diff options
Diffstat (limited to 'src/H5Dio.c')
| -rw-r--r-- | src/H5Dio.c | 650 |
1 files changed, 511 insertions, 139 deletions
diff --git a/src/H5Dio.c b/src/H5Dio.c index c1f6d4b..731b4c7 100644 --- a/src/H5Dio.c +++ b/src/H5Dio.c @@ -65,9 +65,10 @@ typedef struct fm_map { H5TB_TREE *fsel; /* TBBT containing file dataspaces for all chunks */ H5TB_TREE *msel; /* TBBT containing memory dataspaces for all chunks */ hsize_t last_index; /* Index of last chunk operated on */ - H5S_t *last_fchunk; /* Pointer to last file chunk's dataspace */ + H5S_t *file_space; /* Pointer to the file dataspace */ + H5S_t *mem_space; /* Pointer to the memory dataspace */ + hsize_t f_dims[H5O_LAYOUT_NDIMS]; /* File dataspace dimensions */ H5S_t *last_mchunk; /* Pointer to last memory chunk's dataspace */ - H5S_t *fchunk_tmpl; /* Dataspace template for new file chunks */ H5S_t *mchunk_tmpl; /* Dataspace template for new memory chunks */ unsigned f_ndims; /* Number of dimensions for file dataspace */ H5S_sel_iter_t mem_iter; /* Iterator for elements in memory selection */ @@ -120,7 +121,9 @@ static void H5D_free_fchunk_info(void *fchunk_info); static void H5D_free_mchunk_info(void *mchunk_info); static herr_t H5D_chunk_coords_assist(hssize_t *coords, size_t ndims, hsize_t chunks[], hsize_t chunk_idx); -static herr_t H5D_chunk_cb(void *elem, hid_t type_id, hsize_t ndims, +static herr_t H5D_create_chunk_file_map(fm_map *fm); +static herr_t H5D_create_chunk_mem_map(fm_map *fm); +static herr_t H5D_chunk_mem_cb(void *elem, hid_t type_id, hsize_t ndims, hssize_t *coords, void *fm); static herr_t H5D_fill(const void *fill, const H5T_t *fill_type, void *buf, const H5T_t *buf_type, const H5S_t *space, hid_t dxpl_id); @@ -1837,9 +1840,27 @@ nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, FUNC_ENTER_NOINIT(H5D_chunk_write); +#ifdef QAK +{ + int mpi_rank; + double time; + MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); + time = MPI_Wtime(); + HDfprintf(stderr,"%s: rank=%d - Entering, time=%f\n",FUNC,mpi_rank,time); +} +#endif /* QAK */ /* Map elements between file and memory for each chunk*/ if(H5D_create_chunk_map(dataset, mem_type, file_space, mem_space, &fm)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't build chunk mapping"); +#ifdef QAK +{ + int mpi_rank; + double time; + MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); + time = MPI_Wtime(); + HDfprintf(stderr,"%s: rank=%d - After creating chunk map, time=%f\n",FUNC,mpi_rank,time); +} +#endif /* QAK */ /* * If there is no type conversion then write directly from the @@ -1849,6 +1870,15 @@ nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif +#ifdef QAK +{ + int mpi_rank; + double time; + MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); + time = MPI_Wtime(); + HDfprintf(stderr,"%s: rank=%d - Performing optimized I/O, time=%f\n",FUNC,mpi_rank,time); +} +#endif /* QAK */ /* Get first node in chunk trees */ fchunk_node=H5TB_first(fm.fsel->root); mchunk_node=H5TB_first(fm.msel->root); @@ -1896,6 +1926,15 @@ nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, */ assert((fchunk_node && mchunk_node) || (!fchunk_node && !mchunk_node)); } /* end while */ +#ifdef QAK +{ + int mpi_rank; + double time; + MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); + time = MPI_Wtime(); + HDfprintf(stderr,"%s: rank=%d - Done performing optimized I/O, time=%f\n",FUNC,mpi_rank,time); +} +#endif /* QAK */ #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[0].write_timer), &timer); @@ -1906,6 +1945,13 @@ nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, /* direct xfer accomplished successfully */ HGOTO_DONE(SUCCEED); } /* end if */ +#ifdef QAK +{ + int mpi_rank; + MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); + HDfprintf(stderr,"%s: rank=%d - Performing NON-optimized I/O\n",FUNC,mpi_rank); +} +#endif /* QAK */ /* * This is the general case(type conversion). @@ -2242,14 +2288,13 @@ static herr_t H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_space, const H5S_t *mem_space, fm_map *fm) { - H5S_t *tmp_fspace=NULL, /* Temporary file dataspace */ - *tmp_mspace=NULL; /* Temporary memory dataspace */ + H5S_t *tmp_mspace=NULL; /* Temporary memory dataspace */ hid_t f_tid=(-1); /* Temporary copy of file datatype for iteration */ size_t elmt_size; /* Memory datatype size */ hbool_t iter_init=0; /* Selection iteration info has been initialized */ unsigned f_ndims; /* The number of dimensions of the file's dataspace */ int sm_ndims; /* The number of dimensions of the memory buffer's dataspace (signed) */ - hsize_t f_dims[H5O_LAYOUT_NDIMS]; /* Dimensionality of file dataspace */ + hsize_t offset[H5O_LAYOUT_NDIMS]; /* Offset of selection for chunk */ hsize_t nchunks, last_nchunks; /* Number of chunks in dataset */ H5TB_NODE *curr_node; /* Current node in TBBT */ char bogus; /* "bogus" buffer to pass to selection iterator */ @@ -2257,6 +2302,15 @@ H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_sp herr_t ret_value = SUCCEED; /*return value */ FUNC_ENTER_NOINIT(H5D_create_chunk_map); +#ifdef QAK +{ + int mpi_rank; + double time; + MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); + time = MPI_Wtime(); + HDfprintf(stderr,"%s: rank=%d - Entering, time=%f\n",FUNC,mpi_rank,time); +} +#endif /* QAK */ /* Initialize fm_map structure */ HDmemset(fm, 0, sizeof(fm_map)); @@ -2264,34 +2318,29 @@ H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_sp /* Get layout for dataset */ fm->layout = &(dataset->layout); - /* Create a file space of a chunk's size, instead of whole file space*/ - if(NULL==(tmp_fspace=H5S_create_simple((dataset->layout.ndims-1),dataset->layout.dim,NULL))) - HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create simple dataspace"); - /*make a copy of mem_space*/ if((tmp_mspace = H5S_copy(mem_space))==NULL) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space"); - /*de-select the file space and mem space copies*/ - if(H5S_select_none(tmp_fspace)<0) - HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to de-select file space"); - if(H5S_select_none(tmp_mspace)<0) - HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to de-select memory space"); - /* Get dim number and dimensionality for each dataspace */ fm->f_ndims=f_ndims=dataset->layout.ndims-1; if((sm_ndims = H5S_get_simple_extent_ndims(tmp_mspace))<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimension number"); fm->m_ndims=sm_ndims; - if(H5S_get_simple_extent_dims(file_space, f_dims, NULL)<0) + /* De-select the mem space copy */ + if(H5S_select_none(tmp_mspace)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to de-select memory space"); + + if(H5S_get_simple_extent_dims(file_space, fm->f_dims, NULL)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimensionality"); /* Decide the number of chunks in each dimension*/ last_nchunks=0; nchunks=1; for(u=0; u<f_ndims; u++) { - fm->chunks[u] = ((f_dims[u]+dataset->layout.dim[u])-1) / dataset->layout.dim[u]; + /* Round up to the next integer # of chunks, to accomodate partial chunks */ + fm->chunks[u] = ((fm->f_dims[u]+dataset->layout.dim[u])-1) / dataset->layout.dim[u]; /* Track total number of chunks in dataset */ nchunks *= fm->chunks[u]; @@ -2312,28 +2361,47 @@ H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_sp if((fm->msel=H5TB_fast_dmake(H5TB_FAST_HSIZE_COMPARE))==NULL) HGOTO_ERROR(H5E_DATASET,H5E_CANTMAKETREE,FAIL,"can't create TBBT for memory chunk selections"); - /* Save chunk template information */ - fm->fchunk_tmpl=tmp_fspace; - fm->mchunk_tmpl=tmp_mspace; + /* Save chunk template information */ + fm->mchunk_tmpl=tmp_mspace; - /* Initialize "last chunk" information */ - fm->last_index=(hsize_t)-1; - fm->last_fchunk=fm->last_mchunk=NULL; - - /* Create temporary datatypes for selection iteration */ - if((f_tid = H5I_register(H5I_DATATYPE, H5T_copy(dataset->type, H5T_COPY_ALL)))<0) - HGOTO_ERROR (H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register file datatype"); - - /* Create selection iterator for memory selection */ - if((elmt_size=H5T_get_size(mem_type))==0) - HGOTO_ERROR(H5E_DATATYPE, H5E_BADSIZE, FAIL, "datatype size invalid"); - if (H5S_select_iter_init(&(fm->mem_iter), mem_space, elmt_size)<0) - HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator"); - iter_init=1; /* Selection iteration info has been initialized */ + /* Initialize "last chunk" information */ + fm->last_index=(hsize_t)-1; + fm->last_mchunk=NULL; + + /* Copy the file dataspace */ + if((fm->file_space = H5S_copy(file_space))==NULL) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file dataspace"); + if(H5S_hyper_convert(fm->file_space)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to convert selection to span trees"); - /* Build the file & memory selection for each chunk */ - if(H5S_select_iterate(&bogus, f_tid, file_space, H5D_chunk_cb, fm)<0) - HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to iterate file space"); + /* Copy the memory dataspace */ + if((fm->mem_space = H5S_copy(mem_space))==NULL) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory dataspace"); + if(H5S_hyper_convert(fm->mem_space)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to convert selection to span trees"); + +#ifdef QAK +{ + int mpi_rank; + double time; + MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); + time = MPI_Wtime(); + HDfprintf(stderr,"%s: rank=%d - Before creating chunk selections, time=%f\n",FUNC,mpi_rank,time); +} +#endif /* QAK */ + /* Build the file selection for each chunk */ + if(H5D_create_chunk_file_map(fm)<0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections"); +#ifdef QAK +{ + int mpi_rank; + double time; + MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); + time = MPI_Wtime(); + HDfprintf(stderr,"%s: rank=%d - After creating file chunk selections, time=%f\n",FUNC,mpi_rank,time); + HDfprintf(stderr,"%s: rank=%d - H5S_select_shape_same=%d\n",FUNC,mpi_rank,H5S_select_shape_same(file_space,mem_space)); +} +#endif /* QAK */ /* Clean file chunks' hyperslab span "scratch" information */ curr_node=H5TB_first(fm->fsel->root); @@ -2352,34 +2420,64 @@ H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_sp curr_node=H5TB_next(curr_node); } /* end while */ - /* Clean memory chunks' hyperslab span "scratch" information */ - curr_node=H5TB_first(fm->msel->root); - while(curr_node) { - H5D_mchunk_info_t *chunk_info; /* Pointer chunk information */ - - /* Get pointer to chunk's information */ - chunk_info=curr_node->data; - assert(chunk_info); - - /* Clean hyperslab span's "scratch" information */ - if(H5S_hyper_reset_scratch(chunk_info->space)<0) - HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset span scratch info"); + /* Build the memory selection for each chunk */ + if(H5S_select_shape_same(file_space,mem_space)==TRUE) { + /* If the selections are the same shape, use the file chunk information + * to generate the memory chunk information quickly. + */ + if(H5D_create_chunk_mem_map(fm)<0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create memory chunk selections"); + } /* end if */ + else { + /* Create temporary datatypes for selection iteration */ + if((f_tid = H5I_register(H5I_DATATYPE, H5T_copy(dataset->type, H5T_COPY_ALL)))<0) + HGOTO_ERROR (H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register file datatype"); + + /* Create selection iterator for memory selection */ + if((elmt_size=H5T_get_size(mem_type))==0) + HGOTO_ERROR(H5E_DATATYPE, H5E_BADSIZE, FAIL, "datatype size invalid"); + if (H5S_select_iter_init(&(fm->mem_iter), mem_space, elmt_size)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator"); + iter_init=1; /* Selection iteration info has been initialized */ + + /* Spaces aren't the same shape, iterate over the memory selection directly */ + if(H5S_select_iterate(&bogus, f_tid, file_space, H5D_chunk_mem_cb, fm)<0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create memory chunk selections"); + + /* Clean memory chunks' hyperslab span "scratch" information */ + curr_node=H5TB_first(fm->msel->root); + while(curr_node) { + H5D_mchunk_info_t *chunk_info; /* Pointer chunk information */ + + /* Get pointer to chunk's information */ + chunk_info=curr_node->data; + assert(chunk_info); + + /* Clean hyperslab span's "scratch" information */ + if(H5S_hyper_reset_scratch(chunk_info->space)<0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset span scratch info"); + + /* Get the next chunk node in the TBBT */ + curr_node=H5TB_next(curr_node); + } /* end while */ + } /* end else */ - /* Get the next chunk node in the TBBT */ - curr_node=H5TB_next(curr_node); - } /* end while */ +#ifdef QAK +{ + int mpi_rank; + double time; + MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); + time = MPI_Wtime(); + HDfprintf(stderr,"%s: rank=%d - After creating chunk selections, time=%f\n",FUNC,mpi_rank,time); +} +#endif /* QAK */ done: /* Release the [potentially partially built] chunk mapping information if an error occurs */ if(ret_value<0) { - if(tmp_fspace && !fm->fchunk_tmpl) { - if(H5S_close(tmp_fspace)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release file chunk dataspace template"); - } /* end if */ - if(tmp_mspace && !fm->mchunk_tmpl) { if(H5S_close(tmp_mspace)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release memory chunk dataspace template"); + HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release memory chunk dataspace template"); } /* end if */ if (H5D_destroy_chunk_map(fm)<0) @@ -2393,6 +2491,15 @@ done: if(f_tid!=(-1)) H5Tclose(f_tid); +#ifdef QAK +{ + int mpi_rank; + double time; + MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); + time = MPI_Wtime(); + HDfprintf(stderr,"%s: rank=%d - Leaving, time=%f\n",FUNC,mpi_rank,time); +} +#endif /* QAK */ FUNC_LEAVE_NOAPI(ret_value); } /* end H5D_create_chunk_map() */ @@ -2500,10 +2607,15 @@ H5D_destroy_chunk_map(fm_map *fm) if(fm->msel) H5TB_dfree(fm->msel,H5D_free_mchunk_info,NULL); - /* Free the file chunk dataspace template */ - if(fm->fchunk_tmpl) - if(H5S_close(fm->fchunk_tmpl)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release file chunk dataspace template"); + /* Free the file dataspace */ + if(fm->file_space) + if(H5S_close(fm->file_space)<0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release file dataspace"); + + /* Free the memory dataspace */ + if(fm->mem_space) + if(H5S_close(fm->mem_space)<0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release memory dataspace"); /* Free the memory chunk dataspace template */ if(fm->mchunk_tmpl) @@ -2516,10 +2628,338 @@ done: /*------------------------------------------------------------------------- - * Function: H5D_chunk_cb + * Function: H5D_create_chunk_file_map + * + * Purpose: Create all chunk selections in file. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * Thursday, May 29, 2003 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D_create_chunk_file_map(fm_map *fm) +{ + H5S_t *tmp_fspace=NULL; /* Temporary file dataspace */ + hssize_t sel_points; /* Number of elements in file selection */ + hsize_t sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */ + hsize_t sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */ + hssize_t start_coords[H5O_LAYOUT_NDIMS]; /* Starting coordinates of selection */ + hssize_t coords[H5O_LAYOUT_NDIMS]; /* Current coordinates of chunk */ + hsize_t count[H5O_LAYOUT_NDIMS]; /* Hyperslab count information */ + hsize_t chunk_index; /* Index of chunk */ + int curr_dim; /* Current dimension to increment */ + unsigned u; /* Local index variable */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOINIT(H5D_create_chunk_file_map); + + /* Make a copy of file dataspace */ + if((tmp_fspace = H5S_copy(fm->file_space))==NULL) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space"); + + /* Get number of elements selected in file */ + if((sel_points=H5S_get_select_npoints(tmp_fspace))<0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection # of elements"); + + /* Get offset of first block in file selection */ + if(H5S_get_select_bounds(tmp_fspace, sel_start, sel_end)<0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound info"); + + /* Set initial chunk location & hyperslab size */ + for(u=0; u<fm->f_ndims; u++) { + start_coords[u]=(sel_start[u]/fm->layout->dim[u])*fm->layout->dim[u]; + coords[u]=start_coords[u]; + count[u]=fm->layout->dim[u]; + } /* end for */ + + /* Select initial chunk as hyperslab */ + if(H5S_select_hyperslab(tmp_fspace,H5S_SELECT_SET,coords,NULL,count,NULL)<0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't create hyperslab selection"); + + /* Calculate the index of this chunk */ + if(H5V_chunk_index(fm->f_ndims,coords,fm->layout->dim,fm->chunks,fm->down_chunks,&chunk_index)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index"); + + /* Iterate through each chunk in the dataset */ + while(1) { + /* Check for intersection of temporary chunk and file selection */ + if(H5S_hyper_intersect(tmp_fspace,fm->file_space)==TRUE) { + H5S_t *tmp_fchunk; /* Temporary file dataspace */ + H5D_fchunk_info_t *new_fchunk_info; /* File chunk information to insert into tree */ + hssize_t chunk_points; /* Number of elements in chunk selection */ + + /* Create "temporary" chunk for selection operations (copy file space) */ + if((tmp_fchunk = H5S_copy(fm->file_space))==NULL) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space"); + + /* "AND" temporary chunk and current chunk */ + if(H5S_select_hyperslab(tmp_fchunk,H5S_SELECT_AND,coords,NULL,count,NULL)<0) { + H5S_close(tmp_fchunk); + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't create chunk selection"); + } /* end if */ + + /* Resize chunk's dataspace dimensions to size of chunk */ + if(H5S_set_extent_real(tmp_fchunk,count)<0) { + H5S_close(tmp_fchunk); + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk dimensions"); + } /* end if */ + + /* Move selection back to have correct offset in chunk */ + if(H5S_hyper_adjust(tmp_fchunk,coords)<0) { + H5S_close(tmp_fchunk); + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk selection"); + } /* end if */ + + /* Add temporary chunk to the list of file chunks */ + + /* Allocate the file & memory chunk information */ + if (NULL==(new_fchunk_info = H5FL_MALLOC (H5D_fchunk_info_t))) { + H5S_close(tmp_fchunk); + HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate file chunk info"); + } /* end if */ + + /* Initialize the file chunk information */ + + /* Set the chunk index */ + new_fchunk_info->index=chunk_index; + + /* Set the file chunk dataspace */ + new_fchunk_info->space=tmp_fchunk; + + /* Compute the chunk's coordinates */ + H5D_chunk_coords_assist(new_fchunk_info->coords, fm->f_ndims, fm->chunks, chunk_index); + + /* Insert the new file chunk into the TBBT tree */ + if(H5TB_dins(fm->fsel,new_fchunk_info,new_fchunk_info)==NULL) { + H5D_free_fchunk_info(new_fchunk_info); + HGOTO_ERROR(H5E_DATASPACE,H5E_CANTINSERT,FAIL,"can't insert file chunk into TBBT"); + } /* end if */ + + /* Get number of elements selected in chunk */ + if((chunk_points=H5S_get_select_npoints(tmp_fchunk))<0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection # of elements"); + + /* Decrement # of points left in file selection */ + sel_points-=chunk_points; + + /* Leave if we are done */ + if(sel_points==0) + HGOTO_DONE(SUCCEED); + assert(sel_points>0); + } /* end if */ + + /* Increment chunk index */ + chunk_index++; + + /* Set current increment dimension */ + curr_dim=fm->f_ndims-1; + + /* Increment chunk location in fastest changing dimension */ + coords[curr_dim]+=count[curr_dim]; + + /* Bring chunk location back into bounds, if necessary */ + if(coords[curr_dim]>sel_end[curr_dim]) { + do { + /* Reset current dimension's location to 0 */ + coords[curr_dim]=start_coords[curr_dim]; + + /* Decrement current dimension */ + curr_dim--; + + /* Increment chunk location in current dimension */ + coords[curr_dim]+=count[curr_dim]; + } while(coords[curr_dim]>sel_end[curr_dim]); + + /* Re-Calculate the index of this chunk */ + if(H5V_chunk_index(fm->f_ndims,coords,fm->layout->dim,fm->chunks,fm->down_chunks,&chunk_index)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index"); + } /* end if */ + + /* Move template chunk's offset to current location of chunk */ + if(H5S_hyper_move(tmp_fspace,coords)<0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't move chunk selection"); + } /* end while */ + +done: + if(tmp_fspace) + if(H5S_close(tmp_fspace)<0) + HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release file dataspace copy"); + FUNC_LEAVE_NOAPI(ret_value); +} /* end H5D_create_chunk_file_map() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_create_chunk_mem_map + * + * Purpose: Create all chunk selections in memory by copying the file + * chunk selections and adjusting their offsets to be correct + * for the memory. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * Thursday, May 29, 2003 + * + * Assumptions: That the file and memory selections are the same shape. + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D_create_chunk_mem_map(fm_map *fm) +{ + H5TB_NODE *curr_node; /* Current node in TBBT */ + hsize_t file_off[H5O_LAYOUT_NDIMS*2]; /* Offset of first block in file selection */ + hsize_t mem_off[H5O_LAYOUT_NDIMS*2]; /* Offset of first block in memory selection */ + hssize_t adjust[H5O_LAYOUT_NDIMS]; /* Adjustment to make to all file chunks */ + hssize_t chunk_adjust[H5O_LAYOUT_NDIMS]; /* Adjustment to make to a particular chunk */ + unsigned u; /* Local index variable */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOINIT(H5D_create_chunk_mem_map); +#ifdef QAK +{ + hsize_t mem_dims[H5O_LAYOUT_NDIMS]; /* Dimensions of memory space */ + + if(H5S_get_simple_extent_dims(fm->mem_space, mem_dims, NULL)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimensionality"); + + HDfprintf(stderr,"%s: mem_dims={",FUNC); + for(u=0; u<fm->m_ndims; u++) + HDfprintf(stderr,"%Hd%s",mem_dims[u],(u<(fm->m_ndims-1) ? ", " : "}\n")); +} +#endif /* QAK */ + + /* Get offset of first block in file selection */ + if(H5S_get_select_hyper_blocklist(fm->file_space, 0, 1, file_off)<0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection block info"); + + /* Get offset of first block in memory selection */ + if(H5S_get_select_hyper_blocklist(fm->mem_space, 0, 1, mem_off)<0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection block info"); + + /* Calculate the adjustment for memory selection from file selection */ + assert(fm->m_ndims==fm->f_ndims); + for(u=0; u<fm->f_ndims; u++) + adjust[u]=file_off[u]-mem_off[u]; +#ifdef QAK +{ + int mpi_rank; + MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); + if(mpi_rank==1) { + HDfprintf(stderr,"%s: rank=%d - adjust={",FUNC,mpi_rank); + for(u=0; u<fm->f_ndims; u++) + HDfprintf(stderr,"%Hd%s",adjust[u],(u<(fm->f_ndims-1) ? ", " : "}\n")); + } /* end if */ +} +#endif /* QAK */ +#ifdef QAK +HDfprintf(stderr,"%s: adjust={",FUNC); +for(u=0; u<fm->f_ndims; u++) + HDfprintf(stderr,"%Hd%s",adjust[u],(u<(fm->f_ndims-1) ? ", " : "}\n")); +#endif /* QAK */ + + /* Iterate over each chunk in the file chunk list */ + curr_node=H5TB_first(fm->fsel->root); + while(curr_node) { + H5D_fchunk_info_t *fchunk_info; /* Pointer to file chunk information */ + H5D_mchunk_info_t *mchunk_info; /* Pointer to memory chunk information */ + + /* Get pointer to chunk's information */ + fchunk_info=curr_node->data; + assert(fchunk_info); + + /* Allocate space for the memory chunk information */ + if (NULL==(mchunk_info = H5FL_MALLOC (H5D_mchunk_info_t))) + HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate memory chunk info"); + + /* Copy the information */ + + /* Set the chunk index */ + mchunk_info->index=fchunk_info->index; + + /* Copy the memory dataspace */ + if((mchunk_info->space = H5S_copy(fm->mem_space))==NULL) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space"); + + /* Release the current selection */ + if(H5S_select_release(mchunk_info->space)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection"); + + /* Copy the file chunk's selection */ + if(H5S_select_copy(mchunk_info->space,fchunk_info->space)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy selection"); + + /* Compensate for the chunk offset */ + for(u=0; u<fm->f_ndims; u++) + chunk_adjust[u]=adjust[u]-(fchunk_info->coords[u]*fm->layout->dim[u]); +#ifdef QAK +{ + int mpi_rank; + MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); + if(mpi_rank==1) { + HDfprintf(stderr,"%s: rank=%d - Before adjusting memory selection\n",FUNC,mpi_rank); + HDfprintf(stderr,"%s: rank=%d - chunk_adjust={",FUNC,mpi_rank); + for(u=0; u<fm->f_ndims; u++) + HDfprintf(stderr,"%Hd%s",chunk_adjust[u],(u<(fm->f_ndims-1) ? ", " : "}\n")); + } /* end if */ +} +#endif /* QAK */ +#ifdef QAK +HDfprintf(stderr,"%s: Before adjusting memory selection\n",FUNC); +HDfprintf(stderr,"%s: chunk_adjust={",FUNC); +for(u=0; u<fm->f_ndims; u++) + HDfprintf(stderr,"%Hd%s",chunk_adjust[u],(u<(fm->f_ndims-1) ? ", " : "}\n")); +#endif /* QAK */ + /* Adjust the selection */ + if(H5S_hyper_adjust(mchunk_info->space,chunk_adjust)<0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk selection"); +#ifdef QAK +{ + int mpi_rank; + MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); + if(mpi_rank==1) + HDfprintf(stderr,"%s: rank=%d - After adjusting memory selection\n",FUNC,mpi_rank); +} +#endif /* QAK */ +#ifdef QAK +HDfprintf(stderr,"%s: After adjusting memory selection\n",FUNC); + +{ + hsize_t mem_dims[H5O_LAYOUT_NDIMS]; /* Dimensions of memory space */ + + if(H5S_get_simple_extent_dims(mchunk_info->space, mem_dims, NULL)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimensionality"); + + HDfprintf(stderr,"%s: mem_dims={",FUNC); + for(u=0; u<fm->m_ndims; u++) + HDfprintf(stderr,"%Hd%s",mem_dims[u],(u<(fm->m_ndims-1) ? ", " : "}\n")); +} +#endif /* QAK */ + /* Insert the new memory chunk into the TBBT tree */ + if(H5TB_dins(fm->msel,mchunk_info,mchunk_info)==NULL) + HGOTO_ERROR(H5E_DATASPACE,H5E_CANTINSERT,FAIL,"can't insert memory chunk into TBBT"); + + /* Get the next chunk node in the TBBT */ + curr_node=H5TB_next(curr_node); + } /* end while */ + +done: + FUNC_LEAVE_NOAPI(ret_value); +} /* end H5D_create_chunk_mem_map() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_chunk_mem_cb * * Purpose: Callback routine for file selection iterator. Used when - * creating selections in memory and each chunk for each chunk. + * creating selections in memory for each chunk. * * Return: Non-negative on success/Negative on failure * @@ -2533,54 +2973,26 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D_chunk_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize_t *coords, void *_fm) +H5D_chunk_mem_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize_t *coords, void *_fm) { fm_map *fm = (fm_map*)_fm; /* File<->memory chunk mapping info */ - H5S_t *fspace; /* File chunk's dataspace */ H5S_t *mspace; /* Memory chunk's dataspace */ - hssize_t coords_in_chunk[H5O_LAYOUT_NDIMS]; /* Coordinates of element in chunk */ hssize_t coords_in_mem[H5O_LAYOUT_NDIMS]; /* Coordinates of element in memory */ hsize_t chunk_index; /* Chunk index */ hsize_t u; /* Local index variables */ herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_NOINIT(H5D_chunk_cb); -#ifdef QAK -{ - unsigned u; - HDfprintf(stderr,"%s: coords={",FUNC); - for(u=0; u<ndims; u++) - HDfprintf(stderr,"%Hd%s",coords[u],(u<(ndims-1)?", ":"}\n")); -} -#endif /* QAK */ + FUNC_ENTER_NOINIT(H5D_chunk_mem_cb); /* Calculate the index of this chunk */ if(H5V_chunk_index((unsigned)ndims,coords,fm->layout->dim,fm->chunks,fm->down_chunks,&chunk_index)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index"); -#ifdef QAK -HDfprintf(stderr,"%s: chunk_index=%Hu\n",FUNC,chunk_index); -#endif /* QAK */ - - /*convert coords from relative to whole file space to relative to its chunk space, - *pass into H5S_select_hyperslab.*/ - for(u=0; u<ndims; u++) - coords_in_chunk[u] = coords[u] % fm->layout->dim[u]; - -#ifdef QAK -{ - unsigned u; - HDfprintf(stderr,"%s: coords_in_chunk={",FUNC); - for(u=0; u<ndims; u++) - HDfprintf(stderr,"%Hd%s",coords_in_chunk[u],(u<(ndims-1)?", ":"}\n")); -} -#endif /* QAK */ /* Find correct chunk in file & memory TBBTs */ if(chunk_index==fm->last_index) { /* If the chunk index is the same as the last chunk index we used, * get the cached spaces to operate on. */ - fspace=fm->last_fchunk; mspace=fm->last_mchunk; } /* end if */ else { @@ -2589,48 +3001,22 @@ HDfprintf(stderr,"%s: chunk_index=%Hu\n",FUNC,chunk_index); * find the chunk in the tree. */ /* Get the chunk node from the TBBT */ - if((chunk_node=H5TB_dfind(fm->fsel,&chunk_index,NULL))!=NULL) { + if((chunk_node=H5TB_dfind(fm->msel,&chunk_index,NULL))!=NULL) { /* We found the correct chunk already in the tree */ - /* Get the file space information from the node */ - fspace=((H5D_fchunk_info_t *)(chunk_node->data))->space; - - /* Look up the memory space information for the chunk */ - if((chunk_node=H5TB_dfind(fm->msel,&chunk_index,NULL))==NULL) - HGOTO_ERROR (H5E_DATASPACE, H5E_NOTFOUND, FAIL, "can't find memory chunk info"); - - /* Get the file space information from the node */ + /* Get the memory space information from the node */ mspace=((H5D_mchunk_info_t *)(chunk_node->data))->space; } /* end if */ else { - H5D_fchunk_info_t *new_fchunk_info; /* File chunk information to insert into tree */ H5D_mchunk_info_t *new_mchunk_info; /* Memory chunk information to insert into tree */ /* The correct chunk is not already in the tree, create a new node */ /* in both the file and memory chunk trees */ - /* Allocate the file & memory chunk information */ - if (NULL==(new_fchunk_info = H5FL_MALLOC (H5D_fchunk_info_t))) - HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate file chunk info"); + /* Allocate the memory chunk information */ if (NULL==(new_mchunk_info = H5FL_MALLOC (H5D_mchunk_info_t))) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate memory chunk info"); - /* Initialize the file chunk information */ - - /* Set the chunk index */ - new_fchunk_info->index=chunk_index; - - /* Copy the template file chunk dataspace */ - if((new_fchunk_info->space = H5S_copy(fm->fchunk_tmpl))==NULL) - HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file space"); - - /* Compute the chunk's coordinates */ - H5D_chunk_coords_assist(new_fchunk_info->coords, fm->f_ndims, fm->chunks, chunk_index); - - /* Insert the new file chunk into the TBBT tree */ - if(H5TB_dins(fm->fsel,new_fchunk_info,new_fchunk_info)==NULL) - HGOTO_ERROR(H5E_DATASPACE,H5E_CANTINSERT,FAIL,"can't insert file chunk into TBBT"); - /* Initialize the memory chunk information */ /* Set the chunk index */ @@ -2645,32 +3031,18 @@ HDfprintf(stderr,"%s: chunk_index=%Hu\n",FUNC,chunk_index); HGOTO_ERROR(H5E_DATASPACE,H5E_CANTINSERT,FAIL,"can't insert memory chunk into TBBT"); /* Get the dataspaces for use in this routine */ - fspace=new_fchunk_info->space; mspace=new_mchunk_info->space; } /* end else */ /* Update the "last chunk seen" information */ fm->last_index=chunk_index; - fm->last_fchunk=fspace; fm->last_mchunk=mspace; } /* end else */ - /* Add point to file selection for chunk */ - if(H5S_hyper_add_span_element(fspace, fm->f_ndims, coords_in_chunk)<0) - HGOTO_ERROR (H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element"); - /* Get coordinates of selection iterator for memory */ if(H5S_select_iter_coords(&fm->mem_iter,coords_in_mem)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get iterator coordinates"); -#ifdef QAK -{ - unsigned u; - HDfprintf(stderr,"%s: coords_in_mem={",FUNC); - for(u=0; u<fm->m_ndims; u++) - HDfprintf(stderr,"%Hd%s",coords_in_mem[u],(u<(fm->m_ndims-1)?", ":"}\n")); -} -#endif /* QAK */ /* Add point to memory selection for chunk */ if(H5S_hyper_add_span_element(mspace, fm->m_ndims, coords_in_mem)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element"); @@ -2681,4 +3053,4 @@ HDfprintf(stderr,"%s: chunk_index=%Hu\n",FUNC,chunk_index); done: FUNC_LEAVE_NOAPI(ret_value); -} /* end H5D_chunk_cb() */ +} /* end H5D_chunk_mem_cb() */ |