Conda Multi-Account Setup on HiPerGator

Experiment Overview

Context

On HiPerGator, users often belong to multiple research groups with separate storage allocations under /blue/. Each group may have its own conda installation and environments. The challenge is accessing environments from a different group's storage location.

The Problem

Default conda only knows about environments in:

• ~/.conda/envs/ (home directory)
• The base conda installation's envs/ directory

Environments created under /blue/othergroup/username/ are not visible.

Verified Workflow

Solution: Create a Sourcing Script

Create ~/.use_conda_<groupname>.sh for each group's conda:

#!/bin/bash
# ~/.use_conda_maigan.sh - Switch to maigan group's conda

# Initialize conda for this shell
source /blue/maigan/smith6jt/miniforge3/etc/profile.d/conda.sh

# Add environment search paths
export CONDA_ENVS_DIRS="/blue/maigan/smith6jt/miniforge3/envs:$HOME/.conda/envs"

# Optional: Set package cache to shared location
export CONDA_PKGS_DIRS="/blue/maigan/smith6jt/miniforge3/pkgs:$HOME/.conda/pkgs"

Usage Pattern

# At start of session, source the appropriate conda
source ~/.use_conda_maigan.sh

# Now conda sees all environments
conda env list
# Shows environments from /blue/maigan/smith6jt/miniforge3/envs/

# Activate environment from that location
conda activate KINTSUGI

For Multiple Groups

Create separate scripts for each group:

# ~/.use_conda_maigan.sh - for maigan group
source /blue/maigan/smith6jt/miniforge3/etc/profile.d/conda.sh
export CONDA_ENVS_DIRS="/blue/maigan/smith6jt/miniforge3/envs:$HOME/.conda/envs"

# ~/.use_conda_othergroup.sh - for another group
source /blue/othergroup/smith6jt/miniforge3/etc/profile.d/conda.sh
export CONDA_ENVS_DIRS="/blue/othergroup/smith6jt/miniforge3/envs:$HOME/.conda/envs"

Integration with Claude Code

Add the sourcing command to Claude Code permissions in .claude/settings.local.json:

{
  "permissions": {
    "allow": [
      "Bash(source ~/.use_conda_maigan.sh)",
      "Bash(conda activate:*)",
      "Bash(conda env list:*)",
      "Bash(pip install:*)"
    ]
  }
}

Failed Attempts (Critical)

Final Parameters

Directory Structure

/blue/maigan/smith6jt/
├── miniforge3/           # Conda installation
│   ├── etc/profile.d/
│   │   └── conda.sh      # Source this to initialize
│   ├── envs/
│   │   └── KINTSUGI/     # Your environments here
│   └── pkgs/             # Package cache
└── KINTSUGI/             # Project directory

~/.use_conda_maigan.sh    # Sourcing script

The Sourcing Script

#!/bin/bash
# ~/.use_conda_maigan.sh

# Initialize conda (REQUIRED - sets up conda command)
source /blue/maigan/smith6jt/miniforge3/etc/profile.d/conda.sh

# Tell conda where to find environments
export CONDA_ENVS_DIRS="/blue/maigan/smith6jt/miniforge3/envs:$HOME/.conda/envs"

# Share package cache to save space
export CONDA_PKGS_DIRS="/blue/maigan/smith6jt/miniforge3/pkgs:$HOME/.conda/pkgs"

echo "Conda configured for maigan group"
conda env list

Key Insights

• conda.sh sourcing is required before any conda commands work
• CONDA_ENVS_DIRS is colon-separated list of paths to search for environments
• The first path in CONDA_ENVS_DIRS is where new environments are created
• Don't run conda init for multiple installations - it modifies .bashrc
• Miniforge is preferred over Anaconda for HPC (faster, BSD licensed)
• Package cache (CONDA_PKGS_DIRS) can be shared to save quota

Environment Creation

When creating new environments with this setup:

source ~/.use_conda_maigan.sh

# Create from environment file
conda env create -f envs/env-linux.yml

# Or create manually
conda create -n myenv python=3.10

# Environment will be created in /blue/maigan/smith6jt/miniforge3/envs/

References

• Conda configuration: https://docs.conda.io/projects/conda/en/latest/user-guide/configuration/
• HiPerGator documentation: https://help.rc.ufl.edu/doc/Conda
• Miniforge: https://github.com/conda-forge/miniforge