---

name: conda-multi-account-hipergator description: "Set up conda with multiple group storage locations on HiPerGator" author: KINTSUGI Team date: 2025-12-11

Conda Multi-Account Setup on HiPerGator

Experiment Overview

Item	Details
Date	2025-12-11
Goal	Configure conda to use environments from multiple group storage locations
Environment	HiPerGator (UF), RHEL 9, multiple /blue/group/ directories
Status	Success

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)

Attempt	Why it Failed	Lesson Learned
Adding paths to .condarc envs_dirs	Only works after conda init, path issues with multiple condas	Use environment variables instead
Symlinking envs to home directory	Permissions issues, clutters home	Keep envs in original location
Using full paths to activate	Verbose, error-prone	Sourcing script is cleaner
Running conda init for multiple condas	Conflicts in .bashrc, breaks shell	Use separate sourcing scripts
Using module load conda	HiPerGator module may not have your custom envs	Use your own miniforge installation

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