File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 55688ms, 87.43% of 63694ms total Dropped 876 nodes (cum <= 318.47ms) flat flat% sum% cum cum% 0 0% 0% 63617ms 99.88% __libc_start_call_main 0 0% 0% 63617ms 99.88% __libc_start_main_impl 0 0% 0% 63617ms 99.88% _start 0 0% 0% 63600ms 99.85% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 63600ms 99.85% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 63600ms 99.85% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 63600ms 99.85% main 0 0% 0% 63567ms 99.80% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 63567ms 99.80% CxxTest::TestRunner::runTest (inline) 0 0% 0% 63567ms 99.80% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 63304ms 99.39% AbstractCellBasedSimulation::Solve 0 0% 0% 52426ms 82.31% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 52381ms 82.24% MeshBasedCellPopulation::Update 0 0% 0% 30807ms 48.37% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 30807ms 48.37% MeshBasedCellPopulation::TessellateIfNeeded 219ms 0.34% 0.34% 26914ms 42.26% VertexMesh::VertexMesh 0 0% 0.34% 17278ms 27.13% MutableMesh::ReMesh 531ms 0.83% 1.18% 13168ms 20.67% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.18% 12706ms 19.95% tetgen::tetrahedralize 1ms 0.0016% 1.18% 12567ms 19.73% tetgen::tetgenmesh::delaunizevertices 6ms 0.0094% 1.19% 12562ms 19.72% tetgen::tetgenmesh::incrflipdelaunay 583ms 0.92% 2.10% 11186ms 17.56% tetgen::tetgenmesh::lawson 22ms 0.035% 2.14% 10623ms 16.68% std::set::insert (inline) 3108ms 4.88% 7.02% 10240ms 16.08% std::_Rb_tree::_M_lower_bound (inline) 201ms 0.32% 7.33% 10101ms 15.86% std::_Rb_tree::_M_insert_unique 251ms 0.39% 7.73% 9513ms 14.94% std::_Rb_tree::find (inline) 394ms 0.62% 8.35% 9458ms 14.85% VertexElement::AddFace 0 0% 8.35% 8933ms 14.02% std::set::count (inline) 6825ms 10.72% 19.06% 6825ms 10.72% std::_Rb_tree_increment 102ms 0.16% 19.22% 6779ms 10.64% std::less::operator() (inline) 6737ms 10.58% 29.80% 6737ms 10.58% std::operator< (inline) 259ms 0.41% 30.21% 5864ms 9.21% std::_Rb_tree::_M_insert_ (inline) 0 0% 30.21% 5755ms 9.04% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 30.21% 5597ms 8.79% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0047% 30.21% 5569ms 8.74% AbstractNumericalMethod::ComputeForcesIncludingDamping 194ms 0.3% 30.51% 5443ms 8.55% operator new 1055ms 1.66% 32.17% 5173ms 8.12% __GI___libc_malloc 0 0% 32.17% 4976ms 7.81% AbstractCellPopulation::WriteResultsToFiles 1ms 0.0016% 32.17% 4633ms 7.27% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.0047% 32.18% 4624ms 7.26% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 48ms 0.075% 32.25% 4549ms 7.14% std::__new_allocator::allocate (inline) 7ms 0.011% 32.26% 4544ms 7.13% std::_Rb_tree::~_Rb_tree (inline) 1890ms 2.97% 35.23% 4536ms 7.12% std::_Rb_tree::_M_erase 0 0% 35.23% 4528ms 7.11% std::allocator_traits::allocate (inline) 0 0% 35.23% 4471ms 7.02% std::set::~set (inline) 16ms 0.025% 35.26% 4469ms 7.02% MeshBasedCellPopulation::SpringIterator::operator++ 1239ms 1.95% 37.20% 4369ms 6.86% std::_Rb_tree::_M_get_insert_unique_pos 6ms 0.0094% 37.21% 4334ms 6.80% std::set_intersection (inline) 236ms 0.37% 37.58% 4328ms 6.79% std::__set_intersection 33ms 0.052% 37.63% 4205ms 6.60% Node::AddElement 1153ms 1.81% 39.44% 4059ms 6.37% __GI___libc_free 3955ms 6.21% 45.65% 3955ms 6.21% std::_Rb_tree::_S_right (inline) 0 0% 45.65% 3919ms 6.15% VertexMesh::~VertexMesh 2735ms 4.29% 49.95% 3767ms 5.91% _int_malloc 245ms 0.38% 50.33% 3727ms 5.85% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 12ms 0.019% 50.35% 3721ms 5.84% TetrahedralMesh::ImportFromMesher 0 0% 50.35% 3633ms 5.70% std::_Rb_tree::_M_create_node (inline) 0 0% 50.35% 3604ms 5.66% std::_Rb_tree::_Alloc_node::operator() (inline) 180ms 0.28% 50.63% 3601ms 5.65% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 50.63% 3583ms 5.63% std::_Rb_tree::_M_get_node (inline) 125ms 0.2% 50.83% 3545ms 5.57% std::__new_allocator::deallocate (inline) 0 0% 50.83% 3522ms 5.53% std::allocator_traits::deallocate (inline) 120ms 0.19% 51.02% 3508ms 5.51% tetgen::tetgenmesh::insphere_sos 2ms 0.0031% 51.02% 3495ms 5.49% std::_Rb_tree_iterator::operator++ (inline) 2ms 0.0031% 51.02% 3492ms 5.48% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 3096ms 4.86% 55.88% 3379ms 5.31% tetgen::insphere 79ms 0.12% 56.01% 3174ms 4.98% MutableElement::AddNode 1181ms 1.85% 57.86% 2903ms 4.56% _int_free 205ms 0.32% 58.18% 2747ms 4.31% Node::~Node 176ms 0.28% 58.46% 2604ms 4.09% tetgen::tetgenmesh::flip23 222ms 0.35% 58.81% 2521ms 3.96% VertexMesh::Clear 2090ms 3.28% 62.09% 2090ms 3.28% std::_Rb_tree_insert_and_rebalance 0 0% 62.09% 1868ms 2.93% std::_Rb_tree::_M_drop_node (inline) 1ms 0.0016% 62.09% 1857ms 2.92% Element::Element 0 0% 62.09% 1850ms 2.90% std::_Rb_tree::_M_put_node (inline) 164ms 0.26% 62.35% 1844ms 2.90% tetgen::tetgenmesh::flip32 1830ms 2.87% 65.22% 1830ms 2.87% Node::GetIndex 1103ms 1.73% 66.95% 1713ms 2.69% malloc_consolidate 17ms 0.027% 66.98% 1689ms 2.65% std::_Vector_base::_M_deallocate (inline) 0 0% 66.98% 1574ms 2.47% std::vector::~vector (inline) 2ms 0.0031% 66.98% 1526ms 2.40% Element::RegisterWithNodes (inline) 223ms 0.35% 67.33% 1518ms 2.38% TetrahedralMesh::Clear 0 0% 67.33% 1510ms 2.37% std::_Vector_base::~_Vector_base (inline) 6ms 0.0094% 67.34% 1486ms 2.33% _int_free_maybe_consolidate 1307ms 2.05% 69.40% 1391ms 2.18% tetgen::orient3d 1293ms 2.03% 71.43% 1293ms 2.03% unlink_chunk 161ms 0.25% 71.68% 1269ms 1.99% tetgen::tetgenmesh::enqueueflipface 62ms 0.097% 71.78% 1262ms 1.98% std::map::operator[] 0 0% 71.78% 1223ms 1.92% VoronoiDataWriter::Visit 40ms 0.063% 71.84% 1171ms 1.84% tetgen::tetgenmesh::locate 48ms 0.075% 71.91% 1139ms 1.79% std::vector::_M_realloc_insert 0 0% 71.91% 1138ms 1.79% std::_Rb_tree::lower_bound (inline) 0 0% 71.91% 1138ms 1.79% std::map::lower_bound (inline) 2ms 0.0031% 71.92% 1134ms 1.78% VertexMesh::GenerateVerticesFromElementCircumcentres 85ms 0.13% 72.05% 1096ms 1.72% tetgen::tetgenmesh::preciselocate 3ms 0.0047% 72.06% 948ms 1.49% std::_Vector_base::_M_allocate (inline) 784ms 1.23% 73.29% 933ms 1.46% AbstractElement::GetNodeGlobalIndex 110ms 0.17% 73.46% 925ms 1.45% std::vector::push_back (inline) 883ms 1.39% 74.85% 883ms 1.39% tetgen::tetgenmesh::triface::triface 2ms 0.0031% 74.85% 834ms 1.31% TetrahedralMesh::RefreshJacobianCachedData 6ms 0.0094% 74.86% 742ms 1.16% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.0016% 74.86% 735ms 1.15% AbstractTwoBodyInteractionForce::AddForceContribution 387ms 0.61% 75.47% 734ms 1.15% tetgen::tetgenmesh::fnextself 298ms 0.47% 75.93% 725ms 1.14% AbstractElement::GetNodeLocation 21ms 0.033% 75.97% 697ms 1.09% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 696ms 1.09% 77.06% 696ms 1.09% tetgen::tetgenmesh::oppo 16ms 0.025% 77.09% 690ms 1.08% AbstractTetrahedralElement::CalculateJacobian 676ms 1.06% 78.15% 676ms 1.06% Node::rGetLocation 24ms 0.038% 78.18% 675ms 1.06% boost::numeric::ublas::vector_assign (inline) 669ms 1.05% 79.24% 669ms 1.05% [libchaste_mesh.so] 5ms 0.0079% 79.24% 645ms 1.01% boost::numeric::ublas::c_vector::c_vector (inline) 611ms 0.96% 80.20% 611ms 0.96% tetgen::tetgenmesh::triface::operator= 50ms 0.079% 80.28% 599ms 0.94% __atan2 592ms 0.93% 81.21% 592ms 0.93% AbstractElement::IsDeleted 19ms 0.03% 81.24% 578ms 0.91% Element::CalculateCircumsphere 0 0% 81.24% 576ms 0.9% std::set::find (inline) 438ms 0.69% 81.93% 549ms 0.86% __ieee754_atan2_fma 0 0% 81.93% 531ms 0.83% std::insert_iterator::operator= (inline) 519ms 0.81% 82.74% 520ms 0.82% std::vector::size (inline) 57ms 0.089% 82.83% 507ms 0.8% AbstractTetrahedralElement::RefreshJacobian 46ms 0.072% 82.90% 491ms 0.77% tetgen::tetgenmesh::enext2fnext 47ms 0.074% 82.98% 475ms 0.75% tetgen::tetgenmesh::enextfnext 0 0% 82.98% 470ms 0.74% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 82.98% 455ms 0.71% boost::numeric::ublas::inner_prod (inline) 6ms 0.0094% 82.99% 450ms 0.71% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 290ms 0.46% 83.44% 446ms 0.7% tetgen::tetgenmesh::sym 23ms 0.036% 83.48% 444ms 0.7% boost::numeric::ublas::vector_scalar_binary::evaluate 20ms 0.031% 83.51% 443ms 0.7% VertexMesh::CalculateUnitNormalToFaceWithArea 9ms 0.014% 83.52% 428ms 0.67% CellPropertyCollection::GetPropertiesType (inline) 124ms 0.19% 83.72% 419ms 0.66% boost::numeric::ublas::indexing_vector_assign 242ms 0.38% 84.10% 404ms 0.63% AbstractTetrahedralMesh::GetElement 3ms 0.0047% 84.10% 404ms 0.63% Cell::GetCellId 15ms 0.024% 84.13% 399ms 0.63% std::_Rb_tree_iterator::operator-- (inline) 0 0% 84.13% 397ms 0.62% VertexMeshWriter::WriteVtkUsingMesh 5ms 0.0079% 84.14% 390ms 0.61% boost::numeric::ublas::c_vector::operator= (inline) 98ms 0.15% 84.29% 388ms 0.61% __dynamic_cast 20ms 0.031% 84.32% 387ms 0.61% tetgen::tetgenmesh::queue::push 284ms 0.45% 84.77% 386ms 0.61% tetgen::tetgenmesh::bond 382ms 0.6% 85.37% 382ms 0.6% boost::numeric::ublas::c_vector::operator() 376ms 0.59% 85.96% 376ms 0.59% tetgen::tetgenmesh::org 174ms 0.27% 86.23% 371ms 0.58% boost::numeric::ublas::vector_inner_prod::apply (inline) 256ms 0.4% 86.63% 364ms 0.57% tetgen::tetgenmesh::link::add 357ms 0.56% 87.19% 357ms 0.56% std::_Rb_tree_decrement 0 0% 87.19% 355ms 0.56% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 9ms 0.014% 87.21% 345ms 0.54% std::vector::insert (inline) 2ms 0.0031% 87.21% 341ms 0.54% AbstractCellProperty::IsSubType (inline) 5ms 0.0079% 87.22% 338ms 0.53% VertexElement::~VertexElement 132ms 0.21% 87.42% 330ms 0.52% Inverse 4ms 0.0063% 87.43% 328ms 0.51% AbstractTetrahedralElement::AbstractTetrahedralElement