File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 17041ms, 83.90% of 20312ms total Dropped 835 nodes (cum <= 101.56ms) flat flat% sum% cum cum% 0 0% 0% 20264ms 99.76% __libc_start_call_main 0 0% 0% 20264ms 99.76% __libc_start_main_impl 0 0% 0% 20264ms 99.76% _start 0 0% 0% 20244ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20244ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20244ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20244ms 99.67% main 0 0% 0% 20205ms 99.47% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20205ms 99.47% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20205ms 99.47% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 20178ms 99.34% AbstractCellBasedSimulation::Solve 0 0% 0% 15576ms 76.68% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0049% 0.0049% 10060ms 49.53% AbstractCellBasedSimulation::DoCellBirth 8ms 0.039% 0.044% 9972ms 49.09% Cell::ReadyToDivide 6ms 0.03% 0.074% 9894ms 48.71% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.074% 9753ms 48.02% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 17ms 0.084% 0.16% 9743ms 47.97% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 6ms 0.03% 0.19% 9722ms 47.86% CellCycleModelOdeHandler::SolveOdeToTime 77ms 0.38% 0.57% 9522ms 46.88% AbstractOneStepIvpOdeSolver::InternalSolve 879ms 4.33% 4.89% 8717ms 42.92% RungeKutta4IvpOdeSolver::CalculateNextYValue 3576ms 17.61% 22.50% 7618ms 37.50% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0049% 22.50% 5380ms 26.49% MeshBasedCellPopulation::Update 4ms 0.02% 22.52% 4175ms 20.55% Cylindrical2dMesh::ReMesh 85ms 0.42% 22.94% 4081ms 20.09% AbstractCellProperty::IsType (inline) 610ms 3.00% 25.95% 2848ms 14.02% AbstractCellProperty::IsSame 1ms 0.0049% 25.95% 2558ms 12.59% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0049% 25.96% 2297ms 11.31% MutableMesh::ReMesh 2ms 0.0098% 25.96% 2240ms 11.03% ForwardEulerNumericalMethod::UpdateAllNodePositions 431ms 2.12% 28.09% 2238ms 11.02% std::type_info::operator== (inline) 12ms 0.059% 28.15% 2199ms 10.83% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0049% 28.15% 2036ms 10.02% AbstractCellPopulation::WriteResultsToFiles 838ms 4.13% 32.28% 1891ms 9.31% std::_Rb_tree::_M_lower_bound (inline) 1786ms 8.79% 41.07% 1786ms 8.79% __strcmp_avx2 136ms 0.67% 41.74% 1742ms 8.58% TetrahedralMesh::EdgeIterator::operator++ 73ms 0.36% 42.10% 1434ms 7.06% std::_Rb_tree::find (inline) 16ms 0.079% 42.18% 1191ms 5.86% TetrahedralMesh::ImportFromMesher 0 0% 42.18% 1166ms 5.74% MeshBasedCellPopulation::UpdateNodePairs 46ms 0.23% 42.40% 1146ms 5.64% operator new 4ms 0.02% 42.42% 1144ms 5.63% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 237ms 1.17% 43.59% 1094ms 5.39% __GI___libc_malloc 14ms 0.069% 43.66% 1038ms 5.11% MeshBasedCellPopulation::SpringIterator::operator++ 48ms 0.24% 43.90% 993ms 4.89% std::__new_allocator::allocate (inline) 0 0% 43.90% 990ms 4.87% std::allocator_traits::allocate (inline) 8ms 0.039% 43.93% 970ms 4.78% std::set::insert (inline) 15ms 0.074% 44.01% 962ms 4.74% std::_Rb_tree::_M_insert_unique 0 0% 44.01% 920ms 4.53% std::set::count (inline) 0 0% 44.01% 809ms 3.98% triangulate 423ms 2.08% 46.09% 766ms 3.77% _int_malloc 1ms 0.0049% 46.10% 736ms 3.62% delaunay 4ms 0.02% 46.12% 733ms 3.61% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 3ms 0.015% 46.13% 733ms 3.61% divconqdelaunay 55ms 0.27% 46.40% 725ms 3.57% std::map::operator[] (partial-inline) 2ms 0.0098% 46.41% 700ms 3.45% AbstractTwoBodyInteractionForce::AddForceContribution 19ms 0.094% 46.50% 680ms 3.35% std::less::operator() (inline) 8ms 0.039% 46.54% 664ms 3.27% CellPopulationElementWriter::Visit 661ms 3.25% 49.80% 661ms 3.25% std::operator< (inline) 184ms 0.91% 50.70% 660ms 3.25% __dynamic_cast 660ms 3.25% 53.95% 660ms 3.25% std::_Rb_tree::_S_right (inline) 0 0% 53.95% 637ms 3.14% std::_Rb_tree::_M_create_node (inline) 16ms 0.079% 54.03% 622ms 3.06% CellPropertyCollection::GetPropertiesType (inline) 21ms 0.1% 54.14% 621ms 3.06% std::_Rb_tree::_M_insert_ (inline) 599ms 2.95% 57.08% 607ms 2.99% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 57.08% 606ms 2.98% std::_Rb_tree::_M_get_node (inline) 21ms 0.1% 57.19% 578ms 2.85% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 2ms 0.0098% 57.20% 574ms 2.83% MeshBasedCellPopulation::AcceptCellWriter 0 0% 57.20% 570ms 2.81% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 57.20% 570ms 2.81% std::_Rb_tree::lower_bound (inline) 0 0% 57.20% 570ms 2.81% std::map::lower_bound (inline) 19ms 0.094% 57.29% 553ms 2.72% AbstractCellPopulation::GetCellUsingLocationIndex 9ms 0.044% 57.34% 538ms 2.65% MutableMesh::ReIndex 6ms 0.03% 57.37% 530ms 2.61% Element::Element 1ms 0.0049% 57.37% 517ms 2.55% std::ostream::operator<< (inline) 73ms 0.36% 57.73% 516ms 2.54% std::ostream::_M_insert 0 0% 57.73% 509ms 2.51% std::map::find (inline) 3ms 0.015% 57.74% 492ms 2.42% AbstractCellProperty::IsSubType (inline) 340ms 1.67% 59.42% 486ms 2.39% AbstractCellMutationState::AbstractCellMutationState 10ms 0.049% 59.47% 484ms 2.38% Cylindrical2dMesh::CorrectNonPeriodicMesh 7ms 0.034% 59.50% 478ms 2.35% Cylindrical2dMesh::ReconstructCylindricalMesh 178ms 0.88% 60.38% 461ms 2.27% __GI___libc_free 3ms 0.015% 60.39% 457ms 2.25% Element::RegisterWithNodes (inline) 7ms 0.034% 60.43% 454ms 2.24% Node::AddElement 145ms 0.71% 61.14% 402ms 1.98% std::_Rb_tree::_M_erase 22ms 0.11% 61.25% 392ms 1.93% divconqrecurse 1ms 0.0049% 61.25% 385ms 1.90% std::_Vector_base::_M_allocate (inline) 9ms 0.044% 61.30% 379ms 1.87% std::_Rb_tree::erase 0 0% 61.30% 379ms 1.87% std::set::erase (inline) 17ms 0.084% 61.38% 375ms 1.85% Node::RemoveElement 123ms 0.61% 61.99% 365ms 1.80% mergehulls 3ms 0.015% 62.00% 363ms 1.79% Cell::GetMutationState 18ms 0.089% 62.09% 363ms 1.79% std::_Rb_tree::~_Rb_tree (inline) 13ms 0.064% 62.16% 340ms 1.67% std::__new_allocator::deallocate (inline) 16ms 0.079% 62.23% 337ms 1.66% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 162ms 0.8% 63.03% 335ms 1.65% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 63.03% 334ms 1.64% std::set::~set (inline) 333ms 1.64% 64.67% 333ms 1.64% std::type_info::name (inline) 0 0% 64.67% 332ms 1.63% std::allocator_traits::deallocate (inline) 30ms 0.15% 64.82% 327ms 1.61% Element::ResetIndex 107ms 0.53% 65.35% 326ms 1.60% std::_Rb_tree::_M_get_insert_unique_pos 9ms 0.044% 65.39% 313ms 1.54% AbstractCellPopulation::GetLocationIndexUsingCell 3ms 0.015% 65.40% 310ms 1.53% NodeLocationWriter::Visit 0 0% 65.40% 301ms 1.48% std::_Rb_tree::_M_drop_node (inline) 1ms 0.0049% 65.41% 298ms 1.47% AbstractCellPopulation::Iterator::operator++ (inline) 3ms 0.015% 65.42% 297ms 1.46% LegacyCellProliferativeTypesWriter::VisitCell 31ms 0.15% 65.58% 294ms 1.45% AbstractCellPopulation::Iterator::IsRealCell 26ms 0.13% 65.71% 289ms 1.42% TetrahedralMesh::Clear 0 0% 65.71% 285ms 1.40% Cell::GetCellProliferativeType 217ms 1.07% 66.77% 283ms 1.39% _int_free 11ms 0.054% 66.83% 275ms 1.35% std::vector::push_back (inline) 274ms 1.35% 68.18% 274ms 1.35% std::vector::operator[] (inline) 0 0% 68.18% 269ms 1.32% std::_Rb_tree::_M_put_node (inline) 24ms 0.12% 68.29% 268ms 1.32% std::num_put::_M_insert_float 1ms 0.0049% 68.30% 262ms 1.29% TetrahedralMesh::RefreshJacobianCachedData 12ms 0.059% 68.36% 262ms 1.29% std::_Rb_tree::_Rb_tree (partial-inline) 1ms 0.0049% 68.36% 257ms 1.27% MeshBasedCellPopulation::GetDampingConstant 3ms 0.015% 68.38% 256ms 1.26% AbstractCentreBasedCellPopulation::GetDampingConstant 22ms 0.11% 68.49% 255ms 1.26% AbstractTetrahedralElement::CalculateJacobian 17ms 0.084% 68.57% 255ms 1.26% std::vector::_M_realloc_insert 8ms 0.039% 68.61% 252ms 1.24% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.015% 68.62% 241ms 1.19% std::set::set (inline) 3ms 0.015% 68.64% 238ms 1.17% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 70ms 0.34% 68.98% 231ms 1.14% ApcOneHitCellMutationState::ApcOneHitCellMutationState 38ms 0.19% 69.17% 230ms 1.13% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 4ms 0.02% 69.19% 229ms 1.13% AbstractCellPopulation::IsCellAttachedToLocationIndex 11ms 0.054% 69.24% 220ms 1.08% std::_Rb_tree::_M_erase_aux (inline) 47ms 0.23% 69.48% 214ms 1.05% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 10ms 0.049% 69.53% 212ms 1.04% AbstractTetrahedralElement::CalculateInverseJacobian 3ms 0.015% 69.54% 210ms 1.03% alternateaxes 8ms 0.039% 69.58% 209ms 1.03% std::__cxx11::collate::do_transform 16ms 0.079% 69.66% 208ms 1.02% std::_Rb_tree::_M_copy (inline) 207ms 1.02% 70.68% 207ms 1.02% [libchaste_cell_based.so] 160ms 0.79% 71.47% 207ms 1.02% malloc_consolidate 182ms 0.9% 72.36% 205ms 1.01% vertexmedian 15ms 0.074% 72.44% 203ms 1% Element::MarkAsDeleted 28ms 0.14% 72.57% 197ms 0.97% AbstractTetrahedralElement::RefreshJacobian 0 0% 72.57% 196ms 0.96% OffLatticeSimulation::ApplyBoundaries 4ms 0.02% 72.59% 196ms 0.96% ___vsnprintf 0 0% 72.59% 192ms 0.95% __vsnprintf_internal (inline) 61ms 0.3% 72.89% 191ms 0.94% std::_Rb_tree::_M_clone_node (inline) 26ms 0.13% 73.02% 189ms 0.93% __printf_buffer 185ms 0.91% 73.93% 185ms 0.91% Node::GetIndex 141ms 0.69% 74.63% 181ms 0.89% AbstractElement::GetNodeGlobalIndex 178ms 0.88% 75.50% 178ms 0.88% unlink_chunk 177ms 0.87% 76.37% 177ms 0.87% std::_Rb_tree_insert_and_rebalance 0 0% 76.37% 172ms 0.85% AbstractCellBasedWriter::OpenOutputFileForAppend 6ms 0.03% 76.40% 172ms 0.85% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.0049% 76.41% 166ms 0.82% OutputFileHandler::OpenOutputFile 13ms 0.064% 76.47% 159ms 0.78% Node::~Node 106ms 0.52% 76.99% 159ms 0.78% std::_Rb_tree::equal_range (inline) 4ms 0.02% 77.01% 154ms 0.76% boost::numeric::ublas::vector_assign (inline) 1ms 0.0049% 77.02% 153ms 0.75% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 152ms 0.75% 77.77% 152ms 0.75% incircle 5ms 0.025% 77.79% 151ms 0.74% __printf_fp_l_buffer 0 0% 77.79% 151ms 0.74% __printf_fp_spec (inline) 65ms 0.32% 78.11% 150ms 0.74% AbstractElement::GetNodeLocation 2ms 0.0098% 78.12% 149ms 0.73% CellProliferativeTypesWriter::VisitCell 7ms 0.034% 78.16% 146ms 0.72% CellPropertyCollection::HasProperty 9ms 0.044% 78.20% 145ms 0.71% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 66ms 0.32% 78.53% 142ms 0.7% __printf_fp_buffer_1 0 0% 78.53% 140ms 0.69% Cell::HasCellProperty (inline) 12ms 0.059% 78.58% 134ms 0.66% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 78.58% 133ms 0.65% AbstractCellBasedSimulation::DoCellRemoval (inline) 7ms 0.034% 78.62% 133ms 0.65% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 23ms 0.11% 78.73% 132ms 0.65% TetrahedralMesh::EdgesEnd 2ms 0.0098% 78.74% 131ms 0.64% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 19ms 0.094% 78.84% 129ms 0.64% std::num_put::_M_insert_int 49ms 0.24% 79.08% 127ms 0.63% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 28ms 0.14% 79.21% 127ms 0.63% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 126ms 0.62% 79.83% 126ms 0.62% AbstractCellProperty::~AbstractCellProperty 55ms 0.27% 80.11% 126ms 0.62% std::__ostream_insert 125ms 0.62% 80.72% 125ms 0.62% std::vector::size (inline) 2ms 0.0098% 80.73% 124ms 0.61% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 122ms 0.6% 81.33% 122ms 0.6% AbstractElement::IsDeleted 118ms 0.58% 81.91% 122ms 0.6% vertexsort 41ms 0.2% 82.11% 120ms 0.59% boost::numeric::ublas::indexing_vector_assign 40ms 0.2% 82.31% 115ms 0.57% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 69ms 0.34% 82.65% 115ms 0.57% Cylindrical2dMesh::GetVectorFromAtoB 112ms 0.55% 83.20% 112ms 0.55% std::_Rb_tree_increment 0 0% 83.20% 112ms 0.55% std::vector::resize (inline) 1ms 0.0049% 83.21% 111ms 0.55% Cell::SetCellProliferativeType 6ms 0.03% 83.24% 111ms 0.55% Cylindrical2dMesh::CreateMirrorNodes 9ms 0.044% 83.28% 111ms 0.55% boost::detail::shared_count::~shared_count (inline) 0 0% 83.28% 111ms 0.55% boost::shared_ptr::~shared_ptr (inline) 2ms 0.0098% 83.29% 111ms 0.55% std::vector::_M_default_append 110ms 0.54% 83.83% 110ms 0.54% AbstractCellMutationState::~AbstractCellMutationState 9ms 0.044% 83.88% 109ms 0.54% std::_Rb_tree_const_iterator::operator++ (inline) 4ms 0.02% 83.90% 107ms 0.53% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 83.90% 105ms 0.52% NodeMap::NodeMap