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-rw-r--r--src/H5Dvirtual.c159
-rw-r--r--src/H5Olayout.c3
-rw-r--r--src/H5Oprivate.h2
-rw-r--r--src/H5Pdcpl.c2
-rw-r--r--src/H5Shyper.c2
-rw-r--r--test/tselect.c5
6 files changed, 118 insertions, 55 deletions
diff --git a/src/H5Dvirtual.c b/src/H5Dvirtual.c
index 226d879..a783a5a 100644
--- a/src/H5Dvirtual.c
+++ b/src/H5Dvirtual.c
@@ -108,8 +108,8 @@ const H5D_layout_ops_t H5D_LOPS_VIRTUAL[1] = {{
H5D__virtual_read,
H5D__virtual_write,
#ifdef H5_HAVE_PARALLEL
- H5D__virtual_collective_read, //VDSINC
- H5D__virtual_collective_write, //VDSINC
+ NULL,
+ NULL,
#endif /* H5_HAVE_PARALLEL */
NULL,
NULL,
@@ -132,9 +132,8 @@ H5FL_DEFINE(H5O_storage_virtual_name_seg_t);
*
* Purpose: Updates the virtual layout's "min_dims" field to take into
* account the "idx"th entry in the mapping list. The entry
- * must be complete, though top level fields list_nused does
- * (and of course min_dims) do not need to take it into
- * account.
+ * must be complete, though top level field list_nused (and
+ * of course min_dims) does not need to take it into account.
*
* Return: Non-negative on success/Negative on failure
*
@@ -206,6 +205,9 @@ herr_t
H5D__virtual_copy_layout(H5O_layout_t *layout)
{
H5O_storage_virtual_ent_t *orig_list = NULL;
+ hid_t orig_source_fapl;
+ hid_t orig_source_dapl;
+ H5P_genplist_t *plist;
size_t i;
herr_t ret_value = SUCCEED;
@@ -214,11 +216,18 @@ H5D__virtual_copy_layout(H5O_layout_t *layout)
HDassert(layout);
HDassert(layout->type == H5D_VIRTUAL);
- if(layout->storage.u.virt.list_nused > 0) {
- HDassert(layout->storage.u.virt.list);
+ /* 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;
- /* Save original entry list for use as the "source" */
- orig_list = layout->storage.u.virt.list;
+ /* Copy entry list */
+ if(layout->storage.u.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))))
@@ -315,13 +324,26 @@ H5D__virtual_copy_layout(H5O_layout_t *layout)
layout->storage.u.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)
+ 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)
+ 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;
done:
/* Release allocated resources on failure */
- if((ret_value < 0) && orig_list
- && (orig_list != layout->storage.u.virt.list))
+ if(ret_value < 0)
if(H5D__virtual_reset_layout(layout) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset virtual layout")
@@ -392,6 +414,14 @@ H5D__virtual_reset_layout(H5O_layout_t *layout)
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));
+ /* Close access property lists */
+ if(layout->storage.u.virt.source_fapl >= 0)
+ if(H5I_dec_ref(layout->storage.u.virt.source_fapl) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "can't close source fapl")
+ if(layout->storage.u.virt.source_dapl >= 0)
+ if(H5I_dec_ref(layout->storage.u.virt.source_dapl) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "can't close source dapl")
+
/* The list is no longer initialized */
layout->storage.u.virt.init = FALSE;
@@ -470,13 +500,11 @@ H5D__virtual_open_source_dset(const H5D_t *vdset,
HDassert(source_dset->dset_name);
/* Get dapl and fapl from current (virtual dataset) location? VDSINC */
- /* Write code to check if these exist and return without opening dset
- * otherwise VDSINC */
/* Check if we need to open the source file */
if(HDstrcmp(source_dset->file_name, ".")) {
/* Open the source file */
- if(NULL == (src_file = H5F_open(source_dset->file_name, H5F_INTENT(vdset->oloc.file) & H5F_ACC_RDWR, H5P_FILE_CREATE_DEFAULT, H5P_FILE_ACCESS_DEFAULT, dxpl_id)))
+ if(NULL == (src_file = H5F_open(source_dset->file_name, H5F_INTENT(vdset->oloc.file) & H5F_ACC_RDWR, H5P_FILE_CREATE_DEFAULT, vdset->shared->layout.storage.u.virt.source_fapl, dxpl_id)))
H5E_clear_stack(NULL); //Quick hack until proper support for H5Fopen with missing file is implemented VDSINC HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENFILE, FAIL, "unable to open source file")
else
src_file_open = TRUE;
@@ -493,7 +521,7 @@ H5D__virtual_open_source_dset(const H5D_t *vdset,
HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "unable to get path for root group")
/* Open the source dataset */
- if(NULL == (source_dset->dset = H5D__open_name(&src_root_loc, source_dset->dset_name, H5P_DATASET_ACCESS_DEFAULT, dxpl_id)))
+ if(NULL == (source_dset->dset = H5D__open_name(&src_root_loc, source_dset->dset_name, vdset->shared->layout.storage.u.virt.source_dapl, dxpl_id)))
H5E_clear_stack(NULL); //Quick hack until proper support for H5Fopen with missing file is implemented VDSINC HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "unable to open dataset")
else
/* Patch the source selection if necessary */
@@ -1443,8 +1471,8 @@ done:
*-------------------------------------------------------------------------
*/
herr_t
-H5D__virtual_init(H5F_t H5_ATTR_UNUSED *f, hid_t H5_ATTR_UNUSED dxpl_id,
- const H5D_t *dset, hid_t dapl_id)
+H5D__virtual_init(H5F_t *f, hid_t H5_ATTR_UNUSED dxpl_id, const H5D_t *dset,
+ hid_t dapl_id)
{
H5O_storage_virtual_t *storage; /* Convenience pointer */
H5P_genplist_t *dapl; /* Data access property list object pointer */
@@ -1484,6 +1512,14 @@ H5D__virtual_init(H5F_t H5_ATTR_UNUSED *f, hid_t H5_ATTR_UNUSED dxpl_id,
else
storage->printf_gap = (hsize_t)0;
+ /* Retrieve VDS file FAPL to layout */
+ if((storage->source_fapl = H5F_get_access_plist(f, FALSE)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get fapl")
+
+ /* Copy DAPL to layout */
+ if((storage->source_dapl = H5P_copy_plist(dapl, FALSE)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't copy dapl")
+
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__virtual_init() */
@@ -1838,6 +1874,12 @@ H5D__virtual_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
storage = &io_info->dset->shared->layout.storage.u.virt;
HDassert((storage->view == H5D_VDS_FIRST_MISSING) || (storage->view == H5D_VDS_LAST_AVAILABLE));
+#ifdef H5_HAVE_PARALLEL
+ /* Parallel reads are not supported (yet) */
+ if(H5F_HAS_FEATURE(io_info->dset->oloc.file, H5FD_FEAT_HAS_MPI))
+ HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "parallel reads not supported on virtual datasets")
+#endif /* H5_HAVE_PARALLEL */
+
/* Prepare for I/O operation */
if(H5D__virtual_pre_io(io_info, storage, file_space, mem_space, &tot_nelmts) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCLIP, FAIL, "unable to prepare for I/O operation")
@@ -1863,47 +1905,56 @@ H5D__virtual_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
/* Fill unmapped part of buffer with fill value */
if(tot_nelmts != nelmts) {
- HDassert(tot_nelmts < nelmts);
+ H5D_fill_value_t fill_status; /* Fill value status */
- /* Start with fill space equal to memory space */
- if(NULL == (fill_space = H5S_copy(mem_space, FALSE, TRUE)))
- HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy memory selection")
+ HDassert(tot_nelmts < nelmts);
- /* Iterate over mappings */
- for(i = 0; i < storage->list_nused; i++)
- /* Check for "printf" source dataset resolution */
- if(storage->list[i].psfn_nsubs || storage->list[i].psdn_nsubs) {
- /* Iterate over sub-source dsets */
- for(j = storage->list[i].sub_dset_io_start;
- j < storage->list[i].sub_dset_io_end; j++)
- if(storage->list[i].sub_dset[j].projected_mem_space)
- if(H5S_select_subtract(fill_space, storage->list[i].sub_dset[j].projected_mem_space) < 0)
+ /* Check the fill value status */
+ if(H5P_is_fill_value_defined(&io_info->dset->shared->dcpl_cache.fill, &fill_status) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't tell if fill value defined")
+
+ /* Always write fill value to memory buffer unless it is undefined */
+ if(fill_status != H5D_FILL_VALUE_UNDEFINED) {
+ /* Start with fill space equal to memory space */
+ if(NULL == (fill_space = H5S_copy(mem_space, FALSE, TRUE)))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy memory selection")
+
+ /* Iterate over mappings */
+ for(i = 0; i < storage->list_nused; i++)
+ /* Check for "printf" source dataset resolution */
+ if(storage->list[i].psfn_nsubs || storage->list[i].psdn_nsubs) {
+ /* Iterate over sub-source dsets */
+ for(j = storage->list[i].sub_dset_io_start;
+ j < storage->list[i].sub_dset_io_end; j++)
+ if(storage->list[i].sub_dset[j].projected_mem_space)
+ if(H5S_select_subtract(fill_space, storage->list[i].sub_dset[j].projected_mem_space) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCLIP, FAIL, "unable to clip fill selection")
+ } /* end if */
+ else
+ if(storage->list[i].source_dset.projected_mem_space)
+ /* Subtract projected memory space from fill space */
+ if(H5S_select_subtract(fill_space, storage->list[i].source_dset.projected_mem_space) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCLIP, FAIL, "unable to clip fill selection")
- } /* end if */
- else
- if(storage->list[i].source_dset.projected_mem_space)
- /* Subtract projected memory space from fill space */
- if(H5S_select_subtract(fill_space, storage->list[i].source_dset.projected_mem_space) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTCLIP, FAIL, "unable to clip fill selection")
- /* Write fill values to memory buffer */
- if(H5D__fill(io_info->dset->shared->dcpl_cache.fill.buf, io_info->dset->shared->type, io_info->u.rbuf, type_info->mem_type, fill_space, io_info->dxpl_id) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "filling buf failed")
+ /* Write fill values to memory buffer */
+ if(H5D__fill(io_info->dset->shared->dcpl_cache.fill.buf, io_info->dset->shared->type, io_info->u.rbuf, type_info->mem_type, fill_space, io_info->dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "filling buf failed")
#ifndef NDEBUG
- /* Make sure the total number of elements written (including fill
- * values) == nelmts */
- {
- hssize_t select_nelmts; /* Number of elements in selection */
-
- /* Get number of elements in fill dataspace */
- if((select_nelmts = (hssize_t)H5S_GET_SELECT_NPOINTS(fill_space)) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "unable to get number of elements in selection")
-
- /* Verify number of elements is correct */
- HDassert((tot_nelmts + (hsize_t)select_nelmts) == nelmts);
- } /* end block */
+ /* Make sure the total number of elements written (including fill
+ * values) == nelmts */
+ {
+ hssize_t select_nelmts; /* Number of elements in selection */
+
+ /* Get number of elements in fill dataspace */
+ if((select_nelmts = (hssize_t)H5S_GET_SELECT_NPOINTS(fill_space)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "unable to get number of elements in selection")
+
+ /* Verify number of elements is correct */
+ HDassert((tot_nelmts + (hsize_t)select_nelmts) == nelmts);
+ } /* end block */
#endif /* NDEBUG */
+ } /* end if */
} /* end if */
done:
@@ -2012,6 +2063,12 @@ H5D__virtual_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
storage = &io_info->dset->shared->layout.storage.u.virt;
HDassert((storage->view == H5D_VDS_FIRST_MISSING) || (storage->view == H5D_VDS_LAST_AVAILABLE));
+#ifdef H5_HAVE_PARALLEL
+ /* Parallel writes are not supported (yet) */
+ if(H5F_HAS_FEATURE(io_info->dset->oloc.file, H5FD_FEAT_HAS_MPI))
+ HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "parallel writes not supported on virtual datasets")
+#endif /* H5_HAVE_PARALLEL */
+
/* Prepare for I/O operation */
if(H5D__virtual_pre_io(io_info, storage, file_space, mem_space, &tot_nelmts) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCLIP, FAIL, "unable to prepare for I/O operation")
diff --git a/src/H5Olayout.c b/src/H5Olayout.c
index 5a388fe..b72d41b 100644
--- a/src/H5Olayout.c
+++ b/src/H5Olayout.c
@@ -253,6 +253,9 @@ H5O_layout_decode(H5F_t *f, hid_t H5_ATTR_UNUSED dxpl_id, H5O_t H5_ATTR_UNUSED *
mesg->storage.u.virt.list_nalloc = 0;
mesg->storage.u.virt.view = H5D_VDS_ERROR;
mesg->storage.u.virt.printf_gap = HSIZE_UNDEF;
+ mesg->storage.u.virt.source_fapl = -1;
+ mesg->storage.u.virt.source_dapl = -1;
+ mesg->storage.u.virt.init = FALSE;
/* Decode heap block if it exists */
if(mesg->storage.u.virt.serial_list_hobjid.addr != HADDR_UNDEF) {
diff --git a/src/H5Oprivate.h b/src/H5Oprivate.h
index a9a5949..bb14d77 100644
--- a/src/H5Oprivate.h
+++ b/src/H5Oprivate.h
@@ -482,6 +482,8 @@ typedef struct H5O_storage_virtual_t {
hsize_t min_dims[H5S_MAX_RANK]; /* Minimum extent of VDS (maximum of all non-unlimited selection bounds) */
H5D_vds_view_t view; /* Method for calculating the extent of the virtual dataset with unlimited selections */
hsize_t printf_gap; /* Maximum number of sequential missing source datasets before terminating the search for more */
+ hid_t source_fapl; /* FAPL to use to open source files */
+ hid_t source_dapl; /* DAPL to use to open source datasets */
hbool_t init; /* Whether all information has been completely initialized */
} H5O_storage_virtual_t;
diff --git a/src/H5Pdcpl.c b/src/H5Pdcpl.c
index 1e2b91e..a900eb0 100644
--- a/src/H5Pdcpl.c
+++ b/src/H5Pdcpl.c
@@ -57,7 +57,7 @@
#define H5D_DEF_STORAGE_CONTIG_INIT {HADDR_UNDEF, (hsize_t)0}
#define H5D_DEF_STORAGE_CHUNK_INIT {H5D_CHUNK_IDX_BTREE, HADDR_UNDEF, NULL, {{HADDR_UNDEF, NULL}}}
#define H5D_DEF_LAYOUT_CHUNK_INIT {(unsigned)0, {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, (uint32_t)0, (hsize_t)0, {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}}
-#define H5D_DEF_STORAGE_VIRTUAL_INIT {{HADDR_UNDEF, 0}, 0, NULL, 0, {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, H5D_VDS_ERROR, HSIZE_UNDEF, FALSE}
+#define H5D_DEF_STORAGE_VIRTUAL_INIT {{HADDR_UNDEF, 0}, 0, NULL, 0, {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, H5D_VDS_ERROR, HSIZE_UNDEF, -1, -1, FALSE}
#ifdef H5_HAVE_C99_DESIGNATED_INITIALIZER
#define H5D_DEF_STORAGE_COMPACT {H5D_COMPACT, { .compact = H5D_DEF_STORAGE_COMPACT_INIT }}
#define H5D_DEF_STORAGE_CONTIG {H5D_CONTIGUOUS, { .contig = H5D_DEF_STORAGE_CONTIG_INIT }}
diff --git a/src/H5Shyper.c b/src/H5Shyper.c
index baeeec2..f0879b6 100644
--- a/src/H5Shyper.c
+++ b/src/H5Shyper.c
@@ -9638,7 +9638,7 @@ done:
REVISION LOG
--------------------------------------------------------------------------*/
herr_t
-H5S__hyper_subtract (H5S_t *space, H5S_t *subtract_space)
+H5S__hyper_subtract(H5S_t *space, H5S_t *subtract_space)
{
H5S_hyper_span_info_t *a_not_b = NULL; /* Span tree for hyperslab spans in old span tree and not in new span tree */
H5S_hyper_span_info_t *a_and_b = NULL; /* Span tree for hyperslab spans in both old and new span trees */
diff --git a/test/tselect.c b/test/tselect.c
index 7e142f3..a665cf2 100644
--- a/test/tselect.c
+++ b/test/tselect.c
@@ -13432,8 +13432,9 @@ test_hyper_unlim(void)
//VDSINC write test saving unlim selection to file as region reference
//VDSINC write tests for more general AND/NOTA/NOTB operations with
- //unlimited selections. Also return values from H5Sget_select_npoints and
- // H5Shyper_get_select_nblocks for unlimited selections
+ //unlimited selections. Also return values from H5Sget_select_npoints,
+ //H5Shyper_get_select_nblocks, and H5Sget_select_bounds for unlimited
+ //selections
/* Close the dataspace */
ret = H5Sclose(sid);
generated by cgit v0.12 at 2024-11-09 11:22:56 (GMT)