File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 41009ms, 86.18% of 47587ms total Dropped 826 nodes (cum <= 237.94ms) flat flat% sum% cum cum% 0 0% 0% 47539ms 99.90% __libc_start_call_main 0 0% 0% 47539ms 99.90% __libc_start_main_impl 0 0% 0% 47539ms 99.90% _start 0 0% 0% 47526ms 99.87% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 47526ms 99.87% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 47526ms 99.87% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 47526ms 99.87% main 0 0% 0% 47493ms 99.80% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 47493ms 99.80% CxxTest::TestRunner::runTest (inline) 0 0% 0% 47492ms 99.80% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 47284ms 99.36% AbstractCellBasedSimulation::Solve 0 0% 0% 40133ms 84.34% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 40102ms 84.27% MeshBasedCellPopulation::Update 0 0% 0% 21495ms 45.17% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 21495ms 45.17% MeshBasedCellPopulation::TessellateIfNeeded 142ms 0.3% 0.3% 19194ms 40.33% VertexMesh::VertexMesh 0 0% 0.3% 15437ms 32.44% MutableMesh::ReMesh 0 0% 0.3% 12428ms 26.12% tetgen::tetrahedralize 0 0% 0.3% 12317ms 25.88% tetgen::tetgenmesh::delaunizevertices 9ms 0.019% 0.32% 12315ms 25.88% tetgen::tetgenmesh::incrflipdelaunay 394ms 0.83% 1.15% 11009ms 23.13% tetgen::tetgenmesh::lawson 489ms 1.03% 2.17% 9591ms 20.15% TetrahedralMesh::EdgeIterator::operator++ 30ms 0.063% 2.24% 7463ms 15.68% std::set::insert (inline) 288ms 0.61% 2.84% 7341ms 15.43% VertexElement::AddFace 2568ms 5.40% 8.24% 7198ms 15.13% std::_Rb_tree::_M_lower_bound (inline) 164ms 0.34% 8.58% 7098ms 14.92% std::_Rb_tree::_M_insert_unique 223ms 0.47% 9.05% 6792ms 14.27% std::_Rb_tree::find (inline) 0 0% 9.05% 6294ms 13.23% std::set::count (inline) 88ms 0.18% 9.24% 4466ms 9.38% std::less::operator() (inline) 4433ms 9.32% 18.55% 4433ms 9.32% std::operator< (inline) 240ms 0.5% 19.06% 4276ms 8.99% std::_Rb_tree::_M_insert_ (inline) 0 0% 19.06% 4215ms 8.86% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 19.06% 4101ms 8.62% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0042% 19.06% 4082ms 8.58% AbstractNumericalMethod::ComputeForcesIncludingDamping 3916ms 8.23% 27.29% 3916ms 8.23% std::_Rb_tree_increment 141ms 0.3% 27.59% 3730ms 7.84% operator new 909ms 1.91% 29.50% 3519ms 7.39% __GI___libc_malloc 0 0% 29.50% 3450ms 7.25% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.0084% 29.50% 3375ms 7.09% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 13ms 0.027% 29.53% 3326ms 6.99% MeshBasedCellPopulation::SpringIterator::operator++ 30ms 0.063% 29.59% 3258ms 6.85% std::__new_allocator::allocate (inline) 0 0% 29.59% 3245ms 6.82% std::allocator_traits::allocate (inline) 6ms 0.013% 29.61% 3178ms 6.68% std::_Rb_tree::~_Rb_tree (inline) 1059ms 2.23% 31.83% 3166ms 6.65% std::_Rb_tree::_M_erase 0 0% 31.83% 3141ms 6.60% std::set::~set (inline) 890ms 1.87% 33.70% 3001ms 6.31% __GI___libc_free 5ms 0.011% 33.71% 2930ms 6.16% std::set_intersection (inline) 173ms 0.36% 34.08% 2925ms 6.15% std::__set_intersection 92ms 0.19% 34.27% 2902ms 6.10% tetgen::tetgenmesh::insphere_sos 999ms 2.10% 36.37% 2876ms 6.04% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 36.37% 2815ms 5.92% AbstractCellPopulation::WriteResultsToFiles 2541ms 5.34% 41.71% 2803ms 5.89% tetgen::insphere 87ms 0.18% 41.89% 2698ms 5.67% tetgen::tetgenmesh::flip23 0 0% 41.89% 2651ms 5.57% std::_Rb_tree::_M_create_node (inline) 123ms 0.26% 42.15% 2647ms 5.56% std::__new_allocator::deallocate (inline) 0 0% 42.15% 2636ms 5.54% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 42.15% 2630ms 5.53% std::_Rb_tree::_M_get_node (inline) 0 0% 42.15% 2629ms 5.52% std::allocator_traits::deallocate (inline) 41ms 0.086% 42.24% 2439ms 5.13% Node::AddElement 5ms 0.011% 42.25% 2429ms 5.10% TetrahedralMesh::ImportFromMesher 142ms 0.3% 42.55% 2388ms 5.02% std::_Rb_tree_const_iterator::operator++ (inline) 1776ms 3.73% 46.28% 2367ms 4.97% _int_malloc 0 0% 46.28% 2315ms 4.86% VertexMesh::~VertexMesh 2300ms 4.83% 51.11% 2300ms 4.83% std::_Rb_tree::_S_right (inline) 1091ms 2.29% 53.40% 2108ms 4.43% _int_free 108ms 0.23% 53.63% 1993ms 4.19% tetgen::tetgenmesh::flip32 58ms 0.12% 53.75% 1945ms 4.09% MutableElement::AddNode 0 0% 53.75% 1938ms 4.07% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 124ms 0.26% 54.01% 1915ms 4.02% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 54.01% 1797ms 3.78% std::_Rb_tree_iterator::operator++ (inline) 113ms 0.24% 54.25% 1746ms 3.67% Node::~Node 0 0% 54.25% 1656ms 3.48% std::_Rb_tree::_M_drop_node (inline) 0 0% 54.25% 1645ms 3.46% std::_Rb_tree::_M_put_node (inline) 118ms 0.25% 54.50% 1555ms 3.27% VertexMesh::Clear 1444ms 3.03% 57.53% 1444ms 3.03% std::_Rb_tree_insert_and_rebalance 160ms 0.34% 57.87% 1410ms 2.96% tetgen::tetgenmesh::enqueueflipface 1222ms 2.57% 60.44% 1222ms 2.57% Node::GetIndex 1125ms 2.36% 62.80% 1178ms 2.48% tetgen::orient3d 8ms 0.017% 62.82% 1148ms 2.41% Element::Element 90ms 0.19% 63.01% 1090ms 2.29% TetrahedralMesh::Clear 27ms 0.057% 63.06% 1054ms 2.21% tetgen::tetgenmesh::locate 18ms 0.038% 63.10% 1002ms 2.11% std::_Vector_base::_M_deallocate (inline) 84ms 0.18% 63.28% 991ms 2.08% tetgen::tetgenmesh::preciselocate 614ms 1.29% 64.57% 964ms 2.03% malloc_consolidate 0 0% 64.57% 946ms 1.99% std::vector::~vector (inline) 1ms 0.0021% 64.57% 903ms 1.90% Element::RegisterWithNodes (inline) 51ms 0.11% 64.68% 886ms 1.86% std::map::operator[] 3ms 0.0063% 64.68% 857ms 1.80% std::_Vector_base::~_Vector_base (inline) 68ms 0.14% 64.83% 844ms 1.77% std::vector::_M_realloc_insert 6ms 0.013% 64.84% 826ms 1.74% _int_free_maybe_consolidate 793ms 1.67% 66.51% 793ms 1.67% tetgen::tetgenmesh::triface::triface 0 0% 66.51% 779ms 1.64% std::_Rb_tree::lower_bound (inline) 0 0% 66.51% 779ms 1.64% std::map::lower_bound (inline) 749ms 1.57% 68.08% 749ms 1.57% tetgen::tetgenmesh::oppo 582ms 1.22% 69.30% 725ms 1.52% AbstractElement::GetNodeGlobalIndex 718ms 1.51% 70.81% 718ms 1.51% unlink_chunk 0 0% 70.81% 693ms 1.46% VoronoiDataWriter::Visit 104ms 0.22% 71.03% 671ms 1.41% std::vector::push_back (inline) 0 0% 71.03% 663ms 1.39% VertexMesh::GenerateVerticesFromElementCircumcentres 244ms 0.51% 71.54% 644ms 1.35% tetgen::tetgenmesh::sym 629ms 1.32% 72.86% 629ms 1.32% [libchaste_mesh.so] 3ms 0.0063% 72.87% 618ms 1.30% std::_Vector_base::_M_allocate (inline) 0 0% 72.87% 566ms 1.19% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 72.87% 566ms 1.19% TetrahedralMesh::RefreshJacobianCachedData 566ms 1.19% 74.06% 566ms 1.19% tetgen::tetgenmesh::triface::operator= 7ms 0.015% 74.07% 539ms 1.13% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 30ms 0.063% 74.14% 534ms 1.12% tetgen::tetgenmesh::queue::push 330ms 0.69% 74.83% 517ms 1.09% tetgen::tetgenmesh::fnextself 6ms 0.013% 74.84% 516ms 1.08% AbstractTetrahedralElement::CalculateInverseJacobian 303ms 0.64% 75.48% 504ms 1.06% tetgen::tetgenmesh::link::add 0 0% 75.48% 495ms 1.04% std::set::find (inline) 168ms 0.35% 75.83% 487ms 1.02% tetgen::tetgenmesh::bond 52ms 0.11% 75.94% 487ms 1.02% tetgen::tetgenmesh::enext2fnext 37ms 0.078% 76.02% 471ms 0.99% __atan2 57ms 0.12% 76.14% 468ms 0.98% tetgen::tetgenmesh::enextfnext 10ms 0.021% 76.16% 456ms 0.96% boost::numeric::ublas::vector_assign (inline) 13ms 0.027% 76.19% 455ms 0.96% AbstractTetrahedralElement::CalculateJacobian 8ms 0.017% 76.21% 443ms 0.93% boost::numeric::ublas::c_vector::c_vector (inline) 340ms 0.71% 76.92% 434ms 0.91% __ieee754_atan2_fma 189ms 0.4% 77.32% 416ms 0.87% AbstractElement::GetNodeLocation 408ms 0.86% 78.17% 408ms 0.86% Node::rGetLocation 408ms 0.86% 79.03% 408ms 0.86% tetgen::tetgenmesh::decode 0 0% 79.03% 406ms 0.85% boost::numeric::ublas::inner_prod (inline) 1ms 0.0021% 79.03% 401ms 0.84% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 34ms 0.071% 79.11% 400ms 0.84% boost::numeric::ublas::vector_scalar_binary::evaluate 1ms 0.0021% 79.11% 388ms 0.82% CellPropertyCollection::GetPropertiesType (inline) 0 0% 79.11% 387ms 0.81% std::insert_iterator::operator= (inline) 381ms 0.8% 79.91% 381ms 0.8% tetgen::tetgenmesh::org 377ms 0.79% 80.70% 377ms 0.79% std::vector::size (inline) 1ms 0.0021% 80.70% 376ms 0.79% Cell::GetCellId 371ms 0.78% 81.48% 371ms 0.78% AbstractElement::IsDeleted 353ms 0.74% 82.22% 353ms 0.74% tetgen::tetgenmesh::pointmark 0 0% 82.22% 335ms 0.7% AbstractCellProperty::IsSubType (inline) 0 0% 82.22% 335ms 0.7% std::_Rb_tree::_M_insert_unique_ (inline) 75ms 0.16% 82.38% 333ms 0.7% __dynamic_cast 158ms 0.33% 82.71% 331ms 0.7% boost::numeric::ublas::vector_inner_prod::apply (inline) 33ms 0.069% 82.78% 329ms 0.69% AbstractTetrahedralElement::RefreshJacobian 173ms 0.36% 83.15% 329ms 0.69% AbstractTetrahedralMesh::GetElement 16ms 0.034% 83.18% 328ms 0.69% Element::CalculateCircumsphere 0 0% 83.18% 314ms 0.66% VertexMeshWriter::WriteVtkUsingMesh 311ms 0.65% 83.83% 311ms 0.65% tetgen::tetgenmesh::encode 14ms 0.029% 83.86% 304ms 0.64% VertexMesh::CalculateUnitNormalToFaceWithArea 3ms 0.0063% 83.87% 301ms 0.63% boost::numeric::ublas::c_vector::operator= (inline) 17ms 0.036% 83.91% 298ms 0.63% std::_Rb_tree_iterator::operator-- (inline) 13ms 0.027% 83.93% 297ms 0.62% std::vector::insert (inline) 293ms 0.62% 84.55% 293ms 0.62% boost::numeric::ublas::c_vector::operator() 4ms 0.0084% 84.56% 292ms 0.61% VertexElement::~VertexElement 74ms 0.16% 84.71% 267ms 0.56% boost::numeric::ublas::indexing_vector_assign 27ms 0.057% 84.77% 262ms 0.55% tetgen::insphereadapt 0 0% 84.77% 258ms 0.54% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 258ms 0.54% 85.31% 258ms 0.54% std::_Rb_tree_decrement 76ms 0.16% 85.47% 249ms 0.52% tetgen::tetgenmesh::queue::pop 248ms 0.52% 85.99% 248ms 0.52% tetgen::tetgenmesh::face::face 87ms 0.18% 86.17% 240ms 0.5% Inverse 1ms 0.0021% 86.18% 239ms 0.5% AbstractTetrahedralElement::AbstractTetrahedralElement