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amdis
Commit 9fc53052 authored by Thomas Witkowski's avatar Thomas Witkowski
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Some performance issues, part I.

parent e4673262
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Showing with 102 additions and 67 deletions
AMDiS/src/parallel/ElementObjectDatabase.cc
View file @ 9fc53052
......@@ -563,9 +563,10 @@ namespace AMDiS {
bool reverseMode =
BoundaryObject::computeReverseMode(obj0, obj1, feSpace, INTERIOR);
edgeReverseMode[make_pair(els[i], els[j])] = reverseMode;
edgeReverseMode[make_pair(els[j], els[i])] = reverseMode;
if (reverseMode) {
edgeReverseMode.insert(make_pair(els[i], els[j]));
edgeReverseMode.insert(make_pair(els[j], els[i]));
}
}
}
}
......@@ -587,9 +588,10 @@ namespace AMDiS {
bool reverseMode =
BoundaryObject::computeReverseMode(obj0, obj1, feSpace, INTERIOR);
faceReverseMode[make_pair(els[i], els[j])] = reverseMode;
faceReverseMode[make_pair(els[j], els[i])] = reverseMode;
if (reverseMode) {
faceReverseMode.insert(make_pair(els[i], els[j]));
faceReverseMode.insert(make_pair(els[j], els[i]));
}
}
}
}
......@@ -615,9 +617,10 @@ namespace AMDiS {
bool reverseMode =
BoundaryObject::computeReverseMode(obj0, obj1, feSpace,
edgeIt->second);
edgeReverseMode[make_pair(edges0[i], edges1[j])] = reverseMode;
edgeReverseMode[make_pair(edges1[j], edges0[i])] = reverseMode;
if (reverseMode) {
edgeReverseMode.insert(make_pair(edges0[i], edges1[j]));
edgeReverseMode.insert(make_pair(edges1[j], edges0[i]));
}
}
}
}
......@@ -638,9 +641,10 @@ namespace AMDiS {
bool reverseMode =
BoundaryObject::computeReverseMode(obj0, obj1, feSpace, faceIt->second);
faceReverseMode[make_pair(faces0[0], faces1[0])] = reverseMode;
faceReverseMode[make_pair(faces1[0], faces0[0])] = reverseMode;
if (reverseMode) {
faceReverseMode.insert(make_pair(faces0[0], faces1[0]));
faceReverseMode.insert(make_pair(faces1[0], faces0[0]));
}
}
}
......@@ -863,19 +867,18 @@ namespace AMDiS {
nSize = edgeReverseMode.size();
SerUtil::serialize(out, nSize);
for (map<pair<ElementObjectData, ElementObjectData>, bool>::iterator it = edgeReverseMode.begin();
for (std::set<pair<ElementObjectData, ElementObjectData> >::iterator it = edgeReverseMode.begin();
it != edgeReverseMode.end(); ++it) {
it->first.first.serialize(out);
it->first.second.serialize(out);
SerUtil::serialize(out, it->second);
it->first.serialize(out);
it->second.serialize(out);
}
nSize = faceReverseMode.size();
SerUtil::serialize(out, nSize);
for (map<pair<ElementObjectData, ElementObjectData>, bool>::iterator it = faceReverseMode.begin();
for (std::set<pair<ElementObjectData, ElementObjectData> >::iterator it = faceReverseMode.begin();
it != faceReverseMode.end(); ++it) {
it->first.first.serialize(out);
it->first.second.serialize(out);
it->first.serialize(out);
it->second.serialize(out);
SerUtil::serialize(out, it->second);
}
}
......@@ -1012,24 +1015,20 @@ namespace AMDiS {
edgeReverseMode.clear();
for (int i = 0; i < nSize; i++) {
ElementObjectData obj0, obj1;
bool reverseMode;
obj0.deserialize(in);
obj1.deserialize(in);
SerUtil::deserialize(in, reverseMode);
edgeReverseMode[make_pair(obj0, obj1)] = reverseMode;
edgeReverseMode.insert(make_pair(obj0, obj1));
}
SerUtil::deserialize(in, nSize);
faceReverseMode.clear();
for (int i = 0; i < nSize; i++) {
ElementObjectData obj0, obj1;
bool reverseMode;
obj0.deserialize(in);
obj1.deserialize(in);
SerUtil::deserialize(in, reverseMode);
faceReverseMode[make_pair(obj0, obj1)] = reverseMode;
faceReverseMode.insert(make_pair(obj0, obj1));
}
}
......@@ -1086,6 +1085,8 @@ namespace AMDiS {
unsigned long ElementObjectDatabase::calculateMemoryUsage()
{
FUNCNAME("ElementObjectDatabase::calculateMemoryUsage()");
const unsigned int structElObjDataSize = sizeof(ElementObjectData);
const unsigned int dofSize = sizeof(DegreeOfFreedom);
const unsigned int edgeSize = sizeof(DofEdge);
......@@ -1093,73 +1094,96 @@ namespace AMDiS {
const unsigned int vectorOverhead = sizeof(vector<int>);
const unsigned int mapOverhead = 48; //sizeof(_Rb_tree<int, int>);
const unsigned int mapEntryOverhead = 40; // sizeof(_Rb_tree_node_base);
const unsigned int setOverhead = 48;
const unsigned int setEntryOverhead = 40;
unsigned long value = 0;
unsigned long tmp = 0;
// vertexElements
value += mapOverhead + vertexElements.size() * mapEntryOverhead;
tmp = mapOverhead + vertexElements.size() * mapEntryOverhead;
for (map<DegreeOfFreedom, vector<ElementObjectData> >::iterator mapIt =
vertexElements.begin(); mapIt != vertexElements.end(); ++mapIt)
value += dofSize + vectorOverhead + mapIt->second.size() * structElObjDataSize;
vertexElements.begin(); mapIt != vertexElements.end(); ++mapIt)
tmp += dofSize + vectorOverhead + mapIt->second.size() * structElObjDataSize;
MSG("EL-OBJ-DB MEM 01: %d\n", tmp);
value += tmp;
// edgeElements
value += mapOverhead + edgeElements.size() * mapEntryOverhead;
tmp = mapOverhead + edgeElements.size() * mapEntryOverhead;
for (map<DofEdge, vector<ElementObjectData> >::iterator mapIt =
edgeElements.begin(); mapIt != edgeElements.end(); ++mapIt)
value += dofSize + vectorOverhead + mapIt->second.size() * structElObjDataSize;
tmp += dofSize + vectorOverhead + mapIt->second.size() * structElObjDataSize;
MSG("EL-OBJ-DB MEM 02: %d\n", tmp);
value += tmp;
// faceElements
value += mapOverhead + faceElements.size() * mapEntryOverhead;
tmp += mapOverhead + faceElements.size() * mapEntryOverhead;
for (map<DofFace, vector<ElementObjectData> >::iterator mapIt =
faceElements.begin(); mapIt != faceElements.end(); ++mapIt)
value += dofSize + vectorOverhead + mapIt->second.size() * structElObjDataSize;
tmp += dofSize + vectorOverhead + mapIt->second.size() * structElObjDataSize;
MSG("EL-OBJ-DB MEM 03: %d\n", tmp);
value += tmp;
tmp = 0;
// vertexLocalMap
value += mapOverhead + vertexLocalMap.size() * (mapEntryOverhead + structElObjDataSize + dofSize);
tmp += mapOverhead + vertexLocalMap.size() * (mapEntryOverhead + structElObjDataSize + dofSize);
// edgeLocalMap
value += mapOverhead + edgeLocalMap.size() * (mapEntryOverhead + structElObjDataSize + edgeSize);
tmp += mapOverhead + edgeLocalMap.size() * (mapEntryOverhead + structElObjDataSize + edgeSize);
// faceLocalMap
value += mapOverhead + faceLocalMap.size() * (mapEntryOverhead + structElObjDataSize + faceSize);
tmp += mapOverhead + faceLocalMap.size() * (mapEntryOverhead + structElObjDataSize + faceSize);
MSG("EL-OBJ-DB MEM 04: %d\n", tmp);
value += tmp;
// vertexInRank
value += mapOverhead + vertexInRank.size() * mapEntryOverhead;
tmp = mapOverhead + vertexInRank.size() * mapEntryOverhead;
for (map<DegreeOfFreedom, map<int, ElementObjectData> >::iterator mapIt =
vertexInRank.begin(); mapIt != vertexInRank.end(); ++mapIt)
value += dofSize + mapOverhead +
tmp += dofSize + mapOverhead +
mapIt->second.size() * (mapEntryOverhead + sizeof(int) + structElObjDataSize);
MSG("EL-OBJ-DB MEM 05: %d\n", tmp);
value += tmp;
// edgeInRank
value += mapOverhead + edgeInRank.size() * mapEntryOverhead;
tmp += mapOverhead + edgeInRank.size() * mapEntryOverhead;
for (map<DofEdge, map<int, ElementObjectData> >::iterator mapIt =
edgeInRank.begin(); mapIt != edgeInRank.end(); ++mapIt)
value += edgeSize + mapOverhead +
tmp += edgeSize + mapOverhead +
mapIt->second.size() * (mapEntryOverhead + sizeof(int) + structElObjDataSize);
MSG("EL-OBJ-DB MEM 06: %d\n", tmp);
value += tmp;
// faceInRank
value += mapOverhead + faceInRank.size() * mapEntryOverhead;
tmp = mapOverhead + faceInRank.size() * mapEntryOverhead;
for (map<DofFace, map<int, ElementObjectData> >::iterator mapIt =
faceInRank.begin(); mapIt != faceInRank.end(); ++mapIt)
value += faceSize + mapOverhead +
tmp += faceSize + mapOverhead +
mapIt->second.size() * (mapEntryOverhead + sizeof(int) + structElObjDataSize);
MSG("EL-OBJ-DB MEM 07: %d\n", tmp);
value += tmp;
tmp = 0;
if (bConnMap.size() || periodicVertices.size() || periodicDofAssoc.size()) {
ERROR_EXIT("Not yet implemented for periodic meshes!\n");
}
// edgeReverseMode
value += mapOverhead + edgeReverseMode.size() * (mapEntryOverhead + 2 * structElObjDataSize + sizeof(bool));
tmp += setOverhead + edgeReverseMode.size() * (setEntryOverhead + 2 * structElObjDataSize);
// faceReverseMode
value += mapOverhead + faceReverseMode.size() * (mapEntryOverhead + 2 * structElObjDataSize + sizeof(bool));
tmp += setOverhead + faceReverseMode.size() * (setEntryOverhead + 2 * structElObjDataSize);
// macroElIndexMap
value += mapOverhead + macroElIndexMap.size() * (mapEntryOverhead + sizeof(int) + sizeof(int*));
tmp += mapOverhead + macroElIndexMap.size() * (mapEntryOverhead + sizeof(int) + sizeof(int*));
// macroElIndexTypeMap
value += mapOverhead + macroElIndexTypeMap.size() * (mapEntryOverhead + sizeof(int) + sizeof(int*));
tmp += mapOverhead + macroElIndexTypeMap.size() * (mapEntryOverhead + sizeof(int) + sizeof(int*));
MSG("EL-OBJ-DB MEM 08: %d\n", tmp);
value += tmp;
return value;
}
......
AMDiS/src/parallel/ElementObjectDatabase.h
View file @ 9fc53052
......@@ -385,19 +385,19 @@ namespace AMDiS {
if (mesh->getDim() == 2)
return true;
TEST_EXIT_DBG(edgeReverseMode.count(make_pair(obj0, obj1)))
("Should not happen!\n");
if (edgeReverseMode.empty())
return false;
return edgeReverseMode[make_pair(obj0, obj1)];
return static_cast<bool>(edgeReverseMode.count(make_pair(obj0, obj1)));
}
inline bool getFaceReverseMode(ElementObjectData &obj0,
ElementObjectData &obj1)
{
TEST_EXIT_DBG(faceReverseMode.count(make_pair(obj0, obj1)))
("Should not happen!\n");
if (faceReverseMode.empty())
return false;
return faceReverseMode[make_pair(obj0, obj1)];
return static_cast<bool>(faceReverseMode.count(make_pair(obj0, obj1)));
}
/// Returns true if there is periodic data.
......@@ -459,15 +459,13 @@ namespace AMDiS {
/// Adds the i-th face of an element to the object database.
void addFace(Element *el, int ith);
/** \brief
* Creates final data of the periodic boundaries. Must be called after all
* elements of the mesh are added to the object database. Then this functions
* search for indirectly connected vertices in periodic boundaries. This is
* only the case, if there are more than one boundary conditions. Then, e.g.,
* in 2D, all edges of a square are iterectly connected. In 3D, if the macro
* mesh is a box, all eight vertex nodes and always four of the 12 edges are
* indirectly connected.
*/
/// Creates final data of the periodic boundaries. Must be called after all
/// elements of the mesh are added to the object database. Then this
/// functions search for indirectly connected vertices in periodic
/// boundaries. This is only the case, if there are more than one boundary
/// conditions. Then, e.g., in 2D, all edges of a square are iterectly
/// connected. In 3D, if the macro mesh is a box, all eight vertex nodes and
/// always four of the 12 edges are indirectly connected.
void createPeriodicData();
/// Creates on all boundaries the reverse mode flag.
......@@ -566,9 +564,11 @@ namespace AMDiS {
/// Stores to each edge all its periodic associations.
map<DofEdge, std::set<DofEdge> > periodicEdgeAssoc;
map<pair<ElementObjectData, ElementObjectData>, bool> edgeReverseMode;
/// Stores all interior edge boundaries which have reverse mode enabled.
std::set<pair<ElementObjectData, ElementObjectData> > edgeReverseMode;
map<pair<ElementObjectData, ElementObjectData>, bool> faceReverseMode;
/// Stores all interior face boundaries which have reverse mode enabled.
std::set<pair<ElementObjectData, ElementObjectData> > faceReverseMode;
map<int, int> *macroElementRankMap;
......
AMDiS/src/parallel/MeshDistributor.cc
View file @ 9fc53052
......@@ -959,6 +959,7 @@ namespace AMDiS {
// === Check the boundaries and adapt mesh if necessary. ===
MSG_DBG("Run checkAndAdaptBoundary ...\n");
double second = MPI::Wtime();
// Check for periodic boundaries within rank's subdomain.
for (InteriorBoundary::iterator it(intBoundary.getPeriodic());
!it.end(); ++it) {
......@@ -973,9 +974,13 @@ namespace AMDiS {
}
}
}
MSG(" -> create mesh structure codes needed %.5f seconds\n", MPI::Wtime() - second);
second = MPI::Wtime();
meshChanged |= checkAndAdaptBoundary(allBound);
MSG(" -> checkAndAdaptBoundary needed %.5f seconds\n", MPI::Wtime() - second);
// === Check on all ranks if at least one rank's mesh has changed. ===
int sendValue = static_cast<int>(meshChanged);
......@@ -1091,6 +1096,8 @@ namespace AMDiS {
map<int, MeshCodeVec> sendCodes;
double first = MPI::Wtime();
for (RankToBoundMap::iterator it = allBound.begin();
it != allBound.end(); ++it) {
for (vector<AtomicBoundary>::iterator boundIt = it->second.begin();
......@@ -1109,6 +1116,8 @@ namespace AMDiS {
stdMpi.startCommunication();
MSG(" -> communicate codes needed %.5f seconds\n", MPI::Wtime() - first);
first = MPI::Wtime();
// === Compare received mesh structure codes. ===
......@@ -1144,6 +1153,8 @@ namespace AMDiS {
}
}
MSG(" -> fitElementToMeshCode needed %.5f seconds\n", MPI::Wtime() - first);
return meshChanged;
}
......@@ -1584,9 +1595,9 @@ namespace AMDiS {
elObjDb.create(partitionMap, levelData);
elObjDb.updateRankData();
// unsigned long memsize = elObjDb.calculateMemoryUsage();
// MSG("Memory usage of element object database = %5.f KByte\n",
// static_cast<double>(memsize / 1024));
unsigned long memsize = elObjDb.calculateMemoryUsage();
MSG("Memory usage of element object database = %5.f KByte\n",
static_cast<double>(memsize / 1024.0));
intBoundary.create(levelData, 0, elObjDb);
ParallelDebug::printBoundaryInfo(intBoundary);
......
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