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Modules

Modules is a utility which helps users manage the complex business of setting up their shell environment in the face of potentially conflicting application versions and libraries.

Viewing Available Modules

When a user logs in, the system looks for a file named .modules in their home directory. This file contains module commands to set up the initial shell environment.

The command

$ module avail

displays a list of all the modules available. The list will look something like:

--- output trimmed ---
velvet/1.2.10/INTEL-14.0.2
vmatch/2.2.2

---------------- /usr/local/packages/Modules/modulefiles/admin -----------------
EasyBuild/1.11.1       GCC/4.9.0              INTEL-140-MPICH/3.1.1
EasyBuild/1.13.0       INTEL/14.0.2           INTEL-140-MVAPICH2/2.0
--- output trimmed ---

The module names take the form appname/version/compiler, providing the application name, the version, and information about how it was compiled (if needed).

Managing Modules

Besides avail, there are other basic module commands to use for manipulating the environment. These include:

List of module commands. Use -h to see full list

Loading / Unloading commands:
  add | load      modulefile [...]  Load modulefile(s)
  rm | unload     modulefile [...]  Remove modulefile(s)
  purge                             Unload all loaded modulefiles
  reload | refresh                  Unload then load all loaded modulefiles
  switch | swap   [mod1] mod2       Unload mod1 and load mod2

Listing / Searching commands:
  list            [-t|-l|-j]        List loaded modules
  avail   [-d|-L] [-t|-l|-j] [-S|-C] [--indepth|--no-indepth] [mod ...]
                                    List all or matching available modules
  aliases                           List all module aliases
  whatis  [-j]    [modulefile ...]  Print whatis information of modulefile(s)
  apropos | keyword | search [-j] str
                                    Search all name and whatis containing str
  is-loaded       [modulefile ...]  Test if any of the modulefile(s) are loaded
  is-avail        modulefile [...]  Is any of the modulefile(s) available
  info-loaded     modulefile        Get full name of matching loaded module(s)

Collection of modules handling commands:
  save            [collection|file] Save current module list to collection
  restore         [collection|file] Restore module list from collection or file
  saverm          [collection]      Remove saved collection
  saveshow        [collection|file] Display information about collection
  savelist        [-t|-l|-j]        List all saved collections
  is-saved        [collection ...]  Test if any of the collection(s) exists

The -h option to module will list all available commands.

How to setup your Environment Modules

Modules is a utility which helps users manage the complex business of setting up their shell environment in the face of potentially conflicting application versions and libraries.

Default Setup

When a user logs in, the system looks for a file named .modules in their home directory. This file contains module commands to set up the initial shell environment.

Shells

A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.

/bin/bash

System resource file: /etc/profile

When one access the shell, the following user files are read in if they exist (in order):

  1. ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
  2. ~/.bashrc (interactive login only)
  3. ~/.profile

When a user logs out of an interactive session, the file ~/.bash_logout is executed if it exists.

The default value of the environmental variable, PATH, is set automatically using Modules. See below for more information.

/bin/tcsh

The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.

Request HPC Software

If a software package you would like to use for your research is not available on a cluster, you can request it to be installed. The software requests are evaluated by the HPC staff on a case-by-case basis. Before you send in a software request, please go through the information below.

Types of requests

Depending on how many users need to use the software, software requests are divided into three types, each of which corresponds to the location where the software is installed:

  • The user's /home directory
    • Software packages installed here will be accessible only to the user.
    • It is suitable for software packages that will be used by a single user.
    • Python, Perl and R modules should be installed here.
  • /project
    • Software packages installed here can be accessed by a group of users.
    • It is suitable for software packages that need to be shared by users from the same research group, or are bigger than the quota on the /home file system.
    • This type of request must be sent by the PI of the research group, who may be asked to apply for a storage allocation.
  • /usr/local/packages
    • Software packages installed here can be accessed by all users.
    • It is suitable for software packages that will be used by users from multiple research groups.
    • This type of request must be sent by the PI of a research group.

How to request

Please send an email with the following information:

  • Your user name
  • The name of cluster where you want to use the requested software
  • The name, version and download link of the software
  • Specific installation instructions if any (e.g. compiler flags, variants and flavor, etc.)
  • Why the software is needed
  • Where the software should be installed (locally, /project, or /usr/local/packages) and justification explaining how many users are expected.

Please note that, once the software is installed, testing and validation are users' responsibility.