Setting Up Your Environment

Shells

• Your account will be set up with the bash shell, unless you asked for a different shell when you requested your account. You can find out your current shell with the command echo $SHELL.

• If you'd like a different shell, please contact us. Click to send email or via telephone: 630-252-8224..

• The commands chsh and ypchsh don't work on the cluster, and have been disabled.

Accessing application software with modules

• The cluster uses the Environment Modules package to manage access to application software.

• modules documentation is available with the command man module.

• To set up your environment so that an application can be used, use the command

module load <module>

at the command line or in your shell's configuration files.

• You can undo the effect of a module load with

module unload <module>

• It's generally not a good idea to load modules for more than one version of the same application. Instead, swap the modules:

module swap some-application/stable some-application/beta

• Your .bashrc or .cshrc contains sample commands for loading the most common modules. Please see the instructions in those files, or in /etc/skel/.bashrc or /etc/skel/.cshrc, which will be the latest versions of the default configuration files.

• Most modules are one of these two forms:

<application type>/<application>/<version>
<application>/<version>

for example

compiler/pathscale/3.1-147
starccm/15.06.008-R8

Omitting the version number will load the latest stable version of the module.

To see what modules are currently loaded in your environment, do

module list

To see what modules are available, do

module avail

• Modules with "-alpha" or "-beta" appended to the name may not work, either because the software or module is broken.

• To use modules in shell scripts, including Torque jobs scripts, see below.

File permissions

By default, you will be in your own Unix group, and your files will be readable and writable only by you (that is, the default umask is 027). If you want files to be readable by everyone working on your project, you will need to

• Have your project leader request that we create a Unix group for the project. They also need to let us know who should be in the group.

• Change the group ownership of the files you want to be group-readable:

chgrp <project-group> <filename>

• Make the file group-readable, and, if user-executable, group-executable:

chmod g+rX <filename>

If you want all your new files to be readable by everyone in your group, you'll need to

• Ask us to change your default group.

Note that a change in your primary group will not affect pre-existing files. To change the group ownership of all your files, do this:

chgrp -R <new-group> ~
chmod -R g+rX ~
chgrp -R $USER ~/.ssh
chmod -R g-rx ~/.ssh

The last two commands are necessary for SSH security; you will lock yourself out of the cluster if you omit them.