Changeset 1024cb for src/Helpers

Timestamp:

May 31, 2010, 5:32:27 PM (15 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:

e08c46

Parents:

42af9e (diff), a7b761b (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

git-author:

Frederik Heber <heber@…> (05/31/10 17:29:30)

git-committer:

Frederik Heber <heber@…> (05/31/10 17:32:27)

Message:

Merge commit 'jupiter/MoleculeStartEndSwitch' into CommandLineActionMapping

Conflicts:

molecuilder/src/Makefile.am
molecuilder/src/builder.cpp
molecuilder/src/config.cpp
molecuilder/src/helpers.hpp
molecuilder/src/molecule.cpp
molecuilder/src/molecule_dynamics.cpp
molecuilder/src/molecule_fragmentation.cpp
molecuilder/src/molecule_geometry.cpp
molecuilder/src/molecule_graph.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp
molecuilder/src/unittests/listofbondsunittest.cpp

Integration of MoleculeStartEndSwitch had the following consequences:

• no more AtomCount -> getAtomCount()
• no more start/end -> begin(), end() and iterator
• no more decent ordering in atomic ids (hence, Simple_configuration/8 and Domain/5, Domain/6 now check by comparing sorted xyz, not confs)

There is still a huge problem with bonds. One test runs into an endless loop.

Signed-off-by: Frederik Heber <heber@…>

Location:

src/Helpers

Files:

• Assert.cpp (modified) (2 diffs)
• MemDebug.cpp (modified) (6 diffs)
• MemDebug.hpp (modified) (2 diffs)

src/Helpers/Assert.cpp

@@ -54 +54 @@
 
 
-
 bool _my_assert::check(const bool res,
                        const char* condition,
@@ -63 +62 @@
 {
   if(!res){
-    cout << "Assertion " << condition << " failed in file " << filename << " at line " << line << endl;
+    cout << "Assertion \"" << condition << "\" failed in file " << filename << " at line " << line << endl;
     cout << "Assertion Message: " << message << std::endl;
     while(true){

src/Helpers/MemDebug.cpp

@@ -9 +9 @@
 #include <cstdlib>
 #include <cstring>
+#include <boost/thread.hpp>
 
 using namespace std;
+
+#ifndef NDBEGUG
+#ifndef NO_MEMDEBUG
 
 namespace Memory {
@@ -40 +44 @@
   };
 
+  boost::mutex memorylock;
+
   // start and end of the doubly-linked list
   entry_t *begin=0;
@@ -127 +133 @@
 
 void *operator new(size_t nbytes,const char* file, int line) throw(std::bad_alloc) {
+
+  // we need to lock, so that no one changes the linked list while we are here
+  boost::mutex::scoped_lock guard(Memory::memorylock);
 
   // to avoid allocations of 0 bytes if someone screws up
@@ -204 +213 @@
 
 void operator delete(void *ptr) throw() {
+  if(!ptr){
+    cerr << "Warning: Deleting NULL pointer" << endl;
+    return;
+  }
+
+  // we need to lock, so the linked list does not changed while we are in here
+  boost::mutex::scoped_lock guard(Memory::memorylock);
+
   // get the size for the entry, including alignment
   static const size_t entrySpace = Memory::doAlign(sizeof(Memory::entry_t));
@@ -212 +229 @@
   // let's see if the checksum is still matching
   if(Memory::calcChecksum(&entry->info)!=entry->checksum){
-    cout << "Possible memory corruption detected!" << endl;
-    cout << "Trying to recover allocation information..." << endl;
-    cout << "Memory was allocated at " << entry->info.file << ":" << entry->info.line << endl;
+    cerr << "Possible memory corruption detected!" << endl;
+    cerr << "Trying to recover allocation information..." << endl;
+    cerr << "Memory was allocated at " << entry->info.file << ":" << entry->info.line << endl;
     terminate();
   }
@@ -241 +258 @@
   operator delete(ptr);
 }
+#endif
+#endif

src/Helpers/MemDebug.hpp

@@ -21 +21 @@
  * your sourcefiles.
  */
+#ifndef NDEBUG
+#ifndef NO_MEMDEBUG
+
+#ifndef MEMDEBUG
+#define MEMDEBUG
+#endif
 
 namespace Memory {
@@ -56 +62 @@
 #define new new(__FILE__,__LINE__)
 
+#endif
+#endif
+
+
+#ifndef MEMDEBUG
+// memory debugging was disabled
+
+namespace Memory {
+  inline void getState(){}
+
+  template <typename T>
+  inline T *ignore(T* ptr){
+    return ptr;
+  }
+}
+
+#endif
 #endif /* MEMDEBUG_HPP_ */