Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing...
Transcript of Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing...
![Page 1: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/1.jpg)
Introducing MadagascarA Computational Platform for Geophysical Data Processing and
Reproducible Numerical Experiments
Sergey Fomel1 Paul Sava2 Felix Herrmann3
1Bureau of Economic GeologyJackson School of Geosciences
University of Texas at Austin
2Colorado School of Mines3University of British Columbia
June 11, 2006
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 1 / 20
![Page 2: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/2.jpg)
From RSF to Madagascar
RSERSF
RSG
RSF
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 2 / 20
![Page 3: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/3.jpg)
Outline
1 New
2 Test Driven Development
3 Open Source
4 Universal File Format
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 3 / 20
![Page 4: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/4.jpg)
Outline
1 New
2 Test Driven Development
3 Open Source
4 Universal File Format
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 3 / 20
![Page 5: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/5.jpg)
Outline
1 New
2 Test Driven Development
3 Open Source
4 Universal File Format
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 3 / 20
![Page 6: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/6.jpg)
Outline
1 New
2 Test Driven Development
3 Open Source
4 Universal File Format
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 3 / 20
![Page 7: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/7.jpg)
Outline
1 New
2 Test Driven Development
3 Open Source
4 Universal File Format
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 4 / 20
![Page 8: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/8.jpg)
History
Started in June 2003
6 main contributors
Version 0.9 released June 2006Development version
2,000 revisions300 main programs (140,000 lines of C)3,000 tests (40,000 lines of Python)30 papers (20,000 lines of LATEX)
http://rsf.sf.net/
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 5 / 20
![Page 9: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/9.jpg)
Heritage
SEPlibRob Clayton, Jon Claerbout, Dave Hale, Stew Levin, RickOttolini, Joe Dellinger, Steve Cole, Dave Nichols, MartinKarrenbach, Biondo Biondi, Bob Clapp
SEP reproducible research systemMartin Karrenbach, Matthias Schwab, Joel Schroeder,Sergey Fomel, Bob Clapp
Seismic Unix
DDS
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 6 / 20
![Page 10: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/10.jpg)
Outline
1 New
2 Test Driven Development
3 Open Source
4 Universal File Format
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 7 / 20
![Page 11: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/11.jpg)
Test Driven Development
XP, agile software engineering, refactoringTests drive development
Computational geophysicsTests are numerical experiments
ScienceReproducible experiments mean progress
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 8 / 20
![Page 12: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/12.jpg)
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 8 / 20
![Page 13: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/13.jpg)
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 8 / 20
![Page 14: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/14.jpg)
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 8 / 20
![Page 15: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/15.jpg)
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 8 / 20
![Page 16: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/16.jpg)
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 8 / 20
![Page 17: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/17.jpg)
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 8 / 20
![Page 18: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/18.jpg)
Inspirational Quotes
Abandoning the habit of secrecy in favor of processtransparency and peer review was the crucial step bywhich alchemy became chemistry. In the same way, itis beginning to appear that open-source developmentmay signal the long-awaited maturation of softwaredevelopment as a discipline.Eric S. Raymond, The art of UNIX programming, 2004
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 9 / 20
![Page 19: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/19.jpg)
Inspirational Quotes
The purpose of reproducible research is to facilitatesomeone going a step further by changing something.The first step that someone will want to make is to besure that your work is reproducible before they changeand improve upon it.Jon F. Claerbout, Reproducible research
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 10 / 20
![Page 20: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/20.jpg)
Inspirational Quotes
An article about computational science in a scientificpublication is not the scholarship itself, it is merelyadvertising of the scholarship. The actual scholarshipis the complete software development environment andthe complete set of instructions which generated thefigures.Jon B. Buckheit and David L. Donoho, WaveLab andreproducible research, 1995
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 11 / 20
![Page 21: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/21.jpg)
Inspirational Quotes
Within the world of science, computation is now rightlyseen as a third vertex of a triangle complementingexperiment and theory. However, as it is now oftenpracticed, one can make a good case that computing isthe last refuge of the scientific scoundrel... Where elsein science can one get away with publishingobservations that are claimed to prove a theory orillustrate the success of a technique without having togive a careful description of the methods used, insufficient detail that others can attempt to repeat theexperiment?Randall J. LeVeque, Wave propagation software,computational science, and reproducible research,2006
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 12 / 20
![Page 22: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/22.jpg)
Reproducible Research Tools
SEPGNU make rulesPerl scriptsShell scriptsLATEX macros
MadagascarSCons (Python replacement for make)
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 13 / 20
![Page 23: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/23.jpg)
Outline
1 New
2 Test Driven Development
3 Open Source
4 Universal File Format
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 14 / 20
![Page 24: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/24.jpg)
Open Source
Open source means freedom to the userFreedom to useFreedom to study and modifyFreedom to redistributeFreedom to improve
Open source means collaboration and peer reviewMadagascar package is 100% open-source
GPL licenseHosted by SourceforgeDeveloped with Subversion
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 15 / 20
![Page 25: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/25.jpg)
Outline
1 New
2 Test Driven Development
3 Open Source
4 Universal File Format
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 16 / 20
![Page 26: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/26.jpg)
Universal File Format
Borrowed from classic SEPlib
Binary data and test headers
N-dimensional hypercubes
Can represent seismic data (regular, irregular, 3-D, 9-D,etc.) as well as any other kind of data
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 17 / 20
![Page 27: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/27.jpg)
Inspirational Quotes
To design a perfect anti-Unix, make all file formatsbinary and opaque, and require heavyweight tools toread and edit them....If you feel an urge to design a complex binary fileformat, or a complex binary application protocol, it isgenerally wise to lie down until the feeling passes.Eric S. Raymond, The art of UNIX programming, 2004
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 18 / 20
![Page 28: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/28.jpg)
Summary
Madagascar is a software package for geophysical dataprocessing and reproducible numerical experiments.
New, test-driven, open-source, using a universal file format
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 19 / 20
![Page 29: Introducing Madagascarreproducibility.org/wikilocal/docs/vienna.pdf · 2008. 10. 9. · Introducing Madagascar A Computational Platform for Geophysical Data Processing and Reproducible](https://reader033.fdocuments.net/reader033/viewer/2022060911/60a6141540f59d01c307a2a3/html5/thumbnails/29.jpg)
Please Visit
http://rsf.sf.netSchool and workshop
Reproducible Research in Computational GeophysicsAugust 30-31, 2006Vancouver BC, Canada
S. Fomel (UT Austin) Introducing Madagascar EAGE Open-Source Software 20 / 20