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Installation Guide install_guide.book Page i Monday, May 11, 2015 8:48 PM Installation Guide Installation Guide Schrödinger Software Release 2015-2 Schrödinger Press install_guide.book Page ii Monday, May 11, 2015 8:48 PM Installation Guide Copyright © 2015 Schrödinger, LLC. All rights reserved. While care has been taken in the preparation of this publication, Schrödinger assumes no responsibility for errors or omissions, or for damages resulting from the use of the information contained herein. Canvas, CombiGlide, ConfGen, Epik, Glide, Impact, Jaguar, Liaison, LigPrep, Maestro, Phase, Prime, PrimeX, QikProp, QikFit, QikSim, QSite, SiteMap, Strike, and WaterMap are trademarks of Schrödinger, LLC. Schrödinger, BioLuminate, and MacroModel are registered trademarks of Schrödinger, LLC. MCPRO is a trademark of William L. Jorgensen. DESMOND is a trademark of D. E. Shaw Research, LLC. Desmond is used with the permission of D. E. Shaw Research. All rights reserved. This publication may contain the trademarks of other companies. Schrödinger software includes software and libraries provided by third parties. For details of the copyrights, and terms and conditions associated with such included third party software, use your browser to open third_party_legal.html, which is in the docs folder of your Schrödinger software installation. This publication may refer to other third party software not included in or with Schrödinger software ("such other third party software"), and provide links to third party Web sites ("linked sites"). References to such other third party software or linked sites do not constitute an endorsement by Schrödinger, LLC or its affiliates. Use of such other third party software and linked sites may be subject to third party license agreements and fees. Schrödinger, LLC and its affiliates have no responsibility or liability, directly or indirectly, for such other third party software and linked sites, or for damage resulting from the use thereof. Any warranties that we make regarding Schrödinger products and services do not apply to such other third party software or linked sites, or to the interaction between, or interoperability of, Schrödinger products and services and such other third party software. May 2015 install_guide.book Page iii Monday, May 11, 2015 8:48 PM Contents Document Conventions ..................................................................................................... ix Chapter 1: Installation Notes .......................................................................................... 1 1.1 Linux Installation Process Summary..................................................................... 1 1.2 Windows Installation Process Summary .............................................................. 2 1.3 Mac Installation Process Summary ....................................................................... 2 Chapter 2: Hardware and Software Requirements......................................... 5 2.1 General Requirements.............................................................................................. 5 2.1.1 Hardware ............................................................................................................ 5 2.1.1.1 CPU, Memory, and Disk ........................................................................... 5 2.1.1.2 Graphics Card and Monitor ...................................................................... 5 2.1.1.3 GPGPU Computing.................................................................................. 6 2.1.1.4 Clusters................................................................................................... 6 2.1.2 Linux ................................................................................................................... 6 2.1.3 Windows ............................................................................................................. 7 2.1.4 Mac ..................................................................................................................... 8 2.1.5 Queueing Systems.............................................................................................. 8 2.2 Disk Space for Installation....................................................................................... 9 2.3 Product Notes ............................................................................................................ 9 2.3.1 Desmond 4.2....................................................................................................... 9 2.3.1.1 Network Recommendations for MPI Use................................................... 9 2.3.1.2 Use of Graphics Processors (GPUs)....................................................... 10 2.3.2 Jaguar 8.8 ......................................................................................................... 10 2.3.3 KNIME Extensions 2.11 .................................................................................... 11 2.3.4 MCPRO+ 3.8..................................................................................................... 11 2.3.5 Prime 4.0........................................................................................................... 11 2.4 Prime Third-Party Software and Databases ....................................................... 11 2.5 Documentation Requirements .............................................................................. 14 Installation Guide iii install_guide.book Page iv Monday, May 11, 2015 8:48 PM Contents Chapter 3: Installing the Products on Linux ....................................................... 15 3.1 Access to the Software .......................................................................................... 15 3.2 Verifying System Compliance............................................................................... 16 3.3 Installing the Software and Documentation ....................................................... 17 3.4 Setting the Environment Variables....................................................................... 19 3.5 Enabling Hardware Stereo Viewing...................................................................... 20 3.6 Installing Prime Third-Party Software and Databases from a Download...... 20 3.7 Installing VMD for Desmond.................................................................................. 23 3.8 Setting Up Access to PyMOL ................................................................................ 24 3.9 Uninstalling the Software....................................................................................... 24 Chapter 4: Installing the Products on Windows .............................................. 25 4.1 Installing Schrödinger Software ........................................................................... 25 4.1.1 Preparing for Installation ................................................................................... 25 4.1.2 Installation Notes .............................................................................................. 26 4.1.3 Installing From the DOS Command Line .......................................................... 28 4.1.4 Troubleshooting................................................................................................. 30 4.2 Installing Prime Third-Party Software and Databases...................................... 31 4.3 Setting Up Access to PyMOL ................................................................................ 33 4.4 Uninstalling Schrödinger Software...................................................................... 34 Chapter 5: Installing the Products on a Mac ..................................................... 35 5.1 Installing Schrödinger Software ........................................................................... 35 5.2 Installing Prime Third-Party Databases............................................................... 35 5.3 Uninstalling Schrödinger Software...................................................................... 36 Chapter 6: Installing and Updating KNIME Extensions ............................. 39 6.1 Installing into an Existing Version of KNIME ..................................................... 39 iv Schrödinger Software Release 2015-2 install_guide.book Page v Monday, May 11, 2015 8:48 PM Contents 6.2 Updating Existing Schrödinger Extensions ....................................................... 43 6.3 Adding New Schrödinger Extensions.................................................................. 44 6.4 Installing Knime Workflows................................................................................... 45 6.5 Installing A Web Service for Node Execution .................................................... 46 Chapter 7: Preparing for Job Submission ........................................................... 47 7.1 The Hosts File .......................................................................................................... 47 7.1.1 The name and host Settings ............................................................................. 51 7.1.2 The user Setting................................................................................................ 52 7.1.3 The tmpdir Setting............................................................................................. 52 7.1.4 The processors and processors_per_node Settings ........................................ 52 7.1.5 The parallel Setting ..........................................................................................
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