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Using installed software

Hierarchical module naming scheme

Starting with the Aurora service and continuing with COSMOS, LUNARC uses a hierarchical module naming scheme. Hierarchical modules ensure that the correct shared libraries are available when running an application while keeping the screen output of standard module commands such as module avail manageable.

Hierarchical naming scheme concept

When logging into the system, you only get access to those modules that do not require any special dynamic libraries. After loading a compiler module you obtain access to those packages that have been built with that specific compiler and depend on its shared libraries. For many compilers, this will include one or more matching MPI libraries. After loading an MPI library additional software packages, depending on this pair (compiler & MPI library), will become available. Users should take note that in many cases loading an MPI library is required for software that doesn't depend on it.

Using Modules

The module system uses the Lua-based Lmod software.

Loading packages

The command

module avail

shows the modules that can currently be accessed. The output will look similar to

--------------------------------- /sw/Modules/modulefiles/Core ---------------------------------
   matlab/8.5

-------------------------------- /sw/easybuild/modules/all/Core --------------------------------
   Bison/3.0.4                    gompi/2015b
   EasyBuild/2.5.0                gompi/2016a                        (D)
   EasyBuild/2.6.0         (D)    icc/2015.3.187-GNU-4.9.3-2.25
   GCC/4.9.3-binutils-2.25        icc/2016.1.150-GCC-4.9.3-2.25      (D)
   GCC/4.9.3-2.25                 iccifort/2015.3.187-GNU-4.9.3-2.25
   GCC/5.3.0               (D)    iccifort/2016.1.150-GCC-4.9.3-2.25 (D)
   GCCcore/4.9.3                  ifort/2015.3.187-GNU-4.9.3-2.25
   GNU/4.9.3-2.25                 ifort/2016.1.150-GCC-4.9.3-2.25    (D)
   Java/1.8.0_72                  iimpi/7.3.5-GNU-4.9.3-2.25
   M4/1.4.17                      iimpi/2016.01-GCC-4.9.3-2.25       (D)
   binutils/2.25                  intel/2015b
   flex/2.5.39                    intel/2016a
   foss/2015b                     intel/2016.01                      (D)
   foss/2016a              (D)    zlib/1.2.8

-------------------------------- /sw/lmod/lmod/modulefiles/Core --------------------------------
   lmod/6.0.24    settarg/6.0.24

In this example, you can see modules and versions located in 3 directories. Any of these modules can be accessed directly. To obtain access to the software inside e.g. the toolchain module foss/2016a one loads the module by issuing

module load foss/2016a

Many modules will load several modules, which they depend on. As the output from module avail version 2016a is marked as the default version, the command

module load foss
would have the same effect unless the default changes, which it may do, if

  • You load a module
  • The LUNARC team installs another version of the software

So if you require a specific version, the LUNARC team strongly recommends not relying on defaults, but explicitly specify the version you are after.

To see what modules you have currently loaded, use

module list

In a hierarchical module naming scheme, the command module avail is not as useful as it is in a flat module naming scheme which LUNARC deployed on earlier services. In many situations module avail resulted in the desired action, one has to use the module spider command which is described in the text below.

Purging the loaded modules

Many modules will load a number extra of modules, which they depend on. When unloading a module, these dependencies will typically not be unloaded. For that reason, we currently recommend using

module purge

when loaded modules are no longer needed. You would then start loading the modules required for the next task you need to accomplish from scratch.

Searching for all software packages

In practical use, the command module spider is key to searching for packages in a Lmod-based hierarchical module naming scheme. To get an overview of the software installed, simply type:

module spider
at the command prompt. This will create an output similar to:

---------------------------------------------------------------------
The following is a list of the modules currently available:
---------------------------------------------------------------------
  Autoconf: Autoconf/2.69

  Automake: Automake/1.15

  Autotools: Autotools/20150215

  Bison: Bison/3.0.4

  Boost: Boost/1.58.0-Python-2.7.9

  CMake: CMake/3.2.2, CMake/3.3.2

  Cube: Cube/4.3

  EasyBuild: EasyBuild/2.5.0, EasyBuild/2.6.0

  FFTW: FFTW/3.3.4

  GCC: GCC/4.9.3-binutils-2.25, GCC/4.9.3-2.25, GCC/5.3.0

  GCCcore: GCCcore/4.9.3

  GLib: GLib/2.42.1, GLib/2.46.0

  GNU: GNU/4.9.3-2.25

  GROMACS: GROMACS/5.0.4-mt, GROMACS/5.0.5-hybrid

  ...
This is a full list of the packages and versions available on the service.

Searching for a specific package

If you are looking for a specific package and have an idea of what its name might be, you can give this as an argument to module spider. This argument is case insensitive.

Example: Accessing a Gromacs version

For example, when looking to run Gromacs:

module spider gromacs

You obtain output similar to:

---------------------------------------------------------------------------------
  GROMACS:
---------------------------------------------------------------------------------
     Versions:
        GROMACS/5.0.4-mt
        GROMACS/5.0.5-hybrid

---------------------------------------------------------------------------------
  To find detailed information about GROMACS please enter the full name.
  For example:

     $ module spider GROMACS/5.0.5-hybrid
---------------------------------------------------------------------------------

This tells you that the multi-threaded version 5.0.4 and the hybrid version 5.0.5 are installed. If you want to use the version 5.0.5 issue the command:

module spider GROMACS/5.0.5-hybrid

You get the following output

---------------------------------------------------------------------------------
  GROMACS: GROMACS/5.0.5-hybrid
---------------------------------------------------------------------------------

    This module can only be loaded through the following modules:

      icc/2016.1.150-GCC-4.9.3-2.25  impi/5.1.2.150
      ifort/2016.1.150-GCC-4.9.3-2.25  impi/5.1.2.150

...

This lists the modules you have to load before accessing Gromacs. In this case, you have two options, we choose the first option. We load

module load icc/2016.1.150-GCC-4.9.3-2.25 impi/5.1.2.150

After which we can load the GROMACS-installation:

module load GROMACS/5.0.5-hybrid

Loading this module will load several additional modules required for GROMACS to work.

Example accessing R

This is another example of how to access a specific software package. This time we want to run the statistical software package R.

module spider R

One gets:

------------------------------------------------------------------
  R:
------------------------------------------------------------------
     Versions:
        R/3.2.1-bare
        R/3.2.1
        R/3.2.3

     Other possible modules matches:
        GCCcore  GROMACS  SuiteSparse  cURL  fixesproto  fontsproto  ...

------------------------------------------------------------------
  To find other possible module matches do:
      module -r spider '.*R.*'

------------------------------------------------------------------
  To find detailed information about R please enter the full name.
  For example:

     $ module spider R/3.2.1-bare
------------------------------------------------------------------

If we are interested in version 3.2.3, we do a

module spider R/3.2.3

next and get the following info:

------------------------------------------------------------------
  R: R/3.2.3
------------------------------------------------------------------

     Other possible modules matches:
        GCCcore, GROMACS, SuiteSparse, cURL, fixesproto, ...

    This module can only be loaded through the following modules:

      GCC/4.9.3-binutils-2.25  OpenMPI/1.8.8

...

The output states the two modules that need loading to get access to this R version. We issue

module load GCC/4.9.3-binutils-2.25
module load OpenMPI/1.8.8
module load R/3.2.3

and have access to R.

Working with a standard set of modules

Many users of the LUNARC systems conduct similar tasks for many days, e.g. using the same pieces of software on different sets of data. In this case, users should consider creating user collections of modules. Working with user collections is a better alternative to e.g. adding module load statements to e.g. your .bashrc file.

Creating and restoring user collections

To create a user collection load the modules required for the task at hand. The command 

module save
would then store the currently loaded modules as a default collection. Alternatively, you can create a named collection

module save collection-name

where you can choose any name you like as collection-name.

Warning

The module system will remember whether a module was loaded as default (no version specified) or whether you loaded a specific version. If you include default modules, the contents of your collection will change whenever the default changes.

When one restores a collection, this has two effects:

  1. Unloading/purging all currently loaded modules
  2. Loading all modules included in the collection

To restore your default collection

module restore
A named collection can be restored as follows

module restore collection-name

Enquiring about user collections

To get a list of all user collections you have created use the sub-command savelist:

module savelist

The sub-command describe shows you the modules included in the collection

module describe collection-name

If you want to remove a collection from your list:

module disable collection-name

which actually renames the collection in a way that it would no longer show with module savelist, but recovery of the collection is possible.

Lmod cache

To improve the performance of the module spider command, lmod caches the entire module structure of the system. The system cache, holding info about the modules installed by the LUNARC team, is updated, every time the LUNARC team installs new software.

Searching for modules graphically

It is also possible to browse the module tree and select the module using a graphical user interface. This interface can be launched from the command with the ml-browse:

ml-browse

Author: Joachim Hein (LUNARC)

Last Updated: 2022-10-06