From c632455129bceaedeef906fadffdc359b253ff06 Mon Sep 17 00:00:00 2001 From: Antonin Portelli Date: Fri, 21 Sep 2018 18:16:01 +0100 Subject: [PATCH] Hadrons: meson field IO fix --- Hadrons/A2AMatrix.hpp | 26 +++++++------- .../Modules/MContraction/A2AMesonField.hpp | 36 +++++++++++-------- 2 files changed, 36 insertions(+), 26 deletions(-) diff --git a/Hadrons/A2AMatrix.hpp b/Hadrons/A2AMatrix.hpp index bcae395a..22eeddd1 100644 --- a/Hadrons/A2AMatrix.hpp +++ b/Hadrons/A2AMatrix.hpp @@ -39,13 +39,14 @@ public: A2AMatrixIo(void) = default; A2AMatrixIo(std::string filename, std::string dataname, const unsigned int nt, const unsigned int ni, - const unsigned int nj, const unsigned int blockSize); + const unsigned int nj); ~A2AMatrixIo(void) = default; - void initFile(const MetadataType &d); - void saveBlock(const T *data, const unsigned int i, const unsigned int j); + void initFile(const MetadataType &d, const unsigned int chunkSize); + void saveBlock(const T *data, const unsigned int i, const unsigned int j, + const unsigned int blockSizei, const unsigned int blockSizej); private: std::string filename_, dataname_; - unsigned int nt_, ni_, nj_, blockSize_; + unsigned int nt_, ni_, nj_; }; template @@ -53,22 +54,21 @@ A2AMatrixIo::A2AMatrixIo(std::string filename, std::string dataname, const unsigned int nt, const unsigned int ni, - const unsigned int nj, - const unsigned int blockSize) + const unsigned int nj) : filename_(filename), dataname_(dataname) -, nt_(nt), ni_(ni), nj_(nj), blockSize_(blockSize) +, nt_(nt), ni_(ni), nj_(nj) {} template -void A2AMatrixIo::initFile(const MetadataType &d) +void A2AMatrixIo::initFile(const MetadataType &d, const unsigned int chunkSize) { #ifdef HAVE_HDF5 std::vector dim = {static_cast(nt_), static_cast(ni_), static_cast(nj_)}, chunk = {static_cast(nt_), - static_cast(blockSize_), - static_cast(blockSize_)}; + static_cast(chunkSize), + static_cast(chunkSize)}; H5NS::DataSpace dataspace(dim.size(), dim.data()); H5NS::DataSet dataset; H5NS::DSetCreatPropList plist; @@ -94,11 +94,13 @@ void A2AMatrixIo::initFile(const MetadataType &d) template void A2AMatrixIo::saveBlock(const T *data, const unsigned int i, - const unsigned int j) + const unsigned int j, + const unsigned int blockSizei, + const unsigned int blockSizej) { #ifdef HAVE_HDF5 Hdf5Reader reader(filename_); - std::vector count = {nt_, blockSize_, blockSize_}, + std::vector count = {nt_, blockSizei, blockSizej}, offset = {0, static_cast(i), static_cast(j)}, stride = {1, 1, 1}, diff --git a/Hadrons/Modules/MContraction/A2AMesonField.hpp b/Hadrons/Modules/MContraction/A2AMesonField.hpp index 0f93a5b9..1a922b49 100644 --- a/Hadrons/Modules/MContraction/A2AMesonField.hpp +++ b/Hadrons/Modules/MContraction/A2AMesonField.hpp @@ -85,6 +85,7 @@ public: MatrixIo io; A2AMesonFieldMetadata metadata; size_t offset; + unsigned int i, j, blockSizei, blockSizej; }; public: // constructor @@ -100,9 +101,9 @@ public: virtual void execute(void); private: // IO - std::string ioname(unsigned int m, unsigned int g) const; - std::string filename(unsigned int m, unsigned int g) const; - void saveBlock(const MF_IO_TYPE *data, IoHelper &h, unsigned int i, unsigned int j); + std::string ioname(const unsigned int m, const unsigned int g) const; + std::string filename(const unsigned int m, const unsigned int g) const; + void saveBlock(const MF_IO_TYPE *data, IoHelper &h); private: bool hasPhase_{false}; std::string momphName_; @@ -350,19 +351,23 @@ void TA2AMesonField::execute(void) const unsigned int m = f/ngamma, g = f % ngamma; IoHelper h; - h.io = MatrixIo(filename(m, g), ioname(m, g), nt, N_i, N_j, block); + h.io = MatrixIo(filename(m, g), ioname(m, g), nt, N_i, N_j); for (auto pmu: mom_[m]) { h.metadata.momentum.push_back(pmu); } h.metadata.gamma = gamma_[g]; - h.offset = (m*ngamma + g)*nt*block*block; + h.i = i; + h.j = j; + h.blockSizei = mfBlock.dimension(3); + h.blockSizej = mfBlock.dimension(4); + h.offset = (m*ngamma + g)*nt*h.blockSizei*h.blockSizej; nodeIo_.push_back(h); } // parallel IO for (auto &h: nodeIo_) { - saveBlock(mfBlock.data(), h, i, j); + saveBlock(mfBlock.data(), h); } env().getGrid()->Barrier(); #else @@ -372,14 +377,18 @@ void TA2AMesonField::execute(void) { IoHelper h; - h.io = MatrixIo(filename(m, g), ioname(m, g), nt, N_i, N_j, block); + h.io = MatrixIo(filename(m, g), ioname(m, g), nt, N_i, N_j); for (auto pmu: mom_[m]) { h.metadata.momentum.push_back(pmu); } h.metadata.gamma = gamma_[g]; - h.offset = (m*ngamma + g)*nt*block*block; - saveBlock(mfBlock.data(), h, i, j); + h.i = i; + h.j = j; + h.blockSizei = mfBlock.dimension(3); + h.blockSizej = mfBlock.dimension(4); + h.offset = (m*ngamma + g)*nt*h.blockSizei*h.blockSizej; + saveBlock(mfBlock.data(), h); } #endif stopTimer("IO: total"); @@ -416,17 +425,16 @@ std::string TA2AMesonField::filename(unsigned int m, unsigned int g) cons } template -void TA2AMesonField::saveBlock(const MF_IO_TYPE *data, IoHelper &h, - unsigned int i, unsigned int j) +void TA2AMesonField::saveBlock(const MF_IO_TYPE *data, IoHelper &h) { - if ((i == 0) and (j == 0)) + if ((h.i == 0) and (h.j == 0)) { startTimer("IO: file creation"); - h.io.initFile(h.metadata); + h.io.initFile(h.metadata, par().block); stopTimer("IO: file creation"); } startTimer("IO: write block"); - h.io.saveBlock(data + h.offset, i, j); + h.io.saveBlock(data + h.offset, h.i, h.j, h.blockSizei, h.blockSizej); stopTimer("IO: write block"); }