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

Gordon can be accessed via Kerberized ssh as follows:

% ssh gordon.navydsrc.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 and the HPC Portal. Neither of these file systems is backed up. You are responsible for managing files in your $WORKDIR and $CENTER directories by backing up files to the archive system and deleting unneeded files. Currently, $WORKDIR files older than 21 days and $CENTER files older than 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 Gordon

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 Gordon login node.

% scp local_file user@gordon.navydsrc.hpc.mil:/target_dir

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

6. Submit jobs to the batch queue

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

7. Batch queues

The following table describes the PBS queues available on Gordon:

Queue Descriptions and Limits on Gordon
Priority Queue
Max Wall
Clock Time
Max Cores
Per Job
Highest urgent 24 Hours 768 Jobs belonging to DoD HPCMP Urgent Projects
Down arrow for decreasing priority frontier 168 Hours 16,000 Designated Frontier projects by DoD HPCMP
high 168 Hours 16,000 Jobs belonging to DoD HPCMP High Priority Projects
debug 30 Minutes 3,072 User diagnostic jobs
standard 168 Hours 8,000 Standard jobs
phi 168 Hours 2,016 Phi-accelerated jobs
bigmem 24 Hours 224 Large-memory jobs
transfer 48 Hours N/A Data transfer for user jobs
Lowest background 4 Hours 3,200 Unrestricted access - no allocation charge

8. Monitoring your job

You can monitor your batch jobs on Gordon using the qpeek, qview, 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
--------         -------- --------  ------- ------ --- --- ------ ----- -  -----
30815.gordon-pbs1  user1  debug     mytest  1766   50  120   --   00:30 R  00:12
31010.gordon-pbs1  user1  frontier  inspect --     100 240   --   06:00 Q   --
31015.gordon-pbs1  user1  standard  45dh8   2584   50  120   --   02:00 R  14:22

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

To delete a job, use the command "qdel jobID".

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

Copy one or more files from the archive system
scp $ARCHIVE_HOST:$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. Gordon 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 which 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 Gordon is available on the software page.

12. Advance Reservation Service

A subset of Gordon'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.