diff options
Diffstat (limited to 'src/H5Dio.c')
| -rw-r--r-- | src/H5Dio.c | 675 |
1 files changed, 333 insertions, 342 deletions
diff --git a/src/H5Dio.c b/src/H5Dio.c index 63ae221..50c474b 100644 --- a/src/H5Dio.c +++ b/src/H5Dio.c @@ -15,55 +15,49 @@ /* Module Setup */ /****************/ -#include "H5Dmodule.h" /* This source code file is part of the H5D module */ - +#include "H5Dmodule.h" /* This source code file is part of the H5D module */ /***********/ /* Headers */ /***********/ -#include "H5private.h" /* Generic Functions */ -#include "H5CXprivate.h" /* API Contexts */ -#include "H5Dpkg.h" /* Dataset functions */ -#include "H5Eprivate.h" /* Error handling */ -#include "H5FLprivate.h" /* Free Lists */ -#include "H5Iprivate.h" /* IDs */ -#include "H5MMprivate.h" /* Memory management */ -#include "H5Sprivate.h" /* Dataspace */ +#include "H5private.h" /* Generic Functions */ +#include "H5CXprivate.h" /* API Contexts */ +#include "H5Dpkg.h" /* Dataset functions */ +#include "H5Eprivate.h" /* Error handling */ +#include "H5FLprivate.h" /* Free Lists */ +#include "H5Iprivate.h" /* IDs */ +#include "H5MMprivate.h" /* Memory management */ +#include "H5Sprivate.h" /* Dataspace */ #include "H5VLnative_private.h" /* Native VOL connector */ - /****************/ /* Local Macros */ /****************/ - /******************/ /* Local Typedefs */ /******************/ - /********************/ /* Local Prototypes */ /********************/ /* Setup/teardown routines */ -static herr_t H5D__ioinfo_init(H5D_t *dset, const H5D_type_info_t *type_info, - H5D_storage_t *store, H5D_io_info_t *io_info); -static herr_t H5D__typeinfo_init(const H5D_t *dset, hid_t mem_type_id, - hbool_t do_write, H5D_type_info_t *type_info); +static herr_t H5D__ioinfo_init(H5D_t *dset, const H5D_type_info_t *type_info, H5D_storage_t *store, + H5D_io_info_t *io_info); +static herr_t H5D__typeinfo_init(const H5D_t *dset, hid_t mem_type_id, hbool_t do_write, + H5D_type_info_t *type_info); #ifdef H5_HAVE_PARALLEL -static herr_t H5D__ioinfo_adjust(H5D_io_info_t *io_info, const H5D_t *dset, - const H5S_t *file_space, const H5S_t *mem_space, const H5D_type_info_t *type_info); +static herr_t H5D__ioinfo_adjust(H5D_io_info_t *io_info, const H5D_t *dset, const H5S_t *file_space, + const H5S_t *mem_space, const H5D_type_info_t *type_info); #endif /* H5_HAVE_PARALLEL */ static herr_t H5D__typeinfo_term(const H5D_type_info_t *type_info); - /*********************/ /* Package Variables */ /*********************/ - /*******************/ /* Local Variables */ /*******************/ @@ -74,8 +68,6 @@ H5FL_BLK_DEFINE(type_conv); /* Declare a free list to manage the H5D_chunk_map_t struct */ H5FL_DEFINE(H5D_chunk_map_t); - - /*------------------------------------------------------------------------- * Function: H5D__get_offset_copy * @@ -93,7 +85,7 @@ herr_t H5D__get_offset_copy(const H5D_t *dset, const hsize_t *offset, hsize_t *offset_copy) { unsigned u; - herr_t ret_value = SUCCEED; /* Return value */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(FAIL) @@ -125,7 +117,6 @@ done: } /* end H5D__get_offset_copy() */ - /*------------------------------------------------------------------------- * Function: H5Dread * @@ -157,15 +148,14 @@ done: *------------------------------------------------------------------------- */ herr_t -H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, - hid_t file_space_id, hid_t dxpl_id, void *buf/*out*/) +H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t dxpl_id, + void *buf /*out*/) { - H5VL_object_t *vol_obj = NULL; - herr_t ret_value = SUCCEED; /* Return value */ + H5VL_object_t *vol_obj = NULL; + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_API(FAIL) - H5TRACE6("e", "iiiiix", dset_id, mem_type_id, mem_space_id, file_space_id, - dxpl_id, buf); + H5TRACE6("e", "iiiiix", dset_id, mem_type_id, mem_space_id, file_space_id, dxpl_id, buf); /* Check arguments */ if (mem_space_id < 0) @@ -180,19 +170,18 @@ H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, /* Get the default dataset transfer property list if the user didn't provide one */ if (H5P_DEFAULT == dxpl_id) dxpl_id = H5P_DATASET_XFER_DEFAULT; - else - if (TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER)) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms") + else if (TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER)) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms") /* Read the data */ - if ((ret_value = H5VL_dataset_read(vol_obj, mem_type_id, mem_space_id, file_space_id, dxpl_id, buf, H5_REQUEST_NULL)) < 0) + if ((ret_value = H5VL_dataset_read(vol_obj, mem_type_id, mem_space_id, file_space_id, dxpl_id, buf, + H5_REQUEST_NULL)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data") done: FUNC_LEAVE_API(ret_value) } /* end H5Dread() */ - /*------------------------------------------------------------------------- * Function: H5Dread_chunk * @@ -206,11 +195,10 @@ done: *--------------------------------------------------------------------------- */ herr_t -H5Dread_chunk(hid_t dset_id, hid_t dxpl_id, const hsize_t *offset, uint32_t *filters, - void *buf) +H5Dread_chunk(hid_t dset_id, hid_t dxpl_id, const hsize_t *offset, uint32_t *filters, void *buf) { - H5VL_object_t *vol_obj = NULL; - herr_t ret_value = SUCCEED; /* Return value */ + H5VL_object_t *vol_obj = NULL; + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_API(FAIL) H5TRACE5("e", "ii*h*Iu*x", dset_id, dxpl_id, offset, filters, buf); @@ -228,19 +216,18 @@ H5Dread_chunk(hid_t dset_id, hid_t dxpl_id, const hsize_t *offset, uint32_t *fil /* Get the default dataset transfer property list if the user didn't provide one */ if (H5P_DEFAULT == dxpl_id) dxpl_id = H5P_DATASET_XFER_DEFAULT; - else - if (TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER)) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dxpl_id is not a dataset transfer property list ID") + else if (TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER)) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dxpl_id is not a dataset transfer property list ID") /* Read the raw chunk */ - if(H5VL_dataset_optional(vol_obj, H5VL_NATIVE_DATASET_CHUNK_READ, dxpl_id, H5_REQUEST_NULL, offset, filters, buf) < 0) + if (H5VL_dataset_optional(vol_obj, H5VL_NATIVE_DATASET_CHUNK_READ, dxpl_id, H5_REQUEST_NULL, offset, + filters, buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read unprocessed chunk data") done: FUNC_LEAVE_API(ret_value) } /* end H5Dread_chunk() */ - /*------------------------------------------------------------------------- * Function: H5Dwrite * @@ -273,15 +260,14 @@ done: *------------------------------------------------------------------------- */ herr_t -H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, - hid_t file_space_id, hid_t dxpl_id, const void *buf) +H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t dxpl_id, + const void *buf) { - H5VL_object_t *vol_obj = NULL; - herr_t ret_value = SUCCEED; /* Return value */ + H5VL_object_t *vol_obj = NULL; + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_API(FAIL) - H5TRACE6("e", "iiiii*x", dset_id, mem_type_id, mem_space_id, file_space_id, - dxpl_id, buf); + H5TRACE6("e", "iiiii*x", dset_id, mem_type_id, mem_space_id, file_space_id, dxpl_id, buf); /* Check arguments */ if (mem_space_id < 0) @@ -296,19 +282,18 @@ H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, /* Get the default dataset transfer property list if the user didn't provide one */ if (H5P_DEFAULT == dxpl_id) dxpl_id = H5P_DATASET_XFER_DEFAULT; - else - if (TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER)) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms") + else if (TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER)) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms") /* Write the data */ - if ((ret_value = H5VL_dataset_write(vol_obj, mem_type_id, mem_space_id, file_space_id, dxpl_id, buf, H5_REQUEST_NULL)) < 0) + if ((ret_value = H5VL_dataset_write(vol_obj, mem_type_id, mem_space_id, file_space_id, dxpl_id, buf, + H5_REQUEST_NULL)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data") done: FUNC_LEAVE_API(ret_value) } /* end H5Dwrite() */ - /*------------------------------------------------------------------------- * Function: H5Dwrite_chunk * @@ -322,12 +307,12 @@ done: *------------------------------------------------------------------------- */ herr_t -H5Dwrite_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, const hsize_t *offset, - size_t data_size, const void *buf) +H5Dwrite_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, const hsize_t *offset, size_t data_size, + const void *buf) { - H5VL_object_t *vol_obj = NULL; - uint32_t data_size_32; /* Chunk data size (limited to 32-bits currently) */ - herr_t ret_value = SUCCEED; /* Return value */ + H5VL_object_t *vol_obj = NULL; + uint32_t data_size_32; /* Chunk data size (limited to 32-bits currently) */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_API(FAIL) H5TRACE6("e", "iiIu*hz*x", dset_id, dxpl_id, filters, offset, data_size, buf); @@ -350,19 +335,18 @@ H5Dwrite_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, const hsize_t *of /* Get the default dataset transfer property list if the user didn't provide one */ if (H5P_DEFAULT == dxpl_id) dxpl_id = H5P_DATASET_XFER_DEFAULT; - else - if (TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER)) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dxpl_id is not a dataset transfer property list ID") + else if (TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER)) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dxpl_id is not a dataset transfer property list ID") /* Write chunk */ - if(H5VL_dataset_optional(vol_obj, H5VL_NATIVE_DATASET_CHUNK_WRITE, dxpl_id, H5_REQUEST_NULL, filters, offset, data_size_32, buf) < 0) + if (H5VL_dataset_optional(vol_obj, H5VL_NATIVE_DATASET_CHUNK_WRITE, dxpl_id, H5_REQUEST_NULL, filters, + offset, data_size_32, buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write unprocessed chunk data") done: FUNC_LEAVE_API(ret_value) } /* end H5Dwrite_chunk() */ - /*------------------------------------------------------------------------- * Function: H5D__read * @@ -377,84 +361,85 @@ done: *------------------------------------------------------------------------- */ herr_t -H5D__read(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space, - const H5S_t *file_space, void *buf/*out*/) +H5D__read(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space, const H5S_t *file_space, + void *buf /*out*/) { - H5D_chunk_map_t *fm = NULL; /* Chunk file<->memory mapping */ - H5D_io_info_t io_info; /* Dataset I/O info */ - H5D_type_info_t type_info; /* Datatype info for operation */ - hbool_t type_info_init = FALSE; /* Whether the datatype info has been initialized */ - H5S_t * projected_mem_space = NULL; /* If not NULL, ptr to dataspace containing a */ - /* projection of the supplied mem_space to a new */ - /* dataspace with rank equal to that of */ - /* file_space. */ - /* */ - /* This field is only used if */ - /* H5S_select_shape_same() returns TRUE when */ - /* comparing the mem_space and the data_space, */ - /* and the mem_space have different rank. */ - /* */ - /* Note that if this variable is used, the */ - /* projected mem space must be discarded at the */ - /* end of the function to avoid a memory leak. */ - H5D_storage_t store; /* union of EFL and chunk pointer in file space */ - hsize_t nelmts; /* total number of elmts */ - hbool_t io_op_init = FALSE; /* Whether the I/O op has been initialized */ - char fake_char; /* Temporary variable for NULL buffer pointers */ - herr_t ret_value = SUCCEED; /* Return value */ + H5D_chunk_map_t *fm = NULL; /* Chunk file<->memory mapping */ + H5D_io_info_t io_info; /* Dataset I/O info */ + H5D_type_info_t type_info; /* Datatype info for operation */ + hbool_t type_info_init = FALSE; /* Whether the datatype info has been initialized */ + H5S_t * projected_mem_space = NULL; /* If not NULL, ptr to dataspace containing a */ + /* projection of the supplied mem_space to a new */ + /* dataspace with rank equal to that of */ + /* file_space. */ + /* */ + /* This field is only used if */ + /* H5S_select_shape_same() returns TRUE when */ + /* comparing the mem_space and the data_space, */ + /* and the mem_space have different rank. */ + /* */ + /* Note that if this variable is used, the */ + /* projected mem space must be discarded at the */ + /* end of the function to avoid a memory leak. */ + H5D_storage_t store; /* union of EFL and chunk pointer in file space */ + hsize_t nelmts; /* total number of elmts */ + hbool_t io_op_init = FALSE; /* Whether the I/O op has been initialized */ + char fake_char; /* Temporary variable for NULL buffer pointers */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE_TAG(dataset->oloc.addr) /* check args */ HDassert(dataset && dataset->oloc.file); - if(!file_space) + if (!file_space) file_space = dataset->shared->space; - if(!mem_space) + if (!mem_space) mem_space = file_space; nelmts = H5S_GET_SELECT_NPOINTS(mem_space); /* Set up datatype info for operation */ - if(H5D__typeinfo_init(dataset, mem_type_id, FALSE, &type_info) < 0) + if (H5D__typeinfo_init(dataset, mem_type_id, FALSE, &type_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set up type info") type_info_init = TRUE; #ifdef H5_HAVE_PARALLEL /* Check for non-MPI-based VFD */ - if(!(H5F_HAS_FEATURE(dataset->oloc.file, H5FD_FEAT_HAS_MPI))) { - H5FD_mpio_xfer_t io_xfer_mode; /* MPI I/O transfer mode */ + if (!(H5F_HAS_FEATURE(dataset->oloc.file, H5FD_FEAT_HAS_MPI))) { + H5FD_mpio_xfer_t io_xfer_mode; /* MPI I/O transfer mode */ /* Get I/O transfer mode */ - if(H5CX_get_io_xfer_mode(&io_xfer_mode) < 0) + if (H5CX_get_io_xfer_mode(&io_xfer_mode) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get MPI-I/O transfer mode") /* Collective access is not permissible without a MPI based VFD */ - if(io_xfer_mode == H5FD_MPIO_COLLECTIVE) + if (io_xfer_mode == H5FD_MPIO_COLLECTIVE) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access for MPI-based drivers only") - } /* end if */ + } /* end if */ #endif /*H5_HAVE_PARALLEL*/ /* Make certain that the number of elements in each selection is the same */ - if(nelmts != H5S_GET_SELECT_NPOINTS(file_space)) - HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest dataspaces have different number of elements selected") + if (nelmts != H5S_GET_SELECT_NPOINTS(file_space)) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, + "src and dest dataspaces have different number of elements selected") /* Check for a NULL buffer, after the H5S_ALL dataspace selection has been handled */ - if(NULL == buf) { + if (NULL == buf) { /* Check for any elements selected (which is invalid) */ - if(nelmts > 0) + if (nelmts > 0) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer") - /* If the buffer is nil, and 0 element is selected, make a fake buffer. - * This is for some MPI package like ChaMPIon on NCSA's tungsten which - * doesn't support this feature. - */ + /* If the buffer is nil, and 0 element is selected, make a fake buffer. + * This is for some MPI package like ChaMPIon on NCSA's tungsten which + * doesn't support this feature. + */ buf = &fake_char; } /* end if */ /* Make sure that both selections have their extents set */ - if(!(H5S_has_extent(file_space))) + if (!(H5S_has_extent(file_space))) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "file dataspace does not have extent set") - if(!(H5S_has_extent(mem_space))) + if (!(H5S_has_extent(mem_space))) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "memory dataspace does not have extent set") /* H5S_select_shape_same() has been modified to accept topologically identical @@ -470,23 +455,23 @@ H5D__read(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space, * Note that in general, this requires us to touch up the memory buffer as * well. */ - if(TRUE == H5S_SELECT_SHAPE_SAME(mem_space, file_space) && - H5S_GET_EXTENT_NDIMS(mem_space) != H5S_GET_EXTENT_NDIMS(file_space)) { - const void *adj_buf = NULL; /* Pointer to the location in buf corresponding */ - /* to the beginning of the projected mem space. */ + if (TRUE == H5S_SELECT_SHAPE_SAME(mem_space, file_space) && + H5S_GET_EXTENT_NDIMS(mem_space) != H5S_GET_EXTENT_NDIMS(file_space)) { + const void *adj_buf = NULL; /* Pointer to the location in buf corresponding */ + /* to the beginning of the projected mem space. */ /* Attempt to construct projected dataspace for memory dataspace */ - if(H5S_select_construct_projection(mem_space, &projected_mem_space, - (unsigned)H5S_GET_EXTENT_NDIMS(file_space), buf, &adj_buf, type_info.dst_type_size) < 0) + if (H5S_select_construct_projection(mem_space, &projected_mem_space, + (unsigned)H5S_GET_EXTENT_NDIMS(file_space), buf, &adj_buf, + type_info.dst_type_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to construct projected memory dataspace") HDassert(projected_mem_space); HDassert(adj_buf); /* Switch to using projected memory dataspace & adjusted buffer */ mem_space = projected_mem_space; - buf = (void *)adj_buf; /* Casting away 'const' OK -QAK */ - } /* end if */ - + buf = (void *)adj_buf; /* Casting away 'const' OK -QAK */ + } /* end if */ /* Retrieve dataset properties */ /* <none needed in the general case> */ @@ -497,26 +482,30 @@ H5D__read(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space, * fill time is NEVER, there is no way to tell whether part of data * has been overwritten. So just proceed in reading. */ - if(nelmts > 0 && dataset->shared->dcpl_cache.efl.nused == 0 && - !(*dataset->shared->layout.ops->is_space_alloc)(&dataset->shared->layout.storage) && - !(dataset->shared->layout.ops->is_data_cached && (*dataset->shared->layout.ops->is_data_cached)(dataset->shared))) { - H5D_fill_value_t fill_status; /* Whether/How the fill value is defined */ + if (nelmts > 0 && dataset->shared->dcpl_cache.efl.nused == 0 && + !(*dataset->shared->layout.ops->is_space_alloc)(&dataset->shared->layout.storage) && + !(dataset->shared->layout.ops->is_data_cached && + (*dataset->shared->layout.ops->is_data_cached)(dataset->shared))) { + H5D_fill_value_t fill_status; /* Whether/How the fill value is defined */ /* Retrieve dataset's fill-value properties */ - if(H5P_is_fill_value_defined(&dataset->shared->dcpl_cache.fill, &fill_status) < 0) + if (H5P_is_fill_value_defined(&dataset->shared->dcpl_cache.fill, &fill_status) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined") /* Should be impossible, but check anyway... */ - if(fill_status == H5D_FILL_VALUE_UNDEFINED && - (dataset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_ALLOC || dataset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_IFSET)) - HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "read failed: dataset doesn't exist, no data can be read") + if (fill_status == H5D_FILL_VALUE_UNDEFINED && + (dataset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_ALLOC || + dataset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_IFSET)) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, + "read failed: dataset doesn't exist, no data can be read") /* If we're never going to fill this dataset, just leave the junk in the user's buffer */ - if(dataset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_NEVER) + if (dataset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_NEVER) HGOTO_DONE(SUCCEED) /* Go fill the user's selection with the dataset's fill value */ - if(H5D__fill(dataset->shared->dcpl_cache.fill.buf, dataset->shared->type, buf, type_info.mem_type, mem_space) < 0) + if (H5D__fill(dataset->shared->dcpl_cache.fill.buf, dataset->shared->type, buf, type_info.mem_type, + mem_space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "filling buf failed") else HGOTO_DONE(SUCCEED) @@ -524,56 +513,56 @@ H5D__read(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space, /* Set up I/O operation */ io_info.op_type = H5D_IO_OP_READ; - io_info.u.rbuf = buf; - if(H5D__ioinfo_init(dataset, &type_info, &store, &io_info) < 0) + io_info.u.rbuf = buf; + if (H5D__ioinfo_init(dataset, &type_info, &store, &io_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to set up I/O operation") /* Sanity check that space is allocated, if there are elements */ - if(nelmts > 0) - HDassert((*dataset->shared->layout.ops->is_space_alloc)(&dataset->shared->layout.storage) - || (dataset->shared->layout.ops->is_data_cached && (*dataset->shared->layout.ops->is_data_cached)(dataset->shared)) - || dataset->shared->dcpl_cache.efl.nused > 0 - || dataset->shared->layout.type == H5D_COMPACT); + if (nelmts > 0) + HDassert((*dataset->shared->layout.ops->is_space_alloc)(&dataset->shared->layout.storage) || + (dataset->shared->layout.ops->is_data_cached && + (*dataset->shared->layout.ops->is_data_cached)(dataset->shared)) || + dataset->shared->dcpl_cache.efl.nused > 0 || dataset->shared->layout.type == H5D_COMPACT); /* Allocate the chunk map */ - if(NULL == (fm = H5FL_CALLOC(H5D_chunk_map_t))) + if (NULL == (fm = H5FL_CALLOC(H5D_chunk_map_t))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate chunk map") /* Call storage method's I/O initialization routine */ - if(io_info.layout_ops.io_init && (*io_info.layout_ops.io_init)(&io_info, &type_info, nelmts, file_space, mem_space, fm) < 0) + if (io_info.layout_ops.io_init && + (*io_info.layout_ops.io_init)(&io_info, &type_info, nelmts, file_space, mem_space, fm) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize I/O info") io_op_init = TRUE; #ifdef H5_HAVE_PARALLEL /* Adjust I/O info for any parallel I/O */ - if(H5D__ioinfo_adjust(&io_info, dataset, file_space, mem_space, &type_info) < 0) + if (H5D__ioinfo_adjust(&io_info, dataset, file_space, mem_space, &type_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to adjust I/O info for parallel I/O") #endif /*H5_HAVE_PARALLEL*/ /* Invoke correct "high level" I/O routine */ - if((*io_info.io_ops.multi_read)(&io_info, &type_info, nelmts, file_space, mem_space, fm) < 0) + if ((*io_info.io_ops.multi_read)(&io_info, &type_info, nelmts, file_space, mem_space, fm) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data") done: /* Shut down the I/O op information */ - if(io_op_init && io_info.layout_ops.io_term && (*io_info.layout_ops.io_term)(fm) < 0) + if (io_op_init && io_info.layout_ops.io_term && (*io_info.layout_ops.io_term)(fm) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down I/O op info") - if(fm) + if (fm) fm = H5FL_FREE(H5D_chunk_map_t, fm); /* Shut down datatype info for operation */ - if(type_info_init && H5D__typeinfo_term(&type_info) < 0) + if (type_info_init && H5D__typeinfo_term(&type_info) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down type info") /* discard projected mem space if it was created */ - if(NULL != projected_mem_space) - if(H5S_close(projected_mem_space) < 0) + if (NULL != projected_mem_space) + if (H5S_close(projected_mem_space) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down projected memory dataspace") FUNC_LEAVE_NOAPI_TAG(ret_value) } /* end H5D__read() */ - /*------------------------------------------------------------------------- * Function: H5D__write * @@ -588,31 +577,31 @@ done: *------------------------------------------------------------------------- */ herr_t -H5D__write(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space, - const H5S_t *file_space, const void *buf) +H5D__write(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space, const H5S_t *file_space, + const void *buf) { - H5D_chunk_map_t *fm = NULL; /* Chunk file<->memory mapping */ - H5D_io_info_t io_info; /* Dataset I/O info */ - H5D_type_info_t type_info; /* Datatype info for operation */ - hbool_t type_info_init = FALSE; /* Whether the datatype info has been initialized */ - H5S_t * projected_mem_space = NULL; /* If not NULL, ptr to dataspace containing a */ - /* projection of the supplied mem_space to a new */ - /* dataspace with rank equal to that of */ - /* file_space. */ - /* */ - /* This field is only used if */ - /* H5S_select_shape_same() returns TRUE when */ - /* comparing the mem_space and the data_space, */ - /* and the mem_space have different rank. */ - /* */ - /* Note that if this variable is used, the */ - /* projected mem space must be discarded at the */ - /* end of the function to avoid a memory leak. */ - H5D_storage_t store; /* union of EFL and chunk pointer in file space */ - hsize_t nelmts; /* total number of elmts */ - hbool_t io_op_init = FALSE; /* Whether the I/O op has been initialized */ - char fake_char; /* Temporary variable for NULL buffer pointers */ - herr_t ret_value = SUCCEED; /* Return value */ + H5D_chunk_map_t *fm = NULL; /* Chunk file<->memory mapping */ + H5D_io_info_t io_info; /* Dataset I/O info */ + H5D_type_info_t type_info; /* Datatype info for operation */ + hbool_t type_info_init = FALSE; /* Whether the datatype info has been initialized */ + H5S_t * projected_mem_space = NULL; /* If not NULL, ptr to dataspace containing a */ + /* projection of the supplied mem_space to a new */ + /* dataspace with rank equal to that of */ + /* file_space. */ + /* */ + /* This field is only used if */ + /* H5S_select_shape_same() returns TRUE when */ + /* comparing the mem_space and the data_space, */ + /* and the mem_space have different rank. */ + /* */ + /* Note that if this variable is used, the */ + /* projected mem space must be discarded at the */ + /* end of the function to avoid a memory leak. */ + H5D_storage_t store; /* union of EFL and chunk pointer in file space */ + hsize_t nelmts; /* total number of elmts */ + hbool_t io_op_init = FALSE; /* Whether the I/O op has been initialized */ + char fake_char; /* Temporary variable for NULL buffer pointers */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE_TAG(dataset->oloc.addr) @@ -620,73 +609,75 @@ H5D__write(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space, HDassert(dataset && dataset->oloc.file); /* All filters in the DCPL must have encoding enabled. */ - if(!dataset->shared->checked_filters) { - if(H5Z_can_apply(dataset->shared->dcpl_id, dataset->shared->type_id) < 0) + if (!dataset->shared->checked_filters) { + if (H5Z_can_apply(dataset->shared->dcpl_id, dataset->shared->type_id) < 0) HGOTO_ERROR(H5E_PLINE, H5E_CANAPPLY, FAIL, "can't apply filters") dataset->shared->checked_filters = TRUE; } /* end if */ /* Check if we are allowed to write to this file */ - if(0 == (H5F_INTENT(dataset->oloc.file) & H5F_ACC_RDWR)) + if (0 == (H5F_INTENT(dataset->oloc.file) & H5F_ACC_RDWR)) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "no write intent on file") /* Set up datatype info for operation */ - if(H5D__typeinfo_init(dataset, mem_type_id, TRUE, &type_info) < 0) + if (H5D__typeinfo_init(dataset, mem_type_id, TRUE, &type_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set up type info") type_info_init = TRUE; /* Various MPI based checks */ #ifdef H5_HAVE_PARALLEL - if(H5F_HAS_FEATURE(dataset->oloc.file, H5FD_FEAT_HAS_MPI)) { + if (H5F_HAS_FEATURE(dataset->oloc.file, H5FD_FEAT_HAS_MPI)) { /* If MPI based VFD is used, no VL or region reference datatype support yet. */ /* This is because they use the global heap in the file and we don't */ /* support parallel access of that yet */ - if(H5T_is_vl_storage(type_info.mem_type) > 0) - HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Parallel IO does not support writing VL or region reference datatypes yet") + if (H5T_is_vl_storage(type_info.mem_type) > 0) + HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, + "Parallel IO does not support writing VL or region reference datatypes yet") } /* end if */ else { - H5FD_mpio_xfer_t io_xfer_mode; /* MPI I/O transfer mode */ + H5FD_mpio_xfer_t io_xfer_mode; /* MPI I/O transfer mode */ /* Get I/O transfer mode */ - if(H5CX_get_io_xfer_mode(&io_xfer_mode) < 0) + if (H5CX_get_io_xfer_mode(&io_xfer_mode) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get MPI-I/O transfer mode") /* Collective access is not permissible without a MPI based VFD */ - if(io_xfer_mode == H5FD_MPIO_COLLECTIVE) + if (io_xfer_mode == H5FD_MPIO_COLLECTIVE) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access for MPI-based driver only") - } /* end else */ + } /* end else */ #endif /*H5_HAVE_PARALLEL*/ /* Initialize dataspace information */ - if(!file_space) + if (!file_space) file_space = dataset->shared->space; - if(!mem_space) + if (!mem_space) mem_space = file_space; nelmts = H5S_GET_SELECT_NPOINTS(mem_space); /* Make certain that the number of elements in each selection is the same */ - if(nelmts != H5S_GET_SELECT_NPOINTS(file_space)) - HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest dataspaces have different number of elements selected") + if (nelmts != H5S_GET_SELECT_NPOINTS(file_space)) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, + "src and dest dataspaces have different number of elements selected") /* Check for a NULL buffer, after the H5S_ALL dataspace selection has been handled */ - if(NULL == buf) { + if (NULL == buf) { /* Check for any elements selected (which is invalid) */ - if(nelmts > 0) + if (nelmts > 0) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer") - /* If the buffer is nil, and 0 element is selected, make a fake buffer. - * This is for some MPI package like ChaMPIon on NCSA's tungsten which - * doesn't support this feature. - */ + /* If the buffer is nil, and 0 element is selected, make a fake buffer. + * This is for some MPI package like ChaMPIon on NCSA's tungsten which + * doesn't support this feature. + */ buf = &fake_char; } /* end if */ /* Make sure that both selections have their extents set */ - if(!(H5S_has_extent(file_space))) + if (!(H5S_has_extent(file_space))) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "file dataspace does not have extent set") - if(!(H5S_has_extent(mem_space))) + if (!(H5S_has_extent(mem_space))) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "memory dataspace does not have extent set") /* H5S_select_shape_same() has been modified to accept topologically @@ -702,21 +693,22 @@ H5D__write(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space, * Note that in general, this requires us to touch up the memory buffer * as well. */ - if(TRUE == H5S_SELECT_SHAPE_SAME(mem_space, file_space) && - H5S_GET_EXTENT_NDIMS(mem_space) != H5S_GET_EXTENT_NDIMS(file_space)) { - const void *adj_buf = NULL; /* Pointer to the location in buf corresponding */ - /* to the beginning of the projected mem space. */ + if (TRUE == H5S_SELECT_SHAPE_SAME(mem_space, file_space) && + H5S_GET_EXTENT_NDIMS(mem_space) != H5S_GET_EXTENT_NDIMS(file_space)) { + const void *adj_buf = NULL; /* Pointer to the location in buf corresponding */ + /* to the beginning of the projected mem space. */ /* Attempt to construct projected dataspace for memory dataspace */ - if(H5S_select_construct_projection(mem_space, &projected_mem_space, - (unsigned)H5S_GET_EXTENT_NDIMS(file_space), buf, &adj_buf, type_info.src_type_size) < 0) + if (H5S_select_construct_projection(mem_space, &projected_mem_space, + (unsigned)H5S_GET_EXTENT_NDIMS(file_space), buf, &adj_buf, + type_info.src_type_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to construct projected memory dataspace") HDassert(projected_mem_space); HDassert(adj_buf); /* Switch to using projected memory dataspace & adjusted buffer */ mem_space = projected_mem_space; - buf = adj_buf; + buf = adj_buf; } /* end if */ /* Retrieve dataset properties */ @@ -724,88 +716,88 @@ H5D__write(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space, /* Set up I/O operation */ io_info.op_type = H5D_IO_OP_WRITE; - io_info.u.wbuf = buf; - if(H5D__ioinfo_init(dataset, &type_info, &store, &io_info) < 0) + io_info.u.wbuf = buf; + if (H5D__ioinfo_init(dataset, &type_info, &store, &io_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set up I/O operation") /* Allocate dataspace and initialize it if it hasn't been. */ - if(nelmts > 0 && dataset->shared->dcpl_cache.efl.nused == 0 && - !(*dataset->shared->layout.ops->is_space_alloc)(&dataset->shared->layout.storage)) { - hssize_t file_nelmts; /* Number of elements in file dataset's dataspace */ - hbool_t full_overwrite; /* Whether we are over-writing all the elements */ + if (nelmts > 0 && dataset->shared->dcpl_cache.efl.nused == 0 && + !(*dataset->shared->layout.ops->is_space_alloc)(&dataset->shared->layout.storage)) { + hssize_t file_nelmts; /* Number of elements in file dataset's dataspace */ + hbool_t full_overwrite; /* Whether we are over-writing all the elements */ /* Get the number of elements in file dataset's dataspace */ - if((file_nelmts = H5S_GET_EXTENT_NPOINTS(file_space)) < 0) + if ((file_nelmts = H5S_GET_EXTENT_NPOINTS(file_space)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "can't retrieve number of elements in file dataset") /* Always allow fill values to be written if the dataset has a VL datatype */ - if(H5T_detect_class(dataset->shared->type, H5T_VLEN, FALSE)) + if (H5T_detect_class(dataset->shared->type, H5T_VLEN, FALSE)) full_overwrite = FALSE; else full_overwrite = (hbool_t)((hsize_t)file_nelmts == nelmts ? TRUE : FALSE); /* Allocate storage */ - if(H5D__alloc_storage(&io_info, H5D_ALLOC_WRITE, full_overwrite, NULL) < 0) + if (H5D__alloc_storage(&io_info, H5D_ALLOC_WRITE, full_overwrite, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage") } /* end if */ /* Allocate the chunk map */ - if(NULL == (fm = H5FL_CALLOC(H5D_chunk_map_t))) + if (NULL == (fm = H5FL_CALLOC(H5D_chunk_map_t))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate chunk map") /* Call storage method's I/O initialization routine */ - if(io_info.layout_ops.io_init && (*io_info.layout_ops.io_init)(&io_info, &type_info, nelmts, file_space, mem_space, fm) < 0) + if (io_info.layout_ops.io_init && + (*io_info.layout_ops.io_init)(&io_info, &type_info, nelmts, file_space, mem_space, fm) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize I/O info") io_op_init = TRUE; #ifdef H5_HAVE_PARALLEL /* Adjust I/O info for any parallel I/O */ - if(H5D__ioinfo_adjust(&io_info, dataset, file_space, mem_space, &type_info) < 0) + if (H5D__ioinfo_adjust(&io_info, dataset, file_space, mem_space, &type_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to adjust I/O info for parallel I/O") #endif /*H5_HAVE_PARALLEL*/ /* Invoke correct "high level" I/O routine */ - if((*io_info.io_ops.multi_write)(&io_info, &type_info, nelmts, file_space, mem_space, fm) < 0) + if ((*io_info.io_ops.multi_write)(&io_info, &type_info, nelmts, file_space, mem_space, fm) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data") #ifdef OLD_WAY -/* - * This was taken out because it can be called in a parallel program with - * independent access, causing the metadata cache to get corrupted. Its been - * disabled for all types of access (serial as well as parallel) to make the - * modification time consistent for all programs. -QAK - * - * We should set a value in the dataset's shared information instead and flush - * it to the file when the dataset is being closed. -QAK - */ + /* + * This was taken out because it can be called in a parallel program with + * independent access, causing the metadata cache to get corrupted. Its been + * disabled for all types of access (serial as well as parallel) to make the + * modification time consistent for all programs. -QAK + * + * We should set a value in the dataset's shared information instead and flush + * it to the file when the dataset is being closed. -QAK + */ /* * Update modification time. We have to do this explicitly because * writing to a dataset doesn't necessarily change the object header. */ - if(H5O_touch(&(dataset->oloc), FALSE) < 0) + if (H5O_touch(&(dataset->oloc), FALSE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update modification time") #endif /* OLD_WAY */ done: /* Shut down the I/O op information */ - if(io_op_init && io_info.layout_ops.io_term && (*io_info.layout_ops.io_term)(fm) < 0) + if (io_op_init && io_info.layout_ops.io_term && (*io_info.layout_ops.io_term)(fm) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down I/O op info") - if(fm) + if (fm) fm = H5FL_FREE(H5D_chunk_map_t, fm); /* Shut down datatype info for operation */ - if(type_info_init && H5D__typeinfo_term(&type_info) < 0) + if (type_info_init && H5D__typeinfo_term(&type_info) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down type info") /* discard projected mem space if it was created */ - if(NULL != projected_mem_space) - if(H5S_close(projected_mem_space) < 0) + if (NULL != projected_mem_space) + if (H5S_close(projected_mem_space) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down projected memory dataspace") FUNC_LEAVE_NOAPI_TAG(ret_value) } /* end H5D__write() */ - /*------------------------------------------------------------------------- * Function: H5D__ioinfo_init * @@ -820,8 +812,7 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__ioinfo_init(H5D_t *dset, const H5D_type_info_t *type_info, - H5D_storage_t *store, H5D_io_info_t *io_info) +H5D__ioinfo_init(H5D_t *dset, const H5D_type_info_t *type_info, H5D_storage_t *store, H5D_io_info_t *io_info) { FUNC_ENTER_STATIC_NOERR @@ -833,31 +824,31 @@ H5D__ioinfo_init(H5D_t *dset, const H5D_type_info_t *type_info, HDassert(io_info); /* Set up "normal" I/O fields */ - io_info->dset = dset; - io_info->f_sh = H5F_SHARED(dset->oloc.file); + io_info->dset = dset; + io_info->f_sh = H5F_SHARED(dset->oloc.file); io_info->store = store; /* Set I/O operations to initial values */ io_info->layout_ops = *dset->shared->layout.ops; /* Set the "high-level" I/O operations for the dataset */ - io_info->io_ops.multi_read = dset->shared->layout.ops->ser_read; + io_info->io_ops.multi_read = dset->shared->layout.ops->ser_read; io_info->io_ops.multi_write = dset->shared->layout.ops->ser_write; /* Set the I/O operations for reading/writing single blocks on disk */ - if(type_info->is_xform_noop && type_info->is_conv_noop) { + if (type_info->is_xform_noop && type_info->is_conv_noop) { /* * If there is no data transform or type conversion then read directly into * the application's buffer. This saves at least one mem-to-mem copy. */ - io_info->io_ops.single_read = H5D__select_read; + io_info->io_ops.single_read = H5D__select_read; io_info->io_ops.single_write = H5D__select_write; } /* end if */ else { /* * This is the general case (type conversion, usually). */ - io_info->io_ops.single_read = H5D__scatgath_read; + io_info->io_ops.single_read = H5D__scatgath_read; io_info->io_ops.single_write = H5D__scatgath_write; } /* end else */ @@ -869,7 +860,6 @@ H5D__ioinfo_init(H5D_t *dset, const H5D_type_info_t *type_info, FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5D__ioinfo_init() */ - /*------------------------------------------------------------------------- * Function: H5D__typeinfo_init * @@ -884,13 +874,12 @@ H5D__ioinfo_init(H5D_t *dset, const H5D_type_info_t *type_info, *------------------------------------------------------------------------- */ static herr_t -H5D__typeinfo_init(const H5D_t *dset, hid_t mem_type_id, hbool_t do_write, - H5D_type_info_t *type_info) +H5D__typeinfo_init(const H5D_t *dset, hid_t mem_type_id, hbool_t do_write, H5D_type_info_t *type_info) { - const H5T_t *src_type; /* Source datatype */ - const H5T_t *dst_type; /* Destination datatype */ - H5Z_data_xform_t *data_transform; /* Data transform info */ - herr_t ret_value = SUCCEED; /* Return value */ + const H5T_t * src_type; /* Source datatype */ + const H5T_t * dst_type; /* Destination datatype */ + H5Z_data_xform_t *data_transform; /* Data transform info */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC @@ -899,26 +888,26 @@ H5D__typeinfo_init(const H5D_t *dset, hid_t mem_type_id, hbool_t do_write, HDassert(dset); /* Patch the top level file pointer for dt->shared->u.vlen.f if needed */ - if(H5T_patch_vlen_file(dset->shared->type, H5F_VOL_OBJ(dset->oloc.file)) < 0 ) + if (H5T_patch_vlen_file(dset->shared->type, H5F_VOL_OBJ(dset->oloc.file)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't patch VL datatype file pointer") /* Initialize type info safely */ HDmemset(type_info, 0, sizeof(*type_info)); /* Get the memory & dataset datatypes */ - if(NULL == (type_info->mem_type = (const H5T_t *)H5I_object_verify(mem_type_id, H5I_DATATYPE))) + if (NULL == (type_info->mem_type = (const H5T_t *)H5I_object_verify(mem_type_id, H5I_DATATYPE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a datatype") type_info->dset_type = dset->shared->type; - if(do_write) { - src_type = type_info->mem_type; - dst_type = dset->shared->type; + if (do_write) { + src_type = type_info->mem_type; + dst_type = dset->shared->type; type_info->src_type_id = mem_type_id; type_info->dst_type_id = dset->shared->type_id; } /* end if */ else { - src_type = dset->shared->type; - dst_type = type_info->mem_type; + src_type = dset->shared->type; + dst_type = type_info->mem_type; type_info->src_type_id = dset->shared->type_id; type_info->dst_type_id = mem_type_id; } /* end else */ @@ -930,73 +919,72 @@ H5D__typeinfo_init(const H5D_t *dset, hid_t mem_type_id, hbool_t do_write, * enough value in xfer_parms since turning off datatype conversion also * turns off background preservation. */ - if(NULL == (type_info->tpath = H5T_path_find(src_type, dst_type))) + if (NULL == (type_info->tpath = H5T_path_find(src_type, dst_type))) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest datatype") /* Retrieve info from API context */ - if(H5CX_get_data_transform(&data_transform) < 0) + if (H5CX_get_data_transform(&data_transform) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get data transform info") /* Precompute some useful information */ type_info->src_type_size = H5T_get_size(src_type); type_info->dst_type_size = H5T_get_size(dst_type); type_info->max_type_size = MAX(type_info->src_type_size, type_info->dst_type_size); - type_info->is_conv_noop = H5T_path_noop(type_info->tpath); + type_info->is_conv_noop = H5T_path_noop(type_info->tpath); type_info->is_xform_noop = H5Z_xform_noop(data_transform); - if(type_info->is_xform_noop && type_info->is_conv_noop) { + if (type_info->is_xform_noop && type_info->is_conv_noop) { type_info->cmpd_subset = NULL; - type_info->need_bkg = H5T_BKG_NO; + type_info->need_bkg = H5T_BKG_NO; } /* end if */ else { - void *tconv_buf; /* Temporary conversion buffer pointer */ - void *bkgr_buf; /* Background conversion buffer pointer */ - size_t max_temp_buf; /* Maximum temporary buffer size */ - H5T_bkg_t bkgr_buf_type; /* Background buffer type */ - size_t target_size; /* Desired buffer size */ + void * tconv_buf; /* Temporary conversion buffer pointer */ + void * bkgr_buf; /* Background conversion buffer pointer */ + size_t max_temp_buf; /* Maximum temporary buffer size */ + H5T_bkg_t bkgr_buf_type; /* Background buffer type */ + size_t target_size; /* Desired buffer size */ /* Get info from API context */ - if(H5CX_get_max_temp_buf(&max_temp_buf) < 0) + if (H5CX_get_max_temp_buf(&max_temp_buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve max. temp. buf size") - if(H5CX_get_tconv_buf(&tconv_buf) < 0) + if (H5CX_get_tconv_buf(&tconv_buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve temp. conversion buffer pointer") - if(H5CX_get_bkgr_buf(&bkgr_buf) < 0) + if (H5CX_get_bkgr_buf(&bkgr_buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve background conversion buffer pointer") - if(H5CX_get_bkgr_buf_type(&bkgr_buf_type) < 0) + if (H5CX_get_bkgr_buf_type(&bkgr_buf_type) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve background buffer type") /* Check if the datatypes are compound subsets of one another */ type_info->cmpd_subset = H5T_path_compound_subset(type_info->tpath); /* Check if we need a background buffer */ - if(do_write && H5T_detect_class(dset->shared->type, H5T_VLEN, FALSE)) + if (do_write && H5T_detect_class(dset->shared->type, H5T_VLEN, FALSE)) type_info->need_bkg = H5T_BKG_YES; else { - H5T_bkg_t path_bkg; /* Type conversion's background info */ + H5T_bkg_t path_bkg; /* Type conversion's background info */ - if((path_bkg = H5T_path_bkg(type_info->tpath))) { + if ((path_bkg = H5T_path_bkg(type_info->tpath))) { /* Retrieve the bkgr buffer property */ type_info->need_bkg = bkgr_buf_type; type_info->need_bkg = MAX(path_bkg, type_info->need_bkg); } /* end if */ else type_info->need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/ - } /* end else */ - + } /* end else */ /* Set up datatype conversion/background buffers */ target_size = max_temp_buf; /* If the buffer is too small to hold even one element, try to make it bigger */ - if(target_size < type_info->max_type_size) { - hbool_t default_buffer_info; /* Whether the buffer information are the defaults */ + if (target_size < type_info->max_type_size) { + hbool_t default_buffer_info; /* Whether the buffer information are the defaults */ /* Detect if we have all default settings for buffers */ - default_buffer_info = (hbool_t)((H5D_TEMP_BUF_SIZE == max_temp_buf) - && (NULL == tconv_buf) && (NULL == bkgr_buf)); + default_buffer_info = + (hbool_t)((H5D_TEMP_BUF_SIZE == max_temp_buf) && (NULL == tconv_buf) && (NULL == bkgr_buf)); /* Check if we are using the default buffer info */ - if(default_buffer_info) + if (default_buffer_info) /* OK to get bigger for library default settings */ target_size = type_info->max_type_size; else @@ -1008,42 +996,43 @@ H5D__typeinfo_init(const H5D_t *dset, hid_t mem_type_id, hbool_t do_write, type_info->request_nelmts = target_size / type_info->max_type_size; /* Sanity check elements in temporary buffer */ - if(type_info->request_nelmts == 0) + if (type_info->request_nelmts == 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small") /* Get a temporary buffer for type conversion unless the app has already * supplied one through the xfer properties. Instead of allocating a * buffer which is the exact size, we allocate the target size. */ - if(NULL == (type_info->tconv_buf = (uint8_t *)tconv_buf)) { + if (NULL == (type_info->tconv_buf = (uint8_t *)tconv_buf)) { /* Allocate temporary buffer */ - if(NULL == (type_info->tconv_buf = H5FL_BLK_CALLOC(type_conv, target_size))) + if (NULL == (type_info->tconv_buf = H5FL_BLK_CALLOC(type_conv, target_size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion") type_info->tconv_buf_allocated = TRUE; } /* end if */ - if(type_info->need_bkg && NULL == (type_info->bkg_buf = (uint8_t *)bkgr_buf)) { - size_t bkg_size; /* Desired background buffer size */ + if (type_info->need_bkg && NULL == (type_info->bkg_buf = (uint8_t *)bkgr_buf)) { + size_t bkg_size; /* Desired background buffer size */ /* Compute the background buffer size */ /* (don't try to use buffers smaller than the default size) */ bkg_size = type_info->request_nelmts * type_info->dst_type_size; - if(bkg_size < max_temp_buf) + if (bkg_size < max_temp_buf) bkg_size = max_temp_buf; /* Allocate background buffer */ /* (Need calloc()-like call since memory needs to be initialized) */ - if(NULL == (type_info->bkg_buf = H5FL_BLK_CALLOC(type_conv, bkg_size))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion") + if (NULL == (type_info->bkg_buf = H5FL_BLK_CALLOC(type_conv, bkg_size))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, + "memory allocation failed for background conversion") type_info->bkg_buf_allocated = TRUE; } /* end if */ - } /* end else */ + } /* end else */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__typeinfo_init() */ #ifdef H5_HAVE_PARALLEL - + /*------------------------------------------------------------------------- * Function: H5D__ioinfo_adjust * @@ -1057,11 +1046,10 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__ioinfo_adjust(H5D_io_info_t *io_info, const H5D_t *dset, - const H5S_t *file_space, const H5S_t *mem_space, - const H5D_type_info_t *type_info) +H5D__ioinfo_adjust(H5D_io_info_t *io_info, const H5D_t *dset, const H5S_t *file_space, const H5S_t *mem_space, + const H5D_type_info_t *type_info) { - herr_t ret_value = SUCCEED; /* Return value */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC @@ -1078,34 +1066,34 @@ H5D__ioinfo_adjust(H5D_io_info_t *io_info, const H5D_t *dset, * the DXPL (if it's non-default) was previously used in a collective * I/O operation. */ - if(!H5CX_is_def_dxpl()) { + if (!H5CX_is_def_dxpl()) { H5CX_set_mpio_actual_chunk_opt(H5D_MPIO_NO_CHUNK_OPTIMIZATION); H5CX_set_mpio_actual_io_mode(H5D_MPIO_NO_COLLECTIVE); } /* end if */ /* Make any parallel I/O adjustments */ - if(io_info->using_mpi_vfd) { + if (io_info->using_mpi_vfd) { H5FD_mpio_xfer_t xfer_mode; /* Parallel transfer for this request */ - htri_t opt; /* Flag whether a selection is optimizable */ + htri_t opt; /* Flag whether a selection is optimizable */ /* Get the original state of parallel I/O transfer mode */ - if(H5CX_get_io_xfer_mode(&xfer_mode) < 0) + if (H5CX_get_io_xfer_mode(&xfer_mode) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get MPI-I/O transfer mode") /* Get MPI communicator */ - if(MPI_COMM_NULL == (io_info->comm = H5F_mpi_get_comm(dset->oloc.file))) + if (MPI_COMM_NULL == (io_info->comm = H5F_mpi_get_comm(dset->oloc.file))) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't retrieve MPI communicator") /* Check if we can set direct MPI-IO read/write functions */ - if((opt = H5D__mpio_opt_possible(io_info, file_space, mem_space, type_info)) < 0) + if ((opt = H5D__mpio_opt_possible(io_info, file_space, mem_space, type_info)) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "invalid check for direct IO dataspace ") /* Check if we can use the optimized parallel I/O routines */ - if(opt == TRUE) { + if (opt == TRUE) { /* Override the I/O op pointers to the MPI-specific routines */ - io_info->io_ops.multi_read = dset->shared->layout.ops->par_read; - io_info->io_ops.multi_write = dset->shared->layout.ops->par_write; - io_info->io_ops.single_read = H5D__mpio_select_read; + io_info->io_ops.multi_read = dset->shared->layout.ops->par_read; + io_info->io_ops.multi_write = dset->shared->layout.ops->par_write; + io_info->io_ops.single_read = H5D__mpio_select_read; io_info->io_ops.single_write = H5D__mpio_select_write; } /* end if */ else { @@ -1114,41 +1102,46 @@ H5D__ioinfo_adjust(H5D_io_info_t *io_info, const H5D_t *dset, * otherwise there will be metadata inconsistencies in the file. */ if (io_info->op_type == H5D_IO_OP_WRITE && io_info->dset->shared->dcpl_cache.pline.nused > 0) { - H5D_mpio_no_collective_cause_t cause; - uint32_t local_no_collective_cause; - uint32_t global_no_collective_cause; - hbool_t local_error_message_previously_written = FALSE; - hbool_t global_error_message_previously_written = FALSE; - size_t idx; - size_t cause_strings_len; - char local_no_collective_cause_string[512] = ""; - char global_no_collective_cause_string[512] = ""; - const char *cause_strings[] = { "independent I/O was requested", - "datatype conversions were required", - "data transforms needed to be applied", - "optimized MPI types flag wasn't set", - "one of the dataspaces was neither simple nor scalar", - "dataset was not contiguous or chunked", - "parallel writes to filtered datasets are disabled", - "an error occurred while checking if collective I/O was possible" }; + H5D_mpio_no_collective_cause_t cause; + uint32_t local_no_collective_cause; + uint32_t global_no_collective_cause; + hbool_t local_error_message_previously_written = FALSE; + hbool_t global_error_message_previously_written = FALSE; + size_t idx; + size_t cause_strings_len; + char local_no_collective_cause_string[512] = ""; + char global_no_collective_cause_string[512] = ""; + const char * cause_strings[] = { + "independent I/O was requested", + "datatype conversions were required", + "data transforms needed to be applied", + "optimized MPI types flag wasn't set", + "one of the dataspaces was neither simple nor scalar", + "dataset was not contiguous or chunked", + "parallel writes to filtered datasets are disabled", + "an error occurred while checking if collective I/O was possible"}; cause_strings_len = sizeof(cause_strings) / sizeof(cause_strings[0]); - if(H5CX_get_mpio_local_no_coll_cause(&local_no_collective_cause) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get local no collective cause value") - if(H5CX_get_mpio_global_no_coll_cause(&global_no_collective_cause) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get global no collective cause value") + if (H5CX_get_mpio_local_no_coll_cause(&local_no_collective_cause) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, + "unable to get local no collective cause value") + if (H5CX_get_mpio_global_no_coll_cause(&global_no_collective_cause) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, + "unable to get global no collective cause value") /* Append each of the "reason for breaking collective I/O" error messages to the * local and global no collective cause strings */ - for (cause = 1, idx = 0; (cause < H5D_MPIO_NO_COLLECTIVE_MAX_CAUSE) && (idx < cause_strings_len); cause <<= 1, idx++) { + for (cause = 1, idx = 0; + (cause < H5D_MPIO_NO_COLLECTIVE_MAX_CAUSE) && (idx < cause_strings_len); + cause <<= 1, idx++) { size_t cause_strlen = HDstrlen(cause_strings[idx]); if (cause & local_no_collective_cause) { - /* Check if there were any previous error messages included. If so, prepend a semicolon - * to separate the messages. + /* Check if there were any previous error messages included. If so, prepend a + * semicolon to separate the messages. */ - if(local_error_message_previously_written) + if (local_error_message_previously_written) HDstrncat(local_no_collective_cause_string, "; ", 2); HDstrncat(local_no_collective_cause_string, cause_strings[idx], cause_strlen); @@ -1156,44 +1149,43 @@ H5D__ioinfo_adjust(H5D_io_info_t *io_info, const H5D_t *dset, local_error_message_previously_written = TRUE; } /* end if */ - if(cause & global_no_collective_cause) { - /* Check if there were any previous error messages included. If so, prepend a semicolon - * to separate the messages. + if (cause & global_no_collective_cause) { + /* Check if there were any previous error messages included. If so, prepend a + * semicolon to separate the messages. */ - if(global_error_message_previously_written) + if (global_error_message_previously_written) HDstrncat(global_no_collective_cause_string, "; ", 2); HDstrncat(global_no_collective_cause_string, cause_strings[idx], cause_strlen); global_error_message_previously_written = TRUE; } /* end if */ - } /* end for */ - - HGOTO_ERROR(H5E_IO, H5E_NO_INDEPENDENT, FAIL, "Can't perform independent write with filters in pipeline.\n" - " The following caused a break from collective I/O:\n" - " Local causes: %s\n" - " Global causes: %s", - local_no_collective_cause_string, - global_no_collective_cause_string); + } /* end for */ + + HGOTO_ERROR(H5E_IO, H5E_NO_INDEPENDENT, FAIL, + "Can't perform independent write with filters in pipeline.\n" + " The following caused a break from collective I/O:\n" + " Local causes: %s\n" + " Global causes: %s", + local_no_collective_cause_string, global_no_collective_cause_string); } /* end if */ /* If we won't be doing collective I/O, but the user asked for * collective I/O, change the request to use independent I/O */ - if(xfer_mode == H5FD_MPIO_COLLECTIVE) { + if (xfer_mode == H5FD_MPIO_COLLECTIVE) { /* Change the xfer_mode to independent for handling the I/O */ - if(H5CX_set_io_xfer_mode(H5FD_MPIO_INDEPENDENT) < 0) + if (H5CX_set_io_xfer_mode(H5FD_MPIO_INDEPENDENT) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set MPI-I/O transfer mode") } /* end if */ - } /* end else */ - } /* end if */ + } /* end else */ + } /* end if */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__ioinfo_adjust() */ #endif /* H5_HAVE_PARALLEL */ - /*------------------------------------------------------------------------- * Function: H5D__typeinfo_term * @@ -1212,15 +1204,14 @@ H5D__typeinfo_term(const H5D_type_info_t *type_info) FUNC_ENTER_STATIC_NOERR /* Check for releasing datatype conversion & background buffers */ - if(type_info->tconv_buf_allocated) { + if (type_info->tconv_buf_allocated) { HDassert(type_info->tconv_buf); (void)H5FL_BLK_FREE(type_conv, type_info->tconv_buf); } /* end if */ - if(type_info->bkg_buf_allocated) { + if (type_info->bkg_buf_allocated) { HDassert(type_info->bkg_buf); (void)H5FL_BLK_FREE(type_conv, type_info->bkg_buf); } /* end if */ FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5D__typeinfo_term() */ - |