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Merge pull request #2766 from boutproject/adios-io-next-rebase
ADIOS 2 I/O
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,62 @@ | ||
| #!/bin/bash | ||
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| set -e | ||
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| if test $BUILD_ADIOS2 ; then | ||
| if [[ ! -d $HOME/local/adios/include/adios2.h ]] || test $1 ; then | ||
| echo "****************************************" | ||
| echo "Building ADIOS2" | ||
| echo "****************************************" | ||
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| branch=${1:-release_29} | ||
| if [ ! -d adios2 ]; then | ||
| git clone -b $branch https://github.com/ornladios/ADIOS2.git adios2 --depth=1 | ||
| fi | ||
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| pushd adios2 | ||
| rm -rf build | ||
| mkdir -p build | ||
| pushd build | ||
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| cmake .. \ | ||
| -DCMAKE_INSTALL_PREFIX=$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 | ||
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| make -j 4 && make install | ||
| popd | ||
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| echo "****************************************" | ||
| echo " Finished building ADIOS2" | ||
| echo "****************************************" | ||
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| else | ||
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| echo "****************************************" | ||
| echo " ADIOS2 already installed" | ||
| echo "****************************************" | ||
| fi | ||
| else | ||
| echo "****************************************" | ||
| echo " ADIOS2 not requested" | ||
| echo "****************************************" | ||
| fi |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,83 @@ | ||
| /*!************************************************************************ | ||
| * Provides access to the ADIOS library, handling initialisation and | ||
| * finalisation. | ||
| * | ||
| * Usage | ||
| * ----- | ||
| * | ||
| * #include <bout/adios_object.hxx> | ||
| * | ||
| **************************************************************************/ | ||
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| #ifndef ADIOS_OBJECT_HXX | ||
| #define ADIOS_OBJECT_HXX | ||
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| #include "bout/build_config.hxx" | ||
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| #if BOUT_HAS_ADIOS | ||
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| #include <adios2.h> | ||
| #include <memory> | ||
| #include <mpi.h> | ||
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| namespace bout { | ||
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| void ADIOSInit(MPI_Comm comm); | ||
| void ADIOSInit(const std::string configFile, MPI_Comm comm); | ||
| void ADIOSFinalize(); | ||
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| using ADIOSPtr = std::shared_ptr<adios2::ADIOS>; | ||
| using EnginePtr = std::shared_ptr<adios2::Engine>; | ||
| using IOPtr = std::shared_ptr<adios2::IO>; | ||
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| ADIOSPtr GetADIOSPtr(); | ||
| IOPtr GetIOPtr(const std::string IOName); | ||
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| 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 | ||
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| /** create or return the ADIOSStream based on the target file name */ | ||
| static ADIOSStream& ADIOSGetStream(const std::string& fname); | ||
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| ~ADIOSStream(); | ||
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| 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; | ||
| } | ||
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| 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; | ||
| } | ||
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| private: | ||
| ADIOSStream(const std::string fname) : fname(fname){}; | ||
| std::string fname; | ||
| }; | ||
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| /** Set user parameters for an IO group */ | ||
| void ADIOSSetParameters(const std::string& input, const char delimKeyValue, | ||
| const char delimItem, adios2::IO& io); | ||
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| } // namespace bout | ||
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| #endif //BOUT_HAS_ADIOS | ||
| #endif //ADIOS_OBJECT_HXX |
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