Changeset f4d063

Timestamp:

Dec 16, 2010, 5:32:23 PM (14 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

ad7270

Parents:

c77ac8

git-author:

Frederik Heber <heber@…> (12/15/10 15:54:40)

git-committer:

Frederik Heber <heber@…> (12/16/10 17:32:23)

Message:

MEMFIX: MemDebug ignores all unknown sources. Removed all dependencies around main(), moved to builder_init.?pp.

• this has been an attempt to fix the warning of a memory leak that actually results into the libboost_filesystem.so over which we have no control. As of now, i I do not quite look through the whole affair. That is, I have a now idea why Till's new memory allocator is used during the initialization of some external library already, but apparently it must have to do with lookup tables present in the exectuable already. Hence, we can not do much about.
• Nonetheless, we split up main() into some initializating functions which have been outsourced to builder_init.cpp.
• The only fix then is that we ignore all values of unknown source in MemDebug.
• Note: We only do accouting of stuff allocated on the heap (e.g. int *test = new int;) and not on stack (int test;)! However, stack space is limited anyway.

Location:

src

Files:

• Helpers/MemDebug.cpp (modified) (2 diffs)
• Helpers/MemDebug.hpp (modified) (1 diff)
• Makefile.am (modified) (2 diffs)
• builder.cpp (modified) (1 diff)
• builder_init.cpp (added)
• builder_init.hpp (added)

src/Helpers/MemDebug.cpp

@@ -380 +380 @@
   // mark the block as not in the list (will be changed by addEntry)
   entry->isIgnored = true;
-  Memory::addEntry(entry);
+  if (line != 0)  { // indicator that we do not know the source
+    Memory::addEntry(entry);
+  }
 
   // get the checksum...
@@ -424 +426 @@
   // mark the block as not in the list (will be changed by addEntry)
   entry->isIgnored = true;
-  Memory::addEntry(entry);
+  if (line != 0)  { // indicator that we do not know the source
+    Memory::addEntry(entry);
+  }
 
   // get the checksum...

src/Helpers/MemDebug.hpp

@@ -52 +52 @@
 #include <boost/shared_ptr.hpp>
 #include <boost/function.hpp>
-#include <boost/program_options.hpp>
 
 

src/Makefile.am

@@ -317 +317 @@
 #molecuilder_CXXFLAGS += -DNO_CACHING
 molecuilder_LDFLAGS = $(BOOST_LIB)
-molecuilder_SOURCES = builder.cpp
+molecuilder_SOURCES = builder.cpp builder_init.cpp builder_init.hpp
 molecuilder_LDADD = \
         UIElements/libMolecuilderUI-@MOLECUILDER_API_VERSION@.la \
@@ -329 +329 @@
 
 #Stuff for building the GUI using Qt
-molecuildergui_SOURCES = builder.cpp
+molecuildergui_SOURCES = builder.cpp builder_init.cpp builder_init.hpp
 molecuildergui_CXXFLAGS = $(BOOST_CPPFLAGS) -DUSE_GUI_QT
 molecuildergui_LDFLAGS = $(BOOST_LIB)

src/builder.cpp

@@ -73 +73 @@
 #endif
 
-#include "Helpers/MemDebug.hpp"
-
-#include "bondgraph.hpp"
-#include "config.hpp"
-#include "Helpers/Log.hpp"
-#include "molecule.hpp"
-#include "periodentafel.hpp"
-#include "tesselationhelpers.hpp"
-#include "UIElements/UIFactory.hpp"
-#include "UIElements/Menu/MenuDescription.hpp"
-#include "UIElements/TextUI/TextUIFactory.hpp"
-#include "UIElements/CommandLineUI/CommandLineUIFactory.hpp"
-#include "UIElements/CommandLineUI/CommandLineParser.hpp"
-#ifdef USE_GUI_QT
-#include "UIElements/Qt4/QtUIFactory.hpp"
-#endif
-#include "UIElements/MainWindow.hpp"
-#include "UIElements/Dialog.hpp"
-//#include "Menu/ActionMenuItem.hpp"
-#include "Helpers/Verbose.hpp"
-#include "World.hpp"
-
-#include "Actions/ActionRegistry.hpp"
-#include "Actions/ActionHistory.hpp"
-
-#include "Parser/ChangeTracker.hpp"
-#include "Parser/FormatParserStorage.hpp"
-
-#include "UIElements/UIFactory.hpp"
-#include "UIElements/TextUI/TextUIFactory.hpp"
-#include "UIElements/CommandLineUI/CommandLineUIFactory.hpp"
-#include "UIElements/MainWindow.hpp"
-#include "UIElements/Dialog.hpp"
-
-#include "version.h"
-
+#include "builder_init.hpp"
 
 /********************************************** Main routine **************************************/
 
-/** In this function all dynamicly allocated member variables to static/global
- * variables are added to the ignore list of Memory/MemDebug.
- *
- * Use this to prevent their listing in the Memory::getState() at the end of the
- * program. Check with valgrind that truely no memory leak occurs!
- */
-void AddStaticEntitiestoIgnoreList()
-{
-  // zeroVec and unitVec are global variables (on the stack) but vectorContent
-  // within is situated on the heap and has to be ignored
-  Memory::ignore(zeroVec.get());
-  Memory::ignore(unitVec[0].get());
-  Memory::ignore(unitVec[1].get());
-  Memory::ignore(unitVec[2].get());
-}
-
-/** Cleans all singleton instances in an orderly fashion.
- * C++ does not guarantee any specific sequence of removal of single instances
- * which have static/global variables. Some singletons depend on others hence we
- * acertain a specific ordering here, which is is used via the atexit() hook.
- */
-void cleanUp(){
-  FormatParserStorage::purgeInstance();
-  ChangeTracker::purgeInstance();
-  World::purgeInstance();
-  MenuDescription::purgeInstance();
-  UIFactory::purgeInstance();
-  ValueStorage::purgeInstance();
-  CommandLineParser::purgeInstance();
-  ActionRegistry::purgeInstance();
-  OptionRegistry::purgeInstance();
-  ActionHistory::purgeInstance();
-  // we have to remove these two static as otherwise their boost::shared_ptrs are still present
-  Action::removeStaticStateEntities();
-  // put some static variables' dynamic contents on the Memory::ignore map to avoid their
-  // admonishing lateron
-  AddStaticEntitiestoIgnoreList();
-  logger::purgeInstance();
-  errorLogger::purgeInstance();
-#ifdef LOG_OBSERVER
-  cout << observerLog().getLog();
-#endif
-  Memory::getState();
-}
-
-void dumpMemory(){
-  ofstream ost("molecuilder.memdump");
-  Memory::dumpMemory(ost);
-}
-
 int main(int argc, char **argv)
 {
-  // while we are non interactive, we want to abort from asserts
-  ASSERT_DO(Assert::Abort);
-  ASSERT_HOOK(dumpMemory);
-  string line;
-  char **Arguments = NULL;
-  int ArgcSize = 0;
-  int ExitFlag = 0;
-  bool ArgumentsCopied = false;
-  std::string BondGraphFileName("\n");
+  initGeneral();
 
-  // print version check and copyright notice
-  cout << MOLECUILDERVERSION << endl;
-  cout << "MoleCuilder comes with ABSOLUTELY NO WARRANTY; for details type" << endl;
-  cout << "`molecuilder --warranty'." << endl;
-  cout << "`MoleCuilder - to create and alter molecular systems." << endl;
-  cout << "Copyright (C) 2010  University Bonn. All rights reserved." << endl;
+  initUI(argc,argv);
 
-  setVerbosity(0);
-  // need to init the history before any action is created
-  ActionHistory::init();
+  doUI();
 
-  // from this moment on, we need to be sure to deeinitialize in the correct order
-  // this is handled by the cleanup function
-  atexit(cleanUp);
-
-  // Parse command line options and if present create respective UI
-  {
-    // construct bond graph
-    if (World::getInstance().getConfig()->BG == NULL) {
-      World::getInstance().getConfig()->BG = new BondGraph(World::getInstance().getConfig()->GetIsAngstroem());
-      if (World::getInstance().getConfig()->BG->LoadBondLengthTable(BondGraphFileName)) {
-        DoLog(0) && (Log() << Verbose(0) << "Bond length table loaded successfully." << endl);
-      } else {
-        DoeLog(1) && (eLog()<< Verbose(1) << "Bond length table loading failed." << endl);
-      }
-    }
-    // handle remaining arguments by CommandLineParser
-    if (argc>1) {
-      CommandLineParser::getInstance().InitializeCommandArguments();
-      CommandLineParser::getInstance().Run(argc,argv);
-      DoLog(0) && (Log() << Verbose(0) << "Setting UI to CommandLine." << endl);
-      UIFactory::registerFactory(new CommandLineUIFactory::description());
-      UIFactory::makeUserInterface("CommandLine");
-    } else {
-      // In the interactive mode, we can leave the user the choice in case of error
-      ASSERT_DO(Assert::Ask);
-      #ifdef USE_GUI_QT
-        DoLog(0) && (Log() << Verbose(0) << "Setting UI to Qt4." << endl);
-        UIFactory::registerFactory(new QtUIFactory::description());
-        UIFactory::makeUserInterface("Qt4");
-      #else
-        DoLog(0) && (Log() << Verbose(0) << "Setting UI to Text." << endl);
-        cout << MOLECUILDERVERSION << endl;
-        UIFactory::registerFactory(new TextUIFactory::description());
-        UIFactory::makeUserInterface("Text");
-      #endif
-    }
-  }
-
-  {
-    MainWindow *mainWindow = UIFactory::getInstance().makeMainWindow();
-    mainWindow->display();
-    delete mainWindow;
-  }
-
-  FormatParserStorage::getInstance().SaveAll();
-  ChangeTracker::getInstance().saveStatus();
-
-  // free the new argv
-  if (ArgumentsCopied) {
-    for (int i=0; i<ArgcSize;i++)
-      delete[](Arguments[i]);
-    delete[](Arguments);
-  }
-  //delete[](ConfigFileName);
-
-  ExitFlag = World::getInstance().getExitFlag();
-  return (ExitFlag == 1 ? 0 : ExitFlag);
+  return saveAll();
 }