Madagascar Software Package Technology for

Reproducible Computational Experiments

Sergey FomelBureau of Economic GeologyJackson School of GeosciencesThe University of Texas at Austin

http://rsf.sf.net/

Scientific Software Day 2007

Outline

Past Seismic Imaging

MIT, Industry, Stanford, …

Present Test-driven development

Reproducible computational experiments

Future Asking for help

Automatic testing, parallel processing, graphics, …

Seismic Imaging Computations 45 clusters on the top 500 list

many missing Europe’s most powerful supercomputer

(CGG/IBM) Data size

Gb (2-D; 1980x) Tb (3-D; 1990x) ?? (4-D, 4-C, multi-azimuth, …; 200x)

History of Seismic Imaging

Norbert Wiener (© RLE/MIT) Enders Robinson

Jon Claerbout

SEPlib Software Innovations Universal data file format (RSF)

Data separated from text headers Conceptual regularly gridded N-dimensional

hypercubes

If you feel an urge to design a complex binary file format, or a complex binary application protocol, it is generally wise to lie down until the feeling passes. -- Eric S. Raymond, TAUP

Universal graphics format (Vplot) Reproducible research 30+ years legacy

R. Clayton, J. Claerbout, D. Hale, S. Levin, J. Dellinger, S. Cole, D. Nichols, M. Karrenbach, B. Biondi, R. Clapp, …

Data

n1=1000 in=“/path/data.rsf@”n2=500 n3=100 d1=0.001 d2=0.1 o2=1

“Madagascar” Innovations

Open source (GPL) Open community (SourceForge) Open science

Command-line modules Data processing scripts Documentation

Monday Get an idea

Tuesday Implement it

Wednesday Test it

ThursdayCommunicate it

Friday Apply it

Technology Transfer

I

2

3

Three Levels of Technology

Implement it (Tuesday) Command-line modules

C (C++, Fortran-77, Fortran-90, Matlab, Python)

400 modules Test it (Wednesday)

Data processing flows Python/SCons 4,000 tests

Communicate it (Thursday) Papers and reports

LaTeX + Python/SCons 60 papers

Reproducible Computations

Test Driven Development Document computational experiments Old experiments become regression

tests

Within the world of science, computation is now rightly seen as a third vertex of a triangle complementing experiment and theory. However, as it is now often practiced, one can make a good case that computing is the last refuge of the scientific scoundrel. –R. LeVeque

Asking for Help

Open problems Automatic reproducibility testing Parallelization Interfaces Graphics …

Open opportunities Summer students Consultants

Information

http://rsf.sourceforge.net/ Wiki, blog, e-mail lists, forums

RSF/Madagascar School in Austin April 20, 2007 Bureau of Economic Geology

http://rsf.sourceforge.net/RSF_Austin_School_2007