Release/v1.2

.gitlab-ci.yml

@@ -17,8 +17,6 @@ build:9-debug-gcc:
     - install/
     name: "$CI_BUILD_NAME"
     expire_in: 6 hrs
-  only:
-  - master
 
 build:9-release-gcc:
   stage: build
@@ -29,8 +27,6 @@ build:9-release-gcc:
     - install/
     name: "$CI_BUILD_NAME"
     expire_in: 6 hrs
-  only:
-  - master
 
 build:9-parallel-debug-gcc:
   stage: build
@@ -41,8 +37,6 @@ build:9-parallel-debug-gcc:
     - install/
     name: "$CI_BUILD_NAME"
     expire_in: 6 hrs
-  only:
-  - master
 
 build:9-parallel-release-gcc:
   stage: build
@@ -53,8 +47,6 @@ build:9-parallel-release-gcc:
     - install/
     name: "$CI_BUILD_NAME"
     expire_in: 6 hrs
-  only:
-  - master
 
 
 # compile the demos
@@ -64,8 +56,6 @@ demo:9-debug-gcc:
   - tools/build_amdis.sh --stage demo --config Debug
   dependencies:
   - build:9-debug-gcc
-  only:
-  - master
 
 demo:9-release-gcc:
   stage: demo
@@ -73,8 +63,6 @@ demo:9-release-gcc:
   - tools/build_amdis.sh --stage demo --config Release
   dependencies:
   - build:9-release-gcc
-  only:
-  - master
 
 demo:9-parallel-debug-gcc:
   stage: demo
@@ -82,8 +70,6 @@ demo:9-parallel-debug-gcc:
   - tools/build_amdis.sh --stage demo --config Debug --parallel
   dependencies:
   - build:9-parallel-debug-gcc
-  only:
-  - master
 
 demo:9-parallel-release-gcc:
   stage: demo
@@ -91,8 +77,6 @@ demo:9-parallel-release-gcc:
   - tools/build_amdis.sh --stage demo --config Release --parallel
   dependencies:
   - build:9-parallel-release-gcc
-  only:
-  - master
 
 
 # compiel and run the tests
@@ -102,8 +86,6 @@ test:9-debug-gcc:
   - tools/build_amdis.sh --stage test --config Debug
   dependencies:
   - build:9-debug-gcc
-  only:
-  - master
 
 test:9-release-gcc:
   stage: test
@@ -111,8 +93,6 @@ test:9-release-gcc:
   - tools/build_amdis.sh --stage test --config Release
   dependencies:
   - build:9-release-gcc
-  only:
-  - master
 
 test:9-parallel-debug-gcc:
   stage: test
@@ -120,8 +100,6 @@ test:9-parallel-debug-gcc:
   - tools/build_amdis.sh --stage test --config Debug --parallel
   dependencies:
   - build:9-parallel-debug-gcc
-  only:
-  - master
 
 test:9-parallel-release-gcc:
   stage: test
@@ -129,5 +107,3 @@ test:9-parallel-release-gcc:
   - tools/build_amdis.sh --stage test --config Release --parallel
   dependencies:
   - build:9-parallel-release-gcc
-  only:
-  - master

AMDiS/CMakeLists.txt

 set(CMAKE_LEGACY_CYGWIN_WIN32 0)
-cmake_minimum_required(VERSION 2.8 FATAL_ERROR)
+cmake_minimum_required(VERSION 2.8.12 FATAL_ERROR)
 project(AMDiS)
 
-set(AMDiS_VERSION "1.1.0")
+set(AMDiS_VERSION "1.2.0")
 
 set(BASE_DIR ${AMDiS_SOURCE_DIR})
 set(SOURCE_DIR ${BASE_DIR}/src)

AMDiS/src/DOFSerializer.cc

@@ -7,34 +7,38 @@
 #include "Traverse.h"
 
 namespace AMDiS
-{    
-    
-// satre values of DOFVector on all macro elements to internal container
+{
+
+// store values of DOFVector on all macro elements to internal container
 void DOFSerializer::gather(DOFVector<double> const* vec, std::vector<double>& values)
 {
   std::fill(visited_.begin(), visited_.end(), false);
   values.clear();
-    
+  values.reserve(numValues_);
+
   for (auto* macroEl : mesh_->getMacroElements())
     gather(macroEl->getIndex(), vec, values, false);
+
+  numValues_ = values.size();
 }
 
 
-// satre values of DOFVector on macro element `macroIndex` to internal container
+// store values of DOFVector on macro element `macroIndex` to internal container
 void DOFSerializer::gather(int macroIndex, DOFVector<double> const* vec, std::vector<double>& values, bool reset)
 {
+  FUNCNAME("DOFSerializer::gather()");
+  TEST_EXIT(mesh_ == vec->getFeSpace()->getMesh())("Incompatible meshes!\n");
+
   if (reset) {
     std::fill(visited_.begin(), visited_.end(), false);
     values.clear();
   }
-  
-  TEST_EXIT(mesh_ == vec->getFeSpace()->getMesh())("Incompatible meshes!\n");
-  
+
   TraverseStack stack;
   ElInfo *elInfo = stack.traverseFirstOneMacro(mesh_, macroIndex, -1, Mesh::CALL_EVERY_EL_PREORDER);
   while (elInfo) {
     Element *el = elInfo->getElement();
-    
+
     if (el->isLeaf()) {
       gather(VERTEX, elInfo, vec, values);
       if (mesh_->getDim() > 1)
@@ -43,14 +47,15 @@ void DOFSerializer::gather(int macroIndex, DOFVector<double> const* vec, std::ve
         gather(FACE, elInfo, vec, values);
       gather(CENTER, elInfo, vec, values);
     }
-    
+
     elInfo = stack.traverseNext(elInfo);
   }
 }
 
 
-void DOFSerializer::gather(GeoIndex geo, ElInfo* elInfo, DOFVector<double> const* vec, std::vector<double>& values) 
+void DOFSerializer::gather(GeoIndex geo, ElInfo* elInfo, DOFVector<double> const* vec, std::vector<double>& values)
 {
+  FUNCNAME_DBG("DOFSerializer::gather()");
   int nd;
   if ((nd = admin_->getNumberOfDofs(geo)))  {
     int entities = mesh_->getGeo(geo);
@@ -59,7 +64,7 @@ void DOFSerializer::gather(GeoIndex geo, ElInfo* elInfo, DOFVector<double> const
     for (int n = 0; n < entities; n++) {
       for(int d = 0; d < nd; d++) {
         DegreeOfFreedom globalDof = elInfo->getElement()->getDof(n0 + n, nd0 + d);
-        TEST_EXIT(globalDof < visited_.size())("visited container not large enough!\n");
+        TEST_EXIT_DBG(globalDof < visited_.size())("visited container not large enough!\n");
         if (!visited_[globalDof]) {
           visited_[globalDof] = true;
           values.push_back((*vec)[globalDof]);
@@ -75,7 +80,7 @@ void DOFSerializer::scatter(std::vector<double> const& values, DOFVector<double>
 {
   std::fill(visited_.begin(), visited_.end(), false);
   counter_ = 0u;
-    
+
   for (auto* macroEl : mesh_->getMacroElements())
     scatter(macroEl->getIndex(), values, vec, false);
 }
@@ -83,19 +88,20 @@ void DOFSerializer::scatter(std::vector<double> const& values, DOFVector<double>
 
 // assign stored values to DOFVector, on macroElement with index `macroIndex`
 void DOFSerializer::scatter(int macroIndex, std::vector<double> const& values, DOFVector<double>* vec, bool reset) const
-{    
+{
+  FUNCNAME("DOFSerializer::scatter()");
+  TEST_EXIT(mesh_ == vec->getFeSpace()->getMesh())("Incompatible meshes!\n");
+
   if (reset) {
     std::fill(visited_.begin(), visited_.end(), false);
     counter_ = 0u;
   }
-  
-  TEST_EXIT(mesh_ == vec->getFeSpace()->getMesh())("Incompatible meshes!\n");
-  
+
   TraverseStack stack;
   ElInfo *elInfo = stack.traverseFirstOneMacro(mesh_, macroIndex, -1, Mesh::CALL_EVERY_EL_PREORDER);
   while (elInfo) {
     Element *el = elInfo->getElement();
-    
+
     if (el->isLeaf()) {
       scatter(VERTEX, elInfo, values, vec);
       if (mesh_->getDim() > 1)
@@ -104,7 +110,7 @@ void DOFSerializer::scatter(int macroIndex, std::vector<double> const& values, D
         scatter(FACE, elInfo, values, vec);
       scatter(CENTER, elInfo, values, vec);
     }
-    
+
     elInfo = stack.traverseNext(elInfo);
   }
 }
@@ -112,6 +118,7 @@ void DOFSerializer::scatter(int macroIndex, std::vector<double> const& values, D
 
 void DOFSerializer::scatter(GeoIndex geo, ElInfo* elInfo, std::vector<double> const& values, DOFVector<double>* vec) const
 {
+  FUNCNAME("DOFSerializer::scatter()");
   int nd;
   if ((nd = admin_->getNumberOfDofs(geo)))  {
     int entities = mesh_->getGeo(geo);
@@ -120,7 +127,7 @@ void DOFSerializer::scatter(GeoIndex geo, ElInfo* elInfo, std::vector<double> co
     for (int n = 0; n < entities; n++) {
       for(int d = 0; d < nd; d++) {
         DegreeOfFreedom globalDof = elInfo->getElement()->getDof(n0 + n, nd0 + d);
-        TEST_EXIT(globalDof < visited_.size())("visited container not large enough!\n");
+        TEST_EXIT_DBG(globalDof < visited_.size())("visited container not large enough!\n");
         if (!visited_[globalDof]) {
           visited_[globalDof] = true;
           TEST_EXIT(counter_ < values.size())("Not enough values in value-container!\n");

AMDiS/src/DOFSerializer.h

@@ -41,47 +41,51 @@ namespace AMDiS
   class DOFSerializer
   {
   public:
-    
+
     /// Constructor, stores a pointer to the DOFAdmin. If the number of values to store can be estimated,
     /// pass a second argument `numValues`
-    DOFSerializer(DOFAdmin* admin, std::size_t numValues = 0)
+    DOFSerializer(DOFAdmin* admin, std::size_t numValues = 0u)
       : admin_(admin)
       , mesh_(admin->getMesh())
       , visited_(admin->getUsedSize(), false)
+      , numValues_(numValues)
     {}
-    
-    
-    // satre values of DOFVector on all macro elements to internal container
+
+
+    // store values of DOFVector on all macro elements to internal container
     void gather(DOFVector<double> const* vec, std::vector<double>& values);
-    
-    // satre values of DOFVector on macro element `macroIndex` to internal container
+
+    // store values of DOFVector on macro element `macroIndex` to internal container
     void gather(int macroIndex, DOFVector<double> const* vec, std::vector<double>& values, bool reset = true);
-    
-    
+
+
     // assign stored values to DOFVector, for all macro elements
     void scatter(std::vector<double> const& values, DOFVector<double>* vec) const;
-    
+
     // assign stored values to DOFVector, on macroElement with index `macroIndex`
     void scatter(int macroIndex, std::vector<double> const& values, DOFVector<double>* vec, bool reset = true) const;
 
-      
+
   protected:
-    
+
     // collect values of one geometry-type
     void gather(GeoIndex geo, ElInfo* elInfo, DOFVector<double> const* vec, std::vector<double>& values);
-    
+
     // assign values of one geometry type
     void scatter(GeoIndex geo, ElInfo* elInfo, std::vector<double> const& values, DOFVector<double>* vec) const;
-    
-    
+
+
   protected:
-    
+
     DOFAdmin* admin_;
     Mesh* mesh_;
-    
+
     // stored which DOFs were already visited during traversal
     mutable std::vector<bool> visited_;
-    
+
+    // estimated number of values
+    std::size_t numValues_ = 0u;
+
     // a counter used during assignment of values. To guarantee the same order as during gather
     mutable std::size_t counter_ = 0u;
   };

AMDiS/src/Initfile.h

@@ -37,7 +37,6 @@
 
 #include <boost/lexical_cast.hpp>
 #include <boost/numeric/conversion/cast.hpp>
-#include <boost/thread/shared_mutex.hpp> // requires c++14
 
 #include <boost/type_traits.hpp>
 
@@ -423,8 +422,6 @@ namespace AMDiS {
     template<typename T>
     static void get(const std::string tag, T& value, int debugInfo = -1)
     {
-//       boost::shared_lock<boost::shared_mutex> lock(singlett().mutex_);
-      
       if (debugInfo == -1)
         debugInfo = singlett().getMsgInfo();
       else {
@@ -498,8 +495,6 @@ namespace AMDiS {
     /// return InitEntry object for tag tag
     static InitEntry get(const std::string tag)
     {
-//       boost::shared_lock<boost::shared_mutex> lock(singlett().mutex_);
-      
       InitEntry result;
 
       std::string valStr;
@@ -527,8 +522,6 @@ else if(error_code == TAG_NOT_FOUND_BREAK)
     template<typename T>
     static void set(const std::string tag, T const& value, int debugInfo=  -1)
     {
-//       boost::unique_lock<boost::shared_mutex> lock(singlett().mutex_);
-      
       if (debugInfo == -1)
         debugInfo = singlett().getMsgInfo();
 
@@ -578,14 +571,14 @@ else if(error_code == TAG_NOT_FOUND_BREAK)
     {
       singlett().clear();
     }
-    
+
 
     /// save singlett-data to file with filename fn
     static void save(std::string fn)
     {
       singlett().write(fn);
     }
-    
+
 
     // list of included filenames
     static std::set< std::string >& getIncludeList()
@@ -593,7 +586,7 @@ else if(error_code == TAG_NOT_FOUND_BREAK)
       static std::set< std::string > include_list;
       return include_list;
     }
-    
+
 protected:
     Initfile()
     : msgInfo(0),
@@ -656,8 +649,6 @@ protected:
     void getInternalParameters();
 
     int msgInfo, msgWait, paramInfo, breakOnMissingTag;
-    
-//     mutable boost::shared_mutex mutex_;
   };
 
   typedef Initfile Parameters;

AMDiS/src/MeshStructure.cc

@@ -280,25 +280,25 @@ namespace AMDiS {
     bool cont = true;
     while (cont) {
       bool cont1;
-// #ifndef NDEBUG
+#ifndef NDEBUG
       bool cont2;
-// #endif
+#endif
       if (structure1->isLeafElement() == structure2->isLeafElement()) {
 	cont1 = structure1->nextElement(result);
-// #ifndef NDEBUG
+#ifndef NDEBUG
 	cont2 = structure2->nextElement();
-// #endif
+#endif
       } else {
 	if (structure1->isLeafElement()) {
 	  cont1 = structure1->nextElement();
-// #ifndef NDEBUG
+#ifndef NDEBUG
 	  cont2 = structure2->skipBranch(result);
-// #endif
+#endif
 	} else {
 	  cont1 = structure1->skipBranch(result);
-// #ifndef NDEBUG
+#ifndef NDEBUG
 	  cont2 = structure2->nextElement();
-// #endif
+#endif
 	}
       }
       TEST_EXIT_DBG(cont1 == cont2)("Structures don't match!\n");
@@ -504,7 +504,7 @@ namespace AMDiS {
       elInfo = stack.traverseNext(elInfo);
     }
   }
-  
+
 
   void MeshStructure::setMeshStructureValues(int macroElIndex,