Final fix with compilation at JCNS, new README with installation instructions,...

Final fix with compilation at JCNS, new README with installation instructions, special profile call for TestFactory.

App/App.pro

@@ -85,14 +85,12 @@ macx {
 LIBS += -lgsl -lgslcblas -lfftw3 -lboost_system -lboost_filesystem -lboost_regex
 
 # here is workaround since JCNS /usr/local doesn't have shared fftw3
-#LIBS += -lgsl -lgslcblas -lboost_system -lboost_filesystem -lboost_regex
-#macx {
-#  LIBS += -lfftw3
-#}
-#!macx:unix {
-#  # telling linker to link with static version of the library with fPIC option
-#  LIBS += -Bstatic -lfftw3f -Bdynamic
-#}
+# qmake CONFIG+=JCNS
+CONFIG(JCNS) {
+  LIBS -= -lfftw3
+  LIBS += -Bstatic -lfftw3 -Bdynamic # request for static (without fPIC option)
+  # "-lfftw3f" - with fPIC option, "-lfftw3" - without fPIC option
+}
 
 
 # -----------------------------------------------------------------------------

App/inc/TestFactory.h

@@ -32,6 +32,9 @@ public:
     //! execute specified test
     void execute(std::string name);
 
+    //! profile specified test
+    void profile(std::string name);
+
     //! execute all registered tests
     void execute_all();
 

App/inc/TestIsGISAXS9.h

@@ -28,7 +28,10 @@ class TestIsGISAXS9 : public IFunctionalTest
 public:
     TestIsGISAXS9();
     virtual ~TestIsGISAXS9();
+
+    virtual void initialise();
     virtual void execute();
+    virtual void finalise();
 
 private:
     void initializeSample();

App/src/CommandLine.cpp

@@ -22,6 +22,7 @@ CommandLine::CommandLine(int argc, char **argv) : m_argc(argc), m_argv(argv)
     m_defined_arguments.push_back("batch");
     m_defined_arguments.push_back("pdfreport");
     m_defined_arguments.push_back("all");
+    m_defined_arguments.push_back("profile");
     // getting info about names of defined functional tests and adding them to the list of defined arguments
     m_defined_functional_tests = TestFactory::instance().get_testnames();
     m_defined_arguments.insert(m_defined_arguments.end(), m_defined_functional_tests.begin(), m_defined_functional_tests.end());
@@ -33,6 +34,7 @@ CommandLine::CommandLine(int argc, char **argv) : m_argc(argc), m_argv(argv)
     m_description["batch"]        = "run application in batch mode (no graphics)";
     m_description["pdfreport"]    = "generate pdf report for functional tests";
     m_description["all"]          = "run all registered functional test";
+    m_description["profile"]      = "profile specified test";
     // default description of functional tests
     for(arguments_t::iterator it = m_defined_functional_tests.begin(); it!=m_defined_functional_tests.end(); ++it ) {
         m_description[ (*it) ]    = "functional test: no description";
@@ -103,6 +105,7 @@ void CommandLine::print_help()
         std::cout << std::setw(15) << std::left << (*it) << " - " << m_description[(*it)] << std::endl;
     }
     std::cout << " " << std::endl;
-    std::cout << "Example: ./App isgisaxs10 pdfreport batch " << std::endl;
+    std::cout << "Example: ./App isgisaxs10 " << std::endl;
+    std::cout << "Example: ./App isgisaxs3 isgisaxs10 pdfreport batch " << std::endl;
 
 }

App/src/TestFactory.cpp

@@ -63,14 +63,35 @@ void TestFactory::execute(std::string name)
         return;
     }
 
+    test->initialise();
     m_benchmark->Start(name.c_str());
     test->execute();
     m_benchmark->Stop(name.c_str());
     m_benchmark->Show(name.c_str());
+    test->finalise();
 
 }
 
 
+void TestFactory::profile(std::string name)
+{
+    //IFunctionalTest *test = TestFactory::instance().createItem( args[i] );
+    IFunctionalTest *test(0);
+    try {
+        test = createItem( name );
+    } catch (std::runtime_error &e) {
+        std::cout << e.what() << std::endl;
+        std::cout << "TestFactory::execute() -> Warning. No test with name '" << name << "' is defined." << std::endl;
+        return;
+    }
+
+    test->initialise();
+    for(int i=0; i<10; i++) test->execute();
+
+}
+
+
+
 /* ************************************************************************* */
 // execute all registered functional tests
 /* ************************************************************************* */

App/src/TestIsGISAXS9.cpp

@@ -30,9 +30,15 @@ TestIsGISAXS9::~TestIsGISAXS9()
     if(mp_intensity_output) delete mp_intensity_output;
 }
 
-void TestIsGISAXS9::execute()
+
+void TestIsGISAXS9::initialise()
 {
     initializeSample();
+}
+
+
+void TestIsGISAXS9::execute()
+{
     GISASExperiment experiment;
     experiment.setSample(mp_sample);
     experiment.setDetectorParameters(0.0*Units::degree, 2.0*Units::degree, 100
@@ -44,6 +50,12 @@ void TestIsGISAXS9::execute()
 
     // saving results to file
     IsGISAXSTools::writeOutputDataToFile(*mp_intensity_output, Utils::FileSystem::GetHomePath()+"./Examples/IsGISAXS_examples/ex-9/this_pyramid_Z0.ima");
+
+}
+
+
+void TestIsGISAXS9::finalise()
+{
     // reading result of IsGISAXS for comparison
     OutputData<double> *isgi_data = IsGISAXSTools::readOutputDataFromFile(Utils::FileSystem::GetHomePath()+"./Examples/IsGISAXS_examples/ex-9/isgi_pyramid_Z0.ima");
 

App/src/main.cpp

@@ -17,6 +17,15 @@ int main(int argc, char **argv)
     CommandLine args(argc, argv);
     if( !args.isGood() ) { args.print_help(); return 0; }
 
+    // profiling code for memory leakages and cpu performance
+    if( args.find("profile") ) {
+        for(size_t i=0; i<args.size(); i++) {
+            if(args.isFunctionalTest( args[i] ))
+            TestFactory::instance().execute( args[i] );
+        }
+        return 0;
+    }
+
     // setting graphics environment
     TApplication theApp("theApp", 0, 0);
     DrawHelper::SetStyle();

Core/Core.pro

@@ -193,15 +193,12 @@ macx {
 LIBS += -lgsl -lgslcblas -lfftw3 -lboost_system -lboost_filesystem -lboost_regex
 
 # here is workaround since JCNS /usr/local doesn't have shared fftw3
-#LIBS += -lgsl -lgslcblas -lboost_system -lboost_filesystem -lboost_regex
-#macx {
-#  LIBS += -lfftw3
-#}
-#!macx:unix {
-#  # telling linker to link with static version of the library with fPIC option
-#  LIBS += -Bstatic -lfftw3f -Bdynamic
-#}
-
+# qmake CONFIG+=JCNS
+CONFIG(JCNS) {
+  LIBS -= -lfftw3
+  LIBS += -Bstatic -lfftw3f -Bdynamic # request for static (with fPIC option)
+  # "-lfftw3f" - with fPIC option, "-lfftw3" - without fPIC option
+}
 
 
 # -----------------------------------------------------------------------------

Macros/CodeProfiling/README

@@ -24,5 +24,5 @@ make
 3) run profiling
 run_gperftools.sh
 
-
+*) When compiled with GPERFTOOLS option, profiling with valgrind (callgrind) wont work.
 

Macros/CodeProfiling/run_gperftools.sh

@@ -5,7 +5,7 @@ mkdir -p ./output
 
 
 application=../../App/App
-arguments="isgisaxs9 batch"
+arguments="isgisaxs9 profile"
 focuson=GISASExperiment
 
 # ------------------------------------------- #

Macros/CodeProfiling/run_valgrind.sh

@@ -6,7 +6,7 @@ mkdir -p ./output
 
 application=../../App/App
 #arguments="isgisaxs9"
-arguments="isgisaxs9 batch"
+arguments="isgisaxs9 profile"
 focuson=GISASExperiment
 
 # ------------------------------------------- #
@@ -16,7 +16,7 @@ profile_cpu=yes
 if [ $profile_cpu = "yes" ]
 then
 #  valgrind --tool=callgrind -v --dump-every-bb=10000000 --dump-instr=yes --trace-jump=yes ./App commandline
-  valgrind  --tool=callgrind --callgrind-out-file=./output/callgrind.output  --log-file=./output/valgrind2.output --dump-instr=yes --trace-jump=yes $application $arguments
+  valgrind  --tool=callgrind --dsymutil=yes --callgrind-out-file=./output/callgrind.output  --log-file=./output/tmplog.output --dump-instr=yes --trace-jump=yes $application $arguments
 # --zero-before=GISASExperiment
 fi
 
@@ -27,7 +27,7 @@ fi
 profile_memory=yes
 if [ $profile_memory = "yes" ]
 then
-  valgrind --log-file=./output/valgrind.output --num-callers=6 --track-origins=yes --leak-check=yes $application $arguments
+  valgrind --log-file=./output/valgrind.output  --dsymutil=yes --num-callers=6 --track-origins=yes --leak-check=yes $application $arguments
 fi
 
 

README

+This is the GISASFW framework.
+
+-------------------------------------------------------------------------------
+Package content:
+-------------------------------------------------------------------------------
+./Core       - the main library of the framework
+./App        - functional tests
+./ThirdParty - third party libraries
+./UnitTests  - collection of cpp unit tests
+./Examples   - usage examples
+./Doc        - documentation
+
+-------------------------------------------------------------------------------
+Installation Instructions
+-------------------------------------------------------------------------------
+
+> Installation in lucky case 
+~ cd <to_the_package_directory>
+~ qmake; make
+
+* 'make clean', and more powerfull 'make distclean' are also available
+
+> Installation of additional libraries might be required before
+* gsl fftw3 boost(>1.46)  - these are dependencies of Core
+* ROOT                    - these are dependencies of App
+* probably also python>=2.6 and Qt>=4.5
+
+* (see explanation about 'root' below)
+
+> Checked on following platforms
+*  MacOS 10.7.3
+*  OpenSuse 12.1
+*  CentOS 5.1 with JCNS setup (see issue below)
+
+> Issue with CentOS from JCNS
+* it has /usr/local with lot of officially installed libraries
+* however
+* fftw3 in /usr/local compiled only statically
+  As a temporary workaround GISASFW package should be compiled with
+  qmake CONFIG+=JCNS; make
+* boost 1.46 which is there, is buggy too
+  As a temporary workaround you have to define environment variable
+  export LC_ALL=C
+  for more information see https://svn.boost.org/trac/boost/ticket/5928 or google for
+  "locale::facet::_S_create_c_locale name not valid"
+
+
+-------------------------------------------------------------------------------
+Installation Instructions +
+-------------------------------------------------------------------------------
+> Words about ROOT.
+ROOT is extremely powerfull, awfully professional and exceptionally supported,
+C++ based analysis framework, see http://root.cern.ch.
+Framework has to be installed to be able to compile App part (containing functional tests). You do not need to install
+ROOT to have only Core library.
+
+> How to install ROOT
+* different ways are explained on site
+* one possible way is following
+*
+* download source from http://root.cern.ch, unpack it somewhere
+* define variable pointing to the directory where ROOT will be installed
+  export ROOTSYS=/home/jamesbond/software/root
+* go to the directory where you unpacked ROOT and run
+  ./configure; make; make install
+
+> Steps after installation
+* ROOT requires couple of system variables to be defined
+* the easiest way to do it is to run
+  source /home/jamesbond/software/root/bin/thisroot.sh
+  each time you are going to use ROOT
+* simply put this call in your .bash_profile
+
+* or you can just define variables by yourself
+  export ROOTSYS=/home/jamesbond/software/root
+  export PATH=$ROOTSYS/bin:$PATH
+  export LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH
+
+
+
+