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-rw-r--r--MANIFEST2
-rw-r--r--src/CMakeLists.txt2
-rw-r--r--src/H5B2.c36
-rw-r--r--src/H5B2private.h3
-rw-r--r--src/H5Dbtree2.c1491
-rw-r--r--src/H5Dchunk.c6
-rw-r--r--src/H5Dearray.c1740
-rw-r--r--src/H5Dint.c5
-rw-r--r--src/H5Dlayout.c140
-rw-r--r--src/H5Dpkg.h27
-rw-r--r--src/H5Dpublic.h4
-rw-r--r--src/H5Dtest.c41
-rw-r--r--src/H5EA.c88
-rw-r--r--src/H5EAprivate.h14
-rw-r--r--src/H5Olayout.c97
-rw-r--r--src/H5Oprivate.h47
-rw-r--r--src/H5VMprivate.h16
-rw-r--r--src/Makefile.am10
-rw-r--r--test/dsets.c25
19 files changed, 3773 insertions, 21 deletions
diff --git a/MANIFEST b/MANIFEST
index ba15450..e02f5fb 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -498,11 +498,13 @@
./src/H5CSprivate.h
./src/H5D.c
./src/H5Dbtree.c
+./src/H5Dbtree2.c
./src/H5Dchunk.c
./src/H5Dcompact.c
./src/H5Dcontig.c
./src/H5Ddbg.c
./src/H5Ddeprec.c
+./src/H5Dearray.c
./src/H5Defl.c
./src/H5Dfill.c
./src/H5Dint.c
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 1e0061f..f65c77f 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -103,11 +103,13 @@ IDE_GENERATED_PROPERTIES ("H5CS" "${H5CS_HDRS}" "${H5CS_SRCS}" )
set (H5D_SRCS
${HDF5_SRC_DIR}/H5D.c
${HDF5_SRC_DIR}/H5Dbtree.c
+ ${HDF5_SRC_DIR}/H5Dbtree2.c
${HDF5_SRC_DIR}/H5Dchunk.c
${HDF5_SRC_DIR}/H5Dcompact.c
${HDF5_SRC_DIR}/H5Dcontig.c
${HDF5_SRC_DIR}/H5Ddbg.c
${HDF5_SRC_DIR}/H5Ddeprec.c
+ ${HDF5_SRC_DIR}/H5Dearray.c
${HDF5_SRC_DIR}/H5Defl.c
${HDF5_SRC_DIR}/H5Dfill.c
${HDF5_SRC_DIR}/H5Dint.c
diff --git a/src/H5B2.c b/src/H5B2.c
index 5cbeadd..bce6a9f 100644
--- a/src/H5B2.c
+++ b/src/H5B2.c
@@ -87,6 +87,8 @@ 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];
extern const H5B2_class_t H5B2_TEST2[1];
const H5B2_class_t *const H5B2_client_class_g[] = {
@@ -100,7 +102,9 @@ const H5B2_class_t *const H5B2_client_class_g[] = {
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 */
- H5B2_TEST2, /* 10 - H5B2_TEST_ID */
+ H5D_BT2, /* 10 - H5B2_CDSET_ID */
+ H5D_BT2_FILT, /* 11 - H5B2_CDSET_FILT_ID */
+ H5B2_TEST2 /* 12 - H5B2_TEST_ID */
};
@@ -1445,3 +1449,33 @@ done:
FUNC_LEAVE_NOAPI(ret_value)
} /* H5B2_delete() */
+
+/*-------------------------------------------------------------------------
+ * Function: H5B2_patch_file
+ *
+ * Purpose: Patch the top-level file pointer contained in bt2
+ * to point to idx_info->f if they are different.
+ * This is possible because the file pointer in bt2 can be
+ * closed out if bt2 remains open.
+ *
+ * Return: SUCCEED
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5B2_patch_file(H5B2_t *bt2, H5F_t *f)
+{
+ FUNC_ENTER_NOAPI_NOINIT_NOERR
+
+ /*
+ * Check arguments.
+ */
+ HDassert(bt2);
+ HDassert(f);
+
+ if(bt2->f != f || bt2->hdr->f != f)
+ bt2->f = bt2->hdr->f = f;
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* H5B2_patch_file() */
+
diff --git a/src/H5B2private.h b/src/H5B2private.h
index b509869..3caf41f 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_TEST2_ID, /* Another B-tree is for testing (do not use for actual data) */
H5B2_NUM_BTREE_ID /* Number of B-tree IDs (must be last) */
} H5B2_subid_t;
@@ -151,6 +153,7 @@ H5_DLL herr_t H5B2_size(H5B2_t *bt2, hid_t dxpl_id,
H5_DLL herr_t H5B2_close(H5B2_t *bt2, hid_t dxpl_id);
H5_DLL herr_t H5B2_delete(H5F_t *f, hid_t dxpl_id, haddr_t addr,
void *ctx_udata, H5B2_remove_t op, void *op_data);
+H5_DLL herr_t H5B2_patch_file(H5B2_t *fa, H5F_t *f);
/* Statistics routines */
H5_DLL herr_t H5B2_stat_info(H5B2_t *bt2, H5B2_stat_t *info);
diff --git a/src/H5Dbtree2.c b/src/H5Dbtree2.c
new file mode 100644
index 0000000..9de609f
--- /dev/null
+++ b/src/H5Dbtree2.c
@@ -0,0 +1,1491 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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 */
+/****************/
+
+#include "H5Dmodule.h" /* This source code file is part of the H5D module */
+
+
+/***********/
+/* Headers */
+/***********/
+#include "H5private.h" /* Generic Functions */
+#include "H5Dpkg.h" /* Datasets */
+#include "H5FLprivate.h" /* Free Lists */
+#include "H5MFprivate.h" /* File space management */
+#include "H5VMprivate.h" /* Vector and array functions */
+
+
+/****************/
+/* Local Macros */
+/****************/
+
+
+/******************/
+/* Local Typedefs */
+/******************/
+/* 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 */
+ uint32_t *dim; /* Size of chunk in elements */
+} H5D_bt2_ctx_ud_t;
+
+/* The callback context */
+typedef struct H5D_bt2_ctx_t {
+ uint32_t chunk_size; /* Size of chunk (bytes; constant for unfiltered object) */
+ 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 in chunk */
+ uint32_t *dim; /* Size of chunk in elements */
+} 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 */
+} H5D_bt2_remove_ud_t;
+
+/* Callback info for iteration over chunks in v2 B-tree */
+typedef struct H5D_bt2_it_ud_t {
+ 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_ud_t {
+ H5D_chunk_rec_t rec; /* The record to search for */
+ unsigned ndims; /* Number of dimensions for the chunked dataset */
+} H5D_bt2_ud_t;
+
+
+/********************/
+/* Local Prototypes */
+/********************/
+
+/* Shared v2 B-tree methods for indexing filtered and non-filtered chunked datasets */
+static void *H5D__bt2_crt_context(void *udata);
+static herr_t H5D__bt2_dst_context(void *ctx);
+static herr_t H5D__bt2_store(void *native, const void *udata);
+static herr_t H5D__bt2_compare(const void *rec1, const void *rec2, int *result);
+
+/* v2 B-tree class for indexing non-filtered chunked datasets */
+static herr_t H5D__bt2_unfilt_encode(uint8_t *raw, const void *native, void *ctx);
+static herr_t H5D__bt2_unfilt_decode(const uint8_t *raw, void *native, void *ctx);
+static herr_t H5D__bt2_unfilt_debug(FILE *stream, 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_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, 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);
+
+/* Callback for H5B2_find() which is called in H5D__bt2_idx_get_addr() */
+static herr_t H5D__bt2_found_cb(const void *nrecord, void *op_data);
+
+/*
+ * Callback for H5B2_remove() and H5B2_delete() which is called
+ * in H5D__bt2_idx_remove() and H5D__bt2_idx_delete().
+ */
+static herr_t H5D__bt2_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_cb(void *_record, void *_op_data, hbool_t *changed);
+
+/* Chunked layout indexing callbacks for v2 B-tree indexing */
+static herr_t H5D__bt2_idx_init(const H5D_chk_idx_info_t *idx_info,
+ const H5S_t *space, haddr_t dset_ohdr_addr);
+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, const H5D_t *dset);
+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] = {{
+ H5D__bt2_idx_init, /* init */
+ H5D__bt2_idx_create, /* create */
+ H5D__bt2_idx_is_space_alloc, /* is_space_alloc */
+ H5D__bt2_idx_insert, /* insert */
+ H5D__bt2_idx_get_addr, /* get_addr */
+ NULL, /* resize */
+ H5D__bt2_idx_iterate, /* iterate */
+ H5D__bt2_idx_remove, /* remove */
+ H5D__bt2_idx_delete, /* delete */
+ H5D__bt2_idx_copy_setup, /* copy_setup */
+ H5D__bt2_idx_copy_shutdown, /* copy_shutdown */
+ H5D__bt2_idx_size, /* size */
+ H5D__bt2_idx_reset, /* reset */
+ H5D__bt2_idx_dump, /* dump */
+ H5D__bt2_idx_dest /* destroy */
+}};
+
+
+/*****************************/
+/* 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_chunk_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_unfilt_encode, /* Record encoding callback */
+ H5D__bt2_unfilt_decode, /* Record decoding callback */
+ H5D__bt2_unfilt_debug /* Record debugging callback */
+}};
+
+/* 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_chunk_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_filt_encode, /* Record encoding callback */
+ H5D__bt2_filt_decode, /* Record decoding callback */
+ H5D__bt2_filt_debug /* Record debugging callback */
+}};
+
+
+/*******************/
+/* Local Variables */
+/*******************/
+
+/* 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 page elements */
+H5FL_BLK_DEFINE(chunk_dim);
+
+
+
+
+/*-------------------------------------------------------------------------
+ * 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 */
+ uint32_t *my_dim = NULL; /* Pointer to copy of chunk dimension size */
+ void *ret_value = NULL; /* Return value */
+
+ FUNC_ENTER_STATIC
+
+ /* 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 set the chunk size and # of dimensions for the dataset */
+ ctx->sizeof_addr = H5F_SIZEOF_ADDR(udata->f);
+ ctx->chunk_size = udata->chunk_size;
+ ctx->ndims = udata->ndims;
+
+ /* Set up the "local" information for this dataset's chunk dimension sizes */
+ if(NULL == (my_dim = (uint32_t *)H5FL_BLK_MALLOC(chunk_dim, H5O_LAYOUT_NDIMS * sizeof(uint32_t))))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, NULL, "can't allocate chunk dims")
+ HDmemcpy(my_dim, udata->dim, H5O_LAYOUT_NDIMS * sizeof(uint32_t));
+ ctx->dim = my_dim;
+
+ /*
+ * 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 + ((H5VM_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_STATIC_NOERR
+
+ /* Sanity check */
+ HDassert(ctx);
+
+ /* Free array for chunk dimension sizes */
+ if(ctx->dim)
+ (void)H5FL_BLK_FREE(chunk_dim, ctx->dim);
+ /* 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)
+{
+ const H5D_bt2_ud_t *udata = (const H5D_bt2_ud_t *)_udata; /* User data */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ *(H5D_chunk_rec_t *)record = udata->rec;
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* H5D__bt2_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, int *result)
+{
+ const H5D_bt2_ud_t *udata = (const H5D_bt2_ud_t *)_udata; /* User data */
+ const H5D_chunk_rec_t *rec1 = &(udata->rec); /* The search record */
+ const H5D_chunk_rec_t *rec2 = (const H5D_chunk_rec_t *)_rec2; /* The native record */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Sanity checks */
+ HDassert(rec1);
+ HDassert(rec2);
+
+ /* Compare the offsets but ignore the other fields */
+ *result = H5VM_vector_cmp_u(udata->ndims, rec1->scaled, rec2->scaled);
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D__bt2_compare() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__bt2_unfilt_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_unfilt_encode(uint8_t *raw, const void *_record, void *_ctx)
+{
+ H5D_bt2_ctx_t *ctx = (H5D_bt2_ctx_t *)_ctx; /* Callback context structure */
+ const H5D_chunk_rec_t *record = (const H5D_chunk_rec_t *)_record; /* The native record */
+ unsigned u; /* Local index varible */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Sanity check */
+ HDassert(ctx);
+
+ /* Encode the record's fields */
+ H5F_addr_encode_len(ctx->sizeof_addr, &raw, record->chunk_addr);
+ /* (Don't encode the chunk size & filter mask for non-filtered B-tree records) */
+ for(u = 0; u < ctx->ndims; u++)
+ UINT64ENCODE(raw, record->scaled[u]);
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* H5D__bt2_unfilt_encode() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__bt2_unfilt_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_unfilt_decode(const uint8_t *raw, void *_record, void *_ctx)
+{
+ H5D_bt2_ctx_t *ctx = (H5D_bt2_ctx_t *)_ctx; /* Callback context structure */
+ H5D_chunk_rec_t *record = (H5D_chunk_rec_t *)_record; /* The native record */
+ unsigned u; /* Local index variable */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Sanity check */
+ HDassert(ctx);
+
+ /* Decode the record's fields */
+ H5F_addr_decode_len(ctx->sizeof_addr, &raw, &record->chunk_addr);
+ record->nbytes = ctx->chunk_size;
+ record->filter_mask = 0;
+ for(u = 0; u < ctx->ndims; u++)
+ UINT64DECODE(raw, record->scaled[u]);
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* H5D__bt2_unfilt_decode() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__bt2_unfilt_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_unfilt_debug(FILE *stream, int indent, int fwidth,
+ const void *_record, const void *_ctx)
+{
+ const H5D_chunk_rec_t *record = (const H5D_chunk_rec_t *)_record; /* The native record */
+ const H5D_bt2_ctx_t *ctx = (const H5D_bt2_ctx_t *)_ctx; /* Callback context */
+ unsigned u; /* Local index variable */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Sanity checks */
+ HDassert(record);
+ HDassert(ctx->chunk_size == record->nbytes);
+ HDassert(0 == record->filter_mask);
+
+ HDfprintf(stream, "%*s%-*s %a\n", indent, "", fwidth, "Chunk address:", record->chunk_addr);
+
+ HDfprintf(stream, "%*s%-*s {", indent, "", fwidth, "Logical offset:");
+ for(u = 0; u < ctx->ndims; u++)
+ HDfprintf(stream, "%s%Hd", u?", ":"", record->scaled[u] * ctx->dim[u]);
+ HDfputs("}\n", stream);
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* H5D__bt2_unfilt_debug() */
+
+
+/*-------------------------------------------------------------------------
+ * 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_chunk_rec_t *record = (const H5D_chunk_rec_t *)_record; /* The native record */
+ unsigned u; /* Local index variable */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Sanity check */
+ HDassert(ctx);
+ HDassert(record);
+ HDassert(H5F_addr_defined(record->chunk_addr));
+ HDassert(0 != record->nbytes);
+
+ /* Encode the record's fields */
+ H5F_addr_encode_len(ctx->sizeof_addr, &raw, record->chunk_addr);
+ UINT64ENCODE_VAR(raw, record->nbytes, ctx->chunk_size_len);
+ UINT32ENCODE(raw, record->filter_mask);
+ for(u = 0; u < ctx->ndims; u++)
+ UINT64ENCODE(raw, record->scaled[u]);
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* H5D__bt2_filt_encode() */
+
+
+/*-------------------------------------------------------------------------
+ * 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_chunk_rec_t *record = (H5D_chunk_rec_t *)_record; /* The native record */
+ unsigned u; /* Local index variable */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Sanity check */
+ HDassert(ctx);
+ HDassert(record);
+
+ /* Decode the record's fields */
+ H5F_addr_decode_len(ctx->sizeof_addr, &raw, &record->chunk_addr);
+ UINT64DECODE_VAR(raw, record->nbytes, ctx->chunk_size_len);
+ UINT32DECODE(raw, record->filter_mask);
+ for(u = 0; u < ctx->ndims; u++)
+ UINT64DECODE(raw, record->scaled[u]);
+
+ /* Sanity checks */
+ HDassert(H5F_addr_defined(record->chunk_addr));
+ HDassert(0 != record->nbytes);
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* H5D__bt2_filt_decode() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__bt2_filt_debug
+ *
+ * Purpose: Debug native form of record (filtered)
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi; June 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__bt2_filt_debug(FILE *stream, int indent, int fwidth,
+ const void *_record, const void *_ctx)
+{
+ const H5D_chunk_rec_t *record = (const H5D_chunk_rec_t *)_record; /* The native record */
+ const H5D_bt2_ctx_t *ctx = (const H5D_bt2_ctx_t *)_ctx; /* Callback context */
+ unsigned u; /* Local index variable */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Sanity checks */
+ HDassert(record);
+ HDassert(H5F_addr_defined(record->chunk_addr));
+ HDassert(0 != record->nbytes);
+
+ HDfprintf(stream, "%*s%-*s %a\n", indent, "", fwidth, "Chunk address:", record->chunk_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 < ctx->ndims; u++)
+ HDfprintf(stream, "%s%Hd", u?", ":"", record->scaled[u] * ctx->dim[u]);
+ HDfputs("}\n", stream);
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* H5D__bt2_filt_debug() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__bt2_idx_init
+ *
+ * Purpose: Initialize the indexing information for a dataset.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Neil Fortner
+ * Wednesday, May 23, 2012
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__bt2_idx_init(const H5D_chk_idx_info_t H5_ATTR_UNUSED *idx_info,
+ const H5S_t H5_ATTR_UNUSED *space, haddr_t dset_ohdr_addr)
+{
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Check args */
+ HDassert(H5F_addr_defined(dset_ohdr_addr));
+
+ idx_info->storage->u.btree2.dset_ohdr_addr = dset_ohdr_addr;
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D__bt2_idx_init() */
+
+
+/*-------------------------------------------------------------------------
+ * 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_STATIC
+
+ /* 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;
+ u_ctx.dim = idx_info->layout->dim;
+
+ /* 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_STATIC
+
+ /* 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 */
+
+ /* General parameters */
+ 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 + ((H5VM_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;
+ } /* end if */
+ 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;
+ u_ctx.dim = idx_info->layout->dim;
+
+ /* 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)
+{
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Check args */
+ HDassert(storage);
+
+ FUNC_LEAVE_NOAPI((hbool_t)H5F_addr_defined(storage->idx_addr))
+} /* end H5D__bt2_idx_is_space_alloc() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__bt2_mod_cb
+ *
+ * Purpose: Modify record for dataset chunk when it is found in a 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_cb(void *_record, void *_op_data, hbool_t *changed)
+{
+ H5D_bt2_ud_t *op_data = (H5D_bt2_ud_t *)_op_data; /* User data for v2 B-tree calls */
+ H5D_chunk_rec_t *record = (H5D_chunk_rec_t *)_record; /* Chunk record */
+
+ FUNC_ENTER_STATIC_NOERR
+
+/* Sanity check */
+#ifndef NDEBUG
+{
+ unsigned u; /* Local index variable */
+
+ for(u = 0; u < op_data->ndims; u++)
+ HDassert(record->scaled[u] == op_data->rec.scaled[u]);
+}
+#endif /* NDEBUG */
+
+ /* Modify record */
+ *record = op_data->rec;
+
+ /* Note that the record changed */
+ *changed = TRUE;
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D__bt2_mod_cb() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__bt2_idx_insert
+ *
+ * Purpose: Insert chunk address into the indexing structure.
+ * 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,
+ const H5D_t H5_ATTR_UNUSED *dset)
+{
+ H5B2_t *bt2; /* v2 B-tree handle for indexing chunks */
+ H5D_bt2_ud_t bt2_udata; /* User data for v2 B-tree calls */
+ unsigned u; /* Local index variable */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC
+
+ /* Sanity checks */
+ 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);
+ HDassert(H5F_addr_defined(udata->chunk_block.offset));
+
+ /* Check if the v2 B-tree is open yet */
+ 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 */
+ else /* Patch the top level file pointer contained in bt2 if needed */
+ if(H5B2_patch_file(idx_info->storage->u.btree2.bt2, idx_info->f) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't patch v2 B-tree file pointer")
+
+ /* Set convenience pointer to v2 B-tree structure */
+ bt2 = idx_info->storage->u.btree2.bt2;
+
+ /* Set up callback info */
+ bt2_udata.ndims = idx_info->layout->ndims - 1;
+ bt2_udata.rec.chunk_addr = udata->chunk_block.offset;
+ if(idx_info->pline->nused > 0) { /* filtered chunk */
+ H5_CHECKED_ASSIGN(bt2_udata.rec.nbytes, uint32_t, udata->chunk_block.length, hsize_t);
+ bt2_udata.rec.filter_mask = udata->filter_mask;
+ } /* end if */
+ else { /* non-filtered chunk */
+ bt2_udata.rec.nbytes = idx_info->layout->size;
+ bt2_udata.rec.filter_mask = 0;
+ } /* end else */
+ for(u = 0; u < (idx_info->layout->ndims - 1); u++)
+ bt2_udata.rec.scaled[u] = udata->common.scaled[u];
+
+ /* Update record for v2 B-tree (could be insert or modify) */
+ if(H5B2_update(bt2, idx_info->dxpl_id, &bt2_udata, H5D__bt2_mod_cb, &bt2_udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTUPDATE, FAIL, "unable to update record in v2 B-tree")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D__bt2_idx_insert() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__bt2_found_cb
+ *
+ * Purpose: Retrieve record for dataset chunk when it is found in a 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_STATIC_NOERR
+
+ *(H5D_chunk_rec_t *)op_data = *(const H5D_chunk_rec_t *)nrecord;
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* H5D__bt2_found_cb() */
+
+
+/*-------------------------------------------------------------------------
+ * 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; /* v2 B-tree handle for indexing chunks */
+ H5D_bt2_ud_t bt2_udata; /* User data for v2 B-tree calls */
+ H5D_chunk_rec_t found_rec; /* Record found from searching for object */
+ unsigned u; /* Local index variable */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC
+
+ /* Sanity checks */
+ 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);
+
+ /* Check if the v2 B-tree is open yet */
+ 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 */
+ else /* Patch the top level file pointer contained in bt2 if needed */
+ if(H5B2_patch_file(idx_info->storage->u.btree2.bt2, idx_info->f) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't patch v2 B-tree file pointer")
+
+ /* Set convenience pointer to v2 B-tree structure */
+ bt2 = idx_info->storage->u.btree2.bt2;
+
+ /* Clear the found record */
+ found_rec.chunk_addr = HADDR_UNDEF;
+ found_rec.nbytes = 0;
+ found_rec.filter_mask = 0;
+
+ /* Prepare user data for compare callback */
+ bt2_udata.rec.chunk_addr = HADDR_UNDEF;
+ bt2_udata.ndims = idx_info->layout->ndims - 1;
+
+ /* Set the chunk offset to be searched for */
+ for(u = 0; u < (idx_info->layout->ndims - 1); u++)
+ bt2_udata.rec.scaled[u] = udata->common.scaled[u];
+
+ /* Go get chunk information from v2 B-tree */
+ if(H5B2_find(bt2, 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")
+
+ /* Set common info for the chunk */
+ udata->chunk_block.offset = found_rec.chunk_addr;
+
+ /* Check for setting other info */
+ if(H5F_addr_defined(udata->chunk_block.offset)) {
+ /* Sanity check */
+ HDassert(0 != found_rec.nbytes);
+
+ /* Set other info for the chunk */
+ if(idx_info->pline->nused > 0) { /* filtered chunk */
+ udata->chunk_block.length = found_rec.nbytes;
+ udata->filter_mask = found_rec.filter_mask;
+ } /* end if */
+ else { /* non-filtered chunk */
+ udata->chunk_block.length = idx_info->layout->size;
+ udata->filter_mask = 0;
+ } /* end else */
+ } /* end if */
+ else {
+ udata->chunk_block.length = 0;
+ udata->filter_mask = 0;
+ } /* end else */
+
+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
+ *
+ *-------------------------------------------------------------------------
+ */
+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 */
+ const H5D_chunk_rec_t *record = (const H5D_chunk_rec_t *)_record; /* Native record */
+ int ret_value = -1; /* Return value */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Make "generic chunk" callback */
+ if((ret_value = (udata->cb)(record, 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)
+{
+ H5B2_t *bt2; /* v2 B-tree handle for indexing chunks */
+ H5D_bt2_it_ud_t udata; /* User data for B-tree iterator callback */
+ int ret_value = FAIL; /* Return value */
+
+ FUNC_ENTER_STATIC
+
+ /* Sanity checks */
+ 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);
+
+ /* Check if the v2 B-tree is open yet */
+ 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 */
+ else /* Patch the top level file pointer contained in bt2 if needed */
+ if(H5B2_patch_file(idx_info->storage->u.btree2.bt2, idx_info->f) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't patch v2 B-tree file pointer")
+
+ /* Set convenience pointer to v2 B-tree structure */
+ bt2 = idx_info->storage->u.btree2.bt2;
+
+ /* Prepare user data for iterate callback */
+ udata.cb = chunk_cb;
+ udata.udata = chunk_udata;
+
+ /* Iterate over the records in the v2 B-tree */
+ if((ret_value = H5B2_iterate(bt2, idx_info->dxpl_id, H5D__bt2_idx_iterate_cb, &udata)) < 0)
+ HERROR(H5E_DATASET, H5E_BADITER, "unable to iterate over chunk v2 B-tree");
+
+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)
+{
+ const H5D_chunk_rec_t *record = (const H5D_chunk_rec_t *)_record; /* The native record */
+ 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_STATIC
+
+ /* Sanity checks */
+ HDassert(udata);
+ HDassert(udata->f);
+
+ /* 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->chunk_addr, (hsize_t)record->nbytes) < 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_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)
+{
+ H5B2_t *bt2; /* v2 B-tree handle for indexing chunks */
+ H5D_bt2_remove_ud_t remove_udata; /* User data for removal callback */
+ H5D_bt2_ud_t bt2_udata; /* User data for v2 B-tree find call */
+ unsigned u; /* Local index variable */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC
+
+ /* Sanity checks */
+ 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);
+
+ /* Check if the v2 B-tree is open yet */
+ 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")
+
+ /* Set convenience pointer to v2 B-tree structure */
+ bt2 = 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;
+
+ /* Prepare user data for compare callback */
+ bt2_udata.ndims = idx_info->layout->ndims - 1;
+
+ /* Initialize the record to search for */
+ for(u = 0; u < (idx_info->layout->ndims - 1); u++)
+ bt2_udata.rec.scaled[u] = udata->scaled[u];
+
+ /* 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(H5B2_remove(bt2, 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")
+
+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
+ *
+ * Modifications:
+ * Vailin Choi; March 2011
+ * Initialize size of an unfiltered chunk.
+ * This is a fix for for the assertion failure in:
+ * [src/H5FSsection.c:968: H5FS_sect_link_size: Assertion `bin < sinfo->nbins' failed.]
+ * which is uncovered by test_unlink_chunked_dataset() in test/unlink.c
+ *
+ *-------------------------------------------------------------------------
+ */
+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_STATIC
+
+ /* 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;
+ u_ctx.dim = idx_info->layout->dim;
+
+ /* Initialize user data for removal callback */
+ remove_udata.f = idx_info->f;
+ remove_udata.dxpl_id = idx_info->dxpl_id;
+
+ /* Set remove operation. */
+ remove_op = 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_STATIC
+
+ /* 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")
+
+ /* 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 H5_ATTR_UNUSED dxpl_id)
+{
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC
+
+ /* 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_STATIC
+
+ /* 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_STATIC_NOERR
+
+ /* Sanity checks */
+ 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_STATIC_NOERR
+
+ /* Sanity checks */
+ 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_STATIC
+
+ /* 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 4d0e2c3..4df493d 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -75,7 +75,9 @@
/* Sanity check on chunk index types: commonly used by a lot of routines in this file */
#define H5D_CHUNK_STORAGE_INDEX_CHK(storage) \
- HDassert((H5D_CHUNK_IDX_BTREE == storage->idx_type && H5D_COPS_BTREE == storage->ops));
+ HDassert((H5D_CHUNK_IDX_EARRAY == storage->idx_type && H5D_COPS_EARRAY == 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));
/*
* Feature: If this constant is defined then every cache preemption and load
@@ -6285,6 +6287,8 @@ H5D__chunk_file_alloc(const H5D_chk_idx_info_t *idx_info, const H5F_block_t *old
/* Actually allocate space for the chunk in the file */
if(alloc_chunk) {
switch(idx_info->storage->idx_type) {
+ case H5D_CHUNK_IDX_EARRAY:
+ case H5D_CHUNK_IDX_BT2:
case H5D_CHUNK_IDX_BTREE:
HDassert(new_chunk->length > 0);
H5_CHECK_OVERFLOW(new_chunk->length, /*From: */uint32_t, /*To: */hsize_t);
diff --git a/src/H5Dearray.c b/src/H5Dearray.c
new file mode 100644
index 0000000..f24c69a
--- /dev/null
+++ b/src/H5Dearray.c
@@ -0,0 +1,1740 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/* Programmer: Quincey Koziol <koziol@hdfgroup.org>
+ * Tuesday, January 27, 2009
+ *
+ * Purpose: Extensible array indexed (chunked) I/O functions. The chunks
+ * are given a single-dimensional index which is used as the
+ * offset in an extensible array that maps a chunk coordinate to
+ * a disk address.
+ *
+ */
+
+/****************/
+/* Module Setup */
+/****************/
+
+#include "H5Dmodule.h" /* This source code file is part of the H5D module */
+
+
+/***********/
+/* Headers */
+/***********/
+#include "H5private.h" /* Generic Functions */
+#include "H5Dpkg.h" /* Datasets */
+#include "H5Eprivate.h" /* Error handling */
+#include "H5EAprivate.h" /* Extensible arrays */
+#include "H5FLprivate.h" /* Free Lists */
+#include "H5MFprivate.h" /* File space management */
+#include "H5VMprivate.h" /* Vector functions */
+
+
+/****************/
+/* Local Macros */
+/****************/
+
+/* Value to fill unset array elements with */
+#define H5D_EARRAY_FILL HADDR_UNDEF
+#define H5D_EARRAY_FILT_FILL {HADDR_UNDEF, 0, 0}
+
+
+/******************/
+/* Local Typedefs */
+/******************/
+
+/* Extensible array create/open user data */
+typedef struct H5D_earray_ctx_ud_t {
+ const H5F_t *f; /* Pointer to file info */
+ uint32_t chunk_size; /* Size of chunk (bytes) */
+} H5D_earray_ctx_ud_t;
+
+/* Extensible array callback context */
+typedef struct H5D_earray_ctx_t {
+ size_t file_addr_len; /* Size of addresses in the file (bytes) */
+ size_t chunk_size_len; /* Size of chunk sizes in the file (bytes) */
+} H5D_earray_ctx_t;
+
+/* User data for chunk callbacks */
+typedef struct H5D_earray_ud_t {
+ H5F_t *f; /* File pointer for operation */
+ hid_t dxpl_id; /* DXPL ID for operation */
+} H5D_earray_ud_t;
+
+/* Extensible Array callback info for iteration over chunks */
+typedef struct H5D_earray_it_ud_t {
+ H5D_chunk_common_ud_t common; /* Common info for Fixed Array user data (must be first) */
+ H5D_chunk_rec_t chunk_rec; /* Generic chunk record for callback */
+ hbool_t filtered; /* Whether the chunks are filtered */
+ H5D_chunk_cb_func_t cb; /* Chunk callback routine */
+ void *udata; /* User data for chunk callback routine */
+} H5D_earray_it_ud_t;
+
+/* Native extensible array element for chunks w/filters */
+typedef struct H5D_earray_filt_elmt_t {
+ haddr_t addr; /* Address of chunk */
+ uint32_t nbytes; /* Size of chunk (in file) */
+ uint32_t filter_mask; /* Excluded filters for chunk */
+} H5D_earray_filt_elmt_t;
+
+
+/********************/
+/* Local Prototypes */
+/********************/
+/* Extensible array iterator callbacks */
+static int H5D__earray_idx_iterate_cb(hsize_t idx, const void *_elmt, void *_udata);
+static int H5D__earray_idx_delete_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata);
+
+/* Extensible array class callbacks for chunks w/o filters */
+static void *H5D__earray_crt_context(void *udata);
+static herr_t H5D__earray_dst_context(void *ctx);
+static herr_t H5D__earray_fill(void *nat_blk, size_t nelmts);
+static herr_t H5D__earray_encode(void *raw, const void *elmt, size_t nelmts,
+ void *ctx);
+static herr_t H5D__earray_decode(const void *raw, void *elmt, size_t nelmts,
+ void *ctx);
+static herr_t H5D__earray_debug(FILE *stream, int indent, int fwidth,
+ hsize_t idx, const void *elmt);
+static void *H5D__earray_crt_dbg_context(H5F_t *f, hid_t dxpl_id, haddr_t obj_addr);
+static herr_t H5D__earray_dst_dbg_context(void *dbg_ctx);
+
+/* Extensible array class callbacks for chunks w/filters */
+/* (some shared with callbacks for chunks w/o filters) */
+static herr_t H5D__earray_filt_fill(void *nat_blk, size_t nelmts);
+static herr_t H5D__earray_filt_encode(void *raw, const void *elmt, size_t nelmts,
+ void *ctx);
+static herr_t H5D__earray_filt_decode(const void *raw, void *elmt, size_t nelmts,
+ void *ctx);
+static herr_t H5D__earray_filt_debug(FILE *stream, int indent, int fwidth,
+ hsize_t idx, const void *elmt);
+
+/* Chunked layout indexing callbacks */
+static herr_t H5D__earray_idx_init(const H5D_chk_idx_info_t *idx_info,
+ const H5S_t *space, haddr_t dset_ohdr_addr);
+static herr_t H5D__earray_idx_create(const H5D_chk_idx_info_t *idx_info);
+static hbool_t H5D__earray_idx_is_space_alloc(const H5O_storage_chunk_t *storage);
+static herr_t H5D__earray_idx_insert(const H5D_chk_idx_info_t *idx_info,
+ H5D_chunk_ud_t *udata, const H5D_t *dset);
+static herr_t H5D__earray_idx_get_addr(const H5D_chk_idx_info_t *idx_info,
+ H5D_chunk_ud_t *udata);
+static herr_t H5D__earray_idx_resize(H5O_layout_chunk_t *layout);
+static int H5D__earray_idx_iterate(const H5D_chk_idx_info_t *idx_info,
+ H5D_chunk_cb_func_t chunk_cb, void *chunk_udata);
+static herr_t H5D__earray_idx_remove(const H5D_chk_idx_info_t *idx_info,
+ H5D_chunk_common_ud_t *udata);
+static herr_t H5D__earray_idx_delete(const H5D_chk_idx_info_t *idx_info);
+static herr_t H5D__earray_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__earray_idx_copy_shutdown(H5O_storage_chunk_t *storage_src,
+ H5O_storage_chunk_t *storage_dst, hid_t dxpl_id);
+static herr_t H5D__earray_idx_size(const H5D_chk_idx_info_t *idx_info,
+ hsize_t *size);
+static herr_t H5D__earray_idx_reset(H5O_storage_chunk_t *storage, hbool_t reset_addr);
+static herr_t H5D__earray_idx_dump(const H5O_storage_chunk_t *storage,
+ FILE *stream);
+static herr_t H5D__earray_idx_dest(const H5D_chk_idx_info_t *idx_info);
+
+/* Generic extensible array routines */
+static herr_t H5D__earray_idx_open(const H5D_chk_idx_info_t *idx_info);
+
+
+/*********************/
+/* Package Variables */
+/*********************/
+
+/* Extensible array indexed chunk I/O ops */
+const H5D_chunk_ops_t H5D_COPS_EARRAY[1] = {{
+ H5D__earray_idx_init, /* init */
+ H5D__earray_idx_create, /* create */
+ H5D__earray_idx_is_space_alloc, /* is_space_alloc */
+ H5D__earray_idx_insert, /* insert */
+ H5D__earray_idx_get_addr, /* get_addr */
+ H5D__earray_idx_resize, /* resize */
+ H5D__earray_idx_iterate, /* iterate */
+ H5D__earray_idx_remove, /* remove */
+ H5D__earray_idx_delete, /* delete */
+ H5D__earray_idx_copy_setup, /* copy_setup */
+ H5D__earray_idx_copy_shutdown, /* copy_shutdown */
+ H5D__earray_idx_size, /* size */
+ H5D__earray_idx_reset, /* reset */
+ H5D__earray_idx_dump, /* dump */
+ H5D__earray_idx_dest /* destroy */
+}};
+
+
+/*****************************/
+/* Library Private Variables */
+/*****************************/
+
+/* Extensible array class callbacks for dataset chunks w/o filters */
+const H5EA_class_t H5EA_CLS_CHUNK[1]={{
+ H5EA_CLS_CHUNK_ID, /* Type of extensible array */
+ "Chunk w/o filters", /* Name of extensible array class */
+ sizeof(haddr_t), /* Size of native element */
+ H5D__earray_crt_context, /* Create context */
+ H5D__earray_dst_context, /* Destroy context */
+ H5D__earray_fill, /* Fill block of missing elements callback */
+ H5D__earray_encode, /* Element encoding callback */
+ H5D__earray_decode, /* Element decoding callback */
+ H5D__earray_debug, /* Element debugging callback */
+ H5D__earray_crt_dbg_context, /* Create debugging context */
+ H5D__earray_dst_dbg_context /* Destroy debugging context */
+}};
+
+/* Extensible array class callbacks for dataset chunks w/filters */
+const H5EA_class_t H5EA_CLS_FILT_CHUNK[1]={{
+ H5EA_CLS_FILT_CHUNK_ID, /* Type of extensible array */
+ "Chunk w/filters", /* Name of extensible array class */
+ sizeof(H5D_earray_filt_elmt_t), /* Size of native element */
+ H5D__earray_crt_context, /* Create context */
+ H5D__earray_dst_context, /* Destroy context */
+ H5D__earray_filt_fill, /* Fill block of missing elements callback */
+ H5D__earray_filt_encode, /* Element encoding callback */
+ H5D__earray_filt_decode, /* Element decoding callback */
+ H5D__earray_filt_debug, /* Element debugging callback */
+ H5D__earray_crt_dbg_context, /* Create debugging context */
+ H5D__earray_dst_dbg_context /* Destroy debugging context */
+}};
+
+
+/*******************/
+/* Local Variables */
+/*******************/
+
+/* Declare a free list to manage the H5D_earray_ctx_t struct */
+/* Declare a free list to manage the H5D_earray_ctx_ud_t struct */
+H5FL_DEFINE_STATIC(H5D_earray_ctx_t);
+H5FL_DEFINE_STATIC(H5D_earray_ctx_ud_t);
+
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_crt_context
+ *
+ * Purpose: Create context for callbacks
+ *
+ * Return: Success: non-NULL
+ * Failure: NULL
+ *
+ * Programmer: Quincey Koziol
+ * Thursday, January 29, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static void *
+H5D__earray_crt_context(void *_udata)
+{
+ H5D_earray_ctx_t *ctx; /* Extensible array callback context */
+ H5D_earray_ctx_ud_t *udata = (H5D_earray_ctx_ud_t *)_udata; /* User data for extensible array context */
+ void *ret_value = NULL; /* Return value */
+
+ FUNC_ENTER_STATIC
+
+ /* Sanity checks */
+ HDassert(udata);
+ HDassert(udata->f);
+ HDassert(udata->chunk_size > 0);
+
+ /* Allocate new context structure */
+ if(NULL == (ctx = H5FL_MALLOC(H5D_earray_ctx_t)))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, NULL, "can't allocate extensible array client callback context")
+
+ /* Initialize the context */
+ ctx->file_addr_len = H5F_SIZEOF_ADDR(udata->f);
+
+ /* 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 + ((H5VM_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)
+} /* end H5D__earray_crt_context() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_dst_context
+ *
+ * Purpose: Destroy context for callbacks
+ *
+ * Return: Success: non-NULL
+ * Failure: NULL
+ *
+ * Programmer: Quincey Koziol
+ * Thursday, January 29, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__earray_dst_context(void *_ctx)
+{
+ H5D_earray_ctx_t *ctx = (H5D_earray_ctx_t *)_ctx; /* Extensible array callback context */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Sanity checks */
+ HDassert(ctx);
+
+ /* Release context structure */
+ ctx = H5FL_FREE(H5D_earray_ctx_t, ctx);
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D__earray_dst_context() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_fill
+ *
+ * Purpose: Fill "missing elements" in block of elements
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Quincey Koziol
+ * Tuesday, January 27, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__earray_fill(void *nat_blk, size_t nelmts)
+{
+ haddr_t fill_val = H5D_EARRAY_FILL; /* Value to fill elements with */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Sanity checks */
+ HDassert(nat_blk);
+ HDassert(nelmts);
+
+ H5VM_array_fill(nat_blk, &fill_val, H5EA_CLS_CHUNK->nat_elmt_size, nelmts);
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D__earray_fill() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_encode
+ *
+ * Purpose: Encode an element from "native" to "raw" form
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Quincey Koziol
+ * Tuesday, January 27, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__earray_encode(void *raw, const void *_elmt, size_t nelmts, void *_ctx)
+{
+ H5D_earray_ctx_t *ctx = (H5D_earray_ctx_t *)_ctx; /* Extensible array callback context */
+ const haddr_t *elmt = (const haddr_t *)_elmt; /* Convenience pointer to native elements */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Sanity checks */
+ HDassert(raw);
+ HDassert(elmt);
+ HDassert(nelmts);
+ HDassert(ctx);
+
+ /* Encode native elements into raw elements */
+ while(nelmts) {
+ /* Encode element */
+ /* (advances 'raw' pointer) */
+ H5F_addr_encode_len(ctx->file_addr_len, (uint8_t **)&raw, *elmt);
+
+ /* Advance native element pointer */
+ elmt++;
+
+ /* Decrement # of elements to encode */
+ nelmts--;
+ } /* end while */
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D__earray_encode() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_decode
+ *
+ * Purpose: Decode an element from "raw" to "native" form
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Quincey Koziol
+ * Thursday, January 29, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__earray_decode(const void *_raw, void *_elmt, size_t nelmts, void *_ctx)
+{
+ H5D_earray_ctx_t *ctx = (H5D_earray_ctx_t *)_ctx; /* Extensible array callback context */
+ haddr_t *elmt = (haddr_t *)_elmt; /* Convenience pointer to native elements */
+ const uint8_t *raw = (const uint8_t *)_raw; /* Convenience pointer to raw elements */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Sanity checks */
+ HDassert(raw);
+ HDassert(elmt);
+ HDassert(nelmts);
+
+ /* Decode raw elements into native elements */
+ while(nelmts) {
+ /* Decode element */
+ /* (advances 'raw' pointer) */
+ H5F_addr_decode_len(ctx->file_addr_len, &raw, elmt);
+
+ /* Advance native element pointer */
+ elmt++;
+
+ /* Decrement # of elements to decode */
+ nelmts--;
+ } /* end while */
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D__earray_decode() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_debug
+ *
+ * Purpose: Display an element for debugging
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Quincey Koziol
+ * Thursday, January 29, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__earray_debug(FILE *stream, int indent, int fwidth, hsize_t idx,
+ const void *elmt)
+{
+ char temp_str[128]; /* Temporary string, for formatting */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Sanity checks */
+ HDassert(stream);
+ HDassert(elmt);
+
+ /* Print element */
+ sprintf(temp_str, "Element #%llu:", (unsigned long long)idx);
+ HDfprintf(stream, "%*s%-*s %a\n", indent, "", fwidth, temp_str,
+ *(const haddr_t *)elmt);
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D__earray_debug() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_filt_fill
+ *
+ * Purpose: Fill "missing elements" in block of elements
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Quincey Koziol
+ * Saturday, January 31, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__earray_filt_fill(void *nat_blk, size_t nelmts)
+{
+ H5D_earray_filt_elmt_t fill_val = H5D_EARRAY_FILT_FILL; /* Value to fill elements with */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Sanity checks */
+ HDassert(nat_blk);
+ HDassert(nelmts);
+ HDassert(sizeof(fill_val) == H5EA_CLS_FILT_CHUNK->nat_elmt_size);
+
+ H5VM_array_fill(nat_blk, &fill_val, H5EA_CLS_FILT_CHUNK->nat_elmt_size, nelmts);
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D__earray_filt_fill() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_filt_encode
+ *
+ * Purpose: Encode an element from "native" to "raw" form
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Quincey Koziol
+ * Saturday, January 31, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__earray_filt_encode(void *_raw, const void *_elmt, size_t nelmts, void *_ctx)
+{
+ H5D_earray_ctx_t *ctx = (H5D_earray_ctx_t *)_ctx; /* Extensible array callback context */
+ uint8_t *raw = (uint8_t *)_raw; /* Convenience pointer to raw elements */
+ const H5D_earray_filt_elmt_t *elmt = (const H5D_earray_filt_elmt_t *)_elmt; /* Convenience pointer to native elements */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Sanity checks */
+ HDassert(raw);
+ HDassert(elmt);
+ HDassert(nelmts);
+ HDassert(ctx);
+
+ /* Encode native elements into raw elements */
+ while(nelmts) {
+ /* Encode element */
+ /* (advances 'raw' pointer) */
+ H5F_addr_encode_len(ctx->file_addr_len, &raw, elmt->addr);
+ UINT64ENCODE_VAR(raw, elmt->nbytes, ctx->chunk_size_len);
+ UINT32ENCODE(raw, elmt->filter_mask);
+
+ /* Advance native element pointer */
+ elmt++;
+
+ /* Decrement # of elements to encode */
+ nelmts--;
+ } /* end while */
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D__earray_filt_encode() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_filt_decode
+ *
+ * Purpose: Decode an element from "raw" to "native" form
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Quincey Koziol
+ * Saturday, January 31, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__earray_filt_decode(const void *_raw, void *_elmt, size_t nelmts, void *_ctx)
+{
+ H5D_earray_ctx_t *ctx = (H5D_earray_ctx_t *)_ctx; /* Extensible array callback context */
+ H5D_earray_filt_elmt_t *elmt = (H5D_earray_filt_elmt_t *)_elmt; /* Convenience pointer to native elements */
+ const uint8_t *raw = (const uint8_t *)_raw; /* Convenience pointer to raw elements */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Sanity checks */
+ HDassert(raw);
+ HDassert(elmt);
+ HDassert(nelmts);
+
+ /* Decode raw elements into native elements */
+ while(nelmts) {
+ /* Decode element */
+ /* (advances 'raw' pointer) */
+ H5F_addr_decode_len(ctx->file_addr_len, &raw, &elmt->addr);
+ UINT64DECODE_VAR(raw, elmt->nbytes, ctx->chunk_size_len);
+ UINT32DECODE(raw, elmt->filter_mask);
+
+ /* Advance native element pointer */
+ elmt++;
+
+ /* Decrement # of elements to decode */
+ nelmts--;
+ } /* end while */
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D__earray_filt_decode() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_filt_debug
+ *
+ * Purpose: Display an element for debugging
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Quincey Koziol
+ * Saturday, January 31, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__earray_filt_debug(FILE *stream, int indent, int fwidth, hsize_t idx,
+ const void *_elmt)
+{
+ const H5D_earray_filt_elmt_t *elmt = (const H5D_earray_filt_elmt_t *)_elmt; /* Convenience pointer to native elements */
+ char temp_str[128]; /* Temporary string, for formatting */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Sanity checks */
+ HDassert(stream);
+ HDassert(elmt);
+
+ /* Print element */
+ sprintf(temp_str, "Element #%llu:", (unsigned long long)idx);
+ HDfprintf(stream, "%*s%-*s {%a, %u, %0x}\n", indent, "", fwidth, temp_str,
+ elmt->addr, elmt->nbytes, elmt->filter_mask);
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D__earray_filt_debug() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_crt_dbg_context
+ *
+ * Purpose: Create context for debugging callback
+ * (get the layout message in the specified object header)
+ *
+ * Return: Success: non-NULL
+ * Failure: NULL
+ *
+ * Programmer: Vailin Choi; July 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static void *
+H5D__earray_crt_dbg_context(H5F_t *f, hid_t dxpl_id, haddr_t obj_addr)
+{
+ H5D_earray_ctx_ud_t *dbg_ctx = NULL; /* Context for fixed array callback */
+ 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 = NULL; /* Return value */
+
+ FUNC_ENTER_STATIC
+
+ /* Sanity checks */
+ HDassert(f);
+ HDassert(H5F_addr_defined(obj_addr));
+
+ /* Allocate context for debugging callback */
+ if(NULL == (dbg_ctx = H5FL_MALLOC(H5D_earray_ctx_ud_t)))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, NULL, "can't allocate extensible array client callback context")
+
+ /* 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")
+
+ /* Create user data */
+ dbg_ctx->f = f;
+ dbg_ctx->chunk_size = layout.u.chunk.size;
+
+ /* Set return value */
+ ret_value = dbg_ctx;
+
+done:
+ /* Cleanup on error */
+ if(ret_value == NULL) {
+ /* Release context structure */
+ if(dbg_ctx)
+ dbg_ctx = H5FL_FREE(H5D_earray_ctx_ud_t, dbg_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)
+} /* end H5D__earray_crt_dbg_context() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_dst_dbg_context
+ *
+ * Purpose: Destroy context for debugging callback
+ * (free the layout message from the specified object header)
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi; July 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__earray_dst_dbg_context(void *_dbg_ctx)
+{
+ H5D_earray_ctx_ud_t *dbg_ctx = (H5D_earray_ctx_ud_t *)_dbg_ctx; /* Context for extensible array callback */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Sanity checks */
+ HDassert(dbg_ctx);
+
+ /* Release context structure */
+ dbg_ctx = H5FL_FREE(H5D_earray_ctx_ud_t, dbg_ctx);
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D__earray_dst_dbg_context() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_idx_open
+ *
+ * Purpose: Opens an existing extensible array.
+ *
+ * Note: This information is passively initialized from each index
+ * operation callback because those abstract chunk index operations
+ * are designed to work with the v1 B-tree chunk indices also,
+ * which don't require an 'open' for the data structure.
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Quincey Koziol
+ * Thursday, January 29, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__earray_idx_open(const H5D_chk_idx_info_t *idx_info)
+{
+ H5D_earray_ctx_ud_t udata; /* User data for extensible array open call */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC
+
+ /* Check args */
+ HDassert(idx_info);
+ HDassert(idx_info->f);
+ HDassert(idx_info->pline);
+ HDassert(idx_info->layout);
+ HDassert(H5D_CHUNK_IDX_EARRAY == idx_info->layout->idx_type);
+ HDassert(idx_info->storage);
+ HDassert(H5D_CHUNK_IDX_EARRAY == idx_info->storage->idx_type);
+ HDassert(H5F_addr_defined(idx_info->storage->idx_addr));
+ HDassert(NULL == idx_info->storage->u.earray.ea);
+
+ /* Set up the user data */
+ udata.f = idx_info->f;
+ udata.chunk_size = idx_info->layout->size;
+
+ /* Open the extensible array for the chunk index */
+ if(NULL == (idx_info->storage->u.earray.ea = H5EA_open(idx_info->f, idx_info->dxpl_id, idx_info->storage->idx_addr, &udata)))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't open extensible array")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__earray_idx_open() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_idx_init
+ *
+ * Purpose: Initialize the indexing information for a dataset.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * Wednesday, May 27, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__earray_idx_init(const H5D_chk_idx_info_t *idx_info, const H5S_t *space,
+ haddr_t dset_ohdr_addr)
+{
+ hsize_t max_dims[H5O_LAYOUT_NDIMS]; /* Max. size of dataset dimensions */
+ int unlim_dim; /* Rank of the dataset's unlimited dimension */
+ int sndims; /* Rank of dataspace */
+ unsigned ndims; /* Rank of dataspace */
+ unsigned u; /* Local index variable */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC
+
+ /* Check args */
+ HDassert(idx_info);
+ HDassert(idx_info->f);
+ HDassert(idx_info->pline);
+ HDassert(idx_info->layout);
+ HDassert(idx_info->storage);
+ HDassert(space);
+ HDassert(H5F_addr_defined(dset_ohdr_addr));
+
+ /* Get the dim info for dataset */
+ if((sndims = H5S_get_simple_extent_dims(space, NULL, max_dims)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataspace dimensions")
+ H5_CHECKED_ASSIGN(ndims, unsigned, sndims, int);
+
+ /* Find the rank of the unlimited dimension */
+ unlim_dim = (-1);
+ for(u = 0; u < ndims; u++) {
+ /* Check for unlimited dimension */
+ if(H5S_UNLIMITED == max_dims[u]) {
+ /* Check if we've already found an unlimited dimension */
+ if(unlim_dim >= 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_ALREADYINIT, FAIL, "already found unlimited dimension")
+
+ /* Set the unlimited dimension */
+ unlim_dim = (int)u;
+ } /* end if */
+ } /* end for */
+
+ /* Check if we didn't find an unlimited dimension */
+ if(unlim_dim < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_UNINITIALIZED, FAIL, "didn't find unlimited dimension")
+
+ /* Set the unlimited dimension for the layout's future use */
+ idx_info->layout->u.earray.unlim_dim = (unsigned)unlim_dim;
+
+ /* Store the dataset's object header address for later */
+ idx_info->storage->u.earray.dset_ohdr_addr = dset_ohdr_addr;
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__earray_idx_init() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_idx_create
+ *
+ * Purpose: Creates a new indexed-storage extensible array and initializes
+ * the layout struct with information about the storage. The
+ * struct should be immediately written to the object header.
+ *
+ * This function must be called before passing LAYOUT to any of
+ * the other indexed storage functions!
+ *
+ * Return: Non-negative on success (with the LAYOUT argument initialized
+ * and ready to write to an object header). Negative on failure.
+ *
+ * Programmer: Quincey Koziol
+ * Tuesday, January 27, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__earray_idx_create(const H5D_chk_idx_info_t *idx_info)
+{
+ H5EA_create_t cparam; /* Extensible array creation parameters */
+ H5D_earray_ctx_ud_t udata; /* User data for extensible array create call */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC
+
+ /* 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(NULL == idx_info->storage->u.earray.ea);
+
+ /* General parameters */
+ 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 + ((H5VM_log2_gen((uint64_t)idx_info->layout->size) + 8) / 8);
+ if(chunk_size_len > 8)
+ chunk_size_len = 8;
+
+ cparam.cls = H5EA_CLS_FILT_CHUNK;
+ cparam.raw_elmt_size = (uint8_t)(H5F_SIZEOF_ADDR(idx_info->f) + chunk_size_len + 4);
+ } /* end if */
+ else {
+ cparam.cls = H5EA_CLS_CHUNK;
+ cparam.raw_elmt_size = (uint8_t)H5F_SIZEOF_ADDR(idx_info->f);
+ } /* end else */
+ cparam.max_nelmts_bits = idx_info->layout->u.earray.cparam.max_nelmts_bits;
+ HDassert(cparam.max_nelmts_bits > 0);
+ cparam.idx_blk_elmts = idx_info->layout->u.earray.cparam.idx_blk_elmts;
+ HDassert(cparam.idx_blk_elmts > 0);
+ cparam.sup_blk_min_data_ptrs = idx_info->layout->u.earray.cparam.sup_blk_min_data_ptrs;
+ HDassert(cparam.sup_blk_min_data_ptrs > 0);
+ cparam.data_blk_min_elmts = idx_info->layout->u.earray.cparam.data_blk_min_elmts;
+ HDassert(cparam.data_blk_min_elmts > 0);
+ cparam.max_dblk_page_nelmts_bits = idx_info->layout->u.earray.cparam.max_dblk_page_nelmts_bits;
+ HDassert(cparam.max_dblk_page_nelmts_bits > 0);
+
+ /* Set up the user data */
+ udata.f = idx_info->f;
+ udata.chunk_size = idx_info->layout->size;
+
+ /* Create the extensible array for the chunk index */
+ if(NULL == (idx_info->storage->u.earray.ea = H5EA_create(idx_info->f, idx_info->dxpl_id, &cparam, &udata)))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't create extensible array")
+
+ /* Get the address of the extensible array in file */
+ if(H5EA_get_addr(idx_info->storage->u.earray.ea, &(idx_info->storage->idx_addr)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't query extensible array address")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__earray_idx_create() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_idx_is_space_alloc
+ *
+ * Purpose: Query if space is allocated for index method
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * Thursday, January 29, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static hbool_t
+H5D__earray_idx_is_space_alloc(const H5O_storage_chunk_t *storage)
+{
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Check args */
+ HDassert(storage);
+
+ FUNC_LEAVE_NOAPI((hbool_t)H5F_addr_defined(storage->idx_addr))
+} /* end H5D__earray_idx_is_space_alloc() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_idx_insert
+ *
+ * Purpose: Insert chunk address into the indexing structure.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Vailin Choi; May 2014
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__earray_idx_insert(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata,
+ const H5D_t H5_ATTR_UNUSED *dset)
+{
+ H5EA_t *ea; /* Pointer to extensible array structure */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC
+
+ /* Sanity checks */
+ 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);
+
+ /* Check if the extensible array is open yet */
+ if(NULL == idx_info->storage->u.earray.ea) {
+ /* Open the extensible array in file */
+ if(H5D__earray_idx_open(idx_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open extensible array")
+ } else /* Patch the top level file pointer contained in ea if needed */
+ H5EA_patch_file(idx_info->storage->u.earray.ea, idx_info->f);
+
+ /* Set convenience pointer to extensible array structure */
+ ea = idx_info->storage->u.earray.ea;
+
+ if(!H5F_addr_defined(udata->chunk_block.offset))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "The chunk should have allocated already")
+ if(udata->chunk_idx != (udata->chunk_idx & 0xffffffff)) /* negative value */
+ HGOTO_ERROR(H5E_ARGS, H5E_BADRANGE, FAIL, "chunk index must be less than 2^32")
+
+ /* Check for filters on chunks */
+ if(idx_info->pline->nused > 0) {
+ H5D_earray_filt_elmt_t elmt; /* Extensible array element */
+
+ elmt.addr = udata->chunk_block.offset;
+ H5_CHECKED_ASSIGN(elmt.nbytes, uint32_t, udata->chunk_block.length, hsize_t);
+ elmt.filter_mask = udata->filter_mask;
+
+ /* Set the info for the chunk */
+ if(H5EA_set(ea, idx_info->dxpl_id, udata->chunk_idx, &elmt) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set chunk info")
+ } /* end if */
+ else {
+ /* Set the address for the chunk */
+ if(H5EA_set(ea, idx_info->dxpl_id, udata->chunk_idx, &udata->chunk_block.offset) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set chunk address")
+ } /* end else */
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D__earray_idx_insert() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_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: Quincey Koziol
+ * Thursday, January 29, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__earray_idx_get_addr(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata)
+{
+ H5EA_t *ea; /* Pointer to extensible array structure */
+ hsize_t idx; /* Array index of chunk */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC
+
+ /* Sanity checks */
+ 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);
+
+ /* Check if the extensible array is open yet */
+ if(NULL == idx_info->storage->u.earray.ea) {
+ /* Open the extensible array in file */
+ if(H5D__earray_idx_open(idx_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open extensible array")
+ } else /* Patch the top level file pointer contained in ea if needed */
+ H5EA_patch_file(idx_info->storage->u.earray.ea, idx_info->f);
+
+ /* Set convenience pointer to extensible array structure */
+ ea = idx_info->storage->u.earray.ea;
+
+ /* Check for unlimited dim. not being the slowest-changing dim. */
+ if(idx_info->layout->u.earray.unlim_dim > 0) {
+ hsize_t swizzled_coords[H5O_LAYOUT_NDIMS]; /* swizzled chunk coordinates */
+ unsigned ndims = (idx_info->layout->ndims - 1); /* Number of dimensions */
+ unsigned u;
+
+ /* Compute coordinate offset from scaled offset */
+ for(u = 0; u < ndims; u++)
+ swizzled_coords[u] = udata->common.scaled[u] * idx_info->layout->dim[u];
+
+ H5VM_swizzle_coords(hsize_t, swizzled_coords, idx_info->layout->u.earray.unlim_dim);
+
+ /* Calculate the index of this chunk */
+ idx = H5VM_chunk_index(ndims, swizzled_coords, idx_info->layout->u.earray.swizzled_dim, idx_info->layout->u.earray.swizzled_down_chunks);
+ } /* end if */
+ else {
+ /* Calculate the index of this chunk */
+ idx = H5VM_array_offset_pre((idx_info->layout->ndims - 1), idx_info->layout->down_chunks, udata->common.scaled);
+ } /* end else */
+
+ udata->chunk_idx = idx;
+
+ /* Check for filters on chunks */
+ if(idx_info->pline->nused > 0) {
+ H5D_earray_filt_elmt_t elmt; /* Extensible array element */
+
+ /* Get the information for the chunk */
+ if(H5EA_get(ea, idx_info->dxpl_id, idx, &elmt) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk info")
+
+ /* Set the info for the chunk */
+ udata->chunk_block.offset = elmt.addr;
+ udata->chunk_block.length = elmt.nbytes;
+ udata->filter_mask = elmt.filter_mask;
+ } /* end if */
+ else {
+ /* Get the address for the chunk */
+ if(H5EA_get(ea, idx_info->dxpl_id, idx, &udata->chunk_block.offset) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk address")
+
+ /* Update the other (constant) information for the chunk */
+ udata->chunk_block.length = idx_info->layout->size;
+ udata->filter_mask = 0;
+ } /* end else */
+
+ if(!H5F_addr_defined(udata->chunk_block.offset))
+ udata->chunk_block.length = 0;
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D__earray_idx_get_addr() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_idx_resize
+ *
+ * Purpose: Calculate/setup the swizzled down chunk array, used for chunk
+ * index calculations.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * Thursday, July 23, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__earray_idx_resize(H5O_layout_chunk_t *layout)
+{
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC
+
+ /* Check args */
+ HDassert(layout);
+
+ /* "Swizzle" constant dimensions for this dataset */
+ if(layout->u.earray.unlim_dim > 0) {
+ hsize_t swizzled_chunks[H5O_LAYOUT_NDIMS]; /* Swizzled form of # of chunks in each dimension */
+
+ /* Get the swizzled chunk dimensions */
+ HDmemcpy(layout->u.earray.swizzled_dim, layout->dim, (layout->ndims - 1) * sizeof(layout->dim[0]));
+ H5VM_swizzle_coords(uint32_t, layout->u.earray.swizzled_dim, layout->u.earray.unlim_dim);
+
+ /* Get the swizzled number of chunks in each dimension */
+ HDmemcpy(swizzled_chunks, layout->chunks, (layout->ndims - 1) * sizeof(swizzled_chunks[0]));
+ H5VM_swizzle_coords(hsize_t, swizzled_chunks, layout->u.earray.unlim_dim);
+
+ /* Get the swizzled "down" sizes for each dimension */
+ if(H5VM_array_down((layout->ndims - 1), swizzled_chunks, layout->u.earray.swizzled_down_chunks) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't compute swizzled 'down' chunk size value")
+ } /* end if */
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__earray_idx_resize() */
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_idx_iterate_cb
+ *
+ * Purpose: Callback routine for extensible array element iteration.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Vailin Choi; Feb 2015
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+H5D__earray_idx_iterate_cb(hsize_t H5_ATTR_UNUSED idx, const void *_elmt, void *_udata)
+{
+ H5D_earray_it_ud_t *udata = (H5D_earray_it_ud_t *)_udata; /* User data */
+ unsigned ndims; /* Rank of chunk */
+ int curr_dim; /* Current dimension */
+ int ret_value = H5_ITER_CONT; /* Return value */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Compose generic chunk record for callback */
+ if(udata->filtered) {
+ const H5D_earray_filt_elmt_t *filt_elmt = (const H5D_earray_filt_elmt_t *)_elmt;
+
+ udata->chunk_rec.chunk_addr = filt_elmt->addr;
+ udata->chunk_rec.nbytes = filt_elmt->nbytes;
+ udata->chunk_rec.filter_mask = filt_elmt->filter_mask;
+ } /* end if */
+ else
+ udata->chunk_rec.chunk_addr = *(const haddr_t *)_elmt;
+
+ /* Make "generic chunk" callback */
+ if(H5F_addr_defined(udata->chunk_rec.chunk_addr))
+ if((ret_value = (udata->cb)(&udata->chunk_rec, udata->udata)) < 0)
+ HERROR(H5E_DATASET, H5E_CALLBACK, "failure in generic chunk iterator callback");
+
+ /* Update coordinates of chunk in dataset */
+ ndims = udata->common.layout->ndims - 1;
+ HDassert(ndims > 0);
+ curr_dim = (int)(ndims - 1);
+ while(curr_dim >= 0) {
+ /* Increment coordinate in current dimension */
+ udata->chunk_rec.scaled[curr_dim]++;
+
+ /* Check if we went off the end of the current dimension */
+ if(udata->chunk_rec.scaled[curr_dim] >= udata->common.layout->chunks[curr_dim]) {
+ /* Reset coordinate & move to next faster dimension */
+ udata->chunk_rec.scaled[curr_dim] = 0;
+ curr_dim--;
+ } /* end if */
+ else
+ break;
+ } /* end while */
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D__earray_idx_iterate_cb() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_idx_iterate
+ *
+ * Purpose: Iterate over the chunks in an index, making a callback
+ * for each one.
+ *
+ * Note: This implementation is slow, particularly for sparse
+ * extensible arrays, replace it with call to H5EA_iterate()
+ * when that's available.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * Thursday, January 29, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+H5D__earray_idx_iterate(const H5D_chk_idx_info_t *idx_info,
+ H5D_chunk_cb_func_t chunk_cb, void *chunk_udata)
+{
+ H5EA_t *ea; /* Pointer to extensible array structure */
+ H5EA_stat_t ea_stat; /* Extensible array statistics */
+ int ret_value = H5_ITER_CONT; /* Return value */
+
+ FUNC_ENTER_STATIC
+
+ /* Sanity checks */
+ 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);
+
+ /* Check if the extensible array is open yet */
+ if(NULL == idx_info->storage->u.earray.ea) {
+ /* Open the extensible array in file */
+ if(H5D__earray_idx_open(idx_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open extensible array")
+ } else /* Patch the top level file pointer contained in ea if needed */
+ H5EA_patch_file(idx_info->storage->u.earray.ea, idx_info->f);
+
+ /* Set convenience pointer to extensible array structure */
+ ea = idx_info->storage->u.earray.ea;
+
+ /* Get the extensible array statistics */
+ if(H5EA_get_stats(ea, &ea_stat) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't query extensible array statistics")
+
+ if(ea_stat.stored.max_idx_set > 0) {
+ H5D_earray_it_ud_t udata; /* User data for iteration callback */
+
+ /* Initialize userdata */
+ HDmemset(&udata, 0, sizeof udata);
+ udata.common.layout = idx_info->layout;
+ udata.common.storage = idx_info->storage;
+ HDmemset(&udata.chunk_rec, 0, sizeof(udata.chunk_rec));
+ udata.filtered = (idx_info->pline->nused > 0);
+ if(!udata.filtered) {
+ udata.chunk_rec.nbytes = idx_info->layout->size;
+ udata.chunk_rec.filter_mask = 0;
+ } /* end if */
+ udata.cb = chunk_cb;
+ udata.udata = chunk_udata;
+
+ /* Iterate over the extensible array elements */
+ if((ret_value = H5EA_iterate(ea, idx_info->dxpl_id, H5D__earray_idx_iterate_cb, &udata)) < 0)
+ HERROR(H5E_DATASET, H5E_BADITER, "unable to iterate over fixed array chunk index");
+ } /* end if */
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__earray_idx_iterate() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_idx_remove
+ *
+ * Purpose: Remove chunk from index.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * Thursday, January 29, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__earray_idx_remove(const H5D_chk_idx_info_t *idx_info, H5D_chunk_common_ud_t *udata)
+{
+ H5EA_t *ea; /* Pointer to extensible array structure */
+ hsize_t idx; /* Array index of chunk */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC
+
+ /* Sanity checks */
+ 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);
+
+ /* Check if the extensible array is open yet */
+ if(NULL == idx_info->storage->u.earray.ea)
+ /* Open the extensible array in file */
+ if(H5D__earray_idx_open(idx_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open extensible array")
+
+ /* Set convenience pointer to extensible array structure */
+ ea = idx_info->storage->u.earray.ea;
+
+ /* Check for unlimited dim. not being the slowest-changing dim. */
+ if(idx_info->layout->u.earray.unlim_dim > 0) {
+ hsize_t swizzled_coords[H5O_LAYOUT_NDIMS]; /* swizzled chunk coordinates */
+ unsigned ndims = (idx_info->layout->ndims - 1); /* Number of dimensions */
+ unsigned u;
+
+ /* Compute coordinate offset from scaled offset */
+ for(u = 0; u < ndims; u++)
+ swizzled_coords[u] = udata->scaled[u] * idx_info->layout->dim[u];
+
+ H5VM_swizzle_coords(hsize_t, swizzled_coords, idx_info->layout->u.earray.unlim_dim);
+
+ /* Calculate the index of this chunk */
+ idx = H5VM_chunk_index(ndims, swizzled_coords, idx_info->layout->u.earray.swizzled_dim, idx_info->layout->u.earray.swizzled_down_chunks);
+ } /* end if */
+ else {
+ /* Calculate the index of this chunk */
+ idx = H5VM_array_offset_pre((idx_info->layout->ndims - 1), idx_info->layout->down_chunks, udata->scaled);
+ } /* end else */
+
+ /* Check for filters on chunks */
+ if(idx_info->pline->nused > 0) {
+ H5D_earray_filt_elmt_t elmt; /* Extensible array element */
+
+ /* Get the info about the chunk for the index */
+ if(H5EA_get(ea, idx_info->dxpl_id, idx, &elmt) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk info")
+
+ /* Remove raw data chunk from file */
+ HDassert(H5F_addr_defined(elmt.addr));
+ H5_CHECK_OVERFLOW(elmt.nbytes, /*From: */uint32_t, /*To: */hsize_t);
+ if(H5MF_xfree(idx_info->f, H5FD_MEM_DRAW, idx_info->dxpl_id, elmt.addr, (hsize_t)elmt.nbytes) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to free chunk")
+
+ /* Reset the info about the chunk for the index */
+ elmt.addr = HADDR_UNDEF;
+ elmt.nbytes = 0;
+ elmt.filter_mask = 0;
+ if(H5EA_set(ea, idx_info->dxpl_id, idx, &elmt) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to reset chunk info")
+ } /* end if */
+ else {
+ haddr_t addr = HADDR_UNDEF; /* Chunk address */
+
+ /* Get the address of the chunk for the index */
+ if(H5EA_get(ea, idx_info->dxpl_id, idx, &addr) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk address")
+
+ /* Remove raw data chunk from file */
+ HDassert(H5F_addr_defined(addr));
+ H5_CHECK_OVERFLOW(idx_info->layout->size, /*From: */uint32_t, /*To: */hsize_t);
+ if(H5MF_xfree(idx_info->f, H5FD_MEM_DRAW, idx_info->dxpl_id, addr, (hsize_t)idx_info->layout->size) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to free chunk")
+
+ /* Reset the address of the chunk for the index */
+ addr = HADDR_UNDEF;
+ if(H5EA_set(ea, idx_info->dxpl_id, idx, &addr) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to reset chunk address")
+ } /* end else */
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D__earray_idx_remove() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_idx_delete_cb
+ *
+ * Purpose: Delete space for chunk in file
+ *
+ * Return: Success: Non-negative
+ * Failure: negative
+ *
+ * Programmer: Quincey Koziol
+ * Saturday, January 31, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+H5D__earray_idx_delete_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
+{
+ H5D_earray_ud_t *udata = (H5D_earray_ud_t *)_udata; /* User data for callback */
+ int ret_value = H5_ITER_CONT; /* Return value */
+
+ FUNC_ENTER_STATIC
+
+ /* Sanity checks */
+ HDassert(chunk_rec);
+ HDassert(H5F_addr_defined(chunk_rec->chunk_addr));
+ HDassert(chunk_rec->nbytes > 0);
+ HDassert(udata);
+ HDassert(udata->f);
+
+ /* Remove raw data chunk from file */
+ H5_CHECK_OVERFLOW(chunk_rec->nbytes, /*From: */uint32_t, /*To: */hsize_t);
+ if(H5MF_xfree(udata->f, H5FD_MEM_DRAW, udata->dxpl_id, chunk_rec->chunk_addr, (hsize_t)chunk_rec->nbytes) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, H5_ITER_ERROR, "unable to free chunk")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__earray_idx_delete_cb() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_idx_delete
+ *
+ * Purpose: Delete index and raw data storage for entire dataset
+ * (i.e. all chunks)
+ *
+ * Note: This implementation is slow, particularly for sparse
+ * extensible arrays, replace it with call to H5EA_iterate()
+ * when that's available.
+ *
+ * Return: Success: Non-negative
+ * Failure: negative
+ *
+ * Programmer: Quincey Koziol
+ * Thursday, January 29, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__earray_idx_delete(const H5D_chk_idx_info_t *idx_info)
+{
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC
+
+ /* 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)) {
+ H5D_earray_ud_t udata; /* User data for callback */
+ H5D_earray_ctx_ud_t ctx_udata; /* User data for extensible array open call */
+
+ /* Initialize user data for callback */
+ udata.f = idx_info->f;
+ udata.dxpl_id = idx_info->dxpl_id;
+
+ /* Iterate over the chunk addresses in the extensible array, deleting each chunk */
+ if(H5D__earray_idx_iterate(idx_info, H5D__earray_idx_delete_cb, &udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to iterate over chunk addresses")
+
+ /* Close extensible array */
+ if(H5EA_close(idx_info->storage->u.earray.ea, idx_info->dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to close extensible array")
+ idx_info->storage->u.earray.ea = NULL;
+
+ /* Set up the context user data */
+ ctx_udata.f = idx_info->f;
+ ctx_udata.chunk_size = idx_info->layout->size;
+
+ /* Delete extensible array */
+ if(H5EA_delete(idx_info->f, idx_info->dxpl_id, idx_info->storage->idx_addr, &ctx_udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTDELETE, FAIL, "unable to delete chunk extensible array")
+ idx_info->storage->idx_addr = HADDR_UNDEF;
+ } /* end if */
+ else
+ HDassert(NULL == idx_info->storage->u.earray.ea);
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__earray_idx_delete() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_idx_copy_setup
+ *
+ * Purpose: Set up any necessary information for copying chunks
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * Saturday, January 31, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__earray_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_STATIC
+
+ /* Check args */
+ HDassert(idx_info_src);
+ HDassert(idx_info_src->f);
+ HDassert(idx_info_src->pline);
+ HDassert(idx_info_src->layout);
+ HDassert(idx_info_src->storage);
+ 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 extensible array is open yet */
+ if(NULL == idx_info_src->storage->u.earray.ea)
+ /* Open the extensible array in file */
+ if(H5D__earray_idx_open(idx_info_src) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open extensible array")
+
+ /* Set copied metadata tag */
+ H5_BEGIN_TAG(idx_info_dst->dxpl_id, H5AC__COPIED_TAG, FAIL);
+
+ /* Create the extensible array that describes chunked storage in the dest. file */
+ if(H5D__earray_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__earray_idx_copy_setup() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_idx_copy_shutdown
+ *
+ * Purpose: Shutdown any information from copying chunks
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * Saturday, January 31, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__earray_idx_copy_shutdown(H5O_storage_chunk_t *storage_src,
+ H5O_storage_chunk_t *storage_dst, hid_t dxpl_id)
+{
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC
+
+ /* Check args */
+ HDassert(storage_src);
+ HDassert(storage_src->u.earray.ea);
+ HDassert(storage_dst);
+ HDassert(storage_dst->u.earray.ea);
+
+ /* Close extensible arrays */
+ if(H5EA_close(storage_src->u.earray.ea, dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to close extensible array")
+ storage_src->u.earray.ea = NULL;
+ if(H5EA_close(storage_dst->u.earray.ea, dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to close extensible array")
+ storage_dst->u.earray.ea = NULL;
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__earray_idx_copy_shutdown() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_idx_size
+ *
+ * Purpose: Retrieve the amount of index storage for chunked dataset
+ *
+ * Return: Success: Non-negative
+ * Failure: negative
+ *
+ * Programmer: Quincey Koziol
+ * Saturday, January 31, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__earray_idx_size(const H5D_chk_idx_info_t *idx_info, hsize_t *index_size)
+{
+ H5EA_t *ea; /* Pointer to extensible array structure */
+ H5EA_stat_t ea_stat; /* Extensible array statistics */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC
+
+ /* 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 the extensible array in file */
+ if(H5D__earray_idx_open(idx_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open extensible array")
+
+ /* Set convenience pointer to extensible array structure */
+ ea = idx_info->storage->u.earray.ea;
+
+ /* Get the extensible array statistics */
+ if(H5EA_get_stats(ea, &ea_stat) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't query extensible array statistics")
+
+ /* Set the size of the extensible array */
+ *index_size = ea_stat.computed.hdr_size + ea_stat.computed.index_blk_size
+ + ea_stat.stored.super_blk_size + ea_stat.stored.data_blk_size;
+
+done:
+ if(idx_info->storage->u.earray.ea) {
+ if(H5EA_close(idx_info->storage->u.earray.ea, idx_info->dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to close extensible array")
+ idx_info->storage->u.earray.ea = NULL;
+ } /* end if */
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__earray_idx_size() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_idx_reset
+ *
+ * Purpose: Reset indexing information.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * Saturday, January 31, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__earray_idx_reset(H5O_storage_chunk_t *storage, hbool_t reset_addr)
+{
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Check args */
+ HDassert(storage);
+
+ /* Reset index info */
+ if(reset_addr) {
+ storage->idx_addr = HADDR_UNDEF;
+ storage->u.earray.dset_ohdr_addr = HADDR_UNDEF;
+ } /* end if */
+ storage->u.earray.ea = NULL;
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D__earray_idx_reset() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_idx_dump
+ *
+ * Purpose: Dump indexing information to a stream.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * Saturday, January 31, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__earray_idx_dump(const H5O_storage_chunk_t *storage, FILE *stream)
+{
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Check args */
+ HDassert(storage);
+ HDassert(stream);
+
+ HDfprintf(stream, " Address: %a\n", storage->idx_addr);
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D__earray_idx_dump() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__earray_idx_dest
+ *
+ * Purpose: Release indexing information in memory.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * Saturday, January 31, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__earray_idx_dest(const H5D_chk_idx_info_t *idx_info)
+{
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC
+
+ /* Check args */
+ HDassert(idx_info);
+ HDassert(idx_info->f);
+ HDassert(idx_info->storage);
+
+ /* Check if the extensible array is open */
+ if(idx_info->storage->u.earray.ea) {
+ /* Close extensible array */
+ if(H5EA_close(idx_info->storage->u.earray.ea, idx_info->dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to close extensible array")
+ idx_info->storage->u.earray.ea = NULL;
+ } /* end if */
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__earray_idx_dest() */
+
diff --git a/src/H5Dint.c b/src/H5Dint.c
index 6c1f24a..0355656 100644
--- a/src/H5Dint.c
+++ b/src/H5Dint.c
@@ -1222,6 +1222,11 @@ H5D__create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id,
if(H5D__layout_set_latest_version(&new_dset->shared->layout, new_dset->shared->space, &new_dset->shared->dcpl_cache) < 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, &new_dset->shared->dcpl_cache) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set latest indexing")
+ } /* end if */
/* Check if this dataset is going into a parallel file and set space allocation time */
if(H5F_HAS_FEATURE(file, H5FD_FEAT_ALLOCATE_EARLY))
diff --git a/src/H5Dlayout.c b/src/H5Dlayout.c
index 7801632..c213140 100644
--- a/src/H5Dlayout.c
+++ b/src/H5Dlayout.c
@@ -96,8 +96,24 @@ H5D__layout_set_io_ops(const H5D_t *dataset)
dataset->shared->layout.ops = H5D_LOPS_CHUNK;
/* Set the chunk operations */
- /* (Only "B-tree" indexing type currently supported) */
- dataset->shared->layout.storage.u.chunk.ops = H5D_COPS_BTREE;
+ switch(dataset->shared->layout.u.chunk.idx_type) {
+ case H5D_CHUNK_IDX_BTREE:
+ dataset->shared->layout.storage.u.chunk.ops = H5D_COPS_BTREE;
+ break;
+
+ case H5D_CHUNK_IDX_EARRAY:
+ dataset->shared->layout.storage.u.chunk.ops = H5D_COPS_EARRAY;
+ break;
+
+ case H5D_CHUNK_IDX_BT2:
+ dataset->shared->layout.storage.u.chunk.ops = H5D_COPS_BT2;
+ break;
+
+ case H5D_CHUNK_IDX_NTYPES:
+ default:
+ HDassert(0 && "Unknown chunk index method!");
+ HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unknown chunk index method")
+ } /* end switch */
break;
case H5D_COMPACT:
@@ -190,8 +206,30 @@ H5D__layout_meta_size(const H5F_t *f, const H5O_layout_t *layout, hbool_t includ
/* Dimension sizes */
ret_value += layout->u.chunk.ndims * layout->u.chunk.enc_bytes_per_dim;
- /* B-tree address */
- ret_value += H5F_SIZEOF_ADDR(f); /* Address of data */
+ /* Type of chunk index */
+ ret_value++;
+
+ switch(layout->u.chunk.idx_type) {
+ case H5D_CHUNK_IDX_BTREE:
+ HGOTO_ERROR(H5E_OHDR, H5E_BADVALUE, 0, "v1 B-tree index type found for layout message >v3")
+
+ case H5D_CHUNK_IDX_EARRAY:
+ /* Extensible array creation parameters */
+ ret_value += H5D_EARRAY_CREATE_PARAM_SIZE;
+ break;
+
+ case H5D_CHUNK_IDX_BT2:
+ /* v2 B-tree creation parameters */
+ ret_value += H5D_BT2_CREATE_PARAM_SIZE;
+ break;
+
+ case H5D_CHUNK_IDX_NTYPES:
+ default:
+ HGOTO_ERROR(H5E_OHDR, H5E_CANTENCODE, 0, "Invalid chunk index type")
+ } /* end switch */
+
+ /* Chunk index address */
+ ret_value += H5F_SIZEOF_ADDR(f);
} /* end else */
break;
@@ -241,12 +279,106 @@ H5D__layout_set_latest_version(H5O_layout_t *layout, const H5S_t *space,
/* Set encoding of layout to latest version */
layout->version = H5O_LAYOUT_VERSION_LATEST;
+ /* Set the latest indexing type for the layout message */
+ if(H5D__layout_set_latest_indexing(layout, space, dcpl_cache) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set latest indexing type")
+
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
+ *
+ * Programmer: Quincey Koziol
+ * Thursday, January 15, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D__layout_set_latest_indexing(H5O_layout_t *layout, const H5S_t *space,
+ const H5D_dcpl_cache_t *dcpl_cache)
+{
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_PACKAGE
+
+ /* Sanity check */
+ HDassert(layout);
+ HDassert(space);
+ HDassert(dcpl_cache);
+
+ /* The indexing methods only apply to chunked datasets (currently) */
+ if(layout->type == H5D_CHUNKED) {
+ int sndims; /* Rank of dataspace */
+ unsigned ndims; /* Rank of dataspace */
+
+ /* Query the dimensionality of the dataspace */
+ if((sndims = H5S_GET_EXTENT_NDIMS(space)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "invalid dataspace rank")
+ ndims = (unsigned)sndims;
+
+ /* Avoid scalar/null dataspace */
+ if(ndims > 0) {
+ hsize_t max_dims[H5O_LAYOUT_NDIMS]; /* Maximum dimension sizes */
+ hsize_t cur_dims[H5O_LAYOUT_NDIMS]; /* Current dimension sizes */
+ unsigned unlim_count = 0; /* Count of unlimited max. dimensions */
+ unsigned u; /* Local index variable */
+
+ /* Query the dataspace's dimensions */
+ if(H5S_get_simple_extent_dims(space, cur_dims, max_dims) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataspace max. dimensions")
+
+ /* Spin through the max. dimensions, looking for unlimited dimensions */
+ for(u = 0; u < ndims; u++)
+ if(max_dims[u] == H5S_UNLIMITED)
+ unlim_count++;
+
+ 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;
+
+ /* Set the extensible array creation parameters */
+ /* (use hard-coded defaults for now, until we give applications
+ * control over this with a property list - QAK)
+ */
+ layout->u.chunk.u.earray.cparam.max_nelmts_bits = H5D_EARRAY_MAX_NELMTS_BITS;
+ layout->u.chunk.u.earray.cparam.idx_blk_elmts = H5D_EARRAY_IDX_BLK_ELMTS;
+ layout->u.chunk.u.earray.cparam.sup_blk_min_data_ptrs = H5D_EARRAY_SUP_BLK_MIN_DATA_PTRS;
+ 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;
+ } /* end if */
+ else {
+ /* 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 */
+ /* (use hard-coded defaults for now, until we give applications
+ * control over this with a property list - QAK)
+ */
+ 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;
+ } /* end else */
+ } /* end if */
+ } /* end if */
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__layout_set_latest_indexing() */
+
+
+/*-------------------------------------------------------------------------
* Function: H5D__layout_oh_create
*
* Purpose: Create layout/pline/efl information for dataset
diff --git a/src/H5Dpkg.h b/src/H5Dpkg.h
index 8fc5cac..bfd0601 100644
--- a/src/H5Dpkg.h
+++ b/src/H5Dpkg.h
@@ -33,6 +33,7 @@
/* Other private headers needed by this file */
#include "H5ACprivate.h" /* Metadata cache */
+#include "H5B2private.h" /* v2 B-trees */
#include "H5Fprivate.h" /* File access */
#include "H5Gprivate.h" /* Groups */
#include "H5SLprivate.h" /* Skip lists */
@@ -67,6 +68,23 @@
#define H5D_MARK_SPACE 0x01
#define H5D_MARK_LAYOUT 0x02
+/* Default creation parameters for chunk index data structures */
+/* See H5O_layout_chunk_t */
+
+/* Extensible array creation values */
+#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 2048
+#define H5D_BT2_SPLIT_PERC 100
+#define H5D_BT2_MERGE_PERC 40
+
/****************************/
/* Package Private Typedefs */
@@ -519,6 +537,12 @@ H5_DLLVAR const H5D_layout_ops_t H5D_LOPS_VIRTUAL[1];
/* Chunked layout operations */
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_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];
/******************************/
@@ -584,6 +608,8 @@ 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, const H5D_dcpl_cache_t *dcpl_cache);
+H5_DLL herr_t H5D__layout_set_latest_indexing(H5O_layout_t *layout,
+ const H5S_t *space, const H5D_dcpl_cache_t *dcpl_cache);
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,
@@ -721,6 +747,7 @@ H5_DLL htri_t H5D__mpio_opt_possible(const H5D_io_info_t *io_info,
#ifdef H5D_TESTING
H5_DLL herr_t H5D__layout_version_test(hid_t did, unsigned *version);
H5_DLL herr_t H5D__layout_contig_size_test(hid_t did, hsize_t *size);
+H5_DLL herr_t H5D__layout_idx_type_test(hid_t did, H5D_chunk_index_t *idx_type);
H5_DLL herr_t H5D__current_cache_size_test(hid_t did, size_t *nbytes_used, int *nused);
#endif /* H5D_TESTING */
diff --git a/src/H5Dpublic.h b/src/H5Dpublic.h
index 39e6aa7..a7bd981 100644
--- a/src/H5Dpublic.h
+++ b/src/H5Dpublic.h
@@ -61,7 +61,9 @@ 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 */
- H5D_CHUNK_IDX_NTYPES /* this one must be last! */
+ H5D_CHUNK_IDX_EARRAY = 4, /* Extensible array (for 1 unlimited dim) */
+ H5D_CHUNK_IDX_BT2 = 5, /* v2 B-tree index (for >1 unlimited dims) */
+ H5D_CHUNK_IDX_NTYPES /*this one must be last! */
} H5D_chunk_index_t;
/* Values for the space allocation time property */
diff --git a/src/H5Dtest.c b/src/H5Dtest.c
index fd8ff71..c3b0b19 100644
--- a/src/H5Dtest.c
+++ b/src/H5Dtest.c
@@ -144,6 +144,47 @@ done:
/*--------------------------------------------------------------------------
NAME
+ H5D__layout_idx_type_test
+ PURPOSE
+ Determine the storage layout index type for a dataset's layout information
+ USAGE
+ herr_t H5D__layout_idx_type_test(did, idx_type)
+ hid_t did; IN: Dataset to query
+ H5D_chunk_index_t *idx_type; OUT: Pointer to location to place index type info
+ RETURNS
+ Non-negative on success, negative on failure
+ DESCRIPTION
+ Checks the index type of the storage layout information for a dataset.
+ GLOBAL VARIABLES
+ COMMENTS, BUGS, ASSUMPTIONS
+ DO NOT USE THIS FUNCTION FOR ANYTHING EXCEPT TESTING
+ EXAMPLES
+ REVISION LOG
+--------------------------------------------------------------------------*/
+herr_t
+H5D__layout_idx_type_test(hid_t did, H5D_chunk_index_t *idx_type)
+{
+ H5D_t *dset; /* Pointer to dataset to query */
+ herr_t ret_value = SUCCEED; /* return value */
+
+ FUNC_ENTER_PACKAGE
+
+ /* Check args */
+ if(NULL == (dset = (H5D_t *)H5I_object_verify(did, H5I_DATASET)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
+ if(dset->shared->layout.type != H5D_CHUNKED)
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dataset is not chunked")
+
+ if(idx_type)
+ *idx_type = dset->shared->layout.u.chunk.idx_type;
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D__layout_idx_type_test() */
+
+
+/*--------------------------------------------------------------------------
+ NAME
H5D__current_cache_size_test
PURPOSE
Determine current the size of the dataset's chunk cache
diff --git a/src/H5EA.c b/src/H5EA.c
index 34173e4..756eb93 100644
--- a/src/H5EA.c
+++ b/src/H5EA.c
@@ -88,6 +88,8 @@ hbool_t H5_PKG_INIT_VAR = FALSE;
* client class..
*/
const H5EA_class_t *const H5EA_client_class_g[] = {
+ H5EA_CLS_CHUNK, /* 0 - H5EA_CLS_CHUNK_ID */
+ H5EA_CLS_FILT_CHUNK, /* 1 - H5EA_CLS_FILT_CHUNK_ID */
H5EA_CLS_TEST, /* ? - H5EA_CLS_TEST_ID */
};
@@ -104,6 +106,8 @@ const H5EA_class_t *const H5EA_client_class_g[] = {
/* Declare a free list to manage the H5EA_t struct */
H5FL_DEFINE_STATIC(H5EA_t);
+/* Declare a PQ free list to manage the element */
+H5FL_BLK_DEFINE(ea_native_elmt);
/*-------------------------------------------------------------------------
@@ -1032,3 +1036,87 @@ CATCH
END_FUNC(PRIV) /* end H5EA_delete() */
+
+/*-------------------------------------------------------------------------
+ * Function: H5EA_iterate
+ *
+ * Purpose: Iterate over the elements of an extensible array
+ * (copied and modified from FA_iterate() in H5FA.c)
+ *
+ * Return: SUCCEED/FAIL
+ *
+ * Programmer: Vailin Choi; Feb 2015
+ *
+ *-------------------------------------------------------------------------
+ */
+BEGIN_FUNC(PRIV, ERR,
+herr_t, SUCCEED, FAIL,
+H5EA_iterate(H5EA_t *ea, hid_t dxpl_id, H5EA_operator_t op, void *udata))
+
+ /* Local variables */
+ uint8_t *elmt = NULL;
+ hsize_t u;
+
+ /*
+ * Check arguments.
+ */
+ HDassert(ea);
+ HDassert(op);
+ HDassert(udata);
+
+ /* Allocate space for a native array element */
+ if(NULL == (elmt = H5FL_BLK_MALLOC(ea_native_elmt, ea->hdr->cparam.cls->nat_elmt_size)))
+ H5E_THROW(H5E_CANTALLOC, "memory allocation failed for extensible array element")
+
+ /* Iterate over all elements in array */
+ for(u = 0; u < ea->hdr->stats.stored.max_idx_set; u++) {
+ int cb_ret; /* Return value from callback */
+
+ /* Get array element */
+ if(H5EA_get(ea, dxpl_id, u, elmt) < 0)
+ H5E_THROW(H5E_CANTGET, "unable to delete fixed array")
+
+ /* Make callback */
+ if((cb_ret = (*op)(u, elmt, udata)) < 0) {
+ H5E_PRINTF(H5E_BADITER, "iterator function failed");
+ H5_LEAVE(cb_ret)
+ } /* end if */
+ } /* end for */
+
+CATCH
+
+ if(elmt)
+ elmt = H5FL_BLK_FREE(ea_native_elmt, elmt);
+
+END_FUNC(PRIV) /* end H5EA_iterate() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5EA_patch_file
+ *
+ * Purpose: Patch the top-level file pointer contained in ea
+ * to point to idx_info->f if they are different.
+ * This is possible because the file pointer in ea can be
+ * closed out if ea remains open.
+ *
+ * Return: SUCCEED
+ *
+ *-------------------------------------------------------------------------
+ */
+BEGIN_FUNC(PRIV, NOERR,
+herr_t, SUCCEED, -,
+H5EA_patch_file(H5EA_t *ea, H5F_t *f))
+
+ /* Local variables */
+
+ /*
+ * Check arguments.
+ */
+ HDassert(ea);
+ HDassert(f);
+
+ if(ea->f != f || ea->hdr->f != f)
+ ea->f = ea->hdr->f = f;
+
+END_FUNC(PRIV) /* end H5EA_patch_file() */
+
diff --git a/src/H5EAprivate.h b/src/H5EAprivate.h
index 9147f39..0a1b945 100644
--- a/src/H5EAprivate.h
+++ b/src/H5EAprivate.h
@@ -49,6 +49,9 @@
/* Extensible array class IDs */
typedef enum H5EA_cls_id_t {
+ H5EA_CLS_CHUNK_ID = 0, /* Extensible array is for indexing dataset chunks w/o filters */
+ H5EA_CLS_FILT_CHUNK_ID, /* Extensible array is for indexing dataset chunks w/filters */
+
/* Start real class IDs at 0 -QAK */
/* (keep these last) */
H5EA_CLS_TEST_ID, /* Extensible array is for testing (do not use for actual data) */
@@ -112,11 +115,20 @@ typedef struct H5EA_stat_t {
/* Extensible array info (forward decl - defined in H5EApkg.h) */
typedef struct H5EA_t H5EA_t;
+/* Define the operator callback function pointer for H5EA_iterate() */
+typedef int (*H5EA_operator_t)(hsize_t idx, const void *_elmt, void *_udata);
+
/*****************************/
/* Library-private Variables */
/*****************************/
+/* The Extensible Array class for dataset chunks w/o filters*/
+H5_DLLVAR const H5EA_class_t H5EA_CLS_CHUNK[1];
+
+/* The Extensible Array class for dataset chunks w/ filters*/
+H5_DLLVAR const H5EA_class_t H5EA_CLS_FILT_CHUNK[1];
+
/***************************************/
/* Library-private Function Prototypes */
@@ -131,8 +143,10 @@ H5_DLL herr_t H5EA_get_addr(const H5EA_t *ea, haddr_t *addr);
H5_DLL herr_t H5EA_set(const H5EA_t *ea, hid_t dxpl_id, hsize_t idx, const void *elmt);
H5_DLL herr_t H5EA_get(const H5EA_t *ea, hid_t dxpl_id, hsize_t idx, void *elmt);
H5_DLL herr_t H5EA_depend(H5AC_info_t *parent_entry, H5EA_t *ea);
+H5_DLL herr_t H5EA_iterate(H5EA_t *fa, hid_t dxpl_id, H5EA_operator_t op, void *udata);
H5_DLL herr_t H5EA_close(H5EA_t *ea, hid_t dxpl_id);
H5_DLL herr_t H5EA_delete(H5F_t *f, hid_t dxpl_id, haddr_t ea_addr, void *ctx_udata);
+H5_DLL herr_t H5EA_patch_file(H5EA_t *fa, H5F_t *f);
/* Statistics routines */
H5_DLL herr_t H5EA_get_stats(const H5EA_t *ea, H5EA_stat_t *stats);
diff --git a/src/H5Olayout.c b/src/H5Olayout.c
index f2af8ef..c19bbfc 100644
--- a/src/H5Olayout.c
+++ b/src/H5Olayout.c
@@ -287,9 +287,52 @@ H5O__layout_decode(H5F_t *f, hid_t H5_ATTR_UNUSED dxpl_id, H5O_t H5_ATTR_UNUSED
for(u = 1, mesg->u.chunk.size = mesg->u.chunk.dim[0]; u < mesg->u.chunk.ndims; u++)
mesg->u.chunk.size *= mesg->u.chunk.dim[u];
- /* Set the chunk operations */
- mesg->storage.u.chunk.idx_type = H5D_CHUNK_IDX_BTREE;
- mesg->storage.u.chunk.ops = H5D_COPS_BTREE;
+ /* Chunk index type */
+ mesg->u.chunk.idx_type = (H5D_chunk_index_t)*p++;
+ if(mesg->u.chunk.idx_type >= H5D_CHUNK_IDX_NTYPES)
+ HGOTO_ERROR(H5E_OHDR, H5E_BADVALUE, NULL, "unknown chunk index type")
+ mesg->storage.u.chunk.idx_type = mesg->u.chunk.idx_type;
+
+ switch(mesg->u.chunk.idx_type) {
+ case H5D_CHUNK_IDX_BTREE:
+ HGOTO_ERROR(H5E_OHDR, H5E_BADVALUE, NULL, "v1 B-tree index type should never be in a v4 layout message")
+ break;
+
+ case H5D_CHUNK_IDX_EARRAY:
+ /* Extensible array creation parameters */
+ mesg->u.chunk.u.earray.cparam.max_nelmts_bits = *p++;
+ if(0 == mesg->u.chunk.u.earray.cparam.max_nelmts_bits)
+ HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL, "invalid extensible array creation parameter")
+ mesg->u.chunk.u.earray.cparam.idx_blk_elmts = *p++;
+ if(0 == mesg->u.chunk.u.earray.cparam.idx_blk_elmts)
+ HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL, "invalid extensible array creation parameter")
+ mesg->u.chunk.u.earray.cparam.sup_blk_min_data_ptrs = *p++;
+ if(0 == mesg->u.chunk.u.earray.cparam.sup_blk_min_data_ptrs)
+ HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL, "invalid extensible array creation parameter")
+ mesg->u.chunk.u.earray.cparam.data_blk_min_elmts = *p++;
+ if(0 == mesg->u.chunk.u.earray.cparam.data_blk_min_elmts)
+ HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL, "invalid extensible array creation parameter")
+ mesg->u.chunk.u.earray.cparam.max_dblk_page_nelmts_bits = *p++;
+ if(0 == mesg->u.chunk.u.earray.cparam.max_dblk_page_nelmts_bits)
+ HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL, "invalid extensible array creation parameter")
+
+ /* Set the chunk operations */
+ mesg->storage.u.chunk.ops = H5D_COPS_EARRAY;
+ break;
+
+ 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++;
+
+ /* Set the chunk operations */
+ mesg->storage.u.chunk.ops = H5D_COPS_BT2;
+ break;
+
+ case H5D_CHUNK_IDX_NTYPES:
+ default:
+ HGOTO_ERROR(H5E_OHDR, H5E_BADVALUE, NULL, "Invalid chunk index type")
+ } /* end switch */
/* Chunk index address */
H5F_addr_decode(f, &p, &(mesg->storage.u.chunk.idx_addr));
@@ -557,6 +600,34 @@ H5O__layout_encode(H5F_t *f, hbool_t H5_ATTR_UNUSED disable_shared, uint8_t *p,
for(u = 0; u < mesg->u.chunk.ndims; u++)
UINT64ENCODE_VAR(p, mesg->u.chunk.dim[u], mesg->u.chunk.enc_bytes_per_dim);
+ /* Chunk index type */
+ *p++ = (uint8_t)mesg->u.chunk.idx_type;
+
+ switch(mesg->u.chunk.idx_type) {
+ case H5D_CHUNK_IDX_BTREE:
+ HGOTO_ERROR(H5E_OHDR, H5E_BADVALUE, FAIL, "v1 B-tree index type should never be in a v4 layout message")
+ break;
+
+ case H5D_CHUNK_IDX_EARRAY:
+ /* Extensible array creation parameters */
+ *p++ = mesg->u.chunk.u.earray.cparam.max_nelmts_bits;
+ *p++ = mesg->u.chunk.u.earray.cparam.idx_blk_elmts;
+ *p++ = mesg->u.chunk.u.earray.cparam.sup_blk_min_data_ptrs;
+ *p++ = mesg->u.chunk.u.earray.cparam.data_blk_min_elmts;
+ *p++ = mesg->u.chunk.u.earray.cparam.max_dblk_page_nelmts_bits;
+ break;
+
+ 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_NTYPES:
+ default:
+ HGOTO_ERROR(H5E_OHDR, H5E_CANTENCODE, FAIL, "Invalid chunk index type")
+ } /* end switch */
+
/*
* Implicit index: Address of the chunks
* Single chunk index: address of the single chunk
@@ -1082,20 +1153,32 @@ H5O__layout_debug(H5F_t H5_ATTR_UNUSED *f, hid_t H5_ATTR_UNUSED dxpl_id, const v
HDfprintf(stream, "}\n");
/* Index information */
- switch(mesg->storage.u.chunk.idx_type) {
+ switch(mesg->u.chunk.idx_type) {
case H5D_CHUNK_IDX_BTREE:
HDfprintf(stream, "%*s%-*s %s\n", indent, "", fwidth,
"Index Type:", "v1 B-tree");
- HDfprintf(stream, "%*s%-*s %a\n", indent, "", fwidth,
- "B-tree address:", mesg->storage.u.chunk.idx_addr);
+ break;
+
+ case H5D_CHUNK_IDX_EARRAY:
+ HDfprintf(stream, "%*s%-*s %s\n", indent, "", fwidth,
+ "Index Type:", "Extensible Array");
+ /* (Should print the extensible array creation parameters) */
+ break;
+
+ case H5D_CHUNK_IDX_BT2:
+ HDfprintf(stream, "%*s%-*s %s\n", indent, "", fwidth,
+ "Index Type:", "v2 B-tree");
+ /* (Should print the v2-Btree creation parameters) */
break;
case H5D_CHUNK_IDX_NTYPES:
default:
HDfprintf(stream, "%*s%-*s %s (%u)\n", indent, "", fwidth,
- "Index Type:", "Unknown", (unsigned)mesg->storage.u.chunk.idx_type);
+ "Index Type:", "Unknown", (unsigned)mesg->u.chunk.idx_type);
break;
} /* end switch */
+ HDfprintf(stream, "%*s%-*s %a\n", indent, "", fwidth,
+ "Index address:", mesg->storage.u.chunk.idx_addr);
break;
case H5D_CONTIGUOUS:
diff --git a/src/H5Oprivate.h b/src/H5Oprivate.h
index 8175bd8..a5f07b2 100644
--- a/src/H5Oprivate.h
+++ b/src/H5Oprivate.h
@@ -416,12 +416,30 @@ typedef struct H5O_storage_chunk_btree_t {
H5UC_t *shared; /* Ref-counted shared info for B-tree nodes */
} H5O_storage_chunk_btree_t;
+/* Forward declaration of structs used below */
+struct H5EA_t; /* Defined in H5EAprivate.h */
+
+typedef struct H5O_storage_chunk_earray_t {
+ haddr_t dset_ohdr_addr; /* File address dataset's object header */
+ struct H5EA_t *ea; /* Pointer to extensible index array struct */
+} H5O_storage_chunk_earray_t;
+
+/* Forward declaration of structs used below */
+struct H5B2_t; /* Defined in H5B2pkg.h */
+
+typedef struct H5O_storage_chunk_bt2_t {
+ haddr_t dset_ohdr_addr; /* File address dataset's object header */
+ struct H5B2_t *bt2; /* Pointer to b-tree 2 struct */
+} H5O_storage_chunk_bt2_t;
+
typedef struct H5O_storage_chunk_t {
H5D_chunk_index_t idx_type; /* Type of chunk index */
haddr_t idx_addr; /* File address of chunk index */
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_earray_t earray; /* Information for extensible array index */
} u;
} H5O_storage_chunk_t;
@@ -516,7 +534,32 @@ typedef struct H5O_storage_t {
} u;
} H5O_storage_t;
+typedef struct H5O_layout_chunk_earray_t {
+ /* Creation parameters for extensible array data structure */
+ struct {
+ uint8_t max_nelmts_bits; /* Log2(Max. # of elements in array) - i.e. # of bits needed to store max. # of elements */
+ uint8_t idx_blk_elmts; /* # of elements to store in index block */
+ uint8_t data_blk_min_elmts; /* Min. # of elements per data block */
+ uint8_t sup_blk_min_data_ptrs; /* Min. # of data block pointers for a super block */
+ uint8_t max_dblk_page_nelmts_bits; /* Log2(Max. # of elements in data block page) - i.e. # of bits needed to store max. # of elements in data block page */
+ } cparam;
+
+ unsigned unlim_dim; /* Rank of unlimited dimension for dataset */
+ uint32_t swizzled_dim[H5O_LAYOUT_NDIMS]; /* swizzled chunk dimensions */
+ hsize_t swizzled_down_chunks[H5O_LAYOUT_NDIMS]; /* swizzled "down" size of number of chunks in each dimension */
+} H5O_layout_chunk_earray_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_t {
+ H5D_chunk_index_t idx_type; /* Type of chunk index */
uint8_t flags; /* Chunk layout flags */
unsigned ndims; /* Num dimensions in chunk */
uint32_t dim[H5O_LAYOUT_NDIMS]; /* Size of chunk in elements */
@@ -528,6 +571,10 @@ typedef struct H5O_layout_chunk_t {
hsize_t max_chunks[H5O_LAYOUT_NDIMS]; /* # of chunks in each dataset's max. dimension */
hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of chunks in each dimension */
hsize_t max_down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of chunks in each max dim */
+ union {
+ 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;
typedef struct H5O_layout_t {
diff --git a/src/H5VMprivate.h b/src/H5VMprivate.h
index 7d3361b..f402b36 100644
--- a/src/H5VMprivate.h
+++ b/src/H5VMprivate.h
@@ -49,6 +49,22 @@ typedef herr_t (*H5VM_opvv_func_t)(hsize_t dst_off, hsize_t src_off,
#define H5VM_vector_zero(N,DST) HDmemset(DST,0,(N)*sizeof(*(DST)))
+/* Given a coordinate offset array (COORDS) of type TYPE, move the unlimited
+ * dimension (UNLIM_DIM) value to offset 0, sliding any intermediate values down
+ * one position. */
+#define H5VM_swizzle_coords(TYPE,COORDS,UNLIM_DIM) { \
+ /* COORDS must be an array of type TYPE */ \
+ HDassert(sizeof(COORDS[0]) == sizeof(TYPE)); \
+ \
+ /* Nothing to do when unlimited dimension is at position 0 */ \
+ if(0 != (UNLIM_DIM)) { \
+ TYPE _tmp = (COORDS)[UNLIM_DIM]; \
+ \
+ HDmemmove(&(COORDS)[1], &(COORDS)[0], sizeof(TYPE) * (UNLIM_DIM)); \
+ (COORDS)[0] = _tmp; \
+ } /* end if */ \
+}
+
/* A null pointer is equivalent to a zero vector */
#define H5VM_ZERO NULL
diff --git a/src/Makefile.am b/src/Makefile.am
index 9f748bf..ca9c4c3 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -47,8 +47,8 @@ libhdf5_la_SOURCES= H5.c H5checksum.c H5dbg.c H5system.c H5timer.c H5trace.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 \
- H5Ddeprec.c H5Defl.c H5Dfill.c H5Dint.c \
+ H5D.c H5Dbtree.c H5Dbtree2.c H5Dchunk.c H5Dcompact.c H5Dcontig.c H5Ddbg.c \
+ H5Ddeprec.c H5Dearray.c H5Defl.c H5Dfill.c H5Dint.c \
H5Dio.c H5Dlayout.c \
H5Doh.c H5Dscatgath.c H5Dselect.c H5Dtest.c H5Dvirtual.c \
H5E.c H5Edeprec.c H5Eint.c \
@@ -84,8 +84,10 @@ libhdf5_la_SOURCES= H5.c H5checksum.c H5dbg.c H5system.c H5timer.c H5trace.c \
H5Olayout.c \
H5Olinfo.c H5Olink.c H5Omessage.c H5Omtime.c \
H5Oname.c H5Onull.c H5Opline.c H5Orefcount.c \
- H5Osdspace.c H5Oshared.c H5Ostab.c \
- H5Oshmesg.c H5Otest.c H5Ounknown.c \
+ H5Osdspace.c H5Oshared.c \
+ H5Oshmesg.c \
+ H5Ostab.c \
+ H5Otest.c H5Ounknown.c \
H5P.c H5Pacpl.c H5Pdapl.c H5Pdcpl.c \
H5Pdeprec.c H5Pdxpl.c H5Pencdec.c \
H5Pfapl.c H5Pfcpl.c H5Pfmpl.c \
diff --git a/test/dsets.c b/test/dsets.c
index b3f11b8..5e92a6e 100644
--- a/test/dsets.c
+++ b/test/dsets.c
@@ -6462,15 +6462,24 @@ 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;
+ hsize_t dzero = 0, dmax = H5S_UNLIMITED, csize = 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");
+ /* Get the file's file access property list */
+ if((fapl = H5Fget_access_plist(file)) < 0) FAIL_STACK_ERROR
+
+ /* Get library format */
+ if(H5Pget_libver_bounds(fapl, &low, NULL) < 0) FAIL_STACK_ERROR
+
/*
* One-dimensional dataset
*/
- if((s = H5Screate_simple(1, &dsize, &dmax)) < 0) FAIL_STACK_ERROR
+ if((s = H5Screate_simple(1, &dzero, &dmax)) < 0) FAIL_STACK_ERROR
/* Try creating chunked dataset with undefined chunk dimensions */
if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0) FAIL_STACK_ERROR
@@ -6486,7 +6495,7 @@ test_zero_dims(hid_t file)
/* Try creating chunked dataset with zero-sized chunk dimensions */
H5E_BEGIN_TRY {
- ret = H5Pset_chunk(dcpl, 1, &dsize);
+ ret = H5Pset_chunk(dcpl, 1, &dzero);
} H5E_END_TRY;
if(ret > 0)
FAIL_PUTS_ERROR("set zero-sized chunk dimensions")
@@ -6498,6 +6507,16 @@ test_zero_dims(hid_t file)
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) FAIL_STACK_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");
+
/* Various no-op writes */
if(H5Dwrite(d, H5T_NATIVE_INT, s, s, H5P_DEFAULT, (void*)911) < 0) FAIL_STACK_ERROR
if(H5Dwrite(d, H5T_NATIVE_INT, s, s, H5P_DEFAULT, NULL) < 0) FAIL_STACK_ERROR