Better Scientific Software

a tutorial presented at

Improving Scientific Software

on 2021-03-25/2021-03-25

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.

Last updated: 2021-07-26

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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 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


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 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).


Stay in Touch


Resources from Presentations

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


Requested Citation

The requested citation the overall tutorial is: David E. Bernholdt, Anshu Dubey, Rinku K. Gupta, and David 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.