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amdis
Commit dfeb9e9e authored by Thomas Witkowski's avatar Thomas Witkowski
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Work on parallel periodic boundary condition in 3D.

parent 32b71148
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Showing with 289 additions and 67 deletions
AMDiS/src/parallel/MeshDistributor.cc
View file @ dfeb9e9e
......@@ -221,6 +221,9 @@ namespace AMDiS {
createPeriodicMap();
#if (DEBUG != 0)
ParallelDebug::testPeriodicBoundary(*this);
#endif
// === Global refinements. ===
......@@ -547,7 +550,7 @@ namespace AMDiS {
for (InteriorBoundary::iterator it(periodicBoundary); !it.end(); ++it) {
if (it.getRank() == mpiRank) {
// ERROR_EXIT("Na, du weisst schon!\n");
WARNING("Na, du weisst schon!\n");
} else {
if ((mesh->getDim() == 2 && it->rankObj.subObj == EDGE) ||
(mesh->getDim() == 3 && it->rankObj.subObj == FACE))
......@@ -1261,8 +1264,6 @@ namespace AMDiS {
{
FUNCNAME("MeshDistributor::createInteriorBoundaryInfo()");
MSG("CREATE BOUNDARY INFO!\n");
createMeshElementData();
createBoundaryData();
......@@ -1274,8 +1275,6 @@ namespace AMDiS {
{
FUNCNAME("MeshDistributor::updateInteriorBoundaryInfo()");
MSG("UPDATE BOUNDARY INFO!\n");
elObjects.createRankData(partitionVec);
createBoundaryData();
......@@ -1328,8 +1327,8 @@ namespace AMDiS {
periodicEdgeAssoc[edge1].insert(edge2);
periodicDofs[std::make_pair(edge1.first, edge2.first)] = boundaryType;
periodicDofs[std::make_pair(edge1.second, edge2.second)] = boundaryType;
periodicVertices[std::make_pair(edge1.first, edge2.first)] = boundaryType;
periodicVertices[std::make_pair(edge1.second, edge2.second)] = boundaryType;
periodicDofAssoc[edge1.first].insert(boundaryType);
periodicDofAssoc[edge1.second].insert(boundaryType);
......@@ -1351,9 +1350,9 @@ namespace AMDiS {
periodicFaces[std::make_pair(face1, face2)] = elInfo->getBoundary(i);
periodicDofs[std::make_pair(face1.get<0>(), face2.get<0>())] = boundaryType;
periodicDofs[std::make_pair(face1.get<1>(), face2.get<1>())] = boundaryType;
periodicDofs[std::make_pair(face1.get<2>(), face2.get<2>())] = boundaryType;
periodicVertices[std::make_pair(face1.get<0>(), face2.get<0>())] = boundaryType;
periodicVertices[std::make_pair(face1.get<1>(), face2.get<1>())] = boundaryType;
periodicVertices[std::make_pair(face1.get<2>(), face2.get<2>())] = boundaryType;
periodicDofAssoc[face1.get<0>()].insert(boundaryType);
periodicDofAssoc[face1.get<1>()].insert(boundaryType);
......@@ -1395,7 +1394,7 @@ namespace AMDiS {
// === Search for interectly connected vertices in periodic boundaries. ===
if (periodicDofs.size() > 0) {
if (periodicVertices.size() > 0) {
// === Search for an unsed boundary index. ===
......@@ -1413,52 +1412,51 @@ namespace AMDiS {
// === Get all vertex DOFs that have multiple periodic associations. ===
std::vector<DegreeOfFreedom> multiplePeriodicDof;
std::map<int, std::vector<DegreeOfFreedom> > multiplePeriodicDof;
for (std::map<DegreeOfFreedom, std::set<BoundaryType> >::iterator it = periodicDofAssoc.begin();
it != periodicDofAssoc.end(); ++it) {
if (mesh->getDim() == 2) {
TEST_EXIT_DBG(it->second.size() <= 2)("Should not happen!\n");
}
if (mesh->getDim() == 3) {
TEST_EXIT_DBG(it->second.size() <= 3)("Should not happen!\n");
}
if ((mesh->getDim() == 2 && it->second.size() == 2) ||
(mesh->getDim() == 3 && it->second.size() == 3))
multiplePeriodicDof.push_back(it->first);
}
if (mesh->getDim() == 2) {
TEST_EXIT_DBG(multiplePeriodicDof.size() == 0 ||
multiplePeriodicDof.size() == 4)
("Should not happen (%d)!\n", multiplePeriodicDof.size());
}
if (mesh->getDim() == 3) {
TEST_EXIT_DBG(multiplePeriodicDof.size() == 0 ||
multiplePeriodicDof.size() == 8)
("Should not happen (%d)!\n", multiplePeriodicDof.size());
TEST_EXIT_DBG((mesh->getDim() == 2 && it->second.size() <= 2) ||
(mesh->getDim() == 3 && it->second.size() <= 3))
("Should not happen!\n");
multiplePeriodicDof[it->second.size()].push_back(it->first);
}
int nMultiplePeriodicDofs = multiplePeriodicDof.size();
for (int i = 0; i < nMultiplePeriodicDofs; i++) {
for (int j = 0; j < nMultiplePeriodicDofs; j++) {
if (i == j)
continue;
std::pair<DegreeOfFreedom, DegreeOfFreedom> perDofs =
std::make_pair(multiplePeriodicDof[i], multiplePeriodicDof[j]);
if (periodicDofs.count(perDofs) == 0)
periodicDofs[perDofs] = newPeriodicBoundaryType;
if (mesh->getDim() == 2)
TEST_EXIT_DBG(multiplePeriodicDof[2].size() == 0 ||
multiplePeriodicDof[2].size() == 4)
("Should not happen (%d)!\n", multiplePeriodicDof[2].size());
if (mesh->getDim() == 3)
TEST_EXIT_DBG(multiplePeriodicDof[3].size() == 0 ||
multiplePeriodicDof[3].size() == 8)
("Should not happen (%d)!\n", multiplePeriodicDof[3].size());
for (int k = 2; k <= 3; k++) {
int nMultiplePeriodicDofs = multiplePeriodicDof[k].size();
for (int i = 0; i < nMultiplePeriodicDofs; i++) {
for (int j = i + 1; j < nMultiplePeriodicDofs; j++) {
std::pair<DegreeOfFreedom, DegreeOfFreedom> perDofs0 =
std::make_pair(multiplePeriodicDof[k][i], multiplePeriodicDof[k][j]);
std::pair<DegreeOfFreedom, DegreeOfFreedom> perDofs1 =
std::make_pair(multiplePeriodicDof[k][j], multiplePeriodicDof[k][i]);
if (periodicVertices.count(perDofs0) == 0) {
TEST_EXIT_DBG(periodicVertices.count(perDofs1) == 0)
("Should not happen!\n");
periodicVertices[perDofs0] = newPeriodicBoundaryType;
periodicVertices[perDofs1] = newPeriodicBoundaryType;
newPeriodicBoundaryType--;
mesh->getPeriodicAssociations()[newPeriodicBoundaryType] =
new VertexVector(feSpace->getAdmin(), "");
}
}
}
}
// === Get all edges that have multiple periodic associations (3D only!). ===
for (std::map<DofEdge, std::set<DofEdge> >::iterator it = periodicEdgeAssoc.begin();
......@@ -1474,10 +1472,47 @@ namespace AMDiS {
periodicEdges[perEdge0] = newPeriodicBoundaryType;
periodicEdges[perEdge1] = newPeriodicBoundaryType;
newPeriodicBoundaryType--;
mesh->getPeriodicAssociations()[newPeriodicBoundaryType] =
new VertexVector(feSpace->getAdmin(), "");
}
}
// === In debug mode we make some tests, if the periodic structures are set ===
// === in a symmetric way, i.e., if A -> B for a specific boundary type, ===
// === there must be a mapping B -> A with the same boundary type. ===
#if (DEBUG != 0)
for (std::map<std::pair<DegreeOfFreedom, DegreeOfFreedom>, BoundaryType>::iterator it = periodicVertices.begin();
it != periodicVertices.end(); ++it) {
std::pair<DegreeOfFreedom, DegreeOfFreedom> testVertex =
std::make_pair(it->first.second, it->first.first);
TEST_EXIT_DBG(periodicVertices.count(testVertex) == 1)("Should not happen!\n");
TEST_EXIT_DBG(periodicVertices[testVertex] == it->second)("Should not happen!\n");
}
for (std::map<std::pair<DofEdge, DofEdge>, BoundaryType>::iterator it = periodicEdges.begin();
it != periodicEdges.end(); ++it) {
std::pair<DofEdge, DofEdge> testEdge =
std::make_pair(it->first.second, it->first.first);
TEST_EXIT_DBG(periodicEdges.count(testEdge) == 1)("Should not happen!\n");
TEST_EXIT_DBG(periodicEdges[testEdge] == it->second)("Should not happen!\n");
}
for (std::map<std::pair<DofFace, DofFace>, BoundaryType>::iterator it = periodicFaces.begin();
it != periodicFaces.end(); ++it) {
std::pair<DofFace, DofFace> testFace =
std::make_pair(it->first.second, it->first.first);
TEST_EXIT_DBG(periodicFaces.count(testFace) == 1)("Should not happen!\n");
TEST_EXIT_DBG(periodicFaces[testFace] == it->second)("Should not happen!\n");
}
#endif
}
}
......@@ -1488,7 +1523,7 @@ namespace AMDiS {
FUNCNAME("MeshDistributor::createBoundaryData()");
// === Clear all relevant data structures, ===
// === Clear all relevant data structures. ===
myIntBoundary.clear();
otherIntBoundary.clear();
......@@ -1578,12 +1613,19 @@ namespace AMDiS {
// === Create periodic boundary data structure. ===
for (std::map<std::pair<DegreeOfFreedom, DegreeOfFreedom>, BoundaryType>::iterator it = periodicDofs.begin();
it != periodicDofs.end(); ++it) {
for (std::map<std::pair<DegreeOfFreedom, DegreeOfFreedom>, BoundaryType>::iterator it = periodicVertices.begin();
it != periodicVertices.end(); ++it) {
if (elObjects.isInRank(it->first.first, mpiRank) == false)
continue;
WorldVector<double> c0, c1;
mesh->getDofIndexCoords(it->first.first, feSpace, c0);
mesh->getDofIndexCoords(it->first.second, feSpace, c1);
MSG("CREATE BOUNDARY FOR DOF MAP: %d (%.3f %.3f %.3f)<-> %d (%.3f %.3f %.3f)\n", it->first.first,
c0[0], c0[1], c0[2], it->first.second, c1[0], c1[1], c1[2]);
ElementObjectData& perDofEl0 = elObjects.getElementsInRank(it->first.first)[mpiRank];
MSG("DATA: %d %d %d\n", perDofEl0.elIndex, VERTEX, perDofEl0.ithObject);
for (std::map<int, ElementObjectData>::iterator elIt = elObjects.getElementsInRank(it->first.second).begin();
elIt != elObjects.getElementsInRank(it->first.second).end(); ++elIt) {
......@@ -2033,6 +2075,8 @@ namespace AMDiS {
for (RankToBoundMap::iterator it = periodicBoundary.boundary.begin();
it != periodicBoundary.boundary.end(); ++it) {
MSG("------------- WITH RANK %d ------------------\n", it->first);
if (it->first == mpiRank) {
TEST_EXIT_DBG(it->second.size() % 2 == 0)("Should not happen!\n");
......@@ -2044,6 +2088,10 @@ namespace AMDiS {
bound.neighObj.el->getVertexDofs(feSpace, bound.neighObj, dofs1);
bound.neighObj.el->getNonVertexDofs(feSpace, bound.neighObj, dofs1);
MSG("BOUND-I %d-%d-%d WITH %d-%d-%d\n",
bound.rankObj.elIndex, bound.rankObj.subObj, bound.rankObj.ithObj,
bound.neighObj.elIndex, bound.neighObj.subObj, bound.neighObj.ithObj);
TEST_EXIT_DBG(dofs0.size() == dofs1.size())("Should not happen!\n");
BoundaryType type = bound.type;
......@@ -2055,6 +2103,8 @@ namespace AMDiS {
if (periodicDofAssociations[globalDof0].count(type) == 0) {
periodicDof[type][globalDof0] = globalDof1;
periodicDofAssociations[globalDof0].insert(type);
MSG("SET(A TYPE %d) DOF %d -> %d\n", type, globalDof0, globalDof1);
}
}
}
......@@ -2066,12 +2116,20 @@ namespace AMDiS {
boundIt != it->second.end(); ++boundIt) {
int nDofs = dofs.size();
MSG("BOUND-R (T = %d) %d-%d-%d WITH %d-%d-%d\n",
boundIt->type,
boundIt->rankObj.elIndex, boundIt->rankObj.subObj, boundIt->rankObj.ithObj,
boundIt->neighObj.elIndex, boundIt->neighObj.subObj, boundIt->neighObj.ithObj);
boundIt->rankObj.el->getVertexDofs(feSpace, boundIt->rankObj, dofs);
boundIt->rankObj.el->getNonVertexDofs(feSpace, boundIt->rankObj, dofs);
for (unsigned int i = 0; i < (dofs.size() - nDofs); i++)
for (unsigned int i = 0; i < (dofs.size() - nDofs); i++) {
MSG(" i = %d DOF = %d\n", nDofs + i, mapLocalGlobalDofs[*(dofs[nDofs + i])]);
rankToDofType[it->first].push_back(boundIt->type);
}
}
// Send the global indices to the rank on the other side.
......@@ -2088,6 +2146,8 @@ namespace AMDiS {
stdMpi.startCommunication<int>(MPI_INT);
MSG("===============================\n");
// === The rank has received the dofs from the rank on the other side of ===
// === the boundary. Now it can use them to create the mapping between ===
// === the periodic dofs in this rank and the corresponding periodic ===
......@@ -2096,6 +2156,9 @@ namespace AMDiS {
for (RankToBoundMap::iterator it = periodicBoundary.boundary.begin();
it != periodicBoundary.boundary.end(); ++it) {
MSG("------------- WITH RANK %d ------------------\n", it->first);
DofContainer& dofs = rankPeriodicDofs[it->first];
std::vector<int>& types = rankToDofType[it->first];
......@@ -2110,24 +2173,29 @@ 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[globalDofIndex].count(type) == 0) {
MSG("SET(B-%d TYPE %d) DOF %d -> %d\n", i, type, globalDofIndex, mapGlobalDofIndex);
periodicDof[type][globalDofIndex] = mapGlobalDofIndex;
periodicDofAssociations[globalDofIndex].insert(type);
} else {
MSG("ASSOC ALREADY SET FOR %d TYPE %d\n", i, type);
}
}
}
#if (DEBUG != 0)
// In 2D, a periodic DOF can have either 1 or 3 associations. Check this!
if (mesh->getDim() == 2) {
for (std::map<int, std::set<BoundaryType> >::iterator it = periodicDofAssociations.begin();
it != periodicDofAssociations.end(); ++it) {
int nAssoc = it->second.size();
TEST_EXIT_DBG(nAssoc == 1 || nAssoc == 3)
("Should not happen! DOF %d has %d periodic associations!\n",
it->first, nAssoc);
}
}
for (std::map<int, std::set<BoundaryType> >::iterator it = periodicDofAssociations.begin();
it != periodicDofAssociations.end(); ++it) {
WorldVector<double> c;
mesh->getDofIndexCoords(it->first, feSpace, c);
int nAssoc = it->second.size();
TEST_EXIT_DBG(nAssoc == 1 || nAssoc == 3 ||
(mesh->getDim() == 3 && (nAssoc == 7 || nAssoc == 11)))
("Should not happen! DOF %d (%e %e %e) has %d periodic associations!\n",
it->first, c[0], c[1], (mesh->getDim() == 2 ? 0.0 : c[2]), nAssoc);
}
#endif
}
......@@ -2179,7 +2247,7 @@ namespace AMDiS {
elObjects.serialize(out);
SerUtil::serialize(out, periodicDofs);
SerUtil::serialize(out, periodicVertices);
SerUtil::serialize(out, periodicEdges);
SerUtil::serialize(out, periodicFaces);
......@@ -2243,7 +2311,7 @@ namespace AMDiS {
elObjects.deserialize(in);
SerUtil::deserialize(in, periodicDofs);
SerUtil::deserialize(in, periodicVertices);
SerUtil::deserialize(in, periodicEdges);
SerUtil::deserialize(in, periodicFaces);
......
AMDiS/src/parallel/MeshDistributor.h
View file @ dfeb9e9e
......@@ -479,7 +479,7 @@ namespace AMDiS {
std::map<int, int> macroElIndexTypeMap;
// The following three data structures store periodic DOFs, edges and faces.
std::map<std::pair<DegreeOfFreedom, DegreeOfFreedom>, BoundaryType> periodicDofs;
std::map<std::pair<DegreeOfFreedom, DegreeOfFreedom>, BoundaryType> periodicVertices;
std::map<std::pair<DofEdge, DofEdge>, BoundaryType> periodicEdges;
std::map<std::pair<DofFace, DofFace>, BoundaryType> periodicFaces;
......
AMDiS/src/parallel/ParallelDebug.cc
View file @ dfeb9e9e
......@@ -139,6 +139,89 @@ namespace AMDiS {
}
void ParallelDebug::testPeriodicBoundary(MeshDistributor &pdb)
{
FUNCNAME("ParallelDebug::testPeriodicBoundary()");
typedef MeshDistributor::PeriodicDofMap PeriodicDofMap;
StdMpi<PeriodicDofMap> stdMpi(pdb.mpiComm, true);
if (pdb.mpiRank == 0) {
for (int i = 1; i < pdb.mpiSize; i++)
stdMpi.recv(i);
} else {
stdMpi.send(0, pdb.periodicDof);
}
stdMpi.startCommunication<int>(MPI_INT);
int foundError = 0;
// === The boundary DOFs are checked only on the zero rank. ===
if (pdb.mpiRank == 0) {
std::map<int, PeriodicDofMap> rankToMaps;
PeriodicDofMap dofMap = pdb.periodicDof;
rankToMaps[0] = dofMap;
for (int i = 1; i < pdb.mpiSize; i++) {
PeriodicDofMap &otherMap = stdMpi.getRecvData(i);
rankToMaps[i] = otherMap;
for (PeriodicDofMap::iterator it = otherMap.begin();
it != otherMap.end(); ++it) {
for (MeshDistributor::DofMapping::iterator dofIt = it->second.begin();
dofIt != it->second.end(); ++dofIt) {
if (dofMap.count(it->first) == 1 &&
dofMap[it->first].count(dofIt->first) == 1) {
TEST_EXIT_DBG(dofMap[it->first][dofIt->first] == dofIt->second)
("Should not happen!\n");
} else {
dofMap[it->first][dofIt->first] = dofIt->second;
}
}
}
}
// === Now we test if global DOF A is mapped to B, then B must be mapped ===
// === to A for the same boundary type. ===
for (PeriodicDofMap::iterator it = dofMap.begin();
it != dofMap.end(); ++it) {
for (MeshDistributor::DofMapping::iterator dofIt = it->second.begin();
dofIt != it->second.end(); ++dofIt) {
if (it->second[dofIt->second] != dofIt->first) {
MSG("[DBG] For boundary type %d: DOF %d -> %d, but %d -> %d!\n",
it ->first,
dofIt->first, dofIt->second,
dofIt->second, it->second[dofIt->second]);
for (int i = 0; i < pdb.mpiSize; i++) {
if (rankToMaps[i][it->first].count(dofIt->first) == 1) {
MSG("[DBG] %d -> %d in rank %d\n",
dofIt->first, rankToMaps[i][it->first][dofIt->first], i);
}
if (rankToMaps[i][it->first].count(dofIt->second) == 1) {
MSG("[DBG] %d -> %d in rank %d\n",
dofIt->second, rankToMaps[i][it->first][dofIt->second], i);
}
}
ERROR("Wrong periodic DOFs!\n");
foundError = 1;
}
}
}
}
mpi::globalAdd(foundError);
TEST_EXIT(foundError == 0)("Error found on at least on rank!\n");
}
void ParallelDebug::testCommonDofs(MeshDistributor &pdb, bool printCoords)
{
FUNCNAME("ParallelDebug::testCommonDofs()");
......@@ -573,7 +656,8 @@ namespace AMDiS {
}
for (InteriorBoundary::iterator it(pdb.periodicBoundary); !it.end(); ++it) {
MSG("Periodic boundary with rank %d: \n", it.getRank());
MSG("Periodic boundary (ID %d) with rank %d: \n",
it->type, it.getRank());
MSG(" ranks obj-ind: %d sub-obj: %d ith-obj: %d\n",
it->rankObj.elIndex, it->rankObj.subObj, it->rankObj.ithObj);
MSG(" neigh obj-ind: %d sub-obj: %d ith-obj: %d\n",
......
AMDiS/src/parallel/ParallelDebug.h
View file @ dfeb9e9e
......@@ -41,6 +41,13 @@ namespace AMDiS {
*/
static void testInteriorBoundary(MeshDistributor &pdb);
/** \brief
* Test if all periodic boundaries are set in a consistent way on all ranks.
*
* \param[in] pdb Parallel problem definition used for debugging.
*/
static void testPeriodicBoundary(MeshDistributor &pdb);
/** \brief
* This function is used for debugging only. It traverses all interior boundaries
* and compares the DOF indices on them with the dof indices of the boundarys
......
AMDiS/src/parallel/StdMpi.cc
View file @ dfeb9e9e
......@@ -83,6 +83,20 @@ namespace AMDiS {
return size;
}
int intSizeOf(std::map<BoundaryType, std::map<DegreeOfFreedom, DegreeOfFreedom> > &data)
{
int size = 1;
for (std::map<BoundaryType, std::map<DegreeOfFreedom, DegreeOfFreedom> >::iterator it = data.begin();
it != data.end(); ++it) {
size += 2 + it->second.size() * 2;
}
MSG("RET SIZE = %d\n", size);
return size;
}
void makeBuf(int &data, int *buf)
{
buf[0] = data;
......@@ -322,4 +336,48 @@ namespace AMDiS {
}
}
void makeBuf(std::map<BoundaryType, std::map<DegreeOfFreedom, DegreeOfFreedom> > &data, int *buf)
{
buf[0] = data.size();
int counter = 1;
for (std::map<BoundaryType, std::map<DegreeOfFreedom, DegreeOfFreedom> >::iterator it = data.begin();
it != data.end(); ++it) {
buf[counter++] = it->first;
buf[counter++] = it->second.size();
for (std::map<DegreeOfFreedom, DegreeOfFreedom>::iterator it2 = it->second.begin();
it2 != it->second.end(); ++it2) {
buf[counter++] = it2->first;
buf[counter++] = it2->second;
}
}
}
void makeFromBuf(std::map<BoundaryType, std::map<DegreeOfFreedom, DegreeOfFreedom> > &data, int *buf, int bufSize)
{
data.clear();
if (bufSize == 0)
return;
int counter = 1;
for (int i = 0; i < buf[0]; i++) {
BoundaryType bound = buf[counter++];
std::map<DegreeOfFreedom, DegreeOfFreedom> dofs;
int nDofs = buf[counter++];
for (int j = 0; j < nDofs; j++) {
DegreeOfFreedom dof0, dof1;
dof0 = buf[counter++];
dof1 = buf[counter++];
dofs[dof0] = dof1;
}
data[bound] = dofs;
}
TEST_EXIT(bufSize == counter)("Should not happen!\n");
}
}
AMDiS/src/parallel/StdMpi.h
View file @ dfeb9e9e
......@@ -55,6 +55,8 @@ namespace AMDiS {
int intSizeOf(std::vector<std::vector<double> > &data);
int intSizeOf(std::map<BoundaryType, std::map<DegreeOfFreedom, DegreeOfFreedom> > &data);
void makeBuf(int &data, int *buf);
void makeFromBuf(int &data, int *buf, int bufSize);
......@@ -98,7 +100,10 @@ namespace AMDiS {
void makeBuf(std::vector<std::vector<double> > &data, double *buf);
void makeFromBuf(std::vector<std::vector<double> > &data, double *buf, int bufSize);
void makeBuf(std::map<BoundaryType, std::map<DegreeOfFreedom, DegreeOfFreedom> > &data, int *buf);
void makeFromBuf(std::map<BoundaryType, std::map<DegreeOfFreedom, DegreeOfFreedom> > &data, int *buf, int bufSize);
template<typename SendT, typename RecvT=SendT>
......
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