Better Scientific Software

a tutorial presented at

ISC High Performance

on 2021-06-24/2021-06-25

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 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

The computational science and engineering (CSE) community is in the midst of an extremely challenging period created by the confluence of disruptive changes in computing architectures, demand for greater scientific reproducibility, and new opportunities for greatly improved simulation capabilities, especially through coupling physics and scales. 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 will provide information and hands-on experience with software practices, processes, and tools explicitly tailored for CSE. Goals are improving the productivity of those who develop CSE software and increasing the sustainability of software artifacts. We discuss practices that are relevant for projects of all sizes, with emphasis on small teams, and on aggregate teams composed of small teams. Topics include software licensing, effective models, tools, and processes for small teams (including agile workflow management), reproducibility, and scientific software testing (including automated testing and continuous integration).


Agenda

Day Time (CEST) Module Topic Presenter Time (EDT)
Thu 2:00pm-2:10pm 00 Introduction and Setup David E. Bernholdt, ORNL 8:00am-8:10am
Thu 2:10pm-2:30pm 01 Motivation and Overview of Best Practices in HPC Software Development David E. Bernholdt, ORNL 8:10am-8:30am
Thu 2:30pm-3:00pm 02 Agile Methodologies Rinku Gupta, ANL 8:30am-9:00am
Thu 3:00pm-3:30pm 03 Git Workflows Patricia A. Grubel, LANL 9:00am-9:30am
Thu 3:30pm-4:00pm 04 Scientific Software Design Anshu Dubey, ANL 9:30am-10:00am
Thu 4:00pm-4:30pm   Break   10:00am-10:30am
Thu 4:30pm-5:00pm 05 Improving Reproducibility Through Better Software Practices David E. Bernholdt, ORNL 10:30am-11:00am
Thu 5:00pm-5:15pm 06 Agile Methodologies Redux Rinku Gupta, ANL 11:00am-11:15am
Thu 5:15pm-6:00pm   Hands-On Activities All 11:15am-12:00pm
           
Fri 2:00pm-2:25pm 07 Software Testing Introduction Patricia A. Grubel, LANL 8:00am-8:25am
Fri 2:25pm-2:40pm 08 Testing Walk-Through David M. Rogers, ORNL 8:25am-8:40am
Fri 2:40pm-3:00pm 09 Testing Complex Software David M. Rogers, ORNL 8:40am-9:00am
Fri 3:00pm-3:30pm 10 Continuous Integration David M. Rogers, ORNL 9:00am-9:30am
Fri 3:30pm-4:00pm   Hands-On Activities All 9:30am-10:00am
Fri 4:00pm-4:30pm   Break   10:00am-1030am
Fri 4:30pm-5:15pm 11 Refactoring Scientific Software Anshu Dubey, ANL 10:30am-11:15am
Fri 5:15pm-5:30pm 12 Summary Anshu Dubey, ANL 11:15am-11:30am
Fri 5:30pm-6:00pm   Hands-On Activities All 11:30am-12:00pm

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-2021-06-isc. 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).


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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, Patricia A. Grubel, and David Rogers, Better Scientific Software tutorial, in ISC High Performance, 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.