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Deploying software on BlueBrain5

Modules on BlueBrain5

Essential software used to build and simulate our brain models is deployed centrally on BlueBrain5, as well as some utilities to facilitate easier software development.

Modules should be available by default, and

$ module avail

should list both archive modules and an unstable one, which will become the next archive module available at the end of the month.

If no modules are available, the following will restore the setup:

$ . /gpfs/bbp.cscs.ch/apps/bsd/config/modules.sh

Updating deployed software versions

To update the version of any of these modules, first we have to make sure that the corresponding software is built by edit the corresponding Spack environment:

$ nvim ${SPACK_ROOT}/bluebrain/deployment/environments/applications_${team}.yaml

The above environment definition provides the end-user software that is developed by BlueBrain, split by team. Version specifications are only required if the deployed version should be static and not change with updates to the package file. Please ensure that:

  • If a module is required, the list spack:modules:default:tcl:include contains the name of the package (no version information required normally)
  • The package name is listed under spack:specs with required variants or special dependencies.

If there are dependencies used in a broader scope/by several software packages, consider adding them to one of the following steps in the deployment chain (all found in ${SPACK_ROOT}/bluebrain/deployment/environments):

  • libraries for general purpose libraries, and dependencies that depend on MPI
  • externals for packages that are rarely changed and for which the dependency graph may be truncated by Spack (e.g. Spark, Python) ­ mainly dependencies for building

Changes to any file should be committed and result in a pull request on Github.

Testing pull requests for updates

Jenkins will build the additional software required, with all output available in a separate directory:

$ ls /gpfs/bbp.cscs.ch/apps/bsd/pulls/12345
config  deploy  mirror  spack

Software packages and modules should be updated upon pull request merge and a nightly basis. The config directory contains the same configuration files as the regular deployment and can be used instead. To test the pull request, clean the environment and source the corresponding modules:

$ module purge     # remove anything that may pollute the shell environment
$ unset MODULEPATH # start with a clean slate, no interference
$ . /gpfs/bbp.cscs.ch/apps/bsd/pulls/${MY_PULL_REQUEST_NUMBER}/config/modules.sh
$ module load unstable
$ module load ${SOFTWARE_I_JUST_UPDATED}