1. Writing your own Madagascar applications Sergey Fomel University of Texas at Austin August 30, 2006 Vancouver, BC

2. August 30, 2006 Vancouver School & Workshop 1 of 17 This Presentation How to add your own low-level programs Programming in C Programming in other languages C++, Fortran-77, Fortran-90, Python, MATLAB How to contribute your programs, tests, and texts Who should contribute and why Copyright and licensing Resources http://rsf.sourceforge.net/wiki/index.php/API http://rsf.sourceforge.net/wiki/index.php/Demo http://rsf.sourceforge.net/wiki/index.php/Adding

3. August 30, 2006 Vancouver School & Workshop 2 of 17 The Easiest Way to Add Programs to Madagascar Create a directory under TOPDIR/user Follow examples from other directories cd TOPDIR/user; scons compiles locally with debugging flags cd TOPDIR; scons install compiles globally with optimization flags installs under $RSFROOT

4. August 30, 2006 Vancouver School & Workshop 3 of 17 Leaky Integration: leakint.c void leakint (int nt /* trace length */, float rho /* leakage */, float *trace /* integrated trace */) /* */ { int it; for (it=1; it < nt; it++) /* integrate */ trace[it] += rho*trace[it-1]; } comment the interface special style comment to generate leakint.h scons generates leakint.h compiles leakint.o

5. August 30, 2006 Vancouver School & Workshop 4 of 17 Leaky Integration: Mleakint.c /* Leaky integration. */ #include #include “leakint.h” int main(int argc, char* argv[]) { int n1, n2, i2; float rho, *pp; sf_file in, out; sf_init(argc,argv); in = sf_input("in"); out = sf_output("out"); if (!sf_histint(in,"n1",&n1)) sf_error("No n1= in input"); n2 = sf_leftsize(in,1); short description main library local subroutine initialize command line special type for files standard input/output trace length number of traces

6. August 30, 2006 Vancouver School & Workshop 5 of 17 Leaky Integration: Mleakint.c if (!sf_getfloat(“rho”,&rho)) rho=1.; /* leakage */ pp = sf_floatalloc(n1); /* loop over traces */ for (i2=0; i2 < n2; i2++) { sf_floatread(pp,n1,in); leakint (n1,rho,pp); sf_floatwrite(pp,n1,out); } exit(0); } read parameter from command line add comment for self-documentation error-checking memory allocation read trace write trace scons compiles sfleakint

7. August 30, 2006 Vancouver School & Workshop 6 of 17 Leaky Integration: leakint.f90 module leakint contains subroutine leakint (rho,trace) ! leaky integration float, intent (in) :: rho ! leakage float, dimension (:) :: trace ! Integrated trace int :: it, nt nt = size(trace) do it=2, nt ! integrate trace(it) = trace(it) + rho*trace(it-1) end do end subroutine end module comment the interface scons generates leakint.mod compiles leakint.o

8. August 30, 2006 Vancouver School & Workshop 7 of 17 Causal integration: Mleakint.f90 ! Leaky integration. program Mleakint use rsf use leakint implicit none integer :: n1, n2, i2 real, dimension (:), allocatable :: trace type (file) :: in, out call sf_init() in = rsf_input() out = rsf_output() call from_par(in,"n1",n1) n2 = filesize(in,1) short description main module local module initialize command line special type for files standard input/output trace length number of traces

9. August 30, 2006 Vancouver School & Workshop 8 of 17 Leaky Integration: Mleakint.f90 call get_par(“rho”,rho,1.) ! leakage allocate (trace (n1)) ! loop over traces do i2=1, n2 call rsf_read(in,trace) call leakint (rho,trace) call rsf_write(out,trace) end do end program Mleakint read parameter from command line read trace write trace scons compiles sfleakint

10. August 30, 2006 Vancouver School & Workshop 9 of 17 Other Language Bindings C++ Fortran-77 Python MATLAB … http://rsf.sourceforge.net/wiki/index.php/API http://rsf.sourceforge.net/wiki/index.php/Demo

11. August 30, 2006 Vancouver School & Workshop 10 of 17 This Presentation How to add your own programs Programming in C Programming in other languages C++, Fortran-77, Fortran-90, Python, MATLAB How to contribute your programs, tests, and texts Who should contribute and why Copyright and licensing Resources http://rsf.sourceforge.net/wiki/index.php/API http://rsf.sourceforge.net/wiki/index.php/Demo http://rsf.sourceforge.net/wiki/index.php/Adding

12. August 30, 2006 Vancouver School & Workshop 11 of 17 Four Reasons to Contribute to Open Source / Free Software To help your neighbor To show your talents To enable scientific progress To improve software quality

13. August 30, 2006 Vancouver School & Workshop 12 of 17 Four Reasons to Contribute to Open Source / Free Software I To help your neighbor “Run a program as you wish, for any purpose you wish, not limited to any narrowly defined application.” “Help yourself by improving the program (which requires access to source code).” “Help your neighbor by sharing a copy of the program with them.” “Help community by sharing the improved copy at large.” To show your talents To enable scientific progress To improve software quality Richard Stallman

14. August 30, 2006 Vancouver School & Workshop 13 of 17 Four Reasons to Contribute to Open Source / Free Software II To help your neighbor To show your talents “Open source is a gift to those who need to hire technical people. With open source, you can track someone’s work and contributions – good and bad – over a lengthy period of time.” “The top software developers are more productive than average software developers not by a factor of 10x or 100x or even 1000x but by 10,000x.” -- Nathan Myhrvold as quoted by Stephen Covey To enable scientific progress To improve software quality 37signals Microsoft

15. August 30, 2006 Vancouver School & Workshop 14 of 17 Four Reasons to Contribute to Open Source / Free Software III To help your neighbor To show your talents To enable scientific progress “Within the world of science, computation is now rightly seen as a third vertex of a triangle complementing experiment and theory. However, as it is now often practiced, one can make a good case that computing is the last refuge of the scientific scoundrel.” To improve software quality R. LeVeque

16. August 30, 2006 Vancouver School & Workshop 15 of 17 Four Reasons to Contribute to Open Source / Free Software IV To help your neighbor To show your talents To enable scientific progress To improve software quality “Given a large enough beta-tester and co-developer base, almost every problem will be characterized quickly and the fix obvious to someone.” "Given enough eyeballs, all bugs are shallow." Eric Raymond

17. August 30, 2006 Vancouver School & Workshop 16 of 17 How to contribute Get a permission to distribute under GPL “Using the GNU GPL will require that all the released improved versions be free software. This means you can avoid the risk of having to compete with a proprietary modified version of your own work.” Add GPL notice to all files. Keep your © Register at SourceForge and send us your login name to be added to the developer list Register at SourceForge Commit your files and directories to the repository using svn add and svn commit.

18. August 30, 2006 Vancouver School & Workshop 17 of 17 Lessons Adding your own programs is easy Pick language of your choice C, C++, Fortran-77, Fortran-90, Python, MATLAB Follow examples and conventions Test Contributing your programs and tests is easy Get permission if you need it Honor GPL Adopt Subversion