Better Scientific Software
a tutorial presented at
NOAA Global Systems Laboratory
on 9:00 am - 5:00 pm MDT (UTC-6) Tuesday 1 August 2023 - Wednesday 2 August 2023
Presenters: David E. Bernholdt (Oak Ridge National Laboratory), Anshu Dubey (Argonne National Laboratory), and Patricia A. Grubel (Los Alamos 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
- Presentation Slides (FigShare)
On this Page
- Description
- Agenda
- Presentation Slides
- How to Participate
- Stay in Touch
- Resources from Presentations
- Requested Citation
- Acknowledgements
Description
The BSSw tutorial focuses on issues of developer productivity, software sustainability, and reproducibility in scientific research software, particularly targeting high-performance computers.
Agenda
| Day | Time (MDT) | Title | Presenter |
|---|---|---|---|
| Tue 1 Aug | 9:00 AM | Introduction | Patricia A. Grubel (LANL) |
| Tue 1 Aug | 9:10 AM | Motivation and Overview of Best Practices in HPC Software Development | Patricia A. Grubel (LANL) |
| Tue 1 Aug | 9:40 AM | Collaborative Software Development | Patricia A. Grubel (LANL) |
| Tue 1 Aug | 10:40 AM | Break | |
| Tue 1 Aug | 10:55 AM | Collaborative Software Development | Patricia A. Grubel (LANL) |
| Tue 1 Aug | 11:25 AM | Software Packaging | David E. Bernholdt (ORNL) |
| Tue 1 Aug | 11:55 AM | Lunch | |
| Tue 1 Aug | 1:30 PM | Scientific Software Design | Anshu Dubey (ANL) |
| Tue 1 Aug | 3:00 PM | Refactoring Scientific Software | Anshu Dubey (ANL) |
| Tue 1 Aug | 3:30 PM | Break | |
| Tue 1 Aug | 3:45 PM | Improving Reproducibility Through Better Software Practices | Patricia A. Grubel (LANL) |
| Tue 1 Aug | 5:00 PM | Adjourn | |
| Wed 2 Aug | 9:00 AM | Lab Notebooks for Computational Mathematics, Sciences, & Engineering | David E. Bernholdt (ORNL) |
| Wed 2 Aug | 10:00 AM | Managing Computational Experiments | Anshu Dubey (ANL) |
| Wed 2 Aug | 10:30 AM | Break | |
| Wed 2 Aug | 10:45 AM | Software Testing and Verification | Anshu Dubey (ANL) |
| Wed 2 Aug | 12:15 PM | Lunch | |
| Wed 2 Aug | 1:45 PM | Documenting your Software | David E. Bernholdt (ORNL) |
| Wed 2 Aug | 2:45 PM | Break | |
| Wed 2 Aug | 3:00 PM | Software Licensing | David E. Bernholdt (ORNL) |
| Wed 2 Aug | 4:00 PM | Summary | David E. Bernholdt (ORNL) |
| Wed 2 Aug | 4:15 PM | General Discussion (optional) | All |
| Wed 2 Aug | 5:00 PM | Adjourn |
Presentation Slides
The latest version of the slides will always be available at https://doi.org/10.6084/m9.figshare.23796606.
Note that these files may include additional slides that will not be discussed during the tutorial, but questions are welcome.
How to Participate
-
We want to interact with you! We find these tutorials most interesting and informative (for everyone) if you ask questions and share experiences! We learn too!
-
Please raise your hand at any time to ask a question
-
We have reserved extra time for discussion following many of our presentations to provide opportunities for deeper discussions of your situations and experiences
- We encourage you to ask questions directly related to our presentations during them
- And save the deeper discussions for after the presentation
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.
-
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
Links from the tutorial presentations are listed here for convenience
- Module 1: Introduction
- Module 2: Motivation and Overview of Best Practices in HPC Software Development
- COVID-19 epidemiology saga
- https://doi.org/10.25561/77482
- https://www.nicholaslewis.org/imperial-college-uk-covid-19-numbers-dont-seem-to-add-up/
- https://www.nature.com/articles/d41586-020-01003-6
- https://www.foxnews.com/world/imperial-college-britain-coronavirus-lockdown-buggy-mess-unreliable
- https://www.telegraph.co.uk/technology/2020/05/16/coding-led-lockdown-totally-unreliable-buggy-mess-say-experts/
- https://github.com/mrc-ide/covid-sim/
- https://philbull.wordpress.com/2020/05/10/why-you-can-ignore-reviews-of-scientific-code-by-commercial-software-developers/amp/
- http://doi.org/10.5281/zenodo.3865491
- Best Practices for Scientific Computing
- Good Enough Practices in Scientific Computing
- Linux Foundation Core Infrastructure Initiative (CII) Best Practices Badging Program
- Rate Your Project Assesment Tool
- Progress Tracking Card (PTC) Examples
- Productivity and Sustainability Improvement Planning
- Better Scientific Software (BSSw)
- COVID-19 epidemiology saga
- Module 3: Collaborative Software Development
- Design Patterns for Git Workflows
- Git Flow (Driessen’s Original Blog)
- 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) - Trilinos
- Open MPI
- FleCSI
- Agile Manifesto
- How to code review in a Pull Request
- Investing in Code Reviews for Better Research Software
- Testing and Code Review Practices in Research Software Development
- Open Source Initiative
- Choose an Open Source License Tool
- Introduction to Software Licensing
- Module 4: Software Packaging
- Simple Heat Equation Example
- https://pyscaffold.org/
- https://github.com/frobnitzem/lib0
- https://code.ornl.gov/99R/mpi-test
- https://cmake.org/cmake/help/git-stage/manual/cmake-packages.7.html#creating-packages
- Fortran resources
- Well documented example
- Modern conventions example
- Fortran standard lib (using fypp meta-programming)
- Fortran Package Index
- Fortran Package Manager
- https://spack.readthedocs.io
- Anatomy of a Spack dependency “spec”
- https://supercontainers.github.io/sc20-tutorial/
- https://fluid-run.readthedocs.io/en/latest/HowTo/setup_your_repo.html
- Article on CI team practices
- https://spack.readthedocs.io/en/latest/packaging_guide.html#dependency-specs
- DCA++
- https://github.com/pyscf/extension-template
- ZFP
- https://github.com/ECP-copa/Cabana
- Intermediate example: C++ with spack
- https://spack-tutorial.readthedocs.io/en/latest/tutorial_packaging.html
- https://spack.readthedocs.io/en/latest/spack.util.html#module-spack.util.prefix
- https://spack.readthedocs.io/en/latest/packaging_guide.html#accessing-dependencies
- Module 5: Scientific Software Design
- Resources for independent exploration
- Code repository in python: https://github.com/abiswas-odu/heateq-design-intersect-2023
- Complete example in C++: https://xsdk-project.github.io/MathPackagesTraining2020/lessons/hand_coded_heat/
- Resources for independent exploration
- Module 6: Refactoring Scientific Software
- Refactoring example code repository: https://github.com/bssw-tutorial/hello-numerical-world
- Module 7: Improving Reproducibility Through Better Software Practices
- Toward a Compatible Reproducibility Taxonomy for Computational and Computing Sciences
- Reproducibility and Replicability in Science
- Many Psychology Findings Not As Strong As Claimed
- The War Over Supercooled Water
- Researchers find bug in Python Script may have affected hundreds of studies
- National Science Foundation Data Management Plan Requirements
- Findable, Accessible, Interoperable, Re-usable
- FAIR Data Principles US
- SC23 Reproducibility Initiative
- ACM Transactions on Mathematical Software (TOMS)
- ACM Artifact Review and Badging
- http://fursin.net/reproducibility.html
- National Information Standards Organization (NISO) on Reproducibility and Badging
- Helpful Tools
- Floating Point Analysis Tools
- Code Ocean (Cloud platforms - publish and reproduce research code and data)
- DOIs and hosting of data, code, documents:
- Other Resources:
- The FAIR Guiding Principles for Scientific Data Management and Stewardship. Mark D. Wilkinson, et al. 2016
- FAIR4RS (previously linked to
www.rd-alliance.org/groups/fair-research-software-fair4rs-wg) - Editorial: ACM TOMS Replicated Computational Results Initiative. Michael A. Heroux. 2015
- Enhancing Reproducibility for Computational Methods
- Simple experiments in reproducibility and technical trust by Mike Heroux and students (work in progress)
- What every scientist should know about floating-point arithmetic. David Goldberg.
- Module 8: Lab Notebooks for Computational Mathematics, Sciences, & Engineering
- Writing the Laboratory Notebook
- HPC and the Lab Manager
- What All Codes Should Do (ATPESC 2019)
- DIKW pyramid
- How to pick an electronic notebook
- Resources – Execution Environments
- Module 9: Managing Computational Experiments
- Dubey A, Calder AC, Daley C, et al. Pragmatic optimizations for better scientific utilization of large supercomputers. The International Journal of High Performance Computing Applications. 2013;27(3):360-373. doi:10.1177/1094342012464404
- Wilfred F. van Gunsteren, and Alan E. Mark. Validation of molecular dynamics simulation. J. Chem. Phys. 108(15), 6109-6116 (1998). doi:10.1063/1.476021
- Module 10: Software Testing and Verification
- CI introduction
- Useful resources on testing (formerly linked to
ideas-productivity.org/resources/howtos/) - Lcov (formerly linked to
ltp.sourceforge.net/coverage/lcov.php) - Additional resources:
- Module 11: Documenting your Software
- API documentation tools
- Flash-X documentation examples
- Diataxis Framework
- Markup languages
- Formatting/generation tools
- Publishing/hosting sites
- Module 12: Software Licensing
- See Additional Resources in lesson
- Module 13: Summary
Requested Citation
The requested citation the overall tutorial is:
David E. Bernholdt, Anshu Dubey, and Patricia A. Grubel, Better Scientific Software tutorial, in NOAA Global Systems Laboratory, Boulder, Colorado, 2023. DOI: 10.6084/m9.figshare.23796606.
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.