diff options
Diffstat (limited to 'src/H5Dmpio.c')
| -rw-r--r-- | src/H5Dmpio.c | 399 |
1 files changed, 40 insertions, 359 deletions
diff --git a/src/H5Dmpio.c b/src/H5Dmpio.c index e216d85..f85c551 100644 --- a/src/H5Dmpio.c +++ b/src/H5Dmpio.c @@ -43,12 +43,6 @@ H5D_mpio_spaces_xfer(H5D_io_info_t *io_info, size_t elmt_size, void *buf/*out*/, hbool_t do_write); -/* For irregular hyperslab selection. */ -static herr_t -H5D_mpio_spaces_span_xfer(H5D_io_info_t *io_info, size_t elmt_size, - const H5S_t *file_space, const H5S_t *mem_space, - void *buf/*out*/, - hbool_t do_write); /*------------------------------------------------------------------------- * Function: H5D_mpio_opt_possible @@ -66,10 +60,10 @@ H5D_mpio_spaces_span_xfer(H5D_io_info_t *io_info, size_t elmt_size, * *------------------------------------------------------------------------- */ + htri_t H5D_mpio_opt_possible( const H5D_t *dset, const H5S_t *mem_space, const H5S_t *file_space, const unsigned flags) { - htri_t c1,c2; /* Flags whether a selection is optimizable */ htri_t ret_value=TRUE; FUNC_ENTER_NOAPI(H5D_mpio_opt_possible, FAIL); @@ -88,16 +82,7 @@ H5D_mpio_opt_possible( const H5D_t *dset, const H5S_t *mem_space, const H5S_t *f && (H5S_SIMPLE==H5S_GET_EXTENT_TYPE(file_space) || H5S_SCALAR==H5S_GET_EXTENT_TYPE(file_space)))) HGOTO_DONE(FALSE); - /* Check whether both selections are "regular" */ - /*#ifndef KYANG*/ -#ifndef H5_MPI_COMPLEX_DERIVED_DATATYPE_WORKS - c1=H5S_SELECT_IS_REGULAR(file_space); - c2=H5S_SELECT_IS_REGULAR(mem_space); - if(c1==FAIL || c2==FAIL) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "invalid check for single selection blocks"); - if(c1==FALSE || c2==FALSE) - HGOTO_DONE(FALSE); -#endif + /* Can't currently handle point selections */ if (H5S_SEL_POINTS==H5S_GET_SELECT_TYPE(mem_space) || H5S_SEL_POINTS==H5S_GET_SELECT_TYPE(file_space)) HGOTO_DONE(FALSE); @@ -107,126 +92,35 @@ H5D_mpio_opt_possible( const H5D_t *dset, const H5S_t *mem_space, const H5S_t *f (flags&H5S_CONV_STORAGE_MASK)!=H5S_CONV_STORAGE_CHUNKED) HGOTO_DONE(FALSE); - if ((flags&H5S_CONV_STORAGE_MASK)==H5S_CONV_STORAGE_CHUNKED) { - hsize_t chunk_dim[H5O_LAYOUT_NDIMS]; /* Chunk dimensions */ - hsize_t startf[H5S_MAX_RANK], /* Selection start bounds */ - endf[H5S_MAX_RANK]; /* Selection end bounds */ - unsigned dim_rankf; /* Number of dimensions of file dataspace */ - int pcheck_hyper,check_hyper, /* Flags for checking if selection is in one chunk */ - tnum_chunkf, /* Number of chunks selection overlaps */ - max_chunkf, /* Maximum number of chunks selection overlaps */ - min_chunkf, /* Minimum number of chunks selection overlaps */ - num_chunks_same; /* Flag indicating whether all processes have the same # of chunks to operate on */ - unsigned dim_chunks; /* Temporary number of chunks in a dimension */ - MPI_Comm comm; /* MPI communicator for file */ - int mpi_rank; /* Rank in MPI communicator */ - int mpi_code; /* MPI return code */ - unsigned u; /* Local index variable */ - - /* Disallow collective I/O if there are any I/O filters on chunks */ - if(dset->shared->dcpl_cache.pline.nused>0) - HGOTO_DONE(FALSE) - - /* Getting MPI communicator and rank */ - if((comm = H5F_mpi_get_comm(dset->ent.file))==MPI_COMM_NULL) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't retrieve MPI communicator") - if((mpi_rank = H5F_mpi_get_rank(dset->ent.file))<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't retrieve MPI rank") - - /* Currently collective chunking storage - inside HDF5 is supported for either one of the following two cases: - 1. All the hyperslabs for one process is inside one chunk. - 2. For single hyperslab selection, the number of chunks that covered - the single selection for all processes should be equal. - KY, 2004/7/14 - */ - - /* Quincey, please read. - This is maybe redundant, I think only when both memory and file space be SCALAR - space, the collective IO can work. Otherwise, SELECT_POINT will be reached,collective - IO shouldn't work. - Please clarify and correct the code on the following, - Quincey said that it was probably okay if only one data space is SCALAR, - Still keep the code here until we added more tests later. - Kent */ - if(H5S_SCALAR==H5S_GET_EXTENT_TYPE(mem_space) || H5S_SCALAR ==H5S_GET_EXTENT_TYPE(file_space)) { - if(!(H5S_SCALAR==H5S_GET_EXTENT_TYPE(mem_space) && H5S_SCALAR ==H5S_GET_EXTENT_TYPE(file_space))) - HGOTO_DONE(FALSE) - else - HGOTO_DONE(TRUE) - } /* end if */ - - dim_rankf = H5S_GET_EXTENT_NDIMS(file_space); - - if(H5S_SELECT_BOUNDS(file_space,startf,endf)==FAIL) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE,FAIL, "invalid check for single selection blocks"); - - for(u=0; u < dset->shared->layout.u.chunk.ndims; u++) - chunk_dim[u] = dset->shared->layout.u.chunk.dim[u]; - - /* Case 1: check whether all hyperslab in this process is inside one chunk. - Note: we don't handle when starting point is less than zero since that may cover - two chunks. */ - - /*for file space checking*/ - pcheck_hyper = 1; - for (u=0; u<dim_rankf; u++) - if(endf[u]/chunk_dim[u]!=startf[u]/chunk_dim[u]) { - pcheck_hyper = 0; - break; - } - - if (MPI_SUCCESS != (mpi_code= MPI_Reduce(&pcheck_hyper,&check_hyper,1,MPI_INT,MPI_LAND,0,comm))) - HMPI_GOTO_ERROR(FAIL, "MPI_Reduce failed", mpi_code) - if (MPI_SUCCESS != (mpi_code= MPI_Bcast(&check_hyper,1,MPI_INT,0,comm))) - HMPI_GOTO_ERROR(FAIL, "MPI_Bcast failed", mpi_code) - - /*if check_hyper is true, condition for collective IO case is fulfilled, no - need to do further test. */ - if(check_hyper) - HGOTO_DONE(TRUE); + /*The handling of memory space is different for chunking + and contiguous storage, + For contigous storage, mem_space and file_space won't + change when it it is doing disk IO. + For chunking storage, mem_space will change for different + chunks. So for chunking storage, whether we can use + collective IO will defer until the each chunk IO is reached. + For contiguous storage, if we find the MPI-IO cannot + support complicated MPI derived data type, we will + set use_par_opt_io = FALSE. + */ + if(dset->shared->layout.type == H5D_CONTIGUOUS) { + +#ifndef H5_MPI_COMPLEX_DERIVED_DATATYPE_WORKS + if((H5S_SELECT_IS_REGULAR(file_space) != TRUE) || + (H5S_SELECT_IS_REGULAR(mem_space) != TRUE)) + HGOTO_DONE(FALSE); +#endif + } - /* Case 2:Check whether the number of chunks that covered the single hyperslab is the same. - If not,no collective chunk IO. - KY, 2004/7/14 - */ - - c1 = H5S_SELECT_IS_SINGLE(file_space); - c2 = H5S_SELECT_IS_SINGLE(mem_space); - - if(c1==FAIL || c2 ==FAIL) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "invalid check for single selection blocks"); - if(c1==FALSE || c2 ==FALSE) - HGOTO_DONE(FALSE); - - /* Compute the number of chunks covered by the selection on this process */ - tnum_chunkf = 1; - for (u=0; u<dim_rankf; u++) { - dim_chunks = (endf[u]/chunk_dim[u]-startf[u]/chunk_dim[u])+1; - tnum_chunkf = dim_chunks*tnum_chunkf; - } - - /* Determine the minimum and maximum # of chunks for all processes */ - if (MPI_SUCCESS != (mpi_code= MPI_Reduce(&tnum_chunkf,&max_chunkf,1,MPI_INT,MPI_MAX,0,comm))) - HMPI_GOTO_ERROR(FAIL, "MPI_Reduce failed", mpi_code) - if (MPI_SUCCESS != (mpi_code= MPI_Reduce(&tnum_chunkf,&min_chunkf,1,MPI_INT,MPI_MIN,0,comm))) - HMPI_GOTO_ERROR(FAIL, "MPI_Reduce failed", mpi_code) - - /* Let the rank==0 process determine if the same number of chunks will be operated on by all processes */ - if(mpi_rank == 0) - num_chunks_same = (max_chunkf==min_chunkf); - - /* Broadcast the flag indicating the number of chunks are the same */ - if (MPI_SUCCESS != (mpi_code= MPI_Bcast(&num_chunks_same,1,MPI_INT,0,comm))) - HMPI_GOTO_ERROR(FAIL, "MPI_Bcast failed", mpi_code) - - /* Can't handle case when number of chunks is different (yet) */ - if(!num_chunks_same) - HGOTO_DONE(FALSE); - } /* end if */ + if(dset->shared->layout.type == H5D_CHUNKED) + if(dset->shared->dcpl_cache.pline.nused>0) + HGOTO_DONE(FALSE); /* Perform the independent write operation */ + + done: FUNC_LEAVE_NOAPI(ret_value); + } /* H5D_mpio_opt_possible() */ @@ -370,281 +264,68 @@ done: FUNC_LEAVE_NOAPI(ret_value); } /* end H5D_mpio_spaces_xfer() */ - -static herr_t -H5D_mpio_spaces_span_xfer(H5D_io_info_t *io_info, - size_t elmt_size, - const H5S_t *file_space, - const H5S_t *mem_space, - void *_buf /*out*/, - hbool_t do_write ) -{ - haddr_t addr; /* Address of dataset (or selection) within file */ - size_t mpi_buf_count, mpi_file_count; /* Number of "objects" to transfer */ - hsize_t mpi_buf_offset, mpi_file_offset; /* Offset within dataset where selection (ie. MPI type) begins */ - MPI_Datatype mpi_buf_type, mpi_file_type; /* MPI types for buffer (memory) and file */ - hbool_t mbt_is_derived=0, /* Whether the buffer (memory) type is derived and needs to be free'd */ - mft_is_derived=0; /* Whether the file type is derived and needs to be free'd */ - hbool_t plist_is_setup=0; /* Whether the dxpl has been customized */ - uint8_t *buf=(uint8_t *)_buf; /* Alias for pointer arithmetic */ - int mpi_code; /* MPI return code */ - herr_t ret_value = SUCCEED; /* Return value */ - - - FUNC_ENTER_NOAPI_NOINIT(H5D_mpio_spaces_span_xfer); - - /* Check args */ - assert (io_info); - assert (io_info->dset); - assert (file_space); - assert (mem_space); - assert (buf); - assert (IS_H5FD_MPIO(io_info->dset->ent.file)); - - /* Make certain we have the correct type of property list */ - assert(TRUE==H5P_isa_class(io_info->dxpl_id,H5P_DATASET_XFER)); - - - /* create the MPI buffer type */ - if(H5S_SELECT_IS_REGULAR(mem_space)==TRUE){ - if (H5S_mpio_space_type( mem_space, elmt_size, - /* out: */ - &mpi_buf_type, - &mpi_buf_count, - &mpi_buf_offset, - &mbt_is_derived )<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't create MPI buf type"); - } - else { - if (H5S_mpio_space_span_type( mem_space, elmt_size, - /* out: */ - &mpi_buf_type, - &mpi_buf_count, - &mpi_buf_offset, - &mbt_is_derived )<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't create MPI buf type"); - } - - /* create the MPI file type */ - - if(H5S_SELECT_IS_REGULAR(file_space)== TRUE){ - if ( H5S_mpio_space_type( file_space, elmt_size, - /* out: */ - &mpi_file_type, - &mpi_file_count, - &mpi_file_offset, - &mft_is_derived )<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't create MPI file type"); - } - else { - if ( H5S_mpio_space_span_type( file_space, elmt_size, - /* out: */ - &mpi_file_type, - &mpi_file_count, - &mpi_file_offset, - &mft_is_derived )<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't create MPI file type"); - } - - /* Get the base address of the contiguous dataset or the chunk */ - if(io_info->dset->shared->layout.type == H5D_CONTIGUOUS) - addr = H5D_contig_get_addr(io_info->dset) + mpi_file_offset; - else { - haddr_t chunk_addr; /* for collective chunk IO */ - assert(io_info->dset->shared->layout.type == H5D_CHUNKED); - chunk_addr=H5D_istore_get_addr(io_info,NULL); - addr = H5F_BASE_ADDR(io_info->dset->ent.file) + chunk_addr + mpi_file_offset; - } - - /* - * Pass buf type, file type to the file driver. Request an MPI type - * transfer (instead of an elementary byteblock transfer). - */ - if(H5FD_mpi_setup_collective(io_info->dxpl_id, mpi_buf_type, mpi_file_type)<0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set MPI-I/O properties"); - plist_is_setup=1; - - /* Adjust the buffer pointer to the beginning of the selection */ - buf+=mpi_buf_offset; - - /* transfer the data */ - if (do_write) { - if (H5F_block_write(io_info->dset->ent.file, H5FD_MEM_DRAW, addr, mpi_buf_count, io_info->dxpl_id, buf) <0) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,"MPI write failed"); - } - else { - if (H5F_block_read (io_info->dset->ent.file, H5FD_MEM_DRAW, addr, mpi_buf_count, io_info->dxpl_id, buf) <0) - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL,"MPI read failed"); - } - -done: - /* Reset the dxpl settings */ - if(plist_is_setup) { - if(H5FD_mpi_teardown_collective(io_info->dxpl_id)<0) - HDONE_ERROR(H5E_DATASPACE, H5E_CANTFREE, FAIL, "unable to reset dxpl values"); - } /* end if */ - - /* free the MPI buf and file types */ - if (mbt_is_derived) { - if (MPI_SUCCESS != (mpi_code= MPI_Type_free( &mpi_buf_type ))) - HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code); - } - if (mft_is_derived) { - if (MPI_SUCCESS != (mpi_code= MPI_Type_free( &mpi_file_type ))) - HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code); - } - - FUNC_LEAVE_NOAPI(ret_value); -} /* end H5D_mpio_spaces_span_xfer() */ - /*------------------------------------------------------------------------- - * Function: H5D_mpio_spaces_read + * Function: H5D_mpio_select_read * * Purpose: MPI-IO function to read directly from app buffer to file. * * Return: non-negative on success, negative on failure. * - * Programmer: rky 980813 + * Programmer: * * Modifications: * - * rky 980918 - * Added must_convert parameter to let caller know we can't optimize the xfer. - * - * QAK - 2002/04/02 - * Removed the must_convert parameter and move preconditions to - * H5S_mpio_opt_possible() routine - * *------------------------------------------------------------------------- */ herr_t -H5D_mpio_spaces_read(H5D_io_info_t *io_info, +H5D_mpio_select_read(H5D_io_info_t *io_info, size_t UNUSED nelmts, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, void *buf/*out*/) { herr_t ret_value; - FUNC_ENTER_NOAPI_NOFUNC(H5D_mpio_spaces_read); + FUNC_ENTER_NOAPI_NOFUNC(H5D_mpio_select_read); - ret_value = H5D_mpio_spaces_xfer(io_info, elmt_size, file_space, + + ret_value = H5D_mpio_spaces_xfer(io_info, elmt_size, file_space, mem_space, buf, 0/*read*/); FUNC_LEAVE_NOAPI(ret_value); -} /* end H5D_mpio_spaces_read() */ +} /* end H5D_mpio_select_read() */ /*------------------------------------------------------------------------- - * Function: H5D_mpio_spaces_write + * Function: H5D_mpio_select_write * * Purpose: MPI-IO function to write directly from app buffer to file. * * Return: non-negative on success, negative on failure. * - * Programmer: rky 980813 + * Programmer: * * Modifications: * - * rky 980918 - * Added must_convert parameter to let caller know we can't optimize the xfer. - * - * QAK - 2002/04/02 - * Removed the must_convert parameter and move preconditions to - * H5S_mpio_opt_possible() routine * *------------------------------------------------------------------------- */ herr_t -H5D_mpio_spaces_write(H5D_io_info_t *io_info, +H5D_mpio_select_write(H5D_io_info_t *io_info, size_t UNUSED nelmts, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, const void *buf) { herr_t ret_value; - FUNC_ENTER_NOAPI_NOFUNC(H5D_mpio_spaces_write); + FUNC_ENTER_NOAPI_NOFUNC(H5D_mpio_select_write); /*OKAY: CAST DISCARDS CONST QUALIFIER*/ - ret_value = H5D_mpio_spaces_xfer(io_info, elmt_size, file_space, - mem_space, (void*)buf, 1/*write*/); + ret_value = H5D_mpio_spaces_xfer(io_info, elmt_size, file_space, + mem_space, (void*)buf, 1/*write*/); FUNC_LEAVE_NOAPI(ret_value); } /* end H5D_mpio_spaces_write() */ - -/*------------------------------------------------------------------------- - * Function: H5D_mpio_spaces_span_read - * - * Purpose: MPI-IO function to read directly from app buffer to file for - span-tree - * - * Return: non-negative on success, negative on failure. - * - * Programmer: KY - * - * Modifications: - * - * - *------------------------------------------------------------------------- - */ -herr_t -H5D_mpio_spaces_span_read(H5D_io_info_t *io_info, - size_t UNUSED nelmts, - size_t elmt_size, - const H5S_t *file_space, - const H5S_t *mem_space, - void *buf/*out*/) -{ - herr_t ret_value; - - FUNC_ENTER_NOAPI_NOFUNC(H5D_mpio_spaces_span_read); - - ret_value = H5D_mpio_spaces_span_xfer(io_info, elmt_size, file_space, - mem_space, buf, 0/*read*/); - - FUNC_LEAVE_NOAPI(ret_value); -} /* end H5D_mpio_spaces_read() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_mpio_spaces_span_write - * - * Purpose: MPI-IO function to write directly from app buffer to file. - * - * Return: non-negative on success, negative on failure. - * - * Programmer: KY - - * - * Modifications: - * - * rky 980918 - * Added must_convert parameter to let caller know we can't optimize the xfer. - * - * QAK - 2002/04/02 - * Removed the must_convert parameter and move preconditions to - * H5S_mpio_opt_possible() routine - * - *------------------------------------------------------------------------- - */ -herr_t -H5D_mpio_spaces_span_write(H5D_io_info_t *io_info, - size_t UNUSED nelmts, - size_t elmt_size, - const H5S_t *file_space, - const H5S_t *mem_space, - const void *buf) -{ - herr_t ret_value; - - FUNC_ENTER_NOAPI_NOFUNC(H5D_mpio_spaces_span_write); - - /*OKAY: CAST DISCARDS CONST QUALIFIER*/ - ret_value = H5D_mpio_spaces_span_xfer(io_info, elmt_size, file_space, - mem_space, (void*)buf, 1/*write*/); - - FUNC_LEAVE_NOAPI(ret_value); -} /* end H5D_mpio_spaces_span_write() */ #endif /* H5_HAVE_PARALLEL */ |