Accessing Installed Software Applications

Environment Modules

The Linux operating system makes extensive use of the “working environment”, which is a collection of individual environment variables. An environment variable is a named object in the Linux shell that contains information used by one or more applications; two of the most used such variables are $HOME, which defines a user’s home directory name, and $PATH, which represents a list paths to different executables. A large number of environment variables are already defined when a Linux shell is open but the environment can be customised, either by defining new environment variables relevant to certain applications (e.g. software license variables) or by modifying existing ones (e.g. adding a new path to $PATH).

module is a Linux utility, which is used to manage of working environment in preparation for running the applications installed on the ARC systems. By loading the module for a certain installed application, the environment variables that are relevant for that application are automatically defined or modified.

The ARC/HTC software environment comprises a mixture of commercial applications, software built using the EasyBuild framework and software built using our own local build recipes. You should use the environment modules system (via the module command) to load applications into your environment on ARC/HTC.

Because the EasyBuild framework adds many new module components into the module list - the best way to search for an application you require on the system is by using the module spider command.

If you wish to browse a current list ARC modules online, you can find it here: ARC Module List

Note

The ARC cluster login nodes reference a different set of modules than the main cluster, so to be sure that the module (or module version) you require is available for use on ARC you should always search for modules in an interactive session on a compute node. e.g:

[software@arc-login01 ~]$ srun -p interactive --pty /bin/bash
srun: CPU resource required, checking settings/requirements...

[software@arc-c304 ~]$ module spider <name>

So, for example, to search for the GROMACS application:

[software@arc-login01 ~]$ srun -p interactive --pty /bin/bash
srun: CPU resource required, checking settings/requirements...

[software@arc-c304 ~]$ module spider gromacs

------------------------------------------------------------------------------------------------------------------------------
  GROMACS:
------------------------------------------------------------------------------------------------------------------------------
  Description:
    GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for
    systems with hundreds to millions of particles. This is a CPU only build, containing both MPI and threadMPI builds.

   Versions:
      GROMACS/2020-fosscuda-2019b
      GROMACS/2020.4-foss-2020a-PLUMED-2.6.2
      GROMACS/2020.4-foss-2020a

Note

module spider is NOT case-sensitive for searching, so:

module spider GROMACS
module spider gromacs
module spider Gromacs

…are all equivalent. However, when loading module using module load you must use the correct case, for example:

[software@arc-c304 ~]$ module load GROMACS/2020.4-foss-2020a

If the software name you are using in “module spider” returns too many options you can use

module -r spider '^name'

for example:

module -r '^Python'
module -r ^R$'

You can also build your own software in your home or data directories using one of the compilers provided (which are also available through the environment modules system). Typically the compiler toolchains, including maths libraries and MPI can be loaded using the modules named foss (e.g. foss/2020a) for free open-source software (i.e. GCC) or intel (e.g. intel/2020a) for the Intel compiler suite.

If no version is specified, the default version of the software is loaded (usually the latest version):

module load GROMACS
module list GROMACS

Currently Loaded Modules Matching: GROMACS
  1) GROMACS/2020.4-foss-2020a

Specific versions, other than the default can be loaded by specifying the version:

module load GROMACS/2020.4-foss-2020a-PLUMED-2.6.2
module list GROMACS

Currently Loaded Modules Matching: GROMACS
  1) GROMACS/2020.4-foss-2020a-PLUMED-2.6.2

A module can be “unloaded” with the unload option, for example:

module unload MATLAB/2020b

Building software against installed modules

If you need to compile your own software but would like to use an ARC built module for its libraries/headers. You need to make use of the EBROOT environment variable which is defined when you load the module. For example: if you need to build against the Boost libraries you first need to load the module:

module load Boost/1.79.0-GCC-11.3.0

Loading the above will define EBROOTBOOST - the variable name is always EBROOT followed by the main module name - this environment variable will contain the path to the Boost software for this specific module:

echo $EBROOTBOOST
/apps/system/easybuild/software/Boost/1.79.0-GCC-11.3.0

ls $EBROOTBOOST
easybuild  include  lib  lib64

So if you need to specify the Boost location to your build, you can supply for example: $EBROOTBOOST/include for the header files and $EBROOTBOOST/lib64 for the library files.