FPGA Accelerated Trading Data Compression
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Contrasting the Performance of Compression Algorithms on Genomic Data
Contrasting the Performance of Compression Algorithms on Genomic Data Cornel Constantinescu, IBM Research Almaden Outline of the Talk: • Introduction / Motivation • Data used in experiments • General purpose compressors comparison • Simple Improvements • Special purpose compression • Transparent compression – working on compressed data (prototype) • Parallelism / Multithreading • Conclusion Introduction / Motivation • Despite the large number of research papers and compression algorithms proposed for compressing genomic data generated by sequencing machines, by far the most commonly used compression algorithm in the industry for FASTQ data is gzip. • The main drawbacks of the proposed alternative special-purpose compression algorithms are: • slow speed of either compression or decompression or both, and also their • brittleness by making various limiting assumptions about the input FASTQ format (for example, the structure of the headers or fixed lengths of the records [1]) in order to further improve their specialized compression. 1. Ibrahim Numanagic, James K Bonfield, Faraz Hach, Jan Voges, Jorn Ostermann, Claudio Alberti, Marco Mattavelli, and S Cenk Sahinalp. Comparison of high-throughput sequencing data compression tools. Nature Methods, 13(12):1005–1008, October 2016. Fast and Efficient Compression of Next Generation Sequencing Data 2 2 General Purpose Compression of Genomic Data As stated earlier, gzip/zlib compression is the method of choice by the industry for FASTQ genomic data. FASTQ genomic data is a text-based format (ASCII readable text) for storing a biological sequence and the corresponding quality scores. Each sequence letter and quality score is encoded with a single ASCII character. FASTQ data is structured in four fields per record (a “read”). The first field is the SEQUENCE ID or the header of the read. -
ROOT I/O Compression Improvements for HEP Analysis
EPJ Web of Conferences 245, 02017 (2020) https://doi.org/10.1051/epjconf/202024502017 CHEP 2019 ROOT I/O compression improvements for HEP analysis Oksana Shadura1;∗ Brian Paul Bockelman2;∗∗ Philippe Canal3;∗∗∗ Danilo Piparo4;∗∗∗∗ and Zhe Zhang1;y 1University of Nebraska-Lincoln, 1400 R St, Lincoln, NE 68588, United States 2Morgridge Institute for Research, 330 N Orchard St, Madison, WI 53715, United States 3Fermilab, Kirk Road and Pine St, Batavia, IL 60510, United States 4CERN, Meyrin 1211, Geneve, Switzerland Abstract. We overview recent changes in the ROOT I/O system, enhancing it by improving its performance and interaction with other data analysis ecosys- tems. Both the newly introduced compression algorithms, the much faster bulk I/O data path, and a few additional techniques have the potential to significantly improve experiment’s software performance. The need for efficient lossless data compression has grown significantly as the amount of HEP data collected, transmitted, and stored has dramatically in- creased over the last couple of years. While compression reduces storage space and, potentially, I/O bandwidth usage, it should not be applied blindly, because there are significant trade-offs between the increased CPU cost for reading and writing files and the reduces storage space. 1 Introduction In the past years, Large Hadron Collider (LHC) experiments are managing about an exabyte of storage for analysis purposes, approximately half of which is stored on tape storages for archival purposes, and half is used for traditional disk storage. Meanwhile for High Lumi- nosity Large Hadron Collider (HL-LHC) storage requirements per year are expected to be increased by a factor of 10 [1]. -
Full Document
R&D Centre for Mobile Applications (RDC) FEE, Dept of Telecommunications Engineering Czech Technical University in Prague RDC Technical Report TR-13-4 Internship report Evaluation of Compressibility of the Output of the Information-Concealing Algorithm Julien Mamelli, [email protected] 2nd year student at the Ecole´ des Mines d'Al`es (N^ımes,France) Internship supervisor: Luk´aˇsKencl, [email protected] August 2013 Abstract Compression is a key element to exchange files over the Internet. By generating re- dundancies, the concealing algorithm proposed by Kencl and Loebl [?], appears at first glance to be particularly designed to be combined with a compression scheme [?]. Is the output of the concealing algorithm actually compressible? We have tried 16 compression techniques on 1 120 files, and the result is that we have not found a solution which could advantageously use repetitions of the concealing method. Acknowledgments I would like to express my gratitude to my supervisor, Dr Luk´aˇsKencl, for his guidance and expertise throughout the course of this work. I would like to thank Prof. Robert Beˇst´akand Mr Pierre Runtz, for giving me the opportunity to carry out my internship at the Czech Technical University in Prague. I would also like to thank all the members of the Research and Development Center for Mobile Applications as well as my colleagues for the assistance they have given me during this period. 1 Contents 1 Introduction 3 2 Related Work 4 2.1 Information concealing method . 4 2.2 Archive formats . 5 2.3 Compression algorithms . 5 2.3.1 Lempel-Ziv algorithm . -
Arxiv:2004.10531V1 [Cs.OH] 8 Apr 2020
ROOT I/O compression improvements for HEP analysis Oksana Shadura1;∗ Brian Paul Bockelman2;∗∗ Philippe Canal3;∗∗∗ Danilo Piparo4;∗∗∗∗ and Zhe Zhang1;y 1University of Nebraska-Lincoln, 1400 R St, Lincoln, NE 68588, United States 2Morgridge Institute for Research, 330 N Orchard St, Madison, WI 53715, United States 3Fermilab, Kirk Road and Pine St, Batavia, IL 60510, United States 4CERN, Meyrin 1211, Geneve, Switzerland Abstract. We overview recent changes in the ROOT I/O system, increasing per- formance and enhancing it and improving its interaction with other data analy- sis ecosystems. Both the newly introduced compression algorithms, the much faster bulk I/O data path, and a few additional techniques have the potential to significantly to improve experiment’s software performance. The need for efficient lossless data compression has grown significantly as the amount of HEP data collected, transmitted, and stored has dramatically in- creased during the LHC era. While compression reduces storage space and, potentially, I/O bandwidth usage, it should not be applied blindly: there are sig- nificant trade-offs between the increased CPU cost for reading and writing files and the reduce storage space. 1 Introduction In the past years LHC experiments are commissioned and now manages about an exabyte of storage for analysis purposes, approximately half of which is used for archival purposes, and half is used for traditional disk storage. Meanwhile for HL-LHC storage requirements per year are expected to be increased by factor 10 [1]. arXiv:2004.10531v1 [cs.OH] 8 Apr 2020 Looking at these predictions, we would like to state that storage will remain one of the major cost drivers and at the same time the bottlenecks for HEP computing. -
ARC File Revision 3.0 Proposal
ARC file Revision 3.0 Proposal Steen Christensen, Det Kongelige Bibliotek <ssc at kb dot dk> Michael Stack, Internet Archive <stack at archive dot org> Edited by Michael Stack Revision History Revision 1 09/09/2004 Initial conversion of wiki working doc. [http://crawler.archive.org/cgi-bin/wiki.pl?ArcRevisionProposal] to docbook. Added suggested edits suggested by Gordon Mohr (Others made are still up for consideration). This revision is what is being submitted to the IIPC Framework Group for review at their London, 09/20/2004 meeting. Table of Contents 1. Introduction ............................................................................................................................2 1.1. IIPC Archival Data Format Requirements .......................................................................... 2 1.2. Input ...........................................................................................................................2 1.3. Scope ..........................................................................................................................3 1.4. Acronyms, Abbreviations and Definitions .......................................................................... 3 2. ARC Record Addressing ........................................................................................................... 4 2.1. Reference ....................................................................................................................4 2.2. The ari Scheme ............................................................................................................ -
Pack, Encrypt, Authenticate Document Revision: 2021 05 02
PEA Pack, Encrypt, Authenticate Document revision: 2021 05 02 Author: Giorgio Tani Translation: Giorgio Tani This document refers to: PEA file format specification version 1 revision 3 (1.3); PEA file format specification version 2.0; PEA 1.01 executable implementation; Present documentation is released under GNU GFDL License. PEA executable implementation is released under GNU LGPL License; please note that all units provided by the Author are released under LGPL, while Wolfgang Ehrhardt’s crypto library units used in PEA are released under zlib/libpng License. PEA file format and PCOMPRESS specifications are hereby released under PUBLIC DOMAIN: the Author neither has, nor is aware of, any patents or pending patents relevant to this technology and do not intend to apply for any patents covering it. As far as the Author knows, PEA file format in all of it’s parts is free and unencumbered for all uses. Pea is on PeaZip project official site: https://peazip.github.io , https://peazip.org , and https://peazip.sourceforge.io For more information about the licenses: GNU GFDL License, see http://www.gnu.org/licenses/fdl.txt GNU LGPL License, see http://www.gnu.org/licenses/lgpl.txt 1 Content: Section 1: PEA file format ..3 Description ..3 PEA 1.3 file format details ..5 Differences between 1.3 and older revisions ..5 PEA 2.0 file format details ..7 PEA file format’s and implementation’s limitations ..8 PCOMPRESS compression scheme ..9 Algorithms used in PEA format ..9 PEA security model .10 Cryptanalysis of PEA format .12 Data recovery from -
Steganography and Vulnerabilities in Popular Archives Formats.| Nyxengine Nyx.Reversinglabs.Com
Hiding in the Familiar: Steganography and Vulnerabilities in Popular Archives Formats.| NyxEngine nyx.reversinglabs.com Contents Introduction to NyxEngine ............................................................................................................................ 3 Introduction to ZIP file format ...................................................................................................................... 4 Introduction to steganography in ZIP archives ............................................................................................. 5 Steganography and file malformation security impacts ............................................................................... 8 References and tools .................................................................................................................................... 9 2 Introduction to NyxEngine Steganography1 is the art and science of writing hidden messages in such a way that no one, apart from the sender and intended recipient, suspects the existence of the message, a form of security through obscurity. When it comes to digital steganography no stone should be left unturned in the search for viable hidden data. Although digital steganography is commonly used to hide data inside multimedia files, a similar approach can be used to hide data in archives as well. Steganography imposes the following data hiding rule: Data must be hidden in such a fashion that the user has no clue about the hidden message or file's existence. This can be achieved by -
Improved Neural Network Based General-Purpose Lossless Compression Mohit Goyal, Kedar Tatwawadi, Shubham Chandak, Idoia Ochoa
JOURNAL OF LATEX CLASS FILES, VOL. 14, NO. 8, AUGUST 2015 1 DZip: improved neural network based general-purpose lossless compression Mohit Goyal, Kedar Tatwawadi, Shubham Chandak, Idoia Ochoa Abstract—We consider lossless compression based on statistical [4], [5] and generative modeling [6]). Neural network based data modeling followed by prediction-based encoding, where an models can typically learn highly complex patterns in the data accurate statistical model for the input data leads to substantial much better than traditional finite context and Markov models, improvements in compression. We propose DZip, a general- purpose compressor for sequential data that exploits the well- leading to significantly lower prediction error (measured as known modeling capabilities of neural networks (NNs) for pre- log-loss or perplexity [4]). This has led to the development of diction, followed by arithmetic coding. DZip uses a novel hybrid several compressors using neural networks as predictors [7]– architecture based on adaptive and semi-adaptive training. Unlike [9], including the recently proposed LSTM-Compress [10], most NN based compressors, DZip does not require additional NNCP [11] and DecMac [12]. Most of the previous works, training data and is not restricted to specific data types. The proposed compressor outperforms general-purpose compressors however, have been tailored for compression of certain data such as Gzip (29% size reduction on average) and 7zip (12% size types (e.g., text [12] [13] or images [14], [15]), where the reduction on average) on a variety of real datasets, achieves near- prediction model is trained in a supervised framework on optimal compression on synthetic datasets, and performs close to separate training data or the model architecture is tuned for specialized compressors for large sequence lengths, without any the specific data type. -
User Commands GZIP ( 1 ) Gzip, Gunzip, Gzcat – Compress Or Expand Files Gzip [ –Acdfhllnnrtvv19 ] [–S Suffix] [ Name ... ]
User Commands GZIP ( 1 ) NAME gzip, gunzip, gzcat – compress or expand files SYNOPSIS gzip [–acdfhlLnNrtvV19 ] [– S suffix] [ name ... ] gunzip [–acfhlLnNrtvV ] [– S suffix] [ name ... ] gzcat [–fhLV ] [ name ... ] DESCRIPTION Gzip reduces the size of the named files using Lempel-Ziv coding (LZ77). Whenever possible, each file is replaced by one with the extension .gz, while keeping the same ownership modes, access and modification times. (The default extension is – gz for VMS, z for MSDOS, OS/2 FAT, Windows NT FAT and Atari.) If no files are specified, or if a file name is "-", the standard input is compressed to the standard output. Gzip will only attempt to compress regular files. In particular, it will ignore symbolic links. If the compressed file name is too long for its file system, gzip truncates it. Gzip attempts to truncate only the parts of the file name longer than 3 characters. (A part is delimited by dots.) If the name con- sists of small parts only, the longest parts are truncated. For example, if file names are limited to 14 characters, gzip.msdos.exe is compressed to gzi.msd.exe.gz. Names are not truncated on systems which do not have a limit on file name length. By default, gzip keeps the original file name and timestamp in the compressed file. These are used when decompressing the file with the – N option. This is useful when the compressed file name was truncated or when the time stamp was not preserved after a file transfer. Compressed files can be restored to their original form using gzip -d or gunzip or gzcat. -
The Ark Handbook
The Ark Handbook Matt Johnston Henrique Pinto Ragnar Thomsen The Ark Handbook 2 Contents 1 Introduction 5 2 Using Ark 6 2.1 Opening Archives . .6 2.1.1 Archive Operations . .6 2.1.2 Archive Comments . .6 2.2 Working with Files . .7 2.2.1 Editing Files . .7 2.3 Extracting Files . .7 2.3.1 The Extract dialog . .8 2.4 Creating Archives and Adding Files . .8 2.4.1 Compression . .9 2.4.2 Password Protection . .9 2.4.3 Multi-volume Archive . 10 3 Using Ark in the Filemanager 11 4 Advanced Batch Mode 12 5 Credits and License 13 Abstract Ark is an archive manager by KDE. The Ark Handbook Chapter 1 Introduction Ark is a program for viewing, extracting, creating and modifying archives. Ark can handle vari- ous archive formats such as tar, gzip, bzip2, zip, rar, 7zip, xz, rpm, cab, deb, xar and AppImage (support for certain archive formats depends on the appropriate command-line programs being installed). In order to successfully use Ark, you need KDE Frameworks 5. The library libarchive version 3.1 or above is needed to handle most archive types, including tar, compressed tar, rpm, deb and cab archives. To handle other file formats, you need the appropriate command line programs, such as zipinfo, zip, unzip, rar, unrar, 7z, lsar, unar and lrzip. 5 The Ark Handbook Chapter 2 Using Ark 2.1 Opening Archives To open an archive in Ark, choose Open... (Ctrl+O) from the Archive menu. You can also open archive files by dragging and dropping from Dolphin. -
How to 'Zip and Unzip' Files
How to 'zip and unzip' files The Windows 10 operating system provides a very easy way to zip-up any file (or folder) you want by using a utility program called 7-zip (Seven Zip). The program is integrated in the context menu which you get when you right-click on anything selected. Here are the basic steps you need to take in order to: Zip a file and create an archive 1. Open a folder in your machine and select any file (by clicking on it once). I selected a single file called 'how-to send an email.docx' 2. Now right click the mouse to have the context menu appear 3. In the context menu you should be able to see some commands like the capture below 4. Since we want to zip up the file you need to select one of the bottom two options a. 'Add to archive' will actually open up a dialog of the 7-zip application and will give you the opportunity to customise the archive. b. 'Add to how-to send an email.zip' is actually the quickest way possible to create an archive. The software uses the name of the file and selects a default compression scheme (.zip) so that you can, with two clicks, create a zip archive containing the original file. 5. Now you can use the 'how-to send an email.zip' file and send it as a 'smaller' email attachment. Now consider that you have just received (via email) the 'how-to send an email.zip' file and you need to get (the correct phrase is extract) the file it contains. -
Unfoldr Dstep
Asymmetric Numeral Systems Jeremy Gibbons WG2.11#19 Salem ANS 2 1. Coding Huffman coding (HC) • efficient; optimally effective for bit-sequence-per-symbol arithmetic coding (AC) • Shannon-optimal (fractional entropy); but computationally expensive asymmetric numeral systems (ANS) • efficiency of Huffman, effectiveness of arithmetic coding applications of streaming (another story) • ANS introduced by Jarek Duda (2006–2013). Now: Facebook (Zstandard), Apple (LZFSE), Google (Draco), Dropbox (DivANS). ANS 3 2. Intervals Pairs of rationals type Interval (Rational, Rational) = with operations unit (0, 1) = weight (l, r) x l (r l) x = + − ⇥ narrow i (p, q) (weight i p, weight i q) = scale (l, r) x (x l)/(r l) = − − widen i (p, q) (scale i p, scale i q) = so that narrow and unit form a monoid, and inverse relationships: weight i x i x unit 2 () 2 weight i x y scale i y x = () = narrow i j k widen i k j = () = ANS 4 3. Models Given counts :: [(Symbol, Integer)] get encodeSym :: Symbol Interval ! decodeSym :: Rational Symbol ! such that decodeSym x s x encodeSym s = () 2 1 1 1 1 Eg alphabet ‘a’, ‘b’, ‘c’ with counts 2, 3, 5 encoded as (0, /5), ( /5, /2), and ( /2, 1). { } ANS 5 4. Arithmetic coding encode1 :: [Symbol ] Rational ! encode1 pick foldl estep unit where = ◦ 1 estep :: Interval Symbol Interval 1 ! ! estep is narrow i (encodeSym s) 1 = decode1 :: Rational [Symbol ] ! decode1 unfoldr dstep where = 1 dstep :: Rational Maybe (Symbol, Rational) 1 ! dstep x let s decodeSym x in Just (s, scale (encodeSym s) x) 1 = = where pick :: Interval Rational satisfies pick i i.