v2.3.0 (#376)

### Changed

- fixed a bug that could lead to diverging results around the spherical axis in non-ideal MHD in 2.5D and 3D (#356)
- refactor of the MPI exchange routines and boundary routines to avoid buildup of roundoff errors at domain faces/edges that could lead to the sudden burst of div(B) or incoherences between MPI sub-domains (#357)
- fixed a bug that could lead to compilations error when targetting AMD APUs (#359)
- fixed a bug that led to the generation of incorrect subviews in 2.5D with vector_potential enabled (#362)
- fixed a bug that could lead to memory corruption when using the UCT_HLLD emf reconstruction scheme and DIMENSIONS < COMPONENTS  (#363)
- reorganise the test to separate specific IO tests from physics tests (#367)

### Added
- magnetic vector potential is now accessible from pydefix when enabled (#361)
- use ccache in the test suite to reduce the runtime of continuous integration (#364)
- automatically detects pybind11 path with cmake when using pydefix (#367)
- skeleton to run the test suite with pytest (#366)
---------------------------------------------------------------------------
Co-authored-by: Clément Robert <cr52@protonmail.com>
Co-authored-by: Sébastien Valat <sebastien.valat.dev@orange.fr>

Author: 3 people

.github/workflows/idefix-ci-jobs.yml

@@ -38,6 +38,8 @@ jobs:
         run: scripts/ci/run-tests $IDEFIX_DIR/test/HD/sod-iso -all $TESTME_OPTIONS
       - name: Mach reflection test
         run: scripts/ci/run-tests $IDEFIX_DIR/test/HD//MachReflection -all $TESTME_OPTIONS
+      - name: Sedov blast wave
+        run: scripts/ci/run-tests $IDEFIX_DIR/test/HD/SedovBlastWave -all $TESTME_OPTIONS
 
   ParabolicHydro:
     runs-on: self-hosted
@@ -68,8 +70,10 @@ jobs:
         run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/sod-iso -all $TESTME_OPTIONS
       - name: Orszag Tang
         run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/OrszagTang -all $TESTME_OPTIONS
-      - name: Orszag Tang 3D+restart tests
+      - name: Orszag Tang 3D
         run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/OrszagTang3D -all $TESTME_OPTIONS
+      - name: Linear wave test
+        run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/LinearWaveTest -all $TESTME_OPTIONS
       - name: Axis Flux tube
         run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/AxisFluxTube -all $TESTME_OPTIONS
 
@@ -221,3 +225,24 @@ jobs:
         run: scripts/ci/run-tests $IDEFIX_DIR/test/utils/dumpImage -all $TESTME_OPTIONS
       - name: Column density
         run: scripts/ci/run-tests $IDEFIX_DIR/test/utils/columnDensity -all $TESTME_OPTIONS
+
+  IOs:
+    needs: [Fargo, Dust, Planet, ShearingBox, SelfGravity]
+    runs-on: self-hosted
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
+        with:
+          submodules: recursive
+          persist-credentials: false
+      - name: Restart dumps
+        run: scripts/ci/run-tests $IDEFIX_DIR/test/IO/dump -all $TESTME_OPTIONS
+      - name: Pydefix
+        run: |
+          python3 -m venv $IDEFIX_DIR/test/IO/pydefix/env
+          source $IDEFIX_DIR/test/IO/pydefix/env/bin/activate
+          python3 -m pip install -r $IDEFIX_DIR/test/IO/pydefix/python_requirements.txt
+          scripts/ci/run-tests $IDEFIX_DIR/test/IO/pydefix -all $TESTME_OPTIONS
+
+      - name: xdmf
+        run: scripts/ci/run-tests $IDEFIX_DIR/test/IO/xdmf -all $TESTME_OPTIONS

.github/workflows/idefix-ci.yml

@@ -32,15 +32,15 @@ jobs:
     name: CPU Jobs (intel OneApi)
     uses: ./.github/workflows/idefix-ci-jobs.yml
     with:
-      TESTME_OPTIONS: -intel -Werror
+      TESTME_OPTIONS: -intel -Werror -ccache
       IDEFIX_COMPILER: icc
 
   gcc-jobs:
     needs: Linter
     name: CPU Jobs (gcc)
     uses: ./.github/workflows/idefix-ci-jobs.yml
     with:
-      TESTME_OPTIONS: -Werror
+      TESTME_OPTIONS: -Werror -ccache
       IDEFIX_COMPILER: gcc
 
   cuda-jobs:

.gitignore

@@ -22,6 +22,9 @@ CMakeFiles
 CMakeCache.txt
 cmake_install.cmake
 Makefile.local
+git-state.txt
+Kokkos_Version_info.*
+
 
 # test artifacts
 test/**/*.o
@@ -36,6 +39,9 @@ test/**/KokkosCore*
 test/**/*.csv
 test/**/*.pyc
 test/**/*.dat
+test/**/cmake_packages*
+test/**/
+idefix-tests.junit.xml
 
 # machine specific cache and hidden files
 .*

.pre-commit-config.yaml

@@ -45,9 +45,10 @@ repos:
         - F403 # ignore import *
 
   - repo: https://github.com/neutrinoceros/inifix
-    rev: v5.0.2
+    rev: v6.1.2
     hooks:
       - id: inifix-format
+        files: ^(test/).*\.(ini)$ # want to skip pytest.ini
 
   - repo: https://github.com/Lucas-C/pre-commit-hooks
     rev: v1.5.5

CHANGELOG.md

@@ -4,6 +4,23 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [2.3.0] 2026-04-21
+### Changed
+
+- fixed a bug that could lead to diverging results around the spherical axis in non-ideal MHD in 2.5D and 3D (#356)
+- refactor of the MPI exchange routines and boundary routines to avoid buildup of roundoff errors at domain faces/edges that could lead to the sudden burst of div(B) or incoherences between MPI sub-domains (#357)
+- fixed a bug that could lead to compilations error when targetting AMD APUs (#359)
+- fixed a bug that led to the generation of incorrect subviews in 2.5D with vector_potential enabled (#362)
+- fixed a bug that could lead to memory corruption when using the UCT_HLLD emf reconstruction scheme and DIMENSIONS < COMPONENTS  (#363)
+- reorganise the test to separate specific IO tests from physics tests (#367)
+
+### Added
+- magnetic vector potential is now accessible from pydefix when enabled (#361)
+- use ccache in the test suite to reduce the runtime of continuous integration (#364)
+- automatically detects pybind11 path with cmake when using pydefix (#367)
+- skeleton to run the test suite with pytest (#366)
+
+
 ## [2.2.02] 2025-10-18
 ### Changed
 
@@ -13,6 +30,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - fixed a bug that led to incorrect BX2 reconstruction when axis is not used on both sides of the domain (#345)
 - fixed a bug that led to incorrect reflective boundary conditions on B when DIMENSIONS < 3 (#345)
 - fixed a bug that led to incorrect dust stopping time when the adiabatic equation of state is used with "size" drag law (#353)
+- fixed div(B) normalisation to avoid "too large div(B)" errors when this is actually due to nulls in |B|
+- fixed insecure github actions settings (#373)
 
 ### Added
 

CMakeLists.txt

@@ -5,17 +5,18 @@ endif()
 set (CMAKE_CXX_STANDARD 17)
 
 set(Idefix_VERSION_MAJOR 2)
-set(Idefix_VERSION_MINOR 2)
-set(Idefix_VERSION_PATCH 02)
+set(Idefix_VERSION_MINOR 3)
+set(Idefix_VERSION_PATCH 0)
 
-project (idefix VERSION 2.2.02)
+project (idefix VERSION 2.3.0)
 option(Idefix_MHD "enable MHD" OFF)
 option(Idefix_MPI "enable Message Passing Interface parallelisation" OFF)
 option(Idefix_HIGH_ORDER_FARGO "Force Fargo to use a PPM reconstruction scheme" OFF)
 option(Idefix_DEBUG "Enable Idefix debug features (makes the code very slow)" OFF)
 option(Idefix_RUNTIME_CHECKS "Enable runtime sanity checks" OFF)
 option(Idefix_WERROR "Treat compiler warnings as errors" OFF)
 option(Idefix_PYTHON "Enable python bindings (requires pybind11)" OFF)
+set(Idefix_PROBLEM_DIR "${CMAKE_BINARY_DIR}" CACHE STRING "Problem directory to build for.")
 set(Idefix_CXX_FLAGS "" CACHE STRING "Additional compiler/linker flag")
 set(Idefix_DEFS "definitions.hpp" CACHE FILEPATH "Problem definition header file")
 option(Idefix_CUSTOM_EOS "Use custom equation of state" OFF)
@@ -34,7 +35,6 @@ set_property(CACHE Idefix_PRECISION PROPERTY STRINGS Double Single)
 set(Idefix_LOOP_PATTERN "Default" CACHE STRING "Loop pattern for idefix_for")
 set_property(CACHE Idefix_LOOP_PATTERN PROPERTY STRINGS Default SIMD Range MDRange TeamPolicy TeamPolicyInnerVector)
 
-
 # load git revision tools
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake/")
 include(GetGitRevisionDescription)
@@ -51,7 +51,7 @@ if(Kokkos_ENABLE_CUDA)
 endif()
 
 # Add kokkos CMAKE files (required early since these set compiler options)
-add_subdirectory(src/kokkos build/kokkos)
+add_subdirectory(src/kokkos ${CMAKE_BINARY_DIR}/build/kokkos)
 include_directories(${Kokkos_INCLUDE_DIRS_RET})
 
 # Add Idefix CXX Flags
@@ -75,20 +75,22 @@ endif()
 add_executable(idefix)
 add_subdirectory(src build)
 
-if(EXISTS ${PROJECT_BINARY_DIR}/setup.cpp)
-  target_sources(idefix PUBLIC ${PROJECT_BINARY_DIR}/setup.cpp)
+# make absolute
+get_filename_component(Idefix_PROBLEM_DIR_ABS ${Idefix_PROBLEM_DIR} ABSOLUTE BASE_DIR ${PROJECT_BINARY_DIR})
+
+if(EXISTS ${Idefix_PROBLEM_DIR_ABS}/setup.cpp)
+  target_sources(idefix PUBLIC ${Idefix_PROBLEM_DIR_ABS}/setup.cpp)
 else()
   message(WARNING "No specific setup.cpp found in the problem directory (this message can be ignored if using python to define your problem)")
 endif()
 
 # If a CMakeLists.txt is in the problem dir (for problem-specific source files)
 # then read it
-if(EXISTS ${PROJECT_BINARY_DIR}/CMakeLists.txt)
-  message(STATUS "Including problem-specific CMakeLists in '${PROJECT_BINARY_DIR}'")
-  add_subdirectory(${PROJECT_BINARY_DIR} build/setup)
+if(EXISTS ${Idefix_PROBLEM_DIR_ABS}/CMakeLists.txt)
+  message(STATUS "Including problem-specific CMakeLists in '${Idefix_PROBLEM_DIR_ABS}'")
+  add_subdirectory(${Idefix_PROBLEM_DIR_ABS} build/setup)
 endif()
 
-
 if(Idefix_MHD)
   add_compile_definitions("MHD=YES")
 else()
@@ -99,10 +101,7 @@ if(Idefix_MPI)
   add_compile_definitions("WITH_MPI")
   find_package(MPI REQUIRED)
   target_link_libraries(idefix MPI::MPI_CXX)
-  target_sources(idefix
-    PUBLIC src/mpi.cpp
-    PUBLIC src/mpi.hpp
-  )
+  add_subdirectory(src/mpi)
 endif()
 
 if(Idefix_HDF5)
@@ -116,14 +115,30 @@ if(Idefix_HDF5)
   )
   find_package(HDF5 REQUIRED)
   target_link_libraries(idefix "${HDF5_LIBRARIES}")
-  target_include_directories(idefix "${HDF5_INCLUDE_DIRS}")
+  message(STATUS "Found HDF5 include directories: ${HDF5_INCLUDE_DIRS}")
+  target_include_directories(idefix PUBLIC "${HDF5_INCLUDE_DIRS}")
+  if(Idefix_MPI)
+    if(NOT HDF5_IS_PARALLEL)
+      message(FATAL_ERROR "Parallel HDF5 required for Idefix_MPI but the found HDF5 library does not support it")
+    endif()
+  endif()
   message(STATUS "XDMF (hdf5+xmf) dumps enabled")
 else()
   set(Idefix_HDF5 OFF)
 endif()
 
 if(Idefix_PYTHON)
   add_compile_definitions("WITH_PYTHON")
+  find_package(Python3 REQUIRED COMPONENTS Interpreter Development)
+
+  execute_process(
+    COMMAND "${Python3_EXECUTABLE}" -m pybind11 --cmakedir
+    OUTPUT_VARIABLE PYBIND11_CMAKE_DIR
+    OUTPUT_STRIP_TRAILING_WHITESPACE
+    COMMAND_ERROR_IS_FATAL ANY
+  )
+
+  list(APPEND CMAKE_PREFIX_PATH "${PYBIND11_CMAKE_DIR}")
   if (NOT DEFINED Python_FIND_FRAMEWORK)
     set(Python_FIND_FRAMEWORK "LAST") # Use Apple's python only at last resort on Macos
   endif ()
@@ -213,7 +228,7 @@ if(${Idefix_PRECISION} STREQUAL "Single")
 endif()
 
 target_include_directories(idefix PUBLIC
-                           "${PROJECT_BINARY_DIR}"
+                           "${Idefix_PROBLEM_DIR_ABS}"
                            )
 target_include_directories(idefix PUBLIC
                            src/kokkos/core/src
@@ -234,6 +249,7 @@ target_include_directories(idefix PUBLIC
                            src/gravity
                            src/utils
                            src/utils/iterativesolver
+                           src/mpi
                            src
                            )
 
@@ -251,6 +267,7 @@ message(STATUS "    Python: ${Idefix_PYTHON}")
 message(STATUS "    Reconstruction: ${Idefix_RECONSTRUCTION}")
 message(STATUS "    Precision: ${Idefix_PRECISION}")
 message(STATUS "    Version: ${Idefix_VERSION}")
+message(STATUS "    Problem directory: '${Idefix_PROBLEM_DIR}'")
 message(STATUS "    Problem definitions: '${Idefix_DEFS}'")
 if(Idefix_CUSTOM_EOS)
   message(STATUS "    EOS: Custom file '${Idefix_CUSTOM_EOS_FILE}'")

doc/python_requirements.txt

@@ -6,12 +6,12 @@
 # python -m pip install -r python_requirements.txt
 
 wheel>=0.38.4 # help forward compatibility for pip with old sphinx plugins
-sphinx==5.3.0
-sphinx_rtd_theme==1.3.0
+sphinx==9.1.0
+sphinx_rtd_theme==3.1.0
 sphinx_git==11.0.0
-breathe==4.34.0
+breathe==4.36.0
 exhale==0.3.7
-m2r2==0.3.2
+m2r2==0.3.4
 sphinx-copybutton==0.5.2
 #sphinxcontrib-applehelp==1.0.7
 matplotlib==3.10.0

doc/source/conf.py

@@ -23,7 +23,7 @@
 author = 'Geoffroy Lesur'
 
 # The full version, including alpha/beta/rc tags
-release = '2.2.02'
+release = '2.3.0'
 
 
 

doc/source/modules/pydefix.rst

@@ -23,7 +23,8 @@ Pydefix usage
 Idefix Configuration
 ++++++++++++++++++++
 
-In order to use Pydefix, you need to switch on ``Idefix_PYTHON`` in cmake. This will auto-detect Python and check that pybind11 can be used effectively.
+In order to use Pydefix, you need to switch on ``Idefix_PYTHON`` in cmake. This will auto-detect Python and check that pybind11 can be used effectively. If you are using a python environement manager such as venv or conda, make sure to activate the right environement *before* running cmake, as idefix
+now includes the full path to python and pybind11 in its executable file.
 
 
 Run Idefix with Pydefix

doc/source/reference/makefile.rst

@@ -59,6 +59,12 @@ Several options can be enabled from the command line (or are accessible with ``c
     The number of ghost cells is automatically adjusted as a function of the order of the reconstruction scheme.
     *Idefix* uses 2 ghost cells when ``ORDER < 4`` and 3 ghost cells when ``ORDER = 4``
 
+``-D Idefix_PROBLEM_DIR=.``
+    Specify where to find the problem directory to build *Idefix* out of source.
+    Place yourself in the ``build`` directory you want to build in and call the ``cmake`` by :
+      + pointing the *Idefix* source directory via ``IDEFIX_DIR`` as usual.
+      + using ``-D Idefix_PROBLEM_DIR`` to point the problem to build.
+
 ``-D Kokkos_ENABLE_OPENMP=ON``
     Enable OpenMP parallelisation on supported compilers. Note that this can be enabled simultaneously with MPI, resulting in a hybrid MPI+OpenMP compilation.