diff --git a/doc/html/FF-IH_FileGroup.gif b/doc/html/FF-IH_FileGroup.gif new file mode 100644 index 0000000000..b0d76f5071 Binary files /dev/null and b/doc/html/FF-IH_FileGroup.gif differ diff --git a/doc/html/FF-IH_FileObject.gif b/doc/html/FF-IH_FileObject.gif new file mode 100644 index 0000000000..8eba623b1d Binary files /dev/null and b/doc/html/FF-IH_FileObject.gif differ diff --git a/doc/html/H5.format.html b/doc/html/H5.format.html index afcd4442b2..8c0d8b208a 100644 --- a/doc/html/H5.format.html +++ b/doc/html/H5.format.html @@ -1,144 +1,169 @@ - HDF5 Disk-Format Specification + HDF5 File Format Specification -

HDF5: Disk Format Implementation

+
+
+ + + + +
+Other HDF5 documents and links 
+Introduction to HDF5 
+		  +HDF5 User Guide 
+HDF5 Reference Manual 
+
+
+
+ +

HDF5 File Format Specification

+ +
+ + + +
    -
  1. - Disk Format Level 0 - File Signature and Boot Block -
  2. - Disk Format Level 1 - File Infrastructure +
  3. Introduction +
  4. Disk Format Level 0 - File Signature and Super Block +
  5. Disk Format Level 1 - File Infrastructure +
      -
    1. - Disk Format Level 1A - B-link Trees -
    2. - Disk Format Level 1B - Symbol Table -
    3. - Disk Format Level 1C - Symbol Table Entry -
    4. - Disk Format Level 1D - Local Heaps -
    5. - Disk Format Level 1E - Global Heap -
    6. - Disk Format Level 1F - Free-Space Index +
    7. Disk Format Level 1A - B-link Trees and B-tree Nodes +
    8. Disk Format Level 1B - Group +
    9. Disk Format Level 1C - Group Entry +
    10. Disk Format Level 1D - Local Heaps +
    11. Disk Format Level 1E - Global Heap +
    12. Disk Format Level 1F - Free-space Index
    -
  6. - Disk Format Level 2 - Data Objects + +
  7. Disk Format Level 2 - Data Objects +
      -
    1. - Disk Format Level 2a - Data Object Headers +
    2. Disk Format Level 2a - Data Object Headers
        -
      1. - Name: NIL -
      2. - Name: Simple Data Space -
      3. - Name: Data-Space -
      4. - Name: Data-Type -
      5. - Name: Data Storage - Fill Value -
      6. - Name: Reserved - not assigned yet -
      7. - Name: Data Storage - Compact -
      8. - Name: Data Storage - External Data Files -
      9. - Name: Data Storage - Layout -
      10. - Name: Reserved - not assigned yet -
      11. - Name: Reserved - not assigned yet -
      12. - Name: Data Storage - Filter Pipeline -
      13. - Name: Attribute -
      14. - Name: Object Name -
      15. - Name: Object Modification Date & Time -
      16. - Name: Shared Object Message -
      17. - Name: Object Header Continuation -
      18. - Name: Symbol Table Message +
      19. Name: NIL +
      20. Name: Simple Dataspace + +
      21. Name: Datatype +
      22. Name: Data Storage - Fill Value +
      23. Name: Reserved - not assigned yet
      -
    3. - Disk Format: Level 2b - Shared Data Object Headers -
    4. - Disk Format: Level 2c - Data Object Data Storage -
    +
+ + 		   +
    + +
  1. Disk Format Level 2 - Data Objects + (Continued) +
      +
    1. Disk Format Level 2a - Data Object Headers(Continued) +
        +
      1. Name: Data Storage - Compact +
      2. Name: Data Storage - External Data Files +
      3. Name: Data Storage - Layout +
      4. Name: Reserved - not assigned yet +
      5. Name: Reserved - not assigned yet +
      6. Name: Data Storage - Filter Pipeline +
      7. Name: Attribute +
      8. Name: Object Name +
      9. Name: Object Modification Date and Time +
      10. Name: Shared Object Message +
      11. Name: Object Header Continuation +
      12. Name: Group Message +
      +
    2. Disk Format: Level 2b - Shared Data Object Headers +
    3. Disk Format: Level 2c - Data Object Data Storage +
    +     +
+
+
+ +

-

Disk Format Implementation

+

Introduction

-

The format of a HDF5 file on disk encompasses several - key ideas of the current HDF4 & AIO file formats as well as - addressing some short-comings therein. The new format is + + + + + + +
  +
+ HDF5 Groups + 		 
  + Figure 1: Relationships among the HDF5 root group, other groups, and objects +
+ 		 
  + HDF5 Objects +  
  + Figure 2: HDF5 objects -- datasets, datatypes, or dataspaces +
+ 		 
+ + +

The format of an HDF5 file on disk encompasses several + key ideas of the HDF4 and AIO file formats as well as + addressing some shortcomings therein. The new format is more self-describing than the HDF4 format and is more uniformly applied to data objects in the file. -

An HDF5 file can be thought of as a directed graph. - The nodes of this graph are the higher-level HDF5 objects, - including groups, datasets, datatypes, and dataspaces. - This document describes the lower-level data objects used by - the HDF5 library to represent those higher-level objects and - their properties. +

An HDF5 file appears to the user as a directed graph. + The nodes of this graph are the higher-level HDF5 objects + that are exposed by the HDF5 APIs: -

At the lowest level, an HDF5 file is made up of the following - objects:

+ +

At the lowest level, as information is actually written to the disk, + an HDF5 file is made up of the following objects: +

- As indicated above, the HDF5 library uses and interprets these - low-level objects to describe the high-level HDF5 objects that - are revealed to the user, and to higher-level applications, - through the HDF5 APIs. + + The HDF5 library uses these lower-level objects to represent the + higher-level objects that are then presented to the user or + to applications through the APIs. + For instance, a group is an object header that contains a message that + points to a local heap and to a B-tree which points to symbol nodes. + A dataset is an object header that contains messages that describe + datatype, space, layout, filters, external files, fill value, etc + with the layout message pointing to either a raw data chunk or to a + B-tree that points to raw data chunks. + + +

This Document

+ +

This document describes the lower-level data objects; + the higher-level objects and their properties are described + in the HDF5 User's Guide. + + - - End of File Address - This is the relative file address of the first byte past - the end of all HDF5 data. It is used to determine if a - file has been accidently truncated and as an address where - file memory allocation can occur if the free list is not - used. - + + End of File Address + This is the relative file address of the first byte past + the end of all HDF5 data. It is used to determine whether a + file has been accidently truncated and as an address where + file data allocation can occur if the free list is not + used. + - - Driver Information Block Address - This is the relative file address of the file driver - information block which contains driver-specific - information needed to reopen the file. If there is no - driver information block then this entry should be the - undefined address (all bits set). - + + Driver Information Block Address + This is the relative file address of the file driver + information block which contains driver-specific + information needed to reopen the file. If there is no + driver information block then this entry should be the + undefined address (all bits set). + - - Root Group Symbol Table Entry - This symbol-table entry (described later in this - document) refers to the entry point into the group - graph. If the file contains a single object, then that - object can be the root object and no groups are used. - - - + + Root Group Address + This is the address of the root group (described later + in this document), which serves as the entry point into + the group graph. + + + -

The file driver information block is an optional region of the + +

The file driver information block is an optional region of the file which contains information needed by the file driver in - order to reopen a file. The format of the driver information + order to reopen a file. The format of the file driver information block is: - +

- - - - - - - + + + + + + + - + @@ -540,12 +568,12 @@ each high-level object.

- Driver Information Block -
bytebytebytebyte
 + Driver Information Block +
bytebytebytebyte
Version Reserved (zero)
- - - - + + + + - + @@ -563,14 +591,15 @@ each high-level object. termination which identifies the driver and version number of the Driver Information block. The predefined drivers supplied with the HDF5 library are identified by the - letters "NCSA" followed by the first four characters of + letters NCSA followed by the first four characters of the driver name. If the Driver Information block is not the original version then the last letter(s) of the identification will be replaced by a version number in - ASCII. For example, the various versions of the "family" - driver will be identified by "NCSAfami", "NCSAfam0", - NCSAfam1", etc. Identification for user-defined drivers is - arbitrary but should be unique. + ASCII. + For example, the various versions of the family driver + will be identified by NCSAfami, NCSAfam0, + NCSAfam1, etc. Identification for user-defined drivers + is arbitrary but should be unique. @@ -584,826 +613,951 @@ each high-level object. -

Disk Format: Level 1A - B-link Trees

- -

B-link trees allow flexible storage for objects which tend to grow - in ways that cause the object to be stored discontiguously. B-trees - are described in various algorithms books including "Introduction to - Algorithms" by Thomas H. Cormen, Charles E. Leiserson, and Ronald - L. Rivest. The B-link tree, in which the sibling nodes at a - particular level in the tree are stored in a doubly-linked list, - is described in the "Efficient Locking for Concurrent Operations - on B-trees" paper by Phillip Lehman and S. Bing Yao as published - in the ACM Transactions on Database Systems, Vol. 6, - No. 4, December 1981. - -

The B-link trees implemented by the file format contain one more - key than the number of children. In other words, each child - pointer out of a B-tree node has a left key and a right key. - The pointers out of internal nodes point to sub-trees while - the pointers out of leaf nodes point to other file data types. - Notwithstanding that difference, internal nodes and leaf nodes - are identical. - -

-

-
Field NameDescription
Field NameDescription
Version The version number of the driver information block. The file format documented here is version zero.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- B-tree Nodes -
bytebytebytebyte
Node Signature
Node TypeNode LevelEntries Used
Address of Left Sibling
Address of Right Sibling
Key 0 (variable size)
Address of Child 0
Key 1 (variable size)
Address of Child 1
...
Key 2K (variable size)
Address of Child 2K
Key 2K+1 (variable size)
-
- -

-

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Field NameDescription
Node SignatureThe value ASCII 'TREE' is used to indicate the - beginning of a B-link tree node. This gives file - consistency checking utilities a better chance of - reconstructing a damaged file.
Node TypeEach B-link tree points to a particular type of data. - This field indicates the type of data as well as - implying the maximum degree K of the tree and - the size of each Key field. -
-
-
0 -
This tree points to symbol table nodes. -
1 -
This tree points to a (partial) linear address space. -
-
Node LevelThe node level indicates the level at which this node - appears in the tree (leaf nodes are at level zero). Not - only does the level indicate whether child pointers - point to sub-trees or to data, but it can also be used - to help file consistency checking utilities reconstruct - damanged trees.
Entries UsedThis determines the number of children to which this - node points. All nodes of a particular type of tree - have the same maximum degree, but most nodes will point - to less than that number of children. The valid child - pointers and keys appear at the beginning of the node - and the unused pointers and keys appear at the end of - the node. The unused pointers and keys have undefined - values.
Address of Left SiblingThis is the file address of the left sibling of the - current node relative to the boot block. If the current - node is the left-most node at this level then this field - is the undefined address (all bits set).
Address of Right SiblingThis is the file address of the right sibling of the - current node relative to the boot block. If the current - node is the right-most node at this level then this - field is the undefined address (all bits set).
Keys and Child PointersEach tree has 2K+1 keys with 2K - child pointers interleaved between the keys. The number - of keys and child pointers actually containing valid - values is determined by the `Entries Used' field. If - that field is N then the B-link tree contains - N child pointers and N+1 keys.
KeyThe format and size of the key values is determined by - the type of data to which this tree points. The keys are - ordered and are boundaries for the contents of the child - pointer. That is, the key values represented by child - N fall between Key N and Key - N+1. Whether the interval is open or closed on - each end is determined by the type of data to which the - tree points.
Address of ChildrenThe tree node contains file addresses of subtrees or - data depending on the node level (0 implies data - addresses).
-
- -

Disk Format: Level 1B - Symbol Table

- -

A symbol table is a group internal to the file that allows - arbitrary nesting of objects (including other symbol - tables). A symbol table maps a set of names to a set of file - address relative to the file boot block. Certain meta data - for an object to which the symbol table points can be cached - in the symbol table in addition to (or in place of?) the - object header. - -

An HDF5 object name space can be stored hierarchically by - partitioning the name into components and storing each - component in a symbol table. The symbol table entry for a - non-ultimate component points to the symbol table containing - the next component. The symbol table entry for the last - component points to the object being named. - -

A symbol table is a collection of symbol table nodes pointed - to by a B-link tree. Each symbol table node contains entries - for one or more symbols. If an attempt is made to add a - symbol to an already full symbol table node containing - 2K entries, then the node is split and one node - contains K symbols and the other contains - K+1 symbols. - -

-

- - - - - - - - - - - - - - - - - - - -
- Symbol Table Node -
bytebytebytebyte
Node Signature
Version NumberReserved for Future UseNumber of Symbols


Symbol Table Entries


-
- -

-

- - - - - - - - - - - - - - - - - - - - - - - - - -
Field NameDescription
Node SignatureThe value ASCII 'SNOD' is used to indicate the - beginning of a symbol table node. This gives file - consistency checking utilities a better chance of - reconstructing a damaged file.
Version NumberThe version number for the symbol table node. This - document describes version 1.
Number of SymbolsAlthough all symbol table nodes have the same length, - most contain fewer than the maximum possible number of - symbol entries. This field indicates how many entries - contain valid data. The valid entries are packed at the - beginning of the symbol table node while the remaining - entries contain undefined values.
Symbol Table EntriesEach symbol has an entry in the symbol table node. - The format of the entry is described below.
-
- -

- Disk Format: Level 1C - Symbol-Table Entry

- -

Each symbol table entry in a symbol table node is designed to allow - for very fast browsing of commonly stored scientific objects. - Toward that design goal, the format of the symbol-table entries - includes space for caching certain constant meta data from the - object header. - -

-

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- Symbol Table Entry -
bytebytebytebyte
Name Offset (<size> bytes)
Object Header Address
Symbol-Type
Reserved


Scratch-pad Space (16 bytes)


-
- -

-

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Field NameDescription
Name OffsetThis is the byte offset into the symbol table local - heap for the name of the symbol. The name is null - terminated.
Object Header AddressEvery object has an object header which serves as a - permanent home for the object's meta data. In addition - to appearing in the object header, the meta data can be - cached in the scratch-pad space.
Symbol-TypeThe symbol type is determined from the object header. - It also determines the format for the scratch-pad space. - The value zero indicates that no object header meta data - is cached in the symbol table entry. -
-
-
0 -
No data is cached by the symbol table entry. This - is guaranteed to be the case when an object header - has a link count greater than one. - -
1 -
Symbol table meta data is cached in the symbol - table entry. This implies that the symbol table - entry refers to another symbol table. - -
2 -
The entry is a symbolic link. The first four bytes - of the scratch pad space are the offset into the local - heap for the link value. The object header address - will be undefined. - -
N -
Other cache values can be defined later and - libraries that don't understand the new values will - still work properly. -
-
ReservedThese for bytes are present so that the scratch pad - space is aligned on an eight-byte boundary. They are - always set to zero.
Scratch-Pad SpaceThis space is used for different purposes, depending - on the value of the Symbol Type field. Any meta-data - about a dataset object represented in the scratch-pad - space is duplicated in the object header for that - dataset. Furthermore, no data is cached in the symbol - table entry scratch-pad space if the object header for - the symbol table entry has a link count greater than - one.
-
- -

The symbol table entry scratch-pad space is formatted - according to the value of the Symbol Type field. If the - Symbol Type field has the value zero then no information is - stored in the scratch pad space. - -

If the Symbol Type field is one, then the scratch pad space - contains cached meta data for another symbol table with the format: - -

-

- - - - - - - - - - - - - - -
- Symbol Table Scratch-Pad Format -
bytebytebytebyte
Address of B-tree
Address of Name Heap
-
- -

-

- - - - - - - - - - - - - - - -
Field NameDescription
Address of B-treeThis is the file address for the symbol table's - B-tree.
Address of Name HeapThis is the file address for the symbol table's local - heap that stores the symbol names.
-
- -

-

- - - - - - - - - - - - - -
- Symbolic Link Scratch-Pad Format -
bytebytebytebyte
Offset to Link Value
-
- -

-

- - - - - - - - - - -
Field NameDescription
Offset to Link ValueThe value of a symbolic link (that is, the name of the - thing to which it points) is stored in the local heap. - This field is the 4-byte offset into the local heap for - the start of the link value, which is null terminated.
-
- -

Disk Format: Level 1D - Local Heaps

- -

A heap is a collection of small heap objects. Objects can be - inserted and removed from the heap at any time and the address - of a heap doesn't change once the heap is created. Note: this - is the "local" version of the heap mostly intended for the - storage of names in a symbol table. The storage of small - objects in a global heap is described below. - -

-

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- Local Heaps -
bytebytebytebyte
Heap Signature
Reserved (zero)
Data Segment Size
Offset to Head of Free-list (<size> bytes)
Address of Data Segment
-
- -

-

- - - - - - - - - - - - - - - - - - - - - - - - - -
Field NameDescription
Heap SignatureThe valid ASCII 'HEAP' is used to indicate the - beginning of a heap. This gives file consistency - checking utilities a better chance of reconstructing a - damaged file.
Data Segment SizeThe total amount of disk memory allocated for the heap - data. This may be larger than the amount of space - required by the object stored in the heap. The extra - unused space holds a linked list of free blocks.
Offset to Head of Free-listThis is the offset within the heap data segment of the - first free block (or all 0xff bytes if there is no free - block). The free block contains <size> bytes that - are the offset of the next free chunk (or all 0xff bytes - if this is the last free chunk) followed by <size> - bytes that store the size of this free chunk.
Address of Data SegmentThe data segment originally starts immediately after - the heap header, but if the data segment must grow as a - result of adding more objects, then the data segment may - be relocated to another part of the file.
-
- -

Objects within the heap should be aligned on an 8-byte boundary. - -

Disk Format: Level 1E - Global Heap

- -

Each HDF5 file has a global heap which stores various types of - information which is typically shared between datasets. The - global heap was designed to satisfy these goals: - -

    -
  1. Repeated access to a heap object must be efficient without - resulting in repeated file I/O requests. Since global heap - objects will typically be shared among several datasets it's - probable that the object will be accessed repeatedly. -

    -
  2. Collections of related global heap objects should result in - fewer and larger I/O requests. For instance, a dataset of - void pointers will have a global heap object for each - pointer. Reading the entire set of void pointer objects - should result in a few large I/O requests instead of one small - I/O request for each object. -

    -
  3. It should be possible to remove objects from the global heap - and the resulting file hole should be eligible to be reclaimed - for other uses. -

    -
-

The implementation of the heap makes use of the memory - management already available at the file level and combines that - with a new top-level object called a collection to - achieve Goal B. The global heap is the set of all collections. - Each global heap object belongs to exactly one collection and - each collection contains one or more global heap objects. For - the purposes of disk I/O and caching, a collection is treated as - an atomic object. -

-

- - +

+ Disk Format: Level 1 - File Infrastructure

+

Disk Format: Level 1A - B-link Trees and B-tree Nodes

+

B-link trees allow flexible storage for objects which tend to grow + in ways that cause the object to be stored discontiguously. B-trees + are described in various algorithms books including "Introduction to + Algorithms" by Thomas H. Cormen, Charles E. Leiserson, and Ronald + L. Rivest. The B-link tree, in which the sibling nodes at a + particular level in the tree are stored in a doubly-linked list, + is described in the "Efficient Locking for Concurrent Operations + on B-trees" paper by Phillip Lehman and S. Bing Yao as published + in the ACM Transactions on Database Systems, Vol. 6, + No. 4, December 1981. + +

The B-link trees implemented by the file format contain one more + key than the number of children. In other words, each child + pointer out of a B-tree node has a left key and a right key. + The pointers out of internal nodes point to sub-trees while + the pointers out of leaf nodes point to symbol nodes and + raw data chunks. + Aside from that difference, internal nodes and leaf nodes + are identical. + +

+

+
- Global Heap Collection -
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ B-tree Nodes +
bytebytebytebyte
Node Signature
Node TypeNode LevelEntries Used
Address of Left Sibling
Address of Right Sibling
Key 0 (variable size)
Address of Child 0
Key 1 (variable size)
Address of Child 1
...
Key 2K (variable size)
Address of Child 2K
Key 2K+1 (variable size)
+
+ +

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Field NameDescription
Node SignatureThe ASCII character string TREE is + used to indicate the + beginning of a B-link tree node. This gives file + consistency checking utilities a better chance of + reconstructing a damaged file.
Node TypeEach B-link tree points to a particular type of data. + This field indicates the type of data as well as + implying the maximum degree K of the tree and + the size of each Key field. +
+
+
0 +
This tree points to group nodes. +
1 +
This tree points to a new data chunk. +
+
Node LevelThe node level indicates the level at which this node + appears in the tree (leaf nodes are at level zero). Not + only does the level indicate whether child pointers + point to sub-trees or to data, but it can also be used + to help file consistency checking utilities reconstruct + damanged trees.
Entries UsedThis determines the number of children to which this + node points. All nodes of a particular type of tree + have the same maximum degree, but most nodes will point + to less than that number of children. The valid child + pointers and keys appear at the beginning of the node + and the unused pointers and keys appear at the end of + the node. The unused pointers and keys have undefined + values.
Address of Left SiblingThis is the file address of the left sibling of the + current node relative to the super block. If the current + node is the left-most node at this level then this field + is the undefined address (all bits set).
Address of Right SiblingThis is the file address of the right sibling of the + current node relative to the super block. If the current + node is the right-most node at this level then this + field is the undefined address (all bits set).
Keys and Child PointersEach tree has 2K+1 keys with 2K + child pointers interleaved between the keys. The number + of keys and child pointers actually containing valid + values is determined by the Entries Used field. If + that field is N then the B-link tree contains + N child pointers and N+1 keys.
KeyThe format and size of the key values is determined by + the type of data to which this tree points. The keys are + ordered and are boundaries for the contents of the child + pointer; that is, the key values represented by child + N fall between Key N and Key + N+1. Whether the interval is open or closed on + each end is determined by the type of data to which the + tree points. +

+ The format of the key depends on the node type. + For nodes of node type 1, the key is formatted as follows: +

+ + + + + + + + + + + +
Bytes 1-4Size of chunk in bytes.
Bytes 4-8Filter mask, a 32-bit bitfield indicating which + filters have been applied to that chunk.
N fields of 8 bytes eachA 64-bit index indicating the offset of the + chunk within the dataset where N is the number + of dimensions of the dataset. For example, if + a chunk in a 3-dimensional dataset begins at the + position [5,5,5], there will be three + such 8-bit indices, each with the value of + 5.
+
+

+ For nodes of node type 0, the key is formatted as follows: +

+ + + + + +
A single field of Size of Lengths + bytesIndicates the byte offset into the local heap + for the first object name in the subtree which + that key describes.
+
+
Child PointersThe tree node contains file addresses of subtrees or + data depending on the node level. Nodes at Level 0 point + to data addresses, either data chunk or group nodes. + Nodes at non-zero levels point to other nodes of the + same B-tree.
+
+ +

+ Each B-tree node looks like this: + +

+ + + + + + + + + + + + + +
key[0]  child[0]  key[1]  child[1]  key[2]  ...  ...  key[N-1]  child[N-1]  key[N]
+
+ + where child[i] is a pointer to a sub-tree (at a level + above Level 0) or to data (at Level 0). + Each key[i] describes an item stored by the B-tree + (a chunk or an object of a group node). The range of values + represented by child[i] are indicated by key[i] + and key[i+1]. + + +

The following question must next be answered: + "Is the value described by key[i] contained in + child[i-1] or in child[i]?" + The answer depends on the type of tree. + In trees for groups (node type 0) the object described by + key[i] is the greatest object contained in + child[i-1] while in chunk trees (node type 1) the + chunk described by key[i] is the least chunk in + child[i]. + +

That means that key[0] for group trees is sometimes unused; + it points to offset zero in the heap, which is always the + empty string and compares as "less-than" any valid object name. + +

And key[N] for chunk trees is sometimes unused; + it contains a chunk offset which compares as "greater-than" + any other chunk offset and has a chunk byte size of zero + to indicate that it is not actually allocated. + + +

Disk Format: Level 1B - Group and Symbol Nodes

+ +

A group is an object internal to the file that allows + arbitrary nesting of objects (including other groups). + A group maps a set of names to a set of file + address relative to the base address. Certain meta data + for an object to which the group points can be duplicated + in the group symbol table in addition to the object header. + +

An HDF5 object name space can be stored hierarchically by + partitioning the name into components and storing each + component in a group. The group entry for a + non-ultimate component points to the group containing + the next component. The group entry for the last + component points to the object being named. + +

A group is a collection of group nodes pointed + to by a B-link tree. Each group node contains entries + for one or more symbols. If an attempt is made to add a + symbol to an already full group node containing + 2K entries, then the node is split and one node + contains K symbols and the other contains + K+1 symbols. + +

+

+ + + + + + + + + + + + + + + + + + + +
+ Group Node (A Leaf of a B-tree) +
bytebytebytebyte
Node Signature
Version NumberReserved for Future UseNumber of Symbols


Group Entries


+
+ +

+

+ + + + + + + + + + + + + + + + + + + + + + + + + +
Field NameDescription
Node SignatureThe ASCII character string SNOD is + used to indicate the + beginning of a group node. This gives file + consistency checking utilities a better chance of + reconstructing a damaged file.
Version NumberThe version number for the group node. This + document describes version 1.
Number of SymbolsAlthough all group nodes have the same length, + most contain fewer than the maximum possible number of + symbol entries. This field indicates how many entries + contain valid data. The valid entries are packed at the + beginning of the group node while the remaining + entries contain undefined values.
Group EntriesEach symbol has an entry in the group node. + The format of the entry is described below.
+
+ +

+ Disk Format: Level 1C - Group Entry

+ +

Each group entry in a group node is designed + to allow for very fast browsing of stored objects. + Toward that design goal, the group entries + include space for caching certain constant meta data from the + object header. + +

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ Group Entry +
bytebytebytebyte
Name Offset (<size> bytes)
Object Header Address
Cache Type
Reserved


Scratch-pad Space (16 bytes)


+
+ +

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Field NameDescription
Name OffsetThis is the byte offset into the group local + heap for the name of the object. The name is null + terminated.
Object Header AddressEvery object has an object header which serves as a + permanent location for the object's meta data. In addition + to appearing in the object header, some meta data can be + cached in the scratch-pad space.
Cache TypeThe cache type is determined from the object header. + It also determines the format for the scratch-pad space. +
+
+
0 +
No data is cached by the group entry. This + is guaranteed to be the case when an object header + has a link count greater than one. + +
1 +
Object header meta data is cached in the group + entry. This implies that the group + entry refers to another group. + +
2 +
The entry is a symbolic link. The first four bytes + of the scratch-pad space are the offset into the local + heap for the link value. The object header address + will be undefined. + +
N +
Other cache values can be defined later and + libraries that do not understand the new values will + still work properly. +
+
ReservedThese four bytes are present so that the scratch-pad + space is aligned on an eight-byte boundary. They are + always set to zero.
Scratch-pad SpaceThis space is used for different purposes, depending + on the value of the Cache Type field. Any meta-data + about a dataset object represented in the scratch-pad + space is duplicated in the object header for that + dataset. This meta data can include the datatype + and the size of the dataspace for a dataset whose datatype + is atomic and whose dataspace is fixed and less than + four dimensions. + Furthermore, no data is cached in the group + entry scratch-pad space if the object header for + the group entry has a link count greater than + one.
+
+ +

Format of the Scratch-pad Space

+ +

The group entry scratch-pad space is formatted + according to the value in the Cache Type field. + +

If the Cache Type field contains the value zero + (0) then no information is + stored in the scratch-pad space. + +

If the Cache Type field contains the value one + (1), then the scratch-pad space + contains cached meta data for another object header + in the following format: + +

+

+ + + + + + + + + + + + + + +
+ Object Header Scratch-pad Format +
bytebytebytebyte
Address of B-tree
Address of Name Heap
+
+ +

+

+ + + + + + + + + + + + + + + +
Field NameDescription
Address of B-treeThis is the file address for the root of the + group's B-tree.
Address of Name HeapThis is the file address for the group's local + heap, in which are stored the symbol names.
+
+ + +

If the Cache Type field contains the value two + (2), then the scratch-pad space + contains cached meta data for another symbolic link + in the following format: + +

+

+ + + + + + + + + + + + + +
+ Symbolic Link Scratch-pad Format +
bytebytebytebyte
Offset to Link Value
+
+ +

+

+ + + + + + + + + + +
Field NameDescription
Offset to Link ValueThe value of a symbolic link (that is, the name of the + thing to which it points) is stored in the local heap. + This field is the 4-byte offset into the local heap for + the start of the link value, which is null terminated.
+
+ +

Disk Format: Level 1D - Local Heaps

+ +

A heap is a collection of small heap objects. Objects can be + inserted and removed from the heap at any time. + The address of a heap does not change once the heap is created. + References to objects are stored in the group table; + the names of those objects are stored in the local heap. + +

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ Local Heaps +
bytebytebytebyte
Heap Signature
Reserved (zero)
Data Segment Size
Offset to Head of Free-list (<size> bytes)
Address of Data Segment
+
+ +

+

+ + + + + + + + + + + + + + + + + + + + + + + + + +
Field NameDescription
Heap SignatureThe ASCII character string HEAP + is used to indicate the + beginning of a heap. This gives file consistency + checking utilities a better chance of reconstructing a + damaged file.
Data Segment SizeThe total amount of disk memory allocated for the heap + data. This may be larger than the amount of space + required by the object stored in the heap. The extra + unused space holds a linked list of free blocks.
Offset to Head of Free-listThis is the offset within the heap data segment of the + first free block (or all 0xff bytes if there is no free + block). The free block contains <size> bytes that + are the offset of the next free chunk (or all 0xff bytes + if this is the last free chunk) followed by <size> + bytes that store the size of this free chunk.
Address of Data SegmentThe data segment originally starts immediately after + the heap header, but if the data segment must grow as a + result of adding more objects, then the data segment may + be relocated, in its entirety, to another part of the + file.
+
+ +

Objects within the heap should be aligned on an 8-byte boundary. + +

Disk Format: Level 1E - Global Heap

+ +

Each HDF5 file has a global heap which stores various types of + information which is typically shared between datasets. The + global heap was designed to satisfy these goals: + +

    +
  1. Repeated access to a heap object must be efficient without + resulting in repeated file I/O requests. Since global heap + objects will typically be shared among several datasets, it is + probable that the object will be accessed repeatedly. + +

    +
  2. Collections of related global heap objects should result in + fewer and larger I/O requests. For instance, a dataset of + void pointers will have a global heap object for each + pointer. Reading the entire set of void pointer objects + should result in a few large I/O requests instead of one small + I/O request for each object. + +

    +
  3. It should be possible to remove objects from the global heap + and the resulting file hole should be eligible to be reclaimed + for other uses. +

    +
+ +

The implementation of the heap makes use of the memory + management already available at the file level and combines that + with a new top-level object called a collection to + achieve Goal B. The global heap is the set of all collections. + Each global heap object belongs to exactly one collection and + each collection contains one or more global heap objects. For + the purposes of disk I/O and caching, a collection is treated as + an atomic object. + +

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ A Global Heap Collection +
bytebytebytebyte
Magic Number
VersionReserved
Collection Size

Global Heap Object 1 + (described below)


Global Heap Object 2


...


Global Heap Object N


Global Heap Object 0 (free space)

+
+ +

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Field NameDescription
Magic NumberThe magic number for global heap collections are the + four bytes G, C, O, + and L.
VersionEach collection has its own version number so that new + collections can be added to old files. This document + describes version zero of the collections. +
Collection Data SizeThis is the size in bytes of the entire collection + including this field. The default (and minimum) + collection size is 4096 bytes which is a typical file + system block size and which allows for 170 16-byte heap + objects plus their overhead.
Object 1 through NThe objects are stored in any order with no + intervening unused space.
Object 0Object 0 (zero), when present, represents the free space in + the collection. Free space always appears at the end of + the collection. If the free space is too small to store + the header for Object 0 (described below) then the + header is implied and the collection contains no free space. +
+
+ +

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ Global Heap Object +
bytebytebytebyte
Object IDReference Count
Reserved
Object Data Size

Object Data

+
+ +

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Field NameDescription
Object IDEach object has a unique identification number within a + collection. The identification numbers are chosen so that + new objects have the smallest value possible with the + exception that the identifier 0 always refers to the + object which represents all free space within the + collection.
Reference CountAll heap objects have a reference count field. An + object which is referenced from some other part of the + file will have a positive reference count. The reference + count for Object 0 is always zero.
ReservedZero padding to align next field on an 8-byte + boundary.
Object Size This is the size of the the fields + above plus the object data stored for the object. The + actual storage size is rounded up to a multiple of + eight.
Object DataThe object data is treated as a one-dimensional array + of bytes to be interpreted by the caller.
+
+ +

Disk Format: Level 1F - Free-space Heap

+ +

The Free-space Index is a collection of blocks of data, + dispersed throughout the file, which are currently not used by + any file objects. + +

The super block contains a pointer to root of the free-space description; + that pointer is currently (i.e., in HDF5 Release 1.2) required + to be the undefined address 0xfff...ff. + +

The free-sapce index is not otherwise publicly defined at this time. + + + -

Disk Format: Level 2 - Data Objects

+ +

+

+ + +

Disk Format: Level 2 - Data Objects

Data objects contain the real information in the file. These objects compose the scientific data and other information which @@ -1500,7 +1661,7 @@ each high-level object. Object Reference Count -
Total Object-Header Size

+
Total Object Header Size

Header Message Type #1 @@ -1539,10 +1700,10 @@ each high-level object. - Version # of the object header + Version number of the object header This value is used to determine the format of the information in the object header. When the format of the - information in the object header is changed, the version # + information in the object header is changed, the version number is incremented and can be used to determine how the information in the object header is formatted. @@ -1563,11 +1724,11 @@ each high-level object. Object Reference Count This value specifies the number of references to this object within the current file. References to the - data-object from external files are not tracked. + data object from external files are not tracked. - Total Object-Header Size + Total Object Header Size This value specifies the total number of bytes of header message data following this length field for the current message as well as any continuation data located elsewhere @@ -1581,7 +1742,7 @@ each high-level object. the type along with a small amount of other information. Bit 15 of the message type is set if the message is constant (constant messages cannot be changed since they - may be cached in symbol table entries throughout the + may be cached in group entries throughout the file). The header message types for the pre-defined header messages will be included in further discussion below. @@ -1602,11 +1763,11 @@ each high-level object.

0
If set, the message data is constant. This is used - for messages like the data type message of a dataset. + for messages like the datatype message of a dataset.
1
If set, the message is stored in the global heap and the Header Message Data field contains a Shared Object - message. and the Size of Header Message Data field + message and the Size of Header Message Data field contains the size of that Shared Object message.
2-7
Reserved @@ -1636,7 +1797,7 @@ each high-level object.

The following is a list of currently defined header messages:

-

Name: NIL

+

Name: NIL

Type: 0x0000
Length: varies
Status: Optional, may be repeated.
@@ -1645,31 +1806,38 @@ each high-level object. which is to be ignored when reading the header messages for a data object. [Probably one which has been deleted for some reason.]
Format of Data: Unspecified.
+ +
-

Name: Simple Data Space

+

Name: Simple Dataspace

Type: 0x0001
- Length: varies
- Status: One of the Simple Data Space or - Data-Space messages is required (but not both) and may - not be repeated.
+ Length: Varies according to the number of dimensions, + as described in the following table
+ Status: The Simple Dataspace message is required + and may not be repeated. This message is currently used with + datasets and named dataspaces.
-

The Simple Dimensionality message describes the number +

The Simple Dataspace message describes the number of dimensions and size of each dimension that the data object has. This message is only used for datasets which have a - simple, rectilinear grid layout, datasets requiring a more - complex layout (irregularly or unstructured grids, etc) must use - the Data-Space message for expressing the space the - dataset inhabits. + simple, rectilinear grid layout; datasets requiring a more + complex layout (irregularly structured or unstructured grids, etc.) + must use the Complex Dataspace message for expressing + the space the dataset inhabits. + (Note: The Complex Dataspace functionality is + not yet implemented (as of HDF5 Release 1.2). It is not described + in this document.)

@@ -1719,6 +1887,15 @@ each high-level object. + + + + +
- Simple Data Space Message + Simple Dataspace Message
Description
Version This value is used to determine the format of the + Simple Dataspace Message. When the format of the + information in the message is changed, the version number + is incremented and can be used to determine how the + information in the object header is formatted.
Dimensionality This value is the number of dimensions that the data @@ -1766,6 +1943,7 @@ each high-level object.
+ + +
-

Name: Data Type

+

Name: Datatype

Type: 0x0003
Length: variable
- Status: One required per dataset
+ Status: One required per dataset or named datatype
-

The data type message defines the data type for each data point - of a dataset. A data type can describe an atomic type like a +

The datatype message defines the datatype for each data point + of a dataset. A datatype can describe an atomic type like a fixed- or floating-point type or a compound type like a C - struct. A data type does not, however, describe how data points - are combined to produce a dataset. Data types are stored on disk - as a data type message, which is a list of data type classes and + struct. A datatype does not, however, describe how data points + are combined to produce a dataset. Datatypes are stored on disk + as a datatype message, which is a list of datatype classes and their associated properties.

@@ -2136,16 +2318,17 @@ each high-level object. on the Type Class, which is the low-order four bits of the Type Class and Version field (the high-order four byte are the version which should be set to the value one). The type class - is one of: 0 (fixed-point number), 1 (floating-point number), 2 - (date and time), 3 (text string), 4 (bit field), 5 (opaque), 6 - (compound). The Class Bit Field is zero and the size of the + is one of 0 (fixed-point number), 1 (floating-point number), + 2 (date and time), 3 (text string), 4 (bit field), 5 (opaque), + 6 (compound), 7 (reference), 8 (enumeration), or 9 (variable-length). + The Class Bit Field is zero and the size of the Properties field is zero except for the cases noted here.

- Data Type Message + Datatype Message
@@ -2184,7 +2367,7 @@ each high-level object.
- Bit Field for Fixed-Point Numbers (Class 0) + Bit Field for Fixed-point Numbers (Class 0)
@@ -2205,7 +2388,7 @@ each high-level object.
- Properties for Fixed-Point Numbers (Class 0) + Properties for Fixed-point Numbers (Class 0)
@@ -2261,7 +2444,7 @@ each high-level object.
- Bit Field for Floating-Point Numbers (Class 1) + Bit Field for Floating-point Numbers (Class 1)
@@ -2459,7 +2642,7 @@ each high-level object. @@ -2471,10 +2654,10 @@ each high-level object.
- Properties for Floating-Point Numbers (Class 1) + Properties for Floating-point Numbers (Class 1)
0-15 Number of Members. This field contains the number - of members defined for the compound data type. The member + of members defined for the compound datatype. The member definitions are listed in the Properties field of the data type message.
-

The Properties field of a compound data type is a list of the - member definitions of the compound data type. The member +

The Properties field of a compound datatype is a list of the + member definitions of the compound datatype. The member definitions appear one after another with no intervening bytes. - The member types are described with a recursive data type + The member types are described with a recursive datatype message.

@@ -2536,11 +2719,88 @@ each high-level object. -

Data type examples are here. +

+

+ + + + + + + + + + + + + + + + + +
+ Bit Field for Enumeration types (Class 8) +
BitsMeaning
0-15Number of Members. The number of name/value + pairs defined for the enumeration type.
16-23Reserved (zero).
+
+ +

+

+ + + + + + + + + + + + + + + + + + + + + + +
+ Properties for Enumeration types (Class 8) +
ByteByteByteByte

Parent Type


Names


Values

+
+ +
+ + + + + + + + + + + +
Parent Type:Each enumeration type is based on some parent type, + usually an integer. The information for that parent type is + described recursively by this field.
Names:The name for each name/value pair. Each name is + stored as a null terminated ASCII string in a multiple of + eight bytes. The names are in no particular order.
Values:The list of values in the same order as the names. + The values are packed (no inter-value padding) and the + size of each value is determined by the parent type.
+
+ +
-

Name: Data Storage - Fill Value

+

Name: Data Storage - Fill Value

Type: 0x0004
Length: varies
Status: Optional, may not be repeated.
@@ -2548,7 +2808,7 @@ each high-level object.

The fill value message stores a single data point value which is returned to the application when an uninitialized data point is read from the dataset. The fill value is interpretted with - the same data type as the dataset. If no fill value message is + the same datatype as the dataset. If no fill value message is present then a fill value of all zero is assumed.

@@ -2591,14 +2851,13 @@ each high-level object. Fill Value The fill value. The bytes of the fill value are - interpreted using the same data type as for the dataset. + interpreted using the same datatype as for the dataset.

-

Name: Reserved - Not Assigned - Yet

+

Name: Reserved - Not Assigned Yet

Type: 0x0005
Length: N/A
Status: N/A
@@ -2606,7 +2865,7 @@ each high-level object.
-

Name: Data Storage - Compact

+

Name: Data Storage - Compact

Type: 0x0006
Length: varies
@@ -2614,23 +2873,25 @@ each high-level object.

This message indicates that the data for the data object is stored within the current HDF file by including the actual - data within the header data for this message. The data is + data as the header data for this message. The data is stored internally in - the "normal" format, i.e. in one chunk, un-compressed, etc. + the normal format, i.e. in one chunk, uncompressed, etc. -

Note that one and only one of the "Data Storage" headers can be +

Note that one and only one of the Data Storage headers can be stored for each data object.

Format of Data: The message data is actually composed of dataset data, so the format will be determined by the dataset format. +

-

Name: Data Storage - - External Data Files

+

Name: Data Storage - + External Data Files

Type: 0x0007
Length: varies
Status: Optional, may not be repeated.
@@ -2686,10 +2947,17 @@ each high-level object. - Heap Address - This is the address of a local name heap which contains - the names for the external files. The name at offset zero - in the heap is always the empty string. + Version + This value is used to determine the format of the + External File List Message. When the format of the + information in the message is changed, the version number + is incremented and can be used to determine how the + information in the object header is formatted. + + + + Reserved + This field is reserved for future use. @@ -2706,8 +2974,10 @@ each high-level object. - Reserved - This field is reserved for future use. + Heap Address + This is the address of a local name heap which contains + the names for the external files. The name at offset zero + in the heap is always the empty string. @@ -2798,7 +3068,7 @@ each high-level object.
-

Name: Data Storage - Layout

+

Name: Data Storage - Layout

Type: 0x0008
Length: varies
@@ -2920,7 +3190,7 @@ each high-level object.
-

Name: Reserved - Not Assigned Yet

+

Name: Reserved - Not Assigned Yet

Type: 0x0009
Length: N/A
Status: N/A
@@ -2928,7 +3198,7 @@ each high-level object. Format of Data: N/A
-

Name: Reserved - Not Assigned Yet

+

Name: Reserved - Not Assigned Yet

Type: 0x000A
Length: N/A
Status: N/A
@@ -2936,7 +3206,7 @@ each high-level object. Format of Data: N/A
-

Name: Data Storage - Filter Pipeline

+

Name: Data Storage - Filter Pipeline

Type: 0x000B
Length: varies
Status: Optional, may not be repeated. @@ -3118,7 +3388,7 @@ each high-level object.
-

Name: Attribute

+

Name: Attribute

Type: 0x000C
Length: varies
Status: Optional, may be repeated.
@@ -3126,7 +3396,7 @@ each high-level object.

Purpose and Description: The Attribute message is used to list objects in the HDF file which are used as attributes, or "meta-data" about the current object. An - attribute is a small dataset; it has a name, a data type, a data + attribute is a small dataset; it has a name, a datatype, a data space, and raw data. Since attributes are stored in the object header they must be relatively small (<64kb) and can be associated with any type of object which has an object header @@ -3189,6 +3459,12 @@ each high-level object. version 1 of attribute messages. + + Reserved + This field is reserved for later use and is set to + zero. + + Name Size The length of the attribute name in bytes including the @@ -3199,24 +3475,18 @@ each high-level object. Type Size - The length of the data type description in the Type + The length of the datatype description in the Type field below. Note that the Type field may contain additional padding not represented by this field. Space Size - The length of the data space description in the Space + The length of the dataspace description in the Space field below. Note that the Space field may contain additional padding not represented by this field. - - Reserved - This field is reserved for later use and is set to - zero. - - Name The null-terminated attribute name. This field is @@ -3226,16 +3496,16 @@ each high-level object. Type - The data type description follows the same format as - described for the data type object header message. This + The datatype description follows the same format as + described for the datatype object header message. This field is padded with additional zero bytes to make it a multiple of eight bytes. Space - The data space description follows the same format as - described for the data space object header message. This + The dataspace description follows the same format as + described for the dataspace object header message. This field is padded with additional zero bytes to make it a multiple of eight bytes. @@ -3243,7 +3513,7 @@ each high-level object. Data The raw data for the attribute. The size is determined - from the data type and data space descriptions. This + from the datatype and dataspace descriptions. This field is not padded with additional zero bytes. @@ -3251,7 +3521,7 @@ each high-level object.

-

Name: Object Name

+

Name: Object Name

Type: 0x000D
Length: varies
@@ -3259,7 +3529,7 @@ each high-level object.

Purpose and Description: The object name or comment is designed to be a short description of an object. An object name - is a sequence of non-zero ('\0') ASCII characters with no other + is a sequence of non-zero (\0) ASCII characters with no other formatting included by the library.

@@ -3298,8 +3568,7 @@ each high-level object.

-

Name: Object Modification Date & - Time

+

Name: Object Modification Date & Time

Type: 0x000E
Length: fixed
@@ -3357,40 +3626,40 @@ each high-level object. Year The four-digit year as an ASCII string. For example, - "1998". All fields of this message should be interpreted + 1998. All fields of this message should be interpreted as coordinated universal time (UTC) Month The month number as a two digit ASCII string where - January is "01" and December is "12". + January is 01 and December is 12. Day of Month The day number within the month as a two digit ASCII - string. The first day of the month is "01". + string. The first day of the month is 01. Hour The hour of the day as a two digit ASCII string where - midnight is "00" and 11:00pm is "23". + midnight is 00 and 11:00pm is 23. Minute The minute of the hour as a two digit ASCII string where - the first minute of the hour is "00" and the last is - "59". + the first minute of the hour is 00 and + the last is 59. Second The second of the minute as a two digit ASCII string - where the first second of the minute is "00" and the last - is "59". + where the first second of the minute is 00 + and the last is 59. @@ -3401,7 +3670,7 @@ each high-level object.

-

Name: Shared Object Message

+

Name: Shared Object Message

Type: 0x000F
Length: 4 Bytes
Status: Optional, may be repeated. @@ -3490,7 +3759,7 @@ each high-level object. the actual message is in the global heap then the pointer is the file address of the global heap collection that holds the message, and a four-byte index into that - collection. Otherwise the pointer is a symbol table entry + collection. Otherwise the pointer is a group entry that points to some other object header. @@ -3498,7 +3767,7 @@ each high-level object.
-

Name: Object Header Continuation

+

Name: Object Header Continuation

Type: 0x0010
Length: fixed
Status: Optional, may be repeated.
@@ -3543,24 +3812,26 @@ the file.
+
-

Name: Symbol Table Message

+

Name: Group Message

Type: 0x0011
Length: fixed
-Status: Required for symbol tables, may not be repeated.
-Purpose and Description: Each symbol table has a B-tree and a +Status: Required for groups, may not be repeated.
+Purpose and Description: Each group has a B-tree and a name heap which are pointed to by this message.
Format of data: -

The symbol table message is formatted as follows: +

The group message is formatted as follows:

@@ -3570,7 +3841,7 @@ name heap which are pointed to by this message.
- + @@ -3579,7 +3850,7 @@ name heap which are pointed to by this message.

-
The elements of the Symbol Table Message are described below: +
The elements of the Group Message are described below:
B-tree Address (<offset> bytes) @@ -3587,13 +3858,13 @@ name heap which are pointed to by this message.
where the B-tree is located.
Heap Address (<offset> bytes)
This value is the offset in bytes from the beginning of the file -where the symbol table name heap is located. +where the group name heap is located.

Disk Format: Level 2b - Shared Data Object Headers

In order to share header messages between several dataset objects, object -header messages may be placed into the global small-data heap. Since these +header messages may be placed into the global heap. Since these messages require additional information beyond the basic object header message information, the format of the shared message is detailed below. @@ -3625,7 +3896,7 @@ information, the format of the shared message is detailed below.

Reference Count of Shared Header Message: (32-bit unsigned integer)
This value is used to keep a count of the number of dataset objects which refer to this message from their dataset headers. When this count reaches zero, -the shared message header may be removed from the global small-data heap. +the shared message header may be removed from the global heap.
Shared Object Header Message: (various lengths)
The data stored for the shared object header message is formatted in the same way as the private object header messages described in the object header @@ -3635,7 +3906,7 @@ description earlier in this document and begins with the header message Type.

Disk Format: Level 2c - Data Object Data Storage

-

The data information for an object is stored separately from the header +

The data for an object is stored separately from the header information in the file and may not actually be located in the HDF5 file itself if the header indicates that the data is stored externally. The information for each record in the object is stored according to the @@ -3648,8 +3919,9 @@ in a different machine format with the architecture-type information from the number-type header message. This means that each architecture will need to [potentially] byte-swap data values into the internal representation for that particular machine. -

Data with a "variable" sized number-type is stored in an data heap -internal to the HDF file [which should not be user-modifiable]. +

Data with a "variable" sized number-type is stored in a data heap +internal to the HDF5 file. Global heap identifiers are stored in the +data object storage.

Data whose elements are composed of pointer number-types are stored in several different ways depending on the particular pointer type involved. Simple pointers are just stored as the dataset offset of the object being pointed to with the @@ -3661,17 +3933,33 @@ format as header message), sub-set start and end information (i.e. a coordinate location for each), and field start and end names (i.e. a [pointer to the] string indicating the first field included and a [pointer to the] string name for the last field). -Browse pointers are stored as an heap-ID (for the name in the file-heap) -followed by a offset of the data object being referenced. -

Data of a compound data-type is stored as a contiguous stream of the items -in the structure, with each item formatted according to it's -data-type. + +

Data of a compound datatype is stored as a contiguous stream of the items +in the structure, with each item formatted according to its datatype.

+
+
-HDF5 Object Header Symbol Table Message Layout +HDF5 Object Header Group Message Layout
byte
B-Tree AddressB-tree Address
Heap Address
+ + + +
+Other HDF5 documents and links 
+Introduction to HDF5 
+		  +HDF5 User Guide 
+HDF5 Reference Manual 
+
+
+
+ + +
HDF Help Desk
-Last modified: Tue Aug 17 10:57:50 EDT 1999 +Last modified: 8 March 2000