Better Scientific Software

a tutorial presented at

Improving Scientific Software

on 9:00 am - 11:20 am MDT (UTC-6), 1:20 pm - 3:40 pm MDT (UTC-6) Thursday 07 April 2022

Presenters: David E. Bernholdt (Oak Ridge National Laboratory), Rinku K. Gupta (Argonne National Laboratory), Patricia A. Grubel (Los Alamos National Laboratory), and David M. Rogers (Oak Ridge National Laboratory)

Helpers: Anshu Dubey (Argonne National Laboratory) and Gregory R. Watson (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.


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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 tutorial distills experience from members of the IDEAS Productivity project and the creators of the BSSw.io community website drawn from many scientific software projects over many years. 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.


Learning Objectives

Participants should be able to…


Agenda

This tutorial comprises two conference sessions. The first session, 9:00am-11:20am MDT, will be a series of presentations. The second session, 1:20pm-3:40pm MDT, will be more open-ended, depending on the interests of the participants. There will be opportunities to:

We will use Zoom breakout rooms to be able to accommodate multiple interests in so far as we can staff them.

Time (MDT)ModuleTitlePresenter
9:00 AM0Introduction and SetupDavid E. Bernholdt (ORNL)
9:05 AM1Motivation and Overview of Best Practices in HPC Software DevelopmentRinku K. Gupta (ANL)
9:15 AM2Agile MethodologiesPatricia A. Grubel (LANL)
9:45 AM3Git WorkflowsPatricia A. Grubel (LANL)
10:00 AMBreak
10:20 AM4Software Testing IntroductionRinku K. Gupta (ANL)
10:40 AM5Scientific Software DesignDavid E. Bernholdt (ORNL)
11:00 AM6Testing Complex SoftwareRinku K. Gupta (ANL)
11:15 AMQ&A
11:20 AMAdjourn morning session
11:20 AMOther conference activities
1:20 PM7Refactoring Scientific SoftwareDavid M. Rogers (ORNL)
1:45 PM8Improving Reproducibility Through Better Software PracticesDavid M. Rogers (ORNL)
2:00 PM9SummaryDavid M. Rogers (ORNL)
2:05 PMHands-on & Discussion (optional)
2:20 PMBreak
2:40 PMHands-on & Discussion (optional)
3:40 PMAdjourn

Presentation Slides

The latest version of the slides will always be available at https://doi.org/10.6084/m9.figshare.19416767.

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


How to Participate


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: bssw-tutorial/hello-numerical-world-2022-04-07-iss.

Note: most of the screenshots will refer to the generic “hello-numerical-world” repository rather than the one specifically for this event.

List of Hands-On Exercises

Note that not every presentation module has exercises (yet).

There are also activities associated with a couple of modules that we didn’t have time to cover in this tutorial. You are welcome to try them out too.


Stay in Touch


Resources from Presentations

Links from the tutorial presentations are listed here for convenience


Requested Citation

The requested citation the overall tutorial is:

David E. Bernholdt, Rinku K. Gupta, Patricia A. Grubel, and David M. Rogers, Better Scientific Software tutorial, in Improving Scientific Software, online, 2022. DOI: 10.6084/m9.figshare.19416767.

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.