Houston 2011

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Workshop - Open Software Tools for Reproducible Computational Geophysics
Sponsored by PTTC Texas/SE New Mexico Region
Photo courtesy of Matt Hall



Open software tools allow the exchange of data and procedures so results can be independently reproduced. This greatly accelerates the transfer of technology and best practices in research and commercial communities.

Reproducible research is a revolutionary concept in organizing and transferring geoscientific technology, both in the public domain and inside individual organizations. Computational experiments with geophysical data are captured in the form of transferable recipes, which can be shared and modified by users of the system. The computational recipes are attached to scientific publications, implementing the publication discipline known as "reproducible research". The economic benefits of reproducible research using open source in computational geophysics are enormous.

There are several open-source software packages for geophysical data analysis that were developed to address different aspects of the problem by different organizations around the world. Example packages are SEPlib, Seismic Unix, FreeUSP, DDS, JavaSeis, Mines JTK, PSEIS, OpendTect, CPSeis, and Madagascar. The packages have individual strengths, are not integrated in a comprehensive system, and some critical components are missing. The workshop will introduce participants to the available software. Those already working on various components will get an update on the recent progress. Users and developers will build the community required to improve collaboration.

Petroleum Technology Transfer Council
A forum for transfer of technology and best- practices within the O&G community

Workshop report

Matt Hall

The Petroleum Technology Transfer Council held a workshop in June on open software for reproducible computational geophysics was held at the Bureau of Economic Geology's Houston Research Center. Organized skillfully by Karl Schleicher and Robert Newsham of the University of Texas at Austin, it was two packed days of presentations, live demos, and spirited discussion. The agenda, and almost all of the presentations are available from the Madagascar wiki [1]. For a quick rundown, read on.

Alex Mihai Popovici, CEO of Z-Terra, gave a great, very practical, overview of the relative merits of three major seismic processing packages: Seismic Unix, Madagascar, and SEPlib. He has a very real need: delivering leading edge seismic processing services to clients all over the world.

Dave Hale, Colorado School of Mines professor, gave an overview of his Mines Java Toolkit, a library of tools for solving all sorts of computational problems, not just in geophysics. He also shared his interest in efficient parallelization, and in the programming languages Scala and Jython.

Chuck Mosher of ConocoPhillips then gave the group a look at JavaSeis, an open source project that makes handling prestack seismic data easy and very, very fast. It has parallelization built into it, and is perfect for large, modern 3D datasets and multi-dimensional processing algorithms.

Eric Jones is CEO of Enthought, the innovators behind (among other things) NumPy/SciPy and the Enthought Python Distribution. His take on the role of Python as an integrator and facilitator, handling data and improving usability for legacy software, was practical and refreshing.

Richard Clarke of BP described the history and future of FreeUSP and FreeDDS, a powerful processing system. FreeDDS is being actively developed and released gradually by BP. It will eventually replace FreeUSP.

German Garabito of the Federal University of Parà, Brazil, generated a lot of interest in BotoSeis, the GUI he has developed to help him teach SeismicUnix. It allows one to build and manage processing flows visually, in a Java-built interface inspired by Focus, ProMax and other proprietary tools.

Karl Schleicher, continuing the usability theme, followed up with a nice look at how he is building scripts to pull field data from the USGS online repository, and perform SU and Madagascar processing flows on them. He hopes he can build a library of such scripts as part of Sergey Fomel's reproducible geophysics efforts.

Bill Menger of Global Geophysical was last up on the first day. He told the group a bit about GeoCraft ad CPSeis, projects he open sourced when he was at ConocoPhillips. His insight on what was required to get them into the open: cet permission, communicate the return on investment, know what you want to get out of it, pick a system to support, and be prepared for the commitment.

Nick Vlad from FusionGeo was first on the second day. He gave us another look at open source systems from a commercial processing shop's perspective. Like Alex (and Renée, later), he gave plenty of evidence that open source is not only compatible with business, but it's good for business.

Yang Zhang from Stanford then showed us how reproducibility is central to SEPlib (as it is to Madagascar). When possible, researchers in the Stanford Exploration Project build figures with makefiles, which can be run by anyone to easily reproduce the figure.

Sergey Fomel of the University of Texas at Austin, while casually downloading and compiling Madagascar (that's how easy it is!), described how it too allows for quick regeneration of figures, even from other sources like Mathematica.

Joe Dellinger from BP explained how he thought some basic interactivity could be added to Vplot, SEP's (and thus also Madagascar's) plotting utility. The goal would not be to build an all-singing, all-dancing graphics tool, but to incrementally improve Vplot.

Bjorn Olofsson of SeaBird Exploration presented, for the first time ever, SeaSeis, a seismic QC and processing system that he has built with his own bare hands. He started the project in 2005 and open-sourced it about 18 months ago; it is used by SeaBird in production. Bjorn appealed for attention and help from interested developers; get in touch with him if you are interested.

Renée Bourque of dGB also opened a lot of eyes with her overview of OpendTect and the Open Seismic Repository. dGB's tools are modern, user-friendly, and flexible. I think many people present realized that these tools could substantially augment many of the processing systems other were presenting, most of which lack graphical user interfaces and 3D rendering engines.

Finally, I told the group a bit about my belief in the usefulness and importance of mobile devices in the lab and workplace. I went on to decribe the geoscience apps I am developing for Android, using a visual programming tool called App Inventor, itself a potentially powerful paradigm for building software and perhaps processing systems too.

It was an inspiring and thought-provoking workshop. Thank you to Karl Schleicher and Robert Newsham for organizing, and Cheers! to the new friends and acquaintances. My own impression was that the greatest challenge ahead for this group is not so much computational, but more about integration and consolidation. I'm looking forward to the next one!


Day 1: Thursday, June 16
8:30-9:00 Continental Breakfast
9:00-9:30 Welcome (Karl Schleicher) Abstract Presentation
9:30-10:00 A Comparison of Open Source Seismic Processing Software (Mihai Popovici) Presentation
10:00-10:45 The Mines Java Toolkit and Multicore Computing + demo (Dave Hale) Abstract Presentation
10:45-11:00 Break
11:00-11:30 JavaSeis (Chuck Mosher)
11:30-12:00 Scientific Python (Eric Jones)
12:00-12:30 FreeDDS and FreeUSP (Richard Clarke) Abstract Presentation
12:30-1:30 Lunch
1:30-2:00 BotoSeis: A new interactive platform for seismic data processing with SU (German Garabito) Abstract Presentation
2:00-2:45 Open Seismic Data with Scripts for Processing with Open Software + demo (Karl Schleicher) Abstract Presentation
2:45-3:00 break
3:00-3:45 CPSeis -- Open-Source Seismic Processing - How it is Used, Lessons Learned + demo (Bill Menger) Abstract Presentation
3:45-4:00 Break
4:00-5:00 Discussion

Open Q&A session of the first day's presentations. Work on install the open source software and problem solving. Please bring your laptop computer with Linux installed to participate.

5:30-8:00 Dinner

Pappadeaux Seafood Kitchen
13080 Northwest Freeway, Houston - (713) 460-1203
Directions from the HRC to Pappadeaux


Day 2: Friday, June 17
8:30-9:00 Continental Breakfast
9:00-9:30 Welcome (Karl Schleicher)
9:30-10:00 Open-source software usage in a geophysical software and services company (Nick Vlad) Abstract Presentation
10:00-10:30 SEPlib (Yang Zhang) Abstract Presentation

Demo (Quicktime)

10:30-10:45 Break
10:45-11:15 Madagascar open-source project (Sergey Fomel) Presentation
11:15-11:45 How can we add interactivity to Madagascar graphics? A proposal. (Joe Dellinger) Abstract Presentation
11:45-12:15 SeaSeis: A simple open-source seismic data processing system (Bjorn Olofsson) Abstract Presentation
12:15-1:15 Lunch
1:15-1:45 OpendTect: driving the open source model into the world of oil and gas (Renee Bourque) Abstract Presentation
1:45-2:15 Mobile Geo-computing in oil and gas (Matt Hall) Abstract Presentation
2:15-3:15 Discussion

Open Q&A session of the presentations. Work on install the open source software and problem solving. Please bring your laptop computer with Linux installed to participate. After the scheduled program participants are welcome to use the meeting room for informal work sessions.



The University of Texas at Austin
Bureau of Economic Geology
Houston Research Center


Dinner Location

Pappadeaux Seafood Kitchen
13080 Northwest Freeway, Houston - (713) 460-1203
Directions from the HRC to Pappadeaux

Speaker biographies

  • Renee Bourque is a Geoscientist at dGB Earth Sciences in Houston, TX. As part of the case studies team, she has interpreted basins around the world and contributed to the development of the HorizonCube and related applications. Her professional interests include educational outreach and helping others to see the geology behind the seismic reflections. Renee received her Bachelor’s in Geology from Texas A&M University, and her Master’s in Hydrogeophysics from the State University of New York at Buffalo.
  • Richard Clarke graduated from Cambridge, England with an engineering degree in 1993. He completed a PhD in geophysics at the Institut Francais de Petrole in 1997 and has spent the last 13 years in the technology group at BP processing seismic data with USP & DDS. He has written numerous modules in DDS.
  • Joe Dellinger graduated from the Stanford Exploration Project in 1991. He is the author of much of the framework underlying vplot, the graphics system used in SEPlib and now Madagascar. Joe currently works in the seismic imaging team at BP in Houston.
  • 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.
  • German Garabito received a Doctor degree in Geophysics from Federal University of Para (UFPA), Brazil, in 2002. He worked at UFPA-Brazil as Professor from 2002 to 2009 and currently work as Professor at UFRN-Brazil. He is responsible for the development of the BotoSeis Project for interactive seismic data processing with the Seismic Unix (SU) package.
  • Dave Hale received a B.S. in physics from Texas A&M University in 1977 and a Ph.D. in geophysics from Stanford University in 1983. At Stanford, he studied with the Stanford Exploration Project. He has worked as a field seismologist and research geophysicist for Western Geophysical, as a senior research geophysicist for Chevron, as an associate professor at the Colorado School of Mines, as a chief geophysicist and software developer for Advance Geophysical, and as a senior research fellow for Landmark Graphics. While at Mines, he worked with the Center for Wave Phenomena. In 2005, he returned to Mines as the C.H. Green Professor of Exploration Geophysics.
  • Matt Hall is a geoscientist based in Nova Scotia. A sedimentologist who found geophysics later in his career, Matt has worked at Statoil in Stavanger, Landmark and ConocoPhillips in Calgary, and is now happily self-employed - - running his company from his world HQ: A small shed conveniently located in his back garden. You can read Matt's blog of the workshop at http://www.agilegeoscience.com/journal/2011/6/16/open-seismic-processing-and-dolphins.html and http://www.agilegeoscience.com/journal/2011/6/18/more-powertools-and-a-gobsmacking.html
  • Bill Menger - Houston HPC Manager for Weinman Geoscience: Bill holds BS degrees in Electrical Engineering and Geophysics from Texas A&M University. He was a nuclear engineer in the US Navy Submarine force for five years, joined Conoco R&D doing work in magnetotellurics, multi-component seismic, and development of a seismic processing system for the Cray X-MP. He moved to Houston with Conoco's Advance Exploration group, building a worldwide database of all its oil and gas data using a distributed database. After a stint in Lafayette as data management supervisor, he left Conoco to join Applied Geophysical Software, where he wrote software for multiple suppression, model-building, tomography, and depth migration. Bill rejoined Conoco in 1998 and assisted with the rewrite of CPS, the seismic processing system for Conoco. From the ConocoPhillips merger in 2002 until March 2009 he supervised a software and HPC group. At ConocoPhillips, Bill was instrumental in obtaining open source licensing for CPS (http://cpseis.org), and for GeoCraft (http://geocraft.org), a framework for general purpose geophysical software. Bill is President of the Society of HPC Professionals.
  • Bjorn Olofsson received a MSc degree in geophysics from the University of Hamburg in 1997. Starting with Geco-Prakla in Stavanger/Norway as a data processor, he worked in seabed seismic data processing for 4 years, then moved into research & development for the following 4 years. In 2005 he joined Multiwave, a small marine seismic service provider based in Bergen/Norway which subsequently was acquired by CGG, as an onboard QC geophysicist. After working offshore for 1 1/2 years, he went back to the office as a research geophysicist and doing onboard processing support. He then had a short stint at Spectraseis doing passive seismic data processing, and has since then worked with Seabird Exploration in ocean bottom node seismic business.
  • Alexander Mihai Popovici is Chief Executive Officer of Z-Terra, a state-of-the-art software, data processing and infrastructure provider. He holds Ph.D. (1995) and M.Sc. (1991) degrees in geophysics from Stanford University, and a B.S. (1985) in geophysical and geological engineering from University of Bucharest, Romania. He escaped from Romania in 1986, crossed two borders and spent a year in a refugee camp in Austria. Popovici is the founder and former CEO of 3DGeo Inc. The company was sold in 2008. Dr. Popovici's industry experience includes work in the seismic processing research department for Halliburton Geophysical Services in Dallas and Houston, and EM acquisition and processing for the University of Bucharest, Romania. He has several patents, over 70 publications and has given numerous invited conference and workshop talks. He has been a member of the SEG Research Committee since 1995, served as Associate Editor (Seismic Migration) for Geophysics, and is a Chairman and founding board member of Geoscientists Without Borders. He was president of Casa Romana (http://www.casaromana.org), a non-profit organization serving Americans of Romanian origin living in the Bay Area. He is Honorary Vice Consul of Romania in Houston. Popovici is director of the Romanian Education Foundation (http://www.roed.org), which he co-founded in 1994, a charitable organization helping students from impoverished families to apply at American and European universities. He is a scuba diving instructor, active fencer (ranked top ten in the veteran division of the US), plays paintball with one of the first established pro teams (The Wild Geese, founded 1985), practices karate, rock climbs, and is working on his private pilot license.
  • Karl Schleicher received a B.S. In Mathematics from the University of Houston in 1974 and an MS in Management from the University of Texas at Dallas n 1988. He has worked in data processing, software testing, and research for GSI, Halliburton Geophysical, Western Geophysical, GDC, PGS and AGS. He is interested in the practical development, implementation, and commercialization of seismic processing technology. He is now retired and works part time as a Senior Research Fellow at University of Texas at Austin
  • Ioan (Nick) Vlad received an Engineer degree in geophysics (2000) from the University of Bucharest and a M.Sc. degree in geophysics (2002) from Stanford University. After three more years of research at Stanford and an internship with ConocoPhillips, he joined Statoil. He did imaging and velocity analysis R&D for Statoil for five years -- four at the Trondheim Research Center, and one as a Visiting Scientist with Colorado School of Mines. He is currently a Senior Research Geophysicist with Fusion Petroleum, Inc. He is a member of the SEG, EAGE, IEEE Computer Society, FSF and the Linux Foundation. He has been a participant in the Madagascar project since 2006.
  • Yang Zhang is now a graduate student in Stanford Exploration Project (SEP) at Stanford Univeristy. Besides doing research in exploration seismology, he is currently in charge of the reproducibility check on the SEP research reports. Previously he earned a bachelor degreee of EE from Tsinghua University in P.R.China in 2007, he spent another year in Microsoft Research Beijing Lab working on projects related to Computer Graphics.

Wrap up and follow up

The Petroleum Technology Transfer Council held a workshop in June on open software for reproducible computational geophysics at the Bureau of Economic Geology's Houston Research Center. It was two packed days of presentations, live demos, and spirited discussion.

As part of the workshop wrap up I am passing on the followup items identified at the end of the workshop along with an update on the progress. Please forward to others that may be interested. The workshop follow up items are:

1- Set up linkedIn group “Open Source Geophysical Software”
http://www.linkedin.com/groups/open-source-geoscience-3974308?trk=myg_ugrp_ovr is setup. Join the group and follow future progress. THIS IS THE MOST IMPROTANT ITEM BECAUSE IT IS THE GATEWAY TO FURTHER DISCUSSION.

2- Write a workshop report
Matt Hall wrote the report published at http://reproducibility.org/wiki/Houston_2011. This report will be submitted to The Leading Edge, First Break, the Geophysical Society of Houston newsletter, and the Texas Bureau of Economic Geology web page.

3- Make presentations available
Most presentations have been posted at http://reproducibility.org/wiki/Houston_2011

4- Work with SEG
Joe Dellinger and Karl Schleicher attended the SEG Online Commitee. The chairman encouraged us to consider creating a collaboration area within SEG Online in addition to the linkedIn group. It is great that SEG wants to collaborate with us.

5- Follow up meetings and presentations
I contacted Houston Geophysical Society Data Processing SIG to ask about occasionally adding open software to their program. We want to have workshop in Europe and one in the US next year. A more frequent study group meeting was suggested.

6- Data distribution
We need to collaborate on data storage and distribution. Data has special license issues. Field data, synthetic data, and source code have three sets of issues.

I thank all the people who made this happen. Many thanks to Sergey Fomel, Robert Newsham, speakers, and attendees. What a group! I was stunned and left wanting more. This workshop is wrapped up! Join the linkedIn group for the sequel!

Karl Schleicher