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Organize ROOT Analyses with Autoconf

Patrick Huck
November 14, 2011

Organize ROOT Analyses with Autoconf

An example-driven introduction to using autoconf/automake (& Doxygen) for the organization of C++ data analysis software within the CERN ROOT framework. A C++ tool has meanwhile been developed which takes care of the setup automatically: http://tschaume.github.com/ckon/

Patrick Huck

November 14, 2011
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Transcript

  1. Why? Macro to Program Class Structure Analysis Software Links
    1 Why?
    2 Macro to Program
    3 Class Structure
    4 Analysis Software
    5 Links
    Using Automake & Doxygen
    for setting up your Analysis Software
    A Step-by-Step Guide using ROOT’s hSimple.C tutorial
    Patrick Huck
    Juniors Day @ STAR Collab. Meeting, LBNL
    (11/14/2011)
    1 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

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  2. Why? Macro to Program Class Structure Analysis Software Links
    Requirements
    – easy to keep tidy
    – compiled programs
    - fast fitting & looping
    - detect bugs during compilation not runtime
    - controlled by main program
    – I/O controlled by program invocation
    - options/parameters
    - no recompilation, no hard-coding
    – easily include foreign classes/code
    – Utility/Database classes
    – GNU standard
    - configure, make [clean, distclean, dist]
    - platform independent
    – documentation within code
    - man-pages, L
    A
    TEX
    - Analysis Homepage
    – simplified Makefiles
    – one ’make’ generates all
    automake
    &
    doxygen
    with a little effort these two in
    combination make all this possible.
    This talk goes through an easy
    example to illustrate the setup and
    usage of automake incl. doxygen.
    Links and files will soon be provided.
    2 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

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  3. Why? Macro to Program Class Structure Analysis Software Links
    General Structure Documentation (HTML/man) L
    ATEXDoc. and Distribution Package
    MySimpleExample/
    README
    configure.ac
    Makefile.am
    src/
    hSimple.cc
    bin/
    hSimple
    out/
    hsimple.root
    pics/
    hSimple.png
    config/
    – README file for instructions
    – configuration file for ./configure
    01: AC INIT([My Simple Example], [11.11.14], [[email protected]], [MySimpleEx-
    ample], [http://www.star.bnl.gov/protected/lfspectra/huck/])
    02: AC PREREQ(2.59)
    03: AM SILENT RULES([yes])
    04: AC CONFIG AUX DIR(config)
    05: AM INIT AUTOMAKE([-Wall no-define])
    06: AC PROG CC
    07: AC PROG CXX
    08: ROOT PATH
    09: AM PROG LIBTOOL
    10: AC SUBST(DEPS CFLAGS)
    11: AC SUBST(DEPS LIBS)
    17: AC CONFIG FILES([Makefile])
    18: AC OUTPUT
    – main program for $ROOTSYS/tutorials/hsimple.C
    – simple Makefile for generating bin/hSimple
    – generate all (program installed in bin/)
    – add MySimpleExample/bin to $PATH in ~/.bashrc
    – run the program specifying the output file
    3 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

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  4. Why? Macro to Program Class Structure Analysis Software Links
    General Structure Documentation (HTML/man) L
    ATEXDoc. and Distribution Package
    MySimpleExample/
    README
    configure.ac
    Makefile.am
    src/
    hSimple.cc
    bin/
    hSimple
    out/
    hsimple.root
    pics/
    hSimple.png
    config/
    – README file for instructions
    – configuration file for ./configure
    – main program for $ROOTSYS/tutorials/hsimple.C
    058: void *hsimple(TFile* hfile) { // hSimple.C code
    106: int main(int argc, char **argv) {
    107: TRint* theApp = new TRint("App", &argc, argv, NULL, 0);
    108: if ( theApp->Argc() == 2 ) {
    109: TString filename = theApp->Argv(1);
    110: TFile* hfile = new TFile(filename,"RECREATE");
    111: hsimple(hfile);
    112: }
    117: theApp->Run();
    118: return 0;
    119: }
    – simple Makefile for generating bin/hSimple
    – generate all (program installed in bin/)
    – add MySimpleExample/bin to $PATH in ~/.bashrc
    – run the program specifying the output file
    4 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

    View full-size slide

  5. Why? Macro to Program Class Structure Analysis Software Links
    General Structure Documentation (HTML/man) L
    ATEXDoc. and Distribution Package
    MySimpleExample/
    README
    configure.ac
    Makefile.am
    src/
    hSimple.cc
    bin/
    hSimple
    out/
    hsimple.root
    pics/
    hSimple.png
    config/
    – README file for instructions
    – configuration file for ./configure
    – main program for $ROOTSYS/tutorials/hsimple.C
    – simple Makefile for generating bin/hSimple
    02: # General Stuff
    03: AUTOMAKE OPTIONS = subdir-objects foreign
    04: ACLOCAL AMFLAGS = -I /Applications/root/build/misc
    05: AM CPPFLAGS = $(DEPS CFLAGS) -I$(ROOTINCDIR)
    06: AM CFLAGS = $(LAYOUT CFLAGS)
    09: # hSimple program
    10: bin PROGRAMS = bin/hSimple
    11: bin hSimple SOURCES = src/hSimple.cc
    12: bin hSimple CXXFLAGS = @ROOTCFLAGS@
    13: bin hSimple LDADD = -L@ROOTLIBDIR@ @ROOTGLIBS@
    @ROOTLIBS@ @LIBS@ ${DEPS LIBS}
    – generate all (program installed in bin/)
    – add MySimpleExample/bin to $PATH in ~/.bashrc
    – run the program specifying the output file
    5 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

    View full-size slide

  6. Why? Macro to Program Class Structure Analysis Software Links
    General Structure Documentation (HTML/man) L
    ATEXDoc. and Distribution Package
    MySimpleExample/
    README
    configure.ac
    Makefile.am
    src/
    hSimple.cc
    bin/
    hSimple
    out/
    hsimple.root
    pics/
    hSimple.png
    config/
    – README file for instructions
    – configuration file for ./configure
    – main program for $ROOTSYS/tutorials/hsimple.C
    – simple Makefile for generating bin/hSimple
    – generate all (program installed in bin/)
    1: autoreconf -v --force --install
    2: ./configure
    3: make
    – add MySimpleExample/bin to $PATH in ~/.bashrc
    – run the program specifying the output file
    6 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

    View full-size slide

  7. Why? Macro to Program Class Structure Analysis Software Links
    General Structure Documentation (HTML/man) L
    ATEXDoc. and Distribution Package
    MySimpleExample/
    README
    configure.ac
    Makefile.am
    src/
    hSimple.cc
    bin/
    hSimple
    out/
    hsimple.root
    pics/
    hSimple.png
    config/
    – README file for instructions
    – configuration file for ./configure
    – main program for $ROOTSYS/tutorials/hsimple.C
    – simple Makefile for generating bin/hSimple
    – generate all (program installed in bin/)
    – add MySimpleExample/bin to $PATH in ~/.bashrc
    1: export PATH=$PATH:[your/top srcdir]/bin
    – run the program specifying the output file
    1: hSimple "out/hsimple.root"
    7 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

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  8. Why? Macro to Program Class Structure Analysis Software Links
    General Structure Documentation (HTML/man) L
    ATEXDoc. and Distribution Package
    MySimpleExample/
    README
    configure.ac
    Makefile.am
    src/
    mainpage.cc
    hSimple.cc
    bin/
    docs/
    Doxyfile.in
    html/
    index.html
    ...
    man/man3/
    hSimple.3
    out/
    pics/
    config/
    – add doxygen support to configure.ac
    12: AC CHECK PROGS([DOXYGEN], [doxygen])
    13: if test -z "$DOXYGEN";
    14: then AC MSG WARN([Doxygen not found - continuing w/o support])
    15: fi
    16: AM CONDITIONAL([HAVE DOXYGEN],[test -n "$DOXYGEN"])
    AM COND IF([HAVE DOXYGEN], [AC CONFIG FILES([docs/Doxyfile])])
    – add doxygen support to Makefile.am
    21: # doxygen
    22: if HAVE DOXYGEN
    23: all-local:
    27: $(DOXYGEN) docs/Doxyfile
    30: endif
    – modify docs/Doxyfile.in
    – add comments at top of src/hSimple.cc
    – generate html start page: src/mainpage.cc
    – html-documentation automatically generated
    – man-pages automatically generated
    8 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

    View full-size slide

  9. Why? Macro to Program Class Structure Analysis Software Links
    General Structure Documentation (HTML/man) L
    ATEXDoc. and Distribution Package
    MySimpleExample/
    README
    configure.ac
    Makefile.am
    src/
    mainpage.cc
    hSimple.cc
    bin/
    docs/
    Doxyfile.in
    html/
    index.html
    ...
    man/man3/
    hSimple.3
    out/
    pics/
    config/
    – add doxygen support to configure.ac and Makefile.am
    – modify docs/Doxyfile.in
    (html, man and latex generation set to YES)
    002: PROJECT NAME = "title"
    003: PROJECT NUMBER = 11.11.14
    004: PROJECT BRIEF = "subtitle"
    005: PROJECT LOGO = [absolute url to logo]
    006: OUTPUT DIRECTORY = [absolute url to docs/]
    099: INPUT = [absolute url to src/]
    142: IMAGE PATH = [absolute url to pics/]
    176: HTML EXTRA FILES = [absolute url to pics/]
    – add comments at top of src/hSimple.cc
    – generate html start page: src/mainpage.cc
    – html-documentation automatically generated
    – man-pages automatically generated
    9 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

    View full-size slide

  10. Why? Macro to Program Class Structure Analysis Software Links
    General Structure Documentation (HTML/man) L
    ATEXDoc. and Distribution Package
    MySimpleExample/
    README
    configure.ac
    Makefile.am
    src/
    mainpage.cc
    hSimple.cc
    bin/
    docs/
    Doxyfile.in
    html/
    index.html
    ...
    man/man3/
    hSimple.3
    out/
    pics/
    config/
    – add doxygen support to configure.ac and Makefile.am
    – modify docs/Doxyfile.in
    – add comments at top of src/hSimple.cc
    001: /*!
    003: * \class hSimple
    004: *
    005: * \brief program for hsimple ROOT tutorial
    006: *
    007: * program description
    011: *
    017: * \par Steps in Detail (see presentation ... url)
    018: * \li mk folders: src,docs,bin,pics,out
    027: *
    028: * \par Images
    029: * \image html ”pics/hSimple.png” ”px distribution”
    030: * \image latex ”pics/hSimple.png” ”px distribution” width=10cm
    031: *
    032: * \par Usage
    033: * hSimple filename
    034: * \param[in] filename filename (incl. dir) for output file
    036: */
    – generate html start page: src/mainpage.cc
    – html-documentation automatically generated
    – man-pages automatically generated
    10 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

    View full-size slide

  11. Why? Macro to Program Class Structure Analysis Software Links
    General Structure Documentation (HTML/man) L
    ATEXDoc. and Distribution Package
    MySimpleExample/
    README
    configure.ac
    Makefile.am
    src/
    mainpage.cc
    hSimple.cc
    bin/
    docs/
    Doxyfile.in
    html/
    index.html
    ...
    man/man3/
    hSimple.3
    out/
    pics/
    config/
    – add doxygen support to configure.ac and Makefile.am
    – modify docs/Doxyfile.in
    – add comments at top of src/hSimple.cc
    – generate html start page: src/mainpage.cc
    01: /*!
    03: * \mainpage Start Page
    04: *
    05: * \note \b Update (Sep 19 2011)

    06: * \li performed and added class for basic RefMult QA (refMultQA)
    10: *
    11: * \par Table of Contents
    12: * The following list outlines the order of programs used for my analysis.\n
    13: * The links lead to the respective documentation.
    14: * \li hSimple
    16: */
    – html-documentation automatically generated
    – man-pages automatically generated
    11 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

    View full-size slide

  12. Why? Macro to Program Class Structure Analysis Software Links
    General Structure Documentation (HTML/man) L
    ATEXDoc. and Distribution Package
    MySimpleExample/
    README
    configure.ac
    Makefile.am
    src/
    mainpage.cc
    hSimple.cc
    bin/
    docs/
    Doxyfile.in
    html/
    index.html
    ...
    man/man3/
    hSimple.3
    out/
    pics/
    config/
    – add doxygen support to configure.ac and Makefile.am
    – modify docs/Doxyfile.in
    – add comments at top of src/hSimple.cc
    – generate html start page: src/mainpage.cc
    – html-documentation automatically generated into
    docs/html/ during make (start page, links, source code)
    – man-pages automatically generated
    12 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

    View full-size slide

  13. Why? Macro to Program Class Structure Analysis Software Links
    General Structure Documentation (HTML/man) L
    ATEXDoc. and Distribution Package
    MySimpleExample/
    README
    configure.ac
    Makefile.am
    src/
    mainpage.cc
    hSimple.cc
    bin/
    docs/
    Doxyfile.in
    html/
    index.html
    ...
    man/man3/
    hSimple.3
    out/
    pics/
    config/
    – add doxygen support to configure.ac and Makefile.am
    – modify docs/Doxyfile.in
    – add comments at top of src/hSimple.cc
    – generate html start page: src/mainpage.cc
    – html-documentation automatically generated into
    docs/html/ during make (start page, links, source code)
    – man-pages automatically generated
    13 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

    View full-size slide

  14. Why? Macro to Program Class Structure Analysis Software Links
    General Structure Documentation (HTML/man) L
    ATEXDoc. and Distribution Package
    MySimpleExample/
    README
    configure.ac
    Makefile.am
    src/
    mainpage.cc
    hSimple.cc
    bin/
    docs/
    Doxyfile.in
    html/
    index.html
    ...
    man/man3/
    hSimple.3
    out/
    pics/
    config/
    – add doxygen support to configure.ac and Makefile.am
    – modify docs/Doxyfile.in
    – add comments at top of src/hSimple.cc
    – generate html start page: src/mainpage.cc
    – html-documentation automatically generated into
    docs/html/ during make (start page, links, source code)
    – man-pages automatically generated
    14 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

    View full-size slide

  15. Why? Macro to Program Class Structure Analysis Software Links
    General Structure Documentation (HTML/man) L
    ATEXDoc. and Distribution Package
    MySimpleExample/
    README
    configure.ac
    Makefile.am
    src/
    mainpage.cc
    hSimple.cc
    bin/
    docs/
    Doxyfile.in
    html/
    index.html
    ...
    man/man3/
    hSimple.3
    out/
    pics/
    config/
    – add doxygen support to configure.ac and Makefile.am
    – modify docs/Doxyfile.in
    – add comments at top of src/hSimple.cc
    – generate html start page: src/mainpage.cc
    – html-documentation automatically generated
    – man-pages automatically generated into docs/man
    → include docs/man/ in $MANPATH to use via man hSimple
    15 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

    View full-size slide

  16. Why? Macro to Program Class Structure Analysis Software Links
    General Structure Documentation (HTML/man) L
    ATEXDoc. and Distribution Package
    MySimpleExample/
    README
    configure.ac
    Makefile.am
    src/
    bin/
    docs/
    Makefile mod
    refman mod.tex
    update texfile.sh
    html/
    latex/
    refman mod.tex
    Makefile mod
    doxygen.sty
    main.tex
    classh simple.tex
    man/
    out/
    pics/
    config/
    MySimpleExample-11.11.14.tar.gz
    – L
    A
    TEX-files generated by doxygen during make
    → doxygen.sty, main.tex, classh simple.tex, ...
    → docs/html/ re-generated
    21: # doxygen
    22: if HAVE DOXYGEN
    23: all-local:
    24: rm -rf $(top srcdir)/docs/html
    25: mkdir docs/html
    26: # ./bin/copy files.sh # copy pics included w/ tag
    27: $(DOXYGEN) docs/Doxyfile
    30: endif
    – include latex mod’s in all-local target in Makefile.am
    – generate pdf-documentation
    – control distribution package
    – generate tar ball for code sharing/distribution
    16 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

    View full-size slide

  17. Why? Macro to Program Class Structure Analysis Software Links
    General Structure Documentation (HTML/man) L
    ATEXDoc. and Distribution Package
    MySimpleExample/
    README
    configure.ac
    Makefile.am
    src/
    bin/
    docs/
    Makefile mod
    refman mod.tex
    update texfile.sh
    html/
    latex/
    refman mod.tex
    Makefile mod
    doxygen.sty
    main.tex
    classh simple.tex
    man/
    out/
    pics/
    config/
    MySimpleExample-11.11.14.tar.gz
    – L
    A
    TEX-files generated by doxygen during make
    – include latex mod’s in all-local target in Makefile.am
    21: # doxygen
    22: if HAVE DOXYGEN
    23: all-local:
    24: rm -rf $(top srcdir)/docs/html
    25: mkdir docs/html
    26: # ./bin/copy files.sh # copy pics included w/ tag
    27: $(DOXYGEN) docs/Doxyfile
    28: cp docs/refman mod.tex docs/latex/
    29: cp docs/Makefile mod docs/latex/
    30: endif
    i) docs/refman_mod.tex includes only necessary
    tex-files in documentation section (change author
    and modify when new class/program is generated)
    ii) docs/update_texfile.sh updates the title page
    in docs/refman_mod.tex (no mod’s needed)
    iii) docs/Makefile_mod calls update_texfile.sh
    when the pdf-file is generated (no mod’s needed)
    – generate pdf-documentation
    – control distribution package
    – generate tar ball for code sharing/distribution
    17 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

    View full-size slide

  18. Why? Macro to Program Class Structure Analysis Software Links
    General Structure Documentation (HTML/man) L
    ATEXDoc. and Distribution Package
    MySimpleExample/
    README
    configure.ac
    Makefile.am
    src/
    bin/
    docs/
    Makefile mod
    refman mod.tex
    update texfile.sh
    html/
    latex/
    refman mod.tex
    Makefile mod
    doxygen.sty
    main.tex
    classh simple.tex
    man/
    out/
    pics/
    config/
    MySimpleExample-11.11.14.tar.gz
    – L
    A
    TEX-files generated by doxygen during make
    – include latex mod’s in all-local target in Makefile.am
    – generate pdf-documentation → refman_mod.pdf
    1: cd docs/latex/
    2: make -f Makefile mod
    – control distribution package
    – generate tar ball for code sharing/distribution
    18 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

    View full-size slide

  19. Why? Macro to Program Class Structure Analysis Software Links
    General Structure Documentation (HTML/man) L
    ATEXDoc. and Distribution Package
    MySimpleExample/
    README
    configure.ac
    Makefile.am
    src/
    bin/
    docs/
    Makefile mod
    refman mod.tex
    update texfile.sh
    html/
    latex/
    refman mod.tex
    Makefile mod
    doxygen.sty
    main.tex
    classh simple.tex
    man/
    out/
    pics/
    config/
    MySimpleExample-11.11.14.tar.gz
    – L
    A
    TEX-files generated by doxygen during make
    – include latex mod’s in all-local target in Makefile.am
    – generate pdf-documentation
    – control distribution package with EXTRA_DIST and
    dist_doc_DATA in Makefile.am
    16: # distribution package extras
    17: EXTRA DIST = src/mainpage.cc configure.ac Makefile.am
    18: dist doc DATA = README
    – generate tar ball for code sharing/distribution
    1: make dist # generate tarball
    2: make clean # remove build files
    3: make distclean # remove everything generated by automake
    19 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

    View full-size slide

  20. Why? Macro to Program Class Structure Analysis Software Links
    Implement Class Structure Add Options Class
    MySimpleExampleClass/
    README
    configure.ac
    Makefile.am
    src/
    mainpage.cc
    runhSimple.cc
    hSimple/
    hSimple.h
    hSimple.cxx
    LinkDef.h
    bin/
    runhSimple
    docs/
    out/
    pics/
    config/
    – split hsimple() of src/hSimple.cc into hSimple.{h,cxx}
    01: /* src/hSimple/hSimple.cxx */
    11: ClassImp(hSimple)
    13: hSimple::hSimple(TFile* pfile) { // init all private class members
    24: void hSimple::Run(Int t niter) { // hSimple.C code
    01: /* src/hSimple/hSimple.h */
    10: #ifndef hSimple h
    11: #define hSimple h
    19: class hSimple {
    20: private:
    21: TH1F *hpx; TH2F *hpxpy; TProfile *hprof;
    22: TNtuple *ntuple; TFile* hfile; TString png name;
    23: public:
    24: hSimple(TFile* pfile); // constructor
    25: virtual ˜hSimple() {}; // destructor
    26: void SetNamePNG(TString str) { png name = str.Data(); }
    27: void Run(Int t niter = 25000) ;
    28: ClassDef(hSimple,0)
    29: };
    30: #endif
    – control class behaviour in src/runhSimple.cc
    – put source code into src/hSimple/ and add LinkDef.h
    – add dictionary generation and linking to Makefile.am
    20 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

    View full-size slide

  21. Why? Macro to Program Class Structure Analysis Software Links
    Implement Class Structure Add Options Class
    MySimpleExampleClass/
    README
    configure.ac
    Makefile.am
    src/
    mainpage.cc
    runhSimple.cc
    hSimple/
    hSimple.h
    hSimple.cxx
    LinkDef.h
    bin/
    runhSimple
    docs/
    out/
    pics/
    config/
    – split hsimple() of src/hSimple.cc into hSimple.{h,cxx}
    – control class behaviour in src/runhSimple.cc
    → create hSimple object, SetNamePNG(), #Iterations
    → no hard coding in hSimple.{h,cxx}!
    56: #include "hSimple/hSimple.h"
    59: int main(int argc, char **argv) {
    60: TRint* theApp = new TRint("App", &argc, argv, NULL, 0);
    61: if ( theApp->Argc() == 2 ) {
    62: TString filename = theApp->Argv(1);
    63: TFile* hfile = new TFile(filename,"RECREATE");
    64: hSimple *hs = new hSimple(hfile);
    65: TString png name = "../pics/hSimple-Class.png";
    66: hs->SetNamePNG(png name);
    67: hs->Run(30000);
    68: }
    73: theApp->Run();
    74: return 0;
    75: }
    – put source code into src/hSimple/ and add LinkDef.h
    – add dictionary generation and linking to Makefile.am
    21 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

    View full-size slide

  22. Why? Macro to Program Class Structure Analysis Software Links
    Implement Class Structure Add Options Class
    MySimpleExampleClass/
    README
    configure.ac
    Makefile.am
    src/
    mainpage.cc
    runhSimple.cc
    hSimple/
    hSimple.h
    hSimple.cxx
    LinkDef.h
    bin/
    runhSimple
    docs/
    out/
    pics/
    config/
    – split hsimple() of src/hSimple.cc into hSimple.{h,cxx}
    – control class behaviour in src/runhSimple.cc
    – put source code into src/hSimple/ and add LinkDef.h
    1: /* src/hSimple/LinkDef.h */
    2: #ifdef CINT
    3: #pragma link off all globals;
    4: #pragma link off all classes;
    5: #pragma link off all functions;
    6: #pragma link C++ nestedclasses;
    7: #pragma link C++ nestedtypedefs;
    8: #pragma link C++ class hSimple;
    9: #endif
    – add dictionary generation and linking to Makefile.am
    22 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

    View full-size slide

  23. Why? Macro to Program Class Structure Analysis Software Links
    Implement Class Structure Add Options Class
    MySimpleExampleClass/
    README
    configure.ac
    Makefile.am
    src/
    mainpage.cc
    runhSimple.cc
    hSimple/
    hSimple.h
    hSimple.cxx
    LinkDef.h
    bin/
    runhSimple
    docs/
    out/
    pics/
    config/
    – split hsimple() of src/hSimple.cc into hSimple.{h,cxx}
    – control class behaviour in src/runhSimple.cc
    – put source code into src/hSimple/ and add LinkDef.h
    – add dictionary generation and linking to Makefile.am
    09: # hSimple dictionary/library
    10: CLEANFILES = src/hSimple/hSimpleDict.cxx src/hSimple/hSimpleDict.h
    11: pkglib LTLIBRARIES = src/hSimple/libhSimple.la
    12: pkginclude HEADERS = src/hSimple/hSimple.h
    13: noinst HEADERS = src/hSimple/LinkDef.h
    14: src hSimple libhSimple la SOURCES = src/hSimple/hSimple.cxx
    15: nodist src hSimple libhSimple la SOURCES = src/hSimple/hSimpleDict.cxx
    16: # run rootcint
    17: src/hSimple/hSimpleDict.cxx src/hSimple/hSimpleDict.h:src/hSimple/hSimple.h
    src/hSimple/LinkDef.h
    18: $(ROOTCINT) -f src/hSimple/hSimpleDict.cxx -c $(AM CPPFLAGS) $ˆ
    19: # runhSimple
    20: bin PROGRAMS = bin/runhSimple
    21: bin runhSimple SOURCES = src/runhSimple.cc
    22: bin runhSimple LDADD = src/hSimple/libhSimple.la
    23: bin runhSimple LDADD += -L@ROOTLIBDIR@ @ROOTGLIBS@
    24: bin runhSimple LDADD += @ROOTLIBS@ @LIBS@ ${DEPS LIBS}
    25: bin runhSimple LDFLAGS = -R $(ROOTLIBDIR) -L$(ROOTLIBDIR)
    26: bin runhSimple CXXFLAGS = @ROOTCFLAGS@
    23 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

    View full-size slide

  24. Why? Macro to Program Class Structure Analysis Software Links
    Implement Class Structure Add Options Class
    MySimpleExampleClass/
    README
    configure.ac
    Makefile.am
    src/
    mainpage.cc
    runhSimple.cc
    hSimple/
    hSimple.h
    hSimple.cxx
    LinkDef.h
    bin/
    runhSimple
    docs/
    out/
    pics/
    config/
    How to avoid hard coding
    entirely? Use program
    options/parameters.
    – split hsimple() of src/hSimple.cc into hSimple.{h,cxx}
    – control class behaviour in src/runhSimple.cc
    – put source code into src/hSimple/ and add LinkDef.h
    – add dictionary generation and linking to Makefile.am
    09: # hSimple dictionary/library
    10: CLEANFILES = src/hSimple/hSimpleDict.cxx src/hSimple/hSimpleDict.h
    11: pkglib LTLIBRARIES = src/hSimple/libhSimple.la
    12: pkginclude HEADERS = src/hSimple/hSimple.h
    13: noinst HEADERS = src/hSimple/LinkDef.h
    14: src hSimple libhSimple la SOURCES = src/hSimple/hSimple.cxx
    15: nodist src hSimple libhSimple la SOURCES = src/hSimple/hSimpleDict.cxx
    16: # run rootcint
    17: src/hSimple/hSimpleDict.cxx src/hSimple/hSimpleDict.h:src/hSimple/hSimple.h
    src/hSimple/LinkDef.h
    18: $(ROOTCINT) -f src/hSimple/hSimpleDict.cxx -c $(AM CPPFLAGS) $ˆ
    19: # runhSimple
    20: bin PROGRAMS = bin/runhSimple
    21: bin runhSimple SOURCES = src/runhSimple.cc
    22: bin runhSimple LDADD = src/hSimple/libhSimple.la
    23: bin runhSimple LDADD += -L@ROOTLIBDIR@ @ROOTGLIBS@
    24: bin runhSimple LDADD += @ROOTLIBS@ @LIBS@ ${DEPS LIBS}
    25: bin runhSimple LDFLAGS = -R $(ROOTLIBDIR) -L$(ROOTLIBDIR)
    26: bin runhSimple CXXFLAGS = @ROOTCFLAGS@
    1: autoreconf -v --force --install
    2: ./configure
    3: make
    24 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

    View full-size slide

  25. Why? Macro to Program Class Structure Analysis Software Links
    Implement Class Structure Add Options Class
    MySimpleExampleClass/
    README
    configure.ac
    Makefile.am
    src/
    mainpage.cc
    runhSimple.cc
    hSimple/
    Options/
    Options.h
    Options.cxx
    LinkDef.h
    bin/
    runhSimple
    docs/
    out/
    pics/
    config/
    – easy to include foreign class Options.{h,cxx} to deal with optional
    program parameters
    i) save source files in separate folder under src/
    ii) add corresponding LinkDef.h file
    iii) include dictionary generation and linking in Makefile.am
    [...]
    09: # Options dictionary/library
    10: CLEANFILES = src/Options/OptionsDict.cxx src/Options/OptionsDict.h
    11: pkglib LTLIBRARIES = src/Options/libOptions.la
    12: pkginclude HEADERS = src/Options/Options.h
    13: noinst HEADERS = src/Options/LinkDef.h
    14: src Options libOptions la SOURCES = src/Options/Options.cxx
    15: nodist src Options libOptions la SOURCES = src/Options/OptionsDict.cxx
    16: # run rootcint
    17: src/Options/OptionsDict.cxx src/Options/OptionsDict.h:src/Options/Options.h src/Options/LinkDef.h
    18: $(ROOTCINT) -f src/Options/OptionsDict.cxx -c $(AM CPPFLAGS) $ˆ
    [...]
    21: # hSimple dictionary/library
    [...]
    28: src hSimple libhSimple la LIBADD = src/Options/libOptions.la
    [...]
    35: bin runhSimple LDADD = src/Options/libOptions.la src/hSimple/libhSimple.la
    [...]
    – modify main-function in src/runhSimple.cc to deal with options
    – fully control the program!
    25 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

    View full-size slide

  26. Why? Macro to Program Class Structure Analysis Software Links
    Implement Class Structure Add Options Class
    MySimpleExampleClass/
    README
    configure.ac
    Makefile.am
    src/
    mainpage.cc
    runhSimple.cc
    hSimple/
    Options/
    Options.h
    Options.cxx
    LinkDef.h
    bin/
    runhSimple
    docs/
    out/
    pics/
    config/
    – easy to include foreign class Options.{h,cxx}
    – modify main-function in src/runhSimple.cc to deal with options
    i) decode options & re-new argc/argv
    ii) rewrite TRint application
    61: // decode options
    62: const char * optv[] = {"N:NIter ","O:NamePNG ",NULL} ;
    63: Int t nit = 30000;
    64: TString pngstr;
    65: Options opts(*argv, optv);
    66: OptArgvIter iter(--argc, ++argv);
    67: const char *optarg;
    68: int argcR = argc;
    69: char **argvR;
    70: while( char optchar = opts(iter, optarg) ) {
    71: switch (optchar) {
    72: case ’N’ :
    73: nit = (Int t)atoi(optarg); argcR=argcR-2; break;
    74: case ’O’ : pngstr = optarg; argcR=argcR-2; break;
    75: default : break;
    76: }
    77: }
    78: argvR = new char*[argcR];
    79: Int t cnter = 0;
    80: if (iter.index() < argc) {
    81: for (int i = iter.index() ; i < argc ; i++) { argvR[cnter] = argv[i]; ++cnter; }
    82: }
    – fully control the program!
    26 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

    View full-size slide

  27. Why? Macro to Program Class Structure Analysis Software Links
    Implement Class Structure Add Options Class
    MySimpleExampleClass/
    README
    configure.ac
    Makefile.am
    src/
    mainpage.cc
    runhSimple.cc
    hSimple/
    Options/
    Options.h
    Options.cxx
    LinkDef.h
    bin/
    runhSimple
    docs/
    out/
    pics/
    config/
    – easy to include foreign class Options.{h,cxx}
    – modify main-function in src/runhSimple.cc to deal with options
    i) decode options & re-new argc/argv
    ii) rewrite TRint application
    84: TRint* theApp = new TRint("App", &argcR, argvR, NULL, 0);
    85: if ( theApp->Argc() == 1 ) {
    86: TString filename = theApp->Argv(0);
    87: TFile* hfile = new TFile(filename,"RECREATE");
    88: hSimple *hs = new hSimple(hfile);
    89: if ( pngstr.Contains("png") ) hs->SetNamePNG(pngstr.Data());
    90: hs->Run(nit);
    91: }
    96: theApp->Run();
    – fully control the program!
    1: runhSimple "out/hsimple.root"
    2: runhSimple -N 1000000 "out/hsimple.root"
    3: runhSimple -O "pics/test.png" "out/hsimple.root"
    4: runhSimple -N 20000 -O "pics/test.png" "out/hsimple.root"
    [...]
    27 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

    View full-size slide

  28. Why? Macro to Program Class Structure Analysis Software Links
    MyAnalysis/
    src/
    BasePlot/
    Bichsel/
    Bichsel.h
    Bichsel.cxx
    dEdxParameterization.h
    dEdxParameterization.cxx
    MyPdgDatabase/
    MyPdgDatabase.h
    MyPdgDatabase.cxx
    database
    Embedding/
    EmbeddingQA.h
    MatchedPairsNT.h
    McTracksNT.h
    MyEventEmbData.h
    SingleElectronNT.h
    eeDecay.h
    *.cxx
    [...]
    [...]
    – from here on it’s easy to fill src/ and create your
    Analysis Software.
    – include foreign classes easily into this structure
    → BasePlot / Bichsel
    – standard libraries with one header and one cxx file
    work like the discussed hSimple example
    – write your own utility classes providing functions or
    databases frequently used (MyPdgDatabase)
    → works like the Options example
    – compile multiple classes in one library and control
    their interplay with the options of a single program
    or with different programs
    – very flexible including the advantages of known
    Unix programs (options, one program for one task)
    Conclusion:
    With little effort one gets tidy, flexible, platform-
    independent & easy-to-share Analysis Software including
    man-pages, pdf-Documentation and Analysis Homepage
    with the three easy commands
    1: autoreconf -v --force --install
    2: ./configure
    3: make
    28 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

    View full-size slide

  29. Why? Macro to Program Class Structure Analysis Software Links
    – http://www.openismus.com/documents/linux/automake/automake
    – http://www.stack.nl/~dimitri/doxygen/index.html
    – http://www.gnu.org/software/hello/manual/autoconf/
    – http://www.gnu.org/software/hello/manual/automake/
    – http://realmike.org/blog/2010/07/18/gnu-automake-by-example/
    – http://chris-miceli.blogspot.com/2011/01/
    integrating-doxygen-with-autotools.html
    – http://ctan.org/tex-archive/macros/generic/dirtree/
    – http://www.gnu.org/s/src-highlite/source-highlight.html
    – http://www.cmcrossroads.com/bradapp/ftp/src/libs/C++/Options.html
    – http://root.cern.ch/svn/root/tags/v5-24-00b/tutorials/hsimple.C
    29 / 29
    Juniors Day @ STAR Collaboration Meeting LBNL (11/14/2011)
    Patrick Huck

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