Better Scientific Software

a tutorial presented at

Improving Scientific Software

on 1:00 pm - 4:00 pm MDT Thursday 25 March 2021

Presenters: David E. Bernholdt (Oak Ridge National Laboratory), Anshu Dubey (Argonne National Laboratory), Rinku K. Gupta (Argonne National Laboratory), and David M. Rogers (Oak Ridge National Laboratory)

This page provides detailed information specific to the tutorial event above. Expect updates to this page up to, and perhaps shortly after, the date of the tutorial. Pages for other tutorial events can be accessed from the main page of this site.

Quick Links

Description

Producing scientific software is a challenge. The high-performance modeling and simulation community, in particular, is dealing with the confluence of disruptive changes in computing architectures and new opportunities (and demands) for greatly improved simulation capabilities, especially through coupling physics and scales. At the same time, computational science and engineering (CSE), as well as other areas of science, are experiencing increasing focus on scientific reproducibility and software quality.

Computer architecture changes require new software design and implementation strategies, including significant refactoring of existing code. Reproducibility demands require more rigor across the entire software endeavor. Code coupling requires aggregate team interactions including integration of software processes and practices. These challenges demand large investments in scientific software development and improved practices. Focusing on improved developer productivity and software sustainability is both urgent and essential.

This half-day tutorial distills multi-project and multi-years experience from members of the IDEAS Productivity project and the creators of the BSSw.io community website. The tutorial will provide information about software practices, processes, and tools explicitly tailored for CSE. Topics to be covered include: Agile methodologies and tools, software design and refactoring, testing and continuous integration, Git workflows for teams, and reproducibility. Material will be mostly at the beginner and intermediate levels. There will also be opportunities to discuss topics raised by the audience.

Agenda

Time (MDT)	Module	Topic	Speaker
1:00pm-1:05pm	00	Introduction	David E. Bernholdt, ORNL
1:05pm-1:15pm	01	Motivation and Overview of Best Practices in HPC Software Development	David E. Bernholdt, ORNL
1:15pm-1:45pm	02	Agile Methodologies	Rinku Gupta, ANL
1:45pm-2:00pm	03	Git Workflows	Rinku Gupta, ANL
2:00pm-2:20pm	04	Software Testing 1	David Rogers, ORNL
2:20pm-2:40pm		Break (optional Q&A)
2:40pm-3:00pm	05	Software Design	Anshu Dubey, ANL
3:00pm-3:15pm	06	Software Testing 2	David Rogers, ORNL
3:15pm-3:40pm	07	Refactoring	Anshu Dubey, ANL
3:40pm-3:55pm	08	Reproducibility	David E. Bernholdt, ORNL
3:55pm-4:00pm	09	Summary	David E. Bernholdt, ORNL

Presentation Slides

The latest version of the slides will always be available at https://doi.org/10.6084/m9.figshare.14256257.

Note that these files may include additional slides that will not be discussed during the tutorial, but questions are welcome.

Version History:
- v2: Corrects a small misstatement about doing demos during breaks in the tutorial
- v1: Provided to ISS organizers

How to Participate

Please use the Sli.do chat to ask questions at any time. We will respond in Sli.do or verbally as opportunities permit.
The schedule includes a break in the middle. We plan to be available for additional Q&A at that time.

Hands-On Exercises

Introduction

The hands-on exercises for this tutorial are based around a simple numerical model using the one-dimensional heat equation. The example is described briefly in the repository’s README file, and in greater detail in the ATPESC Hands-On lesson. The ATPESC version focuses on the numerical aspects of the model. But for this tutorial, we’re focused on how to make the software better from a quality perspective, so you don’t need to understand the math to do these exercises.

For the purposes of these hands-on exercises, you should imagine you’ve inherited an early version of the hello-numerical-world software from a colleague who’s left the project, and you’ve been assigned to get it into better shape so that it can be used in the next ATPESC summer school.

The repository you’ll be working with is on GitHub: bssw-tutorial/hello-numerical-world-2021-03-iss. Note: most of the screenshots will refer to the generic “hello-numerical-world” repository rather than the one specifically for this tutorial.

List of Hands-On Exercises

Note that the exercise numbers align with the presentation modules. Not every module has exercises (yet).

Exercise 0: Setting up the Prerequisites. Setup the accounts needed for these exercises.
Exercise 2: Agile Methodologies. You’ll use GitHub issues and project boards to setup a simple “personal kanban” board.
Exercise 3: Git Workflows. You’ll fork our hello-numerical-world repository, create a feature branch, and make a pull request
Exercise 7a: Agile Redux. You’ll create epic, story, and task issues for the refactoring task and track them on a kanban board
Exercise 7b: Refactoring Part 1. You’ll perform a small, well-defined refactoring exercise
Exercise 7c: Refactoring Part 2. You’ll perform a a more open-ended refactoring exercise
Additional Exercise: Continuous Integration. You’ll establish a simple continuous integration workflow and then refine it, adding code coverage assessment

Stay in Touch

After the tutorial please feel free to email questions or feedback to the BSSw tutorial team at bssw-tutorial@lists.mcs.anl.gov.
If you want to do the hands-on exercises, we’re happy to provide feedback on your pull requests and issues, even after the end of the tutorial.
To find out about future events organized by the IDEAS Productivity Project, you can subscribe to our mailing list (usually ~2 messages/month).
For monthly updates on the Better Scientific Software site, subscribe to our monthly digest.

Resources from Presentations

These are the links included in the tutorial presentations, included here for easier access

Module 0: Introduction
Module 1: Motivation and Overview of Best Practices in HPC Software Development
- none
Module 2: Agile Methodologies
Module 3: Git Workflows
- Atlassian/BitBucket (Comparing Workflows)
- Git Flow (Driessen’s Original Blog)
  - Git extensions
- GitHub Flow (previously linked to ~~scottchacon.com/2011/08/31/github-flow.html~~)
- GitLab Flow (previously linked to ~~docs.gitlab.com/ee/topics/gitlab_flow.html~~)
Module 4: Software Testing 1
- Python Build and Test Framework: pyscaffold.org
- Build-Link-Test CMake Framework: llnl-blt.readthedocs.io
- Static Source Analysis (C++): clang-tidy
- Static Source Analysis (python): flake8 and pylint (updated 2022-03-31 due to dead link)
- Code Coverage Webservices: codecov and coveralls
- Tutorials for code coverage: Online Tutorial, Another example
- Development Practices Survey Article
Module 5: Software Design
- Related Article
Module 6: Software Testing 2
- Useful resources on testing (formerly linked to ~~ideas-productivity.org/resources/howtos/~~)
- Related Articles: 1, 2
Module 7: Refactoring
Module 8: Reproducibility
Module 9: Summary
Additional Module: Continuous Integration

Requested Citation

The requested citation the overall tutorial is:

David E. Bernholdt, Anshu Dubey, Rinku K. Gupta, and David M. Rogers, Better Scientific Software tutorial, in Improving Scientific Software, online, 2021. DOI: 10.6084/m9.figshare.14256257.

Individual modules may be cited as Speaker, Module Title, in Better Scientific Software tutorial…

Acknowledgements

This tutorial is produced by the IDEAS Productivity project.

This work was supported by the U.S. Department of Energy Office of Science, Office of Advanced Scientific Computing Research (ASCR), and by the Exascale Computing Project (17-SC-20-SC), a collaborative effort of the U.S. Department of Energy Office of Science and the National Nuclear Security Administration.