Change log
Overview
This page provides a reverse chronological list of changes made to CCB systems. For all software updates see: modules, Python, R.
Changelog
2026-05-05: R upgraded to 4.6.0, all packages updated
2026-04-15: OpenAI Codex container sandbox
2026-03-23: List rejected software install requests
2026-03-20: Duplicate scan now checks project against databank. A PI may request a scan across all of their projects.
2026-01-29: Update RStudio to 2026.01
2026-01-20: Apply R patch, and update Bioconductor
2026-01-19: Install more GPUs
2025-12-18: Jupyter Slurm integration
2025-11-25: GPU tutorial
2025-10-13: Update RStudio to fix memory usage panel. Fix Numpy matrix performance stuck at 2x threads
2025-10-09: Patch Nextflow to see jobs we moved to unrequested queues
2025-08-29: Patch Python Torch + CUDA module import error
2025-07-21: Increase CPU memory in imm-gn1 (the older GPUs), from 100GB to 250GB.
2025-07-11: R upgrades: R to 4.5.1, all R packages, and RStudio to 2025.05.
2025-04-16: Improve scratch access
2025-02-04: Upgrade Ceph metadata processing: more throughput and prioritise logins
2025-01-22: Apply R patches, and Python patches 1 week before. Also upgraded Bioconductor
2024-10-01: Update RStudio to 2024.09
2024-09-16: Update R to latest version 4.4.1
2024-08-13: Fill gaps in Slurm documentation: scratch storage, job arrays & dependencies. And two new productivity tools sbusy and reportseff. So please review Running jobs and job profiling.
2024-06-24: Interactive project files browser
2024-06-17: Show creating an SSH key, and show how to recover project data from 24-hour backup.
2024-05-28: Announce new L40S GPUs
2024-04-30: Update containers page with new CCB containers including RStudio.
2024-04-03: Show launching IGV in Jupyter
2024-03-20: Fix rare RStudio fault blocking user install of some packages, manifesting in error namespace P X is being loaded, but >= Y is required
2024-03-18: Update R package renv for fix of issue #1671, resolving error namespace 'Matrix' 1.5-4.1 is being loaded, but >= 1.6.1 is required
2024-03-12: Ported Jupyter documentation from Microsoft Word file, added section on launching your own (customisable) Jupyter jobs
2024-01-31: New section on containers
2024-01-25: Improve 'getquota' tool with '-l' argument, to show usage breakdown.
2024-01-05: New cluster documentation website.
2023-11-07: Update R-cbrg to describe interfacing RStudio with Python, see section RStudio talking to Python.
2023-11-01: Update Jupyter PDF tutorial to describe changing folder to e.g. /project/... .
Click new section Changing working directory in PDF linked at welcome.
2023-10-31: New page listing known issues with JADE: known-issues.
2023-10-25: Adjust JADE queues: retire rarely-used jumbo queue, reallocate its resources to long queue, and doubled memory limits of long and short queues.
2023-10-16: New section on setting-up Conda at python-cbrg.
2023-09-18: New pages listing all installed Bioinformatics software: module-installs python-installs R-installs.
2023-08-01: Added flexbar.
2023-07-28: Updated differences with additional information on Bash.
2023-07-27: Removed broken older versions of meme.
2023-07-26: Added vireoSNP to python-cbrg. Added rename to the path.
2023-07-10: Restricted logins to cbrglogin1 and cbrglogin3 to 4 CPU cores and 32GB RAM each.
2023-07-05: Installed feh and xpdf to default path on the login nodes.
2023-06-29: Added Seurat 5 to R-cbrg current. This introduced breaking changes, so reverted to 4.3.0.