.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)
@@ -69,7 +69,7 @@ endif (MSVC)
 
 # parallel of sequential version
 if (ENABLE_PARALLEL_DOMAIN)
-  set(ENABLE_MPI CACHE BOOL "Compile with MPI compiler and library" FORCE)
+  set(ENABLE_MPI 1 CACHE BOOL "Compile with MPI compiler and library" FORCE)
   set(POSTFIX "-p")
 else ()
   set(POSTFIX "-s")

AMDiS/cmake/CMakeLists.txt

@@ -182,6 +182,11 @@ list(APPEND AMDIS_SRC
     ${SOURCE_DIR}/ProblemStatDbg.cc
 )
 
+if (ENABLE_MPI)
+  enable_mpi(COMPILEFLAGS AMDIS_INCLUDE_DIRS _)
+  list(APPEND COMPILEFLAGS "-DHAVE_MPI=1")
+endif (ENABLE_MPI)
+
 include(amdis_parallel)
 include(muparser)
 

AMDiS/cmake/amdis_parallel.cmake

@@ -20,7 +20,6 @@ if (ENABLE_PARALLEL_DOMAIN)
 
     list(APPEND COMPILEFLAGS "-DHAVE_PARALLEL_DOMAIN_AMDIS=1")
 
-    enable_mpi(COMPILEFLAGS AMDIS_INCLUDE_DIRS _)
     enable_petsc(COMPILEFLAGS AMDIS_INCLUDE_DIRS _)
 
     # add support for the zoltan library

AMDiS/cmake3/AMDIS.cmake.in

@@ -78,8 +78,7 @@ target_enable_boost(amdis_base INTERFACE ON)
 # --------------------
 if (AMDIS_NEED_UMFPACK)
   set(AMDIS_SuiteSparse_DIR @SuiteSparse_DIR@)
-  set(AMDIS_UMFPACK_INCLUDE_DIR @UMFPACK_INCLUDE_DIRS@)
-  set(AMDIS_UMFPACK_LIB_DIR ${AMDIS_UMFPACK_INCLUDE_DIR}/../include)
+  set(AMDIS_UMFPACK_ROOT_DIR @UMFPACK_ROOT_DIR@)
   target_enable_umfpack(amdis_base INTERFACE ON)
 endif (AMDIS_NEED_UMFPACK)
 

AMDiS/cmake3/amdis_parallel.cmake

@@ -22,7 +22,6 @@ if (ENABLE_PARALLEL_DOMAIN)
     target_compile_definitions(amdis_parallel INTERFACE
 	   HAVE_PARALLEL_DOMAIN_AMDIS=1)
 
-    target_enable_mpi(amdis_parallel INTERFACE)
     target_enable_petsc(amdis_parallel INTERFACE)
 
     # add support for the zoltan library

AMDiS/cmake3/target_enable_bddcml.cmake

@@ -19,7 +19,7 @@ macro(target_enable_bddcml _TARGET_ _SCOPE_)
       message(FATAL_ERROR "Could not find BDDCML headers.")
     endif()
 
-    if (LINK_EXECUTABLE)
+    if (LINK_EXECUTABLE OR APPLE)
       find_library(BDDCML_LIB bddcml
         HINTS ENV LIBRARY_PATH
         DOC "BDDCML library")
@@ -29,7 +29,7 @@ macro(target_enable_bddcml _TARGET_ _SCOPE_)
       else()
         message(FATAL_ERROR "Could not find the BDDCML library")
       endif()
-    endif (LINK_EXECUTABLE)
+    endif (LINK_EXECUTABLE OR APPLE)
 
     target_compile_definitions(${_TARGET_} ${_SCOPE_} HAVE_BDDCML=1)
 endmacro(target_enable_bddcml)

AMDiS/cmake3/target_enable_boost.cmake

@@ -28,9 +28,9 @@ macro(target_enable_boost _TARGET_ _SCOPE_)
     find_package(Boost ${BOOST_VERSION} REQUIRED ${BOOST_LIBS_REQUIRED})
     target_include_directories(${_TARGET_} ${_SCOPE_} ${Boost_INCLUDE_DIR})
 
-    if (LINK_EXECUTABLE)
+    if (LINK_EXECUTABLE OR APPLE)
       target_link_libraries(${_TARGET_} ${_SCOPE_} ${Boost_LIBRARIES})
-    endif (LINK_EXECUTABLE)
+    endif (LINK_EXECUTABLE OR APPLE)
 
     if (MSVC_SHARED_LIBS AND LINK_EXECUTABLE)
       link_directories(${Boost_LIBRARY_DIRS})

AMDiS/cmake3/target_enable_hypre.cmake

@@ -21,7 +21,7 @@ macro(target_enable_hypre _TARGET_ _SCOPE_)
       target_include_directories(${_TARGET_} ${_SCOPE_} ${HYPRE_INCLUDE_DIRECTORIES})
     endif (_HYPRE_H)
 
-    if (LINK_EXECUTABLE)
+    if (LINK_EXECUTABLE OR APPLE)
       find_library(_HYPRE_LIB HYPRE
         HINTS ${PETSC_LIBRARY_DIRS})
 
@@ -41,10 +41,10 @@ macro(target_enable_hypre _TARGET_ _SCOPE_)
         find_package(LAPACK REQUIRED)
       endif (LAPACK_LIB)
       target_link_libraries(${_TARGET_} ${_SCOPE_} ${LAPACK_LIBRARIES})
-    endif (LINK_EXECUTABLE)
+    endif (LINK_EXECUTABLE OR APPLE)
 
 
-    if (_HYPRE_H AND (NOT LINK_EXECUTABLE OR _HYPRE_LIB))
+    if (_HYPRE_H AND (NOT LINK_EXECUTABLE OR _HYPRE_LIB OR APPLE))
       set(HAVE_HYPRE ON)
       target_compile_definitions(${_TARGET_} ${_SCOPE_} MTL_HAS_HYPRE)
     else ()

AMDiS/cmake3/target_enable_petsc.cmake

@@ -13,7 +13,7 @@ macro(target_enable_mpi _TARGET_ _SCOPE_)
     target_compile_options(${_TARGET_} ${_SCOPE_}
       ${MPI_CXX_COMPILE_FLAGS})
 
-    if (LINK_EXECUTABLE)
+    if (LINK_EXECUTABLE OR APPLE)
       # the parameter --enable-new-dtags causes a linker problem, i.e. some libraries are
       # linked without an rpath (or any other path information) and can not be found while
       # running the executable. The hack below removes this flag manually from the linker flags.
@@ -21,7 +21,7 @@ macro(target_enable_mpi _TARGET_ _SCOPE_)
       string(STRIP "${MY_MPI_CXX_LINK_FLAGS}" MY_MPI_CXX_LINK_FLAGS)
 
       target_link_libraries(${_TARGET_} ${_SCOPE_} ${MPI_CXX_LIBRARIES} ${MY_MPI_CXX_LINK_FLAGS})
-    endif (LINK_EXECUTABLE)
+    endif (LINK_EXECUTABLE OR APPLE)
 endmacro(target_enable_mpi)
 
 macro(target_enable_petsc _TARGET_ _SCOPE_)
@@ -39,7 +39,8 @@ macro(target_enable_petsc _TARGET_ _SCOPE_)
             $ENV{PETSC_ROOT}/lib/pkgconfig
             /usr/lib/petsc/lib/pkgconfig
             /usr/lib/petsc/linux-gnu-cxx-opt/lib/pkgconfig
-            /usr/lib/petsc/linux-gnu-c-opt/lib/pkgconfig)
+            /usr/lib/petsc/linux-gnu-c-opt/lib/pkgconfig
+      PATHS $ENV{PKG_CONFIG_PATH})
     if (PETSC_PKG_CONFIG)
       get_filename_component(PETSC_PKG_CONFIG_PATH "${PETSC_PKG_CONFIG}" PATH CACHE)
       set(ENV{PKG_CONFIG_PATH} ${PETSC_PKG_CONFIG_PATH})
@@ -74,7 +75,7 @@ macro(target_enable_petsc _TARGET_ _SCOPE_)
         PETSC_VERSION=${PETSC_VERSION})
     target_compile_options(${_TARGET_} ${_SCOPE_} ${PETSC_DEFINITIONS})
 
-    if (LINK_EXECUTABLE)
+    if (LINK_EXECUTABLE OR APPLE)
       set(PETSC_LINK_LIBRARIES "")
       foreach (_PETSC_LIB ${PETSC_LIBRARIES})
         find_library(_PETSC_LINK_LIB ${_PETSC_LIB} PATHS ${PETSC_LIBRARY_DIRS} NO_DEFAULT_PATH)
@@ -82,7 +83,7 @@ macro(target_enable_petsc _TARGET_ _SCOPE_)
       endforeach()
       message(STATUS "  Found PETSc library ${PETSC_LINK_LIBRARIES}")
       target_link_libraries(${_TARGET_} ${_SCOPE_} ${PETSC_LINK_LIBRARIES})
-    endif (LINK_EXECUTABLE)
+    endif (LINK_EXECUTABLE OR APPLE)
 
 
     # parmetis is required
@@ -104,7 +105,7 @@ macro(target_enable_petsc _TARGET_ _SCOPE_)
       message(FATAL_ERROR "Could not find ParMetis header file 'parmetis.h'!")
     endif (PARMETIS_HEADER_FILE)
 
-    if (LINK_EXECUTABLE)
+    if (LINK_EXECUTABLE OR APPLE)
       find_library(PARMETIS_LIB parmetis
         HINTS ${PARMETIS_DIR}/lib ${PETSC_LIBRARY_DIRS})
       if (NOT PARMETIS_LIB)
@@ -112,7 +113,7 @@ macro(target_enable_petsc _TARGET_ _SCOPE_)
       endif (NOT PARMETIS_LIB)
       message(STATUS "  Found ParMetis library ${PARMETIS_LIB}")
       target_link_libraries(${_TARGET_} ${_SCOPE_} ${PARMETIS_LIB})
-    endif (LINK_EXECUTABLE)
+    endif (LINK_EXECUTABLE OR APPLE)
 
 
     # metis is required
@@ -125,7 +126,7 @@ macro(target_enable_petsc _TARGET_ _SCOPE_)
       message(FATAL_ERROR "Could not find Metis header file 'metis.h'!")
     endif (METIS_HEADER_FILE)
 
-    if (LINK_EXECUTABLE)
+    if (LINK_EXECUTABLE OR APPLE)
       find_library(METIS_LIB metis
         HINTS ${METIS_DIR}/lib ${PETSC_LIBRARY_DIRS})
       if (NOT METIS_LIB)
@@ -133,11 +134,11 @@ macro(target_enable_petsc _TARGET_ _SCOPE_)
       endif (NOT METIS_LIB)
       message(STATUS "  Found Metis library ${METIS_LIB}")
       target_link_libraries(${_TARGET_} ${_SCOPE_} ${METIS_LIB})
-    endif (LINK_EXECUTABLE)
+    endif (LINK_EXECUTABLE OR APPLE)
 
 
     # blas library is required
-    if (LINK_EXECUTABLE)
+    if (LINK_EXECUTABLE OR APPLE)
       find_library(BLAS_LIB
         NAMES blas fblas openblas
         HINTS ${BLAS_DIR}/lib ${PETSC_LIBRARY_DIRS} /usr/lib/openblas-base /usr/lib/atlas-base)
@@ -147,11 +148,11 @@ macro(target_enable_petsc _TARGET_ _SCOPE_)
         find_package(BLAS REQUIRED)
       endif (BLAS_LIB)
       target_link_libraries(${_TARGET_} ${_SCOPE_} ${BLAS_LIBRARIES})
-    endif (LINK_EXECUTABLE)
+    endif (LINK_EXECUTABLE OR APPLE)
 
 
     # lapack library is required
-    if (LINK_EXECUTABLE)
+    if (LINK_EXECUTABLE OR APPLE)
       find_library(LAPACK_LIB
         NAMES lapack flapack
         HINTS ${LAPACK_DIR}/lib ${PETSC_LIBRARY_DIRS} ${PETSC_DIR}/lib)
@@ -161,5 +162,5 @@ macro(target_enable_petsc _TARGET_ _SCOPE_)
         find_package(LAPACK REQUIRED)
       endif (LAPACK_LIB)
       target_link_libraries(${_TARGET_} ${_SCOPE_} ${LAPACK_LIBRARIES})
-    endif (LINK_EXECUTABLE)
+    endif (LINK_EXECUTABLE OR APPLE)
 endmacro(target_enable_petsc)

AMDiS/cmake3/target_enable_png.cmake

@@ -25,7 +25,7 @@ macro(target_enable_png _TARGET_ _SCOPE_)
     get_filename_component(PNG_PATH ${_PNG_H} PATH)
     target_include_directories(${_TARGET_} ${_SCOPE_} ${PNG_PATH})
 
-    if (LINK_EXECUTABLE)
+    if (LINK_EXECUTABLE OR APPLE)
       find_library(_PNG_LIB png
         HINTS ENV LIBRARY_PATH
         DOC "The PNG library")
@@ -34,7 +34,7 @@ macro(target_enable_png _TARGET_ _SCOPE_)
       else()
         message(FATAL_ERROR "Could not find the PNG library")
       endif()
-    endif (LINK_EXECUTABLE)
+    endif (LINK_EXECUTABLE OR APPLE)
 
     target_compile_definitions(${_TARGET_} ${_SCOPE_} HAVE_PNG=1)
 endmacro(target_enable_png)

AMDiS/cmake3/target_enable_umfpack.cmake

@@ -18,19 +18,22 @@ macro(target_enable_umfpack _TARGET_ _SCOPE_)
     if (SuiteSparse_FOUND)
         message(STATUS "Found SuiteSparse CMake-library")
         include(${USE_SuiteSparse})
-        if (LINK_EXECUTABLE)
+        if (LINK_EXECUTABLE OR APPLE)
           target_link_libraries(${_TARGET_} ${_SCOPE_} ${SuiteSparse_LIBRARIES})
-        endif (LINK_EXECUTABLE)
+        endif (LINK_EXECUTABLE OR APPLE)
         target_include_directories(${_TARGET_} ${_SCOPE_} ${SuiteSparse_INCLUDE_DIR} ${SuiteSparse_METIS_INCLUDE_DIR})
         set(FOUND_SUITESPARSE_LIBS ${SuiteSparse_LIBRARIES})
     else (SuiteSparse_FOUND)
         # find umfpack manually by searching for umfpack.h header file
         find_library(UMFPACK_LIBRARY umfpack
-            HINTS ${AMDIS_UMFPACK_LIB_DIR} ${SUITESPARSE_LIB} $ENV{SUITESPARSE_LIB}
-            DOC "Library file for UMFPACK")
+          HINTS ${AMDIS_UMFPACK_ROOT_DIR}
+          PATHS $ENV{EBROOTSUITESPARSE}
+          PATH_SUFFIXES lib/ lib64/
+	        DOC "Library file for UMFPACK")
         find_file(UMFPACK_H umfpack.h
-            HINTS ${AMDIS_UMFPACK_INCLUDE_DIR} ${SUITESPARSE_INC} $ENV{SUITESPARSE_INC} ENV CPATH /usr/include /usr/include/suitesparse /usr/include/ufsparse
-            DOC "Headerfile umfpack.h for UMFPACK")
+          HINTS ${AMDIS_UMFPACK_ROOT_DIR}/include
+          PATHS /usr/include/suitesparse /usr/include/ufsparse $ENV{EBROOTSUITESPARSE}/include
+	        DOC "Headerfile umfpack.h for UMFPACK")
 
         if (UMFPACK_H AND UMFPACK_LIBRARY)
             get_filename_component(UMFPACK_PATH ${UMFPACK_H} PATH)
@@ -39,7 +42,13 @@ macro(target_enable_umfpack _TARGET_ _SCOPE_)
             get_filename_component(UMFPACK_LIB_PATH ${UMFPACK_LIBRARY} PATH)
             set(FOUND_SUITESPARSE_LIBS ${UMFPACK_LIBRARY})
 
-            if (LINK_EXECUTABLE)
+            # extract root directory from umfpack lib dir
+            set (UMFPACK_ROOT_DIR ${UMFPACK_LIB_PATH}/..)
+            if (NOT EXISTS ${UMFPACK_ROOT_DIR}/include)
+              message(WARNING "directory ${UMFPACK_ROOT_DIR} is not a valid root dir of an umfpack installation.")
+            endif ()
+
+            if (LINK_EXECUTABLE OR APPLE)
 
               # find all connected libraries
               find_library(AMD_LIBRARY amd HINTS ${UMFPACK_LIB_PATH})
@@ -70,15 +79,20 @@ macro(target_enable_umfpack _TARGET_ _SCOPE_)
               endif (SUITESPARSECONFIG_LIBRARY)
 
               target_link_libraries(${_TARGET_} ${_SCOPE_} ${FOUND_SUITESPARSE_LIBS})
-            endif (LINK_EXECUTABLE)
+            endif (LINK_EXECUTABLE OR APPLE)
         else()
-            message(FATAL_ERROR "Could not find the UMFPACK header umfpack.h.")
+            if (NOT UMFPACK_H)
+              message(FATAL_ERROR "Could not find the UMFPACK header umfpack.h.")
+            endif ()
+            if (NOT UMFPACK_LIBRARY)
+              message(FATAL_ERROR "Could not find the UMFPACK library libumfpack.so")
+            endif ()
         endif (UMFPACK_H AND UMFPACK_LIBRARY)
     endif (SuiteSparse_FOUND)
 
 
     # Check for clock_gettime in librt
-    if (NOT WIN32 AND LINK_EXECUTABLE)
+    if (NOT WIN32 AND (LINK_EXECUTABLE OR APPLE))
       include(CheckLibraryExists)
       check_library_exists(rt clock_gettime "time.h" HAVE_CLOCK_GETTIME)
       if (HAVE_CLOCK_GETTIME)
@@ -86,7 +100,7 @@ macro(target_enable_umfpack _TARGET_ _SCOPE_)
       else ()
           check_library_exists(c clock_gettime "" HAVE_CLOCK_GETTIME)
       endif (HAVE_CLOCK_GETTIME)
-    endif (NOT WIN32 AND LINK_EXECUTABLE)
+    endif (NOT WIN32 AND (LINK_EXECUTABLE OR APPLE))
 
 
     # collect informations about umfpack version and found libraries
@@ -98,12 +112,12 @@ macro(target_enable_umfpack _TARGET_ _SCOPE_)
         unset(_UMFPACK_H CACHE)
 
         message(STATUS "UMFPACK version: ${UMFPACK_VERSION}")
-        if (LINK_EXECUTABLE)
+        if (LINK_EXECUTABLE OR APPLE)
           message(STATUS "Found the following SuiteSparse libraries:")
           foreach (lib ${FOUND_SUITESPARSE_LIBS})
               message(STATUS "  ${lib}")
           endforeach ()
-        endif (LINK_EXECUTABLE)
+        endif (LINK_EXECUTABLE OR APPLE)
     endif (FOUND_SUITESPARSE_LIBS)
 
     target_compile_definitions(${_TARGET_} ${_SCOPE_}

AMDiS/cmake3/target_enable_zoltan.cmake

@@ -11,7 +11,7 @@ macro(target_enable_zoltan _TARGET_ _SCOPE_)
       find_file(ZOLTAN_HEADER_FILE "zoltan.h" PATHS ${Zoltan_INCLUDE_DIRS})
       target_include_directories(${_TARGET_} ${_SCOPE_} ${Zoltan_INCLUDE_DIRS})
 
-      if (LINK_EXECUTABLE)
+      if (LINK_EXECUTABLE OR APPLE)
         foreach (LIB_NAME ${Zoltan_LIBRARIES})
           find_library(_ZOLTAN_LIB ${LIB_NAME} HINTS ${Zoltan_LIBRARY_DIRS})
           if (NOT _ZOLTAN_LIB)
@@ -21,7 +21,7 @@ macro(target_enable_zoltan _TARGET_ _SCOPE_)
           endif ()
           unset(_ZOLTAN_LIB CACHE)
         endforeach(LIB_NAME)
-      endif (LINK_EXECUTABLE)
+      endif (LINK_EXECUTABLE OR APPLE)
     else (Zoltan_FOUND)
       find_file(ZOLTAN_HEADER_FILE "zoltan.h" HINTS ${ZOLTAN_DIR}/include ${PETSC_INCLUDE_DIRS})
       if (ZOLTAN_HEADER_FILE)
@@ -31,7 +31,7 @@ macro(target_enable_zoltan _TARGET_ _SCOPE_)
         message(FATAL_ERROR "Could not find Zoltan include file 'zoltan.h'!")
       endif(ZOLTAN_HEADER_FILE)
 
-      if (LINK_EXECUTABLE)
+      if (LINK_EXECUTABLE OR APPLE)
         find_library(ZOLTAN_LIB zoltan
           HINTS ${Zoltan_INCLUDE_DIR}/../lib DOC "Full path to the zoltan library")
         if (NOT ZOLTAN_LIB)
@@ -45,7 +45,7 @@ macro(target_enable_zoltan _TARGET_ _SCOPE_)
         else ()
           message(WARNING "Zoltan configuration file Makefile.export.zoltan not found!")
         endif ()
-      endif (LINK_EXECUTABLE)
+      endif (LINK_EXECUTABLE OR APPLE)
 
       target_compile_definitions(${_TARGET_} ${_SCOPE_} HAVE_ZOLTAN=1)
     endif (Zoltan_FOUND)

AMDiS/src/CreatorInterface.h

@@ -76,13 +76,11 @@ namespace AMDiS {
   class NullCreator : public CreatorInterface<BaseClass>
   {
     /// Creates no object.
-    BaseClass* create()
+    virtual BaseClass* create() override
     {
       return NULL;
     }
 
-    virtual ~NullCreator() {}
-
     /// Implementation of \ref CreatorInterface::isNullCreator()
     virtual bool isNullCreator() override
     {
@@ -101,8 +99,6 @@ namespace AMDiS {
   class CreatorInterfaceName : public CreatorInterface<BaseClass>
   {
   public:
-    virtual ~CreatorInterfaceName() {}
-
     /// Sets \ref name
     void setName(std::string str)
     {

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/DOFVector.hh

@@ -124,10 +124,10 @@ namespace AMDiS {
   {
     this->name = n;
     this->feSpace = f;
-    
+
     if (this->feSpace && this->feSpace->getAdmin())
       (this->feSpace->getAdmin())->addDOFIndexed(this);
-    
+
     this->boundaryManager = new BoundaryManager(f);
 #ifdef HAVE_PARALLEL_DOMAIN_AMDIS
     if (addToSynch && Parallel::MeshDistributor::globalMeshDistributor != NULL)
@@ -142,7 +142,7 @@ namespace AMDiS {
     if ( Parallel::MeshDistributor::globalMeshDistributor != NULL)
       Parallel::MeshDistributor::globalMeshDistributor->removeInterchangeVector(this);
 #endif
-    
+
     #ifdef _OPENMP
     #pragma omp critical
     #endif
@@ -1090,7 +1090,7 @@ namespace AMDiS {
 
     ElInfo *elInfo = mesh->createNewElInfo();
     double value = 0.0;
-    bool inside = false;
+    unsigned short inside = 0;
 
     if (oldElInfo && oldElInfo->getMacroElement()) {
       inside = mesh->findElInfoAtPoint(p, elInfo, lambda, oldElInfo->getMacroElement(), NULL, NULL);
@@ -1101,28 +1101,24 @@ namespace AMDiS {
     if (oldElInfo)
       oldElInfo = elInfo;
 
-    if (inside) {
+    if (inside > 0) {
       basFcts->getLocalIndices(elInfo->getElement(), this->feSpace->getAdmin(), localIndices);
       ElementVector uh(nBasFcts);
       for (int i = 0; i < nBasFcts; i++)
         uh[i] = operator[](localIndices[i]);
       value = basFcts->evalUh(lambda, uh);
-    } else {
-#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
-      value = 0.0;
-#else
-      ERROR_EXIT("Can not eval DOFVector at point p, because point is outside geometry.");
-#endif
     }
 
-
     if (oldElInfo == NULL)
       delete elInfo;
 
 #ifdef HAVE_PARALLEL_DOMAIN_AMDIS
     Parallel::mpi::globalAdd(value);
+    Parallel::mpi::globalAdd(inside);
 #endif
-    return value;
+
+    TEST_EXIT(inside > 0)("Can not eval DOFVector at point p, because point is outside geometry.");
+    return value/inside;
   }
 
 
@@ -1140,7 +1136,7 @@ namespace AMDiS {
     DimVec<double> lambda(dim, NO_INIT);
     ElInfo *elInfo = mesh->createNewElInfo();
     WorldVector<double> value(DEFAULT_VALUE, 0.0);
-    bool inside = false;
+    unsigned short inside = 0;
 
     if (oldElInfo && oldElInfo->getMacroElement()) {
       inside = mesh->findElInfoAtPoint(p, elInfo, lambda, oldElInfo->getMacroElement(), NULL, NULL);
@@ -1151,19 +1147,24 @@ namespace AMDiS {
     if (oldElInfo)
       oldElInfo = elInfo;
 
-    if (inside) {
+    if (inside > 0) {
       basFcts->getLocalIndices(elInfo->getElement(), this->feSpace->getAdmin(), localIndices);
       mtl::dense_vector<WorldVector<double> > uh(nBasFcts);
       for (int i = 0; i < nBasFcts; i++)
         uh[i] = operator[](localIndices[i]);
       value = basFcts->evalUh(lambda, uh);
-    } else {
-      ERROR_EXIT("Can not eval DOFVector at point p, because point is outside geometry.");
     }
 
     if (oldElInfo == NULL)
       delete elInfo;
 
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+    Parallel::mpi::globalAdd(value);
+    Parallel::mpi::globalAdd(inside);
+#endif
+
+    TEST_EXIT(inside > 0)("Can not eval DOFVector at point p, because point is outside geometry.");
+    value *= 1.0/inside;
     return value;
   }
 

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,
 					     DOFVector<double>* vec,
@@ -519,7 +519,7 @@ namespace AMDiS {
     Mesh *mesh = feSpace->getMesh();
     bool feSpaceHasNonVertexDofs = (feSpace->getBasisFcts()->getDegree() > 1);
     int nVertexPreDofs = feSpace->getAdmin()->getNumberOfPreDofs(VERTEX);
-    
+
     std::size_t counter = 0;
     if (withElIndex) {
       TEST_EXIT(static_cast<int>(values[0]) == macroElIndex)

AMDiS/src/expressions/cmath_expr.hpp

@@ -490,7 +490,7 @@ namespace AMDiS
 
       int getDegree() const
       {
-	return std::max(super::term1.getDegree(), super::term2.getDegree());
+	return std::max(super::term1.getDegree(), super::term2.getDegree())+2;
       }
 
       inline value_type operator()(const int& iq) const
@@ -514,7 +514,7 @@ namespace AMDiS
 
       int getDegree() const
       {
-	return std::max(super::term1.getDegree(), super::term2.getDegree());
+	return std::max(super::term1.getDegree(), super::term2.getDegree())+2;
       }
 
       inline value_type operator()(const int& iq) const
@@ -525,6 +525,69 @@ namespace AMDiS
       std::string str() const { return std::string("min(") + super::term1.str() + ", " + super::term2.str() + ")"; }
     };
 
+
+    template<typename Term1>
+    struct Clamp : public LazyOperatorTerm1<Term1>
+    {
+      typedef LazyOperatorTerm1<Term1> super;
+      typedef typename Term1::value_type value_type;
+
+      Clamp(const Term1& term1_, value_type const& lo = 0.0, value_type const& hi = 1.0)
+	: super(term1_)
+        , lo(lo)
+        , hi(hi)
+      {
+        assert( !(hi < lo) );
+      }
+
+      int getDegree() const
+      {
+	return super::term.getDegree()+2;
+      }
+
+      inline value_type operator()(const int& iq) const
+      {
+        value_type v = super::term(iq);
+	return v < lo ? lo : hi < v ? hi : v;
+      }
+
+      std::string str() const { return std::string("clamp(") + super::term.str() + ", " + lo + ", " << hi << ")"; }
+
+      value_type lo, hi;
+    };
+
+
+    // derivative of clamp
+    template<typename Term1>
+    struct DClamp : public LazyOperatorTerm1<Term1>
+    {
+      typedef LazyOperatorTerm1<Term1> super;
+      typedef typename Term1::value_type value_type;
+
+      DClamp(const Term1& term1_, value_type const& lo = 0.0, value_type const& hi = 1.0)
+	: super(term1_)
+        , lo(lo)
+        , hi(hi)
+      {
+        assert( !(hi < lo) );
+      }
+
+      int getDegree() const
+      {
+	return 2;
+      }
+
+      inline value_type operator()(const int& iq) const
+      {
+        value_type v = super::term(iq);
+	return v < lo ? value_type(0) : hi < v ? value_type(0) : value_type(1);
+      }
+
+      std::string str() const { return std::string("dclamp(") + super::term.str() + ", " + lo + ", " << hi << ")"; }
+
+      value_type lo, hi;
+    };
+
   } // end namespace expressions
 
 
@@ -742,6 +805,22 @@ namespace AMDiS
     expressions::Atanh<Term> >::type
   atanh(const Term& t) { return expressions::Atanh<Term>(t); }
 
+  //______________________________________________________________________________
+
+  // clamp between lo and hi
+  template<typename Term, typename T = typename Term::value_type>
+  inline typename boost::enable_if<
+    typename traits::is_expr<Term>::type,
+    expressions::Clamp<Term> >::type
+  clamp(const Term& t, T const& lo, T const& hi) { return expressions::Clamp<Term>(t, lo, hi); }
+
+  // derivative of clamp between lo and hi
+  template<typename Term, typename T = typename Term::value_type>
+  inline typename boost::enable_if<
+    typename traits::is_expr<Term>::type,
+    expressions::DClamp<Term> >::type
+  dclamp(const Term& t, T const& lo, T const& hi) { return expressions::DClamp<Term>(t, lo, hi); }
+
 } // end namespace AMDiS
 
 #endif // AMDIS_CMATH_EXPRESSION_HPP