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Introduction to HDF5 
HDF5 User's Guide 
HDF5 Reference Manual 
HDF5 Application Developer's Guide 

HDF5 File Format Specification Version 2.0

  1. Introduction
  2. Disk Format Level 0 - File Metadata
    1. Disk Format Level 0A - Format Signature and Superblock
    2. Disk Format Level 0B - File Driver Info
    3. Disk Format Level 0C - Superblock Extension
  3. Disk Format Level 1 - File Infrastructure
    1. Disk Format Level 1A - B-Trees
      1. Version 1 B-Trees (B-link trees)
      2. Version 2 B-Trees
    2. Disk Format Level 1B - Group Symbol Table
    3. Disk Format Level 1C - Group Symbol Table Entry
    4. Disk Format Level 1D - Local Heaps
    5. Disk Format Level 1E - Global Heap
    6. Disk Format Level 1F - Fractal Heap
    7. Disk Format Level 1G - Free-Space Manager
    8. Disk Format Level 1H - Shared Object Header Message Table
  4. Disk Format Level 2 - Data Objects
    1. Disk Format Level 2A - Data Object Headers
      1. Disk Format Level 2A1 - Data Object Header Prefix
        1. Version 1 Data Object Header Prefix
        2. Version 2 Data Object Header Prefix
      2. Disk Format Level 2A2 - Data Object Header Messages
        1. NIL
        2. Dataspace
 
  1. Disk Format Level 2 - Data Objects (Continued)
    1. Disk Format Level 2A - Data Object Headers(Continued)
      1. Disk Format Level 2A2 - Data Object Header Messages(Continued)
        1. Link Info
        2. Datatype
        3. Data Storage - Fill Value (Old)
        4. Data Storage - Fill Value
        5. Link Message
        6. Data Storage - External Data Files
        7. Data Storage - Layout
        8. Bogus
        9. Group Info
        10. Data Storage - Filter Pipeline
        11. Attribute
        12. Object Comment
        13. Object Modification Time (Old)
        14. Shared Message Table
        15. Object Header Continuation
        16. Symbol Table
        17. Object Modification Time
        18. B-tree 'K' Values
        19. Driver Info
        20. Attribute Info
        21. Object Reference Count
    2. Disk Format: Level 2B - Data Object Data Storage
  2. Appendix


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 low-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 (for storing the links to objects in the group) and to a B-tree (which indexes the links). A dataset is an object header that contains messages that describe datatype, dataspace, 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 information about the pieces of a file shared by many objects in the file (such as a B-trees and heaps). 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 metadata, 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 superblock and is indicated in this document with a superscripted 'O', and (3) the size of length fields is determined by the Size of Lengths field in the superblock and is indicated in this document with a superscripted 'L'.

Values for all fields in this document should be treated as unsigned integers, unless otherwise noted in the description of a field. Additionally, all metadata fields are stored in little-endian byte order.

All checksums used in the format are computed with the Jenkins' lookup3 algorithm.

Various tables in this document aligned with "This space inserted only to align table nicely". These entries in the table are just to make the table presentation nicer and do not represent any values or padding in the file.



Disk Format: Level 0 - File Metadata

Disk Format: Level 0A - Format Signature and Superblock

The superblock 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 an HDF5 file without requiring the modification of the actual file's information. The superblock is located by searching for the HDF5 format 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 superblock is composed of the format signature, followed by a superblock version number and information that is specific to each version of the superblock. Currently, there are three versions of the superblock format. Version 0 is the default format, while version 1 is basically the same as version 0 with additional information when a non-default B-tree 'K' value is stored. Version 2 is the latest format, with some fields eliminated or compressed and with superblock extension and checksum support.

Version 0 and 1 of the superblock are described below:

Superblock (Versions 0 and 1)
byte byte byte byte

Format Signature (8 bytes)

Version # of Superblock Version # of File Free-space Storage Version # of Root Group Symbol Table Entry Reserved (zero)
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
Indexed Storage Internal Node K1 Reserved (zero)1

Base AddressO


Address of File Free-space InfoO


End of File AddressO


Driver Information Block AddressO

Root Group Symbol Table Entry
(Items marked with an ‘O’ in the above table are
of the size specified in “Size of Offsets.”)
(Items marked with a ‘1’ in the above table are
new in version 1 of the superblock)

Field Name Description
Format 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.)

This field is present in version 0+ of the superblock.

Version Number of the Superblock

This value is used to determine the format of the information in the superblock. When the format of the information in the superblock is changed, the version number is incremented to the next integer and can be used to determine how the information in the superblock is formatted.

Values of 0, 1 and 2 are defined for this field. (The format of version 2 is described below, not here)

This field is present in version 0+ of the superblock.

Version Number of the File Free-Space Information

This value is used to determine the format of the information in the file's free-space Information.

The only value currently valid in this field is '0', which indicates that the free space index is formatted as described below.

This field is present in version 0 and 1 of the superblock.

Version Number of the Root Group Symbol Table Entry

This value is used to determine the format of the information in the Root Group Symbol Table Entry. When the format of the information in that field is changed, the version number is incremented to the next integer and can be used to determine how the information in the field is formatted.

The only value currently valid in this field is '0', which indicates that the root group symbol table entry is formatted as described below.

This field is present in version 0 and 1 of the superblock.

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. Since the format of the shared header messages differs from the other private header messages, a version number is used to identify changes in the format.

The only value currently valid in this field is '0', which indicates that shared header messages are formatted as described below.

This field is present in version 0 and 1 of the superblock.

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 superblock signature. This allows a wrapper to be added after the file is created without invalidating the internal offset locations.

This field is present in version 0+ of the superblock.

Size of Lengths

This value contains the number of bytes used to store the size of an object.

This field is present in version 0+ of the superblock.

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.

This value must be greater than zero.

See the description of B-trees below.

This field is present in version 0 and 1 of the superblock.

Group Internal Node K

Each internal node of a group B-tree will have at least this many entries but not more than twice this many. If the group has only one internal node then it might have fewer entries.

This value must be greater than zero.

See the description of B-trees below.

This field is present in version 0 and 1 of the superblock.

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.

This field is present in version 0+ of the superblock.

Indexed Storage Internal Node K

Each internal node of an indexed storage B-tree will have at least this many entries but not more than twice this many. If the index storage B-tree has only one internal node then it might have fewer entries.

This value must be greater than zero.

See the description of B-trees below.

This field is present in version 1 of the superblock.

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 superblock itself when creating new files; future versions of the library may provide greater flexibility. When opening an existing file and this address does not match the offset of the superblock, the library assumes that the entire contents of the HDF5 file have been adjusted in the file and adjusts the base address and end of file address to reflect their new positions in the file. Unless otherwise noted, all other file addresses are relative to this base address.

This field is present in version 0+ of the superblock.

Address of Global Free-space Index

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.

This field is present in version 0 and 1 of the superblock.

End of File Address

This is the absolute 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 space from the free list is not used.

This field is present in version 0+ of the superblock.

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.

This field is present in version 0 and 1 of the superblock.

Root Group Symbol Table Entry

This is the symbol table entry of the root group, which serves as the entry point into the group graph for the file.

This field is present in version 0 and 1 of the superblock.

Version 2 of the superblock is described below:

Superblock (Version 2)
byte byte byte byte

Format Signature (8 bytes)

Version # of Superblock Size of Offsets Size of Lengths File Consistency Flags

Base AddressO


Superblock Extension AddressO


End of File AddressO


Root Group Object Header AddressO

Superblock Checksum
(Items marked with an ‘O’ in the above table are
of the size specified in “Size of Offsets.”)

Field Name Description
Format Signature

This field is the same as described for versions 0 and 1 of the superblock.

Version Number of the Superblock

This field has a value of 2 and has the same meaning as for versions 0 and 1.

Size of Offsets

This field is the same as described for versions 0 and 1 of the superblock.

Size of Lengths

This field is the same as described for versions 0 and 1 of the superblock.

File Consistency Flags

This field is the same as desribed for versions 0 and 1 except that it is smaller (the number of reserved bits has been reduced from 30 to 6).

Base Address

This field is the same as described for versions 0 and 1 of the superblock.

Superblock Extension Address

The field is the address of the object header for the superblock extension. If there is no extension then this entry should be the undefined address.

End of File Address

This field is the same as described for versions 0 and 1 of the superblock.

Root Group Object Header Address

This is the address of the root group object header, which serves as the entry point into the group graph for the file.

Superblock Checksum

The checksum for the superblock.


Disk Format: Level 0B - File Driver Info

The driver information block is an optional region of the file which contains information needed by the file driver to reopen a file. The format is described below:

Driver Information Block
byte byte byte byte
Version Reserved
Driver Information Size

Driver Identification (8 bytes)



Driver Information (variable size)



Field Name Description
Version

The version number of the Driver Information Block. This document describes version 0.

Driver Information Size

The size in bytes of the Driver Information field.

Driver Identification

This is an eight-byte ASCII string without null termination which identifies the driver and/or version number of the Driver Information Block. The predefined driver encoded in this field by the HDF5 library is 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, starting with 0.

Identification for user-defined drivers is also eight-byte long. It can be arbitrary but should be unique to avoid the four character prefix "NCSA".

Driver Information Driver information is stored in a format defined by the file driver (see description below).

The two drivers encoded in the Driver Identification field are as follows:
The format of the Driver Information field for the above two drivers are described below:

Multi Driver Information
byte byte byte byte
Member Mapping Member Mapping Member Mapping Member Mapping
Member Mapping Member Mapping Reserved Reserved

Address of Member File 1


End of Address for Member File 1


Address of Member File 2


End of Address for Member File 2


... ...


Address of Member File N


End of Address for Member File N


Name of Member File 1 (variable size)


Name of Member File 2 (variable size)


... ...


Name of Member File N (variable size)


Field Name Description
Member Mapping These fields are integer values from 1 to 6 indicating how the data can be mapped to or merged with another type of data.
Member Mapping Description
1 The superblock data.
2 The B-tree data.
3 The raw data.
4 The global heap data.
5 The local heap data.
6 The object header data.

For example, if the third field has the value 3 and all the rest have the value 1, it means there are two files: one for raw data, and one for superblock, B-tree, global heap, local heap, and object header.
Reserved

These fields are reserved and should always be zero.

Address of Member File N

This field Specifies the virtual address at which the member file starts.

N is the number of member files.

End of Address for Member File N

This field is the end of the allocated address for the member file.

Name of Member File N

This field is the null-terminated name of the member file and its length should be multiples of 8 bytes. Additional bytes will be padded with NULLs. The default naming convention is %s-X.h5, where X is one of the letters s (for superblock), b (for B-tree), r (for raw data), g (for global heap), l (for local heap), and o (for object header). The name of the whole HDF5 file will substitute the %s in the string.


Family Driver Information
byte byte byte byte

Size of member file


Field Name Description
Size of member file

This field is the size of the member file in the family of files.


Disk Format: Level 0C - Superblock Extension

The superblock extension is used to store superblock metadata which is either optional or added after the version of the superblock was defined. Superblock extensions may only exist when version 2+ of superblock is used. A superblock extension is an object header which may hold the following messages:



Disk Format: Level 1 - File Infrastructure

Disk Format: Level 1A - B-Trees and B-Tree Nodes

B-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. B-trees are used in several places in the HDF5 file format, when an index is needed for another data structure.

The version 1 B-tree structure described below is the original index structure, but are limited by some bugs in our implementation (mainly in how they handle deleting records). The version 1 B-trees are being phased out in favor of the version 2 B-trees described below, although both types of structures may be found in the same file, depending on application settings when creating the file.

Disk Format: Level 1A1 - Version 1 B-trees

Version 1 B-trees in HDF5 files an implementation of 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-link Tree Nodes
byte byte byte byte
Signature
Node Type Node Level Entries Used

Address of Left SiblingO


Address of Right SiblingO

Key 0 (variable size)

Address of Child 0O

Key 1 (variable size)

Address of Child 1O

...
Key 2K (variable size)

Address of Child 2KO

Key 2K+1 (variable size)
(Items marked with an ‘O’ the above table are
of the size specified in “Size of Offsets.”)

Field Name Description
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.

Node Type Description
0 This tree points to group nodes.
1 This tree points to raw data chunk nodes.
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 relative file address of the left sibling of the current node. If the current node is the left-most node at this level then this field is the undefined address.

Address of Right Sibling

This is the relative file address of the right sibling of the current node. If the current node is the right-most node at this level then this field is the undefined address.

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 node's 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 0 (group nodes), 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.

For nodes of node type 1 (chunked raw data nodes), 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 skipped for this chunk. Each filter has an index number in the pipeline (starting at 0, with the first filter to apply) and if that filter is skipped, the bit corresponding to its index is set.
(D + 1) 64-bit fields: The offset of the chunk within the dataset where D is the number of dimensions of the dataset, and the last value is the offset within the dataset's datatype and should always be zero. For example, if a chunk in a 3-dimensional dataset begins at the position [5,5,5], there will be three such 64-bit values, each with the value of 5, followed by a 0 value.

Child Pointer

The tree node contains file addresses of subtrees or data depending on the node level. Nodes at Level 0 point to data addresses, either raw data chunks or group nodes. Nodes at non-zero levels point to other nodes of the same B-tree.

For raw data chunk nodes, the child pointer is the address of a single raw data chunk. For group nodes, the child pointer points to a symbol table, which contains information for multiple symbol table entries.

Conceptually, 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] is 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 1A2 - Version 2 B-Trees

Version 2 B-trees are "traditional" B-trees, with one major difference. Instead of just using a simple pointer (or address in the file) to a child of an internal node, the pointer to the child node contains two additional pieces of information: the number of records in the child node itself, and the total number of records in the child node and all its descendents. Storing this additional information allows fast array-like indexing to locate the n'th record in the B-tree.

The entry into a version 2 B-tree is a header which contains global information about the structure of the B-tree. The root node address field in the header points to the B-tree root node, which is either an internal or leaf node, depending on the value in the header's depth field. An internal node consists of records plus pointers to further leaf or internal nodes in the tree. A leaf node consists of solely of records. The format of the records depends on the B-tree type (stored in the header).

Version 2 B-tree Header
byte byte byte byte
Signature
Version Type This space inserted only to align table nicely
Node Size
Record Size Depth
Split Percent Merge Percent This space inserted only to align table nicely

Root Node AddressO

Number of Records in Root Node This space inserted only to align table nicely

Total Number of Records in B-treeL

Checksum

Field Name Description
Signature

The ASCII character string "BTHD" is used to indicate the header of a version 2 B-link tree node.

Version

The version number for this B-tree header. This document describes version 0.

Type

This field indicates the type of B-tree:
Value Description
0 A "testing" B-tree, this value should not be used for storing records in actual HDF5 files.
1 This B-tree is used for indexing indirectly accessed, non-filtered 'huge' fractal heap objects.
2 This B-tree is used for indexing indirectly accessed, filtered 'huge' fractal heap objects.
3 This B-tree is used for indexing directly accessed, non-filtered 'huge' fractal heap objects.
4 This B-tree is used for indexing directly accessed, filtered 'huge' fractal heap objects.
5 This B-tree is used for indexing the 'name' field for links in indexed groups.
6 This B-tree is used for indexing the 'creation order' field for links in indexed groups.
7 This B-tree is used for indexing shared object header messages.
8 This B-tree is used for indexing the 'name' field for indexed attributes.
9 This B-tree is used for indexing the 'creation order' field for indexed attributes.

The format of records for each type is described below.

Node Size

This is the size in bytes of all B-tree nodes.

Record Size

This field is the size in bytes of the B-tree record.

Depth

This is the depth of the B-tree.

Split Percent

The percent full that a node needs to increase above before it is split.

Merge Percent

The percent full that a node needs to be decrease below before it is split.

Root Node Address

This is the address of the root B-tree node. A B-tree with no records will have the undefined address in this field.

Number of Records in Root Node

This is the number of records in the root node.

Total Number of Records in B-tree

This is the total number of records in the entire B-tree.

Checksum

This is the checksum for the B-tree header.


Version 2 B-tree Internal Node
byte byte byte byte
Signature
Version Type Records 0, 1, 2...N-1 (variable size)

Child Node Pointer 0O


Number of Records N0 for Child Node 0 (variable size)

Total Number of Records for Child Node 0 (optional, variable size)

Child Node Pointer 1O


Number of Records N1 for Child Node 1 (variable size)

Total Number of Records for Child Node 1 (optional, variable size)
...

Child Node Pointer NO


Number of Records Nnfor Child Node N (variable size)

Total Number of Records for Child Node N (optional, variable size)
Checksum

Field Name Description
Signature

The ASCII character string "BTIN" is used to indicate the internal node of a B-link tree.

Version

The version number for this B-tree internal node. This document describes version 0.

Type

This field is the type of the B-tree node. It should always be the same as the B-tree type in the header.

Records

The size of this field is determined by the number of records for this node and the record size (from the header). The format of records depends on the type of B-tree.

Child Node Pointer

This field is the address of the child node pointed to by the internal node.

Number of Records in Child Node

This is the number of records in the child node pointed to by the corresponding Node Pointer.

The number of bytes used to store this field is determined by the maximum possible number of records able to be stored in the child node.

The maximum number of records in a child node is computed in the following way: Subtract the fixed size overhead for the child node (e.g. it's signature, version, checksum, etc. and one pointer triplet of information for the child node (because there is one more pointer triplet than records in each internal node)) from the size of nodes for the B-tree and dividing that result by the size of a record plus the pointer triplet of information stored to reach each child node from this node.

Note that leaf nodes don't encode any child pointer triplets, so the maximum number of records in a leaf node is just the node size minus the leaf node overhead, divided by the record size.

Also note that the first level of internal nodes above the leaf nodes don't encode the Total Number of Records in Child Node value in the child pointer triplets (since it is the same as the Number of Records in Child Node), so the maximum number of records in these nodes is computed with the equation above, but using (Child Pointer, Number of Records in Child Node) pairs instead of triplets.

The number of bytes used to encode this field is the least number of bytes required to encode the maximum number of records in a child node value for the child nodes below this level in the B-tree.

For example, if the maximum number of child records is 123, one byte will be used to encode these values in this node, if the maximum number of child records is 20000, two bytes will be used to encode these values in this node, etc. The maximum number of bytes used to encode these values is 8 (i.e. an unsigned 64-bit integer).

Total Number of Records in Child Node

This is the total number of records for the node pointed to by the corresponding Node Pointer and all its children. This field exists only in nodes whose depth in the B-tree node is greater than 1 (i.e. the "twig" internal nodes, just above leaf nodes, don't store this field in their child node pointers).

The number of bytes used to store this field is determined by the maximum possible number of records able to be stored in the child node and its descendents.

The maximum possible number of records able to be stored in a child node and its descendents is computed iteratively, in the following way: The maximum number of records in a leaf node is computed, then that value is used to compute the maximum possible number of records in the first level of internal nodes above the leaf nodes. Multiplying these two values together determines the maximum possible number of records in child node pointers for the level of nodes two levels above leaf nodes. This process is continued up to any level in the B-tree.

The number of bytes used to encode this value is computed in the same way as for the Number of Records in Child Node field.

Checksum

This is the checksum for this node.


Version 2 B-tree Leaf Node
byte byte byte byte
Signature
Version Type Record 0, 1, 2...N-1 (variable size)
Checksum

Field Name Description
Signature

The ASCII character string "BTLF" is used to indicate the leaf node of a version 2 B-link tree.

Version

The version number for this B-tree leaf node. This document describes version 0.

Type

This field is the type of the B-tree node. It should always be the same as the B-tree type in the header.

Records

The size of this field is determined by the number of records for this node and the record size (from the header). The format of records depends on the type of B-tree.

Checksum

This is the checksum for this node.

The record layout for each stored (i.e. non-testing) B-tree type is as follows:

Version 2 B-tree, Type 1 Record Layout - Indirectly Accessed, Non-Filtered, 'Huge' Fractal Heap Objects
byte byte byte byte

Huge Object AddressO


Huge Object LengthL


Huge Object IDL


Field Name Description
Huge Object Address

The address of the huge object in the file.

Huge Object Length

The length of the huge object in the file.

Huge Object ID

The heap ID for the huge object.


Version 2 B-tree, Type 2 Record Layout - Indirectly Accessed, Filtered, 'Huge' Fractal Heap Objects
byte byte byte byte

Filtered Huge Object AddressO


Filtered Huge Object LengthL

Filter Mask

Filtered Huge Object Memory SizeL


Huge Object IDL


Field Name Description
Filtered Huge Object Address

The address of the filtered huge object in the file.

Filtered Huge Object Length

The length of the filtered huge object in the file.

Filter Mask

A 32-bit bitfield indicating which filters have been skipped for this chunk. Each filter has an index number in the pipeline (starting at 0, with the first filter to apply) and if that filter is skipped, the bit corresponding to its index is set.

Filtered Huge Object Memory Size

The size of the de-filtered huge object in memory.

Huge Object ID

The heap ID for the huge object.


Version 2 B-tree, Type 3 Record Layout - Directly Accessed, Non-Filtered, 'Huge' Fractal Heap Objects
byte byte byte byte

Huge Object AddressO


Huge Object LengthL


Field Name Description
Huge Object Address

The address of the huge object in the file.

Huge Object Length

The length of the huge object in the file.


Version 2 B-tree, Type 4 Record Layout - Directly Accessed, Filtered, 'Huge' Fractal Heap Objects
byte byte byte byte

Filtered Huge Object AddressO


Filtered Huge Object LengthL

Filter Mask

Filtered Huge Object Memory SizeL


Field Name Description
Filtered Huge Object Address

The address of the filtered huge object in the file.

Filtered Huge Object Length

The length of the filtered huge object in the file.

Filter Mask

A 32-bit bitfield indicating which filters have been skipped for this chunk. Each filter has an index number in the pipeline (starting at 0, with the first filter to apply) and if that filter is skipped, the bit corresponding to its index is set.

Filtered Huge Object Memory Size

The size of the de-filtered huge object in memory.


Version 2 B-tree, Type 5 Record Layout - Link Name for Indexed Group
byte byte byte byte
Hash of Name
ID (bytes 1-4)
ID (bytes 5-7)

Field Name Description
Hash

This field is hash value of the name for the link. The hash value is the Jenkins' lookup3 checksum algorithm applied to the link's name.

ID

This is a 7-byte sequence of bytes and is the heap ID for the link record in the group's fractal heap.


Version 2 B-tree, Type 6 Record Layout - Creation Order for Indexed Group
byte byte byte byte

Creation Order (8 bytes)

ID (bytes 1-4)
ID (bytes 5-7)

Field Name Description
Creation Order

This field is the creation order value for the link.

ID

This is a 7-byte sequence of bytes and is the heap ID for the link record in the group's fractal heap.


Version 2 B-tree, Type 7 Record Layout - Shared Object Header Messages (Sub-Type 0 - Message in Heap)
byte byte byte byte
Message Location This space inserted only to align table nicely
Hash
Reference Count

Heap ID (8 bytes)


Field Name Description
Message Location

This field Indicates the location where the message is stored:
Value Description
0 Shared message is stored in shared message index heap.
1 Shared message is stored in object header.

Hash

This field is hash value of the shared message. The hash value is the Jenkins' lookup3 checksum algorithm applied to the shared message.

Reference Count

The number of objects which reference this message.

Heap ID

This is a 8-byte sequence of bytes and is the heap ID for the shared message in the shared message index's fractal heap.


Version 2 B-tree, Type 7 Record Layout - Shared Object Header Messages (Sub-Type 1 - Message in Object Header)
byte byte byte byte
Message Location This space inserted only to align table nicely
Hash
Reserved (zero) Message Type Object Header Index

Object Header AddressO


Field Name Description
Message Location

This field Indicates the location where the message is stored:
Value Description
0 Shared message is stored in shared message index heap.
1 Shared message is stored in object header.

Hash

This field is hash value of the shared message. The hash value is the Jenkins' lookup3 checksum algorithm applied to the shared message.

Message Type

The object header message type of the shared message.

Object Header Index

This field indicates that the shared message is the n'th message of its type in the specified object header.

Object Header Address

The address of the object header containing the shared message.


Version 2 B-tree, Type 8 Record Layout - Attribute Name for Indexed Attributes
byte byte byte byte

Heap ID (8 bytes)

Message Flags This space inserted only to align table nicely
Creation Order
Hash of Name

Field Name Description
Heap ID

This is a 8-byte sequence of bytes and is the heap ID for the attribute in the object's attribute fractal heap.

Message Flags

The object header message flags for the attribute message.

Creation Order

This field is the creation order value for the attribute.

Hash

This field is hash value of the name for the attribute. The hash value is the Jenkins' lookup3 checksum algorithm applied to the attribute's name.


Version 2 B-tree, Type 9 Record Layout- Creation Order for Indexed Attributes
byte byte byte byte

Heap ID (8 bytes)

Message Flags This space inserted only to align table nicely
Creation Order

Field Name Description
Heap ID

This is a 8-byte sequence of bytes and is the heap ID for the attribute in the object's attribute fractal heap.

Message Flags

The object header message flags for the attribute message.

Creation Order

This field is the creation order value for the attribute.

Disk Format: Level 1B - Group Symbol Table Nodes

A group is an object internal to the file that allows arbitrary nesting of objects within the file (including other groups). A group maps a set of link names in the group to a set of relative file addresses of objects in the file. Certain metadata for an object to which the group points can be cached in the group's symbol table entry in addition to being in the object's header.

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

One implementation of a group is a collection of symbol table nodes indexed by a B-link tree. Each symbol table node contains entries for one or more links. If an attempt is made to add a link 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 (A Leaf of a B-link tree)
byte byte byte byte
Signature
Version Number Reserved (zero) Number of Symbols


Group Entries



Field Name Description
Signature

The ASCII character string "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 Number

The version number for the symbol table node. This document describes version 1. (There is no version '0' of the symbol table node)

Number of Entries

Although all symbol table nodes have the same length, most contain fewer than the maximum possible number of link 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 Entries

Each link has an entry in the symbol table node. The format of the entry is described below. There are 2K entries in each group node, where K is the "Group Leaf Node K" value from the superblock.

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 stored objects. Toward that design goal, the symbol table entries include space for caching certain constant metadata from the object header.

Symbol Table Entry
byte byte byte byte

Link Name OffsetO


Object Header AddressO

Cache Type
Reserved (zero)


Scratch-pad Space (16 bytes)


(Items marked with an ‘O’ the above table are
of the size specified in “Size of Offsets.”)

Field Name Description
Link Name Offset

This is the byte offset into the group's local heap for the name of the link. The name is null terminated.

Object Header Address

Every object has an object header which serves as a permanent location for the object's metadata. In addition to appearing in the object header, some of the object's metadata 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:
Type: Description:
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 Group object header metadata is cached in the scratch-pad space. This implies that the symbol table 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.

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 metadata about an object represented in the scratch-pad space is duplicated in the object header for that object.

Furthermore, no data is cached in the group entry scratch-pad space if the object header for the object has a link count greater than one.

Format of the Scratch-pad Space

The symbol table 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 metadata for another object header in the following format:

Object Header Scratch-pad Format
byte byte byte byte

Address of B-treeO


Address of Name HeapO

(Items marked with an ‘O’ the above table are
of the size specified in “Size of Offsets.”)

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 group's symbol names.

If the Cache Type field contains the value two (2), then the scratch-pad space contains cached metadata for a 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 local heap is a collection of small pieces of data that are particular to a single object in the HDF5 file. 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. For example, a group stores addresses of objects in symbol table nodes with the names of links stored in the group's local heap.


Local Heap
byte byte byte byte
Signature
Version Reserved (zero)

Data Segment SizeL


Offset to Head of Free-listL


Address of Data SegmentO

(Items marked with an ‘L’ the above table are
of the size specified in “Size of Lengths.”)
(Items marked with an ‘O’ the above table are
of the size specified in “Size of Offsets.”)

Field Name Description
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.

Version

Each local heap has its own version number so that new heaps can be added to old files. This document describes version zero (0) of the local heap.

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 objects stored in the heap. The extra unused space in the heap 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 the undefined address if there is no free block). The free block contains "Size of Lengths" bytes that are the offset of the next free block (or the value '1' if this is the last free block) followed by "Size of Lengths" bytes that store the size of this free block. The size of the free block includes the space used to store the offset of the next free block and the size of the current block, making the minimum size of a free block 2 * "Size of Lengths".

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 a local 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 object references will have a global heap object for each reference. Reading the entire set of object references should result in a few large I/O requests instead of one small I/O request for each reference.
  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 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, addressing goal A.

When a global heap object is deleted from a collection (which occurs when its reference count falls to zero), objects located after the deleted object in the collection are packed down toward the beginning of the collection and the collection's global heap object 0 is created (if possible) or its size is increased to account for the recently freed space. There are no gaps between objects in each collection, with the possible exception of the final space in the collection, if it is not large enough to hold the header for the collection's global heap object 0. These features address goal C.

The HDF5 library creates global heap collections as needed, so there may be multiple collections throughout the file. The set of all of them is abstractly called the "global heap", although they don't actually link to each other, and there is no global place in the file where you can discover all of the collections. The collections are found simply by finding a reference to one through another object in the file. For example, data of variable-length datatype elements is stored in the global heap and is accessed via a global heap ID. The format for global heap IDs is described at the end of this section.


A Global Heap Collection
byte byte byte byte
Signature
Version Reserved (zero)

Collection SizeL


Global Heap Object 1


Global Heap Object 2


...


Global Heap Object N


Global Heap Object 0 (free space)


Field Name Description
Signature

The ASCII character string "GCOL" is used to indicate the beginning of a collection. This gives file consistency checking utilities a better chance of reconstructing a damaged file.

Version

Each collection has its own version number so that new collections can be added to old files. This document describes version one (1) of the collections (there is no version zero (0)).

Collection 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. This allows for 127 16-byte heap objects plus their overhead (the collection header of 16 bytes and the 16 bytes of information about each heap object).

Global Heap Object 1 through N

The objects are stored in any order with no intervening unused space.

Global Heap Object 0

Global Heap 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
Heap Object Index Reference Count
Reserved (zero)

Object SizeL


Object Data


Field Name Description
Heap Object Index

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 object data stored for the object. The actual storage space allocated for the object data 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.

(Items marked with an ‘O’ in the above tables are
of the size specified in “Size of Offsets.”)
(Items marked with an ‘L’ the above tables are
of the size specified in “Size of Lengths.”)

The format for the ID used to locate an object in the global heap is described here:

Global Heap ID
byte byte byte byte

Collection AddressO

Object Index

Field Name Description
Collection Address

This field is the address of the global heap collection where the data object is stored.

ID

This field is the index of the data object within the global heap collection.


Disk Format: Level 1F - Fractal Heap

Each fractal heap consists of a header and zero or more direct and indirect blocks (described below). The header contains general information as well as initialization parameters for the doubling table. The Root Block Address in the header points to the first direct or indirect block in the heap.

Fractal heaps are based on a data structure called a doubling table. A doubling table provides a mechanism for quickly extending an array-like data structure that minimizes the number of empty blocks in the heap, while retaining very fast lookup of any element within the array. More information on fractal heaps and doubling tables can be found in the RFC “Private Heaps in HDF5.”

The fractal heap implements the doubling table structure with indirect and direct blocks. Indirect blocks in the heap do not actually contain data for objects in the heap, their "size" is abstract - they represent the indexing structure for locating the direct blocks in the doubling table. Direct blocks contain the actual data for objects stored in the heap.

All indirect blocks have a constant number of block entries in each row, called the width of the doubling table (stored in the heap header). The number of rows for each indirect block in the heap is determined by the size of the block that the indirect block represents in the doubling table (calculation of this is shown below) and is constant, except for the "root" indirect block, which expands and shrinks its number of rows as needed.

Blocks in the first two rows of an indirect block are Starting Block Size number of bytes in size, and the blocks in each subsequent row are twice the size of the blocks in the previous row (i.e. blocks in the third row are twice the Starting Block Size, blocks in the fourth row are four times the Starting Block Size, etc.). Entries for blocks up to the Maximum Direct Block Size point to direct blocks and entries for blocks greater than that size point to further indirect blocks (which have their own entries for direct and indirect blocks, etc).

The number of rows of blocks, nrows, in an indirect block of size iblock_size is given by the following expression:

nrows = (log2(iblock_size) - log2(<Starting Block Size> * <Width>)) + 1

The maximum number of rows of direct blocks, max_dblock_rows, in any indirect block of a fractal heap is given by the following expression:

max_dblock_rows = (log2(<Max. Direct Block Size>) - log2(<Starting Block Size>)) + 2

Using the computed values for nrows and max_dblock_rows, along with the Width of the doubling table, the number of direct and indirect block entries (K and N in the indirect block description, below) in an indirect block can be computed:

K = MIN(nrows, max_dblock_rows) * Width

If nrows is less than or equal to max_dblock_rows, N is 0. Otherwise, N is simply computed:

N = K - (max_dblock_rows * Width)

The size indirect blocks on disk is determined by the number of rows in the indirect block (computed above). The size of direct blocks on disk is exactly the size of the block in the doubling table.


Fractal Heap Header
byte byte byte byte
Signature
Version This space inserted only to align table nicely
Heap ID Length I/O Filters' Encoded Length
Flags This space inserted only to align table nicely
Maximum Size of Managed Objects

Next Huge Object IDL


v2 B-tree Address of Huge ObjectsO


Amount of Free Space in Managed BlocksL


Address of Managed Block Free Space ManagerO


Amount of Managed Space in HeapL


Amount of Allocated Managed Space in HeapL


Offset of Direct Block Allocation Iterator in Managed SpaceL


Number of Managed Objects in HeapL


Size of Huge Objects in HeapL


Number of Huge Objects in HeapL


Size of Tiny Objects in HeapL


Number of Tiny Objects in HeapL

Table Width This space inserted only to align table nicely

Starting Block SizeL


Maximum Direct Block SizeL

Maximum Heap Size Starting # of Rows in Root Indirect Block

Address of Root BlockO

Current # of Rows in Root Indirect Block This space inserted only to align table nicely

Size of Filtered Root Direct Block (optional)L

I/O Filter Mask (optional)
I/O Filter Information (optional, variable size)
Checksum

Field Name Description
Signature

The ASCII character string "FRHP" is used to indicate the beginning of a fractal heap header. This gives file consistency checking utilities a better chance of reconstructing a damaged file.

Version

This document describes version 0.

Heap ID Length

This is the length in bytes of heap object IDs for this heap.

I/O Filters' Encoded Length

This is the size in bytes of the encoded I/O Filter Information.

Flags

This field is the heap status flag and is a bit-field indicating additional information about the fractal heap.
Bit(s) Description
0 If set, the ID value to use for huge object has wrapped around. If the value for the Next Huge Object ID has wrapped around, each new huge object inserted into the heap will require a search for an ID value.
1 If set, the direct blocks in the heap are checksummed.
2-7 Reserved

Maximum Size of Managed Objects

This is the maximum size of managed objects allowed in the heap. Objects greater than this this are 'huge' objects and will be stored in the file directly, rather than in a direct block for the heap.

Next Huge Object ID

This is the next ID value to use for a huge object in the heap.

v2 B-tree Address of Huge Objects

This is the address of the v2 B-tree used to track huge objects in the heap. The type of records stored in the v2 B-tree will be determined by whether the address & length of a huge object can fit into a heap ID (if yes, it's a "directly" accessed huge object) and whether there is a filter used on objects in the heap.

Amount of Free Space in Managed Blocks

This is the total amount of free space in managed direct blocks (in bytes).

Address of Managed Block Free Space Manager

This is the address of the Free-Space Manager for managed blocks.

Amount of Managed Space in Heap

This is the total amount of managed space in the heap (in bytes), essentially the upper bound of the heap's linear address space.

Amount of Allocated Managed Space in Heap

This is the total amount of managed space (in bytes) actually allocated in the heap. This can be less than the Amount of Managed Space in Heap field, if some direct blocks in the heap's linear address space are not allocated.

Offset of Direct Block Allocation Iterator in Managed Space

This is the linear heap offset where the next direct block should be allocated at (in bytes). This may be less than the Amount of Managed Space in Heap value because the heap's address space is increased by a "row" of direct blocks at a time, rather than by single direct block increments.

Number of Managed Objects in Heap

This is the number of managed objects in the heap.

Size of Huge Objects in Heap

This is the total size of huge objects in the heap (in bytes).

Number of Huge Objects in Heap

This is the number of huge objects in the heap.

Size of Tiny Objects in Heap

This is the total size of tiny objects that are packed in heap IDs (in bytes).

Number of Tiny Objects in Heap

This is the number of tiny objects that are packed in heap IDs.

Table Width

This is the number of columns in the doubling table for managed blocks. This value must be a power of two.

Starting Block Size

This is the starting block size to use in the doubling table for managed blocks (in bytes). This value must be a power of two.

Maximum Direct Block Size

This is the maximum size allowed for a managed direct block. Objects inserted into the heap that are larger than this value (less the # of bytes of direct block prefix/suffix) are stored as 'huge' objects. This value must be a power of two.

Maximum Heap Size

This is the maximum size of the heap's linear address space for managed objects (in bytes). The value stored is the log2 of the actual value, that is: the # of bits of the address space. 'Huge' and 'tiny' objects aren't counted in this value, since they don't store objects in the linear address space of the heap.

Starting # of Rows in Root Indirect Block

This is the starting number of rows for the root indirect block. A value of 0 indicates that the root indirect block will have the maximum number of rows needed to address the heap's Maximum Heap Size.

Address of Root Block

This is the address of the root block for the heap. It can be the undefined address if there is no data in the heap. It either points to a direct block (if the Current # of Rows in the Root Indirect Block value is 0), or an indirect block.

Current # of Rows in Root Indirect Block

This is the current number of rows in the root indirect block. A value of 0 indicates that Address of Root Block points to direct block instead of indirect block.

Size of Filtered Root Direct Block

This is the size of the root direct block, if filters are applied to heap objects (in bytes). This field is only stored in the header if the I/O Filters' Encoded Length is greater than 0.

I/O Filter Mask

This is the filter mask for the root direct block, if filters are applied to heap objects. This mask has the same format as that used for the filter mask in chunked raw data records in a v1 B-tree. This field is only stored in the header if the I/O Filters' Encoded Length is greater than 0.

I/O Filter Information

This is the I/O filter information encoding direct blocks and huge objects, if filters are applied to heap objects. This field is encoded as a Filter Pipeline message. The size of this field is determined by I/O Filters' Encoded Length.

Checksum

This is the checksum for the header.


Fractal Heap Direct Block
byte byte byte byte
Signature
Version This space inserted only to align table nicely

Heap Header AddressO

Block Offset (variable size)

Object Data (variable size)

Checksum (optional)

Field Name Description
Signature

The ASCII character string "FHDB" is used to indicate the beginning of a fractal heap direct block. This gives file consistency checking utilities a better chance of reconstructing a damaged file.

Version

This document describes version 0.

Heap Header Address

This is the address for the fractal heap header that this block belongs to. This field is principally used for file integrity checking.

Block Offset

This is the offset of the block within the fractal heap's address space (in bytes). The number of bytes used to encode this field is the Maximum Heap Size (in the heap's header) divided by 8 and rounded up to the next highest integer, for values that aren't a multiple of 8. This value is principally used for file integrity checking.

Object Data

This section of the direct block stores the actual data for objects in the heap. The size of this section is determined by the direct block's size, minus the size of the other fields stored in the direct block (the Signature, Version, etc., including the Checksum if it's present).

Checksum

This is the checksum for the direct block.

This field is only present if bit 1 of Flags in the heap's header is set.


Fractal Heap Indirect Block
byte byte byte byte
Signature
Version This space inserted only to align table nicely

Heap Header AddressO

Block Offset (variable size)

Child Direct Block #0 AddressO


Size of Filtered Direct Block #0 (optional) L

Filter Mask for Direct Block #0 (optional)

Child Direct Block #1 AddressO


Size of Filtered Direct Block #1 (optional)L

Filter Mask for Direct Block #1 (optional)
...

Child Direct Block #K-1 AddressO


Size of Filtered Direct Block #K-1 (optional)L

Filter Mask for Direct Block #K-1 (optional)

Child Indirect Block #0 AddressO


Child Indirect Block #1 AddressO

...

Child Indirect Block #N-1 AddressO

Checksum

Field Name Description
Signature

The ASCII character string "FHIB" is used to indicate the beginning of a fractal heap indirect block. This gives file consistency checking utilities a better chance of reconstructing a damaged file.

Version

This document describes version 0.

Heap Header Address

This is the address for the fractal heap header that this block belongs to. This field is principally used for file integrity checking.

Block Offset

This is the offset of the block within the fractal heap's address space (in bytes). The number of bytes used to encode this field is the Maximum Heap Size (in the heap's header) divided by 8 and rounded up to the next highest integer, for values that aren't a multiple of 8. This value is principally used for file integrity checking.

Child Direct Block #K Address

This field is the address of the child direct block. The size of the [uncompressed] direct block can be computed by its offset in the heap's linear address space.

Size of Filtered Direct Block #K

This is the size of the child direct block after passing through the I/O filters defined for this heap (in bytes). If no I/O filters are present for this heap, this field is not present.

Filter Mask for Direct Block #K

This is the I/O filter mask for the filtered direct block. This mask has the same format as that used for the filter mask in chunked raw data records in a v1 B-tree. If no I/O filters are present for this heap, this field is not present.

Child Indirect Block #N Address

This field is the address of the child indirect block. The size of the indirect block can be computed by its offset in the heap's linear address space.

Checksum

This is the checksum for the indirect block.

(Items marked with an ‘O’ in the above tables are
of the size specified in “Size of Offsets.”)
(Items marked with an ‘L’ the above table are
of the size specified in “Size of Lengths.”)

An object in the fractal heap is identified by means of a fractal heap ID, which encodes information to locate the object in the heap. Currently, the fractal heap stores an object in one of three ways, depending on the object's size:

Type Description
Tiny

When an object is small enough to be encoded in the heap ID, the object's data is embedded in the fractal heap ID itself. There are 2 sub-types for this type of object: normal and extended. The sub-type for tiny heap IDs depends on whether the heap ID is large enough to store objects greater than 16 bytes or not. If the heap ID length is 18 bytes or smaller, the "normal" tiny heap ID form is used. If the heap ID length is greater than 18 bytes in length, the "extented" form is used. See format description below for both sub-types.

Huge

When the size of an object is larger than Maximum Size of Managed Objects in the Fractal Heap Header, the object's data is stored on its own in the file and the object is tracked/indexed via a version 2 B-tree. All huge objects for a particular fractal heap use the same v2 B-tree. All huge objects for a particular fractal heap use the same format for their huge object IDs.

Depending on whether the IDs for a heap are large enough to hold the object's retrieval information and whether I/O pipeline filters are applied to the heap's objects, 4 sub-types are derived for for huge object IDs for this heap:

Sub-type Description
Directly accessed, non-filtered

The object's address and length are embedded in the fractal heap ID itself and the object is directly accessed from them. This allows the object to be accessed without resorting to the B-tree.

Directly accessed, filtered

The filtered object's address, length, filter mask and de-filtered size are embedded in the fractal heap ID itself and the object is accessed directly with them. This allows the object to be accessed without resorting to the B-tree.

Indirectly accessed, non-filtered

The object is located by using a B-tree key embedded in the fractal heap ID to retrieve the address and length from the version 2 B-tree for huge objects. Then, the address and length are used to access the object.

Indirectly accessed, filtered

The object is located by using a B-tree key embedded in the fractal heap ID to retrieve the filtered object's address, length, filter mask and de-filtered size from the version 2 B-ree for huge objects. Then, this information is used to access the object.

Managed

When the size of an object does not meet the above two conditions, the object is stored and managed via the direct and indirect blocks based on the doubling table.

The specific format for each type of heap ID is described below:


Fractal Heap ID for Tiny Objects (sub-type 1 - "Normal")
byte byte byte byte
Version, Type & Length This space inserted only to align table nicely

Data (variable size)

Field Name Description
Version, Type & Length

This is a bit field with the following definition:
Bit Description
6-7 The current version of ID format. This document describes version 0.
4-5 The ID type. Tiny objects have a value of 2.
0-3 The length of the tiny object. The value stored is one less than the actual length (since zero-length objects are not allowed to be stored in the heap). For example, an object of actual length 1 has an encoded length of 0, an object of actual length 2 has an encoded length of 1, etc.

Data

This is the data for the object.


Fractal Heap ID for Tiny Objects (sub-type 2 - "Extended")
byte byte byte byte
Version, Type & Length Extended Length This space inserted only to align table nicely
Data (variable size)

Field Name Description
Version, Type & Length

This is a bit field with the following definition:
Bit Description
6-7 The current version of ID format. This document describes version 0.
4-5 The ID type. Tiny objects have a value of 2.
0-3 These 4 bits, together with the next byte, form an unsigned 12-bit integer for holding the length of the object. These 4-bits are bits 8-11 of the 12-bit integer. See description for the Extended Length field below.

Extended Length

This byte, together with the 4 bits in the previous byte, forms an unsigned 12-bit integer for holding the length of the tiny object. These 8 bits are bits 0-7 of the 12-bit integer formed. The value stored is one less than the actual length (since zero-length objects are not allowed to be stored in the heap). For example, an object of actual length 1 has an encoded length of 0, an object of actual length 2 has an encoded length of 1, etc.

Data

This is the data for the object.


Fractal Heap ID for Huge Objects (sub-type 1 & 2): indirectly accessed, non-filtered/filtered
byte byte byte byte
Version & Type This space inserted only to align table nicely

v2 B-tree KeyL (variable size)


Field Name Description
Version & Type

This is a bit field with the following definition:
Bit Description
6-7 The current version of ID format. This document describes version 0.
4-5 The ID type. Huge objects have a value of 1.
0-3 Reserved.

v2 B-tree Key

This field is the B-tree key for retrieving the information from the version 2 B-tree for huge objects needed to access the object. See the description of v2 B-tree records sub-type 1 & 2 for a description of the fields. New key values are derived from Next Huge Object ID in the Fractal Heap Header.


Fractal Heap ID for Huge Objects (sub-type 3): directly accessed, non-filtered
byte byte byte byte
Version & Type This space inserted only to align table nicely

Address O


Length L


Field Name Description
Version & Type

This is a bit field with the following definition:
Bit Description
6-7 The current version of ID format. This document describes version 0.
4-5 The ID type. Huge objects have a value of 1.
0-3 Reserved.

Address

This field is the address of the object in the file.

Length

This field is the length of the object in the file.


Fractal Heap ID for Huge Objects (sub-type 4): directly accessed, filtered
byte byte byte byte
Version & Type This space inserted only to align table nicely

Address O


Length L

Filter Mask

De-filtered Size L


Field Name Description
Version & Type

This is a bit field with the following definition:
Bit Description
6-7 The current version of ID format. This document describes version 0.
4-5 The ID type. Huge objects have a value of 1.
0-3 Reserved.

Address

This field is the address of the filtered object in the file.

Length

This field is the length of the filtered object in the file.

Filter Mask

This field is the I/O pipeline filter mask for the filtered object in the file.

Filtered Size

This field is the size of the de-flitered object in the file.


Fractal Heap ID for Managed Objects
byte byte byte byte
Version & Type This space inserted only to align table nicely
Offset (variable size)
Length (variable size)

Field Name Description
Version & Type

This is a bit field with the following definition:
Bit Description
6-7 The current version of ID format. This document describes version 0.
4-5 The ID type. Managed objects have a value of 0.
0-3 Reserved.

Offset

This field is the offset of the object in the heap. This field's size is the minimum number of bytes necessary to encode the Maximum Heap Size value (from the Fractal Heap Header). For example, if the value of the Maximum Heap Size is less than 256 bytes, this field is 1 byte in length, a Maximum Heap Size of of 256-65535 bytes uses a 2 byte length, etc.

Length

This field is the length of the object in the heap. It is determined by taking the minimum value of Maximum Direct Block Size and Maximum Size of Managed Objects in the Fractal Heap Header. Again, the minimum number of bytes needed to encode that value is used for the size of this field.


Disk Format: Level 1G - Free-Space Manager

Free-space managers are used to describe space within a heap or the entire HDF5 file that is not currently used for that heap or file.

The superblock contains a pointer to a free-space managers for the whole file, but that pointer is currently required to be the undefined address.

The free-space manager header contains metadata information about the space being tracked, along with the address of the list of free space sections which actually describes the free space. The header records information about free-space sections being tracked, creation parameters for handling free-space sections of a client, and section information used to locate the collection of free-space sections.

The free-space section list stores a collection of free-space sections that is specific to each client of the free-space manager. For example, the fractal heap is a client of the free space manager and uses it to track unused space within the heap. There are 4 types of section records for the fractal heap, each of which has its own format, listed below.


Free-Space Manager Header
byte byte byte byte
Signature
Version Client ID This space inserted only to align table nicely

Total Space TrackedL


Total Number of SectionsL


Number of Serialized SectionsL


Number of Un-Serialized SectionsL

Number of Section Classes This space inserted only to align table nicely
Shrink Percent Expand Percent
Size of Address Space This space inserted only to align table nicely

Maximum Section Size L


Address of Serialized Section ListO


Size of Serialized Section List UsedL


Allocated Size of Serialized Section ListL

Checksum

Field Name Description
Signature

The ASCII character string "FSHD" is used to indicate the beginning of the Free-Space Manager Header. This gives file consistency checking utilities a better chance of reconstructing a damaged file.

Version

This is the version number for the Free-Space Manager Header and this document describes version 0.

Client ID

This is the client ID for identifying the user of this free-space manager:
ID Description
0 Fractal heap
1+ Reserved.

Total Space Tracked

This is the total amount of free space being tracked, in bytes.

Total Number of Sections

This is the total number of free-space sections being tracked.

Number of Serialized Sections

This is the number of serialized free-space sections being tracked.

Number of Un-Serialized Sections

This is the number of un-serialized free-space sections being managed. Un-serialized sections are created by the free-space client when the list of sections is read in.

Number of Section Classes

This is the number of section classes handled by this free space manager for the free-space client.

Shrink Percent

This is the percent of current size to shrink the allocated serialized free-space section list.

Expand Percent

This is the percent of current size to expand the allocated serialized free-space section list.

Size of Address Space

This is the size of the address space that free-space sections are within. This is stored as the log2 of the actual value (i.e. the number of bits required to store values within that address space).

Maximum Section Size

This is the maximum size of a section to be tracked.

Address of Serialized Section List

This is the address where the serialized free-space section list is stored.

Size of Serialized Section List Used

This is the size of the serialized free-space section list used (in bytes). This value must be less than or equal to the allocated size of serialized section list, below.

Allocated Size of Serialized Section List

This is the size of serialized free-space section list actually allocated (in bytes).

Checksum

This is the checksum for the free-space manager header.


The free-space sections being managed are stored in a free-space section list, described below. The sections in the free-space section list are stored in the following way: a count of the number of sections describing a particular size of free space and the size of the free-space desribed (in bytes), followed by a list of section description records; then another section count & size, followed by the list of section descriptions for that size; etc.


Free-Space Section List
byte byte byte byte
Signature
Version This space inserted only to align table nicely

Free-Space Manager Header AddressO

Number of Section Records in Set #0 (variable size)
Size of Free-Space Section Described in Record Set #0 (variable size)
Record Set #0 Section Record #0 Offset(variable size)
Record Set #0 Section Record #0 Type This space inserted only to align table nicely
Record Set #0 Section Record #0 Data (variable size)
...
Record Set #0 Section Record #K-1 Offset(variable size)
Record Set #0 Section Record #K-1 Type This space inserted only to align table nicely
Record Set #0 Section Record #K-1 Data (variable size)
Number of Section Records in Set #1 (variable size)
Size of Free-Space Section Described in Record Set #1 (variable size)
Record Set #1 Section Record #0 Offset(variable size)
Record Set #1 Section Record #0 Type This space inserted only to align table nicely
Record Set #1 Section Record #0 Data (variable size)
...
Record Set #1 Section Record #K-1 Offset(variable size)
Record Set #1 Section Record #K-1 Type This space inserted only to align table nicely
Record Set #1 Section Record #K-1 Data (variable size)
...
...
Number of Section Records in Set #N-1 (variable size)
Size of Free-Space Section Described in Record Set #N-1 (variable size)
Record Set #N-1 Section Record #0 Offset(variable size)
Record Set #N-1 Section Record #0 Type This space inserted only to align table nicely
Record Set #N-1 Section Record #0 Data (variable size)
...
Record Set #N-1 Section Record #K-1 Offset(variable size)
Record Set #N-1 Section Record #K-1 Type This space inserted only to align table nicely
Record Set #N-1 Section Record #K-1 Data (variable size)
Checksum

Field Name Description
Signature

The ASCII character string "FSSE" is used to indicate the beginning of the Free-Space Section Information. This gives file consistency checking utilities a better chance of reconstructing a damaged file.

Version

This is the version number for the Free-Space Section List and this document describes version 0.

Free-Space Manager Header Address

This is the address of the Free-Space Manager Header. This field is principally used for file integrity checking.

Number of Section Records for Set #N

This is the number of free-space section records for set #N. The length of this field is the minimum number of bytes needed to store the number of serialized sections (from the free-space manager header).

The number of sets of free-space section records is determined by the size of serialized section list in the free-space manager header.

Section Size for Record Set #N

This is the size (in bytes) of the free-space section described for all the section records in set #N.

The length of this field is the minimum number of bytes needed to store the maximum section size (from the free-space manager header).

Record Set #N Section #K Offset

This is the offset (in bytes) of the free-space section within the client for the free-space manager.

The length of this field is the minimum number of bytes needed to store the size of address space (from the free-space manager header).

Record Set #N Section #K Type

This is the type of the section record, used to decode the record set #N section #K data information. Currently defined record types are:
Type Description
0 Fractal heap "single" section
1 Fractal heap "first row" section
2 Fractal heap "normal row" section
3 Fractal heap "indirect" section
4+ Reserved.

Record Set #N Section #K Data

This is the section-type specific information for each record in the record set, described below.

Checksum

This is the checksum for the Free-Space Section List.

(Items marked with an ‘O’ in the above tables are
of the size specified in “Size of Offsets.”)
(Items marked with an ‘L’ the above tables are
of the size specified in “Size of Lengths.”)

The section-type specific data for each free-space section record is described below:


Fractal Heap "Single" Section Data Record
No additional record data stored

Fractal Heap "First Row" Section Data Record
Same format as "indirect" section data

Fractal Heap "Normal Row" Section Data Record
No additional record data stored

Fractal Heap "Indirect" Section Data Record
byte byte byte byte
Fractal Heap Indirect Block Offset (variable size)
Block Start Row Block Start Column
Number of Blocks This space inserted only to align table nicely

Field Name Description
Fractal Heap Block Offset

The offset of the indirect block in the fractal heap's address space containing the empty blocks.

The number of bytes used to encode this field is the minimum number of bytes needed to encode values for the Maximum Heap Size (in the fractal heap's header).

Block Start Row

This is the row that the empty blocks start in.

Block Start Column

This is the column that the empty blocks start in.

Number of Blocks

This is the number of empty blocks covered by the section.


Disk Format: Level 1H - Shared Object Header Message Table

The shared object header message table is used to locate object header messages that are shared between two or more object headers in the file. Shared object header messages are stored and indexed in the file in one of two ways: indexed sequentially in a shared header message list or indexed with a v2 B-tree. The shared messages themselves are either stored in a fractal heap (when two or more objects share the message), or remain in an object's header (when only one object uses the message currently, but the message can be shared in the future).

The shared object header message table contains a list of shared message index headers. Each index header records information about the version of the index format, the index storage type, flags for the message types indexed, the number of messages in the index, the address where the index resides, and the fractal heap address if shared messages are stored there.

Each index can be either a list or a v2 B-tree and may transition between those two forms as the number of messages in the index varies. Each shared message record contains information used to locate the shared message from either a fractal heap or an object header. The types of messages that can be shared are: Dataspace, Datatype, Fill Value, Filter Pipeline and Attribute.

The shared object header message table is pointed to from a shared message table message in the superblock extension for a file. This message stores the version of the table format, along with the number of index headers in the table.


Shared Object Header Message Table
byte byte byte byte
Signature
Version for index #0 Index Type for index #0 Message Type Flags for index #0
Minimum Message Size for index #0
List Cutoff for index #0 v2 B-tree Cutoff for index #0
Number of Messages for index #0 This space inserted only to align table nicely

Index AddressO for index #0


Fractal Heap AddressO for index #0

...
...
Version for index #N-1 Index Type for index #N-1 Message Type Flags for index #N-1
Minimum Message Size for index #N-1
List Cutoff for index #N-1 v2 B-tree Cutoff for index #N-1
Number of Messages for index #N-1 This space inserted only to align table nicely

Index AddressO for index #N-1


Fractal Heap AddressO for index #N-1

Checksum

Field Name Description
Signature

The ASCII character string "SMTB" is used to indicate the beginning of the Shared Object Header Message table. This gives file consistency checking utilities a better chance of reconstructing a damaged file.

Version for index #N

This is the version number for the list of shared object header message indexes and this document describes version 0.

Index Type for index #N

The type of index can be an unsorted list or a v2 B-tree.

Message Type Flags for index #N

This field indicates the type of messages tracked in the index, as follows:
Bits Description
0 If set, the index tracks Dataspace Messages.
1 If set, the message tracks Datatype Messages.
2 If set, the message tracks Fill Value Messages.
3 If set, the message tracks Filter Pipeline Messages.
4 If set, the message tracksn Attribute Messages.
5-15 Reserved (zero).

An index can track more than one type of message, but each type of message can only by in one index.

Minimum Message Size for index #N

This is the message size sharing threshold for the index. If the encoded size of the message is less than this value, the message is not shared.

List Cutoff for index #N

This is is the cutoff value for the indexing of messages to switch from a list to a v2 B-tree. If the number of messages is greater than this value, the index should be a v2 B-tree.

v2 B-tree Cutoff for index #N

This is is the cutoff value for the indexing of messages to switch from a v2 B-tree back to a list. If the number of messages is less than this value, the index should be a list.

Number of Messages for index #N

The number of shared messages being tracked for the index.

Index Address for index #N

This field is the address of the list or v2 B-tree where the index nodes reside.

Fractal Heap Address for index #N

This field is the address of the fractal heap if shared messages are stored there.

Checksum

This is the checksum for the table.

(Items marked with an ‘O’ in the above tables are
of the size specified in “Size of Offsets.”)

Shared messages are indexed either with a shared message record list, described below, or using a v2 B-tree (using record type 7). The number of records in the shared message record list is determined in the index's entry in the shared object header message table.


Shared Message Record List
byte byte byte byte
Signature
Shared Message Record #0
Shared Message Record #1
...
Shared Message Record #N-1
Checksum

Field Name Description
Signature

The ASCII character string "SMLI" is used to indicate the beginning of a list of index nodes. This gives file consistency checking utilities a better chance of reconstructing a damaged file.

Shared Message Record #N

The record for locating the shared message, either in the fractal heap for the index, or an object header (see format for index nodes below).

Checksum

This is the checksum for the list.


The record for each shared message in an index is stored in one of the following forms:


Shared Message Record, for messages stored in a fractal heap
byte byte byte byte
Message Location This space inserted only to align table nicely
Hash Value
Reference Count

Fractal Heap ID


Field Name Description
Message Location

This has a value of 0 indicating that the message is stored in the heap.

Hash Value

This is the hash value for the message.

Reference Count

This is the number of times the message is used in the file.

Fractal Heap ID

This is an 8-byte fractal heap ID for the message as stored in the fractal heap for the index.


Shared Message Record, for messages stored in an object header
byte byte byte byte
Message Location This space inserted only to align table nicely
Hash Value
Reserved Message Type Creation Index

Object Header AddressO


Field Name Description
Message Location

This has a value of 1 indicating that the message is stored in an object header.

Hash Value

This is the hash value for the message.

Message Type

This is the message type in the object header.

Creation Index

This is the creation index of the message within the object header.

Object Header Address

This is the address of the object header where the message is located.



Disk Format: Level 2 - Data Objects

Data objects contain the "real" user-visible 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 storing and accessing these data objects.

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

Disk Format: Level 2A - Data Object Headers

The header information of an object is designed to encompass all the information about an object, except for the data itself. This information includes the dataspace, datatype, 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. Information stored by user applications as attributes is also stored in the object's header. 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. The order of the messages in an object header is not significant.

Object headers are composed of a prefix and a set of messages. The prefix contains the information needed to interpret the messages and a small amount of metadata about the object, and the messages contain the majority of the metadata about the object.

Disk Format: Level 2A1 - Data Object Header Prefix

Version 1 Data Object Header Prefix

Header messages are aligned on 8-byte boundaries for version 1 object headers.


Version 1 Object Header
byte byte byte byte
Version Reserved (zero) Total Number of Header Messages
Object Reference Count
Object Header Size
Header Message Type #1 Size of Header Message Data #1
Header Message #1 Flags Reserved (zero)

Header Message Data #1

.
.
.
Header Message Type #n Size of Header Message Data #n
Header Message #n Flags Reserved (zero)

Header Message Data #n


Field Name Description
Version

This value is used to determine the format of the information in the object header. When the format of 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. This is version one (1) (there was no version zero (0)) of the object header.

Total Number of Header Messages

This value determines the total number of messages listed in object headers for this object. This value includes the messages in continuation messages for this object.

Object Reference Count

This value specifies the number of "hard links" to this object within the current file. References to the object from external files, "soft links" in this file and object references in this file are not tracked.

Object Header Size

This value specifies the number of bytes of header message data following this length field that contain object header messages for this object header. This value does not include the size of object header continuation blocks for this object elsewhere in the file.

Header Message #n Type

This value specifies the type of information included in the following header message data. The message types for header messages are defined in sections below.

Size of Header Message #n 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.

Header Message #n Flags

This is a bit field with the following definition:
Bit Description
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 shared and stored in another location than the object header. The Header Message Data field contains a Shared Message (described in the Data Object Header Messages section below) and the Size of Header Message Data field contains the size of that Shared Message.
2 If set, the message should not be shared.
3 If set, the HDF5 decoder should fail to open this object if it doesn't understand the message's type. (Normally, unknown messages should can be ignored by HDF5 decoders)
4 If set, the HDF5 decoder should set bit 5 of this message's flags (this bit-field) if it doesn't understand the message's type and the object is modified in any way. (Normally, unknown messages can just be ignored by HDF5 decoders)
5 If set, this object was modified by software that didn't understand this message. (Normally, unknown messages should just be ignored by HDF5 decoders) (Can be used to invalidate an index or a similar feature)
6 If set, this message is shareable.
7 Reserved

Header Message #n 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.

Version 2 Data Object Headers

Note that the "total number of messages" field has been dropped from the data object header prefix in this version. The number is messages in the data object header is just determined by the messages encountered in all the object header blocks.

Note also that the fields and messages in this version of data object headers have no alignment or padding bytes inserted - they are stored packed together.

Version 2 Object Header
byte byte byte byte
Signature
Version Flags This space inserted only to align table nicely
Access time (optional)
Modification Time (optional)
Change Time (optional)
Birth Time (optional)
Maximum # of compact attributes (optional) Minimum # of dense attributes (optional)
Size of Chunk #0 (variable size) This space inserted only to align table nicely
Header Message Type #1 Size of Header Message Data #1 Header Message #1 Flags
Header Message #1 Creation Order (optional) This space inserted only to align table nicely

Header Message Data #1

.
.
.
Header Message Type #n Size of Header Message Data #n Header Message #n Flags
Header Message #n Creation Order (optional) This space inserted only to align table nicely

Header Message Data #n

Gap (optional, variable size)
Checksum

Field Name Description
Signature

The ASCII character string "OHDR" is used to indicate the beginning of an object header. This gives file consistency checking utilities a better chance of reconstructing a damaged file.

Version

This field has a value of 2 indicating version 2 of the object header.

Flags

This field is a bit-field indicating additional information about the object header.
Bit(s) Description
0-1 This two bit field determines the size of the Size of Chunk #0 field. The values are:
Value Description
0 The Size of Chunk #0 field is 1 byte.
1 The Size of Chunk #0 field is 2 bytes.
2 The Size of Chunk #0 field is 4 bytes.
3 The Size of Chunk #0 field is 8 bytes.
2 If set, attribute creation order is tracked.
3 If set, attribute creation order is indexed.
4 If set, non-default attribute storage phase change values are stored.
5 If set, access, modification, change and birth times are stored.
6-7 Reserved

Access Time

This 32-bit value represents the number of seconds after the UNIX epoch when the object's raw data was last accessed (i.e. read or written).

This field is present if bit 5 of flags is set.

Modification Time

This 32-bit value represents the number of seconds after the UNIX epoch when the object's raw data was last modified (i.e. written).

This field is present if bit 5 of flags is set.

Change Time

This 32-bit value represents the number of seconds after the UNIX epoch when the object's metadata was last changed.

This field is present if bit 5 of flags is set.

Birth Time

This 32-bit value represents the number of seconds after the UNIX epoch when the object was created.

This field is present if bit 5 of flags is set.

Maximum # of compact attributes

This is the maximum number of attributes to store in the compact format before switching to the indexed format.

This field is present if bit 4 of flags is set.

Minimum # of dense attributes

This is the minimum number of attributes to store in the indexed format before switching to the compact format.

This field is present if bit 4 of flags is set.

Size of Chunk #0

This unsigned value specifies the number of bytes of header message data following this field that contain object header information.

This value does not include the size of object header continuation blocks for this object elsewhere in the file.

The length of this field varies depending on bits 0 and 1 of the flags field.

Header Message #n Type

Same format as version 1 of the object header, described above.

Size of Header Message #n 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 of messages in this version does not include any padding bytes.

Header Message #n Flags

Same format as version 1 of the object header, described above.

Header Message #n Creation Order

This field stores the order that a message of a given type was created in.

This field is present if bit 2 of flags is set.

Header Message #n Data

Same format as version 1 of the object header, described above.

Gap

A gap in an object header chunk is inferred by the end of the messages for the chunk before the beginning of the chunk's checksum. Gaps are always smaller than the size of an object header message prefix (message type + message size + message flags).

Gaps are formed when a message (typically an attribute message) in an earlier chunk is deleted and a message from a later chunk that doesn't quite fit into the free space is moved into the earlier chunk.

Checksum

This is the checksum for the object header chunk.

The header message types and the message data associated with them compose the critical "metadata" 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.


Disk Format: Level 2A2 - Data Object Header Messages

Data object header messages are small pieces of metadata that are stored in the data object header for each object in an HDF5 file. Data object header messages provide the metadata required to describe an object and its contents, as well as optional pieces of metadata that annotate the meaning or purpose of the object.

Data object header messages are either stored directly in the data object header for the object or are shared between multiple objects in the file. When a message is shared, a flag in the Message Flags indicates that the actual Message Data portion of that message is stored in another location (such as another data object header, or a heap in the file) and the Message Data field contains the information needed to locate the actual information for the message.

The format of shared message data is described here:

Shared Message (Version 1)
byte byte byte byte
Version Type Reserved (zero)
Reserved (zero)

AddressO


Field Name Description
Version

The version number is used when there are changes in the format of a shared object message and is described here:

Version Description
0 Never used.
1 Used by the library before version 1.6.1.
Type

The type of shared message location:
Value Description
0 Message stored in another object's header (a committed message).

Address

The address of the object header containing the message to be shared.


Shared Message (Version 2)
byte byte byte byte
Version Type This space inserted only to align table nicely

AddressO


Field Name Description
Version

The version number is used when there are changes in the format of a shared object message and is described here:

Version Description
2 Used by the library of version 1.6.1 and after.
Type

The type of shared message location:
Value Description
0 Message stored in another object's header (a committed message).

Address

The address of the object header containing the message to be shared.


Shared Message (Version 3)
byte byte byte byte
Version Type This space inserted only to align table nicely
Location (variable size)

Field Name Description
Version

The version number indicates changes in the format of shared object message and is described here:

Version Description
3 Used by the library of version 1.8 and after. In this version, the Type field can indicate that the message is stored in the fractal heap.
Type

The type of shared message location:
Value Description
0 Message is not shared and is not sharable..
1 Message stored in file's shared object header message heap (a shared message).
2 Message stored in another object's header (a committed message).
3 Message stored is not shared, but is sharable.

Location

This field contains either a Size of Offsets-bytes address of the object header containing the message to be shared, or an 8-byte fractal heap ID for the message in the file's shared object header message heap.

The following is a list of currently defined header messages:


Name: NIL

Header Message 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. [Possibly one which has been deleted for some reason.]

Format of Data: Unspecified.


Name: Dataspace

Header Message Type: 0x0001

Length: Varies according to the number of dimensions, as described in the following table.

Status: Required for dataset objects, may not be repeated.

Description: The dataspace message describes the number of dimensions (i.e. "rank") and size of each dimension that the data object has. This message is only used for datasets which have a simple, rectilinear, array-like layout; datasets requiring a more complex layout are not yet supported.

Format of Data:

Dataspace Message - Version 1
byte byte byte byte
Version Dimensionality Flags Reserved
Reserved

Dimension #1 SizeL

.
.
.

Dimension #n SizeL


Dimension #1 Maximum SizeL (optional)

.
.
.

Dimension #n Maximum SizeL (optional)


Permutation Index #1L (optional)

.
.
.

Permutation Index #nL (optional)

(Items marked with an ‘L’ the above table are
of the size specified in “Size of Lengths.”)

Field Name Description
Version

This value is used to determine the format of the 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. This document describes version one (1) (there was no version zero (0)).

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.

Dimension #n Size

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 #n Maximum Size

This value is the maximum size of the dimension of the data as stored in the file. This value may be the special "unlimited" size which indicates that the data may expand along this dimension indefinitely. If these values are not stored, the maximum size of each dimension is assumed to be the dimension's current size.

Permutation Index #n

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.

Version 2 of the dataspace message dropped the optional permutation index value support, as it was never implemented in the HDF5 library:

Dataspace Message - Version 2
byte byte byte byte
Version Dimensionality Flags Type

Dimension #1 SizeL

.
.
.

Dimension #n SizeL


Dimension #1 Maximum SizeL (optional)

.
.
.

Dimension #n Maximum SizeL (optional)

(Items marked with an ‘L’ the above table are
of the size specified in “Size of Lengths.”)

Field Name Description
Version

This value is used to determine the format of the Dataspace Message. This field should be '2' for version 2 format messages.

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.

Type

This field indicates the type of the dataspace:
Value Description
0 A scalar dataspace, i.e. a dataspace with a single, dimensionless element.
1 A simple dataspace, i.e. a dataspace with a a rank > 0 and an appropriate # of dimensions.
2 A null dataspace, i.e. a dataspace with no elements.

Dimension #n Size

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 #n Maximum Size

This value is the maximum size of the dimension of the data as stored in the file. This value may be the special "unlimited" size which indicates that the data may expand along this dimension indefinitely. If these values are not stored, the maximum size of each dimension is assumed to be the dimension's current size.


Name: Link Info

Header Message Type: 0x002

Length: varies

Status: Optional, may not be repeated.

Description:This message tracks variable information about the current state of the links for a "new style" group's behavior. Variable information will be stored in this message and constant information will be stored in the Group Info message.

Format of Data:

Link Info
byte byte byte byte
Version Flags This space inserted only to align table nicely

Maximum Creation Index (8 bytes, optional)


Fractal Heap AddressO


Address of v2 B-tree for Name IndexO


Address of v2 B-tree for Creation Order IndexO (optional)


Field Name Description
Version

The version number for this message. This document describes version 0.

Flags

This field determines various optional aspects of the link info message:

Bit Description
0 If set, creation order for the links is tracked.
1 If set, creation order for the links is indexed.
2-7 Reserved

Maximum Creation Index

This 64-bit value is the maximum creation order index value stored for a link in this group.

This field is present if bit 0 of flags is set.

Fractal Heap Address

This is the address of the fractal heap to store dense links. Each link stored in the fractal heap is stored as a Link Message.

If there are no links in the group, or the group's links are stored "compactly" (as object header messages), this value will be the undefined address.

Address of v2 B-tree for Name Index

This is the address of the version 2 B-tree to index names of links.

If there are no links in the group, or the group's links are stored "compactly" (as object header messages), this value will be the undefined address.

Address of v2 B-tree for Creation Order Index

This is the address of the version 2 B-tree to index creation order of links.

If there are no links in the group, or the group's links are stored "compactly" (as object header messages), this value will be the undefined address.

This field exists if bit 1 of flags is set.


Name: Datatype

Header Message Type: 0x0003

Length: variable

Status: Required for dataset or named datatype objects, may not be repeated.

Description: The datatype message defines the datatype for each element of a dataset or a common datatype for sharing between multiple datasets. A datatype can describe an atomic type like a fixed- or floating-point type or more complex types like a C struct (compound datatype), array (array datatype) or C++ vector (variable-length datatype).

Datatype messages that are part of a dataset object, do not describe how elements are related to one another, the dataspace message is used for that purpose. Datatype messages that are part of a named datatype message describe a common datatype that can be shared by multiple datasets in the file.

Format of Data:

Datatype Message
byte byte byte byte
Class and Version Class Bit Field, Bits 0-7 Class Bit Field, Bits 8-15 Class Bit Field, Bits 16-23
Size


Properties



Field Name Description
Class and Version

The version of the datatype message and the datatype's class information are packed together in this field. The version number is packed in the top 4 bits of the field and the class is contained in the bottom 4 bits.

The version number information is used for changes in the format of the datatype message and is described here:
Version Description
0 Never used
1 Used by early versions of the library to encode compound datatypes with explicit array fields. See the compound datatype description below for further details.
2 Used when an array datatype needs to be encoded.
3 Used when a VAX byte-ordered type needs to be encoded. Packs various other datatype classes more efficiently also.

The class of the datatype determines the format for the class bit field and properties portion of the datatype message, which are described below. The following classes are currently defined:
Value Description
0 Fixed-Point
1 Floating-Point
2 Time
3 String
4 Bitfield
5 Opaque
6 Compound
7 Reference
8 Enumerated
9 Variable-Length
10 Array

Class Bit Fields

The information in these bit fields is specific to each datatype class and is described below. All bits not defined for a datatype class are set to zero.

Size

The size of a datatype element in bytes.

Properties

This variable-sized sequence of bytes encodes information specific to each datatype class and is described for each class below. If there is no property information specified for a datatype class, the size of this field is zero bytes.

Class specific information for Fixed-Point Numbers (Class 0):

Fixed-Point Bit Field Description
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 bit and bit 2 is the hi_pad bit. 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).

Fixed-Point Property Description
Byte Byte Byte Byte
Bit Offset Bit Precision

Field Name Description
Bit Offset

The bit offset of the first significant bit of the fixed-point value within the datatype. The bit offset specifies the number of bits "to the right of" the value (which are set to the lo_pad bit value).

Bit Precision

The number of bits of precision of the fixed-point value within the datatype. This value, combined with the datatype element's size and the Bit Offset field specifies the number of bits "to the left of" the value (which are set to the hi_pad bit value).

Class specific information for Floating-Point Numbers (Class 1):

Floating-Point Bit Field Description
Bits Meaning
0, 6 Byte Order. These two non-contiguous bits specify the "endianess" of the bytes in the datatype element.
Bit 6 Bit 0 Description
0 0 Byte order is little-endian
0 1 Byte order is big-endian
1 0 Reserved
1 1 Byte order is VAX-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 end or between the sign bit, exponent, or mantissa, then the value of bit 1, 2, or 3 is copied to those locations.
4-5 Mantissa Normalization. This 2-bit bit-field specifies how the most significant bit of the mantissa is managed.
Value Description
0 No normalization
1 The most significant bit of the mantissa is always set (except for 0.0).
2 The most significant bit of the mantissa is not stored, but is implied to be set.
3 Reserved.
7 Reserved (zero).
8-15 Sign Location. This is the bit position of the sign bit. Bits are numbered with the least significant bit zero.
16-23 Reserved (zero).

Floating-Point Property Description
Byte Byte Byte Byte
Bit Offset Bit Precision
Exponent Location Exponent Size Mantissa Location Mantissa Size
Exponent Bias

Field Name Description
Bit Offset

The bit offset of the first significant bit of the floating-point value within the datatype. The bit offset specifies the number of bits "to the right of" the value.

Bit Precision

The number of bits of precision of the floating-point value within the datatype.

Exponent Location

The bit position of the exponent field. Bits are numbered with the least significant bit number zero.

Exponent Size

The size of the exponent field in bits.

Mantissa Location

The bit position of the mantissa field. Bits are numbered with the least significant bit number zero.

Mantissa Size

The size of the mantissa field in bits.

Exponent Bias

The bias of the exponent field.

Class specific information for Time (Class 2):

Time Bit Field Description
Bits Meaning
0 Byte Order. If zero, byte order is little-endian; otherwise, byte order is big endian.
1-23 Reserved (zero).

Time Property Description
Byte Byte
Bit Precision

Field Name Description
Bit Precision

The number of bits of precision of the time value.

Class specific information for Strings (Class 3):

String Bit Field Description
Bits Meaning
0-3 Padding type. This four-bit value determines the type of padding to use for the string. The values are:
Value Description
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
4-7 Character Set. The character set used to encode the string.
Value Description
0 ASCII character set encoding
1 UTF-8 character set encoding
2-15 Reserved
8-23 Reserved (zero).

There are no properties defined for the string class.

Class specific information for Bitfields (Class 4):

Bitfield Bit Field Description
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).

Bitfield Property Description
Byte Byte Byte Byte
Bit Offset Bit Precision

Field Name Description
Bit Offset

The bit offset of the first significant bit of the bitfield within the datatype. The bit offset specifies the number of bits "to the right of" the value.

Bit Precision

The number of bits of precision of the bitfield within the datatype.

Class specific information for Opaque (Class 5):

Opaque Bit Field Description
Bits Meaning
0-7 Length of ASCII tag in bytes.
8-23 Reserved (zero).

Opaque Property Description
Byte Byte Byte Byte

ASCII Tag


Field Name Description
ASCII Tag

This NUL-terminated string provides a description for the opaque type. It is NUL-padded to a multiple of 8 bytes.

Class specific information for Compound (Class 6):

Compound Bit Field Description
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.
16-23 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 (recursively) encoded datatype message.

Note that the property descriptions are different for different versions of the datatype version. Additionally note that the version 0 datatype encoding is deprecated and has been replaced with later encodings in versions of the HDF5 library from the 1.4 release onward.

Compound Properties Description for Datatype Version 1
Byte Byte Byte Byte

Name

Byte Offset of Member
Dimensionality Reserved (zero)
Dimension Permutation
Reserved (zero)
Dimension #1 Size (required)
Dimension #2 Size (required)
Dimension #3 Size (required)
Dimension #4 Size (required)

Member Type Message


Field Name Description
Name

This NUL-terminated string provides a description for the opaque type. It is NUL-padded to a multiple of 8 bytes.

Byte Offset of Member

This is the byte offset of the member within the datatype.

Dimensionality

If set to zero, this field indicates a scalar member. If set to a value greater than zero, this field indicates that the member is an array of values. For array members, the size of the array is indicated by the 'Size of Dimension n' field in this message.

Dimension Permutation

This field was intended to allow an array field to have it's dimensions permuted, but this was never implemented. This field should always be set to zero.

Dimension #n Size

This field is the size of a dimension of the array field 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.

Member Type Message

This field is a datatype message describing the datatype of the member.


Compound Properties Description for Datatype Version 2
Byte Byte Byte Byte

Name

Byte Offset of Member

Member Type Message


Field Name Description
Name

This NUL-terminated string provides a description for the opaque type. It is NUL-padded to a multiple of 8 bytes.

Byte Offset of Member

This is the byte offset of the member within the datatype.

Member Type Message

This field is a datatype message describing the datatype of the member.


Compound Properties Description for Datatype Version 3
Byte Byte Byte Byte

Name

Byte Offset of Member (variable size)

Member Type Message


Field Name Description
Name

This NUL-terminated string provides a description for the opaque type. It is not NUL-padded to a multiple of 8 bytes.

Byte Offset of Member

This is the byte offset of the member within the datatype. The field size is the minimum # of bytes necessary, based on size of the datatype element. For example, a datatype element size of less than 256 bytes uses a 1 byte length, a datatype element size of 256-65535 bytes uses a 2 byte length, etc.

Member Type Message

This field is a datatype message describing the datatype of the member.

Class specific information for Reference (Class 7):

Reference Bit Field Description
Bits Meaning
0-3 Type. This four-bit value contains the type of reference described. The values defined are:
Value Description
0 Object Reference: A reference to another object in this HDF5 file.
1 Dataset Region Reference: A reference to a region within a dataset in this HDF5 file.
2-15 Reserved
4-23 Reserved (zero).

There are no properties defined for the reference class.

Class specific information for Enumeration (Class 8):

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

Enumeration Property Description for Datatype Versions 1 & 2
Byte Byte Byte Byte

Base Type


Names


Values


Field Name Description
Base 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.


Enumeration Property Description for Datatype Version 3
Byte Byte Byte Byte

Base Type


Names


Values


Field Name Description
Base 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, not padded to 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.

Class specific information for Variable-Length (Class 9):

Variable-Length Bit Field Description
Bits Meaning
0-3 Type. This four-bit value contains the type of variable-length datatype described. The values defined are:
Value Description
0 Sequence: A variable-length sequence of any datatype. Variable-length sequences do not have padding or character set information.
1 String: A variable-length sequence of characters. Variable-length strings have padding and character set information.
2-15 Reserved
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:
Value Description
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
This value is set to zero for variable-length sequences.
8-11 Character Set. (variable-length string only) This four-bit value specifies the character set to be used for encoding the string:
Value Description
0 ASCII character set encoding
1 UTF-8 character set encoding
2-15 Reserved
This value is set to zero for variable-length sequences.
12-23 Reserved (zero).

Variable-Length Property Description
Byte Byte Byte Byte

Base Type


Field Name Description
Base Type

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

Class specific information for Array (Class 10):

There are no bit fields defined for the array class.

Note that the dimension information defined in the property for this datatype class is independent of dataspace information for a dataset. The dimension information here describes the dimensionality of the information within a data element (or a component of an element, if the array datatype is nested within another datatype) and the dataspace for a dataset describes the size and locations of the elements in a dataset.


Array Property Description for Datatype Version 2
Byte Byte Byte Byte
Dimensionality Reserved (zero)
Dimension #1 Size
.
.
.
Dimension #n Size
Permutation Index #1
.
.
.
Permutation Index #n

Base Type


Field Name Description
Dimensionality

This value is the number of dimensions that the array has.

Dimension #n Size

This value is the size of the dimension of the array 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.

Permutation Index #n

This value is the index permutation used to map each dimension from the canonical representation to an alternate axis for each dimension. Currently, dimension permutations are not supported and these indices should be set to the index position minus one (i.e. the first dimension should be set to 0, the second dimension should be set to 1, etc.)

Base Type

Each array type is based on some parent type. The information for that parent type is described recursively by this field.


Array Property Description for Datatype Version 3
Byte Byte Byte Byte
Dimensionality This space inserted only to align table nicely
Dimension #1 Size
.
.
.
Dimension #n Size

Base Type


Field Name Description
Dimensionality

This value is the number of dimensions that the array has.

Dimension #n Size

This value is the size of the dimension of the array 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.

Base Type

Each array type is based on some parent type. The information for that parent type is described recursively by this field.


Name: Data Storage - Fill Value (Old)

Header Message Type: 0x0004

Length: varies

Status: Optional, may not be repeated.

Description: The fill value message stores a single data value which is returned to the application when an uninitialized data element is read from a dataset. The fill value is interpreted with the same datatype as the dataset. If no fill value message is present then a fill value of all zero bytes is assumed.

This fill value message is deprecated in favor of the "new" fill value message (Message Type 0x0005) and is only written to the file for forward compatibility with versions of the HDF5 library before the 1.6.0 version. Additionally, it only appears for datasets with a user defined fill value (as opposed to the library default fill value or an explicitly set "undefined" fill value).

Format of Data:

Fill Value Message (Old)
byte byte byte byte
Size

Fill Value (optional, variable size)


Field Name Description
Size

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: Data Storage - Fill Value

Header Message Type: 0x0005

Length: varies

Status: Required for dataset objects, may not be repeated.

Description: The fill value message stores a single data value which is returned to the application when an uninitialized data element is read from a dataset. The fill value is interpreted with the same datatype as the dataset.

Format of Data:

Fill Value Message - Versions 1 & 2
byte byte byte byte
Version Space Allocation Time Fill Value Write Time Fill Value Defined
Size (optional)

Fill Value (optional, variable size)


Field Name Description
Version

The version number information is used for changes in the format of the fill value message and is described here:
Version Description
0 Never used
1 Initial version of this message.
2 In this version, the Size and Fill Value fields are only present if the Fill Value Defined field is set to 1.
3 This version packs the other fields in the message more efficiently than version 2.

Space Allocation Time

When the storage space for the dataset's raw data will be allocated. The allowed values are:
Value Description
0 Not used.
1 Early allocation. Storage space for the entire dataset should be allocated in the file when the dataset is created.
2 Late allocation. Storage space for the entire dataset should not be allocated until the dataset is written to.
3 Incremental allocation. Storage space for the dataset should not be allocated until the portion of the dataset is written to. This is currently used in conjunction with chunked data storage for datasets.

Fill Value Write Time

At the time that storage space for the dataset's raw data is allocated, this value indicates whether the fill value should be written to the raw data storage elements. The allowed values are:
Value Description
0 On allocation. The fill value is always written to the raw data storage when the storage space is allocated.
1 Never. The fill value should never be written to the raw data storage.
2 Fill value written if set by user. The fill value will be written to the raw data storage when the storage space is allocated only if the user explicitly set the fill value. If the fill value is the library default or is undefined, it will not be written to the raw data storage.

Fill Value Defined

This value indicates if a fill value is defined for this dataset. If this value is 0, the fill value is undefined. If this value is 1, a fill value is defined for this dataset. For version 2 or later of the fill value message, this value controls the presence of the Size and Fill Value fields.

Size

This is the size of the Fill Value field in bytes. This field is not present if the Version field is >1 and the Fill Value Defined field is set to 0.

Fill Value

The fill value. The bytes of the fill value are interpreted using the same datatype as for the dataset. This field is not present if the Version field is >1 and the Fill Value Defined field is set to 0.


Fill Value Message - Version 3
byte byte byte byte
Version Flags This space inserted only to align table nicely
Size (optional)

Fill Value (optional, variable size)


Field Name Description
Version

The version number information is used for changes in the format of the fill value message and is described here:
Version Description
0 Never used
1 Initial version of this message.
2 In this version, the Size and Fill Value fields are only present if the Fill Value Defined field is set to 1.
3 This version packs the other fields in the message more efficiently than version 2.

Flags

When the storage space for the dataset's raw data will be allocated. The allowed values are:
Bits Description
0-1 Space Allocation Time, with the same values as versions 1 and 2 of the message.
2-3 Fill Value Write Time, with the same values as versions 1 and 2 of the message.
4 Fill Value Undefined, indicating that the fill value has been marked as "undefined" for this dataset. Bits 4 and 5 can not both be set.
5 Fill Value Defined, with the same values as versions 1 and 2 of the message. Bits 4 and 5 can not both be set.
6-7 Reserved (zero).

Size

This is the size of the Fill Value field in bytes. This field is not present if the Version field is >1 and the Fill Value Defined flag is set to 0.

Fill Value

The fill value. The bytes of the fill value are interpreted using the same datatype as for the dataset. This field is not present if the Version field is >1 and the Fill Value Defined flag is set to 0.


Name: Link Message

Header Message Type: 0x0006

Length: varies

Status: Optional, may be repeated.

Description:This message encodes the information for a link in a group's object header, when the group is storing its links "compactly", or in the group's fractal heap, when the group is storing its links "densely".

A group is storing its links compactly when the fractal heap address in the Link Info Message is set to the "undefined address" value.

Format of Data:

Link Message
byte byte byte byte
Version Flags Link type (optional) This space inserted only to align table nicely

Creation Order (8 bytes, optional)

Link Name Character Set (optional) Length of Link Name (variable size) This space inserted only to align table nicely
Link Name (variable size)

Link Information (variable size)


Field Name Description
Version

The version number for this message. This document describes version 1.

Flags

This field contains information about the link and controls the presence of other fields below.
Bits Description
0-1 Determines the size of the Length of Link Name field.
Value Description
0 The size of the Length of Link Name field is 1 byte.
1 The size of the Length of Link Name field is 2 bytes.
2 The size of the Length of Link Name field is 4 bytes.
3 The size of the Length of Link Name field is 8 bytes.
2 Creation Order Field Present: if set, the Creation Order field is present. If not set, creation order information is not stored for links in this group.
3 Link Type Field Present: if set, the link is not a hard link and the Link Type field is present. If not set, the link is a hard link.
4 Link Name Character Set Field Present: if set, the link name is not represented with the ASCII character set and the Link Name Character Set field is present. If not set, the link name is represented with the ASCII character set.
5-7 Reserved (zero).

Link type

This is the link class type and can be one of the following values:
Value Description
0 A hard link (should never be stored in the file)
1 A soft link.
2-63 Reserved for future HDF5 internal use.
64 An external link.
65-255 Reserved, but available for user-defined link types.

This field is present if bit 3 of Flags is set.

Creation Order

This 64-bit value is an index of the link's creation time within the group. Values start at 0 when the group is created an increment by one for each link added to the group. Removing a link from a group does not change existing links' creation order field.

This field is present if bit 2 of Flags is set.

Link Name Character Set

This is the character set for encoding the link's name:
Value Description
0 ASCII character set encoding (this should never be stored in the file)
1 UTF-8 character set encoding

This field is present if bit 4 of Flags is set.

Length of link name

This is the length of the link's name. The size of this field depends on bits 0 and 1 of Flags.

Link name

This is the name of the link, non-NULL terminated.

Link information

The format of this field depends on the link type.

For hard links, the field is formatted as follows:
Size of Offsets bytes: The address of the object header for the object that the link points to.

For soft links, the field is formatted as follows:
Bytes 1-2: Length of soft link value.
Length of soft link value bytes: A non-NULL-terminated string storing the value of the soft link.

For external links, the field is formatted as follows:
Bytes 1-2: Length of external link value.
Length of external link value bytes: The first byte contains the version number in the upper 4 bits and flags in the lower 4 bits for the external link. Both version and flags are defined to be zero in this document. The remaining bytes consist of two NULL-terminated strings, with no padding between them. The first string is the name of the HDF5 file containing the object linked to and the second string is the full path to the object linked to, within the HDF5 file's group hierarchy.

For user-defined links, the field is formatted as follows:
Bytes 1-2: Length of user-defined data.
Length of used-defined link value bytes: The data supplied for the user-defined link type.


Name: Data Storage - External Data Files

Header Message Type: 0x0007

Length: varies

Status: Optional, may not be repeated.

Purpose and Description: The external data storage 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.

Format of Data:

External File List Message
byte byte byte byte
Version Reserved (zero)
Allocated Slots Used Slots

Heap AddressO


Slot Definitions...


Field Name Description
Version

The version number information is used for changes in the format of External Data Storage Message and is described here:
Version Description
0 Never used.
1 The current version used by the library.

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. (The current library simply uses the number of Used Slots for this message)

Used Slots

The number of initial slots which contains valid information.

Heap Address

This is the address of a local heap which contains the names for the external files (The local heap information can be found in Disk Format Level 1D in this document). 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.


External File List Slot
byte byte byte byte

Name Offset in Local HeapL


Offset in External Data FileL


Data Size in External FileL


Field Name Description
Name Offset in Local Heap

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).

Offset in External Data File

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.

Data Size in External File

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

Header Message 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 stored in the HDF5 file. Three types of data layout are supported:

  1. Contiguous: The array is stored in one contiguous area of the file. This layout requires that the size of the array be constant and does not permit chunking, compression, checksums, encryption, etc. The message stores the total storage size of the array. The offset of an element from the beginning of the storage area is computed as in a C array.
  2. Chunked: The array domain is regularly decomposed into chunks and each chunk is allocted and stored separately. This layout supports arbitrary element traversals, compression, encryption, and checksums, etc. (these features are described in other messages). The message stores the size of a chunk instead of the size of the entire array; the storage size of the entire array can be calculated by traversing the B-tree that stores the chunk addresses.
  3. Compact: The array is stored in one contiguous block, as part of this object header message.

Format of Data:

Data Layout Message (Versions 1 and 2)
byte byte byte byte
Version Dimensionality Layout Class Reserved (zero)
Reserved (zero)

Data AddressO (optional)

Dimension 0 Size
Dimension 1 Size
...
Dimension #n Size
Dataset Element Size (optional)
Compact Data Size (optional)

Compact Data... (variable size, optional)


Field Name Description
Version

The version number information is used for changes in the format of the data layout message and is described here:

Version Description
0 Never used.
1 Used by version 1.4 and before of the library to encode layout information. Data space is always allocated when the data set is created.
2 Used by version 1.6.x of the library to encode layout information. Data space is allocated only when it is necessary.
Dimensionality

An array has a fixed dimensionality. This field specifies the number of dimension size fields later in the message. The value stored for chunked storage is 1 greater than the number of dimensions in the dataset's dataspace (i.e. 2 is stored for a 1 dimensional dataset, etc).

Layout Class

The layout class specifies the type of storage for the data and how the other fields of the layout message are to be interpreted.
Value Description
0 Compact Storage
1 Contiguous Storage
2 Chunked Storage

Data Address

For contiguous storage, this is the address of the raw data in the file. For chunked storage this is the address of the v1 B-tree that is used to look up the addresses of the chunks. This field is not present for compact storage. If the version for this message is >1, the address may have the "undefined address" value, to indicate that storage has not yet been allocated for this array.

Dimension #n Size

For contiguous and compact storage the dimensions define the entire size of the array while for chunked storage they define the size of a single chunk. In all cases, they are in units of array elements (not bytes). The first dimension stored in the list of dimensions is the slowest changing dimension and the last dimension stored is the fastest changing dimension.

Dataset Element Size

The size of a dataset element, in bytes. This field is only present for chunked storage.

Compact Data Size

This field is only present for compact data storage. It contains the size of the raw data for the dataset array, in bytes.

Compact Data

This field is only present for compact data storage. It contains the raw data for the dataset array.


Version 3 of this message re-structured the format into specific properties that are required for each layout class.

Data Layout Message (Version 3)
byte byte byte byte
Version Layout Class This space inserted only to align table nicely

Properties (variable size)


Field Name Description
Version

The version number information is used for changes in the format of layout message and is described here:

Version Description
3 Used by the version 1.6.3 and later of the library to store properties for each layout class.
Layout Class

The layout class specifies the type of storage for the data and how the other fields of the layout message are to be interpreted.
Value Description
0 Compact Storage
1 Contiguous Storage
2 Chunked Storage

Properties

This variable-sized field encodes information specific to each layout class and is described below. If there is no property information specified for a layout class, the size of this field is zero bytes.


Class-specific information for compact layout (Class 0): (Note: The dimensionality information is in the Dataspace message)

Compact Storage Property Description
byte byte byte byte
Size This space inserted only to align table nicely

Raw Data... (variable size)


Field Name Description
Size

This field contains the size of the raw data for the dataset array, in bytes.

Raw Data

This field contains the raw data for the dataset array.


Class-specific information for contiguous layout (Class 1): (Note: The dimensionality information is in the Dataspace message)

Contiguous Storage Property Description
byte byte byte byte

AddressO


SizeL


Field Name Description
Address

This is the address of the raw data in the file. The address may have the "undefined address" value, to indicate that storage has not yet been allocated for this array.

Size

This field contains the size allocated to store the raw data, in bytes.


Class-specific information for chunked layout (Class 2):

Chunked Storage Property Description
byte byte byte byte
Dimensionality This space inserted only to align table nicely

AddressO

Dimension 0 Size
Dimension 1 Size
...
Dimension #n Size
Dataset Element Size

Field Name Description
Dimensionality

A chunk has a fixed dimensionality. This field specifies the number of dimension size fields later in the message.

Address

This is the address of the v1 B-tree that is used to look up the addresses of the chunks that actually store portions of the array data. The address may have the "undefined address" value, to indicate that storage has not yet been allocated for this array.

Dimension #n Size

These values define the dimension size of a single chunk, in units of array elements (not bytes). The first dimension stored in the list of dimensions is the slowest changing dimension and the last dimension stored is the fastest changing dimension.

Dataset Element Size

The size of a dataset element, in bytes.


Name: Bogus

Header Message Type: 0x0009

Length: 4 bytes

Status: For testing only, should never be stored in valid file

Purpose and Description: This message is used for testing the HDF5 library's response to an "unknown" message type and should never be encounted in a valid HDF5 file.

Format of Data:

Bogus Message
byte byte byte byte
Bogus Value

Field Name Description
Bogus Value

This value should always be: 0xdeadbeef.


Name: Group Info

Header Message Type: 0x000A

Length: varies

Status: Optional, may not be repeated.

Description: This message stores information for the constants defining a "new style" group's behavior. Constant information will be stored in this message and variable information will be stored in the Link Info message.

Note: the "estimated entry" information below is used when determining the size of the object header for the group when it is created.

Format of Data:

Group Info Message
byte byte byte byte
Version Flags Link Phase Change: Maximum Compact Value (optional)
Link Phase Change: Minimum Dense Value (optional) Estimated Number of Entries (optional)
Estimated Link Name Length of Entries (optional) This space inserted only to align table nicely

Field Name Description
Version

The version number for this message. This document describes version 0.

Flags

This is the group information flag with the following definition:

Bit Description
0 If set, link phase change values are stored.
1 If set, the estimated entry information is non-default and is stored.
2-7 Reserved
Link Phase Change: Maximum Compact Value

The is the maximum number of links to store "compactly" (in the group's object header).

This field is present if bit 0 of Flags is set.

Link Phase Change: Minimum Dense Value

This is the minimum number of links to store "densely" (in the group's fractal heap). The fractal heap's address is located in the Link Info message.

This field is present if bit 0 of Flags is set.

Estimated Number of Entries

This is the estimated number of entries in groups.

If this field is not present, the default value of 4 will be used for the estimated number of group entries.

This field is present if bit 1 of Flags is set.

Estimated Link Name Length of Entries

This is the estimated length of entry name.

If this field is not present, the default value of 8 will be used for the estimated link name length of group entries.

This field is present if bit 1 of Flags is set.


Name: Data Storage - Filter Pipeline

Header Message Type: 0x000B

Length: varies

Status: Optional, may not be repeated.

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

This message may be present in the object headers of both dataset and group objects. For datasets, it specifies the filters to apply to raw data. For groups, it specifies the filters to apply to the group's fractal heap. Currently, only datasets using chunked data storage use the filter pipeline on their raw data.

Format of Data:

Filter Pipeline Message - Version 1
byte byte byte byte
Version Number of Filters Reserved (zero)
Reserved (zero)

Filter Description List (variable size)


Field Name Description
Version

The version number for this message. This table describes version 1.

Number of Filters

The total number of filters described in this message. The maximum possible number of filters in a message is 32.

Filter Description List

A description of each filter. A filter description appears in the next table.


Filter Description
byte byte byte byte
Filter Identification Value Name Length
Flags Number Client Data Values

Name (variable size, optional)


Client Data (variable size, optional)

Padding (variable size, optional)

Field Name Description
Filter Identification Value

This value, often referred to as a filter identifier, is designed to be a unique identifier for the filter. Values from zero through 32,767 are reserved for filters supported by The HDF Group in the HDF5 library and for filters requested and supported by third parties. Filters supported by The HDF Group are documented immediately below. Information on 3rd-party filters can be found at The HDF Group’s Contributions page.

To request a filter identifier, please contact The HDF Group’s Help Desk at . You will be asked to provide the following information:

  1. Contact information for the developer requesting the new identifier
  2. A short description of the new filter
  3. Links to any relevant information, including licensing information

Values from 32768 to 65535 are reserved for non-distributed uses (for example, internal company usage) or for application usage when testing a feature. The HDF Group does not track or document the use of the filters with identifiers from this range.

The filters currently in library version 1.8.0 are listed below:
Identification Name Description
0 N/A Reserved
1 deflate GZIP deflate compression
2 shuffle Data element shuffling
3 fletcher32 Fletcher32 checksum
4 szip SZIP compression
5 nbit N-bit packing
6 scaleoffset Scale and offset encoded values

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 Description
0 If set then the filter is an optional filter. During output, if an optional filter fails it will be silently skipped in the pipeline.
1-15 Reserved (zero)
Number of Client Data Values

Each filter can store 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, padded to 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.


Filter Pipeline Message - Version 2
byte byte byte byte
Version Number of Filters This space inserted only to align table nicely

Filter Description List (variable size)


Field Name Description
Version

The version number for this message. This table describes version 2.

Number of Filters

The total number of filters described in this message. The maximum possible number of filters in a message is 32.

Filter Description List

A description of each filter. A filter description appears in the next table.


Filter Description
byte byte byte byte
Filter Identification Value Name Length (optional)
Flags Number Client Data Values

Name (variable size, optional)


Client Data (variable size, optional)


Field Name Description
Filter Identification Value

This value, often referred to as a filter identifier, is designed to be a unique identifier for the filter. Values from zero through 32,767 are reserved for filters supported by The HDF Group in the HDF5 library and for filters requested and supported by third parties. Filters supported by The HDF Group are documented immediately below. Information on 3rd-party filters can be found at The HDF Group’s Contributions page.

To request a filter identifier, please contact The HDF Group’s Help Desk at . You will be asked to provide the following information:

  1. Contact information for the developer requesting the new identifier
  2. A short description of the new filter
  3. Links to any relevant information, including licensing information

Values from 32768 to 65535 are reserved for non-distributed uses (for example, internal company usage) or for application usage when testing a feature. The HDF Group does not track or document the use of the filters with identifiers from this range.

The filters currently in library version 1.8.0 are listed below:
Identification Name Description
0 N/A Reserved
1 deflate GZIP deflate compression
2 shuffle Data element shuffling
3 fletcher32 Fletcher32 checksum
4 szip SZIP compression
5 nbit N-bit packing
6 scaleoffset Scale and offset encoded values

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.

Filters with IDs less than 256 (i.e. those that are defined in this format documentation) do not store the Name Length or Name fields.

Flags

The flags indicate certain properties for a filter. The bit values defined so far are:

Bit Description
0 If set then the filter is an optional filter. During output, if an optional filter fails it will be silently skipped in the pipeline.
1-15 Reserved (zero)
Number of Client Data Values

Each filter can store 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, not padded to a multiple of eight. This field contains a non-null-terminated, ASCII character string to serve as a comment/name for the filter.

Filters that are defined in this format documentation (deflate, shuffle, etc.) do not store the Name Length or Name fields.

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.


Name: Attribute

Header Message Type: 0x000C

Length: varies

Status: Optional, may be repeated.

Description: The Attribute message is used to store objects in the HDF5 file which are used as attributes, or “metadata” 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 should be relatively small (in other words, less than 64KB). They can be associated with any type of object which has an object header (groups, datasets, or committed (named) datatypes).

In 1.8.x versions of the library, attributes can be larger than 64KB. See the “Special Issues” section of the Attributes chapter in the HDF5 User's Guide for more information.

Note: Attributes on an object must have unique names (The HDF5 library currently enforces this by causing the creation of an attribute with a duplicate name to fail). Attributes on different objects may have the same name, however.

Format of Data:

Attribute Message (Version 1)
byte byte byte byte
Version Reserved (zero) Name Size
Datatype Size Dataspace Size

Name (variable size)


Datatype (variable size)


Dataspace (variable size)


Data (variable size)


Field Name Description
Version

The version number information is used for changes in the format of the attribute message and is described here:

Version Description
0 Never used.
1 Used by the library before version 1.6 to encode attribute message. This version does not support shared datatypes.
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.

Datatype Size

The length of the datatype description in the Datatype field below. Note that the Datatype field may contain additional padding not represented by this field.

Dataspace Size

The length of the dataspace description in the Dataspace field below. Note that the Dataspace 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.

Datatype

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.

Dataspace

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 bytes.


Attribute Message (Version 2)
byte byte byte byte
Version Flags Name Size
Datatype Size Dataspace Size

Name (variable size)


Datatype (variable size)


Dataspace (variable size)


Data (variable size)


Field Name Description
Version

The version number information is used for changes in the format of the attribute message and is described here:

Version Description
2 Used by the library of version 1.6.x and after to encode attribute messages. This version supports shared datatypes. The fields of name, datatype, and dataspace are not padded with additional bytes of zero.
Flags

This bit-field contains extra information about interpreting the attribute message:

Bit Description
0 If set, datatype is shared.
1 If set, dataspace is shared.
Name Size

The length of the attribute name in bytes including the null terminator.

Datatype Size

The length of the datatype description in the Datatype field below.

Dataspace Size

The length of the dataspace description in the Dataspace field below.

Name

The null-terminated attribute name. This field is not padded with additional bytes.

Datatype

The datatype description follows the same format as described for the datatype object header message.

If the Flag field indicates this attribute's datatype is shared, this field will contain a "shared message" encoding instead of the datatype encoding.

This field is not padded with additional bytes.

Dataspace

The dataspace description follows the same format as described for the dataspace object header message.

If the Flag field indicates this attribute's dataspace is shared, this field will contain a "shared message" encoding instead of the dataspace encoding.

This field is not padded with additional 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.


Attribute Message (Version 3)
byte byte byte byte
Version Flags Name Size
Datatype Size Dataspace Size
Name Character Set Encoding This space inserted only to align table nicely

Name (variable size)


Datatype (variable size)


Dataspace (variable size)


Data (variable size)


Field Name Description
Version

The version number information is used for changes in the format of the attribute message and is described here:

Version Description
3 Used by the library of version 1.8.x and after to encode attribute messages. This version supports attributes with non-ASCII names.
Flags

This bit-field contains extra information about interpreting the attribute message:

Bit Description
0 If set, datatype is shared.
1 If set, dataspace is shared.
Name Size

The length of the attribute name in bytes including the null terminator.

Datatype Size

The length of the datatype description in the Datatype field below.

Dataspace Size

The length of the dataspace description in the Dataspace field below.

Name Character Set Encoding

The character set encoding for the attribute's name:
Value Description
0 ASCII character set encoding
1 UTF-8 character set encoding

Name

The null-terminated attribute name. This field is not padded with additional bytes.

Datatype

The datatype description follows the same format as described for the datatype object header message.

If the Flag field indicates this attribute's datatype is shared, this field will contain a "shared message" encoding instead of the datatype encoding.

This field is not padded with additional bytes.

Dataspace

The dataspace description follows the same format as described for the dataspace object header message.

If the Flag field indicates this attribute's dataspace is shared, this field will contain a "shared message" encoding instead of the dataspace encoding.

This field is not padded with additional 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 Comment

Header Message Type: 0x000D

Length: varies

Status: Optional, may not be repeated.

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

Format of Data:

Name Message
byte byte byte byte

Comment (variable size)


Field Name Description
Name A null terminated ASCII character string.


Name: Object Modification Time (Old)

Header Message Type: 0x000E

Length: fixed

Status: Optional, may not be repeated.

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. All fields of this message should be interpreted as coordinated universal time (UTC).

This modification time message is deprecated in favor of the "new" Object Modification Time message and is no longer written to the file in versions of the HDF5 library after the 1.6.0 version.

Format of Data:

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.

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 Message Table

Header Message Type: 0x000F

Length: fixed

Status: Optional, may not be repeated.

Description: This message is used to locate the table of shared object header message (SOHM) indexes. Each index consists of information to find the shared messages from either the heap or object header. This message is only found in the superblock extension.

Format of Data:

Shared Message Table Message
byte byte byte byte
Version This space inserted only to align table nicely

Shared Object Header Message Table AddressO

Number of Indices This space inserted only to align table nicely

Field Name Description
Version

The version number for this message. This document describes version 0.

Shared Object Header Message Table Address

This field is the address of the master table for shared object header message indexes.

Number of Indices

This field is the number of indices in the master table.


Name: Object Header Continuation

Header Message Type: 0x0010

Length: fixed

Status: Optional, may be repeated.

Description: The object header continuation is the location in the file of a block containing more header messages for the current data object. This can be used when header blocks become too large or are likely to change over time.

Format of Data:

Object Header Continuation Message
byte byte byte byte

OffsetO


LengthL


Field Name Description
Offset

This value is the address in the file where the header continuation block is located.

Length

This value is the length in bytes of the header continuation block in the file.

The format of the header continuation block that this message points to depends on the version of the object header that the message is contained within.

Continuation blocks for version 1 object headers have no special formatting information, they are merely a list of object header message info sequences (type, size, flags, reserved bytes and data for each message sequence). See the description of Version 1 Data Object Header Prefix.

Continuation blocks for version 2 object headers do have special formatting information as described here (see also the description of Version 2 Data Object Header Prefix.):

Version 2 Object Header Continuation Block
byte byte byte byte
Signature
Header Message Type #1 Size of Header Message Data #1 Header Message #1 Flags
Header Message #1 Creation Order (optional) This space inserted only to align table nicely

Header Message Data #1

.
.
.
Header Message Type #n Size of Header Message Data #n Header Message #n Flags
Header Message #n Creation Order (optional) This space inserted only to align table nicely

Header Message Data #n

Gap (optional, variable size)
Checksum

Field Name Description
Signature

The ASCII character string "OCHK" is used to indicate the beginning of an object header continuation block. This gives file consistency checking utilities a better chance of reconstructing a damaged file.

Header Message #n Type

Same format as version 1 of the object header, described above.

Size of Header Message #n Data

Same format as version 1 of the object header, described above.

Header Message #n Flags

Same format as version 1 of the object header, described above.

Header Message #n Creation Order

This field stores the order that a message of a given type was created in.

This field is present if bit 2 of flags is set.

Header Message #n Data

Same format as version 1 of the object header, described above.

Gap

A gap in an object header chunk is inferred by the end of the messages for the chunk before the beginning of the chunk's checksum. Gaps are always smaller than the size of an object header message prefix (message type + message size + message flags).

Gaps are formed when a message (typically an attribute message) in an earlier chunk is deleted and a message from a later chunk that doesn't quite fit into the free space is moved into the earlier chunk.

Checksum

This is the checksum for the object header chunk.


Name: Symbol Table Message

Header Message Type: 0x0011

Length: fixed

Status: Required for "old style" groups, may not be repeated.

Description: Each "old style" group has a v1 B-tree and a local heap for storing symbol table entries, which are located with this message.

Format of data:

Symbol Table Message
byte byte byte byte

v1 B-tree AddressO


Local Heap AddressO


Field Name Description
v1 B-tree Address

This value is the address of the v1 B-tree containing the symbol table entries for the group.

Local Heap Address

This value is the address of the local heap containing the link names for the symbol table entries for the group.


Name: Object Modification Time

Header Message Type: 0x0012

Length: Fixed

Status: Optional, may not be repeated.

Description: The object modification time is a timestamp which indicates the time of 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.

Format of Data:

Modification Time Message
byte byte byte byte
Version Reserved (zero)
Seconds After UNIX Epoch

Field Name Description
Version

The version number is used for changes in the format of Object Modification Time and is described here:

Version Description
0 Never used.
1 Used by Version 1.6.1 and after of the library to encode time. In this version, the time is the seconds after Epoch.
Seconds After UNIX Epoch

A 32-bit unsigned integer value that stores the number of seconds since 0 hours, 0 minutes, 0 seconds, January 1, 1970, Coordinated Universal Time.


Name: B-tree 'K' Values Message

Header Message Type: 0x0013

Length: Fixed

Status: Optional, may not be repeated.

Description:This message retrieves non-default 'K' values for internal and leaf nodes of a group or indexed storage v1 B-trees. This message is only found in the superblock extension.

Format of Data:

B-tree 'K' Values Message
byte byte byte byte
Version Indexed Storage Internal Node K This space inserted only to align table nicely
Group Internal Node K Group Leaf Node K

Field Name Description
Version

The version number for this message. This document describes version 0.

Indexed Storage Internal Node K

This is the node 'K' value for each internal node of an indexed storage v1 B-tree. See the description of this field in version 0 and 1 of the superblock as well the section on v1 B-trees.

Group Internal Node K

This is the node 'K' value for each internal node of a group v1 B-tree. See the description of this field in version 0 and 1 of the superblock as well as the section on v1 B-trees.

Group Leaf Node K

This is the node 'K' value for each leaf node of a group v1 B-tree. See the description of this field in version 0 and 1 of the superblock as well as the section on v1 B-trees.


Name: Driver Info Message

Header Message Type: 0x0014

Length: varies

Status: Optional, may not be repeated.

Description: This message contains information needed by the file driver to reopen a file. This message is only found in the superblock extension: see the “Disk Format: Level 0C - Superblock Extension” section for more information. For more information on the fields in the driver info message, see the “Disk Format : Level 0B - File Driver Info” section; those who use the multi and family file drivers will find this section particularly helpful.

Format of Data:

Driver Info Message
byte byte byte byte
Version This space inserted only to align table nicely

Driver Identification
Driver Information Size This space inserted only to align table nicely


Driver Information (variable size)



Field Name Description
Version

The version number for this message. This document describes version 0.

Driver Identification

This is an eight-byte ASCII string without null termination which identifies the driver.

Driver Information Size

The size in bytes of the Driver Information field of this message.

Driver Information

Driver information is stored in a format defined by the file driver.


Name: Attribute Info Message

Header Message Type: 0x0015

Length: varies

Status: Optional, may not be repeated.

Description:This message stores information about the attributes on an object, such as the maximum creation index for the attributes created and the location of the attribute storage when the attributes are stored "densely".

Format of Data:

Attribute Info Message
byte byte byte byte
Version Flags Maximum Creation Index (optional)

Fractal Heap AddressO


Attribute Name v2 B-tree AddressO


Attribute Creation Order v2 B-tree AddressO (optional)


Field Name Description
Version

The version number for this message. This document describes version 0.

Flags

This is the attribute index information flag with the following definition:

Bit Description
0 If set, creation order for attributes is tracked.
1 If set, creation order for attributes is indexed.
2-7 Reserved

Maximum Creation Index

The is the maximum creation order index value for the attributes on the object.

This field is present if bit 0 of Flags is set.

Fractal Heap Address

This is the address of the fractal heap to store dense attributes.

Attribute Name v2 B-tree Address

This is the address of the version 2 B-tree to index the names of densely stored attributes.

Attribute Creation Order v2 B-tree Address

This is the address of the version 2 B-tree to index the creation order of densely stored attributes.

This field is present if bit 1 of Flags is set.


Name: Object Reference Count

Header Message Type: 0x0016

Length: fixed

Status: Optional, may not be repeated.

Description:This message stores the number of hard links (in groups or objects) pointing to an object (i.e. its reference count).

Format of Data:

Object Reference Count
byte byte byte byte
Version This space inserted only to align table nicely
Reference count

Field Name Description
Version

The version number for this message. This document describes version 0.

Reference Count

The unsigned 32-bit integer is the reference count for the object. This message is only present in "version 2" (or later) object headers, and if not present those object header versions, the reference count for the object is assumed to be 1.


Disk Format: Level 2B - Data Object Data Storage

The data for an object is stored separately from its 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 dataspace header message). Multi-dimensional array data is stored in C order, i.e. the "last" dimension changes fastest.

Data whose elements are composed of atomic datatypes are stored in IEEE format, unless they are specifically defined as being stored in a different machine format with the architecture-type information from the datatype 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-length datatype is stored in the global heap of the HDF5 file. Global heap identifiers are stored in the data object storage.

Data whose elements are composed of reference datatypes are stored in several different ways depending on the particular reference type involved. Object pointers are just stored as the offset of the object header being pointed to with the size of the pointer being the same number of bytes as offsets in the file.

Dataset region references 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.


Appendix

Definitions of various terms used in this document.

The "undefined address" for a file is a file address with all bits set, i.e. 0xffff...ff.

The "unlimited size" for a size is a value with all bits set, i.e. 0xffff...ff.


HDF5 documents and links 
Introduction to HDF5 
HDF5 User's Guide 
HDF5 Reference Manual 
HDF5 Application Developer's Guide 

The HDF Group Help Desk:
Describes HDF5 Release 1.8.14, November 2014.
  Copyright by The HDF Group
and the Board of Trustees of the University of Illinois
Last modified: 21 October 2014