Bodhi HPC User Guide¶

Scheduled Maintenance

Bodhi undergoes scheduled maintenance on the last Thursday of every month. Jobs may be held or killed during the maintenance window. Plan your submissions accordingly.

Welcome to the documentation site for the Bodhi HPC cluster. Use the sections below to find what you need.

SLURM Documentation¶

Bodhi has migrated from IBM Spectrum LSF to SLURM. Our SLURM documentation covers everything you need to get your jobs running:

Directives — #BSUB → #SBATCH mapping
Commands — LSF-to-SLURM command equivalents
Environment Variables — $LSB_* → $SLURM_* mapping
Job Arrays — array job syntax changes
Common Pain Points — OOM debugging, accounts, wall time
Example Scripts — complete before/after job scripts
Converter — automated lsf2slurm.sh helper script
Interactive Sessions — persistent interactive jobs with tmux
Resources — links to official SLURM documentation

Positron / VSCode¶

Remote SSH Setup — using Positron or VSCode over remote SSH

Existing users: redeploy to land on the positron partition

The launcher was updated on 2026-03-29 to submit jobs to the dedicated positron partition (was previously landing in normal). If you set up Positron Remote SSH before then, refresh your copy once:

cd ~/devel/rnabioco/remote-ssh-positron && git pull && make install

Verify with squeue --me after launching a new session — the job should show Partition=positron.

Backups¶

Guidelines for backing up your data on the Bodhi cluster.

Backup Instructions — what to back up, where, and how
PetaLibrary — CU Research Computing PetaLibrary backup system

Getting Help¶

Contacts & Support — who to contact and how to get assistance