https://www.reproducibility.org/wiki2020/api.php?action=feedcontributions&user=Yangliu&feedformat=atomMadagascar - User contributions [en]2024-03-29T13:22:59ZUser contributionsMediaWiki 1.34.0https://www.reproducibility.org/wiki2020/index.php?title=Hefei_2020&diff=3913Hefei 20202020-10-10T15:22:04Z<p>Yangliu: </p>
<hr />
<div>[[Image:Hefei2020.jpg|center|frame|Screenshot courtesy of Zhisheng Zheng]]<br />
<br />
<center><big>'''2020 Madagascar School in Hefei'''</big></center><br />
<br />
&nbsp;<br />
<br />
== Introduction ==<br />
<br />
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. Madagascar school has been organized many times around the word. It provides a platform for Madagascar users to learn and communicate with the developers. This Madagascar school will introduce the fundamental usages for the beginners with less knowledge of Madagascar and focus on the topic about Open-Source Geophysics in China. This Madagascar school is convened by 1st Asia-Pacific Geophysics Student Conference (APGSC) and hosted by Prof. Yang Liu from Jilin University.<br />
<br />
== Dates ==<br />
<br />
September 6, 2020<br />
<br />
== Agenda ==<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Sunday, September 6, 2020<br />
|-<br />
| 8:30-8:40 <br />
! colspan="2" | Welcome<br />
|-<br />
| 8:40-10:10<br />
! colspan="2" | Introduction to Madagascar Software Project (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
The <tt>Madagascar</tt> project has been in public existence for fourteen 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 origin and history of the project, the Madagascar components and design principles, and plans for future development. In this module, you will learn how to take the full advantage of the <tt>Madagascar</tt> environment to enhance research productivity and research collaboration.<br><br><br />
|-<br />
|<br />
| colspan="2" | <br />
[http://www.ahay.org/wikilocal/docs/school2020-introduction.pdf Slides] (5.9M)<br><br><br />
[https://github.com/ahay/src/blob/master/book/rsf/school2020/cmp/SConstruct Example]<br><br />
|-<br />
| 10:10-10:20<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:20-11:50<br />
! colspan="2" | Geophysical data processing with Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Filed data processing is always a tough problem, which is an important test of integrality degree for Open-source geophysics software and the final target for scientific research. We will use a 2D field seismic dataset to illustrate how Madagascar can set up a common seismic data processing workflow. Meanwhile, we also try to setup the initial processing workflows for other geophysical data, e.g., gravity field data and controlled source electromagnetic (CSEM) synthetic data. <br><br><br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.ahay.org/wikilocal/docs/school2020-workflow.pdf Slides] (6.3M)<br><br><br />
[https://github.com/ahay/src/tree/master/book/rsf/school2020/seismic/SConstruct Seismic example]<br><br />
[https://github.com/ahay/src/tree/master/book/rsf/school2020/gravity/SConstruct Gravity example]<br><br />
[https://github.com/ahay/src/tree/master/book/rsf/school2020/csem/SConstruct MCSEM example]<br><br />
|-<br />
| 11:50-13:30<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 13:30-15:00<br />
! colspan="2" | Writing a reproducible paper using Madagascar and SEGTeX (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
From the viewpoint of science, all technical papers should be "reproducible" in the sense that someone of reasonable skill ought to be able to read the paper and then reproduce the results (from '''Joe Dellinger'''). SEGTeX is a LaTeX package for geophysical publications, which is a important component in Madagascar Project. SEGTeX consists of class files for Geophysics papers, SEG expanded abstracts, etc, and cumulative bibliography of geophysical publications. In this module, you will learn how to use the <tt>Madagascar</tt> and SEGTeX to write a reproducible paper. <br><br><br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.ahay.org/wikilocal/docs/school2020-publish.pdf Slides] (1.3M)<br><br><br />
[https://github.com/ahay/src/blob/master/book/rsf/school2020/SConstruct SConstruct]<br><br />
[https://github.com/ahay/src/blob/master/book/rsf/school2020/school2020.tex tex]<br><br />
[https://github.com/ahay/src/blob/master/book/rsf/school2020/school2020.bib bib]<br><br />
|-<br />
| 15:00-15:30<br />
! colspan="2" | Contributing to Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
As a user of Madagascar, you have the right to run the code for any purpose, to make modifications and additions, and to share your modifications with other people under the standard GPL open-source license. Madagascar is an open community, which makes it easy to share your contributions and to collaborate with other users and developers around the world. <br><br><br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.ahay.org/wikilocal/docs/school2020-contributing.pdf Slides] (2.1M)<br><br><br />
|-<br />
| 15:30-15:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 15:40-16:40<br />
! colspan="2" | Practice (Students and Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Learn the functions of Madagascar software platform, and do some exercises about the construction of data processing workflow and the writing of reproducible papers. <br><br><br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.ahay.org/wikilocal/docs/school2020-practice.pdf Slides] (533KB)<br><br><br />
|}<br />
<br />
== Location ==<br />
<br />
Virtual conference (Tencent Meeting), Jilin University, Changchun, China<br />
*Meeting time: 2020/09/06 08:30-17:00<br />
*Meeting link: https://meeting.tencent.com/s/aFCtbWXXt07N<br />
*Meeting ID: 528 567 355<br />
<br />
== Registration ==<br />
<br />
The Madagascar School participation is free.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
You must [[download]] and [[Installation|install]] the Madagascar package in the days before the school. <br />
<br />
== Organizations ==<br />
<br />
The "Madagascar School on Open-Source Geophysics in Hefei 2020" is organized by<br />
* '''Yang Liu''' from College of Geo-exploration Science and Technology, Jilin University (Changchun, China)<br />
* '''1st Asia-Pacific Geophysics Student Conference (APGSC)''' jointly organized by University of Science and Technology of China (USTC) and SEG<br />
and hosted by '''Yang Liu'''<br />
<br />
== Instructors ==<br />
<br />
* '''Yang Liu''' is a 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 nonstationary seismic data processing. http://gest.jlu.edu.cn/info/1183/4673.htm</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Hefei_2020&diff=3907Hefei 20202020-09-06T17:00:34Z<p>Yangliu: </p>
<hr />
<div>[[Image:Hefei2020.jpg|center|frame|Screenshot courtesy of Zhisheng Zheng]]<br />
<br />
<center><big>'''2020 Madagascar School in Hefei'''</big></center><br />
<br />
&nbsp;<br />
<br />
== Introduction ==<br />
<br />
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. Madagascar school has been organized many times around the word. It provides a platform for Madagascar users to learn and communicate with the developers. This Madagascar school will introduce the fundamental usages for the beginners with less knowledge of Madagascar and focus on the topic about Open-Source Geophysics in China. This Madagascar school is convened by 1st Asia-Pacific Geophysics Student Conference (APGSC) and hosted by Prof. Yang Liu from Jilin University.<br />
<br />
== Dates ==<br />
<br />
September 6, 2020<br />
<br />
== Agenda ==<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Sunday, September 6, 2020<br />
|-<br />
| 8:30-8:40 <br />
! colspan="2" | Welcome<br />
|-<br />
| 8:40-10:10<br />
! colspan="2" | Introduction to Madagascar Software Project (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
The <tt>Madagascar</tt> project has been in public existence for fourteen 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 origin and history of the project, the Madagascar components and design principles, and plans for future development. In this module, you will learn how to take the full advantage of the <tt>Madagascar</tt> environment to enhance research productivity and research collaboration.<br><br><br />
|-<br />
|<br />
| colspan="2" | <br />
[http://www.ahay.org/wikilocal/docs/school2020-Introduction.pdf Slides] (5.9M)<br><br><br />
[https://github.com/ahay/src/blob/master/book/rsf/school2020/cmp/SConstruct Example]<br><br />
|-<br />
| 10:10-10:20<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:20-11:50<br />
! colspan="2" | Geophysical data processing with Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Filed data processing is always a tough problem, which is an important test of integrality degree for Open-source geophysics software and the final target for scientific research. We will use a 2D field seismic dataset to illustrate how Madagascar can set up a common seismic data processing workflow. Meanwhile, we also try to setup the initial processing workflows for other geophysical data, e.g., gravity field data and controlled source electromagnetic (CSEM) synthetic data. <br><br><br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.ahay.org/wikilocal/docs/school2020-workflow.pdf Slides] (6.3M)<br><br><br />
[https://github.com/ahay/src/tree/master/book/rsf/school2020/seismic/SConstruct Seismic example]<br><br />
[https://github.com/ahay/src/tree/master/book/rsf/school2020/gravity/SConstruct Gravity example]<br><br />
[https://github.com/ahay/src/tree/master/book/rsf/school2020/csem/SConstruct MCSEM example]<br><br />
|-<br />
| 11:50-13:30<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 13:30-15:00<br />
! colspan="2" | Writing a reproducible paper using Madagascar and SEGTeX (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
From the viewpoint of science, all technical papers should be "reproducible" in the sense that someone of reasonable skill ought to be able to read the paper and then reproduce the results (from '''Joe Dellinger'''). SEGTeX is a LaTeX package for geophysical publications, which is a important component in Madagascar Project. SEGTeX consists of class files for Geophysics papers, SEG expanded abstracts, etc, and cumulative bibliography of geophysical publications. In this module, you will learn how to use the <tt>Madagascar</tt> and SEGTeX to write a reproducible paper. <br><br><br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.ahay.org/wikilocal/docs/school2020-publish.pdf Slides] (1.3M)<br><br><br />
[https://github.com/ahay/src/blob/master/book/rsf/school2020/SConstruct SConstruct]<br><br />
[https://github.com/ahay/src/blob/master/book/rsf/school2020/school2020.tex tex]<br><br />
[https://github.com/ahay/src/blob/master/book/rsf/school2020/school2020.bib bib]<br><br />
|-<br />
| 15:00-15:30<br />
! colspan="2" | Contributing to Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
As a user of Madagascar, you have the right to run the code for any purpose, to make modifications and additions, and to share your modifications with other people under the standard GPL open-source license. Madagascar is an open community, which makes it easy to share your contributions and to collaborate with other users and developers around the world. <br><br><br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.ahay.org/wikilocal/docs/school2020-contributing.pdf Slides] (2.1M)<br><br><br />
|-<br />
| 15:30-15:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 15:40-16:40<br />
! colspan="2" | Practice (Students and Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Learn the functions of Madagascar software platform, and do some exercises about the construction of data processing workflow and the writing of reproducible papers. <br><br><br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.ahay.org/wikilocal/docs/school2020-practice.pdf Slides] (533KB)<br><br><br />
|}<br />
<br />
== Location ==<br />
<br />
Virtual conference (Tencent Meeting), Jilin University, Changchun, China<br />
*Meeting time: 2020/09/06 08:30-17:00<br />
*Meeting link: https://meeting.tencent.com/s/aFCtbWXXt07N<br />
*Meeting ID: 528 567 355<br />
<br />
== Registration ==<br />
<br />
The Madagascar School participation is free.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
You must [[download]] and [[Installation|install]] the Madagascar package in the days before the school. <br />
<br />
== Organizations ==<br />
<br />
The "Madagascar School on Open-Source Geophysics in Hefei 2020" is organized by<br />
* '''Yang Liu''' from College of Geo-exploration Science and Technology, Jilin University (Changchun, China)<br />
* '''1st Asia-Pacific Geophysics Student Conference (APGSC)''' jointly organized by University of Science and Technology of China (USTC) and SEG<br />
and hosted by '''Yang Liu'''<br />
<br />
== Instructors ==<br />
<br />
* '''Yang Liu''' is a 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 nonstationary seismic data processing. http://gest.jlu.edu.cn/info/1183/4673.htm</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=File:Hefei2020.jpg&diff=3906File:Hefei2020.jpg2020-09-06T16:57:05Z<p>Yangliu: Yangliu uploaded a new version of File:Hefei2020.jpg</p>
<hr />
<div></div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=File:Hefei2020.jpg&diff=3905File:Hefei2020.jpg2020-09-06T16:47:19Z<p>Yangliu: </p>
<hr />
<div></div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Hefei_2020&diff=3904Hefei 20202020-09-06T16:23:52Z<p>Yangliu: /* Agenda */</p>
<hr />
<div>&nbsp;<br />
<br />
== Introduction ==<br />
<br />
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. Madagascar school has been organized many times around the word. It provides a platform for Madagascar users to learn and communicate with the developers. This Madagascar school will introduce the fundamental usages for the beginners with less knowledge of Madagascar and focus on the topic about Open-Source Geophysics in China. This Madagascar school is convened by 1st Asia-Pacific Geophysics Student Conference (APGSC) and hosted by Prof. Yang Liu from Jilin University.<br />
<br />
== Dates ==<br />
<br />
September 6, 2020<br />
<br />
== Agenda ==<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Sunday, September 6, 2020<br />
|-<br />
| 8:30-8:40 <br />
! colspan="2" | Welcome<br />
|-<br />
| 8:40-10:10<br />
! colspan="2" | Introduction to Madagascar Software Project (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
The <tt>Madagascar</tt> project has been in public existence for fourteen 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 origin and history of the project, the Madagascar components and design principles, and plans for future development. In this module, you will learn how to take the full advantage of the <tt>Madagascar</tt> environment to enhance research productivity and research collaboration.<br><br><br />
|-<br />
|<br />
| colspan="2" | <br />
[http://www.ahay.org/wikilocal/docs/school2020-Introduction.pdf Slides] (5.9M)<br><br><br />
[https://github.com/ahay/src/blob/master/book/rsf/school2020/cmp/SConstruct Example]<br><br />
|-<br />
| 10:10-10:20<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:20-11:50<br />
! colspan="2" | Geophysical data processing with Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Filed data processing is always a tough problem, which is an important test of integrality degree for Open-source geophysics software and the final target for scientific research. We will use a 2D field seismic dataset to illustrate how Madagascar can set up a common seismic data processing workflow. Meanwhile, we also try to setup the initial processing workflows for other geophysical data, e.g., gravity field data and controlled source electromagnetic (CSEM) synthetic data. <br><br><br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.ahay.org/wikilocal/docs/school2020-workflow.pdf Slides] (6.3M)<br><br><br />
[https://github.com/ahay/src/tree/master/book/rsf/school2020/seismic/SConstruct Seismic example]<br><br />
[https://github.com/ahay/src/tree/master/book/rsf/school2020/gravity/SConstruct Gravity example]<br><br />
[https://github.com/ahay/src/tree/master/book/rsf/school2020/csem/SConstruct MCSEM example]<br><br />
|-<br />
| 11:50-13:30<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 13:30-15:00<br />
! colspan="2" | Writing a reproducible paper using Madagascar and SEGTeX (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
From the viewpoint of science, all technical papers should be "reproducible" in the sense that someone of reasonable skill ought to be able to read the paper and then reproduce the results (from '''Joe Dellinger'''). SEGTeX is a LaTeX package for geophysical publications, which is a important component in Madagascar Project. SEGTeX consists of class files for Geophysics papers, SEG expanded abstracts, etc, and cumulative bibliography of geophysical publications. In this module, you will learn how to use the <tt>Madagascar</tt> and SEGTeX to write a reproducible paper. <br><br><br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.ahay.org/wikilocal/docs/school2020-publish.pdf Slides] (1.3M)<br><br><br />
[https://github.com/ahay/src/blob/master/book/rsf/school2020/SConstruct SConstruct]<br><br />
[https://github.com/ahay/src/blob/master/book/rsf/school2020/school2020.tex tex]<br><br />
[https://github.com/ahay/src/blob/master/book/rsf/school2020/school2020.bib bib]<br><br />
|-<br />
| 15:00-15:30<br />
! colspan="2" | Contributing to Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
As a user of Madagascar, you have the right to run the code for any purpose, to make modifications and additions, and to share your modifications with other people under the standard GPL open-source license. Madagascar is an open community, which makes it easy to share your contributions and to collaborate with other users and developers around the world. <br><br><br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.ahay.org/wikilocal/docs/school2020-contributing.pdf Slides] (2.1M)<br><br><br />
|-<br />
| 15:30-15:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 15:40-16:40<br />
! colspan="2" | Practice (Students and Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Learn the functions of Madagascar software platform, and do some exercises about the construction of data processing workflow and the writing of reproducible papers. <br><br><br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.ahay.org/wikilocal/docs/school2020-practice.pdf Slides] (533KB)<br><br><br />
|}<br />
<br />
== Location ==<br />
<br />
Virtual conference (Tencent Meeting), Jilin University, Changchun, China<br />
*Meeting time: 2020/09/06 08:30-17:00<br />
*Meeting link: https://meeting.tencent.com/s/aFCtbWXXt07N<br />
*Meeting ID: 528 567 355<br />
<br />
== Registration ==<br />
<br />
The Madagascar School participation is free.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
You must [[download]] and [[Installation|install]] the Madagascar package in the days before the school. <br />
<br />
== Organizations ==<br />
<br />
The "Madagascar School on Open-Source Geophysics in Hefei 2020" is organized by<br />
* '''Yang Liu''' from College of Geo-exploration Science and Technology, Jilin University (Changchun, China)<br />
* '''1st Asia-Pacific Geophysics Student Conference (APGSC)''' jointly organized by University of Science and Technology of China (USTC) and SEG<br />
and hosted by '''Yang Liu'''<br />
<br />
== Instructors ==<br />
<br />
* '''Yang Liu''' is a 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 nonstationary seismic data processing. http://gest.jlu.edu.cn/info/1183/4673.htm</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Hefei_2020&diff=3903Hefei 20202020-09-06T15:44:51Z<p>Yangliu: /* Agenda */</p>
<hr />
<div>&nbsp;<br />
<br />
== Introduction ==<br />
<br />
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. Madagascar school has been organized many times around the word. It provides a platform for Madagascar users to learn and communicate with the developers. This Madagascar school will introduce the fundamental usages for the beginners with less knowledge of Madagascar and focus on the topic about Open-Source Geophysics in China. This Madagascar school is convened by 1st Asia-Pacific Geophysics Student Conference (APGSC) and hosted by Prof. Yang Liu from Jilin University.<br />
<br />
== Dates ==<br />
<br />
September 6, 2020<br />
<br />
== Agenda ==<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Sunday, September 6, 2020<br />
|-<br />
| 8:30-8:40 <br />
! colspan="2" | Welcome<br />
|-<br />
| 8:40-10:10<br />
! colspan="2" | Introduction to Madagascar Software Project (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
The <tt>Madagascar</tt> project has been in public existence for fourteen 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 origin and history of the project, the Madagascar components and design principles, and plans for future development. In this module, you will learn how to take the full advantage of the <tt>Madagascar</tt> environment to enhance research productivity and research collaboration.<br><br><br />
|-<br />
|<br />
| colspan="2" | <br />
[http://www.ahay.org/wikilocal/docs/school2020-Introduction.pdf Slides] (5.9M)<br />
|-<br />
| 10:10-10:20<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:20-11:50<br />
! colspan="2" | Geophysical data processing with Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Filed data processing is always a tough problem, which is an important test of integrality degree for Open-source geophysics software and the final target for scientific research. We will use a 2D field seismic dataset to illustrate how Madagascar can set up a common seismic data processing workflow. Meanwhile, we also try to setup the initial processing workflows for other geophysical data, e.g., gravity field data and controlled source electromagnetic (CSEM) synthetic data. <br><br><br />
|-<br />
| 11:50-13:30<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 13:30-15:00<br />
! colspan="2" | Writing a reproducible paper using Madagascar and SEGTeX (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
From the viewpoint of science, all technical papers should be "reproducible" in the sense that someone of reasonable skill ought to be able to read the paper and then reproduce the results (from '''Joe Dellinger'''). SEGTeX is a LaTeX package for geophysical publications, which is a important component in Madagascar Project. SEGTeX consists of class files for Geophysics papers, SEG expanded abstracts, etc, and cumulative bibliography of geophysical publications. In this module, you will learn how to use the <tt>Madagascar</tt> and SEGTeX to write a reproducible paper. <br><br><br />
|-<br />
| 15:00-15:30<br />
! colspan="2" | Contributing to Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
As a user of Madagascar, you have the right to run the code for any purpose, to make modifications and additions, and to share your modifications with other people under the standard GPL open-source license. Madagascar is an open community, which makes it easy to share your contributions and to collaborate with other users and developers around the world. <br><br><br />
|-<br />
| 15:30-15:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 15:40-16:40<br />
! colspan="2" | Practice (Students and Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Learn the functions of Madagascar software platform, and do some exercises about the construction of data processing workflow and the writing of reproducible papers. <br><br><br />
|}<br />
<br />
== Location ==<br />
<br />
Virtual conference (Tencent Meeting), Jilin University, Changchun, China<br />
*Meeting time: 2020/09/06 08:30-17:00<br />
*Meeting link: https://meeting.tencent.com/s/aFCtbWXXt07N<br />
*Meeting ID: 528 567 355<br />
<br />
== Registration ==<br />
<br />
The Madagascar School participation is free.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
You must [[download]] and [[Installation|install]] the Madagascar package in the days before the school. <br />
<br />
== Organizations ==<br />
<br />
The "Madagascar School on Open-Source Geophysics in Hefei 2020" is organized by<br />
* '''Yang Liu''' from College of Geo-exploration Science and Technology, Jilin University (Changchun, China)<br />
* '''1st Asia-Pacific Geophysics Student Conference (APGSC)''' jointly organized by University of Science and Technology of China (USTC) and SEG<br />
and hosted by '''Yang Liu'''<br />
<br />
== Instructors ==<br />
<br />
* '''Yang Liu''' is a 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 nonstationary seismic data processing. http://gest.jlu.edu.cn/info/1183/4673.htm</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Hefei_2020&diff=3902Hefei 20202020-09-03T02:20:43Z<p>Yangliu: /* Location */</p>
<hr />
<div>&nbsp;<br />
<br />
== Introduction ==<br />
<br />
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. Madagascar school has been organized many times around the word. It provides a platform for Madagascar users to learn and communicate with the developers. This Madagascar school will introduce the fundamental usages for the beginners with less knowledge of Madagascar and focus on the topic about Open-Source Geophysics in China. This Madagascar school is convened by 1st Asia-Pacific Geophysics Student Conference (APGSC) and hosted by Prof. Yang Liu from Jilin University.<br />
<br />
== Dates ==<br />
<br />
September 6, 2020<br />
<br />
== Agenda ==<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Sunday, September 6, 2020<br />
|-<br />
| 8:30-8:40 <br />
! colspan="2" | Welcome<br />
|-<br />
| 8:40-10:10<br />
! colspan="2" | Introduction to Madagascar Software Project (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
The <tt>Madagascar</tt> project has been in public existence for fourteen 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 origin and history of the project, the Madagascar components and design principles, and plans for future development. In this module, you will learn how to take the full advantage of the <tt>Madagascar</tt> environment to enhance research productivity and research collaboration.<br><br><br />
|-<br />
| 10:10-10:20<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:20-11:50<br />
! colspan="2" | Geophysical data processing with Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Filed data processing is always a tough problem, which is an important test of integrality degree for Open-source geophysics software and the final target for scientific research. We will use a 2D field seismic dataset to illustrate how Madagascar can set up a common seismic data processing workflow. Meanwhile, we also try to setup the initial processing workflows for other geophysical data, e.g., gravity field data and controlled source electromagnetic (CSEM) synthetic data. <br><br><br />
|-<br />
| 11:50-13:30<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 13:30-15:00<br />
! colspan="2" | Writing a reproducible paper using Madagascar and SEGTeX (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
From the viewpoint of science, all technical papers should be "reproducible" in the sense that someone of reasonable skill ought to be able to read the paper and then reproduce the results (from '''Joe Dellinger'''). SEGTeX is a LaTeX package for geophysical publications, which is a important component in Madagascar Project. SEGTeX consists of class files for Geophysics papers, SEG expanded abstracts, etc, and cumulative bibliography of geophysical publications. In this module, you will learn how to use the <tt>Madagascar</tt> and SEGTeX to write a reproducible paper. <br><br><br />
|-<br />
| 15:00-15:30<br />
! colspan="2" | Contributing to Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
As a user of Madagascar, you have the right to run the code for any purpose, to make modifications and additions, and to share your modifications with other people under the standard GPL open-source license. Madagascar is an open community, which makes it easy to share your contributions and to collaborate with other users and developers around the world. <br><br><br />
|-<br />
| 15:30-15:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 15:40-16:40<br />
! colspan="2" | Practice (Students and Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Learn the functions of Madagascar software platform, and do some exercises about the construction of data processing workflow and the writing of reproducible papers. <br><br><br />
|}<br />
<br />
== Location ==<br />
<br />
Virtual conference (Tencent Meeting), Jilin University, Changchun, China<br />
*Meeting time: 2020/09/06 08:30-17:00<br />
*Meeting link: https://meeting.tencent.com/s/aFCtbWXXt07N<br />
*Meeting ID: 528 567 355<br />
<br />
== Registration ==<br />
<br />
The Madagascar School participation is free.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
You must [[download]] and [[Installation|install]] the Madagascar package in the days before the school. <br />
<br />
== Organizations ==<br />
<br />
The "Madagascar School on Open-Source Geophysics in Hefei 2020" is organized by<br />
* '''Yang Liu''' from College of Geo-exploration Science and Technology, Jilin University (Changchun, China)<br />
* '''1st Asia-Pacific Geophysics Student Conference (APGSC)''' jointly organized by University of Science and Technology of China (USTC) and SEG<br />
and hosted by '''Yang Liu'''<br />
<br />
== Instructors ==<br />
<br />
* '''Yang Liu''' is a 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 nonstationary seismic data processing. http://gest.jlu.edu.cn/info/1183/4673.htm</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Hefei_2020&diff=3901Hefei 20202020-09-03T02:19:39Z<p>Yangliu: /* Location */</p>
<hr />
<div>&nbsp;<br />
<br />
== Introduction ==<br />
<br />
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. Madagascar school has been organized many times around the word. It provides a platform for Madagascar users to learn and communicate with the developers. This Madagascar school will introduce the fundamental usages for the beginners with less knowledge of Madagascar and focus on the topic about Open-Source Geophysics in China. This Madagascar school is convened by 1st Asia-Pacific Geophysics Student Conference (APGSC) and hosted by Prof. Yang Liu from Jilin University.<br />
<br />
== Dates ==<br />
<br />
September 6, 2020<br />
<br />
== Agenda ==<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Sunday, September 6, 2020<br />
|-<br />
| 8:30-8:40 <br />
! colspan="2" | Welcome<br />
|-<br />
| 8:40-10:10<br />
! colspan="2" | Introduction to Madagascar Software Project (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
The <tt>Madagascar</tt> project has been in public existence for fourteen 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 origin and history of the project, the Madagascar components and design principles, and plans for future development. In this module, you will learn how to take the full advantage of the <tt>Madagascar</tt> environment to enhance research productivity and research collaboration.<br><br><br />
|-<br />
| 10:10-10:20<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:20-11:50<br />
! colspan="2" | Geophysical data processing with Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Filed data processing is always a tough problem, which is an important test of integrality degree for Open-source geophysics software and the final target for scientific research. We will use a 2D field seismic dataset to illustrate how Madagascar can set up a common seismic data processing workflow. Meanwhile, we also try to setup the initial processing workflows for other geophysical data, e.g., gravity field data and controlled source electromagnetic (CSEM) synthetic data. <br><br><br />
|-<br />
| 11:50-13:30<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 13:30-15:00<br />
! colspan="2" | Writing a reproducible paper using Madagascar and SEGTeX (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
From the viewpoint of science, all technical papers should be "reproducible" in the sense that someone of reasonable skill ought to be able to read the paper and then reproduce the results (from '''Joe Dellinger'''). SEGTeX is a LaTeX package for geophysical publications, which is a important component in Madagascar Project. SEGTeX consists of class files for Geophysics papers, SEG expanded abstracts, etc, and cumulative bibliography of geophysical publications. In this module, you will learn how to use the <tt>Madagascar</tt> and SEGTeX to write a reproducible paper. <br><br><br />
|-<br />
| 15:00-15:30<br />
! colspan="2" | Contributing to Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
As a user of Madagascar, you have the right to run the code for any purpose, to make modifications and additions, and to share your modifications with other people under the standard GPL open-source license. Madagascar is an open community, which makes it easy to share your contributions and to collaborate with other users and developers around the world. <br><br><br />
|-<br />
| 15:30-15:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 15:40-16:40<br />
! colspan="2" | Practice (Students and Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Learn the functions of Madagascar software platform, and do some exercises about the construction of data processing workflow and the writing of reproducible papers. <br><br><br />
|}<br />
<br />
== Location ==<br />
<br />
Virtual conference (Tencent Meeting), Jilin University, Changchun, China<br />
Meeting time: 2020/09/06 08:30-17:00<br />
Meeting link: https://meeting.tencent.com/s/aFCtbWXXt07N<br />
Meeting ID: 528 567 355<br />
<br />
== Registration ==<br />
<br />
The Madagascar School participation is free.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
You must [[download]] and [[Installation|install]] the Madagascar package in the days before the school. <br />
<br />
== Organizations ==<br />
<br />
The "Madagascar School on Open-Source Geophysics in Hefei 2020" is organized by<br />
* '''Yang Liu''' from College of Geo-exploration Science and Technology, Jilin University (Changchun, China)<br />
* '''1st Asia-Pacific Geophysics Student Conference (APGSC)''' jointly organized by University of Science and Technology of China (USTC) and SEG<br />
and hosted by '''Yang Liu'''<br />
<br />
== Instructors ==<br />
<br />
* '''Yang Liu''' is a 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 nonstationary seismic data processing. http://gest.jlu.edu.cn/info/1183/4673.htm</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Hefei_2020&diff=3900Hefei 20202020-09-01T09:22:46Z<p>Yangliu: /* Agenda */</p>
<hr />
<div>&nbsp;<br />
<br />
== Introduction ==<br />
<br />
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. Madagascar school has been organized many times around the word. It provides a platform for Madagascar users to learn and communicate with the developers. This Madagascar school will introduce the fundamental usages for the beginners with less knowledge of Madagascar and focus on the topic about Open-Source Geophysics in China. This Madagascar school is convened by 1st Asia-Pacific Geophysics Student Conference (APGSC) and hosted by Prof. Yang Liu from Jilin University.<br />
<br />
== Dates ==<br />
<br />
September 6, 2020<br />
<br />
== Agenda ==<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Sunday, September 6, 2020<br />
|-<br />
| 8:30-8:40 <br />
! colspan="2" | Welcome<br />
|-<br />
| 8:40-10:10<br />
! colspan="2" | Introduction to Madagascar Software Project (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
The <tt>Madagascar</tt> project has been in public existence for fourteen 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 origin and history of the project, the Madagascar components and design principles, and plans for future development. In this module, you will learn how to take the full advantage of the <tt>Madagascar</tt> environment to enhance research productivity and research collaboration.<br><br><br />
|-<br />
| 10:10-10:20<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:20-11:50<br />
! colspan="2" | Geophysical data processing with Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Filed data processing is always a tough problem, which is an important test of integrality degree for Open-source geophysics software and the final target for scientific research. We will use a 2D field seismic dataset to illustrate how Madagascar can set up a common seismic data processing workflow. Meanwhile, we also try to setup the initial processing workflows for other geophysical data, e.g., gravity field data and controlled source electromagnetic (CSEM) synthetic data. <br><br><br />
|-<br />
| 11:50-13:30<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 13:30-15:00<br />
! colspan="2" | Writing a reproducible paper using Madagascar and SEGTeX (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
From the viewpoint of science, all technical papers should be "reproducible" in the sense that someone of reasonable skill ought to be able to read the paper and then reproduce the results (from '''Joe Dellinger'''). SEGTeX is a LaTeX package for geophysical publications, which is a important component in Madagascar Project. SEGTeX consists of class files for Geophysics papers, SEG expanded abstracts, etc, and cumulative bibliography of geophysical publications. In this module, you will learn how to use the <tt>Madagascar</tt> and SEGTeX to write a reproducible paper. <br><br><br />
|-<br />
| 15:00-15:30<br />
! colspan="2" | Contributing to Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
As a user of Madagascar, you have the right to run the code for any purpose, to make modifications and additions, and to share your modifications with other people under the standard GPL open-source license. Madagascar is an open community, which makes it easy to share your contributions and to collaborate with other users and developers around the world. <br><br><br />
|-<br />
| 15:30-15:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 15:40-16:40<br />
! colspan="2" | Practice (Students and Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Learn the functions of Madagascar software platform, and do some exercises about the construction of data processing workflow and the writing of reproducible papers. <br><br><br />
|}<br />
<br />
== Location ==<br />
<br />
Virtual conference (Tencent Meeting), Jilin University, Changchun, China<br />
<br />
== Registration ==<br />
<br />
The Madagascar School participation is free.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
You must [[download]] and [[Installation|install]] the Madagascar package in the days before the school. <br />
<br />
== Organizations ==<br />
<br />
The "Madagascar School on Open-Source Geophysics in Hefei 2020" is organized by<br />
* '''Yang Liu''' from College of Geo-exploration Science and Technology, Jilin University (Changchun, China)<br />
* '''1st Asia-Pacific Geophysics Student Conference (APGSC)''' jointly organized by University of Science and Technology of China (USTC) and SEG<br />
and hosted by '''Yang Liu'''<br />
<br />
== Instructors ==<br />
<br />
* '''Yang Liu''' is a 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 nonstationary seismic data processing. http://gest.jlu.edu.cn/info/1183/4673.htm</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Package_overview&diff=3899Package overview2020-08-23T10:36:30Z<p>Yangliu: /* Estimated Cost */</p>
<hr />
<div>[[Image:Fotolia_5127720_XS.jpg|right|]]<br />
<br />
The mission of the Madagascar project is to provide a '''shared research environment''' for computational data analysis in geophysics and related fields.<br />
<br />
The Madagascar environment consists of:<br />
# Standalone programs for out-of-core data analysis;<br />
# Standalone programs for geophysical data processing and imaging;<br />
# A development kit for C, C++, Java, Fortran-77, Fortran-90, Python, Matlab, and Octave;<br />
# A framework for reproducible numerical experiments, based on [http://www.scons.org/ SCons];<br />
# A framework for scientific publications, based on [http://www.scons.org/ SCons] and [http://en.wikipedia.org/wiki/LaTeX LaTeX];<br />
# A collection of reproducible scientific articles also used as usage examples and regression tests for the standalone programs;<br />
# A collection of datasets used as input to reproducible numerical experiments.<br />
<br />
This guide serves as a brief introduction of different components and shows how they all fit together.<br />
<br />
==How to obtain Madagascar==<br />
<br />
See [[Download|download]] and [[Installation | installation instructions]]. Madagascar runs on Unix/Linux platforms, including MacOS X and Unix emulations under Miscrosoft Windows. Its installation requires, at a minimum, a working C compiler and Python. <br />
<br />
==How to find your way around Madagascar==<br />
<br />
Start by checking the [[Reproducible_Documents|list of reproducible papers]]. If any of these papers looks close to your interests, follow the links until you find a figure with a "wrench" button under it [[Image:configure.png]]. Click on the wrench, and it will open a computational recipe used for generating the figure (the <tt>SConstruct</tt> file). <br />
<syntaxhighlight lang="python"><br />
from rsf.proj import *<br />
Flow('rose',None,<br />
'''<br />
math n1=629 d1=0.01 o1=0 n2=40 d2=1 o2=5 <br />
output="x2*(8+sin(6*x1+x2/10))" |<br />
rtoc |<br />
math output="input*exp(I*x1)"<br />
''')<br />
Result('rose',<br />
'graph title=Rose screenratio=1 wantaxis=n')<br />
End()<br />
</syntaxhighlight><br />
You can copy this recipe to your computer or simply find it already existing in the "book" subtree under the Madagascar source directory. For example, the recipe at http://www.reproducibility.org/RSF/book/rsf/rsf/sfmath.html also exists in the file <tt>RSFSRC/book/rsf/rsf/sfmath/SConstruct</tt>. After copying or locating the appropriate <tt>SConstruct</tt> file,<br />
run<br />
<pre><br />
scons view<br />
</pre><br />
on the command line to generate all the figures in the selected project and to display them on your screen. For example, try<br />
<pre><br />
bash$ cd RSFSRC/book/rsf/rsf/sfmath<br />
bash$ scons view<br />
</pre><br />
where <tt>bash$</tt> stands for the Unix prompt and <tt>RSFSRC</tt> stands for the Madagascar source directory. The output should look like<br />
<pre><br />
scons: Reading SConscript files ...<br />
scons: done reading SConscript files.<br />
scons: Building targets ...<br />
/RSFROOT/bin/sfmath n1=629 d1=0.01 o1=0 n2=40 d2=1 o2=5 output="x2*(8+sin(6*x1+x2/10))" | /RSFROOT/bin/sfrtoc | <br />
/RSFROOT/bin/sfmath output="input*exp(I*x1)" > rose.rsf<br />
< rose.rsf /RSFROOT/bin/sfgraph title=Rose screenratio=1 wantaxis=n > Fig/rose.vpl<br />
/RSFROOT/bin/sfpen Fig/rose.vpl<br />
scons: done building targets.<br />
</pre><br />
with a picture appearing on your screen.<br />
[[Image:rose.png|frame|center]]<br />
If there are several figures in the recipe, you can run<br />
<pre><br />
scons figurename.view<br />
</pre><br />
(e.g. <tt>scons rose.view</tt>) to display individual figures. To remove all files that <tt>scons view</tt> generated, run<br />
<pre><br />
scons -c view<br />
</pre><br />
If you want to know in advance what commands will be executed to generate the figures, try<br />
<pre><br />
scons -n view<br />
</pre><br />
You can output this command to a file<br />
<pre><br />
scons -n -Q view > script.sh<br />
</pre><br />
and use <tt>script.sh</tt> as a shell script. If you are to make modifications to the data processing recipe (changing parameters or trying new data), working with SCons is more powerful and convenient than running shell scripts.<br />
<br />
A computational recipe puts together individual commands through Unix pipes and SCons rules. These commands act like Lego blocks for creating complex data analysis constructions. In the example above, three "blocks" are used: <tt>sfmath</tt>, <tt>sfrtoc</tt>, and <tt>sfgraph</tt>. To find out what a particular command is doing, you can follow the links from the bottom of the web page http://www.reproducibility.org/RSF/book/rsf/rsf/sfmath.html<br />
Alternatively, run the command without arguments on the command line. Running<br />
<pre><br />
bash$ sfrtoc<br />
</pre><br />
produces something like<br />
<pre><br />
NAME<br />
sfrtoc<br />
DESCRIPTION<br />
Convert real data to complex (by adding zero imaginary part).<br />
SYNOPSIS<br />
sfrtoc < real.rsf > cmplx.rsf<br />
COMMENTS <br />
See also: sfcmplx<br />
USED IN<br />
bei/ft1/plane4<br />
bei/ft1/autocor<br />
bei/ft1/brad<br />
[...]<br />
SOURCE<br />
user/main/rtoc.c<br />
DOCUMENTATION<br />
http://reproducibility.org/wiki/Guide_to_madagascar_programs#sfrtoc<br />
</pre><br />
<br />
The <b>DOCUMENTATION</b> section provides a link to a more detailed documentation on the web. The most useful part is the <b>USED IN</b> section, which points to more examples of using the program. As an exercise, change directory to <tt>RSFSRC/book/bei/ft1/plane4</tt> or any other example directory, examine the <tt>SConstruct</tt> file, and run <tt>scons view</tt>. Alternatively, look at http://www.reproducibility.org/RSF/book/bei/ft1/plane4.html<br />
<br />
Want to find a program by keywords? Try <tt>sfdoc -k</tt>.<br />
<pre><br />
bash$ sfdoc -k complex<br />
sfsort: Sort a float/complex vector by absolute values.<br />
sfrtoc: Convert real data to complex (by adding zero imaginary part).<br />
sfjacobi2: Find eigenvalues of a general complex matrix by Jacobi-like iteration. <br />
sfboolcmp: Element-wise boolean comparison of values. For int/float/complex data-sets.<br />
sfcmatmult: Simple matrix multiplication for complex matrices <br />
sfimag: Extract real (sfreal) or imaginary (sfimag) part of a complex dataset. <br />
sfthr: Threshold float/complex inputs given a constant/varying threshold level.<br />
sfcpef: 1-D prediction-error filter estimation from complex data <br />
sfroots: Find roots of a complex polynomial. <br />
sfreal: Extract real (sfreal) or imaginary (sfimag) part of a complex dataset. <br />
sfcmplx: Create a complex dataset from its real and imaginary parts.<br />
sfsin: Simple operations with complex sinusoids <br />
sfcdottest: Generic dot-product test for complex linear operators with adjoints <br />
sfcconjgrad: Generic conjugate-gradient solver for linear inversion with complex data<br />
</pre><br />
<br />
Individual components of the Madagascar environment are described in more details below.<br />
<br />
==Madagascar components==<br />
<br />
===Standalone programs===<br />
The list of all standalone programs is available [http://www.reproducibility.org/RSF/ online]. Most programs act as filters on input data and can be chained through Unix pipes, i.e.:<br />
<bash><br />
< data.rsf sfwindow n1=100 | sfbandpass fhi=60 > data2.rsf<br />
</bash><br />
This approach follows the Unix philosophy, as formulated by Doug McIlroy, the inventor of Unix pipes (Salus, 1994<ref>Salus, P. H., 1994, A quarter-century of Unix: Addison-Wesley.</ref>): <br />
#Write programs that do one thing and do it well. <br />
#Write programs to work together. <br />
#Write programs to handle text streams, because that is a universal interface. <br />
<br />
Following the Unix convention, programs have brief <tt>man</tt> pages, which explain the program purpose and parameters. You can access this documentation by running a program without parameters. To search for a program by a keyword, use <tt>sfdoc -k <keyword></tt>. <br />
<br />
The [[guide to madagascar programs]] provides more detailed documentation for selected programs while the [[task-centric program list]] attempts to categorize them. You can see the programs in actual use in the [[Reproducible Documents]].<br />
<br />
===Data format===<br />
<br />
For data, Madagascar uses the [[Guide to RSF file format| Regularly Sampled Format]] (RSF), which is based on the concept of hypercubes (n-D arrays, or regularly sampled functions of several variables), much like the SEPlib (its closest relative), DDS, or the regularly-sampled version of the Javaseis format (SVF). Up to 9 dimensions are supported. For 1D it is conceptually analogous to a time series, for 2D to a raster image, and for 3D to a [http://en.wikipedia.org/wiki/Voxel voxel volume]. The format (actually a [http://en.wikipedia.org/wiki/Meta meta]format) makes use of a ASCII file with metadata (information about the data), including a pointer (<tt>in=</tt> parameter) to the location of the file with the actual data values. Irregularly sampled data are currently handled as a pair of datasets, one containing data and the second containing the corresponding irregular geometry information. Programs for conversion to and from other formats such as SEG-Y and SU are provided. <br />
<br />
For graphics, Madagascar currently uses the Vplot vector graphics format. Converters to other graphics formats (Postscript, PNG, GIF, JPEG) are also provided.<br />
<br />
===Reproducible documents===<br />
<br />
A reproducible document consists of LaTeX source combined with SCons rules required to fully build the documents. These rules are expressed in terms of SCons extensions that are provided as part of Madagascar. <br />
<br />
This is the key to the reproducibility aspect of Madagascar. An introduction to reproducible Madagascar documents is at [[Reproducible_computational_experiments_using_SCons]] .<br />
<br />
===Vplot graphics===<br />
<br />
In contrast to most other Madagascar Components, graphics components produce Vplot data as output.<br />
<br />
Vplot is a device independent graphics format that allows both vector and raster elements (as such, <br />
it is comparable to Postscript). Vplot files are interpreted by a number of output devices. Its typical usage is for a visual display in X-windows. A list of them is [[Guide to madagascar programs#Plotting programs | provided on the wiki]].<br />
<br />
Here is an example of a Madagascar pipe. In this case it takes a subsection of a file, low-pass <br />
filters it, and saves the result<br />
<br />
<syntaxhighlight lang="bash"><br />
< data.rsf sfwindow n1=100 | sfbandpass fhi=60 > data2.rsf <br />
</syntaxhighlight><br />
<br />
In this more elaborate case, the final output is passed to a graphics program and plotted.<br />
<br />
<syntaxhighlight lang="bash"><br />
< data.rsf sfwindow n1=100 | sfbandpass fhi=60 | sfcontour | xtpen<br />
</syntaxhighlight><br />
<br />
More extensive examples are seen in [[Guide to madagascar programs]] . The novice reader should probably read the material below before proceeding to that page.<br />
<br />
===Reproducibility and Project Management===<br />
<br />
Madagascar uses and extends [http://www.scons.org/ SCons], an open-source <br />
software construction package, to document and maintain data processing flows. Documented projects become <br />
computational recipes that can be easily exchanged among Madagascar users. <br />
<br />
SCons is a rule-based package in Python typically used as a build system analogous to <tt>make</tt>. Familiarity with any build system will<br />
be helpful in understanding SCons. SCons statements, as python statements, are invoked in the sequence they are <br />
written, but as such they only define rules. The rules are invoked in accordance with a dependency graph which<br />
SCons builds based on those rules. Components regarded as "up-to-date" are not rebuilt. <br />
<br />
SCons allows for user-contributed Builders (meta-rule categories) and Madagascar uses this capability extensively. <br />
The idea is that building an output file based on a workflow chain is very much analogous to building a <br />
software package based on a software tool chain. The calculation is seen simply as a build with dependencies. <br />
This is a considerable benefit in developing alternative workflows using a given dataset. The system <br />
maintains an awareness of already completed calculations. Without user intervention, redundant calculations <br />
are avoided.<br />
<br />
Madagascar calculations are thus expressed as SCons scripts (<tt>SConstruct</tt> files). SCons extensions follow SCons conventions in beginning <br />
with an uppercase letter. The most common Madagascar extensions are <tt>Flow()</tt>, <tt>Result()</tt>, and <tt>End()</tt>. A <tt>Flow()</tt> invocation wraps Madagascar computational components. <tt>Result()</tt> is a version of <tt>Flow()</tt> with a graphical output. Finally an<br />
End() actually invokes the default rules for multiple results. <br />
<br />
Finally, Madagascar enables a collection of reproducible documents, organized in living books. Each <br />
reproducible book contains a collection of Madagascar recipes (<tt>SConstruct</tt> files) used to generate book figures. The recipes <br />
cover a variety of data processing and imaging tasks described in the books. Figures and recipes serve <br />
dual purpose with respect to Madagascar maintenance. They provide demos for introducing new users to the <br />
functionality of the package and, at the same time, [[Automatic Testing|regression tests]] for assuring the system stability <br />
under change.<br />
<br />
==Madagascar Trivia==<br />
<br />
===Why the Name "Madagascar"?===<br />
<br />
[http://ahay.org/blog/2006/04/19/madagascar/ Whimsy, really]. It seems easier to remember than the previous name "RSF", and it provides us interesting [http://ahay.org/blog/2008/10/21/ahay/ mascots].<br />
<br />
===License===<br />
<br />
The Madagascar package is released in an open-source form under the standard [http://www.gnu.org/copyleft/gpl.html GNU GPL] license. In simple <br />
words, there are no restrictions on the use of the software (including copying, modifying, selling, etc.) <br />
However, there are restrictions on the software redistribution intended to prevent the package from losing <br />
its open-source status. Users are encouraged to [[Contributing new programs to Madagascar|submit their modifications]] back to the original distribution for the benefit of the whole [[Package_overview#Community|community]].<br />
<br />
===Community===<br />
<br />
Madagascar seeks to be an open and active community. Mailing lists are maintained, and annual meetings take place. See <br />
* [[Conferences]]<br />
* [http://ahay.org/blog/ Development blog]<br />
* [https://lists.sourceforge.net/lists/listinfo/rsf-user RSF-user mailing list] <br />
* [https://lists.sourceforge.net/lists/listinfo/rsf-devel RSF-devel mailing list] <br />
* [http://www.linkedin.com/e/vgh/1847746 LinkedIn group]<br />
Your participation is welcome.<br />
<br />
===History=== <br />
<br />
Madagascar was first publicly presented at the [[Conferences#Vienna_2006_.28EAGE.29|EAGE Workshop]] in Vienna in June 2006. The work on the package (previously named RSF) was started by Sergey Fomel in 2003. Since then, many people have contributed to it. See [https://github.com/ahay/src/blob/master/AUTHORS.txt AUTHORS.txt] for an incomplete list.<br />
<br />
While being written mostly from scratch, Madagascar borrows ideas from the design of [http://sepwww.stanford.ed/doku.php?id=sep:software:seplib SEPlib], a package maintained by Bob Clapp at the Stanford Exploration Project (SEP). Generations of SEP students and researchers contributed to SEPlib. Most important contributions came from Rob Clayton, Jon Claerbout, Dave Hale, Stew Levin, Rick Ottolini, Joe Dellinger, Steve Cole, Dave Nichols, Martin Karrenbach, Biondo Biondi, and Bob Clapp.<br />
<br />
Madagascar also borrows ideas from [http://timna.mines.edu/cwpcodes/ Seismic Unix] (SU), an open-source package maintained by John Stockwell at the Center for Wave Phenomena (CWP) at the Colorado School of Mines (Stockwell, 1997<ref>Stockwell, J. W., 1997, Free software in education: A case study of CWP/SU: Seismic Unix: The Leading Edge, '''16''', 1045--1049.</ref>;Stockwell, 1999<ref>--------, 1999, The CWP/SU: Seismic Un*x package: Computers and Geosciences, '''25''', 415--419.</ref>). Main contributors to SU included Einar Kjartansson, Shuki Ronen, Jack Cohen, Chris Liner, Dave Hale, and John Stockwell. SU adopted an open-source BSD-style license starting with release 40 (April 10, 2007).<br />
<br />
<references/><br />
<br />
===Estimated Cost=== <br />
<br />
The Project Cost Calculator on Madagascar's [https://www.openhub.net/p/m8r Open Hub (formerly Ohloh) metrics page] shows the estimated cost of the project about $ 19,945,109 using the Basic COCOMO Model by April 20, 2020.</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Package_overview&diff=3898Package overview2020-08-23T10:30:17Z<p>Yangliu: /* Estimated Cost */</p>
<hr />
<div>[[Image:Fotolia_5127720_XS.jpg|right|]]<br />
<br />
The mission of the Madagascar project is to provide a '''shared research environment''' for computational data analysis in geophysics and related fields.<br />
<br />
The Madagascar environment consists of:<br />
# Standalone programs for out-of-core data analysis;<br />
# Standalone programs for geophysical data processing and imaging;<br />
# A development kit for C, C++, Java, Fortran-77, Fortran-90, Python, Matlab, and Octave;<br />
# A framework for reproducible numerical experiments, based on [http://www.scons.org/ SCons];<br />
# A framework for scientific publications, based on [http://www.scons.org/ SCons] and [http://en.wikipedia.org/wiki/LaTeX LaTeX];<br />
# A collection of reproducible scientific articles also used as usage examples and regression tests for the standalone programs;<br />
# A collection of datasets used as input to reproducible numerical experiments.<br />
<br />
This guide serves as a brief introduction of different components and shows how they all fit together.<br />
<br />
==How to obtain Madagascar==<br />
<br />
See [[Download|download]] and [[Installation | installation instructions]]. Madagascar runs on Unix/Linux platforms, including MacOS X and Unix emulations under Miscrosoft Windows. Its installation requires, at a minimum, a working C compiler and Python. <br />
<br />
==How to find your way around Madagascar==<br />
<br />
Start by checking the [[Reproducible_Documents|list of reproducible papers]]. If any of these papers looks close to your interests, follow the links until you find a figure with a "wrench" button under it [[Image:configure.png]]. Click on the wrench, and it will open a computational recipe used for generating the figure (the <tt>SConstruct</tt> file). <br />
<syntaxhighlight lang="python"><br />
from rsf.proj import *<br />
Flow('rose',None,<br />
'''<br />
math n1=629 d1=0.01 o1=0 n2=40 d2=1 o2=5 <br />
output="x2*(8+sin(6*x1+x2/10))" |<br />
rtoc |<br />
math output="input*exp(I*x1)"<br />
''')<br />
Result('rose',<br />
'graph title=Rose screenratio=1 wantaxis=n')<br />
End()<br />
</syntaxhighlight><br />
You can copy this recipe to your computer or simply find it already existing in the "book" subtree under the Madagascar source directory. For example, the recipe at http://www.reproducibility.org/RSF/book/rsf/rsf/sfmath.html also exists in the file <tt>RSFSRC/book/rsf/rsf/sfmath/SConstruct</tt>. After copying or locating the appropriate <tt>SConstruct</tt> file,<br />
run<br />
<pre><br />
scons view<br />
</pre><br />
on the command line to generate all the figures in the selected project and to display them on your screen. For example, try<br />
<pre><br />
bash$ cd RSFSRC/book/rsf/rsf/sfmath<br />
bash$ scons view<br />
</pre><br />
where <tt>bash$</tt> stands for the Unix prompt and <tt>RSFSRC</tt> stands for the Madagascar source directory. The output should look like<br />
<pre><br />
scons: Reading SConscript files ...<br />
scons: done reading SConscript files.<br />
scons: Building targets ...<br />
/RSFROOT/bin/sfmath n1=629 d1=0.01 o1=0 n2=40 d2=1 o2=5 output="x2*(8+sin(6*x1+x2/10))" | /RSFROOT/bin/sfrtoc | <br />
/RSFROOT/bin/sfmath output="input*exp(I*x1)" > rose.rsf<br />
< rose.rsf /RSFROOT/bin/sfgraph title=Rose screenratio=1 wantaxis=n > Fig/rose.vpl<br />
/RSFROOT/bin/sfpen Fig/rose.vpl<br />
scons: done building targets.<br />
</pre><br />
with a picture appearing on your screen.<br />
[[Image:rose.png|frame|center]]<br />
If there are several figures in the recipe, you can run<br />
<pre><br />
scons figurename.view<br />
</pre><br />
(e.g. <tt>scons rose.view</tt>) to display individual figures. To remove all files that <tt>scons view</tt> generated, run<br />
<pre><br />
scons -c view<br />
</pre><br />
If you want to know in advance what commands will be executed to generate the figures, try<br />
<pre><br />
scons -n view<br />
</pre><br />
You can output this command to a file<br />
<pre><br />
scons -n -Q view > script.sh<br />
</pre><br />
and use <tt>script.sh</tt> as a shell script. If you are to make modifications to the data processing recipe (changing parameters or trying new data), working with SCons is more powerful and convenient than running shell scripts.<br />
<br />
A computational recipe puts together individual commands through Unix pipes and SCons rules. These commands act like Lego blocks for creating complex data analysis constructions. In the example above, three "blocks" are used: <tt>sfmath</tt>, <tt>sfrtoc</tt>, and <tt>sfgraph</tt>. To find out what a particular command is doing, you can follow the links from the bottom of the web page http://www.reproducibility.org/RSF/book/rsf/rsf/sfmath.html<br />
Alternatively, run the command without arguments on the command line. Running<br />
<pre><br />
bash$ sfrtoc<br />
</pre><br />
produces something like<br />
<pre><br />
NAME<br />
sfrtoc<br />
DESCRIPTION<br />
Convert real data to complex (by adding zero imaginary part).<br />
SYNOPSIS<br />
sfrtoc < real.rsf > cmplx.rsf<br />
COMMENTS <br />
See also: sfcmplx<br />
USED IN<br />
bei/ft1/plane4<br />
bei/ft1/autocor<br />
bei/ft1/brad<br />
[...]<br />
SOURCE<br />
user/main/rtoc.c<br />
DOCUMENTATION<br />
http://reproducibility.org/wiki/Guide_to_madagascar_programs#sfrtoc<br />
</pre><br />
<br />
The <b>DOCUMENTATION</b> section provides a link to a more detailed documentation on the web. The most useful part is the <b>USED IN</b> section, which points to more examples of using the program. As an exercise, change directory to <tt>RSFSRC/book/bei/ft1/plane4</tt> or any other example directory, examine the <tt>SConstruct</tt> file, and run <tt>scons view</tt>. Alternatively, look at http://www.reproducibility.org/RSF/book/bei/ft1/plane4.html<br />
<br />
Want to find a program by keywords? Try <tt>sfdoc -k</tt>.<br />
<pre><br />
bash$ sfdoc -k complex<br />
sfsort: Sort a float/complex vector by absolute values.<br />
sfrtoc: Convert real data to complex (by adding zero imaginary part).<br />
sfjacobi2: Find eigenvalues of a general complex matrix by Jacobi-like iteration. <br />
sfboolcmp: Element-wise boolean comparison of values. For int/float/complex data-sets.<br />
sfcmatmult: Simple matrix multiplication for complex matrices <br />
sfimag: Extract real (sfreal) or imaginary (sfimag) part of a complex dataset. <br />
sfthr: Threshold float/complex inputs given a constant/varying threshold level.<br />
sfcpef: 1-D prediction-error filter estimation from complex data <br />
sfroots: Find roots of a complex polynomial. <br />
sfreal: Extract real (sfreal) or imaginary (sfimag) part of a complex dataset. <br />
sfcmplx: Create a complex dataset from its real and imaginary parts.<br />
sfsin: Simple operations with complex sinusoids <br />
sfcdottest: Generic dot-product test for complex linear operators with adjoints <br />
sfcconjgrad: Generic conjugate-gradient solver for linear inversion with complex data<br />
</pre><br />
<br />
Individual components of the Madagascar environment are described in more details below.<br />
<br />
==Madagascar components==<br />
<br />
===Standalone programs===<br />
The list of all standalone programs is available [http://www.reproducibility.org/RSF/ online]. Most programs act as filters on input data and can be chained through Unix pipes, i.e.:<br />
<bash><br />
< data.rsf sfwindow n1=100 | sfbandpass fhi=60 > data2.rsf<br />
</bash><br />
This approach follows the Unix philosophy, as formulated by Doug McIlroy, the inventor of Unix pipes (Salus, 1994<ref>Salus, P. H., 1994, A quarter-century of Unix: Addison-Wesley.</ref>): <br />
#Write programs that do one thing and do it well. <br />
#Write programs to work together. <br />
#Write programs to handle text streams, because that is a universal interface. <br />
<br />
Following the Unix convention, programs have brief <tt>man</tt> pages, which explain the program purpose and parameters. You can access this documentation by running a program without parameters. To search for a program by a keyword, use <tt>sfdoc -k <keyword></tt>. <br />
<br />
The [[guide to madagascar programs]] provides more detailed documentation for selected programs while the [[task-centric program list]] attempts to categorize them. You can see the programs in actual use in the [[Reproducible Documents]].<br />
<br />
===Data format===<br />
<br />
For data, Madagascar uses the [[Guide to RSF file format| Regularly Sampled Format]] (RSF), which is based on the concept of hypercubes (n-D arrays, or regularly sampled functions of several variables), much like the SEPlib (its closest relative), DDS, or the regularly-sampled version of the Javaseis format (SVF). Up to 9 dimensions are supported. For 1D it is conceptually analogous to a time series, for 2D to a raster image, and for 3D to a [http://en.wikipedia.org/wiki/Voxel voxel volume]. The format (actually a [http://en.wikipedia.org/wiki/Meta meta]format) makes use of a ASCII file with metadata (information about the data), including a pointer (<tt>in=</tt> parameter) to the location of the file with the actual data values. Irregularly sampled data are currently handled as a pair of datasets, one containing data and the second containing the corresponding irregular geometry information. Programs for conversion to and from other formats such as SEG-Y and SU are provided. <br />
<br />
For graphics, Madagascar currently uses the Vplot vector graphics format. Converters to other graphics formats (Postscript, PNG, GIF, JPEG) are also provided.<br />
<br />
===Reproducible documents===<br />
<br />
A reproducible document consists of LaTeX source combined with SCons rules required to fully build the documents. These rules are expressed in terms of SCons extensions that are provided as part of Madagascar. <br />
<br />
This is the key to the reproducibility aspect of Madagascar. An introduction to reproducible Madagascar documents is at [[Reproducible_computational_experiments_using_SCons]] .<br />
<br />
===Vplot graphics===<br />
<br />
In contrast to most other Madagascar Components, graphics components produce Vplot data as output.<br />
<br />
Vplot is a device independent graphics format that allows both vector and raster elements (as such, <br />
it is comparable to Postscript). Vplot files are interpreted by a number of output devices. Its typical usage is for a visual display in X-windows. A list of them is [[Guide to madagascar programs#Plotting programs | provided on the wiki]].<br />
<br />
Here is an example of a Madagascar pipe. In this case it takes a subsection of a file, low-pass <br />
filters it, and saves the result<br />
<br />
<syntaxhighlight lang="bash"><br />
< data.rsf sfwindow n1=100 | sfbandpass fhi=60 > data2.rsf <br />
</syntaxhighlight><br />
<br />
In this more elaborate case, the final output is passed to a graphics program and plotted.<br />
<br />
<syntaxhighlight lang="bash"><br />
< data.rsf sfwindow n1=100 | sfbandpass fhi=60 | sfcontour | xtpen<br />
</syntaxhighlight><br />
<br />
More extensive examples are seen in [[Guide to madagascar programs]] . The novice reader should probably read the material below before proceeding to that page.<br />
<br />
===Reproducibility and Project Management===<br />
<br />
Madagascar uses and extends [http://www.scons.org/ SCons], an open-source <br />
software construction package, to document and maintain data processing flows. Documented projects become <br />
computational recipes that can be easily exchanged among Madagascar users. <br />
<br />
SCons is a rule-based package in Python typically used as a build system analogous to <tt>make</tt>. Familiarity with any build system will<br />
be helpful in understanding SCons. SCons statements, as python statements, are invoked in the sequence they are <br />
written, but as such they only define rules. The rules are invoked in accordance with a dependency graph which<br />
SCons builds based on those rules. Components regarded as "up-to-date" are not rebuilt. <br />
<br />
SCons allows for user-contributed Builders (meta-rule categories) and Madagascar uses this capability extensively. <br />
The idea is that building an output file based on a workflow chain is very much analogous to building a <br />
software package based on a software tool chain. The calculation is seen simply as a build with dependencies. <br />
This is a considerable benefit in developing alternative workflows using a given dataset. The system <br />
maintains an awareness of already completed calculations. Without user intervention, redundant calculations <br />
are avoided.<br />
<br />
Madagascar calculations are thus expressed as SCons scripts (<tt>SConstruct</tt> files). SCons extensions follow SCons conventions in beginning <br />
with an uppercase letter. The most common Madagascar extensions are <tt>Flow()</tt>, <tt>Result()</tt>, and <tt>End()</tt>. A <tt>Flow()</tt> invocation wraps Madagascar computational components. <tt>Result()</tt> is a version of <tt>Flow()</tt> with a graphical output. Finally an<br />
End() actually invokes the default rules for multiple results. <br />
<br />
Finally, Madagascar enables a collection of reproducible documents, organized in living books. Each <br />
reproducible book contains a collection of Madagascar recipes (<tt>SConstruct</tt> files) used to generate book figures. The recipes <br />
cover a variety of data processing and imaging tasks described in the books. Figures and recipes serve <br />
dual purpose with respect to Madagascar maintenance. They provide demos for introducing new users to the <br />
functionality of the package and, at the same time, [[Automatic Testing|regression tests]] for assuring the system stability <br />
under change.<br />
<br />
==Madagascar Trivia==<br />
<br />
===Why the Name "Madagascar"?===<br />
<br />
[http://ahay.org/blog/2006/04/19/madagascar/ Whimsy, really]. It seems easier to remember than the previous name "RSF", and it provides us interesting [http://ahay.org/blog/2008/10/21/ahay/ mascots].<br />
<br />
===License===<br />
<br />
The Madagascar package is released in an open-source form under the standard [http://www.gnu.org/copyleft/gpl.html GNU GPL] license. In simple <br />
words, there are no restrictions on the use of the software (including copying, modifying, selling, etc.) <br />
However, there are restrictions on the software redistribution intended to prevent the package from losing <br />
its open-source status. Users are encouraged to [[Contributing new programs to Madagascar|submit their modifications]] back to the original distribution for the benefit of the whole [[Package_overview#Community|community]].<br />
<br />
===Community===<br />
<br />
Madagascar seeks to be an open and active community. Mailing lists are maintained, and annual meetings take place. See <br />
* [[Conferences]]<br />
* [http://ahay.org/blog/ Development blog]<br />
* [https://lists.sourceforge.net/lists/listinfo/rsf-user RSF-user mailing list] <br />
* [https://lists.sourceforge.net/lists/listinfo/rsf-devel RSF-devel mailing list] <br />
* [http://www.linkedin.com/e/vgh/1847746 LinkedIn group]<br />
Your participation is welcome.<br />
<br />
===History=== <br />
<br />
Madagascar was first publicly presented at the [[Conferences#Vienna_2006_.28EAGE.29|EAGE Workshop]] in Vienna in June 2006. The work on the package (previously named RSF) was started by Sergey Fomel in 2003. Since then, many people have contributed to it. See [https://github.com/ahay/src/blob/master/AUTHORS.txt AUTHORS.txt] for an incomplete list.<br />
<br />
While being written mostly from scratch, Madagascar borrows ideas from the design of [http://sepwww.stanford.ed/doku.php?id=sep:software:seplib SEPlib], a package maintained by Bob Clapp at the Stanford Exploration Project (SEP). Generations of SEP students and researchers contributed to SEPlib. Most important contributions came from Rob Clayton, Jon Claerbout, Dave Hale, Stew Levin, Rick Ottolini, Joe Dellinger, Steve Cole, Dave Nichols, Martin Karrenbach, Biondo Biondi, and Bob Clapp.<br />
<br />
Madagascar also borrows ideas from [http://timna.mines.edu/cwpcodes/ Seismic Unix] (SU), an open-source package maintained by John Stockwell at the Center for Wave Phenomena (CWP) at the Colorado School of Mines (Stockwell, 1997<ref>Stockwell, J. W., 1997, Free software in education: A case study of CWP/SU: Seismic Unix: The Leading Edge, '''16''', 1045--1049.</ref>;Stockwell, 1999<ref>--------, 1999, The CWP/SU: Seismic Un*x package: Computers and Geosciences, '''25''', 415--419.</ref>). Main contributors to SU included Einar Kjartansson, Shuki Ronen, Jack Cohen, Chris Liner, Dave Hale, and John Stockwell. SU adopted an open-source BSD-style license starting with release 40 (April 10, 2007).<br />
<br />
<references/><br />
<br />
===Estimated Cost=== <br />
<br />
The Project Cost Calculator on Madagascar's [https://www.openhub.net/p/m8r Open Hub (formerly Ohloh) metrics page] shows the estimated cost of the project about $ 19,945,109 using the Basic COCOMO Model by the end of April 20, 2020.</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Package_overview&diff=3897Package overview2020-08-23T10:27:08Z<p>Yangliu: </p>
<hr />
<div>[[Image:Fotolia_5127720_XS.jpg|right|]]<br />
<br />
The mission of the Madagascar project is to provide a '''shared research environment''' for computational data analysis in geophysics and related fields.<br />
<br />
The Madagascar environment consists of:<br />
# Standalone programs for out-of-core data analysis;<br />
# Standalone programs for geophysical data processing and imaging;<br />
# A development kit for C, C++, Java, Fortran-77, Fortran-90, Python, Matlab, and Octave;<br />
# A framework for reproducible numerical experiments, based on [http://www.scons.org/ SCons];<br />
# A framework for scientific publications, based on [http://www.scons.org/ SCons] and [http://en.wikipedia.org/wiki/LaTeX LaTeX];<br />
# A collection of reproducible scientific articles also used as usage examples and regression tests for the standalone programs;<br />
# A collection of datasets used as input to reproducible numerical experiments.<br />
<br />
This guide serves as a brief introduction of different components and shows how they all fit together.<br />
<br />
==How to obtain Madagascar==<br />
<br />
See [[Download|download]] and [[Installation | installation instructions]]. Madagascar runs on Unix/Linux platforms, including MacOS X and Unix emulations under Miscrosoft Windows. Its installation requires, at a minimum, a working C compiler and Python. <br />
<br />
==How to find your way around Madagascar==<br />
<br />
Start by checking the [[Reproducible_Documents|list of reproducible papers]]. If any of these papers looks close to your interests, follow the links until you find a figure with a "wrench" button under it [[Image:configure.png]]. Click on the wrench, and it will open a computational recipe used for generating the figure (the <tt>SConstruct</tt> file). <br />
<syntaxhighlight lang="python"><br />
from rsf.proj import *<br />
Flow('rose',None,<br />
'''<br />
math n1=629 d1=0.01 o1=0 n2=40 d2=1 o2=5 <br />
output="x2*(8+sin(6*x1+x2/10))" |<br />
rtoc |<br />
math output="input*exp(I*x1)"<br />
''')<br />
Result('rose',<br />
'graph title=Rose screenratio=1 wantaxis=n')<br />
End()<br />
</syntaxhighlight><br />
You can copy this recipe to your computer or simply find it already existing in the "book" subtree under the Madagascar source directory. For example, the recipe at http://www.reproducibility.org/RSF/book/rsf/rsf/sfmath.html also exists in the file <tt>RSFSRC/book/rsf/rsf/sfmath/SConstruct</tt>. After copying or locating the appropriate <tt>SConstruct</tt> file,<br />
run<br />
<pre><br />
scons view<br />
</pre><br />
on the command line to generate all the figures in the selected project and to display them on your screen. For example, try<br />
<pre><br />
bash$ cd RSFSRC/book/rsf/rsf/sfmath<br />
bash$ scons view<br />
</pre><br />
where <tt>bash$</tt> stands for the Unix prompt and <tt>RSFSRC</tt> stands for the Madagascar source directory. The output should look like<br />
<pre><br />
scons: Reading SConscript files ...<br />
scons: done reading SConscript files.<br />
scons: Building targets ...<br />
/RSFROOT/bin/sfmath n1=629 d1=0.01 o1=0 n2=40 d2=1 o2=5 output="x2*(8+sin(6*x1+x2/10))" | /RSFROOT/bin/sfrtoc | <br />
/RSFROOT/bin/sfmath output="input*exp(I*x1)" > rose.rsf<br />
< rose.rsf /RSFROOT/bin/sfgraph title=Rose screenratio=1 wantaxis=n > Fig/rose.vpl<br />
/RSFROOT/bin/sfpen Fig/rose.vpl<br />
scons: done building targets.<br />
</pre><br />
with a picture appearing on your screen.<br />
[[Image:rose.png|frame|center]]<br />
If there are several figures in the recipe, you can run<br />
<pre><br />
scons figurename.view<br />
</pre><br />
(e.g. <tt>scons rose.view</tt>) to display individual figures. To remove all files that <tt>scons view</tt> generated, run<br />
<pre><br />
scons -c view<br />
</pre><br />
If you want to know in advance what commands will be executed to generate the figures, try<br />
<pre><br />
scons -n view<br />
</pre><br />
You can output this command to a file<br />
<pre><br />
scons -n -Q view > script.sh<br />
</pre><br />
and use <tt>script.sh</tt> as a shell script. If you are to make modifications to the data processing recipe (changing parameters or trying new data), working with SCons is more powerful and convenient than running shell scripts.<br />
<br />
A computational recipe puts together individual commands through Unix pipes and SCons rules. These commands act like Lego blocks for creating complex data analysis constructions. In the example above, three "blocks" are used: <tt>sfmath</tt>, <tt>sfrtoc</tt>, and <tt>sfgraph</tt>. To find out what a particular command is doing, you can follow the links from the bottom of the web page http://www.reproducibility.org/RSF/book/rsf/rsf/sfmath.html<br />
Alternatively, run the command without arguments on the command line. Running<br />
<pre><br />
bash$ sfrtoc<br />
</pre><br />
produces something like<br />
<pre><br />
NAME<br />
sfrtoc<br />
DESCRIPTION<br />
Convert real data to complex (by adding zero imaginary part).<br />
SYNOPSIS<br />
sfrtoc < real.rsf > cmplx.rsf<br />
COMMENTS <br />
See also: sfcmplx<br />
USED IN<br />
bei/ft1/plane4<br />
bei/ft1/autocor<br />
bei/ft1/brad<br />
[...]<br />
SOURCE<br />
user/main/rtoc.c<br />
DOCUMENTATION<br />
http://reproducibility.org/wiki/Guide_to_madagascar_programs#sfrtoc<br />
</pre><br />
<br />
The <b>DOCUMENTATION</b> section provides a link to a more detailed documentation on the web. The most useful part is the <b>USED IN</b> section, which points to more examples of using the program. As an exercise, change directory to <tt>RSFSRC/book/bei/ft1/plane4</tt> or any other example directory, examine the <tt>SConstruct</tt> file, and run <tt>scons view</tt>. Alternatively, look at http://www.reproducibility.org/RSF/book/bei/ft1/plane4.html<br />
<br />
Want to find a program by keywords? Try <tt>sfdoc -k</tt>.<br />
<pre><br />
bash$ sfdoc -k complex<br />
sfsort: Sort a float/complex vector by absolute values.<br />
sfrtoc: Convert real data to complex (by adding zero imaginary part).<br />
sfjacobi2: Find eigenvalues of a general complex matrix by Jacobi-like iteration. <br />
sfboolcmp: Element-wise boolean comparison of values. For int/float/complex data-sets.<br />
sfcmatmult: Simple matrix multiplication for complex matrices <br />
sfimag: Extract real (sfreal) or imaginary (sfimag) part of a complex dataset. <br />
sfthr: Threshold float/complex inputs given a constant/varying threshold level.<br />
sfcpef: 1-D prediction-error filter estimation from complex data <br />
sfroots: Find roots of a complex polynomial. <br />
sfreal: Extract real (sfreal) or imaginary (sfimag) part of a complex dataset. <br />
sfcmplx: Create a complex dataset from its real and imaginary parts.<br />
sfsin: Simple operations with complex sinusoids <br />
sfcdottest: Generic dot-product test for complex linear operators with adjoints <br />
sfcconjgrad: Generic conjugate-gradient solver for linear inversion with complex data<br />
</pre><br />
<br />
Individual components of the Madagascar environment are described in more details below.<br />
<br />
==Madagascar components==<br />
<br />
===Standalone programs===<br />
The list of all standalone programs is available [http://www.reproducibility.org/RSF/ online]. Most programs act as filters on input data and can be chained through Unix pipes, i.e.:<br />
<bash><br />
< data.rsf sfwindow n1=100 | sfbandpass fhi=60 > data2.rsf<br />
</bash><br />
This approach follows the Unix philosophy, as formulated by Doug McIlroy, the inventor of Unix pipes (Salus, 1994<ref>Salus, P. H., 1994, A quarter-century of Unix: Addison-Wesley.</ref>): <br />
#Write programs that do one thing and do it well. <br />
#Write programs to work together. <br />
#Write programs to handle text streams, because that is a universal interface. <br />
<br />
Following the Unix convention, programs have brief <tt>man</tt> pages, which explain the program purpose and parameters. You can access this documentation by running a program without parameters. To search for a program by a keyword, use <tt>sfdoc -k <keyword></tt>. <br />
<br />
The [[guide to madagascar programs]] provides more detailed documentation for selected programs while the [[task-centric program list]] attempts to categorize them. You can see the programs in actual use in the [[Reproducible Documents]].<br />
<br />
===Data format===<br />
<br />
For data, Madagascar uses the [[Guide to RSF file format| Regularly Sampled Format]] (RSF), which is based on the concept of hypercubes (n-D arrays, or regularly sampled functions of several variables), much like the SEPlib (its closest relative), DDS, or the regularly-sampled version of the Javaseis format (SVF). Up to 9 dimensions are supported. For 1D it is conceptually analogous to a time series, for 2D to a raster image, and for 3D to a [http://en.wikipedia.org/wiki/Voxel voxel volume]. The format (actually a [http://en.wikipedia.org/wiki/Meta meta]format) makes use of a ASCII file with metadata (information about the data), including a pointer (<tt>in=</tt> parameter) to the location of the file with the actual data values. Irregularly sampled data are currently handled as a pair of datasets, one containing data and the second containing the corresponding irregular geometry information. Programs for conversion to and from other formats such as SEG-Y and SU are provided. <br />
<br />
For graphics, Madagascar currently uses the Vplot vector graphics format. Converters to other graphics formats (Postscript, PNG, GIF, JPEG) are also provided.<br />
<br />
===Reproducible documents===<br />
<br />
A reproducible document consists of LaTeX source combined with SCons rules required to fully build the documents. These rules are expressed in terms of SCons extensions that are provided as part of Madagascar. <br />
<br />
This is the key to the reproducibility aspect of Madagascar. An introduction to reproducible Madagascar documents is at [[Reproducible_computational_experiments_using_SCons]] .<br />
<br />
===Vplot graphics===<br />
<br />
In contrast to most other Madagascar Components, graphics components produce Vplot data as output.<br />
<br />
Vplot is a device independent graphics format that allows both vector and raster elements (as such, <br />
it is comparable to Postscript). Vplot files are interpreted by a number of output devices. Its typical usage is for a visual display in X-windows. A list of them is [[Guide to madagascar programs#Plotting programs | provided on the wiki]].<br />
<br />
Here is an example of a Madagascar pipe. In this case it takes a subsection of a file, low-pass <br />
filters it, and saves the result<br />
<br />
<syntaxhighlight lang="bash"><br />
< data.rsf sfwindow n1=100 | sfbandpass fhi=60 > data2.rsf <br />
</syntaxhighlight><br />
<br />
In this more elaborate case, the final output is passed to a graphics program and plotted.<br />
<br />
<syntaxhighlight lang="bash"><br />
< data.rsf sfwindow n1=100 | sfbandpass fhi=60 | sfcontour | xtpen<br />
</syntaxhighlight><br />
<br />
More extensive examples are seen in [[Guide to madagascar programs]] . The novice reader should probably read the material below before proceeding to that page.<br />
<br />
===Reproducibility and Project Management===<br />
<br />
Madagascar uses and extends [http://www.scons.org/ SCons], an open-source <br />
software construction package, to document and maintain data processing flows. Documented projects become <br />
computational recipes that can be easily exchanged among Madagascar users. <br />
<br />
SCons is a rule-based package in Python typically used as a build system analogous to <tt>make</tt>. Familiarity with any build system will<br />
be helpful in understanding SCons. SCons statements, as python statements, are invoked in the sequence they are <br />
written, but as such they only define rules. The rules are invoked in accordance with a dependency graph which<br />
SCons builds based on those rules. Components regarded as "up-to-date" are not rebuilt. <br />
<br />
SCons allows for user-contributed Builders (meta-rule categories) and Madagascar uses this capability extensively. <br />
The idea is that building an output file based on a workflow chain is very much analogous to building a <br />
software package based on a software tool chain. The calculation is seen simply as a build with dependencies. <br />
This is a considerable benefit in developing alternative workflows using a given dataset. The system <br />
maintains an awareness of already completed calculations. Without user intervention, redundant calculations <br />
are avoided.<br />
<br />
Madagascar calculations are thus expressed as SCons scripts (<tt>SConstruct</tt> files). SCons extensions follow SCons conventions in beginning <br />
with an uppercase letter. The most common Madagascar extensions are <tt>Flow()</tt>, <tt>Result()</tt>, and <tt>End()</tt>. A <tt>Flow()</tt> invocation wraps Madagascar computational components. <tt>Result()</tt> is a version of <tt>Flow()</tt> with a graphical output. Finally an<br />
End() actually invokes the default rules for multiple results. <br />
<br />
Finally, Madagascar enables a collection of reproducible documents, organized in living books. Each <br />
reproducible book contains a collection of Madagascar recipes (<tt>SConstruct</tt> files) used to generate book figures. The recipes <br />
cover a variety of data processing and imaging tasks described in the books. Figures and recipes serve <br />
dual purpose with respect to Madagascar maintenance. They provide demos for introducing new users to the <br />
functionality of the package and, at the same time, [[Automatic Testing|regression tests]] for assuring the system stability <br />
under change.<br />
<br />
==Madagascar Trivia==<br />
<br />
===Why the Name "Madagascar"?===<br />
<br />
[http://ahay.org/blog/2006/04/19/madagascar/ Whimsy, really]. It seems easier to remember than the previous name "RSF", and it provides us interesting [http://ahay.org/blog/2008/10/21/ahay/ mascots].<br />
<br />
===License===<br />
<br />
The Madagascar package is released in an open-source form under the standard [http://www.gnu.org/copyleft/gpl.html GNU GPL] license. In simple <br />
words, there are no restrictions on the use of the software (including copying, modifying, selling, etc.) <br />
However, there are restrictions on the software redistribution intended to prevent the package from losing <br />
its open-source status. Users are encouraged to [[Contributing new programs to Madagascar|submit their modifications]] back to the original distribution for the benefit of the whole [[Package_overview#Community|community]].<br />
<br />
===Community===<br />
<br />
Madagascar seeks to be an open and active community. Mailing lists are maintained, and annual meetings take place. See <br />
* [[Conferences]]<br />
* [http://ahay.org/blog/ Development blog]<br />
* [https://lists.sourceforge.net/lists/listinfo/rsf-user RSF-user mailing list] <br />
* [https://lists.sourceforge.net/lists/listinfo/rsf-devel RSF-devel mailing list] <br />
* [http://www.linkedin.com/e/vgh/1847746 LinkedIn group]<br />
Your participation is welcome.<br />
<br />
===History=== <br />
<br />
Madagascar was first publicly presented at the [[Conferences#Vienna_2006_.28EAGE.29|EAGE Workshop]] in Vienna in June 2006. The work on the package (previously named RSF) was started by Sergey Fomel in 2003. Since then, many people have contributed to it. See [https://github.com/ahay/src/blob/master/AUTHORS.txt AUTHORS.txt] for an incomplete list.<br />
<br />
While being written mostly from scratch, Madagascar borrows ideas from the design of [http://sepwww.stanford.ed/doku.php?id=sep:software:seplib SEPlib], a package maintained by Bob Clapp at the Stanford Exploration Project (SEP). Generations of SEP students and researchers contributed to SEPlib. Most important contributions came from Rob Clayton, Jon Claerbout, Dave Hale, Stew Levin, Rick Ottolini, Joe Dellinger, Steve Cole, Dave Nichols, Martin Karrenbach, Biondo Biondi, and Bob Clapp.<br />
<br />
Madagascar also borrows ideas from [http://timna.mines.edu/cwpcodes/ Seismic Unix] (SU), an open-source package maintained by John Stockwell at the Center for Wave Phenomena (CWP) at the Colorado School of Mines (Stockwell, 1997<ref>Stockwell, J. W., 1997, Free software in education: A case study of CWP/SU: Seismic Unix: The Leading Edge, '''16''', 1045--1049.</ref>;Stockwell, 1999<ref>--------, 1999, The CWP/SU: Seismic Un*x package: Computers and Geosciences, '''25''', 415--419.</ref>). Main contributors to SU included Einar Kjartansson, Shuki Ronen, Jack Cohen, Chris Liner, Dave Hale, and John Stockwell. SU adopted an open-source BSD-style license starting with release 40 (April 10, 2007).<br />
<br />
<references/><br />
<br />
===Estimated Cost=== <br />
<br />
The Project Cost Calculator on Madagascar's [https://www.openhub.net/p/m8r Open Hub (formerly Ohloh) metrics page] shows the estimated cost of the project using the Basic COCOMO Model.</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Package_overview&diff=3896Package overview2020-08-23T10:01:15Z<p>Yangliu: /* Community */</p>
<hr />
<div>[[Image:Fotolia_5127720_XS.jpg|right|]]<br />
<br />
The mission of the Madagascar project is to provide a '''shared research environment''' for computational data analysis in geophysics and related fields.<br />
<br />
The Madagascar environment consists of:<br />
# Standalone programs for out-of-core data analysis;<br />
# Standalone programs for geophysical data processing and imaging;<br />
# A development kit for C, C++, Java, Fortran-77, Fortran-90, Python, Matlab, and Octave;<br />
# A framework for reproducible numerical experiments, based on [http://www.scons.org/ SCons];<br />
# A framework for scientific publications, based on [http://www.scons.org/ SCons] and [http://en.wikipedia.org/wiki/LaTeX LaTeX];<br />
# A collection of reproducible scientific articles also used as usage examples and regression tests for the standalone programs;<br />
# A collection of datasets used as input to reproducible numerical experiments.<br />
<br />
This guide serves as a brief introduction of different components and shows how they all fit together.<br />
<br />
==How to obtain Madagascar==<br />
<br />
See [[Download|download]] and [[Installation | installation instructions]]. Madagascar runs on Unix/Linux platforms, including MacOS X and Unix emulations under Miscrosoft Windows. Its installation requires, at a minimum, a working C compiler and Python. <br />
<br />
==How to find your way around Madagascar==<br />
<br />
Start by checking the [[Reproducible_Documents|list of reproducible papers]]. If any of these papers looks close to your interests, follow the links until you find a figure with a "wrench" button under it [[Image:configure.png]]. Click on the wrench, and it will open a computational recipe used for generating the figure (the <tt>SConstruct</tt> file). <br />
<syntaxhighlight lang="python"><br />
from rsf.proj import *<br />
Flow('rose',None,<br />
'''<br />
math n1=629 d1=0.01 o1=0 n2=40 d2=1 o2=5 <br />
output="x2*(8+sin(6*x1+x2/10))" |<br />
rtoc |<br />
math output="input*exp(I*x1)"<br />
''')<br />
Result('rose',<br />
'graph title=Rose screenratio=1 wantaxis=n')<br />
End()<br />
</syntaxhighlight><br />
You can copy this recipe to your computer or simply find it already existing in the "book" subtree under the Madagascar source directory. For example, the recipe at http://www.reproducibility.org/RSF/book/rsf/rsf/sfmath.html also exists in the file <tt>RSFSRC/book/rsf/rsf/sfmath/SConstruct</tt>. After copying or locating the appropriate <tt>SConstruct</tt> file,<br />
run<br />
<pre><br />
scons view<br />
</pre><br />
on the command line to generate all the figures in the selected project and to display them on your screen. For example, try<br />
<pre><br />
bash$ cd RSFSRC/book/rsf/rsf/sfmath<br />
bash$ scons view<br />
</pre><br />
where <tt>bash$</tt> stands for the Unix prompt and <tt>RSFSRC</tt> stands for the Madagascar source directory. The output should look like<br />
<pre><br />
scons: Reading SConscript files ...<br />
scons: done reading SConscript files.<br />
scons: Building targets ...<br />
/RSFROOT/bin/sfmath n1=629 d1=0.01 o1=0 n2=40 d2=1 o2=5 output="x2*(8+sin(6*x1+x2/10))" | /RSFROOT/bin/sfrtoc | <br />
/RSFROOT/bin/sfmath output="input*exp(I*x1)" > rose.rsf<br />
< rose.rsf /RSFROOT/bin/sfgraph title=Rose screenratio=1 wantaxis=n > Fig/rose.vpl<br />
/RSFROOT/bin/sfpen Fig/rose.vpl<br />
scons: done building targets.<br />
</pre><br />
with a picture appearing on your screen.<br />
[[Image:rose.png|frame|center]]<br />
If there are several figures in the recipe, you can run<br />
<pre><br />
scons figurename.view<br />
</pre><br />
(e.g. <tt>scons rose.view</tt>) to display individual figures. To remove all files that <tt>scons view</tt> generated, run<br />
<pre><br />
scons -c view<br />
</pre><br />
If you want to know in advance what commands will be executed to generate the figures, try<br />
<pre><br />
scons -n view<br />
</pre><br />
You can output this command to a file<br />
<pre><br />
scons -n -Q view > script.sh<br />
</pre><br />
and use <tt>script.sh</tt> as a shell script. If you are to make modifications to the data processing recipe (changing parameters or trying new data), working with SCons is more powerful and convenient than running shell scripts.<br />
<br />
A computational recipe puts together individual commands through Unix pipes and SCons rules. These commands act like Lego blocks for creating complex data analysis constructions. In the example above, three "blocks" are used: <tt>sfmath</tt>, <tt>sfrtoc</tt>, and <tt>sfgraph</tt>. To find out what a particular command is doing, you can follow the links from the bottom of the web page http://www.reproducibility.org/RSF/book/rsf/rsf/sfmath.html<br />
Alternatively, run the command without arguments on the command line. Running<br />
<pre><br />
bash$ sfrtoc<br />
</pre><br />
produces something like<br />
<pre><br />
NAME<br />
sfrtoc<br />
DESCRIPTION<br />
Convert real data to complex (by adding zero imaginary part).<br />
SYNOPSIS<br />
sfrtoc < real.rsf > cmplx.rsf<br />
COMMENTS <br />
See also: sfcmplx<br />
USED IN<br />
bei/ft1/plane4<br />
bei/ft1/autocor<br />
bei/ft1/brad<br />
[...]<br />
SOURCE<br />
user/main/rtoc.c<br />
DOCUMENTATION<br />
http://reproducibility.org/wiki/Guide_to_madagascar_programs#sfrtoc<br />
</pre><br />
<br />
The <b>DOCUMENTATION</b> section provides a link to a more detailed documentation on the web. The most useful part is the <b>USED IN</b> section, which points to more examples of using the program. As an exercise, change directory to <tt>RSFSRC/book/bei/ft1/plane4</tt> or any other example directory, examine the <tt>SConstruct</tt> file, and run <tt>scons view</tt>. Alternatively, look at http://www.reproducibility.org/RSF/book/bei/ft1/plane4.html<br />
<br />
Want to find a program by keywords? Try <tt>sfdoc -k</tt>.<br />
<pre><br />
bash$ sfdoc -k complex<br />
sfsort: Sort a float/complex vector by absolute values.<br />
sfrtoc: Convert real data to complex (by adding zero imaginary part).<br />
sfjacobi2: Find eigenvalues of a general complex matrix by Jacobi-like iteration. <br />
sfboolcmp: Element-wise boolean comparison of values. For int/float/complex data-sets.<br />
sfcmatmult: Simple matrix multiplication for complex matrices <br />
sfimag: Extract real (sfreal) or imaginary (sfimag) part of a complex dataset. <br />
sfthr: Threshold float/complex inputs given a constant/varying threshold level.<br />
sfcpef: 1-D prediction-error filter estimation from complex data <br />
sfroots: Find roots of a complex polynomial. <br />
sfreal: Extract real (sfreal) or imaginary (sfimag) part of a complex dataset. <br />
sfcmplx: Create a complex dataset from its real and imaginary parts.<br />
sfsin: Simple operations with complex sinusoids <br />
sfcdottest: Generic dot-product test for complex linear operators with adjoints <br />
sfcconjgrad: Generic conjugate-gradient solver for linear inversion with complex data<br />
</pre><br />
<br />
Individual components of the Madagascar environment are described in more details below.<br />
<br />
==Madagascar components==<br />
<br />
===Standalone programs===<br />
The list of all standalone programs is available [http://www.reproducibility.org/RSF/ online]. Most programs act as filters on input data and can be chained through Unix pipes, i.e.:<br />
<bash><br />
< data.rsf sfwindow n1=100 | sfbandpass fhi=60 > data2.rsf<br />
</bash><br />
This approach follows the Unix philosophy, as formulated by Doug McIlroy, the inventor of Unix pipes (Salus, 1994<ref>Salus, P. H., 1994, A quarter-century of Unix: Addison-Wesley.</ref>): <br />
#Write programs that do one thing and do it well. <br />
#Write programs to work together. <br />
#Write programs to handle text streams, because that is a universal interface. <br />
<br />
Following the Unix convention, programs have brief <tt>man</tt> pages, which explain the program purpose and parameters. You can access this documentation by running a program without parameters. To search for a program by a keyword, use <tt>sfdoc -k <keyword></tt>. <br />
<br />
The [[guide to madagascar programs]] provides more detailed documentation for selected programs while the [[task-centric program list]] attempts to categorize them. You can see the programs in actual use in the [[Reproducible Documents]].<br />
<br />
===Data format===<br />
<br />
For data, Madagascar uses the [[Guide to RSF file format| Regularly Sampled Format]] (RSF), which is based on the concept of hypercubes (n-D arrays, or regularly sampled functions of several variables), much like the SEPlib (its closest relative), DDS, or the regularly-sampled version of the Javaseis format (SVF). Up to 9 dimensions are supported. For 1D it is conceptually analogous to a time series, for 2D to a raster image, and for 3D to a [http://en.wikipedia.org/wiki/Voxel voxel volume]. The format (actually a [http://en.wikipedia.org/wiki/Meta meta]format) makes use of a ASCII file with metadata (information about the data), including a pointer (<tt>in=</tt> parameter) to the location of the file with the actual data values. Irregularly sampled data are currently handled as a pair of datasets, one containing data and the second containing the corresponding irregular geometry information. Programs for conversion to and from other formats such as SEG-Y and SU are provided. <br />
<br />
For graphics, Madagascar currently uses the Vplot vector graphics format. Converters to other graphics formats (Postscript, PNG, GIF, JPEG) are also provided.<br />
<br />
===Reproducible documents===<br />
<br />
A reproducible document consists of LaTeX source combined with SCons rules required to fully build the documents. These rules are expressed in terms of SCons extensions that are provided as part of Madagascar. <br />
<br />
This is the key to the reproducibility aspect of Madagascar. An introduction to reproducible Madagascar documents is at [[Reproducible_computational_experiments_using_SCons]] .<br />
<br />
===Vplot graphics===<br />
<br />
In contrast to most other Madagascar Components, graphics components produce Vplot data as output.<br />
<br />
Vplot is a device independent graphics format that allows both vector and raster elements (as such, <br />
it is comparable to Postscript). Vplot files are interpreted by a number of output devices. Its typical usage is for a visual display in X-windows. A list of them is [[Guide to madagascar programs#Plotting programs | provided on the wiki]].<br />
<br />
Here is an example of a Madagascar pipe. In this case it takes a subsection of a file, low-pass <br />
filters it, and saves the result<br />
<br />
<syntaxhighlight lang="bash"><br />
< data.rsf sfwindow n1=100 | sfbandpass fhi=60 > data2.rsf <br />
</syntaxhighlight><br />
<br />
In this more elaborate case, the final output is passed to a graphics program and plotted.<br />
<br />
<syntaxhighlight lang="bash"><br />
< data.rsf sfwindow n1=100 | sfbandpass fhi=60 | sfcontour | xtpen<br />
</syntaxhighlight><br />
<br />
More extensive examples are seen in [[Guide to madagascar programs]] . The novice reader should probably read the material below before proceeding to that page.<br />
<br />
===Reproducibility and Project Management===<br />
<br />
Madagascar uses and extends [http://www.scons.org/ SCons], an open-source <br />
software construction package, to document and maintain data processing flows. Documented projects become <br />
computational recipes that can be easily exchanged among Madagascar users. <br />
<br />
SCons is a rule-based package in Python typically used as a build system analogous to <tt>make</tt>. Familiarity with any build system will<br />
be helpful in understanding SCons. SCons statements, as python statements, are invoked in the sequence they are <br />
written, but as such they only define rules. The rules are invoked in accordance with a dependency graph which<br />
SCons builds based on those rules. Components regarded as "up-to-date" are not rebuilt. <br />
<br />
SCons allows for user-contributed Builders (meta-rule categories) and Madagascar uses this capability extensively. <br />
The idea is that building an output file based on a workflow chain is very much analogous to building a <br />
software package based on a software tool chain. The calculation is seen simply as a build with dependencies. <br />
This is a considerable benefit in developing alternative workflows using a given dataset. The system <br />
maintains an awareness of already completed calculations. Without user intervention, redundant calculations <br />
are avoided.<br />
<br />
Madagascar calculations are thus expressed as SCons scripts (<tt>SConstruct</tt> files). SCons extensions follow SCons conventions in beginning <br />
with an uppercase letter. The most common Madagascar extensions are <tt>Flow()</tt>, <tt>Result()</tt>, and <tt>End()</tt>. A <tt>Flow()</tt> invocation wraps Madagascar computational components. <tt>Result()</tt> is a version of <tt>Flow()</tt> with a graphical output. Finally an<br />
End() actually invokes the default rules for multiple results. <br />
<br />
Finally, Madagascar enables a collection of reproducible documents, organized in living books. Each <br />
reproducible book contains a collection of Madagascar recipes (<tt>SConstruct</tt> files) used to generate book figures. The recipes <br />
cover a variety of data processing and imaging tasks described in the books. Figures and recipes serve <br />
dual purpose with respect to Madagascar maintenance. They provide demos for introducing new users to the <br />
functionality of the package and, at the same time, [[Automatic Testing|regression tests]] for assuring the system stability <br />
under change.<br />
<br />
==Madagascar Trivia==<br />
<br />
===Why the Name "Madagascar"?===<br />
<br />
[http://ahay.org/blog/2006/04/19/madagascar/ Whimsy, really]. It seems easier to remember than the previous name "RSF", and it provides us interesting [http://ahay.org/blog/2008/10/21/ahay/ mascots].<br />
<br />
===License===<br />
<br />
The Madagascar package is released in an open-source form under the standard [http://www.gnu.org/copyleft/gpl.html GNU GPL] license. In simple <br />
words, there are no restrictions on the use of the software (including copying, modifying, selling, etc.) <br />
However, there are restrictions on the software redistribution intended to prevent the package from losing <br />
its open-source status. Users are encouraged to [[Contributing new programs to Madagascar|submit their modifications]] back to the original distribution for the benefit of the whole [[Package_overview#Community|community]].<br />
<br />
===Community===<br />
<br />
Madagascar seeks to be an open and active community. Mailing lists are maintained, and annual meetings take place. See <br />
* [[Conferences]]<br />
* [http://ahay.org/blog/ Development blog]<br />
* [https://lists.sourceforge.net/lists/listinfo/rsf-user RSF-user mailing list] <br />
* [https://lists.sourceforge.net/lists/listinfo/rsf-devel RSF-devel mailing list] <br />
* [http://www.linkedin.com/e/vgh/1847746 LinkedIn group]<br />
Your participation is welcome.<br />
<br />
===History=== <br />
<br />
Madagascar was first publicly presented at the [[Conferences#Vienna_2006_.28EAGE.29|EAGE Workshop]] in Vienna in June 2006. The work on the package (previously named RSF) was started by Sergey Fomel in 2003. Since then, many people have contributed to it. See [https://github.com/ahay/src/blob/master/AUTHORS.txt AUTHORS.txt] for an incomplete list.<br />
<br />
While being written mostly from scratch, Madagascar borrows ideas from the design of [http://sepwww.stanford.ed/doku.php?id=sep:software:seplib SEPlib], a package maintained by Bob Clapp at the Stanford Exploration Project (SEP). Generations of SEP students and researchers contributed to SEPlib. Most important contributions came from Rob Clayton, Jon Claerbout, Dave Hale, Stew Levin, Rick Ottolini, Joe Dellinger, Steve Cole, Dave Nichols, Martin Karrenbach, Biondo Biondi, and Bob Clapp.<br />
<br />
Madagascar also borrows ideas from [http://timna.mines.edu/cwpcodes/ Seismic Unix] (SU), an open-source package maintained by John Stockwell at the Center for Wave Phenomena (CWP) at the Colorado School of Mines (Stockwell, 1997<ref>Stockwell, J. W., 1997, Free software in education: A case study of CWP/SU: Seismic Unix: The Leading Edge, '''16''', 1045--1049.</ref>;Stockwell, 1999<ref>--------, 1999, The CWP/SU: Seismic Un*x package: Computers and Geosciences, '''25''', 415--419.</ref>). Main contributors to SU included Einar Kjartansson, Shuki Ronen, Jack Cohen, Chris Liner, Dave Hale, and John Stockwell. SU adopted an open-source BSD-style license starting with release 40 (April 10, 2007).<br />
<br />
<references/></div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Package_overview&diff=3895Package overview2020-08-23T08:25:08Z<p>Yangliu: /* History */</p>
<hr />
<div>[[Image:Fotolia_5127720_XS.jpg|right|]]<br />
<br />
The mission of the Madagascar project is to provide a '''shared research environment''' for computational data analysis in geophysics and related fields.<br />
<br />
The Madagascar environment consists of:<br />
# Standalone programs for out-of-core data analysis;<br />
# Standalone programs for geophysical data processing and imaging;<br />
# A development kit for C, C++, Java, Fortran-77, Fortran-90, Python, Matlab, and Octave;<br />
# A framework for reproducible numerical experiments, based on [http://www.scons.org/ SCons];<br />
# A framework for scientific publications, based on [http://www.scons.org/ SCons] and [http://en.wikipedia.org/wiki/LaTeX LaTeX];<br />
# A collection of reproducible scientific articles also used as usage examples and regression tests for the standalone programs;<br />
# A collection of datasets used as input to reproducible numerical experiments.<br />
<br />
This guide serves as a brief introduction of different components and shows how they all fit together.<br />
<br />
==How to obtain Madagascar==<br />
<br />
See [[Download|download]] and [[Installation | installation instructions]]. Madagascar runs on Unix/Linux platforms, including MacOS X and Unix emulations under Miscrosoft Windows. Its installation requires, at a minimum, a working C compiler and Python. <br />
<br />
==How to find your way around Madagascar==<br />
<br />
Start by checking the [[Reproducible_Documents|list of reproducible papers]]. If any of these papers looks close to your interests, follow the links until you find a figure with a "wrench" button under it [[Image:configure.png]]. Click on the wrench, and it will open a computational recipe used for generating the figure (the <tt>SConstruct</tt> file). <br />
<syntaxhighlight lang="python"><br />
from rsf.proj import *<br />
Flow('rose',None,<br />
'''<br />
math n1=629 d1=0.01 o1=0 n2=40 d2=1 o2=5 <br />
output="x2*(8+sin(6*x1+x2/10))" |<br />
rtoc |<br />
math output="input*exp(I*x1)"<br />
''')<br />
Result('rose',<br />
'graph title=Rose screenratio=1 wantaxis=n')<br />
End()<br />
</syntaxhighlight><br />
You can copy this recipe to your computer or simply find it already existing in the "book" subtree under the Madagascar source directory. For example, the recipe at http://www.reproducibility.org/RSF/book/rsf/rsf/sfmath.html also exists in the file <tt>RSFSRC/book/rsf/rsf/sfmath/SConstruct</tt>. After copying or locating the appropriate <tt>SConstruct</tt> file,<br />
run<br />
<pre><br />
scons view<br />
</pre><br />
on the command line to generate all the figures in the selected project and to display them on your screen. For example, try<br />
<pre><br />
bash$ cd RSFSRC/book/rsf/rsf/sfmath<br />
bash$ scons view<br />
</pre><br />
where <tt>bash$</tt> stands for the Unix prompt and <tt>RSFSRC</tt> stands for the Madagascar source directory. The output should look like<br />
<pre><br />
scons: Reading SConscript files ...<br />
scons: done reading SConscript files.<br />
scons: Building targets ...<br />
/RSFROOT/bin/sfmath n1=629 d1=0.01 o1=0 n2=40 d2=1 o2=5 output="x2*(8+sin(6*x1+x2/10))" | /RSFROOT/bin/sfrtoc | <br />
/RSFROOT/bin/sfmath output="input*exp(I*x1)" > rose.rsf<br />
< rose.rsf /RSFROOT/bin/sfgraph title=Rose screenratio=1 wantaxis=n > Fig/rose.vpl<br />
/RSFROOT/bin/sfpen Fig/rose.vpl<br />
scons: done building targets.<br />
</pre><br />
with a picture appearing on your screen.<br />
[[Image:rose.png|frame|center]]<br />
If there are several figures in the recipe, you can run<br />
<pre><br />
scons figurename.view<br />
</pre><br />
(e.g. <tt>scons rose.view</tt>) to display individual figures. To remove all files that <tt>scons view</tt> generated, run<br />
<pre><br />
scons -c view<br />
</pre><br />
If you want to know in advance what commands will be executed to generate the figures, try<br />
<pre><br />
scons -n view<br />
</pre><br />
You can output this command to a file<br />
<pre><br />
scons -n -Q view > script.sh<br />
</pre><br />
and use <tt>script.sh</tt> as a shell script. If you are to make modifications to the data processing recipe (changing parameters or trying new data), working with SCons is more powerful and convenient than running shell scripts.<br />
<br />
A computational recipe puts together individual commands through Unix pipes and SCons rules. These commands act like Lego blocks for creating complex data analysis constructions. In the example above, three "blocks" are used: <tt>sfmath</tt>, <tt>sfrtoc</tt>, and <tt>sfgraph</tt>. To find out what a particular command is doing, you can follow the links from the bottom of the web page http://www.reproducibility.org/RSF/book/rsf/rsf/sfmath.html<br />
Alternatively, run the command without arguments on the command line. Running<br />
<pre><br />
bash$ sfrtoc<br />
</pre><br />
produces something like<br />
<pre><br />
NAME<br />
sfrtoc<br />
DESCRIPTION<br />
Convert real data to complex (by adding zero imaginary part).<br />
SYNOPSIS<br />
sfrtoc < real.rsf > cmplx.rsf<br />
COMMENTS <br />
See also: sfcmplx<br />
USED IN<br />
bei/ft1/plane4<br />
bei/ft1/autocor<br />
bei/ft1/brad<br />
[...]<br />
SOURCE<br />
user/main/rtoc.c<br />
DOCUMENTATION<br />
http://reproducibility.org/wiki/Guide_to_madagascar_programs#sfrtoc<br />
</pre><br />
<br />
The <b>DOCUMENTATION</b> section provides a link to a more detailed documentation on the web. The most useful part is the <b>USED IN</b> section, which points to more examples of using the program. As an exercise, change directory to <tt>RSFSRC/book/bei/ft1/plane4</tt> or any other example directory, examine the <tt>SConstruct</tt> file, and run <tt>scons view</tt>. Alternatively, look at http://www.reproducibility.org/RSF/book/bei/ft1/plane4.html<br />
<br />
Want to find a program by keywords? Try <tt>sfdoc -k</tt>.<br />
<pre><br />
bash$ sfdoc -k complex<br />
sfsort: Sort a float/complex vector by absolute values.<br />
sfrtoc: Convert real data to complex (by adding zero imaginary part).<br />
sfjacobi2: Find eigenvalues of a general complex matrix by Jacobi-like iteration. <br />
sfboolcmp: Element-wise boolean comparison of values. For int/float/complex data-sets.<br />
sfcmatmult: Simple matrix multiplication for complex matrices <br />
sfimag: Extract real (sfreal) or imaginary (sfimag) part of a complex dataset. <br />
sfthr: Threshold float/complex inputs given a constant/varying threshold level.<br />
sfcpef: 1-D prediction-error filter estimation from complex data <br />
sfroots: Find roots of a complex polynomial. <br />
sfreal: Extract real (sfreal) or imaginary (sfimag) part of a complex dataset. <br />
sfcmplx: Create a complex dataset from its real and imaginary parts.<br />
sfsin: Simple operations with complex sinusoids <br />
sfcdottest: Generic dot-product test for complex linear operators with adjoints <br />
sfcconjgrad: Generic conjugate-gradient solver for linear inversion with complex data<br />
</pre><br />
<br />
Individual components of the Madagascar environment are described in more details below.<br />
<br />
==Madagascar components==<br />
<br />
===Standalone programs===<br />
The list of all standalone programs is available [http://www.reproducibility.org/RSF/ online]. Most programs act as filters on input data and can be chained through Unix pipes, i.e.:<br />
<bash><br />
< data.rsf sfwindow n1=100 | sfbandpass fhi=60 > data2.rsf<br />
</bash><br />
This approach follows the Unix philosophy, as formulated by Doug McIlroy, the inventor of Unix pipes (Salus, 1994<ref>Salus, P. H., 1994, A quarter-century of Unix: Addison-Wesley.</ref>): <br />
#Write programs that do one thing and do it well. <br />
#Write programs to work together. <br />
#Write programs to handle text streams, because that is a universal interface. <br />
<br />
Following the Unix convention, programs have brief <tt>man</tt> pages, which explain the program purpose and parameters. You can access this documentation by running a program without parameters. To search for a program by a keyword, use <tt>sfdoc -k <keyword></tt>. <br />
<br />
The [[guide to madagascar programs]] provides more detailed documentation for selected programs while the [[task-centric program list]] attempts to categorize them. You can see the programs in actual use in the [[Reproducible Documents]].<br />
<br />
===Data format===<br />
<br />
For data, Madagascar uses the [[Guide to RSF file format| Regularly Sampled Format]] (RSF), which is based on the concept of hypercubes (n-D arrays, or regularly sampled functions of several variables), much like the SEPlib (its closest relative), DDS, or the regularly-sampled version of the Javaseis format (SVF). Up to 9 dimensions are supported. For 1D it is conceptually analogous to a time series, for 2D to a raster image, and for 3D to a [http://en.wikipedia.org/wiki/Voxel voxel volume]. The format (actually a [http://en.wikipedia.org/wiki/Meta meta]format) makes use of a ASCII file with metadata (information about the data), including a pointer (<tt>in=</tt> parameter) to the location of the file with the actual data values. Irregularly sampled data are currently handled as a pair of datasets, one containing data and the second containing the corresponding irregular geometry information. Programs for conversion to and from other formats such as SEG-Y and SU are provided. <br />
<br />
For graphics, Madagascar currently uses the Vplot vector graphics format. Converters to other graphics formats (Postscript, PNG, GIF, JPEG) are also provided.<br />
<br />
===Reproducible documents===<br />
<br />
A reproducible document consists of LaTeX source combined with SCons rules required to fully build the documents. These rules are expressed in terms of SCons extensions that are provided as part of Madagascar. <br />
<br />
This is the key to the reproducibility aspect of Madagascar. An introduction to reproducible Madagascar documents is at [[Reproducible_computational_experiments_using_SCons]] .<br />
<br />
===Vplot graphics===<br />
<br />
In contrast to most other Madagascar Components, graphics components produce Vplot data as output.<br />
<br />
Vplot is a device independent graphics format that allows both vector and raster elements (as such, <br />
it is comparable to Postscript). Vplot files are interpreted by a number of output devices. Its typical usage is for a visual display in X-windows. A list of them is [[Guide to madagascar programs#Plotting programs | provided on the wiki]].<br />
<br />
Here is an example of a Madagascar pipe. In this case it takes a subsection of a file, low-pass <br />
filters it, and saves the result<br />
<br />
<syntaxhighlight lang="bash"><br />
< data.rsf sfwindow n1=100 | sfbandpass fhi=60 > data2.rsf <br />
</syntaxhighlight><br />
<br />
In this more elaborate case, the final output is passed to a graphics program and plotted.<br />
<br />
<syntaxhighlight lang="bash"><br />
< data.rsf sfwindow n1=100 | sfbandpass fhi=60 | sfcontour | xtpen<br />
</syntaxhighlight><br />
<br />
More extensive examples are seen in [[Guide to madagascar programs]] . The novice reader should probably read the material below before proceeding to that page.<br />
<br />
===Reproducibility and Project Management===<br />
<br />
Madagascar uses and extends [http://www.scons.org/ SCons], an open-source <br />
software construction package, to document and maintain data processing flows. Documented projects become <br />
computational recipes that can be easily exchanged among Madagascar users. <br />
<br />
SCons is a rule-based package in Python typically used as a build system analogous to <tt>make</tt>. Familiarity with any build system will<br />
be helpful in understanding SCons. SCons statements, as python statements, are invoked in the sequence they are <br />
written, but as such they only define rules. The rules are invoked in accordance with a dependency graph which<br />
SCons builds based on those rules. Components regarded as "up-to-date" are not rebuilt. <br />
<br />
SCons allows for user-contributed Builders (meta-rule categories) and Madagascar uses this capability extensively. <br />
The idea is that building an output file based on a workflow chain is very much analogous to building a <br />
software package based on a software tool chain. The calculation is seen simply as a build with dependencies. <br />
This is a considerable benefit in developing alternative workflows using a given dataset. The system <br />
maintains an awareness of already completed calculations. Without user intervention, redundant calculations <br />
are avoided.<br />
<br />
Madagascar calculations are thus expressed as SCons scripts (<tt>SConstruct</tt> files). SCons extensions follow SCons conventions in beginning <br />
with an uppercase letter. The most common Madagascar extensions are <tt>Flow()</tt>, <tt>Result()</tt>, and <tt>End()</tt>. A <tt>Flow()</tt> invocation wraps Madagascar computational components. <tt>Result()</tt> is a version of <tt>Flow()</tt> with a graphical output. Finally an<br />
End() actually invokes the default rules for multiple results. <br />
<br />
Finally, Madagascar enables a collection of reproducible documents, organized in living books. Each <br />
reproducible book contains a collection of Madagascar recipes (<tt>SConstruct</tt> files) used to generate book figures. The recipes <br />
cover a variety of data processing and imaging tasks described in the books. Figures and recipes serve <br />
dual purpose with respect to Madagascar maintenance. They provide demos for introducing new users to the <br />
functionality of the package and, at the same time, [[Automatic Testing|regression tests]] for assuring the system stability <br />
under change.<br />
<br />
==Madagascar Trivia==<br />
<br />
===Why the Name "Madagascar"?===<br />
<br />
[http://ahay.org/blog/2006/04/19/madagascar/ Whimsy, really]. It seems easier to remember than the previous name "RSF", and it provides us interesting [http://ahay.org/blog/2008/10/21/ahay/ mascots].<br />
<br />
===License===<br />
<br />
The Madagascar package is released in an open-source form under the standard [http://www.gnu.org/copyleft/gpl.html GNU GPL] license. In simple <br />
words, there are no restrictions on the use of the software (including copying, modifying, selling, etc.) <br />
However, there are restrictions on the software redistribution intended to prevent the package from losing <br />
its open-source status. Users are encouraged to [[Contributing new programs to Madagascar|submit their modifications]] back to the original distribution for the benefit of the whole [[Package_overview#Community|community]].<br />
<br />
===Community===<br />
<br />
Madagascar seeks to be an open and active community. Mailing lists are maintained, and annual meetings take place. See <br />
* [[Conferences]]<br />
* [http://www.ahay.org/rsflog Development blog]<br />
* [https://lists.sourceforge.net/lists/listinfo/rsf-user RSF-user mailing list] <br />
* [https://lists.sourceforge.net/lists/listinfo/rsf-devel RSF-devel mailing list] <br />
* [http://www.linkedin.com/e/vgh/1847746 LinkedIn group]<br />
Your participation is welcome.<br />
<br />
===History=== <br />
<br />
Madagascar was first publicly presented at the [[Conferences#Vienna_2006_.28EAGE.29|EAGE Workshop]] in Vienna in June 2006. The work on the package (previously named RSF) was started by Sergey Fomel in 2003. Since then, many people have contributed to it. See [https://github.com/ahay/src/blob/master/AUTHORS.txt AUTHORS.txt] for an incomplete list.<br />
<br />
While being written mostly from scratch, Madagascar borrows ideas from the design of [http://sepwww.stanford.ed/doku.php?id=sep:software:seplib SEPlib], a package maintained by Bob Clapp at the Stanford Exploration Project (SEP). Generations of SEP students and researchers contributed to SEPlib. Most important contributions came from Rob Clayton, Jon Claerbout, Dave Hale, Stew Levin, Rick Ottolini, Joe Dellinger, Steve Cole, Dave Nichols, Martin Karrenbach, Biondo Biondi, and Bob Clapp.<br />
<br />
Madagascar also borrows ideas from [http://timna.mines.edu/cwpcodes/ Seismic Unix] (SU), an open-source package maintained by John Stockwell at the Center for Wave Phenomena (CWP) at the Colorado School of Mines (Stockwell, 1997<ref>Stockwell, J. W., 1997, Free software in education: A case study of CWP/SU: Seismic Unix: The Leading Edge, '''16''', 1045--1049.</ref>;Stockwell, 1999<ref>--------, 1999, The CWP/SU: Seismic Un*x package: Computers and Geosciences, '''25''', 415--419.</ref>). Main contributors to SU included Einar Kjartansson, Shuki Ronen, Jack Cohen, Chris Liner, Dave Hale, and John Stockwell. SU adopted an open-source BSD-style license starting with release 40 (April 10, 2007).<br />
<br />
<references/></div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Package_overview&diff=3894Package overview2020-08-23T08:17:42Z<p>Yangliu: /* Why the Name "Madagascar"? */</p>
<hr />
<div>[[Image:Fotolia_5127720_XS.jpg|right|]]<br />
<br />
The mission of the Madagascar project is to provide a '''shared research environment''' for computational data analysis in geophysics and related fields.<br />
<br />
The Madagascar environment consists of:<br />
# Standalone programs for out-of-core data analysis;<br />
# Standalone programs for geophysical data processing and imaging;<br />
# A development kit for C, C++, Java, Fortran-77, Fortran-90, Python, Matlab, and Octave;<br />
# A framework for reproducible numerical experiments, based on [http://www.scons.org/ SCons];<br />
# A framework for scientific publications, based on [http://www.scons.org/ SCons] and [http://en.wikipedia.org/wiki/LaTeX LaTeX];<br />
# A collection of reproducible scientific articles also used as usage examples and regression tests for the standalone programs;<br />
# A collection of datasets used as input to reproducible numerical experiments.<br />
<br />
This guide serves as a brief introduction of different components and shows how they all fit together.<br />
<br />
==How to obtain Madagascar==<br />
<br />
See [[Download|download]] and [[Installation | installation instructions]]. Madagascar runs on Unix/Linux platforms, including MacOS X and Unix emulations under Miscrosoft Windows. Its installation requires, at a minimum, a working C compiler and Python. <br />
<br />
==How to find your way around Madagascar==<br />
<br />
Start by checking the [[Reproducible_Documents|list of reproducible papers]]. If any of these papers looks close to your interests, follow the links until you find a figure with a "wrench" button under it [[Image:configure.png]]. Click on the wrench, and it will open a computational recipe used for generating the figure (the <tt>SConstruct</tt> file). <br />
<syntaxhighlight lang="python"><br />
from rsf.proj import *<br />
Flow('rose',None,<br />
'''<br />
math n1=629 d1=0.01 o1=0 n2=40 d2=1 o2=5 <br />
output="x2*(8+sin(6*x1+x2/10))" |<br />
rtoc |<br />
math output="input*exp(I*x1)"<br />
''')<br />
Result('rose',<br />
'graph title=Rose screenratio=1 wantaxis=n')<br />
End()<br />
</syntaxhighlight><br />
You can copy this recipe to your computer or simply find it already existing in the "book" subtree under the Madagascar source directory. For example, the recipe at http://www.reproducibility.org/RSF/book/rsf/rsf/sfmath.html also exists in the file <tt>RSFSRC/book/rsf/rsf/sfmath/SConstruct</tt>. After copying or locating the appropriate <tt>SConstruct</tt> file,<br />
run<br />
<pre><br />
scons view<br />
</pre><br />
on the command line to generate all the figures in the selected project and to display them on your screen. For example, try<br />
<pre><br />
bash$ cd RSFSRC/book/rsf/rsf/sfmath<br />
bash$ scons view<br />
</pre><br />
where <tt>bash$</tt> stands for the Unix prompt and <tt>RSFSRC</tt> stands for the Madagascar source directory. The output should look like<br />
<pre><br />
scons: Reading SConscript files ...<br />
scons: done reading SConscript files.<br />
scons: Building targets ...<br />
/RSFROOT/bin/sfmath n1=629 d1=0.01 o1=0 n2=40 d2=1 o2=5 output="x2*(8+sin(6*x1+x2/10))" | /RSFROOT/bin/sfrtoc | <br />
/RSFROOT/bin/sfmath output="input*exp(I*x1)" > rose.rsf<br />
< rose.rsf /RSFROOT/bin/sfgraph title=Rose screenratio=1 wantaxis=n > Fig/rose.vpl<br />
/RSFROOT/bin/sfpen Fig/rose.vpl<br />
scons: done building targets.<br />
</pre><br />
with a picture appearing on your screen.<br />
[[Image:rose.png|frame|center]]<br />
If there are several figures in the recipe, you can run<br />
<pre><br />
scons figurename.view<br />
</pre><br />
(e.g. <tt>scons rose.view</tt>) to display individual figures. To remove all files that <tt>scons view</tt> generated, run<br />
<pre><br />
scons -c view<br />
</pre><br />
If you want to know in advance what commands will be executed to generate the figures, try<br />
<pre><br />
scons -n view<br />
</pre><br />
You can output this command to a file<br />
<pre><br />
scons -n -Q view > script.sh<br />
</pre><br />
and use <tt>script.sh</tt> as a shell script. If you are to make modifications to the data processing recipe (changing parameters or trying new data), working with SCons is more powerful and convenient than running shell scripts.<br />
<br />
A computational recipe puts together individual commands through Unix pipes and SCons rules. These commands act like Lego blocks for creating complex data analysis constructions. In the example above, three "blocks" are used: <tt>sfmath</tt>, <tt>sfrtoc</tt>, and <tt>sfgraph</tt>. To find out what a particular command is doing, you can follow the links from the bottom of the web page http://www.reproducibility.org/RSF/book/rsf/rsf/sfmath.html<br />
Alternatively, run the command without arguments on the command line. Running<br />
<pre><br />
bash$ sfrtoc<br />
</pre><br />
produces something like<br />
<pre><br />
NAME<br />
sfrtoc<br />
DESCRIPTION<br />
Convert real data to complex (by adding zero imaginary part).<br />
SYNOPSIS<br />
sfrtoc < real.rsf > cmplx.rsf<br />
COMMENTS <br />
See also: sfcmplx<br />
USED IN<br />
bei/ft1/plane4<br />
bei/ft1/autocor<br />
bei/ft1/brad<br />
[...]<br />
SOURCE<br />
user/main/rtoc.c<br />
DOCUMENTATION<br />
http://reproducibility.org/wiki/Guide_to_madagascar_programs#sfrtoc<br />
</pre><br />
<br />
The <b>DOCUMENTATION</b> section provides a link to a more detailed documentation on the web. The most useful part is the <b>USED IN</b> section, which points to more examples of using the program. As an exercise, change directory to <tt>RSFSRC/book/bei/ft1/plane4</tt> or any other example directory, examine the <tt>SConstruct</tt> file, and run <tt>scons view</tt>. Alternatively, look at http://www.reproducibility.org/RSF/book/bei/ft1/plane4.html<br />
<br />
Want to find a program by keywords? Try <tt>sfdoc -k</tt>.<br />
<pre><br />
bash$ sfdoc -k complex<br />
sfsort: Sort a float/complex vector by absolute values.<br />
sfrtoc: Convert real data to complex (by adding zero imaginary part).<br />
sfjacobi2: Find eigenvalues of a general complex matrix by Jacobi-like iteration. <br />
sfboolcmp: Element-wise boolean comparison of values. For int/float/complex data-sets.<br />
sfcmatmult: Simple matrix multiplication for complex matrices <br />
sfimag: Extract real (sfreal) or imaginary (sfimag) part of a complex dataset. <br />
sfthr: Threshold float/complex inputs given a constant/varying threshold level.<br />
sfcpef: 1-D prediction-error filter estimation from complex data <br />
sfroots: Find roots of a complex polynomial. <br />
sfreal: Extract real (sfreal) or imaginary (sfimag) part of a complex dataset. <br />
sfcmplx: Create a complex dataset from its real and imaginary parts.<br />
sfsin: Simple operations with complex sinusoids <br />
sfcdottest: Generic dot-product test for complex linear operators with adjoints <br />
sfcconjgrad: Generic conjugate-gradient solver for linear inversion with complex data<br />
</pre><br />
<br />
Individual components of the Madagascar environment are described in more details below.<br />
<br />
==Madagascar components==<br />
<br />
===Standalone programs===<br />
The list of all standalone programs is available [http://www.reproducibility.org/RSF/ online]. Most programs act as filters on input data and can be chained through Unix pipes, i.e.:<br />
<bash><br />
< data.rsf sfwindow n1=100 | sfbandpass fhi=60 > data2.rsf<br />
</bash><br />
This approach follows the Unix philosophy, as formulated by Doug McIlroy, the inventor of Unix pipes (Salus, 1994<ref>Salus, P. H., 1994, A quarter-century of Unix: Addison-Wesley.</ref>): <br />
#Write programs that do one thing and do it well. <br />
#Write programs to work together. <br />
#Write programs to handle text streams, because that is a universal interface. <br />
<br />
Following the Unix convention, programs have brief <tt>man</tt> pages, which explain the program purpose and parameters. You can access this documentation by running a program without parameters. To search for a program by a keyword, use <tt>sfdoc -k <keyword></tt>. <br />
<br />
The [[guide to madagascar programs]] provides more detailed documentation for selected programs while the [[task-centric program list]] attempts to categorize them. You can see the programs in actual use in the [[Reproducible Documents]].<br />
<br />
===Data format===<br />
<br />
For data, Madagascar uses the [[Guide to RSF file format| Regularly Sampled Format]] (RSF), which is based on the concept of hypercubes (n-D arrays, or regularly sampled functions of several variables), much like the SEPlib (its closest relative), DDS, or the regularly-sampled version of the Javaseis format (SVF). Up to 9 dimensions are supported. For 1D it is conceptually analogous to a time series, for 2D to a raster image, and for 3D to a [http://en.wikipedia.org/wiki/Voxel voxel volume]. The format (actually a [http://en.wikipedia.org/wiki/Meta meta]format) makes use of a ASCII file with metadata (information about the data), including a pointer (<tt>in=</tt> parameter) to the location of the file with the actual data values. Irregularly sampled data are currently handled as a pair of datasets, one containing data and the second containing the corresponding irregular geometry information. Programs for conversion to and from other formats such as SEG-Y and SU are provided. <br />
<br />
For graphics, Madagascar currently uses the Vplot vector graphics format. Converters to other graphics formats (Postscript, PNG, GIF, JPEG) are also provided.<br />
<br />
===Reproducible documents===<br />
<br />
A reproducible document consists of LaTeX source combined with SCons rules required to fully build the documents. These rules are expressed in terms of SCons extensions that are provided as part of Madagascar. <br />
<br />
This is the key to the reproducibility aspect of Madagascar. An introduction to reproducible Madagascar documents is at [[Reproducible_computational_experiments_using_SCons]] .<br />
<br />
===Vplot graphics===<br />
<br />
In contrast to most other Madagascar Components, graphics components produce Vplot data as output.<br />
<br />
Vplot is a device independent graphics format that allows both vector and raster elements (as such, <br />
it is comparable to Postscript). Vplot files are interpreted by a number of output devices. Its typical usage is for a visual display in X-windows. A list of them is [[Guide to madagascar programs#Plotting programs | provided on the wiki]].<br />
<br />
Here is an example of a Madagascar pipe. In this case it takes a subsection of a file, low-pass <br />
filters it, and saves the result<br />
<br />
<syntaxhighlight lang="bash"><br />
< data.rsf sfwindow n1=100 | sfbandpass fhi=60 > data2.rsf <br />
</syntaxhighlight><br />
<br />
In this more elaborate case, the final output is passed to a graphics program and plotted.<br />
<br />
<syntaxhighlight lang="bash"><br />
< data.rsf sfwindow n1=100 | sfbandpass fhi=60 | sfcontour | xtpen<br />
</syntaxhighlight><br />
<br />
More extensive examples are seen in [[Guide to madagascar programs]] . The novice reader should probably read the material below before proceeding to that page.<br />
<br />
===Reproducibility and Project Management===<br />
<br />
Madagascar uses and extends [http://www.scons.org/ SCons], an open-source <br />
software construction package, to document and maintain data processing flows. Documented projects become <br />
computational recipes that can be easily exchanged among Madagascar users. <br />
<br />
SCons is a rule-based package in Python typically used as a build system analogous to <tt>make</tt>. Familiarity with any build system will<br />
be helpful in understanding SCons. SCons statements, as python statements, are invoked in the sequence they are <br />
written, but as such they only define rules. The rules are invoked in accordance with a dependency graph which<br />
SCons builds based on those rules. Components regarded as "up-to-date" are not rebuilt. <br />
<br />
SCons allows for user-contributed Builders (meta-rule categories) and Madagascar uses this capability extensively. <br />
The idea is that building an output file based on a workflow chain is very much analogous to building a <br />
software package based on a software tool chain. The calculation is seen simply as a build with dependencies. <br />
This is a considerable benefit in developing alternative workflows using a given dataset. The system <br />
maintains an awareness of already completed calculations. Without user intervention, redundant calculations <br />
are avoided.<br />
<br />
Madagascar calculations are thus expressed as SCons scripts (<tt>SConstruct</tt> files). SCons extensions follow SCons conventions in beginning <br />
with an uppercase letter. The most common Madagascar extensions are <tt>Flow()</tt>, <tt>Result()</tt>, and <tt>End()</tt>. A <tt>Flow()</tt> invocation wraps Madagascar computational components. <tt>Result()</tt> is a version of <tt>Flow()</tt> with a graphical output. Finally an<br />
End() actually invokes the default rules for multiple results. <br />
<br />
Finally, Madagascar enables a collection of reproducible documents, organized in living books. Each <br />
reproducible book contains a collection of Madagascar recipes (<tt>SConstruct</tt> files) used to generate book figures. The recipes <br />
cover a variety of data processing and imaging tasks described in the books. Figures and recipes serve <br />
dual purpose with respect to Madagascar maintenance. They provide demos for introducing new users to the <br />
functionality of the package and, at the same time, [[Automatic Testing|regression tests]] for assuring the system stability <br />
under change.<br />
<br />
==Madagascar Trivia==<br />
<br />
===Why the Name "Madagascar"?===<br />
<br />
[http://ahay.org/blog/2006/04/19/madagascar/ Whimsy, really]. It seems easier to remember than the previous name "RSF", and it provides us interesting [http://ahay.org/blog/2008/10/21/ahay/ mascots].<br />
<br />
===License===<br />
<br />
The Madagascar package is released in an open-source form under the standard [http://www.gnu.org/copyleft/gpl.html GNU GPL] license. In simple <br />
words, there are no restrictions on the use of the software (including copying, modifying, selling, etc.) <br />
However, there are restrictions on the software redistribution intended to prevent the package from losing <br />
its open-source status. Users are encouraged to [[Contributing new programs to Madagascar|submit their modifications]] back to the original distribution for the benefit of the whole [[Package_overview#Community|community]].<br />
<br />
===Community===<br />
<br />
Madagascar seeks to be an open and active community. Mailing lists are maintained, and annual meetings take place. See <br />
* [[Conferences]]<br />
* [http://www.ahay.org/rsflog Development blog]<br />
* [https://lists.sourceforge.net/lists/listinfo/rsf-user RSF-user mailing list] <br />
* [https://lists.sourceforge.net/lists/listinfo/rsf-devel RSF-devel mailing list] <br />
* [http://www.linkedin.com/e/vgh/1847746 LinkedIn group]<br />
Your participation is welcome.<br />
<br />
===History=== <br />
<br />
Madagascar was first publicly presented at the [[Conferences#Vienna_2006_.28EAGE.29|EAGE Workshop]] in Vienna in June 2006. The work on the package (previously named RSF) was started by Sergey Fomel in 2003. Since then, many people have contributed to it. See [http://rsf.svn.sourceforge.net/viewvc/rsf/trunk/AUTHORS.txt?view=markup AUTHORS.txt] for an incomplete list.<br />
<br />
While being written mostly from scratch, Madagascar borrows ideas from the design of [http://sepwww.stanford.ed/doku.php?id=sep:software:seplib SEPlib], a package maintained by Bob Clapp at the Stanford Exploration Project (SEP). Generations of SEP students and researchers contributed to SEPlib. Most important contributions came from Rob Clayton, Jon Claerbout, Dave Hale, Stew Levin, Rick Ottolini, Joe Dellinger, Steve Cole, Dave Nichols, Martin Karrenbach, Biondo Biondi, and Bob Clapp.<br />
<br />
Madagascar also borrows ideas from [http://timna.mines.edu/cwpcodes/ Seismic Unix] (SU), an open-source package maintained by John Stockwell at the Center for Wave Phenomena (CWP) at the Colorado School of Mines (Stockwell, 1997<ref>Stockwell, J. W., 1997, Free software in education: A case study of CWP/SU: Seismic Unix: The Leading Edge, '''16''', 1045--1049.</ref>;Stockwell, 1999<ref>--------, 1999, The CWP/SU: Seismic Un*x package: Computers and Geosciences, '''25''', 415--419.</ref>). Main contributors to SU included Einar Kjartansson, Shuki Ronen, Jack Cohen, Chris Liner, Dave Hale, and John Stockwell. SU adopted an open-source BSD-style license starting with release 40 (April 10, 2007).<br />
<br />
<references/></div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Package_overview&diff=3893Package overview2020-08-23T08:14:18Z<p>Yangliu: /* Madagascar Trivia */</p>
<hr />
<div>[[Image:Fotolia_5127720_XS.jpg|right|]]<br />
<br />
The mission of the Madagascar project is to provide a '''shared research environment''' for computational data analysis in geophysics and related fields.<br />
<br />
The Madagascar environment consists of:<br />
# Standalone programs for out-of-core data analysis;<br />
# Standalone programs for geophysical data processing and imaging;<br />
# A development kit for C, C++, Java, Fortran-77, Fortran-90, Python, Matlab, and Octave;<br />
# A framework for reproducible numerical experiments, based on [http://www.scons.org/ SCons];<br />
# A framework for scientific publications, based on [http://www.scons.org/ SCons] and [http://en.wikipedia.org/wiki/LaTeX LaTeX];<br />
# A collection of reproducible scientific articles also used as usage examples and regression tests for the standalone programs;<br />
# A collection of datasets used as input to reproducible numerical experiments.<br />
<br />
This guide serves as a brief introduction of different components and shows how they all fit together.<br />
<br />
==How to obtain Madagascar==<br />
<br />
See [[Download|download]] and [[Installation | installation instructions]]. Madagascar runs on Unix/Linux platforms, including MacOS X and Unix emulations under Miscrosoft Windows. Its installation requires, at a minimum, a working C compiler and Python. <br />
<br />
==How to find your way around Madagascar==<br />
<br />
Start by checking the [[Reproducible_Documents|list of reproducible papers]]. If any of these papers looks close to your interests, follow the links until you find a figure with a "wrench" button under it [[Image:configure.png]]. Click on the wrench, and it will open a computational recipe used for generating the figure (the <tt>SConstruct</tt> file). <br />
<syntaxhighlight lang="python"><br />
from rsf.proj import *<br />
Flow('rose',None,<br />
'''<br />
math n1=629 d1=0.01 o1=0 n2=40 d2=1 o2=5 <br />
output="x2*(8+sin(6*x1+x2/10))" |<br />
rtoc |<br />
math output="input*exp(I*x1)"<br />
''')<br />
Result('rose',<br />
'graph title=Rose screenratio=1 wantaxis=n')<br />
End()<br />
</syntaxhighlight><br />
You can copy this recipe to your computer or simply find it already existing in the "book" subtree under the Madagascar source directory. For example, the recipe at http://www.reproducibility.org/RSF/book/rsf/rsf/sfmath.html also exists in the file <tt>RSFSRC/book/rsf/rsf/sfmath/SConstruct</tt>. After copying or locating the appropriate <tt>SConstruct</tt> file,<br />
run<br />
<pre><br />
scons view<br />
</pre><br />
on the command line to generate all the figures in the selected project and to display them on your screen. For example, try<br />
<pre><br />
bash$ cd RSFSRC/book/rsf/rsf/sfmath<br />
bash$ scons view<br />
</pre><br />
where <tt>bash$</tt> stands for the Unix prompt and <tt>RSFSRC</tt> stands for the Madagascar source directory. The output should look like<br />
<pre><br />
scons: Reading SConscript files ...<br />
scons: done reading SConscript files.<br />
scons: Building targets ...<br />
/RSFROOT/bin/sfmath n1=629 d1=0.01 o1=0 n2=40 d2=1 o2=5 output="x2*(8+sin(6*x1+x2/10))" | /RSFROOT/bin/sfrtoc | <br />
/RSFROOT/bin/sfmath output="input*exp(I*x1)" > rose.rsf<br />
< rose.rsf /RSFROOT/bin/sfgraph title=Rose screenratio=1 wantaxis=n > Fig/rose.vpl<br />
/RSFROOT/bin/sfpen Fig/rose.vpl<br />
scons: done building targets.<br />
</pre><br />
with a picture appearing on your screen.<br />
[[Image:rose.png|frame|center]]<br />
If there are several figures in the recipe, you can run<br />
<pre><br />
scons figurename.view<br />
</pre><br />
(e.g. <tt>scons rose.view</tt>) to display individual figures. To remove all files that <tt>scons view</tt> generated, run<br />
<pre><br />
scons -c view<br />
</pre><br />
If you want to know in advance what commands will be executed to generate the figures, try<br />
<pre><br />
scons -n view<br />
</pre><br />
You can output this command to a file<br />
<pre><br />
scons -n -Q view > script.sh<br />
</pre><br />
and use <tt>script.sh</tt> as a shell script. If you are to make modifications to the data processing recipe (changing parameters or trying new data), working with SCons is more powerful and convenient than running shell scripts.<br />
<br />
A computational recipe puts together individual commands through Unix pipes and SCons rules. These commands act like Lego blocks for creating complex data analysis constructions. In the example above, three "blocks" are used: <tt>sfmath</tt>, <tt>sfrtoc</tt>, and <tt>sfgraph</tt>. To find out what a particular command is doing, you can follow the links from the bottom of the web page http://www.reproducibility.org/RSF/book/rsf/rsf/sfmath.html<br />
Alternatively, run the command without arguments on the command line. Running<br />
<pre><br />
bash$ sfrtoc<br />
</pre><br />
produces something like<br />
<pre><br />
NAME<br />
sfrtoc<br />
DESCRIPTION<br />
Convert real data to complex (by adding zero imaginary part).<br />
SYNOPSIS<br />
sfrtoc < real.rsf > cmplx.rsf<br />
COMMENTS <br />
See also: sfcmplx<br />
USED IN<br />
bei/ft1/plane4<br />
bei/ft1/autocor<br />
bei/ft1/brad<br />
[...]<br />
SOURCE<br />
user/main/rtoc.c<br />
DOCUMENTATION<br />
http://reproducibility.org/wiki/Guide_to_madagascar_programs#sfrtoc<br />
</pre><br />
<br />
The <b>DOCUMENTATION</b> section provides a link to a more detailed documentation on the web. The most useful part is the <b>USED IN</b> section, which points to more examples of using the program. As an exercise, change directory to <tt>RSFSRC/book/bei/ft1/plane4</tt> or any other example directory, examine the <tt>SConstruct</tt> file, and run <tt>scons view</tt>. Alternatively, look at http://www.reproducibility.org/RSF/book/bei/ft1/plane4.html<br />
<br />
Want to find a program by keywords? Try <tt>sfdoc -k</tt>.<br />
<pre><br />
bash$ sfdoc -k complex<br />
sfsort: Sort a float/complex vector by absolute values.<br />
sfrtoc: Convert real data to complex (by adding zero imaginary part).<br />
sfjacobi2: Find eigenvalues of a general complex matrix by Jacobi-like iteration. <br />
sfboolcmp: Element-wise boolean comparison of values. For int/float/complex data-sets.<br />
sfcmatmult: Simple matrix multiplication for complex matrices <br />
sfimag: Extract real (sfreal) or imaginary (sfimag) part of a complex dataset. <br />
sfthr: Threshold float/complex inputs given a constant/varying threshold level.<br />
sfcpef: 1-D prediction-error filter estimation from complex data <br />
sfroots: Find roots of a complex polynomial. <br />
sfreal: Extract real (sfreal) or imaginary (sfimag) part of a complex dataset. <br />
sfcmplx: Create a complex dataset from its real and imaginary parts.<br />
sfsin: Simple operations with complex sinusoids <br />
sfcdottest: Generic dot-product test for complex linear operators with adjoints <br />
sfcconjgrad: Generic conjugate-gradient solver for linear inversion with complex data<br />
</pre><br />
<br />
Individual components of the Madagascar environment are described in more details below.<br />
<br />
==Madagascar components==<br />
<br />
===Standalone programs===<br />
The list of all standalone programs is available [http://www.reproducibility.org/RSF/ online]. Most programs act as filters on input data and can be chained through Unix pipes, i.e.:<br />
<bash><br />
< data.rsf sfwindow n1=100 | sfbandpass fhi=60 > data2.rsf<br />
</bash><br />
This approach follows the Unix philosophy, as formulated by Doug McIlroy, the inventor of Unix pipes (Salus, 1994<ref>Salus, P. H., 1994, A quarter-century of Unix: Addison-Wesley.</ref>): <br />
#Write programs that do one thing and do it well. <br />
#Write programs to work together. <br />
#Write programs to handle text streams, because that is a universal interface. <br />
<br />
Following the Unix convention, programs have brief <tt>man</tt> pages, which explain the program purpose and parameters. You can access this documentation by running a program without parameters. To search for a program by a keyword, use <tt>sfdoc -k <keyword></tt>. <br />
<br />
The [[guide to madagascar programs]] provides more detailed documentation for selected programs while the [[task-centric program list]] attempts to categorize them. You can see the programs in actual use in the [[Reproducible Documents]].<br />
<br />
===Data format===<br />
<br />
For data, Madagascar uses the [[Guide to RSF file format| Regularly Sampled Format]] (RSF), which is based on the concept of hypercubes (n-D arrays, or regularly sampled functions of several variables), much like the SEPlib (its closest relative), DDS, or the regularly-sampled version of the Javaseis format (SVF). Up to 9 dimensions are supported. For 1D it is conceptually analogous to a time series, for 2D to a raster image, and for 3D to a [http://en.wikipedia.org/wiki/Voxel voxel volume]. The format (actually a [http://en.wikipedia.org/wiki/Meta meta]format) makes use of a ASCII file with metadata (information about the data), including a pointer (<tt>in=</tt> parameter) to the location of the file with the actual data values. Irregularly sampled data are currently handled as a pair of datasets, one containing data and the second containing the corresponding irregular geometry information. Programs for conversion to and from other formats such as SEG-Y and SU are provided. <br />
<br />
For graphics, Madagascar currently uses the Vplot vector graphics format. Converters to other graphics formats (Postscript, PNG, GIF, JPEG) are also provided.<br />
<br />
===Reproducible documents===<br />
<br />
A reproducible document consists of LaTeX source combined with SCons rules required to fully build the documents. These rules are expressed in terms of SCons extensions that are provided as part of Madagascar. <br />
<br />
This is the key to the reproducibility aspect of Madagascar. An introduction to reproducible Madagascar documents is at [[Reproducible_computational_experiments_using_SCons]] .<br />
<br />
===Vplot graphics===<br />
<br />
In contrast to most other Madagascar Components, graphics components produce Vplot data as output.<br />
<br />
Vplot is a device independent graphics format that allows both vector and raster elements (as such, <br />
it is comparable to Postscript). Vplot files are interpreted by a number of output devices. Its typical usage is for a visual display in X-windows. A list of them is [[Guide to madagascar programs#Plotting programs | provided on the wiki]].<br />
<br />
Here is an example of a Madagascar pipe. In this case it takes a subsection of a file, low-pass <br />
filters it, and saves the result<br />
<br />
<syntaxhighlight lang="bash"><br />
< data.rsf sfwindow n1=100 | sfbandpass fhi=60 > data2.rsf <br />
</syntaxhighlight><br />
<br />
In this more elaborate case, the final output is passed to a graphics program and plotted.<br />
<br />
<syntaxhighlight lang="bash"><br />
< data.rsf sfwindow n1=100 | sfbandpass fhi=60 | sfcontour | xtpen<br />
</syntaxhighlight><br />
<br />
More extensive examples are seen in [[Guide to madagascar programs]] . The novice reader should probably read the material below before proceeding to that page.<br />
<br />
===Reproducibility and Project Management===<br />
<br />
Madagascar uses and extends [http://www.scons.org/ SCons], an open-source <br />
software construction package, to document and maintain data processing flows. Documented projects become <br />
computational recipes that can be easily exchanged among Madagascar users. <br />
<br />
SCons is a rule-based package in Python typically used as a build system analogous to <tt>make</tt>. Familiarity with any build system will<br />
be helpful in understanding SCons. SCons statements, as python statements, are invoked in the sequence they are <br />
written, but as such they only define rules. The rules are invoked in accordance with a dependency graph which<br />
SCons builds based on those rules. Components regarded as "up-to-date" are not rebuilt. <br />
<br />
SCons allows for user-contributed Builders (meta-rule categories) and Madagascar uses this capability extensively. <br />
The idea is that building an output file based on a workflow chain is very much analogous to building a <br />
software package based on a software tool chain. The calculation is seen simply as a build with dependencies. <br />
This is a considerable benefit in developing alternative workflows using a given dataset. The system <br />
maintains an awareness of already completed calculations. Without user intervention, redundant calculations <br />
are avoided.<br />
<br />
Madagascar calculations are thus expressed as SCons scripts (<tt>SConstruct</tt> files). SCons extensions follow SCons conventions in beginning <br />
with an uppercase letter. The most common Madagascar extensions are <tt>Flow()</tt>, <tt>Result()</tt>, and <tt>End()</tt>. A <tt>Flow()</tt> invocation wraps Madagascar computational components. <tt>Result()</tt> is a version of <tt>Flow()</tt> with a graphical output. Finally an<br />
End() actually invokes the default rules for multiple results. <br />
<br />
Finally, Madagascar enables a collection of reproducible documents, organized in living books. Each <br />
reproducible book contains a collection of Madagascar recipes (<tt>SConstruct</tt> files) used to generate book figures. The recipes <br />
cover a variety of data processing and imaging tasks described in the books. Figures and recipes serve <br />
dual purpose with respect to Madagascar maintenance. They provide demos for introducing new users to the <br />
functionality of the package and, at the same time, [[Automatic Testing|regression tests]] for assuring the system stability <br />
under change.<br />
<br />
==Madagascar Trivia==<br />
<br />
===Why the Name "Madagascar"?===<br />
<br />
[http://www.reproducibility.org/rsflog/index.php?/archives/67-Madagascar.html Whimsy, really]. It seems easier to remember than the previous name "RSF", and it provides us interesting [http://ahay.org/blog/2008/10/21/ahay/ mascots].<br />
<br />
===License===<br />
<br />
The Madagascar package is released in an open-source form under the standard [http://www.gnu.org/copyleft/gpl.html GNU GPL] license. In simple <br />
words, there are no restrictions on the use of the software (including copying, modifying, selling, etc.) <br />
However, there are restrictions on the software redistribution intended to prevent the package from losing <br />
its open-source status. Users are encouraged to [[Contributing new programs to Madagascar|submit their modifications]] back to the original distribution for the benefit of the whole [[Package_overview#Community|community]].<br />
<br />
===Community===<br />
<br />
Madagascar seeks to be an open and active community. Mailing lists are maintained, and annual meetings take place. See <br />
* [[Conferences]]<br />
* [http://www.ahay.org/rsflog Development blog]<br />
* [https://lists.sourceforge.net/lists/listinfo/rsf-user RSF-user mailing list] <br />
* [https://lists.sourceforge.net/lists/listinfo/rsf-devel RSF-devel mailing list] <br />
* [http://www.linkedin.com/e/vgh/1847746 LinkedIn group]<br />
Your participation is welcome.<br />
<br />
===History=== <br />
<br />
Madagascar was first publicly presented at the [[Conferences#Vienna_2006_.28EAGE.29|EAGE Workshop]] in Vienna in June 2006. The work on the package (previously named RSF) was started by Sergey Fomel in 2003. Since then, many people have contributed to it. See [http://rsf.svn.sourceforge.net/viewvc/rsf/trunk/AUTHORS.txt?view=markup AUTHORS.txt] for an incomplete list.<br />
<br />
While being written mostly from scratch, Madagascar borrows ideas from the design of [http://sepwww.stanford.ed/doku.php?id=sep:software:seplib SEPlib], a package maintained by Bob Clapp at the Stanford Exploration Project (SEP). Generations of SEP students and researchers contributed to SEPlib. Most important contributions came from Rob Clayton, Jon Claerbout, Dave Hale, Stew Levin, Rick Ottolini, Joe Dellinger, Steve Cole, Dave Nichols, Martin Karrenbach, Biondo Biondi, and Bob Clapp.<br />
<br />
Madagascar also borrows ideas from [http://timna.mines.edu/cwpcodes/ Seismic Unix] (SU), an open-source package maintained by John Stockwell at the Center for Wave Phenomena (CWP) at the Colorado School of Mines (Stockwell, 1997<ref>Stockwell, J. W., 1997, Free software in education: A case study of CWP/SU: Seismic Unix: The Leading Edge, '''16''', 1045--1049.</ref>;Stockwell, 1999<ref>--------, 1999, The CWP/SU: Seismic Un*x package: Computers and Geosciences, '''25''', 415--419.</ref>). Main contributors to SU included Einar Kjartansson, Shuki Ronen, Jack Cohen, Chris Liner, Dave Hale, and John Stockwell. SU adopted an open-source BSD-style license starting with release 40 (April 10, 2007).<br />
<br />
<references/></div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Why_Madagascar&diff=3892Why Madagascar2020-08-23T08:01:18Z<p>Yangliu: /* Why not rewrite Madagascar in-house? */</p>
<hr />
<div>Different people and different organizations act for different reasons. Madagascar can mean a lot of things for a lot of people. Feel free to add below your messages, as text, images or movies, for any category of potential users!<br />
==Individuals==<br />
===Graduate student in small research group===<br />
[[Image:marketing_errmsg_gs.png]]<br />
===Academic researcher with strong theoretical background===<br />
[[Image:marketing_errmsg_sj.png]]<br />
<br />
===Professional researcher===<br />
[[Image:marketing_errmsg_pg.png]]<br />
===Project manager===<br />
[[Image:marketing_errmsg_pm.png]]<br />
<br />
==Corporations==<br />
===Disorganized company===<br />
[[Image:marketing_errmsg_dc.png]]<br />
===Tightly-run company with managers that never did professional programming===<br />
[[Image:marketing_errmsg_tc.png]]<br />
===Academic research group or small company===<br />
[[Image:marketing_errmsg_ag.png]]<br />
===Start-up company===<br />
[[Image:marketing_errmsg_su.png]]<br />
===Geophysical services company===<br />
[[Image:marketing_errmsg_sc.png]]<br />
===Computer hardware company===<br />
[[Image:marketing_errmsg_hc.png]]<br />
===Geophysical acquisition systems company===<br />
[[Image:marketing_errmsg_ga.png]]<br />
<br />
==Why not another open-source package?==<br />
Most of the reasons above apply to any open-source package as well. Madagascar [[Other open-source geophysical packages | is not the only open-source geophysical package]], but it is the only one to provide all the components of a '''shared research environment''' as described at the beginning of the [[Package overview | Overview]]. Also, it has an active, diverse community of developers (as opposed to a single owner and a mass of passive users) and its current and future freedom is guaranteed by the [http://en.wikipedia.org/wiki/GNU_General_Public_License GNU General Public License] (2 or higher).<br />
==Why not rewrite Madagascar in-house?==<br />
The Project Cost Calculator on Madagascar's [https://www.openhub.net/p/m8r Open Hub (formerly Ohloh) metrics page] shows the estimated cost for a project of this size. You are getting all this for free!</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Why_Madagascar&diff=3891Why Madagascar2020-08-23T07:54:36Z<p>Yangliu: /* Why not rewrite Madagascar in-house? */</p>
<hr />
<div>Different people and different organizations act for different reasons. Madagascar can mean a lot of things for a lot of people. Feel free to add below your messages, as text, images or movies, for any category of potential users!<br />
==Individuals==<br />
===Graduate student in small research group===<br />
[[Image:marketing_errmsg_gs.png]]<br />
===Academic researcher with strong theoretical background===<br />
[[Image:marketing_errmsg_sj.png]]<br />
<br />
===Professional researcher===<br />
[[Image:marketing_errmsg_pg.png]]<br />
===Project manager===<br />
[[Image:marketing_errmsg_pm.png]]<br />
<br />
==Corporations==<br />
===Disorganized company===<br />
[[Image:marketing_errmsg_dc.png]]<br />
===Tightly-run company with managers that never did professional programming===<br />
[[Image:marketing_errmsg_tc.png]]<br />
===Academic research group or small company===<br />
[[Image:marketing_errmsg_ag.png]]<br />
===Start-up company===<br />
[[Image:marketing_errmsg_su.png]]<br />
===Geophysical services company===<br />
[[Image:marketing_errmsg_sc.png]]<br />
===Computer hardware company===<br />
[[Image:marketing_errmsg_hc.png]]<br />
===Geophysical acquisition systems company===<br />
[[Image:marketing_errmsg_ga.png]]<br />
<br />
==Why not another open-source package?==<br />
Most of the reasons above apply to any open-source package as well. Madagascar [[Other open-source geophysical packages | is not the only open-source geophysical package]], but it is the only one to provide all the components of a '''shared research environment''' as described at the beginning of the [[Package overview | Overview]]. Also, it has an active, diverse community of developers (as opposed to a single owner and a mass of passive users) and its current and future freedom is guaranteed by the [http://en.wikipedia.org/wiki/GNU_General_Public_License GNU General Public License] (2 or higher).<br />
==Why not rewrite Madagascar in-house?==<br />
The Project Cost Calculator on Madagascar's [https://www.openhub.net/p/m8r Ohloh metrics page] shows the estimated cost for a project of this size. You are getting all this for free!</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Hefei_2020&diff=3890Hefei 20202020-08-14T08:11:23Z<p>Yangliu: /* Introduction */</p>
<hr />
<div>&nbsp;<br />
<br />
== Introduction ==<br />
<br />
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. Madagascar school has been organized many times around the word. It provides a platform for Madagascar users to learn and communicate with the developers. This Madagascar school will introduce the fundamental usages for the beginners with less knowledge of Madagascar and focus on the topic about Open-Source Geophysics in China. This Madagascar school is convened by 1st Asia-Pacific Geophysics Student Conference (APGSC) and hosted by Prof. Yang Liu from Jilin University.<br />
<br />
== Dates ==<br />
<br />
September 6, 2020<br />
<br />
== Agenda ==<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Sunday, September 6, 2020<br />
|-<br />
| 8:30-8:40 <br />
! colspan="2" | Welcome<br />
|-<br />
| 8:40-10:10<br />
! colspan="2" | Introduction to Madagascar Project (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
The <tt>Madagascar</tt> project has been in public existence for fourteen 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 origin and history of the project, the Madagascar components and design principles, and plans for future development. In this module, you will learn how to take the full advantage of the <tt>Madagascar</tt> environment to enhance research productivity and research collaboration.<br><br><br />
|-<br />
| 10:10-10:20<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:20-11:50<br />
! colspan="2" | Geophysical data processing with Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Filed data processing is always a tough problem, which is an important test of integrality degree for Open-source geophysics software and the final target for scientific research. We will use a 2D field seismic dataset to illustrate how Madagascar can set up a common seismic data processing workflow. Meanwhile, we also try to setup the initial processing workflows for other geophysical data, e.g., gravity field data and controlled source electromagnetic (CSEM) synthetic data. <br><br><br />
|-<br />
| 11:50-13:30<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 13:30-15:00<br />
! colspan="2" | Writing a reproducible paper using Madagascar and SEGTeX (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
From the viewpoint of science, all technical papers should be "reproducible" in the sense that someone of reasonable skill ought to be able to read the paper and then reproduce the results (from '''Joe Dellinger'''). SEGTeX is a LaTeX package for geophysical publications, which is a important component in Madagascar Project. SEGTeX consists of class files for Geophysics papers, SEG expanded abstracts, etc, and cumulative bibliography of geophysical publications. In this module, you will learn how to use the <tt>Madagascar</tt> and SEGTeX to write a reproducible paper. <br><br><br />
|-<br />
| 15:00-15:30<br />
! colspan="2" | Contributing to Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
As a user of Madagascar, you have the right to run the code for any purpose, to make modifications and additions, and to share your modifications with other people under the standard GPL open-source license. Madagascar is an open community, which makes it easy to share your contributions and to collaborate with other users and developers around the world. <br><br><br />
|-<br />
| 15:30-15:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 15:40-16:40<br />
! colspan="2" | Practice (Students and Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Learn the functions of Madagascar software platform, and do some exercises about the construction of data processing workflow and the writing of reproducible papers. <br><br><br />
|}<br />
<br />
== Location ==<br />
<br />
Virtual conference (Tencent Meeting), Jilin University, Changchun, China<br />
<br />
== Registration ==<br />
<br />
The Madagascar School participation is free.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
You must [[download]] and [[Installation|install]] the Madagascar package in the days before the school. <br />
<br />
== Organizations ==<br />
<br />
The "Madagascar School on Open-Source Geophysics in Hefei 2020" is organized by<br />
* '''Yang Liu''' from College of Geo-exploration Science and Technology, Jilin University (Changchun, China)<br />
* '''1st Asia-Pacific Geophysics Student Conference (APGSC)''' jointly organized by University of Science and Technology of China (USTC) and SEG<br />
and hosted by '''Yang Liu'''<br />
<br />
== Instructors ==<br />
<br />
* '''Yang Liu''' is a 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 nonstationary seismic data processing. http://gest.jlu.edu.cn/info/1183/4673.htm</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Hefei_2020&diff=3889Hefei 20202020-08-14T07:58:56Z<p>Yangliu: /* Agenda */</p>
<hr />
<div>&nbsp;<br />
<br />
== Introduction ==<br />
<br />
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. Madagascar school has been organized many times around the word. It provides a platform for Madagascar users to learn and communicate with the developers. This Madagascar school will introduce the advanced usages for the users with fundamental knowledge of Madagascar and focus on the topic of Open-Source Geophysics in China. This Madagascar school is convened by 1st Asia-Pacific Geophysics Student Conference (APGSC) and hosted by Prof. Yang Liu from Jilin University.<br />
<br />
== Dates ==<br />
<br />
September 6, 2020<br />
<br />
== Agenda ==<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Sunday, September 6, 2020<br />
|-<br />
| 8:30-8:40 <br />
! colspan="2" | Welcome<br />
|-<br />
| 8:40-10:10<br />
! colspan="2" | Introduction to Madagascar Project (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
The <tt>Madagascar</tt> project has been in public existence for fourteen 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 origin and history of the project, the Madagascar components and design principles, and plans for future development. In this module, you will learn how to take the full advantage of the <tt>Madagascar</tt> environment to enhance research productivity and research collaboration.<br><br><br />
|-<br />
| 10:10-10:20<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:20-11:50<br />
! colspan="2" | Geophysical data processing with Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Filed data processing is always a tough problem, which is an important test of integrality degree for Open-source geophysics software and the final target for scientific research. We will use a 2D field seismic dataset to illustrate how Madagascar can set up a common seismic data processing workflow. Meanwhile, we also try to setup the initial processing workflows for other geophysical data, e.g., gravity field data and controlled source electromagnetic (CSEM) synthetic data. <br><br><br />
|-<br />
| 11:50-13:30<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 13:30-15:00<br />
! colspan="2" | Writing a reproducible paper using Madagascar and SEGTeX (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
From the viewpoint of science, all technical papers should be "reproducible" in the sense that someone of reasonable skill ought to be able to read the paper and then reproduce the results (from '''Joe Dellinger'''). SEGTeX is a LaTeX package for geophysical publications, which is a important component in Madagascar Project. SEGTeX consists of class files for Geophysics papers, SEG expanded abstracts, etc, and cumulative bibliography of geophysical publications. In this module, you will learn how to use the <tt>Madagascar</tt> and SEGTeX to write a reproducible paper. <br><br><br />
|-<br />
| 15:00-15:30<br />
! colspan="2" | Contributing to Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
As a user of Madagascar, you have the right to run the code for any purpose, to make modifications and additions, and to share your modifications with other people under the standard GPL open-source license. Madagascar is an open community, which makes it easy to share your contributions and to collaborate with other users and developers around the world. <br><br><br />
|-<br />
| 15:30-15:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 15:40-16:40<br />
! colspan="2" | Practice (Students and Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Learn the functions of Madagascar software platform, and do some exercises about the construction of data processing workflow and the writing of reproducible papers. <br><br><br />
|}<br />
<br />
== Location ==<br />
<br />
Virtual conference (Tencent Meeting), Jilin University, Changchun, China<br />
<br />
== Registration ==<br />
<br />
The Madagascar School participation is free.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
You must [[download]] and [[Installation|install]] the Madagascar package in the days before the school. <br />
<br />
== Organizations ==<br />
<br />
The "Madagascar School on Open-Source Geophysics in Hefei 2020" is organized by<br />
* '''Yang Liu''' from College of Geo-exploration Science and Technology, Jilin University (Changchun, China)<br />
* '''1st Asia-Pacific Geophysics Student Conference (APGSC)''' jointly organized by University of Science and Technology of China (USTC) and SEG<br />
and hosted by '''Yang Liu'''<br />
<br />
== Instructors ==<br />
<br />
* '''Yang Liu''' is a 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 nonstationary seismic data processing. http://gest.jlu.edu.cn/info/1183/4673.htm</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Hefei_2020&diff=3888Hefei 20202020-08-14T07:58:29Z<p>Yangliu: /* Agenda */</p>
<hr />
<div>&nbsp;<br />
<br />
== Introduction ==<br />
<br />
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. Madagascar school has been organized many times around the word. It provides a platform for Madagascar users to learn and communicate with the developers. This Madagascar school will introduce the advanced usages for the users with fundamental knowledge of Madagascar and focus on the topic of Open-Source Geophysics in China. This Madagascar school is convened by 1st Asia-Pacific Geophysics Student Conference (APGSC) and hosted by Prof. Yang Liu from Jilin University.<br />
<br />
== Dates ==<br />
<br />
September 6, 2020<br />
<br />
== Agenda ==<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Sunday, September 6, 2020<br />
|-<br />
| 8:30-8:40 <br />
! colspan="2" | Welcome<br />
|-<br />
| 8:40-10:10<br />
! colspan="2" | Introduction to Madagascar Project (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
The <tt>Madagascar</tt> project has been in public existence for fourteen 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 origin and history of the project, the Madagascar components and design principles, and plans for future development. In this module, you will learn how to take the full advantage of the <tt>Madagascar</tt> environment to enhance research productivity and research collaboration.<br><br><br />
|-<br />
| 10:10-10:20<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:20-11:50<br />
! colspan="2" | Geophysical data processing with Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Filed data processing is always a tough problem, which is an important test of integrality degree for Open-source geophysics software and the final target for scientific research. We will use a 2D field seismic dataset to illustrate how Madagascar can set up a common seismic data processing workflow. Meanwhile, we also try to setup the initial processing workflows for other geophysical data, e.g., gravity field data and controlled source electromagnetic (CSEM) synthetic data. <br><br><br />
|-<br />
| 11:50-13:30<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 13:30-15:00<br />
! colspan="2" | Writing a reproducible paper using Madagascar and SEGTeX (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
From the viewpoint of science, all technical papers should be "reproducible" in the sense that someone of reasonable skill ought to be able to read the paper and then reproduce the results (From '''Joe Dellinger'''). SEGTeX is a LaTeX package for geophysical publications, which is a important component in Madagascar Project. SEGTeX consists of class files for Geophysics papers, SEG expanded abstracts, etc, and cumulative bibliography of geophysical publications. In this module, you will learn how to use the <tt>Madagascar</tt> and SEGTeX to write a reproducible paper. <br><br><br />
|-<br />
| 15:00-15:30<br />
! colspan="2" | Contributing to Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
As a user of Madagascar, you have the right to run the code for any purpose, to make modifications and additions, and to share your modifications with other people under the standard GPL open-source license. Madagascar is an open community, which makes it easy to share your contributions and to collaborate with other users and developers around the world. <br><br><br />
|-<br />
| 15:30-15:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 15:40-16:40<br />
! colspan="2" | Practice (Students and Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Learn the functions of Madagascar software platform, and do some exercises about the construction of data processing workflow and the writing of reproducible papers. <br><br><br />
|}<br />
<br />
== Location ==<br />
<br />
Virtual conference (Tencent Meeting), Jilin University, Changchun, China<br />
<br />
== Registration ==<br />
<br />
The Madagascar School participation is free.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
You must [[download]] and [[Installation|install]] the Madagascar package in the days before the school. <br />
<br />
== Organizations ==<br />
<br />
The "Madagascar School on Open-Source Geophysics in Hefei 2020" is organized by<br />
* '''Yang Liu''' from College of Geo-exploration Science and Technology, Jilin University (Changchun, China)<br />
* '''1st Asia-Pacific Geophysics Student Conference (APGSC)''' jointly organized by University of Science and Technology of China (USTC) and SEG<br />
and hosted by '''Yang Liu'''<br />
<br />
== Instructors ==<br />
<br />
* '''Yang Liu''' is a 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 nonstationary seismic data processing. http://gest.jlu.edu.cn/info/1183/4673.htm</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Hefei_2020&diff=3887Hefei 20202020-08-14T07:57:20Z<p>Yangliu: /* Agenda */</p>
<hr />
<div>&nbsp;<br />
<br />
== Introduction ==<br />
<br />
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. Madagascar school has been organized many times around the word. It provides a platform for Madagascar users to learn and communicate with the developers. This Madagascar school will introduce the advanced usages for the users with fundamental knowledge of Madagascar and focus on the topic of Open-Source Geophysics in China. This Madagascar school is convened by 1st Asia-Pacific Geophysics Student Conference (APGSC) and hosted by Prof. Yang Liu from Jilin University.<br />
<br />
== Dates ==<br />
<br />
September 6, 2020<br />
<br />
== Agenda ==<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Sunday, September 6, 2020<br />
|-<br />
| 8:30-8:40 <br />
! colspan="2" | Welcome<br />
|-<br />
| 8:40-10:10<br />
! colspan="2" | Introduction to Madagascar Project (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
The <tt>Madagascar</tt> project has been in public existence for fourteen 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 origin and history of the project, the Madagascar components and design principles, and plans for future development. In this module, you will learn how to take the full advantage of the <tt>Madagascar</tt> environment to enhance research productivity and research collaboration.<br><br><br />
|-<br />
| 10:10-10:20<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:20-11:50<br />
! colspan="2" | Geophysical data processing with Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Filed data processing is always a tough problem, which is an important test of integrality degree for Open-source geophysics software and the final target for scientific research. We will use a 2D field seismic dataset to illustrate how Madagascar can set up a common seismic data processing workflow. Meanwhile, we also try to setup the initial processing workflows for other geophysical data, e.g., gravity field data and controlled source electromagnetic (CSEM) synthetic data. <br><br><br />
|-<br />
| 11:50-13:30<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 13:30-15:00<br />
! colspan="2" | Writing a reproducible paper using Madagascar and SEGTeX (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
From the viewpoint of science, all technical papers should be "reproducible" in the sense that someone of reasonable skill ought to be able to read the paper and then reproduce the results (From <tt>Joe Dellinger</tt>). SEGTeX is a LaTeX package for geophysical publications, which is a important component in Madagascar Project. SEGTeX consists of class files for Geophysics papers, SEG expanded abstracts, etc, and cumulative bibliography of geophysical publications. In this module, you will learn how to use the <tt>Madagascar</tt> and SEGTeX to write a reproducible paper. <br><br><br />
|-<br />
| 15:00-15:30<br />
! colspan="2" | Contributing to Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
As a user of Madagascar, you have the right to run the code for any purpose, to make modifications and additions, and to share your modifications with other people under the standard GPL open-source license. Madagascar is an open community, which makes it easy to share your contributions and to collaborate with other users and developers around the world. <br><br><br />
|-<br />
| 15:30-15:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 15:40-16:40<br />
! colspan="2" | Practice (Students and Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Learn the functions of Madagascar software platform, and do some exercises about the construction of data processing workflow and the writing of reproducible papers. <br><br><br />
|}<br />
<br />
== Location ==<br />
<br />
Virtual conference (Tencent Meeting), Jilin University, Changchun, China<br />
<br />
== Registration ==<br />
<br />
The Madagascar School participation is free.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
You must [[download]] and [[Installation|install]] the Madagascar package in the days before the school. <br />
<br />
== Organizations ==<br />
<br />
The "Madagascar School on Open-Source Geophysics in Hefei 2020" is organized by<br />
* '''Yang Liu''' from College of Geo-exploration Science and Technology, Jilin University (Changchun, China)<br />
* '''1st Asia-Pacific Geophysics Student Conference (APGSC)''' jointly organized by University of Science and Technology of China (USTC) and SEG<br />
and hosted by '''Yang Liu'''<br />
<br />
== Instructors ==<br />
<br />
* '''Yang Liu''' is a 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 nonstationary seismic data processing. http://gest.jlu.edu.cn/info/1183/4673.htm</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Hefei_2020&diff=3886Hefei 20202020-08-14T07:56:56Z<p>Yangliu: /* Agenda */</p>
<hr />
<div>&nbsp;<br />
<br />
== Introduction ==<br />
<br />
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. Madagascar school has been organized many times around the word. It provides a platform for Madagascar users to learn and communicate with the developers. This Madagascar school will introduce the advanced usages for the users with fundamental knowledge of Madagascar and focus on the topic of Open-Source Geophysics in China. This Madagascar school is convened by 1st Asia-Pacific Geophysics Student Conference (APGSC) and hosted by Prof. Yang Liu from Jilin University.<br />
<br />
== Dates ==<br />
<br />
September 6, 2020<br />
<br />
== Agenda ==<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Sunday, September 6, 2020<br />
|-<br />
| 8:30-8:40 <br />
! colspan="2" | Welcome<br />
|-<br />
| 8:40-10:10<br />
! colspan="2" | Introduction to Madagascar Project (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
The <tt>Madagascar</tt> project has been in public existence for fourteen 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 origin and history of the project, the Madagascar components and design principles, and plans for future development. In this module, you will learn how to take the full advantage of the <tt>Madagascar</tt> environment to enhance research productivity and research collaboration.<br><br><br />
|-<br />
| 10:10-10:20<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:20-11:50<br />
! colspan="2" | Geophysical data processing with Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Filed data processing is always a tough problem, which is an important test of integrality degree for Open-source geophysics software and the final target for scientific research. We will use a 2D field seismic dataset to illustrate how Madagascar can set up a common seismic data processing workflow. Meanwhile, we also try to setup the initial processing workflows for other geophysical data, e.g., gravity field data and controlled source electromagnetic (CSEM) synthetic data. <br><br><br />
|-<br />
| 11:50-13:30<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 13:30-15:00<br />
! colspan="2" | Writing a reproducible paper using Madagascar and SEGTeX (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
From the viewpoint of science, all technical papers should be "reproducible" in the sense that someone of reasonable skill ought to be able to read the paper and then reproduce the results (From <tt>Joe Dellinger<tt>). SEGTeX is a LaTeX package for geophysical publications, which is a important component in Madagascar Project. SEGTeX consists of class files for Geophysics papers, SEG expanded abstracts, etc, and cumulative bibliography of geophysical publications. In this module, you will learn how to use the <tt>Madagascar</tt> and SEGTeX to write a reproducible paper. <br><br><br />
|-<br />
| 15:00-15:30<br />
! colspan="2" | Contributing to Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
As a user of Madagascar, you have the right to run the code for any purpose, to make modifications and additions, and to share your modifications with other people under the standard GPL open-source license. Madagascar is an open community, which makes it easy to share your contributions and to collaborate with other users and developers around the world. <br><br><br />
|-<br />
| 15:30-15:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 15:40-16:40<br />
! colspan="2" | Practice (Students and Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Learn the functions of Madagascar software platform, and do some exercises about the construction of data processing workflow and the writing of reproducible papers. <br><br><br />
|}<br />
<br />
== Location ==<br />
<br />
Virtual conference (Tencent Meeting), Jilin University, Changchun, China<br />
<br />
== Registration ==<br />
<br />
The Madagascar School participation is free.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
You must [[download]] and [[Installation|install]] the Madagascar package in the days before the school. <br />
<br />
== Organizations ==<br />
<br />
The "Madagascar School on Open-Source Geophysics in Hefei 2020" is organized by<br />
* '''Yang Liu''' from College of Geo-exploration Science and Technology, Jilin University (Changchun, China)<br />
* '''1st Asia-Pacific Geophysics Student Conference (APGSC)''' jointly organized by University of Science and Technology of China (USTC) and SEG<br />
and hosted by '''Yang Liu'''<br />
<br />
== Instructors ==<br />
<br />
* '''Yang Liu''' is a 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 nonstationary seismic data processing. http://gest.jlu.edu.cn/info/1183/4673.htm</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Hefei_2020&diff=3885Hefei 20202020-08-14T07:54:28Z<p>Yangliu: /* Agenda */</p>
<hr />
<div>&nbsp;<br />
<br />
== Introduction ==<br />
<br />
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. Madagascar school has been organized many times around the word. It provides a platform for Madagascar users to learn and communicate with the developers. This Madagascar school will introduce the advanced usages for the users with fundamental knowledge of Madagascar and focus on the topic of Open-Source Geophysics in China. This Madagascar school is convened by 1st Asia-Pacific Geophysics Student Conference (APGSC) and hosted by Prof. Yang Liu from Jilin University.<br />
<br />
== Dates ==<br />
<br />
September 6, 2020<br />
<br />
== Agenda ==<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Sunday, September 6, 2020<br />
|-<br />
| 8:30-8:40 <br />
! colspan="2" | Welcome<br />
|-<br />
| 8:40-10:10<br />
! colspan="2" | Introduction to Madagascar Project (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
The <tt>Madagascar</tt> project has been in public existence for fourteen 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 origin and history of the project, the Madagascar components and design principles, and plans for future development. In this module, you will learn how to take the full advantage of the <tt>Madagascar</tt> environment to enhance research productivity and research collaboration.<br><br><br />
|-<br />
| 10:10-10:20<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:20-11:50<br />
! colspan="2" | Geophysical data processing with Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Filed data processing is always a tough problem, which is an important test of integrality degree for Open-source geophysics software and the final target for scientific research. We will use a 2D field seismic dataset to illustrate how Madagascar can set up a common seismic data processing workflow. Meanwhile, we also try to setup the initial processing workflows for other geophysical data, e.g., gravity field data and controlled source electromagnetic (CSEM) synthetic data. <br><br><br />
|-<br />
| 11:50-13:30<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 13:30-15:00<br />
! colspan="2" | Writing a reproducible paper using Madagascar and SEGTeX (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
From the viewpoint of science, all technical papers should be "reproducible" in the sense that someone of reasonable skill ought to be able to read the paper and then reproduce the results. SEGTeX is a LaTeX package for geophysical publications, which is a important component in Madagascar Project. SEGTeX consists of class files for Geophysics papers, SEG expanded abstracts, etc, and cumulative bibliography of geophysical publications. In this module, you will learn how to use the <tt>Madagascar</tt> and SEGTeX to write a reproducible paper. <br><br><br />
|-<br />
| 15:00-15:30<br />
! colspan="2" | Contributing to Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
As a user of Madagascar, you have the right to run the code for any purpose, to make modifications and additions, and to share your modifications with other people under the standard GPL open-source license. Madagascar is an open community, which makes it easy to share your contributions and to collaborate with other users and developers around the world. <br><br><br />
|-<br />
| 15:30-15:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 15:40-16:40<br />
! colspan="2" | Practice (Students and Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Learn the functions of Madagascar software platform, and do some exercises about the construction of data processing workflow and the writing of reproducible papers. <br><br><br />
|}<br />
<br />
== Location ==<br />
<br />
Virtual conference (Tencent Meeting), Jilin University, Changchun, China<br />
<br />
== Registration ==<br />
<br />
The Madagascar School participation is free.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
You must [[download]] and [[Installation|install]] the Madagascar package in the days before the school. <br />
<br />
== Organizations ==<br />
<br />
The "Madagascar School on Open-Source Geophysics in Hefei 2020" is organized by<br />
* '''Yang Liu''' from College of Geo-exploration Science and Technology, Jilin University (Changchun, China)<br />
* '''1st Asia-Pacific Geophysics Student Conference (APGSC)''' jointly organized by University of Science and Technology of China (USTC) and SEG<br />
and hosted by '''Yang Liu'''<br />
<br />
== Instructors ==<br />
<br />
* '''Yang Liu''' is a 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 nonstationary seismic data processing. http://gest.jlu.edu.cn/info/1183/4673.htm</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Hefei_2020&diff=3884Hefei 20202020-08-14T07:53:39Z<p>Yangliu: /* Agenda */</p>
<hr />
<div>&nbsp;<br />
<br />
== Introduction ==<br />
<br />
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. Madagascar school has been organized many times around the word. It provides a platform for Madagascar users to learn and communicate with the developers. This Madagascar school will introduce the advanced usages for the users with fundamental knowledge of Madagascar and focus on the topic of Open-Source Geophysics in China. This Madagascar school is convened by 1st Asia-Pacific Geophysics Student Conference (APGSC) and hosted by Prof. Yang Liu from Jilin University.<br />
<br />
== Dates ==<br />
<br />
September 6, 2020<br />
<br />
== Agenda ==<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Sunday, September 6, 2020<br />
|-<br />
| 8:30-8:40 <br />
! colspan="2" | Welcome<br />
|-<br />
| 8:40-10:10<br />
! colspan="2" | Introduction to Madagascar Project (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
The <tt>Madagascar</tt> project has been in public existence for fourteen 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 origin and history of the project, the Madagascar components and design principles, and plans for future development. In this module, you will learn how to take the full advantage of the <tt>Madagascar</tt> environment to enhance research productivity and research collaboration.<br><br><br />
|-<br />
| 10:10-10:20<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:20-11:50<br />
! colspan="2" | Geophysical data processing with Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Filed data processing is always a tough problem, which is an important test of integrality degree for Open-source geophysics software and the final target for scientific research. We will use a 2D field seismic dataset to illustrate how Madagascar can set up a common seismic data processing workflow. Meanwhile, we also try to setup the initial processing workflows for other geophysical data, e.g., gravity field data and controlled source electromagnetic (CSEM) synthetic data. <br><br><br />
|-<br />
| 11:50-13:30<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 13:30-15:00<br />
! colspan="2" | Writing a reproducible paper using Madagascar and SEGTeX (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
From the viewpoint of science, all technical papers should be "reproducible" in the sense that someone of reasonable skill ought to be able to read the paper and then reproduce the results. SEGTeX is a LaTeX package for geophysical publications, which is a important component in Madagascar Project. SEGTeX consists of class files for Geophysics papers, SEG expanded abstracts, etc, and cumulative bibliography of geophysical publications. In this module, you will learn how to use the <tt>Madagascar</tt> and SEGTeX to write a reproducible paper. <br><br><br />
|-<br />
| 15:00-15:30<br />
! colspan="2" | Contributing to Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
As a user of Madagascar, you have the right to run the code for any purpose, to make modifications and additions, and to share your modifications with other people. Madagascar is an open community, which makes it easy to share your contributions and to collaborate with other users and developers around the world. <br><br><br />
|-<br />
| 15:30-15:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 15:40-16:40<br />
! colspan="2" | Practice (Students and Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Learn the functions of Madagascar software platform, and do some exercises about the construction of data processing workflow and the writing of reproducible papers. <br><br><br />
|}<br />
<br />
== Location ==<br />
<br />
Virtual conference (Tencent Meeting), Jilin University, Changchun, China<br />
<br />
== Registration ==<br />
<br />
The Madagascar School participation is free.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
You must [[download]] and [[Installation|install]] the Madagascar package in the days before the school. <br />
<br />
== Organizations ==<br />
<br />
The "Madagascar School on Open-Source Geophysics in Hefei 2020" is organized by<br />
* '''Yang Liu''' from College of Geo-exploration Science and Technology, Jilin University (Changchun, China)<br />
* '''1st Asia-Pacific Geophysics Student Conference (APGSC)''' jointly organized by University of Science and Technology of China (USTC) and SEG<br />
and hosted by '''Yang Liu'''<br />
<br />
== Instructors ==<br />
<br />
* '''Yang Liu''' is a 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 nonstationary seismic data processing. http://gest.jlu.edu.cn/info/1183/4673.htm</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Hefei_2020&diff=3883Hefei 20202020-08-14T07:52:18Z<p>Yangliu: /* Agenda */</p>
<hr />
<div>&nbsp;<br />
<br />
== Introduction ==<br />
<br />
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. Madagascar school has been organized many times around the word. It provides a platform for Madagascar users to learn and communicate with the developers. This Madagascar school will introduce the advanced usages for the users with fundamental knowledge of Madagascar and focus on the topic of Open-Source Geophysics in China. This Madagascar school is convened by 1st Asia-Pacific Geophysics Student Conference (APGSC) and hosted by Prof. Yang Liu from Jilin University.<br />
<br />
== Dates ==<br />
<br />
September 6, 2020<br />
<br />
== Agenda ==<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Sunday, September 6, 2020<br />
|-<br />
| 8:30-8:40 <br />
! colspan="2" | Welcome<br />
|-<br />
| 8:40-10:10<br />
! colspan="2" | Introduction to Madagascar Project (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
The <tt>Madagascar</tt> project has been in public existence for fourteen 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 origin and history of the project, the Madagascar components and design principles, and plans for future development. In this module, you will learn how to take the full advantage of the <tt>Madagascar</tt> environment to enhance research productivity and research collaboration.<br><br><br />
|-<br />
| 10:10-10:20<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:20-11:50<br />
! colspan="2" | Geophysical data processing with Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Filed data processing is always a tough problem, which is an important test of integrality degree for Open-source geophysics software and the final target for scientific research. We will use a 2D field seismic dataset to illustrate how Madagascar can set up a common seismic data processing workflow. Meanwhile, we also try to setup the initial processing workflows for other geophysical data, e.g., gravity field data and controlled source electromagnetic (CSEM) synthetic data. <br><br><br />
|-<br />
| 11:50-13:30<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 13:30-15:00<br />
! colspan="2" | Writing a reproducible paper using Madagascar and SEGTeX (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
From the viewpoint of science, all technical papers should be "reproducible" in the sense that someone of reasonable skill ought to be able to read the paper and then reproduce the results. SEGTeX is a LaTeX package for geophysical publications, which is a important component in Madagascar Project. SEGTeX consists of class files for Geophysics papers, SEG expanded abstracts, etc, and cumulative bibliography of geophysical publications. In this module, you will learn how to use the <tt>Madagascar</tt> and SEGTeX to write a reproducible paper. <br><br><br />
|-<br />
| 15:00-15:30<br />
! colspan="2" | Contributing to Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
As a user of Madagascar, you have the right to run the code for any purpose, to make modifications and additions, and to share your modifications with other people. Madagascar is an open community, which makes it easy to share your contributions and to collaborate with other users and developers around the world. <br><br><br />
|-<br />
| 15:30-15:50<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 15:50-16:50<br />
! colspan="2" | Practice (Students and Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
Learn the functions of Madagascar software platform, and do some exercises about the construction of data processing workflow and the writing of reproducible papers. <br><br><br />
|}<br />
<br />
== Location ==<br />
<br />
Virtual conference (Tencent Meeting), Jilin University, Changchun, China<br />
<br />
== Registration ==<br />
<br />
The Madagascar School participation is free.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
You must [[download]] and [[Installation|install]] the Madagascar package in the days before the school. <br />
<br />
== Organizations ==<br />
<br />
The "Madagascar School on Open-Source Geophysics in Hefei 2020" is organized by<br />
* '''Yang Liu''' from College of Geo-exploration Science and Technology, Jilin University (Changchun, China)<br />
* '''1st Asia-Pacific Geophysics Student Conference (APGSC)''' jointly organized by University of Science and Technology of China (USTC) and SEG<br />
and hosted by '''Yang Liu'''<br />
<br />
== Instructors ==<br />
<br />
* '''Yang Liu''' is a 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 nonstationary seismic data processing. http://gest.jlu.edu.cn/info/1183/4673.htm</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Hefei_2020&diff=3882Hefei 20202020-08-14T06:56:10Z<p>Yangliu: /* Agenda */</p>
<hr />
<div>&nbsp;<br />
<br />
== Introduction ==<br />
<br />
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. Madagascar school has been organized many times around the word. It provides a platform for Madagascar users to learn and communicate with the developers. This Madagascar school will introduce the advanced usages for the users with fundamental knowledge of Madagascar and focus on the topic of Open-Source Geophysics in China. This Madagascar school is convened by 1st Asia-Pacific Geophysics Student Conference (APGSC) and hosted by Prof. Yang Liu from Jilin University.<br />
<br />
== Dates ==<br />
<br />
September 6, 2020<br />
<br />
== Agenda ==<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Sunday, September 6, 2020<br />
|-<br />
| 8:30-8:40 <br />
! colspan="2" | Welcome<br />
|-<br />
| 8:40-10:10<br />
! colspan="2" | Introduction to Madagascar Project (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
The <tt>Madagascar</tt> project has been in public existence for fourteen 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 origin and history of the project, the Madagascar components and design principles, and plans for future development. In this module, you will learn how to take the full advantage of the <tt>Madagascar</tt> environment to enhance research productivity and research collaboration.<br><br><br />
|-<br />
| 10:10-10:20<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:20-11:50<br />
! colspan="2" | Geophysical data processing with Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[]<br />
|-<br />
| 11:50-13:30<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 13:30-15:00<br />
! colspan="2" | Writing a reproducible paper using Madagascar and SEGTex (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[]<br />
|-<br />
| 15:00-15:30<br />
! colspan="2" | Contributing to Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[]<br />
|-<br />
| 15:30-15:50<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 15:50-16:50<br />
! colspan="2" | Practice (Students and Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[] <br />
|}<br />
<br />
== Location ==<br />
<br />
Virtual conference (Tencent Meeting), Jilin University, Changchun, China<br />
<br />
== Registration ==<br />
<br />
The Madagascar School participation is free.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
You must [[download]] and [[Installation|install]] the Madagascar package in the days before the school. <br />
<br />
== Organizations ==<br />
<br />
The "Madagascar School on Open-Source Geophysics in Hefei 2020" is organized by<br />
* '''Yang Liu''' from College of Geo-exploration Science and Technology, Jilin University (Changchun, China)<br />
* '''1st Asia-Pacific Geophysics Student Conference (APGSC)''' jointly organized by University of Science and Technology of China (USTC) and SEG<br />
and hosted by '''Yang Liu'''<br />
<br />
== Instructors ==<br />
<br />
* '''Yang Liu''' is a 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 nonstationary seismic data processing. http://gest.jlu.edu.cn/info/1183/4673.htm</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Hefei_2020&diff=3881Hefei 20202020-08-14T06:50:53Z<p>Yangliu: /* Location */</p>
<hr />
<div>&nbsp;<br />
<br />
== Introduction ==<br />
<br />
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. Madagascar school has been organized many times around the word. It provides a platform for Madagascar users to learn and communicate with the developers. This Madagascar school will introduce the advanced usages for the users with fundamental knowledge of Madagascar and focus on the topic of Open-Source Geophysics in China. This Madagascar school is convened by 1st Asia-Pacific Geophysics Student Conference (APGSC) and hosted by Prof. Yang Liu from Jilin University.<br />
<br />
== Dates ==<br />
<br />
September 6, 2020<br />
<br />
== Agenda ==<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Sunday, September 6, 2020<br />
|-<br />
| 8:30-8:40 <br />
! colspan="2" | Welcome<br />
|-<br />
| 8:40-9:30<br />
! colspan="2" | Introduction to Madagascar Project (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
The <tt>Madagascar</tt> project has been in public existence for fourteen 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 origin and history of the project, the Madagascar components and design principles, and plans for future development. In this module, you will learn how to take the full advantage of the <tt>Madagascar</tt> environment to enhance research productivity and research collaboration.<br><br><br />
|-<br />
| 9:30-9:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 9:40-10:30<br />
! colspan="2" | Geophysical data processing with Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[]<br />
|-<br />
| 10:30-11:30<br />
! colspan="2" | Writing a reproducible paper using Madagascar and SEGTex (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[]<br />
|-<br />
| 11:30-14:00<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 14:00-15:30<br />
! colspan="2" | Contributing to Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[]<br />
|-<br />
| 15:30-15:50<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 15:50-17:00<br />
! colspan="2" | Practice (Students and Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[] <br />
|}<br />
<br />
== Location ==<br />
<br />
Virtual conference (Tencent Meeting), Jilin University, Changchun, China<br />
<br />
== Registration ==<br />
<br />
The Madagascar School participation is free.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
You must [[download]] and [[Installation|install]] the Madagascar package in the days before the school. <br />
<br />
== Organizations ==<br />
<br />
The "Madagascar School on Open-Source Geophysics in Hefei 2020" is organized by<br />
* '''Yang Liu''' from College of Geo-exploration Science and Technology, Jilin University (Changchun, China)<br />
* '''1st Asia-Pacific Geophysics Student Conference (APGSC)''' jointly organized by University of Science and Technology of China (USTC) and SEG<br />
and hosted by '''Yang Liu'''<br />
<br />
== Instructors ==<br />
<br />
* '''Yang Liu''' is a 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 nonstationary seismic data processing. http://gest.jlu.edu.cn/info/1183/4673.htm</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Hefei_2020&diff=3880Hefei 20202020-08-14T06:45:15Z<p>Yangliu: </p>
<hr />
<div>&nbsp;<br />
<br />
== Introduction ==<br />
<br />
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. Madagascar school has been organized many times around the word. It provides a platform for Madagascar users to learn and communicate with the developers. This Madagascar school will introduce the advanced usages for the users with fundamental knowledge of Madagascar and focus on the topic of Open-Source Geophysics in China. This Madagascar school is convened by 1st Asia-Pacific Geophysics Student Conference (APGSC) and hosted by Prof. Yang Liu from Jilin University.<br />
<br />
== Dates ==<br />
<br />
September 6, 2020<br />
<br />
== Agenda ==<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Sunday, September 6, 2020<br />
|-<br />
| 8:30-8:40 <br />
! colspan="2" | Welcome<br />
|-<br />
| 8:40-9:30<br />
! colspan="2" | Introduction to Madagascar Project (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
The <tt>Madagascar</tt> project has been in public existence for fourteen 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 origin and history of the project, the Madagascar components and design principles, and plans for future development. In this module, you will learn how to take the full advantage of the <tt>Madagascar</tt> environment to enhance research productivity and research collaboration.<br><br><br />
|-<br />
| 9:30-9:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 9:40-10:30<br />
! colspan="2" | Geophysical data processing with Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[]<br />
|-<br />
| 10:30-11:30<br />
! colspan="2" | Writing a reproducible paper using Madagascar and SEGTex (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[]<br />
|-<br />
| 11:30-14:00<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 14:00-15:30<br />
! colspan="2" | Contributing to Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[]<br />
|-<br />
| 15:30-15:50<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 15:50-17:00<br />
! colspan="2" | Practice (Students and Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[] <br />
|}<br />
<br />
== Location ==<br />
<br />
Virtual conference, Jilin University, Changchun, China<br />
<br />
== Registration ==<br />
<br />
The Madagascar School participation is free.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
You must [[download]] and [[Installation|install]] the Madagascar package in the days before the school. <br />
<br />
== Organizations ==<br />
<br />
The "Madagascar School on Open-Source Geophysics in Hefei 2020" is organized by<br />
* '''Yang Liu''' from College of Geo-exploration Science and Technology, Jilin University (Changchun, China)<br />
* '''1st Asia-Pacific Geophysics Student Conference (APGSC)''' jointly organized by University of Science and Technology of China (USTC) and SEG<br />
and hosted by '''Yang Liu'''<br />
<br />
== Instructors ==<br />
<br />
* '''Yang Liu''' is a 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 nonstationary seismic data processing. http://gest.jlu.edu.cn/info/1183/4673.htm</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Harbin_2015&diff=3879Harbin 20152020-08-14T06:40:46Z<p>Yangliu: /* Agenda */</p>
<hr />
<div>[[Image:Harbin_2015.jpg|center|frame]]<br />
<br />
<center><big>'''Madagascar School in Harbin 2015'''</big></center><br />
<br />
&nbsp;<br />
<br />
== Dates ==<br />
<br />
January 7-8, 2015.<br />
<br />
== Agenda ==<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 1: Wednesday, January 7, 2015<br />
|-<br />
| 10:00-3:00<br />
! colspan="2" | Bring your laptop with Madagascar package (stable version 1.6) and get help with installing Madagascar<br />
|-<br />
|<br />
! colspan="2" | Sergey Fomel, Yang Liu, Jeffrey Shragge, Junzhe Sun, Pengliang Yang<br />
|-<br />
| <br />
| colspan="2" | <br />
[http://ahay.org/RSF/book/rsf/school2015/paper_html/ Madagascar tutorial]<br />
|}<br />
<br />
&nbsp;<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 2: Thursday, January 8, 2015<br />
|-<br />
| 9:00-9:10<br />
! colspan="2" | Welcome (Jianwei Ma)<br />
<br />
|-<br />
| 9:10-10:10<br />
! colspan="2" | Introduction (Sergey Fomel)<br />
|-<br />
| <br />
| colspan="2" | <br />
The Madagascar project has been in public existence for nine 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.<br><br><br />
[http://www.ahay.org/wikilocal/docs/Madagascar-Harbin.pdf Slides] (18M)<br />
<br />
|-<br />
| 10:10-10:25<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:25-11:25<br />
! colspan="2" | Command-line, plotting, papers and beyond (Pengliang Yang)<br />
|-<br />
|<br />
| colspan="2" | <br />
Madagascar provides excellent plotting tools for displaying 2D and 3D seismic data volume. I will cover some fundamentals of Madagascar's command-line usage, plotting, and reproducing papers. I will share my experience of using Madagascar as a great resource to obtain public datasets, to take the free open course and to share research outcomes.<br />
<br><br><br />
[http://www.ahay.org/wikilocal/docs/school2015.pdf Slides] (2.5M)<br />
|-<br />
| 11:25-12:25<br />
! colspan="2" | Developing workflows using SCons (Sergey Fomel)<br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.scons.org/ SCons] (from '''S'''oftware '''Cons'''truction) is a superior alternative to the classic '''make''' utility. SCons is implemented as a [http://www.python.org Python] script, its "configuration files" (<tt>SConstruct</tt> files) are also Python scripts. Madagascar uses SCons to compile software, to manage data processing flowing, and to assemble [[Reproducible Documents|reproducible documents]].<br><br><br />
|-<br />
| 12:25-1:25<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 1:25-2:25<br />
! colspan="2" | Wave-equation modeling and migration (Junzhe Sun)<br />
|-<br />
|<br />
| colspan="2" | <br />
In this module we will first briefly review wave equation modeling and imaging using the exploding reflector concept. Next, the numerical experiment includes implementing this technique in Madagascar and applying it on a simple geological model generated by Madagascar programs.<br />
<br><br><br />
[http://www.ahay.org/wikilocal/docs/exploding_modmig_Sun.pdf Slides] (1M)<br />
<br><br />
[http://www.ahay.org/RSF/book/rsf/school2015/modmig.html SConstruct]<br />
|-<br />
| 2:25-3:25<br />
! colspan="2" | Developing your own programs in Madagascar (Jeffrey Shragge)<br />
|-<br />
|<br />
| colspan="2" | <br />
There are many programs already built into the Madagascar project, but if you use Madagascar long enough you will eventually run into a problem that you cannot solve using only provided codes. Fortunately, Madagascar has a variety of programming language APIs already built, that allow you to: design, code, and integrate your programs into the Madagascar framework. By the end of the session, you should have a good starting point for developing your own codes, and adding them to the growing library of open-source software available in Madagascar. <br />
<br><br><br />
[http://www.ahay.org/wikilocal/docs/RSF_SCHOOL.pdf Slides] (204K)<br />
<br><br />
[http://www.ahay.org/wikilocal/docs/PROGRAM.pdf Program example] (104K)<br />
|-<br />
| 3:25-3:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 3:40-4:40<br />
! colspan="2" | Seismic data processing example (Yang Liu)<br />
|-<br />
|<br />
| colspan="2" | <br />
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.<br><br><br />
[http://www.ahay.org/wikilocal/docs/Field_data_example.pdf Slides] (4.9M)<br />
<br><br />
[http://www.ahay.org/RSF/book/rsf/school/data.html SConstruct]<br />
|-<br />
| 4:40-5:10<br />
! colspan="2" | Contributing to Madagascar (Sergey Fomel)<br />
|-<br />
|<br />
| colspan="2" |<br />
As a user of Madagascar, you have the right to run the code for any purpose, to make modifications and additions, and to share your modifications with other people. Madagascar is an open community, which makes it easy to share your contributions and to collaborate with other users and developers around the world. <br><br><br />
[http://www.ahay.org/wikilocal/docs/Contributing-Harbin.pdf Slides] (4.6M)<br />
|-<br />
| 5:10-5:40<br />
! colspan="2" | Awarding certificates and closing<br />
|-<br />
|}<br />
<br />
== Location ==<br />
<br />
Room no. 331 in the New Active Center, Harbin Institute of Technology (HIT), China<br />
<br />
哈尔滨工业大学,新活动中心331会议室,黑龙江省哈尔滨市南岗区西大直街92号<br />
<br />
== Registration ==<br />
The workshop participation is free but requires an application. <br />
<br />
The deadline is January 1, 2015.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
Please try to [[download]] and [[Installation|install]] the Madagascar package ([http://sourceforge.net/projects/rsf/files/latest/download?source=files stable version 1.6]) in the days before the workshop according to the instructions on the left margin of this webpage. If issues come up, there will an opportunity to install the package at the start of the workshop. Remember to bring your laptop (Linux, Mac, or Windows) to the session!<br />
<br />
== Instructors ==<br />
<br />
* '''Sergey Fomel''' is a Professor at the Jackson School of Geosciences, the University of Texas at Austin. He received a Ph.D. in Geophysics from Stanford University in 2001. Sergey started work on Madagascar (at that time named RSF for Regularly Sampled Format) in 2003. http://www.jsg.utexas.edu/researcher/sergey_fomel/<br />
* '''Yang Liu''' is a 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. http://gest.jlu.edu.cn/?mod=info&act=view&id=54<br />
* '''Jeffrey Shragge''' is an Associate 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). https://www.socrates.uwa.edu.au/Staff/StaffProfile.aspx?Person=JeffreyShragge<br />
* '''Junzhe Sun''' graduated from a joint education program between China University of Petroleum-East China and Missouri University of Science and Technology with a Bachelor's Degree in Geophysics in 2012. He worked with Prof. Stephen Gao on seismic anisotropy and mantle flow when he was at Missouri S&T. He is currently a Ph.D student working with Prof. Sergey Fomel. http://www.linkedin.com/pub/junzhe-sun/44/749/3b<br />
* '''Pengliang Yang''' received his bachelor's degree in 2009 from Nanjing University of Aeronautics and Astronautics and is currently pursuing a Ph.D. at Xi'an Jiaotong University. Previously, he worked on sparsity-based seismic data reconstruction using the theory of compressed sensing. His current research is mainly on reverse time migration and sparse inversion.</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Hefei_2020&diff=3878Hefei 20202020-08-14T06:25:29Z<p>Yangliu: /* Agenda */</p>
<hr />
<div>&nbsp;<br />
<br />
== Introduction ==<br />
<br />
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. Madagascar school has been organized many times around the word. It provides a platform for Madagascar users to learn and communicate with the developers. This Madagascar school will introduce the advanced usages for the users with fundamental knowledge of Madagascar and focus on the topic of Open-Source Geophysics in China. This Madagascar school is convened by 1st Asia-Pacific Geophysics Student Conference (APGSC) and hosted by Prof. Yang Liu from Jilin University.<br />
<br />
== Dates ==<br />
<br />
September 6, 2020<br />
<br />
== Agenda ==<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Sunday, September 6, 2020<br />
|-<br />
| 8:30-8:40 <br />
! colspan="2" | Welcome<br />
|-<br />
| 8:40-9:30<br />
! colspan="2" | Introduction to Madagascar Project (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[] <br />
|-<br />
| 9:30-9:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 9:40-10:30<br />
! colspan="2" | Geophysical data processing with Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[]<br />
|-<br />
| 10:30-11:30<br />
! colspan="2" | Writing a reproducible paper using Madagascar and SEGTex (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[]<br />
|-<br />
| 11:30-14:00<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 14:00-15:30<br />
! colspan="2" | Contributing to Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[]<br />
|-<br />
| 15:30-15:50<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 15:50-17:00<br />
! colspan="2" | Practice (Students and Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[] <br />
|}<br />
<br />
== Location ==<br />
<br />
Virtual conference, Jilin University, Changchun, China<br />
<br />
== Registration ==<br />
<br />
The Madagascar School participation is free.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
You must [[download]] and [[Installation|install]] the Madagascar package in the days before the school. <br />
<br />
== Organizations ==<br />
<br />
The "Madagascar School on Open-Source Geophysics in Hefei 2020" is organized by<br />
* '''Yang Liu''' from College of Geo-exploration Science and Technology, Jilin University (Changchun, China)<br />
* '''1st Asia-Pacific Geophysics Student Conference (APGSC)''' jointly organized by University of Science and Technology of China (USTC) and SEG<br />
and hosted by '''Yang Liu'''<br />
<br />
== Instructors ==<br />
<br />
* '''Yang Liu''' is a 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 nonstationary seismic data processing. http://gest.jlu.edu.cn/info/1183/4673.htm</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Hefei_2020&diff=3877Hefei 20202020-08-13T16:46:36Z<p>Yangliu: </p>
<hr />
<div>&nbsp;<br />
<br />
== Introduction ==<br />
<br />
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. Madagascar school has been organized many times around the word. It provides a platform for Madagascar users to learn and communicate with the developers. This Madagascar school will introduce the advanced usages for the users with fundamental knowledge of Madagascar and focus on the topic of Open-Source Geophysics in China. This Madagascar school is convened by 1st Asia-Pacific Geophysics Student Conference (APGSC) and hosted by Prof. Yang Liu from Jilin University.<br />
<br />
== Dates ==<br />
<br />
September 6, 2020<br />
<br />
== Agenda ==<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Sunday, September 6, 2020<br />
|-<br />
| 8:30-8:40 <br />
! colspan="2" | Welcome (UTSC)<br />
|-<br />
| 8:40-9:30<br />
! colspan="2" | About Madagascar Project (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[] <br />
|-<br />
| 9:30-9:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 9:40-10:30<br />
! colspan="2" | Geophysical data processing with Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[]<br />
|-<br />
| 10:30-11:30<br />
! colspan="2" | Writing a reproducible paper using LaTeX and Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[]<br />
|-<br />
| 11:30-14:00<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 14:00-15:30<br />
! colspan="2" | Contributing to Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[]<br />
|-<br />
| 15:30-15:50<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 15:50-17:00<br />
! colspan="2" | Practice (Students and Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[] <br />
|}<br />
<br />
== Location ==<br />
<br />
Virtual conference, Jilin University, Changchun, China<br />
<br />
== Registration ==<br />
<br />
The Madagascar School participation is free.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
You must [[download]] and [[Installation|install]] the Madagascar package in the days before the school. <br />
<br />
== Organizations ==<br />
<br />
The "Madagascar School on Open-Source Geophysics in Hefei 2020" is organized by<br />
* '''Yang Liu''' from College of Geo-exploration Science and Technology, Jilin University (Changchun, China)<br />
* '''1st Asia-Pacific Geophysics Student Conference (APGSC)''' jointly organized by University of Science and Technology of China (USTC) and SEG<br />
and hosted by '''Yang Liu'''<br />
<br />
== Instructors ==<br />
<br />
* '''Yang Liu''' is a 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 nonstationary seismic data processing. http://gest.jlu.edu.cn/info/1183/4673.htm</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Conferences&diff=3876Conferences2020-08-13T16:26:17Z<p>Yangliu: </p>
<hr />
<div>[[Image:Conferences.png|right|]]<br />
In reverse chronological order.<br />
<br />
==Schools, Workshops, and Working Workshops==<br />
[[Hefei_2020|Madagascar School on Open-Source Geophysics in Hefei 2020]]<br />
<br />
[[HoustonWW2018|SEG Working Workshop - Python and Julia for Geophysics, Houston August 8-11, 2018]]<br />
<br />
[[HoustonWW2017|SEG Working Workshop in Houston 2017]]<br />
<br />
[[Shanghai_2017|Madagascar School of Reproducible Computational Geophysics Shanghai 2017]]<br />
<br />
[[Houston_2017|Madagascar School at the University of Houston 2017]]<br />
<br />
[[SEG_3D_Seismic_Processing_Working_Workshop_Houston_2016-_Land_3D|SEG Land 3D Seismic Processing Working Workshop Houston 2016]]<br />
<br />
[[Zurich 2016|Madagascar School on Reproducible Computational Geophysics in Zürich 2016]]<br />
<br />
[[Vienna_2016|Workshop - Open-source Software in Applied Geosciences Vienna 2016]]<br />
<br />
[[Qingdao_2015|Madagascar School for Advanced Users in Qingdao 2015]]<br />
<br />
[[SEG 3D Seismic Processing Working Workshop Houston 2015- Land 3D|SEG 3D Land Seismic Processing Working Workshop Houston 2015]]<br />
<br />
[[Harbin_2015|School in Harbin 2015]]<br />
<br />
[[Houston_2014|Second Madagascar Working Workshop Houston 2014]]<br />
<br />
[[Petersburg_2014|Workshop at EAGE/St. Petersburg 2014]]<br />
<br />
[[Melbourne_2013|Workshop at ASEG 2013]]<br />
<br />
[[Austin_2013|First Madagascar Working Workshop Austin 2013]]<br />
<br />
[[Austin_2012|Madagascar School and Workshop on Reproducible Computational Geophysics Austin 2012]]<br />
<br />
[[Copenhagen_2012|Workshop - Open-source E&P Software - Six Years Later Copenhagen 2012]]<br />
<br />
[[Beijing_2011|Madagascar School of Reproducible Computational Geophysics Beijing 2011]]<br />
<br />
[[Houston_2011|Workshop - Open Software Tools for Reproducible Computational Geophysics Houston 2011]]<br />
<br />
[[Houston_2010|Madagascar School of Reproducible Computational Geophysics and Hands-On School Houston 2010]]<br />
<br />
[[Salvador_2009|Madagascar School on Reproducible Computational Geophysics Salvador 2009]]<br />
<br />
[[Delft_2009|Madagascar School on Reproducible Computational Geophysics Delft 2009]]<br />
<br />
[[2008_Implementation_Workshop|Towards full automation and better robustness Coding Sprint Golden 2008]] <br />
<br />
[[RSF_Austin_School_2007|Using and Extending RSF/Madagascar School Austin 2007]].<br />
<br />
[[RSF_School_and_Workshop%2C_Vancouver_2006|Reproducible Research in Computational Geophysics School and Workshop Vancouver 2006]].<br />
<br />
==Conference presentations==<br />
<br />
===Lausanne 2016 (PASC)===<br />
<br />
Two presentations about <tt>Madagascar</tt> were presented in the minisymposium on '''Open Source Software (OSS) and High Performance Computing (HPC)''' at the [http://www.pasc16.org/ Platform for Advanced Scientific Computing] conference in Lausanne, Switzerland, on June 9, 2016. See presentation slides: <br />
* [http://reproducibility.org/wikilocal/docs/FOMEL-PASC2016.pdf Data-Parallel Processing Using Madagascar Open-Source Software Package] <br />
* [http://reproducibility.org/wikilocal/docs/POTTER-SHRAGGE-PASC2016.pdf Leveraging the Madagascar Framework for Reproducible Large-scale Cluster and Cloud Computing]<br />
<br />
===San Francisco 2015 (AGU)===<br />
<br />
<tt>Madagascar</tt> was presented in the session on '''Informatics and Intelligent Systems in Reproducible Geoscience Research''' at the [http://fallmeeting.agu.org/2015/ AGU Fall Meeting] in San Francisco, California, on December 17, 2015. See presentation [http://reproducibility.org/wikilocal/docs/Madagascar-AGU-2015.pdf slides] and the [https://agu.confex.com/agu/fm15/meetingapp.cgi/Session/10540 session program].<br />
<br />
===Stanford 2015 (SIAM Geosciences)===<br />
<br />
<tt>Madagascar</tt> was presented in the minisymposium on '''Advances in Software for Computational Geosciences''' at the [http://www.siam.org/meetings/gs15/ SIAM Conference on Mathematical & Computational Issues in the Geosciences] in Stanford, California, on June 30, 2015. See presentation [http://reproducibility.org/wikilocal/docs/Fomel-SIAM-Geosciences-2015.pdf slides] and the [http://meetings.siam.org/sess/dsp_programsess.cfm?SESSIONCODE=21097 minisymposium program].<br />
<br />
===New York 2013 (NYU Poly)===<br />
<br />
<tt>Madagascar</tt> was presented at the Workshop on [http://www.reproduciblescience.org/index.php/Workshop_on_Software_Infrastructure_for_Reproducibility_in_Science_--_May_30th-31st,_2013 Software Infrastructure for Reproducibility in Science] at the Polytechnic Institute of New York University in Brooklyn, New York, on May 30, 2013. See presentation [http://reproducibility.org/wikilocal/docs/Madagascar-NYC.pdf slides]. <br />
<br />
The workshop was supported by the [http://www.sloan.org/ Alfred P. Sloan Foundation]. Juliana Freire provides the complete [http://vgc.poly.edu/~juliana/ReproducibleScience/SoftwareInfrastructure/agenda.pdf workshop program].<br />
<br />
===Providence 2012 (ICERM)===<br />
<br />
<tt>Madagascar</tt> was presented at the [http://icerm.brown.edu/tw12-5-rcem Reproducibility in Computational and Experimental Mathematics] Workshop at the Institute for Computational and Experimental Research in Mathematics (ICERM) in Providence, Rhode Island, on December 13, 2012.<br />
<br />
See presentation [http://reproducibility.org/wikilocal/docs/ICERM.pptx slides], the complete [http://icerm.brown.edu/tw12-5-rcem workshop program], and Victoria Stodden's [http://wiki.stodden.net/ICERM_Reproducibility_in_Computational_and_Experimental_Mathematics:_Readings_and_References wiki page].<br />
<br />
===Austin 2012 (SciPy)===<br />
<br />
The Python interface to <tt>Madagascar</tt> was presented at the [http://conference.scipy.org/scipy2012/ Scientific Computing with Python Conference] in Austin, Texas, on July 19, 2012. See the poster by clicking on the image below<br />
.<br><br />
<br />
[[Image:SciPy2012Poster.png|link=http://www.ahay.org/wikilocal/docs/SciPy2012Poster.pdf]]<br />
<br />
===Cary 2011 (Interface)===<br />
<tt>Madagascar</tt> was presented in the special session on '''Reproducible Research''' at the [http://www.interfacesymposia.org/Interface2011/ 42nd Symposium on the Interface] (Statistical, Machine Learning, and Visualization Algorithms) in Cary, North Carolina, on June 1, 2011. See the [http://www.interfacesymposia.org/Interface2011/Program.pdf symposium program].<br />
<br />
===Long Beach 2011 (SIAM Geosciences)===<br />
<br />
<tt>Madagascar</tt> was presented in the minisymposium on '''Reproducible Science and Open-Source Software in the Geosciences''' at the [http://www.siam.org/meetings/gs11/ SIAM Conference on Mathematical & Computational Issues in the Geosciences] in Long Beach, California, on March 23, 2011. See presentation [http://reproducibility.org/wikilocal/docs/longbeach2011.pdf slides] and the minisymposium program: [http://meetings.siam.org/sess/dsp_programsess.cfm?SESSIONCODE=11822 Part 1] and [http://meetings.siam.org/sess/dsp_programsess.cfm?SESSIONCODE=11823 Part 2].<br />
<br />
===Reno 2011 (SIAM CS&E)===<br />
<br />
<tt>Madagascar</tt> was presented in the minisymposium on '''Verifiable, Reproducible Research and Computational Science''' at the [http://www.siam.org/meetings/cse11/ SIAM Conference on Computational Science and Engineering] in Reno, Nevada, on March 4, 2011. See presentation [http://reproducibility.org/wikilocal/docs/reno2011.pdf slides]. <br />
<br />
Jarrod Millman provides a complete [http://jarrodmillman.com/events/siam2011.html session program].<br />
<br />
===Austin 2010 (SciPy)===<br />
<br />
<tt>Madagascar</tt> was presented at the [http://conference.scipy.org/scipy2010/ Python in Scientific Computing Conference] in Austin, Texas, on July 1, 2010. See presentation [http://reproducibility.org/wikilocal/docs/scipy2010.pdf slides] and [http://conference.scipy.org/scipy2010/schedule.html complete program].<br />
<br />
===Salt Lake City 2010 (NSF Archive Workshop)===<br />
<br />
<tt>Madagascar</tt> was presented at the [http://users.emulab.net/trac/archive10/ NSF Workshop on Archiving Experiments to Raise Scientific Standards] in Salt Lake City on May 25, 2010. See presentation [http://reproducibility.org/wikilocal/docs/slc.pdf slides] and [http://users.emulab.net/trac/archive10/wiki/WorkshopSchedule complete program].<br />
<br />
===Düsseldorf 2008 (Berlin 6) ===<br />
<br />
<tt>Madagascar</tt> was mentioned in the special session on '''Open Data and Reproducible Research''' at the [http://www.berlin6.org/ Berlin 6 Open Access Conference] in Düsseldorf, Germany, on November 12, 2008. See presentation [http://reproducibility.org/wikilocal/docs/Berlin-6.ppt slides]. <br />
<br />
Mark Liberman provides a complete [http://ldc.upenn.edu/myl/Berlin6Session5/Overview.html session program].<br />
<br />
===Austin 2008 (Texas Python Unconference)===<br />
<br />
''New Directions in Literate Programming with Madagascar'' was presented at the Second Annual Texas Python Unconference hosted by Enthought Corporation on the UT campus on October 4, 2008. See presentation [http://www.ig.utexas.edu/people/staff/tobis/MadLiter/madliter.html slides].<br />
<br />
===Austin 2008 (Scientific Software Days)===<br />
<br />
<tt>Madagascar</tt> was presented at the Second Annual Scientific Software Days at the University of Texas at Austin on May 15, 2008. See presentation [http://reproducibility.org/wikilocal/docs/ssd2.pdf slides] and [http://www.tacc.utexas.edu/softwareday/ complete program].<br />
<br />
===Rio de Janeiro 2007 (SBGf)===<br />
<br />
<tt>Madagascar</tt> and reproducible scientific computing were presented at the 2007 [http://www.sbgf.org.br Congress of the Brazilian Geophysical Society] in Rio de Janeiro. See presentation [http://reproducibility.org/wikilocal/docs/2007_SBGf_ReproducibleScientificComputingUsingMadagascar.pdf slides].<br />
<br />
===Vancouver 2007 (AIP)===<br />
<br />
<tt>Madagascar</tt> was presented at a minisymposium on '''Software for Inverse Problems''' at the [http://www.pims.math.ca/science/2007/07aip/ Conference on Applied Inverse Problems] in Vancouver on June 29, 2007. See presentation [http://reproducibility.org/wikilocal/docs/Fomel-AIP.ppt slides].<br />
<br />
===Honolulu 2007 (ICASSP)===<br />
<br />
The paper [http://reproducibility.org/wikilocal/docs/scons.pdf Reproducible computational experiments using SCons] was presented in the [http://www.icassp2007.org/Papers/PublicSessionIndex3.asp?Sessionid=1168 special session] on '''Reproducible Signal Processing Research''' at the [http://www.icassp2007.org/ International Conference on Acoustics, Speech, and Signal Processing] in Honolulu on April 18, 2007 . See presentation [http://reproducibility.org/wikilocal/docs/SCons.ppt slides].<br />
<br />
Patrick Vandewalle provides a complete [http://lcavwww.epfl.ch/reproducible_research/ICASSP07/ session program].<br />
<br />
===Austin 2007 (Scientific Software Day)===<br />
<br />
<tt>Madagascar</tt> was presented at the First Annual Scientific Software Day at the University of Texas at Austin on April 2, 2007. See presentation [http://reproducibility.org/wikilocal/docs/Madagascar-SSD.ppt slides].<br />
<br />
===New Orleans 2006 (SEG)===<br />
<br />
These advertising posters were prepared for the SEG Annual Meeting in New Orleans. The idea by Gilles Hennenfent, implementation by Scott Rodgers.<br />
<br />
[[Image:Poker_comp_BEG.png]] [[Image:Poker_comp_CSM.png]] [[Image:Poker_comp_UBC.png]]<br />
<br />
===Vienna 2006 (EAGE)===<br />
<br />
RSF/Madagascar was first presented at the EAGE Workshop [http://www.eage.org/events/index.php?evp=274&eventid=1&ActiveMenu=16&Opendivs=s2,s11,s13 Open Source E&P Software – Putting the Pieces Together] in Vienna on June 11, 2006. See presentation [http://reproducibility.org/wikilocal/docs/vienna.pdf slides].<br />
<br />
Joe Dellinger provides a complete [http://sepwww.stanford.edu/oldsep/joe/Vienna/ workshop program with abstracts].</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Hefei_2020&diff=3875Hefei 20202020-08-13T16:25:46Z<p>Yangliu: </p>
<hr />
<div>&nbsp;<br />
<br />
== Introduction ==<br />
<br />
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. Madagascar school has been organized many times around the word. It provides a platform for Madagascar users to learn and communicate with the developers. This Madagascar school will introduce the advanced usages for the users with fundamental knowledge of Madagascar and focus on the topic of Open-Source Geophysics in China. This Madagascar school is convened by 1st Asia-Pacific Geophysics Student Conference, USTC, Hefei, Anhui, China and hosted by Prof. Yang Liu from Jilin University.<br />
<br />
== Dates ==<br />
<br />
September 6, 2020<br />
<br />
== Agenda ==<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Sunday, September 6, 2020<br />
|-<br />
| 8:30-8:40 <br />
! colspan="2" | Welcome (UTSC)<br />
|-<br />
| 8:40-9:30<br />
! colspan="2" | About Madagascar Project (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[] <br />
|-<br />
| 9:30-9:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 9:40-10:30<br />
! colspan="2" | Geophysical data processing with Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[]<br />
|-<br />
| 10:30-11:30<br />
! colspan="2" | Writing a reproducible paper using LaTeX and Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[]<br />
|-<br />
| 11:30-14:00<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 14:00-15:30<br />
! colspan="2" | Contributing to Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[]<br />
|-<br />
| 15:30-15:50<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 15:50-17:00<br />
! colspan="2" | Practice (Students and Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[] <br />
|}<br />
<br />
== Location ==<br />
<br />
Virtual conference, Jilin University, Changchun, China<br />
<br />
== Registration ==<br />
<br />
The Madagascar School participation is free.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
You must [[download]] and [[Installation|install]] the Madagascar package in the days before the school. <br />
<br />
== Organizations ==<br />
<br />
The "Madagascar School on Open-Source Geophysics in Hefei 2020" is organized by<br />
* '''Yang Liu''' from College of Geo-exploration Science and Technology, Jilin University (Changchun, China)<br />
* '''1st Asia-Pacific Geophysics Student Conference''' from UTSC (Hefei, China)<br />
and hosted by '''Yang Liu'''<br />
<br />
== Instructors ==<br />
<br />
* '''Yang Liu''' is a 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 nonstationary seismic data processing. http://gest.jlu.edu.cn/info/1183/4673.htm</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Hefei_2020&diff=3874Hefei 20202020-08-13T16:24:16Z<p>Yangliu: Created page with "&nbsp; == Introduction == Madagascar provides a complete environment for organizing one's research, from new software development to running computational experiments to pub..."</p>
<hr />
<div>&nbsp;<br />
<br />
== Introduction ==<br />
<br />
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. Madagascar school has been organized many times around the word. It provides a platform for Madagascar users to learn and communicate with the developers. This Madagascar school will introduce the advanced usages for the users with fundamental knowledge of Madagascar and focus on the topic of Open-Source Geophysics in China. This Madagascar school is convened by 1st Asia-Pacific Geophysics Student Conference, USTC, Hefei, Anhui, China and hosted by Prof. Yang Liu from Jilin University.<br />
<br />
== Dates ==<br />
<br />
September 6, 2020<br />
<br />
== Agenda ==<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Sunday, September 6, 2020<br />
|-<br />
| 8:30-8:40 <br />
! colspan="2" | Welcome (UTSC)<br />
|-<br />
| 8:40-9:30<br />
! colspan="2" | About Madagascar Project (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[] <br />
|-<br />
| 9:30-9:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 9:40-10:30<br />
! colspan="2" | Geophysical data processing with Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[]<br />
|-<br />
| 10:30-11:30<br />
! colspan="2" | Writing a reproducible paper using LaTeX and Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[]<br />
|-<br />
| 11:30-14:00<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 14:00-15:30<br />
! colspan="2" | Contributing to Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[]<br />
|-<br />
| 15:30-15:50<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 15:50-17:00<br />
! colspan="2" | Practice (Students and Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[] <br />
|}<br />
<br />
== Location ==<br />
<br />
Virtual conference, Jilin University, Changchun, China<br />
<br />
== Registration ==<br />
<br />
The Madagascar School participation is free.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
You must [[download]] and [[Installation|install]] the Madagascar package in the days before the school. <br />
<br />
== Organizations ==<br />
<br />
The "Madagascar School of Reproducible Computational Geophysics Shanghai 2017" is organized by<br />
* '''Yang Liu''' from College of Geo-exploration Science and Technology, Jilin University (Changchun, China)<br />
* '''1st Asia-Pacific Geophysics Student Conference''' from UTSC (Hefei, China)<br />
and hosted by '''Yang Liu'''<br />
<br />
== Instructors ==<br />
<br />
* '''Yang Liu''' is a 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 nonstationary seismic data processing. http://gest.jlu.edu.cn/info/1183/4673.htm</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Conferences&diff=3873Conferences2020-08-13T15:57:01Z<p>Yangliu: /* Schools, Workshops, and Working Workshops */</p>
<hr />
<div>[[Image:Conferences.png|right|]]<br />
In reverse chronological order.<br />
<br />
==Schools, Workshops, and Working Workshops==<br />
[[Hefei_2020|Madagascar School on Open-Source Geophysics in Hefei 2010]]<br />
<br />
[[HoustonWW2018|SEG Working Workshop - Python and Julia for Geophysics, Houston August 8-11, 2018]]<br />
<br />
[[HoustonWW2017|SEG Working Workshop in Houston 2017]]<br />
<br />
[[Shanghai_2017|Madagascar School of Reproducible Computational Geophysics Shanghai 2017]]<br />
<br />
[[Houston_2017|Madagascar School at the University of Houston 2017]]<br />
<br />
[[SEG_3D_Seismic_Processing_Working_Workshop_Houston_2016-_Land_3D|SEG Land 3D Seismic Processing Working Workshop Houston 2016]]<br />
<br />
[[Zurich 2016|Madagascar School on Reproducible Computational Geophysics in Zürich 2016]]<br />
<br />
[[Vienna_2016|Workshop - Open-source Software in Applied Geosciences Vienna 2016]]<br />
<br />
[[Qingdao_2015|Madagascar School for Advanced Users in Qingdao 2015]]<br />
<br />
[[SEG 3D Seismic Processing Working Workshop Houston 2015- Land 3D|SEG 3D Land Seismic Processing Working Workshop Houston 2015]]<br />
<br />
[[Harbin_2015|School in Harbin 2015]]<br />
<br />
[[Houston_2014|Second Madagascar Working Workshop Houston 2014]]<br />
<br />
[[Petersburg_2014|Workshop at EAGE/St. Petersburg 2014]]<br />
<br />
[[Melbourne_2013|Workshop at ASEG 2013]]<br />
<br />
[[Austin_2013|First Madagascar Working Workshop Austin 2013]]<br />
<br />
[[Austin_2012|Madagascar School and Workshop on Reproducible Computational Geophysics Austin 2012]]<br />
<br />
[[Copenhagen_2012|Workshop - Open-source E&P Software - Six Years Later Copenhagen 2012]]<br />
<br />
[[Beijing_2011|Madagascar School of Reproducible Computational Geophysics Beijing 2011]]<br />
<br />
[[Houston_2011|Workshop - Open Software Tools for Reproducible Computational Geophysics Houston 2011]]<br />
<br />
[[Houston_2010|Madagascar School of Reproducible Computational Geophysics and Hands-On School Houston 2010]]<br />
<br />
[[Salvador_2009|Madagascar School on Reproducible Computational Geophysics Salvador 2009]]<br />
<br />
[[Delft_2009|Madagascar School on Reproducible Computational Geophysics Delft 2009]]<br />
<br />
[[2008_Implementation_Workshop|Towards full automation and better robustness Coding Sprint Golden 2008]] <br />
<br />
[[RSF_Austin_School_2007|Using and Extending RSF/Madagascar School Austin 2007]].<br />
<br />
[[RSF_School_and_Workshop%2C_Vancouver_2006|Reproducible Research in Computational Geophysics School and Workshop Vancouver 2006]].<br />
<br />
==Conference presentations==<br />
<br />
===Lausanne 2016 (PASC)===<br />
<br />
Two presentations about <tt>Madagascar</tt> were presented in the minisymposium on '''Open Source Software (OSS) and High Performance Computing (HPC)''' at the [http://www.pasc16.org/ Platform for Advanced Scientific Computing] conference in Lausanne, Switzerland, on June 9, 2016. See presentation slides: <br />
* [http://reproducibility.org/wikilocal/docs/FOMEL-PASC2016.pdf Data-Parallel Processing Using Madagascar Open-Source Software Package] <br />
* [http://reproducibility.org/wikilocal/docs/POTTER-SHRAGGE-PASC2016.pdf Leveraging the Madagascar Framework for Reproducible Large-scale Cluster and Cloud Computing]<br />
<br />
===San Francisco 2015 (AGU)===<br />
<br />
<tt>Madagascar</tt> was presented in the session on '''Informatics and Intelligent Systems in Reproducible Geoscience Research''' at the [http://fallmeeting.agu.org/2015/ AGU Fall Meeting] in San Francisco, California, on December 17, 2015. See presentation [http://reproducibility.org/wikilocal/docs/Madagascar-AGU-2015.pdf slides] and the [https://agu.confex.com/agu/fm15/meetingapp.cgi/Session/10540 session program].<br />
<br />
===Stanford 2015 (SIAM Geosciences)===<br />
<br />
<tt>Madagascar</tt> was presented in the minisymposium on '''Advances in Software for Computational Geosciences''' at the [http://www.siam.org/meetings/gs15/ SIAM Conference on Mathematical & Computational Issues in the Geosciences] in Stanford, California, on June 30, 2015. See presentation [http://reproducibility.org/wikilocal/docs/Fomel-SIAM-Geosciences-2015.pdf slides] and the [http://meetings.siam.org/sess/dsp_programsess.cfm?SESSIONCODE=21097 minisymposium program].<br />
<br />
===New York 2013 (NYU Poly)===<br />
<br />
<tt>Madagascar</tt> was presented at the Workshop on [http://www.reproduciblescience.org/index.php/Workshop_on_Software_Infrastructure_for_Reproducibility_in_Science_--_May_30th-31st,_2013 Software Infrastructure for Reproducibility in Science] at the Polytechnic Institute of New York University in Brooklyn, New York, on May 30, 2013. See presentation [http://reproducibility.org/wikilocal/docs/Madagascar-NYC.pdf slides]. <br />
<br />
The workshop was supported by the [http://www.sloan.org/ Alfred P. Sloan Foundation]. Juliana Freire provides the complete [http://vgc.poly.edu/~juliana/ReproducibleScience/SoftwareInfrastructure/agenda.pdf workshop program].<br />
<br />
===Providence 2012 (ICERM)===<br />
<br />
<tt>Madagascar</tt> was presented at the [http://icerm.brown.edu/tw12-5-rcem Reproducibility in Computational and Experimental Mathematics] Workshop at the Institute for Computational and Experimental Research in Mathematics (ICERM) in Providence, Rhode Island, on December 13, 2012.<br />
<br />
See presentation [http://reproducibility.org/wikilocal/docs/ICERM.pptx slides], the complete [http://icerm.brown.edu/tw12-5-rcem workshop program], and Victoria Stodden's [http://wiki.stodden.net/ICERM_Reproducibility_in_Computational_and_Experimental_Mathematics:_Readings_and_References wiki page].<br />
<br />
===Austin 2012 (SciPy)===<br />
<br />
The Python interface to <tt>Madagascar</tt> was presented at the [http://conference.scipy.org/scipy2012/ Scientific Computing with Python Conference] in Austin, Texas, on July 19, 2012. See the poster by clicking on the image below<br />
.<br><br />
<br />
[[Image:SciPy2012Poster.png|link=http://www.ahay.org/wikilocal/docs/SciPy2012Poster.pdf]]<br />
<br />
===Cary 2011 (Interface)===<br />
<tt>Madagascar</tt> was presented in the special session on '''Reproducible Research''' at the [http://www.interfacesymposia.org/Interface2011/ 42nd Symposium on the Interface] (Statistical, Machine Learning, and Visualization Algorithms) in Cary, North Carolina, on June 1, 2011. See the [http://www.interfacesymposia.org/Interface2011/Program.pdf symposium program].<br />
<br />
===Long Beach 2011 (SIAM Geosciences)===<br />
<br />
<tt>Madagascar</tt> was presented in the minisymposium on '''Reproducible Science and Open-Source Software in the Geosciences''' at the [http://www.siam.org/meetings/gs11/ SIAM Conference on Mathematical & Computational Issues in the Geosciences] in Long Beach, California, on March 23, 2011. See presentation [http://reproducibility.org/wikilocal/docs/longbeach2011.pdf slides] and the minisymposium program: [http://meetings.siam.org/sess/dsp_programsess.cfm?SESSIONCODE=11822 Part 1] and [http://meetings.siam.org/sess/dsp_programsess.cfm?SESSIONCODE=11823 Part 2].<br />
<br />
===Reno 2011 (SIAM CS&E)===<br />
<br />
<tt>Madagascar</tt> was presented in the minisymposium on '''Verifiable, Reproducible Research and Computational Science''' at the [http://www.siam.org/meetings/cse11/ SIAM Conference on Computational Science and Engineering] in Reno, Nevada, on March 4, 2011. See presentation [http://reproducibility.org/wikilocal/docs/reno2011.pdf slides]. <br />
<br />
Jarrod Millman provides a complete [http://jarrodmillman.com/events/siam2011.html session program].<br />
<br />
===Austin 2010 (SciPy)===<br />
<br />
<tt>Madagascar</tt> was presented at the [http://conference.scipy.org/scipy2010/ Python in Scientific Computing Conference] in Austin, Texas, on July 1, 2010. See presentation [http://reproducibility.org/wikilocal/docs/scipy2010.pdf slides] and [http://conference.scipy.org/scipy2010/schedule.html complete program].<br />
<br />
===Salt Lake City 2010 (NSF Archive Workshop)===<br />
<br />
<tt>Madagascar</tt> was presented at the [http://users.emulab.net/trac/archive10/ NSF Workshop on Archiving Experiments to Raise Scientific Standards] in Salt Lake City on May 25, 2010. See presentation [http://reproducibility.org/wikilocal/docs/slc.pdf slides] and [http://users.emulab.net/trac/archive10/wiki/WorkshopSchedule complete program].<br />
<br />
===Düsseldorf 2008 (Berlin 6) ===<br />
<br />
<tt>Madagascar</tt> was mentioned in the special session on '''Open Data and Reproducible Research''' at the [http://www.berlin6.org/ Berlin 6 Open Access Conference] in Düsseldorf, Germany, on November 12, 2008. See presentation [http://reproducibility.org/wikilocal/docs/Berlin-6.ppt slides]. <br />
<br />
Mark Liberman provides a complete [http://ldc.upenn.edu/myl/Berlin6Session5/Overview.html session program].<br />
<br />
===Austin 2008 (Texas Python Unconference)===<br />
<br />
''New Directions in Literate Programming with Madagascar'' was presented at the Second Annual Texas Python Unconference hosted by Enthought Corporation on the UT campus on October 4, 2008. See presentation [http://www.ig.utexas.edu/people/staff/tobis/MadLiter/madliter.html slides].<br />
<br />
===Austin 2008 (Scientific Software Days)===<br />
<br />
<tt>Madagascar</tt> was presented at the Second Annual Scientific Software Days at the University of Texas at Austin on May 15, 2008. See presentation [http://reproducibility.org/wikilocal/docs/ssd2.pdf slides] and [http://www.tacc.utexas.edu/softwareday/ complete program].<br />
<br />
===Rio de Janeiro 2007 (SBGf)===<br />
<br />
<tt>Madagascar</tt> and reproducible scientific computing were presented at the 2007 [http://www.sbgf.org.br Congress of the Brazilian Geophysical Society] in Rio de Janeiro. See presentation [http://reproducibility.org/wikilocal/docs/2007_SBGf_ReproducibleScientificComputingUsingMadagascar.pdf slides].<br />
<br />
===Vancouver 2007 (AIP)===<br />
<br />
<tt>Madagascar</tt> was presented at a minisymposium on '''Software for Inverse Problems''' at the [http://www.pims.math.ca/science/2007/07aip/ Conference on Applied Inverse Problems] in Vancouver on June 29, 2007. See presentation [http://reproducibility.org/wikilocal/docs/Fomel-AIP.ppt slides].<br />
<br />
===Honolulu 2007 (ICASSP)===<br />
<br />
The paper [http://reproducibility.org/wikilocal/docs/scons.pdf Reproducible computational experiments using SCons] was presented in the [http://www.icassp2007.org/Papers/PublicSessionIndex3.asp?Sessionid=1168 special session] on '''Reproducible Signal Processing Research''' at the [http://www.icassp2007.org/ International Conference on Acoustics, Speech, and Signal Processing] in Honolulu on April 18, 2007 . See presentation [http://reproducibility.org/wikilocal/docs/SCons.ppt slides].<br />
<br />
Patrick Vandewalle provides a complete [http://lcavwww.epfl.ch/reproducible_research/ICASSP07/ session program].<br />
<br />
===Austin 2007 (Scientific Software Day)===<br />
<br />
<tt>Madagascar</tt> was presented at the First Annual Scientific Software Day at the University of Texas at Austin on April 2, 2007. See presentation [http://reproducibility.org/wikilocal/docs/Madagascar-SSD.ppt slides].<br />
<br />
===New Orleans 2006 (SEG)===<br />
<br />
These advertising posters were prepared for the SEG Annual Meeting in New Orleans. The idea by Gilles Hennenfent, implementation by Scott Rodgers.<br />
<br />
[[Image:Poker_comp_BEG.png]] [[Image:Poker_comp_CSM.png]] [[Image:Poker_comp_UBC.png]]<br />
<br />
===Vienna 2006 (EAGE)===<br />
<br />
RSF/Madagascar was first presented at the EAGE Workshop [http://www.eage.org/events/index.php?evp=274&eventid=1&ActiveMenu=16&Opendivs=s2,s11,s13 Open Source E&P Software – Putting the Pieces Together] in Vienna on June 11, 2006. See presentation [http://reproducibility.org/wikilocal/docs/vienna.pdf slides].<br />
<br />
Joe Dellinger provides a complete [http://sepwww.stanford.edu/oldsep/joe/Vienna/ workshop program with abstracts].</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Conferences&diff=3872Conferences2020-08-13T15:56:27Z<p>Yangliu: /* Schools, Workshops, and Working Workshops */</p>
<hr />
<div>[[Image:Conferences.png|right|]]<br />
In reverse chronological order.<br />
<br />
==Schools, Workshops, and Working Workshops==<br />
[[Hefei_2020|Madagascar School on Open-Source Geophysics Hefei 2010]]<br />
<br />
[[HoustonWW2018|SEG Working Workshop - Python and Julia for Geophysics, Houston August 8-11, 2018]]<br />
<br />
[[HoustonWW2017|SEG Working Workshop in Houston 2017]]<br />
<br />
[[Shanghai_2017|Madagascar School of Reproducible Computational Geophysics Shanghai 2017]]<br />
<br />
[[Houston_2017|Madagascar School at the University of Houston 2017]]<br />
<br />
[[SEG_3D_Seismic_Processing_Working_Workshop_Houston_2016-_Land_3D|SEG Land 3D Seismic Processing Working Workshop Houston 2016]]<br />
<br />
[[Zurich 2016|Madagascar School on Reproducible Computational Geophysics in Zürich 2016]]<br />
<br />
[[Vienna_2016|Workshop - Open-source Software in Applied Geosciences Vienna 2016]]<br />
<br />
[[Qingdao_2015|Madagascar School for Advanced Users in Qingdao 2015]]<br />
<br />
[[SEG 3D Seismic Processing Working Workshop Houston 2015- Land 3D|SEG 3D Land Seismic Processing Working Workshop Houston 2015]]<br />
<br />
[[Harbin_2015|School in Harbin 2015]]<br />
<br />
[[Houston_2014|Second Madagascar Working Workshop Houston 2014]]<br />
<br />
[[Petersburg_2014|Workshop at EAGE/St. Petersburg 2014]]<br />
<br />
[[Melbourne_2013|Workshop at ASEG 2013]]<br />
<br />
[[Austin_2013|First Madagascar Working Workshop Austin 2013]]<br />
<br />
[[Austin_2012|Madagascar School and Workshop on Reproducible Computational Geophysics Austin 2012]]<br />
<br />
[[Copenhagen_2012|Workshop - Open-source E&P Software - Six Years Later Copenhagen 2012]]<br />
<br />
[[Beijing_2011|Madagascar School of Reproducible Computational Geophysics Beijing 2011]]<br />
<br />
[[Houston_2011|Workshop - Open Software Tools for Reproducible Computational Geophysics Houston 2011]]<br />
<br />
[[Houston_2010|Madagascar School of Reproducible Computational Geophysics and Hands-On School Houston 2010]]<br />
<br />
[[Salvador_2009|Madagascar School on Reproducible Computational Geophysics Salvador 2009]]<br />
<br />
[[Delft_2009|Madagascar School on Reproducible Computational Geophysics Delft 2009]]<br />
<br />
[[2008_Implementation_Workshop|Towards full automation and better robustness Coding Sprint Golden 2008]] <br />
<br />
[[RSF_Austin_School_2007|Using and Extending RSF/Madagascar School Austin 2007]].<br />
<br />
[[RSF_School_and_Workshop%2C_Vancouver_2006|Reproducible Research in Computational Geophysics School and Workshop Vancouver 2006]].<br />
<br />
==Conference presentations==<br />
<br />
===Lausanne 2016 (PASC)===<br />
<br />
Two presentations about <tt>Madagascar</tt> were presented in the minisymposium on '''Open Source Software (OSS) and High Performance Computing (HPC)''' at the [http://www.pasc16.org/ Platform for Advanced Scientific Computing] conference in Lausanne, Switzerland, on June 9, 2016. See presentation slides: <br />
* [http://reproducibility.org/wikilocal/docs/FOMEL-PASC2016.pdf Data-Parallel Processing Using Madagascar Open-Source Software Package] <br />
* [http://reproducibility.org/wikilocal/docs/POTTER-SHRAGGE-PASC2016.pdf Leveraging the Madagascar Framework for Reproducible Large-scale Cluster and Cloud Computing]<br />
<br />
===San Francisco 2015 (AGU)===<br />
<br />
<tt>Madagascar</tt> was presented in the session on '''Informatics and Intelligent Systems in Reproducible Geoscience Research''' at the [http://fallmeeting.agu.org/2015/ AGU Fall Meeting] in San Francisco, California, on December 17, 2015. See presentation [http://reproducibility.org/wikilocal/docs/Madagascar-AGU-2015.pdf slides] and the [https://agu.confex.com/agu/fm15/meetingapp.cgi/Session/10540 session program].<br />
<br />
===Stanford 2015 (SIAM Geosciences)===<br />
<br />
<tt>Madagascar</tt> was presented in the minisymposium on '''Advances in Software for Computational Geosciences''' at the [http://www.siam.org/meetings/gs15/ SIAM Conference on Mathematical & Computational Issues in the Geosciences] in Stanford, California, on June 30, 2015. See presentation [http://reproducibility.org/wikilocal/docs/Fomel-SIAM-Geosciences-2015.pdf slides] and the [http://meetings.siam.org/sess/dsp_programsess.cfm?SESSIONCODE=21097 minisymposium program].<br />
<br />
===New York 2013 (NYU Poly)===<br />
<br />
<tt>Madagascar</tt> was presented at the Workshop on [http://www.reproduciblescience.org/index.php/Workshop_on_Software_Infrastructure_for_Reproducibility_in_Science_--_May_30th-31st,_2013 Software Infrastructure for Reproducibility in Science] at the Polytechnic Institute of New York University in Brooklyn, New York, on May 30, 2013. See presentation [http://reproducibility.org/wikilocal/docs/Madagascar-NYC.pdf slides]. <br />
<br />
The workshop was supported by the [http://www.sloan.org/ Alfred P. Sloan Foundation]. Juliana Freire provides the complete [http://vgc.poly.edu/~juliana/ReproducibleScience/SoftwareInfrastructure/agenda.pdf workshop program].<br />
<br />
===Providence 2012 (ICERM)===<br />
<br />
<tt>Madagascar</tt> was presented at the [http://icerm.brown.edu/tw12-5-rcem Reproducibility in Computational and Experimental Mathematics] Workshop at the Institute for Computational and Experimental Research in Mathematics (ICERM) in Providence, Rhode Island, on December 13, 2012.<br />
<br />
See presentation [http://reproducibility.org/wikilocal/docs/ICERM.pptx slides], the complete [http://icerm.brown.edu/tw12-5-rcem workshop program], and Victoria Stodden's [http://wiki.stodden.net/ICERM_Reproducibility_in_Computational_and_Experimental_Mathematics:_Readings_and_References wiki page].<br />
<br />
===Austin 2012 (SciPy)===<br />
<br />
The Python interface to <tt>Madagascar</tt> was presented at the [http://conference.scipy.org/scipy2012/ Scientific Computing with Python Conference] in Austin, Texas, on July 19, 2012. See the poster by clicking on the image below<br />
.<br><br />
<br />
[[Image:SciPy2012Poster.png|link=http://www.ahay.org/wikilocal/docs/SciPy2012Poster.pdf]]<br />
<br />
===Cary 2011 (Interface)===<br />
<tt>Madagascar</tt> was presented in the special session on '''Reproducible Research''' at the [http://www.interfacesymposia.org/Interface2011/ 42nd Symposium on the Interface] (Statistical, Machine Learning, and Visualization Algorithms) in Cary, North Carolina, on June 1, 2011. See the [http://www.interfacesymposia.org/Interface2011/Program.pdf symposium program].<br />
<br />
===Long Beach 2011 (SIAM Geosciences)===<br />
<br />
<tt>Madagascar</tt> was presented in the minisymposium on '''Reproducible Science and Open-Source Software in the Geosciences''' at the [http://www.siam.org/meetings/gs11/ SIAM Conference on Mathematical & Computational Issues in the Geosciences] in Long Beach, California, on March 23, 2011. See presentation [http://reproducibility.org/wikilocal/docs/longbeach2011.pdf slides] and the minisymposium program: [http://meetings.siam.org/sess/dsp_programsess.cfm?SESSIONCODE=11822 Part 1] and [http://meetings.siam.org/sess/dsp_programsess.cfm?SESSIONCODE=11823 Part 2].<br />
<br />
===Reno 2011 (SIAM CS&E)===<br />
<br />
<tt>Madagascar</tt> was presented in the minisymposium on '''Verifiable, Reproducible Research and Computational Science''' at the [http://www.siam.org/meetings/cse11/ SIAM Conference on Computational Science and Engineering] in Reno, Nevada, on March 4, 2011. See presentation [http://reproducibility.org/wikilocal/docs/reno2011.pdf slides]. <br />
<br />
Jarrod Millman provides a complete [http://jarrodmillman.com/events/siam2011.html session program].<br />
<br />
===Austin 2010 (SciPy)===<br />
<br />
<tt>Madagascar</tt> was presented at the [http://conference.scipy.org/scipy2010/ Python in Scientific Computing Conference] in Austin, Texas, on July 1, 2010. See presentation [http://reproducibility.org/wikilocal/docs/scipy2010.pdf slides] and [http://conference.scipy.org/scipy2010/schedule.html complete program].<br />
<br />
===Salt Lake City 2010 (NSF Archive Workshop)===<br />
<br />
<tt>Madagascar</tt> was presented at the [http://users.emulab.net/trac/archive10/ NSF Workshop on Archiving Experiments to Raise Scientific Standards] in Salt Lake City on May 25, 2010. See presentation [http://reproducibility.org/wikilocal/docs/slc.pdf slides] and [http://users.emulab.net/trac/archive10/wiki/WorkshopSchedule complete program].<br />
<br />
===Düsseldorf 2008 (Berlin 6) ===<br />
<br />
<tt>Madagascar</tt> was mentioned in the special session on '''Open Data and Reproducible Research''' at the [http://www.berlin6.org/ Berlin 6 Open Access Conference] in Düsseldorf, Germany, on November 12, 2008. See presentation [http://reproducibility.org/wikilocal/docs/Berlin-6.ppt slides]. <br />
<br />
Mark Liberman provides a complete [http://ldc.upenn.edu/myl/Berlin6Session5/Overview.html session program].<br />
<br />
===Austin 2008 (Texas Python Unconference)===<br />
<br />
''New Directions in Literate Programming with Madagascar'' was presented at the Second Annual Texas Python Unconference hosted by Enthought Corporation on the UT campus on October 4, 2008. See presentation [http://www.ig.utexas.edu/people/staff/tobis/MadLiter/madliter.html slides].<br />
<br />
===Austin 2008 (Scientific Software Days)===<br />
<br />
<tt>Madagascar</tt> was presented at the Second Annual Scientific Software Days at the University of Texas at Austin on May 15, 2008. See presentation [http://reproducibility.org/wikilocal/docs/ssd2.pdf slides] and [http://www.tacc.utexas.edu/softwareday/ complete program].<br />
<br />
===Rio de Janeiro 2007 (SBGf)===<br />
<br />
<tt>Madagascar</tt> and reproducible scientific computing were presented at the 2007 [http://www.sbgf.org.br Congress of the Brazilian Geophysical Society] in Rio de Janeiro. See presentation [http://reproducibility.org/wikilocal/docs/2007_SBGf_ReproducibleScientificComputingUsingMadagascar.pdf slides].<br />
<br />
===Vancouver 2007 (AIP)===<br />
<br />
<tt>Madagascar</tt> was presented at a minisymposium on '''Software for Inverse Problems''' at the [http://www.pims.math.ca/science/2007/07aip/ Conference on Applied Inverse Problems] in Vancouver on June 29, 2007. See presentation [http://reproducibility.org/wikilocal/docs/Fomel-AIP.ppt slides].<br />
<br />
===Honolulu 2007 (ICASSP)===<br />
<br />
The paper [http://reproducibility.org/wikilocal/docs/scons.pdf Reproducible computational experiments using SCons] was presented in the [http://www.icassp2007.org/Papers/PublicSessionIndex3.asp?Sessionid=1168 special session] on '''Reproducible Signal Processing Research''' at the [http://www.icassp2007.org/ International Conference on Acoustics, Speech, and Signal Processing] in Honolulu on April 18, 2007 . See presentation [http://reproducibility.org/wikilocal/docs/SCons.ppt slides].<br />
<br />
Patrick Vandewalle provides a complete [http://lcavwww.epfl.ch/reproducible_research/ICASSP07/ session program].<br />
<br />
===Austin 2007 (Scientific Software Day)===<br />
<br />
<tt>Madagascar</tt> was presented at the First Annual Scientific Software Day at the University of Texas at Austin on April 2, 2007. See presentation [http://reproducibility.org/wikilocal/docs/Madagascar-SSD.ppt slides].<br />
<br />
===New Orleans 2006 (SEG)===<br />
<br />
These advertising posters were prepared for the SEG Annual Meeting in New Orleans. The idea by Gilles Hennenfent, implementation by Scott Rodgers.<br />
<br />
[[Image:Poker_comp_BEG.png]] [[Image:Poker_comp_CSM.png]] [[Image:Poker_comp_UBC.png]]<br />
<br />
===Vienna 2006 (EAGE)===<br />
<br />
RSF/Madagascar was first presented at the EAGE Workshop [http://www.eage.org/events/index.php?evp=274&eventid=1&ActiveMenu=16&Opendivs=s2,s11,s13 Open Source E&P Software – Putting the Pieces Together] in Vienna on June 11, 2006. See presentation [http://reproducibility.org/wikilocal/docs/vienna.pdf slides].<br />
<br />
Joe Dellinger provides a complete [http://sepwww.stanford.edu/oldsep/joe/Vienna/ workshop program with abstracts].</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Shanghai_2017&diff=3871Shanghai 20172020-08-13T15:38:35Z<p>Yangliu: </p>
<hr />
<div>[[Image:Shanghai2017.jpg|center|frame|800px]]<br />
<br />
<center><big>'''2017 Madagascar School in Shanghai'''</big></center><br />
<br />
&nbsp;<br />
<br />
== Introduction ==<br />
<br />
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. Madagascar school has been organized many times around the word. It provides a platform for Madagascar users to learn and communicate with the developers. This Madagascar school will introduce the advanced usages for the users with fundamental knowledge of Madagascar. Besides the lecture section, this school will also features a discussion section, in which the participants are welcome to share the research experiences using Madagascar. This Madagascar school is convened by Prof. Sergey Fomel from the University of Texas at Austin and hosted by Prof. Jiubing Cheng from Tongji University.<br />
<br />
== Dates ==<br />
<br />
July 10-11, 2017<br />
<br />
== Agenda ==<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Before the school: Sunday, July 9, 2017<br />
|-<br />
| 14:00-18:00<br />
! colspan="2" | Bring your laptop and get individual help with Madagascar<br />
|-<br />
|<br />
! colspan="2" | Peng Zou, Chenlong Wang, Gang Fang<br />
|-<br />
|}<br />
<br />
&nbsp;<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 1: Monday, July 10, 2017<br />
|-<br />
| 8:30-8:40 <br />
! colspan="2" | Welcome (Jiubing Cheng)<br />
|-<br />
| 8:40-9:30<br />
! colspan="2" | Madagascar principles (Sergey Fomel)<br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.ahay.org/wikilocal/docs/Madagascar-Shanghai.pdf Slides] (29M)<br />
|-<br />
| 9:30-9:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 9:40-10:30<br />
! colspan="2" | Madagascar development: writing programs in C, C++, Fortran-90, and Python (Gang Fang)<br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.ahay.org/wikilocal/docs/Madagascar2017_GangFang.pdf Slides] (4.9M)<br><br><br />
[https://github.com/ahay/src/tree/master/book/rsf/school2017/c C example]<br><br />
[https://github.com/ahay/src/tree/master/book/rsf/school2017/c++ C++ example]<br><br />
[https://github.com/ahay/src/tree/master/book/rsf/school2017/f90 Fortran-90 example]<br><br />
[https://github.com/ahay/src/tree/master/book/rsf/school2017/python Python example]<br />
|-<br />
| 10:30-11:30<br />
! colspan="2" | Plotting Guidance and SConstruct Flow (Xufei Gong)<br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.ahay.org/wikilocal/docs/xufeigong.pdf Slides] (1.5M)<br><br />
[https://github.com/ahay/src/tree/master/book/rsf/school2017/modeling Modeling example]<br />
|-<br />
| 11:30-14:00<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 14:00-15:30<br />
! colspan="2" | Parallel programming (MPI, OpenMP, Pscons) in Madagascar (Chenlong Wang)<br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.ahay.org/wikilocal/docs/chenlongw.pdf Slides] (484K)<br />
|-<br />
| 15:30-15:50<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 15:50-17:00<br />
! colspan="2" |Writing a reproducible paper using LaTeX and Madagascar (Jiubing Cheng)<br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.ahay.org/wikilocal/docs/WritingAPaper.pdf Slides] (3.7M)<br><br />
[https://github.com/ahay/src/tree/master/book/tutorial/authors/geophys Example]<br />
|}<br />
<br />
&nbsp;<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 2: Tuesday, July 11, 2017<br />
|-<br />
| 8:30-10:00 <br />
! colspan="2" | Geophysical data processing with Madagascar (Yang Liu)<br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.ahay.org/wikilocal/docs/Yangliu2017.pdf Slides] (8.1M)<br><br><br />
[http://ahay.org/RSF/book/rsf/school2017/seismic.html Seismic example]<br><br />
[http://ahay.org/RSF/book/rsf/school2017/gravity.html Gravity example]<br><br />
[http://ahay.org/RSF/book/rsf/school2017/csem.html CSEM example]<br />
<br />
|-<br />
| 10:00-10:30<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:30-11:30<br />
! colspan="2" |Additional topics (Sergey Fomel)<br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.ahay.org/wikilocal/docs/Additional-Shanghai.pdf Slides] (6.4M)<br><br />
[https://github.com/sfomel/ipython/blob/master/Shanghai.ipynb Example Jypyter notebook]<br />
|-<br />
| 11:30-14:00<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 14:00-17:00<br />
! colspan="2" | Sharing experience in Madagascar<br />
|-<br />
| <br />
! colspan="2" | Guoning Wu (China University of Petroleum - Beijing)<br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.ahay.org/wikilocal/docs/Wuguoning.pdf Slides] (14M)<br />
|-<br />
| <br />
! colspan="2" | Peng Zou (Tongji University)<br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.ahay.org/wikilocal/docs/Pengzou.pdf Slides] (1.6M)<br />
|-<br />
| <br />
! colspan="2" | Yufeng Wang (China University of Petroleum - Beijing)<br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.ahay.org/wikilocal/docs/cuQRTM.pdf Slides] (2.3M)<br />
|}<br />
<br />
== Location ==<br />
<br />
Room 205B, Rui’an Building, Tongji University, Shanghai, China<br />
<br />
同济大学,瑞安楼 205B室,上海市杨浦区四平路1239号<br />
<br />
== Registration ==<br />
<br />
The Madagascar School participation is free but requires an application. Please send your name and affiliation to [mailto:1533006@tongji.edu.cn 1533006@tongji.edu.cn]. '''The deadline is July 5, 2017.'''<br />
== Pre-workshop Assignment ==<br />
<br />
You must [[download]] and [[Installation|install]] the Madagascar package in the days before the school. If issues come up, there will an opportunity to get installation help on Sunday, July 9. Remember to bring your laptop (Linux, Mac) to the session!<br />
=== Additional Installation Requirements ===<br />
#Latex<br />
#MPICH2/OPENMPI<br />
<br />
=== QQ group ===<br />
<br />
Madagascar advanced school QQ group: 468749704<br />
<br />
== Organizations ==<br />
<br />
The "Madagascar School of Reproducible Computational Geophysics Shanghai 2017" is organized by<br />
* '''Jiubing Cheng''' from School of Ocean and Earth Science, Tongji University (Shanghai, China)<br />
* '''Sergey Fomel''' from Jackson School of Geosciences, The University of Texas at Austin (Austin, USA)<br />
* '''Yang Liu''' from College of Geo-exploration Science and Technology, Jilin University (Changchun, China)<br />
* '''Gang Fang''' from Qingdao Institute of Marine Geology, China Geological Survey (Qingdao, China)<br />
and hosted by '''Jiubing Cheng'''<br />
<br />
== Instructors ==<br />
<br />
* '''Jiubing Cheng''' is a Professor of School of Ocean and Earth Science, Tongji University. He received a Ph.D. in Geophysics from Tongji University in 2003. http://mgg.tongji.edu.cn/space/cjb/<br />
* '''Sergey Fomel'''is a Professor at the Jackson School of Geosciences, the University of Texas at Austin. He received a Ph.D. in Geophysics from Stanford University in 2001. Sergey started work on Madagascar (at that time named RSF for Regularly Sampled Format) in 2003. http://www.jsg.utexas.edu/researcher/sergey_fomel/<br />
* '''Yang Liu''' is a 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. http://gest.jlu.edu.cn/?mod=info&act=view&id=2296<br />
* '''Gang Fang''' is an assistant research fellow at Qingdao Institute of Marine Geology, China Geological Survey. He received a Ph.D in Geophysics from China University of Petroleum (East China) in 2014 and was a visiting Ph.D student at Bureau of Economic Geology, The University of Texas at Austin from 2012 to 2013 sponsored by China State Scholarship Fund. His research interests are seismic modeling and seismic imaging. https://www.linkedin.com/profile/view?id=92186291</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Working_Workshops&diff=3022Working Workshops2015-01-14T05:01:49Z<p>Yangliu: /* Future workshops */</p>
<hr />
<div>"Working workshops" as opposed to "talking workshops" are meetings where the participants work together (possibly divided into pairs or small teams) to develop new software code or to conduct computational experiments addressing a particular problem. Working workshops are a cross between scientific workshops and [http://en.wikipedia.org/wiki/Sprint_%28software_development%29 coding sprints] or [http://en.wikipedia.org/wiki/Hackathon hackathons] common among open-source software communities. <br />
<br />
== Previous workshops ==<br />
<br />
[[Austin_2013|First Madagascar Working Workshop]]<br />
<br />
=== Reproducibility ===<br />
<br />
During this workshop, published papers that are not currently reproducible would be made reproducible and included with Madagascar (with permission from the authors). This includes both recent papers and old historical papers.<br />
<br />
=== Migration Gallery ===<br />
<br />
Migration gallery is a matrix where rows are different benchmark datasets and columns are different seismic migration methods. The goal of the workshop is to fill missing entries in the matrix and to add new rows and columns to it.<br />
<br />
[[Houston_2014|Second Madagascar Working Workshop]]<br />
<br />
=== Parallel Computing ===<br />
<br />
The parallel computing workshop uses resources of a supercomputing center. The goal is to peform a number of large-scale parallel computations and to test and document different styles of simplifying parallel computing tasks in Madagascar.<br />
<br />
==Future workshops==<br />
<br />
Here are some suggestions for future working workshops for the Madagascar community.<br />
<br />
=== Documentation ===<br />
<br />
The goal of this workshop would be to improve the existing Madagascar documentation and to create new documents (books, papers, user manuals).<br />
<br />
=== Seismic Data Processing ===<br />
<br />
In the data processing workshop, a particular field seismic dataset is selected for processing by different people and possibly different processing packages. A clear metric is developed for comparing results at different stages of data processing. The goal is to learn about the best data processing practices, to improve the existing tools, and to build reproducible examples.<br />
<br />
=== Seismic Interpretation ===<br />
<br />
Seismic interpreters can access the Madagascar functionality through the [http://opendtect.org OpendTect] interface. However, they are lacking particular examples of data analysis tasks relevant to seismic interpretation. This workshop will bring together Madagascar/OpendTect developers and practicing interpreters to go through case studies and to build necessary tools.<br />
<br />
=== C++/Java/Python/Fortran/Matlab Interface ===<br />
<br />
The goal of this workshop would be to extend the [[Guide_to_madagascar_API|Madagascar interface]] to the corresponding language and to create examples of its usage.<br />
<br />
=== Non-seismic Geophysics ===<br />
<br />
Develop programs and examples for non-seismic geophysics: potential-field methods (gravity and magnetics), controlled-source electromagnetics (CSEM), ground-penetrating radar (GPR), etc.</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Harbin_2015&diff=3008Harbin 20152015-01-07T08:57:08Z<p>Yangliu: /* Agenda */</p>
<hr />
<div>[[File:Example.jpg]][[Image:Harbin.jpg|center|frame]]<br />
<br />
<center><big>'''Madagascar School in Harbin 2015'''</big></center><br />
<br />
&nbsp;<br />
<br />
== Dates ==<br />
<br />
January 7-8, 2015.<br />
<br />
== Agenda ==<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 1: Wednesday, January 7, 2015<br />
|-<br />
| 10:00-3:00<br />
! colspan="2" | Bring your laptop with Madagascar package (stable version 1.6) and get help with installing Madagascar<br />
|-<br />
|<br />
! colspan="2" | Sergey Fomel, Yang Liu, Jeffrey Shragge, Junzhe Sun, Pengliang Yang<br />
|-<br />
<br />
|}<br />
<br />
&nbsp;<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 2: Thursday, January 8, 2015<br />
|-<br />
| 9:00-9:10<br />
! colspan="2" | Welcome (Jianwei Ma)<br />
<br />
|-<br />
| 9:10-10:10<br />
! colspan="2" | Introduction (Sergey Fomel)<br />
|-<br />
| <br />
| colspan="2" | <br />
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.<br><br><br />
<br />
|-<br />
| 10:10-10:25<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:25-11:25<br />
! colspan="2" | Command-line, plotting, papers and beyond (Pengliang Yang)<br />
|-<br />
|<br />
| colspan="2" | <br />
Madagascar provides excellent plotting tools for displaying 2D and 3D seismic data volume. I will cover some fundamentals of Madagascar's command-line usage, plotting, and reproducing papers. I will share my experience of using Madagascar as a great resource to obtain public datasets, to take the free open course and to share research outcomes.<br />
<br><br />
|-<br />
| 11:25-12:25<br />
! colspan="2" | Developing workflows using SCons (Sergey Fomel)<br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.scons.org/ SCons] (from '''S'''oftware '''Cons'''truction) is a superior alternative to the classic '''make''' utility. SCons is implemented as a [http://www.python.org Python] script, its "configuration files" (<tt>SConstruct</tt> files) are also Python scripts. Madagascar uses SCons to compile software, to manage data processing flowing, and to assemble [[Reproducible Documents|reproducible documents]].<br><br><br />
|-<br />
| 12:25-1:25<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 1:25-2:25<br />
! colspan="2" | Wave-equation modeling and migration (Junzhe Sun)<br />
|-<br />
|<br />
| colspan="2" | <br />
In this module we will first briefly review wave equation modeling and imaging using the exploding reflector concept. Next, the numerical experiment includes implementing this technique in Madagascar and applying it on a simple geological model generated by Madagascar programs.<br />
|-<br />
| 2:25-3:25<br />
! colspan="2" | Developing your own programs in Madagascar (Jeffrey Shragge)<br />
|-<br />
|<br />
| colspan="2" | <br />
There are many programs already built into the Madagascar project, but if you use Madagascar long enough you will eventually run into a problem that you cannot solve using only provided codes. Fortunately, Madagascar has a variety of programming language APIs already built, that allow you to: design, code, and integrate your programs into the Madagascar framework. By the end of the session, you should have a good starting point for developing your own codes, and adding them to the growing library of open-source software available in Madagascar. <br />
<br><br><br />
[http://www.ahay.org/wikilocal/docs/RSF_SCHOOL.pdf Slides] (204K)<br />
<br><br />
[http://www.ahay.org/wikilocal/docs/PROGRAM.pdf Program example] (104K)<br />
|-<br />
| 3:25-3:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 3:40-4:40<br />
! colspan="2" | Seismic data processing example (Yang Liu)<br />
|-<br />
|<br />
| colspan="2" | <br />
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.<br><br><br />
|-<br />
| 4:40-5:10<br />
! colspan="2" | Contributing to Madagascar (Sergey Fomel)<br />
|-<br />
|<br />
| colspan="2" |<br />
As a user of Madagascar, you have the right to run the code for any purpose, to make modifications and additions, and to share your modifications with other people. Madagascar is an open community, which makes it easy to share your contributions and to collaborate with other users and developers around the world. <br><br><br />
|-<br />
| 5:10-5:40<br />
! colspan="2" | Awarding certificates and closing<br />
|-<br />
|}<br />
<br />
== Location ==<br />
<br />
Room no. 331 in the New Active Center, Harbin Institute of Technology (HIT), China<br />
<br />
哈尔滨工业大学,新活动中心331会议室,黑龙江省哈尔滨市南岗区西大直街92号<br />
<br />
== Registration ==<br />
The workshop participation is free but requires an application. <br />
<br />
To register, please send [mailto:rsfschool@gmail.com an email] with your name. <br />
<br />
The deadline is January 1, 2015.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
Please try to [[download]] and [[Installation|install]] the Madagascar package ([http://sourceforge.net/projects/rsf/files/latest/download?source=files stable version 1.6]) in the days before the workshop according to the instructions on the left margin of this webpage. If issues come up, there will an opportunity to install the package at the start of the workshop. Remember to bring your laptop (Linux, Mac, or Windows) to the session!<br />
<br />
== Instructors ==<br />
<br />
* '''Sergey Fomel''' is a Professor at the Jackson School of Geosciences, the University of Texas at Austin. He received a Ph.D. in Geophysics from Stanford University in 2001. Sergey started work on Madagascar (at that time named RSF for Regularly Sampled Format) in 2003. http://www.jsg.utexas.edu/researcher/sergey_fomel/<br />
* '''Yang Liu''' is a 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. http://gest.jlu.edu.cn/?mod=info&act=view&id=54<br />
* '''Jeffrey Shragge''' is an Associate 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). https://www.socrates.uwa.edu.au/Staff/StaffProfile.aspx?Person=JeffreyShragge<br />
* '''Junzhe Sun''' graduated from a joint education program between China University of Petroleum-East China and Missouri University of Science and Technology with a Bachelor's Degree in Geophysics in 2012. He worked with Prof. Stephen Gao on seismic anisotropy and mantle flow when he was at Missouri S&T. He is currently a Ph.D student working with Prof. Sergey Fomel. http://www.linkedin.com/pub/junzhe-sun/44/749/3b<br />
* '''Pengliang Yang''' received his bachelor's degree in 2009 from Nanjing University of Aeronautics and Astronautics and is currently pursuing a Ph.D. at Xi'an Jiaotong University. Previously, he worked on sparsity-based seismic data reconstruction using the theory of compressed sensing. His current research is mainly on reverse time migration and sparse inversion.</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Harbin_2015&diff=3007Harbin 20152015-01-07T08:36:56Z<p>Yangliu: /* Agenda */</p>
<hr />
<div>[[File:Example.jpg]][[Image:Harbin.jpg|center|frame]]<br />
<br />
<center><big>'''Madagascar School in Harbin 2015'''</big></center><br />
<br />
&nbsp;<br />
<br />
== Dates ==<br />
<br />
January 7-8, 2015.<br />
<br />
== Agenda ==<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 1: Wednesday, January 7, 2015<br />
|-<br />
| 10:00-3:00<br />
! colspan="2" | Bring your laptop with Madagascar package (stable version 1.6) and get help with installing Madagascar<br />
|-<br />
|<br />
! colspan="2" | Sergey Fomel, Yang Liu, Jeffrey Shragge, Junzhe Sun, Pengliang Yang<br />
|-<br />
<br />
|}<br />
<br />
&nbsp;<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 2: Thursday, January 8, 2015<br />
|-<br />
| 9:00-9:10<br />
! colspan="2" | Welcome (Jianwei Ma)<br />
<br />
|-<br />
| 9:10-10:10<br />
! colspan="2" | Introduction (Sergey Fomel)<br />
|-<br />
| <br />
| colspan="2" | <br />
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.<br><br><br />
<br />
|-<br />
| 10:10-10:25<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:25-11:25<br />
! colspan="2" | Command-line, plotting, papers and beyond (Pengliang Yang)<br />
|-<br />
|<br />
| colspan="2" | <br />
Madagascar provides excellent plotting tools for displaying 2D and 3D seismic data volume. I will cover some fundamentals of Madagascar's command-line usage, plotting, and reproducing papers. I will share my experience of using Madagascar as a great resource to obtain public datasets, to take the free open course and to share research outcomes.<br />
<br><br />
|-<br />
| 11:25-12:25<br />
! colspan="2" | Developing workflows using SCons (Sergey Fomel)<br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.scons.org/ SCons] (from '''S'''oftware '''Cons'''truction) is a superior alternative to the classic '''make''' utility. SCons is implemented as a [http://www.python.org Python] script, its "configuration files" (<tt>SConstruct</tt> files) are also Python scripts. Madagascar uses SCons to compile software, to manage data processing flowing, and to assemble [[Reproducible Documents|reproducible documents]].<br><br><br />
|-<br />
| 12:25-1:25<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 1:25-2:25<br />
! colspan="2" | Seismic data processing example (Yang Liu) <br />
|-<br />
|<br />
| colspan="2" | <br />
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.<br><br><br />
|-<br />
| 2:25-3:25<br />
! colspan="2" | Developing your own programs in Madagascar (Jeffrey Shragge)<br />
|-<br />
|<br />
| colspan="2" | <br />
There are many programs already built into the Madagascar project, but if you use Madagascar long enough you will eventually run into a problem that you cannot solve using only provided codes. Fortunately, Madagascar has a variety of programming language APIs already built, that allow you to: design, code, and integrate your programs into the Madagascar framework. By the end of the session, you should have a good starting point for developing your own codes, and adding them to the growing library of open-source software available in Madagascar. <br />
<br><br><br />
[http://www.ahay.org/wikilocal/docs/RSF_SCHOOL.pdf Slides] (204K)<br />
<br><br />
[http://www.ahay.org/wikilocal/docs/PROGRAM.pdf Program example] (104K)<br />
|-<br />
| 3:25-3:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 3:40-4:40<br />
! colspan="2" | Wave-equation modeling and migration (Junzhe Sun)<br />
|-<br />
|<br />
| colspan="2" | <br />
In this module we will first briefly review wave equation modeling and imaging using the exploding reflector concept. Next, the numerical experiment includes implementing this technique in Madagascar and applying it on a simple geological model generated by Madagascar programs.<br />
|-<br />
| 4:40-5:10<br />
! colspan="2" | Contributing to Madagascar (Sergey Fomel)<br />
|-<br />
|<br />
| colspan="2" |<br />
As a user of Madagascar, you have the right to run the code for any purpose, to make modifications and additions, and to share your modifications with other people. Madagascar is an open community, which makes it easy to share your contributions and to collaborate with other users and developers around the world. <br><br><br />
|-<br />
| 5:10-5:40<br />
! colspan="2" | Awarding certificates and closing<br />
|-<br />
|}<br />
<br />
== Location ==<br />
<br />
Room no. 331 in the New Active Center, Harbin Institute of Technology (HIT), China<br />
<br />
哈尔滨工业大学,新活动中心331会议室,黑龙江省哈尔滨市南岗区西大直街92号<br />
<br />
== Registration ==<br />
The workshop participation is free but requires an application. <br />
<br />
To register, please send [mailto:rsfschool@gmail.com an email] with your name. <br />
<br />
The deadline is January 1, 2015.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
Please try to [[download]] and [[Installation|install]] the Madagascar package ([http://sourceforge.net/projects/rsf/files/latest/download?source=files stable version 1.6]) in the days before the workshop according to the instructions on the left margin of this webpage. If issues come up, there will an opportunity to install the package at the start of the workshop. Remember to bring your laptop (Linux, Mac, or Windows) to the session!<br />
<br />
== Instructors ==<br />
<br />
* '''Sergey Fomel''' is a Professor at the Jackson School of Geosciences, the University of Texas at Austin. He received a Ph.D. in Geophysics from Stanford University in 2001. Sergey started work on Madagascar (at that time named RSF for Regularly Sampled Format) in 2003. http://www.jsg.utexas.edu/researcher/sergey_fomel/<br />
* '''Yang Liu''' is a 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. http://gest.jlu.edu.cn/?mod=info&act=view&id=54<br />
* '''Jeffrey Shragge''' is an Associate 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). https://www.socrates.uwa.edu.au/Staff/StaffProfile.aspx?Person=JeffreyShragge<br />
* '''Junzhe Sun''' graduated from a joint education program between China University of Petroleum-East China and Missouri University of Science and Technology with a Bachelor's Degree in Geophysics in 2012. He worked with Prof. Stephen Gao on seismic anisotropy and mantle flow when he was at Missouri S&T. He is currently a Ph.D student working with Prof. Sergey Fomel. http://www.linkedin.com/pub/junzhe-sun/44/749/3b<br />
* '''Pengliang Yang''' received his bachelor's degree in 2009 from Nanjing University of Aeronautics and Astronautics and is currently pursuing a Ph.D. at Xi'an Jiaotong University. Previously, he worked on sparsity-based seismic data reconstruction using the theory of compressed sensing. His current research is mainly on reverse time migration and sparse inversion.</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Harbin_2015&diff=3005Harbin 20152015-01-07T06:00:15Z<p>Yangliu: /* Agenda */</p>
<hr />
<div>[[File:Example.jpg]][[Image:Harbin.jpg|center|frame]]<br />
<br />
<center><big>'''Madagascar School in Harbin 2015'''</big></center><br />
<br />
&nbsp;<br />
<br />
== Dates ==<br />
<br />
January 7-8, 2015.<br />
<br />
== Agenda ==<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 1: Wednesday, January 7, 2015<br />
|-<br />
| 10:00-3:00<br />
! colspan="2" | Bring your laptop with Madagascar package (stable version 1.6) and get help with installing Madagascar<br />
|-<br />
|<br />
! colspan="2" | Sergey Fomel, Yang Liu, Jeffrey Shragge, Junzhe Sun, Pengliang Yang<br />
|-<br />
<br />
|}<br />
<br />
&nbsp;<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 2: Thursday, January 8, 2015<br />
|-<br />
| 9:00-9:10<br />
! colspan="2" | Welcome (Jianwei Ma)<br />
<br />
|-<br />
| 9:10-10:10<br />
! colspan="2" | Introduction (Sergey Fomel)<br />
|-<br />
| <br />
| colspan="2" | <br />
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.<br><br><br />
<br />
|-<br />
| 10:10-10:25<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:25-11:25<br />
! colspan="2" | Command-line, plotting, papers and beyond (Pengliang Yang)<br />
|-<br />
|<br />
| colspan="2" | <br />
Madagascar provides excellent plotting tools for displaying 2D and 3D seismic data volume. I will cover some fundamentals of Madagascar's command-line usage, plotting, and reproducing papers. I will share my experience of using Madagascar as a great resource to obtain public datasets, to take the free open course and to share research outcomes.<br />
<br><br />
|-<br />
| 11:25-12:25<br />
! colspan="2" | Developing workflows using SCons (Sergey Fomel)<br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.scons.org/ SCons] (from '''S'''oftware '''Cons'''truction) is a superior alternative to the classic '''make''' utility. SCons is implemented as a [http://www.python.org Python] script, its "configuration files" (<tt>SConstruct</tt> files) are also Python scripts. Madagascar uses SCons to compile software, to manage data processing flowing, and to assemble [[Reproducible Documents|reproducible documents]].<br><br><br />
|-<br />
| 12:25-1:25<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 1:25-2:25<br />
! colspan="2" | Seismic data processing example (Yang Liu) <br />
|-<br />
|<br />
| colspan="2" | <br />
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.<br><br><br />
|-<br />
| 2:25-3:25<br />
! colspan="2" | Developing your own programs in Madagascar (Jeffrey Shragge)<br />
|-<br />
|<br />
| colspan="2" | <br />
There are many programs already built into the Madagascar project, but if you use Madagascar long enough you will eventually run into a problem that you cannot solve using only provided codes. Fortunately, Madagascar has a variety of programming language APIs already built, that allow you to: design, code, and integrate your programs into the Madagascar framework. By the end of the session, you should have a good starting point for developing your own codes, and adding them to the growing library of open-source software available in Madagascar. <br />
<br><br><br />
|-<br />
| 3:25-3:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 3:40-4:40<br />
! colspan="2" | TBA (Junzhe Sun)<br />
|-<br />
|<br />
| colspan="2" | <br />
content<br />
|-<br />
| 4:40-5:10<br />
! colspan="2" | Contributing to Madagascar (Sergey Fomel)<br />
|-<br />
|<br />
| colspan="2" |<br />
As a user of Madagascar, you have the right to run the code for any purpose, to make modifications and additions, and to share your modifications with other people. Madagascar is an open community, which makes it easy to share your contributions and to collaborate with other users and developers around the world. <br><br><br />
|-<br />
| 5:10-5:40<br />
! colspan="2" | Awarding certificates and closing<br />
|-<br />
|}<br />
<br />
== Location ==<br />
<br />
Room no. 331 in the New Active Center, Harbin Institute of Technology (HIT), China<br />
<br />
哈尔滨工业大学,新活动中心331会议室,黑龙江省哈尔滨市南岗区西大直街92号<br />
<br />
== Registration ==<br />
The workshop participation is free but requires an application. <br />
<br />
To register, please send [mailto:rsfschool@gmail.com an email] with your name. <br />
<br />
The deadline is January 1, 2015.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
Please try to [[download]] and [[Installation|install]] the Madagascar package ([http://sourceforge.net/projects/rsf/files/latest/download?source=files stable version 1.6]) in the days before the workshop according to the instructions on the left margin of this webpage. If issues come up, there will an opportunity to install the package at the start of the workshop. Remember to bring your laptop (Linux, Mac, or Windows) to the session!<br />
<br />
== Instructors ==<br />
<br />
* '''Sergey Fomel''' is a Professor at the Jackson School of Geosciences, the University of Texas at Austin. He received a Ph.D. in Geophysics from Stanford University in 2001. Sergey started work on Madagascar (at that time named RSF for Regularly Sampled Format) in 2003. http://www.jsg.utexas.edu/researcher/sergey_fomel/<br />
* '''Yang Liu''' is a 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. http://gest.jlu.edu.cn/?mod=info&act=view&id=54<br />
* '''Jeffrey Shragge''' is an Associate 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). https://www.socrates.uwa.edu.au/Staff/StaffProfile.aspx?Person=JeffreyShragge<br />
* '''Junzhe Sun''' graduated from a joint education program between China University of Petroleum-East China and Missouri University of Science and Technology with a Bachelor's Degree in Geophysics in 2012. He worked with Prof. Stephen Gao on seismic anisotropy and mantle flow when he was at Missouri S&T. He is currently a Ph.D student working with Prof. Sergey Fomel. http://www.linkedin.com/pub/junzhe-sun/44/749/3b<br />
* '''Pengliang Yang''' received his bachelor's degree in 2009 from Nanjing University of Aeronautics and Astronautics and is currently pursuing a Ph.D. at Xi'an Jiaotong University. Previously, he worked on sparsity-based seismic data reconstruction using the theory of compressed sensing. His current research is mainly on reverse time migration and sparse inversion.</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Harbin_2015&diff=3004Harbin 20152015-01-07T05:34:57Z<p>Yangliu: /* Agenda */</p>
<hr />
<div>[[File:Example.jpg]][[Image:Harbin.jpg|center|frame]]<br />
<br />
<center><big>'''Madagascar School in Harbin 2015'''</big></center><br />
<br />
&nbsp;<br />
<br />
== Dates ==<br />
<br />
January 7-8, 2015.<br />
<br />
== Agenda ==<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 1: Wednesday, January 7, 2015<br />
|-<br />
| 10:00-3:00<br />
! colspan="2" | Bring your laptop with Madagascar package (stable version 1.6) and get help with installing Madagascar<br />
|-<br />
|<br />
! colspan="2" | Sergey Fomel, Yang Liu, Jeffrey Shragge, Junzhe Sun, Pengliang Yang<br />
|-<br />
<br />
|}<br />
<br />
&nbsp;<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 2: Thursday, January 8, 2015<br />
|-<br />
| 9:00-9:10<br />
! colspan="2" | Welcome (Jianwei Ma)<br />
<br />
|-<br />
| 9:10-10:10<br />
! colspan="2" | Introduction (Sergey Fomel)<br />
|-<br />
| <br />
| colspan="2" | <br />
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.<br><br><br />
<br />
|-<br />
| 10:10-10:25<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:25-11:25<br />
! colspan="2" | Command-line, plotting, papers and beyond (Pengliang Yang)<br />
|-<br />
|<br />
| colspan="2" | <br />
<br />
<br><br />
|-<br />
| 11:25-12:25<br />
! colspan="2" | Developing workflows using SCons (Sergey Fomel)<br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.scons.org/ SCons] (from '''S'''oftware '''Cons'''truction) is a superior alternative to the classic '''make''' utility. SCons is implemented as a [http://www.python.org Python] script, its "configuration files" (<tt>SConstruct</tt> files) are also Python scripts. Madagascar uses SCons to compile software, to manage data processing flowing, and to assemble [[Reproducible Documents|reproducible documents]].<br><br><br />
|-<br />
| 12:25-1:25<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 1:25-2:25<br />
! colspan="2" | Seismic data processing example (Yang Liu) <br />
|-<br />
|<br />
| colspan="2" | <br />
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.<br><br><br />
|-<br />
| 2:25-3:25<br />
! colspan="2" | Developing your own programs in Madagascar (Jeffrey Shragge)<br />
|-<br />
|<br />
| colspan="2" | <br />
There are many programs already built into the Madagascar project, but if you use Madagascar long enough you will eventually run into a problem that you cannot solve using only provided codes. Fortunately, Madagascar has a variety of programming language APIs already built, that allow you to: design, code, and integrate your programs into the Madagascar framework. By the end of the session, you should have a good starting point for developing your own codes, and adding them to the growing library of open-source software available in Madagascar. <br />
<br><br><br />
|-<br />
| 3:25-3:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 3:40-4:40<br />
! colspan="2" | TBA (Junzhe Sun)<br />
|-<br />
|<br />
| colspan="2" | <br />
content<br />
|-<br />
| 4:40-5:10<br />
! colspan="2" | Contributing to Madagascar (Sergey Fomel)<br />
|-<br />
|<br />
| colspan="2" |<br />
As a user of Madagascar, you have the right to run the code for any purpose, to make modifications and additions, and to share your modifications with other people. Madagascar is an open community, which makes it easy to share your contributions and to collaborate with other users and developers around the world. <br><br><br />
|-<br />
| 5:10-5:40<br />
! colspan="2" | Awarding certificates and closing<br />
|-<br />
|}<br />
<br />
== Location ==<br />
<br />
Room no. 331 in the New Active Center, Harbin Institute of Technology (HIT), China<br />
<br />
哈尔滨工业大学,新活动中心331会议室,黑龙江省哈尔滨市南岗区西大直街92号<br />
<br />
== Registration ==<br />
The workshop participation is free but requires an application. <br />
<br />
To register, please send [mailto:rsfschool@gmail.com an email] with your name. <br />
<br />
The deadline is January 1, 2015.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
Please try to [[download]] and [[Installation|install]] the Madagascar package ([http://sourceforge.net/projects/rsf/files/latest/download?source=files stable version 1.6]) in the days before the workshop according to the instructions on the left margin of this webpage. If issues come up, there will an opportunity to install the package at the start of the workshop. Remember to bring your laptop (Linux, Mac, or Windows) to the session!<br />
<br />
== Instructors ==<br />
<br />
* '''Sergey Fomel''' is a Professor at the Jackson School of Geosciences, the University of Texas at Austin. He received a Ph.D. in Geophysics from Stanford University in 2001. Sergey started work on Madagascar (at that time named RSF for Regularly Sampled Format) in 2003. http://www.jsg.utexas.edu/researcher/sergey_fomel/<br />
* '''Yang Liu''' is a 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. http://gest.jlu.edu.cn/?mod=info&act=view&id=54<br />
* '''Jeffrey Shragge''' is an Associate 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). https://www.socrates.uwa.edu.au/Staff/StaffProfile.aspx?Person=JeffreyShragge<br />
* '''Junzhe Sun''' graduated from a joint education program between China University of Petroleum-East China and Missouri University of Science and Technology with a Bachelor's Degree in Geophysics in 2012. He worked with Prof. Stephen Gao on seismic anisotropy and mantle flow when he was at Missouri S&T. He is currently a Ph.D student working with Prof. Sergey Fomel. http://www.linkedin.com/pub/junzhe-sun/44/749/3b<br />
* '''Pengliang Yang''' received his bachelor's degree in 2009 from Nanjing University of Aeronautics and Astronautics and is currently pursuing a Ph.D. at Xi'an Jiaotong University. Previously, he worked on sparsity-based seismic data reconstruction using the theory of compressed sensing. His current research is mainly on reverse time migration and sparse inversion.</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Harbin_2015&diff=2992Harbin 20152014-11-13T07:38:05Z<p>Yangliu: /* Agenda */</p>
<hr />
<div>[[Image:Harbin.jpg|center|frame]]<br />
<br />
<center><big>'''Madagascar School in Harbin 2015'''</big></center><br />
<br />
&nbsp;<br />
<br />
== Dates ==<br />
<br />
January 7-8, 2015.<br />
<br />
== Agenda ==<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 1: Wednesday, January 7, 2015<br />
|-<br />
| 10:00-3:00<br />
! colspan="2" | Bring your laptop with Madagascar package (stable version 1.6) and get help with installing Madagascar<br />
|-<br />
|<br />
! colspan="2" | Sergey Fomel, Yang Liu, Jeffrey Shragge, Junzhe Sun, Pengliang Yang<br />
|-<br />
<br />
|}<br />
<br />
&nbsp;<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 2: Thursday, January 8, 2015<br />
|-<br />
| 9:00-9:10<br />
! colspan="2" | Welcome (Jianwei Ma)<br />
<br />
|-<br />
| 9:10-10:10<br />
! colspan="2" | Introduction (Sergey Fomel)<br />
|-<br />
| <br />
| colspan="2" | <br />
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.<br><br><br />
<br />
|-<br />
| 10:10-10:25<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:25-11:25<br />
! colspan="2" | title (Pengliang Yang)<br />
|-<br />
|<br />
| colspan="2" | <br />
content<br />
<br><br />
|-<br />
| 11:25-12:25<br />
! colspan="2" | Developing workflows using SCons (Sergey Fomel)<br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.scons.org/ SCons] (from '''S'''oftware '''Cons'''truction) is a superior alternative to the classic '''make''' utility. SCons is implemented as a [http://www.python.org Python] script, its "configuration files" (<tt>SConstruct</tt> files) are also Python scripts. Madagascar uses SCons to compile software, to manage data processing flowing, and to assemble [[Reproducible Documents|reproducible documents]].<br><br><br />
|-<br />
| 12:25-1:25<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 1:25-2:25<br />
! colspan="2" | Seismic data processing example (Yang Liu) <br />
|-<br />
|<br />
| colspan="2" | <br />
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.<br><br><br />
|-<br />
| 2:25-3:25<br />
! colspan="2" | Developing your own programs in Madagascar (Jeffrey Shragge)<br />
|-<br />
|<br />
| colspan="2" | <br />
There are many programs already built into the Madagascar project, but if you use Madagascar long enough you will eventually run into a problem that you cannot solve using only provided codes. Fortunately, Madagascar has a variety of programming language APIs already built, that allow you to: design, code, and integrate your programs into the Madagascar framework. By the end of the session, you should have a good starting point for developing your own codes, and adding them to the growing library of open-source software available in Madagascar. <br><br><br />
|-<br />
| 3:25-3:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 3:40-4:40<br />
! colspan="2" | title (Junzhe Sun)<br />
|-<br />
|<br />
| colspan="2" | <br />
content<br />
|-<br />
| 4:40-5:10<br />
! colspan="2" | Contributing to Madagascar (Sergey Fomel)<br />
|-<br />
|<br />
| colspan="2" |<br />
As a user of Madagascar, you have the right to run the code for any purpose, to make modifications and additions, and to share your modifications with other people. Madagascar is an open community, which makes it easy to share your contributions and to collaborate with other users and developers around the world. <br><br><br />
|-<br />
| 5:10-5:40<br />
! colspan="2" | Awarding certificates and closing<br />
|-<br />
|}<br />
<br />
== Location ==<br />
<br />
The 503 Gewu Building, Department of Mathematics, Harbin Institute of Technology (HIT), China, or Xiyuan Hotel in the HIT campus<br />
<br />
哈尔滨工业大学数学系,格物楼503,黑龙江省哈尔滨市南岗区西大直街92号<br />
<br />
== Registration ==<br />
The workshop participation is free but requires an application. <br />
<br />
The application deadline was December 25, 2014.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
Please try to [[download]] and [[Installation|install]] the Madagascar package ([http://sourceforge.net/projects/rsf/files/latest/download?source=files stable version 1.6]) in the days before the workshop according to the instructions on the left margin of this webpage. If issues come up, there will an opportunity to install the package at the start of the workshop. Remember to bring your laptop (Linux, Mac, or Windows) to the session!<br />
<br />
== Instructors ==<br />
<br />
* '''Sergey Fomel''' is a Professor at the Jackson School of Geosciences, the University of Texas at Austin. He received a Ph.D. in Geophysics from Stanford University in 2001. Sergey started work on Madagascar (at that time named RSF for Regularly Sampled Format) in 2003. http://www.jsg.utexas.edu/researcher/sergey_fomel/<br />
* '''Yang Liu''' is a 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. http://gest.jlu.edu.cn/?mod=info&act=view&id=54<br />
* '''Jeffrey Shragge''' is an Associate 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). https://www.socrates.uwa.edu.au/Staff/StaffProfile.aspx?Person=JeffreyShragge<br />
* '''Junzhe Sun''' graduated from a joint education program between China University of Petroleum-East China and Missouri University of Science and Technology with a Bachelor's Degree in Geophysics in 2012. He worked with Prof. Stephen Gao on seismic anisotropy and mantle flow when he was at Missouri S&T. He is currently a Ph.D student working with Prof. Sergey Fomel. http://www.linkedin.com/pub/junzhe-sun/44/749/3b<br />
* '''Pengliang Yang''' received his bachelor's degree in 2009 from Nanjing University of Aeronautics and Astronautics and is currently pursuing a Ph.D. at Xi'an Jiaotong University. Previously, he worked on sparsity-based seismic data reconstruction using the theory of compressed sensing. His current research is mainly on reverse time migration and sparse inversion.</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Harbin_2015&diff=2991Harbin 20152014-11-13T07:18:16Z<p>Yangliu: /* Registration */</p>
<hr />
<div>[[Image:Harbin.jpg|center|frame]]<br />
<br />
<center><big>'''Madagascar School in Harbin 2015'''</big></center><br />
<br />
&nbsp;<br />
<br />
== Dates ==<br />
<br />
January 7-8, 2015.<br />
<br />
== Agenda ==<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 1: Wednesday, January 7, 2015<br />
|-<br />
| 10:00-3:00<br />
! colspan="2" | Bring your laptop with Madagascar package (stable version 1.6) and get help with installing Madagascar<br />
|-<br />
|<br />
! colspan="2" | Sergey Fomel, Jeffrey Shragge , Yang Liu<br />
|-<br />
<br />
|}<br />
<br />
&nbsp;<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 2: Thursday, January 8, 2015<br />
|-<br />
| 9:00-9:10<br />
! colspan="2" | Welcome (Jianwei Ma)<br />
<br />
|-<br />
| 9:10-10:10<br />
! colspan="2" | Introduction (Sergey Fomel)<br />
|-<br />
| <br />
| colspan="2" | <br />
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.<br><br><br />
<br />
|-<br />
| 10:10-10:25<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:25-11:25<br />
! colspan="2" | title (Pengliang Yang)<br />
|-<br />
|<br />
| colspan="2" | <br />
content<br />
<br><br />
|-<br />
| 11:25-12:25<br />
! colspan="2" | Developing workflows using SCons (Sergey Fomel)<br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.scons.org/ SCons] (from '''S'''oftware '''Cons'''truction) is a superior alternative to the classic '''make''' utility. SCons is implemented as a [http://www.python.org Python] script, its "configuration files" (<tt>SConstruct</tt> files) are also Python scripts. Madagascar uses SCons to compile software, to manage data processing flowing, and to assemble [[Reproducible Documents|reproducible documents]].<br><br><br />
|-<br />
| 12:25-1:25<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 1:25-2:25<br />
! colspan="2" | Seismic data processing example (Yang Liu) <br />
|-<br />
|<br />
| colspan="2" | <br />
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.<br><br><br />
|-<br />
| 2:25-3:25<br />
! colspan="2" | Developing your own programs in Madagascar (Jeffrey Shragge)<br />
|-<br />
|<br />
| colspan="2" | <br />
There are many programs already built into the Madagascar project, but if you use Madagascar long enough you will eventually run into a problem that you cannot solve using only provided codes. Fortunately, Madagascar has a variety of programming language APIs already built, that allow you to: design, code, and integrate your programs into the Madagascar framework. By the end of the session, you should have a good starting point for developing your own codes, and adding them to the growing library of open-source software available in Madagascar. <br><br><br />
|-<br />
| 3:25-3:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 3:40-4:40<br />
! colspan="2" | title (Junzhe Sun)<br />
|-<br />
|<br />
| colspan="2" | <br />
content<br />
|-<br />
| 4:40-5:10<br />
! colspan="2" | Contributing to Madagascar (Sergey Fomel)<br />
|-<br />
|<br />
| colspan="2" |<br />
As a user of Madagascar, you have the right to run the code for any purpose, to make modifications and additions, and to share your modifications with other people. Madagascar is an open community, which makes it easy to share your contributions and to collaborate with other users and developers around the world. <br><br><br />
|-<br />
| 5:10-5:40<br />
! colspan="2" | Awarding certificates and closing<br />
|-<br />
|}<br />
<br />
== Location ==<br />
<br />
The 503 Gewu Building, Department of Mathematics, Harbin Institute of Technology (HIT), China, or Xiyuan Hotel in the HIT campus<br />
<br />
哈尔滨工业大学数学系,格物楼503,黑龙江省哈尔滨市南岗区西大直街92号<br />
<br />
== Registration ==<br />
The workshop participation is free but requires an application. <br />
<br />
The application deadline was December 25, 2014.<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
Please try to [[download]] and [[Installation|install]] the Madagascar package ([http://sourceforge.net/projects/rsf/files/latest/download?source=files stable version 1.6]) in the days before the workshop according to the instructions on the left margin of this webpage. If issues come up, there will an opportunity to install the package at the start of the workshop. Remember to bring your laptop (Linux, Mac, or Windows) to the session!<br />
<br />
== Instructors ==<br />
<br />
* '''Sergey Fomel''' is a Professor at the Jackson School of Geosciences, the University of Texas at Austin. He received a Ph.D. in Geophysics from Stanford University in 2001. Sergey started work on Madagascar (at that time named RSF for Regularly Sampled Format) in 2003. http://www.jsg.utexas.edu/researcher/sergey_fomel/<br />
* '''Yang Liu''' is a 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. http://gest.jlu.edu.cn/?mod=info&act=view&id=54<br />
* '''Jeffrey Shragge''' is an Associate 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). https://www.socrates.uwa.edu.au/Staff/StaffProfile.aspx?Person=JeffreyShragge<br />
* '''Junzhe Sun''' graduated from a joint education program between China University of Petroleum-East China and Missouri University of Science and Technology with a Bachelor's Degree in Geophysics in 2012. He worked with Prof. Stephen Gao on seismic anisotropy and mantle flow when he was at Missouri S&T. He is currently a Ph.D student working with Prof. Sergey Fomel. http://www.linkedin.com/pub/junzhe-sun/44/749/3b<br />
* '''Pengliang Yang''' received his bachelor's degree in 2009 from Nanjing University of Aeronautics and Astronautics and is currently pursuing a Ph.D. at Xi'an Jiaotong University. Previously, he worked on sparsity-based seismic data reconstruction using the theory of compressed sensing. His current research is mainly on reverse time migration and sparse inversion.</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Harbin_2015&diff=2990Harbin 20152014-11-13T07:16:58Z<p>Yangliu: /* Location */</p>
<hr />
<div>[[Image:Harbin.jpg|center|frame]]<br />
<br />
<center><big>'''Madagascar School in Harbin 2015'''</big></center><br />
<br />
&nbsp;<br />
<br />
== Dates ==<br />
<br />
January 7-8, 2015.<br />
<br />
== Agenda ==<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 1: Wednesday, January 7, 2015<br />
|-<br />
| 10:00-3:00<br />
! colspan="2" | Bring your laptop with Madagascar package (stable version 1.6) and get help with installing Madagascar<br />
|-<br />
|<br />
! colspan="2" | Sergey Fomel, Jeffrey Shragge , Yang Liu<br />
|-<br />
<br />
|}<br />
<br />
&nbsp;<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 2: Thursday, January 8, 2015<br />
|-<br />
| 9:00-9:10<br />
! colspan="2" | Welcome (Jianwei Ma)<br />
<br />
|-<br />
| 9:10-10:10<br />
! colspan="2" | Introduction (Sergey Fomel)<br />
|-<br />
| <br />
| colspan="2" | <br />
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.<br><br><br />
<br />
|-<br />
| 10:10-10:25<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:25-11:25<br />
! colspan="2" | title (Pengliang Yang)<br />
|-<br />
|<br />
| colspan="2" | <br />
content<br />
<br><br />
|-<br />
| 11:25-12:25<br />
! colspan="2" | Developing workflows using SCons (Sergey Fomel)<br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.scons.org/ SCons] (from '''S'''oftware '''Cons'''truction) is a superior alternative to the classic '''make''' utility. SCons is implemented as a [http://www.python.org Python] script, its "configuration files" (<tt>SConstruct</tt> files) are also Python scripts. Madagascar uses SCons to compile software, to manage data processing flowing, and to assemble [[Reproducible Documents|reproducible documents]].<br><br><br />
|-<br />
| 12:25-1:25<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 1:25-2:25<br />
! colspan="2" | Seismic data processing example (Yang Liu) <br />
|-<br />
|<br />
| colspan="2" | <br />
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.<br><br><br />
|-<br />
| 2:25-3:25<br />
! colspan="2" | Developing your own programs in Madagascar (Jeffrey Shragge)<br />
|-<br />
|<br />
| colspan="2" | <br />
There are many programs already built into the Madagascar project, but if you use Madagascar long enough you will eventually run into a problem that you cannot solve using only provided codes. Fortunately, Madagascar has a variety of programming language APIs already built, that allow you to: design, code, and integrate your programs into the Madagascar framework. By the end of the session, you should have a good starting point for developing your own codes, and adding them to the growing library of open-source software available in Madagascar. <br><br><br />
|-<br />
| 3:25-3:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 3:40-4:40<br />
! colspan="2" | title (Junzhe Sun)<br />
|-<br />
|<br />
| colspan="2" | <br />
content<br />
|-<br />
| 4:40-5:10<br />
! colspan="2" | Contributing to Madagascar (Sergey Fomel)<br />
|-<br />
|<br />
| colspan="2" |<br />
As a user of Madagascar, you have the right to run the code for any purpose, to make modifications and additions, and to share your modifications with other people. Madagascar is an open community, which makes it easy to share your contributions and to collaborate with other users and developers around the world. <br><br><br />
|-<br />
| 5:10-5:40<br />
! colspan="2" | Awarding certificates and closing<br />
|-<br />
|}<br />
<br />
== Location ==<br />
<br />
The 503 Gewu Building, Department of Mathematics, Harbin Institute of Technology (HIT), China, or Xiyuan Hotel in the HIT campus<br />
<br />
哈尔滨工业大学数学系,格物楼503,黑龙江省哈尔滨市南岗区西大直街92号<br />
<br />
== Registration ==<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
Please try to [[download]] and [[Installation|install]] the Madagascar package ([http://sourceforge.net/projects/rsf/files/latest/download?source=files stable version 1.6]) in the days before the workshop according to the instructions on the left margin of this webpage. If issues come up, there will an opportunity to install the package at the start of the workshop. Remember to bring your laptop (Linux, Mac, or Windows) to the session!<br />
<br />
== Instructors ==<br />
<br />
* '''Sergey Fomel''' is a Professor at the Jackson School of Geosciences, the University of Texas at Austin. He received a Ph.D. in Geophysics from Stanford University in 2001. Sergey started work on Madagascar (at that time named RSF for Regularly Sampled Format) in 2003. http://www.jsg.utexas.edu/researcher/sergey_fomel/<br />
* '''Yang Liu''' is a 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. http://gest.jlu.edu.cn/?mod=info&act=view&id=54<br />
* '''Jeffrey Shragge''' is an Associate 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). https://www.socrates.uwa.edu.au/Staff/StaffProfile.aspx?Person=JeffreyShragge<br />
* '''Junzhe Sun''' graduated from a joint education program between China University of Petroleum-East China and Missouri University of Science and Technology with a Bachelor's Degree in Geophysics in 2012. He worked with Prof. Stephen Gao on seismic anisotropy and mantle flow when he was at Missouri S&T. He is currently a Ph.D student working with Prof. Sergey Fomel. http://www.linkedin.com/pub/junzhe-sun/44/749/3b<br />
* '''Pengliang Yang''' received his bachelor's degree in 2009 from Nanjing University of Aeronautics and Astronautics and is currently pursuing a Ph.D. at Xi'an Jiaotong University. Previously, he worked on sparsity-based seismic data reconstruction using the theory of compressed sensing. His current research is mainly on reverse time migration and sparse inversion.</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Harbin_2015&diff=2989Harbin 20152014-11-13T07:12:16Z<p>Yangliu: /* Instructors */</p>
<hr />
<div>[[Image:Harbin.jpg|center|frame]]<br />
<br />
<center><big>'''Madagascar School in Harbin 2015'''</big></center><br />
<br />
&nbsp;<br />
<br />
== Dates ==<br />
<br />
January 7-8, 2015.<br />
<br />
== Agenda ==<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 1: Wednesday, January 7, 2015<br />
|-<br />
| 10:00-3:00<br />
! colspan="2" | Bring your laptop with Madagascar package (stable version 1.6) and get help with installing Madagascar<br />
|-<br />
|<br />
! colspan="2" | Sergey Fomel, Jeffrey Shragge , Yang Liu<br />
|-<br />
<br />
|}<br />
<br />
&nbsp;<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 2: Thursday, January 8, 2015<br />
|-<br />
| 9:00-9:10<br />
! colspan="2" | Welcome (Jianwei Ma)<br />
<br />
|-<br />
| 9:10-10:10<br />
! colspan="2" | Introduction (Sergey Fomel)<br />
|-<br />
| <br />
| colspan="2" | <br />
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.<br><br><br />
<br />
|-<br />
| 10:10-10:25<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:25-11:25<br />
! colspan="2" | title (Pengliang Yang)<br />
|-<br />
|<br />
| colspan="2" | <br />
content<br />
<br><br />
|-<br />
| 11:25-12:25<br />
! colspan="2" | Developing workflows using SCons (Sergey Fomel)<br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.scons.org/ SCons] (from '''S'''oftware '''Cons'''truction) is a superior alternative to the classic '''make''' utility. SCons is implemented as a [http://www.python.org Python] script, its "configuration files" (<tt>SConstruct</tt> files) are also Python scripts. Madagascar uses SCons to compile software, to manage data processing flowing, and to assemble [[Reproducible Documents|reproducible documents]].<br><br><br />
|-<br />
| 12:25-1:25<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 1:25-2:25<br />
! colspan="2" | Seismic data processing example (Yang Liu) <br />
|-<br />
|<br />
| colspan="2" | <br />
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.<br><br><br />
|-<br />
| 2:25-3:25<br />
! colspan="2" | Developing your own programs in Madagascar (Jeffrey Shragge)<br />
|-<br />
|<br />
| colspan="2" | <br />
There are many programs already built into the Madagascar project, but if you use Madagascar long enough you will eventually run into a problem that you cannot solve using only provided codes. Fortunately, Madagascar has a variety of programming language APIs already built, that allow you to: design, code, and integrate your programs into the Madagascar framework. By the end of the session, you should have a good starting point for developing your own codes, and adding them to the growing library of open-source software available in Madagascar. <br><br><br />
|-<br />
| 3:25-3:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 3:40-4:40<br />
! colspan="2" | title (Junzhe Sun)<br />
|-<br />
|<br />
| colspan="2" | <br />
content<br />
|-<br />
| 4:40-5:10<br />
! colspan="2" | Contributing to Madagascar (Sergey Fomel)<br />
|-<br />
|<br />
| colspan="2" |<br />
As a user of Madagascar, you have the right to run the code for any purpose, to make modifications and additions, and to share your modifications with other people. Madagascar is an open community, which makes it easy to share your contributions and to collaborate with other users and developers around the world. <br><br><br />
|-<br />
| 5:10-5:40<br />
! colspan="2" | Awarding certificates and closing<br />
|-<br />
|}<br />
<br />
== Registration location ==<br />
<br />
The 503 Gewu Building, Department of Mathematics, Harbin Institute of Technology (HIT), China, or Xiyuan Hotel in the HIT campus<br />
<br />
哈尔滨工业大学数学系,格物楼503,黑龙江省哈尔滨市南岗区西大直街92号<br />
<br />
== Registration ==<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
Please try to [[download]] and [[Installation|install]] the Madagascar package ([http://sourceforge.net/projects/rsf/files/latest/download?source=files stable version 1.6]) in the days before the workshop according to the instructions on the left margin of this webpage. If issues come up, there will an opportunity to install the package at the start of the workshop. Remember to bring your laptop (Linux, Mac, or Windows) to the session!<br />
<br />
== Instructors ==<br />
<br />
* '''Sergey Fomel''' is a Professor at the Jackson School of Geosciences, the University of Texas at Austin. He received a Ph.D. in Geophysics from Stanford University in 2001. Sergey started work on Madagascar (at that time named RSF for Regularly Sampled Format) in 2003. http://www.jsg.utexas.edu/researcher/sergey_fomel/<br />
* '''Yang Liu''' is a 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. http://gest.jlu.edu.cn/?mod=info&act=view&id=54<br />
* '''Jeffrey Shragge''' is an Associate 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). https://www.socrates.uwa.edu.au/Staff/StaffProfile.aspx?Person=JeffreyShragge<br />
* '''Junzhe Sun''' graduated from a joint education program between China University of Petroleum-East China and Missouri University of Science and Technology with a Bachelor's Degree in Geophysics in 2012. He worked with Prof. Stephen Gao on seismic anisotropy and mantle flow when he was at Missouri S&T. He is currently a Ph.D student working with Prof. Sergey Fomel. http://www.linkedin.com/pub/junzhe-sun/44/749/3b<br />
* '''Pengliang Yang''' received his bachelor's degree in 2009 from Nanjing University of Aeronautics and Astronautics and is currently pursuing a Ph.D. at Xi'an Jiaotong University. Previously, he worked on sparsity-based seismic data reconstruction using the theory of compressed sensing. His current research is mainly on reverse time migration and sparse inversion.</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Harbin_2015&diff=2988Harbin 20152014-11-13T07:06:13Z<p>Yangliu: /* Registration location */</p>
<hr />
<div>[[Image:Harbin.jpg|center|frame]]<br />
<br />
<center><big>'''Madagascar School in Harbin 2015'''</big></center><br />
<br />
&nbsp;<br />
<br />
== Dates ==<br />
<br />
January 7-8, 2015.<br />
<br />
== Agenda ==<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 1: Wednesday, January 7, 2015<br />
|-<br />
| 10:00-3:00<br />
! colspan="2" | Bring your laptop with Madagascar package (stable version 1.6) and get help with installing Madagascar<br />
|-<br />
|<br />
! colspan="2" | Sergey Fomel, Jeffrey Shragge , Yang Liu<br />
|-<br />
<br />
|}<br />
<br />
&nbsp;<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 2: Thursday, January 8, 2015<br />
|-<br />
| 9:00-9:10<br />
! colspan="2" | Welcome (Jianwei Ma)<br />
<br />
|-<br />
| 9:10-10:10<br />
! colspan="2" | Introduction (Sergey Fomel)<br />
|-<br />
| <br />
| colspan="2" | <br />
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.<br><br><br />
<br />
|-<br />
| 10:10-10:25<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:25-11:25<br />
! colspan="2" | title (Pengliang Yang)<br />
|-<br />
|<br />
| colspan="2" | <br />
content<br />
<br><br />
|-<br />
| 11:25-12:25<br />
! colspan="2" | Developing workflows using SCons (Sergey Fomel)<br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.scons.org/ SCons] (from '''S'''oftware '''Cons'''truction) is a superior alternative to the classic '''make''' utility. SCons is implemented as a [http://www.python.org Python] script, its "configuration files" (<tt>SConstruct</tt> files) are also Python scripts. Madagascar uses SCons to compile software, to manage data processing flowing, and to assemble [[Reproducible Documents|reproducible documents]].<br><br><br />
|-<br />
| 12:25-1:25<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 1:25-2:25<br />
! colspan="2" | Seismic data processing example (Yang Liu) <br />
|-<br />
|<br />
| colspan="2" | <br />
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.<br><br><br />
|-<br />
| 2:25-3:25<br />
! colspan="2" | Developing your own programs in Madagascar (Jeffrey Shragge)<br />
|-<br />
|<br />
| colspan="2" | <br />
There are many programs already built into the Madagascar project, but if you use Madagascar long enough you will eventually run into a problem that you cannot solve using only provided codes. Fortunately, Madagascar has a variety of programming language APIs already built, that allow you to: design, code, and integrate your programs into the Madagascar framework. By the end of the session, you should have a good starting point for developing your own codes, and adding them to the growing library of open-source software available in Madagascar. <br><br><br />
|-<br />
| 3:25-3:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 3:40-4:40<br />
! colspan="2" | title (Junzhe Sun)<br />
|-<br />
|<br />
| colspan="2" | <br />
content<br />
|-<br />
| 4:40-5:10<br />
! colspan="2" | Contributing to Madagascar (Sergey Fomel)<br />
|-<br />
|<br />
| colspan="2" |<br />
As a user of Madagascar, you have the right to run the code for any purpose, to make modifications and additions, and to share your modifications with other people. Madagascar is an open community, which makes it easy to share your contributions and to collaborate with other users and developers around the world. <br><br><br />
|-<br />
| 5:10-5:40<br />
! colspan="2" | Awarding certificates and closing<br />
|-<br />
|}<br />
<br />
== Registration location ==<br />
<br />
The 503 Gewu Building, Department of Mathematics, Harbin Institute of Technology (HIT), China, or Xiyuan Hotel in the HIT campus<br />
<br />
哈尔滨工业大学数学系,格物楼503,黑龙江省哈尔滨市南岗区西大直街92号<br />
<br />
== Registration ==<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
Please try to [[download]] and [[Installation|install]] the Madagascar package ([http://sourceforge.net/projects/rsf/files/latest/download?source=files stable version 1.6]) in the days before the workshop according to the instructions on the left margin of this webpage. If issues come up, there will an opportunity to install the package at the start of the workshop. Remember to bring your laptop (Linux, Mac, or Windows) to the session!<br />
<br />
== Instructors ==<br />
<br />
* '''Sergey Fomel''' is a Professor at the Jackson School of Geosciences, the University of Texas at Austin. He received a Ph.D. in Geophysics from Stanford University in 2001. Sergey started work on Madagascar (at that time named RSF for Regularly Sampled Format) in 2003. http://www.jsg.utexas.edu/researcher/sergey_fomel/<br />
* '''Yang Liu''' is a 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. http://gest.jlu.edu.cn/?mod=info&act=view&id=54<br />
* '''Jeffrey Shragge''' is an Associate 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). https://www.socrates.uwa.edu.au/Staff/StaffProfile.aspx?Person=JeffreyShragge</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Harbin_2015&diff=2987Harbin 20152014-11-13T03:20:45Z<p>Yangliu: /* Agenda */</p>
<hr />
<div>[[Image:Harbin.jpg|center|frame]]<br />
<br />
<center><big>'''Madagascar School in Harbin 2015'''</big></center><br />
<br />
&nbsp;<br />
<br />
== Dates ==<br />
<br />
January 7-8, 2015.<br />
<br />
== Agenda ==<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 1: Wednesday, January 7, 2015<br />
|-<br />
| 10:00-3:00<br />
! colspan="2" | Bring your laptop with Madagascar package (stable version 1.6) and get help with installing Madagascar<br />
|-<br />
|<br />
! colspan="2" | Sergey Fomel, Jeffrey Shragge , Yang Liu<br />
|-<br />
<br />
|}<br />
<br />
&nbsp;<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 2: Thursday, January 8, 2015<br />
|-<br />
| 9:00-9:10<br />
! colspan="2" | Welcome (Jianwei Ma)<br />
<br />
|-<br />
| 9:10-10:10<br />
! colspan="2" | Introduction (Sergey Fomel)<br />
|-<br />
| <br />
| colspan="2" | <br />
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.<br><br><br />
<br />
|-<br />
| 10:10-10:25<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:25-11:25<br />
! colspan="2" | title (Pengliang Yang)<br />
|-<br />
|<br />
| colspan="2" | <br />
content<br />
<br><br />
|-<br />
| 11:25-12:25<br />
! colspan="2" | Developing workflows using SCons (Sergey Fomel)<br />
|-<br />
| <br />
| colspan="2" | <br />
[http://www.scons.org/ SCons] (from '''S'''oftware '''Cons'''truction) is a superior alternative to the classic '''make''' utility. SCons is implemented as a [http://www.python.org Python] script, its "configuration files" (<tt>SConstruct</tt> files) are also Python scripts. Madagascar uses SCons to compile software, to manage data processing flowing, and to assemble [[Reproducible Documents|reproducible documents]].<br><br><br />
|-<br />
| 12:25-1:25<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 1:25-2:25<br />
! colspan="2" | Seismic data processing example (Yang Liu) <br />
|-<br />
|<br />
| colspan="2" | <br />
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.<br><br><br />
|-<br />
| 2:25-3:25<br />
! colspan="2" | Developing your own programs in Madagascar (Jeffrey Shragge)<br />
|-<br />
|<br />
| colspan="2" | <br />
There are many programs already built into the Madagascar project, but if you use Madagascar long enough you will eventually run into a problem that you cannot solve using only provided codes. Fortunately, Madagascar has a variety of programming language APIs already built, that allow you to: design, code, and integrate your programs into the Madagascar framework. By the end of the session, you should have a good starting point for developing your own codes, and adding them to the growing library of open-source software available in Madagascar. <br><br><br />
|-<br />
| 3:25-3:40<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 3:40-4:40<br />
! colspan="2" | title (Junzhe Sun)<br />
|-<br />
|<br />
| colspan="2" | <br />
content<br />
|-<br />
| 4:40-5:10<br />
! colspan="2" | Contributing to Madagascar (Sergey Fomel)<br />
|-<br />
|<br />
| colspan="2" |<br />
As a user of Madagascar, you have the right to run the code for any purpose, to make modifications and additions, and to share your modifications with other people. Madagascar is an open community, which makes it easy to share your contributions and to collaborate with other users and developers around the world. <br><br><br />
|-<br />
| 5:10-5:40<br />
! colspan="2" | Awarding certificates and closing<br />
|-<br />
|}<br />
<br />
== Registration location ==<br />
<br />
The 503 Gewu Building, Department of Mathematics, Harbin Institute of Technology (HIT), China, or Xiyuan Hotel in the HIT campus<br />
<br />
哈尔滨工业大学,格物楼503,哈尔滨市南岗区西大直街92号<br />
<br />
== Registration ==<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
Please try to [[download]] and [[Installation|install]] the Madagascar package ([http://sourceforge.net/projects/rsf/files/latest/download?source=files stable version 1.6]) in the days before the workshop according to the instructions on the left margin of this webpage. If issues come up, there will an opportunity to install the package at the start of the workshop. Remember to bring your laptop (Linux, Mac, or Windows) to the session!<br />
<br />
== Instructors ==<br />
<br />
* '''Sergey Fomel''' is a Professor at the Jackson School of Geosciences, the University of Texas at Austin. He received a Ph.D. in Geophysics from Stanford University in 2001. Sergey started work on Madagascar (at that time named RSF for Regularly Sampled Format) in 2003. http://www.jsg.utexas.edu/researcher/sergey_fomel/<br />
* '''Yang Liu''' is a 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. http://gest.jlu.edu.cn/?mod=info&act=view&id=54<br />
* '''Jeffrey Shragge''' is an Associate 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). https://www.socrates.uwa.edu.au/Staff/StaffProfile.aspx?Person=JeffreyShragge</div>Yangliuhttps://www.reproducibility.org/wiki2020/index.php?title=Harbin_2015&diff=2986Harbin 20152014-11-13T02:19:20Z<p>Yangliu: /* Registration location */</p>
<hr />
<div>[[Image:Harbin.jpg|center|frame]]<br />
<br />
<center><big>'''Madagascar School in Harbin 2015'''</big></center><br />
<br />
&nbsp;<br />
<br />
== Dates ==<br />
<br />
January 7-8, 2015.<br />
<br />
== Agenda ==<br />
<br />
== Registration location ==<br />
<br />
The 503 Gewu Building, Department of Mathematics, Harbin Institute of Technology (HIT), China, or Xiyuan Hotel in the HIT campus<br />
<br />
哈尔滨工业大学,格物楼503,哈尔滨市南岗区西大直街92号<br />
<br />
== Registration ==<br />
<br />
== Pre-workshop Assignment ==<br />
<br />
Please try to [[download]] and [[Installation|install]] the Madagascar package ([http://sourceforge.net/projects/rsf/files/latest/download?source=files stable version 1.6]) in the days before the workshop according to the instructions on the left margin of this webpage. If issues come up, there will an opportunity to install the package at the start of the workshop. Remember to bring your laptop (Linux, Mac, or Windows) to the session!<br />
<br />
== Instructors ==<br />
<br />
* '''Sergey Fomel''' is a Professor at the Jackson School of Geosciences, the University of Texas at Austin. He received a Ph.D. in Geophysics from Stanford University in 2001. Sergey started work on Madagascar (at that time named RSF for Regularly Sampled Format) in 2003. http://www.jsg.utexas.edu/researcher/sergey_fomel/<br />
* '''Yang Liu''' is a 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. http://gest.jlu.edu.cn/?mod=info&act=view&id=54<br />
* '''Jeffrey Shragge''' is an Associate 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). https://www.socrates.uwa.edu.au/Staff/StaffProfile.aspx?Person=JeffreyShragge</div>Yangliu