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author | Quincey Koziol <koziol@hdfgroup.org> | 2005-06-18 05:10:36 (GMT) |
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committer | Quincey Koziol <koziol@hdfgroup.org> | 2005-06-18 05:10:36 (GMT) |
commit | 47bd0eecd65317c8ffbae0b403e0f412d6d17551 (patch) | |
tree | d58593770d4183bb52bc11e131cc7a540d6667e1 /src | |
parent | c5ec1ebfbc6ae66d1ddfafbe02c6b6a9d5a08cac (diff) | |
download | hdf5-47bd0eecd65317c8ffbae0b403e0f412d6d17551.zip hdf5-47bd0eecd65317c8ffbae0b403e0f412d6d17551.tar.gz hdf5-47bd0eecd65317c8ffbae0b403e0f412d6d17551.tar.bz2 |
[svn-r10952] Purpose:
Bug fix
Description:
Hyperslab selections that had a selection offset and were applied to a
chunked dataset could get into an infinite loop or core dump if the same
selection was used multiple times, with different selection offsets.
Solution:
"Normalize" the selection with the selection offset, generate the
selections for the chunks overlapped and then "denormalize" the selection.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
Diffstat (limited to 'src')
-rw-r--r-- | src/H5Dio.c | 24 | ||||
-rw-r--r-- | src/H5Shyper.c | 78 | ||||
-rw-r--r-- | src/H5Sprivate.h | 3 |
3 files changed, 82 insertions, 23 deletions
diff --git a/src/H5Dio.c b/src/H5Dio.c index d8becd0..fd9b6c9 100644 --- a/src/H5Dio.c +++ b/src/H5Dio.c @@ -2325,6 +2325,8 @@ H5D_create_chunk_map(const H5D_t *dataset, const H5T_t *mem_type, const H5S_t *f H5S_t *tmp_mspace=NULL; /* Temporary memory dataspace */ H5S_t *equiv_mspace=NULL; /* Equivalent memory dataspace */ hbool_t equiv_mspace_init=0;/* Equivalent memory dataspace was created */ + hssize_t old_offset[H5O_LAYOUT_NDIMS]; /* Old selection offset */ + hbool_t file_space_normalized = FALSE; /* File dataspace was normalized */ hid_t f_tid=(-1); /* Temporary copy of file datatype for iteration */ hbool_t iter_init=0; /* Selection iteration info has been initialized */ unsigned f_ndims; /* The number of dimensions of the file's dataspace */ @@ -2371,6 +2373,16 @@ H5D_create_chunk_map(const H5D_t *dataset, const H5T_t *mem_type, const H5S_t *f if(H5S_get_simple_extent_dims(file_space, fm->f_dims, NULL)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimensionality") + /* Normalize hyperslab selections by adjusting them by the offset */ + /* (It might be worthwhile to normalize both the file and memory dataspaces + * before any (contiguous, chunked, etc) file I/O operation, in order to + * speed up hyperslab calculations by removing the extra checks and/or + * additions involving the offset and the hyperslab selection -QAK) + */ + if(H5S_hyper_normalize_offset(file_space, old_offset)<0) + HGOTO_ERROR (H5E_DATASET, H5E_BADSELECT, FAIL, "unable to normalize dataspace by offset") + file_space_normalized = TRUE; + /* Decide the number of chunks in each dimension*/ for(u=0; u<f_ndims; u++) { /* Keep the size of the chunk dimensions as hsize_t for various routines */ @@ -2386,7 +2398,7 @@ H5D_create_chunk_map(const H5D_t *dataset, const H5T_t *mem_type, const H5S_t *f /* Initialize skip list for chunk selections */ if((fm->fsel=H5SL_create(H5SL_TYPE_HSIZE,0.5,H5D_DEFAULT_SKIPLIST_HEIGHT))==NULL) - HGOTO_ERROR(H5E_DATASET,H5E_CANTMAKETREE,FAIL,"can't create skip list for chunk selections") + HGOTO_ERROR(H5E_DATASET,H5E_CANTCREATE,FAIL,"can't create skip list for chunk selections") /* Initialize "last chunk" information */ fm->last_index=(hsize_t)-1; @@ -2531,6 +2543,10 @@ done: if(H5I_dec_ref(f_tid)<0) HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID") } /* end if */ + if(file_space_normalized) { + if(H5S_hyper_denormalize_offset(file_space, old_offset)<0) + HGOTO_ERROR (H5E_DATASET, H5E_BADSELECT, FAIL, "unable to normalize dataspace by offset") + } /* end if */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_create_chunk_map() */ @@ -2689,12 +2705,6 @@ H5D_create_chunk_file_map_hyper(const fm_map *fm) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to convert selection to span trees") } /* end if */ - /* Normalize hyperslab selections by adjusting them by the offset */ - if(H5S_hyper_normalize_offset(tmp_fchunk)<0) { - (void)H5S_close(tmp_fchunk); - HGOTO_ERROR (H5E_DATASET, H5E_BADSELECT, FAIL, "unable to normalize dataspace by offset") - } /* end if */ - /* "AND" temporary chunk and current chunk */ if(H5S_select_hyperslab(tmp_fchunk,H5S_SELECT_AND,coords,NULL,fm->chunk_dim,NULL)<0) { (void)H5S_close(tmp_fchunk); diff --git a/src/H5Shyper.c b/src/H5Shyper.c index 9360432..f3b5d22 100644 --- a/src/H5Shyper.c +++ b/src/H5Shyper.c @@ -3667,7 +3667,7 @@ done: REVISION LOG --------------------------------------------------------------------------*/ static htri_t -H5S_hyper_intersect_block_helper (const H5S_hyper_span_info_t *spans, hssize_t *offset, hsize_t *start, hsize_t *end) +H5S_hyper_intersect_block_helper (const H5S_hyper_span_info_t *spans, hsize_t *start, hsize_t *end) { H5S_hyper_span_t *curr; /* Pointer to current span in 1st span tree */ htri_t status; /* Status from recursive call */ @@ -3677,7 +3677,6 @@ H5S_hyper_intersect_block_helper (const H5S_hyper_span_info_t *spans, hssize_t * /* Sanity check */ assert(spans); - assert(offset); assert(start); assert(end); @@ -3687,11 +3686,11 @@ H5S_hyper_intersect_block_helper (const H5S_hyper_span_info_t *spans, hssize_t * /* Iterate over the spans in the tree */ while(curr!=NULL) { /* Check for span entirely before block */ - if(((hssize_t)curr->high+*offset)<(hssize_t)*start) + if(curr->high < *start) /* Advance to next span in this dimension */ curr=curr->next; /* If this span is past the end of the block, then we're done in this dimension */ - else if(((hssize_t)curr->low+*offset)>(hssize_t)*end) + else if(curr->low > *end) HGOTO_DONE(FALSE) /* block & span overlap */ else { @@ -3699,7 +3698,7 @@ H5S_hyper_intersect_block_helper (const H5S_hyper_span_info_t *spans, hssize_t * HGOTO_DONE(TRUE) else { /* Recursively check spans in next dimension down */ - if((status=H5S_hyper_intersect_block_helper(curr->down,offset+1,start+1,end+1))<0) + if((status=H5S_hyper_intersect_block_helper(curr->down,start+1,end+1))<0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADSELECT, FAIL, "can't perform hyperslab intersection check"); /* If there is a span intersection in the down dimensions, the span trees overlap */ @@ -3759,7 +3758,7 @@ H5S_hyper_intersect_block (H5S_t *space, hsize_t *start, hsize_t *end) HGOTO_ERROR(H5E_DATASPACE, H5E_UNINITIALIZED, FAIL, "dataspace does not have span tree"); /* Perform the span-by-span intersection check */ - if((ret_value=H5S_hyper_intersect_block_helper(space->select.sel_info.hslab->span_lst,space->select.offset,start,end))<0) + if((ret_value=H5S_hyper_intersect_block_helper(space->select.sel_info.hslab->span_lst,start,end))<0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADSELECT, FAIL, "can't perform hyperslab intersection check"); done: @@ -4102,20 +4101,22 @@ done: "Normalize" a hyperslab selection by adjusting it's coordinates by the amount of the selection offset. USAGE - herr_t H5S_hyper_normalize_offset(space) + herr_t H5S_hyper_normalize_offset(space, old_offset) H5S_t *space; IN/OUT: Pointer to dataspace to move + hssize_t *old_offset; OUT: Pointer to space to store old offset RETURNS Non-negative on success, negative on failure DESCRIPTION - Moves the hyperslab selection by the selection offset and then resets - the selection offset to zeros. + Copies the current selection offset into the array provided, then + inverts the selection offset, subtracts the offset from the hyperslab + selection and resets the offset to zero. GLOBAL VARIABLES COMMENTS, BUGS, ASSUMPTIONS EXAMPLES REVISION LOG --------------------------------------------------------------------------*/ herr_t -H5S_hyper_normalize_offset(H5S_t *space) +H5S_hyper_normalize_offset(H5S_t *space, hssize_t *old_offset) { unsigned u; /* Local index variable */ herr_t ret_value=SUCCEED; /* Return value */ @@ -4127,17 +4128,18 @@ H5S_hyper_normalize_offset(H5S_t *space) /* Check for 'all' selection, instead of a hyperslab selection */ /* (Technically, this check shouldn't be in the "hyperslab" routines...) */ if(H5S_GET_SELECT_TYPE(space)!=H5S_SEL_ALL) { - /* Invert the selection offset */ - for(u=0; u<space->extent.rank; u++) - space->select.offset[u] =- space->select.offset[u]; + /* Copy & invert the selection offset */ + for(u=0; u<space->extent.rank; u++) { + old_offset[u] = space->select.offset[u]; + space->select.offset[u] = -space->select.offset[u]; + } /* end for */ /* Call the existing 'adjust' routine */ if(H5S_hyper_adjust_s(space, space->select.offset)<0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADSELECT, FAIL, "can't perform hyperslab normalization"); /* Zero out the selection offset */ - for(u=0; u<space->extent.rank; u++) - space->select.offset[u] = 0; + HDmemset(space->select.offset, 0, sizeof(hssize_t) * space->extent.rank); } /* end if */ done: @@ -4147,6 +4149,52 @@ done: /*-------------------------------------------------------------------------- NAME + H5S_hyper_denormalize_offset + PURPOSE + "Denormalize" a hyperslab selection by reverse adjusting it's coordinates + by the amount of the former selection offset. + USAGE + herr_t H5S_hyper_normalize_offset(space, old_offset) + H5S_t *space; IN/OUT: Pointer to dataspace to move + hssize_t *old_offset; IN: Pointer to old offset array + RETURNS + Non-negative on success, negative on failure + DESCRIPTION + Subtracts the old offset from the current selection (canceling out the + effect of the "normalize" routine), then restores the old offset into + the dataspace. + GLOBAL VARIABLES + COMMENTS, BUGS, ASSUMPTIONS + EXAMPLES + REVISION LOG +--------------------------------------------------------------------------*/ +herr_t +H5S_hyper_denormalize_offset(H5S_t *space, const hssize_t *old_offset) +{ + herr_t ret_value=SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT(H5S_hyper_denormalize_offset); + + assert(space); + + /* Check for 'all' selection, instead of a hyperslab selection */ + /* (Technically, this check shouldn't be in the "hyperslab" routines...) */ + if(H5S_GET_SELECT_TYPE(space)!=H5S_SEL_ALL) { + /* Call the existing 'adjust' routine */ + if(H5S_hyper_adjust_s(space, old_offset)<0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADSELECT, FAIL, "can't perform hyperslab normalization"); + + /* Copy the selection offset over */ + HDmemcpy(space->select.offset, old_offset, sizeof(hssize_t) * space->extent.rank); + } /* end if */ + +done: + FUNC_LEAVE_NOAPI(ret_value); +} /* H5S_hyper_denormalize_offset() */ + + +/*-------------------------------------------------------------------------- + NAME H5S_hyper_append_span PURPOSE Create a new span and append to span list diff --git a/src/H5Sprivate.h b/src/H5Sprivate.h index 06c9f02..ac6a297 100644 --- a/src/H5Sprivate.h +++ b/src/H5Sprivate.h @@ -258,7 +258,8 @@ H5_DLL htri_t H5S_hyper_intersect_block (H5S_t *space, hsize_t *start, hsize_t * H5_DLL herr_t H5S_hyper_adjust_u(H5S_t *space, const hsize_t *offset); H5_DLL herr_t H5S_hyper_adjust_s(H5S_t *space, const hssize_t *offset); H5_DLL herr_t H5S_hyper_move(H5S_t *space, const hssize_t *offset); -H5_DLL herr_t H5S_hyper_normalize_offset(H5S_t *space); +H5_DLL herr_t H5S_hyper_normalize_offset(H5S_t *space, hssize_t *old_offset); +H5_DLL herr_t H5S_hyper_denormalize_offset(H5S_t *space, const hssize_t *old_offset); /* Operations on selection iterators */ H5_DLL herr_t H5S_select_iter_init(H5S_sel_iter_t *iter, const H5S_t *space, size_t elmt_size); |