As the number of pages on the Wiki grows, the navbar starts becoming insufficient for proper organization of all documentation. A top-down view of all materials about Madagascar is also useful for determining whether gaps in coverage exist. This page will stay in the Sandbox for a long while -- until all gaps have been filled.

Ideally the manual will only consist of either links to wiki pages, or own content. "Forking", i.e. creating a modified copy of a page especially for the manual, invariably ends up with one version getting out of synch.

How nice would it be, and what publicity would bring, calling this manual "Reproducible data analysis with Madagascar" and getting it on SEG Bookmart's shelf :-)

1 About Madagascar
2 Downloading and installing Madagascar
- 2.1 Download
- 2.2 Install
3 Using Madagascar
4 Developing in Madagascar
- 4.1 Writing your own programs
- 4.2 Madagascar framework development
  - 4.2.1 cfortran.h
  - 4.2.2 Automated code checks
5 Datasets distributed with Madagascar
6 Other open-source data analysis packages
- 6.1 Geophysical software
- 6.2 Other tools

About Madagascar

What is Madagascar?

Madagascar description and features from the main page of the wiki. Sections 1 and 2 (What is in Madagascar; Copyright) from Introduction to madagascar.

For people who do not read manuals

Point them to Download, Short Install Guide, and the SEPlib Tour Revisited.

Why use Madagascar?

An articulate description of the reasons on the Why Madagascar page. Have some spectacular pictures obtained with algorithms that are not present in other packages. Describe algorithms/tools unavailable in other open-source geophysical data analysis packages.

Community

A description of the current Madagascar community, with the map of downloads and an estimate of the number of installs, who are the biggest users, outstanding research results obtained with Madagascar, etc. Links to the blog, user mailing list, developer mailing list. Also mention the bug tracker and feature request tracker, encouraging the community to use them more. Mention forums as an alternative for those who want to ask questions or conduct discussions without subscribing to a mailing list.

History

A history of Madagascar, with the SEPlib/SU part of the "Alternatives" section of the Introduction, and mentions of landmark events (short descriptions where necessary):

when and where it was started
2004-08 (?): made available to selected alpha users
2005-02-16: RSF Blog started
2006-03-17: Registered on Sourceforge
2006-04-19: Name change from RSF to Madagascar
2006-06-11: Public launch at the Open Source E&P Software EAGE Workshop (Vienna)
2006-06-18: First stable version (0.9.1). Mailing lists created
2006-07-23: Madagascar logo created by Scott Rodgers (BEG)
2006-08-30/31: Madagascar School and Workshop (Vancouver) (How many participants, from how many universities and how many companies?)
2007-04-20: Madagascar School (Austin)
2008-05-23/26: Madagascar Implementation Workshop (Golden)

More details can be found on the Conferences page.

Downloading and installing Madagascar

Download

Install

Using Madagascar

The lightning-quick tour

The revisited SEP Tour

The Madagascar file formats

The Regularly Sampled Format (RSF)

The current Guide to RSF file format

Handling irregularly sampled data

Explain the principle of the current method (sfheadermath/sfheaderwindow used on the trace header block output by su/segyread)

Calling existing Madagascar programs

Finding out what program you need

sfdoc -k
Task-centric program list and all its subordinate nodes
Collection of 1-2 page reproducible papers -- "How to do raytracing in Madagascar"; "How to do modeling in Madagascar"; etc
SU to m8r dictionary
SEPlib to m8r dictionary
Other such dictionaries, for free or proprietary seismic processing packages. Such dictionaries are also useful because they will highlight algorithms/utilities present in such packages but missing from m8r.

This chapter is now just a sketch, should get quite big. Users approach tools in a task-centric fashion, i.e. Q1:"how do I do X with Madagascar?", A1:"With feature Y"; Q2: "How do I use feature Y to this end?" M8r is very good at answering Q2, but people ask Q1 first. Many of the reproducible papers included so far contain cutting-edge research. Users learning how to use Madagascar need to start with something much more simple, where they do not have to focus on understanding research on top of understanding software.

Learning how to use a given program

Command-line self-doc
Local html self-doc ($RSFROOT/doc/index.html). Contains all programs installed on the user's machine and only those programs.
Online self-doc
The wiki Guide to Programs.
The ultimate guide are the repro papers; pointer to relevant section of the manual ("Exploring reproducible papers")

What is reproducibility

The whole Reproducibility page, combined with Section 1 from Reproducible computational experiments using SCons

Exploring existing reproducible papers

Papers and books included in the Madagascar distribution

Reproducible Documents and more.

How to reproduce specific figures in existing papers

Finding the paper directory: If the interesting article has been found by browsing/hyperlink to Reproducible Documents, then the reproducibility package corresponding to
```
http://www.reproducibility.org/RSF/book/<bookname>/<papername>/paper_html/
```
can be found in
```
RSFSRC/book/<bookname>/<papername>/
```
Finding result names: Use the html version of the paper, or grep in all .tex files in the directory for a text string that occurs in the figure legend. Multiple-panel figures may have individual names for each panel. [Note: In pdf versions obtained with scons pdf in paper directory, neither the book name nor paper directory name nor figure names are given. LaTeX options to have figure names as well as a Geophysics-style header/footer with more details on the first page may be in order]
Command that should be typed in a paper directory to reproduce individual results, when their name is known.

How to reproduce entire papers

See the previous section for how to find the paper directory
The relevant SCons commands to reproduce the paper (scons pdf and scons read). Troubleshooting:
- If it fails with this kind of messages (details here), you miss TeX system dependencies. Install a TeX system. Tex Live should have it all. Note: It's a 1 Gb download. Too large for many individual users to bother with it and for most IT departments of companies to review for security. We should implement individual dependency checking, like we do in the installation. Otherwise it is equivalent to telling the user that in order to install Madagascar, he should install Debian with all 30000 packages in the repository... the dependencies will be among them.
- If scons pdf in the paper directory pdf figures already in place in order to work, run sftour scons lock.
- Tell the user to expect conditional reproducibility: If Matlab is not present, rsftex will not try to build the figures but will use the stored PDF files (same goes for Mathematica, xfig, etc.)

How to reproduce whole books

The 2006-12-22 rsf-user thread, the 2007-04-08 blog entry and more.

Writing a LaTeX paper in the Madagascar framework

Follows the natural progression of learning of somebody who may even not know LaTeX, let alone SCons.

A paper with no figures.
A paper with NR-only figures

Creating a reproducible paper

Sections 2 3 from Reproducible computational experiments using SCons. Also, mention the "SCons macros" in book/packages.

Creating a reproducible book

Developing in Madagascar

Writing your own programs

The Madagascar API

The existing data clipping API demo
A more complex finite differences API demo – add Python, F77 and Matlab APIs to it

Madagascar framework development

Description of m8r's inner works for those who want to help improve and maintain Madagascar. This section does not have a structure yet, and is so far just a place for gathering content.

cfortran.h

This source code file provides a machine-independent interface between C procedures, Fortran procedures and global data (more details on the website of its initial author). It is a dependency of the F77 and F90 APIs, as well as of vplot. It is included in m8r in three (!) places. Version 4.3 (2002) is still distributed through the website of the original author. Another version (fork?) is maintained at CERN and distributed in the include directory of the interface to event generators in the Monte Carlo libraries in the CERN Program Library (CERNlib). Debian distributes the Free Software part of this package as cernlib. Under Fedora, cfortran.h is included in cernlib-g77-devel and cernlib-devel, which happily overwrite each other's files and create copies of cfortran.h in two different locations deeply nested under /usr/include. CERNlib's Debian maintainer states that "CERNlib is an ancient mass of mostly Fortran code" and that "Most components of CERNLIB are completely broken on modern 64-bit architectures", so m8r developers should be aware that CERNlib will probably be superseded at some point in the future by ROOT, with upstream cfortran.h maintenance possibly continuing this way.

Automated code checks

Madagascar contains the beginning of an implementation of static code checks for security vulnerabilities and coding mistakes with Splint. This is visible in the code through the presence of comments like /*@out@*/ and /*@null@*/, which instruct Splint about the intent of different variables and function return values. Future plans include using also dynamic checking by Valgrind or IBM's Rational Purify.

Datasets distributed with Madagascar

Description of datasets – pictures of the velocity model, of sample gathers, zero-offset sections, migrated image.
Comment on which are the main problems they illustrate (internal multiples? overturning waves? etc). Algorithm used for generating them, references to published literature describing the datasets
Command line options for correctly reading them from the storage format (SEG-Y, most probably) into RSF
In general, expand the datasets section of Reproducible Documents page to include other datasets

Other open-source data analysis packages

Geophysical software

Other open-source geophysical packages. Briefly discuss each of them. Mention "dictionaries" from them to m8r where available (should attempt to have dictionaries for all of them)

Other tools

Mention other open-source codes that are commonly used by geophysicists:

SciPY
FFTW
BLAS/Atlas

etc

Manual

Contents