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Merge pull request #2804 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:final_1_10_prs to hdf5_1_10

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* commit '41da55dfe836551936032a33aa7b0acb9d4dc7cb':
  Adds missing HDstrtoumax for S3 VFD
  Merge of develop PRs to 1.10
This commit is contained in:
Dana Robinson
2020-08-18 11:59:15 -05:00
parent de8830ca7f 41da55dfe8
commit bc6a36e125
6 changed files with 158 additions and 97 deletions
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204
src/H5Dvirtual.c
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@@ -313,6 +313,8 @@ done:
herr_t
H5D_virtual_update_min_dims(H5O_layout_t *layout, size_t idx)
{
H5O_storage_virtual_t *virt = &layout->storage.u.virt;
H5O_storage_virtual_ent_t *ent = &virt->list[idx];
H5S_sel_type sel_type;
int rank;
hsize_t bounds_start[H5S_MAX_RANK];
@@ -324,10 +326,10 @@ H5D_virtual_update_min_dims(H5O_layout_t *layout, size_t idx)
HDassert(layout);
HDassert(layout->type == H5D_VIRTUAL);
HDassert(idx < layout->storage.u.virt.list_nalloc);
HDassert(idx < virt->list_nalloc);
/* Get type of selection */
if(H5S_SEL_ERROR == (sel_type = H5S_GET_SELECT_TYPE(layout->storage.u.virt.list[idx].source_dset.virtual_select)))
if(H5S_SEL_ERROR == (sel_type = H5S_GET_SELECT_TYPE(ent->source_dset.virtual_select)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get selection type")
/* Do not update min_dims for "all" or "none" selections */
@@ -335,19 +337,19 @@ H5D_virtual_update_min_dims(H5O_layout_t *layout, size_t idx)
HGOTO_DONE(SUCCEED)
/* Get rank of vspace */
if((rank = H5S_GET_EXTENT_NDIMS(layout->storage.u.virt.list[idx].source_dset.virtual_select)) < 0)
if((rank = H5S_GET_EXTENT_NDIMS(ent->source_dset.virtual_select)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get number of dimensions")
/* Get selection bounds */
if(H5S_SELECT_BOUNDS(layout->storage.u.virt.list[idx].source_dset.virtual_select, bounds_start, bounds_end) < 0)
if(H5S_SELECT_BOUNDS(ent->source_dset.virtual_select, bounds_start, bounds_end) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get selection bounds")
/* Update min_dims */
for(i = 0; i < rank; i++)
/* Don't check unlimited dimensions in the selection */
if((i != layout->storage.u.virt.list[idx].unlim_dim_virtual)
&& (bounds_end[i] >= layout->storage.u.virt.min_dims[i]))
layout->storage.u.virt.min_dims[i] = bounds_end[i] + (hsize_t)1;
if((i != ent->unlim_dim_virtual)
&& (bounds_end[i] >= virt->min_dims[i]))
virt->min_dims[i] = bounds_end[i] + (hsize_t)1;
done:
FUNC_LEAVE_NOAPI(ret_value)
@@ -419,6 +421,7 @@ done:
herr_t
H5D__virtual_store_layout(H5F_t *f, H5O_layout_t *layout)
{
H5O_storage_virtual_t *virt = &layout->storage.u.virt;
uint8_t *heap_block = NULL; /* Block to add to heap */
size_t *str_size = NULL; /* Array for VDS entry string lengths */
uint8_t *heap_block_p; /* Pointer into the heap block, while encoding */
@@ -433,16 +436,16 @@ H5D__virtual_store_layout(H5F_t *f, H5O_layout_t *layout)
/* Sanity checking */
HDassert(f);
HDassert(layout);
HDassert(layout->storage.u.virt.serial_list_hobjid.addr == HADDR_UNDEF);
HDassert(virt->serial_list_hobjid.addr == HADDR_UNDEF);
/* Create block if # of used entries > 0 */
if(layout->storage.u.virt.list_nused > 0) {
if(virt->list_nused > 0) {
/* Set the low/high bounds according to 'f' for the API context */
H5CX_set_libver_bounds(f);
/* Allocate array for caching results of strlen */
if(NULL == (str_size = (size_t *)H5MM_malloc(2 * layout->storage.u.virt.list_nused * sizeof(size_t))))
if(NULL == (str_size = (size_t *)H5MM_malloc(2 * virt->list_nused * sizeof(size_t))))
HGOTO_ERROR(H5E_OHDR, H5E_RESOURCE, FAIL, "unable to allocate string length array")
/*
@@ -453,29 +456,30 @@ H5D__virtual_store_layout(H5F_t *f, H5O_layout_t *layout)
block_size = (size_t)1 + H5F_SIZEOF_SIZE(f);
/* Calculate size of each entry */
for(i = 0; i < layout->storage.u.virt.list_nused; i++) {
for(i = 0; i < virt->list_nused; i++) {
H5O_storage_virtual_ent_t *ent = &virt->list[i];
hssize_t select_serial_size; /* Size of serialized selection */
HDassert(layout->storage.u.virt.list[i].source_file_name);
HDassert(layout->storage.u.virt.list[i].source_dset_name);
HDassert(layout->storage.u.virt.list[i].source_select);
HDassert(layout->storage.u.virt.list[i].source_dset.virtual_select);
HDassert(ent->source_file_name);
HDassert(ent->source_dset_name);
HDassert(ent->source_select);
HDassert(ent->source_dset.virtual_select);
/* Source file name */
str_size[2 * i] = HDstrlen(layout->storage.u.virt.list[i].source_file_name) + (size_t)1;
str_size[2 * i] = HDstrlen(ent->source_file_name) + (size_t)1;
block_size += str_size[2 * i];
/* Source dset name */
str_size[(2 * i) + 1] = HDstrlen(layout->storage.u.virt.list[i].source_dset_name) + (size_t)1;
str_size[(2 * i) + 1] = HDstrlen(ent->source_dset_name) + (size_t)1;
block_size += str_size[(2 * i) + 1];
/* Source selection */
if((select_serial_size = H5S_SELECT_SERIAL_SIZE(layout->storage.u.virt.list[i].source_select)) < 0)
if((select_serial_size = H5S_SELECT_SERIAL_SIZE(ent->source_select)) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTENCODE, FAIL, "unable to check dataspace selection size")
block_size += (size_t)select_serial_size;
/* Virtual dataset selection */
if((select_serial_size = H5S_SELECT_SERIAL_SIZE(layout->storage.u.virt.list[i].source_dset.virtual_select)) < 0)
if((select_serial_size = H5S_SELECT_SERIAL_SIZE(ent->source_dset.virtual_select)) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTENCODE, FAIL, "unable to check dataspace selection size")
block_size += (size_t)select_serial_size;
} /* end for */
@@ -498,25 +502,26 @@ H5D__virtual_store_layout(H5F_t *f, H5O_layout_t *layout)
*heap_block_p++ = (uint8_t)H5O_LAYOUT_VDS_GH_ENC_VERS;
/* Number of entries */
tmp_nentries = (hsize_t)layout->storage.u.virt.list_nused;
tmp_nentries = (hsize_t)virt->list_nused;
H5F_ENCODE_LENGTH(f, heap_block_p, tmp_nentries)
/* Encode each entry */
for(i = 0; i < layout->storage.u.virt.list_nused; i++) {
for(i = 0; i < virt->list_nused; i++) {
H5O_storage_virtual_ent_t *ent = &virt->list[i];
/* Source file name */
H5MM_memcpy((char *)heap_block_p, layout->storage.u.virt.list[i].source_file_name, str_size[2 * i]);
H5MM_memcpy((char *)heap_block_p, ent->source_file_name, str_size[2 * i]);
heap_block_p += str_size[2 * i];
/* Source dataset name */
H5MM_memcpy((char *)heap_block_p, layout->storage.u.virt.list[i].source_dset_name, str_size[(2 * i) + 1]);
H5MM_memcpy((char *)heap_block_p, ent->source_dset_name, str_size[(2 * i) + 1]);
heap_block_p += str_size[(2 * i) + 1];
/* Source selection */
if(H5S_SELECT_SERIALIZE(layout->storage.u.virt.list[i].source_select, &heap_block_p) < 0)
if(H5S_SELECT_SERIALIZE(ent->source_select, &heap_block_p) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to serialize source selection")
/* Virtual selection */
if(H5S_SELECT_SERIALIZE(layout->storage.u.virt.list[i].source_dset.virtual_select, &heap_block_p) < 0)
if(H5S_SELECT_SERIALIZE(ent->source_dset.virtual_select, &heap_block_p) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to serialize virtual selection")
} /* end for */
@@ -525,7 +530,7 @@ H5D__virtual_store_layout(H5F_t *f, H5O_layout_t *layout)
UINT32ENCODE(heap_block_p, chksum)
/* Insert block into global heap */
if(H5HG_insert(f, block_size, heap_block, &(layout->storage.u.virt.serial_list_hobjid)) < 0) /* Casting away const OK --NAF */
if(H5HG_insert(f, block_size, heap_block, &(virt->serial_list_hobjid)) < 0) /* Casting away const OK --NAF */
HGOTO_ERROR(H5E_OHDR, H5E_CANTINSERT, FAIL, "unable to insert virtual dataset heap block")
} /* end if */
@@ -556,6 +561,7 @@ herr_t
H5D__virtual_copy_layout(H5O_layout_t *layout)
{
H5O_storage_virtual_ent_t *orig_list = NULL;
H5O_storage_virtual_t *virt = &layout->storage.u.virt;
hid_t orig_source_fapl;
hid_t orig_source_dapl;
H5P_genplist_t *plist;
@@ -569,127 +575,129 @@ H5D__virtual_copy_layout(H5O_layout_t *layout)
/* Save original entry list and top-level property lists and reset in layout
* so the originals aren't closed on error */
orig_source_fapl = layout->storage.u.virt.source_fapl;
layout->storage.u.virt.source_fapl = -1;
orig_source_dapl = layout->storage.u.virt.source_dapl;
layout->storage.u.virt.source_dapl = -1;
orig_list = layout->storage.u.virt.list;
layout->storage.u.virt.list = NULL;
orig_source_fapl = virt->source_fapl;
virt->source_fapl = -1;
orig_source_dapl = virt->source_dapl;
virt->source_dapl = -1;
orig_list = virt->list;
virt->list = NULL;
/* Copy entry list */
if(layout->storage.u.virt.list_nused > 0) {
if(virt->list_nused > 0) {
HDassert(orig_list);
/* Allocate memory for the list */
if(NULL == (layout->storage.u.virt.list = (H5O_storage_virtual_ent_t *)H5MM_calloc(layout->storage.u.virt.list_nused * sizeof(H5O_storage_virtual_ent_t))))
if(NULL == (virt->list = H5MM_calloc(virt->list_nused * sizeof(virt->list[0]))))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate memory for virtual dataset entry list")
layout->storage.u.virt.list_nalloc = layout->storage.u.virt.list_nused;
virt->list_nalloc = virt->list_nused;
/* Copy the list entries, though set source_dset.dset and sub_dset to
* NULL */
for(i = 0; i < layout->storage.u.virt.list_nused; i++) {
for(i = 0; i < virt->list_nused; i++) {
H5O_storage_virtual_ent_t *ent = &virt->list[i];
/* Copy virtual selection */
if(NULL == (layout->storage.u.virt.list[i].source_dset.virtual_select
if(NULL == (ent->source_dset.virtual_select
= H5S_copy(orig_list[i].source_dset.virtual_select, FALSE, TRUE)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy virtual selection")
/* Copy original source names */
if(NULL == (layout->storage.u.virt.list[i].source_file_name
if(NULL == (ent->source_file_name
= H5MM_strdup(orig_list[i].source_file_name)))
HGOTO_ERROR(H5E_DATASET, H5E_RESOURCE, FAIL, "unable to duplicate source file name")
if(NULL == (layout->storage.u.virt.list[i].source_dset_name
if(NULL == (ent->source_dset_name
= H5MM_strdup(orig_list[i].source_dset_name)))
HGOTO_ERROR(H5E_DATASET, H5E_RESOURCE, FAIL, "unable to duplicate source dataset name")
/* Copy source selection */
if(NULL == (layout->storage.u.virt.list[i].source_select
if(NULL == (ent->source_select
= H5S_copy(orig_list[i].source_select, FALSE, TRUE)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy source selection")
/* Initialize clipped selections */
if(orig_list[i].unlim_dim_virtual < 0) {
layout->storage.u.virt.list[i].source_dset.clipped_source_select = layout->storage.u.virt.list[i].source_select;
layout->storage.u.virt.list[i].source_dset.clipped_virtual_select = layout->storage.u.virt.list[i].source_dset.virtual_select;
ent->source_dset.clipped_source_select = ent->source_select;
ent->source_dset.clipped_virtual_select = ent->source_dset.virtual_select;
} /* end if */
/* Copy parsed names */
if(H5D__virtual_copy_parsed_name(&layout->storage.u.virt.list[i].parsed_source_file_name, orig_list[i].parsed_source_file_name) < 0)
if(H5D__virtual_copy_parsed_name(&ent->parsed_source_file_name, orig_list[i].parsed_source_file_name) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy parsed source file name")
layout->storage.u.virt.list[i].psfn_static_strlen = orig_list[i].psfn_static_strlen;
layout->storage.u.virt.list[i].psfn_nsubs = orig_list[i].psfn_nsubs;
if(H5D__virtual_copy_parsed_name(&layout->storage.u.virt.list[i].parsed_source_dset_name, orig_list[i].parsed_source_dset_name) < 0)
ent->psfn_static_strlen = orig_list[i].psfn_static_strlen;
ent->psfn_nsubs = orig_list[i].psfn_nsubs;
if(H5D__virtual_copy_parsed_name(&ent->parsed_source_dset_name, orig_list[i].parsed_source_dset_name) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy parsed source dataset name")
layout->storage.u.virt.list[i].psdn_static_strlen = orig_list[i].psdn_static_strlen;
layout->storage.u.virt.list[i].psdn_nsubs = orig_list[i].psdn_nsubs;
ent->psdn_static_strlen = orig_list[i].psdn_static_strlen;
ent->psdn_nsubs = orig_list[i].psdn_nsubs;
/* Copy source names in source dset or add reference as appropriate
*/
if(orig_list[i].source_dset.file_name) {
if(orig_list[i].source_dset.file_name
== orig_list[i].source_file_name)
layout->storage.u.virt.list[i].source_dset.file_name = layout->storage.u.virt.list[i].source_file_name;
ent->source_dset.file_name = ent->source_file_name;
else if(orig_list[i].parsed_source_file_name
&& (orig_list[i].source_dset.file_name
!= orig_list[i].parsed_source_file_name->name_segment)) {
HDassert(layout->storage.u.virt.list[i].parsed_source_file_name);
HDassert(layout->storage.u.virt.list[i].parsed_source_file_name->name_segment);
layout->storage.u.virt.list[i].source_dset.file_name = layout->storage.u.virt.list[i].parsed_source_file_name->name_segment;
HDassert(ent->parsed_source_file_name);
HDassert(ent->parsed_source_file_name->name_segment);
ent->source_dset.file_name = ent->parsed_source_file_name->name_segment;
} /* end if */
else
if(NULL == (layout->storage.u.virt.list[i].source_dset.file_name
if(NULL == (ent->source_dset.file_name
= H5MM_strdup(orig_list[i].source_dset.file_name)))
HGOTO_ERROR(H5E_DATASET, H5E_RESOURCE, FAIL, "unable to duplicate source file name")
} /* end if */
if(orig_list[i].source_dset.dset_name) {
if(orig_list[i].source_dset.dset_name
== orig_list[i].source_dset_name)
layout->storage.u.virt.list[i].source_dset.dset_name = layout->storage.u.virt.list[i].source_dset_name;
ent->source_dset.dset_name = ent->source_dset_name;
else if(orig_list[i].parsed_source_dset_name
&& (orig_list[i].source_dset.dset_name
!= orig_list[i].parsed_source_dset_name->name_segment)) {
HDassert(layout->storage.u.virt.list[i].parsed_source_dset_name);
HDassert(layout->storage.u.virt.list[i].parsed_source_dset_name->name_segment);
layout->storage.u.virt.list[i].source_dset.dset_name = layout->storage.u.virt.list[i].parsed_source_dset_name->name_segment;
HDassert(ent->parsed_source_dset_name);
HDassert(ent->parsed_source_dset_name->name_segment);
ent->source_dset.dset_name = ent->parsed_source_dset_name->name_segment;
} /* end if */
else
if(NULL == (layout->storage.u.virt.list[i].source_dset.dset_name
if(NULL == (ent->source_dset.dset_name
= H5MM_strdup(orig_list[i].source_dset.dset_name)))
HGOTO_ERROR(H5E_DATASET, H5E_RESOURCE, FAIL, "unable to duplicate source dataset name")
} /* end if */
/* Copy other fields in entry */
layout->storage.u.virt.list[i].unlim_dim_source = orig_list[i].unlim_dim_source;
layout->storage.u.virt.list[i].unlim_dim_virtual = orig_list[i].unlim_dim_virtual;
layout->storage.u.virt.list[i].unlim_extent_source = orig_list[i].unlim_extent_source;
layout->storage.u.virt.list[i].unlim_extent_virtual = orig_list[i].unlim_extent_virtual;
layout->storage.u.virt.list[i].clip_size_source = orig_list[i].clip_size_source;
layout->storage.u.virt.list[i].clip_size_virtual = orig_list[i].clip_size_virtual;
layout->storage.u.virt.list[i].source_space_status = orig_list[i].source_space_status;
layout->storage.u.virt.list[i].virtual_space_status = orig_list[i].virtual_space_status;
ent->unlim_dim_source = orig_list[i].unlim_dim_source;
ent->unlim_dim_virtual = orig_list[i].unlim_dim_virtual;
ent->unlim_extent_source = orig_list[i].unlim_extent_source;
ent->unlim_extent_virtual = orig_list[i].unlim_extent_virtual;
ent->clip_size_source = orig_list[i].clip_size_source;
ent->clip_size_virtual = orig_list[i].clip_size_virtual;
ent->source_space_status = orig_list[i].source_space_status;
ent->virtual_space_status = orig_list[i].virtual_space_status;
} /* end for */
} /* end if */
else {
/* Zero out other fields related to list, just to be sure */
layout->storage.u.virt.list = NULL;
layout->storage.u.virt.list_nalloc = 0;
virt->list = NULL;
virt->list_nalloc = 0;
} /* end else */
/* Copy property lists */
if(orig_source_fapl >= 0) {
if(NULL == (plist = (H5P_genplist_t *)H5I_object_verify(orig_source_fapl, H5I_GENPROP_LST)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a property list")
if((layout->storage.u.virt.source_fapl = H5P_copy_plist(plist, FALSE)) < 0)
if((virt->source_fapl = H5P_copy_plist(plist, FALSE)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't copy fapl")
} /* end if */
if(orig_source_dapl >= 0) {
if(NULL == (plist = (H5P_genplist_t *)H5I_object_verify(orig_source_dapl, H5I_GENPROP_LST)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a property list")
if((layout->storage.u.virt.source_dapl = H5P_copy_plist(plist, FALSE)) < 0)
if((virt->source_dapl = H5P_copy_plist(plist, FALSE)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't copy dapl")
} /* end if */
/* New layout is not fully initialized */
layout->storage.u.virt.init = FALSE;
virt->init = FALSE;
done:
/* Release allocated resources on failure */
@@ -721,6 +729,7 @@ herr_t
H5D__virtual_reset_layout(H5O_layout_t *layout)
{
size_t i, j;
H5O_storage_virtual_t *virt = &layout->storage.u.virt;
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
@@ -731,53 +740,54 @@ H5D__virtual_reset_layout(H5O_layout_t *layout)
/* Free the list entries. Note we always attempt to free everything even in
* the case of a failure. Because of this, and because we free the list
* afterwards, we do not need to zero out the memory in the list. */
for(i = 0; i < layout->storage.u.virt.list_nused; i++) {
for(i = 0; i < virt->list_nused; i++) {
H5O_storage_virtual_ent_t *ent = &virt->list[i];
/* Free source_dset */
if(H5D__virtual_reset_source_dset(&layout->storage.u.virt.list[i], &layout->storage.u.virt.list[i].source_dset) < 0)
if(H5D__virtual_reset_source_dset(ent, &ent->source_dset) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset source dataset")
/* Free original source names */
(void)H5MM_xfree(layout->storage.u.virt.list[i].source_file_name);
(void)H5MM_xfree(layout->storage.u.virt.list[i].source_dset_name);
(void)H5MM_xfree(ent->source_file_name);
(void)H5MM_xfree(ent->source_dset_name);
/* Free sub_dset */
for(j = 0; j < layout->storage.u.virt.list[i].sub_dset_nalloc; j++)
if(H5D__virtual_reset_source_dset(&layout->storage.u.virt.list[i], &layout->storage.u.virt.list[i].sub_dset[j]) < 0)
for(j = 0; j < ent->sub_dset_nalloc; j++)
if(H5D__virtual_reset_source_dset(ent, &ent->sub_dset[j]) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset source dataset")
layout->storage.u.virt.list[i].sub_dset = (H5O_storage_virtual_srcdset_t *)H5MM_xfree(layout->storage.u.virt.list[i].sub_dset);
ent->sub_dset = H5MM_xfree(ent->sub_dset);
/* Free source_select */
if(layout->storage.u.virt.list[i].source_select)
if(H5S_close(layout->storage.u.virt.list[i].source_select) < 0)
if(ent->source_select)
if(H5S_close(ent->source_select) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release source selection")
/* Free parsed_source_file_name */
H5D_virtual_free_parsed_name(layout->storage.u.virt.list[i].parsed_source_file_name);
H5D_virtual_free_parsed_name(ent->parsed_source_file_name);
/* Free parsed_source_dset_name */
H5D_virtual_free_parsed_name(layout->storage.u.virt.list[i].parsed_source_dset_name);
} /* end for */
H5D_virtual_free_parsed_name(ent->parsed_source_dset_name);
}
/* Free the list */
layout->storage.u.virt.list = (H5O_storage_virtual_ent_t *)H5MM_xfree(layout->storage.u.virt.list);
layout->storage.u.virt.list_nalloc = (size_t)0;
layout->storage.u.virt.list_nused = (size_t)0;
(void)HDmemset(layout->storage.u.virt.min_dims, 0, sizeof(layout->storage.u.virt.min_dims));
virt->list = H5MM_xfree(virt->list);
virt->list_nalloc = (size_t)0;
virt->list_nused = (size_t)0;
(void)HDmemset(virt->min_dims, 0, sizeof(virt->min_dims));
/* Close access property lists */
if(layout->storage.u.virt.source_fapl >= 0) {
if(H5I_dec_ref(layout->storage.u.virt.source_fapl) < 0)
if(virt->source_fapl >= 0) {
if(H5I_dec_ref(virt->source_fapl) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "can't close source fapl")
layout->storage.u.virt.source_fapl = -1;
} /* end if */
if(layout->storage.u.virt.source_dapl >= 0) {
if(H5I_dec_ref(layout->storage.u.virt.source_dapl) < 0)
virt->source_fapl = -1;
}
if(virt->source_dapl >= 0) {
if(H5I_dec_ref(virt->source_dapl) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "can't close source dapl")
layout->storage.u.virt.source_dapl = -1;
} /* end if */
virt->source_dapl = -1;
}
/* The list is no longer initialized */
layout->storage.u.virt.init = FALSE;
virt->init = FALSE;
/* Note the lack of a done: label. This is because there are no HGOTO_ERROR
* calls. If one is added, a done: label must also be added */
@@ -2781,7 +2791,7 @@ H5D__virtual_write_one(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
* extent in the unlimited dimension. -NAF */
/* Project intersection of file space and mapping virtual space onto
* mapping source space */
if(H5S_select_project_intersection(source_dset->virtual_select, source_dset->clipped_source_select, file_space, &projected_src_space, TRUE) < 0)
if(H5S_select_project_intersection(source_dset->clipped_virtual_select, source_dset->clipped_source_select, file_space, &projected_src_space, TRUE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCLIP, FAIL, "can't project virtual intersection onto source space")
/* Perform write on source dataset */

4
src/H5FDcore.c
View File

@@ -381,7 +381,9 @@ H5FD__core_write_to_bstore(H5FD_core_t *file, haddr_t addr, size_t size)
int myerrno = errno;
time_t mytime = HDtime(NULL);
#ifndef H5_HAVE_PREADWRITE
offset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR);
#endif /* H5_HAVE_PREADWRITE */
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "write to backing store failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', ptr = %p, total write size = %llu, bytes this sub-write = %llu, bytes actually written = %llu, offset = %llu", HDctime(&mytime), file->name, file->fd, myerrno, HDstrerror(myerrno), ptr, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_wrote, (unsigned long long)offset);
} /* end if */
@@ -803,7 +805,9 @@ H5FD__core_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr
int myerrno = errno;
time_t mytime = HDtime(NULL);
#ifndef H5_HAVE_PREADWRITE
offset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR);
#endif /* H5_HAVE_PREADWRITE */
HGOTO_ERROR(H5E_IO, H5E_READERROR, NULL, "file read failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', file->mem = %p, total read size = %llu, bytes this sub-read = %llu, bytes actually read = %llu, offset = %llu", HDctime(&mytime), file->name, file->fd, myerrno, HDstrerror(myerrno), file->mem, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_read, (unsigned long long)offset);
} /* end if */

21
src/H5FDlog.c
View File

@@ -81,8 +81,10 @@ typedef struct H5FD_log_t {
int fd; /* the unix file */
haddr_t eoa; /* end of allocated region */
haddr_t eof; /* end of file; current file size */
#ifndef H5_HAVE_PREADWRITE
haddr_t pos; /* current file I/O position */
H5FD_file_op_t op; /* last operation */
#endif /* H5_HAVE_PREADWRITE */
hbool_t ignore_disabled_file_locks;
char filename[H5FD_MAX_FILENAME_LEN]; /* Copy of file name from open operation */
#ifndef H5_HAVE_WIN32_API
@@ -571,8 +573,10 @@ H5FD__log_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr)
file->fd = fd;
H5_CHECKED_ASSIGN(file->eof, haddr_t, sb.st_size, h5_stat_size_t);
#ifndef H5_HAVE_PREADWRITE
file->pos = HADDR_UNDEF;
file->op = OP_UNKNOWN;
#endif /* H5_HAVE_PREADWRITE */
#ifdef H5_HAVE_WIN32_API
file->hFile = (HANDLE)_get_osfhandle(fd);
if(INVALID_HANDLE_VALUE == file->hFile)
@@ -1280,7 +1284,9 @@ H5FD__log_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, had
int myerrno = errno;
time_t mytime = HDtime(NULL);
#ifndef H5_HAVE_PREADWRITE
offset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR);
#endif /* H5_HAVE_PREADWRITE */
if(file->fa.flags & H5FD_LOG_LOC_READ)
HDfprintf(file->logfp, "Error! Reading: %10a-%10a (%10Zu bytes)\n", orig_addr, (orig_addr + orig_size) - 1, orig_size);
@@ -1337,15 +1343,19 @@ H5FD__log_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, had
HDfprintf(file->logfp, "\n");
} /* end if */
#ifndef H5_HAVE_PREADWRITE
/* Update current position */
file->pos = addr;
file->op = OP_READ;
#endif /* H5_HAVE_PREADWRITE */
done:
if(ret_value < 0) {
#ifndef H5_HAVE_PREADWRITE
/* Reset last file I/O information */
file->pos = HADDR_UNDEF;
file->op = OP_UNKNOWN;
#endif /* H5_HAVE_PREADWRITE */
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
@@ -1489,7 +1499,9 @@ H5FD__log_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, ha
int myerrno = errno;
time_t mytime = HDtime(NULL);
#ifndef H5_HAVE_PREADWRITE
offset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR);
#endif /* H5_HAVE_PREADWRITE */
if(file->fa.flags & H5FD_LOG_LOC_WRITE)
HDfprintf(file->logfp, "Error! Writing: %10a-%10a (%10Zu bytes)\n", orig_addr, (orig_addr + orig_size) - 1, orig_size);
@@ -1541,17 +1553,24 @@ H5FD__log_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, ha
HDfprintf(file->logfp, "\n");
} /* end if */
#ifndef H5_HAVE_PREADWRITE
/* Update current position and eof */
file->pos = addr;
file->op = OP_WRITE;
if(file->pos > file->eof)
file->eof = file->pos;
#else /* H5_HAVE_PREADWRITE */
if(addr > file->eof)
file->eof = addr;
#endif /* H5_HAVE_PREADWRITE */
done:
if(ret_value < 0) {
#ifndef H5_HAVE_PREADWRITE
/* Reset last file I/O information */
file->pos = HADDR_UNDEF;
file->op = OP_UNKNOWN;
#endif /* H5_HAVE_PREADWRITE */
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
@@ -1656,9 +1675,11 @@ H5FD__log_truncate(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, hbool_t H5_ATTR_
/* Update the eof value */
file->eof = file->eoa;
#ifndef H5_HAVE_PREADWRITE
/* Reset last file I/O information */
file->pos = HADDR_UNDEF;
file->op = OP_UNKNOWN;
#endif /* H5_HAVE_PREADWRITE */
} /* end if */
done:

2
src/H5FDprivate.h
View File

@@ -59,12 +59,14 @@ typedef struct H5FD_class_mpi_t {
/* Library Private Typedefs */
/****************************/
#ifndef H5_HAVE_PREADWRITE
/* File operations */
typedef enum {
OP_UNKNOWN = 0, /* Unknown last file operation */
OP_READ = 1, /* Last file I/O operation was a read */
OP_WRITE = 2 /* Last file I/O operation was a write */
} H5FD_file_op_t;
#endif /* H5_HAVE_PREADWRITE */
/* Define structure to hold initial file image and other relevant information */

21
src/H5FDsec2.c
View File

@@ -58,8 +58,10 @@ typedef struct H5FD_sec2_t {
int fd; /* the filesystem file descriptor */
haddr_t eoa; /* end of allocated region */
haddr_t eof; /* end of file; current file size */
#ifndef H5_HAVE_PREADWRITE
haddr_t pos; /* current file I/O position */
H5FD_file_op_t op; /* last operation */
#endif /* H5_HAVE_PREADWRITE */
hbool_t ignore_disabled_file_locks;
char filename[H5FD_MAX_FILENAME_LEN]; /* Copy of file name from open operation */
#ifndef H5_HAVE_WIN32_API
@@ -369,8 +371,10 @@ H5FD__sec2_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr
file->fd = fd;
H5_CHECKED_ASSIGN(file->eof, haddr_t, sb.st_size, h5_stat_size_t);
#ifndef H5_HAVE_PREADWRITE
file->pos = HADDR_UNDEF;
file->op = OP_UNKNOWN;
#endif /* H5_HAVE_PREADWRITE */
#ifdef H5_HAVE_WIN32_API
file->hFile = (HANDLE)_get_osfhandle(fd);
if(INVALID_HANDLE_VALUE == file->hFile)
@@ -748,7 +752,9 @@ H5FD__sec2_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU
int myerrno = errno;
time_t mytime = HDtime(NULL);
#ifndef H5_HAVE_PREADWRITE
offset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR);
#endif /* H5_HAVE_PREADWRITE */
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total read size = %llu, bytes this sub-read = %llu, bytes actually read = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_read, (unsigned long long)offset);
} /* end if */
@@ -767,15 +773,19 @@ H5FD__sec2_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU
buf = (char *)buf + bytes_read;
} /* end while */
#ifndef H5_HAVE_PREADWRITE
/* Update current position */
file->pos = addr;
file->op = OP_READ;
#endif /* H5_HAVE_PREADWRITE */
done:
if(ret_value < 0) {
#ifndef H5_HAVE_PREADWRITE
/* Reset last file I/O information */
file->pos = HADDR_UNDEF;
file->op = OP_UNKNOWN;
#endif /* H5_HAVE_PREADWRITE */
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
@@ -851,7 +861,9 @@ H5FD__sec2_write(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UN
int myerrno = errno;
time_t mytime = HDtime(NULL);
#ifndef H5_HAVE_PREADWRITE
offset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR);
#endif /* H5_HAVE_PREADWRITE */
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total write size = %llu, bytes this sub-write = %llu, bytes actually written = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_wrote, (unsigned long long)offset);
} /* end if */
@@ -864,17 +876,24 @@ H5FD__sec2_write(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UN
buf = (const char *)buf + bytes_wrote;
} /* end while */
#ifndef H5_HAVE_PREADWRITE
/* Update current position and eof */
file->pos = addr;
file->op = OP_WRITE;
if(file->pos > file->eof)
file->eof = file->pos;
#else /* H5_HAVE_PREADWRITE */
if(addr > file->eof)
file->eof = addr;
#endif /* H5_HAVE_PREADWRITE */
done:
if(ret_value < 0) {
#ifndef H5_HAVE_PREADWRITE
/* Reset last file I/O information */
file->pos = HADDR_UNDEF;
file->op = OP_UNKNOWN;
#endif /* H5_HAVE_PREADWRITE */
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
@@ -940,9 +959,11 @@ H5FD__sec2_truncate(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, hbool_t H5_ATTR
/* Update the eof value */
file->eof = file->eoa;
#ifndef H5_HAVE_PREADWRITE
/* Reset last file I/O information */
file->pos = HADDR_UNDEF;
file->op = OP_UNKNOWN;
#endif /* H5_HAVE_PREADWRITE */
} /* end if */
done:

3
src/H5private.h
View File

@@ -1512,6 +1512,9 @@ typedef off_t h5_stat_size_t;
#ifndef HDstrtoull
#define HDstrtoull(S,R,N) strtoull(S,R,N)
#endif /* HDstrtoul */
#ifndef HDstrtoumax
#define HDstrtoumax(S,R,N) strtoumax(S,R,N)
#endif /* HDstrtoumax */
#ifndef HDstrxfrm
#define HDstrxfrm(X,Y,Z) strxfrm(X,Y,Z)
#endif /* HDstrxfrm */