diff --git a/src/hdf5_interface.F90 b/src/hdf5_interface.F90 index 562e35661e..f1de90d726 100644 --- a/src/hdf5_interface.F90 +++ b/src/hdf5_interface.F90 @@ -44,12 +44,12 @@ module hdf5_interface end interface write_dataset interface read_dataset - module procedure read_double + module procedure read_double_0D module procedure read_double_1D module procedure read_double_2D module procedure read_double_3D module procedure read_double_4D - module procedure read_integer + module procedure read_integer_0D module procedure read_integer_1D module procedure read_integer_2D module procedure read_integer_3D @@ -114,6 +114,15 @@ module hdf5_interface logical(C_BOOL), intent(in) :: indep end subroutine read_double_c + subroutine read_int_c(obj_id, name, buffer, indep) & + bind(C, name='read_int') + import HID_T, C_INT, C_BOOL, C_PTR + integer(HID_T), value :: obj_id + type(C_PTR), value :: name + integer(C_INT), intent(in) :: buffer(*) + logical(C_BOOL), intent(in) :: indep + end subroutine read_int_c + subroutine write_double_c(group_id, ndim, dims, name, buffer, indep) & bind(C, name='write_double') import HID_T, HSIZE_T, C_INT, C_DOUBLE, C_CHAR, C_BOOL @@ -402,49 +411,6 @@ contains ! READ_DOUBLE reads double precision scalar data !=============================================================================== - subroutine read_double(buffer, obj_id, name, indep) - real(8), 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 :: data_xfer_mode -#ifdef PHDF5 - integer(HID_T) :: plist ! property list -#endif - integer(HID_T) :: dset_id - type(c_ptr) :: f_ptr - - ! 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) - else - dset_id = obj_id - end if - - ! 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_DOUBLE, f_ptr, hdf5_err, xfer_prp=plist) - call h5pclose_f(plist, hdf5_err) -#endif - else - call h5dread_f(dset_id, H5T_NATIVE_DOUBLE, f_ptr, hdf5_err) - end if - - if (present(name)) call h5dclose_f(dset_id, hdf5_err) - end subroutine read_double !=============================================================================== ! WRITE_DOUBLE_ND writes double precision N-D array data @@ -535,6 +501,30 @@ contains ! READ_DOUBLE_ND reads double precision N-D array data !=============================================================================== + subroutine read_double_0D(buffer, obj_id, name, indep) + real(8), target, intent(inout) :: buffer + integer(HID_T), intent(in) :: obj_id + character(*), optional, intent(in) :: name + logical, optional, intent(in) :: indep ! independent I/O + + real(C_DOUBLE) :: buffer_(1) + 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 + name_ = to_c_string(name) + call read_double_c(obj_id, c_loc(name_), buffer_, indep_) + else + call read_double_c(obj_id, C_NULL_PTR, buffer_, indep_) + end if + buffer = buffer_(1) + end subroutine read_double_0D + subroutine read_double_1D(buffer, obj_id, name, indep) real(8), target, intent(inout) :: buffer(:) integer(HID_T), intent(in) :: obj_id @@ -627,50 +617,6 @@ contains ! READ_INTEGER reads integer precision scalar data !=============================================================================== - subroutine read_integer(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 :: data_xfer_mode -#ifdef PHDF5 - integer(HID_T) :: plist ! property list -#endif - integer(HID_T) :: dset_id - type(c_ptr) :: f_ptr - - ! 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) - else - dset_id = obj_id - end if - - ! 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 - - if (present(name)) call h5dclose_f(dset_id, hdf5_err) - end subroutine read_integer - !=============================================================================== ! WRITE_INTEGER_ND writes integer precision N-D array data !=============================================================================== @@ -757,269 +703,121 @@ contains end subroutine write_integer_4D !=============================================================================== -! READ_INTEGER_1D reads integer precision 1-D array data +! READ_INTEGER_ND reads integer precision N-D array data !=============================================================================== + subroutine read_integer_0D(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(C_INT) :: buffer_(1) + 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 + name_ = to_c_string(name) + call read_int_c(obj_id, c_loc(name_), buffer_, indep_) + else + call read_int_c(obj_id, C_NULL_PTR, buffer_, indep_) + end if + buffer = buffer_(1) + end subroutine read_integer_0D + subroutine read_integer_1D(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(1) + 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_1D_explicit(dset_id, dims, buffer, indep) - else - call read_integer_1D_explicit(dset_id, dims, buffer) - end if - - if (present(name)) call h5dclose_f(dset_id, hdf5_err) end subroutine read_integer_1D - subroutine read_integer_1D_explicit(dset_id, dims, buffer, indep) - integer(HID_T), intent(in) :: dset_id - integer(HSIZE_T), intent(in) :: dims(1) - integer, target, intent(inout) :: buffer(dims(1)) - 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_1D_explicit - -!=============================================================================== -! READ_INTEGER_2D reads integer precision 2-D array data -!=============================================================================== - subroutine read_integer_2D(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(2) + 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_2D_explicit(dset_id, dims, buffer, indep) - else - call read_integer_2D_explicit(dset_id, dims, buffer) - end if - - if (present(name)) call h5dclose_f(dset_id, hdf5_err) end subroutine read_integer_2D - subroutine read_integer_2D_explicit(dset_id, dims, buffer, indep) - integer(HID_T), intent(in) :: dset_id - integer(HSIZE_T), intent(in) :: dims(2) - integer, target, intent(inout) :: buffer(dims(1),dims(2)) - 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_2D_explicit - -!=============================================================================== -! READ_INTEGER_3D reads integer precision 3-D array data -!=============================================================================== - subroutine read_integer_3D(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(3) + 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_3D_explicit(dset_id, dims, buffer, indep) - else - call read_integer_3D_explicit(dset_id, dims, buffer) - end if - - if (present(name)) call h5dclose_f(dset_id, hdf5_err) end subroutine read_integer_3D - subroutine read_integer_3D_explicit(dset_id, dims, buffer, indep) - integer(HID_T), intent(in) :: dset_id - integer(HSIZE_T), intent(in) :: dims(3) - integer, target, intent(inout) :: buffer(dims(1),dims(2),dims(3)) - 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_3D_explicit - -!=============================================================================== -! 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 !=============================================================================== diff --git a/src/hdf5_interface.cpp b/src/hdf5_interface.cpp index 349c1876de..76b3d6feae 100644 --- a/src/hdf5_interface.cpp +++ b/src/hdf5_interface.cpp @@ -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) diff --git a/src/hdf5_interface.h b/src/hdf5_interface.h index f2bef3b0b7..b3efda48c2 100644 --- a/src/hdf5_interface.h +++ b/src/hdf5_interface.h @@ -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);