Merge branch 'par-bc-cleanup' into par-bc-improve

.build_adios2_for_ci.sh

@@ -0,0 +1,62 @@
+#!/bin/bash
+
+set -e
+
+if test $BUILD_ADIOS2 ; then
+    if [[ ! -d $HOME/local/adios/include/adios2.h ]] || test $1 ; then
+	echo "****************************************"
+	echo "Building ADIOS2"
+	echo "****************************************"
+
+	branch=${1:-release_29}
+    if [ ! -d adios2 ]; then
+    	git clone -b $branch https://github.com/ornladios/ADIOS2.git adios2 --depth=1
+    fi
+
+	pushd adios2
+    rm -rf build
+    mkdir -p build
+    pushd build
+
+    cmake .. \
+        -DCMAKE_INSTALL_PREFIX=$HOME/local \
+        -DADIOS2_USE_MPI=ON \
+        -DADIOS2_USE_Fortran=OFF \
+        -DADIOS2_USE_Python=OFF \
+        -DADIOS2_BUILD_EXAMPLES=OFF \
+        -DCMAKE_BUILD_TYPE=Release \
+        -DCMAKE_POSITION_INDEPENDENT_CODE=ON \
+        -DBUILD_TESTING=OFF \
+        -DADIOS2_USE_SST=OFF \
+        -DADIOS2_USE_MGARD=OFF \
+        -DADIOS2_USE_HDF5=OFF \
+        -DADIOS2_USE_BZip2=OFF \
+        -DADIOS2_USE_Blosc2=OFF \
+        -DADIOS2_USE_SZ=OFF \
+        -DADIOS2_USE_ZFP=OFF \
+        -DADIOS2_USE_DAOS=OFF \
+        -DADIOS2_USE_UCX=OFF \
+        -DADIOS2_USE_LIBPRESSIO=OFF \
+        -DADIOS2_USE_Sodium=OFF \
+        -DADIOS2_USE_ZeroMQ=OFF \
+        -DADIOS2_USE_MHS=OFF \
+        -DADIOS2_USE_DataMan=OFF
+
+	make -j 4 && make install
+	popd
+
+	echo "****************************************"
+	echo " Finished building ADIOS2"
+	echo "****************************************"
+
+    else
+
+	echo "****************************************"
+	echo " ADIOS2 already installed"
+	echo "****************************************"
+    fi
+else
+    echo "****************************************"
+    echo " ADIOS2 not requested"
+    echo "****************************************"
+fi

.ci_fedora.sh

@@ -56,6 +56,7 @@ else
     . /etc/profile.d/modules.sh
     module load mpi/${1}-x86_64
     export OMPI_MCA_rmaps_base_oversubscribe=yes
+    export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe
     export TRAVIS=true
     export FLEXIBLAS=NETLIB
     cd

.github/workflows/clang-tidy-review.yml

@@ -32,7 +32,7 @@ jobs:
           # the unit tests until they're fixed or ignored upstream
           exclude: "tests/unit/*cxx"
           cmake_command: |
-            pip install cmake && \
+            pip install --break-system-packages cmake && \
             cmake --version && \
             git config --global --add safe.directory "$GITHUB_WORKSPACE" && \
             cmake . -B build -DBUILD_SHARED_LIBS=ON \

.github/workflows/tests.yml

@@ -28,6 +28,7 @@ jobs:
       OMP_NUM_THREADS: ${{ matrix.config.omp_num_threads }}
       PYTHONPATH: ${{ github.workspace }}/tools/pylib
       OMPI_MCA_rmaps_base_oversubscribe: yes
+      PRTE_MCA_rmaps_default_mapping_policy: ":oversubscribe"
       MPIRUN: mpiexec -np
     strategy:
       fail-fast: true
@@ -38,20 +39,23 @@ jobs:
         is_cron:
           - ${{ github.event_name == 'cron' }}
         config:
-          - name: "CMake, PETSc unreleased"
+          - name: "CMake, PETSc unreleased, ADIOS"
             os: ubuntu-20.04
             cmake_options: "-DBUILD_SHARED_LIBS=ON
                             -DBOUT_ENABLE_METRIC_3D=ON
                             -DBOUT_ENABLE_OPENMP=ON
                             -DBOUT_USE_PETSC=ON
                             -DBOUT_USE_SLEPC=ON
                             -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_USE_ADIOS2=ON
                             -DBOUT_ENABLE_PYTHON=ON
+                            -DADIOS2_ROOT=/home/runner/local/adios2
                             -DSUNDIALS_ROOT=/home/runner/local
                             -DPETSC_DIR=/home/runner/local/petsc
                             -DSLEPC_DIR=/home/runner/local/slepc"
             build_petsc: -petsc-main
             build_petsc_branch: main
+            build_adios2: true
             on_cron: true
 
           - name: "Default options, Ubuntu 20.04"
@@ -185,9 +189,8 @@ jobs:
 
       - name: Install pip packages
         run: |
-          ./.pip_install_for_ci.sh 'cython~=0.29' 'netcdf4~=1.5' 'sympy~=1.5' 'gcovr' 'cmake' zoidberg fastcov
-          # Add the pip install location to the runner's PATH
-          echo ~/.local/bin >> $GITHUB_PATH
+          python -m pip install --upgrade pip setuptools
+          python -m pip install -r requirements.txt
 
       - name: Cache SUNDIALS build
         uses: actions/cache@v3
@@ -201,6 +204,9 @@ jobs:
       - name: Build PETSc
         run: BUILD_PETSC=${{ matrix.config.build_petsc }} ./.build_petsc_for_ci.sh ${{ matrix.config.build_petsc_branch }}
 
+      - name: Build ADIOS2
+        run: BUILD_ADIOS2=${{ matrix.config.build_adios2 }} ./.build_adios2_for_ci.sh 
+
       - name: Build BOUT++
         run: UNIT_ONLY=${{ matrix.config.unit_only }} ./.ci_with_cmake.sh ${{ matrix.config.cmake_options }}
 

CHANGELOG.md

@@ -6,6 +6,8 @@
 ### Breaking changes
 
 - The autotools `./configure` build system has been removed
+- Parsing of booleans has changed [\#2828][https://github.com/boutproject/BOUT-dev/pull/2828] ([bendudson][https://github.com/bendudson]).
+  See the [manual page](https://bout-dev.readthedocs.io/en/stable/user_docs/bout_options.html#boolean-expressions) for details.
 
 
 ## [v5.1.0](https://github.com/boutproject/BOUT-dev/tree/v5.1.0)

CMakeLists.txt

@@ -83,6 +83,7 @@ function(bout_update_submodules)
 endfunction()
 
 set(BOUT_SOURCES
+  ./include/bout/adios_object.hxx
   ./include/bout/array.hxx
   ./include/bout/assert.hxx
   ./include/bout/boundary_factory.hxx
@@ -146,7 +147,7 @@ set(BOUT_SOURCES
   ./include/bout/openmpwrap.hxx
   ./include/bout/operatorstencil.hxx
   ./include/bout/options.hxx
-  ./include/bout/options_netcdf.hxx
+  ./include/bout/options_io.hxx
   ./include/bout/optionsreader.hxx
   ./include/bout/output.hxx
   ./include/bout/output_bout_types.hxx
@@ -325,6 +326,7 @@ set(BOUT_SOURCES
   ./src/solver/impls/split-rk/split-rk.cxx
   ./src/solver/impls/split-rk/split-rk.hxx
   ./src/solver/solver.cxx
+  ./src/sys/adios_object.cxx
   ./src/sys/bout_types.cxx
   ./src/sys/boutcomm.cxx
   ./src/sys/boutexception.cxx
@@ -338,7 +340,11 @@ set(BOUT_SOURCES
   ./src/sys/options/optionparser.hxx
   ./src/sys/options/options_ini.cxx
   ./src/sys/options/options_ini.hxx
+  ./src/sys/options/options_io.cxx
   ./src/sys/options/options_netcdf.cxx
+  ./src/sys/options/options_netcdf.hxx
+  ./src/sys/options/options_adios.cxx
+  ./src/sys/options/options_adios.hxx
   ./src/sys/optionsreader.cxx
   ./src/sys/output.cxx
   ./src/sys/petsclib.cxx
@@ -462,7 +468,7 @@ set_target_properties(bout++ PROPERTIES
 # Set some variables for the bout-config script
 set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} -L\$BOUT_LIB_PATH -lbout++")
 set(BOUT_INCLUDE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/include")
-set(CONFIG_CFLAGS "${CONFIG_CFLAGS} -I\${BOUT_INCLUDE_PATH} -I${CMAKE_CURRENT_BINARY_DIR}/include ${CMAKE_CXX_FLAGS}")
+set(CONFIG_CFLAGS "${CONFIG_CFLAGS} -I\${BOUT_INCLUDE_PATH} -I${CMAKE_CURRENT_BINARY_DIR}/include ${CMAKE_CXX_FLAGS} -std=c++17")
 
 target_compile_features(bout++ PUBLIC cxx_std_17)
 set_target_properties(bout++ PROPERTIES CXX_EXTENSIONS OFF)
@@ -930,6 +936,7 @@ message("
    SUNDIALS support         : ${BOUT_HAS_SUNDIALS}
    HYPRE support            : ${BOUT_HAS_HYPRE}
    NetCDF support           : ${BOUT_HAS_NETCDF}
+   ADIOS support            : ${BOUT_HAS_ADIOS}
    FFTW support             : ${BOUT_HAS_FFTW}
    LAPACK support           : ${BOUT_HAS_LAPACK}
    OpenMP support           : ${BOUT_USE_OPENMP}

README.md

@@ -26,8 +26,11 @@ For example, the following set of equations for magnetohydrodynamics
 (MHD):
 
 ![ddt_rho](http://latex.codecogs.com/png.latex?%5Cfrac%7B%5Cpartial%20%5Crho%7D%7B%5Cpartial%20t%7D%20%3D%20-%5Cmathbf%7Bv%7D%5Ccdot%5Cnabla%5Crho%20-%20%5Crho%5Cnabla%5Ccdot%5Cmathbf%7Bv%7D)
+
 ![ddt_p](http://latex.codecogs.com/png.latex?%5Cfrac%7B%5Cpartial%20p%7D%7B%5Cpartial%20t%7D%20%3D%20-%5Cmathbf%7Bv%7D%5Ccdot%5Cnabla%20p%20-%20%5Cgamma%20p%5Cnabla%5Ccdot%5Cmathbf%7Bv%7D)
+
 ![ddt_v](http://latex.codecogs.com/png.latex?%5Cfrac%7B%5Cpartial%20%5Cmathbf%7Bv%7D%7D%7B%5Cpartial%20t%7D%20%3D%20-%5Cmathbf%7Bv%7D%5Ccdot%5Cnabla%5Cmathbf%7Bv%7D%20+%20%5Cfrac%7B1%7D%7B%5Crho%7D%28-%5Cnabla%20p%20+%20%28%5Cnabla%5Ctimes%5Cmathbf%7BB%7D%29%5Ctimes%5Cmathbf%7BB%7D%29)
+
 ![ddt_B](http://latex.codecogs.com/png.latex?%7B%7B%5Cfrac%7B%5Cpartial%20%5Cmathbf%7BB%7D%7D%7B%5Cpartial%20t%7D%7D%7D%20%3D%20%5Cnabla%5Ctimes%28%5Cmathbf%7Bv%7D%5Ctimes%5Cmathbf%7BB%7D%29)
 
 can be written simply as:
@@ -43,7 +46,7 @@ The full code for this example can be found in the [orszag-tang
 example](examples/orszag-tang/mhd.cxx).
 
 Jointly developed by University of York (UK), LLNL, CCFE, DCU, DTU,
-and other international partners.
+and other international partners. See the Git logs for author details.
 
 
 Homepage found at [http://boutproject.github.io/](http://boutproject.github.io/)
@@ -52,7 +55,6 @@ Homepage found at [http://boutproject.github.io/](http://boutproject.github.io/)
 * [Requirements](#requirements)
 * [Usage and installation](#usage-and-installation)
 * [Terms of use](#terms-of-use)
-* [Overview of files](#overview-of-files)
 * [Contributing](#contributing)
 * [License](#license)
 
@@ -66,18 +68,17 @@ BOUT++ needs the following:
 
 BOUT++ has the following optional dependencies:
 
-* FFTW3 (strongly recommended!)
-* OpenMP
-* PETSc
-* SLEPc
-* ARKODE
-* IDA
-* CVODE
+* [FFTW3](https://www.fftw.org/) (strongly recommended!)
+* [SUNDIALS](https://computing.llnl.gov/projects/sundials): CVODE, IDA, ARKODE
+* [PETSc](https://petsc.org)
+* [ADIOS2](https://adios2.readthedocs.io/)
+* [SLEPc](https://slepc.upv.es/)
 * LAPACK
+* OpenMP
 * Score-p (for performance diagnostics)
 
 ## Usage and installation
-Please see the [users manual](http://bout-dev.readthedocs.io)
+Please see the [users manual](http://bout-dev.readthedocs.io).
 
 ## Terms of use
 
@@ -105,58 +106,14 @@ You can convert the CITATION.cff file into a Bibtex file as follows:
     pip3 install --user cffconvert
     cffconvert -if CITATION.cff -f bibtex -of CITATION.bib
 
-## Overview of files
-
-This directory contains
-
-* **bin**                   Files for setting the BOUT++ configuration
-* **examples**              Example models and test codes
-* **externalpackages**      External packages needed for installing BOUT++
-* **include**               Header files used in BOUT++
-* **manual**                Manuals and documentation (also [doxygen](http://www.stack.nl/~dimitri/doxygen/) documentation)
-* **src**                   The main code directory
-* **CITATION**              Contains the paper citation for BOUT++
-* **LICENSE**               LGPL license
-* **LICENSE.GPL**           GPL license
-* **tools**                 Tools for helping with analysis, mesh generation, and data managment
-
-  * **archiving**               Routines for managing input/output files e.g. compressing data, converting formats, and managing runs
-  * **cyl_and_helimak_grids**   IDL codes for generating cylindrical and helimak grids
-  * **eigensolver**             Matlab routines for solving eigenmodes
-  * **idllib**                  Analysis codes in IDL. Add this to your IDL_PATH environment variable
-  * **line_tracing**            IDL routines for line tracing of field lines
-  * **line_tracing_v2**         Newer version of the IDL routines for line tracing of field lines
-  * **mathematicalib**          Library for post processing using Mathematica
-  * **matlablib**               Library for post processing using MATLAB
-  * **numlib**                  Numerical IDL routines
-  * **octave**                  Routines for post processing using octave
-  * **plasmalib**               IDL routines for calculation of plasma parameters
-  * **pdb2idl**                 Library to read Portable Data Binary (PDB) files into IDL
-  * **pylib**                   Analysis codes in Python
-
-    * **boutdata**        Routines to simplify accessing BOUT++ output
-    * **boututils**       Some useful routines for accessing and plotting data
-    * **post_bout**       Routines for post processing in BOUT++
-
-  * **slab**              IDL routine for grid generation of a slab
-  * **tokamak_grids**     Code to generate input grids for tokamak equilibria
-
-    * **gridgen**         Grid generator in IDL. Hypnotoad GUI for converting G-EQDSK files into a flux-aligned orthogonal grid.
-    * **elite**           Convert ELITE .eqin files into an intermediate binary file
-    * **gato**            Convert DSKGATO files into intermediate binary format
-    * **all**             Convert the intermediate binary file into BOUT++ input grid
-    * **coils**           Routines for calculating the field due to external RMP coils and adding to existing equilibria
-    * **cyclone**         Generate cyclone test cases (concentric circle "equilibrium" for local flux-surface calculations)
-    * **py_gridgen**      Translation" into python of the corresponding IDL routines in the folder gridgen
-    * **shifted_circle**  Produce shifted cirle equilibria input grids
 
 
 ## Contributing
 
-See [CONTRIBUTING.md](CONTRIBUTING.md).
+See [CONTRIBUTING.md](CONTRIBUTING.md) and the [manual page](https://bout-dev.readthedocs.io/en/stable/developer_docs/contributing.html)
 
 ## License
-Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
+Copyright 2010-2024 BOUT++ contributors
 
 BOUT++ is free software: you can redistribute it and/or modify
 it under the terms of the GNU Lesser General Public License as published by
@@ -171,15 +128,7 @@ GNU Lesser General Public License for more details.
 A copy of the LGPL license is in [LICENSE](LICENSE). Since this is based
 on (and refers to) the GPL, this is included in [LICENSE.GPL](LICENSE.GPL).
 
-Some of the autoconf macros under [m4](m4) are licensed under
-GPLv3. These are not necessary to either build or run BOUT++, but are
-used in the creation of [configure](configure) from
-[configure.ac](configure.ac), and are provided as a courtesy to
-developers. You are free to substitute them with other autoconf macros
-that provide equivalent functionality.
-
 BOUT++ links by default with some GPL licensed libraries. Thus if you
 compile BOUT++ with any of them, BOUT++ will automatically be licensed
 as GPL. Thus if you want to use BOUT++ with GPL non-compatible code,
 make sure to compile without GPLed code.
-

bin/bout-config.in

@@ -29,6 +29,7 @@ idlpath="@IDLCONFIGPATH@"
 pythonpath="@PYTHONCONFIGPATH@"
 
 has_netcdf="@BOUT_HAS_NETCDF@"
+has_adios="@BOUT_HAS_ADIOS@"
 has_legacy_netcdf="@BOUT_HAS_LEGACY_NETCDF@"
 has_pnetcdf="@BOUT_HAS_PNETCDF@"
 has_pvode="@BOUT_HAS_PVODE@"
@@ -71,6 +72,7 @@ Available values for OPTION include:
   --python       Python path
 
   --has-netcdf  NetCDF file support
+  --has-adios   ADIOS file support
   --has-legacy-netcdf  Legacy NetCDF file support
   --has-pnetcdf Parallel NetCDF file support
   --has-pvode   PVODE solver support
@@ -109,6 +111,7 @@ all()
         echo "  --python      -> $pythonpath"
         echo
         echo "  --has-netcdf  -> $has_netcdf"
+        echo "  --has-adios   -> $has_adios"
         echo "  --has-legacy-netcdf  -> $has_legacy_netcdf"
         echo "  --has-pnetcdf -> $has_pnetcdf"
         echo "  --has-pvode   -> $has_pvode"
@@ -197,6 +200,10 @@ while test $# -gt 0; do
         echo $has_netcdf
         ;;
 
+    --has-adios)
+        echo $has_adios
+        ;;
+
     --has-legacy-netcdf)
         echo $has_legacy_netcdf
         ;;

bout++Config.cmake.in

@@ -15,6 +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_FFTW @BOUT_HAS_FFTW@)
 set(BOUT_HAS_LAPACK @BOUT_HAS_LAPACK@)
 set(BOUT_HAS_PETSC @BOUT_HAS_PETSC@)