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Hadrons: meson field IO fix

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This commit is contained in:
Antonin Portelli 2018-09-21 18:16:01 +01:00
parent c012899ed5
commit c632455129
2 changed files with 36 additions and 26 deletions
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26
Hadrons/A2AMatrix.hpp
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@ -39,13 +39,14 @@ public:
A2AMatrixIo(void) = default; A2AMatrixIo(void) = default;
A2AMatrixIo(std::string filename, std::string dataname, A2AMatrixIo(std::string filename, std::string dataname,
const unsigned int nt, const unsigned int ni, const unsigned int nt, const unsigned int ni,
const unsigned int nj, const unsigned int blockSize); const unsigned int nj);
~A2AMatrixIo(void) = default; ~A2AMatrixIo(void) = default;
void initFile(const MetadataType &d); void initFile(const MetadataType &d, const unsigned int chunkSize);
void saveBlock(const T *data, const unsigned int i, const unsigned int j); void saveBlock(const T *data, const unsigned int i, const unsigned int j,
const unsigned int blockSizei, const unsigned int blockSizej);
private: private:
std::string filename_, dataname_; std::string filename_, dataname_;
unsigned int nt_, ni_, nj_, blockSize_; unsigned int nt_, ni_, nj_;
}; };
template <typename T, typename MetadataType> template <typename T, typename MetadataType>
@ -53,22 +54,21 @@ A2AMatrixIo<T, MetadataType>::A2AMatrixIo(std::string filename,
std::string dataname, std::string dataname,
const unsigned int nt, const unsigned int nt,
const unsigned int ni, const unsigned int ni,
const unsigned int nj, const unsigned int nj)
const unsigned int blockSize)
: filename_(filename), dataname_(dataname) : filename_(filename), dataname_(dataname)
, nt_(nt), ni_(ni), nj_(nj), blockSize_(blockSize) , nt_(nt), ni_(ni), nj_(nj)
{} {}
template <typename T, typename MetadataType> template <typename T, typename MetadataType>
void A2AMatrixIo<T, MetadataType>::initFile(const MetadataType &d) void A2AMatrixIo<T, MetadataType>::initFile(const MetadataType &d, const unsigned int chunkSize)
{ {
#ifdef HAVE_HDF5 #ifdef HAVE_HDF5
std::vector<hsize_t> dim = {static_cast<hsize_t>(nt_), std::vector<hsize_t> dim = {static_cast<hsize_t>(nt_),
static_cast<hsize_t>(ni_), static_cast<hsize_t>(ni_),
static_cast<hsize_t>(nj_)}, static_cast<hsize_t>(nj_)},
chunk = {static_cast<hsize_t>(nt_), chunk = {static_cast<hsize_t>(nt_),
static_cast<hsize_t>(blockSize_), static_cast<hsize_t>(chunkSize),
static_cast<hsize_t>(blockSize_)}; static_cast<hsize_t>(chunkSize)};
H5NS::DataSpace dataspace(dim.size(), dim.data()); H5NS::DataSpace dataspace(dim.size(), dim.data());
H5NS::DataSet dataset; H5NS::DataSet dataset;
H5NS::DSetCreatPropList plist; H5NS::DSetCreatPropList plist;
@ -94,11 +94,13 @@ void A2AMatrixIo<T, MetadataType>::initFile(const MetadataType &d)
template <typename T, typename MetadataType> template <typename T, typename MetadataType>
void A2AMatrixIo<T, MetadataType>::saveBlock(const T *data, void A2AMatrixIo<T, MetadataType>::saveBlock(const T *data,
const unsigned int i, const unsigned int i,
const unsigned int j) const unsigned int j,
const unsigned int blockSizei,
const unsigned int blockSizej)
{ {
#ifdef HAVE_HDF5 #ifdef HAVE_HDF5
Hdf5Reader reader(filename_); Hdf5Reader reader(filename_);
std::vector<hsize_t> count = {nt_, blockSize_, blockSize_}, std::vector<hsize_t> count = {nt_, blockSizei, blockSizej},
offset = {0, static_cast<hsize_t>(i), offset = {0, static_cast<hsize_t>(i),
static_cast<hsize_t>(j)}, static_cast<hsize_t>(j)},
stride = {1, 1, 1}, stride = {1, 1, 1},

36
Hadrons/Modules/MContraction/A2AMesonField.hpp
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@ -85,6 +85,7 @@ public:
MatrixIo io; MatrixIo io;
A2AMesonFieldMetadata metadata; A2AMesonFieldMetadata metadata;
size_t offset; size_t offset;
unsigned int i, j, blockSizei, blockSizej;
}; };
public: public:
// constructor // constructor
@ -100,9 +101,9 @@ public:
virtual void execute(void); virtual void execute(void);
private: private:
// IO // IO
std::string ioname(unsigned int m, unsigned int g) const; std::string ioname(const unsigned int m, const unsigned int g) const;
std::string filename(unsigned int m, 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, unsigned int i, unsigned int j); void saveBlock(const MF_IO_TYPE *data, IoHelper &h);
private: private:
bool hasPhase_{false}; bool hasPhase_{false};
std::string momphName_; std::string momphName_;
@ -350,19 +351,23 @@ void TA2AMesonField<FImpl>::execute(void)
const unsigned int m = f/ngamma, g = f % ngamma; const unsigned int m = f/ngamma, g = f % ngamma;
IoHelper h; 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]) for (auto pmu: mom_[m])
{ {
h.metadata.momentum.push_back(pmu); h.metadata.momentum.push_back(pmu);
} }
h.metadata.gamma = gamma_[g]; 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); nodeIo_.push_back(h);
} }
// parallel IO // parallel IO
for (auto &h: nodeIo_) for (auto &h: nodeIo_)
{ {
saveBlock(mfBlock.data(), h, i, j); saveBlock(mfBlock.data(), h);
} }
env().getGrid()->Barrier(); env().getGrid()->Barrier();
#else #else
@ -372,14 +377,18 @@ void TA2AMesonField<FImpl>::execute(void)
{ {
IoHelper h; 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]) for (auto pmu: mom_[m])
{ {
h.metadata.momentum.push_back(pmu); h.metadata.momentum.push_back(pmu);
} }
h.metadata.gamma = gamma_[g]; h.metadata.gamma = gamma_[g];
h.offset = (m*ngamma + g)*nt*block*block; h.i = i;
saveBlock(mfBlock.data(), h, i, j); 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 #endif
stopTimer("IO: total"); stopTimer("IO: total");
@ -416,17 +425,16 @@ std::string TA2AMesonField<FImpl>::filename(unsigned int m, unsigned int g) cons
} }
template <typename FImpl> template <typename FImpl>
void TA2AMesonField<FImpl>::saveBlock(const MF_IO_TYPE *data, IoHelper &h, void TA2AMesonField<FImpl>::saveBlock(const MF_IO_TYPE *data, IoHelper &h)
unsigned int i, unsigned int j)
{ {
if ((i == 0) and (j == 0)) if ((h.i == 0) and (h.j == 0))
{ {
startTimer("IO: file creation"); startTimer("IO: file creation");
h.io.initFile(h.metadata); h.io.initFile(h.metadata, par().block);
stopTimer("IO: file creation"); stopTimer("IO: file creation");
} }
startTimer("IO: write block"); 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"); stopTimer("IO: write block");
} }