diff --git a/AMDiS/src/InteriorBoundary.cc b/AMDiS/src/InteriorBoundary.cc
index 4da79698d67505f8bfce5c8748aca88fa1e618df..2594017e9b09a3c66e9feaa8b568f5649077e651 100644
--- a/AMDiS/src/InteriorBoundary.cc
+++ b/AMDiS/src/InteriorBoundary.cc
@@ -8,4 +8,11 @@ namespace AMDiS {
return boundary[rank][boundary[rank].size() - 1];
}
+ void InteriorBoundary::serialize(std::ostream &out)
+ {
+ }
+
+ void InteriorBoundary::deserialize(std::istream &in)
+ {
+ }
}
diff --git a/AMDiS/src/InteriorBoundary.h b/AMDiS/src/InteriorBoundary.h
index 6de459da1f08f88d1b8ba6011014aca9e830af53..74e9eef95d425c86167608af0c2370427e085a76 100644
--- a/AMDiS/src/InteriorBoundary.h
+++ b/AMDiS/src/InteriorBoundary.h
@@ -81,6 +81,10 @@ namespace AMDiS {
AtomicBoundary& getNewAtomicBoundary(int rank);
+ void serialize(std::ostream &out);
+
+ void deserialize(std::istream &in);
+
public:
RankToBoundMap boundary;
};
diff --git a/AMDiS/src/ParallelDomainBase.cc b/AMDiS/src/ParallelDomainBase.cc
index b0e857f977e5da1991ceac812a5e197e159b89d8..fd75308e4a0d3af004695b89ae491374505b8f31 100644
--- a/AMDiS/src/ParallelDomainBase.cc
+++ b/AMDiS/src/ParallelDomainBase.cc
@@ -16,6 +16,7 @@
#include "ProblemStatBase.h"
#include "StandardProblemIteration.h"
#include "ElementFileWriter.h"
+#include "Serializer.h"
#include "petscksp.h"
@@ -45,7 +46,7 @@ namespace AMDiS {
mesh(fe->getMesh()),
refinementManager(refineManager),
initialPartitionMesh(true),
- nRankDOFs(0),
+ nRankDofs(0),
rstart(0),
nComponents(1)
{
@@ -92,11 +93,11 @@ namespace AMDiS {
// Set of all DOFs of the rank.
std::vector<const DegreeOfFreedom*> rankDOFs;
// Number of DOFs in ranks partition that are owned by the rank.
- nRankDOFs = 0;
+ nRankDofs = 0;
// Number of all DOFs in the macro mesh.
int nOverallDOFs = 0;
- createLocalGlobalNumbering(rankDOFs, nRankDOFs, nOverallDOFs);
+ createLocalGlobalNumbering(rankDOFs, nRankDofs, nOverallDOFs);
// === Create interior boundary information ===
@@ -130,7 +131,7 @@ namespace AMDiS {
DbgCreateElementMap(elMap);
#endif
- updateLocalGlobalNumbering(nRankDOFs, nOverallDOFs);
+ updateLocalGlobalNumbering(nRankDofs, nOverallDOFs);
updateDofAdmins();
@@ -144,7 +145,7 @@ namespace AMDiS {
DbgTestCommonDofs(true);
#endif
- nRankRows = nRankDOFs * nComponents;
+ nRankRows = nRankDofs * nComponents;
nOverallRows = nOverallDOFs * nComponents;
}
@@ -535,7 +536,7 @@ namespace AMDiS {
PetscScalar *vecPointer;
VecGetArray(petscSolVec, &vecPointer);
- for (int i = 0; i < nRankDOFs; i++)
+ for (int i = 0; i < nRankDofs; i++)
(*vec)[mapLocalToDofIndex[i]] = vecPointer[i];
VecRestoreArray(petscSolVec, &vecPointer);
@@ -613,7 +614,7 @@ namespace AMDiS {
for (int i = 0; i < nComponents; i++) {
DOFVector<double> *dofvec = vec.getDOFVector(i);
- for (int j = 0; j < nRankDOFs; j++)
+ for (int j = 0; j < nRankDofs; j++)
(*dofvec)[mapLocalToDofIndex[j]] = vecPointer[j * nComponents + i];
}
@@ -895,7 +896,7 @@ namespace AMDiS {
void ParallelDomainBase::createLocalGlobalNumbering(DofContainer& rankDOFs,
- int& nRankDOFs,
+ int& nRankDofs,
int& nOverallDOFs)
{
FUNCNAME("ParallelDomainBase::createLocalGlobalNumbering()");
@@ -909,15 +910,15 @@ namespace AMDiS {
createDOFMemberInfo(partitionDOFs, rankDOFs, rankAllDofs, boundaryDofs, vertexDof);
- nRankDOFs = rankDOFs.size();
+ nRankDofs = rankDOFs.size();
nOverallDOFs = partitionDOFs.size();
// === Get starting position for global rank dof ordering. ====
rstart = 0;
- mpiComm.Scan(&nRankDOFs, &rstart, 1, MPI_INT, MPI_SUM);
- rstart -= nRankDOFs;
+ mpiComm.Scan(&nRankDofs, &rstart, 1, MPI_INT, MPI_SUM);
+ rstart -= nRankDofs;
// === Create for all dofs in rank new indices. The new index must start at ===
@@ -1115,7 +1116,7 @@ namespace AMDiS {
}
- void ParallelDomainBase::updateLocalGlobalNumbering(int& nRankDOFs, int& nOverallDOFs)
+ void ParallelDomainBase::updateLocalGlobalNumbering(int& nRankDofs, int& nOverallDOFs)
{
FUNCNAME("ParallelDomainBase::updateLocalGlobalNumbering()");
@@ -1220,17 +1221,17 @@ namespace AMDiS {
}
}
- nRankDOFs = rankDOFs.size();
+ nRankDofs = rankDOFs.size();
// === Get starting position for global rank dof ordering. ====
- mpiComm.Scan(&nRankDOFs, &rstart, 1, MPI_INT, MPI_SUM);
- rstart -= nRankDOFs;
+ mpiComm.Scan(&nRankDofs, &rstart, 1, MPI_INT, MPI_SUM);
+ rstart -= nRankDofs;
// === Calculate number of overall DOFs of all partitions. ===
- mpiComm.Allreduce(&nRankDOFs, &nOverallDOFs, 1, MPI_INT, MPI_SUM);
+ mpiComm.Allreduce(&nRankDofs, &nOverallDOFs, 1, MPI_INT, MPI_SUM);
// Do not change the indices now, but create a new indexing a store it here.
@@ -1510,6 +1511,57 @@ namespace AMDiS {
}
+ Flag ParallelDomainBase::oneIteration(AdaptInfo *adaptInfo, Flag toDo)
+ {
+ FUNCNAME("ParallelDomainBase::oneIteration()");
+
+ Flag flag = dynamic_cast<StandardProblemIteration*>(iterationIF)->
+ buildAndAdapt(adaptInfo, toDo);
+
+ if (toDo.isSet(SOLVE))
+ solve();
+
+ if (toDo.isSet(SOLVE_RHS))
+ ERROR_EXIT("Not yet implemented!\n");
+
+ if (toDo.isSet(ESTIMATE))
+ iterationIF->getProblem()->estimate(adaptInfo);
+
+ return flag;
+ }
+
+
+ void ParallelDomainBase::serialize(std::ostream &out)
+ {
+ SerUtil::serialize(out, elemWeights);
+ SerUtil::serialize(out, &initialPartitionMesh);
+ SerUtil::serialize(out, partitionVec);
+ SerUtil::serialize(out, oldPartitionVec);
+ SerUtil::serialize(out, &nRankDofs);
+
+ myIntBoundary.serialize(out);
+ otherIntBoundary.serialize(out);
+
+ // SerUtil::serialize(out, sendDofs);
+ // SerUtil::serialize(out, recvDofs);
+
+ SerUtil::serialize(out, mapLocalGlobalDOFs);
+ SerUtil::serialize(out, mapLocalToDofIndex);
+ SerUtil::serialize(out, isRankDof);
+
+ // SerUtil::serialize(out, vertexDof);
+
+ SerUtil::serialize(out, &rstart);
+ SerUtil::serialize(out, &nRankRows);
+ SerUtil::serialize(out, &nOverallRows);
+ }
+
+
+ void ParallelDomainBase::deserialize(std::istream &in)
+ {
+ }
+
+
void ParallelDomainBase::DbgCreateElementMap(ElementIdxToDofs &elMap)
{
FUNCNAME("ParallelDomainBase::DbgCreateElementMap()");
@@ -1793,24 +1845,4 @@ namespace AMDiS {
ElementFileWriter::writeFile(vec, feSpace, filename);
}
-
- Flag ParallelDomainBase::oneIteration(AdaptInfo *adaptInfo, Flag toDo)
- {
- FUNCNAME("ParallelDomainBase::oneIteration()");
-
- Flag flag = dynamic_cast<StandardProblemIteration*>(iterationIF)->
- buildAndAdapt(adaptInfo, toDo);
-
- if (toDo.isSet(SOLVE))
- solve();
-
- if (toDo.isSet(SOLVE_RHS))
- ERROR_EXIT("Not yet implemented!\n");
-
- if (toDo.isSet(ESTIMATE))
- iterationIF->getProblem()->estimate(adaptInfo);
-
- return flag;
- }
-
}
diff --git a/AMDiS/src/ParallelDomainBase.h b/AMDiS/src/ParallelDomainBase.h
index 3ab82d43579347e3f54aa6d5b11e14670e37fb5f..36538590373fe49e696212beba239e970f607eca 100644
--- a/AMDiS/src/ParallelDomainBase.h
+++ b/AMDiS/src/ParallelDomainBase.h
@@ -163,9 +163,9 @@ namespace AMDiS {
}
/// Returns \ref nRankDOFs, the number of DOFs in the rank mesh.
- int getNumberRankDOFs()
+ int getNumberRankDofs()
{
- return nRankDOFs;
+ return nRankDofs;
}
void fillPetscMatrix(DOFMatrix *mat, DOFVector<double> *vec);
@@ -181,10 +181,9 @@ namespace AMDiS {
return NULL;
}
- virtual void serialize(std::ostream&) {}
-
- virtual void deserialize(std::istream&) {}
+ virtual void serialize(std::ostream &out);
+ virtual void deserialize(std::istream &in);
protected:
/** \brief
@@ -376,16 +375,17 @@ namespace AMDiS {
*/
std::map<int, int> oldPartitionVec;
+ /// Petsc's matrix structure.
Mat petscMatrix;
- Vec petscRhsVec;
+ /** \brief
+ * Petsc's vector structures for the rhs vector, the solution vector and a
+ * temporary vector for calculating the final residuum.
+ */
+ Vec petscRhsVec, petscSolVec, petscTmpVec;
- Vec petscSolVec;
-
- Vec petscTmpVec;
-
/// Number of DOFs in the rank mesh.
- int nRankDOFs;
+ int nRankDofs;
/** \brief
* Defines the interior boundaries of the domain that result from partitioning
@@ -430,12 +430,19 @@ namespace AMDiS {
DofToBool vertexDof;
+ /// Is the index of the first row of the linear system, which is owned by the rank.
int rstart;
+ /** \brief
+ * Number of components of the equation. Is used to calculate the exact number
+ * of rows in the the overall linear system.
+ */
int nComponents;
+ /// Number of rows of the whole linear system that are stored on this rank.
int nRankRows;
+ /// Overall number of the rows in the lineary system.
int nOverallRows;
};
diff --git a/AMDiS/src/ProblemVec.cc b/AMDiS/src/ProblemVec.cc
index 3e8860d697cfb108a07e7a12c51f8aafe3f0ca5d..c3474cfbfe463f74c35b3d5c1c36f52a2a301433 100644
--- a/AMDiS/src/ProblemVec.cc
+++ b/AMDiS/src/ProblemVec.cc
@@ -1309,7 +1309,7 @@ namespace AMDiS {
{
FUNCNAME("ProblemVec::serialize()");
- SerializerUtil::serializeBool(out, &allowFirstRef);
+ SerUtil::serialize(out, &allowFirstRef);
for (int i = 0; i < static_cast<int>(meshes.size()); i++)
meshes[i]->serialize(out);
@@ -1321,7 +1321,7 @@ namespace AMDiS {
{
FUNCNAME("ProblemVec::deserialize()");
- SerializerUtil::deserializeBool(in, &allowFirstRef);
+ SerUtil::deserialize(in, &allowFirstRef);
for (int i = 0; i < static_cast<int>(meshes.size()); i++)
meshes[i]->deserialize(in);
diff --git a/AMDiS/src/Serializer.h b/AMDiS/src/Serializer.h
index e1818a3a7c0277a172b440f721e44a242c69b917..06c4798696f63500ca8f99409174493ef4c6ebc1 100644
--- a/AMDiS/src/Serializer.h
+++ b/AMDiS/src/Serializer.h
@@ -22,6 +22,7 @@
#ifndef AMDIS_SERIALIZER_H
#define AMDIS_SERIALIZER_H
+#include <map>
#include "FileWriter.h"
#include "Parameters.h"
#include "AdaptInfo.h"
@@ -33,17 +34,17 @@ namespace AMDiS {
class Serializer : public FileWriterInterface
{
public:
- Serializer(ProblemType *problem)
- : name_(""),
- problem_(problem),
- tsModulo_(1),
- timestepNumber_(-1)
+ Serializer(ProblemType *prob)
+ : name(""),
+ problem(prob),
+ tsModulo(1),
+ timestepNumber(-1)
{
- 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");
+ 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");
}
virtual ~Serializer() {}
@@ -56,76 +57,65 @@ namespace AMDiS {
{
FUNCNAME("Serializer::writeFiles()");
- timestepNumber_++;
- timestepNumber_ %= tsModulo_;
- if ((timestepNumber_ != 0) && !force)
+ timestepNumber++;
+ timestepNumber %= tsModulo;
+ if ((timestepNumber != 0) && !force)
return;
TEST_EXIT(adaptInfo)("No AdaptInfo\n");
- std::ofstream out(name_.c_str());
+ std::ofstream out(name.c_str());
TEST_EXIT(out.is_open())("Cannot open serialization file!\n");
- problem_->serialize(out);
+ problem->serialize(out);
adaptInfo->serialize(out);
out.close();
- MSG("problem serialized to %s \n", name_.c_str());
- }
-
- void writeDelayedFiles() {}
-
- bool isWritingDelayed()
- {
- return false;
+ MSG("problem serialized to %s \n", name.c_str());
}
protected:
/// Name of file to which the problem is serialized.
- std::string name_;
+ std::string name;
/// Pointer to the problem.
- ProblemType *problem_;
+ ProblemType *problem;
/// The problem is serialized every tsModulo-th timestep.
- int tsModulo_;
+ int tsModulo;
/// Current timestep number.
- int timestepNumber_;
+ int timestepNumber;
};
+ namespace SerUtil {
- class SerializerUtil {
- public:
- static void serializeInt(std::ostream &out, int* ptrInt)
- {
- out.write(reinterpret_cast<const char*>(ptrInt), sizeof(int));
- }
-
- static void serializeDouble(std::ostream &out, double* ptrInt)
- {
- out.write(reinterpret_cast<const char*>(ptrInt), sizeof(double));
- }
-
- static void serializeBool(std::ostream &out, bool* ptrBool)
- {
- out.write(reinterpret_cast<const char*>(ptrBool), sizeof(bool));
- }
-
- static void deserializeInt(std::istream &in, int* ptrInt)
+ template<typename T>
+ void serialize(std::ostream &out, T *data)
{
- in.read(reinterpret_cast<char*>(ptrInt), sizeof(int));
- }
+ out.write(reinterpret_cast<const char*>(data), sizeof(T));
+ }
- static void deserializeDouble(std::istream &in, double* ptrInt)
+ template<typename T>
+ void deserialize(std::istream &in, T *data)
{
- in.read(reinterpret_cast<char*>(ptrInt), sizeof(double));
- }
+ in.read(reinterpret_cast<char*>(data), sizeof(T));
+ }
- static void deserializeBool(std::istream &in, bool* ptrBool)
+ template<typename T1, typename T2>
+ void serialize(std::ostream &out, std::map<T1, T2> &data)
{
- in.read(reinterpret_cast<char*>(ptrBool), sizeof(bool));
+ int mapSize = data.size();
+ serialize(out, &mapSize);
+
+ for (typename std::map<T1,T2>::iterator it = data.begin();
+ it != data.end(); ++it) {
+ T1 v1 = it->first;
+ T2 v2 = it->second;
+ serialize(out, &v1);
+ serialize(out, &v2);
+ }
}
+ }
- };
}
#endif