From bc08d8a6b8ddf812433a3ec84a0e0642b4bbf91a Mon Sep 17 00:00:00 2001 From: Sterling Harper Date: Thu, 12 Dec 2019 17:24:03 -0500 Subject: [PATCH] Explicitly name lowlevel HDF5 read/write dataset --- include/openmc/hdf5_interface.h | 99 +++++++++++++++++++-------------- src/hdf5_interface.cpp | 53 +++++++++++------- src/state_point.cpp | 2 +- 3 files changed, 90 insertions(+), 64 deletions(-) diff --git a/include/openmc/hdf5_interface.h b/include/openmc/hdf5_interface.h index ee3419fa22..72eaa39368 100644 --- a/include/openmc/hdf5_interface.h +++ b/include/openmc/hdf5_interface.h @@ -26,13 +26,17 @@ namespace openmc { //============================================================================== void read_attr(hid_t obj_id, const char* name, hid_t mem_type_id, - void* buffer); + void* buffer); + void write_attr(hid_t obj_id, int ndim, const hsize_t* dims, const char* name, - hid_t mem_type_id, const void* buffer); -void read_dataset(hid_t obj_id, const char* name, hid_t mem_type_id, - void* buffer, bool indep); -void write_dataset(hid_t group_id, int ndim, const hsize_t* dims, const char* name, - hid_t mem_type_id, const void* buffer, bool indep); + hid_t mem_type_id, const void* buffer); + +void read_dataset_lowlevel(hid_t obj_id, const char* name, hid_t mem_type_id, + void* buffer, bool indep); + +void write_dataset_lowlevel(hid_t group_id, int ndim, const hsize_t* dims, + const char* name, hid_t mem_type_id, const void* buffer, bool indep); + bool using_mpio_device(hid_t obj_id); //============================================================================== @@ -86,34 +90,32 @@ extern "C" { void read_attr_string(hid_t obj_id, const char* name, size_t slen, char* buffer); void read_complex(hid_t obj_id, const char* name, - std::complex* buffer, bool indep); - void read_double(hid_t obj_id, const char* name, double* buffer, - bool indep); - void read_int(hid_t obj_id, const char* name, int* buffer, - bool indep); + std::complex* buffer, bool indep); + void read_double(hid_t obj_id, const char* name, double* buffer, bool indep); + void read_int(hid_t obj_id, const char* name, int* buffer, bool indep); void read_llong(hid_t obj_id, const char* name, long long* buffer, - bool indep); - void read_string(hid_t obj_id, const char* name, size_t slen, - char* buffer, bool indep); + bool indep); + void read_string(hid_t obj_id, const char* name, size_t slen, char* buffer, + bool indep); - void read_tally_results(hid_t group_id, hsize_t n_filter, - hsize_t n_score, double* results); + void read_tally_results(hid_t group_id, hsize_t n_filter, hsize_t n_score, + double* results); void write_attr_double(hid_t obj_id, int ndim, const hsize_t* dims, - const char* name, const double* buffer); + const char* name, const double* buffer); void write_attr_int(hid_t obj_id, int ndim, const hsize_t* dims, - const char* name, const int* buffer); + const char* name, const int* buffer); void write_attr_string(hid_t obj_id, const char* name, const char* buffer); void write_double(hid_t group_id, int ndim, const hsize_t* dims, - const char* name, const double* buffer, bool indep); + const char* name, const double* buffer, bool indep); void write_int(hid_t group_id, int ndim, const hsize_t* dims, - const char* name, const int* buffer, bool indep); + const char* name, const int* buffer, bool indep); void write_llong(hid_t group_id, int ndim, const hsize_t* dims, - const char* name, const long long* buffer, bool indep); + const char* name, const long long* buffer, bool indep); void write_string(hid_t group_id, int ndim, const hsize_t* dims, size_t slen, - const char* name, char const* buffer, bool indep); + const char* name, char const* buffer, bool indep); void write_tally_results(hid_t group_id, hsize_t n_filter, hsize_t n_score, - const double* results); + const double* results); } // extern "C" //============================================================================== @@ -233,7 +235,7 @@ template inline std::enable_if_t>::value> read_dataset(hid_t obj_id, const char* name, T& buffer, bool indep=false) { - read_dataset(obj_id, name, H5TypeMap::type_id, &buffer, indep); + read_dataset_lowlevel(obj_id, name, H5TypeMap::type_id, &buffer, indep); } // overload for std::string @@ -251,9 +253,11 @@ read_dataset(hid_t obj_id, const char* name, std::string& str, bool indep=false) // array version template inline void -read_dataset(hid_t dset, const char* name, std::array& buffer, bool indep=false) +read_dataset(hid_t dset, const char* name, std::array& buffer, + bool indep=false) { - read_dataset(dset, name, H5TypeMap::type_id, buffer.data(), indep); + read_dataset_lowlevel(dset, name, H5TypeMap::type_id, buffer.data(), + indep); } // vector version @@ -267,11 +271,13 @@ void read_dataset(hid_t dset, std::vector& vec, bool indep=false) vec.resize(shape[0]); // Read data into vector - read_dataset(dset, nullptr, H5TypeMap::type_id, vec.data(), indep); + read_dataset_lowlevel(dset, nullptr, H5TypeMap::type_id, vec.data(), + indep); } template -void read_dataset(hid_t obj_id, const char* name, std::vector& vec, bool indep=false) +void read_dataset(hid_t obj_id, const char* name, std::vector& vec, + bool indep=false) { hid_t dset = open_dataset(obj_id, name); read_dataset(dset, vec, indep); @@ -291,14 +297,17 @@ void read_dataset(hid_t dset, xt::xarray& arr, bool indep=false) arr.resize(shape); // Read data from attribute - read_dataset(dset, nullptr, H5TypeMap::type_id, arr.data(), indep); + read_dataset_lowlevel(dset, nullptr, H5TypeMap::type_id, arr.data(), + indep); } template<> -void read_dataset(hid_t dset, xt::xarray>& arr, bool indep); +void read_dataset(hid_t dset, xt::xarray>& arr, + bool indep); template -void read_dataset(hid_t obj_id, const char* name, xt::xarray& arr, bool indep=false) +void read_dataset(hid_t obj_id, const char* name, xt::xarray& arr, + bool indep=false) { // Open dataset and read array hid_t dset = open_dataset(obj_id, name); @@ -308,7 +317,8 @@ void read_dataset(hid_t obj_id, const char* name, xt::xarray& arr, bool indep template -void read_dataset(hid_t obj_id, const char* name, xt::xtensor& arr, bool indep=false) +void read_dataset(hid_t obj_id, const char* name, xt::xtensor& arr, + bool indep=false) { // Open dataset and read array hid_t dset = open_dataset(obj_id, name); @@ -346,7 +356,7 @@ read_dataset(hid_t obj_id, const char* name, Position& r, bool indep=false) template inline void read_dataset_as_shape(hid_t obj_id, const char* name, - xt::xtensor& arr, bool indep=false) + xt::xtensor& arr, bool indep=false) { hid_t dset = open_dataset(obj_id, name); @@ -357,7 +367,8 @@ inline void read_dataset_as_shape(hid_t obj_id, const char* name, std::vector buffer(size); // Read data from attribute - read_dataset(dset, nullptr, H5TypeMap::type_id, buffer.data(), indep); + read_dataset_lowlevel(dset, nullptr, H5TypeMap::type_id, buffer.data(), + indep); // Adapt into xarray arr = xt::adapt(buffer, arr.shape()); @@ -367,8 +378,8 @@ inline void read_dataset_as_shape(hid_t obj_id, const char* name, template -inline void read_nd_vector(hid_t obj_id, const char* name, xt::xtensor& result, - bool must_have=false) +inline void read_nd_vector(hid_t obj_id, const char* name, + xt::xtensor& result, bool must_have=false) { if (object_exists(obj_id, name)) { read_dataset_as_shape(obj_id, name, result, true); @@ -431,7 +442,8 @@ template inline std::enable_if_t>::value> write_dataset(hid_t obj_id, const char* name, T buffer) { - write_dataset(obj_id, 0, nullptr, name, H5TypeMap::type_id, &buffer, false); + write_dataset_lowlevel(obj_id, 0, nullptr, name, H5TypeMap::type_id, + &buffer, false); } inline void @@ -444,11 +456,13 @@ template inline void write_dataset(hid_t obj_id, const char* name, const std::array& buffer) { hsize_t dims[] {N}; - write_dataset(obj_id, 1, dims, name, H5TypeMap::type_id, buffer.data(), false); + write_dataset_lowlevel(obj_id, 1, dims, name, H5TypeMap::type_id, + buffer.data(), false); } inline void -write_dataset(hid_t obj_id, const char* name, const std::vector& buffer) +write_dataset(hid_t obj_id, const char* name, + const std::vector& buffer) { auto n {buffer.size()}; hsize_t dims[] {n}; @@ -477,7 +491,8 @@ template inline void write_dataset(hid_t obj_id, const char* name, const std::vector& buffer) { hsize_t dims[] {buffer.size()}; - write_dataset(obj_id, 1, dims, name, H5TypeMap::type_id, buffer.data(), false); + write_dataset_lowlevel(obj_id, 1, dims, name, H5TypeMap::type_id, + buffer.data(), false); } // Template for xarray, xtensor, etc. @@ -487,8 +502,8 @@ write_dataset(hid_t obj_id, const char* name, const xt::xcontainer& arr) using T = typename D::value_type; auto s = arr.shape(); std::vector dims {s.cbegin(), s.cend()}; - write_dataset(obj_id, dims.size(), dims.data(), name, H5TypeMap::type_id, - arr.data(), false); + write_dataset_lowlevel(obj_id, dims.size(), dims.data(), name, + H5TypeMap::type_id, arr.data(), false); } inline void diff --git a/src/hdf5_interface.cpp b/src/hdf5_interface.cpp index b1a90cb8f7..d4434225a2 100644 --- a/src/hdf5_interface.cpp +++ b/src/hdf5_interface.cpp @@ -49,7 +49,8 @@ get_shape(hid_t obj_id, hsize_t* dims) } else if (type == H5I_ATTR) { dspace = H5Aget_space(obj_id); } else { - throw std::runtime_error{"Expected dataset or attribute in call to get_shape."}; + throw std::runtime_error{ + "Expected dataset or attribute in call to get_shape."}; } H5Sget_simple_extent_dims(dspace, dims, nullptr); H5Sclose(dspace); @@ -74,7 +75,8 @@ std::vector object_shape(hid_t obj_id) } else if (type == H5I_ATTR) { dspace = H5Aget_space(obj_id); } else { - throw std::runtime_error{"Expected dataset or attribute in call to object_shape."}; + throw std::runtime_error{ + "Expected dataset or attribute in call to object_shape."}; } int n = H5Sget_simple_extent_ndims(dspace); @@ -471,8 +473,8 @@ read_attr_string(hid_t obj_id, const char* name, size_t slen, char* buffer) void -read_dataset(hid_t obj_id, const char* name, hid_t mem_type_id, - void* buffer, bool indep) +read_dataset_lowlevel(hid_t obj_id, const char* name, hid_t mem_type_id, + void* buffer, bool indep) { hid_t dset = obj_id; if (name) dset = open_dataset(obj_id, name); @@ -520,26 +522,27 @@ void read_dataset(hid_t dset, xt::xarray>& arr, bool indep) void read_double(hid_t obj_id, const char* name, double* buffer, bool indep) { - read_dataset(obj_id, name, H5T_NATIVE_DOUBLE, buffer, indep); + read_dataset_lowlevel(obj_id, name, H5T_NATIVE_DOUBLE, buffer, indep); } void read_int(hid_t obj_id, const char* name, int* buffer, bool indep) { - read_dataset(obj_id, name, H5T_NATIVE_INT, buffer, indep); + read_dataset_lowlevel(obj_id, name, H5T_NATIVE_INT, buffer, indep); } void read_llong(hid_t obj_id, const char* name, long long* buffer, bool indep) { - read_dataset(obj_id, name, H5T_NATIVE_LLONG, buffer, indep); + read_dataset_lowlevel(obj_id, name, H5T_NATIVE_LLONG, buffer, indep); } void -read_string(hid_t obj_id, const char* name, size_t slen, char* buffer, bool indep) +read_string(hid_t obj_id, const char* name, size_t slen, char* buffer, + bool indep) { // Create datatype for a string hid_t datatype = H5Tcopy(H5T_C_S1); @@ -548,7 +551,7 @@ read_string(hid_t obj_id, const char* name, size_t slen, char* buffer, bool inde H5Tset_strpad(datatype, H5T_STR_NULLPAD); // Read data into buffer - read_dataset(obj_id, name, datatype, buffer, indep); + read_dataset_lowlevel(obj_id, name, datatype, buffer, indep); // Free resources H5Tclose(datatype); @@ -556,7 +559,8 @@ read_string(hid_t obj_id, const char* name, size_t slen, char* buffer, bool inde void -read_complex(hid_t obj_id, const char* name, std::complex* buffer, bool indep) +read_complex(hid_t obj_id, const char* name, std::complex* buffer, + bool indep) { // Create compound datatype for complex numbers struct complex_t { @@ -569,7 +573,7 @@ read_complex(hid_t obj_id, const char* name, std::complex* buffer, bool H5Tinsert(complex_id, "i", HOFFSET(complex_t, im), H5T_NATIVE_DOUBLE); // Read data - read_dataset(obj_id, name, complex_id, buffer, indep); + read_dataset_lowlevel(obj_id, name, complex_id, buffer, indep); // Free resources H5Tclose(complex_id); @@ -577,7 +581,8 @@ read_complex(hid_t obj_id, const char* name, std::complex* buffer, bool void -read_tally_results(hid_t group_id, hsize_t n_filter, hsize_t n_score, double* results) +read_tally_results(hid_t group_id, hsize_t n_filter, hsize_t n_score, + double* results) { // Create dataspace for hyperslab in memory hsize_t dims[] {n_filter, n_score, 3}; @@ -654,8 +659,8 @@ write_attr_string(hid_t obj_id, const char* name, const char* buffer) void -write_dataset(hid_t group_id, int ndim, const hsize_t* dims, const char* name, - hid_t mem_type_id, const void* buffer, bool indep) +write_dataset_lowlevel(hid_t group_id, int ndim, const hsize_t* dims, + const char* name, hid_t mem_type_id, const void* buffer, bool indep) { // If array is given, create a simple dataspace. Otherwise, create a scalar // datascape. @@ -696,7 +701,8 @@ void write_double(hid_t group_id, int ndim, const hsize_t* dims, const char* name, const double* buffer, bool indep) { - write_dataset(group_id, ndim, dims, name, H5T_NATIVE_DOUBLE, buffer, indep); + write_dataset_lowlevel(group_id, ndim, dims, name, H5T_NATIVE_DOUBLE, buffer, + indep); } @@ -704,7 +710,8 @@ void write_int(hid_t group_id, int ndim, const hsize_t* dims, const char* name, const int* buffer, bool indep) { - write_dataset(group_id, ndim, dims, name, H5T_NATIVE_INT, buffer, indep); + write_dataset_lowlevel(group_id, ndim, dims, name, H5T_NATIVE_INT, buffer, + indep); } @@ -712,7 +719,8 @@ void write_llong(hid_t group_id, int ndim, const hsize_t* dims, const char* name, const long long* buffer, bool indep) { - write_dataset(group_id, ndim, dims, name, H5T_NATIVE_LLONG, buffer, indep); + write_dataset_lowlevel(group_id, ndim, dims, name, H5T_NATIVE_LLONG, buffer, + indep); } @@ -725,7 +733,7 @@ write_string(hid_t group_id, int ndim, const hsize_t* dims, size_t slen, hid_t datatype = H5Tcopy(H5T_C_S1); H5Tset_size(datatype, slen); - write_dataset(group_id, ndim, dims, name, datatype, buffer, indep); + write_dataset_lowlevel(group_id, ndim, dims, name, datatype, buffer, indep); // Free resources H5Tclose(datatype); @@ -734,14 +742,17 @@ write_string(hid_t group_id, int ndim, const hsize_t* dims, size_t slen, void -write_string(hid_t group_id, const char* name, const std::string& buffer, bool indep) +write_string(hid_t group_id, const char* name, const std::string& buffer, + bool indep) { - write_string(group_id, 0, nullptr, buffer.length(), name, buffer.c_str(), indep); + write_string(group_id, 0, nullptr, buffer.length(), name, buffer.c_str(), + indep); } void -write_tally_results(hid_t group_id, hsize_t n_filter, hsize_t n_score, const double* results) +write_tally_results(hid_t group_id, hsize_t n_filter, hsize_t n_score, + const double* results) { // Set dimensions of sum/sum_sq hyperslab to store hsize_t count[] {n_filter, n_score, 2}; diff --git a/src/state_point.cpp b/src/state_point.cpp index 4c159c1678..31454ec4df 100644 --- a/src/state_point.cpp +++ b/src/state_point.cpp @@ -418,7 +418,7 @@ void load_state_point() if (mpi::master) { #endif // Read global tally data - read_dataset(file_id, "global_tallies", H5T_NATIVE_DOUBLE, + read_dataset_lowlevel(file_id, "global_tallies", H5T_NATIVE_DOUBLE, simulation::global_tallies.data(), false); // Check if tally results are present