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Reproducible Computational Experiments Using MADAGASCAR Software Package

Reproducible Computational Experiments Using MADAGASCAR Software Package. Sergey Fomel Bureau of Economic Geology University of Texas at Austin. Applied Inverse Problems Vancouver BC June 29, 2007. http://rsf.sf.net/. Principles of Scientific Software. Encapsulation File Formats

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Reproducible Computational Experiments Using MADAGASCAR Software Package

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  1. Reproducible Computational Experiments Using MADAGASCAR Software Package Sergey Fomel Bureau of Economic Geology University of Texas at Austin Applied Inverse Problems Vancouver BC June 29, 2007 http://rsf.sf.net/

  2. Principles of Scientific Software • Encapsulation • File Formats • Testing • Reproducibility • Maintenance http://rsf.sourceforge.net/

  3. Principles of Scientific Software • Encapsulation • File Formats • Testing • Reproducibility • Maintenance http://rsf.sourceforge.net/

  4. Encapsulation • Information hiding (Parnas, 1972) • Separation of concerns (Dijkstra, 1974) • Separate physics from mathematics • A is physics • Going from b to is mathematics http://rsf.sourceforge.net/

  5. Example: Velocity Transform http://rsf.sourceforge.net/

  6. Physics of Velocity Transform http://rsf.sourceforge.net/

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  8. http://rsf.sourceforge.net/

  9. Encapsulation in Programming • Separation of concerns • Classes or templates (C++) • Function pointers (C) • Function interfaces (Fortran-90) /* initialize velocity transform (A) */ veltran_init (true, x0, dx, nx, s0, ds, nv, o1, d1, nt, s02, anti, psun1, psun2); /* least-squares minimization of |A x – b|^2, x=vscan, b=cmp */ sf_solver (veltran_lop, sf_cgstep, ntv, ntx, vscan, cmp, niter, "err", error, "nmem", 0, "nfreq", miter, "mwt", mask, "end"); http://rsf.sourceforge.net/

  10. Encapsulation in UNIX • Write programs that do one thing and do it well. • Write programs to work together. • Write programs to handle text streams, because that is a universal interface. http://rsf.sourceforge.net/

  11. Encapsulation in UNIX Shell bash$ sfveltran < cmp.rsf > vtran.rsf adj=y v0=1 dv=0.025 nv=60 bash$ sfdottest sfveltran mod=vtran.rsf dat=cmp.rsf v0=1 dv=0.025 nv=60 sfdottest: L[m]*d=21665.9 sfdottest: L'[d]*m=21665.9 bash$ sfdottest sfveltran mod=vtran.rsf dat=cmp.rsf v0=1 dv=0.025 nv=60 sfdottest: L[m]*d=21906.2 sfdottest: L'[d]*m=21906.2 bash$ sfconjgrad sfveltran < cmp.rsf > vtran.rsf niter=3 v0=1 dv=0.025 nv=60 sfconjgrad: iter 1 of 3 sfconjgrad: grad=6.36797e+09 sfconjgrad: iter 2 of 3 sfconjgrad: grad=1.39068e+09 sfconjgrad: iter 3 of 3 sfconjgrad: grad=7.50257e+08 http://rsf.sourceforge.net/

  12. Principles of Scientific Software • Encapsulation • File Formats • Testing • Reproducibility • Maintenance http://rsf.sourceforge.net/

  13. The Art of UNIX Programming • (Raymond, 2004) • To design a perfect anti-Unix, make all file formats binary and opaque, and require heavyweight tools to read and edit them. • If you feel an urge to design a complex binary file format, or a complex binary application protocol, it is generally wise to lie down until the feeling passes. http://rsf.sourceforge.net/

  14. n1=1000 in=“/path/data.rsf@” n2=500 n3=100 d1=0.001 d2=0.1 o2=1 Data RSF (Regularly Sampled Format) • SEPlib (Stanford Exploration Project) • Data separated from text headers • Conceptually N-dimensional hypercubes • Multiple files for complex geometries • Not application specific http://rsf.sourceforge.net/

  15. Principles of Scientific Software • Encapsulation • File Formats • Testing • Reproducibility • Maintenance http://rsf.sourceforge.net/

  16. Testing • Test-driven development (Beck, 2003) • YAGNI principle • Always implement things when you actually need them, never when you just foresee that you need them. • In scientific software development, tests are computational experiments http://rsf.sourceforge.net/

  17. http://www.scons.org Testing with SCons • Software Construction • Replacement for “make” • reliable and extensible dependency analysis • configuration files are Python scripts • cross-platform • open-source http://rsf.sourceforge.net/

  18. SConstruct File # Mobil AVO CMP gather 807 at well4 location Fetch('cmp807_raw.HH','rad') # Preprocessing Flow('cmp','cmp807_raw.HH', 'dd form=native | tpow tpow=2 | mutter half=n v0=1.3 tp=0.2') Plot('cmp','grey title="Input CMP Gather" ‘) # Velocity Transform Flow('veltran','cmp','veltran s02=0.25 v0=1.250 dv=0.025 nv=60 adj=y') Plot('veltran','grey title="Velocity Scan" ') # Display Side by Side Result('veltran','cmp veltran','SideBySideAniso') http://rsf.sourceforge.net/

  19. Experimenting with SCons bash$ scons retrieve(["cmp807_raw.HH"], []) < cmp807_raw.HH sfdd form=native | sftpow tpow=2 | sfmutter half=n v0=1.3 tp=0.2 > cmp.rsf < cmp.rsf sfgrey title="Input CMP Gather" > cmp.vpl < cmp.rsf sfveltran s02=0.25 v0=1.250 dv=0.025 nv=60 adj=y > veltran.rsf < veltran.rsf sfgrey title="Velocity Scan" > veltran.vpl vppen yscale=2 vpstyle=n gridnum=2,1 cmp.vpl veltran.vpl > Fig/veltran.vpl bash$ sed s/Velocity/Slowness/ < SConstruct > SConstruct2 bash$ mv SConstruct2 SConstruct bash$ scons < veltran.rsf sfgrey title=“Slowness Scan" > veltran.vpl vppen yscale=2 vpstyle=n gridnum=2,1 cmp.vpl veltran.vpl > Fig/veltran.vpl http://rsf.sourceforge.net/

  20. Principles of Scientific Software • Encapsulation • File Formats • Testing • Reproducibility • Maintenance http://rsf.sourceforge.net/

  21. Reproducible Research at Stanford • (Knuth, 1992) • A computer program should be written with human readability as a primary goal. • (Claerbout and Karrenbach, 1992) • The purpose of reproducible research is to facilitate someone going a step further by changing something. • (Buckheit and Donoho, 1995) • An article about computational science in a scientific publication is not the scholarship itself, it is merely advertising of the scholarship. http://rsf.sourceforge.net/

  22. Reproducible Experiments • 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 […] Where else in science can one get away with publishing observations that are claimed to prove a theory or illustrate the success of a technique without having to give a careful description of the methods used, in sufficient detail that others can attempt to repeat the experiment?(LeVeque, 2006) http://rsf.sourceforge.net/

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  25. Principles of Scientific Software • Encapsulation • File Formats • Testing • Reproducibility • Maintenance http://rsf.sourceforge.net/

  26. Maintenance • Computational experiments that are not continuously maintained loose reproducibility. • Regression testing (Brooks, 1975) • Contribute computational software and experiments to a community-maintained repository to enable research productivity. http://rsf.sourceforge.net/

  27. Open Science http://rsf.sourceforge.net/

  28. http://rsf.sf.net/ Conclusions • Principles of Scientific Software • Encapsulation • File Formats • Testing • Reproducibility • Maintenance • Madagascar software package • Open source, open community, open science http://rsf.sourceforge.net/

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