From ad3bb0b43acc4ec0ac8b338041205d9f37737904 Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Wed, 18 Apr 2018 22:54:51 -0500 Subject: [PATCH] Handle most writing of attributes in C++ --- src/hdf5_interface.F90 | 189 ++++++++++++----------------------------- src/hdf5_interface.cpp | 52 +++++++++++- src/hdf5_interface.h | 13 ++- 3 files changed, 115 insertions(+), 139 deletions(-) diff --git a/src/hdf5_interface.F90 b/src/hdf5_interface.F90 index 1d056e1dcd..bd14245526 100644 --- a/src/hdf5_interface.F90 +++ b/src/hdf5_interface.F90 @@ -105,6 +105,19 @@ module hdf5_interface integer(HID_T), value :: file_id end subroutine file_close + subroutine get_shape_c(obj_id, dims) bind(C, name='get_shape') + import HID_T, HSIZE_T + integer(HID_T), value :: obj_id + integer(HSIZE_T), intent(out) :: dims(*) + end subroutine get_shape_c + + subroutine get_shape_attr(obj_id, name, dims) bind(C) + import HID_T, HSIZE_T, C_CHAR + integer(HID_T), value :: obj_id + character(kind=C_CHAR), intent(in) :: name(*) + integer(HSIZE_T), intent(out) :: dims(*) + end subroutine get_shape_attr + subroutine read_double_c(obj_id, name, buffer, indep) & bind(C, name='read_double') import HID_T, C_DOUBLE, C_BOOL, C_PTR @@ -114,6 +127,22 @@ module hdf5_interface logical(C_BOOL), intent(in) :: indep end subroutine read_double_c + subroutine read_attr_int_c(obj_id, name, buffer) & + bind(C, name='read_attr_int') + import HID_T, C_CHAR, C_INT + integer(HID_T), value :: obj_id + character(kind=C_CHAR), intent(in) :: name(*) + integer(C_INT), intent(in) :: buffer(*) + end subroutine read_attr_int_c + + subroutine read_attr_double_c(obj_id, name, buffer) & + bind(C, name='read_attr_double') + import HID_T, C_CHAR, C_DOUBLE + integer(HID_T), value :: obj_id + character(kind=C_CHAR), intent(in) :: name(*) + real(C_DOUBLE), intent(in) :: buffer(*) + end subroutine read_attr_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 @@ -1178,14 +1207,10 @@ contains integer(HID_T), intent(in) :: obj_id character(*), intent(in) :: name - integer :: hdf5_err - integer(HID_T) :: attr_id - type(c_ptr) :: f_ptr + real(C_DOUBLE) :: buffer_(1) - call h5aopen_f(obj_id, trim(name), attr_id, hdf5_err) - f_ptr = c_loc(buffer) - call h5aread_f(attr_id, H5T_NATIVE_DOUBLE, f_ptr, hdf5_err) - call h5aclose_f(attr_id, hdf5_err) + call read_attr_double_c(obj_id, to_c_string(name), buffer_) + buffer = buffer_(1) end subroutine read_attribute_double subroutine write_attribute_double(obj_id, name, buffer) @@ -1205,39 +1230,16 @@ contains integer(HID_T), intent(in) :: obj_id character(*), intent(in) :: name - integer :: hdf5_err - integer(HID_T) :: space_id - integer(HID_T) :: attr_id integer(HSIZE_T) :: dims(1) - integer(HSIZE_T) :: maxdims(1) - call h5aopen_f(obj_id, trim(name), attr_id, hdf5_err) - - if (allocated(buffer)) then - dims(:) = shape(buffer) - else - call h5aget_space_f(attr_id, space_id, hdf5_err) - call h5sget_simple_extent_dims_f(space_id, dims, maxdims, hdf5_err) + if (.not. allocated(buffer)) then + call get_shape_attr(obj_id, to_c_string(name), dims) allocate(buffer(dims(1))) - call h5sclose_f(space_id, hdf5_err) end if - call read_attribute_double_1D_explicit(attr_id, dims, buffer) - call h5aclose_f(attr_id, hdf5_err) + call read_attr_double_c(obj_id, to_c_string(name), buffer) end subroutine read_attribute_double_1D - subroutine read_attribute_double_1D_explicit(attr_id, dims, buffer) - integer(HID_T), intent(in) :: attr_id - integer(HSIZE_T), intent(in) :: dims(1) - real(8), target, intent(inout) :: buffer(dims(1)) - - integer :: hdf5_err - type(c_ptr) :: f_ptr - - f_ptr = c_loc(buffer) - call h5aread_f(attr_id, H5T_NATIVE_DOUBLE, f_ptr, hdf5_err) - end subroutine read_attribute_double_1D_explicit - subroutine write_attribute_double_1D(obj_id, name, buffer) integer(HID_T), intent(in) :: obj_id character(*), intent(in) :: name @@ -1254,52 +1256,25 @@ contains integer(HID_T), intent(in) :: obj_id character(*), intent(in) :: name - integer :: hdf5_err - integer(HID_T) :: space_id - integer(HID_T) :: attr_id integer(HSIZE_T) :: dims(2) - integer(HSIZE_T) :: maxdims(2) - call h5aopen_f(obj_id, trim(name), attr_id, hdf5_err) - - if (allocated(buffer)) then - dims(:) = shape(buffer) - else - call h5aget_space_f(attr_id, space_id, hdf5_err) - call h5sget_simple_extent_dims_f(space_id, dims, maxdims, hdf5_err) - allocate(buffer(dims(1), dims(2))) - call h5sclose_f(space_id, hdf5_err) + if (.not. allocated(buffer)) then + call get_shape_attr(obj_id, to_c_string(name), dims) + allocate(buffer(dims(2), dims(1))) end if - call read_attribute_double_2D_explicit(attr_id, dims, buffer) - call h5aclose_f(attr_id, hdf5_err) + call read_attr_double_c(obj_id, to_c_string(name), buffer) end subroutine read_attribute_double_2D - subroutine read_attribute_double_2D_explicit(attr_id, dims, buffer) - integer(HID_T), intent(in) :: attr_id - integer(HSIZE_T), intent(in) :: dims(2) - real(8), target, intent(inout) :: buffer(dims(1),dims(2)) - - integer :: hdf5_err - type(c_ptr) :: f_ptr - - f_ptr = c_loc(buffer) - call h5aread_f(attr_id, H5T_NATIVE_DOUBLE, f_ptr, hdf5_err) - end subroutine read_attribute_double_2D_explicit - subroutine read_attribute_integer(buffer, obj_id, name) integer, intent(inout), target :: buffer integer(HID_T), intent(in) :: obj_id character(*), intent(in) :: name - integer :: hdf5_err - integer(HID_T) :: attr_id - type(c_ptr) :: f_ptr + integer(C_INT) :: buffer_(1) - call h5aopen_f(obj_id, trim(name), attr_id, hdf5_err) - f_ptr = c_loc(buffer) - call h5aread_f(attr_id, H5T_NATIVE_INTEGER, f_ptr, hdf5_err) - call h5aclose_f(attr_id, hdf5_err) + call read_attr_int_c(obj_id, to_c_string(name), buffer_) + buffer = buffer_(1) end subroutine read_attribute_integer subroutine write_attribute_integer(obj_id, name, buffer) @@ -1319,39 +1294,16 @@ contains integer(HID_T), intent(in) :: obj_id character(*), intent(in) :: name - integer :: hdf5_err - integer(HID_T) :: space_id - integer(HID_T) :: attr_id integer(HSIZE_T) :: dims(1) - integer(HSIZE_T) :: maxdims(1) - call h5aopen_f(obj_id, trim(name), attr_id, hdf5_err) - - if (allocated(buffer)) then - dims(:) = shape(buffer) - else - call h5aget_space_f(attr_id, space_id, hdf5_err) - call h5sget_simple_extent_dims_f(space_id, dims, maxdims, hdf5_err) + if (.not. allocated(buffer)) then + call get_shape_attr(obj_id, to_c_string(name), dims) allocate(buffer(dims(1))) - call h5sclose_f(space_id, hdf5_err) end if - call read_attribute_integer_1D_explicit(attr_id, dims, buffer) - call h5aclose_f(attr_id, hdf5_err) + call read_attr_int_c(obj_id, to_c_string(name), buffer) end subroutine read_attribute_integer_1D - subroutine read_attribute_integer_1D_explicit(attr_id, dims, buffer) - integer(HID_T), intent(in) :: attr_id - integer(HSIZE_T), intent(in) :: dims(1) - integer, target, intent(inout) :: buffer(dims(1)) - - integer :: hdf5_err - type(c_ptr) :: f_ptr - - f_ptr = c_loc(buffer) - call h5aread_f(attr_id, H5T_NATIVE_INTEGER, f_ptr, hdf5_err) - end subroutine read_attribute_integer_1D_explicit - subroutine write_attribute_integer_1D(obj_id, name, buffer) integer(HID_T), intent(in) :: obj_id character(*), intent(in) :: name @@ -1368,39 +1320,16 @@ contains integer(HID_T), intent(in) :: obj_id character(*), intent(in) :: name - integer :: hdf5_err - integer(HID_T) :: space_id - integer(HID_T) :: attr_id integer(HSIZE_T) :: dims(2) - integer(HSIZE_T) :: maxdims(2) - call h5aopen_f(obj_id, trim(name), attr_id, hdf5_err) - - if (allocated(buffer)) then - dims(:) = shape(buffer) - else - call h5aget_space_f(attr_id, space_id, hdf5_err) - call h5sget_simple_extent_dims_f(space_id, dims, maxdims, hdf5_err) - allocate(buffer(dims(1), dims(2))) - call h5sclose_f(space_id, hdf5_err) + if (.not. allocated(buffer)) then + call get_shape_attr(obj_id, to_c_string(name), dims) + allocate(buffer(dims(2), dims(1))) end if - call read_attribute_integer_2D_explicit(attr_id, dims, buffer) - call h5aclose_f(attr_id, hdf5_err) + call read_attr_int_C(obj_id, to_c_string(name), buffer) end subroutine read_attribute_integer_2D - subroutine read_attribute_integer_2D_explicit(attr_id, dims, buffer) - integer(HID_T), intent(in) :: attr_id - integer(HSIZE_T), intent(in) :: dims(2) - integer, target, intent(inout) :: buffer(dims(1),dims(2)) - - integer :: hdf5_err - type(c_ptr) :: f_ptr - - f_ptr = c_loc(buffer) - call h5aread_f(attr_id, H5T_NATIVE_INTEGER, f_ptr, hdf5_err) - end subroutine read_attribute_integer_2D_explicit - subroutine read_attribute_string(buffer, obj_id, name) character(*), intent(inout) :: buffer ! read data to here integer(HID_T), intent(in) :: obj_id @@ -1533,21 +1462,13 @@ contains integer(HID_T), intent(in) :: obj_id integer(HSIZE_T), intent(out) :: dims(:) - integer :: hdf5_err - integer :: type - integer(HID_T) :: space_id - integer(HSIZE_T) :: maxdims(size(dims)) + integer :: i + integer(HSIZE_T) :: dims_c(size(dims)) - call h5iget_type_f(obj_id, type, hdf5_err) - if (type == H5I_DATASET_F) then - call h5dget_space_f(obj_id, space_id, hdf5_err) - call h5sget_simple_extent_dims_f(space_id, dims, maxdims, hdf5_err) - call h5sclose_f(space_id, hdf5_err) - elseif (type == H5I_ATTR_F) then - call h5aget_space_f(obj_id, space_id, hdf5_err) - call h5sget_simple_extent_dims_f(space_id, dims, maxdims, hdf5_err) - call h5sclose_f(space_id, hdf5_err) - end if + call get_shape_c(obj_id, dims_c) + do i = 1, size(dims) + dims(i) = dims_c(size(dims) - i + 1) + end do end subroutine get_shape subroutine get_ndims(obj_id, ndims) diff --git a/src/hdf5_interface.cpp b/src/hdf5_interface.cpp index f482285f26..3e906a94ab 100644 --- a/src/hdf5_interface.cpp +++ b/src/hdf5_interface.cpp @@ -31,6 +31,32 @@ using_mpio_device(hid_t obj_id) } +void +get_shape(hid_t obj_id, hsize_t* dims) +{ + auto type = H5Iget_type(obj_id); + hid_t dspace; + if (type == H5I_DATASET) { + dspace = H5Dget_space(obj_id); + } else if (type == H5I_ATTR) { + dspace = H5Aget_space(obj_id); + } + H5Sget_simple_extent_dims(dspace, dims, nullptr); + H5Sclose(dspace); +} + + +void +get_shape_attr(hid_t obj_id, const char* name, hsize_t* dims) +{ + hid_t attr = H5Aopen(obj_id, name, H5P_DEFAULT); + hid_t dspace = H5Aget_space(attr); + H5Sget_simple_extent_dims(dspace, dims, nullptr); + H5Sclose(dspace); + H5Aclose(attr); +} + + hid_t create_group(hid_t parent_id, char const *name) { @@ -159,10 +185,32 @@ open_group(hid_t group_id, const char* name) } } +void +read_attr(hid_t obj_id, const char* name, hid_t mem_type_id, void* buffer) +{ + hid_t attr = H5Aopen(obj_id, name, H5P_DEFAULT); + H5Aread(attr, mem_type_id, buffer); + H5Aclose(attr); +} + + +void +read_attr_double(hid_t obj_id, const char* name, double* buffer) +{ + read_attr(obj_id, name, H5T_NATIVE_DOUBLE, buffer); +} + + +void +read_attr_int(hid_t obj_id, const char* name, int* buffer) +{ + read_attr(obj_id, name, H5T_NATIVE_INT, buffer); +} + void read_dataset(hid_t obj_id, const char* name, hid_t mem_type_id, - void* buffer, bool indep) + void* buffer, bool indep) { hid_t dset = obj_id; if (name) dset = H5Dopen(obj_id, name, H5P_DEFAULT); @@ -176,7 +224,7 @@ read_dataset(hid_t obj_id, const char* name, hid_t mem_type_id, hid_t plist = H5Pcreate(H5P_DATASET_XFER); H5Pset_dxpl_mpio(plist, data_xfer_mode); - // Write data + // Read data H5Dread(dset, mem_type_id, H5S_ALL, H5S_ALL, plist, buffer); H5Pclose(plist); #endif diff --git a/src/hdf5_interface.h b/src/hdf5_interface.h index 615bed24c7..ca5e27e7e8 100644 --- a/src/hdf5_interface.h +++ b/src/hdf5_interface.h @@ -11,7 +11,6 @@ namespace openmc { -bool using_mpio_device(hid_t obj_id); hid_t create_group(hid_t parent_id, const char* name); hid_t create_group(hid_t parent_id, const std::string& name); void close_dataset(hid_t dataset_id); @@ -19,9 +18,12 @@ void close_group(hid_t group_id); extern "C" hid_t file_open(const char* filename, char mode, bool parallel); hid_t file_open(const std::string& filename, char mode, bool parallel); extern "C" void file_close(hid_t file_id); +extern "C" void get_shape(hid_t obj_if, hsize_t* dims); +extern "C" void get_shape_attr(hid_t obj_if, const char* name, hsize_t* dims); bool object_exists(hid_t object_id, const char* name); hid_t open_dataset(hid_t group_id, const char* name); hid_t open_group(hid_t group_id, const char* name); +bool using_mpio_device(hid_t obj_id); template void @@ -41,8 +43,13 @@ write_double_1D(hid_t group_id, char const *name, H5Dclose(dataset); } -void read_dataset(hid_t obj_id, const char* name, double* buffer, - hid_t mem_type_id, bool indep); +void read_attr(hid_t obj_id, const char* name, hid_t mem_type_id, + const void* buffer); +extern "C" void read_attr_double(hid_t obj_id, const char* name, double* buffer); +extern "C" void read_attr_int(hid_t obj_id, const char* name, int* buffer); + +void read_dataset(hid_t obj_id, const char* name, hid_t mem_type_id, + void* buffer, 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,