1. Madagascar Installation
Sergey Fomel
University of Texas at Austin
August 30, 2006
Vancouver, BC

2. Vancouver School & Workshop
This Presentation
Introductory remarks
History
Goals
Design principles
Installation and compilation
Downloading
Software construction with SCons
File structure
August 30, 2006
Vancouver School & Workshop

3. Vancouver School & Workshop
Madagascar Story
Started in 2003
Publicly open in June 2006
Open-source
Standing on SEPlib/SU shoulders
RSF (regularly sampled format)
August 30, 2006
Vancouver School & Workshop

4. Cumulative Downloads Registered at freshmeat.net
Vancouver School announced
August 30, 2006
Vancouver School & Workshop

5. Vancouver School & Workshop
August 30, 2006
Vancouver School & Workshop

6. Source Referral (August 2006)
Vancouver School & Workshop

7. Vancouver School & Workshop
Goal
To make our research* productive
To make technology transfer efficient
*computational experiments
August 30, 2006
Vancouver School & Workshop

8. One Week Technology Transfer
Monday
Get an idea
Tuesday
Implement it
Wednesday
Test it
Thursday
Communicate it
Friday
Commercialize it a b c
August 30, 2006
Vancouver School & Workshop

9. Madagascar Design Principles
Document computational experiments
Old experiments are regression tests
New experiments become unit tests
Test Driven Development
August 30, 2006
Vancouver School & Workshop

10. Vancouver School & Workshop
This Presentation
Introductory remarks
History
Goal
Design principles
Installation and compilation
Downloading
Compiling with SCons
File structure
August 30, 2006
Vancouver School & Workshop

11. Downloading Madagascar
Stable version
madagascar-0.9.3
SourceForge
Unstable (development) version
svn co rsf
Update with svn update
Commit with svn commit (developers)
Browse at
Subversion facilitates collaboration and version control
August 30, 2006
Vancouver School & Workshop

12. Cumulative Subversion Access
August 30, 2006
Vancouver School & Workshop

13. SCons (Software Construction)
“make” replacement
Built-in “autoconf/automake” functionality
Written in
Open-source
Used for compiling Madagascar
Used for managing processing flows
SCons is an easier, more reliable and faster way to build software.
August 30, 2006
Vancouver School & Workshop

14. Vancouver School & Workshop
From Tim O’Reilly’s blog “O’Reilly Radar”
August 30, 2006
Vancouver School & Workshop

15. Installing from Source
Unpack
tar xvzf madagascar tgz
Prerequisites
Install Python and SCons if necessary
Set environmental variables
Build
scons config (generates config.py)
scons install
$RSFROOT
root of installation
$PYTHONPATH
add $RSFROOT/lib
$DATAPATH
home for binary files
August 30, 2006
Vancouver School & Workshop

16. Vancouver School & Workshop
Open Source
created by scons install
madagascar-0.9.3/
Sconstruct
config.py
api/
book/
filt/
user/
pens/
plot/
python/ convenience Python scripts
scons/ SCons sources
$RSFROOT/
bin/
lib/
include/
doc/
figs/
August 30, 2006
Vancouver School & Workshop

17. Vancouver School & Workshop
Look Inside I
madagascar-0.9.3/
Sconstruct top software construction
config.py created by scons config
ENV = {'PATH': '/usr/local/bin:/bin:/usr/bin'}
AR = 'ar'
JPEG = 'jpeg'
PPM = None
CC = 'gcc'
CCFLAGS = '-O2 -std=gnu99 -Wall -pedantic -DNO_COMPLEX'
CPPPATH = []
LIBPATH = []
LIBS = ['m', 'rpc']
XLIBPATH = ['/usr/X11R6/lib']
XLIBS = ['Xaw', 'Xt', 'X11']
XINC = ['/usr/X11R6/include']
CXX = 'g++'
August 30, 2006
Vancouver School & Workshop

18. Vancouver School & Workshop
Look Inside II
api/ API tests C++/Fortran/MATLAB…
book/ reproducible research tests
gee/ book
ajt/ chapter/paper
SConstruct
paper.tex (LaTeX)
causint/ project
conv/ …
hlx/
bei/
geo391/
from rsfproj import *
Flow('data1',None,'spike n1=30 k1=15 label1=')
Flow('data2','data1','causint')
Flow('data3','data1','causint adj=y')
Flow('data4',None,
'spike n1=30 nsp=2 k1=10,15 mag=1,-1 label1= ')
Flow('data5','data4','causint')
Flow('data6','data4','causint adj=y')
Flow('data7','data5','causint')
August 30, 2006
Vancouver School & Workshop

19. Vancouver School & Workshop
Look Inside III
filt/ program sources arranged by subject
lib/ sources for rsf.h, librsf.a and API bindings
SConstruct
alloc.c …
main/ most common data manipulation programs
add.c
proc/ “processing”
imag/ “imaging”
user/ program sources arranged by author
fomels/
slim/
… easily extensible
August 30, 2006
Vancouver School & Workshop

20. Vancouver School & Workshop
Look Inside IV
plot/ sources for Vplot generation
lib/ sources for rsfplot.h, librsfplot.a
SConstruct
axis.c …
main/ RSF to Vplot
contour.c
test/ Vplot from source
pens/ sources for Vplot manipulation
main/
pspen.c Vplot to PostScript
August 30, 2006
Vancouver School & Workshop

21. Vancouver School & Workshop
Lessons
Madagascar goal
To make our research productive
To make technology transfer efficient
Multiple levels
(Tuesday) implement – main modules, C
(Wednesday) test – projects, SCons/Python
(Thursday) communicate – papers, LaTeX
If you don’t like it, please voice your concerns.
Wiki | Blog | Mailing list | Forums | Bug tracking | Feature requests
August 30, 2006
Vancouver School & Workshop