diff options
Diffstat (limited to 'src/H5Dio.c')
| -rw-r--r-- | src/H5Dio.c | 1560 |
1 files changed, 998 insertions, 562 deletions
diff --git a/src/H5Dio.c b/src/H5Dio.c index 104a632..26e02c5 100644 --- a/src/H5Dio.c +++ b/src/H5Dio.c @@ -49,25 +49,27 @@ /* Local Prototypes */ /********************/ -/* Internal I/O routines */ -static herr_t H5D__pre_write(H5D_t *dset, hbool_t direct_write, hid_t mem_type_id, - const H5S_t *mem_space, const H5S_t *file_space, hid_t dxpl_id, const void *buf); +/* Internal I/O routines for single-dset */ +static herr_t H5D__pre_read(hid_t file_id, hid_t dxpl_id, size_t count, + H5D_dset_info_t *dset_info); +static herr_t H5D__pre_write(hid_t file_id, hid_t dxpl_id, size_t count, + H5D_dset_info_t *dset_info); + +/* Internal I/O routines for multi-dset */ + /* Setup/teardown routines */ static herr_t H5D__ioinfo_init(H5D_t *dset, #ifndef H5_HAVE_PARALLEL -const + const #endif /* H5_HAVE_PARALLEL */ - H5D_dxpl_cache_t *dxpl_cache, - hid_t dxpl_id, const H5D_type_info_t *type_info, H5D_storage_t *store, - H5D_io_info_t *io_info); + H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, H5D_dset_info_t *dset_info, + H5D_storage_t *store, H5D_io_info_t *io_info); static herr_t H5D__typeinfo_init(const H5D_t *dset, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, 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, - hid_t dxpl_id, const H5S_t *file_space, const H5S_t *mem_space, - const H5D_type_info_t *type_info, const H5D_chunk_map_t *fm); +static herr_t H5D__ioinfo_adjust(const size_t count, H5D_io_info_t *io_info, hid_t dxpl_id); static herr_t H5D__ioinfo_term(H5D_io_info_t *io_info); #endif /* H5_HAVE_PARALLEL */ static herr_t H5D__typeinfo_term(const H5D_type_info_t *type_info); @@ -86,8 +88,96 @@ static herr_t H5D__typeinfo_term(const H5D_type_info_t *type_info); H5FL_BLK_DEFINE(type_conv); /* Declare a free list to manage the H5D_chunk_map_t struct */ -H5FL_DEFINE(H5D_chunk_map_t); +/* H5FL_DEFINE(H5D_chunk_map_t); */ + + +/*------------------------------------------------------------------------- + * Function: H5D__init_dset_info + * + * Purpose: Initializes a H5D_dset_info_t from a set of user parameters, + * while checking parameters too. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * Friday, August 29, 2014 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__init_dset_info(H5D_dset_info_t *dset_info, hid_t dset_id, + hid_t mem_type_id, hid_t mem_space_id, hid_t dset_space_id, + const H5D_dset_buf_t *u_buf) +{ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_STATIC + + /* Get dataset */ + if(NULL == (dset_info->dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") + if(NULL == dset_info->dset->oloc.file) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a file") + /* Check for invalid space IDs */ + if(mem_space_id < 0 || dset_space_id < 0) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace") + + /* Get file dataspace */ + if(H5S_ALL != dset_space_id) { + if(NULL == (dset_info->file_space = (const H5S_t *)H5I_object_verify(dset_space_id, H5I_DATASPACE))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace") + + /* Check for valid selection */ + if(H5S_SELECT_VALID(dset_info->file_space) != TRUE) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "file selection+offset not within extent") + } /* end if */ + else + dset_info->file_space = dset_info->dset->shared->space; + + /* Get memory dataspace */ + if(H5S_ALL != mem_space_id) { + if(NULL == (dset_info->mem_space = (const H5S_t *)H5I_object_verify(mem_space_id, H5I_DATASPACE))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace") + + /* Check for valid selection */ + if(H5S_SELECT_VALID(dset_info->mem_space) != TRUE) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "memory selection+offset not within extent") + } /* end if */ + else + dset_info->mem_space = dset_info->file_space; + + /* Get memory datatype */ + dset_info->mem_type_id = mem_type_id; + + /* Get buffer */ + dset_info->u = *u_buf; + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__init_dset_info() */ + +static hid_t +H5D__verify_location(size_t count, const H5D_dset_info_t *info) +{ + hid_t file_id; + size_t u; + hid_t ret_value = FAIL; /* Return value */ + + FUNC_ENTER_STATIC + + file_id = H5F_FILE_ID(info[0].dset->oloc.file); + + for(u = 1; u < count; u++) { + if(file_id != H5F_FILE_ID(info[u].dset->oloc.file)) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dataset's file ID doesn't match file_id parameter") + } /* end for */ + + ret_value = file_id; + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__verify_location */ /*------------------------------------------------------------------------- @@ -122,107 +212,241 @@ H5FL_DEFINE(H5D_chunk_map_t); */ herr_t H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, - hid_t file_space_id, hid_t plist_id, void *buf/*out*/) + hid_t file_space_id, hid_t dxpl_id, void *buf/*out*/) { - H5D_t *dset = NULL; - const H5S_t *mem_space = NULL; - const H5S_t *file_space = NULL; - H5P_genplist_t *plist; /* Property list pointer */ - hsize_t *direct_offset = NULL; - hbool_t direct_read = FALSE; - uint32_t direct_filters = 0; - herr_t ret_value = SUCCEED; /* Return value */ + H5D_dset_info_t *dset_info = NULL; /* Internal multi-dataset info placeholder */ + H5D_dset_buf_t u_buf; /* Buffer pointer */ + hid_t file_id; /* File ID for operation */ + 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, - plist_id, buf); + dxpl_id, buf); - /* check arguments */ - if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") - if(NULL == dset->oloc.file) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") + /* 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") - if(mem_space_id < 0 || file_space_id < 0) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space") + /* Alloc dset_info */ + if(NULL == (dset_info = (H5D_dset_info_t *)H5MM_calloc(sizeof(H5D_dset_info_t)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate dset info array buffer") - if(H5S_ALL != mem_space_id) { - if(NULL == (mem_space = (const H5S_t *)H5I_object_verify(mem_space_id, H5I_DATASPACE))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space") + /* Translate public multi-dataset info to internal structure */ + /* (And check parameters) */ + u_buf.rbuf = buf; + if(H5D__init_dset_info(dset_info, dset_id, mem_type_id, mem_space_id, file_space_id, &u_buf) < 0) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't init dataset info") - /* Check for valid selection */ - if(H5S_SELECT_VALID(mem_space) != TRUE) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent") - } /* end if */ + /* Retrieve file_id */ + file_id = H5F_FILE_ID(dset_info->dset->oloc.file); - if(H5S_ALL != file_space_id) { - if(NULL == (file_space = (const H5S_t *)H5I_object_verify(file_space_id, H5I_DATASPACE))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space") + /* Call common pre-read routine */ + if(H5D__pre_read(file_id, dxpl_id, 1, dset_info) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't prepare for reading data") - /* Check for valid selection */ - if(H5S_SELECT_VALID(file_space) != TRUE) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent") - } /* end if */ +done: + if(dset_info) + H5MM_xfree(dset_info); + + FUNC_LEAVE_API(ret_value) +} /* end H5Dread() */ + + +/*------------------------------------------------------------------------- + * Function: H5Dread_multi + * + * Purpose: Multi-version of H5Dread(), which reads selections from + * multiple datasets from a file into application memory BUFS. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Jonathan Kim Nov, 2013 + * + *------------------------------------------------------------------------- + */ +herr_t +H5Dread_multi(hid_t dxpl_id, size_t count, H5D_rw_multi_t *info) +{ + H5D_dset_info_t *dset_info = NULL; /* Pointer to internal list of multi-dataset info */ + size_t u; /* Local index variable */ + hid_t file_id; /* file ID where datasets are located */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_API(FAIL) + H5TRACE3("e", "iz*Dm", dxpl_id, count, info); + + if(count <= 0) + HGOTO_DONE(SUCCEED) /* Get the default dataset transfer property list if the user didn't provide one */ - if (H5P_DEFAULT == plist_id) - plist_id= H5P_DATASET_XFER_DEFAULT; + if(H5P_DEFAULT == dxpl_id) + dxpl_id = H5P_DATASET_XFER_DEFAULT; else - if(TRUE != H5P_isa_class(plist_id, H5P_DATASET_XFER)) + if(TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER)) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms") + /* Alloc dset_info */ + if(NULL == (dset_info = (H5D_dset_info_t *)H5MM_calloc(count * sizeof(H5D_dset_info_t)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate dset info array buffer") + + /* Translate public multi-dataset info to internal structure */ + /* (And check parameters) */ + for(u = 0; u < count; u++) { + if(H5D__init_dset_info(&dset_info[u], info[u].dset_id, info[u].mem_type_id, info[u].mem_space_id, + info[u].dset_space_id, &(info[u].u.rbuf)) < 0) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't init dataset info") + } /* end for */ + + if((file_id = H5D__verify_location(count, dset_info)) < 0) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "datasets are not in the same file") + + /* Call common pre-read routine */ + if(H5D__pre_read(file_id, dxpl_id, count, dset_info) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't prepare for reading data") + +done: + if(dset_info) + H5MM_xfree(dset_info); + + FUNC_LEAVE_API(ret_value) +} /* end H5Dread_multi() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__pre_read + * + * Purpose: Sets up a read operation. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Neil Fortner Apr, 2014 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__pre_read(hid_t file_id, hid_t dxpl_id, size_t count, + H5D_dset_info_t *dset_info) +{ + H5FD_mpio_xfer_t xfer_mode; /* Parallel I/O transfer mode */ + hbool_t broke_mdset = FALSE; /* Whether to break multi-dataset option */ + size_t u; /* Local index variable */ + H5P_genplist_t *plist; /* Property list pointer */ + H5P_genplist_t *plist_chunk; /* Property list pointer */ + hsize_t *direct_offset = NULL; + hbool_t direct_read = FALSE; + uint32_t direct_filters = 0; + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_STATIC + + /* check args */ + HDassert(dxpl_id > 0); + HDassert(count > 0); + HDassert(dset_info); + + /* Retrieve DXPL for queries below */ + if(NULL == (plist = H5P_object_verify(dxpl_id, H5P_DATASET_XFER))) + HGOTO_ERROR(H5E_PLIST, H5E_BADTYPE, FAIL, "not a dxpl") + + /* Get the transfer mode */ + if(H5P_get(plist, H5D_XFER_IO_XFER_MODE_NAME, &xfer_mode) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "unable to get value") + /* Get the dataset transfer property list */ - if(NULL == (plist = (H5P_genplist_t *)H5I_object(plist_id))) + if(NULL == (plist_chunk = (H5P_genplist_t *)H5I_object(dxpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list") /* Retrieve the 'direct read' flag */ - if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_READ_FLAG_NAME, &direct_read) < 0) + if(H5P_get(plist_chunk, H5D_XFER_DIRECT_CHUNK_READ_FLAG_NAME, &direct_read) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error getting flag for direct chunk read") if(direct_read) { - unsigned u; hsize_t internal_offset[H5O_LAYOUT_NDIMS]; - if(H5D_CHUNKED != dset->shared->layout.type) + if(H5D_CHUNKED != dset_info[0].dset->shared->layout.type) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset") /* Get the direct chunk offset property */ - if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_READ_OFFSET_NAME, &direct_offset) < 0) + if(H5P_get(plist_chunk, H5D_XFER_DIRECT_CHUNK_READ_OFFSET_NAME, &direct_offset) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error getting direct offset from xfer properties") /* The library's chunking code requires the offset terminates with a zero. So transfer the * offset array to an internal offset array */ - for(u = 0; u < dset->shared->ndims; u++) { + for(u = 0; u < dset_info[0].dset->shared->ndims; u++) { /* Make sure the offset doesn't exceed the dataset's dimensions */ - if(direct_offset[u] > dset->shared->curr_dims[u]) + if(direct_offset[u] > dset_info[0].dset->shared->curr_dims[u]) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset exceeds dimensions of dataset") /* Make sure the offset fall right on a chunk's boundary */ - if(direct_offset[u] % dset->shared->layout.u.chunk.dim[u]) + if(direct_offset[u] % dset_info[0].dset->shared->layout.u.chunk.dim[u]) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset doesn't fall on chunks's boundary") internal_offset[u] = direct_offset[u]; } /* end for */ /* Terminate the offset with a zero */ - internal_offset[dset->shared->ndims] = 0; - + internal_offset[dset_info[0].dset->shared->ndims] = 0; /* Read the raw chunk */ - if(H5D__chunk_direct_read(dset, plist_id, internal_offset, &direct_filters, buf) < 0) + if(H5D__chunk_direct_read(dset_info[0].dset, dxpl_id, internal_offset, &direct_filters, dset_info[0].u.rbuf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read chunk directly") /* Set the chunk filter mask property */ - if(H5P_set(plist, H5D_XFER_DIRECT_CHUNK_READ_FILTERS_NAME, &direct_filters) < 0) + if(H5P_set(plist_chunk, H5D_XFER_DIRECT_CHUNK_READ_FILTERS_NAME, &direct_filters) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error setting filter mask xfer property") } else { - /* read raw data */ - if(H5D__read(dset, mem_type_id, mem_space, file_space, plist_id, buf/*out*/) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data") + + /* In independent mode or with an unsupported layout, for now just + read each dataset individually */ + if(xfer_mode == H5FD_MPIO_INDEPENDENT) + broke_mdset = TRUE; + else { + /* Multi-dset I/O currently supports CHUNKED and internal CONTIGUOUS + * only, not external CONTIGUOUS (EFL) or COMPACT. Fall back to + * individual dataset reads if any dataset uses an unsupported layout. + */ + for(u = 0; u < count; u++) { + if(!(dset_info[u].dset->shared->layout.type == H5D_CHUNKED || + (dset_info[u].dset->shared->layout.type == H5D_CONTIGUOUS && + dset_info[u].dset->shared->layout.ops != H5D_LOPS_EFL))) { + broke_mdset = TRUE; + break; + } + } /* end for */ + } + + if(broke_mdset) { + /* Read raw data from each dataset by iteself */ + for(u = 0; u < count; u++) + if(H5D__read(file_id, dxpl_id, 1, &dset_info[u]) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data") + } /* end if */ + else { + HDassert(xfer_mode == H5FD_MPIO_COLLECTIVE); + + if(count > 0) { + if(H5D__read(file_id, dxpl_id, count, dset_info) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data") + } /* end if */ +#ifdef H5_HAVE_PARALLEL + /* MSC - I do not think we should allow for this. I think we + should make the multi dataset APIs enforce a uniform list + of datasets among all processes, and users would enter a + NULL selection when a process does not have anything to + write to a particulat dataset. */ + else { + if(H5D__match_coll_calls(file_id, plist, TRUE) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "failed in matching collective MPI calls") + } /* end else */ +#endif /* H5_HAVE_PARALLEL */ + } /* end else */ } done: - FUNC_LEAVE_API(ret_value) -} /* end H5Dread() */ + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__pre_read() */ /*------------------------------------------------------------------------- @@ -260,23 +484,15 @@ 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) { - H5D_t *dset = NULL; - H5P_genplist_t *plist; /* Property list pointer */ - const H5S_t *mem_space = NULL; - const H5S_t *file_space = NULL; - hbool_t direct_write = FALSE; - herr_t ret_value = SUCCEED; /* Return value */ + H5D_dset_info_t *dset_info = NULL; /* Internal multi-dataset info placeholder */ + H5D_dset_buf_t u_buf; /* Buffer pointer */ + hid_t file_id; /* File ID for operation */ + 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); - /* check arguments */ - if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") - if(NULL == dset->oloc.file) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a file") - /* 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; @@ -284,43 +500,88 @@ H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, if(TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER)) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms") - /* Get the dataset transfer property list */ - if(NULL == (plist = (H5P_genplist_t *)H5I_object(dxpl_id))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list") + /* Alloc dset_info */ + if(NULL == (dset_info = (H5D_dset_info_t *)H5MM_calloc(sizeof(H5D_dset_info_t)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate dset info array buffer") - /* Retrieve the 'direct write' flag */ - if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME, &direct_write) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error getting flag for direct chunk write") + /* Translate public multi-dataset info to internal structure */ + /* (And check parameters) */ + u_buf.wbuf = buf; + if(H5D__init_dset_info(dset_info, dset_id, mem_type_id, mem_space_id, file_space_id, &u_buf) < 0) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't init dataset info") - /* Check dataspace selections if this is not a direct write */ - if(!direct_write) { - if(mem_space_id < 0 || file_space_id < 0) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace") + /* Retrieve file_id */ + file_id = H5F_FILE_ID(dset_info->dset->oloc.file); - if(H5S_ALL != mem_space_id) { - if(NULL == (mem_space = (const H5S_t *)H5I_object_verify(mem_space_id, H5I_DATASPACE))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace") + /* Call common pre-write routine */ + if(H5D__pre_write(file_id, dxpl_id, 1, dset_info) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't prepare for writing data") - /* Check for valid selection */ - if(H5S_SELECT_VALID(mem_space) != TRUE) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "memory selection+offset not within extent") - } /* end if */ - if(H5S_ALL != file_space_id) { - if(NULL == (file_space = (const H5S_t *)H5I_object_verify(file_space_id, H5I_DATASPACE))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace") +done: + if(dset_info) + H5MM_xfree(dset_info); + FUNC_LEAVE_API(ret_value) +} /* end H5Dwrite() */ - /* Check for valid selection */ - if(H5S_SELECT_VALID(file_space) != TRUE) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "file selection+offset not within extent") - } /* end if */ + +/*------------------------------------------------------------------------- + * Function: H5Dwrite_multi + * + * Purpose: Multi-version of H5Dwrite(), which writes selections from + * application memory BUFs into multiple datasets in a file. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Jonathan Kim Nov, 2013 + * + *------------------------------------------------------------------------- + */ +herr_t +H5Dwrite_multi(hid_t dxpl_id, size_t count, const H5D_rw_multi_t *info) +{ + H5D_dset_info_t *dset_info = NULL; /* Pointer to internal list of multi-dataset info */ + size_t u; /* Local index variable */ + hid_t file_id; /* file ID where datasets are located */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_API(FAIL) + H5TRACE3("e", "iz*Dm", dxpl_id, count, info); + + if(count <= 0) + HGOTO_DONE(SUCCEED) + + /* 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") + + /* Alloc dset_info */ + if(NULL == (dset_info = (H5D_dset_info_t *)H5MM_calloc(count * sizeof(H5D_dset_info_t)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate dset info array buffer") + + /* Translate public multi-dataset info to internal structure */ + /* (And check parameters) */ + for(u = 0; u < count; u++) { + if(H5D__init_dset_info(&dset_info[u], info[u].dset_id, info[u].mem_type_id, info[u].mem_space_id, + info[u].dset_space_id, &(info[u].u.wbuf)) < 0) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't init dataset info") } - if(H5D__pre_write(dset, direct_write, mem_type_id, mem_space, file_space, dxpl_id, buf) < 0) + if((file_id = H5D__verify_location(count, dset_info)) < 0) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "datasets are not in the same file") + + /* Call common pre-write routine */ + if(H5D__pre_write(file_id, dxpl_id, count, dset_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't prepare for writing data") done: + if(dset_info) + H5MM_xfree(dset_info); + FUNC_LEAVE_API(ret_value) -} /* end H5Dwrite() */ +} /* end H5Dwrite_multi() */ /*------------------------------------------------------------------------- @@ -330,34 +591,49 @@ done: * * Return: Non-negative on success/Negative on failure * - * Programmer: Raymond Lu - * 2 November 2012 + * Programmer: Jonathan Kim Nov, 2013 * *------------------------------------------------------------------------- */ static herr_t -H5D__pre_write(H5D_t *dset, hbool_t direct_write, hid_t mem_type_id, - const H5S_t *mem_space, const H5S_t *file_space, - hid_t dxpl_id, const void *buf) +H5D__pre_write(hid_t file_id, hid_t dxpl_id, size_t count, + H5D_dset_info_t *dset_info) { - herr_t ret_value = SUCCEED; /* Return value */ + H5P_genplist_t *plist; /* DXPL property list pointer */ + hbool_t direct_write = FALSE; /* Flag for direct writing */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC - /* Direct chunk write */ - if(direct_write) { - H5P_genplist_t *plist; /* Property list pointer */ - uint32_t direct_filters; - hsize_t *direct_offset; - uint32_t direct_datasize; - hsize_t internal_offset[H5O_LAYOUT_NDIMS]; - unsigned u; /* Local index variable */ + /* check args */ + HDassert(dxpl_id > 0); + HDassert(count > 0); + HDassert(dset_info); + + /* Retrieve DXPL for queries below */ + if(NULL == (plist = H5P_object_verify(dxpl_id, H5P_DATASET_XFER))) + HGOTO_ERROR(H5E_PLIST, H5E_BADTYPE, FAIL, "not a dxpl") - /* Get the dataset transfer property list */ - if(NULL == (plist = (H5P_genplist_t *)H5I_object(dxpl_id))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list") + /* Check if direct write or not */ + if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME, &direct_write) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error getting flag for direct chunk write") - if(H5D_CHUNKED != dset->shared->layout.type) + /* Direct chunk write */ + if(direct_write) { + uint32_t direct_filters; /* Filters already applied to chunk */ + hsize_t *direct_offset; /* Offset of chunk */ + uint32_t direct_datasize; /* [Pre-compressed] size of chunk */ + int sndims; /* Dataspace rank (signed) */ + unsigned ndims; /* Dataspace rank */ + hsize_t dims[H5O_LAYOUT_NDIMS]; /* Dataspace dimensions */ + hsize_t internal_offset[H5O_LAYOUT_NDIMS]; /* Internal copy of the chunk offset */ + unsigned u; /* Local index variable */ + + /* Sanity check */ + HDassert(count == 1); + + /* Verify dataset is chunked */ + if(H5D_CHUNKED != dset_info[0].dset->shared->layout.type) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset") /* Retrieve parameters for direct chunk write */ @@ -368,31 +644,87 @@ H5D__pre_write(H5D_t *dset, hbool_t direct_write, hid_t mem_type_id, if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_NAME, &direct_datasize) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error getting data size for direct chunk write") - /* The library's chunking code requires the offset terminates with a zero. So transfer the - * offset array to an internal offset array */ - for(u = 0; u < dset->shared->ndims; u++) { + /* The library's chunking code requires the offset terminates with a + * zero. So transfer the offset array to an internal offset array */ + if((sndims = H5S_get_simple_extent_dims(dset_info[0].dset->shared->space, dims, NULL)) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't retrieve dataspace extent dims") + H5_CHECKED_ASSIGN(ndims, unsigned, sndims, int); + + /* Sanity check chunk offset and set up internal offset array */ + for(u = 0; u < ndims; u++) { /* Make sure the offset doesn't exceed the dataset's dimensions */ - if(direct_offset[u] > dset->shared->curr_dims[u]) + if(direct_offset[u] > dset_info[0].dset->shared->curr_dims[u]) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset exceeds dimensions of dataset") /* Make sure the offset fall right on a chunk's boundary */ - if(direct_offset[u] % dset->shared->layout.u.chunk.dim[u]) + if(direct_offset[u] % dset_info[0].dset->shared->layout.u.chunk.dim[u]) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset doesn't fall on chunks's boundary") internal_offset[u] = direct_offset[u]; } /* end for */ - - /* Terminate the offset with a zero */ - internal_offset[dset->shared->ndims] = 0; - /* write raw data */ - if(H5D__chunk_direct_write(dset, dxpl_id, direct_filters, internal_offset, direct_datasize, buf) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write chunk directly") - } /* end if */ - else { /* Normal write */ + /* Terminate the offset with a zero */ + internal_offset[ndims] = 0; + /* write raw data */ - if(H5D__write(dset, mem_type_id, mem_space, file_space, dxpl_id, buf) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data") + if(H5D__chunk_direct_write(dset_info[0].dset, dxpl_id, direct_filters, internal_offset, + direct_datasize, dset_info[0].u.wbuf) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write chunk directly") + } /* end if */ + else { + size_t u; /* Local index variable */ + hbool_t broke_mdset = FALSE; /* Whether to break multi-dataset option */ + H5FD_mpio_xfer_t xfer_mode; /* Parallel I/O transfer mode */ + + /* Get the transfer mode */ + if(H5P_get(plist, H5D_XFER_IO_XFER_MODE_NAME, &xfer_mode) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "unable to get value") + + /* In independent mode or with an unsupported layout, for now + just write each dataset individually */ + if(xfer_mode == H5FD_MPIO_INDEPENDENT) + broke_mdset = TRUE; + else { + /* Multi-dset I/O currently supports CHUNKED and internal CONTIGUOUS + * only, not external CONTIGUOUS (EFL) or COMPACT. Fall back to + * individual dataset writes if any dataset uses an unsupported layout. + */ + for(u = 0; u < count; u++) { + if(!(dset_info[u].dset->shared->layout.type == H5D_CHUNKED || + (dset_info[u].dset->shared->layout.type == H5D_CONTIGUOUS && + dset_info[u].dset->shared->layout.ops != H5D_LOPS_EFL))) { + broke_mdset = TRUE; + break; + } + } /* end for */ + } + + if(broke_mdset) { + /* Write raw data to each dataset by iteself */ + for(u = 0; u < count; u++) + if(H5D__write(file_id, dxpl_id, 1, &dset_info[u]) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data") + } /* end if */ + else { + HDassert(xfer_mode == H5FD_MPIO_COLLECTIVE); + + if(count > 0) { + if(H5D__write(file_id, dxpl_id, count, dset_info) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data") + } /* end if */ + +#ifdef H5_HAVE_PARALLEL + /* MSC - I do not think we should allow for this. I think we + should make the multi dataset APIs enforce a uniform list + of datasets among all processes, and users would enter a + NULL selection when a process does not have anything to + write to a particulat dataset. */ + else { + if(H5D__match_coll_calls(file_id, plist, FALSE) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "failed in matching collective MPI calls") + } /* end else */ +#endif /* H5_HAVE_PARALLEL */ + } /* end else */ } /* end else */ done: @@ -403,25 +735,22 @@ done: /*------------------------------------------------------------------------- * Function: H5D__read * - * Purpose: Reads (part of) a DATASET into application memory BUF. See - * H5Dread() for complete details. + * Purpose: Reads multiple (part of) DATASETs into application memory BUFs. + * See H5Dread_multi() for complete details. * * Return: Non-negative on success/Negative on failure * - * Programmer: Robb Matzke - * Thursday, December 4, 1997 + * Programmer: Jonathan Kim Nov, 2013 * *------------------------------------------------------------------------- */ herr_t -H5D__read(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space, - const H5S_t *file_space, hid_t dxpl_id, void *buf/*out*/) +H5D__read(hid_t file_id, hid_t dxpl_id, size_t count, + H5D_dset_info_t *dset_info) { - 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 */ + H5D_io_info_t io_info; /* Dataset I/O info for multi dsets */ + size_t type_info_init = 0; /* Number of datatype info structs that have been initialized */ + H5S_t ** projected_mem_space; /* If not NULL, ptr to dataspace containing a */ /* projection of the supplied mem_space to a new */ /* data space with rank equal to that of */ /* file_space. */ @@ -434,171 +763,236 @@ H5D__read(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space, /* 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 */ - hssize_t snelmts; /*total number of elmts (signed) */ - hsize_t nelmts; /*total number of elmts */ + H5D_storage_t *store = NULL; /* Union of EFL and chunk pointer in file space */ + hssize_t snelmts; /* Total number of elmts (signed) */ + hsize_t nelmts; /* Total number of elmts */ hbool_t io_info_init = FALSE; /* Whether the I/O info has been initialized */ - hbool_t io_op_init = FALSE; /* Whether the I/O op has been initialized */ + size_t io_op_init = 0; /* Number I/O ops that have been initialized */ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */ + size_t i; /* Local index variable */ char fake_char; /* Temporary variable for NULL buffer pointers */ herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_PACKAGE_TAG(dxpl_id, dataset->oloc.addr, FAIL) + FUNC_ENTER_NOAPI(FAIL) - /* check args */ - HDassert(dataset && dataset->oloc.file); + /* init io_info */ + io_info.sel_pieces = NULL; + io_info.store_faddr = 0; + io_info.base_maddr_r = NULL; - if(!file_space) - file_space = dataset->shared->space; - if(!mem_space) - mem_space = file_space; - if((snelmts = H5S_GET_SELECT_NPOINTS(mem_space)) < 0) - HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "dst dataspace has invalid selection") - H5_CHECKED_ASSIGN(nelmts, hsize_t, snelmts, hssize_t); + /* Create global piece skiplist */ + if(NULL == (io_info.sel_pieces = H5SL_create(H5SL_TYPE_HADDR, NULL))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't create skip list for piece selections") - /* Fill the DXPL cache values for later use */ - if(H5D__get_dxpl_cache(dxpl_id, &dxpl_cache) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache") + /* Use provided dset_info */ + io_info.dsets_info = dset_info; - /* Set up datatype info for operation */ - if(H5D__typeinfo_init(dataset, dxpl_cache, dxpl_id, mem_type_id, FALSE, &type_info) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set up type info") - type_info_init = TRUE; + /* Allocate other buffers */ + if(NULL == (projected_mem_space = (H5S_t **)H5MM_calloc(count * sizeof(H5S_t*)))) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "couldn't allocate dset space array ptr") + if(NULL == (store = (H5D_storage_t *)H5MM_malloc(count * sizeof(H5D_storage_t)))) + HGOTO_ERROR(H5E_STORAGE, H5E_CANTALLOC, FAIL, "couldn't allocate dset storage info array buffer") -#ifdef H5_HAVE_PARALLEL - /* Collective access is not permissible without a MPI based VFD */ - if(dxpl_cache->xfer_mode == H5FD_MPIO_COLLECTIVE && - !(H5F_HAS_FEATURE(dataset->oloc.file, H5FD_FEAT_HAS_MPI))) - HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access for MPI-based drivers only") -#endif /*H5_HAVE_PARALLEL*/ + /* init both dxpls to the original one */ + io_info.md_dxpl_id = dxpl_id; + io_info.raw_dxpl_id = dxpl_id; - /* Make certain that the number of elements in each selection is the same */ - if(nelmts != (hsize_t)H5S_GET_SELECT_NPOINTS(file_space)) - HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest data spaces have different sizes") + /* set the dxpl IO type for sanity checking at the FD layer */ +#ifdef H5_DEBUG_BUILD + if(H5D_set_io_info_dxpls(&io_info, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't set metadata and raw data dxpls") +#endif /* H5_DEBUG_BUILD */ - /* Check for a NULL buffer, after the H5S_ALL dataspace selection has been handled */ - if(NULL == buf) { - /* Check for any elements selected (which is invalid) */ - if(nelmts > 0) - HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer") + /* iterate over all dsets and construct I/O information necessary to do I/O */ + for(i = 0; i < count; i++) { + /* check args */ + if(NULL == dset_info[i].dset) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") + if(NULL == dset_info[i].dset->oloc.file) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a file") - /* 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 */ + /* Fill the DXPL cache values for later use */ + if(H5D__get_dxpl_cache(dxpl_id, &dxpl_cache) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache") - /* Make sure that both selections have their extents set */ - 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))) - 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 - * selections with different rank as having the same shape (if the most - * rapidly changing coordinates match up), but the I/O code still has - * difficulties with the notion. - * - * To solve this, we check to see if H5S_select_shape_same() returns true, - * and if the ranks of the mem and file spaces are different. If the are, - * construct a new mem space that is equivalent to the old mem space, and - * use that instead. - * - * 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)) { - 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, (const void **)&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 = adj_buf; - } /* end if */ + /* Set up datatype info for operation */ + if(H5D__typeinfo_init(dset_info[i].dset, dxpl_cache, dxpl_id, dset_info[i].mem_type_id, + FALSE, &(dset_info[i].type_info)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set up type info") + type_info_init++; +#ifdef H5_HAVE_PARALLEL + /* Collective access is not permissible without a MPI based VFD */ + if(dxpl_cache->xfer_mode == H5FD_MPIO_COLLECTIVE && + !(H5F_HAS_FEATURE(dset_info[i].dset->oloc.file, H5FD_FEAT_HAS_MPI))) + HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access for MPI-based drivers only") +#endif /*H5_HAVE_PARALLEL*/ - /* Retrieve dataset properties */ - /* <none needed in the general case> */ + if((snelmts = H5S_GET_SELECT_NPOINTS(dset_info[i].mem_space)) < 0) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "dst dataspace has invalid selection") + H5_CHECKED_ASSIGN(nelmts, hsize_t, snelmts, hssize_t); - /* If space hasn't been allocated and not using external storage, - * return fill value to buffer if fill time is upon allocation, or - * do nothing if fill time is never. If the dataset is compact and - * 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)) { - 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) - 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 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) - 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, dxpl_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "filling buf failed") - else - HGOTO_DONE(SUCCEED) - } /* end if */ + /* Make certain that the number of elements in each selection is the same */ + if(nelmts != (hsize_t)H5S_GET_SELECT_NPOINTS(dset_info[i].file_space)) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest dataspace have different sizes") - /* Set up I/O operation */ - io_info.op_type = H5D_IO_OP_READ; - io_info.u.rbuf = buf; - if(H5D__ioinfo_init(dataset, dxpl_cache, dxpl_id, &type_info, &store, &io_info) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to set up I/O operation") - io_info_init = TRUE; + /* Check for a NULL buffer, after the H5S_ALL dataspace selection has been handled */ + if(NULL == dset_info[i].u.rbuf) { + /* Check for any elements selected (which is invalid) */ + if(nelmts > 0) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer") - /* 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->dcpl_cache.efl.nused > 0 - || dataset->shared->layout.type == H5D_COMPACT); + /* 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. + */ + dset_info[i].u.rbuf = &fake_char; + } /* end if */ + + /* Make sure that both selections have their extents set */ + if(!(H5S_has_extent(dset_info[i].file_space))) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "file dataspace does not have extent set") + if(!(H5S_has_extent(dset_info[i].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 selections with different rank as having the same shape + * (if the most rapidly changing coordinates match up), but the I/O + * code still has difficulties with the notion. + * + * To solve this, we check to see if H5S_select_shape_same() returns + * true, and if the ranks of the mem and file spaces are different. + * If the are, construct a new mem space that is equivalent to the + * old mem space, and use that instead. + * + * Note that in general, this requires us to touch up the memory buffer + * as well. + */ + if(TRUE == H5S_select_shape_same(dset_info[i].mem_space, dset_info[i].file_space) && + H5S_GET_EXTENT_NDIMS(dset_info[i].mem_space) != H5S_GET_EXTENT_NDIMS(dset_info[i].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(dset_info[i].mem_space, &(projected_mem_space[i]), + (unsigned)H5S_GET_EXTENT_NDIMS(dset_info[i].file_space), dset_info[i].u.rbuf, + (const void **)&adj_buf, + (hsize_t)dset_info[i].type_info.dst_type_size) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to construct projected memory dataspace") + HDassert(projected_mem_space[i]); + HDassert(adj_buf); + + /* Switch to using projected memory dataspace & adjusted buffer */ + dset_info[i].mem_space = projected_mem_space[i]; + dset_info[i].u.rbuf = (void *)adj_buf; + } /* end if */ - /* Allocate the chunk map */ - if(NULL == (fm = H5FL_CALLOC(H5D_chunk_map_t))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate chunk map") + /* Retrieve dataset properties */ + /* <none needed in the general case> */ - /* 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) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize I/O info") - io_op_init = TRUE; + /* If space hasn't been allocated and not using external storage, + * return fill value to buffer if fill time is upon allocation, or + * do nothing if fill time is never. If the dataset is compact and + * 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 && dset_info[i].dset->shared->dcpl_cache.efl.nused == 0 && + !(*dset_info[i].dset->shared->layout.ops->is_space_alloc)(&dset_info[i].dset->shared->layout.storage)) { + 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(&dset_info[i].dset->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 && + (dset_info[i].dset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_ALLOC || + dset_info[i].dset->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(dset_info[i].dset->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(dset_info[i].dset->shared->dcpl_cache.fill.buf, dset_info[i].dset->shared->type, + dset_info[i].u.rbuf, dset_info[i].type_info.mem_type, dset_info[i].mem_space, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "filling buf failed") + else + HGOTO_DONE(SUCCEED) + } /* end if */ + + /* Set up I/O operation */ + io_info.op_type = H5D_IO_OP_READ; + if(H5D__ioinfo_init(dset_info[i].dset, dxpl_cache, dxpl_id, &(dset_info[i]), + &(store[i]), &io_info) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to set up I/O operation") + io_info_init = TRUE; + + /* Sanity check that space is allocated, if there are elements */ + if(nelmts > 0) + HDassert((*dset_info[i].dset->shared->layout.ops->is_space_alloc) + (&dset_info[i].dset->shared->layout.storage) + || dset_info[i].dset->shared->dcpl_cache.efl.nused > 0 + || dset_info[i].dset->shared->layout.type == H5D_COMPACT); + + /* Call storage method's I/O initialization routine */ + /* Init io_info.dset_info[] and generate piece_info in skip list */ + if(dset_info[i].layout_ops.io_init && + (*dset_info[i].layout_ops.io_init)(&io_info, &(dset_info[i].type_info), nelmts, + dset_info[i].file_space, dset_info[i].mem_space, + &(dset_info[i])) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize I/O info") + io_op_init++; + } /* end of for loop */ + + assert(type_info_init == count); + assert(io_op_init == count); #ifdef H5_HAVE_PARALLEL /* Adjust I/O info for any parallel I/O */ - if(H5D__ioinfo_adjust(&io_info, dataset, dxpl_id, file_space, mem_space, &type_info, fm) < 0) + if(H5D__ioinfo_adjust(count, &io_info, dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to adjust I/O info for parallel I/O") +#else + io_info.is_coll_broken = TRUE; #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) - HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data") + /* If collective mode is broken, perform read IO in independent mode via + * single-dset path with looping. + * Multiple-dset path can not be called since it is not supported, so make + * detour through single-dset path */ + if(TRUE == io_info.is_coll_broken) { + haddr_t prev_tag = HADDR_UNDEF; + + /* Loop with serial & single-dset read IO path */ + for(i = 0; i < count; i++) { + /* set metadata tagging with dset oheader addr */ + if(H5AC_tag(io_info.md_dxpl_id, dset_info[i].dset->oloc.addr, &prev_tag) < 0) + HGOTO_ERROR(H5E_CACHE, H5E_CANTTAG, FAIL, "unable to apply metadata tag") + + io_info.dsets_info = &(dset_info[i]); + + if((*io_info.io_ops.multi_read)(&io_info, &(dset_info[i].type_info), nelmts, dset_info[i].file_space, + dset_info[i].mem_space, &dset_info[i]) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data") + + /* Reset metadata tagging */ + if(H5AC_tag(io_info.md_dxpl_id, prev_tag, NULL) < 0) + HDONE_ERROR(H5E_CACHE, H5E_CANTTAG, FAIL, "unable to apply metadata tag") + } + } /* end if */ + else + if((*io_info.io_ops.multi_read_md)(file_id, count, &io_info) < 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) - HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down I/O op info") - if(fm) - fm = H5FL_FREE(H5D_chunk_map_t, fm); + for(i = 0; i < io_op_init; i++) + if(dset_info[i].layout_ops.io_term && (*dset_info[i].layout_ops.io_term)(&io_info, &(dset_info[i])) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down I/O op info") + if(io_info_init) { #ifdef H5_DEBUG_BUILD @@ -614,40 +1008,52 @@ done: } /* Shut down datatype info for operation */ - if(type_info_init && H5D__typeinfo_term(&type_info) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down type info") + for(i = 0; i < type_info_init; i++) + if(H5D__typeinfo_term(&(dset_info[i].type_info)) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down type info") + + /* Discard projected mem spaces if they were created */ + for(i = 0; i < count; i++) + if(NULL != projected_mem_space[i]) + if(H5S_close(projected_mem_space[i]) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down projected memory dataspace") + + /* Free global piece skiplist */ + if(io_info.sel_pieces) + if(H5SL_close(io_info.sel_pieces) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "can't close dataset skip list") + + /* io_info.dsets_info was allocated in calling function */ + if(projected_mem_space) + H5MM_xfree(projected_mem_space); + if(store) + H5MM_xfree(store); - /* discard projected mem space if it was created */ - 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, FAIL) + FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__read() */ /*------------------------------------------------------------------------- * Function: H5D__write * - * Purpose: Writes (part of) a DATASET to a file from application memory - * BUF. See H5Dwrite() for complete details. + * Purpose: Writes multiple (part of) DATASETs to a file from application + * memory BUFs. See H5Dwrite_multi() for complete details. + * + * This was referred from H5D__write for multi-dset work. * * Return: Non-negative on success/Negative on failure * - * Programmer: Robb Matzke - * Thursday, December 4, 1997 + * Programmer: Jonathan Kim Nov, 2013 * *------------------------------------------------------------------------- */ herr_t -H5D__write(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space, - const H5S_t *file_space, hid_t dxpl_id, 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 */ +H5D__write(hid_t file_id, hid_t dxpl_id, size_t count, + H5D_dset_info_t *dset_info) +{ + H5D_io_info_t io_info; /* Dataset I/O info for multi dsets */ + size_t type_info_init = 0; /* Number of datatype info structs that have 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 */ /* data space with rank equal to that of */ /* file_space. */ @@ -660,180 +1066,259 @@ H5D__write(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space, /* 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 */ - hssize_t snelmts; /*total number of elmts (signed) */ - hsize_t nelmts; /*total number of elmts */ + H5D_storage_t *store = NULL; /* Union of EFL and chunk pointer in file space */ + hssize_t snelmts; /* Total number of elmts (signed) */ + hsize_t nelmts; /* Total number of elmts */ hbool_t io_info_init = FALSE; /* Whether the I/O info has been initialized */ - hbool_t io_op_init = FALSE; /* Whether the I/O op has been initialized */ + size_t io_op_init = 0; /* Number I/O ops that have been initialized */ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */ + size_t i; /* Local index variable */ char fake_char; /* Temporary variable for NULL buffer pointers */ herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_PACKAGE_TAG(dxpl_id, dataset->oloc.addr, FAIL) + FUNC_ENTER_NOAPI(FAIL) - /* check args */ - HDassert(dataset && dataset->oloc.file); + /* Init io_info */ + io_info.sel_pieces = NULL; + io_info.store_faddr = 0; + io_info.base_maddr_w = NULL; - /* 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) - HGOTO_ERROR(H5E_PLINE, H5E_CANAPPLY, FAIL, "can't apply filters") + /* Create global piece skiplist */ + if(NULL == (io_info.sel_pieces = H5SL_create(H5SL_TYPE_HADDR, NULL))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't create skip list for piece selections") - dataset->shared->checked_filters = TRUE; - } /* end if */ + /* Use provided dset_info */ + io_info.dsets_info = dset_info; + + /* Allocate other buffers */ + if(NULL == (projected_mem_space = (H5S_t **)H5MM_calloc(count * sizeof(H5S_t*)))) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "couldn't allocate dset space array ptr") + if(NULL == (store = (H5D_storage_t *)H5MM_malloc(count * sizeof(H5D_storage_t)))) + HGOTO_ERROR(H5E_STORAGE, H5E_CANTALLOC, FAIL, "couldn't allocate dset storage info array buffer") + + /* init both dxpls to the original one */ + io_info.md_dxpl_id = dxpl_id; + io_info.raw_dxpl_id = dxpl_id; + + /* set the dxpl IO type for sanity checking at the FD layer */ +#ifdef H5_DEBUG_BUILD + if(H5D_set_io_info_dxpls(&io_info, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't set metadata and raw data dxpls") +#endif /* H5_DEBUG_BUILD */ + + /* iterate over all dsets and construct I/O information */ + for(i = 0; i < count; i++) { + haddr_t prev_tag = HADDR_UNDEF; + + /* check args */ + if(NULL == dset_info[i].dset) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") + if(NULL == dset_info[i].dset->oloc.file) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a file") - /* Check if we are allowed to write to this file */ - if(0 == (H5F_INTENT(dataset->oloc.file) & H5F_ACC_RDWR)) - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "no write intent on file") + /* set metadata tagging with dset oheader addr */ + if(H5AC_tag(io_info.md_dxpl_id, dset_info[i].dset->oloc.addr, &prev_tag) < 0) + HGOTO_ERROR(H5E_CACHE, H5E_CANTTAG, FAIL, "unable to apply metadata tag") - /* Fill the DXPL cache values for later use */ - if(H5D__get_dxpl_cache(dxpl_id, &dxpl_cache) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache") + /* All filters in the DCPL must have encoding enabled. */ + if(!dset_info[i].dset->shared->checked_filters) { + if(H5Z_can_apply(dset_info[i].dset->shared->dcpl_id, dset_info[i].dset->shared->type_id) < 0) + HGOTO_ERROR(H5E_PLINE, H5E_CANAPPLY, FAIL, "can't apply filters") - /* Set up datatype info for operation */ - if(H5D__typeinfo_init(dataset, dxpl_cache, dxpl_id, mem_type_id, TRUE, &type_info) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set up type info") - type_info_init = TRUE; + dset_info[i].dset->shared->checked_filters = TRUE; + } /* end if */ + + /* Check if we are allowed to write to this file */ + if(0 == (H5F_INTENT(dset_info[i].dset->oloc.file) & H5F_ACC_RDWR)) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "no write intent on file") + + /* Fill the DXPL cache values for later use */ + if(H5D__get_dxpl_cache(dxpl_id, &dxpl_cache) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache") + + /* Set up datatype info for operation */ + if(H5D__typeinfo_init(dset_info[i].dset, dxpl_cache, dxpl_id, dset_info[i].mem_type_id, + TRUE, &(dset_info[i].type_info)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set up type info") + type_info_init++; /* Various MPI based checks */ #ifdef H5_HAVE_PARALLEL - if H5F_HAS_FEATURE(dataset->oloc.file, H5FD_FEAT_HAS_MPI) { - /* If MPI based VFD is used, no VL 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_detect_class(type_info.mem_type, H5T_VLEN, FALSE) > 0) - HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Parallel IO does not support writing VL datatypes yet") - - /* If MPI based VFD is used, no VL datatype support yet. */ - /* This is because they use the global heap in the file and we don't */ - /* support parallel access of that yet */ - /* We should really use H5T_detect_class() here, but it will be difficult - * to detect the type of the reference if it is nested... -QAK - */ - if(H5T_get_class(type_info.mem_type, TRUE) == H5T_REFERENCE && - H5T_get_ref_type(type_info.mem_type) == H5R_DATASET_REGION) - HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Parallel IO does not support writing region reference datatypes yet") - } /* end if */ - else { - /* Collective access is not permissible without a MPI based VFD */ - if(dxpl_cache->xfer_mode == H5FD_MPIO_COLLECTIVE) - HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access for MPI-based driver only") - } /* end else */ + if H5F_HAS_FEATURE(dset_info[i].dset->oloc.file, H5FD_FEAT_HAS_MPI) { + /* If MPI based VFD is used, no VL 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_detect_class(dset_info[i].type_info.mem_type, H5T_VLEN, FALSE) > 0) + HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Parallel IO does not support writing VL datatypes yet") + + /* If MPI based VFD is used, no VL datatype support yet. */ + /* This is because they use the global heap in the file and we don't */ + /* support parallel access of that yet */ + /* We should really use H5T_detect_class() here, but it will be difficult + * to detect the type of the reference if it is nested... -QAK + */ + if(H5T_get_class(dset_info[i].type_info.mem_type, TRUE) == H5T_REFERENCE && + H5T_get_ref_type(dset_info[i].type_info.mem_type) == H5R_DATASET_REGION) + HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Parallel IO does not support writing region reference datatypes yet") + + /* Can't write to chunked datasets with filters, in parallel */ + if(dset_info[i].dset->shared->layout.type == H5D_CHUNKED && + dset_info[i].dset->shared->dcpl_cache.pline.nused > 0) + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot write to chunked storage with filters in parallel") + } /* end if */ + else { + /* Collective access is not permissible without a MPI based VFD */ + if(dxpl_cache->xfer_mode == H5FD_MPIO_COLLECTIVE) + HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access for MPI-based driver only") + } /* end else */ #endif /*H5_HAVE_PARALLEL*/ - /* Initialize dataspace information */ - if(!file_space) - file_space = dataset->shared->space; - if(!mem_space) - mem_space = file_space; + if((snelmts = H5S_GET_SELECT_NPOINTS(dset_info[i].mem_space)) < 0) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "src dataspace has invalid selection") + H5_CHECKED_ASSIGN(nelmts, hsize_t, snelmts, hssize_t); - if((snelmts = H5S_GET_SELECT_NPOINTS(mem_space)) < 0) - HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "src dataspace has invalid selection") - H5_CHECKED_ASSIGN(nelmts, hsize_t, snelmts, hssize_t); + /* Make certain that the number of elements in each selection is the same */ + if(nelmts != (hsize_t)H5S_GET_SELECT_NPOINTS(dset_info[i].file_space)) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest data space have different sizes") - /* Make certain that the number of elements in each selection is the same */ - if(nelmts != (hsize_t)H5S_GET_SELECT_NPOINTS(file_space)) - HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest data spaces have different sizes") + /* Check for a NULL buffer, after the H5S_ALL dataspace selection has been handled */ + if(NULL == dset_info[i].u.wbuf) { + /* Check for any elements selected (which is invalid) */ + if(nelmts > 0) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer") - /* Check for a NULL buffer, after the H5S_ALL dataspace selection has been handled */ - if(NULL == buf) { - /* Check for any elements selected (which is invalid) */ - 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. + */ + dset_info[i].u.wbuf = &fake_char; + } /* end if */ - /* 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(dset_info[i].file_space))) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "file dataspace does not have extent set") + if(!(H5S_has_extent(dset_info[i].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 selections with different rank as having the same shape + * (if the most rapidly changing coordinates match up), but the I/O + * code still has difficulties with the notion. + * + * To solve this, we check to see if H5S_select_shape_same() returns + * true, and if the ranks of the mem and file spaces are different. + * If the are, construct a new mem space that is equivalent to the + * old mem space, and use that instead. + * + * Note that in general, this requires us to touch up the memory buffer + * as well. + */ + if(TRUE == H5S_select_shape_same(dset_info[i].mem_space, dset_info[i].file_space) && + H5S_GET_EXTENT_NDIMS(dset_info[i].mem_space) != H5S_GET_EXTENT_NDIMS(dset_info[i].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(dset_info[i].mem_space, &(projected_mem_space[i]), + (unsigned)H5S_GET_EXTENT_NDIMS(dset_info[i].file_space), + dset_info[i].u.wbuf, (const void **)&adj_buf, + (hsize_t)dset_info[i].type_info.src_type_size) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to construct projected memory dataspace") + HDassert(projected_mem_space[i]); + HDassert(adj_buf); + + /* Switch to using projected memory dataspace & adjusted buffer */ + dset_info[i].mem_space = projected_mem_space[i]; + dset_info[i].u.wbuf = adj_buf; + } /* end if */ - /* Make sure that both selections have their extents set */ - 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))) - 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 selections with different rank as having the same shape - * (if the most rapidly changing coordinates match up), but the I/O - * code still has difficulties with the notion. - * - * To solve this, we check to see if H5S_select_shape_same() returns - * true, and if the ranks of the mem and file spaces are different. - * If the are, construct a new mem space that is equivalent to the - * old mem space, and use that instead. - * - * 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)) { - 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, (const void **)&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; - } /* end if */ + /* Retrieve dataset properties */ + /* <none needed currently> */ - /* Retrieve dataset properties */ - /* <none needed currently> */ - - /* Set up I/O operation */ - io_info.op_type = H5D_IO_OP_WRITE; - io_info.u.wbuf = buf; - if(H5D__ioinfo_init(dataset, dxpl_cache, dxpl_id, &type_info, &store, &io_info) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set up I/O operation") - io_info_init = TRUE; - - /* Allocate data space 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 */ - - /* Get the number of elements in file dataset's dataspace */ - 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)) - 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) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage") - } /* end if */ + /* Set up I/O operation */ + io_info.op_type = H5D_IO_OP_WRITE; + if(H5D__ioinfo_init(dset_info[i].dset, dxpl_cache, dxpl_id, &(dset_info[i]), + &(store[i]), &io_info) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set up I/O operation") +#ifdef H5_HAVE_PARALLEL + io_info_init = TRUE; +#endif /*H5_HAVE_PARALLEL*/ - /* Allocate the chunk map */ - if(NULL == (fm = H5FL_CALLOC(H5D_chunk_map_t))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate chunk map") + /* Allocate dataspace and initialize it if it hasn't been. */ + if(nelmts > 0 && dset_info[i].dset->shared->dcpl_cache.efl.nused == 0 && + !(*dset_info[i].dset->shared->layout.ops->is_space_alloc)(&dset_info[i].dset->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(dset_info[i].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(dset_info[i].dset->shared->type, H5T_VLEN, FALSE)) + full_overwrite = FALSE; + else + full_overwrite = (hbool_t)((hsize_t)file_nelmts == nelmts ? TRUE : FALSE); + + io_info.dset = dset_info[i].dset; + /* Allocate storage */ + 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 */ - /* 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) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize I/O info") - io_op_init = TRUE; + /* Call storage method's I/O initialization routine */ + /* Init io_info.dset_info[] and generate piece_info in skip list */ + if(dset_info[i].layout_ops.io_init && + (*dset_info[i].layout_ops.io_init)(&io_info, &(dset_info[i].type_info), nelmts, + dset_info[i].file_space, dset_info[i].mem_space, + &(dset_info[i])) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize I/O info") + io_op_init++; + + /* Reset metadata tagging */ + if(H5AC_tag(io_info.md_dxpl_id, prev_tag, NULL) < 0) + HDONE_ERROR(H5E_CACHE, H5E_CANTTAG, FAIL, "unable to apply metadata tag") + } /* end of Count for loop */ + assert(type_info_init == count); + assert(io_op_init == count); #ifdef H5_HAVE_PARALLEL /* Adjust I/O info for any parallel I/O */ - if(H5D__ioinfo_adjust(&io_info, dataset, dxpl_id, file_space, mem_space, &type_info, fm) < 0) + if(H5D__ioinfo_adjust(count, &io_info, dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to adjust I/O info for parallel I/O") +#else + io_info.is_coll_broken = TRUE; #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) - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data") + /* If collective mode is broken, perform write IO in independent mode via + * single-dset path with looping. + * Multiple-dset path can not be called since it is not supported, so make + * detour through single-dset path */ + if(TRUE == io_info.is_coll_broken) { + haddr_t prev_tag = HADDR_UNDEF; + + /* loop with serial & single-dset write IO path */ + for(i = 0; i < count; i++) { + /* set metadata tagging with dset oheader addr */ + if(H5AC_tag(io_info.md_dxpl_id, dset_info->dset->oloc.addr, &prev_tag) < 0) + HGOTO_ERROR(H5E_CACHE, H5E_CANTTAG, FAIL, "unable to apply metadata tag") + + io_info.dsets_info = &(dset_info[i]); + + /* Invoke correct "high level" I/O routine */ + if((*io_info.io_ops.multi_write)(&io_info, &(dset_info[i].type_info), nelmts, dset_info[i].file_space, + dset_info[i].mem_space, &dset_info[i]) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data") + /* Reset metadata tagging */ + if(H5AC_tag(io_info.md_dxpl_id, prev_tag, NULL) < 0) + HDONE_ERROR(H5E_CACHE, H5E_CANTTAG, FAIL, "unable to apply metadata tag") + } + } /* end if */ + else + /* Invoke correct "high level" I/O routine */ + if((*io_info.io_ops.multi_write_md)(file_id, count, &io_info) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data") #ifdef OLD_WAY /* @@ -855,10 +1340,10 @@ H5D__write(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space, 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) - HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down I/O op info") - if(fm) - fm = H5FL_FREE(H5D_chunk_map_t, fm); + for(i = 0; i < io_op_init; i++) + if(dset_info[i].layout_ops.io_term && (*dset_info[i].layout_ops.io_term)(&io_info, &(dset_info[i])) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down I/O op info") + if(io_info_init) { #ifdef H5_DEBUG_BUILD @@ -874,38 +1359,50 @@ done: } /* Shut down datatype info for operation */ - if(type_info_init && H5D__typeinfo_term(&type_info) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down type info") + for(i = 0; i < type_info_init; i++) + if(H5D__typeinfo_term(&(dset_info[i].type_info)) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down type info") + + /* Discard projected mem spaces if they were created */ + for(i = 0; i < count; i++) + if(NULL != projected_mem_space[i]) + if(H5S_close(projected_mem_space[i]) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down projected memory dataspace") + + /* Free global piece skiplist */ + if(io_info.sel_pieces) + if(H5SL_close(io_info.sel_pieces) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "can't close dataset skip list") + + /* io_info.dsets_info was allocated in calling function */ + if(projected_mem_space) + H5MM_xfree(projected_mem_space); + if(store) + H5MM_xfree(store); - /* discard projected mem space if it was created */ - 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, FAIL) -} /* end H5D__write() */ + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__write */ /*------------------------------------------------------------------------- * Function: H5D__ioinfo_init * - * Purpose: Routine for determining correct I/O operations for - * each I/O action. + * Purpose: Routine for determining correct I/O operations for each I/O action. * - * Return: Non-negative on success/Negative on failure + * This was derived from H5D__ioinfo_init for multi-dset work. * - * Programmer: Quincey Koziol - * Thursday, September 30, 2004 + * Return: Non-negative on success/Negative on failure * + * Programmer: Jonathan Kim Nov, 2013 *------------------------------------------------------------------------- */ static herr_t H5D__ioinfo_init(H5D_t *dset, #ifndef H5_HAVE_PARALLEL -const + const #endif /* H5_HAVE_PARALLEL */ - H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, - const H5D_type_info_t *type_info, H5D_storage_t *store, H5D_io_info_t *io_info) + H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, + H5D_dset_info_t *dset_info, H5D_storage_t *store, H5D_io_info_t *io_info) { herr_t ret_value = SUCCEED; @@ -914,34 +1411,25 @@ const /* check args */ HDassert(dset); HDassert(dset->oloc.file); - HDassert(type_info); - HDassert(type_info->tpath); + //HDassert(&(dset_info->type_info)); + HDassert(dset_info->type_info.tpath); HDassert(io_info); - /* init both dxpls to the original one */ - io_info->md_dxpl_id = dxpl_id; - io_info->raw_dxpl_id = dxpl_id; - - /* set the dxpl IO type for sanity checking at the FD layer */ -#ifdef H5_DEBUG_BUILD - if(H5D_set_io_info_dxpls(io_info, dxpl_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't set metadata and raw data dxpls") -#endif /* H5_DEBUG_BUILD */ - /* Set up "normal" I/O fields */ - io_info->dset = dset; + dset_info->dset = dset; io_info->dxpl_cache = dxpl_cache; - io_info->store = store; + io_info->is_coll_broken = FALSE; /* is collective broken? */ + dset_info->store = store; /* Set I/O operations to initial values */ - io_info->layout_ops = *dset->shared->layout.ops; + dset_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_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(dset_info->type_info.is_xform_noop && dset_info->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. @@ -1133,18 +1621,17 @@ done: * * Purpose: Adjust operation's I/O info for any parallel I/O * - * Return: Non-negative on success/Negative on failure + * This was derived from H5D__ioinfo_adjust for multi-dset work. * - * Programmer: Quincey Koziol - * Thursday, March 27, 2008 + * Return: Non-negative on success/Negative on failure * + * Programmer: Jonathan Kim Nov, 2013 *------------------------------------------------------------------------- */ static herr_t -H5D__ioinfo_adjust(H5D_io_info_t *io_info, const H5D_t *dset, hid_t dxpl_id, - const H5S_t *file_space, const H5S_t *mem_space, - const H5D_type_info_t *type_info, const H5D_chunk_map_t *fm) +H5D__ioinfo_adjust(const size_t count, H5D_io_info_t *io_info, hid_t dxpl_id) { + H5D_t *dset0; /* only the first dset , also for single dsets case */ H5P_genplist_t *dx_plist; /* Data transer property list */ H5D_mpio_actual_chunk_opt_mode_t actual_chunk_opt_mode; /* performed chunk optimization */ H5D_mpio_actual_io_mode_t actual_io_mode; /* performed io mode */ @@ -1153,14 +1640,14 @@ H5D__ioinfo_adjust(H5D_io_info_t *io_info, const H5D_t *dset, hid_t dxpl_id, FUNC_ENTER_STATIC /* check args */ - HDassert(dset); - HDassert(dset->oloc.file); - HDassert(mem_space); - HDassert(file_space); - HDassert(type_info); - HDassert(type_info->tpath); + HDassert(count > 0); HDassert(io_info); + /* check the first dset, should exist either single or multi dset cases */ + HDassert(io_info->dsets_info[0].dset); + dset0 = io_info->dsets_info[0].dset; + HDassert(dset0->oloc.file); + /* Get the dataset transfer property list */ if(NULL == (dx_plist = (H5P_genplist_t *)H5I_object(dxpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list") @@ -1182,87 +1669,32 @@ H5D__ioinfo_adjust(H5D_io_info_t *io_info, const H5D_t *dset, hid_t dxpl_id, /* Record the original state of parallel I/O transfer options */ io_info->orig.xfer_mode = io_info->dxpl_cache->xfer_mode; io_info->orig.coll_opt_mode = io_info->dxpl_cache->coll_opt_mode; + /* single-dset */ io_info->orig.io_ops.single_read = io_info->io_ops.single_read; io_info->orig.io_ops.single_write = io_info->io_ops.single_write; + /* multi-dset */ + io_info->orig.io_ops.single_read_md = io_info->io_ops.single_read_md; + io_info->orig.io_ops.single_write_md = io_info->io_ops.single_write_md; - /* Get MPI communicator */ - if(MPI_COMM_NULL == (io_info->comm = H5F_mpi_get_comm(dset->oloc.file))) + /* Get MPI communicator from the first dset */ + if(MPI_COMM_NULL == (io_info->comm = H5F_mpi_get_comm(dset0->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, dx_plist)) < 0) + if((opt = H5D__mpio_opt_possible(count, io_info, dx_plist)) < 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) { /* 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.single_write = H5D__mpio_select_write; + io_info->io_ops.multi_read = NULL; + io_info->io_ops.multi_write = NULL; + io_info->io_ops.multi_read_md = dset0->shared->layout.ops->par_read; + io_info->io_ops.multi_write_md = dset0->shared->layout.ops->par_write; + io_info->io_ops.single_read_md = H5D__mpio_select_read; + io_info->io_ops.single_write_md = H5D__mpio_select_write; } /* end if */ else { - /* Check if there are any filters in the pipeline. If there are, - * we cannot break to independent I/O if this is a write operation; - * 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 index; - char local_no_collective_cause_string[256] = ""; - char global_no_collective_cause_string[256] = ""; - 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" }; - - if (H5P_get(dx_plist, H5D_MPIO_LOCAL_NO_COLLECTIVE_CAUSE_NAME, &local_no_collective_cause) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "unable to get local no collective cause value") - if (H5P_get(dx_plist, H5D_MPIO_GLOBAL_NO_COLLECTIVE_CAUSE_NAME, &global_no_collective_cause) < 0) - HGOTO_ERROR(H5E_PLIST, 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, index = 0; cause < H5D_MPIO_NO_COLLECTIVE_MAX_CAUSE; cause <<= 1, index++) { - size_t cause_strlen = strlen(cause_strings[index]); - - if (cause & local_no_collective_cause) { - /* Check if there were any previous error messages included. If so, prepend a semicolon - * to separate the messages. - */ - if (local_error_message_previously_written) strncat(local_no_collective_cause_string, "; ", 2); - - strncat(local_no_collective_cause_string, cause_strings[index], cause_strlen); - - 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 (global_error_message_previously_written) strncat(global_no_collective_cause_string, "; ", 2); - - strncat(global_no_collective_cause_string, cause_strings[index], 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 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, but * mark it so that we remember to revert the change. @@ -1272,10 +1704,14 @@ H5D__ioinfo_adjust(H5D_io_info_t *io_info, const H5D_t *dset, hid_t dxpl_id, io_info->dxpl_cache->xfer_mode = H5FD_MPIO_INDEPENDENT; if(H5P_set(dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &io_info->dxpl_cache->xfer_mode) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set transfer mode") + io_info->is_coll_broken = TRUE; } /* end if */ + else if(io_info->dxpl_cache->xfer_mode == H5FD_MPIO_INDEPENDENT) + io_info->is_coll_broken = TRUE; } /* end else */ } /* end if */ - + else + io_info->is_coll_broken = TRUE; done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__ioinfo_adjust() */ @@ -1285,13 +1721,13 @@ done: * Function: H5D__ioinfo_term * * Purpose: Common logic for terminating an I/O info object - * (Only used for restoring MPI transfer mode currently) + * (Only used for restoring MPI transfer mode currently) * - * Return: Non-negative on success/Negative on failure + * This was derived from H5D__ioinfo_term for multi-dset work. * - * Programmer: Quincey Koziol - * Friday, February 6, 2004 + * Return: Non-negative on success/Negative on failure * + * Programmer: Jonathan Kim Nov, 2013 *------------------------------------------------------------------------- */ static herr_t |