Beijing 2011

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Madagascar School on Reproducible Computational Geophysics
China Beijing.png



July 21-22, 2011


Day 0: Wednesday, July 20
10:00-3:00 Bring your laptop with CD-ROM and get help with installing Madagascar
Tariq Alkhalifah, Sergey Fomel, Yang Liu, Xuxin Ma, Jeffrey Shragge


Day 1: Thursday, July 21
9:00-9:10 Welcome (Yike Liu)
9:10-10:40 Introduction (Sergey Fomel)

The Madagascar project has been in public existence for five years. Madagascar provides a complete environment for organizing one's research, from new software development to running computational experiments to publishing the experimental results in papers and reports, archiving them for future usage, and sharing them with colleagues and sponsors. The introductory presentation will describe the history of the project, the Madagascar components and design principles, and the future development goals.

10:40-10:55 break
10:55-12:15 Command-line usage, RSF file format, Vplot graphics (Xuxin Ma)

Madagascar programs are designed to run from UNIX shell. In this tutorial I will show command-line usage of some basic Madagascar programs and how to manage data flow between different programs. I will also explain the working mechanism of RSF format and how to represent RSF dataset graphically using Madagascar programs.

Command-line usage (0.8M)

12:15-1:15 Lunch
1:15-2:45 Developing workflows using SCons (Sergey Fomel)
2:45-3:00 break
3:00-4:30 Writing papers using Madagascar (Tariq Alkhalifah)

Writing a Geophysics paper using Madagascar offers features beyond the conventional LeTeX package. It first adheres to reproducible principals, which allows for seamless team work and access to your work by others and by your self down the road. It also offers a treasure chest of reproducible papers, which can serve as templates and examples. We will look into these features and write a reproducible paper, at least start one, together.

Day 2: Friday, July 22
9:00-10:30 Wave-equation modeling and migration (Paul Sava)

The theoretical part of this module provides an overview of reverse-time imaging methodology applied to wavefield seismic data. The main technique discussed is reverse-time migration with emphasis on modern imaging conditions which enable migration velocity analysis and amplitude-versus-angle analysis. The applied part demonstrates this technique on a complex geologic model using Madagascar codes in a fully reproducible setup.

10:30-10:45 break
10:45-12:15 Seismic data processing example (Yang Liu)

Field data processing is an important test of integrality degree for open-source software and the final target for scientific research. We will use a 2-D field dataset to illustrate how Madagascar can set up a common seismic data processing workflow.

12:15-1:15 Lunch
1:15-2:45 Developing your own programs in Madagascar (Jeffrey Shragge)
2:45-3:00 break
3:00-4:30 Contributing to Madagascar (Sergey Fomel)


Conference Hall in new office building, Institute of Geology and Geophysics, Chinese Academy of Sciences

No.19 Beitucheng Xilu, Chaoyang District, Beijing, China

中国科学院地质与地球物理研究所, 新办公楼报告厅, 北京市朝阳区北土城西路19号

Location map


Attendance is free for each participant but registration is required. To register, please send an email.


Participating Organizations

Bureau of Economic Geology, The University of Texas at Austin (Austin, USA)

Institute of Geology and Geophysics, Chinese Academy of Sciences (Beijing, China)

College of Geo-exploration Science and Technology, Jilin University (Changchun, China)

College of Geophysics and Information Engineering, China University of Petroleum (Beijing, China)

Contact information

Sergey Fomel, E-mail:

Yibo Wang, E-mail:

Yang Liu (JLU), E-mail:

Yang Liu (CUP), E-mail:


  • Tariq Alkhalifah is currently a Professor of Geophysics at KAUST in Saudi Arabia. He graduated with a PhD from Colorado School of Mines, Golden, Colorado, in 1996, and served afterwards as a Post Doc at Stanford University for 2 years sharing an office with Sergey Fomel. I used to be a devote SU Unix follower for most of my research carrier even as a Post Doc at Stanford (SEPlib people), but I have recently seen the light and converted to Madagascar.
  • Sergey Fomel has been working at the Bureau of Economic Geology at the University of Texas at Austin since 2002 and currently has an Associate Professor appointment, jointly with the Department of Geological Sciences. He received a Ph.D. in Geophysics from Stanford University in 2001 and worked previously at the Institute of Geophysics in Novosibirsk, Russia, and the Lawrence Berkeley National Laboratory. Sergey started work on Madagascar (at that time named RSF for Regularly Sampled Format) in 2003.
  • Yang Liu is currently an Associate Professor of Geophysics at College of Geo-exploration science and technology at Jilin University, China. He received a Ph.D. in Geophysics from Jilin University in 2006 and was a Postdoctoral fellow at Bureau of Economic Geology, The University of Texas at Austin from 2007 to 2010. His research focuses mainly on seismic data processing.
  • Xuxin Ma is currently an MS student in the Seismic Wave Analysis Group (SWAG) at KAUST, Saudi Arabia. He received BS in Thermal engineering from Tsinghua University, China (2006). His research interest includes wave-equation migration and waveform inversion.
  • Paul Sava is an Associate Professor of Geophysics and a member of the Center for Wave Phenomena at Colorado School of Mines. He holds an Engineering degree in Geophysics (1995) from the University of Bucharest, an M.Sc. (1998) and a Ph.D. (2004) in Geophysics from Stanford University where he was a member of the Stanford Exploration Project. His research interests are in wavefield seismic imaging, stochastic imaging and inversion, computational methods for wave propagation, numeric optimization and high performance computing.
  • Jeff Shragge is a Research Assistant Professor with the Centre for Petroleum Geoscience and CO2 Sequestration in the School of Earth and Environment at the University of Western Australia. He received his Ph.D. (Geophysics) in 2009 in seismic imaging with the Stanford Exploration Project at Stanford University. His research interests are in the fields of seismic imaging (migration, time-lapse imaging and velocity inversion) and high-performance computing (parallel computation, GPU programming).