Changeset b0b2d2 for LinearAlgebra

Timestamp:

Aug 28, 2014, 8:53:32 AM (11 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:

185e6f

Parents:

7f1a1a

git-author:

Frederik Heber <heber@…> (08/26/14 21:07:40)

git-committer:

Frederik Heber <heber@…> (08/28/14 08:53:32)

Message:

MEMFIX: RealSpaceMatrix's and MatrixContent's serialization leaked memory.

• serialization always works on fully instantiated RealSpaceMatrix, hence neither createViews nor re-creating content ptr instance is necessary.
• MatrixContent newly allocated content but for RealSpaceMatrix it was still present as matrix dimensions have been set. Now it is freed when free_content_on_exit is true.
• similar fixes to VectorContent.

Location:

LinearAlgebra/src/LinearAlgebra

Files:

• MatrixContent.cpp (modified) (1 diff)
• MatrixContent.hpp (modified) (1 diff)
• RealSpaceMatrix.hpp (modified) (1 diff)
• VectorContent.cpp (modified) (3 diffs)

LinearAlgebra/src/LinearAlgebra/MatrixContent.cpp

@@ -88 +88 @@
 MatrixContent::MatrixContent(size_t _rows, size_t _columns, MatrixBaseCase) :
     MatrixDimension(_rows,_columns),
-    free_content_on_exit(true)
+    free_content_on_exit(false)
 {}
 

LinearAlgebra/src/LinearAlgebra/MatrixContent.hpp

@@ -189 +189 @@
   {
     ar & boost::serialization::base_object<MatrixDimension>(*this);
+    if (free_content_on_exit)
+      gsl_matrix_free(content);
     content = gsl_matrix_calloc(getRows(), getColumns());
     ar & content->size1;

LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.hpp

@@ -179 +179 @@
   void save(Archive & ar, const unsigned int version) const
   {
-    ar & content;
+    ar & *content;
   }
   template<class Archive>
   void load(Archive & ar, const unsigned int version)
   {
-    ar & content;
-    createViews();
+    ar & *content;
   }
   BOOST_SERIALIZATION_SPLIT_MEMBER()

LinearAlgebra/src/LinearAlgebra/VectorContent.cpp

@@ -55 +55 @@
   VectorDimension(0),
   content(NULL),
-  free_content_on_exit(true)
+  free_content_on_exit(false)
 {}
 
@@ -78 +78 @@
 VectorContent::VectorContent(VectorBaseCase) :
     VectorDimension(0),
+    content(NULL),
     free_content_on_exit(false)
 {}
@@ -112 +113 @@
 VectorContent::VectorContent(const size_t _dimension, std::istream &inputstream) :
   VectorDimension(_dimension),
-  content(NULL),
   free_content_on_exit(true)
 {