Customizing the Runtime Environment

The default login environment is configured with Intel compilers, math libraries and an MPI library (see module list when logged in to see the full list of what is loaded). So normally, you won't need to change anything to have a functional environment when you login.

The module program allows you to conveniently customize your environment as needed (details). In order to make such customizations permanent for your login environment, you can insert the module commands in your ~/.profile (or ~/.bash_profile). For example,

# add these to your ~/.profile
module rm env
module load env/intel-11.1-openmpi-1.3

This will replace the default environment with one that has Intel 11.1.x compilers, OpenMPI 1.3.x libraries, and some compatible MKL library. There are several preset environment modules available, run module avail env to see a list. You may of course prefer not to use any env presets, but instead fine tune your environment by loading a more precise set of modules.

Your job scripts also execute in an environment identical to your login environment. So once you inflict the customizations in your ~/.profile you do not need to load/unload the same modules in your job scripts.

These customizations do not apply to or affect the applications (such as Molpro, LAMMPS, etc.). A given application is pre-compiled under some custom environment which is known to the application maintainer only, and is most likely different than your own environment, or even the defaults. Therefore, the correct runtime for the application should be set by the application module, and is usually in conflict with the user environment. So, the correct way to load an application is:

# reset all environment customizations
module purge 
# load (the correct runtime for) the application
module load lammps

Never try to run an application directly from its installation directory (given, of course, that you took the trouble to actually fish this out) without loading the application module.