX)
+    cmake_parse_arguments(DOWNLOAD_ARGS "" "${oneValueArgs}" "" ${ARGN})
+
+    if(DOWNLOAD_ARGS_PREFIX)
+        set(DOWNLOAD_TEST_NAME "${DOWNLOAD_ARGS_PREFIX}_download_mesh_${MESH_NAME}")
+    else()
+        set(DOWNLOAD_TEST_NAME "download_mesh_${MESH_NAME}")
+    endif()
+
+    add_test(
+        NAME ${DOWNLOAD_TEST_NAME}
+        COMMAND ${CMAKE_COMMAND}
+            -DSOURCE_DIR=${CMAKE_SOURCE_DIR}
+            -DMESH_NAME=${MESH_NAME}
+            -P ${CMAKE_SOURCE_DIR}/tests/integration/mesh_download.cmake
+    )
+
+    set_tests_properties(${DOWNLOAD_TEST_NAME} PROPERTIES
+        TIMEOUT 1200  # 20 minutes for download
+        FIXTURES_SETUP "mesh_${MESH_NAME}"
+        LABELS "download_mesh"
+    )
+
+    message(STATUS "Added mesh download fixture: ${DOWNLOAD_TEST_NAME}")
+endfunction()
+
+# Function to add mesh partition fixture  
+function(add_mesh_partition_fixture MESH_NAME NUM_PROCESSES)
+    # Parse optional prefix argument
+    set(oneValueArgs PREFIX)
+    cmake_parse_arguments(PARTITION_ARGS "" "${oneValueArgs}" "" ${ARGN})
+
+    if(PARTITION_ARGS_PREFIX)
+        set(PARTITION_TEST_NAME "${PARTITION_ARGS_PREFIX}_partition_mesh_${MESH_NAME}_${NUM_PROCESSES}")
+    else()
+        set(PARTITION_TEST_NAME "partition_mesh_${MESH_NAME}_${NUM_PROCESSES}")
+    endif()
+
+    add_test(
+        NAME ${PARTITION_TEST_NAME}
+        COMMAND ${CMAKE_COMMAND}
+            -DSOURCE_DIR=${CMAKE_SOURCE_DIR}
+            -DBUILD_DIR=${CMAKE_BINARY_DIR}
+            -DMESH_NAME=${MESH_NAME}
+            -DNUM_PROCESSES=${NUM_PROCESSES}
+            -P ${CMAKE_SOURCE_DIR}/tests/integration/mesh_partition.cmake
+    )
+
+    set_tests_properties(${PARTITION_TEST_NAME} PROPERTIES
+        TIMEOUT 1200  # 20 minutes for partitioning
+        FIXTURES_SETUP "mesh_${MESH_NAME}_${NUM_PROCESSES}"
+        FIXTURES_REQUIRED "mesh_${MESH_NAME}"
+        LABELS "partition_mesh"
+    )
+
+    message(STATUS "Added mesh partition fixture: ${PARTITION_TEST_NAME}")
+endfunction()
+
+# Function to add complete mesh pipeline (download + multiple partitions)
+function(add_mesh_pipeline MESH_NAME)
+    # Parse arguments
+    set(oneValueArgs PREFIX)
+    set(multiValueArgs PROCESS_COUNTS)
+    cmake_parse_arguments(PIPELINE_ARGS "" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+
+    # Use remaining args as process counts if not specified
+    if(NOT PIPELINE_ARGS_PROCESS_COUNTS)
+        set(PIPELINE_ARGS_PROCESS_COUNTS ${PIPELINE_ARGS_UNPARSED_ARGUMENTS})
+        if(NOT PIPELINE_ARGS_PROCESS_COUNTS)
+            set(PIPELINE_ARGS_PROCESS_COUNTS 2 4)  # Default process counts
+        endif()
+    endif()
+
+    # Add download fixture
+    if(PIPELINE_ARGS_PREFIX)
+        add_mesh_download_fixture(${MESH_NAME} PREFIX ${PIPELINE_ARGS_PREFIX})
+    else()
+        add_mesh_download_fixture(${MESH_NAME})
+    endif()
+
+    # Add partition fixtures for each process count
+    foreach(NP ${PIPELINE_ARGS_PROCESS_COUNTS})
+        if(PIPELINE_ARGS_PREFIX)
+            add_mesh_partition_fixture(${MESH_NAME} ${NP} PREFIX ${PIPELINE_ARGS_PREFIX})
+        else()
+            add_mesh_partition_fixture(${MESH_NAME} ${NP})
+        endif()
+    endforeach()
+
+    message(STATUS "Added complete mesh pipeline for '${MESH_NAME}' with process counts: ${PIPELINE_ARGS_PROCESS_COUNTS}")
+endfunction()
+
+# Enhanced function to add FESOM test with mesh pipeline integration
+function(add_fesom_mesh_test TEST_NAME MESH_NAME NP)
+    set(options MPI_TEST)
+    set(oneValueArgs TIMEOUT)
+    set(multiValueArgs)
+    cmake_parse_arguments(FESOM_TEST "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+
+    # Set defaults
+    if(NOT DEFINED FESOM_TEST_TIMEOUT)
+        set(FESOM_TEST_TIMEOUT 900)  # 15 minutes default
+    endif()
+
+    # Parse mesh configuration from registry
+    set(MESH_REGISTRY "${CMAKE_SOURCE_DIR}/tests/mesh_registry.json")
+    if(EXISTS "${MESH_REGISTRY}")
+        file(READ "${MESH_REGISTRY}" REGISTRY_CONTENT)
+
+        # Extract mesh configuration
+        string(REGEX MATCH "\"${MESH_NAME}\"[^}]*\"force_rotation\"[ ]*:[ ]*([^,}]+)" ROTATION_MATCH "${REGISTRY_CONTENT}")
+        if(ROTATION_MATCH)
+            string(STRIP "${CMAKE_MATCH_1}" FORCE_ROTATION_RAW)
+            string(REPLACE "true" ".true." FORCE_ROTATION "${FORCE_ROTATION_RAW}")
+            string(REPLACE "false" ".false." FORCE_ROTATION "${FORCE_ROTATION}")
+        else()
+            set(FORCE_ROTATION ".true.")  # Default
+        endif()
+
+        string(REGEX MATCH "\"${MESH_NAME}\"[^}]*\"use_cavity\"[ ]*:[ ]*([^,}]+)" CAVITY_MATCH "${REGISTRY_CONTENT}")
+        if(CAVITY_MATCH)
+            string(STRIP "${CMAKE_MATCH_1}" USE_CAVITY_RAW)
+            string(REPLACE "true" ".true." USE_CAVITY "${USE_CAVITY_RAW}")
+            string(REPLACE "false" ".false." USE_CAVITY "${USE_CAVITY}")
+        else()
+            set(USE_CAVITY ".false.")  # Default
+        endif()
+
+        # Extract timing parameters
+        string(REGEX MATCH "\"${MESH_NAME}\"[^}]*\"step_per_day\"[ ]*:[ ]*([^,}]+)" SPD_MATCH "${REGISTRY_CONTENT}")
+        if(SPD_MATCH)
+            string(STRIP "${CMAKE_MATCH_1}" STEP_PER_DAY)
+        else()
+            set(STEP_PER_DAY "288")  # Default
+        endif()
+
+        string(REGEX MATCH "\"${MESH_NAME}\"[^}]*\"run_length\"[ ]*:[ ]*([^,}]+)" RL_MATCH "${REGISTRY_CONTENT}")
+        if(RL_MATCH)
+            string(STRIP "${CMAKE_MATCH_1}" RUN_LENGTH)
+        else()
+            set(RUN_LENGTH "1")  # Default
+        endif()
+
+        string(REGEX MATCH "\"${MESH_NAME}\"[^}]*\"run_length_unit\"[ ]*:[ ]*\"([^\"]+)\"" RLU_MATCH "${REGISTRY_CONTENT}")
+        if(RLU_MATCH)
+            string(STRIP "${CMAKE_MATCH_1}" RUN_LENGTH_UNIT)
+        else()
+            set(RUN_LENGTH_UNIT "s")  # Default
+        endif()
+    else()
+        # Fallback defaults
+        set(FORCE_ROTATION ".true.")
+        set(USE_CAVITY ".false.")
+        set(STEP_PER_DAY "288")
+        set(RUN_LENGTH "1")
+        set(RUN_LENGTH_UNIT "s")
+    endif()
+
+    # Create FESOM test with appropriate configuration from registry
+    add_fesom_test_with_options(${TEST_NAME}
+        "${MESH_NAME}" "${STEP_PER_DAY}" "${RUN_LENGTH}" "${RUN_LENGTH_UNIT}" "1" "d" "10" "${FORCE_ROTATION}" "${USE_CAVITY}"
+        MPI_TEST
+        NP ${NP}
+        TIMEOUT ${FESOM_TEST_TIMEOUT}
+    )
+
+    # Add mesh pipeline dependency
+    set_tests_properties(${TEST_NAME} PROPERTIES
+        FIXTURES_REQUIRED "mesh_${MESH_NAME}_${NP}"
+        LABELS "mesh_simulation"
+    )
+
+    message(STATUS "Added FESOM mesh test: ${TEST_NAME} (mesh: ${MESH_NAME}, ${NP} processes)")
+    message(STATUS "  Configuration: force_rotation=${FORCE_ROTATION}, use_cavity=${USE_CAVITY}")
+    message(STATUS "  Timing: step_per_day=${STEP_PER_DAY}, run_length=${RUN_LENGTH} ${RUN_LENGTH_UNIT}")
+endfunction()
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
@@ -16,7 +16,6 @@ if(NOT TARGET fesom)
 endif()
 
 # Testing configuration options
-option(ENABLE_INTEGRATION_TESTS "Enable integration tests that run FESOM" ON)
 option(ENABLE_MPI_TESTS "Enable MPI tests (requires mpiexec/mpirun)" ON)
 set(TEST_TIMEOUT 600 CACHE STRING "Default timeout for tests in seconds")
 
@@ -56,26 +55,28 @@ endif()
 
 # Print test configuration
 message(STATUS "FESOM2 Testing Configuration:")
-message(STATUS "  Integration tests: ${ENABLE_INTEGRATION_TESTS}")
 message(STATUS "  MPI tests: ${ENABLE_MPI_TESTS}")
 message(STATUS "  Test timeout: ${TEST_TIMEOUT}s")
 message(STATUS "  Test data directory: ${TEST_DATA_DIR}")
 message(STATUS "  MPI executable: ${MPIEXEC_EXECUTABLE}")
 
-# Add integration tests if enabled
-if(ENABLE_INTEGRATION_TESTS)
-    add_subdirectory(integration)
-endif()
+# Add integration tests
+add_subdirectory(integration)
+
+# Add mesh partitioner tests
+add_subdirectory(meshpartitioner)
+
+
+# Add remote mesh pipeline tests
+add_subdirectory(remote)
 
 # Add unit tests (for future expansion)
 if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/unit/CMakeLists.txt")
     add_subdirectory(unit)
 endif()
 
-# Add ecbundle tests if ecbundle is available
-if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/ecbundle/CMakeLists.txt")
-    add_subdirectory(ecbundle)
-endif()
+# Add ecbundle tests
+add_subdirectory(ecbundle)
 
 # Create a convenience target to run all tests
 add_custom_target(run_tests
@@ -106,9 +107,19 @@ endif()
 # Create target to run only meshdiag tests (if BUILD_MESHDIAG is enabled)
 if(BUILD_MESHDIAG)
     add_custom_target(run_meshdiag_tests
-        COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure -R "meshdiag_"
+        COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure -R "(meshdiag_|generate_meshdiag_)"
         WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
         COMMENT "Running FESOM2 meshdiag tests"
         VERBATIM
     )
 endif()
+
+# Create target to run only mesh partitioner tests (if BUILD_MESHPARTITIONER is enabled)
+if(BUILD_MESHPARTITIONER)
+    add_custom_target(run_meshpartitioner_tests
+        COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure -L "meshpartitioner"
+        WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+        COMMENT "Running FESOM2 mesh partitioner tests"
+        VERBATIM
+    )
+endif()