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Commit b3b829c3 authored by Thomas Witkowski's avatar Thomas Witkowski
Browse files

Refactoring of using periodic DOF mapping in parallel computations.

parent eada967c
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Showing with 409 additions and 317 deletions
AMDiS/src/AMDiS.h
View file @ b3b829c3
......@@ -81,7 +81,6 @@
#include "Operator.h"
#include "OperatorTerm.h"
#include "Parametric.h"
#include "PeriodicMap.h"
#include "PeriodicBC.h"
#include "ProblemStat.h"
#include "ProblemInstat.h"
......
AMDiS/src/Mesh.cc
View file @ b3b829c3
......@@ -34,7 +34,6 @@
#include "CoarseningManager.h"
#include "DOFIterator.h"
#include "VertexVector.h"
#include "PeriodicMap.h"
#include "Projection.h"
#include "ElInfoStack.h"
#include "Serializer.h"
......
AMDiS/src/PeriodicMap.h deleted 100644 → 0
View file @ eada967c
// ============================================================================
// == ==
// == AMDiS - Adaptive multidimensional simulations ==
// == ==
// == http://www.amdis-fem.org ==
// == ==
// ============================================================================
//
// Software License for AMDiS
//
// Copyright (c) 2010 Dresden University of Technology
// All rights reserved.
// Authors: Simon Vey, Thomas Witkowski et al.
//
// This file is part of AMDiS
//
// See also license.opensource.txt in the distribution.
/** \file PeriodicMap.h */
#ifndef AMDIS_PERIODICMAP_H
#define AMDIS_PERIODICMAP_H
#include "Global.h"
#include <map>
namespace AMDiS {
class PeriodicMap
{
public:
void setEntry(DegreeOfFreedom key, DegreeOfFreedom entry) {
// no trivial entries!
if (key == entry)
return;
// if a key equal to entry exists ...
if (getEntry(entry) >= 0) {
if (getEntry(entry) == key) {
return;
}
// ... let it be equal entries
setEntry(key, getEntry(entry));
return;
}
// replace entries equal to key
std::map<DegreeOfFreedom, DegreeOfFreedom>::iterator it;
for (it = periodicMap.begin(); it != periodicMap.end(); ++it) {
if (it->second == key) {
it->second = entry;
}
}
// if key exists already
if (getEntry(key) >= 0) {
// insert new entry with old entry as key
setEntry(getEntry(key), entry);
}
// set entry
periodicMap[key] = entry;
};
DegreeOfFreedom getEntry(DegreeOfFreedom key) {
std::map<DegreeOfFreedom, DegreeOfFreedom>::iterator it;
it = periodicMap.find(key);
if (it != periodicMap.end()) {
return it->second;
} else {
return -1;
}
};
protected:
std::map<DegreeOfFreedom, DegreeOfFreedom> periodicMap;
};
}
#endif
AMDiS/src/io/MacroReader.cc
View file @ b3b829c3
......@@ -10,6 +10,10 @@
// See also license.opensource.txt in the distribution.
#include <string.h>
#include <map>
#include <iostream>
#include <fstream>
#include "MacroReader.h"
#include "MacroWriter.h"
#include "MacroElement.h"
......@@ -17,17 +21,12 @@
#include "Boundary.h"
#include "FiniteElemSpace.h"
#include "Mesh.h"
#include <string.h>
#include "FixVec.h"
#include "PeriodicMap.h"
#include "ElInfo.h"
#include "Initfile.h"
#include "DOFIterator.h"
#include "LeafData.h"
#include "VertexVector.h"
#include <map>
#include <iostream>
#include <fstream>
namespace AMDiS {
......@@ -64,7 +63,7 @@ namespace AMDiS {
int mode = -1; // 0: drop dofs, 1: associate dofs
int result;
BoundaryType boundaryType;
PeriodicMap periodicMap;
MacroReader::PeriodicMap periodicMap;
fscanf(file, "%*s %d", &n);
fscanf(file, "%*s %*s %*s %*s %*s %*s %*s %*s %*s %*s %*s");
......
AMDiS/src/io/MacroReader.h
View file @ b3b829c3
......@@ -41,6 +41,53 @@ namespace AMDiS {
*/
class MacroReader
{
// Is used to read periodic macros
class PeriodicMap
{
public:
void setEntry(DegreeOfFreedom key, DegreeOfFreedom entry)
{
// no trivial entries!
if (key == entry)
return;
// if a key equal to entry exists ...
if (getEntry(entry) >= 0) {
if (getEntry(entry) == key)
return;
// ... let it be equal entries
setEntry(key, getEntry(entry));
return;
}
// replace entries equal to key
for (map<DegreeOfFreedom, DegreeOfFreedom>::iterator it =
periodicMap.begin(); it != periodicMap.end(); ++it)
if (it->second == key)
it->second = entry;
// if key exists already, insert new entry with old entry as key
if (getEntry(key) >= 0)
setEntry(getEntry(key), entry);
// set entry
periodicMap[key] = entry;
}
DegreeOfFreedom getEntry(DegreeOfFreedom key)
{
map<DegreeOfFreedom, DegreeOfFreedom>::iterator it = periodicMap.find(key);
if (it != periodicMap.end())
return it->second;
return -1;
}
protected:
map<DegreeOfFreedom, DegreeOfFreedom> periodicMap;
};
public:
/// Creates a Mesh by reading the macro file with the given filename.
static MacroInfo* readMacro(std::string filename,
......
AMDiS/src/parallel/InteriorBoundary.h
View file @ b3b829c3
......@@ -95,6 +95,8 @@ namespace AMDiS {
ExcludeList excludedSubstructures;
};
/** \brief
* Defines one atomic part of the boundary, i.e., two boundary objects where the
* boundary goes through.
......@@ -118,6 +120,8 @@ namespace AMDiS {
BoundaryType type;
};
/** \brief
* Defines the interior boundary, i.e. a bound within the domain. It is used for
* the classical domain decomposition parallelization.
......
AMDiS/src/parallel/MeshDistributor.cc
View file @ b3b829c3
......@@ -2014,8 +2014,7 @@ namespace AMDiS {
// Clear all periodic DOF mappings calculated before. We do it from scratch.
periodicDofs.clear();
periodicDofMap.clear();
periodicDofAssociations.clear();
periodicMap.clear();
for (unsigned int i = 0; i < feSpaces.size(); i++)
createPeriodicMap(feSpaces[i]);
......@@ -2064,10 +2063,8 @@ namespace AMDiS {
DegreeOfFreedom globalDof1 =
dofFeData[feSpace].mapLocalGlobalDofs[*(dofs1[j])];
if (periodicDofAssociations[feSpace][globalDof0].count(type) == 0) {
periodicDofMap[feSpace][type][globalDof0] = globalDof1;
periodicDofAssociations[feSpace][globalDof0].insert(type);
}
if (!periodicMap.isPeriodicOnBound(feSpace, type, globalDof0))
periodicMap.add(feSpace, type, globalDof0, globalDof1);
}
}
......@@ -2121,10 +2118,8 @@ namespace AMDiS {
// Check if this global DOF with the corresponding boundary type was
// not added before by another periodic boundary from other rank.
if (periodicDofAssociations[feSpace][globalDofIndex].count(type) == 0) {
periodicDofMap[feSpace][type][globalDofIndex] = mapGlobalDofIndex;
periodicDofAssociations[feSpace][globalDofIndex].insert(type);
}
if (!periodicMap.isPeriodicOnBound(feSpace, type, globalDofIndex))
periodicMap.add(feSpace, type, globalDofIndex, mapGlobalDofIndex);
}
}
......@@ -2151,17 +2146,15 @@ namespace AMDiS {
DegreeOfFreedom globalDof =
dofFeData[feSpace].mapLocalGlobalDofs[*dofs[i]];
TEST_EXIT_DBG(periodicDofAssociations[feSpace].count(globalDof))
("Should hot happen!\n");
std::set<BoundaryType>& assoc =
periodicMap.getAssociations(feSpace, globalDof);
TEST_EXIT_DBG(assoc.size() > 0)("Should not happen!\n");
for (std::set<BoundaryType>::iterator perAscIt = periodicDofAssociations[feSpace][globalDof].begin();
perAscIt != periodicDofAssociations[feSpace][globalDof].end(); ++perAscIt)
if (*perAscIt >= -3) {
TEST_EXIT_DBG(periodicDofMap[feSpace][*perAscIt].count(globalDof) == 1)
("Should not happen!\n");
for (std::set<BoundaryType>::iterator perAscIt = assoc.begin();
perAscIt != assoc.end(); ++perAscIt)
if (*perAscIt >= -3)
perObjMap[*perAscIt][globalDof] =
periodicDofMap[feSpace][*perAscIt][globalDof];
}
periodicMap.map(feSpace, *perAscIt, globalDof);
}
}
......@@ -2172,19 +2165,12 @@ namespace AMDiS {
stdMpi2.startCommunication();
for (map<int, PeriodicDofMap>::iterator it = stdMpi2.getRecvData().begin();
it != stdMpi2.getRecvData().end(); ++it) {
it != stdMpi2.getRecvData().end(); ++it)
for (PeriodicDofMap::iterator perIt = it->second.begin();
perIt != it->second.end(); ++perIt) {
perIt != it->second.end(); ++perIt)
for (DofMapping::iterator dofIt = perIt->second.begin();
dofIt != perIt->second.end(); ++dofIt) {
TEST_EXIT_DBG(periodicDofMap[feSpace][perIt->first].count(dofIt->second) == 0 ||
periodicDofMap[feSpace][perIt->first][dofIt->second] == dofIt->first)
("Should not happen!\n");
periodicDofMap[feSpace][perIt->first][dofIt->second] = dofIt->first;
}
}
}
dofIt != perIt->second.end(); ++dofIt)
periodicMap.add(feSpace, perIt->first, dofIt->second, dofIt->first);
}
......@@ -2275,11 +2261,7 @@ namespace AMDiS {
SerUtil::serialize(out, dofFeData[feSpaces[i]].mapLocalDofIndex);
}
for (unsigned int i = 0; i < nFeSpace; i++)
serialize(out, periodicDofMap[feSpaces[i]]);
for (unsigned int i = 0; i < nFeSpace; i++)
serialize(out, periodicDofAssociations[feSpaces[i]]);
periodicMap.serialize(out, feSpaces);
SerUtil::serialize(out, macroElementNeighbours);
......@@ -2352,12 +2334,7 @@ namespace AMDiS {
SerUtil::deserialize(in, dofFeData[feSpaces[i]].mapLocalDofIndex);
}
for (unsigned int i = 0; i < nFeSpace; i++)
deserialize(in, periodicDofMap[feSpaces[i]]);
for (unsigned int i = 0; i < nFeSpace; i++)
deserialize(in, periodicDofAssociations[feSpaces[i]]);
periodicMap.deserialize(in, feSpaces);
SerUtil::deserialize(in, macroElementNeighbours);
......@@ -2379,73 +2356,4 @@ namespace AMDiS {
deserialized = true;
}
void MeshDistributor::serialize(ostream &out, PeriodicDofMap &data)
{
int mapSize = data.size();
SerUtil::serialize(out, mapSize);
for (PeriodicDofMap::iterator it = data.begin(); it != data.end(); ++it) {
int type = it->first;
DofMapping dofMap = it->second;
SerUtil::serialize(out, type);
SerUtil::serialize(out, dofMap);
}
}
void MeshDistributor::serialize(ostream &out, map<int, std::set<int> >& data)
{
int mapSize = data.size();
SerUtil::serialize(out, mapSize);
for (map<int, std::set<int> >::iterator it = data.begin(); it != data.end(); ++it) {
int dof = it->first;
std::set<int> typeSet = it->second;
SerUtil::serialize(out, dof);
SerUtil::serialize(out, typeSet);
}
}
void MeshDistributor::deserialize(istream &in, PeriodicDofMap &data)
{
data.clear();
int mapSize = 0;
SerUtil::deserialize(in, mapSize);
for (int i = 0; i < mapSize; i++) {
int type;
DofMapping dofMap;
SerUtil::deserialize(in, type);
SerUtil::deserialize(in, dofMap);
data[type] = dofMap;
}
}
void MeshDistributor::deserialize(istream &in,
map<int, std::set<int> >& data)
{
data.clear();
int mapSize = 0;
SerUtil::deserialize(in, mapSize);
for (int i = 0; i < mapSize; i++) {
int dof;
std::set<int> typeSet;
SerUtil::deserialize(in, dof);
SerUtil::deserialize(in, typeSet);
data[dof] = typeSet;
}
}
}
AMDiS/src/parallel/MeshDistributor.h
View file @ b3b829c3
......@@ -30,6 +30,7 @@
#include "parallel/ParallelTypes.h"
#include "parallel/MeshPartitioner.h"
#include "parallel/InteriorBoundary.h"
#include "parallel/PeriodicMap.h"
#include "parallel/StdMpi.h"
#include "AMDiS_fwd.h"
#include "Global.h"
......@@ -277,58 +278,10 @@ namespace AMDiS {
return dofFeData[feSpace].mapLocalDofIndex[dof];
}
/// Returns the periodic mapping for all boundary DOFs in rank.
inline PeriodicDofMap& getPeriodicMapping(const FiniteElemSpace *feSpace)
/// Returns the periodic mapping handler, \ref periodicMap.
inline PeriodicMap& getPeriodicMap()
{
return periodicDofMap[feSpace];
}
/// Returns for a global DOF index of a given FE space its periodic mapping
/// for a given boundary type.
inline int getPeriodicMapping(const FiniteElemSpace *feSpace,
BoundaryType type,
int globalDofIndex)
{
FUNCNAME("MeshDistributor::getPeriodicMapping()");
TEST_EXIT_DBG(periodicDofMap.count(feSpace))("Should not happen!\n");
TEST_EXIT_DBG(periodicDofMap[feSpace][type].count(globalDofIndex) == 1)
("There is no periodic association for global DOF %d for boundary type %d!\n",
globalDofIndex, type);
return periodicDofMap[feSpace][type][globalDofIndex];
}
/// For a given global DOF index, this function returns the set of periodic
/// associations, i.e., the boundary types the DOF is associated to, for
/// this DOF.
inline std::set<BoundaryType>& getPerDofAssociations(const FiniteElemSpace* feSpace,
int globalDofIndex)
{
FUNCNAME("MeshDistributor::getPerDofAssociations()");
TEST_EXIT_DBG(periodicDofAssociations.count(feSpace))
("Should not happen!\n");
TEST_EXIT_DBG(periodicDofAssociations[feSpace].count(globalDofIndex))
("Should not happen!\n");
return periodicDofAssociations[feSpace][globalDofIndex];
}
/// Returns true, if the DOF (global index) is a periodic DOF.
inline bool isPeriodicDof(const FiniteElemSpace *feSpace, int globalDofIndex)
{
return (periodicDofAssociations[feSpace].count(globalDofIndex) > 0 &&
periodicDofAssociations[feSpace][globalDofIndex].size() > 0);
}
/// Returns true, if the DOF (global index) of a given FE space is a
/// periodic DOF for the given boundary type.
inline bool isPeriodicDof(const FiniteElemSpace *feSpace,
BoundaryType type,
int globalDofIndex)
{
return (periodicDofMap[feSpace][type].count(globalDofIndex) > 0);
return periodicMap;
}
DofComm& getSendDofs()
......@@ -556,16 +509,6 @@ namespace AMDiS {
map<int, map<const FiniteElemSpace*, DofContainer> > &data,
map<const FiniteElemSpace*, map<int, const DegreeOfFreedom*> > &dofMap);
/// Writes a periodic dof mapping to an output stream.
void serialize(ostream &out, PeriodicDofMap &data);
void serialize(ostream &out, map<int, std::set<int> >& data);
/// Reads a periodic dof mapping from an input stream.
void deserialize(istream &in, PeriodicDofMap &data);
void deserialize(istream &in, map<int, std::set<int> >& data);
/// Writes a mapping from dof pointers to some values to an output stream.
template<typename T>
void serialize(ostream &out, map<const DegreeOfFreedom*, T> &data)
......@@ -710,24 +653,8 @@ namespace AMDiS {
*/
DofComm periodicDofs;
/** \brief
* If periodic boundaries are used, this map stores, for each periodic
* boundary type, for all DOFs in rank's partition (that are on periodic
* boundaries), the corresponding mapped periodic DOFs. The mapping is
* defined by using global DOF indices.
*/
PeriodicDofMapFeSpace periodicDofMap;
/** \brief
* If periodic boundaries are used, this map stores to each periodic DOF in
* rank's partition the set of periodic boundaries the DOF is associated to.
* In 2D, most DOFs are only on one periodic boundary. Only, e.g., in a box
* with all boundaries being periodic, the four corners are associated by
* two different boundaries.
*/
map<const FiniteElemSpace*, map<DegreeOfFreedom, std::set<BoundaryType> > > periodicDofAssociations;
PeriodicMap periodicMap;
/// This set of values must be interchanged between ranks when the mesh is
/// repartitioned.
vector<DOFVector<double>*> interchangeVectors;
......
AMDiS/src/parallel/ParallelDebug.cc
View file @ b3b829c3
......@@ -157,9 +157,11 @@ namespace AMDiS {
// === 1. check: All periodic DOFs should have at least a correct number ===
// === of periodic associations. ===
for (map<int, std::set<BoundaryType> >::iterator it = pdb.periodicDofAssociations[feSpace].begin();
it != pdb.periodicDofAssociations[feSpace].end(); ++it) {
PeriodicMap &perMap = pdb.getPeriodicMap();
for (map<int, std::set<BoundaryType> >::iterator it =
perMap.periodicDofAssociations[feSpace].begin();
it != perMap.periodicDofAssociations[feSpace].end(); ++it) {
WorldVector<double> c;
pdb.mesh->getDofIndexCoords(it->first, pdb.feSpaces[0], c);
int nAssoc = it->second.size();
......@@ -178,7 +180,7 @@ namespace AMDiS {
for (int i = 1; i < pdb.mpiSize; i++)
stdMpi.recv(i);
} else {
stdMpi.send(0, pdb.periodicDofMap[feSpace]);
stdMpi.send(0, perMap.periodicDofMap[feSpace]);
}
stdMpi.startCommunication();
......@@ -190,7 +192,7 @@ namespace AMDiS {
if (pdb.mpiRank == 0) {
// Stores to each rank the periodic DOF mappings of this rank.
map<int, PeriodicDofMap> rankToMaps;
PeriodicDofMap dofMap = pdb.periodicDofMap[feSpace];
PeriodicDofMap dofMap = perMap.periodicDofMap[feSpace];
rankToMaps[0] = dofMap;
for (int i = 1; i < pdb.mpiSize; i++) {
......@@ -678,6 +680,8 @@ namespace AMDiS {
ERROR_EXIT("Function must be rewritten!\n");
#if 0
PeriodicMap &perMap = pdb.getPeriodicMap();
const FiniteElemSpace* feSpace = pdb.feSpaces[0];
typedef map<DegreeOfFreedom, DegreeOfFreedom> DofMapping;
......@@ -686,8 +690,8 @@ namespace AMDiS {
if (rank == -1 || pdb.mpiRank == rank) {
cout << "====== DOF MAP PERIODIC ====== " << endl;
for (PeriodicDofMap::iterator it = pdb.periodicDofMap.begin();
it != pdb.periodicDofMap.end(); ++it) {
for (PeriodicDofMap::iterator it = perMap.periodicDofMap.begin();
it != perMap.periodicDofMap.end(); ++it) {
cout << "DOF MAP " << it->first << ": ";
for (std::set<DegreeOfFreedom>::iterator dofit = it->second.begin();
dofit != it->second.end(); ++dofit)
......
AMDiS/src/parallel/ParallelTypes.h
View file @ b3b829c3
......@@ -62,12 +62,6 @@ namespace AMDiS {
typedef map<const DegreeOfFreedom*, DegreeOfFreedom> DofIndexMap;
/// Mapps a boundar type, i.e., a boundary identifier index, to a periodic
/// DOF mapping.
typedef map<BoundaryType, DofMapping> PeriodicDofMap;
typedef map<const FiniteElemSpace*, PeriodicDofMap> PeriodicDofMapFeSpace;
typedef vector<MeshStructure> MeshCodeVec;
}
......
AMDiS/src/parallel/PeriodicMap.cc 0 → 100644
View file @ b3b829c3
//
// Software License for AMDiS
//
// Copyright (c) 2010 Dresden University of Technology
// All rights reserved.
// Authors: Simon Vey, Thomas Witkowski et al.
//
// This file is part of AMDiS
//
// See also license.opensource.txt in the distribution.
#include <fstream>
#include "parallel/PeriodicMap.h"
namespace AMDiS {
void PeriodicMap::serialize(ostream &out,
vector<const FiniteElemSpace*> feSpaces)
{
FUNCNAME("PeriodicMap::serialize()");
int nFeSpace = static_cast<int>(feSpaces.size());
for (int i = 0; i < nFeSpace; i++)
serialize(out, periodicDofMap[feSpaces[i]]);
for (int i = 0; i < nFeSpace; i++)
serialize(out, periodicDofAssociations[feSpaces[i]]);
}
void PeriodicMap::deserialize(istream &in,
vector<const FiniteElemSpace*> feSpaces)