Better Scientific Software

a tutorial presented at

The International Conference for High-Performance Computing, Networking, Storage, and Analysis (SC21)

on 8:00 am - 5:00 pm CST Monday 15 November 2021

Presenters: David E. Bernholdt (Oak Ridge National Laboratory), Anshu Dubey (Argonne National Laboratory), Patricia A. Grubel (Los Alamos National Laboratory), Rinku K. Gupta (Argonne National Laboratory), and Gregory R. Watson (Oak Ridge National Laboratory)

Helper: 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.

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Description

Computational science and engineering (CSE) is in the midst of an extremely challenging period created by the confluence of disruptive changes in computing architectures, demand for greater scientific reproducibility, sustainability, and quality, and new opportunities for greatly improved simulation capabilities, especially through coupling physics and scales. These challenges demand increased investments in scientific software development and improved practices. Focusing on improved developer productivity and software sustainability is both urgent and essential. Key practices include code refactoring, flexible and extensible design, thoughtful testing, attention to reproducibility at all stages, and effective collaboration around code.

This tutorial presents software practices, processes, and tools explicitly tailored for CSE and HPC. Goals are improving the productivity of those who develop CSE software and increasing the sustainability of software artifacts. Topics include the software processes for (small) teams, including agile processes, collaboration via version control workflows, reproducibility, and scientific software design, refactoring, and testing.

Agenda

Time (CST)ModuleTitlePresenter
8:00 AM0Introduction and Setup David E. Bernholdt (ORNL)
8:10 AM1Motivation and Overview of Best Practices in HPC Software Development Patricia A. Grubel (LANL)
8:30 AM2Git Workflows Patricia A. Grubel (LANL)
9:00 AM3Agile Methodologies Rinku K. Gupta (ANL)
9:30 AM4Scientific Software Design David E. Bernholdt (ORNL)
10:00 AMBreak with optional discussion or hands-on activities
10:30 AM5Agile Methodologies Redux Rinku K. Gupta (ANL)
10:45 AM6Improving Reproducibility Through Better Software Practices David E. Bernholdt (ORNL)
11:30 AMHands-on & Discussion
12:00 PMLunch break with optional discussion or hands-on activities
1:00 PM7Software Testing Introduction Gregory R. Watson (ORNL)
1:30 PM8Continuous Integration Gregory R. Watson (ORNL)
1:55 PM9Testing Complex Software Anshu Dubey (ANL)
2:15 PM10Refactoring Scientific Software Anshu Dubey (ANL)
3:00 PMBreak with optional discussion or hands-on activities
3:30 PM11Summary David E. Bernholdt (ORNL)
3:45 PMHands-on & Discussion
5:00 PMAdjourn

Presentation Slides

The latest version of the slides will always be available at https://doi.org/10.6084/m9.figshare.16556628.

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

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-2021-11-15-sc.

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).

If you’re interested in this tutorial, you might be interested in this list of other software-related events taking place in the SC21 conference. And remember that since much of SC21’s content will be available on-demand, you may be able to “catch up” with events that you miss.

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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, Anshu Dubey, Patricia A. Grubel, Rinku K. Gupta, and Gregory R. Watson, Better Scientific Software tutorial, in The International Conference for High-Performance Computing, Networking, Storage, and Analysis (SC21), St. Louis, Missouri and online, 2021. DOI: 10.6084/m9.figshare.16556628.

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.