Installing software packages locally with Anaconda

Audience: Faculty, Postdocs, Researchers, Staff and Students

This KB Article References: High Performance Computing
This Information is Intended for: Faculty, Postdocs, Researchers, Staff, Students
Last Updated: June 28, 2018

When HPC users have need of software that is not currently installed on SeaWulf, there are two basic approaches that can be taken to get the programs installed:

1. You are welcome to submit a ticket and ask the HPC support staff to install the software package.  This may be preferable if the program is widely used and likely to be of interest to multiple users.  

2.  Alternatively, you may install the program locally in your home or project directory.  The easiest way to install many software packages is by using the Anaconda package manager.  First load the appropriate module (either Anaconda2 or Anaconda3, depending on which version of Python is desired):

module load anaconda/2

In order to ensure that there is no conflict between the software you'd like to install and existing programs (e.g., dependency version conflicts), it's best to create a custom Anaconda environment.  This can be accomplished using the following command:

conda create --name my_env

This will create a custom environment entitled "my_env".  By default (i.e., if you don't specify a directory using the "--path" argument in the above command), custom environments will be placed at

/gpfs/home/NETID/.conda/envs/

If you prefer to create the environement in a specific directory, you may use the following command. 

conda create --prefix /path/to/my/env/ 

Once you've created a custom environment, you need to "activate: it with the following:

source activate my_env

By doing this, the environmental variables  associated with your custom Anaconda environment (including the path to executable files) will become active.  

From here, you may install packages using the "conda install" command.  For example, if you would like to install the "scipy" package, type the following:

conda install scipy

After the package has been installed, any associated executable files will be placed within a bin folder in your environment directory (this is automatically added to your path):

.../my_env/bin/

Likewise, the directory system for any libraries installed with conda can be found at:

.../my_env/lib/

Once you're done installing and using your Anaconda packages, you may return to the default environment by typing:

source deactivate

To read more about installing and managing environments with Anaconda, please see the conda documentation.  

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