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authorVailin Choi <vchoi@hdfgroup.org>2010-09-13 21:57:00 (GMT)
committerVailin Choi <vchoi@hdfgroup.org>2010-09-13 21:57:00 (GMT)
commitae7d45d612db414c8f9f8d21d732974ab33bb651 (patch)
tree989c7c5a6d48cb81249bac73602e6a3b53ba2abb
parentc348f9405e134e722edfb0c26133c471c926c64d (diff)
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[svn-r19378] Modifications to using v2 B-tree as index for chunked datasets with >1 unlimited dimensions.
h5committested.
-rw-r--r--src/H5B2.c8
-rw-r--r--src/H5B2dbg.c30
-rw-r--r--src/H5B2pkg.h6
-rw-r--r--src/H5B2private.h16
-rw-r--r--src/H5B2test.c1
-rw-r--r--src/H5Dbtree2.c1769
-rw-r--r--src/H5Dchunk.c94
-rw-r--r--src/H5Dint.c7
-rw-r--r--src/H5Dlayout.c80
-rw-r--r--src/H5Dpkg.h31
-rw-r--r--src/H5Dpublic.h3
-rw-r--r--src/H5HFbtree2.c1
-rw-r--r--src/H5Olayout.c28
-rw-r--r--src/H5Oprivate.h18
-rw-r--r--src/H5Ostorage.c18
-rwxr-xr-xsrc/H5SMbtree2.c1
-rwxr-xr-xsrc/Makefile.am2
-rw-r--r--src/Makefile.in19
-rw-r--r--test/dsets.c618
-rwxr-xr-xtest/objcopy.c3
-rw-r--r--test/set_extent.c3
-rw-r--r--tools/h5dump/h5dumpgentest.c15
-rw-r--r--tools/misc/h5debug.c58
-rw-r--r--tools/testfiles/tdset_idx.h5bin6760 -> 10562 bytes
24 files changed, 2642 insertions, 187 deletions
diff --git a/src/H5B2.c b/src/H5B2.c
index 0ed90a4..d31f0cf 100644
--- a/src/H5B2.c
+++ b/src/H5B2.c
@@ -82,6 +82,8 @@ extern const H5B2_class_t H5G_BT2_CORDER[1];
extern const H5B2_class_t H5SM_INDEX[1];
extern const H5B2_class_t H5A_BT2_NAME[1];
extern const H5B2_class_t H5A_BT2_CORDER[1];
+extern const H5B2_class_t H5D_BT2[1];
+extern const H5B2_class_t H5D_BT2_FILT[1];
const H5B2_class_t *const H5B2_client_class_g[] = {
H5B2_TEST, /* 0 - H5B2_TEST_ID */
@@ -90,10 +92,12 @@ const H5B2_class_t *const H5B2_client_class_g[] = {
H5HF_HUGE_BT2_DIR, /* 3 - H5B2_FHEAP_HUGE_DIR_ID */
H5HF_HUGE_BT2_FILT_DIR, /* 4 - H5B2_FHEAP_HUGE_FILT_DIR_ID */
H5G_BT2_NAME, /* 5 - H5B2_GRP_DENSE_NAME_ID */
- H5G_BT2_CORDER, /* 6 - H5B2_GRP_DENSE_CORDER_ID */
+ H5G_BT2_CORDER, /* 6 - H5B2_GRP_DENSE_CORDER_ID */
H5SM_INDEX, /* 7 - H5B2_SOHM_INDEX_ID */
H5A_BT2_NAME, /* 8 - H5B2_ATTR_DENSE_NAME_ID */
- H5A_BT2_CORDER, /* 9 - H5B2_ATTR_DENSE_CORDER_ID */
+ H5A_BT2_CORDER, /* 9 - H5B2_ATTR_DENSE_CORDER_ID */
+ H5D_BT2, /* 10 - H5B2_CDSET_ID */
+ H5D_BT2_FILT /* 11 - H5B2_CDSET_FILT_ID */
};
diff --git a/src/H5B2dbg.c b/src/H5B2dbg.c
index cf7301d..1199edf 100644
--- a/src/H5B2dbg.c
+++ b/src/H5B2dbg.c
@@ -84,11 +84,14 @@
* koziol@ncsa.uiuc.edu
* Feb 2 2005
*
- *-------------------------------------------------------------------------
+ * Modifications:
+ * Vailin Choi; August 2010
+ * Created debugging context so that the header can be loaded correctly.
+ *--------------------------------------------------------------------------
*/
herr_t
H5B2_hdr_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE *stream, int indent, int fwidth,
- const H5B2_class_t *type)
+ const H5B2_class_t *type, haddr_t obj_addr)
{
H5B2_hdr_t *hdr = NULL; /* B-tree header info */
void *dbg_ctx = NULL; /* v2 B-tree debugging context */
@@ -104,6 +107,7 @@ H5B2_hdr_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE *stream, int indent,
*/
HDassert(f);
HDassert(H5F_addr_defined(addr));
+ HDassert(H5F_addr_defined(obj_addr));
HDassert(stream);
HDassert(indent >= 0);
HDassert(fwidth >= 0);
@@ -114,7 +118,7 @@ H5B2_hdr_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE *stream, int indent,
/* Check for debugging context callback available */
if(type->crt_dbg_ctx) {
/* Create debugging context */
- if(NULL == (dbg_ctx = (type->crt_dbg_ctx)(f, dxpl_id, addr)))
+ if(NULL == (dbg_ctx = (type->crt_dbg_ctx)(f, dxpl_id, obj_addr)))
HGOTO_ERROR(H5E_BTREE, H5E_CANTGET, FAIL, "unable to create v2 B-tree debugging context")
} /* end if */
@@ -198,11 +202,14 @@ done:
* koziol@ncsa.uiuc.edu
* Feb 4 2005
*
+ * Modifications:
+ * Vailin Choi; August 2010
+ * Created debugging context so that the header can be loaded correctly.
*-------------------------------------------------------------------------
*/
herr_t
H5B2_int_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE *stream, int indent, int fwidth,
- const H5B2_class_t *type, haddr_t hdr_addr, unsigned nrec, unsigned depth)
+ const H5B2_class_t *type, haddr_t hdr_addr, unsigned nrec, unsigned depth, haddr_t obj_addr)
{
H5B2_hdr_t *hdr = NULL; /* B-tree header */
H5B2_internal_t *internal = NULL; /* B-tree internal node */
@@ -226,12 +233,13 @@ H5B2_int_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE *stream, int indent,
HDassert((type->crt_dbg_ctx && type->dst_dbg_ctx) ||
(NULL == type->crt_dbg_ctx && NULL == type->dst_dbg_ctx));
HDassert(H5F_addr_defined(hdr_addr));
+ HDassert(H5F_addr_defined(obj_addr));
HDassert(nrec > 0);
/* Check for debugging context callback available */
if(type->crt_dbg_ctx) {
/* Create debugging context */
- if(NULL == (dbg_ctx = (type->crt_dbg_ctx)(f, dxpl_id, addr)))
+ if(NULL == (dbg_ctx = (type->crt_dbg_ctx)(f, dxpl_id, obj_addr)))
HGOTO_ERROR(H5E_BTREE, H5E_CANTGET, FAIL, "unable to create v2 B-tree debugging context")
} /* end if */
@@ -292,7 +300,7 @@ H5B2_int_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE *stream, int indent,
temp_str);
HDassert(H5B2_INT_NREC(internal, hdr, u));
(void)(type->debug)(stream, f, dxpl_id, indent + 6, MAX (0, fwidth-6),
- H5B2_INT_NREC(internal, hdr, u), NULL);
+ H5B2_INT_NREC(internal, hdr, u), dbg_ctx);
} /* end for */
/* Print final node pointer */
@@ -329,11 +337,14 @@ done:
* koziol@ncsa.uiuc.edu
* Feb 7 2005
*
+ * Modifications:
+ * Vailin Choi; August 2010
+ * Created debugging context so that the header can be loaded correctly.
*-------------------------------------------------------------------------
*/
herr_t
H5B2_leaf_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE *stream, int indent, int fwidth,
- const H5B2_class_t *type, haddr_t hdr_addr, unsigned nrec)
+ const H5B2_class_t *type, haddr_t hdr_addr, unsigned nrec, haddr_t obj_addr)
{
H5B2_hdr_t *hdr = NULL; /* B-tree header */
H5B2_leaf_t *leaf = NULL; /* B-tree leaf node */
@@ -357,12 +368,13 @@ H5B2_leaf_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE *stream, int indent,
HDassert((type->crt_dbg_ctx && type->dst_dbg_ctx) ||
(NULL == type->crt_dbg_ctx && NULL == type->dst_dbg_ctx));
HDassert(H5F_addr_defined(hdr_addr));
+ HDassert(H5F_addr_defined(obj_addr));
HDassert(nrec > 0);
/* Check for debugging context callback available */
if(type->crt_dbg_ctx) {
/* Create debugging context */
- if(NULL == (dbg_ctx = (type->crt_dbg_ctx)(f, dxpl_id, addr)))
+ if(NULL == (dbg_ctx = (type->crt_dbg_ctx)(f, dxpl_id, obj_addr)))
HGOTO_ERROR(H5E_BTREE, H5E_CANTGET, FAIL, "unable to create v2 B-tree debugging context")
} /* end if */
@@ -412,7 +424,7 @@ H5B2_leaf_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE *stream, int indent,
temp_str);
HDassert(H5B2_LEAF_NREC(leaf, hdr, u));
(void)(type->debug)(stream, f, dxpl_id, indent + 6, MAX (0, fwidth-6),
- H5B2_LEAF_NREC(leaf, hdr, u), NULL);
+ H5B2_LEAF_NREC(leaf, hdr, u), dbg_ctx);
} /* end for */
done:
diff --git a/src/H5B2pkg.h b/src/H5B2pkg.h
index 543fa3f..b820853 100644
--- a/src/H5B2pkg.h
+++ b/src/H5B2pkg.h
@@ -346,13 +346,13 @@ H5_DLL herr_t H5B2_delete_node(H5B2_hdr_t *hdr, hid_t dxpl_id, unsigned depth,
/* Debugging routines for dumping file structures */
H5_DLL herr_t H5B2_hdr_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr,
- FILE *stream, int indent, int fwidth, const H5B2_class_t *type);
+ FILE *stream, int indent, int fwidth, const H5B2_class_t *type, haddr_t obj_addr);
H5_DLL herr_t H5B2_int_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr,
FILE *stream, int indent, int fwidth, const H5B2_class_t *type,
- haddr_t hdr_addr, unsigned nrec, unsigned depth);
+ haddr_t hdr_addr, unsigned nrec, unsigned depth, haddr_t obj_addr);
H5_DLL herr_t H5B2_leaf_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr,
FILE *stream, int indent, int fwidth, const H5B2_class_t *type,
- haddr_t hdr_addr, unsigned nrec);
+ haddr_t hdr_addr, unsigned nrec, haddr_t obj_addr);
/* Testing routines */
#ifdef H5B2_TESTING
diff --git a/src/H5B2private.h b/src/H5B2private.h
index 4880ab2..8ec9954 100644
--- a/src/H5B2private.h
+++ b/src/H5B2private.h
@@ -54,6 +54,8 @@ typedef enum H5B2_subid_t {
H5B2_SOHM_INDEX_ID, /* B-tree is an index for shared object header messages */
H5B2_ATTR_DENSE_NAME_ID, /* B-tree is for indexing 'name' field for "dense" attribute storage on objects */
H5B2_ATTR_DENSE_CORDER_ID, /* B-tree is for indexing 'creation order' field for "dense" attribute storage on objects */
+ H5B2_CDSET_ID, /* B-tree is for non-filtered chunked dataset storage w/ >1 unlim dims */
+ H5B2_CDSET_FILT_ID, /* B-tree is for filtered chunked dataset storage w/ >1 unlim dims */
H5B2_NUM_BTREE_ID /* Number of B-tree IDs (must be last) */
} H5B2_subid_t;
@@ -88,13 +90,13 @@ struct H5B2_class_t {
/* Extensible array client callback methods */
void *(*crt_context)(void *udata); /* Create context for other client callbacks */
herr_t (*dst_context)(void *ctx); /* Destroy client callback context */
- herr_t (*store)(void *nrecord, const void *udata); /* Store application record in native record table */
- herr_t (*compare)(const void *rec1, const void *rec2); /* Compare two native records */
- herr_t (*encode)(uint8_t *raw, const void *record, void *ctx); /* Encode record from native form to disk storage form */
- herr_t (*decode)(const uint8_t *raw, void *record, void *ctx); /* Decode record from disk storage form to native form */
- herr_t (*debug)(FILE *stream, const H5F_t *f, hid_t dxpl_id, /* Print a record for debugging */
- int indent, int fwidth, const void *record, const void *udata);
- void *(*crt_dbg_ctx)(H5F_t *f, hid_t dxpl_id, haddr_t obj_addr); /* Create debugging context */
+ herr_t (*store)(void *nrecord, const void *udata); /* Store application record in native record table */
+ herr_t (*compare)(const void *rec1, const void *rec2); /* Compare two native records */
+ herr_t (*encode)(uint8_t *raw, const void *record, void *ctx); /* Encode record from native form to disk storage form */
+ herr_t (*decode)(const uint8_t *raw, void *record, void *ctx); /* Decode record from disk storage form to native form */
+ herr_t (*debug)(FILE *stream, const H5F_t *f, hid_t dxpl_id, /* Print a record for debugging */
+ int indent, int fwidth, const void *record, const void *ctx);
+ void *(*crt_dbg_ctx)(H5F_t *f, hid_t dxpl_id, haddr_t obj_addr); /* Create debugging context */
herr_t (*dst_dbg_ctx)(void *dbg_ctx); /* Destroy debugging context */
};
diff --git a/src/H5B2test.c b/src/H5B2test.c
index a0508fe..8076343 100644
--- a/src/H5B2test.c
+++ b/src/H5B2test.c
@@ -333,7 +333,6 @@ H5B2_test_crt_dbg_context(H5F_t *f, hid_t UNUSED dxpl_id, haddr_t UNUSED addr)
/* Sanity check */
HDassert(f);
- HDassert(H5F_addr_defined(addr));
/* Allocate callback context */
if(NULL == (ctx = H5FL_MALLOC(H5B2_test_ctx_t)))
diff --git a/src/H5Dbtree2.c b/src/H5Dbtree2.c
new file mode 100644
index 0000000..1b014e5
--- /dev/null
+++ b/src/H5Dbtree2.c
@@ -0,0 +1,1769 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+
+ * Copyright by The HDF Group. *
+ * Copyright by the Board of Trustees of the University of Illinois. *
+ * All rights reserved. *
+ * *
+ * This file is part of HDF5. The full HDF5 copyright notice, including *
+ * terms governing use, modification, and redistribution, is contained in *
+ * the files COPYING and Copyright.html. COPYING can be found at the root *
+ * of the source code distribution tree; Copyright.html can be found at the *
+ * root level of an installed copy of the electronic HDF5 document set and *
+ * is linked from the top-level documents page. It can also be found at *
+ * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
+ * access to either file, you may request a copy from help@hdfgroup.org. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*
+ *
+ * Purpose: v2 B-tree indexing for chunked datasets with > 1 unlimited dimensions.
+ * Each dataset chunk in the b-tree is identified by its dimensional offset.
+ *
+ */
+
+/****************/
+/* Module Setup */
+/****************/
+
+#define H5D_PACKAGE /*suppress error about including H5Dpkg */
+
+
+/***********/
+/* Headers */
+/***********/
+#include "H5private.h" /* Generic Functions */
+#include "H5Dpkg.h" /* Datasets */
+#include "H5FLprivate.h" /* Free Lists */
+#include "H5MFprivate.h" /* File space management */
+#include "H5Vprivate.h" /* Vector and array functions */
+
+/****************/
+/* Local Macros */
+/****************/
+
+/******************/
+/* Local Typedefs */
+/******************/
+/* Typedef for non-filtered object's records in v2 B-tree */
+typedef struct H5D_bt2_rec_t {
+ haddr_t addr; /* Address of the chunk in the file */
+ hsize_t offset[H5O_LAYOUT_NDIMS]; /* logical offset to start*/
+} H5D_bt2_rec_t;
+
+/* Typedef for filtered object's records in v2 B-tree */
+typedef struct H5D_bt2_filt_rec_t {
+ haddr_t addr; /* Address of the filtered object in the file */
+ uint32_t nbytes; /* Length of the filtered object in the file */
+ uint32_t filter_mask; /* I/O pipeline filter mask for filtered object in the file */
+ hsize_t offset[H5O_LAYOUT_NDIMS]; /* logical offset to start*/
+} H5D_bt2_filt_rec_t;
+
+/* User data for creating callback context */
+typedef struct H5D_bt2_ctx_ud_t {
+ const H5F_t *f; /* Pointer to file info */
+ uint32_t chunk_size; /* Size of chunk (bytes; for filtered object) */
+ unsigned ndims; /* Number of dimensions */
+} H5D_bt2_ctx_ud_t;
+
+/* The callback context */
+typedef struct H5D_bt2_ctx_t {
+ size_t sizeof_addr; /* Size of file addresses in the file (bytes) */
+ size_t chunk_size_len; /* Size of chunk sizes in the file (bytes) */
+ unsigned ndims; /* Number of dimensions */
+} H5D_bt2_ctx_t;
+
+/* User data for the chunk's removal callback routine */
+typedef struct H5D_bt2_remove_ud_t {
+ H5F_t *f; /* File pointer for operation */
+ hid_t dxpl_id; /* DXPL ID for operation */
+ uint32_t unfilt_size; /* Size of unfiltered chunk in bytes */
+} H5D_bt2_remove_ud_t;
+
+/* Callback info for iteration over chunks in v2 B-tree */
+typedef struct H5D_bt2_it_ud_t {
+ H5D_chunk_common_ud_t common; /* Common info for v2 B-tree user data (must be first) */
+ H5D_chunk_rec_t chunk_rec; /* Generic chunk record for callback */
+ hbool_t filtered; /* The chunk is filtered or not */
+ H5D_chunk_cb_func_t cb; /* Callback routine for the chunk */
+ void *udata; /* User data for the chunk's callback routine */
+} H5D_bt2_it_ud_t;
+
+/* User data for compare callback */
+typedef struct H5D_bt2_find_ud_t {
+ void *rec; /* The record to search for */
+ unsigned ndims; /* Number of dimensions for the chunked dataset */
+} H5D_bt2_find_ud_t;
+
+/********************/
+/* Local Prototypes */
+/********************/
+
+/* v2 B-tree class for indexing non-filtered chunked datasets */
+static void *H5D_bt2_crt_context(void *udata);
+static herr_t H5D_bt2_dst_context(void *ctx);
+static void *H5D_bt2_crt_dbg_context(H5F_t *f, hid_t dxpl_id, haddr_t obj_addr);
+static herr_t H5D_bt2_dst_dbg_context(void *_u_ctx);
+
+static herr_t H5D_bt2_store(void *native, const void *udata);
+static herr_t H5D_bt2_compare(const void *rec1, const void *rec2);
+static herr_t H5D_bt2_encode(uint8_t *raw, const void *native, void *ctx);
+static herr_t H5D_bt2_decode(const uint8_t *raw, void *native, void *ctx);
+static herr_t H5D_bt2_debug(FILE *stream, const H5F_t *f, hid_t dxpl_id,
+ int indent, int fwidth, const void *record, const void *u_ctx);
+
+/* v2 B-tree class for indexing filtered chunked datasets */
+static herr_t H5D_bt2_filt_store(void *native, const void *udata);
+static herr_t H5D_bt2_filt_compare(const void *rec1, const void *rec2);
+static herr_t H5D_bt2_filt_encode(uint8_t *raw, const void *native, void *ctx);
+static herr_t H5D_bt2_filt_decode(const uint8_t *raw, void *native, void *ctx);
+static herr_t H5D_bt2_filt_debug(FILE *stream, const H5F_t *f, hid_t dxpl_id,
+ int indent, int fwidth, const void *record, const void *u_ctx);
+
+/* Helper routine */
+static herr_t H5D_bt2_idx_open(const H5D_chk_idx_info_t *idx_info);
+
+/* Callback for H5B2_iterate() which is called in H5D_bt2_idx_iterate() */
+static int H5D_bt2_idx_iterate_cb(const void *_record, void *_udata);
+
+/* Callbacks for H5B2_find() which are called in H5D_bt2_idx_get_addr() and H5D_bt2_idx_insert() */
+static herr_t H5D_bt2_found_cb(const void *nrecord, void *op_data);
+static herr_t H5D_bt2_filt_found_cb(const void *nrecord, void *op_data);
+
+/*
+ * Callbacks for H5B2_remove() and H5B2_delete() which are called
+ * in H5D_bt2_idx_remove() and H5D_bt2_idx_delete().
+ */
+static herr_t H5D_bt2_remove_cb(const void *nrecord, void *_udata);
+static herr_t H5D_bt2_filt_remove_cb(const void *nrecord, void *_udata);
+
+/* Callback for H5B2_modify() which is called in H5D_bt2_idx_insert() */
+static herr_t H5D_bt2_mod_filt_cb(void *_record, void *_op_data, hbool_t *changed);
+
+/* Chunked dataset I/O ops for v2 B-tree indexing */
+static herr_t H5D_bt2_idx_create(const H5D_chk_idx_info_t *idx_info);
+static hbool_t H5D_bt2_idx_is_space_alloc(const H5O_storage_chunk_t *storage);
+static herr_t H5D_bt2_idx_insert(const H5D_chk_idx_info_t *idx_info,
+ H5D_chunk_ud_t *udata);
+static herr_t H5D_bt2_idx_get_addr(const H5D_chk_idx_info_t *idx_info,
+ H5D_chunk_ud_t *udata);
+static int H5D_bt2_idx_iterate(const H5D_chk_idx_info_t *idx_info,
+ H5D_chunk_cb_func_t chunk_cb, void *chunk_udata);
+static herr_t H5D_bt2_idx_remove(const H5D_chk_idx_info_t *idx_info,
+ H5D_chunk_common_ud_t *udata);
+static herr_t H5D_bt2_idx_delete(const H5D_chk_idx_info_t *idx_info);
+static herr_t H5D_bt2_idx_copy_setup(const H5D_chk_idx_info_t *idx_info_src,
+ const H5D_chk_idx_info_t *idx_info_dst);
+static herr_t H5D_bt2_idx_copy_shutdown(H5O_storage_chunk_t *storage_src,
+ H5O_storage_chunk_t *storage_dst, hid_t dxpl_id);
+static herr_t H5D_bt2_idx_size(const H5D_chk_idx_info_t *idx_info, hsize_t *size);
+static herr_t H5D_bt2_idx_reset(H5O_storage_chunk_t *storage, hbool_t reset_addr);
+static herr_t H5D_bt2_idx_dump(const H5O_storage_chunk_t *storage,
+ FILE *stream);
+static herr_t H5D_bt2_idx_dest(const H5D_chk_idx_info_t *idx_info);
+
+/*********************/
+/* Package Variables */
+/*********************/
+
+/* Chunked dataset I/O ops for v2 B-tree indexing */
+const H5D_chunk_ops_t H5D_COPS_BT2[1] = {{
+ FALSE,
+ NULL,
+ H5D_bt2_idx_create,
+ H5D_bt2_idx_is_space_alloc,
+ H5D_bt2_idx_insert,
+ H5D_bt2_idx_get_addr,
+ NULL,
+ H5D_bt2_idx_iterate,
+ H5D_bt2_idx_remove,
+ H5D_bt2_idx_delete,
+ H5D_bt2_idx_copy_setup,
+ H5D_bt2_idx_copy_shutdown,
+ H5D_bt2_idx_size,
+ H5D_bt2_idx_reset,
+ NULL,
+ NULL,
+ H5D_bt2_idx_dump,
+ H5D_bt2_idx_dest
+}};
+
+
+/*****************************/
+/* Library Private Variables */
+/*****************************/
+
+/* v2 B-tree class for indexing non-filtered chunked datasets */
+const H5B2_class_t H5D_BT2[1] = {{ /* B-tree class information */
+ H5B2_CDSET_ID, /* Type of B-tree */
+ "H5B2_CDSET_ID", /* Name of B-tree class */
+ sizeof(H5D_bt2_rec_t), /* Size of native record */
+ H5D_bt2_crt_context, /* Create client callback context */
+ H5D_bt2_dst_context, /* Destroy client callback context */
+ H5D_bt2_store, /* Record storage callback */
+ H5D_bt2_compare, /* Record comparison callback */
+ H5D_bt2_encode, /* Record encoding callback */
+ H5D_bt2_decode, /* Record decoding callback */
+ H5D_bt2_debug, /* Record debugging callback */
+ H5D_bt2_crt_dbg_context, /* Create debugging context */
+ H5D_bt2_dst_dbg_context /* Destroy debugging context */
+}};
+
+/* v2 B-tree class for indexing filtered chunked datasets */
+const H5B2_class_t H5D_BT2_FILT[1] = {{ /* B-tree class information */
+ H5B2_CDSET_FILT_ID, /* Type of B-tree */
+ "H5B2_CDSET_FILT_ID", /* Name of B-tree class */
+ sizeof(H5D_bt2_filt_rec_t), /* Size of native record */
+ H5D_bt2_crt_context, /* Create client callback context */
+ H5D_bt2_dst_context, /* Destroy client callback context */
+ H5D_bt2_filt_store, /* Record storage callback */
+ H5D_bt2_filt_compare, /* Record comparison callback */
+ H5D_bt2_filt_encode, /* Record encoding callback */
+ H5D_bt2_filt_decode, /* Record decoding callback */
+ H5D_bt2_filt_debug, /* Record debugging callback */
+ H5D_bt2_crt_dbg_context, /* Create debugging context */
+ H5D_bt2_dst_dbg_context /* Destroy debugging context */
+}};
+
+/* Declare a free list to manage the H5D_bt2_ctx_t struct */
+H5FL_DEFINE_STATIC(H5D_bt2_ctx_t);
+/* Declare a free list to manage the H5D_bt2_ctx_ud_t struct */
+H5FL_DEFINE_STATIC(H5D_bt2_ctx_ud_t);
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_crt_context
+ *
+ * Purpose: Create client callback context
+ *
+ * Return: Success: non-NULL
+ * Failure: NULL
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static void *
+H5D_bt2_crt_context(void *_udata)
+{
+ H5D_bt2_ctx_ud_t *udata = (H5D_bt2_ctx_ud_t *)_udata; /* User data for building callback context */
+ H5D_bt2_ctx_t *ctx; /* Callback context structure */
+ void *ret_value; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_bt2_crt_context)
+
+ /* Sanity check */
+ HDassert(udata);
+ HDassert(udata->f);
+ HDassert(udata->ndims > 0 && udata->ndims < H5O_LAYOUT_NDIMS);
+
+ /* Allocate callback context */
+ if(NULL == (ctx = H5FL_MALLOC(H5D_bt2_ctx_t)))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, NULL, "can't allocate callback context")
+
+ /* Determine the size of addresses and # of dimensions for the dataset */
+ ctx->sizeof_addr = H5F_SIZEOF_ADDR(udata->f);
+ ctx->ndims = udata->ndims;
+
+ /*
+ * Compute the size required for encoding the size of a chunk,
+ * allowing for an extra byte, in case the filter makes the chunk larger.
+ */
+ ctx->chunk_size_len = 1 + ((H5V_log2_gen((uint64_t)udata->chunk_size) + 8) / 8);
+ if(ctx->chunk_size_len > 8)
+ ctx->chunk_size_len = 8;
+
+ /* Set return value */
+ ret_value = ctx;
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D_bt2_crt_context() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_dst_context
+ *
+ * Purpose: Destroy client callback context
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_dst_context(void *_ctx)
+{
+ H5D_bt2_ctx_t *ctx = (H5D_bt2_ctx_t *)_ctx; /* Callback context structure */
+
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_bt2_dst_context)
+
+ /* Sanity check */
+ HDassert(ctx);
+
+ /* Release callback context */
+ ctx = H5FL_FREE(H5D_bt2_ctx_t, ctx);
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* H5D_bt2_dst_context() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_store
+ *
+ * Purpose: Store native information into record for v2 B-tree
+ * (non-filtered)
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_store(void *record, const void *_udata)
+{
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_bt2_store)
+
+ const H5D_bt2_find_ud_t *udata = (const H5D_bt2_find_ud_t *)_udata; /* User data */
+
+ *(H5D_bt2_rec_t *)record = *(const H5D_bt2_rec_t *)udata->rec;
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* H5D_bt2_store() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_filt_store
+ *
+ * Purpose: Store native information into record for v2 B-tree
+ * (filtered)
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_filt_store(void *record, const void *_udata)
+{
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_bt2_filt_store)
+
+ const H5D_bt2_find_ud_t *udata = (const H5D_bt2_find_ud_t *)_udata; /* User data */
+
+ *(H5D_bt2_filt_rec_t *)record = *(const H5D_bt2_filt_rec_t *)udata->rec;
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* H5D_bt2_filt_store() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_compare
+ *
+ * Purpose: Compare two native information records, according to some key
+ * (non-filtered)
+ *
+ * Return: <0 if rec1 < rec2
+ * =0 if rec1 == rec2
+ * >0 if rec1 > rec2
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_compare(const void *_udata, const void *_rec2)
+{
+ const H5D_bt2_find_ud_t *udata = (const H5D_bt2_find_ud_t *)_udata; /* User data */
+
+ const H5D_bt2_rec_t *rec1 = (const H5D_bt2_rec_t *)udata->rec; /* The native record */
+ const H5D_bt2_rec_t *rec2 = (const H5D_bt2_rec_t *)_rec2; /* The native record */
+ herr_t ret_value; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_bt2_compare)
+
+ HDassert(rec1);
+ HDassert(rec2);
+
+ /* Compare the offsets but ignore the other fields */
+ ret_value = H5V_vector_cmp_u(udata->ndims, rec1->offset, rec2->offset);
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D_bt2_compare() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_filt_compare
+ *
+ * Purpose: Compare two native information records, according to some key
+ * (filtered)
+ *
+ * Return: <0 if rec1 < rec2
+ * =0 if rec1 == rec2
+ * >0 if rec1 > rec2
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_filt_compare(const void *_udata, const void *_rec2)
+{
+ const H5D_bt2_find_ud_t *udata = (const H5D_bt2_find_ud_t *)_udata; /* User data */
+
+ const H5D_bt2_filt_rec_t *rec1 = (const H5D_bt2_filt_rec_t *)udata->rec; /* The native record */
+ const H5D_bt2_filt_rec_t *rec2 = (const H5D_bt2_filt_rec_t *)_rec2; /* The native record */
+ herr_t ret_value; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_bt2_filt_compare)
+
+ HDassert(rec1);
+ HDassert(rec2);
+
+ /* Compare the offsets but ignore the other fields */
+ ret_value = H5V_vector_cmp_u(udata->ndims, rec1->offset, rec2->offset);
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D_bt2_filt_compare() */
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_encode
+ *
+ * Purpose: Encode native information into raw form for storing on disk
+ * (non-filtered)
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_encode(uint8_t *raw, const void *_record, void *_ctx)
+{
+ H5D_bt2_ctx_t *ctx = (H5D_bt2_ctx_t *)_ctx; /* Callback context structure */
+ const H5D_bt2_rec_t *record = (const H5D_bt2_rec_t *)_record; /* The native record */
+ unsigned i; /* Local index varible */
+
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_bt2_encode)
+
+ /* Sanity check */
+ HDassert(ctx);
+
+ /* Encode the record's fields */
+ H5F_addr_encode_len(ctx->sizeof_addr, &raw, record->addr);
+ for(i = 0; i < ctx->ndims; i++)
+ UINT64ENCODE(raw, record->offset[i]);
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* H5D_bt2_encode() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_filt_encode
+ *
+ * Purpose: Encode native information into raw form for storing on disk
+ * (filtered)
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_filt_encode(uint8_t *raw, const void *_record, void *_ctx)
+{
+ H5D_bt2_ctx_t *ctx = (H5D_bt2_ctx_t *)_ctx; /* Callback context structure */
+ const H5D_bt2_filt_rec_t *record = (const H5D_bt2_filt_rec_t *)_record; /* The native record */
+ unsigned i; /* Local index variable */
+
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_bt2_filt_encode)
+
+ /* Sanity check */
+ HDassert(ctx);
+
+ /* Encode the record's fields */
+ H5F_addr_encode_len(ctx->sizeof_addr, &raw, record->addr);
+ UINT64ENCODE_VAR(raw, record->nbytes, ctx->chunk_size_len);
+ UINT32ENCODE(raw, record->filter_mask);
+ for(i = 0; i < ctx->ndims; i++)
+ UINT64ENCODE(raw, record->offset[i]);
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* H5D_bt2_filt_encode() */
+
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_decode
+ *
+ * Purpose: Decode raw disk form of record into native form
+ * (non-filtered)
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_decode(const uint8_t *raw, void *_record, void *_ctx)
+{
+ H5D_bt2_ctx_t *ctx = (H5D_bt2_ctx_t *)_ctx; /* Callback context structure */
+ H5D_bt2_rec_t *record = (H5D_bt2_rec_t *)_record; /* The native record */
+ unsigned i; /* Local index variable */
+
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_bt2_decode)
+
+ /* Sanity check */
+ HDassert(ctx);
+
+ /* Decode the record's fields */
+ H5F_addr_decode_len(ctx->sizeof_addr, &raw, &record->addr);
+ for(i = 0; i < ctx->ndims; i++)
+ UINT64DECODE(raw, record->offset[i]);
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* H5D_bt2_decode() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_filt_decode
+ *
+ * Purpose: Decode raw disk form of record into native form
+ * (filtered)
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_filt_decode(const uint8_t *raw, void *_record, void *_ctx)
+{
+ H5D_bt2_ctx_t *ctx = (H5D_bt2_ctx_t *)_ctx; /* Callback context structure */
+ H5D_bt2_filt_rec_t *record = (H5D_bt2_filt_rec_t *)_record; /* The native record */
+ unsigned i; /* Local index variable */
+
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_bt2_filt_decode)
+
+ /* Sanity check */
+ HDassert(ctx);
+
+ /* Decode the record's fields */
+ H5F_addr_decode_len(ctx->sizeof_addr, &raw, &record->addr);
+ UINT64DECODE_VAR(raw, record->nbytes, ctx->chunk_size_len);
+ UINT32DECODE(raw, record->filter_mask);
+ for(i = 0; i < ctx->ndims; i++)
+ UINT64DECODE(raw, record->offset[i]);
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* H5D_bt2_filt_decode() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_debug
+ *
+ * Purpose: Debug native form of record (non-filtered)
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_debug(FILE *stream, const H5F_t UNUSED *f, hid_t UNUSED dxpl_id,
+ int indent, int fwidth, const void *_record, const void *_u_ctx)
+{
+ const H5D_bt2_rec_t *record = (const H5D_bt2_rec_t *)_record; /* The native record */
+ const H5D_bt2_ctx_ud_t *u_ctx = (const H5D_bt2_ctx_ud_t *)_u_ctx; /* User data for creating callback context */
+ unsigned u; /* Local index variable */
+
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_bt2_debug)
+
+ HDassert(record);
+
+ HDfprintf(stream, "%*s%-*s %a\n", indent, "", fwidth, "Chunk address:", (unsigned)record->addr);
+ HDfprintf(stream, "%*s%-*s {", indent, "", fwidth, "Logical offset:");
+ for(u = 0; u < u_ctx->ndims; u++)
+ HDfprintf(stream, "%s%Hd", u?", ":"", record->offset[u]);
+ HDfputs("}\n", stream);
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* H5D_bt2_debug() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_filt_debug
+ *
+ * Purpose: Debug native form of record (filterd)
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_filt_debug(FILE *stream, const H5F_t UNUSED *f, hid_t UNUSED dxpl_id,
+ int indent, int fwidth, const void *_record, const void *_u_ctx)
+{
+ const H5D_bt2_filt_rec_t *record = (const H5D_bt2_filt_rec_t *)_record; /* The native record */
+ const H5D_bt2_ctx_ud_t *u_ctx = (const H5D_bt2_ctx_ud_t *)_u_ctx; /* User data for creating callback context */
+ unsigned u; /* Local index variable */
+
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_bt2_filt_debug)
+
+ HDassert(record);
+
+ HDfprintf(stream, "%*s%-*s %a\n", indent, "", fwidth, "Chunk address:", (unsigned)record->addr);
+ HDfprintf(stream, "%*s%-*s %u bytes\n", indent, "", fwidth, "Chunk size:", (unsigned)record->nbytes);
+ HDfprintf(stream, "%*s%-*s 0x%08x\n", indent, "", fwidth, "Filter mask:", record->filter_mask);
+
+ HDfprintf(stream, "%*s%-*s {", indent, "", fwidth, "Logical offset:");
+ for(u = 0; u < u_ctx->ndims; u++)
+ HDfprintf(stream, "%s%Hd", u?", ":"", record->offset[u]);
+ HDfputs("}\n", stream);
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* H5D_bt2_filt_debug() */
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_crt_dbg_context
+ *
+ * Purpose: Create user data for debugged callback context
+ *
+ * Return: Success: non-NULL
+ * Failure: NULL
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static void *
+H5D_bt2_crt_dbg_context(H5F_t *f, hid_t UNUSED dxpl_id, haddr_t obj_addr)
+{
+ H5D_bt2_ctx_ud_t *u_ctx; /* User data for creating callback context */
+ H5O_loc_t obj_loc; /* Pointer to an object's location */
+ hbool_t obj_opened = FALSE; /* Flag to indicate that the object header was opened */
+ H5O_layout_t layout; /* Layout message */
+ void *ret_value; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_bt2_crt_dbg_context)
+
+ /* Sanity check */
+ HDassert(f);
+ HDassert(H5F_addr_defined(obj_addr));
+
+ /* Set up the object header location info */
+ H5O_loc_reset(&obj_loc);
+ obj_loc.file = f;
+ obj_loc.addr = obj_addr;
+
+ /* Open the object header where the layout message resides */
+ if(H5O_open(&obj_loc) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, NULL, "can't open object header")
+ obj_opened = TRUE;
+
+ /* Read the layout message */
+ if(NULL == H5O_msg_read(&obj_loc, H5O_LAYOUT_ID, &layout, dxpl_id))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, NULL, "can't get layout info")
+
+ /* close the object header */
+ if(H5O_close(&obj_loc) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, NULL, "can't close object header")
+
+ /* Allocate structure for storing user data to create callback context */
+ if(NULL == (u_ctx = H5FL_MALLOC(H5D_bt2_ctx_ud_t)))
+ HGOTO_ERROR(H5E_HEAP, H5E_CANTALLOC, NULL, "can't allocate user data context structure ")
+
+ /* Set information for context structure */
+ u_ctx->f = f;
+ u_ctx->chunk_size = layout.u.chunk.size;
+ u_ctx->ndims = layout.u.chunk.ndims - 1;
+
+ /* Set return value */
+ ret_value = u_ctx;
+
+done:
+ /* Cleanup on error */
+ if(ret_value == NULL) {
+ /* Release context structure */
+ if(u_ctx)
+ u_ctx = H5FL_FREE(H5D_bt2_ctx_ud_t, u_ctx);
+
+ /* Close object header */
+ if(obj_opened) {
+ if(H5O_close(&obj_loc) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, NULL, "can't close object header")
+ } /* end if */
+ } /* end if */
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D_bt2_crt_dbg_context() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_dst_dbg_context
+ *
+ * Purpose: Destroy client callback context
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_dst_dbg_context(void *_u_ctx)
+{
+ H5D_bt2_ctx_ud_t *u_ctx = (H5D_bt2_ctx_ud_t *)_u_ctx; /* User data for creating callback context */
+
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_bt2_dst_dbg_context)
+
+ /* Sanity check */
+ HDassert(u_ctx);
+
+ /* Release user data for creating callback context */
+ u_ctx = H5FL_FREE(H5D_bt2_ctx_ud_t, u_ctx);
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* H5D_bt2_dst_dbg_context() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_idx_open()
+ *
+ * Purpose: Opens an existing v2 B-tree.
+ *
+ * Note: This information is passively initialized from each index
+ * operation callback because those abstract chunk index operations
+ * are designed to work with the v2 B-tree chunk indices also,
+ * which don't require an 'open' for the data structure.
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_idx_open(const H5D_chk_idx_info_t *idx_info)
+{
+ H5D_bt2_ctx_ud_t u_ctx; /* user data for creating context */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_bt2_idx_open)
+
+ /* Check args */
+ HDassert(idx_info);
+ HDassert(idx_info->f);
+ HDassert(idx_info->pline);
+ HDassert(idx_info->layout);
+ HDassert(H5D_CHUNK_IDX_BT2 == idx_info->layout->idx_type);
+ HDassert(idx_info->storage);
+ HDassert(H5F_addr_defined(idx_info->storage->idx_addr));
+ HDassert(NULL == idx_info->storage->u.btree2.bt2);
+
+ /* Set up the user data */
+ u_ctx.f = idx_info->f;
+ u_ctx.ndims = idx_info->layout->ndims - 1;
+ u_ctx.chunk_size = idx_info->layout->size;
+
+ /* Open v2 B-tree for the chunk index */
+ if(NULL == (idx_info->storage->u.btree2.bt2 = H5B2_open(idx_info->f, idx_info->dxpl_id, idx_info->storage->idx_addr , &u_ctx)))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't open v2 B-tree for tracking chunked dataset")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_bt2_idx_open() */
+
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_idx_create
+ *
+ * Purpose: Create the v2 B-tree for tracking dataset chunks
+ *
+ * Return: SUCCEED/FAIL
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_idx_create(const H5D_chk_idx_info_t *idx_info)
+{
+ H5B2_create_t bt2_cparam; /* v2 B-tree creation parameters */
+ H5D_bt2_ctx_ud_t u_ctx; /* data for context call */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_bt2_idx_create)
+
+ /* Check args */
+ HDassert(idx_info);
+ HDassert(idx_info->f);
+ HDassert(idx_info->pline);
+ HDassert(idx_info->layout);
+ HDassert(idx_info->storage);
+ HDassert(!H5F_addr_defined(idx_info->storage->idx_addr));
+
+ bt2_cparam.rrec_size = H5F_SIZEOF_ADDR(idx_info->f) /* Address of chunk */
+ + (idx_info->layout->ndims - 1) * 8; /* # of dimensions x 64-bit chunk offsets */
+
+ if(idx_info->pline->nused > 0) {
+ unsigned chunk_size_len; /* Size of encoded chunk size */
+ /*
+ * Compute the size required for encoding the size of a chunk,
+ * allowing for an extra byte, in case the filter makes the chunk larger.
+ */
+ chunk_size_len = 1 + ((H5V_log2_gen((uint64_t)idx_info->layout->size) + 8) / 8);
+ if(chunk_size_len > 8)
+ chunk_size_len = 8;
+
+ bt2_cparam.rrec_size += chunk_size_len + 4; /* Size of encoded chunk size & filter mask */
+ bt2_cparam.cls = H5D_BT2_FILT;
+ } else
+ bt2_cparam.cls = H5D_BT2;
+
+ bt2_cparam.node_size = idx_info->layout->u.btree2.cparam.node_size;
+ bt2_cparam.split_percent = idx_info->layout->u.btree2.cparam.split_percent;
+ bt2_cparam.merge_percent = idx_info->layout->u.btree2.cparam.merge_percent;
+
+ u_ctx.f = idx_info->f;
+ u_ctx.ndims = idx_info->layout->ndims - 1;
+ u_ctx.chunk_size = idx_info->layout->size;
+
+ /* Create the v2 B-tree for the chunked dataset */
+ if(NULL == (idx_info->storage->u.btree2.bt2 = H5B2_create(idx_info->f, idx_info->dxpl_id, &bt2_cparam, &u_ctx)))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't create v2 B-tree for tracking chunked dataset")
+
+ /* Retrieve the v2 B-tree's address in the file */
+ if(H5B2_get_addr(idx_info->storage->u.btree2.bt2, &(idx_info->storage->idx_addr)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get v2 B-tree address for tracking chunked dataset")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_bt2_idx_create() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_idx_is_space_alloc
+ *
+ * Purpose: Query if space is allocated for index method
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static hbool_t
+H5D_bt2_idx_is_space_alloc(const H5O_storage_chunk_t *storage)
+{
+ hbool_t ret_value; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_bt2_idx_is_space_alloc)
+
+ /* Check args */
+ HDassert(storage);
+
+ /* Set return value */
+ ret_value = (hbool_t)H5F_addr_defined(storage->idx_addr);
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_bt2_idx_is_space_alloc() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_found_cb
+ *
+ * Purpose: Retrieve record (non-filtered) for dataset chunk when it is found
+ * in the v2 B-tree.
+ * This is the callback for H5B2_find() which is called in
+ * H5D_bt2_idx_get_addr() and H5D_bt2_idx_insert().
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_found_cb(const void *nrecord, void *op_data)
+{
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_bt2_found_cb)
+
+ *(H5D_bt2_rec_t *)op_data = *(const H5D_bt2_rec_t *)nrecord;
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* H5D_bt2_found_cb() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_filt_found_cb
+ *
+ * Purpose: Retrieve record (filtered) for dataset chunk when it is found
+ * in the v2 B-tree.
+ * This is the callback for H5B2_find() which is called in
+ * H5D_bt2_idx_get_addr() and H5D_bt2_idx_insert().
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_filt_found_cb(const void *nrecord, void *op_data)
+{
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_bt2_filt_found_cb)
+
+ *(H5D_bt2_filt_rec_t *)op_data = *(const H5D_bt2_filt_rec_t *)nrecord;
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* H5D_bt2_filt_found_cb() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_mod_filt_cb
+ *
+ * Purpose: Modify record (filtered) for dataset chunk when it is found
+ * in the v2 B-tree.
+ * This is the callback for H5B2_modify() which is called in
+ * H5D_bt2_idx_insert().
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_mod_filt_cb(void *_record, void *_op_data, hbool_t *changed)
+{
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_bt2_mod_filt_cb)
+
+ *(H5D_bt2_filt_rec_t *)_record = *(H5D_bt2_filt_rec_t *)_op_data;
+
+ /* Note that the record changed */
+ *changed = TRUE;
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D_bt2_mod_filt_cb() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_idx_insert
+ *
+ * Purpose: A non-filtered chunk:
+ * Should not exist
+ * Allocate the chunk and pass chunk address back up
+ * A filtered chunk:
+ * If it was not found, create the chunk and pass chunk address back up
+ * If it was found but its size changed, reallocate the chunk and pass chunk address back up
+ * If it was found but its size was the same, pass chunk address back up
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_idx_insert(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata)
+{
+ H5B2_t *bt2_cdset = NULL; /* v2 B-tree handle for indexing chunks */
+ H5D_bt2_find_ud_t bt2_udata;
+ unsigned u; /* local index variable */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_bt2_idx_insert)
+
+ HDassert(idx_info);
+ HDassert(idx_info->f);
+ HDassert(idx_info->pline);
+ HDassert(idx_info->layout);
+ HDassert(idx_info->storage);
+ HDassert(H5F_addr_defined(idx_info->storage->idx_addr));
+ HDassert(udata);
+
+ if(NULL == idx_info->storage->u.btree2.bt2) {
+ /* Open existing v2 B-tree */
+ if(H5D_bt2_idx_open(idx_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open v2 B-tree")
+ } /* end if */
+
+ bt2_cdset = idx_info->storage->u.btree2.bt2;
+
+ /* Check for filters on chunks */
+ if(idx_info->pline->nused > 0) { /* filtered chunk */
+ unsigned allow_chunk_size_len; /* Allowed size of encoded chunk size */
+ unsigned new_chunk_size_len; /* Size of encoded chunk size */
+ H5D_bt2_filt_rec_t rec; /* Record for searching object */
+ H5D_bt2_filt_rec_t found_rec; /* Record found from searching for object */
+
+ /*
+ * Compute the size required for encoding the size of a chunk,
+ * allowing for an extra byte, in case the filter makes the chunk larger.
+ */
+ allow_chunk_size_len = 1 + ((H5V_log2_gen((uint64_t)idx_info->layout->size) + 8) / 8);
+ if(allow_chunk_size_len > 8)
+ allow_chunk_size_len = 8;
+
+ /* Compute encoded size of chunk */
+ new_chunk_size_len = (H5V_log2_gen((uint64_t)udata->nbytes) + 8) / 8;
+ if(new_chunk_size_len > 8)
+ HGOTO_ERROR(H5E_DATASET, H5E_BADRANGE, FAIL, "encoded chunk size is more than 8 bytes?!?")
+
+ /* Check if the chunk became too large to be encoded */
+ if(new_chunk_size_len > allow_chunk_size_len)
+ HGOTO_ERROR(H5E_DATASET, H5E_BADRANGE, FAIL, "chunk size can't be encoded")
+
+ /* Initialize record information */
+ rec.nbytes = udata->nbytes;
+ rec.filter_mask = udata->filter_mask;
+ for(u = 0; u < (idx_info->layout->ndims - 1); u++)
+ rec.offset[u] = udata->common.offset[u];
+
+ found_rec.addr = HADDR_UNDEF;
+ found_rec.nbytes = 0;
+ found_rec.filter_mask = 0;
+
+ /* Prepare user data for compare callback */
+ bt2_udata.rec = &rec;
+ bt2_udata.ndims = idx_info->layout->ndims - 1;
+
+ /* Try to find the chunked record */
+ if(H5B2_find(bt2_cdset, idx_info->dxpl_id, &bt2_udata, H5D_bt2_filt_found_cb, &found_rec) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, FAIL, "can't find object in v2 B-tree")
+
+ /* Check for previous chunk */
+ if(H5F_addr_defined(found_rec.addr)) { /* Found it */
+ /* Sanity check */
+ HDassert(!H5F_addr_defined(udata->addr) || H5F_addr_eq(udata->addr, found_rec.addr));
+
+ /* Check for chunk being same size */
+ if(udata->nbytes != found_rec.nbytes) {
+
+ H5_CHECK_OVERFLOW(found_rec.nbytes, uint32_t, hsize_t);
+
+ /* Free the original chunk */
+ if(H5MF_xfree(idx_info->f, H5FD_MEM_DRAW, idx_info->dxpl_id, found_rec.addr, (hsize_t)found_rec.nbytes) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to free chunk")
+
+ /* Allocate a new chunk */
+ H5_CHECK_OVERFLOW(udata->nbytes, uint32_t, hsize_t);
+ rec.addr = udata->addr = H5MF_alloc(idx_info->f, H5FD_MEM_DRAW, idx_info->dxpl_id, (hsize_t)udata->nbytes);
+
+ if(!H5F_addr_defined(udata->addr))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate chunk")
+
+ /* Modify record for object in v2 B-tree */
+ if(H5B2_modify(bt2_cdset, idx_info->dxpl_id, &bt2_udata, H5D_bt2_mod_filt_cb, &rec) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to modify record in v2 B-tree")
+
+ } else
+ /* Don't need to reallocate chunk, but send its address back up */
+ udata->addr = found_rec.addr;
+ } else { /* Not found */
+ H5_CHECK_OVERFLOW(udata->nbytes, uint32_t, hsize_t);
+
+ /* Allocate a new chunk */
+ rec.addr = udata->addr = H5MF_alloc(idx_info->f, H5FD_MEM_DRAW, idx_info->dxpl_id, (hsize_t)udata->nbytes);
+ if(!H5F_addr_defined(udata->addr))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate chunk")
+
+ /* Insert record for object in v2 B-tree */
+ if(H5B2_insert(bt2_cdset, idx_info->dxpl_id, &bt2_udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "couldn't insert record in v2 B-tree")
+ }
+ } else { /* non-filtered chunk */
+ H5D_bt2_rec_t rec;
+
+ /* The record should not be there */
+ HDassert(!H5F_addr_defined(udata->addr));
+ HDassert(udata->nbytes == idx_info->layout->size);
+
+ /* Prepare user data for compare callback */
+ bt2_udata.rec = &rec;
+ bt2_udata.ndims = idx_info->layout->ndims - 1;
+
+ for(u = 0; u < (idx_info->layout->ndims - 1); u++)
+ rec.offset[u] = udata->common.offset[u];
+
+ /* Allocate storage for the new chunk */
+ H5_CHECK_OVERFLOW(udata->nbytes, uint32_t, hsize_t);
+ rec.addr = udata->addr = H5MF_alloc(idx_info->f, H5FD_MEM_DRAW, idx_info->dxpl_id, (hsize_t)udata->nbytes);
+
+ if(!H5F_addr_defined(udata->addr))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate chunk")
+
+ /* Insert record for object in v2 B-tree */
+ if(H5B2_insert(bt2_cdset, idx_info->dxpl_id, &bt2_udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "couldn't insert record in v2 B-tree")
+ } /* end else */
+ HDassert(H5F_addr_defined(udata->addr));
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D_bt2_idx_insert() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_idx_get_addr
+ *
+ * Purpose: Get the file address of a chunk if file space has been
+ * assigned. Save the retrieved information in the udata
+ * supplied.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_idx_get_addr(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata)
+{
+ H5B2_t *bt2_cdset = NULL; /* v2 B-tree handle for indexing chunks */
+ unsigned u; /* Local index variable */
+ H5D_bt2_find_ud_t bt2_udata;
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_bt2_idx_get_addr)
+
+ HDassert(idx_info);
+ HDassert(idx_info->f);
+ HDassert(idx_info->pline);
+ HDassert(idx_info->layout);
+ HDassert(idx_info->layout->ndims > 0);
+ HDassert(idx_info->storage);
+ HDassert(H5F_addr_defined(idx_info->storage->idx_addr));
+ HDassert(udata);
+
+ if(NULL == idx_info->storage->u.btree2.bt2) {
+ /* Open existing v2 B-tree */
+ if(H5D_bt2_idx_open(idx_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open v2 B-tree")
+ } /* end if */
+
+ bt2_cdset = idx_info->storage->u.btree2.bt2;
+
+ /* Check for filters on chunks */
+ if(idx_info->pline->nused > 0) { /* filtered chunk */
+ H5D_bt2_filt_rec_t search_rec; /* Record for searching object */
+ H5D_bt2_filt_rec_t found_rec; /* Record found from searching for object */
+
+ /* Set the chunk offset to be searched for */
+ for(u = 0; u < (idx_info->layout->ndims - 1); u++)
+ search_rec.offset[u] = udata->common.offset[u];
+
+ found_rec.addr = HADDR_UNDEF;
+ found_rec.nbytes = 0;
+ found_rec.filter_mask = 0;
+
+ /* Prepare user data for compare callback */
+ bt2_udata.rec = &search_rec;
+ bt2_udata.ndims = idx_info->layout->ndims - 1;
+
+ /* Go get chunk information from v2 B-tree */
+ if(H5B2_find(bt2_cdset, idx_info->dxpl_id, &bt2_udata, H5D_bt2_filt_found_cb, &found_rec) < 0)
+ HGOTO_ERROR(H5E_HEAP, H5E_NOTFOUND, FAIL, "can't find object in v2 B-tree")
+
+ /* Set info for the chunk */
+ udata->addr = found_rec.addr;
+ udata->nbytes = found_rec.nbytes;
+ udata->filter_mask = found_rec.filter_mask;
+ } else { /* non-filtered chunk */
+ H5D_bt2_rec_t search_rec; /* Record for searching object */
+ H5D_bt2_rec_t found_rec; /* Record found from searching for object */
+
+ /* Set the chunk offset to be searched for */
+ for(u = 0; u < (idx_info->layout->ndims - 1); u++)
+ search_rec.offset[u] = udata->common.offset[u];
+
+ search_rec.addr = HADDR_UNDEF;
+ found_rec.addr = HADDR_UNDEF;
+
+ /* Prepare user data for compare callback */
+ bt2_udata.rec = &search_rec;
+ bt2_udata.ndims = idx_info->layout->ndims - 1;
+
+ /* Go get chunk information from v2 B-tree */
+ if(H5B2_find(bt2_cdset, idx_info->dxpl_id, &bt2_udata, H5D_bt2_found_cb, &found_rec) < 0)
+ HGOTO_ERROR(H5E_HEAP, H5E_NOTFOUND, FAIL, "can't find object in v2 B-tree")
+
+ udata->addr = found_rec.addr;
+
+ /* Update the other (constant) information for the chunk */
+ udata->nbytes = idx_info->layout->size;
+ udata->filter_mask = 0;
+ }
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D_bt2_idx_get_addr() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_idx_iterate_cb
+ *
+ * Purpose: Translate the B-tree specific chunk record into a generic
+ * form and make the callback to the generic chunk callback
+ * routine.
+ * This is the callback for H5B2_iterate() which is called in
+ * H5D_bt2_idx_iterate().
+ *
+ * Return: Success: Non-negative
+ * Failure: Negative
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+/* ARGSUSED */
+static int
+H5D_bt2_idx_iterate_cb(const void *_record, void *_udata)
+{
+ H5D_bt2_it_ud_t *udata = (H5D_bt2_it_ud_t *)_udata; /* User data */
+ unsigned u; /* Local index variable */
+ int ret_value; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOERR(H5D_bt2_idx_iterate_cb, -)
+
+ /* Compose generic chunk record for callback */
+ if(udata->filtered) { /* filtered record */
+ const H5D_bt2_filt_rec_t *filt_rec = (const H5D_bt2_filt_rec_t *)_record;
+
+ udata->chunk_rec.chunk_addr = filt_rec->addr;
+ udata->chunk_rec.nbytes = filt_rec->nbytes;
+ udata->chunk_rec.filter_mask = filt_rec->filter_mask;
+ for(u = 0; u < (udata->common.layout->ndims - 1); u++)
+ udata->chunk_rec.offset[u] = filt_rec->offset[u];
+ } else { /* non-filtered record */
+ const H5D_bt2_rec_t *rec = (const H5D_bt2_rec_t *)_record;
+
+ udata->chunk_rec.chunk_addr = rec->addr;
+ udata->chunk_rec.nbytes = udata->common.layout->size;
+ udata->chunk_rec.filter_mask = 0;
+ for(u = 0; u < (udata->common.layout->ndims - 1); u++)
+ udata->chunk_rec.offset[u] = rec->offset[u];
+ }
+
+ /* Make "generic chunk" callback */
+ if((ret_value = (udata->cb)(&udata->chunk_rec, udata->udata)) < 0)
+ HERROR(H5E_DATASET, H5E_CALLBACK, "failure in generic chunk iterator callback");
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D_bt2_idx_iterate_cb() */
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_idx_iterate
+ *
+ * Purpose: Iterate over the chunks in an index, making a callback
+ * for each one.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+H5D_bt2_idx_iterate(const H5D_chk_idx_info_t *idx_info,
+ H5D_chunk_cb_func_t chunk_cb, void *chunk_udata)
+{
+ H5D_bt2_it_ud_t udata; /* User data for B-tree iterator callback */
+ H5B2_t *bt2_cdset = NULL; /* v2 B-tree handle for indexing chunks */
+ int ret_value; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_bt2_idx_iterate)
+
+ HDassert(idx_info);
+ HDassert(idx_info->f);
+ HDassert(idx_info->pline);
+ HDassert(idx_info->layout);
+ HDassert(idx_info->storage);
+ HDassert(H5F_addr_defined(idx_info->storage->idx_addr));
+ HDassert(chunk_cb);
+ HDassert(chunk_udata);
+
+ /* Initialize user data */
+ HDmemset(&udata, 0, sizeof udata);
+ udata.common.layout = idx_info->layout;
+ udata.common.storage = idx_info->storage;
+ udata.filtered = idx_info->pline->nused > 0;
+ HDmemset(&udata.chunk_rec, 0, sizeof(udata.chunk_rec));
+
+ if(NULL == idx_info->storage->u.btree2.bt2) {
+ /* Open existing v2 B-tree */
+ if(H5D_bt2_idx_open(idx_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open v2 B-tree")
+ } /* end if */
+
+ bt2_cdset = idx_info->storage->u.btree2.bt2;
+
+ udata.cb = chunk_cb;
+ udata.udata = chunk_udata;
+
+ /* Iterate over the records in the v2 B-tree */
+ if((ret_value = H5B2_iterate(bt2_cdset, idx_info->dxpl_id, H5D_bt2_idx_iterate_cb, &udata)) < 0)
+ HERROR(H5E_DATASET, H5E_BADITER, "unable to iterate over v2 B-tree for dataset chunks");
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_bt2_idx_iterate() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_remove_cb()
+ *
+ * Purpose: Free space for 'dataset chunk' object as v2 B-tree
+ * is being deleted or v2 B-tree node is removed.
+ * This is the callback for H5B2_remove() and H5B2_delete() which
+ * which are called in H5D_bt2_idx_remove() and H5D_bt2_idx_delete().
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_remove_cb(const void *record, void *_udata)
+{
+ H5D_bt2_remove_ud_t *udata = (H5D_bt2_remove_ud_t *)_udata; /* User data for removal callback */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_bt2_remove_cb)
+
+ /* Free the space in the file for the object being removed */
+ H5_CHECK_OVERFLOW(udata->unfilt_size, uint32_t, hsize_t);
+ if(H5MF_xfree(udata->f, H5FD_MEM_DRAW, udata->dxpl_id, ((const H5D_bt2_rec_t *)record)->addr, (hsize_t)udata->unfilt_size) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to free chunk")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D_bt2_remove_cb() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_filt_remove_cb
+ *
+ * Purpose: Free space for 'filtered dataset chunk' object as v2 B-tree
+ * is being deleted or v2 B-tree node is removed
+ * This is the callback for H5B2_remove() and H5B2_delete() which
+ * which are called in H5D_bt2_idx_remove() and H5D_bt2_idx_delete().
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_filt_remove_cb(const void *_record, void *_udata)
+{
+ H5D_bt2_remove_ud_t *udata = (H5D_bt2_remove_ud_t *)_udata; /* User data for removal callback */
+ const H5D_bt2_filt_rec_t *record = (const H5D_bt2_filt_rec_t *)_record; /* The native record */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_bt2_filt_remove_cb)
+
+ /* Free the space in the file for the object being removed */
+ H5_CHECK_OVERFLOW(record->nbytes, uint32_t, hsize_t);
+ if(H5MF_xfree(udata->f, H5FD_MEM_DRAW, udata->dxpl_id, record->addr, (hsize_t)record->nbytes) < 0)
+ HGOTO_ERROR(H5E_HEAP, H5E_CANTFREE, FAIL, "unable to free chunk")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D_bt2_filt_remove_cb() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_idx_remove
+ *
+ * Purpose: Remove chunk from index.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_idx_remove(const H5D_chk_idx_info_t *idx_info, H5D_chunk_common_ud_t *udata)
+{
+ H5D_bt2_remove_ud_t remove_udata; /* User data for removal callback */
+ H5B2_t *bt2_cdset = NULL; /* v2 B-tree handle for indexing chunks */
+ H5D_bt2_find_ud_t bt2_udata;
+ unsigned u; /* Local index variable */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_bt2_idx_remove)
+
+ HDassert(idx_info);
+ HDassert(idx_info->f);
+ HDassert(idx_info->pline);
+ HDassert(idx_info->layout);
+ HDassert(idx_info->storage);
+ HDassert(H5F_addr_defined(idx_info->storage->idx_addr));
+ HDassert(udata);
+
+ if(NULL == idx_info->storage->u.btree2.bt2) {
+ /* Open existing v2 B-tree */
+ if(H5D_bt2_idx_open(idx_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open v2 B-tree")
+ } /* end if */
+
+ bt2_cdset = idx_info->storage->u.btree2.bt2;
+
+ /* Initialize user data for removal callback */
+ remove_udata.f = idx_info->f;
+ remove_udata.dxpl_id = idx_info->dxpl_id;
+
+ /* Remove the record for the "dataset chunk" object from the v2 B-tree */
+ /* (space in the file for the object is freed in the 'remove' callback) */
+ if(idx_info->pline->nused > 0) { /* filtered chunk */
+ H5D_bt2_filt_rec_t search_rec; /* Record for searching for object */
+
+ /* Initialize the record to search for */
+ for(u = 0; u < (idx_info->layout->ndims - 1); u++)
+ search_rec.offset[u] = udata->offset[u];
+
+ bt2_udata.rec = &search_rec;
+ bt2_udata.ndims = idx_info->layout->ndims - 1;
+
+ if(H5B2_remove(bt2_cdset, idx_info->dxpl_id, &bt2_udata, H5D_bt2_filt_remove_cb, &remove_udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "can't remove object from B-tree")
+ } else { /* non-filtered chunk */
+ H5D_bt2_rec_t search_rec; /* Record for searching for object */
+
+ remove_udata.unfilt_size = idx_info->layout->size;
+
+ /* Initialize the record to search for */
+ for(u = 0; u < (idx_info->layout->ndims - 1); u++)
+ search_rec.offset[u] = udata->offset[u];
+
+ bt2_udata.rec = &search_rec;
+ bt2_udata.ndims = idx_info->layout->ndims - 1;
+
+ if(H5B2_remove(bt2_cdset, idx_info->dxpl_id, &bt2_udata, H5D_bt2_remove_cb, &remove_udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "can't remove object from B-tree")
+ } /* end else */
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D_bt2_idx_remove() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_idx_delete
+ *
+ * Purpose: Delete index and raw data storage for entire dataset
+ * (i.e. all chunks)
+ *
+ * Return: Success: Non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_idx_delete(const H5D_chk_idx_info_t *idx_info)
+{
+ H5D_bt2_remove_ud_t remove_udata; /* User data for removal callback */
+ H5B2_remove_t remove_op; /* The removal callback */
+ H5D_bt2_ctx_ud_t u_ctx; /* data for context call */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_bt2_idx_delete)
+
+ /* Sanity checks */
+ HDassert(idx_info);
+ HDassert(idx_info->f);
+ HDassert(idx_info->pline);
+ HDassert(idx_info->layout);
+ HDassert(idx_info->storage);
+
+ /* Check if the index data structure has been allocated */
+ if(H5F_addr_defined(idx_info->storage->idx_addr)) {
+
+ /* Set up user data for creating context */
+ u_ctx.f = idx_info->f;
+ u_ctx.ndims = idx_info->layout->ndims - 1;
+ u_ctx.chunk_size = idx_info->layout->size;
+
+ /* Initialize user data for removal callback */
+ remove_udata.f = idx_info->f;
+ remove_udata.dxpl_id = idx_info->dxpl_id;
+
+ remove_op = idx_info->pline->nused > 0 ? H5D_bt2_filt_remove_cb : H5D_bt2_remove_cb;
+
+ /* Delete the v2 B-tree */
+ /*(space in the file for each object is freed in the 'remove' callback) */
+ if(H5B2_delete(idx_info->f, idx_info->dxpl_id, idx_info->storage->idx_addr, &u_ctx, remove_op, &remove_udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTDELETE, FAIL, "can't delete v2 B-tree")
+
+ idx_info->storage->idx_addr = HADDR_UNDEF;
+ } /* end if */
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_bt2_idx_delete() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_idx_copy_setup
+ *
+ * Purpose: Set up any necessary information for copying chunks
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_idx_copy_setup(const H5D_chk_idx_info_t *idx_info_src,
+ const H5D_chk_idx_info_t *idx_info_dst)
+{
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_bt2_idx_copy_setup)
+
+ /* Source file */
+ HDassert(idx_info_src);
+ HDassert(idx_info_src->f);
+ HDassert(idx_info_src->pline);
+ HDassert(idx_info_src->layout);
+ HDassert(idx_info_src->storage);
+
+ /* Destination file */
+ HDassert(idx_info_dst);
+ HDassert(idx_info_dst->f);
+ HDassert(idx_info_dst->pline);
+ HDassert(idx_info_dst->layout);
+ HDassert(idx_info_dst->storage);
+ HDassert(!H5F_addr_defined(idx_info_dst->storage->idx_addr));
+
+ /* Check if the source v2 B-tree is open yet */
+ if(NULL == idx_info_src->storage->u.btree2.bt2) {
+ if(H5D_bt2_idx_open(idx_info_src) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open v2 B-tree")
+ } /* end if */
+
+ /* Set copied metadata tag */
+ H5_BEGIN_TAG(idx_info_dst->dxpl_id, H5AC__COPIED_TAG, FAIL);
+
+ /* Create v2 B-tree that describes the chunked dataset in the destination file */
+ if(H5D_bt2_idx_create(idx_info_dst) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize chunked storage")
+ HDassert(H5F_addr_defined(idx_info_dst->storage->idx_addr));
+
+ /* Reset metadata tag */
+ H5_END_TAG(FAIL);
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_bt2_idx_copy_setup() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_idx_copy_shutdown
+ *
+ * Purpose: Shutdown any information from copying chunks
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_idx_copy_shutdown(H5O_storage_chunk_t *storage_src,
+ H5O_storage_chunk_t *storage_dst, hid_t UNUSED dxpl_id)
+{
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_bt2_idx_copy_shutdown)
+
+ /* Check args */
+ HDassert(storage_src);
+ HDassert(storage_src->u.btree2.bt2);
+ HDassert(storage_dst);
+ HDassert(storage_dst->u.btree2.bt2);
+
+ /* Close v2 B-tree for source file */
+ if(H5B2_close(storage_src->u.btree2.bt2, dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to close v2 B-tree")
+ storage_src->u.btree2.bt2 = NULL;
+
+ /* Close v2 B-tree for destination file */
+ if(H5B2_close(storage_dst->u.btree2.bt2, dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to close v2 B-tree")
+ storage_dst->u.btree2.bt2 = NULL;
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_bt2_idx_copy_shutdown() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_idx_size
+ *
+ * Purpose: Retrieve the amount of index storage for chunked dataset
+ *
+ * Return: Success: Non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_idx_size(const H5D_chk_idx_info_t *idx_info, hsize_t *index_size)
+{
+ H5B2_t *bt2_cdset = NULL; /* Pointer to v2 B-tree structure */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5D_bt2_idx_size, FAIL)
+
+ /* Check args */
+ HDassert(idx_info);
+ HDassert(idx_info->f);
+ HDassert(idx_info->pline);
+ HDassert(idx_info->layout);
+ HDassert(idx_info->storage);
+ HDassert(H5F_addr_defined(idx_info->storage->idx_addr));
+ HDassert(index_size);
+
+ /* Open v2 B-tree */
+ if(H5D_bt2_idx_open(idx_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open v2 B-tree")
+
+ /* Set convenience pointer to v2 B-tree structure */
+ bt2_cdset = idx_info->storage->u.btree2.bt2;
+
+ /* Get v2 B-tree size for indexing chunked dataset */
+ if(H5B2_size(bt2_cdset, idx_info->dxpl_id, index_size) < 0)
+ HGOTO_ERROR(H5E_SYM, H5E_CANTGET, FAIL, "can't retrieve v2 B-tree storage info for chunked dataset")
+done:
+ /* Close v2 B-tree index */
+ if(bt2_cdset && H5B2_close(bt2_cdset, idx_info->dxpl_id) < 0)
+ HDONE_ERROR(H5E_SYM, H5E_CLOSEERROR, FAIL, "can't close v2 B-tree for tracking chunked dataset")
+ idx_info->storage->u.btree2.bt2 = NULL;
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_bt2_idx_size() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_idx_reset
+ *
+ * Purpose: Reset indexing information.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_idx_reset(H5O_storage_chunk_t *storage, hbool_t reset_addr)
+{
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_bt2_idx_reset)
+
+ HDassert(storage);
+
+ /* Reset index info */
+ if(reset_addr)
+ storage->idx_addr = HADDR_UNDEF;
+ storage->u.btree2.bt2 = NULL;
+
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D_bt2_idx_reset() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_idx_dump
+ *
+ * Purpose: Dump indexing information to a stream.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_idx_dump(const H5O_storage_chunk_t *storage, FILE *stream)
+{
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_bt2_idx_dump)
+
+ HDassert(storage);
+ HDassert(stream);
+
+ HDfprintf(stream, " Address: %a\n", storage->idx_addr);
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D_bt2_idx_dump() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_bt2_idx_dest
+ *
+ * Purpose: Release indexing information in memory.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_bt2_idx_dest(const H5D_chk_idx_info_t *idx_info)
+{
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_bt2_idx_dest)
+
+ /* Check args */
+ HDassert(idx_info);
+ HDassert(idx_info->f);
+ HDassert(idx_info->storage);
+
+ /* Check if the v2-btree is open */
+ if(idx_info->storage->u.btree2.bt2) {
+ /* Close v2 B-tree */
+ if(H5B2_close(idx_info->storage->u.btree2.bt2, idx_info->dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "can't close v2 B-tree")
+ idx_info->storage->u.btree2.bt2 = NULL;
+ } /* end if */
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_bt2_idx_dest() */
+
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index 0deb578..e70a7b0 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -464,6 +464,10 @@ done:
* Programmer: Robb Matzke
* Monday, May 18, 1998
*
+ * Modifications:
+ * Vailin Choi; August 2010
+ * Added v2-btree indexing
+ *
*-------------------------------------------------------------------------
*/
herr_t
@@ -483,6 +487,8 @@ H5D_chunk_init(H5F_t *f, hid_t dxpl_id, const H5D_t *dset, hid_t dapl_id)
H5D_COPS_EARRAY == dset->shared->layout.storage.u.chunk.ops) ||
(H5D_CHUNK_IDX_FARRAY == dset->shared->layout.storage.u.chunk.idx_type &&
H5D_COPS_FARRAY == dset->shared->layout.storage.u.chunk.ops) ||
+ (H5D_CHUNK_IDX_BT2 == dset->shared->layout.storage.u.chunk.idx_type &&
+ H5D_COPS_BT2 == dset->shared->layout.storage.u.chunk.ops) ||
(H5D_CHUNK_IDX_BTREE == dset->shared->layout.storage.u.chunk.idx_type &&
H5D_COPS_BTREE == dset->shared->layout.storage.u.chunk.ops));
@@ -547,6 +553,10 @@ done:
* Programmer: Quincey Koziol
* Thursday, January 15, 2009
*
+ * Modifications:
+ * Vailin Choi; August 2010
+ * Added v2-btree indexing
+ *
*-------------------------------------------------------------------------
*/
hbool_t
@@ -562,6 +572,8 @@ H5D_chunk_is_space_alloc(const H5O_storage_t *storage)
H5D_COPS_EARRAY == storage->u.chunk.ops) ||
(H5D_CHUNK_IDX_FARRAY == storage->u.chunk.idx_type &&
H5D_COPS_FARRAY == storage->u.chunk.ops) ||
+ (H5D_CHUNK_IDX_BT2 == storage->u.chunk.idx_type &&
+ H5D_COPS_BT2 == storage->u.chunk.ops) ||
(H5D_CHUNK_IDX_BTREE == storage->u.chunk.idx_type &&
H5D_COPS_BTREE == storage->u.chunk.ops));
@@ -2044,6 +2056,10 @@ done:
* Programmer: Quincey Koziol
* Thursday, January 15, 2009
*
+ * Modifications:
+ * Vailin Choi; August 2010
+ * Added v2-btree indexing
+ *
*-------------------------------------------------------------------------
*/
herr_t
@@ -2060,6 +2076,8 @@ H5D_chunk_idx_reset(H5O_storage_chunk_t *storage, hbool_t reset_addr)
H5D_COPS_EARRAY == storage->ops) ||
(H5D_CHUNK_IDX_FARRAY == storage->idx_type &&
H5D_COPS_FARRAY == storage->ops) ||
+ (H5D_CHUNK_IDX_BT2 == storage->idx_type &&
+ H5D_COPS_BT2 == storage->ops) ||
(H5D_CHUNK_IDX_BTREE == storage->idx_type &&
H5D_COPS_BTREE == storage->ops));
@@ -2201,6 +2219,10 @@ done:
* Programmer: Quincey Koziol
* Thursday, May 22, 2008
*
+ * Modifications:
+ * Vailin Choi; August 2010
+ * Added v2-btree indexing
+ *
*-------------------------------------------------------------------------
*/
herr_t
@@ -2219,6 +2241,8 @@ H5D_chunk_create(H5D_t *dset /*in,out*/, hid_t dxpl_id)
H5D_COPS_EARRAY == dset->shared->layout.storage.u.chunk.ops) ||
(H5D_CHUNK_IDX_FARRAY == dset->shared->layout.storage.u.chunk.idx_type &&
H5D_COPS_FARRAY == dset->shared->layout.storage.u.chunk.ops) ||
+ (H5D_CHUNK_IDX_BT2 == dset->shared->layout.storage.u.chunk.idx_type &&
+ H5D_COPS_BT2 == dset->shared->layout.storage.u.chunk.ops) ||
(H5D_CHUNK_IDX_BTREE == dset->shared->layout.storage.u.chunk.idx_type &&
H5D_COPS_BTREE == dset->shared->layout.storage.u.chunk.ops));
#ifndef NDEBUG
@@ -2257,6 +2281,10 @@ done:
* Programmer: Albert Cheng
* June 27, 1998
*
+ * Modifications:
+ * Vailin Choi; August 2010
+ * Added v2-btree indexing
+ *
*-------------------------------------------------------------------------
*/
herr_t
@@ -2276,6 +2304,8 @@ H5D_chunk_lookup(const H5D_t *dset, hid_t dxpl_id, const hsize_t *chunk_offset,
H5D_COPS_EARRAY == dset->shared->layout.storage.u.chunk.ops) ||
(H5D_CHUNK_IDX_FARRAY == dset->shared->layout.storage.u.chunk.idx_type &&
H5D_COPS_FARRAY == dset->shared->layout.storage.u.chunk.ops) ||
+ (H5D_CHUNK_IDX_BT2 == dset->shared->layout.storage.u.chunk.idx_type &&
+ H5D_COPS_BT2 == dset->shared->layout.storage.u.chunk.ops) ||
(H5D_CHUNK_IDX_BTREE == dset->shared->layout.storage.u.chunk.idx_type &&
H5D_COPS_BTREE == dset->shared->layout.storage.u.chunk.ops));
HDassert(chunk_offset);
@@ -2350,6 +2380,10 @@ done:
* Programmer: Robb Matzke
* Thursday, May 21, 1998
*
+ * Modifications:
+ * Vailin Choi; August 2010
+ * Added v2-btree indexing
+ *
*-------------------------------------------------------------------------
*/
herr_t
@@ -2368,6 +2402,8 @@ H5D_chunk_flush_entry(const H5D_t *dset, hid_t dxpl_id, const H5D_dxpl_cache_t *
H5D_COPS_EARRAY == dset->shared->layout.storage.u.chunk.ops) ||
(H5D_CHUNK_IDX_FARRAY == dset->shared->layout.storage.u.chunk.idx_type &&
H5D_COPS_FARRAY == dset->shared->layout.storage.u.chunk.ops) ||
+ (H5D_CHUNK_IDX_BT2 == dset->shared->layout.storage.u.chunk.idx_type &&
+ H5D_COPS_BT2 == dset->shared->layout.storage.u.chunk.ops) ||
(H5D_CHUNK_IDX_BTREE == dset->shared->layout.storage.u.chunk.idx_type &&
H5D_COPS_BTREE == dset->shared->layout.storage.u.chunk.ops));
HDassert(dxpl_cache);
@@ -3279,6 +3315,10 @@ H5D_chunk_allocated_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
* Programmer: Quincey Koziol
* Tuesday, May 20, 2008
*
+ * Modifications:
+ * Vailin Choi; August 2010
+ * Added v2-btree indexing
+ *
*-------------------------------------------------------------------------
*/
herr_t
@@ -3300,6 +3340,8 @@ H5D_chunk_allocated(H5D_t *dset, hid_t dxpl_id, hsize_t *nbytes)
H5D_COPS_EARRAY == dset->shared->layout.storage.u.chunk.ops) ||
(H5D_CHUNK_IDX_FARRAY == dset->shared->layout.storage.u.chunk.idx_type &&
H5D_COPS_FARRAY == dset->shared->layout.storage.u.chunk.ops) ||
+ (H5D_CHUNK_IDX_BT2 == dset->shared->layout.storage.u.chunk.idx_type &&
+ H5D_COPS_BT2 == dset->shared->layout.storage.u.chunk.ops) ||
(H5D_CHUNK_IDX_BTREE == dset->shared->layout.storage.u.chunk.idx_type &&
H5D_COPS_BTREE == dset->shared->layout.storage.u.chunk.ops));
@@ -3345,6 +3387,10 @@ done:
* Programmer: Albert Cheng
* June 26, 1998
*
+ * Modifications:
+ * Vailin Choi; August 2010
+ * Added v2-btree indexing
+ *
*-------------------------------------------------------------------------
*/
herr_t
@@ -3399,6 +3445,8 @@ H5D_chunk_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite,
H5D_COPS_EARRAY == layout->storage.u.chunk.ops) ||
(H5D_CHUNK_IDX_FARRAY == layout->storage.u.chunk.idx_type &&
H5D_COPS_FARRAY == layout->storage.u.chunk.ops) ||
+ (H5D_CHUNK_IDX_BT2 == layout->storage.u.chunk.idx_type &&
+ H5D_COPS_BT2 == layout->storage.u.chunk.ops) ||
(H5D_CHUNK_IDX_BTREE == layout->storage.u.chunk.idx_type &&
H5D_COPS_BTREE == layout->storage.u.chunk.ops));
HDassert(TRUE == H5P_isa_class(dxpl_id, H5P_DATASET_XFER));
@@ -3846,6 +3894,8 @@ H5D_chunk_update_old_edge_chunks(H5D_t *dset, hid_t dxpl_id, hsize_t old_dim[])
H5D_COPS_EARRAY == layout->storage.u.chunk.ops) ||
(H5D_CHUNK_IDX_FARRAY == layout->storage.u.chunk.idx_type &&
H5D_COPS_FARRAY == layout->storage.u.chunk.ops) ||
+ (H5D_CHUNK_IDX_BT2 == layout->storage.u.chunk.idx_type &&
+ H5D_COPS_BT2 == layout->storage.u.chunk.ops) ||
(H5D_CHUNK_IDX_BTREE == layout->storage.u.chunk.idx_type &&
H5D_COPS_BTREE == layout->storage.u.chunk.ops));
HDassert(TRUE == H5P_isa_class(dxpl_id, H5P_DATASET_XFER));
@@ -4214,6 +4264,9 @@ done:
* To release the chunks, we traverse the B-tree to obtain a list of unused
* allocated chunks, and then call H5B_remove() for each chunk.
*
+ * Vailin Choi; August 2010
+ * Added v2-btree indexing
+ *
*-------------------------------------------------------------------------
*/
herr_t
@@ -4264,6 +4317,8 @@ H5D_chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dim)
H5D_COPS_EARRAY == layout->storage.u.chunk.ops) ||
(H5D_CHUNK_IDX_FARRAY == layout->storage.u.chunk.idx_type &&
H5D_COPS_FARRAY == layout->storage.u.chunk.ops) ||
+ (H5D_CHUNK_IDX_BT2 == layout->storage.u.chunk.idx_type &&
+ H5D_COPS_BT2 == layout->storage.u.chunk.ops) ||
(H5D_CHUNK_IDX_BTREE == layout->storage.u.chunk.idx_type &&
H5D_COPS_BTREE == layout->storage.u.chunk.ops));
HDassert(dxpl_cache);
@@ -4441,7 +4496,7 @@ H5D_chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dim)
dims_outside_fill[i] = FALSE;
carry = FALSE;
- } /* end if */
+ } /* end if */
while(!carry) {
/* Calculate the index of this chunk */
@@ -4629,6 +4684,10 @@ done:
* Programmer: Kent Yang
* November 15, 2005
*
+ * Modifications:
+ * Vailin Choi; August 2010
+ * Added v2-btree indexing
+ *
*-------------------------------------------------------------------------
*/
herr_t
@@ -4647,6 +4706,8 @@ H5D_chunk_addrmap(const H5D_io_info_t *io_info, haddr_t chunk_addr[])
H5D_COPS_EARRAY == dset->shared->layout.storage.u.chunk.ops) ||
(H5D_CHUNK_IDX_FARRAY == dset->shared->layout.storage.u.chunk.idx_type &&
H5D_COPS_FARRAY == dset->shared->layout.storage.u.chunk.ops) ||
+ (H5D_CHUNK_IDX_BT2 == dset->shared->layout.storage.u.chunk.idx_type &&
+ H5D_COPS_BT2 == dset->shared->layout.storage.u.chunk.ops) ||
(H5D_CHUNK_IDX_BTREE == dset->shared->layout.storage.u.chunk.idx_type &&
H5D_COPS_BTREE == dset->shared->layout.storage.u.chunk.ops));
HDassert(chunk_addr);
@@ -4685,6 +4746,10 @@ done:
* Programmer: Quincey Koziol
* Thursday, March 20, 2003
*
+ * Modifications:
+ * Vailin Choi; August 2010
+ * Added v2-btree indexing
+ *
*-------------------------------------------------------------------------
*/
herr_t
@@ -4708,6 +4773,8 @@ H5D_chunk_delete(H5F_t *f, hid_t dxpl_id, H5O_t *oh, H5O_storage_t *storage)
H5D_COPS_EARRAY == storage->u.chunk.ops) ||
(H5D_CHUNK_IDX_FARRAY == storage->u.chunk.idx_type &&
H5D_COPS_FARRAY == storage->u.chunk.ops) ||
+ (H5D_CHUNK_IDX_BT2 == storage->u.chunk.idx_type &&
+ H5D_COPS_BT2 == storage->u.chunk.ops) ||
(H5D_CHUNK_IDX_BTREE == storage->u.chunk.idx_type &&
H5D_COPS_BTREE == storage->u.chunk.ops));
@@ -5049,6 +5116,9 @@ done:
* Programmer: Peter Cao
* August 20, 2005
*
+ * Vailin Choi; August 2010
+ * Added v2-btree indexing
+ *
*-------------------------------------------------------------------------
*/
herr_t
@@ -5090,6 +5160,8 @@ H5D_chunk_copy(H5F_t *f_src, H5O_storage_chunk_t *storage_src,
H5D_COPS_EARRAY == storage_src->ops) ||
(H5D_CHUNK_IDX_FARRAY == storage_src->idx_type &&
H5D_COPS_FARRAY == storage_src->ops) ||
+ (H5D_CHUNK_IDX_BT2 == storage_src->idx_type &&
+ H5D_COPS_BT2 == storage_src->ops) ||
(H5D_CHUNK_IDX_BTREE == storage_src->idx_type &&
H5D_COPS_BTREE == storage_src->ops));
HDassert(layout_src);
@@ -5099,6 +5171,8 @@ H5D_chunk_copy(H5F_t *f_src, H5O_storage_chunk_t *storage_src,
H5D_COPS_EARRAY == storage_dst->ops) ||
(H5D_CHUNK_IDX_FARRAY == storage_dst->idx_type &&
H5D_COPS_FARRAY == storage_dst->ops) ||
+ (H5D_CHUNK_IDX_BT2 == storage_dst->idx_type &&
+ H5D_COPS_BT2 == storage_dst->ops) ||
(H5D_CHUNK_IDX_BTREE == storage_dst->idx_type &&
H5D_COPS_BTREE == storage_dst->ops));
HDassert(ds_extent_src);
@@ -5324,6 +5398,10 @@ done:
* Programmer: Vailin Choi
* June 8, 2007
*
+ * Modifications:
+ * Vailin Choi; August 2010
+ * Added v2-btree indexing
+ *
*-------------------------------------------------------------------------
*/
herr_t
@@ -5342,6 +5420,8 @@ H5D_chunk_bh_info(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout,
H5D_COPS_EARRAY == layout->storage.u.chunk.ops) ||
(H5D_CHUNK_IDX_FARRAY == layout->storage.u.chunk.idx_type &&
H5D_COPS_FARRAY == layout->storage.u.chunk.ops) ||
+ (H5D_CHUNK_IDX_BT2 == layout->storage.u.chunk.idx_type &&
+ H5D_COPS_BT2 == layout->storage.u.chunk.ops) ||
(H5D_CHUNK_IDX_BTREE == layout->storage.u.chunk.idx_type &&
H5D_COPS_BTREE == layout->storage.u.chunk.ops));
HDassert(pline);
@@ -5421,6 +5501,10 @@ H5D_chunk_dump_index_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
* Programmer: Robb Matzke
* Wednesday, April 28, 1999
*
+ * Modifications:
+ * Vailin Choi; August 2010
+ * Added v2-btree indexing
+ *
*-------------------------------------------------------------------------
*/
herr_t
@@ -5436,6 +5520,8 @@ H5D_chunk_dump_index(H5D_t *dset, hid_t dxpl_id, FILE *stream)
H5D_COPS_EARRAY == dset->shared->layout.storage.u.chunk.ops) ||
(H5D_CHUNK_IDX_FARRAY == dset->shared->layout.storage.u.chunk.idx_type &&
H5D_COPS_FARRAY == dset->shared->layout.storage.u.chunk.ops) ||
+ (H5D_CHUNK_IDX_BT2 == dset->shared->layout.storage.u.chunk.idx_type &&
+ H5D_COPS_BT2 == dset->shared->layout.storage.u.chunk.ops) ||
(H5D_CHUNK_IDX_BTREE == dset->shared->layout.storage.u.chunk.idx_type &&
H5D_COPS_BTREE == dset->shared->layout.storage.u.chunk.ops));
@@ -5481,6 +5567,10 @@ done:
* Programmer: Robb Matzke
* Thursday, May 21, 1998
*
+ * Modifications:
+ * Vailin Choi; August 2010
+ * Added v2-btree indexing
+ *
*-------------------------------------------------------------------------
*/
herr_t
@@ -5502,6 +5592,8 @@ H5D_chunk_dest(H5F_t *f, hid_t dxpl_id, H5D_t *dset)
H5D_COPS_EARRAY == dset->shared->layout.storage.u.chunk.ops) ||
(H5D_CHUNK_IDX_FARRAY == dset->shared->layout.storage.u.chunk.idx_type &&
H5D_COPS_FARRAY == dset->shared->layout.storage.u.chunk.ops) ||
+ (H5D_CHUNK_IDX_BT2 == dset->shared->layout.storage.u.chunk.idx_type &&
+ H5D_COPS_BT2 == dset->shared->layout.storage.u.chunk.ops) ||
(H5D_CHUNK_IDX_BTREE == dset->shared->layout.storage.u.chunk.idx_type &&
H5D_COPS_BTREE == dset->shared->layout.storage.u.chunk.ops));
diff --git a/src/H5Dint.c b/src/H5Dint.c
index 8c4d8cd..381323c 100644
--- a/src/H5Dint.c
+++ b/src/H5Dint.c
@@ -1116,6 +1116,7 @@ H5D_create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id,
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve external file list")
} /* end if */
+
/* Set the latest version of the layout, pline & fill messages, if requested */
if(H5F_USE_LATEST_FORMAT(file)) {
/* Set the latest version for the I/O pipeline message */
@@ -1129,7 +1130,11 @@ H5D_create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id,
/* Set the latest version for the layout message */
if(H5D_layout_set_latest_version(&new_dset->shared->layout, new_dset->shared->space) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set latest version of layout")
- } /* end if */
+ } else if(new_dset->shared->layout.version >= H5O_LAYOUT_VERSION_4) {
+ /* Use latest indexing type for layout message version >= 4 */
+ if(H5D_layout_set_latest_indexing(&new_dset->shared->layout, new_dset->shared->space) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set latest indexing")
+ }
/* Check if this dataset is going into a parallel file and set space allocation time */
if(IS_H5FD_MPI(file))
diff --git a/src/H5Dlayout.c b/src/H5Dlayout.c
index 1505f0e..bc3a77f 100644
--- a/src/H5Dlayout.c
+++ b/src/H5Dlayout.c
@@ -71,6 +71,9 @@
* Programmer: Quincey Koziol
* Thursday, March 20, 2008
*
+ * Modifications:
+ * Vailin Choi; August 2010
+ * Added v2 B-tree indexing.
*-------------------------------------------------------------------------
*/
herr_t
@@ -101,6 +104,10 @@ H5D_layout_set_io_ops(const H5D_t *dataset)
dataset->shared->layout.storage.u.chunk.ops = H5D_COPS_BTREE;
break;
+ case H5D_CHUNK_IDX_BT2:
+ dataset->shared->layout.storage.u.chunk.ops = H5D_COPS_BT2;
+ break;
+
case H5D_CHUNK_IDX_FARRAY:
dataset->shared->layout.storage.u.chunk.ops = H5D_COPS_FARRAY;
break;
@@ -143,6 +150,10 @@ done:
* Programmer: Raymond Lu
* August 14, 2002
*
+ * Modifications:
+ * Vailin Choi; August 2010
+ * Added v2 B-tree indexing.
+ * Removed v1 B-tree support for layout message version >= 4.
*-------------------------------------------------------------------------
*/
size_t
@@ -209,18 +220,19 @@ H5D_layout_meta_size(const H5F_t *f, const H5O_layout_t *layout, hbool_t include
ret_value++;
switch(layout->u.chunk.idx_type) {
- case H5D_CHUNK_IDX_BTREE: /* Remove this when v2 B-tree indices added */
- /* Nothing to do */
+ case H5D_CHUNK_IDX_BT2:
+ /* v2 B-tree creation parameters */
+ ret_value += H5D_BT2_CREATE_PARAM_SIZE;
break;
case H5D_CHUNK_IDX_FARRAY:
/* Fixed array creation parameters */
- ret_value += 1;
+ ret_value += H5D_FARRAY_CREATE_PARAM_SIZE;
break;
case H5D_CHUNK_IDX_EARRAY:
/* Extensible array creation parameters */
- ret_value += 5;
+ ret_value += H5D_EARRAY_CREATE_PARAM_SIZE;
break;
default:
@@ -244,6 +256,42 @@ done:
* Function: H5D_layout_set_latest_version
*
* Purpose: Set the encoding for a layout to the latest version.
+ * Part of the coding in this routine is moved to
+ * H5D_layout_set_latest_indexing().
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * Thursday, January 15, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_layout_set_latest_version(H5O_layout_t *layout, const H5S_t *space)
+{
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5D_layout_set_latest_version, FAIL)
+
+ /* Sanity check */
+ HDassert(layout);
+
+ /* Set encoding of layout to latest version */
+ layout->version = H5O_LAYOUT_VERSION_LATEST;
+
+ /* Set the latest indexing type for the layout message */
+ ret_value = H5D_layout_set_latest_indexing(layout, space);
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_layout_set_latest_version() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_layout_set_latest_indexing
+ *
+ * Purpose: Set the latest indexing type for a layout message
+ * This is moved from H5D_layout_set_latest_version().
*
* Return: Non-negative on success/Negative on failure
*
@@ -255,23 +303,22 @@ done:
* Modified to use Fixed Array indexing for extendible chunked dataset.
* (fixed max. dim. setting but exclude H5S_UNLIMITED)
*
+ * Vailin Choi; August 2010
+ * Added v2 B-tree indexing for chunked dataset >1 unlimited dimensions.
*-------------------------------------------------------------------------
*/
herr_t
-H5D_layout_set_latest_version(H5O_layout_t *layout, const H5S_t *space)
+H5D_layout_set_latest_indexing(H5O_layout_t *layout, const H5S_t *space)
{
int sndims; /* Rank of dataspace */
unsigned ndims; /* Rank of dataspace */
herr_t ret_value = SUCCEED; /* Return value */
- FUNC_ENTER_NOAPI(H5D_layout_set_latest_version, FAIL)
+ FUNC_ENTER_NOAPI(H5D_layout_set_latest_indexing, FAIL)
/* Sanity check */
HDassert(layout);
- /* Set encoding of layout to latest version */
- layout->version = H5O_LAYOUT_VERSION_LATEST;
-
/* Query the dimensionality of the dataspace */
if((sndims = H5S_GET_EXTENT_NDIMS(space)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "invalid dataspace rank")
@@ -299,6 +346,7 @@ H5D_layout_set_latest_version(H5O_layout_t *layout, const H5S_t *space)
HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "dataset with unlimited dimensions is not chunked")
if(1 == unlim_count) { /* Chunked dataset with only 1 unlimited dimension */
+ /* Set the chunk index type to an extensible array */
layout->u.chunk.idx_type = H5D_CHUNK_IDX_EARRAY;
layout->storage.u.chunk.idx_type = H5D_CHUNK_IDX_EARRAY;
layout->storage.u.chunk.ops = H5D_COPS_EARRAY;
@@ -313,8 +361,16 @@ H5D_layout_set_latest_version(H5O_layout_t *layout, const H5S_t *space)
layout->u.chunk.u.earray.cparam.data_blk_min_elmts = H5D_EARRAY_DATA_BLK_MIN_ELMTS;
layout->u.chunk.u.earray.cparam.max_dblk_page_nelmts_bits = H5D_EARRAY_MAX_DBLOCK_PAGE_NELMTS_BITS;
} else { /* Chunked dataset with > 1 unlimited dimensions */
- /* Add setup to use v2 B-tree chunk indices here */
- }
+ /* Set the chunk index type to v2 B-tree */
+ layout->u.chunk.idx_type = H5D_CHUNK_IDX_BT2;
+ layout->storage.u.chunk.idx_type = H5D_CHUNK_IDX_BT2;
+ layout->storage.u.chunk.ops = H5D_COPS_BT2;
+
+ /* Set the v2 B-tree creation parameters */
+ layout->u.chunk.u.btree2.cparam.node_size = H5D_BT2_NODE_SIZE;
+ layout->u.chunk.u.btree2.cparam.split_percent = H5D_BT2_SPLIT_PERC;
+ layout->u.chunk.u.btree2.cparam.merge_percent = H5D_BT2_MERGE_PERC;
+ }
} else if(layout->type == H5D_CHUNKED) {
/* Chunked dataset with fixed dimensions (with or without max. dimension setting) */
/* Set the chunk index type to Fixed Array */
@@ -332,7 +388,7 @@ H5D_layout_set_latest_version(H5O_layout_t *layout, const H5S_t *space)
done:
FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5D_layout_set_latest_version() */
+} /* end H5D_layout_set_latest_indexing() */
/*-------------------------------------------------------------------------
diff --git a/src/H5Dpkg.h b/src/H5Dpkg.h
index 63cc010..fa7eacf 100644
--- a/src/H5Dpkg.h
+++ b/src/H5Dpkg.h
@@ -34,6 +34,7 @@
/* Other private headers needed by this file */
#include "H5ACprivate.h" /* Metadata cache */
#include "H5Gprivate.h" /* Groups */
+#include "H5B2private.h" /* v2 B-trees */
#include "H5SLprivate.h" /* Skip lists */
#include "H5Tprivate.h" /* Datatypes */
@@ -66,17 +67,25 @@
#define H5D_CHUNK_HASH(D, ADDR) H5F_addr_hash(ADDR, (D)->cache.chunk.nslots)
/* Default creation parameters for chunk index data structures */
+/* See H5O_layout_chunk_t */
/* Fixed array creation values */
-#define H5D_FARRAY_MAX_DBLK_PAGE_NELMTS_BITS 10 /* i.e. 1024 elements per data block page */
+#define H5D_FARRAY_CREATE_PARAM_SIZE 1 /* Size of the creation parameters in bytes */
+#define H5D_FARRAY_MAX_DBLK_PAGE_NELMTS_BITS 10 /* i.e. 1024 elements per data block page */
/* Extensible array creation values */
-#define H5D_EARRAY_MAX_NELMTS_BITS 32 /* i.e. 4 giga-elements */
-#define H5D_EARRAY_IDX_BLK_ELMTS 4
-#define H5D_EARRAY_SUP_BLK_MIN_DATA_PTRS 4
-#define H5D_EARRAY_DATA_BLK_MIN_ELMTS 16
-#define H5D_EARRAY_MAX_DBLOCK_PAGE_NELMTS_BITS 10 /* i.e. 1024 elements per data block page */
-
+#define H5D_EARRAY_CREATE_PARAM_SIZE 5 /* Size of the creation parameters in bytes */
+#define H5D_EARRAY_MAX_NELMTS_BITS 32 /* i.e. 4 giga-elements */
+#define H5D_EARRAY_IDX_BLK_ELMTS 4
+#define H5D_EARRAY_SUP_BLK_MIN_DATA_PTRS 4
+#define H5D_EARRAY_DATA_BLK_MIN_ELMTS 16
+#define H5D_EARRAY_MAX_DBLOCK_PAGE_NELMTS_BITS 10 /* i.e. 1024 elements per data block page */
+
+/* v2 B-tree creation values for raw meta_size */
+#define H5D_BT2_CREATE_PARAM_SIZE 6 /* Size of the creation parameters in bytes */
+#define H5D_BT2_NODE_SIZE 512
+#define H5D_BT2_SPLIT_PERC 100
+#define H5D_BT2_MERGE_PERC 40
/****************************/
/* Package Private Typedefs */
@@ -554,6 +563,12 @@ H5_DLLVAR const H5D_layout_ops_t H5D_LOPS_CHUNK[1];
H5_DLLVAR const H5D_chunk_ops_t H5D_COPS_BTREE[1];
H5_DLLVAR const H5D_chunk_ops_t H5D_COPS_EARRAY[1];
H5_DLLVAR const H5D_chunk_ops_t H5D_COPS_FARRAY[1];
+H5_DLLVAR const H5D_chunk_ops_t H5D_COPS_BT2[1];
+
+/* The v2 B-tree class for indexing chunked datasets with >1 unlimited dimensions */
+H5_DLLVAR const H5B2_class_t H5D_BT2[1];
+H5_DLLVAR const H5B2_class_t H5D_BT2_FILT[1];
+
/******************************/
@@ -606,6 +621,8 @@ H5_DLL size_t H5D_layout_meta_size(const H5F_t *f, const H5O_layout_t *layout,
hbool_t include_compact_data);
H5_DLL herr_t H5D_layout_set_latest_version(H5O_layout_t *layout,
const H5S_t *space);
+H5_DLL herr_t H5D_layout_set_latest_indexing(H5O_layout_t *layout,
+ const H5S_t *space);
H5_DLL herr_t H5D_layout_oh_create(H5F_t *file, hid_t dxpl_id, H5O_t *oh,
H5D_t *dset, hid_t dapl_id);
H5_DLL herr_t H5D_layout_oh_read(H5D_t *dset, hid_t dxpl_id, hid_t dapl_id,
diff --git a/src/H5Dpublic.h b/src/H5Dpublic.h
index 972b33b..f4c62c9 100644
--- a/src/H5Dpublic.h
+++ b/src/H5Dpublic.h
@@ -53,9 +53,10 @@ typedef enum H5D_layout_t {
/* Types of chunk index data structures */
typedef enum H5D_chunk_index_t {
- H5D_CHUNK_IDX_BTREE = 0, /* v1 B-tree index (default) */
+ H5D_CHUNK_IDX_BTREE = 0, /* v1 B-tree index (default) */
H5D_CHUNK_IDX_FARRAY = 1, /* Fixed array (for 0 unlimited dims) */
H5D_CHUNK_IDX_EARRAY = 2, /* Extensible array (for 1 unlimited dim) */
+ H5D_CHUNK_IDX_BT2 = 3, /* v2 B-tree index (for >1 unlimited dims) */
H5D_CHUNK_IDX_NTYPES /*this one must be last! */
} H5D_chunk_index_t;
diff --git a/src/H5HFbtree2.c b/src/H5HFbtree2.c
index 3f208e7..bce58b7 100644
--- a/src/H5HFbtree2.c
+++ b/src/H5HFbtree2.c
@@ -287,7 +287,6 @@ H5HF_huge_bt2_crt_dbg_context(H5F_t *f, hid_t UNUSED dxpl_id, haddr_t UNUSED add
/* Sanity check */
HDassert(f);
- HDassert(H5F_addr_defined(addr));
/* Allocate callback context */
if(NULL == (ctx = H5FL_MALLOC(H5HF_huge_bt2_ctx_t)))
diff --git a/src/H5Olayout.c b/src/H5Olayout.c
index debc169..bbebb8e 100644
--- a/src/H5Olayout.c
+++ b/src/H5Olayout.c
@@ -96,6 +96,11 @@ H5FL_DEFINE(H5O_layout_t);
* Programmer: Robb Matzke
* Wednesday, October 8, 1997
*
+ * Modifications:
+ * Vailin Choi; Aug 2010
+ * Added v2 B-tree index.
+ * Removed v1 B-tree support for layout message version > 4.
+ *
*-------------------------------------------------------------------------
*/
static void *
@@ -306,8 +311,10 @@ H5O_layout_decode(H5F_t *f, hid_t UNUSED dxpl_id, H5O_t UNUSED *open_oh,
mesg->storage.u.chunk.idx_type = mesg->u.chunk.idx_type;
switch(mesg->u.chunk.idx_type) {
- case H5D_CHUNK_IDX_BTREE: /* Remove this when v2 B-tree indices added */
- /* Nothing to do */
+ case H5D_CHUNK_IDX_BT2: /* v2 B-tree index */
+ UINT32DECODE(p, mesg->u.chunk.u.btree2.cparam.node_size);
+ mesg->u.chunk.u.btree2.cparam.split_percent = *p++;
+ mesg->u.chunk.u.btree2.cparam.merge_percent = *p++;
break;
case H5D_CHUNK_IDX_FARRAY:
@@ -394,6 +401,10 @@ done:
* Added version number 4 case to allow different kinds of indices for
* looking up chunks.
*
+ * Vailin Choi; Aug 2010
+ * Added v2 B-tree index.
+ * Removed v1 B-tree support for layout message version > 4.
+ *
*-------------------------------------------------------------------------
*/
static herr_t
@@ -480,8 +491,10 @@ H5O_layout_encode(H5F_t *f, hbool_t UNUSED disable_shared, uint8_t *p, const voi
*p++ = (uint8_t)mesg->u.chunk.idx_type;
switch(mesg->u.chunk.idx_type) {
- case H5D_CHUNK_IDX_BTREE: /* Remove this when v2 B-tree indices added */
- /* Nothing to do */
+ case H5D_CHUNK_IDX_BT2: /* v2 B-tree index */
+ UINT32ENCODE(p, mesg->u.chunk.u.btree2.cparam.node_size);
+ *p++ = mesg->u.chunk.u.btree2.cparam.split_percent;
+ *p++ = mesg->u.chunk.u.btree2.cparam.merge_percent;
break;
case H5D_CHUNK_IDX_FARRAY:
@@ -887,6 +900,8 @@ done:
* Wednesday, October 8, 1997
*
* Modifications:
+ * Vailin Choi; Aug 2010
+ * Added v2 B-tree index.
*
*-------------------------------------------------------------------------
*/
@@ -929,6 +944,11 @@ H5O_layout_debug(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, const void *_mesg,
"Index Type:", "v1 B-tree");
break;
+ case H5D_CHUNK_IDX_BT2:
+ HDfprintf(stream, "%*s%-*s %s\n", indent, "", fwidth,
+ "Index Type:", "v2 B-tree");
+ break;
+
case H5D_CHUNK_IDX_FARRAY:
HDfprintf(stream, "%*s%-*s %s\n", indent, "", fwidth,
"Index Type:", "Fixed Array");
diff --git a/src/H5Oprivate.h b/src/H5Oprivate.h
index b062b95..a736e7c 100644
--- a/src/H5Oprivate.h
+++ b/src/H5Oprivate.h
@@ -396,6 +396,13 @@ typedef struct H5O_storage_chunk_btree_t {
} H5O_storage_chunk_btree_t;
/* Forward declaration of structs used below */
+struct H5B2_t; /* Defined in H5B2pkg.h */
+
+typedef struct H5O_storage_chunk_bt2_t {
+ struct H5B2_t *bt2;
+} H5O_storage_chunk_bt2_t;
+
+/* Forward declaration of structs used below */
struct H5FA_t; /* Defined in H5FAprivate.h */
typedef struct H5O_storage_chunk_farray_t {
@@ -416,6 +423,7 @@ typedef struct H5O_storage_chunk_t {
const struct H5D_chunk_ops_t *ops; /* Pointer to chunked storage operations */
union {
H5O_storage_chunk_btree_t btree; /* Information for v1 B-tree index */
+ H5O_storage_chunk_bt2_t btree2; /* Information for v2 B-tree index */
H5O_storage_chunk_farray_t farray; /* Information for fixed array index */
H5O_storage_chunk_earray_t earray; /* Information for extensible array index */
} u;
@@ -436,6 +444,15 @@ typedef struct H5O_storage_t {
} u;
} H5O_storage_t;
+typedef struct H5O_layout_chunk_bt2_t {
+ /* Creation parameters for v2 B-tree data structure */
+ struct {
+ uint32_t node_size; /* Size of each node (in bytes) */
+ uint8_t split_percent; /* % full to split nodes */
+ uint8_t merge_percent; /* % full to merge nodes */
+ } cparam;
+} H5O_layout_chunk_bt2_t;
+
typedef struct H5O_layout_chunk_farray_t {
/* Creation parameters for fixed array data structure */
struct {
@@ -475,6 +492,7 @@ typedef struct H5O_layout_chunk_t {
union {
H5O_layout_chunk_farray_t farray; /* Information for fixed array index */
H5O_layout_chunk_earray_t earray; /* Information for extensible array index */
+ H5O_layout_chunk_bt2_t btree2; /* Information for v2 B-tree index */
} u;
} H5O_layout_chunk_t;
diff --git a/src/H5Ostorage.c b/src/H5Ostorage.c
index f6891d7..2995e47 100644
--- a/src/H5Ostorage.c
+++ b/src/H5Ostorage.c
@@ -103,6 +103,11 @@ H5FL_DEFINE_STATIC(H5O_storage_t);
* Programmer: Quincey Koziol
* Wednesday, July 29, 2009
*
+ * Modifications:
+ * Vailin Choi; Aug 2010
+ * Added v2 B-tree index.
+ * Removed v1 B-tree support.
+ *
*-------------------------------------------------------------------------
*/
static void *
@@ -173,9 +178,9 @@ H5O_storage_decode(H5F_t *f, hid_t UNUSED dxpl_id, H5O_t UNUSED *open_oh,
/* Chunk index type */
mesg->u.chunk.idx_type = (H5D_chunk_index_t)*p++;
switch(mesg->u.chunk.idx_type) {
- case H5D_CHUNK_IDX_BTREE: /* Remove this when v2 B-tree indices added */
+ case H5D_CHUNK_IDX_BT2: /* v2 B-tree index */
/* Set the chunk operations */
- mesg->u.chunk.ops = H5D_COPS_BTREE;
+ mesg->u.chunk.ops = H5D_COPS_BT2;
break;
case H5D_CHUNK_IDX_FARRAY:
@@ -603,6 +608,10 @@ done:
* Programmer: Quincey Koziol
* Thursday, July 30, 2009
*
+ * Modifications:
+ * Vailin Choi; Aug 2010
+ * Added v2 B-tree index.
+ *
*-------------------------------------------------------------------------
*/
static herr_t
@@ -634,6 +643,11 @@ H5O_storage_debug(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, const void *_mesg,
"Index Type:", "v1 B-tree");
break;
+ case H5D_CHUNK_IDX_BT2:
+ HDfprintf(stream, "%*s%-*s %s\n", indent, "", fwidth,
+ "Index Type:", "v2 B-tree");
+ break;
+
case H5D_CHUNK_IDX_FARRAY:
HDfprintf(stream, "%*s%-*s %s\n", indent, "", fwidth,
"Index Type:", "Fixed Array");
diff --git a/src/H5SMbtree2.c b/src/H5SMbtree2.c
index 95527f9..156a6c5 100755
--- a/src/H5SMbtree2.c
+++ b/src/H5SMbtree2.c
@@ -240,7 +240,6 @@ H5SM_bt2_crt_dbg_context(H5F_t *f, hid_t UNUSED dxpl_id, haddr_t UNUSED addr)
/* Sanity check */
HDassert(f);
- HDassert(H5F_addr_defined(addr));
/* Allocate callback context */
if(NULL == (ctx = H5FL_MALLOC(H5SM_bt2_ctx_t)))
diff --git a/src/Makefile.am b/src/Makefile.am
index 5dd6b36..6f93c4e 100755
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -46,7 +46,7 @@ libhdf5_la_SOURCES= H5.c H5checksum.c H5dbg.c H5system.c H5timer.c H5trace.c \
H5AC.c H5B.c H5Bcache.c H5Bdbg.c \
H5B2.c H5B2cache.c H5B2dbg.c H5B2hdr.c H5B2int.c H5B2stat.c H5B2test.c \
H5C.c H5CS.c \
- H5D.c H5Dbtree.c H5Dchunk.c H5Dcompact.c H5Dcontig.c H5Ddbg.c \
+ H5D.c H5Dbtree.c H5Dbtree2.c H5Dchunk.c H5Dcompact.c H5Dcontig.c H5Ddbg.c \
H5Ddeprec.c H5Dearray.c H5Defl.c H5Dfarray.c H5Dfill.c H5Dint.c \
H5Dio.c H5Dlayout.c H5Dmpio.c H5Doh.c H5Dproxy.c H5Dscatgath.c \
H5Dselect.c H5Dtest.c \
diff --git a/src/Makefile.in b/src/Makefile.in
index 1fa47ad..8dbba32 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -100,14 +100,14 @@ am_libhdf5_la_OBJECTS = H5.lo H5checksum.lo H5dbg.lo H5system.lo \
H5Adeprec.lo H5Aint.lo H5Atest.lo H5AC.lo H5B.lo H5Bcache.lo \
H5Bdbg.lo H5B2.lo H5B2cache.lo H5B2dbg.lo H5B2hdr.lo \
H5B2int.lo H5B2stat.lo H5B2test.lo H5C.lo H5CS.lo H5D.lo \
- H5Dbtree.lo H5Dchunk.lo H5Dcompact.lo H5Dcontig.lo H5Ddbg.lo \
- H5Ddeprec.lo H5Dearray.lo H5Defl.lo H5Dfarray.lo H5Dfill.lo \
- H5Dint.lo H5Dio.lo H5Dlayout.lo H5Dmpio.lo H5Doh.lo \
- H5Dproxy.lo H5Dscatgath.lo H5Dselect.lo H5Dtest.lo H5E.lo \
- H5Edeprec.lo H5Eint.lo H5EA.lo H5EAcache.lo H5EAdbg.lo \
- H5EAdblkpage.lo H5EAdblock.lo H5EAhdr.lo H5EAiblock.lo \
- H5EAint.lo H5EAsblock.lo H5EAstat.lo H5EAtest.lo H5F.lo \
- H5Faccum.lo H5Fdbg.lo H5Fdeprec.lo H5Ffake.lo H5Fio.lo \
+ H5Dbtree.lo H5Dbtree2.lo H5Dchunk.lo H5Dcompact.lo \
+ H5Dcontig.lo H5Ddbg.lo H5Ddeprec.lo H5Dearray.lo H5Defl.lo \
+ H5Dfarray.lo H5Dfill.lo H5Dint.lo H5Dio.lo H5Dlayout.lo \
+ H5Dmpio.lo H5Doh.lo H5Dproxy.lo H5Dscatgath.lo H5Dselect.lo \
+ H5Dtest.lo H5E.lo H5Edeprec.lo H5Eint.lo H5EA.lo H5EAcache.lo \
+ H5EAdbg.lo H5EAdblkpage.lo H5EAdblock.lo H5EAhdr.lo \
+ H5EAiblock.lo H5EAint.lo H5EAsblock.lo H5EAstat.lo H5EAtest.lo \
+ H5F.lo H5Faccum.lo H5Fdbg.lo H5Fdeprec.lo H5Ffake.lo H5Fio.lo \
H5Fmount.lo H5Fmpi.lo H5Fquery.lo H5Fsfile.lo H5Fsuper.lo \
H5Fsuper_cache.lo H5Ftest.lo H5FA.lo H5FAcache.lo H5FAdbg.lo \
H5FAdblock.lo H5FAdblkpage.lo H5FAhdr.lo H5FAstat.lo \
@@ -468,7 +468,7 @@ libhdf5_la_SOURCES = H5.c H5checksum.c H5dbg.c H5system.c H5timer.c H5trace.c \
H5AC.c H5B.c H5Bcache.c H5Bdbg.c \
H5B2.c H5B2cache.c H5B2dbg.c H5B2hdr.c H5B2int.c H5B2stat.c H5B2test.c \
H5C.c H5CS.c \
- H5D.c H5Dbtree.c H5Dchunk.c H5Dcompact.c H5Dcontig.c H5Ddbg.c \
+ H5D.c H5Dbtree.c H5Dbtree2.c H5Dchunk.c H5Dcompact.c H5Dcontig.c H5Ddbg.c \
H5Ddeprec.c H5Dearray.c H5Defl.c H5Dfarray.c H5Dfill.c H5Dint.c \
H5Dio.c H5Dlayout.c H5Dmpio.c H5Doh.c H5Dproxy.c H5Dscatgath.c \
H5Dselect.c H5Dtest.c \
@@ -694,6 +694,7 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5CS.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5D.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5Dbtree.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5Dbtree2.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5Dchunk.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5Dcompact.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5Dcontig.Plo@am__quote@
diff --git a/test/dsets.c b/test/dsets.c
index 3d42efc..ae23e7e 100644
--- a/test/dsets.c
+++ b/test/dsets.c
@@ -130,7 +130,6 @@ const char *FILENAME[] = {
#define DSET_FIXED_MAX "DSET_FIXED_MAX"
#define DSET_FIXED_NOMAX "DSET_FIXED_NOMAX"
#define DSET_FIXED_BIG "DSET_FIXED_BIG"
-
#define POINTS 72
#define POINTS_BIG 2500
@@ -183,9 +182,11 @@ const char *FILENAME[] = {
/* Names for zero-dim test */
#define ZERODIM_DATASET "zerodim"
+#define ZERODIM_DATASET2 "zerodim2"
/* Parameters for zero-dim test */
#define MISSING_CHUNK_DATASET "missing_chunk"
+#define MISSING_CHUNK_DATASET2 "missing_chunk2"
#define MISSING_CHUNK_DIM 100
/* Names for random chunks test */
@@ -210,6 +211,10 @@ const char *FILENAME[] = {
/* Parameters for testing bypassing chunk cache */
#define BYPASS_DATASET1 "Dset1"
#define BYPASS_DATASET2 "Dset2"
+
+#define T_BYPASS_DATASET1 "T_Dset1"
+#define T_BYPASS_DATASET2 "T_Dset2"
+
#define BYPASS_DIM 1000
#define BYPASS_CHUNK_DIM 500
#define BYPASS_FILL_VALUE 7
@@ -923,8 +928,8 @@ error:
/* Close file */
H5Sclose(space);
H5Pclose(plist);
- H5Fclose(file);
H5Dclose(dataset);
+ H5Fclose(file);
} H5E_END_TRY;
return -1;
@@ -6411,22 +6416,43 @@ error:
* Programmer: Quincey Koziol
* Tuesday, July 27, 2004
*
+ * Modifications:
+ * Vailin Choi; June 2010
+ * Added dataset with > 1 unlimited dimensions to the test.
+ *
*-------------------------------------------------------------------------
*/
static herr_t
test_zero_dims(hid_t file)
{
hid_t s=-1, d=-1, dcpl=-1;
- hsize_t dsize=0, dmax=H5S_UNLIMITED, csize=5;
+ hid_t s2 = -1, d2 = -1, dcpl2 = -1;
+ hsize_t dsize = 0, dmax = H5S_UNLIMITED, csize = 5;
+ hsize_t dsize2[2] = {0, 0};
+ hsize_t dmax2[2] = {H5S_UNLIMITED, H5S_UNLIMITED};
+ hsize_t csize2[2] = {5, 5};
+ hid_t fapl; /* File access property list */
+ H5D_chunk_index_t idx_type; /* Dataset chunk index type */
+ H5F_libver_t low; /* File format low bound */
herr_t ret;
TESTING("I/O on datasets with zero-sized dims");
- if((s = H5Screate_simple(1, &dsize, &dmax)) < 0) FAIL_STACK_ERROR
+ /* Get the file's file access property list */
+ if((fapl = H5Fget_access_plist(file)) < 0) TEST_ERROR;
- /* Try creating chunked dataset with zero-sized chunk dimensions */
- if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0) FAIL_STACK_ERROR
+ /* Get library format */
+ if(H5Pget_libver_bounds(fapl, &low, NULL) < 0) TEST_ERROR;
+
+ /*
+ * One-dimensional dataset
+ */
+ if((s = H5Screate_simple(1, &dsize, &dmax)) < 0) TEST_ERROR;
+
+ /* Try creating chunked dataset with undefined chunk dimensions */
+ if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0) TEST_ERROR;
if(H5Pset_layout(dcpl, H5D_CHUNKED) < 0) FAIL_STACK_ERROR
+
H5E_BEGIN_TRY {
d = H5Dcreate2(file, ZERODIM_DATASET, H5T_NATIVE_INT, s, H5P_DEFAULT, dcpl, H5P_DEFAULT);
} H5E_END_TRY;
@@ -6435,6 +6461,7 @@ test_zero_dims(hid_t file)
FAIL_PUTS_ERROR("created dataset with undefined chunk dimensions")
} /* end if */
+ /* Try creating chunked dataset with zero-sized chunk dimensions */
H5E_BEGIN_TRY {
ret = H5Pset_chunk(dcpl, 1, &dsize);
} H5E_END_TRY;
@@ -6443,17 +6470,78 @@ test_zero_dims(hid_t file)
if(H5Pclose(dcpl) < 0) FAIL_STACK_ERROR
+ /* Create the zero-sized extendible dataset */
if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0) FAIL_STACK_ERROR
if(H5Pset_chunk(dcpl, 1, &csize) < 0) FAIL_STACK_ERROR
if((d = H5Dcreate2(file, ZERODIM_DATASET, H5T_NATIVE_INT, s, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0) FAIL_STACK_ERROR
+ /* Get the chunk index type */
+ if(H5D_layout_idx_type_test(d, &idx_type) < 0) TEST_ERROR;
+
+ /* Verify index type */
+ if(low == H5F_LIBVER_LATEST) {
+ if(idx_type != H5D_CHUNK_IDX_EARRAY)
+ FAIL_PUTS_ERROR("should be using extensible array as index");
+ } else if(idx_type != H5D_CHUNK_IDX_BTREE)
+ FAIL_PUTS_ERROR("should be using v1 B-tree as index");
+
+ /* Just a no-op */
if(H5Dwrite(d, H5T_NATIVE_INT, s, s, H5P_DEFAULT, (void*)911) < 0) FAIL_STACK_ERROR
if(H5Dclose(d) < 0) FAIL_STACK_ERROR
if(H5Pclose(dcpl) < 0) FAIL_STACK_ERROR
-
if(H5Sclose(s) < 0) FAIL_STACK_ERROR
+ /*
+ * Two-dimensional dataset
+ */
+ if((s2 = H5Screate_simple(2, dsize2, dmax2)) < 0) TEST_ERROR;
+
+ /* Try creating chunked dataset with undefined chunk dimensions */
+ if((dcpl2 = H5Pcreate(H5P_DATASET_CREATE)) < 0) TEST_ERROR;
+ if(H5Pset_layout(dcpl2, H5D_CHUNKED) < 0) FAIL_STACK_ERROR
+
+ H5E_BEGIN_TRY {
+ d2 = H5Dcreate2(file, ZERODIM_DATASET2, H5T_NATIVE_INT, s2, H5P_DEFAULT, dcpl2, H5P_DEFAULT);
+ } H5E_END_TRY;
+ if(d2 > 0) {
+ H5Dclose(d2);
+ FAIL_PUTS_ERROR("created dataset with undefined chunk dimensions")
+ } /* end if */
+
+ /* Try creating chunked dataset with zero-sized chunk dimensions */
+ H5E_BEGIN_TRY {
+ ret = H5Pset_chunk(dcpl2, 2, dsize2);
+ } H5E_END_TRY;
+ if(ret > 0)
+ FAIL_PUTS_ERROR("set zero-sized chunk dimensions")
+
+ if(H5Pclose(dcpl2) < 0) FAIL_STACK_ERROR
+
+ /* Write to the zero-sized extendible dataset */
+ if((dcpl2 = H5Pcreate(H5P_DATASET_CREATE)) < 0) FAIL_STACK_ERROR
+ if(H5Pset_chunk(dcpl2, 2, csize2) < 0) FAIL_STACK_ERROR
+
+ /* Create the dataset */
+ if((d2 = H5Dcreate2(file, ZERODIM_DATASET2, H5T_NATIVE_INT, s2, H5P_DEFAULT, dcpl2, H5P_DEFAULT)) < 0) FAIL_STACK_ERROR
+
+ /* Get the chunk index type */
+ if(H5D_layout_idx_type_test(d2, &idx_type) < 0) TEST_ERROR;
+
+ /* Verify index type */
+ if(low == H5F_LIBVER_LATEST) {
+ if(idx_type != H5D_CHUNK_IDX_BT2)
+ FAIL_PUTS_ERROR("should be using v2 B-tree as index");
+ } else if(idx_type != H5D_CHUNK_IDX_BTREE)
+ FAIL_PUTS_ERROR("should be using v1 B-tree as index");
+
+ /* Just a no-op */
+ if(H5Dwrite(d2, H5T_NATIVE_INT, s2, s2, H5P_DEFAULT, (void*)911) < 0) FAIL_STACK_ERROR
+
+ if(H5Dclose(d2) < 0) FAIL_STACK_ERROR
+ if(H5Pclose(dcpl2) < 0) FAIL_STACK_ERROR
+ if(H5Sclose(s2) < 0) FAIL_STACK_ERROR
+
PASSED();
return 0;
@@ -6462,6 +6550,10 @@ error:
H5Pclose(dcpl);
H5Dclose(d);
H5Sclose(s);
+
+ H5Pclose(dcpl2);
+ H5Dclose(d2);
+ H5Sclose(s2);
} H5E_END_TRY;
return -1;
} /* end test_zero_dims() */
@@ -6481,46 +6573,98 @@ error:
* Tuesday, August 25, 2004
*
* Modifications:
+ * Vailin Choi; June 2010
+ * Added dataset with >1 unlimited dimensions to the test.
*
*-------------------------------------------------------------------------
*/
static herr_t
test_missing_chunk(hid_t file)
{
- hid_t s=-1, d=-1, dcpl=-1;
- hsize_t hs_start[1];
- hsize_t hs_stride[1],
- hs_count[1],
- hs_block[1];
+ hid_t d = -1, did2 = -1, dcpl=-1, dcpl2 = -1; /* Dataset & dataset creation property IDs */
+ hid_t s = -1, sid2 = -1; /* Dataspace ID */
+ hsize_t hs_start[1], hs_stride[1], hs_count[1], hs_block[1]; /* Hyperslab setting */
+ hsize_t hs_start2[2], hs_stride2[2], hs_count2[2], hs_block2[2];/* Hyperslab setting */
+
+ /* Buffers for reading/writing dataset */
int wdata[MISSING_CHUNK_DIM],
rdata[MISSING_CHUNK_DIM];
- hsize_t dsize=100, dmax=H5S_UNLIMITED, csize=5;
- size_t u;
+ int wdata2[MISSING_CHUNK_DIM][MISSING_CHUNK_DIM],
+ rdata2[MISSING_CHUNK_DIM][MISSING_CHUNK_DIM];
+
+ /* Setting for 1-D dataset */
+ hsize_t dsize=100, dmax=H5S_UNLIMITED;
+ hsize_t csize=5;
+
+ /* Setting for 2-D dataset */
+ hsize_t dsize2[2] = {100, 100}, dmax2[2] = {H5S_UNLIMITED, H5S_UNLIMITED};
+ hsize_t csize2[2] = {5, 5};
+ size_t u, i, j; /* Local Index variable */
+
+ hid_t fapl; /* File access property list */
+ H5F_libver_t low; /* File format low bound */
+ H5D_chunk_index_t idx_type, idx_type2; /* Dataset chunk index types */
TESTING("Read dataset with unwritten chunk & undefined fill value");
- /* Initialize data */
- for(u=0; u<MISSING_CHUNK_DIM; u++) {
- wdata[u]=(int)u;
- rdata[u]=911;
+ /* Get the file's file access property list */
+ if((fapl = H5Fget_access_plist(file)) < 0) TEST_ERROR;
+
+ /* Get library format */
+ if(H5Pget_libver_bounds(fapl, &low, NULL) < 0) TEST_ERROR;
+
+ /* Initialize data for 1-D dataset */
+ for(u = 0; u < MISSING_CHUNK_DIM; u++) {
+ wdata[u] = (int)u;
+ rdata[u] = 911;
+ } /* end for */
+
+ /* Initialize data for 2-D dataset */
+ for(i = 0; i < MISSING_CHUNK_DIM; i++) {
+ for(j = 0; j < MISSING_CHUNK_DIM; j++) {
+ wdata2[i][j] = (int)j + (i * MISSING_CHUNK_DIM);
+ rdata2[i][j] = 911;
+ }
} /* end for */
/* Create dataspace */
if((s = H5Screate_simple(1, &dsize, &dmax)) < 0) TEST_ERROR;
+ if((sid2 = H5Screate_simple(2, dsize2, dmax2)) < 0) TEST_ERROR;
/* Create dataset creation property list */
if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0) TEST_ERROR;
+ if((dcpl2 = H5Pcreate(H5P_DATASET_CREATE)) < 0) TEST_ERROR;
/* Set to chunked */
if(H5Pset_chunk(dcpl, 1, &csize) < 0) TEST_ERROR;
+ if(H5Pset_chunk(dcpl2, 2, csize2) < 0) TEST_ERROR;
/* Undefine fill value */
if(H5Pset_fill_value(dcpl, H5T_NATIVE_INT, NULL) < 0) TEST_ERROR;
+ if(H5Pset_fill_value(dcpl2, H5T_NATIVE_INT, NULL) < 0) TEST_ERROR;
- /* Create dataset */
+ /* Create the 1-D & 2-D datasets */
if((d = H5Dcreate2(file, MISSING_CHUNK_DATASET, H5T_NATIVE_INT, s, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0) TEST_ERROR;
+ if((did2 = H5Dcreate2(file, MISSING_CHUNK_DATASET2, H5T_NATIVE_INT, sid2, H5P_DEFAULT, dcpl2, H5P_DEFAULT)) < 0) TEST_ERROR;
+
+ /* Get the chunk index types */
+ if(H5D_layout_idx_type_test(d, &idx_type) < 0) TEST_ERROR;
+ if(H5D_layout_idx_type_test(did2, &idx_type2) < 0) TEST_ERROR;
+
+ /* Verify index type */
+ if(low == H5F_LIBVER_LATEST) {
+ if(idx_type != H5D_CHUNK_IDX_EARRAY)
+ FAIL_PUTS_ERROR("should be using Extensible Array as index");
+ if(idx_type2 != H5D_CHUNK_IDX_BT2)
+ FAIL_PUTS_ERROR("should be using v2 B-tree as index");
+ } else {
+ if(idx_type != H5D_CHUNK_IDX_BTREE)
+ FAIL_PUTS_ERROR("should be using v1 B-tree as index");
+ if(idx_type2 != H5D_CHUNK_IDX_BTREE)
+ FAIL_PUTS_ERROR("should be using v1 B-tree as index");
+ }
- /* Select elements in every other chunk */
+ /* Select elements in every other chunk for 1-D dataset */
hs_start[0]=0;
hs_stride[0]=10;
hs_count[0]=10;
@@ -6528,13 +6672,23 @@ test_missing_chunk(hid_t file)
if(H5Sselect_hyperslab(s, H5S_SELECT_SET, hs_start, hs_stride, hs_count,
hs_block) < 0) TEST_ERROR;
- /* Write selected data */
+ /* Select elements in every other chunk for 2-D dataset */
+ hs_start2[0] = hs_start2[1] = 0;
+ hs_stride2[0] = hs_stride2[1] = 10;
+ hs_count2[0] = hs_count2[1] = 10;
+ hs_block2[0] = hs_block2[1] = 5;
+ if(H5Sselect_hyperslab(sid2, H5S_SELECT_SET, hs_start2, hs_stride2, hs_count2,
+ hs_block2) < 0) TEST_ERROR;
+
+ /* Write selected data to the datasets */
if(H5Dwrite(d, H5T_NATIVE_INT, s, s, H5P_DEFAULT, wdata) < 0) TEST_ERROR;
+ if(H5Dwrite(did2, H5T_NATIVE_INT, sid2, sid2, H5P_DEFAULT, wdata2) < 0) TEST_ERROR;
- /* Read all data */
+ /* Read all data from the datasets */
if(H5Dread(d, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata) < 0) TEST_ERROR;
+ if(H5Dread(did2, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata2) < 0) TEST_ERROR;
- /* Validata values read */
+ /* Validata values read for the 1-D dataset */
for(u=0; u<MISSING_CHUNK_DIM; u++) {
if((u%10)>=5) {
if(rdata[u]!=911) {
@@ -6550,10 +6704,34 @@ test_missing_chunk(hid_t file)
} /* end else */
} /* end for */
+ /* Validata values read for the 2-D dataset */
+ for(i = 0; i < MISSING_CHUNK_DIM; i++) {
+ for(j = 0; j < MISSING_CHUNK_DIM; j++) {
+
+ if((i % 10) >= 5 || (j % 10) >= 5) {
+ if(rdata2[i][j] != 911) {
+ printf(" Line %d: Incorrect value, rdata2[%u][%u] = %d\n",
+ __LINE__,(unsigned)i, (unsigned)j, rdata2[i][j]);
+ TEST_ERROR;
+ } /* end if */
+ } /* end if */
+ else {
+ if(rdata2[i][j] != wdata2[i][j]) {
+ printf(" Line %d: Incorrect value, wdata2[%u][%u] = %d, rdata2[%u][%u] = %d\n",
+ __LINE__,(unsigned)i, (unsigned)j, wdata2[i][j],(unsigned)i, (unsigned)j, rdata2[i][j]);
+ TEST_ERROR;
+ } /* end if */
+ } /* end else */
+ } /* end for */
+ } /* end for */
+
/* Close everything */
if(H5Pclose(dcpl) < 0) TEST_ERROR;
+ if(H5Pclose(dcpl2) < 0) TEST_ERROR;
if(H5Sclose(s) < 0) TEST_ERROR;
+ if(H5Sclose(sid2) < 0) TEST_ERROR;
if(H5Dclose(d) < 0) TEST_ERROR;
+ if(H5Dclose(did2) < 0) TEST_ERROR;
PASSED();
return 0;
@@ -6561,8 +6739,11 @@ test_missing_chunk(hid_t file)
error:
H5E_BEGIN_TRY {
H5Pclose(dcpl);
+ H5Pclose(dcpl2);
H5Dclose(d);
+ H5Dclose(did2);
H5Sclose(s);
+ H5Sclose(sid2);
} H5E_END_TRY;
return -1;
} /* end test_missing_chunk() */
@@ -6583,6 +6764,8 @@ error:
* Monday, March 26, 2007
*
* Modifications:
+ * Vailin Choi; June 2010
+ * Added dataset with >1 unlimited dimensions to the test.
*
*-------------------------------------------------------------------------
*/
@@ -6600,6 +6783,8 @@ test_random_chunks(hid_t fapl)
const char dname[]="dataset";
int chunk_row, chunk_col;
size_t i, j;
+ H5D_chunk_index_t idx_type; /* Dataset chunk index type */
+ H5F_libver_t low; /* File format low bound */
TESTING("Write/read on randomly selected chunks");
@@ -6609,7 +6794,7 @@ test_random_chunks(hid_t fapl)
h5_fixname(FILENAME[6], fapl, filename, sizeof filename);
/* Create file for first test */
- if((file = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR;
+ if((file = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl)) < 0) TEST_ERROR;
/* Create dataspace */
if((s = H5Screate_simple(2, dsize, NULL)) < 0) TEST_ERROR;
@@ -6693,7 +6878,9 @@ test_random_chunks(hid_t fapl)
/* Create file for second test */
- if((file = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR;
+ if(H5Pget_libver_bounds(fapl, &low, NULL) < 0) TEST_ERROR;
+
+ if((file = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl)) < 0) TEST_ERROR;
/* Create dataspace with unlimited maximum dimensions */
if((s = H5Screate_simple(2, dsize, dmax)) < 0) TEST_ERROR;
@@ -6710,6 +6897,16 @@ test_random_chunks(hid_t fapl)
/* Create dataset */
if((d = H5Dcreate2(file, dname, H5T_NATIVE_INT, s, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0) TEST_ERROR;
+ /* Get the chunk index type */
+ if(H5D_layout_idx_type_test(d, &idx_type) < 0) TEST_ERROR;
+
+ /* Verify index type */
+ if(low == H5F_LIBVER_LATEST) {
+ if(idx_type != H5D_CHUNK_IDX_BT2)
+ FAIL_PUTS_ERROR("should be using v2 B-tree as index");
+ } else if(idx_type != H5D_CHUNK_IDX_BTREE)
+ FAIL_PUTS_ERROR("should be using v1 B-tree as index");
+
/* Extend both dimensions of the dataset */
if(H5Dset_extent(d, nsize) < 0) TEST_ERROR;
@@ -7345,29 +7542,45 @@ error:
* Programmer: Raymond Lu
* 11 Feb 2009
*
+ * Modifications:
+ * Vailin Choi; June 2010
+ * Added 2-D dataset with unlimited dimensions to the test.
*-------------------------------------------------------------------------
*/
static herr_t
test_big_chunks_bypass_cache(hid_t fapl)
{
char filename[FILENAME_BUF_SIZE];
- hid_t fid = -1; /* File ID */
- hid_t fapl_local = -1; /* File access property list ID */
- hid_t dcpl = -1; /* Dataset creation property list ID */
- hid_t sid = -1; /* Dataspace ID */
- hid_t dsid = -1; /* Dataset ID */
- hsize_t dim, chunk_dim; /* Dataset and chunk dimensions */
- size_t rdcc_nelmts, rdcc_nbytes;
- int fvalue = BYPASS_FILL_VALUE;
- hsize_t count, stride, offset, block;
+ hid_t fid = -1; /* File ID */
+ hid_t fapl_local = -1; /* File access property list ID */
+ hid_t dcpl = -1, t_dcpl = -1; /* Dataset creation property list ID */
+ hid_t sid = -1, t_sid = -1; /* Dataspace ID */
+ hid_t mid; /* Memory space ID */
+ hid_t dsid = -1, t_dsid = -1; /* Dataset ID */
+ hsize_t dim, chunk_dim; /* Dataset and chunk dimensions */
+ hsize_t t_dim[2], t_max[2], t_chunk_dim[2]; /* Dataset and chunk dimensions */
+ size_t rdcc_nelmts, rdcc_nbytes; /* Chunk cache parameters */
+ int fvalue = BYPASS_FILL_VALUE; /* Fill value */
+ hsize_t count, stride, offset, block; /* Setting for hyperslab (1-D) */
+ hsize_t t_count[2], t_stride[2], t_offset[2], t_block[2]; /* Setting for hyperslab (2-D) */
+ /* Buffer for reading and writing data (1-D) */
static int wdata[BYPASS_CHUNK_DIM/2], rdata1[BYPASS_DIM],
- rdata2[BYPASS_CHUNK_DIM/2];
- int i, j;
+ rdata2[BYPASS_CHUNK_DIM/2];
+ /* Buffer for reading and writing data (2-D) */
+ static int t_wdata[BYPASS_CHUNK_DIM/2][BYPASS_CHUNK_DIM/2], t_rdata1[BYPASS_DIM][BYPASS_DIM],
+ t_rdata2[BYPASS_CHUNK_DIM/2][BYPASS_CHUNK_DIM/2];
+ int i, j; /* Local index variables */
+ H5F_libver_t low; /* File format low bound */
+ H5D_chunk_index_t idx_type, t_idx_type; /* Dataset chunk index types */
+
TESTING("big chunks bypassing the cache");
h5_fixname(FILENAME[9], fapl, filename, sizeof filename);
+ /* Check if we are using the latest version of the format */
+ if(H5Pget_libver_bounds(fapl, &low, NULL) < 0) FAIL_STACK_ERROR
+
/* Copy fapl passed to this function (as we will be modifying it) */
if((fapl_local = H5Pcopy(fapl)) < 0) FAIL_STACK_ERROR
@@ -7379,52 +7592,101 @@ test_big_chunks_bypass_cache(hid_t fapl)
/* Create file */
if((fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_local)) < 0) FAIL_STACK_ERROR
- /* Create 1-D dataspace */
- dim = BYPASS_DIM;
+ /* Create 1-D & 2-D dataspace */
+ dim = t_dim[0] = t_dim[1] = BYPASS_DIM;
+ t_max[0] = t_max[1] = H5S_UNLIMITED;
if((sid = H5Screate_simple(1, &dim, NULL)) < 0) FAIL_STACK_ERROR
+ if((t_sid = H5Screate_simple(2, t_dim, t_max)) < 0) FAIL_STACK_ERROR
- /* Create dataset creation property list */
+ /* Create 1-D & 2-D dataset creation property list */
if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0) FAIL_STACK_ERROR
+ if((t_dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0) FAIL_STACK_ERROR
- /* Define chunk size. There will be only 2 chunks in the dataset. */
- chunk_dim = BYPASS_CHUNK_DIM;
+ /* Define chunk size. */
+ /* There will be 2 chunks in 1-D dataset & 4 chunks in the 2-D dataset */
+ chunk_dim = t_chunk_dim[0] = t_chunk_dim[1] = BYPASS_CHUNK_DIM;
if(H5Pset_chunk(dcpl, 1, &chunk_dim) < 0) FAIL_STACK_ERROR
+ if(H5Pset_chunk(t_dcpl, 2, t_chunk_dim) < 0) FAIL_STACK_ERROR
/* Define fill value, fill time, and chunk allocation time */
if(H5Pset_fill_value(dcpl, H5T_NATIVE_INT, &fvalue) < 0) FAIL_STACK_ERROR
+ if(H5Pset_fill_value(t_dcpl, H5T_NATIVE_INT, &fvalue) < 0) FAIL_STACK_ERROR
+
if(H5Pset_fill_time(dcpl, H5D_FILL_TIME_IFSET) < 0) FAIL_STACK_ERROR
+ if(H5Pset_fill_time(t_dcpl, H5D_FILL_TIME_IFSET) < 0) FAIL_STACK_ERROR
+
if(H5Pset_alloc_time(dcpl, H5D_ALLOC_TIME_INCR) < 0) FAIL_STACK_ERROR
+ if(H5Pset_alloc_time(t_dcpl, H5D_ALLOC_TIME_INCR) < 0) FAIL_STACK_ERROR
- /* Create a first dataset */
+ /* Create the first 1-D dataset */
if((dsid = H5Dcreate2(fid, BYPASS_DATASET1, H5T_NATIVE_INT, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
FAIL_STACK_ERROR
+ /* Create the first 2-D dataset */
+ if((t_dsid = H5Dcreate2(fid, T_BYPASS_DATASET1, H5T_NATIVE_INT, t_sid, H5P_DEFAULT, t_dcpl, H5P_DEFAULT)) < 0)
+ FAIL_STACK_ERROR
+
+ /* Get the chunk index types for 1-D and 2-d datasets */
+ if(H5D_layout_idx_type_test(dsid, &idx_type) < 0) FAIL_STACK_ERROR
+ if(H5D_layout_idx_type_test(t_dsid, &t_idx_type) < 0) FAIL_STACK_ERROR
+
+ /* Chunk index type expected depends on whether we are using the latest version of the format */
+ if(low == H5F_LIBVER_LATEST) {
+ /* Verify index type */
+ if(idx_type != H5D_CHUNK_IDX_FARRAY) FAIL_PUTS_ERROR("should be using Fixed Array as index");
+ if(t_idx_type != H5D_CHUNK_IDX_BT2) FAIL_PUTS_ERROR("should be using v2 B-tree as index");
+ } else {
+ /* Verify index type */
+ if(idx_type != H5D_CHUNK_IDX_BTREE) FAIL_PUTS_ERROR("should be using v1 B-tree as index");
+ if(t_idx_type != H5D_CHUNK_IDX_BTREE) FAIL_PUTS_ERROR("should be using v1 B-tree as index");
+ } /* end else */
+
/* Select first chunk to write the data */
- offset = 0;
- count = 1;
- stride = 1;
- block = BYPASS_CHUNK_DIM / 2;
+ offset = t_offset[0] = t_offset[1] = 0;
+ count = t_count[0] = t_count[1] = 1;
+ stride = t_stride[0] = t_stride[1] = 1;
+ block = t_block[0] = t_block[1] = BYPASS_CHUNK_DIM / 2;
if(H5Sselect_hyperslab(sid, H5S_SELECT_SET, &offset, &stride, &count, &block) < 0)
FAIL_STACK_ERROR
- /* Initialize data to write */
+ if(H5Sselect_hyperslab(t_sid, H5S_SELECT_SET, t_offset, t_stride, t_count, t_block) < 0)
+ FAIL_STACK_ERROR
+
+ /* Initialize data to write for 1-D dataset */
for(i = 0; i < BYPASS_CHUNK_DIM / 2; i++)
wdata[i] = i;
+ /* Initialize data to write for 2-D dataset */
+ for(i = 0; i < BYPASS_CHUNK_DIM / 2; i++)
+ for(j = 0; j < BYPASS_CHUNK_DIM / 2; j++)
+ t_wdata[i][j] = j;
+
+ /* Set up memory space for the 2-D dataset */
+ mid = H5Screate_simple(2, t_block, NULL);
+
+ /* Write to the first 1-D & 2-D datasets */
/* This write should go through the cache because fill value is used. */
if(H5Dwrite(dsid, H5T_NATIVE_INT, H5S_ALL, sid, H5P_DEFAULT, wdata) < 0)
FAIL_STACK_ERROR
+ if(H5Dwrite(t_dsid, H5T_NATIVE_INT, mid, t_sid, H5P_DEFAULT, t_wdata) < 0)
+ FAIL_STACK_ERROR
+ /* Close the first 1-D & 2-D datasets */
if(H5Dclose(dsid) < 0) FAIL_STACK_ERROR
+ if(H5Dclose(t_dsid) < 0) FAIL_STACK_ERROR
- /* Reopen the dataset */
+ /* Reopen the first 1-D & 2-D datasets */
if((dsid = H5Dopen2(fid, BYPASS_DATASET1, H5P_DEFAULT)) < 0) FAIL_STACK_ERROR
+ if((t_dsid = H5Dopen2(fid, T_BYPASS_DATASET1, H5P_DEFAULT)) < 0) FAIL_STACK_ERROR
/* Reads both 2 chunks. Reading the second chunk should bypass the cache because the
* chunk is bigger than the cache size and it isn't allocated on disk. */
if(H5Dread(dsid, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata1) < 0)
FAIL_STACK_ERROR
+ if(H5Dread(t_dsid, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, t_rdata1) < 0)
+ FAIL_STACK_ERROR
+ /* Verify data for the first 1-D dataset */
for(i = 0; i < BYPASS_CHUNK_DIM / 2; i++)
if(rdata1[i] != i) {
printf(" Read different values than written in the 1st chunk.\n");
@@ -7439,41 +7701,88 @@ test_big_chunks_bypass_cache(hid_t fapl)
TEST_ERROR
} /* end if */
- /* Close the first dataset */
+ /* Verify data for the first 2-D dataset */
+ for(i = 0; i < BYPASS_CHUNK_DIM / 2; i++)
+ for(j = 0; j < BYPASS_CHUNK_DIM / 2; j++)
+ if(t_rdata1[i][j] != j) {
+ printf(" Read different values than written in the 1st chunk.\n");
+ printf(" At line %d and index (%d, %d), t_rdata1 = %d. It should be %d.\n",
+ __LINE__, i, j, t_rdata1[i][j], j);
+ TEST_ERROR
+ } /* end if */
+
+ for(i = BYPASS_CHUNK_DIM / 2; i < BYPASS_DIM; i++)
+ for(j = BYPASS_CHUNK_DIM / 2; j < BYPASS_DIM; j++)
+ if(t_rdata1[i][j] != fvalue) {
+ printf(" Read different values than written in the 2nd chunk.\n");
+ printf(" At line %d and index (%d, %d), t_rdata1 = %d. It should be %d.\n",
+ __LINE__, i, j, t_rdata1[i][j], fvalue);
+ TEST_ERROR
+ } /* end if */
+
+ /* Close the first 1-D & 2-D datasets */
if(H5Dclose(dsid) < 0) FAIL_STACK_ERROR
+ if(H5Dclose(t_dsid) < 0) FAIL_STACK_ERROR
/* Create a second dataset without fill value. This time, both write
* and read should bypass the cache because the chunk is bigger than the
* cache size and it's not allocated on disk. */
if(H5Pset_fill_time(dcpl, H5D_FILL_TIME_NEVER) < 0) FAIL_STACK_ERROR
+ if(H5Pset_fill_time(t_dcpl, H5D_FILL_TIME_NEVER) < 0) FAIL_STACK_ERROR
+ /* Create a second 1-D & 2-D dataset */
if((dsid = H5Dcreate2(fid, BYPASS_DATASET2, H5T_NATIVE_INT, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
FAIL_STACK_ERROR
+ if((t_dsid = H5Dcreate2(fid, T_BYPASS_DATASET2, H5T_NATIVE_INT, t_sid, H5P_DEFAULT, t_dcpl, H5P_DEFAULT)) < 0)
+ FAIL_STACK_ERROR
+ /* Write to the second 1-D & 2-D dataset */
if(H5Dwrite(dsid, H5T_NATIVE_INT, H5S_ALL, sid, H5P_DEFAULT, wdata) < 0)
FAIL_STACK_ERROR
+ if(H5Dwrite(t_dsid, H5T_NATIVE_INT, mid, t_sid, H5P_DEFAULT, t_wdata) < 0)
+ FAIL_STACK_ERROR
+ /* Close the second 1-D & 2-D dataset */
if(H5Dclose(dsid) < 0) FAIL_STACK_ERROR
+ if(H5Dclose(t_dsid) < 0) FAIL_STACK_ERROR
- /* Reopen the dataset */
+ /* Reopen the second 1-d dataset and 2-d dataset */
if((dsid = H5Dopen2(fid, BYPASS_DATASET2, H5P_DEFAULT)) < 0) FAIL_STACK_ERROR
+ if((t_dsid = H5Dopen2(fid, T_BYPASS_DATASET2, H5P_DEFAULT)) < 0) FAIL_STACK_ERROR
/* Read back only the part that was written to the file. Reading the
* half chunk should bypass the cache because the chunk is bigger than
* the cache size. */
if(H5Dread(dsid, H5T_NATIVE_INT, H5S_ALL, sid, H5P_DEFAULT, rdata2) < 0)
+ FAIL_STACK_ERROR
+ if(H5Dread(t_dsid, H5T_NATIVE_INT, mid, t_sid, H5P_DEFAULT, t_rdata2) < 0)
+ FAIL_STACK_ERROR
+ /* Verify data for the second 1-D dataset */
for(i = 0; i < BYPASS_CHUNK_DIM / 2; i++)
- if(rdata2[i] != i) {
+ if(rdata2[i] != i) {
printf(" Read different values than written in the chunk.\n");
printf(" At line %d and index %d, rdata2 = %d. It should be %d.\n", __LINE__, i, rdata2[i], i);
TEST_ERROR
} /* end if */
+ /* Verify data for the second 2-D dataset */
+ for(i = 0; i < BYPASS_CHUNK_DIM / 2; i++)
+ for(j = 0; j < BYPASS_CHUNK_DIM / 2; j++)
+ if(t_rdata2[i][j] != j) {
+ printf(" Read different values than written in the chunk.\n");
+ printf(" At line %d and index (%d, %d), t_rdata2 = %d. It should be %d.\n",
+ __LINE__, i, j, t_rdata2[i][j], j);
+ TEST_ERROR
+ } /* end if */
+
/* Close IDs */
if(H5Sclose(sid) < 0) FAIL_STACK_ERROR
+ if(H5Sclose(t_sid) < 0) FAIL_STACK_ERROR
if(H5Dclose(dsid) < 0) FAIL_STACK_ERROR
+ if(H5Dclose(t_dsid) < 0) FAIL_STACK_ERROR
if(H5Pclose(dcpl) < 0) FAIL_STACK_ERROR
+ if(H5Pclose(t_dcpl) < 0) FAIL_STACK_ERROR
if(H5Pclose(fapl_local) < 0) FAIL_STACK_ERROR
if(H5Fclose(fid) < 0) FAIL_STACK_ERROR
@@ -7483,9 +7792,12 @@ test_big_chunks_bypass_cache(hid_t fapl)
error:
H5E_BEGIN_TRY {
H5Pclose(dcpl);
+ H5Pclose(t_dcpl);
H5Pclose(fapl_local);
H5Dclose(dsid);
+ H5Dclose(t_dsid);
H5Sclose(sid);
+ H5Sclose(t_sid);
H5Fclose(fid);
} H5E_END_TRY;
return -1;
@@ -8025,26 +8337,32 @@ filter_expand(unsigned int flags, size_t UNUSED cd_nelmts,
* Programmer: Quincey Koziol
* Tuesday, March 31, 2009
*
+ * Modifications:
+ * Vailin Choi; June 2010
+ * Added 2-D dataset with unlimited dimensions to the test.
+ *
*-------------------------------------------------------------------------
*/
static herr_t
test_chunk_expand(hid_t fapl)
{
char filename[FILENAME_BUF_SIZE];
- hid_t fid = -1; /* File ID */
- hid_t dcpl = -1; /* Dataset creation property list ID */
- hid_t sid = -1; /* Dataspace ID */
- hid_t scalar_sid = -1;/* Scalar dataspace ID */
- hid_t dsid = -1; /* Dataset ID */
- hsize_t dim, max_dim, chunk_dim; /* Dataset and chunk dimensions */
- H5D_chunk_index_t idx_type; /* Dataset chunk index type */
- H5F_libver_t low, high; /* File format bounds */
- hsize_t hs_offset; /* Hyperslab offset */
- hsize_t hs_size; /* Hyperslab size */
- H5D_alloc_time_t alloc_time; /* Storage allocation time */
- unsigned write_elem, read_elem; /* Element written/read */
- unsigned u; /* Local index variable */
- herr_t status; /* Generic return value */
+ hid_t fid = -1; /* File ID */
+ hid_t dcpl = -1, dcpl2 = -1; /* Dataset creation property list ID */
+ hid_t sid = -1, sid2 = -1; /* Dataspace ID */
+ hid_t scalar_sid = -1; /* Scalar dataspace ID */
+ hid_t dsid = -1, dsid2 = -1; /* Dataset ID */
+ hsize_t dim, max_dim, chunk_dim; /* Dataset and chunk dimensions */
+ hsize_t dim2[2], max_dim2[2], chunk_dim2[2]; /* Dataset and chunk dimensions */
+ H5D_chunk_index_t idx_type, idx_type2; /* Dataset chunk index type */
+ H5F_libver_t low, high; /* File format bounds */
+ hsize_t hs_offset, hs_offset2[2]; /* Hyperslab offset */
+ hsize_t hs_size, hs_size2[2]; /* Hyperslab size */
+ H5D_alloc_time_t alloc_time; /* Storage allocation time */
+ unsigned write_elem, read_elem; /* Element written/read */
+ unsigned write_elem2, read_elem2; /* Element written/read */
+ unsigned u; /* Local index variable */
+ herr_t status; /* Generic return value */
TESTING("filter expanding chunks too much");
@@ -8066,34 +8384,41 @@ test_chunk_expand(hid_t fapl)
/* Loop over storage allocation time */
for(alloc_time = H5D_ALLOC_TIME_EARLY; alloc_time <= H5D_ALLOC_TIME_INCR; alloc_time++) {
+
/* Create file */
if((fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl)) < 0) FAIL_STACK_ERROR
/* Create dataset creation property list */
if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0) FAIL_STACK_ERROR
+ if((dcpl2 = H5Pcreate(H5P_DATASET_CREATE)) < 0) FAIL_STACK_ERROR
/* Set chunking */
- chunk_dim = 10;
+ chunk_dim = chunk_dim2[0] = chunk_dim2[1] = 10;
if(H5Pset_chunk(dcpl, 1, &chunk_dim) < 0) FAIL_STACK_ERROR
+ if(H5Pset_chunk(dcpl2, 2, chunk_dim2) < 0) FAIL_STACK_ERROR
/* Set fill time */
if(H5Pset_fill_time(dcpl, H5D_FILL_TIME_ALLOC) < 0) FAIL_STACK_ERROR
+ if(H5Pset_fill_time(dcpl2, H5D_FILL_TIME_ALLOC) < 0) FAIL_STACK_ERROR
/* Set allocation time */
if(H5Pset_alloc_time(dcpl, alloc_time) < 0) FAIL_STACK_ERROR
+ if(H5Pset_alloc_time(dcpl2, alloc_time) < 0) FAIL_STACK_ERROR
/* Set "expand" filter */
if(H5Pset_filter(dcpl, H5Z_FILTER_EXPAND, 0, (size_t)0, NULL) < 0) FAIL_STACK_ERROR
+ if(H5Pset_filter(dcpl2, H5Z_FILTER_EXPAND, 0, (size_t)0, NULL) < 0) FAIL_STACK_ERROR
/* Create scalar dataspace */
if((scalar_sid = H5Screate(H5S_SCALAR)) < 0) FAIL_STACK_ERROR
- /* Create 1-D dataspace */
- dim = 100;
- max_dim = H5S_UNLIMITED;
+ /* Create 1-D and 2-D dataspace */
+ dim = dim2[0] = dim2[1] = 100;
+ max_dim = max_dim2[0] = max_dim2[1] = H5S_UNLIMITED;
if((sid = H5Screate_simple(1, &dim, &max_dim)) < 0) FAIL_STACK_ERROR
+ if((sid2 = H5Screate_simple(2, dim2, max_dim2)) < 0) FAIL_STACK_ERROR
- /* Create chunked dataset */
+ /* Create 1-D & 2-D chunked datasets */
if(H5D_ALLOC_TIME_EARLY == alloc_time) {
/* Make the expansion factor large enough to cause failure right away */
filter_expand_factor_g = 8;
@@ -8102,202 +8427,272 @@ test_chunk_expand(hid_t fapl)
dsid = H5Dcreate2(fid, "dset", H5T_NATIVE_UINT, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT);
} H5E_END_TRY;
if(dsid >= 0) FAIL_PUTS_ERROR("should fail to create dataset when allocation time is early");
+
+ H5E_BEGIN_TRY {
+ dsid2 = H5Dcreate2(fid, "dset2", H5T_NATIVE_UINT, sid2, H5P_DEFAULT, dcpl2, H5P_DEFAULT);
+ } H5E_END_TRY;
+ if(dsid2 >= 0) FAIL_PUTS_ERROR("should fail to create dataset when allocation time is early");
+
} /* end if */
else {
if((dsid = H5Dcreate2(fid, "dset", H5T_NATIVE_UINT, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
FAIL_STACK_ERROR
+ if((dsid2 = H5Dcreate2(fid, "dset2", H5T_NATIVE_UINT, sid2, H5P_DEFAULT, dcpl2, H5P_DEFAULT)) < 0)
+ FAIL_STACK_ERROR
+
/* Get the chunk index type */
if(H5D_layout_idx_type_test(dsid, &idx_type) < 0) FAIL_STACK_ERROR
+ if(H5D_layout_idx_type_test(dsid2, &idx_type2) < 0) FAIL_STACK_ERROR
- /* Chunk index tyepe expected depends on whether we are using the latest version of the format */
+ /* Chunk index type expected depends on whether we are using the latest version of the format */
if(low == H5F_LIBVER_LATEST) {
/* Verify index type */
if(idx_type != H5D_CHUNK_IDX_EARRAY) FAIL_PUTS_ERROR("should be using extensible array as index");
+ if(idx_type2 != H5D_CHUNK_IDX_BT2) FAIL_PUTS_ERROR("should be using v2 B-tree as index");
} /* end if */
else {
/* Verify index type */
if(idx_type != H5D_CHUNK_IDX_BTREE) FAIL_PUTS_ERROR("should be using v1 B-tree as index");
+ if(idx_type2 != H5D_CHUNK_IDX_BTREE) FAIL_PUTS_ERROR("should be using v1 B-tree as index");
} /* end else */
/* Fill elements */
- hs_size = 1;
+ hs_size = hs_size2[0] = hs_size2[1] = 1;
for(u = 0; u < 100; u++) {
- /* Select a single element in the dataset */
- hs_offset = u;
+
+ hs_offset = hs_offset2[0] = hs_offset2[1] = u;
+
+ /* Select a single element in the 1-D dataset */
if(H5Sselect_hyperslab(sid, H5S_SELECT_SET, &hs_offset, NULL, &hs_size, NULL) < 0) FAIL_STACK_ERROR
+ /* Select a single element in the 2-D dataset; NOT every element is selected */
+ if(H5Sselect_hyperslab(sid2, H5S_SELECT_SET, hs_offset2, NULL, hs_size2, NULL) < 0) FAIL_STACK_ERROR
+
/* Read (unwritten) element from dataset */
- read_elem = 1;
+ read_elem = read_elem2 = 1;
if(H5Dread(dsid, H5T_NATIVE_UINT, scalar_sid, sid, H5P_DEFAULT, &read_elem) < 0) FAIL_STACK_ERROR
+ if(H5Dread(dsid2, H5T_NATIVE_UINT, scalar_sid, sid2, H5P_DEFAULT, &read_elem2) < 0) FAIL_STACK_ERROR
/* Verify unwritten element is fill value (0) */
if(read_elem != 0) FAIL_PUTS_ERROR("invalid unwritten element read");
+ if(read_elem2 != 0) FAIL_PUTS_ERROR("invalid unwritten element read");
/* Don't expand chunks yet */
filter_expand_factor_g = 0;
- /* Write element to dataset */
- write_elem = u;
+ /* Write element to the datasets */
+ write_elem = write_elem2 = u;
if(H5Dwrite(dsid, H5T_NATIVE_UINT, scalar_sid, sid, H5P_DEFAULT, &write_elem) < 0) FAIL_STACK_ERROR
+ if(H5Dwrite(dsid2, H5T_NATIVE_UINT, scalar_sid, sid2, H5P_DEFAULT, &write_elem2) < 0) FAIL_STACK_ERROR
- /* Read element from dataset */
+ /* Read element from the datasets */
read_elem = write_elem + 1;
+ read_elem2 = write_elem2 + 1;
if(H5Dread(dsid, H5T_NATIVE_UINT, scalar_sid, sid, H5P_DEFAULT, &read_elem) < 0) FAIL_STACK_ERROR
+ if(H5Dread(dsid2, H5T_NATIVE_UINT, scalar_sid, sid2, H5P_DEFAULT, &read_elem2) < 0) FAIL_STACK_ERROR
/* Verify written element is read in */
if(read_elem != write_elem) FAIL_PUTS_ERROR("invalid written element read");
+ if(read_elem2 != write_elem2) FAIL_PUTS_ERROR("invalid written element read");
/* Expand chunks now */
filter_expand_factor_g = 8;
- /* Write element to dataset */
- write_elem = u;
+ /* Write element to the datasets */
+ write_elem = write_elem2 = u;
H5E_BEGIN_TRY {
status = H5Dwrite(dsid, H5T_NATIVE_UINT, scalar_sid, sid, H5P_DEFAULT, &write_elem);
} H5E_END_TRY;
if(status >= 0) FAIL_PUTS_ERROR("should fail to write to dataset when allocation time is not early");
+
+ H5E_BEGIN_TRY {
+ status = H5Dwrite(dsid2, H5T_NATIVE_UINT, scalar_sid, sid2, H5P_DEFAULT, &write_elem2);
+ } H5E_END_TRY;
+ if(status >= 0) FAIL_PUTS_ERROR("should fail to write to dataset when allocation time is not early");
} /* end for */
/* Incrementally extend dataset and verify write/reads */
while(dim < 1000) {
- /* Extend dataset */
+ /* Extend the datasets */
dim += 100;
+ dim2[0] += 100;
+ dim2[1] += 100;
if(H5Dset_extent(dsid, &dim) < 0) FAIL_STACK_ERROR
+ if(H5Dset_extent(dsid2, dim2) < 0) FAIL_STACK_ERROR
/* Close old dataspace */
if(H5Sclose(sid) < 0) FAIL_STACK_ERROR
+ if(H5Sclose(sid2) < 0) FAIL_STACK_ERROR
- /* Get dataspace for dataset now */
+ /* Get dataspace for the datasets now */
if((sid = H5Dget_space(dsid)) < 0) FAIL_STACK_ERROR
+ if((sid2 = H5Dget_space(dsid2)) < 0) FAIL_STACK_ERROR
/* Fill new elements */
- hs_size = 1;
+ hs_size = hs_size2[0] = hs_size2[1] = 1;
for(u = 0; u < 100; u++) {
- /* Select a single element in the dataset */
+ /* Select a single element in the datasets */
hs_offset = (dim + u) - 100;
+ hs_offset2[0] = (dim2[0] + u) - 100;
+ hs_offset2[1] = (dim2[1] + u) - 100;
if(H5Sselect_hyperslab(sid, H5S_SELECT_SET, &hs_offset, NULL, &hs_size, NULL) < 0) FAIL_STACK_ERROR
+ if(H5Sselect_hyperslab(sid2, H5S_SELECT_SET, hs_offset2, NULL, hs_size2, NULL) < 0) FAIL_STACK_ERROR
- /* Read (unwritten) element from dataset */
- read_elem = 1;
+ /* Read (unwritten) element from the datasets */
+ read_elem = read_elem2 = 1;
if(H5Dread(dsid, H5T_NATIVE_UINT, scalar_sid, sid, H5P_DEFAULT, &read_elem) < 0) FAIL_STACK_ERROR
+ if(H5Dread(dsid2, H5T_NATIVE_UINT, scalar_sid, sid2, H5P_DEFAULT, &read_elem2) < 0) FAIL_STACK_ERROR
/* Verify unwritten element is fill value (0) */
if(read_elem != 0) FAIL_PUTS_ERROR("invalid unwritten element read");
+ if(read_elem2 != 0) FAIL_PUTS_ERROR("invalid unwritten element read");
/* Don't expand chunks yet */
filter_expand_factor_g = 0;
- /* Write element to dataset */
- write_elem = u;
+ /* Write element to the datasets */
+ write_elem = write_elem2 = u;
if(H5Dwrite(dsid, H5T_NATIVE_UINT, scalar_sid, sid, H5P_DEFAULT, &write_elem) < 0) FAIL_STACK_ERROR
+ if(H5Dwrite(dsid2, H5T_NATIVE_UINT, scalar_sid, sid2, H5P_DEFAULT, &write_elem2) < 0) FAIL_STACK_ERROR
- /* Read element from dataset */
+ /* Read element from the datasets */
read_elem = write_elem + 1;
+ read_elem2 = write_elem2 + 1;
if(H5Dread(dsid, H5T_NATIVE_UINT, scalar_sid, sid, H5P_DEFAULT, &read_elem) < 0) FAIL_STACK_ERROR
+ if(H5Dread(dsid2, H5T_NATIVE_UINT, scalar_sid, sid2, H5P_DEFAULT, &read_elem2) < 0) FAIL_STACK_ERROR
/* Verify written element is read in */
if(read_elem != write_elem) FAIL_PUTS_ERROR("invalid written element read");
+ if(read_elem2 != write_elem2) FAIL_PUTS_ERROR("invalid written element read");
/* Expand chunks now */
filter_expand_factor_g = 8;
- /* Write element to dataset */
- write_elem = u;
+ /* Write element to the datasets */
+ write_elem = write_elem2 = u;
H5E_BEGIN_TRY {
status = H5Dwrite(dsid, H5T_NATIVE_UINT, scalar_sid, sid, H5P_DEFAULT, &write_elem);
} H5E_END_TRY;
if(status >= 0) FAIL_PUTS_ERROR("should fail to write to dataset when allocation time is not early");
+
+ H5E_BEGIN_TRY {
+ status = H5Dwrite(dsid2, H5T_NATIVE_UINT, scalar_sid, sid2, H5P_DEFAULT, &write_elem2);
+ } H5E_END_TRY;
+ if(status >= 0) FAIL_PUTS_ERROR("should fail to write to dataset when allocation time is not early");
} /* end for */
} /* end while */
- /* Close dataset */
+ /* Close the datasets */
if(H5Dclose(dsid) < 0) FAIL_STACK_ERROR
+ if(H5Dclose(dsid2) < 0) FAIL_STACK_ERROR
} /* end else */
/* Close everything */
if(H5Sclose(sid) < 0) FAIL_STACK_ERROR
+ if(H5Sclose(sid2) < 0) FAIL_STACK_ERROR
if(H5Sclose(scalar_sid) < 0) FAIL_STACK_ERROR
if(H5Pclose(dcpl) < 0) FAIL_STACK_ERROR
+ if(H5Pclose(dcpl2) < 0) FAIL_STACK_ERROR
if(H5Fclose(fid) < 0) FAIL_STACK_ERROR
/* If the dataset was created, do some extra testing */
if(H5D_ALLOC_TIME_EARLY != alloc_time) {
- /* Re-open file & dataset */
+ /* Re-open file & datasets */
if((fid = H5Fopen(filename, H5F_ACC_RDWR, fapl)) < 0) FAIL_STACK_ERROR
- /* Open dataset */
+ /* Open the datasets */
if((dsid = H5Dopen2(fid, "dset", H5P_DEFAULT)) < 0) FAIL_STACK_ERROR
+ if((dsid2 = H5Dopen2(fid, "dset2", H5P_DEFAULT)) < 0) FAIL_STACK_ERROR
- /* Get the chunk index type */
+ /* Get the chunk index type for the two datasets */
if(H5D_layout_idx_type_test(dsid, &idx_type) < 0) FAIL_STACK_ERROR
+ if(H5D_layout_idx_type_test(dsid2, &idx_type2) < 0) FAIL_STACK_ERROR
- /* Chunk index tyepe expected depends on whether we are using the latest version of the format */
+ /* Chunk index type expected depends on whether we are using the latest version of the format */
if(low == H5F_LIBVER_LATEST) {
/* Verify index type */
if(idx_type != H5D_CHUNK_IDX_EARRAY) FAIL_PUTS_ERROR("should be using extensible array as index");
+ if(idx_type2 != H5D_CHUNK_IDX_BT2) FAIL_PUTS_ERROR("should be using v2 B-tree as index");
} /* end if */
else {
/* Verify index type */
if(idx_type != H5D_CHUNK_IDX_BTREE) FAIL_PUTS_ERROR("should be using v1 B-tree as index");
+ if(idx_type2 != H5D_CHUNK_IDX_BTREE) FAIL_PUTS_ERROR("should be using v1 B-tree as index");
} /* end else */
/* Create scalar dataspace */
if((scalar_sid = H5Screate(H5S_SCALAR)) < 0) FAIL_STACK_ERROR
- /* Get dataspace for dataset now */
+ /* Get dataspace for the datasets now */
if((sid = H5Dget_space(dsid)) < 0) FAIL_STACK_ERROR
+ if((sid2 = H5Dget_space(dsid2)) < 0) FAIL_STACK_ERROR
/* Read elements */
- hs_size = 1;
+ hs_size = hs_size2[0] = hs_size2[1] = 1;
for(u = 0; u < 1000; u++) {
- /* Select a single element in the dataset */
- hs_offset = u;
+ /* Select a single element in the datasets */
+ hs_offset = hs_offset2[0] = hs_offset2[1] = u;
if(H5Sselect_hyperslab(sid, H5S_SELECT_SET, &hs_offset, NULL, &hs_size, NULL) < 0) FAIL_STACK_ERROR
+ if(H5Sselect_hyperslab(sid2, H5S_SELECT_SET, hs_offset2, NULL, hs_size2, NULL) < 0) FAIL_STACK_ERROR
- /* Read element from dataset */
- read_elem = u + 1;
+ /* Read element from the datasets */
+ read_elem = read_elem2 = u + 1;
if(H5Dread(dsid, H5T_NATIVE_UINT, scalar_sid, sid, H5P_DEFAULT, &read_elem) < 0) FAIL_STACK_ERROR
+ if(H5Dread(dsid2, H5T_NATIVE_UINT, scalar_sid, sid2, H5P_DEFAULT, &read_elem2) < 0) FAIL_STACK_ERROR
/* Verify unwritten element is proper value */
if(read_elem != (u % 100)) FAIL_PUTS_ERROR("invalid element read");
+ if(read_elem2 != (u % 100)) FAIL_PUTS_ERROR("invalid element read");
/* Don't expand chunks yet */
filter_expand_factor_g = 0;
- /* Write element to dataset */
- write_elem = u % 100;
+ /* Write element to the datasets */
+ write_elem = write_elem2 = u % 100;
if(H5Dwrite(dsid, H5T_NATIVE_UINT, scalar_sid, sid, H5P_DEFAULT, &write_elem) < 0) FAIL_STACK_ERROR
+ if(H5Dwrite(dsid2, H5T_NATIVE_UINT, scalar_sid, sid2, H5P_DEFAULT, &write_elem2) < 0) FAIL_STACK_ERROR
- /* Read element from dataset */
+ /* Read element from the datasets */
read_elem = write_elem + 1;
+ read_elem2 = write_elem2 + 1;
if(H5Dread(dsid, H5T_NATIVE_UINT, scalar_sid, sid, H5P_DEFAULT, &read_elem) < 0) FAIL_STACK_ERROR
+ if(H5Dread(dsid2, H5T_NATIVE_UINT, scalar_sid, sid2, H5P_DEFAULT, &read_elem2) < 0) FAIL_STACK_ERROR
/* Verify written element is read in */
if(read_elem != write_elem) FAIL_PUTS_ERROR("invalid written element read");
+ if(read_elem2 != write_elem2) FAIL_PUTS_ERROR("invalid written element read");
/* Expand chunks now */
filter_expand_factor_g = 8;
- /* Write element to dataset */
- write_elem = u % 100;
+ /* Write element to the datasets */
+ write_elem = write_elem2 = u % 100;
H5E_BEGIN_TRY {
status = H5Dwrite(dsid, H5T_NATIVE_UINT, scalar_sid, sid, H5P_DEFAULT, &write_elem);
} H5E_END_TRY;
if(status >= 0) FAIL_PUTS_ERROR("should fail to write to dataset when allocation time is not early");
+
+ H5E_BEGIN_TRY {
+ status = H5Dwrite(dsid2, H5T_NATIVE_UINT, scalar_sid, sid2, H5P_DEFAULT, &write_elem2);
+ } H5E_END_TRY;
+ if(status >= 0) FAIL_PUTS_ERROR("should fail to write to dataset when allocation time is not early");
} /* end for */
/* Close everything */
if(H5Sclose(sid) < 0) FAIL_STACK_ERROR
+ if(H5Sclose(sid2) < 0) FAIL_STACK_ERROR
if(H5Sclose(scalar_sid) < 0) FAIL_STACK_ERROR
if(H5Dclose(dsid) < 0) FAIL_STACK_ERROR
+ if(H5Dclose(dsid2) < 0) FAIL_STACK_ERROR
if(H5Fclose(fid) < 0) FAIL_STACK_ERROR
/* Re-open file */
if((fid = H5Fopen(filename, H5F_ACC_RDWR, fapl)) < 0) FAIL_STACK_ERROR
- /* Delete dataset */
+ /* Delete the datasets */
if(H5Ldelete(fid, "dset", H5P_DEFAULT) < 0) FAIL_STACK_ERROR
+ if(H5Ldelete(fid, "dset2", H5P_DEFAULT) < 0) FAIL_STACK_ERROR
/* Close everything */
if(H5Fclose(fid) < 0) FAIL_STACK_ERROR
@@ -8318,8 +8713,11 @@ test_chunk_expand(hid_t fapl)
error:
H5E_BEGIN_TRY {
H5Pclose(dcpl);
+ H5Pclose(dcpl2);
H5Dclose(dsid);
+ H5Dclose(dsid2);
H5Sclose(sid);
+ H5Sclose(sid2);
H5Sclose(scalar_sid);
H5Fclose(fid);
} H5E_END_TRY;
@@ -8522,8 +8920,7 @@ test_fixed_array(hid_t fapl)
if(low == H5F_LIBVER_LATEST) {
if(idx_type != H5D_CHUNK_IDX_FARRAY)
FAIL_PUTS_ERROR("should be using Fixed Array as index");
- } /* end if */
- else {
+ } else {
if(idx_type != H5D_CHUNK_IDX_BTREE)
FAIL_PUTS_ERROR("should be using v1 B-tree as index");
} /* end else */
@@ -8712,6 +9109,7 @@ error:
return -1;
} /* end test_fixed_array() */
+
/*-------------------------------------------------------------------------
*
* test_idx_compatible():
diff --git a/test/objcopy.c b/test/objcopy.c
index edeca09..941d113 100755
--- a/test/objcopy.c
+++ b/test/objcopy.c
@@ -3062,7 +3062,8 @@ test_copy_dataset_no_edge_filt(hid_t fcpl_src, hid_t fcpl_dst, hid_t fapl)
/* open the destination dataset */
if((did2 = H5Dopen2(fid_dst, NAME_DATASET_CHUNKED, H5P_DEFAULT)) < 0) TEST_ERROR
- if(compare_idx_type(fapl, did2, H5D_CHUNK_IDX_FARRAY, H5D_CHUNK_IDX_BTREE) != TRUE)
+ /* H5Pset_chunk_opts() will set layout version to 4 which will use latest indexing available */
+ if(compare_idx_type(fapl, did2, H5D_CHUNK_IDX_FARRAY, H5D_CHUNK_IDX_FARRAY) != TRUE)
TEST_ERROR
/* Check if the datasets are equal */
diff --git a/test/set_extent.c b/test/set_extent.c
index 8de5649..b99d1c3 100644
--- a/test/set_extent.c
+++ b/test/set_extent.c
@@ -2765,7 +2765,8 @@ static int test_random_rank4( hid_t fapl, hid_t dcpl, hbool_t do_fillvalue,
/*!FIXME Skip the test if a fixed array index is requested, as resizing
* fixed arrays is broken now. Extensible arrays are also broken. Remove
* these lines as appropriate when these problems are fixed. */
- if(index_type == RANK4_INDEX_FARRAY || index_type == RANK4_INDEX_EARRAY)
+ /* Fixed Array index type is now fixed */
+ if(index_type == RANK4_INDEX_EARRAY)
return 0;
/* create a new file */
diff --git a/tools/h5dump/h5dumpgentest.c b/tools/h5dump/h5dumpgentest.c
index e8c888c..196e5e9 100644
--- a/tools/h5dump/h5dumpgentest.c
+++ b/tools/h5dump/h5dumpgentest.c
@@ -6786,13 +6786,18 @@ gent_fs_strategy_threshold(void)
}
/*
- * Create a file with new format.
- * Create one dataset with (set_chunk, fixed dimension)
+ * Create a file with new format:
+ * Create one dataset with (set_chunk, fixed dims, null max. dims)
* so that Fixed Array indexing will be used.
- * Create one dataset with (set_chunk, fixed dimension, filter)
+ * Create one dataset with (set_chunk, fixed dims, null max. dims, filter)
* so that Fixed Array indexing will be used.
- * Create one dataset with (set_chunk, non-fixed dimension)
- * so that B-tree indexing will be used.
+ * Create one dataset with (set_chunk, fixed dims, fixed max. dims)
+ * so that Fixed Array indexing will be used.
+ *
+ * Modifications:
+ * Fixed Array indexing will be used for chunked dataset
+ * with fixed max. dims setting.
+ *
*/
static void
gent_dataset_idx(void)
diff --git a/tools/misc/h5debug.c b/tools/misc/h5debug.c
index 50d81d0..ff8cdf0 100644
--- a/tools/misc/h5debug.c
+++ b/tools/misc/h5debug.c
@@ -24,6 +24,7 @@
*-------------------------------------------------------------------------
*/
#define H5A_PACKAGE /*suppress error about including H5Apkg */
+#define H5D_PACKAGE /*suppress error about including H5Dpkg */
#define H5B2_PACKAGE /*suppress error about including H5B2pkg */
#define H5B2_TESTING /*suppress warning about H5B2 testing funcs*/
#define H5EA_PACKAGE /*suppress error about including H5EApkg */
@@ -39,7 +40,7 @@
#include "H5private.h" /* Generic Functions */
#include "H5Apkg.h" /* Attributes */
#include "H5B2pkg.h" /* v2 B-trees */
-#include "H5Dprivate.h" /* Datasets */
+#include "H5Dpkg.h" /* Datasets */
#include "H5Eprivate.h" /* Error handling */
#include "H5EApkg.h" /* Extensible Arrays */
#include "H5FApkg.h" /* Fixed Arrays */
@@ -71,7 +72,10 @@
* koziol@hdfgroup.org
* Sep 11 2008
*
- *-------------------------------------------------------------------------
+ * Modifications:
+ * Vailin Choi; August 2010
+ * Added v2 B-tree indexing for chunked dataset >1 unlimited dimensions.
+ *---------------------------------------------------------------------------
*/
static const H5B2_class_t *
get_H5B2_class(const uint8_t *sig)
@@ -120,6 +124,14 @@ get_H5B2_class(const uint8_t *sig)
cls = H5A_BT2_CORDER;
break;
+ case H5B2_CDSET_ID:
+ cls = H5D_BT2;
+ break;
+
+ case H5B2_CDSET_FILT_ID:
+ cls = H5D_BT2_FILT;
+ break;
+
default:
fprintf(stderr, "Unknown B-tree subtype %u\n", (unsigned)(subtype));
HDexit(4);
@@ -228,6 +240,9 @@ get_H5FA_class(const uint8_t *sig)
* matzke@llnl.gov
* Jul 18 1997
*
+ * Modifications:
+ * Vailin Choi; August 2010
+ * Modified to handle v2 B-tree indexing for chunked dataset >1 unlimited dimensions.
*-------------------------------------------------------------------------
*/
int
@@ -235,7 +250,7 @@ main(int argc, char *argv[])
{
hid_t fid, fapl, dxpl;
H5F_t *f;
- haddr_t addr = 0, extra = 0, extra2 = 0, extra3 = 0;
+ haddr_t addr = 1, extra = 0, extra2 = 0, extra3 = 0, extra4 = 0;
uint8_t sig[H5F_SIGNATURE_LEN];
size_t u;
herr_t status = SUCCEED;
@@ -290,6 +305,8 @@ main(int argc, char *argv[])
extra2 = (haddr_t)HDstrtoll(argv[4], NULL, 0);
if(argc > 5)
extra3 = (haddr_t)HDstrtoll(argv[5], NULL, 0);
+ if(argc > 6)
+ extra4 = (haddr_t)HDstrtoll(argv[6], NULL, 0);
/*
* Read the signature at the specified file position.
@@ -376,7 +393,15 @@ main(int argc, char *argv[])
*/
const H5B2_class_t *cls = get_H5B2_class(sig);
HDassert(cls);
- status = H5B2_hdr_debug(f, H5P_DATASET_XFER_DEFAULT, addr, stdout, 0, VCOL, cls);
+
+ if((cls == H5D_BT2 || cls == H5D_BT2_FILT) && extra == 0) {
+ fprintf(stderr, "ERROR: Need v2 B-tree header address and object header address containing the layout message in order to dump header\n");
+ fprintf(stderr, "v2 B-tree hdr usage:\n");
+ fprintf(stderr, "\th5debug <filename> <v2 B-tree header address> <object header address>\n");
+ HDexit(4);
+ }
+
+ status = H5B2_hdr_debug(f, H5P_DATASET_XFER_DEFAULT, addr, stdout, 0, VCOL, cls, (haddr_t)extra);
} else if(!HDmemcmp(sig, H5B2_INT_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
/*
@@ -386,7 +411,16 @@ main(int argc, char *argv[])
HDassert(cls);
/* Check for enough valid parameters */
- if(extra == 0 || extra2 == 0 || extra3 == 0) {
+ if((cls == H5D_BT2 || cls == H5D_BT2_FILT) &&
+ (extra == 0 || extra2 == 0 || extra3 == 0 || extra4 == 0)) {
+
+ fprintf(stderr, "ERROR: Need v2 B-tree header address, the node's number of records, depth, and object header address containing the layout message in order to dump internal node\n");
+ fprintf(stderr, "NOTE: Leaf nodes are depth 0, the internal nodes above them are depth 1, etc.\n");
+ fprintf(stderr, "v2 B-tree internal node usage:\n");
+ fprintf(stderr, "\th5debug <filename> <internal node address> <v2 B-tree header address> <number of records> <depth> <object header address>\n");
+ HDexit(4);
+
+ } else if(extra == 0 || extra2 == 0 || extra3 == 0) {
fprintf(stderr, "ERROR: Need v2 B-tree header address and the node's number of records and depth in order to dump internal node\n");
fprintf(stderr, "NOTE: Leaf nodes are depth 0, the internal nodes above them are depth 1, etc.\n");
fprintf(stderr, "v2 B-tree internal node usage:\n");
@@ -394,7 +428,7 @@ main(int argc, char *argv[])
HDexit(4);
} /* end if */
- status = H5B2_int_debug(f, H5P_DATASET_XFER_DEFAULT, addr, stdout, 0, VCOL, cls, extra, (unsigned)extra2, (unsigned)extra3);
+ status = H5B2_int_debug(f, H5P_DATASET_XFER_DEFAULT, addr, stdout, 0, VCOL, cls, extra, (unsigned)extra2, (unsigned)extra3, (haddr_t)extra4);
} else if(!HDmemcmp(sig, H5B2_LEAF_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
/*
@@ -404,14 +438,22 @@ main(int argc, char *argv[])
HDassert(cls);
/* Check for enough valid parameters */
- if(extra == 0 || extra2 == 0) {
+ if((cls == H5D_BT2 || cls == H5D_BT2_FILT) &&
+ (extra == 0 || extra2 == 0 || extra3 == 0 )) {
+
+ fprintf(stderr, "ERROR: Need v2 B-tree header address, number of records, and object header address containing the layout message in order to dump leaf node\n");
+ fprintf(stderr, "v2 B-tree leaf node usage:\n");
+ fprintf(stderr, "\th5debug <filename> <leaf node address> <v2 B-tree header address> <number of records> <object header address>\n");
+ HDexit(4);
+
+ } else if(extra == 0 || extra2 == 0) {
fprintf(stderr, "ERROR: Need v2 B-tree header address and number of records in order to dump leaf node\n");
fprintf(stderr, "v2 B-tree leaf node usage:\n");
fprintf(stderr, "\th5debug <filename> <leaf node address> <v2 B-tree header address> <number of records>\n");
HDexit(4);
} /* end if */
- status = H5B2_leaf_debug(f, H5P_DATASET_XFER_DEFAULT, addr, stdout, 0, VCOL, cls, extra, (unsigned)extra2);
+ status = H5B2_leaf_debug(f, H5P_DATASET_XFER_DEFAULT, addr, stdout, 0, VCOL, cls, extra, (unsigned)extra2, (haddr_t)extra3);
} else if(!HDmemcmp(sig, H5HF_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
/*
diff --git a/tools/testfiles/tdset_idx.h5 b/tools/testfiles/tdset_idx.h5
index 809aee6..d1d910b 100644
--- a/tools/testfiles/tdset_idx.h5
+++ b/tools/testfiles/tdset_idx.h5
Binary files differ