Merge branch 'master' of https://gitlab.math.tu-dresden.de/iwr/amdis

AMDiS/src/config/Config_defaults.h

@@ -63,8 +63,8 @@ typedef size_t aligned_size_t;
 
 // C++11 features
 // --------------
-#ifndef HAS_CXX11
-  #define HAS_CXX11 0
+#ifndef AMDIS_HAS_CXX11
+  #define AMDIS_HAS_CXX11 0
 #endif
 
 #ifndef HAS_VARIADIC_TEMPLATES

AMDiS/src/config/Config_gcc.h

@@ -47,7 +47,7 @@ typedef size_t aligned_size_t   __attribute__ ((aligned(CACHE_LINE)));
 
 // C++11 features
 // --------------
-#if HAS_CXX11
+#if AMDIS_HAS_CXX11
 
 #if GCC_VERSION >= 40300 && !defined(HAS_VARIADIC_TEMPLATES)
   #define HAS_VARIADIC_TEMPLATES 1

AMDiS/src/config/Config_intel.h

@@ -51,7 +51,7 @@ typedef __declspec(align(CACHE_LINE)) size_t aligned_size_t;
 
 // C++11 features
 // --------------
-#if HAS_CXX11
+#if AMDIS_HAS_CXX11
 
 #if INTEL_VERSION >= 1201 && !defined(HAS_VARIADIC_TEMPLATES)
   #define HAS_VARIADIC_TEMPLATES 1

AMDiS/src/config/Config_msc.h

@@ -52,6 +52,19 @@ typedef __declspec(align(CACHE_LINE)) size_t aligned_size_t;
 #define ALWAYS_INLINE    __forceinline
 #define OPENMODE         std::ios::open_mode
 
+#ifdef max
+#undef max
+#undef min
+#endif
+
+#ifdef NONE
+#undef NONE
+#endif
+
+#ifdef THIS
+#undef THIS
+#endif
+
 #if MSC_VERSION >= 1800 && !defined(HAS_VARIADIC_TEMPLATES)
   #define HAS_VARIADIC_TEMPLATES 1
 #endif

AMDiS/src/io/FileWriter.hh

@@ -233,7 +233,7 @@ namespace AMDiS
 
       if (writeParaViewVectorFormat) {
 	io::VtkVectorWriter::Aux<T> vtkVectorWriter(&dataCollectors, writeAs3dVector);
-#ifdef HAVE_COMPRESSION
+#ifdef AMDIS_HAS_COMPRESSION
 	vtkVectorWriter.setCompression(compression);
 #endif
 	vtkVectorWriter.writeFile(fn + paraviewFileExt);

AMDiS/src/io/detail/Arh2Reader.cc

@@ -10,7 +10,7 @@
 #include <boost/filesystem.hpp>
 #include <boost/iostreams/filtering_streambuf.hpp>
 #include <boost/iostreams/copy.hpp>
-#ifdef HAVE_COMPRESSION
+#ifdef AMDIS_HAS_COMPRESSION
 #include <boost/iostreams/filter/zlib.hpp>
 #endif
 
@@ -242,12 +242,12 @@ namespace AMDiS { namespace io {
 	if(minor >= 1)
 	  file.read(const_cast<char*>(cps.data()), 4);
 
-#ifdef HAVE_COMPRESSION
+#if HAMDIS_HAS_COMPRESSION
 	TEST_EXIT(cps == "null" || cps == "zlib")
 	  ("Cannot read Arh2 file. Currently only support zlib compression.\n");
 #else
 	TEST_EXIT(cps == "null")
-	  ("HAVE_COMPRESSION OFF. Cannot read compressed Arh2 file.\n");
+	  ("AMDIS_HAS_COMPRESSION==OFF. Cannot read compressed Arh2 file.\n");
 #endif
 
 	TEST_EXIT(dow == (unsigned)mesh->getGeo(WORLD))
@@ -371,7 +371,7 @@ namespace AMDiS { namespace io {
 	  file.read(buffer, size);
 	  dataStream.write(buffer, size);
 	  delete[] buffer;
-#ifdef HAVE_COMPRESSION
+#ifdef AMDIS_HAS_COMPRESSION
 	  if(cps == "zlib") {
 	    stringstream tmp(ios::out | ios::in);
 	    boost::iostreams::filtering_streambuf<boost::iostreams::input> in;
@@ -554,12 +554,12 @@ namespace AMDiS { namespace io {
 	if(minor > 0)
 	  file.read(const_cast<char*>(cps.data()), 4);
 
-#ifdef HAVE_COMPRESSION
+#ifdef AMDIS_HAS_COMPRESSION
 	TEST_EXIT(cps == "null" || cps == "zlib")
 	  ("Cannot read Arh2 file. Currently only support zlib compression.\n");
 #else
 	TEST_EXIT(cps == "null")
-	  ("HAVE_COMPRESSION OFF. Cannot read compressed Arh2 file.\n");
+	  ("AMDIS_HAS_COMPRESSION OFF. Cannot read compressed Arh2 file.\n");
 #endif
 
 	vector<int> macroElIndex(nMacroElements);
@@ -600,7 +600,7 @@ namespace AMDiS { namespace io {
 	  dataStream.write(buffer, size);
 	  delete[] buffer;
 
-#ifdef HAVE_COMPRESSION
+#ifdef AMDIS_HAS_COMPRESSION
 	  if(cps == "zlib") {
 	    stringstream tmp(ios::out | ios::in);
 	    boost::iostreams::filtering_streambuf<boost::iostreams::input> in;

AMDiS/src/io/detail/Arh2Writer.cc

@@ -11,7 +11,7 @@
 
 #include <boost/iostreams/filtering_streambuf.hpp>
 #include <boost/iostreams/copy.hpp>
-#ifdef HAVE_COMPRESSION
+#ifdef AMDIS_HAS_COMPRESSION
 #include <boost/iostreams/filter/zlib.hpp>
 #endif
 
@@ -151,7 +151,7 @@ namespace AMDiS { namespace io {
 			     namesLen + 	     //value vector table
 			     nValueVectors * 8;      //also value vector table
         string typeId = "arh2", cps("null");
-#ifdef HAVE_COMPRESSION
+#ifdef AMDIS_HAS_COMPRESSION
 	cps = "zlib";
 #endif
         uint8_t *major = const_cast<uint8_t*>(&(AMDiS::io::Arh2Writer::MAJOR));
@@ -426,7 +426,7 @@ namespace AMDiS { namespace io {
         }
 	stringstream tmp(ios::out | ios::in | ios::binary);
         boost::iostreams::filtering_streambuf<boost::iostreams::input> in;
-#ifdef HAVE_COMPRESSION
+#ifdef AMDIS_HAS_COMPRESSION
 	in.push(boost::iostreams::zlib_compressor());
 #endif
 	in.push(dataStream);

AMDiS/src/io/detail/Arh3Reader.cc

@@ -14,7 +14,7 @@
 #include <boost/filesystem.hpp>
 #include <boost/iostreams/filtering_streambuf.hpp>
 #include <boost/iostreams/copy.hpp>
-#ifdef HAVE_COMPRESSION
+#ifdef AMDIS_HAS_COMPRESSION
 #include <boost/iostreams/filter/zlib.hpp>
 #include <boost/iostreams/filter/bzip2.hpp>
 #endif
@@ -251,14 +251,14 @@ namespace AMDiS { namespace io {
 	file.read(reinterpret_cast<char*>(&cpsflag), 4);
 	cps = static_cast<Cpsformat::Value>(cpsflag);
 
-#ifdef HAVE_COMPRESSION
+#ifdef AMDIS_HAS_COMPRESSION
 	TEST_EXIT(cps == Cpsformat::ZLIB  ||
 		  cps == Cpsformat::BZIP2 ||
 		  cps == Cpsformat::NONE)
 	  ("Cannot read Arh3 file. Currently only support zlib and bzip2 compression.\n");
 #else
 	TEST_EXIT(cps == Cpsformat::NONE)
-	  ("HAVE_COMPRESSION OFF. Cannot read compressed Arh3 file.\n");
+	  ("AMDIS_HAS_COMPRESSION OFF. Cannot read compressed Arh3 file.\n");
 #endif
 
 	TEST_EXIT(dow == (unsigned)mesh->getGeo(WORLD))
@@ -421,7 +421,7 @@ namespace AMDiS { namespace io {
 	  file.read(buffer, size);
 	  dataStream.write(buffer, size);
 	  delete[] buffer;
-#ifdef HAVE_COMPRESSION
+#ifdef AMDIS_HAS_COMPRESSION
 	  stringstream tmp(ios::out | ios::in);
 	  boost::iostreams::filtering_streambuf<boost::iostreams::input> in;
 	  switch(cps)
@@ -649,14 +649,14 @@ namespace AMDiS { namespace io {
 	file.read(reinterpret_cast<char*>(&cpsflag), 4);
 	cps = static_cast<Cpsformat::Value>(cpsflag);
 
-#ifdef HAVE_COMPRESSION
+#ifdef AMDIS_HAS_COMPRESSION
 	TEST_EXIT(cps == Cpsformat::ZLIB  ||
 		  cps == Cpsformat::BZIP2 ||
 		  cps == Cpsformat::NONE)
 	  ("Cannot read Arh3 file. Currently only support zlib and bzip2 compression.\n");
 #else
 	TEST_EXIT(cps == Cpsformat::NONE)
-	  ("HAVE_COMPRESSION OFF. Cannot read compressed Arh3 file.\n");
+	  ("AMDIS_HAS_COMPRESSION OFF. Cannot read compressed Arh3 file.\n");
 #endif
 
 	vector<int> macroElIndex(nMacroElements);
@@ -715,7 +715,7 @@ namespace AMDiS { namespace io {
 	  dataStream.write(buffer, size);
 	  delete[] buffer;
 
-#ifdef HAVE_COMPRESSION
+#ifdef AMDIS_HAS_COMPRESSION
 	  stringstream tmp(ios::out | ios::in);
 	  boost::iostreams::filtering_streambuf<boost::iostreams::input> in;
 	  switch(cps)

AMDiS/src/io/detail/Arh3Writer.cc

@@ -15,7 +15,7 @@
 #include <boost/iostreams/filtering_streambuf.hpp>
 #include <boost/iostreams/device/file_descriptor.hpp>
 #include <boost/iostreams/copy.hpp>
-#ifdef HAVE_COMPRESSION
+#ifdef AMDIS_HAS_COMPRESSION
 #include <boost/iostreams/filter/zlib.hpp>
 #include <boost/iostreams/filter/bzip2.hpp>
 #endif
@@ -140,7 +140,7 @@ namespace AMDiS { namespace io {
 	      macroFilename + ';' + perFilename;
 
 	    macroFile_nl = macroFile.length();
-	  } else if (writeMacro == Macroformat::THIS) {
+	  } else if (writeMacro == Macroformat::SELF) {
 	    macroFile_nl = 13;
 	    readFileToString(macroFilename, macroData);
 
@@ -163,7 +163,7 @@ namespace AMDiS { namespace io {
 	}
 
 	// write macro and periodic file
-	if (writeMacro == Macroformat::THIS && macroFilename.length()) {
+	if (writeMacro == Macroformat::SELF && macroFilename.length()) {
 	  file.seekp(0, ios_base::end);
 	  long macroPos = file.tellp(), perPos = 0;
 	  file.write(macroData.c_str(), macroData.length());
@@ -354,7 +354,7 @@ namespace AMDiS { namespace io {
 	      macroFilename + ';' + perFilename;
 
 	    macroFile_nl = macroFile.length();
-	  } else if (writeMacro == Macroformat::THIS) {
+	  } else if (writeMacro == Macroformat::SELF) {
 	    macroFile_nl = perFilename.length() ? 27 : 13;
 	    macroFile.resize(macroFile_nl, ' ');
 	  }
@@ -371,7 +371,7 @@ namespace AMDiS { namespace io {
 			     4 +			  //macroFile_nl
 			     macroFile_nl;		  //macroFile
         string typeId = "sarh";
-#ifndef HAVE_COMPRESSION
+#if !AMDIS_HAS_COMPRESSION
 	cps = Cpsformat::NONE;
 #endif
         uint8_t *major = const_cast<uint8_t*>(&(AMDiS::io::Arh3Reader::MAJOR));
@@ -604,7 +604,7 @@ namespace AMDiS { namespace io {
 	//reset the macro positions in file
 	setMacrosPos(file, headerLen, macroSize);
 
-	if (writeMacro == Macroformat::THIS)
+	if (writeMacro == Macroformat::SELF)
 	  setMacroFile(file, headerLen, mesh, writeMacro);
 
         file.close();
@@ -634,8 +634,8 @@ namespace AMDiS { namespace io {
       {
 	FUNCNAME("setMacroFile()");
 
-	TEST_EXIT(writeMacro == Macroformat::THIS)
-	  ("This function should only be called under Macroformat::THIS.\n");
+	TEST_EXIT(writeMacro == Macroformat::SELF)
+	  ("This function should only be called under Macroformat::SELF.\n");
 
 	string macroFilename = "", perFilename = "";
 	string macroData = "", periodicData = "";
@@ -716,7 +716,7 @@ namespace AMDiS { namespace io {
         }
 	stringstream tmp(ios::out | ios::in | ios::binary);
         boost::iostreams::filtering_streambuf<boost::iostreams::input> in;
-#ifdef HAVE_COMPRESSION
+#ifdef AMDIS_HAS_COMPRESSION
 	switch(cps)
 	{
 	  case Cpsformat::ZLIB:

AMDiS/src/io/detail/Arh3Writer.h

@@ -27,7 +27,7 @@ namespace AMDiS { namespace io {
       typedef enum{
 	  NONE = 0, 		// no macro
 	  PT_MACROFILE = 1, 	// pointer to macro file
-	  THIS = 2		// pointer to this file, at the end of this file
+	  SELF = 2		// pointer to this file, at the end of this file
       } Value;
     };
 

AMDiS/src/io/detail/VtkReader.h

@@ -32,7 +32,7 @@
 #include <boost/archive/iterators/transform_width.hpp>
 #include <boost/iostreams/filtering_streambuf.hpp>
 #include <boost/iostreams/copy.hpp>
-#ifdef HAVE_COMPRESSION
+#ifdef AMDIS_HAS_COMPRESSION
 #include <boost/iostreams/filter/zlib.hpp>
 #endif
 #include "DOFVector.h"
@@ -95,7 +95,7 @@ namespace AMDiS
 	  return result;
 	}
 
-#ifdef HAVE_COMPRESSION
+#ifdef AMDIS_HAS_COMPRESSION
 	inline std::string decompress(std::string text)
 	{
 	  std::stringstream tmp1, tmp2;
@@ -120,7 +120,7 @@ namespace AMDiS
 	  string header = "", body = "", data = "";
 
 	  if(zlib) {
-#ifdef HAVE_COMPRESSION
+#ifdef AMDIS_HAS_COMPRESSION
 	    string s = input.substr(0, 8);
 	    if (base64)
 	      s = detail::base64ToStr(s);
@@ -151,7 +151,7 @@ namespace AMDiS
 	      offset += *ptr;
 	    }
 #else
-            ERROR_EXIT("HAVE_COMPRESSION OFF. VtkReader cannot read APPENDED_COMPRESSED vtu files.\n");
+            ERROR_EXIT("AMDIS_HAS_COMPRESSION OFF. VtkReader cannot read APPENDED_COMPRESSED vtu files.\n");
 #endif
 	  } else {
  	    header = (base64) ? detail::base64ToStr(input) : input;

AMDiS/src/io/detail/VtkVectorWriter.h

@@ -28,7 +28,7 @@
 #include "io/DataCollector.h"
 #include "SystemVector.h"
 
-#ifdef HAVE_COMPRESSION
+#ifdef AMDIS_HAS_COMPRESSION
 #include "io/FileCompression.h"
 #endif
 
@@ -43,7 +43,7 @@ namespace AMDiS
       struct Aux {
 	Aux(std::vector<DataCollector<S>*> *dc, bool writeAs3dVector_=false)
 	  : dataCollector(dc)
-#ifdef HAVE_COMPRESSION
+#ifdef AMDIS_HAS_COMPRESSION
 	    , compress(NONE)
 #endif
 	    , writeAs3dVector(writeAs3dVector_)
@@ -61,7 +61,7 @@ namespace AMDiS
 			      std::string fnPrefix, std::string fnPostfix);
 
 
-#ifdef HAVE_COMPRESSION
+#ifdef AMDIS_HAS_COMPRESSION
 	/// Set a compressing method for file output.
 	void setCompression(FileCompression c)
 	{
@@ -154,7 +154,7 @@ namespace AMDiS
 	/// List of DataCollectors, for each component of the problem one.
 	std::vector<DataCollector<S>*> *dataCollector;
 
-#ifdef HAVE_COMPRESSION
+#ifdef AMDIS_HAS_COMPRESSION
 	/** \brief
 	* Defines if the file has to be compressed for ouput, and with which
 	* kind of compress method.

AMDiS/src/io/detail/VtkVectorWriter.hh

@@ -42,7 +42,7 @@
 #include <boost/iostreams/device/file_descriptor.hpp>
 #include <boost/lexical_cast.hpp>
 
-#ifdef HAVE_COMPRESSION
+#ifdef AMDIS_HAS_COMPRESSION
 // #include <boost/iostreams/filter/gzip.hpp>
 // #include <boost/iostreams/filter/bzip2.hpp>
 #endif
@@ -67,7 +67,7 @@ namespace AMDiS
 	FUNCNAME("Aux<S>::writeFile()");
 
 	boost::iostreams::filtering_ostream file;
-#ifdef HAVE_COMPRESSION
+#ifdef AMDIS_HAS_COMPRESSION
 // 	switch (compress) {
 // 	case GZIP:
 // 	  file.push(boost::iostreams::gzip_compressor());

AMDiS/src/io/detail/VtkWriter.cc

@@ -33,7 +33,7 @@
 #include <boost/iostreams/filtering_stream.hpp>
 #include <boost/iostreams/device/file_descriptor.hpp>
 #include <boost/iostreams/copy.hpp>
-#ifdef HAVE_COMPRESSION
+#ifdef AMDIS_HAS_COMPRESSION
 #include <boost/iostreams/filter/zlib.hpp>
 #endif
 #include "AdaptInfo.h"
@@ -86,7 +86,7 @@ namespace AMDiS  { namespace io {
 	    break;
 	  }
 	  case APPENDED_COMPRESSED: {
-#ifdef HAVE_COMPRESSION
+#ifdef AMDIS_HAS_COMPRESSION
 	    BinaryStream hstream;
 	    int nBlocks = bstream.getSize() / AMDIS_ZLIB_BLOCK_SIZE + 1;
 	    int finalsize = bstream.getSize() % AMDIS_ZLIB_BLOCK_SIZE;
@@ -232,7 +232,7 @@ namespace AMDiS  { namespace io {
 	  FUNCNAME("writeParallelFile()");
 	  using boost::lexical_cast;
 
-#ifndef HAVE_COMPRESSION
+#ifndef AMDIS_HAS_COMPRESSION
 	  if(format == APPENDED_COMPRESSED)
 	    format = APPENDED;
 #endif

AMDiS/src/io/detail/VtkWriter.h

@@ -119,11 +119,11 @@ namespace AMDiS  { namespace io {
 	    bstream(hp),
 	    writeAsVector(writeAsVector_)
 	{
-#ifndef HAVE_COMPRESSION
+#ifndef AMDIS_HAS_COMPRESSION
 	  FUNCNAME("VtkWriter::Aux::Aux()");
 	  if(f == APPENDED_COMPRESSED) {
 	    f = APPENDED;
-	    WARNING("HAVE_COMPRESSION OFF. So vtuformat is automatically changed from APPENDED_COMPRESSED to APPENDED.\n");
+	    WARNING("AMDIS_HAS_COMPRESSION OFF. So vtuformat is automatically changed from APPENDED_COMPRESSED to APPENDED.\n");
 	  }
 #endif
           degree = (*dataCollector)[0]->getFeSpace()->getBasisFcts()->getDegree();

AMDiS/src/parallel/PetscHelper.cc

@@ -304,16 +304,12 @@ namespace AMDiS
 	PCSetFromOptions(pc);
 
 #ifndef NDEBUG
-    MSG("PetscOptionsView:\n");
-    PetscViewer viewer;
-    PetscViewerCreate(PETSC_COMM_WORLD, &viewer);
-    PetscViewerSetType(viewer, PETSCVIEWERASCII);
-#if (PETSC_VERSION_MINOR >= 7)
-    PetscOptionsView(PETSC_NULL, viewer);
-#else
-    PetscOptionsView(viewer);
-#endif
-    PetscViewerDestroy(&viewer);
+        MSG("PetscOptionsView:\n");
+        PetscViewer viewer;
+        PetscViewerCreate(PETSC_COMM_WORLD, &viewer);
+        PetscViewerSetType(viewer, PETSCVIEWERASCII);
+        petsc::options_view(viewer);
+        PetscViewerDestroy(&viewer);
 #endif
       }
 
@@ -334,19 +330,15 @@ namespace AMDiS
       void createSolver(MPI::Intracomm comm, KSP &ksp, Mat m, std::string kspPrefix, int info)
       {
 	KSPCreate(comm, &ksp);
-	#if (PETSC_VERSION_MINOR >= 5)
-	  KSPSetOperators(ksp, m, m);
-	#else
-	  KSPSetOperators(ksp, m, m, SAME_NONZERO_PATTERN);
-	#endif
+        petsc::ksp_set_operators(ksp, m, m);
 	KSPSetTolerances(ksp, 0.0, 1e-8, PETSC_DEFAULT, PETSC_DEFAULT);
 	KSPSetType(ksp, KSPBCGS);
 	KSPSetOptionsPrefix(ksp, kspPrefix.c_str());
 
 	if (info >= 10)
-	  KSPMonitorSet(ksp, PETSC_MONITOR_CAST(KSPMonitorDefault), PETSC_NULL, PETSC_NULL);
+	  petsc::ksp_monitor_set(ksp, KSPMonitorDefault);
 	else if (info >= 20)
-	  KSPMonitorSet(ksp, PETSC_MONITOR_CAST(KSPMonitorTrueResidualNorm), PETSC_NULL, PETSC_NULL);
+	  petsc::ksp_monitor_set(ksp, KSPMonitorTrueResidualNorm);
       }
 
     } // end namespace petsc_helper

AMDiS/src/parallel/PetscHelper.h

@@ -31,13 +31,6 @@
 #include <petsc.h>
 #include "AMDiS_fwd.h"
 
-#if (PETSC_VERSION_MINOR >= 7)
-  #define PETSC_MONITOR_CAST(...) \
-    (PetscErrorCode (*)(KSP,PetscInt,PetscReal,void*))(__VA_ARGS__)
-#else
-  #define PETSC_MONITOR_CAST(...) __VA_ARGS__
-#endif
-
 namespace AMDiS
 {
   namespace Parallel
@@ -126,7 +119,82 @@ namespace AMDiS
       void createSolver(MPI::Intracomm comm, KSP &ksp, Mat m, std::string kspPrefix = "", int info = 0);
 
     } // 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/parallel/PetscSolver.cc

@@ -26,6 +26,7 @@
 #include "parallel/MeshDistributor.h"
 #include "parallel/MpiHelper.h"
 #include "parallel/ParallelDofMapping.h"
+#include "parallel/PetscHelper.h"
 #include "parallel/PetscSolver.h"
 #include "parallel/StdMpi.h"
 
@@ -49,7 +50,7 @@ namespace AMDiS { namespace Parallel {
       Parameters::get(name + "->ksp", kspStr);
 
     if (kspStr != "")
-      petsc_options_insert_string(kspStr.c_str());
+      petsc::options_insert_string(kspStr.c_str());
 
     Parameters::get(name + "->remove rhs null space", removeRhsNullspace);
     Parameters::get(name + "->has constant null space", hasConstantNullspace);

AMDiS/src/parallel/PetscSolverCahnHilliard.cc

@@ -85,15 +85,11 @@ namespace AMDiS { namespace Parallel {
   {
     // Create FGMRES based outer solver
     KSPCreate(meshDistributor->getMpiComm(0), &ksp);
-#if (PETSC_VERSION_MINOR >= 5)
-    KSPSetOperators(ksp, getMatInterior(), getMatInterior());
-#else
-    KSPSetOperators(ksp, getMatInterior(), getMatInterior(), SAME_NONZERO_PATTERN);
-#endif
+    petsc::ksp_set_operators(ksp, getMatInterior(), getMatInterior());
     if (getInfo() >= 10)
-      KSPMonitorSet(ksp, PETSC_MONITOR_CAST(KSPMonitorDefault), PETSC_NULL, PETSC_NULL);
+      petsc::ksp_monitor_set(ksp, KSPMonitorDefault);
     else if (getInfo() >= 20)
-      KSPMonitorSet(ksp, PETSC_MONITOR_CAST(KSPMonitorTrueResidualNorm), PETSC_NULL, PETSC_NULL);
+      petsc::ksp_monitor_set(ksp, KSPMonitorTrueResidualNorm);
     petsc_helper::setSolver(ksp, "ch_", KSPFGMRES, PCNONE, getRelative(), getTolerance(), getMaxIterations());
     KSPSetFromOptions(ksp);
 

AMDiS/src/parallel/PetscSolverCahnHilliard2.cc

@@ -67,11 +67,7 @@ namespace AMDiS { namespace Parallel {
     /// create new solver for S
     KSP kspS;
     KSPCreate(*data->mpiCommGlobal, &kspS);
-#if (PETSC_VERSION_MINOR >= 5)
-    KSPSetOperators(kspS, S, S);
-#else
-    KSPSetOperators(kspS, S, S, SAME_NONZERO_PATTERN);
-#endif
+    petsc::ksp_set_operators(kspS, S, S);
     petsc_helper::setSolver(kspS, "S_", KSPFGMRES, PCSHELL, 1e-6, 1e-8, 1);
     {
       PC pc;
@@ -117,15 +113,11 @@ namespace AMDiS { namespace Parallel {