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Convert HDF5 read_integer to C++
This commit is contained in:
Paul Romano
parent
46270774c5
commit
8338c0022e
3 changed files with 114 additions and 297 deletions
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@ -44,12 +44,12 @@ module hdf5_interface
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end interface write_dataset
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interface read_dataset
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module procedure read_double
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module procedure read_double_0D
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module procedure read_double_1D
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module procedure read_double_2D
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module procedure read_double_3D
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module procedure read_double_4D
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module procedure read_integer
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module procedure read_integer_0D
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module procedure read_integer_1D
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module procedure read_integer_2D
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module procedure read_integer_3D
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@ -114,6 +114,15 @@ module hdf5_interface
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logical(C_BOOL), intent(in) :: indep
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end subroutine read_double_c
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subroutine read_int_c(obj_id, name, buffer, indep) &
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bind(C, name='read_int')
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import HID_T, C_INT, 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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integer(C_INT), intent(in) :: buffer(*)
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logical(C_BOOL), intent(in) :: indep
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end subroutine read_int_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
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@ -402,49 +411,6 @@ contains
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! READ_DOUBLE reads double precision scalar data
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!===============================================================================
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subroutine read_double(buffer, obj_id, name, indep)
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real(8), target, intent(inout) :: buffer
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integer(HID_T), intent(in) :: obj_id
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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 :: 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_id
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type(c_ptr) :: f_ptr
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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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else
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dset_id = obj_id
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end if
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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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if (present(name)) call h5dclose_f(dset_id, hdf5_err)
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end subroutine read_double
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!===============================================================================
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! WRITE_DOUBLE_ND writes double precision N-D array data
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@ -535,6 +501,30 @@ contains
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! READ_DOUBLE_ND reads double precision N-D array data
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!===============================================================================
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subroutine read_double_0D(buffer, obj_id, name, indep)
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real(8), target, intent(inout) :: buffer
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integer(HID_T), intent(in) :: obj_id
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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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real(C_DOUBLE) :: buffer_(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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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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call read_double_c(obj_id, C_NULL_PTR, buffer_, indep_)
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end if
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buffer = buffer_(1)
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end subroutine read_double_0D
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subroutine read_double_1D(buffer, obj_id, name, indep)
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real(8), target, intent(inout) :: buffer(:)
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integer(HID_T), intent(in) :: obj_id
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@ -627,50 +617,6 @@ contains
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! READ_INTEGER reads integer precision scalar data
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!===============================================================================
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subroutine read_integer(buffer, obj_id, name, indep)
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integer, target, intent(inout) :: buffer
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integer(HID_T), intent(in) :: obj_id
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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 :: 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_id
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type(c_ptr) :: f_ptr
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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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else
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dset_id = obj_id
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end if
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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_INTEGER, 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_INTEGER, f_ptr, hdf5_err)
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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_integer
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!===============================================================================
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! WRITE_INTEGER_ND writes integer precision N-D array data
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!===============================================================================
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@ -757,269 +703,121 @@ contains
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end subroutine write_integer_4D
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!===============================================================================
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! READ_INTEGER_1D reads integer precision 1-D array data
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! READ_INTEGER_ND reads integer precision N-D array data
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!===============================================================================
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subroutine read_integer_0D(buffer, obj_id, name, indep)
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integer, target, intent(inout) :: buffer
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integer(HID_T), intent(in) :: obj_id
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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(C_INT) :: buffer_(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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name_ = to_c_string(name)
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call read_int_c(obj_id, c_loc(name_), buffer_, indep_)
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else
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call read_int_c(obj_id, C_NULL_PTR, buffer_, indep_)
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end if
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buffer = buffer_(1)
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end subroutine read_integer_0D
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subroutine read_integer_1D(buffer, obj_id, name, indep)
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integer, target, intent(inout) :: buffer(:)
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integer(HID_T), intent(in) :: obj_id
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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_int_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_int_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_integer_1D_explicit(dset_id, dims, buffer, indep)
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else
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call read_integer_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_integer_1D
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subroutine read_integer_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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integer, 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_INTEGER, 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_INTEGER, f_ptr, hdf5_err)
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end if
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end subroutine read_integer_1D_explicit
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!===============================================================================
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! READ_INTEGER_2D reads integer precision 2-D array data
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!===============================================================================
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subroutine read_integer_2D(buffer, obj_id, name, indep)
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integer, target, intent(inout) :: buffer(:,:)
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integer(HID_T), intent(in) :: obj_id
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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_int_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_int_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_integer_2D_explicit(dset_id, dims, buffer, indep)
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else
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call read_integer_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_integer_2D
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subroutine read_integer_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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integer, 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_INTEGER, 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_INTEGER, f_ptr, hdf5_err)
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end if
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end subroutine read_integer_2D_explicit
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!===============================================================================
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! READ_INTEGER_3D reads integer precision 3-D array data
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!===============================================================================
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subroutine read_integer_3D(buffer, obj_id, name, indep)
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integer, target, intent(inout) :: buffer(:,:,:)
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integer(HID_T), intent(in) :: obj_id
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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_int_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_int_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_integer_3D_explicit(dset_id, dims, buffer, indep)
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else
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call read_integer_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_integer_3D
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subroutine read_integer_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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integer, 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_INTEGER, 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_INTEGER, f_ptr, hdf5_err)
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end if
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end subroutine read_integer_3D_explicit
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!===============================================================================
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! READ_INTEGER_4D reads integer precision 4-D array data
|
||||
!===============================================================================
|
||||
|
||||
subroutine read_integer_4D(buffer, obj_id, name, indep)
|
||||
integer, target, intent(inout) :: buffer(:,:,:,:)
|
||||
integer(HID_T), intent(in) :: obj_id
|
||||
character(*), optional, intent(in) :: name
|
||||
logical, optional, intent(in) :: indep ! independent I/O
|
||||
|
||||
integer :: hdf5_err
|
||||
integer(HID_T) :: dset_id
|
||||
integer(HSIZE_T) :: dims(4)
|
||||
logical(C_BOOL) :: indep_
|
||||
character(kind=C_CHAR), target, allocatable :: name_(:)
|
||||
|
||||
indep_ = .false.
|
||||
if (present(indep)) indep_ = indep
|
||||
|
||||
! If 'name' argument is passed, obj_id is interpreted to be a group and
|
||||
! 'name' is the name of the dataset we should read from
|
||||
if (present(name)) then
|
||||
call h5dopen_f(obj_id, trim(name), dset_id, hdf5_err)
|
||||
name_ = to_c_string(name)
|
||||
call read_int_c(obj_id, c_loc(name_), buffer, indep_)
|
||||
else
|
||||
dset_id = obj_id
|
||||
call read_int_c(obj_id, C_NULL_PTR, buffer, indep_)
|
||||
end if
|
||||
|
||||
dims(:) = shape(buffer)
|
||||
|
||||
if (present(indep)) then
|
||||
call read_integer_4D_explicit(dset_id, dims, buffer, indep)
|
||||
else
|
||||
call read_integer_4D_explicit(dset_id, dims, buffer)
|
||||
end if
|
||||
|
||||
if (present(name)) call h5dclose_f(dset_id, hdf5_err)
|
||||
end subroutine read_integer_4D
|
||||
|
||||
subroutine read_integer_4D_explicit(dset_id, dims, buffer, indep)
|
||||
integer(HID_T), intent(in) :: dset_id
|
||||
integer(HSIZE_T), intent(in) :: dims(4)
|
||||
integer, target, intent(inout) :: buffer(dims(1),dims(2),dims(3),dims(4))
|
||||
logical, optional, intent(in) :: indep ! independent I/O
|
||||
|
||||
integer :: hdf5_err
|
||||
integer :: data_xfer_mode
|
||||
#ifdef PHDF5
|
||||
integer(HID_T) :: plist ! property list
|
||||
#endif
|
||||
type(c_ptr) :: f_ptr
|
||||
|
||||
! Set up collective vs. independent I/O
|
||||
data_xfer_mode = H5FD_MPIO_COLLECTIVE_F
|
||||
if (present(indep)) then
|
||||
if (indep) data_xfer_mode = H5FD_MPIO_INDEPENDENT_F
|
||||
end if
|
||||
|
||||
f_ptr = c_loc(buffer)
|
||||
|
||||
if (using_mpio_device(dset_id)) then
|
||||
#ifdef PHDF5
|
||||
call h5pcreate_f(H5P_DATASET_XFER_F, plist, hdf5_err)
|
||||
call h5pset_dxpl_mpio_f(plist, data_xfer_mode, hdf5_err)
|
||||
call h5dread_f(dset_id, H5T_NATIVE_INTEGER, f_ptr, hdf5_err, xfer_prp=plist)
|
||||
call h5pclose_f(plist, hdf5_err)
|
||||
#endif
|
||||
else
|
||||
call h5dread_f(dset_id, H5T_NATIVE_INTEGER, f_ptr, hdf5_err)
|
||||
end if
|
||||
end subroutine read_integer_4D_explicit
|
||||
|
||||
!===============================================================================
|
||||
! WRITE_LONG writes long integer scalar data
|
||||
!===============================================================================
|
||||
|
|
|
|||
|
|
@ -160,7 +160,8 @@ open_group(hid_t group_id, const char* name)
|
|||
|
||||
|
||||
void
|
||||
read_double(hid_t obj_id, const char* name, double* buffer, bool indep)
|
||||
read_array(hid_t obj_id, const char* name, hid_t mem_type_id,
|
||||
void* buffer, bool indep)
|
||||
{
|
||||
hid_t dset = obj_id;
|
||||
if (name) dset = H5Dopen(obj_id, name, H5P_DEFAULT);
|
||||
|
|
@ -175,17 +176,31 @@ read_double(hid_t obj_id, const char* name, double* buffer, bool indep)
|
|||
H5Pset_dxpl_mpio(plist, data_xfer_mode);
|
||||
|
||||
// Write data
|
||||
H5Dread(dset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, plist, buffer);
|
||||
H5Dread(dset, mem_type_id, H5S_ALL, H5S_ALL, plist, buffer);
|
||||
H5Pclose(plist);
|
||||
#endif
|
||||
} else {
|
||||
H5Dread(dset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, buffer);
|
||||
H5Dread(dset, mem_type_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buffer);
|
||||
}
|
||||
|
||||
if (name) H5Dclose(dset);
|
||||
}
|
||||
|
||||
|
||||
void
|
||||
read_double(hid_t obj_id, const char* name, double* buffer, bool indep)
|
||||
{
|
||||
read_array(obj_id, name, H5T_NATIVE_DOUBLE, buffer, indep);
|
||||
}
|
||||
|
||||
|
||||
void
|
||||
read_int(hid_t obj_id, const char* name, int* buffer, bool indep)
|
||||
{
|
||||
read_array(obj_id, name, H5T_NATIVE_INT, buffer, indep);
|
||||
}
|
||||
|
||||
|
||||
void
|
||||
write_array(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
|
||||
hid_t mem_type_id, const void* buffer, bool indep)
|
||||
|
|
|
|||
|
|
@ -41,8 +41,12 @@ write_double_1D(hid_t group_id, char const *name,
|
|||
H5Dclose(dataset);
|
||||
}
|
||||
|
||||
void read_array(hid_t obj_id, const char* name, double* buffer,
|
||||
hid_t mem_type_id, bool indep);
|
||||
extern "C" void read_double(hid_t obj_id, const char* name, double* buffer,
|
||||
bool indep);
|
||||
extern "C" void read_int(hid_t obj_id, const char* name, int* buffer,
|
||||
bool indep);
|
||||
|
||||
void write_array(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
|
||||
hid_t mem_type_id, const void* buffer, bool indep);
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue