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Commit 1a6ac357 authored by Thomas Witkowski's avatar Thomas Witkowski
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Modified Serializer for parallel serialization.

parent ded81b7f
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Showing with 180 additions and 119 deletions
AMDiS/src/ElementData.cc
View file @ 1a6ac357
......@@ -7,32 +7,31 @@ namespace AMDiS {
Element* otherChild,
int elTypeParent)
{
if (decorated_) {
PartitionElementData* ped=NULL;
ped=dynamic_cast<PartitionElementData*> (thisChild->getElementData(PARTITION_ED));
ped=NULL;
ped=dynamic_cast<PartitionElementData*> (otherChild->getElementData(PARTITION_ED));
ped=NULL;
ped=dynamic_cast<PartitionElementData*> (parent->getElementData(PARTITION_ED));
decorated_->coarsenElementData(parent, thisChild, otherChild, elTypeParent);
delete decorated_;
decorated_ = NULL;
if (decorated) {
PartitionElementData* ped = NULL;
ped = dynamic_cast<PartitionElementData*>(thisChild->getElementData(PARTITION_ED));
ped = NULL;
ped = dynamic_cast<PartitionElementData*>(otherChild->getElementData(PARTITION_ED));
ped = NULL;
ped = dynamic_cast<PartitionElementData*> (parent->getElementData(PARTITION_ED));
decorated->coarsenElementData(parent, thisChild, otherChild, elTypeParent);
delete decorated;
decorated = NULL;
}
}
bool ElementData::deleteDecorated(int typeID)
{
if (decorated_) {
if (decorated_->isOfType(typeID)) {
ElementData *tmp = decorated_;
decorated_ = decorated_->decorated_;
if (decorated) {
if (decorated->isOfType(typeID)) {
ElementData *tmp = decorated;
decorated = decorated->decorated;
delete tmp;
tmp = NULL;
return true;
} else {
return decorated_->deleteDecorated(typeID);
return decorated->deleteDecorated(typeID);
}
}
return false;
......@@ -40,9 +39,9 @@ namespace AMDiS {
void ElementData::deleteDecorated()
{
if (decorated_) {
decorated_->deleteDecorated();
delete decorated_;
if (decorated) {
decorated->deleteDecorated();
delete decorated;
}
}
......@@ -53,10 +52,10 @@ namespace AMDiS {
void ElementData::serialize(std::ostream& out)
{
std::string decoratedType;
if (decorated_) {
decoratedType = decorated_->getTypeName();
if (decorated) {
decoratedType = decorated->getTypeName();
out << decoratedType << "\n";
decorated_->serialize(out);
decorated->serialize(out);
} else {
out << "NULL\n";
}
......@@ -64,16 +63,16 @@ namespace AMDiS {
void ElementData::deserialize(std::istream& in)
{
TEST_EXIT(decorated_ == NULL)
TEST_EXIT(decorated == NULL)
("there are already decorated element data\n");
std::string decoratedType;
in >> decoratedType;
in.get();
if (decoratedType != "NULL") {
decorated_ = CreatorMap<ElementData>::getCreator(decoratedType)->create();
decorated_->deserialize(in);
decorated = CreatorMap<ElementData>::getCreator(decoratedType)->create();
decorated->deserialize(in);
} else {
decorated_ = NULL;
decorated = NULL;
}
}
......
AMDiS/src/ElementData.h
View file @ 1a6ac357
......@@ -43,8 +43,8 @@ namespace AMDiS {
{
public:
/// constructor
ElementData(ElementData *decorated = NULL)
: decorated_(decorated)
ElementData(ElementData *dec = NULL)
: decorated(dec)
{}
/// destructor
......@@ -56,14 +56,14 @@ namespace AMDiS {
Element* child2,
int elType)
{
if (decorated_) {
if (decorated) {
bool remove =
decorated_->refineElementData(parent, child1, child2, elType);
decorated->refineElementData(parent, child1, child2, elType);
if (remove) {
ElementData *tmp = decorated_->decorated_;
delete decorated_;
decorated_ = tmp;
ElementData *tmp = decorated->decorated;
delete decorated;
decorated = tmp;
}
}
return false;
......@@ -78,8 +78,8 @@ namespace AMDiS {
/// Returns a copy of this ElementData object including all decorated data.
virtual ElementData *clone() const
{
if (decorated_)
return decorated_->clone();
if (decorated)
return decorated->clone();
return NULL;
}
......@@ -108,32 +108,32 @@ namespace AMDiS {
if (this->isOfType(typeID)) {
return this;
} else {
if (decorated_)
return decorated_->getElementData(typeID);
if (decorated)
return decorated->getElementData(typeID);
}
return NULL;
}
inline ElementData *getDecorated(int typeID)
{
if (decorated_)
return decorated_->getElementData(typeID);
if (decorated)
return decorated->getElementData(typeID);
return NULL;
}
/** \ref
* Search the \ref decorated_ chain for a specific type ID, and delets
* Search the \ref decorated chain for a specific type ID, and delets
* this entry.
*/
bool deleteDecorated(int typeID);
/// Delets the whole \ref decorated_ chain.
/// Delets the whole \ref decorated chain.
void deleteDecorated();
inline ElementData *getDecorated()
{
return decorated_;
return decorated;
}
inline void setDecorated(ElementData *d)
......@@ -142,12 +142,12 @@ namespace AMDiS {
if (d != NULL)
std::cout << "leafdata decorated with nonzero" << std::endl;
decorated_ = d;
decorated = d;
}
protected:
/// Pointer to next ElementData object in the chain of responsibility.
ElementData *decorated_;
ElementData *decorated;
};
}
......
AMDiS/src/ElementRegion_ED.h
View file @ 1a6ac357
......@@ -17,10 +17,10 @@
// == ==
// ============================================================================
/** \file ElementRegion_ED.h */
/** \file ElementRegionED.h */
#ifndef AMDIS_ELEMENTREGION_ED_H
#define AMDIS_ELEMENTREGION_ED_H
#ifndef AMDIS_ELEMENTREGIONED_H
#define AMDIS_ELEMENTREGIONED_H
#include "ElementData.h"
#include "FixVec.h"
......@@ -48,7 +48,7 @@ namespace AMDiS {
ElementRegion_ED(ElementData *decorated = NULL)
: ElementData(decorated),
region_(-1)
region(-1)
{}
bool refineElementData(Element* parent,
......@@ -61,11 +61,11 @@ namespace AMDiS {
ElementRegion_ED *ep;
ep = new ElementRegion_ED(child1->getElementData());
ep->region_ = region_;
ep->region = region;
child1->setElementData(ep);
ep = new ElementRegion_ED(child2->getElementData());
ep->region_ = region_;
ep->region = region;
child2->setElementData(ep);
return false;
......@@ -74,14 +74,14 @@ namespace AMDiS {
ElementData *clone() const
{
ElementRegion_ED *newObj = new ElementRegion_ED;
newObj->region_ = region_;
newObj->decorated_ = ElementData::clone();
newObj->region = region;
newObj->decorated = ElementData::clone();
return newObj;
}
inline std::string getTypeName() const
{
return "ElementRegion_ED";
return "ElementRegionED";
}
inline const int getTypeID() const
......@@ -92,27 +92,27 @@ namespace AMDiS {
void serialize(std::ostream& out)
{
ElementData::serialize(out);
out.write(reinterpret_cast<const char*>(&region_), sizeof(int));
out.write(reinterpret_cast<const char*>(&region), sizeof(int));
}
void deserialize(std::istream& in)
{
ElementData::deserialize(in);
in.read(reinterpret_cast<char*>(&region_), sizeof(int));
in.read(reinterpret_cast<char*>(&region), sizeof(int));
}
inline void setRegion(int region)
inline void setRegion(int r)
{
region_ = region;
region = r;
}
inline int getRegion() const
{
return region_;
return region;
}
protected:
int region_;
int region;
};
}
......
AMDiS/src/LeafData.h
View file @ 1a6ac357
......@@ -102,7 +102,7 @@ namespace AMDiS {
newObj->errorEstimate = errorEstimate;
// clone decorated element data (=> deep copy)
newObj->decorated_ = ElementData::clone();
newObj->decorated = ElementData::clone();
// return the clone
return newObj;
......@@ -193,7 +193,7 @@ namespace AMDiS {
newObj->errorEstimate = errorEstimate;
// clone decorated element data (=> deep copy)
newObj->decorated_ = ElementData::clone();
newObj->decorated = ElementData::clone();
// return the clone
return newObj;
......@@ -298,7 +298,7 @@ namespace AMDiS {
LeafDataCoarsenable *newObj = new LeafDataCoarsenable(NULL);
// clone decorated element data (=> deep copy)
newObj->decorated_ = ElementData::clone();
newObj->decorated = ElementData::clone();
// return the clone
return newObj;
......@@ -377,7 +377,7 @@ namespace AMDiS {
newObj->coarseningError = coarseningError;
// clone decorated leaf data (=> deep copy)
newObj->decorated_ = ElementData::clone();
newObj->decorated = ElementData::clone();
// return the clone
return newObj;
......@@ -547,7 +547,7 @@ namespace AMDiS {
inline ElementData *clone() const
{
LeafDataPeriodic *newObj = new LeafDataPeriodic;
newObj->decorated_ = ElementData::clone();
newObj->decorated = ElementData::clone();
return newObj;
}
......
AMDiS/src/ParallelDomainScal.cc
View file @ 1a6ac357
......@@ -14,6 +14,12 @@ namespace AMDiS {
probScal(problem)
{
info = problem->getInfo();
// Create parallel serialization file writer, if needed.
int writeSerialization = 0;
GET_PARAMETER(0, name + "->output->write serialization", "%d", &writeSerialization);
if (writeSerialization)
problem->getFileWriterList().push_back(new Serializer<ParallelDomainScal>(this));
}
void ParallelDomainScal::initParallelization(AdaptInfo *adaptInfo)
......
AMDiS/src/ParallelDomainScal.h
View file @ 1a6ac357
......@@ -23,6 +23,7 @@
#define AMDIS_PARALLELDOMAINSCAL_H
#include "ParallelDomainBase.h"
#include "ProblemScal.h"
namespace AMDiS {
......@@ -34,6 +35,20 @@ namespace AMDiS {
void initParallelization(AdaptInfo *adaptInfo);
// Writes all data of this object to an output stream.
virtual void serialize(std::ostream &out)
{
probScal->serialize(out);
ParallelDomainBase::serialize(out);
}
// Reads the object data from an input stream.
virtual void deserialize(std::istream &in)
{
probScal->deserialize(in);
ParallelDomainBase::deserialize(in);
}
protected:
/// Starts the solution of the linear system using Petsc.
void solve();
......
AMDiS/src/ParallelDomainVec.cc
View file @ 1a6ac357
......@@ -2,6 +2,7 @@
#include "ProblemVec.h"
#include "ProblemInstat.h"
#include "SystemVector.h"
#include "Serializer.h"
namespace AMDiS {
......@@ -18,10 +19,18 @@ namespace AMDiS {
info = probVec->getInfo();
nComponents = probVec->getNumComponents();
// Test if all fe spaces are equal. Yet, different fe spaces are not supported for
// domain parallelization.
const FiniteElemSpace *fe = probVec->getFESpace(0);
for (int i = 0; i < nComponents; i++)
TEST_EXIT(fe == probVec->getFESpace(i))
("Parallelization does not supported different FE spaces!\n");
// Create parallel serialization file writer, if needed.
int writeSerialization = 0;
GET_PARAMETER(0, name + "->output->write serialization", "%d", &writeSerialization);
if (writeSerialization)
problem->getFileWriterList().push_back(new Serializer<ParallelDomainVec>(this));
}
......
AMDiS/src/ParallelDomainVec.h
View file @ 1a6ac357
......@@ -42,6 +42,20 @@ namespace AMDiS {
synchVectors(*(probVec->getSolution()));
}
// Writes all data of this object to an output stream.
virtual void serialize(std::ostream &out)
{
probVec->serialize(out);
ParallelDomainBase::serialize(out);
}
// Reads the object data from an input stream.
virtual void deserialize(std::istream &in)
{
probVec->deserialize(in);
ParallelDomainBase::deserialize(in);
}
protected:
/// Starts the solution of the linear system using Petsc.
void solve();
......
AMDiS/src/PartitionElementData.h
View file @ 1a6ac357
......@@ -40,16 +40,18 @@ namespace AMDiS {
class PartitionElementData : public ElementData
{
public:
inline bool isOfType(int typeID) const {
inline bool isOfType(int typeID) const
{
if (typeID == PARTITION_ED)
return true;
return true;
return false;
}
class Creator : public CreatorInterface<ElementData>
{
public:
ElementData* create() {
ElementData* create()
{
return new PartitionElementData;
}
};
......@@ -68,10 +70,12 @@ namespace AMDiS {
Element* child2,
int elType)
{
ElementData::refineElementData(parent, child1, child2, elType);
ElementData::refineElementData(parent, child1, child2, elType);
PartitionElementData *child1Data = new PartitionElementData(child1->getElementData());
PartitionElementData *child2Data = new PartitionElementData(child2->getElementData());
PartitionElementData *child1Data =
new PartitionElementData(child1->getElementData());
PartitionElementData *child2Data =
new PartitionElementData(child2->getElementData());
child1Data->setPartitionStatus(status);
child2Data->setPartitionStatus(status);
child1Data->setLevel(level + 1);
......@@ -79,51 +83,58 @@ namespace AMDiS {
child1->setElementData(child1Data);
child2->setElementData(child2Data);
return false;
};
}
ElementData *clone() const {
ElementData *clone() const
{
PartitionElementData *newObj = new PartitionElementData;
newObj->decorated_ = ElementData::clone();
newObj->decorated = ElementData::clone();
return newObj;
};
}
inline std::string getTypeName() const {
inline std::string getTypeName() const
{
return "PartitionElementData";
};
}
inline const int getTypeID() const {
inline const int getTypeID() const
{
return PARTITION_ED;
};
}
void serialize(std::ostream& out)
{
ElementData::serialize(out);
out.write(reinterpret_cast<const char*>(&status), sizeof(PartitionStatus));
out.write(reinterpret_cast<const char*>(&level), sizeof(int));
};
}
void deserialize(std::istream& in)
{
ElementData::deserialize(in);
in.read(reinterpret_cast<char*>(&status), sizeof(PartitionStatus));
in.read(reinterpret_cast<char*>(&level), sizeof(int));
};
}
inline void setPartitionStatus(PartitionStatus status_) {
inline void setPartitionStatus(PartitionStatus status_)
{
status = status_;
};
}
inline PartitionStatus getPartitionStatus() {
inline PartitionStatus getPartitionStatus()
{
return status;
};
}
inline void setLevel(int level_) {
level = level_;
};
inline void setLevel(int l)
{
level = l;
}
inline int getLevel() {
inline int getLevel()
{
return level;
};
}
void descend(Element *element)
{
......@@ -145,7 +156,7 @@ namespace AMDiS {
child0Data->descend(child0);
child1Data->descend(child1);
}
};
}
protected:
PartitionStatus status;
......
AMDiS/src/ProblemScal.h
View file @ 1a6ac357
......@@ -186,7 +186,7 @@ namespace AMDiS {
/// Adds robin boundary conditions.
virtual void addRobinBC(BoundaryType type,
DOFVector<double> *n,
DOFVector<double> *n,
DOFVector<double> *r);
/// Adds Neumann boundary conditions.
......@@ -317,7 +317,7 @@ namespace AMDiS {
virtual void deserialize(std::istream &in);
/// Returns \ref fileWriters.
std::vector<FileWriterInterface*> getFileWriterList()
std::vector<FileWriterInterface*>& getFileWriterList()
{
return fileWriters;
}
......
AMDiS/src/Serializer.h
View file @ 1a6ac357
......@@ -40,11 +40,17 @@ namespace AMDiS {
tsModulo(1),
timestepNumber(-1)
{
GET_PARAMETER(0, problem->getName() + "->output->serialization filename",
&name);
GET_PARAMETER(0, problem->getName() + "->output->write every i-th timestep",
FUNCNAME("Serializer::Serializer()");
GET_PARAMETER(0, problem->getName() + "->output->serialization filename", &name);
GET_PARAMETER(0, problem->getName() + "->output->write every i-th timestep",
"%d", &tsModulo);
TEST_EXIT(name != "")("no filename\n");
#if HAVE_PARALLEL_DOMAIN_AMDIS
name += ".p";
name += MPI::COMM_WORLD.Get_rank();
#endif
}
virtual ~Serializer() {}
......
AMDiS/src/SurfaceRegion_ED.h
View file @ 1a6ac357
......@@ -30,7 +30,8 @@ namespace AMDiS {
class SurfaceRegion_ED : public ElementData
{
public:
inline bool isOfType(int typeID) const {
inline bool isOfType(int typeID) const
{
if (typeID == SURFACE_REGION)
return true;
return false;
......@@ -47,8 +48,8 @@ namespace AMDiS {
SurfaceRegion_ED(ElementData *decorated = NULL)
: ElementData(decorated),
side_(-1),
region_(-1)
side(-1),
region(-1)
{}
bool refineElementData(Element* parent,
......@@ -61,19 +62,19 @@ namespace AMDiS {
int sideOfChild;
SurfaceRegion_ED *surfaceRegion;
sideOfChild = parent->getSideOfChild(0, side_, elType);
sideOfChild = parent->getSideOfChild(0, side, elType);
if (sideOfChild >= 0) {
surfaceRegion = new SurfaceRegion_ED(child1->getElementData());
surfaceRegion->setSide(sideOfChild);
surfaceRegion->setRegion(region_);
surfaceRegion->setRegion(region);
child1->setElementData(surfaceRegion);
}
sideOfChild = parent->getSideOfChild(1, side_, elType);
sideOfChild = parent->getSideOfChild(1, side, elType);
if (sideOfChild >= 0) {
surfaceRegion = new SurfaceRegion_ED(child2->getElementData());
surfaceRegion->side_ = sideOfChild;
surfaceRegion->region_ = region_;
surfaceRegion->side = sideOfChild;
surfaceRegion->region = region;
child2->setElementData(surfaceRegion);
}
......@@ -83,9 +84,9 @@ namespace AMDiS {
ElementData *clone() const
{
SurfaceRegion_ED *newObj = new SurfaceRegion_ED;