Python on Pelle¶
Welcome to the UPPMAX Python user guide for Pelle cluster.
Here we, as a start, present Pelle specific topics that are different from Bianca and Rackham
We describe that there are multiple Python versions.
Then, we show how to load Python and to deal with Python packages and how to include more Python packages by loading Python bundles.
Info
General things can be found on the general Python page.
- Running Python
- Use Python to run a Python script
- Use Python in an interactive session
- Programming in Python
- UPPMAX Python-related courses
- Installing Python packages
Python versions¶
Python (or to be precise: the Python interpreter) has different versions. The current major version of Python is Python 3. Python 3 is not backwards compatible with Python 2. This means that you need to use the correct Python version to run a Python script.
Which version of Python is python?
To determine which version python is, in a terminal, type:
to see which Python version you are using now.
Which version of Python is python3?
To determine which version python3 is, in a terminal, type:
to see which Python version you are using now.
Loading Python¶
The different versions of Python are available via the module system on all UPPMAX clusters. Loading a Python module also makes some Python packages available.
Forgot what the module system is?
UPPMAX modules or Python modules?
At this page, we will use the word 'modules' for UPPMAX modules and 'packages' for Python modules, to be clear in what is meant. The word 'package' is used in multiple other languages, such as R, with a similar definition as a Python module.
To find out which Python modules there are, use module spider python.
What is the output of that command?
The output of module spider python on the day of writing, is:
[user@pelle ~]$ module spider python
---------------------------------------------------------------------------------------------------------------------------------------
Python:
---------------------------------------------------------------------------------------------------------------------------------------
Description:
Python is a programming language that lets you work more quickly and integrate your systems more effectively.
Versions:
Python/2.7.15-fosscuda-2018b
Python/2.7.18-GCCcore-10.2.0
Python/2.7.18-GCCcore-13.3.0
Python/3.7.4-GCCcore-8.3.0
Python/3.8.6-GCCcore-10.2.0
Python/3.9.6-GCCcore-11.2.0-bare
Python/3.9.6-GCCcore-11.2.0
Python/3.10.4-GCCcore-11.3.0-bare
Python/3.10.4-GCCcore-11.3.0
Python/3.11.3-GCCcore-12.3.0
Python/3.11.3-GCCcore-13.3.0
Python/3.11.5-GCCcore-13.2.0
Python/3.11.5-GCCcore-13.3.0
Python/3.12.3-GCCcore-13.3.0
Python/3.13.1-GCCcore-14.2.0
Other possible modules matches:
Biopython IPython Python-bundle-PyPI
---------------------------------------------------------------------------------------
To find other possible module matches execute:
$ module -r spider '.*python.*'
-------------------------------------------------------------------------------------------------------------------------
For detailed information about a specific "Python" package (including how to load the modules) use the module's full name.
Note that names that have a trailing (E) are extensions provided by other modules.
For example:
$ module spider Python/3.13.1-GCCcore-14.2.0
-------------------------------------------------------------------------------------------------------------------------
To load a specific version of Python into your environment,
type module load python/[version],
where [version] is a Python version,
for example, module load Python/3.11.5-GCCcore-13.2.0
Do I really need to load a Python module?
It is recommended to load a Python module, but in some case you will not get into trouble.
When you do not load a module, the system-installed Python version are used.
These is python version 3.9.21.
If using those older versions give you no trouble, all is well, for example, when running basic Python scripts that have no package imports.
However, when any problem occurs, load those newer modules.
After loading a Python module, one can start the Python interpreter:
How does this look like?
After loading Python/3.13.1-GCCcore-14.2.0 and starting the Python interpreter with python it looks like this:
Warning
The sections below needs updates
Python packages¶
Terminology
A Python package consists out of one or more Python modules. In this document, we avoid using this term, to avoid confusion with the UPPMAX modules.
Many scientific tools are distributed as Python packages,
which allows any user to run complex tools from a terminal or script.
For example, the following Python code imports the functionality
of the pandas library:
Some packages/tools are preinstalled on all UPPMAX clusters. To load such a package:
- determine if it comes with your Python version
- determine if it comes as a module
Determine if a Python package comes with your Python module¶
To determine if a Python package comes with your Python module, there are multiple ways:
- Using
pip list - Using the module help
- Importing the package
Using pip list¶
To determine if a Python package comes with your Python module,
pip list is one of the ways to do so.
On a terminal, type:
This shows a list of Python packages that are installed.
How does the output of pip list look like?
Here is an example:
Using the module help¶
Determine if a Python package comes with your Python module using the module help, in a terminal, type:
where [module_version] is a version of a Python module,
for example:
What is the output of module help Python/3.13.1-GCCcore-14.2.0?
--------------------------------- Module Specific Help for "Python/3.13.1-GCCcore-14.2.0" ----------------------------------
Description
===========
Python is a programming language that lets you work more quickly and integrate your systems
more effectively.
More information
================
- Homepage: https://python.org/
Included extensions
===================
flit_core-3.10.1, packaging-24.2, pip-24.3.1, setuptools-75.6.0,
setuptools_scm-8.1.0, tomli-2.2.1, typing_extensions-4.12.2, wheel-0.45.1
Warning
- Note that the ordinary Python module contains much fewer packages than the ones on Bianca, Rackham and Snowy
- It does though contain the so called "base", including packages like
sysandmath.
Importing the package¶
Importing a Python package is a way to determine if a Python package comes with your Python module installed. From the terminal do:
What does that -c do?
python -c will run the text after it as Python code.
In this way, you can directly run code, i.e.
you do not need to create a file to run.
where [your_package] is the name of a Python package,
for example:
What is the output if the Python package is found?
The output if the Python package is found is nothing.
What is the output if the Python package is not found?
Here an absent package is loaded, with the nonsense name absentpackage:
This results in the following error:
Stand-alone tools¶
Some Python packages are working as stand-alone tools, for instance in
bioinformatics. The tool may be already installed as a module. Check if it is
there by using the module system spider function:
where [tool_name] is (part of) the name of the tool. module spider
is case-insensitive, hence YourTool and yourtool give similar results.
system](../cluster_guides/modules.md)
Load Python bundle modules¶
- We have so-called Bundle modules containing python packages.
- To get a python package that is not available in the base installation, try to load a Python bundle.
- If you for instance need
numpy,pandasand matplotlib, do:
- For more bundles, see Python_bundles on Pelle.
General things¶
General things can be found on the general Python page.
- Running Python
- Use Python to run a Python script
- Use Python in an interactive session
- Programming in Python
- UPPMAX Python-related courses
- Installing Python packages