mirror of
https://github.com/openmc-dev/openmc.git
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Convert HDF5 read_double to C++
This commit is contained in:
Paul Romano
parent
dcde6a331a
commit
ef1956e811
3 changed files with 104 additions and 235 deletions
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@ -105,9 +105,18 @@ module hdf5_interface
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integer(HID_T), value :: file_id
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end subroutine file_close
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subroutine read_double_c(obj_id, name, buffer, indep) &
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bind(C, name='read_double')
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import HID_T, C_DOUBLE, C_BOOL, C_PTR
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integer(HID_T), value :: obj_id
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type(C_PTR), value :: name
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real(C_DOUBLE), intent(in) :: buffer(*)
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logical(C_BOOL), intent(in) :: indep
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end subroutine read_double_c
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subroutine write_double_c(group_id, ndim, dims, name, buffer, indep) &
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bind(C, name='write_double')
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import HID_T, HSIZE_T, C_INT, C_DOUBLE, C_CHAR, C_BOOL, C_PTR
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import HID_T, HSIZE_T, C_INT, C_DOUBLE, C_CHAR, C_BOOL
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integer(HID_T), value :: group_id
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integer(C_INT), value :: ndim
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integer(HSIZE_T), intent(in) :: dims(*)
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@ -388,40 +397,15 @@ contains
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real(8), intent(in), target :: buffer ! data to write
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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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type(c_ptr) :: f_ptr
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integer(HSIZE_T) :: dims(0)
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logical(C_BOOL) :: indep_
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real(C_DOUBLE) :: value(1)
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! Set up independentive 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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value(1) = buffer
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! Create dataspace and 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), H5T_NATIVE_DOUBLE, &
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dspace, dset, hdf5_err)
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f_ptr = c_loc(buffer)
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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, H5T_NATIVE_DOUBLE, 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, H5T_NATIVE_DOUBLE, 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 write_double_c(group_id, 0, dims, to_c_string(name), value, indep_)
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end subroutine write_double
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!===============================================================================
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@ -502,62 +486,22 @@ contains
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character(*), optional, intent(in) :: name
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logical, optional, intent(in) :: indep ! independent I/O
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integer :: hdf5_err
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integer(HID_T) :: dset_id
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integer(HSIZE_T) :: dims(1)
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logical(C_BOOL) :: indep_
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character(kind=C_CHAR), target, allocatable :: name_(:)
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indep_ = .false.
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if (present(indep)) indep_ = indep
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! If 'name' argument is passed, obj_id is interpreted to be a group and
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! 'name' is the name of the dataset we should read from
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if (present(name)) then
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call h5dopen_f(obj_id, trim(name), dset_id, hdf5_err)
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name_ = to_c_string(name)
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call read_double_c(obj_id, c_loc(name_), buffer, indep_)
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else
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dset_id = obj_id
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call read_double_c(obj_id, C_NULL_PTR, buffer, indep_)
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end if
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dims(:) = shape(buffer)
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if (present(indep)) then
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call read_double_1D_explicit(dset_id, dims, buffer, indep)
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else
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call read_double_1D_explicit(dset_id, dims, buffer)
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end if
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if (present(name)) call h5dclose_f(dset_id, hdf5_err)
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end subroutine read_double_1D
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subroutine read_double_1D_explicit(dset_id, dims, buffer, indep)
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integer(HID_T), intent(in) :: dset_id
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integer(HSIZE_T), intent(in) :: dims(1)
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real(8), target, intent(inout) :: buffer(dims(1))
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logical, optional, intent(in) :: 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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type(c_ptr) :: f_ptr
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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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f_ptr = c_loc(buffer)
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if (using_mpio_device(dset_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 h5dread_f(dset_id, H5T_NATIVE_DOUBLE, 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 h5dread_f(dset_id, H5T_NATIVE_DOUBLE, f_ptr, hdf5_err)
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end if
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end subroutine read_double_1D_explicit
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!===============================================================================
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! WRITE_DOUBLE_2D writes double precision 2-D array data
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!===============================================================================
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@ -588,62 +532,22 @@ contains
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character(*), optional, intent(in) :: name
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logical, optional, intent(in) :: indep ! independent I/O
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integer :: hdf5_err
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integer(HID_T) :: dset_id
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integer(HSIZE_T) :: dims(2)
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logical(C_BOOL) :: indep_
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character(kind=C_CHAR), target, allocatable :: name_(:)
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indep_ = .false.
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if (present(indep)) indep_ = indep
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! If 'name' argument is passed, obj_id is interpreted to be a group and
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! 'name' is the name of the dataset we should read from
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if (present(name)) then
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call h5dopen_f(obj_id, trim(name), dset_id, hdf5_err)
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name_ = to_c_string(name)
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call read_double_c(obj_id, c_loc(name_), buffer, indep_)
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else
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dset_id = obj_id
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call read_double_c(obj_id, C_NULL_PTR, buffer, indep_)
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end if
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dims(:) = shape(buffer)
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if (present(indep)) then
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call read_double_2D_explicit(dset_id, dims, buffer, indep)
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else
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call read_double_2D_explicit(dset_id, dims, buffer)
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end if
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if (present(name)) call h5dclose_f(dset_id, hdf5_err)
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end subroutine read_double_2D
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subroutine read_double_2D_explicit(dset_id, dims, buffer, indep)
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integer(HID_T), intent(in) :: dset_id
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integer(HSIZE_T), intent(in) :: dims(2)
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real(8), target, intent(inout) :: buffer(dims(1),dims(2))
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logical, optional, intent(in) :: 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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type(c_ptr) :: f_ptr
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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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f_ptr = c_loc(buffer)
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if (using_mpio_device(dset_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 h5dread_f(dset_id, H5T_NATIVE_DOUBLE, 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 h5dread_f(dset_id, H5T_NATIVE_DOUBLE, f_ptr, hdf5_err)
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end if
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end subroutine read_double_2D_explicit
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!===============================================================================
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! WRITE_DOUBLE_3D writes double precision 3-D array data
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!===============================================================================
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@ -674,62 +578,22 @@ contains
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character(*), optional, intent(in) :: name
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logical, optional, intent(in) :: indep ! independent I/O
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integer :: hdf5_err
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integer(HID_T) :: dset_id
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integer(HSIZE_T) :: dims(3)
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logical(C_BOOL) :: indep_
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character(kind=C_CHAR), target, allocatable :: name_(:)
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indep_ = .false.
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if (present(indep)) indep_ = indep
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! If 'name' argument is passed, obj_id is interpreted to be a group and
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! 'name' is the name of the dataset we should read from
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if (present(name)) then
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call h5dopen_f(obj_id, trim(name), dset_id, hdf5_err)
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name_ = to_c_string(name)
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call read_double_c(obj_id, c_loc(name_), buffer, indep_)
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else
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dset_id = obj_id
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call read_double_c(obj_id, C_NULL_PTR, buffer, indep_)
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end if
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dims(:) = shape(buffer)
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if (present(indep)) then
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call read_double_3D_explicit(dset_id, dims, buffer, indep)
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else
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call read_double_3D_explicit(dset_id, dims, buffer)
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end if
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if (present(name)) call h5dclose_f(dset_id, hdf5_err)
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end subroutine read_double_3D
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subroutine read_double_3D_explicit(dset_id, dims, buffer, indep)
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integer(HID_T), intent(in) :: dset_id
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integer(HSIZE_T), intent(in) :: dims(3)
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real(8), target, intent(inout) :: buffer(dims(1),dims(2),dims(3))
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logical, optional, intent(in) :: 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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type(c_ptr) :: f_ptr
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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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f_ptr = c_loc(buffer)
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if (using_mpio_device(dset_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 h5dread_f(dset_id, H5T_NATIVE_DOUBLE, 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 h5dread_f(dset_id, H5T_NATIVE_DOUBLE, f_ptr, hdf5_err)
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end if
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end subroutine read_double_3D_explicit
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!===============================================================================
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! WRITE_DOUBLE_4D writes double precision 4-D array data
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!===============================================================================
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@ -760,62 +624,22 @@ contains
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character(*), optional, intent(in) :: name
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logical, optional, intent(in) :: indep ! independent I/O
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integer :: hdf5_err
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integer(HID_T) :: dset_id
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integer(HSIZE_T) :: dims(4)
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logical(C_BOOL) :: indep_
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character(kind=C_CHAR), target, allocatable :: name_(:)
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indep_ = .false.
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if (present(indep)) indep_ = indep
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! If 'name' argument is passed, obj_id is interpreted to be a group and
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! 'name' is the name of the dataset we should read from
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if (present(name)) then
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call h5dopen_f(obj_id, trim(name), dset_id, hdf5_err)
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name_ = to_c_string(name)
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call read_double_c(obj_id, c_loc(name_), buffer, indep_)
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else
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dset_id = obj_id
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call read_double_c(obj_id, C_NULL_PTR, buffer, indep_)
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end if
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dims(:) = shape(buffer)
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if (present(indep)) then
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call read_double_4D_explicit(dset_id, dims, buffer, indep)
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else
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call read_double_4D_explicit(dset_id, dims, buffer)
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end if
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if (present(name)) call h5dclose_f(dset_id, hdf5_err)
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end subroutine read_double_4D
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subroutine read_double_4D_explicit(dset_id, dims, buffer, indep)
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integer(HID_T), intent(in) :: dset_id
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integer(HSIZE_T), intent(in) :: dims(4)
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real(8), target, intent(inout) :: buffer(dims(1),dims(2),dims(3),dims(4))
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logical, optional, intent(in) :: 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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type(c_ptr) :: f_ptr
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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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f_ptr = c_loc(buffer)
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if (using_mpio_device(dset_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 h5dread_f(dset_id, H5T_NATIVE_DOUBLE, 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 h5dread_f(dset_id, H5T_NATIVE_DOUBLE, f_ptr, hdf5_err)
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end if
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end subroutine read_double_4D_explicit
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!===============================================================================
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! WRITE_INTEGER writes integer precision scalar data
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!===============================================================================
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@ -11,7 +11,8 @@
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namespace openmc {
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bool
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using_mpio_device(hid_t obj_id) {
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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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@ -109,16 +110,19 @@ file_open(const char* filename, char mode, bool parallel)
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}
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hid_t
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file_open(const std::string& filename, char mode, bool parallel=false) {
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file_open(const std::string& filename, char mode, bool parallel=false)
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{
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file_open(filename.c_str(), mode, parallel);
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}
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void file_close(hid_t file_id) {
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void file_close(hid_t file_id)
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{
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H5Fclose(file_id);
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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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object_exists(hid_t object_id, const char* name)
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{
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htri_t out = H5LTpath_valid(object_id, name, true);
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if (out < 0) {
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std::stringstream err_msg;
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@ -130,7 +134,8 @@ object_exists(hid_t object_id, const char* name) {
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hid_t
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open_dataset(hid_t group_id, const char* name){
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open_dataset(hid_t group_id, const char* name)
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{
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if (object_exists(group_id, name)) {
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return H5Dopen(group_id, name, H5P_DEFAULT);
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} else {
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@ -142,7 +147,8 @@ open_dataset(hid_t group_id, const char* name){
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hid_t
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open_group(hid_t group_id, const char* name){
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open_group(hid_t group_id, const char* name)
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{
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if (object_exists(group_id, name)) {
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return H5Gopen(group_id, name, H5P_DEFAULT);
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} else {
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@ -153,10 +159,46 @@ open_group(hid_t group_id, const char* name){
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}
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||||
|
||||
void
|
||||
read_double(hid_t obj_id, const char* name, double* buffer, bool indep)
|
||||
{
|
||||
hid_t dset = obj_id;
|
||||
if (name) dset = H5Dopen(obj_id, name, H5P_DEFAULT);
|
||||
|
||||
if (using_mpio_device(dset)) {
|
||||
#ifdef PHDF5
|
||||
// Set up collective vs independent I/O
|
||||
auto data_xfer_mode {indep ? H5FD_MPIO_INDEPENDENT : H5FD_MPIO_COLLECTIVE};
|
||||
|
||||
// Create dataset transfer property list
|
||||
hid_t plist = H5Pcreate(H5P_DATASET_XFER);
|
||||
H5Pset_dxpl_mpio(plist, data_xfer_mode);
|
||||
|
||||
// Write data
|
||||
H5Dread(dset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, plist, buffer);
|
||||
H5Pclose(plist);
|
||||
#endif
|
||||
} else {
|
||||
H5Dread(dset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, buffer);
|
||||
}
|
||||
|
||||
if (name) H5Dclose(dset);
|
||||
}
|
||||
|
||||
|
||||
void
|
||||
write_double(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
|
||||
const double* buffer, bool indep) {
|
||||
hid_t dspace = H5Screate_simple(ndim, dims, nullptr);
|
||||
const double* buffer, bool indep)
|
||||
{
|
||||
// If array is given, create a simple dataspace. Otherwise, create a scalar
|
||||
// datascape.
|
||||
hid_t dspace;
|
||||
if (ndim > 0) {
|
||||
dspace = H5Screate_simple(ndim, dims, nullptr);
|
||||
} else {
|
||||
dspace = H5Screate(H5S_SCALAR);
|
||||
}
|
||||
|
||||
hid_t dset = H5Dcreate(group_id, name, H5T_NATIVE_DOUBLE, dspace,
|
||||
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
||||
|
||||
|
|
|
|||
|
|
@ -41,8 +41,11 @@ write_double_1D(hid_t group_id, char const *name,
|
|||
H5Dclose(dataset);
|
||||
}
|
||||
|
||||
extern "C" void write_double(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
|
||||
const double* buffer, bool indep);
|
||||
extern "C" void read_double(hid_t obj_id, const char* name, double* buffer,
|
||||
bool indep);
|
||||
|
||||
extern "C" void write_double(hid_t group_id, int ndim, const hsize_t* dims,
|
||||
const char* name, const double* buffer, bool indep);
|
||||
|
||||
void write_string(hid_t group_id, char const *name, char const *buffer);
|
||||
void write_string(hid_t group_id, char const *name, const std::string &buffer);
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue