GPU-Accelerated Applications for HPC Industries| NVIDIA
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
VMD User's Guide
VMD User’s Guide Version 1.9.4a48 October 13, 2020 NIH Biomedical Research Center for Macromolecular Modeling and Bioinformatics Theoretical and Computational Biophysics Group1 Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign 405 N. Mathews Urbana, IL 61801 http://www.ks.uiuc.edu/Research/vmd/ Description The VMD User’s Guide describes how to run and use the molecular visualization and analysis program VMD. This guide documents the user interfaces displaying and grapically manipulating molecules, and describes how to use the scripting interfaces for analysis and to customize the behavior of VMD. VMD development is supported by the National Institutes of Health grant numbers NIH P41- GM104601. 1http://www.ks.uiuc.edu/ Contents 1 Introduction 11 1.1 Contactingtheauthors. ....... 12 1.2 RegisteringVMD.................................. 12 1.3 CitationReference ............................... ...... 12 1.4 Acknowledgments................................. ..... 13 1.5 Copyright and Disclaimer Notices . .......... 13 1.6 For information on our other software . .......... 15 2 Hardware and Software Requirements 17 2.1 Basic Hardware and Software Requirements . ........... 17 2.2 Multi-core CPUs and GPU Acceleration . ......... 17 2.3 Parallel Computing on Clusters and Supercomputers . .............. 18 3 Tutorials 19 3.1 RapidIntroductiontoVMD. ...... 19 3.2 Viewing a molecule: Myoglobin . ........ 19 3.3 RenderinganImage ................................ 21 3.4 AQuickAnimation................................. 21 3.5 An Introduction to Atom Selection . ......... 22 3.6 ComparingTwoStructures . ...... 22 3.7 SomeNiceRepresenations . ....... 23 3.8 Savingyourwork.................................. 24 3.9 Tracking Script Command Versions of the GUI Actions . ............ 24 4 Loading A Molecule 26 4.1 Notes on common molecular file formats . ......... 26 4.2 Whathappenswhenafileisloaded? . ....... 27 4.3 Babelinterface ................................. -
Gpu-Accelerated Applications Gpu‑Accelerated Applications
GPU-ACCELERATED APPLICATIONS GPU-ACCELERATED APPLICATIONS Accelerated computing has revolutionized a broad range of industries with over five hundred applications optimized for GPUs to help you accelerate your work. CONTENTS 1 Computational Finance 2 Climate, Weather and Ocean Modeling 2 Data Science & Analytics 4 Deep Learning and Machine Learning 8 Defense and Intelligence 9 Manufacturing/AEC: CAD and CAE COMPUTATIONAL FLUID DYNAMICS COMPUTATIONAL STRUCTURAL MECHANICS DESIGN AND VISUALIZATION ELECTRONIC DESIGN AUTOMATION 17 Media & Entertainment ANIMATION, MODELING AND RENDERING COLOR CORRECTION AND GRAIN MANAGEMENT COMPOSITING, FINISHING AND EFFECTS EDITING ENCODING AND DIGITAL DISTRIBUTION ON-AIR GRAPHICS ON-SET, REVIEW AND STEREO TOOLS WEATHER GRAPHICS 24 Medical Imaging 27 Oil and Gas 28 Research: Higher Education and Supercomputing COMPUTATIONAL CHEMISTRY AND BIOLOGY NUMERICAL ANALYTICS PHYSICS SCIENTIFIC VISUALIZATION 39 Safety and Security 42 Tools and Management Computational Finance APPLICATION NAME COMPANY/DEVELOPER PRODUCT DESCRIPTION SUPPORTED FEATURES GPU SCALING Accelerated Elsen Secure, accessible, and accelerated back- • Web-like API with Native bindings for Multi-GPU Computing Engine testing, scenario analysis, risk analytics Python, R, Scala, C Single Node and real-time trading designed for easy • Custom models and data streams are integration and rapid development. easy to add Adaptiv Analytics SunGard A flexible and extensible engine for fast • Existing models code in C# supported Multi-GPU calculations of a wide variety of pricing transparently, with minimal code Single Node and risk measures on a broad range of changes asset classes and derivatives. • Supports multiple backends including CUDA and OpenCL • Switches transparently between multiple GPUs and CPUS depending on the deal support and load factors. -
Gpu-Accelerated Applications Gpu‑Accelerated Applications
GPU-ACCELERATED APPLICATIONS GPU-ACCELERATED APPLICATIONS Accelerated computing has revolutionized a broad range of industries with over five hundred applications optimized for GPUs to help you accelerate your work. CONTENTS 1 Computational Finance 2 Climate, Weather and Ocean Modeling 2 Data Science and Analytics 4 Artificial Intelligence DEEP LEARNING AND MACHINE LEARNING 8 Federal, Defense and Intelligence 10 Design for Manufacturing/Construction: CAD/CAE/CAM COMPUTATIONAL FLUID DYNAMICS COMPUTATIONAL STRUCTURAL MECHANICS DESIGN AND VISUALIZATION ELECTRONIC DESIGN AUTOMATION INDUSTRIAL INSPECTION 19 Media & Entertainment ANIMATION, MODELING AND RENDERING COLOR CORRECTION AND GRAIN MANAGEMENT Test Drive the COMPOSITING, FINISHING AND EFFECTS World’s Fastest EDITING ENCODING AND DIGITAL DISTRIBUTION Accelerator – Free! ON-AIR GRAPHICS ON-SET, REVIEW AND STEREO TOOLS Take the GPU Test Drive, a free and WEATHER GRAPHICS easy way to experience accelerated computing on GPUs. You can run 29 Medical Imaging your own application or try one of the preloaded ones, all running on a 30 Oil and Gas remote cluster. Try it today. 31 Research: Higher Education and Supercomputing www.nvidia.com/gputestdrive COMPUTATIONAL CHEMISTRY AND BIOLOGY NUMERICAL ANALYTICS PHYSICS SCIENTIFIC VISUALIZATION 47 Safety and Security 49 Tools and Management Computational Finance APPLICATION NAME COMPANY/DEVELOPER PRODUCT DESCRIPTION SUPPORTED FEATURES GPU SCALING Accelerated Elsen Secure, accessible, and accelerated back- • Web-like API with Native bindings for Multi-GPU Computing Engine testing, scenario analysis, risk analytics Python, R, Scala, C Single Node and real-time trading designed for easy • Custom models and data streams are integration and rapid development. easy to add Adaptiv Analytics SunGard A flexible and extensible engine for fast • Existing models code in C# supported Multi-GPU calculations of a wide variety of pricing transparently, with minimal code Single Node and risk measures on a broad range of changes asset classes and derivatives. -
Image Fx 1.5 Plus!
IMAGE FX We show you how to manipulate scan s and Hi Quality Version Available on AMIGALAND.COMclip art like this! All the software you need on this months coverdisksl UTILITY DISK AH Araigas with 2Mb IMAGE FX 1.5 PLUS! The best image processing program lor the Amiga! RAM speed test: AMIGA S S S L , 110 Blinara 1230 III Siren Apollo - 4 * BOctaM I E 0 6 I L; ' / P Test your skills \ \ , / < with this superb renewed > > * ■ d cup challenge ^ ‘*en10 *,om x J Impressions f i' I e long wait is over - see page 20 antes: 977096300903706 I Primal Rage i Sensible Golf » High Seas Trader i Pizza Tycoon 9 ( fU V O D UUYUJI I Ultimate Soccer June 1995 f 3 99 USSJ.95 ■ CAS9 95 ■ 0M2D ■ PIA1.150 ■ II 3.600 Manager ■ ASCHWO An (nap Piblitdtan LEISURE SUIT LARRY 1 ................. LEMMINGS 2 .................................... HOP * w ill not work on 4500 Phn, LOROS OF THE REALM 2149 4600 or 41200 A-TRAIN - CONSTRUCTION SET .......... 1049 MICRO MACHINES (512K) ................. 12 99 ACID BLITZ COMPILER VERSION 2. 17 BIT COLLECTION 2 CD S. MASSIVE 2 CO I MONOPOLY (5I2K) ......................... 13 99 THE LATEST UPOATE TO THE POPULAR SET OF GAMES. DEMOS. EDUCATION. MUSIC HOI2; w ill not work on 41200 A.T.R ITEAM 17) ..................................1649 A10 TANK KILLER............................... 1299 MORTAL KOMBAT ........................ 11 99 BLITZ BASIC IWHICH WAS USED TO MAKE ANO GRAPHICS 31JB j 5124 = will work onSOkn ALIEN BREED • TOWER ASSAUIJ (512K) 1349 MORTAL KOMBAT 2 19 49 SKIDMARKS AND GUARDIAN) WITH 1 CO S OF 17 Bn CONTINUATION. -
Rhorix: an Interface Between Quantum Chemical Topology and the 3D Graphics Program Blender
Lawrence Berkeley National Laboratory Recent Work Title Rhorix: An interface between quantum chemical topology and the 3D graphics program blender. Permalink https://escholarship.org/uc/item/18n454gq Journal Journal of computational chemistry, 38(29) ISSN 0192-8651 Authors Mills, Matthew JL Sale, Kenneth L Simmons, Blake A et al. Publication Date 2017-11-01 DOI 10.1002/jcc.25054 Peer reviewed eScholarship.org Powered by the California Digital Library University of California SOFTWARE NEWS AND UPDATES WWW.C-CHEM.ORG Rhorix: An Interface between Quantum Chemical Topology and the 3D Graphics Program Blender Matthew J. L. Mills ,[a,b] Kenneth L. Sale,[a,b] Blake A. Simmons,[a,c] and Paul L. A. Popelier [d] Chemical research is assisted by the creation of visual repre- topological objects and their 3D representations. Possible sentations that map concepts (such as atoms and bonds) to mappings are discussed and a canonical example is suggested, 3D objects. These concepts are rooted in chemical theory that which has been implemented as a Python “Add-On” named predates routine solution of the Schrodinger€ equation for sys- Rhorix for the state-of-the-art 3D modeling program Blender. tems of interesting size. The method of Quantum Chemical This allows chemists to use modern drawing tools and artists Topology (QCT) provides an alternative, parameter-free means to access QCT data in a familiar context. A number of exam- to understand chemical phenomena directly from quantum ples are discussed. VC 2017 The Authors. Journal of Computa- mechanical principles. Representation of the topological ele- tional Chemistry Published by Wiley Periodicals, Inc. -
Software and Peripherals Are Sent by Post, Hardware by White Arrow 2 MB RAM
Make your Amiga faster for under a tenner SPECIAL CELEBRATION COVERDISK NO. 100! WORTH d ir ec to r y OPUS4 Hi Quality Version Available on AMIGALAND.COM Clipart and utilities All Ailligas m ill 1 r.lli • Pto» die complete Stsl level m out demo ol this fanUslic RPC hom Black Legend Game Reviews: • Shadow Fighter • Lemmings III • Dragonstone • Kick Off 3 Euro • MKH-full review and players guidel S A V E 1 £ 9 M s / w e 1 l / ? , | F ' F A P f f V I CANNON h ODDER SAVE S O C f L i SETTLERS T2 | ' CHAOS ENGINE | £ 1 5 V CANNON FODDER 2 PREM MGR 2 PREM MGR 3 THEME PARK MONKEY ISLAND 2 BEAU JOLLY COMP RISE OF THE ROBOTS FIFA INTN L SOCCER MORTAL KOMBAT 19.99 8.99 16.99 23.99 a l l f o r m a t s 1 2 .9 9 25.99 27.49 o r 2 5 .9 9 A1200 23.49 20.99 PGA GO LF INDY 500 ADVANTAGE TENNIS EURO CHAMPS 92 TOWER ASSAULT ALADDIN JUNGLE STRIKE PGA EUROPEAN TOUR SENSIBLE SOCCER UFO 1 4 .9 9 OR 1 9 .9 9 CD32 2 0 . 4 9 A1200 1 8 .4 9 OR 1 9 .4 9 A12001 8 .4 9 OR 1 9 .4 9 A1200 4 .9 9 2 3 .9 9 A12001 9 .9 9 CD32 CANNON FODDER SAVE S a v e m £ ff k £ g RISE OF THE ROBOTS GUARDIAN MEGA RACE SUPER STARDUST SIMON TH E SO RCERER JUNGLE STRIKE CANNON FODDER POWER DRIVE 2 3 . -
Scalable Molecular Visualization and Analysis Tools in VMD
ATPESC Track 4: Scalable Molecular Visualization and Analysis Tools in VMD John E. Stone Theoretical and Computational Biophysics Group Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign http://www.ks.uiuc.edu/Research/vmd/ Argonne Training Program on Exascale Computing (ATPESC) 3:45pm-4:30pm, St. Charles Amphitheater, Q Center, St. Charles, IL, Monday August 5th, 2019 Biomedical Technology Research Center for Macromolecular Modeling and Bioinformatics Beckman Institute, University of Illinois at Urbana-Champaign - www.ks.uiuc.edu VMD – “Visual Molecular Dynamics” • 100,000 active users worldwide • Visualization and analysis of: – Molecular dynamics simulations – Lattice cell simulations – Quantum chemistry calculations – Cryo-EM densities, volumetric data • User extensible scripting and plugins • http://www.ks.uiuc.edu/Research/vmd/ Cell-Scale Modeling MD Simulation Biomedical Technology Research Center for Macromolecular Modeling and Bioinformatics Beckman Institute, University of Illinois at Urbana-Champaign - www.ks.uiuc.edu VMD Hands-On Tutorials • http://www.ks.uiuc.edu/Training/Tutorials/#vmd – Main VMD tutorial – QwikMD simulation preparation and analysis plugin – VMD images and movies tutorial – Structure check – VMD quantum chemistry visualization tutorial – Visualization and analysis of CPMD data with VMD – Parameterizing small molecules using ffTK Biomedical Technology Research Center for Macromolecular Modeling and Bioinformatics Beckman Institute, University of Illinois at Urbana-Champaign -
GPU-Accelerated Applications for HPC Industries| NVIDIA
GPU-ACCELERATED APPLICATIONS GPU‑ACCELERATED APPLICATIONS Accelerated computing has revolutionized a broad range of industries with over two hundred applications optimized for GPUs to help you accelerate your work. CONTENTS 01 Computational Finance 02 Defense and Intelligence 03 Manufacturing: CAD and CAE COMPUTER AIDED DESIGN COMPUTATIONAL FLUID DYNAMICS COMPUTATIONAL STRUCTURAL MECHANICS ELECTRONIC DESIGN AUTOMATION 05 Media and Entertainment ANIMATION, MODELING AND RENDERING COLOR CORRECTION AND GRAIN MANAGEMENT COMPOSITING, FINISHING AND EFFECTS EDITING ENCODING AND DIGITAL DISTRIBUTION ON-AIR GRAPHICS ON-SET, REVIEW AND STEREO TOOLS SIMULATION WEATHER GRAPHICS 08 Oil and Gas 09 Research: Higher Education and Supercomputing COMPUTATIONAL CHEMISTRY AND BIOLOGY NUMERICAL ANALYTICS PHYSICS Computational Finance APPLICATION DESCRIPTION SUPPORTED FEATURES MULTI-GPU SUPPORT Aaon Benfield Specialized platform for real-time hedging, Spreadsheet-like modeling interfaces, Yes Pathwise™ valuation, pricing and risk management Python-based scripting environment and Grid middleware Altimesh’s Hybridizer C# Multi-target C# framework for data parallel C# with translation to GPU or Multi-Core Yes computing. Xeon Global Valuation Esther In-memory risk analytics system for OTC High quality models not admitting closed Yes portfolios with a particular focus on XVA form solutions, efficient solvers based on metrics and balance sheet simulations. full matrix linear algebra powered by GPUs and Monte Carlo algorithms. Hanweck Associates Real-time options analytical engine (Volera) Real-time options analytics engine Yes MiAccLib 2.0.1 High Speed Multi-Algorithm Search Engine Exact Text match Search, Approximate\ Yes library providing high speed text string Similarity Text Search, Wild Card search with scalability of searching text Text Search, Proximity & Percentage and/or keywords on hundreds millions of Text Search, MultiKeyword and records and/or text data. -
Metadefender Core V4.11.1
MetaDefender Core v4.11.1 © 2018 OPSWAT, Inc. All rights reserved. OPSWAT®, MetadefenderTM and the OPSWAT logo are trademarks of OPSWAT, Inc. All other trademarks, trade names, service marks, service names, and images mentioned and/or used herein belong to their respective owners. Table of Contents About This Guide 13 Key Features of Metadefender Core 14 1. Quick Start with Metadefender Core 15 1.1. Installation 15 Operating system invariant initial steps 15 Basic setup 16 1.1.1. Configuration wizard 16 1.2. License Activation 22 1.3. Scan Files with Metadefender Core 22 2. Installing or Upgrading Metadefender Core 23 2.1. Recommended System Requirements 23 System Requirements For Server 23 Browser Requirements for the Metadefender Core Management Console 25 2.2. Installing Metadefender 26 Installation 26 Installation notes 26 2.2.1. Installing Metadefender Core using command line 26 2.2.2. Installing Metadefender Core using the Install Wizard 28 2.3. Upgrading MetaDefender Core 28 Upgrading from MetaDefender Core 3.x 28 Upgrading from MetaDefender Core 4.x 28 2.4. Metadefender Core Licensing 29 2.4.1. Activating Metadefender Licenses 29 2.4.2. Checking Your Metadefender Core License 35 2.5. Performance and Load Estimation 36 What to know before reading the results: Some factors that affect performance 36 How test results are calculated 37 Test Reports 37 Performance Report - Multi-Scanning On Linux 37 Performance Report - Multi-Scanning On Windows 41 2.6. Special installation options 46 Use RAMDISK for the tempdirectory 46 3. Configuring Metadefender Core 50 3.1. Management Console 50 3.2. -
Gpu-Accelerated Applications Gpu‑Accelerated Applications
GPU-ACCELERATED APPLICATIONS GPU-ACCELERATED APPLICATIONS Accelerated computing has revolutionized a broad range of industries with over six hundred applications optimized for GPUs to help you accelerate your work. CONTENTS 1 Computational Finance 62 Research: Higher Education and Supercomputing NUMERICAL ANALYTICS 2 Climate, Weather and Ocean Modeling PHYSICS 2 Data Science and Analytics SCIENTIFIC VISUALIZATION 5 Artificial Intelligence 68 Safety and Security DEEP LEARNING AND MACHINE LEARNING 71 Tools and Management 13 Federal, Defense and Intelligence 79 Agriculture 14 Design for Manufacturing/Construction: 79 Business Process Optimization CAD/CAE/CAM CFD (MFG) CFD (RESEARCH DEVELOPMENTS) COMPUTATIONAL STRUCTURAL MECHANICS DESIGN AND VISUALIZATION ELECTRONIC DESIGN AUTOMATION INDUSTRIAL INSPECTION Test Drive the 29 Media and Entertainment ANIMATION, MODELING AND RENDERING World’s Fastest COLOR CORRECTION AND GRAIN MANAGEMENT COMPOSITING, FINISHING AND EFFECTS Accelerator – Free! (VIDEO) EDITING Take the GPU Test Drive, a free and (IMAGE & PHOTO) EDITING easy way to experience accelerated ENCODING AND DIGITAL DISTRIBUTION computing on GPUs. You can run ON-AIR GRAPHICS your own application or try one of ON-SET, REVIEW AND STEREO TOOLS the preloaded ones, all running on a WEATHER GRAPHICS remote cluster. Try it today. www.nvidia.com/gputestdrive 44 Medical Imaging 47 Oil and Gas 48 Life Sciences BIOINFORMATICS MICROSCOPY MOLECULAR DYNAMICS QUANTUM CHEMISTRY (MOLECULAR) VISUALIZATION AND DOCKING Computational Finance APPLICATION NAME COMPANYNAME PRODUCT DESCRIPTION SUPPORTED FEATURES GPU SCALING Accelerated Elsen Secure, accessible, and accelerated • Web-like API with Native bindings for Multi-GPU Computing Engine back-testing, scenario analysis, Python, R, Scala, C Single Node risk analytics and real-time trading • Custom models and data streams designed for easy integration and rapid development. -
Metadefender Core V4.16.3
MetaDefender Core v4.16.3 © 2019 OPSWAT, Inc. All rights reserved. OPSWAT®, MetadefenderTM and the OPSWAT logo are trademarks of OPSWAT, Inc. All other trademarks, trade names, service marks, service names, and images mentioned and/or used herein belong to their respective owners. Table of Contents About This Guide 12 Key Features of MetaDefender Core 13 1. Quick Start with MetaDefender Core 14 1.1. Installation 14 Operating system invariant initial steps 14 Basic setup 15 1.1.1. Configuration wizard 15 1.2. License Activation 20 1.3. Process Files with MetaDefender Core 20 2. Installing or Upgrading MetaDefender Core 21 2.1. System Requirements 21 System Requirements For Server 21 Browser Requirements for the Metadefender Core Management Console 25 2.2. Installing MetaDefender 26 Installation 26 Installation notes 26 2.2.1. Installing Metadefender Core using command line 27 2.2.2. Installing Metadefender Core using the Install Wizard 30 2.3. Upgrading MetaDefender Core 30 Upgrading from MetaDefender Core 3.x 30 Upgrading from MetaDefender Core 4.x 30 2.4. MetaDefender Core Licensing 30 2.4.1. Activating Metadefender Licenses 31 2.4.2. Checking Your Metadefender Core License 36 2.5. Performance and Load Estimation 37 What to know before reading the results: Some factors that affect performance 37 How test results are calculated 38 Test Reports 38 Performance Report - Multi-Scanning On Linux 38 Performance Report - Multi-Scanning On Windows 42 2.6. Special installation options 45 Use RAMDISK for the tempdirectory 45 3. Configuring MetaDefender Core 49 3.1. Management Console 49 3.1.1. -
NVIDIA GPU Accelerated Applications Catalog
POPULAR GPU‑ACCELERATED APPLICATIONS CONTENTS 02 Research: Higher Education and Supercomputing COMPUTATIONAL CHEMISTRY AND BIOLOGY NUMERICAL ANALYTICS PHYSICS WEATHER AND CLIMATE FORECASTING 06 Defense and Intelligence 07 Computational Finance 08 Manufacturing: CAD and CAE COMPUTER AIDED DESIGN COMPUTATIONAL FLUID DYNAMICS COMPUTATIONAL STRUCTURAL MECHANICS ELECTRONIC DESIGN AUTOMATION 10 Media and Entertainment ANIMATION, MODELING AND RENDERING COLOR CORRECTION AND GRAIN MANAGEMENT COMPOSITING, FINISHING AND EFFECTS EDITING ENCODING AND DIGITAL DISTRIBUTION ON-AIR GRAPHICS ON-SET, REVIEW AND STEREO TOOLS SIMULATION WEATHER GRAPHICS 14 Oil and Gas Research: Higher Education and Supercomputing COMPUTATIONAL CHEMISTRY AND BIOLOGY Bioinformatics APPLICATION DESCRIPTION SUPPORTED FEATURES EXPECTED SPEED UP* RECOMMENDED GPU ** MULTI-GPU SUPPORT RELEASE STATUS BarraCUDA Sequence mapping software Alignment of short 6-10x T 2075, 2090, Yes Available now sequencing reads K10, K20, K20X Version 0.6.2 CUDASW++ Open source software for Smith- Parallel search of Smith- 10-50x T 2075, 2090, Yes Available now Waterman protein database searches Waterman database K10, K20, K20X Version 2.0.8 on GPUs CUSHAW Parallelized short read aligner Parallel, accurate long read 10x T 2075, 2090, Yes Available now aligner - gapped alignments K10, K20, K20X Version 1.0.40 to large genomes GPU-BLAST Local search with fast k-tuple Protein alignment according 3-4x T 2075, 2090, Single only Available now heuristic to blastp, multi cpu threads K10, K20, K20X Version 2.2.26