Query Execution and Effect of Compression on Nosql Column Oriented Data-Store Using Hadoop and Hbase Priyanka Raichand, Rinkle Rani
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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. -
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 -
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 Network Data Storage Model Based on the HTML
Proceedings of the 2nd International Conference on Computer Science and Electronics Engineering (ICCSEE 2013) The network data storage model based on the HTML Lei Li1, Jianping Zhou2 Runhua Wang3, Yi Tang4 1Network Information Center 3Teaching Quality and Assessment Office Chongqing University of Science and Technology Chongqing University of Science and Technology Chongqing, China Chongqing, China [email protected] [email protected] 2Network Information Center 4School of Electronic and Information Engineering Chongqing University of Science and Technology Chongqing University of Science and Technology Chongqing, China Chongqing, China [email protected] [email protected] Abstract—in this paper, the mass oriented HTML data refers popular NoSQL for HTML database. This article describes to those large enough for HTML data, that can no longer use the SMAQ stack model and those who today may be traditional methods of treatment. In the past, has been the included in the model under mass oriented HTML data Web search engine creators have to face this problem be the processing tools. first to bear the brunt. Today, various social networks, mobile applications and various sensors and scientific fields are II. MAPREDUCE created daily with PB for HTML data. In order to deal with MapReduce is a Google for creating web webpage index the massive data processing challenges for HTML, Google created MapReduce. Google and Yahoo created Hadoop created. MapReduce framework has become today most hatching out of an intact mass oriented HTML data processing mass oriented HTML data processing plant. MapReduce is tools for ecological system. the key, will be oriented in the HTML data collection of a query division, then at multiple nodes to execute in parallel. -
Projects – Other Than Hadoop! Created By:-Samarjit Mahapatra [email protected]
Projects – other than Hadoop! Created By:-Samarjit Mahapatra [email protected] Mostly compatible with Hadoop/HDFS Apache Drill - provides low latency ad-hoc queries to many different data sources, including nested data. Inspired by Google's Dremel, Drill is designed to scale to 10,000 servers and query petabytes of data in seconds. Apache Hama - is a pure BSP (Bulk Synchronous Parallel) computing framework on top of HDFS for massive scientific computations such as matrix, graph and network algorithms. Akka - a toolkit and runtime for building highly concurrent, distributed, and fault tolerant event-driven applications on the JVM. ML-Hadoop - Hadoop implementation of Machine learning algorithms Shark - is a large-scale data warehouse system for Spark designed to be compatible with Apache Hive. It can execute Hive QL queries up to 100 times faster than Hive without any modification to the existing data or queries. Shark supports Hive's query language, metastore, serialization formats, and user-defined functions, providing seamless integration with existing Hive deployments and a familiar, more powerful option for new ones. Apache Crunch - Java library provides a framework for writing, testing, and running MapReduce pipelines. Its goal is to make pipelines that are composed of many user-defined functions simple to write, easy to test, and efficient to run Azkaban - batch workflow job scheduler created at LinkedIn to run their Hadoop Jobs Apache Mesos - is a cluster manager that provides efficient resource isolation and sharing across distributed applications, or frameworks. It can run Hadoop, MPI, Hypertable, Spark, and other applications on a dynamically shared pool of nodes. -
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. -
Database Software Market: Billy Fitzsimmons +1 312 364 5112
Equity Research Technology, Media, & Communications | Enterprise and Cloud Infrastructure March 22, 2019 Industry Report Jason Ader +1 617 235 7519 [email protected] Database Software Market: Billy Fitzsimmons +1 312 364 5112 The Long-Awaited Shake-up [email protected] Naji +1 212 245 6508 [email protected] Please refer to important disclosures on pages 70 and 71. Analyst certification is on page 70. William Blair or an affiliate does and seeks to do business with companies covered in its research reports. As a result, investors should be aware that the firm may have a conflict of interest that could affect the objectivity of this report. This report is not intended to provide personal investment advice. The opinions and recommendations here- in do not take into account individual client circumstances, objectives, or needs and are not intended as recommen- dations of particular securities, financial instruments, or strategies to particular clients. The recipient of this report must make its own independent decisions regarding any securities or financial instruments mentioned herein. William Blair Contents Key Findings ......................................................................................................................3 Introduction .......................................................................................................................5 Database Market History ...................................................................................................7 Market Definitions -
Big Data: a Survey the New Paradigms, Methodologies and Tools
Big Data: A Survey The New Paradigms, Methodologies and Tools Enrico Giacinto Caldarola1,2 and Antonio Maria Rinaldi1,3 1Department of Electrical Engineering and Information Technologies, University of Naples Federico II, Napoli, Italy 2Institute of Industrial Technologies and Automation, National Research Council, Bari, Italy 3IKNOS-LAB Intelligent and Knowledge Systems, University of Naples Federico II, LUPT 80134, via Toledo, 402-Napoli, Italy Keywords: Big Data, NoSQL, NewSQL, Big Data Analytics, Data Management, Map-reduce. Abstract: For several years we are living in the era of information. Since any human activity is carried out by means of information technologies and tends to be digitized, it produces a humongous stack of data that becomes more and more attractive to different stakeholders such as data scientists, entrepreneurs or just privates. All of them are interested in the possibility to gain a deep understanding about people and things, by accurately and wisely analyzing the gold mine of data they produce. The reason for such interest derives from the competitive advantage and the increase in revenues expected from this deep understanding. In order to help analysts in revealing the insights hidden behind data, new paradigms, methodologies and tools have emerged in the last years. There has been a great explosion of technological solutions that arises the need for a review of the current state of the art in the Big Data technologies scenario. Thus, after a characterization of the new paradigm under study, this work aims at surveying the most spread technologies under the Big Data umbrella, throughout a qualitative analysis of their characterizing features. -
Arrow: Integration to 'Apache' 'Arrow'
Package ‘arrow’ September 5, 2021 Title Integration to 'Apache' 'Arrow' Version 5.0.0.2 Description 'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language development platform for in-memory data. It specifies a standardized language-independent columnar memory format for flat and hierarchical data, organized for efficient analytic operations on modern hardware. This package provides an interface to the 'Arrow C++' library. Depends R (>= 3.3) License Apache License (>= 2.0) URL https://github.com/apache/arrow/, https://arrow.apache.org/docs/r/ BugReports https://issues.apache.org/jira/projects/ARROW/issues Encoding UTF-8 Language en-US SystemRequirements C++11; for AWS S3 support on Linux, libcurl and openssl (optional) Biarch true Imports assertthat, bit64 (>= 0.9-7), methods, purrr, R6, rlang, stats, tidyselect, utils, vctrs RoxygenNote 7.1.1.9001 VignetteBuilder knitr Suggests decor, distro, dplyr, hms, knitr, lubridate, pkgload, reticulate, rmarkdown, stringi, stringr, testthat, tibble, withr Collate 'arrowExports.R' 'enums.R' 'arrow-package.R' 'type.R' 'array-data.R' 'arrow-datum.R' 'array.R' 'arrow-tabular.R' 'buffer.R' 'chunked-array.R' 'io.R' 'compression.R' 'scalar.R' 'compute.R' 'config.R' 'csv.R' 'dataset.R' 'dataset-factory.R' 'dataset-format.R' 'dataset-partition.R' 'dataset-scan.R' 'dataset-write.R' 'deprecated.R' 'dictionary.R' 'dplyr-arrange.R' 'dplyr-collect.R' 'dplyr-eval.R' 'dplyr-filter.R' 'expression.R' 'dplyr-functions.R' 1 2 R topics documented: 'dplyr-group-by.R' 'dplyr-mutate.R' 'dplyr-select.R' 'dplyr-summarize.R' -
Gzip, Bzip2 and Tar EXPERT PACKING
LINUXUSER Command Line: gzip, bzip2, tar gzip, bzip2 and tar EXPERT PACKING A short command is all it takes to pack your data or extract it from an archive. BY HEIKE JURZIK rchiving provides many bene- fits: packed and compressed Afiles occupy less space on your disk and require less bandwidth on the Internet. Linux has both GUI-based pro- grams, such as File Roller or Ark, and www.sxc.hu command-line tools for creating and un- packing various archive types. This arti- cle examines some shell tools for ar- chiving files and demonstrates the kind of expert packing that clever combina- tained by the packing process. If you A gzip file can be unpacked using either tions of Linux commands offer the com- prefer to use a different extension, you gunzip or gzip -d. If the tool discovers a mand line user. can set the -S (suffix) flag to specify your file of the same name in the working di- own instead. For example, the command rectory, it prompts you to make sure that Nicely Packed with “gzip” you know you are overwriting this file: The gzip (GNU Zip) program is the de- gzip -S .z image.bmp fault packer on Linux. Gzip compresses $ gunzip screenie.jpg.gz simple files, but it does not create com- creates a compressed file titled image. gunzip: screenie.jpg U plete directory archives. In its simplest bmp.z. form, the gzip command looks like this: The size of the compressed file de- Listing 1: Compression pends on the distribution of identical Compared gzip file strings in the original file. -
Parquet Data Format Performance
Parquet data format performance Jim Pivarski Princeton University { DIANA-HEP February 21, 2018 1 / 22 What is Parquet? 1974 HBOOK tabular rowwise FORTRAN first ntuples in HEP 1983 ZEBRA hierarchical rowwise FORTRAN event records in HEP 1989 PAW CWN tabular columnar FORTRAN faster ntuples in HEP 1995 ROOT hierarchical columnar C++ object persistence in HEP 2001 ProtoBuf hierarchical rowwise many Google's RPC protocol 2002 MonetDB tabular columnar database “first” columnar database 2005 C-Store tabular columnar database also early, became HP's Vertica 2007 Thrift hierarchical rowwise many Facebook's RPC protocol 2009 Avro hierarchical rowwise many Hadoop's object permanance and interchange format 2010 Dremel hierarchical columnar C++, Java Google's nested-object database (closed source), became BigQuery 2013 Parquet hierarchical columnar many open source object persistence, based on Google's Dremel paper 2016 Arrow hierarchical columnar many shared-memory object exchange 2 / 22 What is Parquet? 1974 HBOOK tabular rowwise FORTRAN first ntuples in HEP 1983 ZEBRA hierarchical rowwise FORTRAN event records in HEP 1989 PAW CWN tabular columnar FORTRAN faster ntuples in HEP 1995 ROOT hierarchical columnar C++ object persistence in HEP 2001 ProtoBuf hierarchical rowwise many Google's RPC protocol 2002 MonetDB tabular columnar database “first” columnar database 2005 C-Store tabular columnar database also early, became HP's Vertica 2007 Thrift hierarchical rowwise many Facebook's RPC protocol 2009 Avro hierarchical rowwise many Hadoop's object permanance and interchange format 2010 Dremel hierarchical columnar C++, Java Google's nested-object database (closed source), became BigQuery 2013 Parquet hierarchical columnar many open source object persistence, based on Google's Dremel paper 2016 Arrow hierarchical columnar many shared-memory object exchange 2 / 22 Developed independently to do the same thing Google Dremel authors claimed to be unaware of any precedents, so this is an example of convergent evolution.