merge of branch solver-preconditioner with trunk

AMDiS/AMDISConfig.cmake.in

@@ -68,6 +68,8 @@ set(AMDIS_NEED_ZOLTAN @ENABLE_ZOLTAN@)
 set(AMDIS_HAS_PARALLEL_DOMAIN @ENABLE_PARALLEL_DOMAIN@)
 set(AMDIS_OPENMP @ENABLE_OPENMP@)
 set(AMDIS_NEED_UMFPACK @ENABLE_UMFPACK@)
+set(AMDIS_NEED_HYPRE @ENABLE_HYPRE@)
+set(AMDIS_NEED_PETSC @ENABLE_PETSC@)
 set(AMDIS_NEED_PNG @ENABLE_PNG@)
 set(AMDIS_NEED_BDDCML @ENABLE_BDDCML@)
 set(AMDIS_NEED_MKL @ENABLE_MKL@)

AMDiS/AMDISUse.cmake

@@ -32,7 +32,42 @@ if(AMDIS_HAS_PARALLEL_DOMAIN)
 			message(FATAL_ERROR "could not find the metis libraries needed by amdis")
 		endif(METIS_LIB)
 	endif()
-endif(AMDIS_HAS_PARALLEL_DOMAIN)
+	
+elseif(AMDIS_NEED_PETSC)
+    find_package(MPI REQUIRED)
+    if(MPI_FOUND)
+	    list(APPEND AMDIS_LIBRARIES ${MPI_LIBRARIES})
+	    list(APPEND AMDIS_COMPILEFLAGS ${MPI_COMPILE_FLAGS})
+	    list(APPEND AMDIS_INCLUDE_DIRS ${MPI_INCLUDE_PATH})
+    endif(MPI_FOUND)
+	
+  set(CMAKE_MODULE_PATH ${AMDIS_DIR})
+    set(PETSC_EXECUTABLE_RUNS ON)
+    find_package(PETSc REQUIRED)
+    if(PETSC_FOUND)
+	    list(APPEND AMDIS_LIBRARIES ${PETSC_LIBRARY_SYS} ${PETSC_LIBRARIES})
+	    list(APPEND AMDIS_INCLUDE_DIRS ${PETSC_INCLUDES})
+    else()
+	    message(FATAL_ERROR "Could not find PETSc!")
+    endif(PETSC_FOUND)
+endif()
+
+if(AMDIS_NEED_HYPRE)
+  find_package(HYPRE REQUIRED)
+  if(HAVE_HYPRE)
+    if(NOT MPI_FOUND)
+      find_package(MPI REQUIRED)
+      if(MPI_FOUND)
+	    list(APPEND AMDIS_LIBRARIES ${MPI_LIBRARIES})
+	    list(APPEND AMDIS_COMPILEFLAGS ${MPI_COMPILE_FLAGS})
+	    list(APPEND AMDIS_INCLUDE_DIRS ${MPI_INCLUDE_PATH})
+      endif()
+    endif()
+    list(APPEND AMDIS_INCLUDE_DIRS ${HYPRE_INCLUDE_DIRECTORIES})
+    list(APPEND AMDIS_COMPILEFLAGS "-DMTL_HAS_HYPRE")
+    list(APPEND AMDIS_LIBRARIES ${HYPRE_LIBRARIES} )
+  endif()
+endif(AMDIS_NEED_HYPRE)
 
 #thats bad because it affects each target
 add_definitions(${AMDIS_COMPILEFLAGS})

AMDiS/CMakeLists.txt

@@ -40,12 +40,14 @@ endif()
 SET(ENABLE_PARALLEL_DOMAIN "OFF" CACHE STRING "use parallel domain decomposition. please set to one of: PMTL, PETSC, OFF" )
 option(USE_PETSC_DEV false)
 option(ENABLE_ZOLTAN false)
+option(ENABLE_PETSC "Use sequential PETSc solvers" false)
 option(ENABLE_UMFPACK "Use of UMFPACK solver" false)
+option(ENABLE_HYPRE "Use HYPRE AMG solver" false)
 option(ENABLE_PNG "use png reader/writer" false)
 option(ENABLE_BDDCML "Use of BDDCML library" false)
 option(ENABLE_EXTENSIONS "Use extensions" false)
 option(ENABLE_OPENMP "Use OpenMP" false)
-option(ENABLE_OUTPUT "AMDiS output priniting, disable only for debugging!" true)
+option(ENABLE_OUTPUT "AMDiS output printing, disable only for debugging!" true)
 
 
 mark_as_advanced(ENABLE_OUTPUT)
@@ -80,7 +82,7 @@ SET(AMDIS_SRC ${SOURCE_DIR}/AdaptBase.cc
 	      ${SOURCE_DIR}/CoarseningManager2d.cc
 	      ${SOURCE_DIR}/CoarseningManager3d.cc
 	      ${SOURCE_DIR}/ComponentTraverseInfo.cc
-              ${SOURCE_DIR}/CouplingIterationInterface.cc
+	      ${SOURCE_DIR}/CouplingIterationInterface.cc
 	      ${SOURCE_DIR}/CreatorMap.cc
 	      ${SOURCE_DIR}/DOFAdmin.cc
 	      ${SOURCE_DIR}/DOFIndexed.cc
@@ -105,7 +107,7 @@ SET(AMDIS_SRC ${SOURCE_DIR}/AdaptBase.cc
 	      ${SOURCE_DIR}/Global.cc
 	      ${SOURCE_DIR}/GlobalDOFNumbering.cc
 	      ${SOURCE_DIR}/GlobalElementNumbering.cc
-              ${SOURCE_DIR}/Initfile.cc
+	      ${SOURCE_DIR}/Initfile.cc
 	      ${SOURCE_DIR}/Lagrange.cc
 	      ${SOURCE_DIR}/LeafData.cc
 	      ${SOURCE_DIR}/Line.cc
@@ -139,7 +141,6 @@ SET(AMDIS_SRC ${SOURCE_DIR}/AdaptBase.cc
 	      ${SOURCE_DIR}/SecondOrderTerm.cc
 	      ${SOURCE_DIR}/Serializer.cc
 	      ${SOURCE_DIR}/StandardProblemIteration.cc
-	      ${SOURCE_DIR}/SolverMatrix.cc
 	      ${SOURCE_DIR}/SubAssembler.cc
 	      ${SOURCE_DIR}/SubElInfo.cc
 	      ${SOURCE_DIR}/SubQuadrature.cc
@@ -175,6 +176,7 @@ SET(AMDIS_SRC ${SOURCE_DIR}/AdaptBase.cc
 	      ${SOURCE_DIR}/io/VtkWriter.cc
 	      ${SOURCE_DIR}/io/VtkVectorWriter.cc
 	      ${SOURCE_DIR}/nonlin/ProblemNonLin.cc
+	      ${SOURCE_DIR}/solver/SolverMatrix.cc
 	      ${SOURCE_DIR}/time/RosenbrockAdaptInstationary.cc
 	      ${SOURCE_DIR}/time/RosenbrockMethod.cc
 	      ${SOURCE_DIR}/time/RosenbrockStationary.cc
@@ -230,11 +232,11 @@ if(ENABLE_PARALLEL_DOMAIN)
 
 	list(APPEND COMPILEFLAGS "-DHAVE_PARALLEL_DOMAIN_AMDIS=1")
 	SET(PARALLEL_DOMAIN_AMDIS_SRC
+		${SOURCE_DIR}/parallel/BddcMlSolver.cc
                	${SOURCE_DIR}/parallel/DofComm.cc
 		${SOURCE_DIR}/parallel/CheckerPartitioner.cc
 		${SOURCE_DIR}/parallel/ElementObjectDatabase.cc
 		${SOURCE_DIR}/parallel/InteriorBoundary.cc
-		${SOURCE_DIR}/parallel/MatrixNnzStructure.cc
 		${SOURCE_DIR}/parallel/MeshDistributor.cc 
 		${SOURCE_DIR}/parallel/MeshLevelData.cc 
 		${SOURCE_DIR}/parallel/MeshManipulation.cc
@@ -242,9 +244,10 @@ if(ENABLE_PARALLEL_DOMAIN)
 		${SOURCE_DIR}/parallel/MpiHelper.cc
 		${SOURCE_DIR}/parallel/ParallelDebug.cc
 		${SOURCE_DIR}/parallel/ParallelDofMapping.cc
-		${SOURCE_DIR}/parallel/ParallelProblemStatBase.cc
+		${SOURCE_DIR}/parallel/ParallelProblemStat.cc
+		${SOURCE_DIR}/parallel/ParallelSolver.cc
 		${SOURCE_DIR}/parallel/PeriodicMap.cc
-                ${SOURCE_DIR}/parallel/ParMetisPartitioner.cc
+		${SOURCE_DIR}/parallel/ParMetisPartitioner.cc
 		${SOURCE_DIR}/parallel/StdMpi.cc
 		${SOURCE_DIR}/parallel/ZoltanPartitioner.cc)
 		
@@ -253,13 +256,13 @@ if(ENABLE_PARALLEL_DOMAIN)
 		set(PETSC_EXECUTABLE_RUNS ON)
 		find_package(PETSc REQUIRED)
 		include_directories(${PETSC_DIR}/include ${PETSC_DIR}/${PETSC_ARCH}/include)
+		list(APPEND COMPILEFLAGS "-DHAVE_PARALLEL_PETSC")
 		list(APPEND AMDIS_INCLUDE_DIRS ${PETSC_DIR}/include ${PETSC_DIR}/${PETSC_ARCH}/include)
 		list(APPEND PARALLEL_DOMAIN_AMDIS_SRC 
-			${SOURCE_DIR}/parallel/BddcMlSolver.cc
+			${SOURCE_DIR}/parallel/MatrixNnzStructure.cc
 			${SOURCE_DIR}/parallel/ParallelCoarseSpaceSolver.cc
 			${SOURCE_DIR}/parallel/PetscHelper.cc
 			${SOURCE_DIR}/parallel/PetscSolver.cc
-			${SOURCE_DIR}/parallel/PetscProblemStat.cc
 			${SOURCE_DIR}/parallel/PetscSolverFeti.cc
 			${SOURCE_DIR}/parallel/PetscSolverFetiDebug.cc
 			${SOURCE_DIR}/parallel/PetscSolverFetiMonitor.cc
@@ -269,14 +272,17 @@ if(ENABLE_PARALLEL_DOMAIN)
 			${SOURCE_DIR}/parallel/PetscSolverGlobalBlockMatrix.cc
 			${SOURCE_DIR}/parallel/PetscSolverNavierStokes.cc
 			${SOURCE_DIR}/parallel/PetscSolverNSCH.cc
-                        ${SOURCE_DIR}/parallel/PetscSolverCahnHilliard2.cc
-                        ${SOURCE_DIR}/parallel/PetscSolverCahnHilliard.cc                        
-			${SOURCE_DIR}/parallel/PetscSolverSchur.cc)
+			${SOURCE_DIR}/parallel/PetscSolverCahnHilliard2.cc
+			${SOURCE_DIR}/parallel/PetscSolverCahnHilliard.cc                        
+			${SOURCE_DIR}/parallel/PetscSolverSchur.cc
+			${SOURCE_DIR}/solver/PetscTypes.cc)
 	elseif(ENABLE_PARALLEL_DOMAIN STREQUAL "PMTL")
 		set(MTL_INCLUDE_DIR "")
 		find_package(MTL REQUIRED)
 		list(APPEND COMPILEFLAGS "-DMTL_HAS_MPI" "-DHAVE_PARALLEL_MTL4")
-		list(APPEND PARALLEL_DOMAIN_AMDIS_SRC ${SOURCE_DIR}/parallel/Mtl4Solver.cc)
+# 		list(APPEND PARALLEL_DOMAIN_AMDIS_SRC 
+# 			${SOURCE_DIR}/parallel/PMTL_ProblemStat.cc
+# 			)
 		list(APPEND AMDIS_LIBS ${MTL_LIBRARIES})
 	else()
 		message(SEND_ERROR "Set the domain-decomposition version correctly.")
@@ -290,6 +296,24 @@ if(ENABLE_PARALLEL_DOMAIN)
 endif(ENABLE_PARALLEL_DOMAIN)
 
 
+if(ENABLE_PETSC)
+  find_package(MPI REQUIRED)
+  if(MPI_FOUND)
+    list(APPEND COMPILEFLAGS "${MPI_COMPILE_FLAGS}")
+    include_directories(${MPI_INCLUDE_PATH})
+  endif(MPI_FOUND)
+	
+  set(CMAKE_MODULE_PATH "${CMAKE_MODULE_PATH};/usr/share/cmake-2.8/Modules/;${CMAKE_SOURCE_DIR}/")
+  set(PETSC_EXECUTABLE_RUNS ON)
+  find_package(PETSc REQUIRED)
+  include_directories(${PETSC_DIR}/include ${PETSC_DIR}/${PETSC_ARCH}/include)
+  list(APPEND AMDIS_INCLUDE_DIRS ${PETSC_DIR}/include ${PETSC_DIR}/${PETSC_ARCH}/include)
+  list(APPEND COMPILEFLAGS "-DHAVE_PETSC" "-DPETSC_VERSION=${PETSC_VERSION}")
+  
+  list(APPEND AMDIS_SRC   
+	${SOURCE_DIR}/solver/PetscSolver.cc
+	${SOURCE_DIR}/solver/PetscTypes.cc)
+endif(ENABLE_PETSC)
 
 if(ENABLE_UMFPACK)
 	find_file(UMFPACK_H umfpack.h
@@ -306,6 +330,24 @@ if(ENABLE_UMFPACK)
 endif(ENABLE_UMFPACK)
 
 
+if(ENABLE_HYPRE)
+  include(FindHYPRE.cmake)
+  message("have hypre: ${HAVE_HYPRE}")
+  if(HAVE_HYPRE)
+    if(NOT MPI_FOUND)
+      find_package(MPI REQUIRED)
+      if(MPI_FOUND)
+	list(APPEND COMPILEFLAGS "${MPI_COMPILE_FLAGS}")
+	include_directories(${MPI_INCLUDE_PATH})
+      endif()
+    endif()
+    include_directories(${HYPRE_INCLUDE_DIRECTORIES})
+    list(APPEND COMPILEFLAGS "-DMTL_HAS_HYPRE")
+    list(APPEND MYLIBS ${HYPRE_LIBRARIES} )
+  endif()
+endif(ENABLE_HYPRE)
+  
+  
 if(ENABLE_PNG)
 	find_file(PNG_H png.h
 			    HINTS ENV CPATH /usr/include
@@ -374,6 +416,13 @@ if(ENABLE_EXTENSIONS)
 	      ${EXTENSIONS_DIR}/POperators.cc
 	      ${EXTENSIONS_DIR}/time/ExtendedRosenbrockStationary.cc
 	      ${EXTENSIONS_DIR}/pugixml/src/pugixml.cpp)
+	      
+      if(ENABLE_PETSC)
+	list(APPEND EXTENSIONS_SRC
+	      ${EXTENSIONS_DIR}/preconditioner/PetscPreconPfc.cc
+	      ${EXTENSIONS_DIR}/preconditioner/PetscPreconCahnHilliard.cc)
+      endif(ENABLE_PETSC)
+      
       list(APPEND COMPILEFLAGS "-DHAVE_EXTENSIONS=1")
       list(APPEND AMDIS_INCLUDE_DIRS ${EXTENSIONS_DIR})
       list(APPEND AMDIS_INCLUDE_DIRS ${EXTENSIONS_DIR}/time)
@@ -401,6 +450,13 @@ if(ENABLE_EXTENSIONS)
       FILE(GLOB HEADERS "${EXTENSIONS_DIR}/time/*.hh")
       INSTALL(FILES ${HEADERS}
 	      DESTINATION include/amdis/extensions/time/)
+	      
+      FILE(GLOB HEADERS "${EXTENSIONS_DIR}/preconditioner/*.h")
+      INSTALL(FILES ${HEADERS}
+	      DESTINATION include/amdis/extensions/preconditioner/)
+      FILE(GLOB HEADERS "${EXTENSIONS_DIR}/preconditioner/*.hh")
+      INSTALL(FILES ${HEADERS}
+	      DESTINATION include/amdis/extensions/preconditioner/)
 
       list(APPEND deb_add_dirs "include/amdis/extensions/time")
 
@@ -438,7 +494,7 @@ if(ENABLE_EXTENSIONS)
 		  ${EXTENSIONS_DIR}/base_problems/NavierStokes_TH_MultiPhase_RB.cc
 		  ${EXTENSIONS_DIR}/base_problems/PhaseFieldCrystal_Base.cc
     # 	      ${EXTENSIONS_DIR}/base_problems/PhaseFieldCrystal.cc
-# 		  ${EXTENSIONS_DIR}/base_problems/PhaseFieldCrystal_Phase.cc
+		  ${EXTENSIONS_DIR}/base_problems/PhaseFieldCrystal_Phase.cc
 		  ${EXTENSIONS_DIR}/base_problems/PhaseFieldCrystal_RB.cc)
 	list(APPEND COMPILEFLAGS "-DHAVE_BASE_PROBLEMS=1")
 	list(APPEND AMDIS_INCLUDE_DIRS ${EXTENSIONS_DIR}/base_problems)
@@ -562,10 +618,20 @@ INSTALL(FILES ${HEADERS}
 	DESTINATION include/amdis/time/)
 list(APPEND deb_add_dirs "include/amdis/time")
 
-FILE(GLOB HEADERS "${SOURCE_DIR}/itl/*.hpp")
+FILE(GLOB HEADERS "${SOURCE_DIR}/solver/*.h")
+INSTALL(FILES ${HEADERS} 
+	DESTINATION include/amdis/solver)
+list(APPEND deb_add_dirs "include/amdis/solver")
+
+FILE(GLOB HEADERS "${SOURCE_DIR}/solver/*.hh")
+INSTALL(FILES ${HEADERS} 
+	DESTINATION include/amdis/solver)
+list(APPEND deb_add_dirs "include/amdis/solver")
+
+FILE(GLOB HEADERS "${SOURCE_DIR}/solver/itl/*.hpp")
 INSTALL(FILES ${HEADERS} 
-	DESTINATION include/amdis/itl)
-list(APPEND deb_add_dirs "include/amdis/itl")
+	DESTINATION include/amdis/solver/itl)
+list(APPEND deb_add_dirs "include/amdis/solver/itl")
 
 FILE(GLOB HEADERS "${SOURCE_DIR}/io/*.h")
 INSTALL(FILES ${HEADERS}
@@ -604,7 +670,10 @@ INSTALL(FILES ${AMDIS_BINARY_DIR}/AMDISConfig.cmake
 	DESTINATION share/amdis/)
 list(APPEND deb_add_dirs "share/amdis/")
 
-INSTALL(FILES ${AMDIS_SOURCE_DIR}/AMDISUse.cmake 
+# INSTALL(FILES ${AMDIS_SOURCE_DIR}/AMDISUse.cmake 
+# 	DESTINATION share/amdis/)
+FILE(GLOB CMAKE_FILES "${AMDIS_SOURCE_DIR}/*.cmake")
+INSTALL(FILES ${CMAKE_FILES}
 	DESTINATION share/amdis/)