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

Koehr can be accessed via Kerberized ssh as follows:

% ssh koehr.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 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 Koehr

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 Koehr login node.

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

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

6. Submit Jobs to the Batch Queue

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

7. Batch Queues

The following table describes the PBS queues available on Koehr:

Queue Descriptions and Limits
Priority Queue
Name
Job
Class
Max Wall
Clock Time
Max Cores
Per Job
Comments
Highest urgent Urgent 24 Hours 768 Designated urgent projects by DoD HPCMP
Down Arrow for decreasing priority frontier Frontier 168 Hours 19,200 Frontier projects only
high High 168 Hours 15,840 Designated high-priority projects by service/agency
debug Debug 30 Minutes 2,400 User diagnostic jobs
standard Standard 168 Hours 8,168 Normal priority user jobs
gpu N/A 24 Hours 48 GPU-accelerated jobs
transfer N/A 48 Hours N/A Data transfer jobs
bigmem N/A 96 Hours 768 Large-memory jobs
Lowest background Background 4 Hours 1,200 User jobs that will not be charged against the project allocation.

8. Monitoring your job

You can monitor your batch jobs on Koehr 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. 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
scp file1 $ARCHIVE_HOST:$ARCHIVE_HOME/

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. Koehr 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 Koehr is available on the software page.

12. Advance Reservation Service

A subset of Koehr'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.