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

HDF5 File Format Specification

  1. Introduction
  2. Disk Format Level 0 - File Signature and Super Block
  3. Disk Format Level 1 - File Infrastructure
    1. Disk Format Level 1A - B-link Trees and B-tree Nodes
    2. Disk Format Level 1B - Group
    3. Disk Format Level 1C - Group Entry
    4. Disk Format Level 1D - Local Heaps
    5. Disk Format Level 1E - Global Heap
    6. Disk Format Level 1F - Free-space Index
  4. Disk Format Level 2 - Data Objects
    1. Disk Format Level 2a - Data Object Headers
      1. Name: NIL
      2. Name: Simple Dataspace
      3. Name: Datatype
      4. Name: Data Storage - Fill Value
      5. Name: Reserved - not assigned yet
  
  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


Introduction

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

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.

Three levels of information comprise the file format. Level 0 contains basic information for identifying and defining information about the file. Level 1 information contains the group information (stored as a B-tree) and is used as the index for all the objects in the file. Level 2 is the rest of the file and contains all of the data objects, with each object partitioned into header information, also known as meta information, and data.

The sizes of various fields in the following layout tables are determined by looking at the number of columns the field spans in the table. There are three exceptions: (1) The size may be overridden by specifying a size in parentheses, (2) the size of addresses is determined by the Size of Offsets field in the super block, and (3) the size of size fields is determined by the Size of Lengths field in the super block.



Disk Format: Level 0 - File Signature and Super Block

The super block may begin at certain predefined offsets within the HDF5 file, allowing a block of unspecified content for users to place additional information at the beginning (and end) of the HDF5 file without limiting the HDF5 library's ability to manage the objects within the file itself. This feature was designed to accommodate wrapping an HDF5 file in another file format or adding descriptive information to the file without requiring the modification of the actual file's information. The super block is located by searching for the HDF5 file signature at byte offset 0, byte offset 512 and at successive locations in the file, each a multiple of two of the previous location, i.e. 0, 512, 1024, 2048, etc.

The super block is composed of a file signature, followed by super block and group version numbers, information about the sizes of offset and length values used to describe items within the file, the size of each group page, and a group entry for the root object in the file.

HDF5 Super Block Layout
byte byte byte byte

HDF5 File Signature (8 bytes)

Version # of Super Block Version # of Global Free-space Storage Version # of Group Reserved
Version # of Shared Header Message Format Size of Offsets Size of Lengths Reserved (zero)
Group Leaf Node K Group Internal Node K
File Consistency Flags
Base Address*
Address of Global Free-space Heap*
End of File Address*
Driver Information Block Address*
Root Group Address*
(Items marked with an asterisk (*) in the above table
are of the size specified in "Size of Offsets.")

Field Name Description
File Signature This field contains a constant value and can be used to quickly identify a file as being an HDF5 file. The constant value is designed to allow easy identification of an HDF5 file and to allow certain types of data corruption to be detected. The file signature of an HDF5 file always contains the following values:

decimal 137 72 68 70 13 10 26 10
hexadecimal 89 48 44 46 0d 0a 1a 0a
ASCII C Notation \211 H D F \r \n \032 \n

This signature both identifies the file as an HDF5 file and provides for immediate detection of common file-transfer problems. The first two bytes distinguish HDF5 files on systems that expect the first two bytes to identify the file type uniquely. The first byte is chosen as a non-ASCII value to reduce the probability that a text file may be misrecognized as an HDF5 file; also, it catches bad file transfers that clear bit 7. Bytes two through four name the format. The CR-LF sequence catches bad file transfers that alter newline sequences. The control-Z character stops file display under MS-DOS. The final line feed checks for the inverse of the CR-LF translation problem. (This is a direct descendent of the PNG file signature.)
Version Number of the Super Block This value is used to determine the format of the information in the super block. When the format of the information in the super block is changed, the version number is incremented to the next integer and can be used to determine how the information in the super block is formatted.
Version Number of the Global Free-space Heap This value is used to determine the format of the information in the Global Free-space Heap.
Version Number of the Group This value is used to determine the format of the information in the Group. When the format of the information in the Group is changed, the version number is incremented to the next integer and can be used to determine how the information in the Group is formatted.
Version Number of the Shared Header Message Format This value is used to determine the format of the information in a shared object header message, which is stored in the global small-data heap. Since the format of the shared header messages differs from the private header messages, a version number is used to identify changes in the format.
Size of Offsets This value contains the number of bytes used to store addresses in the file. The values for the addresses of objects in the file are offsets relative to a base address, usually the address of the super block signature. This allows a wrapper to be added after the file is created without invalidating the internal offset locations.
Size of Lengths This value contains the number of bytes used to store the size of an object.
Group Leaf Node K Each leaf node of a group B-tree will have at least this many entries but not more than twice this many. If a group has a single leaf node then it may have fewer entries.
Group Internal Node K Each internal node of a group B-tree will have at least K pointers to other nodes but not more than 2K pointers. If the group has only one internal node then it might have fewer than K pointers.
Bytes per B-tree Page This value contains the number of bytes used for symbol pairs per page of the B-trees used in the file. All B-tree pages will have the same size per page.
For 32-bit file offsets, 340 objects is the maximum per 4KB page; for 64-bit file offset, 254 objects will fit per 4KB page. In general, the equation is:
   <number of objects> =
       FLOOR((<page size> - <offset size>) /
          (<Symbol size> + <offset size>)) - 1
File Consistency Flags This value contains flags to indicate information about the consistency of the information contained within the file. Currently, the following bit flags are defined:
  • Bit 0 set indicates that the file is opened for write-access.
  • Bit 1 set indicates that the file has been verified for consistency and is guaranteed to be consistent with the format defined in this document.
  • Bits 2-31 are reserved for future use.
Bit 0 should be set as the first action when a file is opened for write access and should be cleared only as the final action when closing a file. Bit 1 should be cleared during normal access to a file and only set after the file's consistency is guaranteed by the library or a consistency utility.
Base Address This is the absolute file address of the first byte of the HDF5 data within the file. The library currently constrains this value to be the absolute file address of the super block itself when creating new files; future versions of the library may provide greater flexibility. Unless otherwise noted, all other file addresses are relative to this base address.
Address of Global Free-space Heap Free-space management is not yet defined in the HDF5 file format and is not handled by the library. Currently this field always contains the undefined address 0xfff...ff.
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).
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 file which contains information needed by the file driver in order to reopen a file. The format of the file driver information block is:

Driver Information Block
byte byte byte byte
Version Reserved (zero)
Driver Information Size (4 bytes)

Driver Identification (8 bytes)



Driver Information


Field Name Description
Version The version number of the driver information block. The file format documented here is version zero.
Driver Information Size The size in bytes of the Driver Information part of this structure.
Driver Identification This is an eight-byte ASCII string without null 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 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. (NCSAfami is simply NCSAfamily truncated to eight characters. Subsequent identifiers will be created by substituting sequential numerical values for the final character, starting with zero.)

Identification for user-defined drivers is arbitrary but should be unique.

Driver Information Driver information is stored in a format defined by the file driver and encoded/decoded by the driver callbacks invoked from the H5FD_sb_encode and H5FD_sb_decode functions.




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.

B-tree Nodes
byte byte byte byte
Node Signature
Node Type Node Level Entries 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 Name Description
Node Signature The 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 Type Each 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 Level The 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 Used This 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 Sibling This 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 Sibling This 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 Pointers Each 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.
Key The 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 1-4 Size of chunk in bytes.
Bytes 4-8 Filter mask, a 32-bit bitfield indicating which filters have been applied to that chunk.
N fields of 8 bytes each A 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 bytes Indicates the byte offset into the local heap for the first object name in the subtree which that key describes.
Child Pointers The 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)
byte byte byte byte
Node Signature
Version Number Reserved for Future Use Number of Symbols


Group Entries


Field Name Description
Node Signature The 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 Number The version number for the group node. This document describes version 1.
Number of Symbols Although 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 Entries Each 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
byte byte byte byte
Name Offset (<size> bytes)
Object Header Address
Cache Type
Reserved


Scratch-pad Space (16 bytes)


Field Name Description
Name Offset This is the byte offset into the group local heap for the name of the object. The name is null terminated.
Object Header Address Every 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 Type The 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.
Reserved These 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 Space This 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
byte byte byte byte
Address of B-tree
Address of Name Heap

Field Name Description
Address of B-tree This is the file address for the root of the group's B-tree.
Address of Name Heap This 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
byte byte byte byte
Offset to Link Value

Field Name Description
Offset to Link Value The 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
byte byte byte byte
Heap Signature
Reserved (zero)
Data Segment Size
Offset to Head of Free-list (<size> bytes)
Address of Data Segment

Field Name Description
Heap Signature The 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 Size The 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-list This 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 Segment The 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
byte byte byte byte
Magic Number
Version Reserved
Collection Size

Global Heap Object 1 (described below)


Global Heap Object 2


...


Global Heap Object N


Global Heap Object 0 (free space)

Field Name Description
Magic Number The magic number for global heap collections are the four bytes G, C, O, and L.
Version Each 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 Size This 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 N The objects are stored in any order with no intervening unused space.
Object 0 Object 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
byte byte byte byte
Object ID Reference Count
Reserved
Object Data Size

Object Data

Field Name Description
Object ID Each 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 Count All 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.
Reserved Zero 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 Data The 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

Data objects contain the real information in the file. These objects compose the scientific data and other information which are generally thought of as "data" by the end-user. All the other information in the file is provided as a framework for these data objects.

A data object is composed of header information and data information. The header information contains the information needed to interpret the data information for the data object as well as additional "meta-data" or pointers to additional "meta-data" used to describe or annotate each data object.

Disk Format: Level 2a - Data Object Headers

The header information of an object is designed to encompass all the information about an object which would be desired to be known, except for the data itself. This information includes the dimensionality, number-type, information about how the data is stored on disk (in external files, compressed, broken up in blocks, etc.), as well as other information used by the library to speed up access to the data objects or maintain a file's integrity. The header of each object is not necessarily located immediately prior to the object's data in the file and in fact may be located in any position in the file.

Object Headers
byte byte byte byte
Version # of Object Header Reserved Number of Header Messages
Object Reference Count

Total Object Header Size

Header Message Type #1 Size of Header Message Data #1
Flags Reserved

Header Message Data #1

.
.
.
Header Message Type #n Size of Header Message Data #n
Flags Reserved

Header Message Data #n

Field Name Description
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 number is incremented and can be used to determine how the information in the object header is formatted.
Reserved Always set to zero.
Number of header messages This value determines the number of messages listed in this object header. This provides a fast way for software to prepare storage for the messages in the header.
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.
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 in the file.
Header Message Type The header message type specifies the type of information included in the header message data following 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 group entries throughout the file). The header message types for the pre-defined header messages will be included in further discussion below.
Size of Header Message Data This value specifies the number of bytes of header message data following the header message type and length information for the current message. The size includes padding bytes to make the message a multiple of eight bytes.
Flags This is a bit field with the following definition:
0
If set, the message data is constant. This is used 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 contains the size of that Shared Object message.
2-7
Reserved
Header Message Data The format and length of this field is determined by the header message type and size respectively. Some header message types do not require any data and this information can be eliminated by setting the length of the message to zero. The data is padded with enough zeros to make the size a multiple of eight.

The header message types and the message data associated with them compose the critical "meta-data" about each object. Some header messages are required for each object while others are optional. Some optional header messages may also be repeated several times in the header itself, the requirements and number of times allowed in the header will be noted in each header message description below.

The following is a list of currently defined header messages:


Name: NIL

Type: 0x0000
Length: varies
Status: Optional, may be repeated.
Purpose and Description: The NIL message is used to indicate a message 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 Dataspace

Type: 0x0001
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 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 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.)

Simple Dataspace Message
byte byte byte byte
Version Dimensionality Flags Reserved
Reserved
Dimension Size #1 (<size> bytes)
.
.
.
Dimension Size #n (<size> bytes)
Dimension Maximum #1 (<size> bytes)
.
.
.
Dimension Maximum #n (<size> bytes)
Permutation Index #1
.
.
.
Permutation Index #n

Field Name 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 object has.
Flags This field is used to store flags to indicate the presence of parts of this message. Bit 0 (the least significant bit) is used to indicate that maximum dimensions are present. Bit 1 is used to indicate that permutation indices are present for each dimension.
Dimension Size #n (<size> bytes) This value is the current size of the dimension of the data as stored in the file. The first dimension stored in the list of dimensions is the slowest changing dimension and the last dimension stored is the fastest changing dimension.
Dimension Maximum #n (<size> bytes) This value is the maximum size of the dimension of the data as stored in the file. This value may be the special value <UNLIMITED> (all bits set) which indicates that the data may expand along this dimension indefinitely. If these values are not stored, the maximum value of each dimension is assumed to be the same as the current size value.
Permutation Index #n (4 bytes) This value is the index permutation used to map each dimension from the canonical representation to an alternate axis for each dimension. If these values are not stored, the first dimension stored in the list of dimensions is the slowest changing dimension and the last dimension stored is the fastest changing dimension.

Name: Datatype

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

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 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.

Datatype Message
byte byte byte byte
Type Class and Version Class Bit Field
Size in Bytes (4 bytes)


Properties


The Class Bit Field and Properties fields vary depending on the Type Class, which is the low-order four bits of the Type Class and Version field (the high-order four bits 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), 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.

Bit Field for Fixed-point Numbers (Class 0)
Bits Meaning
0 Byte Order. If zero, byte order is little-endian; otherwise, byte order is big endian.
1, 2 Padding type. Bit 1 is the lo_pad type and bit 2 is the hi_pad type. If a datum has unused bits at either end, then the lo_pad or hi_pad bit is copied to those locations.
3 Signed. If this bit is set then the fixed-point number is in 2's complement form.
4-23 Reserved (zero).

Properties for Fixed-point Numbers (Class 0)
Byte Byte Byte Byte
Bit Offset Bit Precision

Bit Field for Floating-point Numbers (Class 1)
Bits Meaning
0 Byte Order. If zero, byte order is little-endian; otherwise, byte order is big endian.
1, 2, 3 Padding type. Bit 1 is the low bits pad type, bit 2 is the high bits pad type, and bit 3 is the internal bits pad type. If a datum has unused bits at either or between the sign bit, exponent, or mantissa, then the value of bit 1, 2, or 3 is copied to those locations.
4-5 Normalization. The value can be 0 if there is no normalization, 1 if the most significant bit of the mantissa is always set (except for 0.0), and 2 if the most signficant bit of the mantissa is not stored but is implied to be set. The value 3 is reserved and will not appear in this field.
6-7 Reserved (zero).
8-15 Sign. This is the bit position of the sign bit.
16-23 Reserved (zero).

Properties for Floating-point Numbers (Class 1)
Byte Byte Byte Byte
Bit Offset Bit Precision
Exponent Location Exponent Size in Bits Mantissa Location Mantissa Size in Bits
Exponent Bias

Bit Field for Strings (Class 3)
Bits Meaning
0-3 Padding type. This four-bit value determines the type of padding to use for the string. The values are:
0 Null terminate.
A zero byte marks the end of the string and is guaranteed to be present after converting a long string to a short string. When converting a short string to a long string the value is padded with additional null characters as necessary.

1 Null pad.
Null characters are added to the end of the value during conversions from short values to long values but conversion in the opposite direction simply truncates the value.

2 Space pad.
Space characters are added to the end of the value during conversions from short values to long values but conversion in the opposite direction simply truncates the value. This is the Fortran representation of the string.

3-15 Reserved.
These values are reserved for future use.
4-7 Character Set. The character set to use for encoding the string. The only character set supported is the 8-bit ASCII (zero) so no translations have been defined yet.
8-23 Reserved (zero).

Bit Field for Bitfield Types (Class 4)
Bits Meaning
0 Byte Order. If zero, byte order is little-endian; otherwise, byte order is big endian.
1, 2 Padding type. Bit 1 is the lo_pad type and bit 2 is the hi_pad type. If a datum has unused bits at either end, then the lo_pad or hi_pad bit is copied to those locations.
3-23 Reserved (zero).

Properties for Bitfield Types (Class 4)
Byte Byte Byte Byte
Bit Offset Bit Precision

Bit Field for Opaque Types (Class 5)
Bits Meaning
0-23 Reserved (zero).

Properties for Opaque Types (Class 5)
Byte Byte Byte Byte

Null-terminated ASCII Tag
(multiple of 8 bytes)

Bit Field for Compound Types (Class 6)
Bits Meaning
0-15 Number of Members. This field contains the number of members defined for the compound datatype. The member definitions are listed in the Properties field of the data type message.
15-23 Reserved (zero).

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 datatype message.

Properties for Compound Types (Class 6)
Byte Byte Byte Byte


Name (null terminated, multiple of eight bytes)


Byte Offset of Member in Compound Instance
Dimensionality reserved
Dimension Permutation
Reserved
Size of Dimension 0 (required)
Size of Dimension 1 (required)
Size of Dimension 2 (required)
Size of Dimension 3 (required)


Member Type Message


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

Properties for Enumeration Types (Class 8)
Byte Byte Byte Byte

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.

Bit Field for Variable-length Types (Class 9)
Bits Meaning
0-3
Type
0 Variable-length sequence
This variable-length datatype can be of any sequence of data. Variable-length sequences do not have padding or character set information.
1 Variable-length string
This variable-length datatype is composed of a series of characters. Variable-length strings have padding and character set information.
4-7
Padding type (variable-length string only)
This four-bit value determines the type of padding used for variable-length strings. The values are the same as for the string padding type, as follows:
0 Null terminate
A zero byte marks the end of a string and is guaranteed to be present after converting a long string to a short string. When converting a short string to a long string, the value is padded with additional null characters as necessary.
1 Null pad
Null characters are added to the end of the value during conversion from a short string to a longer string. Conversion from a long string to a shorter string simply truncates the value.
2 Space pad
Space characters are added to the end of the value during conversion from a short string to a longer string. Conversion from a long string to a shorter string simply truncates the value. This is the Fortran representation of the string.
3-15 Reserved
These values are reserved for future use.
8-11
Character set (variable-length string only)
This four-bit value specifies the character set to be used for encoding the string.
0 8-bit ASCII
As of this writing (July 2002, Release 1.4.4), 8-bit ASCII is the only character set supported. Therefore, no translations have been defined.
12-23 Reserved (zero).

Properties for Variable-length Types (Class 9)
Byte Byte Byte Byte

Parent Type

Parent Type: Each variable-length type is based on some parent type. The information for that parent type is described recursively by this field.


Name: Data Storage - Fill Value

Type: 0x0004
Length: varies
Status: Optional, may not be repeated.

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 datatype as the dataset. If no fill value message is present then a fill value of all zero is assumed.

Fill Value Message
byte byte byte byte
Size (4 bytes)

Fill Value

Field Name Description
Size (4 bytes) This is the size of the Fill Value field in bytes.
Fill Value The fill value. The bytes of the fill value are interpreted using the same datatype as for the dataset.

Name: Reserved - Not Assigned Yet

Type: 0x0005
Length: N/A
Status: N/A

Name: Data Storage - Compact

Type: 0x0006
Length: varies
Status: Optional, may not be repeated.

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

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

Type: 0x0007
Length: varies
Status: Optional, may not be repeated.

Purpose and Description: The external object message indicates that the data for an object is stored outside the HDF5 file. The filename of the object is stored as a Universal Resource Location (URL) of the actual filename containing the data. An external file list record also contains the byte offset of the start of the data within the file and the amount of space reserved in the file for that data.

External File List Message
byte byte byte byte
Version Reserved
Allocated Slots Used Slots

Heap Address


Slot Definitions...

Field Name Description
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.
Allocated Slots The total number of slots allocated in the message. Its value must be at least as large as the value contained in the Used Slots field.
Used Slots The number of initial slots which contain valid information. The remaining slots are zero filled.
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.
Slot Definitions The slot definitions are stored in order according to the array addresses they represent. If more slots have been allocated than what has been used then the defined slots are all at the beginning of the list.

External File List Slot
byte byte byte byte

Name Offset (<size> bytes)


File Offset (<size> bytes)


Size

Field Name Description
Name Offset (<size> bytes) The byte offset within the local name heap for the name of the file. File names are stored as a URL which has a protocol name, a host name, a port number, and a file name: protocol:port//host/file. If the protocol is omitted then "file:" is assumed. If the port number is omitted then a default port for that protocol is used. If both the protocol and the port number are omitted then the colon can also be omitted. If the double slash and host name are omitted then "localhost" is assumed. The file name is the only mandatory part, and if the leading slash is missing then it is relative to the application's current working directory (the use of relative names is not recommended).
File Offset (<size> bytes) This is the byte offset to the start of the data in the specified file. For files that contain data for a single dataset this will usually be zero.
Size This is the total number of bytes reserved in the specified file for raw data storage. For a file that contains exactly one complete dataset which is not extendable, the size will usually be the exact size of the dataset. However, by making the size larger one allows HDF5 to extend the dataset. The size can be set to a value larger than the entire file since HDF5 will read zeros past the end of the file without failing.

Name: Data Storage - Layout

Type: 0x0008
Length: varies
Status: Required for datasets, may not be repeated.

Purpose and Description: 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 supported:

  1. The array can be stored in one contiguous area of the file. The layout requires that the size of the array be constant and does not permit chunking, compression, checksums, encryption, etc. The message stores the total size of the array and the offset of an element from the beginning of the storage area is computed as in C.
  2. The array domain can be regularly decomposed into chunks and each chunk is allocated separately. This layout supports arbitrary element traversals, compression, encryption, and checksums, and the chunks can be distributed across external raw data files (these features are described in other messages). The message stores the size of a chunk instead of 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.

Data Layout Message
byte byte byte byte
Version Dimensionality Layout Class Reserved
Reserved

Address

Dimension 0 (4-bytes)
Dimension 1 (4-bytes)
...

Field Name Description
Version A version number for the layout message. This documentation describes version one.
Dimensionality An array has a fixed dimensionality. This field specifies the number of dimension size fields later in the message.
Layout Class 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 in the future.
Address 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.
Dimensions For contiguous storage the dimensions define the entire size of the array while for chunked storage they define the size of a single chunk.

Name: Reserved - Not Assigned Yet

Type: 0x0009
Length: N/A
Status: N/A
Purpose and Description: N/A
Format of Data: N/A

Name: Reserved - Not Assigned Yet

Type: 0x000A
Length: N/A
Status: N/A
Purpose and Description: N/A
Format of Data: N/A

Name: Data Storage - Filter Pipeline

Type: 0x000B
Length: varies
Status: Optional, may not be repeated.

Purpose and Description: This message describes the filter pipeline which should be applied to the data stream by providing filter identification numbers, flags, a name, an client data.

Filter Pipeline Message
byte byte byte byte
Version Number of Filters Reserved
Reserved

Filter List

Field Name Description
Version The version number for this message. This document describes version one.
Number of Filters The total number of filters described by this message. The maximum possible number of filters in a message is 32.
Filter List A description of each filter. A filter description appears in the next table.

Filter Pipeline Message
byte byte byte byte
Filter Identification Name Length
Flags Client Data Number of Values

Name


Client Data

Padding

Field Name Description
Filter Identification This is a unique (except in the case of testing) identifier for the filter. Values from zero through 255 are reserved for filters defined by the NCSA HDF5 library. Values 256 through 511 have been set aside for use when developing/testing new filters. The remaining values are allocated to specific filters by contacting the HDF5 Development Team.
Name Length Each filter has an optional null-terminated ASCII name and this field holds the length of the name including the null termination padded with nulls to be a multiple of eight. If the filter has no name then a value of zero is stored in this field.
Flags The flags indicate certain properties for a filter. The bit values defined so far are:
bit 1
If set then the filter is an optional filter. During output, if an optional filter fails it will be silently removed from the pipeline.
Client Data Number of Values Each filter can store a few integer values to control how the filter operates. The number of entries in the Client Data array is stored in this field.
Name If the Name Length field is non-zero then it will contain the size of this field, a multiple of eight. This field contains a null-terminated, ASCII character string to serve as a comment/name for the filter.
Client Data This is an array of four-byte integers which will be passed to the filter function. The Client Data Number of Values determines the number of elements in the array.
Padding Four bytes of zeros are added to the message at this point if the Client Data Number of Values field contains an odd number.

Name: Attribute

Type: 0x000C
Length: varies
Status: Optional, may be repeated.

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 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 (groups, datasets, named types and spaces, etc.).

Attribute Message
byte byte byte byte
Version Reserved Name Size
Type Size Space Size

Name


Type


Space


Data

Field Name Description
Version Version number for the message. This document describes 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 null terminator. Note that the Name field below may contain additional padding not represented by this field.
Type Size 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 dataspace description in the Space field below. Note that the Space field may contain additional padding not represented by this field.
Name The null-terminated attribute name. This field is padded with additional null characters to make it a multiple of eight bytes.
Type 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 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.
Data The raw data for the attribute. The size is determined from the datatype and dataspace descriptions. This field is not padded with additional zero bytes.

Name: Object Name

Type: 0x000D
Length: varies
Status: Optional, may not be repeated.

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 formatting included by the library.

Name Message
byte byte byte byte

Name

Field Name Description
Name A null terminated ASCII character string.

Name: Object Modification Date & Time

Type: 0x000E
Length: fixed
Status: Optional, may not be repeated.

Purpose and Description: The object modification date and time is a timestamp which indicates (using ISO-8601 date and time format) 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.

Modification Time Message
byte byte byte byte
Year
Month Day of Month
Hour Minute
Second Reserved

Field Name Description
Year The four-digit year as an ASCII string. For example, 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.
Day of Month The day number within the month as a two digit ASCII 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.
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.
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.
Reserved This field is reserved and should always be zero.

Name: Shared Object Message

Type: 0x000F
Length: 4 Bytes
Status: Optional, may be repeated.

A constant message can be shared among several object headers by writing that message in the global heap and having the object headers all point to it. The pointing is accomplished with a Shared Object message which is understood directly by the object header layer of the library. It is also possible to have a message of one object header point to a message in some other object header, but care must be exercised to prevent cycles.

If a message is shared, then the message appears in the global heap and its message ID appears in the Header Message Type field of the object header. Also, the Flags field in the object header for that message will have bit two set (the H5O_FLAG_SHARED bit). The message body in the object header will be that of a Shared Object message defined here and not that of the pointed-to message.

Shared Message Message
byte byte byte byte
Version Flags Reserved
Reserved

Pointer

Field Name Description
Version The version number for the message. This document describes version one of shared messages.
Flags The Shared Message message points to a message which is shared among multiple object headers. The Flags field describes the type of sharing:
Bit 0
If this bit is clear then the actual message is the first message in some other object header; otherwise the actual message is stored in the global heap.
Bits 2-7
Reserved (always zero)
Pointer This field points to the actual message. The format of the pointer depends on the value of the Flags field. If 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 group entry that points to some other object header.

Name: Object Header Continuation

Type: 0x0010
Length: fixed
Status: Optional, may be repeated.
Purpose and Description: The object header continuation is the location in the file of more header messages for the current data object. This can be used when header blocks are large, or likely to change over time.
Format of Data:

The object header continuation is formatted as follows (assuming a 4-byte length & offset are being used in the current file):

HDF5 Object Header Continuation Message Layout
byte byte byte byte
Header Continuation Offset
Header Continuation Length

The elements of the Header Continuation Message are described below:
Header Continuation Offset: (<offset> bytes)
This value is the offset in bytes from the beginning of the file where the header continuation information is located.
Header Continuation Length: (<length> bytes)
This value is the length in bytes of the header continuation information in the file.

Name: Group Message

Type: 0x0011
Length: fixed
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 group message is formatted as follows:

HDF5 Object Header Group Message Layout
byte byte byte byte
B-tree Address
Heap Address

The elements of the Group Message are described below:
B-tree Address (<offset> bytes)
This value is the offset in bytes from the beginning of the file 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 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 heap. Since these messages require additional information beyond the basic object header message information, the format of the shared message is detailed below.

HDF5 Shared Object Header Message
byte byte byte byte
Reference Count of Shared Header Message

Shared Object Header Message

The elements of the shared object header message are described 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 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 description earlier in this document and begins with the header message Type.

Disk Format: Level 2c - Data Object Data Storage

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 dimensionality of the object (indicated in the dimensionality header message). Multi-dimensional data is stored in C order [same as current scheme], i.e. the "last" dimension changes fastest.

Data whose elements are composed of simple number-types are stored in native-endian IEEE format, unless they are specifically defined as being stored 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 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 size of the pointer being the same number of bytes as offsets in the file. Partial-object pointers are stored as a heap-ID which points to the following information within the file-heap: an offset of the object pointed to, number-type information (same format as header message), dimensionality information (same 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).

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.


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

HDF Help Desk
Last modified: 1 July 2002
Describes HDF5 Release 1.4.4, July 2002