Skip to content

GitLab

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

Refactoring of using periodic DOF mapping in parallel computations.

parent eada967c
Hide whitespace changes
Inline Side-by-side
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)