Merge branch 'master' into 'issue/cmake_configuration'

# Conflicts:
#   AMDiS/cmake3/CMakeLists.txt

.gitlab-ci.yml

@@ -6,7 +6,6 @@ cache:
 
 before_script:
   - tools/install_boost.sh
-  - tools/install_petsc.sh
 
 build:9-debug-gcc:
   stage: build
@@ -28,6 +27,7 @@ build:9-parallel-debug-gcc:
   stage: build
   image: duneci/base:9
   script:
+  - tools/install_petsc.sh
   - tools/build_parallel_amdis.sh Debug
   only:
   - master
@@ -36,6 +36,7 @@ build:9-parallel-release-gcc:
   stage: build
   image: duneci/base:9
   script:
+  - tools/install_petsc.sh
   - tools/build_parallel_amdis.sh Release
   only:
   - master

AMDiS/cmake/CMakeLists.txt

@@ -19,11 +19,6 @@ endif()
 #TODO: use the cmake build type
 SET(MTL_INCLUDE_DIR ${LIB_DIR}/mtl4/ CACHE PATH "mtl4 directory")
 
-# set global compile_definitions for all target, depending on build-type
-set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS
-    $<$<CONFIG:Debug>:DEBUG=1>
-    $<$<CONFIG:Release>:DEBUG=0>)
-
 # find_package(Subversion QUIET)
 # if(Subversion_FOUND)
 #   Subversion_WC_INFO(${CMAKE_CURRENT_SOURCE_DIR} svn_info)

AMDiS/cmake3/CMakeLists.txt

@@ -193,10 +193,7 @@ add_library(amdis
     ${SOURCE_DIR}/time/RosenbrockAdaptInstationary.cc
     ${SOURCE_DIR}/time/RosenbrockMethod.cc
     ${SOURCE_DIR}/time/RosenbrockStationary.cc
-)
-
-add_library(amdis_debug INTERFACE)
-target_sources(amdis_debug INTERFACE
+# debugging files
     ${SOURCE_DIR}/Debug.cc
     ${SOURCE_DIR}/GlobalDOFNumbering.cc      # not used by any other class
     ${SOURCE_DIR}/GlobalElementNumbering.cc  # not used by any other class
@@ -233,8 +230,7 @@ if (MSVC)
       _CRT_SECURE_NO_WARNINGS)
 endif (MSVC)
 
-target_link_libraries(amdis AMDiS::base muparser
-    $<$<NOT:$<CONFIG:Release>>:amdis_debug>)
+target_link_libraries(amdis AMDiS::base muparser)
 
 # specify how to install this target:
 # -----------------------------------
@@ -259,4 +255,4 @@ configure_file(${BASE_DIR}/cmake3/AMDISConfig.cmake.in
 
 install(FILES ${AMDiS_BINARY_DIR}/AMDISConfig.cmake DESTINATION share/amdis/)
 install(FILES ${BASE_DIR}/cmake3/AMDISUse.cmake DESTINATION share/amdis/)
-install(FILES ${BASE_DIR}/cmake3/test_compile_features.cmake DESTINATION share/amdis/)
+install(FILES ${BASE_DIR}/cmake3/test_compile_features.cmake DESTINATION share/amdis/)
\ No newline at end of file

AMDiS/cmake3/amdis_parallel.cmake

@@ -14,6 +14,7 @@ if (ENABLE_PARALLEL_DOMAIN)
         ${SOURCE_DIR}/parallel/MeshManipulation.cc
         ${SOURCE_DIR}/parallel/MeshPartitioner.cc
         ${SOURCE_DIR}/parallel/MpiHelper.cc
+        ${SOURCE_DIR}/parallel/ParallelDebug.cc
         ${SOURCE_DIR}/parallel/ParallelDofMapping.cc
         ${SOURCE_DIR}/parallel/ParallelProblemStat.cc
         ${SOURCE_DIR}/parallel/ParallelSolver.cc
@@ -22,10 +23,6 @@ if (ENABLE_PARALLEL_DOMAIN)
         ${SOURCE_DIR}/parallel/StdMpi.cc
     )
 
-    target_sources(amdis_debug INTERFACE
-        ${SOURCE_DIR}/parallel/ParallelDebug.cc
-    )
-
     target_compile_definitions(amdis_parallel INTERFACE
 	   HAVE_PARALLEL_DOMAIN_AMDIS=1)
 

AMDiS/lib/mtl4/boost/numeric/mtl/utility/view_code.hpp

@@ -59,8 +59,8 @@ struct view_code<mtl::matrix::hermitian_view<Matrix> >
 template <unsigned Value>
 struct view_normalize_const
 {
-      static const unsigned tmp2= Value == 0 || Value == 4 ? Value | 1 : Value, // if matrix ref or transposed, make it const
-	                    value= (tmp2 & 3) == 3 ? tmp2 ^ 1 : tmp2;           // for conj turn off const
+      static const unsigned tmp2= Value == 0 || Value == 4 ? Value | 1 : Value; // if matrix ref or transposed, make it const
+	  static const unsigned value= (tmp2 & 3) == 3 ? tmp2 ^ 1 : tmp2;           // for conj turn off const
 };
 
 template <typename ViewCode>

AMDiS/src/BoundaryObject.cc

@@ -73,7 +73,7 @@ namespace AMDiS {
       if (obj0.subObj == EDGE) {
 	int el0_v0 = obj0.el->getVertexOfEdge(obj0.ithObj, 0);
 	int el1_v0 = obj0.el->getVertexOfEdge(obj1.ithObj, 0);
-#if DEBUG != 0
+#ifndef NDEBUG
 	int el0_v1 = obj0.el->getVertexOfEdge(obj0.ithObj, 1);
 	int el1_v1 = obj0.el->getVertexOfEdge(obj1.ithObj, 1);
 #endif

AMDiS/src/Config.h

@@ -29,15 +29,6 @@
 #define AMDIS_VERSION  "AMDiS: Version 0.9.1"
 #endif
 
-#ifdef DEBUG
-#undef DEBUG
-#endif
-#ifdef NDEBUG
-#define DEBUG 0
-#else
-#define DEBUG 1
-#endif
-
 #include <boost/config.hpp>
 
 #define CACHE_LINE 16

AMDiS/src/FiniteElemSpace.cc

@@ -122,7 +122,7 @@ namespace AMDiS {
     feSpaces.resize(0);
   }
 
-#if DEBUG
+#ifndef NDEBUG
   FiniteElemSpace* FiniteElemSpace::provideFeSpace(Mesh *mesh)
   {
     FUNCNAME("FiniteElemSpace::provideFeSpace()");

AMDiS/src/FiniteElemSpace.h

@@ -53,7 +53,7 @@ namespace AMDiS {
 
     static void destroyFeSpaces();
 
-#if DEBUG
+#ifndef NDEBUG
     /// For debugging it may be useful to get some FE space for a given mesh at a
     /// position in code where it is not possible to access the FE space directly. The
     /// function assumes that there is only one FE space defined for the mesh.

AMDiS/src/Global.cc

@@ -187,7 +187,7 @@ namespace AMDiS {
     vsprintf(buff, format, arg);
     PRINT_LINE((*error), buff);
     va_end(arg);
-#if defined HAVE_PARALLEL_DOMAIN_AMDIS && !defined HAVE_PARALLEL_MTL4 && (DEBUG == 0 || defined NDEBUG)
+#if defined HAVE_PARALLEL_DOMAIN_AMDIS && !defined HAVE_PARALLEL_MTL4 && (defined NDEBUG)
   #if (PETSC_VERSION_MINOR >= 5)
     PetscError(MPI_COMM_WORLD, __LINE__, "Msg::print_error_exit", "Global.cc", 1, PETSC_ERROR_INITIAL, buff);
   #else
@@ -220,11 +220,9 @@ namespace AMDiS {
 				const char *file,
 				int line)
   {
-#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
-#if (DEBUG == 0)
+#if defined(HAVE_PARALLEL_DOMAIN_AMDIS) && defined(NDEBUG)
     if (outputMainRank && MPI::COMM_WORLD.Get_rank() != 0)
       return;
-#endif
 #endif
 
     static int old_line = -1;
@@ -256,11 +254,9 @@ namespace AMDiS {
 
   void Msg::print_warn(const char *format, ...)
   {
-#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
-#if (DEBUG == 0)
+#if defined(HAVE_PARALLEL_DOMAIN_AMDIS) && defined(NDEBUG)
     if (outputMainRank && MPI::COMM_WORLD.Get_rank() != 0)
       return;
-#endif
 #endif
     va_list arg;
     char buff[255];

AMDiS/src/Mesh.cc

@@ -1161,7 +1161,7 @@ namespace AMDiS {
     in >> name;
     in.get();
 
-#if DEBUG != 0
+#ifndef NDEBUG
     int oldVal = dim;
 #endif
     SerUtil::deserialize(in, dim);
@@ -1178,7 +1178,7 @@ namespace AMDiS {
 
     SerUtil::deserialize(in, preserveCoarseDOFs);
 
-#if DEBUG != 0
+#ifndef NDEBUG
     oldVal = nDofEl;
 #endif
     SerUtil::deserialize(in, nDofEl);
@@ -1186,7 +1186,7 @@ namespace AMDiS {
 
     nDof.deserialize(in);
 
-#if DEBUG != 0
+#ifndef NDEBUG
     oldVal = nNodeEl;
 #endif
     SerUtil::deserialize(in, nNodeEl);

AMDiS/src/MeshStructure.cc

@@ -280,23 +280,23 @@ namespace AMDiS {
     bool cont = true;
     while (cont) {
       bool cont1;
-#if DEBUG != 0
+#ifndef NDEBUG
       bool cont2;
 #endif
       if (structure1->isLeafElement() == structure2->isLeafElement()) {
 	cont1 = structure1->nextElement(result);
-#if DEBUG != 0
+#ifndef NDEBUG
 	cont2 = structure2->nextElement();
 #endif
       } else {
 	if (structure1->isLeafElement()) {
 	  cont1 = structure1->nextElement();
-#if DEBUG != 0
+#ifndef NDEBUG
 	  cont2 = structure2->skipBranch(result);
 #endif
 	} else {
 	  cont1 = structure1->skipBranch(result);
-#if DEBUG != 0
+#ifndef NDEBUG
 	  cont2 = structure2->nextElement();
 #endif
 	}
@@ -385,7 +385,7 @@ namespace AMDiS {
       }
 
       if (!finished) {
-#if (DEBUG != 0)
+#ifndef NDEBUG
 	int oldMeshIndex = mesh->getChangeIndex();
 #endif
 
@@ -394,7 +394,7 @@ namespace AMDiS {
 	else
 	  manager->refineMacroElement(mesh, macroElIndex);
 
-#if (DEBUG != 0)
+#ifndef NDEBUG
 	TEST_EXIT(oldMeshIndex != mesh->getChangeIndex())
 	  ("Mesh has not been changed by refinement procedure!\n");
 #endif

AMDiS/src/MeshStructure.h

@@ -32,10 +32,10 @@
 #include "Global.h"
 #include "BoundaryObject.h"
 
-#if (DEBUG != 0)
-#define WITH_ELINDEX true
+#ifndef NDEBUG
+  #define WITH_ELINDEX true
 #else
-#define WITH_ELINDEX false
+  #define WITH_ELINDEX false
 #endif
 
 namespace AMDiS {

AMDiS/src/OpenMP.h

@@ -47,7 +47,7 @@ namespace AMDiS {
 
     inline T& get()
     {
-#if (DEBUG != 0)
+#ifndef NDEBUG
       if (omp_get_thread_num() >= data.size()) {
 	std::cout << "Error in ThreadPrivate::get()!\n";
 	exit(0);
@@ -58,7 +58,7 @@ namespace AMDiS {
 
     inline void set(T& val)
     {
-#if (DEBUG != 0)
+#ifndef NDEBUG
       if (omp_get_thread_num() >= data.size()) {
 	std::cout << "Error in ThreadPrivate::set()!\n";
 	exit(0);

AMDiS/src/ProblemStat.h

@@ -703,7 +703,7 @@ namespace AMDiS {
 			 public StandardProblemIteration
     {
       using ProblemStatType::getName;
-      using ProblemStatSeq::info;
+      using ProblemStatType::info;
 
       /// Constructor
       ProblemStat(std::string nameStr,

AMDiS/src/RefinementManager3d.cc

@@ -422,7 +422,7 @@ namespace AMDiS {
       return true;
 
     int oppVertex = (*elInfo)->getOppVertex(localNeighbour);
-#if DEBUG
+#ifndef NDEBUG
     int testIndex = (*elInfo)->getNeighbour(localNeighbour)->getIndex();
 #endif
     ElInfo *neighInfo = stack->traverseNeighbour3d((*elInfo), localNeighbour);
@@ -573,7 +573,7 @@ namespace AMDiS {
 	if (neighInfo->getNeighbour(i)) {
 	  oppVertex = neighInfo->getOppVertex(i);
 
-#if DEBUG
+#ifndef NDEBUG
 	  int testIndex = neighInfo->getNeighbour(i)->getIndex();
 #endif
 
@@ -607,7 +607,7 @@ namespace AMDiS {
 	("While looping back domains boundary was reached or i == 0\n");
       oppVertex = refineList.getOppVertex(i--, 0);
 
-#if DEBUG
+#ifndef NDEBUG
       int testIndex = neighInfo->getNeighbour(oppVertex)->getIndex();
 #endif
       neighInfo = stack->traverseNeighbour3d(neighInfo, oppVertex);

AMDiS/src/est/ResidualEstimator.cc

@@ -194,7 +194,7 @@ namespace AMDiS {
     Parallel::InteriorBoundary &intBoundary =
       Parallel::MeshDistributor::globalMeshDistributor->getIntBoundary(0);
 
-#if (DEBUG != 0)
+#ifndef NDEBUG
     // Make sure interior boundary is correct
     Parallel::ParallelDebug::testInteriorBoundary(*(Parallel::MeshDistributor::globalMeshDistributor));
 #endif

AMDiS/src/io/MacroReader.cc

@@ -228,7 +228,7 @@ namespace AMDiS { namespace io {
 	  }
 
 	  for (int j = 0; j < dim; j++) {
-#ifdef DEBUG
+#ifndef NDEBUG
 	  {
 		  unsigned initData(melVertex[el1][verticesEl1[j]]);
 		  unsigned oldData((*associated)[melVertex[el1][verticesEl1[j]]]);
@@ -272,7 +272,7 @@ namespace AMDiS { namespace io {
 	}
       }
 
-#if (DEBUG != 0)
+#ifndef NDEBUG
       std::map<BoundaryType, VertexVector*>::iterator assoc;
       std::map<BoundaryType, VertexVector*>::iterator assocEnd =
 	mesh->periodicAssociations.end();

AMDiS/src/parallel/DofComm.cc

@@ -54,7 +54,7 @@ namespace AMDiS { namespace Parallel {
     createContainer(mesh, boundary, boundary.getOwn(), sendDofs);
     createContainer(mesh, boundary, boundary.getOther(), recvDofs);
 
-#if (DEBUG != 0)
+#ifndef NDEBUG
     {
       std::set<DegreeOfFreedom> sds;
       for (DofComm::Iterator it(sendDofs, feSpaces[0]);

AMDiS/src/parallel/ElementObjectDatabase.cc

@@ -452,7 +452,7 @@ namespace AMDiS { namespace Parallel {
     // === in a symmetric way, i.e., if A -> B for a specific boundary type,    ===
     // === there must be a mapping B -> A with the same boundary type.          ===
 
-#if (DEBUG != 0)
+#ifndef NDEBUG
     for (PerBoundMap<DegreeOfFreedom>::iterator it = periodicVertices.begin();
 	 it != periodicVertices.end(); ++it) {
       pair<DegreeOfFreedom, DegreeOfFreedom> testVertex =