File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 58366ms, 87.04% of 67056ms total Dropped 847 nodes (cum <= 335.28ms) flat flat% sum% cum cum% 0 0% 0% 66986ms 99.90% __libc_start_call_main 0 0% 0% 66986ms 99.90% __libc_start_main_impl 0 0% 0% 66986ms 99.90% _start 0 0% 0% 66968ms 99.87% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 66968ms 99.87% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 66968ms 99.87% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 66968ms 99.87% main 0 0% 0% 66929ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 66929ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 66929ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 66645ms 99.39% AbstractCellBasedSimulation::Solve 0 0% 0% 56126ms 83.70% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 56078ms 83.63% MeshBasedCellPopulation::Update 0 0% 0% 31168ms 46.48% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 31168ms 46.48% MeshBasedCellPopulation::TessellateIfNeeded 207ms 0.31% 0.31% 27765ms 41.41% VertexMesh::VertexMesh 0 0% 0.31% 20434ms 30.47% MutableMesh::ReMesh 0 0% 0.31% 16171ms 24.12% tetgen::tetrahedralize 4ms 0.006% 0.31% 16018ms 23.89% tetgen::tetgenmesh::delaunizevertices 15ms 0.022% 0.34% 16009ms 23.87% tetgen::tetgenmesh::incrflipdelaunay 512ms 0.76% 1.10% 14272ms 21.28% tetgen::tetgenmesh::lawson 584ms 0.87% 1.97% 13857ms 20.66% TetrahedralMesh::EdgeIterator::operator++ 27ms 0.04% 2.01% 10651ms 15.88% std::set::insert (inline) 3161ms 4.71% 6.73% 10591ms 15.79% std::_Rb_tree::_M_lower_bound (inline) 267ms 0.4% 7.12% 10211ms 15.23% std::_Rb_tree::_M_insert_unique 396ms 0.59% 7.71% 10198ms 15.21% VertexElement::AddFace 287ms 0.43% 8.14% 9885ms 14.74% std::_Rb_tree::find (inline) 0 0% 8.14% 9282ms 13.84% std::set::count (inline) 114ms 0.17% 8.31% 7037ms 10.49% std::less::operator() (inline) 6978ms 10.41% 18.72% 6978ms 10.41% std::operator< (inline) 6293ms 9.38% 28.10% 6293ms 9.38% std::_Rb_tree_increment 0 0% 28.10% 6036ms 9.00% OffLatticeSimulation::UpdateCellLocationsAndTopology 325ms 0.48% 28.59% 5996ms 8.94% std::_Rb_tree::_M_insert_ (inline) 0 0% 28.59% 5883ms 8.77% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.003% 28.59% 5858ms 8.74% AbstractNumericalMethod::ComputeForcesIncludingDamping 179ms 0.27% 28.86% 5533ms 8.25% operator new 1176ms 1.75% 30.61% 5272ms 7.86% __GI___libc_malloc 5ms 0.0075% 30.62% 4898ms 7.30% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1ms 0.0015% 30.62% 4862ms 7.25% MeshBasedCellPopulation::UpdateNodePairs 39ms 0.058% 30.68% 4747ms 7.08% std::__new_allocator::allocate (inline) 0 0% 30.68% 4732ms 7.06% std::allocator_traits::allocate (inline) 6ms 0.0089% 30.69% 4701ms 7.01% MeshBasedCellPopulation::SpringIterator::operator++ 5ms 0.0075% 30.70% 4411ms 6.58% std::set_intersection (inline) 271ms 0.4% 31.10% 4406ms 6.57% std::__set_intersection 12ms 0.018% 31.12% 4375ms 6.52% std::_Rb_tree::~_Rb_tree (inline) 1638ms 2.44% 33.56% 4362ms 6.51% std::_Rb_tree::_M_erase 0 0% 33.56% 4319ms 6.44% std::set::~set (inline) 0 0% 33.56% 4308ms 6.42% AbstractCellPopulation::WriteResultsToFiles 1301ms 1.94% 35.50% 4215ms 6.29% std::_Rb_tree::_M_get_insert_unique_pos 1175ms 1.75% 37.25% 4034ms 6.02% __GI___libc_free 43ms 0.064% 37.32% 3827ms 5.71% Node::AddElement 0 0% 37.32% 3783ms 5.64% std::_Rb_tree::_M_create_node (inline) 117ms 0.17% 37.49% 3783ms 5.64% tetgen::tetgenmesh::insphere_sos 0 0% 37.49% 3757ms 5.60% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 37.49% 3745ms 5.58% std::_Rb_tree::_M_get_node (inline) 2691ms 4.01% 41.50% 3708ms 5.53% _int_malloc 3692ms 5.51% 47.01% 3692ms 5.51% std::_Rb_tree::_S_right (inline) 200ms 0.3% 47.31% 3671ms 5.47% std::_Rb_tree_const_iterator::operator++ (inline) 3375ms 5.03% 52.34% 3654ms 5.45% tetgen::insphere 141ms 0.21% 52.55% 3535ms 5.27% std::__new_allocator::deallocate (inline) 0 0% 52.55% 3525ms 5.26% std::allocator_traits::deallocate (inline) 131ms 0.2% 52.75% 3485ms 5.20% tetgen::tetgenmesh::flip23 10ms 0.015% 52.76% 3443ms 5.13% TetrahedralMesh::ImportFromMesher 0 0% 52.76% 3427ms 5.11% VertexMesh::~VertexMesh 193ms 0.29% 53.05% 3126ms 4.66% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 2ms 0.003% 53.05% 3006ms 4.48% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 53.05% 2951ms 4.40% std::_Rb_tree_iterator::operator++ (inline) 64ms 0.095% 53.15% 2857ms 4.26% MutableElement::AddNode 1302ms 1.94% 55.09% 2856ms 4.26% _int_free 143ms 0.21% 55.30% 2666ms 3.98% tetgen::tetgenmesh::flip32 167ms 0.25% 55.55% 2426ms 3.62% Node::~Node 167ms 0.25% 55.80% 2198ms 3.28% VertexMesh::Clear 0 0% 55.80% 2080ms 3.10% std::_Rb_tree::_M_drop_node (inline) 0 0% 55.80% 2061ms 3.07% std::_Rb_tree::_M_put_node (inline) 2031ms 3.03% 58.83% 2031ms 3.03% Node::GetIndex 2009ms 3.00% 61.83% 2009ms 3.00% std::_Rb_tree_insert_and_rebalance 228ms 0.34% 62.17% 1977ms 2.95% tetgen::tetgenmesh::enqueueflipface 1ms 0.0015% 62.17% 1785ms 2.66% Element::Element 976ms 1.46% 63.62% 1577ms 2.35% malloc_consolidate 1485ms 2.21% 65.84% 1568ms 2.34% tetgen::orient3d 17ms 0.025% 65.86% 1481ms 2.21% std::_Vector_base::_M_deallocate (inline) 6ms 0.0089% 65.87% 1446ms 2.16% Element::RegisterWithNodes (inline) 0 0% 65.87% 1425ms 2.13% std::vector::~vector (inline) 55ms 0.082% 65.95% 1401ms 2.09% tetgen::tetgenmesh::locate 82ms 0.12% 66.08% 1363ms 2.03% TetrahedralMesh::Clear 71ms 0.11% 66.18% 1353ms 2.02% std::map::operator[] 9ms 0.013% 66.20% 1337ms 1.99% _int_free_maybe_consolidate 0 0% 66.20% 1334ms 1.99% std::_Vector_base::~_Vector_base (inline) 87ms 0.13% 66.33% 1317ms 1.96% tetgen::tetgenmesh::preciselocate 1236ms 1.84% 68.17% 1236ms 1.84% unlink_chunk 0 0% 68.17% 1203ms 1.79% std::_Rb_tree::lower_bound (inline) 0 0% 68.17% 1203ms 1.79% std::map::lower_bound (inline) 63ms 0.094% 68.26% 1154ms 1.72% std::vector::_M_realloc_insert 857ms 1.28% 69.54% 1054ms 1.57% AbstractElement::GetNodeGlobalIndex 1054ms 1.57% 71.11% 1054ms 1.57% tetgen::tetgenmesh::oppo 1043ms 1.56% 72.67% 1043ms 1.56% tetgen::tetgenmesh::triface::triface 1ms 0.0015% 72.67% 1039ms 1.55% VoronoiDataWriter::Visit 5ms 0.0075% 72.68% 1004ms 1.50% VertexMesh::GenerateVerticesFromElementCircumcentres 7ms 0.01% 72.69% 994ms 1.48% std::_Vector_base::_M_allocate (inline) 141ms 0.21% 72.90% 987ms 1.47% std::vector::push_back (inline) 831ms 1.24% 74.14% 831ms 1.24% [libchaste_mesh.so] 0 0% 74.14% 798ms 1.19% TetrahedralMesh::RefreshJacobianCachedData 332ms 0.5% 74.63% 764ms 1.14% tetgen::tetgenmesh::sym 0 0% 74.63% 751ms 1.12% AbstractTwoBodyInteractionForce::AddForceContribution 9ms 0.013% 74.65% 720ms 1.07% AbstractTetrahedralElement::CalculateInverseJacobian 313ms 0.47% 75.11% 714ms 1.06% AbstractElement::GetNodeLocation 15ms 0.022% 75.13% 710ms 1.06% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 702ms 1.05% 76.18% 702ms 1.05% tetgen::tetgenmesh::triface::operator= 683ms 1.02% 77.20% 683ms 1.02% Node::rGetLocation 371ms 0.55% 77.75% 679ms 1.01% tetgen::tetgenmesh::fnextself 49ms 0.073% 77.83% 671ms 1.00% __atan2 12ms 0.018% 77.84% 666ms 0.99% AbstractTetrahedralElement::CalculateJacobian 40ms 0.06% 77.90% 658ms 0.98% tetgen::tetgenmesh::queue::push 620ms 0.92% 78.83% 620ms 0.92% AbstractElement::IsDeleted 498ms 0.74% 79.57% 616ms 0.92% __ieee754_atan2_fma 378ms 0.56% 80.13% 616ms 0.92% tetgen::tetgenmesh::link::add 16ms 0.024% 80.16% 606ms 0.9% boost::numeric::ublas::vector_assign (inline) 45ms 0.067% 80.23% 600ms 0.89% tetgen::tetgenmesh::enextfnext 0 0% 80.23% 596ms 0.89% std::set::find (inline) 12ms 0.018% 80.24% 569ms 0.85% boost::numeric::ublas::c_vector::c_vector (inline) 569ms 0.85% 81.09% 569ms 0.85% std::vector::size (inline) 58ms 0.086% 81.18% 558ms 0.83% tetgen::tetgenmesh::enext2fnext 226ms 0.34% 81.52% 546ms 0.81% tetgen::tetgenmesh::bond 55ms 0.082% 81.60% 528ms 0.79% AbstractTetrahedralElement::RefreshJacobian 0 0% 81.60% 522ms 0.78% boost::numeric::ublas::inner_prod (inline) 54ms 0.081% 81.68% 520ms 0.78% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 81.68% 520ms 0.78% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 21ms 0.031% 81.71% 512ms 0.76% Element::CalculateCircumsphere 503ms 0.75% 82.46% 503ms 0.75% tetgen::tetgenmesh::org 0 0% 82.46% 464ms 0.69% std::insert_iterator::operator= (inline) 451ms 0.67% 83.13% 451ms 0.67% tetgen::tetgenmesh::pointmark 448ms 0.67% 83.80% 448ms 0.67% tetgen::tetgenmesh::decode 182ms 0.27% 84.07% 417ms 0.62% AbstractTetrahedralMesh::GetElement 17ms 0.025% 84.10% 416ms 0.62% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 84.10% 410ms 0.61% std::_Rb_tree::_M_insert_unique_ (inline) 166ms 0.25% 84.34% 407ms 0.61% boost::numeric::ublas::vector_inner_prod::apply (inline) 117ms 0.17% 84.52% 404ms 0.6% __dynamic_cast 24ms 0.036% 84.55% 404ms 0.6% std::_Rb_tree_iterator::operator-- (inline) 1ms 0.0015% 84.56% 393ms 0.59% CellPropertyCollection::GetPropertiesType (inline) 2ms 0.003% 84.56% 391ms 0.58% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 84.56% 390ms 0.58% Cell::GetCellId 0 0% 84.56% 386ms 0.58% VertexMeshWriter::WriteVtkUsingMesh 6ms 0.0089% 84.57% 376ms 0.56% VertexElement::~VertexElement 117ms 0.17% 84.74% 370ms 0.55% boost::numeric::ublas::indexing_vector_assign 369ms 0.55% 85.29% 369ms 0.55% tetgen::tetgenmesh::face::face 368ms 0.55% 85.84% 368ms 0.55% boost::numeric::ublas::c_vector::operator() 0 0% 85.84% 363ms 0.54% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 85.84% 357ms 0.53% tcache_get (inline) 357ms 0.53% 86.37% 357ms 0.53% tcache_get_n (inline) 355ms 0.53% 86.90% 355ms 0.53% std::_Rb_tree_decrement 83ms 0.12% 87.03% 354ms 0.53% tetgen::tetgenmesh::queue::pop 9ms 0.013% 87.04% 340ms 0.51% AbstractTetrahedralElement::AbstractTetrahedralElement