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diff --git a/src/H5Dfarray.c b/src/H5Dfarray.c
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+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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: Vailin Choi <vchoi@hdfgroup.org>
+ * Thursday, April 30, 2009
+ *
+ * Purpose: Fixed array indexed (chunked) I/O functions.
+ * The chunk coordinate is mapped as an index into an array of
+ * disk addresses for the chunks.
+ *
+ */
+
+/****************/
+/* 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 "H5FAprivate.h" /* Fixed 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_FARRAY_FILL HADDR_UNDEF
+#define H5D_FARRAY_FILT_FILL {HADDR_UNDEF, 0, 0}
+
+
+/******************/
+/* Local Typedefs */
+/******************/
+
+/* Fixed array create/open user data */
+typedef struct H5D_farray_ctx_ud_t {
+ const H5F_t *f; /* Pointer to file info */
+ uint32_t chunk_size; /* Size of chunk (bytes) */
+} H5D_farray_ctx_ud_t;
+
+/* Fixed array callback context */
+typedef struct H5D_farray_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_farray_ctx_t;
+
+/* User data for chunk deletion callback */
+typedef struct H5D_farray_del_ud_t {
+ H5F_t *f; /* File pointer for operation */
+ hid_t dxpl_id; /* DXPL ID for operation */
+ hbool_t filtered; /* Whether the chunks are filtered */
+ uint32_t unfilt_size; /* Size of unfiltered chunk in bytes */
+} H5D_farray_del_ud_t;
+
+/* Fixed Array callback info for iteration over chunks */
+typedef struct H5D_farray_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_farray_it_ud_t;
+
+/* Native fixed array element for chunks w/filters */
+typedef struct H5D_farray_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_farray_filt_elmt_t;
+
+
+/********************/
+/* Local Prototypes */
+/********************/
+
+/* Fixed Array iterator callbacks */
+static int H5D__farray_idx_iterate_cb(hsize_t idx, const void *_elmt, void *_udata);
+static int H5D__farray_idx_delete_cb(hsize_t idx, const void *_elmt, void *_udata);
+
+/* Fixed array class callbacks for chunks w/o filters */
+static void *H5D__farray_crt_context(void *udata);
+static herr_t H5D__farray_dst_context(void *ctx);
+static herr_t H5D__farray_fill(void *nat_blk, size_t nelmts);
+static herr_t H5D__farray_encode(void *raw, const void *elmt, size_t nelmts,
+ void *ctx);
+static herr_t H5D__farray_decode(const void *raw, void *elmt, size_t nelmts,
+ void *ctx);
+static herr_t H5D__farray_debug(FILE *stream, int indent, int fwidth,
+ hsize_t idx, const void *elmt);
+static void *H5D__farray_crt_dbg_context(H5F_t *f, hid_t dxpl_id,
+ haddr_t obj_addr);
+static herr_t H5D__farray_dst_dbg_context(void *dbg_ctx);
+
+/* Fixed array class callbacks for chunks w/filters */
+/* (some shared with callbacks for chunks w/o filters) */
+static herr_t H5D__farray_filt_fill(void *nat_blk, size_t nelmts);
+static herr_t H5D__farray_filt_encode(void *raw, const void *elmt, size_t nelmts,
+ void *ctx);
+static herr_t H5D__farray_filt_decode(const void *raw, void *elmt, size_t nelmts,
+ void *ctx);
+static herr_t H5D__farray_filt_debug(FILE *stream, int indent, int fwidth,
+ hsize_t idx, const void *elmt);
+
+/* Chunked layout indexing callbacks */
+static herr_t H5D__farray_idx_init(const H5D_chk_idx_info_t *idx_info,
+ const H5S_t *space, haddr_t dset_ohdr_addr);
+static herr_t H5D__farray_idx_create(const H5D_chk_idx_info_t *idx_info);
+static hbool_t H5D__farray_idx_is_space_alloc(const H5O_storage_chunk_t *storage);
+static herr_t H5D__farray_idx_insert(const H5D_chk_idx_info_t *idx_info,
+ H5D_chunk_ud_t *udata, const H5D_t *dset);
+static herr_t H5D__farray_idx_get_addr(const H5D_chk_idx_info_t *idx_info,
+ H5D_chunk_ud_t *udata);
+static int H5D__farray_idx_iterate(const H5D_chk_idx_info_t *idx_info,
+ H5D_chunk_cb_func_t chunk_cb, void *chunk_udata);
+static herr_t H5D__farray_idx_remove(const H5D_chk_idx_info_t *idx_info,
+ H5D_chunk_common_ud_t *udata);
+static herr_t H5D__farray_idx_delete(const H5D_chk_idx_info_t *idx_info);
+static herr_t H5D__farray_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__farray_idx_copy_shutdown(H5O_storage_chunk_t *storage_src,
+ H5O_storage_chunk_t *storage_dst, hid_t dxpl_id);
+static herr_t H5D__farray_idx_size(const H5D_chk_idx_info_t *idx_info,
+ hsize_t *size);
+static herr_t H5D__farray_idx_reset(H5O_storage_chunk_t *storage, hbool_t reset_addr);
+static herr_t H5D__farray_idx_dump(const H5O_storage_chunk_t *storage, FILE *stream);
+static herr_t H5D__farray_idx_dest(const H5D_chk_idx_info_t *idx_info);
+
+/* Generic extensible array routines */
+static herr_t H5D__farray_idx_open(const H5D_chk_idx_info_t *idx_info);
+
+/*********************/
+/* Package Variables */
+/*********************/
+
+/* Fixed array indexed chunk I/O ops */
+const H5D_chunk_ops_t H5D_COPS_FARRAY[1] = {{
+ H5D__farray_idx_init, /* init */
+ H5D__farray_idx_create, /* create */
+ H5D__farray_idx_is_space_alloc, /* is_space_alloc */
+ H5D__farray_idx_insert, /* insert */
+ H5D__farray_idx_get_addr, /* get_addr */
+ NULL, /* resize */
+ H5D__farray_idx_iterate, /* iterate */
+ H5D__farray_idx_remove, /* remove */
+ H5D__farray_idx_delete, /* delete */
+ H5D__farray_idx_copy_setup, /* copy_setup */
+ H5D__farray_idx_copy_shutdown, /* copy_shutdown */
+ H5D__farray_idx_size, /* size */
+ H5D__farray_idx_reset, /* reset */
+ H5D__farray_idx_dump, /* dump */
+ H5D__farray_idx_dest /* destroy */
+}};
+
+
+/*****************************/
+/* Library Private Variables */
+/*****************************/
+
+
+/*******************/
+/* Local Variables */
+/*******************/
+
+/* Fixed array class callbacks for dataset chunks w/o filters */
+const H5FA_class_t H5FA_CLS_CHUNK[1]={{
+ H5FA_CLS_CHUNK_ID, /* Type of fixed array */
+ "Chunk w/o filters", /* Name of fixed array class */
+ sizeof(haddr_t), /* Size of native element */
+ H5D__farray_crt_context, /* Create context */
+ H5D__farray_dst_context, /* Destroy context */
+ H5D__farray_fill, /* Fill block of missing elements callback */
+ H5D__farray_encode, /* Element encoding callback */
+ H5D__farray_decode, /* Element decoding callback */
+ H5D__farray_debug, /* Element debugging callback */
+ H5D__farray_crt_dbg_context, /* Create debugging context */
+ H5D__farray_dst_dbg_context /* Destroy debugging context */
+}};
+
+/* Fixed array class callbacks for dataset chunks w/filters */
+const H5FA_class_t H5FA_CLS_FILT_CHUNK[1]={{
+ H5FA_CLS_FILT_CHUNK_ID, /* Type of fixed array */
+ "Chunk w/filters", /* Name of fixed array class */
+ sizeof(H5D_farray_filt_elmt_t), /* Size of native element */
+ H5D__farray_crt_context, /* Create context */
+ H5D__farray_dst_context, /* Destroy context */
+ H5D__farray_filt_fill, /* Fill block of missing elements callback */
+ H5D__farray_filt_encode, /* Element encoding callback */
+ H5D__farray_filt_decode, /* Element decoding callback */
+ H5D__farray_filt_debug, /* Element debugging callback */
+ H5D__farray_crt_dbg_context, /* Create debugging context */
+ H5D__farray_dst_dbg_context /* Destroy debugging context */
+}};
+
+/* Declare a free list to manage the H5D_farray_ctx_t struct */
+H5FL_DEFINE_STATIC(H5D_farray_ctx_t);
+
+/* Declare a free list to manage the H5D_farray_ctx_ud_t struct */
+H5FL_DEFINE_STATIC(H5D_farray_ctx_ud_t);
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_crt_context
+ *
+ * Purpose: Create context for callbacks
+ *
+ * Return: Success: non-NULL
+ * Failure: NULL
+ *
+ * Programmer: Vailin Choi
+ * Thursday, April 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static void *
+H5D__farray_crt_context(void *_udata)
+{
+ H5D_farray_ctx_t *ctx; /* Fixed array callback context */
+ H5D_farray_ctx_ud_t *udata = (H5D_farray_ctx_ud_t *)_udata; /* User data for fixed 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_farray_ctx_t)))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, NULL, "can't allocate fixed 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__farray_crt_context() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_dst_context
+ *
+ * Purpose: Destroy context for callbacks
+ *
+ * Return: Success: non-NULL
+ * Failure: NULL
+ *
+ * Programmer: Vailin Choi
+ * Thursday, April 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__farray_dst_context(void *_ctx)
+{
+ H5D_farray_ctx_t *ctx = (H5D_farray_ctx_t *)_ctx; /* Fixed array callback context */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Sanity checks */
+ HDassert(ctx);
+
+ /* Release context structure */
+ ctx = H5FL_FREE(H5D_farray_ctx_t, ctx);
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D__farray_dst_context() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_fill
+ *
+ * Purpose: Fill "missing elements" in block of elements
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi
+ * Thursday, April 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__farray_fill(void *nat_blk, size_t nelmts)
+{
+ haddr_t fill_val = H5D_FARRAY_FILL; /* Value to fill elements with */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Sanity checks */
+ HDassert(nat_blk);
+ HDassert(nelmts);
+
+ H5VM_array_fill(nat_blk, &fill_val, H5FA_CLS_CHUNK->nat_elmt_size, nelmts);
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D__farray_fill() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_encode
+ *
+ * Purpose: Encode an element from "native" to "raw" form
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi
+ * Thursday, April 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__farray_encode(void *raw, const void *_elmt, size_t nelmts, void *_ctx)
+{
+ H5D_farray_ctx_t *ctx = (H5D_farray_ctx_t *)_ctx; /* Fixed 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__farray_encode() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_decode
+ *
+ * Purpose: Decode an element from "raw" to "native" form
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi
+ * Thursday, April 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__farray_decode(const void *_raw, void *_elmt, size_t nelmts, void *_ctx)
+{
+ H5D_farray_ctx_t *ctx = (H5D_farray_ctx_t *)_ctx; /* Fixed 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__farray_decode() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_debug
+ *
+ * Purpose: Display an element for debugging
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi
+ * Thursday, April 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__farray_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__farray_debug() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_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
+ * 5th August, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static void *
+H5D__farray_crt_dbg_context(H5F_t *f, hid_t dxpl_id, haddr_t obj_addr)
+{
+ H5D_farray_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_farray_ctx_ud_t)))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, NULL, "can't allocate fixed 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_farray_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__farray_crt_dbg_context() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_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: Quincey Koziol
+ * 24th September, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__farray_dst_dbg_context(void *_dbg_ctx)
+{
+ H5D_farray_ctx_ud_t *dbg_ctx = (H5D_farray_ctx_ud_t *)_dbg_ctx; /* Context for fixed array callback */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Sanity checks */
+ HDassert(dbg_ctx);
+
+ /* Release context structure */
+ dbg_ctx = H5FL_FREE(H5D_farray_ctx_ud_t, dbg_ctx);
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D__farray_dst_dbg_context() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_filt_fill
+ *
+ * Purpose: Fill "missing elements" in block of elements
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi
+ * Thursday, April 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__farray_filt_fill(void *nat_blk, size_t nelmts)
+{
+ H5D_farray_filt_elmt_t fill_val = H5D_FARRAY_FILT_FILL; /* Value to fill elements with */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Sanity checks */
+ HDassert(nat_blk);
+ HDassert(nelmts);
+ HDassert(sizeof(fill_val) == H5FA_CLS_FILT_CHUNK->nat_elmt_size);
+
+ H5VM_array_fill(nat_blk, &fill_val, H5FA_CLS_FILT_CHUNK->nat_elmt_size, nelmts);
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D__farray_filt_fill() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_filt_encode
+ *
+ * Purpose: Encode an element from "native" to "raw" form
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi
+ * Thursday, April 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__farray_filt_encode(void *_raw, const void *_elmt, size_t nelmts, void *_ctx)
+{
+ H5D_farray_ctx_t *ctx = (H5D_farray_ctx_t *)_ctx; /* Fixed array callback context */
+ uint8_t *raw = (uint8_t *)_raw; /* Convenience pointer to raw elements */
+ const H5D_farray_filt_elmt_t *elmt = (const H5D_farray_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__farray_filt_encode() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_filt_decode
+ *
+ * Purpose: Decode an element from "raw" to "native" form
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi
+ * Thursday, April 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__farray_filt_decode(const void *_raw, void *_elmt, size_t nelmts, void *_ctx)
+{
+ H5D_farray_ctx_t *ctx = (H5D_farray_ctx_t *)_ctx; /* Fixed array callback context */
+ H5D_farray_filt_elmt_t *elmt = (H5D_farray_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__farray_filt_decode() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_filt_debug
+ *
+ * Purpose: Display an element for debugging
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi
+ * Thursday, April 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__farray_filt_debug(FILE *stream, int indent, int fwidth, hsize_t idx,
+ const void *_elmt)
+{
+ const H5D_farray_filt_elmt_t *elmt = (const H5D_farray_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__farray_filt_debug() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_idx_init
+ *
+ * Purpose: Initialize the indexing information for a dataset.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Neil Fortner
+ * Wednensday, May 23, 2012
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__farray_idx_init(const H5D_chk_idx_info_t *idx_info, const H5S_t H5_ATTR_UNUSED *space, haddr_t dset_ohdr_addr)
+{
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Check args */
+ HDassert(idx_info);
+ HDassert(idx_info->storage);
+ HDassert(H5F_addr_defined(dset_ohdr_addr));
+
+ idx_info->storage->u.farray.dset_ohdr_addr = dset_ohdr_addr;
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D__farray_idx_init() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_idx_open
+ *
+ * Purpose: Opens an existing fixed array and initializes
+ * the layout struct with information about the storage.
+ *
+ * Return: Success: non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi
+ * Thursday, April 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__farray_idx_open(const H5D_chk_idx_info_t *idx_info)
+{
+ H5D_farray_ctx_ud_t udata; /* User data for fixed 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_FARRAY == idx_info->layout->idx_type);
+ HDassert(idx_info->storage);
+ HDassert(H5D_CHUNK_IDX_FARRAY == idx_info->storage->idx_type);
+ HDassert(H5F_addr_defined(idx_info->storage->idx_addr));
+ HDassert(NULL == idx_info->storage->u.farray.fa);
+
+ /* Set up the user data */
+ udata.f = idx_info->f;
+ udata.chunk_size = idx_info->layout->size;
+
+ /* Open the fixed array for the chunk index */
+ if(NULL == (idx_info->storage->u.farray.fa = H5FA_open(idx_info->f, idx_info->dxpl_id, idx_info->storage->idx_addr, &udata)))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't open fixed array")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__farray_idx_open() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_idx_create
+ *
+ * Purpose: Creates a new indexed-storage fixed 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: Vailin Choi
+ * Thursday, April 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__farray_idx_create(const H5D_chk_idx_info_t *idx_info)
+{
+ H5FA_create_t cparam; /* Fixed array creation parameters */
+ H5D_farray_ctx_ud_t udata; /* User data for fixed 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.farray.fa);
+ HDassert(idx_info->layout->nchunks);
+
+ /* 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 = H5FA_CLS_FILT_CHUNK;
+ cparam.raw_elmt_size = (uint8_t)(H5F_SIZEOF_ADDR(idx_info->f) + chunk_size_len + 4);
+ } /* end if */
+ else {
+ cparam.cls = H5FA_CLS_CHUNK;
+ cparam.raw_elmt_size = (uint8_t)H5F_SIZEOF_ADDR(idx_info->f);
+ } /* end else */
+ cparam.max_dblk_page_nelmts_bits = idx_info->layout->u.farray.cparam.max_dblk_page_nelmts_bits;
+ HDassert(cparam.max_dblk_page_nelmts_bits > 0);
+ cparam.nelmts = idx_info->layout->max_nchunks;
+
+ /* Set up the user data */
+ udata.f = idx_info->f;
+ udata.chunk_size = idx_info->layout->size;
+
+ /* Create the fixed array for the chunk index */
+ if(NULL == (idx_info->storage->u.farray.fa = H5FA_create(idx_info->f, idx_info->dxpl_id, &cparam, &udata)))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't create fixed array")
+
+ /* Get the address of the fixed array in file */
+ if(H5FA_get_addr(idx_info->storage->u.farray.fa, &(idx_info->storage->idx_addr)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't query fixed array address")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__farray_idx_create() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_idx_is_space_alloc
+ *
+ * Purpose: Query if space is allocated for index method
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Vailin Choi
+ * Thursday, April 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static hbool_t
+H5D__farray_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__farray_idx_is_space_alloc() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_idx_insert
+ *
+ * Purpose: Insert chunk address into the indexing structure.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Vailin Choi; 5 May 2014
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__farray_idx_insert(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata,
+ const H5D_t H5_ATTR_UNUSED *dset)
+{
+ H5FA_t *fa; /* Pointer to fixed 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 fixed array is open yet */
+ if(NULL == idx_info->storage->u.farray.fa) {
+ /* Open the fixed array in file */
+ if(H5D__farray_idx_open(idx_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open fixed array")
+ } else /* Patch the top level file pointer contained in fa if needed */
+ H5FA_patch_file(idx_info->storage->u.farray.fa, idx_info->f);
+
+ /* Set convenience pointer to fixed array structure */
+ fa = idx_info->storage->u.farray.fa;
+
+ 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_farray_filt_elmt_t elmt; /* Fixed 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(H5FA_set(fa, 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(H5FA_set(fa, 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__farray_idx_insert() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_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
+ * Thursday, April 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__farray_idx_get_addr(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata)
+{
+ H5FA_t *fa; /* Pointer to fixed 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 fixed array is open yet */
+ if(NULL == idx_info->storage->u.farray.fa) {
+ /* Open the fixed array in file */
+ if(H5D__farray_idx_open(idx_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open fixed array")
+ } else /* Patch the top level file pointer contained in fa if needed */
+ H5FA_patch_file(idx_info->storage->u.farray.fa, idx_info->f);
+
+ /* Set convenience pointer to fixed array structure */
+ fa = idx_info->storage->u.farray.fa;
+
+ /* Calculate the index of this chunk */
+ idx = H5VM_array_offset_pre((idx_info->layout->ndims - 1), idx_info->layout->max_down_chunks, udata->common.scaled);
+
+ udata->chunk_idx = idx;
+
+ /* Check for filters on chunks */
+ if(idx_info->pline->nused > 0) {
+ H5D_farray_filt_elmt_t elmt; /* Fixed array element */
+
+ /* Get the information for the chunk */
+ if(H5FA_get(fa, 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(H5FA_get(fa, 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__farray_idx_get_addr() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_idx_iterate_cb
+ *
+ * Purpose: Callback routine for fixed array element iteration.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Vailin Choi
+ * Thursday, April 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+H5D__farray_idx_iterate_cb(hsize_t H5_ATTR_UNUSED idx, const void *_elmt, void *_udata)
+{
+ H5D_farray_it_ud_t *udata = (H5D_farray_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_farray_filt_elmt_t *filt_elmt = (const H5D_farray_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__farray_idx_iterate_cb() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_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
+ * Thursday, April 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+H5D__farray_idx_iterate(const H5D_chk_idx_info_t *idx_info,
+ H5D_chunk_cb_func_t chunk_cb, void *chunk_udata)
+{
+ H5FA_t *fa; /* Pointer to fixed array structure */
+ H5FA_stat_t fa_stat; /* Fixed array statistics */
+ 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 fixed array is open yet */
+ if(NULL == idx_info->storage->u.farray.fa) {
+ /* Open the fixed array in file */
+ if(H5D__farray_idx_open(idx_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open fixed array")
+ } else /* Patch the top level file pointer contained in fa if needed */
+ H5FA_patch_file(idx_info->storage->u.farray.fa, idx_info->f);
+
+ /* Set convenience pointer to fixed array structure */
+ fa = idx_info->storage->u.farray.fa;
+
+ /* Get the fixed array statistics */
+ if(H5FA_get_stats(fa, &fa_stat) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't query fixed array statistics")
+
+ /* Check if there are any array elements */
+ if(fa_stat.nelmts > 0) {
+ H5D_farray_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 fixed array elements */
+ if((ret_value = H5FA_iterate(fa, idx_info->dxpl_id, H5D__farray_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__farray_idx_iterate() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_idx_remove
+ *
+ * Purpose: Remove chunk from index.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Vailin Choi
+ * Thursday, April 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__farray_idx_remove(const H5D_chk_idx_info_t *idx_info, H5D_chunk_common_ud_t *udata)
+{
+ H5FA_t *fa; /* Pointer to fixed 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 fixed array is open yet */
+ if(NULL == idx_info->storage->u.farray.fa)
+ /* Open the fixed array in file */
+ if(H5D__farray_idx_open(idx_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open fixed array")
+
+ /* Set convenience pointer to fixed array structure */
+ fa = idx_info->storage->u.farray.fa;
+
+ /* Calculate the index of this chunk */
+ idx = H5VM_array_offset_pre((idx_info->layout->ndims - 1), idx_info->layout->max_down_chunks, udata->scaled);
+
+ /* Check for filters on chunks */
+ if(idx_info->pline->nused > 0) {
+ H5D_farray_filt_elmt_t elmt; /* Fixed array element */
+
+ /* Get the info about the chunk for the index */
+ if(H5FA_get(fa, 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(H5FA_set(fa, 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(H5FA_get(fa, 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(H5FA_set(fa, 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__farray_idx_remove() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_idx_delete_cb
+ *
+ * Purpose: Delete space for chunk in file
+ *
+ * Return: Success: Non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi
+ * Thursday, April 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+H5D__farray_idx_delete_cb(hsize_t H5_ATTR_UNUSED idx, const void *_elmt, void *_udata)
+{
+ H5D_farray_del_ud_t *udata = (H5D_farray_del_ud_t *)_udata; /* User data for callback */
+ haddr_t chunk_addr; /* Address of chunk */
+ uint32_t nbytes; /* Size of chunk */
+ int ret_value = H5_ITER_CONT; /* Return value */
+
+ FUNC_ENTER_STATIC
+
+ /* Sanity checks */
+ HDassert(_elmt);
+ HDassert(udata);
+ HDassert(udata->f);
+
+ /* Check for filtered elements */
+ if(udata->filtered) {
+ const H5D_farray_filt_elmt_t *filt_elmt = (const H5D_farray_filt_elmt_t *)_elmt;
+
+ chunk_addr = filt_elmt->addr;
+ nbytes = filt_elmt->nbytes;
+ } /* end if */
+ else {
+ chunk_addr = *(const haddr_t *)_elmt;
+ nbytes = udata->unfilt_size;
+ } /* end else */
+
+ /* Remove raw data chunk from file */
+ H5_CHECK_OVERFLOW(nbytes, /*From: */uint32_t, /*To: */hsize_t);
+ if(H5MF_xfree(udata->f, H5FD_MEM_DRAW, udata->dxpl_id, chunk_addr, (hsize_t)nbytes) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, H5_ITER_ERROR, "unable to free chunk")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__farray_idx_delete_cb() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_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
+ * Thursday, April 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__farray_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)) {
+ H5FA_t *fa; /* Pointer to fixed array structure */
+ H5FA_stat_t fa_stat; /* Fixed array statistics */
+ H5D_farray_ctx_ud_t ctx_udata; /* User data for fixed array open call */
+
+ /* Check if the fixed array is open yet */
+ if(NULL == idx_info->storage->u.farray.fa)
+ /* Open the fixed array in file */
+ if(H5D__farray_idx_open(idx_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open fixed array")
+
+ /* Set convenience pointer to fixed array structure */
+ fa = idx_info->storage->u.farray.fa;
+
+ /* Get the fixed array statistics */
+ if(H5FA_get_stats(fa, &fa_stat) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't query fixed array statistics")
+
+ /* Check if there are any array elements */
+ if(fa_stat.nelmts > 0) {
+ H5D_farray_del_ud_t udata; /* User data for callback */
+
+ /* Initialize user data for callback */
+ udata.f = idx_info->f;
+ udata.dxpl_id = idx_info->dxpl_id;
+ udata.filtered = (idx_info->pline->nused > 0);
+ udata.unfilt_size = idx_info->layout->size;
+
+ /* Iterate over the chunk addresses in the fixed array, deleting each chunk */
+ if(H5FA_iterate(fa, idx_info->dxpl_id, H5D__farray_idx_delete_cb, &udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to iterate over chunk addresses")
+ } /* end if */
+
+ /* Close fixed array */
+ if(H5FA_close(idx_info->storage->u.farray.fa, idx_info->dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to close fixed array")
+ idx_info->storage->u.farray.fa = NULL;
+
+ /* Set up the user data */
+ ctx_udata.f = idx_info->f;
+ ctx_udata.chunk_size = idx_info->layout->size;
+
+ /* Delete fixed array */
+ if(H5FA_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 fixed array")
+ idx_info->storage->idx_addr = HADDR_UNDEF;
+ } /* end if */
+ else
+ HDassert(NULL == idx_info->storage->u.farray.fa);
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__farray_idx_delete() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_idx_copy_setup
+ *
+ * Purpose: Set up any necessary information for copying chunks
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Vailin Choi
+ * Thursday, April 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__farray_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 fixed array is open yet */
+ if(NULL == idx_info_src->storage->u.farray.fa)
+ /* Open the fixed array in file */
+ if(H5D__farray_idx_open(idx_info_src) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open fixed array")
+
+ /* Set copied metadata tag */
+ H5_BEGIN_TAG(idx_info_dst->dxpl_id, H5AC__COPIED_TAG, FAIL);
+
+ /* Create the fixed array that describes chunked storage in the dest. file */
+ if(H5D__farray_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__farray_idx_copy_setup() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_idx_copy_shutdown
+ *
+ * Purpose: Shutdown any information from copying chunks
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Vailin Choi
+ * Thursday, April 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__farray_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.farray.fa);
+ HDassert(storage_dst);
+ HDassert(storage_dst->u.farray.fa);
+
+ /* Close fixed arrays */
+ if(H5FA_close(storage_src->u.farray.fa, dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to close fixed array")
+ storage_src->u.farray.fa = NULL;
+ if(H5FA_close(storage_dst->u.farray.fa, dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to close fixed array")
+ storage_dst->u.farray.fa = NULL;
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__farray_idx_copy_shutdown() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_idx_size
+ *
+ * Purpose: Retrieve the amount of index storage for chunked dataset
+ *
+ * Return: Success: Non-negative
+ * Failure: negative
+ *
+ * Programmer: Vailin Choi
+ * Thursday, April 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__farray_idx_size(const H5D_chk_idx_info_t *idx_info, hsize_t *index_size)
+{
+ H5FA_t *fa; /* Pointer to fixed array structure */
+ H5FA_stat_t fa_stat; /* Fixed 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 fixed array in file */
+ if(H5D__farray_idx_open(idx_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open fixed array")
+
+ /* Set convenience pointer to fixed array structure */
+ fa = idx_info->storage->u.farray.fa;
+
+ /* Get the fixed array statistics */
+ if(H5FA_get_stats(fa, &fa_stat) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't query fixed array statistics")
+
+ *index_size = fa_stat.hdr_size;
+ *index_size += fa_stat.dblk_size;
+
+done:
+ if(idx_info->storage->u.farray.fa) {
+ if(H5FA_close(idx_info->storage->u.farray.fa, idx_info->dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to close fixed array")
+ idx_info->storage->u.farray.fa = NULL;
+ } /* end if */
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__farray_idx_size() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_idx_reset
+ *
+ * Purpose: Reset indexing information.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Vailin Choi
+ * Thursday, April 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__farray_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.farray.fa = NULL;
+
+ FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D__farray_idx_reset() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_idx_dump
+ *
+ * Purpose: Dump indexing information to a stream.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Vailin Choi
+ * Thursday, April 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__farray_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__farray_idx_dump() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__farray_idx_dest
+ *
+ * Purpose: Release indexing information in memory.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Vailin Choi
+ * Thursday, April 30, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__farray_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 fixed array is open */
+ if(idx_info->storage->u.farray.fa) {
+ /* Close fixed array */
+ if(H5FA_close(idx_info->storage->u.farray.fa, idx_info->dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to close fixed array")
+ idx_info->storage->u.farray.fa = NULL;
+ } /* end if */
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__farray_idx_dest() */
+