Python

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.

Python on Niagara

We currently have two families of Python installed on Niagara.

• Regular Python
• Intel Python (a variant of anaconda)

Here we describe the differences between these packages.

Note that it is highly recommended that you use the NiaEnv/2019b stack by loading the corresponding module, ie.:

   module load NiaEnv/2019b

If you do not, you are using the 2018a stack whose python setup is less optimal.

Regular Python

Python versions 2.7 and 3.6 have been installed from source and are optimized for Niagara. We call these 'regular' python versions because they are not dependent on other distribution mechanisms like (ana)conda. Such distributions do not play well with the rest of the software stack, so the 'regular' python modules should be your first choice.

In the Niagara Software Stack version 2019b, i.e., NiaEnv/2019b, the specific versions are 2.7.15 and 3.6.8, so you can load python 2 or python 3 using

   module load python/2.7.15
   module load python/3.6.8

Both these installations come with the following optimized python packages preinstalled:

   virtualenv
   intel-numpy
   intel-scipy
   intel-scikit-learn
   ipp
   daal
   jinja2
   cython 
   matplotlib
   ipython
   numba
   numexpr
   pandas
   line_profiler
   memory_profiler
   funcsigs
   pycosat
   pyeditline
   pyOpenSSL
   PySocks
   PyYAML
   requests 
   xgboost

In this list, a intel-PACKAGE package provides an Intel-optimized version of PACKAGE, often using Intel's high performance Math Kernel Library. You use these package in python the same way you would non-optimized versions, i.e., import PACKAGE.

In the previous NiaEnv/2018a stack, the regular python versions did not have these packages, and users needed to install them in their own home directory. This was wasteful in terms of storage and has occasional led to quota issues, so we highly recommend using the NiaEnv/2019b packages.

Additional packages in these module should be installed in virtual environments.

Intel Python

The Intel Python modules are based on the Anaconda package, a python distribution that aims to simplify package management. 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. These modifications have also been incorporated in the intel-PACKAGES included in the regular python modules discussed above, but with Intel Python, you also get the conda command. You can load the python 2 version or the python 3 version of intel python with

   module load intelpython2
   module load intelpython3

Packages in this module can be installed in so-called conda environments (see below), although virtualenv also works.

A word of caution: conda environment are very wasteful when it comes to the number of files that they store in your home directory, and there is a good chance you will hit your quote of 250,000 files with only a few conda environments. And conda being a package manager on its own means that it does not always work well in combination with the rest of the software stack.

Miniconda and Anaconda

If your are looking for anaconda or miniconda, you should find that intelpython is a good substitute. In the NiaEnv/2019b stack, we no longer provide anaconda modules, but we do have aliases conda2 and conda3 for intelpython2 and intelpython3.

We advice against installing your own anaconda or miniconda in your home directory. Instead, start from one of the intelpython modules and use conda environments, or, even better, start from a regular python module and create a virtualenv in which you can install your own packages. Installing your own anaconda or miniconda would cause many more files to be installed in your $HOME directory, and this might cause trouble with the quota on the number of files.

Installing your own Python Modules

If you need to install your own Python modules, either in regular python or with conda, you should set up a virtual or conda environment. Visit the Installing your own Python Modules page for instructions on how to set this up.

We would urge you do remove any conda or virtual environments that you are not using, to help reduce the number of files on the $HOME file system.

Python virtual environments are documented on the Alliance wiki: https://docs.alliancecan.ca/wiki/Python#Creating_and_using_a_virtual_environment

That page covers the current modules and job examples for Trillium. For SciNet-specific access, see Trillium Quickstart.

Running serial Python jobs

As with all serial jobs, if your Python computation does not use multiple cores, you should bundle them up so the 40 cores of a node are all performing work. Examples of this can be found on this page.

Using a Jupyter Notebook

You may develop your Python scripts in a Jupyter Notebook on Niagara. A node has been set aside as a Jupyter Hub. See this page for details on how to access that node, and develop your code.

Producing Matplotlib Figures on Niagara 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 Niagara 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.

Using mpi4py

Several of the Python installations contain mpi4py preinstalled. However, using mpi4py requires loading an MPI module. There are several combinations of compiler/MPI/python modules which can be used.

Using intelpython

Using the either the NiaEnv/2019b or NiaEnv/2018a stack (the most-recent software stack is always recommended), the intelpython modules all have mpi4py, and should all work if an MPI module is also loaded. An example of this, using the NiaEnv/2019b stack, might be

   $ module load NiaEnv/2019b
   $ module load intel/2019u4 intelmpi/2019u4
   $ module load intelpython3/2019u4

Other combinations of compilers (intel/gcc) or MPI module (intelmpi/openmpi) will also work with intelpython.

Using anaconda

Under the NiaEnv/2018a stack anaconda is available as a module. This module does not come with mpi4py, but can be installed using the usual steps:

 $ module load gcc/7.3.0 openmpi/3.1.1
 $ module load anaconda3/2018.12
 $
 $ conda create -n myenv
 $ 
 $ source activate myenv
 (myenv) $ 
 (myenv) $ conda install mpi4py
 (myenv) $

Using the source Python module

The Python module compiled from source does not come with mpi4py. If you need to use this module you will need to install mpi4py in your own storage space, preferably in a virtual environment.

Error messages

If you get an error of this type:

    pml_ucx.c:285  Error: UCP worker does not support MPI_THREAD_MULTIPLE

Add the following lines to your Python script, BEFORE you import the mpi4py package:

   import mpi4py.rc
   mpi4py.rc.threads = False

SciNet's Python Classes

There is a dizzying amount of documentation available for programming in Python on the Python.org webpage. That begin said, each fall, SciNet runs two 4-week classes on using Python for research:

• SCMP142: Introduction to Programming with Python. This class is intended for those with little-to-no programming experience who wish to learn how to program.
• SCMP112: Introduction to Scientific Computing with Python. This class focusses on using Python to perform research computing.

An excellent set of material for teaching scientists to program in Python is also available at the Software Carpentry homepage.