PBS Professional 13.0 User’s Guide

1 PBS Works is a division ofPBS Professional s Guide Y ou are reading the Altair PBS Professional user s Guide (UG) Updated 6/7/15 Copyright 2003-2015 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 and inter-national laws and treaties. All other marks are the property of their respective ENGINEERING INC. Proprietary and Confidential. Contains Trade Secret Informa-tion. Not for use or disclosure 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.

2 Copyright notice does not imply information on the End user License Agreement terms and conditions and the terms and conditions governing third party codes included in the Altair Software, please see the Release Notes. Documentation and Contact Information Contact Altair at: www . pbssales@altair .com T echnical Support This document is proprietary information of Altair Engineering, Inc. Location T elephone e-mail North America +1 248 614 2425 pbssupport@altair .com China +86 (0)21 61 17 1666 es@altair . France +33 (0)1 4133 0992 francesupport@altair .com Germany +49 (0)7031 6208 22 hwsupport@altair .de India +91 80 66 29 4500 .com Italy +39 800 905595 Japan +81 3 5396 2881 Korea +82 70 4050 9200 support@altair . Scandinavia +46 (0) 46 460 2828 support@altair.

3 Se UK +44 (0)1926 468 600 .com PBS Professional user s Guide UG-iii Contents About PBS Documentation vii1 New Features1 New Features in PBS .. 1 Changes in Previous Releases .. 2 Deprecations .. 4 Backward Compatibility .. 5 2 Getting Started with PBS 7 Why Use PBS? .. 7 PBS Tasks and Components .. 7 Interfaces to PBS .. 9 Setting Up Your Environment .. 12 3 Submitting a PBS Job 21 Introduction to the PBS Job .. 21 The PBS Job Script .. 25 Submitting a PBS Job .. 31 Job Submission Recommendations and Advice .. 39 Job Submission Options .. 39 4 Job Input & Output Files 49 Introduction to Job File I/O in PBS .. 49 Input/Output File Staging .. 49 Managing Output and Error Files .. 62 Contents UG-iv PBS Professional user s Guide 5 Allocating Resources & Placing Jobs 71 What is a Vnode?

4 71 PBS Resources .. 72 Requesting Resources .. 74 How Resources are Allocated to Jobs .. 84 Limits on Resource Usage .. 88 Viewing Resources .. Job Placement.. Compatibility.. 1016 Multiprocessor Multiprocessor Jobs .. MPI with PBS .. PVM with PBS.. OpenMP with PBS .. MPI-OpenMP Jobs.. 1587 Controlling How Your Job Job Exit Status .. Job Dependencies .. Job Running Time.. Checkpointing.. and Releasing Jobs .. Your Job to be Re-run.. Number of Times Job is Re-run .. qsub Wait Until Job Ends.. Execution.. Priority for Your Job .. Your Job Interactively.. Which Jobs to Preempt .. 1908 Reserving Resources Ahead of .. for Reserving Resources.. and Using Reservations .. the Status of a Reservation.. Your Reservation.

5 Caveats and Errors.. 205 ContentsPBS Professional user s GuideUG-v9 Job of Job Arrays.. of Job Arrays .. a Job Array .. Status of a Job Array.. PBS Commands with Job Arrays .. Array Caveats.. 22910 Working with PBS vs. Historical Jobs .. Job Attributes .. Jobs.. Messages to Jobs.. Signals to Jobs .. Order of Jobs .. Jobs Between Queues .. 24011 Checking Job & System Job Status .. Server Status.. Queue Status .. Job & System Status with xpbs.. a List of Jobs.. Job Progress Using xpbs TrackJob Feature.. License Availability .. 26812 Submitting Cray .. Jobs on the Cray.. Resources for the Cray.. for Submitting Jobs on the Cray .. for Submitting Cray Jobs.. Cray Job Information.. and Advice .. and Logging .. 296 ContentsUG-viPBS Professional user s Guide13 Using.

6 Provisioning Works.. and Restrictions.. Provisioning.. and Errors.. 30414 Special Circumstances and for Large Page Mode on AIX.. Comprehensive System Accounting.. 30715 Using the xpbs the xpbs command.. xpbs: Definitions of Terms.. the xpbs Main Display.. xpbs Preferences.. Between PBS and xpbs .. to Submit a Job Using xpbs .. xpbs.. xpbs Configuration File.. Preferences.. 323 Index 327 PBS Professional user s GuideUG-viiAbout PBS DocumentationThe PBS Professional DocumentationThe documentation for PBS Professional includes the following:PBS Professional Administrators Guide :How to configure and manage PBS Professional . For the PBS Professional Quick Start Guide :Quick overview of PBS Professional installation and license file Professional Installation & Upgrade Guide : How to install and upgrade PBS Professional .

7 For the Professional Users Guide : How to submit, monitor, track, delete, and manipulate jobs. For the job Professional Programmers Guide : Discusses the PBS application programming interface (API). For Professional Reference Guide : Covers PBS reference Manual Pages:PBS commands, resources, attributes, to Keep the DocumentationTo make cross-references work, put all of the PBS guides in the same directory. Ordering Software and PublicationsTo order additional copies of this manual and other PBS publications, or to purchase addi-tional software licenses, contact your Altair sales representative at PBS DocumentationUG-viiiPBS Professional user s GuideDocument ConventionsPBS documentation uses the following typographic conventions:abbreviationThe shortest acceptable abbreviation of a command or subcommand is such as qmgr and scpinputCommand-line instructionsmanpage(x)File and path names.

8 Manual page references include the section number in parentheses appended to the manual page , template, synopsisAttributesAttributes, parameters, objects, variable names, resources, typesValuesKeywords, instances, states, values, labelsDefinitionsTerms being definedOutputOutput, example code, or file contentsExamplesExamples FilenameName of fileUtilityName of utility, such as a program1 PBS Professional user s GuideUG-1 New Features in PBS Preemption TargetsYou can specify which jobs can be preempted by a given job. See section , How Preemption Targets Work , on page qsub in the ForegroundBy default, the qsub command runs in the background. You can run it in the foreground using the -f option. See qsub on page 225 of the PBS Professional Reference Users can Use UNC PathsWindows users can use UNC paths for job submission and file staging.

9 See "Set up Paths", on page 16 of the PBS Professional user s Guide and "Using UNC Paths", on page 54 of the PBS Professional user s Job and Reservation NamesYou can use job and reservation names up to 236 characters in length. See Formats on page 421 of the PBS Professional Reference for Hydra Process Manager in Intel MPI Intel MPI is integrated with PBS. See "Integrating Intel MPI On Linux/UNIX Using Environment Variables on page to pbsnodes Command You can now use the pbsnodes command to edit the comment attribute of a host, to write out host information, and to operate on specific vnodes. See "pbsnodes on page Group of Job Owner or Reservation Creator Automatically Added to Job group_list The job submitter s and reservation creator s primary group is automatically added to the job or reservation group_list attribute.

10 See "qsub on page 225 and "pbs_rsub on page 1 New FeaturesUG-2 PBS Professional user s GuideIntel MPI Integrated under WindowsMPI is integrated with PBS under Windows (as well as Linux/UNIX). See "Integrating Intel MPI on Windows Using Wrapper Script on page Integrated under WindowsMPICH2 is integrated with PBS under Windows (as well as Linux/UNIX). See "Integrating MPICH2 on Windows Using Wrapper Script on page pbsdsh Command Available under WindowsThe pbsdsh command is available under Windows. See "pbsdsh on page TM APIs Available under WindowsThe PBS TM APIs are available under Windows. See "TM Library on page 91 of the PBS Professional Programmer s pbs_attach Command Available under WindowsThe pbs_attach command is available under Windows.