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HDF5 Last Updated on 2025-10-31
The HDF5 Field Guide
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The HDF5 h5repack Tool

Navigate back: Main / HDF5 User Guide / Command Line Tools for HDF5 Files

h5repack

Introduction

With h5repack, you can write an HDF5 file to a new file and change the layout for objects in the new file.

Usage

h5repack [OPTIONS] file1 file2

  • file1 Input HDF5 File
  • file2 Output HDF5 File

Error Report Option

  • –enable-error-stack Prints messages from the HDF5 error stack as they occur. Optional value 2 also prints file open errors, –enable-error-stack=2.

Options

  • –help Print a usage message and exit
  • –verbose=N Verbose mode, print object information. N - is an integer greater than 1, 2 displays read/write timing
  • –version Print the library version number and exit
  • –native Use a native HDF5 type when repacking
  • –page-buffer-size=N Set the page buffer cache size, N=non-negative integers
  • –src-vol-value Value (ID) of the VOL connector to use for opening the input HDF5 file specified
  • –src-vol-name Name of the VOL connector to use for opening the input HDF5 file specified
  • –src-vol-info VOL-specific info to pass to the VOL connector used for opening the input HDF5 file specified
  • –dst-vol-value Value (ID) of the VOL connector to use for opening the output HDF5 file specified
  • –dst-vol-name Name of the VOL connector to use for opening the output HDF5 file specified
  • –dst-vol-info VOL-specific info to pass to the VOL connector used for opening the output HDF5 file specified
  • –src-vfd-value Value (ID) of the VFL driver to use for opening the input HDF5 file specified
  • –src-vfd-name Name of the VFL driver to use for opening the input HDF5 file specified
  • –src-vfd-info VFD-specific info to pass to the VFL driver used for opening the input HDF5 file specified
  • –dst-vfd-value Value (ID) of the VFL driver to use for opening the output HDF5 file specified
  • –dst-vfd-name Name of the VFL driver to use for opening the output HDF5 file specified
  • –dst-vfd-info VFD-specific info to pass to the VFL driver used for opening the output HDF5 file specified
  • –latest Use latest version of file format This option will take precedence over the options –low and –high
  • –low=BOUND The low bound for library release versions to use when creating objects in the file (default is H5F_LIBVER_EARLIEST)
  • –high=BOUND The high bound for library release versions to use when creating objects in the file (default is H5F_LIBVER_LATEST)
  • –merge Follow external soft link recursively and merge data
  • –prune Do not follow external soft links and remove link
  • –merge –prune Follow external link, merge data and remove dangling link
  • –compact=L1 Maximum number of links in header messages
  • –indexed=L2 Minimum number of links in the indexed format
  • –ssize=S[:F] Shared object header message minimum size
  • –minimum=M Do not apply the filter to datasets smaller than M
  • –file=E Name of file E with the –file and –layout options
  • –ublock=U Name of file U with user block data to be added
  • –block=B Size of user block to be added
  • –metadata_block_size=A Metadata block size for H5Pset_meta_block_size
  • –threshold=T Threshold value for H5Pset_alignment
  • –alignment=A Alignment value for H5Pset_alignment
  • –sort_by=Q Sort groups and attributes by index Q
  • –sort_order=Z Sort groups and attributes by order Z
  • –filter=FILT Filter type
  • –layout=LAYT Layout type
  • –fs_strategy=FS_STRATEGY File space management strategy for H5Pset_file_space_strategy
  • –fs_persist=FS_PERSIST Persisting or not persisting free-space for H5Pset_file_space_strategy
  • –fs_threshold=FS_THRESHOLD : Free-space section threshold for H5Pset_file_space_strategy
  • –fs_pagesize=FS_PAGESIZE File space page size for H5Pset_file_space_page_size

Arguments to Certain Options

  • M - is an integer greater than 1, size of dataset in bytes (default is 0)
  • E - is a filename.
  • S - is an integer
  • U - is a filename.
  • T - is an integer
  • A - is an integer greater than zero
  • Q - is the sort index type for the input file. It can be "name" or "creation_order" (default)
  • Z - is the sort order type for the input file. It can be "descending" or "ascending" (default)
  • B - is the user block size, any value that is 512 or greater and is a power of 2 (1024 default)
  • F - is the shared object header message type, any of <dspace|dtype|fill| pline|attr>. If F is not specified, S applies to all messages

Library Version Bounds

BOUND is an integer indicating the library release versions to use when creating objects in the file (see H5Pset_libver_bounds()):

File Strategy Settings

FS_STRATEGY is a string indicating the file space strategy used:

  • FSM_AGGR The mechanisms used in managing file space are free-space managers, aggregators and virtual file driver.
  • PAGE The mechanisms used in managing file space are free-space managers with embedded paged aggregation and virtual file driver.
  • AGGR The mechanisms used in managing file space are aggregators and virtual file driver.
  • NONE The mechanisms used in managing file space are virtual file driver.
  • The default strategy when not set is FSM_AGGR without persisting free-space.
  • FS_PERSIST is 1 for persisting free-space or 0 for not persisting free-space. The default when not set is not persisting free-space. The value is ignored for AGGR and NONE strategies.
  • FS_THRESHOLD is the minimum size (in bytes) of free-space sections to be tracked by the library. The default when not set is 1. The value is ignored for AGGR and NONE strategies.
  • FS_PAGESIZE is the size (in bytes) >=512 that is used by the library when the file space strategy PAGE is used. The default when not set is 4096.

Applying a Third-party Filter

FILT - is a string with the format:

  • <objects list>:<name of filter>=<filter parameters>
  • <objects list> is a comma separated list of object names, meaning apply compression only to those objects. If no names are specified, the filter is applied to all objects
  • <name of filter> can be:
    • 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 NBIT filter (NBIT compression)
    • SOFF to apply the HDF5 Scale/Offset filter
    • UD to apply a user defined filter
    • NONE to remove all filters
  • <filter parameters> is optional filter parameter information
    • GZIP=<deflation level> from 1-9
    • SZIP=<pixels per block,coding> pixels per block is a even number in 2-32 and coding method is either EC or NN
    • SHUF (no parameter)
    • FLET (no parameter)
    • NBIT (no parameter)
    • SOFF=<scale_factor,scale_type> scale_factor is an integer and scale_type is either IN or DS
    • UD=<filter_number,filter_flag,cd_value_count,value1[,value2,...,valueN]>
      • Required values filter_number, filter_flag, cd_value_count, value1
      • Optional values value2 to valueN
      • filter_flag 1 is OPTIONAL or 0 is MANDATORY
    • NONE (no parameter)

Layout Settings

LAYT - is a string with the format:

  • <objects list>:<layout type>=<layout parameters>
  • <objects list> is a comma separated list of object names, meaning that layout information is supplied for those objects. If no names are specified, the layout type is applied to all objects
  • <layout type> can be:
    • CHUNK to apply chunking layout
    • COMPA to apply compact layout
    • CONTI to apply contiguous layout
  • <layout parameters> is optional layout information
    • CHUNK=DIM[xDIM...xDIM], the chunk size of each dimension
    • COMPA (no parameter)
    • CONTI (no parameter)

NOTE

The environment variable H5TOOLS_BUFSIZE can be set to the number of MBs to change the default hyperslab buffer size from 32MB.

setenv H5TOOLS_BUFSIZE=64 to double the hyperslab buffer.

Usage Examples

  • 1) h5repack –verbose –filter=GZIP=1 file1 file2 
     GZIP compression with level 1 to all objects
  • 2) h5repack –verbose –filter=dset1:SZIP=8,NN file1 file2 
     SZIP compression with 8 pixels per block and NN coding method to object dset1
  • 3) h5repack –verbose –layout=dset1,dset2:CHUNK=20x10 –filter=dset3,dset4,dset5:NONE file1 file2 
     Chunked layout, with a layout size of 20x10, to objects dset1 and dset2
 and remove filters to objects dset3, dset4, dset5
  • 4) h5repack –latest –compact=10 –ssize=20:dtype file1 file2 
     Using latest file format with maximum compact group size of 10 and
 minimum shared datatype size of 20
  • 5) h5repack –filter=SHUF –filter=GZIP=1 file1 file2 
     Add both filters SHUF and GZIP in this order to all datasets
  • 6) h5repack –filter=UD=307,0,1,9 file1 file2 
     Add bzip2 filter to all datasets
  • 7) h5repack –low=0 –high=1 file1 file2 
     Set low=H5F_LIBVER_EARLIEST and high=H5F_LIBVER_V18 via
 H5Pset_libver_bounds() when creating the repacked file, file2

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