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-usage: h5repack [OPTIONS] file1 file2
- file1 Input HDF5 File
- file2 Output HDF5 File
- ERROR
- --enable-error-stack Prints messages from the HDF5 error stack as they occur.
- Optional value 2 also prints file open errors.
- OPTIONS
- -h, --help Print a usage message and exit
- -v N, --verbose=N Verbose mode, print object information.
- N - is an integer greater than 1, 2 displays read/write timing
- -V, --version Print version number and exit
- -n, --native Use a native HDF5 type when repacking
- --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
- -L, --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
- -c L1, --compact=L1 Maximum number of links in header messages
- -d L2, --indexed=L2 Minimum number of links in the indexed format
- -s S[:F], --ssize=S[:F] Shared object header message minimum size
- -m M, --minimum=M Do not apply the filter to datasets smaller than M
- -e E, --file=E Name of file E with the -f and -l options
- -u U, --ublock=U Name of file U with user block data to be added
- -b B, --block=B Size of user block to be added
- -M A, --metadata_block_size=A Metadata block size for H5Pset_meta_block_size
- -t T, --threshold=T Threshold value for H5Pset_alignment
- -a A, --alignment=A Alignment value for H5Pset_alignment
- -q Q, --sort_by=Q Sort groups and attributes by index Q
- -z Z, --sort_order=Z Sort groups and attributes by order Z
- -f FILT, --filter=FILT Filter type
- -l LAYT, --layout=LAYT Layout type
- -S FS_STRATEGY, --fs_strategy=FS_STRATEGY File space management strategy for
- H5Pset_file_space_strategy
- -P FS_PERSIST, --fs_persist=FS_PERSIST Persisting or not persisting free-
- space for H5Pset_file_space_strategy
- -T FS_THRESHOLD, --fs_threshold=FS_THRESHOLD Free-space section threshold
- for H5Pset_file_space_strategy
- -G FS_PAGESIZE, --fs_pagesize=FS_PAGESIZE File space page size for
- H5Pset_file_space_page_size
-
- 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
-
- BOUND is an integer indicating the library release versions to use when
- creating objects in the file (see H5Pset_libver_bounds()):
- 0: This is H5F_LIBVER_EARLIEST in H5F_libver_t struct
- 1: This is H5F_LIBVER_V18 in H5F_libver_t struct
- 2: This is H5F_LIBVER_V110 in H5F_libver_t struct
- 3: This is H5F_LIBVER_V112 in H5F_libver_t struct
- 4: This is H5F_LIBVER_V114 in H5F_libver_t struct
- (H5F_LIBVER_LATEST is aliased to H5F_LIBVER_V114 for this release
-
- 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 to persisting free-space or 0 to 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.
-
- FILT - 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 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)
-
- LAYT - is a string with the 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 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)
-
-Examples of use:
-
-1) h5repack -v -f GZIP=1 file1 file2
-
- GZIP compression with level 1 to all objects
-
-2) h5repack -v -f dset1:SZIP=8,NN file1 file2
-
- SZIP compression with 8 pixels per block and NN coding method to object dset1
-
-3) h5repack -v -l dset1,dset2:CHUNK=20x10 -f 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 -L -c 10 -s 20:dtype file1 file2
-
- Using latest file format with maximum compact group size of 10 and
- minimum shared datatype size of 20
-
-5) h5repack -f SHUF -f GZIP=1 file1 file2
-
- Add both filters SHUF and GZIP in this order to all datasets
-
-6) h5repack -f 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
-