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authorJerome Soumagne <jsoumagne@hdfgroup.org>2015-09-25 00:11:50 (GMT)
committerJerome Soumagne <jsoumagne@hdfgroup.org>2016-11-29 23:42:31 (GMT)
commitdcc46c56f6cdbfebbf33fbf48d82931d5d0b60a2 (patch)
tree528c1d71d47d8daa263f3a5064b8cc79771b40ee /src
parent6ce8e4ba64133f8175fd6ec4fe039793a16751ed (diff)
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Use core VFD to store H5Q view
Update H5Q after H5R changes and use H5R_REGION Fix H5Q view write
Diffstat (limited to 'src')
-rw-r--r--src/H5Q.c122
1 files changed, 92 insertions, 30 deletions
diff --git a/src/H5Q.c b/src/H5Q.c
index 819d905..8f22ee3 100644
--- a/src/H5Q.c
+++ b/src/H5Q.c
@@ -35,6 +35,7 @@
#include "H5Dprivate.h" /* Datasets */
#include "H5Rprivate.h" /* References */
#include "H5Aprivate.h" /* Attributes */
+#include "H5FDcore.h" /* Core driver */
/****************/
@@ -163,6 +164,7 @@ struct { \
{H5Q_QUEUE_HEAD_INITIALIZER(view.reg_refs), H5Q_QUEUE_HEAD_INITIALIZER(view.obj_refs), H5Q_QUEUE_HEAD_INITIALIZER(view.attr_refs)}
#define H5Q_VIEW_REF_NTYPES 3 /* number of reference types */
+#define H5Q_VIEW_CORE_INCREMENT 1024 /* increment for core VFD */
//#define H5Q_DEBUG
@@ -195,12 +197,12 @@ typedef enum H5Q_match_type_t { /* The different kinds of native types we can ma
typedef struct H5Q_ref_entry_t H5Q_ref_entry_t;
struct H5Q_ref_entry_t {
+ H5R_type_t ref_type;
union {
- hdset_reg_ref_t reg;
+ hreg_ref_t reg;
hobj_ref_t obj;
hattr_ref_t attr;
} ref;
- H5R_type_t ref_type; /* TODO maybe not necessary */
H5Q_QUEUE_ENTRY(H5Q_ref_entry_t) entry;
};
@@ -391,14 +393,14 @@ H5Q_top_term_package(void)
FUNC_ENTER_NOAPI_NOINIT_NOERR
- if(H5Q_top_package_initialize_s) {
- if(H5I_nmembers(H5I_QUERY) > 0) {
+ if (H5Q_top_package_initialize_s) {
+ if (H5I_nmembers(H5I_QUERY) > 0) {
(void)H5I_clear_type(H5I_QUERY, FALSE, FALSE);
n++; /*H5I*/
} /* end if */
/* Mark closed */
- if(0 == n)
+ if (0 == n)
H5Q_top_package_initialize_s = FALSE;
} /* end if */
@@ -429,7 +431,7 @@ H5Q_term_package(void)
FUNC_ENTER_NOAPI_NOINIT_NOERR
- if(H5_PKG_INIT_VAR) {
+ if (H5_PKG_INIT_VAR) {
/* Sanity checks */
HDassert(0 == H5I_nmembers(H5I_QUERY));
@@ -437,7 +439,7 @@ H5Q_term_package(void)
n += (H5I_dec_type_ref(H5I_QUERY) > 0);
/* Mark closed */
- if(0 == n)
+ if (0 == n)
H5_PKG_INIT_VAR = FALSE;
} /* end if */
@@ -1435,11 +1437,12 @@ H5Qapply_atom(hid_t query_id, hbool_t *result, ...)
break;
}
- va_end(ap);
-
done:
if (native_type)
H5T_close(native_type);
+
+ va_end(ap);
+
FUNC_LEAVE_API(ret_value)
} /* end H5Qapply_atom() */
@@ -1889,6 +1892,11 @@ H5Q_apply(const H5G_loc_t *loc, hid_t loc_id, const H5Q_t *query, unsigned *resu
H5Q_view_t view = H5Q_VIEW_INITIALIZER(view); /* Resulting view */
H5G_t *ret_grp = NULL; /* New group created */
H5G_t *ret_value = NULL; /* Return value */
+ H5P_genclass_t *pclass = NULL;
+ unsigned flags;
+ hid_t fapl_id = FAIL;
+ H5F_t *new_file = NULL;
+ H5G_loc_t file_loc;
FUNC_ENTER_NOAPI_NOINIT
@@ -1899,10 +1907,6 @@ H5Q_apply(const H5G_loc_t *loc, hid_t loc_id, const H5Q_t *query, unsigned *resu
/* First check and optimize query */
/* TODO */
- /* Create the new group & get its ID */
- if (NULL == (ret_grp = H5G_create_anon(loc, H5P_GROUP_CREATE_DEFAULT, H5P_GROUP_ACCESS_DEFAULT)))
- HGOTO_ERROR(H5E_SYM, H5E_CANTINIT, NULL, "unable to create group");
-
/* Create new view and init args */
args.query = query;
args.result = result;
@@ -1919,6 +1923,31 @@ H5Q_apply(const H5G_loc_t *loc, hid_t loc_id, const H5Q_t *query, unsigned *resu
if (!H5Q_QUEUE_EMPTY(&view.attr_refs))
H5Q_LOG_DEBUG("Number of attr refs: %zu\n", view.attr_refs.n_elem);
+ /* Get property list class */
+ if (NULL == (pclass = (H5P_genclass_t *)H5I_object_verify(H5P_FILE_ACCESS, H5I_GENPROP_CLS)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a property list class");
+
+ /* Create the new property list */
+ if (FAIL == (fapl_id = H5P_create_id(pclass, TRUE)))
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTCREATE, NULL, "unable to create property list");
+
+ /* Use the core VFD to store the view */
+ if (FAIL == H5Pset_fapl_core(fapl_id, H5Q_VIEW_CORE_INCREMENT, FALSE))
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, NULL, "unable to set property list to core VFD");
+
+ /* Create a new file or truncate an existing file. */
+ flags = H5F_ACC_EXCL | H5F_ACC_RDWR | H5F_ACC_CREAT;
+ if (NULL == (new_file = H5F_open("view", flags, H5P_FILE_CREATE_DEFAULT, fapl_id, H5AC_dxpl_id)))
+ HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to create file");
+
+ /* Construct a group location for root group of the file */
+ if (FAIL == H5G_root_loc(new_file, &file_loc))
+ HGOTO_ERROR(H5E_SYM, H5E_BADVALUE, NULL, "unable to create location for file")
+
+ /* Create the new group & get its ID */
+ if (NULL == (ret_grp = H5G_create_anon(&file_loc, H5P_GROUP_CREATE_DEFAULT, H5P_GROUP_ACCESS_DEFAULT)))
+ HGOTO_ERROR(H5E_SYM, H5E_CANTINIT, NULL, "unable to create group");
+
/* Write view */
if (FAIL == H5Q__view_write(ret_grp, &view))
HGOTO_ERROR(H5E_QUERY, H5E_WRITEERROR, NULL, "can't write view");
@@ -1942,9 +1971,19 @@ done:
/* Cleanup on failure */
if (NULL == ret_value)
if (ret_grp && (FAIL == H5G_close(ret_grp)))
- HDONE_ERROR(H5E_SYM, H5E_CLOSEERROR, NULL, "unable to release group")
+ HDONE_ERROR(H5E_SYM, H5E_CLOSEERROR, NULL, "unable to release group");
+ /* Close the property list */
+ if ((fapl_id != FAIL) && (H5I_dec_app_ref(fapl_id) < 0))
+ HDONE_ERROR(H5E_PLIST, H5E_CANTFREE, NULL, "can't close");
+
+ /* Attempt to close the file/mount hierarchy */
+ if (new_file && (FAIL == H5F_try_close(new_file)))
+ HDONE_ERROR(H5E_FILE, H5E_CANTCLOSEFILE, NULL, "can't close file")
+
+ /* Free the view */
H5Q__view_free(&view);
+
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5Q_apply() */
@@ -2108,9 +2147,9 @@ H5Q__apply_object_link(H5G_loc_t *loc, const char *name, const H5O_info_t *oinfo
H5Q_LOG_DEBUG("Match link name: %s (%s)\n", link_name, name);
/* Keep object reference */
- if (FAIL == H5R_create(&ref_buf, loc, name, H5AC_dxpl_id, H5R_OBJECT))
+ if (FAIL == H5R_create(&ref_buf, H5R_OBJECT, loc, name, H5AC_dxpl_id))
HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't create region reference");
- if (FAIL == H5Q__view_append(args->view, H5R_DATASET_REGION, &ref_buf))
+ if (FAIL == H5Q__view_append(args->view, H5R_OBJECT, &ref_buf))
HGOTO_ERROR(H5E_QUERY, H5E_CANTAPPEND, FAIL, "can't append region reference to view");
done:
@@ -2130,7 +2169,7 @@ static herr_t
H5Q__apply_object_data(H5G_loc_t *loc, const char *name, const H5O_info_t *oinfo,
void *udata)
{
- hdset_reg_ref_t ref_buf;
+ hreg_ref_t ref_buf = H5R_REG_REF_INITIALIZER;
H5Q_apply_arg_t *args = (H5Q_apply_arg_t *) udata;
hid_t obj_id = FAIL;
H5S_t *dataspace = NULL;
@@ -2169,9 +2208,15 @@ H5Q__apply_object_data(H5G_loc_t *loc, const char *name, const H5O_info_t *oinfo
*(args->result) = H5Q_REF_REG;
/* Keep dataset region reference */
- if (FAIL == H5R_create(&ref_buf, loc, name, H5AC_dxpl_id, H5R_DATASET_REGION, dataspace))
+ if (FAIL == H5R_create(&ref_buf, H5R_REGION, loc, name, H5AC_dxpl_id, dataspace))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't get buffer size for region reference");
+ if (NULL == (ref_buf.buf = H5MM_malloc(ref_buf.buf_size)))
+ HGOTO_ERROR(H5E_QUERY, H5E_NOSPACE, FAIL, "can't allocate region reference buffer");
+ if (FAIL == H5R_create(&ref_buf, H5R_REGION, loc, name, H5AC_dxpl_id, dataspace))
HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't create region reference");
- if (FAIL == H5Q__view_append(args->view, H5R_DATASET_REGION, &ref_buf))
+
+ H5Q_LOG_DEBUG("Region reference size: %zu\n", ref_buf.buf_size);
+ if (FAIL == H5Q__view_append(args->view, H5R_REGION, &ref_buf))
HGOTO_ERROR(H5E_QUERY, H5E_CANTAPPEND, FAIL, "can't append region reference to view");
done:
@@ -2322,7 +2367,7 @@ H5Q__apply_object_attr_name(H5A_t *attr, void *udata)
H5Q_LOG_DEBUG("Match attribute name: %s\n", (const char *) name);
/* Keep object reference */
- if (FAIL == H5R_create(&ref_buf, args->loc, args->loc_name, H5AC_dxpl_id, H5R_ATTR, (const char *) name))
+ if (FAIL == H5R_create(&ref_buf, H5R_ATTR, args->loc, args->loc_name, H5AC_dxpl_id, (const char *) name))
HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't create region reference");
if (FAIL == H5Q__view_append(args->apply_args->view, H5R_ATTR, &ref_buf))
HGOTO_ERROR(H5E_QUERY, H5E_CANTAPPEND, FAIL, "can't append region reference to view");
@@ -2417,7 +2462,7 @@ H5Q__apply_object_attr_value(H5A_t *iter_attr, void *udata)
H5Q_LOG_DEBUG("Match value of attribute name: %s\n", (const char *) name);
/* Keep object reference */
- if (FAIL == H5R_create(&ref_buf, args->loc, args->loc_name, H5AC_dxpl_id, H5R_ATTR, (const char *) name))
+ if (FAIL == H5R_create(&ref_buf, H5R_ATTR, args->loc, args->loc_name, H5AC_dxpl_id, (const char *) name))
HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't create region reference");
if (FAIL == H5Q__view_append(args->apply_args->view, H5R_ATTR, &ref_buf))
HGOTO_ERROR(H5E_QUERY, H5E_CANTAPPEND, FAIL, "can't append region reference to view");
@@ -2490,18 +2535,19 @@ H5Q__view_append(H5Q_view_t *view, H5R_type_t ref_type, void *ref)
ref_entry->ref_type = ref_type;
switch (ref_type) {
- case H5R_ATTR:
- HDmemcpy(&ref_entry->ref.attr, ref, sizeof(hattr_ref_t));
- H5Q_QUEUE_INSERT_TAIL(&view->attr_refs, ref_entry, entry);
- break;
- case H5R_DATASET_REGION:
- HDmemcpy(&ref_entry->ref.reg, ref, sizeof(hdset_reg_ref_t));
+ case H5R_REGION:
+ HDmemcpy(&ref_entry->ref.reg, ref, sizeof(hreg_ref_t));
H5Q_QUEUE_INSERT_TAIL(&view->reg_refs, ref_entry, entry);
break;
case H5R_OBJECT:
HDmemcpy(&ref_entry->ref.obj, ref, sizeof(hobj_ref_t));
H5Q_QUEUE_INSERT_TAIL(&view->obj_refs, ref_entry, entry);
break;
+ case H5R_ATTR:
+ HDmemcpy(&ref_entry->ref.attr, ref, sizeof(hattr_ref_t));
+ H5Q_QUEUE_INSERT_TAIL(&view->attr_refs, ref_entry, entry);
+ break;
+ case H5R_DATASET_REGION:
case H5R_BADTYPE:
case H5R_MAXTYPE:
default:
@@ -2601,12 +2647,13 @@ H5Q__view_write(H5G_t *grp, H5Q_view_t *view)
{
H5G_loc_t loc;
H5D_t *dset = NULL;
+ H5S_t *mem_space = NULL;
H5S_t *space = NULL;
H5Q_ref_head_t *refs[H5Q_VIEW_REF_NTYPES] = { &view->reg_refs, &view->obj_refs,
&view->attr_refs };
const char *dset_name[H5Q_VIEW_REF_NTYPES] = { H5Q_VIEW_REF_REG_NAME,
H5Q_VIEW_REF_OBJ_NAME, H5Q_VIEW_REF_ATTR_NAME };
- hid_t ref_types[H5Q_VIEW_REF_NTYPES] = { H5T_STD_REF_DSETREG,
+ hid_t ref_types[H5Q_VIEW_REF_NTYPES] = { H5T_STD_REF_REG,
H5T_STD_REF_OBJ, H5T_STD_REF_ATTR };
herr_t ret_value = SUCCEED; /* Return value */
int i;
@@ -2619,10 +2666,11 @@ H5Q__view_write(H5G_t *grp, H5Q_view_t *view)
loc.oloc = H5G_oloc(grp);
loc.path = H5G_nameof(grp);
- /* Write region references if any */
+ /* Iterate over reference types and write references if any */
for (i = 0; i < H5Q_VIEW_REF_NTYPES; i++) {
H5Q_ref_entry_t *ref_entry = NULL;
hsize_t n_elem = refs[i]->n_elem;
+ hsize_t start = 0;
if (!n_elem)
break;
@@ -2637,10 +2685,23 @@ H5Q__view_write(H5G_t *grp, H5Q_view_t *view)
H5P_DATASET_ACCESS_DEFAULT, H5AC_dxpl_id)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "unable to create dataset");
+ /* Iterate over reference entries in view */
H5Q_QUEUE_FOREACH(ref_entry, refs[i], entry) {
- if (FAIL == H5D_write(dset, FALSE, ref_types[i], NULL, space,
+ hsize_t count = 1;
+
+ if (NULL == (mem_space = H5S_create_simple(1, &count, NULL)))
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "unable to create dataspace");
+ if (FAIL == H5S_select_hyperslab(space, H5S_SELECT_SET, &start, NULL, &count, NULL))
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to set hyperslab selection")
+ if (FAIL == H5D_write(dset, FALSE, ref_types[i], mem_space, space,
H5P_DATASET_XFER_DEFAULT, &ref_entry->ref))
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to write dataset");
+ if (FAIL == H5S_close(mem_space))
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCLOSEOBJ, FAIL, "unable to close dataspace");
+ mem_space = NULL;
+
+ /* Increment reference position in file */
+ start++;
}
if (FAIL == H5D_close(dset))
@@ -2654,6 +2715,7 @@ H5Q__view_write(H5G_t *grp, H5Q_view_t *view)
done:
if (dset) H5D_close(dset);
if (space) H5S_close(space);
+ if (mem_space) H5S_close(mem_space);
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5Q__view_write */