Manual

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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 research and processing with Madagascar" and getting it on SEG Bookmart's shelf :-)

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.

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, mailing lists, forums.

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):

More details can be found on the Conferences page.

Other free seismic processing and interpretation packages

Briefly mention SEPlib and SU, saying that they were covered in the History section. Follow with Free USP and the rest of the "Alternatives" section of the Introduction.

Downloading and installing Madagascar

Download

Download

Install

  1. Short installation guide
  2. Advanced installation guide

Using Madagascar

The lightning-quick tour

The revisited SEP Tour

Calling existing Madagascar programs

RSF, the Madagascar file format

The existing Guide to RSF file format

Finding out what program you need

  1. sfdoc -k
  2. Task-centric program list and all its subordinate nodes
  3. Collection of 1-2 page reproducible papers -- "How to do raytracing in Madagascar"; "How to do modeling in Madagascar"; etc
  4. SU to m8r dictionary
  5. 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

  1. Self-doc
  2. Local html self-doc ($RSFROOT/doc/index.html). Contains only and all programs installed on the user's machine.
  3. Online self-doc
  4. The wiki Guide to Programs.
  5. 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 results in existing papers

  1. 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>/
    Figure names are given in the html version too. [Note: In pdf versions obtained with scons pdf in paper directory, neither the book name nor paper directory name nor figure names are given. Figure names as well as a Geophysics-style header/footer with more details on the first page may be in order]
  2. 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.

  1. A paper with no figures.
  2. 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

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

How to add your program

The relevant section in "Adding programs"

How to document your program

The relevant section in "Adding programs"

Style guide

The relevant section in "Adding programs"

How to test your program

The relevant section in "Adding programs"

Tips and tricks

The relevant section in "Adding programs"

Madagascar library reference

Library Reference

Madagascar framework development

Description of Madagascar's inner works for those who want to help improve and maintain Madagascar.

Exploring RSFSRC

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.

Auto-generated documentation mechanism