File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16153ms, 87.62% of 18435ms total Dropped 762 nodes (cum <= 92.17ms) flat flat% sum% cum cum% 0 0% 0% 18393ms 99.77% __libc_start_call_main 0 0% 0% 18393ms 99.77% __libc_start_main_impl 0 0% 0% 18393ms 99.77% _start 0 0% 0% 18370ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 18370ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 18370ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 18370ms 99.65% main 0 0% 0% 18334ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 18334ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 18334ms 99.45% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 18310ms 99.32% AbstractCellBasedSimulation::Solve 0 0% 0% 13913ms 75.47% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 8473ms 45.96% AbstractCellBasedSimulation::DoCellBirth 5ms 0.027% 0.027% 8363ms 45.36% Cell::ReadyToDivide 2ms 0.011% 0.038% 8312ms 45.09% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.038% 8145ms 44.18% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 6ms 0.033% 0.071% 8141ms 44.16% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 0.071% 8132ms 44.11% CellCycleModelOdeHandler::SolveOdeToTime 64ms 0.35% 0.42% 7972ms 43.24% AbstractOneStepIvpOdeSolver::InternalSolve 807ms 4.38% 4.80% 7055ms 38.27% RungeKutta4IvpOdeSolver::CalculateNextYValue 3143ms 17.05% 21.84% 5934ms 32.19% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.011% 21.86% 5313ms 28.82% MeshBasedCellPopulation::Update 5ms 0.027% 21.88% 4029ms 21.86% Cylindrical2dMesh::ReMesh 276ms 1.50% 23.38% 2914ms 15.81% AbstractCellProperty::IsType (inline) 0 0% 23.38% 2552ms 13.84% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 23.38% 2204ms 11.96% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 23.38% 2199ms 11.93% MutableMesh::ReMesh 3ms 0.016% 23.40% 2155ms 11.69% AbstractNumericalMethod::ComputeForcesIncludingDamping 888ms 4.82% 28.21% 1951ms 10.58% std::_Rb_tree::_M_lower_bound (inline) 174ms 0.94% 29.16% 1844ms 10.00% TetrahedralMesh::EdgeIterator::operator++ 0 0% 29.16% 1840ms 9.98% AbstractCellPopulation::WriteResultsToFiles 35ms 0.19% 29.35% 1503ms 8.15% std::_Rb_tree::find (inline) 0 0% 29.35% 1245ms 6.75% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.016% 29.36% 1209ms 6.56% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 51ms 0.28% 29.64% 1201ms 6.51% operator new 387ms 2.10% 31.74% 1141ms 6.19% __GI___libc_malloc 17ms 0.092% 31.83% 1116ms 6.05% MeshBasedCellPopulation::SpringIterator::operator++ 13ms 0.071% 31.90% 1114ms 6.04% std::set::insert (inline) 16ms 0.087% 31.99% 1101ms 5.97% std::_Rb_tree::_M_insert_unique 4ms 0.022% 32.01% 1088ms 5.90% TetrahedralMesh::ImportFromMesher 151ms 0.82% 32.83% 1052ms 5.71% AbstractCellProperty::IsSame 33ms 0.18% 33.01% 1030ms 5.59% std::__new_allocator::allocate (inline) 0 0% 33.01% 1023ms 5.55% std::allocator_traits::allocate (inline) 996ms 5.40% 38.41% 996ms 5.40% [libchaste_cell_based.so] 0 0% 38.41% 938ms 5.09% std::set::count (inline) 13ms 0.071% 38.48% 901ms 4.89% std::type_info::operator== (inline) 0 0% 38.48% 842ms 4.57% triangulate 839ms 4.55% 43.03% 839ms 4.55% __strcmp_evex 0 0% 43.03% 761ms 4.13% delaunay 0 0% 43.03% 761ms 4.13% divconqdelaunay 20ms 0.11% 43.14% 739ms 4.01% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 718ms 3.89% 47.04% 718ms 3.89% std::_Rb_tree::_S_right (inline) 43ms 0.23% 47.27% 714ms 3.87% std::_Rb_tree::_M_insert_ (inline) 0 0% 47.27% 699ms 3.79% std::_Rb_tree::_M_create_node (inline) 64ms 0.35% 47.62% 697ms 3.78% std::map::operator[] (partial-inline) 4ms 0.022% 47.64% 687ms 3.73% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 47.64% 684ms 3.71% std::_Rb_tree::_M_get_node (inline) 668ms 3.62% 51.26% 668ms 3.62% WntCellCycleOdeSystem::CalculateStoppingEvent 13ms 0.071% 51.33% 663ms 3.60% CellPopulationElementWriter::Visit 391ms 2.12% 53.45% 636ms 3.45% _int_malloc 0 0% 53.45% 629ms 3.41% std::_Rb_tree::_Alloc_node::operator() (inline) 25ms 0.14% 53.59% 619ms 3.36% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 18ms 0.098% 53.69% 612ms 3.32% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 53.69% 564ms 3.06% std::map::find (inline) 14ms 0.076% 53.76% 560ms 3.04% MeshBasedCellPopulation::AcceptCellWriter 169ms 0.92% 54.68% 548ms 2.97% __dynamic_cast 2ms 0.011% 54.69% 541ms 2.93% Element::Element 1ms 0.0054% 54.69% 540ms 2.93% CellPropertyCollection::GetPropertiesType (inline) 6ms 0.033% 54.73% 534ms 2.90% Element::RegisterWithNodes (inline) 40ms 0.22% 54.94% 531ms 2.88% Cylindrical2dMesh::ReconstructCylindricalMesh 19ms 0.1% 55.05% 531ms 2.88% Node::AddElement 0 0% 55.05% 523ms 2.84% std::_Rb_tree::lower_bound (inline) 0 0% 55.05% 523ms 2.84% std::map::lower_bound (inline) 11ms 0.06% 55.11% 519ms 2.82% std::less::operator() (inline) 508ms 2.76% 57.86% 508ms 2.76% std::operator< (inline) 237ms 1.29% 59.15% 505ms 2.74% AbstractCellMutationState::AbstractCellMutationState 108ms 0.59% 59.73% 502ms 2.72% __GI___libc_free 8ms 0.043% 59.78% 498ms 2.70% MutableMesh::ReIndex 4ms 0.022% 59.80% 484ms 2.63% Cylindrical2dMesh::CorrectNonPeriodicMesh 0 0% 59.80% 448ms 2.43% std::_Rb_tree::_M_drop_node (inline) 19ms 0.1% 59.90% 434ms 2.35% std::__new_allocator::deallocate (inline) 2ms 0.011% 59.91% 426ms 2.31% AbstractCellProperty::IsSubType (inline) 0 0% 59.91% 426ms 2.31% std::allocator_traits::deallocate (inline) 13ms 0.071% 59.98% 423ms 2.29% std::_Rb_tree::erase 13ms 0.071% 60.05% 422ms 2.29% Node::RemoveElement 0 0% 60.05% 422ms 2.29% std::set::erase (inline) 417ms 2.26% 62.32% 417ms 2.26% [libchaste_crypt.so] 0 0% 62.32% 407ms 2.21% std::ostream::operator<< (inline) 54ms 0.29% 62.61% 406ms 2.20% std::_Rb_tree::~_Rb_tree (inline) 51ms 0.28% 62.89% 402ms 2.18% std::ostream::_M_insert 72ms 0.39% 63.28% 400ms 2.17% std::_Rb_tree::_M_erase 10ms 0.054% 63.33% 396ms 2.15% divconqrecurse 327ms 1.77% 65.10% 389ms 2.11% _int_free 0 0% 65.10% 383ms 2.08% std::set::~set (inline) 104ms 0.56% 65.67% 373ms 2.02% mergehulls 147ms 0.8% 66.47% 371ms 2.01% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 66.47% 356ms 1.93% std::_Rb_tree::_M_put_node (inline) 13ms 0.071% 66.54% 349ms 1.89% Element::ResetIndex 0 0% 66.54% 339ms 1.84% std::_Vector_base::_M_allocate (inline) 0 0% 66.54% 327ms 1.77% AbstractCellPopulation::Iterator::operator++ (inline) 38ms 0.21% 66.74% 326ms 1.77% AbstractCellPopulation::Iterator::IsRealCell (inline) 25ms 0.14% 66.88% 325ms 1.76% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 1ms 0.0054% 66.88% 319ms 1.73% Cell::GetMutationState 300ms 1.63% 68.51% 308ms 1.67% std::vector::operator[] (inline) 5ms 0.027% 68.54% 301ms 1.63% LegacyCellProliferativeTypesWriter::VisitCell 7ms 0.038% 68.58% 301ms 1.63% boost::detail::shared_count::~shared_count (inline) 0 0% 68.58% 301ms 1.63% boost::shared_ptr::~shared_ptr (inline) 17ms 0.092% 68.67% 300ms 1.63% std::_Rb_tree::_Rb_tree 3ms 0.016% 68.68% 299ms 1.62% Cell::GetCellProliferativeType 287ms 1.56% 70.24% 288ms 1.56% boost::detail::sp_counted_base::release 1ms 0.0054% 70.25% 288ms 1.56% std::set::set (inline) 7ms 0.038% 70.28% 285ms 1.55% std::_Rb_tree::_M_erase_aux (inline) 14ms 0.076% 70.36% 281ms 1.52% std::vector::push_back (inline) 9ms 0.049% 70.41% 280ms 1.52% AbstractCellPopulation::GetLocationIndexUsingCell 37ms 0.2% 70.61% 279ms 1.51% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.016% 70.63% 275ms 1.49% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 70.63% 272ms 1.48% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 124ms 0.67% 71.30% 270ms 1.46% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 71.30% 261ms 1.42% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 26ms 0.14% 71.44% 257ms 1.39% std::_Rb_tree::_M_copy (inline) 8ms 0.043% 71.48% 255ms 1.38% std::vector::_M_realloc_insert 0 0% 71.48% 251ms 1.36% NodeLocationWriter::Visit 2ms 0.011% 71.49% 250ms 1.36% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 4ms 0.022% 71.52% 246ms 1.33% alternateaxes 0 0% 71.52% 242ms 1.31% TetrahedralMesh::RefreshJacobianCachedData 229ms 1.24% 72.76% 242ms 1.31% vertexmedian 0 0% 72.76% 237ms 1.29% OffLatticeSimulation::ApplyBoundaries 113ms 0.61% 73.37% 225ms 1.22% std::_Rb_tree::_M_clone_node (inline) 12ms 0.065% 73.44% 223ms 1.21% std::num_put::_M_insert_float 0 0% 73.44% 222ms 1.20% ApcOneHitCellMutationState::ApcOneHitCellMutationState 222ms 1.20% 74.64% 222ms 1.20% [libchaste_mesh.so] 3ms 0.016% 74.66% 220ms 1.19% Element::MarkAsDeleted 5ms 0.027% 74.68% 214ms 1.16% AbstractTetrahedralElement::CalculateInverseJacobian 17ms 0.092% 74.78% 213ms 1.16% AbstractTetrahedralElement::CalculateJacobian 3ms 0.016% 74.79% 199ms 1.08% std::__cxx11::collate::do_transform 1ms 0.0054% 74.80% 191ms 1.04% ___vsnprintf 3ms 0.016% 74.81% 190ms 1.03% MeshBasedCellPopulation::GetDampingConstant 1ms 0.0054% 74.82% 190ms 1.03% __vsnprintf_internal (inline) 43ms 0.23% 75.05% 189ms 1.03% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 1ms 0.0054% 75.06% 187ms 1.01% AbstractCentreBasedCellPopulation::GetDampingConstant 13ms 0.071% 75.13% 185ms 1.00% __printf_buffer 174ms 0.94% 76.07% 174ms 0.94% incircle 174ms 0.94% 77.02% 174ms 0.94% std::_Rb_tree_insert_and_rebalance 37ms 0.2% 77.22% 169ms 0.92% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 125ms 0.68% 77.90% 166ms 0.9% malloc_consolidate 4ms 0.022% 77.92% 165ms 0.9% __printf_fp_l_buffer 0 0% 77.92% 165ms 0.9% __printf_fp_spec (inline) 37ms 0.2% 78.12% 164ms 0.89% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 3ms 0.016% 78.13% 164ms 0.89% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 2ms 0.011% 78.14% 157ms 0.85% TetrahedralMesh::Clear 56ms 0.3% 78.45% 154ms 0.84% __printf_fp_buffer_1 60ms 0.33% 78.77% 152ms 0.82% AbstractElement::GetNodeGlobalIndex 145ms 0.79% 79.56% 145ms 0.79% AbstractCellProperty::AbstractCellProperty 5ms 0.027% 79.59% 145ms 0.79% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 9ms 0.049% 79.64% 142ms 0.77% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 22ms 0.12% 79.76% 141ms 0.76% AbstractTetrahedralElement::RefreshJacobian 5ms 0.027% 79.78% 141ms 0.76% Cell::SetCellProliferativeType 138ms 0.75% 80.53% 138ms 0.75% std::vector::size (inline) 68ms 0.37% 80.90% 137ms 0.74% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 80.90% 135ms 0.73% CellProliferativeTypesWriter::VisitCell 1ms 0.0054% 80.91% 133ms 0.72% boost::numeric::ublas::vector_assign (inline) 69ms 0.37% 81.28% 131ms 0.71% std::_Rb_tree::equal_range (inline) 1ms 0.0054% 81.29% 130ms 0.71% CellPropertyCollection::HasProperty 6ms 0.033% 81.32% 130ms 0.71% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 81.32% 129ms 0.7% Cell::HasCellProperty (inline) 128ms 0.69% 82.01% 128ms 0.69% std::type_info::name (inline) 0 0% 82.01% 126ms 0.68% AbstractCellBasedSimulation::DoCellRemoval (inline) 2ms 0.011% 82.02% 123ms 0.67% AbstractTetrahedralElement::AbstractTetrahedralElement 7ms 0.038% 82.06% 121ms 0.66% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 16ms 0.087% 82.15% 121ms 0.66% TetrahedralMesh::EdgesEnd 6ms 0.033% 82.18% 119ms 0.65% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 8ms 0.043% 82.22% 118ms 0.64% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 4ms 0.022% 82.25% 113ms 0.61% std::_Rb_tree_const_iterator::operator++ (inline) 111ms 0.6% 82.85% 111ms 0.6% std::_Rb_tree::_S_left (inline) 4ms 0.022% 82.87% 110ms 0.6% boost::numeric::ublas::c_vector::c_vector (inline) 2ms 0.011% 82.88% 110ms 0.6% std::_Rb_tree::_M_emplace_hint_unique 110ms 0.6% 83.48% 110ms 0.6% std::_Rb_tree_rebalance_for_erase 98ms 0.53% 84.01% 108ms 0.59% vertexsort 3ms 0.016% 84.02% 107ms 0.58% Cylindrical2dMesh::CreateMirrorNodes 42ms 0.23% 84.25% 106ms 0.57% AbstractElement::GetNodeLocation 105ms 0.57% 84.82% 105ms 0.57% [libchaste_ode.so] 104ms 0.56% 85.39% 104ms 0.56% std::_Rb_tree_increment 102ms 0.55% 85.94% 102ms 0.55% Node::GetIndex 0 0% 85.94% 99ms 0.54% tcache_get (inline) 99ms 0.54% 86.48% 99ms 0.54% tcache_get_n (inline) 98ms 0.53% 87.01% 98ms 0.53% unlink_chunk 17ms 0.092% 87.10% 94ms 0.51% MeshBasedCellPopulation::SpringIterator::SpringIterator 23ms 0.12% 87.23% 94ms 0.51% std::num_put::_M_insert_int 73ms 0.4% 87.62% 93ms 0.5% TetrahedralMesh::EdgeIterator::EdgeIterator