Using Modules

To run jobs on MOGON, you need to set up your environment correctly. This wiki page will help you to do so.

What are environment modules? #

Environment modules, or module files, are a way to set up a working environment under Linux dynamically. HPC system administration has to be rather conservative: In order to provide a consistent environment, it is not possible to install the newest (untested) piece of software (or kernel stuff) system-wide. On the other hand, the requirement to run state of the art scientific software has to be fulfilled. This is where environment modules step in rather handy:

So, loading a particular module will set up an environment? This is mainly done by exporting environment variables, particularly PATH and (LD)_LIBRARY_PATH and others. Usually modulefiles contain code to sanitize the setup, e.g. reporting conflicts with other loaded modules or deprecation warnings.

Lmod: A New Environment Module System #

Lmod is a Lua based module system that easily handles the MODULEPATH Hierarchical problem. Environment Modules provide a convenient way to dynamically change the users’ environment through modulefiles. This includes easily adding or removing directories to the PATH environment variable. Modulefiles for Library packages provide environment variables that specify where the library and header files can be found.

— Lmod Documentation

Working with Lmod #

Frequently Used Commands #

Finding Modules #

In many cases there are several versions of the same compiler/program installed. You have to check that your desired version is available.

module avail #

You can get an overview of all available modules using the command

module avail

or

module av

You can use the search capabilities to refine your search, e.g.:

module av mathematica

gives

JGU HPC Modules

------------------- /cluster/easybuild/broadwell/modules/all -------------------
   math/Mathematica/11.1.1    math/Mathematica/12.2.0 (D)

  Where:
   D:  Default Module
Questions? contact us at hpc@uni-mainz.de
yet more ...

Area Specific Modules #

EasyBuild, our software installation framework, provides prefixes – at least the way we install software – for modulefiles: bio, chem and phys. This classification is a bit arbitrary at times, but you can search for the respective strings and look whether your desired application is already available.

Other classes include lib and compiler. Of particular relevance is sometimes the lang category, e.g. for providing scripting languages with their correct version (see for example the entries on Python, R and BioConductor and Perl).

For example with

module av phys

you get all the Modules in phys:

module avail phys
  JGU HPC Modules

  ------------------- /cluster/easybuild/broadwell/modules/all -------------------
    phys/ESPResSo++/2.0.1-foss-2018b
    phys/HOOMD/2.5.1-fosscuda-2019b-double
    phys/HOOMD/2.9.1-fosscuda-2019b-double
    phys/HOOMD/2.9.1-fosscuda-2019b-single
    phys/HOOMD/2.9.6-fosscuda-2019b-single
    phys/HOOMD/2.9.6-fosscuda-2020b-double
    phys/HOOMD/2.9.6-fosscuda-2020b-single (D)
    phys/UDUNITS/2.2.26-GCCcore-8.3.0
    phys/UDUNITS/2.2.26                    (D)

    Where:
    D:  Default Module
  Questions? contact us at hpc@uni-mainz.de
  yet more ...

module spider #

The command module spider lists all modules that can be loaded on MOGON.

module spider mathematica

gives

----------------------------------------------------------------------------
  math/Mathematica:
----------------------------------------------------------------------------
    Description:
      Mathematica is a computational software program used in many
      scientific, engineering, mathematical and computing fields.

     Versions:
        math/Mathematica/11.1.1
        math/Mathematica/12.2.0

----------------------------------------------------------------------------
  For detailed information about a specific "math/Mathematica" package (including how to load the modules) use the module's full name.
  Note that names that have a trailing (E) are extensions provided by other modules.
  For example:

     $ module spider math/Mathematica/12.2.0
----------------------------------------------------------------------------

Loading Modules #

Now, knowing the modules that are available, you can go on by loading the module(s) you need. This will happen using the command module load [module] or module add [module].

Example: Maybe you want to load gcc (version 10.2.0) and OpenMPI, so you would do

module load mpi/OpenMPI/4.0.5-GCC-10.2.0

That’s all - OpenMPI (version 4.0.5) was compiled with gcc 10.2.0 as the version string indicates, but mpicc depends on the specific compiler (and libraries), hence gcc is also provided in the correct version.

Listing active Modules #

module list

From the example above:

Currently Loaded Modules:
  1) compiler/GCCcore/10.2.0        4) lib/libfabric/1.11.0-GCCcore-10.2.0
  2) compiler/GCC/10.2.0            5) lib/PMIx/3.1.5-GCCcore-10.2.0
  3) lib/UCX/1.9.0-GCCcore-10.2.0   6) mpi/OpenMPI/4.0.5-GCC-10.2.0

Unload Modules #

To expel a specific module you can use the command

module rm [module]

or

module unload [module]

If you want to unload all your loaded modules, use

module purge

Displaying contents of a Module #

module show

ml - A convenient Tool #

For those of you who can’t type the mdoule, moduel, err module command correctly, Lmod has a tool for you. With ml you won’t have to type the module command again. The two most common commands are module list and module load <something> and ml does both:

— Lmod Documentation

ml

means module list. And

ml foo

means module load foo.

ml -bar

means module unload bar. It is not surprising that these can be combined:

ml foo -bar

means module unload bar; module load foo.

You can do all the module commands:

ml spider
ml avail
ml show foo

User Collections #

User defined initial list of login modules

module load module1 module2 ...

On MOGON, users can create as many collections as they like. You can save to a named collection with:

module save <collection_name>

The collection is restored with:

module restore <collection_name>

You can display the contents of a name collection with

module describe <collection_name>

Use the following command to list the collections you already have:

module savelist

Finally, you can deactivate a collection with:

module disable <collection_name>

If no <collection_name> is specified, the default is disabled. Note that the collection is not removed, only renamed. If you disable the collection foo, the file foo is renamed to foo~. To restore the foo collection, you must do the following:

cd ~/.lmod.d; mv foo~ foo

Working with Environment Modules #

In order to use the old Environment Modules system, the file ~/.nolmod should be present in your home directory.

List of useful module commands #

Before we really start, the most frequently used commands at a glance:

Show modules #

In many cases there are several versions of the same compiler/program installed. You have to check that your desired version is available. You can get an overview of all available modules using the command module avail¹.

As module reports on standard error, a grep for a particular module can be done like:

module avail |& grep <your_module_you_are_looking_for>

Area Specific Modules #

EasyBuild, our software installation framework provides prefixes – at least the way we install software – for modulefiles: bio, chem and phys. This classification is a bit arbitrary at times, but you can search for the respective strings and look whether your desired application is already available.

Other classes include lib and compiler. Of particular relevance is sometimes the lang category, e.g. for providing scripting languages with their correct version (see for example the entries on Python, R and BioConductor and Perl).

Loading modules #

Now, knowing the modules that are available you can go on by loading the module(s) you need. This will happen using the command module load [module] or module add [module] ((They are equal. It’s yours to chose which you like more)).

Example: Maybe you want to load gcc (version 6.3.0) and OpenMPI, so you would do:

module load mpi/OpenMPI/2.0.2-GCC-6.3.0

That’s all - OpenMPI (version 2.0.2) was compiled with gcc 6.3.0 as the version string indicates, but mpicc depends on the specific compiler (and libraries), hence gcc is also provided in the correct version.

Listing active modules #

If you want to check your loaded modules, simply use module list.

From the example above:

module list
Currently Loaded Modulefiles:
  1) compiler/GCCcore/6.3.0        3) mpi/OpenMPI/2.0.2-GCC-6.3.0
  2) compiler/GCC/6.3.0

Unload modules #

To expel a specific module you can use the command module rm [module] or module unload [module]. If you want to unload all your loaded modules, use module purge.

Example:

module unload compiler/GCCcore/6.3.0
module purge

Footnotes #