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Centennial 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 Centennial. For more detailed information, see the Centennial 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 Centennial. 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 Centennial

Centennial can be accessed via Kerberized ssh as follows:

% ssh centennial.arl.hpc.mil

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. 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 21 days and $CENTER files that have not been accessed in 120 days are subject to being purged.

If it is determined as part of the normal purge cycle that files in your $WORKDIR directory must be deleted, you WILL NOT be notified prior to deletion. You are responsible to monitor your workspace to prevent data loss.

5. Transfer Files and Data to Centennial

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 Centennial login node.

% scp local_file centennial.arl.hpc.mil:/target_dir

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

6. Submit Jobs to the Batch Queue

The Portable Batch System (PBS Professional ™) is the workload management system for Centennial. 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 Centennial User Guide, the Centennial PBS Guide, or the sample script examples found in the $SAMPLES_HOME directory on Centennial.

7. Batch Queues

The following table describes the PBS queues available on Centennial:

Queue Descriptions and Limits
Priority Queue
Name
Job
Class
Max Wall
Clock Time
Max Cores
Per Job
Comments
Highest debug Debug 1 Hour N/A User diagnostic jobs
Down Arrow for decreasing priority transfer N/A 48 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
frontier Frontier 168 Hours N/A Frontier 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 Normal 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 Centennial 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.centenn  user1   backgrou  tw2      14658   1    1   --   12:00 R  01:12
64495.centenn  user1   standard  45dh8    21308   2    1   --   02:00 R  00:22
64513.centenn  user1   frontier  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. Archiving 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
archive put file1

Copy one or more files from the archive system
archive get 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. Centennial 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 Centennial is available on the software page.

12. Advance Reservation Service

A subset of Centennial's nodes has been set aside for use as part of the Advance 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 https://reservation.hpc.mil. Authenticated access is required. The ARS User Guide is available on HPC Centers.