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Application of Bagit-Serialized Research Object Bundles for Packaging and Re-Execution of Computational Analyses
Application of BagIt-Serialized Research Object Bundles for Packaging and Re-execution of Computational Analyses Kyle Chard Bertram Ludascher¨ Thomas Thelen Computation Institute School of Information Sciences NCEAS University of Chicago University of Illinois at Urbana-Champaign University of California at Santa Barbara Chicago, IL Champaign, IL Santa Barbara, CA [email protected] [email protected] [email protected] Niall Gaffney Jarek Nabrzyski Matthew J. Turk Texas Advanced Computing Center Center for Research Computing School of Information Sciences University of Texas at Austin University of Notre Dame University of Illinois at Urbana-Champaign Austin, TX South Bend, IN Champaign, IL [email protected] [email protected] [email protected] Matthew B. Jones Victoria Stodden Craig Willisy NCEAS School of Information Sciences NCSA University of California at Santa Barbara University of Illinois at Urbana-Champaign University of Illinois at Urbana-Champaign Santa Barbara, CA Champaign, IL Champaign, IL [email protected] [email protected] [email protected] Kacper Kowalik Ian Taylor yCorresponding author NCSA Center for Research Computing University of Illinois at Urbana-Champaign University of Notre Dame Champaign, IL South Bend, IN [email protected] [email protected] Abstract—In this paper we describe our experience adopting and can be used for verification of computational reproducibil- the Research Object Bundle (RO-Bundle) format with BagIt ity, for example as part of the peer-review process. serialization (BagIt-RO) for the design and implementation of Since its inception, the Whole Tale platform has been “tales” in the Whole Tale platform. A tale is an executable research object intended for the dissemination of computational designed to bring together existing open science infrastructure. -
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. -
My Sons Postponed to March 18-19 Artist Series Please: Return Those Books!
» LWA Darlings Don Colonial Garb for Minuet Ans^nsçhuetz, Bekkdal, Jensen and Ladw ig Lib*.Ire Honored at Traditional Banquet A dainty Mozart minuet intro-1 duced Lawrence college’s four Best tian. president of the Spanish Loved senior women at the annual club. « colonial banquet last Monday eve Tekla Bekkedal as vice-president ning in the dining hall of the First of the Student Christian association, Congregational church. Chosen for the Best Loved honor this year and is active in the International were Mary Anschuetz, Tekla Bek- Relations club, the German club kedal, Mary Ellen Jensen and Joan tind on The Lawrentian staff. She Ladwig. Complete with powdered wras chosen for membership in hair, they were dressed in tradi Sigrna, underclass scholastic group, tional colonial costumes of George and is now a counselor to freshman and Martha Washington and James women. and Dolly Madison. Miss Jensen is yico-president and The best loved tradition, which Pled*e mistress of Alpha Chi Ome- has been observed for more than 20 *?a- ^lcr social sorority, and also is years, is sponsored by the Lawrencei^fHiated w'ith Sigma Alpha Iota, Women’s association, under the so- professional music sorority. A music Cial chairmanship this year of Viv- major, she sings in the college con- ia n Grady and Betty Wheeler. V iv - cert choir and plays in several in- ia n was toastmistress for the ban- strumental groups. Last fall she was quet and Mrs. Kenneth Davis, Ap-¡chosen attendant to the homecom- pleton. a Best Loved in 1947, gave ¡ ‘ " 8 queen and she has also served a toast to the new electees and pre- as a counselor to freshman women, tented them with small bracelets on! Best Loved banquets are not behalf of last year’s group. -
Real Time Operating Systems Rootfs Creation: Summing Up
Real Time Operating Systems RootFS Creation: Summing Up Luca Abeni Real Time Operating Systems – p. System Boot System boot → the CPU starts executing from a well-known address ROM address: BIOS → read the first sector on the boot device, and executes it Bootloader (GRUB, LILO, U-Boot, . .) In general, load a kernel and an “intial ram disk” The initial fs image isn’t always needed (example: netboot) Kernel: from arm-test-*.tar.gz Initial filesystem? Loaded in RAM without the kernel help Generally contains the boot scripts and binaries Real Time Operating Systems – p. Initial Filesystem Old (2.4) kernels: Init Ram Disk (initrd); New (2.6) kernels: Init Ram Filesystem (initramfs) Generally used for modularized disk and FS drivers Example: if IDE drivers and Ext2 FS are modules (not inside the kernel), how can the kernel load them from disk? Solution: boot drivers can be on initrd / initramfs The bootloader loads it from disk with the kernel The kernel creates a “fake” fs based on it Modules are loaded from it Embedded systems can use initial FS for all the binaries Qemu does not need a bootloader to load kernel and initial FS (-kernel and -initrd) Real Time Operating Systems – p. Init Ram Filesystem Used in 2.6 kernels It is only a RAM FS: no real filesystem metadata on a storage medium All the files that must populate the FS are stored in a cpio package (similar to tar or zip file) The bootloader loads the cpio file in ram At boot time, the kernel “uncompresses” it, creating the RAM FS, and populating it with the files contained in the archive The cpio archive can be created by using the cpio -o -H newc command (see man cpio) Full command line: find . -
CA SOLVE:FTS Installation Guide
CA SOLVE:FTS Installation Guide Release 12.1 This Documentation, which includes embedded help systems and electronically distributed materials, (hereinafter referred to as the “Documentation”) is for your informational purposes only and is subject to change or withdrawal by CA at any time. This Documentation may not be copied, transferred, reproduced, disclosed, modified or duplicated, in whole or in part, without the prior written consent of CA. This Documentation is confidential and proprietary information of CA and may not be disclosed by you or used for any purpose other than as may be permitted in (i) a separate agreement between you and CA governing your use of the CA software to which the Documentation relates; or (ii) a separate confidentiality agreement between you and CA. Notwithstanding the foregoing, if you are a licensed user of the software product(s) addressed in the Documentation, you may print or otherwise make available a reasonable number of copies of the Documentation for internal use by you and your employees in connection with that software, provided that all CA copyright notices and legends are affixed to each reproduced copy. The right to print or otherwise make available copies of the Documentation is limited to the period during which the applicable license for such software remains in full force and effect. Should the license terminate for any reason, it is your responsibility to certify in writing to CA that all copies and partial copies of the Documentation have been returned to CA or destroyed. TO THE EXTENT PERMITTED BY APPLICABLE LAW, CA PROVIDES THIS DOCUMENTATION “AS IS” WITHOUT WARRANTY OF ANY KIND, INCLUDING WITHOUT LIMITATION, ANY IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NONINFRINGEMENT. -
Bagit File Packaging Format (V0.97) Draft-Kunze-Bagit-07.Txt
Network Working Group A. Boyko Internet-Draft Expires: October 4, 2012 J. Kunze California Digital Library J. Littman L. Madden Library of Congress B. Vargas April 2, 2012 The BagIt File Packaging Format (V0.97) draft-kunze-bagit-07.txt Abstract This document specifies BagIt, a hierarchical file packaging format for storage and transfer of arbitrary digital content. A "bag" has just enough structure to enclose descriptive "tags" and a "payload" but does not require knowledge of the payload's internal semantics. This BagIt format should be suitable for disk-based or network-based storage and transfer. Status of this Memo This Internet-Draft is submitted in full conformance with the provisions of BCP 78 and BCP 79. Internet-Drafts are working documents of the Internet Engineering Task Force (IETF). Note that other groups may also distribute working documents as Internet-Drafts. The list of current Internet- Drafts is at http://datatracker.ietf.org/drafts/current/. Internet-Drafts are draft documents valid for a maximum of six months and may be updated, replaced, or obsoleted by other documents at any time. It is inappropriate to use Internet-Drafts as reference material or to cite them other than as "work in progress." This Internet-Draft will expire on October 4, 2012. Copyright Notice Copyright (c) 2012 IETF Trust and the persons identified as the document authors. All rights reserved. This document is subject to BCP 78 and the IETF Trust's Legal Provisions Relating to IETF Documents (http://trustee.ietf.org/license-info) in effect on the date of Boyko, et al. -
Lossless Compression of Internal Files in Parallel Reservoir Simulation
Lossless Compression of Internal Files in Parallel Reservoir Simulation Suha Kayum Marcin Rogowski Florian Mannuss 9/26/2019 Outline • I/O Challenges in Reservoir Simulation • Evaluation of Compression Algorithms on Reservoir Simulation Data • Real-world application - Constraints - Algorithm - Results • Conclusions 2 Challenge Reservoir simulation 1 3 Reservoir Simulation • Largest field in the world are represented as 50 million – 1 billion grid block models • Each runs takes hours on 500-5000 cores • Calibrating the model requires 100s of runs and sophisticated methods • “History matched” model is only a beginning 4 Files in Reservoir Simulation • Internal Files • Input / Output Files - Interact with pre- & post-processing tools Date Restart/Checkpoint Files 5 Reservoir Simulation in Saudi Aramco • 100’000+ simulations annually • The largest simulation of 10 billion cells • Currently multiple machines in TOP500 • Petabytes of storage required 600x • Resources are Finite • File Compression is one solution 50x 6 Compression algorithm evaluation 2 7 Compression ratio Tested a number of algorithms on a GRID restart file for two models 4 - Model A – 77.3 million active grid blocks 3.5 - Model K – 8.7 million active grid blocks 3 - 15.6 GB and 7.2 GB respectively 2.5 2 Compression ratio is between 1.5 1 compression ratio compression - From 2.27 for snappy (Model A) 0.5 0 - Up to 3.5 for bzip2 -9 (Model K) Model A Model K lz4 snappy gzip -1 gzip -9 bzip2 -1 bzip2 -9 8 Compression speed • LZ4 and Snappy significantly outperformed other algorithms -
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 Do You Download Driver Fron 7 Zip Download Arduino and Install Arduino Driver
how do you download driver fron 7 zip Download Arduino and install Arduino driver. You can direct download the latest version from this page: http://arduino.cc/en/Main/Software, When the download finishes, unzip the downloaded file. Make sure to preserve the folder structure. Double-click the folder to open it. There should be a few files and sub-folders inside. Connect Seeeduino to PC. Connect the Seeeduino board to your computer using the USB cable. The green power LED (labeled PWR) should go on. Install the driver. Installing drivers for the Seeeduino with window7. Plug in your board and wait for Windows to begin its driver installation process. After a few moments, the process will fail. Open the Device Manager by right clicking “My computer” and selecting control panel. Look under Ports (COM & LPT). You should see an open port named "USB Serial Port" Right click on the "USB Serial Port" and choose the "Update Driver Software" option. Next, choose the "Browse my computer for Driver software" option. Finally, select the driver file named "FTDI USB Drivers", located in the "Drivers" folder of the Arduino Software download. Note: the FTDI USB Drivers are from Arduino. But when you install drivers for other Controllers, such as Xadow Main Board, Seeeduino Clio, Seeeduino Lite, you need to download corresponding driver file and save it. And select the driver file you have downloaded. The below dialog boxes automatically appears if you have installed driver successfully. You can check that the drivers have been installed by opening the Windows Device Manager. Look for a "USB Serial Port" in the Ports section. -
How to Extract a Deb Package on Debian, Ubuntu, Mint Linux and Other Non Debian Based Distributions
? Walking in Light with Christ - Faith, Computers, Freedom Free Software GNU Linux, FreeBSD, Unix, Windows, Mac OS - Hacks, Goodies, Tips and Tricks and The True Meaning of life http://www.pc-freak.net/blog How to extract a deb package on Debian, Ubuntu, Mint Linux and other non debian based distributions Author : admin How to extract a deb package? Have you ever had a debian .deb package which contains image files you need, but the dependencies doesn't allow you to install it on your Debian / Ubuntu / Mint Linux release? I had just recently downloaded the ultimate-edition-themes latest release v 0.0.7 a large pack of GNOME Themes and wanted to install it on my Debian Stretch Linux but I faced problems because of dependencies when trying to install with dpkg. That is why I took another appoarch and decided to only extract the necessery themes from the archive only with dpkg. Here is how I have extracted ultimate-edition-themes-.0.0.7_all.deb ; dpkg -x ultimate-edition-themes-.0.0.7_all.deb /tmp/ultimate-edition-themes 1 / 3 ? Walking in Light with Christ - Faith, Computers, Freedom Free Software GNU Linux, FreeBSD, Unix, Windows, Mac OS - Hacks, Goodies, Tips and Tricks and The True Meaning of life http://www.pc-freak.net/blog So how dpkg extracts the .deb file? Debian .deb packages are a regular more in Wikipedia - Unix archive files (ar) . The structure of a deb file consists of another 3 files (2 tar.gzs and one binary) as follows: debian-binary: regular text file, contains the version of the deb package format control.tar.gz: compressed file, contains file md5sums and control directory for the deb package data.tar.gz: compressed file, contains all the files which will be installed Basicly if you're on a Linux distribution that lacks dpkg you can easily extract .deb binary using GNU AR command (used to create, modify extract Unix ar files and is the GNU / Linux equivallent of the UNIX ar command). -
Breaking Antivirus Software Joxean Koret, COSEINC 44CON, 2014
Breaking Antivirus Software Joxean Koret, COSEINC 44CON, 2014 Breaking antivirus software Introduction Attacking antivirus engines Finding vulnerabilities Exploiting antivirus engines Antivirus vulnerabilities Conclusions Recommendations Antivirus Engines Common features of AV engines: Written in C/C++. Signatures based engine + heuristics. On-access scanners. Command line/GUI on-demand scanners. Support for compressed file archives. Support for packers. Support for miscellaneous file formats. Advanced common features: Packet filters and firewalls. Drivers to protect the product, anti-rootkits, etc... Anti-exploiting toolkits. Antivirus products or engines An antivirus engine is just the core, the kernel, of an antivirus product. Some antivirus engines are used by multiple products. For example, BitDefender is the most widely used antivirus kernel. It's used by so many products like QiHoo360, G-Data, eScan, F-Secure, etc... Most “big” antivirus companies have their own engine but not all. And some companies, like F-Secure, integrate 3rd party engines in their products. In general, during this talk I will refer to AV engines, to the kernels, except when specified the word “product”. Attack surface Fact: installing an application in your computer makes you a bit more vulnerable. You just increased your attack surface. If the application is local: your local attack surface increased. If the application is remote: your remote attack surface increased. If your application runs with the highest privileges, installs kernel drivers, a packet filter and tries to handle anything your computer may do... Your attack surface dramatically increased. Myths and reality Antivirus propaganda: “We make your computer safer with no performance penalty!” “We protect against unknown zero day attacks!”. -
Bzip2 and Libbzip2, Version 1.0.8 a Program and Library for Data Compression
bzip2 and libbzip2, version 1.0.8 A program and library for data compression Julian Seward, https://sourceware.org/bzip2/ bzip2 and libbzip2, version 1.0.8: A program and library for data compression by Julian Seward Version 1.0.8 of 13 July 2019 Copyright© 1996-2019 Julian Seward This program, bzip2, the associated library libbzip2, and all documentation, are copyright © 1996-2019 Julian Seward. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: • Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. • The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required. • Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. • The name of the author may not be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DIS- CLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.