cbe

Plugin cbe from marketplace clip-hpc in CLIP-HPC/skills. Commands read from the repo's manifest — 2 days ago.

Skills (9)

• cbe-data

  Choose storage and transfer methods on CBE.next; stage job data, restore files from snapshots, check quotas, retention, automatic deletion, and permissions, or archive results. Use before deleting, moving, renaming, or overwriting any file or directory under /groups (rm, mv, find -delete, rsync --de

• cbe-migrate

  Port job scripts, sbatch files, modules, conda environments, containers, data, and interactive JupyterHub, RStudio, or XPRA workflows from legacy CBE to CBE.next. Use for legacy cbe.vbc.ac.at, clip-login-* or clip-* hosts, /scratch-cbe, old QOS settings such as c_short, m_long, or g_rapid, and prepa

• cbe-next

  Work on CBE.next, the Vienna BioCenter HPC cluster (SSH alias cbe.next, login cbenext.vbc.ac.at, nodes cbe-c3-*, cbe-g3-*, cbe-g4-*, cbe-g5-*, cbe-m2-*, cbe-m3-*): connect over SSH, choose Slurm partitions c, g, and m and Slurm accounts, pick NVIDIA B200, A100, or RTX 6000 GPUs or MIG slices, and wr

• cbe-python

  Set up, repair, and maintain reproducible Python and conda environments on CBE.next with uv, conda, or mamba (global Miniforge), including conda environments for R and Bioconda tools: a project in a git repository whose dependencies are tracked in pyproject.toml and uv.lock, or environment.yml and c

• cbe-queue

  Explain why a CBE.next Slurm job is pending or waits long to start, and why jobs start in the order they do: job priority, Fair Tree fair-share across holding, institute, lab, and user accounts, usage decay, job age, QOS, backfill, and limits. Use for questions such as why is my job still pending, w

• cbe-software

  Find, load, install, or run software on CBE.next using Lmod modules (EESSI/2025.06 and CBE/2025.06 stacks, module spider, collections), CVMFS repositories (Galaxy BioContainers, Refgenie reference data, CERN unpacked images), SBGrid in /programs, Apptainer, uv Python environments, or conda from the

• cbe-ticket

  Write and open an HPC Servicedesk ticket (Jira project ISD, request type CLIP Support) for a CBE.next or OpenOnDemand problem: failed or hanging jobs, broken nodes, storage, mount, or permission errors, login and SSH problems, OpenOnDemand sessions (Jupyter, RStudio, VS Code, Remote Desktop) that do

• cbe-triage

  Diagnose failed, crashed, killed, cancelled, timed-out, out-of-memory, hanging, or incorrect Slurm jobs on CBE.next using job logs and accounting data. Check system-side causes such as exceeded quota, scratch deletion, node failure, network or storage errors, and maintenance; compare with successful

• cbe-tuning

  Improve Slurm job performance and resource efficiency on CBE.next using measured accounting data (sacct, jobeff, jobinfo) and small parameter sweeps. Use for slow jobs, shortening queue waits by right-sizing requests, over- or under-requested CPU, memory, GPU, or time, thread settings, job arrays fo

Hooks (1)

• PreToolUse

  command -v python3 >/dev/null 2>&1 || exit 0; exec python3 -I "${CLAUDE_PLUGIN_ROOT}/hooks/guard_groups.py"

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