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HDF5 Tools

HDF5 Tool Interfaces

HDF5-related tools are available to assist the user in a variety of activities, including examining or managing HDF5 files, converting raw data between HDF5 and other special-purpose formats, moving data and files between the HDF4 and HDF5 formats, measuring HDF5 library performance, and managing HDF5 library and application compilation, installation and configuration. Unless otherwise specified below, these tools are distributed and installed with HDF5.


Last modified: 23 August 2013
Tool Name: h5dump
Syntax:
h5dump [OPTIONS] files

Purpose:
Displays HDF5 file contents.

Description:
h5dump enables the user to examine the contents of an HDF5 file and dump those contents, in human readable form, to an ASCII file.

h5dump dumps HDF5 file content to standard output. It can display the contents of the entire HDF5 file or selected objects, which can be groups, datasets, a subset of a dataset, links, attributes, or datatypes.

The --header option displays object header information only.

Names are the absolute names of the objects. h5dump displays objects in the order same as the command order. If a name does not start with a slash, h5dump begins searching for the specified object starting at the root group.

If an object is hard linked with multiple names, h5dump displays the content of the object in the first occurrence. Only the link information is displayed in later occurrences.

h5dump assigns a name for any unnamed datatype in the form of #oid1:oid2, where oid1 and oid2 are the object identifiers assigned by the library. The unnamed types are displayed within the root group.

Datatypes are displayed with standard type names. For example, if a dataset is created with H5T_NATIVE_INT type and the standard type name for integer on that machine is H5T_STD_I32BE, h5dump displays H5T_STD_I32BE as the type of the dataset.

h5dump can also dump a subset of a dataset. This feature operates in much the same way as hyperslabs in HDF5; the parameters specified on the command line are passed to the function H5Sselect_hyperslab and the resulting selection is displayed.

The h5dump output is described in detail in the DDL for HDF5, the Data Description Language document.

Note: It is not permissible to specify multiple attributes, datasets, datatypes, groups, or soft links with one flag. For example, one may not issue the command
         WRONG:   h5dump -a /attr1 /attr2 foo.h5
to display both /attr1 and /attr2. One must issue the following command:
         CORRECT:   h5dump -a /attr1 -a /attr2 foo.h5

One byte integer type data is displayed in decimal by default. When displayed in ASCII, a non-printable code is displayed in 3 octal digits preceeded by a back-slash unless there is a C language escape sequence for it. For example, CR and LF are printed as \r and \n. Though the NUL code is represented as \0 in C, it is printed as \000 to avoid ambiguity as illustrated in the following 1 byte char data (since this is not a string, embedded NUL is possible).

        141 142 143 000 060 061 062 012
          a   b   c  \0   0   1   2  \n 
h5dump prints them as "abc\000012\n". But if h5dump prints NUL as \0, the output is "abc\0012\n" which is ambiguous.

Using file drivers:
It is possible to select the file driver with which to open an HDF5 file by using the --filedriver (or -f) command-line option. Valid values for the --filedriver option are  sec2,  family,  split,  and  multi. If the file driver flag is not specified, then the file will be opened with each driver in turn, and in the order specified above, until one driver succeeds in opening the file.

Special file naming restrictions apply when using h5dump with either the split or the multi driver.

To dump a split file, h5dump requires that the metadata and raw data filenames end with -m.h5 and -r.h5, respectively, and that the entire virtual HDF5 file, or the logical HDF5 file, be referred to on the command line by the common portion of the filename preceding the -m and -r.

For example, assume that a split HDF5 file has its metadata in a file named splitfile-m.h5 and its raw data in a file named splitfile-r.h5. The following command would dump the contents of this logical HDF5 file:
     h5dump --filedriver="split" splitfile

Note that the above split filename restrictions are specific to h5dump; HDF5 applications do not necessarily have the same limitations.

To dump a multi file, h5dump requires that the metadata and raw data filenames end with a subset of the following:
     -s.h5   for userblock, superblock, and driver information block data
     -b.h5   for B-tree node information
     -r.h5   for dataset raw data
     -g.h5   for global heap data
     -l.h5   for local heap data (object names)
     -o.h5   for object headers
The entire virtual HDF5 file must also be referred to on the command line by the common portion of the filename preceding those special tags.

For example, assume that a multi HDF5 file has its userblock, superblock, and driver information block data in a file named multifile-s.h5, its B-tree node information in a file named multifile-b.h5, its raw data in a file named multifile-r.h5, its global heap data in a file named multifile-g.h5, et cetera. The following command would dump the contents of this logical HDF5 file:
     h5dump --filedriver="multi" multifile

Note that the above multi filename restrictions are specific to h5dump; HDF5 applications do not necessarily have the same limitations.

To dump a family file, h5dump requires that the logical file’s name on the command line include the printf(3c)-style integer format specifier that specifies the format of the family file member numbers. For example, if an HDF5 family of files consists of the files family_000.h5, family_001.h5, family_002.h5, and family_003.h5, the logical HDF5 file would be specified on the command line as family_%3d.h5.

The following command would dump the contents of this logical HDF5 file:
     h5dump --filedriver="family" family_%3d.h5

XML Output:
With the --xml option, h5dump generates XML output. This output contains a complete description of the file, marked up in XML. The XML conforms to the HDF5 Document Type Definition (DTD) available at “HDF5 XML Software.”

The XML output is suitable for use with other tools, including the HDF5 Java Products.

Options and Parameters:
-h   or   --help Print a usage message and exit.
-V   or   --version Print version number and exit.
  
Formatting options:
-e   or   --escape Escape non-printing characters.
-r   or   --string Print 1-byte integer datasets as ASCII.
-y   or   --noindex Do not print array indices with data.
-m T   or   --format=T Set the floating point output format.
T is a string defining the floating point format, e.g., '%.3f'.
-q Q   or   --sort_by=Q Sort groups and attributes by the specified index type, Q. Valid values of Q are as follows:
     name              Alpha-numeric index by name (Default)
     creation_order    Index by creation order
-z Z   or   --sort_order=Z Sort groups and attributes in the specified order, Z. Valid values of Z are as follows:
     ascending    Sort in ascending order (Default)
     descending   Sort in descending order
--enable-error-stack Prints messages from the HDF5 error stack as they occur.

Injects error stack information, which is normally suppressed, directly into the output stream. This will disrupt normal h5dump output but is a useful diagnostic tool when data is not being correctly dumped. Consider the case when an h5dump call produces this message:

    dump error: unable to print data
h5dump can be called again with ‘--enable-error-stack’ plus the original options to reveal error stack messages.
--no-compact-subset Enables recognition of the left square bracket ( [ ) as a character in a dataset name.

This option must disable compact subsetting, which is described at the end of this “Options and Parameters” section.

-w N   or   --width=N Set the number of columns of output.
A value of 0 (zero) sets the number of columns to the maximum (65535).
Default width is 80 columns.
File options:
-n   or   --contents Print a list of the file contents and exit.
-n 1   or   --contents=1 The optional value 1 (one) on the -n, --contents option adds attributes to the output.
-B   or   --superblock Print the content of the superblock.
-H   or   --header Print the header only; no data is displayed.
-f D   or   --filedriver=D Specify which driver to open the file with.
-o F   or   --output=F Output raw data into file F.

The files specified for the -o and -O options must be different files. The output from these options must not be comingled.

To suppress the raw data display, use this option with no filename, as in either of the following examples. This has the effect of sending the output to a NULL file:
     -o
     --output=

-b B   or   --binary=B Output dataset to a binary file using the datatype specified by B.
B must have one of the following values:
     LE        Little-endian
     BE        Big-endian
     MEMORY    Memory datatype
     FILE      File datatype
Recommended usage is with the -d and -o options.
-O F   or   --ddl=F Output DDL text into file F.

The files specified for the -o and -O options must be different files. The output from these options must not be comingled.

h5import can use the files output by the -o and -O when importing HDF5 data. See “Using h5dump to create input for h5import.”

To suppress the DDL display, use this option with no filename, as in either of the following examples. This has the effect of sending the output to a NULL file:
     -O
     --ddl=

Object options:
-a P  or  --attribute=P     Print the specified attribute.
-d P   or   --dataset=P Print the specified dataset.
-g P   or   --group=P Print the specified group and all members.
-l P   or   --soft-link=P Print the value(s) of the specified soft link.
-t P   or   --datatype=P Print the specified named datatype.
-A   or   --onlyattr Print the header and value of attributes; data of datasets is not displayed.
-A 0   or   --onlyattr=0 The optional value 0 (zero) on the -A, --onlyattr option prints everything except attributes.
-N P   or   --any-path=P Print any attribute, dataset, datatype, group, or link whose path matches P.
P may match either the absolute path or any portion of the path.
Object property options:
-i   or   --object-ids Print the object ids.
-p   or   --properties
                           
Print information regarding dataset properties, including filters, storage layout, fill value, and allocation time.
The filter output lists any filters used with a dataset, including the type of filter, its name, and any filter parameters.
The storage layout output specifies the dataset layout (chunked, compact, or contiguous), the size in bytes of the dataset on disk, and, if a compression filter is associated with the dataset, the compression ratio. The compression ratio is computed as (uncompressed size)/(compressed size).
The fill value output includes the fill value datatype and value.
The allocation time output displays the allocation time as specified with H5Pset_alloc_time.
-M L   or   --packedbits=L Print packed bits as unsigned integers, using the mask format L for an integer dataset specified with option -d.
L is a list of offset,length values, separated by commas.
offset is the beginning bit in the data value.
length is the number of bits in the mask.
-R   or   --region Print dataset pointed by region references.
XML options:
-x   or   --xml Output XML using XML schema (default) instead of DDL.
-u   or   --use-dtd Output XML using XML DTD instead of DDL.
-D U   or   --xml-dtd=U In XML output, refer to the DTD or schema at U instead of the default schema/DTD.
-X S   or   --xml-ns=S In XML output, (XML Schema) use qualified names in the XML:
      ":": no namespace, default: "hdf5:"
Subsetting options and compact subsetting:
  Subsetting is available by using the following options with the dataset option, -d or --dataset. Subsetting is accomplished by selecting a hyperslab from the data, so the options mirror those for performing a hyperslab selection.

At least one of the START, COUNT, STRIDE, or BLOCK options is mandatory if you do subsetting; the remainder are optional, with default values as follows:
STRIDE, COUNT, and BLOCK default to 1 in each dimension.
START defaults to 0 in each dimension.

-s START   or
  --start=START
Offset of start of subsetting selection.
Default: 0 in all dimensions, specifying the beginning of the dataset.

Each of START, STRIDE, COUNT, and BLOCK must be a comma-separated list of integers with one integer for each dimension of the dataset.

-S STRIDE   or
  --stride=STRIDE
Hyperslab stride.
Default: 1 in all dimensions.
-c COUNT   or
  --count=COUNT
Number of blocks to include in the selection.
Default: 1 in all dimensions.
-k BLOCK   or
  --block=BLOCK
Size of block in hyperslab.
Default: 1 in all dimensions.

Compact subsetting:
Subsetting parameters can also be expressed in a convenient compact form, as follows:
         --dataset="/foo/mydataset[START;STRIDE;COUNT;BLOCK]"

It is not required to use all parameters, but until the last parameter value used, all of the semicolons (;) are required, even when a parameter value is not specified. Example:
         --dataset="/foo/mydataset[START;;COUNT]"
         --dataset="/foo/mydataset[START]"

Each of START, STRIDE, COUNT, and BLOCK must be a comma-separated list of integers with one integer for each dimension of the dataset.

When not specified, default parameter values are used: zeros ( 0 ) for START and ones ( 1 ) for STRIDE, COUNT, and BLOCK.

Option Argument Conventions:
-- Two dashes followed by whitespace.
Indicates that the following argument is not an option.

For example, this structure can be used to dump a file called -f:

    h5dump -- -f
This option is necessary only when the name of the file to be examined starts with a dash (-), which could confuse the tool’s command-line parser.
Option parameters appearing above are defined as follows:
D File driver to use in opening the file
Valid values are  sec2,  family,  split, and  multi.
Without the file driver option, the file will be opened with each driver in turn, and in the order specified immediately above, until one driver succeeds in opening the file.
P Path to the object
For most options, this must be the absolute path from the root group to the object.
With the -N, --any-path option, this may be either the absolute path or a partial path.
F A filename
N An integer greater than 1
START,  STRIDE,
     COUNT, and BLOCK
Comma-separated lists of integers
Each of these option parameters must be a list of integers with one integer for each dimension of the dataspace being queried.
U A URI (as defined in [IETF RFC 2396], updated by [IETF RFC 2732]) that refers to the DTD to be used to validate the XML
B The form of binary output:
    MEMORY    for a memory type
    FILE      for the file type
    LE or BE   for pre-existing little- or big-endian types
Files parameter:
files File or files to be examined; one or more files may be listed.

The file name may include a printf(3C) integer format such as %05d to open a file family.

On Unix, Linux, and Mac OS X systems, multiple files can be examined through the use of Unix-style wildcards. For example, assume that we are working with the files FileA.h5, FileB.h5, FileC.h5, and FileAB.h5:

  • File[AB].h5 will pick up any file that begins with File, followed by any one of the characters contained in the square brackets, and ending with .h5.

    In this case, File[AB].h5 will pick up the files FileA.h5 and FileB.h5.

  • File?.h5 will pick up all files whose names are File, followed by exactly 1 character (any character), followed by .h5.

    In this case, File?.h5 will pick up the files FileA.h5 and FileB.h5, and FileC.h5.

  • File*.h5 will pick up all files whose names begin with File and end with .h5.

    In this case, File*.h5 will pick up all four files.

The wildcard capability is not currently available on Windows systems.

Exit Status:
0 Succeeded.
> 0     An error occurred.

Examples:
  1. Dump the group /GroupFoo/GroupBar in the file quux.h5:
         h5dump -g /GroupFoo/GroupBar quux.h5

  2. Dump the dataset Fnord, which is in the group /GroupFoo/GroupBar in the file quux.h5:
         h5dump -d /GroupFoo/GroupBar/Fnord quux.h5

  3. Dump the attribute metadata of the dataset Fnord, which is in the group /GroupFoo/GroupBar in the file quux.h5:
         h5dump -a /GroupFoo/GroupBar/Fnord/metadata quux.h5

  4. Dump the attribute metadata which is an attribute of the root group in the file quux.h5:
         h5dump -a /metadata quux.h5

  5. Produce an XML listing of the file bobo.h5, saving the listing in the file bobo.h5.xml:
         h5dump --xml bobo.h5 > bobo.h5.xml

  6. Dump a subset of the dataset /GroupFoo/databar/ in the file quux.h5:
         h5dump -d /GroupFoo/databar --start="1,1" --stride="2,3"
                --count="3,19" --block="1,1" quux.h5


  7. The same example, using the short form to specify the subsetting parameters:
         h5dump -d "/GroupFoo/databar[1,1;2,3;3,19;1,1]" quux.h5

  8. Dump a binary copy of the dataset /GroupD/FreshData/ in the file quux.h5, with data written in little-endian form, to the output file FreshDataD.bin:
         h5dump -d "/GroupD/FreshData" -b LE
                -o "FreshDataD.bin" quux.h5


  9. Display two sets of packed bits (bits 0-1 and bits 4-6) in the dataset /dset of the file quux.h5:
         h5dump -d /dset -M 0,1,4,3 quux.h5

  10. Dump the dataset /GroupFoo/GroupBar/Fnord to the file quux.h5 and output the DDL into the file ddl.txt and the raw data into the file data.txt:
         h5dump -d /GroupFoo/GroupBar/Fnord --ddl=ddl.txt -y
                -o data.txt quux.h5


  11. Dump the dataset /GroupFoo/GroupBar/Fnord to the file quux.h5, suppress the DDL output, and output the raw data into the file data.txt:
         h5dump -d /GroupFoo/GroupBar/Fnord --ddl= -y
                -o data.txt quux.h5


Current Status:
The current version of h5dump displays the following information:

See Also:
  • HDF5 Data Description Language syntax at DDL for HDF5
  • HDF5 XML Schema at http://www.hdfgroup.org/HDF5/XML/schema/HDF5-File.xsd
  • HDF5 XML information at http://www.hdfgroup.org/HDF5/XML/
  • History:
    Release     Change
    1.8.12 Optional value of 0 (zero) for the -A, --onlyattr option added in this release.

    Option added in this release:
       -N P or --any-path=P

    1.8.11 Option added in this release:
       -O F or --ddl=F
    This option can be used to suppress the DDL output.
    This option, combined with the '--output=F' (or '-o F') option will generate files that can be used as input to h5import.

    h5dump updated in this release to display the compression ratio for user-defined filters.

    In h5dump output, UNKNOWN_FILTER has been changed to USER_DEFINED_FILTER.

    1.8.9 Option added in this release:
       --no-compact-subset

    h5dump output has been updated for this release to improve compliance with the HDF5 DDL specification and to improve readablilty. This output is now fully compliant with the HDF5 DDL specification, but these changes may affect some user scripts:

    • Whitespace has been modified.
    • Display errors, such as misplaced brackets, have been fixed.
    • When printing superblock content, user block content is now properly displayed within the superblock.
    1.8.7 Option added in this release:
       --enable-error-stack

    Tool updated in this release to correctly display reference type:
       H5T_REFERENCE {H5T_STD_REF_OBJ} for object references
       H5T_REFERENCE {H5T_STD_REF_DSETREG} for dataset region references

    1.8.5 Bitfield display fixed in this release.

    Option added in this release for packed bits data display:
       -M or --packedbits option

    1.8.4 Option added in this release for region reference display:
       -R or --region option
    1.8.1 Compression ratio added to output of -p or --properties option in this release.
    1.8.0 Options added in this release:
       -q or --sort_by
       -z or --sort_order
    1.6.5 Options added in this release:
       -n or --contents
       -e or --escape
       -y or --noindex
       -p or --properties
       -b or --binary

    Last modified: 12 March 2013
    Tool Name: h5ls
    Syntax:
    h5ls [OPTIONS]   file[/OBJECT]   [file[/OBJECT]...]

    Purpose:
    Prints information about one or more HDF5 files or objects.

    Description:
    h5ls prints selected information about specified HDF5 file(s) and/or object(s) in the specified format. In some cases, information regarding symbolic links is also provided.

    Options and Parameters:

    Exit Status:
    0 Succeeded.
    >0     An error occurred.

    Examples:
    1. Display root group in file quux.h5:
          h5ls quux.h5 
    2. Display datasets in file quux.h5:
          h5ls -d quux.h5/dset1 
    3. Display target objects of symbolic links (soft and external links) in file quux.h5:
          h5ls --follow-symlinks quux.h5 
    4. Display all group information in group g1 recursively, avoiding cycles, in file quux.h5:
          h5ls -r -g quux.h5/g1 

    History:
    Release     Change
    1.8.5 Options added in this release:
         --follow-symlinks
         --no-dangling-links
    1.8.7 Option name --enable-error-stack replaces deprecated option name --error in this release.

    Last modified: 29 April 2014
    Tool Name: h5diff    
    Syntax:
    h5diff [OPTIONS] file1 file2 [object1 [object2 ] ]

    ph5diff [OPTIONS] file1 file2 [object1 [object2 ] ]

    Purpose:
    Compare two HDF5 files and report the differences.

    Description:
    h5diff and ph5diff are command line tools that compare two HDF5 files, file1 and file2, and report the differences between them. h5diff is for serial use while ph5diff is for use in parallel environments.

    Optionally, h5diff and ph5diff will compare two objects within these files. If only one object, object1, is specified, h5diff will compare object1 in file1 with object1 in file2. If two objects, object1 and object2, are specified, h5diff will compare object1 in file1 with object2 in file2.

    object1 and object2 can be groups, datasets, named datatypes, or symbolic links (soft links or external links) and must be expressed as absolute paths from the respective file’s root group.

    Output modes:
    h5diff and ph5diff have the following output modes:

    Default        Prints the number of differences found and where they occurred.
    If no differences are found, h5diff and ph5diff produce no output.
    This normal behavior is achieved by using none of the following output mode options.
    Report mode -r Prints the above plus the differences.
    Verbose mode     -v Prints all of the above plus a list of objects and warnings.
    Verbose mode    
        with levels
    -vn Prints a selectable level of detail.
    For details, see “Options and Parameters” below.
    Quiet mode -q Prints no output.
    The h5diff exit code will be the only feedback provided.

    Difference controls:
    h5diff offers several mutually-exclusive criteria for analyzing differences in raw data:

    h5diff and NaNs:
    h5diff detects when a value in a dataset is a NaN (a "not a number" value), but does not differentiate among various types of NaNs. Thus, when one NaN is compared with another NaN, h5diff treats them as equal; when a NaN is compared with a valid number, h5diff treats them as not equal.

    Note that NaN detection is computationally expensive and slows h5diff performance dramatically. If you do not have NaNs in your files, or do not care about NaNs, use the -N option to turn off NaN detection. Similarly, if h5diff -N produces unexpected differences, running h5diff without -N should reveal whether any of the differences are associated with NaN values.

    Difference between h5diff and ph5diff:
    With the following exception, h5diff and ph5diff behave identically. With ph5diff, the comparison of objects is shared across multiple processors, with the comparison of each pair of objects assigned to a single processor. This work assignment means that ph5diff will not speed up the comparison of any given pair of datasets, as the comparison of the pair will still occur on a single processor.

    Options and Parameters:
    Exit Status for h5diff:
    0 No differences were found.
    1 Some differences were found.
    >1     An error occurred.

    Exit Status for ph5diff:
    Because of the limitations in the MPI standard, the return value is not defined.

    Examples:
    Compare the object /a/b in file1 with the object /a/c in file2:
        h5diff file1 file2 /a/b /a/c

    Compare the object /a/b in file1 with the same object in file2:
        h5diff file1 file2 /a/b

    Compare all objects in both files:
        h5diff file1 file2

    Comparisons executed with the verbose options can produce object and attribute status reports as illustrated below:
        h5diff -v file1 file2

        ...
        file1     file2
        ---------------------------------------
            x      x    /              
                   x    /dset          
            x           /g2            
            x      x    /g3            
        ...
            
    The sample output above shows that the dataset dset exists only in file2, the group /g2 exists only in file1, and the group /g3 and the root group exist in both files. Only objects that exist in both files will be compared. More verbose levels can produce more information:
        h5diff -v2 file1 file2
        ...
        group  : ‹/g2› and ‹/g2›
        0 differences found              
           obj1   obj2
         --------------------------------------
            x      x    float2         
            x           float3         
            x      x    integer1       
        Attributes status:  2 common, 1 only in obj1, 0 only in obj2
        ...
            
    In this illustration, both objects, obj1 and obj2, have attributes named float2 and integer1, while only obj1 has an attribute named float3. Only attributes that exist on both objects will be compared.

    The “Attributes status:” line reports that there are two attributes common to both objects: one attribute attached only to obj1, and zero attributes attached only to obj2.

    To see the “Attributes status:” line independently of the immediately-preceding table, use the -v1 option.
        h5diff -v1 file1 file2

        ...
        group  : ‹/g2› and ‹/g2›
        0 differences found              
        Attributes status:  2 common, 1 only in obj1, 0 only in obj2
        ...
            

    History:
    Release     Change
    1.6.0 h5diff introduced in this release.
    1.8.0 ph5diff introduced in this release.
    h5diff command line syntax changed in this release.
    1.8.2 and 1.6.8 Return value on failure changed in this release.
    1.8.4 and 1.6.10     --use-system-epsilon option added in this release.
    1.8.5 --follow-symlinks option added in this release.
    --no-dangling-links option added in this release.
    1.8.6 --exclude-path option added in this release.
    1.8.7 -vn, --verbose=n  option, specifying levels of verbose output, added in this release.

    Last modified: 10 September 2013
    Tool Name: h5repack
    Syntax:
    h5repack [OPTIONS] in_file out_file

    h5repack -i in_file -o out_file [OPTIONS]

    Purpose:
    Copies an HDF5 file to a new file with or without compression and/or chunking.

    Description:
    h5repack is a command line tool that applies HDF5 filters to an input file in_file, saving the output in a new output file, out_file.

    Options and Parameters:
    -i in_file
    Input HDF5 file

    -o out_file
    Output HDF5 file

    -h   or  --help
    Print help message.

    -v   or  --verbose
    Print verbose output.

    -V   or  --version
    Print version number.

    -n   or  --native
    Use native HDF5 datatypes when repacking.
    (Default behavior is to use original file datatypes.)
    Note that this is a change in default behavior; prior to Release 1.6.6, h5repack generated files only with native datatypes.

    -L   or  --latest
    Use latest version of the HDF5 file format.

    -c max_compact_links   or  --compact=max_compact_links
    Set the maximum number of links, max_compact_links, that can be stored in a group header message (compact format).

    -d min_indexed_links   or  --indexed=min_indexed_links
    Set the minimum number of links, min_indexed_links, in the indexed format.

    max_compact_links and min_indexed_links are closely related and the first must be equal to or greater than the second. In the general case, however, performance will suffer, possibly dramatically, if they are equal; performance can be improved by tuning the gap between the two values to minimize unnecessary thrashing between the compact storage and indexed storage modes as group size waxes and wanes. The relationship between max_compact_links and min_indexed_links is most important when group sizes are highly dynamic; that relationship is much less important in files with a stable structure. Compact mode is space and performance-efficient when groups have small numbers of members; indexed mode requires slightly more storage space, but provides increasingly better performance as the number of members in each group increases.

    -m size   or  --minimum=size
    Apply filter(s) only to objects whose size in bytes is equal to or greater than size.
    size must be an integer greater than one ( 1 ).

    Default:  If no size is specified, a threshold of 1024 bytes is assumed.

    -u file   or  --ublock=file
    Specify name of file containing user block data to be added.

    -b user_block_size   or  --block=user_block_size
    Set size in bytes of user block to be added.
    user_block_size must be 512 or greater and a power of 2.

    Default:  1024

    -M size   or  --metadata_block_size=size
    Metadata block size to be used when h5repack calls H5Pset_meta_block_size.
    size must be a non-negative integer.

    -t alignment_threshold   or  --threshold=alignment_threshold
    Set threshold value for H5Pset_alignment call.
    alignment_threshold must be an integer.

    -a alignment   or  --alignment=alignment
    Set alignment value for H5Pset_alignment call.
    alignment must be a positive integer.

    -s min_size[:header_type]   or  --ssize=min_size[:header_type]
    Set the minimum size of optionally specified types of shared object header messages.

    min_size is the minimum size, in bytes, of a shared object header message. Header messages smaller than the specified size will not be shared.

    header_type specifies the type(s) of header message that this minimum size is to be applied to. Valid values of header_type are any of the following:
      dspace  for dataspace header messages
      dtype   for datatype header messages
      fill    for fill values
      pline   for property list header messages
      attr    for attribute header messages
    If header_type is not specified, min_size will be applied to all header messages.

    -f filter   or  --filter=filter
    Filter type

    filter is a string of the following format:

    list_of_objects : name_of_filter[=filter_parameters]

    list_of_objects is a comma separated list of object names meaning apply the filter(s) only to those objects. If no object names are specified, the filter is applied to all objects.

    name_of_filter can be one of the following:
         GZIP, to apply the HDF5 GZIP filter (GZIP compression)
         SZIP, to apply the HDF5 SZIP filter (SZIP compression)
         SHUF, to apply the HDF5 shuffle filter
         FLET, to apply the HDF5 checksum filter
         NBIT, to apply the HDF5 N-bit filter
         SOFF, to apply the HDF5 scale/offset filter
         UD, to apply a user-defined filter
         NONE, to remove any filter(s)

    filter_parameters conveys optional compression information:
         GZIP=deflation_level from 1-9
         SZIP=pixels_per_block,coding_method
             pixels_per_block is a even number in the range 2-32.
             coding_method is EC or NN.
         SHUF (no parameter)
         FLET (no parameter)
         NBIT (no parameter)
         SOFF=scale_factor,scale_type
             scale_factor is an integer.
             scale_type is either IN or DS.
         UD=filter_id,nfilter_params,value_1[,value_2,....,value_n]
             filter_id is the filter identifier.
             nfilter_params is the number of filter parameters.
             value_1 through value_n are the values of each filter parameter.
                     Number of values must match the value of nfilter_params.
         NONE (no parameter)

    -l layout   or  --layout=layout
    Layout type

    layout is a string of the following format:

    list_of_objects : layout_type[=layout_parameters]

    list_of_objects is a comma separated list of object names, meaning that layout information is supplied for those objects. If no object names are specified, the layout is applied to all objects.

    layout_type can be one of the following:
         CHUNK, to apply chunking layout
         COMPA, to apply compact layout
         CONTI, to apply contiguous layout

    layout_parameters is present only in the CHUNK case and specifies the chunk size of each dimension in the following format with no intervening spaces:
         dim_1 × dim_2 × ... dim_n

    -e file   or  --file=file
    File containing values to be passed in for the -f (or --filter) and -l (or --layout) options.
    This file contains only the filter and layout flags.

    in_file
    Input HDF5 file

    out_file
    Output HDF5 file

    Exit Status:
    0 Succeeded.
    >0     An error occurred.
    Examples:
    1. h5repack -f GZIP=1 -v file1 file2
      Applies GZIP compression to all objects in file1 and saves the output in file2. Prints verbose output.
       
    2. h5repack -f dset1:SZIP=8,NN file1 file2
      Applies SZIP compression only to object dset1.
       
    3. h5repack -l dset1,dset2:CHUNK=20x10 file1 file2
      Applies chunked layout to objects dset1 and dset2.
       
    4. h5repack -f UD=307,1,9 file1 file2
      Adds bzip2 filter to all datasets.

    History:
    Release     Change
    1.8.12 Added user-defined filter parameter (UD) to -f filter, --filter=filter option for use in read and write operations.
    1.8.9 -M number, --medata_block_size=number option introduced in this release.
    1.8.1 Original syntax restored; both the new and the original syntax are now supported.
    1.8.0 h5repack command line syntax changed in this release.
    1.6.2 h5repack introduced in this release.

    Tool Name: h5repart
    Syntax:
    h5repart [-v] [-V] [-[b|m]N[g|m|k]] [-family_to_sec2] source_file dest_file
    Purpose:
    Repartitions a file or family of files.
    Description:
    h5repart joins a family of files into a single file, or copies one family of files to another while changing the size of the family members. h5repart can also be used to copy a single file to a single file with holes. At this stage, h5repart can not split a single non-family file into a family of file(s).

    To convert a family of file(s) to a single non-family file (sec2 file), the option -family_to_sec2 has to be used.

    Sizes associated with the -b and -m options may be suffixed with g for gigabytes, m for megabytes, or k for kilobytes.

    File family names include an integer printf format such as %d.

    Options and Parameters:
    Exit Status:
    0 Succeeded.
    >0     An error occurred.

    Last modified: 16 August 2012
    Tool Name: h5jam/h5unjam
    Syntax:
    h5jam -u user_block -i in_file.h5 [-o out_file.h5] [--clobber]
    h5jam -h
     
    h5unjam -i in_file.h5 [-u user_block | --delete] [-o out_file.h5]
    h5unjam -h

    Purpose:
    h5jam: Adds user block to front of an HDF5 file, to create a new concatenated file.
    h5unjam: Splits user block and HDF5 file into two files: user block data and HDF5 data.

    Description:
    h5jam:
    h5jam  concatenates a user_block file and an HDF5 file to create an HDF5 file with a user block.

    If out_file.h5 is given, a new file is created with the user_block followed by the contents of in_file.h5. In this case, infile.h5 is unchanged.

    If out_file.h5 is not specified, the user_block is added to in_file.h5.

    If in_file.h5 already has a user block, the contents of user_block will be added to the end of the existing user block, and the file shifted to the next boundary. If --clobber is set, any existing user block will be overwritten.

    A user block can contain either binary or text data.

    The minimum size of a user block is 512 bytes. As needed, the user block can be any power of 2 greater than that: 1024 bytes, 2048 bytes, etc. The user block in the output file is padded so that the HDF5 header begins on the first appropriate boundary. For example, if only 8 bytes of data are inserted for the user block, the HDF5 header will be found at byte 512; if 1100 bytes of data are inserted for the user block, the HDF5 header will be found at byte 2048.

    h5unjam:
    h5unjam splits an HDF5 file, writing the user block to a file or to stdout and the HDF5 file to an HDF5 file with a header at byte zero (0, i.e., with no user block).

    If out_file.h5 is given, a new file is created with the contents of in_file.h5 without the user block. In this case, infile.h5 is unchanged.

    If out_file.h5 is not specified, the user_block is removed and in_file.h5 is rewritten, starting at byte 0.

    If user_block is set, the user block will be written to user_block. If user_block is not set, the user block, if any, will be written to stdout. If --delete is selected, the user block will not be written.

    The last portion of a returned user block may contain padding or undefined data (see discussion below: “h5jam and h5unjam not necessarily transitive”). It is the user’s or the user application’s responsibility to handle this correctly.

    Examples:
    Create new file, newfile.h5, with the text in file mytext.txt as the user block for the HDF5 file file.h5.
        h5jam -u mytext.txt -i file.h5 -o newfile.h5
    Add text in file mytext.txt to front of HDF5 dataset, file.h5.
        h5jam -u mytext.txt -i file.h5 
    Overwrite the user block, if any, in file.h5 with the contents of mytext.txt.
        h5jam -u mytext.txt -i file.h5 --clobber
    For an HDF5 file, with_ub.h5, with a user block, extract the user block to user_block.txt and the HDF5 portion of the file to wo_ub.h5.
        h5unjam -i with_ub.h5 -u user_block.txt -o wo_ub.h5

    Exit Status:
    0 Succeeded.
    >0     An error occurred.

    Caveats:
    These tools copy all the data sequentially in the file(s) to new offsets. For a large file, this copy will take a long time.

    The most efficient way to create a user block is to create the file with a user block (see H5Pset_userblock), and write the user block data into that space from a program.

    The user block is completely opaque to the HDF5 library and to the h5jam and h5unjam tools. The user block is read or written in a single block as a string of bytes; it can contain text or any kind of binary data; and it is up to the user to know what the user block content means and how to process it.

    When the user block is extracted, its entire contents are written as a single block of output, including any padding or uninitialized data.

    This tool moves the HDF5 portion of the file through byte copies; i.e., it does not read or interpret the HDF5 objects.

    h5jam and h5unjam not necessarily transitive:
    Note that h5jam and h5unjam are not necessarily transitive operations. Any amount of data can be inserted into a user block, but an HDF5 user block itself has specific size requirements. The minimum size is 512 bytes; beyond that, the user block can be 512 bytes times any positive power of 2. That is, a user block’s size will be one of the following: 512 bytes, 1024 bytes, 2048 bytes, 4096 bytes, et cetera.

    If h5jam is used to insert a 700 byte file into the user block, h5jam will create a user block of 1024 bytesa and insert the user’s file as the first 700 bytes of that block. The remaining 324 bytes will be undefined. If the remaining bytes must have a particular fill value, for instance, the user must modify the input file by padding it to exactly 1024 bytes with the required fill value before inserting it with h5jam.

    When h5unjam is asked to return the above user block, it will be returned with the padding in the last 324 bytes if the user defined it or with undefined data in the last 324 bytes if the user took no action to insert the padding.

    If the file must be cleaned up for use, it is the user’s or the user application’s responsibility.

    If a community of users employs user block data that must be cleaned up after the use of h5unjam, the community should establish a protocol for that process so that every community member knows what is required. The community may prefer to create and provide a tool to perform standard cleanup. A simple protocol might be for a user community to declare that the first N bytes of the user block will always contain the length or size of the valid user block content, much as a Pascal string starts with the length of the string data. Also see the HDF5 source code for examples of examining or reading the user block without modifying the file in any way. The relevant source files are the test programs tools/h5jam/tellub.c and tools/h5jam/getub.c.


    Last modified: 12 April 2011
    Tool Name: h5copy
    Syntax:
    h5copy [OPTIONS] [OBJECTS]

    Purpose:
    Copies an HDF5 object within an HDF5 file or from one HDF5 file to another.

    Description:
    h5copy  copies an HDF5 object (a dataset, named datatype, or group) from an input HDF5 file to an output HDF5 file.

    If a group is specified as the input object, any objects in that group will be recursively copied.

    The output file may or may not already exist.

    h5copy will fail if the destination object name already exists.

    Arguments:
    Options and Parameters:
    -h   or   --help
    Print a usage message and exit.
    -v   or   --verbose
    Produce verbose output, printing information regarding the specified options and objects.
    -V   or   --Version
    Print version information.
    -p   or   --parents
    Create parent or intermediate groups as required. (There is no error if they already exist.)
    -f flag_type   or   --flag=flag_type
    Specify one or more of several copy options; flag_type may be one of the following strings or a logical AND of two or more:
    shallow  Copy only immediate members of a group.
    (Default: Recursively copy all objects below the group.)
    soft  Expand soft links to copy target objects.
    (Default: Keep soft links as they are.)
    ext  Expand external links to copy external objects.
    (Default: Keep external links as they are.)
    ref  Copy references and any referenced objects, i.e., objects that the references point to.

    Referenced objects are copied in addition to the objects specified on the command line and reference datasets are populated with correct reference values. Copies of referenced datasets outside the copy range specified on the command line will normally have a different name from the original.

    (Default:Without this option, reference value(s) in any reference datasets are set to NULL and referenced objects are not copied unless they are otherwise within the copy range specified on the command line.)

    attr  Copy objects without copying attributes.
    (Default: Copy objects and all attributes.)
    allflags   Switch each setting above from the default to the setting described in this table.
    Equivalent to logical AND of all flags above.

    Objects (all required):
    -i input_file   or   --input=input_file
    Input HDF5 file name
    -o output_file   or   --output=output_file
    Output HDF5 file name (existing or non-existing)
    -s source_object   or   --source=source_object
    Input HDF5 object name within the input file
    -d destination_object   or   --destination=destination_object
    Output HDF5 object name within the output file
     

    Exit Status:
    0 Succeeded.
    >0     An error occurred.

    Example Usage
    In verbose mode, create a new file, test1.out.h5, containing the object array in the root group, copied from the existing file test1.h5 and object array.
        h5copy -v -i "test1.h5" -o "test1.out.h5" -s "/array" -d "/array
            

    In verbose mode and using the flag shallow to prevent recursion in the file hierarchy, create a new file, test1.out.h5, containing the object array in the root group, copied from the existing file test1.h5 and object array.

        h5copy -v -f shallow -i "test1.h5" -s "/array" -o test1.out.h5" -d "/array"

    History:

    Tool Name: h5mkgrp
    Syntax:
    h5mkgrp [OPTIONS] file_name group_name...
    Purpose:
    Creates new group(s) in an HDF5 file.

    Description:
    h5mkgrp  creates one or more new groups in an HDF5 file.

    Options and Parameters:
    file_name
    Name of HDF5 file within which new group is to be created.
    group_name
    Name of group to be created; specified as full path name from the root group, i.e., starting with a slash (/).
     
    Options:
    -h, --help
    Print a usage message and exit.
    -l, --latest
    Use latest version of file format to create new group.
    -p, --parents
    Create parent or intervening groups as needed. Issue no error if intervening groups or new group already exist.
    -v, --verbose
    Print verbose output, including information about file, group(s), and options.
    -V, --version
    Print tool version number then exit. Tool version number is that of the corresponding HDF5 Library.

    Exit Status:
    0 Succeeded.
    >0     An error occurred.
    Example Usage
    Create a new group, new_group,  within the existing group /a/b in the file HDF5_file.
        h5mkgrp "HDF5_file" "/a/b/new_group"
    Create a new group, new_group,  within the group /a/b in the file HDF5_file. Create the groups a and b if they do not already exist. Issue no error if the intervening groups or the new group already exist.
        h5mkgrp -p "HDF5_file" "/a/b/new_group"
    Create the new groups /a/b/new_c  and /a/x/new_4  in the file HDF5_file. The groups /a/b  and /a/x  must already exist.
        h5mkgrp -p "HDF5_file" "/a/b/new_c" "/a/x/new_4"

    History:

    Last modified: 22 March 2013
    Tool Name: h5import
    Syntax:
    h5import infile in_options [infile in_options ...] -o outfile
    h5import infile in_options [infile in_options ...] -outfile outfile
    h5import -h
    h5import -help

    Purpose:
    Imports data into an existing or new HDF5 file.

    Description:
    h5import converts data from one or more ASCII or binary files, infile, into the same number of HDF5 datasets in the existing or new HDF5 file, outfile. Data conversion is performed in accordance with the user-specified type and storage properties specified in in_options.

    The primary objective of h5import is to import floating point or integer data. The utility's design allows for future versions that accept ASCII text files and store the contents as a compact array of one-dimensional strings, but that capability is not implemented in HDF5 Release 1.6.

    Input data and options:
    Input data can be provided in one of the following forms:

    Each input file, infile, contains a single n-dimensional array of values of one of the above types expressed in the order of fastest-changing dimensions first.

    Floating point data in an ASCII input file may be expressed either in the fixed-point form (e.g., 323.56) or in scientific notation (e.g., 3.23E+02) in an ASCII input file.

    Each input file can be associated with options specifying the datatype and storage properties. These options can be specified either as command line arguments or in a configuration file. Note that exactly one of these approaches must be used with a single input file.

    Command line arguments, best used with simple input files, can be used to specify the class, size, dimensions of the input data and a path identifying the output dataset.

    The recommended means of specifying input data options is in a configuration file; this is also the only means of specifying advanced storage features. See further discussion in "The configuration file" below.

    The only required option for input data is dimension sizes; defaults are available for all others.

    h5import will accept up to 30 input files in a single call. Other considerations, such as the maximum length of a command line, may impose a more stringent limitation.

    Output data and options:
    The name of the output file is specified following the -o or -output option in outfile. The data from each input file is stored as a separate dataset in this output file. outfile may be an existing file. If it does not yet exist, h5import will create it.

    Output dataset information and storage properties can be specified only by means of a configuration file.
      Dataset path If the groups in the path leading to the dataset do not exist, h5import will create them.
    If no group is specified, the dataset will be created as a member of the root group.
    If no dataset name is specified, the default name is dataset0 for the first input dataset, dataset1 for the second input dataset, dataset2 for the third input dataset, etc.
    h5import does not overwrite a pre-existing dataset of the specified or default name. When an existing dataset of a conflicting name is encountered, h5import quits with an error; the current input file and any subsequent input files are not processed.
      Output type Datatype parameters for output data
          Output data class Signed or unsigned integer or floating point
          Output data size 8-, 16-, 32-, or 64-bit integer
    32- or 64-bit floating point
          Output architecture IEEE
    STD
    NATIVE (Default)
    Other architectures are included in the h5import design but are not implemented in this release.
          Output byte order Little- or big-endian.
    Relevant only if output architecture is IEEE, UNIX, or STD; fixed for other architectures.
      Dataset layout and storage  
            properties
    Denote how raw data is to be organized on the disk. If none of the following are specified, the default configuration is contiguous layout and with no compression.
          Layout Contiguous (Default)
    Chunked
          External storage Allows raw data to be stored in a non-HDF5 file or in an external HDF5 file.
    Requires contiguous layout.
          Compressed Sets the type of compression and the level to which the dataset must be compressed.
    Requires chunked layout.
          Extendable Allows the dimensions of the dataset increase over time and/or to be unlimited.
    Requires chunked layout.
          Compressed and
            extendable
    Requires chunked layout.
       

    Command-line arguments:
    The h5import syntax for the command-line arguments, in_options, is as follows:
         h5import infile -d dim_list [-p pathname] [-t input_class] [-s input_size] [infile ...] -o outfile
    or
    h5import infile -dims dim_list [-path pathname] [-type input_class] [-size input_size] [infile ...] -outfile outfile
    or
    h5import infile -c config_file [infile ...] -outfile outfile

    Note the following:

    Using h5dump to create input for h5import:
    h5import can use the output of h5dump as input to create a dataset or file. As in all uses of h5import, an import action is limited to a single dataset with an atomic numeric or text datatype.

    h5dump must first create two files:
        •  A DDL file, which will be used as an h5import configuration file
        •  A raw data file containing the data to be imported

    The DDL file must be generated with the h5dump -p option, to generate properties.

    The raw data file may contain either numeric or string data. Numeric data can be imported by this method only if h5dump writes it to a binary file. String data must be written with the h5dump -y and --width=1 options, generating a single column of strings without indices.

    Two examples follow: The first imports a dataset with a numeric datatype. Note that numeric data requires use of the h5dump -b option to produce a binary data file.

        h5dump -p -d "/int/buin/16-bit" --ddl=binuin16.h5.dmp -o binuin16.h5.bin \
               -b binuin16.h5 
        h5import binuin16.h5.bin -c binuin16.h5.dmp -o new_binuin16.h5 

    The second example imports a dataset containing text data. Note that string data requires use of the h5dump -y option to exclude indexes and the h5dump --width=1 option to generate a single column of strings.

        h5dump -p -d "/mytext/data" -O txtstr.h5.dmp -o txtstr.h5.bin            \
               -y --width=1 xtstr.h5 
        h5import txtstr.h5.bin -c txtstr.h5.dmp -o new_txtstr.h5 

    The configuration file:
    A configuration file is specified with the -c config_file option:
         h5import infile -c config_file [infile -c config_file2 ...] -outfile outfile

    The configuration file is an ASCII file and must be organized as "Configuration_Keyword Value" pairs, with one pair on each line. For example, the line indicating that the input data class (configuration keyword INPUT-CLASS) is floating point in a text file (value TEXTFP) would appear as follows:
        INPUT-CLASS TEXTFP

    A configuration file may have the following keywords each followed by one of the following defined values. One entry for each of the first two keywords, RANK and DIMENSION-SIZES, is required; all other keywords are optional.


    Keyword  
        Value

    Description

    RANK  

    The number of dimensions in the dataset. (Required)
        rank An integer specifying the number of dimensions in the dataset.
    Example:   4   for a 4-dimensional dataset.

    DIMENSION-SIZES

    Sizes of the dataset dimensions. (Required)
        dim_sizes A string of space-separated integers specifying the sizes of the dimensions in the dataset. The number of sizes in this entry must match the value in the RANK entry. The fastest-changing dimension must be listed first.
    Example:   4 3 4 38   for a 38x4x3x4 dataset.

    PATH

    Path of the output dataset.
        path The full HDF5 pathname identifying the output dataset relative to the root group within the output file.
    I.e., path is a string consisting of optional group names, each followed by a slash, and ending with a dataset name. If the groups in the path do no exist, they will be created.
    If PATH is not specified, the output dataset is stored as a member of the root group and the default dataset name is dataset0 for the first input dataset, dataset1 for the second input dataset, dataset2 for the third input dataset, etc.
    Note that h5import does not overwrite a pre-existing dataset of the specified or default name. When an existing dataset of a conflicting name is encountered, h5import quits with an error; the current input file and any subsequent input files are not processed.
    Example: The configuration file entry
         PATH grp1/grp2/dataset1
    indicates that the output dataset dataset1 will be written in the group grp2/ which is in the group grp1/, a member of the root group in the output file.

    INPUT-CLASS  

    A string denoting the type of input data.
        TEXTIN Input is signed integer data in an ASCII file.
        TEXTUIN Input is unsigned integer data in an ASCII file.
        TEXTFP Input is floating point data in either fixed-point notation (e.g., 325.34) or scientific notation (e.g., 3.2534E+02) in an ASCII file.
        IN Input is signed integer data in a binary file.
        UIN Input is unsigned integer data in a binary file.
        FP Input is floating point data in a binary file. (Default)
        STR Input is character data in an ASCII file. With this value, the configuration keywords RANK, DIMENSION-SIZES, OUTPUT-CLASS, OUTPUT-SIZE, OUTPUT-ARCHITECTURE, and OUTPUT-BYTE-ORDER will be ignored.
    (Not implemented in this release.)

    INPUT-SIZE

    An integer denoting the size of the input data, in bits.
        8
        16
        32
        64
    For signed and unsigned integer data: TEXTIN, TEXTUIN, IN, or UIN. (Default: 32)
        32
        64
    For floating point data: TEXTFP or FP. (Default: 32)

    OUTPUT-CLASS  

    A string denoting the type of output data.
        IN Output is signed integer data.
    (Default if INPUT-CLASS is IN or TEXTIN)
        UIN Output is unsigned integer data.
    (Default if INPUT-CLASS is UIN or TEXTUIN)
        FP Output is floating point data.
    (Default if INPUT-CLASS is not specified or is FP or TEXTFP)
        STR Output is character data, to be written as a 1-dimensional array of strings.
    (Default if INPUT-CLASS is STR)
    (Not implemented in this release.)

    OUTPUT-SIZE

    An integer denoting the size of the output data, in bits.
        8
        16
        32
        64
    For signed and unsigned integer data: IN or UIN. (Default: Same as INPUT-SIZE, else 32)
        32
        64
    For floating point data: FP. (Default: Same as INPUT-SIZE, else 32)

    OUTPUT-ARCHITECTURE

    A string denoting the type of output architecture.
        NATIVE
        STD
        IEEE
        INTEL *
        CRAY *
        MIPS *
        ALPHA *
        UNIX *
    See the "Predefined Atomic Types" section in the "HDF5 Datatypes" chapter of the HDF5 User's Guide for a discussion of these architectures.
    Values marked with an asterisk (*) are not implemented in this release.
    (Default: NATIVE)

    OUTPUT-BYTE-ORDER

    A string denoting the output byte order. This entry is ignored if the OUTPUT-ARCHITECTURE is not specified or if it is not specified as IEEE, UNIX, or STD.
        BE Big-endian. (Default)
        LE Little-endian.

    The following options are disabled by default, making the default storage properties no chunking, no compression, no external storage, and no extensible dimensions.

    CHUNKED-DIMENSION-SIZES

    Dimension sizes of the chunk for chunked output data.
        chunk_dims A string of space-separated integers specifying the dimension sizes of the chunk for chunked output data. The number of dimensions must correspond to the value of RANK.
    The presence of this field indicates that the output dataset is to be stored in chunked layout; if this configuration field is absent, the dataset will be stored in contiguous layout.

    COMPRESSION-TYPE

    Type of compression to be used with chunked storage. Requires that CHUNKED-DIMENSION-SIZES be specified.
        GZIP Gzip compression.
    Other compression algorithms are not implemented in this release of h5import.

    COMPRESSION-PARAM

    Compression level. Required if COMPRESSION-TYPE is specified.
        1 through 9 Gzip compression levels: 1 will result in the fastest compression while 9 will result in the best compression ratio.
    (Default: 6. The default gzip compression level is 6; not all compression methods will have a default level.)

    EXTERNAL-STORAGE

    Name of an external file in which to create the output dataset. Cannot be used with CHUNKED-DIMENSIONS-SIZES, COMPRESSION-TYPE, OR MAXIMUM-DIMENSIONS.
        external_file        A string specifying the name of an external file.

    MAXIMUM-DIMENSIONS

    Maximum sizes of all dimensions. Requires that CHUNKED-DIMENSION-SIZES be specified.
        max_dims A string of space-separated integers specifying the maximum size of each dimension of the output dataset. A value of -1 for any dimension implies unlimited size for that particular dimension.
    The number of dimensions must correspond to the value of RANK.


    Options and Parameters:
    infile(s) Name of the Input file(s).
    in_options Input options. Note that while only the -dims argument is required, arguments must used in the order in which they are listed below.
      -d dim_list  
      -dims dim_list Input data dimensions. dim_list is a string of comma-separated numbers with no spaces describing the dimensions of the input data. For example, a 50 x 100 2-dimensional array would be specified as -dims 50,100.
    Required argument: if no configuration file is used, this command-line argument is mandatory.
      -p pathname  
      -pathname pathname  
                          
    pathname is a string consisting of one or more strings separated by slashes (/) specifying the path of the dataset in the output file. If the groups in the path do no exist, they will be created.
    Optional argument: if not specified, the default path is dataset1 for the first input dataset, dataset2 for the second input dataset, dataset3 for the third input dataset, etc.
    h5import does not overwrite a pre-existing dataset of the specified or default name. When an existing dataset of a conflicting name is encountered, h5import quits with an error; the current input file and any subsequent input files are not processed.
      -t input_class  
      -type input_class   input_class specifies the class of the input data and determines the class of the output data.
    Valid values are as defined in the Keyword/Values table in the section "The configuration file" above.
    Optional argument: if not specified, the default value is FP.
      -s input_size  
      -size input_size input_size specifies the size in bits of the input data and determines the size of the output data.
    Valid values for signed or unsigned integers are 8, 16, 32, and 64.
    Valid values for floating point data are 32 and 64.
    Optional argument: if not specified, the default value is 32.
      -c config_file config_file specifies a configuration file.
    This argument replaces all other arguments except infile and -o outfile
      -h  
      -help Prints the h5import usage summary:
    h5import -h[elp], OR
    h5import <infile> <options> [<infile> <options>...] -o[utfile] <outfile>

    Then exits.
    outfile Name of the HDF5 output file.

    Exit Status:
    0 Succeeded.
    >0     An error occurred.

    Examples:
    Using command-line arguments:
    h5import infile -dims 2,3,4 -type TEXTIN -size 32 -o out1
         This command creates a file out1 containing a single 2x3x4 32-bit integer dataset. Since no pathname is specified, the dataset is stored in out1 as /dataset1.
    h5import infile -dims 20,50 -path bin1/dset1 -type FP -size 64 -o out2
         This command creates a file out2 containing a single a 20x50 64-bit floating point dataset. The dataset is stored in out2 as /bin1/dset1.

     

    Sample configuration files:
    The following configuration file specifies the following:
    – The input data is a 5x2x4 floating point array in an ASCII file.
    – The output dataset will be saved in chunked layout, with chunk dimension sizes of 2x2x2.
    – The output datatype will be 64-bit floating point, little-endian, IEEE.
    – The output dataset will be stored in outfile at /work/h5/pkamat/First-set.
    – The maximum dimension sizes of the output dataset will be 8x8x(unlimited).
                PATH work/h5/pkamat/First-set
                INPUT-CLASS TEXTFP
                RANK 3
                DIMENSION-SIZES 5 2 4
                OUTPUT-CLASS FP
                OUTPUT-SIZE 64
                OUTPUT-ARCHITECTURE IEEE
                OUTPUT-BYTE-ORDER LE
                CHUNKED-DIMENSION-SIZES 2 2 2 
                MAXIMUM-DIMENSIONS 8 8 -1
            
    The next configuration file specifies the following:
    – The input data is a 6x3x5x2x4 integer array in a binary file.
    – The output dataset will be saved in chunked layout, with chunk dimension sizes of 2x2x2x2x2.
    – The output datatype will be 32-bit integer in NATIVE format (as the output architecture is not specified).
    – The output dataset will be compressed using Gzip compression with a compression level of 7.
    – The output dataset will be stored in outfile at /Second-set.
                PATH Second-set
                INPUT-CLASS IN
                RANK 5
                DIMENSION-SIZES 6 3 5 2 4
                OUTPUT-CLASS IN
                OUTPUT-SIZE 32
                CHUNKED-DIMENSION-SIZES 2 2 2 2 2
                COMPRESSION-TYPE GZIP
                COMPRESSION-PARAM 7
            

    History:
    Release     Change
    1.6.0 Tool introduced in this release.
    1.8.10 Tool updated to accept h5dump output.
    1.8.11 Process simplified for using h5dump output. See “Using h5dump to create input for h5import.”

    Last modified: 4 January 2011
    Tool Name: gif2h5
    Syntax:
    gif2h5 gif_file h5_file

    Purpose:
    Converts a GIF file to an HDF5 file.

    Description:
    gif2h5 accepts as input the GIF file gif_file and produces the HDF5 file h5_file as output.

    Options and Parameters:
    gif_file     The name of the input GIF file
    h5_file The name of the output HDF5 file

    Exit Status:
    0 Succeeded.
    > 0     An error occurred.

    History:
    Release     Change
    1.8.5 Tool exit status codes updated.

    Last modified: 4 January 2011
    Tool Name: h52gif
    Syntax:
    h52gif h5_file gif_file -i h5_image [-p h5_palette]

    Purpose:
    Converts an HDF5 file to a GIF file.

    Description:
    h52gif accepts as input the HDF5 file h5_file and the names of images and associated palettes within that file as input and produces the GIF file gif_file, containing those images, as output.

    h52gif expects at least one h5_image. You may repeat
         -i h5_image [-p h5_palette]
    up to 50 times, for a maximum of 50 images.

    Options and Parameters:
    h5_file The name of the input HDF5 file
    gif_file The name of the output GIF file
    -i h5_image Image option, specifying the name of an HDF5 image or dataset containing an image to be converted
    -p h5_palette     Palette option, specifying the name of an HDF5 dataset containing a palette to be used in an image conversion

    Exit Status:
    0 Succeeded.
    > 0     An error occurred.

    History:
    Release     Change
    1.8.5 Tool exit status codes updated.

    Last modified: 17 July 2013
    Tool Name: h5toh4
    The h5toh4 command-line utility is distributed with the H4toH5 Conversion Library and documented in the “H4toH5 Conversion Library Reference Manual.”

    Last modified: 17 July 2013
    Tool Name: h4toh5
    The h4toh5 command-line utility is distributed with the H4toH5 Conversion Library and documented in the “H4toH5 Conversion Library Reference Manual.”

    Last modified: 20 August 2013
    Tool Name: h5stat
    Syntax:
    h5stat [OPTIONSfile

    Purpose:
    Reports statistics about an HDF5 file and its objects.

    Description:
    h5stat reports selected statistics regarding an HDF5 file and the objects in that file.

    Options and Parameters:
    -h   or   --help Print a usage message and exit.
    -V   or   --version Print version of HDF5 and exit.
      
    -f   or   --file Print file information.
    -F   or   --filemetadata Print file space information for file metadata.
    -g   or   --group Print group information.
    -l N   or   --links=N Set the threshold for the number of links when printing information for small groups.
    N is an integer greater than 0. The default threshold is 10.
    -G   or   --groupmetadata    Print file space information for group metadata.
    -d   or   --dset Print dataset information.
    -m N   or   --dims=N Set the threshold for the dimension sizes when printing information for small datasets.
    N is an integer greater than 0. The default threshold is 10.
    -D   or   --dsetmetadata Print file space information for dataset metadata.
    -T   or   --dtypemetadata Print dataset datatype information.
    -A   or   --attribute Print attribute information.
    -a N   or   --numattrs=N Set the threshold for the number of of attributes when printing information for small numbers of attributes.
    N is an integer greater than 0. The default threshold is 10.
    -S   or   --summary Print summary of file space information.

    Exit Status:
    0 Succeeded.
    > 0     An error occurred.

    History:
    Release     Change
    1.8.12 Options added in this release:
         -l N,   --links=N
         -m N,   --dims=N
         -a N,   --numattrs=N
    1.8.9 Option added in this release:
         -S,   --summary
    1.8.0 Tool introduced in this release.

    Last modified: 10 November 2010
    Tool Name: h5check
    Syntax:
    h5check [OPTIONS] file

    Purpose:
    Verifies that an HDF5 file is encoded according to the HDF5 specification.

    Motivation:
    h5check is a validation tool designed to verify that an HDF5 file is encoded according to the HDF5 File Format Specification. The purpose is to ensure data model integrity and long-term compatibility between evolving versions of the HDF5 Library.

    Independent Verification Tool: Note that h5check is designed to operate independently of the HDF5 Library:

    Description:
    Given a file, h5check scans through the encoded content, verifying it against the defined library format. If it finds any non-compliance, h5check prints the error and the reason behind the non-compliance; if possible, it continues the scanning. If h5check does not find any non-compliance, it prints an approval statement upon completion.

    By default, the file is verified against the latest version of the file format; as of this writing, that is the format recognized by the HDF5 Release 1.8.x series. A format version can be explicitly specified with the -fn (or --format=n) option. For example, -f16 (or --format=16) would specify verification against the format recognized by the HDF5 Release 1.6.x series.

    Options:
    -h, --help
    Print usage message and exit.
    -V, --version
    Print version number and exit.
    -vn, --verbose n
    Set verbose mode:
    n=0 Terse Indicate only whether file is compliant.
    n=1 Normal Print progress and all errors found.   (Default)
    n=2 Verbose Print all known information; usually used for debugging.
    -e, --external
    Validate external links existing in the file.
    -fn, --format n
    Set library release version against which the file is to be validated:
    n=16 Validate according to HDF5 Release 1.6.x series.
    n=18 Validate according to HDF5 Release 1.8.x series.   (Default)
    -oa, --object a
    Check object header, where a is the address of the object header to be validated.

    Exit Status:
    0 Succeeded.
    1 Command failures, such as argument errors.
    2 Format compliance errors found.

    History:
    Release     Change
    1.8.5 Tool first distributed shortly before this release.

    Last modified: 24 April 2014
    Tool Name: h5perf
    Syntax:
    h5perf [-h | --help]
    h5perf [options]

    Purpose:
    Tests Parallel HDF5 performance.

    Description:
    h5perf is a tool for testing the performance of the Parallel HDF5 Library. The tool can perform testing with 1-dimensional and 2-dimensional buffers and datasets. For details regarding data organization and access, see the “h5perf User Guide.”

    The following environment variables have the following effects on h5perf behavior:
         HDF5_NOCLEANUP If set, h5perf does not remove data files.
    (Default: Data files are removed.)
      HDF5_MPI_INFO Must be set to a string containing a list of semi-colon separated key=value pairs for the MPI INFO object.
    Example:
      HDF5_PARAPREFIX   Sets the prefix for parallel output data files.

    Options and Parameters:

    Exit Status:
    0 Succeeded.
    >0     An error occurred.
    History:

    Tool Name: h5perf_serial
    Syntax:
    h5perf_serial [-h | --help]
    h5perf_serial [options]

    Purpose:
    Tests HDF5 serial performance.

    Description:
    h5perf_serial provides tools for testing the performance of the HDF5 Library in serial mode.

    See “h5perf_serial, a Serial File System Benchmarking Tool” for a complete description of this tool.

    The following environment variable can be set to control the specfied aspect of h5perf_serial behavior:
         HDF5_NOCLEANUP      If set, h5perf_serial does not remove data files.
    (Default: Data files are removed.)
         HDF5_PREFIX      Sets the prefix for output data files.

    Options and Parameters:

    Exit Status:
    0 Succeeded.
    >0     An error occurred.
    History:

    Last modified: 10 May 2013
    Tool Name: h5redeploy
    Syntax:
    h5redeploy [help | -help]
    h5redeploy [-echo] [-force] [-prefix=dir] [-exec-prefix=dir] [-libdir=dir] [-includedir=dir] [-tool=tool] [-show]

    Purpose:
    Updates HDF5 compiler tools after an HDF5 software installation in a new location.

    Description:
    h5redeploy updates the HDF5 compiler tools after the HDF5 software has been installed in a new location.

    Options and Parameters:
    help, -help Prints a help message.
    -echo Shows all the shell commands executed.
    -force Performs the requested action without offering any prompt requesting confirmation.
    -prefix=dir Specifies a new directory in which to find the HDF5 subdirectories lib/ and include/.
    (Default: current working directory)
    -exec-prefix=dir
                      
    Specifies a new directory in which to find the HDF5 lib/ subdirectory.
    (Default: prefix)
    -libdir=dir Specifies a new directory for the HDF5 lib/ directory.
    (Default: exec-prefix/lib)
    -includedir=dir Specifies a new directory for the HDF5 include/ directory.
    (Default: prefix/include)
    -tool=tool Specifies the tool to update.
    tool must be in the current directory and must be writable.
    (Default: h5cc h5pcc h5fc h5pfc h5c++)
    -show Shows all of the shell commands to be executed without actually executing them.

    Exit Status:
    0 Succeeded.
    > 0     An error occurred.

    History:
    Release     Command Line Tool
    1.8.11 -exec-prefix, -libdir, and -includedir options added.
    1.8.5 Tool exit status codes updated.
    1.6.0 Tool introduced in this release.

    Last modified: 25 September 2013
    Tool Name: h5cc and h5pcc
    Syntax:
    h5cc [OPTIONS] <compile line>
    h5pcc [OPTIONS] <compile_line>

    Purpose:
    Helper scripts to compile HDF5 applications.

    Description:
    h5cc and h5pcc can be used in much the same way as mpicc by MPICH is used to compile an HDF5 program. These tools take care of specifying on the command line the locations of the HDF5 header files and libraries. h5cc is for use in serial computing environments; h5pcc is for parallel environments.

    h5cc and h5pcc subsume all other compiler scripts in that if you have used a set of scripts to compile the HDF5 library, then h5cc and h5pcc also use those scripts. For example, when compiling an MPICH program, you use the mpicc script. If you have built HDF5 using MPICH, then h5cc uses the MPICH program for compilation.

    Some programs use HDF5 in only a few modules. It is not necessary to use h5cc or h5pcc to compile those modules which do not use HDF5. In fact, since h5cc and h5pcc are only convenience scripts, you can still compile HDF5 modules in the normal manner, though you will have to specify the HDF5 libraries and include paths yourself. Use the -show option to see the details. For example, running h5cc for an HDF5 library built using gcc with --disable-shared, zlib and szlib, all installed in /usr/local/lib would provide this compile command:

    gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE      \
        -D_BSD_SOURCE -L/usr/local/lib /usr/local/lib/libhdf5_hl.a            \
        /usr/local/lib/libhdf5.a /usr/local/lib/libsz.a /usr/local/lib/libz.a \
        -lm -W1,-rpath -W1,/usr/local/lib   [OPTIONS] <compile line>                          

    An example of how to use h5cc to compile the program hdf_prog, which consists of the modules prog1.c and prog2.c and uses the HDF5 shared library, would be as follows. h5pcc is used in an identical manner.

         # h5cc -c prog1.c
         # h5cc -c prog2.c
         # h5cc -shlib -o hdf_prog prog1.o prog2.o

    Options and Parameters:

    Environment Variables:
    When set, these environment variables override some of the built-in h5cc and h5pcc defaults.

    The last four of these environment variables have corresponding variables with names ending in BASE that can also be set by editing their values in the "Things You Can Modify to Override HDF5 Library Build Components" section of the h5cc and h5pcc scripts.

    Note that adding library paths to HDF5_LDFLAGS where another HDF5 version is located may link your program with that other HDF5 Library version.

    Exit Status:
    0 Succeeded.
    > 0     An error occurred.

    History:

    Last modified: 25 September 2013
    Tool Name: h5fc and h5pfc
    Syntax:
    h5fc [OPTIONS] <compile line>
    h5pfc [OPTIONS] <compile_line>

    Purpose:
    Helper scripts to compile HDF5 Fortran applications.

    Description:
    h5fc and h5pfc can be used in much the same way mpif90 by MPICH is used to compile an HDF5 program. These tools take care of specifying on the command line the locations of the HDF5 header files and libraries. h5fc is for use in serial computing environments; h5pfc is for parallel environments.

    h5fc and h5pfc subsume all other compiler scripts in that if you have used a set of scripts to compile the HDF5 Fortran library, then h5fc and h5pfc also use those scripts. For example, when compiling an MPICH program, you use the mpif90 script. If you have built HDF5 using MPICH, then h5fc uses the MPICH program for compilation.

    Some programs use HDF5 in only a few modules. It is not necessary to use h5fc and h5pfc to compile those modules which do not use HDF5. In fact, since h5fc and h5pfc are only convenience scripts, you can still compile HDF5 Fortran modules in the normal manner, though you will have to specify the HDF5 libraries and include paths yourself. Use the -show option to see the details.

    An example of how to use h5fc to compile the program hdf_prog, which consists of the modules prog1.f90 and prog2.f90 and uses the HDF5 Fortran library, would be as follows. h5pfc is used in an identical manner.

            # h5fc -c prog1.f90
            # h5fc -c prog2.f90
            # h5fc -o hdf_prog prog1.o prog2.o 

    Options and Parameters:
    -help Prints a help message.
    -echo Show all the shell commands executed.
    -prefix=DIR Use the directory DIR to find HDF5 lib/ and include/ subdirectories.
    Default: prefix specified when configuring HDF5.
    -show Show the commands without executing them.
    -shlib Compile using shared HDF5 libraries.
    Default for HDF5 built without static libraries.
    -noshlib Compile using static HDF5 libraries.
    Default for HDF5 built with static libraries.
    <compile line>     The normal compile line options for your compiler.
    h5fc and h5pfc use the the same compiler you used to compile HDF5. Check your compiler's manual for more information on which options are needed.

    Environment Variables:
    When set, these environment variables override some of the built-in h5fc and h5pfc defaults.
    HDF5_FC Use a different Fortran compiler.
    HDF5_FLINKER Use a different linker.
    HDF5_USE_SHLIB=[yes|no]   Use shared version of the HDF5 library.
    Default: no, except when HDF5 built with only shared libraries.
    HDF5_FFLAGS Use additional Fortran compiler flags.
    HDF5_LDFLAGS Use additional library paths.
    HDF5_LIBS Use additional libraries.

    The last three of these environment variables have corresponding variables with names ending in BASE that can also be set by editing their values in the "Things You Can Modify to Override HDF5 Library Build Components" section of the h5fc and h5pfc scripts.

    Note that adding library paths to HDF5_LDFLAGS where another HDF5 version is located may link your program with that other HDF5 Library version.

    Exit Status:
    0 Succeeded.
    > 0     An error occurred.

    History:
    Release     Change
    1.8.12 Tool modified to switch default to link to shared libraries when HDF5 configured with --disable-static.
    1.8.11 Tool updated to recognize .f95, .f03, and .f08 file extensions.
    1.8.6 Three compiler flags and environment variables added.
    1.8.5 Tool exit status codes updated.
    1.6.0 Tool introduced in this release.

    Last modified: 25 September 2013
    Tool Name: h5c++
    Syntax:
    h5c++ [OPTIONS] <compile line>

    Purpose:
    Helper script to compile HDF5 C++ applications.

    Description:

    h5c++ can be used in much the same way MPIch is used to compile an HDF5 program. It takes care of specifying where the HDF5 header files and libraries are on the command line.

    h5c++ supersedes all other compiler scripts in that if you've used one set of compiler scripts to compile the HDF5 C++ library, then h5c++ uses those same scripts. For example, when compiling an MPIch program, you use the mpiCC script.

    Some programs use HDF5 in only a few modules. It isn't necessary to use h5c++ to compile those modules which don't use HDF5. In fact, since h5c++ is only a convenience script, you are still able to compile HDF5 C++ modules in the normal way. In that case, you will have to specify the HDF5 libraries and include paths yourself. Use the -show option to see the details.

    An example of how to use h5c++ to compile the program hdf_prog, which consists of modules prog1.cpp and prog2.cpp and uses the HDF5 C++ library, would be as follows:

            # h5c++ -c prog1.cpp
            # h5c++ -c prog2.cpp
            # h5c++ -o hdf_prog prog1.o prog2.o

    Options and Parameters:
    -help Prints a help message.
    -echo Show all the shell commands executed.
    -prefix=DIR Use the directory DIR to find HDF5 lib/ and include/ subdirectories
    Default: prefix specified when configuring HDF5.
    -show Show the commands without executing them.
    -shlib Compile using shared HDF5 libraries.
    Default for HDF5 built without static libraries.
    -noshlib Compile using static HDF5 libraries.
    Default for HDF5 built with static libraries.
    <compile line>
                    
    The normal compile line options for your compiler. h5c++ uses the same compiler you used to compile HDF5. Check your compiler's manual for more information on which options are needed.

    Environment Variables:
    When set, these environment variables override some of the built-in defaults of h5c++.

    The last four of these environment variables have corresponding variables with names ending in BASE that can also be set by editing their values in the "Things You Can Modify to Override HDF5 Library Build Components" section of the h5c++ script.

    Note that adding library paths to HDF5_LDFLAGS where another HDF5 version is located may link your program with that other HDF5 Library version.

    Exit Status:
    0 Succeeded.
    > 0     An error occurred.

    History:
    Release     Command Line Tool
    1.8.12 Tool modified to switch default to link to shared libraries when HDF5 configured with --disable-static.
    1.8.6 Four compiler flags and environment variables added.
    1.8.5 Tool exit status codes updated.
    1.6.0 Tool introduced in this release.

    HDF5 documents and links 
    Introduction to HDF5 
    HDF5 User Guide 
    In the HDF5 Reference Manual 
    H5DS   H5IM   H5LT   H5PT   H5TB  Optimized 
    H5   H5A   H5D   H5E   H5F   H5G   H5I 
    H5L   H5O   H5P   H5R   H5S   H5T   H5Z 
    Tools   Datatypes   Fortran   Compatibility Macros 
    Collective Calls in Parallel 

    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