Python user guide

Welcome to the UPPMAX Python user guide.

We describe what Python is and that there are multiple Python versions.

Then, we show how to load Python and to load Python packages after which you can run Python.

Finally, you can find UPPMAX Python-related courses and these more advanced topics:

• Programming in Python
• Installing Python packages
• Virtual environments in Python
• How to run parallel jobs in Python

What is Python?

Python is a high-level, general-purpose programming language. Its design philosophy emphasizes code readability with the use of significant indentation [Kuhlman, 2009].

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.

Could you give me an example of a difference between Python 2 and 3?

One example is how Python 2 and Python 3 dividetwo integers. Here is an example that will work on all UPMMAX clusters.

Load Python 2.7.15:

module load python/2.7.15

Then

python -c "print(1/2)"

will print 0, as this is an integer division: two fits zero times in one.

Load Python 3.11.4:

module load python/3.11.4

Then

python -c "print(1/2)"

will print 0.5, as this is turned into a floating point division, equivalent to 1.0 / 2.0.

Which version of Python is python?

To determine which version python is, in a terminal, type:

python --version

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:

python3 --version

to see which Python version you are using now.

Loading Python

Prefer seeing a video?

A video that shows how to load the Python module can be found here.

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?

See the UPPMAX pages on the module system here.

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@rackham1 ~]$ module spider python

---------------------------------------------------------------------------------------
  python:
---------------------------------------------------------------------------------------
     Versions:
        python/2.7.6
        python/2.7.9
        python/2.7.11
        python/2.7.15
        python/3.3
        python/3.3.1
        python/3.4.3
        python/3.5.0
        python/3.6.0
        python/3.6.8
        python/3.7.2
        python/3.8.7
        python/3.9.5
        python/3.10.8
        python/3.11.4
     Other possible modules matches:
        Biopython  Boost.Python  GitPython  IPython  Python  biopython  flatbuffers-python
 ...

---------------------------------------------------------------------------------------
  To find other possible module matches execute:

      $ module -r spider '.*python.*'

---------------------------------------------------------------------------------------
  For detailed information about a specific "python" package (including how to load the mod
ules) 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/3.11.4
---------------------------------------------------------------------------------------

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/3.11.4

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 are python version 2.7.5, and python3 version 3.6.8.

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.

Why are there both python/3.X.Y and python3/3.X.Y modules?

Sometimes existing software might use python2 and there’s nothing you can do about that.

In pipelines and other toolchains the different tools may together require both python2 and python3.

How to deal with tools that require both python2 and python3?

You can run two python modules at the same time if one of the modules is python/2.X.Y and the other module is python3/3.X.Y (i.e. not python/3.X.Y).

Loading Python package modules

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.

For more complex complex Python packages, there exist UPPMAX modules to load these:

• python_GIS_packages: for geographic information system packages
• python_ML_packages: for machine learning Python packages

How could I find these modules myself?

Use:

module spider packages

Loading 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:

import pandas

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:

pip list

This shows a list of Python packages that are installed.

How does the output of pip list look like?

Here is an example:

Package                   Version
------------------------- ---------------
anndata                   0.10.5.post1
anyio                     4.2.0
appdirs                   1.4.4
argon2-cffi               23.1.0
argon2-cffi-bindings      21.2.0
[more Python packages]
Werkzeug                  3.0.1
wheel                     0.42.0
widgetsnbextension        4.0.9
zipp                      3.17.0
zope.interface            6.1

Using the module help

Determine if a Python package comes with your Python module using the module help, in a terminal, type:

module help python/[module_version]

where [module_version] is a version of a Python module, for example:

module help python/3.11.4

What is the output of module help python/3.11.4?

Here is part of the output of module help python/3.11.4:

------------------------ Module Specific Help for "python/3.11.4" -------------------------
    Python - use Python

    Version 3.11.4


This module provides the executable names 'python' and 'python3'.

Several additional python packages are also installed in this module. The complete list of
packages in this module, produced using 'pip list', is:

Package                   Version
------------------------- -----------
anndata                   0.9.2
anyio                     3.7.1
argon2-cffi               21.3.0
...
widgetsnbextension        4.0.8
zipp                      3.16.2
zope.interface            6.0

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:

python -c "import [your_package]"

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:

python -c "import pandas"

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:

python -c "import absentpackage"

This results in the following error:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'absentpackage'

Determine if a Python package comes with a module

If the Python package is not pre-installed with your version of Python, use the UPPMAX module system to search for it.

Not all packages are easy to find, as some are part of super-packages, for example the TensorFlow Python libraries, which are part of the python_ML_packages/[version]-{cpu,gpu}, for example python_ML_packages/3.11.8-cpu.

Want to see a list of Python packages in python_ML_packages/3.11.8-cpu that are not in python/3.11.8?

Here you go:

• absl-py
• array-record
• astunparse
• cachetools
• cons
• dill
• dm-tree
• ducc0
• etils
• etuples
• flatbuffers
• gast
• google-auth
• google-auth-oauthlib
• google-pasta
• googleapis-common-protos
• grpcio
• imbalanced-learn
• importlib_resources
• keras
• libclang
• llvmlite
• logical-unification
• miniKanren
• ml-dtypes
• multipledispatch
• nlp
• numba
• oauthlib
• opt-einsum
• patsy
• promise
• protobuf
• pyasn1
• pyasn1-modules
• pytensor
• requests-oauthlib
• rsa
• scikit-learn
• seaborn
• statsmodels
• tensorboard
• tensorboard-data-server
• tensorflow-cpu
• tensorflow-datasets
• tensorflow-estimator
• tensorflow-io-gcs-filesyst
• tensorflow-metadata
• tensorflow-probability
• termcolor
• threadpoolctl
• toml
• torch
• torchaudio
• torchvision
• wrapt
• xxhash

It may not always be easy to find your Python package within the many modules. Do not hesitate to contact support so that you can spend time on your research and we figure this out :-)

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:

module spider [tool_name]

where [tool_name] is (part of) the name of the tool. module spider is case-insensitive, hence YourTool and yourtool give similar results.

What are UPPMAX modules?

See the page about the UPPMAX module system here

Running Python

You can run Python in multiple ways:

• use Python to run a Python script
• use Python in an interactive session

To program in Python, there are more ways, which are discussed at the UPPMAX page on Python programming here

Use Python to run a Python script

You can run a Python script in the shell by:

python example_script.py

or, if you loaded a python3 module:

python3 example_script.py

Use Python in an interactive session

You start a python session by typing:

python

or

python3

The python prompt looks like this:

>>>

Exit with <Ctrl-D>, quit() or exit().

Programming in Python

To program in Python, there are more ways, which are discussed at the UPPMAX page on Python programming here

UPPMAX Python-related courses

See the UPPMAX workshops and courses to find UPPMAX courses related to Python.

Installing Python packages

How to install Python packages is described here.

Virtual environments in Python

How to use virtual environments in Python is described here.

How to run parallel jobs in Python

How to run parallel jobs in Python is described here.

References

• [Kuhlman, 2009] Kuhlman, Dave. A python book: Beginning python, advanced python, and python exercises. Lutz: Dave Kuhlman, 2009.

Links

• Official Python documentation
• Python forum
• Free online book: 'How to Think Like a Computer Scientist'
• UPPMAX TensorFlow guide
• UPPMAX PyTorch guide