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HIVE Cluster Migration Tools

This repository contains scripts to help migrate from the old HPC cluster to the new HIVE cluster.

Table of Contents

HIVE vs Cacao Comparison

Key Differences Between Clusters

Component Cacao (Old Cluster) HIVE (New Cluster)
Storage Path /share/siegellab/ /quobyte/jbsiegelgrp/
Home Directory Size 1GB limit 20GB limit
Shell Config .bash_profile .bashrc (with minimal .bash_profile)
Conda/Python Local installations (~/miniconda3, etc.) module load conda/latest
CUDA Various local installations module load cuda/12.6.2
GPU Partition jbsiegel-gpu gpu-a100
GPU Account Not required --account=genome-center-grp required
CPU Partitions production low (3 day max) or high (30 day max)
Job Requeue Not standard --requeue flag for low partition

Software Locations

Software Cacao Path HIVE Path
ColabFold /toolbox/LocalColabFold/ /quobyte/jbsiegelgrp/software/LocalColabFold/
LigandMPNN /toolbox/ligandMPNN/ /quobyte/jbsiegelgrp/ligandMPNN/
RFdiffusion Various (~/RFdiffusion, /toolbox/RFdiffusion, etc.) /quobyte/jbsiegelgrp/software/RFdiffusion/
RFdiff Conda Env Various (SE3nv, rfdiffusion, etc.) /quobyte/jbsiegelgrp/software/envs/SE3nv
Rosetta /share/siegellab/software/kschu/Rosetta/main/ /quobyte/jbsiegelgrp/software/Rosetta_314/rosetta/main/
Rosetta Version Older version Rosetta 3.14
Rosetta Binaries .default.linuxgccrelease .static.linuxgccrelease

Storage Management

Storage Type Cacao HIVE
Conda Packages ~/.conda/pkgs /quobyte/jbsiegelgrp/{user}/.conda/pkgs
Conda Environments ~/.conda/envs or local /quobyte/jbsiegelgrp/{user}/.conda/envs
Pip Cache ~/.cache/pip /quobyte/jbsiegelgrp/{user}/.cache/pip
HuggingFace Cache ~/.cache/huggingface /quobyte/jbsiegelgrp/{user}/.cache/huggingface
PyTorch Cache ~/.cache/torch /quobyte/jbsiegelgrp/{user}/.cache/torch
Transformers Cache ~/.cache/transformers /quobyte/jbsiegelgrp/{user}/.cache/transformers

SLURM Changes

Parameter Cacao HIVE
GPU Jobs #SBATCH -p jbsiegel-gpu #SBATCH -p gpu-a100
#SBATCH --account=genome-center-grp
CPU Jobs #SBATCH -p production #SBATCH -p low (default) or
#SBATCH -p high (long jobs)
Low Priority N/A #SBATCH --requeue (auto-requeue if preempted)
Time Limits 30 days max low: 3 days max
high: 30 days max

Interactive Sessions

The bash_profile_migration.py script adds these convenient aliases for requesting interactive sessions:

Command Resources Partition
sandbox 8 CPU, 16GB RAM, 1 day high
sandboxlow 16 CPU, 32GB RAM, 1 day low
sandboxgpu 8 CPU, 16GB RAM, 1 GPU, 1 day high
sandboxlowgpu 8 CPU, 16GB RAM, 1 GPU, 1 day low

Quick Start

Step 1: Migrate Your Shell Configuration (Run from Cacao/Barbera)

IMPORTANT: Run this from your old cluster (cacao/barbera), NOT from HIVE!

# SSH to cacao or barbera first
ssh username@cacao.genomecenter.ucdavis.edu

# Download just the bash profile migration script
wget https://raw.githubusercontent.com/ianandersonlol/HiveTransition/main/bash_profile_migration.py

# Run it
python bash_profile_migration.py <ssh_username> <quobyte_dir>

# Example:
python bash_profile_migration.py jdoe john

Step 2: Fix Your Job Scripts

For fixing job scripts, clone the repository where YOUR scripts are located:

git clone https://github.com/ianandersonlol/HiveTransition.git
cd HiveTransition

# Fix individual scripts
python colab_fix.py /path/to/colabfold_job.sh      # For ColabFold
python ligandmpnn_fix.py /path/to/ligandmpnn_job.sh # For LigandMPNN
python rfdiffusion_fix.py /path/to/rfdiff_job.sh    # For RFdiffusion
python rosetta_fix.py /path/to/rosetta_job.sh       # For Rosetta

# Or update all paths at once (no SLURM changes)
python pathMigrator.py /path/to/scripts/directory    # Update all software paths

Available Scripts

1. pathMigrator.py (Comprehensive Path Migration)

Updates ALL software paths in a directory:

  • Combines path fixes from all other scripts
  • Does NOT modify SLURM settings
  • Can process entire directories at once
  • Includes all software: ColabFold, LigandMPNN, RFdiffusion, Rosetta

Full Documentation

2. bash_profile_migration.py

Migrates your shell configuration to HIVE:

  • Converts .bash_profile to .bashrc
  • Sets up conda in quobyte directory
  • Adds interactive session aliases
  • Updates paths and modules

Full Documentation

3. colab_fix.py

Updates ColabFold scripts:

  • Fixes ColabFold installation path
  • Updates GPU partition settings
  • Migrates storage paths

Full Documentation

4. ligandmpnn_fix.py

Updates LigandMPNN scripts:

  • Fixes LigandMPNN installation path
  • Updates GPU partition settings
  • Migrates storage paths

Full Documentation

5. rfdiffusion_fix.py

Updates RFdiffusion scripts:

  • Standardizes RFdiffusion installation path
  • Updates conda environment to shared SE3nv
  • Updates GPU partition settings

Full Documentation

8. rf_diffusion_aa.sh

Example script for running RFdiffusion for amino acid design:

  • Demonstrates how to set up and run RFdiffusion jobs on a SLURM cluster.
  • Configurable parameters for protein design tasks.

Full Documentation

6. rosetta_fix.py

Updates Rosetta scripts:

  • Migrates to Rosetta 3.14
  • Changes binary names (.default. → .static.)
  • Handles CPU partition selection
  • Enforces time limits

Full Documentation

7. broken.py

Reports issues with scripts:

  • Generates GitHub issue URL
  • Pre-fills script content
  • Auto-assigns to maintainer

Full Documentation

Common Migration Tasks

Setting Up Your Environment

  1. Run the migration script from old cluster (cacao/barbera):

    python bash_profile_migration.py myusername mydirectory

  2. Log into HIVE:

    ssh myusername@hive.hpc.ucdavis.edu

  3. Source your configuration:

    source ~/.bashrc

Migrating Job Scripts

  1. Identify script type (ColabFold, Rosetta, etc.)

  2. Run appropriate fix script:

    python <tool>_fix.py myscript.sh

  3. Review changes:

    diff myscript.sh myscript_fixed.sh

  4. Test on HIVE:

    sbatch myscript_fixed.sh

Interactive Sessions

Use the aliases added by bash_profile_migration.py:

sandbox      # 8 CPU, 16GB RAM, high priority
sandboxlow   # 16 CPU, 32GB RAM, low priority
sandboxgpu   # 8 CPU, 16GB RAM, 1 GPU, high priority
sandboxlowgpu # 8 CPU, 16GB RAM, 1 GPU, low priority

Important Notes

Storage Management

  • Home directory: 20GB limit
  • Store everything in /quobyte/jbsiegelgrp/{your_directory}/
  • Conda environments go in .conda/envs/
  • Package caches go in .cache/

Module Loading

Instead of local conda:

module load conda/latest
module load cuda/12.6.2  # For GPU jobs Good to have even when you're not using a GPU so you have the drivers up!

IF YOU USED MY BASH MIGRATION TOOL IT WILL PUT IT IN YOUR BASHRC

Partition Selection

  • Use low for most jobs (< 3 days)
  • Use high for long jobs (> 3 days)
  • GPU jobs need --account=genome-center-grp

Troubleshooting

Common Issues

  1. "Module not found"

    • Use module avail <name> to find the new module name
    • Some modules have different names on HIVE

  2. "Permission denied"

    • Check you're writing to your quobyte directory
    • Create directories if they don't exist

  3. "Command not found"

    • Ensure you've sourced ~/.bashrc
    • Check if software is in a different location

  4. Time limit errors

    • Use --high flag for Rosetta jobs > 3 days
    • Break large jobs into smaller chunks

Getting Help

  1. Check documentation:

    • See docs/ folder for detailed guides
    • Each script has --help option

  2. Report issues:

    python broken.py problematic_script.sh

  3. GitHub Issues:

Contributing

If you find issues or have improvements:

  1. Use broken.py to report script issues
  2. Submit pull requests for fixes
  3. Share working examples with the community

File Structure

/Users/iananderson/Desktop/HiveTransition/
├───.gitignore
├───bash_profile_migration.py
├───broken.py
├───colab_fix.py
├───ligandmpnn_fix.py
├───pathMigrator.py
├───README.md
├───rfdiffusion_fix.py
├───rosetta_fix.py
├───.claude/
│   └───settings.local.json
├───.git/...
├───.github/
│   └───ISSUE_TEMPLATE/
│       └───script_not_working.yml
├───docs/
│   ├───bash_profile_migration.md
│   ├───broken.md
│   ├───chai_with_msa.md
│   ├───colab_fix.md
│   ├───colabfold.md
│   ├───galigand_dock.md
│   ├───ligandmpnn_fix.md
│   ├───ligandmpnn.md
│   ├───pathMigrator.md
│   ├───relax.md
│   ├───rfdiffusion_fix.py
│   ├───rosetta_fix.py
│   ├───run_chai.md
│   └───submit_chai.md
└───example_scripts/
    ├───design/
    │   ├───Diffusion/
    │   │   └───rf_diffusion_aa.sh
    │   └───LigandMPNN/
    │       └───submit_ligandMPNN.sh
    ├───docking/
    │   ├───galigand_dock/
    │   │   ├───4Epimv7.cst
    │   │   ├───DF6.params
    │   │   ├───docking.xml
    │   │   ├───flags
    │   │   ├───GatZ_F6P.pdb
    │   │   └───submit.sh
    │   └───relaxation/
    │       └───relax.sh
    └───folding/
        ├───Alphafold2/
        │   └───colabfold.sh
        └───Chai/
            ├───chai_with_msa.py
            ├───run_chai.py
            ├───submit_chai_with_msa.sh
            └───submit_chai.sh

Example Scripts

This project includes example scripts to demonstrate how to run common bioinformatics tools in a cluster environment.

ColabFold

  • Script: example_scripts/folding/Alphafold2/colabfold.sh
  • Description: A SLURM submission script for running ColabFold. It is pre-configured with resource requests and sets up the necessary environment.
  • Full Documentation

Chai

run_chai.py

  • Script: example_scripts/folding/Chai/run_chai.py
  • Description: A script to run protein structure prediction using the chai_lab library.
  • Full Documentation

chai_with_msa.py

  • Script: example_scripts/folding/Chai/chai_with_msa.py
  • Description: A script to run protein structure prediction using the chai_lab library with MSA support.
  • Full Documentation

submit_chai.sh & submit_chai_with_msa.sh

  • Scripts: example_scripts/folding/Chai/submit_chai.sh, example_scripts/folding/Chai/submit_chai_with_msa.sh
  • Description: SLURM submission scripts for run_chai.py and chai_with_msa.py.
  • Full Documentation

LigandMPNN

  • Script: example_scripts/design/LigandMPNN/submit_ligandMPNN.sh
  • Description: A SLURM submission script for running LigandMPNN. It is pre-configured with resource requests and sets up the necessary environment.
  • Full Documentation

RFdiffusion

  • Script: example_scripts/design/Diffusion/rf_diffusion_aa.sh
  • Description: A SLURM submission script for running RFdiffusion for de novo protein design. It is pre-configured with common parameters for protein design tasks.
  • Full Documentation

GaliGand Dock

  • Script: example_scripts/docking/galigand_dock/submit.sh
  • Description: A SLURM submission script for running the GaliGand docking protocol. It is pre-configured with resource requests and sets up the necessary environment.
  • Full Documentation

Relaxation

  • Script: example_scripts/docking/relaxation/relax.sh
  • Description: A SLURM submission script for running Rosetta relaxation. It is pre-configured with resource requests and sets up the necessary environment.
  • Full Documentation

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