1. Introduction

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

Gaffney can be accessed via Kerberized ssh as follows:

% ssh gaffney.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. 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 180 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 Gaffney

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 Gaffney login node.

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

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

6. Submit Jobs to the Batch Queue

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

7. Batch Queues

The following table describes the PBS queues available on Gaffney:

Queue Descriptions and Limits on Gaffney
Priority Queue Name Max Wall Clock Time Max Cores Per Job Description
Highest urgent 24 Hours 768 Jobs belonging to DoD HPCMP Urgent Projects
Down arrow for decreasing priority debug 30 Minutes 2,400 Time/resource-limited for user testing and debug purposes
HIE 24 Hours 384 Rapid response for interactive work. For more information see the HPC Interactive Environment (HIE) User Guide.
high 168 Hours 15,840 Jobs belonging to DoD HPCMP High Priority Projects
frontier 168 Hours 14,400 Jobs belonging to DoD HPCMP Frontier Projects
standard 168 Hours 8,160 Standard jobs
gpu 24 Hours 384 GPU-accelerated jobs
serial 168 Hours 1 Serial jobs
bigmem 96 Hours 720 Large-memory jobs
transfer 48 Hours N/A Data transfer for user jobs. See the Navy DSRC Archive Guide, section 5.2.
Lowest background 4 Hours 1,200 User jobs that are not charged against the project allocation

8. Monitoring Your Job

You can monitor your batch jobs on Gaffney 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
--------         -------- --------  ------- ------ --- --- ------ ----- -  -----
3403.pbsserver   user1    debug     mytest  435354   1  48   --   00:30 R  00:12
3404.pbsserver   user1    frontier  inspect --     100 480   --   06:00 Q   --
3405.pbsserver   user1    standard  45dh8   2584     2  96   --   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. 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 [-C path ] [-D] [-s] file1 [file2 ...]

Copy one or more files from the archive system
archive get [-C path ] [-s] file1 [file2 ...]

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. Gaffney 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 Gaffney is available on the software page.

12. Advance Reservation Service

A subset of Gaffney'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.