Merge branch 'next' into hermes3-temp

.ci_fedora.sh

@@ -50,7 +50,7 @@ then
     cp -a /tmp/BOUT-dev /home/test/
     chown -R test /home/test
     chmod u+rwX /home/test -R
-    sudo -u test ${0/\/tmp/\/home\/test} $mpi
+    su - test -c "${0/\/tmp/\/home\/test} $mpi"
 ## If we are called as normal user, run test
 else
     . /etc/profile.d/modules.sh

.clang-format

@@ -109,6 +109,8 @@ SpacesInParentheses: false
 SpacesInSquareBrackets: false
 StatementMacros:
   - BOUT_OMP
+  - BOUT_OMP_PERF
+  - BOUT_OMP_SAFE
 Standard:        c++14
 TabWidth:        8
 UseTab:          Never

.clang-tidy

@@ -2,15 +2,14 @@
 Checks:          'clang-diagnostic-*,clang-analyzer-*,performance-*,readability-*,bugprone-*,clang-analyzer-*,cppcoreguidelines-*,mpi-*,misc-*,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers,-misc-non-private-member-variables-in-classes,-clang-analyzer-optin.mpi*,-bugprone-exception-escape,-cppcoreguidelines-pro-bounds-pointer-arithmetic,-readability-function-cognitive-complexity,-misc-no-recursion,-bugprone-easily-swappable-parameters'
 WarningsAsErrors: ''
 HeaderFilterRegex: ''
-AnalyzeTemporaryDtors: false
 FormatStyle:     file
 CheckOptions:
 
   # Allow some common short names
   - key:             readability-identifier-length.IgnoredVariableNames
     value:           '^[dn]?[xyz]$'
   - key:             readability-identifier-length.IgnoredParameterNames
-    value:           '^[fijkxyz][01xyz]?$'
+    value:           '^[dfijknxyz][01xyz]?$'
   - key:             readability-identifier-length.IgnoredLoopCounterNames
     value:           '^[ijkxyz_]$'
 

.github/workflows/tests.yml

@@ -39,7 +39,7 @@ jobs:
         is_cron:
           - ${{ github.event_name == 'cron' }}
         config:
-          - name: "CMake, PETSc unreleased, ADIOS"
+          - name: "CMake, PETSc unreleased, ADIOS2"
             os: ubuntu-20.04
             cmake_options: "-DBUILD_SHARED_LIBS=ON
                             -DBOUT_ENABLE_METRIC_3D=ON

.gitignore

@@ -85,3 +85,5 @@ coverage/
 /_version.txt
 /BOUT++-v*.tar.gz
 /BOUT++-v*.tar.xz
+/CMakeCache.txt
+/CMakeFiles/cmake.check_cache

CMakeLists.txt

@@ -366,7 +366,7 @@ else()
   set(BOUT_GENERATE_FIELDOPS_DEFAULT OFF)
 endif()
 
-execute_process(COMMAND ${Python3_EXECUTABLE} -c "import zoidberg"
+execute_process(COMMAND ${Python3_EXECUTABLE} -c "import importlib.util ; import sys; sys.exit(importlib.util.find_spec(\"zoidberg\") is None)"
   RESULT_VARIABLE zoidberg_FOUND)
 if (zoidberg_FOUND EQUAL 0)
   set(zoidberg_FOUND ON)
@@ -774,7 +774,7 @@ set(BOUT_HAS_PNETCDF OFF)
 # while for static builds we need the dependencies too
 if (BUILD_SHARED_LIBS)
   # Include rpath linker flag so user doesn't need to set LD_LIBRARY_PATH
-  set(CONFIG_LDFLAGS "${CMAKE_SHARED_LIBRARY_RUNTIME_CXX_FLAG}\$BOUT_LIB_PATH -L\$BOUT_LIB_PATH -lbout++ -lfmt")
+  set(CONFIG_LDFLAGS "${CMAKE_SHARED_LIBRARY_RUNTIME_CXX_FLAG}\$BOUT_LIB_PATH -L\$BOUT_LIB_PATH -lbout++ -lfmt ${CONFIG_LDFLAGS_SHARED}")
 else()
   set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS}")
 endif()
@@ -935,7 +935,7 @@ message("
    SUNDIALS support         : ${BOUT_HAS_SUNDIALS}
    HYPRE support            : ${BOUT_HAS_HYPRE}
    NetCDF support           : ${BOUT_HAS_NETCDF}
-   ADIOS support            : ${BOUT_HAS_ADIOS}
+   ADIOS2 support           : ${BOUT_HAS_ADIOS2}
    FFTW support             : ${BOUT_HAS_FFTW}
    LAPACK support           : ${BOUT_HAS_LAPACK}
    OpenMP support           : ${BOUT_USE_OPENMP}

bin/bout-build-deps.sh

@@ -98,7 +98,7 @@ netcdf() {
 
 nccxx() {
     cd $BUILD
-    wget -c ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-cxx4-$NCCXXVER.tar.gz || :
+    wget -c https://downloads.unidata.ucar.edu/netcdf-cxx/$NCCXXVER/netcdf-cxx4-$NCCXXVER.tar.gz || :
     tar -xf netcdf-cxx4-$NCCXXVER.tar.gz
     cd netcdf-cxx4-$NCCXXVER
     CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib/" ./configure --prefix=$PREFIX $NCCXXFLAGS
@@ -286,17 +286,17 @@ set -x
 ## Setup folders and links
 setup
 ## Build and install hdf5
-hdf5
+test $NO_HDF5 || hdf5
 ## Build and install netcdf
-netcdf
+test $NO_NETCDF || netcdf
 ## Build and install C++ interface for netcdf
-nccxx
+test $NO_NCXX || nccxx
 ## Build and install FFTW
-fftw
+test $NO_FFTW || fftw
 ## Build and install Sundials
-sundials
+test $NO_SUNDIALS || sundials
 ## Build and install PETSc
-petsc
+test $NO_PETSC || petsc
 ## Download BOUT++ submodules
 submod
 # Install python packages

bin/bout-config.in

@@ -29,7 +29,7 @@ idlpath="@IDLCONFIGPATH@"
 pythonpath="@PYTHONCONFIGPATH@"
 
 has_netcdf="@BOUT_HAS_NETCDF@"
-has_adios="@BOUT_HAS_ADIOS@"
+has_adios2="@BOUT_HAS_ADIOS2@"
 has_legacy_netcdf="@BOUT_HAS_LEGACY_NETCDF@"
 has_pnetcdf="@BOUT_HAS_PNETCDF@"
 has_pvode="@BOUT_HAS_PVODE@"
@@ -71,18 +71,18 @@ Available values for OPTION include:
   --idl          IDL path
   --python       Python path
 
-  --has-netcdf  NetCDF file support
-  --has-adios   ADIOS file support
+  --has-netcdf   NetCDF file support
+  --has-adios2   ADIOS2 file support
   --has-legacy-netcdf  Legacy NetCDF file support
-  --has-pnetcdf Parallel NetCDF file support
-  --has-pvode   PVODE solver support
-  --has-cvode   SUNDIALS CVODE solver support
-  --has-ida     SUNDIALS IDA solver support
-  --has-lapack  LAPACK support
-  --has-petsc   PETSc support
-  --has-hypre   Hypre support
-  --has-slepc   SLEPc support
-  --has-nls     Natural Language Support
+  --has-pnetcdf  Parallel NetCDF file support
+  --has-pvode    PVODE solver support
+  --has-cvode    SUNDIALS CVODE solver support
+  --has-ida      SUNDIALS IDA solver support
+  --has-lapack   LAPACK support
+  --has-petsc    PETSc support
+  --has-hypre    Hypre support
+  --has-slepc    SLEPc support
+  --has-nls      Natural Language Support
 
   --petsc-has-sundials 
 
@@ -123,6 +123,7 @@ all()
         echo "  --has-slepc   -> $has_slepc"
         echo "  --has-arkode  -> $has_arkode"
         echo "  --has-nls     -> $has_nls"
+        echo "  --has-openmp  -> $has_openmp"
         echo
         echo "  --petsc-has-sundials -> $petsc_has_sundials"
         echo

bout++Config.cmake.in

@@ -15,7 +15,7 @@ set(BOUT_USE_METRIC_3D @BOUT_USE_METRIC_3D@)
 
 set(BOUT_HAS_PVODE @BOUT_HAS_PVODE@)
 set(BOUT_HAS_NETCDF @BOUT_HAS_NETCDF@)
-set(BOUT_HAS_ADIOS @BOUT_HAS_ADIOS@)
+set(BOUT_HAS_ADIOS2 @BOUT_HAS_ADIOS2@)
 set(BOUT_HAS_FFTW @BOUT_HAS_FFTW@)
 set(BOUT_HAS_LAPACK @BOUT_HAS_LAPACK@)
 set(BOUT_HAS_PETSC @BOUT_HAS_PETSC@)

cmake/FindCython.cmake

@@ -10,7 +10,7 @@
 #   CYTHON_FOUND - true if Cython was found
 #   CYTHON_VERSION - Cython version
 
-execute_process(COMMAND ${Python_EXECUTABLE} -c "import cython ; print(cython.__version__)"
+execute_process(COMMAND ${Python3_EXECUTABLE} -c "import cython ; print(cython.__version__)"
   RESULT_VARIABLE _cython_runs
   OUTPUT_VARIABLE CYTHON_VERSION
   OUTPUT_STRIP_TRAILING_WHITESPACE

cmake/FindNumpy.cmake

@@ -12,32 +12,32 @@
 #   Numpy_INCLUDE_DIR
 
 
-find_package(Python 3.6 COMPONENTS Interpreter Development)
+find_package(Python3 3.6 COMPONENTS Interpreter Development)
 
-if (NOT Python_FOUND)
+if (NOT Python3_FOUND)
   message(STATUS "Could not find numpy as python was not found. Maybe the developement package is missing?")
-  set(Numpy_FOUND ${Python_FOUND})
+  set(Numpy_FOUND ${Python3_FOUND})
   return()
 endif()
 
 if (NOT Numpy_FOUND)
-  execute_process(COMMAND ${Python_EXECUTABLE} -c "import numpy ; print(numpy.__version__)"
+  execute_process(COMMAND ${Python3_EXECUTABLE} -c "import numpy ; print(numpy.__version__)"
     OUTPUT_STRIP_TRAILING_WHITESPACE
     OUTPUT_VARIABLE Numpy_VERSION
     )
-  execute_process(COMMAND ${Python_EXECUTABLE} -c "import numpy ; print(numpy.get_include())"
+  execute_process(COMMAND ${Python3_EXECUTABLE} -c "import numpy ; print(numpy.get_include())"
     OUTPUT_STRIP_TRAILING_WHITESPACE
     OUTPUT_VARIABLE _numpy_include_dirs
     )
 endif()
 
 if (Numpy_DEBUG)
-  message(STATUS "Looking for numpy headers in: ${_numpy_include_dirs} ${PYTHON_INCLUDE_DIR}")
+  message(STATUS "Looking for numpy headers in: ${_numpy_include_dirs} ${Python3_INCLUDE_DIRS}")
 endif()
 
 find_path(Numpy_INCLUDE_DIR
   numpy/arrayobject.h
-  PATHS "${_numpy_include_dirs}" "${PYTHON_INCLUDE_DIR}"
+  PATHS "${_numpy_include_dirs}" "${Python3_INCLUDE_DIRS}"
   PATH_SUFFIXES numpy/core/include
   )
 

cmake/FindSUNDIALS.cmake

@@ -104,16 +104,8 @@ endforeach()
 
 if (SUNDIALS_INCLUDE_DIR)
   file(READ "${SUNDIALS_INCLUDE_DIR}/sundials_config.h" SUNDIALS_CONFIG_FILE)
-  string(FIND "${SUNDIALS_CONFIG_FILE}" "SUNDIALS_PACKAGE_VERSION" index)
-  if("${index}" LESS 0)
-    # Version >3
-    set(SUNDIALS_VERSION_REGEX_PATTERN
-      ".*#define SUNDIALS_VERSION \"([0-9]+)\\.([0-9]+)\\.([0-9]+)\".*")
-  else()
-    # Version <3
-    set(SUNDIALS_VERSION_REGEX_PATTERN
-      ".*#define SUNDIALS_PACKAGE_VERSION \"([0-9]+)\\.([0-9]+)\\.([0-9]+)\".*")
-  endif()
+  set(SUNDIALS_VERSION_REGEX_PATTERN
+    ".*#define SUNDIALS_VERSION \"([0-9]+)\\.([0-9]+)\\.([0-9]+)\".*")
   string(REGEX MATCH ${SUNDIALS_VERSION_REGEX_PATTERN} _ "${SUNDIALS_CONFIG_FILE}")
   set(SUNDIALS_VERSION_MAJOR ${CMAKE_MATCH_1} CACHE STRING "")
   set(SUNDIALS_VERSION_MINOR ${CMAKE_MATCH_2} CACHE STRING "")

cmake/SetupBOUTThirdParty.cmake

@@ -8,6 +8,9 @@ endif ()
 # determined in SetupCompilers.cmake
 if (BOUT_USE_OPENMP)
   target_link_libraries(bout++ PUBLIC OpenMP::OpenMP_CXX)
+  set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} -fopenmp")
+  set(CONFIG_LDFLAGS_SHARED "${CONFIG_LDFLAGS_SHARED} -fopenmp")
+  set(CONFIG_CFLAGS "${CONFIG_CFLAGS} -fopenmp")
 endif()
 
 # determined in SetupCompilers.cmake
@@ -187,10 +190,10 @@ endif()
 message(STATUS "NetCDF support: ${BOUT_USE_NETCDF}")
 set(BOUT_HAS_NETCDF ${BOUT_USE_NETCDF})
 
-option(BOUT_USE_ADIOS "Enable support for ADIOS output" ON)
-option(BOUT_DOWNLOAD_ADIOS "Download and build ADIOS2" OFF)
-if (BOUT_USE_ADIOS)
-  if (BOUT_DOWNLOAD_ADIOS)
+option(BOUT_USE_ADIOS2 "Enable support for ADIOS output" ON)
+option(BOUT_DOWNLOAD_ADIOS2 "Download and build ADIOS2" OFF)
+if (BOUT_USE_ADIOS2)
+  if (BOUT_DOWNLOAD_ADIOS2)
     message(STATUS "Downloading and configuring ADIOS2")
     include(FetchContent)
     FetchContent_Declare(
@@ -217,12 +220,12 @@ if (BOUT_USE_ADIOS)
       find_package(MPI REQUIRED COMPONENTS C)
       target_link_libraries(bout++ PUBLIC adios2::cxx11_mpi MPI::MPI_C)
     else()
-      set(BOUT_USE_ADIOS OFF)
+      set(BOUT_USE_ADIOS2 OFF)
     endif()
   endif()
 endif()
-message(STATUS "ADIOS support: ${BOUT_USE_ADIOS}")
-set(BOUT_HAS_ADIOS ${BOUT_USE_ADIOS})
+message(STATUS "ADIOS2 support: ${BOUT_USE_ADIOS2}")
+set(BOUT_HAS_ADIOS2 ${BOUT_USE_ADIOS2})
 
 
 option(BOUT_USE_FFTW "Enable support for FFTW" ON)
@@ -278,8 +281,8 @@ if (BOUT_USE_SUNDIALS)
     include(FetchContent)
     FetchContent_Declare(
       sundials
-      GIT_REPOSITORY https://github.com/ZedThree/sundials
-      GIT_TAG        cmake-export-fixes
+      GIT_REPOSITORY https://github.com/LLNL/sundials
+      GIT_TAG        v7.0.0
       )
     # Note: These are settings for building SUNDIALS
     set(EXAMPLES_ENABLE_C OFF CACHE BOOL "" FORCE)
@@ -294,7 +297,11 @@ if (BOUT_USE_SUNDIALS)
     FetchContent_MakeAvailable(sundials)
     message(STATUS "SUNDIALS done configuring")
   else()
+    enable_language(C)
     find_package(SUNDIALS REQUIRED)
+    if (SUNDIALS_VERSION VERSION_LESS 4.0.0)
+      message(FATAL_ERROR "SUNDIALS_VERSION 4.0.0 or newer is required. Found version ${SUNDIALS_VERSION}.")
+    endif()
   endif()
   target_link_libraries(bout++ PUBLIC SUNDIALS::nvecparallel)
   target_link_libraries(bout++ PUBLIC SUNDIALS::cvode)

cmake_build_defines.hxx.in

@@ -13,7 +13,7 @@
 #cmakedefine01 BOUT_HAS_IDA
 #cmakedefine01 BOUT_HAS_LAPACK
 #cmakedefine01 BOUT_HAS_NETCDF
-#cmakedefine01 BOUT_HAS_ADIOS
+#cmakedefine01 BOUT_HAS_ADIOS2
 #cmakedefine01 BOUT_HAS_PETSC
 #cmakedefine01 BOUT_HAS_PRETTY_FUNCTION
 #cmakedefine01 BOUT_HAS_PVODE

examples/CMakeLists.txt

@@ -11,6 +11,7 @@ add_subdirectory(backtrace)
 add_subdirectory(blob2d)
 add_subdirectory(blob2d-outerloop)
 add_subdirectory(blob2d-laplacexz)
+add_subdirectory(boutpp)
 add_subdirectory(boundary-conditions/advection)
 add_subdirectory(conducting-wall-mode)
 add_subdirectory(conduction)

examples/blob2d/blob2d.cxx

@@ -25,7 +25,6 @@ class Blob2D : public PhysicsModel {
   BoutReal rho_s;   ///< Bohm gyro radius
   BoutReal Omega_i; ///< Ion cyclotron frequency
   BoutReal c_s;     ///< Bohm sound speed
-  BoutReal n0;      ///< Reference density
 
   // Constants to calculate the parameters
   BoutReal Te0; ///< Isothermal temperature [eV]
@@ -61,7 +60,6 @@ class Blob2D : public PhysicsModel {
     m_i = options["m_i"].withDefault(2 * 1.667e-27);
     m_e = options["m_e"].withDefault(9.11e-31);
 
-    n0 = options["n0"].doc("Background density in cubic m").withDefault(1e19);
     D_vort = options["D_vort"].doc("Viscous diffusion coefficient").withDefault(0.0);
     D_n = options["D_n"].doc("Density diffusion coefficient").withDefault(0.0);
 

examples/blob2d/delta_0.25/BOUT.inp

@@ -87,8 +87,6 @@ flags = 49152  # set_rhs i.e. identity matrix in boundaries
 
 Te0 = 5    # Electron Temperature (eV)
 
-n0 = 2e+18  # Background plasma density (m^-3)
-
 compressible = false  # Compressibility?
 
 boussinesq = true  # Boussinesq approximation (no perturbed n in vorticity)

examples/blob2d/delta_1/BOUT.inp

@@ -87,8 +87,6 @@ flags = 49152  # set_rhs i.e. identity matrix in boundaries
 
 Te0 = 5    # Electron Temperature (eV)
 
-n0 = 2e+18  # Background plasma density (m^-3)
-
 compressible = false  # Compressibility?
 
 boussinesq = true  # Boussinesq approximation (no perturbed n in vorticity)

examples/blob2d/delta_10/BOUT.inp

@@ -87,8 +87,6 @@ flags = 49152  # set_rhs i.e. identity matrix in boundaries
 
 Te0 = 5    # Electron Temperature (eV)
 
-n0 = 2e+18  # Background plasma density (m^-3)
-
 compressible = false  # Compressibility?
 
 boussinesq = true  # Boussinesq approximation (no perturbed n in vorticity)

examples/boutpp/CMakeLists.txt

@@ -0,0 +1,10 @@
+cmake_minimum_required(VERSION 3.13)
+
+if (NOT TARGET bout++::bout++)
+  find_package(bout++ REQUIRED)
+endif()
+
+bout_copy_file(runexample)
+bout_copy_file(blob2d.py)
+bout_copy_file(simulation.py)
+bout_copy_file(data/BOUT.inp)