Nautilus Quick Start Guide

1. Introduction

This document provides a brief summary of information you'll need to quickly begin working on Nautilus. For more detailed information, see the Nautilus 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 Nautilus. A Kerberos client kit must be installed on your desktop to get a Kerberos ticket. Information about installing Kerberos clients on your Windows desktop can be found on the Kerberos & Authentication page.

3. Connect to Nautilus

Nautilus can be accessed via Kerberized ssh as follows:

% ssh

4. Home, Working, and Center-wide Directories

Each user has file space in the $HOME, $WORKDIR, $WORKDIR2, and $CENTER directories. The $HOME, $WORKDIR, $WORKDIR2, 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 and $WORKDIR2 are "scratch" file systems, and $CENTER is a center-wide file system accessible to all Navy DSRC production systems. Neither of these file systems is backed up. You are responsible for managing files in your $WORKDIR, $WORKDIR2, and $CENTER directories by backing up files to the archive system and deleting unneeded files. Currently, $WORKDIR and $WORKDIR2 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 or $WORKDIR2 directories 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 Nautilus

File transfers to DSRC systems must be performed using Kerberized versions of the following tools: scp, sftp, and mpscp. For example, the command below uses secure copy (scp) to copy a local file into a destination directory on a Nautilus login node.

% scp local_file

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

6. Submit Jobs to the Batch Queue

The Slurm Workload Manager (Slurm) is the workload management system for Nautilus. To submit a batch job, use the following command:

sbatch [ options ] my_job_script

where my_job_script is the name of the file containing your batch script. For more information on using Slurm or job scripts, see the Nautilus User Guide, the Nautilus Slurm Guide, or the sample script examples in the $SAMPLES_HOME directory on Nautilus.

7. Batch Queues

The following table describes the Slurm queues available on Nautilus:

Queue Descriptions and Limits on Nautilus
Priority Queue Name Max Wall Clock Time Max Cores Per Job Description
Highest urgent 24 Hours 16,384 Jobs belonging to DoD HPCMP Urgent Projects
Down arrow for decreasing priority debug 30 Minutes 10,752 Time/resource-limited for user testing and debug purposes
HIE 24 Hours 3,072 Rapid response for interactive work. For more information see the HPC Interactive Environment (HIE) User Guide.
frontier 168 Hours 65,536 Jobs belonging to DoD HPCMP Frontier Projects
high 168 Hours 65,536 Jobs belonging to DoD HPCMP High Priority Projects
serial 168 Hours 1 Single-core serial jobs
standard 168 Hours 16,384 Standard jobs
transfer 48 Hours 1 Data transfer for user jobs. See the Navy DSRC Archive Guide, section 5.2.
Lowest background 4 Hours 4,096 User jobs that are not charged against the project allocation

8. Monitoring Your Job

You can monitor your batch jobs on Nautilus using the squeue command.

The squeue command lists all jobs in the queue. The -u username option shows only jobs owned by the given user, as follows:

% squeue -u user1
184628   general   mytest user1  R 1:50:59    40 n[0067-0071,0808-0842]
184626   general slurmJob user1  R 5:53:50    10 nautilus-mla[23-32]
184612   general mat_test user1  R 8:42:48    44 n[056-0604]
184624   general  inspect user1  R 6:03:14     1 n0144

Notice the output contains the JobID for each job. This ID can be used with the qview, squeue, and scancel commands.

To delete a job, use the command scancel jobID.

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 Navy DSRC Archive Guide.

10. Modules

Software modules are a very convenient way to set needed environment variables and include necessary directories in your path so commands for particular applications can be found. Nautilus uses modules to initialize your environment with COTS application software, system commands and libraries, compiler suites, environment variables, and Slurm batch system commands.

Several modules are loaded automatically as soon as you log in. To view the currently loaded modules, use module list. To see the entire list of available modules, use 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 Navy DSRC Modules Guide.

11. Available Software

A list of software on Nautilus is available on the Software page.

12. Advance Reservation Service (ARS)

A subset of Nautilus's nodes has been set aside for use as part of the 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 at Authenticated access is required. For more information on ARS, see the ARS User Guide.