https://www.reproducibility.org/wiki2020/api.php?action=feedcontributions&user=Psava&feedformat=atomMadagascar - User contributions [en]2024-03-29T05:11:48ZUser contributionsMediaWiki 1.34.0https://www.reproducibility.org/wiki2020/index.php?title=Petersburg_2014&diff=2898Petersburg 20142014-04-15T12:57:03Z<p>Psava: /* Registration */</p>
<hr />
<div>[[Image:Petersburg.jpg|center|frame]]<br />
<br />
<center><big>'''Madagascar Workshop at EAGE-St.Petersburg 2014'''</big></center><br />
<br />
&nbsp;<br />
<br />
== Date ==<br />
<br />
Friday, April 11, 2014<br />
<br />
== Agenda ==<br />
<br />
The tentative workshop agenda is the following:<br />
<br />
{| border="1" cellpadding="5" cellspacing="0" <br />
! style="background:#ffdead;" align="center" | TIME <br />
! style="background:#ffdead;" align="center" | ACTIVITY<br />
|-<br />
| 9:00-9:15am <br />
| Welcome <br />
<br> Speaker: Paul Sava<br />
|-<br />
| 9:15-11am<br />
| Madagascar: command-line usage<br />
<br> Speaker: Paul Sava<br />
|-<br />
! style="background:#efefef;" | 11:00-11:15am <br />
! style="background:#efefef;" | BREAK <br />
|-<br />
| 11:15am-12:00pm <br />
| Madagascar: reproducible numeric experiments <br />
<br> Speaker: Paul Sava<br />
|-<br />
! style="background:#efefef;" | 12:00-1:15pm <br />
! style="background:#efefef;" | LUNCH<br />
|-<br />
| 1:15pm-2:00pm <br />
| Data processing exercise<br />
<br> Speaker: Luke Decker<br />
|-<br />
! style="background:#efefef;" | 2:00-2:15pm <br />
! style="background:#efefef;" | BREAK <br />
|-<br />
| 2:15-3:15pm <br />
| Wavefield modeling/imaging<br />
<br> Speaker: Paul Sava <br />
|-<br />
! style="background:#efefef;" | 3:15-3:30pm <br />
! style="background:#efefef;" | BREAK <br />
|-<br />
| 3:30-5:00pm <br />
| Fast research using Madagascar <br />
<br> Speaker: Tariq Alkhalifah<br />
|-<br />
! style="background:#efefef;" | 5:00-5:15pm <br />
! style="background:#efefef;" | Discussion and wrap up<br />
|}<br />
<br />
== Location ==<br />
<br />
The Congress Centre of the [http://www.parkinn.com/hotelpulkovskaya-stpetersburg Park Inn by Radisson Pulkovskaya] hotel <br />
* Pobedy Square 1<br />
* 196240 St. Petersburg, Russia<br />
<br />
== Registration ==<br />
<br />
The best way to register is by using the [http://www.eage.org/events/index.php?evp=10534&ActiveMenu=10&Opendivs=s3,s10 online registration form]. You can also register using the [http://www.eage.org/images/cms/files/Education/16273-STP14%20registration%20form.pdf PDF form] and returning it to:<br />
<br />
EAGE Europe Office<br><br />
Registration Department<br><br />
PO Box 59<br><br />
3990 DB Houten<br><br />
The Netherlands<br><br />
Tel.: +31 88 9955055<br><br />
Fax: +31 306343534<br><br />
E-mail: registration@eage.org<br><br />
<br />
The workshop registration price varies from €75 for early-registration EAGE student member to €230 for late-registration non-member.<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 />
* '''Tariq Alkhalifah''' is currently a Professor of Geophysics at KAUST in Saudi Arabia. He graduated with a PhD from Colorado School of Mines, Golden, Colorado, in 1996, and served afterwards as a Post Doc at Stanford University. He used to be a devoted SU Unix follower for most of his research career even as a Post Doc at Stanford (SEPlib people), but has recently seen the light and converted to Madagascar. https://sites.google.com/a/kaust.edu.sa/tariq/<br />
* '''Luke Decker''' is a Master's student at the Jackson School of Geosciences, the University of Texas at Austin, studying under Professor Sergey Fomel. He holds undergraduate degrees in Physics (2008) from Whitman College in Walla Walla, Washington, and Geophysics (2011) from Western Washington University in Bellingham, Washington. He worked for several years as a mudlogger for King Canyon Buffalo, Inc., and his research focus is seismic diffraction imaging.<br />
* '''Paul Sava''' is an Associate Professor of Geophysics and a member of the Center for Wave Phenomena at Colorado School of Mines. He holds an Engineering degree in Geophysics (1995) from the University of Bucharest, an M.Sc. (1998) and a Ph.D. (2004) in Geophysics from Stanford University. His research interests are in wavefield seismic imaging, stochastic imaging and inversion, computational methods for wave propagation, numeric optimization and high performance computing. http://newton.mines.edu/paul/home.php</div>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=Petersburg_2014&diff=2897Petersburg 20142014-04-15T12:56:09Z<p>Psava: /* Agenda */</p>
<hr />
<div>[[Image:Petersburg.jpg|center|frame]]<br />
<br />
<center><big>'''Madagascar Workshop at EAGE-St.Petersburg 2014'''</big></center><br />
<br />
&nbsp;<br />
<br />
== Date ==<br />
<br />
Friday, April 11, 2014<br />
<br />
== Agenda ==<br />
<br />
The tentative workshop agenda is the following:<br />
<br />
{| border="1" cellpadding="5" cellspacing="0" <br />
! style="background:#ffdead;" align="center" | TIME <br />
! style="background:#ffdead;" align="center" | ACTIVITY<br />
|-<br />
| 9:00-9:15am <br />
| Welcome <br />
<br> Speaker: Paul Sava<br />
|-<br />
| 9:15-11am<br />
| Madagascar: command-line usage<br />
<br> Speaker: Paul Sava<br />
|-<br />
! style="background:#efefef;" | 11:00-11:15am <br />
! style="background:#efefef;" | BREAK <br />
|-<br />
| 11:15am-12:00pm <br />
| Madagascar: reproducible numeric experiments <br />
<br> Speaker: Paul Sava<br />
|-<br />
! style="background:#efefef;" | 12:00-1:15pm <br />
! style="background:#efefef;" | LUNCH<br />
|-<br />
| 1:15pm-2:00pm <br />
| Data processing exercise<br />
<br> Speaker: Luke Decker<br />
|-<br />
! style="background:#efefef;" | 2:00-2:15pm <br />
! style="background:#efefef;" | BREAK <br />
|-<br />
| 2:15-3:15pm <br />
| Wavefield modeling/imaging<br />
<br> Speaker: Paul Sava <br />
|-<br />
! style="background:#efefef;" | 3:15-3:30pm <br />
! style="background:#efefef;" | BREAK <br />
|-<br />
| 3:30-5:00pm <br />
| Fast research using Madagascar <br />
<br> Speaker: Tariq Alkhalifah<br />
|-<br />
! style="background:#efefef;" | 5:00-5:15pm <br />
! style="background:#efefef;" | Discussion and wrap up<br />
|}<br />
<br />
== Location ==<br />
<br />
The Congress Centre of the [http://www.parkinn.com/hotelpulkovskaya-stpetersburg Park Inn by Radisson Pulkovskaya] hotel <br />
* Pobedy Square 1<br />
* 196240 St. Petersburg, Russia<br />
<br />
== Registration ==<br />
<br />
The best way to register is by using the [http://www.eage.org/events/index.php?evp=10534&ActiveMenu=10&Opendivs=s3,s10 online registration form]. You can also register using the [http://www.eage.org/images/cms/files/Education/16273-STP14%20registration%20form.pdf PDF form] and returning it to:<br />
<br />
EAGE Europe Office<br><br />
Registration Department<br><br />
PO Box 59<br><br />
3990 DB Houten<br><br />
The Netherlands<br><br />
Tel.: +31 88 9955055<br><br />
Fax: +31 306343534<br><br />
E-mail: registration@eage.org<br><br />
<br />
The workshop registration price varies from €75 for early-registration EAGE student member to €230 for late-registration non-member.<br />
<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 />
* '''Tariq Alkhalifah''' is currently a Professor of Geophysics at KAUST in Saudi Arabia. He graduated with a PhD from Colorado School of Mines, Golden, Colorado, in 1996, and served afterwards as a Post Doc at Stanford University. He used to be a devoted SU Unix follower for most of his research career even as a Post Doc at Stanford (SEPlib people), but has recently seen the light and converted to Madagascar. https://sites.google.com/a/kaust.edu.sa/tariq/<br />
* '''Luke Decker''' is a Master's student at the Jackson School of Geosciences, the University of Texas at Austin, studying under Professor Sergey Fomel. He holds undergraduate degrees in Physics (2008) from Whitman College in Walla Walla, Washington, and Geophysics (2011) from Western Washington University in Bellingham, Washington. He worked for several years as a mudlogger for King Canyon Buffalo, Inc., and his research focus is seismic diffraction imaging.<br />
* '''Paul Sava''' is an Associate Professor of Geophysics and a member of the Center for Wave Phenomena at Colorado School of Mines. He holds an Engineering degree in Geophysics (1995) from the University of Bucharest, an M.Sc. (1998) and a Ph.D. (2004) in Geophysics from Stanford University. His research interests are in wavefield seismic imaging, stochastic imaging and inversion, computational methods for wave propagation, numeric optimization and high performance computing. http://newton.mines.edu/paul/home.php</div>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=Petersburg_2014&diff=2896Petersburg 20142014-04-15T12:54:32Z<p>Psava: /* Agenda */</p>
<hr />
<div>[[Image:Petersburg.jpg|center|frame]]<br />
<br />
<center><big>'''Madagascar Workshop at EAGE-St.Petersburg 2014'''</big></center><br />
<br />
&nbsp;<br />
<br />
== Date ==<br />
<br />
Friday, April 11, 2014<br />
<br />
== Agenda ==<br />
<br />
The tentative workshop agenda is the following:<br />
<br />
{| border="1" cellpadding="5" cellspacing="0" <br />
! style="background:#ffdead;" align="center" | TIME <br />
! style="background:#ffdead;" align="center" | ACTIVITY<br />
|-<br />
| 9:00-9:15am <br />
| Welcome <br />
<br> Speaker: Paul Sava<br />
|-<br />
| 9:15-11am<br />
| Madagascar: command-line usage<br />
<br> Speaker: Paul Sava<br />
|-<br />
! style="background:#efefef;" | 11:00-11:15am <br />
! style="background:#efefef;" | BREAK <br />
|-<br />
| 11:15am-12:00pm <br />
| Madagascar: reproducible numeric experiments <br />
<br> Speaker: Paul Sava<br />
|-<br />
! style="background:#efefef;" | 12:00-1:15pm <br />
! style="background:#efefef;" | LUNCH<br />
|-<br />
| 1:15pm-2:00pm <br />
| Data processing exercise<br />
<br> Speaker: Luke Decker<br />
|-<br />
! style="background:#efefef;" | 2:00-2:15pm <br />
! style="background:#efefef;" | BREAK <br />
|-<br />
| 2:15-3:00pm <br />
| Wavefield modeling/imaging<br />
<br> Speaker: Paul Sava <br />
|-<br />
! style="background:#efefef;" | 3:00-3:15pm <br />
! style="background:#efefef;" | BREAK <br />
|-<br />
| 3:15-5:00pm <br />
| Fast research using Madagascar <br />
<br> Speaker: Tariq Alkhalifah<br />
|-<br />
! style="background:#efefef;" | 5:00-5:15pm <br />
! style="background:#efefef;" | Discussion and wrap up<br />
|}<br />
<br />
== Location ==<br />
<br />
The Congress Centre of the [http://www.parkinn.com/hotelpulkovskaya-stpetersburg Park Inn by Radisson Pulkovskaya] hotel <br />
* Pobedy Square 1<br />
* 196240 St. Petersburg, Russia<br />
<br />
== Registration ==<br />
<br />
The best way to register is by using the [http://www.eage.org/events/index.php?evp=10534&ActiveMenu=10&Opendivs=s3,s10 online registration form]. You can also register using the [http://www.eage.org/images/cms/files/Education/16273-STP14%20registration%20form.pdf PDF form] and returning it to:<br />
<br />
EAGE Europe Office<br><br />
Registration Department<br><br />
PO Box 59<br><br />
3990 DB Houten<br><br />
The Netherlands<br><br />
Tel.: +31 88 9955055<br><br />
Fax: +31 306343534<br><br />
E-mail: registration@eage.org<br><br />
<br />
The workshop registration price varies from €75 for early-registration EAGE student member to €230 for late-registration non-member.<br />
<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 />
* '''Tariq Alkhalifah''' is currently a Professor of Geophysics at KAUST in Saudi Arabia. He graduated with a PhD from Colorado School of Mines, Golden, Colorado, in 1996, and served afterwards as a Post Doc at Stanford University. He used to be a devoted SU Unix follower for most of his research career even as a Post Doc at Stanford (SEPlib people), but has recently seen the light and converted to Madagascar. https://sites.google.com/a/kaust.edu.sa/tariq/<br />
* '''Luke Decker''' is a Master's student at the Jackson School of Geosciences, the University of Texas at Austin, studying under Professor Sergey Fomel. He holds undergraduate degrees in Physics (2008) from Whitman College in Walla Walla, Washington, and Geophysics (2011) from Western Washington University in Bellingham, Washington. He worked for several years as a mudlogger for King Canyon Buffalo, Inc., and his research focus is seismic diffraction imaging.<br />
* '''Paul Sava''' is an Associate Professor of Geophysics and a member of the Center for Wave Phenomena at Colorado School of Mines. He holds an Engineering degree in Geophysics (1995) from the University of Bucharest, an M.Sc. (1998) and a Ph.D. (2004) in Geophysics from Stanford University. His research interests are in wavefield seismic imaging, stochastic imaging and inversion, computational methods for wave propagation, numeric optimization and high performance computing. http://newton.mines.edu/paul/home.php</div>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=Petersburg_2014&diff=2895Petersburg 20142014-04-15T12:53:52Z<p>Psava: /* Agenda */</p>
<hr />
<div>[[Image:Petersburg.jpg|center|frame]]<br />
<br />
<center><big>'''Madagascar Workshop at EAGE-St.Petersburg 2014'''</big></center><br />
<br />
&nbsp;<br />
<br />
== Date ==<br />
<br />
Friday, April 11, 2014<br />
<br />
== Agenda ==<br />
<br />
The tentative workshop agenda is the following:<br />
<br />
{| border="1" cellpadding="5" cellspacing="0" <br />
! style="background:#ffdead;" align="center" | TIME <br />
! style="background:#ffdead;" align="center" | ACTIVITY<br />
|-<br />
| 9:00-9:15am <br />
| Welcome <br />
<br> Speaker: Paul Sava<br />
|-<br />
| 9:15-11am<br />
| Madagascar: command-line usage<br />
| Madagascar: reproducible numeric experiments <br />
<br> Speaker: Paul Sava<br />
|-<br />
! style="background:#efefef;" | 11:00-11:15am <br />
! style="background:#efefef;" | BREAK <br />
|-<br />
| 11:15am-12:00pm <br />
| Data processing exercise (part 1)<br />
<br> Speaker: Luke Decker<br />
|-<br />
! style="background:#efefef;" | 12:00-1:15pm <br />
! style="background:#efefef;" | LUNCH<br />
|-<br />
| 1:15pm-2:00pm <br />
| Data processing exercise (part 2)<br />
<br> Speaker: Luke Decker<br />
|-<br />
! style="background:#efefef;" | 2:00-2:15pm <br />
! style="background:#efefef;" | BREAK <br />
|-<br />
| 2:15-3:00pm <br />
| Wavefield modeling/imaging<br />
<br> Speaker: Paul Sava <br />
|-<br />
! style="background:#efefef;" | 3:00-3:15pm <br />
! style="background:#efefef;" | BREAK <br />
|-<br />
| 3:15-5:00pm <br />
| Fast research using Madagascar <br />
<br> Speaker: Tariq Alkhalifah<br />
|-<br />
! style="background:#efefef;" | 5:00-5:15pm <br />
! style="background:#efefef;" | Discussion and wrap up<br />
|}<br />
<br />
== Location ==<br />
<br />
The Congress Centre of the [http://www.parkinn.com/hotelpulkovskaya-stpetersburg Park Inn by Radisson Pulkovskaya] hotel <br />
* Pobedy Square 1<br />
* 196240 St. Petersburg, Russia<br />
<br />
== Registration ==<br />
<br />
The best way to register is by using the [http://www.eage.org/events/index.php?evp=10534&ActiveMenu=10&Opendivs=s3,s10 online registration form]. You can also register using the [http://www.eage.org/images/cms/files/Education/16273-STP14%20registration%20form.pdf PDF form] and returning it to:<br />
<br />
EAGE Europe Office<br><br />
Registration Department<br><br />
PO Box 59<br><br />
3990 DB Houten<br><br />
The Netherlands<br><br />
Tel.: +31 88 9955055<br><br />
Fax: +31 306343534<br><br />
E-mail: registration@eage.org<br><br />
<br />
The workshop registration price varies from €75 for early-registration EAGE student member to €230 for late-registration non-member.<br />
<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 />
* '''Tariq Alkhalifah''' is currently a Professor of Geophysics at KAUST in Saudi Arabia. He graduated with a PhD from Colorado School of Mines, Golden, Colorado, in 1996, and served afterwards as a Post Doc at Stanford University. He used to be a devoted SU Unix follower for most of his research career even as a Post Doc at Stanford (SEPlib people), but has recently seen the light and converted to Madagascar. https://sites.google.com/a/kaust.edu.sa/tariq/<br />
* '''Luke Decker''' is a Master's student at the Jackson School of Geosciences, the University of Texas at Austin, studying under Professor Sergey Fomel. He holds undergraduate degrees in Physics (2008) from Whitman College in Walla Walla, Washington, and Geophysics (2011) from Western Washington University in Bellingham, Washington. He worked for several years as a mudlogger for King Canyon Buffalo, Inc., and his research focus is seismic diffraction imaging.<br />
* '''Paul Sava''' is an Associate Professor of Geophysics and a member of the Center for Wave Phenomena at Colorado School of Mines. He holds an Engineering degree in Geophysics (1995) from the University of Bucharest, an M.Sc. (1998) and a Ph.D. (2004) in Geophysics from Stanford University. His research interests are in wavefield seismic imaging, stochastic imaging and inversion, computational methods for wave propagation, numeric optimization and high performance computing. http://newton.mines.edu/paul/home.php</div>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=Petersburg_2014&diff=2795Petersburg 20142014-04-03T19:14:01Z<p>Psava: /* Agenda */</p>
<hr />
<div>[[Image:Petersburg.jpg|center|frame]]<br />
<br />
<center><big>'''Madagascar Workshop at EAGE-St.Petersburg 2014'''</big></center><br />
<br />
&nbsp;<br />
<br />
== Date ==<br />
<br />
Friday, April 11, 2014<br />
<br />
== Agenda ==<br />
<br />
The tentative workshop agenda is the following:<br />
<br />
{| border="1" cellpadding="5" cellspacing="0" <br />
! style="background:#ffdead;" align="center" | TIME <br />
! style="background:#ffdead;" align="center" | ACTIVITY<br />
|-<br />
| 9:00-9:15am <br />
| Welcome <br />
<br> Speaker: Paul Sava<br />
|-<br />
| 9:15-11am<br />
| Madagascar fundamentals<br />
<br> Speaker: Paul Sava<br />
|-<br />
! style="background:#efefef;" | 11:00-11:15am <br />
! style="background:#efefef;" | BREAK <br />
|-<br />
| 11:15am-12:00pm <br />
| Data processing exercise (part 1)<br />
<br> Speaker: Luke Decker<br />
|-<br />
! style="background:#efefef;" | 12:00-1:15pm <br />
! style="background:#efefef;" | LUNCH<br />
|-<br />
| 1:15pm-2:00pm <br />
| Data processing exercise (part 2)<br />
<br> Speaker: Luke Decker<br />
|-<br />
! style="background:#efefef;" | 2:00-2:15pm <br />
! style="background:#efefef;" | BREAK <br />
|-<br />
| 2:15-3:00pm <br />
| Wavefield modeling/imaging<br />
<br> Speaker: Paul Sava <br />
|-<br />
! style="background:#efefef;" | 3:00-3:15pm <br />
! style="background:#efefef;" | BREAK <br />
|-<br />
| 3:15-5:00pm <br />
| Fast research using Madagascar <br />
<br> Speaker: Tariq Alkhalifah<br />
|-<br />
! style="background:#efefef;" | 5:00-5:15pm <br />
! style="background:#efefef;" | Discussion and wrap up<br />
|}<br />
<br />
== Location ==<br />
<br />
The Congress Centre of the [http://www.parkinn.com/hotelpulkovskaya-stpetersburg Park Inn by Radisson Pulkovskaya] hotel <br />
* Pobedy Square 1<br />
* 196240 St. Petersburg, Russia<br />
<br />
== Registration ==<br />
<br />
The best way to register is by using the [http://www.eage.org/events/index.php?evp=10534&ActiveMenu=10&Opendivs=s3,s10 online registration form]. You can also register using the [http://www.eage.org/images/cms/files/Education/16273-STP14%20registration%20form.pdf PDF form] and returning it to:<br />
<br />
EAGE Europe Office<br><br />
Registration Department<br><br />
PO Box 59<br><br />
3990 DB Houten<br><br />
The Netherlands<br><br />
Tel.: +31 88 9955055<br><br />
Fax: +31 306343534<br><br />
E-mail: registration@eage.org<br><br />
<br />
The workshop registration price varies from €75 for early-registration EAGE student member to €230 for late-registration non-member.<br />
<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 />
* '''Tariq Alkhalifah''' is currently a Professor of Geophysics at KAUST in Saudi Arabia. He graduated with a PhD from Colorado School of Mines, Golden, Colorado, in 1996, and served afterwards as a Post Doc at Stanford University. He used to be a devoted SU Unix follower for most of his research career even as a Post Doc at Stanford (SEPlib people), but has recently seen the light and converted to Madagascar. https://sites.google.com/a/kaust.edu.sa/tariq/<br />
* '''Luke Decker''' is a Master's student at the Jackson School of Geosciences, the University of Texas at Austin, studying under Professor Sergey Fomel. He holds undergraduate degrees in Physics (2008) from Whitman College in Walla Walla, Washington, and Geophysics (2011) from Western Washington University in Bellingham, Washington. He worked for several years as a mudlogger for King Canyon Buffalo, Inc., and his research focus is seismic diffraction imaging.<br />
* '''Paul Sava''' is an Associate Professor of Geophysics and a member of the Center for Wave Phenomena at Colorado School of Mines. He holds an Engineering degree in Geophysics (1995) from the University of Bucharest, an M.Sc. (1998) and a Ph.D. (2004) in Geophysics from Stanford University. His research interests are in wavefield seismic imaging, stochastic imaging and inversion, computational methods for wave propagation, numeric optimization and high performance computing. http://newton.mines.edu/paul/home.php</div>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=Conferences&diff=2794Conferences2014-04-01T21:47:52Z<p>Psava: /* Featured events */</p>
<hr />
<div>[[Image:Conferences.png|right|]]<br />
In reverse chronological order.<br />
<br />
==Featured events==<br />
<br />
===School in St. Petersburg 2014===<br />
<br />
[[Petersburg_2014|Workshop at EAGE/St. Petersburg]]<br />
<br />
===School in Melbourne 2013===<br />
<br />
[[Melbourne_2013|Workshop at ASEG]]<br />
<br />
===Working Workshop in Austin 2013===<br />
<br />
[[Austin_2013|First Madagascar Working Workshop]]<br />
<br />
===School in Austin 2012===<br />
<br />
[[Austin_2012|Madagascar School and Workshop on Reproducible Computational Geophysics]]<br />
<br />
===Workshop in Copenhagen 2012===<br />
<br />
[[Copenhagen_2012|Workshop - Open-source E&P Software - Six Years Later]]<br />
<br />
===School in Bejing 2011===<br />
<br />
[[Beijing_2011|Madagascar School of Reproducible Computational Geophysics]]<br />
<br />
===Workshop in Houston 2011===<br />
<br />
[[Houston_2011|Workshop - Open Software Tools for Reproducible Computational Geophysics]]<br />
<br />
===School in Houston 2010===<br />
<br />
[[Houston_2010|Madagascar School of Reproducible Computational Geophysics and Hands-On Workshop]]<br />
<br />
===School in Salvador 2009===<br />
<br />
[[Salvador_2009|Madagascar School on Reproducible Computational Geophysics]]<br />
<br />
===School in Delft 2009===<br />
<br />
[[Delft_2009|Madagascar School on Reproducible Computational Geophysics]]<br />
<br />
===Coding Sprint in Golden 2008===<br />
<br />
Implementation Workshop [[2008_Implementation_Workshop|Towards full automation and better robustness]] <br />
<br />
===School in Austin 2007===<br />
<br />
Short Course [[RSF_Austin_School_2007|Using and Extending RSF/Madagascar]].<br />
<br />
===School in Vancouver 2006===<br />
<br />
School and Workshop [[RSF_School_and_Workshop%2C_Vancouver_2006|Reproducible Research in Computational Geophysics]].<br />
<br />
==Conference presentations==<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>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=Petersburg_2014&diff=2777Petersburg 20142014-03-25T22:34:00Z<p>Psava: /* Instructors */</p>
<hr />
<div>[[Image:Petersburg.jpg|center|frame]]<br />
<br />
<center><big>'''Madagascar Workshop at EAGE-St.Petersburg 2014'''</big></center><br />
<br />
&nbsp;<br />
<br />
== Date ==<br />
<br />
Friday, April 11, 2014<br />
<br />
== Agenda ==<br />
<br />
The tentative workshop agenda is the following:<br />
<br />
{| border="1" cellpadding="5" cellspacing="0" <br />
! style="background:#ffdead;" align="center" | TIME <br />
! style="background:#ffdead;" align="center" | ACTIVITY<br />
|-<br />
| 9:00-10:00am <br />
| Welcome and Madagascar Fundamentals <br />
<br> Speaker: Paul Sava<br />
|-<br />
| 10:00-12:00am <br />
| Workflow I: An introductory exercise <br />
<br> Speaker: Luke Decker<br />
|-<br />
! style="background:#efefef;" | 12:00-1:100 pm <br />
! style="background:#efefef;" | LUNCH<br />
|-<br />
| 1:00-2:30pm <br />
| Workflow II: Finite-differences modeling & migration<br />
<br> Speaker: Paul Sava <br />
|-<br />
! style="background:#efefef;" | 2:30-2:45 am <br />
! style="background:#efefef;" | BREAK <br />
|-<br />
| 2:45-4:15 pm <br />
| Fast research using Madagascar <br />
<br> Speaker: Tariq Alkhalifah<br />
|-<br />
! style="background:#efefef;" | 4:15-5:00pm <br />
! style="background:#efefef;" | Discussion and wrap up<br />
|}<br />
<br />
== Location ==<br />
<br />
The Congress Centre of the [http://www.parkinn.com/hotelpulkovskaya-stpetersburg Park Inn by Radisson Pulkovskaya] hotel <br />
* Pobedy Square 1<br />
* 196240 St. Petersburg, Russia<br />
<br />
== Registration ==<br />
<br />
The best way to register is by using the [http://www.eage.org/events/index.php?evp=10534&ActiveMenu=10&Opendivs=s3,s10 online registration form]. You can also register using the [http://www.eage.org/images/cms/files/Education/16273-STP14%20registration%20form.pdf PDF form] and returning it to:<br />
<br />
EAGE Europe Office<br><br />
Registration Department<br><br />
PO Box 59<br><br />
3990 DB Houten<br><br />
The Netherlands<br><br />
Tel.: +31 88 9955055<br><br />
Fax: +31 306343534<br><br />
E-mail: registration@eage.org<br><br />
<br />
The workshop registration price varies from €75 for early-registration EAGE student member to €230 for late-registration non-member.<br />
<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 />
* '''Tariq Alkhalifah''' is currently a Professor of Geophysics at KAUST in Saudi Arabia. He graduated with a PhD from Colorado School of Mines, Golden, Colorado, in 1996, and served afterwards as a Post Doc at Stanford University. He used to be a devoted SU Unix follower for most of his research career even as a Post Doc at Stanford (SEPlib people), but has recently seen the light and converted to Madagascar. https://sites.google.com/a/kaust.edu.sa/tariq/<br />
* '''Luke Decker''' is a Master's student at the Jackson School of Geosciences, the University of Texas at Austin, studying under Professor Sergey Fomel. He holds undergraduate degrees in Physics (2008) from Whitman College in Walla Walla, Washington, and Geophysics (2011) from Western Washington University in Bellingham, Washington. He worked for several years as a mudlogger for King Canyon Buffalo, Inc., and his research focus is seismic diffraction imaging.<br />
* '''Paul Sava''' is an Associate Professor of Geophysics and a member of the Center for Wave Phenomena at Colorado School of Mines. He holds an Engineering degree in Geophysics (1995) from the University of Bucharest, an M.Sc. (1998) and a Ph.D. (2004) in Geophysics from Stanford University. His research interests are in wavefield seismic imaging, stochastic imaging and inversion, computational methods for wave propagation, numeric optimization and high performance computing. http://newton.mines.edu/paul/home.php</div>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=Petersburg_2014&diff=2776Petersburg 20142014-03-25T22:32:10Z<p>Psava: /* Instructors */</p>
<hr />
<div>[[Image:Petersburg.jpg|center|frame]]<br />
<br />
<center><big>'''Madagascar Workshop at EAGE-St.Petersburg 2014'''</big></center><br />
<br />
&nbsp;<br />
<br />
== Date ==<br />
<br />
Friday, April 11, 2014<br />
<br />
== Agenda ==<br />
<br />
The tentative workshop agenda is the following:<br />
<br />
{| border="1" cellpadding="5" cellspacing="0" <br />
! style="background:#ffdead;" align="center" | TIME <br />
! style="background:#ffdead;" align="center" | ACTIVITY<br />
|-<br />
| 9:00-10:00am <br />
| Welcome and Madagascar Fundamentals <br />
<br> Speaker: Paul Sava<br />
|-<br />
| 10:00-12:00am <br />
| Workflow I: An introductory exercise <br />
<br> Speaker: Luke Decker<br />
|-<br />
! style="background:#efefef;" | 12:00-1:100 pm <br />
! style="background:#efefef;" | LUNCH<br />
|-<br />
| 1:00-2:30pm <br />
| Workflow II: Finite-differences modeling & migration<br />
<br> Speaker: Paul Sava <br />
|-<br />
! style="background:#efefef;" | 2:30-2:45 am <br />
! style="background:#efefef;" | BREAK <br />
|-<br />
| 2:45-4:15 pm <br />
| Fast research using Madagascar <br />
<br> Speaker: Tariq Alkhalifah<br />
|-<br />
! style="background:#efefef;" | 4:15-5:00pm <br />
! style="background:#efefef;" | Discussion and wrap up<br />
|}<br />
<br />
== Location ==<br />
<br />
The Congress Centre of the [http://www.parkinn.com/hotelpulkovskaya-stpetersburg Park Inn by Radisson Pulkovskaya] hotel <br />
* Pobedy Square 1<br />
* 196240 St. Petersburg, Russia<br />
<br />
== Registration ==<br />
<br />
The best way to register is by using the [http://www.eage.org/events/index.php?evp=10534&ActiveMenu=10&Opendivs=s3,s10 online registration form]. You can also register using the [http://www.eage.org/images/cms/files/Education/16273-STP14%20registration%20form.pdf PDF form] and returning it to:<br />
<br />
EAGE Europe Office<br><br />
Registration Department<br><br />
PO Box 59<br><br />
3990 DB Houten<br><br />
The Netherlands<br><br />
Tel.: +31 88 9955055<br><br />
Fax: +31 306343534<br><br />
E-mail: registration@eage.org<br><br />
<br />
The workshop registration price varies from €75 for early-registration EAGE student member to €230 for late-registration non-member.<br />
<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 />
* '''Tariq Alkhalifah''' is currently a Professor of Geophysics at KAUST in Saudi Arabia. He graduated with a PhD from Colorado School of Mines, Golden, Colorado, in 1996, and served afterwards as a Post Doc at Stanford University. He used to be a devote SU Unix follower for most of his research carrier even as a Post Doc at Stanford (SEPlib people), but have recently seen the light and converted to Madagascar. https://sites.google.com/a/kaust.edu.sa/tariq/<br />
* '''Luke Decker''' is a Master's student at the Jackson School of Geosciences, the University of Texas at Austin, studying under Professor Sergey Fomel. He holds undergraduate degrees in Physics (2008) from Whitman College in Walla Walla, Washington, and Geophysics (2011) from Western Washington University in Bellingham, Washington. He worked for several years as a mudlogger for King Canyon Buffalo, Inc., and his research focus is seismic diffraction imaging.<br />
* '''Paul Sava''' is an Associate Professor of Geophysics and a member of the Center for Wave Phenomena at Colorado School of Mines. He holds an Engineering degree in Geophysics (1995) from the University of Bucharest, an M.Sc. (1998) and a Ph.D. (2004) in Geophysics from Stanford University. His research interests are in wavefield seismic imaging, stochastic imaging and inversion, computational methods for wave propagation, numeric optimization and high performance computing. http://newton.mines.edu/paul/home.php</div>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=Petersburg_2014&diff=2761Petersburg 20142014-02-05T00:52:17Z<p>Psava: /* Agenda */</p>
<hr />
<div>[[Image:Petersburg.jpg|center|frame]]<br />
<br />
<center><big>'''Madagascar Workshop at EAGE-St.Petersburg 2014'''</big></center><br />
<br />
&nbsp;<br />
<br />
== Agenda ==<br />
<br />
The tentative 2013 ASEG Madagascar workshop agenda is the following:<br />
<br />
{| border="1" cellpadding="5" cellspacing="0" <br />
! style="background:#ffdead;" align="center" | TIME <br />
! style="background:#ffdead;" align="center" | ACTIVITY<br />
|-<br />
| 9:00-10:00am <br />
| Welcome and Background Installation<br />
<br> Speaker: Sergey Fomel<br />
|-<br />
| 10:00-10:45am <br />
| Madagascar Fundamentals <br />
<br> Speaker: ?<br />
|-<br />
! style="background:#efefef;" | 10:45-11:00am <br />
! style="background:#efefef;" | BREAK <br />
|-<br />
| 11:00-11:45am <br />
| Workflow I: An introductory exercise <br />
<br> Speaker: ?<br />
|-<br />
| 11:45-12:30pm <br />
| Workflow II: Finite-differences modeling & migration<br />
<br> Speaker: Paul Sava <br />
|-<br />
! style="background:#efefef;" | 12:30-1:30pm <br />
! style="background:#efefef;" | LUNCH <br />
|-<br />
| 1:30-3:15pm <br />
| Workflow III: Field seismic data processing example<br />
<br> Speaker: ?<br />
|-<br />
| 3:15-3:30pm <br />
| BREAK <br />
|-<br />
| 3:30-4:15pm <br />
| Developing Madagascar programs <br />
<br> Speaker: ?<br />
|-<br />
| 4:15-5:00pm <br />
| Contributing to Madagascar <br />
<br> Speaker: Sergey Fomel<br />
|-<br />
| 5:00-5:30pm <br />
| Discussion and wrap up<br />
|}<br />
<br />
== Location ==<br />
<br />
The Congress Centre of the [http://www.parkinn.com/hotelpulkovskaya-stpetersburg Park Inn by Radisson Pulkovskaya] hotel <br />
* Pobedy Square 1<br />
* 196240 St. Petersburg, Russia<br />
<br />
== Registration ==<br />
<br />
The best way to register is by using the [http://www.eage.org/events/index.php?evp=10534&ActiveMenu=10&Opendivs=s3,s10 online registration form]. You can also register using the [http://www.eage.org/images/cms/files/Education/16273-STP14%20registration%20form.pdf PDF form] and returning it to:<br />
<br />
EAGE Europe Office<br><br />
Registration Department<br><br />
PO Box 59<br><br />
3990 DB Houten<br><br />
The Netherlands<br><br />
Tel.: +31 88 9955055<br><br />
Fax: +31 306343534<br><br />
E-mail: registration@eage.org<br><br />
<br />
The workshop registration price varies from €75 for early-registration EAGE student member to €230 for late-registration non-member.<br />
<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 />
* '''Tariq Alkhalifah'''<br />
* '''Luke Decker'''<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 and worked previously at the Institute of Geophysics in Russia and the Lawrence Berkeley National Laboratory. Sergey started work on Madagascar (at that time named RSF for Regularly Sampled Format) in 2003. http://www.jsg.utexas.edu/researcher/sergey_fomel/<br />
* '''Paul Sava''' is an Associate Professor of Geophysics and a member of the Center for Wave Phenomena at Colorado School of Mines. He holds an Engineering degree in Geophysics (1995) from the University of Bucharest, an M.Sc. (1998) and a Ph.D. (2004) in Geophysics from Stanford University where he was a member of the Stanford Exploration Project. His research interests are in wavefield seismic imaging, stochastic imaging and inversion, computational methods for wave propagation, numeric optimization and high performance computing. http://newton.mines.edu/paul/home.php<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>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=Petersburg_2014&diff=2760Petersburg 20142014-02-05T00:32:51Z<p>Psava: /* Agenda */</p>
<hr />
<div>[[Image:Petersburg.jpg|center|frame]]<br />
<br />
<center><big>'''Madagascar Workshop at EAGE-St.Petersburg 2014'''</big></center><br />
<br />
&nbsp;<br />
<br />
== Agenda ==<br />
<br />
The tentative 2013 ASEG Madagascar workshop agenda is the following:<br />
<br />
{| border="1" cellpadding="5" cellspacing="0" <br />
! style="background:#ffdead;" align="center" | TIME <br />
! style="background:#ffdead;" align="center" | ACTIVITY<br />
|-<br />
| 9:00-10:00am <br />
| Welcome and Background Installation<br />
<br> Speaker: Sergey Fomel<br />
|-<br />
| 10:00-10:45am <br />
| Madagascar Fundamentals <br />
<br> Speaker: ?<br />
|-<br />
! style="background:#efefef;" | 10:45-11:00am <br />
! style="background:#efefef;" | BREAK <br />
|-<br />
| 11:00-11:45am <br />
| Workflow I: An introductory exercise <br />
<br> Speaker: ?<br />
|-<br />
| 11:45-12:30pm <br />
| Workflow II: Finite-differences modeling & migration<br />
<br> Speaker: Paul Sava <br />
|-<br />
! style="background:#efefef;" | 12:30-1:30pm <br />
! style="background:#efefef;" | LUNCH <br />
|-<br />
| 1:30-3:15pm <br />
| Workflow III: Field seismic data processing example<br />
<br> Speaker: ?<br />
|-<br />
| 3:15-3:30pm <br />
| BREAK <br />
|-<br />
| 3:30-4:15pm <br />
| Developing your own Madagascar programs <br />
<br> Speaker: ?<br />
|-<br />
| 4:15-5:00pm <br />
| Contributing to Madagascar <br />
<br> Speaker: Sergey Fomel<br />
|-<br />
| 5:00-5:30pm <br />
| Discussion and wrap up<br />
|}<br />
<br />
== Location ==<br />
<br />
The Congress Centre of the [http://www.parkinn.com/hotelpulkovskaya-stpetersburg Park Inn by Radisson Pulkovskaya] hotel <br />
* Pobedy Square 1<br />
* 196240 St. Petersburg, Russia<br />
<br />
== Registration ==<br />
<br />
The best way to register is by using the [http://www.eage.org/events/index.php?evp=10534&ActiveMenu=10&Opendivs=s3,s10 online registration form]. You can also register using the [http://www.eage.org/images/cms/files/Education/16273-STP14%20registration%20form.pdf PDF form] and returning it to:<br />
<br />
EAGE Europe Office<br><br />
Registration Department<br><br />
PO Box 59<br><br />
3990 DB Houten<br><br />
The Netherlands<br><br />
Tel.: +31 88 9955055<br><br />
Fax: +31 306343534<br><br />
E-mail: registration@eage.org<br><br />
<br />
The workshop registration price varies from €75 for early-registration EAGE student member to €230 for late-registration non-member.<br />
<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 />
* '''Tariq Alkhalifah'''<br />
* '''Luke Decker'''<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 and worked previously at the Institute of Geophysics in Russia and the Lawrence Berkeley National Laboratory. Sergey started work on Madagascar (at that time named RSF for Regularly Sampled Format) in 2003. http://www.jsg.utexas.edu/researcher/sergey_fomel/<br />
* '''Paul Sava''' is an Associate Professor of Geophysics and a member of the Center for Wave Phenomena at Colorado School of Mines. He holds an Engineering degree in Geophysics (1995) from the University of Bucharest, an M.Sc. (1998) and a Ph.D. (2004) in Geophysics from Stanford University where he was a member of the Stanford Exploration Project. His research interests are in wavefield seismic imaging, stochastic imaging and inversion, computational methods for wave propagation, numeric optimization and high performance computing. http://newton.mines.edu/paul/home.php<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>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=Petersburg_2014&diff=2759Petersburg 20142014-02-05T00:19:25Z<p>Psava: /* Agenda */</p>
<hr />
<div>[[Image:Petersburg.jpg|center|frame]]<br />
<br />
<center><big>'''Madagascar Workshop at EAGE-St.Petersburg 2014'''</big></center><br />
<br />
&nbsp;<br />
<br />
== Agenda ==<br />
<br />
The tentative 2013 ASEG Madagascar workshop agenda is the following:<br />
<br />
{| border="1" cellpadding="5" cellspacing="0" <br />
! style="background:#ffdead;" align="center" | TIME <br />
! style="background:#ffdead;" align="center" | ACTIVITY<br />
|-<br />
| 9:00-9:30am <br />
| Welcome and Background Installation<br />
<br><br />
[http://www.ahay.org/wikilocal/docs/Madagascar_Installation.pdf Installation Handout] (204K)<br />
<br><br />
[http://www.ahay.org/wikilocal/docs/Madagascar-ASEG.pdf Slides] (15M)<br />
|-<br />
| 9:30-10:00am <br />
| [http://opendtect.org/ OpendTect] and Madagascar (Jan Stellingwerf)<br />
|-<br />
| 10:00-10:45am <br />
| Madagascar Fundamentals <br />
<br><br />
[http://www.ahay.org/wikilocal/docs/Fundamentals-ASEG.pdf Slides] (308K)<br />
|-<br />
! style="background:#efefef;" | 10:45-11:00am <br />
! style="background:#efefef;" | BREAK <br />
|-<br />
| 11:00-11:45am <br />
| Building workflows I: An introductory exercise <br />
<br><br />
[http://www.ahay.org/wikilocal/docs/4-ASSIGNMENT.pdf Handout] (88K)<br />
|-<br />
| 11:45-12:30pm <br />
| Building workflows II: Acoustic/Elastic modelling <br />
<br><br />
[http://www.ahay.org/RSF/book/rsf/school/modeling.html SConstruct]<br />
<br><br />
[http://www.ahay.org/wikilocal/docs/Modeling-ASEG.pdf Handout] (711K)<br />
|-<br />
! style="background:#efefef;" | 12:30-1:30pm <br />
! style="background:#efefef;" | LUNCH <br />
|-<br />
| 1:30-3:15pm <br />
| Field seismic data processing example<br />
<br><br />
[http://www.ahay.org/RSF/book/rsf/school/data.html SConstruct]<br />
<br><br />
[http://www.ahay.org/wikilocal/docs/school2013-Field_data_example.pdf Slides] (4.2M)<br />
|-<br />
| 3:15-3:30pm <br />
| BREAK <br />
|-<br />
| 3:30-4:15pm <br />
| Developing your own Madagascar programs <br />
<br><br />
[http://www.ahay.org/wikilocal/docs/7-LECTURE.pdf Slides] (200K)<br />
|-<br />
| 4:15-4:40pm <br />
| Contributing to Madagascar <br />
<br><br />
[http://www.ahay.org/wikilocal/docs/Contributing-ASEG.pdf Slides] (4.7M)<br />
|-<br />
| 4:40-5:00pm <br />
| Discussion and wrap up<br />
|}<br />
<br />
== Location ==<br />
<br />
The Congress Centre of the [http://www.parkinn.com/hotelpulkovskaya-stpetersburg Park Inn by Radisson Pulkovskaya] hotel <br />
* Pobedy Square 1<br />
* 196240 St. Petersburg, Russia<br />
<br />
== Registration ==<br />
<br />
The best way to register is by using the [http://www.eage.org/events/index.php?evp=10534&ActiveMenu=10&Opendivs=s3,s10 online registration form]. You can also register using the [http://www.eage.org/images/cms/files/Education/16273-STP14%20registration%20form.pdf PDF form] and returning it to:<br />
<br />
EAGE Europe Office<br><br />
Registration Department<br><br />
PO Box 59<br><br />
3990 DB Houten<br><br />
The Netherlands<br><br />
Tel.: +31 88 9955055<br><br />
Fax: +31 306343534<br><br />
E-mail: registration@eage.org<br><br />
<br />
The workshop registration price varies from €75 for early-registration EAGE student member to €230 for late-registration non-member.<br />
<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 />
* '''Tariq Alkhalifah'''<br />
* '''Luke Decker'''<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 and worked previously at the Institute of Geophysics in Russia and the Lawrence Berkeley National Laboratory. Sergey started work on Madagascar (at that time named RSF for Regularly Sampled Format) in 2003. http://www.jsg.utexas.edu/researcher/sergey_fomel/<br />
* '''Paul Sava''' is an Associate Professor of Geophysics and a member of the Center for Wave Phenomena at Colorado School of Mines. He holds an Engineering degree in Geophysics (1995) from the University of Bucharest, an M.Sc. (1998) and a Ph.D. (2004) in Geophysics from Stanford University where he was a member of the Stanford Exploration Project. His research interests are in wavefield seismic imaging, stochastic imaging and inversion, computational methods for wave propagation, numeric optimization and high performance computing. http://newton.mines.edu/paul/home.php<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>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=Petersburg_2014&diff=2758Petersburg 20142014-02-05T00:15:14Z<p>Psava: /* Instructors */</p>
<hr />
<div>[[Image:Petersburg.jpg|center|frame]]<br />
<br />
<center><big>'''Madagascar Workshop at EAGE-St.Petersburg 2014'''</big></center><br />
<br />
&nbsp;<br />
<br />
== Agenda ==<br />
<br />
TBA<br />
<br />
== Location ==<br />
<br />
The Congress Centre of the [http://www.parkinn.com/hotelpulkovskaya-stpetersburg Park Inn by Radisson Pulkovskaya] hotel <br />
* Pobedy Square 1<br />
* 196240 St. Petersburg, Russia<br />
<br />
== Registration ==<br />
<br />
The best way to register is by using the [http://www.eage.org/events/index.php?evp=10534&ActiveMenu=10&Opendivs=s3,s10 online registration form]. You can also register using the [http://www.eage.org/images/cms/files/Education/16273-STP14%20registration%20form.pdf PDF form] and returning it to:<br />
<br />
EAGE Europe Office<br><br />
Registration Department<br><br />
PO Box 59<br><br />
3990 DB Houten<br><br />
The Netherlands<br><br />
Tel.: +31 88 9955055<br><br />
Fax: +31 306343534<br><br />
E-mail: registration@eage.org<br><br />
<br />
The workshop registration price varies from €75 for early-registration EAGE student member to €230 for late-registration non-member.<br />
<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 />
* '''Tariq Alkhalifah'''<br />
* '''Luke Decker'''<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 and worked previously at the Institute of Geophysics in Russia and the Lawrence Berkeley National Laboratory. Sergey started work on Madagascar (at that time named RSF for Regularly Sampled Format) in 2003. http://www.jsg.utexas.edu/researcher/sergey_fomel/<br />
* '''Paul Sava''' is an Associate Professor of Geophysics and a member of the Center for Wave Phenomena at Colorado School of Mines. He holds an Engineering degree in Geophysics (1995) from the University of Bucharest, an M.Sc. (1998) and a Ph.D. (2004) in Geophysics from Stanford University where he was a member of the Stanford Exploration Project. His research interests are in wavefield seismic imaging, stochastic imaging and inversion, computational methods for wave propagation, numeric optimization and high performance computing. http://newton.mines.edu/paul/home.php<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>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=Advanced_Installation&diff=2344Advanced Installation2012-07-28T18:45:01Z<p>Psava: /* Mac OS X */</p>
<hr />
<div>[[Image:Fotolia_419157_XS.jpg|right|]]<br />
Before reading this document, please familiarize yourself with the [[Installation|short Installation guide]].<br />
=What the installation process does=<br />
The term "installation" in the title is used for brevity, and it actually covers all three steps: configuration, build and install.<br />
# Configure: determine what tools are available on the system and how they should be used to built the software. Creates a layer of abstraction so that the build is platform-independent. Should ideally either solve or flag all problems, so that the build either works, or does not proceed at all.<br />
# Build: compiles the software and documentation using RSFSRC/build as a "workplace"<br />
# Install: moves the compiled executables and the documentation to the final locations in $RSFROOT, sometimes changing filenames. Kept separate from build so that it can be done by root, and to avoid build failures leaving junk files all over the system.<br />
A successful installation will have created in <tt>$RSFROOT</tt> the following directories:<br />
* <tt>bin/</tt>: executable programs<br />
* <tt>doc/</tt>: auto-generated HTML documentation<br />
* <tt>include/</tt>: header files with info on library procedures; fonts<br />
* <tt>lib/</tt>: libraries and Python modules<br />
<br />
=Old (1.0 and 1.1) version installation=<br />
<br />
Use <tt>$RSFROOT/etc/madagascar/</tt> as the location of <tt>env</tt> scripts instead of <tt>$RSFROOT/share/madagascar/etc/</tt>.<br />
<br />
=Old (0.9.9) version installation=<br />
<br />
====Environment variables====<br />
Example configuration for <tt>bash</tt>:<br />
<bash><br />
export RSFROOT=/usr/local/rsf # directory where Madagascar will be installed. <br />
if [ -n "$PYTHONPATH" ]; then<br />
export PYTHONPATH=${PYTHONPATH}:$RSFROOT/lib<br />
else<br />
export PYTHONPATH=$RSFROOT/lib<br />
fi<br />
export PATH=$RSFROOT/bin:$PATH<br />
export DATAPATH=/var/tmp/<br />
export MANPATH=$RSFROOT/share/man:$(manpath)<br />
export LD_LIBRARY_PATH=$RSFROOT/lib:$LD_LIBRARY_PATH<br />
</bash><br />
Notice the slash at the end of the <tt>DATAPATH</tt> variable. <br />
<br />
Example configuration for <tt>csh</tt> and <tt>tcsh</tt>:<br />
<pre><br />
setenv RSFROOT /usr/local/rsf<br />
if ($?PYTHONPATH) then<br />
setenv PYTHONPATH ${PYTHONPATH}:$RSFROOT/lib<br />
else<br />
setenv PYTHONPATH $RSFROOT/lib<br />
endif<br />
set path = ($RSFROOT/bin $path)<br />
setenv DATAPATH /var/tmp/<br />
setenv MANPATH $RSFROOT/share/man:`manpath`<br />
setenv LD_LIBRARY_PATH $RSFROOT/lib:$LD_LIBRARY_PATH<br />
</pre><br />
Notice the backticks surrounding the call to <tt>manpath</tt>.<br />
<br />
Be aware that on some systems /var/tmp gets automatically cleaned at some intervals, so if you want to keep your data binaries for a long time, set <tt>DATAPATH</tt> to another location where you have write access and that allows large files.<br />
<br />
====Software construction====<br />
<br />
#Configuration. Change to the top source directory and run <pre>./configure</pre> You can examine the <tt>config.py</tt> file that this command generates. Additional options are available. You can obtain a full list of customizable variables by running <tt>scons -h</tt>. For example, to install C++ and Fortran-90 API bindings in addition to the basic package, run <pre>./configure API=c++,fortran-90</pre> <br />
#Building and installing the package. Run <tt>scons install</tt> or the following two commands in succession: <pre>make; make install</pre> or <pre>scons; scons install</pre> If you need "root" privileges for installing under <tt>&#36;RSFROOT</tt>, you may need to run <pre>su; scons install </pre> or <pre>sudo scons install</pre><br />
#Cleaning. To clean all intermediate files generated by SCons, run <pre>make clean</pre> or <pre>scons -c</pre><br />
<br />
=Prerequisites=<br />
Basic prerequisites are described in the [[Installation|short Installation guide]]. Here are some additional details. <br />
==Compilers==<br />
Madagascar has been built successfully with the following compilers, and possibly with others:<br />
* gcc<br />
* Intel (icc/ifort)<br />
* open64<br />
* clang<br />
* cc (Solaris)<br />
<br />
==Python and SCons==<br />
As described below under [[Advanced Installation#Platform-specific installation advice | Platform-specific installation advice]], Madagascar supports the oldest non-deprecated Python version currently supported by the latest stable version of [http://scons.org/ SCons]. If your version of Python is older and you experience problems you should probably [http://www.python.org/ upgrade].<br />
<br />
Madagascar includes the latest stable version of SCons and the configure scripts will try to install it for you in RSFROOT if you don't have it already. However, if you have an older version of SCons the configure scripts will not try to install the newer version. Your older version might work fine, but Madagascar attempts to support only the latest stable version of SCons, so if you have problems you should upgrade.<br />
<br />
To install the SCons bundled with Madagascar go to <tt>RSFSRC/scons</tt>, unpack the tar file, and type<br />
<br />
<bash><br />
python setup.py install<br />
</bash><br />
<br />
This will install SCons in the standard location. You might need root privileges. If you don't have root privileges, or you don't want to interfere with the system SCons you can install it somewhere else with a --prefix option. A logical choice is to put it in RSFROOT like this:<br />
<br />
<bash><br />
python setup.py install --prefix=$RSFROOT<br />
</bash><br />
<br />
==Location==<br />
As long as you set the environment variables and directory permissions correctly, it does not matter in what part of your filesystem you place the install. If you have the luxury of installing anywhere, it is good practice to follow the [http://en.wikipedia.org/wiki/Filesystem_Hierarchy_Standard Filesystem Hierarchy Standard] and either:<br />
# Install everything (including <tt>figs</tt> if you do testing) under <tt>/usr/local/rsf</tt>, with the source tree in <tt>/usr/local/rsf/src</tt>, OR <br />
# Put the source tree in <tt>/usr/local/src/rsf</tt>, and specify <tt>RSFROOT=/usr/local</tt>, so that header files and binaries go in <tt>/usr/local/bin</tt> and <tt>/usr/local/include</tt>. To follow the standard, before installing set <tt>RSFDOC=/usr/local/share/rsf/doc</tt> and create the appropriate directories. The auto-generated HTML documentation will get put there. Also, if installed, the figs directory for testing should be <tt>/usr/local/share/rsf/figs/</tt>.<br />
# Package Madagascar (i.e. build a RPM, etc) and install it in the default locations. For RPMs, those are as like the ones from the previous option, just directly in the <tt>/usr/</tt> hierarchy, instead of in the <tt>/usr/local/</tt> one.<br />
<br />
==Disk space==<br />
At present (Feb 2007, r2530), the source directory containing the build tree from the development version was approx. 200Mb, the full installation (<tt>bin/</tt>, <tt>doc/</tt>, <tt>include/</tt> and <tt>lib</tt>) is 31Mb, and <tt>figs/</tt> (the optional directory if you want to do testing) is about 10 Gb. The stable version is significantly smaller.<br />
<br />
The only Madagascar-related directory where disk space can be an issue is <tt>$DATAPATH</tt>. Real 3-D seismic datasets can be measured in Terabytes. Buggy programs/processing flows can fill up <tt>$DATAPATH</tt>. A real problem are "disk memory leaks" -- removing header files with anything else than <tt>sfrm</tt> will leave the binaries intact. Crashed jobs which start to write to binary but never get to write the header also produce "leaks". Experience has shown that over time <tt>$DATAPATH</tt> inexorably fills up. You may need to <br />
# keep irreplaceable data and expensive results in a separate place;<br />
# remove the oldest files in <tt>$DATAPATH</tt> whenever the amount of free space declines under a preset threshold.<br />
<br />
==Dependencies==<br />
Some platforms feature complete lists of dependencies. See [[Advanced Installation#Platform-specific installation advice | Platform-specific installation advice]] for details.<br />
===C++ API===<br />
A C++ compiler. SCons is smart and will try to find it for you. If it does not work specify the path to your compiler in the <tt>CXX</tt> environment variable (can be passed as an option to the configuration script, like the <tt>API</tt> one).<br />
===F77 API===<br />
A Fortran 77 compiler. If SCons does not find one, then you can either specify its path through the <tt>F77</tt> variable, or if the executable is in your path, add its name to the list of F77 compilers in <tt>RSFSRC/configure.py</tt> .<br />
===F90 API===<br />
Same as for Fortran 77 &ndash; just substitute <tt>F90</tt>. If using the <tt>gfortran</tt> compiler, make sure to get [http://gcc.gnu.org/wiki/GFortranBinaries the latest version]. If you have more than one compiler installed on your system, specify the desired one at configuration time:<br />
<bash><br />
./configure API=f90 F90=/path/to/preferred/compiler<br />
</bash><br />
<br />
===Java API===<br />
There are two styles of API, old (1.0 release and previous) and new. The two APIs are not compatible with each other.<br />
<br />
The "old" interface requires the Mines Java Toolkit for fast Java file IO. The Mines JTK, is an open-source Java package that can be downloaded from [http://inside.mines.edu/~dhale/jtk/ Mines JTK]. Currently, the "old" interface will also build alongside the new one if the MINESJTK environment variable exists, and can be used as was previously.<br />
<br />
To install the new API, you need the (Oracle) JDK. Set your JAVA_HOME environment variable to the location of the jdk (on Ubuntu 10.04 this is: /usr/lib/jvm/java-6-openjdk), then reconfigure (./configure API=java ...) and reinstall. <br />
<br />
Ignore the SWIG warnings (there are lots). <br />
<br />
Make sure to set your LD_LIBRARY_PATH to $RSFROOT/lib .<br />
<br />
If you want to include additional Java packages, you can set them using your shell's CLASSPATH variable. This environment variable is now automatically passed onto all Java classes in SCons.<br />
<br />
The installation can be tested using the example demonstrating the new API in api/java/test .<br />
<br />
===Matlab API===<br />
Besides Matlab itself, you need Mex, which compiles C code into regular Matlab functions. Use the <tt>MATLAB</tt> and <tt>MEX</tt> environment variables to specify their paths if they are installed, but not found.<br />
===Octave API===<br />
The Octave function compiler (<tt>mkoctfile</tt>) is sometimes bundled in a separate package, so it may be missing from the Octave installation.<br />
<br />
===Python API===<br />
This API requires [http://www.swig.org/ SWIG], [http://numpy.scipy.org/ numpy] and the Python development kit. Numpy requires Python 2.4 or newer (i.e. RHEL 5 or newer). However, these dependencies are unnecessary for the common case when Python is just used as [http://en.wikipedia.org/wiki/Glue_language glue] to create chains of programs, and it only needs to read the RSF header, and not the binary. To allow Python [http://en.wikipedia.org/wiki/Meta-programs metaprograms] in madagascar to function, and programming in this style to be done, a fallback development kit implementing only the header-related functionality will be installed in the lack of these dependencies.<br />
<br />
===Python modules in user space===<br />
Python is an evolving language. Many large systems have old versions for stability reasons, and administrators of such large systems tend to not install all software users may wish, and to not allow access to rpm either. To install a module in your user space, download the tarball, unzip it, cd into the directory and run: <br />
<br />
<pre>python setup.py install --prefix=/path/to/your/place</pre><br />
<br />
The installer will create a subdirectory named <tt>lib</tt>, or <tt>lib64</tt> under the directory above. These <tt>lib*</tt> dirs will have a directory named <tt>python</tt>, or <tt>python2.3</tt> for example, and those will have a subdirectory named <tt>site-packages</tt>. Add all paths to these <tt>site-packages</tt> subdirectories in your <tt>PYTHONPATH</tt> environment variable. Some (<tt>numpy</tt>) may create a <tt>bin</tt> directory that needs to be added to <tt>PATH</tt>.<br />
<br />
=Environment variables=<br />
Besides the variables defined in env.sh or env.csh (see the [[Installation|short Installation guide]]), Madagascar programs may read the variables below. They usually have reasonable defaults and were introduced just to provide more power to the advanced user.<br />
<br />
For future documentation writers: the environment variables read by Madagascar that have not been documented below can be found by running the script <tt>$RSFSRC/admin/find_env_var.py</tt>. If the script does not exist or does not work, a summary of all environment variable calls can be obtained by going to $RSFSRC, temporarily moving the directory <tt>build/</tt> outside RSFSRC, and typing<br />
<bash><br />
grep environ.get *.py */*.py */*/*.py */*/*/*.py<br />
grep getenv */*.c */*/*.c */*/*/*.c<br />
</bash><br />
<br />
==Used by the Madagascar core==<br />
<br />
{|class="wikitable" align="center" cellspacing="0" border="1"<br />
|-<br />
! colspan="3" style="background:#ffdead;"|Variables introduced by Madagascar's non-graphic programs<br />
|-<br />
| '''Name''' || '''Default''' || Meaning<br />
|-<br />
| RSF_DATASERVER || <nowiki>ftp://egl.beg.utexas.edu/</nowiki> || Data server for benchmark datasets<br />
|-<br />
| RSFDOC || $RSFROOT/doc || Directory for the HTML self-doc<br />
|-<br />
| RSFFIGS || $RSFROOT/figs || Directory with figures for testing examples in $RSFSRC/book<br />
|-<br />
|-<br />
| RSFALTFIGS || $RSFFIGS || Alternate directory with figures for testing examples not in $RSFSRC/book<br />
|-<br />
| RSFMEMSIZE || 100 || Maximum RAM (Mb) to be used by some programs <br />
|-<br />
| RSFSRC || undefined || Root of the Madagascar source tree<br />
|-<br />
| TMPDATAPATH || $DATAPATH || Datapath for temporary files on local disk.<br />
|-<br />
| LATEX2HTML || undefined || LateX2HTML customization directory<br />
|}<br />
<br />
<br />
{|class="wikitable" align="center" cellspacing="0" border="1"<br />
|-<br />
! colspan="3" style="background:#ffdead;"|Variables introduced by Madagascar graphics programs <br />
|-<br />
| '''Name''' || '''Default''' || Meaning<br />
|-<br />
| DEFAULT_PAPER_SIZE || "letter" || For pspen. Other options: legal, a3, a4, a5.<br />
|-<br />
| FATMULT || ? || Fatness multiplication factor. <br />
|-<br />
| GIFBORDER || 0.25 || For vplot2gif (spacing)<br />
|-<br />
| GIFDELAY || 100 || For vplot2gif (for animations)<br />
|-<br />
| IMAGE_TYPE || 'png' || Icon type for LateX2HTML <br />
|-<br />
| PATTERNMULT || None || Pattern multiplication factor <br />
|-<br />
| PLOTSTYLE || None || Used in vplot<br />
|-<br />
| PPI || 75 || For vplot2gif (screen resolution)<br />
|-<br />
| PPMSCALE || 1 || For vplot2gif<br />
|-<br />
| PSBORDER || 0.05 || For vplot2eps (border around the plot)<br />
|-<br />
| PSPRINTER || postscript or colorps || For pspen<br />
|-<br />
| PSTEXPENOPTS || color=n fat=1 fatmult=1.5 invras=y || Other vplot2eps options <br />
|-<br />
| VPLOTFONTDIR || $RSFROOT/include || Dir with backup fonts in case the runtime-loaded vplot fonts are not found<br />
|-<br />
| VPLOTSPOOLDIR || /tmp || Where to put vplot tmp files<br />
|-<br />
| WSTYPE || "default" || Workstation type.<br />
|}<br />
<br />
<br />
{|class="wikitable" align="center" cellspacing="0" border="1"<br />
|-<br />
! colspan="2" style="background:#ffdead;"| Variables set by OS/other apps, read-only to Madagascar<br />
|-<br />
| '''Name''' || '''Primarily used/set by'''<br />
|-<br />
| CWPROOT || Seismic Unix<br />
|-<br />
| DISPLAY || Operating System (OS)<br />
|-<br />
| HOME || OS<br />
|-<br />
| LD_LIBRARY_PATH || linker<br />
|-<br />
| MATLABPATH || Matlab<br />
|-<br />
| XAUTHORITY || X-Windows<br />
|}<br />
<br />
==Used by the Madagascar build process and parallelization utilities==<br />
Type <tt>scons -h</tt> in RSFSRC to get a list of environment variables that affect the build process, with explanations, defaults and actual values. Below are more detailed explanations for some of them:<br />
* <tt>RSF_THREADS</tt>: used by <tt>pscons</tt> to determine on how many threads to run on the local node, overriding the number of threads detected by Madagascar<br />
* <tt>RSF_CLUSTER</tt>: used by <tt>pscons</tt> to determine on which cluster nodes to run, and on how many CPUs<br />
<br />
==Used by the Matlab API==<br />
To use the Matlab API, you need to add <tt>$RSFROOT/lib</tt> to <tt>MATLABPATH</tt><br />
==Used by the Octave API==<br />
To use the Octave API, you need to add <tt>$RSFROOT/lib</tt> to Octave's path. Determine Octave's version with<br />
<bash><br />
octave -v | head -1<br />
</bash><br />
If your version is lower than 2.9.6, type at a Unix command line:<br />
<bash><br />
echo 'LOADPATH = "::$RSFROOT/lib/octave"' >> ~/.octaverc<br />
</bash><br />
For later versions, use:<br />
<bash><br />
echo 'addpath([getenv("RSFROOT") "/lib/octave"])' >> ~/.octaverc<br />
</bash><br />
==Used by the Java API==<br />
New-style (post-1.0) API: Needs <tt>JAVA_HOME</tt><br />
<br />
Old-style API (1.0 and before): The path to the downloaded Mines JTK must be specified in the MINESJTK environment variable in order to install the Java API. For example:<br />
<bash><br />
export MINESJTK=/home/user/edu_mines_jtk.jar<br />
</bash><br />
<br />
==RSFROOT for NFS-shared user home directories==<br />
Heterogeneous networks with user home directories shared through [http://en.wikipedia.org/wiki/Network_File_System_(protocol) NFS] are quite common in many institutions. In addition, even when the architecture is the same (i.e. 64-bit) and the operating system is the same (i.e. [http://en.wikipedia.org/wiki/RHEL RHEL]), the difference between operating system versions may be very significant because clusters may run legacy versions, while desktop workstations may run the latest-and-greatest (even beta), and entirely different Madagascar versions may be needed to support both. <br />
<br />
One possible solution of detecting the distribution version and architecture and setting RSFROOT appropriately is shown below. In the example network, all RHEL4 machines have the same architecture, but there are RHEL 3 machines with several architectures:<br />
<bash><br />
REDHAT_RELEASE=`awk -F'release' '{ print $2 }' /etc/redhat-release | awk -F' ' '{ print $1 }'`<br />
<br />
RSFROOT=/usr/local/rsf/rhel$REDHAT_RELEASE<br />
<br />
if [ $REDHAT_RELEASE == '4' ] ; then<br />
export RSFROOT<br />
elif [ $REDHAT_RELEASE == '3' ] ; then<br />
export RSFROOT=$RSFROOT/$ARCH<br />
fi<br />
</bash><br />
Of course, the Madagascar administrator will have to download appropriate versions of Madagascar to each $RSFROOT, and compile them on the appropriate system.<br />
<br />
If you have many kinds of systems to maintain, with multiple versions of Madagascar, and users have more than one shell, you may find it easy to outsource the complex logic to the easy-to-debug Python, i.e.:<br />
<br />
<bash><br />
export RSFROOT=`$M8R_SETUP/get_rsfroot.py`<br />
export PYTHONPATH=`$M8R_SETUP/edit_pythonpath.py`<br />
export PATH=`$M8R_SETUP/edit_path.py`<br />
</bash><br />
<br />
and similarly for (t)csh. The Python scripts determine the operating system and its version, determine the machine name, and simply print to stdout the desired string.<br />
<br />
==Eclipse + Pydev==<br />
If you use [http://eclipse.org/ Eclipse] with [http://pydev.org/ Pydev], [http://pydev.org/manual_101_interpreter.html#id2 configure the interpreter] by adding <tt>$RSFROOT/lib</tt> to the <tt>PYTHONPATH</tt> for your chosen interpreter.<br />
<br />
=Platform-specific installation advice=<br />
==Supported platforms==<br />
Madagascar attempts to support any [http://en.wikipedia.org/wiki/POSIX POSIX-compliant] operating system demanded by users. For systems that bundle Python (i.e. Linux distributions, BSDs), backwards compatibility will attempt to cover those systems that were bundled with the oldest non-deprecated Python version currently supported by the latest stable version of [http://scons.org/ SCons]. For example, in early 2009 the stable SCons release (1.2) supported Python 2.2 or newer. [http://distrowatch.com/table.php?distribution=redhat Python 2.2 was bundled by RHEL3], so RHEL 3 and newer are supported. <br />
<br />
Attempts for backward compatibility with a given operating system are also stopped if the operating system itself becomes unsupported. For example, Python 2.2 was bundled by Fedora 1 and newer, but in January 2010 only Fedora 11 and 12 are actively maintained. Thus, in January 2010 Madagascar was not attempting to support Fedora 1, even though it included Python 2.2.<br />
<br />
Please keep in mind that the above statements constitute only general guidelines for what will be attempted, and do not constitute in any way a warranty of support. An application of the above guidelines to some Linux distributions follows:<br />
<br />
'''Support info'''<br />
{| class="wikitable" align="center" cellspacing="0" border="1"<br />
|-<br />
! style="background:#ffdead;" | Distribution<br />
! style="background:#ffdead;" | Life Cycle<br />
! style="background:#ffdead;" | Supported versions<br />
|-<br />
| RHEL/CentOS/Scientific Linux<br />
| [https://www.redhat.com/security/updates/errata/ 7 years]<br />
| <br />
* 6 until 2017-11-30<br />
* 5 until 2014-03-31<br />
* 4 until 2012-02-29<br />
|-<br />
| Fedora<br />
| [http://fedoraproject.org/wiki/Fedora_Release_Life_Cycle Release X maintained until one month after the release of X+2]<br />
| <br />
* 15 until 2012-06-24<br />
* 14 until 2011-12-02<br />
|-<br />
| Ubuntu<br />
| Releases every 6 mo, maintained for 1.5 yrs; LTS versions every 2 yrs, maintained for 5 yrs<br />
| <br />
* 11.10 until end of April 2013<br />
* 11.04 until end of October 2012<br />
* 10.10 until end of April 2012<br />
* 10.04 until end of October 2011<br />
* 8.04 LTS Server until end of April 2013<br />
|-<br />
| Debian<br />
| [http://wiki.debian.org/DebianLenny Usually: stable releases every 1.5-3 yrs, release X maintained 1 yr after release X+1]<br />
| <br />
* 6 until its TBD end of life (approx. 2014)<br />
* 5 until 2012-04<br />
|- <br />
| openSUSE<br />
| [http://en.opensuse.org/Lifetime openSUSE releases Lifetime of 1.5-2.5 years]<br />
| <br />
* 11.4 until 2012-09-10<br />
* 11.3 until 2012-01-15<br />
|}<br />
<br />
==Ubuntu==<br />
In '''Ubuntu 12.04 ''Precise Pangolin''''', you can install all of Madagascar's dependencies by running<br />
<pre><br />
sudo apt-get install scons openmpi-bin libopenmpi-dev freeglut3-dev g++ gfortran libgd2-xpm-dev libglew1.6-dev \<br />
libx11-dev libxaw7-dev libnetpbm10-dev swig python-dev python-scipy python-numpy libtiff4-dev scons units \<br />
libblas-dev liblapack-dev libcairo2-dev liblapack-devlibavcodec-dev python-epydoc<br />
</pre><br />
<br />
In Ubuntu 10.10 ''Maverick Meerkat'', you can install all of Madagascar's dependencies by running <br />
<pre><br />
sudo apt-get install freeglut3-dev g++ gfortran libgd2-xpm-dev libglew1.5-dev libjpeg62-dev libx11-dev \<br />
libxaw7-dev libnetpbm10-dev swig python-dev python-scipy python-numpy libtiff4-dev scons units libblas-dev \<br />
libcairo2-dev libavcodec-dev libplplot-dev <br />
</pre><br />
<br />
In Ubuntu 9.04 ''Jaunty Jackalope'', the corresponding command is<br />
<pre><br />
sudo apt-get install freeglut3-dev g++ gfortran libc6-dev libgd2-xpm-dev libglew1.5-dev libjpeg62-dev \<br />
libx11-dev libxaw7-dev libnetpbm10-dev swig python-dev python-scipy python-numpy libtiff4-dev scons units <br />
</pre><br />
<br />
Earlier versions may work with<br />
<pre><br />
sudo apt-get install mesa-libGL-devel g++ g77 libc6-dev libgd2-xpm-dev libglew-dev libjpeg62-dev \<br />
libx11-dev libxaw7-dev libnetpbm10-dev swig python-dev python-scipy python-numpy libtiff4-dev scons units <br />
</pre><br />
<br />
If working with the development version, you will also need <tt>subversion</tt>.<br />
<br />
==Fedora, CentOS, Scientific Linux, openSUSE==<br />
<br />
Dependency package names, sorted by Linux distribution and m8r feature they provide. Packages that are not included in the standard distro repositories are hyperlinked to their providers. The tables below cover build dependencies. <br />
<br />
Names of packages that are runtime dependencies are '''highlighted''' in the tables below (task under construction).<br />
<br />
''Note: In the future, it should be possible for the configuration scripts to output the dependency tables below, so that they are guaranteed to be in synch with a given m8r version''<br />
<br />
'''Minimal install ("Core"), publishing and development'''<br />
<br />
{| class="wikitable" align="center" cellspacing="0" border="1"<br />
|-<br />
|<br />
! style="background:#ffdead;" | Core<br />
! style="background:#ffdead;" | LaTeX<br />
! style="background:#ffdead;" | Development version<br />
! style="background:#ffdead;" | C++ API<br />
! style="background:#ffdead;" | F77 API, F90 API<br />
! style="background:#ffdead;" | Python API<br />
! style="background:#ffdead;" | Java API<br />
! style="background:#ffdead;" | Octave API<br />
! style="background:#ffdead;" | Matlab API<br />
|-<br />
! style="background:#ffdead;" | Fedora 15<br />
| binutils, gcc, glibc-headers, python, scons <br />
| texlive-latex<br />
| subversion<br />
| gcc-c++<br />
| gcc-gfortran<br />
| numpy, swig, python-devel<br />
| Java (Sun's? IcedTea?)<br />
| octave, octave-devel<br />
| [http://www.mathworks.com/ Matlab] with Mex<br />
|-<br />
! style="background:#ffdead;" | Fedora 14<br />
| binutils, gcc, glibc-headers, python, scons <br />
| texlive-latex<br />
| subversion<br />
| gcc-c++<br />
| gcc-gfortran<br />
| numpy, swig<br />
| Java (Sun's? IcedTea?)<br />
| octave, octave-devel<br />
| [http://www.mathworks.com/ Matlab] with Mex<br />
|-<br />
! style="background:#ffdead;" | Fedora 13<br />
| binutils, gcc, glibc-headers, python, scons<br />
| texlive-latex<br />
| subversion<br />
| gcc-c++<br />
| gcc-gfortran<br />
| numpy, swig<br />
| Java (Sun's? IcedTea?)<br />
| octave, octave-devel<br />
| [http://www.mathworks.com/ Matlab]<br />
|-<br />
! style="background:#ffdead;" | CentOS 5<br />
| binutils, gcc, glibc-headers; python, scons (needs [http://dag.wieers.com/rpm/FAQ.php#B2 RPMforge's RHEL5 repository])<br />
| ?<br />
| subversion<br />
| gcc-c++<br />
| gcc-gfortran<br />
| numpy, swig<br />
| Java (Sun's? IcedTea?), [http://inside.mines.edu/~dhale/jtk/ Mines JTK]<br />
| [http://www.gnu.org/software/octave/ Octave, octave-devel]<br />
| [http://www.mathworks.com/ Matlab]<br />
|-<br />
! style="background:#ffdead;" | openSUSE 11.0<br />
| gcc, python, scons<br />
| texlive-latex<br />
| subversion<br />
| gcc-c++<br />
| gcc-fortran<br />
| [http://numpy.scipy.org/ NumPy], swig<br />
| Java (Sun's? IcedTea?), [http://inside.mines.edu/~dhale/jtk/ Mines JTK]<br />
| [http://www.gnu.org/software/octave/ Octave]<br />
| [http://www.mathworks.com/ Matlab]<br />
|}<br />
<br />
'''Numerical and file manipulation utilities'''<br />
<br />
{| class="wikitable" align="center" cellspacing="0" border="1"<br />
|-<br />
|<br />
! style="background:#ffdead;" | OpenMP<br />
! style="background:#ffdead;" | MPI<br />
! style="background:#ffdead;" | BLAS/ATLAS<br />
! style="background:#ffdead;" | Interface to the Fast Discrete Curvelet Transform<br />
! style="background:#ffdead;" | sfunits<br />
|-<br />
! style="background:#ffdead;" | Fedora 13<br />
| libgomp<br />
| openmpi, openmpi-devel; openmpi-libs (?)<br />
| blas, blas-devel, atlas, atlas-devel<br />
| [https://wave.eos.ubc.ca/Software/Licenced/ pyct]<br />
| units<br />
|-<br />
! style="background:#ffdead;" | CentOS 5<br />
| ?<br />
| ?<br />
| ?<br />
| [https://wave.eos.ubc.ca/Software/Licenced/ pyct]<br />
| [http://www.gnu.org/software/units/units.html Gnu Units]<br />
|}<br />
<br />
'''Graphics and visualization'''<br />
<br />
{| class="wikitable" align="center" cellspacing="0" border="1"<br />
|-<br />
|<br />
! style="background:#ffdead;" | vplot2gif<br />
! style="background:#ffdead;" | vplot2avi<br />
! style="background:#ffdead;" | Some sort of movies?<br />
! style="background:#ffdead;" | TIFF output<br />
! style="background:#ffdead;" | JPEG output<br />
! style="background:#ffdead;" | PLplot graphics<br />
! style="background:#ffdead;" | OpenGL graphics<br />
! style="background:#ffdead;" | X11 graphics<br />
! style="background:#ffdead;" | ppm (?)<br />
! style="background:#ffdead;" | unknown<br />
|-<br />
! style="background:#ffdead;" | Fedora 13<br />
| gifsicle<br />
| ffmpeg (needs the [http://rpmfusion.org/ RPM Fusion] repository enabled)<br />
| ffmpeg-devel (needs the [http://rpmfusion.org/ RPM Fusion] repository enabled)<br />
| libtiff-devel<br />
| libjpeg-devel<br />
| plplot-devel<br />
| mesa-libGL-devel, freeglut, freeglut-devel<br />
| libXaw-devel<br />
| netpbm-devel<br />
| ?<br />
|-<br />
! style="background:#ffdead;" | openSUSE 11.0<br />
| ?<br />
| ?<br />
| ?<br />
| libtiff-devel<br />
| libjpeg-devel<br />
| plplot-devel<br />
| mesa-libGL-devel, freeglut, freeglut-devel<br />
| xorg-x11-devel<br />
| netpbm-devel<br />
| cairo-devel, gd-devel, glew-devel<br />
|}<br />
<br />
'''Other'''<br />
<br />
{| class="wikitable" align="center" cellspacing="0" border="1"<br />
|-<br />
|<br />
! style="background:#ffdead;" | Inclusions from Seismic Unix<br />
|-<br />
! style="background:#ffdead;" | Fedora 14, 15<br />
| [http://www.cwp.mines.edu/cwpcodes/ Seismic Unix]<br />
|-<br />
! style="background:#ffdead;" | CentOS 5<br />
| [http://www.cwp.mines.edu/cwpcodes/ Seismic Unix]<br />
<br />
|}<br />
<br />
'''Command to install all dependencies present in the public repositories'''<br />
<br />
Usually package management software will not install again a package that is already installed, so it should be safe to copy and paste the command below to a command line:<br />
<br />
{| class="wikitable" align="center" cellspacing="0" border="1"<br />
|-<br />
! style="background:#ffdead;" | Fedora 15<br />
| '''yum -y install''' binutils gcc glibc-headers scons texlive-latex subversion gcc-c++ gcc-gfortran numpy python python-devel swig octave octave-devel libgomp openmpi openmpi-devel blas blas-devel atlas atlas-devel units gifsicle ffmpeg ffmpeg-devel libtiff-devel libjpeg-devel plplot-devel mesa-libGL-devel freeglut freeglut-devel libXaw-devel netpbm-devel<br />
|-<br />
! style="background:#ffdead;" | Fedora 13<br />
| '''yum -y install''' binutils gcc glibc-headers scons texlive-latex subversion gcc-c++ gcc-gfortran numpy python swig octave octave-devel libgomp openmpi openmpi-devel blas blas-devel atlas atlas-devel units gifsicle ffmpeg ffmpeg-devel libtiff-devel libjpeg-devel plplot-devel mesa-libGL-devel freeglut freeglut-devel libXaw-devel netpbm-devel<br />
|-<br />
! style="background:#ffdead;" | CentOS 5<br />
| '''yum -y install''' binutils freeglut freeglut-devel gcc gcc-c++ gcc-gfortran glibc-headers libjpeg-devel libXaw-devel netpbm-devel<br />
|-<br />
! style="background:#ffdead;" | openSUSE 11.0<br />
| '''zypper install''' cairo-devel gcc gcc-c++ gcc-fortran gd-devel glew-devel libjpeg-devel libtiff-devel octave scons subversion texlive-latex xorg-x11-devel<br />
|}<br />
<br />
'''List of runtime dependencies only'''<br />
(needed by packagers of Madagascar in order to properly list dependencies):<br />
UNDER CONSTRUCTION<br />
<br />
==Debian 5==<br />
Specific dependencies:<br />
* Debian 5.0 ("Lenny"): Please make sure you have the <tt>libc6-dev</tt> package before trying to compile from source. The <tt>libXaw7-dev</tt> package might be a dependency for <tt>xtpen</tt> (was in Debian 4.0)<br />
<br />
==Yellow Dog Linux 6.1 on Sony PlayStation 3==<br />
See [http://www.reproducibility.org/rsflog/uploads/Friday_Seminar_Madagascar_on_PS3.ppt Will Burnett's guide (PowerPoint)]<br />
<br />
==Mac OS X==<br />
<br />
Install necessary Mac OS X applications using:<br />
* [http://www.macports.org/ MacPorts], an easy-to-use system for compiling, installing, and upgrading open-source software on Mac OS X.<br />
* [http://www.finkproject.org/ Fink], a tool that brings the full world of Unix Open Source software to Mac OS X. <br />
<br />
Installation on Mac OS X Mountain Lion requires the following:<br />
# <b>Xcode</b>: Download and install the development tools from Apple using their App Store application. In Xcode, enable and install the command-line tools in Xcode/Preferences/Downloads to get access to programs like <b>svn</b>, <b>make</b>, etc.<br />
# <b>X11</b>: Install X11 libraries from [http://xquartz.macosforge.org Xquartz]. After installation, make a symbolic link from /usr/X11 to /opt/X11 and restart your computer.<br />
# <b>gcc</b>: Install the Gnu C compiler from [http://hpc.sourceforge.net HPC Mac OS X]. The Lion version also works on Mountain Lion.<br />
# [[SEGTeX]]: To use <b>SEGTeX</b>, you may need [http://www.tug.org/texlive/ TeX Live]. <b>MacPorts</b> and <b>Fink</b> provide an easy way to install it with commands <tt>sudo port install texlive</tt> or <tt>sudo fink install texlive</tt>.<br />
Proceed with configuration and installation following the normal procedure.<br />
<br />
<br />
<!---<br />
The following might help. <br />
# <b>C compiler</b> for Mac OS X. You can download the precompiled binary package of <b>Xcode</b> tools, including the <b>gcc</b> compiler, from [http://developer.apple.com/tools/xcode/ Apple]. Other sources are:<br />
#* [http://www.macports.org/ MacPorts], an easy-to-use system for compiling, installing, and upgrading open-source software on Mac OS X.<br />
#* [http://www.finkproject.org/ Fink], a tool that brings the full world of Unix Open Source software to Mac OS X. <br />
# [http://subversion.tigris.org/ Subversion] client for Mac OS X. There are two methods to install Subversion in Mac OS X: you can use <b>MacPorts</b> or <b>Fink</b> to update <b>Subversion client</b> package or the precompiled binary. Some useful information can be found on the [http://www.wikihow.com/Install-Subversion-on-Mac-OS-X Wikihow website] and [http://downloads.open.collab.net/binaries.html Collab]. You can use <b>Subversion</b> to [[Download#Current_development_version|download the development version]] of the <tt>Madagascar</tt> source code. Next, follow [[Installation|Installation instructions]] to install. <br />
# [[SEGTeX]], a <b>LaTeX</b> package for geophysical publications. To use <b>SEGTeX</b>, you may need [http://www.tug.org/texlive/ TeX Live]. <b>MacPorts</b> and <b>Fink</b> provide an easy way to install it with commands <tt>sudo port install texlive</tt> or <tt>sudo fink install texlive</tt>.<br />
--><br />
<br />
==OpenSolaris==<br />
<br />
Use <tt>pkg</tt> to install missing components such as X11 headers.<br />
<br />
<bash><br />
pfexec pkg install SUNWxorg-headers<br />
</bash><br />
<br />
==MS Windows==<br />
Due to its size, this topic has been assigned [[Windows | its own Wiki page]].<br />
<br />
==How to adapt Madagascar to a new platform==<br />
The most laborious part of adapting madagascar to a new platform is finding the proper dependency names. This usually proceeds as follows: dependency X fails with a "missing file" error either as a header file in <tt>config.log</tt>, or a missing library during the build step. Possible package names are found through an internet search for the missing file name and the distribution name or by using specific [http://rpm.pbone.net/ rpm search tools]. Packages are installed and the configure (and, if necessary) build processes are repeated until the error goes away.<br />
<br />
=Multi-user installs=<br />
Some organizations may find it desirable to deny write access of some users to all RSFSRC/RSFROOT except their own user directory. Fortunately, this can be easily done by placing the restricted user dirs outside RSFSRC/RSFROOT, i.e. in their home dirs, say /home/joe/rsfsrc. In order to move a user's directory out of RSFSRC, you must:<br />
* "tell" the SConstruct in the user's dir where to find RSFSRC so that when the user builds in his directory, it can import <tt>configure.py</tt> and <tt>config.py</tt> You do that by setting the environment variable RSFSRC to the absolute path of the Madagascar source root, and by making sure that lines 2 and 3 in the users' SConstruct files are<br />
<python><br />
srcroot = os.environ.get('RSFSRC', '../..')<br />
sys.path.append(srcroot)<br />
</python> <br />
and then replace <tt>../..</tt> throughout the SConstruct using <tt>os.path.join</tt> and the <tt>srcroot</tt> variable.<br />
* "tell" the build scripts about the user's dir, so that it is included in the builds launched from RSFSRC. You do that with a symbolic link:<br />
<bash><br />
ln -s /home/joe/rsfsrc $RSFSRC/user/joe<br />
</bash><br />
''When the link exists'', those of Joe's programs that are mentioned in the "prog" string in SConstruct get included in the distribution, complete with self-doc. If Joe is just learning how to code and his stuff breaks the build, just remove the symbolic link. Even if build+installs are done after the link is removed, his stable programs and self-doc will continue to remain installed system-wide as long as the admin does not type <tt>scons -c install</tt> (not likely).<br />
* point the user's RSFDOC environment variable to a location where the user has write access<br />
* edit the users' SConstruct so that it uses the RSF library and headers already installed in $RSFROOT/lib and $RSFROOT/include , instead of building again the whole <tt>librsf</tt> with user-specific flags in <tt>RSFSRC/filt/lib/</tt>. To do that, replace in the user's SConstruct the env.Prepend statement with<br />
<python><br />
rsfroot = os.environ.get('RSFROOT','/usr/local/rsf')<br />
<br />
env.Prepend(CPPPATH=[os.path.join(rsfroot,'include')],<br />
LIBPATH=[os.path.join(rsfroot,'lib')],<br />
LIBS=['rsf'])<br />
</python><br />
* If the link from RSFSRC to Joe's directory was not made, add Joe's directory to his own path so that he can execute his own binaries.<br />
<br />
To understand how $DATAPATH disk space issues may become an issue in a multi-user environment, refer to the [[Advanced_Installation#Disk_space|Disk Space subsection]] at the beginning of this document.<br />
<br />
=Keeping your stuff separate=<br />
A user may add his own programs and recipes to the Madagascar system. He may also create his own computational examples, data, and locked figures for testing. All of these components can be placed in their default locations, but it is not necessary to make them public. To keep these items private simply do not add them to the repository.<br />
<br />
However, it might be desirable to keep these components in separate places. For example, if you keep your private programs in RSFSRC/user you will have to remember to make a copy somewhere else if you ever want to delete the Madagascar installation to perform a fresh install. Yup, I deleted all my programs that way once. Good thing I had a back up! Fortunately, it is easy to keep each of these components in a separate place if desired.<br />
<br />
==Keeping programs separate==<br />
User programs are ordinarily kept in a subdirectory of RSFSRC/user. However, if you want to keep your programs separate all you have to do is put your subdirectory somewhere else and make a link to it in RSFSRC/user:<br />
<bash><br />
ln -s path_to_my_programs $RSFSRC/user/my_programs<br />
</bash><br />
The additional instructions above for "multi-user installs" are for the case where the other users do not have write access to RSFSRC. However, if you have full write access and only want to keep the programs in a separate place the link is the only thing you need.<br />
<br />
==Keeping recipes separate==<br />
Computational recipes written in Python and imported by the SConstruct file of a workflow are normally stored in RSFSRC/book/Recipes. The install process copies these recipes to a directory like $RSFROOT/lib/python2.5/site-packages/rsf/recipes and adds this directory to your PYTHONPATH so that Python can find them.<br />
<br />
However, you can put you own recipes anywhere you want. You only have to add that place to your PYTHONPATH like this (bash):<br />
<bash><br />
export PYTHONPATH=${PYTHONPATH}:path_to_my_recipes<br />
</bash><br />
Or like this (csh):<br />
<bash><br />
setenv PYTHONPATH=${PYTHONPATH}:path_to_my_recipes<br />
</bash><br />
<br />
==Keeping examples separate==<br />
Madagascar's public collection of example workflows are stored in RSFSRC/book, but you can put your private workflows anywhere you want. No special instructions are required.<br />
<br />
However, Madagascar assumes that the workflows are organized into a three-level book/chapter/section directory hierarchy when it creates a directory tree for the data and locked figures associated with your workflow. It is not required, but it might be easier to find the data and locked figures if you put your workflows in a three-level directory tree something like this: path_to_my_book/chapter/section/SConstruct.<br />
<br />
==Keeping data separate==<br />
The location of the data portion of your *.rsf files is controlled by your DATAPATH environment variable. However, you may want to keep the data for your private workflows in a different place, or several different places, than the data created by the public examples in RSFSRC/book. The way to do that is to temporarily change the DATAPATH variable in the SConstruct ''before'' importing rsf.proj like this:<br />
<python><br />
import os<br />
os.environ['DATAPATH'] = 'path_to_my_private_data'<br />
<br />
from rsf.proj import *<br />
</python><br />
<br />
==Keeping locked figures separate==<br />
The command "scons lock" in the directory of a workflow will store a "locked" copy of your figures for regression testing. Normally these figures are stored in the location pointed to by your RSFFIGS variable, and that is where the figures from the figures repository should be stored for testing in RSFSRC/book.<br />
<br />
However, you may want to keep your private figures in a different place. The way to do that is to temporarily change the RSFFIGS variable in the SConstruct ''before'' importing rsf.proj like this:<br />
<python><br />
import os<br />
os.environ['RSFFIGS'] = 'path_to_my_private_figures'<br />
<br />
from rsf.proj import *<br />
</python><br />
If you also create a RSFALTFIGS environment variable pointing to path_to_my_private_figures, then the testing script sffiglist will automatically test your figures against those in RSFALTFIGS when the sffiglist command is executed from a location outside of RSFSRC/book.<br />
<br />
=Capturing error and warning messages=<br />
The messages during configuration are few and their importance quite high, so they should be watched "in person". A complete log of the configuration process is recorded in RSFSRC/configure.log<br />
<br />
Console messages generated during the build step can be captured to a log file and observed at the same time with a command like this (tcsh):<br />
<bash><br />
nice +10 nohup /usr/bin/time -p scons -k |& tee log_build.asc<br />
</bash><br />
The log file can be of course named otherwise than <tt>log_build.asc</tt>. The file can be later grepped for error and warnings with commands such as:<br />
<bash><br />
grep -c error log_build.asc<br />
grep error log_build.asc | awk '/error.c/ {next}; /error.h/ {next}; /error.o/ {next}; {print}'<br />
grep -c warning log_build.asc<br />
grep warning log_build.asc | awk '/imaginary constants are a GCC extension/ {next}; {print}'<br />
</bash><br />
<br />
=Advanced troubleshooting=<br />
* If you removed one of your programs or changed its name, and <tt>scons install</tt> fails with "Source <tt>oldprogname</tt> not found, needed by target install", and you cleaned everything there was to clean but still get this message, remove <tt>RSFSRC/.sconsign*</tt><br />
* If during <tt>scons install</tt> you get a <tt>DBAccessError : (13, 'Permission denied')</tt> in some reproducible papers, check permissions in your <tt>$DATAPATH</tt> directory. This is where SCons places database ".sconsign" files for its dependencies (according to the rules in <tt>rsf.proj</tt> and <tt>rsf.tex</tt>).<br />
* If <tt>scons</tt> or <tt>scons install</tt> fail due to an a bug introduced in a tool you are certain you will not use, a quick workaround for the problem is already built into scons: the <tt>-k</tt> option, which means "keep going". Thus, if you use <tt>scons -k</tt> or <tt>scons -k install</tt>, SCons will not be able to build the failed component, or anything that depends on it, but it will keep going and make everything else that it can.<br />
<br />
=Further support=<br />
Subscribe to the [https://lists.sourceforge.net/lists/listinfo/rsf-user rsf-user mailing list].</div>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=Advanced_Installation&diff=2343Advanced Installation2012-07-28T18:40:11Z<p>Psava: /* Mac OS X */</p>
<hr />
<div>[[Image:Fotolia_419157_XS.jpg|right|]]<br />
Before reading this document, please familiarize yourself with the [[Installation|short Installation guide]].<br />
=What the installation process does=<br />
The term "installation" in the title is used for brevity, and it actually covers all three steps: configuration, build and install.<br />
# Configure: determine what tools are available on the system and how they should be used to built the software. Creates a layer of abstraction so that the build is platform-independent. Should ideally either solve or flag all problems, so that the build either works, or does not proceed at all.<br />
# Build: compiles the software and documentation using RSFSRC/build as a "workplace"<br />
# Install: moves the compiled executables and the documentation to the final locations in $RSFROOT, sometimes changing filenames. Kept separate from build so that it can be done by root, and to avoid build failures leaving junk files all over the system.<br />
A successful installation will have created in <tt>$RSFROOT</tt> the following directories:<br />
* <tt>bin/</tt>: executable programs<br />
* <tt>doc/</tt>: auto-generated HTML documentation<br />
* <tt>include/</tt>: header files with info on library procedures; fonts<br />
* <tt>lib/</tt>: libraries and Python modules<br />
<br />
=Old (1.0 and 1.1) version installation=<br />
<br />
Use <tt>$RSFROOT/etc/madagascar/</tt> as the location of <tt>env</tt> scripts instead of <tt>$RSFROOT/share/madagascar/etc/</tt>.<br />
<br />
=Old (0.9.9) version installation=<br />
<br />
====Environment variables====<br />
Example configuration for <tt>bash</tt>:<br />
<bash><br />
export RSFROOT=/usr/local/rsf # directory where Madagascar will be installed. <br />
if [ -n "$PYTHONPATH" ]; then<br />
export PYTHONPATH=${PYTHONPATH}:$RSFROOT/lib<br />
else<br />
export PYTHONPATH=$RSFROOT/lib<br />
fi<br />
export PATH=$RSFROOT/bin:$PATH<br />
export DATAPATH=/var/tmp/<br />
export MANPATH=$RSFROOT/share/man:$(manpath)<br />
export LD_LIBRARY_PATH=$RSFROOT/lib:$LD_LIBRARY_PATH<br />
</bash><br />
Notice the slash at the end of the <tt>DATAPATH</tt> variable. <br />
<br />
Example configuration for <tt>csh</tt> and <tt>tcsh</tt>:<br />
<pre><br />
setenv RSFROOT /usr/local/rsf<br />
if ($?PYTHONPATH) then<br />
setenv PYTHONPATH ${PYTHONPATH}:$RSFROOT/lib<br />
else<br />
setenv PYTHONPATH $RSFROOT/lib<br />
endif<br />
set path = ($RSFROOT/bin $path)<br />
setenv DATAPATH /var/tmp/<br />
setenv MANPATH $RSFROOT/share/man:`manpath`<br />
setenv LD_LIBRARY_PATH $RSFROOT/lib:$LD_LIBRARY_PATH<br />
</pre><br />
Notice the backticks surrounding the call to <tt>manpath</tt>.<br />
<br />
Be aware that on some systems /var/tmp gets automatically cleaned at some intervals, so if you want to keep your data binaries for a long time, set <tt>DATAPATH</tt> to another location where you have write access and that allows large files.<br />
<br />
====Software construction====<br />
<br />
#Configuration. Change to the top source directory and run <pre>./configure</pre> You can examine the <tt>config.py</tt> file that this command generates. Additional options are available. You can obtain a full list of customizable variables by running <tt>scons -h</tt>. For example, to install C++ and Fortran-90 API bindings in addition to the basic package, run <pre>./configure API=c++,fortran-90</pre> <br />
#Building and installing the package. Run <tt>scons install</tt> or the following two commands in succession: <pre>make; make install</pre> or <pre>scons; scons install</pre> If you need "root" privileges for installing under <tt>&#36;RSFROOT</tt>, you may need to run <pre>su; scons install </pre> or <pre>sudo scons install</pre><br />
#Cleaning. To clean all intermediate files generated by SCons, run <pre>make clean</pre> or <pre>scons -c</pre><br />
<br />
=Prerequisites=<br />
Basic prerequisites are described in the [[Installation|short Installation guide]]. Here are some additional details. <br />
==Compilers==<br />
Madagascar has been built successfully with the following compilers, and possibly with others:<br />
* gcc<br />
* Intel (icc/ifort)<br />
* open64<br />
* clang<br />
* cc (Solaris)<br />
<br />
==Python and SCons==<br />
As described below under [[Advanced Installation#Platform-specific installation advice | Platform-specific installation advice]], Madagascar supports the oldest non-deprecated Python version currently supported by the latest stable version of [http://scons.org/ SCons]. If your version of Python is older and you experience problems you should probably [http://www.python.org/ upgrade].<br />
<br />
Madagascar includes the latest stable version of SCons and the configure scripts will try to install it for you in RSFROOT if you don't have it already. However, if you have an older version of SCons the configure scripts will not try to install the newer version. Your older version might work fine, but Madagascar attempts to support only the latest stable version of SCons, so if you have problems you should upgrade.<br />
<br />
To install the SCons bundled with Madagascar go to <tt>RSFSRC/scons</tt>, unpack the tar file, and type<br />
<br />
<bash><br />
python setup.py install<br />
</bash><br />
<br />
This will install SCons in the standard location. You might need root privileges. If you don't have root privileges, or you don't want to interfere with the system SCons you can install it somewhere else with a --prefix option. A logical choice is to put it in RSFROOT like this:<br />
<br />
<bash><br />
python setup.py install --prefix=$RSFROOT<br />
</bash><br />
<br />
==Location==<br />
As long as you set the environment variables and directory permissions correctly, it does not matter in what part of your filesystem you place the install. If you have the luxury of installing anywhere, it is good practice to follow the [http://en.wikipedia.org/wiki/Filesystem_Hierarchy_Standard Filesystem Hierarchy Standard] and either:<br />
# Install everything (including <tt>figs</tt> if you do testing) under <tt>/usr/local/rsf</tt>, with the source tree in <tt>/usr/local/rsf/src</tt>, OR <br />
# Put the source tree in <tt>/usr/local/src/rsf</tt>, and specify <tt>RSFROOT=/usr/local</tt>, so that header files and binaries go in <tt>/usr/local/bin</tt> and <tt>/usr/local/include</tt>. To follow the standard, before installing set <tt>RSFDOC=/usr/local/share/rsf/doc</tt> and create the appropriate directories. The auto-generated HTML documentation will get put there. Also, if installed, the figs directory for testing should be <tt>/usr/local/share/rsf/figs/</tt>.<br />
# Package Madagascar (i.e. build a RPM, etc) and install it in the default locations. For RPMs, those are as like the ones from the previous option, just directly in the <tt>/usr/</tt> hierarchy, instead of in the <tt>/usr/local/</tt> one.<br />
<br />
==Disk space==<br />
At present (Feb 2007, r2530), the source directory containing the build tree from the development version was approx. 200Mb, the full installation (<tt>bin/</tt>, <tt>doc/</tt>, <tt>include/</tt> and <tt>lib</tt>) is 31Mb, and <tt>figs/</tt> (the optional directory if you want to do testing) is about 10 Gb. The stable version is significantly smaller.<br />
<br />
The only Madagascar-related directory where disk space can be an issue is <tt>$DATAPATH</tt>. Real 3-D seismic datasets can be measured in Terabytes. Buggy programs/processing flows can fill up <tt>$DATAPATH</tt>. A real problem are "disk memory leaks" -- removing header files with anything else than <tt>sfrm</tt> will leave the binaries intact. Crashed jobs which start to write to binary but never get to write the header also produce "leaks". Experience has shown that over time <tt>$DATAPATH</tt> inexorably fills up. You may need to <br />
# keep irreplaceable data and expensive results in a separate place;<br />
# remove the oldest files in <tt>$DATAPATH</tt> whenever the amount of free space declines under a preset threshold.<br />
<br />
==Dependencies==<br />
Some platforms feature complete lists of dependencies. See [[Advanced Installation#Platform-specific installation advice | Platform-specific installation advice]] for details.<br />
===C++ API===<br />
A C++ compiler. SCons is smart and will try to find it for you. If it does not work specify the path to your compiler in the <tt>CXX</tt> environment variable (can be passed as an option to the configuration script, like the <tt>API</tt> one).<br />
===F77 API===<br />
A Fortran 77 compiler. If SCons does not find one, then you can either specify its path through the <tt>F77</tt> variable, or if the executable is in your path, add its name to the list of F77 compilers in <tt>RSFSRC/configure.py</tt> .<br />
===F90 API===<br />
Same as for Fortran 77 &ndash; just substitute <tt>F90</tt>. If using the <tt>gfortran</tt> compiler, make sure to get [http://gcc.gnu.org/wiki/GFortranBinaries the latest version]. If you have more than one compiler installed on your system, specify the desired one at configuration time:<br />
<bash><br />
./configure API=f90 F90=/path/to/preferred/compiler<br />
</bash><br />
<br />
===Java API===<br />
There are two styles of API, old (1.0 release and previous) and new. The two APIs are not compatible with each other.<br />
<br />
The "old" interface requires the Mines Java Toolkit for fast Java file IO. The Mines JTK, is an open-source Java package that can be downloaded from [http://inside.mines.edu/~dhale/jtk/ Mines JTK]. Currently, the "old" interface will also build alongside the new one if the MINESJTK environment variable exists, and can be used as was previously.<br />
<br />
To install the new API, you need the (Oracle) JDK. Set your JAVA_HOME environment variable to the location of the jdk (on Ubuntu 10.04 this is: /usr/lib/jvm/java-6-openjdk), then reconfigure (./configure API=java ...) and reinstall. <br />
<br />
Ignore the SWIG warnings (there are lots). <br />
<br />
Make sure to set your LD_LIBRARY_PATH to $RSFROOT/lib .<br />
<br />
If you want to include additional Java packages, you can set them using your shell's CLASSPATH variable. This environment variable is now automatically passed onto all Java classes in SCons.<br />
<br />
The installation can be tested using the example demonstrating the new API in api/java/test .<br />
<br />
===Matlab API===<br />
Besides Matlab itself, you need Mex, which compiles C code into regular Matlab functions. Use the <tt>MATLAB</tt> and <tt>MEX</tt> environment variables to specify their paths if they are installed, but not found.<br />
===Octave API===<br />
The Octave function compiler (<tt>mkoctfile</tt>) is sometimes bundled in a separate package, so it may be missing from the Octave installation.<br />
<br />
===Python API===<br />
This API requires [http://www.swig.org/ SWIG], [http://numpy.scipy.org/ numpy] and the Python development kit. Numpy requires Python 2.4 or newer (i.e. RHEL 5 or newer). However, these dependencies are unnecessary for the common case when Python is just used as [http://en.wikipedia.org/wiki/Glue_language glue] to create chains of programs, and it only needs to read the RSF header, and not the binary. To allow Python [http://en.wikipedia.org/wiki/Meta-programs metaprograms] in madagascar to function, and programming in this style to be done, a fallback development kit implementing only the header-related functionality will be installed in the lack of these dependencies.<br />
<br />
===Python modules in user space===<br />
Python is an evolving language. Many large systems have old versions for stability reasons, and administrators of such large systems tend to not install all software users may wish, and to not allow access to rpm either. To install a module in your user space, download the tarball, unzip it, cd into the directory and run: <br />
<br />
<pre>python setup.py install --prefix=/path/to/your/place</pre><br />
<br />
The installer will create a subdirectory named <tt>lib</tt>, or <tt>lib64</tt> under the directory above. These <tt>lib*</tt> dirs will have a directory named <tt>python</tt>, or <tt>python2.3</tt> for example, and those will have a subdirectory named <tt>site-packages</tt>. Add all paths to these <tt>site-packages</tt> subdirectories in your <tt>PYTHONPATH</tt> environment variable. Some (<tt>numpy</tt>) may create a <tt>bin</tt> directory that needs to be added to <tt>PATH</tt>.<br />
<br />
=Environment variables=<br />
Besides the variables defined in env.sh or env.csh (see the [[Installation|short Installation guide]]), Madagascar programs may read the variables below. They usually have reasonable defaults and were introduced just to provide more power to the advanced user.<br />
<br />
For future documentation writers: the environment variables read by Madagascar that have not been documented below can be found by running the script <tt>$RSFSRC/admin/find_env_var.py</tt>. If the script does not exist or does not work, a summary of all environment variable calls can be obtained by going to $RSFSRC, temporarily moving the directory <tt>build/</tt> outside RSFSRC, and typing<br />
<bash><br />
grep environ.get *.py */*.py */*/*.py */*/*/*.py<br />
grep getenv */*.c */*/*.c */*/*/*.c<br />
</bash><br />
<br />
==Used by the Madagascar core==<br />
<br />
{|class="wikitable" align="center" cellspacing="0" border="1"<br />
|-<br />
! colspan="3" style="background:#ffdead;"|Variables introduced by Madagascar's non-graphic programs<br />
|-<br />
| '''Name''' || '''Default''' || Meaning<br />
|-<br />
| RSF_DATASERVER || <nowiki>ftp://egl.beg.utexas.edu/</nowiki> || Data server for benchmark datasets<br />
|-<br />
| RSFDOC || $RSFROOT/doc || Directory for the HTML self-doc<br />
|-<br />
| RSFFIGS || $RSFROOT/figs || Directory with figures for testing examples in $RSFSRC/book<br />
|-<br />
|-<br />
| RSFALTFIGS || $RSFFIGS || Alternate directory with figures for testing examples not in $RSFSRC/book<br />
|-<br />
| RSFMEMSIZE || 100 || Maximum RAM (Mb) to be used by some programs <br />
|-<br />
| RSFSRC || undefined || Root of the Madagascar source tree<br />
|-<br />
| TMPDATAPATH || $DATAPATH || Datapath for temporary files on local disk.<br />
|-<br />
| LATEX2HTML || undefined || LateX2HTML customization directory<br />
|}<br />
<br />
<br />
{|class="wikitable" align="center" cellspacing="0" border="1"<br />
|-<br />
! colspan="3" style="background:#ffdead;"|Variables introduced by Madagascar graphics programs <br />
|-<br />
| '''Name''' || '''Default''' || Meaning<br />
|-<br />
| DEFAULT_PAPER_SIZE || "letter" || For pspen. Other options: legal, a3, a4, a5.<br />
|-<br />
| FATMULT || ? || Fatness multiplication factor. <br />
|-<br />
| GIFBORDER || 0.25 || For vplot2gif (spacing)<br />
|-<br />
| GIFDELAY || 100 || For vplot2gif (for animations)<br />
|-<br />
| IMAGE_TYPE || 'png' || Icon type for LateX2HTML <br />
|-<br />
| PATTERNMULT || None || Pattern multiplication factor <br />
|-<br />
| PLOTSTYLE || None || Used in vplot<br />
|-<br />
| PPI || 75 || For vplot2gif (screen resolution)<br />
|-<br />
| PPMSCALE || 1 || For vplot2gif<br />
|-<br />
| PSBORDER || 0.05 || For vplot2eps (border around the plot)<br />
|-<br />
| PSPRINTER || postscript or colorps || For pspen<br />
|-<br />
| PSTEXPENOPTS || color=n fat=1 fatmult=1.5 invras=y || Other vplot2eps options <br />
|-<br />
| VPLOTFONTDIR || $RSFROOT/include || Dir with backup fonts in case the runtime-loaded vplot fonts are not found<br />
|-<br />
| VPLOTSPOOLDIR || /tmp || Where to put vplot tmp files<br />
|-<br />
| WSTYPE || "default" || Workstation type.<br />
|}<br />
<br />
<br />
{|class="wikitable" align="center" cellspacing="0" border="1"<br />
|-<br />
! colspan="2" style="background:#ffdead;"| Variables set by OS/other apps, read-only to Madagascar<br />
|-<br />
| '''Name''' || '''Primarily used/set by'''<br />
|-<br />
| CWPROOT || Seismic Unix<br />
|-<br />
| DISPLAY || Operating System (OS)<br />
|-<br />
| HOME || OS<br />
|-<br />
| LD_LIBRARY_PATH || linker<br />
|-<br />
| MATLABPATH || Matlab<br />
|-<br />
| XAUTHORITY || X-Windows<br />
|}<br />
<br />
==Used by the Madagascar build process and parallelization utilities==<br />
Type <tt>scons -h</tt> in RSFSRC to get a list of environment variables that affect the build process, with explanations, defaults and actual values. Below are more detailed explanations for some of them:<br />
* <tt>RSF_THREADS</tt>: used by <tt>pscons</tt> to determine on how many threads to run on the local node, overriding the number of threads detected by Madagascar<br />
* <tt>RSF_CLUSTER</tt>: used by <tt>pscons</tt> to determine on which cluster nodes to run, and on how many CPUs<br />
<br />
==Used by the Matlab API==<br />
To use the Matlab API, you need to add <tt>$RSFROOT/lib</tt> to <tt>MATLABPATH</tt><br />
==Used by the Octave API==<br />
To use the Octave API, you need to add <tt>$RSFROOT/lib</tt> to Octave's path. Determine Octave's version with<br />
<bash><br />
octave -v | head -1<br />
</bash><br />
If your version is lower than 2.9.6, type at a Unix command line:<br />
<bash><br />
echo 'LOADPATH = "::$RSFROOT/lib/octave"' >> ~/.octaverc<br />
</bash><br />
For later versions, use:<br />
<bash><br />
echo 'addpath([getenv("RSFROOT") "/lib/octave"])' >> ~/.octaverc<br />
</bash><br />
==Used by the Java API==<br />
New-style (post-1.0) API: Needs <tt>JAVA_HOME</tt><br />
<br />
Old-style API (1.0 and before): The path to the downloaded Mines JTK must be specified in the MINESJTK environment variable in order to install the Java API. For example:<br />
<bash><br />
export MINESJTK=/home/user/edu_mines_jtk.jar<br />
</bash><br />
<br />
==RSFROOT for NFS-shared user home directories==<br />
Heterogeneous networks with user home directories shared through [http://en.wikipedia.org/wiki/Network_File_System_(protocol) NFS] are quite common in many institutions. In addition, even when the architecture is the same (i.e. 64-bit) and the operating system is the same (i.e. [http://en.wikipedia.org/wiki/RHEL RHEL]), the difference between operating system versions may be very significant because clusters may run legacy versions, while desktop workstations may run the latest-and-greatest (even beta), and entirely different Madagascar versions may be needed to support both. <br />
<br />
One possible solution of detecting the distribution version and architecture and setting RSFROOT appropriately is shown below. In the example network, all RHEL4 machines have the same architecture, but there are RHEL 3 machines with several architectures:<br />
<bash><br />
REDHAT_RELEASE=`awk -F'release' '{ print $2 }' /etc/redhat-release | awk -F' ' '{ print $1 }'`<br />
<br />
RSFROOT=/usr/local/rsf/rhel$REDHAT_RELEASE<br />
<br />
if [ $REDHAT_RELEASE == '4' ] ; then<br />
export RSFROOT<br />
elif [ $REDHAT_RELEASE == '3' ] ; then<br />
export RSFROOT=$RSFROOT/$ARCH<br />
fi<br />
</bash><br />
Of course, the Madagascar administrator will have to download appropriate versions of Madagascar to each $RSFROOT, and compile them on the appropriate system.<br />
<br />
If you have many kinds of systems to maintain, with multiple versions of Madagascar, and users have more than one shell, you may find it easy to outsource the complex logic to the easy-to-debug Python, i.e.:<br />
<br />
<bash><br />
export RSFROOT=`$M8R_SETUP/get_rsfroot.py`<br />
export PYTHONPATH=`$M8R_SETUP/edit_pythonpath.py`<br />
export PATH=`$M8R_SETUP/edit_path.py`<br />
</bash><br />
<br />
and similarly for (t)csh. The Python scripts determine the operating system and its version, determine the machine name, and simply print to stdout the desired string.<br />
<br />
==Eclipse + Pydev==<br />
If you use [http://eclipse.org/ Eclipse] with [http://pydev.org/ Pydev], [http://pydev.org/manual_101_interpreter.html#id2 configure the interpreter] by adding <tt>$RSFROOT/lib</tt> to the <tt>PYTHONPATH</tt> for your chosen interpreter.<br />
<br />
=Platform-specific installation advice=<br />
==Supported platforms==<br />
Madagascar attempts to support any [http://en.wikipedia.org/wiki/POSIX POSIX-compliant] operating system demanded by users. For systems that bundle Python (i.e. Linux distributions, BSDs), backwards compatibility will attempt to cover those systems that were bundled with the oldest non-deprecated Python version currently supported by the latest stable version of [http://scons.org/ SCons]. For example, in early 2009 the stable SCons release (1.2) supported Python 2.2 or newer. [http://distrowatch.com/table.php?distribution=redhat Python 2.2 was bundled by RHEL3], so RHEL 3 and newer are supported. <br />
<br />
Attempts for backward compatibility with a given operating system are also stopped if the operating system itself becomes unsupported. For example, Python 2.2 was bundled by Fedora 1 and newer, but in January 2010 only Fedora 11 and 12 are actively maintained. Thus, in January 2010 Madagascar was not attempting to support Fedora 1, even though it included Python 2.2.<br />
<br />
Please keep in mind that the above statements constitute only general guidelines for what will be attempted, and do not constitute in any way a warranty of support. An application of the above guidelines to some Linux distributions follows:<br />
<br />
'''Support info'''<br />
{| class="wikitable" align="center" cellspacing="0" border="1"<br />
|-<br />
! style="background:#ffdead;" | Distribution<br />
! style="background:#ffdead;" | Life Cycle<br />
! style="background:#ffdead;" | Supported versions<br />
|-<br />
| RHEL/CentOS/Scientific Linux<br />
| [https://www.redhat.com/security/updates/errata/ 7 years]<br />
| <br />
* 6 until 2017-11-30<br />
* 5 until 2014-03-31<br />
* 4 until 2012-02-29<br />
|-<br />
| Fedora<br />
| [http://fedoraproject.org/wiki/Fedora_Release_Life_Cycle Release X maintained until one month after the release of X+2]<br />
| <br />
* 15 until 2012-06-24<br />
* 14 until 2011-12-02<br />
|-<br />
| Ubuntu<br />
| Releases every 6 mo, maintained for 1.5 yrs; LTS versions every 2 yrs, maintained for 5 yrs<br />
| <br />
* 11.10 until end of April 2013<br />
* 11.04 until end of October 2012<br />
* 10.10 until end of April 2012<br />
* 10.04 until end of October 2011<br />
* 8.04 LTS Server until end of April 2013<br />
|-<br />
| Debian<br />
| [http://wiki.debian.org/DebianLenny Usually: stable releases every 1.5-3 yrs, release X maintained 1 yr after release X+1]<br />
| <br />
* 6 until its TBD end of life (approx. 2014)<br />
* 5 until 2012-04<br />
|- <br />
| openSUSE<br />
| [http://en.opensuse.org/Lifetime openSUSE releases Lifetime of 1.5-2.5 years]<br />
| <br />
* 11.4 until 2012-09-10<br />
* 11.3 until 2012-01-15<br />
|}<br />
<br />
==Ubuntu==<br />
In '''Ubuntu 12.04 ''Precise Pangolin''''', you can install all of Madagascar's dependencies by running<br />
<pre><br />
sudo apt-get install scons openmpi-bin libopenmpi-dev freeglut3-dev g++ gfortran libgd2-xpm-dev libglew1.6-dev \<br />
libx11-dev libxaw7-dev libnetpbm10-dev swig python-dev python-scipy python-numpy libtiff4-dev scons units \<br />
libblas-dev liblapack-dev libcairo2-dev liblapack-devlibavcodec-dev python-epydoc<br />
</pre><br />
<br />
In Ubuntu 10.10 ''Maverick Meerkat'', you can install all of Madagascar's dependencies by running <br />
<pre><br />
sudo apt-get install freeglut3-dev g++ gfortran libgd2-xpm-dev libglew1.5-dev libjpeg62-dev libx11-dev \<br />
libxaw7-dev libnetpbm10-dev swig python-dev python-scipy python-numpy libtiff4-dev scons units libblas-dev \<br />
libcairo2-dev libavcodec-dev libplplot-dev <br />
</pre><br />
<br />
In Ubuntu 9.04 ''Jaunty Jackalope'', the corresponding command is<br />
<pre><br />
sudo apt-get install freeglut3-dev g++ gfortran libc6-dev libgd2-xpm-dev libglew1.5-dev libjpeg62-dev \<br />
libx11-dev libxaw7-dev libnetpbm10-dev swig python-dev python-scipy python-numpy libtiff4-dev scons units <br />
</pre><br />
<br />
Earlier versions may work with<br />
<pre><br />
sudo apt-get install mesa-libGL-devel g++ g77 libc6-dev libgd2-xpm-dev libglew-dev libjpeg62-dev \<br />
libx11-dev libxaw7-dev libnetpbm10-dev swig python-dev python-scipy python-numpy libtiff4-dev scons units <br />
</pre><br />
<br />
If working with the development version, you will also need <tt>subversion</tt>.<br />
<br />
==Fedora, CentOS, Scientific Linux, openSUSE==<br />
<br />
Dependency package names, sorted by Linux distribution and m8r feature they provide. Packages that are not included in the standard distro repositories are hyperlinked to their providers. The tables below cover build dependencies. <br />
<br />
Names of packages that are runtime dependencies are '''highlighted''' in the tables below (task under construction).<br />
<br />
''Note: In the future, it should be possible for the configuration scripts to output the dependency tables below, so that they are guaranteed to be in synch with a given m8r version''<br />
<br />
'''Minimal install ("Core"), publishing and development'''<br />
<br />
{| class="wikitable" align="center" cellspacing="0" border="1"<br />
|-<br />
|<br />
! style="background:#ffdead;" | Core<br />
! style="background:#ffdead;" | LaTeX<br />
! style="background:#ffdead;" | Development version<br />
! style="background:#ffdead;" | C++ API<br />
! style="background:#ffdead;" | F77 API, F90 API<br />
! style="background:#ffdead;" | Python API<br />
! style="background:#ffdead;" | Java API<br />
! style="background:#ffdead;" | Octave API<br />
! style="background:#ffdead;" | Matlab API<br />
|-<br />
! style="background:#ffdead;" | Fedora 15<br />
| binutils, gcc, glibc-headers, python, scons <br />
| texlive-latex<br />
| subversion<br />
| gcc-c++<br />
| gcc-gfortran<br />
| numpy, swig, python-devel<br />
| Java (Sun's? IcedTea?)<br />
| octave, octave-devel<br />
| [http://www.mathworks.com/ Matlab] with Mex<br />
|-<br />
! style="background:#ffdead;" | Fedora 14<br />
| binutils, gcc, glibc-headers, python, scons <br />
| texlive-latex<br />
| subversion<br />
| gcc-c++<br />
| gcc-gfortran<br />
| numpy, swig<br />
| Java (Sun's? IcedTea?)<br />
| octave, octave-devel<br />
| [http://www.mathworks.com/ Matlab] with Mex<br />
|-<br />
! style="background:#ffdead;" | Fedora 13<br />
| binutils, gcc, glibc-headers, python, scons<br />
| texlive-latex<br />
| subversion<br />
| gcc-c++<br />
| gcc-gfortran<br />
| numpy, swig<br />
| Java (Sun's? IcedTea?)<br />
| octave, octave-devel<br />
| [http://www.mathworks.com/ Matlab]<br />
|-<br />
! style="background:#ffdead;" | CentOS 5<br />
| binutils, gcc, glibc-headers; python, scons (needs [http://dag.wieers.com/rpm/FAQ.php#B2 RPMforge's RHEL5 repository])<br />
| ?<br />
| subversion<br />
| gcc-c++<br />
| gcc-gfortran<br />
| numpy, swig<br />
| Java (Sun's? IcedTea?), [http://inside.mines.edu/~dhale/jtk/ Mines JTK]<br />
| [http://www.gnu.org/software/octave/ Octave, octave-devel]<br />
| [http://www.mathworks.com/ Matlab]<br />
|-<br />
! style="background:#ffdead;" | openSUSE 11.0<br />
| gcc, python, scons<br />
| texlive-latex<br />
| subversion<br />
| gcc-c++<br />
| gcc-fortran<br />
| [http://numpy.scipy.org/ NumPy], swig<br />
| Java (Sun's? IcedTea?), [http://inside.mines.edu/~dhale/jtk/ Mines JTK]<br />
| [http://www.gnu.org/software/octave/ Octave]<br />
| [http://www.mathworks.com/ Matlab]<br />
|}<br />
<br />
'''Numerical and file manipulation utilities'''<br />
<br />
{| class="wikitable" align="center" cellspacing="0" border="1"<br />
|-<br />
|<br />
! style="background:#ffdead;" | OpenMP<br />
! style="background:#ffdead;" | MPI<br />
! style="background:#ffdead;" | BLAS/ATLAS<br />
! style="background:#ffdead;" | Interface to the Fast Discrete Curvelet Transform<br />
! style="background:#ffdead;" | sfunits<br />
|-<br />
! style="background:#ffdead;" | Fedora 13<br />
| libgomp<br />
| openmpi, openmpi-devel; openmpi-libs (?)<br />
| blas, blas-devel, atlas, atlas-devel<br />
| [https://wave.eos.ubc.ca/Software/Licenced/ pyct]<br />
| units<br />
|-<br />
! style="background:#ffdead;" | CentOS 5<br />
| ?<br />
| ?<br />
| ?<br />
| [https://wave.eos.ubc.ca/Software/Licenced/ pyct]<br />
| [http://www.gnu.org/software/units/units.html Gnu Units]<br />
|}<br />
<br />
'''Graphics and visualization'''<br />
<br />
{| class="wikitable" align="center" cellspacing="0" border="1"<br />
|-<br />
|<br />
! style="background:#ffdead;" | vplot2gif<br />
! style="background:#ffdead;" | vplot2avi<br />
! style="background:#ffdead;" | Some sort of movies?<br />
! style="background:#ffdead;" | TIFF output<br />
! style="background:#ffdead;" | JPEG output<br />
! style="background:#ffdead;" | PLplot graphics<br />
! style="background:#ffdead;" | OpenGL graphics<br />
! style="background:#ffdead;" | X11 graphics<br />
! style="background:#ffdead;" | ppm (?)<br />
! style="background:#ffdead;" | unknown<br />
|-<br />
! style="background:#ffdead;" | Fedora 13<br />
| gifsicle<br />
| ffmpeg (needs the [http://rpmfusion.org/ RPM Fusion] repository enabled)<br />
| ffmpeg-devel (needs the [http://rpmfusion.org/ RPM Fusion] repository enabled)<br />
| libtiff-devel<br />
| libjpeg-devel<br />
| plplot-devel<br />
| mesa-libGL-devel, freeglut, freeglut-devel<br />
| libXaw-devel<br />
| netpbm-devel<br />
| ?<br />
|-<br />
! style="background:#ffdead;" | openSUSE 11.0<br />
| ?<br />
| ?<br />
| ?<br />
| libtiff-devel<br />
| libjpeg-devel<br />
| plplot-devel<br />
| mesa-libGL-devel, freeglut, freeglut-devel<br />
| xorg-x11-devel<br />
| netpbm-devel<br />
| cairo-devel, gd-devel, glew-devel<br />
|}<br />
<br />
'''Other'''<br />
<br />
{| class="wikitable" align="center" cellspacing="0" border="1"<br />
|-<br />
|<br />
! style="background:#ffdead;" | Inclusions from Seismic Unix<br />
|-<br />
! style="background:#ffdead;" | Fedora 14, 15<br />
| [http://www.cwp.mines.edu/cwpcodes/ Seismic Unix]<br />
|-<br />
! style="background:#ffdead;" | CentOS 5<br />
| [http://www.cwp.mines.edu/cwpcodes/ Seismic Unix]<br />
<br />
|}<br />
<br />
'''Command to install all dependencies present in the public repositories'''<br />
<br />
Usually package management software will not install again a package that is already installed, so it should be safe to copy and paste the command below to a command line:<br />
<br />
{| class="wikitable" align="center" cellspacing="0" border="1"<br />
|-<br />
! style="background:#ffdead;" | Fedora 15<br />
| '''yum -y install''' binutils gcc glibc-headers scons texlive-latex subversion gcc-c++ gcc-gfortran numpy python python-devel swig octave octave-devel libgomp openmpi openmpi-devel blas blas-devel atlas atlas-devel units gifsicle ffmpeg ffmpeg-devel libtiff-devel libjpeg-devel plplot-devel mesa-libGL-devel freeglut freeglut-devel libXaw-devel netpbm-devel<br />
|-<br />
! style="background:#ffdead;" | Fedora 13<br />
| '''yum -y install''' binutils gcc glibc-headers scons texlive-latex subversion gcc-c++ gcc-gfortran numpy python swig octave octave-devel libgomp openmpi openmpi-devel blas blas-devel atlas atlas-devel units gifsicle ffmpeg ffmpeg-devel libtiff-devel libjpeg-devel plplot-devel mesa-libGL-devel freeglut freeglut-devel libXaw-devel netpbm-devel<br />
|-<br />
! style="background:#ffdead;" | CentOS 5<br />
| '''yum -y install''' binutils freeglut freeglut-devel gcc gcc-c++ gcc-gfortran glibc-headers libjpeg-devel libXaw-devel netpbm-devel<br />
|-<br />
! style="background:#ffdead;" | openSUSE 11.0<br />
| '''zypper install''' cairo-devel gcc gcc-c++ gcc-fortran gd-devel glew-devel libjpeg-devel libtiff-devel octave scons subversion texlive-latex xorg-x11-devel<br />
|}<br />
<br />
'''List of runtime dependencies only'''<br />
(needed by packagers of Madagascar in order to properly list dependencies):<br />
UNDER CONSTRUCTION<br />
<br />
==Debian 5==<br />
Specific dependencies:<br />
* Debian 5.0 ("Lenny"): Please make sure you have the <tt>libc6-dev</tt> package before trying to compile from source. The <tt>libXaw7-dev</tt> package might be a dependency for <tt>xtpen</tt> (was in Debian 4.0)<br />
<br />
==Yellow Dog Linux 6.1 on Sony PlayStation 3==<br />
See [http://www.reproducibility.org/rsflog/uploads/Friday_Seminar_Madagascar_on_PS3.ppt Will Burnett's guide (PowerPoint)]<br />
<br />
==Mac OS X==<br />
<br />
Installation on Mac OS X Mountain Lion requires the following:<br />
# <b>Xcode</b>: Download and install the development tools from Apple using their App Store application. In Xcode, enable and install the command-line tools in Xcode/Preferences/Downloads to get access to programs like <b>svn</b>, <b>make</b>, etc.<br />
# <b>X11</b>: Install X11 libraries from [http://xquartz.macosforge.org Xquartz]. After installation, make a symbolic link from /usr/X11 to /opt/X11 and restart your computer.<br />
# <b>gcc</b>: Install the Gnu C compiler from [http://hpc.sourceforge.net HPC Mac OS X]. The Lion version also works on Mountain Lion.<br />
Proceed with installation following the normal procedure.<br />
<br />
<br />
<!---<br />
The following might help. <br />
# <b>C compiler</b> for Mac OS X. You can download the precompiled binary package of <b>Xcode</b> tools, including the <b>gcc</b> compiler, from [http://developer.apple.com/tools/xcode/ Apple]. Other sources are:<br />
#* [http://www.macports.org/ MacPorts], an easy-to-use system for compiling, installing, and upgrading open-source software on Mac OS X.<br />
#* [http://www.finkproject.org/ Fink], a tool that brings the full world of Unix Open Source software to Mac OS X. <br />
# [http://subversion.tigris.org/ Subversion] client for Mac OS X. There are two methods to install Subversion in Mac OS X: you can use <b>MacPorts</b> or <b>Fink</b> to update <b>Subversion client</b> package or the precompiled binary. Some useful information can be found on the [http://www.wikihow.com/Install-Subversion-on-Mac-OS-X Wikihow website] and [http://downloads.open.collab.net/binaries.html Collab]. You can use <b>Subversion</b> to [[Download#Current_development_version|download the development version]] of the <tt>Madagascar</tt> source code. Next, follow [[Installation|Installation instructions]] to install. <br />
# [[SEGTeX]], a <b>LaTeX</b> package for geophysical publications. To use <b>SEGTeX</b>, you may need [http://www.tug.org/texlive/ TeX Live]. <b>MacPorts</b> and <b>Fink</b> provide an easy way to install it with commands <tt>sudo port install texlive</tt> or <tt>sudo fink install texlive</tt>.<br />
--><br />
<br />
==OpenSolaris==<br />
<br />
Use <tt>pkg</tt> to install missing components such as X11 headers.<br />
<br />
<bash><br />
pfexec pkg install SUNWxorg-headers<br />
</bash><br />
<br />
==MS Windows==<br />
Due to its size, this topic has been assigned [[Windows | its own Wiki page]].<br />
<br />
==How to adapt Madagascar to a new platform==<br />
The most laborious part of adapting madagascar to a new platform is finding the proper dependency names. This usually proceeds as follows: dependency X fails with a "missing file" error either as a header file in <tt>config.log</tt>, or a missing library during the build step. Possible package names are found through an internet search for the missing file name and the distribution name or by using specific [http://rpm.pbone.net/ rpm search tools]. Packages are installed and the configure (and, if necessary) build processes are repeated until the error goes away.<br />
<br />
=Multi-user installs=<br />
Some organizations may find it desirable to deny write access of some users to all RSFSRC/RSFROOT except their own user directory. Fortunately, this can be easily done by placing the restricted user dirs outside RSFSRC/RSFROOT, i.e. in their home dirs, say /home/joe/rsfsrc. In order to move a user's directory out of RSFSRC, you must:<br />
* "tell" the SConstruct in the user's dir where to find RSFSRC so that when the user builds in his directory, it can import <tt>configure.py</tt> and <tt>config.py</tt> You do that by setting the environment variable RSFSRC to the absolute path of the Madagascar source root, and by making sure that lines 2 and 3 in the users' SConstruct files are<br />
<python><br />
srcroot = os.environ.get('RSFSRC', '../..')<br />
sys.path.append(srcroot)<br />
</python> <br />
and then replace <tt>../..</tt> throughout the SConstruct using <tt>os.path.join</tt> and the <tt>srcroot</tt> variable.<br />
* "tell" the build scripts about the user's dir, so that it is included in the builds launched from RSFSRC. You do that with a symbolic link:<br />
<bash><br />
ln -s /home/joe/rsfsrc $RSFSRC/user/joe<br />
</bash><br />
''When the link exists'', those of Joe's programs that are mentioned in the "prog" string in SConstruct get included in the distribution, complete with self-doc. If Joe is just learning how to code and his stuff breaks the build, just remove the symbolic link. Even if build+installs are done after the link is removed, his stable programs and self-doc will continue to remain installed system-wide as long as the admin does not type <tt>scons -c install</tt> (not likely).<br />
* point the user's RSFDOC environment variable to a location where the user has write access<br />
* edit the users' SConstruct so that it uses the RSF library and headers already installed in $RSFROOT/lib and $RSFROOT/include , instead of building again the whole <tt>librsf</tt> with user-specific flags in <tt>RSFSRC/filt/lib/</tt>. To do that, replace in the user's SConstruct the env.Prepend statement with<br />
<python><br />
rsfroot = os.environ.get('RSFROOT','/usr/local/rsf')<br />
<br />
env.Prepend(CPPPATH=[os.path.join(rsfroot,'include')],<br />
LIBPATH=[os.path.join(rsfroot,'lib')],<br />
LIBS=['rsf'])<br />
</python><br />
* If the link from RSFSRC to Joe's directory was not made, add Joe's directory to his own path so that he can execute his own binaries.<br />
<br />
To understand how $DATAPATH disk space issues may become an issue in a multi-user environment, refer to the [[Advanced_Installation#Disk_space|Disk Space subsection]] at the beginning of this document.<br />
<br />
=Keeping your stuff separate=<br />
A user may add his own programs and recipes to the Madagascar system. He may also create his own computational examples, data, and locked figures for testing. All of these components can be placed in their default locations, but it is not necessary to make them public. To keep these items private simply do not add them to the repository.<br />
<br />
However, it might be desirable to keep these components in separate places. For example, if you keep your private programs in RSFSRC/user you will have to remember to make a copy somewhere else if you ever want to delete the Madagascar installation to perform a fresh install. Yup, I deleted all my programs that way once. Good thing I had a back up! Fortunately, it is easy to keep each of these components in a separate place if desired.<br />
<br />
==Keeping programs separate==<br />
User programs are ordinarily kept in a subdirectory of RSFSRC/user. However, if you want to keep your programs separate all you have to do is put your subdirectory somewhere else and make a link to it in RSFSRC/user:<br />
<bash><br />
ln -s path_to_my_programs $RSFSRC/user/my_programs<br />
</bash><br />
The additional instructions above for "multi-user installs" are for the case where the other users do not have write access to RSFSRC. However, if you have full write access and only want to keep the programs in a separate place the link is the only thing you need.<br />
<br />
==Keeping recipes separate==<br />
Computational recipes written in Python and imported by the SConstruct file of a workflow are normally stored in RSFSRC/book/Recipes. The install process copies these recipes to a directory like $RSFROOT/lib/python2.5/site-packages/rsf/recipes and adds this directory to your PYTHONPATH so that Python can find them.<br />
<br />
However, you can put you own recipes anywhere you want. You only have to add that place to your PYTHONPATH like this (bash):<br />
<bash><br />
export PYTHONPATH=${PYTHONPATH}:path_to_my_recipes<br />
</bash><br />
Or like this (csh):<br />
<bash><br />
setenv PYTHONPATH=${PYTHONPATH}:path_to_my_recipes<br />
</bash><br />
<br />
==Keeping examples separate==<br />
Madagascar's public collection of example workflows are stored in RSFSRC/book, but you can put your private workflows anywhere you want. No special instructions are required.<br />
<br />
However, Madagascar assumes that the workflows are organized into a three-level book/chapter/section directory hierarchy when it creates a directory tree for the data and locked figures associated with your workflow. It is not required, but it might be easier to find the data and locked figures if you put your workflows in a three-level directory tree something like this: path_to_my_book/chapter/section/SConstruct.<br />
<br />
==Keeping data separate==<br />
The location of the data portion of your *.rsf files is controlled by your DATAPATH environment variable. However, you may want to keep the data for your private workflows in a different place, or several different places, than the data created by the public examples in RSFSRC/book. The way to do that is to temporarily change the DATAPATH variable in the SConstruct ''before'' importing rsf.proj like this:<br />
<python><br />
import os<br />
os.environ['DATAPATH'] = 'path_to_my_private_data'<br />
<br />
from rsf.proj import *<br />
</python><br />
<br />
==Keeping locked figures separate==<br />
The command "scons lock" in the directory of a workflow will store a "locked" copy of your figures for regression testing. Normally these figures are stored in the location pointed to by your RSFFIGS variable, and that is where the figures from the figures repository should be stored for testing in RSFSRC/book.<br />
<br />
However, you may want to keep your private figures in a different place. The way to do that is to temporarily change the RSFFIGS variable in the SConstruct ''before'' importing rsf.proj like this:<br />
<python><br />
import os<br />
os.environ['RSFFIGS'] = 'path_to_my_private_figures'<br />
<br />
from rsf.proj import *<br />
</python><br />
If you also create a RSFALTFIGS environment variable pointing to path_to_my_private_figures, then the testing script sffiglist will automatically test your figures against those in RSFALTFIGS when the sffiglist command is executed from a location outside of RSFSRC/book.<br />
<br />
=Capturing error and warning messages=<br />
The messages during configuration are few and their importance quite high, so they should be watched "in person". A complete log of the configuration process is recorded in RSFSRC/configure.log<br />
<br />
Console messages generated during the build step can be captured to a log file and observed at the same time with a command like this (tcsh):<br />
<bash><br />
nice +10 nohup /usr/bin/time -p scons -k |& tee log_build.asc<br />
</bash><br />
The log file can be of course named otherwise than <tt>log_build.asc</tt>. The file can be later grepped for error and warnings with commands such as:<br />
<bash><br />
grep -c error log_build.asc<br />
grep error log_build.asc | awk '/error.c/ {next}; /error.h/ {next}; /error.o/ {next}; {print}'<br />
grep -c warning log_build.asc<br />
grep warning log_build.asc | awk '/imaginary constants are a GCC extension/ {next}; {print}'<br />
</bash><br />
<br />
=Advanced troubleshooting=<br />
* If you removed one of your programs or changed its name, and <tt>scons install</tt> fails with "Source <tt>oldprogname</tt> not found, needed by target install", and you cleaned everything there was to clean but still get this message, remove <tt>RSFSRC/.sconsign*</tt><br />
* If during <tt>scons install</tt> you get a <tt>DBAccessError : (13, 'Permission denied')</tt> in some reproducible papers, check permissions in your <tt>$DATAPATH</tt> directory. This is where SCons places database ".sconsign" files for its dependencies (according to the rules in <tt>rsf.proj</tt> and <tt>rsf.tex</tt>).<br />
* If <tt>scons</tt> or <tt>scons install</tt> fail due to an a bug introduced in a tool you are certain you will not use, a quick workaround for the problem is already built into scons: the <tt>-k</tt> option, which means "keep going". Thus, if you use <tt>scons -k</tt> or <tt>scons -k install</tt>, SCons will not be able to build the failed component, or anything that depends on it, but it will keep going and make everything else that it can.<br />
<br />
=Further support=<br />
Subscribe to the [https://lists.sourceforge.net/lists/listinfo/rsf-user rsf-user mailing list].</div>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=Austin_2012&diff=2262Austin 20122012-06-29T22:12:55Z<p>Psava: /* Agenda */</p>
<hr />
<div>[[Image:Austin2.jpg|center|frame]]<br />
<br />
<center><big>'''Madagascar School and Workshop on Reproducible Computational Geophysics'''</big></center><br />
<br />
&nbsp;<br />
<br />
==Agenda==<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 1: Friday, July 20, 2012<br />
|-<br />
| 8:00-9:00<br />
! colspan="2" | Coffee/pastries/installation<br />
|-<br />
| <br />
| colspan="2" | <br />
Bring your laptop and get help getting Madagascar installed.<br />
|-<br />
| 9:00-10:15<br />
! colspan="2" | Introduction (Sergey Fomel)<br />
|-<br />
| <br />
| colspan="2" | <br />
The Madagascar open-source project has been in public existence for six years. Madagascar provides a complete environment for organizing one's research, from new software development to running computational experiments to publishing the computational results in papers and reports, archiving them for future usage, and sharing them with colleagues or sponsors. The introductory presentation will describe the history of the project, the Madagascar main components and design principles, and the plans for future development.<br />
|-<br />
| 10:15-10:30<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:30-12:00<br />
! colspan="2" | Introductory exercise (Siwei Li)<br />
|-<br />
|<br />
| colspan="2" | <br />
|-<br />
| 12:00-1:00<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 1:00-1:45<br />
! colspan="2" | RSF file format<br />
|-<br />
| <br />
| colspan="2" | <br />
|-<br />
| 1:45-2:30<br />
! colspan="2" | Command-line versus SCons<br />
|-<br />
| <br />
| colspan="2" | <br />
|-<br />
| 2:30-2:45<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 2:45-3:30<br />
! colspan="2" | Vplot graphics<br />
|-<br />
| <br />
| colspan="2" |<br />
|-<br />
| 3:30-5:00<br />
! colspan="2" | Seismic Field Data Processing<br />
|-<br />
|<br />
| colspan="2" |<br />
|-<br />
| 5:30-8:30<br />
! colspan="2" style="background:#ccff99;" | Wine reception and dinner at Maggiano's<br />
|-<br />
|}<br />
<br />
&nbsp;<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 2: Saturday, July 21, 2012<br />
|-<br />
| 8:00-9:00<br />
! colspan="2" | Coffee/pastries/installation<br />
|-<br />
| <br />
| colspan="2" | <br />
Bring your laptop and get help getting Madagascar installed.<br />
|-<br />
| 9:00-12:00<br />
! colspan="2" | Seismic wavefield imaging and Writing Research Papers (Paul Sava)<br />
|-<br />
| <br />
| colspan="2" | <br />
The theoretical part of this module provides an overview of reverse-time imaging methodology applied to wavefield seismic data. The main technique discussed is reverse-time migration developed under the single-scattering assumption. The applied part demonstrates this technique on a complex geologic model using Madagascar codes in a fully reproducible setup. We will conclude by generating reproducible documents constructed using LaTeX.<br />
|-<br />
| 12:00-1:00<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 1:00-1:45<br />
! colspan="2" | Developing Madagascar code in C and C++ (Jingwei Hu)<br />
|-<br />
| <br />
| colspan="2" | <br />
|-<br />
| 1:45-2:30<br />
! colspan="2" | Python and Graphical User Interfaces (Sergey Fomel)<br />
|-<br />
| <br />
| colspan="2" | <br />
|-<br />
| 2:30-2:45<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 2:45-3:30<br />
! colspan="2" | Parallel processing with Madagascar<br />
|-<br />
|<br />
| colspan="2" |<br />
|-<br />
| 3:30-4:15<br />
! colspan="2" | Contributing your code to Madagascar (Sergey Fomel)<br />
|-<br />
|<br />
| colspan="2" |<br />
|-<br />
| 4:15-5:00<br />
! colspan="2" | Discussion<br />
|-<br />
|<br />
| colspan="2" |<br />
Open Q&A session and discussions on the future development of Madagascar<br />
|}<br />
<br />
==Registration==<br />
<br />
Registration is required to attend this event. The registration deadline is July 12, 2012.<br />
<br />
The registration fee is $200. Registration includes lunch and dinner and is complimentary for students.<br />
<br />
Please register by [http://www.cvent.com/d/scqq5f following this link].<br />
<br />
==Location==<br />
<br />
[[Image:ROC.jpg]]<br />
<br />
Room ROC 1.603<br><br />
Texas Advanced Computing Center<br><br />
The University of Texas at Austin<br />
<br />
'''Address'''<br />
* J.J. Pickle Research Campus, Building 196<br />
* 10100 Burnet Road (R2200)<br />
* Austin, Texas 78758-4445, USA<br />
* [http://www.tacc.utexas.edu/about/contact-us/directions/ Directions]<br />
* [http://www.tacc.utexas.edu/about/hotels/ Nearby hotels]<br />
<br />
<br clear=all/><br />
<br />
===Dinner Location===<br />
<br />
[[Image:maggianos.jpg|left]]<br />
'''Maggiano's'''<br />
* 10910 Domain Drive, Suite 100<br />
* Austin, Texas 78758<br />
* [http://www.maggianos.com/en/Austin_Austin_TX/Pages/LocationLanding.aspx# Directions]<br />
<br />
<br clear=all/><br />
<br />
==Host Organization==<br />
<br />
Bureau of Economic Geology<br><br />
The University of Texas at Austin<br />
<br />
== Speakers ==<br />
<br />
* '''Sergey Fomel''' has been working at the Bureau of Economic Geology at the University of Texas at Austin since 2002 and currently has an Associate Professor appointment, jointly with the Department of Geological Sciences. He received a Ph.D. in Geophysics from Stanford University in 2001 and worked previously at the Institute of Geophysics in Novosibirsk, Russia, and the Lawrence Berkeley National Laboratory. Sergey started work on Madagascar (at that time named RSF for Regularly Sampled Format) in 2003. http://www.jsg.utexas.edu/researcher/sergey_fomel/<br />
* '''Jingwei Hu''' is a postdoctoral fellow at the Institute for Computational Engineering and Sciences (ICES), the University of Texas at Austin. Jingwei received her BS degree (2006) in computational mathematics from Peking University, China, and her PhD degree (2011) in mathematics from the University of Wisconsin-Madison. Her interests are numerical methods and applied analysis for kinetic theory, conservation laws, quantum mechanics, high frequency waves, and seismic imaging. http://users.ices.utexas.edu/~hu/ <br />
* '''Siwei Li''' graduated from Peking University with a Bachelor's Degree in Geophysics and is currently pursuing a Ph.D. degree at the University of Texas at Austin. <br />
* '''Paul Sava''' is an Associate Professor of Geophysics and a member of the Center for Wave Phenomena at Colorado School of Mines. He holds an Engineering degree in Geophysics (1995) from the University of Bucharest, an M.Sc. (1998) and a Ph.D. (2004) in Geophysics from Stanford University where he was a member of the Stanford Exploration Project. His research interests are in wavefield seismic imaging, stochastic imaging and inversion, computational methods for wave propagation, numeric optimization and high performance computing. http://newton.mines.edu/paul/home.php<br />
<br />
==Neighbor Conferences==<br />
<br />
* [http://conference.scipy.org/scipy2012/ SciPy 2012], Scientific Computing with Python</div>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=Conferences&diff=1899Conferences2011-07-12T21:48:50Z<p>Psava: </p>
<hr />
<div>[[Image:Conferences.png|right|]]<br />
In reverse chronological order.<br />
<br />
==Featured events==<br />
<br />
===School in Bejing 2011===<br />
<br />
[[Beijing_2011|Madagascar School of Reproducible Computational Geophysics]]<br />
<br />
===Workshop in Houston 2011===<br />
<br />
[[Houston_2011|Workshop - Open Software Tools for Reproducible Computational Geophysics]]<br />
<br />
===School in Houston 2010===<br />
<br />
[[Houston_2010|Madagascar School of Reproducible Computational Geophysics and Hands-On Workshop]]<br />
<br />
===School in Salvador 2009===<br />
<br />
[[Salvador_2009|Madagascar School on Reproducible Computational Geophysics]]<br />
<br />
===School in Delft 2009===<br />
<br />
[[Delft_2009|Madagascar School on Reproducible Computational Geophysics]]<br />
<br />
===Coding Sprint in Golden 2008===<br />
<br />
Implementation Workshop [[2008_Implementation_Workshop|Towards full automation and better robustness]] <br />
<br />
===School in Austin 2007===<br />
<br />
Short Course [[RSF_Austin_School_2007|Using and Extending RSF/Madagascar]].<br />
<br />
===School in Vancouver 2006===<br />
<br />
School and Workshop [[RSF_School_and_Workshop%2C_Vancouver_2006|Reproducible Research in Computational Geophysics]].<br />
<br />
==Conference presentations==<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 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://www.protogeni.net/trac/archive10/wiki 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://www.protogeni.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>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=Beijing_2011&diff=1876Beijing 20112011-07-08T03:24:44Z<p>Psava: /* Instructors */</p>
<hr />
<div><center><big>'''Madagascar School on Reproducible Computational Geophysics'''</big></center><br />
<br />
[[Image:China_Beijing.png|center]]<br />
<br />
&nbsp;<br />
<br />
==Dates==<br />
<br />
July 21-22, 2011<br />
<br />
==Program==<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 0: Wednesday, July 20<br />
|-<br />
| 10:00-3:00<br />
! colspan="2" | Bring your laptop and get help with installing Madagascar<br />
|-<br />
|<br />
! colspan="2" | Tariq Alkhalifah, Sergey Fomel, Yang Liu, Jeffrey Shragge <br />
|-<br />
<br />
|}<br />
<br />
&nbsp;<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 1: Thursday, July 21<br />
|-<br />
| 8:50-9:00<br />
! colspan="2" | Welcome (Yike Liu)<br />
<br />
|-<br />
| 9:00-10:30<br />
! colspan="2" | Introduction (Sergey Fomel)<br />
|-<br />
|<br />
| colspan="2" | <br />
|-<br />
| 10:30-10:45<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:45-12:15<br />
<br />
! colspan="2" | Command-line usage, RSF file format, Vplot graphics <br />
|-<br />
|<br />
| colspan="2" | <br />
|-<br />
| 12:15-1:15<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 1:15-2:45<br />
! colspan="2" | Developing workflows using SCons <br />
|-<br />
|<br />
| colspan="2" | <br />
|-<br />
| 2:45-3:00<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 3:00-4:30<br />
! colspan="2" | Writing reproducible papers (Tariq Alkhalifah)<br />
|-<br />
|<br />
| colspan="2" |<br />
|-<br />
|}<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 2: Friday, July 22<br />
|-<br />
| 9:00-10:30<br />
! colspan="2" | Wave-equation modeling and migration (Paul Sava) <br />
|-<br />
|<br />
| colspan="2" | <br />
The theoretical part of this module provides an overview of reverse-time imaging methodology applied to wavefield seismic data. The main technique discussed is reverse-time migration with emphasis on modern imaging conditions which enable migration velocity analysis and amplitude-versus-angle analysis. The applied part demonstrates this technique on a complex geologic model using Madagascar codes in a fully reproducible setup.<br />
|-<br />
| 10:30-10:45<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:45-12:15<br />
<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 />
| 12:15-1:15<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 1:15-2:45<br />
! colspan="2" | Developing your own programs in Madagascar<br />
|-<br />
|<br />
| colspan="2" | <br />
|-<br />
| 2:45-3:00<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 3:00-4:30<br />
! colspan="2" | Contributing to Madagascar (Sergey Fomel)<br />
|-<br />
|<br />
| colspan="2" |<br />
|-<br />
|}<br />
<br />
==Location==<br />
<br />
Conference Hall in new office building, Institute of Geology and Geophysics, Chinese Academy of Sciences<br />
<br />
No.19 Beitucheng Xilu, Chaoyang District, Beijing, China<br />
<br />
中国科学院地质与地球物理研究所, 新办公楼会议室, 北京市朝阳区北土城西路19号<br />
<br />
[http://www.ahay.org/wikilocal/docs/map.pdf Location map]<br />
<br />
==Registration==<br />
<br />
Attendance is free for students but registration is required. To register, please send [mailto:wyb1982@gmail.com an email].<br />
<br />
==Participating Organizations==<br />
<br />
Bureau of Economic Geology, The University of Texas at Austin (Austin, USA)<br />
<br />
Institute of Geology and Geophysics, Chinese Academy of Sciences (Beijing, China)<br />
<br />
College of Geo-exploration Science and Technology, Jilin University (Changchun, China)<br />
<br />
College of Geophysics and Information Engineering, China University of Petroleum (Beijing, China)<br />
<br />
==Contact information ==<br />
<br />
Sergey Fomel, E-mail: sergey.fomel@beg.utexas.edu<br />
<br />
Yibo Wang, E-mail: wyb1982@gmail.com<br />
<br />
Yang Liu (JLU), E-mail: yangliu1979@gmail.com<br />
<br />
Yang Liu (CUP), E-mail: wliuyang@vip.sina.com<br />
<br />
== Instructors ==<br />
<br />
* '''Tariq Alkhalifah''' is currently a Professor of Geophysics at KAUST in Saudi Arabia. He graduated with a PhD from Colorado School of Mines, Golden, Colorado, in 1996, and served afterwards as a Post Doc at Stanford University for 2 years sharing an office with Sergey Fomel. I used to be a devote SU Unix follower for most of my research carrier even as a Post Doc at Stanford (SEPlib people), but I have recently seen the light and converted to Madagascar. https://sites.google.com/a/kaust.edu.sa/tariq/ <br />
* '''Sergey Fomel''' has been working at the Bureau of Economic Geology at the University of Texas at Austin since 2002 and currently has an Associate Professor appointment, jointly with the Department of Geological Sciences. He received a Ph.D. in Geophysics from Stanford University in 2001 and worked previously at the Institute of Geophysics in Novosibirsk, Russia, and the Lawrence Berkeley National Laboratory. Sergey started work on Madagascar (at that time named RSF for Regularly Sampled Format) in 2003. http://www.beg.utexas.edu/fomel/<br />
* '''Yang Liu''' is currently an Associate Professor of Geophysics at College of Geo-exploration science and technology at Jilin University, China. He received a Ph.D. in Geophysics from Jilin University in 2006 and was a Postdoctoral fellow at Bureau of Economic Geology, The University of Texas at Austin from 2007 to 2010. His research focuses mainly on seismic data processing. http://gest.jlu.edu.cn/index.php/teacher/read/id/249<br />
* '''Xuxin Ma'''<br />
* '''Paul Sava''' is an Associate Professor of Geophysics and a member of the Center for Wave Phenomena at Colorado School of Mines. He holds an Engineering degree in Geophysics (1995) from the University of Bucharest, an M.Sc. (1998) and a Ph.D. (2004) in Geophysics from Stanford University where he was a member of the Stanford Exploration Project. His research interests are in wavefield seismic imaging, stochastic imaging and inversion, computational methods for wave propagation, numeric optimization and high performance computing. http://newton.mines.edu/paul/home.php<br />
* '''Jeff Shragge''' is a Research Assistant Professor with the Centre for Petroleum Geoscience and CO2 Sequestration in the School of Earth and Environment at the University of Western Australia. He received his Ph.D. (Geophysics) in 2009 in seismic imaging with the Stanford Exploration Project at Stanford University. His research interests are in the fields of seismic imaging (migration, time-lapse imaging and velocity inversion) and high-performance computing (parallel computation, GPU programming).</div>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=Beijing_2011&diff=1871Beijing 20112011-07-07T05:32:27Z<p>Psava: /* Program */</p>
<hr />
<div><center><big>'''Madagascar School on Reproducible Computational Geophysics'''</big></center><br />
<br />
[[Image:China_Beijing.png|center]]<br />
<br />
&nbsp;<br />
<br />
==Dates==<br />
<br />
July 21-22, 2011<br />
<br />
==Program==<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 0: Wednesday, July 20<br />
|-<br />
| 10:00-3:00<br />
! colspan="2" | Bring your laptop and get help with installing Madagascar<br />
|-<br />
|<br />
! colspan="2" | Sergey Fomel, Tariq Alkhalifah, 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 1: Thursday, July 21<br />
|-<br />
| 8:50-9:00<br />
! colspan="2" | Welcome (Yike Liu)<br />
<br />
|-<br />
| 9:00-10:30<br />
! colspan="2" | Introduction (Sergey Fomel)<br />
|-<br />
|<br />
| colspan="2" | <br />
|-<br />
| 10:30-10:45<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:45-12:15<br />
<br />
! colspan="2" | <br />
|-<br />
|<br />
| colspan="2" | <br />
|-<br />
| 12:15-1:15<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 1:15-2:45<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 />
| 2:45-3:00<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 3:00-4:30<br />
! colspan="2" | <br />
|-<br />
|<br />
| colspan="2" |<br />
|-<br />
|}<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 2: Friday, July 22<br />
|-<br />
| 9:00-10:30<br />
! colspan="2" | Wave-equation modeling and migration (Paul Sava) <br />
|-<br />
|<br />
| colspan="2" | <br />
The theoretical part of this module provides an overview of reverse-time imaging methodology applied to wavefield seismic data. The main technique discussed is reverse-time migration with emphasis on modern imaging conditions which enable migration velocity analysis and amplitude-versus-angle analysis. The applied part demonstrates this technique on a complex geologic model using Madagascar codes in a fully reproducible setup.<br />
|-<br />
| 10:30-10:45<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:45-12:15<br />
<br />
! colspan="2" | <br />
|-<br />
|<br />
| colspan="2" | <br />
|-<br />
| 12:15-1:15<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 1:15-2:45<br />
! colspan="2" | <br />
|-<br />
|<br />
| colspan="2" | <br />
|-<br />
| 2:45-3:00<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 3:00-4:30<br />
! colspan="2" | <br />
|-<br />
|<br />
| colspan="2" |<br />
|-<br />
|}<br />
<br />
==Location==<br />
<br />
Conference Hall in new office building, Institute of Geology and Geophysics, Chinese Academy of Sciences<br />
<br />
No.19 Beitucheng Xilu, Chaoyang District, Beijing, China<br />
<br />
中国科学院地质与地球物理研究所, 新办公楼会议室, 北京市朝阳区北土城西路19号<br />
<br />
==Registration==<br />
<br />
No registration fee for students, but need send email to wyb1982@gmail.com to register.<br />
<br />
==Participating Organizations==<br />
<br />
Bureau of Economic Geology, The University of Texas at Austin (Austin, USA)<br />
<br />
Institute of Geology and Geophysics, Chinese Academy of Sciences (Beijing, China)<br />
<br />
College of Geo-exploration Science and Technology, Jilin University (Changchun, China)<br />
<br />
College of Geophysics and Information Engineering, China University of Petroleum (Beijing, China)<br />
<br />
==Contact information ==<br />
<br />
Sergey Fomel, E-mail: sergey.fomel@beg.utexas.edu<br />
<br />
Yibo Wang, E-mail: wyb1982@gmail.com<br />
<br />
Yang Liu (JLU), E-mail: yangliu1979@gmail.com<br />
<br />
Yang Liu (CUP), E-mail: wliuyang@vip.sina.com<br />
<br />
== Instructors ==<br />
<br />
* '''Tariq Alkhalifah''' is currently a Professor of Geophysics at KAUST in Saudi Arabia. He graduated with a PhD from Colorado School of Mines, Golden, Colorado, in 1996, and served afterwards as a Post Doc at Stanford University for 2 years sharing an office with Sergey Fomel. I used to be a devote SU Unix follower for most of my research carrier even as a Post Doc at Stanford (SEPlib people), but I have recently seen the light and converted to Madagascar. https://sites.google.com/a/kaust.edu.sa/tariq/ <br />
* '''Sergey Fomel''' has been working at the Bureau of Economic Geology at the University of Texas at Austin since 2002 and currently has an Associate Professor appointment, jointly with the Department of Geological Sciences. He received a Ph.D. in Geophysics from Stanford University in 2001 and worked previously at the Institute of Geophysics in Novosibirsk, Russia, and the Lawrence Berkeley National Laboratory. Sergey started work on Madagascar (at that time named RSF for Regularly Sampled Format) in 2003. http://www.beg.utexas.edu/fomel/<br />
* '''Yang Liu''' is currently an Associate Professor of Geophysics at College of Geo-exploration science and technology at Jilin University, China. He received a Ph.D. in Geophysics from Jilin University in 2006 and was a Postdoctoral fellow at Bureau of Economic Geology, The University of Texas at Austin from 2007-2010. His research focuses mainly on seismic data processing. http://gest.jlu.edu.cn/index.php/teacher/read/id/249<br />
* '''Xuxin Ma'''<br />
* '''Paul Sava''' is an Assistant Professor of Geophysics and a member of the Center for Wave Phenomena at Colorado School of Mines. He holds an Engineering degree in Geophysics (1995) from the University of Bucharest, an M.Sc. (1998) and a Ph.D. (2004) in Geophysics from Stanford University where he was a member of the Stanford Exploration Project. His research interests are in wavefield seismic imaging, stochastic imaging and inversion, computational methods for wave propagation, numeric optimization and high performance computing. http://newton.mines.edu/paul/home.php<br />
* '''Jeff Shragge''' is a Research Assistant Professor with the Centre for Petroleum Geoscience and CO2 Sequestration in the School of Earth and Environment at the University of Western Australia. He received his Ph.D. (Geophysics) in 2009 in seismic imaging with the Stanford Exploration Project at Stanford University. His research interests are in the fields of seismic imaging (migration, time-lapse imaging and velocity inversion) and high-performance computing (parallel computation, GPU programming).</div>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=Houston_2010&diff=1310Houston 20102010-07-14T15:08:58Z<p>Psava: </p>
<hr />
<div>[[Image:PTTC.jpg|left|link=http://www.beg.utexas.edu/pttc/workshops.htm ]]<br />
<br />
[[Image:BEG.png|left|link=http://www.beg.utexas.edu/ ]]<br />
<br />
[[Image:Fotolia_3744441_XS.jpg|center]]<br />
<br />
&nbsp;<br />
<br />
<center><big>'''Madagascar School on Reproducible Computational Geophysics and Hands-On Workshop'''<br><br />
Sponsored by [http://www.beg.utexas.edu/pttc/workshops.htm PTTC Texas/SE New Mexico Region]</big></center><br />
<br />
&nbsp;<br />
<br />
==Program==<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 1: Friday, July 23<br />
|-<br />
| 9:00-10:30<br />
! colspan="2" | Introduction (Sergey Fomel)<br />
|-<br />
|<br />
| colspan="2" | <br />
The Madagascar project has been in public existence for four years. Madagascar provides a complete environment for organizing one's research, from new software development to running computational experiments to publishing the experimental results in papers and reports, archiving them for future usage, and sharing them with colleagues and sponsors. The introductory presentation will describe the history of the project, the Madagascar components and design principles, and the future development goals. <br />
|-<br />
| 10:30-10:45<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:45-12:15<br />
<br />
! colspan="2" | Seismic finite-difference modeling and migration example (Paul Sava)<br />
|-<br />
|<br />
| colspan="2" | <br />
The theoretical part of this module provides an overview of reverse-time imaging methodology applied to wavefield seismic data. The main technique discussed is reverse-time migration with emphasis on modern imaging conditions which enable migration velocity analysis and amplitude-versus-angle analysis. The applied part demonstrates this technique on a complex geologic model using Madagascar codes in a fully reproducible setup.<br />
|-<br />
|<br />
| colspan="2" |<br />
<br />
|-<br />
| 12:15-1:15<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 1:15-2:45<br />
! colspan="2" | Workflows in SCons and automatic testing (Jim Jennings)<br />
|-<br />
|<br />
| colspan="2" | <br />
The rich and well-documented Python syntax used in SConstruct files provides great flexibility when coding Madagascar SCons workflows. In the first part of this module a few geostatistical workflows will be presented to illustrate some useful techniques.<br />
<br />
Two important components of the Madagascar design goals are reproducibility and regression testing. In the second part of this module our progress towards these goals will be discussed and some of the built-in tools for automatic testing will be presented.<br />
|-<br />
| 2:45-3:00<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 3:00-4:30<br />
! colspan="2" | Discussion<br />
|-<br />
|<br />
| colspan="2" |<br />
Open Q&A session and discussions on the future development of Madagascar<br />
|-<br />
| 5:30-8:00<br />
! colspan="2" style="background:#ccff99;" | Dinner and Madagascar 1.0 celebration<br />
|-<br />
|}<br />
<br />
&nbsp;<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Day 2: Saturday, July 24<br />
|-<br />
| 9:00-9:30<br />
! colspan="2" | Learning Madagascar (Tariq Alkhalifah)<br />
|-<br />
|<br />
| colspan="2" |<br />
Why Madagascar was easy for me? The art of the Madagascar template! In a year, I managed to write 7-8 papers using Madagascar, and the papers are still coming. Considering that I have used SU (Seismic Unix) all my life and taking into account my not-so-young age, I think Madagascar was good to me. In the presentation, I will share my experience (no Python background knowledge is needed!) and share some insights on how to use Madagascar efficiently.<br />
|-<br />
| 9:30-10:30<br />
! colspan="2" | Programming with Madagascar (Jeff Godwin)<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. This session will discuss an overview of the Madagascar APIs, and then focus in particular on the C and Python APIs. 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 />
| colspan="2" |<br />
<br />
|-<br />
| 10:30-10:45<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 10:45-11:15<br />
! colspan="2" | Vplot graphics language - past, present, and future (Joe Dellinger)<br />
|-<br />
|<br />
| colspan="2" |<br />
<br />
<br />
|-<br />
| 11:15-12:15<br />
! colspan="2" | Plotting and high-performance computing with Madagascar (Vladimir Bashkardin)<br />
|-<br />
|<br />
| colspan="2" |<br />
The first part of this module will cover visualization and preparation of data plots with Madagascar tools. Major available styles of plots will be explained as long as the mechanism of creating figures in reproducible fashion for papers and presentations. The second part will be a tutorial for using Madagascar in a high-performance environment. Different types of such environments will be described and principal approaches to handling parallel problems with Madagascar will be unfolded. This module will specifically address how to run data-parallel tasks and how to create Madagascar programs with MPI and GPU(CUDA) routines.<br />
|-<br />
| 12:15-1:15<br />
! colspan="2" style="background:#efefef;" | Lunch<br />
|-<br />
| 1:15-2:45<br />
! colspan="2" | Seismic field data processing example (Ioan Vlad)<br />
|-<br />
|<br />
| colspan="2" | <br />
<br />
|-<br />
| 2:45-3:00<br />
! colspan="2" style="background:#efefef;" | break<br />
|-<br />
| 3:00-4:30<br />
! colspan="2" | Discussion<br />
|-<br />
|<br />
| colspan="2" |<br />
Open Q&A session and discussions on the future development of Madagascar<br />
|-<br />
|}<br />
<br />
== Location ==<br />
<br />
[[Image:HRC.png|right]]<br />
<br />
The University of Texas at Austin<br><br />
Bureau of Economic Geology<br><br />
[http://www.beg.utexas.edu/info/hrc_facil.php Houston Research Center]<br />
<br />
'''Address'''<br />
* 11611 West Little York Rd<br />
* Houston, Texas 77041, USA<br />
* [http://www.beg.utexas.edu/info/pdf/Directions_to_HRC.pdf Driving directions]<br />
<br />
<br clear=all/><br />
<br />
== Registration ==<br />
<br />
Register by filling the [http://www.beg.utexas.edu/pttc/madagascar.php Registration Form].<br />
<br />
The registration cost is $300 and includes morning refreshments, lunch, Friday dinner, and instructor handouts. <br />
<br />
The registration is '''<font color="red">free for graduate students</font>'''. If you are a graduate student, please e-mail<br />
[mailto:pttc@beg.utexas.edu pttc@beg.utexas.edu] to obtain a discount code.<br />
<br />
== Speaker biographies ==<br />
<br />
* '''Tariq Alkhalifah''' is currently a Professor of Geophysics at KAUST in Saudi Arabia. He graduated with a PhD from Colorado School of Mines, Golden, Colorado, in 1996, and served afterwards as a Post Doc at Stanford University for 2 years sharing an office with Sergey Fomel. I used to be a devote SU Unix follower for most of my research carrier even as a Post Doc at Stanford (SEPlib people), but I have recently seen the light and converted to Madagascar. https://sites.google.com/a/kaust.edu.sa/tariq/ <br />
* '''Vladimir Bashkardin''' is currently a PhD student in geophysics at The University of Texas at Austin. Before joining the research group of Dr. Sergey Fomel at UT Austin, he worked as a software engineer for Paradigm (former Paradigm Geophysical) with specialization in seismic data visualization and interpretation. He also was a part-time lecturer at Gubkin Oil and Gas University (Moscow, Russia), an industry-oriented school from which he holds a degree in exploration geophysics.<br />
* '''Joe Dellinger''' graduated with a PhD in Geophysics from the Stanford Exploration Project in 1991 and currently works for BP in Houston, specializing in anisotropy and multicomponent seismology. Joe has often provided advice to the SEG (much of it unsolicited) on how they should best advance into the brave new online/digital world, for which he was awarded Life Membership in 2001. Joe currently is the editor of the Software and Algorithms section of GEOPHYSICS, and maintains the accompanying software and data website. http://software.seg.org<br />
* '''Sergey Fomel''' has been working at the Bureau of Economic Geology at the University of Texas at Austin since 2002 and currently has an Associate Professor appointment, jointly with the Department of Geological Sciences. He received a Ph.D. in Geophysics from Stanford University in 2001 and worked previously at the Institute of Geophysics in Novosibirsk, Russia, and the Lawrence Berkeley National Laboratory. Sergey started work on Madagascar (at that time named RSF for Regularly Sampled Format) in 2003. http://www.beg.utexas.edu/fomel/<br />
* '''Jeff Godwin''' is currently a MS student in geophysics in the Center for Wave Phenomena (CWP) at the Colorado School of Mines (CSM). He received his undergraduate degree in Geophysics (2009) from CSM as well, and has interned with Hess, Marathon Oil, and Landmark Graphics in various positions. His research interests include: high performance computing, inverse methods, and seismic imaging. <br />
* '''Jim Jennings''' currently works for Shell International Exploration and Production in Houston Texas as a company consultant on carbonate reservoir modeling, but he contributes to Madagascar as a hobby and will be participating in the workshop on his own time. Before joining Shell in 2007 he worked for 23 years at the Bureau of Economic Geology, Arco, and BP. Jim has a PhD in Petroleum Engineering from Texas A&M University (1983), was chairman for an SPE reprint volume on Advances in Reservoir Characterization (2006), and was a Distinguished Lecturer for the AAPG (2008-2009). http://www.aapg.org/education/dist_lect/jennings.cfm<br />
* '''Paul Sava''' is an Assistant Professor of Geophysics and a member of the Center for Wave Phenomena at Colorado School of Mines. He holds an Engineering degree in Geophysics (1995) from the University of Bucharest, an M.Sc. (1998) and a Ph.D. (2004) in Geophysics from Stanford University where he was a member of the Stanford Exploration Project. His research interests are in wavefield seismic imaging, stochastic imaging and inversion, computational methods for wave propagation, numeric optimization and high performance computing. http://newton.mines.edu/paul/home.php<br />
* '''Ioan "Nick" Vlad''' received an Engineer degree in Geophysics (2000) from University of Bucharest and a M.Sc. degree in Geophysics (2002) from Stanford University. After three more years of research at Stanford and an internship with ConocoPhillips, he joined Statoil and started working at the Trondheim Research Center in 2005 on imaging and velocity analysis problems. He is a Visiting Scholar at CWP for the year of 2010, working with Prof. Paul Sava on Wave-Equation MVA. He is a member of SEG and EAGE and a participant in the Madagascar open-source project.</div>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=Salvador_2009&diff=959Salvador 20092009-09-15T02:45:56Z<p>Psava: </p>
<hr />
<div><center><big>'''Madagascar School on Reproducible Computational Geophysics'''</big><br />
<br />
[[Image:salvador.jpg|400px]]<br />
<br />
</center><br />
<br />
<hr><br />
<br />
<tt>Madagascar</tt> 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 and archiving them for future usage. This shared environment enables an efficient exchange of research results with colleagues and sponsors. In this course, 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 />
The theoretical part of the course provides an overview of reverse-time imaging methodology applied to wavefield seismic data. The main technique discussed is reverse-time migration with emphasis on modern imaging conditions which enable migration velocity analysis and amplitude-versus-angle analysis. The applied part demonstrates this technique on a complex geologic model using <tt>Madagascar</tt> codes in a fully reproducible setup.<br><br><br />
[http://reproducibility.org/wikilocal/docs/slides.pdf Seismic imaging tutorial]<br><br />
[http://reproducibility.org/RSF/book/rsf/school/sigsbee.html SConstruct]<br />
<br />
<br />
== Location ==<br />
<br />
Bahia Convention Center <br><br />
Av. Simon Bolívar, s/n – Jardim Armação <br><br />
41750-230 – Salvador -BA <br><br />
Brazil <br clear="all"><br><br />
<br />
== Instructor ==<br />
<br />
Paul Sava (Colorado School of Mines)</div>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=Salvador_2009&diff=958Salvador 20092009-09-15T02:45:29Z<p>Psava: </p>
<hr />
<div><center><big>'''Madagascar School on Reproducible Computational Geophysics'''</big><br />
<br />
[[Image:salvador.jpg|400px]]<br />
<br />
</center><br />
<br />
<hr><br />
<br />
<tt>Madagascar</tt> 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 and archiving them for future usage. This shared environment enables an efficient exchange of research results with colleagues and sponsors. In this course, 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 />
The theoretical part of the course provides an overview of reverse-time imaging methodology applied to wavefield seismic data. The main technique discussed is reverse-time migration with emphasis on modern imaging conditions which enable migration velocity analysis and amplitude-versus-angle analysis. The applied part demonstrates this technique on a complex geologic model using <tt>Madagascar</tt> codes in a fully reproducible setup.<br><br><br />
[http://reproducibility.org/wikilocal/docs/slides.pdf Seismic imaging tutorial]<br><br />
[http://reproducibility.org/RSF/book/rsf/school/sigsbee.html SConstruct]<br />
<br />
<br />
== Location ==<br />
<br />
Bahia Convention Center <br><br />
Av. Simon Bolívar, s/n – Jardim Armação <br><br />
41750-230 – Salvador -BA <br><br />
Brazil <br clear="all"><br><br />
<br />
== Instructor ==<br />
<br />
* Paul Sava (Colorado School of Mines)</div>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=Salvador_2009&diff=957Salvador 20092009-09-15T02:44:44Z<p>Psava: </p>
<hr />
<div><center><big>'''Madagascar School on Reproducible Computational Geophysics'''</big><br />
<br />
[[Image:salvador.jpg|500px]]<br />
<br />
</center><br />
<br />
<hr><br />
<br />
<tt>Madagascar</tt> 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 and archiving them for future usage. This shared environment enables an efficient exchange of research results with colleagues and sponsors. In this course, 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 />
The theoretical part of the course provides an overview of reverse-time imaging methodology applied to wavefield seismic data. The main technique discussed is reverse-time migration with emphasis on modern imaging conditions which enable migration velocity analysis and amplitude-versus-angle analysis. The applied part demonstrates this technique on a complex geologic model using <tt>Madagascar</tt> codes in a fully reproducible setup.<br><br><br />
[http://reproducibility.org/wikilocal/docs/slides.pdf Seismic imaging tutorial]<br><br />
[http://reproducibility.org/RSF/book/rsf/school/sigsbee.html SConstruct]<br />
<br />
<br />
== Location ==<br />
<br />
Bahia Convention Center <br><br />
Av. Simon Bolívar, s/n – Jardim Armação <br><br />
41750-230 – Salvador -BA <br><br />
Brazil <br clear="all"><br><br />
<br />
== Instructor ==<br />
<br />
* Paul Sava (Colorado School of Mines)</div>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=Salvador_2009&diff=956Salvador 20092009-09-15T02:38:11Z<p>Psava: </p>
<hr />
<div><center><big>'''Madagascar School on Reproducible Computational Geophysics'''</big><br />
<br />
[[Image:salvador.jpg|500px]]<br />
<br />
<hr></div>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=File:Salvador.jpg&diff=955File:Salvador.jpg2009-09-15T02:35:47Z<p>Psava: </p>
<hr />
<div></div>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=Salvador_2009&diff=954Salvador 20092009-09-15T02:31:14Z<p>Psava: New page: <center><big>'''Madagascar School on Reproducible Computational Geophysics'''</big> Image:salvador.jpg <hr></p>
<hr />
<div><center><big>'''Madagascar School on Reproducible Computational Geophysics'''</big><br />
<br />
[[Image:salvador.jpg]]<br />
<br />
<hr></div>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=Conferences&diff=953Conferences2009-09-15T02:25:30Z<p>Psava: /* Madagascar-featured events */</p>
<hr />
<div>[[Image:Conferences.png|right|]]<br />
In reverse chronological order.<br />
<br />
==Madagascar-featured events==<br />
<br />
===School in Salvador 2009===<br />
<br />
[[Salvador_2009|Madagascar School on Reproducible Computational Geophysics]]<br />
<br />
===School in Delft 2009===<br />
<br />
[[Delft_2009|Madagascar School on Reproducible Computational Geophysics]]<br />
<br />
===Coding Sprint in Golden 2008===<br />
<br />
Implementation Workshop [[2008_Implementation_Workshop|Towards full automation and better robustness]] <br />
<br />
===School in Austin 2007===<br />
<br />
Short Course [[RSF_Austin_School_2007|Using and Extending RSF/Madagascar]].<br />
<br />
===School in Vancouver 2006===<br />
<br />
School and Workshop [[RSF_School_and_Workshop%2C_Vancouver_2006|Reproducible Research in Computational Geophysics]].<br />
<br />
==Conference presentations==<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>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=Delft_2009&diff=660Delft 20092009-02-26T05:47:17Z<p>Psava: </p>
<hr />
<div><center><big>'''Madagascar School on Reproducible Computational Geophysics'''</big><br />
<br />
[[Image:View-of-delft.jpg]]<br />
<br />
<hr><br />
<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Program<br />
|-<br />
! Day 1 <br />
! colspan="2" | Friday, June 12<br />
|-<br />
| 9:00-12:00<br />
! colspan="2" | Madagascar as a framework for reproducible research<br />
|-<br />
|<br />
| colspan="2" | <br />
<tt>Madagascar</tt> 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 and archiving them for future usage. This shared environment enables an efficient exchange of research results with colleagues and sponsors. 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 />
| 13:00-16:00<br />
! colspan="3" | Seismic interpretation (via OpendTect and <tt>Madagascar</tt>)<br />
|-<br />
! Day 2 <br />
! colspan="2" | Saturday, June 13<br />
|-<br />
| 9:00-12:00<br />
! colspan="2" | Wavefield seismic imaging <br />
|-<br />
|<br />
| colspan="2" | <br />
The theoretical part of this module provides an overview of reverse-time imaging methodology applied to wavefield seismic data. The main technique discussed is reverse-time migration with emphasis on modern imaging conditions which enable migration velocity analysis and amplitude-versus-angle analysis. The applied part demonstrates this technique on a complex geologic model using <tt>Madagascar</tt> codes in a fully reproducible setup.<br />
|-<br />
| 13:00-16:00<br />
! colspan="3" | Seismic interferometry<br />
|-<br />
|}<br />
<br />
</center><br />
<br />
== Location ==<br />
<br />
[[Image:TU.gif|left]]<br />
<br />
Department of Geotechnology<br><br />
Delft University of Technology (TU Delft)<br><br />
The Netherlands<br clear="all"><br />
<br />
== Instructors ==<br />
<br />
* Sergey Fomel (University of Texas at Austin)<br />
* Paul Sava (Colorado School of Mines)<br />
* Ivan Vasconcelos (ION Geophysical)<br />
<br />
== Registration ==<br />
<br />
Attendance is free but registration is required. To register, please send [mailto:rsfschool@gmail.com an email].</div>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=Delft_2009&diff=659Delft 20092009-02-26T05:44:25Z<p>Psava: </p>
<hr />
<div><center><big>'''Madagascar School on Reproducible Computational Geophysics'''</big><br />
<br />
[[Image:View-of-delft.jpg]]<br />
<br />
<hr><br />
<br />
<br />
<br />
{| align="center" border="1" cellpadding="5" cellspacing="0" <br />
! colspan="3" style="background:#ffdead;" | Program<br />
|-<br />
! Day 1 <br />
! colspan="2" | Friday, June 12<br />
|-<br />
| 9:00-12:00<br />
! colspan="2" | Madagascar as a framework for reproducible research<br />
|-<br />
|<br />
| colspan="2" | <br />
<tt>Madagascar</tt> 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 and archiving them for future usage. This shared environment enables an efficient exchange of research results with colleagues and sponsors. 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 />
! colspan="3" | Seismic interpretation (via OpendTect and <tt>Madagascar</tt>)<br />
|-<br />
! Day 2 <br />
! colspan="2" | Saturday, June 13<br />
|-<br />
| 9:00-12:00<br />
! colspan="2" | Wavefield seismic imaging <br />
|-<br />
|<br />
| colspan="2" | <br />
The theoretical part of this module provides an overview of reverse-time imaging methodology applied to wavefield seismic data. The main technique discussed is reverse-time migration with emphasis on modern imaging conditions which enable migration velocity analysis and amplitude-versus-angle analysis. The applied part demonstrates this technique on a complex geologic model using <tt>Madagascar</tt> codes in a fully reproducible setup.<br />
|-<br />
|<br />
! colspan="3" | Seismic interferometry<br />
|-<br />
|}<br />
<br />
</center><br />
<br />
== Location ==<br />
<br />
[[Image:TU.gif|left]]<br />
<br />
Department of Geotechnology<br><br />
Delft University of Technology (TU Delft)<br><br />
The Netherlands<br clear="all"><br />
<br />
== Instructors ==<br />
<br />
* Sergey Fomel (University of Texas at Austin)<br />
* Paul Sava (Colorado School of Mines)<br />
* Ivan Vasconcelos (ION Geophysical)<br />
<br />
== Registration ==<br />
<br />
Attendance is free but registration is required. To register, please send [mailto:rsfschool@gmail.com an email].</div>Psavahttps://www.reproducibility.org/wiki2020/index.php?title=Delft_2009&diff=657Delft 20092009-02-24T05:11:15Z<p>Psava: </p>
<hr />
<div><center><big>'''Madagascar School on Reproducible Computational Geophysics'''</big><br />
<br />
[[Image:View-of-delft.jpg]]<br />
<br />
<hr><br />
<br />
{| align="center" <br />
! colspan="3" style="background:#ffdead;" | Program<br />
|-<br />
! Day 1 <br />
! colspan="2" | Friday, June 12<br />
|-<br />
|<br />
! colspan="3" | Madagascar as a framework for reproducible research<br />
|-<br />
|<br />
! colspan="3" | Seismic interpretation (via OpendTect and Madagascar)<br />
|-<br />
! Day 2 <br />
! colspan="2" | Saturday, June 13<br />
|-<br />
|<br />
! colspan="3" | Wavefield seismic imaging<br />
The theoretical part of this module provides an overview of reverse-time imaging methodology applied to wavefield seismic data. The main technique discussed is reverse-time migration with emphasis on modern imaging conditions which enable migration velocity analysis and amplitude-versus-angle analysis. The applied part demonstrates this technique on a complex geologic model using Madagascar codes in a fully reproducible setup.<br />
|-<br />
|<br />
! colspan="3" | Seismic interferometry<br />
|-<br />
|}<br />
<br />
</center><br />
<br />
== Location ==<br />
<br />
[[Image:TU.gif|left]]<br />
<br />
Department of Geotechnology<br><br />
Delft University of Technology (TU Delft)<br><br />
The Netherlands<br clear="all"><br />
<br />
== Instructors ==<br />
<br />
* Sergey Fomel (University of Texas at Austin)<br />
* Paul Sava (Colorado School of Mines)<br />
* Ivan Vasconcelos (ION Geophysical)<br />
<br />
== Registration ==<br />
<br />
Attendance is free but registration is required. To register, please send [mailto:rsfschool@gmail.com an email].</div>Psava