File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16094ms, 86.98% of 18504ms total Dropped 755 nodes (cum <= 92.52ms) flat flat% sum% cum cum% 0 0% 0% 18466ms 99.79% __libc_start_call_main 0 0% 0% 18466ms 99.79% __libc_start_main_impl 0 0% 0% 18466ms 99.79% _start 0 0% 0% 18447ms 99.69% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 18447ms 99.69% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 18447ms 99.69% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 18447ms 99.69% main 0 0% 0% 18414ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 18414ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 18414ms 99.51% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 18391ms 99.39% AbstractCellBasedSimulation::Solve 0 0% 0% 13763ms 74.38% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 8359ms 45.17% AbstractCellBasedSimulation::DoCellBirth 8ms 0.043% 0.043% 8253ms 44.60% Cell::ReadyToDivide 3ms 0.016% 0.059% 8167ms 44.14% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0054% 0.065% 8012ms 43.30% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 10ms 0.054% 0.12% 8009ms 43.28% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.011% 0.13% 7996ms 43.21% CellCycleModelOdeHandler::SolveOdeToTime 54ms 0.29% 0.42% 7775ms 42.02% AbstractOneStepIvpOdeSolver::InternalSolve 877ms 4.74% 5.16% 7002ms 37.84% RungeKutta4IvpOdeSolver::CalculateNextYValue 2977ms 16.09% 21.25% 5959ms 32.20% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 21.25% 5290ms 28.59% MeshBasedCellPopulation::Update 5ms 0.027% 21.28% 4136ms 22.35% Cylindrical2dMesh::ReMesh 236ms 1.28% 22.55% 3138ms 16.96% AbstractCellProperty::IsType (inline) 0 0% 22.55% 2591ms 14.00% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.011% 22.56% 2322ms 12.55% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0054% 22.57% 2298ms 12.42% MutableMesh::ReMesh 2ms 0.011% 22.58% 2290ms 12.38% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 22.58% 2026ms 10.95% AbstractCellPopulation::WriteResultsToFiles 718ms 3.88% 26.46% 1726ms 9.33% std::_Rb_tree::_M_lower_bound (inline) 158ms 0.85% 27.31% 1687ms 9.12% TetrahedralMesh::EdgeIterator::operator++ 279ms 1.51% 28.82% 1435ms 7.76% AbstractCellProperty::IsSame 61ms 0.33% 29.15% 1364ms 7.37% std::_Rb_tree::find (inline) 52ms 0.28% 29.43% 1255ms 6.78% operator new 14ms 0.076% 29.51% 1216ms 6.57% TetrahedralMesh::ImportFromMesher 426ms 2.30% 31.81% 1171ms 6.33% __GI___libc_malloc 174ms 0.94% 32.75% 1156ms 6.25% std::type_info::operator== (inline) 7ms 0.038% 32.79% 1135ms 6.13% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 3ms 0.016% 32.80% 1119ms 6.05% MeshBasedCellPopulation::UpdateNodePairs 16ms 0.086% 32.89% 1103ms 5.96% std::set::insert (inline) 12ms 0.065% 32.96% 1087ms 5.87% std::_Rb_tree::_M_insert_unique 1074ms 5.80% 38.76% 1074ms 5.80% __strcmp_evex 35ms 0.19% 38.95% 1065ms 5.76% std::__new_allocator::allocate (inline) 0 0% 38.95% 1062ms 5.74% std::allocator_traits::allocate (inline) 9ms 0.049% 39.00% 994ms 5.37% MeshBasedCellPopulation::SpringIterator::operator++ 882ms 4.77% 43.76% 882ms 4.77% [libchaste_cell_based.so] 20ms 0.11% 43.87% 850ms 4.59% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 43.87% 837ms 4.52% std::set::count (inline) 1ms 0.0054% 43.88% 805ms 4.35% triangulate 3ms 0.016% 43.89% 786ms 4.25% AbstractTwoBodyInteractionForce::AddForceContribution 242ms 1.31% 45.20% 771ms 4.17% __dynamic_cast 0 0% 45.20% 755ms 4.08% std::_Rb_tree::_M_create_node (inline) 11ms 0.059% 45.26% 751ms 4.06% CellPropertyCollection::GetPropertiesType (inline) 7ms 0.038% 45.30% 739ms 3.99% CellPopulationElementWriter::Visit 0 0% 45.30% 729ms 3.94% delaunay 5ms 0.027% 45.33% 729ms 3.94% divconqdelaunay 0 0% 45.33% 727ms 3.93% std::_Rb_tree::_M_get_node (inline) 46ms 0.25% 45.57% 719ms 3.89% std::_Rb_tree::_M_insert_ (inline) 23ms 0.12% 45.70% 703ms 3.80% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 45.70% 673ms 3.64% std::_Rb_tree::_Alloc_node::operator() (inline) 12ms 0.065% 45.76% 660ms 3.57% MeshBasedCellPopulation::AcceptCellWriter 76ms 0.41% 46.17% 649ms 3.51% std::map::operator[] (partial-inline) 364ms 1.97% 48.14% 635ms 3.43% _int_malloc 16ms 0.086% 48.23% 631ms 3.41% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.022% 48.25% 610ms 3.30% Element::Element 598ms 3.23% 51.48% 598ms 3.23% std::_Rb_tree::_S_right (inline) 595ms 3.22% 54.70% 595ms 3.22% WntCellCycleOdeSystem::CalculateStoppingEvent 13ms 0.07% 54.77% 586ms 3.17% Element::RegisterWithNodes (inline) 8ms 0.043% 54.81% 581ms 3.14% AbstractCellProperty::IsSubType (inline) 10ms 0.054% 54.86% 570ms 3.08% Node::AddElement 114ms 0.62% 55.48% 552ms 2.98% __GI___libc_free 21ms 0.11% 55.59% 527ms 2.85% std::less::operator() (inline) 0 0% 55.59% 527ms 2.85% std::map::find (inline) 20ms 0.11% 55.70% 517ms 2.79% Cylindrical2dMesh::ReconstructCylindricalMesh 506ms 2.73% 58.44% 506ms 2.73% std::operator< (inline) 56ms 0.3% 58.74% 505ms 2.73% std::_Rb_tree::~_Rb_tree (inline) 9ms 0.049% 58.79% 496ms 2.68% MutableMesh::ReIndex 115ms 0.62% 59.41% 495ms 2.68% std::_Rb_tree::_M_erase 0 0% 59.41% 478ms 2.58% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.41% 471ms 2.55% std::set::~set (inline) 249ms 1.35% 60.75% 467ms 2.52% AbstractCellMutationState::AbstractCellMutationState 459ms 2.48% 63.23% 459ms 2.48% [libchaste_crypt.so] 0 0% 63.23% 452ms 2.44% std::_Rb_tree::lower_bound (inline) 0 0% 63.23% 452ms 2.44% std::map::lower_bound (inline) 14ms 0.076% 63.31% 439ms 2.37% Cylindrical2dMesh::CorrectNonPeriodicMesh 361ms 1.95% 65.26% 431ms 2.33% _int_free 12ms 0.065% 65.33% 431ms 2.33% std::__new_allocator::deallocate (inline) 0 0% 65.33% 426ms 2.30% std::allocator_traits::deallocate (inline) 3ms 0.016% 65.34% 426ms 2.30% std::ostream::operator<< (inline) 76ms 0.41% 65.75% 416ms 2.25% std::ostream::_M_insert 0 0% 65.75% 404ms 2.18% Cell::GetMutationState 6ms 0.032% 65.79% 396ms 2.14% std::_Rb_tree::erase 0 0% 65.79% 395ms 2.13% std::set::erase (inline) 9ms 0.049% 65.83% 392ms 2.12% Node::RemoveElement 4ms 0.022% 65.86% 388ms 2.10% Cell::GetCellProliferativeType 171ms 0.92% 66.78% 380ms 2.05% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 66.78% 362ms 1.96% std::_Rb_tree::_M_put_node (inline) 121ms 0.65% 67.43% 356ms 1.92% std::_Rb_tree::_M_get_insert_unique_pos 14ms 0.076% 67.51% 355ms 1.92% divconqrecurse 21ms 0.11% 67.62% 338ms 1.83% Element::ResetIndex 1ms 0.0054% 67.63% 338ms 1.83% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 67.63% 335ms 1.81% std::_Vector_base::_M_allocate (inline) 96ms 0.52% 68.15% 328ms 1.77% mergehulls 23ms 0.12% 68.27% 308ms 1.66% boost::detail::shared_count::~shared_count (inline) 0 0% 68.27% 308ms 1.66% boost::shared_ptr::~shared_ptr (inline) 13ms 0.07% 68.34% 307ms 1.66% std::_Rb_tree::_Rb_tree 0 0% 68.34% 297ms 1.61% std::set::set (inline) 21ms 0.11% 68.46% 294ms 1.59% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 1ms 0.0054% 68.46% 287ms 1.55% MeshBasedCellPopulation::GetDampingConstant 4ms 0.022% 68.48% 287ms 1.55% std::vector::push_back (inline) 3ms 0.016% 68.50% 284ms 1.53% AbstractCentreBasedCellPopulation::GetDampingConstant 9ms 0.049% 68.55% 277ms 1.50% AbstractCellPopulation::IsCellAttachedToLocationIndex 274ms 1.48% 70.03% 277ms 1.50% boost::detail::sp_counted_base::release 28ms 0.15% 70.18% 272ms 1.47% std::_Rb_tree::_M_copy (inline) 10ms 0.054% 70.23% 266ms 1.44% std::vector::_M_realloc_insert 3ms 0.016% 70.25% 256ms 1.38% std::_Rb_tree::_M_erase_aux (inline) 0 0% 70.25% 254ms 1.37% AbstractCellPopulation::Iterator::operator++ (inline) 26ms 0.14% 70.39% 249ms 1.35% AbstractCellPopulation::Iterator::IsRealCell (inline) 2ms 0.011% 70.40% 245ms 1.32% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 0 0% 70.40% 245ms 1.32% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.011% 70.41% 244ms 1.32% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 15ms 0.081% 70.49% 236ms 1.28% AbstractTetrahedralElement::CalculateJacobian 97ms 0.52% 71.02% 235ms 1.27% std::_Rb_tree::_M_clone_node (inline) 5ms 0.027% 71.04% 234ms 1.26% ApcOneHitCellMutationState::ApcOneHitCellMutationState 4ms 0.022% 71.07% 233ms 1.26% alternateaxes 9ms 0.049% 71.11% 230ms 1.24% AbstractCellPopulation::GetLocationIndexUsingCell 217ms 1.17% 72.29% 228ms 1.23% vertexmedian 1ms 0.0054% 72.29% 227ms 1.23% NodeLocationWriter::Visit 13ms 0.07% 72.36% 225ms 1.22% Element::MarkAsDeleted 10ms 0.054% 72.42% 225ms 1.22% TetrahedralMesh::Clear 224ms 1.21% 73.63% 224ms 1.21% [libchaste_mesh.so] 19ms 0.1% 73.73% 214ms 1.16% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 12ms 0.065% 73.79% 204ms 1.10% std::num_put::_M_insert_float 1ms 0.0054% 73.80% 201ms 1.09% CellProliferativeTypesWriter::VisitCell 11ms 0.059% 73.86% 198ms 1.07% AbstractTetrahedralElement::CalculateInverseJacobian 182ms 0.98% 74.84% 182ms 0.98% std::_Rb_tree::_S_left (inline) 0 0% 74.84% 178ms 0.96% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 6ms 0.032% 74.88% 172ms 0.93% std::__cxx11::collate::do_transform 25ms 0.14% 75.01% 171ms 0.92% AbstractTetrahedralElement::RefreshJacobian 2ms 0.011% 75.02% 167ms 0.9% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 3ms 0.016% 75.04% 166ms 0.9% CellPropertyCollection::HasProperty 0 0% 75.04% 164ms 0.89% Cell::HasCellProperty (inline) 4ms 0.022% 75.06% 162ms 0.88% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 130ms 0.7% 75.76% 160ms 0.86% malloc_consolidate 158ms 0.85% 76.62% 160ms 0.86% std::vector::operator[] (inline) 1ms 0.0054% 76.62% 157ms 0.85% ___vsnprintf 0 0% 76.62% 156ms 0.84% __vsnprintf_internal (inline) 11ms 0.059% 76.68% 154ms 0.83% __printf_buffer 154ms 0.83% 77.51% 154ms 0.83% std::_Rb_tree_insert_and_rebalance 5ms 0.027% 77.54% 153ms 0.83% Cylindrical2dMesh::CreateMirrorNodes 0 0% 77.54% 153ms 0.83% OffLatticeSimulation::ApplyBoundaries 1ms 0.0054% 77.55% 151ms 0.82% boost::numeric::ublas::vector_assign (inline) 5ms 0.027% 77.57% 147ms 0.79% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 14ms 0.076% 77.65% 147ms 0.79% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.011% 77.66% 146ms 0.79% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 95ms 0.51% 78.17% 144ms 0.78% AbstractElement::GetNodeGlobalIndex 8ms 0.043% 78.22% 142ms 0.77% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 41ms 0.22% 78.44% 141ms 0.76% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 85ms 0.46% 78.90% 141ms 0.76% std::_Rb_tree::equal_range (inline) 139ms 0.75% 79.65% 139ms 0.75% unlink_chunk 3ms 0.016% 79.66% 136ms 0.73% AbstractTetrahedralElement::AbstractTetrahedralElement 136ms 0.73% 80.40% 136ms 0.73% incircle 8ms 0.043% 80.44% 135ms 0.73% __printf_fp_l_buffer 0 0% 80.44% 135ms 0.73% __printf_fp_spec (inline) 9ms 0.049% 80.49% 131ms 0.71% boost::numeric::ublas::c_vector::c_vector (inline) 128ms 0.69% 81.18% 128ms 0.69% std::type_info::name (inline) 119ms 0.64% 81.83% 128ms 0.69% vertexsort 127ms 0.69% 82.51% 127ms 0.69% std::_Rb_tree_increment 77ms 0.42% 82.93% 123ms 0.66% AbstractElement::GetNodeLocation 67ms 0.36% 83.29% 121ms 0.65% Cylindrical2dMesh::GetVectorFromAtoB 7ms 0.038% 83.33% 121ms 0.65% MeshBasedCellPopulation::SpringsEnd (inline) 4ms 0.022% 83.35% 121ms 0.65% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.016% 83.37% 119ms 0.64% Cell::SetCellProliferativeType 3ms 0.016% 83.38% 119ms 0.64% Node::~Node 55ms 0.3% 83.68% 119ms 0.64% __printf_fp_buffer_1 27ms 0.15% 83.83% 119ms 0.64% boost::numeric::ublas::indexing_vector_assign 0 0% 83.83% 117ms 0.63% std::__new_allocator::destroy (inline) 0 0% 83.83% 117ms 0.63% std::allocator_traits::destroy (inline) 0 0% 83.83% 116ms 0.63% std::_Rb_tree::_M_destroy_node (inline) 0 0% 83.83% 113ms 0.61% AbstractCellBasedSimulation::DoCellRemoval (inline) 5ms 0.027% 83.85% 110ms 0.59% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 27ms 0.15% 84.00% 109ms 0.59% std::num_put::_M_insert_int 18ms 0.097% 84.10% 102ms 0.55% MeshBasedCellPopulation::SpringIterator::SpringIterator 101ms 0.55% 84.64% 101ms 0.55% [libstdc++.so.6.0.33] 100ms 0.54% 85.18% 100ms 0.54% TetrahedralMesh::EdgeIterator::operator!= 0 0% 85.18% 97ms 0.52% tcache_get (inline) 97ms 0.52% 85.71% 97ms 0.52% tcache_get_n (inline) 96ms 0.52% 86.22% 96ms 0.52% std::_Rb_tree_rebalance_for_erase 40ms 0.22% 86.44% 95ms 0.51% std::__ostream_insert 94ms 0.51% 86.95% 94ms 0.51% std::vector::size (inline) 5ms 0.027% 86.98% 93ms 0.5% CryptSimulationBoundaryCondition::VerifyBoundaryCondition