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Pershing Quick Start Guide

Table of Contents

1. Introduction

This document provides a brief summary of information that you'll need to know to quickly get started working on Pershing. For more detailed information, see the Pershing User Guide.

2. Get a Kerberos Ticket

For security purposes, you must have a current Kerberos ticket on your computer before attempting to connect to Pershing. A Kerberos client kit must be installed on your desktop to enable you to get a Kerberos ticket. Information about installing Kerberos clients on your Windows desktop can be found at HPC Centers: Kerberos & Authentication.

3. Connect to Pershing

Pershing can be accessed via Kerberized ssh as follows:

% ssh

4. Home, working, and center-wide directories

Each user has file space in the $HOME, $WORKDIR, and $CENTER directories. The $HOME, $WORKDIR, and $CENTER environment variables are predefined for you and point to the appropriate locations in the file systems. You are strongly encouraged to use these variables in your scripts.

NOTE: $WORKDIR is a "scratch" file system, and $CENTER is a center-wide file system that is accessible to all center production machines, including the Utility Server. The $WORKDIR file system is not backed up. You are responsible for managing files in your $WORKDIR directories by backing up files to the archive system and deleting unneeded files. Currently, $WORKDIR files that have not been accessed in 15 days are subject to being purged.

5. Transfer files and data to Pershing

File transfers to DSRC systems must be performed using Kerberized versions of the following tools: scp, ftp, sftp, and mpscp. For example, the command below uses secure copy (scp) to copy a local file into a destination directory on a Pershing login node.

% scp local_file

For additional information on file transfers to and from Pershing, see the File Transfers section of the Pershing User Guide.

6. Submit jobs to the batch queue

The Portable Batch System (PBS Professional ™) is the workload management system for Pershing. To submit a batch job, use the following command:

qsub [ options ] my_job_script

where my_job_script is the name of the file containing your batch script. For more information on using PBS or on job scripts, see the Pershing User Guide, the Pershing PBS Guide, or the sample script examples found in the $SAMPLES_HOME directory on Pershing.

7. Batch queues

The following table describes the PBS queues available on Pershing:

Queue Descriptions and Limits
Priority Queue
Max Wall
Clock Time
Max Cores
Per Job
Highest debug Debug 1 Hour 512 User diagnostic jobs
Down Arrow for decreasing priority transfer N/A 24 Hours 1 Data transfer for user jobs
urgent Urgent 96 Hours N/A Designated urgent jobs by DoD HPCMP
staff N/A 368 Hours N/A ARL DSRC staff testing only. System testing and user support.
high High 96 Hours N/A Designated high-priority jobs by DoD HPCMP
challenge Challenge 168 Hours N/A Challenge projects only
cots Standard 96 Hours N/A Abaqus, Fluent, and Cobalt jobs
interactive Standard 12 Hours N/A Interactive jobs
standard-long Standard 200 Hours N/A ARL DSRC permission required
standard Standard 168 Hours N/A Non-Challenge user jobs
Lowest background Background 24 Hours N/A User jobs that will not be charged against the project allocation.

* The running job limit on the debug queue per user is 4.
** The running job limit on the background queue per user is 1.

8. Monitoring your job

You can monitor your batch jobs on Pershing using the qpeek or qstat commands.

The qstat command lists all jobs in the queue. The "-u username" option shows only jobs owned by the given user, as follows:

% qstat -u user1
                                                         Req'd  Req'd    Elap
Job ID        Username Queue    Jobname   SessID NDS TSK Memory Time  S  Time
-----------   -------- -------- --------- ------ --- --- ------ ----- -  -----
64485.pershin  user1   backgrou  tw2      14658   1    1   --   12:00 R  01:12
64495.pershin  user1   standard  45dh8    21308   2    1   --   02:00 R  00:22
64513.pershin  user1   challeng  inspect    --   16  256   --   06:00 Q   --

Notice that the output contains the JobID for each job. This ID can be used with the qpeek, qstat, and qdel commands.

To delete a job, use the command "qdel jobID".
To delete all of your jobs, use "qdel `qselect -u username`".
To delete all of your running jobs (R status), use "qdel `qselect -u username -s R`".
To delete all of your queued (Q status), use "qdel `qselect -u username -s Q`".

To view a partially completed output file, use the "qpeek jobID" command.

9. Saving your work

When your job is finished, you should archive any important data to prevent automatic deletion by the purge scripts.

Copy one or more files to the archive system
cp file1 $ARCHIVE_HOME

Copy one or more files from the archive system
cp $ARCHIVE_HOME/my_data/file1 .

For more information on archiving your files, see the Archive Guide.

10. Modules

Software modules are a very convenient way to set needed environment variables and include necessary directories in your path so that commands for particular applications can be found. Pershing uses "modules" to initialize your environment with COTS application software, system commands and libraries, compiler suites, environment variables, and PBS batch system commands.

A number of modules are loaded automatically as soon as you log in. To see the modules that are currently loaded, run "module list". To see the entire list of available modules, run "module avail". You can modify the configuration of your environment by loading and unloading modules. For complete information on how to do this, see the Modules User Guide.

11. Available software

A list of software on Pershing is available on the software page.

12. Advance Reservation Service

A subset of Pershing's nodes has been set aside for use as part of the Advanced Reservation Service (ARS). The ARS allows users to reserve a user-designated number of nodes for a specified number of hours starting at a specific date/time. This service enables users to execute interactive or other time-critical jobs within the batch system environment. The ARS is accessible via most modern web browsers at Authenticated access is required. Windows Internet Explorer users may authenticate with either CAC or YubiKey. Non-Windows users must use YubiKey. An ARS User's Guide is available online once you have logged in.