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
pythoncommand 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
- 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
bashshell is loaded. To permanently prevent the Anaconda enviroment from loading, one have to manually edit
==> For the changes to take effect, please close and reopen your current shell. <==
- According to the sugestion, we close the shell (Ctrl + D or
On the next usage:
- Open the
- 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.