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Hadrons: dedicated IO class for A2A matrices
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Hadrons/A2AMatrix.hpp
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97
Hadrons/A2AMatrix.hpp
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@ -0,0 +1,97 @@
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#ifndef A2A_Matrix_hpp_
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#define A2A_Matrix_hpp_
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#include <Hadrons/Global.hpp>
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BEGIN_HADRONS_NAMESPACE
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template <typename T, typename MetadataType>
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class A2AMatrixIo
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{
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public:
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A2AMatrixIo(void) = default;
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A2AMatrixIo(std::string filename, std::string dataname,
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const unsigned int nt, const unsigned int ni,
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const unsigned int nj, const unsigned int blockSize);
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~A2AMatrixIo(void) = default;
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void initFile(const MetadataType &d);
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void saveBlock(const T *data, const unsigned int i, const unsigned int j);
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private:
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std::string filename_, dataname_;
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unsigned int nt_, ni_, nj_, blockSize_;
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};
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template <typename T, typename MetadataType>
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A2AMatrixIo<T, MetadataType>::A2AMatrixIo(std::string filename,
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std::string dataname,
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const unsigned int nt,
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const unsigned int ni,
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const unsigned int nj,
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const unsigned int blockSize)
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: filename_(filename), dataname_(dataname)
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, nt_(nt), ni_(ni), nj_(nj), blockSize_(blockSize)
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{}
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template <typename T, typename MetadataType>
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void A2AMatrixIo<T, MetadataType>::initFile(const MetadataType &d)
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{
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#ifdef HAVE_HDF5
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std::vector<hsize_t> dim = {static_cast<hsize_t>(nt_),
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static_cast<hsize_t>(ni_),
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static_cast<hsize_t>(nj_)},
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chunk = {static_cast<hsize_t>(nt_),
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static_cast<hsize_t>(blockSize_),
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static_cast<hsize_t>(blockSize_)};
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H5NS::DataSpace dataspace(dim.size(), dim.data());
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H5NS::DataSet dataset;
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H5NS::DSetCreatPropList plist;
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// create empty file just with metadata
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{
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Hdf5Writer writer(filename_);
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write(writer, dataname_, d);
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}
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// create the dataset
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Hdf5Writer writer(filename_);
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push(writer, dataname_);
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auto &group = writer.getGroup();
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plist.setChunk(chunk.size(), chunk.data());
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dataset = group.createDataSet("data", Hdf5Type<T>::type(), dataspace, plist);
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#else
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HADRONS_ERROR(Implementation, "all-to-all matrix I/O needs HDF5 library");
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#endif
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}
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template <typename T, typename MetadataType>
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void A2AMatrixIo<T, MetadataType>::saveBlock(const T *data,
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const unsigned int i,
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const unsigned int j)
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{
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#ifdef HAVE_HDF5
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Hdf5Reader reader(filename_);
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std::vector<hsize_t> count = {nt_, blockSize_, blockSize_},
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offset = {0, static_cast<hsize_t>(i),
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static_cast<hsize_t>(j)},
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stride = {1, 1, 1},
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block = {1, 1, 1};
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H5NS::DataSpace memspace(count.size(), count.data()), dataspace;
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H5NS::DataSet dataset;
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size_t shift;
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push(reader, dataname_);
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auto &group = reader.getGroup();
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dataset = group.openDataSet("data");
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dataspace = dataset.getSpace();
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dataspace.selectHyperslab(H5S_SELECT_SET, count.data(), offset.data(),
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stride.data(), block.data());
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dataset.write(data, Hdf5Type<T>::type(), memspace, dataspace);
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#else
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HADRONS_ERROR(Implementation, "all-to-all matrix I/O needs HDF5 library");
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#endif
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}
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END_HADRONS_NAMESPACE
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#endif // A2A_Matrix_hpp_
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@ -15,7 +15,9 @@ libHadrons_adir = $(includedir)/Hadrons
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nobase_libHadrons_a_HEADERS = \
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$(modules_hpp) \
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A2AVectors.hpp \
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A2AMatrix.hpp \
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Application.hpp \
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DilutedNoise.hpp \
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EigenPack.hpp \
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Environment.hpp \
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Exceptions.hpp \
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@ -34,6 +34,7 @@ See the full license in the file "LICENSE" in the top level distribution directo
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#include <Hadrons/Module.hpp>
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#include <Hadrons/ModuleFactory.hpp>
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#include <Hadrons/A2AVectors.hpp>
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#include <Hadrons/A2AMatrix.hpp>
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#include <Hadrons/Modules/MSolver/A2AVectors.hpp>
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#include <Hadrons/Modules/MContraction/A2AMesonFieldKernels.hpp>
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@ -62,6 +63,14 @@ class A2AMesonFieldPar: Serializable
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std::vector<std::string>, mom);
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};
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class A2AMesonFieldMetadata: Serializable
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{
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public:
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GRID_SERIALIZABLE_CLASS_MEMBERS(A2AMesonFieldMetadata,
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std::vector<RealF>, momentum,
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Gamma::Algebra, gamma);
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};
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template <typename FImpl>
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class TA2AMesonField : public Module<A2AMesonFieldPar>
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{
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@ -70,6 +79,13 @@ public:
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SOLVER_TYPE_ALIASES(FImpl,);
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typedef Eigen::TensorMap<Eigen::Tensor<Complex, 5, Eigen::RowMajor>> MesonField;
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typedef Eigen::TensorMap<Eigen::Tensor<MF_IO_TYPE, 5, Eigen::RowMajor>> MesonFieldIo;
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typedef A2AMatrixIo<MF_IO_TYPE, A2AMesonFieldMetadata> MatrixIo;
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struct IoHelper
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{
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MatrixIo io;
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A2AMesonFieldMetadata metadata;
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size_t offset;
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};
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public:
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// constructor
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TA2AMesonField(const std::string name);
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@ -86,16 +102,13 @@ private:
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// IO
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std::string ioname(unsigned int m, unsigned int g) const;
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std::string filename(unsigned int m, unsigned int g) const;
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void initFile(unsigned int m, unsigned int g);
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void saveBlock(const MesonFieldIo &mf,
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unsigned int m, unsigned int g,
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unsigned int i, unsigned int j);
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void saveBlock(MF_IO_TYPE *data, IoHelper &h, unsigned int i, unsigned int j);
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private:
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bool hasPhase_{false};
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std::string momphName_;
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std::vector<Gamma::Algebra> gamma_;
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std::vector<std::vector<Real>> mom_;
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std::vector<std::pair<unsigned int, unsigned int>> nodeFile_;
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std::vector<IoHelper> nodeIo_;
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};
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MODULE_REGISTER(A2AMesonField, ARG(TA2AMesonField<FIMPL>), MContraction);
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@ -331,29 +344,25 @@ void TA2AMesonField<FImpl>::execute(void)
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makeFileDir(filename(0, 0), env().getGrid());
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#ifdef MF_PARALLEL_IO
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env().getGrid()->Barrier();
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nodeFile_.clear();
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nodeIo_.clear();
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for(int f = myRank; f < nmom*ngamma; f += nRank)
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{
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std::pair<unsigned int, unsigned int> file;
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const unsigned int m = f/ngamma, g = f % ngamma;
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IoHelper h;
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file.first = f/ngamma;
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file.second = f % ngamma;
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nodeFile_.push_back(file);
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h.io = MatrixIo(filename(m, g), ioname(m, g), nt, N_i, N_j, block);
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for (auto pmu: mom_[m])
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{
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h.metadata.momentum.push_back(pmu);
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}
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h.metadata.gamma = gamma_[g];
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h.offset = (m*ngamma + g)*nt*block*block;
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nodeIo_.push_back(h);
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}
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// parallel IO
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for (auto &f: nodeFile_)
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for (auto &h: nodeIo_)
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{
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auto m = f.first, g = f.second;
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if ((i == 0) and (j == 0))
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{
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startTimer("IO: file creation");
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initFile(m, g);
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stopTimer("IO: file creation");
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}
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startTimer("IO: write block");
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saveBlock(mfBlock, m, g, i, j);
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stopTimer("IO: write block");
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saveBlock(mfBlock.data(), h, i, j);
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}
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env().getGrid()->Barrier();
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#else
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@ -361,21 +370,16 @@ void TA2AMesonField<FImpl>::execute(void)
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for(int m = 0; m < nmom; m++)
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for(int g = 0; g < ngamma; g++)
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{
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if ((i == 0) and (j == 0))
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IoHelper h;
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h.io = MatrixIo(filename(m, g), ioname(m, g), nt, N_i, N_j, block);
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for (auto pmu: mom_[m])
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{
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startTimer("IO: file creation");
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if (env().getGrid()->IsBoss())
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{
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initFile(m, g);
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}
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stopTimer("IO: file creation");
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h.metadata.momentum.push_back(pmu);
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}
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startTimer("IO: write block");
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if (env().getGrid()->IsBoss())
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{
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saveBlock(mfBlock, m, g, i, j);
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}
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stopTimer("IO: write block");
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h.metadata.gamma = gamma_[g];
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h.offset = (m*ngamma + g)*nt*block*block;
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saveBlock(mfBlock.data(), h, i, j);
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}
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#endif
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stopTimer("IO: total");
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@ -412,71 +416,18 @@ std::string TA2AMesonField<FImpl>::filename(unsigned int m, unsigned int g) cons
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}
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template <typename FImpl>
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void TA2AMesonField<FImpl>::initFile(unsigned int m, unsigned int g)
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{
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#ifdef HAVE_HDF5
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std::string f = filename(m, g);
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auto &v = envGet(std::vector<FermionField>, par().v);
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auto &w = envGet(std::vector<FermionField>, par().w);
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int nt = env().getDim().back();
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int N_i = w.size();
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int N_j = v.size();
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Hdf5Writer writer(f);
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std::vector<hsize_t> dim = {static_cast<hsize_t>(nt),
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static_cast<hsize_t>(N_i),
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static_cast<hsize_t>(N_j)},
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chunk = {static_cast<hsize_t>(nt),
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static_cast<hsize_t>(par().block),
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static_cast<hsize_t>(par().block)};
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H5NS::DataSpace dataspace(dim.size(), dim.data());
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H5NS::DataSet dataset;
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H5NS::DSetCreatPropList plist;
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push(writer, ioname(m, g));
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write(writer, "momentum", mom_[m]);
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write(writer, "gamma", gamma_[g]);
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auto &group = writer.getGroup();
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plist.setChunk(chunk.size(), chunk.data());
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dataset = group.createDataSet("mesonField", Hdf5Type<MF_IO_TYPE>::type(),
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dataspace, plist);
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#else
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HADRONS_ERROR(Implementation, "meson field I/O needs HDF5 library");
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#endif
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}
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template <typename FImpl>
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void TA2AMesonField<FImpl>::saveBlock(const MesonFieldIo &mf,
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unsigned int m, unsigned int g,
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void TA2AMesonField<FImpl>::saveBlock(MF_IO_TYPE *data, IoHelper &h,
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unsigned int i, unsigned int j)
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{
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#ifdef HAVE_HDF5
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std::string f = filename(m, g);
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Hdf5Reader reader(f);
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hsize_t nt = mf.dimension(2),
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Ni = mf.dimension(3),
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Nj = mf.dimension(4);
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std::vector<hsize_t> count = {nt, Ni, Nj},
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offset = {0, static_cast<hsize_t>(i),
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static_cast<hsize_t>(j)},
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stride = {1, 1, 1},
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block = {1, 1, 1};
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H5NS::DataSpace memspace(count.size(), count.data()), dataspace;
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H5NS::DataSet dataset;
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size_t shift;
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push(reader, ioname(m, g));
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auto &group = reader.getGroup();
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dataset = group.openDataSet("mesonField");
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dataspace = dataset.getSpace();
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dataspace.selectHyperslab(H5S_SELECT_SET, count.data(), offset.data(),
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stride.data(), block.data());
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shift = (m*mf.dimension(1) + g)*nt*Ni*Nj;
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dataset.write(mf.data() + shift, Hdf5Type<MF_IO_TYPE>::type(), memspace,
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dataspace);
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#else
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HADRONS_ERROR(Implementation, "meson field I/O needs HDF5 library");
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#endif
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if ((i == 0) and (j == 0))
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{
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startTimer("IO: file creation");
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h.io.initFile(h.metadata);
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stopTimer("IO: file creation");
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}
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startTimer("IO: write block");
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h.io.saveBlock(data + h.offset, i, j);
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stopTimer("IO: write block");
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}
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END_MODULE_NAMESPACE
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