Bodhi HPC User Guide

Documentation site for the Bodhi HPC cluster — SLURM usage, backups, and support contacts.

Live site: https://rnabioco.github.io/bodhi-docs/

Local development

Requires pixi:

# Serve docs locally at http://localhost:8000
pixi run docs

# Build the site (strict mode)
pixi run build

Installing the scripts

The sinteractive and bodhi-splash helpers install via make:

# Per-user install (default): copies into ~/.local/bin
make install

# System-wide install (as root): sinteractive to /usr/local/bin and the
# login splash to /etc/profile.d/bodhi-splash.sh
sudo make install

Override the per-user location with PREFIX, e.g. make install PREFIX=~/bin.

There is also a Claude Code skill that teaches agents to run compute work through sinteractive (headless launch, srun --overlap, time budgets) instead of on the login node:

# Per-user: copies to ~/.claude/skills/bodhi-compute
make skill-install

Upgrading tmux

sinteractive runs tmux on the allocated compute node, and /usr/local is node-local, so the latest tmux must be installed on every node. These targets build the latest tmux release from source and fan it out to the cluster. They must be run as root on the head node:

# One-time: install build dependencies (RHEL/Rocky 9)
sudo make tmux-deps

# Download, build, and install into /usr/local
sudo make tmux

# Copy the built binary to every Slurm compute node
sudo make tmux-push

# Or do the build + push in one step
sudo make tmux-all

• Bump the version with TMUX_VERSION, e.g. sudo make tmux TMUX_VERSION=3.8.
• Restrict the push to specific nodes with NODES, e.g. sudo make tmux-push NODES="compute00 compute01" (defaults to all Slurm nodes from sinfo).
• tmux-push copies to a temp name and renames into place, so running sinteractive sessions aren't disturbed.

Converter script

A sed-based helper that converts common #BSUB directives and $LSB_* variables to SLURM equivalents:

bash scripts/lsf2slurm.sh myjob.lsf > myjob.slurm

See the converter documentation for details on what it does and doesn't handle.

Deployment

Pushes to main automatically build and deploy to GitHub Pages via GitHub Actions. The site is served from the gh-pages branch.

To enable: Settings → Pages → Source → gh-pages branch.