File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 47692ms, 86.01% of 55447ms total Dropped 851 nodes (cum <= 277.24ms) flat flat% sum% cum cum% 0 0% 0% 55390ms 99.90% __libc_start_call_main 0 0% 0% 55390ms 99.90% __libc_start_main_impl 0 0% 0% 55390ms 99.90% _start 0 0% 0% 55375ms 99.87% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 55375ms 99.87% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 55375ms 99.87% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 55375ms 99.87% main 0 0% 0% 55337ms 99.80% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 55337ms 99.80% CxxTest::TestRunner::runTest (inline) 0 0% 0% 55337ms 99.80% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 55078ms 99.33% AbstractCellBasedSimulation::Solve 0 0% 0% 46706ms 84.24% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 46665ms 84.16% MeshBasedCellPopulation::Update 0 0% 0% 26203ms 47.26% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 26202ms 47.26% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 168ms 0.3% 0.3% 23290ms 42.00% VertexMesh::VertexMesh 0 0% 0.3% 16812ms 30.32% MutableMesh::ReMesh 1ms 0.0018% 0.3% 12951ms 23.36% tetgen::tetrahedralize 1ms 0.0018% 0.31% 12803ms 23.09% tetgen::tetgenmesh::delaunizevertices 5ms 0.009% 0.32% 12797ms 23.08% tetgen::tetgenmesh::incrflipdelaunay 548ms 0.99% 1.30% 11349ms 20.47% tetgen::tetgenmesh::lawson 604ms 1.09% 2.39% 11167ms 20.14% TetrahedralMesh::EdgeIterator::operator++ 30ms 0.054% 2.45% 9448ms 17.04% std::set::insert (inline) 213ms 0.38% 2.83% 8929ms 16.10% std::_Rb_tree::_M_insert_unique 349ms 0.63% 3.46% 8864ms 15.99% VertexElement::AddFace 3090ms 5.57% 9.03% 8450ms 15.24% std::_Rb_tree::_M_lower_bound (inline) 253ms 0.46% 9.49% 7926ms 14.29% std::_Rb_tree::find (inline) 0 0% 9.49% 7383ms 13.32% std::set::count (inline) 274ms 0.49% 9.98% 5397ms 9.73% std::_Rb_tree::_M_insert_ (inline) 116ms 0.21% 10.19% 5246ms 9.46% std::less::operator() (inline) 5196ms 9.37% 19.56% 5196ms 9.37% std::operator< (inline) 0 0% 19.56% 4976ms 8.97% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 19.56% 4866ms 8.78% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.0072% 19.57% 4845ms 8.74% AbstractNumericalMethod::ComputeForcesIncludingDamping 213ms 0.38% 19.96% 4668ms 8.42% operator new 1082ms 1.95% 21.91% 4376ms 7.89% __GI___libc_malloc 4356ms 7.86% 29.76% 4356ms 7.86% std::_Rb_tree_increment 38ms 0.069% 29.83% 4039ms 7.28% std::__new_allocator::allocate (inline) 0 0% 29.83% 4015ms 7.24% std::allocator_traits::allocate (inline) 1ms 0.0018% 29.83% 3992ms 7.20% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.011% 29.84% 3991ms 7.20% std::_Rb_tree::~_Rb_tree (inline) 1457ms 2.63% 32.47% 3985ms 7.19% std::_Rb_tree::_M_erase 3ms 0.0054% 32.48% 3980ms 7.18% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 32.48% 3947ms 7.12% std::set::~set (inline) 16ms 0.029% 32.51% 3853ms 6.95% MeshBasedCellPopulation::SpringIterator::operator++ 1208ms 2.18% 34.69% 3653ms 6.59% std::_Rb_tree::_M_get_insert_unique_pos 103ms 0.19% 34.87% 3543ms 6.39% tetgen::tetgenmesh::insphere_sos 1107ms 2.00% 36.87% 3517ms 6.34% __GI___libc_free 3ms 0.0054% 36.87% 3472ms 6.26% std::set_intersection (inline) 221ms 0.4% 37.27% 3469ms 6.26% std::__set_intersection 3134ms 5.65% 42.92% 3421ms 6.17% tetgen::insphere 0 0% 42.92% 3272ms 5.90% std::_Rb_tree::_M_create_node (inline) 0 0% 42.92% 3253ms 5.87% AbstractCellPopulation::WriteResultsToFiles 0 0% 42.92% 3249ms 5.86% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 42.92% 3244ms 5.85% std::_Rb_tree::_M_get_node (inline) 34ms 0.061% 42.99% 3226ms 5.82% Node::AddElement 6ms 0.011% 43.00% 3105ms 5.60% TetrahedralMesh::ImportFromMesher 126ms 0.23% 43.22% 3100ms 5.59% std::__new_allocator::deallocate (inline) 0 0% 43.22% 3076ms 5.55% std::allocator_traits::deallocate (inline) 2244ms 4.05% 47.27% 2976ms 5.37% _int_malloc 0 0% 47.27% 2936ms 5.30% VertexMesh::~VertexMesh 2922ms 5.27% 52.54% 2922ms 5.27% std::_Rb_tree::_S_right (inline) 201ms 0.36% 52.90% 2764ms 4.98% std::_Rb_tree_const_iterator::operator++ (inline) 219ms 0.39% 53.30% 2735ms 4.93% tetgen::tetgenmesh::flip23 67ms 0.12% 53.42% 2563ms 4.62% MutableElement::AddNode 1181ms 2.13% 55.55% 2407ms 4.34% _int_free 144ms 0.26% 55.81% 2202ms 3.97% Node::~Node 4ms 0.0072% 55.82% 2156ms 3.89% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 197ms 0.36% 56.17% 2089ms 3.77% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 169ms 0.3% 56.48% 2007ms 3.62% VertexMesh::Clear 1946ms 3.51% 59.99% 1946ms 3.51% std::_Rb_tree_insert_and_rebalance 0 0% 59.99% 1900ms 3.43% std::_Rb_tree_iterator::operator++ (inline) 0 0% 59.99% 1894ms 3.42% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.99% 1880ms 3.39% std::_Rb_tree::_M_put_node (inline) 141ms 0.25% 60.24% 1858ms 3.35% tetgen::tetgenmesh::flip32 7ms 0.013% 60.25% 1461ms 2.63% Element::Element 1327ms 2.39% 62.65% 1423ms 2.57% tetgen::orient3d 187ms 0.34% 62.98% 1385ms 2.50% tetgen::tetgenmesh::enqueueflipface 199ms 0.36% 63.34% 1332ms 2.40% TetrahedralMesh::Clear 1241ms 2.24% 65.58% 1241ms 2.24% Node::GetIndex 36ms 0.065% 65.64% 1214ms 2.19% tetgen::tetgenmesh::locate 16ms 0.029% 65.67% 1212ms 2.19% std::_Vector_base::_M_deallocate (inline) 758ms 1.37% 67.04% 1196ms 2.16% malloc_consolidate 8ms 0.014% 67.06% 1158ms 2.09% Element::RegisterWithNodes (inline) 0 0% 67.06% 1137ms 2.05% std::vector::~vector (inline) 101ms 0.18% 67.24% 1129ms 2.04% tetgen::tetgenmesh::preciselocate 66ms 0.12% 67.36% 1087ms 1.96% std::map::operator[] 1ms 0.0018% 67.36% 1045ms 1.88% std::_Vector_base::~_Vector_base (inline) 2ms 0.0036% 67.36% 1013ms 1.83% _int_free_maybe_consolidate 52ms 0.094% 67.46% 991ms 1.79% std::vector::_M_realloc_insert 0 0% 67.46% 967ms 1.74% std::_Rb_tree::lower_bound (inline) 0 0% 67.46% 967ms 1.74% std::map::lower_bound (inline) 951ms 1.72% 69.17% 951ms 1.72% tetgen::tetgenmesh::triface::triface 930ms 1.68% 70.85% 930ms 1.68% unlink_chunk 2ms 0.0036% 70.85% 865ms 1.56% VoronoiDataWriter::Visit 3ms 0.0054% 70.86% 828ms 1.49% VertexMesh::GenerateVerticesFromElementCircumcentres 669ms 1.21% 72.06% 821ms 1.48% AbstractElement::GetNodeGlobalIndex 395ms 0.71% 72.78% 778ms 1.40% tetgen::tetgenmesh::fnextself 6ms 0.011% 72.79% 777ms 1.40% std::_Vector_base::_M_allocate (inline) 98ms 0.18% 72.96% 774ms 1.40% std::vector::push_back (inline) 0 0% 72.96% 734ms 1.32% TetrahedralMesh::RefreshJacobianCachedData 25ms 0.045% 73.01% 720ms 1.30% boost::numeric::ublas::vector_assign (inline) 0 0% 73.01% 715ms 1.29% AbstractTwoBodyInteractionForce::AddForceContribution 704ms 1.27% 74.28% 704ms 1.27% tetgen::tetgenmesh::oppo 677ms 1.22% 75.50% 677ms 1.22% [libchaste_mesh.so] 5ms 0.009% 75.51% 675ms 1.22% AbstractTetrahedralElement::CalculateInverseJacobian 8ms 0.014% 75.52% 670ms 1.21% boost::numeric::ublas::c_vector::c_vector (inline) 14ms 0.025% 75.55% 658ms 1.19% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 614ms 1.11% 76.66% 614ms 1.11% tetgen::tetgenmesh::triface::operator= 44ms 0.079% 76.73% 612ms 1.10% __atan2 19ms 0.034% 76.77% 600ms 1.08% AbstractTetrahedralElement::CalculateJacobian 435ms 0.78% 77.55% 568ms 1.02% __ieee754_atan2_fma 0 0% 77.55% 542ms 0.98% std::set::find (inline) 235ms 0.42% 77.98% 521ms 0.94% AbstractElement::GetNodeLocation 0 0% 77.98% 515ms 0.93% std::insert_iterator::operator= (inline) 43ms 0.078% 78.05% 498ms 0.9% tetgen::tetgenmesh::enext2fnext 41ms 0.074% 78.13% 495ms 0.89% tetgen::tetgenmesh::enextfnext 0 0% 78.13% 466ms 0.84% boost::numeric::ublas::inner_prod (inline) 6ms 0.011% 78.14% 463ms 0.84% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 123ms 0.22% 78.36% 462ms 0.83% boost::numeric::ublas::indexing_vector_assign 462ms 0.83% 79.19% 462ms 0.83% std::vector::size (inline) 0 0% 79.19% 460ms 0.83% std::_Rb_tree::_M_insert_unique_ (inline) 23ms 0.041% 79.24% 457ms 0.82% Element::CalculateCircumsphere 30ms 0.054% 79.29% 457ms 0.82% boost::numeric::ublas::vector_scalar_binary::evaluate 449ms 0.81% 80.10% 449ms 0.81% Node::rGetLocation 18ms 0.032% 80.13% 443ms 0.8% tetgen::tetgenmesh::queue::push 272ms 0.49% 80.62% 432ms 0.78% tetgen::tetgenmesh::sym 41ms 0.074% 80.70% 427ms 0.77% AbstractTetrahedralElement::RefreshJacobian 294ms 0.53% 81.23% 424ms 0.76% tetgen::tetgenmesh::link::add 20ms 0.036% 81.26% 422ms 0.76% VertexMesh::CalculateUnitNormalToFaceWithArea 416ms 0.75% 82.01% 416ms 0.75% boost::numeric::ublas::c_vector::operator() 7ms 0.013% 82.03% 416ms 0.75% boost::numeric::ublas::c_vector::operator= (inline) 75ms 0.14% 82.16% 406ms 0.73% __dynamic_cast 399ms 0.72% 82.88% 399ms 0.72% AbstractElement::IsDeleted 5ms 0.009% 82.89% 389ms 0.7% CellPropertyCollection::GetPropertiesType (inline) 0 0% 82.89% 389ms 0.7% VertexMeshWriter::WriteVtkUsingMesh 25ms 0.045% 82.94% 387ms 0.7% std::_Rb_tree_iterator::operator-- (inline) 387ms 0.7% 83.63% 387ms 0.7% tetgen::tetgenmesh::org 1ms 0.0018% 83.63% 380ms 0.69% Cell::GetCellId 209ms 0.38% 84.01% 376ms 0.68% AbstractTetrahedralMesh::GetElement 162ms 0.29% 84.30% 368ms 0.66% boost::numeric::ublas::vector_inner_prod::apply (inline) 24ms 0.043% 84.35% 351ms 0.63% std::vector::insert (inline) 253ms 0.46% 84.80% 348ms 0.63% tetgen::tetgenmesh::bond 343ms 0.62% 85.42% 343ms 0.62% std::_Rb_tree_decrement 7ms 0.013% 85.43% 337ms 0.61% AbstractCellProperty::IsSubType (inline) 10ms 0.018% 85.45% 325ms 0.59% VertexElement::~VertexElement 138ms 0.25% 85.70% 321ms 0.58% Inverse 58ms 0.1% 85.81% 307ms 0.55% boost::numeric::ublas::vector_reference::operator() (inline) 3ms 0.0054% 85.81% 296ms 0.53% AbstractTetrahedralElement::AbstractTetrahedralElement 8ms 0.014% 85.83% 289ms 0.52% VertexMesh::GetVolumeOfElement 35ms 0.063% 85.89% 287ms 0.52% tetgen::insphereadapt 69ms 0.12% 86.01% 284ms 0.51% tetgen::tetgenmesh::queue::pop