Using environment modules ========================= .. _envmods: 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: .. code-block:: console ------------------------------ /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``: .. code-block:: console --------------------------- /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: .. code-block:: console 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: .. code-block:: console 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: .. code-block:: console module add intel/21.0u4 To view the modules currently added to your environment, use the ``module list`` command: .. code-block:: console wayland-2022% module list Currently Loaded Modulefiles: 1) intel/21.0u4 To remove modules from your environment, use the ``module rm`` command: .. code-block:: console 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: .. code-block:: console 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: .. code-block:: console 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: .. code-block:: console 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 -------------------------------------------------------------------