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Convert HDF5 read/write_tally_results (and fix attribute bug)

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This commit is contained in:
Paul Romano 2018-04-19 14:44:10 -05:00
parent f78e6e0fc3
commit 4fdfd51ab9
4 changed files with 84 additions and 58 deletions
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4
src/hdf5_interface.F90
View file

@ -1342,7 +1342,7 @@ contains
! Allocate a C char array to get strings
n = attribute_typesize(obj_id, to_c_string(name))
m = size(buffer)
allocate(buffer_(n*m))
allocate(buffer_((n+1)*m))
! Read attribute
call read_attr_string_c(obj_id, to_c_string(name), n, buffer_)
@ -1351,7 +1351,7 @@ contains
do i = 1, m
buffer(i) = ''
do j = 1, n
k = (i-1)*n + j
k = (i-1)*(n+1) + j
if (buffer_(k) == C_NULL_CHAR) exit
buffer(i)(j:j) = buffer_(k)
end do

47
src/hdf5_interface.cpp
View file

@ -350,6 +350,26 @@ read_complex(hid_t obj_id, const char* name, double _Complex* buffer, bool indep
}
void
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};
hsize_t start[] {0, 0, 1};
hsize_t count[] {n_filter, n_score, 2};
hid_t memspace = H5Screate_simple(3, dims, nullptr);
H5Sselect_hyperslab(memspace, H5S_SELECT_SET, start, nullptr, count, nullptr);
// Create and write dataset
hid_t dset = H5Dopen(group_id, "results", H5P_DEFAULT);
H5Dread(dset, H5T_NATIVE_DOUBLE, memspace, H5S_ALL, H5P_DEFAULT, results);
// Free resources
H5Dclose(dset);
H5Sclose(memspace);
}
void
write_attr(hid_t obj_id, int ndim, const hsize_t* dims, const char* name,
hid_t mem_type_id, const void* buffer)
@ -488,9 +508,34 @@ write_string(hid_t group_id, int ndim, const hsize_t* dims, size_t slen,
void
write_string(hid_t group_id, char const* 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);
}
void
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};
hid_t dspace = H5Screate_simple(3, count, nullptr);
// Set dimensions of results array
hsize_t dims[] {n_filter, n_score, 3};
hsize_t start[] {0, 0, 1};
hid_t memspace = H5Screate_simple(3, dims, nullptr);
H5Sselect_hyperslab(memspace, H5S_SELECT_SET, start, nullptr, count, nullptr);
// Create and write dataset
hid_t dset = H5Dcreate(group_id, "results", H5T_NATIVE_DOUBLE, dspace,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dwrite(dset, H5T_NATIVE_DOUBLE, memspace, H5S_ALL, H5P_DEFAULT, results);
// Free resources
H5Dclose(dset);
H5Sclose(memspace);
H5Sclose(dspace);
}
} // namespace openmc

7
src/hdf5_interface.h
View file

@ -68,6 +68,9 @@ extern "C" void read_string(hid_t obj_id, const char* name, size_t slen,
extern "C" void read_complex(hid_t obj_id, const char* name,
double _Complex* buffer, bool indep);
extern "C" void read_tally_results(hid_t group_id, hsize_t n_filter,
hsize_t n_score, double* results);
void write_attr(hid_t obj_id, int ndim, const hsize_t* dims, const char* name,
hid_t mem_type_id, const void* buffer);
extern "C" void write_attr_double(hid_t obj_id, int ndim, const hsize_t* dims,
@ -90,5 +93,9 @@ extern "C" void write_string(hid_t group_id, int ndim, const hsize_t* dims, size
const char* name, char const* buffer, bool indep);
void write_string(hid_t group_id, const char* name, const std::string& buffer, bool indep);
extern "C" void write_tally_results(hid_t group_id, hsize_t n_filter, hsize_t n_score,
const double* results);
} // namespace openmc
#endif //HDF5_INTERFACE_H

84
src/tallies/tally_header.F90
View file

@ -2,11 +2,10 @@ module tally_header
use, intrinsic :: ISO_C_BINDING
use hdf5
use constants
use error
use dict_header, only: DictIntInt
use hdf5_interface, only: HID_T, HSIZE_T
use message_passing, only: n_procs
use nuclide_header, only: nuclide_dict
use settings, only: reduce_tallies, run_mode
@ -200,67 +199,42 @@ contains
class(TallyObject), intent(in) :: this
integer(HID_T), intent(in) :: group_id
integer :: hdf5_err
integer(HID_T) :: dset, dspace
integer(HID_T) :: memspace
integer(HSIZE_T) :: dims(3)
integer(HSIZE_T) :: dims_slab(3)
integer(HSIZE_T) :: offset(3) = [1,0,0]
integer(HSIZE_T) :: n_filter, n_score
interface
subroutine write_tally_results(group_id, n_filter, n_score, results) &
bind(C)
import HID_T, HSIZE_T, C_DOUBLE
integer(HID_T), value :: group_id
integer(HSIZE_T), value :: n_filter
integer(HSIZE_T), value :: n_score
real(C_DOUBLE), intent(in) :: results(*)
end subroutine write_tally_results
end interface
! Create file dataspace
dims_slab(:) = shape(this % results)
dims_slab(1) = 2
call h5screate_simple_f(3, dims_slab, dspace, hdf5_err)
! Create memory dataspace that contains only SUM and SUM_SQ values
dims(:) = shape(this % results)
call h5screate_simple_f(3, dims, memspace, hdf5_err)
call h5sselect_hyperslab_f(memspace, H5S_SELECT_SET_F, offset, dims_slab, &
hdf5_err)
! Create and write to dataset
call h5dcreate_f(group_id, "results", H5T_NATIVE_DOUBLE, dspace, dset, &
hdf5_err)
call h5dwrite_f(dset, H5T_NATIVE_DOUBLE, this % results, dims_slab, &
hdf5_err, mem_space_id=memspace)
! Close identifiers
call h5dclose_f(dset, hdf5_err)
call h5sclose_f(memspace, hdf5_err)
call h5sclose_f(dspace, hdf5_err)
n_filter = size(this % results, 3)
n_score = size(this % results, 2)
call write_tally_results(group_id, n_filter, n_score, this % results)
end subroutine tally_write_results_hdf5
subroutine tally_read_results_hdf5(this, group_id)
class(TallyObject), intent(inout) :: this
integer(HID_T), intent(in) :: group_id
integer :: hdf5_err
integer(HID_T) :: dset, dspace
integer(HID_T) :: memspace
integer(HSIZE_T) :: dims(3)
integer(HSIZE_T) :: dims_slab(3)
integer(HSIZE_T) :: offset(3) = [1,0,0]
integer(HSIZE_T) :: n_filter, n_score
interface
subroutine read_tally_results(group_id, n_filter, n_score, results) &
bind(C)
import HID_T, HSIZE_T, C_DOUBLE
integer(HID_T), value :: group_id
integer(HSIZE_T), value :: n_filter
integer(HSIZE_T), value :: n_score
real(C_DOUBLE), intent(out) :: results(*)
end subroutine read_tally_results
end interface
! Create file dataspace
dims_slab(:) = shape(this % results)
dims_slab(1) = 2
call h5screate_simple_f(3, dims_slab, dspace, hdf5_err)
! Create memory dataspace that contains only SUM and SUM_SQ values
dims(:) = shape(this % results)
call h5screate_simple_f(3, dims, memspace, hdf5_err)
call h5sselect_hyperslab_f(memspace, H5S_SELECT_SET_F, offset, dims_slab, &
hdf5_err)
! Create and write to dataset
call h5dopen_f(group_id, "results", dset, hdf5_err)
call h5dread_f(dset, H5T_NATIVE_DOUBLE, this % results, dims_slab, &
hdf5_err, mem_space_id=memspace)
! Close identifiers
call h5dclose_f(dset, hdf5_err)
call h5sclose_f(memspace, hdf5_err)
call h5sclose_f(dspace, hdf5_err)
n_filter = size(this % results, 3)
n_score = size(this % results, 2)
call read_tally_results(group_id, n_filter, n_score, this % results)
end subroutine tally_read_results_hdf5
!===============================================================================