Beowulf Compute Cluster - Using Environment Modules

Using 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.

**The module command**

$ module avail	list all available package modules
$ module whatis [module-name]	list module description
$ module list	list the modules already loaded
$ module load module-name	load the named module
$ module unload module-name	unload the named module
$ module switch old-module-name new-module-name	swap the old module and new modules
$ module purge	unassign all module definitions
$ module display module-name	list the rules that define a module

Examples

$ module avail

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

------------------------------ /share/apps/modulefiles ------------------------------
gnumpich        intel/10.1      ldm             pgi/5.2         torque
gromacs         intel/ict-3.0   lsf             pgi/6.0
idl             intel/vtune-9.0 pbs             pgi/7.0

$ module whatis pbs
pbs                  : pbs: (aka TORQUE) an open source resource manager providing control
                            over batch jobs and distributed compute nodes

$ module load intel/10.1

$ module list
Currently Loaded Modulefiles:
  1) pbs          2) intel/10.1

**Using the module command with batch jobs**

To set up package environment variables for batch first use the module command in your terminal session and then use qsub to export the variables to batch. For example, assume your job requires access to the shared Intel Math Kernel libraries.

First, use the modules command to load variables for the Intel Compiler package:

$ module load intel/10.1

Then submit the job script using the option to export the variables to your batch job:

$ qsub -V myjob.sh

If you prefer, the option can be enabled in the job script itself with the PBS command:

#PBS -V