Conda Environment Configuration Guide

Overview

The system-wide Conda installation is located at:

/tem/al9/system/miniconda3-py312_25.1.1-2

The default envs directory is read-only and managed by the system administrator:

/tem/al9/system/miniconda3-py312_25.1.1-2/envs

To create and manage your own Conda environments, you must add a writable envs directory under your group's scratch space. This guide explains how to configure it.

Directory Structure

Path	Description
`/tem/al9/system/miniconda3-py312_25.1.1-2`	System Conda installation (read-only)
`/tem/al9/system/miniconda3-py312_25.1.1-2/envs`	System default envs directory (read-only)
`/tem/home/<UserID>`	Your home directory
`/tem/scratch/<GroupDir>`	Your group's scratch directory
`/tem/scratch/<GroupDir>/envs`	Recommended location for your group's environments

Replace <UserID> with your actual user ID and <GroupDir> with your group's scratch directory name.

Step 1: Load the Conda Module

Before using Conda, load the module:

module load miniconda3/py312_25.1.1-2

Verify that Conda is available:

conda --version
# conda 25.1.1

Step 2: Create the Group Envs Directory

Create the envs directory under your group's scratch space if it does not already exist:

mkdir -p /tem/scratch/<GroupDir>/envs

Note: This directory is shared within your group. Coordinate with your group members to avoid naming conflicts when creating environments.

Step 3: Add the Custom Envs Directory to Conda Config

Register the group envs directory as an additional environment path using conda config:

conda config --add envs_dirs /tem/scratch/<GroupDir>/envs

Verify the configuration was applied:

conda config --show envs_dirs

Expected output:

envs_dirs:
  - /tem/scratch/<GroupDir>/envs
  - /tem/al9/system/miniconda3-py312_25.1.1-2/envs

The newly added path is prepended to the list, so Conda will search it first when looking up environments.

Step 4: Create a Conda Environment

Create a new environment in your group's envs directory:

conda create --prefix /tem/scratch/<GroupDir>/envs/<env-name> python=3.12

Or, since the directory is already registered, you can use the shorthand --name option:

conda create --name <env-name> python=3.12

When using --name, Conda will automatically place the environment in the first writable path listed in envs_dirs — which is /tem/scratch/<GroupDir>/envs.

Step 5: Activate and Use the Environment

Activate the environment by name:

conda activate <env-name>

Or by full path:

conda activate /tem/scratch/<GroupDir>/envs/<env-name>

Deactivate when done:

conda deactivate

If the Active Environment Name Is Not Shown in the Prompt

After activation, the shell prompt should display the active environment name, for example:

(<env-name>) [user@hostname ~]$

If the environment name does not appear in your prompt, set the following environment variable before activating:

export BASH_POWERLINE=yes
conda activate <env-name>

To make this setting persistent across sessions, add it to your ~/.bashrc:

echo 'export BASH_POWERLINE=yes' >> ~/.bashrc
source ~/.bashrc

Step 6: List Available Environments

conda env list

Example output:

# conda environments:
#
base                  /tem/al9/system/miniconda3-py312_25.1.1-2
<env-name>         *  /tem/scratch/<GroupDir>/envs/<env-name>

Removing a Custom Envs Directory from Config

If you need to remove the custom path from your Conda configuration:

conda config --remove envs_dirs /tem/scratch/<GroupDir>/envs

Notes and Best Practices

Module must be loaded first. Always run module load miniconda3/py312_25.1.1-2 before using Conda in a new shell session. Consider adding it to your ~/.bashrc or job script.
The conda config change is persistent. It is saved to ~/.condarc in your home directory and applies to all future sessions automatically.
Do not install packages into the base environment. The base environment is system-managed and read-only. Always create and activate a dedicated environment.
Disk quota. Conda environments can be large. Monitor your group's scratch usage periodically:

cluster.mydata