experi 0.3.4

An interface for managing computational experiments with many independent variables.

Experi

A framework for running command line applications with a range of different variables.

Documentation is available on Read the Docs

How to use

Actually running experi is a simple process, in a directory with an experiment.yml file run the command

$ experi

If for whatever reason you want to name the file something other than experiment.yml or to run a file in a different directory a custom file can be specified with the -f flag

$ experi -f not_an_experiment.yml

Note that since this is designed to keep the specification of the experiment with the results, the commands will be run in the same directory as the specified file.

The complicated part of getting everything running is the specification of the experiment in the experiment.yml file. The details on configuring this file is available in the documentation.

Why should I use this?

When running a series of experiments it can be difficult to remember the exact parameters of the experiment, or even how to run the simulation again. Additionally for a complex experiment with many variables, iterating through all the combinations of variables can be unwieldy, error prone, and plain frustrating.

Experi aims to keep all the information about running an experiment in an experiment.yml file which sits in the same directory as the experiment. Supporting complex iteration of variables incorporated into easily the easily readable yaml syntax, it is easy to quickly understand the experimental conditions. Additionally by keeping the configuration file with the results there is a quick reference to the experimental conditions and replication is as simple as running experi.

For more information I have written a blog post which goes into more depth on how this tool has helped my workflow.

Project Goals

The primary goals of this project detailed below. They act as the guiding principles for the design decisions which are made.

• Human centric

  • Interactions should be simple, intuitive, and frictionless
  • Shouldn't need to constantly consult documentation to use
  • Minimal expertise required to understand

• Sensible Defaults

  • Testing a job on a scheduler should be simple, requiring a minimal specification

• Fast Errors

  • Errors in the code should be picked up as soon as possible, i.e. shouldn't arise after waiting in the job queue.
  • Allow for testing locally using the shell, before running on HPC

Where current functionality doesn't meet these goals please raise an issue, I am more than happy to discuss. Although do note that these goals are somewhat opinionated.

What about ...?

• Sumatra is a tool for managing and tracking projects, with a focus on running a single experiment at a time and the reproducibility of the results. Experi is more about running many simulations with a range of parameters, the reproducibility aspect is a byproduct of the way these parameters are specified. Also Sumatra does a much better job of the reproducibility than experi, capturing version numbers and executable paths.

• SciPipe is a workflow manager similar to SciLuigi, Airflow or any number of other examples. These tools can be incredibly powerful, specifying complex networks of dependent tasks and managing their completion. However, they have a learning curve and can be difficult to configure with a task scheduler on a HPC. Experi is about simplicity; taking the workflow you already use and making it more powerful. Experi also uses the task scheduler for the management of dependent jobs, albeit the functionality is currently very basic.

• Snakemake is a workflow management tool, very similar to GNU Make which supports submitting jobs to a HPC scheduler. I personally have no experience using it, however from reading the documentation it is a highly configurable tool with far more functionality than Experi. Experi is more suitable is the handling of complex specification of variables and using the scheduler for control of scheduling.

Installation

Experi is currently compatible with python>==3.6

pip3 install experi

Note that for the command experi to work the directory containing the executable needs to be in the PATH variable. In most cases this will probably be $HOME/.local/bin although this is installation dependent. If you don't know where the executable is, on *nix systems the command

find $HOME -name experi

will search everywhere in your home directory to find it. Alternatively replacing $HOME with / will search everywhere.

For installation from source

git clone https://github.com/malramsay64/experi.git
cd experi
pip3 install .

To install a development version, pipenv is required which can be installed by running

pip3 install pipenv

and installing the dependencies by running

pipenv install --dev --three

which will create a virtual environment for the project. Activating the virtualenv is can be done by running

pipenv shell

which creates a new shell with the environment activated. Alternatively a single command (like the test cases) can be run using

pipenv run pytest

For those of you trying to run this on a cluster with only user privileges including the --user flag will resolve issues with pip requiring elevated permissions installing to your home directory rather than for everyone.

pip3 install --user experi

For more information documentation is available on Read the Docs.