File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 53088ms, 86.66% of 61259ms total Dropped 875 nodes (cum <= 306.30ms) flat flat% sum% cum cum% 0 0% 0% 61201ms 99.91% __libc_start_call_main 0 0% 0% 61201ms 99.91% __libc_start_main_impl 0 0% 0% 61201ms 99.91% _start 0 0% 0% 61185ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 61185ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 61185ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 61185ms 99.88% main 0 0% 0% 61147ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 61147ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 61147ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 60873ms 99.37% AbstractCellBasedSimulation::Solve 0 0% 0% 51782ms 84.53% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 51732ms 84.45% MeshBasedCellPopulation::Update 0 0% 0% 27598ms 45.05% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 27598ms 45.05% MeshBasedCellPopulation::TessellateIfNeeded 185ms 0.3% 0.3% 24926ms 40.69% VertexMesh::VertexMesh 0 0% 0.3% 20129ms 32.86% MutableMesh::ReMesh 0 0% 0.3% 16420ms 26.80% tetgen::tetrahedralize 2ms 0.0033% 0.31% 16277ms 26.57% tetgen::tetgenmesh::delaunizevertices 14ms 0.023% 0.33% 16274ms 26.57% tetgen::tetgenmesh::incrflipdelaunay 531ms 0.87% 1.19% 14588ms 23.81% tetgen::tetgenmesh::lawson 617ms 1.01% 2.20% 12340ms 20.14% TetrahedralMesh::EdgeIterator::operator++ 21ms 0.034% 2.24% 9849ms 16.08% std::set::insert (inline) 356ms 0.58% 2.82% 9644ms 15.74% VertexElement::AddFace 286ms 0.47% 3.28% 9441ms 15.41% std::_Rb_tree::_M_insert_unique 3235ms 5.28% 8.57% 9158ms 14.95% std::_Rb_tree::_M_lower_bound (inline) 235ms 0.38% 8.95% 8617ms 14.07% std::_Rb_tree::find (inline) 0 0% 8.95% 8037ms 13.12% std::set::count (inline) 94ms 0.15% 9.10% 5813ms 9.49% std::less::operator() (inline) 5778ms 9.43% 18.53% 5778ms 9.43% std::operator< (inline) 316ms 0.52% 19.05% 5457ms 8.91% std::_Rb_tree::_M_insert_ (inline) 1ms 0.0016% 19.05% 5412ms 8.83% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 19.05% 5278ms 8.62% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0016% 19.05% 5252ms 8.57% AbstractNumericalMethod::ComputeForcesIncludingDamping 4971ms 8.11% 27.17% 4971ms 8.11% std::_Rb_tree_increment 143ms 0.23% 27.40% 4664ms 7.61% operator new 1139ms 1.86% 29.26% 4445ms 7.26% __GI___libc_malloc 0 0% 29.26% 4381ms 7.15% MeshBasedCellPopulation::UpdateNodePairs 9ms 0.015% 29.28% 4354ms 7.11% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 17ms 0.028% 29.30% 4250ms 6.94% MeshBasedCellPopulation::SpringIterator::operator++ 35ms 0.057% 29.36% 4058ms 6.62% std::__new_allocator::allocate (inline) 0 0% 29.36% 4051ms 6.61% std::allocator_traits::allocate (inline) 1359ms 2.22% 31.58% 3954ms 6.45% std::_Rb_tree::_M_get_insert_unique_pos 7ms 0.011% 31.59% 3884ms 6.34% std::_Rb_tree::~_Rb_tree (inline) 1334ms 2.18% 33.77% 3875ms 6.33% std::_Rb_tree::_M_erase 103ms 0.17% 33.94% 3844ms 6.27% tetgen::tetgenmesh::insphere_sos 0 0% 33.94% 3833ms 6.26% std::set::~set (inline) 1ms 0.0016% 33.94% 3754ms 6.13% std::set_intersection (inline) 253ms 0.41% 34.35% 3753ms 6.13% std::__set_intersection 3438ms 5.61% 39.96% 3717ms 6.07% tetgen::insphere 1052ms 1.72% 41.68% 3594ms 5.87% __GI___libc_free 133ms 0.22% 41.90% 3544ms 5.79% tetgen::tetgenmesh::flip23 0 0% 41.90% 3522ms 5.75% AbstractCellPopulation::WriteResultsToFiles 0 0% 41.90% 3320ms 5.42% std::_Rb_tree::_M_create_node (inline) 0 0% 41.90% 3294ms 5.38% std::_Rb_tree::_M_get_node (inline) 0 0% 41.90% 3291ms 5.37% std::_Rb_tree::_Alloc_node::operator() (inline) 146ms 0.24% 42.14% 3202ms 5.23% std::__new_allocator::deallocate (inline) 0 0% 42.14% 3186ms 5.20% std::allocator_traits::deallocate (inline) 44ms 0.072% 42.21% 3086ms 5.04% Node::AddElement 196ms 0.32% 42.53% 3066ms 5.00% std::_Rb_tree_const_iterator::operator++ (inline) 2148ms 3.51% 46.03% 2960ms 4.83% _int_malloc 11ms 0.018% 46.05% 2959ms 4.83% TetrahedralMesh::ImportFromMesher 2941ms 4.80% 50.85% 2941ms 4.80% std::_Rb_tree::_S_right (inline) 0 0% 50.85% 2690ms 4.39% VertexMesh::~VertexMesh 143ms 0.23% 51.09% 2604ms 4.25% tetgen::tetgenmesh::flip32 1312ms 2.14% 53.23% 2540ms 4.15% _int_free 83ms 0.14% 53.36% 2497ms 4.08% MutableElement::AddNode 5ms 0.0082% 53.37% 2399ms 3.92% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 174ms 0.28% 53.66% 2398ms 3.91% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1ms 0.0016% 53.66% 2240ms 3.66% std::_Rb_tree_iterator::operator++ (inline) 126ms 0.21% 53.86% 2023ms 3.30% Node::~Node 0 0% 53.86% 2016ms 3.29% std::_Rb_tree::_M_drop_node (inline) 0 0% 53.86% 2008ms 3.28% std::_Rb_tree::_M_put_node (inline) 228ms 0.37% 54.24% 1947ms 3.18% tetgen::tetgenmesh::enqueueflipface 1887ms 3.08% 57.32% 1887ms 3.08% std::_Rb_tree_insert_and_rebalance 145ms 0.24% 57.55% 1781ms 2.91% VertexMesh::Clear 1576ms 2.57% 60.13% 1663ms 2.71% tetgen::orient3d 1541ms 2.52% 62.64% 1541ms 2.52% Node::GetIndex 6ms 0.0098% 62.65% 1419ms 2.32% Element::Element 38ms 0.062% 62.71% 1368ms 2.23% tetgen::tetgenmesh::locate 75ms 0.12% 62.83% 1284ms 2.10% tetgen::tetgenmesh::preciselocate 76ms 0.12% 62.96% 1268ms 2.07% TetrahedralMesh::Clear 23ms 0.038% 63.00% 1201ms 1.96% std::_Vector_base::_M_deallocate (inline) 772ms 1.26% 64.26% 1188ms 1.94% malloc_consolidate 72ms 0.12% 64.37% 1133ms 1.85% std::map::operator[] 0 0% 64.37% 1116ms 1.82% std::vector::~vector (inline) 10ms 0.016% 64.39% 1080ms 1.76% Element::RegisterWithNodes (inline) 1061ms 1.73% 66.12% 1061ms 1.73% tetgen::tetgenmesh::oppo 57ms 0.093% 66.22% 1039ms 1.70% std::vector::_M_realloc_insert 1ms 0.0016% 66.22% 1015ms 1.66% std::_Vector_base::~_Vector_base (inline) 1010ms 1.65% 67.87% 1010ms 1.65% tetgen::tetgenmesh::triface::triface 10ms 0.016% 67.88% 1009ms 1.65% _int_free_maybe_consolidate 0 0% 67.88% 985ms 1.61% std::_Rb_tree::lower_bound (inline) 0 0% 67.88% 985ms 1.61% std::map::lower_bound (inline) 934ms 1.52% 69.41% 934ms 1.52% unlink_chunk 726ms 1.19% 70.59% 909ms 1.48% AbstractElement::GetNodeGlobalIndex 0 0% 70.59% 883ms 1.44% VoronoiDataWriter::Visit 111ms 0.18% 70.77% 852ms 1.39% std::vector::push_back (inline) 305ms 0.5% 71.27% 823ms 1.34% tetgen::tetgenmesh::sym 2ms 0.0033% 71.27% 794ms 1.30% VertexMesh::GenerateVerticesFromElementCircumcentres 781ms 1.27% 72.55% 781ms 1.27% [libchaste_mesh.so] 9ms 0.015% 72.56% 766ms 1.25% std::_Vector_base::_M_allocate (inline) 748ms 1.22% 73.79% 748ms 1.22% tetgen::tetgenmesh::triface::operator= 0 0% 73.79% 731ms 1.19% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 73.79% 729ms 1.19% TetrahedralMesh::RefreshJacobianCachedData 6ms 0.0098% 73.79% 687ms 1.12% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 8ms 0.013% 73.81% 676ms 1.10% AbstractTetrahedralElement::CalculateInverseJacobian 16ms 0.026% 73.83% 671ms 1.10% boost::numeric::ublas::vector_assign (inline) 15ms 0.024% 73.86% 658ms 1.07% boost::numeric::ublas::c_vector::c_vector (inline) 42ms 0.069% 73.93% 655ms 1.07% tetgen::tetgenmesh::queue::push 72ms 0.12% 74.04% 632ms 1.03% tetgen::tetgenmesh::enext2fnext 382ms 0.62% 74.67% 630ms 1.03% tetgen::tetgenmesh::fnextself 53ms 0.087% 74.75% 623ms 1.02% __atan2 13ms 0.021% 74.78% 615ms 1.00% AbstractTetrahedralElement::CalculateJacobian 376ms 0.61% 75.39% 613ms 1.00% tetgen::tetgenmesh::link::add 0 0% 75.39% 575ms 0.94% std::set::find (inline) 214ms 0.35% 75.74% 572ms 0.93% tetgen::tetgenmesh::bond 226ms 0.37% 76.11% 570ms 0.93% AbstractElement::GetNodeLocation 49ms 0.08% 76.19% 565ms 0.92% tetgen::tetgenmesh::enextfnext 446ms 0.73% 76.92% 564ms 0.92% __ieee754_atan2_fma 562ms 0.92% 77.83% 562ms 0.92% Node::rGetLocation 552ms 0.9% 78.73% 552ms 0.9% tetgen::tetgenmesh::pointmark 541ms 0.88% 79.62% 541ms 0.88% std::vector::size (inline) 540ms 0.88% 80.50% 540ms 0.88% tetgen::tetgenmesh::decode 510ms 0.83% 81.33% 510ms 0.83% tetgen::tetgenmesh::org 0 0% 81.33% 500ms 0.82% boost::numeric::ublas::inner_prod (inline) 1ms 0.0016% 81.33% 499ms 0.81% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 35ms 0.057% 81.39% 498ms 0.81% boost::numeric::ublas::vector_scalar_binary::evaluate 13ms 0.021% 81.41% 446ms 0.73% Element::CalculateCircumsphere 441ms 0.72% 82.13% 441ms 0.72% AbstractElement::IsDeleted 35ms 0.057% 82.19% 440ms 0.72% AbstractTetrahedralElement::RefreshJacobian 0 0% 82.19% 439ms 0.72% std::insert_iterator::operator= (inline) 5ms 0.0082% 82.20% 434ms 0.71% boost::numeric::ublas::c_vector::operator= (inline) 22ms 0.036% 82.23% 431ms 0.7% std::_Rb_tree_iterator::operator-- (inline) 198ms 0.32% 82.56% 427ms 0.7% AbstractTetrahedralMesh::GetElement 109ms 0.18% 82.73% 424ms 0.69% boost::numeric::ublas::indexing_vector_assign 420ms 0.69% 83.42% 420ms 0.69% boost::numeric::ublas::c_vector::operator() 101ms 0.16% 83.58% 414ms 0.68% __dynamic_cast 168ms 0.27% 83.86% 403ms 0.66% boost::numeric::ublas::vector_inner_prod::apply (inline) 12ms 0.02% 83.88% 391ms 0.64% VertexMesh::CalculateUnitNormalToFaceWithArea 3ms 0.0049% 83.88% 390ms 0.64% CellPropertyCollection::GetPropertiesType (inline) 0 0% 83.88% 386ms 0.63% std::_Rb_tree::_M_insert_unique_ (inline) 384ms 0.63% 84.51% 384ms 0.63% std::_Rb_tree_decrement 0 0% 84.51% 380ms 0.62% VertexMeshWriter::WriteVtkUsingMesh 7ms 0.011% 84.52% 366ms 0.6% Cell::GetCellId 352ms 0.57% 85.10% 352ms 0.57% tetgen::tetgenmesh::face::face 345ms 0.56% 85.66% 345ms 0.56% tetgen::tetgenmesh::encode 137ms 0.22% 85.88% 341ms 0.56% Inverse 7ms 0.011% 85.89% 333ms 0.54% AbstractTetrahedralElement::AbstractTetrahedralElement 9ms 0.015% 85.91% 328ms 0.54% VertexElement::~VertexElement 2ms 0.0033% 85.91% 325ms 0.53% AbstractCellProperty::IsSubType (inline) 52ms 0.085% 86.00% 325ms 0.53% boost::numeric::ublas::vector_reference::operator() (inline) 16ms 0.026% 86.02% 325ms 0.53% std::vector::insert (inline) 80ms 0.13% 86.15% 315ms 0.51% tetgen::tetgenmesh::queue::pop 0 0% 86.15% 311ms 0.51% tcache_get (inline) 311ms 0.51% 86.66% 311ms 0.51% tcache_get_n (inline)