File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95563ms, 87.73% of 108925ms total Dropped 1095 nodes (cum <= 544.62ms) flat flat% sum% cum cum% 0 0% 0% 108568ms 99.67% __libc_start_call_main 0 0% 0% 108568ms 99.67% __libc_start_main_impl 0 0% 0% 108568ms 99.67% _start 0 0% 0% 108546ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108546ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108546ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108546ms 99.65% main 0 0% 0% 108497ms 99.61% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108497ms 99.61% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108497ms 99.61% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 5ms 0.0046% 0.0046% 108488ms 99.60% AbstractCellBasedSimulation::Solve 18ms 0.017% 0.021% 56431ms 51.81% OffLatticeSimulation::UpdateCellLocationsAndTopology 8ms 0.0073% 0.028% 53128ms 48.77% ForwardEulerNumericalMethod::UpdateAllNodePositions 144ms 0.13% 0.16% 52025ms 47.76% AbstractNumericalMethod::ComputeForcesIncludingDamping 322ms 0.3% 0.46% 39981ms 36.71% NagaiHondaForce::AddForceContribution 0 0% 0.46% 38811ms 35.63% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00092% 0.46% 23783ms 21.83% VertexBasedCellPopulation::Update 1ms 0.00092% 0.46% 23627ms 21.69% MutableVertexMesh::ReMesh 14760ms 13.55% 14.01% 23482ms 21.56% Cylindrical2dVertexMesh::GetVectorFromAtoB 73ms 0.067% 14.08% 17922ms 16.45% Cell::ReadyToDivide 71ms 0.065% 14.14% 16651ms 15.29% AbstractPhaseBasedCellCycleModel::ReadyToDivide 386ms 0.35% 14.50% 14690ms 13.49% NagaiHondaForce::GetAdhesionParameter 148ms 0.14% 14.63% 14343ms 13.17% SimpleWntCellCycleModel::UpdateCellCyclePhase 451ms 0.41% 15.05% 13856ms 12.72% boost::numeric::ublas::c_vector::c_vector (partial-inline) 102ms 0.094% 15.14% 13643ms 12.53% CellPropertyCollection::GetPropertiesType (inline) 324ms 0.3% 15.44% 12396ms 11.38% boost::numeric::ublas::vector_assign (inline) 139ms 0.13% 15.56% 11774ms 10.81% MutableVertexMesh::CheckForIntersections 3346ms 3.07% 18.64% 11767ms 10.80% __dynamic_cast 102ms 0.094% 18.73% 11665ms 10.71% AbstractCellProperty::IsSubType (inline) 85ms 0.078% 18.81% 11488ms 10.55% VertexBasedCellPopulation::GetDampingConstant 55ms 0.05% 18.86% 10725ms 9.85% AbstractTargetAreaModifier::UpdateTargetAreas 36ms 0.033% 18.89% 10658ms 9.78% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 25ms 0.023% 18.91% 10441ms 9.59% AbstractCellBasedSimulation::DoCellBirth 1319ms 1.21% 20.12% 9963ms 9.15% std::__new_allocator::allocate (inline) 0 0% 20.12% 9432ms 8.66% std::allocator_traits::allocate (inline) 2826ms 2.59% 22.72% 9418ms 8.65% boost::numeric::ublas::indexing_vector_assign 0 0% 22.72% 9378ms 8.61% std::_Rb_tree::_M_create_node (inline) 332ms 0.3% 23.02% 9314ms 8.55% VertexMesh::GetNextEdgeGradientOfElementAtNode 1289ms 1.18% 24.21% 9106ms 8.36% std::_Rb_tree::_M_erase 25ms 0.023% 24.23% 8978ms 8.24% VertexBasedCellPopulation::GetLocationOfCellCentre 87ms 0.08% 24.31% 8798ms 8.08% Cell::GetMutationState 0 0% 24.31% 8762ms 8.04% std::_Rb_tree::_M_get_node (inline) 754ms 0.69% 25.00% 8718ms 8.00% operator new 847ms 0.78% 25.78% 8654ms 7.94% VertexMesh::ElementIncludesPoint 455ms 0.42% 26.20% 8502ms 7.81% VertexMesh::GetCentroidOfElement 282ms 0.26% 26.46% 8304ms 7.62% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.46% 8220ms 7.55% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.46% 8215ms 7.54% std::_Rb_tree::_Alloc_node::operator() (inline) 221ms 0.2% 26.66% 7930ms 7.28% std::__new_allocator::deallocate (inline) 0 0% 26.66% 7921ms 7.27% std::allocator_traits::deallocate (inline) 0 0% 26.66% 7919ms 7.27% std::set::~set (inline) 0 0% 26.66% 7861ms 7.22% std::_Rb_tree::_M_put_node (inline) 3012ms 2.77% 29.42% 7784ms 7.15% __GI___libc_malloc 479ms 0.44% 29.86% 7674ms 7.05% std::map::operator[] (partial-inline) 24ms 0.022% 29.89% 7565ms 6.95% MutableVertexMesh::RemoveDeletedNodesAndElements 3096ms 2.84% 32.73% 7481ms 6.87% __GI___libc_free 1285ms 1.18% 33.91% 7413ms 6.81% AbstractMesh::GetDistanceBetweenNodes 172ms 0.16% 34.07% 7102ms 6.52% std::_Rb_tree::_Rb_tree (partial-inline) 6709ms 6.16% 40.23% 6709ms 6.16% __strcmp_avx2 717ms 0.66% 40.88% 6696ms 6.15% std::_Rb_tree::_M_copy (inline) 25ms 0.023% 40.91% 6630ms 6.09% std::set::set (inline) 110ms 0.1% 41.01% 6569ms 6.03% SimpleWntCellCycleModel::GetWntLevel 174ms 0.16% 41.17% 6372ms 5.85% WntConcentration::GetWntLevel 6178ms 5.67% 46.84% 6178ms 5.67% boost::numeric::ublas::c_vector::operator() 2527ms 2.32% 49.16% 6017ms 5.52% std::_Rb_tree::_M_lower_bound (inline) 803ms 0.74% 49.90% 5738ms 5.27% std::_Rb_tree::_M_clone_node (inline) 2910ms 2.67% 52.57% 5663ms 5.20% __cxxabiv1::__si_class_type_info::__do_dyncast 1987ms 1.82% 54.39% 5357ms 4.92% boost::numeric::ublas::c_vector::operator[] (inline) 25ms 0.023% 54.42% 5351ms 4.91% MutableVertexMesh::RemoveDeletedNodes 38ms 0.035% 54.45% 5151ms 4.73% EdgeHelper::RemoveDeletedEdges 0 0% 54.45% 5142ms 4.72% std::set::insert (inline) 0 0% 54.45% 4962ms 4.56% std::_Rb_tree::lower_bound (inline) 0 0% 54.45% 4962ms 4.56% std::map::lower_bound (inline) 45ms 0.041% 54.49% 4867ms 4.47% EdgeHelper::UpdateEdgesMapKey 0 0% 54.49% 4576ms 4.20% AbstractCellBasedSimulation::DoCellRemoval (inline) 189ms 0.17% 54.67% 4575ms 4.20% MutableElement::ResetIndex 3942ms 3.62% 58.28% 4375ms 4.02% _int_free 132ms 0.12% 58.41% 4370ms 4.01% AbstractCellPopulation::GetCellUsingLocationIndex 506ms 0.46% 58.87% 4312ms 3.96% std::_Rb_tree::_M_insert_ (inline) 122ms 0.11% 58.98% 4304ms 3.95% std::set_intersection (inline) 254ms 0.23% 59.22% 4182ms 3.84% std::__set_intersection 51ms 0.047% 59.26% 3919ms 3.60% Cell::GetCellProliferativeType 3786ms 3.48% 62.74% 3786ms 3.48% boost::numeric::ublas::same_impl_ex 51ms 0.047% 62.78% 3754ms 3.45% AbstractCellProperty::IsType (inline) 12ms 0.011% 62.80% 3491ms 3.20% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.80% 3216ms 2.95% std::insert_iterator::operator= (inline) 82ms 0.075% 62.87% 3203ms 2.94% Cell::SetCellProliferativeType 2270ms 2.08% 64.95% 3195ms 2.93% _int_malloc 921ms 0.85% 65.80% 3074ms 2.82% AbstractElement::GetNodeLocation 72ms 0.066% 65.87% 2912ms 2.67% std::_Rb_tree::erase 2863ms 2.63% 68.49% 2863ms 2.63% std::_Rb_tree::_S_right (inline) 12ms 0.011% 68.51% 2781ms 2.55% std::_Rb_tree::_M_insert_unique_ (inline) 22ms 0.02% 68.53% 2681ms 2.46% CellPropertyCollection::HasProperty 236ms 0.22% 68.74% 2638ms 2.42% VertexMesh::GetAreaGradientOfElementAtNode 728ms 0.67% 69.41% 2621ms 2.41% AbstractCellProperty::IsSame 0 0% 69.41% 2585ms 2.37% Cell::HasCellProperty (inline) 600ms 0.55% 69.96% 2573ms 2.36% boost::numeric::ublas::vector_binary::size (inline) 237ms 0.22% 70.18% 2546ms 2.34% std::_Rb_tree_const_iterator::operator++ (inline) 32ms 0.029% 70.21% 2521ms 2.31% Cell::GetCellData 0 0% 70.21% 2517ms 2.31% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 70.21% 2494ms 2.29% boost::numeric::ublas::c_vector::assign (inline) 0 0% 70.21% 2484ms 2.28% AbstractCellPopulation::WriteResultsToFiles 1ms 0.00092% 70.21% 2361ms 2.17% std::_Rb_tree::_M_insert_unique 88ms 0.081% 70.29% 2333ms 2.14% VertexMesh::GetVolumeOfElement 41ms 0.038% 70.33% 2216ms 2.03% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 32ms 0.029% 70.36% 2197ms 2.02% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.0028% 70.36% 2175ms 2.00% AbstractCellPopulation::Iterator::operator++ (inline) 183ms 0.17% 70.53% 2170ms 1.99% AbstractCellPopulation::Iterator::IsRealCell (inline) 2ms 0.0018% 70.53% 2062ms 1.89% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.53% 2062ms 1.89% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 2061ms 1.89% 72.42% 2061ms 1.89% std::_Rb_tree_increment 0 0% 72.42% 2019ms 1.85% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 72.42% 2006ms 1.84% VertexBasedCellPopulation::WriteCellVtkResultsToFile 427ms 0.39% 72.81% 1893ms 1.74% std::type_info::operator== (inline) 1234ms 1.13% 73.95% 1877ms 1.72% std::_Rb_tree::equal_range (inline) 65ms 0.06% 74.01% 1849ms 1.70% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 74.01% 1800ms 1.65% VertexMeshWriter::WriteVtkUsingMesh 23ms 0.021% 74.03% 1666ms 1.53% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 34ms 0.031% 74.06% 1564ms 1.44% VertexMesh::GetSurfaceAreaOfElement 46ms 0.042% 74.10% 1528ms 1.40% AbstractCellPopulation::GetLocationIndexUsingCell 90ms 0.083% 74.18% 1476ms 1.36% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 39ms 0.036% 74.22% 1421ms 1.30% Node::RemoveElement 55ms 0.05% 74.27% 1398ms 1.28% boost::numeric::ublas::vector_reference::operator() (inline) 7ms 0.0064% 74.28% 1384ms 1.27% std::set::erase (inline) 3ms 0.0028% 74.28% 1378ms 1.27% OffLatticeSimulation::ApplyBoundaries 0 0% 74.28% 1377ms 1.26% tcache_get (inline) 1377ms 1.26% 75.54% 1377ms 1.26% tcache_get_n (inline) 190ms 0.17% 75.72% 1352ms 1.24% CellPropertyCollection::AddProperty 0 0% 75.72% 1343ms 1.23% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 75.72% 1335ms 1.23% boost::numeric::ublas::norm_2 (inline) 591ms 0.54% 76.26% 1325ms 1.22% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1311ms 1.20% 77.46% 1311ms 1.20% [libchaste_cell_based.so] 70ms 0.064% 77.53% 1299ms 1.19% std::less::operator() (inline) 986ms 0.91% 78.43% 1229ms 1.13% std::operator< (inline) 21ms 0.019% 78.45% 1179ms 1.08% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 78.45% 1163ms 1.07% std::_Rb_tree::_Auto_node::_Auto_node (inline) 88ms 0.081% 78.53% 1155ms 1.06% std::_Rb_tree::_M_erase_aux (partial-inline) 20ms 0.018% 78.55% 1122ms 1.03% CellPropertyRegistry::Get 1111ms 1.02% 79.57% 1111ms 1.02% std::_Rb_tree_insert_and_rebalance 0 0% 79.57% 1086ms 1% std::_Rb_tree::clear (inline) 0 0% 79.57% 1061ms 0.97% std::map::clear (inline) 79ms 0.073% 79.64% 1057ms 0.97% std::_Rb_tree::find (inline) 148ms 0.14% 79.78% 1049ms 0.96% boost::detail::shared_count::~shared_count (inline) 0 0% 79.78% 1049ms 0.96% boost::shared_ptr::~shared_ptr (inline) 0 0% 79.78% 1044ms 0.96% boost::numeric::ublas::c_vector::assign_temporary (inline) 15ms 0.014% 79.79% 1044ms 0.96% boost::numeric::ublas::c_vector::swap (inline) 5ms 0.0046% 79.80% 1039ms 0.95% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 77ms 0.071% 79.87% 1029ms 0.94% std::swap_ranges (inline) 15ms 0.014% 79.88% 1026ms 0.94% boost::numeric::ublas::detail::expression_type_check (inline) 205ms 0.19% 80.07% 1001ms 0.92% boost::numeric::ublas::detail::equals 1000ms 0.92% 80.99% 1000ms 0.92% Node::rGetLocation 0 0% 80.99% 952ms 0.87% std::iter_swap (inline) 952ms 0.87% 81.86% 952ms 0.87% std::swap (inline) 0 0% 81.86% 879ms 0.81% std::map::find (inline) 835ms 0.77% 82.63% 862ms 0.79% boost::detail::sp_counted_base::release 1ms 0.00092% 82.63% 855ms 0.78% VertexMeshWriter::MakeVtkMesh 90ms 0.083% 82.71% 802ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 82.71% 796ms 0.73% CellPropertyCollection::~CellPropertyCollection (inline) 788ms 0.72% 83.44% 788ms 0.72% std::vector::size (inline) 16ms 0.015% 83.45% 781ms 0.72% MutableElement::RegisterWithEdges (inline) 28ms 0.026% 83.48% 774ms 0.71% Edge::AddElement 420ms 0.39% 83.86% 741ms 0.68% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 379ms 0.35% 84.21% 728ms 0.67% Edge::GetMapIndex 0 0% 84.21% 728ms 0.67% boost::numeric::ublas::norm_inf (inline) 377ms 0.35% 84.56% 728ms 0.67% boost::numeric::ublas::vector_norm_inf::apply (inline) 716ms 0.66% 85.21% 716ms 0.66% [libchaste_mesh.so] 169ms 0.16% 85.37% 703ms 0.65% boost::shared_ptr::shared_ptr (inline) 0 0% 85.37% 697ms 0.64% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 204ms 0.19% 85.56% 681ms 0.63% std::__new_allocator::construct (inline) 0 0% 85.56% 681ms 0.63% std::allocator_traits::construct (inline) 0 0% 85.56% 670ms 0.62% std::_Rb_tree::_Auto_node::_M_insert (inline) 16ms 0.015% 85.57% 670ms 0.62% std::_Rb_tree::_M_insert_node (inline) 2ms 0.0018% 85.57% 667ms 0.61% std::_Vector_base::_M_allocate (inline) 124ms 0.11% 85.69% 644ms 0.59% MutableElement::GetNodeLocalIndex 622ms 0.57% 86.26% 622ms 0.57% Node::GetIndex 0 0% 86.26% 616ms 0.57% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.26% 610ms 0.56% vtkPolygon::New 0 0% 86.26% 610ms 0.56% vtkPolygon::vtkPolygon 372ms 0.34% 86.60% 593ms 0.54% CellPropertyCollection::GetProperty 34ms 0.031% 86.63% 589ms 0.54% MutableElement::RegisterWithNodes (inline) 589ms 0.54% 87.17% 589ms 0.54% [libstdc++.so.6.0.33] 29ms 0.027% 87.20% 560ms 0.51% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.20% 560ms 0.51% boost::numeric::ublas::vector::vector (inline) 23ms 0.021% 87.22% 557ms 0.51% Node::AddElement 9ms 0.0083% 87.23% 556ms 0.51% std::vector::_M_default_append (inline) 550ms 0.5% 87.73% 550ms 0.5% boost::shared_ptr::operator-> (inline)