---
name: "h5repack"
section: "1"
platform: "linux"
package: "hdf5-tools"
version: "1.14.5+repack-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/h5repack"
---

# h5repack(1)

Copy an HDF5 file to a new file with or without compression/chunking

## NAME

h5repack - Copy an HDF5 file to a new file with or without compression/chunking

## SYNOPSIS

**h5repack** **-i** *file1* **-o** *file2* \[**-h**\] \[**-v**\] \[**-f** *´filter´*\] \[**-l** *´layout´*\] \[**-m** *number*\] \[**-e** *file*\]

## DESCRIPTION

**h5repack** is a command line tool that applies HDF5 filters to a input  file *file1*, saving the output in a new file,  *file2*.

*´filter´* is a string with the format\
 	\<list of objects\> : \<name of filter\> = \<filter parameters\>.

*\<list of objects\>* is a comma separated list of object names meaning  apply compression only to those objects. If no object 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\
     NONE, to remove the filter

*\<filter parameters\>* contains the optional compression information:\
     SHUF (no parameter) \
     FLET (no parameter) \
     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 'EC' or 'NN')

*´layout´ is a string with the format*\
     \<list of objects\> : \<layout type\>

*\<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: \
     CHUNK, to apply chunking layout \
     COMPA, to apply compact layout \
     CONTI, to apply continuous layout

*\<layout parameters\>* is present for the chunk case only it is the  chunk size of each dimension: *\<dim\_1 x dim\_2 x ... dim\_n\>*

## OPTIONS

- *file1*,*file2*

  The input and output HDF5 files

- **-h**

  Print a help message

- **-f** *filter*

  Filter type

- **-l** *layout*

  Layout type

- **-v**

  Verbose mode. Print output (list of objects in the file, filters and  layout applied).

- **-e** *file*

  File with the **-f** and **-l** options (only filter and layout flags)

- **-d** *delta*

  Print only differences that are greater than the limit *delta*. *delta* must be a positive number. The comparison criterion is whether the  absolute value of the difference of two corresponding values is greater  than *delta* (e.g., \|*a*-*b*\| \>  *delta*, where *a* is a value in *file1* and *b* is a value in  *file2*).

- **-m** *number*

  Do not apply the filter to objects which size in bytes is smaller  than number. If no size is specified a minimum of 1024 bytes is assumed.

## EXAMPLES

Apply GZIP compression to all objects in *file1* and save the output in  *file2*:

	h5repack -i file1 -o file2 -f GZIP=1 -v

Apply SZIP compression only to object *´dset1´*:

	h5repack -i file1 -o file2 -f dset1:SZIP=8,NN -v

Apply a chunked layout to objects *´dset1´* and *´dset2´*:

	h5repack -i file1 -o file2 -l dset1,dset2:CHUNK=20x10 -v

## SEE ALSO

[*h5dump*(1)](/h5dump/1.md), [*h5ls*(1)](/h5ls/1.md), [*h5diff*(1)](/h5diff/1.md), [*h5import*(1)](/h5import/1.md), [*gif2h5*(1)](/gif2h5/1.md), [*h52gif*(1)](/h52gif/1.md), *h5perf*(1), [*h5repart*(1)](/h5repart/1.md).