Merge branch 'issue/petsc_3-7' into 'master'

sequential petsc corrected

See merge request !19

AMDiS/cmake/enable_hypre.cmake

@@ -17,7 +17,7 @@ macro(enable_hypre _FLAGS_ _INC_DIRS_ _LIBS_)
       HINTS ${PETSC_INCLUDE_DIRS})
 
     if (_HYPRE_H)
-      get_filename_component(HYPRE_INCLUDE_DIRECTORIES ${HYPRE_H} PATH)
+      get_filename_component(HYPRE_INCLUDE_DIRECTORIES ${_HYPRE_H} PATH)
       list(APPEND ${_INC_DIRS_} ${HYPRE_INCLUDE_DIRECTORIES})
     endif (_HYPRE_H)
 

AMDiS/cmake3/amdis_seq_petsc.cmake

 if (ENABLE_SEQ_PETSC)
-  target_enable_mpi(amdis PRIVATE)
-  target_enable_petsc(amdis PRIVATE)
+  target_enable_mpi(amdis PUBLIC)
+  target_enable_petsc(amdis PUBLIC)
 
-  target_compile_definitions(amdis PRIVATE HAVE_SEQ_PETSC=1)
+  target_compile_definitions(amdis PUBLIC HAVE_SEQ_PETSC=1)
 
   target_sources(amdis PRIVATE
 	${SOURCE_DIR}/solver/PetscSolver.cc

AMDiS/cmake3/target_enable_hypre.cmake

@@ -17,7 +17,7 @@ macro(target_enable_hypre _TARGET_ _SCOPE_)
       HINTS ${PETSC_INCLUDE_DIRS})
 
     if (_HYPRE_H)
-      get_filename_component(HYPRE_INCLUDE_DIRECTORIES ${HYPRE_H} PATH)
+      get_filename_component(HYPRE_INCLUDE_DIRECTORIES ${_HYPRE_H} PATH)
       target_include_directories(${_TARGET_} ${_SCOPE_} ${HYPRE_INCLUDE_DIRECTORIES})
     endif (_HYPRE_H)
 

AMDiS/src/ProblemStat.cc

@@ -566,14 +566,16 @@ namespace AMDiS {
     FUNCNAME("ProblemStat::createSolver()");
 
     // definition of standard-backends
-#if defined HAVE_PARALLEL_PETSC
-    string backend("p_petsc");
-#elif defined HAVE_PARALLEL_MTL
-    string backend("p_mtl");
-#elif defined HAVE_SEQ_PETSC
-    string backend("petsc");
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+      std::string backend = "p_";
+#else
+      std::string backend = "";
+#endif
+
+#if defined(HAVE_PARALLEL_PETSC) || defined(HAVE_SEQ_PETSC)
+      backend += "petsc";
 #else
-    string backend("mtl");
+      backend += "mtl";
 #endif
 
     // === read backend-name ===

AMDiS/src/parallel/PetscHelper.h

@@ -30,6 +30,7 @@
 #include <vector>
 #include <petsc.h>
 #include "AMDiS_fwd.h"
+#include "utility/PetscWrapper.h"
 
 namespace AMDiS
 {
@@ -121,80 +122,4 @@ namespace AMDiS
     } // end namespace petsc_helper
 
   } // end namespace Parallel
-
-
-  // functions for PETSc API changes
-  namespace petsc
-  {
-    inline PetscErrorCode options_view(PetscViewer viewer)
-    {
-#if (PETSC_VERSION_MINOR >= 7)
-      return PetscOptionsView(PETSC_NULL, viewer);
-#else
-      return PetscOptionsView(viewer);
-#endif
-    }
-
-    inline PetscErrorCode options_insert_string(const char in_str[])
-    {
-#if (PETSC_VERSION_MINOR >= 7)
-      return PetscOptionsInsertString(PETSC_NULL, in_str);
-#else
-      return PetscOptionsInsertString(in_str);
-#endif
-    }
-
-    inline PetscErrorCode ksp_set_operators(KSP ksp, Mat Amat,Mat Pmat)
-    {
-#if (PETSC_VERSION_MINOR >= 5)
-      return KSPSetOperators(ksp, Amat, Pmat);
-#else
-      return KSPSetOperators(ksp, Amat, Pmat, SAME_NONZERO_PATTERN);
-#endif
-    }
-
-    inline PetscErrorCode ksp_get_operators(KSP ksp, Mat *Amat,Mat *Pmat)
-    {
-#if (PETSC_VERSION_MINOR >= 5)
-      return KSPGetOperators(ksp, Amat, Pmat);
-#else
-      return KSPGetOperators(ksp, Amat, Pmat, SAME_NONZERO_PATTERN);
-#endif
-    }
-
-    template <class Monitor>
-    inline PetscErrorCode ksp_monitor_set(KSP ksp, Monitor monitor)
-    {
-#if (PETSC_VERSION_MINOR >= 7)
-      PetscViewerAndFormat *vf;
-      PetscErrorCode ierr;
-      ierr = PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_DEFAULT,&vf);CHKERRQ(ierr);
-      ierr = KSPMonitorSet(ksp,(PetscErrorCode (*)(KSP,PetscInt,PetscReal,void*))monitor,vf,(PetscErrorCode (*)(void**))PetscViewerAndFormatDestroy);CHKERRQ(ierr);
-      return ierr;
-#else
-      return KSPMonitorSet(ksp, monitor, PETSC_NULL, PETSC_NULL);
-#endif
-    }
-
-    inline PetscErrorCode mat_create_vecs(Mat mat,Vec *right,Vec *left)
-    {
-#if (PETSC_VERSION_MINOR >= 6)
-      return MatCreateVecs(mat, right, left);
-#else
-      return MatGetVecs(mat, right, left);
-#endif
-    }
-
-    inline PetscErrorCode mat_nullspace_remove(MatNullSpace sp,Vec vec)
-    {
-#if (PETSC_VERSION_MINOR >= 5)
-      return MatNullSpaceRemove(sp, vec);
-#else
-      return MatNullSpaceRemove(sp, vec, PETSC_NULL);
-#endif
-    }
-
-  } // end namespace petsc
 } // end namespace AMDiS
-
-#endif

AMDiS/src/solver/BlockPreconditioner.h

@@ -91,14 +91,16 @@ namespace AMDiS {
 				int max_iter = 100, double tol = 1.e-8)
     {
       // definition of standard-backends
-#if defined HAVE_PARALLEL_PETSC
-      std::string backend("p_petsc");
-#elif defined HAVE_PARALLEL_MTL
-      std::string backend("p_mtl");
-#elif defined HAVE_PETSC
-      std::string backend("petsc");
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+      std::string backend = "p_";
 #else
-      std::string backend("mtl");
+      std::string backend = "";
+#endif
+
+#if defined(HAVE_PARALLEL_PETSC) || defined(HAVE_SEQ_PETSC)
+      backend += "petsc";
+#else
+      backend += "mtl";
 #endif
 
       // === read backend-name ===

AMDiS/src/solver/KrylovPreconditioner.h

@@ -70,15 +70,16 @@ namespace AMDiS {
 	solver(NULL),
 	runner(NULL)
     {
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+      std::string backend = "p_";
+#else
+      std::string backend = "";
+#endif
 
-#if defined HAVE_PARALLEL_PETSC
-      std::string backend("p_petsc");
-#elif defined HAVE_PARALLEL_MTL
-      std::string backend("p_mtl");
-#elif defined HAVE_PETSC || defined HAVE_SEQ_PETSC
-      std::string backend("petsc");
+#if defined(HAVE_PARALLEL_PETSC) || defined(HAVE_SEQ_PETSC)
+      backend += "petsc";
 #else
-      std::string backend("mtl");
+      backend += "mtl";
 #endif
 
       // === read backend-name ===

AMDiS/src/solver/PetscSolver.h

@@ -29,6 +29,7 @@
 #include "solver/LinearSolver.h"
 #include "solver/PetscTypes.h"
 #include "solver/MatrixStreams.h"
+#include "utility/PetscWrapper.h"
 #include "Timer.h"
 #include <vector>
 #include <iostream>
@@ -58,7 +59,7 @@ namespace AMDiS {
 
     virtual void init(PC pc, const SolverMatrix<Matrix<DOFMatrix*> >& A, const MatrixType& fullMatrix)
     {
-      petsc_options_insert_string(("-" + prefix + "pc_type " + name).c_str());
+      petsc::options_insert_string(("-" + prefix + "pc_type " + name).c_str());
       PCSetFromOptions(pc);
     }
 

AMDiS/src/utility/PetscWrapper.h

+/******************************************************************************
+ *
+ * AMDiS - Adaptive multidimensional simulations
+ *
+ * Copyright (C) 2013 Dresden University of Technology. All Rights Reserved.
+ * Web: https://fusionforge.zih.tu-dresden.de/projects/amdis
+ *
+ * Authors:
+ * Simon Vey, Thomas Witkowski, Andreas Naumann, Simon Praetorius, et al.
+ *
+ * This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+ * WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+ *
+ *
+ * This file is part of AMDiS
+ *
+ * See also license.opensource.txt in the distribution.
+ *
+ ******************************************************************************/
+
+
+
+/** \file PetscWrapper.h */
+
+#ifndef AMDIS_PETSCWRAPPER_H
+#define AMDIS_PETSCWRAPPER_H
+
+#include <mpi.h>
+#include <petsc.h>
+
+namespace AMDiS
+{
+
+  // functions for PETSc API changes
+  namespace petsc
+  {
+    inline PetscErrorCode options_view(PetscViewer viewer)
+    {
+#if (PETSC_VERSION_MINOR >= 7)
+      return PetscOptionsView(PETSC_NULL, viewer);
+#else
+      return PetscOptionsView(viewer);
+#endif
+    }
+
+    inline PetscErrorCode options_insert_string(const char in_str[])
+    {
+#if (PETSC_VERSION_MINOR >= 7)
+      return PetscOptionsInsertString(PETSC_NULL, in_str);
+#else
+      return PetscOptionsInsertString(in_str);
+#endif
+    }
+
+    inline PetscErrorCode ksp_set_operators(KSP ksp, Mat Amat,Mat Pmat)
+    {
+#if (PETSC_VERSION_MINOR >= 5)
+      return KSPSetOperators(ksp, Amat, Pmat);
+#else
+      return KSPSetOperators(ksp, Amat, Pmat, SAME_NONZERO_PATTERN);
+#endif
+    }
+
+    inline PetscErrorCode ksp_get_operators(KSP ksp, Mat *Amat,Mat *Pmat)
+    {
+#if (PETSC_VERSION_MINOR >= 5)
+      return KSPGetOperators(ksp, Amat, Pmat);
+#else
+      return KSPGetOperators(ksp, Amat, Pmat, SAME_NONZERO_PATTERN);
+#endif
+    }
+
+    template <class Monitor>
+    inline PetscErrorCode ksp_monitor_set(KSP ksp, Monitor monitor)
+    {
+#if (PETSC_VERSION_MINOR >= 7)
+      PetscViewerAndFormat *vf;
+      PetscErrorCode ierr;
+      ierr = PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_DEFAULT,&vf);CHKERRQ(ierr);
+      ierr = KSPMonitorSet(ksp,(PetscErrorCode (*)(KSP,PetscInt,PetscReal,void*))monitor,vf,(PetscErrorCode (*)(void**))PetscViewerAndFormatDestroy);CHKERRQ(ierr);
+      return ierr;
+#else
+      return KSPMonitorSet(ksp, monitor, PETSC_NULL, PETSC_NULL);
+#endif
+    }
+
+    inline PetscErrorCode mat_create_vecs(Mat mat,Vec *right,Vec *left)
+    {
+#if (PETSC_VERSION_MINOR >= 6)
+      return MatCreateVecs(mat, right, left);
+#else
+      return MatGetVecs(mat, right, left);
+#endif
+    }
+
+    inline PetscErrorCode mat_nullspace_remove(MatNullSpace sp,Vec vec)
+    {
+#if (PETSC_VERSION_MINOR >= 5)
+      return MatNullSpaceRemove(sp, vec);
+#else
+      return MatNullSpaceRemove(sp, vec, PETSC_NULL);
+#endif
+    }
+
+  } // end namespace petsc
+} // end namespace AMDiS
+
+#endif

extensions/demo/pfc/CMakeLists.txt

@@ -2,21 +2,18 @@ project("extensions_demo_pfc")
 cmake_minimum_required(VERSION 2.8)
 
 find_package(AMDIS REQUIRED)
+include(${AMDIS_USE_FILE})
 
-if(AMDIS_FOUND)
-	message("amdis was found\n")
-	include(${AMDIS_USE_FILE})
-	SET(BASIS_LIBS ${AMDIS_LIBRARIES})
-endif(AMDIS_FOUND)
+add_definitions(-DUSE_MTL=1)
 
 set(pfc src/pfc.cc)
 add_executable("pfc" ${pfc})
-target_link_libraries("pfc" ${BASIS_LIBS})
+target_link_libraries("pfc" ${AMDIS_LIBRARIES})
 
 set(pfc_rb src/pfc_rb.cc)
 add_executable("pfc_rb" ${pfc_rb})
-target_link_libraries("pfc_rb" ${BASIS_LIBS})
+target_link_libraries("pfc_rb" ${AMDIS_LIBRARIES})
 
 set(vpfc src/vpfc.cc)
 add_executable("vpfc" ${vpfc})
-target_link_libraries("vpfc" ${BASIS_LIBS})
+target_link_libraries("vpfc" ${AMDIS_LIBRARIES})

extensions/demo/pfc/init/pfc.dat.2d

@@ -28,16 +28,8 @@ pfc->space->dim: 2
 
 
 % ================== SOLVER ======================================
-%#include "init/pfc_solver.inc"
-pfc->space->solver: cg
-pfc->space->MG->number of levels:   10
-pfc->space->MG->max iteration:      100
-pfc->space->MG->tolerance:          1.e-8
-pfc->space->MG->nu1:                20
-pfc->space->MG->nu2:                20
-pfc->space->MG->gamma:              1
-pfc->space->MG->mu:                 3
-pfc->space->MG->fine level:         12
+pfc->space->solver->backend: bpetsc
+#include "init/pfc_solver.mtl.inc"
 
 % ==================== TIMESTEPS ===============================
 adapt->timestep:      1.e-1

extensions/demo/pfc/init/pfc_rb.mtl.dat.2d

@@ -29,6 +29,7 @@ pfc->space->dim: 2
 
 
 % ================== SOLVER ======================================
+pfc->space->solver->backend: mtl
 #include "init/pfc_solver.mtl.inc"
 
 

extensions/demo/pfc/init/pfc_solver.inc

-%pfc->space->solver->backend: p_petsc
+pfc->space->solver->backend: petsc
 pfc->space->solver->petsc prefix: pfc_
 pfc->space->solver: pfc
 pfc->space->solver->ksp_type: fgmres
@@ -26,4 +26,4 @@ precon_pfc_MpL2->max iteration: 1000
 precon_pfc_MpL2->relative tolerance: 1.e-3
 precon_pfc_MpL2->use direct solver: 0
 precon_pfc_MpL2->solver: cg
-precon_pfc_MpL2->use AMG: 0
+precon_pfc_MpL2->use AMG: 0
\ No newline at end of file

extensions/demo/pfc/src/pfc.cc

@@ -2,13 +2,11 @@
 #include "Helpers.h"
 #include "PhaseFieldCrystal.h"
 
-#if (defined HAVE_SEQ_PETSC) || (defined HAVE_PETSC)
+#if defined(USE_SEQ_PETSC)
 #include "preconditioner/PetscPreconPfc.h"
-#endif
-#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+#elif defined(USE_PARALLEL_PETSC)
 #include "preconditioner/PetscSolverPfc.h"
-#endif
-#if (!defined HAVE_SEQ_PETSC) && (!defined HAVE_PETSC) && (!defined HAVE_PARALLEL_DOMAIN_AMDIS)
+#elif defined(USE_MTL)
 #include "preconditioner/MTLPreconPfc.h"
 #endif
 
@@ -30,33 +28,24 @@ public:
   {
     super::finalizeData();
 
-#ifdef USE_PRECON
-
+#if defined(USE_SEQ_PETSC)
     // sequential PFC preconditioner
-#if (defined HAVE_SEQ_PETSC) || (defined HAVE_PETSC)
     PetscPreconPfc* precon = dynamic_cast<PetscPreconPfc*>(prob->getSolver()->getRightPrecon());
     if (precon) {
       precon->setData(getTau(), M0);
     }
-//     PetscPreconPfcDiag* precon2 = dynamic_cast<PetscPreconPfcDiag*>(prob->getSolver()->getRightPrecon());
-//     if (precon2) {
-//       precon2->setData(getTau(), M0);
-    }
-#elif !defined(HAVE_PARALLEL_DOMAIN_AMDIS)
-     MTLPreconPfc* precon = dynamic_cast<MTLPreconPfc*>(prob->getSolver()->getRightPrecon());
-     if (precon)
-	precon->setData(getTau(), M0);
-#else
+#elif defined(USE_PARALLEL_PETSC)
     // parallel PFC preconditioner
     Parallel::PetscSolverPfc* solver = dynamic_cast<Parallel::PetscSolverPfc*>(prob->getSolver());
-    if (solver)
+    if (solver) {
       solver->setData(getTau(), M0);
-
-//     Parallel::PetscSolverPfcDiag* solver2 = dynamic_cast<Parallel::PetscSolverPfcDiag*>(prob->getSolver());
-//     if (solver2)
-//       solver2->setData(getTau(), M0);
-#endif
-
+    }
+#elif defined(USE_MTL)
+    // mtl4 preconditioner
+    MTLPreconPfc* precon = dynamic_cast<MTLPreconPfc*>(prob->getSolver()->getRightPrecon());
+    if (precon) {
+      precon->setData(getTau(), M0);
+    }
 #endif
   }
 
@@ -82,20 +71,13 @@ int main(int argc, char** argv)
   AMDiS::init(argc, argv);
   Timer t;
 
-#ifdef USE_PRECON
-
   // add preconditioner / solver to the parameter list. Must be added before problem is initialized.
-#if (defined HAVE_SEQ_PETSC) || (defined HAVE_PETSC)
+#if defined(USE_SEQ_PETSC)
   CreatorMap<PetscPreconditionerNested>::addCreator("pfc", new PetscPreconPfc::Creator);
-//   CreatorMap<PetscPreconditionerNested>::addCreator("pfc_diag", new PetscPreconPfcDiag::Creator);
-#elif !defined(HAVE_PARALLEL_DOMAIN_AMDIS)
-  CreatorMap<typename MTLPreconPfc::precon_base>::addCreator("pfc", new MTLPreconPfc::Creator);
-//   CreatorMap<typename MTLPreconPfc_Diag::base_precon>::addCreator("pfc", new MTLPreconPfc::Creator);
-#else
+#elif defined(USE_PARALLEL_PETSC)
   CreatorMap<LinearSolverInterface>::addCreator("p_petsc_pfc", new Parallel::PetscSolverPfc::Creator);
-//   CreatorMap<LinearSolverInterface>::addCreator("p_petsc_pfc_diag", new Parallel::PetscSolverPfcDiag::Creator);
-#endif
-
+#elif defined(USE_MTL)
+  CreatorMap<typename MTLPreconPfc::precon_base>::addCreator("pfc", new MTLPreconPfc::Creator);
 #endif
 
   // create and initialize the PFC BaseProblem

extensions/demo/pfc/src/pfc_rb.cc

@@ -2,13 +2,11 @@
 #include "Helpers.h"
 #include "PhaseFieldCrystal.h"
 
-#if (defined HAVE_SEQ_PETSC) || (defined HAVE_PETSC)
+#if defined(USE_SEQ_PETSC)
 #include "preconditioner/PetscPreconPfc.h"
-#endif
-#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+#elif defined(USE_PARALLEL_PETSC)
 #include "preconditioner/PetscSolverPfc.h"
-#endif
-#if (!defined HAVE_SEQ_PETSC) && (!defined HAVE_PETSC) && (!defined HAVE_PARALLEL_DOMAIN_AMDIS)
+#elif defined(USE_MTL)
 #include "preconditioner/MTLPreconPfc.h"
 #endif
 
@@ -49,24 +47,19 @@ public:
   {
     super::initData();
 
+#if defined(USE_SEQ_PETSC)
     // sequential PFC preconditioner
-#if (defined HAVE_SEQ_PETSC) || (defined HAVE_PETSC)
     PetscPreconPfc* runner = dynamic_cast<PetscPreconPfc*>(prob->getSolver()->getRunner());
     if (runner) {
-      dynamic_cast<PetscSolver<PetscPreconPfc>*>(prob->getSolver())->setNested(true);
       runner->setData(getTau());
     }
-#endif
-
+#elif defined(USE_PARALLEL_PETSC)
     // parallel PFC preconditioner
-#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
     Parallel::PetscSolverPfc* solver = dynamic_cast<Parallel::PetscSolverPfc*>(prob->getSolver());
     if (solver)
       solver->setData(getTau());