File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 38636ms, 86.90% of 44462ms total Dropped 780 nodes (cum <= 222.31ms) flat flat% sum% cum cum% 0 0% 0% 44426ms 99.92% __libc_start_call_main 0 0% 0% 44426ms 99.92% __libc_start_main_impl 0 0% 0% 44426ms 99.92% _start 0 0% 0% 44411ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 44411ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 44411ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 44411ms 99.89% main 0 0% 0% 44375ms 99.80% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 44375ms 99.80% CxxTest::TestRunner::runTest (inline) 0 0% 0% 44375ms 99.80% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 44209ms 99.43% AbstractCellBasedSimulation::Solve 0 0% 0% 36884ms 82.96% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 36843ms 82.86% MeshBasedCellPopulation::Update 1ms 0.0022% 0.0022% 22885ms 51.47% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0.0022% 22885ms 51.47% MeshBasedCellPopulation::TessellateIfNeeded 225ms 0.51% 0.51% 20579ms 46.28% VertexMesh::VertexMesh 0 0% 0.51% 10843ms 24.39% MutableMesh::ReMesh 402ms 0.9% 1.41% 9806ms 22.05% TetrahedralMesh::EdgeIterator::operator++ 22ms 0.049% 1.46% 8416ms 18.93% std::set::insert (inline) 125ms 0.28% 1.74% 8003ms 18.00% std::_Rb_tree::_M_insert_unique 1ms 0.0022% 1.75% 7815ms 17.58% tetgen::tetrahedralize 3ms 0.0067% 1.75% 7727ms 17.38% tetgen::tetgenmesh::delaunizevertices 2ms 0.0045% 1.76% 7719ms 17.36% tetgen::tetgenmesh::incrflipdelaunay 184ms 0.41% 2.17% 7666ms 17.24% VertexElement::AddFace 2773ms 6.24% 8.41% 7522ms 16.92% std::_Rb_tree::_M_lower_bound (inline) 123ms 0.28% 8.68% 7147ms 16.07% std::_Rb_tree::find (inline) 341ms 0.77% 9.45% 6778ms 15.24% tetgen::tetgenmesh::lawson 0 0% 9.45% 6707ms 15.08% std::set::count (inline) 164ms 0.37% 9.82% 5255ms 11.82% operator new 230ms 0.52% 10.34% 5210ms 11.72% std::_Rb_tree::_M_insert_ (inline) 1469ms 3.30% 13.64% 5042ms 11.34% __GI___libc_malloc 58ms 0.13% 13.77% 4507ms 10.14% std::__new_allocator::allocate (inline) 0 0% 13.77% 4489ms 10.10% std::allocator_traits::allocate (inline) 4427ms 9.96% 23.73% 4427ms 9.96% std::_Rb_tree_increment 0 0% 23.73% 4336ms 9.75% OffLatticeSimulation::UpdateCellLocationsAndTopology 46ms 0.1% 23.83% 4211ms 9.47% std::less::operator() (inline) 4208ms 9.46% 33.30% 4208ms 9.46% std::operator< (inline) 1ms 0.0022% 33.30% 4197ms 9.44% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0045% 33.30% 4177ms 9.39% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 33.30% 3671ms 8.26% std::_Rb_tree::_M_create_node (inline) 0 0% 33.30% 3649ms 8.21% std::_Rb_tree::_M_get_node (inline) 0 0% 33.30% 3630ms 8.16% std::_Rb_tree::_Alloc_node::operator() (inline) 221ms 0.5% 33.80% 3513ms 7.90% std::__set_intersection 0 0% 33.80% 3513ms 7.90% std::set_intersection (inline) 565ms 1.27% 35.07% 3408ms 7.66% __GI___libc_free 5ms 0.011% 35.08% 3381ms 7.60% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 35.08% 3363ms 7.56% MeshBasedCellPopulation::UpdateNodePairs 2657ms 5.98% 41.06% 3255ms 7.32% _int_malloc 15ms 0.034% 41.09% 3246ms 7.30% MeshBasedCellPopulation::SpringIterator::operator++ 50ms 0.11% 41.20% 2987ms 6.72% std::__new_allocator::deallocate (inline) 0 0% 41.20% 2985ms 6.71% std::allocator_traits::deallocate (inline) 14ms 0.031% 41.24% 2931ms 6.59% std::_Rb_tree::~_Rb_tree (inline) 999ms 2.25% 43.48% 2927ms 6.58% std::_Rb_tree::_M_get_insert_unique_pos 775ms 1.74% 45.23% 2907ms 6.54% std::_Rb_tree::_M_erase 0 0% 45.23% 2907ms 6.54% std::set::~set (inline) 181ms 0.41% 45.63% 2887ms 6.49% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 45.63% 2867ms 6.45% AbstractCellPopulation::WriteResultsToFiles 1404ms 3.16% 48.79% 2828ms 6.36% _int_free 62ms 0.14% 48.93% 2820ms 6.34% Node::AddElement 2627ms 5.91% 54.84% 2627ms 5.91% std::_Rb_tree::_S_right (inline) 3ms 0.0067% 54.84% 2410ms 5.42% TetrahedralMesh::ImportFromMesher 0 0% 54.84% 2321ms 5.22% VertexMesh::~VertexMesh 57ms 0.13% 54.97% 2179ms 4.90% tetgen::tetgenmesh::insphere_sos 202ms 0.45% 55.43% 2162ms 4.86% std::_Rb_tree_iterator::operator++ (inline) 3ms 0.0067% 55.43% 2155ms 4.85% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1933ms 4.35% 59.78% 2103ms 4.73% tetgen::insphere 1ms 0.0022% 59.78% 2057ms 4.63% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 38ms 0.085% 59.87% 1940ms 4.36% MutableElement::AddNode 0 0% 59.87% 1766ms 3.97% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.87% 1736ms 3.90% std::_Rb_tree::_M_put_node (inline) 160ms 0.36% 60.23% 1569ms 3.53% tetgen::tetgenmesh::flip23 1560ms 3.51% 63.74% 1560ms 3.51% [libchaste_mesh.so] 4ms 0.009% 63.75% 1463ms 3.29% Element::Element 1419ms 3.19% 66.94% 1419ms 3.19% std::_Rb_tree_insert_and_rebalance 825ms 1.86% 68.79% 1386ms 3.12% malloc_consolidate 17ms 0.038% 68.83% 1347ms 3.03% Node::~Node 13ms 0.029% 68.86% 1261ms 2.84% std::_Vector_base::_M_deallocate (inline) 10ms 0.022% 68.88% 1260ms 2.83% VertexMesh::Clear 3ms 0.0067% 68.89% 1224ms 2.75% _int_free_maybe_consolidate 5ms 0.011% 68.90% 1221ms 2.75% Element::RegisterWithNodes (inline) 0 0% 68.90% 1171ms 2.63% std::vector::~vector (inline) 0 0% 68.90% 1144ms 2.57% std::_Vector_base::~_Vector_base (inline) 1101ms 2.48% 71.38% 1101ms 2.48% Node::GetIndex 1056ms 2.38% 73.75% 1099ms 2.47% tetgen::orient3d 133ms 0.3% 74.05% 1027ms 2.31% tetgen::tetgenmesh::flip32 927ms 2.08% 76.14% 927ms 2.08% unlink_chunk 31ms 0.07% 76.21% 908ms 2.04% std::vector::_M_realloc_insert 52ms 0.12% 76.32% 880ms 1.98% std::map::operator[] (partial-inline) 6ms 0.013% 76.34% 846ms 1.90% std::_Vector_base::_M_allocate (inline) 14ms 0.031% 76.37% 818ms 1.84% tetgen::tetgenmesh::locate 4ms 0.009% 76.38% 798ms 1.79% VertexMesh::GenerateVerticesFromElementCircumcentres 62ms 0.14% 76.52% 776ms 1.75% tetgen::tetgenmesh::preciselocate 54ms 0.12% 76.64% 754ms 1.70% std::vector::push_back (inline) 0 0% 76.64% 750ms 1.69% std::_Rb_tree::lower_bound (inline) 0 0% 76.64% 750ms 1.69% std::map::lower_bound (inline) 108ms 0.24% 76.88% 697ms 1.57% tetgen::tetgenmesh::enqueueflipface 5ms 0.011% 76.89% 662ms 1.49% TetrahedralMesh::Clear 0 0% 76.89% 658ms 1.48% VoronoiDataWriter::Visit 397ms 0.89% 77.79% 629ms 1.41% AbstractElement::GetNodeGlobalIndex 0 0% 77.79% 596ms 1.34% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.0022% 77.79% 593ms 1.33% AbstractTwoBodyInteractionForce::AddForceContribution 6ms 0.013% 77.80% 566ms 1.27% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 555ms 1.25% 79.05% 555ms 1.25% Node::rGetLocation 6ms 0.013% 79.06% 528ms 1.19% AbstractTetrahedralElement::CalculateInverseJacobian 244ms 0.55% 79.61% 513ms 1.15% AbstractElement::GetNodeLocation 5ms 0.011% 79.62% 489ms 1.10% AbstractTetrahedralElement::CalculateJacobian 0 0% 79.62% 438ms 0.99% std::set::find (inline) 429ms 0.96% 80.59% 429ms 0.96% tetgen::tetgenmesh::oppo 6ms 0.013% 80.60% 428ms 0.96% boost::numeric::ublas::vector_assign (inline) 11ms 0.025% 80.63% 414ms 0.93% boost::numeric::ublas::c_vector::c_vector (inline) 240ms 0.54% 81.17% 410ms 0.92% tetgen::tetgenmesh::sym 25ms 0.056% 81.22% 404ms 0.91% __atan2 0 0% 81.22% 404ms 0.91% std::insert_iterator::operator= (inline) 22ms 0.049% 81.27% 394ms 0.89% AbstractTetrahedralElement::RefreshJacobian 381ms 0.86% 82.13% 381ms 0.86% std::vector::size (inline) 337ms 0.76% 82.89% 377ms 0.85% __ieee754_atan2_fma 0 0% 82.89% 365ms 0.82% std::_Rb_tree::_M_insert_unique_ (inline) 8ms 0.018% 82.90% 361ms 0.81% Element::CalculateCircumsphere 2ms 0.0045% 82.91% 351ms 0.79% Cell::GetCellId 11ms 0.025% 82.93% 341ms 0.77% CellPropertyCollection::GetPropertiesType (inline) 34ms 0.076% 83.01% 312ms 0.7% std::_Rb_tree_iterator::operator-- (inline) 0 0% 83.01% 273ms 0.61% VertexMeshWriter::WriteVtkUsingMesh 0 0% 83.01% 260ms 0.58% tcache_get (inline) 260ms 0.58% 83.59% 260ms 0.58% tcache_get_n (inline) 258ms 0.58% 84.18% 258ms 0.58% std::_Rb_tree_decrement 204ms 0.46% 84.63% 258ms 0.58% tetgen::tetgenmesh::fnextself 12ms 0.027% 84.66% 255ms 0.57% std::vector::insert (inline) 190ms 0.43% 85.09% 254ms 0.57% AbstractTetrahedralMesh::GetElement 23ms 0.052% 85.14% 252ms 0.57% tetgen::tetgenmesh::enext2fnext 0 0% 85.14% 251ms 0.56% boost::numeric::ublas::inner_prod (inline) 16ms 0.036% 85.18% 251ms 0.56% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 85.18% 251ms 0.56% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 245ms 0.55% 85.73% 245ms 0.55% AbstractElement::IsDeleted 0 0% 85.73% 242ms 0.54% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 73ms 0.16% 85.89% 238ms 0.54% __dynamic_cast 4ms 0.009% 85.90% 237ms 0.53% AbstractTetrahedralElement::AbstractTetrahedralElement 3ms 0.0067% 85.91% 232ms 0.52% boost::numeric::ublas::c_vector::operator= (inline) 88ms 0.2% 86.10% 231ms 0.52% Inverse 231ms 0.52% 86.62% 231ms 0.52% boost::numeric::ublas::c_vector::operator() 25ms 0.056% 86.68% 231ms 0.52% tetgen::tetgenmesh::enextfnext 45ms 0.1% 86.78% 226ms 0.51% boost::numeric::ublas::indexing_vector_assign 51ms 0.11% 86.90% 225ms 0.51% tetgen::tetgenmesh::queue::pop