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HPC software environment


On UBELIX the default shell is Bash. With the operation system, a list of basic tools (mainly command line tools) are provided, including editors, file analyzing and manipulation tools, packing and transfer tools etc. This commands are accessible all the time.

Other software packages (libraries and applications) are available via the LMOD (lua modules) modules. By the help of this tool a lot of different packages even in different versions can be provided, without unwanted influences.

Furthermore, software stacks are provided one for each CPU architecture. These are loaded automatically on the related architecture, transparent to the user.

Additionally to our software stack, VITAL-IT provides a software stack targeting mainly bioinformatics users, see Bioinformatics Software.

Basic concept

Many Linux settings are in environment variables. These include search paths for applications ($PATH) and libraries ($LD_LIBRARY_PATH). Adding or removing a directory to these lists, provides access or remove access to additional software.

The LMOD modules are an user friendly way to search and manage software packages without dealing with complicated directory names.

In general every software package has its related module. When loading the module the software package and its dependencies get accessible.

But let’s do it step by step.

List available Modules

There are various ways to search for a software package. You can list all currently available packages using:

module avail

You can search for an packages starting with a specific string, e.g. all version of GCC:

module avail GCC

Furthermore, the following command lists you all the modules containing a certain sub-string in the name, even in other software stacks, e.g.:

module spider Assembler

In the example above all modules with the sub-string Assembler will be listed, in this case the ones from the Vital-It software stack.

Load/Add a Modules

Loading a module will provide access to the software package and it will additionally load all required dependencies.

module load OpenMPI/3.1.3-GCC-8.2.0-2.31.1

or equivalently:

$ module add OpenMPI/3.1.3-GCC-8.2.0-2.31.1

This will provide access to OpenMPI, but also to GCC and other libraries. With this principle it is verified that the library versions are loaded, which were used to build the package.

List all Loaded Modules

You can list the currently loaded modules using

$ module list

Currently Loaded Modules:
  1) GCCcore/8.2.0
  2) zlib/.1.2.11-GCCcore-8.2.0       (H)
  3) binutils/.2.31.1-GCCcore-8.2.0   (H)
  4) GCC/8.2.0-2.31.1
  5) numactl/2.0.12-GCCcore-8.2.0
  6) XZ/.5.2.4-GCCcore-8.2.0          (H)
  7) libxml2/.2.9.8-GCCcore-8.2.0     (H)
  8) libpciaccess/.0.14-GCCcore-8.2.0 (H)
  9) hwloc/1.11.11-GCCcore-8.2.0
 10) OpenMPI/3.1.3-GCC-8.2.0-2.31.1

   H:  Hidden Module

Toolchains / version consistency

When loading multiple modules it is strongly suggested to stay within one toolchain version.

A toolchain is a set of modules all building on top of each other. The related packages and versions can be listed with the command above. There are two basic toolchains which are build up on top of GCC and Intel:

Toolchain packages
GCC GCC compiler
gompi GCC, OpenMPI
gompic GCC, OpenMPI, CUDA
fosscuda GCC, OpenMPI, OpenBLAS, FFTW, ScaLAPACK, CUDA
intel Intel compiler, (GCC required), MKL, Intel MPI
iompi Intel compiler, OpenMPI
iomkl Intel compiler, OpenMPI, MKL

Furthermore, toolchains are provided in different versions and updated regularly.

When loading multiple packages, they should be based on the same toolchain and the same version.

In the following are two examples where netCDF and FFTW should be loaded, but the based toolchains and versions do not match.

Problematic example: different toolchains

module load netCDF/4.7.3-gompi-2019b
module load FFTW/3.3.8-intel-2019b
NetCDF is loaded in the gompi toolchain, including OpenMPI. FFTW is loaded in the intel toolchain, including iimpi (IntelMPI). Beside other, now two different MPI implementation are loaded. We cannot verify that each package uses the MPI library it is build with. In best case this leads to errors during run time. In worse case results are incorrect.

Problematic example: toolchain versions

$ module load netCDF/4.7.4-gompi-2020b
$ module load FFTW/3.3.7-gompi-2018a

The following have been reloaded with a version change:
  1) GCC/10.2.0 => GCC/6.4.0-2.28                                      5) gompi/2020b => gompi/2018a
  2) GCCcore/10.2.0 => GCCcore/6.4.0                                   6) hwloc/2.2.0-GCCcore-10.2.0 => hwloc/1.11.8-GCCcore-6.4.0
  3) OpenMPI/4.0.5-GCC-10.2.0 => OpenMPI/2.1.2-GCC-6.4.0-2.28          7) numactl/2.0.13-GCCcore-10.2.0 => numactl/2.0.11-GCCcore-6.4.0
  4) binutils/.2.35-GCCcore-10.2.0 => binutils/.2.28-GCCcore-6.4.0

LMOD already notes the version changes. In this case, netCDF build with 2020a version will utilize libraries of 2018a. If interfaces have changed, errors may occur.

Unload/remove Modules

To prevent unwanted influences between software packages, it is advisable to keep the loaded software stack small and clean.

Certain modules can be unloaded using:

$ module unload OpenMPI/3.1.3-GCC-8.2.0-2.31.1
or equivalently:

$ module rm OpenMPI/3.1.3-GCC-8.2.0-2.31.1

This will only unload the specified module. Dependencies stay loaded, which were automatically loaded when loading the specified modulefile. A clean environment can be obtained with purge (see below).

Purge all Modules

All currently loaded modules an be unloaded using:

$ module purge

Show information

Most modules provide a short description which software package they contain and a link to the homepage, as well as information about the changes of environment undertaken. From short to full detail:

$ module whatis OpenMPI
$ module help OpenMPI
$ module show OpenMPI

Environment definitions

Working on different projects or with different types of task may require to load different sets of modules.

There are two ways of providing a user environment setups, e.g. for development, production, post processing etc., a custom module (also for Workspaces) or a module user collections (per user).

Adding module load into .bashrc may lead to issues. If you diverge from this “default” environment and additionally load conflicting modules, e.g. form another toolchain.

Custom Modules

A so called “Meta Module” can be used to specify a set of modules. Additionally, environment variables can be defined. These custom modules can be placed in the custom software stack, e.g. in a Workspace. Thus default working environments could be defined for the users that workspace. You may want to decide if you want to specify the environment with all versions of the modules (advisable), or always the latest versions (no version specified).

The modules can be placed into $WORKSPACE/modulefiles/$NAME/$VERSION.lua.

Example: Lua module for development environment

Here an environment is defined using foss and netCDF of version 2021a. Additionally an environment variable WS_ENV is set to devel. Therefore, a file $WORKSPACE/modulefiles/WS_devel/2021a.lua is created with the following content:

whatis([==[Description: Workspace XXX development environment]==])
if not ( isloaded("foss/2021a") ) then
if not ( isloaded("netCDF/4.8.0-gompi-2021a") ) then
setenv("WS_ENV", "devel")
setenv("CFLAGS", "-DNDEBUG")

The all workspace members can load this environment using:

module purge   ### better start with a clean environment
module load Workspace WS_devel

Module User Collections

Sets of modules can be stored and reloaded in LMOD using the “user collection” feature.

As an example, a set of module for development consiting of SciPy-bundle and netCDF should be stored under the name devel. Further module lists can be managed in the same way (here lists for test and prod already exist).

$ module load SciPy-bundle netCDF
$ module save devel
Saved current collection of modules to: "devel"
$ module savelist
Named collection list :
  1) devel  2) test  3) prod
Therewith the set of modules can be loaded using:

$ module restore devel

This will unload all other previously loaded modules beforehand and then load the set specified in the collection.

This method is preferred against defining/loading a set of modules in Bash configuration like .bashrc.

More information can be found in the LMOD documentation

Bioinformatics Software

In co-operation with the Vital-IT Group of the SIB Swiss Institute of Bioinformatics, a large set of bioinformatics software tools and databases is available to the life science community.

To list all modulefiles provided by Vital-IT, you have to first load the vital-it module:

Loading the vital-it modulefile automatically configures the environment to use specific versions of selected software, e.g. python v2.7.5, and gcc v4.9.1

 $ module load vital-it && module avail

Modules background

Architectural software stacks

On our HPCs we use LMOD (Lua modules) to provide access to different software packages and different versions. Beside different packages and versions, we provide software stacks build for the different CPU architectures. This enables us to have the packages build e.g. with AVX2 for Broadwell CPUs, but also a version with only SSE4 for Ivybridge CPUs. These software stacks are completely transparent to the user and will be used automatically when loading a module on the related architecture.

If you want to build your own software build for specific Hardware, we provide tools which help you, see Installing Custom Software

Scientific Software Management

Our scientific software stack, available via module files are mainly build with EasyBuild. This tool helps us to install and maintain software packages and recycle existing installation procedures. There are plenty of install instructions available EasyBuild/Easyconfigs, which can be installed also in the user space with low effort, see Installing Custom Software

Custom modules

Modules are able to define the users environment. This includes accessibility to software packages, including settings for libraries and setting environment variables.

On UBELIX we use LMOD. Therewith, lua as well as TCL modules can be used.

Last update: 2023-11-17