File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 36763ms, 86.72% of 42392ms total Dropped 805 nodes (cum <= 211.96ms) flat flat% sum% cum cum% 0 0% 0% 42346ms 99.89% __libc_start_call_main 0 0% 0% 42346ms 99.89% __libc_start_main_impl 0 0% 0% 42346ms 99.89% _start 0 0% 0% 42334ms 99.86% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 42334ms 99.86% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 42334ms 99.86% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 42334ms 99.86% main 0 0% 0% 42302ms 99.79% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 42302ms 99.79% CxxTest::TestRunner::runTest (inline) 0 0% 0% 42302ms 99.79% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 42143ms 99.41% AbstractCellBasedSimulation::Solve 0 0% 0% 35928ms 84.75% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 35881ms 84.64% MeshBasedCellPopulation::Update 0 0% 0% 21283ms 50.21% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 21283ms 50.21% MeshBasedCellPopulation::TessellateIfNeeded 119ms 0.28% 0.28% 18337ms 43.26% VertexMesh::VertexMesh 1ms 0.0024% 0.28% 11650ms 27.48% MutableMesh::ReMesh 433ms 1.02% 1.30% 8864ms 20.91% TetrahedralMesh::EdgeIterator::operator++ 1ms 0.0024% 1.31% 8554ms 20.18% tetgen::tetrahedralize 2ms 0.0047% 1.31% 8496ms 20.04% tetgen::tetgenmesh::delaunizevertices 3ms 0.0071% 1.32% 8493ms 20.03% tetgen::tetgenmesh::incrflipdelaunay 34ms 0.08% 1.40% 7628ms 17.99% std::set::insert (inline) 327ms 0.77% 2.17% 7514ms 17.73% tetgen::tetgenmesh::lawson 142ms 0.33% 2.51% 7336ms 17.31% std::_Rb_tree::_M_insert_unique 234ms 0.55% 3.06% 6660ms 15.71% VertexElement::AddFace 2434ms 5.74% 8.80% 6145ms 14.50% std::_Rb_tree::_M_lower_bound (inline) 159ms 0.38% 9.17% 5772ms 13.62% std::_Rb_tree::find (partial-inline) 0 0% 9.17% 5416ms 12.78% std::set::count (inline) 149ms 0.35% 9.53% 4696ms 11.08% operator new 207ms 0.49% 10.01% 4538ms 10.70% std::_Rb_tree::_M_insert_ (inline) 1496ms 3.53% 13.54% 4497ms 10.61% __GI___libc_malloc 39ms 0.092% 13.63% 3877ms 9.15% std::__new_allocator::allocate (inline) 0 0% 13.63% 3862ms 9.11% std::allocator_traits::allocate (inline) 3799ms 8.96% 22.60% 3799ms 8.96% std::_Rb_tree_increment 0 0% 22.60% 3759ms 8.87% OffLatticeSimulation::UpdateCellLocationsAndTopology 88ms 0.21% 22.80% 3674ms 8.67% std::less::operator() (inline) 0 0% 22.80% 3665ms 8.65% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0024% 22.81% 3654ms 8.62% AbstractNumericalMethod::ComputeForcesIncludingDamping 3640ms 8.59% 31.39% 3641ms 8.59% std::operator< (inline) 6ms 0.014% 31.41% 3450ms 8.14% std::_Rb_tree::~_Rb_tree (inline) 1216ms 2.87% 34.28% 3441ms 8.12% std::_Rb_tree::_M_erase 0 0% 34.28% 3406ms 8.03% std::set::~set (inline) 874ms 2.06% 36.34% 3383ms 7.98% __GI___libc_free 0 0% 36.34% 3198ms 7.54% std::_Rb_tree::_M_create_node (inline) 0 0% 36.34% 3172ms 7.48% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 36.34% 3170ms 7.48% MeshBasedCellPopulation::UpdateNodePairs 0 0% 36.34% 3162ms 7.46% std::_Rb_tree::_M_get_node (inline) 2ms 0.0047% 36.34% 3104ms 7.32% std::set_intersection (inline) 213ms 0.5% 36.84% 3102ms 7.32% std::__set_intersection 4ms 0.0094% 36.85% 3094ms 7.30% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 7ms 0.017% 36.87% 3069ms 7.24% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 36.87% 2963ms 6.99% VertexMesh::~VertexMesh 922ms 2.17% 39.05% 2822ms 6.66% std::_Rb_tree::_M_get_insert_unique_pos 72ms 0.17% 39.21% 2799ms 6.60% std::__new_allocator::deallocate (inline) 0 0% 39.21% 2790ms 6.58% std::allocator_traits::deallocate (inline) 2049ms 4.83% 44.05% 2785ms 6.57% _int_malloc 23ms 0.054% 44.10% 2773ms 6.54% Node::AddElement 3ms 0.0071% 44.11% 2579ms 6.08% TetrahedralMesh::ImportFromMesher 136ms 0.32% 44.43% 2571ms 6.06% std::_Rb_tree_const_iterator::operator++ (inline) 1263ms 2.98% 47.41% 2506ms 5.91% _int_free 0 0% 47.41% 2356ms 5.56% AbstractCellPopulation::WriteResultsToFiles 85ms 0.2% 47.61% 2259ms 5.33% tetgen::tetgenmesh::insphere_sos 2224ms 5.25% 52.86% 2224ms 5.25% std::_Rb_tree::_S_right (inline) 57ms 0.13% 52.99% 2201ms 5.19% MutableElement::AddNode 129ms 0.3% 53.30% 2199ms 5.19% Node::~Node 1982ms 4.68% 57.97% 2164ms 5.10% tetgen::insphere 73ms 0.17% 58.14% 2025ms 4.78% VertexMesh::Clear 0 0% 58.14% 1701ms 4.01% std::_Rb_tree::_M_drop_node (inline) 0 0% 58.14% 1682ms 3.97% std::_Rb_tree::_M_put_node (inline) 106ms 0.25% 58.39% 1653ms 3.90% tetgen::tetgenmesh::flip23 1ms 0.0024% 58.40% 1599ms 3.77% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 84ms 0.2% 58.59% 1597ms 3.77% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 2ms 0.0047% 58.60% 1521ms 3.59% std::_Rb_tree_iterator::operator++ (inline) 1227ms 2.89% 61.49% 1227ms 2.89% std::_Rb_tree_insert_and_rebalance 74ms 0.17% 61.67% 1185ms 2.80% TetrahedralMesh::Clear 848ms 2.00% 63.67% 1172ms 2.76% malloc_consolidate 53ms 0.13% 63.79% 1135ms 2.68% tetgen::tetgenmesh::flip32 23ms 0.054% 63.85% 1131ms 2.67% std::_Vector_base::_M_deallocate (inline) 4ms 0.0094% 63.86% 1118ms 2.64% Element::Element 0 0% 63.86% 1111ms 2.62% std::vector::~vector (inline) 0 0% 63.86% 1033ms 2.44% std::_Vector_base::~_Vector_base (inline) 6ms 0.014% 63.87% 1011ms 2.38% _int_free_maybe_consolidate 918ms 2.17% 66.04% 979ms 2.31% tetgen::orient3d 690ms 1.63% 67.66% 929ms 2.19% AbstractElement::GetNodeGlobalIndex 4ms 0.0094% 67.67% 915ms 2.16% Element::RegisterWithNodes (inline) 82ms 0.19% 67.87% 854ms 2.01% tetgen::tetgenmesh::enqueueflipface 849ms 2.00% 69.87% 849ms 2.00% unlink_chunk 24ms 0.057% 69.93% 834ms 1.97% tetgen::tetgenmesh::locate 52ms 0.12% 70.05% 798ms 1.88% std::vector::_M_realloc_insert 85ms 0.2% 70.25% 785ms 1.85% tetgen::tetgenmesh::preciselocate 59ms 0.14% 70.39% 733ms 1.73% std::map::operator[] 720ms 1.70% 72.09% 720ms 1.70% Node::GetIndex 1ms 0.0024% 72.09% 701ms 1.65% std::_Vector_base::_M_allocate (inline) 6ms 0.014% 72.10% 693ms 1.63% VertexMesh::GenerateVerticesFromElementCircumcentres 679ms 1.60% 73.70% 679ms 1.60% [libchaste_mesh.so] 0 0% 73.70% 617ms 1.46% std::_Rb_tree::lower_bound (inline) 0 0% 73.70% 617ms 1.46% std::map::lower_bound (inline) 617ms 1.46% 75.16% 617ms 1.46% tetgen::tetgenmesh::oppo 49ms 0.12% 75.28% 604ms 1.42% std::vector::push_back (inline) 592ms 1.40% 76.67% 592ms 1.40% std::vector::size (inline) 0 0% 76.67% 588ms 1.39% VoronoiDataWriter::Visit 306ms 0.72% 77.39% 551ms 1.30% tetgen::tetgenmesh::sym 537ms 1.27% 78.66% 537ms 1.27% AbstractElement::IsDeleted 1ms 0.0024% 78.66% 500ms 1.18% TetrahedralMesh::RefreshJacobianCachedData 251ms 0.59% 79.26% 495ms 1.17% AbstractElement::GetNodeLocation 2ms 0.0047% 79.26% 459ms 1.08% AbstractTwoBodyInteractionForce::AddForceContribution 9ms 0.021% 79.28% 444ms 1.05% AbstractTetrahedralElement::CalculateJacobian 9ms 0.021% 79.30% 442ms 1.04% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 5ms 0.012% 79.31% 431ms 1.02% AbstractTetrahedralElement::CalculateInverseJacobian 376ms 0.89% 80.20% 376ms 0.89% Node::rGetLocation 21ms 0.05% 80.25% 372ms 0.88% __atan2 0 0% 80.25% 355ms 0.84% std::set::find (inline) 8ms 0.019% 80.27% 352ms 0.83% boost::numeric::ublas::vector_assign (inline) 250ms 0.59% 80.86% 351ms 0.83% tetgen::tetgenmesh::fnextself 279ms 0.66% 81.52% 349ms 0.82% __ieee754_atan2_fma 6ms 0.014% 81.53% 339ms 0.8% VertexElement::~VertexElement 337ms 0.79% 82.33% 337ms 0.79% tetgen::tetgenmesh::triface::operator= 7ms 0.017% 82.34% 336ms 0.79% boost::numeric::ublas::c_vector::c_vector (inline) 155ms 0.37% 82.71% 333ms 0.79% AbstractTetrahedralMesh::GetElement 26ms 0.061% 82.77% 332ms 0.78% AbstractTetrahedralElement::RefreshJacobian 5ms 0.012% 82.78% 328ms 0.77% Element::CalculateCircumsphere 312ms 0.74% 83.52% 312ms 0.74% boost::numeric::ublas::c_vector::operator() 30ms 0.071% 83.59% 308ms 0.73% tetgen::tetgenmesh::enext2fnext 0 0% 83.59% 293ms 0.69% std::insert_iterator::operator= (inline) 0 0% 83.59% 289ms 0.68% boost::numeric::ublas::inner_prod (inline) 3ms 0.0071% 83.60% 289ms 0.68% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 12ms 0.028% 83.62% 286ms 0.67% boost::numeric::ublas::vector_scalar_binary::evaluate 11ms 0.026% 83.65% 265ms 0.63% VertexMesh::CalculateUnitNormalToFaceWithArea 265ms 0.63% 84.28% 265ms 0.63% tetgen::tetgenmesh::org 65ms 0.15% 84.43% 262ms 0.62% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 84.43% 258ms 0.61% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 84.43% 256ms 0.6% VertexMeshWriter::WriteVtkUsingMesh 38ms 0.09% 84.52% 255ms 0.6% tetgen::tetgenmesh::enextfnext 255ms 0.6% 85.12% 255ms 0.6% tetgen::tetgenmesh::pointmark 19ms 0.045% 85.16% 254ms 0.6% boost::numeric::ublas::vector_reference::operator() (inline) 253ms 0.6% 85.76% 253ms 0.6% tetgen::tetgenmesh::triface::triface 4ms 0.0094% 85.77% 251ms 0.59% std::vector::insert (inline) 108ms 0.25% 86.03% 250ms 0.59% tetgen::tetgenmesh::queue::pop 0 0% 86.03% 244ms 0.58% Cell::GetCellId 30ms 0.071% 86.10% 244ms 0.58% std::_Rb_tree_iterator::operator-- (inline) 0 0% 86.10% 240ms 0.57% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 2ms 0.0047% 86.10% 240ms 0.57% Element::~Element 4ms 0.0094% 86.11% 235ms 0.55% CellPropertyCollection::GetPropertiesType (inline) 233ms 0.55% 86.66% 233ms 0.55% tetgen::tetgenmesh::decode 20ms 0.047% 86.71% 229ms 0.54% tetgen::tetgenmesh::queue::push 3ms 0.0071% 86.71% 228ms 0.54% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 86.71% 220ms 0.52% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 3ms 0.0071% 86.72% 215ms 0.51% VertexMesh::GetVolumeOfElement