Help:HPCC Env Modules

Environment Modules

Several software packages on the cluster require correct definition of certain environment variables. These variables establish the package's configuration and influence its behavior. For example, PATH and LD_LIBRARY_PATH specify the location of package binary files.

Environment Modules is a tool to manage package environment variables.

With simple command line options, you can prepare the environment for any package available on the cluster. In the case of packages with multiple versions, there are options to switch between one version and another - defining and undefining variables as needed. If there is a conflict between two packages, module will alert you.

Cheat Sheet

Command	Description
module avail	List available modules
module load <module-name>	Load module named <module-name>
module unload <module-name>	Unload module named <module-name>
module whatis <module-name>	Give description of module <module-name>
module list	List modules that are loaded in your environment
module purge	Unload all currently loaded modules from your environment
module display <module-name>	Give the rules for module <module-name>

Set Up Environment Modules

To use Environment Modules you will have to add a couple of things to your startup RC file. The module command is initialized by sourcing a shell-specific initialization file. You will find the initialization files /usr/local/modules/init. To initialize modules,

source /usr/local/modules/init/<shell>

Where <shell> is the name of your shell. To have this done automatically when you login, add this command to the end of your startup RC file. You should now be able to use the module command.

Use beach-Specific Modules

For module to recognize the modules install on the cluster, you must tell module to use the local modulefiles,

module use /data/progs/localmodules

You can also add this to your RC file after the previous initialization command.

Examples

The following examples assume that you have executed (either interactively or in a login RC file) the previous two commands.

List all available modules,

> module avail
---------------------------------------------------------- /data/progs/localmodules -----------------------------------------------------------
cca/eric                glib2                   mpich2/1.1              petsc                   sedflux/mars
cca/stable(default)     gnu                     mvapich2/1.2            python/2.4              sedflux/nightly
cca/yanb                hdf5                    netcdf                  python/2.5              sedflux/stable(default)
cmake                   intel/11.0              null                    python/2.6(default)     subversion
gcc/4.1                 libxml2                 openmi/1.4              scons                   torque
gcc/4.3(default)        matlab/2008b            openmpi/1.3             sedflux/intel           udunits

-------------------------------------------------- /usr/local/modules-3.2.6/Modules/versions --------------------------------------------------
3.2.6

--------------------------------------------- /usr/local/modules-3.2.6/Modules/3.2.6/modulefiles ----------------------------------------------
dot         module-cvs  module-info modules     null        use.own

Load python 2.6,

> which python
/usr/bin/python
> module load python/2.6
> which python
/usr/local/bin/python/bin/python

Get the name of your shell

If you're not sure what shell you are running, try running the following command,

> grep <username> /etc/passwd | cut -d: -f7

Substitute your username for <username>.

Get the name of your startup RC file

The following table lists user RC files for shells available on the cluster.

	sh	ksh	csh	tcsh	bash
~/.tcshrc				always
~/.cshrc			always	always
~/.login			login	login
~/.logout			login	login
~/.profile	login	login			login
~/.bash_profile					login
~/.bash_login					login
~/.bash_logout					login
~/.bashrc					! login

Explanation:

• Blank means the file is not read by the shell at all.
• always means the file is always read by the shell upon startup.
• login means the file is read if the shell is a login shell.
• ! login means the file is read if the shell is not a login shell.