diff options
| -rw-r--r-- | MANIFEST | 3 | ||||
| -rw-r--r-- | doc/html/H5.format.html | 250 | ||||
| -rw-r--r-- | src/H5A.c | 6 | ||||
| -rw-r--r-- | src/H5D.c | 248 | ||||
| -rw-r--r-- | src/H5Dcompact.c | 6 | ||||
| -rw-r--r-- | src/H5Dcontig.c | 29 | ||||
| -rw-r--r-- | src/H5Dio.c | 92 | ||||
| -rw-r--r-- | src/H5Distore.c | 222 | ||||
| -rw-r--r-- | src/H5Dpkg.h | 7 | ||||
| -rw-r--r-- | src/H5Dprivate.h | 2 | ||||
| -rw-r--r-- | src/H5Dseq.c | 4 | ||||
| -rw-r--r-- | src/H5Dtest.c | 116 | ||||
| -rw-r--r-- | src/H5Fcompact.c | 6 | ||||
| -rw-r--r-- | src/H5Fcontig.c | 29 | ||||
| -rw-r--r-- | src/H5Fistore.c | 222 | ||||
| -rw-r--r-- | src/H5Fseq.c | 4 | ||||
| -rw-r--r-- | src/H5Oattr.c | 2 | ||||
| -rw-r--r-- | src/H5Olayout.c | 310 | ||||
| -rw-r--r-- | src/H5Oprivate.h | 33 | ||||
| -rw-r--r-- | src/H5Pdcpl.c | 28 | ||||
| -rw-r--r-- | src/H5S.c | 6 | ||||
| -rw-r--r-- | src/H5Sall.c | 4 | ||||
| -rw-r--r-- | src/H5Smpio.c | 6 | ||||
| -rw-r--r-- | src/H5Sprivate.h | 2 | ||||
| -rw-r--r-- | src/H5V.c | 8 | ||||
| -rw-r--r-- | src/H5Vprivate.h | 6 | ||||
| -rw-r--r-- | src/H5Z.c | 7 | ||||
| -rw-r--r-- | src/Makefile.in | 33 | ||||
| -rw-r--r-- | test/dsets.c | 2 | ||||
| -rw-r--r-- | test/gen_old_layout.c | 95 | ||||
| -rw-r--r-- | test/tlayouto.h5 | bin | 0 -> 1576 bytes | |||
| -rw-r--r-- | test/tmisc.c | 189 |
32 files changed, 1372 insertions, 605 deletions
@@ -782,6 +782,7 @@ ./src/H5Dprivate.h ./src/H5Dpublic.h ./src/H5Dpkg.h +./src/H5Dtest.c ./src/H5Ztrans.c ./src/H5E.c ./src/H5Edefin.h @@ -997,6 +998,7 @@ ./test/gen_old_array.c _DO_NOT_DISTRIBUTE_ ./test/gen_new_array.c _DO_NOT_DISTRIBUTE_ ./test/gen_new_fill.c _DO_NOT_DISTRIBUTE_ +./test/gen_old_layout.c _DO_NOT_DISTRIBUTE_ ./test/gen_old_mtime.c _DO_NOT_DISTRIBUTE_ ./test/gen_new_mtime.c _DO_NOT_DISTRIBUTE_ ./test/gen_new_super.c _DO_NOT_DISTRIBUTE_ @@ -1022,6 +1024,7 @@ ./test/th5s.h5 ./test/theap.c ./test/titerate.c +./test/tlayouto.h5 ./test/tmeta.c ./test/tmisc.c ./test/tmtimen.h5 diff --git a/doc/html/H5.format.html b/doc/html/H5.format.html index 1868138..ae1ff23 100644 --- a/doc/html/H5.format.html +++ b/doc/html/H5.format.html @@ -130,8 +130,7 @@ TABLE.list TD { border:none; } <li><a href="#AttributeMessage">Name: Attribute</a> <!-- 0x000c --> <li><a href="#CommentMessage">Name: Object Comment</a> <!-- 0x000d --> <li><a href="#OldModifiedMessage">Name: Object Modification Date and Time (Old)</a> <!-- 0x000e --> -<!-- <li><a href="#SharedMessage">Name: Shared Object Message</a> --> <!-- 0x000f --> - <li><a href="#ReservedMessage_000F">Name: Reserved - not assigned yet</a> <!-- 0x000f --> + <li><a href="#SharedMessage">Name: Shared Object Message</a> <!-- 0x000f --> <li><a href="#ContinuationMessage">Name: Object Header Continuation</a> <!-- 0x0010 --> <li><a href="#SymbolTableMessage">Name: Group Message</a> <!-- 0x0011 --> <li><a href="#ModifiedMessage">Name: Object Modification Date and Time</a> <!-- 0x0012 --> @@ -4729,14 +4728,17 @@ TABLE.list TD { border:none; } addresses. <li>The array can be stored in one contiguous block, as part of - this object header message. + this object header message (this is called "compact" storage below). </ol> + + <P>Version 3 of this message re-structured the format into specific + properties that are required for each layout class. <p> <center> <table border cellpadding=4 width="80%"> <caption align=top> - <B>Data Layout Message</B> + <B>Data Layout Message, Versions 1 and 2</B> </caption> <tr align=center> @@ -4850,6 +4852,233 @@ TABLE.list TD { border:none; } </table> </center> + <p> + <center> + <table border cellpadding=4 width="80%"> + <caption align=top> + <B>Data Layout Message, Version 3</B> + </caption> + + <tr align=center> + <th width="25%">byte</th> + <th width="25%">byte</th> + <th width="25%">byte</th> + <th width="25%">byte</th> + </tr> + + <tr align=center> + <td>Version</td> + <td>Layout Class</td> + </tr> + + <tr align=center> + <td colspan=4>Properties</td> + </tr> + + </table> + </center> + + <p> + <center> + <table align=center width="80%"> + <tr align=left> + <th width="30%"><U><font size=+1>Field Name</font></U></th> + <th><U><font size=+1>Description</font></U></th> + </tr> + + <tr valign=top> + <td>Version</td> + <td>A version number for the layout message. This value can be + either 1, 2 or 3.</td> + </tr> + + <tr valign=top> + <td>Layout Class</td> + <td>The layout class specifies how the other fields of the + layout message are to be interpreted. A value of one + indicates contiguous storage, a value of two + indicates chunked storage, + while a value of three + indicates compact storage.</td> + </tr> + + <tr valign=top> + <td>Properties</td> + <td>This variable-sized field encodes information specific to each + layout class and is described below. If there is no property + information specified for a layout class, the size of this field + is zero bytes.</td> + </tr> + + </table> + </center> + + <P>Class-specific information for contiguous layout (Class 0): + + <p> + <center> + <table border cellpadding=4 width="80%"> + <caption align=top> + <B>Property Descriptions</B> + </caption> + + <tr align=center> + <th width="25%">byte</th> + <th width="25%">byte</th> + <th width="25%">byte</th> + <th width="25%">byte</th> + </tr> + + <tr align=center> + <td colspan=4><br>Address<br><br></td> + </tr> + + <tr align=center> + <td colspan=4><br>Size<br><br></td> + </tr> + </table> + </center> + + <p> + <center> + <table align=center width="80%"> + <tr align=left> + <th width="30%"><U><font size=+1>Field Name</font></U></th> + <th><U><font size=+1>Description</font></U></th> + </tr> + + <tr valign=top> + <td>Address</td> + <td>This is the address of the first byte of raw data storage. + The address may have the "undefined address" value, to indicate + that storage has not yet been allocated for this array.</td> + </tr> + + <tr valign=top> + <td>Size</td> + <td>This field contains the size allocated to store the raw data.</td> + </table> + </center> + + <P>Class-specific information for chunked layout (Class 1): + + <p> + <center> + <table border cellpadding=4 width="80%"> + <caption align=top> + <B>Property Descriptions</B> + </caption> + + <tr align=center> + <th width="25%">byte</th> + <th width="25%">byte</th> + <th width="25%">byte</th> + <th width="25%">byte</th> + </tr> + + <tr align=center> + <td>Dimensionality</td> + </tr> + + <tr align=center> + <td colspan=4><br>Address<br><br></td> + </tr> + + <tr align=center> + <td colspan=4>Dimension 0 (4-bytes)</td> + </tr> + + <tr align=center> + <td colspan=4>Dimension 1 (4-bytes)</td> + </tr> + + <tr align=center> + <td colspan=4>...</td> + </tr> + </table> + </center> + + <p> + <center> + <table align=center width="80%"> + <tr align=left> + <th width="30%"><U><font size=+1>Field Name</font></U></th> + <th><U><font size=+1>Description</font></U></th> + </tr> + + <tr valign=top> + <td>Dimensionality</td> + <td>A chunk has a fixed dimensionality. This field + specifies the number of dimension size fields later in the + message.</td> + </tr> + + <tr valign=top> + <td>Address</td> + <td>This is the address + of the B-tree that is used to look up the addresses of the + chunks. + The address + may have the "undefined address" value, to indicate that + storage has not yet been allocated for this array.</td> + </tr> + + <tr valign=top> + <td>Dimensions</td> + <td>The dimension sizes define the size of a single chunk.</td> + </tr> + </table> + </center> + + <P>Class-specific information for compact layout (Class 2): + + <p> + <center> + <table border cellpadding=4 width="80%"> + <caption align=top> + <B>Property Descriptions</B> + </caption> + + <tr align=center> + <th width="25%">byte</th> + <th width="25%">byte</th> + <th width="25%">byte</th> + <th width="25%">byte</th> + </tr> + + <tr align=center> + <td colspan=2>Size</td> + </tr> + + <tr align=center> + <td colspan=4>Raw Data</td> + </tr> + + <tr align=center> + <td colspan=4>...</td> + </tr> + </table> + </center> + + <p> + <center> + <table align=center width="80%"> + <tr align=left> + <th width="30%"><U><font size=+1>Field Name</font></U></th> + <th><U><font size=+1>Description</font></U></th> + </tr> + + <tr valign=top> + <td>Size</td> + <td>This field contains the size of the raw data for the dataset array.</td> + + <tr valign=top> + <td>Raw Data</td> + <td>This field contains the raw data for the dataset array.</td> + </tr> + </table> + </center> + <hr> <h4><a name="ReservedMessage_0009">Name: Reserved - Not Assigned Yet</a></h4> @@ -5348,7 +5577,6 @@ TABLE.list TD { border:none; } </table> </center> -<!-- <hr> <h4><a name="SharedMessage">Name: Shared Object Message</a></h4> <b>Header Message Type:</b> 0x000F<br> @@ -5444,20 +5672,8 @@ TABLE.list TD { border:none; } </tr> </table> </center> ---> - <hr> - <h4><a name="ReservedMessage_000F">Name: Reserved - Not Assigned Yet</a></h4> - <b>Header Message Type:</b> 0x000F<BR> - <b>Length:</b> N/A<BR> - <b>Status:</b> N/A<BR> - <b>Format of Data:</b> N/A<BR> - - <p><b>Purpose and Description:</b> This message type was skipped during - the initial specification of the file format and may be used in a - future expansion to the format. - <hr> <h4><a name="ContinuationMessage">Name: Object Header Continuation</a></h4> <b>Header Message Type:</b> 0x0010<BR> @@ -269,7 +269,7 @@ H5A_create(const H5G_entry_t *ent, const char *name, const H5T_t *type, assert(attr->dt_size>0); attr->ds_size=H5O_raw_size(H5O_SDSPACE_ID,attr->ent.file,&(space->extent)); assert(attr->ds_size>0); - H5_ASSIGN_OVERFLOW(attr->data_size,H5S_get_simple_extent_npoints(attr->ds)*H5T_get_size(attr->dt),hssize_t,size_t); + H5_ASSIGN_OVERFLOW(attr->data_size,H5S_GET_SIMPLE_EXTENT_NPOINTS(attr->ds)*H5T_get_size(attr->dt),hssize_t,size_t); /* Hold the symbol table entry (and file) open */ if (H5O_open(&(attr->ent)) < 0) @@ -629,7 +629,7 @@ H5A_write(H5A_t *attr, const H5T_t *mem_type, const void *buf, hid_t dxpl_id) assert(buf); /* Create buffer for data to store on disk */ - if((snelmts=H5S_get_simple_extent_npoints (attr->ds))<0) + if((snelmts=H5S_GET_SIMPLE_EXTENT_NPOINTS(attr->ds))<0) HGOTO_ERROR (H5E_ATTR, H5E_CANTCOUNT, FAIL, "dataspace is invalid") nelmts=(hsize_t)snelmts; @@ -778,7 +778,7 @@ H5A_read(const H5A_t *attr, const H5T_t *mem_type, void *buf, hid_t dxpl_id) assert(buf); /* Create buffer for data to store on disk */ - if((snelmts=H5S_get_simple_extent_npoints (attr->ds))<0) + if((snelmts=H5S_GET_SIMPLE_EXTENT_NPOINTS(attr->ds))<0) HGOTO_ERROR (H5E_ATTR, H5E_CANTCOUNT, FAIL, "dataspace is invalid") nelmts=(hsize_t)snelmts; @@ -189,7 +189,7 @@ H5D_init_interface(void) H5P_genclass_t *crt_pclass; H5D_layout_t layout = H5D_CRT_LAYOUT_DEF; unsigned chunk_ndims = H5D_CRT_CHUNK_DIM_DEF; - hsize_t chunk_size[H5O_LAYOUT_NDIMS] = H5D_CRT_CHUNK_SIZE_DEF; + size_t chunk_size[H5O_LAYOUT_NDIMS] = H5D_CRT_CHUNK_SIZE_DEF; H5O_fill_t fill = H5D_CRT_FILL_VALUE_DEF; H5D_alloc_time_t alloc_time = H5D_CRT_ALLOC_TIME_DEF; H5D_fill_time_t fill_time = H5D_CRT_FILL_TIME_DEF; @@ -1443,7 +1443,7 @@ H5D_get_space_status(const H5D_t *dset, H5D_space_status_t *allocation, hid_t dx assert(space); /* Get the total number of elements in dataset's dataspace */ - if((total_elem=H5S_get_simple_extent_npoints(space))<0) + if((total_elem=H5S_GET_SIMPLE_EXTENT_NPOINTS(space))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "unable to get # of dataspace elements") /* Get the size of the dataset's datatype */ @@ -1788,7 +1788,7 @@ H5D_update_entry_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset, H5P_genplist_t *p /* Add the dataset's raw data size to the size of the header, if the raw data will be stored as compact */ if (layout->type == H5D_COMPACT) - ohdr_size += layout->size; + ohdr_size += layout->u.compact.size; /* Create (open for write access) an object header */ if (H5O_create(file, dxpl_id, ohdr_size, ent) < 0) @@ -2031,10 +2031,8 @@ H5D_create(H5G_entry_t *loc, const char *name, hid_t type_id, const H5S_t *space H5D_t *new_dset = NULL; int i, ndims; unsigned u; - hsize_t max_dim[H5O_LAYOUT_NDIMS]={0}; H5F_t *file=NULL; unsigned chunk_ndims = 0; /* Dimensionality of chunk */ - hsize_t chunk_size[H5O_LAYOUT_NDIMS]={0}; H5P_genplist_t *dc_plist=NULL; /* New Property list */ hbool_t has_vl_type=FALSE; /* Flag to indicate a VL-type for dataset */ H5D_t *ret_value; /* Return value */ @@ -2159,80 +2157,88 @@ H5D_create(H5G_entry_t *loc, const char *name, hid_t type_id, const H5S_t *space /* Check if this dataset is going into a parallel file and set space allocation time */ if(IS_H5FD_MPI(file)) new_dset->alloc_time=H5D_ALLOC_TIME_EARLY; - - /* Set up layout information */ - if((ndims=H5S_GET_SIMPLE_EXTENT_NDIMS(new_dset->space))<0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, NULL, "unable to get rank") - new_dset->layout.ndims = (unsigned)ndims + 1; - assert((unsigned)(new_dset->layout.ndims) <= NELMTS(new_dset->layout.dim)); - new_dset->layout.dim[new_dset->layout.ndims-1] = H5T_get_size(new_dset->type); - new_dset->layout.addr = HADDR_UNDEF; /* Initialize to no address */ switch (new_dset->layout.type) { case H5D_CONTIGUOUS: - /* - * The maximum size of the dataset cannot exceed the storage size. - * Also, only the slowest varying dimension of a simple data space - * can be extendible. - */ - if ((ndims=H5S_get_simple_extent_dims(new_dset->space, new_dset->layout.dim, max_dim))<0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize contiguous storage") - for (i=1; i<ndims; i++) { - if (max_dim[i]>new_dset->layout.dim[i]) - HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "only the first dimension can be extendible") - } - if (new_dset->efl.nused>0) { - hsize_t max_points = H5S_get_npoints_max (new_dset->space); - hsize_t max_storage = H5O_efl_total_size (&new_dset->efl); - - if (H5S_UNLIMITED==max_points) { - if (H5O_EFL_UNLIMITED!=max_storage) - HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "unlimited data space but finite storage") - } else if (max_points * H5T_get_size (type) < max_points) { - HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "data space * type size overflowed") - } else if (max_points * H5T_get_size (type) > max_storage) { - HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "data space size exceeds external storage size") + { + hssize_t tmp_size; /* Temporary holder for raw data size */ + hsize_t dim[H5O_LAYOUT_NDIMS]; /* Current size of data in elements */ + hsize_t max_dim[H5O_LAYOUT_NDIMS]; /* Maximum size of data in elements */ + + /* + * The maximum size of the dataset cannot exceed the storage size. + * Also, only the slowest varying dimension of a simple data space + * can be extendible (currently only for external data storage). + */ + new_dset->layout.u.contig.addr = HADDR_UNDEF; /* Initialize to no address */ + + if ((ndims=H5S_get_simple_extent_dims(new_dset->space, dim, max_dim))<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize contiguous storage") + for (i=1; i<ndims; i++) + if (max_dim[i]>dim[i]) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "only the first dimension can be extendible") + if (new_dset->efl.nused>0) { + hsize_t max_points = H5S_get_npoints_max (new_dset->space); + hsize_t max_storage = H5O_efl_total_size (&new_dset->efl); + + if (H5S_UNLIMITED==max_points) { + if (H5O_EFL_UNLIMITED!=max_storage) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "unlimited data space but finite storage") + } else if (max_points * H5T_get_size (type) < max_points) { + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "data space * type size overflowed") + } else if (max_points * H5T_get_size (type) > max_storage) { + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "data space size exceeds external storage size") + } + } else if (ndims>0 && max_dim[0]>dim[0]) { + HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, NULL, "extendible contiguous non-external dataset") } - } else if (ndims>0 && max_dim[0]>new_dset->layout.dim[0]) { - HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, NULL, "extendible contiguous non-external dataset") - } - /* Compute the total size of a chunk */ - for (u=1, new_dset->layout.chunk_size=new_dset->layout.dim[0]; u<new_dset->layout.ndims; u++) - new_dset->layout.chunk_size *= new_dset->layout.dim[u]; + /* Compute the total size of a chunk */ + tmp_size = H5S_GET_SIMPLE_EXTENT_NPOINTS(new_dset->space) * + H5T_get_size(new_dset->type); + H5_ASSIGN_OVERFLOW(new_dset->layout.u.contig.size,tmp_size,hssize_t,hsize_t); + } /* end case */ break; case H5D_CHUNKED: - /* - * Chunked storage allows any type of data space extension, so we - * don't even bother checking. - */ - if(chunk_ndims != (unsigned)H5S_GET_SIMPLE_EXTENT_NDIMS(new_dset->space)) - HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "dimensionality of chunks doesn't match the data space") - if (new_dset->efl.nused>0) - HGOTO_ERROR (H5E_DATASET, H5E_BADVALUE, NULL, "external storage not supported with chunked layout") - - /* - * The chunk size of a dimension with a fixed size cannot exceed - * the maximum dimension size - */ - if(H5P_get(dc_plist, H5D_CRT_CHUNK_SIZE_NAME, chunk_size) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve chunk size") - - if (H5S_get_simple_extent_dims(new_dset->space, NULL, max_dim)<0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to query maximum dimensions") - for (u=0; u<new_dset->layout.ndims-1; u++) { - if(max_dim[u] != H5S_UNLIMITED && max_dim[u] < chunk_size[u]) - HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "chunk size must be <= maximum dimension size for fixed-sized dimensions") - } + { + hsize_t max_dim[H5O_LAYOUT_NDIMS]; /* Maximum size of data in elements */ + + /* Set up layout information */ + if((ndims=H5S_GET_SIMPLE_EXTENT_NDIMS(new_dset->space))<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, NULL, "unable to get rank") + new_dset->layout.u.chunk.ndims = (unsigned)ndims + 1; + assert((unsigned)(new_dset->layout.u.chunk.ndims) <= NELMTS(new_dset->layout.u.chunk.dim)); - /* Set the dataset's chunk sizes from the property list's chunk sizes */ - for (u=0; u<new_dset->layout.ndims-1; u++) - new_dset->layout.dim[u] = chunk_size[u]; + new_dset->layout.u.chunk.addr = HADDR_UNDEF; /* Initialize to no address */ + + /* + * Chunked storage allows any type of data space extension, so we + * don't even bother checking. + */ + if(chunk_ndims != ndims) + HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "dimensionality of chunks doesn't match the data space") + if (new_dset->efl.nused>0) + HGOTO_ERROR (H5E_DATASET, H5E_BADVALUE, NULL, "external storage not supported with chunked layout") - /* Compute the total size of a chunk */ - for (u=1, new_dset->layout.chunk_size=new_dset->layout.dim[0]; u<new_dset->layout.ndims; u++) - new_dset->layout.chunk_size *= new_dset->layout.dim[u]; + /* + * The chunk size of a dimension with a fixed size cannot exceed + * the maximum dimension size + */ + if(H5P_get(dc_plist, H5D_CRT_CHUNK_SIZE_NAME, new_dset->layout.u.chunk.dim) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve chunk size") + new_dset->layout.u.chunk.dim[new_dset->layout.u.chunk.ndims-1] = H5T_get_size(new_dset->type); + + if (H5S_get_simple_extent_dims(new_dset->space, NULL, max_dim)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to query maximum dimensions") + for (u=0; u<new_dset->layout.u.chunk.ndims-1; u++) + if(max_dim[u] != H5S_UNLIMITED && max_dim[u] < new_dset->layout.u.chunk.dim[u]) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "chunk size must be <= maximum dimension size for fixed-sized dimensions") + + /* Compute the total size of a chunk */ + for (u=1, new_dset->layout.u.chunk.size=new_dset->layout.u.chunk.dim[0]; u<new_dset->layout.u.chunk.ndims; u++) + new_dset->layout.u.chunk.size *= new_dset->layout.u.chunk.dim[u]; + } /* end case */ break; case H5D_COMPACT: @@ -2244,19 +2250,17 @@ H5D_create(H5G_entry_t *loc, const char *name, hid_t type_id, const H5S_t *space * Compact dataset is stored in dataset object header message of * layout. */ - tmp_size = H5S_get_simple_extent_npoints(space) * + tmp_size = H5S_GET_SIMPLE_EXTENT_NPOINTS(space) * H5T_get_size(new_dset->type); - H5_ASSIGN_OVERFLOW(new_dset->layout.size,tmp_size,hssize_t,size_t); + H5_ASSIGN_OVERFLOW(new_dset->layout.u.compact.size,tmp_size,hssize_t,size_t); + /* Verify data size is smaller than maximum header message size * (64KB) minus other layout message fields. */ comp_data_size=H5O_MAX_SIZE-H5O_layout_meta_size(file, &(new_dset->layout)); - if(new_dset->layout.size > comp_data_size) + if(new_dset->layout.u.compact.size > comp_data_size) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "compact dataset size is bigger than header message maximum size") - if (H5S_get_simple_extent_dims(space, new_dset->layout.dim, NULL)<0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize dimension size of compact dataset storage"); - } - + } /* end case */ break; default: @@ -2464,7 +2468,6 @@ H5D_open_oid(const H5G_entry_t *ent, hid_t dxpl_id) H5O_fill_new_t fill = {NULL, 0, NULL, H5D_ALLOC_TIME_LATE, H5D_CRT_FILL_TIME_DEF, TRUE}; H5O_fill_t *fill_prop; /* Pointer to dataset's fill value area */ H5O_pline_t pline; /* I/O pipeline information */ - H5D_layout_t layout; /* Dataset layout */ H5P_genplist_t *plist; /* Property list */ H5D_t *ret_value = NULL; /*return value */ @@ -2517,11 +2520,21 @@ H5D_open_oid(const H5G_entry_t *ent, hid_t dxpl_id) */ if (NULL==H5O_read(&(dataset->ent), H5O_LAYOUT_ID, 0, &(dataset->layout), dxpl_id)) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to read data layout message") + if(H5P_set(plist, H5D_CRT_LAYOUT_NAME, &dataset->layout.type) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set layout") switch (dataset->layout.type) { case H5D_CONTIGUOUS: - layout = H5D_CONTIGUOUS; - if(H5P_set(plist, H5D_CRT_LAYOUT_NAME, &layout) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set layout") + /* 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->layout.version<3) { + hssize_t tmp_size; /* Temporary holder for raw data size */ + + tmp_size = H5S_GET_SIMPLE_EXTENT_NPOINTS(dataset->space) * + H5T_get_size(dataset->type); + H5_ASSIGN_OVERFLOW(dataset->layout.u.contig.size,tmp_size,hssize_t,hsize_t); + } /* end if */ break; case H5D_CHUNKED: @@ -2533,23 +2546,18 @@ H5D_open_oid(const H5G_entry_t *ent, hid_t dxpl_id) { unsigned chunk_ndims; /* Dimensionality of chunk */ - layout = H5D_CHUNKED; - chunk_ndims = dataset->layout.ndims - 1; + chunk_ndims = dataset->layout.u.chunk.ndims - 1; - if(H5P_set(plist, H5D_CRT_LAYOUT_NAME, &layout) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set layout") if(H5P_set(plist, H5D_CRT_CHUNK_DIM_NAME, &chunk_ndims) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set chunk dimensions") - if(H5P_set(plist, H5D_CRT_CHUNK_SIZE_NAME, dataset->layout.dim) < 0) + if(H5P_set(plist, H5D_CRT_CHUNK_SIZE_NAME, dataset->layout.u.chunk.dim) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set chunk size") } break; case H5D_COMPACT: - layout = H5D_COMPACT; - if(H5P_set(plist, H5D_CRT_LAYOUT_NAME, &layout) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set layout") break; + default: HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet") } /* end switch */ @@ -2617,19 +2625,22 @@ H5D_open_oid(const H5G_entry_t *ent, hid_t dxpl_id) /* Get the external file list message, which might not exist. Space is * also undefined when space allocate time is H5D_ALLOC_TIME_LATE. */ - if( !H5F_addr_defined(dataset->layout.addr)) { + if((dataset->layout.type==H5D_CONTIGUOUS && !H5F_addr_defined(dataset->layout.u.contig.addr)) + || (dataset->layout.type==H5D_CHUNKED && !H5F_addr_defined(dataset->layout.u.chunk.addr))) { HDmemset(&dataset->efl,0,sizeof(H5O_efl_t)); if(NULL != H5O_read(&(dataset->ent), H5O_EFL_ID, 0, &dataset->efl, dxpl_id)) if(H5P_set(plist, H5D_CRT_EXT_FILE_LIST_NAME, &dataset->efl) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set external file list") } + /* * Make sure all storage is properly initialized. * This is important only for parallel I/O where the space must * be fully allocated before I/O can happen. */ if ((H5F_get_intent(dataset->ent.file) & H5F_ACC_RDWR) - && (dataset->layout.type!=H5D_COMPACT && dataset->layout.addr==HADDR_UNDEF) + && ((dataset->layout.type==H5D_CONTIGUOUS && !H5F_addr_defined(dataset->layout.u.contig.addr)) + || (dataset->layout.type==H5D_CHUNKED && !H5F_addr_defined(dataset->layout.u.chunk.addr))) && IS_H5FD_MPI(dataset->ent.file)) { if (H5D_alloc_storage(dataset->ent.file, dxpl_id, dataset,H5D_ALLOC_OPEN, TRUE, FALSE)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize file storage") @@ -2708,10 +2719,10 @@ H5D_close(H5D_t *dataset) H5I_dec_ref(dataset->dcpl_id) < 0); /* Update header message of layout for compact dataset. */ - if(dataset->layout.type==H5D_COMPACT && dataset->layout.dirty) { + if(dataset->layout.type==H5D_COMPACT && dataset->layout.u.compact.dirty) { if(H5O_modify(&(dataset->ent), H5O_LAYOUT_ID, 0, 0, 1, &(dataset->layout), H5AC_dxpl_id)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout message") - dataset->layout.dirty = FALSE; + dataset->layout.u.compact.dirty = FALSE; } /* end if */ /* Remove the dataset from the list of opened objects in the file */ @@ -2732,7 +2743,7 @@ H5D_close(H5D_t *dataset) dataset->ent.file = NULL; /* Free the buffer for the raw data for compact datasets */ if(dataset->layout.type==H5D_COMPACT) - dataset->layout.buf=H5MM_xfree(dataset->layout.buf); + dataset->layout.u.compact.buf=H5MM_xfree(dataset->layout.u.compact.buf); H5FL_FREE(H5D_t,dataset); if (free_failed) @@ -2924,13 +2935,13 @@ H5D_alloc_storage (H5F_t *f, hid_t dxpl_id, H5D_t *dset/*in,out*/, H5D_time_allo * We assume that external storage is already * allocated by the caller, or at least will be before I/O is performed. */ - if(dset->efl.nused==0) { + if(!(H5S_NULL == H5S_GET_SIMPLE_EXTENT_TYPE(dset->space) || dset->efl.nused>0)) { /* Get a pointer to the dataset's layout information */ layout=&(dset->layout); switch (layout->type) { case H5D_CONTIGUOUS: - if(layout->addr==HADDR_UNDEF) { + if(layout->u.contig.addr==HADDR_UNDEF) { /* Reserve space in the file for the entire array */ if (H5F_contig_create (f, dxpl_id, layout/*out*/)<0) HGOTO_ERROR (H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize contiguous storage") @@ -2944,7 +2955,7 @@ H5D_alloc_storage (H5F_t *f, hid_t dxpl_id, H5D_t *dset/*in,out*/, H5D_time_allo break; case H5D_CHUNKED: - if(layout->addr==HADDR_UNDEF) { + if(layout->u.chunk.addr==HADDR_UNDEF) { /* Create the root of the B-tree that describes chunked storage */ if (H5F_istore_create (f, dxpl_id, layout/*out*/)<0) HGOTO_ERROR (H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize chunked storage") @@ -2967,12 +2978,12 @@ H5D_alloc_storage (H5F_t *f, hid_t dxpl_id, H5D_t *dset/*in,out*/, H5D_time_allo case H5D_COMPACT: /* Check if space is already allocated */ - if(layout->buf==NULL) { + if(layout->u.compact.buf==NULL) { /* Reserve space in layout header message for the entire array. */ - assert(layout->size>0); - if (NULL==(layout->buf=H5MM_malloc(layout->size))) + assert(layout->u.compact.size>0); + if (NULL==(layout->u.compact.buf=H5MM_malloc(layout->u.compact.size))) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate memory for compact dataset") - layout->dirty = TRUE; + layout->u.compact.dirty = TRUE; /* Indicate that we set the storage addr */ addr_set=1; @@ -3073,7 +3084,7 @@ H5D_init_storage(H5D_t *dset, hbool_t full_overwrite, hid_t dxpl_id) space=dset->space; /* Get the number of elements in the dataset's dataspace */ - snpoints = H5S_get_simple_extent_npoints(space); + snpoints = H5S_GET_SIMPLE_EXTENT_NPOINTS(space); assert(snpoints>=0); H5_ASSIGN_OVERFLOW(npoints,snpoints,hssize_t,size_t); @@ -3084,9 +3095,9 @@ H5D_init_storage(H5D_t *dset, hbool_t full_overwrite, hid_t dxpl_id) /* If the fill value is defined, initialize the data buffer with it */ if(dset->fill.buf) /* Initialize the cached data buffer with the fill value */ - H5V_array_fill(dset->layout.buf, dset->fill.buf, dset->fill.size, npoints); + H5V_array_fill(dset->layout.u.compact.buf, dset->fill.buf, dset->fill.size, npoints); else /* If the fill value is default, zero set data buf. */ - HDmemset(dset->layout.buf, 0, dset->layout.size); + HDmemset(dset->layout.u.compact.buf, 0, dset->layout.u.compact.size); } /* end if */ break; @@ -3117,7 +3128,7 @@ H5D_init_storage(H5D_t *dset, hbool_t full_overwrite, hid_t dxpl_id) /* We only handle simple data spaces so far */ if ((ndims=H5S_get_simple_extent_dims(space, dim, NULL))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get simple data space info") - dim[ndims] = dset->layout.dim[ndims]; + dim[ndims] = dset->layout.u.chunk.dim[ndims]; if (H5F_istore_allocate(dset->ent.file, dxpl_id, &(dset->layout), dim, plist, full_overwrite)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset") @@ -3204,25 +3215,23 @@ H5D_get_storage_size(const H5D_t *dset, hid_t dxpl_id) switch(dset->layout.type) { case H5D_CHUNKED: - if(dset->layout.addr == HADDR_UNDEF) + if(dset->layout.u.chunk.addr == HADDR_UNDEF) ret_value=0; else - ret_value = H5F_istore_allocated(dset->ent.file, dxpl_id, dset->layout.ndims, - dset->layout.addr); + ret_value = H5F_istore_allocated(dset->ent.file, dxpl_id, dset->layout.u.chunk.ndims, + dset->layout.u.chunk.addr); break; case H5D_CONTIGUOUS: /* Datasets which are not allocated yet are using no space on disk */ - if(dset->layout.addr == HADDR_UNDEF) + if(dset->layout.u.contig.addr == HADDR_UNDEF) ret_value=0; - else { - for (u=0, ret_value=1; u<dset->layout.ndims; u++) - ret_value *= dset->layout.dim[u]; - } /* end else */ + else + ret_value=dset->layout.u.contig.size; break; case H5D_COMPACT: - ret_value = dset->layout.size; + ret_value = dset->layout.u.compact.size; break; default: @@ -3313,9 +3322,9 @@ H5D_get_offset(const H5D_t *dset) /* If there's user block in file, returns the absolute dataset offset * from the beginning of file. */ if(base_addr!=HADDR_UNDEF) - ret_value = dset->layout.addr + base_addr; + ret_value = dset->layout.u.contig.addr + base_addr; else - ret_value = dset->layout.addr; + ret_value = dset->layout.u.contig.addr; break; default: @@ -3879,10 +3888,11 @@ H5D_flush(const H5F_t *f, hid_t dxpl_id) for(j=0; j<num_dsets; j++) { if(NULL==(dataset=H5I_object_verify(id_list[j], H5I_DATASET))) HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to get dataset object") - if(dataset->layout.type==H5D_COMPACT && dataset->layout.dirty) + if(dataset->layout.type==H5D_COMPACT && dataset->layout.u.compact.dirty) { if(H5O_modify(&(dataset->ent), H5O_LAYOUT_ID, 0, 0, 1, &(dataset->layout), dxpl_id)<0) HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to update layout message") - dataset->layout.dirty = FALSE; + dataset->layout.u.compact.dirty = FALSE; + } /* end if */ } } /* end if */ @@ -3925,9 +3935,9 @@ H5Ddebug(hid_t dset_id) /* Print B-tree information */ if (H5D_CHUNKED==dset->layout.type) { - (void)H5F_istore_dump_btree(dset->ent.file, H5AC_dxpl_id, stdout, dset->layout.ndims, dset->layout.addr); + (void)H5F_istore_dump_btree(dset->ent.file, H5AC_dxpl_id, stdout, dset->layout.u.chunk.ndims, dset->layout.u.chunk.addr); } else if (H5D_CONTIGUOUS==dset->layout.type) { - HDfprintf(stdout, " %-10s %a\n", "Address:", dset->layout.addr); + HDfprintf(stdout, " %-10s %a\n", "Address:", dset->layout.u.contig.addr); } done: diff --git a/src/H5Dcompact.c b/src/H5Dcompact.c index 96e9955..4f5b75e 100644 --- a/src/H5Dcompact.c +++ b/src/H5Dcompact.c @@ -70,7 +70,7 @@ H5F_compact_readvv(H5F_t UNUSED *f, const H5O_layout_t *layout, FUNC_ENTER_NOAPI(H5F_compact_readvv, FAIL); /* Use the vectorized memory copy routine to do actual work */ - if((ret_value=H5V_memcpyvv(buf,mem_max_nseq,mem_curr_seq,mem_size_arr,mem_offset_arr,layout->buf,dset_max_nseq,dset_curr_seq,dset_size_arr,dset_offset_arr))<0) + if((ret_value=H5V_memcpyvv(buf,mem_max_nseq,mem_curr_seq,mem_size_arr,mem_offset_arr,layout->u.compact.buf,dset_max_nseq,dset_curr_seq,dset_size_arr,dset_offset_arr))<0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vectorized memcpy failed"); done: @@ -112,10 +112,10 @@ H5F_compact_writevv(H5F_t UNUSED *f, H5O_layout_t *layout, FUNC_ENTER_NOAPI(H5F_compact_writevv, FAIL); /* Use the vectorized memory copy routine to do actual work */ - if((ret_value=H5V_memcpyvv(layout->buf,dset_max_nseq,dset_curr_seq,dset_size_arr,dset_offset_arr,buf,mem_max_nseq,mem_curr_seq,mem_size_arr,mem_offset_arr))<0) + if((ret_value=H5V_memcpyvv(layout->u.compact.buf,dset_max_nseq,dset_curr_seq,dset_size_arr,dset_offset_arr,buf,mem_max_nseq,mem_curr_seq,mem_size_arr,mem_offset_arr))<0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vectorized memcpy failed"); - layout->dirty = TRUE; + layout->u.compact.dirty = TRUE; done: FUNC_LEAVE_NOAPI(ret_value); diff --git a/src/H5Dcontig.c b/src/H5Dcontig.c index 09be560..1255922 100644 --- a/src/H5Dcontig.c +++ b/src/H5Dcontig.c @@ -75,8 +75,6 @@ H5FL_BLK_DEFINE_STATIC(zero_fill); herr_t H5F_contig_create(H5F_t *f, hid_t dxpl_id, struct H5O_layout_t *layout) { - hsize_t size; /* Size of contiguous block of data */ - unsigned u; /* Local index variable */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5F_contig_create, FAIL); @@ -85,14 +83,8 @@ H5F_contig_create(H5F_t *f, hid_t dxpl_id, struct H5O_layout_t *layout) assert(f); assert(layout); - /* Compute size */ - size=layout->dim[0]; - for (u = 1; u < layout->ndims; u++) - size *= layout->dim[u]; - assert (size>0); - /* Allocate space for the contiguous data */ - if (HADDR_UNDEF==(layout->addr=H5MF_alloc(f, H5FD_MEM_DRAW, dxpl_id, size))) + if (HADDR_UNDEF==(layout->u.contig.addr=H5MF_alloc(f, H5FD_MEM_DRAW, dxpl_id, layout->u.contig.size))) HGOTO_ERROR (H5E_IO, H5E_NOSPACE, FAIL, "unable to reserve file space"); done: @@ -145,8 +137,8 @@ H5F_contig_fill(H5F_t *f, hid_t dxpl_id, struct H5O_layout_t *layout, assert(f); assert(TRUE==H5P_isa_class(dxpl_id,H5P_DATASET_XFER)); assert(layout && H5D_CONTIGUOUS==layout->type); - assert(layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS); - assert(H5F_addr_defined(layout->addr)); + assert(H5F_addr_defined(layout->u.contig.addr)); + assert(layout->u.contig.size>0); assert(space); assert(elmt_size>0); @@ -167,7 +159,7 @@ H5F_contig_fill(H5F_t *f, hid_t dxpl_id, struct H5O_layout_t *layout, #endif /* H5_HAVE_PARALLEL */ /* Get the number of elements in the dataset's dataspace */ - snpoints = H5S_get_simple_extent_npoints(space); + snpoints = H5S_GET_SIMPLE_EXTENT_NPOINTS(space); assert(snpoints>=0); H5_ASSIGN_OVERFLOW(npoints,snpoints,hssize_t,size_t); @@ -214,7 +206,7 @@ H5F_contig_fill(H5F_t *f, hid_t dxpl_id, struct H5O_layout_t *layout, } /* end else */ /* Start at the beginning of the dataset */ - addr = layout->addr; + addr = layout->u.contig.addr; /* Loop through writing the fill value to the dataset */ while (npoints>0) { @@ -290,8 +282,6 @@ done: herr_t H5F_contig_delete(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout) { - hsize_t size; /* Size of contiguous block of data */ - unsigned u; /* Local index variable */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5F_contig_delete, FAIL); @@ -300,17 +290,12 @@ H5F_contig_delete(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout) assert(f); assert(layout); - /* Compute size */ - size=layout->dim[0]; - for (u = 1; u < layout->ndims; u++) - size *= layout->dim[u]; - /* Check for overlap with the sieve buffer and reset it */ - if (H5F_sieve_overlap_clear(f, dxpl_id, layout->addr, size)<0) + if (H5F_sieve_overlap_clear(f, dxpl_id, layout->u.contig.addr, layout->u.contig.size)<0) HGOTO_ERROR(H5E_OHDR, H5E_CANTFREE, FAIL, "unable to clear sieve buffer"); /* Free the file space for the chunk */ - if (H5MF_xfree(f, H5FD_MEM_DRAW, dxpl_id, layout->addr, size)<0) + if (H5MF_xfree(f, H5FD_MEM_DRAW, dxpl_id, layout->u.contig.addr, layout->u.contig.size)<0) HGOTO_ERROR(H5E_OHDR, H5E_CANTFREE, FAIL, "unable to free object header"); done: diff --git a/src/H5Dio.c b/src/H5Dio.c index 985089e..a465413 100644 --- a/src/H5Dio.c +++ b/src/H5Dio.c @@ -63,6 +63,7 @@ typedef struct fm_map { H5S_sel_iter_t mem_iter; /* Iterator for elements in memory selection */ unsigned m_ndims; /* Number of dimensions for memory dataspace */ hsize_t chunks[H5O_LAYOUT_NDIMS]; /* Number of chunks in each dimension */ + hsize_t chunk_dim[H5O_LAYOUT_NDIMS]; /* Size of chunk in each dimension */ hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of chunks in each dimension */ H5O_layout_t *layout; /* Dataset layout information*/ H5S_sel_type msel_type; /* Selection type in memory */ @@ -694,8 +695,9 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, * fill time is NEVER, there is no way to tell whether part of data * has been overwritten. So just proceed in reading. */ - if(nelmts > 0 && dataset->efl.nused==0 && dataset->layout.type!=H5D_COMPACT - && dataset->layout.addr==HADDR_UNDEF) { + if(nelmts > 0 && dataset->efl.nused==0 && + ((dataset->layout.type==H5D_CONTIGUOUS && !H5F_addr_defined(dataset->layout.u.contig.addr)) + || (dataset->layout.type==H5D_CHUNKED && !H5F_addr_defined(dataset->layout.u.chunk.addr)))) { H5D_fill_value_t fill_status; /* Whether/How the fill value is defined */ /* Retrieve dataset's fill-value properties */ @@ -912,13 +914,14 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, /* <none needed currently> */ /* Allocate data space and initialize it if it hasn't been. */ - if(nelmts > 0 && dataset->efl.nused==0 && dataset->layout.type!=H5D_COMPACT - && dataset->layout.addr==HADDR_UNDEF) { + if(nelmts > 0 && dataset->efl.nused==0 && + ((dataset->layout.type==H5D_CONTIGUOUS && !H5F_addr_defined(dataset->layout.u.contig.addr)) + || (dataset->layout.type==H5D_CHUNKED && !H5F_addr_defined(dataset->layout.u.chunk.addr)))) { hssize_t file_nelmts; /* Number of elements in file dataset's dataspace */ hbool_t full_overwrite; /* Whether we are over-writing all the elements */ /* Get the number of elements in file dataset's dataspace */ - if((file_nelmts=H5S_get_simple_extent_npoints(file_space))<0) + if((file_nelmts=H5S_GET_SIMPLE_EXTENT_NPOINTS(file_space))<0) HGOTO_ERROR (H5E_DATASET, H5E_BADVALUE, FAIL, "can't retrieve number of elements in file dataset") /* Always allow fill values to be written if the dataset has a VL datatype */ @@ -1081,7 +1084,9 @@ H5D_contig_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, H5_timer_begin(&timer); #endif /* Sanity check dataset, then read it */ - assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 || + assert(((dataset->layout.type==H5D_CONTIGUOUS && H5F_addr_defined(dataset->layout.u.contig.addr)) + || (dataset->layout.type==H5D_CHUNKED && H5F_addr_defined(dataset->layout.u.chunk.addr))) + || dataset->efl.nused>0 || H5S_NULL == H5S_GET_SIMPLE_EXTENT_TYPE(file_space) || dataset->layout.type==H5D_COMPACT); H5_CHECK_OVERFLOW(nelmts,hsize_t,size_t); @@ -1178,7 +1183,9 @@ H5D_contig_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, H5_timer_begin(&timer); #endif /* Sanity check that space is allocated, then read data from it */ - assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 || + assert(((dataset->layout.type==H5D_CONTIGUOUS && H5F_addr_defined(dataset->layout.u.contig.addr)) + || (dataset->layout.type==H5D_CHUNKED && H5F_addr_defined(dataset->layout.u.chunk.addr))) + || dataset->efl.nused>0 || dataset->layout.type==H5D_COMPACT); n = H5S_select_fgath(dataset->ent.file, &(dataset->layout), &dataset->dcpl_cache, (H5D_storage_t *)&(dataset->efl), file_space, @@ -1580,8 +1587,9 @@ UNUSED H5_timer_begin(&timer); #endif /* Sanity check dataset, then read it */ - assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 || - dataset->layout.type==H5D_COMPACT); + assert(((dataset->layout.type==H5D_CONTIGUOUS && H5F_addr_defined(dataset->layout.u.contig.addr)) + || (dataset->layout.type==H5D_CHUNKED && H5F_addr_defined(dataset->layout.u.chunk.addr))) + || dataset->efl.nused>0 || dataset->layout.type==H5D_COMPACT); /* Get first node in chunk tree */ chunk_node=H5TB_first(fm.fsel->root); @@ -1709,8 +1717,9 @@ UNUSED H5_timer_begin(&timer); #endif /* Sanity check that space is allocated, then read data from it */ - assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 || - dataset->layout.type==H5D_COMPACT); + assert(((dataset->layout.type==H5D_CONTIGUOUS && H5F_addr_defined(dataset->layout.u.contig.addr)) + || (dataset->layout.type==H5D_CHUNKED && H5F_addr_defined(dataset->layout.u.chunk.addr))) + || dataset->efl.nused>0 || dataset->layout.type==H5D_COMPACT); n = H5S_select_fgath(dataset->ent.file, &(dataset->layout), &dataset->dcpl_cache, &store, chunk_info->fspace, &file_iter, smine_nelmts, dxpl_cache, dxpl_id, tconv_buf/*out*/); @@ -2324,16 +2333,16 @@ H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_sp hsize_t dims[H5O_LAYOUT_NDIMS]; /* Temporary dimension information */ /* Set up "equivalent" n-dimensional dataspace with size '1' in each dimension */ - for(u=0; u<dataset->layout.ndims-1; u++) + for(u=0; u<dataset->layout.u.chunk.ndims-1; u++) dims[u]=1; - if((equiv_mspace = H5S_create_simple(dataset->layout.ndims-1,dims,NULL))==NULL) + if((equiv_mspace = H5S_create_simple(dataset->layout.u.chunk.ndims-1,dims,NULL))==NULL) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCREATE, FAIL, "unable to create equivalent dataspace for scalar space") /* Indicate that this space needs to be released */ equiv_mspace_init=1; /* Set the number of dimensions for the memory dataspace */ - fm->m_ndims=dataset->layout.ndims-1; + fm->m_ndims=dataset->layout.u.chunk.ndims-1; } /* end else */ else { equiv_mspace=(H5S_t *)mem_space; /* Casting away 'const' OK... */ @@ -2343,7 +2352,7 @@ H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_sp } /* end else */ /* Get dim number and dimensionality for each dataspace */ - fm->f_ndims=f_ndims=dataset->layout.ndims-1; + fm->f_ndims=f_ndims=dataset->layout.u.chunk.ndims-1; if(H5S_get_simple_extent_dims(file_space, fm->f_dims, NULL)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimensionality") @@ -2352,8 +2361,11 @@ H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_sp last_nchunks=0; nchunks=1; for(u=0; u<f_ndims; u++) { + /* Keep the size of the chunk dimensions as hsize_t for various routines */ + fm->chunk_dim[u]=fm->layout->u.chunk.dim[u]; + /* Round up to the next integer # of chunks, to accomodate partial chunks */ - fm->chunks[u] = ((fm->f_dims[u]+dataset->layout.dim[u])-1) / dataset->layout.dim[u]; + fm->chunks[u] = ((fm->f_dims[u]+dataset->layout.u.chunk.dim[u])-1) / dataset->layout.u.chunk.dim[u]; /* Track total number of chunks in dataset */ nchunks *= fm->chunks[u]; @@ -2653,7 +2665,6 @@ H5D_create_chunk_file_map_hyper(fm_map *fm) hssize_t sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */ hssize_t start_coords[H5O_LAYOUT_NDIMS]; /* Starting coordinates of selection */ hssize_t coords[H5O_LAYOUT_NDIMS]; /* Current coordinates of chunk */ - hsize_t count[H5O_LAYOUT_NDIMS]; /* Hyperslab count information */ hssize_t end[H5O_LAYOUT_NDIMS]; /* Current coordinates of chunk */ hsize_t chunk_index; /* Index of chunk */ int curr_dim; /* Current dimension to increment */ @@ -2675,21 +2686,21 @@ H5D_create_chunk_file_map_hyper(fm_map *fm) /* Set initial chunk location & hyperslab size */ for(u=0; u<fm->f_ndims; u++) { - H5_CHECK_OVERFLOW(fm->layout->dim[u],hsize_t,hssize_t); - start_coords[u]=(sel_start[u]/(hssize_t)fm->layout->dim[u])*(hssize_t)fm->layout->dim[u]; + H5_CHECK_OVERFLOW(fm->layout->u.chunk.dim[u],hsize_t,hssize_t); + start_coords[u]=(sel_start[u]/(hssize_t)fm->layout->u.chunk.dim[u])*(hssize_t)fm->layout->u.chunk.dim[u]; coords[u]=start_coords[u]; - count[u]=fm->layout->dim[u]; - end[u]=(coords[u]+count[u])-1; + end[u]=(coords[u]+fm->chunk_dim[u])-1; } /* end for */ /* Calculate the index of this chunk */ - if(H5V_chunk_index(fm->f_ndims,coords,fm->layout->dim,fm->down_chunks,&chunk_index)<0) + if(H5V_chunk_index(fm->f_ndims,coords,fm->layout->u.chunk.dim,fm->down_chunks,&chunk_index)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") /* Iterate through each chunk in the dataset */ while(sel_points) { /* Check for intersection of temporary chunk and file selection */ - if(H5S_hyper_intersect_block(fm->file_space,coords,end)==TRUE) { + /* (Casting away const OK - QAK) */ + if(H5S_hyper_intersect_block((H5S_t *)fm->file_space,coords,end)==TRUE) { H5S_t *tmp_fchunk; /* Temporary file dataspace */ H5D_chunk_info_t *new_chunk_info; /* chunk information to insert into tree */ hssize_t schunk_points; /* Number of elements in chunk selection */ @@ -2707,13 +2718,13 @@ H5D_create_chunk_file_map_hyper(fm_map *fm) HGOTO_ERROR (H5E_DATASET, H5E_BADSELECT, FAIL, "unable to normalize dataspace by offset") /* "AND" temporary chunk and current chunk */ - if(H5S_select_hyperslab(tmp_fchunk,H5S_SELECT_AND,coords,NULL,count,NULL)<0) { + if(H5S_select_hyperslab(tmp_fchunk,H5S_SELECT_AND,coords,NULL,fm->chunk_dim,NULL)<0) { (void)H5S_close(tmp_fchunk); HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't create chunk selection") } /* end if */ /* Resize chunk's dataspace dimensions to size of chunk */ - if(H5S_set_extent_real(tmp_fchunk,count)<0) { + if(H5S_set_extent_real(tmp_fchunk,fm->chunk_dim)<0) { (void)H5S_close(tmp_fchunk); HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk dimensions") } /* end if */ @@ -2775,9 +2786,9 @@ H5D_create_chunk_file_map_hyper(fm_map *fm) curr_dim=(int)fm->f_ndims-1; /* Increment chunk location in fastest changing dimension */ - H5_CHECK_OVERFLOW(count[curr_dim],hsize_t,hssize_t); - coords[curr_dim]+=(hssize_t)count[curr_dim]; - end[curr_dim]+=(hssize_t)count[curr_dim]; + H5_CHECK_OVERFLOW(fm->chunk_dim[curr_dim],hsize_t,hssize_t); + coords[curr_dim]+=(hssize_t)fm->chunk_dim[curr_dim]; + end[curr_dim]+=(hssize_t)fm->chunk_dim[curr_dim]; /* Bring chunk location back into bounds, if necessary */ if(coords[curr_dim]>sel_end[curr_dim]) { @@ -2789,12 +2800,12 @@ H5D_create_chunk_file_map_hyper(fm_map *fm) curr_dim--; /* Increment chunk location in current dimension */ - coords[curr_dim]+=(hssize_t)count[curr_dim]; - end[curr_dim]=(coords[curr_dim]+(hssize_t)count[curr_dim])-1; + coords[curr_dim]+=(hssize_t)fm->chunk_dim[curr_dim]; + end[curr_dim]=(coords[curr_dim]+(hssize_t)fm->chunk_dim[curr_dim])-1; } while(coords[curr_dim]>sel_end[curr_dim]); /* Re-Calculate the index of this chunk */ - if(H5V_chunk_index(fm->f_ndims,coords,fm->layout->dim,fm->down_chunks,&chunk_index)<0) + if(H5V_chunk_index(fm->f_ndims,coords,fm->layout->u.chunk.dim,fm->down_chunks,&chunk_index)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") } /* end if */ } /* end while */ @@ -2871,7 +2882,8 @@ H5D_create_chunk_mem_map_hyper(const fm_map *fm) } /* end if */ else { /* Just point at the memory dataspace & selection */ - chunk_info->mspace=fm->mem_space; + /* (Casting away const OK -QAK) */ + chunk_info->mspace=(H5S_t *)fm->mem_space; /* Indicate that the chunk's memory space is shared */ chunk_info->mspace_shared=1; @@ -2931,10 +2943,8 @@ H5D_create_chunk_mem_map_hyper(const fm_map *fm) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy selection") /* Compensate for the chunk offset */ - for(u=0; u<fm->f_ndims; u++) { - H5_CHECK_OVERFLOW(fm->layout->dim[u],hsize_t,hssize_t); + for(u=0; u<fm->f_ndims; u++) chunk_adjust[u]=adjust[u]-chunk_info->coords[u]; /*lint !e771 The adjust array will always be initialized */ - } /* end for */ #ifdef QAK { int mpi_rank; @@ -3016,7 +3026,7 @@ H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_file_cb) /* Calculate the index of this chunk */ - if(H5V_chunk_index((unsigned)ndims,coords,fm->layout->dim,fm->down_chunks,&chunk_index)<0) + if(H5V_chunk_index((unsigned)ndims,coords,fm->layout->u.chunk.dim,fm->down_chunks,&chunk_index)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") /* Find correct chunk in file & memory TBBTs */ @@ -3047,7 +3057,7 @@ H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize new_chunk_info->index=chunk_index; /* Create a dataspace for the chunk */ - if((fspace = H5S_create_simple(fm->f_ndims,fm->layout->dim,NULL))==NULL) { + if((fspace = H5S_create_simple(fm->f_ndims,fm->chunk_dim,NULL))==NULL) { H5FL_FREE(H5D_chunk_info_t,new_chunk_info); HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCREATE, FAIL, "unable to create dataspace for chunk") } /* end if */ @@ -3071,8 +3081,8 @@ H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize /* Compute the chunk's coordinates */ for(u=0; u<fm->f_ndims; u++) { - H5_CHECK_OVERFLOW(fm->layout->dim[u],hsize_t,hssize_t); - new_chunk_info->coords[u]=(coords[u]/(hssize_t)fm->layout->dim[u])*(hssize_t)fm->layout->dim[u]; + H5_CHECK_OVERFLOW(fm->layout->u.chunk.dim[u],hsize_t,hssize_t); + new_chunk_info->coords[u]=(coords[u]/(hssize_t)fm->layout->u.chunk.dim[u])*(hssize_t)fm->layout->u.chunk.dim[u]; } /* end for */ new_chunk_info->coords[fm->f_ndims]=0; @@ -3096,7 +3106,7 @@ H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize /* Get the coordinates of the element in the chunk */ for(u=0; u<fm->f_ndims; u++) - coords_in_chunk[u]=coords[u]%fm->layout->dim[u]; + coords_in_chunk[u]=coords[u]%fm->layout->u.chunk.dim[u]; /* Add point to file selection for chunk */ if(H5S_select_elements(chunk_info->fspace,H5S_SELECT_APPEND,1,(const hssize_t **)coords_in_chunk)<0) @@ -3140,7 +3150,7 @@ H5D_chunk_mem_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize_ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_mem_cb) /* Calculate the index of this chunk */ - if(H5V_chunk_index((unsigned)ndims,coords,fm->layout->dim,fm->down_chunks,&chunk_index)<0) + if(H5V_chunk_index((unsigned)ndims,coords,fm->layout->u.chunk.dim,fm->down_chunks,&chunk_index)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") /* Find correct chunk in file & memory TBBTs */ diff --git a/src/H5Distore.c b/src/H5Distore.c index 861c28f..2434cc2 100644 --- a/src/H5Distore.c +++ b/src/H5Distore.c @@ -248,11 +248,11 @@ H5F_istore_sizeof_rkey(H5F_t UNUSED *f, const void *_udata) FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5F_istore_sizeof_rkey); assert(udata); - assert(udata->mesg.ndims > 0 && udata->mesg.ndims <= H5O_LAYOUT_NDIMS); + assert(udata->mesg.u.chunk.ndims > 0 && udata->mesg.u.chunk.ndims <= H5O_LAYOUT_NDIMS); nbytes = 4 + /*storage size */ 4 + /*filter mask */ - udata->mesg.ndims*8; /*dimension indices */ + udata->mesg.u.chunk.ndims*8; /*dimension indices */ FUNC_LEAVE_NOAPI(nbytes); } @@ -375,7 +375,7 @@ H5F_istore_debug_key (FILE *stream, H5F_t UNUSED *f, hid_t UNUSED dxpl_id, int i "Filter mask:", key->filter_mask); HDfprintf(stream, "%*s%-*s {", indent, "", fwidth, "Logical offset:"); - for (u=0; u<udata->mesg.ndims; u++) + for (u=0; u<udata->mesg.u.chunk.ndims; u++) HDfprintf (stream, "%s%Hd", u?", ":"", key->offset[u]); HDfputs ("}\n", stream); @@ -419,10 +419,10 @@ H5F_istore_cmp2(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, void *_lt_key, void *_uda assert(lt_key); assert(rt_key); assert(udata); - assert(udata->mesg.ndims > 0 && udata->mesg.ndims <= H5O_LAYOUT_NDIMS); + assert(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_s(udata->mesg.ndims, lt_key->offset, rt_key->offset); + ret_value = H5V_vector_cmp_s(udata->mesg.u.chunk.ndims, lt_key->offset, rt_key->offset); done: FUNC_LEAVE_NOAPI(ret_value); @@ -472,12 +472,12 @@ H5F_istore_cmp3(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, void *_lt_key, void *_uda assert(lt_key); assert(rt_key); assert(udata); - assert(udata->mesg.ndims > 0 && udata->mesg.ndims <= H5O_LAYOUT_NDIMS); + assert(udata->mesg.u.chunk.ndims > 0 && udata->mesg.u.chunk.ndims <= H5O_LAYOUT_NDIMS); - if (H5V_vector_lt_s(udata->mesg.ndims, udata->key.offset, + if (H5V_vector_lt_s(udata->mesg.u.chunk.ndims, udata->key.offset, lt_key->offset)) { ret_value = -1; - } else if (H5V_vector_ge_s(udata->mesg.ndims, udata->key.offset, + } else if (H5V_vector_ge_s(udata->mesg.u.chunk.ndims, udata->key.offset, rt_key->offset)) { ret_value = 1; } @@ -525,7 +525,7 @@ H5F_istore_new_node(H5F_t *f, hid_t dxpl_id, H5B_ins_t op, assert(lt_key); assert(rt_key); assert(udata); - assert(udata->mesg.ndims > 0 && udata->mesg.ndims < H5O_LAYOUT_NDIMS); + assert(udata->mesg.u.chunk.ndims > 0 && udata->mesg.u.chunk.ndims < H5O_LAYOUT_NDIMS); assert(addr_p); /* Allocate new storage */ @@ -541,7 +541,7 @@ H5F_istore_new_node(H5F_t *f, hid_t dxpl_id, H5B_ins_t op, */ lt_key->nbytes = udata->key.nbytes; lt_key->filter_mask = udata->key.filter_mask; - for (u=0; u<udata->mesg.ndims; u++) + for (u=0; u<udata->mesg.u.chunk.ndims; u++) lt_key->offset[u] = udata->key.offset[u]; /* @@ -551,12 +551,11 @@ H5F_istore_new_node(H5F_t *f, hid_t dxpl_id, H5B_ins_t op, if (H5B_INS_LEFT != op) { rt_key->nbytes = 0; rt_key->filter_mask = 0; - for (u=0; u<udata->mesg.ndims; u++) { - assert (udata->mesg.dim[u] < HSSIZET_MAX); - assert (udata->key.offset[u]+(hssize_t)(udata->mesg.dim[u]) > + for (u=0; u<udata->mesg.u.chunk.ndims; u++) { + assert (udata->key.offset[u]+(hssize_t)(udata->mesg.u.chunk.dim[u]) > udata->key.offset[u]); rt_key->offset[u] = udata->key.offset[u] + - (hssize_t)(udata->mesg.dim[u]); + (hssize_t)(udata->mesg.u.chunk.dim[u]); } } @@ -610,8 +609,8 @@ H5F_istore_found(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, haddr_t addr, const void assert(lt_key); /* Is this *really* the requested chunk? */ - for (u=0; u<udata->mesg.ndims; u++) { - if (udata->key.offset[u] >= lt_key->offset[u]+(hssize_t)(udata->mesg.dim[u])) + for (u=0; u<udata->mesg.u.chunk.ndims; u++) { + if (udata->key.offset[u] >= lt_key->offset[u]+(hssize_t)(udata->mesg.u.chunk.dim[u])) HGOTO_DONE(FAIL); } @@ -620,7 +619,7 @@ H5F_istore_found(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, haddr_t addr, const void udata->key.nbytes = lt_key->nbytes; udata->key.filter_mask = lt_key->filter_mask; assert (lt_key->nbytes>0); - for (u = 0; u < udata->mesg.ndims; u++) + for (u = 0; u < udata->mesg.u.chunk.ndims; u++) udata->key.offset[u] = lt_key->offset[u]; done: @@ -696,7 +695,7 @@ H5F_istore_insert(H5F_t *f, hid_t dxpl_id, haddr_t addr, void *_lt_key, assert("HDF5 INTERNAL ERROR -- see rpm" && 0); HGOTO_ERROR(H5E_STORAGE, H5E_UNSUPPORTED, H5B_INS_ERROR, "internal error"); - } else if (H5V_vector_eq_s (udata->mesg.ndims, + } else if (H5V_vector_eq_s (udata->mesg.u.chunk.ndims, udata->key.offset, lt_key->offset) && lt_key->nbytes>0) { /* @@ -735,20 +734,20 @@ H5F_istore_insert(H5F_t *f, hid_t dxpl_id, haddr_t addr, void *_lt_key, ret_value = H5B_INS_NOOP; } - } else if (H5V_hyper_disjointp(udata->mesg.ndims, - lt_key->offset, udata->mesg.dim, - udata->key.offset, udata->mesg.dim)) { - assert(H5V_hyper_disjointp(udata->mesg.ndims, - rt_key->offset, udata->mesg.dim, - udata->key.offset, udata->mesg.dim)); + } else if (H5V_hyper_disjointp(udata->mesg.u.chunk.ndims, + lt_key->offset, udata->mesg.u.chunk.dim, + udata->key.offset, udata->mesg.u.chunk.dim)) { + assert(H5V_hyper_disjointp(udata->mesg.u.chunk.ndims, + rt_key->offset, udata->mesg.u.chunk.dim, + udata->key.offset, udata->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->key.nbytes; md_key->filter_mask = udata->key.filter_mask; - for (u=0; u<udata->mesg.ndims; u++) { - assert(0 == udata->key.offset[u] % udata->mesg.dim[u]); + for (u=0; u<udata->mesg.u.chunk.ndims; u++) { + assert(0 == udata->key.offset[u] % udata->mesg.u.chunk.dim[u]); md_key->offset[u] = udata->key.offset[u]; } @@ -847,7 +846,7 @@ H5F_istore_iter_dump (H5F_t UNUSED *f, hid_t UNUSED dxpl_id, void *_lt_key, hadd } HDfprintf(bt_udata->stream, " 0x%08x %8Zu %10a [", lt_key->filter_mask, lt_key->nbytes, addr); - for (u=0; u<bt_udata->mesg.ndims; u++) + for (u=0; u<bt_udata->mesg.u.chunk.ndims; u++) HDfprintf(bt_udata->stream, "%s%Hd", u?", ":"", lt_key->offset[u]); HDfputs("]\n", bt_udata->stream); @@ -936,7 +935,7 @@ H5F_istore_flush_entry(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, udata.key.filter_mask = 0; udata.addr = HADDR_UNDEF; udata.key.nbytes = ent->chunk_size; - for (u=0; u<ent->layout.ndims; u++) + for (u=0; u<ent->layout.u.chunk.ndims; u++) udata.key.offset[u] = ent->offset[u]; alloc = ent->alloc_size; @@ -974,7 +973,7 @@ H5F_istore_flush_entry(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, * 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(f, dxpl_id, H5B_ISTORE, ent->layout.addr, &udata)<0) + if (H5B_insert(f, dxpl_id, H5B_ISTORE, ent->layout.u.chunk.addr, &udata)<0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to allocate chunk"); if (H5F_block_write(f, H5FD_MEM_DRAW, udata.addr, udata.key.nbytes, dxpl_id, buf)<0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file"); @@ -1365,22 +1364,22 @@ H5F_istore_lock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, con assert(TRUE==H5P_isa_class(dxpl_id,H5P_DATASET_XFER)); /* Get the chunk's size */ - assert(layout->chunk_size>0); - H5_ASSIGN_OVERFLOW(chunk_size,layout->chunk_size,hsize_t,size_t); + 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) { - for (u=0, temp_idx=0; u<layout->ndims; u++) { + for (u=0, temp_idx=0; u<layout->u.chunk.ndims; u++) { temp_idx += offset[u]; - temp_idx *= layout->dim[u]; + temp_idx *= layout->u.chunk.dim[u]; } - temp_idx += (hsize_t)(layout->addr); + temp_idx += (hsize_t)(layout->u.chunk.addr); idx=H5F_HASH(f,temp_idx); ent = rdcc->slot[idx]; - if (ent && layout->ndims==ent->layout.ndims && - H5F_addr_eq(layout->addr, ent->layout.addr)) { - for (u=0, found=TRUE; u<ent->layout.ndims; u++) { + if (ent && layout->u.chunk.ndims==ent->layout.u.chunk.ndims && + H5F_addr_eq(layout->u.chunk.addr, ent->layout.u.chunk.addr)) { + for (u=0, found=TRUE; u<ent->layout.u.chunk.ndims; u++) { if (offset[u]!=ent->offset[u]) { found = FALSE; break; @@ -1508,7 +1507,7 @@ H5F_istore_lock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, con ent->alloc_size = chunk_size; H5O_copy(H5O_LAYOUT_ID, layout, &ent->layout); H5O_copy(H5O_PLINE_ID, pline, &ent->pline); - for (u=0; u<layout->ndims; u++) + for (u=0; u<layout->u.chunk.ndims; u++) ent->offset[u] = offset[u]; ent->rd_count = chunk_size; ent->wr_count = chunk_size; @@ -1645,10 +1644,10 @@ H5F_istore_unlock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, x.dirty = TRUE; H5O_copy (H5O_LAYOUT_ID, layout, &x.layout); H5O_copy (H5O_PLINE_ID, pline, &x.pline); - for (u=0; u<layout->ndims; u++) + for (u=0; u<layout->u.chunk.ndims; u++) x.offset[u] = offset[u]; - assert(layout->chunk_size>0); - H5_ASSIGN_OVERFLOW(x.chunk_size,layout->chunk_size,hsize_t,size_t); + 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; @@ -1709,7 +1708,7 @@ H5F_istore_readvv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, hid_t dxp assert(f); assert(dxpl_cache); assert(layout && H5D_CHUNKED==layout->type); - assert(layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS); + assert(layout->u.chunk.ndims>0 && layout->u.chunk.ndims<=H5O_LAYOUT_NDIMS); assert(dcpl_cache); assert(chunk_len_arr); assert(chunk_offset_arr); @@ -1718,19 +1717,19 @@ H5F_istore_readvv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, hid_t dxp assert(buf); #ifndef NDEBUG - for (u=0; u<layout->ndims; u++) + for (u=0; u<layout->u.chunk.ndims; u++) assert(chunk_coords[u]>=0); /*negative coordinates not supported (yet) */ #endif /* Get the address of this chunk on disk */ #ifdef QAK HDfprintf(stderr,"%s: chunk_coords={",FUNC); -for(u=0; u<layout->ndims; u++) - HDfprintf(stderr,"%Hd%s",chunk_coords[u],(u<(layout->ndims-1) ? ", " : "}\n")); +for(u=0; u<layout->u.chunk.ndims; u++) + HDfprintf(stderr,"%Hd%s",chunk_coords[u],(u<(layout->u.chunk.ndims-1) ? ", " : "}\n")); #endif /* QAK */ chunk_addr=H5F_istore_get_addr(f, dxpl_id, layout, chunk_coords, &udata); #ifdef QAK -HDfprintf(stderr,"%s: chunk_addr=%a, chunk_size=%Hu\n",FUNC,chunk_addr,layout->chunk_size); +HDfprintf(stderr,"%s: chunk_addr=%a, chunk_size=%Hu\n",FUNC,chunk_addr,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]); @@ -1743,9 +1742,9 @@ HDfprintf(stderr,"%s: mem_offset_arr[%Zu]=%Hu\n",FUNC,*mem_curr_seq,mem_offset_a * for the chunk has been defined, then don't load the chunk into the * cache, just write the data to it directly. */ - if (layout->chunk_size>f->shared->rdcc_nbytes && dcpl_cache->pline.nused==0 && + if (layout->u.chunk.size>f->shared->rdcc_nbytes && dcpl_cache->pline.nused==0 && chunk_addr!=HADDR_UNDEF) { - if ((ret_value=H5F_contig_readvv(f, layout->chunk_size, chunk_addr, chunk_max_nseq, chunk_curr_seq, chunk_len_arr, chunk_offset_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, dxpl_id, buf))<0) + if ((ret_value=H5F_contig_readvv(f, (hsize_t)layout->u.chunk.size, chunk_addr, chunk_max_nseq, chunk_curr_seq, chunk_len_arr, chunk_offset_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, dxpl_id, buf))<0) HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "unable to read raw data to file"); } /* end if */ else { @@ -1813,7 +1812,7 @@ H5F_istore_writevv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, assert(f); assert(dxpl_cache); assert(layout && H5D_CHUNKED==layout->type); - assert(layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS); + assert(layout->u.chunk.ndims>0 && layout->u.chunk.ndims<=H5O_LAYOUT_NDIMS); assert(dcpl_cache); assert(chunk_len_arr); assert(chunk_offset_arr); @@ -1822,19 +1821,19 @@ H5F_istore_writevv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, assert(buf); #ifndef NDEBUG - for (u=0; u<layout->ndims; u++) + for (u=0; u<layout->u.chunk.ndims; u++) assert(chunk_coords[u]>=0); /*negative coordinates not supported (yet) */ #endif /* Get the address of this chunk on disk */ #ifdef QAK HDfprintf(stderr,"%s: chunk_coords={",FUNC); -for(u=0; u<layout->ndims; u++) - HDfprintf(stderr,"%Hd%s",chunk_coords[u],(u<(layout->ndims-1) ? ", " : "}\n")); +for(u=0; u<layout->u.chunk.ndims; u++) + HDfprintf(stderr,"%Hd%s",chunk_coords[u],(u<(layout->u.chunk.ndims-1) ? ", " : "}\n")); #endif /* QAK */ chunk_addr=H5F_istore_get_addr(f, dxpl_id, layout, chunk_coords, &udata); #ifdef QAK -HDfprintf(stderr,"%s: chunk_addr=%a, chunk_size=%Hu\n",FUNC,chunk_addr,layout->chunk_size); +HDfprintf(stderr,"%s: chunk_addr=%a, chunk_size=%Hu\n",FUNC,chunk_addr,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]); @@ -1852,14 +1851,14 @@ HDfprintf(stderr,"%s: mem_offset_arr[%Zu]=%Hu\n",FUNC,*mem_curr_seq,mem_offset_a * writing to other elements in the same chunk. Do a direct * write-through of only the elements requested. */ - if ((layout->chunk_size>f->shared->rdcc_nbytes && dcpl_cache->pline.nused==0 && chunk_addr!=HADDR_UNDEF) + if ((layout->u.chunk.size>f->shared->rdcc_nbytes && dcpl_cache->pline.nused==0 && chunk_addr!=HADDR_UNDEF) || (IS_H5FD_MPI(f) && (H5F_ACC_RDWR & f->shared->flags))) { #ifdef H5_HAVE_PARALLEL /* Additional sanity check when operating in parallel */ if (chunk_addr==HADDR_UNDEF || dcpl_cache->pline.nused>0) HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to locate raw data chunk"); #endif /* H5_HAVE_PARALLEL */ - if ((ret_value=H5F_contig_writevv(f, layout->chunk_size, chunk_addr, chunk_max_nseq, chunk_curr_seq, chunk_len_arr, chunk_offset_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, dxpl_id, buf))<0) + if ((ret_value=H5F_contig_writevv(f, (hsize_t)layout->u.chunk.size, chunk_addr, chunk_max_nseq, chunk_curr_seq, chunk_len_arr, chunk_offset_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, dxpl_id, buf))<0) HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file"); } /* end if */ else { @@ -1872,7 +1871,7 @@ HDfprintf(stderr,"%s: mem_offset_arr[%Zu]=%Hu\n",FUNC,*mem_curr_seq,mem_offset_a * Lock the chunk, copy from application to chunk, then unlock the * chunk. */ - if(chunk_max_nseq==1 && chunk_len_arr[0] == layout->chunk_size) + if(chunk_max_nseq==1 && chunk_len_arr[0] == layout->u.chunk.size) relax = TRUE; else relax = FALSE; @@ -1933,14 +1932,14 @@ H5F_istore_create(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout /*out */ ) /* Check args */ assert(f); assert(layout && H5D_CHUNKED == layout->type); - assert(layout->ndims > 0 && layout->ndims <= H5O_LAYOUT_NDIMS); + assert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS); #ifndef NDEBUG - for (u = 0; u < layout->ndims; u++) - assert(layout->dim[u] > 0); + for (u = 0; u < layout->u.chunk.ndims; u++) + assert(layout->u.chunk.dim[u] > 0); #endif - udata.mesg.ndims = layout->ndims; - if (H5B_create(f, dxpl_id, H5B_ISTORE, &udata, &(layout->addr)/*out*/) < 0) + udata.mesg.u.chunk.ndims = layout->u.chunk.ndims; + 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: @@ -1976,7 +1975,7 @@ H5F_istore_allocated(H5F_t *f, hid_t dxpl_id, unsigned ndims, haddr_t addr) FUNC_ENTER_NOAPI(H5F_istore_allocated, 0); HDmemset(&udata, 0, sizeof udata); - udata.mesg.ndims = ndims; + udata.mesg.u.chunk.ndims = ndims; if (H5B_iterate(f, dxpl_id, H5B_ISTORE, H5F_istore_iter_allocated, addr, &udata)<0) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, 0, "unable to iterate over chunk B-tree"); @@ -2018,20 +2017,20 @@ H5F_istore_get_addr(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, FUNC_ENTER_NOAPI_NOINIT(H5F_istore_get_addr); assert(f); - assert(layout && (layout->ndims > 0)); + assert(layout && (layout->u.chunk.ndims > 0)); assert(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<layout->ndims; u++) + for (u=0; u<layout->u.chunk.ndims; u++) udata->key.offset[u] = offset[u]; udata->mesg = *layout; udata->addr = HADDR_UNDEF; /* Go get the chunk information */ - if (H5B_find (f, dxpl_id, H5B_ISTORE, layout->addr, udata)<0) { + if (H5B_find (f, dxpl_id, H5B_ISTORE, layout->u.chunk.addr, udata)<0) { H5E_clear(NULL); HGOTO_ERROR(H5E_BTREE,H5E_NOTFOUND,HADDR_UNDEF,"Can't locate chunk info"); @@ -2189,8 +2188,8 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, assert(f); assert(space_dim); assert(layout && H5D_CHUNKED==layout->type); - assert(layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS); - assert(H5F_addr_defined(layout->addr)); + assert(layout->u.chunk.ndims>0 && layout->u.chunk.ndims<=H5O_LAYOUT_NDIMS); + assert(H5F_addr_defined(layout->u.chunk.addr)); assert(TRUE==H5P_isa_class(dxpl_id,H5P_DATASET_XFER)); assert(dc_plist); @@ -2230,9 +2229,9 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, * Setup indice to go through all chunks. (Future improvement * should allocate only chunks that have no file space assigned yet. */ - for (u=0; u<layout->ndims; u++) + for (u=0; u<layout->u.chunk.ndims; u++) chunk_offset[u] = 0; - chunk_size = layout->chunk_size; + chunk_size = layout->u.chunk.size; /* Check the dataset's fill-value status */ if (H5P_is_fill_value_defined(&fill, &fill_status) < 0) @@ -2297,12 +2296,12 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, /* Look for chunk in cache */ for(ent = rdcc->head; ent && !chunk_exists; ent = ent->next) { /* Make certain we are dealing with the correct B-tree, etc */ - if (layout->ndims==ent->layout.ndims && - H5F_addr_eq(layout->addr, ent->layout.addr)) { + if (layout->u.chunk.ndims==ent->layout.u.chunk.ndims && + H5F_addr_eq(layout->u.chunk.addr, ent->layout.u.chunk.addr)) { /* Assume a match */ chunk_exists = 1; - for(u = 0; u < layout->ndims && chunk_exists; u++) { + for(u = 0; u < layout->u.chunk.ndims && chunk_exists; u++) { if(ent->offset[u] != chunk_offset[u]) chunk_exists = 0; /* Reset if no match */ } /* end for */ @@ -2317,11 +2316,11 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, udata.addr = HADDR_UNDEF; H5_CHECK_OVERFLOW(chunk_size,hsize_t,size_t); udata.key.nbytes = (size_t)chunk_size; - for (u=0; u<layout->ndims; u++) + for (u=0; u<layout->u.chunk.ndims; u++) udata.key.offset[u] = chunk_offset[u]; /* Allocate the chunk with all processes */ - if (H5B_insert(f, dxpl_id, H5B_ISTORE, layout->addr, &udata)<0) + if (H5B_insert(f, dxpl_id, H5B_ISTORE, 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 */ @@ -2350,8 +2349,8 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, } /* end if */ /* Increment indices */ - for (i=layout->ndims-1, carry=1; i>=0 && carry; --i) { - chunk_offset[i] += layout->dim[i]; + for (i=layout->u.chunk.ndims-1, carry=1; i>=0 && carry; --i) { + chunk_offset[i] += layout->u.chunk.dim[i]; if (chunk_offset[i] >= (hssize_t)(space_dim[i])) chunk_offset[i] = 0; else @@ -2498,8 +2497,8 @@ H5F_istore_prune_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, /* Check args */ assert(f); assert(layout && H5D_CHUNKED == layout->type); - assert(layout->ndims > 0 && layout->ndims <= H5O_LAYOUT_NDIMS); - assert(H5F_addr_defined(layout->addr)); + assert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS); + assert(H5F_addr_defined(layout->u.chunk.addr)); assert(space); /* Go get the rank & dimensions */ @@ -2515,10 +2514,10 @@ H5F_istore_prune_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, next = ent->next; /* Make certain we are dealing with the correct B-tree, etc */ - if (layout->ndims==ent->layout.ndims && - H5F_addr_eq(layout->addr, ent->layout.addr)) { + if (layout->u.chunk.ndims==ent->layout.u.chunk.ndims && + H5F_addr_eq(layout->u.chunk.addr, ent->layout.u.chunk.addr)) { found = 0; - for(u = 0; u < ent->layout.ndims - 1; u++) { + for(u = 0; u < ent->layout.u.chunk.ndims - 1; u++) { if((hsize_t)ent->offset[u] > curr_dims[u]) { found = 1; break; @@ -2529,7 +2528,7 @@ H5F_istore_prune_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, if(found) { #if defined (H5F_ISTORE_DEBUG) HDfputs("cache:remove:[", stdout); - for(u = 0; u < ent->layout.ndims - 1; u++) { + for(u = 0; u < ent->layout.u.chunk.ndims - 1; u++) { HDfprintf(stdout, "%s%Hd", u ? ", " : "", ent->offset[u]); } HDfputs("]\n", stdout); @@ -2548,13 +2547,13 @@ H5F_istore_prune_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, HDmemset(&udata, 0, sizeof udata); udata.stream = stdout; - udata.mesg.addr = layout->addr; - udata.mesg.ndims = layout->ndims; - for(u = 0; u < udata.mesg.ndims; u++) - udata.mesg.dim[u] = layout->dim[u]; + udata.mesg.u.chunk.addr = layout->u.chunk.addr; + udata.mesg.u.chunk.ndims = layout->u.chunk.ndims; + for(u = 0; u < udata.mesg.u.chunk.ndims; u++) + udata.mesg.u.chunk.dim[u] = layout->u.chunk.dim[u]; udata.dims = curr_dims; - if(H5B_iterate(f, dxpl_id, H5B_ISTORE, H5F_istore_prune_extent, layout->addr, &udata) < 0) + if(H5B_iterate(f, dxpl_id, H5B_ISTORE, H5F_istore_prune_extent, layout->u.chunk.addr, &udata) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, 0, "unable to iterate over B-tree"); done: @@ -2596,11 +2595,11 @@ H5F_istore_prune_extent(H5F_t *f, hid_t dxpl_id, void *_lt_key, haddr_t UNUSED a FUNC_ENTER_NOAPI_NOINIT(H5F_istore_prune_extent); /* Figure out what chunks are no longer in use for the specified extent and release them */ - for(u = 0; u < bt_udata->mesg.ndims - 1; u++) + for(u = 0; u < bt_udata->mesg.u.chunk.ndims - 1; u++) if((hsize_t)lt_key->offset[u] > bt_udata->dims[u]) { #if defined (H5F_ISTORE_DEBUG) HDfputs("b-tree:remove:[", bt_udata->stream); - for(u = 0; u < bt_udata->mesg.ndims - 1; u++) { + for(u = 0; u < bt_udata->mesg.u.chunk.ndims - 1; u++) { HDfprintf(bt_udata->stream, "%s%Hd", u ? ", " : "", lt_key->offset[u]); } @@ -2612,7 +2611,7 @@ H5F_istore_prune_extent(H5F_t *f, hid_t dxpl_id, void *_lt_key, haddr_t UNUSED a udata.mesg = bt_udata->mesg; /* Remove */ - if(H5B_remove(f, dxpl_id, H5B_ISTORE, bt_udata->mesg.addr, &udata) < 0) + if(H5B_remove(f, dxpl_id, H5B_ISTORE, bt_udata->mesg.u.chunk.addr, &udata) < 0) HGOTO_ERROR(H5E_SYM, H5E_CANTINIT, H5B_ITER_ERROR, "unable to remove entry"); break; } /* end if */ @@ -2709,6 +2708,7 @@ H5F_istore_initialize_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_ca 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 */ int srank; /*current # of dimensions (signed) */ unsigned rank; /*current # of dimensions */ @@ -2725,8 +2725,8 @@ H5F_istore_initialize_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_ca /* Check args */ assert(f); assert(layout && H5D_CHUNKED == layout->type); - assert(layout->ndims > 0 && layout->ndims <= H5O_LAYOUT_NDIMS); - assert(H5F_addr_defined(layout->addr)); + assert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS); + assert(H5F_addr_defined(layout->u.chunk.addr)); assert(space); /* Get necessary properties from property list */ @@ -2749,10 +2749,12 @@ H5F_istore_initialize_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_ca /* Copy current dimensions */ for(u = 0; u < rank; u++) size[u] = curr_dims[u]; - size[u] = layout->dim[u]; + size[u] = layout->u.chunk.dim[u]; /* Create a data space for a chunk & set the extent */ - if(NULL == (space_chunk = H5S_create_simple(rank,layout->dim,NULL))) + 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"); /* @@ -2760,18 +2762,18 @@ H5F_istore_initialize_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_ca * loop through the chunks copying each chunk from the application to the * chunk cache. */ - for(u = 0; u < layout->ndims; u++) { - idx_max[u] = (size[u] - 1) / layout->dim[u] + 1; + 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 */ /* Loop over all chunks */ carry=0; while(carry==0) { - for(u = 0, naccessed = 1; u < layout->ndims; u++) { + 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] * (hssize_t)(layout->dim[u]); - sub_size[u] = MIN((idx_cur[u] + 1) * layout->dim[u], + chunk_offset[u] = idx_cur[u] * (hssize_t)(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 */ @@ -2780,8 +2782,8 @@ H5F_istore_initialize_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_ca * 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 < layout->ndims - 1; u++) { - end_chunk = chunk_offset[u] + layout->dim[u]; + for(u = 0, found = 0; u < layout->u.chunk.ndims - 1; u++) { + end_chunk = chunk_offset[u] + layout->u.chunk.dim[u]; if(end_chunk > size[u]) { found = 1; break; @@ -2798,15 +2800,15 @@ H5F_istore_initialize_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_ca 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->dim[u], size[u] - chunk_offset[u]); + count[u] = MIN((idx_cur[u] + 1) * layout->u.chunk.dim[u], size[u] - chunk_offset[u]); #if defined (H5F_ISTORE_DEBUG) HDfputs("cache:initialize:offset:[", stdout); - for(u = 0; u < layout->ndims - 1; u++) + for(u = 0; u < layout->u.chunk.ndims - 1; u++) HDfprintf(stdout, "%s%Hd", u ? ", " : "", chunk_offset[u]); HDfputs("]", stdout); HDfputs(":count:[", stdout); - for(u = 0; u < layout->ndims - 1; u++) + for(u = 0; u < layout->u.chunk.ndims - 1; u++) HDfprintf(stdout, "%s%Hd", u ? ", " : "", count[u]); HDfputs("]\n", stdout); #endif @@ -2829,7 +2831,7 @@ H5F_istore_initialize_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_ca } /*found */ /* Increment indices */ - for(i = layout->ndims - 1, carry = 1; i >= 0 && carry; --i) { + for(i = layout->u.chunk.ndims - 1, carry = 1; i >= 0 && carry; --i) { if(++idx_cur[i] >= idx_max[i]) idx_cur[i] = 0; else @@ -2876,14 +2878,14 @@ H5F_istore_delete(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache") /* Check if the B-tree has been created in the file */ - if(H5F_addr_defined(layout->addr)) { + if(H5F_addr_defined(layout->u.chunk.addr)) { /* Iterate through the entries in the cache, checking for the chunks to be deleted */ for (ent=rdcc->head; ent; ent=next) { /* Get pointer to next node, in case this one is deleted */ next=ent->next; /* Is the chunk to be deleted this cache entry? */ - if(layout->addr==ent->layout.addr) + if(layout->u.chunk.addr==ent->layout.u.chunk.addr) /* Remove entry without flushing */ if (H5F_istore_preempt(f, &dxpl_cache, dxpl_id, ent, FALSE )<0) HGOTO_ERROR (H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks"); @@ -2894,7 +2896,7 @@ H5F_istore_delete(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout) udata.mesg = *layout; /* Delete entire B-tree */ - if(H5B_delete(f, dxpl_id, H5B_ISTORE, layout->addr, &udata)<0) + if(H5B_delete(f, dxpl_id, H5B_ISTORE, layout->u.chunk.addr, &udata)<0) HGOTO_ERROR(H5E_IO, H5E_CANTDELETE, 0, "unable to delete chunk B-tree"); } /* end if */ @@ -2930,7 +2932,7 @@ H5F_istore_dump_btree(H5F_t *f, hid_t dxpl_id, FILE *stream, unsigned ndims, had FUNC_ENTER_NOAPI(H5F_istore_dump_btree, FAIL); HDmemset(&udata, 0, sizeof udata); - udata.mesg.ndims = ndims; + udata.mesg.u.chunk.ndims = ndims; udata.stream = stream; if(stream) HDfprintf(stream, " Address: %a\n",addr); @@ -3034,7 +3036,7 @@ H5F_istore_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE * stream, int inden FUNC_ENTER_NOAPI(H5F_istore_debug, FAIL); HDmemset (&udata, 0, sizeof udata); - udata.mesg.ndims = ndims; + udata.mesg.u.chunk.ndims = ndims; H5B_debug (f, dxpl_id, addr, stream, indent, fwidth, H5B_ISTORE, &udata); diff --git a/src/H5Dpkg.h b/src/H5Dpkg.h index b9047a6..8a4abae 100644 --- a/src/H5Dpkg.h +++ b/src/H5Dpkg.h @@ -86,4 +86,11 @@ extern H5D_dxpl_cache_t H5D_def_dxpl_cache; H5_DLL herr_t H5D_alloc_storage (H5F_t *f, hid_t dxpl_id, H5D_t *dset, H5D_time_alloc_t time_alloc, hbool_t update_time, hbool_t full_overwrite); + +/* Testing functions */ +#ifdef H5D_TESTING +H5_DLL herr_t H5D_layout_version_test(hid_t did, unsigned *version); +H5_DLL herr_t H5D_layout_contig_size_test(hid_t did, hsize_t *size); +#endif /* H5D_TESTING */ + #endif /*_H5Dpkg_H*/ diff --git a/src/H5Dprivate.h b/src/H5Dprivate.h index 63532c8..985d935 100644 --- a/src/H5Dprivate.h +++ b/src/H5Dprivate.h @@ -46,7 +46,7 @@ #define H5D_CRT_CHUNK_DIM_DEF 1 /* Definitions for chunk size */ #define H5D_CRT_CHUNK_SIZE_NAME "chunk_size" -#define H5D_CRT_CHUNK_SIZE_SIZE sizeof(hsize_t[H5O_LAYOUT_NDIMS]) +#define H5D_CRT_CHUNK_SIZE_SIZE sizeof(size_t[H5O_LAYOUT_NDIMS]) #define H5D_CRT_CHUNK_SIZE_DEF {1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,\ 1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1} /* Definitions for fill value. size=0 means fill value will be 0 as diff --git a/src/H5Dseq.c b/src/H5Dseq.c index dcd12cc..9bf10e7 100644 --- a/src/H5Dseq.c +++ b/src/H5Dseq.c @@ -227,7 +227,7 @@ H5F_seq_readvv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_i HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "external data read failed"); } else { /* Pass along the vector of sequences to read */ - if((ret_value=H5F_contig_readvv(f, layout->chunk_size, layout->addr, + if((ret_value=H5F_contig_readvv(f, layout->u.contig.size, layout->u.contig.addr, dset_max_nseq, dset_curr_seq, dset_len_arr, dset_offset_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, dxpl_id, buf))<0) @@ -336,7 +336,7 @@ H5F_seq_writevv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "external data write failed"); } else { /* Pass along the vector of sequences to write */ - if ((ret_value=H5F_contig_writevv(f, layout->chunk_size, layout->addr, + if ((ret_value=H5F_contig_writevv(f, layout->u.contig.size, layout->u.contig.addr, dset_max_nseq, dset_curr_seq, dset_len_arr, dset_offset_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, dxpl_id, buf))<0) diff --git a/src/H5Dtest.c b/src/H5Dtest.c new file mode 100644 index 0000000..d3339df --- /dev/null +++ b/src/H5Dtest.c @@ -0,0 +1,116 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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: Quincey Koziol <koziol@ncsa.uiuc.edu> + * Thusdayr, May 27, 2004 + * + * Purpose: Dataset testing functions. + */ + +#define H5D_PACKAGE /*suppress error about including H5Dpkg */ +#define H5D_TESTING /*suppress warning about H5D testing funcs*/ + +/* Pablo information */ +/* (Put before include files to avoid problems with inline functions) */ +#define PABLO_MASK H5Dtest_mask + +#include "H5private.h" /* Generic Functions */ +#include "H5Dpkg.h" /* Datasets */ +#include "H5Eprivate.h" /* Error handling */ +#include "H5Iprivate.h" /* ID Functions */ + +/* Interface initialization */ +#define INTERFACE_INIT NULL +static int interface_initialize_g = 0; + + +/*-------------------------------------------------------------------------- + NAME + H5D_layout_version_test + PURPOSE + Determine the storage layout version for a dataset's layout information + USAGE + herr_t H5D_layout_version_test(did, version) + hid_t did; IN: Dataset to query + unsigned *version; OUT: Pointer to location to place version info + RETURNS + Non-negative on success, negative on failure + DESCRIPTION + Checks the version of the storage layout information for a dataset. + GLOBAL VARIABLES + COMMENTS, BUGS, ASSUMPTIONS + DO NOT USE THIS FUNCTION FOR ANYTHING EXCEPT TESTING + EXAMPLES + REVISION LOG +--------------------------------------------------------------------------*/ +herr_t +H5D_layout_version_test(hid_t did, unsigned *version) +{ + H5D_t *dset; /* Pointer to dataset to query */ + herr_t ret_value=SUCCEED; /* return value */ + + FUNC_ENTER_NOAPI(H5D_layout_version_test, FAIL); + + /* Check args */ + if (NULL==(dset=H5I_object_verify(did, H5I_DATASET))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") + + if(version) + *version=dset->layout.version; + +done: + FUNC_LEAVE_NOAPI(ret_value); +} /* H5D_layout_version_test() */ + + +/*-------------------------------------------------------------------------- + NAME + H5D_layout_contig_size_test + PURPOSE + Determine the size of a contiguous layout for a dataset's layout information + USAGE + herr_t H5D_layout_contig_size_test(did, size) + hid_t did; IN: Dataset to query + hsize_t *size; OUT: Pointer to location to place size info + RETURNS + Non-negative on success, negative on failure + DESCRIPTION + Checks the size of a contiguous dataset's storage. + GLOBAL VARIABLES + COMMENTS, BUGS, ASSUMPTIONS + DO NOT USE THIS FUNCTION FOR ANYTHING EXCEPT TESTING + EXAMPLES + REVISION LOG +--------------------------------------------------------------------------*/ +herr_t +H5D_layout_contig_size_test(hid_t did, hsize_t *size) +{ + H5D_t *dset; /* Pointer to dataset to query */ + herr_t ret_value=SUCCEED; /* return value */ + + FUNC_ENTER_NOAPI(H5D_layout_contig_size_test, FAIL); + + /* Check args */ + if (NULL==(dset=H5I_object_verify(did, H5I_DATASET))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") + + if(size) { + assert(dset->layout.type==H5D_CONTIGUOUS); + *size=dset->layout.u.contig.size; + } /* end if */ + +done: + FUNC_LEAVE_NOAPI(ret_value); +} /* H5D_layout_contig_size_test() */ + diff --git a/src/H5Fcompact.c b/src/H5Fcompact.c index 96e9955..4f5b75e 100644 --- a/src/H5Fcompact.c +++ b/src/H5Fcompact.c @@ -70,7 +70,7 @@ H5F_compact_readvv(H5F_t UNUSED *f, const H5O_layout_t *layout, FUNC_ENTER_NOAPI(H5F_compact_readvv, FAIL); /* Use the vectorized memory copy routine to do actual work */ - if((ret_value=H5V_memcpyvv(buf,mem_max_nseq,mem_curr_seq,mem_size_arr,mem_offset_arr,layout->buf,dset_max_nseq,dset_curr_seq,dset_size_arr,dset_offset_arr))<0) + if((ret_value=H5V_memcpyvv(buf,mem_max_nseq,mem_curr_seq,mem_size_arr,mem_offset_arr,layout->u.compact.buf,dset_max_nseq,dset_curr_seq,dset_size_arr,dset_offset_arr))<0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vectorized memcpy failed"); done: @@ -112,10 +112,10 @@ H5F_compact_writevv(H5F_t UNUSED *f, H5O_layout_t *layout, FUNC_ENTER_NOAPI(H5F_compact_writevv, FAIL); /* Use the vectorized memory copy routine to do actual work */ - if((ret_value=H5V_memcpyvv(layout->buf,dset_max_nseq,dset_curr_seq,dset_size_arr,dset_offset_arr,buf,mem_max_nseq,mem_curr_seq,mem_size_arr,mem_offset_arr))<0) + if((ret_value=H5V_memcpyvv(layout->u.compact.buf,dset_max_nseq,dset_curr_seq,dset_size_arr,dset_offset_arr,buf,mem_max_nseq,mem_curr_seq,mem_size_arr,mem_offset_arr))<0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vectorized memcpy failed"); - layout->dirty = TRUE; + layout->u.compact.dirty = TRUE; done: FUNC_LEAVE_NOAPI(ret_value); diff --git a/src/H5Fcontig.c b/src/H5Fcontig.c index 09be560..1255922 100644 --- a/src/H5Fcontig.c +++ b/src/H5Fcontig.c @@ -75,8 +75,6 @@ H5FL_BLK_DEFINE_STATIC(zero_fill); herr_t H5F_contig_create(H5F_t *f, hid_t dxpl_id, struct H5O_layout_t *layout) { - hsize_t size; /* Size of contiguous block of data */ - unsigned u; /* Local index variable */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5F_contig_create, FAIL); @@ -85,14 +83,8 @@ H5F_contig_create(H5F_t *f, hid_t dxpl_id, struct H5O_layout_t *layout) assert(f); assert(layout); - /* Compute size */ - size=layout->dim[0]; - for (u = 1; u < layout->ndims; u++) - size *= layout->dim[u]; - assert (size>0); - /* Allocate space for the contiguous data */ - if (HADDR_UNDEF==(layout->addr=H5MF_alloc(f, H5FD_MEM_DRAW, dxpl_id, size))) + if (HADDR_UNDEF==(layout->u.contig.addr=H5MF_alloc(f, H5FD_MEM_DRAW, dxpl_id, layout->u.contig.size))) HGOTO_ERROR (H5E_IO, H5E_NOSPACE, FAIL, "unable to reserve file space"); done: @@ -145,8 +137,8 @@ H5F_contig_fill(H5F_t *f, hid_t dxpl_id, struct H5O_layout_t *layout, assert(f); assert(TRUE==H5P_isa_class(dxpl_id,H5P_DATASET_XFER)); assert(layout && H5D_CONTIGUOUS==layout->type); - assert(layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS); - assert(H5F_addr_defined(layout->addr)); + assert(H5F_addr_defined(layout->u.contig.addr)); + assert(layout->u.contig.size>0); assert(space); assert(elmt_size>0); @@ -167,7 +159,7 @@ H5F_contig_fill(H5F_t *f, hid_t dxpl_id, struct H5O_layout_t *layout, #endif /* H5_HAVE_PARALLEL */ /* Get the number of elements in the dataset's dataspace */ - snpoints = H5S_get_simple_extent_npoints(space); + snpoints = H5S_GET_SIMPLE_EXTENT_NPOINTS(space); assert(snpoints>=0); H5_ASSIGN_OVERFLOW(npoints,snpoints,hssize_t,size_t); @@ -214,7 +206,7 @@ H5F_contig_fill(H5F_t *f, hid_t dxpl_id, struct H5O_layout_t *layout, } /* end else */ /* Start at the beginning of the dataset */ - addr = layout->addr; + addr = layout->u.contig.addr; /* Loop through writing the fill value to the dataset */ while (npoints>0) { @@ -290,8 +282,6 @@ done: herr_t H5F_contig_delete(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout) { - hsize_t size; /* Size of contiguous block of data */ - unsigned u; /* Local index variable */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5F_contig_delete, FAIL); @@ -300,17 +290,12 @@ H5F_contig_delete(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout) assert(f); assert(layout); - /* Compute size */ - size=layout->dim[0]; - for (u = 1; u < layout->ndims; u++) - size *= layout->dim[u]; - /* Check for overlap with the sieve buffer and reset it */ - if (H5F_sieve_overlap_clear(f, dxpl_id, layout->addr, size)<0) + if (H5F_sieve_overlap_clear(f, dxpl_id, layout->u.contig.addr, layout->u.contig.size)<0) HGOTO_ERROR(H5E_OHDR, H5E_CANTFREE, FAIL, "unable to clear sieve buffer"); /* Free the file space for the chunk */ - if (H5MF_xfree(f, H5FD_MEM_DRAW, dxpl_id, layout->addr, size)<0) + if (H5MF_xfree(f, H5FD_MEM_DRAW, dxpl_id, layout->u.contig.addr, layout->u.contig.size)<0) HGOTO_ERROR(H5E_OHDR, H5E_CANTFREE, FAIL, "unable to free object header"); done: diff --git a/src/H5Fistore.c b/src/H5Fistore.c index 861c28f..2434cc2 100644 --- a/src/H5Fistore.c +++ b/src/H5Fistore.c @@ -248,11 +248,11 @@ H5F_istore_sizeof_rkey(H5F_t UNUSED *f, const void *_udata) FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5F_istore_sizeof_rkey); assert(udata); - assert(udata->mesg.ndims > 0 && udata->mesg.ndims <= H5O_LAYOUT_NDIMS); + assert(udata->mesg.u.chunk.ndims > 0 && udata->mesg.u.chunk.ndims <= H5O_LAYOUT_NDIMS); nbytes = 4 + /*storage size */ 4 + /*filter mask */ - udata->mesg.ndims*8; /*dimension indices */ + udata->mesg.u.chunk.ndims*8; /*dimension indices */ FUNC_LEAVE_NOAPI(nbytes); } @@ -375,7 +375,7 @@ H5F_istore_debug_key (FILE *stream, H5F_t UNUSED *f, hid_t UNUSED dxpl_id, int i "Filter mask:", key->filter_mask); HDfprintf(stream, "%*s%-*s {", indent, "", fwidth, "Logical offset:"); - for (u=0; u<udata->mesg.ndims; u++) + for (u=0; u<udata->mesg.u.chunk.ndims; u++) HDfprintf (stream, "%s%Hd", u?", ":"", key->offset[u]); HDfputs ("}\n", stream); @@ -419,10 +419,10 @@ H5F_istore_cmp2(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, void *_lt_key, void *_uda assert(lt_key); assert(rt_key); assert(udata); - assert(udata->mesg.ndims > 0 && udata->mesg.ndims <= H5O_LAYOUT_NDIMS); + assert(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_s(udata->mesg.ndims, lt_key->offset, rt_key->offset); + ret_value = H5V_vector_cmp_s(udata->mesg.u.chunk.ndims, lt_key->offset, rt_key->offset); done: FUNC_LEAVE_NOAPI(ret_value); @@ -472,12 +472,12 @@ H5F_istore_cmp3(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, void *_lt_key, void *_uda assert(lt_key); assert(rt_key); assert(udata); - assert(udata->mesg.ndims > 0 && udata->mesg.ndims <= H5O_LAYOUT_NDIMS); + assert(udata->mesg.u.chunk.ndims > 0 && udata->mesg.u.chunk.ndims <= H5O_LAYOUT_NDIMS); - if (H5V_vector_lt_s(udata->mesg.ndims, udata->key.offset, + if (H5V_vector_lt_s(udata->mesg.u.chunk.ndims, udata->key.offset, lt_key->offset)) { ret_value = -1; - } else if (H5V_vector_ge_s(udata->mesg.ndims, udata->key.offset, + } else if (H5V_vector_ge_s(udata->mesg.u.chunk.ndims, udata->key.offset, rt_key->offset)) { ret_value = 1; } @@ -525,7 +525,7 @@ H5F_istore_new_node(H5F_t *f, hid_t dxpl_id, H5B_ins_t op, assert(lt_key); assert(rt_key); assert(udata); - assert(udata->mesg.ndims > 0 && udata->mesg.ndims < H5O_LAYOUT_NDIMS); + assert(udata->mesg.u.chunk.ndims > 0 && udata->mesg.u.chunk.ndims < H5O_LAYOUT_NDIMS); assert(addr_p); /* Allocate new storage */ @@ -541,7 +541,7 @@ H5F_istore_new_node(H5F_t *f, hid_t dxpl_id, H5B_ins_t op, */ lt_key->nbytes = udata->key.nbytes; lt_key->filter_mask = udata->key.filter_mask; - for (u=0; u<udata->mesg.ndims; u++) + for (u=0; u<udata->mesg.u.chunk.ndims; u++) lt_key->offset[u] = udata->key.offset[u]; /* @@ -551,12 +551,11 @@ H5F_istore_new_node(H5F_t *f, hid_t dxpl_id, H5B_ins_t op, if (H5B_INS_LEFT != op) { rt_key->nbytes = 0; rt_key->filter_mask = 0; - for (u=0; u<udata->mesg.ndims; u++) { - assert (udata->mesg.dim[u] < HSSIZET_MAX); - assert (udata->key.offset[u]+(hssize_t)(udata->mesg.dim[u]) > + for (u=0; u<udata->mesg.u.chunk.ndims; u++) { + assert (udata->key.offset[u]+(hssize_t)(udata->mesg.u.chunk.dim[u]) > udata->key.offset[u]); rt_key->offset[u] = udata->key.offset[u] + - (hssize_t)(udata->mesg.dim[u]); + (hssize_t)(udata->mesg.u.chunk.dim[u]); } } @@ -610,8 +609,8 @@ H5F_istore_found(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, haddr_t addr, const void assert(lt_key); /* Is this *really* the requested chunk? */ - for (u=0; u<udata->mesg.ndims; u++) { - if (udata->key.offset[u] >= lt_key->offset[u]+(hssize_t)(udata->mesg.dim[u])) + for (u=0; u<udata->mesg.u.chunk.ndims; u++) { + if (udata->key.offset[u] >= lt_key->offset[u]+(hssize_t)(udata->mesg.u.chunk.dim[u])) HGOTO_DONE(FAIL); } @@ -620,7 +619,7 @@ H5F_istore_found(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, haddr_t addr, const void udata->key.nbytes = lt_key->nbytes; udata->key.filter_mask = lt_key->filter_mask; assert (lt_key->nbytes>0); - for (u = 0; u < udata->mesg.ndims; u++) + for (u = 0; u < udata->mesg.u.chunk.ndims; u++) udata->key.offset[u] = lt_key->offset[u]; done: @@ -696,7 +695,7 @@ H5F_istore_insert(H5F_t *f, hid_t dxpl_id, haddr_t addr, void *_lt_key, assert("HDF5 INTERNAL ERROR -- see rpm" && 0); HGOTO_ERROR(H5E_STORAGE, H5E_UNSUPPORTED, H5B_INS_ERROR, "internal error"); - } else if (H5V_vector_eq_s (udata->mesg.ndims, + } else if (H5V_vector_eq_s (udata->mesg.u.chunk.ndims, udata->key.offset, lt_key->offset) && lt_key->nbytes>0) { /* @@ -735,20 +734,20 @@ H5F_istore_insert(H5F_t *f, hid_t dxpl_id, haddr_t addr, void *_lt_key, ret_value = H5B_INS_NOOP; } - } else if (H5V_hyper_disjointp(udata->mesg.ndims, - lt_key->offset, udata->mesg.dim, - udata->key.offset, udata->mesg.dim)) { - assert(H5V_hyper_disjointp(udata->mesg.ndims, - rt_key->offset, udata->mesg.dim, - udata->key.offset, udata->mesg.dim)); + } else if (H5V_hyper_disjointp(udata->mesg.u.chunk.ndims, + lt_key->offset, udata->mesg.u.chunk.dim, + udata->key.offset, udata->mesg.u.chunk.dim)) { + assert(H5V_hyper_disjointp(udata->mesg.u.chunk.ndims, + rt_key->offset, udata->mesg.u.chunk.dim, + udata->key.offset, udata->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->key.nbytes; md_key->filter_mask = udata->key.filter_mask; - for (u=0; u<udata->mesg.ndims; u++) { - assert(0 == udata->key.offset[u] % udata->mesg.dim[u]); + for (u=0; u<udata->mesg.u.chunk.ndims; u++) { + assert(0 == udata->key.offset[u] % udata->mesg.u.chunk.dim[u]); md_key->offset[u] = udata->key.offset[u]; } @@ -847,7 +846,7 @@ H5F_istore_iter_dump (H5F_t UNUSED *f, hid_t UNUSED dxpl_id, void *_lt_key, hadd } HDfprintf(bt_udata->stream, " 0x%08x %8Zu %10a [", lt_key->filter_mask, lt_key->nbytes, addr); - for (u=0; u<bt_udata->mesg.ndims; u++) + for (u=0; u<bt_udata->mesg.u.chunk.ndims; u++) HDfprintf(bt_udata->stream, "%s%Hd", u?", ":"", lt_key->offset[u]); HDfputs("]\n", bt_udata->stream); @@ -936,7 +935,7 @@ H5F_istore_flush_entry(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, udata.key.filter_mask = 0; udata.addr = HADDR_UNDEF; udata.key.nbytes = ent->chunk_size; - for (u=0; u<ent->layout.ndims; u++) + for (u=0; u<ent->layout.u.chunk.ndims; u++) udata.key.offset[u] = ent->offset[u]; alloc = ent->alloc_size; @@ -974,7 +973,7 @@ H5F_istore_flush_entry(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, * 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(f, dxpl_id, H5B_ISTORE, ent->layout.addr, &udata)<0) + if (H5B_insert(f, dxpl_id, H5B_ISTORE, ent->layout.u.chunk.addr, &udata)<0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to allocate chunk"); if (H5F_block_write(f, H5FD_MEM_DRAW, udata.addr, udata.key.nbytes, dxpl_id, buf)<0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file"); @@ -1365,22 +1364,22 @@ H5F_istore_lock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, con assert(TRUE==H5P_isa_class(dxpl_id,H5P_DATASET_XFER)); /* Get the chunk's size */ - assert(layout->chunk_size>0); - H5_ASSIGN_OVERFLOW(chunk_size,layout->chunk_size,hsize_t,size_t); + 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) { - for (u=0, temp_idx=0; u<layout->ndims; u++) { + for (u=0, temp_idx=0; u<layout->u.chunk.ndims; u++) { temp_idx += offset[u]; - temp_idx *= layout->dim[u]; + temp_idx *= layout->u.chunk.dim[u]; } - temp_idx += (hsize_t)(layout->addr); + temp_idx += (hsize_t)(layout->u.chunk.addr); idx=H5F_HASH(f,temp_idx); ent = rdcc->slot[idx]; - if (ent && layout->ndims==ent->layout.ndims && - H5F_addr_eq(layout->addr, ent->layout.addr)) { - for (u=0, found=TRUE; u<ent->layout.ndims; u++) { + if (ent && layout->u.chunk.ndims==ent->layout.u.chunk.ndims && + H5F_addr_eq(layout->u.chunk.addr, ent->layout.u.chunk.addr)) { + for (u=0, found=TRUE; u<ent->layout.u.chunk.ndims; u++) { if (offset[u]!=ent->offset[u]) { found = FALSE; break; @@ -1508,7 +1507,7 @@ H5F_istore_lock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, con ent->alloc_size = chunk_size; H5O_copy(H5O_LAYOUT_ID, layout, &ent->layout); H5O_copy(H5O_PLINE_ID, pline, &ent->pline); - for (u=0; u<layout->ndims; u++) + for (u=0; u<layout->u.chunk.ndims; u++) ent->offset[u] = offset[u]; ent->rd_count = chunk_size; ent->wr_count = chunk_size; @@ -1645,10 +1644,10 @@ H5F_istore_unlock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, x.dirty = TRUE; H5O_copy (H5O_LAYOUT_ID, layout, &x.layout); H5O_copy (H5O_PLINE_ID, pline, &x.pline); - for (u=0; u<layout->ndims; u++) + for (u=0; u<layout->u.chunk.ndims; u++) x.offset[u] = offset[u]; - assert(layout->chunk_size>0); - H5_ASSIGN_OVERFLOW(x.chunk_size,layout->chunk_size,hsize_t,size_t); + 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; @@ -1709,7 +1708,7 @@ H5F_istore_readvv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, hid_t dxp assert(f); assert(dxpl_cache); assert(layout && H5D_CHUNKED==layout->type); - assert(layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS); + assert(layout->u.chunk.ndims>0 && layout->u.chunk.ndims<=H5O_LAYOUT_NDIMS); assert(dcpl_cache); assert(chunk_len_arr); assert(chunk_offset_arr); @@ -1718,19 +1717,19 @@ H5F_istore_readvv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, hid_t dxp assert(buf); #ifndef NDEBUG - for (u=0; u<layout->ndims; u++) + for (u=0; u<layout->u.chunk.ndims; u++) assert(chunk_coords[u]>=0); /*negative coordinates not supported (yet) */ #endif /* Get the address of this chunk on disk */ #ifdef QAK HDfprintf(stderr,"%s: chunk_coords={",FUNC); -for(u=0; u<layout->ndims; u++) - HDfprintf(stderr,"%Hd%s",chunk_coords[u],(u<(layout->ndims-1) ? ", " : "}\n")); +for(u=0; u<layout->u.chunk.ndims; u++) + HDfprintf(stderr,"%Hd%s",chunk_coords[u],(u<(layout->u.chunk.ndims-1) ? ", " : "}\n")); #endif /* QAK */ chunk_addr=H5F_istore_get_addr(f, dxpl_id, layout, chunk_coords, &udata); #ifdef QAK -HDfprintf(stderr,"%s: chunk_addr=%a, chunk_size=%Hu\n",FUNC,chunk_addr,layout->chunk_size); +HDfprintf(stderr,"%s: chunk_addr=%a, chunk_size=%Hu\n",FUNC,chunk_addr,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]); @@ -1743,9 +1742,9 @@ HDfprintf(stderr,"%s: mem_offset_arr[%Zu]=%Hu\n",FUNC,*mem_curr_seq,mem_offset_a * for the chunk has been defined, then don't load the chunk into the * cache, just write the data to it directly. */ - if (layout->chunk_size>f->shared->rdcc_nbytes && dcpl_cache->pline.nused==0 && + if (layout->u.chunk.size>f->shared->rdcc_nbytes && dcpl_cache->pline.nused==0 && chunk_addr!=HADDR_UNDEF) { - if ((ret_value=H5F_contig_readvv(f, layout->chunk_size, chunk_addr, chunk_max_nseq, chunk_curr_seq, chunk_len_arr, chunk_offset_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, dxpl_id, buf))<0) + if ((ret_value=H5F_contig_readvv(f, (hsize_t)layout->u.chunk.size, chunk_addr, chunk_max_nseq, chunk_curr_seq, chunk_len_arr, chunk_offset_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, dxpl_id, buf))<0) HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "unable to read raw data to file"); } /* end if */ else { @@ -1813,7 +1812,7 @@ H5F_istore_writevv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, assert(f); assert(dxpl_cache); assert(layout && H5D_CHUNKED==layout->type); - assert(layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS); + assert(layout->u.chunk.ndims>0 && layout->u.chunk.ndims<=H5O_LAYOUT_NDIMS); assert(dcpl_cache); assert(chunk_len_arr); assert(chunk_offset_arr); @@ -1822,19 +1821,19 @@ H5F_istore_writevv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, assert(buf); #ifndef NDEBUG - for (u=0; u<layout->ndims; u++) + for (u=0; u<layout->u.chunk.ndims; u++) assert(chunk_coords[u]>=0); /*negative coordinates not supported (yet) */ #endif /* Get the address of this chunk on disk */ #ifdef QAK HDfprintf(stderr,"%s: chunk_coords={",FUNC); -for(u=0; u<layout->ndims; u++) - HDfprintf(stderr,"%Hd%s",chunk_coords[u],(u<(layout->ndims-1) ? ", " : "}\n")); +for(u=0; u<layout->u.chunk.ndims; u++) + HDfprintf(stderr,"%Hd%s",chunk_coords[u],(u<(layout->u.chunk.ndims-1) ? ", " : "}\n")); #endif /* QAK */ chunk_addr=H5F_istore_get_addr(f, dxpl_id, layout, chunk_coords, &udata); #ifdef QAK -HDfprintf(stderr,"%s: chunk_addr=%a, chunk_size=%Hu\n",FUNC,chunk_addr,layout->chunk_size); +HDfprintf(stderr,"%s: chunk_addr=%a, chunk_size=%Hu\n",FUNC,chunk_addr,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]); @@ -1852,14 +1851,14 @@ HDfprintf(stderr,"%s: mem_offset_arr[%Zu]=%Hu\n",FUNC,*mem_curr_seq,mem_offset_a * writing to other elements in the same chunk. Do a direct * write-through of only the elements requested. */ - if ((layout->chunk_size>f->shared->rdcc_nbytes && dcpl_cache->pline.nused==0 && chunk_addr!=HADDR_UNDEF) + if ((layout->u.chunk.size>f->shared->rdcc_nbytes && dcpl_cache->pline.nused==0 && chunk_addr!=HADDR_UNDEF) || (IS_H5FD_MPI(f) && (H5F_ACC_RDWR & f->shared->flags))) { #ifdef H5_HAVE_PARALLEL /* Additional sanity check when operating in parallel */ if (chunk_addr==HADDR_UNDEF || dcpl_cache->pline.nused>0) HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to locate raw data chunk"); #endif /* H5_HAVE_PARALLEL */ - if ((ret_value=H5F_contig_writevv(f, layout->chunk_size, chunk_addr, chunk_max_nseq, chunk_curr_seq, chunk_len_arr, chunk_offset_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, dxpl_id, buf))<0) + if ((ret_value=H5F_contig_writevv(f, (hsize_t)layout->u.chunk.size, chunk_addr, chunk_max_nseq, chunk_curr_seq, chunk_len_arr, chunk_offset_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, dxpl_id, buf))<0) HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file"); } /* end if */ else { @@ -1872,7 +1871,7 @@ HDfprintf(stderr,"%s: mem_offset_arr[%Zu]=%Hu\n",FUNC,*mem_curr_seq,mem_offset_a * Lock the chunk, copy from application to chunk, then unlock the * chunk. */ - if(chunk_max_nseq==1 && chunk_len_arr[0] == layout->chunk_size) + if(chunk_max_nseq==1 && chunk_len_arr[0] == layout->u.chunk.size) relax = TRUE; else relax = FALSE; @@ -1933,14 +1932,14 @@ H5F_istore_create(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout /*out */ ) /* Check args */ assert(f); assert(layout && H5D_CHUNKED == layout->type); - assert(layout->ndims > 0 && layout->ndims <= H5O_LAYOUT_NDIMS); + assert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS); #ifndef NDEBUG - for (u = 0; u < layout->ndims; u++) - assert(layout->dim[u] > 0); + for (u = 0; u < layout->u.chunk.ndims; u++) + assert(layout->u.chunk.dim[u] > 0); #endif - udata.mesg.ndims = layout->ndims; - if (H5B_create(f, dxpl_id, H5B_ISTORE, &udata, &(layout->addr)/*out*/) < 0) + udata.mesg.u.chunk.ndims = layout->u.chunk.ndims; + 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: @@ -1976,7 +1975,7 @@ H5F_istore_allocated(H5F_t *f, hid_t dxpl_id, unsigned ndims, haddr_t addr) FUNC_ENTER_NOAPI(H5F_istore_allocated, 0); HDmemset(&udata, 0, sizeof udata); - udata.mesg.ndims = ndims; + udata.mesg.u.chunk.ndims = ndims; if (H5B_iterate(f, dxpl_id, H5B_ISTORE, H5F_istore_iter_allocated, addr, &udata)<0) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, 0, "unable to iterate over chunk B-tree"); @@ -2018,20 +2017,20 @@ H5F_istore_get_addr(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, FUNC_ENTER_NOAPI_NOINIT(H5F_istore_get_addr); assert(f); - assert(layout && (layout->ndims > 0)); + assert(layout && (layout->u.chunk.ndims > 0)); assert(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<layout->ndims; u++) + for (u=0; u<layout->u.chunk.ndims; u++) udata->key.offset[u] = offset[u]; udata->mesg = *layout; udata->addr = HADDR_UNDEF; /* Go get the chunk information */ - if (H5B_find (f, dxpl_id, H5B_ISTORE, layout->addr, udata)<0) { + if (H5B_find (f, dxpl_id, H5B_ISTORE, layout->u.chunk.addr, udata)<0) { H5E_clear(NULL); HGOTO_ERROR(H5E_BTREE,H5E_NOTFOUND,HADDR_UNDEF,"Can't locate chunk info"); @@ -2189,8 +2188,8 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, assert(f); assert(space_dim); assert(layout && H5D_CHUNKED==layout->type); - assert(layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS); - assert(H5F_addr_defined(layout->addr)); + assert(layout->u.chunk.ndims>0 && layout->u.chunk.ndims<=H5O_LAYOUT_NDIMS); + assert(H5F_addr_defined(layout->u.chunk.addr)); assert(TRUE==H5P_isa_class(dxpl_id,H5P_DATASET_XFER)); assert(dc_plist); @@ -2230,9 +2229,9 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, * Setup indice to go through all chunks. (Future improvement * should allocate only chunks that have no file space assigned yet. */ - for (u=0; u<layout->ndims; u++) + for (u=0; u<layout->u.chunk.ndims; u++) chunk_offset[u] = 0; - chunk_size = layout->chunk_size; + chunk_size = layout->u.chunk.size; /* Check the dataset's fill-value status */ if (H5P_is_fill_value_defined(&fill, &fill_status) < 0) @@ -2297,12 +2296,12 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, /* Look for chunk in cache */ for(ent = rdcc->head; ent && !chunk_exists; ent = ent->next) { /* Make certain we are dealing with the correct B-tree, etc */ - if (layout->ndims==ent->layout.ndims && - H5F_addr_eq(layout->addr, ent->layout.addr)) { + if (layout->u.chunk.ndims==ent->layout.u.chunk.ndims && + H5F_addr_eq(layout->u.chunk.addr, ent->layout.u.chunk.addr)) { /* Assume a match */ chunk_exists = 1; - for(u = 0; u < layout->ndims && chunk_exists; u++) { + for(u = 0; u < layout->u.chunk.ndims && chunk_exists; u++) { if(ent->offset[u] != chunk_offset[u]) chunk_exists = 0; /* Reset if no match */ } /* end for */ @@ -2317,11 +2316,11 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, udata.addr = HADDR_UNDEF; H5_CHECK_OVERFLOW(chunk_size,hsize_t,size_t); udata.key.nbytes = (size_t)chunk_size; - for (u=0; u<layout->ndims; u++) + for (u=0; u<layout->u.chunk.ndims; u++) udata.key.offset[u] = chunk_offset[u]; /* Allocate the chunk with all processes */ - if (H5B_insert(f, dxpl_id, H5B_ISTORE, layout->addr, &udata)<0) + if (H5B_insert(f, dxpl_id, H5B_ISTORE, 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 */ @@ -2350,8 +2349,8 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, } /* end if */ /* Increment indices */ - for (i=layout->ndims-1, carry=1; i>=0 && carry; --i) { - chunk_offset[i] += layout->dim[i]; + for (i=layout->u.chunk.ndims-1, carry=1; i>=0 && carry; --i) { + chunk_offset[i] += layout->u.chunk.dim[i]; if (chunk_offset[i] >= (hssize_t)(space_dim[i])) chunk_offset[i] = 0; else @@ -2498,8 +2497,8 @@ H5F_istore_prune_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, /* Check args */ assert(f); assert(layout && H5D_CHUNKED == layout->type); - assert(layout->ndims > 0 && layout->ndims <= H5O_LAYOUT_NDIMS); - assert(H5F_addr_defined(layout->addr)); + assert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS); + assert(H5F_addr_defined(layout->u.chunk.addr)); assert(space); /* Go get the rank & dimensions */ @@ -2515,10 +2514,10 @@ H5F_istore_prune_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, next = ent->next; /* Make certain we are dealing with the correct B-tree, etc */ - if (layout->ndims==ent->layout.ndims && - H5F_addr_eq(layout->addr, ent->layout.addr)) { + if (layout->u.chunk.ndims==ent->layout.u.chunk.ndims && + H5F_addr_eq(layout->u.chunk.addr, ent->layout.u.chunk.addr)) { found = 0; - for(u = 0; u < ent->layout.ndims - 1; u++) { + for(u = 0; u < ent->layout.u.chunk.ndims - 1; u++) { if((hsize_t)ent->offset[u] > curr_dims[u]) { found = 1; break; @@ -2529,7 +2528,7 @@ H5F_istore_prune_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, if(found) { #if defined (H5F_ISTORE_DEBUG) HDfputs("cache:remove:[", stdout); - for(u = 0; u < ent->layout.ndims - 1; u++) { + for(u = 0; u < ent->layout.u.chunk.ndims - 1; u++) { HDfprintf(stdout, "%s%Hd", u ? ", " : "", ent->offset[u]); } HDfputs("]\n", stdout); @@ -2548,13 +2547,13 @@ H5F_istore_prune_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, HDmemset(&udata, 0, sizeof udata); udata.stream = stdout; - udata.mesg.addr = layout->addr; - udata.mesg.ndims = layout->ndims; - for(u = 0; u < udata.mesg.ndims; u++) - udata.mesg.dim[u] = layout->dim[u]; + udata.mesg.u.chunk.addr = layout->u.chunk.addr; + udata.mesg.u.chunk.ndims = layout->u.chunk.ndims; + for(u = 0; u < udata.mesg.u.chunk.ndims; u++) + udata.mesg.u.chunk.dim[u] = layout->u.chunk.dim[u]; udata.dims = curr_dims; - if(H5B_iterate(f, dxpl_id, H5B_ISTORE, H5F_istore_prune_extent, layout->addr, &udata) < 0) + if(H5B_iterate(f, dxpl_id, H5B_ISTORE, H5F_istore_prune_extent, layout->u.chunk.addr, &udata) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, 0, "unable to iterate over B-tree"); done: @@ -2596,11 +2595,11 @@ H5F_istore_prune_extent(H5F_t *f, hid_t dxpl_id, void *_lt_key, haddr_t UNUSED a FUNC_ENTER_NOAPI_NOINIT(H5F_istore_prune_extent); /* Figure out what chunks are no longer in use for the specified extent and release them */ - for(u = 0; u < bt_udata->mesg.ndims - 1; u++) + for(u = 0; u < bt_udata->mesg.u.chunk.ndims - 1; u++) if((hsize_t)lt_key->offset[u] > bt_udata->dims[u]) { #if defined (H5F_ISTORE_DEBUG) HDfputs("b-tree:remove:[", bt_udata->stream); - for(u = 0; u < bt_udata->mesg.ndims - 1; u++) { + for(u = 0; u < bt_udata->mesg.u.chunk.ndims - 1; u++) { HDfprintf(bt_udata->stream, "%s%Hd", u ? ", " : "", lt_key->offset[u]); } @@ -2612,7 +2611,7 @@ H5F_istore_prune_extent(H5F_t *f, hid_t dxpl_id, void *_lt_key, haddr_t UNUSED a udata.mesg = bt_udata->mesg; /* Remove */ - if(H5B_remove(f, dxpl_id, H5B_ISTORE, bt_udata->mesg.addr, &udata) < 0) + if(H5B_remove(f, dxpl_id, H5B_ISTORE, bt_udata->mesg.u.chunk.addr, &udata) < 0) HGOTO_ERROR(H5E_SYM, H5E_CANTINIT, H5B_ITER_ERROR, "unable to remove entry"); break; } /* end if */ @@ -2709,6 +2708,7 @@ H5F_istore_initialize_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_ca 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 */ int srank; /*current # of dimensions (signed) */ unsigned rank; /*current # of dimensions */ @@ -2725,8 +2725,8 @@ H5F_istore_initialize_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_ca /* Check args */ assert(f); assert(layout && H5D_CHUNKED == layout->type); - assert(layout->ndims > 0 && layout->ndims <= H5O_LAYOUT_NDIMS); - assert(H5F_addr_defined(layout->addr)); + assert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS); + assert(H5F_addr_defined(layout->u.chunk.addr)); assert(space); /* Get necessary properties from property list */ @@ -2749,10 +2749,12 @@ H5F_istore_initialize_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_ca /* Copy current dimensions */ for(u = 0; u < rank; u++) size[u] = curr_dims[u]; - size[u] = layout->dim[u]; + size[u] = layout->u.chunk.dim[u]; /* Create a data space for a chunk & set the extent */ - if(NULL == (space_chunk = H5S_create_simple(rank,layout->dim,NULL))) + 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"); /* @@ -2760,18 +2762,18 @@ H5F_istore_initialize_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_ca * loop through the chunks copying each chunk from the application to the * chunk cache. */ - for(u = 0; u < layout->ndims; u++) { - idx_max[u] = (size[u] - 1) / layout->dim[u] + 1; + 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 */ /* Loop over all chunks */ carry=0; while(carry==0) { - for(u = 0, naccessed = 1; u < layout->ndims; u++) { + 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] * (hssize_t)(layout->dim[u]); - sub_size[u] = MIN((idx_cur[u] + 1) * layout->dim[u], + chunk_offset[u] = idx_cur[u] * (hssize_t)(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 */ @@ -2780,8 +2782,8 @@ H5F_istore_initialize_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_ca * 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 < layout->ndims - 1; u++) { - end_chunk = chunk_offset[u] + layout->dim[u]; + for(u = 0, found = 0; u < layout->u.chunk.ndims - 1; u++) { + end_chunk = chunk_offset[u] + layout->u.chunk.dim[u]; if(end_chunk > size[u]) { found = 1; break; @@ -2798,15 +2800,15 @@ H5F_istore_initialize_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_ca 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->dim[u], size[u] - chunk_offset[u]); + count[u] = MIN((idx_cur[u] + 1) * layout->u.chunk.dim[u], size[u] - chunk_offset[u]); #if defined (H5F_ISTORE_DEBUG) HDfputs("cache:initialize:offset:[", stdout); - for(u = 0; u < layout->ndims - 1; u++) + for(u = 0; u < layout->u.chunk.ndims - 1; u++) HDfprintf(stdout, "%s%Hd", u ? ", " : "", chunk_offset[u]); HDfputs("]", stdout); HDfputs(":count:[", stdout); - for(u = 0; u < layout->ndims - 1; u++) + for(u = 0; u < layout->u.chunk.ndims - 1; u++) HDfprintf(stdout, "%s%Hd", u ? ", " : "", count[u]); HDfputs("]\n", stdout); #endif @@ -2829,7 +2831,7 @@ H5F_istore_initialize_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_ca } /*found */ /* Increment indices */ - for(i = layout->ndims - 1, carry = 1; i >= 0 && carry; --i) { + for(i = layout->u.chunk.ndims - 1, carry = 1; i >= 0 && carry; --i) { if(++idx_cur[i] >= idx_max[i]) idx_cur[i] = 0; else @@ -2876,14 +2878,14 @@ H5F_istore_delete(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache") /* Check if the B-tree has been created in the file */ - if(H5F_addr_defined(layout->addr)) { + if(H5F_addr_defined(layout->u.chunk.addr)) { /* Iterate through the entries in the cache, checking for the chunks to be deleted */ for (ent=rdcc->head; ent; ent=next) { /* Get pointer to next node, in case this one is deleted */ next=ent->next; /* Is the chunk to be deleted this cache entry? */ - if(layout->addr==ent->layout.addr) + if(layout->u.chunk.addr==ent->layout.u.chunk.addr) /* Remove entry without flushing */ if (H5F_istore_preempt(f, &dxpl_cache, dxpl_id, ent, FALSE )<0) HGOTO_ERROR (H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks"); @@ -2894,7 +2896,7 @@ H5F_istore_delete(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout) udata.mesg = *layout; /* Delete entire B-tree */ - if(H5B_delete(f, dxpl_id, H5B_ISTORE, layout->addr, &udata)<0) + if(H5B_delete(f, dxpl_id, H5B_ISTORE, layout->u.chunk.addr, &udata)<0) HGOTO_ERROR(H5E_IO, H5E_CANTDELETE, 0, "unable to delete chunk B-tree"); } /* end if */ @@ -2930,7 +2932,7 @@ H5F_istore_dump_btree(H5F_t *f, hid_t dxpl_id, FILE *stream, unsigned ndims, had FUNC_ENTER_NOAPI(H5F_istore_dump_btree, FAIL); HDmemset(&udata, 0, sizeof udata); - udata.mesg.ndims = ndims; + udata.mesg.u.chunk.ndims = ndims; udata.stream = stream; if(stream) HDfprintf(stream, " Address: %a\n",addr); @@ -3034,7 +3036,7 @@ H5F_istore_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE * stream, int inden FUNC_ENTER_NOAPI(H5F_istore_debug, FAIL); HDmemset (&udata, 0, sizeof udata); - udata.mesg.ndims = ndims; + udata.mesg.u.chunk.ndims = ndims; H5B_debug (f, dxpl_id, addr, stream, indent, fwidth, H5B_ISTORE, &udata); diff --git a/src/H5Fseq.c b/src/H5Fseq.c index dcd12cc..9bf10e7 100644 --- a/src/H5Fseq.c +++ b/src/H5Fseq.c @@ -227,7 +227,7 @@ H5F_seq_readvv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_i HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "external data read failed"); } else { /* Pass along the vector of sequences to read */ - if((ret_value=H5F_contig_readvv(f, layout->chunk_size, layout->addr, + if((ret_value=H5F_contig_readvv(f, layout->u.contig.size, layout->u.contig.addr, dset_max_nseq, dset_curr_seq, dset_len_arr, dset_offset_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, dxpl_id, buf))<0) @@ -336,7 +336,7 @@ H5F_seq_writevv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "external data write failed"); } else { /* Pass along the vector of sequences to write */ - if ((ret_value=H5F_contig_writevv(f, layout->chunk_size, layout->addr, + if ((ret_value=H5F_contig_writevv(f, layout->u.contig.size, layout->u.contig.addr, dset_max_nseq, dset_curr_seq, dset_len_arr, dset_offset_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, dxpl_id, buf))<0) diff --git a/src/H5Oattr.c b/src/H5Oattr.c index 2fd4677..4cd3a62 100644 --- a/src/H5Oattr.c +++ b/src/H5Oattr.c @@ -200,7 +200,7 @@ H5O_attr_decode(H5F_t *f, hid_t dxpl_id, const uint8_t *p, H5O_shared_t UNUSED * p += attr->ds_size; /* Compute the size of the data */ - H5_ASSIGN_OVERFLOW(attr->data_size,H5S_get_simple_extent_npoints(attr->ds)*H5T_get_size(attr->dt),hsize_t,size_t); + H5_ASSIGN_OVERFLOW(attr->data_size,H5S_GET_SIMPLE_EXTENT_NPOINTS(attr->ds)*H5T_get_size(attr->dt),hsize_t,size_t); /* Go get the data */ if(attr->data_size) { diff --git a/src/H5Olayout.c b/src/H5Olayout.c index 5dca442..63c41bc 100644 --- a/src/H5Olayout.c +++ b/src/H5Olayout.c @@ -58,9 +58,11 @@ const H5O_class_t H5O_LAYOUT[1] = {{ }}; /* For forward and backward compatibility. Version is 1 when space is - * allocated; 2 when space is delayed for allocation. */ + * allocated; 2 when space is delayed for allocation; 3 is default now and + * is revised to just store information needed for each storage type. */ #define H5O_LAYOUT_VERSION_1 1 #define H5O_LAYOUT_VERSION_2 2 +#define H5O_LAYOUT_VERSION_3 3 /* Interface initialization */ #define PABLO_MASK H5O_layout_mask @@ -92,13 +94,18 @@ H5FL_DEFINE(H5O_layout_t); * Added version number 2 case depends on if space has been allocated * at the moment when layout header message is updated. * + * Quincey Koziol, 2004-5-21 + * Added version number 3 case to straighten out problems with contiguous + * layout's sizes (was encoding them as 4-byte values when they were + * really n-byte values (where n usually is 8)) and additionally clean up + * the information written out. + * *------------------------------------------------------------------------- */ static void * H5O_layout_decode(H5F_t *f, hid_t UNUSED dxpl_id, const uint8_t *p, H5O_shared_t UNUSED *sh) { H5O_layout_t *mesg = NULL; - int version; unsigned u; void *ret_value; /* Return value */ @@ -114,44 +121,108 @@ H5O_layout_decode(H5F_t *f, hid_t UNUSED dxpl_id, const uint8_t *p, H5O_shared_t HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed"); /* Version. 1 when space allocated; 2 when space allocation is delayed */ - version = *p++; - if (version!=H5O_LAYOUT_VERSION_1 && version!=H5O_LAYOUT_VERSION_2) + mesg->version = *p++; + if (mesg->version<H5O_LAYOUT_VERSION_1 || mesg->version>H5O_LAYOUT_VERSION_3) HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL, "bad version number for layout message"); - /* Dimensionality */ - mesg->ndims = *p++; - if (mesg->ndims>H5O_LAYOUT_NDIMS) - HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL, "dimensionality is too large"); - - /* Layout class */ - mesg->type = *p++; - assert(H5D_CONTIGUOUS == mesg->type || H5D_CHUNKED == mesg->type || H5D_COMPACT == mesg->type); - - /* Reserved bytes */ - p += 5; - - /* Address */ - if(mesg->type!=H5D_COMPACT) - H5F_addr_decode(f, &p, &(mesg->addr)); - - /* Read the size */ - for (u = 0; u < mesg->ndims; u++) - UINT32DECODE(p, mesg->dim[u]); - - if(mesg->type == H5D_COMPACT) { - UINT32DECODE(p, mesg->size); - if(mesg->size > 0) { - if(NULL==(mesg->buf=H5MM_malloc(mesg->size))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for fill value"); - HDmemcpy(mesg->buf, p, mesg->size); - p += mesg->size; + if(mesg->version < H5O_LAYOUT_VERSION_3) { + unsigned ndims; /* Num dimensions in chunk */ + + /* Dimensionality */ + ndims = *p++; + if (ndims>H5O_LAYOUT_NDIMS) + HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL, "dimensionality is too large"); + + /* Layout class */ + mesg->type = *p++; + assert(H5D_CONTIGUOUS == mesg->type || H5D_CHUNKED == mesg->type || H5D_COMPACT == mesg->type); + + /* Reserved bytes */ + p += 5; + + /* Address */ + if(mesg->type==H5D_CONTIGUOUS) + H5F_addr_decode(f, &p, &(mesg->u.contig.addr)); + else if(mesg->type==H5D_CHUNKED) + H5F_addr_decode(f, &p, &(mesg->u.chunk.addr)); + + /* Read the size */ + if(mesg->type!=H5D_CHUNKED) { + size_t temp_dim[H5O_LAYOUT_NDIMS]; + + for (u = 0; u < ndims; u++) + UINT32DECODE(p, temp_dim[u]); + + /* Don't compute size of contiguous storage here, due to possible + * truncation of the dimension sizes when they were stored in this + * version of the layout message. Compute the contiguous storage + * size in the dataset code, where we've got the dataspace + * information available also. - QAK 5/26/04 + */ + } /* end if */ + else { + mesg->u.chunk.ndims=ndims; + for (u = 0; u < ndims; u++) + UINT32DECODE(p, mesg->u.chunk.dim[u]); + + /* Compute chunk size */ + for (u=1, mesg->u.chunk.size=mesg->u.chunk.dim[0]; u<ndims; u++) + mesg->u.chunk.size *= mesg->u.chunk.dim[u]; + } /* end if */ + + if(mesg->type == H5D_COMPACT) { + UINT32DECODE(p, mesg->u.compact.size); + if(mesg->u.compact.size > 0) { + if(NULL==(mesg->u.compact.buf=H5MM_malloc(mesg->u.compact.size))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for compact data buffer"); + HDmemcpy(mesg->u.compact.buf, p, mesg->u.compact.size); + p += mesg->u.compact.size; + } } - } - else if(mesg->type == H5D_CHUNKED || mesg->type == H5D_CONTIGUOUS) { - /* Compute chunk size */ - for (u=1, mesg->chunk_size=mesg->dim[0]; u<mesg->ndims; u++) - mesg->chunk_size *= mesg->dim[u]; } /* end if */ + else { + /* Layout class */ + mesg->type = *p++; + + /* Interpret the rest of the message according to the layout class */ + switch(mesg->type) { + case H5D_CONTIGUOUS: + H5F_addr_decode(f, &p, &(mesg->u.contig.addr)); + H5F_DECODE_LENGTH(f, p, mesg->u.contig.size); + break; + + case H5D_CHUNKED: + /* Dimensionality */ + mesg->u.chunk.ndims = *p++; + if (mesg->u.chunk.ndims>H5O_LAYOUT_NDIMS) + HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL, "dimensionality is too large"); + + /* B-tree address */ + H5F_addr_decode(f, &p, &(mesg->u.chunk.addr)); + + /* Chunk dimensions */ + for (u = 0; u < mesg->u.chunk.ndims; u++) + UINT32DECODE(p, mesg->u.chunk.dim[u]); + + /* Compute chunk size */ + for (u=1, mesg->u.chunk.size=mesg->u.chunk.dim[0]; u<mesg->u.chunk.ndims; u++) + mesg->u.chunk.size *= mesg->u.chunk.dim[u]; + break; + + case H5D_COMPACT: + UINT16DECODE(p, mesg->u.compact.size); + if(mesg->u.compact.size > 0) { + if(NULL==(mesg->u.compact.buf=H5MM_malloc(mesg->u.compact.size))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for compact data buffer"); + HDmemcpy(mesg->u.compact.buf, p, mesg->u.compact.size); + p += mesg->u.compact.size; + } /* end if */ + break; + + default: + HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL, "Invalid layout class"); + } /* end switch */ + } /* end else */ /* Set return value */ ret_value=mesg; @@ -175,6 +246,10 @@ done: * Programmer: Robb Matzke * Wednesday, October 8, 1997 * + * Note: + * Quincey Koziol, 2004-5-21 + * We write out version 3 messages by default now. + * * Modifications: * Robb Matzke, 1998-07-20 * Rearranged the message to add a version number at the beginning. @@ -183,6 +258,12 @@ done: * Added version number 2 case depends on if space has been allocated * at the moment when layout header message is updated. * + * Quincey Koziol, 2004-5-21 + * Added version number 3 case to straighten out problems with contiguous + * layout's sizes (was encoding them as 4-byte values when they were + * really n-byte values (where n usually is 8)) and additionally clean up + * the information written out. + * *------------------------------------------------------------------------- */ static herr_t @@ -197,46 +278,50 @@ H5O_layout_encode(H5F_t *f, uint8_t *p, const void *_mesg) /* check args */ assert(f); assert(mesg); - assert(mesg->ndims > 0 && mesg->ndims <= H5O_LAYOUT_NDIMS); assert(p); - /* Version: 1 when space allocated; 2 when space allocation is delayed */ - if(mesg->type==H5D_CONTIGUOUS) { - if(mesg->addr==HADDR_UNDEF) - *p++ = H5O_LAYOUT_VERSION_2; - else - *p++ = H5O_LAYOUT_VERSION_1; - } else if(mesg->type==H5D_COMPACT) { - *p++ = H5O_LAYOUT_VERSION_2; - } else - *p++ = H5O_LAYOUT_VERSION_1; - - /* number of dimensions */ - *p++ = mesg->ndims; - - /* layout class */ + /* Version 3 by default now. */ + *p++ = H5O_LAYOUT_VERSION_3; + + /* Layout class */ *p++ = mesg->type; - /* reserved bytes should be zero */ - for (u=0; u<5; u++) - *p++ = 0; + /* Write out layout class specific information */ + switch(mesg->type) { + case H5D_CONTIGUOUS: + H5F_addr_encode(f, &p, mesg->u.contig.addr); + H5F_ENCODE_LENGTH(f, p, mesg->u.contig.size); + break; - /* data or B-tree address */ - if(mesg->type!=H5D_COMPACT) - H5F_addr_encode(f, &p, mesg->addr); + case H5D_CHUNKED: + /* Number of dimensions */ + assert(mesg->u.chunk.ndims > 0 && mesg->u.chunk.ndims <= H5O_LAYOUT_NDIMS); + *p++ = mesg->u.chunk.ndims; - /* dimension size */ - for (u = 0; u < mesg->ndims; u++) - UINT32ENCODE(p, mesg->dim[u]); + /* B-tree address */ + H5F_addr_encode(f, &p, mesg->u.chunk.addr); + + /* Dimension sizes */ + for (u = 0; u < mesg->u.chunk.ndims; u++) + UINT32ENCODE(p, mesg->u.chunk.dim[u]); + break; + + case H5D_COMPACT: + /* Size of raw data */ + UINT16ENCODE(p, mesg->u.compact.size); + + /* Raw data */ + if(mesg->u.compact.size>0 && mesg->u.compact.buf) { + HDmemcpy(p, mesg->u.compact.buf, mesg->u.compact.size); + p += mesg->u.compact.size; + } /* end if */ + break; + + default: + HGOTO_ERROR(H5E_OHDR, H5E_CANTENCODE, FAIL, "Invalid layout class"); + break; + } /* end switch */ - if(mesg->type==H5D_COMPACT) { - UINT32ENCODE(p, mesg->size); - if(mesg->size>0 && mesg->buf) { - HDmemcpy(p, mesg->buf, mesg->size); - p += mesg->size; - } - } - done: FUNC_LEAVE_NOAPI(ret_value); } @@ -279,11 +364,11 @@ H5O_layout_copy(const void *_mesg, void *_dest) /* Deep copy the buffer for compact datasets also */ if(mesg->type==H5D_COMPACT) { /* Allocate memory for the raw data */ - if (NULL==(dest->buf=H5MM_malloc(dest->size))) + if (NULL==(dest->u.compact.buf=H5MM_malloc(dest->u.compact.size))) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "unable to allocate memory for compact dataset"); /* Copy over the raw data */ - HDmemcpy(dest->buf,mesg->buf,dest->size); + HDmemcpy(dest->u.compact.buf,mesg->u.compact.buf,dest->u.compact.size); } /* end if */ /* Set return value */ @@ -323,18 +408,37 @@ H5O_layout_meta_size(H5F_t *f, const void *_mesg) /* check args */ assert(f); assert(mesg); - assert(mesg->ndims > 0 && mesg->ndims <= H5O_LAYOUT_NDIMS); ret_value = 1 + /* Version number */ - 1 + /* layout class type */ - 1 + /* dimensionality */ - 5 + /* reserved bytes */ - mesg->ndims * 4; /* size of each dimension */ + 1; /* layout class type */ - if(mesg->type==H5D_COMPACT) - ret_value += 4; /* size field for compact dataset */ - else - ret_value += H5F_SIZEOF_ADDR(f); /* file address of data or B-tree for chunked dataset */ + switch(mesg->type) { + case H5D_CONTIGUOUS: + ret_value += H5F_SIZEOF_ADDR(f); /* Address of data */ + ret_value += H5F_SIZEOF_SIZE(f); /* Length of data */ + break; + + case H5D_CHUNKED: + /* Number of dimensions (1 byte) */ + assert(mesg->u.chunk.ndims > 0 && mesg->u.chunk.ndims <= H5O_LAYOUT_NDIMS); + ret_value++; + + /* B-tree address */ + ret_value += H5F_SIZEOF_ADDR(f); /* Address of data */ + + /* Dimension sizes */ + ret_value += mesg->u.chunk.ndims*4; + break; + + case H5D_COMPACT: + /* Size of raw data */ + ret_value+=2; + break; + + default: + HGOTO_ERROR(H5E_OHDR, H5E_CANTENCODE, 0, "Invalid layout class"); + break; + } /* end switch */ done: FUNC_LEAVE_NOAPI(ret_value); @@ -370,11 +474,10 @@ H5O_layout_size(H5F_t *f, const void *_mesg) /* check args */ assert(f); assert(mesg); - assert(mesg->ndims > 0 && mesg->ndims <= H5O_LAYOUT_NDIMS); ret_value = H5O_layout_meta_size(f, mesg); if(mesg->type==H5D_COMPACT) - ret_value += mesg->size;/* data for compact dataset */ + ret_value += mesg->u.compact.size;/* data for compact dataset */ done: FUNC_LEAVE_NOAPI(ret_value); } @@ -406,7 +509,7 @@ H5O_layout_reset (void *_mesg) if(mesg) { /* Free the compact storage buffer */ if(mesg->type==H5D_COMPACT) - mesg->buf=H5MM_xfree(mesg->buf); + mesg->u.compact.buf=H5MM_xfree(mesg->u.compact.buf); /* Reset the message */ mesg->type=H5D_CONTIGUOUS; @@ -443,7 +546,7 @@ H5O_layout_free (void *_mesg) /* Free the compact storage buffer */ if(mesg->type==H5D_COMPACT) - mesg->buf=H5MM_xfree(mesg->buf); + mesg->u.compact.buf=H5MM_xfree(mesg->u.compact.buf); H5FL_FREE(H5O_layout_t,mesg); @@ -536,21 +639,30 @@ H5O_layout_debug(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, const void *_mesg, FILE assert(indent >= 0); assert(fwidth >= 0); - HDfprintf(stream, "%*s%-*s %a\n", indent, "", fwidth, - H5D_CHUNKED == mesg->type ? "B-tree address:" : "Data address:", - mesg->addr); - - HDfprintf(stream, "%*s%-*s %lu\n", indent, "", fwidth, - "Number of dimensions:", - (unsigned long) (mesg->ndims)); - - /* Size */ - HDfprintf(stream, "%*s%-*s {", indent, "", fwidth, "Size:"); - for (u = 0; u < mesg->ndims; u++) { - HDfprintf(stream, "%s%lu", u ? ", " : "", - (unsigned long) (mesg->dim[u])); - } - HDfprintf(stream, "}\n"); + if(mesg->type==H5D_CHUNKED) { + HDfprintf(stream, "%*s%-*s %a\n", indent, "", fwidth, + "B-tree address:", mesg->u.chunk.addr); + HDfprintf(stream, "%*s%-*s %lu\n", indent, "", fwidth, + "Number of dimensions:", + (unsigned long) (mesg->u.chunk.ndims)); + /* Size */ + HDfprintf(stream, "%*s%-*s {", indent, "", fwidth, "Size:"); + for (u = 0; u < mesg->u.chunk.ndims; u++) { + HDfprintf(stream, "%s%lu", u ? ", " : "", + (unsigned long) (mesg->u.chunk.dim[u])); + } + HDfprintf(stream, "}\n"); + } /* end if */ + else if(mesg->type==H5D_CONTIGUOUS) { + HDfprintf(stream, "%*s%-*s %a\n", indent, "", fwidth, + "Data address:", mesg->u.contig.addr); + HDfprintf(stream, "%*s%-*s %Hu\n", indent, "", fwidth, + "Data Size:", mesg->u.contig.size); + } /* end if */ + else { + HDfprintf(stream, "%*s%-*s %Zu\n", indent, "", fwidth, + "Data Size:", mesg->u.compact.size); + } /* end else */ done: FUNC_LEAVE_NOAPI(ret_value); diff --git a/src/H5Oprivate.h b/src/H5Oprivate.h index 2686784..6520877 100644 --- a/src/H5Oprivate.h +++ b/src/H5Oprivate.h @@ -123,15 +123,32 @@ typedef struct H5O_efl_t { */ #define H5O_LAYOUT_NDIMS (H5S_MAX_RANK+1) +typedef struct H5O_layout_contig_t { + haddr_t addr; /* File address of data */ + hsize_t size; /* Size of data in bytes */ +} H5O_layout_contig_t; + +typedef struct H5O_layout_chunk_t { + haddr_t addr; /* File address of B-tree */ + unsigned ndims; /* Num dimensions in chunk */ + size_t dim[H5O_LAYOUT_NDIMS]; /* Size of chunk in elements */ + size_t size; /* Size of chunk in bytes */ +} H5O_layout_chunk_t; + +typedef struct H5O_layout_compact_t { + hbool_t dirty; /* Dirty flag for compact dataset */ + size_t size; /* Size of buffer in bytes */ + void *buf; /* Buffer for compact dataset */ +} H5O_layout_compact_t; + typedef struct H5O_layout_t { - int type; /*type of layout, H5D_layout_t */ - haddr_t addr; /*file address of data or B-tree */ - unsigned ndims; /*num dimensions in stored data */ - hsize_t dim[H5O_LAYOUT_NDIMS]; /*size of data or chunk in bytes */ - hsize_t chunk_size; /*size of chunk in bytes */ - hbool_t dirty; /*dirty flag for compact dataset */ - size_t size; /*size of compact dataset in bytes */ - void *buf; /*buffer for compact dataset */ + H5D_layout_t type; /* Type of layout */ + unsigned version; /* Version of message */ + union { + H5O_layout_contig_t contig; /* Information for contiguous layout */ + H5O_layout_chunk_t chunk; /* Information for chunked layout */ + H5O_layout_compact_t compact; /* Information for compact layout */ + } u; } H5O_layout_t; /* Enable reading/writing "bogus" messages */ diff --git a/src/H5Pdcpl.c b/src/H5Pdcpl.c index 1ae97b2..d2b57df 100644 --- a/src/H5Pdcpl.c +++ b/src/H5Pdcpl.c @@ -151,7 +151,7 @@ herr_t H5Pset_chunk(hid_t plist_id, int ndims, const hsize_t dim[/*ndims*/]) { int i; - hsize_t real_dims[H5O_LAYOUT_NDIMS]; /* Full-sized array to hold chunk dims */ + size_t real_dims[H5O_LAYOUT_NDIMS]; /* Full-sized array to hold chunk dims */ H5D_layout_t layout; H5P_genplist_t *plist; /* Property list pointer */ herr_t ret_value=SUCCEED; /* return value */ @@ -172,12 +172,14 @@ H5Pset_chunk(hid_t plist_id, int ndims, const hsize_t dim[/*ndims*/]) HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't find object for ID"); /* Initialize chunk dims to 0s */ - HDmemset(real_dims,0,H5O_LAYOUT_NDIMS*sizeof(hsize_t)); + HDmemset(real_dims,0,sizeof(real_dims)); for (i=0; i<ndims; i++) { - if (dim[i] <= 0) + if (dim[i] == 0) HGOTO_ERROR(H5E_ARGS, H5E_BADRANGE, FAIL, "all chunk dimensions must be positive"); + if (dim[i] != (dim[i]&0xffffffff)) + HGOTO_ERROR(H5E_ARGS, H5E_BADRANGE, FAIL, "all chunk dimensions must be less than 2^32"); real_dims[i]=dim[i]; /* Store user's chunk dimensions */ - } + } /* end for */ layout = H5D_CHUNKED; if(H5P_set(plist, H5D_CRT_LAYOUT_NAME, &layout) < 0) @@ -219,10 +221,8 @@ done: int H5Pget_chunk(hid_t plist_id, int max_ndims, hsize_t dim[]/*out*/) { - int i; int ndims; H5D_layout_t layout; - hsize_t chunk_size[H5O_LAYOUT_NDIMS]; H5P_genplist_t *plist; /* Property list pointer */ int ret_value; @@ -238,14 +238,20 @@ H5Pget_chunk(hid_t plist_id, int max_ndims, hsize_t dim[]/*out*/) if(H5D_CHUNKED != layout) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "not a chunked storage layout"); - if(H5P_get(plist, H5D_CRT_CHUNK_SIZE_NAME, chunk_size) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get chunk size"); if(H5P_get(plist, H5D_CRT_CHUNK_DIM_NAME, &ndims) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get chunk dimensionality"); - /* Get the dimension sizes */ - for (i=0; i<ndims && i<max_ndims && dim; i++) - dim[i] = chunk_size[i]; + if(dim) { + int i; + size_t chunk_size[H5O_LAYOUT_NDIMS]; + + if(H5P_get(plist, H5D_CRT_CHUNK_SIZE_NAME, chunk_size) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get chunk size"); + + /* Get the dimension sizes */ + for (i=0; i<ndims && i<max_ndims; i++) + dim[i] = chunk_size[i]; + } /* end if */ /* Set the return value */ ret_value=ndims; @@ -752,6 +752,10 @@ done: * Programmer: Robb Matzke * Tuesday, December 9, 1997 * + * Note: This routine participates in the "Inlining C function pointers" + * pattern, don't call it directly, use the appropriate macro + * defined in H5Sprivate.h. + * * Modifications: * Changed Name - QAK 7/7/98 * @@ -805,7 +809,7 @@ H5Sget_simple_extent_npoints(hid_t space_id) if (NULL == (ds = H5I_object_verify(space_id, H5I_DATASPACE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space"); - ret_value = H5S_get_simple_extent_npoints(ds); + ret_value = H5S_GET_SIMPLE_EXTENT_NPOINTS(ds); done: FUNC_LEAVE_API(ret_value); diff --git a/src/H5Sall.c b/src/H5Sall.c index 19a0a02..fafbf09 100644 --- a/src/H5Sall.c +++ b/src/H5Sall.c @@ -380,7 +380,7 @@ H5S_all_copy (H5S_t *dst, const H5S_t *src) assert(dst); /* Set number of elements in selection */ - dst->select.num_elem=(hsize_t)H5S_get_simple_extent_npoints(dst); + dst->select.num_elem=(hsize_t)H5S_GET_SIMPLE_EXTENT_NPOINTS(dst); done: FUNC_LEAVE_NOAPI(ret_value); @@ -723,7 +723,7 @@ H5S_select_all (H5S_t *space, unsigned rel_prev) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTDELETE, FAIL, "can't release selection"); /* Set number of elements in selection */ - space->select.num_elem=(hsize_t)H5S_get_simple_extent_npoints(space); + space->select.num_elem=(hsize_t)H5S_GET_SIMPLE_EXTENT_NPOINTS(space); /* Set selection type */ space->select.type=H5S_SEL_ALL; diff --git a/src/H5Smpio.c b/src/H5Smpio.c index 2fc3eea..0d8b537 100644 --- a/src/H5Smpio.c +++ b/src/H5Smpio.c @@ -106,7 +106,6 @@ H5S_mpio_all_type( const H5S_t *space, size_t elmt_size, hsize_t total_bytes; hssize_t snelmts; /*total number of elmts (signed) */ hsize_t nelmts; /*total number of elmts */ - unsigned u; herr_t ret_value = SUCCEED; FUNC_ENTER_NOAPI_NOINIT(H5S_mpio_all_type); @@ -115,7 +114,7 @@ H5S_mpio_all_type( const H5S_t *space, size_t elmt_size, assert (space); /* Just treat the entire extent as a block of bytes */ - if((snelmts = H5S_get_simple_extent_npoints(space))<0) + if((snelmts = H5S_GET_SIMPLE_EXTENT_NPOINTS(space))<0) HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "src dataspace has invalid selection") H5_ASSIGN_OVERFLOW(nelmts,snelmts,hssize_t,hsize_t); @@ -678,7 +677,8 @@ H5S_mpio_spaces_xfer(H5F_t *f, const H5O_layout_t *layout, size_t elmt_size, * the address to read from. This should be used as the diplacement for * a call to MPI_File_set_view() in the read or write call. */ - addr = f->shared->base_addr + layout->addr + mpi_file_offset; + assert(layout->type==H5D_CONTIGUOUS); + addr = f->shared->base_addr + layout->u.contig.addr + mpi_file_offset; #ifdef H5Smpi_DEBUG HDfprintf(stderr, "spaces_xfer: addr=%a\n", addr ); #endif diff --git a/src/H5Sprivate.h b/src/H5Sprivate.h index 8b5a5b8..59174fc 100644 --- a/src/H5Sprivate.h +++ b/src/H5Sprivate.h @@ -176,6 +176,7 @@ typedef struct H5S_conv_t { #ifdef H5S_PACKAGE #define H5S_GET_SIMPLE_EXTENT_TYPE(S) ((S)->extent.type) #define H5S_GET_SIMPLE_EXTENT_NDIMS(S) ((S)->extent.u.simple.rank) +#define H5S_GET_SIMPLE_EXTENT_NPOINTS(S) ((S)->extent.nelem) #define H5S_GET_SELECT_NPOINTS(S) ((S)->select.num_elem) #define H5S_GET_SELECT_TYPE(S) ((S)->select.type) #define H5S_SELECT_GET_SEQ_LIST(S,FLAGS,ITER,MAXSEQ,MAXBYTES,NSEQ,NBYTES,OFF,LEN) ((*(S)->select.get_seq_list)(S,FLAGS,ITER,MAXSEQ,MAXBYTES,NSEQ,NBYTES,OFF,LEN)) @@ -197,6 +198,7 @@ typedef struct H5S_conv_t { #else /* H5S_PACKAGE */ #define H5S_GET_SIMPLE_EXTENT_TYPE(S) (H5S_get_simple_extent_type(S)) #define H5S_GET_SIMPLE_EXTENT_NDIMS(S) (H5S_get_simple_extent_ndims(S)) +#define H5S_GET_SIMPLE_EXTENT_NPOINTS(S) (H5S_get_simple_extent_npoints(S)) #define H5S_GET_SELECT_NPOINTS(S) (H5S_get_select_npoints(S)) #define H5S_GET_SELECT_TYPE(S) (H5S_get_select_type(S)) #define H5S_SELECT_GET_SEQ_LIST(S,FLAGS,ITER,MAXSEQ,MAXBYTES,NSEQ,NBYTES,OFF,LEN) (H5S_select_get_seq_list(S,FLAGS,ITER,MAXSEQ,MAXBYTES,NSEQ,NBYTES,OFF,LEN)) @@ -433,8 +433,8 @@ done: */ htri_t H5V_hyper_disjointp(unsigned n, - const hssize_t *offset1, const hsize_t *size1, - const hssize_t *offset2, const hsize_t *size2) + const hssize_t *offset1, const size_t *size1, + const hssize_t *offset2, const size_t *size2) { unsigned u; htri_t ret_value=FALSE; /* Return value */ @@ -1229,7 +1229,7 @@ done: *------------------------------------------------------------------------- */ herr_t -H5V_chunk_index(unsigned ndims, const hssize_t *coord, const hsize_t *chunk, +H5V_chunk_index(unsigned ndims, const hssize_t *coord, const size_t *chunk, const hsize_t *down_nchunks, hsize_t *chunk_idx) { hssize_t scaled_coord[H5V_HYPER_NDIMS]; /* Scaled, coordinates, in terms of chunks */ @@ -1246,7 +1246,7 @@ H5V_chunk_index(unsigned ndims, const hssize_t *coord, const hsize_t *chunk, /* Compute the scaled coordinates for actual coordinates */ for(u=0; u<ndims; u++) { - H5_CHECK_OVERFLOW(chunk[u],hsize_t,hssize_t); + H5_CHECK_OVERFLOW(chunk[u],size_t,hssize_t); scaled_coord[u]=coord[u]/(hssize_t)chunk[u]; } /* end for */ diff --git a/src/H5Vprivate.h b/src/H5Vprivate.h index 3ed0707..24cfc19 100644 --- a/src/H5Vprivate.h +++ b/src/H5Vprivate.h @@ -50,9 +50,9 @@ H5_DLL hsize_t H5V_hyper_stride(unsigned n, const hsize_t *size, const hssize_t *offset, hssize_t *stride); H5_DLL htri_t H5V_hyper_disjointp(unsigned n, const hssize_t *offset1, - const hsize_t *size1, + const size_t *size1, const hssize_t *offset2, - const hsize_t *size2); + const size_t *size2); H5_DLL htri_t H5V_hyper_eq(int n, const hssize_t *offset1, const hsize_t *size1, const hssize_t *offset2, const hsize_t *size2); @@ -82,7 +82,7 @@ H5_DLL hsize_t H5V_array_offset(unsigned n, const hsize_t *total_size, H5_DLL herr_t H5V_array_calc(hsize_t offset, unsigned n, const hsize_t *total_size, hssize_t *coords); H5_DLL herr_t H5V_chunk_index(unsigned ndims, const hssize_t *coord, - const hsize_t *chunk, const hsize_t *down_nchunks, hsize_t *chunk_idx); + const size_t *chunk, const hsize_t *down_nchunks, hsize_t *chunk_idx); H5_DLL ssize_t H5V_memcpyvv(void *_dst, size_t dst_max_nseq, size_t *dst_curr_seq, size_t dst_len_arr[], hsize_t dst_off_arr[], const void *_src, @@ -481,7 +481,8 @@ H5Z_prelude_callback(hid_t dcpl_id, hid_t type_id, H5Z_prelude_type_t prelude_ty /* Check if the chunks have filters */ if(dcpl_pline.nused > 0) { unsigned chunk_ndims; /* # of chunk dimensions */ - hsize_t chunk_size[H5O_LAYOUT_NDIMS]; /* Size of chunk dimensions */ + size_t chunk_size[H5O_LAYOUT_NDIMS]; /* Size of chunk dimensions */ + hsize_t chunk_dims[H5O_LAYOUT_NDIMS]; /* Size of chunk dimensions */ H5S_t *space; /* Dataspace describing chunk */ hid_t space_id; /* ID for dataspace describing chunk */ size_t u; /* Local index variable */ @@ -493,7 +494,9 @@ H5Z_prelude_callback(hid_t dcpl_id, hid_t type_id, H5Z_prelude_type_t prelude_ty HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve chunk size") /* Create a data space for a chunk & set the extent */ - if(NULL == (space = H5S_create_simple(chunk_ndims,chunk_size,NULL))) + for(u=0; u<chunk_ndims; u++) + chunk_dims[u]=chunk_size[u]; + if(NULL == (space = H5S_create_simple(chunk_ndims,chunk_dims,NULL))) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create simple dataspace") /* Get ID for dataspace to pass to filter routines */ diff --git a/src/Makefile.in b/src/Makefile.in index c08141a..1160238 100644 --- a/src/Makefile.in +++ b/src/Makefile.in @@ -30,22 +30,23 @@ LIB=libhdf5.la DISTCLEAN=libhdf5.settings ## Source and object files for the library (lexicographically)... -LIB_SRC=H5.c H5A.c H5AC.c H5B.c H5D.c H5Dio.c H5E.c H5F.c H5Fcontig.c \ - H5Fcompact.c H5Fdbg.c H5Fistore.c H5Fseq.c H5FD.c H5FDcore.c \ - H5FDfamily.c H5FDfphdf5.c H5FDgass.c H5FDlog.c H5FDmpi.c H5FDmpio.c \ - H5FDmpiposix.c H5FDmulti.c H5FDsec2.c H5FDsrb.c H5FDstdio.c \ - H5FDstream.c H5FL.c H5FO.c H5FP.c H5FPclient.c H5FPserver.c H5FS.c \ - H5G.c H5Gent.c H5Gnode.c H5Gstab.c H5HG.c H5HGdbg.c H5HL.c H5HLdbg.c \ - H5HP.c H5I.c H5MF.c H5MM.c H5O.c H5Oattr.c H5Obogus.c H5Ocont.c \ - H5Odtype.c H5Oefl.c H5Ofill.c H5Olayout.c H5Omtime.c H5Oname.c \ - H5Onull.c H5Opline.c H5Osdspace.c H5Oshared.c H5Ostab.c H5P.c \ - H5Pdcpl.c H5Pdxpl.c H5Pfapl.c H5Pfcpl.c H5Ptest.c H5R.c H5RS.c H5S.c \ - H5Sall.c H5Shyper.c H5Smpio.c H5Snone.c H5Spoint.c H5Sselect.c \ - H5Stest.c H5ST.c H5T.c H5Tarray.c H5Tbit.c H5Tcommit.c H5Tcompound.c \ - H5Tconv.c H5Tcset.c H5Tenum.c H5Tfields.c H5Tfixed.c H5Tfloat.c \ - H5Tinit.c H5Tnative.c H5Toffset.c H5Topaque.c H5Torder.c H5Tpad.c \ - H5Tprecis.c H5Tstrpad.c H5Tvlen.c H5TB.c H5TS.c H5V.c H5Z.c \ - H5Zdeflate.c H5Zfletcher32.c H5Zshuffle.c H5Zszip.c H5Ztrans.c +LIB_SRC=H5.c H5A.c H5AC.c H5B.c H5D.c H5Dio.c H5Dtest.c H5E.c H5F.c \ + H5Fcontig.c H5Fcompact.c H5Fdbg.c H5Fistore.c H5Fseq.c H5FD.c \ + H5FDcore.c H5FDfamily.c H5FDfphdf5.c H5FDgass.c H5FDlog.c H5FDmpi.c \ + H5FDmpio.c H5FDmpiposix.c H5FDmulti.c H5FDsec2.c H5FDsrb.c \ + H5FDstdio.c H5FDstream.c H5FL.c H5FO.c H5FP.c H5FPclient.c \ + H5FPserver.c H5FS.c H5G.c H5Gent.c H5Gnode.c H5Gstab.c H5HG.c \ + H5HGdbg.c H5HL.c H5HLdbg.c H5HP.c H5I.c H5MF.c H5MM.c H5O.c H5Oattr.c \ + H5Obogus.c H5Ocont.c H5Odtype.c H5Oefl.c H5Ofill.c H5Olayout.c \ + H5Omtime.c H5Oname.c H5Onull.c H5Opline.c H5Osdspace.c H5Oshared.c \ + H5Ostab.c H5P.c H5Pdcpl.c H5Pdxpl.c H5Pfapl.c H5Pfcpl.c H5Ptest.c \ + H5R.c H5RS.c H5S.c H5Sall.c H5Shyper.c H5Smpio.c H5Snone.c \ + H5Spoint.c H5Sselect.c H5Stest.c H5ST.c H5T.c H5Tarray.c H5Tbit.c \ + H5Tcommit.c H5Tcompound.c H5Tconv.c H5Tcset.c H5Tenum.c H5Tfields.c \ + H5Tfixed.c H5Tfloat.c H5Tinit.c H5Tnative.c H5Toffset.c H5Topaque.c \ + H5Torder.c H5Tpad.c H5Tprecis.c H5Tstrpad.c H5Tvlen.c H5TB.c H5TS.c \ + H5V.c H5Z.c H5Zdeflate.c H5Zfletcher32.c H5Zshuffle.c H5Zszip.c \ + H5Ztrans.c LIB_OBJ=$(LIB_SRC:.c=.lo) diff --git a/test/dsets.c b/test/dsets.c index deaba61..79ff80b 100644 --- a/test/dsets.c +++ b/test/dsets.c @@ -578,6 +578,8 @@ test_compact_io(hid_t fapl) H5_FAILED(); printf(" Read different values than written.\n"); printf(" At index %d,%d\n", i, j); + printf(" wbuf[%d][%d]=%d\n", i, j, wbuf[i][j]); + printf(" rbuf[%d][%d]=%d\n", i, j, rbuf[i][j]); goto error; } } diff --git a/test/gen_old_layout.c b/test/gen_old_layout.c new file mode 100644 index 0000000..473b3d3 --- /dev/null +++ b/test/gen_old_layout.c @@ -0,0 +1,95 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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: Quincey Koziol <koziol@ncsa.uiuc.edu> + * Thursday, May 27, 2004 + * + * Purpose: Create two datasets (one for version 1 and one for version 2 of + * the layout message), which should have dimensions too large to + * represent in version 1 & 2 of the storage layout message. + * This program is used to create the test file `tlayouto.h5' which + * has truncated dimension information and can be used to verify that the + * library has fixed up the storage size correctly. + * To build the test file, this program MUST be compiled and linked + * with version hdf5-1.6.2 or _earlier_ libraries and the generated test + * file must be put into the 'test' directory in the 1.7+ (or 1.6+) branch + * of the library. + */ + +#include "hdf5.h" + +#define TESTFILE "tlayouto.h5" +#define SPACE_RANK 2 +#define SPACE_DIM0 (8*1024*1024*1024ULL) +#define SPACE_DIM1 ((4*1024*1024*1024ULL)+1ULL) + + +/*------------------------------------------------------------------------- + * Function: main + * + * Purpose: + * + * Return: Success: + * + * Failure: + * + * Programmer: Quincey Koziol + * Friday, January 3, 2003 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +int +main(void) +{ + hid_t file, space, dset, dcpl; + herr_t ret; + unsigned rank=SPACE_RANK; /* Rank of dataspace */ + hsize_t big_dims[SPACE_RANK]={SPACE_DIM0,SPACE_DIM1}; /* Large dimensions */ + + /* Create the file */ + file = H5Fcreate(TESTFILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); + if(file<0) + printf("file<0!\n"); + + /* Create the dataspace (for dataset) */ + space = H5Screate_simple(rank,big_dims,NULL); + if(space<0) + printf("space<0!\n"); + + /* Create a dataset creation property list */ + dcpl = H5Pcreate(H5P_DATASET_CREATE); + if(dcpl<0) + printf("dcpl<0!\n"); + + /* Make certain that the dataset's storage doesn't get allocated :-) */ + ret = H5Pset_alloc_time(dcpl,H5D_ALLOC_TIME_LATE); + if(ret<0) + printf("H5Pset_alloc_time() failed!\n"); + + /* Create the dataset with deferred storage allocation */ + dset = H5Dcreate(file, "Dataset", H5T_NATIVE_INT, space, dcpl); + if(dset<0) + printf("dset<0!\n"); + + H5Dclose(dset); + H5Sclose(space); + H5Pclose(dcpl); + H5Fclose(file); + + return 0; +} + diff --git a/test/tlayouto.h5 b/test/tlayouto.h5 Binary files differnew file mode 100644 index 0000000..5dba556 --- /dev/null +++ b/test/tlayouto.h5 diff --git a/test/tmisc.c b/test/tmisc.c index 87534fa..b1d1691 100644 --- a/test/tmisc.c +++ b/test/tmisc.c @@ -22,8 +22,14 @@ * *************************************************************/ +#define H5D_PACKAGE /*suppress error about including H5Dpkg */ + +/* Define this macro to indicate that the testing APIs should be available */ +#define H5D_TESTING + #include "hdf5.h" #include "testhdf5.h" +#include "H5Dpkg.h" /* Datasets */ /* Definitions for misc. test #1 */ #define MISC1_FILE "tmisc1.h5" @@ -217,6 +223,17 @@ unsigned m13_rdata[MISC13_DIM1][MISC13_DIM2]; /* Data read from dataset #define MISC19_ATTR_NAME "Attribute" #define MISC19_GROUP_NAME "Group" +/* Definitions for misc. test #20 */ +#define MISC20_FILE "tmisc20.h5" +#define MISC20_FILE_OLD "tlayouto.h5" +#define MISC20_DSET_NAME "Dataset" +#define MISC20_DSET2_NAME "Dataset2" +#define MISC20_SPACE_RANK 2 +#define MISC20_SPACE_DIM0 (8*1024*1024*1024ULL) +#define MISC20_SPACE_DIM1 ((4*1024*1024*1024ULL)+1ULL) +#define MISC20_SPACE2_DIM0 8 +#define MISC20_SPACE2_DIM1 4 + /**************************************************************** ** ** test_misc1(): test unlinking a dataset from a group and immediately @@ -3288,6 +3305,176 @@ test_misc19(void) /**************************************************************** ** +** test_misc20(): Test problems with version 2 of storage layout +** message truncating dimensions +** +****************************************************************/ +static void +test_misc20(void) +{ + hid_t fid; /* File ID */ + hid_t sid; /* 'Space ID */ + hid_t did; /* Dataset ID */ + hid_t dcpl; /* Dataset creation property list ID */ + unsigned rank=MISC20_SPACE_RANK; /* Rank of dataspace */ + hsize_t big_dims[MISC20_SPACE_RANK]={MISC20_SPACE_DIM0,MISC20_SPACE_DIM1}; /* Large dimensions */ + hsize_t small_dims[MISC20_SPACE_RANK]={MISC20_SPACE2_DIM0,MISC20_SPACE2_DIM1}; /* Small dimensions */ + unsigned version; /* Version of storage layout info */ + hsize_t contig_size; /* Size of contiguous storage size from layout into */ + char testfile[512]=""; /* Character buffer for corrected test file name */ + char *srcdir = HDgetenv("srcdir"); /* Pointer to the directory the source code is located within */ + herr_t ret; /* Generic return value */ + + /* Output message about test being performed */ + MESSAGE(5, ("Testing large dimension truncation fix\n")); + + /* Verify that chunks with dimensions that are too large get rejected */ + + /* Create a dataset creation property list */ + dcpl = H5Pcreate(H5P_DATASET_CREATE); + CHECK(dcpl, FAIL, "H5Pcreate"); + + /* Use chunked storage for this dataset */ + ret = H5Pset_chunk(dcpl,rank,big_dims); + VERIFY(ret, FAIL, "H5Pset_chunk"); + + /* Verify that the storage for the dataset is the correct size and hasn't + * been truncated. + */ + + /* Create the file */ + fid = H5Fcreate(MISC20_FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); + CHECK(fid, FAIL, "H5Fcreate"); + + /* Create dataspace with _really_ big dimensions */ + sid = H5Screate_simple(rank,big_dims,NULL); + CHECK(sid, FAIL, "H5Screate_simple"); + + /* Make certain that the dataset's storage doesn't get allocated :-) */ + ret = H5Pset_alloc_time(dcpl,H5D_ALLOC_TIME_LATE); + CHECK(ret, FAIL, "H5Pset_alloc_time"); + + /* Create dataset with big dataspace */ + did = H5Dcreate(fid, MISC20_DSET_NAME, H5T_NATIVE_INT, sid, dcpl); + CHECK(did, FAIL, "H5Dcreate"); + + /* Close datasset */ + ret=H5Dclose(did); + CHECK(ret, FAIL, "H5Dclose"); + + /* Close dataspace */ + ret=H5Sclose(sid); + CHECK(ret, FAIL, "H5Sclose"); + + /* Create dataspace with small dimensions */ + sid = H5Screate_simple(rank,small_dims,NULL); + CHECK(sid, FAIL, "H5Screate_simple"); + + /* Create dataset with big dataspace */ + did = H5Dcreate(fid, MISC20_DSET2_NAME, H5T_NATIVE_INT, sid, dcpl); + CHECK(did, FAIL, "H5Dcreate"); + + /* Close datasset */ + ret=H5Dclose(did); + CHECK(ret, FAIL, "H5Dclose"); + + /* Close dataspace */ + ret=H5Sclose(sid); + CHECK(ret, FAIL, "H5Sclose"); + + /* Close dataset creation property list */ + ret=H5Pclose(dcpl); + CHECK(ret, FAIL, "H5Pclose"); + + /* Close file */ + ret = H5Fclose(fid); + CHECK(ret, FAIL, "H5Fclose"); + + /* Re-open the file */ + fid = H5Fopen(MISC20_FILE, H5F_ACC_RDONLY, H5P_DEFAULT); + CHECK(fid, FAIL, "H5Fopen"); + + /* Open dataset with big dimensions */ + did = H5Dopen(fid, MISC20_DSET_NAME); + CHECK(did, FAIL, "H5Dopen"); + + /* Get the layout version */ + ret = H5D_layout_version_test(did,&version); + CHECK(ret, FAIL, "H5D_layout_version_test"); + VERIFY(version,3,"H5D_layout_version_test"); + + /* Get the layout contiguous storage size */ + ret = H5D_layout_contig_size_test(did,&contig_size); + CHECK(ret, FAIL, "H5D_layout_contig_size_test"); + VERIFY(contig_size, MISC20_SPACE_DIM0*MISC20_SPACE_DIM1*H5Tget_size(H5T_NATIVE_INT), "H5D_layout_contig_size_test"); + + /* Close datasset */ + ret=H5Dclose(did); + CHECK(ret, FAIL, "H5Dclose"); + + /* Open dataset with small dimensions */ + did = H5Dopen(fid, MISC20_DSET2_NAME); + CHECK(did, FAIL, "H5Dopen"); + + /* Get the layout version */ + ret = H5D_layout_version_test(did,&version); + CHECK(ret, FAIL, "H5D_layout_version_test"); + VERIFY(version,3,"H5D_layout_version_test"); + + /* Get the layout contiguous storage size */ + ret = H5D_layout_contig_size_test(did,&contig_size); + CHECK(ret, FAIL, "H5D_layout_contig_size_test"); + VERIFY(contig_size, MISC20_SPACE2_DIM0*MISC20_SPACE2_DIM1*H5Tget_size(H5T_NATIVE_INT), "H5D_layout_contig_size_test"); + + /* Close datasset */ + ret=H5Dclose(did); + CHECK(ret, FAIL, "H5Dclose"); + + /* Close file */ + ret = H5Fclose(fid); + CHECK(ret, FAIL, "H5Fclose"); + + /* Verify that the storage size is computed correctly for older versions of layout info */ + + /* Generate the correct name for the test file, by prepending the source path */ + if (srcdir && ((HDstrlen(srcdir) + HDstrlen(MISC20_FILE_OLD) + 1) < sizeof(testfile))) { + HDstrcpy(testfile, srcdir); + HDstrcat(testfile, "/"); + } + HDstrcat(testfile, MISC20_FILE_OLD); + + /* + * Open the old file and the dataset and get old settings. + */ + fid = H5Fopen(testfile, H5F_ACC_RDONLY, H5P_DEFAULT); + CHECK(fid, FAIL, "H5Fopen"); + + /* Open dataset with small dimensions */ + did = H5Dopen(fid, MISC20_DSET_NAME); + CHECK(did, FAIL, "H5Dopen"); + + /* Get the layout version */ + ret = H5D_layout_version_test(did,&version); + CHECK(ret, FAIL, "H5D_layout_version_test"); + VERIFY(version,2,"H5D_layout_version_test"); + + /* Get the layout contiguous storage size */ + ret = H5D_layout_contig_size_test(did,&contig_size); + CHECK(ret, FAIL, "H5D_layout_contig_size_test"); + VERIFY(contig_size, MISC20_SPACE_DIM0*MISC20_SPACE_DIM1*H5Tget_size(H5T_NATIVE_INT), "H5D_layout_contig_size_test"); + + /* Close datasset */ + ret=H5Dclose(did); + CHECK(ret, FAIL, "H5Dclose"); + + /* Close file */ + ret = H5Fclose(fid); + CHECK(ret, FAIL, "H5Fclose"); + +} /* end test_misc20() */ + +/**************************************************************** +** ** test_misc(): Main misc. test routine. ** ****************************************************************/ @@ -3316,6 +3503,7 @@ test_misc(void) test_misc17(); /* Test array of ASCII character */ test_misc18(); /* Test new object header information in H5G_stat_t struct */ test_misc19(); /* Test incrementing & decrementing ref count on IDs */ + test_misc20(); /* Test problems with truncated dimensions in version 2 of storage layout message */ } /* test_misc() */ @@ -3359,4 +3547,5 @@ cleanup_misc(void) HDremove(MISC17_FILE); HDremove(MISC18_FILE); HDremove(MISC19_FILE); + HDremove(MISC20_FILE); } |