Using environment modules
About environment modules
The environment modules are a system that allows you to quickly and easily modify your shell environment to access different software packages. The HEC offers a large (and growing) number of software packages to users, and each package may contain several tools, manual pages and libraries, or may require special setup to work properly. Some software packages come in several versions or flavours, many of which conflict with each other. Modules allow you to tailor your shell to access exactly the versions of packages you need by setting up the relevant environment variables for you, and automatically avoiding many possible conflicts between packages.
Viewing available modules
To view the available modules, use the command module avail
A typical output would look like this:
------------------------------ /usr/shared_apps/Nmodules/apps ------------------------------
abaqus/2019 dynare/4.4.3 mercurial/3.2 turbomole/6.6
adf/test e4d/Mar2017-dev mpb/1.5-mpi turbomole/6.6-smp
amber/18 emacs/27.1 mpb/test-ser turbomole/7.3-mpi
--------------------------- /usr/shared_apps/Nmodules/compilers ----------------------------
gcc/4.8.1 intel/16.0 java/13.0.1 openmpi/1.10.1-intel pgi/12.5
gcc/4.9.2 intel/16.0u3 mono/4.2.2 openmpi/1.10.4-gcc pgi/13.5
--------------------------- /usr/shared_apps/Nmodules/libraries ----------------------------
armadillo/test fftw/3.3.6 hdf5/1.8.13-intel petsc/3.6.3
boost/1.54.0-gcc fftw/3.3.8 hdf5/1.10.5-ompi-intel petsc/3.12.5
For each available module, the name of the software package is listed first, followed by an optional forward slash (/) and the version or flavour of the package offered. Where multiple versions or flavours of a package exist, the default version is indicated. The default version can be accessed using just the module name, rather than the full name.
As the full list of modules is lengthy, you can type module avail packagename
to list versions of the specified package name. For example you can view the available
versions of the intel compiler suite with the command module avail intel:
--------------------------- /usr/shared_apps/Nmodules/compilers ----------------------------
intel/12.1 intel/15.0 intel/16.0u3 intel/18.0u5 intel/20.0u3
intel/13.0 intel/16.0 intel/17.0u4 intel/19.0u5 intel/21.0u4
Key:
default-version modulepath
A brief description of each software package can be obtained with the
module whatis command:
wayland-2022% module whatis intel/21.0u4
--------------------------- /usr/shared_apps/Nmodules/compilers ----------------------------
intel/21.0u4: the intel oneapi compiler suite, 2021 version 4
homepage: https://www.intel.com/content/www/us/en/developer/tools/oneapi/toolkits.html#base-kit
Using modules
To setup up your job script or login shell environment to access the required package,
use the module add command. For example:
module add intel
The above command will configure your environment to use the current default
version of the Intel Compiler Suite tools, which in the example output from
module avail above would version 20.0u4. To request a specific version of a
package (e.g. version 11.1), use the full module name:
module add intel/21.0u4
To view the modules currently added to your environment, use the module list command:
wayland-2022% module list
Currently Loaded Modulefiles:
1) intel/21.0u4
To remove modules from your environment, use the module rm command:
wayland-2022% module rm intel
wayland-2022% module list
No Modulefiles Currently Loaded.
Module conflicts
There are certain module combinations which may cause problems when both are present in your environment. Examples include cases where modules offer applications or libraries with identical names (which may cause confusion as to exactly which one is being used), or when an application is strongly dependent on a specific compiler and its libraries (in which case the module will itself set up access to the required compiler version)
In such cases, modules are designed to conflict. Attempting to load a module which conflicts with one already added to your environment will generate a warning message and the conflicting module will not be loaded. For example, compiler suites are set to conflict with each other so that you only ever have a single compiler and its associated libraries available in your environment at any one time:
wayland-2022% module add intel
wayland-2022% module add pgi
Loading pgi/19.4
ERROR: Module cannot be loaded due to a conflict.
HINT: Might try "module unload intel/20.0u3" first.
To resolve a conflict simply remove the currently loaded conflicting module before adding the new one.
Customising your environment
Module instructions do not persist across sessions; if you log out and log back in again, no modules will be loaded in your new login session. If there are a core set of packages which you access regularly, you can place relevant module add commands into your shell startup script - $HOME/.profile for bash.
Switching to different versions of modules
Sometimes you may wish to switch between different versions of a software
package. Rather than invoke module rm followed by module add, you can
simply use module switch instead:
wayland-2022% module add intel/21.0u4
wayland-2022% module list
Currently Loaded Modulefiles:
1) intel/21.0u4
wayland-2022% module switch intel/19.0u5
wayland-2022% module list
Currently Loaded Modulefiles:
1) intel/19.0u5
Viewing module contents
If you want to see what environment setup a module is doing behind the scenes,
use the command module show. For example:
wayland-2022% module show ImageMagick/7.0.9
-------------------------------------------------------------------
/usr/shared_apps/Nmodules/apps/ImageMagick/7.0.9:
module-whatis {The ImageMagick image editting package
homepage: https://imagemagick.org//}
setenv IM_HOME /usr/shared_apps/packages/ImageMagick-7.0.9-14
prepend-path PATH /usr/shared_apps/packages/ImageMagick-7.0.9-14/bin
prepend-path MANPATH /usr/shared_apps/packages/ImageMagick-7.0.9-14/share/man
prepend-path LD_LIRBARY_PATH /usr/shared_apps/packages/ImageMagick-7.0.9-14/lib
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