ADIOS 2 I/O

.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

.github/workflows/tests.yml

@@ -39,20 +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"
@@ -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 }}
 

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
@@ -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}

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@)

cmake/SetupBOUTThirdParty.cmake

@@ -156,6 +156,7 @@ option(BOUT_USE_NETCDF "Enable support for NetCDF output" ON)
 option(BOUT_DOWNLOAD_NETCDF_CXX4 "Download and build netCDF-cxx4" OFF)
 if (BOUT_USE_NETCDF)
   if (BOUT_DOWNLOAD_NETCDF_CXX4)
+    message(STATUS "Downloading and configuring NetCDF-cxx4")
     include(FetchContent)
     FetchContent_Declare(
       netcdf-cxx4
@@ -185,6 +186,44 @@ 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)
+    message(STATUS "Downloading and configuring ADIOS2")
+    include(FetchContent)
+    FetchContent_Declare(
+      adios2
+      GIT_REPOSITORY https://github.com/ornladios/ADIOS2.git
+      GIT_TAG origin/master
+      GIT_SHALLOW 1
+      )
+    set(ADIOS2_USE_MPI ON CACHE BOOL "" FORCE)
+    set(ADIOS2_USE_Fortran OFF CACHE BOOL "" FORCE)
+    set(ADIOS2_USE_Python OFF CACHE BOOL "" FORCE)
+    set(ADIOS2_BUILD_EXAMPLES OFF CACHE BOOL "" FORCE)
+    # Disable testing, or ADIOS will try to find or install GTEST
+    set(BUILD_TESTING OFF CACHE BOOL "" FORCE)
+    # Note: SST requires <rdma/fabric.h> but doesn't check at configure time
+    set(ADIOS2_USE_SST OFF CACHE BOOL "" FORCE)
+    FetchContent_MakeAvailable(adios2)
+    target_link_libraries(bout++ PUBLIC adios2::cxx11_mpi)
+    message(STATUS "ADIOS2 done configuring")
+  else()
+    find_package(ADIOS2)
+    if (ADIOS2_FOUND)
+      ENABLE_LANGUAGE(C)
+      find_package(MPI REQUIRED COMPONENTS C)
+      target_link_libraries(bout++ PUBLIC adios2::cxx11_mpi MPI::MPI_C)
+    else()
+      set(BOUT_USE_ADIOS OFF)
+    endif()
+  endif()
+endif()
+message(STATUS "ADIOS support: ${BOUT_USE_ADIOS}")
+set(BOUT_HAS_ADIOS ${BOUT_USE_ADIOS})
+
+
 option(BOUT_USE_FFTW "Enable support for FFTW" ON)
 if (BOUT_USE_FFTW)
   find_package(FFTW REQUIRED)

cmake_build_defines.hxx.in

@@ -13,6 +13,7 @@
 #cmakedefine01 BOUT_HAS_IDA
 #cmakedefine01 BOUT_HAS_LAPACK
 #cmakedefine01 BOUT_HAS_NETCDF
+#cmakedefine01 BOUT_HAS_ADIOS
 #cmakedefine01 BOUT_HAS_PETSC
 #cmakedefine01 BOUT_HAS_PRETTY_FUNCTION
 #cmakedefine01 BOUT_HAS_PVODE

include/bout/adios_object.hxx

@@ -0,0 +1,83 @@
+/*!************************************************************************
+ * Provides access to the ADIOS library, handling initialisation and
+ * finalisation.
+ *
+ * Usage
+ * -----
+ *
+ * #include <bout/adios_object.hxx>
+ *
+ **************************************************************************/
+
+#ifndef ADIOS_OBJECT_HXX
+#define ADIOS_OBJECT_HXX
+
+#include "bout/build_config.hxx"
+
+#if BOUT_HAS_ADIOS
+
+#include <adios2.h>
+#include <memory>
+#include <mpi.h>
+
+namespace bout {
+
+void ADIOSInit(MPI_Comm comm);
+void ADIOSInit(const std::string configFile, MPI_Comm comm);
+void ADIOSFinalize();
+
+using ADIOSPtr = std::shared_ptr<adios2::ADIOS>;
+using EnginePtr = std::shared_ptr<adios2::Engine>;
+using IOPtr = std::shared_ptr<adios2::IO>;
+
+ADIOSPtr GetADIOSPtr();
+IOPtr GetIOPtr(const std::string IOName);
+
+class ADIOSStream {
+public:
+  adios2::IO io;
+  adios2::Engine engine;
+  adios2::Variable<double> vTime;
+  adios2::Variable<int> vStep;
+  int adiosStep = 0;
+  bool isInStep = false; // true if BeginStep was called and EndStep was not yet called
+
+  /** create or return the ADIOSStream based on the target file name */
+  static ADIOSStream& ADIOSGetStream(const std::string& fname);
+
+  ~ADIOSStream();
+
+  template <class T>
+  adios2::Variable<T> GetValueVariable(const std::string& varname) {
+    auto v = io.InquireVariable<T>(varname);
+    if (!v) {
+      v = io.DefineVariable<T>(varname);
+    }
+    return v;
+  }
+
+  template <class T>
+  adios2::Variable<T> GetArrayVariable(const std::string& varname, adios2::Dims& shape) {
+    adios2::Variable<T> v = io.InquireVariable<T>(varname);
+    if (!v) {
+      adios2::Dims start(shape.size());
+      v = io.DefineVariable<T>(varname, shape, start, shape);
+    } else {
+      v.SetShape(shape);
+    }
+    return v;
+  }
+
+private:
+  ADIOSStream(const std::string fname) : fname(fname){};
+  std::string fname;
+};
+
+/** Set user parameters for an IO group */
+void ADIOSSetParameters(const std::string& input, const char delimKeyValue,
+                        const char delimItem, adios2::IO& io);
+
+} // namespace bout
+
+#endif //BOUT_HAS_ADIOS
+#endif //ADIOS_OBJECT_HXX

include/bout/bout.hxx

@@ -2,8 +2,6 @@
  *
  * @mainpage BOUT++
  *
- * @version 3.0
- *
  * @par Description
  * Framework for the solution of partial differential
  * equations, in particular fluid models in plasma physics.
@@ -33,8 +31,8 @@
  *
  **************************************************************************/
 
-#ifndef __BOUT_H__
-#define __BOUT_H__
+#ifndef BOUT_H
+#define BOUT_H
 
 #include "bout/build_config.hxx"
 
@@ -44,7 +42,7 @@
 #include "bout/field3d.hxx"
 #include "bout/globals.hxx"
 #include "bout/mesh.hxx"
-#include "bout/options_netcdf.hxx"
+#include "bout/options_io.hxx"
 #include "bout/output.hxx"
 #include "bout/smoothing.hxx" // Smoothing functions
 #include "bout/solver.hxx"
@@ -206,4 +204,4 @@ private:
  */
 int BoutFinalise(bool write_settings = true);
 
-#endif // __BOUT_H__
+#endif // BOUT_H

include/bout/build_config.hxx

@@ -17,6 +17,7 @@ constexpr auto has_gettext = static_cast<bool>(BOUT_HAS_GETTEXT);
 constexpr auto has_lapack = static_cast<bool>(BOUT_HAS_LAPACK);
 constexpr auto has_legacy_netcdf = static_cast<bool>(BOUT_HAS_LEGACY_NETCDF);
 constexpr auto has_netcdf = static_cast<bool>(BOUT_HAS_NETCDF);
+constexpr auto has_adios = static_cast<bool>(BOUT_HAS_ADIOS);
 constexpr auto has_petsc = static_cast<bool>(BOUT_HAS_PETSC);
 constexpr auto has_hypre = static_cast<bool>(BOUT_HAS_HYPRE);
 constexpr auto has_umpire = static_cast<bool>(BOUT_HAS_UMPIRE);

include/bout/generic_factory.hxx

@@ -1,8 +1,8 @@
 /// Base type for factories
 
 #pragma once
-#ifndef __BOUT_GENERIC_FACTORY_H__
-#define __BOUT_GENERIC_FACTORY_H__
+#ifndef BOUT_GENERIC_FACTORY_H
+#define BOUT_GENERIC_FACTORY_H
 
 #include "bout/boutexception.hxx"
 #include "bout/options.hxx"
@@ -259,4 +259,4 @@ public:
   };
 };
 
-#endif // __BOUT_GENERIC_FACTORY_H__
+#endif // BOUT_GENERIC_FACTORY_H