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Accessing the Bon Echo cluster (updated January 2026)

Starting in early 2026, the Scientific Computing is implementing changes to the Bon Echo environment that will affect how users access the cluster and run workflows there. There are several key changes that are being rolled out, with an expectation that these will all go live in February.

Notable changes include:

  • The original login nodes (ie. v.vectorinstitute.ai and vlogin.vectorinstitute.ai) are being retired and replaced.
  • All the GPU nodes are getting an OS upgrade to Ubuntu 24. This means that old Python environments and installed packages may no longer work.
  • The system software modules listed under module avail (for example python/3.12.0 or pytorch2.1-cuda11.8-python3.10) will be different.
  • Many changes to the file system layout.

This document demonstrates all the new login instructions, explains all the changes in detail and shows what to do to update your workflows to work in the new environment.

Logging into Bon Echo

Log into the new Bon Echo environment by SSH-ing into one of the following two login nodes:

  • blogin01.bonecho.vectorinstitute.ai
  • blogin02.bonecho.vectorinstitute.ai

Bon Echo 2026 Updates

You'll need to make several updates to your workflow so they work on the updated environment.

Python Environments

Any python environment that was created previously using venv, uv, or conda will most likely not work anymore on the updated cluster.

System Software Modules

The list of software modules available with module avail is different in the new environment. Modules that used to be available in the old environment (ie. pytorch2.1-cuda11.8-python3.10) may not be available anymore, or might be listed under different names.

Use module avail to view the new list of modules:

coatsworth@blogin02:~$ module avail

----------------------------------------------------------------------------------------------------------- MPI-dependent avx2 modules ------------------------------------------------------------------------------------------------------------
   abyss/2.3.7        (bio)       febio/4.7                                kahip/3.16           (D)       netcdf-c++4-mpi/4.3.1      (io)        pcl/1.14.1            (math)      siesta/4.1.5           (chem)
   adol-c/2.7.2                   ferret/7.6.0                 (vis)       lammps-omp/20250722  (chem)    netcdf-fortran-mpi/4.6.1   (io)        petsc-64bits/3.21.6   (t)         simnibs/4.1.0
   ambertools/23.5    (chem)      fftw-mpi/3.3.10              (math)      libmesh/1.7.5        (math)    netcdf-mpi/4.9.2           (io)        petsc-64bits/3.23.4   (t,D)       slepc-complex/3.20.1
The module avail command sometimes returns an error message starting with /cvmfs/soft.computecanada.ca/custom/software/lua/bin/lua: ...anada.ca/custom/software/lmod/lmod/libexec/Cache.lua:340: bad argument #1 to 'next' (table expected, got boolean).

This error is related to module caching. Fix it by running rm -rf ~/.cache/lmod.

Singularity is now Apptainer

The Singularity project has been renamed to Apptainer (https://apptainer.org/). There is no functional difference under the hood, but you'll need to make 2 small changes in your code:

  • Replace any Singularity module loads in your shell scripts with: module load apptainer/1.3.5
  • Change any singularity commands in your shell scripts to apptainer.
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