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Merge pull request #409 in HDFFV/hdf5 from ~VCHOI/my_hdf5_fork:develop to develop

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* commit '7eda1e3c6a57f79b59fc35518816db4e3a2b382d':
  Fix for H5Dset_extent test failure with extensive array indexing (HDFFV-9771) 1) Calculate chunk index for extensive array index based on swizzled max chunks when unlim_dim > 0 2) Minor fixes to test/fheap.c that somehow were missed from last check in.  See pull request #396 review comments.
This commit is contained in:
Vailin Choi 2017-04-11 19:19:51 -05:00
commit 6efca6717c
4 changed files with 44 additions and 52 deletions
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15
src/H5Dearray.c
View File

@ -1137,7 +1137,7 @@ H5D__earray_idx_get_addr(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *uda
H5VM_swizzle_coords(hsize_t, swizzled_coords, idx_info->layout->u.earray.unlim_dim);
/* Calculate the index of this chunk */
idx = H5VM_chunk_index(ndims, swizzled_coords, idx_info->layout->u.earray.swizzled_dim, idx_info->layout->u.earray.swizzled_down_chunks);
idx = H5VM_chunk_index(ndims, swizzled_coords, idx_info->layout->u.earray.swizzled_dim, idx_info->layout->u.earray.swizzled_max_down_chunks);
} /* end if */
else {
/* Calculate the index of this chunk */
@ -1202,7 +1202,8 @@ H5D__earray_idx_resize(H5O_layout_chunk_t *layout)
/* "Swizzle" constant dimensions for this dataset */
if(layout->u.earray.unlim_dim > 0) {
hsize_t swizzled_chunks[H5O_LAYOUT_NDIMS]; /* Swizzled form of # of chunks in each dimension */
hsize_t swizzled_chunks[H5O_LAYOUT_NDIMS]; /* Swizzled form of # of chunks in each dimension */
hsize_t swizzled_max_chunks[H5O_LAYOUT_NDIMS]; /* Swizzled form of max # of chunks in each dimension */
/* Get the swizzled chunk dimensions */
HDmemcpy(layout->u.earray.swizzled_dim, layout->dim, (layout->ndims - 1) * sizeof(layout->dim[0]));
@ -1215,6 +1216,14 @@ H5D__earray_idx_resize(H5O_layout_chunk_t *layout)
/* Get the swizzled "down" sizes for each dimension */
if(H5VM_array_down((layout->ndims - 1), swizzled_chunks, layout->u.earray.swizzled_down_chunks) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't compute swizzled 'down' chunk size value")
/* Get the swizzled max number of chunks in each dimension */
HDmemcpy(swizzled_max_chunks, layout->max_chunks, (layout->ndims - 1) * sizeof(swizzled_max_chunks[0]));
H5VM_swizzle_coords(hsize_t, swizzled_max_chunks, layout->u.earray.unlim_dim);
/* Get the swizzled max "down" sizes for each dimension */
if(H5VM_array_down((layout->ndims - 1), swizzled_max_chunks, layout->u.earray.swizzled_max_down_chunks) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't compute swizzled 'down' chunk size value")
} /* end if */
done:
@ -1414,7 +1423,7 @@ H5D__earray_idx_remove(const H5D_chk_idx_info_t *idx_info, H5D_chunk_common_ud_t
H5VM_swizzle_coords(hsize_t, swizzled_coords, idx_info->layout->u.earray.unlim_dim);
/* Calculate the index of this chunk */
idx = H5VM_chunk_index(ndims, swizzled_coords, idx_info->layout->u.earray.swizzled_dim, idx_info->layout->u.earray.swizzled_down_chunks);
idx = H5VM_chunk_index(ndims, swizzled_coords, idx_info->layout->u.earray.swizzled_dim, idx_info->layout->u.earray.swizzled_max_down_chunks);
} /* end if */
else {
/* Calculate the index of this chunk */

1
src/H5Oprivate.h
View File

@ -584,6 +584,7 @@ typedef struct H5O_layout_chunk_earray_t {
unsigned unlim_dim; /* Rank of unlimited dimension for dataset */
uint32_t swizzled_dim[H5O_LAYOUT_NDIMS]; /* swizzled chunk dimensions */
hsize_t swizzled_down_chunks[H5O_LAYOUT_NDIMS]; /* swizzled "down" size of number of chunks in each dimension */
hsize_t swizzled_max_down_chunks[H5O_LAYOUT_NDIMS]; /* swizzled max "down" size of number of chunks in each dimension */
} H5O_layout_chunk_earray_t;
typedef struct H5O_layout_chunk_bt2_t {

62
test/fheap.c
View File

@ -553,7 +553,7 @@ begin_test(fheap_test_param_t *tparam, const char *base_desc,
del_str = get_del_string(tparam);
HDassert(del_str);
test_desc = (char *)H5MM_malloc(HDstrlen(del_str) + HDstrlen(base_desc));
sprintf(test_desc, base_desc, del_str);
HDsprintf(test_desc, base_desc, del_str);
TESTING(test_desc);
H5MM_xfree(del_str);
H5MM_xfree(test_desc);
@ -7683,10 +7683,10 @@ test_man_incr_insert_remove(hid_t fapl, H5HF_create_t *cparam, fheap_test_param_
TESTING("incremental object insertion and removal")
for(i = 0; i < 100; i++) {
sprintf(obj1.b, "%s%d", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", i);
HDsprintf(obj1.b, "%s%d", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", i);
for(j = 0; j < i; j++) {
sprintf(obj2.b, "%s%d", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", j);
HDsprintf(obj2.b, "%s%d", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", j);
if(H5HF_remove(fh, dxpl, heap_id[j]) < 0)
FAIL_STACK_ERROR
@ -16393,7 +16393,7 @@ main(void)
* running time will be long.
*/
if(ExpressMode > 1)
printf("***Express test mode on. Some tests may be skipped\n");
HDprintf("***Express test mode on. Some tests may be skipped\n");
else if(ExpressMode == 0)
num_pb_fs = NUM_PB_FS;
@ -16475,12 +16475,12 @@ main(void)
switch(curr_test) {
/* "Normal" testing parameters */
case FHEAP_TEST_NORMAL:
puts("Testing with normal parameters");
HDputs("Testing with normal parameters");
break;
/* "Re-open heap" testing parameters */
case FHEAP_TEST_REOPEN:
puts("Testing with reopen heap flag set");
HDputs("Testing with reopen heap flag set");
tparam.reopen_heap = FHEAP_TEST_REOPEN;
break;
@ -16512,12 +16512,12 @@ main(void)
switch(fill) {
/* "Bulk fill" heap blocks with 'large' objects */
case FHEAP_TEST_FILL_LARGE:
puts("Bulk-filling blocks w/large objects");
HDputs("Bulk-filling blocks w/large objects");
break;
/* "Bulk fill" heap blocks with 'single' objects */
case FHEAP_TEST_FILL_SINGLE:
puts("Bulk-filling blocks w/single object");
HDputs("Bulk-filling blocks w/single object");
break;
/* An unknown test? */
@ -16568,25 +16568,25 @@ main(void)
* level of complexity gradually. -QAK
*/
if(ExpressMode > 1)
printf("***Express test mode on. test_man_start_5th_recursive_indirect is skipped\n");
HDprintf("***Express test mode on. test_man_start_5th_recursive_indirect is skipped\n");
else
nerrors += test_man_start_5th_recursive_indirect(fapl, &small_cparam, &tparam);
/*
* Test fractal heap object deletion
*/
/* Simple removal */
nerrors += test_man_remove_bogus(fapl, &small_cparam, &tparam);
nerrors += test_man_remove_one(fapl, &small_cparam, &tparam);
nerrors += test_man_remove_two(fapl, &small_cparam, &tparam);
nerrors += test_man_remove_one_larger(fapl, &small_cparam, &tparam);
tparam.del_dir = FHEAP_DEL_FORWARD;
nerrors += test_man_remove_two_larger(fapl, &small_cparam, &tparam);
tparam.del_dir = FHEAP_DEL_REVERSE;
nerrors += test_man_remove_two_larger(fapl, &small_cparam, &tparam);
tparam.del_dir = FHEAP_DEL_FORWARD;
nerrors += test_man_remove_three_larger(fapl, &small_cparam, &tparam);
tparam.del_dir = FHEAP_DEL_REVERSE;
/* Simple removal */
nerrors += test_man_remove_bogus(fapl, &small_cparam, &tparam);
nerrors += test_man_remove_one(fapl, &small_cparam, &tparam);
nerrors += test_man_remove_two(fapl, &small_cparam, &tparam);
nerrors += test_man_remove_one_larger(fapl, &small_cparam, &tparam);
tparam.del_dir = FHEAP_DEL_FORWARD;
nerrors += test_man_remove_two_larger(fapl, &small_cparam, &tparam);
tparam.del_dir = FHEAP_DEL_REVERSE;
nerrors += test_man_remove_two_larger(fapl, &small_cparam, &tparam);
tparam.del_dir = FHEAP_DEL_FORWARD;
nerrors += test_man_remove_three_larger(fapl, &small_cparam, &tparam);
tparam.del_dir = FHEAP_DEL_REVERSE;
nerrors += test_man_remove_three_larger(fapl, &small_cparam, &tparam);
/* Incremental insert & removal */
@ -16613,7 +16613,7 @@ main(void)
nerrors += test_man_remove_first_two_rows(fapl, &small_cparam, &tparam);
nerrors += test_man_remove_first_four_rows(fapl, &small_cparam, &tparam);
if(ExpressMode > 1)
printf("***Express test mode on. Some tests skipped\n");
HDprintf("***Express test mode on. Some tests skipped\n");
else {
nerrors += test_man_remove_all_root_direct(fapl, &small_cparam, &tparam);
nerrors += test_man_remove_2nd_indirect(fapl, &small_cparam, &tparam);
@ -16643,7 +16643,7 @@ main(void)
nerrors += test_man_fill_3rd_direct_less_one_fill_direct_wrap_start_block_add_skipped(fapl, &small_cparam, &tparam);
nerrors += test_man_fill_1st_row_3rd_direct_fill_2nd_direct_less_one_wrap_start_block_add_skipped(fapl, &small_cparam, &tparam);
if(ExpressMode > 1)
printf("***Express test mode on. Some tests skipped\n");
HDprintf("***Express test mode on. Some tests skipped\n");
else {
nerrors += test_man_fill_3rd_direct_fill_direct_skip_start_block_add_skipped(fapl, &small_cparam, &tparam);
nerrors += test_man_fill_3rd_direct_fill_2nd_direct_fill_direct_skip_3rd_indirect_start_block_add_skipped(fapl, &small_cparam, &tparam);
@ -16684,12 +16684,12 @@ main(void)
switch(id_len) {
/* Use "normal" form for 'huge' object's heap IDs */
case 0:
puts("Using 'normal' heap ID format for 'huge' objects");
HDputs("Using 'normal' heap ID format for 'huge' objects");
break;
/* Use "direct" form for 'huge' object's heap IDs */
case 1:
puts("Using 'direct' heap ID format for 'huge' objects");
HDputs("Using 'direct' heap ID format for 'huge' objects");
/* Adjust actual length of heap IDs for directly storing 'huge' object's file offset & length in heap ID */
tparam.actual_id_len = 17; /* 1 + 8 (file address size) + 8 (file length size) */
@ -16698,7 +16698,7 @@ main(void)
/* Use "direct" storage for 'huge' objects and larger IDs for 'tiny' objects */
case 2:
small_cparam.id_len = 37;
puts("Using 'direct' heap ID format for 'huge' objects and larger IDs for 'tiny' objects");
HDputs("Using 'direct' heap ID format for 'huge' objects and larger IDs for 'tiny' objects");
tparam.actual_id_len = 37;
break;
@ -16756,10 +16756,10 @@ main(void)
/* Random object insertion & deletion */
if(ExpressMode > 1)
printf("***Express test mode on. Some tests skipped\n");
HDprintf("***Express test mode on. Some tests skipped\n");
else {
/* Random tests using "small" heap creation parameters */
puts("Using 'small' heap creation parameters");
HDputs("Using 'small' heap creation parameters");
/* (reduce size of tests when re-opening each time) */
/* XXX: Try to speed things up enough that these tests don't have to be reduced when re-opening */
@ -16772,7 +16772,7 @@ main(void)
nerrors += test_random_pow2((curr_test == FHEAP_TEST_NORMAL ? (hsize_t)(100*1000*1000) : (hsize_t)(4*1000*1000)), fapl, &small_cparam, &tparam);
/* Random tests using "large" heap creation parameters */
puts("Using 'large' heap creation parameters");
HDputs("Using 'large' heap creation parameters");
tparam.actual_id_len = LARGE_HEAP_ID_LEN;
/* (reduce size of tests when re-opening each time) */
@ -16818,7 +16818,7 @@ main(void)
if(nerrors)
goto error;
puts("All fractal heap tests passed.");
HDputs("All fractal heap tests passed.");
/* Release space for the shared objects */
H5MM_xfree(shared_wobj_g);
@ -16840,7 +16840,7 @@ HDfprintf(stderr, "Uncomment cleanup!\n");
return 0;
error:
puts("*** TESTS FAILED ***");
HDputs("*** TESTS FAILED ***");
H5E_BEGIN_TRY {
H5MM_xfree(shared_wobj_g);
H5MM_xfree(shared_robj_g);

18
test/set_extent.c
View File

@ -2603,15 +2603,6 @@ static int test_random_rank4( hid_t fapl, hid_t dcpl, hbool_t do_fillvalue,
volatile unsigned i, j, k, l, m; /* Local indices */
char filename[NAME_BUF_SIZE];
/* *** FIXME ***
* Skip the test if an extensible array index is requested, as resizing
* them is broken.
*
* Remove these lines as appropriate when these problems are fixed.
*/
if(index_type == RANK4_INDEX_EARRAY)
return 0;
/* create a new file */
h5_fixname(FILENAME[4], fapl, filename, sizeof filename);
if ((file = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl)) < 0)
@ -2816,15 +2807,6 @@ static int test_random_rank4_vl( hid_t fapl, hid_t dcpl, hbool_t do_fillvalue,
volatile unsigned i, j, k, l, m; /* Local indices */
char filename[NAME_BUF_SIZE];
/* *** FIXME ***
* Skip the test if an extensible array index is requested, as resizing
* them is broken.
*
* Remove these lines as appropriate when these problems are fixed.
*/
if(index_type == RANK4_INDEX_EARRAY)
return 0;
/* Initialize fill value buffers so they aren't freed in case of an error */
fill_value.len = 0;
fill_value.p = NULL;