Madagascar - User contributions [en]

Houston 2010

2010-07-02T06:20:52Z

Vbashkardin: /* Program */

[[Image:PTTC.jpg|left|link=http://www.beg.utexas.edu/pttc/workshops.htm ]]

[[Image:BEG.png|left|link=http://www.beg.utexas.edu/ ]]

[[Image:Fotolia_3744441_XS.jpg|center]]

 

<center><big>'''Madagascar School on Reproducible Computational Geophysics and Hands-On Workshop''' 
Sponsored by [http://www.beg.utexas.edu/pttc/workshops.htm PTTC Texas/SE New Mexico Region]</big></center>

 

==Program==

{| align="center" border="1" cellpadding="5" cellspacing="0"
! colspan="3" style="background:#ffdead;" | Day 1: Friday, July 23
|-
| 9:00-10:30
! colspan="2" | Introduction (Sergey Fomel)
|-
|
| colspan="2" |
The Madagascar project has been in public existence for four 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.
|-
| 10:30-10:45
! colspan="2" style="background:#efefef;" | break
|-
| 10:45-12:15
! colspan="2" | Workflows in SCons and automatic testing (Jim Jennings)
|-
|
| colspan="2" |
The rich and well-documented Python syntax used in SConstruct files provides great flexibility when coding Madagascar SCons workflows. In the first part of this module a few geostatistical workflows will be presented to illustrate some useful techniques.

Two important components of the Madagascar design goals are reproducibility and regression testing. In the second part of this module our progress towards these goals will be discussed and some of the built-in tools for automatic testing will be presented.
|-
|
| colspan="2" |

|-
| 12:15-1:15
! colspan="2" style="background:#efefef;" | Lunch
|-
| 1:15-2:45
! colspan="2" | Seismic finite-difference modeling and migration example (Paul Sava)
|-
|
| colspan="2" |
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.
|-
| 2:45-3:00
! colspan="2" style="background:#efefef;" | break
|-
| 3:00-4:30
! colspan="2" | Discussion
|-
|
| colspan="2" |
Open Q&A session and discussions on the future development of Madagascar
|-
| 5:30-8:00
! colspan="2" style="background:#ccff99;" | Dinner and Madagascar 1.0 celebration
|-
|}

 

{| align="center" border="1" cellpadding="5" cellspacing="0"
! colspan="3" style="background:#ffdead;" | Day 2: Saturday, July 24
|-
| 9:00-9:30
! colspan="2" | Learning Madagascar (Tariq Alkhalifah)
|-
|
| colspan="2" |
Why Madagascar was easy for me? The art of the Madagascar template! In a year, I managed to write 7-8 papers using Madagascar, and the papers are still coming. Considering that I have used SU (Seismic Unix) all my life and taking into account my not-so-young age, I think Madagascar was good to me. In the presentation, I will share my experience (no Python background knowledge is needed!) and share some insights on how to use Madagascar efficiently.
|-
| 9:30-10:30
! colspan="2" | Programming with Madagascar (Jeff Godwin)
|-
|
| colspan="2" |

|-
| 10:30-10:45
! colspan="2" style="background:#efefef;" | break
|-
| 10:45-11:15
! colspan="2" | Vplot graphics language - past, present, and future (Joe Dellinger)
|-
|
| colspan="2" |

|-
| 11:15-12:15
! colspan="2" | Plotting and high-performance computing with Madagascar (Vladimir Bashkardin)
|-
|
| colspan="2" |
The first part of this module will cover visualization and preparation of data plots with Madagascar tools. Major available styles of plots will be explained as long as the mechanism of creating figures in reproducible fashion for papers and presentations. The second part will be a tutorial for using Madagascar in a high-performance environment. Different types of such environments will be described and principal approaches to handling parallel problems with Madagascar will be unfolded. This module will specifically address how to run data-parallel tasks and how to create Madagascar programs with MPI and GPU(CUDA) routines.
|-
| 12:15-1:15
! colspan="2" style="background:#efefef;" | Lunch
|-
| 1:15-2:45
! colspan="2" | Seismic field data processing example (Ioan Vlad)
|-
|
| colspan="2" |

|-
| 2:45-3:00
! colspan="2" style="background:#efefef;" | break
|-
| 3:00-4:30
! colspan="2" | Discussion
|-
|
| colspan="2" |
Open Q&A session and discussions on the future development of Madagascar
|-
|}

== Location ==

[[Image:HRC.png|right]]

The University of Texas at Austin 
Bureau of Economic Geology 
[http://www.beg.utexas.edu/info/hrc_facil.php Houston Research Center]

'''Address'''
* 11611 West Little York Rd
* Houston, Texas 77041, USA
* [http://www.beg.utexas.edu/info/pdf/Directions_to_HRC.pdf Driving directions]

 

== Registration ==

Register by filling the [http://www.beg.utexas.edu/pttc/madagascar.php Registration Form].

The registration cost is $300 and includes morning refreshments, lunch, Friday dinner, and instructor handouts.

The registration is '''free for graduate students'''. If you are a graduate student, please e-mail
[mailto:pttc@beg.utexas.edu pttc@beg.utexas.edu] to obtain a discount code.

== Speaker biographies ==

* '''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. https://sites.google.com/a/kaust.edu.sa/tariq/
* '''Vladimir Bashkardin''' is currently a PhD student in geophysics at The University of Texas at Austin. Before joining the research group of Dr. Sergey Fomel at UT Austin, he worked as a software engineer for Paradigm (former Paradigm Geophysical) with specialization in seismic data visualization and interpretation. He also was a part-time lecturer at Gubkin Oil and Gas University (Moscow, Russia), an industry-oriented school from which he holds a degree in exploration geophysics.
* '''Joe Dellinger''' graduated with a PhD in Geophysics from the Stanford Exploration Project in 1991 and currently works for BP in Houston, specializing in anisotropy and multicomponent seismology. Joe has often provided advice to the SEG (much of it unsolicited) on how they should best advance into the brave new online/digital world, for which he was awarded Life Membership in 2001. Joe currently is the editor of the Software and Algorithms section of GEOPHYSICS, and maintains the accompanying software and data website. http://software.seg.org
* '''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. http://www.beg.utexas.edu/fomel/
* '''Jeff Godwin'''
* '''Jim Jennings''' currently works for Shell International Exploration and Production in Houston Texas as a company consultant on carbonate reservoir modeling, but he contributes to Madagascar as a hobby and will be participating in the workshop on his own time. Before joining Shell in 2007 he worked for 23 years at the Bureau of Economic Geology, Arco, and BP. Jim has a PhD in Petroleum Engineering from Texas A&M University (1983), was chairman for an SPE reprint volume on Advances in Reservoir Characterization (2006), and was a Distinguished Lecturer for the AAPG (2008-2009). http://www.aapg.org/education/dist_lect/jennings.cfm
* '''Paul Sava''' is an Assistant 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. http://newton.mines.edu/paul/home.php
* '''Ioan "Nick" Vlad''' received an Engineer degree in Geophysics (2000) from 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 and started working at the Trondheim Research Center in 2005 on imaging and velocity analysis problems. He is a Visiting Scholar at CWP for the year of 2010, working with Prof. Paul Sava on Wave-Equation MVA. He is a member of SEG and EAGE and a participant in the Madagascar open-source project.

Houston 2010

2010-06-28T17:10:43Z

Vbashkardin: /* Speaker biographies */

GSOC2009

2009-02-23T23:33:20Z

Vbashkardin: /* Mentors */

{|border="1" cellpadding="5" cellspacing="0"
|-
| style="background:#efefef;" |
[http://code.google.com/opensource/gsoc/2009/faqs.html Google Summer of Code] is a program that offers student developers stipends to write code for various open source projects. Google will be working with several open source, free software, and technology-related groups to identify and fund several projects over a three month period.
|}

 

[[Image:Google2.png|frame|right|[http://code.google.com/soc/ Google Summer of Code]]]

=Project Ideas=
See also [http://sourceforge.net/tracker/?group_id=162909&atid=825648 feature request tracker]

==Graphical User Interface==
* Add an option to [http://rsf.svn.sourceforge.net/viewvc/rsf/trunk/framework/rsfdoc.py?view=markup sfdoc] to output spec files in the format defined for [http://www.henrythorson.com/interface.htm TKSU]. This should make '''TKSU''' immediately applicable. Spec files can be generated automatically at the compile time.
* Rewrite '''TKSU''' in Python, possibly using [http://wiki.python.org/moin/TkInter TkInter]
* See http://sourceforge.net/forum/forum.php?thread_id=1579059&forum_id=552249 for more discussions.
* Investigate alternative solutions.
* Migrate 2D rendering OpenGL-based code from GSEGYView to Madagascar and create an interactive viewer with zooming/panning features.
* Migrate 3D rendering GLSL-based code from GSEGYView to Madagascar and create a viewer with the support of pluggable shader programs.
* Finish 3D rays viewer
* Create a set of alternatives to sfgraph, sfgrey, sfcontour programs, that would use PLPLOT library instead of VPlot; also, create "pens", that could read from those programs and generate ps, pdf, png output; analyze flexibility of PLPLOT and the possibility to fully mimic VPlot's output (including animation).

==Java API==
* Add a Java interface to [[Guide to madagascar API|other supported interfaces]]
* Possibly use [http://en.wikipedia.org/wiki/Java_Native_Interface JNI]
* Investigate possible connections with [http://www.mines.edu/~dhale/jtk/ Mines JTK] and [http://sourceforge.net/projects/javaseis/ JavaSeis]

==Binary Packages==
* Generate binary packages to simplify installation on multiple platforms.
** [http://en.wikipedia.org/wiki/RPM_Package_Manager RPM]
** [http://www.debian.org/doc/manuals/maint-guide/index.en.html Debian] and [https://wiki.ubuntu.com/PackagingGuide/Complete Ubuntu]
** [http://www.cygwin.com/setup.html Cygwin]
* Given Madagascar's dependencies, and a standardized way of finding other package's dependencies come up with a way/apply a tool to determine the minimum number of packages that make a self-contained Linux distributions that runs Madagascar. Build such a distribution starting from an existing well-supported distribution. Build a virtual appliance from that distribution.
==Geophysics / Numerical Analysis==
* Implement an optimal algorithm for parallel transposes of arrays with 4 or 5 dimensions, up to a few tens of terabytes in volume, on a multi-node Linux cluster
* As a bonus, FFT one of the transposed dimensions
* Implement a hardware-adaptive transpose algorithm for a 1-node, SMP machine of 8 nodes or more. Investigate speed of transfers, size of caches, memory arrangement, etc, and make it hardware-adaptive. Bonus for out-of-core capabilities.
* Implement 3-D seismic data header storage using the fastest open-source database, then compare header I/O times with the classic approach of having a simple table. Which is the fastest way of implementing a large database knowing that the values it will hold are all bools, ints and floats?

=Mentors=
*Sergey Fomel
*Paul Sava
*Nick Vlad
*Vladimir Bashkardin

GSOC2009

2009-02-23T23:32:55Z

Vbashkardin: /* Graphical User Interface */