File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16844ms, 84.21% of 20003ms total Dropped 793 nodes (cum <= 100.02ms) flat flat% sum% cum cum% 0 0% 0% 19959ms 99.78% __libc_start_call_main 0 0% 0% 19959ms 99.78% __libc_start_main_impl 0 0% 0% 19959ms 99.78% _start 0 0% 0% 19940ms 99.69% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19940ms 99.69% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19940ms 99.69% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19940ms 99.69% main 0 0% 0% 19906ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19906ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19906ms 99.52% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19879ms 99.38% AbstractCellBasedSimulation::Solve 0 0% 0% 15486ms 77.42% AbstractCellBasedSimulation::UpdateCellPopulation 5ms 0.025% 0.025% 10301ms 51.50% AbstractCellBasedSimulation::DoCellBirth 8ms 0.04% 0.065% 10199ms 50.99% Cell::ReadyToDivide 3ms 0.015% 0.08% 10136ms 50.67% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.01% 0.09% 9985ms 49.92% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 12ms 0.06% 0.15% 9973ms 49.86% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.015% 0.16% 9957ms 49.78% CellCycleModelOdeHandler::SolveOdeToTime 62ms 0.31% 0.47% 9771ms 48.85% AbstractOneStepIvpOdeSolver::InternalSolve 929ms 4.64% 5.12% 8937ms 44.68% RungeKutta4IvpOdeSolver::CalculateNextYValue 3612ms 18.06% 23.18% 7776ms 38.87% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.01% 23.19% 5083ms 25.41% MeshBasedCellPopulation::Update 163ms 0.81% 24.00% 4206ms 21.03% AbstractCellProperty::IsType (inline) 8ms 0.04% 24.04% 3974ms 19.87% Cylindrical2dMesh::ReMesh 524ms 2.62% 26.66% 2935ms 14.67% AbstractCellProperty::IsSame 2ms 0.01% 26.67% 2434ms 12.17% OffLatticeSimulation::UpdateCellLocationsAndTopology 443ms 2.21% 28.89% 2411ms 12.05% std::type_info::operator== (inline) 0 0% 28.89% 2117ms 10.58% MutableMesh::ReMesh 0 0% 28.89% 2112ms 10.56% ForwardEulerNumericalMethod::UpdateAllNodePositions 15ms 0.075% 28.96% 2073ms 10.36% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 28.96% 1954ms 9.77% AbstractCellPopulation::WriteResultsToFiles 832ms 4.16% 33.12% 1862ms 9.31% std::_Rb_tree::_M_lower_bound (inline) 1733ms 8.66% 41.78% 1733ms 8.66% __strcmp_avx2 171ms 0.85% 42.64% 1614ms 8.07% TetrahedralMesh::EdgeIterator::operator++ 53ms 0.26% 42.90% 1354ms 6.77% std::_Rb_tree::find (inline) 57ms 0.28% 43.19% 1093ms 5.46% operator new 4ms 0.02% 43.21% 1091ms 5.45% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 15ms 0.075% 43.28% 1084ms 5.42% TetrahedralMesh::ImportFromMesher 1ms 0.005% 43.29% 1075ms 5.37% MeshBasedCellPopulation::UpdateNodePairs 251ms 1.25% 44.54% 1026ms 5.13% __GI___libc_malloc 7ms 0.035% 44.58% 975ms 4.87% std::set::insert (inline) 13ms 0.065% 44.64% 968ms 4.84% std::_Rb_tree::_M_insert_unique 8ms 0.04% 44.68% 952ms 4.76% MeshBasedCellPopulation::SpringIterator::operator++ 45ms 0.22% 44.91% 942ms 4.71% std::__new_allocator::allocate (inline) 0 0% 44.91% 935ms 4.67% std::allocator_traits::allocate (inline) 0 0% 44.91% 787ms 3.93% std::set::count (inline) 1ms 0.005% 44.91% 776ms 3.88% triangulate 3ms 0.015% 44.93% 731ms 3.65% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 711ms 3.55% 48.48% 711ms 3.55% std::_Rb_tree::_S_right (inline) 416ms 2.08% 50.56% 702ms 3.51% _int_malloc 2ms 0.01% 50.57% 696ms 3.48% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 50.57% 696ms 3.48% delaunay 2ms 0.01% 50.58% 696ms 3.48% divconqdelaunay 52ms 0.26% 50.84% 689ms 3.44% std::map::operator[] (partial-inline) 9ms 0.045% 50.89% 676ms 3.38% CellPopulationElementWriter::Visit 619ms 3.09% 53.98% 632ms 3.16% WntCellCycleOdeSystem::CalculateStoppingEvent 186ms 0.93% 54.91% 603ms 3.01% __dynamic_cast 0 0% 54.91% 598ms 2.99% std::_Rb_tree::_M_create_node (inline) 30ms 0.15% 55.06% 598ms 2.99% std::less::operator() (inline) 27ms 0.13% 55.20% 590ms 2.95% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 28ms 0.14% 55.34% 571ms 2.85% std::_Rb_tree::_M_insert_ (inline) 0 0% 55.34% 568ms 2.84% std::_Rb_tree::_M_get_node (inline) 568ms 2.84% 58.18% 568ms 2.84% std::operator< (inline) 5ms 0.025% 58.20% 565ms 2.82% MeshBasedCellPopulation::AcceptCellWriter 0 0% 58.20% 560ms 2.80% std::_Rb_tree::lower_bound (inline) 0 0% 58.20% 560ms 2.80% std::map::find (inline) 0 0% 58.20% 560ms 2.80% std::map::lower_bound (inline) 10ms 0.05% 58.25% 551ms 2.75% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 58.25% 548ms 2.74% std::_Rb_tree::_Alloc_node::operator() (inline) 7ms 0.035% 58.29% 542ms 2.71% CellPropertyCollection::GetPropertiesType (inline) 6ms 0.03% 58.32% 542ms 2.71% Element::Element 7ms 0.035% 58.35% 542ms 2.71% MutableMesh::ReIndex 17ms 0.085% 58.44% 515ms 2.57% Cylindrical2dMesh::CorrectNonPeriodicMesh 369ms 1.84% 60.28% 514ms 2.57% AbstractCellMutationState::AbstractCellMutationState 10ms 0.05% 60.33% 498ms 2.49% Element::RegisterWithNodes (inline) 77ms 0.38% 60.72% 483ms 2.41% std::ostream::_M_insert 0 0% 60.72% 483ms 2.41% std::ostream::operator<< (inline) 3ms 0.015% 60.73% 481ms 2.40% Node::AddElement 16ms 0.08% 60.81% 480ms 2.40% Cylindrical2dMesh::ReconstructCylindricalMesh 0 0% 60.81% 442ms 2.21% AbstractCellProperty::IsSubType (inline) 440ms 2.20% 63.01% 440ms 2.20% std::type_info::name (inline) 145ms 0.72% 63.74% 419ms 2.09% __GI___libc_free 142ms 0.71% 64.45% 384ms 1.92% std::_Rb_tree::_M_get_insert_unique_pos 5ms 0.025% 64.47% 380ms 1.90% std::_Rb_tree::erase 0 0% 64.47% 377ms 1.88% std::set::erase (inline) 11ms 0.055% 64.53% 374ms 1.87% Node::RemoveElement 1ms 0.005% 64.53% 368ms 1.84% std::_Vector_base::_M_allocate (inline) 26ms 0.13% 64.66% 366ms 1.83% Element::ResetIndex 16ms 0.08% 64.74% 347ms 1.73% divconqrecurse 119ms 0.59% 65.34% 347ms 1.73% std::_Rb_tree::_M_erase 6ms 0.03% 65.37% 346ms 1.73% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 15ms 0.075% 65.44% 340ms 1.70% std::__new_allocator::deallocate (inline) 0 0% 65.44% 336ms 1.68% std::allocator_traits::deallocate (inline) 96ms 0.48% 65.92% 327ms 1.63% mergehulls 23ms 0.11% 66.04% 317ms 1.58% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.015% 66.05% 307ms 1.53% NodeLocationWriter::Visit 170ms 0.85% 66.90% 304ms 1.52% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 66.90% 301ms 1.50% std::_Rb_tree::_M_drop_node (inline) 1ms 0.005% 66.90% 298ms 1.49% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.005% 66.91% 293ms 1.46% Cell::GetMutationState 4ms 0.02% 66.93% 291ms 1.45% Cell::GetCellProliferativeType 0 0% 66.93% 289ms 1.44% std::set::~set (inline) 1ms 0.005% 66.93% 288ms 1.44% LegacyCellProliferativeTypesWriter::VisitCell 2ms 0.01% 66.94% 285ms 1.42% AbstractCellPopulation::Iterator::operator++ (inline) 42ms 0.21% 67.15% 282ms 1.41% AbstractCellPopulation::Iterator::IsRealCell (inline) 279ms 1.39% 68.55% 280ms 1.40% std::vector::operator[] (inline) 14ms 0.07% 68.62% 277ms 1.38% std::_Rb_tree::_Rb_tree (partial-inline) 233ms 1.16% 69.78% 274ms 1.37% _int_free 0 0% 69.78% 268ms 1.34% std::_Rb_tree::_M_put_node (inline) 17ms 0.085% 69.87% 260ms 1.30% std::num_put::_M_insert_float 2ms 0.01% 69.88% 257ms 1.28% std::set::set (inline) 5ms 0.025% 69.90% 254ms 1.27% AbstractCellPopulation::IsCellAttachedToLocationIndex 253ms 1.26% 71.17% 253ms 1.26% [libchaste_cell_based.so] 8ms 0.04% 71.21% 243ms 1.21% std::vector::push_back (inline) 52ms 0.26% 71.47% 241ms 1.20% ApcOneHitCellMutationState::ApcOneHitCellMutationState 18ms 0.09% 71.56% 232ms 1.16% std::vector::_M_realloc_insert 40ms 0.2% 71.76% 230ms 1.15% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 33ms 0.16% 71.92% 230ms 1.15% std::_Rb_tree::_M_copy (inline) 5ms 0.025% 71.95% 230ms 1.15% std::_Rb_tree::_M_erase_aux (inline) 1ms 0.005% 71.95% 226ms 1.13% alternateaxes 9ms 0.045% 72.00% 225ms 1.12% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 1ms 0.005% 72.00% 225ms 1.12% TetrahedralMesh::RefreshJacobianCachedData 211ms 1.05% 73.06% 225ms 1.12% vertexmedian 19ms 0.095% 73.15% 224ms 1.12% AbstractTetrahedralElement::CalculateJacobian 2ms 0.01% 73.16% 215ms 1.07% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 79ms 0.39% 73.56% 214ms 1.07% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 3ms 0.015% 73.57% 208ms 1.04% std::__cxx11::collate::do_transform 156ms 0.78% 74.35% 205ms 1.02% AbstractElement::GetNodeGlobalIndex 1ms 0.005% 74.36% 202ms 1.01% OffLatticeSimulation::ApplyBoundaries 2ms 0.01% 74.37% 202ms 1.01% ___vsnprintf 0 0% 74.37% 200ms 1% __vsnprintf_internal (inline) 21ms 0.1% 74.47% 197ms 0.98% __printf_buffer 19ms 0.095% 74.57% 196ms 0.98% Element::MarkAsDeleted 144ms 0.72% 75.29% 195ms 0.97% malloc_consolidate 49ms 0.24% 75.53% 195ms 0.97% std::_Rb_tree::_M_clone_node (inline) 10ms 0.05% 75.58% 180ms 0.9% AbstractTetrahedralElement::CalculateInverseJacobian 16ms 0.08% 75.66% 177ms 0.88% TetrahedralMesh::Clear 4ms 0.02% 75.68% 171ms 0.85% AbstractTetrahedralElement::AbstractTetrahedralElement 20ms 0.1% 75.78% 169ms 0.84% AbstractTetrahedralElement::RefreshJacobian 1ms 0.005% 75.79% 169ms 0.84% MeshBasedCellPopulation::GetDampingConstant 0 0% 75.79% 168ms 0.84% AbstractCentreBasedCellPopulation::GetDampingConstant 1ms 0.005% 75.79% 162ms 0.81% __printf_fp_spec (inline) 9ms 0.045% 75.84% 161ms 0.8% __printf_fp_l_buffer 159ms 0.79% 76.63% 159ms 0.79% Node::GetIndex 3ms 0.015% 76.65% 158ms 0.79% CellProliferativeTypesWriter::VisitCell 157ms 0.78% 77.43% 157ms 0.78% std::_Rb_tree_insert_and_rebalance 94ms 0.47% 77.90% 154ms 0.77% std::_Rb_tree::equal_range (inline) 6ms 0.03% 77.93% 148ms 0.74% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 73ms 0.36% 78.30% 145ms 0.72% __printf_fp_buffer_1 144ms 0.72% 79.02% 144ms 0.72% std::vector::size (inline) 141ms 0.7% 79.72% 141ms 0.7% incircle 47ms 0.23% 79.96% 140ms 0.7% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 4ms 0.02% 79.98% 140ms 0.7% CellPropertyCollection::HasProperty 139ms 0.69% 80.67% 139ms 0.69% unlink_chunk 0 0% 80.67% 138ms 0.69% Cell::HasCellProperty (inline) 78ms 0.39% 81.06% 137ms 0.68% AbstractElement::GetNodeLocation 4ms 0.02% 81.08% 137ms 0.68% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 3ms 0.015% 81.10% 133ms 0.66% boost::numeric::ublas::vector_assign (inline) 44ms 0.22% 81.32% 130ms 0.65% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 83ms 0.41% 81.73% 129ms 0.64% Cylindrical2dMesh::GetVectorFromAtoB 5ms 0.025% 81.76% 125ms 0.62% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 13ms 0.065% 81.82% 119ms 0.59% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 25ms 0.12% 81.95% 118ms 0.59% TetrahedralMesh::EdgesEnd 8ms 0.04% 81.99% 115ms 0.57% MeshBasedCellPopulation::SpringsEnd (inline) 22ms 0.11% 82.10% 114ms 0.57% std::num_put::_M_insert_int 57ms 0.28% 82.38% 113ms 0.56% std::__ostream_insert 7ms 0.035% 82.42% 112ms 0.56% boost::numeric::ublas::c_vector::c_vector (inline) 2ms 0.01% 82.43% 110ms 0.55% Cell::SetCellProliferativeType 3ms 0.015% 82.44% 110ms 0.55% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 102ms 0.51% 82.95% 109ms 0.54% vertexsort 106ms 0.53% 83.48% 106ms 0.53% AbstractElement::IsDeleted 104ms 0.52% 84.00% 104ms 0.52% std::_Rb_tree_increment 23ms 0.11% 84.12% 103ms 0.51% boost::numeric::ublas::indexing_vector_assign 18ms 0.09% 84.21% 102ms 0.51% boost::detail::shared_count::~shared_count (inline) 0 0% 84.21% 102ms 0.51% boost::shared_ptr::~shared_ptr (inline)