Environment Modules

Introduction

Environment Modules, or short Modules are the means by which most of the installed scientific software is provided on the bwHPC clusters.
The use of different compilers, libraries and software packages requires users to set up a specific session environment suited for the program they want to run. The bwHPC clusters provide users with the possibility to load and unload complete environments for compilers, libraries and software packages by a single command. This happens usually in the beginning of the jobscript.

Documentation

For an extensive help on how to use Environment Modules, i.e., the command module, execute 'module help' or use 'man modules' to show manpage for the manual command.

An extensive online documentation is available on the Environment Modules Website.

Usage

Module categories, versions and defaults

The bwHPC clusters (such as bwUniCluster) traditionally provide a large variety of software and software versions. Therefore Modules are divided in category folders containing subfolders of modulefiles again containing modulefile versions, and must be addressed as follows:

category/softwarename/version

For instance the Intel compiler X.Y belongs to the category of compilers, therefore the modulefile X.Y is placed under the category compiler and intel.
In case of multiple software versions, one version will be always defined as the default version. The Module of the default can be addressed by simply omitting the version number:

category/softwarename

Currently all bwHPC software packages are assigned to the following Module categories:

• bio
• cae
• chem
• compiler
• devel
• math
• mpi
• numlib
• phys
• system
• vis

Display and search available Modules

Available Modules are modulefiles that can be loaded by the user. A Module must be loaded before it provides changes to your environment. You can display all available Modules on the system by executing:

$ module available

The short form the command is:

$ module av

You can selectively list software in one of those categories using, e.g. for the category "compiler"

$ module avail compiler/

This would list all available versions of the GCC compiler suite

$ module avail compiler/gnu

Loading Modules

You can load a Module software in to your environment to enable easier access to software that you want to use by executing:

$ module load category/softwarename/version

or

$ module add category/softwarename/version

Loading a Module in this manner affects ONLY your environment for the current session.

Loading conflicts

By default you can not load different versions of same software Module in same session. Loading for example Intel compiler version X while Intel compiler version Y is loaded results in error message as follows:

Module 'compiler/intel/X' conflicts with the currently loaded module(s) 'compiler/intel/Y'

The solution is unloading or switching Modules.

Showing the changes introduced by a Module

Loading a Module will change the environment of the current shell session. For instance the $PATH variable will be expanded by the software's binary directory. Other Module variables may even change the behavior of the current shell session or the software program(s) in a more drastic way.
Loaded Modules may also invoke an additional set of environment variables, which e.g. point to directories or destinations of documentation and examples. Their nomenclature is systematic:

Variable	Pointing to
$SWN_HOME	Root directory of the software package
$SWN_DOC_DIR	Documentation
$SWN_EXA_DIR	Examples
$SWN_BPR_URL	URL of software's Wiki article
and many many more...

with SWN being the place holder of the software Module name.
All the changes to the current shell session to be invoked by loading the Module can be reviewed using 'module show category/softwarename/version'.

$ module show compiler/gnu/9.2
-------------------------------------------------------------------
/opt/bwhpc/common/modulefiles/compiler/gnu/9.2:

setenv           GNU_VERSION 9.2.0 
setenv           GNU_HOME /opt/bwhpc/common/compiler/gnu/9.2.0 
setenv           GNU_BIN_DIR /opt/bwhpc/common/compiler/gnu/9.2.0/bin 
setenv           GNU_MAN_DIR /opt/bwhpc/common/compiler/gnu/9.2.0/man 
setenv           GNU_LIB_DIR /opt/bwhpc/common/compiler/gnu/9.2.0/lib64 
setenv           GNU_LIB_DIR2 /opt/bwhpc/common/compiler/gnu/9.2.0/lib 
prepend-path     PATH /opt/bwhpc/common/compiler/gnu/9.2.0/bin 
prepend-path     MANPATH /opt/bwhpc/common/compiler/gnu/9.2.0/man 
prepend-path     LD_LIBRARY_PATH /opt/bwhpc/common/compiler/gnu/9.2.0/lib64:/opt/bwhpc/common/compiler/gnu/9.2.0/lib 
setenv           CC gcc 
setenv           CXX g++ 
setenv           F77 gfortran 
setenv           FC gfortran 
setenv           F90 gfortran 
module-whatis    GNU compiler suite version 9.2.0 (gcc, g++, gfortran, gccgo) 
conflict         compiler/gnu 
-------------------------------------------------------------------

Modules depending on Modules

Some program Modules depend on libraries to be loaded to the user environment. Therefore the corresponding Modules of the software must be loaded together with the Modules of the libraries.
By default such software Modules try to load required Modules and corresponding versions automatically. However, automatic loading might fail if a different version of that required Module is already loaded (cf. Loading conflicts).

Display your loaded Modules

All Modules that are currently loaded for you can be displayed by the command 'module list'.

$ module list
No Modulefiles Currently Loaded.
$ module load compiler/gnu/9.2
$ module list
Currently Loaded Modulefiles:
  1) compiler/gnu/9.2

Unloading Modules

To unload or to remove a software Module execute:

$ module unload category/softwarename/version

or

$ module remove category/softwarename/version

Unloading all loaded modules

In order to remove all previously loaded software modules from your environment issue the command 'module purge'.

$ module list
Currently Loaded Modulefiles:
  1) devel/gdb/7.7
  2) compiler/intel/14.0
  3) mpi/openmpi/1.8-intel-14.0(default)
$
$ module purge
$ module list
No Modulefiles Currently Loaded.
$ 

Other Module commands

module whatis

A short description for a specific Module can be displayed with 'module whatis category/softwarename/version'

$ module whatis compiler/gnu/9.2 
compiler/gnu/9.2     : GNU compiler suite version 9.2.0 (gcc, g++, gfortran, gccgo)

module help

A help message for a specific Module can be displayed with 'module help category/softwarename/version'.
The help message usually contains additional information about the software and points to the software website and documentation.

$ module help compiler/gnu/9.2 

----------- Module Specific Help for 'compiler/gnu/9.2' -----------


This module provides the GNU compiler collection version 9.2.0 via commands
[... rest of the output is omitted in the Wiki for clarity ...]

Software job examples

The Modules installed on bwHPC systems provide job examples to help you get started using the software or submitting jobs with this software. Examples can be found via a convenient variable $SWN_EXA_DIR (for a Module called SWN). It is advisable to copy the whole example folder to your $HOME directory, so you can edit those job examples.
For copying the entire job examples folder of software swn to your working directory, execute:

$ module load catogory/softwarename
$ cp -R $SWN_EXA_DIR .

---