Anaconda on Cheaha¶
For additional general information on using Anaconda please see Anaconda Environments.
If you are using Jupyter Notebook, please see our section on Packages for Jupyter.
Anaconda is installed on Cheaha as a family of modules, and does not need to be installed by Researchers. Instead, the most recent version of Anaconda installed on Cheaha may be loaded using the command
module load Anaconda3. Other versions may be discovered using the command
module avail Anaconda. We recommend always using the latest version.
If you are using Open OnDemand Jupyter Notebook you do not need to use the
module load command as part of creating the job.
Anaconda on Cheaha works like it does on any other system, once the module has been loaded, with a couple of important differences in the callouts below.
base environment is installed in a shared location and cannot be modified by researchers. Other environments are installed in your home directory by default.
Only create environments on compute nodes. Anaconda environment creation consumes substantial resources and should not be run on the login node.
The Cheaha operating system has a version of Python installed. This version is used by
python calls when Anaconda has not been loaded. This can cause unexpected errors. Be sure you've loaded the Anaconda environment you need before using Python.
Do not use
conda init on Cheaha! Anaconda is managed as a module, including script setup. Using
conda init at any point can cause hard-to-diagnose issues with Open OnDemand Interactive Jobs. Please see this ask.ci FAQ for how to undo what
conda init does.
If the Anaconda software instructs you to use
conda init while on Cheaha, please ignore it to avoid future issues with Open OnDemand.
For more information on usage with examples, see Anaconda Environments.
Speedups Using Mamba¶
Mamba is not installed in the base environment on Cheaha, and cannot be installed in the base environment by researchers. We are working on installing Mamba in the base environment as part of our module installation process change. In the meantime if you need the speed Mamba provides, you can follow these instructions to make it available for yourself.
module load Anaconda3
- Create a new environment with only Mamba using
conda create --name mamba -c conda-forge mamba
conda activate mamba
- Use Mamba to install environments as needed. Be aware you must use the flag
--prefix=~/.conda/envs/to put the environment in the correct location to be seen by Anaconda.
Containers are a very useful resource for installing software without needing administrator permission. Please read the full documentation about singularity and containers on our main Singularity page.