🐍Conda Environments

Setting up Conda environments on the cluster is very similar to how you would do it on your local computer. It is highly recommended that you use Conda environments when running code the HPC.

To create a Conda environment and install packages, first log in to a frontend on SciClone with a terminal (i.e., ssh @bora.sciclone.em.edu). After you log in, copy these two lines into your terminal and hit enter.

source "/usr/local/anaconda3-2021.05/etc/profile.d/conda.csh"
module load anaconda3/2021.05

This will source and load the Anaconda module so it is ready for you to use.

Next, follow the standard steps for creating a Conda environment. Use the following line to create your environment and type y when prompted Proceed ([y]/n)?

conda create -n [ENVNAME]

(note some of the scikit learn examples assume your envname is "aml35" and you use python=3.5, i.e. conda create -n "aml35" python=3.5)

Next, activate your new environment by typing:

conda activate [ENVNAME]

To see a list of all the environments you've created, type:

conda info --envs

Once you've activated your environment, you can install any packages you need for a program using standard pip install commands. I.e.:

conda install pandas