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[svn-r7259] Purpose:
Bug fix
Description:
I/O on chunked datasets with point selections was not working correctly.
Solution:
Re-wrote some parts of raw data I/O routines that build the selections for
each chunk to correctly handle point selections.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
This commit is contained in:
Quincey Koziol
parent
77f6e46b81
commit
b0e350c2d6
@ -57,6 +57,8 @@ Bug Fixes since HDF5-1.6.0 release
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Library
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-------
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- Corrected errors with using point selections to access data in
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chunked datasets. QAK - 2003/07/23
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- Corrected error with variable-length datatypes and chunked datasets
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which caused H5Dwrite to fail sometimes. QAK - 2003/07/19
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- Modified library and file format to support storing indexed storage
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626
src/H5Dio.c
626
src/H5Dio.c
File diff suppressed because it is too large
Load Diff
@ -38,8 +38,6 @@
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static int interface_initialize_g = 0;
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/* Static function prototypes */
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static herr_t H5S_select_elements (H5S_t *space, H5S_seloper_t op,
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size_t num_elem, const hssize_t **coord);
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static herr_t H5S_point_iter_coords(const H5S_sel_iter_t *iter, hssize_t *coords);
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static herr_t H5S_point_iter_block(const H5S_sel_iter_t *iter, hssize_t *start, hssize_t *end);
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static hsize_t H5S_point_iter_nelmts(const H5S_sel_iter_t *iter);
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@ -522,7 +520,7 @@ done:
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EXAMPLES
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REVISION LOG
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--------------------------------------------------------------------------*/
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static herr_t
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herr_t
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H5S_select_elements (H5S_t *space, H5S_seloper_t op, size_t num_elem,
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const hssize_t **coord)
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{
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@ -219,8 +219,18 @@ H5_DLL herr_t H5S_select_offset(H5S_t *space, const hssize_t *offset);
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H5_DLL herr_t H5S_select_copy(H5S_t *dst, const H5S_t *src);
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H5_DLL htri_t H5S_select_shape_same(const H5S_t *space1, const H5S_t *space2);
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H5_DLL herr_t H5S_select_release(H5S_t *ds);
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/* Operations on all selections */
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H5_DLL herr_t H5S_select_all(H5S_t *space, unsigned rel_prev);
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/* Operations on none selections */
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H5_DLL herr_t H5S_select_none(H5S_t *space);
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/* Operations on point selections */
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H5_DLL herr_t H5S_select_elements (H5S_t *space, H5S_seloper_t op,
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size_t num_elem, const hssize_t **coord);
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/* Operations on hyperslab selections */
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H5_DLL herr_t H5S_select_hyperslab (H5S_t *space, H5S_seloper_t op, const hssize_t start[],
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const hsize_t *stride, const hsize_t count[], const hsize_t *block);
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H5_DLL herr_t H5S_get_select_hyper_blocklist(H5S_t *space, hsize_t startblock,
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201
test/tselect.c
201
test/tselect.c
@ -87,6 +87,9 @@
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#define SPACE7_DIM1 10
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#define SPACE7_DIM2 10
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#define SPACE7_FILL 254
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#define SPACE7_CHUNK_DIM1 5
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#define SPACE7_CHUNK_DIM2 5
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#define SPACE7_NPOINTS 8
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/* 4-D dataset with fixed dimensions */
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#define SPACE8_NAME "Space8"
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@ -3986,6 +3989,201 @@ test_select_hyper_chunk(hid_t fapl_plist, hid_t xfer_plist)
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free (data_out);
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} /* test_select_hyper_chunk() */
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/****************************************************************
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**
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** test_select_point_chunk(): Test basic H5S (dataspace) selection code.
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** Tests combinations of hyperslab and point selections on
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** chunked datasets.
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**
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****************************************************************/
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static void
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test_select_point_chunk(void)
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{
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hsize_t dimsf[SPACE7_RANK]; /* dataset dimensions */
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hsize_t chunk_dimsf[SPACE7_RANK] = {SPACE7_CHUNK_DIM1,SPACE7_CHUNK_DIM2}; /* chunk sizes */
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unsigned *data; /* data to write */
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unsigned *tmpdata; /* data to write */
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/*
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* Data and output buffer initialization.
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*/
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hid_t file, dataset; /* handles */
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hid_t dataspace;
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hid_t pnt1_space; /* Dataspace to hold 1st point selection */
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hid_t pnt2_space; /* Dataspace to hold 2nd point selection */
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hid_t hyp1_space; /* Dataspace to hold 1st hyperslab selection */
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hid_t hyp2_space; /* Dataspace to hold 2nd hyperslab selection */
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hid_t dcpl;
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herr_t ret; /* Generic return value */
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unsigned *data_out; /* output buffer */
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#ifdef LATER
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unsigned *tmpdata_out; /* output buffer */
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#endif /* LATER */
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hssize_t start[SPACE7_RANK]; /* hyperslab offset */
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hsize_t count[SPACE7_RANK]; /* size of the hyperslab */
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hssize_t points[SPACE7_NPOINTS][SPACE7_RANK]; /* points for selection */
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unsigned i, j; /* Local index variables */
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/* Output message about test being performed */
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MESSAGE(5, ("Testing Point Selections on Chunked Datasets\n"));
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/* Allocate the transfer buffers */
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data = (unsigned*)HDmalloc(sizeof(unsigned)*SPACE7_DIM1*SPACE7_DIM2);
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data_out = (unsigned*)HDcalloc(SPACE7_DIM1*SPACE7_DIM2,sizeof(unsigned));
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/*
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* Data buffer initialization.
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*/
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tmpdata = data;
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for (i = 0; i < SPACE7_DIM1; i++)
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for (j = 0; j < SPACE7_DIM1; j++)
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*tmpdata++ = ((i*SPACE7_DIM2)+j)%256;
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/*
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* Create a new file using H5F_ACC_TRUNC access,
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* the default file creation properties and file
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* access properties.
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*/
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file = H5Fcreate (FILENAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
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CHECK(file, FAIL, "H5Fcreate");
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/* Create file dataspace */
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dimsf[0] = SPACE7_DIM1;
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dimsf[1] = SPACE7_DIM2;
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dataspace = H5Screate_simple (SPACE7_RANK, dimsf, NULL);
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CHECK(dataspace, FAIL, "H5Screate_simple");
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/*
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* Create a new dataset within the file using defined dataspace and
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* chunking properties.
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*/
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dcpl = H5Pcreate (H5P_DATASET_CREATE);
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CHECK(dcpl, FAIL, "H5Pcreate");
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ret = H5Pset_chunk (dcpl, SPACE7_RANK, chunk_dimsf);
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CHECK(ret, FAIL, "H5Pset_chunk");
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dataset = H5Dcreate (file, DATASETNAME, H5T_NATIVE_UCHAR, dataspace, dcpl);
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CHECK(dataset, FAIL, "H5Dcreate");
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/* Create 1st point selection */
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pnt1_space = H5Scopy (dataspace);
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CHECK(pnt1_space, FAIL, "H5Scopy");
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points[0][0]=3;
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points[0][1]=3;
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points[1][0]=3;
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points[1][1]=8;
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points[2][0]=8;
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points[2][1]=3;
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points[3][0]=8;
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points[3][1]=8;
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points[4][0]=1; /* In same chunk as point #0, but "earlier" in chunk */
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points[4][1]=1;
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points[5][0]=1; /* In same chunk as point #1, but "earlier" in chunk */
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points[5][1]=6;
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points[6][0]=6; /* In same chunk as point #2, but "earlier" in chunk */
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points[6][1]=1;
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points[7][0]=6; /* In same chunk as point #3, but "earlier" in chunk */
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points[7][1]=6;
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ret = H5Sselect_elements(pnt1_space,H5S_SELECT_SET,SPACE7_NPOINTS,(const hssize_t **)points);
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CHECK(ret, FAIL, "H5Sselect_elements");
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/* Create 1st hyperslab selection */
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hyp1_space = H5Scopy (dataspace);
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CHECK(hyp1_space, FAIL, "H5Scopy");
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start[0]=2; start[1]=2;
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count[0]=4; count[1]=2;
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ret = H5Sselect_hyperslab(hyp1_space,H5S_SELECT_SET,start,NULL,count,NULL);
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CHECK(ret, FAIL, "H5Sselect_hyperslab");
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/* Write out data using 1st point selection for file & hyperslab for memory */
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ret=H5Dwrite(dataset,H5T_NATIVE_UINT,hyp1_space,pnt1_space,H5P_DEFAULT,data);
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CHECK(ret, FAIL, "H5Dwrite");
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/* Create 2nd point selection */
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pnt2_space = H5Scopy (dataspace);
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CHECK(pnt2_space, FAIL, "H5Scopy");
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points[0][0]=4;
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points[0][1]=4;
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points[1][0]=4;
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points[1][1]=9;
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points[2][0]=9;
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points[2][1]=4;
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points[3][0]=9;
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points[3][1]=9;
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points[4][0]=2; /* In same chunk as point #0, but "earlier" in chunk */
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points[4][1]=2;
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points[5][0]=2; /* In same chunk as point #1, but "earlier" in chunk */
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points[5][1]=7;
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points[6][0]=7; /* In same chunk as point #2, but "earlier" in chunk */
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points[6][1]=2;
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points[7][0]=7; /* In same chunk as point #3, but "earlier" in chunk */
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points[7][1]=7;
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ret = H5Sselect_elements(pnt2_space,H5S_SELECT_SET,SPACE7_NPOINTS,(const hssize_t **)points);
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CHECK(ret, FAIL, "H5Sselect_elements");
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/* Create 2nd hyperslab selection */
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hyp2_space = H5Scopy (dataspace);
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CHECK(hyp2_space, FAIL, "H5Scopy");
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start[0]=2; start[1]=4;
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count[0]=4; count[1]=2;
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ret = H5Sselect_hyperslab(hyp2_space,H5S_SELECT_SET,start,NULL,count,NULL);
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CHECK(ret, FAIL, "H5Sselect_hyperslab");
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/* Write out data using 2nd hyperslab selection for file & point for memory */
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ret=H5Dwrite(dataset,H5T_NATIVE_UINT,pnt2_space,hyp2_space,H5P_DEFAULT,data);
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CHECK(ret, FAIL, "H5Dwrite");
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/* Close everything (except selections) */
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ret=H5Pclose (dcpl);
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CHECK(ret, FAIL, "H5Pclose");
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ret=H5Sclose (dataspace);
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CHECK(ret, FAIL, "H5Sclose");
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ret=H5Dclose (dataset);
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CHECK(ret, FAIL, "H5Dclose");
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ret=H5Fclose (file);
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CHECK(ret, FAIL, "H5Fclose");
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/* Re-open file & dataset */
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file = H5Fopen (FILENAME, H5F_ACC_RDONLY, H5P_DEFAULT);
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CHECK(file, FAIL, "H5Fopen");
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dataset = H5Dopen (file, DATASETNAME);
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CHECK(dataset, FAIL, "H5Dopen");
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/* Read data using 1st point selection for file and hyperslab for memory */
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ret=H5Dread(dataset,H5T_NATIVE_UINT,hyp1_space,pnt1_space,H5P_DEFAULT,data_out);
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CHECK(ret, FAIL, "H5Dread");
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/* Verify data (later) */
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/* Read data using 2nd hyperslab selection for file and point for memory */
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ret=H5Dread(dataset,H5T_NATIVE_UINT,pnt2_space,hyp2_space,H5P_DEFAULT,data_out);
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CHECK(ret, FAIL, "H5Dread");
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/* Verify data (later) */
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/* Close everything (inclusing selections) */
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ret=H5Sclose (pnt1_space);
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CHECK(ret, FAIL, "H5Sclose");
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ret=H5Sclose (pnt2_space);
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CHECK(ret, FAIL, "H5Sclose");
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ret=H5Sclose (hyp1_space);
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CHECK(ret, FAIL, "H5Sclose");
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ret=H5Sclose (hyp2_space);
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CHECK(ret, FAIL, "H5Sclose");
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ret=H5Dclose (dataset);
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CHECK(ret, FAIL, "H5Dclose");
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ret=H5Fclose (file);
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CHECK(ret, FAIL, "H5Fclose");
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free (data);
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free (data_out);
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} /* test_select_point_chunk() */
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/****************************************************************
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**
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** test_select_valid(): Test basic H5S (dataspace) selection code.
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@ -6267,6 +6465,9 @@ test_select(void)
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/* Test "same shape" routine */
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test_shape_same();
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/* Test point selections in chunked datasets */
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test_select_point_chunk();
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} /* test_select() */
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