File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 72112ms, 87.09% of 82798ms total Dropped 1020 nodes (cum <= 413.99ms) flat flat% sum% cum cum% 0 0% 0% 82483ms 99.62% __libc_start_call_main 0 0% 0% 82483ms 99.62% __libc_start_main_impl 0 0% 0% 82483ms 99.62% _start 0 0% 0% 82467ms 99.60% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 82467ms 99.60% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 82467ms 99.60% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 82467ms 99.60% main 0 0% 0% 82428ms 99.55% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 82428ms 99.55% CxxTest::TestRunner::runTest (inline) 0 0% 0% 82428ms 99.55% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0036% 0.0036% 82422ms 99.55% AbstractCellBasedSimulation::Solve 9ms 0.011% 0.014% 43004ms 51.94% OffLatticeSimulation::UpdateCellLocationsAndTopology 18ms 0.022% 0.036% 40427ms 48.83% ForwardEulerNumericalMethod::UpdateAllNodePositions 87ms 0.11% 0.14% 39546ms 47.76% AbstractNumericalMethod::ComputeForcesIncludingDamping 231ms 0.28% 0.42% 30566ms 36.92% NagaiHondaForce::AddForceContribution 0 0% 0.42% 29471ms 35.59% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.0036% 0.42% 18153ms 21.92% VertexBasedCellPopulation::Update 11256ms 13.59% 14.02% 18055ms 21.81% Cylindrical2dVertexMesh::GetVectorFromAtoB 1ms 0.0012% 14.02% 18030ms 21.78% MutableVertexMesh::ReMesh 83ms 0.1% 14.12% 13340ms 16.11% Cell::ReadyToDivide 56ms 0.068% 14.19% 12380ms 14.95% AbstractPhaseBasedCellCycleModel::ReadyToDivide 274ms 0.33% 14.52% 11123ms 13.43% NagaiHondaForce::GetAdhesionParameter 333ms 0.4% 14.92% 10828ms 13.08% boost::numeric::ublas::c_vector::c_vector (partial-inline) 98ms 0.12% 15.04% 10638ms 12.85% SimpleWntCellCycleModel::UpdateCellCyclePhase 84ms 0.1% 15.14% 10502ms 12.68% CellPropertyCollection::GetPropertiesType (inline) 215ms 0.26% 15.40% 9686ms 11.70% boost::numeric::ublas::vector_assign (inline) 115ms 0.14% 15.54% 9228ms 11.15% MutableVertexMesh::CheckForIntersections 2509ms 3.03% 18.57% 9017ms 10.89% __dynamic_cast 40ms 0.048% 18.62% 8930ms 10.79% AbstractCellProperty::IsSubType (inline) 94ms 0.11% 18.73% 8603ms 10.39% VertexBasedCellPopulation::GetDampingConstant 51ms 0.062% 18.79% 7997ms 9.66% AbstractTargetAreaModifier::UpdateTargetAreas 36ms 0.043% 18.84% 7929ms 9.58% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 26ms 0.031% 18.87% 7778ms 9.39% AbstractCellBasedSimulation::DoCellBirth 914ms 1.10% 19.97% 7384ms 8.92% std::__new_allocator::allocate (inline) 2206ms 2.66% 22.64% 7337ms 8.86% boost::numeric::ublas::indexing_vector_assign 289ms 0.35% 22.98% 7276ms 8.79% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 22.98% 7029ms 8.49% std::_Rb_tree::_M_create_node (inline) 0 0% 22.98% 6938ms 8.38% std::allocator_traits::allocate (inline) 857ms 1.04% 24.02% 6816ms 8.23% std::_Rb_tree::_M_erase 705ms 0.85% 24.87% 6813ms 8.23% VertexMesh::ElementIncludesPoint 68ms 0.082% 24.95% 6760ms 8.16% Cell::GetMutationState 27ms 0.033% 24.99% 6687ms 8.08% VertexBasedCellPopulation::GetLocationOfCellCentre 589ms 0.71% 25.70% 6514ms 7.87% operator new 0 0% 25.70% 6452ms 7.79% std::_Rb_tree::_M_get_node (inline) 370ms 0.45% 26.14% 6440ms 7.78% VertexMesh::GetCentroidOfElement 129ms 0.16% 26.30% 6259ms 7.56% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.30% 6252ms 7.55% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.30% 6205ms 7.49% std::_Rb_tree::_Alloc_node::operator() (inline) 184ms 0.22% 26.52% 6079ms 7.34% std::__new_allocator::deallocate (inline) 0 0% 26.52% 6061ms 7.32% std::allocator_traits::deallocate (inline) 0 0% 26.52% 6003ms 7.25% std::_Rb_tree::_M_put_node (inline) 0 0% 26.52% 5954ms 7.19% std::set::~set (inline) 1061ms 1.28% 27.80% 5759ms 6.96% AbstractMesh::GetDistanceBetweenNodes 2246ms 2.71% 30.52% 5732ms 6.92% __GI___libc_malloc 15ms 0.018% 30.53% 5649ms 6.82% MutableVertexMesh::RemoveDeletedNodesAndElements 1827ms 2.21% 32.74% 5609ms 6.77% __GI___libc_free 393ms 0.47% 33.22% 5495ms 6.64% std::map::operator[] (partial-inline) 143ms 0.17% 33.39% 5324ms 6.43% std::_Rb_tree::_Rb_tree (partial-inline) 5190ms 6.27% 39.66% 5190ms 6.27% __strcmp_evex 587ms 0.71% 40.37% 4962ms 5.99% std::_Rb_tree::_M_copy (inline) 20ms 0.024% 40.39% 4944ms 5.97% std::set::set (inline) 99ms 0.12% 40.51% 4855ms 5.86% SimpleWntCellCycleModel::GetWntLevel 4811ms 5.81% 46.32% 4811ms 5.81% boost::numeric::ublas::c_vector::operator() 125ms 0.15% 46.47% 4689ms 5.66% WntConcentration::GetWntLevel 1871ms 2.26% 48.73% 4206ms 5.08% std::_Rb_tree::_M_lower_bound (inline) 2262ms 2.73% 51.46% 4185ms 5.05% __cxxabiv1::__si_class_type_info::__do_dyncast 576ms 0.7% 52.16% 4180ms 5.05% std::_Rb_tree::_M_clone_node (inline) 1545ms 1.87% 54.02% 4158ms 5.02% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 54.02% 3989ms 4.82% std::set::insert (inline) 15ms 0.018% 54.04% 3890ms 4.70% MutableVertexMesh::RemoveDeletedNodes 3423ms 4.13% 58.18% 3765ms 4.55% _int_free 16ms 0.019% 58.20% 3758ms 4.54% EdgeHelper::RemoveDeletedEdges 0 0% 58.20% 3527ms 4.26% AbstractCellBasedSimulation::DoCellRemoval (inline) 17ms 0.021% 58.22% 3512ms 4.24% EdgeHelper::UpdateEdgesMapKey 136ms 0.16% 58.38% 3437ms 4.15% MutableElement::ResetIndex 0 0% 58.38% 3415ms 4.12% std::_Rb_tree::lower_bound (inline) 0 0% 58.38% 3415ms 4.12% std::map::lower_bound (inline) 371ms 0.45% 58.83% 3373ms 4.07% std::_Rb_tree::_M_insert_ (inline) 92ms 0.11% 58.94% 3352ms 4.05% std::set_intersection (inline) 166ms 0.2% 59.14% 3260ms 3.94% std::__set_intersection 77ms 0.093% 59.23% 3027ms 3.66% AbstractCellPopulation::GetCellUsingLocationIndex 2985ms 3.61% 62.84% 2985ms 3.61% boost::numeric::ublas::same_impl_ex 34ms 0.041% 62.88% 2963ms 3.58% Cell::GetCellProliferativeType 44ms 0.053% 62.93% 2826ms 3.41% AbstractCellProperty::IsType (inline) 11ms 0.013% 62.95% 2725ms 3.29% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.95% 2512ms 3.03% std::insert_iterator::operator= (inline) 654ms 0.79% 63.74% 2323ms 2.81% AbstractElement::GetNodeLocation 1581ms 1.91% 65.65% 2297ms 2.77% _int_malloc 42ms 0.051% 65.70% 2296ms 2.77% Cell::SetCellProliferativeType 8ms 0.0097% 65.71% 2204ms 2.66% std::_Rb_tree::_M_insert_unique_ (inline) 46ms 0.056% 65.76% 2162ms 2.61% std::_Rb_tree::erase 477ms 0.58% 66.34% 2030ms 2.45% AbstractCellProperty::IsSame 156ms 0.19% 66.53% 2021ms 2.44% VertexMesh::GetAreaGradientOfElementAtNode 447ms 0.54% 67.07% 2012ms 2.43% boost::numeric::ublas::vector_binary::size (inline) 20ms 0.024% 67.09% 2007ms 2.42% CellPropertyCollection::HasProperty 0 0% 67.09% 1977ms 2.39% boost::numeric::ublas::c_vector::assign (inline) 0 0% 67.09% 1974ms 2.38% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 67.09% 1935ms 2.34% Cell::HasCellProperty (inline) 0 0% 67.09% 1922ms 2.32% AbstractCellPopulation::WriteResultsToFiles 176ms 0.21% 67.30% 1897ms 2.29% std::_Rb_tree_const_iterator::operator++ (inline) 22ms 0.027% 67.33% 1860ms 2.25% Cell::GetCellData 1860ms 2.25% 69.58% 1860ms 2.25% std::_Rb_tree::_S_right (inline) 64ms 0.077% 69.65% 1835ms 2.22% VertexMesh::GetVolumeOfElement 3ms 0.0036% 69.66% 1785ms 2.16% std::_Rb_tree::_M_insert_unique 0 0% 69.66% 1702ms 2.06% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 69.66% 1702ms 2.06% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 30ms 0.036% 69.69% 1675ms 2.02% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 29ms 0.035% 69.73% 1647ms 1.99% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.0012% 69.73% 1629ms 1.97% AbstractCellPopulation::Iterator::operator++ (inline) 119ms 0.14% 69.87% 1625ms 1.96% AbstractCellPopulation::Iterator::IsRealCell (inline) 1571ms 1.90% 71.77% 1571ms 1.90% std::_Rb_tree_increment 0 0% 71.77% 1570ms 1.90% VertexBasedCellPopulation::WriteVtkResultsToFile 3ms 0.0036% 71.77% 1563ms 1.89% VertexBasedCellPopulation::WriteCellVtkResultsToFile 353ms 0.43% 72.20% 1553ms 1.88% std::type_info::operator== (inline) 49ms 0.059% 72.26% 1415ms 1.71% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 72.26% 1411ms 1.70% VertexMeshWriter::WriteVtkUsingMesh 919ms 1.11% 73.37% 1349ms 1.63% std::_Rb_tree::equal_range (inline) 10ms 0.012% 73.38% 1255ms 1.52% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 33ms 0.04% 73.42% 1217ms 1.47% VertexMesh::GetSurfaceAreaOfElement 38ms 0.046% 73.47% 1157ms 1.40% AbstractCellPopulation::GetLocationIndexUsingCell 73ms 0.088% 73.55% 1102ms 1.33% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 56ms 0.068% 73.62% 1086ms 1.31% boost::numeric::ublas::vector_reference::operator() (inline) 45ms 0.054% 73.68% 1078ms 1.30% Node::RemoveElement 2ms 0.0024% 73.68% 1051ms 1.27% OffLatticeSimulation::ApplyBoundaries 0 0% 73.68% 1042ms 1.26% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 73.68% 1036ms 1.25% tcache_get (inline) 1036ms 1.25% 74.93% 1036ms 1.25% tcache_get_n (inline) 10ms 0.012% 74.94% 1035ms 1.25% std::set::erase (inline) 0 0% 74.94% 1030ms 1.24% boost::numeric::ublas::norm_2 (inline) 435ms 0.53% 75.47% 1021ms 1.23% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 103ms 0.12% 75.59% 1005ms 1.21% CellPropertyCollection::AddProperty 54ms 0.065% 75.66% 950ms 1.15% std::less::operator() (inline) 930ms 1.12% 76.78% 930ms 1.12% [libchaste_cell_based.so] 55ms 0.066% 76.85% 912ms 1.10% std::_Rb_tree::_M_erase_aux (partial-inline) 748ms 0.9% 77.75% 896ms 1.08% std::operator< (inline) 17ms 0.021% 77.77% 895ms 1.08% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 877ms 1.06% 78.83% 877ms 1.06% std::_Rb_tree_insert_and_rebalance 24ms 0.029% 78.86% 875ms 1.06% CellPropertyRegistry::Get 0 0% 78.86% 846ms 1.02% boost::numeric::ublas::c_vector::assign_temporary (inline) 7ms 0.0085% 78.87% 846ms 1.02% boost::numeric::ublas::c_vector::swap (inline) 3ms 0.0036% 78.87% 840ms 1.01% boost::numeric::ublas::detail::expression_type_check (inline) 74ms 0.089% 78.96% 839ms 1.01% std::swap_ranges (inline) 126ms 0.15% 79.11% 832ms 1.00% boost::numeric::ublas::detail::equals 0 0% 79.11% 824ms 1% std::_Rb_tree::_Auto_node::_Auto_node (inline) 77ms 0.093% 79.21% 806ms 0.97% std::_Rb_tree::find (inline) 85ms 0.1% 79.31% 772ms 0.93% boost::detail::shared_count::~shared_count (inline) 0 0% 79.31% 772ms 0.93% boost::shared_ptr::~shared_ptr (inline) 8ms 0.0097% 79.32% 767ms 0.93% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 766ms 0.93% 80.24% 766ms 0.93% std::swap (inline) 0 0% 80.24% 765ms 0.92% std::iter_swap (inline) 753ms 0.91% 81.15% 753ms 0.91% Node::rGetLocation 0 0% 81.15% 693ms 0.84% std::_Rb_tree::clear (inline) 0 0% 81.15% 685ms 0.83% VertexMeshWriter::MakeVtkMesh 0 0% 81.15% 685ms 0.83% std::map::clear (inline) 0 0% 81.15% 673ms 0.81% boost::numeric::ublas::norm_inf (inline) 307ms 0.37% 81.52% 673ms 0.81% boost::numeric::ublas::vector_norm_inf::apply (inline) 637ms 0.77% 82.29% 660ms 0.8% boost::detail::sp_counted_base::release 648ms 0.78% 83.08% 648ms 0.78% std::vector::size (inline) 0 0% 83.08% 643ms 0.78% std::map::find (inline) 637ms 0.77% 83.85% 637ms 0.77% [libstdc++.so.6.0.33] 187ms 0.23% 84.07% 618ms 0.75% std::__new_allocator::construct (inline) 0 0% 84.07% 618ms 0.75% std::allocator_traits::construct (inline) 59ms 0.071% 84.14% 608ms 0.73% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 84.14% 591ms 0.71% CellPropertyCollection::~CellPropertyCollection (inline) 142ms 0.17% 84.31% 587ms 0.71% boost::shared_ptr::shared_ptr (inline) 17ms 0.021% 84.33% 584ms 0.71% MutableElement::RegisterWithEdges (inline) 23ms 0.028% 84.36% 579ms 0.7% Edge::AddElement 0 0% 84.36% 577ms 0.7% std::_Rb_tree::_M_construct_node (inline) 330ms 0.4% 84.76% 571ms 0.69% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 565ms 0.68% 85.44% 565ms 0.68% [libchaste_mesh.so] 288ms 0.35% 85.79% 548ms 0.66% Edge::GetMapIndex 0 0% 85.79% 539ms 0.65% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 85.79% 532ms 0.64% std::_Rb_tree::_Auto_node::_M_insert (inline) 17ms 0.021% 85.81% 532ms 0.64% std::_Rb_tree::_M_insert_node (inline) 1ms 0.0012% 85.81% 497ms 0.6% vtkPolygon::New 0 0% 85.81% 495ms 0.6% vtkPolygon::vtkPolygon 0 0% 85.81% 485ms 0.59% std::_Vector_base::_M_allocate (inline) 119ms 0.14% 85.96% 479ms 0.58% MutableElement::GetNodeLocalIndex 22ms 0.027% 85.98% 468ms 0.57% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 85.98% 468ms 0.57% boost::numeric::ublas::vector::vector (inline) 431ms 0.52% 86.50% 445ms 0.54% boost::detail::shared_count::shared_count (inline) 29ms 0.035% 86.54% 438ms 0.53% MutableElement::RegisterWithNodes (inline) 430ms 0.52% 87.06% 430ms 0.52% Node::GetIndex 24ms 0.029% 87.09% 418ms 0.5% AbstractNumericalMethod::SafeNodePositionUpdate 6ms 0.0072% 87.09% 416ms 0.5% std::vector::_M_default_append (inline)