H5Z-SPERR

This is an HDF5 Plugin for the SPERR compressor. It is registered with the HDF Group with a plugin ID of 32028.

Build and Install

Needless to say, H5Z-SPERR depends on both HDF5 and SPERR. After HDF5 and SPERR are installed, H5Z-SPERR can be configured and built using cmake:

export HDF5_ROOT=/path/to/your/preferred/HDF5/installation
mkdir build-H5-SPERR && cd build-H5-SPERR
cmake -DSPERR_INSTALL_DIR=/path/to/SPERR/installation     \
      -DCMAKE_INSTALL_PREFIX=/path/to/install/this/plugin \
      /path/to/H5Z-SPERR/source/code
make install

The plugin library file libh5z-sperr.so will be placed at directory /path/to/install/this/plugin.

Use As a Dynamically Loaded Plugin

Using the dynamically loaded plugin mechanism by HDF5, one may use H5Z-SPERR by simply setting the environment variable HDF5_PLUGIN_PATH to the directory containing the plugin library file:

export HDF5_PLUGIN_PATH=/path/to/install/this/plugin

The user program does not need to link to this plugin or SPERR; it only needs to specify the plugin ID of 32028.

Use in Python

H5Z-SPERR version 0.1.3 is supported by the Python package hdf5plugin since version 5.0.0. One can install the package by issuing

pip install hdf5plugin [--user]           # using pip
conda install -c conda-forge hdf5plugin   # using conda

and use it by importing these two packages:

import h5py         # provide general HDF5 support
import hdf5plugin   # provide HDF5 plugin support

Handling of Missing Values

Simulation models sometimes use a special value (i.e., missing value) to indicate that there's no meaningful value at that specific location. For example, in an ocean simulation, all the land area is marked by missing values. The most often seen missing values are either NaN, or an extremely large value, such as 1e35 or -9.9e35. When these missing values participate in compression, they easily introduce numeric error and result in data corruption.

H5Z-SPERR can handle common missing values with a little help from the user. Specifically, a user can indicate that there's potentially missing values, and H5Z-SPERR will use a compact bitmask to keep track of where exactly those missing values are. H5Z-SPERR then replaces them with a value that is friendly to SPERR compression before passing the field to the SPERR compressor.

During decompression, H5Z-SPERR fills the original missing value at locations indicated by the compact bitmask. Specifically, if the original missing values are NaN, then NaN will be filled. If the orignal missing values are values with a magnitude larger than 1e35, then the first occurance of such values will be used to fill in all missing value locations.

Users use an integer to indicate the potential existance of missing values:

• Mode 0: no missing values;
• Mode 1: there are potential NaNs;
• Mode 2: there are potential values with a magnitude larger than 1e35.

H5Z-SPERR behaves accordingly: (1e35 denotes the first occurance of such values)

Mode	Actual Input Data	Filter Behavior
0	No NaN, no 1e35	✔️ Normal SPERR compression
0	Has NaN or 1e35	❌ Likely numeric error
1	No NaN, no 1e35	✔️ Normal SPERR compression
1	Has NaN, no 1e35	✔️ Normal SPERR compression; NaN is restored at its exact locations
1	Regardless of NaN, has 1e35	❌ Likely numeric error
2	No NaN, no 1e35	✔️ Normal SPERR compression
2	No NaN, has 1e35	✔️ Normal SPERR compression; 1e35 is restored at its exact locations
2	Has NaN, regardless of 1e35	❌ Likely numeric error

Final note: if a variable is indicated to have missing values, but it actually does not, then there's no bitmasks involved thus no storage overhead!

Find cd_values[]

To apply SPERR compression using the HDF5 plugin, one needs to specify 1) what compression mode and 2) what compression quality to use. Supported compression modes and qualities are summarized below:

Mode No.	Mode Meaning	Meaningful Quality Range
1	Fixed bit-per-pixel (BPP)	0.0 < quality < 64.0
2	Fixed peak signal-to-noise ratio (PSNR)	0.0 < quality
3	Fixed point-wise error (PWE)	0.0 < quality

In addition, the rank order needs to be swapped sometimes to achieve the best compression. For example, if a 2D slice of dimensions (64, 128) has the dim=128 rank being the fastest varying rank, then this slice needs a "rank order swap" to achieve the best compression. In general, given dimensions of (NX, NY, NZ), we want the X rank to be varying the fastest, and the Z rank to be varying the slowest, before the data is passed to the compressor. "Rank order swap" helps to achieve it.

The HDF5 libraries takes in these compression parameters as one or more 32-bit unsigned int values, which are named cd_values[] in most HDF5 routines. In the case of H5Z-SPERR, there is exactly one unsigned int used to carry compression-related information, and possibly one more unsigned int to indicate the potential existance of missing values.

Find cd_values[] Using the Programming Interface

Using the HDF5 programming interface, cd_values[] carrying the compression parameters are passed to HDF5 routines such as H5Pset_filter(). To find the correct cd_values[], a user needs to include the header h5z-sperr.h from this repository and call the unsigned int H5Z_SPERR_make_cd_values(int mode, double quality, int swap) function to have these two pieces of information correctly encoded. For example:

int mode = 3;              /* Fixed PWE compression */
double quality = 1e-6;     /* PWE tolerance = 1e-6 */
int swap = 1;              /* Enable rank order swap */
unsigned int cd_values = H5Z_SPERR_make_cd_values(mode, quality, swap);   /* Generate cd_values */
H5Pset_filter(prop, 32028, H5Z_FLAG_MANDATORY, 1, &cd_values);            /* Specify SPERR compression in HDF5 */

See a complete example here.

Find cd_values[] Using the CLI Tool generate_cd_values

After building H5Z-SPERR, a command line tool named generate_cd_values becomes available to encode 1) SPERR compression mode, 2) quality, and 3) if to perform rank order swap into a single unsigned int. The produced value can then be used in other command line tools such as h5repack. In the following example, generate_cd_values reports that 268651725u encodes fixed-rate compression with a bitrate of 3.3 bit-per-value, without doing rank order swap.

$ ./bin/generate_cd_values 1 3.3
For fixed-rate compression with a bitrate of 3.3, without swapping rank orders,
H5Z-SPERR cd_values = 268651725u (Filter ID = 32028).
Please use this value as a single 32-bit unsigned integer in your applications.

Note: an integer produced by generate_cd_values can be decoded by another command line tool, decode_cd_values, to show the coded compression parameters.

Examples

Assume using the nccopy tool:

# Compress variable VAR0, using fixed-rate compression, bitrate = 3.3, no special handling of missing values.
nccopy -F "VAR0, 268651725u" <input_file> <output_file>
nccopy -F "VAR0, 268651725u, 0" <input_file> <output_file>

# Compress variable VAR1, using fixed-rate compression, bitrate = 3.3. VAR1 might have NaNs!
nccopy -F "VAR1, 268651725u, 1" <input_file> <output_file>

# Compress variable VAR2, using fixed-rate compression, bitrate = 3.3. VAR2 might have values such as 1e35!
nccopy -F "VAR2, 268651725u, 2" <input_file> <output_file>