MHPCC
MHPCC Maintenance - FY15 Rollover - October 1 & 2, 2014
09 September 2014
The MHPCC Riptide system will be undergoing scheduled maintenance on Wednesday, October 1st, 2014 0000 - Thursday, October 2nd, 2014 1700 (HST).

MHPCC will forego the scheduled September maintenance period.

Logins to Riptide will be suspended starting at 2359 (HST).

Please plan accordingly.

Thank You,
MHPCC User Services

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Riptide Quick Start Guide

Table Of Contents

Introduction
Get a Kerberos Ticket
Connect to Riptide
Home, Working, and Center-Wide Directories
Transfer Files and Data to Riptide
Submit Jobs to the Batch Queue
Batch Queues
Monitoring Your Job
Saving Your Work
Modules
Available Software
Advance Reservation Service

Introduction

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

Get a Kerberos Ticket

For security purposes, you must have a current Kerberos ticket on your computer before attempting to connect to Riptide. 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 the HPC Centers: Customer Service

Connect to Riptide

Riptide can be accessed via Kerberized ssh as follows:

  • Kerberized SSH
    % ssh riptide.mhpcc.hpc.mil
  • Kerberized rlogin and telnet are also allowed.
or by the following Login Nodes:

riptide01.mhpcc.hpc.mil
riptide02.mhpcc.hpc.mil
riptide03.mhpcc.hpc.mil
riptide04.mhpcc.hpc.mil

Login nodes are shared access points for Riptide. 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.

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, including the Utility Server. 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.

Transfer Files and Data to Riptide

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 Riptide login node.

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

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

Submit Jobs to the Batch Queue

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

Batch Queues

The following table describes the PBS queues available on Riptide:

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

Monitoring Your Job

You can monitor your batch jobs on Riptide 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.riptide  user1   backgrou  tw2      14658   1    1   --   12:00 R  01:12
64495.riptide  user1   standard  45dh8    21308   2    1   --   02:00 R  00:22
64513.riptide  user1   challeng  inspect    --   16  256   --   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.

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
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.

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. Riptide uses "modules" to initialize your environment with COTS/COST 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.

Available Software

A list of software on Riptide is available on the software page.

Advance Reservation Service

Due to MHPCC's involvment with DSPs, Advance Reservation Service is not used on Riptide.

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