Infrastructure/software/python

Background

In mid-2018 at least, the Python programming language takes a central role in much data science and machine learning work. Comprehensive programming environments like SciKitLearn, PyTorch, or TensorFlow often make it possible to deploy advanced machine learning techniques with a few lines of ‘glue’ code in Python. The Python ecosystem is characterized by high degrees of evolution and fragmentation: The core language still develops, there are two mutually incompatible major versions still in common use, and even inbetween minor versions there have at times been incompatible changes. On top of this dynamically evolving core, there is a vast landscape of independently developed add-on modules, of which some are near-universally used (e.g. NumPy or MatPlotLib. For these reasons, maintaining a Python environment for NLPL that is to some degree standardized and parallel across the various instances of the virtual laboratory is no small challenge.

Basic Principles

NLPL standardizes on Python 3.x. In mid-2018, we use Python version 3.5 as the default starting point for NLPL-specific installations of add-on modules, on both Abel and Taito. The general philosophy is to emphasize (a) parallelism, (b) modularity, and (c) replicability. The NLPL software environment should behave the same across different systems on which the virtual laboratory is instantiated. Within reason, it should be possible to ‘mix and match’ modules from the NLPL software (and data) repository. Finally, a specific version of a module should not change (in a user-visible way) once installed and announced. From these principles, it follows that NLPL avoids module ‘bundling’ to the largest possible degree; individual add-on components are provisioned as separate modules, each with its own version history.

Typically, users may not care deeply about specific module versions and just ask for the (current) default version. However, as newer versions are installed, what is the default version will change over time. Preserving older modules unchanged (rather than revising incrementally) means that users are offered full control to select (combinations of) specific module versions. With great power comes great responsibility.

Mixing and Matching

The ‘right’ way of balancing modularity vs. user convenience remains yet to be determined. In mid-2018, for example, the Keras abstraction layer is tightly coupled to TensorFlow; hence, Keras is not currently isolated as a separate module. Likewise, there are some add-on modules that are tightly coupled to the core language, almost to the point of forming an ‘extended standard library’; NumPy is a prime example in this category. Middle-ground candidates for modularization, arguably, are SciKitLearn and what is at times called the SciPy ecosystem, which (besides NumPy) bundles, among others, MatPlotLib, IPython, and Pandas. The NLPL infrastructure task force will be grateful for feedback on how to best cut this pie!

module use -a /proj*/nlpl/software/modulefilkes

module load nlpl-nltk nlpl-gensim nlpl-tensorflow

Random Ideas

In principle, one could reduce most of the virtual environments to just the wheels that they provide, i.e. remove everything else from the standard virtual environment creation, including the binaries. As the wheels are organized in a directory hierarchy relative to each Python minor version, this should make it possible to install the code for add-on components (like MatPlotLib, GenSim, or NLTK) for multiple Python versions into the same module.

As the NLPL collection of modules grows, it may well be helpful to define common ‘environment’ modules, e.g. a combination of individual components (in specific versions) that are often used in conjunction and are known to be mutually interoperable.

Packaging Ideas

Component	102018	122018	022019
NumPy	1.14.6
SciPy Library	1.1. 0
MatPlotLib	3.3.0
IPython	7.0.1
Pandas	0.23.4