From Montana Tech High Performance Computing
Revision as of 11:40, 18 September 2020 by Bdeng
The default Python installed is 2.7.5 and 3.4.10, compiled by GCC 4.8.5.
We also have Miniconda3 and Anaconda3 installed so that you can create your own Python development environments. The difference between Miniconda and Anaconda is that Anaconda has a lot more numeric and scientific libraries installed by default.
Loading the anaconda module
Once logged into HPC, you can use the module command to load the anaconda module.
module load anaconda
module load miniconda
Please note that you can only use one of the "conda" modules at a time. If you have anaonda loaded, but need to switch to miniconda, you will first need to unload the anaconda module:
module unload anaconda
module load miniconda
Creating Anaconda or Miniconda Python environment
You can use the
conda create command to create a new Python environment.
For example, to create a Python environment named mypy38 with Python 3.8:
conda create --name mypy38 python=3.8
You'll then be provided with the location of the environment being created and the packages will be installed. Then type y to confirm the installation.
By default, this will create the environment in your home directory at
~/.conda/env/. If you would like to save it to another location, you can use the
conda create -p /PATH/mypy38 python=3.8
Please note, after the creation, you may be told to use "conda activate mypy38" to activate the environment. If you use the command, you'll then be told to do "conda init". You probably don't want to do that, as it'll alter your basrc file and load one of the conda version by default.
Using a Python Environment in miniconda or anaconda
To get a list of available conda environment, you can use the command:
conda env list. You will get a list of the available Python environment.
# conda environments:
base * /opt/ohpc/pub/apps/anaconda3
Activating a Python environment
To use the mypy38 environment, use the command:
source activate mypy38
You'll then notice the environment name prepended to the command prompt, for example:
(mypy38) [username@oredigger ~]$
Now you can check your python version:
(mypy38) [username@oredigger ~]$ python -V
Installing new Python packages
Once your Python environment is activated, you can install additional packages for your project.
For example, to install the
scipy package, use the command:
(mypy38) [username@oredigger ~]$ conda install scipy
For some packages, you may need to specify the channel using the
-c option. Refer to the documentations of the package you'll need.
To get a list of conda packages installed, use:
(mypy38) [username@oredigger ~]$ conda list
Deactivating a Python environment
When you finished with your environment or you need to switch to a different environment. You can deactivate the current environment with:
(mypy38) [username@oredigger ~]$ conda deactivate
You'll see the environment name removed from the command prompt:
Additional conda commands
To remove a conda environment:
conda env remove --name environment_name
(if environment not in default path, use:
conda env remove -p /PATH/environment_name)
To export a conda environment, first activate the environment, then use:
conda env export > environment.yml
This will export a list of your environment's packages to the file environment.yml