1. Introduction

This document provides a brief summary of information you'll need to quickly begin working on Coral. For more detailed information, see the Coral 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 Coral. 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 Coral

Coral can be accessed via Kerberized ssh as follows:

% ssh user@coral.mhpcc.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 accessible to all MHPCC DSRC production systems. 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, we will notify you via email six days prior to deletion. You are responsible to monitor your workspace to prevent data loss.

5. Transfer Files and Data to Coral

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

% scp local_file user@coral.mhpcc.hpc.mil:/target_dir

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

6. Submit Jobs to the Batch Queue

The Slurm Workload Manager (Slurm) is the workload management system for Coral. 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 Coral User Guide, the Coral Slurm Guide, or the sample script examples in the $SAMPLES_HOME directory on Coral.

7. Batch Queues

The following table describes the Slurm queues available on Coral:

8. Monitoring Your Job

You can monitor your batch jobs on Coral 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 username 
% squeue -u username -t RUNNING 
% squeue -u username -t PENDING

[smithp@coral1 ~]$ squeue -u smith
JOBID PARTITION    NAME     USER 	ST    TIME  NODES NODELIST(REASON)
1009  standard 	hvab_col smith  	R	4:24:17     1 cr2cn4

Notice the output contains the JobID for each job. This ID can be used with the scontrol, sstat, sacct, and scancel commands.

Delete Jobs

Job Deletion Commands

Delete What?	Command
A specific job	scancel jobID
All your jobs	scancel -u username
All your pending jobs	scancel -t PENDING -u username
All your jobs by jobname	scancel -name myJobName

Get Job Information

For detailed information about queued/running jobs

% scontrol show JobID -dd JobID
% sstat --format=AveCPU,AvePages,AveRSS,AveVMSize,JobID -j --allsteps

For detailed information about completed jobs

% sacct -j JobID --format=AveCPU,AvePages,AveRSS,AveVMSize,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.
cp file1 [file2 ...] $ARCHIVE_HOME

Copy one or more files from the archive system.
cp $ARCHIVE_HOME/{file1, [file2 ...]}

For more information on archiving your files, see the MHPCC 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. Coral 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 MHPCC DSRC Modules Guide.

11. Available Software

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

12. Advance Reservation Service (ARS)

A subset of Coral'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 https://reservation.hpc.mil. Authenticated access is required. For more information on ARS, see the ARS User Guide.