PL

Anaconda

Configuration

The Anaconda module is available on the Topola and Okeanos supercomputers.

If it is required to use the Python libraries available in the Anaconda system, the user have to install them her/himself using the virtual environment. This can be done by following the instructions below.

Launch the interactive session.

For the first time, an additional configuration may be required.

Load the Anaconda module from the list of available modules.

To verify that the setup works fine, check the list of default libraries by typing conda list, the type the ca python command in the terminal.

$ conda list
$ python
Python 3.8.3 (default, July 2, 2020, 16:21:59)
[GCC 7.3.0] :: Anaconda, Inc. on Linux
Type "help", "copyright", "credits", or "license" for more information.

Log into the new shell bash -l
Create a virtual environment conda create --prefix $HOME/envs/my_env_name python=3
Activates the environment conda activate $HOME/envs/ my_env_name

An error like the one below may occur during the first time use:

CommandNotFoundError: Your shell is not properly configured to use the "conda Activate" function.
To initialize the shell, run

    $ conda init <SHELL_NAME>

Follow the suggestion and initialize the environment by typing conda init bash. The do command will add Anaconda's variables to the file ~/.bashrc; This file is automatically read when the bash shell is loaded. To permanently prevent the Anaconda enviroment from loading, one have to manually edit ~/.bashrc file.

==> For the changes to take effect, please close and reopen your current shell. <==

According to the sugestion, we close the shell (Ctrl + D or exit).

On the next usage:

Open the bash -l shell.
Activate the virtual environment conda activate $HOME/envs/my_env_name
Install the required libraries conda install --channel $URL $PACKAGE_NAME
The virtual environment is ready. After completing the work, it is enough to type conda deactivate. To return to work the user shall remember to activate the enviroment (point 1,2) - then the previously installed libriaries will become available.

Useful links: