Chaste  Release::2018.1
DistanceMapCalculator.cpp
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35 
36 #include "DistanceMapCalculator.hpp"
37 #include "DistributedTetrahedralMesh.hpp" // For dynamic cast
38 
39 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
42  : mrMesh(rMesh),
43  mWorkOnEntireMesh(true),
44  mNumHalosPerProcess(nullptr),
45  mRoundCounter(0u),
46  mPopCounter(0u),
47  mTargetNodeIndex(UINT_MAX),
48  mSingleTarget(false)
49 {
50  mNumNodes = mrMesh.GetNumNodes();
51 
53  if (PetscTools::IsSequential() || p_distributed_mesh == nullptr)
54  {
55  // It's a non-distributed mesh
56  mLo = 0;
57  mHi = mNumNodes;
58  }
59  else
60  {
61  // It's a parallel (distributed) mesh (p_parallel_mesh is non-null and we are running in parallel)
62  mWorkOnEntireMesh = false;
63  mLo = mrMesh.GetDistributedVectorFactory()->GetLow();
64  mHi = mrMesh.GetDistributedVectorFactory()->GetHigh();
65 
66  // Get local halo information
67  p_distributed_mesh->GetHaloNodeIndices(mHaloNodeIndices);
68 
69  // Share information on the number of halo nodes
70  unsigned my_size = mHaloNodeIndices.size();
72  MPI_Allgather(&my_size, 1, MPI_UNSIGNED, mNumHalosPerProcess, 1, MPI_UNSIGNED, PETSC_COMM_WORLD);
73  }
74 }
75 
76 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
78  const std::vector<unsigned>& rSourceNodeIndices,
79  std::vector<double>& rNodeDistances)
80 {
81  rNodeDistances.resize(mNumNodes);
82  for (unsigned index=0; index<mNumNodes; index++)
83  {
84  rNodeDistances[index] = DBL_MAX;
85  }
86  assert(mActivePriorityNodeIndexQueue.empty());
87 
88  if (mSingleTarget)
89  {
90  assert(rSourceNodeIndices.size() == 1);
91  unsigned source_node_index = rSourceNodeIndices[0];
92 
93  // We need to make sure this is local, so that we can use the geometry
94  if (mLo<=source_node_index && source_node_index<mHi)
95  {
96  double heuristic_correction = norm_2(mrMesh.GetNode(source_node_index)->rGetLocation()-mTargetNodePoint);
97  PushLocal(heuristic_correction, source_node_index);
98  rNodeDistances[source_node_index] = heuristic_correction;
99  }
100  }
101  else
102  {
103  for (unsigned source_index=0; source_index<rSourceNodeIndices.size(); source_index++)
104  {
105  unsigned source_node_index = rSourceNodeIndices[source_index];
106  PushLocal(0.0, source_node_index);
107  rNodeDistances[source_node_index] = 0.0;
108  }
109  }
110 
111  bool non_empty_queue = true;
112  mRoundCounter = 0;
113  mPopCounter = 0;
114  while (non_empty_queue)
115  {
116  bool termination = WorkOnLocalQueue(rNodeDistances);
117 
118  // Sanity - check that we aren't doing this very many times
119  if (mRoundCounter++ > 10 * PetscTools::GetNumProcs())
120  {
121  // This line will be hit if there's a parallel distributed mesh with a really bad partition
123  }
124  if (mSingleTarget && PetscTools::ReplicateBool(termination))
125  {
126  // A single process found the target already
127  break;
128  }
129  non_empty_queue = UpdateQueueFromRemote(rNodeDistances);
130  }
131 
132  if (mWorkOnEntireMesh == false)
133  {
134  // Update all processes with the best values from everywhere
135  // Take a local copy
136  std::vector<double> local_distances = rNodeDistances;
137 
138  // Share it back into the vector
139  MPI_Allreduce( &local_distances[0], &rNodeDistances[0], mNumNodes, MPI_DOUBLE, MPI_MIN, PETSC_COMM_WORLD);
140  }
141 }
142 
143 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
145 {
146  if (mWorkOnEntireMesh)
147  {
148  // This update does nowt
149  return !mActivePriorityNodeIndexQueue.empty();
150  }
151  for (unsigned bcast_process=0; bcast_process<PetscTools::GetNumProcs(); bcast_process++)
152  {
153  // Process packs cart0/cart1/...euclid/index into a 1-d array
154  double* dist_exchange = new double[ mNumHalosPerProcess[bcast_process] ];
155  unsigned* index_exchange = new unsigned[ mNumHalosPerProcess[bcast_process] ];
156  if (PetscTools::GetMyRank() == bcast_process)
157  {
158  // Broadcaster fills the array
159  for (unsigned index=0; index<mHaloNodeIndices.size();index++)
160  {
161  dist_exchange[index] = rNodeDistances[mHaloNodeIndices[index]];
162  index_exchange[index] = mHaloNodeIndices[index];
163  }
164  }
165 
166  /*
167  * Broadcast - this is can be done by casting indices to double and
168  * packing everything into a single array. That would be better for
169  * latency, but this is probably more readable.
170  */
171  MPI_Bcast(dist_exchange, mNumHalosPerProcess[bcast_process], MPI_DOUBLE,
172  bcast_process, PETSC_COMM_WORLD);
173  MPI_Bcast(index_exchange, mNumHalosPerProcess[bcast_process], MPI_UNSIGNED,
174  bcast_process, PETSC_COMM_WORLD);
175  if (PetscTools::GetMyRank() != bcast_process)
176  {
177  // Receiving process take updates
178  for (unsigned index=0; index<mNumHalosPerProcess[bcast_process];index++)
179  {
180  unsigned global_index=index_exchange[index];
181  // Is it a better answer?
182  if (dist_exchange[index] < rNodeDistances[global_index]*(1.0-2*DBL_EPSILON) )
183  {
184  // Copy across - this may be unnecessary when PushLocal isn't going to push because it's not local
185  rNodeDistances[global_index] = dist_exchange[index];
186  PushLocal(rNodeDistances[global_index], global_index);
187  }
188  }
189  }
190  delete [] dist_exchange;
191  delete [] index_exchange;
192  }
193  // Is any queue non-empty?
194  bool non_empty_queue = PetscTools::ReplicateBool(!mActivePriorityNodeIndexQueue.empty());
195  return(non_empty_queue);
196 }
197 
198 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
200 {
201  unsigned pop_stop = mNumNodes/(PetscTools::GetNumProcs()*20);
202  while (!mActivePriorityNodeIndexQueue.empty())
203  {
204  // Get the next index in the queue
205  unsigned current_node_index = mActivePriorityNodeIndexQueue.top().second;
206  double distance_when_queued = -mActivePriorityNodeIndexQueue.top().first;
207  mActivePriorityNodeIndexQueue.pop();
208 
209  // Only act on nodes which haven't been acted on already
210  // (It's possible that a better distance has been found and already been dealt with)
211  if (distance_when_queued == rNodeDistances[current_node_index])
212  {
213  mPopCounter++;
214  Node<SPACE_DIM>* p_current_node = mrMesh.GetNode(current_node_index);
215  double current_heuristic = 0.0;
216  if (mSingleTarget)
217  {
218  current_heuristic=norm_2(p_current_node->rGetLocation()-mTargetNodePoint);
219  }
220 
221  // Loop over the elements containing the given node
222  for (typename Node<SPACE_DIM>::ContainingElementIterator element_iterator = p_current_node->ContainingElementsBegin();
223  element_iterator != p_current_node->ContainingElementsEnd();
224  ++element_iterator)
225  {
226  // Get a pointer to the container element
227  Element<ELEMENT_DIM, SPACE_DIM>* p_containing_element = mrMesh.GetElement(*element_iterator);
228 
229  // Loop over the nodes of the element
230  for (unsigned node_local_index=0;
231  node_local_index<p_containing_element->GetNumNodes();
232  node_local_index++)
233  {
234  Node<SPACE_DIM>* p_neighbour_node = p_containing_element->GetNode(node_local_index);
235  unsigned neighbour_node_index = p_neighbour_node->GetIndex();
236 
237  // Avoid revisiting the active node
238  if (neighbour_node_index != current_node_index)
239  {
240 
241  double neighbour_heuristic=0.0;
242  if (mSingleTarget)
243  {
244  neighbour_heuristic=norm_2(p_neighbour_node->rGetLocation()-mTargetNodePoint);
245  }
246  // Test if we have found a shorter path from the source to the neighbour through current node
247  double updated_distance = rNodeDistances[current_node_index] +
248  norm_2(p_neighbour_node->rGetLocation() - p_current_node->rGetLocation())
249  - current_heuristic + neighbour_heuristic;
250  if (updated_distance < rNodeDistances[neighbour_node_index] * (1.0-2*DBL_EPSILON))
251  {
252  rNodeDistances[neighbour_node_index] = updated_distance;
253  PushLocal(updated_distance, neighbour_node_index);
254  }
255  }
256  }
257  }
258  if (mSingleTarget)
259  {
260  if (current_node_index == mTargetNodeIndex)
261  {
262  // Premature termination if there is a single goal in mind (and we found it)
263  return true;
264  }
265  if (mPopCounter%pop_stop == 0)
266  {
267  // Premature termination -- in case the work has been done
268  return false;
269  }
270  }
271  }
272  }
273  return false;
274 }
275 
276 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
277 double DistanceMapCalculator<ELEMENT_DIM, SPACE_DIM>::SingleDistance(unsigned sourceNodeIndex, unsigned targetNodeIndex)
278 {
279  std::vector<unsigned> source_node_index_vector;
280  source_node_index_vector.push_back(sourceNodeIndex);
281 
282  // We are re-using the mCachedDistances vector...
283  mTargetNodeIndex = targetNodeIndex; // For premature termination
284  mSingleTarget = true;
285 
286  // Set up information on target (for A* guidance)
287  c_vector<double, SPACE_DIM> target_point = zero_vector<double>(SPACE_DIM);
288  if (mrMesh.GetDistributedVectorFactory()->IsGlobalIndexLocal(mTargetNodeIndex))
289  {
290  // Owner of target node sets target_point (others have zero)
291  target_point = mrMesh.GetNode(mTargetNodeIndex)->rGetLocation();
292  }
293 
294  // Communicate for wherever to everyone
295  MPI_Allreduce(&target_point[0], &mTargetNodePoint[0], SPACE_DIM, MPI_DOUBLE, MPI_SUM, PETSC_COMM_WORLD);
296 
297  //mTargetNodePoint;
298  std::vector<double> distances;
299  ComputeDistanceMap(source_node_index_vector, distances);
300 
302 
303  // Reset target, so we don't terminate early next time.
304  mSingleTarget = false;
305 
306  // Make sure that there isn't a non-empty queue from a previous calculation
307  if (!mActivePriorityNodeIndexQueue.empty())
308  {
309  mActivePriorityNodeIndexQueue = std::priority_queue<std::pair<double, unsigned> >();
310  }
311 
312  return distances[targetNodeIndex];
313 }
314 
315 // Explicit instantiation
316 template class DistanceMapCalculator<1, 1>;
317 template class DistanceMapCalculator<1, 2>;
318 template class DistanceMapCalculator<2, 2>;
319 template class DistanceMapCalculator<1, 3>;
320 //template class DistanceMapCalculator<2, 3>;
321 template class DistanceMapCalculator<3, 3>;
Definition: Node.hpp:58
static bool ReplicateBool(bool flag)
Definition: PetscTools.cpp:186
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > & mrMesh
std::vector< unsigned > mHaloNodeIndices
void GetHaloNodeIndices(std::vector< unsigned > &rHaloIndices) const
#define NEVER_REACHED
Definition: Exception.hpp:206
Node< SPACE_DIM > * GetNode(unsigned localIndex) const
static bool IsSequential()
Definition: PetscTools.cpp:91
ContainingElementIterator ContainingElementsBegin() const
Definition: Node.hpp:485
unsigned GetNumNodes() const
bool UpdateQueueFromRemote(std::vector< double > &rNodeDistances)
const c_vector< double, SPACE_DIM > & rGetLocation() const
Definition: Node.cpp:139
bool WorkOnLocalQueue(std::vector< double > &rNodeDistances)
static unsigned GetNumProcs()
Definition: PetscTools.cpp:108
unsigned GetIndex() const
Definition: Node.cpp:158
static unsigned GetMyRank()
Definition: PetscTools.cpp:114
void ComputeDistanceMap(const std::vector< unsigned > &rSourceNodeIndices, std::vector< double > &rNodeDistances)
DistanceMapCalculator(AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)
ContainingElementIterator ContainingElementsEnd() const
Definition: Node.hpp:493
double SingleDistance(unsigned sourceNodeIndex, unsigned destinationNodeIndex)