mirror of
https://github.com/HDFGroup/hdf5.git
synced 2025-01-18 15:15:56 +08:00
[svn-r17243] Description:
Refactor how the layout message is created/written/read in the
dataset's object header.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.7 (amazon) in debug mode
Mac OS X/32 10.5.7 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
This commit is contained in:
Quincey Koziol
parent
c1ad3676c4
commit
6909bc4319
1
MANIFEST
1
MANIFEST
@ -482,6 +482,7 @@
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./src/H5Dfill.c
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./src/H5Dint.c
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./src/H5Dio.c
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./src/H5Dlayout.c
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./src/H5Dmpio.c
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./src/H5Doh.c
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./src/H5Dpkg.h
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111
src/H5Dchunk.c
111
src/H5Dchunk.c
@ -181,6 +181,7 @@ static herr_t H5D_chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type
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static herr_t H5D_chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
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hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space,
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H5D_chunk_map_t *fm);
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static herr_t H5D_chunk_flush(H5D_t *dset, hid_t dxpl_id, unsigned flags);
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static herr_t H5D_chunk_io_term(const H5D_chunk_map_t *fm);
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/* "Nonexistent" layout operation callback */
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@ -206,7 +207,10 @@ static herr_t H5D_chunk_file_cb(void *elem, hid_t type_id, unsigned ndims,
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const hsize_t *coords, void *fm);
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static herr_t H5D_chunk_mem_cb(void *elem, hid_t type_id, unsigned ndims,
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const hsize_t *coords, void *fm);
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static herr_t H5D_chunk_flush_entry(const H5D_t *dset, hid_t dxpl_id,
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const H5D_dxpl_cache_t *dxpl_cache, H5D_rdcc_ent_t *ent, hbool_t reset);
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static herr_t H5D_chunk_cache_evict(const H5D_t *dset, hid_t dxpl_id,
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const H5D_dxpl_cache_t *dxpl_cache, H5D_rdcc_ent_t *ent, hbool_t flush);
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/*********************/
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@ -227,6 +231,7 @@ const H5D_layout_ops_t H5D_LOPS_CHUNK[1] = {{
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#endif /* H5_HAVE_PARALLEL */
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NULL,
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NULL,
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H5D_chunk_flush,
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H5D_chunk_io_term
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}};
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@ -249,6 +254,7 @@ const H5D_layout_ops_t H5D_LOPS_NONEXISTENT[1] = {{
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#endif /* H5_HAVE_PARALLEL */
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H5D_nonexistent_readvv,
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NULL,
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NULL,
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NULL
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}};
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@ -1921,6 +1927,61 @@ done:
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FUNC_LEAVE_NOAPI(ret_value)
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} /* H5D_chunk_write() */
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/*-------------------------------------------------------------------------
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* Function: H5D_chunk_flush
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*
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* Purpose: Writes all dirty chunks to disk and optionally preempts them
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* from the cache.
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*
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* Return: Non-negative on success/Negative on failure
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*
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* Programmer: Robb Matzke
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* Thursday, May 21, 1998
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*
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*-------------------------------------------------------------------------
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*/
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static herr_t
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H5D_chunk_flush(H5D_t *dset, hid_t dxpl_id, unsigned flags)
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{
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H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
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H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
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H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk);
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unsigned nerrors = 0;
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H5D_rdcc_ent_t *ent, *next;
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herr_t ret_value = SUCCEED; /* Return value */
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FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_flush)
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/* Sanity check */
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HDassert(dset);
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/* Flush any data caught in sieve buffer */
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if(H5D_flush_sieve_buf(dset, dxpl_id) < 0)
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HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "unable to flush sieve buffer")
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/* Fill the DXPL cache values for later use */
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if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0)
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HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
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/* Loop over all entries in the chunk cache */
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for(ent = rdcc->head; ent; ent = next) {
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next = ent->next;
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if((flags & H5F_FLUSH_INVALIDATE)) {
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if(H5D_chunk_cache_evict(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0)
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nerrors++;
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} else {
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if(H5D_chunk_flush_entry(dset, dxpl_id, dxpl_cache, ent, FALSE) < 0)
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nerrors++;
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}
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} /* end for */
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if(nerrors)
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HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks")
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done:
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FUNC_LEAVE_NOAPI(ret_value)
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} /* end H5D_chunk_flush() */
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/*-------------------------------------------------------------------------
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* Function: H5D_chunk_io_term
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@ -2911,54 +2972,6 @@ done:
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FUNC_LEAVE_NOAPI(ret_value)
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} /* end H5D_chunk_unlock() */
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/*-------------------------------------------------------------------------
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* Function: H5D_chunk_flush
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*
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* Purpose: Writes all dirty chunks to disk and optionally preempts them
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* from the cache.
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*
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* Return: Non-negative on success/Negative on failure
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*
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* Programmer: Robb Matzke
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* Thursday, May 21, 1998
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*
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*-------------------------------------------------------------------------
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*/
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herr_t
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H5D_chunk_flush(H5D_t *dset, hid_t dxpl_id, unsigned flags)
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{
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H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
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H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
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H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk);
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unsigned nerrors = 0;
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H5D_rdcc_ent_t *ent, *next;
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herr_t ret_value = SUCCEED; /* Return value */
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FUNC_ENTER_NOAPI(H5D_chunk_flush, FAIL)
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/* Fill the DXPL cache values for later use */
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if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0)
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HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
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/* Loop over all entries in the chunk cache */
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for(ent = rdcc->head; ent; ent = next) {
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next = ent->next;
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if((flags & H5F_FLUSH_INVALIDATE)) {
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if(H5D_chunk_cache_evict(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0)
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nerrors++;
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} else {
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if(H5D_chunk_flush_entry(dset, dxpl_id, dxpl_cache, ent, FALSE) < 0)
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nerrors++;
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}
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} /* end for */
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if(nerrors)
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HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks")
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done:
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FUNC_LEAVE_NOAPI(ret_value)
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} /* end H5D_chunk_flush() */
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/*-------------------------------------------------------------------------
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* Function: H5D_chunk_allocated_cb
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@ -68,6 +68,7 @@ static ssize_t H5D_compact_readvv(const H5D_io_info_t *io_info,
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static ssize_t H5D_compact_writevv(const H5D_io_info_t *io_info,
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size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_size_arr[], hsize_t dset_offset_arr[],
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size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_size_arr[], hsize_t mem_offset_arr[]);
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static herr_t H5D_compact_flush(H5D_t *dset, hid_t dxpl_id, unsigned flags);
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/*********************/
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@ -88,6 +89,7 @@ const H5D_layout_ops_t H5D_LOPS_COMPACT[1] = {{
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#endif /* H5_HAVE_PARALLEL */
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H5D_compact_readvv,
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H5D_compact_writevv,
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H5D_compact_flush,
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NULL
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}};
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@ -330,6 +332,40 @@ done:
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FUNC_LEAVE_NOAPI(ret_value)
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} /* end H5D_compact_writevv() */
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/*-------------------------------------------------------------------------
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* Function: H5D_compact_flush
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*
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* Purpose: Writes dirty compact data to object header
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*
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* Return: Non-negative on success/Negative on failure
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*
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* Programmer: Quincey Koziol
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* Monday, July 27, 2009
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*
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*-------------------------------------------------------------------------
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*/
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static herr_t
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H5D_compact_flush(H5D_t *dset, hid_t dxpl_id, unsigned UNUSED flags)
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{
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herr_t ret_value = SUCCEED; /* Return value */
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FUNC_ENTER_NOAPI_NOINIT(H5D_compact_flush)
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/* Sanity check */
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HDassert(dset);
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/* Check if the buffered compact information is dirty */
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if(dset->shared->layout.u.compact.dirty) {
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if(H5O_msg_write(&(dset->oloc), H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, &(dset->shared->layout), dxpl_id) < 0)
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HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to update layout message")
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dset->shared->layout.u.compact.dirty = FALSE;
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} /* end if */
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done:
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FUNC_LEAVE_NOAPI(ret_value)
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} /* end H5D_compact_flush() */
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/*-------------------------------------------------------------------------
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* Function: H5D_compact_copy
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@ -66,6 +66,7 @@ static hbool_t H5D_contig_is_space_alloc(const H5O_layout_t *layout);
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static herr_t H5D_contig_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
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hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space,
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H5D_chunk_map_t *cm);
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static herr_t H5D_contig_flush(H5D_t *dset, hid_t dxpl_id, unsigned flags);
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/* Helper routines */
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static herr_t H5D_contig_write_one(H5D_io_info_t *io_info, hsize_t offset,
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@ -90,6 +91,7 @@ const H5D_layout_ops_t H5D_LOPS_CONTIG[1] = {{
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#endif /* H5_HAVE_PARALLEL */
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H5D_contig_readvv,
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H5D_contig_writevv,
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H5D_contig_flush,
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NULL
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}};
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@ -1171,6 +1173,37 @@ done:
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FUNC_LEAVE_NOAPI(ret_value)
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} /* end H5D_contig_writevv() */
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/*-------------------------------------------------------------------------
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* Function: H5D_contig_flush
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*
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* Purpose: Writes all dirty data to disk.
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*
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* Return: Non-negative on success/Negative on failure
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*
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* Programmer: Quincey Koziol
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* Monday, July 27, 2009
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*
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*-------------------------------------------------------------------------
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*/
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static herr_t
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H5D_contig_flush(H5D_t *dset, hid_t dxpl_id, unsigned UNUSED flags)
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{
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herr_t ret_value = SUCCEED; /* Return value */
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FUNC_ENTER_NOAPI_NOINIT(H5D_contig_flush)
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/* Sanity check */
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HDassert(dset);
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/* Flush any data in sieve buffer */
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if(H5D_flush_sieve_buf(dset, dxpl_id) < 0)
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HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "unable to flush sieve buffer")
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done:
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FUNC_LEAVE_NOAPI(ret_value)
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} /* end H5D_contig_flush() */
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/*-------------------------------------------------------------------------
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* Function: H5D_contig_copy
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@ -86,6 +86,7 @@ const H5D_layout_ops_t H5D_LOPS_EFL[1] = {{
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#endif /* H5_HAVE_PARALLEL */
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H5D_efl_readvv,
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H5D_efl_writevv,
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NULL,
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NULL
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}};
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329
src/H5Dint.c
329
src/H5Dint.c
@ -30,7 +30,6 @@
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#include "H5Dpkg.h" /* Datasets */
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#include "H5Eprivate.h" /* Error handling */
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#include "H5FOprivate.h" /* File objects */
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#include "H5HLprivate.h" /* Local heaps */
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#include "H5Iprivate.h" /* IDs */
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#include "H5Lprivate.h" /* Links */
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#include "H5MMprivate.h" /* Memory management */
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@ -64,7 +63,6 @@ static H5D_shared_t *H5D_new(hid_t dcpl_id, hbool_t creating, hbool_t vl_type);
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static herr_t H5D_init_type(H5F_t *file, const H5D_t *dset, hid_t type_id,
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const H5T_t *type);
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static herr_t H5D_init_space(H5F_t *file, const H5D_t *dset, const H5S_t *space);
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static herr_t H5D_set_io_ops(H5D_t *dataset);
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static herr_t H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset,
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hid_t dapl_id);
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static herr_t H5D_open_oid(H5D_t *dataset, hid_t dapl_id, hid_t dxpl_id);
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@ -690,58 +688,6 @@ done:
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FUNC_LEAVE_NOAPI(ret_value)
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} /* end H5D_init_space() */
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/*-------------------------------------------------------------------------
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* Function: H5D_set_io_ops
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*
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* Purpose: Set the I/O operation function pointers for a dataset
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*
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* Return: Non-negative on success/Negative on failure
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*
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* Programmer: Quincey Koziol
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* Thursday, March 20, 2008
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*
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*-------------------------------------------------------------------------
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*/
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static herr_t
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H5D_set_io_ops(H5D_t *dataset)
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{
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herr_t ret_value = SUCCEED; /* Return value */
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FUNC_ENTER_NOAPI_NOINIT(H5D_set_io_ops)
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/* check args */
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HDassert(dataset);
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/* Set the I/O functions for each layout type */
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switch(dataset->shared->layout.type) {
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case H5D_CONTIGUOUS:
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if(dataset->shared->dcpl_cache.efl.nused > 0)
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dataset->shared->layout.ops = H5D_LOPS_EFL;
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else
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dataset->shared->layout.ops = H5D_LOPS_CONTIG;
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break;
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case H5D_CHUNKED:
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dataset->shared->layout.ops = H5D_LOPS_CHUNK;
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/* Set the chunk operations */
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/* (Only "B-tree" indexing type currently supported */
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dataset->shared->layout.u.chunk.ops = H5D_COPS_BTREE;
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break;
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case H5D_COMPACT:
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dataset->shared->layout.ops = H5D_LOPS_COMPACT;
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break;
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default:
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HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unknown storage method")
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} /* end switch */ /*lint !e788 All appropriate cases are covered */
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done:
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FUNC_LEAVE_NOAPI(ret_value)
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} /* end H5D_set_io_ops() */
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/*-------------------------------------------------------------------------
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* Function: H5D_update_oh_info
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@ -876,86 +822,13 @@ H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset, hid_t dapl_id)
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if(H5S_append(file, dxpl_id, oh, dset->shared->space) < 0)
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HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update dataspace header message")
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/* Update the filters message, if this is a chunked dataset */
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if(layout->type == H5D_CHUNKED) {
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H5O_pline_t *pline; /* Dataset's I/O pipeline information */
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pline = &dset->shared->dcpl_cache.pline;
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if(pline->nused > 0 && H5O_msg_append_oh(file, dxpl_id, oh, H5O_PLINE_ID, H5O_MSG_FLAG_CONSTANT, 0, pline) < 0)
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HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update filter header message")
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} /* end if */
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/* Initialize the layout information for the new dataset */
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if(dset->shared->layout.ops->init && (dset->shared->layout.ops->init)(file, dxpl_id, dset, dapl_id) < 0)
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HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize layout information")
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/* Update/create the layout (and I/O pipeline & EFL) messages */
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if(H5D_layout_oh_create(file, dxpl_id, oh, dset, dapl_id) < 0)
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HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout/pline/efl header message")
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/* Indicate that the layout information was initialized */
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layout_init = TRUE;
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/*
|
||||
* Allocate storage if space allocate time is early; otherwise delay
|
||||
* allocation until later.
|
||||
*/
|
||||
if(fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY)
|
||||
if(H5D_alloc_storage(dset, dxpl_id, H5D_ALLOC_CREATE, FALSE) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage")
|
||||
|
||||
/* Update external storage message, if it's used */
|
||||
if(dset->shared->dcpl_cache.efl.nused > 0) {
|
||||
H5O_efl_t *efl = &dset->shared->dcpl_cache.efl; /* Dataset's external file list */
|
||||
H5HL_t *heap; /* Pointer to local heap for EFL file names */
|
||||
size_t heap_size = H5HL_ALIGN(1);
|
||||
size_t u;
|
||||
|
||||
/* Determine size of heap needed to stored the file names */
|
||||
for(u = 0; u < efl->nused; ++u)
|
||||
heap_size += H5HL_ALIGN(HDstrlen(efl->slot[u].name) + 1);
|
||||
|
||||
/* Create the heap for the EFL file names */
|
||||
if(H5HL_create(file, dxpl_id, heap_size, &efl->heap_addr/*out*/) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create EFL file name heap")
|
||||
|
||||
/* Pin the heap down in memory */
|
||||
if(NULL == (heap = H5HL_protect(file, dxpl_id, efl->heap_addr, H5AC_WRITE)))
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTPROTECT, FAIL, "unable to protect EFL file name heap")
|
||||
|
||||
/* Insert "empty" name first */
|
||||
if((size_t)(-1) == H5HL_insert(file, dxpl_id, heap, (size_t)1, "")) {
|
||||
H5HL_unprotect(file, dxpl_id, heap, efl->heap_addr);
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert file name into heap")
|
||||
} /* end if */
|
||||
|
||||
for(u = 0; u < efl->nused; ++u) {
|
||||
size_t offset; /* Offset of file name in heap */
|
||||
|
||||
/* Insert file name into heap */
|
||||
if((size_t)(-1) == (offset = H5HL_insert(file, dxpl_id, heap,
|
||||
HDstrlen(efl->slot[u].name) + 1, efl->slot[u].name))) {
|
||||
H5HL_unprotect(file, dxpl_id, heap, efl->heap_addr);
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert file name into heap")
|
||||
} /* end if */
|
||||
|
||||
/* Store EFL file name offset */
|
||||
HDassert(0 == efl->slot[u].name_offset);
|
||||
efl->slot[u].name_offset = offset;
|
||||
} /* end for */
|
||||
|
||||
/* Release the heap */
|
||||
if(H5HL_unprotect(file, dxpl_id, heap, efl->heap_addr) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTUNPROTECT, FAIL, "unable to unprotect EFL file name heap")
|
||||
heap = NULL;
|
||||
|
||||
/* Insert EFL message into dataset object header */
|
||||
if(H5O_msg_append_oh(file, dxpl_id, oh, H5O_EFL_ID, H5O_MSG_FLAG_CONSTANT, 0, efl) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update external file list message")
|
||||
} /* end if */
|
||||
|
||||
/* Create layout message */
|
||||
/* (Don't make layout message constant unless allocation time is early, since space may not be allocated) */
|
||||
/* (Note: this is relying on H5D_alloc_storage not calling H5O_msg_write during dataset creation) */
|
||||
if(H5O_msg_append_oh(file, dxpl_id, oh, H5O_LAYOUT_ID, ((fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY && H5D_COMPACT != layout->type) ? H5O_MSG_FLAG_CONSTANT : 0), 0, layout) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout")
|
||||
|
||||
#ifdef H5O_ENABLE_BOGUS
|
||||
{
|
||||
H5P_genplist_t *dc_plist; /* Dataset's creation property list */
|
||||
@ -1150,7 +1023,7 @@ H5D_create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id,
|
||||
new_dset->shared->dcpl_cache.fill.alloc_time = H5D_ALLOC_TIME_EARLY;
|
||||
|
||||
/* Set the dataset's I/O operations */
|
||||
if(H5D_set_io_ops(new_dset) < 0)
|
||||
if(H5D_layout_set_io_ops(new_dset) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize I/O operations")
|
||||
|
||||
/* Create the layout information for the new dataset */
|
||||
@ -1158,7 +1031,7 @@ H5D_create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id,
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to construct layout information")
|
||||
|
||||
/* Update the dataset's object header info. */
|
||||
if(H5D_update_oh_info(file, dxpl_id, new_dset, dapl_id) != SUCCEED)
|
||||
if(H5D_update_oh_info(file, dxpl_id, new_dset, dapl_id) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't update the metadata cache")
|
||||
|
||||
/* Indicate that the layout information was initialized */
|
||||
@ -1360,105 +1233,9 @@ H5D_open_oid(H5D_t *dataset, hid_t dapl_id, hid_t dxpl_id)
|
||||
if(NULL == (plist = (H5P_genplist_t *)H5I_object(dataset->shared->dcpl_id)))
|
||||
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't get dataset creation property list")
|
||||
|
||||
/* Get the optional filters message */
|
||||
if((msg_exists = H5O_msg_exists(&(dataset->oloc), H5O_PLINE_ID, dxpl_id)) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't check if message exists")
|
||||
if(msg_exists) {
|
||||
/* Retrieve the I/O pipeline message */
|
||||
if(NULL == H5O_msg_read(&(dataset->oloc), H5O_PLINE_ID, &dataset->shared->dcpl_cache.pline, dxpl_id))
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve message")
|
||||
|
||||
/* Set the I/O pipeline info in the property list */
|
||||
if(H5P_set(plist, H5D_CRT_DATA_PIPELINE_NAME, &dataset->shared->dcpl_cache.pline) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set pipeline")
|
||||
} /* end if */
|
||||
|
||||
/*
|
||||
* Get the raw data layout info. It's actually stored in two locations:
|
||||
* the storage message of the dataset (dataset->storage) and certain
|
||||
* values are copied to the dataset create plist so the user can query
|
||||
* them.
|
||||
*/
|
||||
if(NULL == H5O_msg_read(&(dataset->oloc), H5O_LAYOUT_ID, &(dataset->shared->layout), dxpl_id))
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data layout message")
|
||||
|
||||
/* Check for external file list message (which might not exist) */
|
||||
if((msg_exists = H5O_msg_exists(&(dataset->oloc), H5O_EFL_ID, dxpl_id)) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't check if message exists")
|
||||
if(msg_exists) {
|
||||
/* Retrieve the EFL message */
|
||||
if(NULL == H5O_msg_read(&(dataset->oloc), H5O_EFL_ID, &dataset->shared->dcpl_cache.efl, dxpl_id))
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve message")
|
||||
|
||||
/* Set the EFL info in the property list */
|
||||
if(H5P_set(plist, H5D_CRT_EXT_FILE_LIST_NAME, &dataset->shared->dcpl_cache.efl) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set external file list")
|
||||
|
||||
/* Set the dataset's I/O operations */
|
||||
dataset->shared->layout.ops = H5D_LOPS_EFL;
|
||||
} /* end if */
|
||||
|
||||
/* Sanity check that the layout operations are set up */
|
||||
HDassert(dataset->shared->layout.ops);
|
||||
|
||||
/* Adjust chunk dimensions to omit datatype size (in last dimension) for creation property */
|
||||
if(H5D_CHUNKED == dataset->shared->layout.type)
|
||||
dataset->shared->layout.u.chunk.ndims--;
|
||||
/* Copy layout to the DCPL */
|
||||
if(H5P_set(plist, H5D_CRT_LAYOUT_NAME, &dataset->shared->layout) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set layout")
|
||||
/* Adjust chunk dimensions back again (*sigh*) */
|
||||
if(H5D_CHUNKED == dataset->shared->layout.type)
|
||||
dataset->shared->layout.u.chunk.ndims++;
|
||||
|
||||
switch(dataset->shared->layout.type) {
|
||||
case H5D_CONTIGUOUS:
|
||||
/* Compute the size of the contiguous storage for versions of the
|
||||
* layout message less than version 3 because versions 1 & 2 would
|
||||
* truncate the dimension sizes to 32-bits of information. - QAK 5/26/04
|
||||
*/
|
||||
if(dataset->shared->layout.version < 3) {
|
||||
hssize_t snelmts; /* Temporary holder for number of elements in dataspace */
|
||||
hsize_t nelmts; /* Number of elements in dataspace */
|
||||
size_t dt_size; /* Size of datatype */
|
||||
hsize_t tmp_size; /* Temporary holder for raw data size */
|
||||
|
||||
/* Retrieve the number of elements in the dataspace */
|
||||
if((snelmts = H5S_GET_EXTENT_NPOINTS(dataset->shared->space)) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve number of elements in dataspace")
|
||||
nelmts = (hsize_t)snelmts;
|
||||
|
||||
/* Get the datatype's size */
|
||||
if(0 == (dt_size = H5T_GET_SIZE(dataset->shared->type)))
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve size of datatype")
|
||||
|
||||
/* Compute the size of the dataset's contiguous storage */
|
||||
tmp_size = nelmts * dt_size;
|
||||
|
||||
/* Check for overflow during multiplication */
|
||||
if(nelmts != (tmp_size / dt_size))
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_OVERFLOW, FAIL, "size of dataset's storage overflowed")
|
||||
|
||||
/* Assign the dataset's contiguous storage size */
|
||||
dataset->shared->layout.u.contig.size = tmp_size;
|
||||
} /* end if */
|
||||
|
||||
/* Get the sieve buffer size for this dataset */
|
||||
dataset->shared->cache.contig.sieve_buf_size = H5F_SIEVE_BUF_SIZE(dataset->oloc.file);
|
||||
break;
|
||||
|
||||
case H5D_CHUNKED:
|
||||
/* Initialize the chunk cache for the dataset */
|
||||
if(H5D_chunk_init(dataset->oloc.file, dxpl_id, dataset, dapl_id) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize chunk cache")
|
||||
break;
|
||||
|
||||
case H5D_COMPACT:
|
||||
break;
|
||||
|
||||
default:
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unknown storage method")
|
||||
} /* end switch */ /*lint !e788 All appropriate cases are covered */
|
||||
/* Get the layout/pline/efl message information */
|
||||
if(H5D_layout_oh_read(dataset, dxpl_id, dapl_id, plist) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get layout/pline/efl info")
|
||||
|
||||
/* Point at dataset's copy, to cache it for later */
|
||||
fill_prop = &dataset->shared->dcpl_cache.fill;
|
||||
@ -1849,9 +1626,6 @@ H5D_alloc_storage(H5D_t *dset/*in,out*/, hid_t dxpl_id, H5D_time_alloc_t time_al
|
||||
HDmemset(layout->u.compact.buf, 0, layout->u.compact.size);
|
||||
layout->u.compact.dirty = TRUE;
|
||||
|
||||
/* Indicate that we set the storage addr */
|
||||
addr_set = TRUE;
|
||||
|
||||
/* Indicate that we should initialize storage space */
|
||||
must_init_space = TRUE;
|
||||
} /* end if */
|
||||
@ -2404,6 +2178,47 @@ done:
|
||||
FUNC_LEAVE_NOAPI(ret_value)
|
||||
} /* end H5D_set_extent() */
|
||||
|
||||
|
||||
/*-------------------------------------------------------------------------
|
||||
* Function: H5D_flush_sieve_buf
|
||||
*
|
||||
* Purpose: Flush any dataset sieve buffer info cached in memory
|
||||
*
|
||||
* Return: Success: Non-negative
|
||||
* Failure: Negative
|
||||
*
|
||||
* Programmer: Quincey Koziol
|
||||
* July 27, 2009
|
||||
*
|
||||
*-------------------------------------------------------------------------
|
||||
*/
|
||||
herr_t
|
||||
H5D_flush_sieve_buf(H5D_t *dataset, hid_t dxpl_id)
|
||||
{
|
||||
herr_t ret_value = SUCCEED; /* Return value */
|
||||
|
||||
FUNC_ENTER_NOAPI_NOINIT(H5D_flush_sieve_buf)
|
||||
|
||||
/* Check args */
|
||||
HDassert(dataset);
|
||||
|
||||
/* Flush the raw data buffer, if we have a dirty one */
|
||||
if(dataset->shared->cache.contig.sieve_buf && dataset->shared->cache.contig.sieve_dirty) {
|
||||
HDassert(dataset->shared->layout.type != H5D_COMPACT); /* We should never have a sieve buffer for compact storage */
|
||||
|
||||
/* Write dirty data sieve buffer to file */
|
||||
if(H5F_block_write(dataset->oloc.file, H5FD_MEM_DRAW, dataset->shared->cache.contig.sieve_loc,
|
||||
dataset->shared->cache.contig.sieve_size, dxpl_id, dataset->shared->cache.contig.sieve_buf) < 0)
|
||||
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed")
|
||||
|
||||
/* Reset sieve buffer dirty flag */
|
||||
dataset->shared->cache.contig.sieve_dirty = FALSE;
|
||||
} /* end if */
|
||||
|
||||
done:
|
||||
FUNC_LEAVE_NOAPI(ret_value)
|
||||
} /* end H5D_flush_sieve_buf() */
|
||||
|
||||
|
||||
/*-------------------------------------------------------------------------
|
||||
* Function: H5D_flush_real
|
||||
@ -2439,8 +2254,8 @@ H5D_flush_real(H5D_t *dataset, hid_t dxpl_id, unsigned flags)
|
||||
|
||||
/* Update the layout on disk, if it's been changed */
|
||||
if(dataset->shared->layout_dirty) {
|
||||
if(H5O_msg_write_oh(dataset->oloc.file, dxpl_id, oh, H5O_LAYOUT_ID, H5O_MSG_FLAG_CONSTANT, update_flags, &dataset->shared->layout) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update layout message")
|
||||
if(H5D_layout_oh_write(dataset, dxpl_id, oh, update_flags) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update layout/pline/efl info")
|
||||
dataset->shared->layout_dirty = FALSE;
|
||||
|
||||
/* Reset the "update the modification time" flag, so we only do it once */
|
||||
@ -2461,44 +2276,10 @@ H5D_flush_real(H5D_t *dataset, hid_t dxpl_id, unsigned flags)
|
||||
HDassert(update_flags == 0);
|
||||
} /* end if */
|
||||
|
||||
/* Flush the raw data buffer, if we have a dirty one */
|
||||
if(dataset->shared->cache.contig.sieve_buf && dataset->shared->cache.contig.sieve_dirty) {
|
||||
HDassert(dataset->shared->layout.type != H5D_COMPACT); /* We should never have a sieve buffer for compact storage */
|
||||
|
||||
/* Write dirty data sieve buffer to file */
|
||||
if(H5F_block_write(dataset->oloc.file, H5FD_MEM_DRAW, dataset->shared->cache.contig.sieve_loc,
|
||||
dataset->shared->cache.contig.sieve_size, dxpl_id, dataset->shared->cache.contig.sieve_buf) < 0)
|
||||
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed")
|
||||
|
||||
/* Reset sieve buffer dirty flag */
|
||||
dataset->shared->cache.contig.sieve_dirty = FALSE;
|
||||
} /* end if */
|
||||
|
||||
/* Flush cached information for each kind of dataset */
|
||||
switch(dataset->shared->layout.type) {
|
||||
case H5D_CONTIGUOUS:
|
||||
break;
|
||||
|
||||
case H5D_CHUNKED:
|
||||
/* Flush the raw data cache */
|
||||
if(H5D_chunk_flush(dataset, dxpl_id, flags & H5F_FLUSH_INVALIDATE) < 0)
|
||||
HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "unable to flush raw data cache")
|
||||
break;
|
||||
|
||||
case H5D_COMPACT:
|
||||
if(dataset->shared->layout.u.compact.dirty) {
|
||||
if(H5O_msg_write(&(dataset->oloc), H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, &(dataset->shared->layout), dxpl_id) < 0)
|
||||
HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to update layout message")
|
||||
dataset->shared->layout.u.compact.dirty = FALSE;
|
||||
} /* end if */
|
||||
break;
|
||||
|
||||
default:
|
||||
HDassert("not implemented yet" && 0);
|
||||
#ifdef NDEBUG
|
||||
HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout")
|
||||
#endif /* NDEBUG */
|
||||
} /* end switch */ /*lint !e788 All appropriate cases are covered */
|
||||
/* Flush cached raw data for each kind of dataset layout */
|
||||
if(dataset->shared->layout.ops->flush &&
|
||||
(dataset->shared->layout.ops->flush)(dataset, dxpl_id, flags) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "unable to flush raw data")
|
||||
|
||||
done:
|
||||
/* Release pointer to object header */
|
||||
|
||||
403
src/H5Dlayout.c
Normal file
403
src/H5Dlayout.c
Normal file
@ -0,0 +1,403 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* All rights reserved. *
|
||||
* *
|
||||
* This file is part of HDF5. The full HDF5 copyright notice, including *
|
||||
* terms governing use, modification, and redistribution, is contained in *
|
||||
* the files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
|
||||
* access to either file, you may request a copy from help@hdfgroup.org. *
|
||||
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
|
||||
|
||||
/****************/
|
||||
/* Module Setup */
|
||||
/****************/
|
||||
|
||||
#define H5D_PACKAGE /*suppress error about including H5Dpkg */
|
||||
|
||||
|
||||
/***********/
|
||||
/* Headers */
|
||||
/***********/
|
||||
#include "H5private.h" /* Generic Functions */
|
||||
#include "H5Dpkg.h" /* Datasets */
|
||||
#include "H5Eprivate.h" /* Error handling */
|
||||
#include "H5HLprivate.h" /* Local heaps */
|
||||
|
||||
|
||||
/****************/
|
||||
/* Local Macros */
|
||||
/****************/
|
||||
|
||||
|
||||
/******************/
|
||||
/* Local Typedefs */
|
||||
/******************/
|
||||
|
||||
|
||||
/********************/
|
||||
/* Local Prototypes */
|
||||
/********************/
|
||||
|
||||
|
||||
/*********************/
|
||||
/* Package Variables */
|
||||
/*********************/
|
||||
|
||||
|
||||
/*****************************/
|
||||
/* Library Private Variables */
|
||||
/*****************************/
|
||||
|
||||
|
||||
/*******************/
|
||||
/* Local Variables */
|
||||
/*******************/
|
||||
|
||||
|
||||
|
||||
/*-------------------------------------------------------------------------
|
||||
* Function: H5D_layout_set_io_ops
|
||||
*
|
||||
* Purpose: Set the I/O operation function pointers for a dataset,
|
||||
* according to the dataset's layout
|
||||
*
|
||||
* Return: Non-negative on success/Negative on failure
|
||||
*
|
||||
* Programmer: Quincey Koziol
|
||||
* Thursday, March 20, 2008
|
||||
*
|
||||
*-------------------------------------------------------------------------
|
||||
*/
|
||||
herr_t
|
||||
H5D_layout_set_io_ops(const H5D_t *dataset)
|
||||
{
|
||||
herr_t ret_value = SUCCEED; /* Return value */
|
||||
|
||||
FUNC_ENTER_NOAPI(H5D_layout_set_io_ops, FAIL)
|
||||
|
||||
/* check args */
|
||||
HDassert(dataset);
|
||||
|
||||
/* Set the I/O functions for each layout type */
|
||||
switch(dataset->shared->layout.type) {
|
||||
case H5D_CONTIGUOUS:
|
||||
if(dataset->shared->dcpl_cache.efl.nused > 0)
|
||||
dataset->shared->layout.ops = H5D_LOPS_EFL;
|
||||
else
|
||||
dataset->shared->layout.ops = H5D_LOPS_CONTIG;
|
||||
break;
|
||||
|
||||
case H5D_CHUNKED:
|
||||
dataset->shared->layout.ops = H5D_LOPS_CHUNK;
|
||||
|
||||
/* Set the chunk operations */
|
||||
/* (Only "B-tree" indexing type currently supported */
|
||||
dataset->shared->layout.u.chunk.ops = H5D_COPS_BTREE;
|
||||
break;
|
||||
|
||||
case H5D_COMPACT:
|
||||
dataset->shared->layout.ops = H5D_LOPS_COMPACT;
|
||||
break;
|
||||
|
||||
default:
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unknown storage method")
|
||||
} /* end switch */ /*lint !e788 All appropriate cases are covered */
|
||||
|
||||
done:
|
||||
FUNC_LEAVE_NOAPI(ret_value)
|
||||
} /* end H5D_layout_set_io_ops() */
|
||||
|
||||
|
||||
/*-------------------------------------------------------------------------
|
||||
* Function: H5D_layout_oh_create
|
||||
*
|
||||
* Purpose: Create layout/pline/efl information for dataset
|
||||
*
|
||||
* Return: Success: SUCCEED
|
||||
* Failure: FAIL
|
||||
*
|
||||
* Programmer: Quincey Koziol
|
||||
* Monday, July 27, 2009
|
||||
*
|
||||
*-------------------------------------------------------------------------
|
||||
*/
|
||||
herr_t
|
||||
H5D_layout_oh_create(H5F_t *file, hid_t dxpl_id, H5O_t *oh, H5D_t *dset,
|
||||
hid_t dapl_id)
|
||||
{
|
||||
H5O_layout_t *layout; /* Dataset's layout information */
|
||||
const H5O_fill_t *fill_prop; /* Pointer to dataset's fill value information */
|
||||
hbool_t layout_init = FALSE; /* Flag to indicate that chunk information was initialized */
|
||||
herr_t ret_value = SUCCEED; /* Return value */
|
||||
|
||||
FUNC_ENTER_NOAPI_NOINIT(H5D_layout_oh_create)
|
||||
|
||||
/* Sanity checking */
|
||||
HDassert(file);
|
||||
HDassert(oh);
|
||||
HDassert(dset);
|
||||
|
||||
/* Set some local variables, for convenience */
|
||||
layout = &dset->shared->layout;
|
||||
fill_prop = &dset->shared->dcpl_cache.fill;
|
||||
|
||||
/* Update the filters message, if this is a chunked dataset */
|
||||
if(layout->type == H5D_CHUNKED) {
|
||||
H5O_pline_t *pline; /* Dataset's I/O pipeline information */
|
||||
|
||||
pline = &dset->shared->dcpl_cache.pline;
|
||||
if(pline->nused > 0 && H5O_msg_append_oh(file, dxpl_id, oh, H5O_PLINE_ID, H5O_MSG_FLAG_CONSTANT, 0, pline) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update filter header message")
|
||||
} /* end if */
|
||||
|
||||
/* Initialize the layout information for the new dataset */
|
||||
if(dset->shared->layout.ops->init && (dset->shared->layout.ops->init)(file, dxpl_id, dset, dapl_id) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize layout information")
|
||||
|
||||
/* Indicate that the layout information was initialized */
|
||||
layout_init = TRUE;
|
||||
|
||||
/*
|
||||
* Allocate storage if space allocate time is early; otherwise delay
|
||||
* allocation until later.
|
||||
*/
|
||||
if(fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY)
|
||||
if(H5D_alloc_storage(dset, dxpl_id, H5D_ALLOC_CREATE, FALSE) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage")
|
||||
|
||||
/* Update external storage message, if it's used */
|
||||
if(dset->shared->dcpl_cache.efl.nused > 0) {
|
||||
H5O_efl_t *efl = &dset->shared->dcpl_cache.efl; /* Dataset's external file list */
|
||||
H5HL_t *heap; /* Pointer to local heap for EFL file names */
|
||||
size_t heap_size = H5HL_ALIGN(1);
|
||||
size_t u;
|
||||
|
||||
/* Determine size of heap needed to stored the file names */
|
||||
for(u = 0; u < efl->nused; ++u)
|
||||
heap_size += H5HL_ALIGN(HDstrlen(efl->slot[u].name) + 1);
|
||||
|
||||
/* Create the heap for the EFL file names */
|
||||
if(H5HL_create(file, dxpl_id, heap_size, &efl->heap_addr/*out*/) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create EFL file name heap")
|
||||
|
||||
/* Pin the heap down in memory */
|
||||
if(NULL == (heap = H5HL_protect(file, dxpl_id, efl->heap_addr, H5AC_WRITE)))
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTPROTECT, FAIL, "unable to protect EFL file name heap")
|
||||
|
||||
/* Insert "empty" name first */
|
||||
if((size_t)(-1) == H5HL_insert(file, dxpl_id, heap, (size_t)1, "")) {
|
||||
H5HL_unprotect(file, dxpl_id, heap, efl->heap_addr);
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert file name into heap")
|
||||
} /* end if */
|
||||
|
||||
for(u = 0; u < efl->nused; ++u) {
|
||||
size_t offset; /* Offset of file name in heap */
|
||||
|
||||
/* Insert file name into heap */
|
||||
if((size_t)(-1) == (offset = H5HL_insert(file, dxpl_id, heap,
|
||||
HDstrlen(efl->slot[u].name) + 1, efl->slot[u].name))) {
|
||||
H5HL_unprotect(file, dxpl_id, heap, efl->heap_addr);
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert file name into heap")
|
||||
} /* end if */
|
||||
|
||||
/* Store EFL file name offset */
|
||||
HDassert(0 == efl->slot[u].name_offset);
|
||||
efl->slot[u].name_offset = offset;
|
||||
} /* end for */
|
||||
|
||||
/* Release the heap */
|
||||
if(H5HL_unprotect(file, dxpl_id, heap, efl->heap_addr) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTUNPROTECT, FAIL, "unable to unprotect EFL file name heap")
|
||||
heap = NULL;
|
||||
|
||||
/* Insert EFL message into dataset object header */
|
||||
if(H5O_msg_append_oh(file, dxpl_id, oh, H5O_EFL_ID, H5O_MSG_FLAG_CONSTANT, 0, efl) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update external file list message")
|
||||
} /* end if */
|
||||
|
||||
/* Create layout message */
|
||||
/* (Don't make layout message constant unless allocation time is early, since space may not be allocated) */
|
||||
/* (Note: this is relying on H5D_alloc_storage not calling H5O_msg_write during dataset creation) */
|
||||
if(H5O_msg_append_oh(file, dxpl_id, oh, H5O_LAYOUT_ID, ((fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY && H5D_COMPACT != layout->type) ? H5O_MSG_FLAG_CONSTANT : 0), 0, layout) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout")
|
||||
|
||||
done:
|
||||
/* Error cleanup */
|
||||
if(ret_value < 0) {
|
||||
if(dset->shared->layout.type == H5D_CHUNKED && layout_init) {
|
||||
if(H5D_chunk_dest(file, dxpl_id, dset) < 0)
|
||||
HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy chunk cache")
|
||||
} /* end if */
|
||||
} /* end if */
|
||||
|
||||
FUNC_LEAVE_NOAPI(ret_value)
|
||||
} /* end H5D_layout_oh_create() */
|
||||
|
||||
|
||||
/*-------------------------------------------------------------------------
|
||||
* Function: H5D_layout_oh_read
|
||||
*
|
||||
* Purpose: Read layout/pline/efl information for dataset
|
||||
*
|
||||
* Return: Success: SUCCEED
|
||||
* Failure: FAIL
|
||||
*
|
||||
* Programmer: Quincey Koziol
|
||||
* Monday, July 27, 2009
|
||||
*
|
||||
*-------------------------------------------------------------------------
|
||||
*/
|
||||
herr_t
|
||||
H5D_layout_oh_read(H5D_t *dataset, hid_t dxpl_id, hid_t dapl_id, H5P_genplist_t *plist)
|
||||
{
|
||||
htri_t msg_exists; /* Whether a particular type of message exists */
|
||||
herr_t ret_value = SUCCEED; /* Return value */
|
||||
|
||||
FUNC_ENTER_NOAPI_NOINIT(H5D_layout_oh_read)
|
||||
|
||||
/* Sanity checking */
|
||||
HDassert(dataset);
|
||||
HDassert(plist);
|
||||
|
||||
/* Get the optional filters message */
|
||||
if((msg_exists = H5O_msg_exists(&(dataset->oloc), H5O_PLINE_ID, dxpl_id)) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't check if message exists")
|
||||
if(msg_exists) {
|
||||
/* Retrieve the I/O pipeline message */
|
||||
if(NULL == H5O_msg_read(&(dataset->oloc), H5O_PLINE_ID, &dataset->shared->dcpl_cache.pline, dxpl_id))
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve message")
|
||||
|
||||
/* Set the I/O pipeline info in the property list */
|
||||
if(H5P_set(plist, H5D_CRT_DATA_PIPELINE_NAME, &dataset->shared->dcpl_cache.pline) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set pipeline")
|
||||
} /* end if */
|
||||
|
||||
/*
|
||||
* Get the raw data layout info. It's actually stored in two locations:
|
||||
* the storage message of the dataset (dataset->storage) and certain
|
||||
* values are copied to the dataset create plist so the user can query
|
||||
* them.
|
||||
*/
|
||||
if(NULL == H5O_msg_read(&(dataset->oloc), H5O_LAYOUT_ID, &(dataset->shared->layout), dxpl_id))
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data layout message")
|
||||
|
||||
/* Check for external file list message (which might not exist) */
|
||||
if((msg_exists = H5O_msg_exists(&(dataset->oloc), H5O_EFL_ID, dxpl_id)) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't check if message exists")
|
||||
if(msg_exists) {
|
||||
/* Retrieve the EFL message */
|
||||
if(NULL == H5O_msg_read(&(dataset->oloc), H5O_EFL_ID, &dataset->shared->dcpl_cache.efl, dxpl_id))
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve message")
|
||||
|
||||
/* Set the EFL info in the property list */
|
||||
if(H5P_set(plist, H5D_CRT_EXT_FILE_LIST_NAME, &dataset->shared->dcpl_cache.efl) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set external file list")
|
||||
|
||||
/* Set the dataset's I/O operations */
|
||||
dataset->shared->layout.ops = H5D_LOPS_EFL;
|
||||
} /* end if */
|
||||
|
||||
/* Sanity check that the layout operations are set up */
|
||||
HDassert(dataset->shared->layout.ops);
|
||||
|
||||
/* Adjust chunk dimensions to omit datatype size (in last dimension) for creation property */
|
||||
if(H5D_CHUNKED == dataset->shared->layout.type)
|
||||
dataset->shared->layout.u.chunk.ndims--;
|
||||
/* Copy layout to the DCPL */
|
||||
if(H5P_set(plist, H5D_CRT_LAYOUT_NAME, &dataset->shared->layout) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set layout")
|
||||
/* Adjust chunk dimensions back again (*sigh*) */
|
||||
if(H5D_CHUNKED == dataset->shared->layout.type)
|
||||
dataset->shared->layout.u.chunk.ndims++;
|
||||
|
||||
switch(dataset->shared->layout.type) {
|
||||
case H5D_CONTIGUOUS:
|
||||
/* Compute the size of the contiguous storage for versions of the
|
||||
* layout message less than version 3 because versions 1 & 2 would
|
||||
* truncate the dimension sizes to 32-bits of information. - QAK 5/26/04
|
||||
*/
|
||||
if(dataset->shared->layout.version < 3) {
|
||||
hssize_t snelmts; /* Temporary holder for number of elements in dataspace */
|
||||
hsize_t nelmts; /* Number of elements in dataspace */
|
||||
size_t dt_size; /* Size of datatype */
|
||||
hsize_t tmp_size; /* Temporary holder for raw data size */
|
||||
|
||||
/* Retrieve the number of elements in the dataspace */
|
||||
if((snelmts = H5S_GET_EXTENT_NPOINTS(dataset->shared->space)) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve number of elements in dataspace")
|
||||
nelmts = (hsize_t)snelmts;
|
||||
|
||||
/* Get the datatype's size */
|
||||
if(0 == (dt_size = H5T_GET_SIZE(dataset->shared->type)))
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve size of datatype")
|
||||
|
||||
/* Compute the size of the dataset's contiguous storage */
|
||||
tmp_size = nelmts * dt_size;
|
||||
|
||||
/* Check for overflow during multiplication */
|
||||
if(nelmts != (tmp_size / dt_size))
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_OVERFLOW, FAIL, "size of dataset's storage overflowed")
|
||||
|
||||
/* Assign the dataset's contiguous storage size */
|
||||
dataset->shared->layout.u.contig.size = tmp_size;
|
||||
} /* end if */
|
||||
|
||||
/* Get the sieve buffer size for this dataset */
|
||||
dataset->shared->cache.contig.sieve_buf_size = H5F_SIEVE_BUF_SIZE(dataset->oloc.file);
|
||||
break;
|
||||
|
||||
case H5D_CHUNKED:
|
||||
/* Initialize the chunk cache for the dataset */
|
||||
if(H5D_chunk_init(dataset->oloc.file, dxpl_id, dataset, dapl_id) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize chunk cache")
|
||||
break;
|
||||
|
||||
case H5D_COMPACT:
|
||||
break;
|
||||
|
||||
default:
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unknown storage method")
|
||||
} /* end switch */ /*lint !e788 All appropriate cases are covered */
|
||||
|
||||
done:
|
||||
FUNC_LEAVE_NOAPI(ret_value)
|
||||
} /* end H5D_layout_oh_read() */
|
||||
|
||||
|
||||
/*-------------------------------------------------------------------------
|
||||
* Function: H5D_layout_oh_write
|
||||
*
|
||||
* Purpose: Read layout/pline/efl information for dataset
|
||||
*
|
||||
* Return: Success: SUCCEED
|
||||
* Failure: FAIL
|
||||
*
|
||||
* Programmer: Quincey Koziol
|
||||
* Monday, July 27, 2009
|
||||
*
|
||||
*-------------------------------------------------------------------------
|
||||
*/
|
||||
herr_t
|
||||
H5D_layout_oh_write(H5D_t *dataset, hid_t dxpl_id, H5O_t *oh, unsigned update_flags)
|
||||
{
|
||||
herr_t ret_value = SUCCEED; /* Return value */
|
||||
|
||||
FUNC_ENTER_NOAPI_NOINIT(H5D_layout_oh_write)
|
||||
|
||||
/* Sanity checking */
|
||||
HDassert(dataset);
|
||||
HDassert(oh);
|
||||
|
||||
/* Write the layout message to the dataset's header */
|
||||
if(H5O_msg_write_oh(dataset->oloc.file, dxpl_id, oh, H5O_LAYOUT_ID, H5O_MSG_FLAG_CONSTANT, update_flags, &dataset->shared->layout) < 0)
|
||||
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update layout message")
|
||||
|
||||
done:
|
||||
FUNC_LEAVE_NOAPI(ret_value)
|
||||
} /* end H5D_layout_oh_write() */
|
||||
|
||||
14
src/H5Dpkg.h
14
src/H5Dpkg.h
@ -118,6 +118,8 @@ typedef ssize_t (*H5D_layout_readvv_func_t)(const struct H5D_io_info_t *io_info,
|
||||
typedef ssize_t (*H5D_layout_writevv_func_t)(const struct H5D_io_info_t *io_info,
|
||||
size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_len_arr[], hsize_t dset_offset_arr[],
|
||||
size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[]);
|
||||
typedef herr_t (*H5D_layout_flush_func_t)(H5D_t *dataset, hid_t dxpl_id,
|
||||
unsigned flags);
|
||||
typedef herr_t (*H5D_layout_io_term_func_t)(const struct H5D_chunk_map_t *cm);
|
||||
|
||||
/* Typedef for grouping layout I/O routines */
|
||||
@ -134,6 +136,7 @@ typedef struct H5D_layout_ops_t {
|
||||
#endif /* H5_HAVE_PARALLEL */
|
||||
H5D_layout_readvv_func_t readvv; /* Low-level I/O routine for reading data */
|
||||
H5D_layout_writevv_func_t writevv; /* Low-level I/O routine for writing data */
|
||||
H5D_layout_flush_func_t flush; /* Low-level I/O routine for flushing raw data */
|
||||
H5D_layout_io_term_func_t io_term; /* I/O shutdown routine */
|
||||
} H5D_layout_ops_t;
|
||||
|
||||
@ -533,6 +536,7 @@ H5_DLL herr_t H5D_vlen_get_buf_size(void *elem, hid_t type_id, unsigned ndim,
|
||||
H5_DLL herr_t H5D_check_filters(H5D_t *dataset);
|
||||
H5_DLL herr_t H5D_set_extent(H5D_t *dataset, const hsize_t *size, hid_t dxpl_id);
|
||||
H5_DLL herr_t H5D_get_dxpl_cache(hid_t dxpl_id, H5D_dxpl_cache_t **cache);
|
||||
H5_DLL herr_t H5D_flush_sieve_buf(H5D_t *dataset, hid_t dxpl_id);
|
||||
|
||||
/* Functions that perform direct serial I/O operations */
|
||||
H5_DLL herr_t H5D_select_read(const H5D_io_info_t *io_info,
|
||||
@ -553,6 +557,15 @@ H5_DLL herr_t H5D_scatgath_write(const H5D_io_info_t *io_info,
|
||||
const H5D_type_info_t *type_info,
|
||||
hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space);
|
||||
|
||||
/* Functions that operate on dataset's layout information */
|
||||
H5_DLL herr_t H5D_layout_set_io_ops(const H5D_t *dataset);
|
||||
H5_DLL herr_t H5D_layout_oh_create(H5F_t *file, hid_t dxpl_id, H5O_t *oh,
|
||||
H5D_t *dset, hid_t dapl_id);
|
||||
H5_DLL herr_t H5D_layout_oh_read(H5D_t *dset, hid_t dxpl_id, hid_t dapl_id,
|
||||
H5P_genplist_t *plist);
|
||||
H5_DLL herr_t H5D_layout_oh_write(H5D_t *dataset, hid_t dxpl_id, H5O_t *oh,
|
||||
unsigned update_flags);
|
||||
|
||||
/* Functions that operate on contiguous storage */
|
||||
H5_DLL herr_t H5D_contig_alloc(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout);
|
||||
H5_DLL herr_t H5D_contig_fill(H5D_t *dset, hid_t dxpl_id);
|
||||
@ -588,7 +601,6 @@ H5_DLL void *H5D_chunk_lock(const H5D_io_info_t *io_info,
|
||||
H5_DLL herr_t H5D_chunk_unlock(const H5D_io_info_t *io_info,
|
||||
const H5D_chunk_ud_t *udata, hbool_t dirty, unsigned idx_hint, void *chunk,
|
||||
uint32_t naccessed);
|
||||
H5_DLL herr_t H5D_chunk_flush(H5D_t *dset, hid_t dxpl_id, unsigned flags);
|
||||
H5_DLL herr_t H5D_chunk_allocated(H5D_t *dset, hid_t dxpl_id, hsize_t *nbytes);
|
||||
H5_DLL herr_t H5D_chunk_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite);
|
||||
H5_DLL herr_t H5D_chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id,
|
||||
|
||||
@ -48,7 +48,7 @@ libhdf5_la_SOURCES= H5.c H5checksum.c H5dbg.c H5system.c H5timer.c H5trace.c \
|
||||
H5C.c H5CS.c \
|
||||
H5D.c H5Dbtree.c H5Dchunk.c H5Dcompact.c H5Dcontig.c H5Ddbg.c \
|
||||
H5Ddeprec.c H5Defl.c H5Dfill.c H5Dint.c \
|
||||
H5Dio.c \
|
||||
H5Dio.c H5Dlayout.c \
|
||||
H5Dmpio.c H5Doh.c H5Dscatgath.c H5Dselect.c H5Dtest.c \
|
||||
H5E.c H5Edeprec.c H5Eint.c \
|
||||
H5EA.c H5EAcache.c H5EAdbg.c H5EAdblkpage.c H5EAdblock.c H5EAhdr.c \
|
||||
|
||||
@ -84,7 +84,7 @@ am_libhdf5_la_OBJECTS = H5.lo H5checksum.lo H5dbg.lo H5system.lo \
|
||||
H5Bdbg.lo H5B2.lo H5B2cache.lo H5B2dbg.lo H5B2int.lo \
|
||||
H5B2stat.lo H5B2test.lo H5C.lo H5CS.lo H5D.lo H5Dbtree.lo \
|
||||
H5Dchunk.lo H5Dcompact.lo H5Dcontig.lo H5Ddbg.lo H5Ddeprec.lo \
|
||||
H5Defl.lo H5Dfill.lo H5Dint.lo H5Dio.lo H5Dmpio.lo H5Doh.lo \
|
||||
H5Defl.lo H5Dfill.lo H5Dint.lo H5Dio.lo H5Dlayout.lo H5Dmpio.lo H5Doh.lo \
|
||||
H5Dscatgath.lo H5Dselect.lo H5Dtest.lo H5E.lo H5Edeprec.lo \
|
||||
H5Eint.lo H5EA.lo H5EAcache.lo H5EAdbg.lo H5EAdblkpage.lo \
|
||||
H5EAdblock.lo H5EAhdr.lo H5EAiblock.lo H5EAint.lo \
|
||||
@ -434,7 +434,7 @@ libhdf5_la_SOURCES = H5.c H5checksum.c H5dbg.c H5system.c H5timer.c H5trace.c \
|
||||
H5C.c H5CS.c \
|
||||
H5D.c H5Dbtree.c H5Dchunk.c H5Dcompact.c H5Dcontig.c H5Ddbg.c \
|
||||
H5Ddeprec.c H5Defl.c H5Dfill.c H5Dint.c \
|
||||
H5Dio.c \
|
||||
H5Dio.c H5Dlayout.c \
|
||||
H5Dmpio.c H5Doh.c H5Dscatgath.c H5Dselect.c H5Dtest.c \
|
||||
H5E.c H5Edeprec.c H5Eint.c \
|
||||
H5EA.c H5EAcache.c H5EAdbg.c H5EAdblkpage.c H5EAdblock.c H5EAhdr.c \
|
||||
@ -650,6 +650,7 @@ distclean-compile:
|
||||
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5Dfill.Plo@am__quote@
|
||||
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5Dint.Plo@am__quote@
|
||||
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5Dio.Plo@am__quote@
|
||||
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5Dlayout.Plo@am__quote@
|
||||
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5Dmpio.Plo@am__quote@
|
||||
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5Doh.Plo@am__quote@
|
||||
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5Dscatgath.Plo@am__quote@
|
||||
|
||||
Loading…
Reference in New Issue
Block a user