Migrating build system to CMake

.gitignore

@@ -1,3 +1,9 @@
+# CMake
+/build/
+CMakeUserPresets.json
+/CMakeCache.txt
+/CMakeFiles/
+
 *.bck
 *.o
 *.mod

CMakeLists.txt

@@ -0,0 +1,167 @@
+cmake_minimum_required(VERSION 3.20)
+
+# The version header embeds the compile flags, so languages must be enabled
+# before we can generate it. Fortran is the primary language; C and C++ are
+# needed for tools/*.c, the r-tree, the sparse-solver shims and Catalyst.
+project(JOREK
+  LANGUAGES Fortran C CXX
+  DESCRIPTION "Non-linear extended MHD code for toroidal X-point geometries")
+
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
+
+if(CMAKE_SOURCE_DIR STREQUAL CMAKE_BINARY_DIR)
+  message(FATAL_ERROR
+    "In-source builds are not supported. Configure into a separate directory, "
+    "e.g. cmake --preset pitagora-intel")
+endif()
+
+set(CMAKE_Fortran_MODULE_DIRECTORY "${CMAKE_BINARY_DIR}/modules")
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+  set(CMAKE_BUILD_TYPE Release CACHE STRING "Build type" FORCE)
+endif()
+
+include(JorekOptions)         # cache options, replaces Makefile.inc switches
+include(JorekModelConfig)     # derive -D flags from the model settings files
+include(JorekCompilerFlags)   # per-compiler flag sets, replaces defaults.mk
+include(JorekDependencies)    # MPI, HDF5, FFTW, BLAS/LAPACK, sparse solvers
+include(JorekVersion)         # git-derived version.h
+include(JorekSources)         # source discovery, program/library split
+
+# --- Usage requirements shared by every JOREK target ------------------------
+add_library(jorek_common INTERFACE)
+target_include_directories(jorek_common INTERFACE
+  "${CMAKE_BINARY_DIR}/generated"        # version.h
+  "${JOREK_GENERATED_INCLUDE_DIR}"       # rhs/amat/aux_automatic.h
+  "${CMAKE_CURRENT_SOURCE_DIR}/tools"    # r3_info.h
+  "${CMAKE_CURRENT_SOURCE_DIR}/models"
+  ${JOREK_INCLUDE_DIRS})
+target_compile_definitions(jorek_common INTERFACE ${JOREK_DEFINES})
+target_link_libraries(jorek_common INTERFACE ${JOREK_LIBRARIES})
+
+# --- The code generator (semianalytical models only) ------------------------
+#
+# Built before, and independently of, the core library -- see JorekSources for
+# why it cannot simply link against it. Its objects are compiled a second time
+# into jorek_core; that is a dozen files, and it keeps the graph acyclic.
+if(JOREK_SEMIANALYTICAL)
+  add_library(jorek_codegen STATIC ${JOREK_CODEGEN_SOURCES})
+  add_dependencies(jorek_codegen jorek_version_header)
+  target_link_libraries(jorek_codegen PRIVATE jorek_common)
+  # Its own module directory: these sources are also compiled into jorek_core,
+  # and the two must not fight over the same .mod files.
+  set_target_properties(jorek_codegen PROPERTIES
+    Fortran_MODULE_DIRECTORY "${CMAKE_BINARY_DIR}/modules_codegen")
+
+  # algexpr2fort evaluates the model's symbolic equations and writes the
+  # RHS/AMAT/AUX Fortran that mod_elt_matrix{,_fft}.f90 #include. It hard-codes
+  # its output path as "models/model<NNN>/<name>.h" relative to the working
+  # directory, so run it from the build tree to keep the source tree clean.
+  add_executable(algexpr2fort "${CMAKE_CURRENT_SOURCE_DIR}/models/algexpr2fort.f90")
+  target_link_libraries(algexpr2fort PRIVATE jorek_codegen jorek_common)
+  set_target_properties(algexpr2fort PROPERTIES
+    Fortran_MODULE_DIRECTORY "${CMAKE_BINARY_DIR}/modules_codegen"
+    RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}"
+    LINKER_LANGUAGE Fortran)
+
+  set(JOREK_GENERATED_HEADERS
+    "${JOREK_GENERATED_INCLUDE_DIR}/rhs_automatic.h"
+    "${JOREK_GENERATED_INCLUDE_DIR}/amat_automatic.h"
+    "${JOREK_GENERATED_INCLUDE_DIR}/aux_automatic.h")
+
+  add_custom_command(
+    OUTPUT ${JOREK_GENERATED_HEADERS}
+    COMMAND "$<TARGET_FILE:algexpr2fort>"
+    WORKING_DIRECTORY "${CMAKE_BINARY_DIR}/generated"
+    DEPENDS algexpr2fort
+    COMMENT "Generating element-matrix code for ${JOREK_MODEL}"
+    VERBATIM)
+  add_custom_target(jorek_generated_code DEPENDS ${JOREK_GENERATED_HEADERS})
+endif()
+
+# --- The core library -------------------------------------------------------
+#
+# The Make build discovered each executable's objects by scanning for `call`
+# statements and linking whatever file was named after the callee. Here every
+# non-program source instead goes into one static archive, and the linker
+# extracts what each executable actually references. Keeping it a single archive
+# matters: JOREK is full of bare external subroutines, so any split into two
+# libraries would leave them referencing each other across the link line.
+add_library(jorek_core STATIC ${JOREK_LIB_SOURCES})
+add_dependencies(jorek_core jorek_version_header)
+target_link_libraries(jorek_core PUBLIC jorek_common)
+target_include_directories(jorek_core PUBLIC "${CMAKE_Fortran_MODULE_DIRECTORY}")
+
+if(JOREK_SEMIANALYTICAL)
+  add_dependencies(jorek_core jorek_generated_code)
+endif()
+
+# --- Executables ------------------------------------------------------------
+#
+# Only the main solver is built by default, mirroring `make`. Every other
+# program is a named target; `make most` builds the regression-tested subset.
+foreach(_prog_src IN LISTS JOREK_PROGRAM_SOURCES)
+  get_filename_component(_prog "${_prog_src}" NAME_WE)
+
+  if(_prog STREQUAL "jorek2_main")
+    add_executable(jorek2_main "${_prog_src}")
+    set_target_properties(jorek2_main PROPERTIES
+      OUTPUT_NAME "jorek_model${JOREK_MODEL_NUMBER}")
+  else()
+    add_executable(${_prog} EXCLUDE_FROM_ALL "${_prog_src}")
+  endif()
+
+  target_link_libraries(${_prog} PRIVATE jorek_core)
+  set_target_properties(${_prog} PROPERTIES
+    RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}"
+    # The core library mixes Fortran, C and C++ objects, and CMake would
+    # otherwise pick the C++ driver to link -- which does not supply the
+    # Fortran runtime's main(). Every JOREK program is a Fortran program.
+    LINKER_LANGUAGE Fortran)
+endforeach()
+
+if(TARGET eqdsk2jorek AND JOREK_DIERCKX_LIBRARIES)
+  target_link_libraries(eqdsk2jorek PRIVATE ${JOREK_DIERCKX_LIBRARIES})
+endif()
+
+# The set of diagnostics that must keep compiling for regression testing to
+# pass. Kept in sync with the `most:` target of the legacy Makefile.
+set(JOREK_MOST_TARGETS
+  jorek2_connection2
+  jorek2_connection_stan
+  jorek2_connection_flux_aligned
+  jorek2_diagno
+  jorek2_diagno_spi
+  jorek2_fieldlines_vtk
+  jorek2_four
+  CARIDDI_wall_curr
+  jorek2_poincare
+  jorek2_powers
+  jorek2_target2vtk
+  jorek2vtk_3d
+  jorek2vtk
+  jorek2vtk_GaussVortTerms
+  test_gvec2jorek_import
+  jorek_to_helena
+  new_diag_demo
+  jorek2_postproc
+  rst_bin2hdf5
+  rst_hdf52bin
+  jorek2_main)
+if(JOREK_USE_IMAS)
+  list(APPEND JOREK_MOST_TARGETS jorek2_IDS)
+endif()
+
+set(_most_existing "")
+foreach(_t IN LISTS JOREK_MOST_TARGETS)
+  if(TARGET ${_t})
+    list(APPEND _most_existing ${_t})
+  else()
+    message(WARNING "'most' target references unknown program '${_t}'")
+  endif()
+endforeach()
+add_custom_target(most DEPENDS ${_most_existing})
+
+include(JorekSummary)

CMakePresets.json

@@ -0,0 +1,174 @@
+{
+  "version": 3,
+  "cmakeMinimumRequired": {
+    "major": 3,
+    "minor": 20,
+    "patch": 0
+  },
+  "configurePresets": [
+    {
+      "name": "base",
+      "hidden": true,
+      "binaryDir": "${sourceDir}/build/${presetName}",
+      "cacheVariables": {
+        "CMAKE_BUILD_TYPE": "Release",
+        "JOREK_MODEL": "model600"
+      }
+    },
+    {
+      "name": "pitagora-intel",
+      "inherits": "base",
+      "displayName": "Pitagora CPU - Intel oneAPI + MKL + STRUMPACK",
+      "description": "Requires: module load intel-oneapi-mpi intel-oneapi-compilers intel-oneapi-mkl/2024.0.0--intel-oneapi-mpi--2021.12.1 hdf5/1.14.3--intel-oneapi-mpi--2021.12.1--oneapi--2024.1.0 cmake",
+      "cacheVariables": {
+        "CMAKE_Fortran_COMPILER": "mpiifx",
+        "CMAKE_C_COMPILER": "mpiicx",
+        "CMAKE_CXX_COMPILER": "mpiicpx",
+        "CMAKE_Fortran_FLAGS": "-mcmodel=medium -march=skylake-avx512 -axCORE-AVX512",
+        "CMAKE_C_FLAGS": "-mcmodel=medium -march=skylake-avx512 -axCORE-AVX512",
+        "CMAKE_CXX_FLAGS": "-mcmodel=medium -march=skylake-avx512 -axCORE-AVX512",
+        "JOREK_USE_MKL": "ON",
+        "JOREK_USE_STRUMPACK": "ON",
+        "JOREK_USE_MUMPS": "OFF",
+        "JOREK_USE_PASTIX": "OFF",
+        "JOREK_USE_HDF5": "ON",
+        "JOREK_USE_FFTW": "ON",
+        "JOREK_USE_BLOCK": "ON",
+        "JOREK_LIB_DIR": "/pitagora_work/FUPA1_MHD/JOREK_LIBRARIES/libraries_recompile_amd",
+        "STRUMPACK_ROOT": "/pitagora_work/FUPA1_MHD/JOREK_LIBRARIES/libraries_recompile_amd/STRUMPACK/install",
+        "METIS_ROOT": "/pitagora_work/FUPA1_MHD/JOREK_LIBRARIES/libraries_recompile_amd/METIS/install",
+        "PARMETIS_ROOT": "/pitagora_work/FUPA1_MHD/JOREK_LIBRARIES/libraries_recompile_amd/ParMETIS/install",
+        "GKLIB_ROOT": "/pitagora_work/FUPA1_MHD/JOREK_LIBRARIES/libraries_recompile_amd/GKlib/install"
+      }
+    },
+    {
+      "name": "pitagora-intel-debug",
+      "inherits": "pitagora-intel",
+      "displayName": "Pitagora CPU - Intel oneAPI, debug build",
+      "cacheVariables": {
+        "CMAKE_BUILD_TYPE": "Debug"
+      }
+    },
+    {
+      "name": "viper-intel",
+      "inherits": "base",
+      "displayName": "Viper CPU - Intel oneAPI + MKL + STRUMPACK (AMD Genoa/Zen4)",
+      "description": "Requires: module purge && module load intel/2025.3 impi/2021.17 mkl/2025.3 hdf5-mpi/2.0.0 fftw-mpi/3.3.10 cmake",
+      "cacheVariables": {
+        "CMAKE_Fortran_COMPILER": "mpiifx",
+        "CMAKE_C_COMPILER": "mpiicx",
+        "CMAKE_CXX_COMPILER": "mpiicpx",
+        "CMAKE_Fortran_FLAGS": "-mcmodel=medium -march=znver4",
+        "CMAKE_C_FLAGS": "-mcmodel=medium -march=znver4",
+        "CMAKE_CXX_FLAGS": "-mcmodel=medium -march=znver4",
+        "JOREK_USE_MKL": "ON",
+        "JOREK_USE_STRUMPACK": "ON",
+        "JOREK_USE_MUMPS": "OFF",
+        "JOREK_USE_PASTIX": "OFF",
+        "JOREK_USE_HDF5": "ON",
+        "JOREK_USE_FFTW": "ON",
+        "JOREK_USE_BLOCK": "ON",
+        "JOREK_LIB_DIR": "/u/edocarr/libs/intel_25_03/",
+        "STRUMPACK_ROOT": "/u/edocarr/libs/intel_25_03/STRUMPACK/install",
+        "METIS_ROOT": "/u/edocarr/libs/intel_25_03/METIS/install",
+        "PARMETIS_ROOT": "/u/edocarr/libs/intel_25_03/ParMETIS/install",
+        "GKLIB_ROOT": "/u/edocarr/libs/intel_25_03/GKlib/install"
+      }
+    },
+    {
+      "name": "viper-intel-debug",
+      "inherits": "viper-intel",
+      "displayName": "Viper CPU - Intel oneAPI, debug build",
+      "cacheVariables": {
+        "CMAKE_BUILD_TYPE": "Debug"
+      }
+    },
+    {
+      "name": "tok-intel",
+      "inherits": "base",
+      "displayName": "TOK CPU - Intel oneAPI + MKL + STRUMPACK (IPP Garching)",
+      "description": "Requires: module purge && module load intel/2025.1 impi/2021.15 mkl fftw-mpi hdf5-mpi cmake",
+      "cacheVariables": {
+        "CMAKE_Fortran_COMPILER": "mpiifx",
+        "CMAKE_C_COMPILER": "mpiicx",
+        "CMAKE_CXX_COMPILER": "mpiicpx",
+        "CMAKE_Fortran_FLAGS": "-mcmodel=medium -march=native",
+        "CMAKE_C_FLAGS": "-mcmodel=medium -march=native",
+        "CMAKE_CXX_FLAGS": "-mcmodel=medium -march=native",
+        "JOREK_USE_MKL": "ON",
+        "JOREK_USE_STRUMPACK": "ON",
+        "JOREK_USE_MUMPS": "OFF",
+        "JOREK_USE_PASTIX": "OFF",
+        "JOREK_USE_HDF5": "ON",
+        "JOREK_USE_FFTW": "ON",
+        "JOREK_USE_BLOCK": "ON",
+        "JOREK_LIB_DIR": "/tokp/work/mhoelzl/bin-of-ihol/intel",
+        "STRUMPACK_ROOT": "/tokp/work/mhoelzl/bin-of-ihol/intel/STRUMPACK-7.1.3/install",
+        "METIS_ROOT": "/tokp/work/mhoelzl/bin-of-ihol/intel/metis_git/install",
+        "PARMETIS_ROOT": "/tokp/work/mhoelzl/bin-of-ihol/intel/ParMETIS_git/install",
+        "GKLIB_ROOT": "/tokp/work/mhoelzl/bin-of-ihol/intel/GKlib_git/install"
+      }
+    },
+    {
+      "name": "tok-intel-debug",
+      "inherits": "tok-intel",
+      "displayName": "TOK CPU - Intel oneAPI, debug build",
+      "cacheVariables": {
+        "CMAKE_BUILD_TYPE": "Debug"
+      }
+    }
+  ],
+  "buildPresets": [
+    {
+      "name": "pitagora-intel",
+      "configurePreset": "pitagora-intel",
+      "jobs": 16
+    },
+    {
+      "name": "pitagora-intel-most",
+      "configurePreset": "pitagora-intel",
+      "displayName": "Main solver plus the regression-tested diagnostics",
+      "targets": ["most"],
+      "jobs": 16
+    },
+    {
+      "name": "pitagora-intel-debug",
+      "configurePreset": "pitagora-intel-debug",
+      "jobs": 16
+    },
+    {
+      "name": "viper-intel",
+      "configurePreset": "viper-intel",
+      "jobs": 16
+    },
+    {
+      "name": "viper-intel-most",
+      "configurePreset": "viper-intel",
+      "displayName": "Main solver plus the regression-tested diagnostics",
+      "targets": ["most"],
+      "jobs": 16
+    },
+    {
+      "name": "viper-intel-debug",
+      "configurePreset": "viper-intel-debug",
+      "jobs": 16
+    },
+    {
+      "name": "tok-intel",
+      "configurePreset": "tok-intel",
+      "jobs": 16
+    },
+    {
+      "name": "tok-intel-most",
+      "configurePreset": "tok-intel",
+      "displayName": "Main solver plus the regression-tested diagnostics",
+      "targets": ["most"],
+      "jobs": 16
+    },
+    {
+      "name": "tok-intel-debug",
+      "configurePreset": "tok-intel-debug",
+      "jobs": 16
+    }
+  ]
+}

README.txt

@@ -6,6 +6,40 @@
 
 For a documentation about the code, see jorek.eu/wiki
 
+
+=======================================================
+ Building with CMake (recommended)
+=======================================================
+
+Each supported machine is a CMake preset in CMakePresets.json. To list them:
+
+  cmake --list-presets
+
+Pick the preset for your machine (e.g. viper-intel, pitagora-intel; add
+-debug for a debug build). Each preset's "description" field states the exact
+`module load` line to run first.
+
+  # 1. load the modules listed in the preset's description
+  # 2. configure once
+  cmake --preset <preset>
+
+  # 3. build (build tree is build/<preset>/)
+  cmake --build build/<preset> -j 16                        # default: main solver
+  cmake --build build/<preset> --target jorek2_diagno -j 16 # a specific program
+  cmake --build build/<preset> --target help                # list all targets
+
+Every .f90 file with a `program` statement becomes a target named after the
+file; the built executables land in build/<preset>/. Set the model and options
+per preset in CMakePresets.json (JOREK_MODEL, JOREK_USE_*), not in Makefile.inc.
+
+
+=======================================================
+ Building with Makefile.inc (DEPRECATED)
+=======================================================
+
+NOTE: the Makefile.inc / `make` build below is deprecated. Prefer the CMake
+build above. The instructions are kept for reference only.
+
 to build jorek2:
 
 - edit the Makefile.inc file to match your environment