diff options
| -rw-r--r-- | MANIFEST | 3 | ||||
| -rw-r--r-- | doc/html/H5.format.html | 428 | ||||
| -rw-r--r-- | src/H5A.c | 12 | ||||
| -rw-r--r-- | src/H5D.c | 302 | ||||
| -rw-r--r-- | src/H5Dcompact.c | 6 | ||||
| -rw-r--r-- | src/H5Dcontig.c | 40 | ||||
| -rw-r--r-- | src/H5Dio.c | 116 | ||||
| -rw-r--r-- | src/H5Distore.c | 226 | ||||
| -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/H5Fcompact.c | 6 | ||||
| -rw-r--r-- | src/H5Fcontig.c | 40 | ||||
| -rw-r--r-- | src/H5Fistore.c | 226 | ||||
| -rw-r--r-- | src/H5Fseq.c | 4 | ||||
| -rw-r--r-- | src/H5Oattr.c | 11 | ||||
| -rw-r--r-- | src/H5Olayout.c | 387 | ||||
| -rw-r--r-- | src/H5Oprivate.h | 46 | ||||
| -rw-r--r-- | src/H5Pdcpl.c | 29 | ||||
| -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 | 12 | ||||
| -rw-r--r-- | src/H5Vprivate.h | 8 | ||||
| -rw-r--r-- | src/H5Z.c | 16 | ||||
| -rw-r--r-- | src/Makefile.in | 4 | ||||
| -rw-r--r-- | test/dsets.c | 2 | ||||
| -rw-r--r-- | test/tmisc.c | 189 |
29 files changed, 1476 insertions, 668 deletions
@@ -850,6 +850,7 @@ ./src/H5Dprivate.h ./src/H5Dpublic.h ./src/H5Dpkg.h +./src/H5Dtest.c ./src/H5E.c ./src/H5Eprivate.h ./src/H5Epublic.h @@ -1050,6 +1051,7 @@ ./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_ @@ -1075,6 +1077,7 @@ ./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 76a9058..ae1ff23 100644 --- a/doc/html/H5.format.html +++ b/doc/html/H5.format.html @@ -104,6 +104,7 @@ TABLE.list TD { border:none; } <li><a href="#NILMessage">Name: NIL</a> <!-- 0x0000 --> <li><a href="#SimpleDataSpace">Name: Simple Dataspace</a> <!-- 0x0001 --> <!-- <li><a href="#DataSpaceMessage">Name: Complex Dataspace</a> --> <!-- 0x0002 --> + <li><a href="#ReservedMessage_0002">Name: Reserved - not assigned yet</a> <!-- 0x0002 --> <li><a href="#DataTypeMessage">Name: Datatype</a> <!-- 0x0003 --> <li><a href="#OldFillValueMessage">Name: Data Storage - Fill Value (Old)</a> <!-- 0x0004 --> <li><a href="#FillValueMessage">Name: Data Storage - Fill Value</a> <!-- 0x0005 --> @@ -119,18 +120,20 @@ TABLE.list TD { border:none; } <ol type=A> <li><a href="#ObjectHeader">Disk Format Level 2a - Data Object Headers</a><i>(Continued)</i> <ol type=1 start=6> - <li><a href="#CompactDataStorageMessage">Name: Data Storage - Compact</a> <!-- 0x0006 --> +<!-- <li><a href="#CompactDataStorageMessage">Name: Data Storage - Compact</a> --> <!-- 0x0006 --> + <li><a href="#ReservedMessage_0006">Name: Reserved - not assigned yet</a> <!-- 0x0006 --> <li><a href="#ExternalFileListMessage">Name: Data Storage - External Data Files</a> <!-- 0x0007 --> <li><a href="#LayoutMessage">Name: Data Storage - Layout</a> <!-- 0x0008 --> <li><a href="#ReservedMessage_0009">Name: Reserved - not assigned yet</a> <!-- 0x0009 --> <li><a href="#ReservedMessage_000A">Name: Reserved - not assigned yet</a> <!-- 0x000a --> - <li><a href="#FilterMessage">Name: Data Storage - Filter Pipeline</a> <!-- 0x000b --> + <li><a href="#FilterMessage">Name: Data Storage - Filter Pipeline</a> <!-- 0x000b --> <li><a href="#AttributeMessage">Name: Attribute</a> <!-- 0x000c --> - <li><a href="#NameMessage">Name: Object Name</a> <!-- 0x000d --> - <li><a href="#ModifiedMessage">Name: Object Modification Date and Time</a> <!-- 0x000e --> - <li><a href="#SharedMessage">Name: Shared Object Message</a> <!-- 0x000f --> + <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="#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 --> </ol> <li><a href="#SharedObjectHeader">Disk Format: Level 2b - Shared Data Object Headers</a> <li><a href="#DataStorage">Disk Format: Level 2c - Data Object Data Storage</a> @@ -1620,10 +1623,13 @@ TABLE.list TD { border:none; } first free block (or the <A href="#UndefinedAddress">undefined address</A> if there is no free block). The free block contains "Size of Lengths" bytes that - are the offset of the next free chunk (or the - <A href="#UndefinedAddress">undefined address</A> if this is the - last free chunk) followed by "Size of Lengths" bytes that store - the size of this free chunk. + are the offset of the next free block (or the + value '1' if this is the + last free block) followed by "Size of Lengths" bytes that store + the size of this free block. The size of the free block includes + the space used to store the offset of the next free block and + the of the current block, making the minimum size of a free block + 2 * "Size of Lengths". </P> </td> </tr> @@ -2719,6 +2725,17 @@ TABLE.list TD { border:none; } </center> --> + <hr> + <h4><a name="ReservedMessage_0002">Name: Reserved - Not Assigned Yet</a></h4> + <b>Header Message Type:</b> 0x0002<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="DataTypeMessage">Name: Datatype</a></h4> @@ -3428,7 +3445,12 @@ TABLE.list TD { border:none; } </tr> <tr> - <td>0-23</td> + <td>0-7</td> + <td>Length of ASCII tag in bytes.</td> + </tr> + + <tr> + <td>8-23</td> <td>Reserved (zero).</td> </tr> </table> @@ -3521,7 +3543,7 @@ TABLE.list TD { border:none; } <div align=center> <table class=format> <caption> - Properties Description for Datatype Version 0 + Properties Description for Datatype Version 1 </caption> <tr> @@ -3649,7 +3671,7 @@ TABLE.list TD { border:none; } <div align=center> <table class=format> <caption> - Properties Description for Datatype Version 1 + Properties Description for Datatype Version 2 </caption> <tr> @@ -4338,7 +4360,8 @@ TABLE.list TD { border:none; } <tr> <td align=center><code>2</code></td> <td>The current version used by the library (version - 1.7.3 or later). In this version, the Size field is + 1.7.3 or later). In this version, the Size and + Fill Value fields are only present if the Fill Value Defined field is set to 1. </td> @@ -4453,7 +4476,9 @@ TABLE.list TD { border:none; } <td>Fill Value</td> <td> <P>The fill value. The bytes of the fill value are interpreted - using the same datatype as for the dataset. + using the same datatype as for the dataset. This field is + not present if the Version field is >1 and the Fill Value + Defined field is set to 0. </P> </td> </tr> @@ -4461,6 +4486,7 @@ TABLE.list TD { border:none; } </div> </P> +<!-- <hr> <h4><a name="CompactDataStorageMessage">Name: Data Storage - Compact</a></h4> @@ -4480,6 +4506,18 @@ TABLE.list TD { border:none; } <P><b>Format of Data:</b> The message data is actually composed of dataset data, so the format will be determined by the dataset format. +--> + + <hr> + <h4><a name="ReservedMessage_0006">Name: Reserved - Not Assigned Yet</a></h4> + <b>Header Message Type:</b> 0x0006<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="ExternalFileListMessage">Name: Data Storage - @@ -4668,7 +4706,7 @@ TABLE.list TD { border:none; } <p><b>Purpose and Description:</b> Data layout describes how the elements of a multi-dimensional array are arranged in the linear - address space of the file. Two types of data layout are + address space of the file. Three types of data layout are supported: <ol> @@ -4688,13 +4726,19 @@ TABLE.list TD { border:none; } the size of the entire array; the size of the entire array can be calculated by traversing the B-tree that stores the chunk addresses. + + <li>The array can be stored in one contiguous block, as part of + 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> @@ -4730,6 +4774,18 @@ TABLE.list TD { border:none; } <tr align=center> <td colspan=4>...</td> </tr> + + <tr align=center> + <td colspan=4>Compact Data Size (4-bytes)</td> + </tr> + + <tr align=center> + <td colspan=4>Compact Data</td> + </tr> + + <tr align=center> + <td colspan=4>...</td> + </tr> </table> </center> @@ -4743,8 +4799,8 @@ TABLE.list TD { border:none; } <tr valign=top> <td>Version</td> - <td>A version number for the layout message. This - documentation describes version one.</td> + <td>A version number for the layout message. This value can be + either 1 or 2.</td> </tr> <tr valign=top> @@ -4758,8 +4814,10 @@ TABLE.list TD { border:none; } <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 while a value of two - indicates chunked storage. Other values will be defined + indicates contiguous storage, a value of two + indicates chunked storage, + while a value of three + indicates compact storage. Other values will be defined in the future.</td> </tr> @@ -4768,7 +4826,10 @@ TABLE.list TD { border:none; } <td>For contiguous storage, this is the address of the first byte of storage. For chunked storage this is the address of the B-tree that is used to look up the addresses of the - chunks.</td> + chunks. This field is not present for compact storage. + If the version for this message is set to 2, 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> @@ -4777,6 +4838,244 @@ TABLE.list TD { border:none; } size of the array while for chunked storage they define the size of a single chunk.</td> </tr> + + <tr valign=top> + <td>Compact Data Size</td> + <td>This field is only present for compact data storage. + It contains the size of the raw data for the dataset array.</td> + + <tr valign=top> + <td>Compact Data</td> + <td>This field is only present for compact data storage. + It contains the raw data for the dataset array.</td> + </tr> + </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> @@ -5124,14 +5423,14 @@ TABLE.list TD { border:none; } </center> <hr> - <h4><a name="NameMessage">Name: Object Name</a></h4> + <h4><a name="CommentMessage">Name: Object Comment</a></h4> <p><b>Header Message Type:</b> 0x000D<br> <b>Length:</b> varies<br> <b>Status:</b> Optional, may not be repeated. - <p><b>Purpose and Description:</b> The object name or comment is - designed to be a short description of an object. An object name + <p><b>Purpose and Description:</b> The object comment is + designed to be a short description of an object. An object comment is a sequence of non-zero (<code>\0</code>) ASCII characters with no other formatting included by the library. @@ -5150,7 +5449,7 @@ TABLE.list TD { border:none; } </tr> <tr align=center> - <td colspan=4><br>Name<br><br></td> + <td colspan=4><br>Comment<br><br></td> </tr> </table> </center> @@ -5171,7 +5470,7 @@ TABLE.list TD { border:none; } </center> <hr> - <h4><a name="ModifiedMessage">Name: Object Modification Date & Time</a></h4> + <h4><a name="OldModifiedMessage">Name: Object Modification Date & Time (Old)</a></h4> <p><b>Header Message Type:</b> 0x000E<br> <b>Length:</b> fixed<br> @@ -5183,6 +5482,12 @@ TABLE.list TD { border:none; } updated when any object header message changes according to the system clock where the change was posted. + <p>This modification time message is deprecated in favor of the "new" + modification time message (Message Type 0x0012) and is no longer written + to the file in versions of the HDF5 library after the 1.6.0 version. + </p> + + <p> <center> <table border align=center cellpadding=4 width="80%"> @@ -5460,6 +5765,75 @@ where the group name heap is located. </dl> </dl> + <hr> + <h4><a name="ModifiedMessage">Name: Object Modification Date & Time</a></h4> + + <P class=item><B>Header Message Type:</B> 0x0012 + </P> + <P class=item><B>Length:</B> Fixed + </P> + <P class=item><B>Status:</B> Optional, may not be repeated. + </P> + + <P class=item><B>Description:</B> The object modification date + and time is a timestamp which indicates + the last modification of an object. The time is + updated when any object header message changes according to the + system clock where the change was posted. + </P> + + <p> + <center> + <table border align=center cellpadding=4 width="80%"> + <caption align=top> + <b>Modification Time Message</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=1>Version</td> + <td colspan=3>Reserved</td> + </tr> + + <tr align=center> + <td colspan=4>Seconds After Epoch</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>The version number for the message. This document + describes version one of the new modification time message.</td> + </tr> + + <tr valign=top> + <td>Reserved</td> + <td>This field is reserved and should always be zero.</td> + </tr> + + <tr valign=top> + <td>Seconds After Epoch</td> + <td>The number of seconds since 0 hours, 0 + minutes, 0 seconds, January 1, 1970, Coordinated Universal Time. + </tr> + </table> + </center> + <h3><a name="SharedObjectHeader">Disk Format: Level 2b - Shared Data Object Headers</a></h3> <P>In order to share header messages between several dataset objects, object header messages may be placed into the global heap. Since these @@ -5570,7 +5944,7 @@ value with all bits set, i.e. <code>0xffff...ff</code>. <!-- #BeginLibraryItem "/ed_libs/Footer.lbi" --><address> <a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a> <br> -Describes HDF5 Release 1.6.2, February 2004 +Describes HDF5 Release 1.7, the unreleased development branch; working toward HDF5 Release 1.8.0 </address><!-- #EndLibraryItem --><!-- hhmts start --> Last modified: 5 July 2002 <!-- hhmts end --> @@ -272,7 +272,7 @@ 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.u.simple)); 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) @@ -613,6 +613,7 @@ H5A_write(H5A_t *attr, const H5T_t *mem_type, const void *buf, hid_t dxpl_id) { uint8_t *tconv_buf = NULL; /* data type conv buffer */ uint8_t *bkg_buf = NULL; /* temp conversion buffer */ + hssize_t snelmts; /* elements in attribute */ hsize_t nelmts; /* elements in attribute */ H5T_path_t *tpath = NULL; /* conversion information*/ hid_t src_id = -1, dst_id = -1;/* temporary type atoms */ @@ -629,7 +630,9 @@ 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 */ - nelmts=H5S_get_simple_extent_npoints (attr->ds); + if((snelmts=H5S_GET_SIMPLE_EXTENT_NPOINTS(attr->ds))<0) + HGOTO_ERROR (H5E_ATTR, H5E_CANTCOUNT, FAIL, "dataspace is invalid") + nelmts=(hsize_t)snelmts; /* Get the memory and file datatype sizes */ src_type_size = H5T_get_size(mem_type); @@ -761,6 +764,7 @@ H5A_read(H5A_t *attr, const H5T_t *mem_type, void *buf, hid_t dxpl_id) { uint8_t *tconv_buf = NULL; /* data type conv buffer*/ uint8_t *bkg_buf = NULL; /* background buffer */ + hssize_t snelmts; /* elements in attribute */ hsize_t nelmts; /* elements in attribute*/ H5T_path_t *tpath = NULL; /* type conversion info */ hid_t src_id = -1, dst_id = -1;/* temporary type atoms*/ @@ -776,7 +780,9 @@ H5A_read(H5A_t *attr, const H5T_t *mem_type, void *buf, hid_t dxpl_id) assert(buf); /* Create buffer for data to store on disk */ - nelmts=H5S_get_simple_extent_npoints (attr->ds); + if((snelmts=H5S_GET_SIMPLE_EXTENT_NPOINTS(attr->ds))<0) + HGOTO_ERROR (H5E_ATTR, H5E_CANTCOUNT, FAIL, "dataspace is invalid") + nelmts=(hsize_t)snelmts; /* Get the memory and file datatype sizes */ src_type_size = H5T_get_size(attr->dt); @@ -189,7 +189,7 @@ H5D_init_interface(void) H5P_genclass_t *crt_pclass; H5D_layout_t layout = H5D_CRT_LAYOUT_DEF; int 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; @@ -1322,8 +1322,8 @@ H5D_get_space_status(H5D_t *dset, H5D_space_status_t *allocation, hid_t dxpl_id) assert(space); /* Get the total number of elements in dataset's dataspace */ - if((total_elem=H5S_get_simple_extent_npoints(space))<0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "unable to get # of dataspace elements"); + 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 */ if((type_size=H5T_get_size(dset->type))==0) @@ -1665,7 +1665,7 @@ 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) @@ -1910,10 +1910,8 @@ 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; int chunk_ndims = 0; - 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 */ @@ -2040,100 +2038,114 @@ H5D_create(H5G_entry_t *loc, const char *name, hid_t type_id, const H5S_t *space new_dset->alloc_time=H5D_ALLOC_TIME_EARLY; /* Set up layout information */ - new_dset->layout.ndims = H5S_GET_SIMPLE_EXTENT_NDIMS(new_dset->space) + 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 */ + new_dset->layout.unused.ndims = H5S_GET_SIMPLE_EXTENT_NDIMS(new_dset->space) + 1; + assert((unsigned)(new_dset->layout.unused.ndims) <= NELMTS(new_dset->layout.unused.dim)); + if (H5S_get_simple_extent_dims(new_dset->space, new_dset->layout.unused.dim, NULL)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize storage info") + new_dset->layout.unused.dim[new_dset->layout.unused.ndims-1] = H5T_get_size(new_dset->type); 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 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, NULL, 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.unused.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]>new_dset->layout.unused.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 != 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: { hssize_t tmp_size; /* Temporary holder for raw data size */ - hsize_t comp_data_size; + hsize_t comp_data_size; /* * 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) - 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"); - } - + 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") + } /* end case */ break; default: @@ -2328,13 +2340,11 @@ static H5D_t * H5D_open_oid(H5G_entry_t *ent, hid_t dxpl_id) { H5D_t *dataset = NULL; /*new dataset struct */ - H5D_t *ret_value = NULL; /*return value */ 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 */ - int chunk_ndims; - H5P_genplist_t *plist; /* Property list */ + H5O_pline_t pline; /* I/O pipeline information */ + H5P_genplist_t *plist; /* Property list */ + H5D_t *ret_value = NULL; /*return value */ FUNC_ENTER_NOAPI(H5D_open_oid, NULL); @@ -2384,11 +2394,21 @@ H5D_open_oid(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: @@ -2397,22 +2417,21 @@ H5D_open_oid(H5G_entry_t *ent, hid_t dxpl_id) * the chunk dimension because the chunk includes a dimension for the * individual bytes of the data type. */ - layout = H5D_CHUNKED; - chunk_ndims = dataset->layout.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) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set chunk size"); + { + unsigned chunk_ndims; /* Dimensionality of chunk */ + + chunk_ndims = dataset->layout.u.chunk.ndims - 1; + + 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.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 */ @@ -2479,20 +2498,23 @@ H5D_open_oid(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) - && (IS_H5FD_MPIO(dataset->ent.file) || IS_H5FD_MPIPOSIX(dataset->ent.file) || IS_H5FD_FPHDF5(dataset->ent.file))) { + && ((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"); } @@ -2564,10 +2586,10 @@ 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; + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout message") + dataset->layout.u.compact.dirty = FALSE; } /* end if */ /* Remove the dataset from the list of opened objects in the file */ @@ -2587,7 +2609,7 @@ 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) @@ -2785,7 +2807,7 @@ H5D_alloc_storage (H5F_t *f, hid_t dxpl_id, H5D_t *dset/*in,out*/, H5D_time_allo 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"); @@ -2799,7 +2821,7 @@ 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"); @@ -2822,12 +2844,12 @@ 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))) - HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate memory for compact dataset"); - layout->dirty = TRUE; + 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->u.compact.dirty = TRUE; /* Indicate that we set the storage addr */ addr_set=1; @@ -2926,7 +2948,7 @@ 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); @@ -2937,9 +2959,9 @@ 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; @@ -2969,13 +2991,19 @@ 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]; + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get simple data space info") + 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"); } /* end if */ break; + + default: + assert ("not implemented yet" && 0); +#ifdef NDEBUG + HGOTO_ERROR (H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout") +#endif /* NDEBUG */ } /* end switch */ done: @@ -3044,32 +3072,29 @@ done: static hsize_t H5D_get_storage_size(H5D_t *dset, hid_t dxpl_id) { - unsigned u; /* Index variable */ hsize_t ret_value; FUNC_ENTER_NOAPI(H5D_get_storage_size, 0); 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: @@ -3138,7 +3163,7 @@ done: static haddr_t H5D_get_offset(H5D_t *dset) { - haddr_t ret_value; + haddr_t ret_value=HADDR_UNDEF; haddr_t base_addr; H5F_t *f; @@ -3149,7 +3174,6 @@ H5D_get_offset(H5D_t *dset) switch(dset->layout.type) { case H5D_CHUNKED: case H5D_COMPACT: - ret_value = HADDR_UNDEF; break; case H5D_CONTIGUOUS: @@ -3161,13 +3185,16 @@ H5D_get_offset(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: - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, HADDR_UNDEF, "unknown dataset layout type"); + assert ("not implemented yet" && 0); +#ifdef NDEBUG + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, HADDR_UNDEF, "unknown dataset layout type") +#endif /* NDEBUG */ } done: @@ -3516,7 +3543,7 @@ done: * Purpose: Modifies the dimensions of a dataset, based on H5Dextend. * Can change to a lower dimension. * - * Return: Success: 0, Failure: -1 + * Return: Success: SUCCEED, Failure: FAIL * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * Robb Matzke @@ -3559,7 +3586,7 @@ done: * Purpose: Based in H5D_extend, allows change to a lower dimension, * calls H5S_set_extent and H5F_istore_prune_by_extent instead * - * Return: Success: 0, Failure: -1 + * Return: Success: SUCCEED, Failure: FAIL * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * Robb Matzke @@ -3710,11 +3737,12 @@ H5D_flush(H5F_t *f, hid_t dxpl_id) HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to get dataset ID list"); 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) + HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to get dataset object") + 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; + HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to update layout message") + dataset->layout.u.compact.dirty = FALSE; + } /* end if */ } } /* end if */ @@ -3757,9 +3785,9 @@ H5Ddebug(hid_t dset_id, unsigned UNUSED flags) /* Print B-tree information */ if (H5D_CHUNKED==dset->layout.type) { - 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 9b1ad40..35b9700 100644 --- a/src/H5Dcontig.c +++ b/src/H5Dcontig.c @@ -31,10 +31,10 @@ #include "H5private.h" /* Generic Functions */ #include "H5Dprivate.h" /* Dataset functions */ #include "H5Eprivate.h" /* Error handling */ -#include "H5Fpkg.h" -#include "H5FDprivate.h" /*file driver */ -#include "H5FLprivate.h" /*Free Lists */ -#include "H5MFprivate.h" /*file memory management */ +#include "H5Fpkg.h" /* Files */ +#include "H5FDprivate.h" /* File drivers */ +#include "H5FLprivate.h" /* Free Lists */ +#include "H5MFprivate.h" /* File memory management */ #include "H5Oprivate.h" /* Object headers */ #include "H5Pprivate.h" /* Property lists */ #include "H5Sprivate.h" /* Dataspace functions */ @@ -46,8 +46,7 @@ #include "H5FDmpiposix.h" /* Private prototypes */ -static herr_t -H5F_contig_write(H5F_t *f, hsize_t max_data, haddr_t addr, +static herr_t H5F_contig_write(H5F_t *f, hsize_t max_data, haddr_t addr, const size_t size, hid_t dxpl_id, const void *buf); /* Interface initialization */ @@ -81,8 +80,6 @@ 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); @@ -91,14 +88,8 @@ 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: @@ -151,8 +142,8 @@ 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); @@ -199,7 +190,7 @@ 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); @@ -246,7 +237,7 @@ 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) { @@ -322,8 +313,6 @@ 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); @@ -332,17 +321,12 @@ 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 d39112d..d8a8f3c 100644 --- a/src/H5Dio.c +++ b/src/H5Dio.c @@ -43,7 +43,7 @@ /* Structure holding information about a chunk's selection for mapping */ typedef struct H5D_chunk_info_t { hsize_t index; /* "Index" of chunk in dataset (must be first for TBBT routines) */ - hsize_t chunk_points; /* Number of elements selected in chunk */ + size_t chunk_points; /* Number of elements selected in chunk */ H5S_t *fspace; /* Dataspace describing chunk & selection in it */ hssize_t coords[H5O_LAYOUT_NDIMS]; /* Coordinates of chunk in file dataset's dataspace */ H5S_t *mspace; /* Dataspace describing selection in memory corresponding to this chunk */ @@ -64,6 +64,7 @@ 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 */ @@ -690,8 +691,9 @@ 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 */ @@ -908,14 +910,15 @@ 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) - HGOTO_ERROR (H5E_DATASET, H5E_BADVALUE, FAIL, "can't retrieve number of elements in file dataset"); + 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 */ if(H5T_detect_class(dataset->type, H5T_VLEN)) @@ -1073,7 +1076,9 @@ 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 || dataset->layout.type==H5D_COMPACT); H5_CHECK_OVERFLOW(nelmts,hsize_t,size_t); status = (sconv->read)(dataset->ent.file, &(dataset->layout), @@ -1169,7 +1174,9 @@ 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, @@ -1537,8 +1544,9 @@ 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); @@ -1666,8 +1674,9 @@ 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*/); @@ -2262,16 +2271,16 @@ 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... */ @@ -2281,7 +2290,7 @@ 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"); @@ -2290,8 +2299,11 @@ 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]; @@ -2418,9 +2430,9 @@ H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_sp /* Spaces aren't the same shape, iterate over the memory selection directly */ if(H5S_select_iterate(&bogus, f_tid, file_space, H5D_chunk_mem_cb, fm)<0) - HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create memory chunk selections"); + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create memory chunk selections") - /* Clean memory chunks' hyperslab span "scratch" information */ + /* Clean up hyperslab stuff, if necessary */ if(fm->msel_type!=H5S_SEL_POINTS) { /* Clean memory chunks' hyperslab span "scratch" information */ curr_node=H5TB_first(fm->fsel->root); @@ -2591,7 +2603,6 @@ 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 */ @@ -2613,21 +2624,21 @@ 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) - HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index"); + 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 */ @@ -2645,15 +2656,15 @@ 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) { - H5S_close(tmp_fchunk); - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't create chunk selection"); + 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) { - H5S_close(tmp_fchunk); - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk dimensions"); + 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 */ /* Move selection back to have correct offset in chunk */ @@ -2695,7 +2706,7 @@ H5D_create_chunk_file_map_hyper(fm_map *fm) /* Get number of elements selected in chunk */ if((schunk_points=H5S_GET_SELECT_NPOINTS(tmp_fchunk))<0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection # of elements") - H5_ASSIGN_OVERFLOW(new_chunk_info->chunk_points,schunk_points,hssize_t,hsize_t); + H5_ASSIGN_OVERFLOW(new_chunk_info->chunk_points,schunk_points,hssize_t,size_t); /* Decrement # of points left in file selection */ sel_points-=schunk_points; @@ -2713,9 +2724,9 @@ 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]) { @@ -2727,13 +2738,13 @@ 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) - HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index"); + 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 */ @@ -2809,7 +2820,8 @@ 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; @@ -2869,10 +2881,8 @@ 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; @@ -2954,7 +2964,7 @@ 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 */ @@ -2985,7 +2995,7 @@ 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 */ @@ -3009,8 +3019,8 @@ 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; @@ -3034,7 +3044,7 @@ 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) @@ -3077,8 +3087,8 @@ 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) - HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index"); + 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 */ if(chunk_index==fm->last_index) { diff --git a/src/H5Distore.c b/src/H5Distore.c index 43045b1..2775548 100644 --- a/src/H5Distore.c +++ b/src/H5Distore.c @@ -252,11 +252,11 @@ 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); } @@ -379,7 +379,7 @@ 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); @@ -423,10 +423,10 @@ 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); @@ -476,12 +476,12 @@ 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; } @@ -529,7 +529,7 @@ 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 */ @@ -545,7 +545,7 @@ 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]; /* @@ -555,12 +555,11 @@ 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]); } } @@ -614,8 +613,8 @@ 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); } @@ -624,7 +623,7 @@ 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: @@ -700,7 +699,7 @@ 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) { /* @@ -739,20 +738,20 @@ 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]; } @@ -851,7 +850,7 @@ 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); @@ -940,7 +939,7 @@ 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; @@ -978,7 +977,7 @@ 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"); @@ -1369,22 +1368,22 @@ 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; @@ -1512,7 +1511,7 @@ 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; @@ -1649,10 +1648,10 @@ 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; @@ -1713,7 +1712,7 @@ 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); @@ -1722,19 +1721,19 @@ 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]); @@ -1747,9 +1746,9 @@ 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.nfilters==0 && + if (layout->u.chunk.size>f->shared->rdcc_nbytes && dcpl_cache->pline.nfilters==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 { @@ -1817,7 +1816,7 @@ 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); @@ -1826,19 +1825,19 @@ 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]); @@ -1856,16 +1855,14 @@ 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.nfilters==0 && - chunk_addr!=HADDR_UNDEF) - || ((IS_H5FD_MPIO(f) ||IS_H5FD_MPIPOSIX(f) || IS_H5FD_FPHDF5(f)) && - (H5F_ACC_RDWR & f->shared->flags))) { + if ((layout->u.chunk.size>f->shared->rdcc_nbytes && dcpl_cache->pline.nfilters==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.nfilters>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 { @@ -1878,7 +1875,7 @@ 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; @@ -1939,14 +1936,14 @@ 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: @@ -1982,7 +1979,7 @@ 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"); @@ -2024,20 +2021,20 @@ 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(); HGOTO_ERROR(H5E_BTREE,H5E_NOTFOUND,HADDR_UNDEF,"Can't locate chunk info"); @@ -2195,8 +2192,8 @@ 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); @@ -2262,9 +2259,9 @@ 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) @@ -2329,12 +2326,12 @@ 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 */ @@ -2349,11 +2346,11 @@ 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 */ @@ -2382,8 +2379,8 @@ 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 @@ -2530,8 +2527,8 @@ 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 */ @@ -2547,10 +2544,10 @@ 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; @@ -2561,7 +2558,7 @@ 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); @@ -2580,13 +2577,13 @@ 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: @@ -2628,11 +2625,11 @@ 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]); } @@ -2644,7 +2641,7 @@ 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 */ @@ -2741,6 +2738,7 @@ 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 */ @@ -2757,8 +2755,8 @@ 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 */ @@ -2781,10 +2779,12 @@ 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"); /* @@ -2792,18 +2792,18 @@ 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 */ @@ -2812,8 +2812,8 @@ 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; @@ -2830,15 +2830,15 @@ 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 @@ -2861,7 +2861,7 @@ 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 @@ -2908,14 +2908,14 @@ 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"); @@ -2926,7 +2926,7 @@ 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 */ @@ -2962,7 +2962,7 @@ 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); @@ -3066,7 +3066,7 @@ 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 7f90465..688d3e3 100644 --- a/src/H5Dprivate.h +++ b/src/H5Dprivate.h @@ -47,7 +47,7 @@ #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 a51e554..6fd583c 100644 --- a/src/H5Dseq.c +++ b/src/H5Dseq.c @@ -231,7 +231,7 @@ 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) @@ -340,7 +340,7 @@ 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/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 9b1ad40..35b9700 100644 --- a/src/H5Fcontig.c +++ b/src/H5Fcontig.c @@ -31,10 +31,10 @@ #include "H5private.h" /* Generic Functions */ #include "H5Dprivate.h" /* Dataset functions */ #include "H5Eprivate.h" /* Error handling */ -#include "H5Fpkg.h" -#include "H5FDprivate.h" /*file driver */ -#include "H5FLprivate.h" /*Free Lists */ -#include "H5MFprivate.h" /*file memory management */ +#include "H5Fpkg.h" /* Files */ +#include "H5FDprivate.h" /* File drivers */ +#include "H5FLprivate.h" /* Free Lists */ +#include "H5MFprivate.h" /* File memory management */ #include "H5Oprivate.h" /* Object headers */ #include "H5Pprivate.h" /* Property lists */ #include "H5Sprivate.h" /* Dataspace functions */ @@ -46,8 +46,7 @@ #include "H5FDmpiposix.h" /* Private prototypes */ -static herr_t -H5F_contig_write(H5F_t *f, hsize_t max_data, haddr_t addr, +static herr_t H5F_contig_write(H5F_t *f, hsize_t max_data, haddr_t addr, const size_t size, hid_t dxpl_id, const void *buf); /* Interface initialization */ @@ -81,8 +80,6 @@ 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); @@ -91,14 +88,8 @@ 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: @@ -151,8 +142,8 @@ 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); @@ -199,7 +190,7 @@ 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); @@ -246,7 +237,7 @@ 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) { @@ -322,8 +313,6 @@ 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); @@ -332,17 +321,12 @@ 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 43045b1..2775548 100644 --- a/src/H5Fistore.c +++ b/src/H5Fistore.c @@ -252,11 +252,11 @@ 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); } @@ -379,7 +379,7 @@ 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); @@ -423,10 +423,10 @@ 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); @@ -476,12 +476,12 @@ 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; } @@ -529,7 +529,7 @@ 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 */ @@ -545,7 +545,7 @@ 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]; /* @@ -555,12 +555,11 @@ 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]); } } @@ -614,8 +613,8 @@ 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); } @@ -624,7 +623,7 @@ 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: @@ -700,7 +699,7 @@ 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) { /* @@ -739,20 +738,20 @@ 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]; } @@ -851,7 +850,7 @@ 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); @@ -940,7 +939,7 @@ 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; @@ -978,7 +977,7 @@ 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"); @@ -1369,22 +1368,22 @@ 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; @@ -1512,7 +1511,7 @@ 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; @@ -1649,10 +1648,10 @@ 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; @@ -1713,7 +1712,7 @@ 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); @@ -1722,19 +1721,19 @@ 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]); @@ -1747,9 +1746,9 @@ 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.nfilters==0 && + if (layout->u.chunk.size>f->shared->rdcc_nbytes && dcpl_cache->pline.nfilters==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 { @@ -1817,7 +1816,7 @@ 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); @@ -1826,19 +1825,19 @@ 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]); @@ -1856,16 +1855,14 @@ 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.nfilters==0 && - chunk_addr!=HADDR_UNDEF) - || ((IS_H5FD_MPIO(f) ||IS_H5FD_MPIPOSIX(f) || IS_H5FD_FPHDF5(f)) && - (H5F_ACC_RDWR & f->shared->flags))) { + if ((layout->u.chunk.size>f->shared->rdcc_nbytes && dcpl_cache->pline.nfilters==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.nfilters>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 { @@ -1878,7 +1875,7 @@ 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; @@ -1939,14 +1936,14 @@ 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: @@ -1982,7 +1979,7 @@ 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"); @@ -2024,20 +2021,20 @@ 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(); HGOTO_ERROR(H5E_BTREE,H5E_NOTFOUND,HADDR_UNDEF,"Can't locate chunk info"); @@ -2195,8 +2192,8 @@ 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); @@ -2262,9 +2259,9 @@ 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) @@ -2329,12 +2326,12 @@ 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 */ @@ -2349,11 +2346,11 @@ 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 */ @@ -2382,8 +2379,8 @@ 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 @@ -2530,8 +2527,8 @@ 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 */ @@ -2547,10 +2544,10 @@ 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; @@ -2561,7 +2558,7 @@ 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); @@ -2580,13 +2577,13 @@ 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: @@ -2628,11 +2625,11 @@ 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]); } @@ -2644,7 +2641,7 @@ 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 */ @@ -2741,6 +2738,7 @@ 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 */ @@ -2757,8 +2755,8 @@ 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 */ @@ -2781,10 +2779,12 @@ 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"); /* @@ -2792,18 +2792,18 @@ 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 */ @@ -2812,8 +2812,8 @@ 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; @@ -2830,15 +2830,15 @@ 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 @@ -2861,7 +2861,7 @@ 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 @@ -2908,14 +2908,14 @@ 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"); @@ -2926,7 +2926,7 @@ 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 */ @@ -2962,7 +2962,7 @@ 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); @@ -3066,7 +3066,7 @@ 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 a51e554..6fd583c 100644 --- a/src/H5Fseq.c +++ b/src/H5Fseq.c @@ -231,7 +231,7 @@ 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) @@ -340,7 +340,7 @@ 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 f5bd52b..2ae0278 100644 --- a/src/H5Oattr.c +++ b/src/H5Oattr.c @@ -16,6 +16,10 @@ #define H5O_PACKAGE /*suppress error about including H5Opkg */ #define H5S_PACKAGE /*suppress error about including H5Spkg */ +/* Pablo information */ +/* (Put before include files to avoid problems with inline functions) */ +#define PABLO_MASK H5O_attr_mask + #include "H5private.h" /* Generic Functions */ #include "H5Apkg.h" /* Attributes */ #include "H5Eprivate.h" /* Error handling */ @@ -25,8 +29,6 @@ #include "H5Opkg.h" /* Object headers */ #include "H5Spkg.h" /* Dataspaces */ -#define PABLO_MASK H5O_attr_mask - /* PRIVATE PROTOTYPES */ static herr_t H5O_attr_encode (H5F_t *f, uint8_t *p, const void *mesg); static void *H5O_attr_decode (H5F_t *f, hid_t dxpl_id, const uint8_t *p, H5O_shared_t *sh); @@ -201,13 +203,14 @@ H5O_attr_decode(H5F_t *f, hid_t dxpl_id, const uint8_t *p, H5O_shared_t UNUSED * /* Default to entire dataspace being selected */ if(H5S_select_all(attr->ds,0)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTSET, NULL, "unable to set all selection"); + if(version < H5O_ATTR_VERSION_NEW) p += H5O_ALIGN(attr->ds_size); else 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 (NULL==(attr->data = H5MM_malloc(attr->data_size))) @@ -262,7 +265,7 @@ H5O_attr_encode(H5F_t *f, uint8_t *p, const void *mesg) size_t name_len; /* Attribute name length */ unsigned version; /* Attribute version */ hbool_t type_shared; /* Flag to indicate that a shared datatype is used for this attribute */ - herr_t ret_value=SUCCEED; /* Return value */ + herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5O_attr_encode, FAIL); diff --git a/src/H5Olayout.c b/src/H5Olayout.c index 5dca442..15013ee 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 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 @@ -98,7 +100,6 @@ 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 +115,108 @@ 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) { + mesg->unused.ndims=ndims; + + for (u = 0; u < ndims; u++) + UINT32DECODE(p, mesg->unused.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; @@ -197,45 +262,87 @@ 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(mesg->version>0); 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 */ - *p++ = mesg->type; - - /* reserved bytes should be zero */ - for (u=0; u<5; u++) - *p++ = 0; - - /* data or B-tree address */ - if(mesg->type!=H5D_COMPACT) - H5F_addr_encode(f, &p, mesg->addr); - - /* dimension size */ - for (u = 0; u < mesg->ndims; u++) - UINT32ENCODE(p, mesg->dim[u]); - - if(mesg->type==H5D_COMPACT) { - UINT32ENCODE(p, mesg->size); - if(mesg->size>0 && mesg->buf) { - HDmemcpy(p, mesg->buf, mesg->size); - p += mesg->size; + /* Version */ + *p++ = mesg->version; + + /* Check for which information to write */ + if(mesg->version<3) { + /* number of dimensions */ + assert(mesg->unused.ndims > 0 && mesg->unused.ndims <= H5O_LAYOUT_NDIMS); + *p++ = mesg->unused.ndims; + + /* layout class */ + *p++ = mesg->type; + + /* reserved bytes should be zero */ + for (u=0; u<5; u++) + *p++ = 0; + + /* data or B-tree address */ + if(mesg->type==H5D_CONTIGUOUS) + H5F_addr_encode(f, &p, mesg->u.contig.addr); + else if(mesg->type==H5D_CHUNKED) + H5F_addr_encode(f, &p, mesg->u.chunk.addr); + + /* dimension size */ + if(mesg->type!=H5D_CHUNKED) + for (u = 0; u < mesg->unused.ndims; u++) + UINT32ENCODE(p, mesg->unused.dim[u]) + else + for (u = 0; u < mesg->u.chunk.ndims; u++) + UINT32ENCODE(p, mesg->u.chunk.dim[u]); + + if(mesg->type==H5D_COMPACT) { + UINT32ENCODE(p, mesg->u.compact.size); + 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 */ + else { + /* Layout class */ + *p++ = mesg->type; + + /* 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; + + case H5D_CHUNKED: + /* Number of dimensions */ + assert(mesg->u.chunk.ndims > 0 && mesg->u.chunk.ndims <= H5O_LAYOUT_NDIMS); + *p++ = mesg->u.chunk.ndims; + + /* 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 */ + } /* end else */ done: FUNC_LEAVE_NOAPI(ret_value); @@ -279,11 +386,11 @@ 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 */ @@ -315,7 +422,8 @@ done: size_t H5O_layout_meta_size(H5F_t *f, const void *_mesg) { - const H5O_layout_t *mesg = (const H5O_layout_t *) _mesg; + /* Casting away const OK - QAK */ + H5O_layout_t *mesg = (H5O_layout_t *) _mesg; size_t ret_value; FUNC_ENTER_NOAPI(H5O_layout_meta_size, 0); @@ -323,18 +431,80 @@ 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 */ + /* Check version information for new datasets */ + if(mesg->version==0) { + unsigned u; + + /* Check for dimension that would be truncated */ + assert(mesg->unused.ndims > 0 && mesg->unused.ndims <= H5O_LAYOUT_NDIMS); + for (u = 0; u < mesg->unused.ndims; u++) + if(mesg->unused.dim[u]!=(0xffffffff&mesg->unused.dim[u])) { + /* Make certain the message is encoded with the new version */ + mesg->version=3; + break; + } /* end if */ + + /* If the message doesn't _have_ to be encoded with the new version */ + if(mesg->version==0) { + /* Version: 1 when space allocated; 2 when space allocation is delayed */ + if(mesg->type==H5D_CONTIGUOUS) { + if(mesg->u.contig.addr==HADDR_UNDEF) + mesg->version = H5O_LAYOUT_VERSION_2; + else + mesg->version = H5O_LAYOUT_VERSION_1; + } else if(mesg->type==H5D_COMPACT) { + mesg->version = H5O_LAYOUT_VERSION_2; + } else + mesg->version = H5O_LAYOUT_VERSION_1; + } /* end if */ + } /* end if */ + assert(mesg->version>0); - 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 */ + if(mesg->version<H5O_LAYOUT_VERSION_3) { + ret_value = 1 + /* Version number */ + 1 + /* layout class type */ + 1 + /* dimensionality */ + 5 + /* reserved bytes */ + mesg->unused.ndims * 4; /* size of each dimension */ + + 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 */ + } /* end if */ + else { + ret_value = 1 + /* Version number */ + 1; /* layout class type */ + + 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 */ + } /* end else */ done: FUNC_LEAVE_NOAPI(ret_value); @@ -370,11 +540,10 @@ 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); } @@ -406,10 +575,11 @@ 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; + mesg->version=0; } /* end if */ done: @@ -443,7 +613,7 @@ 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 +706,30 @@ 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 6dd8a79..574c516 100644 --- a/src/H5Oprivate.h +++ b/src/H5Oprivate.h @@ -48,17 +48,20 @@ /* Flags which are part of a message */ #define H5O_FLAG_CONSTANT 0x01u #define H5O_FLAG_SHARED 0x02u -#define H5O_FLAG_BITS 0x03u +#define H5O_FLAG_BITS (H5O_FLAG_CONSTANT|H5O_FLAG_SHARED) /* Header message IDs */ #define H5O_NULL_ID 0x0000 /* Null Message. */ #define H5O_SDSPACE_ID 0x0001 /* Simple Dataspace Message. */ +/* Complex dataspace is/was planned for message 0x0002 */ #define H5O_DTYPE_ID 0x0003 /* Datatype Message. */ #define H5O_FILL_ID 0x0004 /* Fill Value Message. (Old) */ #define H5O_FILL_NEW_ID 0x0005 /* Fill Value Message. (New) */ +/* Compact data storage is/was planned for message 0x0006 */ #define H5O_EFL_ID 0x0007 /* External File List Message */ #define H5O_LAYOUT_ID 0x0008 /* Data Storage Layout Message. */ #define H5O_BOGUS_ID 0x0009 /* "Bogus" Message. */ +/* message 0x000a appears unused... */ #define H5O_PLINE_ID 0x000b /* Filter pipeline message. */ #define H5O_ATTR_ID 0x000c /* Attribute Message. */ #define H5O_NAME_ID 0x000d /* Object name message. */ @@ -68,7 +71,6 @@ #define H5O_STAB_ID 0x0011 /* Symbol table message. */ #define H5O_MTIME_NEW_ID 0x0012 /* Modification time message. (New) */ - /* * Fill Value Message. (Old) * (Data structure in memory) @@ -102,7 +104,7 @@ typedef struct H5O_fill_new_t { #define H5O_EFL_UNLIMITED H5F_UNLIMITED /*max possible file size */ typedef struct H5O_efl_entry_t { - size_t name_offset; /*offset of name within heap */ + size_t name_offset; /*offset of name within heap */ char *name; /*malloc'd name */ off_t offset; /*offset of data within file */ hsize_t size; /*size allocated within file */ @@ -121,15 +123,37 @@ 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 */ + /* Structure for "unused" dimension information */ + struct { + unsigned ndims; /*num dimensions in stored data */ + hsize_t dim[H5O_LAYOUT_NDIMS]; /*size of data or chunk in bytes */ + } unused; + 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 1906fb9..cafd036 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; @@ -1591,7 +1597,6 @@ done: FUNC_LEAVE_API(ret_value); } - /*------------------------------------------------------------------------- * Function: H5Premove_filter * @@ -751,6 +751,10 @@ 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 * @@ -804,7 +808,7 @@ 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 bea5982..0158d14 100644 --- a/src/H5Smpio.c +++ b/src/H5Smpio.c @@ -107,7 +107,6 @@ 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); @@ -116,7 +115,7 @@ 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)) @@ -413,8 +413,8 @@ 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 */ @@ -1192,7 +1192,7 @@ 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 */ @@ -1208,8 +1208,10 @@ H5V_chunk_index(unsigned ndims, const hssize_t *coord, const hsize_t *chunk, assert(chunk_idx); /* Compute the scaled coordinates for actual coordinates */ - for(u=0; u<ndims; u++) - scaled_coord[u]=coord[u]/chunk[u]; + for(u=0; u<ndims; u++) { + H5_CHECK_OVERFLOW(chunk[u],size_t,hssize_t); + scaled_coord[u]=coord[u]/(hssize_t)chunk[u]; + } /* end for */ /* Compute the chunk index */ *chunk_idx=H5V_array_offset_pre(ndims,down_nchunks,scaled_coord); diff --git a/src/H5Vprivate.h b/src/H5Vprivate.h index e56ddf0..71d9489 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); @@ -85,14 +85,14 @@ H5_DLL herr_t H5V_array_fill(void *_dst, const void *src, size_t size, size_t count); H5_DLL herr_t H5V_array_down(unsigned n, const hsize_t *total_size, hsize_t *down); -H5_DLL hsize_t H5V_array_offset_pre(unsigned n, +H5_DLL hsize_t H5V_array_offset_pre(unsigned n, const hsize_t *acc, const hssize_t *offset); H5_DLL hsize_t H5V_array_offset(unsigned n, const hsize_t *total_size, const hssize_t *offset); 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, @@ -14,6 +14,10 @@ #define H5Z_PACKAGE /*suppress error about including H5Zpkg */ +/* Pablo mask */ +/* (Put before include files to avoid problems with inline functions) */ +#define PABLO_MASK H5Z_mask + #include "H5private.h" /* Generic Functions */ #include "H5Dprivate.h" /* Dataset functions */ #include "H5Eprivate.h" /* Error handling */ @@ -24,9 +28,6 @@ #include "H5Sprivate.h" /* Dataspace functions */ #include "H5Zpkg.h" /* Data filters */ -/* Pablo mask */ -#define PABLO_MASK H5Z_mask - /* Interface initialization */ #define INTERFACE_INIT H5Z_init_interface static int interface_initialize_g = 0; @@ -530,7 +531,8 @@ 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.nfilters > 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 */ @@ -542,8 +544,10 @@ 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))) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create simple dataspace"); + 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 */ if ((space_id=H5I_register (H5I_DATASPACE, space))<0) { diff --git a/src/Makefile.in b/src/Makefile.in index a448175..9a1b7d3 100644 --- a/src/Makefile.in +++ b/src/Makefile.in @@ -30,8 +30,8 @@ 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 H5Fistore.c H5Fseq.c H5FD.c H5FDcore.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 H5Fistore.c H5Fseq.c H5FD.c H5FDcore.c \ H5FDfamily.c H5FDfphdf5.c H5FDgass.c H5FDlog.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 \ diff --git a/test/dsets.c b/test/dsets.c index 176f64e..71379cb 100644 --- a/test/dsets.c +++ b/test/dsets.c @@ -1976,7 +1976,7 @@ test_missing_filter(hid_t file) /* Query the dataset's size on disk */ if((dset_size=H5Dget_storage_size(dsid))==0) { H5_FAILED(); - printf(" Line %d: Error querying dataset size\n",__LINE__); + printf(" Line %d: Error querying dataset size, dset_size=%lu\n",__LINE__,(unsigned long)dset_size); goto error; } /* end if */ diff --git a/test/tmisc.c b/test/tmisc.c index 05a5ccd..b60a0a7 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 @@ -3203,6 +3220,176 @@ 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 */ + int 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,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_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. ** ****************************************************************/ @@ -3231,6 +3418,7 @@ 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() */ @@ -3274,4 +3462,5 @@ cleanup_misc(void) HDremove(MISC17_FILE); HDremove(MISC18_FILE); HDremove(MISC19_FILE); + HDremove(MISC20_FILE); } |