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Conda Environments

Conda on the HPC

It is often desirable to download your own python packages into a conda environment. We will quickly go through how to create one and add packages to that conda environment.

  • Login to the HPC cluster either by Command Line or the OnDemand Website. For information on how to log into the cluster check out:

Navigate To The Cluster

  • Start an interactive session on the Tufts HPC Cluster to work on a compute node. To learn more about how to set up an interactive session visit:

Start an Interative Session

  • Load relevant modules:
module load anaconda/2021.11

Info

You may need to load other modules, such as cuda if you plan to utilize GPUs:

module load cuda/11.0

Create your conda environment

  • Now you can create your own conda env:
cd /cluster/tufts/XXXXlab/$USER/condaenv/
conda create -p yourenvname
  • Or if you have a specific version of python you need to use, e.g. 3.8 (Recommended!):
conda create -p yourenvname python=3.8

Note

you will need to have python and pip installed inside the env to pip install packages inside the env.

  • Activate the environment (needs to be executed whenever you need to use the conda env you have created)
source activate yourenvname
  • If you are using system installed conda, please DO NOT use conda activate to activate your environment Install yourpackage in the conda env
conda install yourpackage
  • Or if you have python (comes with pip) installed
pip install yourpackage
  • Or follow the instruction on package website. Check what's installed in your conda environment:
conda list
  • When you are done, deactivate the environment:
conda deactivate

Additional Information for Jupyter Users: Run conda env as a kernel in Jupyter

  • If you would like to use JupyterNotebook or JupyterLab from OnDemand, you can follow the instructions below and run your conda env as a kernel in Jupyter.
  • Make sure with python 3.7+ and make sure you load cluster's anaconda module (this only works with py3.7+)
  • Activate your conda env from terminal. Install ipykernel with:
pip install ipykernel

Note

this assumes you installed python and pip in your env, otherwise, use "--user" flag

  • Add your env to jupyter with:
python -m ipykernel install --user --name=myenvname
  • Restart Jupyter from OnDemand