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(1) Address the feedback from the PR review

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(2) Add release notes
This commit is contained in:
Vailin Choi 2019-09-26 14:10:56 -05:00
parent 52fef3c6d2
commit 7924eee0e5
3 changed files with 27 additions and 15 deletions
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13
release_docs/RELEASE.txt
View File

@ -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

7
src/H5Dchunk.c
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@ -255,7 +255,7 @@ 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, hsize_t nelmts, H5D_chunk_map_t *fm);
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);
@ -1160,7 +1160,7 @@ 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, nelmts, fm) < 0)
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:
@ -1189,8 +1189,7 @@ done:
*-------------------------------------------------------------------------
*/
static herr_t
H5D__chunk_io_init_selections(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
hsize_t nelmts, H5D_chunk_map_t *fm)
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 */

22
test/tselect.c
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@ -15329,7 +15329,7 @@ test_select_intersect_block(void)
** 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-20585
** 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.
@ -15361,22 +15361,22 @@ test_hyper_io_1d(void)
/* Create the file file */
fid = H5Fcreate(FILENAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
CHECK(fid, FAIL, "H5Fcreate");
CHECK(fid, H5I_INVALID_HID, "H5Fcreate");
/* Create file dataspace */
dims[0] = CHUNKSZ;
maxdims[0] = H5S_UNLIMITED;
sid = H5Screate_simple(RANK, dims, maxdims);
CHECK(sid, FAIL, "H5Pcreate");
CHECK(sid, H5I_INVALID_HID, "H5Pcreate");
/* Create memory dataspace */
dimsm[0] = CHUNKSZ;
mid = H5Screate_simple(RANK, dimsm, NULL);
CHECK(mid, FAIL, "H5Pcreate");
CHECK(mid, H5I_INVALID_HID, "H5Pcreate");
/* Set up to create a chunked dataset */
dcpl = H5Pcreate(H5P_DATASET_CREATE);
CHECK(dcpl, FAIL, "H5Pcreate");
CHECK(dcpl, H5I_INVALID_HID, "H5Pcreate");
chunk_dims[0] = CHUNKSZ;
ret = H5Pset_chunk(dcpl, RANK, chunk_dims);
@ -15384,7 +15384,7 @@ test_hyper_io_1d(void)
/* Create a chunked dataset */
did = H5Dcreate2(fid, DNAME, H5T_NATIVE_INT, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT);
CHECK(did, FAIL, "H5Dcreate2");
CHECK(did, H5I_INVALID_HID, "H5Dcreate2");
/* Set up hyperslab selection for file dataspace */
offset[0] = 0;
@ -15411,7 +15411,7 @@ test_hyper_io_1d(void)
/* Get the dataset's current dataspace */
sid = H5Dget_space(did);
CHECK(sid, FAIL, "H5Dget_space");
CHECK(sid, H5I_INVALID_HID, "H5Dget_space");
}
}
@ -15429,11 +15429,11 @@ test_hyper_io_1d(void)
/* Open the file */
fid = H5Fopen(FILENAME, H5F_ACC_RDONLY, H5P_DEFAULT);
CHECK(fid, FAIL, "H5Fopen");
CHECK(fid, H5I_INVALID_HID, "H5Fopen");
/* Open the dataset */
did = H5Dopen(fid, DNAME, H5P_DEFAULT);
CHECK(did, FAIL, "H5Dopen");
CHECK(did, H5I_INVALID_HID, "H5Dopen");
/* Set up to read every 10th element in file dataspace */
offset[0] = 1;
@ -15443,14 +15443,14 @@ test_hyper_io_1d(void)
/* Get the dataset's dataspace */
sid = H5Dget_space(did);
CHECK(sid, FAIL, "H5Pcreate");
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, FAIL, "H5Screate");
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);