UserSession5 22 18

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Attention: Research Computing Documentation has Moved

Please use the new documentation url for all Research Computing documentation needs.

As a result of this move, we have deprecated use of this wiki for documentation. We are providing read-only access to the content to facilitate migration of bookmarks and to serve as an historical record. All content updates should be made at the new documentation site. The original wiki will not receive further updates.

Thank you,

The Research Computing Team

HPC User session 5/22/2018 The CAFÉ – The Edge of Chaos 1.00 p.m. – 2.30 p.m.


1. Introduction a. Cheaha b. Hardware - Compute & storage

2. Logging on – MAC(linux) and Windows (putty) a. LOGIN NODE – Do not use

3. Storage types and moving data – a. $HOME - 20GB b. /data/user/$USER - 5TB c. /data/project/group_name - 50TB d. /data/scratch/$USER -500TB (scratch)

4. Partitions – a. policies, time limits b. types of jobs – sbatch, sinteractive, srun, salloc c. types of nodes – regular/ GPU

5. Software a. Modules b. Requesting installs c. Self install in $HOME

6. Demo a. Sbatch script b. Sinteractive

7. If time permits a. Jypyter notebook b. R Studio

8. Requesting support – docs wiki, email

9. Questions

Logging ON

This section will cover steps to configure Windows, Linux and Mac OS X clients to connect to Cheaha.


Linux systems, regardless of the flavor (RedHat, SuSE, Ubuntu, etc...), should already have an SSH client on the system as part of the default install.

  1. Start a terminal (on RedHat click Applications -> Accessories -> Terminal, on Ubuntu Ctrl+Alt+T)
  2. At the prompt, enter the following command to connect to Cheaha (Replace blazerid with your Cheaha userid)

Mac OS X

Mac OS X is a Unix operating system (BSD) and has a built in ssh client.

  1. Start a terminal (click Finder, type Terminal and double click on Terminal under the Applications category)
  2. At the prompt, enter the following command to connect to Cheaha (Replace blazerid with your Cheaha userid)


There are many SSH clients available for Windows, some commercial and some that are free (GPL). This section will cover two clients that are commonly found on UAB Windows systems.


PuTTY is a free suite of SSH and telnet tools written and maintained by Simon Tatham. PuTTY supports SSH, secure FTP (SFTP), and X forwarding (XTERM) among other tools.

  • Start PuTTY (Click START -> All Programs -> PuTTY -> PuTTY). The 'PuTTY Configuration' window will open
  • Use these settings for each of the clusters that you would like to configure
Field Cheaha Settings
Host Name (or IP address)
Port 22
Protocol SSH
Saved Sessions
  • Click Save to save the configuration, repeat the previous steps for the other clusters
  • The next time you start PuTTY, simply double click on the cluster name under the 'Saved Sessions' list