Managing Environments with Conda

Conda is a package manager in Anaconda that allows you to create and manage multiple environments where you can pick and choose which packages you want to use. To use Conda you must load an Anaconda module:

$ module load anaconda

Many packages are pre-installed in the global environment. To see these packages:

$ conda list

To create your own custom environment:

$ conda create --name MyEnvName python=2.7 FirstPackageName SecondPackageName -y

The --name option specifies that the environment created will be named MyEnvName. You can include as many packages as you require separated by a space. Including the -y option lets you skip the prompt to install the package. By default environments are created and stored in the $HOME/.conda directory.

To create an environment at a custom location:

$ conda create --prefix=$HOME/MyEnvName python=2.7 PackageName -y

To see a list of your environments:

$ conda env list

To remove unwanted environments:

$ conda remove --name MyEnvName --all

To add packages to your environment:

$ conda install --name MyEnvName PackageNames

To remove a package from an environment:

$ conda remove --name MyEnvName PackageName

Installing packages when creating your environment, instead of one at a time, will help you avoid dependency issues.

To activate or deactivate an environment you have created:

$ source activate MyEnvName
$ source deactivate MyEnvName

If you created your conda environment at a custom location using --prefix option, then you can activate or deactivate it using the full path.

$ source activate $HOME/MyEnvName
$ source deactivate $HOME/MyEnvName

To use a custom environment inside a job you must load the module and activate the environment inside your job submission script. Add the following lines to your submission script:

$ module load anaconda
$ source activate MyEnvName

For more information about Python:


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