File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 46647ms, 86.74% of 53778ms total Dropped 853 nodes (cum <= 268.89ms) flat flat% sum% cum cum% 0 0% 0% 53714ms 99.88% __libc_start_call_main 0 0% 0% 53714ms 99.88% __libc_start_main_impl 0 0% 0% 53714ms 99.88% _start 0 0% 0% 53698ms 99.85% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 53698ms 99.85% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 53698ms 99.85% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 53698ms 99.85% main 0 0% 0% 53662ms 99.78% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 53662ms 99.78% CxxTest::TestRunner::runTest (inline) 0 0% 0% 53662ms 99.78% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 53413ms 99.32% AbstractCellBasedSimulation::Solve 0 0% 0% 44764ms 83.24% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 44720ms 83.16% MeshBasedCellPopulation::Update 0 0% 0% 24958ms 46.41% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 24956ms 46.41% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 210ms 0.39% 0.39% 22243ms 41.36% VertexMesh::VertexMesh 0 0% 0.39% 16146ms 30.02% MutableMesh::ReMesh 0 0% 0.39% 12660ms 23.54% tetgen::tetrahedralize 1ms 0.0019% 0.39% 12510ms 23.26% tetgen::tetgenmesh::delaunizevertices 3ms 0.0056% 0.4% 12503ms 23.25% tetgen::tetgenmesh::incrflipdelaunay 554ms 1.03% 1.43% 11045ms 20.54% tetgen::tetgenmesh::lawson 585ms 1.09% 2.52% 10958ms 20.38% TetrahedralMesh::EdgeIterator::operator++ 27ms 0.05% 2.57% 9047ms 16.82% std::set::insert (inline) 311ms 0.58% 3.14% 8969ms 16.68% VertexElement::AddFace 2992ms 5.56% 8.71% 8532ms 15.87% std::_Rb_tree::_M_lower_bound (inline) 194ms 0.36% 9.07% 8519ms 15.84% std::_Rb_tree::_M_insert_unique 258ms 0.48% 9.55% 8053ms 14.97% std::_Rb_tree::find (inline) 0 0% 9.55% 7442ms 13.84% std::set::count (inline) 114ms 0.21% 9.76% 5432ms 10.10% std::less::operator() (inline) 5367ms 9.98% 19.74% 5367ms 9.98% std::operator< (inline) 292ms 0.54% 20.28% 5248ms 9.76% std::_Rb_tree::_M_insert_ (inline) 0 0% 20.28% 5017ms 9.33% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0019% 20.29% 4896ms 9.10% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0019% 20.29% 4862ms 9.04% AbstractNumericalMethod::ComputeForcesIncludingDamping 208ms 0.39% 20.67% 4420ms 8.22% operator new 1169ms 2.17% 22.85% 4139ms 7.70% __GI___libc_malloc 4086ms 7.60% 30.45% 4086ms 7.60% std::_Rb_tree_increment 0 0% 30.45% 3953ms 7.35% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.0074% 30.45% 3934ms 7.32% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 49ms 0.091% 30.54% 3895ms 7.24% std::__new_allocator::allocate (inline) 0 0% 30.54% 3865ms 7.19% std::allocator_traits::allocate (inline) 10ms 0.019% 30.56% 3841ms 7.14% std::_Rb_tree::~_Rb_tree (inline) 11ms 0.02% 30.58% 3838ms 7.14% MeshBasedCellPopulation::SpringIterator::operator++ 1376ms 2.56% 33.14% 3828ms 7.12% std::_Rb_tree::_M_erase 0 0% 33.14% 3786ms 7.04% std::set::~set (inline) 0 0% 33.14% 3491ms 6.49% AbstractCellPopulation::WriteResultsToFiles 112ms 0.21% 33.35% 3437ms 6.39% tetgen::tetgenmesh::insphere_sos 1188ms 2.21% 35.56% 3404ms 6.33% std::_Rb_tree::_M_get_insert_unique_pos 1052ms 1.96% 37.52% 3362ms 6.25% __GI___libc_free 3033ms 5.64% 43.16% 3313ms 6.16% tetgen::insphere 0 0% 43.16% 3157ms 5.87% std::_Rb_tree::_M_create_node (inline) 0 0% 43.16% 3132ms 5.82% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 43.16% 3130ms 5.82% std::_Rb_tree::_M_get_node (inline) 119ms 0.22% 43.38% 3046ms 5.66% std::__new_allocator::deallocate (inline) 0 0% 43.38% 3024ms 5.62% std::allocator_traits::deallocate (inline) 5ms 0.0093% 43.39% 2907ms 5.41% std::set_intersection (inline) 202ms 0.38% 43.76% 2902ms 5.40% std::__set_intersection 14ms 0.026% 43.79% 2735ms 5.09% TetrahedralMesh::ImportFromMesher 0 0% 43.79% 2727ms 5.07% VertexMesh::~VertexMesh 32ms 0.06% 43.85% 2723ms 5.06% Node::AddElement 186ms 0.35% 44.19% 2662ms 4.95% tetgen::tetgenmesh::flip23 2597ms 4.83% 49.02% 2597ms 4.83% std::_Rb_tree::_S_right (inline) 1995ms 3.71% 52.73% 2589ms 4.81% _int_malloc 4ms 0.0074% 52.74% 2340ms 4.35% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 207ms 0.38% 53.12% 2339ms 4.35% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1188ms 2.21% 55.33% 2308ms 4.29% _int_free 181ms 0.34% 55.67% 2230ms 4.15% std::_Rb_tree_const_iterator::operator++ (inline) 60ms 0.11% 55.78% 2151ms 4.00% MutableElement::AddNode 0 0% 55.78% 2139ms 3.98% std::_Rb_tree_iterator::operator++ (inline) 138ms 0.26% 56.04% 1985ms 3.69% Node::~Node 0 0% 56.04% 1926ms 3.58% std::_Rb_tree::_M_drop_node (inline) 0 0% 56.04% 1912ms 3.56% std::_Rb_tree::_M_put_node (inline) 1903ms 3.54% 59.58% 1903ms 3.54% std::_Rb_tree_insert_and_rebalance 137ms 0.25% 59.83% 1889ms 3.51% VertexMesh::Clear 142ms 0.26% 60.10% 1816ms 3.38% tetgen::tetgenmesh::flip32 1295ms 2.41% 62.50% 1388ms 2.58% tetgen::orient3d 7ms 0.013% 62.52% 1368ms 2.54% Element::Element 164ms 0.3% 62.82% 1318ms 2.45% tetgen::tetgenmesh::enqueueflipface 1266ms 2.35% 65.18% 1266ms 2.35% Node::GetIndex 35ms 0.065% 65.24% 1253ms 2.33% tetgen::tetgenmesh::locate 115ms 0.21% 65.45% 1168ms 2.17% tetgen::tetgenmesh::preciselocate 20ms 0.037% 65.49% 1132ms 2.10% std::_Vector_base::_M_deallocate (inline) 0 0% 65.49% 1085ms 2.02% std::vector::~vector (inline) 107ms 0.2% 65.69% 1075ms 2.00% TetrahedralMesh::Clear 77ms 0.14% 65.83% 1057ms 1.97% std::map::operator[] 654ms 1.22% 67.05% 1036ms 1.93% malloc_consolidate 7ms 0.013% 67.06% 1032ms 1.92% Element::RegisterWithNodes (inline) 54ms 0.1% 67.16% 994ms 1.85% std::vector::_M_realloc_insert 0 0% 67.16% 944ms 1.76% std::_Vector_base::~_Vector_base (inline) 0 0% 67.16% 928ms 1.73% VoronoiDataWriter::Visit 0 0% 67.16% 917ms 1.71% std::_Rb_tree::lower_bound (inline) 0 0% 67.16% 917ms 1.71% std::map::lower_bound (inline) 8ms 0.015% 67.18% 910ms 1.69% _int_free_maybe_consolidate 873ms 1.62% 68.80% 873ms 1.62% tetgen::tetgenmesh::triface::triface 3ms 0.0056% 68.81% 812ms 1.51% VertexMesh::GenerateVerticesFromElementCircumcentres 96ms 0.18% 68.99% 773ms 1.44% std::vector::push_back (inline) 769ms 1.43% 70.42% 769ms 1.43% unlink_chunk 2ms 0.0037% 70.42% 763ms 1.42% AbstractTwoBodyInteractionForce::AddForceContribution 13ms 0.024% 70.44% 746ms 1.39% boost::numeric::ublas::vector_assign (inline) 9ms 0.017% 70.46% 744ms 1.38% std::_Vector_base::_M_allocate (inline) 736ms 1.37% 71.83% 736ms 1.37% tetgen::tetgenmesh::oppo 0 0% 71.83% 730ms 1.36% TetrahedralMesh::RefreshJacobianCachedData 18ms 0.033% 71.86% 708ms 1.32% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 385ms 0.72% 72.58% 698ms 1.30% tetgen::tetgenmesh::fnextself 5ms 0.0093% 72.59% 690ms 1.28% AbstractTetrahedralElement::CalculateInverseJacobian 672ms 1.25% 73.84% 672ms 1.25% [libchaste_mesh.so] 6ms 0.011% 73.85% 670ms 1.25% boost::numeric::ublas::c_vector::c_vector (inline) 513ms 0.95% 74.80% 638ms 1.19% AbstractElement::GetNodeGlobalIndex 46ms 0.086% 74.89% 637ms 1.18% __atan2 17ms 0.032% 74.92% 618ms 1.15% AbstractTetrahedralElement::CalculateJacobian 608ms 1.13% 76.05% 608ms 1.13% tetgen::tetgenmesh::triface::operator= 0 0% 76.05% 606ms 1.13% std::set::find (inline) 476ms 0.89% 76.93% 590ms 1.10% __ieee754_atan2_fma 0 0% 76.93% 514ms 0.96% std::insert_iterator::operator= (inline) 195ms 0.36% 77.30% 512ms 0.95% AbstractElement::GetNodeLocation 503ms 0.94% 78.23% 503ms 0.94% boost::numeric::ublas::c_vector::operator() 0 0% 78.23% 497ms 0.92% boost::numeric::ublas::inner_prod (inline) 4ms 0.0074% 78.24% 494ms 0.92% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 32ms 0.06% 78.30% 490ms 0.91% boost::numeric::ublas::vector_scalar_binary::evaluate 27ms 0.05% 78.35% 483ms 0.9% Element::CalculateCircumsphere 341ms 0.63% 78.98% 482ms 0.9% tetgen::tetgenmesh::sym 45ms 0.084% 79.07% 473ms 0.88% tetgen::tetgenmesh::enextfnext 134ms 0.25% 79.32% 470ms 0.87% boost::numeric::ublas::indexing_vector_assign 0 0% 79.32% 465ms 0.86% std::_Rb_tree::_M_insert_unique_ (inline) 44ms 0.082% 79.40% 448ms 0.83% tetgen::tetgenmesh::enext2fnext 439ms 0.82% 80.21% 439ms 0.82% Node::rGetLocation 433ms 0.81% 81.02% 433ms 0.81% std::vector::size (inline) 4ms 0.0074% 81.03% 425ms 0.79% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.0074% 81.03% 422ms 0.78% Cell::GetCellId 25ms 0.046% 81.08% 419ms 0.78% VertexMesh::CalculateUnitNormalToFaceWithArea 40ms 0.074% 81.16% 416ms 0.77% AbstractTetrahedralElement::RefreshJacobian 165ms 0.31% 81.46% 407ms 0.76% boost::numeric::ublas::vector_inner_prod::apply (inline) 219ms 0.41% 81.87% 406ms 0.75% AbstractTetrahedralMesh::GetElement 4ms 0.0074% 81.88% 401ms 0.75% boost::numeric::ublas::c_vector::operator= (inline) 89ms 0.17% 82.04% 400ms 0.74% __dynamic_cast 0 0% 82.04% 399ms 0.74% VertexMeshWriter::WriteVtkUsingMesh 26ms 0.048% 82.09% 391ms 0.73% std::_Rb_tree_iterator::operator-- (inline) 46ms 0.086% 82.18% 371ms 0.69% boost::numeric::ublas::vector_reference::operator() (inline) 265ms 0.49% 82.67% 361ms 0.67% tetgen::tetgenmesh::bond 35ms 0.065% 82.73% 355ms 0.66% tetgen::tetgenmesh::queue::push 141ms 0.26% 83.00% 352ms 0.65% Inverse 346ms 0.64% 83.64% 346ms 0.64% tetgen::tetgenmesh::org 3ms 0.0056% 83.65% 342ms 0.64% AbstractCellProperty::IsSubType (inline) 3ms 0.0056% 83.65% 339ms 0.63% VertexElement::~VertexElement 339ms 0.63% 84.28% 339ms 0.63% std::_Rb_tree_decrement 11ms 0.02% 84.30% 335ms 0.62% std::vector::insert (inline) 2ms 0.0037% 84.31% 329ms 0.61% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 84.31% 323ms 0.6% tcache_get (inline) 323ms 0.6% 84.91% 323ms 0.6% tcache_get_n (inline) 238ms 0.44% 85.35% 319ms 0.59% tetgen::tetgenmesh::link::add 236ms 0.44% 85.79% 292ms 0.54% boost::numeric::ublas::c_matrix::operator() 288ms 0.54% 86.32% 288ms 0.54% AbstractElement::IsDeleted 0 0% 86.32% 286ms 0.53% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 34ms 0.063% 86.39% 280ms 0.52% tetgen::insphereadapt 64ms 0.12% 86.51% 278ms 0.52% tetgen::tetgenmesh::queue::pop 126ms 0.23% 86.74% 276ms 0.51% Determinant