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Convert HDF5 write_string to C++
This commit is contained in:
Paul Romano
parent
aa5a5cf7db
commit
2760bce679
4 changed files with 56 additions and 95 deletions
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@ -164,6 +164,15 @@ module hdf5_interface
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integer(C_LONG_LONG), intent(in) :: buffer(*)
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logical(C_BOOL), intent(in) :: indep
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end subroutine write_llong_c
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subroutine write_string_c(group_id, name, buffer, indep) &
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bind(C, name='write_string')
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import HID_T, HSIZE_T, C_CHAR, C_BOOL
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integer(HID_T), value :: group_id
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character(kind=C_CHAR), intent(in) :: name(*)
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character(kind=C_CHAR), intent(in) :: buffer(*)
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logical(C_BOOL), intent(in) :: indep
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end subroutine write_string_c
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end interface
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contains
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@ -888,58 +897,12 @@ contains
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character(*), intent(in), target :: buffer ! read data to here
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logical, intent(in), optional :: indep ! independent I/O
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integer :: hdf5_err
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integer :: data_xfer_mode
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#ifdef PHDF5
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integer(HID_T) :: plist ! property list
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#endif
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integer(HID_T) :: dset ! data set handle
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integer(HID_T) :: dspace ! data or file space handle
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integer(HID_T) :: filetype
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integer(SIZE_T) :: i, n
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character(kind=C_CHAR), allocatable, target :: temp_buffer(:)
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type(c_ptr) :: f_ptr
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logical(C_BOOL) :: indep_
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! Set up collective vs. independent I/O
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data_xfer_mode = H5FD_MPIO_COLLECTIVE_F
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if (present(indep)) then
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if (indep) data_xfer_mode = H5FD_MPIO_INDEPENDENT_F
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end if
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indep_ = .false.
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if (present(indep)) indep_ = indep
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! Create datatype for HDF5 file based on C char
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n = len_trim(buffer)
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if (n > 0) then
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call h5tcopy_f(H5T_C_S1, filetype, hdf5_err)
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call h5tset_size_f(filetype, n, hdf5_err)
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! Create dataspace/dataset
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call h5screate_f(H5S_SCALAR_F, dspace, hdf5_err)
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call h5dcreate_f(group_id, trim(name), filetype, dspace, dset, hdf5_err)
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! Copy string to temporary buffer
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allocate(temp_buffer(n))
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do i = 1, n
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temp_buffer(i) = buffer(i:i)
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end do
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! Get pointer to start of string
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f_ptr = c_loc(temp_buffer(1))
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if (using_mpio_device(group_id)) then
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#ifdef PHDF5
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call h5pcreate_f(H5P_DATASET_XFER_F, plist, hdf5_err)
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call h5pset_dxpl_mpio_f(plist, data_xfer_mode, hdf5_err)
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call h5dwrite_f(dset, filetype, f_ptr, hdf5_err, xfer_prp=plist)
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call h5pclose_f(plist, hdf5_err)
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#endif
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else
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call h5dwrite_f(dset, filetype, f_ptr, hdf5_err)
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end if
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call h5dclose_f(dset, hdf5_err)
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call h5sclose_f(dspace, hdf5_err)
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call h5tclose_f(filetype, hdf5_err)
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end if
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call write_string_c(group_id, to_c_string(name), to_c_string(buffer), indep_)
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end subroutine write_string
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!===============================================================================
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@ -5,6 +5,7 @@
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#include "hdf5_hl.h"
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#include <array>
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#include <cstring>
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#include <string>
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#include <sstream>
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@ -160,7 +161,7 @@ open_group(hid_t group_id, const char* name)
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void
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read_array(hid_t obj_id, const char* name, hid_t mem_type_id,
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read_data(hid_t obj_id, const char* name, hid_t mem_type_id,
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void* buffer, bool indep)
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{
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hid_t dset = obj_id;
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@ -190,26 +191,26 @@ read_array(hid_t obj_id, const char* name, hid_t mem_type_id,
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void
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read_double(hid_t obj_id, const char* name, double* buffer, bool indep)
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{
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read_array(obj_id, name, H5T_NATIVE_DOUBLE, buffer, indep);
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read_data(obj_id, name, H5T_NATIVE_DOUBLE, buffer, indep);
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}
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void
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read_int(hid_t obj_id, const char* name, int* buffer, bool indep)
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{
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read_array(obj_id, name, H5T_NATIVE_INT, buffer, indep);
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read_data(obj_id, name, H5T_NATIVE_INT, buffer, indep);
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}
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void
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read_llong(hid_t obj_id, const char* name, long long* buffer, bool indep)
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{
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read_array(obj_id, name, H5T_NATIVE_LLONG, buffer, indep);
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read_data(obj_id, name, H5T_NATIVE_LLONG, buffer, indep);
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}
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void
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write_array(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
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write_data(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
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hid_t mem_type_id, const void* buffer, bool indep)
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{
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// If array is given, create a simple dataspace. Otherwise, create a scalar
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@ -251,7 +252,7 @@ void
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write_double(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
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const double* buffer, bool indep)
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{
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write_array(group_id, ndim, dims, name, H5T_NATIVE_DOUBLE, buffer, indep);
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write_data(group_id, ndim, dims, name, H5T_NATIVE_DOUBLE, buffer, indep);
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}
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@ -259,7 +260,7 @@ void
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write_int(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
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const int* buffer, bool indep)
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{
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write_array(group_id, ndim, dims, name, H5T_NATIVE_INT, buffer, indep);
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write_data(group_id, ndim, dims, name, H5T_NATIVE_INT, buffer, indep);
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}
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@ -267,34 +268,31 @@ void
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write_llong(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
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const long long* buffer, bool indep)
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{
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write_array(group_id, ndim, dims, name, H5T_NATIVE_LLONG, buffer, indep);
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write_data(group_id, ndim, dims, name, H5T_NATIVE_LLONG, buffer, indep);
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}
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void
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write_string(hid_t group_id, char const *name, char const *buffer)
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write_string(hid_t group_id, char const* name, const char* buffer, bool indep)
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{
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size_t buffer_len = strlen(buffer);
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hid_t datatype = H5Tcopy(H5T_C_S1);
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H5Tset_size(datatype, buffer_len);
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if (buffer_len > 0) {
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// Set up appropriate datatype for a fixed-length string
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hid_t datatype = H5Tcopy(H5T_C_S1);
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H5Tset_size(datatype, buffer_len);
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hid_t dataspace = H5Screate(H5S_SCALAR);
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write_data(group_id, 0, nullptr, name, datatype, buffer, indep);
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hid_t dataset = H5Dcreate(group_id, name, datatype, dataspace,
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H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
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H5Dwrite(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, buffer);
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H5Tclose(datatype);
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H5Sclose(dataspace);
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H5Dclose(dataset);
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// Free resources
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H5Tclose(datatype);
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}
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}
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void
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write_string(hid_t group_id, char const *name, const std::string &buffer)
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write_string(hid_t group_id, char const* name, const std::string& buffer, bool indep)
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{
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write_string(group_id, name, buffer.c_str());
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write_string(group_id, name, buffer.c_str(), indep);
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}
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}
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@ -41,8 +41,8 @@ write_double_1D(hid_t group_id, char const *name,
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H5Dclose(dataset);
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}
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void read_array(hid_t obj_id, const char* name, double* buffer,
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hid_t mem_type_id, bool indep);
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void read_data(hid_t obj_id, const char* name, double* buffer,
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hid_t mem_type_id, bool indep);
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extern "C" void read_double(hid_t obj_id, const char* name, double* buffer,
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bool indep);
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extern "C" void read_int(hid_t obj_id, const char* name, int* buffer,
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@ -50,8 +50,8 @@ extern "C" void read_int(hid_t obj_id, const char* name, int* buffer,
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extern "C" void read_llong(hid_t obj_id, const char* name, long long* buffer,
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bool indep);
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void write_array(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
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hid_t mem_type_id, const void* buffer, bool indep);
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void write_data(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
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hid_t mem_type_id, const void* buffer, bool indep);
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extern "C" void write_double(hid_t group_id, int ndim, const hsize_t* dims,
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const char* name, const double* buffer, bool indep);
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extern "C" void write_int(hid_t group_id, int ndim, const hsize_t* dims,
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@ -59,8 +59,8 @@ extern "C" void write_int(hid_t group_id, int ndim, const hsize_t* dims,
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extern "C" void write_llong(hid_t group_id, int ndim, const hsize_t* dims,
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const char* name, const long long* buffer, bool indep);
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void write_string(hid_t group_id, char const *name, char const *buffer);
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void write_string(hid_t group_id, char const *name, const std::string &buffer);
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extern "C" void write_string(hid_t group_id, char const *name, char const *buffer, bool indep);
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void write_string(hid_t group_id, char const *name, const std::string &buffer, bool indep);
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} // namespace openmc
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#endif //HDF5_INTERFACE_H
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@ -202,21 +202,21 @@ Surface::to_hdf5(hid_t group_id) const
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switch(bc) {
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case BC_TRANSMIT :
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write_string(surf_group, "boundary_type", "transmission");
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write_string(surf_group, "boundary_type", "transmission", false);
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break;
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case BC_VACUUM :
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write_string(surf_group, "boundary_type", "vacuum");
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write_string(surf_group, "boundary_type", "vacuum", false);
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break;
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case BC_REFLECT :
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write_string(surf_group, "boundary_type", "reflective");
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write_string(surf_group, "boundary_type", "reflective", false);
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break;
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case BC_PERIODIC :
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write_string(surf_group, "boundary_type", "periodic");
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write_string(surf_group, "boundary_type", "periodic", false);
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break;
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}
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if (!name.empty()) {
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write_string(surf_group, "name", name);
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write_string(surf_group, "name", name, false);
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}
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to_hdf5_inner(surf_group);
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@ -297,7 +297,7 @@ inline void SurfaceXPlane::normal(const double xyz[3], double uvw[3]) const
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void SurfaceXPlane::to_hdf5_inner(hid_t group_id) const
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{
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write_string(group_id, "type", "x-plane");
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write_string(group_id, "type", "x-plane", false);
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std::array<double, 1> coeffs {{x0}};
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write_double_1D(group_id, "coefficients", coeffs);
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}
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@ -362,7 +362,7 @@ inline void SurfaceYPlane::normal(const double xyz[3], double uvw[3]) const
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void SurfaceYPlane::to_hdf5_inner(hid_t group_id) const
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{
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write_string(group_id, "type", "y-plane");
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write_string(group_id, "type", "y-plane", false);
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std::array<double, 1> coeffs {{y0}};
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write_double_1D(group_id, "coefficients", coeffs);
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}
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@ -428,7 +428,7 @@ inline void SurfaceZPlane::normal(const double xyz[3], double uvw[3]) const
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void SurfaceZPlane::to_hdf5_inner(hid_t group_id) const
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{
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write_string(group_id, "type", "z-plane");
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write_string(group_id, "type", "z-plane", false);
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std::array<double, 1> coeffs {{z0}};
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write_double_1D(group_id, "coefficients", coeffs);
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}
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@ -489,7 +489,7 @@ SurfacePlane::normal(const double xyz[3], double uvw[3]) const
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void SurfacePlane::to_hdf5_inner(hid_t group_id) const
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{
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write_string(group_id, "type", "plane");
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write_string(group_id, "type", "plane", false);
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std::array<double, 4> coeffs {{A, B, C, D}};
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write_double_1D(group_id, "coefficients", coeffs);
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}
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@ -621,7 +621,7 @@ inline void SurfaceXCylinder::normal(const double xyz[3], double uvw[3]) const
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void SurfaceXCylinder::to_hdf5_inner(hid_t group_id) const
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{
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write_string(group_id, "type", "x-cylinder");
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write_string(group_id, "type", "x-cylinder", false);
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std::array<double, 3> coeffs {{y0, z0, r}};
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write_double_1D(group_id, "coefficients", coeffs);
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}
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@ -655,7 +655,7 @@ inline void SurfaceYCylinder::normal(const double xyz[3], double uvw[3]) const
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void SurfaceYCylinder::to_hdf5_inner(hid_t group_id) const
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{
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write_string(group_id, "type", "y-cylinder");
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write_string(group_id, "type", "y-cylinder", false);
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std::array<double, 3> coeffs {{x0, z0, r}};
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write_double_1D(group_id, "coefficients", coeffs);
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}
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@ -689,7 +689,7 @@ inline void SurfaceZCylinder::normal(const double xyz[3], double uvw[3]) const
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void SurfaceZCylinder::to_hdf5_inner(hid_t group_id) const
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{
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write_string(group_id, "type", "z-cylinder");
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write_string(group_id, "type", "z-cylinder", false);
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std::array<double, 3> coeffs {{x0, y0, r}};
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write_double_1D(group_id, "coefficients", coeffs);
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}
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@ -760,7 +760,7 @@ inline void SurfaceSphere::normal(const double xyz[3], double uvw[3]) const
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void SurfaceSphere::to_hdf5_inner(hid_t group_id) const
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{
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write_string(group_id, "type", "sphere");
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write_string(group_id, "type", "sphere", false);
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std::array<double, 4> coeffs {{x0, y0, z0, r}};
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write_double_1D(group_id, "coefficients", coeffs);
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}
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@ -877,7 +877,7 @@ inline void SurfaceXCone::normal(const double xyz[3], double uvw[3]) const
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void SurfaceXCone::to_hdf5_inner(hid_t group_id) const
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{
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write_string(group_id, "type", "x-cone");
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write_string(group_id, "type", "x-cone", false);
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std::array<double, 4> coeffs {{x0, y0, z0, r_sq}};
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write_double_1D(group_id, "coefficients", coeffs);
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}
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@ -911,7 +911,7 @@ inline void SurfaceYCone::normal(const double xyz[3], double uvw[3]) const
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void SurfaceYCone::to_hdf5_inner(hid_t group_id) const
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{
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write_string(group_id, "type", "y-cone");
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write_string(group_id, "type", "y-cone", false);
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std::array<double, 4> coeffs {{x0, y0, z0, r_sq}};
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write_double_1D(group_id, "coefficients", coeffs);
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}
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@ -945,7 +945,7 @@ inline void SurfaceZCone::normal(const double xyz[3], double uvw[3]) const
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void SurfaceZCone::to_hdf5_inner(hid_t group_id) const
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{
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write_string(group_id, "type", "z-cone");
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write_string(group_id, "type", "z-cone", false);
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std::array<double, 4> coeffs {{x0, y0, z0, r_sq}};
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write_double_1D(group_id, "coefficients", coeffs);
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}
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@ -1039,7 +1039,7 @@ SurfaceQuadric::normal(const double xyz[3], double uvw[3]) const
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void SurfaceQuadric::to_hdf5_inner(hid_t group_id) const
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{
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write_string(group_id, "type", "quadric");
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write_string(group_id, "type", "quadric", false);
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std::array<double, 10> coeffs {{A, B, C, D, E, F, G, H, J, K}};
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write_double_1D(group_id, "coefficients", coeffs);
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}
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