File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 42502ms, 87.48% of 48585ms total Dropped 836 nodes (cum <= 242.93ms) flat flat% sum% cum cum% 0 0% 0% 48521ms 99.87% __libc_start_call_main 0 0% 0% 48521ms 99.87% __libc_start_main_impl 0 0% 0% 48521ms 99.87% _start 0 0% 0% 48504ms 99.83% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 48504ms 99.83% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 48504ms 99.83% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 48504ms 99.83% main 0 0% 0% 48467ms 99.76% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 48467ms 99.76% CxxTest::TestRunner::runTest (inline) 0 0% 0% 48467ms 99.76% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 48253ms 99.32% AbstractCellBasedSimulation::Solve 0 0% 0% 41004ms 84.40% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0021% 0.0021% 40972ms 84.33% MeshBasedCellPopulation::Update 0 0% 0.0021% 22158ms 45.61% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0.0021% 22157ms 45.60% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 185ms 0.38% 0.38% 19779ms 40.71% VertexMesh::VertexMesh 0 0% 0.38% 15601ms 32.11% MutableMesh::ReMesh 0 0% 0.38% 12475ms 25.68% tetgen::tetrahedralize 2ms 0.0041% 0.39% 12357ms 25.43% tetgen::tetgenmesh::delaunizevertices 7ms 0.014% 0.4% 12351ms 25.42% tetgen::tetgenmesh::incrflipdelaunay 388ms 0.8% 1.20% 11056ms 22.76% tetgen::tetgenmesh::lawson 474ms 0.98% 2.18% 9826ms 20.22% TetrahedralMesh::EdgeIterator::operator++ 18ms 0.037% 2.21% 7822ms 16.10% std::set::insert (inline) 258ms 0.53% 2.74% 7608ms 15.66% VertexElement::AddFace 198ms 0.41% 3.15% 7475ms 15.39% std::_Rb_tree::_M_insert_unique 2524ms 5.20% 8.35% 7297ms 15.02% std::_Rb_tree::_M_lower_bound (inline) 160ms 0.33% 8.68% 6831ms 14.06% std::_Rb_tree::find (inline) 0 0% 8.68% 6379ms 13.13% std::set::count (inline) 81ms 0.17% 8.84% 4643ms 9.56% std::less::operator() (inline) 4607ms 9.48% 18.32% 4607ms 9.48% std::operator< (inline) 252ms 0.52% 18.84% 4501ms 9.26% std::_Rb_tree::_M_insert_ (inline) 1ms 0.0021% 18.85% 4275ms 8.80% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 18.85% 4157ms 8.56% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0021% 18.85% 4136ms 8.51% AbstractNumericalMethod::ComputeForcesIncludingDamping 4039ms 8.31% 27.16% 4039ms 8.31% std::_Rb_tree_increment 152ms 0.31% 27.47% 3934ms 8.10% operator new 925ms 1.90% 29.38% 3703ms 7.62% __GI___libc_malloc 0 0% 29.38% 3504ms 7.21% MeshBasedCellPopulation::UpdateNodePairs 21ms 0.043% 29.42% 3428ms 7.06% std::__new_allocator::allocate (inline) 6ms 0.012% 29.43% 3423ms 7.05% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 29.43% 3412ms 7.02% std::allocator_traits::allocate (inline) 12ms 0.025% 29.46% 3381ms 6.96% MeshBasedCellPopulation::SpringIterator::operator++ 3ms 0.0062% 29.46% 3285ms 6.76% std::_Rb_tree::~_Rb_tree (inline) 1129ms 2.32% 31.79% 3280ms 6.75% std::_Rb_tree::_M_erase 0 0% 31.79% 3241ms 6.67% std::set::~set (inline) 2ms 0.0041% 31.79% 3070ms 6.32% std::set_intersection (inline) 217ms 0.45% 32.24% 3068ms 6.31% std::__set_intersection 914ms 1.88% 34.12% 3063ms 6.30% __GI___libc_free 1029ms 2.12% 36.24% 2957ms 6.09% std::_Rb_tree::_M_get_insert_unique_pos 82ms 0.17% 36.41% 2934ms 6.04% tetgen::tetgenmesh::insphere_sos 0 0% 36.41% 2852ms 5.87% AbstractCellPopulation::WriteResultsToFiles 2629ms 5.41% 41.82% 2845ms 5.86% tetgen::insphere 0 0% 41.82% 2823ms 5.81% std::_Rb_tree::_M_create_node (inline) 0 0% 41.82% 2798ms 5.76% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 41.82% 2793ms 5.75% std::_Rb_tree::_M_get_node (inline) 96ms 0.2% 42.02% 2694ms 5.54% tetgen::tetgenmesh::flip23 104ms 0.21% 42.23% 2673ms 5.50% std::__new_allocator::deallocate (inline) 0 0% 42.23% 2664ms 5.48% std::allocator_traits::deallocate (inline) 3ms 0.0062% 42.24% 2533ms 5.21% TetrahedralMesh::ImportFromMesher 42ms 0.086% 42.32% 2532ms 5.21% Node::AddElement 1772ms 3.65% 45.97% 2492ms 5.13% _int_malloc 143ms 0.29% 46.26% 2481ms 5.11% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 46.26% 2393ms 4.93% VertexMesh::~VertexMesh 2323ms 4.78% 51.04% 2323ms 4.78% std::_Rb_tree::_S_right (inline) 1083ms 2.23% 53.27% 2145ms 4.41% _int_free 98ms 0.2% 53.48% 2042ms 4.20% tetgen::tetgenmesh::flip32 59ms 0.12% 53.60% 2026ms 4.17% MutableElement::AddNode 1ms 0.0021% 53.60% 1938ms 3.99% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 133ms 0.27% 53.87% 1936ms 3.98% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 130ms 0.27% 54.14% 1822ms 3.75% Node::~Node 2ms 0.0041% 54.14% 1811ms 3.73% std::_Rb_tree_iterator::operator++ (inline) 0 0% 54.14% 1664ms 3.42% std::_Rb_tree::_M_drop_node (inline) 0 0% 54.14% 1651ms 3.40% std::_Rb_tree::_M_put_node (inline) 147ms 0.3% 54.45% 1588ms 3.27% VertexMesh::Clear 1491ms 3.07% 57.52% 1491ms 3.07% std::_Rb_tree_insert_and_rebalance 168ms 0.35% 57.86% 1429ms 2.94% tetgen::tetgenmesh::enqueueflipface 1290ms 2.66% 60.52% 1290ms 2.66% Node::GetIndex 1175ms 2.42% 62.94% 1245ms 2.56% tetgen::orient3d 64ms 0.13% 63.07% 1186ms 2.44% TetrahedralMesh::Clear 4ms 0.0082% 63.08% 1147ms 2.36% Element::Element 41ms 0.084% 63.16% 1076ms 2.21% tetgen::tetgenmesh::locate 17ms 0.035% 63.19% 1030ms 2.12% std::_Vector_base::_M_deallocate (inline) 648ms 1.33% 64.53% 1028ms 2.12% malloc_consolidate 64ms 0.13% 64.66% 1004ms 2.07% tetgen::tetgenmesh::preciselocate 0 0% 64.66% 983ms 2.02% std::vector::~vector (inline) 903ms 1.86% 66.52% 903ms 1.86% tetgen::tetgenmesh::triface::triface 6ms 0.012% 66.53% 900ms 1.85% Element::RegisterWithNodes (inline) 0 0% 66.53% 893ms 1.84% std::_Vector_base::~_Vector_base (inline) 7ms 0.014% 66.55% 879ms 1.81% _int_free_maybe_consolidate 56ms 0.12% 66.66% 861ms 1.77% std::map::operator[] 859ms 1.77% 68.43% 859ms 1.77% unlink_chunk 38ms 0.078% 68.51% 823ms 1.69% std::vector::_M_realloc_insert 790ms 1.63% 70.13% 790ms 1.63% tetgen::tetgenmesh::oppo 611ms 1.26% 71.39% 769ms 1.58% AbstractElement::GetNodeGlobalIndex 0 0% 71.39% 744ms 1.53% std::_Rb_tree::lower_bound (inline) 0 0% 71.39% 744ms 1.53% std::map::lower_bound (inline) 0 0% 71.39% 724ms 1.49% VoronoiDataWriter::Visit 4ms 0.0082% 71.40% 669ms 1.38% VertexMesh::GenerateVerticesFromElementCircumcentres 652ms 1.34% 72.74% 652ms 1.34% [libchaste_mesh.so] 77ms 0.16% 72.90% 647ms 1.33% std::vector::push_back (inline) 243ms 0.5% 73.40% 645ms 1.33% tetgen::tetgenmesh::sym 2ms 0.0041% 73.40% 621ms 1.28% std::_Vector_base::_M_allocate (inline) 594ms 1.22% 74.63% 594ms 1.22% tetgen::tetgenmesh::triface::operator= 1ms 0.0021% 74.63% 586ms 1.21% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 74.63% 577ms 1.19% TetrahedralMesh::RefreshJacobianCachedData 287ms 0.59% 75.22% 558ms 1.15% tetgen::tetgenmesh::fnextself 10ms 0.021% 75.24% 557ms 1.15% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 8ms 0.016% 75.26% 539ms 1.11% AbstractTetrahedralElement::CalculateInverseJacobian 41ms 0.084% 75.34% 525ms 1.08% tetgen::tetgenmesh::enextfnext 18ms 0.037% 75.38% 492ms 1.01% boost::numeric::ublas::vector_assign (inline) 39ms 0.08% 75.46% 481ms 0.99% __atan2 174ms 0.36% 75.82% 481ms 0.99% tetgen::tetgenmesh::bond 10ms 0.021% 75.84% 473ms 0.97% boost::numeric::ublas::c_vector::c_vector (inline) 52ms 0.11% 75.94% 470ms 0.97% tetgen::tetgenmesh::enext2fnext 28ms 0.058% 76.00% 462ms 0.95% tetgen::tetgenmesh::queue::push 15ms 0.031% 76.03% 451ms 0.93% AbstractTetrahedralElement::CalculateJacobian 0 0% 76.03% 447ms 0.92% std::set::find (inline) 337ms 0.69% 76.73% 437ms 0.9% __ieee754_atan2_fma 307ms 0.63% 77.36% 434ms 0.89% tetgen::tetgenmesh::link::add 194ms 0.4% 77.76% 426ms 0.88% AbstractElement::GetNodeLocation 414ms 0.85% 78.61% 414ms 0.85% Node::rGetLocation 414ms 0.85% 79.46% 414ms 0.85% std::vector::size (inline) 401ms 0.83% 80.29% 401ms 0.83% tetgen::tetgenmesh::decode 388ms 0.8% 81.08% 388ms 0.8% AbstractElement::IsDeleted 0 0% 81.08% 379ms 0.78% boost::numeric::ublas::inner_prod (inline) 26ms 0.054% 81.14% 374ms 0.77% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 81.14% 374ms 0.77% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 81.14% 367ms 0.76% std::insert_iterator::operator= (inline) 13ms 0.027% 81.16% 354ms 0.73% Element::CalculateCircumsphere 345ms 0.71% 81.88% 345ms 0.71% tetgen::tetgenmesh::org 1ms 0.0021% 81.88% 344ms 0.71% Cell::GetCellId 165ms 0.34% 82.22% 342ms 0.7% AbstractTetrahedralMesh::GetElement 6ms 0.012% 82.23% 338ms 0.7% CellPropertyCollection::GetPropertiesType (inline) 63ms 0.13% 82.36% 329ms 0.68% __dynamic_cast 0 0% 82.36% 326ms 0.67% std::_Rb_tree::_M_insert_unique_ (inline) 13ms 0.027% 82.39% 317ms 0.65% VertexMesh::CalculateUnitNormalToFaceWithArea 317ms 0.65% 83.04% 317ms 0.65% boost::numeric::ublas::c_vector::operator() 24ms 0.049% 83.09% 314ms 0.65% AbstractTetrahedralElement::RefreshJacobian 0 0% 83.09% 311ms 0.64% VertexMeshWriter::WriteVtkUsingMesh 69ms 0.14% 83.23% 307ms 0.63% boost::numeric::ublas::indexing_vector_assign 15ms 0.031% 83.26% 302ms 0.62% std::_Rb_tree_iterator::operator-- (inline) 4ms 0.0082% 83.27% 298ms 0.61% boost::numeric::ublas::c_vector::operator= (inline) 129ms 0.27% 83.53% 297ms 0.61% boost::numeric::ublas::vector_inner_prod::apply (inline) 39ms 0.08% 83.61% 297ms 0.61% tetgen::tetgenmesh::queue::pop 295ms 0.61% 84.22% 295ms 0.61% tetgen::tetgenmesh::encode 5ms 0.01% 84.23% 292ms 0.6% Element::~Element 1ms 0.0021% 84.23% 287ms 0.59% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 6ms 0.012% 84.25% 284ms 0.58% VertexElement::~VertexElement 108ms 0.22% 84.47% 283ms 0.58% Inverse 20ms 0.041% 84.51% 283ms 0.58% std::vector::insert (inline) 0 0% 84.51% 278ms 0.57% AbstractCellProperty::IsSubType (inline) 271ms 0.56% 85.07% 271ms 0.56% std::_Rb_tree_decrement 269ms 0.55% 85.62% 269ms 0.55% tetgen::tetgenmesh::pointmark 0 0% 85.62% 261ms 0.54% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 156ms 0.32% 85.94% 255ms 0.52% tetgen::tetgenmesh::link::deletenode 253ms 0.52% 86.46% 253ms 0.52% tetgen::tetgenmesh::face::face 246ms 0.51% 86.97% 246ms 0.51% tetgen::tetgenmesh::dest 0 0% 86.97% 245ms 0.5% tcache_get (inline) 245ms 0.5% 87.47% 245ms 0.5% tcache_get_n (inline) 3ms 0.0062% 87.48% 243ms 0.5% AbstractTetrahedralElement::AbstractTetrahedralElement