Changes in / [d3dfe18:87e2e39]

Files:

• Makefile.am (modified) (1 diff, 1 prop)
• configure.ac (modified) (2 diffs, 1 prop)
• src/Makefile.am (modified) (1 diff)
• src/builder.cpp (modified) (1 prop)
• src/helpers.cpp (modified) (1 diff, 1 prop)
• src/helpers.hpp (modified) (1 diff)
• src/memoryallocator.hpp (modified) (1 diff, 1 prop)
• src/memoryallocatorunittest.cpp (deleted)
• src/memoryallocatorunittest.hpp (deleted)
• src/memoryusageobserver.cpp (modified) (2 diffs)
• src/memoryusageobserver.hpp (modified) (1 diff)
• src/memoryusageobserverunittest.cpp (deleted)
• src/memoryusageobserverunittest.hpp (deleted)
• src/tesselationunittest.cpp (deleted)
• src/tesselationunittest.hpp (deleted)
• src/unittests/Makefile.am (added)
• src/unittests/memoryallocatorunittest.cpp (added)
• src/unittests/memoryallocatorunittest.hpp (added)
• src/unittests/memoryusageobserverunittest.cpp (added)
• src/unittests/memoryusageobserverunittest.hpp (added)
• src/unittests/tesselationunittest.cpp (added)
• src/unittests/tesselationunittest.hpp (added)
• src/unittests/vectorunittest.cpp (added)
• src/unittests/vectorunittest.hpp (added)
• src/vectorunittest.cpp (deleted)
• src/vectorunittest.hpp (deleted)

Makefile.am

@@ -1 +1 @@
 ACLOCAL_AMFLAGS = -I m4
-SUBDIRS = src doc tests
+SUBDIRS = src src/unittests doc tests 
 
 EXTRA_DIST = autogen.sh

configure.ac

@@ -14 +14 @@
 AC_PROG_CXX
 AC_PROG_CC
+AC_PROG_RANLIB
 AC_PROG_INSTALL
 AC_CHECK_PROG([LATEX],[latex],[latex],[:])
@@ -79 +80 @@
 AC_CONFIG_FILES([tests/molecuilder], [chmod +x tests/molecuilder])
 AC_CONFIG_FILES([doc/molecuilder.xml])
-AC_CONFIG_FILES([Makefile src/Makefile doc/Makefile])
+AC_CONFIG_FILES([Makefile src/Makefile doc/Makefile src/unittests/Makefile])
 AC_OUTPUT

src/Makefile.am

@@ -1 @@
-SOURCE = atom.cpp bond.cpp boundary.cpp config.cpp element.cpp ellipsoid.cpp helpers.cpp leastsquaremin.cpp linkedcell.cpp moleculelist.cpp molecules.cpp parser.cpp periodentafel.cpp tesselation.cpp tesselationhelpers.cpp vector.cpp verbose.cpp
-HEADER = atom.hpp bond.hpp boundary.hpp config.hpp defs.hpp element.hpp ellipsoid.hpp helpers.hpp leastsquaremin.hpp linkedcell.hpp memoryallocator.hpp memoryusageobserver.cpp memoryusageobserver.hpp molecules.hpp parser.hpp periodentafel.hpp stackclass.hpp tesselation.hpp tesselationhelpers.hpp vector.hpp verbose.hpp
+SOURCE = atom.cpp bond.cpp boundary.cpp config.cpp          element.cpp ellipsoid.cpp helpers.cpp leastsquaremin.cpp linkedcell.cpp memoryusageobserver.cpp molecules.cpp moleculelist.cpp parser.cpp periodentafel.cpp                tesselation.cpp tesselationhelpers.cpp vector.cpp verbose.cpp
+HEADER = atom.hpp bond.hpp boundary.hpp config.hpp defs.hpp element.hpp ellipsoid.hpp helpers.hpp leastsquaremin.hpp linkedcell.hpp memoryusageobserver.hpp molecules.hpp                  parser.hpp periodentafel.hpp stackclass.hpp tesselation.hpp tesselationhelpers.hpp vector.hpp verbose.hpp
 
-noinst_PROGRAMS =  VectorUnitTest MemoryAllocatorUnitTest MemoryUsageObserverUnitTest
+INCLUDES = -I$(top_srcdir)/src/unittests
 
+noinst_LIBRARIES = libmolecuilder.a
 bin_PROGRAMS = molecuilder joiner analyzer
 molecuilderdir = ${bindir}
+libmolecuilder_a_SOURCES = ${SOURCE} ${HEADER}
 molecuilder_DATA = elements.db valence.db orbitals.db Hbonddistance.db Hbondangle.db
-molecuilder_SOURCES =  ${SOURCE} builder.cpp  ${HEADER}
-joiner_SOURCES = joiner.cpp datacreator.cpp element.cpp helpers.cpp memoryallocator.hpp memoryusageobserver.cpp memoryusageobserver.hpp periodentafel.cpp parser.cpp verbose.cpp datacreator.hpp helpers.hpp parser.hpp periodentafel.hpp 
-analyzer_SOURCES = analyzer.cpp datacreator.cpp element.cpp helpers.cpp memoryallocator.hpp memoryusageobserver.cpp memoryusageobserver.hpp periodentafel.cpp parser.cpp verbose.cpp helpers.hpp periodentafel.hpp parser.hpp datacreator.hpp 
+molecuilder_SOURCES = builder.cpp
+molecuilder_LDADD = libmolecuilder.a
+joiner_SOURCES = joiner.cpp datacreator.cpp parser.cpp datacreator.hpp helpers.hpp parser.hpp periodentafel.hpp
+joiner_LDADD = libmolecuilder.a 
+analyzer_SOURCES = analyzer.cpp datacreator.cpp parser.cpp helpers.hpp periodentafel.hpp parser.hpp datacreator.hpp 
+analyzer_LDADD = libmolecuilder.a 
 
-TESTS = VectorUnitTest MemoryAllocatorUnitTest
-check_PROGRAMS = $(TESTS)
-VectorUnitTest_SOURCES = defs.hpp helpers.cpp helpers.hpp leastsquaremin.cpp leastsquaremin.hpp memoryallocator.hpp memoryusageobserver.cpp memoryusageobserver.hpp vectorunittest.cpp vectorunittest.hpp vector.cpp vector.hpp verbose.cpp verbose.hpp 
-VectorUnitTest_CXXFLAGS = $(CPPUNIT_CFLAGS)
-VectorUnitTest_LDFLAGS = $(CPPUNIT_LIBS) -ldl
-
-MemoryAllocatorUnitTest_SOURCES = defs.hpp helpers.cpp helpers.hpp memoryallocatorunittest.cpp memoryallocatorunittest.hpp memoryallocator.hpp memoryusageobserver.cpp memoryusageobserver.hpp verbose.cpp verbose.hpp 
-MemoryAllocatorUnitTest_CXXFLAGS = $(CPPUNIT_CFLAGS)
-MemoryAllocatorUnitTest_LDFLAGS = $(CPPUNIT_LIBS) -ldl
-
-MemoryUsageObserverUnitTest_SOURCES = defs.hpp helpers.cpp helpers.hpp memoryusageobserverunittest.cpp memoryusageobserverunittest.hpp memoryusageobserver.hpp memoryusageobserver.cpp verbose.cpp verbose.hpp 
-MemoryUsageObserverUnitTest_CXXFLAGS = $(CPPUNIT_CFLAGS)
-MemoryUsageObserverUnitTest_LDFLAGS = $(CPPUNIT_LIBS) -ldl
-
-EXTRA_DIST = ${molecuilder_DATA}
+#EXTRA_DIST = ${molecuilder_DATA}

src/helpers.cpp

@@ -144 +144 @@
 };
 
+/**
+ * Frees all memory registered by the memory observer and calls exit(225) afterwards.
+ */
+void performCriticalExit() {
+  map<void*, size_t> pointers = MemoryUsageObserver::getInstance()->getPointersToAllocatedMemory();
+  for (map<void*, size_t>::iterator runner = pointers.begin(); runner != pointers.end(); runner++) {
+    Free(((void**) &runner->first));
+  }
 
+  exit(255);
+}

src/helpers.hpp

@@ -51 +51 @@
 void flip(double *x, double *y);
 int pot(int base, int n);
-//void * Malloc(size_t size, const char* output);
-//void * Calloc(size_t size, const char* output);
-//void * ReAlloc(void * OldPointer, size_t size, const char* output);
-//char* MallocString(size_t size, const char* output);
-//void Free(void ** buffer, const char* output);
 char *FixedDigitNumber(const int FragmentNumber, const int digits);
 bool IsValidNumber( const char *string);
+static void performCriticalExit();
 
 /********************************************** helpful template functions *********************************/

src/memoryallocator.hpp

@@ -111 +111 @@
  * \param pointer to the allocated memory range to free; may be NULL, this function is a no-op then
  */
-template <typename X> void Free(X** buffer)
+template <typename X> void Free(X** buffer, const char *msg = NULL)
 {
   if ((buffer == NULL) || (*buffer == NULL))
     return;
 
-  MemoryUsageObserver::getInstance()->removeMemory(*buffer);
+  MemoryUsageObserver::getInstance()->removeMemory(*buffer, msg);
   free(*buffer);
   *buffer = NULL;

src/memoryusageobserver.cpp

@@ -78 +78 @@
  * \param pointer to the allocated piece of memory
  */
-void MemoryUsageObserver::removeMemory(void* pointer) {
+void MemoryUsageObserver::removeMemory(void* pointer, const char *msg) {
   map<void*, size_t>::iterator current = memoryUsers.find(pointer);
 
   if (current == memoryUsers.end()) {
     cout << "WARNING: There is non-tracked memory to be freed. Pointer "
-      << pointer << " is not registered by MemoryUsageObserver." << endl;
+      << pointer << " is not registered by MemoryUsageObserver";
+    if (msg != NULL)
+      cout << ": " << msg;
+    cout << "." << endl;
     return;
   }
@@ -104 +107 @@
   return maximumSize;
 }
+
+/**
+ * Gets a map with pointers to the currently allocated memory ranges as keys and
+ * the allocated size as value.
+ */
+map<void*, size_t> MemoryUsageObserver::getPointersToAllocatedMemory() {
+  return memoryUsers;
+}

src/memoryusageobserver.hpp

@@ -28 +28 @@
   static void purgeInstance();
   void addMemory(void* pointer, size_t size);
-  void removeMemory(void* pointer);
+  void removeMemory(void* pointer, const char *msg = NULL);
   size_t getUsedMemorySize();
   size_t getMaximumUsedMemory();
+  map<void*, size_t> getPointersToAllocatedMemory();
 
 protected: