Python

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Python is programing language that continues to grow in popularity for scientific computing. It is very fast to write code in, but the software that results is much much slower than C or Fortran; one should be wary of doing too much compute-intensive work in Python.

There is a dizzying amount of documentation available for programming in Python on the Python.org webpage; SciNet has given a mini-course of 8 lectures on Research Computing with Python in the Fall of 2013. An excellent set of material for teaching scientists to program in Python is also available at the Software Carpentry homepage.


Python on Niagara

We currently have three families of Python installed.

  • Anaconda
  • Intel Python
  • regular Python

Here we describe the differences between these packages.

Anaconda

Anaconda is a pre-assembled set of commonly-used self-consistent Python packages. The source for this collection is here. There are two types of Anaconda Python available:

  • The whole Anaconda software stack (the anacondaX/A.B.C modules).
  • Anaconda's Python, with all the Python packages, but without the rest of the Anaconda stack (gcc, bzip2, HDF5/NetCDF tools, etc) (the python/A.B.C-anacondaX.Y.Z modules).

As of 9 July 2018 the following Anaconda modules are available: 

   $ module avail anaconda
   ----------------- /scinet/niagara/software/2018a/modules/base ------------------
    anaconda2/5.1.0    python/2.7.14-anaconda5.1.0    r/3.4.3-anaconda5.1.0
    anaconda3/5.1.0    python/3.6.4-anaconda5.1.0

Note that none of these modules require a compiler to be loaded. Also, note the presence of the R module. Anaconda now also comes with R; this package is the R analogy to the Anaconda Python modules.

You load the module in the usual way: 

    $ module load anaconda3/5.1.0
    $ python
    >>>

Intel Python

The Intel Python modules are based on the Anaconda package. Intel has modified the package, and optimized the libraries to use the MKL libraries, which should make them faster than the Anaconda modules for some calculations.

As of 9 July 2018 the following Intel Python modules are available: 

   $ module avail intelpython
   ----------------- /scinet/niagara/software/2018a/modules/base ------------------
    intelpython2/2018.2    intelpython3/2018.2

Regular Python

The base Python program has also been installed from source. This installation comes with no Python packages installed other than virtualenv and pip. You can use this module, in concert with virtualenv and pip, to build your own virtual environment. 

    $ module avail python
    ----------------- /scinet/niagara/software/2018a/modules/base ------------------
    intelpython2/2018.2            python/2.7.14
    intelpython3/2018.2            python/3.6.4-anaconda5.1.0
    python/2.7.14-anaconda5.1.0    python/3.6.5               (D)

    $ module load python/3.6.5
    $ python
    >>>

Producing Matplotlib Figures on GPC Compute Nodes and in Job Scripts

The conventional way of producing figures from python using matplotlib i.e., 

   import matplotlib.pyplot as plt
   plt.plot(.....)
   plt.savefig(...)

will not work on the GPC compute nodes. The reason is that pyplot will try to open the figure in a window on the screen, but the compute nodes do not have screens or window managers. There is an easy workaround, however, that sets up a different 'backend' to matplotlib, one that does not try to open a window, as follows: 

   import matplotlib as mpl
   mpl.use('Agg')
   import matplotlib.pyplot as plt
   plt.plot(.....)
   plt.savefig(...)

It is essential that the mpl.use('Agg') command precedes the importing of pyplot.

Installing your own Python Modules

Python provides an easy way for users to install the libraries they need in their home directories rather than having them installed system-wide. There are so many optional packages for Python people could potentially want (see e.g. http://pypi.python.org/pypi), that we recommend users install these additional packages locally in their home directories. This is almost certainly the easiest way to deal with the wide range of packages, ensure they're up to date, and ensure that users' package choices don't conflict.

To install your own Python modules, follow the instructions below. Where the instructions say python2.X, type python2.6 or python2.7 depending on the version of python you are using.

  • First, create a directory in your home directory, ${HOME}/lib/python2.X/site-packages, where the packages will go.
  • Next, in your .bashrc, *after* you module load python and in the "GPC" section, add the following line:
export PYTHONPATH=${PYTHONPATH}:${HOME}/lib/python2.X/site-packages/
  • Re-load the modified .bashrc by typing source ~/.bashrc.
  • Now, if it's a standard python package and instructions say that you can use easy_intall to install it,
    • install with the following command. where packagename is the name of the package you are installing:
easy_install --prefix=${HOME} -O1 [packagename]
    • Continue doing this until all of the packages you need to install are successfully installed.
    • If, upon importing the new python package, you get error messages like undefined symbol: __stack_chk_guard, you may need to use the following command instead:
LDFLAGS=-fstack-protector easy_install --prefix=${HOME} -O1 [packagename]
  • If easy_install isn't an option for your package, and the installation instructions instead talk about downloading a file and using python setup.py install then instead:
    • Download the relevant files
    • You will probably have to uncompress and untar them: tar -xzvf packagename.tgz or tar -xjvf packagename.bz2.
    • cd into the newly created directory, and run
python setup.py install --prefix=${HOME}
  • Now, the install process may have added some .egg files or directories to your path. For each .egg directory, add that to your python path as well in your .bashrc, in the same place as you had updated PYTHONPATH before: eg,
export PYTHONPATH=${PYTHONPATH}:${HOME}/lib/python2.X/site-packages:${HOME}/lib/python2.X/site-packages/packagename1-x.y.z-yy2.X.egg:${HOME}/lib/python2.X/site-packages/packagename2-a.b.c-py2.X.egg
  • You should now be done! Now, re-source your .bashrc and test your new python modules.
  • In order to keep your .bashrc relatively uncluttered, and to avoid potential conflicts among software modules, we recommend that users create their own modules (for the "module" system, not specifically python modules).

Here is an example module for the Brian package, including instructions for the installation of the python Brian package itself.

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