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authorVailin Choi <vchoi@hdfgroup.org>2019-09-27 17:39:31 (GMT)
committerVailin Choi <vchoi@hdfgroup.org>2019-09-27 17:39:31 (GMT)
commita19de0ec83487963316085e0ea6bcea38aa2f0ae (patch)
tree3a2c351b8f9b5f2d53dc4ac363cdb497fb2e776e
parent270a363cdc3f88cbc6199fc03805e6ac7ec013d1 (diff)
parent7924eee0e5ee0745b784c635042b8633886fb799 (diff)
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Merge pull request #1934 in HDFFV/hdf5 from ~VCHOI/my_third_fork:bugfix/HDFFV-10585-investigate-slowness-of-regular to develop
* commit '7924eee0e5ee0745b784c635042b8633886fb799': (1) Address the feedback from the PR review (2) Add release notes Fix for HDFFV-10585 investigate hyperslab slowness: 1) Improve hyperslab performance when doing I/O from 1-d disjoint file dataspace to 1-d contiguous memory dataspace. 2) Move coding in H5D__chunk_io_init() that is constructing the chunk mappings to a separate routine.
-rw-r--r--release_docs/RELEASE.txt13
-rw-r--r--src/H5Dchunk.c204
-rw-r--r--test/tselect.c162
3 files changed, 343 insertions, 36 deletions
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index f9547f3..b861914 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -362,6 +362,19 @@ Bug Fixes since HDF5-1.10.3 release
Library
-------
+ - Fixed the slowness of regular hyperslab selection in a chunked dataset
+
+ It was reported that the selection of every 10th element from a 20G
+ chunked dataset was extremely slow and sometimes could hang the system.
+ The problem was due to the iteration and the building of the span tree
+ for all the selected elements in file space.
+
+ As the selected elements are going to a 1-d contiguous single block
+ memory space, the problem was fixed by building regular hyperslab selections
+ in memory space for the selected elements in file space.
+
+ (VC - 2019/09/26, HDFFV-10585)
+
- Fixed a bug caused by bad tag value when condensing object header
messages
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index e3bbd59..ed82b3b 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -254,6 +254,8 @@ static herr_t H5D__chunk_init(H5F_t *f, const H5D_t *dset, hid_t dapl_id);
static herr_t H5D__chunk_io_init(const H5D_io_info_t *io_info,
const H5D_type_info_t *type_info, hsize_t nelmts, const H5S_t *file_space,
const H5S_t *mem_space, H5D_chunk_map_t *fm);
+static herr_t H5D__chunk_io_init_selections(const H5D_io_info_t *io_info,
+ const H5D_type_info_t *type_info, H5D_chunk_map_t *fm);
static herr_t H5D__chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space,
H5D_chunk_map_t *fm);
@@ -297,6 +299,9 @@ static herr_t H5D__create_chunk_file_map_all(H5D_chunk_map_t *fm,
const H5D_io_info_t *io_info);
static herr_t H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm,
const H5D_io_info_t *io_info);
+
+static herr_t H5D__create_chunk_mem_map_1d(const H5D_chunk_map_t *fm);
+
static herr_t H5D__create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm);
static herr_t H5D__chunk_file_cb(void *elem, const H5T_t *type, unsigned ndims,
const hsize_t *coords, void *fm);
@@ -1095,7 +1100,6 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf
H5D_chunk_map_t *fm)
{
const H5D_t *dataset = io_info->dset; /* Local pointer to dataset info */
- const H5T_t *mem_type = type_info->mem_type; /* Local pointer to memory datatype */
H5S_t *tmp_mspace = NULL; /* Temporary memory dataspace */
hssize_t old_offset[H5O_LAYOUT_NDIMS]; /* Old selection offset */
htri_t file_space_normalized = FALSE; /* File dataspace was normalized */
@@ -1156,13 +1160,54 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf
fm->file_space = file_space;
fm->mem_space = mem_space;
+ if(H5D__chunk_io_init_selections(io_info, type_info, fm) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file and memory chunk selections")
+
+done:
+ /* Reset the global dataspace info */
+ fm->file_space = NULL;
+ fm->mem_space = NULL;
+
+ if(file_space_normalized == TRUE)
+ if(H5S_hyper_denormalize_offset((H5S_t *)file_space, old_offset) < 0) /* (Casting away const OK -QAK) */
+ HDONE_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't denormalize selection")
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__chunk_io_init() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__chunk_io_init_selections
+ *
+ * Purpose: Initialize the chunk mappings
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * Thursday, March 20, 2008
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__chunk_io_init_selections(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info, H5D_chunk_map_t *fm)
+{
+ const H5D_t *dataset = io_info->dset; /* Local pointer to dataset info */
+ const H5T_t *mem_type = type_info->mem_type; /* Local pointer to memory datatype */
+ H5S_t *tmp_mspace = NULL; /* Temporary memory dataspace */
+ H5T_t *file_type = NULL; /* Temporary copy of file datatype for iteration */
+ hbool_t iter_init = FALSE; /* Selection iteration info has been initialized */
+ char bogus; /* "bogus" buffer to pass to selection iterator */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC
+
/* Special case for only one element in selection */
/* (usually appending a record) */
- if(nelmts == 1
+ if(fm->nelmts == 1
#ifdef H5_HAVE_PARALLEL
&& !(io_info->using_mpi_vfd)
#endif /* H5_HAVE_PARALLEL */
- && H5S_SEL_ALL != H5S_GET_SELECT_TYPE(file_space)) {
+ && H5S_SEL_ALL != H5S_GET_SELECT_TYPE(fm->file_space)) {
/* Initialize skip list for chunk selections */
fm->sel_chunks = NULL;
fm->use_single = TRUE;
@@ -1170,7 +1215,7 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf
/* Initialize single chunk dataspace */
if(NULL == dataset->shared->cache.chunk.single_space) {
/* Make a copy of the dataspace for the dataset */
- if((dataset->shared->cache.chunk.single_space = H5S_copy(file_space, TRUE, FALSE)) == NULL)
+ if((dataset->shared->cache.chunk.single_space = H5S_copy(fm->file_space, TRUE, FALSE)) == NULL)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file space")
/* Resize chunk's dataspace dimensions to size of chunk */
@@ -1212,9 +1257,9 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf
fm->use_single = FALSE;
/* Get type of selection on disk & in memory */
- if((fm->fsel_type = H5S_GET_SELECT_TYPE(file_space)) < H5S_SEL_NONE)
+ if((fm->fsel_type = H5S_GET_SELECT_TYPE(fm->file_space)) < H5S_SEL_NONE)
HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to get type of selection")
- if((fm->msel_type = H5S_GET_SELECT_TYPE(mem_space)) < H5S_SEL_NONE)
+ if((fm->msel_type = H5S_GET_SELECT_TYPE(fm->mem_space)) < H5S_SEL_NONE)
HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to get type of selection")
/* If the selection is NONE or POINTS, set the flag to FALSE */
@@ -1223,22 +1268,22 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf
else
sel_hyper_flag = TRUE;
- /* Check if file selection is a not a hyperslab selection */
- if(sel_hyper_flag) {
- /* Build the file selection for each chunk */
- if(H5S_SEL_ALL == fm->fsel_type) {
- if(H5D__create_chunk_file_map_all(fm, io_info) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections")
+ /* Check if file selection is a not a hyperslab selection */
+ if(sel_hyper_flag) {
+ /* Build the file selection for each chunk */
+ if(H5S_SEL_ALL == fm->fsel_type) {
+ if(H5D__create_chunk_file_map_all(fm, io_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections")
+ } /* end if */
+ else {
+ /* Sanity check */
+ HDassert(fm->fsel_type == H5S_SEL_HYPERSLABS);
+
+ if(H5D__create_chunk_file_map_hyper(fm, io_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections")
+ } /* end else */
} /* end if */
else {
- /* Sanity check */
- HDassert(fm->fsel_type == H5S_SEL_HYPERSLABS);
-
- if(H5D__create_chunk_file_map_hyper(fm, io_info) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections")
- } /* end else */
- } /* end if */
- else {
H5S_sel_iter_op_t iter_op; /* Operator for iteration */
H5D_chunk_file_iter_ud_t udata; /* User data for iteration */
@@ -1256,7 +1301,7 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf
iter_op.u.lib_op = H5D__chunk_file_cb;
/* Spaces might not be the same shape, iterate over the file selection directly */
- if(H5S_select_iterate(&bogus, file_type, file_space, &iter_op, &udata) < 0)
+ if(H5S_select_iterate(&bogus, file_type, fm->file_space, &iter_op, &udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections")
/* Reset "last chunk" info */
@@ -1265,7 +1310,7 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf
} /* end else */
/* Build the memory selection for each chunk */
- if(sel_hyper_flag && H5S_SELECT_SHAPE_SAME(file_space, mem_space) == TRUE) {
+ if(sel_hyper_flag && H5S_SELECT_SHAPE_SAME(fm->file_space, fm->mem_space) == TRUE) {
/* Reset chunk template information */
fm->mchunk_tmpl = NULL;
@@ -1275,12 +1320,19 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf
if(H5D__create_chunk_mem_map_hyper(fm) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create memory chunk selections")
} /* end if */
- else {
+ else if(sel_hyper_flag &&
+ fm->f_ndims == 1 && fm->m_ndims == 1 &&
+ H5S_SELECT_IS_REGULAR(fm->mem_space) && H5S_SELECT_IS_SINGLE(fm->mem_space)) {
+
+ if(H5D__create_chunk_mem_map_1d(fm) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections")
+
+ } else {
H5S_sel_iter_op_t iter_op; /* Operator for iteration */
size_t elmt_size; /* Memory datatype size */
/* Make a copy of equivalent memory space */
- if((tmp_mspace = H5S_copy(mem_space, TRUE, FALSE)) == NULL)
+ if((tmp_mspace = H5S_copy(fm->mem_space, TRUE, FALSE)) == NULL)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space")
/* De-select the mem space copy */
@@ -1291,14 +1343,14 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf
fm->mchunk_tmpl = tmp_mspace;
/* Create temporary datatypes for selection iteration */
- if(!file_type)
- if(NULL == (file_type = H5T_copy(dataset->shared->type, H5T_COPY_ALL)))
+ if(!file_type)
+ if(NULL == (file_type = H5T_copy(dataset->shared->type, H5T_COPY_ALL)))
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTCOPY, FAIL, "unable to copy file datatype")
/* Create selection iterator for memory selection */
if(0 == (elmt_size = H5T_get_size(mem_type)))
HGOTO_ERROR(H5E_DATATYPE, H5E_BADSIZE, FAIL, "datatype size invalid")
- if(H5S_select_iter_init(&(fm->mem_iter), mem_space, elmt_size, 0) < 0)
+ if(H5S_select_iter_init(&(fm->mem_iter), fm->mem_space, elmt_size, 0) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator")
iter_init = TRUE; /* Selection iteration info has been initialized */
@@ -1306,7 +1358,7 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf
iter_op.u.lib_op = H5D__chunk_mem_cb;
/* Spaces aren't the same shape, iterate over the memory selection directly */
- if(H5S_select_iterate(&bogus, file_type, file_space, &iter_op, fm) < 0)
+ if(H5S_select_iterate(&bogus, file_type, fm->file_space, &iter_op, fm) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create memory chunk selections")
} /* end else */
} /* end else */
@@ -1323,20 +1375,13 @@ done:
HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release chunk mapping")
} /* end if */
- /* Reset the global dataspace info */
- fm->file_space = NULL;
- fm->mem_space = NULL;
-
if(iter_init && H5S_SELECT_ITER_RELEASE(&(fm->mem_iter)) < 0)
HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator")
if(file_type && (H5T_close_real(file_type) < 0))
HDONE_ERROR(H5E_DATATYPE, H5E_CANTFREE, FAIL, "Can't free temporary datatype")
- if(file_space_normalized == TRUE)
- if(H5S_hyper_denormalize_offset((H5S_t *)file_space, old_offset) < 0) /* (Casting away const OK -QAK) */
- HDONE_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't denormalize selection")
FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D__chunk_io_init() */
+} /* end H5D__chunk_io_init_selections() */
/*-------------------------------------------------------------------------
@@ -2075,6 +2120,93 @@ done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__create_chunk_mem_map_hyper() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__create_mem_map_1d
+ *
+ * Purpose: Create all chunk selections for 1-dimensional regular memory space
+ * that has only one single block in the selection
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Vailin Choi
+ * Sept 18, 2019
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__create_chunk_mem_map_1d(const H5D_chunk_map_t *fm)
+{
+ H5D_chunk_info_t *chunk_info; /* Pointer to chunk information */
+ H5SL_node_t *curr_node; /* Current node in skip list */
+ hsize_t file_sel_start[H5S_MAX_RANK]; /* Offset of low bound of file selection */
+ hsize_t file_sel_end[H5S_MAX_RANK]; /* Offset of high bound of file selection */
+ hsize_t mem_sel_start[H5S_MAX_RANK]; /* Offset of low bound of file selection */
+ hsize_t mem_sel_end[H5S_MAX_RANK]; /* Offset of high bound of file selection */
+ hssize_t adjust[H5S_MAX_RANK]; /* Adjustment to make to all file chunks */
+ unsigned u; /* Local index variable */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC
+
+ /* Sanity check */
+ HDassert(fm->f_ndims>0);
+
+ /* Check for all I/O going to a single chunk */
+ if(H5SL_count(fm->sel_chunks)==1) {
+ /* Get the node */
+ curr_node = H5SL_first(fm->sel_chunks);
+
+ /* Get pointer to chunk's information */
+ chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node);
+ HDassert(chunk_info);
+
+ /* Just point at the memory dataspace & selection */
+ /* (Casting away const OK -QAK) */
+ chunk_info->mspace = (H5S_t *)fm->mem_space;
+
+ /* Indicate that the chunk's memory space is shared */
+ chunk_info->mspace_shared = TRUE;
+ } /* end if */
+ else {
+ HDassert(fm->m_ndims == 1);
+ hsize_t mem_sel_start[H5S_MAX_RANK]; /* Offset of low bound of file selection */
+ hsize_t mem_sel_end[H5S_MAX_RANK]; /* Offset of high bound of file selection */
+
+ if(H5S_SELECT_BOUNDS(fm->mem_space, mem_sel_start, mem_sel_end) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound info")
+
+ /* Iterate over each chunk in the chunk list */
+ curr_node = H5SL_first(fm->sel_chunks);
+ while(curr_node) {
+ hssize_t schunk_points; /* Number of elements in chunk selection */
+ hsize_t tmp_count = 1;
+
+ /* Get pointer to chunk's information */
+ chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node);
+ HDassert(chunk_info);
+
+ /* Copy the memory dataspace */
+ if((chunk_info->mspace = H5S_copy(fm->mem_space, TRUE, FALSE)) == NULL)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space")
+
+ schunk_points = H5S_GET_SELECT_NPOINTS(chunk_info->fspace);
+
+ if(H5S_select_hyperslab(chunk_info->mspace, H5S_SELECT_SET, mem_sel_start, NULL, &tmp_count, &schunk_points) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, FAIL, "can't create chunk memory selection")
+
+ mem_sel_start[0] += schunk_points;
+
+ /* Get the next chunk node in the skip list */
+ curr_node = H5SL_next(curr_node);
+ } /* end while */
+ } /* end else */
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__create_chunk_mem_map_1d() */
+
/*-------------------------------------------------------------------------
* Function: H5D__chunk_file_cb
diff --git a/test/tselect.c b/test/tselect.c
index 9cfa922..91da4c4 100644
--- a/test/tselect.c
+++ b/test/tselect.c
@@ -177,6 +177,13 @@
#define SEL_ITER_MAX_SEQ 256
+/* Defines for test_hyper_io_1d() */
+#define DNAME "DSET_1D"
+#define RANK 1
+#define NUMCHUNKS 3
+#define CHUNKSZ 20
+#define NUM_ELEMENTS NUMCHUNKS * CHUNKSZ
+
/* Location comparison function */
static int compare_size_t(const void *s1, const void *s2);
@@ -15316,7 +15323,158 @@ test_select_intersect_block(void)
CHECK(ret, FAIL, "H5Sclose");
} /* test_select_intersect_block() */
+
+/****************************************************************
+**
+** test_hyper_io_1d():
+** Test to verify all the selected 10th element in the 1-d file
+** dataspace is read correctly into the 1-d contiguous memory space.
+** This is modeled after the test scenario described in HDFFV-10585
+** that demonstrated the hyperslab slowness. A fix to speed up
+** performance is in place to handle the special case for 1-d disjoint
+** file dataspace into 1-d single block contiguous memory space.
+**
+****************************************************************/
+static void
+test_hyper_io_1d(void)
+{
+ hid_t fid; /* File ID */
+ hid_t did; /* Dataset ID */
+ hid_t sid, mid; /* Dataspace IDs */
+ hid_t dcpl; /* Dataset creation property list ID */
+ hsize_t dims[1], maxdims[1], dimsm[1]; /* Dataset dimension sizes */
+ hsize_t chunk_dims[1]; /* Chunk dimension size */
+ hsize_t offset[1]; /* Starting offset for hyperslab */
+ hsize_t stride[1]; /* Distance between blocks in the hyperslab selection */
+ hsize_t count[1]; /* # of blocks in the the hyperslab selection */
+ hsize_t block[1]; /* Size of block in the hyperslab selection */
+ unsigned int wdata[CHUNKSZ]; /* Data to be written */
+ unsigned int rdata[NUM_ELEMENTS/10]; /* Data to be read */
+ herr_t ret; /* Generic return value */
+ unsigned i; /* Local index variable */
+
+ /* Output message about test being performed */
+ MESSAGE(6, ("Testing Hyperslab I/O for 1-d single block memory space\n"));
+
+ for (i = 0; i < CHUNKSZ; i++)
+ wdata[i] = i;
+
+ /* Create the file file */
+ fid = H5Fcreate(FILENAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+ CHECK(fid, H5I_INVALID_HID, "H5Fcreate");
+ /* Create file dataspace */
+ dims[0] = CHUNKSZ;
+ maxdims[0] = H5S_UNLIMITED;
+ sid = H5Screate_simple(RANK, dims, maxdims);
+ CHECK(sid, H5I_INVALID_HID, "H5Pcreate");
+
+ /* Create memory dataspace */
+ dimsm[0] = CHUNKSZ;
+ mid = H5Screate_simple(RANK, dimsm, NULL);
+ CHECK(mid, H5I_INVALID_HID, "H5Pcreate");
+
+ /* Set up to create a chunked dataset */
+ dcpl = H5Pcreate(H5P_DATASET_CREATE);
+ CHECK(dcpl, H5I_INVALID_HID, "H5Pcreate");
+
+ chunk_dims[0] = CHUNKSZ;
+ ret = H5Pset_chunk(dcpl, RANK, chunk_dims);
+ CHECK(ret, FAIL, "H5Pset_chunk");
+
+ /* Create a chunked dataset */
+ did = H5Dcreate2(fid, DNAME, H5T_NATIVE_INT, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT);
+ CHECK(did, H5I_INVALID_HID, "H5Dcreate2");
+
+ /* Set up hyperslab selection for file dataspace */
+ offset[0] = 0;
+ stride[0] = 1;
+ count[0] = 1;
+ block[0] = CHUNKSZ;
+
+ /* Write to each chunk in the dataset */
+ for (i = 0; i < NUMCHUNKS; i++) {
+ /* Set the hyperslab selection */
+ ret = H5Sselect_hyperslab(sid, H5S_SELECT_SET, offset, stride, count, block);
+ CHECK(ret, FAIL, "H5Sselect_hyperslab");
+
+ /* Write to the dataset */
+ ret = H5Dwrite(did, H5T_NATIVE_INT, mid, sid, H5P_DEFAULT, wdata);
+ CHECK(ret, FAIL, "H5Dwrite");
+
+ /* Extend the dataset's dataspace */
+ if(i < (NUMCHUNKS - 1)) {
+ offset[0] = offset[0] + CHUNKSZ;
+ dims[0] = dims[0] + CHUNKSZ;
+ ret = H5Dset_extent(did, dims);
+ CHECK(ret, FAIL, "H5Dset_extent");
+
+ /* Get the dataset's current dataspace */
+ sid = H5Dget_space(did);
+ CHECK(sid, H5I_INVALID_HID, "H5Dget_space");
+ }
+ }
+
+ /* Closing */
+ ret = H5Sclose(sid);
+ CHECK(ret, FAIL, "H5Sclose");
+ ret = H5Sclose(mid);
+ CHECK(ret, FAIL, "H5Sclose");
+ ret = H5Dclose(did);
+ CHECK(ret, FAIL, "H5Dclose");
+ ret = H5Pclose(dcpl);
+ CHECK(ret, FAIL, "H5Pclose");
+ ret = H5Fclose(fid);
+ CHECK(ret, FAIL, "H5Fclose");
+
+ /* Open the file */
+ fid = H5Fopen(FILENAME, H5F_ACC_RDONLY, H5P_DEFAULT);
+ CHECK(fid, H5I_INVALID_HID, "H5Fopen");
+
+ /* Open the dataset */
+ did = H5Dopen(fid, DNAME, H5P_DEFAULT);
+ CHECK(did, H5I_INVALID_HID, "H5Dopen");
+
+ /* Set up to read every 10th element in file dataspace */
+ offset[0] = 1;
+ stride[0] = 10;
+ count[0] = NUM_ELEMENTS/10;
+ block[0] = 1;
+
+ /* Get the dataset's dataspace */
+ sid = H5Dget_space(did);
+ CHECK(sid, H5I_INVALID_HID, "H5Pcreate");
+ ret = H5Sselect_hyperslab(sid, H5S_SELECT_SET, offset, stride, count, block);
+ CHECK(ret, FAIL, "H5Sselect_hyperslab");
+
+ /* Set up contiguous memory dataspace for the selected elements */
+ dimsm[0] = count[0];
+ mid = H5Screate_simple(RANK, dimsm, NULL);
+ CHECK(mid, H5I_INVALID_HID, "H5Screate");
+
+ /* Read all the selected 10th elements in the dataset into "rdata" */
+ ret = H5Dread(did, H5T_NATIVE_INT, mid, sid, H5P_DEFAULT, rdata);
+ CHECK(ret, FAIL, "H5Dread");
+
+ /* Verify data read is correct */
+ for(i = 0; i < 6; i += 2) {
+ VERIFY(rdata[i], 1, "H5Dread\n");
+ VERIFY(rdata[i+1], 11, "H5Dread\n");
+ }
+
+ /* Closing */
+ ret = H5Sclose(mid);
+ CHECK(ret, FAIL, "H5Sclose");
+ ret = H5Sclose(sid);
+ CHECK(ret, FAIL, "H5Sclose");
+ ret = H5Dclose(did);
+ CHECK(ret, FAIL, "H5Dclose");
+ ret = H5Fclose(fid);
+ CHECK(ret, FAIL, "H5Fclose");
+
+} /* test_hyper_io_1d() */
+
+
/****************************************************************
**
** test_select(): Main H5S selection testing routine.
@@ -15499,6 +15657,10 @@ test_select(void)
/* Test selection intersection with block */
test_select_intersect_block();
+
+ /* Test reading of 1-d disjoint file space to 1-d single block memory space */
+ test_hyper_io_1d();
+
} /* test_select() */