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Add C++ routines for HDF5 get_groups, get_datasets, get_name
This commit is contained in:
Paul Romano
parent
70173aa25c
commit
1a77f8afee
3 changed files with 201 additions and 78 deletions
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@ -13,13 +13,12 @@ module hdf5_interface
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use, intrinsic :: ISO_C_BINDING
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use hdf5
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use h5lt
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use error, only: fatal_error
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#ifdef PHDF5
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use message_passing, only: mpi_intracomm, MPI_INFO_NULL
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#endif
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use string, only: to_c_string
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use string, only: to_c_string, to_f_string
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implicit none
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private
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@ -316,31 +315,37 @@ contains
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integer(HID_T), intent(in) :: object_id
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character(len=150), allocatable, intent(out) :: names(:)
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integer :: n_members, i, group_count, type
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integer :: hdf5_err
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character(len=150) :: name
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integer :: i
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integer(C_INT) :: n
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character(len=150,kind=C_CHAR), target, allocatable :: names_(:)
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type(C_PTR), allocatable :: name_ptrs(:)
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! Get number of members in this location
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call h5gn_members_f(object_id, './', n_members, hdf5_err)
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interface
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function get_num_groups(group_id) result(n) bind(C)
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import HID_T, C_INT
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integer(HID_T), value :: group_id
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integer(C_INT) :: n
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end function get_num_groups
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subroutine get_groups_c(group_id, name) bind(C, name='get_groups')
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import HID_T, C_PTR
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integer(HID_T), value :: group_id
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type(C_PTR) :: name(*)
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end subroutine get_groups_c
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end interface
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! Get the number of groups
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group_count = 0
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do i = 0, n_members - 1
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call h5gget_obj_info_idx_f(object_id, "./", i, name, type, hdf5_err)
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if (type == H5G_GROUP_F) then
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group_count = group_count + 1
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end if
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! Determine number of groups and allocate
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n = get_num_groups(object_id)
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allocate(names(n), names_(n), name_ptrs(n))
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! Set C pointers to beginning of each string
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do i = 1, size(names)
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name_ptrs(i) = c_loc(names_(i))
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end do
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! Now we can allocate the storage for the ids
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allocate(names(group_count))
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group_count = 0
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do i = 0, n_members - 1
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call h5gget_obj_info_idx_f(object_id, "./", i, name, type, hdf5_err)
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if (type == H5G_GROUP_F) then
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group_count = group_count + 1
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names(group_count) = trim(name)
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end if
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! Get names of groups and copy to Fortran strings
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call get_groups_c(object_id, name_ptrs)
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do i = 1, size(names)
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names(i) = to_f_string(names_(i))
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end do
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end subroutine get_groups
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@ -398,32 +403,37 @@ contains
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integer(HID_T), intent(in) :: object_id
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character(len=150), allocatable, intent(out) :: names(:)
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integer :: n_members, i, dset_count, type
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integer :: hdf5_err
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character(len=150) :: name
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integer :: i
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integer(C_INT) :: n
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character(len=150,kind=C_CHAR), target, allocatable :: names_(:)
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type(C_PTR), allocatable :: name_ptrs(:)
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interface
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function get_num_datasets(group_id) result(n) bind(C)
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import HID_T, C_INT
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integer(HID_T), value :: group_id
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integer(C_INT) :: n
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end function get_num_datasets
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subroutine get_datasets_c(group_id, name) bind(C, name='get_datasets')
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import HID_T, C_PTR
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integer(HID_T), value :: group_id
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type(C_PTR) :: name(*)
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end subroutine get_datasets_c
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end interface
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! Get number of members in this location
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call h5gn_members_f(object_id, './', n_members, hdf5_err)
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! Determine number of datasets and allocate
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n = get_num_datasets(object_id)
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allocate(names(n), names_(n), name_ptrs(n))
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! Get the number of datasets
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dset_count = 0
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do i = 0, n_members - 1
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call h5gget_obj_info_idx_f(object_id, "./", i, name, type, hdf5_err)
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if (type == H5G_DATASET_F ) then
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dset_count = dset_count + 1
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end if
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! Set C pointers to beginning of each string
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do i = 1, size(names)
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name_ptrs(i) = c_loc(names_(i))
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end do
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! Now we can allocate the storage for the ids
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allocate(names(dset_count))
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dset_count = 0
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do i = 0, n_members - 1
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call h5gget_obj_info_idx_f(object_id, "./", i, name, type, hdf5_err)
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if (type == H5G_DATASET_F ) then
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dset_count = dset_count + 1
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names(dset_count) = trim(name)
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end if
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! Get names of datasets and copy to Fortran strings
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call get_datasets_c(object_id, name_ptrs)
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do i = 1, size(names)
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names(i) = to_f_string(names_(i))
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end do
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end subroutine get_datasets
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@ -432,21 +442,22 @@ contains
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! GET_NAME Obtains the name of the current group in group_id
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!===============================================================================
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function get_name(group_id, name_len_) result(name)
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integer(HID_T), intent(in) :: group_id
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function get_name(object_id, name_len_) result(name)
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integer(HID_T), intent(in) :: object_id
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integer(SIZE_T), optional, intent(in) :: name_len_
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character(len=150) :: name ! name of group
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integer(SIZE_T) :: name_len, name_file_len
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integer :: hdf5_err ! HDF5 error code
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character(150) :: name ! name of object
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character(kind=C_CHAR) :: name_(150)
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interface
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subroutine get_name_c(obj_id, name) bind(C, name='get_name')
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import HID_T, C_CHAR
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integer(HID_T), value :: obj_id
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character(kind=C_CHAR), intent(out) :: name(*)
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end subroutine get_name_c
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end interface
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if (present(name_len_)) then
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name_len = name_len_
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else
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name_len = 150
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end if
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call h5iget_name_f(group_id, name, name_len, name_file_len, hdf5_err)
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call get_name_c(object_id, name_)
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name = to_f_string(name_)
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end function get_name
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!===============================================================================
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@ -36,26 +36,6 @@ attribute_typesize(hid_t obj_id, const char* name)
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}
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bool
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using_mpio_device(hid_t obj_id)
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{
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// Determine file that this object is part of
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hid_t file_id = H5Iget_file_id(obj_id);
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// Get file access property list
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hid_t fapl_id = H5Fget_access_plist(file_id);
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// Get low-level driver identifier
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hid_t driver = H5Pget_driver(fapl_id);
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// Free resources
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H5Pclose(fapl_id);
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H5Fclose(file_id);
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return driver == H5FD_MPIO;
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}
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void
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get_shape(hid_t obj_id, hsize_t* dims)
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{
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@ -199,6 +179,113 @@ void file_close(hid_t file_id)
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H5Fclose(file_id);
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}
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void
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get_name(hid_t obj_id, char* name)
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{
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size_t size = 1 + H5Iget_name(obj_id, nullptr, 0);
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H5Iget_name(obj_id, name, size);
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}
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int get_num_datasets(hid_t group_id)
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{
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// Determine number of links in the group
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H5G_info_t info;
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H5Gget_info(group_id, &info);
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// Iterate over links to get number of groups
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H5O_info_t oinfo;
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int ndatasets = 0;
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for (hsize_t i = 0; i < info.nlinks; ++i) {
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// Determine type of object (and skip non-group)
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H5Oget_info_by_idx(group_id, ".", H5_INDEX_NAME, H5_ITER_INC, i, &oinfo,
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H5P_DEFAULT);
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if (oinfo.type == H5O_TYPE_DATASET) ndatasets += 1;
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}
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return ndatasets;
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}
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int get_num_groups(hid_t group_id)
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{
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// Determine number of links in the group
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H5G_info_t info;
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H5Gget_info(group_id, &info);
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// Iterate over links to get number of groups
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H5O_info_t oinfo;
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int ngroups = 0;
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for (hsize_t i = 0; i < info.nlinks; ++i) {
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// Determine type of object (and skip non-group)
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H5Oget_info_by_idx(group_id, ".", H5_INDEX_NAME, H5_ITER_INC, i, &oinfo,
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H5P_DEFAULT);
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if (oinfo.type == H5O_TYPE_GROUP) ngroups += 1;
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}
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return ngroups;
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}
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void
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get_datasets(hid_t group_id, char* name[])
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{
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// Determine number of links in the group
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H5G_info_t info;
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H5Gget_info(group_id, &info);
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// Iterate over links to get names
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H5O_info_t oinfo;
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hsize_t count = 0;
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size_t size;
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for (hsize_t i = 0; i < info.nlinks; ++i) {
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// Determine type of object (and skip non-group)
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H5Oget_info_by_idx(group_id, ".", H5_INDEX_NAME, H5_ITER_INC, i, &oinfo,
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H5P_DEFAULT);
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if (oinfo.type != H5O_TYPE_DATASET) continue;
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// Get size of name
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size = 1 + H5Lget_name_by_idx(group_id, ".", H5_INDEX_NAME, H5_ITER_INC,
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i, nullptr, 0, H5P_DEFAULT);
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// Read name
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H5Lget_name_by_idx(group_id, ".", H5_INDEX_NAME, H5_ITER_INC, i,
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name[count], size, H5P_DEFAULT);
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count += 1;
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}
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}
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void
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get_groups(hid_t group_id, char* name[])
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{
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// Determine number of links in the group
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H5G_info_t info;
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H5Gget_info(group_id, &info);
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// Iterate over links to get names
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H5O_info_t oinfo;
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hsize_t count = 0;
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size_t size;
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for (hsize_t i = 0; i < info.nlinks; ++i) {
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// Determine type of object (and skip non-group)
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H5Oget_info_by_idx(group_id, ".", H5_INDEX_NAME, H5_ITER_INC, i, &oinfo,
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H5P_DEFAULT);
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if (oinfo.type != H5O_TYPE_GROUP) continue;
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// Get size of name
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size = 1 + H5Lget_name_by_idx(group_id, ".", H5_INDEX_NAME, H5_ITER_INC,
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i, nullptr, 0, H5P_DEFAULT);
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// Read name
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H5Lget_name_by_idx(group_id, ".", H5_INDEX_NAME, H5_ITER_INC, i,
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name[count], size, H5P_DEFAULT);
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count += 1;
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}
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}
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bool
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object_exists(hid_t object_id, const char* name)
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{
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@ -548,4 +635,24 @@ write_tally_results(hid_t group_id, hsize_t n_filter, hsize_t n_score, const dou
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H5Sclose(dspace);
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}
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bool
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using_mpio_device(hid_t obj_id)
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{
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// Determine file that this object is part of
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hid_t file_id = H5Iget_file_id(obj_id);
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// Get file access property list
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hid_t fapl_id = H5Fget_access_plist(file_id);
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// Get low-level driver identifier
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hid_t driver = H5Pget_driver(fapl_id);
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// Free resources
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H5Pclose(fapl_id);
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H5Fclose(file_id);
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return driver == H5FD_MPIO;
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}
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} // namespace openmc
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@ -23,8 +23,13 @@ extern "C" size_t dataset_typesize(hid_t dset);
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extern "C" hid_t file_open(const char* filename, char mode, bool parallel);
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hid_t file_open(const std::string& filename, char mode, bool parallel);
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extern "C" void file_close(hid_t file_id);
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extern "C" void get_shape(hid_t obj_if, hsize_t* dims);
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extern "C" void get_shape_attr(hid_t obj_if, const char* name, hsize_t* dims);
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extern "C" void get_name(hid_t obj_id, char* name);
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extern "C" int get_num_datasets(hid_t group_id);
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extern "C" int get_num_groups(hid_t group_id);
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extern "C" void get_datasets(hid_t group_id, char* name[]);
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extern "C" void get_groups(hid_t group_id, char* name[]);
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extern "C" void get_shape(hid_t obj_id, hsize_t* dims);
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extern "C" void get_shape_attr(hid_t obj_id, const char* name, hsize_t* dims);
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extern "C" bool object_exists(hid_t object_id, const char* name);
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extern "C" hid_t open_dataset(hid_t group_id, const char* name);
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extern "C" hid_t open_group(hid_t group_id, const char* name);
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