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Hokule'a 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 Hokule'a. For more detailed information, see the Hokule'a 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 Hokule'a. 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 Hokule'a

hokulea can be accessed via Kerberized ssh as follows:

% ssh hokulea.mhpcc.hpc.mil

or by the following Login Node:

hokulea.mhpcc.hpc.mil

Login nodes are shared access points for Hokule'a. Therefore, users should not run resource intensive processes on these nodes. MHPCC reserves the right to kill user processes without notice that may be affecting primary access functionality of the login nodes.

In accordance with HPCMP policy, users are limited to 24 hour session lifetimes. After 24 hours users will be automatically logged out and will need to re-login to the cluster.

4. Home, Working, and Center-wide Directories

Each user has file space in the $HOME and $WORKDIR directories. The $HOME and $WORKDIR 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 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 60 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 Hokule'a

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 an Hokule'a login node.

% scp local_file hokulea.mhpcc.hpc.mil:/target_dir

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

6. Submit Jobs to the Batch Queue

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

7. Batch Queues

The following table describes the PBS queues available on Hokule'a:

Queue Name Description
urgent Approved by HPCMP Director only
high Must be approved by Service/Agency Principal
frontier Must be a Frontier project approved by HPCMP
debug LESS than 30 minutes and LESS than or EQUAL to 64 processors
standard Must be an approved HPCMP project
background Lowest priority, 8 hour limit, no allocation subtraction

8. Monitoring Your Job

You can monitor your batch jobs on Hokule'a 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.hokulea  user1   backgrou  tw2      14658   1    1   --   12:00 R  01:12
64495.hokulea  user1   standard  45dh8    21308   2   64   --   02:00 R  00:22
64513.hokulea  user1   challeng  inspect    --   16  512   --   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
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. Hokule'a 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 Hokule'a is available on the software page.