File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 48001ms, 86.80% of 55299ms total Dropped 847 nodes (cum <= 276.50ms) flat flat% sum% cum cum% 0 0% 0% 55235ms 99.88% __libc_start_call_main 0 0% 0% 55235ms 99.88% __libc_start_main_impl 0 0% 0% 55235ms 99.88% _start 0 0% 0% 55220ms 99.86% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 55220ms 99.86% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 55220ms 99.86% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 55220ms 99.86% main 0 0% 0% 55187ms 99.80% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 55187ms 99.80% CxxTest::TestRunner::runTest (inline) 1ms 0.0018% 0.0018% 55187ms 99.80% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0.0018% 54935ms 99.34% AbstractCellBasedSimulation::Solve 0 0% 0.0018% 46367ms 83.85% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0018% 0.0036% 46321ms 83.76% MeshBasedCellPopulation::Update 0 0% 0.0036% 25676ms 46.43% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0.0036% 25675ms 46.43% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 162ms 0.29% 0.3% 22728ms 41.10% VertexMesh::VertexMesh 0 0% 0.3% 16946ms 30.64% MutableMesh::ReMesh 0 0% 0.3% 12922ms 23.37% tetgen::tetrahedralize 1ms 0.0018% 0.3% 12779ms 23.11% tetgen::tetgenmesh::delaunizevertices 6ms 0.011% 0.31% 12773ms 23.10% tetgen::tetgenmesh::incrflipdelaunay 560ms 1.01% 1.32% 11343ms 20.51% tetgen::tetgenmesh::lawson 539ms 0.97% 2.30% 11197ms 20.25% TetrahedralMesh::EdgeIterator::operator++ 29ms 0.052% 2.35% 9352ms 16.91% std::set::insert (inline) 389ms 0.7% 3.05% 8885ms 16.07% VertexElement::AddFace 181ms 0.33% 3.38% 8851ms 16.01% std::_Rb_tree::_M_insert_unique 3031ms 5.48% 8.86% 8741ms 15.81% std::_Rb_tree::_M_lower_bound (inline) 257ms 0.46% 9.33% 8288ms 14.99% std::_Rb_tree::find (inline) 0 0% 9.33% 7730ms 13.98% std::set::count (inline) 99ms 0.18% 9.50% 5551ms 10.04% std::less::operator() (inline) 5505ms 9.95% 19.46% 5505ms 9.95% std::operator< (inline) 299ms 0.54% 20.00% 5398ms 9.76% std::_Rb_tree::_M_insert_ (inline) 0 0% 20.00% 4977ms 9.00% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 20.00% 4874ms 8.81% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0054% 20.01% 4848ms 8.77% AbstractNumericalMethod::ComputeForcesIncludingDamping 200ms 0.36% 20.37% 4738ms 8.57% operator new 1066ms 1.93% 22.30% 4478ms 8.10% __GI___libc_malloc 4312ms 7.80% 30.09% 4312ms 7.80% std::_Rb_tree_increment 40ms 0.072% 30.17% 4083ms 7.38% std::__new_allocator::allocate (inline) 0 0% 30.17% 4062ms 7.35% std::allocator_traits::allocate (inline) 1ms 0.0018% 30.17% 4041ms 7.31% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.009% 30.18% 4001ms 7.24% std::_Rb_tree::~_Rb_tree (inline) 1499ms 2.71% 32.89% 3995ms 7.22% std::_Rb_tree::_M_erase 7ms 0.013% 32.90% 3989ms 7.21% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 32.90% 3953ms 7.15% std::set::~set (inline) 16ms 0.029% 32.93% 3896ms 7.05% MeshBasedCellPopulation::SpringIterator::operator++ 1225ms 2.22% 35.14% 3570ms 6.46% std::_Rb_tree::_M_get_insert_unique_pos 1035ms 1.87% 37.02% 3494ms 6.32% __GI___libc_free 114ms 0.21% 37.22% 3485ms 6.30% tetgen::tetgenmesh::insphere_sos 0 0% 37.22% 3448ms 6.24% AbstractCellPopulation::WriteResultsToFiles 3074ms 5.56% 42.78% 3358ms 6.07% tetgen::insphere 0 0% 42.78% 3309ms 5.98% std::_Rb_tree::_M_create_node (inline) 0 0% 42.78% 3278ms 5.93% std::_Rb_tree::_M_get_node (inline) 0 0% 42.78% 3271ms 5.92% std::_Rb_tree::_Alloc_node::operator() (inline) 9ms 0.016% 42.80% 3255ms 5.89% TetrahedralMesh::ImportFromMesher 15ms 0.027% 42.82% 3214ms 5.81% Node::AddElement 134ms 0.24% 43.07% 3135ms 5.67% std::__new_allocator::deallocate (inline) 0 0% 43.07% 3116ms 5.63% std::allocator_traits::deallocate (inline) 1ms 0.0018% 43.07% 3068ms 5.55% std::set_intersection (inline) 226ms 0.41% 43.48% 3067ms 5.55% std::__set_intersection 2334ms 4.22% 47.70% 3051ms 5.52% _int_malloc 0 0% 47.70% 2964ms 5.36% VertexMesh::~VertexMesh 2812ms 5.09% 52.78% 2812ms 5.09% std::_Rb_tree::_S_right (inline) 194ms 0.35% 53.13% 2705ms 4.89% tetgen::tetgenmesh::flip23 1209ms 2.19% 55.32% 2457ms 4.44% _int_free 167ms 0.3% 55.62% 2422ms 4.38% std::_Rb_tree_const_iterator::operator++ (inline) 79ms 0.14% 55.76% 2355ms 4.26% MutableElement::AddNode 200ms 0.36% 56.13% 2333ms 4.22% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 2ms 0.0036% 56.13% 2328ms 4.21% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 144ms 0.26% 56.39% 2189ms 3.96% Node::~Node 0 0% 56.39% 2144ms 3.88% std::_Rb_tree_iterator::operator++ (inline) 146ms 0.26% 56.65% 1994ms 3.61% VertexMesh::Clear 138ms 0.25% 56.90% 1916ms 3.46% tetgen::tetgenmesh::flip32 1897ms 3.43% 60.33% 1897ms 3.43% std::_Rb_tree_insert_and_rebalance 0 0% 60.33% 1888ms 3.41% std::_Rb_tree::_M_drop_node (inline) 0 0% 60.33% 1880ms 3.40% std::_Rb_tree::_M_put_node (inline) 3ms 0.0054% 60.34% 1671ms 3.02% Element::Element 1321ms 2.39% 62.73% 1410ms 2.55% tetgen::orient3d 226ms 0.41% 63.14% 1382ms 2.50% tetgen::tetgenmesh::enqueueflipface 5ms 0.009% 63.15% 1363ms 2.46% Element::RegisterWithNodes (inline) 161ms 0.29% 63.44% 1263ms 2.28% TetrahedralMesh::Clear 1249ms 2.26% 65.70% 1249ms 2.26% Node::GetIndex 13ms 0.024% 65.72% 1249ms 2.26% std::_Vector_base::_M_deallocate (inline) 785ms 1.42% 67.14% 1211ms 2.19% malloc_consolidate 32ms 0.058% 67.20% 1206ms 2.18% tetgen::tetgenmesh::locate 0 0% 67.20% 1177ms 2.13% std::vector::~vector (inline) 94ms 0.17% 67.37% 1136ms 2.05% tetgen::tetgenmesh::preciselocate 0 0% 67.37% 1056ms 1.91% std::_Vector_base::~_Vector_base (inline) 6ms 0.011% 67.38% 1042ms 1.88% _int_free_maybe_consolidate 66ms 0.12% 67.50% 1026ms 1.86% std::map::operator[] 60ms 0.11% 67.61% 1019ms 1.84% std::vector::_M_realloc_insert 0 0% 67.61% 891ms 1.61% VoronoiDataWriter::Visit 0 0% 67.61% 888ms 1.61% std::_Rb_tree::lower_bound (inline) 0 0% 67.61% 888ms 1.61% std::map::lower_bound (inline) 878ms 1.59% 69.19% 878ms 1.59% tetgen::tetgenmesh::triface::triface 873ms 1.58% 70.77% 873ms 1.58% unlink_chunk 6ms 0.011% 70.78% 846ms 1.53% VertexMesh::GenerateVerticesFromElementCircumcentres 122ms 0.22% 71.00% 824ms 1.49% std::vector::push_back (inline) 4ms 0.0072% 71.01% 788ms 1.42% std::_Vector_base::_M_allocate (inline) 434ms 0.78% 71.80% 759ms 1.37% tetgen::tetgenmesh::fnextself 0 0% 71.80% 751ms 1.36% TetrahedralMesh::RefreshJacobianCachedData 579ms 1.05% 72.84% 731ms 1.32% AbstractElement::GetNodeGlobalIndex 0 0% 72.84% 705ms 1.27% AbstractTwoBodyInteractionForce::AddForceContribution 705ms 1.27% 74.12% 705ms 1.27% tetgen::tetgenmesh::oppo 11ms 0.02% 74.14% 681ms 1.23% AbstractTetrahedralElement::CalculateInverseJacobian 17ms 0.031% 74.17% 680ms 1.23% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 11ms 0.02% 74.19% 651ms 1.18% boost::numeric::ublas::vector_assign (inline) 628ms 1.14% 75.32% 628ms 1.14% [libchaste_mesh.so] 11ms 0.02% 75.34% 610ms 1.10% AbstractTetrahedralElement::CalculateJacobian 9ms 0.016% 75.36% 602ms 1.09% boost::numeric::ublas::c_vector::c_vector (inline) 63ms 0.11% 75.47% 583ms 1.05% __atan2 237ms 0.43% 75.90% 572ms 1.03% AbstractElement::GetNodeLocation 0 0% 75.90% 553ms 1.00% std::set::find (inline) 544ms 0.98% 76.89% 544ms 0.98% tetgen::tetgenmesh::triface::operator= 0 0% 76.89% 525ms 0.95% boost::numeric::ublas::inner_prod (inline) 413ms 0.75% 77.63% 520ms 0.94% __ieee754_atan2_fma 2ms 0.0036% 77.64% 518ms 0.94% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 31ms 0.056% 77.69% 516ms 0.93% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 77.69% 511ms 0.92% std::insert_iterator::operator= (inline) 499ms 0.9% 78.59% 499ms 0.9% Node::rGetLocation 55ms 0.099% 78.69% 498ms 0.9% tetgen::tetgenmesh::enextfnext 46ms 0.083% 78.78% 492ms 0.89% tetgen::tetgenmesh::enext2fnext 309ms 0.56% 79.34% 472ms 0.85% tetgen::tetgenmesh::sym 22ms 0.04% 79.38% 470ms 0.85% Element::CalculateCircumsphere 451ms 0.82% 80.19% 451ms 0.82% std::vector::size (inline) 23ms 0.042% 80.23% 451ms 0.82% tetgen::tetgenmesh::queue::push 43ms 0.078% 80.31% 449ms 0.81% AbstractTetrahedralElement::RefreshJacobian 0 0% 80.31% 445ms 0.8% std::_Rb_tree::_M_insert_unique_ (inline) 302ms 0.55% 80.86% 425ms 0.77% tetgen::tetgenmesh::link::add 6ms 0.011% 80.87% 422ms 0.76% CellPropertyCollection::GetPropertiesType (inline) 32ms 0.058% 80.93% 413ms 0.75% std::_Rb_tree_iterator::operator-- (inline) 412ms 0.75% 81.67% 412ms 0.75% boost::numeric::ublas::c_vector::operator() 181ms 0.33% 82.00% 412ms 0.75% boost::numeric::ublas::vector_inner_prod::apply (inline) 2ms 0.0036% 82.00% 411ms 0.74% Cell::GetCellId 110ms 0.2% 82.20% 404ms 0.73% __dynamic_cast 400ms 0.72% 82.92% 400ms 0.72% tetgen::tetgenmesh::org 103ms 0.19% 83.11% 397ms 0.72% boost::numeric::ublas::indexing_vector_assign 1ms 0.0018% 83.11% 392ms 0.71% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 83.11% 381ms 0.69% VertexMeshWriter::WriteVtkUsingMesh 54ms 0.098% 83.21% 378ms 0.68% tetgen::tetgenmesh::queue::pop 216ms 0.39% 83.60% 375ms 0.68% AbstractTetrahedralMesh::GetElement 274ms 0.5% 84.10% 369ms 0.67% tetgen::tetgenmesh::bond 15ms 0.027% 84.12% 366ms 0.66% VertexMesh::CalculateUnitNormalToFaceWithArea 358ms 0.65% 84.77% 358ms 0.65% AbstractElement::IsDeleted 1ms 0.0018% 84.77% 350ms 0.63% AbstractCellProperty::IsSubType (inline) 348ms 0.63% 85.40% 348ms 0.63% std::_Rb_tree_decrement 14ms 0.025% 85.43% 347ms 0.63% std::vector::insert (inline) 56ms 0.1% 85.53% 330ms 0.6% boost::numeric::ublas::vector_reference::operator() (inline) 8ms 0.014% 85.54% 324ms 0.59% VertexElement::~VertexElement 213ms 0.39% 85.93% 322ms 0.58% tetgen::tetgenmesh::link::deletenode 133ms 0.24% 86.17% 318ms 0.58% Inverse 5ms 0.009% 86.18% 305ms 0.55% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 86.18% 305ms 0.55% tcache_get (inline) 305ms 0.55% 86.73% 305ms 0.55% tcache_get_n (inline) 0 0% 86.73% 290ms 0.52% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 41ms 0.074% 86.80% 284ms 0.51% tetgen::insphereadapt