Python

Python is a high-level, multi-paradigm programming language that is both easy to learn and useful in a wide variety of applications.  Python has a large standard library as well as a large number of third-party extensions, most of which are completely free and open source. 

Availability and Restrictions

Versions

Python is available on Pitzer and Owens Clusters. The versions currently available at OSC are:

Version Owens Pitzer Ascend Notes
2.7 X      
3.5  X      
3.6 X      
2.7-conda5.2 X X   Anaconda 5.2 with Python 2.7
3.6-conda5.2 X* X*   Anaconda 5.2 with Python 3.6

3.7-2019.10

X X   Anaconda 2019.10 with Python 3.7
3.9-2022.05 X X   Anaconda 2022.05 with Python 3.9
3.9     X*  
* Current default version; A = installed as an integrated package Anaconda 

You can use module spider python to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

Python is available for use by all OSC users.

Publisher/Vendor/Repository and License Type

Python Software Foundation, Open source

Usage

Usage on Owens

Set-up

To load the default version of Python module, use module load python . To select a particular software version, use module load python/version. For example, use module load python/3.5 to load the latest version of Python 3.5. After the module is loaded, you can run the interpreter by using the command python. To unload the latest version of Python 3.5 module, use the command module unload python/3.5

Installed Modules

We have installed a number of Python packages and tuned them for optimal performance on our systems.  When using the Anaconda distributions of python you can run conda list to view the installed packages.

NOTE:
  • Due to architecture differences between our supercomputers, we recommend NOT installing your own packages in  ~/.local. Instead, you should install them in some other directory and set $PYTHONPATH in your default environment. For more information about installing your own Python modules, please see our HOWTO.

Batch Usage

When you log into owens.osc.edu you are actually logged into a linux box referred to as the login node. To gain access to the mutiple processors in the computing environment, you must submit your job to the batch system for execution. Batch jobs can request mutiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info. 

Interactive Batch Session

For an interactive batch session one can run the following command:

 sinteractive -A <project-account> -N 2 -n 28 -t 01:00:00
which requests two nodes with 28 cores (-N 1 -n 28), for a walltime of 20 minutes (-t 00:20:00). You may adjust the numbers per your need.

Usage on Pitzer

Set-up

To load the default version of Python module, use module load python

Installed Modules

We have installed a number of Python packages and tuned them for optimal performance on our systems. When Python module is loaded, executing module help python will help you view the current list of packages available.

NOTE:
  • numpy and scipy have been compiled to use MKL for best performance
  • Due to architecture differences between our supercomputers, we recommend NOT installing your own packages in ~/.local. Instead, you should install them in some other directory and set $PYTHONPATH in your default environment. For more information about installing your own Python modules, please see our HOWTO.

Known Issues

Incorrect MPI launcher and compiler wrappers with Conda environments

Updated: March 2020
Versions Affected: Python 2.7, 3.6 & Conda 5.2
Users may encounter under-performing MPI jobs or failures of compiling MPI applications if you are using Conda from system. We found pre-installed mpich2 package in some Conda environments overrides default MPI path. The affected Conda packages are python/2.7-conda5.2 and python/3.6-conda5.2. If users experience these issues, please re-load MPI module, e.g. module load mvapich2 after setting up your Conda environment.

Further reading

Extensive documentation of the Python programming language and software downloads can be found at the Official Python Website.  

See Also

HOWTO: Install your own python modules

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