tcl.git - Tcl is a high-level, general-purpose, interpreted, dynamic programming language. It was designed with the goal of being very simple but powerful.

	Commit message (Expand)	Author	Age	Files	Lines
*	* README, generic/tcl.h, tools/tcl.wse.in: bumped to	hobbs	2004-07-13	1	-1/+1

*	* win/configure:	hobbs	2004-04-07	1	-4/+16

*	update patchlevel to 8.4.6	hobbs	2004-02-13	1	-1/+1

*	* generic/tcl.h: Bumped patch level to 8.4.5.1 to distinguish	dgp	2003-12-03	1	-1/+1

*	* README: Bumped patch level to 8.4.6 to distinguish	dgp	2003-12-02	1	-1/+1

*	* README: Bumped patch level to 8.4.5 to prepare	dgp	2003-10-02	1	-67/+61

*	* README: Bumped patch level to 8.4.4 in anticipation	dgp	2003-07-15	1	-1/+1

*	bumped version to 8.4.3	hobbs	2003-05-15	1	-1/+1

*	* win/configure: Regen.	mdejong	2003-04-03	1	-12/+16

*	* win/configure:	hobbs	2003-03-01	1	-2/+2

*	* README: Bumped to version 8.4.2.	hobbs	2003-02-15	1	-1/+1

*	* win/configure:	mdejong	2003-02-11	1	-47/+48

*	* win/configure: Regen.	mdejong	2003-01-27	1	-25/+67

*	* win/configure:	mdejong	2003-01-25	1	-31/+38

*	* win/configure: Regen.	mdejong	2003-01-24	1	-25/+70

*	* win/configure: Regen.	mdejong	2003-01-21	1	-15/+20

*	* win/configure: Regen.	mdejong	2003-01-13	1	-2/+2

*	* generic/tcl.h: Skip Tcl's define of CHAR,	mdejong	2003-01-13	1	-25/+72

*	* win/configure: Regen.	mdejong	2003-01-13	1	-25/+70

*	* unix/configure.in: Updated configure of CVS snapshots to reflect	dgp	2002-12-13	1	-1/+1

*	* unix/configure: Regen.	mdejong	2002-11-06	1	-35/+45

*	* win/Makefile.in: removed @MEM_DEBUG_FLAGS@ subst.	hobbs	2002-10-22	1	-76/+83

*	* library/reg/pkgIndex.tcl:	hobbs	2002-10-18	1	-2/+2

*	* win/configure: add workaround for cygwin windres	hobbs	2002-10-17	1	-13/+39

*	* win/configure:	hobbs	2002-10-11	1	-16/+22

*	* README: Bumped to version 8.4.1 to avoid confusion	dgp	2002-09-27	1	-1/+1

*	2002-09-18 Mumit Khan <khan@nanotech.wisc.edu>	hobbs	2002-09-27	1	-34/+103

*	Bumped version number to 8.4.0	hobbs	2002-09-02	1	-1/+1

*	* win/Makefile.in (CFLAGS):	andreas_kupries	2002-08-22	1	-43/+66

*	* README: Bumped version number to 8.4b3 to distinguish	dgp	2002-08-20	1	-1/+1

*	* unix/configure:	mdejong	2002-07-19	1	-43/+44

*	* Bumped HEAD to version 8.4b2 so we can distinguish it from	dgp	2002-07-14	1	-1/+1

*	Regen	dkf	2002-06-22	1	-1/+1

*	* tcl.m4: Enabled COFF as well as CV style debug info with	hobbs	2002-04-12	1	-1/+1

*	* win/configure: Regen.	mdejong	2002-03-15	1	-24/+76

*	* unix/configure: Regen.	mdejong	2002-01-11	1	-42/+44

*	* win/configure: Regen.	mdejong	2001-11-25	1	-2/+2

*	Define TCL_INCLUDE_SPEC in tclConfig.sh. It should be	mdejong	2001-11-08	1	-0/+6

*	* win/README: Change minimum VC++ version to 5.X since	mdejong	2001-11-07	1	-24/+29

*	fixed dangling ;	hobbs	2001-10-15	1	-1/+2

*	* unix/configure:	hobbs	2001-10-15	1	-67/+105

*	added Win64 SDK RC1 compilation support	hobbs	2001-10-01	1	-39/+66

*	* win/Makefile.in:	andreas_kupries	2001-09-14	1	-41/+69

*	Bumped up patchlevel to 8.4a4 to distinguish	dgp	2001-08-08	1	-1/+1

*	* win/configure: regenerated	hobbs	2001-08-04	1	-15/+17

*	* unix/Makefile.in: Add AR variable for use in STLIB_LD.	mdejong	2001-07-11	1	-15/+14

*	* win/configure: Regen.	mdejong	2001-07-06	1	-12/+19

*	* win/Makefile.in: Subst DEPARG directly instead	mdejong	2001-07-06	1	-16/+24

*	* win/Makefile.in: Remove PATHTYPE variable.	mdejong	2001-07-04	1	-24/+44

*	* win/tcl.m4 (SC_CONFIG_CFLAGS): Don't pass the v flag	mdejong	2001-07-03	1	-1/+1

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 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://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have * * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* Programmer: Robb Matzke <matzke@llnl.gov> * Wednesday, October 8, 1997 * * Purpose: Indexed (chunked) I/O functions. The logical * multi-dimensional data space is regularly partitioned into * same-sized "chunks", the first of which is aligned with the * logical origin. The chunks are given a multi-dimensional * index which is used as a lookup key in a B-tree that maps * chunk index to disk address. Each chunk can be compressed * independently and the chunks may move around in the file as * their storage requirements change. * * Cache: Disk I/O is performed in units of chunks and H5MF_alloc() * contains code to optionally align chunks on disk block * boundaries for performance. * * The chunk cache is an extendible hash indexed by a function * of storage B-tree address and chunk N-dimensional offset * within the dataset. Collisions are not resolved -- one of * the two chunks competing for the hash slot must be preempted * from the cache. All entries in the hash also participate in * a doubly-linked list and entries are penalized by moving them * toward the front of the list. When a new chunk is about to * be added to the cache the heap is pruned by preempting * entries near the front of the list to make room for the new * entry which is added to the end of the list. */ /****************/ /* Module Setup */ /****************/ #define H5B_PACKAGE /*suppress error about including H5Bpkg */ #define H5D_PACKAGE /*suppress error about including H5Dpkg */ /***********/ /* Headers */ /***********/ #include "H5private.h" /* Generic Functions */ #include "H5Bpkg.h" /* B-link trees */ #include "H5Dpkg.h" /* Datasets */ #include "H5Eprivate.h" /* Error handling */ #include "H5Fprivate.h" /* Files */ #include "H5FDprivate.h" /* File drivers */ #include "H5FLprivate.h" /* Free Lists */ #include "H5Iprivate.h" /* IDs */ #include "H5MFprivate.h" /* File space management */ #include "H5MMprivate.h" /* Memory management */ #include "H5Oprivate.h" /* Object headers */ #include "H5Pprivate.h" /* Property lists */ #include "H5Sprivate.h" /* Dataspaces */ #include "H5Vprivate.h" /* Vector and array functions */ /****************/ /* Local Macros */ /****************/ /* * Feature: If this constant is defined then every cache preemption and load * causes a character to be printed on the standard error stream: * * `.': Entry was preempted because it has been completely read or * completely written but not partially read and not partially * written. This is often a good reason for preemption because such * a chunk will be unlikely to be referenced in the near future. * * `:': Entry was preempted because it hasn't been used recently. * * `#': Entry was preempted because another chunk collided with it. This * is usually a relatively bad thing. If there are too many of * these then the number of entries in the cache can be increased. * * c: Entry was preempted because the file is closing. * * w: A chunk read operation was eliminated because the library is * about to write new values to the entire chunk. This is a good * thing, especially on files where the chunk size is the same as * the disk block size, chunks are aligned on disk block boundaries, * and the operating system can also eliminate a read operation. */ /*#define H5D_ISTORE_DEBUG */ /* * Given a B-tree node return the dimensionality of the chunks pointed to by * that node. */ #define H5D_ISTORE_NDIMS(X) (((X)->sizeof_rkey-8)/8) #define H5D_HASH(D,ADDR) H5F_addr_hash(ADDR,(D)->cache.chunk.nslots) /******************/ /* Local Typedefs */ /******************/ /* Raw data chunks are cached. Each entry in the cache is: */ typedef struct H5D_rdcc_ent_t { hbool_t locked; /*entry is locked in cache */ hbool_t dirty; /*needs to be written to disk? */ hsize_t offset[H5O_LAYOUT_NDIMS]; /*chunk name */ size_t rd_count; /*bytes remaining to be read */ size_t wr_count; /*bytes remaining to be written */ size_t chunk_size; /*size of a chunk */ size_t alloc_size; /*amount allocated for the chunk */ uint8_t *chunk; /*the unfiltered chunk data */ unsigned idx; /*index in hash table */ struct H5D_rdcc_ent_t *next;/*next item in doubly-linked list */ struct H5D_rdcc_ent_t *prev;/*previous item in doubly-linked list */ } H5D_rdcc_ent_t; typedef H5D_rdcc_ent_t *H5D_rdcc_ent_ptr_t; /* For free lists */ /* * B-tree key. A key contains the minimum logical N-dimensional address and * the logical size of the chunk to which this key refers. The * fastest-varying dimension is assumed to reference individual bytes of the * array, so a 100-element 1-d array of 4-byte integers would really be a 2-d * array with the slow varying dimension of size 100 and the fast varying * dimension of size 4 (the storage dimensionality has very little to do with * the real dimensionality). * * Only the first few values of the OFFSET and SIZE fields are actually * stored on disk, depending on the dimensionality. * * The chunk's file address is part of the B-tree and not part of the key. */ typedef struct H5D_istore_key_t { size_t nbytes; /*size of stored data */ hsize_t offset[H5O_LAYOUT_NDIMS]; /*logical offset to start*/ unsigned filter_mask; /*excluded filters */ } H5D_istore_key_t; /* * Common data exchange structure for indexed storage nodes. This structure is * passed through the B-link tree layer to the methods for the objects * to which the B-link tree points. */ typedef struct H5D_istore_bt_ud_common_t { /* downward */ H5D_istore_key_t key; /*key values */ const H5O_layout_t *mesg; /*layout message */ } H5D_istore_bt_ud_common_t; /* * Data exchange structure for indexed storage nodes. This structure is * passed through the B-link tree layer to the methods for the objects * to which the B-link tree points for operations which require no * additional information. * * (Just an alias for the "common" info). */ typedef H5D_istore_bt_ud_common_t H5D_istore_ud0_t; typedef struct H5D_istore_ud1_t { H5D_istore_bt_ud_common_t common; /* Common info for B-tree user data (must be first) */ haddr_t addr; /*file address of chunk */ } H5D_istore_ud1_t; /* B-tree callback info for iteration to total allocated space */ typedef struct H5D_istore_it_ud1_t { H5D_istore_bt_ud_common_t common; /* Common info for B-tree user data (must be first) */ hsize_t total_storage; /*output from iterator */ } H5D_istore_it_ud1_t; /* B-tree callback info for iteration to dump node's info */ typedef struct H5D_istore_it_ud2_t { H5D_istore_bt_ud_common_t common; /* Common info for B-tree user data (must be first) */ FILE *stream; /*debug output stream */ hbool_t header_displayed; /* Node's header is displayed? */ } H5D_istore_it_ud2_t; /* B-tree callback info for iteration to prune chunks */ typedef struct H5D_istore_it_ud3_t { H5D_istore_bt_ud_common_t common; /* Common info for B-tree user data (must be first) */ hsize_t *dims; /*dataset dimensions */ } H5D_istore_it_ud3_t; /* B-tree callback info for iteration to copy data */ typedef struct H5D_istore_it_ud4_t { H5D_istore_bt_ud_common_t common; /* Common info for B-tree user data (must be first) */ H5F_t *file_src; /* Source file for copy */ haddr_t addr_dst; /* Address of dest. B-tree */ void *buf; /* Buffer to hold chunk data for read/write */ void *bkg; /* Buffer for background information during type conversion */ size_t buf_size; /* Buffer size */ /* needed for converting variable-length data */ hid_t tid_src; /* Datatype ID for source datatype */ hid_t tid_dst; /* Datatype ID for destination datatype */ hid_t tid_mem; /* Datatype ID for memory datatype */ H5T_t *dt_src; /* Source datatype */ H5T_path_t *tpath_src_mem; /* Datatype conversion path from source file to memory */ H5T_path_t *tpath_mem_dst; /* Datatype conversion path from memory to dest. file */ void *reclaim_buf; /* Buffer for reclaiming data */ size_t reclaim_buf_size; /* Reclaim buffer size */ size_t nelmts; /* Number of elements in buffer */ H5S_t *buf_space; /* Dataspace describing buffer */ /* needed for compressed variable-length data */ H5O_pline_t *pline; /* Filter pipeline */ /* needed for copy object pointed by refs */ H5F_t *file_dst; /* Destination file for copy */ H5O_copy_t *cpy_info; /* Copy options */ } H5D_istore_it_ud4_t; /* B-tree callback info for iteration to obtain chunk address and the index of the chunk for all chunks in the B-tree. */ typedef struct H5D_istore_it_ud5_t { H5D_istore_bt_ud_common_t common; /* Common info for B-tree user data (must be first) */ hsize_t* down_chunks; haddr_t *chunk_addr; } H5D_istore_it_ud5_t; /********************/ /* Local Prototypes */ /********************/ static void *H5D_istore_chunk_alloc(size_t size, const H5O_pline_t *pline); static void *H5D_istore_chunk_xfree(void *chk, const H5O_pline_t *pline); static herr_t H5D_istore_shared_create (const H5F_t *f, H5O_layout_t *layout); static herr_t H5D_istore_shared_free (void *page); /* B-tree iterator callbacks */ static int H5D_istore_iter_chunkmap(H5F_t *f, hid_t dxpl_id, const void *left_key, haddr_t addr, const void *right_key, void *_udata); static int H5D_istore_iter_allocated(H5F_t *f, hid_t dxpl_id, const void *left_key, haddr_t addr, const void *right_key, void *_udata); static int H5D_istore_iter_dump(H5F_t *f, hid_t dxpl_id, const void *left_key, haddr_t addr, const void *right_key, void *_udata); static int H5D_istore_prune_extent(H5F_t *f, hid_t dxpl_id, const void *_lt_key, haddr_t addr, const void *_rt_key, void *_udata); static int H5D_istore_iter_copy(H5F_t *f, hid_t dxpl_id, const void *_lt_key, haddr_t addr, const void *_rt_key, void *_udata); /* B-tree callbacks */ static H5RC_t *H5D_istore_get_shared(const H5F_t *f, const void *_udata); static herr_t H5D_istore_new_node(H5F_t *f, hid_t dxpl_id, H5B_ins_t, void *_lt_key, void *_udata, void *_rt_key, haddr_t *addr_p /*out*/); static int H5D_istore_cmp2(H5F_t *f, hid_t dxpl_id, void *_lt_key, void *_udata, void *_rt_key); static int H5D_istore_cmp3(H5F_t *f, hid_t dxpl_id, void *_lt_key, void *_udata, void *_rt_key); static herr_t H5D_istore_found(H5F_t *f, hid_t dxpl_id, haddr_t addr, const void *_lt_key, void *_udata); static H5B_ins_t H5D_istore_insert(H5F_t *f, hid_t dxpl_id, haddr_t addr, void *_lt_key, hbool_t *lt_key_changed, void *_md_key, void *_udata, void *_rt_key, hbool_t *rt_key_changed, haddr_t *new_node/*out*/); static H5B_ins_t H5D_istore_remove( H5F_t *f, hid_t dxpl_id, haddr_t addr, void *_lt_key, hbool_t *lt_key_changed, void *_udata, void *_rt_key, hbool_t *rt_key_changed); static herr_t H5D_istore_decode_key(const H5F_t *f, const H5B_t *bt, const uint8_t *raw, void *_key); static herr_t H5D_istore_encode_key(const H5F_t *f, const H5B_t *bt, uint8_t *raw, void *_key); static herr_t H5D_istore_debug_key(FILE *stream, H5F_t *f, hid_t dxpl_id, int indent, int fwidth, const void *key, const void *udata); /* inherits B-tree like properties from H5B */ H5B_class_t H5B_ISTORE[1] = {{ H5B_ISTORE_ID, /*id */ sizeof(H5D_istore_key_t), /*sizeof_nkey */ H5D_istore_get_shared, /*get_shared */ H5D_istore_new_node, /*new */ H5D_istore_cmp2, /*cmp2 */ H5D_istore_cmp3, /*cmp3 */ H5D_istore_found, /*found */ H5D_istore_insert, /*insert */ FALSE, /*follow min branch? */ FALSE, /*follow max branch? */ H5D_istore_remove, /*remove */ H5D_istore_decode_key, /*decode */ H5D_istore_encode_key, /*encode */ H5D_istore_debug_key, /*debug */ }}; /*********************/ /* Package Variables */ /*********************/ /*****************************/ /* Library Private Variables */ /*****************************/ /*******************/ /* Local Variables */ /*******************/ /* Declare a free list to manage H5F_rdcc_ent_t objects */ H5FL_DEFINE_STATIC(H5D_rdcc_ent_t); /* Declare a free list to manage the H5F_rdcc_ent_ptr_t sequence information */ H5FL_SEQ_DEFINE_STATIC(H5D_rdcc_ent_ptr_t); /* Declare a free list to manage the chunk sequence information */ H5FL_BLK_DEFINE_STATIC(chunk); /* Declare a free list to manage the native key offset sequence information */ H5FL_SEQ_DEFINE_STATIC(size_t); /* Declare a free list to manage the raw page information */ H5FL_BLK_DEFINE_STATIC(chunk_page); /* Declare extern the free list to manage blocks of type conversion data */ H5FL_BLK_EXTERN(type_conv); /*------------------------------------------------------------------------- * Function: H5D_istore_get_shared * * Purpose: Returns the shared B-tree info for the specified UDATA. * * Return: Success: Pointer to the raw B-tree page for this dataset * * Failure: Can't fail * * Programmer: Quincey Koziol * Monday, July 5, 2004 * *------------------------------------------------------------------------- */ /* ARGSUSED */ static H5RC_t * H5D_istore_get_shared(const H5F_t UNUSED *f, const void *_udata) { const H5D_istore_ud0_t *udata = (const H5D_istore_ud0_t *) _udata; FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_get_shared) HDassert(udata); HDassert(udata->mesg); HDassert(udata->mesg->u.chunk.btree_shared); /* Increment reference count on B-tree info */ H5RC_INC(udata->mesg->u.chunk.btree_shared); /* Return the pointer to the ref-count object */ FUNC_LEAVE_NOAPI(udata->mesg->u.chunk.btree_shared) } /* end H5D_istore_get_shared() */ /*------------------------------------------------------------------------- * Function: H5D_istore_decode_key * * Purpose: Decodes a raw key into a native key for the B-tree * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Friday, October 10, 1997 * *------------------------------------------------------------------------- */ static herr_t H5D_istore_decode_key(const H5F_t UNUSED *f, const H5B_t *bt, const uint8_t *raw, void *_key) { H5D_istore_key_t *key = (H5D_istore_key_t *) _key; H5B_shared_t *shared; /* Pointer to shared B-tree info */ size_t ndims; unsigned u; FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_decode_key) /* check args */ assert(f); assert(bt); shared=H5RC_GET_OBJ(bt->rc_shared); HDassert(shared); assert(raw); assert(key); ndims = H5D_ISTORE_NDIMS(shared); assert(ndims<=H5O_LAYOUT_NDIMS); /* decode */ UINT32DECODE(raw, key->nbytes); UINT32DECODE(raw, key->filter_mask); for (u=0; u<ndims; u++) UINT64DECODE(raw, key->offset[u]); FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5D_istore_decode_key() */ /*------------------------------------------------------------------------- * Function: H5D_istore_encode_key * * Purpose: Encode a key from native format to raw format. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Friday, October 10, 1997 * *------------------------------------------------------------------------- */ static herr_t H5D_istore_encode_key(const H5F_t UNUSED *f, const H5B_t *bt, uint8_t *raw, void *_key) { H5D_istore_key_t *key = (H5D_istore_key_t *) _key; H5B_shared_t *shared; /* Pointer to shared B-tree info */ size_t ndims; unsigned u; FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_encode_key) /* check args */ assert(f); assert(bt); shared=H5RC_GET_OBJ(bt->rc_shared); HDassert(shared); assert(raw); assert(key); ndims = H5D_ISTORE_NDIMS(shared); assert(ndims<=H5O_LAYOUT_NDIMS); /* encode */ UINT32ENCODE(raw, key->nbytes); UINT32ENCODE(raw, key->filter_mask); for (u=0; u<ndims; u++) UINT64ENCODE(raw, key->offset[u]); FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5D_istore_encode_key() */ /*------------------------------------------------------------------------- * Function: H5D_istore_debug_key * * Purpose: Prints a key. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Thursday, April 16, 1998 * *------------------------------------------------------------------------- */ /* ARGSUSED */ static herr_t H5D_istore_debug_key(FILE *stream, H5F_t UNUSED *f, hid_t UNUSED dxpl_id, int indent, int fwidth, const void *_key, const void *_udata) { const H5D_istore_key_t *key = (const H5D_istore_key_t *)_key; const H5D_istore_ud0_t *udata = (const H5D_istore_ud0_t *)_udata; unsigned u; FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_debug_key) HDassert(key); HDfprintf(stream, "%*s%-*s %Zd bytes\n", indent, "", fwidth, "Chunk size:", key->nbytes); HDfprintf(stream, "%*s%-*s 0x%08x\n", indent, "", fwidth, "Filter mask:", key->filter_mask); HDfprintf(stream, "%*s%-*s {", indent, "", fwidth, "Logical offset:"); for(u = 0; u < udata->mesg->u.chunk.ndims; u++) HDfprintf(stream, "%s%Hd", u?", ":"", key->offset[u]); HDfputs("}\n", stream); FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5D_istore_debug_key() */ /*------------------------------------------------------------------------- * Function: H5D_istore_cmp2 * * Purpose: Compares two keys sort of like strcmp(). The UDATA pointer * is only to supply extra information not carried in the keys * (in this case, the dimensionality) and is not compared * against the keys. * * Return: Success: -1 if LT_KEY is less than RT_KEY; * 1 if LT_KEY is greater than RT_KEY; * 0 if LT_KEY and RT_KEY are equal. * * Failure: FAIL (same as LT_KEY<RT_KEY) * * Programmer: Robb Matzke * Thursday, November 6, 1997 * *------------------------------------------------------------------------- */ /* ARGSUSED */ static int H5D_istore_cmp2(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, void *_lt_key, void *_udata, void *_rt_key) { H5D_istore_key_t *lt_key = (H5D_istore_key_t *) _lt_key; H5D_istore_key_t *rt_key = (H5D_istore_key_t *) _rt_key; H5D_istore_ud0_t *udata = (H5D_istore_ud0_t *) _udata; int ret_value; FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_cmp2) HDassert(lt_key); HDassert(rt_key); HDassert(udata); HDassert(udata->mesg->u.chunk.ndims > 0 && udata->mesg->u.chunk.ndims <= H5O_LAYOUT_NDIMS); /* Compare the offsets but ignore the other fields */ ret_value = H5V_vector_cmp_u(udata->mesg->u.chunk.ndims, lt_key->offset, rt_key->offset); FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_cmp2() */ /*------------------------------------------------------------------------- * Function: H5D_istore_cmp3 * * Purpose: Compare the requested datum UDATA with the left and right * keys of the B-tree. * * Return: Success: negative if the min_corner of UDATA is less * than the min_corner of LT_KEY. * * positive if the min_corner of UDATA is * greater than or equal the min_corner of * RT_KEY. * * zero otherwise. The min_corner of UDATA is * not necessarily contained within the address * space represented by LT_KEY, but a key that * would describe the UDATA min_corner address * would fall lexicographically between LT_KEY * and RT_KEY. * * Failure: FAIL (same as UDATA < LT_KEY) * * Programmer: Robb Matzke * Wednesday, October 8, 1997 * *------------------------------------------------------------------------- */ /* ARGSUSED */ static int H5D_istore_cmp3(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, void *_lt_key, void *_udata, void *_rt_key) { H5D_istore_key_t *lt_key = (H5D_istore_key_t *) _lt_key; H5D_istore_key_t *rt_key = (H5D_istore_key_t *) _rt_key; H5D_istore_ud0_t *udata = (H5D_istore_ud0_t *) _udata; int ret_value = 0; FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_cmp3) HDassert(lt_key); HDassert(rt_key); HDassert(udata); HDassert(udata->mesg->u.chunk.ndims > 0 && udata->mesg->u.chunk.ndims <= H5O_LAYOUT_NDIMS); /* Special case for faster checks on 1-D chunks */ /* (Checking for ndims==2 because last dimension is the datatype size) */ /* The additional checking for the right key is necessary due to the */ /* slightly odd way the library initializes the right-most node in the */ /* indexed storage B-tree... */ /* (Dump the B-tree with h5debug to look at it) -QAK */ if(udata->mesg->u.chunk.ndims==2) { if(udata->key.offset[0]>rt_key->offset[0]) ret_value=1; else if(udata->key.offset[0]==rt_key->offset[0] && udata->key.offset[1]>=rt_key->offset[1]) ret_value=1; else if(udata->key.offset[0]<lt_key->offset[0]) ret_value=(-1); } /* end if */ else { if (H5V_vector_ge_u(udata->mesg->u.chunk.ndims, udata->key.offset, rt_key->offset)) ret_value = 1; else if (H5V_vector_lt_u(udata->mesg->u.chunk.ndims, udata->key.offset, lt_key->offset)) ret_value = -1; } /* end else */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_cmp3() */ /*------------------------------------------------------------------------- * Function: H5D_istore_new_node * * Purpose: Adds a new entry to an i-storage B-tree. We can assume that * the domain represented by UDATA doesn't intersect the domain * already represented by the B-tree. * * Return: Success: Non-negative. The address of leaf is returned * through the ADDR argument. It is also added * to the UDATA. * * Failure: Negative * * Programmer: Robb Matzke * Tuesday, October 14, 1997 * *------------------------------------------------------------------------- */ static herr_t H5D_istore_new_node(H5F_t *f, hid_t dxpl_id, H5B_ins_t op, void *_lt_key, void *_udata, void *_rt_key, haddr_t *addr_p/*out*/) { H5D_istore_key_t *lt_key = (H5D_istore_key_t *) _lt_key; H5D_istore_key_t *rt_key = (H5D_istore_key_t *) _rt_key; H5D_istore_ud1_t *udata = (H5D_istore_ud1_t *) _udata; unsigned u; herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_istore_new_node) /* check args */ HDassert(f); HDassert(lt_key); HDassert(rt_key); HDassert(udata); HDassert(udata->common.mesg->u.chunk.ndims > 0 && udata->common.mesg->u.chunk.ndims < H5O_LAYOUT_NDIMS); HDassert(addr_p); /* Allocate new storage */ HDassert(udata->common.key.nbytes > 0); H5_CHECK_OVERFLOW(udata->common.key.nbytes ,size_t, hsize_t); if(HADDR_UNDEF == (*addr_p = H5MF_alloc(f, H5FD_MEM_DRAW, dxpl_id, (hsize_t)udata->common.key.nbytes))) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "couldn't allocate new file storage") udata->addr = *addr_p; /* * The left key describes the storage of the UDATA chunk being * inserted into the tree. */ lt_key->nbytes = udata->common.key.nbytes; lt_key->filter_mask = udata->common.key.filter_mask; for (u=0; u<udata->common.mesg->u.chunk.ndims; u++) lt_key->offset[u] = udata->common.key.offset[u]; /* * The right key might already be present. If not, then add a zero-width * chunk. */ if (H5B_INS_LEFT != op) { rt_key->nbytes = 0; rt_key->filter_mask = 0; for (u=0; u<udata->common.mesg->u.chunk.ndims; u++) { HDassert(udata->common.key.offset[u]+udata->common.mesg->u.chunk.dim[u] > udata->common.key.offset[u]); rt_key->offset[u] = udata->common.key.offset[u] + udata->common.mesg->u.chunk.dim[u]; } } done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_new_node() */ /*------------------------------------------------------------------------- * Function: H5D_istore_found * * Purpose: This function is called when the B-tree search engine has * found the leaf entry that points to a chunk of storage that * contains the beginning of the logical address space * represented by UDATA. The LT_KEY is the left key (the one * that describes the chunk) and RT_KEY is the right key (the * one that describes the next or last chunk). * * Note: It's possible that the chunk isn't really found. For * instance, in a sparse dataset the requested chunk might fall * between two stored chunks in which case this function is * called with the maximum stored chunk indices less than the * requested chunk indices. * * Return: Non-negative on success with information about the chunk * returned through the UDATA argument. Negative on failure. * * Programmer: Robb Matzke * Thursday, October 9, 1997 * *------------------------------------------------------------------------- */ /* ARGSUSED */ static herr_t H5D_istore_found(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, haddr_t addr, const void *_lt_key, void *_udata) { H5D_istore_ud1_t *udata = (H5D_istore_ud1_t *) _udata; const H5D_istore_key_t *lt_key = (const H5D_istore_key_t *) _lt_key; unsigned u; herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_found) /* Check arguments */ HDassert(f); HDassert(H5F_addr_defined(addr)); HDassert(udata); HDassert(lt_key); /* Is this *really* the requested chunk? */ for(u = 0; u < udata->common.mesg->u.chunk.ndims; u++) if(udata->common.key.offset[u] >= lt_key->offset[u] + udata->common.mesg->u.chunk.dim[u]) HGOTO_DONE(FAIL) /* Initialize return values */ udata->addr = addr; udata->common.key.nbytes = lt_key->nbytes; udata->common.key.filter_mask = lt_key->filter_mask; HDassert(lt_key->nbytes>0); for(u = 0; u < udata->common.mesg->u.chunk.ndims; u++) udata->common.key.offset[u] = lt_key->offset[u]; done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_found() */ /*------------------------------------------------------------------------- * Function: H5D_istore_insert * * Purpose: This function is called when the B-tree insert engine finds * the node to use to insert new data. The UDATA argument * points to a struct that describes the logical addresses being * added to the file. This function allocates space for the * data and returns information through UDATA describing a * file chunk to receive (part of) the data. * * The LT_KEY is always the key describing the chunk of file * memory at address ADDR. On entry, UDATA describes the logical * addresses for which storage is being requested (through the * `offset' and `size' fields). On return, UDATA describes the * logical addresses contained in a chunk on disk. * * Return: Success: An insertion command for the caller, one of * the H5B_INS_* constants. The address of the * new chunk is returned through the NEW_NODE * argument. * * Failure: H5B_INS_ERROR * * Programmer: Robb Matzke * Thursday, October 9, 1997 * *------------------------------------------------------------------------- */ /* ARGSUSED */ static H5B_ins_t H5D_istore_insert(H5F_t *f, hid_t dxpl_id, haddr_t addr, void *_lt_key, hbool_t *lt_key_changed, void *_md_key, void *_udata, void *_rt_key, hbool_t UNUSED *rt_key_changed, haddr_t *new_node_p/*out*/) { H5D_istore_key_t *lt_key = (H5D_istore_key_t *) _lt_key; H5D_istore_key_t *md_key = (H5D_istore_key_t *) _md_key; H5D_istore_key_t *rt_key = (H5D_istore_key_t *) _rt_key; H5D_istore_ud1_t *udata = (H5D_istore_ud1_t *) _udata; int cmp; unsigned u; H5B_ins_t ret_value; FUNC_ENTER_NOAPI_NOINIT(H5D_istore_insert) /* check args */ HDassert(f); HDassert(H5F_addr_defined(addr)); HDassert(lt_key); HDassert(lt_key_changed); HDassert(md_key); HDassert(udata); HDassert(rt_key); HDassert(new_node_p); cmp = H5D_istore_cmp3(f, dxpl_id, lt_key, udata, rt_key); HDassert(cmp <= 0); if (cmp < 0) { /* Negative indices not supported yet */ HGOTO_ERROR(H5E_STORAGE, H5E_UNSUPPORTED, H5B_INS_ERROR, "internal error") } else if (H5V_vector_eq_u (udata->common.mesg->u.chunk.ndims, udata->common.key.offset, lt_key->offset) && lt_key->nbytes>0) { /* * Already exists. If the new size is not the same as the old size * then we should reallocate storage. */ if (lt_key->nbytes != udata->common.key.nbytes) { /* Currently, the old chunk data is "thrown away" after the space is reallocated, * so avoid data copy in H5MF_realloc() call by just free'ing the space and * allocating new space. * * This should keep the file smaller also, by freeing the space and then * allocating new space, instead of vice versa (in H5MF_realloc). * * QAK - 11/19/2002 */ #ifdef OLD_WAY if(HADDR_UNDEF == (*new_node_p = H5MF_realloc(f, H5FD_MEM_DRAW, addr, (hsize_t)lt_key->nbytes, (hsize_t)udata->common.key.nbytes))) HGOTO_ERROR(H5E_STORAGE, H5E_NOSPACE, H5B_INS_ERROR, "unable to reallocate chunk storage") #else /* OLD_WAY */ H5_CHECK_OVERFLOW( lt_key->nbytes ,size_t, hsize_t); if(H5MF_xfree(f, H5FD_MEM_DRAW, dxpl_id, addr, (hsize_t)lt_key->nbytes)<0) HGOTO_ERROR(H5E_STORAGE, H5E_CANTFREE, H5B_INS_ERROR, "unable to free chunk") H5_CHECK_OVERFLOW(udata->common.key.nbytes ,size_t, hsize_t); if(HADDR_UNDEF == (*new_node_p = H5MF_alloc(f, H5FD_MEM_DRAW, dxpl_id, (hsize_t)udata->common.key.nbytes))) HGOTO_ERROR(H5E_STORAGE, H5E_NOSPACE, H5B_INS_ERROR, "unable to reallocate chunk") #endif /* OLD_WAY */ lt_key->nbytes = udata->common.key.nbytes; lt_key->filter_mask = udata->common.key.filter_mask; *lt_key_changed = TRUE; udata->addr = *new_node_p; ret_value = H5B_INS_CHANGE; } else { udata->addr = addr; ret_value = H5B_INS_NOOP; } } else if (H5V_hyper_disjointp(udata->common.mesg->u.chunk.ndims, lt_key->offset, udata->common.mesg->u.chunk.dim, udata->common.key.offset, udata->common.mesg->u.chunk.dim)) { HDassert(H5V_hyper_disjointp(udata->common.mesg->u.chunk.ndims, rt_key->offset, udata->common.mesg->u.chunk.dim, udata->common.key.offset, udata->common.mesg->u.chunk.dim)); /* * Split this node, inserting the new new node to the right of the * current node. The MD_KEY is where the split occurs. */ md_key->nbytes = udata->common.key.nbytes; md_key->filter_mask = udata->common.key.filter_mask; for(u = 0; u < udata->common.mesg->u.chunk.ndims; u++) { HDassert(0 == udata->common.key.offset[u] % udata->common.mesg->u.chunk.dim[u]); md_key->offset[u] = udata->common.key.offset[u]; } /* * Allocate storage for the new chunk */ H5_CHECK_OVERFLOW(udata->common.key.nbytes ,size_t, hsize_t); if(HADDR_UNDEF == (*new_node_p = H5MF_alloc(f, H5FD_MEM_DRAW, dxpl_id, (hsize_t)udata->common.key.nbytes))) HGOTO_ERROR(H5E_STORAGE, H5E_NOSPACE, H5B_INS_ERROR, "file allocation failed") udata->addr = *new_node_p; ret_value = H5B_INS_RIGHT; } else { HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, H5B_INS_ERROR, "internal error") } done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_insert() */ /*------------------------------------------------------------------------- * Function: H5D_istore_iter_allocated * * Purpose: Simply counts the number of chunks for a dataset. * * Return: Success: Non-negative * * Failure: Negative * * Programmer: Robb Matzke * Wednesday, April 21, 1999 * *------------------------------------------------------------------------- */ /* ARGSUSED */ static int H5D_istore_iter_allocated (H5F_t UNUSED *f, hid_t UNUSED dxpl_id, const void *_lt_key, haddr_t UNUSED addr, const void UNUSED *_rt_key, void *_udata) { H5D_istore_it_ud1_t *udata = (H5D_istore_it_ud1_t *)_udata; const H5D_istore_key_t *lt_key = (const H5D_istore_key_t *)_lt_key; FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_iter_allocated) udata->total_storage += lt_key->nbytes; FUNC_LEAVE_NOAPI(H5B_ITER_CONT) } /* H5D_istore_iter_allocated() */ /*------------------------------------------------------------------------- * Function: H5D_istore_iter_chunkmap * * Purpose: obtain chunk address and the corresponding index * * Return: Success: Non-negative * * Failure: Negative * * Programmer: Kent Yang * Tuesday, November 15, 2005 * *------------------------------------------------------------------------- */ /* ARGSUSED */ static int H5D_istore_iter_chunkmap (H5F_t UNUSED *f, hid_t UNUSED dxpl_id, const void *_lt_key, haddr_t addr, const void UNUSED *_rt_key, void *_udata) { H5D_istore_it_ud5_t *udata = (H5D_istore_it_ud5_t *)_udata; const H5D_istore_key_t *lt_key = (const H5D_istore_key_t *)_lt_key; unsigned rank; hsize_t chunk_index; int ret_value = H5B_ITER_CONT; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_istore_iter_chunkmap); rank = udata->common.mesg->u.chunk.ndims - 1; if(H5V_chunk_index(rank,lt_key->offset,udata->common.mesg->u.chunk.dim,udata->down_chunks,&chunk_index)<0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") udata->chunk_addr[chunk_index] = addr; done: FUNC_LEAVE_NOAPI(ret_value) } /* H5D_istore_iter_allocated() */ /*------------------------------------------------------------------------- * Function: H5D_istore_iter_dump * * Purpose: If the UDATA.STREAM member is non-null then debugging * information is written to that stream. * * Return: Success: Non-negative * * Failure: Negative * * Programmer: Robb Matzke * Wednesday, April 21, 1999 * *------------------------------------------------------------------------- */ /* ARGSUSED */ static int H5D_istore_iter_dump (H5F_t UNUSED *f, hid_t UNUSED dxpl_id, const void *_lt_key, haddr_t UNUSED addr, const void UNUSED *_rt_key, void *_udata) { H5D_istore_it_ud2_t *udata = (H5D_istore_it_ud2_t *)_udata; const H5D_istore_key_t *lt_key = (const H5D_istore_key_t *)_lt_key; unsigned u; FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_iter_dump) if(udata->stream) { if(!udata->header_displayed) { HDfprintf(udata->stream, " Flags Bytes Address Logical Offset\n"); HDfprintf(udata->stream, " ========== ======== ========== ==============================\n"); /* Set flag that the headers has been printed */ udata->header_displayed = TRUE; } /* end if */ HDfprintf(udata->stream, " 0x%08x %8Zu %10a [", lt_key->filter_mask, lt_key->nbytes, addr); for(u = 0; u < udata->common.mesg->u.chunk.ndims; u++) HDfprintf(udata->stream, "%s%Hd", (u ? ", " : ""), lt_key->offset[u]); HDfputs("]\n", udata->stream); } /* end if */ FUNC_LEAVE_NOAPI(H5B_ITER_CONT) } /* H5D_istore_iter_dump() */ /*------------------------------------------------------------------------- * Function: H5D_istore_iter_copy * * Purpose: copy chunked raw data from source file and insert to the * B-tree node in the destination file * * Return: Non-negative on success/Negative on failure * * Programmer: Peter Cao * August 20, 2005 * *------------------------------------------------------------------------- */ static int H5D_istore_iter_copy(H5F_t *f_src, hid_t dxpl_id, const void *_lt_key, haddr_t addr_src, const void UNUSED *_rt_key, void *_udata) { H5D_istore_it_ud4_t *udata = (H5D_istore_it_ud4_t *)_udata; const H5D_istore_key_t *lt_key = (const H5D_istore_key_t *)_lt_key; H5D_istore_ud1_t udata_dst; /* User data about new destination chunk */ hbool_t is_vlen = FALSE; hbool_t fix_ref = FALSE; /* General information about chunk copy */ void *bkg = udata->bkg; void *buf = udata->buf; size_t buf_size = udata->buf_size; H5O_pline_t *pline = udata->pline; /* needed for commpressed variable length data */ hbool_t is_compressed = FALSE; H5Z_EDC_t edc_read = H5Z_NO_EDC; size_t nbytes = lt_key->nbytes; H5Z_cb_t cb_struct; int ret_value = H5B_ITER_CONT; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_istore_iter_copy) /* Check parameter for type conversion */ if(udata->dt_src) { if(H5T_detect_class(udata->dt_src, H5T_VLEN) > 0) is_vlen = TRUE; else if((H5T_get_class(udata->dt_src, FALSE) == H5T_REFERENCE) && (udata->file_src != udata->file_dst)) fix_ref = TRUE; else HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy dataset elements") } /* end if */ /* Check for filtered chunks */ if(pline && pline->nused) { is_compressed = TRUE; cb_struct.func = NULL; /* no callback function when failed */ } /* end if */ /* Resize the buf if it is too small to hold the data */ if(nbytes > buf_size) { /* Re-allocate memory for copying the chunk */ if(NULL == (udata->buf = H5MM_realloc(udata->buf, nbytes))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, H5B_ITER_ERROR, "memory allocation failed for raw data chunk") if(udata->bkg) { if(NULL == (udata->bkg = H5MM_realloc(udata->bkg, nbytes))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, H5B_ITER_ERROR, "memory allocation failed for raw data chunk") if(!udata->cpy_info->expand_ref) HDmemset((uint8_t *)udata->bkg + buf_size, 0, (size_t)(nbytes - buf_size)); bkg = udata->bkg; } /* end if */ buf = udata->buf; udata->buf_size = buf_size = nbytes; } /* end if */ /* read chunk data from the source file */ if(H5F_block_read(f_src, H5FD_MEM_DRAW, addr_src, nbytes, dxpl_id, buf) < 0) HGOTO_ERROR(H5E_IO, H5E_READERROR, H5B_ITER_ERROR, "unable to read raw data chunk") /* Need to uncompress variable-length & reference data elements */ if(is_compressed && (is_vlen || fix_ref)) { unsigned filter_mask = lt_key->filter_mask; if(H5Z_pipeline(pline, H5Z_FLAG_REVERSE, &filter_mask, edc_read, cb_struct, &nbytes, &buf_size, &buf) < 0) HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, H5B_ITER_ERROR, "data pipeline read failed") } /* end if */ /* Perform datatype conversion, if necessary */ if(is_vlen) { H5T_path_t *tpath_src_mem = udata->tpath_src_mem; H5T_path_t *tpath_mem_dst = udata->tpath_mem_dst; H5S_t *buf_space = udata->buf_space; hid_t tid_src = udata->tid_src; hid_t tid_dst = udata->tid_dst; hid_t tid_mem = udata->tid_mem; size_t nelmts = udata->nelmts; void *reclaim_buf = udata->reclaim_buf; size_t reclaim_buf_size = udata->reclaim_buf_size; /* Convert from source file to memory */ if(H5T_convert(tpath_src_mem, tid_src, tid_mem, nelmts, (size_t)0, (size_t)0, buf, NULL, dxpl_id) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, H5B_ITER_ERROR, "datatype conversion failed") /* Copy into another buffer, to reclaim memory later */ HDmemcpy(reclaim_buf, buf, reclaim_buf_size); /* Set background buffer to all zeros */ HDmemset(bkg, 0, buf_size); /* Convert from memory to destination file */ if(H5T_convert(tpath_mem_dst, tid_mem, tid_dst, nelmts, (size_t)0, (size_t)0, buf, bkg, dxpl_id) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, H5B_ITER_ERROR, "datatype conversion failed") /* Reclaim space from variable length data */ if(H5D_vlen_reclaim(tid_mem, buf_space, H5P_DATASET_XFER_DEFAULT, reclaim_buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_BADITER, H5B_ITER_ERROR, "unable to reclaim variable-length data") } /* end if */ else if(fix_ref) { /* Check for expanding references */ /* (background buffer has already been zeroed out, if not expanding) */ if(udata->cpy_info->expand_ref) { size_t ref_count; /* Determine # of reference elements to copy */ ref_count = nbytes / H5T_get_size(udata->dt_src); /* Copy the reference elements */ if(H5O_copy_expand_ref(f_src, buf, dxpl_id, udata->file_dst, bkg, ref_count, H5T_get_ref_type(udata->dt_src), udata->cpy_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy reference attribute") } /* end if */ /* After fix ref, copy the new reference elements to the buffer to write out */ HDmemcpy(buf, bkg, buf_size); } /* end if */ /* Copy source chunk callback information for insertion */ HDmemset(&udata_dst, 0, sizeof(udata_dst)); HDmemcpy(&(udata_dst.common.key), lt_key, sizeof(H5D_istore_key_t)); udata_dst.common.mesg = udata->common.mesg; /* Share this pointer for a short while */ /* Need to compress variable-length & reference data elements before writing to file */ if(is_compressed && (is_vlen || fix_ref) ) { if(H5Z_pipeline(pline, 0, &(udata_dst.common.key.filter_mask), edc_read, cb_struct, &nbytes, &buf_size, &buf) < 0) HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, H5B_ITER_ERROR, "output pipeline failed") udata_dst.common.key.nbytes = nbytes; udata->buf = buf; udata->buf_size = buf_size; } /* end if */ /* Insert chunk into the destination Btree */ if(H5B_insert(udata->file_dst, dxpl_id, H5B_ISTORE, udata->addr_dst, &udata_dst) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, H5B_ITER_ERROR, "unable to allocate chunk") /* Write chunk data to destination file */ HDassert(H5F_addr_defined(udata_dst.addr)); if(H5F_block_write(udata->file_dst, H5FD_MEM_DRAW, udata_dst.addr, nbytes, dxpl_id, buf) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, H5B_ITER_ERROR, "unable to write raw data to file") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_iter_copy() */ /*------------------------------------------------------------------------- * Function: H5D_istore_init * * Purpose: Initialize the raw data chunk cache for a dataset. This is * called when the dataset is initialized. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Monday, May 18, 1998 * *------------------------------------------------------------------------- */ herr_t H5D_istore_init (const H5F_t *f, const H5D_t *dset) { H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_istore_init, FAIL) if (H5F_RDCC_NBYTES(f)>0 && H5F_RDCC_NELMTS(f)>0) { rdcc->nbytes=H5F_RDCC_NBYTES(f); rdcc->nslots = H5F_RDCC_NELMTS(f); rdcc->slot = H5FL_SEQ_CALLOC (H5D_rdcc_ent_ptr_t,rdcc->nslots); if (NULL==rdcc->slot) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") } /* end if */ /* Allocate the shared structure */ if(H5D_istore_shared_create(f, &dset->shared->layout)<0) HGOTO_ERROR(H5E_RESOURCE, H5E_CANTINIT, FAIL, "can't create wrapper for shared B-tree info") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_init() */ /*------------------------------------------------------------------------- * Function: H5D_istore_flush_entry * * Purpose: Writes a chunk to disk. If RESET is non-zero then the * entry is cleared -- it's slightly faster to flush a chunk if * the RESET flag is turned on because it results in one fewer * memory copy. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Thursday, May 21, 1998 * *------------------------------------------------------------------------- */ static herr_t H5D_istore_flush_entry(const H5D_io_info_t *io_info, H5D_rdcc_ent_t *ent, hbool_t reset) { herr_t ret_value=SUCCEED; /*return value */ unsigned u; /*counters */ void *buf=NULL; /*temporary buffer */ size_t alloc; /*bytes allocated for BUF */ hbool_t point_of_no_return = FALSE; FUNC_ENTER_NOAPI_NOINIT(H5D_istore_flush_entry) assert(io_info); assert(io_info->dset); assert(ent); assert(!ent->locked); buf = ent->chunk; if (ent->dirty) { H5D_istore_ud1_t udata; /*pass through B-tree */ udata.common.mesg = &io_info->dset->shared->layout; udata.common.key.filter_mask = 0; udata.addr = HADDR_UNDEF; udata.common.key.nbytes = ent->chunk_size; for (u=0; u<io_info->dset->shared->layout.u.chunk.ndims; u++) udata.common.key.offset[u] = ent->offset[u]; alloc = ent->alloc_size; /* Should the chunk be filtered before writing it to disk? */ if (io_info->dset->shared->dcpl_cache.pline.nused) { if (!reset) { /* * Copy the chunk to a new buffer before running it through * the pipeline because we'll want to save the original buffer * for later. */ alloc = ent->chunk_size; if (NULL==(buf = H5MM_malloc(alloc))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for pipeline") HDmemcpy(buf, ent->chunk, ent->chunk_size); } else { /* * If we are reseting and something goes wrong after this * point then it's too late to recover because we may have * destroyed the original data by calling H5Z_pipeline(). * The only safe option is to continue with the reset * even if we can't write the data to disk. */ point_of_no_return = TRUE; ent->chunk = NULL; } if (H5Z_pipeline(&(io_info->dset->shared->dcpl_cache.pline), 0, &(udata.common.key.filter_mask), io_info->dxpl_cache->err_detect, io_info->dxpl_cache->filter_cb, &(udata.common.key.nbytes), &alloc, &buf)<0) HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "output pipeline failed") } /* * Create the chunk it if it doesn't exist, or reallocate the chunk if * its size changed. Then write the data into the file. */ if(H5B_insert(io_info->dset->oloc.file, io_info->dxpl_id, H5B_ISTORE, io_info->dset->shared->layout.u.chunk.addr, &udata)<0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to allocate chunk") if(H5F_block_write(io_info->dset->oloc.file, H5FD_MEM_DRAW, udata.addr, udata.common.key.nbytes, io_info->dxpl_id, buf) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file") /* Mark cache entry as clean */ ent->dirty = FALSE; #ifdef H5D_ISTORE_DEBUG io_info->dset->shared->cache.chunk.nflushes++; #endif /* H5D_ISTORE_DEBUG */ } /* end if */ /* Reset, but do not free or removed from list */ if (reset) { point_of_no_return = FALSE; if(buf==ent->chunk) buf = NULL; if(ent->chunk!=NULL) ent->chunk = H5D_istore_chunk_xfree(ent->chunk,&(io_info->dset->shared->dcpl_cache.pline)); } /* end if */ done: /* Free the temp buffer only if it's different than the entry chunk */ if (buf!=ent->chunk) H5MM_xfree(buf); /* * If we reached the point of no return then we have no choice but to * reset the entry. This can only happen if RESET is true but the * output pipeline failed. Do not free the entry or remove it from the * list. */ if (ret_value<0 && point_of_no_return) { if(ent->chunk) ent->chunk = H5D_istore_chunk_xfree(ent->chunk,&(io_info->dset->shared->dcpl_cache.pline)); } /* end if */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_flush_entry() */ /*------------------------------------------------------------------------- * Function: H5D_istore_preempt * * Purpose: Preempts the specified entry from the cache, flushing it to * disk if necessary. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Thursday, May 21, 1998 * *------------------------------------------------------------------------- */ static herr_t H5D_istore_preempt(const H5D_io_info_t *io_info, H5D_rdcc_ent_t * ent, hbool_t flush) { H5D_rdcc_t *rdcc = &(io_info->dset->shared->cache.chunk); herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_istore_preempt) assert(io_info); assert(ent); assert(!ent->locked); assert(ent->idx < rdcc->nslots); if(flush) { /* Flush */ if(H5D_istore_flush_entry(io_info, ent, TRUE) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer") } else { /* Don't flush, just free chunk */ if(ent->chunk != NULL) ent->chunk = H5D_istore_chunk_xfree(ent->chunk,&(io_info->dset->shared->dcpl_cache.pline)); } /* Unlink from list */ if(ent->prev) ent->prev->next = ent->next; else rdcc->head = ent->next; if(ent->next) ent->next->prev = ent->prev; else rdcc->tail = ent->prev; ent->prev = ent->next = NULL; /* Remove from cache */ rdcc->slot[ent->idx] = NULL; ent->idx = UINT_MAX; rdcc->nbytes -= ent->chunk_size; --rdcc->nused; /* Free */ H5FL_FREE(H5D_rdcc_ent_t, ent); done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_preempt() */ /*------------------------------------------------------------------------- * Function: H5D_istore_flush * * Purpose: Writes all dirty chunks to disk and optionally preempts them * from the cache. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Thursday, May 21, 1998 * *------------------------------------------------------------------------- */ herr_t H5D_istore_flush (H5D_t *dset, hid_t dxpl_id, unsigned flags) { H5D_io_info_t io_info; /* Temporary I/O info object */ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ H5D_dxpl_cache_t *dxpl_cache=&_dxpl_cache; /* Data transfer property cache */ H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); int nerrors=0; H5D_rdcc_ent_t *ent=NULL, *next=NULL; herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_istore_flush, FAIL) /* Fill the DXPL cache values for later use */ if (H5D_get_dxpl_cache(dxpl_id,&dxpl_cache)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache") /* Construct dataset I/O info */ H5D_BUILD_IO_INFO(&io_info,dset,dxpl_cache,dxpl_id,NULL); for (ent=rdcc->head; ent; ent=next) { next = ent->next; if ((flags&H5F_FLUSH_INVALIDATE)) { if (H5D_istore_preempt(&io_info, ent, TRUE )<0) nerrors++; } else { if (H5D_istore_flush_entry(&io_info, ent, FALSE)<0) nerrors++; } } /* end for */ if (nerrors) HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_flush() */ /*------------------------------------------------------------------------- * Function: H5D_istore_dest * * Purpose: Destroy the entire chunk cache by flushing dirty entries, * preempting all entries, and freeing the cache itself. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Thursday, May 21, 1998 * *------------------------------------------------------------------------- */ herr_t H5D_istore_dest (H5D_t *dset, hid_t dxpl_id) { H5D_io_info_t io_info; /* Temporary I/O info object */ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ H5D_dxpl_cache_t *dxpl_cache=&_dxpl_cache; /* Data transfer property cache */ H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); int nerrors=0; H5D_rdcc_ent_t *ent=NULL, *next=NULL; herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_istore_dest, FAIL) assert(dset); /* Fill the DXPL cache values for later use */ if (H5D_get_dxpl_cache(dxpl_id,&dxpl_cache)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache") /* Construct dataset I/O info */ H5D_BUILD_IO_INFO(&io_info,dset,dxpl_cache,dxpl_id,NULL); /* Flush all the cached chunks */ for (ent=rdcc->head; ent; ent=next) { #ifdef H5D_ISTORE_DEBUG HDfputc('c', stderr); HDfflush(stderr); #endif next = ent->next; if (H5D_istore_preempt(&io_info, ent, TRUE )<0) nerrors++; } if (nerrors) HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks") if(rdcc->slot) H5FL_SEQ_FREE (H5D_rdcc_ent_ptr_t,rdcc->slot); HDmemset (rdcc, 0, sizeof(H5D_rdcc_t)); /* Free the raw B-tree node buffer */ if(dset->shared->layout.u.chunk.btree_shared==NULL) HGOTO_ERROR(H5E_IO, H5E_CANTFREE, FAIL, "ref-counted page nil") if(H5RC_DEC(dset->shared->layout.u.chunk.btree_shared)<0) HGOTO_ERROR(H5E_IO, H5E_CANTFREE, FAIL, "unable to decrement ref-counted page") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_dest() */ /*------------------------------------------------------------------------- * Function: H5D_istore_shared_create * * Purpose: Create & initialize B-tree shared info * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Monday, September 27, 2004 * *------------------------------------------------------------------------- */ static herr_t H5D_istore_shared_create (const H5F_t *f, H5O_layout_t *layout) { H5B_shared_t *shared; /* Shared B-tree node info */ size_t u; /* Local index variable */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_istore_shared_create) /* Allocate space for the shared structure */ if(NULL==(shared=H5FL_MALLOC(H5B_shared_t))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for shared B-tree info") /* Set up the "global" information for this file's groups */ shared->type= H5B_ISTORE; shared->two_k=2*H5F_KVALUE(f,H5B_ISTORE); shared->sizeof_rkey = 4 + /*storage size */ 4 + /*filter mask */ layout->u.chunk.ndims*8; /*dimension indices */ assert(shared->sizeof_rkey); shared->sizeof_rnode = H5B_nodesize(f, shared, &shared->sizeof_keys); assert(shared->sizeof_rnode); if(NULL==(shared->page=H5FL_BLK_MALLOC(chunk_page,shared->sizeof_rnode))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for B-tree page") #ifdef H5_USING_PURIFY HDmemset(shared->page,0,shared->sizeof_rnode); #endif /* H5_USING_PURIFY */ if(NULL==(shared->nkey=H5FL_SEQ_MALLOC(size_t,(size_t)(2*H5F_KVALUE(f,H5B_ISTORE)+1)))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for B-tree page") /* Initialize the offsets into the native key buffer */ for(u=0; u<(2*H5F_KVALUE(f,H5B_ISTORE)+1); u++) shared->nkey[u]=u*H5B_ISTORE[0].sizeof_nkey; /* Make shared B-tree info reference counted */ if(NULL==(layout->u.chunk.btree_shared=H5RC_create(shared,H5D_istore_shared_free))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't create ref-count wrapper for shared B-tree info") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_shared_create() */ /*------------------------------------------------------------------------- * Function: H5D_istore_shared_free * * Purpose: Free B-tree shared info * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, July 8, 2004 * *------------------------------------------------------------------------- */ static herr_t H5D_istore_shared_free (void *_shared) { H5B_shared_t *shared = (H5B_shared_t *)_shared; FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_shared_free) /* Free the raw B-tree node buffer */ H5FL_BLK_FREE(chunk_page,shared->page); /* Free the B-tree native key offsets buffer */ H5FL_SEQ_FREE(size_t,shared->nkey); /* Free the shared B-tree info */ H5FL_FREE(H5B_shared_t,shared); FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5D_istore_shared_free() */ /*------------------------------------------------------------------------- * Function: H5D_istore_prune * * Purpose: Prune the cache by preempting some things until the cache has * room for something which is SIZE bytes. Only unlocked * entries are considered for preemption. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Thursday, May 21, 1998 * *------------------------------------------------------------------------- */ static herr_t H5D_istore_prune (const H5D_io_info_t *io_info, size_t size) { int i, j, nerrors=0; const H5D_rdcc_t *rdcc = &(io_info->dset->shared->cache.chunk); size_t total = rdcc->nbytes; const int nmeth=2; /*number of methods */ int w[1]; /*weighting as an interval */ H5D_rdcc_ent_t *p[2], *cur; /*list pointers */ H5D_rdcc_ent_t *n[2]; /*list next pointers */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_istore_prune) /* * Preemption is accomplished by having multiple pointers (currently two) * slide down the list beginning at the head. Pointer p(N+1) will start * traversing the list when pointer pN reaches wN percent of the original * list. In other words, preemption method N gets to consider entries in * approximate least recently used order w0 percent before method N+1 * where 100% means tha method N will run to completion before method N+1 * begins. The pointers participating in the list traversal are each * given a chance at preemption before any of the pointers are advanced. */ w[0] = (int)(rdcc->nused * H5F_RDCC_W0(io_info->dset->oloc.file)); p[0] = rdcc->head; p[1] = NULL; while ((p[0] || p[1]) && rdcc->nbytes+size>total) { /* Introduce new pointers */ for (i=0; i<nmeth-1; i++) if (0==w[i]) p[i+1] = rdcc->head; /* Compute next value for each pointer */ for (i=0; i<nmeth; i++) n[i] = p[i] ? p[i]->next : NULL; /* Give each method a chance */ for (i=0; i<nmeth && rdcc->nbytes+size>total; i++) { if (0==i && p[0] && !p[0]->locked && ((0==p[0]->rd_count && 0==p[0]->wr_count) || (0==p[0]->rd_count && p[0]->chunk_size==p[0]->wr_count) || (p[0]->chunk_size==p[0]->rd_count && 0==p[0]->wr_count))) { /* * Method 0: Preempt entries that have been completely written * and/or completely read but not entries that are partially * written or partially read. */ cur = p[0]; #ifdef H5D_ISTORE_DEBUG HDputc('.', stderr); HDfflush(stderr); #endif } else if (1==i && p[1] && !p[1]->locked) { /* * Method 1: Preempt the entry without regard to * considerations other than being locked. This is the last * resort preemption. */ cur = p[1]; #ifdef H5D_ISTORE_DEBUG HDputc(':', stderr); HDfflush(stderr); #endif } else { /* Nothing to preempt at this point */ cur= NULL; } if (cur) { for (j=0; j<nmeth; j++) { if (p[j]==cur) p[j] = NULL; if (n[j]==cur) n[j] = cur->next; } if (H5D_istore_preempt(io_info, cur, TRUE)<0) nerrors++; } } /* Advance pointers */ for (i=0; i<nmeth; i++) p[i] = n[i]; for (i=0; i<nmeth-1; i++) w[i] -= 1; } if (nerrors) HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to preempt one or more raw data cache entry") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_prune() */ /*------------------------------------------------------------------------- * Function: H5D_istore_lock * * Purpose: Return a pointer to a dataset chunk. The pointer points * directly into the chunk cache and should not be freed * by the caller but will be valid until it is unlocked. The * input value IDX_HINT is used to speed up cache lookups and * it's output value should be given to H5F_istore_unlock(). * IDX_HINT is ignored if it is out of range, and if it points * to the wrong entry then we fall back to the normal search * method. * * If RELAX is non-zero and the chunk isn't in the cache then * don't try to read it from the file, but just allocate an * uninitialized buffer to hold the result. This is intended * for output functions that are about to overwrite the entire * chunk. * * Return: Success: Ptr to a file chunk. * * Failure: NULL * * Programmer: Robb Matzke * Thursday, May 21, 1998 * *------------------------------------------------------------------------- */ static void * H5D_istore_lock(const H5D_io_info_t *io_info, H5D_istore_ud1_t *udata, hbool_t relax, unsigned *idx_hint/*in,out*/) { H5D_t *dset=io_info->dset; /* Local pointer to the dataset info */ const H5O_pline_t *pline=&(dset->shared->dcpl_cache.pline); /* I/O pipeline info */ const H5O_layout_t *layout=&(dset->shared->layout); /* Dataset layout */ const H5O_fill_t *fill=&(dset->shared->dcpl_cache.fill); /* Fill value info */ H5D_fill_time_t fill_time=dset->shared->dcpl_cache.fill_time; /* Fill time */ H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk);/*raw data chunk cache*/ H5D_rdcc_ent_t *ent = NULL; /*cache entry */ unsigned idx=0; /*hash index number */ hbool_t found = FALSE; /*already in cache? */ unsigned u; /*counters */ size_t chunk_size=0; /*size of a chunk */ void *chunk=NULL; /*the file chunk */ void *ret_value; /*return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_istore_lock) assert(io_info); assert(dset); assert(io_info->dxpl_cache); assert(io_info->store); assert(TRUE==H5P_isa_class(io_info->dxpl_id,H5P_DATASET_XFER)); /* Get the chunk's size */ assert(layout->u.chunk.size>0); H5_ASSIGN_OVERFLOW(chunk_size,layout->u.chunk.size,hsize_t,size_t); /* Search for the chunk in the cache */ if (rdcc->nslots>0) { idx=H5D_HASH(dset->shared,io_info->store->chunk.index); ent = rdcc->slot[idx]; if (ent) { for (u=0, found=TRUE; u<layout->u.chunk.ndims; u++) { if (io_info->store->chunk.offset[u]!=ent->offset[u]) { found = FALSE; break; } /* end if */ } /* end for */ } /* end if */ } /* end if */ if (found) { /* * Already in the cache. Count a hit. */ #ifdef H5D_ISTORE_DEBUG rdcc->nhits++; #endif /* H5D_ISTORE_DEBUG */ } else if (relax) { /* * Not in the cache, but we're about to overwrite the whole thing * anyway, so just allocate a buffer for it but don't initialize that * buffer with the file contents. Count this as a hit instead of a * miss because we saved ourselves lots of work. */ #ifdef H5D_ISTORE_DEBUG HDputc('w', stderr); HDfflush(stderr); rdcc->nhits++; #endif if (NULL==(chunk=H5D_istore_chunk_alloc (chunk_size,pline))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk") } else { H5D_istore_ud1_t tmp_udata; /*B-tree pass-through */ haddr_t chunk_addr; /* Address of chunk on disk */ if(udata!=NULL) chunk_addr = udata->addr; else { /* Point at temporary storage for B-tree pass through */ udata = &tmp_udata; /* * Not in the cache. Read it from the file and count this as a miss * if it's in the file or an init if it isn't. */ chunk_addr = H5D_istore_get_addr(io_info, udata); } /* end else */ if (H5F_addr_defined(chunk_addr)) { size_t chunk_alloc = 0; /*allocated chunk size */ /* * The chunk exists on disk. */ /* Chunk size on disk isn't [likely] the same size as the final chunk * size in memory, so allocate memory big enough. */ chunk_alloc = udata->common.key.nbytes; if(NULL == (chunk = H5D_istore_chunk_alloc (chunk_alloc, pline))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk") if(H5F_block_read(dset->oloc.file, H5FD_MEM_DRAW, chunk_addr, udata->common.key.nbytes, io_info->dxpl_id, chunk) < 0) HGOTO_ERROR(H5E_IO, H5E_READERROR, NULL, "unable to read raw data chunk") if(pline->nused) { if(H5Z_pipeline(pline, H5Z_FLAG_REVERSE, &(udata->common.key.filter_mask), io_info->dxpl_cache->err_detect, io_info->dxpl_cache->filter_cb, &(udata->common.key.nbytes), &chunk_alloc, &chunk) < 0) HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, NULL, "data pipeline read failed") } /* end if */ #ifdef H5D_ISTORE_DEBUG rdcc->nmisses++; #endif /* H5D_ISTORE_DEBUG */ } else { H5D_fill_value_t fill_status; #ifdef OLD_WAY /* Clear the error stack from not finding the chunk on disk */ H5E_clear_stack(NULL); #endif /* OLD_WAY */ /* Chunk size on disk isn't [likely] the same size as the final chunk * size in memory, so allocate memory big enough. */ if (NULL==(chunk = H5D_istore_chunk_alloc (chunk_size,pline))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk") if (H5P_is_fill_value_defined(fill, &fill_status) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't tell if fill value defined") if(fill_time==H5D_FILL_TIME_ALLOC || (fill_time==H5D_FILL_TIME_IFSET && fill_status==H5D_FILL_VALUE_USER_DEFINED)) { if (fill && fill->buf) { /* * The chunk doesn't exist in the file. Replicate the fill * value throughout the chunk. */ assert(0==chunk_size % fill->size); H5V_array_fill(chunk, fill->buf, fill->size, chunk_size/fill->size); } else { /* * The chunk doesn't exist in the file and no fill value was * specified. Assume all zeros. */ HDmemset (chunk, 0, chunk_size); } /* end else */ } /* end if */ #ifdef H5_USING_PURIFY else HDmemset(chunk,0,chunk_size); #endif /* H5_USING_PURIFY */ #ifdef H5D_ISTORE_DEBUG rdcc->ninits++; #endif /* H5D_ISTORE_DEBUG */ } /* end else */ } assert (found || chunk_size>0); if (!found && rdcc->nslots>0 && chunk_size<=rdcc->nbytes && (!ent || !ent->locked)) { /* * Add the chunk to the cache only if the slot is not already locked. * Preempt enough things from the cache to make room. */ if (ent) { #ifdef H5D_ISTORE_DEBUG HDputc('#', stderr); HDfflush(stderr); #endif if (H5D_istore_preempt(io_info, ent, TRUE)<0) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, NULL, "unable to preempt chunk from cache") } if (H5D_istore_prune(io_info, chunk_size)<0) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, NULL, "unable to preempt chunk(s) from cache") /* Create a new entry */ ent = H5FL_MALLOC(H5D_rdcc_ent_t); ent->locked = 0; ent->dirty = FALSE; ent->chunk_size = chunk_size; ent->alloc_size = chunk_size; for (u=0; u<layout->u.chunk.ndims; u++) ent->offset[u] = io_info->store->chunk.offset[u]; ent->rd_count = chunk_size; ent->wr_count = chunk_size; ent->chunk = chunk; /* Add it to the cache */ assert(NULL==rdcc->slot[idx]); rdcc->slot[idx] = ent; ent->idx = idx; rdcc->nbytes += chunk_size; rdcc->nused++; /* Add it to the linked list */ ent->next = NULL; if (rdcc->tail) { rdcc->tail->next = ent; ent->prev = rdcc->tail; rdcc->tail = ent; } else { rdcc->head = rdcc->tail = ent; ent->prev = NULL; } found = TRUE; } else if (!found) { /* * The chunk is larger than the entire cache so we don't cache it. * This is the reason all those arguments have to be repeated for the * unlock function. */ ent = NULL; idx = UINT_MAX; } else { /* * The chunk is not at the beginning of the cache; move it backward * by one slot. This is how we implement the LRU preemption * algorithm. */ assert(ent); if (ent->next) { if (ent->next->next) ent->next->next->prev = ent; else rdcc->tail = ent; ent->next->prev = ent->prev; if (ent->prev) ent->prev->next = ent->next; else rdcc->head = ent->next; ent->prev = ent->next; ent->next = ent->next->next; ent->prev->next = ent; } } /* Lock the chunk into the cache */ if (ent) { assert (!ent->locked); ent->locked = TRUE; chunk = ent->chunk; } if (idx_hint) *idx_hint = idx; /* Set return value */ ret_value = chunk; done: if (!ret_value) if(chunk) chunk=H5D_istore_chunk_xfree (chunk,pline); FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_lock() */ /*------------------------------------------------------------------------- * Function: H5D_istore_unlock * * Purpose: Unlocks a previously locked chunk. The LAYOUT, COMP, and * OFFSET arguments should be the same as for H5F_rdcc_lock(). * The DIRTY argument should be set to non-zero if the chunk has * been modified since it was locked. The IDX_HINT argument is * the returned index hint from the lock operation and BUF is * the return value from the lock. * * The NACCESSED argument should be the number of bytes accessed * for reading or writing (depending on the value of DIRTY). * It's only purpose is to provide additional information to the * preemption policy. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Thursday, May 21, 1998 * *------------------------------------------------------------------------- */ static herr_t H5D_istore_unlock(const H5D_io_info_t *io_info, hbool_t dirty, unsigned idx_hint, uint8_t *chunk, size_t naccessed) { const H5O_layout_t *layout=&(io_info->dset->shared->layout); /* Dataset layout */ const H5D_rdcc_t *rdcc = &(io_info->dset->shared->cache.chunk); H5D_rdcc_ent_t *ent = NULL; unsigned u; herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_istore_unlock) assert(io_info); if (UINT_MAX==idx_hint) { /* * It's not in the cache, probably because it's too big. If it's * dirty then flush it to disk. In any case, free the chunk. * Note: we have to copy the layout and filter messages so we * don't discard the `const' qualifier. */ if (dirty) { H5D_rdcc_ent_t x; HDmemset (&x, 0, sizeof x); x.dirty = TRUE; for (u=0; u<layout->u.chunk.ndims; u++) x.offset[u] = io_info->store->chunk.offset[u]; assert(layout->u.chunk.size>0); H5_ASSIGN_OVERFLOW(x.chunk_size,layout->u.chunk.size,hsize_t,size_t); x.alloc_size = x.chunk_size; x.chunk = chunk; if (H5D_istore_flush_entry(io_info, &x, TRUE)<0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer") } else { if(chunk) chunk=H5D_istore_chunk_xfree (chunk,&(io_info->dset->shared->dcpl_cache.pline)); } } else { /* Sanity check */ assert(idx_hint<rdcc->nslots); assert(rdcc->slot[idx_hint]); assert(rdcc->slot[idx_hint]->chunk==chunk); /* * It's in the cache so unlock it. */ ent = rdcc->slot[idx_hint]; assert (ent->locked); if (dirty) { ent->dirty = TRUE; ent->wr_count -= MIN (ent->wr_count, naccessed); } else { ent->rd_count -= MIN (ent->rd_count, naccessed); } ent->locked = FALSE; } done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_unlock() */ /*------------------------------------------------------------------------- * Function: H5D_istore_readvv * * Purpose: Reads a multi-dimensional buffer from (part of) an indexed raw * storage array. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Wednesday, May 7, 2003 * *------------------------------------------------------------------------- */ ssize_t H5D_istore_readvv(const H5D_io_info_t *io_info, size_t chunk_max_nseq, size_t *chunk_curr_seq, size_t chunk_len_arr[], hsize_t chunk_offset_arr[], size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[], void *buf) { H5D_t *dset=io_info->dset; /* Local pointer to the dataset info */ H5D_istore_ud1_t udata; /*B-tree pass-through */ haddr_t chunk_addr; /* Chunk address on disk */ size_t u; /* Local index variables */ ssize_t ret_value; /* Return value */ FUNC_ENTER_NOAPI(H5D_istore_readvv, FAIL) /* Check args */ HDassert(io_info); HDassert(dset && H5D_CHUNKED==dset->shared->layout.type); HDassert(dset->shared->layout.u.chunk.ndims>0 && dset->shared->layout.u.chunk.ndims<=H5O_LAYOUT_NDIMS); HDassert(io_info->dxpl_cache); HDassert(io_info->store); HDassert(chunk_len_arr); HDassert(chunk_offset_arr); HDassert(mem_len_arr); HDassert(mem_offset_arr); HDassert(buf); /* Get the address of this chunk on disk */ #ifdef QAK HDfprintf(stderr,"%s: io_info->store->chunk.offset={",FUNC); for(u=0; u<dset->shared->layout.u.chunk.ndims; u++) HDfprintf(stderr,"%Hd%s",io_info->store->chunk.offset[u],(u<(dset->shared->layout.u.chunk.ndims-1) ? ", " : "}\n")); #endif /* QAK */ chunk_addr = H5D_istore_get_addr(io_info, &udata); #ifdef QAK HDfprintf(stderr,"%s: chunk_addr=%a, chunk_size=%Zu\n",FUNC,chunk_addr,dset->shared->layout.u.chunk.size); HDfprintf(stderr,"%s: chunk_len_arr[%Zu]=%Zu\n",FUNC,*chunk_curr_seq,chunk_len_arr[*chunk_curr_seq]); HDfprintf(stderr,"%s: chunk_offset_arr[%Zu]=%Hu\n",FUNC,*chunk_curr_seq,chunk_offset_arr[*chunk_curr_seq]); HDfprintf(stderr,"%s: mem_len_arr[%Zu]=%Zu\n",FUNC,*mem_curr_seq,mem_len_arr[*mem_curr_seq]); HDfprintf(stderr,"%s: mem_offset_arr[%Zu]=%Hu\n",FUNC,*mem_curr_seq,mem_offset_arr[*mem_curr_seq]); HDfprintf(stderr,"%s: buf=%p\n",FUNC,buf); #endif /* QAK */ /* * If the chunk is too large to load into the cache and it has no * filters in the pipeline (i.e. not compressed) and if the address * for the chunk has been defined, then don't load the chunk into the * cache, just read the data from it directly. * * If MPI based VFD is used, must bypass the * chunk-cache scheme because other MPI processes could be * writing to other elements in the same chunk. Do a direct * read-through of only the elements requested. */ if (dset->shared->dcpl_cache.pline.nused==0 && ((dset->shared->layout.u.chunk.size>dset->shared->cache.chunk.nbytes && chunk_addr!=HADDR_UNDEF) || (IS_H5FD_MPI(dset->oloc.file) && (H5F_ACC_RDWR & H5F_get_intent(dset->oloc.file))))) { H5D_io_info_t chk_io_info; /* Temporary I/O info object */ H5D_storage_t chk_store; /* Chunk storage information */ /* Set up the storage information for the chunk */ chk_store.contig.dset_addr=chunk_addr; chk_store.contig.dset_size=(hsize_t)dset->shared->layout.u.chunk.size; /* Set up new dataset I/O info */ H5D_BUILD_IO_INFO(&chk_io_info,dset,io_info->dxpl_cache,io_info->dxpl_id,&chk_store); /* Do I/O directly on chunk without reading it into the cache */ if ((ret_value=H5D_contig_readvv(&chk_io_info, chunk_max_nseq, chunk_curr_seq, chunk_len_arr, chunk_offset_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, buf))<0) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data to file") } /* end if */ else { uint8_t *chunk; /* Pointer to cached chunk in memory */ unsigned idx_hint=0; /* Cache index hint */ ssize_t naccessed; /* Number of bytes accessed in chunk */ /* If the chunk address is not defined, check if the fill value is * undefined also. If both situations hold, don't bother copying * values to the destination buffer, since they will just be * garbage. * * Ideally, this will eventually be checked at a higher level and * the entire I/O operation on the chunk will be skipped. -QAK */ if(!H5F_addr_defined(chunk_addr)) { const H5O_fill_t *fill=&(dset->shared->dcpl_cache.fill); /* Fill value info */ H5D_fill_time_t fill_time=dset->shared->dcpl_cache.fill_time; /* Fill time */ H5D_fill_value_t fill_status; H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk);/*raw data chunk cache*/ hbool_t found = FALSE; /*already in cache? */ /* Check if the chunk is in the cache (but hasn't been written to disk yet) */ if (rdcc->nslots>0) { unsigned idx=H5D_HASH(dset->shared, io_info->store->chunk.index); /* Cache entry index */ H5D_rdcc_ent_t *ent = rdcc->slot[idx]; /* Cache entry */ /* Potential match... */ if (ent) { for (u=0, found=TRUE; u<dset->shared->layout.u.chunk.ndims; u++) { if (io_info->store->chunk.offset[u]!=ent->offset[u]) { found = FALSE; break; } /* end if */ } /* end for */ } /* end if */ } /* end if */ /* If the chunk is in the cache, then it must have valid data */ if(!found) { /* Check if the fill value is defined */ if (H5P_is_fill_value_defined(fill, &fill_status) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined") /* If we are never to return fill values, or if we would return them * but they aren't set, process the entire set of I/O vectors and * get out now. */ if(fill_time==H5D_FILL_TIME_NEVER || (fill_time==H5D_FILL_TIME_IFSET && fill_status!=H5D_FILL_VALUE_USER_DEFINED)) { size_t size; /* Size of sequence in bytes */ size_t v; /* Local index variable */ ssize_t bytes_processed=0; /* Eventual return value */ /* Work through all the sequences */ for(u=*mem_curr_seq, v=*chunk_curr_seq; u<mem_max_nseq && v<chunk_max_nseq; ) { /* Choose smallest buffer to write */ if(chunk_len_arr[v]<mem_len_arr[u]) size=chunk_len_arr[v]; else size=mem_len_arr[u]; /* Update source information */ chunk_len_arr[v]-=size; chunk_offset_arr[v]+=size; if(chunk_len_arr[v]==0) v++; /* Update destination information */ mem_len_arr[u]-=size; mem_offset_arr[u]+=size; if(mem_len_arr[u]==0) u++; /* Increment number of bytes copied */ bytes_processed+=(ssize_t)size; } /* end for */ /* Update current sequence vectors */ *mem_curr_seq=u; *chunk_curr_seq=v; HGOTO_DONE(bytes_processed) } /* end if */ } /* end if */ } /* end if */ /* * Lock the chunk, copy from application to chunk, then unlock the * chunk. */ if (NULL==(chunk=H5D_istore_lock(io_info, &udata, FALSE, &idx_hint))) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk") /* Use the vectorized memory copy routine to do actual work */ if((naccessed=H5V_memcpyvv(buf,mem_max_nseq,mem_curr_seq,mem_len_arr,mem_offset_arr,chunk,chunk_max_nseq,chunk_curr_seq,chunk_len_arr,chunk_offset_arr))<0) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "vectorized memcpy failed") H5_CHECK_OVERFLOW(naccessed,ssize_t,size_t); if (H5D_istore_unlock(io_info, FALSE, idx_hint, chunk, (size_t)naccessed)<0) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk") /* Set return value */ ret_value=naccessed; } /* end else */ done: FUNC_LEAVE_NOAPI(ret_value) } /* H5D_istore_readvv() */ /*------------------------------------------------------------------------- * Function: H5D_istore_writevv * * Purpose: Writes a multi-dimensional buffer to (part of) an indexed raw * storage array. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Friday, May 2, 2003 * *------------------------------------------------------------------------- */ ssize_t H5D_istore_writevv(const H5D_io_info_t *io_info, size_t chunk_max_nseq, size_t *chunk_curr_seq, size_t chunk_len_arr[], hsize_t chunk_offset_arr[], size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[], const void *buf) { H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */ H5D_istore_ud1_t udata; /*B-tree pass-through */ haddr_t chunk_addr; /* Chunk address on disk */ size_t u; /* Local index variables */ ssize_t ret_value; /* Return value */ FUNC_ENTER_NOAPI(H5D_istore_writevv, FAIL) /* Check args */ HDassert(io_info); HDassert(dset && H5D_CHUNKED==dset->shared->layout.type); HDassert(dset->shared->layout.u.chunk.ndims>0 && dset->shared->layout.u.chunk.ndims<=H5O_LAYOUT_NDIMS); HDassert(io_info->dxpl_cache); HDassert(io_info->store); HDassert(chunk_len_arr); HDassert(chunk_offset_arr); HDassert(mem_len_arr); HDassert(mem_offset_arr); HDassert(buf); /* Get the address of this chunk on disk */ #ifdef QAK HDfprintf(stderr,"%s: io_info->store->chunk.offset={",FUNC); for(u=0; u<dset->shared->layout.u.chunk.ndims; u++) HDfprintf(stderr,"%Hd%s",io_info->store->chunk.offset[u],(u<(dset->shared->layout.u.chunk.ndims-1) ? ", " : "}\n")); #endif /* QAK */ chunk_addr = H5D_istore_get_addr(io_info, &udata); #ifdef QAK HDfprintf(stderr,"%s: chunk_addr=%a, chunk_size=%Zu\n",FUNC,chunk_addr,dset->shared->layout.u.chunk.size); HDfprintf(stderr,"%s: chunk_len_arr[%Zu]=%Zu\n",FUNC,*chunk_curr_seq,chunk_len_arr[*chunk_curr_seq]); HDfprintf(stderr,"%s: chunk_offset_arr[%Zu]=%Hu\n",FUNC,*chunk_curr_seq,chunk_offset_arr[*chunk_curr_seq]); HDfprintf(stderr,"%s: mem_len_arr[%Zu]=%Zu\n",FUNC,*mem_curr_seq,mem_len_arr[*mem_curr_seq]); HDfprintf(stderr,"%s: mem_offset_arr[%Zu]=%Hu\n",FUNC,*mem_curr_seq,mem_offset_arr[*mem_curr_seq]); #endif /* QAK */ /* * If the chunk is too large to load into the cache and it has no * filters in the pipeline (i.e. not compressed) and if the address * for the chunk has been defined, then don't load the chunk into the * cache, just write the data to it directly. * * If MPI based VFD is used, must bypass the * chunk-cache scheme because other MPI processes could be * writing to other elements in the same chunk. Do a direct * write-through of only the elements requested. */ #ifdef H5_HAVE_PARALLEL /* Additional sanity checks when operating in parallel */ if(IS_H5FD_MPI(dset->oloc.file)) { if (chunk_addr==HADDR_UNDEF) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to locate raw data chunk") if (dset->shared->dcpl_cache.pline.nused>0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot write to chunked storage with filters in parallel") } /* end if */ #endif /* H5_HAVE_PARALLEL */ if (dset->shared->dcpl_cache.pline.nused==0 && ((dset->shared->layout.u.chunk.size>dset->shared->cache.chunk.nbytes && chunk_addr!=HADDR_UNDEF) || (IS_H5FD_MPI(dset->oloc.file) && (H5F_ACC_RDWR & H5F_get_intent(dset->oloc.file))))) { H5D_io_info_t chk_io_info; /* Temporary I/O info object */ H5D_storage_t chk_store; /* Chunk storage information */ /* Set up the storage information for the chunk */ chk_store.contig.dset_addr=chunk_addr; chk_store.contig.dset_size=(hsize_t)dset->shared->layout.u.chunk.size; /* Set up new dataset I/O info */ H5D_BUILD_IO_INFO(&chk_io_info,dset,io_info->dxpl_cache,io_info->dxpl_id,&chk_store); /* Do I/O directly on chunk without reading it into the cache */ if ((ret_value=H5D_contig_writevv(&chk_io_info, chunk_max_nseq, chunk_curr_seq, chunk_len_arr, chunk_offset_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, buf))<0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file") } /* end if */ else { uint8_t *chunk; /* Pointer to cached chunk in memory */ unsigned idx_hint=0; /* Cache index hint */ ssize_t naccessed; /* Number of bytes accessed in chunk */ size_t total_bytes; /* Total # of bytes accessed on disk & memory */ hbool_t relax; /* Whether whole chunk is selected */ /* * Lock the chunk, copy from application to chunk, then unlock the * chunk. */ #ifdef OLD_WAY /* Note that this is technically OK, since eventually all the data in the chunk * will be overwritten. However, it seems risky and a better approach would * be to lock the chunk in the dataset I/O routine (setting the relax flag * appropriately) and then unlock it after all the I/O the chunk was finished. -QAK */ if(chunk_max_nseq==1 && chunk_len_arr[0] == dset->shared->layout.u.chunk.size) relax = TRUE; else relax = FALSE; #else /* OLD_WAY */ relax=TRUE; total_bytes=0; for(u=*chunk_curr_seq; u<chunk_max_nseq; u++) total_bytes+=chunk_len_arr[u]; if(total_bytes!=dset->shared->layout.u.chunk.size) relax=FALSE; if(relax) { total_bytes=0; for(u=*mem_curr_seq; u<mem_max_nseq; u++) total_bytes+=mem_len_arr[u]; if(total_bytes!=dset->shared->layout.u.chunk.size) relax=FALSE; } /* end if */ #endif /* OLD_WAY */ if (NULL==(chunk=H5D_istore_lock(io_info, &udata, relax, &idx_hint))) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to read raw data chunk") /* Use the vectorized memory copy routine to do actual work */ if((naccessed=H5V_memcpyvv(chunk,chunk_max_nseq,chunk_curr_seq,chunk_len_arr,chunk_offset_arr,buf,mem_max_nseq,mem_curr_seq,mem_len_arr,mem_offset_arr))<0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vectorized memcpy failed") H5_CHECK_OVERFLOW(naccessed,ssize_t,size_t); if (H5D_istore_unlock(io_info, TRUE, idx_hint, chunk, (size_t)naccessed)<0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "uanble to unlock raw data chunk") /* Set return value */ ret_value=naccessed; } /* end else */ done: FUNC_LEAVE_NOAPI(ret_value) } /* H5D_istore_writevv() */ /*------------------------------------------------------------------------- * Function: H5D_istore_create * * Purpose: Creates a new indexed-storage B-tree and initializes the * istore struct with information about the storage. The * struct should be immediately written to the object header. * * This function must be called before passing ISTORE to any of * the other indexed storage functions! * * Return: Non-negative on success (with the ISTORE argument initialized * and ready to write to an object header). Negative on failure. * * Programmer: Robb Matzke * Tuesday, October 21, 1997 * *------------------------------------------------------------------------- */ herr_t H5D_istore_create(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout /*out */) { H5D_istore_ud0_t udata; #ifndef NDEBUG unsigned u; #endif herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_istore_create, FAIL) /* Check args */ HDassert(f); HDassert(layout && H5D_CHUNKED == layout->type); HDassert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS); #ifndef NDEBUG for(u = 0; u < layout->u.chunk.ndims; u++) HDassert(layout->u.chunk.dim[u] > 0); #endif /* Initialize "user" data for B-tree callbacks, etc. */ udata.mesg = layout; if(H5B_create(f, dxpl_id, H5B_ISTORE, &udata, &(layout->u.chunk.addr)/*out*/) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "can't create B-tree") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_create() */ /*------------------------------------------------------------------------- * Function: H5D_istore_allocated * * Purpose: Return the number of bytes allocated in the file for storage * of raw data under the specified B-tree (ADDR is the address * of the B-tree). * * Return: Success: Number of bytes stored in all chunks. * * Failure: 0 * * Programmer: Robb Matzke * Wednesday, April 21, 1999 * *------------------------------------------------------------------------- */ hsize_t H5D_istore_allocated(H5D_t *dset, hid_t dxpl_id) { H5D_io_info_t io_info; /* Temporary I/O info object */ const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache */ H5D_rdcc_ent_t *ent; /*cache entry */ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ H5D_dxpl_cache_t *dxpl_cache=&_dxpl_cache; /* Data transfer property cache */ H5D_istore_it_ud1_t udata; hsize_t ret_value; /* Return value */ FUNC_ENTER_NOAPI(H5D_istore_allocated, 0) HDassert(dset); /* Fill the DXPL cache values for later use */ if (H5D_get_dxpl_cache(dxpl_id,&dxpl_cache)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, 0, "can't fill dxpl cache") /* Construct dataset I/O info */ H5D_BUILD_IO_INFO(&io_info,dset,dxpl_cache,dxpl_id,NULL); /* Search for cached chunks that haven't been written out */ for(ent = rdcc->head; ent; ent = ent->next) { /* Flush the chunk out to disk, to make certain the size is correct later */ if (H5D_istore_flush_entry(&io_info, ent, FALSE)<0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, 0, "cannot flush indexed storage buffer") } /* end for */ HDmemset(&udata, 0, sizeof udata); udata.common.mesg = &dset->shared->layout; if(H5B_iterate(dset->oloc.file, dxpl_id, H5B_ISTORE, H5D_istore_iter_allocated, dset->shared->layout.u.chunk.addr, &udata) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, 0, "unable to iterate over chunk B-tree") /* Set return value */ ret_value = udata.total_storage; done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_allocated() */ /*------------------------------------------------------------------------- * Function: H5D_istore_chunkmap * * Purpose: obtain the chunk address and corresponding chunk index * * Return: Success: Non-negative on succeed. * * Failure: negative value * * Programmer: Kent Yang * November 15, 2005 * *------------------------------------------------------------------------- */ herr_t H5D_istore_chunkmap(const H5D_io_info_t *io_info, haddr_t chunk_addr[],hsize_t down_chunks[]) { H5D_t *dset=io_info->dset; /* Local pointer to dataset info */ #if 0 const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache */ H5D_rdcc_ent_t *ent; /*cache entry */ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ H5D_dxpl_cache_t *dxpl_cache=&_dxpl_cache; /* Data transfer property cache */ #endif H5D_istore_it_ud5_t udata; hid_t dxpl_id = io_info->dxpl_id; herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_istore_chunkmap, FAIL) HDassert(dset); #if 0 /* Fill the DXPL cache values for later use */ if (H5D_get_dxpl_cache(dxpl_id,&dxpl_cache)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache") /* Construct dataset I/O info */ H5D_BUILD_IO_INFO(&io_info,dset,dxpl_cache,dxpl_id,NULL); /* Search for cached chunks that haven't been written out */ for(ent = rdcc->head; ent; ent = ent->next) { /* Flush the chunk out to disk, to make certain the size is correct later */ if (H5D_istore_flush_entry(&io_info, ent, FALSE)<0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer") } /* end for */ #endif HDmemset(&udata, 0, sizeof udata); udata.common.mesg = &dset->shared->layout; udata.down_chunks = down_chunks; udata.chunk_addr = chunk_addr; if (H5B_iterate(dset->oloc.file, dxpl_id, H5B_ISTORE, H5D_istore_iter_chunkmap, dset->shared->layout.u.chunk.addr, &udata)<0) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to iterate over chunk B-tree") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_chunkmap() */ /*------------------------------------------------------------------------- * Function: H5D_istore_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: Albert Cheng * June 27, 1998 * *------------------------------------------------------------------------- */ haddr_t H5D_istore_get_addr(const H5D_io_info_t *io_info, H5D_istore_ud1_t *_udata) { H5D_istore_ud1_t tmp_udata; /* Information about a chunk */ H5D_istore_ud1_t *udata; /* Pointer to information about a chunk */ unsigned u; haddr_t ret_value; /* Return value */ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_get_addr) HDassert(io_info); HDassert(io_info->dset); HDassert(io_info->dset->shared->layout.u.chunk.ndims > 0); HDassert(io_info->store->chunk.offset); /* Check for udata struct to return */ udata = (_udata != NULL ? _udata : &tmp_udata); /* Initialize the information about the chunk we are looking for */ for(u = 0; u < io_info->dset->shared->layout.u.chunk.ndims; u++) udata->common.key.offset[u] = io_info->store->chunk.offset[u]; udata->common.mesg = &(io_info->dset->shared->layout); udata->addr = HADDR_UNDEF; /* Go get the chunk information */ if (H5B_find (io_info->dset->oloc.file, io_info->dxpl_id, H5B_ISTORE, io_info->dset->shared->layout.u.chunk.addr, udata)<0) { /* Note: don't push error on stack, leave that to next higher level, * since many times the B-tree is searched in order to determine * if a chunk exists in the B-tree or not. -QAK */ #ifdef OLD_WAY H5E_clear_stack(NULL); HGOTO_ERROR(H5E_BTREE,H5E_NOTFOUND,HADDR_UNDEF,"Can't locate chunk info") #else /* OLD_WAY */ HGOTO_DONE(HADDR_UNDEF) #endif /* OLD_WAY */ } /* end if */ /* Success! Set the return value */ ret_value=udata->addr; done: FUNC_LEAVE_NOAPI(ret_value) } /* H5D_istore_get_addr() */ /*------------------------------------------------------------------------- * Function: H5D_istore_chunk_alloc * * Purpose: Allocate space for a chunk in memory. This routine allocates * memory space for non-filtered chunks from a block free list * and uses malloc()/free() for filtered chunks. * * Return: Pointer to memory for chunk on success/NULL on failure * * Programmer: Quincey Koziol * April 22, 2004 * *------------------------------------------------------------------------- */ static void * H5D_istore_chunk_alloc(size_t size, const H5O_pline_t *pline) { void *ret_value = NULL; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_istore_chunk_alloc) HDassert(size); HDassert(pline); if(pline->nused > 0) ret_value = H5MM_malloc(size); else ret_value = H5FL_BLK_MALLOC(chunk, size); FUNC_LEAVE_NOAPI(ret_value) } /* H5D_istore_chunk_alloc() */ /*------------------------------------------------------------------------- * Function: H5D_istore_chunk_xfree * * Purpose: Free space for a chunk in memory. This routine allocates * memory space for non-filtered chunks from a block free list * and uses malloc()/free() for filtered chunks. * * Return: NULL (never fails) * * Programmer: Quincey Koziol * April 22, 2004 * *------------------------------------------------------------------------- */ static void * H5D_istore_chunk_xfree(void *chk, const H5O_pline_t *pline) { FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_istore_chunk_xfree) assert(pline); if(chk) { if(pline->nused>0) H5MM_xfree(chk); else H5FL_BLK_FREE(chunk,chk); } /* end if */ FUNC_LEAVE_NOAPI(NULL) } /* H5D_istore_chunk_xfree() */ /*------------------------------------------------------------------------- * Function: H5D_istore_allocate * * Purpose: Allocate file space for all chunks that are not allocated yet. * Return SUCCEED if all needed allocation succeed, otherwise * FAIL. * * Return: Non-negative on success/Negative on failure * * Note: Current implementation relies on cache_size being 0, * thus no chunk is cashed and written to disk immediately * when a chunk is unlocked (via H5F_istore_unlock) * This should be changed to do a direct flush independent * of the cache value. * * This routine might be called before the dcpl_cache is set up * correctly, so don't use those values. * * Programmer: Albert Cheng * June 26, 1998 * *------------------------------------------------------------------------- */ herr_t H5D_istore_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite) { H5D_io_info_t io_info; /* Dataset I/O info */ H5D_storage_t store; /* Dataset storage information */ hsize_t chunk_offset[H5O_LAYOUT_NDIMS]; /* Offset of current chunk */ hsize_t chunk_size; /* Size of chunk in bytes */ unsigned filter_mask=0; /* Filter mask for chunks that have them */ H5O_pline_t pline; /* I/O pipeline information */ hbool_t pline_initialized=FALSE; /* Flag to indicate that pline has valid info */ H5O_fill_t fill; /* Fill value information */ H5D_fill_time_t fill_time; /* When to write fill values */ H5D_fill_value_t fill_status; /* The fill value status */ unsigned should_fill=0; /* Whether fill values should be written */ void *chunk=NULL; /* Chunk buffer for writing fill values */ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ H5D_dxpl_cache_t *dxpl_cache=&_dxpl_cache; /* Data transfer property cache */ #ifdef H5_HAVE_PARALLEL MPI_Comm mpi_comm=MPI_COMM_NULL; /* MPI communicator for file */ int mpi_rank=(-1); /* This process's rank */ int mpi_code; /* MPI return code */ unsigned blocks_written=0; /* Flag to indicate that chunk was actually written */ unsigned using_mpi=0; /* Flag to indicate that the file is being accessed with an MPI-capable file driver */ #endif /* H5_HAVE_PARALLEL */ int carry; /* Flag to indicate that chunk increment carrys to higher dimension (sorta) */ unsigned chunk_exists; /* Flag to indicate whether a chunk exists already */ int i; /* Local index variable */ unsigned u; /* Local index variable */ H5P_genplist_t *dc_plist; /* Property list */ int space_ndims; /* Dataset's space rank */ hsize_t space_dim[H5O_LAYOUT_NDIMS]; /* Dataset's dataspace dimensions */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_istore_allocate, FAIL) /* Check args */ assert(dset && H5D_CHUNKED==dset->shared->layout.type); assert(dset->shared->layout.u.chunk.ndims>0 && dset->shared->layout.u.chunk.ndims<=H5O_LAYOUT_NDIMS); assert(H5F_addr_defined(dset->shared->layout.u.chunk.addr)); assert(TRUE==H5P_isa_class(dxpl_id,H5P_DATASET_XFER)); /* Get dataset's creation property list */ if (NULL == (dc_plist = H5I_object(dset->shared->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list") /* We only handle simple data spaces so far */ if ((space_ndims=H5S_get_simple_extent_dims(dset->shared->space, space_dim, NULL))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get simple data space info") space_dim[space_ndims] = dset->shared->layout.u.chunk.dim[space_ndims]; /* Get necessary properties from dataset creation property list */ if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0) HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL, "can't get fill value") if(H5P_get(dc_plist, H5D_CRT_DATA_PIPELINE_NAME, &pline) < 0) HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL, "can't get data pipeline") pline_initialized=TRUE; if(H5P_get(dc_plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve fill time") /* Fill the DXPL cache values for later use */ if (H5D_get_dxpl_cache(dxpl_id,&dxpl_cache)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache") #ifdef H5_HAVE_PARALLEL /* Retrieve MPI parameters */ if(IS_H5FD_MPI(dset->oloc.file)) { /* Get the MPI communicator */ if(MPI_COMM_NULL == (mpi_comm = H5F_mpi_get_comm(dset->oloc.file))) HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator") /* Get the MPI rank */ if((mpi_rank = H5F_mpi_get_rank(dset->oloc.file))<0) HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank") /* Set the MPI-capable file driver flag */ using_mpi=1; } /* end if */ #endif /* H5_HAVE_PARALLEL */ /* * Setup indice to go through all chunks. (Future improvement * should allocate only chunks that have no file space assigned yet. */ for (u=0; u<dset->shared->layout.u.chunk.ndims; u++) chunk_offset[u] = 0; chunk_size = dset->shared->layout.u.chunk.size; /* Check the dataset's fill-value status */ if (H5P_is_fill_value_defined(&fill, &fill_status) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined") /* If we are filling the dataset on allocation or "if set" and * the fill value _is_ set, _and_ we are not overwriting the new blocks, * or if there are any pipeline filters defined, * set the "should fill" flag */ if((!full_overwrite && (fill_time == H5D_FILL_TIME_ALLOC || (fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED))) || pline.nused > 0) should_fill = 1; /* Check if fill values should be written to blocks */ if(should_fill) { /* Allocate chunk buffer for processes to use when writing fill values */ H5_CHECK_OVERFLOW(chunk_size, hsize_t, size_t); if(NULL == (chunk = H5D_istore_chunk_alloc((size_t)chunk_size, &pline))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for chunk") /* Fill the chunk with the proper values */ if(fill.buf) { /* * Replicate the fill value throughout the chunk. */ assert(0==chunk_size % fill.size); H5V_array_fill(chunk, fill.buf, fill.size, (size_t)chunk_size/fill.size); } else { /* * No fill value was specified, assume all zeros. */ HDmemset (chunk, 0, (size_t)chunk_size); } /* end else */ /* Check if there are filters which need to be applied to the chunk */ if (pline.nused>0) { size_t buf_size=(size_t)chunk_size; size_t nbytes=(size_t)chunk_size; /* Push the chunk through the filters */ if (H5Z_pipeline(&pline, 0, &filter_mask, dxpl_cache->err_detect, dxpl_cache->filter_cb, &nbytes, &buf_size, &chunk)<0) HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "output pipeline failed") /* Keep the number of bytes the chunk turned in to */ chunk_size=nbytes; } /* end if */ } /* end if */ /* Set up dataset I/O info */ store.chunk.offset=chunk_offset; H5D_BUILD_IO_INFO(&io_info,dset,dxpl_cache,dxpl_id,&store); /* Loop over all chunks */ carry=0; while (carry==0) { /* Check if the chunk exists yet on disk */ chunk_exists=1; if(H5D_istore_get_addr(&io_info,NULL)==HADDR_UNDEF) { const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache */ H5D_rdcc_ent_t *ent = NULL; /*cache entry */ /* Didn't find the chunk on disk */ chunk_exists = 0; /* Look for chunk in cache */ for(ent = rdcc->head; ent && !chunk_exists; ent = ent->next) { /* Assume a match */ chunk_exists = 1; for(u = 0; u < dset->shared->layout.u.chunk.ndims && chunk_exists; u++) { if(ent->offset[u] != chunk_offset[u]) chunk_exists = 0; /* Reset if no match */ } /* end for */ } /* end for */ } /* end if */ if(!chunk_exists) { H5D_istore_ud1_t udata; /* B-tree pass-through for creating chunk */ /* Initialize the chunk information */ udata.common.mesg = &dset->shared->layout; udata.common.key.filter_mask = filter_mask; udata.addr = HADDR_UNDEF; H5_CHECK_OVERFLOW(chunk_size,hsize_t,size_t); udata.common.key.nbytes = (size_t)chunk_size; for(u = 0; u < dset->shared->layout.u.chunk.ndims; u++) udata.common.key.offset[u] = chunk_offset[u]; /* Allocate the chunk with all processes */ if(H5B_insert(dset->oloc.file, dxpl_id, H5B_ISTORE, dset->shared->layout.u.chunk.addr, &udata)<0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to allocate chunk") /* Check if fill values should be written to blocks */ if(should_fill) { #ifdef H5_HAVE_PARALLEL /* Check if this file is accessed with an MPI-capable file driver */ if(using_mpi) { /* Write the chunks out from only one process */ /* !! Use the internal "independent" DXPL!! -QAK */ if(H5_PAR_META_WRITE==mpi_rank) { if(H5F_block_write(dset->oloc.file, H5FD_MEM_DRAW, udata.addr, udata.common.key.nbytes, H5AC_ind_dxpl_id, chunk) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file") } /* end if */ /* Indicate that blocks are being written */ blocks_written=1; } /* end if */ else { #endif /* H5_HAVE_PARALLEL */ if(H5F_block_write(dset->oloc.file, H5FD_MEM_DRAW, udata.addr, udata.common.key.nbytes, dxpl_id, chunk) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file") #ifdef H5_HAVE_PARALLEL } /* end else */ #endif /* H5_HAVE_PARALLEL */ } /* end if */ } /* end if */ /* Increment indices */ for (i=(int)dset->shared->layout.u.chunk.ndims-1, carry=1; i>=0 && carry; --i) { chunk_offset[i] += dset->shared->layout.u.chunk.dim[i]; if (chunk_offset[i] >= space_dim[i]) chunk_offset[i] = 0; else carry = 0; } /* end for */ } /* end while */ #ifdef H5_HAVE_PARALLEL /* Only need to block at the barrier if we actually allocated a chunk */ /* And if we are using an MPI-capable file driver */ if(using_mpi && blocks_written) { /* Wait at barrier to avoid race conditions where some processes are * still writing out chunks and other processes race ahead to read * them in, getting bogus data. */ if (MPI_SUCCESS != (mpi_code=MPI_Barrier(mpi_comm))) HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code); } /* end if */ #endif /* H5_HAVE_PARALLEL */ done: /* Free the chunk for fill values */ if(chunk!=NULL && pline_initialized) chunk=H5D_istore_chunk_xfree(chunk,&pline); FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_allocate() */ /*------------------------------------------------------------------------- * Function: H5D_istore_prune_by_extent * * Purpose: This function searches for chunks that are no longer necessary both in the * raw data cache and in the B-tree. * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * Algorithm: Robb Matzke * * Date: March 27, 2002 * * The algorithm is: * * For chunks that are no longer necessary: * * 1. Search in the raw data cache for each chunk * 2. If found then preempt it from the cache * 3. Search in the B-tree for each chunk * 4. If found then remove it from the B-tree and deallocate file storage for the chunk * * This example shows a 2d dataset of 90x90 with a chunk size of 20x20. * * * 0 20 40 60 80 90 100 * 0 +---------+---------+---------+---------+-----+...+ * |:::::X:::::::::::::: : : | : * |:::::::X:::::::::::: : : | : Key * |::::::::::X::::::::: : : | : -------- * |::::::::::::X::::::: : : | : +-+ Dataset * 20+::::::::::::::::::::.........:.........:.....+...: | | Extent * | :::::X::::: : : | : +-+ * | ::::::::::: : : | : * | ::::::::::: : : | : ... Chunk * | :::::::X::: : : | : : : Boundary * 40+.........:::::::::::.........:.........:.....+...: :.: * | : : : : | : * | : : : : | : ... Allocated * | : : : : | : ::: & Filled * | : : : : | : ::: Chunk * 60+.........:.........:.........:.........:.....+...: * | : :::::::X::: : | : X Element * | : ::::::::::: : | : Written * | : ::::::::::: : | : * | : ::::::::::: : | : * 80+.........:.........:::::::::::.........:.....+...: O Fill Val * | : : ::::::::::: | : Explicitly * | : : ::::::X:::: | : Written * 90+---------+---------+---------+---------+-----+ : * : : : ::::::::::: : * 100:.........:.........:.........:::::::::::.........: * * * We have 25 total chunks for this dataset, 5 of which have space * allocated in the file because they were written to one or more * elements. These five chunks (and only these five) also have entries in * the storage B-tree for this dataset. * * Now lets say we want to shrink the dataset down to 70x70: * * * 0 20 40 60 70 80 90 100 * 0 +---------+---------+---------+----+----+-----+...+ * |:::::X:::::::::::::: : | : | : * |:::::::X:::::::::::: : | : | : Key * |::::::::::X::::::::: : | : | : -------- * |::::::::::::X::::::: : | : | : +-+ Dataset * 20+::::::::::::::::::::.........:....+....:.....|...: | | Extent * | :::::X::::: : | : | : +-+ * | ::::::::::: : | : | : * | ::::::::::: : | : | : ... Chunk * | :::::::X::: : | : | : : : Boundary * 40+.........:::::::::::.........:....+....:.....|...: :.: * | : : : | : | : * | : : : | : | : ... Allocated * | : : : | : | : ::: & Filled * | : : : | : | : ::: Chunk * 60+.........:.........:.........:....+....:.....|...: * | : :::::::X::: | : | : X Element * | : ::::::::::: | : | : Written * +---------+---------+---------+----+ : | : * | : ::::::::::: : | : * 80+.........:.........:::::::::X:.........:.....|...: O Fill Val * | : : ::::::::::: | : Explicitly * | : : ::::::X:::: | : Written * 90+---------+---------+---------+---------+-----+ : * : : : ::::::::::: : * 100:.........:.........:.........:::::::::::.........: * * * That means that the nine chunks along the bottom and right side should * no longer exist. Of those nine chunks, (0,80), (20,80), (40,80), * (60,80), (80,80), (80,60), (80,40), (80,20), and (80,0), one is actually allocated * that needs to be released. * To release the chunks, we traverse the B-tree to obtain a list of unused * allocated chunks, and then call H5B_remove() for each chunk. * *------------------------------------------------------------------------- */ herr_t H5D_istore_prune_by_extent(const H5D_io_info_t *io_info) { H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */ const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache */ H5D_rdcc_ent_t *ent = NULL, *next = NULL; /*cache entry */ unsigned u; /*counters */ int found; /*remove this entry */ H5D_istore_it_ud3_t udata; /*B-tree pass-through */ hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /*current dataspace dimensions */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_istore_prune_by_extent, FAIL) /* Check args */ assert(io_info); assert(dset && H5D_CHUNKED == dset->shared->layout.type); assert(dset->shared->layout.u.chunk.ndims > 0 && dset->shared->layout.u.chunk.ndims <= H5O_LAYOUT_NDIMS); assert(H5F_addr_defined(dset->shared->layout.u.chunk.addr)); /* Go get the rank & dimensions */ if(H5S_get_simple_extent_dims(dset->shared->space, curr_dims, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions") /*------------------------------------------------------------------------- * Figure out what chunks are no longer in use for the specified extent * and release them from the linked list raw data cache *------------------------------------------------------------------------- */ found = 0; for(ent = rdcc->head; ent; ent = next) { next = ent->next; for(u = 0; u < dset->shared->layout.u.chunk.ndims - 1; u++) { if((hsize_t)ent->offset[u] > curr_dims[u]) { found = 1; break; } /* end if */ } /* end for */ if(found) { #ifdef H5D_ISTORE_DEBUG HDfputs("cache:remove:[", stderr); for(u = 0; u < dset->shared->layout.u.chunk.ndims - 1; u++) HDfprintf(stderr, "%s%Hd", u ? ", " : "", ent->offset[u]); HDfputs("]\n", stderr); #endif /* Preempt the entry from the cache, but do not flush it to disk */ if(H5D_istore_preempt(io_info, ent, FALSE) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, 0, "unable to preempt chunk") found=0; } } /*------------------------------------------------------------------------- * Check if there are any chunks on the B-tree *------------------------------------------------------------------------- */ HDmemset(&udata, 0, sizeof udata); udata.common.mesg = &dset->shared->layout; udata.dims = curr_dims; if(H5B_iterate(dset->oloc.file, io_info->dxpl_id, H5B_ISTORE, H5D_istore_prune_extent, dset->shared->layout.u.chunk.addr, &udata) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, 0, "unable to iterate over B-tree") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_prune_by_extent() */ /*------------------------------------------------------------------------- * Function: H5D_istore_prune_extent * * Purpose: Search for chunks that are no longer necessary in the B-tree. * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: March 26, 2002 * * Comments: Called by H5D_prune_by_extent * *------------------------------------------------------------------------- */ /* ARGSUSED */ static int H5D_istore_prune_extent(H5F_t *f, hid_t dxpl_id, const void *_lt_key, haddr_t UNUSED addr, const void UNUSED *_rt_key, void *_udata) { H5D_istore_it_ud3_t *udata = (H5D_istore_it_ud3_t *)_udata; const H5D_istore_key_t *lt_key = (const H5D_istore_key_t *)_lt_key; unsigned u; int ret_value = H5B_ITER_CONT; /* Return value */ /* The LT_KEY is the left key (the one that describes the chunk). It points to a chunk of * storage that contains the beginning of the logical address space represented by UDATA. */ FUNC_ENTER_NOAPI_NOINIT(H5D_istore_prune_extent) /* Figure out what chunks are no longer in use for the specified extent and release them */ for(u = 0; u < udata->common.mesg->u.chunk.ndims - 1; u++) if((hsize_t)lt_key->offset[u] > udata->dims[u]) { H5D_istore_ud0_t bt_udata; HDmemset(&bt_udata, 0, sizeof bt_udata); bt_udata.key = *lt_key; bt_udata.mesg = udata->common.mesg; /* Remove */ if(H5B_remove(f, dxpl_id, H5B_ISTORE, udata->common.mesg->u.chunk.addr, &bt_udata) < 0) HGOTO_ERROR(H5E_SYM, H5E_CANTINIT, H5B_ITER_ERROR, "unable to remove entry") break; } /* end if */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_prune_extent() */ /*------------------------------------------------------------------------- * Function: H5D_istore_remove * * Purpose: Removes chunks that are no longer necessary in the B-tree. * * Return: Success: 0, Failure: -1 * * Programmer: Robb Matzke * Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: March 28, 2002 * * Comments: Part of H5B_ISTORE * *------------------------------------------------------------------------- */ /* ARGSUSED */ static H5B_ins_t H5D_istore_remove(H5F_t *f, hid_t dxpl_id, haddr_t addr, void *_lt_key /*in,out */ , hbool_t *lt_key_changed /*out */ , void UNUSED * _udata /*in,out */ , void UNUSED * _rt_key /*in,out */ , hbool_t *rt_key_changed /*out */ ) { H5D_istore_key_t *lt_key = (H5D_istore_key_t *)_lt_key; H5B_ins_t ret_value=H5B_INS_REMOVE; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_istore_remove) /* Remove raw data chunk from file */ if(H5MF_xfree(f, H5FD_MEM_DRAW, dxpl_id, addr, (hsize_t)lt_key->nbytes)<0) HGOTO_ERROR(H5E_STORAGE, H5E_CANTFREE, H5B_INS_ERROR, "unable to free chunk") /* Mark keys as unchanged */ *lt_key_changed = FALSE; *rt_key_changed = FALSE; done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_remove() */ /*------------------------------------------------------------------------- * Function: H5D_istore_initialize_by_extent * * Purpose: This function searches for chunks that have to be initialized with the fill * value both in the raw data cache and in the B-tree. * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: April 4, 2002 * * Comments: * * (See the example of H5D_istore_prune_by_extent) * Next, there are seven chunks where the database extent boundary is * within the chunk. We find those seven just like we did with the previous nine. * Fot the ones that are allocated we initialize the part that lies outside the boundary * with the fill value. * *------------------------------------------------------------------------- */ herr_t H5D_istore_initialize_by_extent(H5D_io_info_t *io_info) { const H5O_layout_t *layout=&(io_info->dset->shared->layout); /* Dataset layout */ uint8_t *chunk = NULL; /*the file chunk */ unsigned idx_hint = 0; /*input value for H5F_istore_lock */ hsize_t chunk_offset[H5O_LAYOUT_NDIMS]; /*logical location of the chunks */ hsize_t idx_cur[H5O_LAYOUT_NDIMS]; /*multi-dimensional counters */ hsize_t idx_max[H5O_LAYOUT_NDIMS]; hsize_t sub_size[H5O_LAYOUT_NDIMS]; hsize_t naccessed; /*bytes accessed in chunk */ hsize_t end_chunk; /*chunk position counter */ hsize_t start[H5O_LAYOUT_NDIMS]; /*starting location of hyperslab */ hsize_t count[H5O_LAYOUT_NDIMS]; /*element count of hyperslab */ hsize_t size[H5O_LAYOUT_NDIMS]; /*current size of dimensions */ H5S_t *space_chunk = NULL; /*dataspace for a chunk */ hsize_t chunk_dims[H5O_LAYOUT_NDIMS]; /*current chunk dimensions */ hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /*current dataspace dimensions */ hsize_t chunks[H5O_LAYOUT_NDIMS]; /*current number of chunks in each dimension */ hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of elements in each dimension */ int srank; /*current # of dimensions (signed) */ unsigned rank; /*current # of dimensions */ int i, carry; /*counters */ unsigned u; int found = 0; /*initialize this entry */ H5P_genplist_t *dc_plist; /* Property list */ H5O_pline_t pline; /* I/O pipeline information */ H5O_fill_t fill; /* Fill value information */ H5D_fill_time_t fill_time; /* Fill time information */ H5D_storage_t store; /* Dataset storage information */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_istore_initialize_by_extent, FAIL) /* Check args */ assert(io_info); assert(io_info->dset && H5D_CHUNKED == layout->type); assert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS); assert(H5F_addr_defined(layout->u.chunk.addr)); /* Get dataset's creation property list */ if (NULL == (dc_plist = H5I_object(io_info->dset->shared->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list") /* Get necessary properties from property list */ if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get fill value") if(H5P_get(dc_plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get fill time") if(H5P_get(dc_plist, H5D_CRT_DATA_PIPELINE_NAME, &pline) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get data pipeline") /* Reset start & count arrays */ HDmemset(start, 0, sizeof(start)); HDmemset(count, 0, sizeof(count)); /* Go get the rank & dimensions */ if((srank = H5S_get_simple_extent_dims(io_info->dset->shared->space, curr_dims, NULL)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions"); H5_ASSIGN_OVERFLOW(rank,srank,int,unsigned); /* Copy current dimensions */ for(u = 0; u < rank; u++) { size[u] = curr_dims[u]; /* Round up to the next integer # of chunks, to accomodate partial chunks */ chunks[u] = ((curr_dims[u]+layout->u.chunk.dim[u])-1) / layout->u.chunk.dim[u]; } /* end for */ size[u] = layout->u.chunk.dim[u]; /* Get the "down" sizes for each dimension */ if(H5V_array_down(rank,chunks,down_chunks)<0) HGOTO_ERROR(H5E_INTERNAL, H5E_BADVALUE, FAIL, "can't compute 'down' sizes") /* Create a data space for a chunk & set the extent */ for(u = 0; u < rank; u++) chunk_dims[u] = layout->u.chunk.dim[u]; if(NULL == (space_chunk = H5S_create_simple(rank,chunk_dims,NULL))) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create simple dataspace") /* * Set up multi-dimensional counters (idx_max, and idx_cur) and * loop through the chunks copying each chunk from the application to the * chunk cache. */ for(u = 0; u < layout->u.chunk.ndims; u++) { idx_max[u] = (size[u] - 1) / layout->u.chunk.dim[u] + 1; idx_cur[u] = 0; } /* end for */ /* Point to local dataset storage info */ assert(io_info->store==NULL); /* Make certain we aren't blowing anything away */ io_info->store=&store; /* Loop over all chunks */ carry=0; while(carry==0) { for(u = 0, naccessed = 1; u < layout->u.chunk.ndims; u++) { /* The location and size of the chunk being accessed */ chunk_offset[u] = idx_cur[u] * layout->u.chunk.dim[u]; sub_size[u] = MIN((idx_cur[u] + 1) * layout->u.chunk.dim[u], size[u]) - chunk_offset[u]; naccessed *= sub_size[u]; } /* end for */ /* * Figure out what chunks have to be initialized. These are the chunks where the dataspace * extent boundary is within the chunk */ for(u = 0, found = 0; u < rank; u++) { end_chunk = chunk_offset[u] + layout->u.chunk.dim[u]; if(end_chunk > size[u]) { found = 1; break; } } /* end for */ if(found) { /* Calculate the index of this chunk */ if(H5V_chunk_index(rank,chunk_offset,layout->u.chunk.dim,down_chunks,&store.chunk.index)<0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") store.chunk.offset=chunk_offset; if(NULL == (chunk = H5D_istore_lock(io_info, NULL, FALSE, &idx_hint))) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to read raw data chunk") if(H5S_select_all(space_chunk,1) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to select space") for(u = 0; u < rank; u++) count[u] = MIN((idx_cur[u] + 1) * layout->u.chunk.dim[u], size[u] - chunk_offset[u]); #ifdef H5D_ISTORE_DEBUG HDfputs("cache:initialize:offset:[", stdout); for(u = 0; u < rank; u++) HDfprintf(stdout, "%s%Hd", u ? ", " : "", chunk_offset[u]); HDfputs("]", stdout); HDfputs(":count:[", stdout); for(u = 0; u < rank; u++) HDfprintf(stdout, "%s%Hd", u ? ", " : "", count[u]); HDfputs("]\n", stdout); #endif if(H5S_select_hyperslab(space_chunk, H5S_SELECT_NOTB, start, NULL, count, NULL) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to select hyperslab") /* Fill the selection in the memory buffer */ /* Use the size of the elements in the chunk directly instead of */ /* relying on the fill.size, which might be set to 0 if there is */ /* no fill-value defined for the dataset -QAK */ H5_CHECK_OVERFLOW(size[rank],hsize_t,size_t); if(H5S_select_fill(fill.buf, (size_t)size[rank], space_chunk, chunk) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "filling selection failed") if(H5D_istore_unlock(io_info, TRUE, idx_hint, chunk, (size_t)naccessed) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to unlock raw data chunk") } /*found */ /* Increment indices */ for(i = (int)rank, carry = 1; i >= 0 && carry; --i) { if(++idx_cur[i] >= idx_max[i]) idx_cur[i] = 0; else carry = 0; } /* end for */ } /* end while */ done: if(space_chunk) if(H5S_close(space_chunk)<0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataspace") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_initialize_by_extent() */ /*------------------------------------------------------------------------- * Function: H5D_istore_delete * * Purpose: Delete raw data storage for entire dataset (i.e. all chunks) * * Return: Success: Non-negative * Failure: negative * * Programmer: Quincey Koziol * Thursday, March 20, 2003 * *------------------------------------------------------------------------- */ herr_t H5D_istore_delete(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout) { herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_istore_delete, FAIL) /* Check if the B-tree has been created in the file */ if(H5F_addr_defined(layout->u.chunk.addr)) { H5O_layout_t tmp_layout=*layout;/* Local copy of layout info */ H5D_istore_ud0_t udata; /* User data for B-tree iterator call */ /* Set up user data for B-tree deletion */ HDmemset(&udata, 0, sizeof udata); udata.mesg = &tmp_layout; /* Allocate the shared structure */ if(H5D_istore_shared_create(f, &tmp_layout)<0) HGOTO_ERROR(H5E_RESOURCE, H5E_CANTINIT, FAIL, "can't create wrapper for shared B-tree info") /* Delete entire B-tree */ if(H5B_delete(f, dxpl_id, H5B_ISTORE, tmp_layout.u.chunk.addr, &udata)<0) HGOTO_ERROR(H5E_IO, H5E_CANTDELETE, 0, "unable to delete chunk B-tree") /* Free the raw B-tree node buffer */ if(tmp_layout.u.chunk.btree_shared==NULL) HGOTO_ERROR(H5E_IO, H5E_CANTFREE, FAIL, "ref-counted page nil") if(H5RC_DEC(tmp_layout.u.chunk.btree_shared)<0) HGOTO_ERROR(H5E_IO, H5E_CANTFREE, FAIL, "unable to decrement ref-counted page") } /* end if */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_delete() */ /*------------------------------------------------------------------------- * Function: H5D_istore_update_cache * * Purpose: Update any cached chunks index values after the dataspace * size has changed * * Return: Success: Non-negative * Failure: negative * * Programmer: Quincey Koziol * Saturday, May 29, 2004 * *------------------------------------------------------------------------- */ herr_t H5D_istore_update_cache(H5D_t *dset, hid_t dxpl_id) { H5D_io_info_t io_info; /* Temporary I/O info object */ H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache */ H5D_rdcc_ent_t *ent, *next; /*cache entry */ H5D_rdcc_ent_t *old_ent; /* Old cache entry */ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ H5D_dxpl_cache_t *dxpl_cache=&_dxpl_cache; /* Data transfer property cache */ unsigned rank; /*current # of dimensions */ hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /*current dataspace dimensions */ hsize_t chunks[H5O_LAYOUT_NDIMS]; /*current number of chunks in each dimension */ hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of elements in each dimension */ hsize_t idx; /* Chunk index */ unsigned old_idx; /* Previous index number */ unsigned u; /*counters */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_istore_update_cache, FAIL) /* Check args */ assert(dset && H5D_CHUNKED == dset->shared->layout.type); assert(dset->shared->layout.u.chunk.ndims > 0 && dset->shared->layout.u.chunk.ndims <= H5O_LAYOUT_NDIMS); /* Go get the rank & dimensions */ rank = dset->shared->layout.u.chunk.ndims-1; if(H5S_get_simple_extent_dims(dset->shared->space, curr_dims, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions") /* Round up to the next integer # of chunks, to accomodate partial chunks */ for(u = 0; u < rank; u++) chunks[u] = ((curr_dims[u]+dset->shared->layout.u.chunk.dim[u])-1) / dset->shared->layout.u.chunk.dim[u]; /* Get the "down" sizes for each dimension */ if(H5V_array_down(rank,chunks,down_chunks)<0) HGOTO_ERROR(H5E_INTERNAL, H5E_BADVALUE, FAIL, "can't compute 'down' sizes") /* Fill the DXPL cache values for later use */ if (H5D_get_dxpl_cache(dxpl_id,&dxpl_cache)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache") /* Construct dataset I/O info */ H5D_BUILD_IO_INFO(&io_info,dset,dxpl_cache,dxpl_id,NULL); /* Recompute the index for each cached chunk that is in a dataset */ for(ent = rdcc->head; ent; ent = next) { next=ent->next; /* Calculate the index of this chunk */ if(H5V_chunk_index(rank,ent->offset,dset->shared->layout.u.chunk.dim,down_chunks,&idx)<0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") /* Compute the index for the chunk entry */ old_idx=ent->idx; /* Save for later */ ent->idx=H5D_HASH(dset->shared,idx); if(old_idx!=ent->idx) { /* Check if there is already a chunk at this chunk's new location */ old_ent = rdcc->slot[ent->idx]; if(old_ent!=NULL) { assert(old_ent->locked==0); /* Check if we are removing the entry we would walk to next */ if(old_ent==next) next=old_ent->next; /* Remove the old entry from the cache */ if (H5D_istore_preempt(&io_info, old_ent, TRUE )<0) HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks") } /* end if */ /* Insert this chunk into correct location in hash table */ rdcc->slot[ent->idx]=ent; /* Null out previous location */ rdcc->slot[old_idx]=NULL; } /* end if */ } /* end for */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5F_istore_update_cache() */ /*------------------------------------------------------------------------- * Function: H5D_istore_copy * * Purpose: copy an indexed storage B-tree from SRC file to DST file. * * Return: Non-negative on success (with the ISTORE argument initialized * and ready to write to an object header). Negative on failure. * * Programmer: Peter Cao * August 20, 2005 * *------------------------------------------------------------------------- */ herr_t H5D_istore_copy(H5F_t *f_src, H5O_layout_t *layout_src, H5F_t *f_dst, H5O_layout_t *layout_dst, H5T_t *dt_src, H5O_copy_t *cpy_info, H5O_pline_t *pline, hid_t dxpl_id) { H5D_istore_it_ud4_t udata; H5T_path_t *tpath_src_mem = NULL, *tpath_mem_dst = NULL; /* Datatype conversion paths */ hid_t tid_src = -1; /* Datatype ID for source datatype */ hid_t tid_dst = -1; /* Datatype ID for destination datatype */ hid_t tid_mem = -1; /* Datatype ID for memory datatype */ size_t buf_size; /* Size of copy buffer */ size_t reclaim_buf_size; /* Size of reclaim buffer */ void *buf = NULL; /* Buffer for copying data */ void *bkg = NULL; /* Buffer for background during type conversion */ void *reclaim_buf = NULL; /* Buffer for reclaiming data */ H5S_t *buf_space = NULL; /* Dataspace describing buffer */ hid_t sid_buf = -1; /* ID for buffer dataspace */ size_t nelmts = 0; /* Number of elements in buffer */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_istore_copy, FAIL) /* Check args */ HDassert(f_src); HDassert(f_dst); HDassert(layout_src && H5D_CHUNKED == layout_src->type); HDassert(layout_dst && H5D_CHUNKED == layout_dst->type); /* Create shared B-tree info for each file */ if(H5D_istore_shared_create(f_src, layout_src) < 0) HGOTO_ERROR(H5E_RESOURCE, H5E_CANTINIT, FAIL, "can't create wrapper for shared B-tree info") if(H5D_istore_shared_create(f_dst, layout_dst) < 0) HGOTO_ERROR(H5E_RESOURCE, H5E_CANTINIT, FAIL, "can't create wrapper for shared B-tree info") /* Check if we need to create the B-tree in the dest. file */ if(layout_dst->u.chunk.addr == HADDR_UNDEF) { /* Create the root of the B-tree that describes chunked storage */ if(H5D_istore_create(f_dst, dxpl_id, layout_dst) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize chunked storage") } /* end if */ /* If there's a source datatype, set up type conversion information */ if(dt_src) { if(H5T_detect_class(dt_src, H5T_VLEN) > 0) { H5T_t *dt_dst; /* Destination datatype */ H5T_t *dt_mem; /* Memory datatype */ size_t mem_dt_size; /* Memory datatype size */ size_t tmp_dt_size; /* Temp. datatype size */ size_t max_dt_size; /* Max atatype size */ hsize_t buf_dim; /* Dimension for buffer */ unsigned u; /* Create datatype ID for src datatype */ if((tid_src = H5I_register(H5I_DATATYPE, dt_src)) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register source file datatype") /* create a memory copy of the variable-length datatype */ if(NULL == (dt_mem = H5T_copy(dt_src, H5T_COPY_TRANSIENT))) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to copy") if((tid_mem = H5I_register(H5I_DATATYPE, dt_mem)) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register memory datatype") /* create variable-length datatype at the destinaton file */ if(NULL == (dt_dst = H5T_copy(dt_src, H5T_COPY_TRANSIENT))) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to copy") if(H5T_set_loc(dt_dst, f_dst, H5T_LOC_DISK) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "cannot mark datatype on disk") if((tid_dst = H5I_register(H5I_DATATYPE, dt_dst)) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register destination file datatype") /* Set up the conversion functions */ if(NULL == (tpath_src_mem = H5T_path_find(dt_src, dt_mem, NULL, NULL, dxpl_id, FALSE))) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between src and mem datatypes") if(NULL == (tpath_mem_dst = H5T_path_find(dt_mem, dt_dst, NULL, NULL, dxpl_id, FALSE))) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between mem and dst datatypes") /* Determine largest datatype size */ if(0 == (max_dt_size = H5T_get_size(dt_src))) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size") if(0 == (mem_dt_size = H5T_get_size(dt_mem))) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size") max_dt_size = MAX(max_dt_size, mem_dt_size); if(0 == (tmp_dt_size = H5T_get_size(dt_dst))) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size") max_dt_size = MAX(max_dt_size, tmp_dt_size); /* Compute the number of elements per chunk */ nelmts = 1; for(u = 0; u < (layout_src->u.chunk.ndims - 1); u++) nelmts *= layout_src->u.chunk.dim[u]; /* Create the space and set the initial extent */ buf_dim = nelmts; if(NULL == (buf_space = H5S_create_simple((unsigned)1, &buf_dim, NULL))) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create simple dataspace") /* Atomize */ if((sid_buf = H5I_register(H5I_DATASPACE, buf_space)) < 0) { H5S_close(buf_space); HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register dataspace ID") } /* end if */ /* Set initial buffer sizes */ buf_size = nelmts * max_dt_size; reclaim_buf_size = nelmts * mem_dt_size; /* Allocate memory for reclaim buf */ if(NULL == (reclaim_buf = H5MM_malloc(reclaim_buf_size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for raw data chunk") } /* end if */ else { /* Create datatype ID for source datatype, so it gets freed */ if(H5T_get_class(dt_src, FALSE) == H5T_REFERENCE) { /* Create datatype ID for src datatype */ if((tid_src = H5I_register(H5I_DATATYPE, dt_src)) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register source file datatype") } /* end if */ buf_size = layout_src->u.chunk.size; reclaim_buf_size = 0; } /* end else */ /* Allocate background memory for converting the chunk */ if(NULL == (bkg = H5MM_malloc(buf_size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for raw data chunk") /* Check for reference datatype and no expanding references & clear background buffer */ if(!cpy_info->expand_ref && ((H5T_get_class(dt_src, FALSE) == H5T_REFERENCE) && (f_src != f_dst))) /* Reset value to zero */ HDmemset(bkg, 0, buf_size); } /* end if */ else { buf_size = layout_src->u.chunk.size; reclaim_buf_size = 0; } /* end else */ /* Allocate memory for copying the chunk */ if(NULL == (buf = H5MM_malloc(buf_size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for raw data chunk") /* Initialize the callback structure for the source */ HDmemset(&udata, 0, sizeof udata); udata.common.mesg = layout_src; udata.file_src = f_src; udata.addr_dst = layout_dst->u.chunk.addr; udata.buf = buf; udata.bkg = bkg; udata.buf_size = buf_size; udata.tid_src = tid_src; udata.tid_mem = tid_mem; udata.tid_dst = tid_dst; udata.dt_src = dt_src; udata.tpath_src_mem = tpath_src_mem; udata.tpath_mem_dst = tpath_mem_dst; udata.reclaim_buf = reclaim_buf; udata.reclaim_buf_size = reclaim_buf_size; udata.buf_space = buf_space; udata.nelmts = nelmts; udata.pline = pline; udata.file_dst = f_dst; udata.cpy_info = cpy_info; /* copy the chunked data by iteration */ if(H5B_iterate(f_src, dxpl_id, H5B_ISTORE, H5D_istore_iter_copy, layout_src->u.chunk.addr, &udata) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to iterate over chunk B-tree") /* I/O buffers may have been re-allocated */ buf = udata.buf; bkg = udata.bkg; done: if(sid_buf > 0) if(H5I_dec_ref(sid_buf) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary dataspace ID") if(tid_src > 0) if(H5I_dec_ref(tid_src) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID") if(tid_dst > 0) if(H5I_dec_ref(tid_dst) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID") if(tid_mem > 0) if(H5I_dec_ref(tid_mem) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID") if(buf) H5MM_xfree(buf); if(bkg) H5MM_xfree(bkg); if(reclaim_buf) H5MM_xfree(reclaim_buf); if(H5RC_DEC(layout_src->u.chunk.btree_shared) < 0) HDONE_ERROR(H5E_IO, H5E_CANTFREE, FAIL, "unable to decrement ref-counted page") if(H5RC_DEC(layout_dst->u.chunk.btree_shared) < 0) HDONE_ERROR(H5E_IO, H5E_CANTFREE, FAIL, "unable to decrement ref-counted page") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_copy() */ /*------------------------------------------------------------------------- * Function: H5D_istore_dump_btree * * Purpose: Prints information about the storage B-tree to the specified * stream. * * Return: Success: Non-negative * * Failure: negative * * Programmer: Robb Matzke * Wednesday, April 28, 1999 * *------------------------------------------------------------------------- */ herr_t H5D_istore_dump_btree(H5F_t *f, hid_t dxpl_id, FILE *stream, unsigned ndims, haddr_t addr) { H5O_layout_t layout; H5D_istore_it_ud2_t udata; herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_istore_dump_btree, FAIL) HDmemset(&udata, 0, sizeof udata); layout.u.chunk.ndims = ndims; udata.common.mesg = &layout; udata.stream = stream; if(stream) HDfprintf(stream, " Address: %a\n", addr); if(H5B_iterate(f, dxpl_id, H5B_ISTORE, H5D_istore_iter_dump, addr, &udata)<0) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, 0, "unable to iterate over chunk B-tree") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_dump_btree() */ #ifdef H5D_ISTORE_DEBUG /*------------------------------------------------------------------------- * Function: H5D_istore_stats * * Purpose: Print raw data cache statistics to the debug stream. If * HEADERS is non-zero then print table column headers, * otherwise assume that the H5AC layer has already printed them. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Thursday, May 21, 1998 * *------------------------------------------------------------------------- */ herr_t H5D_istore_stats (H5D_t *dset, hbool_t headers) { H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); double miss_rate; char ascii[32]; herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_istore_stats, FAIL) if (!H5DEBUG(AC)) HGOTO_DONE(SUCCEED) if (headers) { fprintf(H5DEBUG(AC), "H5D: raw data cache statistics\n"); fprintf(H5DEBUG(AC), " %-18s %8s %8s %8s %8s+%-8s\n", "Layer", "Hits", "Misses", "MissRate", "Inits", "Flushes"); fprintf(H5DEBUG(AC), " %-18s %8s %8s %8s %8s-%-8s\n", "-----", "----", "------", "--------", "-----", "-------"); } #ifdef H5AC_DEBUG if (H5DEBUG(AC)) headers = TRUE; #endif if (headers) { if (rdcc->nhits>0 || rdcc->nmisses>0) { miss_rate = 100.0 * rdcc->nmisses / (rdcc->nhits + rdcc->nmisses); } else { miss_rate = 0.0; } if (miss_rate > 100) { sprintf(ascii, "%7d%%", (int) (miss_rate + 0.5)); } else { sprintf(ascii, "%7.2f%%", miss_rate); } fprintf(H5DEBUG(AC), " %-18s %8u %8u %7s %8d+%-9ld\n", "raw data chunks", rdcc->nhits, rdcc->nmisses, ascii, rdcc->ninits, (long)(rdcc->nflushes)-(long)(rdcc->ninits)); } done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_stats() */ #endif /* H5D_ISTORE_DEBUG */ /*------------------------------------------------------------------------- * Function: H5D_istore_debug * * Purpose: Debugs a B-tree node for indexed raw data storage. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Thursday, April 16, 1998 * *------------------------------------------------------------------------- */ herr_t H5D_istore_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE * stream, int indent, int fwidth, unsigned ndims) { H5O_layout_t layout; H5D_istore_ud0_t udata; /* B-tree user data */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_istore_debug,FAIL) layout.u.chunk.ndims = ndims; /* Allocate the shared structure */ if(H5D_istore_shared_create(f, &layout)<0) HGOTO_ERROR(H5E_RESOURCE, H5E_CANTINIT, FAIL, "can't create wrapper for shared B-tree info") /* Set up B-tree user data */ HDmemset(&udata, 0, sizeof udata); udata.mesg = &layout; (void)H5B_debug(f, dxpl_id, addr, stream, indent, fwidth, H5B_ISTORE, &udata); /* Free the raw B-tree node buffer */ if(layout.u.chunk.btree_shared==NULL) HGOTO_ERROR(H5E_IO, H5E_CANTFREE, FAIL, "ref-counted page nil") if(H5RC_DEC(layout.u.chunk.btree_shared)<0) HGOTO_ERROR(H5E_IO, H5E_CANTFREE, FAIL, "unable to decrement ref-counted page") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_istore_debug() */