File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16684ms, 83.86% of 19895ms total Dropped 782 nodes (cum <= 99.47ms) flat flat% sum% cum cum% 0 0% 0% 19850ms 99.77% __libc_start_call_main 0 0% 0% 19850ms 99.77% __libc_start_main_impl 0 0% 0% 19850ms 99.77% _start 0 0% 0% 19831ms 99.68% main 0 0% 0% 19830ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19830ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19830ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19793ms 99.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19793ms 99.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19793ms 99.49% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19766ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0% 15353ms 77.17% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.015% 0.015% 10146ms 51.00% AbstractCellBasedSimulation::DoCellBirth 3ms 0.015% 0.03% 10068ms 50.61% Cell::ReadyToDivide 8ms 0.04% 0.07% 10001ms 50.27% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.005% 0.075% 9849ms 49.50% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 12ms 0.06% 0.14% 9840ms 49.46% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 6ms 0.03% 0.17% 9828ms 49.40% CellCycleModelOdeHandler::SolveOdeToTime 75ms 0.38% 0.54% 9645ms 48.48% AbstractOneStepIvpOdeSolver::InternalSolve 823ms 4.14% 4.68% 8829ms 44.38% RungeKutta4IvpOdeSolver::CalculateNextYValue 3725ms 18.72% 23.40% 7796ms 39.19% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 23.40% 5093ms 25.60% MeshBasedCellPopulation::Update 182ms 0.91% 24.32% 4123ms 20.72% AbstractCellProperty::IsType (inline) 5ms 0.025% 24.34% 3919ms 19.70% Cylindrical2dMesh::ReMesh 542ms 2.72% 27.07% 2905ms 14.60% AbstractCellProperty::IsSame 1ms 0.005% 27.07% 2482ms 12.48% OffLatticeSimulation::UpdateCellLocationsAndTopology 407ms 2.05% 29.12% 2363ms 11.88% std::type_info::operator== (inline) 0 0% 29.12% 2126ms 10.69% MutableMesh::ReMesh 0 0% 29.12% 2117ms 10.64% ForwardEulerNumericalMethod::UpdateAllNodePositions 16ms 0.08% 29.20% 2069ms 10.40% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 29.20% 1927ms 9.69% AbstractCellPopulation::WriteResultsToFiles 1905ms 9.58% 38.77% 1905ms 9.58% __strcmp_avx2 765ms 3.85% 42.62% 1806ms 9.08% std::_Rb_tree::_M_lower_bound (inline) 155ms 0.78% 43.40% 1682ms 8.45% TetrahedralMesh::EdgeIterator::operator++ 51ms 0.26% 43.65% 1375ms 6.91% std::_Rb_tree::find (inline) 0 0% 43.65% 1145ms 5.76% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.02% 43.67% 1122ms 5.64% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 20ms 0.1% 43.77% 1071ms 5.38% TetrahedralMesh::ImportFromMesher 48ms 0.24% 44.02% 1035ms 5.20% operator new 15ms 0.075% 44.09% 1008ms 5.07% MeshBasedCellPopulation::SpringIterator::operator++ 208ms 1.05% 45.14% 981ms 4.93% __GI___libc_malloc 11ms 0.055% 45.19% 904ms 4.54% std::set::insert (inline) 38ms 0.19% 45.38% 900ms 4.52% std::__new_allocator::allocate (inline) 20ms 0.1% 45.48% 893ms 4.49% std::_Rb_tree::_M_insert_unique 0 0% 45.48% 893ms 4.49% std::allocator_traits::allocate (inline) 0 0% 45.48% 838ms 4.21% std::set::count (inline) 0 0% 45.48% 807ms 4.06% triangulate 0 0% 45.48% 723ms 3.63% delaunay 3ms 0.015% 45.50% 723ms 3.63% divconqdelaunay 1ms 0.005% 45.50% 703ms 3.53% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 58ms 0.29% 45.80% 678ms 3.41% std::map::operator[] (partial-inline) 377ms 1.89% 47.69% 677ms 3.40% _int_malloc 3ms 0.015% 47.71% 669ms 3.36% AbstractTwoBodyInteractionForce::AddForceContribution 660ms 3.32% 51.02% 660ms 3.32% std::_Rb_tree::_S_right (inline) 6ms 0.03% 51.05% 657ms 3.30% CellPopulationElementWriter::Visit 16ms 0.08% 51.13% 639ms 3.21% std::less::operator() (inline) 194ms 0.98% 52.11% 636ms 3.20% __dynamic_cast 623ms 3.13% 55.24% 623ms 3.13% std::operator< (inline) 606ms 3.05% 58.29% 613ms 3.08% WntCellCycleOdeSystem::CalculateStoppingEvent 13ms 0.065% 58.35% 579ms 2.91% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 58.35% 576ms 2.90% std::_Rb_tree::_M_create_node (inline) 7ms 0.035% 58.39% 569ms 2.86% MeshBasedCellPopulation::AcceptCellWriter 7ms 0.035% 58.42% 567ms 2.85% CellPropertyCollection::GetPropertiesType (inline) 22ms 0.11% 58.53% 566ms 2.84% std::_Rb_tree::_M_insert_ (inline) 0 0% 58.53% 554ms 2.78% std::_Rb_tree::_M_get_node (inline) 19ms 0.096% 58.63% 542ms 2.72% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.025% 58.65% 537ms 2.70% Element::Element 0 0% 58.65% 533ms 2.68% std::map::find (inline) 8ms 0.04% 58.69% 530ms 2.66% MutableMesh::ReIndex 0 0% 58.69% 519ms 2.61% std::_Rb_tree::lower_bound (inline) 0 0% 58.69% 519ms 2.61% std::map::lower_bound (inline) 0 0% 58.69% 513ms 2.58% std::_Rb_tree::_Alloc_node::operator() (inline) 1ms 0.005% 58.70% 502ms 2.52% std::ostream::operator<< (inline) 68ms 0.34% 59.04% 500ms 2.51% std::ostream::_M_insert 6ms 0.03% 59.07% 493ms 2.48% Cylindrical2dMesh::ReconstructCylindricalMesh 335ms 1.68% 60.75% 485ms 2.44% AbstractCellMutationState::AbstractCellMutationState 175ms 0.88% 61.63% 475ms 2.39% __GI___libc_free 10ms 0.05% 61.68% 474ms 2.38% Cylindrical2dMesh::CorrectNonPeriodicMesh 3ms 0.015% 61.70% 464ms 2.33% AbstractCellProperty::IsSubType (inline) 14ms 0.07% 61.77% 460ms 2.31% Element::RegisterWithNodes (inline) 12ms 0.06% 61.83% 438ms 2.20% Node::AddElement 5ms 0.025% 61.85% 393ms 1.98% std::_Rb_tree::erase 1ms 0.005% 61.86% 391ms 1.97% std::set::erase (inline) 7ms 0.035% 61.89% 384ms 1.93% Node::RemoveElement 6ms 0.03% 61.93% 369ms 1.85% std::__new_allocator::deallocate (inline) 15ms 0.075% 62.00% 364ms 1.83% divconqrecurse 0 0% 62.00% 359ms 1.80% std::allocator_traits::deallocate (inline) 92ms 0.46% 62.46% 354ms 1.78% std::_Rb_tree::_M_erase 4ms 0.02% 62.48% 343ms 1.72% std::_Vector_base::_M_allocate (inline) 108ms 0.54% 63.03% 341ms 1.71% mergehulls 22ms 0.11% 63.14% 340ms 1.71% Element::ResetIndex 0 0% 63.14% 335ms 1.68% std::_Rb_tree::_M_drop_node (inline) 20ms 0.1% 63.24% 328ms 1.65% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.015% 63.25% 321ms 1.61% Cell::GetCellProliferativeType 24ms 0.12% 63.37% 320ms 1.61% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 152ms 0.76% 64.14% 311ms 1.56% __cxxabiv1::__si_class_type_info::__do_dyncast 309ms 1.55% 65.69% 309ms 1.55% std::type_info::name (inline) 118ms 0.59% 66.28% 307ms 1.54% std::_Rb_tree::_M_get_insert_unique_pos 2ms 0.01% 66.29% 301ms 1.51% NodeLocationWriter::Visit 247ms 1.24% 67.53% 298ms 1.50% _int_free 0 0% 67.53% 297ms 1.49% LegacyCellProliferativeTypesWriter::VisitCell 7ms 0.035% 67.57% 296ms 1.49% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 67.57% 291ms 1.46% std::set::~set (inline) 0 0% 67.57% 287ms 1.44% std::_Rb_tree::_M_put_node (inline) 3ms 0.015% 67.58% 282ms 1.42% Cell::GetMutationState 33ms 0.17% 67.75% 270ms 1.36% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 67.75% 270ms 1.36% AbstractCellPopulation::Iterator::operator++ (inline) 266ms 1.34% 69.09% 269ms 1.35% std::vector::operator[] (inline) 20ms 0.1% 69.19% 265ms 1.33% std::num_put::_M_insert_float 16ms 0.08% 69.27% 251ms 1.26% AbstractTetrahedralElement::CalculateJacobian 11ms 0.055% 69.32% 248ms 1.25% std::vector::push_back (inline) 15ms 0.075% 69.40% 247ms 1.24% std::_Rb_tree::_M_erase_aux (inline) 14ms 0.07% 69.47% 240ms 1.21% std::_Rb_tree::_Rb_tree (partial-inline) 8ms 0.04% 69.51% 234ms 1.18% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 230ms 1.16% 70.67% 230ms 1.16% [libchaste_cell_based.so] 4ms 0.02% 70.69% 230ms 1.16% alternateaxes 10ms 0.05% 70.74% 229ms 1.15% std::vector::_M_realloc_insert 48ms 0.24% 70.98% 226ms 1.14% ApcOneHitCellMutationState::ApcOneHitCellMutationState 215ms 1.08% 72.06% 226ms 1.14% vertexmedian 1ms 0.005% 72.06% 225ms 1.13% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.005% 72.07% 218ms 1.10% std::set::set (inline) 1ms 0.005% 72.07% 216ms 1.09% std::__cxx11::collate::do_transform 2ms 0.01% 72.08% 212ms 1.07% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 42ms 0.21% 72.29% 212ms 1.07% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 5ms 0.025% 72.32% 209ms 1.05% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 72.32% 209ms 1.05% OffLatticeSimulation::ApplyBoundaries 1ms 0.005% 72.32% 205ms 1.03% ___vsnprintf 0 0% 72.32% 204ms 1.03% __vsnprintf_internal (inline) 29ms 0.15% 72.47% 202ms 1.02% __printf_buffer 12ms 0.06% 72.53% 200ms 1.01% Element::MarkAsDeleted 21ms 0.11% 72.64% 195ms 0.98% std::_Rb_tree::_M_copy (inline) 53ms 0.27% 72.90% 194ms 0.98% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 15ms 0.075% 72.98% 189ms 0.95% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.005% 72.98% 188ms 0.94% AbstractTetrahedralElement::AbstractTetrahedralElement 22ms 0.11% 73.09% 183ms 0.92% AbstractTetrahedralElement::RefreshJacobian 0 0% 73.09% 178ms 0.89% MeshBasedCellPopulation::GetDampingConstant 136ms 0.68% 73.78% 178ms 0.89% malloc_consolidate 0 0% 73.78% 177ms 0.89% AbstractCentreBasedCellPopulation::GetDampingConstant 134ms 0.67% 74.45% 177ms 0.89% AbstractElement::GetNodeGlobalIndex 58ms 0.29% 74.74% 173ms 0.87% std::_Rb_tree::_M_clone_node (inline) 171ms 0.86% 75.60% 171ms 0.86% std::_Rb_tree_insert_and_rebalance 10ms 0.05% 75.65% 170ms 0.85% TetrahedralMesh::Clear 2ms 0.01% 75.66% 168ms 0.84% CellProliferativeTypesWriter::VisitCell 163ms 0.82% 76.48% 163ms 0.82% Node::GetIndex 9ms 0.045% 76.53% 160ms 0.8% __printf_fp_l_buffer 0 0% 76.53% 160ms 0.8% __printf_fp_spec (inline) 10ms 0.05% 76.58% 158ms 0.79% CellPropertyCollection::HasProperty 103ms 0.52% 77.09% 155ms 0.78% std::_Rb_tree::equal_range (inline) 0 0% 77.09% 151ms 0.76% Cell::HasCellProperty (inline) 151ms 0.76% 77.85% 151ms 0.76% incircle 72ms 0.36% 78.22% 148ms 0.74% __printf_fp_buffer_1 8ms 0.04% 78.26% 146ms 0.73% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 143ms 0.72% 78.97% 143ms 0.72% unlink_chunk 1ms 0.005% 78.98% 142ms 0.71% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 50ms 0.25% 79.23% 140ms 0.7% AbstractElement::GetNodeLocation 13ms 0.065% 79.30% 140ms 0.7% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 79ms 0.4% 79.69% 137ms 0.69% Cylindrical2dMesh::GetVectorFromAtoB 54ms 0.27% 79.96% 135ms 0.68% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 3ms 0.015% 79.98% 135ms 0.68% MeshBasedCellPopulation::SpringsEnd (inline) 27ms 0.14% 80.12% 133ms 0.67% TetrahedralMesh::EdgesEnd (partial-inline) 3ms 0.015% 80.13% 131ms 0.66% boost::numeric::ublas::vector_assign (inline) 44ms 0.22% 80.35% 126ms 0.63% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 126ms 0.63% 80.99% 126ms 0.63% std::vector::size (inline) 0 0% 80.99% 125ms 0.63% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 80.99% 124ms 0.62% OutputFileHandler::OpenOutputFile 0 0% 80.99% 118ms 0.59% Cell::SetCellProliferativeType 117ms 0.59% 81.57% 117ms 0.59% AbstractElement::IsDeleted 11ms 0.055% 81.63% 117ms 0.59% boost::numeric::ublas::c_vector::c_vector (inline) 109ms 0.55% 82.18% 116ms 0.58% vertexsort 1ms 0.005% 82.18% 114ms 0.57% boost::shared_ptr::~shared_ptr (inline) 0 0% 82.18% 113ms 0.57% AbstractCellBasedSimulation::DoCellRemoval (inline) 17ms 0.085% 82.27% 113ms 0.57% boost::detail::shared_count::~shared_count (inline) 32ms 0.16% 82.43% 111ms 0.56% std::num_put::_M_insert_int 0 0% 82.43% 110ms 0.55% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 14ms 0.07% 82.50% 110ms 0.55% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 1ms 0.005% 82.50% 109ms 0.55% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 1ms 0.005% 82.51% 109ms 0.55% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 43ms 0.22% 82.72% 105ms 0.53% std::__ostream_insert 104ms 0.52% 83.25% 104ms 0.52% std::_Rb_tree_rebalance_for_erase 19ms 0.096% 83.34% 102ms 0.51% MeshBasedCellPopulation::SpringIterator::SpringIterator 2ms 0.01% 83.35% 101ms 0.51% std::_Rb_tree::_M_emplace_hint_unique 100ms 0.5% 83.86% 100ms 0.5% AbstractCellMutationState::~AbstractCellMutationState 1ms 0.005% 83.86% 100ms 0.5% CryptSimulationBoundaryCondition::VerifyBoundaryCondition