You are reading the Altair PBS Professional 14.2 User’s Guide (UG) Updated 1/23/17 Please send any questions or suggestions for improvements to [email protected]. Copyright © 2003-2017 Altair Engineering, Inc. All rights reserved. PBS™, PBS Works™, PBS GridWorks®, PBS Professional®, PBS Analytics™, PBS Catalyst™, e-Compute™, and e- Render™ are trademarks of Altair Engineering, Inc. and are protected under U.S. and international laws and treaties. All other marks are the property of their respective owners. ALTAIR ENGINEERING INC. Proprietary and Confidential. Contains Trade Secret Information. Not for use or disclo- sure outside ALTAIR and its licensed clients. Information contained herein shall not be decompiled, disassembled, duplicated or disclosed in whole or in part for any purpose. Usage of the software is only as explicitly permitted in the end user software license agreement. Copyright notice does not imply publication. Terms of use for this software are available online at http://www.pbspro.com/UserArea/agreement.html This document is proprietary information of Altair Engineering, Inc. Please send any questions or suggestions for improvements to [email protected]. Contact Us For the most recent information, go to the PBS Works website, www.pbsworks.com, select "My PBS", and log in with your site ID and password. Altair Altair Engineering, Inc., 1820 E. Big Beaver Road, Troy, MI 48083-2031 USA www.pbsworks.com Sales [email protected] 248.614.2400 Technical Support Need technical support? We are available from 8am to 5pm local times: Location Telephone e-mail Australia +1 800 174 396 [email protected] China +86 (0)21 6117 1666 [email protected] France +33 (0)1 4133 0992 [email protected] Germany +49 (0)7031 6208 22 [email protected] India +91 80 66 29 4500 [email protected] +1 800 425 0234 (Toll Free) Italy +39 800 905595 [email protected] Japan +81 3 5396 2881 [email protected] Korea +82 70 4050 9200 [email protected] Malaysia +91 80 66 29 4500 [email protected] +1 800 425 0234 (Toll Free) North America +1 248 614 2425 [email protected] Russia +49 7031 6208 22 [email protected] Scandinavia +46 (0)46 460 2828 [email protected] Singapore +91 80 66 29 4500 [email protected] +1 800 425 0234 (Toll Free) South America +55 11 3884 0414 [email protected] UK +44 (0)1926 468 600 [email protected] Contents About PBS Documentation ix 1 New Features 1 1.1 New Features in PBS 14.2 . 1 1.2 Changes in Previous Releases . 1 1.3 Deprecations . 3 1.4 Backward Compatibility. 4 2 Getting Started with PBS 5 2.1 Why Use PBS? . 5 2.2 PBS Tasks and Components . 5 2.3 Interfaces to PBS . 7 2.4 Setting Up Your Environment . 9 3 Submitting a PBS Job 15 3.1 Introduction to the PBS Job. 15 3.2 The PBS Job Script. 18 3.3 Submitting a PBS Job . 22 3.4 Job Submission Recommendations and Advice . 28 3.5 Job Submission Options . 28 4 Job Input & Output Files 37 4.1 Introduction to Job File I/O in PBS . 37 4.2 Input/Output File Staging. 37 4.3 Managing Output and Error Files . 45 5 Allocating Resources & Placing Jobs 53 5.1 What is a Vnode? . 53 5.2 PBS Resources. 53 5.3 Requesting Resources . 55 5.4 How Resources are Allocated to Jobs . 62 5.5 Limits on Resource Usage . 64 5.6 Viewing Resources . 66 5.7 Specifying Job Placement. 67 5.8 Backward Compatibility. 73 6 Multiprocessor Jobs 79 6.1 Submitting Multiprocessor Jobs . 79 6.2 Using MPI with PBS . 83 6.3 Using PVM with PBS. 106 6.4 Using OpenMP with PBS . 107 6.5 Hybrid MPI-OpenMP Jobs. 108 PBS Professional 14.2 User’s Guide UG-v Contents 7 Controlling How Your Job Runs 111 7.1 Using Job Exit Status . 111 7.2 Using Job Dependencies . 111 7.3 Adjusting Job Running Time . 113 7.4 Using Checkpointing . 117 7.5 Holding and Releasing Jobs . 118 7.6 Allowing Your Job to be Re-run. 122 7.7 Controlling Number of Times Job is Re-run . 123 7.8 Making qsub Wait Until Job Ends. 123 7.9 Deferring Execution. 124 7.10 Setting Priority for Your Job . 125 7.11 Running Your Job Interactively . 125 7.12 Specifying Which Jobs to Preempt . 131 8 Reserving Resources Ahead of Time 133 8.1 Glossary . 133 8.2 Prerequisites for Reserving Resources. 133 8.3 Creating and Using Reservations . 134 8.4 Viewing the Status of a Reservation . 138 8.5 Using Your Reservation . 141 8.6 Reservation Caveats and Errors . 142 9 Job Arrays 145 9.1 Advantages of Job Arrays . 145 9.2 Glossary . 145 9.3 Description of Job Arrays . 145 9.4 Submitting a Job Array . 148 9.5 Viewing Status of a Job Array . 154 9.6 Using PBS Commands with Job Arrays . 157 9.7 Job Array Caveats. ..