pragzip 0.6.0
Parallel random access to gzip files
License: MIT
Requires Python: >=3.6

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# Pragzip: Parallel Random Access Gzip

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(Alternative Name: Rapidgzip: Random Access Parallel (Indexed) Decompression for Gzip Files)

This repository contains the command line tool `pragzip`, which can be used for parallel decompression of almost any gzip file.

The Python module provides a `PragzipFile` class, which can be used to seek inside gzip files without having to decompress them first.
Alternatively, you can use this simply as a **parallelized** gzip decoder as a replacement for Python's builtin `gzip` module in order to fully utilize all your cores.

The random seeking support is the same as provided by [indexed_gzip](https://github.com/pauldmccarthy/indexed_gzip) but further speedups are realized at the cost of higher memory usage thanks to a least-recently-used cache in combination with a parallelized prefetcher.

[This](https://github.com/mxmlnkn/pragzip) repository is a light-weight fork of the [indexed_bzip2](https://github.com/mxmlnkn/indexed_bzip2) repository, in which the main development takes place.
This repository was created for visibility reasons and in order to keep indexed_bzip2 and pragzip releases separate.
It will be updated at least for each release.
Issues regarding pragzip should be opened [here](https://github.com/mxmlnkn/pragzip/issues).


# Table of Contents

1. [Performance](#performance-comparison-with-gzip-module)
   1. [Decompression with Existing Index](#decompression-with-existing-index)
   2. [Decompression from Scratch](#decompression-from-scratch)
2. [Installation](#installation)
3. [Usage](#usage)
   1. [Command Line Tool](#command-line-tool)
   2. [Python Library](#python-library)
   3. [Via Ratarmount](#via-ratarmount)
   4. [C++ Library](#c-library)
4. [Citation](#citation)
5. [Internal Architecture](#internal-architecture)
6. [Tracing the Decoder](#tracing-the-decoder)


# Performance

These are simple timing tests for reading all the contents of a gzip file sequentially.

Results are shown for an AMD Ryzen 3900X 12-core (24 virtual cores) processor and with `gzipFilePath="4GiB-base64.gz"`, which is a 4 GiB gzip compressed file with base64 random data.

Be aware that the chunk size requested from the Python code does influence the performance heavily.
This benchmarks use a chunk size of 512 KiB.

## Decompression with Existing Index

|                      | 4GiB-base64                  | 4GiB-base64     | | 20x-silesia                   | 20x-silesia
|----------------------|------------------------------|-----------------|-|-------------------------------|---------
| Uncompressed Size    | 4 GiB                        |                 | | 3.95 GiB                      |
| Compressed Size      | 3.04 GiB                     |                 | | 1.27 GiB                      |
| **Module**           | **Bandwidth <br/> / (MB/s)** | **Speedup**     | |  **Bandwidth <br/> / (MB/s)** | **Speedup**
| gzip                 |  250                         |    1            | |   293                         |  1
| pragzip (0  threads) | 4480                         | 17.9            | |  4830                         | 16.5
| pragzip (1  threads) |  294                         |  1.2            | |   350                         |  1.2
| pragzip (2  threads) |  580                         |  2.3            | |   678                         |  2.3
| pragzip (6  threads) | 1680                         |  6.7            | |  1940                         |  6.6
| pragzip (12 threads) | 3110                         | 12.5            | |  3460                         | 11.8
| pragzip (24 threads) | 4510                         | 18.0            | |  5070                         | 17.3
| pragzip (32 threads) | 4330                         | 17.3            | |  4720                         | 16.1


## Decompression from Scratch

### Python

|                      | 4GiB-base64                  | 4GiB-base64     | | 20x-silesia                   | 20x-silesia
|----------------------|------------------------------|-----------------|-|-------------------------------|---------
| Uncompressed Size    | 4 GiB                        |                 | | 3.95 GiB                      |
| Compressed Size      | 3.04 GiB                     |                 | | 1.27 GiB                      |
| **Module**           | **Bandwidth <br/> / (MB/s)** | **Speedup**     | |  **Bandwidth <br/> / (MB/s)** | **Speedup**
| gzip                 |  250                         |    1            | |   293                         |  1
| pragzip (0  threads) | 3280                         | 13.1            | |  2280                         |  7.8
| pragzip (1  threads) |  222                         |  0.9            | |   236                         |  0.8
| pragzip (2  threads) |  428                         |  1.7            | |   411                         |  1.4
| pragzip (6  threads) | 1250                         |  5.0            | |  1095                         |  3.7
| pragzip (12 threads) | 2290                         |  9.2            | |  1390                         |  4.8
| pragzip (24 threads) | 3300                         | 13.2            | |  2280                         |  7.8
| pragzip (32 threads) | 3180                         | 12.7            | |  2480                         |  8.5

Note that pragzip is generally faster when given an index because it can delegate the decompression to zlib while it has to use its own gzip decompression engine when no index exists yet.

Note that values deviate roughly by 10% and therefore are rounded.

The code used for benchmarking can be found [here](results/benchmarkPythonModule.py).


# Installation

You can simply install it from PyPI:

```
python3 -m pip install --upgrade pip  # Recommended for newer manylinux wheels
python3 -m pip install pragzip
```

The latest unreleased development version can be tested out with:

```bash
python3 -m pip install --force-reinstall 'git+https://github.com/mxmlnkn/indexed_bzip2.git@master#egginfo=pragzip&subdirectory=python/pragzip'
```

And to build locally, you can use `build` and install the wheel:

```bash
cd python/pragzip
rm -rf dist
python3 -m build .
python3 -m pip install --force-reinstall --user dist/*.whl
```


# Usage

## Command Line Tool

```bash
pragzip --help

# Parallel decoding: 1.7 s
time pragzip -d -c -P 0 sample.gz | wc -c

# Serial decoding: 22 s
time gzip -d -c sample.gz | wc -c
```


## Python Library

### Simple open, seek, read, and close

```python3
from pragzip import PragzipFile

file = PragzipFile( "example.gz", parallelization = os.cpu_count() )

# You can now use it like a normal file
file.seek( 123 )
data = file.read( 100 )
file.close()
```

The first call to seek will ensure that the block offset list is complete and therefore might create them first.
Because of this the first call to seek might take a while.


### Use with context manager

```python3
import os
import pragzip

with pragzip.open( "example.gz", parallelization = os.cpu_count() ) as file:
    file.seek( 123 )
    data = file.read( 100 )
```


### Storing and loading the block offset map

The creation of the list of gzip blocks can take a while because it has to decode the gzip file completely.
To avoid this setup when opening a gzip file, the block offset list can be exported and imported.


### Open a pure Python file-like object for indexed reading

```python3
import io
import os
import pragzip as pragzip

with open( "example.gz", 'rb' ) as file:
    in_memory_file = io.BytesIO( file.read() )

with pragzip.open( in_memory_file, parallelization = os.cpu_count() ) as file:
    file.seek( 123 )
    data = file.read( 100 )
```


## Via Ratarmount

`pragzip` is **planned** to be used as a backend inside ratarmount with version 0.12.
Then, you can use [ratarmount](https://github.com/mxmlnkn/ratarmount) to mount single gzip files easily.

```bash
base64 /dev/urandom | head -c $(( 4 * 1024 * 1024 * 1024 )) | gzip > sample.gz
# Serial decoding: 23 s
time gzip -c -d sample.gz | wc -c

python3 -m pip install --user ratarmount
ratarmount sample.gz mounted

# Parallel decoding: 3.5 s
time cat mounted/sample | wc -c

# Random seeking to the middle of the file and reading 1 MiB: 0.287 s
time dd if=mounted/sample bs=$(( 1024 * 1024 )) \
       iflag=skip_bytes,count_bytes skip=$(( 2 * 1024 * 1024 * 1024 )) count=$(( 1024 * 1024 )) | wc -c
```


# C++ library

Because it is written in C++, it can of course also be used as a C++ library.
In order to make heavy use of templates and to simplify compiling with Python `setuptools`, it is mostly header-only so that integration it into another project should be easy.
The license is also permissive enough for most use cases.

I currently did not yet test integrating it into other projects other than simply manually copying the source in `src/core`, `src/pragzip`, and if integrated zlib is desired also `src/external/zlib`.
If you have suggestions and wishes like support with CMake or Conan, please open an issue.


# Citation

A paper describing the implementation details and showing the scaling behavior with up to 128 cores has been submitted to and [accepted](https://www.hpdc.org/2023/program/technical-sessions/) in [ACM HPDC'23](https://www.hpdc.org/2023/), The 32nd International Symposium on High-Performance Parallel and Distributed Computing. If you use this software for your scientific publication, please cite it as:

This is preliminiary. The final citation will become available end of June 2023.

```bibtex
@inproceedings{rapidgzip,
    author    = {Knespel, Maximilian and Brunst, Holger},
    title     = {Rapidgzip: Parallel Decompression and Seeking in Gzip Files Using Cache Prefetching},
    year      = {2023},
    % isbn    = {},  % To be released end of June
    publisher = {Association for Computing Machinery},
    address   = {New York, NY, USA},
    url       = {https://doi.org/10.1145/3588195.3592992},
    doi       = {10.1145/3588195.3592992},
    abstract  = {Gzip is a file compression format, which is ubiquitously used. Although a multitude of gzip implementations exist, only pugz can fully utilize current multi-core processor architectures for decompression. Yet, pugz cannot decompress arbitrary gzip files. It requires the decompressed stream to only contain byte values 9–126. In this work, we present a generalization of the parallelization scheme used by pugz that can be reliably applied to arbitrary gzip-compressed data without compromising performance. We show that the requirements on the file contents posed by pugz can be dropped by implementing an architecture based on a cache and a parallelized prefetcher. This architecture can safely handle faulty decompression results, which can appear when threads start decompressing in the middle of a gzip file by using trial and error. Using 128 cores, our implementation reaches 8.7 GB/s decompression bandwidth for gzip-compressed base64-encoded data, a speedup of 55 over the single-threaded GNU gzip, and 5.6 GB/s for the Silesia corpus, a speedup of 33 over GNU gzip.},
    booktitle = {Proceedings of the 32nd International Symposium on High-Performance Parallel and Distributed Computing},
    % pages   = {16–29},  % To be released end of June
    numpages  = {13},
    keywords  = {Gzip, Decompression, Parallel Algorithm, Performance, Random Access},
    location  = {Orlando, FL, USA},
    series    = {HPDC '23},
}
```


# Internal Architecture

The main part of the [internal architecture](https://github.com/mxmlnkn/indexed_bzip2/tree/master/python/indexed_bzip2#internal-architecture) used for parallelizing is the same as used for [indexed_bzip2](https://github.com/mxmlnkn/indexed_bzip2).


# Tracing the Decoder


Performance profiling and tracing is done with [Score-P](https://www.vi-hps.org/projects/score-p/) for instrumentation and [Vampir](https://vampir.eu/) for visualization.
This is one way, you could install Score-P with most of the functionalities on Ubuntu 22.04.

## Installation of Dependencies

<details>
<summary>Installation steps for Score-P</summary>

```bash
sudo apt-get install libopenmpi-dev openmpi-bin gcc-11-plugin-dev llvm-dev libclang-dev libunwind-dev \
                     libopen-trace-format-dev otf-trace libpapi-dev

# Install Score-P (to /opt/scorep)
SCOREP_VERSION=8.0
wget "https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-${SCOREP_VERSION}/scorep-${SCOREP_VERSION}.tar.gz"
tar -xf "scorep-${SCOREP_VERSION}.tar.gz"
cd "scorep-${SCOREP_VERSION}"
./configure --with-mpi=openmpi --enable-shared --without-llvm --without-shmem --without-cubelib --prefix="/opt/scorep-${SCOREP_VERSION}"
make -j $( nproc )
make install

# Add /opt/scorep to your path variables on shell start
cat <<EOF >> ~/.bashrc
if test -d /opt/scorep; then
    export SCOREP_ROOT=/opt/scorep
    export PATH=$SCOREP_ROOT/bin:$PATH
    export LD_LIBRARY_PATH=$SCOREP_ROOT/lib:$LD_LIBRARY_PATH
fi
EOF

echo -1 | sudo tee /proc/sys/kernel/perf_event_paranoid

# Check whether it works
scorep --version
scorep-info config-summary
```

</details>

## Tracing

### Results for a version from 2023-02-04

![](https://raw.githubusercontent.com/mxmlnkn/indexed_bzip2/master/results/Screenshot_2023-01-28_17-16-49.png)

### Comparison without and with rpmalloc preloaded

![](https://raw.githubusercontent.com/mxmlnkn/indexed_bzip2/master/results/benchmarks/malloc/Summary_Timeline_scorep-pragzip-2023-02-04-without-rpmalloc.png)
![](https://raw.githubusercontent.com/mxmlnkn/indexed_bzip2/master/results/benchmarks/malloc/Summary_Timeline_scorep-pragzip-2023-02-04-with-rpmalloc.png)