[svn-r29738] Description:

    Bring "single" chunk index from revise_chunks branch to trunk.

Tested on:
    MacOSX/64 10.11.4 (amazon) w/serial, parallel & production (w/check-vfd)
    (h5committest forthcoming)

1 files changed, 556 insertions, 0 deletions

diff --git a/src/H5Dsingle.c b/src/H5Dsingle.c
new file mode 100644
index 0000000..e09a5cf
--- /dev/null
+++ b/src/H5Dsingle.c
@@ -0,0 +1,556 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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>
+ *	       	May 2011; updated 10/2015
+ *
+ * Purpose:	Single Chunk I/O functions.  
+ *		This is used when the dataset has only 1 chunk (with or without filter):
+ *			cur_dims[] is equal to max_dims[] is equal to the chunk dims[]
+ *		non-filter chunk record: [address of the chunk]
+ *		filtered chunk record: 	[address of the chunk, chunk size, filter mask]
+ *
+ */
+
+/****************/
+/* 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 "H5FLprivate.h"	/* Free Lists                           */
+#include "H5MFprivate.h"	/* File space management		*/
+#include "H5VMprivate.h"         /* Vector functions			*/
+
+
+/****************/
+/* Local Macros */
+/****************/
+
+
+/******************/
+/* Local Typedefs */
+/******************/
+
+
+/********************/
+/* Local Prototypes */
+/********************/
+
+/* Single Chunk Index chunking I/O ops */
+static herr_t H5D__single_idx_init(const H5D_chk_idx_info_t *idx_info,
+    const H5S_t *space, haddr_t dset_ohdr_addr);
+static herr_t H5D__single_idx_create(const H5D_chk_idx_info_t *idx_info);
+static hbool_t H5D__single_idx_is_space_alloc(const H5O_storage_chunk_t *storage);
+static herr_t H5D__single_idx_insert(const H5D_chk_idx_info_t *idx_info,
+    H5D_chunk_ud_t *udata, const H5D_t *dset);
+static herr_t H5D__single_idx_get_addr(const H5D_chk_idx_info_t *idx_info,
+    H5D_chunk_ud_t *udata);
+static int H5D__single_idx_iterate(const H5D_chk_idx_info_t *idx_info,
+    H5D_chunk_cb_func_t chunk_cb, void *chunk_udata);
+static herr_t H5D__single_idx_remove(const H5D_chk_idx_info_t *idx_info,
+    H5D_chunk_common_ud_t *udata);
+static herr_t H5D__single_idx_delete(const H5D_chk_idx_info_t *idx_info);
+static herr_t H5D__single_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__single_idx_size(const H5D_chk_idx_info_t *idx_info,
+    hsize_t *size);
+static herr_t H5D__single_idx_reset(H5O_storage_chunk_t *storage, hbool_t reset_addr);
+static herr_t H5D__single_idx_dump(const H5O_storage_chunk_t *storage, FILE *stream);
+
+
+/*********************/
+/* Package Variables */
+/*********************/
+
+/* Non Index chunk I/O ops */
+const H5D_chunk_ops_t H5D_COPS_SINGLE[1] = {{
+    H5D__single_idx_init,		/* init */
+    H5D__single_idx_create,		/* create */
+    H5D__single_idx_is_space_alloc, 	/* is_space_alloc */
+    H5D__single_idx_insert,	        /* insert */
+    H5D__single_idx_get_addr,		/* get_addr */
+    NULL,				/* resize */
+    H5D__single_idx_iterate,		/* iterate */
+    H5D__single_idx_remove,		/* remove */
+    H5D__single_idx_delete,		/* delete */
+    H5D__single_idx_copy_setup,		/* copy_setup */
+    NULL,				/* copy_shutdown */
+    H5D__single_idx_size,		/* size */
+    H5D__single_idx_reset,		/* reset */
+    H5D__single_idx_dump,		/* dump */
+    NULL				/* destroy */
+}};
+
+
+/*****************************/
+/* Library Private Variables */
+/*****************************/
+
+
+/*******************/
+/* Local Variables */
+/*******************/
+
+
+
+/*-------------------------------------------------------------------------
+ * Function:    H5D__single_idx_init
+ *
+ * Purpose:     Initialize the indexing information for a dataset.
+ *
+ * Return:      Non-negative on success/Negative on failure
+ *
+ * Programmer:  Vailin Choi
+ *              July, 2011
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__single_idx_init(const H5D_chk_idx_info_t *idx_info,
+    const H5S_t H5_ATTR_UNUSED *space, haddr_t H5_ATTR_UNUSED dset_ohdr_addr)
+{
+    FUNC_ENTER_STATIC_NOERR
+
+    /* Check args */
+    HDassert(idx_info);
+    HDassert(idx_info->f);
+    HDassert(idx_info->pline);
+    HDassert(idx_info->layout);
+    HDassert(idx_info->storage);
+
+    if(idx_info->pline->nused)
+	idx_info->layout->flags |= H5O_LAYOUT_CHUNK_SINGLE_INDEX_WITH_FILTER;
+    else
+	idx_info->layout->flags = 0;
+
+    FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D__single_idx_init() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5D__single_idx_create
+ *
+ * Purpose:	Set up Single Chunk Index: filtered or non-filtered
+ *		
+ * Return:	Non-negative on success 
+ *		Negative on failure.
+ *
+ * Programmer:	Vailin Choi; July 2011
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__single_idx_create(const H5D_chk_idx_info_t *idx_info)
+{
+    FUNC_ENTER_STATIC_NOERR
+
+    /* Check args */
+    HDassert(idx_info);
+    HDassert(idx_info->f);
+    HDassert(idx_info->pline);
+    HDassert(idx_info->layout);
+    HDassert(idx_info->storage);
+    HDassert(idx_info->layout->max_nchunks == idx_info->layout->nchunks);
+    HDassert(idx_info->layout->nchunks == 1);
+    HDassert(!H5F_addr_defined(idx_info->storage->idx_addr));
+
+    if(idx_info->pline->nused)
+	HDassert(idx_info->layout->flags & H5O_LAYOUT_CHUNK_SINGLE_INDEX_WITH_FILTER);
+    else
+	HDassert(!(idx_info->layout->flags & H5O_LAYOUT_CHUNK_SINGLE_INDEX_WITH_FILTER));
+
+    FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D__single_idx_create() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5D__single_idx_is_space_alloc
+ *
+ * Purpose:	Query if space is allocated for the single chunk
+ *
+ * Return:	Non-negative on success/Negative on failure
+ *
+ * Programmer:	Vailin Choi; July 2011
+ *
+ *-------------------------------------------------------------------------
+ */
+static hbool_t
+H5D__single_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__single_idx_is_space_alloc() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5D__single_idx_insert
+ *
+ * Purpose:	Allocate space for the single chunk
+ *
+ * Return:	Non-negative on success/Negative on failure
+ *
+ * Programmer:	Vailin Choi; July 2011
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__single_idx_insert(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata,
+    const H5D_t *dset)
+{
+    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(idx_info->layout->nchunks == 1);
+    HDassert(idx_info->layout->max_nchunks == 1);
+    HDassert(udata);
+
+    /* Set the address for the chunk */
+    HDassert(H5F_addr_defined(udata->chunk_block.offset));
+    idx_info->storage->idx_addr = udata->chunk_block.offset;
+
+    if(idx_info->pline->nused > 0) {
+        H5_CHECKED_ASSIGN(idx_info->storage->u.single.nbytes, uint32_t, udata->chunk_block.length, hsize_t);
+	idx_info->storage->u.single.filter_mask = udata->filter_mask;
+    } /* end if */
+
+    if(dset) {
+	if(dset->shared->dcpl_cache.fill.alloc_time != H5D_ALLOC_TIME_EARLY || idx_info->pline->nused > 0) {
+	    /* Mark the layout dirty so that the address of the single chunk will be flushed later */
+	    if(H5D__mark(dset, idx_info->dxpl_id, H5D_MARK_LAYOUT) < 0)
+		HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to mark layout as dirty")
+	} /* end if */
+    } /* end if */
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D__single_idx_insert() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5D__single_idx_get_addr
+ *
+ * Purpose:	Get the file address of a chunk.
+ *		Save the retrieved information in the udata supplied.
+ *
+ * Return:	Non-negative on success/Negative on failure
+ *
+ * Programmer:	Vailin Choi; July 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__single_idx_get_addr(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata)
+{
+    FUNC_ENTER_STATIC_NOERR
+
+    /* Sanity checks */
+    HDassert(idx_info);
+    HDassert(idx_info->f);
+    HDassert(idx_info->pline);
+    HDassert(idx_info->layout);
+    HDassert(idx_info->storage);
+    HDassert(idx_info->layout->nchunks == 1);
+    HDassert(idx_info->layout->max_nchunks == 1);
+    HDassert(udata);
+
+    udata->chunk_block.offset = idx_info->storage->idx_addr;
+    if(idx_info->layout->flags & H5O_LAYOUT_CHUNK_SINGLE_INDEX_WITH_FILTER) {
+	udata->chunk_block.length = idx_info->storage->u.single.nbytes;
+	udata->filter_mask = idx_info->storage->u.single.filter_mask;
+    } /* end if */
+    else {
+	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;
+
+    FUNC_LEAVE_NOAPI(SUCCEED)
+} /* H5D__single_idx_get_addr() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5D__single_idx_iterate
+ *
+ * Purpose:	Make callback for the single chunk
+ *
+ * Return:	Non-negative on success/Negative on failure
+ *
+ * Programmer:	Vailin Choi; July 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+H5D__single_idx_iterate(const H5D_chk_idx_info_t *idx_info,
+    H5D_chunk_cb_func_t chunk_cb, void *chunk_udata)
+{
+    H5D_chunk_rec_t chunk_rec;		/* generic chunk record  */
+    int ret_value = -1;    		/* Return value */
+
+    FUNC_ENTER_STATIC_NOERR
+
+    /* Sanity checks */
+    HDassert(idx_info);
+    HDassert(idx_info->f);
+    HDassert(idx_info->pline);
+    HDassert(idx_info->layout);
+    HDassert(idx_info->storage);
+    HDassert(chunk_cb);
+    HDassert(chunk_udata);
+    HDassert(H5F_addr_defined(idx_info->storage->idx_addr));
+
+    /* Initialize generic chunk record */
+    HDmemset(&chunk_rec, 0, sizeof(chunk_rec));
+    chunk_rec.chunk_addr = idx_info->storage->idx_addr;
+
+    if(idx_info->layout->flags & H5O_LAYOUT_CHUNK_SINGLE_INDEX_WITH_FILTER) {
+	chunk_rec.nbytes = idx_info->storage->u.single.nbytes;
+	chunk_rec.filter_mask = idx_info->storage->u.single.filter_mask;
+    } /* end if */
+    else {
+	chunk_rec.nbytes = idx_info->layout->size;
+	chunk_rec.filter_mask = 0;
+    } /* end else */
+
+    /* Make "generic chunk" callback */
+    if((ret_value = (*chunk_cb)(&chunk_rec, chunk_udata)) < 0)
+	HERROR(H5E_DATASET, H5E_CALLBACK, "failure in generic chunk iterator callback");
+
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__single_idx_iterate() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5D__single_idx_remove
+ *
+ * Purpose:	Remove the single chunk
+ *
+ * Return:	Non-negative on success/Negative on failure
+ *
+ * Programmer:	Vailin Choi; July 2011
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__single_idx_remove(const H5D_chk_idx_info_t *idx_info, H5D_chunk_common_ud_t H5_ATTR_UNUSED *udata)
+{
+    hsize_t nbytes;                 /* Size of all chunks */
+    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));
+
+    if(idx_info->layout->flags & H5O_LAYOUT_CHUNK_SINGLE_INDEX_WITH_FILTER)
+	nbytes = idx_info->storage->u.single.nbytes;
+    else
+	nbytes = idx_info->layout->size;
+
+    if(H5MF_xfree(idx_info->f, H5FD_MEM_DRAW, idx_info->dxpl_id, idx_info->storage->idx_addr, nbytes) < 0)
+        HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, H5_ITER_ERROR, "unable to free dataset chunks")
+
+    idx_info->storage->idx_addr = HADDR_UNDEF;
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D__single_idx_remove() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5D__single_idx_delete
+ *
+ * Purpose:	Delete raw data storage for entire dataset (i.e. the only chunk)
+ *
+ * Return:	Success:	Non-negative
+ *		Failure:	negative
+ *
+ * Programmer:	Vailin Choi; Sept 2011
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__single_idx_delete(const H5D_chk_idx_info_t *idx_info)
+{
+    herr_t ret_value = SUCCEED;     /* Return value */
+
+    FUNC_ENTER_STATIC_NOERR
+
+    /* Sanity checks */
+    HDassert(idx_info);
+    HDassert(idx_info->f);
+    HDassert(idx_info->pline);
+    HDassert(idx_info->layout);
+    HDassert(idx_info->storage);
+
+    if(H5F_addr_defined(idx_info->storage->idx_addr))
+	ret_value = H5D__single_idx_remove(idx_info, NULL);
+    else
+	HDassert(!H5F_addr_defined(idx_info->storage->idx_addr));
+
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__single_idx_delete() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5D__single_idx_copy_setup
+ *
+ * Purpose:	Set up any necessary information for copying the single chunk
+ *
+ * Return:	Non-negative on success/Negative on failure
+ *
+ * Programmer:	Vailin Choi; Sept 2011
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__single_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(H5F_addr_defined(idx_info_src->storage->idx_addr));
+
+    HDassert(idx_info_dst);
+    HDassert(idx_info_dst->f);
+    HDassert(idx_info_dst->pline);
+    HDassert(idx_info_dst->layout);
+    HDassert(idx_info_dst->storage);
+
+    /* Set copied metadata tag */
+    H5_BEGIN_TAG(idx_info_dst->dxpl_id, H5AC__COPIED_TAG, FAIL);
+
+    /* Set up information at the destination file */
+    if(H5D__single_idx_create(idx_info_dst) < 0)
+        HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize chunked storage")
+
+    /* Reset metadata tag */
+    H5_END_TAG(FAIL);
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__single_idx_copy_setup() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:    H5D__single_idx_size
+ *
+ * Purpose:     Retrieve the amount of index storage for the chunked dataset
+ *
+ * Return:      Success:        Non-negative
+ *              Failure:        negative
+ *
+ * Programmer:	Vailin Choi; Sept 2011
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__single_idx_size(const H5D_chk_idx_info_t H5_ATTR_UNUSED *idx_info, hsize_t *index_size)
+{
+    FUNC_ENTER_STATIC_NOERR
+
+    /* Check args */
+    HDassert(index_size);
+
+    *index_size = 0;
+
+    FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D__single_idx_size() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5D__single_idx_reset
+ *
+ * Purpose:	Reset indexing information.
+ *
+ * Return:	Non-negative on success/Negative on failure
+ *
+ * Programmer:	Vailin Choi; Sept 2011
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__single_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;
+
+    FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5D__single_idx_reset() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5D__single_idx_dump
+ *
+ * Purpose:	Dump the address of the single chunk
+ *
+ * Return:	Non-negative on success/Negative on failure
+ *
+ * Programmer:	Vailin Choi; September 2011
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__single_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__single_idx_dump() */
+