Changeset 567357

Timestamp:

Nov 7, 2011, 4:13:17 PM (13 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:

d628da

Parents:

b5d38d

git-author:

Frederik Heber <heber@…> (11/01/11 22:28:03)

git-committer:

Frederik Heber <heber@…> (11/07/11 16:13:17)

Message:

FIX: cleanUp() replaced by module_reinit() and .._exit() in pyMoleCuilder.

• this causes ostream to be set with FormatParserStorage and hence files to be correctly written.
• module_reinit() is python exported as "reinit". This allows for reuse of the module.
• both module_... reside in namespace MoleCuilder::detail.
• ..._reinit() does not use cleanUp() but only purgeStaticInstances().

Location:

src

Files:

• Actions/pyMoleCuilder.cpp (modified) (2 diffs)
• cleanUp.cpp (modified) (3 diffs)
• cleanUp.hpp (modified) (1 diff)

src/Actions/pyMoleCuilder.cpp

@@ -32 +32 @@
 #include "cleanUp.hpp"
 #include "Actions/ActionHistory.hpp"
+#include "cleanUp.hpp"
 
+namespace MoleCuilder {
+
+namespace detail {
+
+void module_exit()
+{
+  // save everything
+  std::cout << "Saving." << std::endl;
+  saveAll();
+  // purge everything
+  std::cout << "Cleaning memory." << std::endl;
+  cleanUp();
+}
+
+void module_reinit()
+{
+  // save everything
+  std::cout << "Saving." << std::endl;
+  saveAll();
+  // purge everything
+  std::cout << "Cleaning static instances from memory." << std::endl;
+  purgeStaticInstances();
+  // need to init the history before any action is created
+  std::cout << "Reinitializing." << std::endl;
+  MoleCuilder::ActionHistory::init();
+}
+
+} /* namespace MoleCuilder */
+} /* namespace detail */
 
 BOOST_PYTHON_MODULE(pyMoleCuilder)
@@ -41 +71 @@
   // from this moment on, we need to be sure to deeinitialize in the correct order
   // this is handled by the cleanup function
-  atexit(cleanUp);
+  atexit(MoleCuilder::detail::module_exit);
 
   // set the docstring of the current module scope
   boost::python::scope().attr("__doc__") = "pyMolecuilder are the python bindings to all Actions of the program suite MoleCuilder.\n\nMoleCuilder is a program to build molecular (dynamics) worlds, allowing you indefinite manipulation, control and analysis over the atoms and molecules within a simulation domain.";
 
+  boost::python::def("reinit", MoleCuilder::detail::module_reinit, "Reinitializes the internal state of the python module as if it had been freshly imported, saves all input files beforehand.");
 #define export_print(z,n,list) \
         BOOST_PP_CAT(export_, BOOST_PP_SEQ_ELEM(n, list))();

src/cleanUp.cpp

@@ -62 +62 @@
 }
 
-/** 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.
+/** purges all static (singleton) instances in correct order of dependency.
+ *
  */
-void cleanUp()
+void purgeStaticInstances()
 {
-  printTimings();
   Chronos::purgeInstance();
-
   RandomNumberDistributionFactory::purgeInstance();
   RandomNumberEngineFactory::purgeInstance();
@@ -85 +81 @@
   MoleCuilder::OptionRegistry::purgeInstance();
   MoleCuilder::ActionHistory::purgeInstance();
+  logger::purgeInstance();
+  errorLogger::purgeInstance();
+}
+
+/** 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()
+{
+  // give timings per Action
+  printTimings();
+  // purge static instances from memory
+  purgeStaticInstances(); 
   // we have to remove these two static as otherwise their boost::shared_ptrs are still present
   MoleCuilder::Action::removeStaticStateEntities();
@@ -90 +101 @@
   // admonishing lateron
   AddStaticEntitiestoIgnoreList();
-  logger::purgeInstance();
-  errorLogger::purgeInstance();
 #ifdef LOG_OBSERVER
   cout << observerLog().getLog();

src/cleanUp.hpp

@@ -18 +18 @@
 void dumpMemory();
 void printTimings();
+void purgeStaticInstances();
 int saveAll();