File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 13634ms, 85.69% of 15910ms total Dropped 773 nodes (cum <= 79.55ms) flat flat% sum% cum cum% 0 0% 0% 15875ms 99.78% __libc_start_call_main 0 0% 0% 15875ms 99.78% __libc_start_main_impl 0 0% 0% 15875ms 99.78% _start 0 0% 0% 15857ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 15857ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 15857ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 15857ms 99.67% main 0 0% 0% 15825ms 99.47% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 15825ms 99.47% CxxTest::TestRunner::runTest (inline) 0 0% 0% 15825ms 99.47% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 15805ms 99.34% AbstractCellBasedSimulation::Solve 0 0% 0% 12073ms 75.88% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 7470ms 46.95% AbstractCellBasedSimulation::DoCellBirth 3ms 0.019% 0.019% 7377ms 46.37% Cell::ReadyToDivide 3ms 0.019% 0.038% 7332ms 46.08% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.038% 7205ms 45.29% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 9ms 0.057% 0.094% 7199ms 45.25% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.013% 0.11% 7187ms 45.17% CellCycleModelOdeHandler::SolveOdeToTime 41ms 0.26% 0.36% 7045ms 44.28% AbstractOneStepIvpOdeSolver::InternalSolve 718ms 4.51% 4.88% 6277ms 39.45% RungeKutta4IvpOdeSolver::CalculateNextYValue 2838ms 17.84% 22.72% 5316ms 33.41% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0063% 22.72% 4505ms 28.32% MeshBasedCellPopulation::Update 2ms 0.013% 22.73% 3392ms 21.32% Cylindrical2dMesh::ReMesh 329ms 2.07% 24.80% 2583ms 16.24% AbstractCellProperty::IsType (inline) 0 0% 24.80% 2189ms 13.76% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 24.80% 1901ms 11.95% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 24.80% 1898ms 11.93% MutableMesh::ReMesh 0 0% 24.80% 1843ms 11.58% AbstractNumericalMethod::ComputeForcesIncludingDamping 729ms 4.58% 29.38% 1669ms 10.49% std::_Rb_tree::_M_lower_bound (inline) 158ms 0.99% 30.38% 1590ms 9.99% TetrahedralMesh::EdgeIterator::operator++ 0 0% 30.38% 1538ms 9.67% AbstractCellPopulation::WriteResultsToFiles 27ms 0.17% 30.55% 1304ms 8.20% std::_Rb_tree::find (inline) 1ms 0.0063% 30.55% 1083ms 6.81% MeshBasedCellPopulation::UpdateNodePairs 122ms 0.77% 31.32% 1025ms 6.44% AbstractCellProperty::IsSame 6ms 0.038% 31.36% 1002ms 6.30% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 40ms 0.25% 31.61% 986ms 6.20% operator new 17ms 0.11% 31.72% 972ms 6.11% MeshBasedCellPopulation::SpringIterator::operator++ 345ms 2.17% 33.88% 934ms 5.87% __GI___libc_malloc 5ms 0.031% 33.92% 911ms 5.73% TetrahedralMesh::ImportFromMesher 907ms 5.70% 39.62% 907ms 5.70% __strcmp_evex 23ms 0.14% 39.76% 903ms 5.68% std::type_info::operator== (inline) 8ms 0.05% 39.81% 891ms 5.60% std::set::insert (inline) 10ms 0.063% 39.87% 883ms 5.55% std::_Rb_tree::_M_insert_unique 0 0% 39.87% 844ms 5.30% std::set::count (inline) 17ms 0.11% 39.98% 831ms 5.22% std::__new_allocator::allocate (inline) 0 0% 39.98% 829ms 5.21% std::allocator_traits::allocate (inline) 797ms 5.01% 44.99% 797ms 5.01% [libchaste_cell_based.so] 0 0% 44.99% 748ms 4.70% triangulate 0 0% 44.99% 688ms 4.32% delaunay 3ms 0.019% 45.01% 688ms 4.32% divconqdelaunay 10ms 0.063% 45.07% 629ms 3.95% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 617ms 3.88% 48.95% 617ms 3.88% std::_Rb_tree::_S_right (inline) 1ms 0.0063% 48.96% 605ms 3.80% AbstractTwoBodyInteractionForce::AddForceContribution 589ms 3.70% 52.66% 589ms 3.70% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 52.66% 567ms 3.56% std::_Rb_tree::_M_create_node (inline) 42ms 0.26% 52.92% 558ms 3.51% std::_Rb_tree::_M_insert_ (inline) 43ms 0.27% 53.19% 558ms 3.51% std::map::operator[] (partial-inline) 9ms 0.057% 53.25% 552ms 3.47% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 53.25% 552ms 3.47% std::_Rb_tree::_M_get_node (inline) 8ms 0.05% 53.30% 535ms 3.36% CellPopulationElementWriter::Visit 14ms 0.088% 53.39% 519ms 3.26% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 53.39% 507ms 3.19% std::_Rb_tree::_Alloc_node::operator() (inline) 131ms 0.82% 54.21% 500ms 3.14% __dynamic_cast 15ms 0.094% 54.31% 491ms 3.09% Cylindrical2dMesh::ReconstructCylindricalMesh 11ms 0.069% 54.37% 485ms 3.05% MeshBasedCellPopulation::AcceptCellWriter 296ms 1.86% 56.24% 485ms 3.05% _int_malloc 1ms 0.0063% 56.24% 473ms 2.97% Element::Element 5ms 0.031% 56.27% 461ms 2.90% CellPropertyCollection::GetPropertiesType (inline) 0 0% 56.27% 457ms 2.87% std::map::find (inline) 12ms 0.075% 56.35% 452ms 2.84% std::less::operator() (inline) 228ms 1.43% 57.78% 441ms 2.77% AbstractCellMutationState::AbstractCellMutationState 6ms 0.038% 57.82% 441ms 2.77% Element::RegisterWithNodes (inline) 440ms 2.77% 60.58% 440ms 2.77% std::operator< (inline) 24ms 0.15% 60.74% 438ms 2.75% Node::AddElement 0 0% 60.74% 425ms 2.67% std::_Rb_tree::lower_bound (inline) 0 0% 60.74% 425ms 2.67% std::map::lower_bound (inline) 81ms 0.51% 61.24% 409ms 2.57% __GI___libc_free 4ms 0.025% 61.27% 376ms 2.36% MutableMesh::ReIndex 2ms 0.013% 61.28% 360ms 2.26% AbstractCellProperty::IsSubType (inline) 14ms 0.088% 61.37% 355ms 2.23% Cylindrical2dMesh::CorrectNonPeriodicMesh 0 0% 61.37% 355ms 2.23% std::_Rb_tree::_M_drop_node (inline) 0 0% 61.37% 355ms 2.23% std::ostream::operator<< (inline) 7ms 0.044% 61.41% 350ms 2.20% divconqrecurse 46ms 0.29% 61.70% 350ms 2.20% std::ostream::_M_insert 11ms 0.069% 61.77% 342ms 2.15% std::__new_allocator::deallocate (inline) 55ms 0.35% 62.12% 335ms 2.11% std::_Rb_tree::_M_erase 43ms 0.27% 62.39% 335ms 2.11% std::_Rb_tree::~_Rb_tree (inline) 0 0% 62.39% 334ms 2.10% std::allocator_traits::deallocate (inline) 92ms 0.58% 62.97% 332ms 2.09% mergehulls 275ms 1.73% 64.70% 320ms 2.01% _int_free 13ms 0.082% 64.78% 320ms 2.01% std::_Rb_tree::erase 0 0% 64.78% 319ms 2.01% std::set::erase (inline) 138ms 0.87% 65.64% 315ms 1.98% std::_Rb_tree::_M_get_insert_unique_pos 9ms 0.057% 65.70% 313ms 1.97% Node::RemoveElement 0 0% 65.70% 312ms 1.96% std::set::~set (inline) 302ms 1.90% 67.60% 302ms 1.90% [libchaste_crypt.so] 7ms 0.044% 67.64% 283ms 1.78% boost::detail::shared_count::~shared_count (inline) 0 0% 67.64% 283ms 1.78% boost::shared_ptr::~shared_ptr (inline) 0 0% 67.64% 277ms 1.74% std::_Rb_tree::_M_put_node (inline) 0 0% 67.64% 277ms 1.74% std::_Vector_base::_M_allocate (inline) 1ms 0.0063% 67.65% 272ms 1.71% Cell::GetMutationState 0 0% 67.65% 271ms 1.70% AbstractCellPopulation::Iterator::operator++ (inline) 23ms 0.14% 67.79% 268ms 1.68% AbstractCellPopulation::Iterator::IsRealCell (inline) 262ms 1.65% 69.44% 265ms 1.67% boost::detail::sp_counted_base::release 1ms 0.0063% 69.45% 259ms 1.63% LegacyCellProliferativeTypesWriter::VisitCell 8ms 0.05% 69.50% 252ms 1.58% std::_Rb_tree::_Rb_tree 124ms 0.78% 70.28% 248ms 1.56% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.013% 70.29% 246ms 1.55% std::set::set (inline) 1ms 0.0063% 70.30% 245ms 1.54% Cell::GetCellProliferativeType 232ms 1.46% 71.75% 240ms 1.51% std::vector::operator[] (inline) 9ms 0.057% 71.81% 234ms 1.47% Element::ResetIndex 21ms 0.13% 71.94% 232ms 1.46% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 8ms 0.05% 71.99% 227ms 1.43% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 71.99% 227ms 1.43% NodeLocationWriter::Visit 6ms 0.038% 72.03% 226ms 1.42% alternateaxes 0 0% 72.03% 225ms 1.41% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 1ms 0.0063% 72.04% 222ms 1.40% ApcOneHitCellMutationState::ApcOneHitCellMutationState 221ms 1.39% 73.43% 221ms 1.39% [libchaste_mesh.so] 27ms 0.17% 73.60% 221ms 1.39% std::_Rb_tree::_M_copy (inline) 0 0% 73.60% 217ms 1.36% TetrahedralMesh::RefreshJacobianCachedData 200ms 1.26% 74.85% 217ms 1.36% vertexmedian 15ms 0.094% 74.95% 216ms 1.36% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 9ms 0.057% 75.00% 214ms 1.35% std::vector::push_back (inline) 16ms 0.1% 75.10% 210ms 1.32% AbstractTetrahedralElement::CalculateJacobian 17ms 0.11% 75.21% 204ms 1.28% std::num_put::_M_insert_float 2ms 0.013% 75.22% 203ms 1.28% AbstractCellPopulation::IsCellAttachedToLocationIndex 16ms 0.1% 75.32% 203ms 1.28% std::_Rb_tree::_M_erase_aux (inline) 0 0% 75.32% 201ms 1.26% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 3ms 0.019% 75.34% 196ms 1.23% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 9ms 0.057% 75.40% 196ms 1.23% std::vector::_M_realloc_insert 1ms 0.0063% 75.41% 194ms 1.22% OffLatticeSimulation::ApplyBoundaries 5ms 0.031% 75.44% 191ms 1.20% AbstractTetrahedralElement::CalculateInverseJacobian 10ms 0.063% 75.50% 189ms 1.19% Element::MarkAsDeleted 90ms 0.57% 76.07% 186ms 1.17% std::_Rb_tree::_M_clone_node (inline) 0 0% 76.07% 170ms 1.07% MeshBasedCellPopulation::GetDampingConstant 4ms 0.025% 76.09% 167ms 1.05% AbstractCentreBasedCellPopulation::GetDampingConstant 2ms 0.013% 76.10% 165ms 1.04% std::__cxx11::collate::do_transform 0 0% 76.10% 160ms 1.01% ___vsnprintf 0 0% 76.10% 160ms 1.01% __vsnprintf_internal (inline) 17ms 0.11% 76.21% 157ms 0.99% __printf_buffer 155ms 0.97% 77.18% 155ms 0.97% incircle 19ms 0.12% 77.30% 151ms 0.95% AbstractTetrahedralElement::RefreshJacobian 28ms 0.18% 77.48% 146ms 0.92% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 53ms 0.33% 77.81% 135ms 0.85% AbstractElement::GetNodeGlobalIndex 132ms 0.83% 78.64% 132ms 0.83% std::vector::size (inline) 5ms 0.031% 78.67% 128ms 0.8% AbstractTetrahedralElement::AbstractTetrahedralElement 5ms 0.031% 78.71% 127ms 0.8% __printf_fp_l_buffer 0 0% 78.71% 127ms 0.8% __printf_fp_spec (inline) 101ms 0.63% 79.34% 127ms 0.8% malloc_consolidate 4ms 0.025% 79.37% 124ms 0.78% boost::numeric::ublas::vector_assign (inline) 3ms 0.019% 79.38% 122ms 0.77% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 0 0% 79.38% 120ms 0.75% CellProliferativeTypesWriter::VisitCell 0 0% 79.38% 120ms 0.75% TetrahedralMesh::Clear 3ms 0.019% 79.40% 118ms 0.74% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 60ms 0.38% 79.78% 118ms 0.74% __printf_fp_buffer_1 118ms 0.74% 80.52% 118ms 0.74% std::_Rb_tree_insert_and_rebalance 45ms 0.28% 80.80% 115ms 0.72% AbstractElement::GetNodeLocation 2ms 0.013% 80.82% 115ms 0.72% CellPropertyCollection::HasProperty 0 0% 80.82% 113ms 0.71% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 113ms 0.71% 81.53% 113ms 0.71% std::type_info::name (inline) 111ms 0.7% 82.23% 111ms 0.7% AbstractCellProperty::AbstractCellProperty 0 0% 82.23% 111ms 0.7% Cell::HasCellProperty (inline) 6ms 0.038% 82.26% 108ms 0.68% boost::numeric::ublas::c_vector::c_vector (inline) 2ms 0.013% 82.28% 107ms 0.67% MeshBasedCellPopulation::SpringsEnd (inline) 55ms 0.35% 82.62% 107ms 0.67% std::_Rb_tree::equal_range (inline) 4ms 0.025% 82.65% 104ms 0.65% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 17ms 0.11% 82.75% 103ms 0.65% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 82.75% 101ms 0.63% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 7ms 0.044% 82.80% 100ms 0.63% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 100ms 0.63% 83.43% 100ms 0.63% std::_Rb_tree::_S_left (inline) 85ms 0.53% 83.96% 98ms 0.62% vertexsort 0 0% 83.96% 97ms 0.61% AbstractCellBasedSimulation::DoCellRemoval (inline) 3ms 0.019% 83.98% 97ms 0.61% Cell::SetCellProliferativeType 1ms 0.0063% 83.98% 93ms 0.58% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 3ms 0.019% 84.00% 93ms 0.58% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 4ms 0.025% 84.03% 91ms 0.57% Cylindrical2dMesh::CreateMirrorNodes 58ms 0.36% 84.39% 91ms 0.57% Cylindrical2dMesh::GetVectorFromAtoB 2ms 0.013% 84.41% 90ms 0.57% std::_Rb_tree::_M_emplace_hint_unique 0 0% 84.41% 89ms 0.56% tcache_get (inline) 89ms 0.56% 84.97% 89ms 0.56% tcache_get_n (inline) 13ms 0.082% 85.05% 85ms 0.53% MeshBasedCellPopulation::SpringIterator::SpringIterator 82ms 0.52% 85.56% 82ms 0.52% Node::GetIndex 0 0% 85.56% 81ms 0.51% std::__new_allocator::destroy (inline) 0 0% 85.56% 81ms 0.51% std::allocator_traits::destroy (inline) 21ms 0.13% 85.69% 80ms 0.5% boost::numeric::ublas::indexing_vector_assign 0 0% 85.69% 80ms 0.5% std::_Rb_tree::_M_destroy_node (inline)