BEAR Application Versions

Every six months we start a new version of our BEAR Applications (bear-apps), which is a default set of tools and libraries that are used as the basis for all the applications we install on the BEAR systems (BlueBEAR, BEARCloud VMs). We only use a bear-apps version for new installations for about one year. The applications in a bear-apps version will be available for several years after we’ve finished using it for new installations - see the details below.

Certain bear-apps versions are loaded automatically. For example, in March 2021 we have bear-apps/2018b, bear-apps/2019a, bear-apps/2019b, and bear-apps/2020a. The latest bear-apps/2020b is not yet loaded automatically, and some pages on our BEAR Applications website include instructions for loading that first. This is just an example, and is correct as of March 2021.

We normally support bear-apps versions from the current year and the previous two years, after which they are deprecated (see below), and later may be removed without warning.

Almost all of our applications are built using EasyBuild, “a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way.” You will sometimes see a bear-apps version with a suffix h, meaning the software had to be installed by hand instead.

Mixing Modules from Different BEAR Apps Versions

It is not possible to load modules from different BEAR Apps versions simultaneously. Where an attempt to load conflicting modules is made you will see an error message, reporting the incompatibility. For example:

$ module load cURL/7.69.1-GCCcore-9.3.0
GCCcore/9.3.0
zlib/1.2.11-GCCcore-9.3.0
cURL/7.69.1-GCCcore-9.3.0
$ module load cURL/7.76.0-GCCcore-10.3.0
Lmod has detected the following error:
    The module load command you have run has failed, as it would result in an incompatible mix of
modules.

    You have the "cURL/7.69.1-GCCcore-9.3.0" module already loaded and the module load command you
have run has attempted to load "cURL/7.76.0-GCCcore-10.3.0".

This is due to how software dependency chains are managed on BlueBEAR.

If you receive the above incompatible mix of modules error message then you will need to modify your module load commands to ensure compatibility. The BEAR Applications website shows the associated “BEAR Apps Version” for each module to assist with this process.

Tip

If you need to run a sequence of commands that use modules from different BEAR Apps versions, you can do this by executing module purge; module load bluebear between the steps of the sequence and loading the new modules as required.

Deprecation

We will usually support bear-apps versions from the current year and the previous two years, after which they may be marked as deprecated and may be removed without warning. For example the following warning is shown when they are loaded:

--------------------------- UNSUPPORTED WARNING ------------------------------
This module is NOT SUPPORTED and may be removed without further warning:
* apps/cytoscape/v3.2.0

Please see https://docs.bear.bham.ac.uk/bluebear/software/bear_apps/ for
further details.

Please see https://bear-apps.bham.ac.uk for alternative versions.
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