Moving the documentation for the parallel index sets to dune-common.

The index sets themselves are already there.

Step 1: copying files from dune-istl to dune-common

[[Imported from SVN: r7110]]

doc/Makefile.am

 # $Id$
 
 # also build these sub directories
-SUBDIRS = doxygen buildsystem
+SUBDIRS = doxygen buildsystem comm
 
 # setting like in dune-web
 CURDIR=doc

doc/comm/Makefile.am

+# $Id: Makefile.am 1681 2012-08-31 11:30:17Z gruenich $
+
+SUBDIRS = figures
+
+MPIPROGRAMS = indexset poosc08 poosc08_test
+
+# programs just to build when "make check" is used
+check_PROGRAMS = $(MPIPROGRAMS)
+# list of tests to run (indicestest is special case)
+TESTS = $(MPIPROGRAMS)
+
+if BUILD_DOCS
+  DOCFILES = communication.pdf
+  EXTRA_DIST = $(DOCFILES)
+  EXTRAINSTALL = $(DOCFILES)
+endif
+
+# setting like in dune-web
+CURDIR=doc/istl/comm
+BASEDIR=../../..
+
+# install the docs
+docdir=$(datadir)/doc/dune-istl/comm
+
+include $(top_srcdir)/am/latex
+include $(top_srcdir)/am/webstuff
+include $(top_srcdir)/am/global-rules
+
+poosc08_SOURCES = poosc08.cc
+poosc08_CPPFLAGS = $(AM_CPPFLAGS)              \
+        $(DUNEMPICPPFLAGS)
+poosc08_LDFLAGS = $(AM_LDFLAGS)                \
+        $(DUNEMPILDFLAGS)
+poosc08_LDADD =                                \
+        $(DUNEMPILIBS)                          \
+        $(LDADD)
+
+poosc08_test_SOURCES = poosc08_test.cc
+poosc08_test_CPPFLAGS = $(AM_CPPFLAGS)              \
+        $(DUNEMPICPPFLAGS)
+poosc08_test_LDFLAGS = $(AM_LDFLAGS)                \
+        $(DUNEMPILDFLAGS)
+poosc08_test_LDADD =                                \
+        $(DUNEMPILIBS)                          \
+        $(LDADD)
+
+indexset_SOURCES = indexset.cc buildindexset.hh reverse.hh
+indexset_CPPFLAGS = $(AM_CPPFLAGS)		\
+	$(DUNEMPICPPFLAGS)
+indexset_LDFLAGS = $(AM_LDFLAGS)		\
+	$(DUNEMPILDFLAGS)
+indexset_LDADD =				\
+	$(DUNEMPILIBS)				\
+	$(LDADD)

doc/comm/buildindexset.hh

+// -*- tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 2 -*-
+// vi: set et ts=4 sw=2 sts=2:
+// $Id: buildindexset.hh 1565 2012-04-30 22:04:34Z mblatt $
+#ifndef BUILDINDEXSET_HH
+#define BUILDINDEXSET_HH
+
+
+#include <dune/common/parallel/indexset.hh>
+#include <dune/common/parallel/plocalindex.hh>
+
+/**
+ * @brief Flag for marking the indices.
+ */
+enum Flag {owner, overlap};
+
+// The type of local index we use
+typedef Dune::ParallelLocalIndex<Flag> LocalIndex;
+
+/**
+ * @brief Add indices to the example index set.
+ * @param indexSet The index set to build.
+ */
+template<class C, class TG, int N>
+void build(C& comm, Dune::ParallelIndexSet<TG,LocalIndex,N>& indexSet)
+{
+
+
+
+
+  // The rank of our process
+  int rank=comm.rank();
+
+  // Indicate that we add or remove indices.
+  indexSet.beginResize();
+
+  if(rank==0) {
+    indexSet.add(0, LocalIndex(0,overlap,true));
+    indexSet.add(2, LocalIndex(1,owner,true));
+    indexSet.add(6, LocalIndex(2,owner,true));
+    indexSet.add(3, LocalIndex(3,owner,true));
+    indexSet.add(5, LocalIndex(4,owner,true));
+  }
+
+  if(rank==1) {
+    indexSet.add(0, LocalIndex(0,owner,true));
+    indexSet.add(1, LocalIndex(1,owner,true));
+    indexSet.add(7, LocalIndex(2,owner,true));
+    indexSet.add(5, LocalIndex(3,overlap,true));
+    indexSet.add(4, LocalIndex(4,owner,true));
+  }
+
+  // Modification is over
+  indexSet.endResize();
+}
+#endif

doc/comm/communication.bib

+@InProceedings{ISTL,
+  author = {Markus Blatt and Peter Bastian},
+  title = 	 {The Iterative Solver Template Library},
+  booktitle = {Applied Parallel Computing. State of the Art in Scientific Computing},
+  editor = 	 {Bo K\r{a}gstr\"om and Erik Elmroth and Jack Dongarra and Jerzy Wa\'sniewski},
+  year = 	 2007,
+  volume = 	 4699,
+  series = 	 {Lecture Notes in Computer Science},
+  publisher =	 {Springer},
+  pages = {666--675}
+}
+
+@Article{dune08-1,
+  author = 	 {Peter Bastian and Markus Blatt and Andreas Dedner and Christian Engwer and Robert Kl\"ofkorn and Mario Ohlberger and Oliver Sander},
+  title = 	 { A generic grid interface for parallel and adaptive scientific computing. Part I: abstract framework},
+  journal = 	 {Computing},
+  year = 	 2008,
+  volume =       82,
+  number = {2--3},
+  pages = {103--119}
+}
+@Article{dune08-2,
+  author = 	 {Peter Bastian and Markus Blatt and Andreas Dedner and Christian Engwer and Robert Kl\"ofkorn and Ralf Kornhuber and Mario Ohlberger and Oliver Sander},
+  title = 	 { A generic grid interface for parallel and adaptive scientific computing. Part II: implementation and test in DUNE},
+  journal = 	 {Computing},
+  year = 	 2008,
+  volume =       82,
+  number = {2--3} ,
+  pages = {121--138}
+}
+@Article{ISTLParallel,
+  author =       {Markus Blatt and Peter Bastian},
+  title =        {On the Generic Parallelisation of Iterative Solvers for
+  the Finite Element Method},
+  journal =      {Int. J. Computational Science and
+    Engineering},
+  volume = {4},
+  number = {1},
+  pages = {56--69},
+  year =         2008
+}
+
+@Misc{DuneWeb,
+  author = {DUNE},
+  howpublished     = {\texttt{http://www.dune-project.org/}}
+}
+@Misc{boost_mpi,
+  author = 	 {D. Gregor and M. Troyer},
+  title = 	 {{B}oost.{M}{P}{I}},
+  howpublished = {\texttt{http://www.boost.org/}},
+  year = 	 2006
+}
+
+@PhdThesis{gerlach02:janus,
+  author = 	 {Jens Gerlach},
+  title = 	 {Domain Engineering and Generic Programming for Parallel Scientific Computing},
+  school = 	 {TU Berlin},
+  year = 	 {2002}
+}
+
+@InProceedings{giloi95:_promot,
+  author = 	 {W.K. Giloi and M. Kessler and A. Schramm},
+  title = 	 {PROMOTER: A High Level, Object-Parallel Programming Language},
+  booktitle = {Proceedings of the International Conference on High Performance Computing},
+  year = 	 {1995},
+  address = 	 {New Dehli, India},
+  month = 	 {December}
+}
+
+@inproceedings{nolte00:_taco,
+ author = {J\"{o}rg Nolte and Mitsuhisa Sato and Yutaka Ishikawa},
+ title = {TACO -- Dynamic Distributed Collections with Templates and Topologies},
+ booktitle = {Euro-Par '00: Proceedings from the 6th International Euro-Par Conference on Parallel Processing},
+ year = {2000},
+ isbn = {3-540-67956-1},
+ pages = {1071--1080},
+ publisher = {Springer-Verlag},
+ address = {London, UK},
+ }
\ No newline at end of file

doc/comm/figures/Makefile.am

+# $Id: $
+EXTRA_DIST=darray.eps distarray.eps distindex.eps
+
+include $(top_srcdir)/am/webstuff
+include $(top_srcdir)/am/global-rules

doc/comm/figures/darray.eps

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doc/comm/indexset.cc

+// -*- tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 2 -*-
+// vi: set et ts=4 sw=2 sts=2:
+// $Id: indexset.cc 1728 2012-11-06 13:06:44Z christi $
+
+#include "config.h"
+
+#include <dune/common/parallel/indexset.hh>
+#include <dune/common/parallel/plocalindex.hh>
+#include <dune/common/parallel/mpihelper.hh>
+#include <iostream>
+#include "buildindexset.hh"
+#include "reverse.hh"
+
+int main(int argc, char **argv)
+{
+  // This is a parallel programm so we need to
+  // initialize mpi first.
+  Dune::MPIHelper& helper = Dune::MPIHelper::instance(argc, argv);
+
+  // The rank of our process
+  int rank = helper.rank();
+
+  // The type used as the local index
+  typedef Dune::ParallelLocalIndex<Flag> LocalIndex;
+
+  // The type used as the global index
+  typedef int GlobalIndex;
+
+  // The index set we use to identify the local indices with the globally
+  // unique ones
+  typedef Dune::ParallelIndexSet<GlobalIndex,LocalIndex,100> ParallelIndexSet;
+
+  // The index set
+  ParallelIndexSet indexSet;
+
+  build(helper, indexSet);
+
+  // Print the index set
+  std::cout<<indexSet<<std::endl;
+
+
+  reverseLocalIndex(indexSet);
+
+  // Print the index set
+  if(rank==0)
+    std::cout<<"Reordered lcoal indices:"<<std::endl;
+
+  // Wait for all processes
+  helper.getCollectiveCommunication().barrier();
+
+  std::cout<<indexSet<<std::endl;
+  // Assign new local indices
+
+  return 0;
+}

doc/comm/poosc08.cc

+// -*- tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 2 -*-
+// vi: set et ts=4 sw=2 sts=2:
+#ifdef HAVE_CONFIG_H
+# include "config.h"
+#endif
+#include <iostream>
+#include <dune/common/exceptions.hh> // We use exceptions
+#include <dune/common/parallel/mpihelper.hh> // An initializer of MPI
+#include <dune/common/parallel/indexset.hh>
+#include <dune/common/parallel/plocalindex.hh>
+
+enum Flags { owner, ghost };
+
+struct Bla
+{
+
+  /** @brief The local index. */
+  size_t localIndex_;
+
+  /** @brief An attribute for the index. */
+  char attribute_;
+
+  /** @brief True if the index is also known to other processors. */
+  bool public_;
+
+  /**
+   * @brief The state of the index.
+   *
+   * Has to be one of LocalIndexState!
+   * @see LocalIndexState.
+   */
+  char state_;
+};
+
+
+template<typename T1, typename T2>
+void buildBlockedIndexSet(T1& indexset, int N, const T2& comm)
+{
+  int rank=comm.rank();
+  int size=comm.size();
+  int localsize=N/size;
+  int bigger=N%size;
+  int start, end;
+  if(rank<bigger) {
+    start=rank*(localsize+1);
+    end=start+(localsize+1);
+  }else{
+    start=bigger*(localsize+1)+(rank-bigger)*localsize;
+    end=start+localsize;
+  }
+
+  indexset.beginResize();
+  int index=0;
+  int gindex=start;
+  typedef typename T1::LocalIndex LocalIndex;
+
+  std::cout<<sizeof(LocalIndex)<<" "<<sizeof(Bla)<<std::endl;
+
+  if(start>0)
+    indexset.add(gindex-1,LocalIndex(index++,ghost));
+
+  for(int i=start; i<end; i++,index++,gindex++)
+    indexset.add(gindex,LocalIndex(index,owner,true));
+
+  if(end<N)
+    indexset.add(gindex,LocalIndex(index,ghost,true));
+}
+int main(int argc, char** argv)
+{
+  int n=100;
+  try{
+    using namespace Dune;
+
+    //Maybe initialize Mpi
+    MPIHelper& helper = MPIHelper::instance(argc, argv);
+    std::cout << "Hello World! This is poosc08." << std::endl;
+    if(Dune::MPIHelper::isFake)
+      std::cout<< "This is a sequential program." << std::endl;
+    else{
+      typedef ParallelIndexSet<int,ParallelLocalIndex<Flags> > IndexSet;
+      IndexSet blockedSet;
+      buildBlockedIndexSet(blockedSet, n, helper.getCollectiveCommunication());
+    }
+    return 0;
+  }
+  catch (Dune::Exception &e) {
+    std::cerr << "Dune reported error: " << e << std::endl;
+  }
+  catch (...) {
+    std::cerr << "Unknown exception thrown!" << std::endl;
+  }
+}

doc/comm/poosc08_test.cc

+// -*- tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 2 -*-
+// vi: set et ts=4 sw=2 sts=2:
+#ifdef HAVE_CONFIG_H
+# include "config.h"
+#endif
+#include <iostream>
+#include <dune/common/exceptions.hh> // We use exceptions
+#include <dune/common/parallel/mpihelper.hh> // An initializer of MPI
+#include <dune/common/parallel/indexset.hh>
+#include <dune/common/parallel/remoteindices.hh>
+#include <dune/common/parallel/communicator.hh>
+#include <dune/common/parallel/plocalindex.hh>
+#include <dune/common/parallel/interface.hh>
+#include <dune/common/enumset.hh>
+
+enum Flags { owner, ghost };
+
+template<typename T>
+struct AddData {
+  typedef typename T::value_type IndexedType;
+
+  static const IndexedType& gather(const T& v, int i){
+    return v[i];
+  }
+
+  static void scatter(T& v, const IndexedType& item, int i){
+    v[i]+=item;
+  }
+};
+
+template<typename T>
+struct CopyData {
+  typedef typename T::value_type IndexedType;
+
+  static const IndexedType& gather(const T& v, int i){
+    return v[i];
+  }
+
+  static void scatter(T& v, const IndexedType& item, int i){
+    v[i]=item;
+  }
+};
+
+
+template<class T>
+void doCalculations(T& t){}
+
+#if HAVE_MPI
+void test()
+{
+  int rank;
+  MPI_Comm comm=(MPI_COMM_WORLD);
+  MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+  using namespace Dune;
+  // shortcut for index set type
+  typedef ParallelLocalIndex<Flags> LocalIndex;
+  typedef ParallelIndexSet<int, LocalIndex > PIndexSet;
+  PIndexSet sis;
+  sis.beginResize();
+  if(rank==0) {
+
+    sis.add(11, LocalIndex(0, ghost));
+    for(int i=1; i<=6; i++)
+      sis.add(i-1, LocalIndex(i, owner, i<=1||i>5));
+    sis.add(6, LocalIndex(7, ghost));
+  }else{
+    sis.add(5, LocalIndex(0, ghost));
+    for(int i=1; i<=6; i++)
+      sis.add(5+i, LocalIndex(i, owner, i<=1||i>5));
+    sis.add(0,LocalIndex(7, ghost));
+  }
+  sis.endResize();
+
+  PIndexSet tis;
+  tis.beginResize();
+  int l=0;
+  for(int i=0; i<2; ++i)
+    for(int j=0; j<5; ++j) {
+      int g=rank*3-1+i*6+j;
+      if(g<0||g>11)
+        continue;
+      Flags flag=(j>0&&j<4) ? owner : ghost;
+      tis.add(g, LocalIndex(l++, flag));
+    }
+  tis.endResize();
+  std::cout<<rank<<" isxset: "<<sis<<std::endl;
+
+  RemoteIndices<PIndexSet> riRedist(sis, tis, comm);
+  riRedist.rebuild<true>();
+
+  std::vector<int> v;
+  RemoteIndices<PIndexSet> riS(sis,sis, comm, v, true);
+  riS.rebuild<false>();
+
+  std::cout<<std::endl<<"begin"<<rank<<" riS="<<riS<<" end"<<rank<<std::endl<<std::endl;
+
+  Combine<EnumItem<Flags,ghost>,EnumItem<Flags,owner>,Flags> ghostFlags;
+  EnumItem<Flags,owner> ownerFlags;
+  Combine<EnumItem<Flags,ghost>, EnumItem<Flags,owner> > allFlags;
+
+  Interface infRedist;
+  Interface infS;
+
+  infRedist.build(riRedist, ownerFlags, allFlags);
+  infS.build(riS, ownerFlags, ghostFlags);
+
+  std::cout<<"inf "<<rank<<": "<<infS<<std::endl;
+
+  typedef std::vector<double> Container;
+  Container s(sis.size(),3), t(tis.size());
+
+  s[sis.size()-1]=-1;
+
+  BufferedCommunicator bComm;
+  BufferedCommunicator bCommRedist;
+  bComm.build(s, s, infS);
+  //bCommRedist.build(s, t, infRedist);
+  for(std::size_t i=0; i<sis.size(); i++)
+    std::cout<<s[i]<<" ";
+  std::cout<<std::endl;
+
+  bComm.forward<CopyData<Container> >(s,s);
+
+  for(std::size_t i=0; i<sis.size(); i++)
+    std::cout<<s[i]<<" ";
+  std::cout<<std::endl;
+  //bCommRedist.forward<CopyData<Container> >(s,t);
+  // calculate on the redistributed array
+  doCalculations(t);
+  bCommRedist.backward<AddData<Container> >(s,t);
+}
+#endif // HAVE_MPI
+
+int main(int argc, char** argv)
+{
+  try{
+    using namespace Dune;
+#if HAVE_MPI
+    //Maybe initialize Mpi
+    MPIHelper& helper = MPIHelper::instance(argc, argv);
+    std::cout << "Hello World! This is poosc08. rank=" <<helper.rank()<< std::endl;
+    test();
+    return 0;
+#else
+    std::cout<< "Test poosc08_test disabled because MPI is not available." << std::endl;
+    return 77;
+#endif // HAVE_MPI
+  }
+  catch (Dune::Exception &e) {
+    std::cerr << "Dune reported error: " << e << std::endl;
+  }
+  catch (...) {
+    std::cerr << "Unknown exception thrown!" << std::endl;
+  }
+}

doc/comm/reverse.hh

+// -*- tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 2 -*-
+// vi: set et ts=4 sw=2 sts=2:
+// $Id: reverse.hh 942 2008-09-10 18:21:57Z christi $
+#ifndef REVERSE_HH
+#define REVERSE_HH
+
+#include "buildindexset.hh"
+
+/**
+ * @brief Reverse the local indices of an index set.
+ *
+ * Let the index set have N entries than the index 0 will become N-1,
+ * 1 become N-2, ..., and N-1 will become 0.
+ * @param indexSet The index set to reverse.
+ */
+template<typename TG, typename TL, int N>
+void reverseLocalIndex(Dune::ParallelIndexSet<TG,TL,N>& indexSet)
+{
+  // reverse the local indices
+  typedef typename Dune::ParallelIndexSet<TG,TL,N>::iterator iterator;
+
+  iterator end = indexSet.end();
+  size_t maxLocal = 0;
+
+  // find the maximal local index
+  for(iterator index = indexSet.begin(); index != end; ++index) {
+    // Get the local index
+    LocalIndex& local = index->local();
+    maxLocal = std::max(maxLocal, local.local());
+  }
+
+  for(iterator index = indexSet.begin(); index != end; ++index) {
+    // Get the local index
+    LocalIndex& local = index->local();
+    local = maxLocal--;
+  }
+
+}
+#endif