File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 13678ms, 85.74% of 15952ms total Dropped 732 nodes (cum <= 79.76ms) flat flat% sum% cum cum% 0 0% 0% 15917ms 99.78% __libc_start_call_main 0 0% 0% 15917ms 99.78% __libc_start_main_impl 0 0% 0% 15917ms 99.78% _start 0 0% 0% 15899ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 15899ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 15899ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 15899ms 99.67% main 0 0% 0% 15865ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 15865ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 15865ms 99.45% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 15844ms 99.32% AbstractCellBasedSimulation::Solve 0 0% 0% 12108ms 75.90% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0063% 0.0063% 7502ms 47.03% AbstractCellBasedSimulation::DoCellBirth 2ms 0.013% 0.019% 7416ms 46.49% Cell::ReadyToDivide 2ms 0.013% 0.031% 7373ms 46.22% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.031% 7241ms 45.39% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 10ms 0.063% 0.094% 7240ms 45.39% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 0.094% 7229ms 45.32% CellCycleModelOdeHandler::SolveOdeToTime 37ms 0.23% 0.33% 7075ms 44.35% AbstractOneStepIvpOdeSolver::InternalSolve 698ms 4.38% 4.70% 6299ms 39.49% RungeKutta4IvpOdeSolver::CalculateNextYValue 2864ms 17.95% 22.66% 5382ms 33.74% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 22.66% 4508ms 28.26% MeshBasedCellPopulation::Update 3ms 0.019% 22.67% 3392ms 21.26% Cylindrical2dMesh::ReMesh 300ms 1.88% 24.55% 2632ms 16.50% AbstractCellProperty::IsType (inline) 0 0% 24.55% 2164ms 13.57% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 24.55% 1896ms 11.89% MutableMesh::ReMesh 0 0% 24.55% 1885ms 11.82% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.013% 24.57% 1845ms 11.57% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0063% 24.57% 1569ms 9.84% AbstractCellPopulation::WriteResultsToFiles 722ms 4.53% 29.10% 1565ms 9.81% std::_Rb_tree::_M_lower_bound (inline) 136ms 0.85% 29.95% 1503ms 9.42% TetrahedralMesh::EdgeIterator::operator++ 44ms 0.28% 30.23% 1197ms 7.50% std::_Rb_tree::find (inline) 0 0% 30.23% 1070ms 6.71% MeshBasedCellPopulation::UpdateNodePairs 134ms 0.84% 31.07% 1029ms 6.45% AbstractCellProperty::IsSame 48ms 0.3% 31.37% 993ms 6.22% operator new 3ms 0.019% 31.39% 989ms 6.20% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 21ms 0.13% 31.52% 951ms 5.96% MeshBasedCellPopulation::SpringIterator::operator++ 346ms 2.17% 33.69% 936ms 5.87% __GI___libc_malloc 8ms 0.05% 33.74% 916ms 5.74% TetrahedralMesh::ImportFromMesher 12ms 0.075% 33.81% 895ms 5.61% std::set::insert (inline) 27ms 0.17% 33.98% 895ms 5.61% std::type_info::operator== (inline) 12ms 0.075% 34.06% 883ms 5.54% std::_Rb_tree::_M_insert_unique 863ms 5.41% 39.47% 863ms 5.41% __strcmp_evex 24ms 0.15% 39.62% 838ms 5.25% std::__new_allocator::allocate (inline) 0 0% 39.62% 834ms 5.23% std::allocator_traits::allocate (inline) 792ms 4.96% 44.58% 792ms 4.96% [libchaste_cell_based.so] 0 0% 44.58% 777ms 4.87% std::set::count (inline) 1ms 0.0063% 44.59% 734ms 4.60% triangulate 0 0% 44.59% 657ms 4.12% delaunay 4ms 0.025% 44.62% 656ms 4.11% divconqdelaunay 8ms 0.05% 44.67% 615ms 3.86% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 4ms 0.025% 44.69% 604ms 3.79% AbstractTwoBodyInteractionForce::AddForceContribution 602ms 3.77% 48.46% 602ms 3.77% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 48.46% 565ms 3.54% std::_Rb_tree::_M_create_node (inline) 35ms 0.22% 48.68% 564ms 3.54% std::map::operator[] (partial-inline) 3ms 0.019% 48.70% 557ms 3.49% CellPopulationElementWriter::Visit 0 0% 48.70% 549ms 3.44% std::_Rb_tree::_M_get_node (inline) 47ms 0.29% 49.00% 549ms 3.44% std::_Rb_tree::_M_insert_ (inline) 27ms 0.17% 49.17% 546ms 3.42% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 543ms 3.40% 52.57% 543ms 3.40% std::_Rb_tree::_S_right (inline) 144ms 0.9% 53.47% 530ms 3.32% __dynamic_cast 0 0% 53.47% 506ms 3.17% std::_Rb_tree::_Alloc_node::operator() (inline) 10ms 0.063% 53.54% 500ms 3.13% AbstractCellPopulation::GetCellUsingLocationIndex 316ms 1.98% 55.52% 498ms 3.12% _int_malloc 27ms 0.17% 55.69% 495ms 3.10% Cylindrical2dMesh::ReconstructCylindricalMesh 13ms 0.081% 55.77% 490ms 3.07% MeshBasedCellPopulation::AcceptCellWriter 256ms 1.60% 57.37% 487ms 3.05% AbstractCellMutationState::AbstractCellMutationState 2ms 0.013% 57.38% 472ms 2.96% Element::Element 3ms 0.019% 57.40% 467ms 2.93% CellPropertyCollection::GetPropertiesType (inline) 15ms 0.094% 57.50% 458ms 2.87% std::less::operator() (inline) 4ms 0.025% 57.52% 449ms 2.81% Element::RegisterWithNodes (inline) 443ms 2.78% 60.30% 443ms 2.78% std::operator< (inline) 18ms 0.11% 60.41% 440ms 2.76% Node::AddElement 0 0% 60.41% 440ms 2.76% std::_Rb_tree::lower_bound (inline) 0 0% 60.41% 440ms 2.76% std::map::lower_bound (inline) 85ms 0.53% 60.95% 417ms 2.61% __GI___libc_free 0 0% 60.95% 417ms 2.61% std::map::find (inline) 0 0% 60.95% 407ms 2.55% std::_Rb_tree::_M_drop_node (inline) 11ms 0.069% 61.01% 381ms 2.39% Cylindrical2dMesh::CorrectNonPeriodicMesh 49ms 0.31% 61.32% 377ms 2.36% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.019% 61.34% 375ms 2.35% AbstractCellProperty::IsSubType (inline) 6ms 0.038% 61.38% 375ms 2.35% MutableMesh::ReIndex 1ms 0.0063% 61.38% 373ms 2.34% std::ostream::operator<< (inline) 57ms 0.36% 61.74% 371ms 2.33% std::ostream::_M_insert 60ms 0.38% 62.12% 368ms 2.31% std::_Rb_tree::_M_erase 0 0% 62.12% 365ms 2.29% std::set::~set (inline) 13ms 0.081% 62.20% 359ms 2.25% std::__new_allocator::deallocate (inline) 0 0% 62.20% 357ms 2.24% std::allocator_traits::deallocate (inline) 340ms 2.13% 64.33% 340ms 2.13% [libchaste_crypt.so] 11ms 0.069% 64.40% 335ms 2.10% divconqrecurse 10ms 0.063% 64.46% 332ms 2.08% std::_Rb_tree::erase 0 0% 64.46% 330ms 2.07% std::set::erase (inline) 281ms 1.76% 66.22% 329ms 2.06% _int_free 133ms 0.83% 67.06% 322ms 2.02% std::_Rb_tree::_M_get_insert_unique_pos 9ms 0.056% 67.11% 321ms 2.01% Node::RemoveElement 101ms 0.63% 67.75% 321ms 2.01% mergehulls 0 0% 67.75% 309ms 1.94% std::_Rb_tree::_M_put_node (inline) 140ms 0.88% 68.62% 287ms 1.80% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 68.62% 285ms 1.79% std::_Vector_base::_M_allocate (inline) 2ms 0.013% 68.64% 274ms 1.72% Cell::GetMutationState 8ms 0.05% 68.69% 271ms 1.70% boost::detail::shared_count::~shared_count (inline) 0 0% 68.69% 271ms 1.70% boost::shared_ptr::~shared_ptr (inline) 3ms 0.019% 68.71% 268ms 1.68% Cell::GetCellProliferativeType 4ms 0.025% 68.73% 264ms 1.65% LegacyCellProliferativeTypesWriter::VisitCell 25ms 0.16% 68.89% 260ms 1.63% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 68.89% 260ms 1.63% AbstractCellPopulation::Iterator::operator++ (inline) 1ms 0.0063% 68.89% 254ms 1.59% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 251ms 1.57% 70.47% 254ms 1.59% boost::detail::sp_counted_base::release 14ms 0.088% 70.56% 254ms 1.59% std::_Rb_tree::_Rb_tree (partial-inline) 15ms 0.094% 70.65% 245ms 1.54% Element::ResetIndex 1ms 0.0063% 70.66% 244ms 1.53% ApcOneHitCellMutationState::ApcOneHitCellMutationState 18ms 0.11% 70.77% 238ms 1.49% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 70.77% 234ms 1.47% std::set::set (inline) 0 0% 70.77% 233ms 1.46% NodeLocationWriter::Visit 6ms 0.038% 70.81% 227ms 1.42% AbstractCellPopulation::IsCellAttachedToLocationIndex 25ms 0.16% 70.96% 226ms 1.42% std::_Rb_tree::_M_copy (inline) 7ms 0.044% 71.01% 226ms 1.42% std::vector::push_back (inline) 7ms 0.044% 71.05% 225ms 1.41% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 71.05% 223ms 1.40% TetrahedralMesh::RefreshJacobianCachedData 209ms 1.31% 72.36% 217ms 1.36% std::vector::operator[] (inline) 13ms 0.081% 72.44% 216ms 1.35% AbstractTetrahedralElement::CalculateJacobian 1ms 0.0063% 72.45% 215ms 1.35% alternateaxes 13ms 0.081% 72.53% 213ms 1.34% std::_Rb_tree::_M_erase_aux (inline) 18ms 0.11% 72.64% 211ms 1.32% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 191ms 1.20% 73.84% 211ms 1.32% vertexmedian 7ms 0.044% 73.88% 210ms 1.32% std::vector::_M_realloc_insert 11ms 0.069% 73.95% 207ms 1.30% Element::MarkAsDeleted 0 0% 73.95% 206ms 1.29% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 8ms 0.05% 74.00% 204ms 1.28% std::num_put::_M_insert_float 6ms 0.038% 74.04% 203ms 1.27% AbstractTetrahedralElement::CalculateInverseJacobian 196ms 1.23% 75.27% 196ms 1.23% [libchaste_mesh.so] 87ms 0.55% 75.81% 196ms 1.23% std::_Rb_tree::_M_clone_node (inline) 4ms 0.025% 75.84% 192ms 1.20% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 75.84% 192ms 1.20% MeshBasedCellPopulation::GetDampingConstant 0 0% 75.84% 191ms 1.20% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 75.84% 179ms 1.12% OffLatticeSimulation::ApplyBoundaries 4ms 0.025% 75.87% 172ms 1.08% std::__cxx11::collate::do_transform 0 0% 75.87% 165ms 1.03% ___vsnprintf 0 0% 75.87% 165ms 1.03% __vsnprintf_internal (inline) 11ms 0.069% 75.93% 162ms 1.02% __printf_buffer 161ms 1.01% 76.94% 161ms 1.01% std::vector::size (inline) 59ms 0.37% 77.31% 155ms 0.97% AbstractElement::GetNodeGlobalIndex 154ms 0.97% 78.28% 154ms 0.97% incircle 16ms 0.1% 78.38% 152ms 0.95% AbstractTetrahedralElement::RefreshJacobian 25ms 0.16% 78.54% 142ms 0.89% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 3ms 0.019% 78.55% 140ms 0.88% __printf_fp_l_buffer 0 0% 78.55% 140ms 0.88% __printf_fp_spec (inline) 60ms 0.38% 78.93% 135ms 0.85% __printf_fp_buffer_1 4ms 0.025% 78.96% 135ms 0.85% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 105ms 0.66% 79.61% 133ms 0.83% malloc_consolidate 2ms 0.013% 79.63% 132ms 0.83% boost::numeric::ublas::vector_assign (inline) 2ms 0.013% 79.64% 127ms 0.8% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 0 0% 79.64% 125ms 0.78% TetrahedralMesh::Clear 16ms 0.1% 79.74% 125ms 0.78% TetrahedralMesh::EdgesEnd (partial-inline) 124ms 0.78% 80.52% 124ms 0.78% AbstractCellProperty::AbstractCellProperty 2ms 0.013% 80.53% 124ms 0.78% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 80.53% 124ms 0.78% CellProliferativeTypesWriter::VisitCell 0 0% 80.53% 119ms 0.75% Cell::HasCellProperty (inline) 0 0% 80.53% 119ms 0.75% CellPropertyCollection::HasProperty 49ms 0.31% 80.84% 115ms 0.72% AbstractElement::GetNodeLocation 1ms 0.0063% 80.84% 114ms 0.71% boost::numeric::ublas::c_vector::c_vector (inline) 114ms 0.71% 81.56% 114ms 0.71% std::type_info::name (inline) 4ms 0.025% 81.58% 113ms 0.71% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 60ms 0.38% 81.96% 113ms 0.71% std::_Rb_tree::equal_range (inline) 113ms 0.71% 82.67% 113ms 0.71% std::_Rb_tree_insert_and_rebalance 1ms 0.0063% 82.67% 107ms 0.67% Cell::SetCellProliferativeType 2ms 0.013% 82.69% 106ms 0.66% MeshBasedCellPopulation::SpringsEnd (inline) 106ms 0.66% 83.35% 106ms 0.66% std::_Rb_tree::_S_left (inline) 0 0% 83.35% 103ms 0.65% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 24ms 0.15% 83.50% 102ms 0.64% boost::numeric::ublas::indexing_vector_assign 0 0% 83.50% 101ms 0.63% std::__new_allocator::destroy (inline) 0 0% 83.50% 101ms 0.63% std::allocator_traits::destroy (inline) 0 0% 83.50% 100ms 0.63% std::_Rb_tree::_M_destroy_node (inline) 43ms 0.27% 83.77% 99ms 0.62% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 83.77% 97ms 0.61% AbstractCellBasedSimulation::DoCellRemoval (inline) 88ms 0.55% 84.32% 96ms 0.6% vertexsort 4ms 0.025% 84.35% 93ms 0.58% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 6ms 0.038% 84.38% 91ms 0.57% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 84.38% 90ms 0.56% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 90ms 0.56% 84.95% 90ms 0.56% Node::GetIndex 69ms 0.43% 85.38% 89ms 0.56% TetrahedralMesh::EdgeIterator::EdgeIterator 7ms 0.044% 85.43% 88ms 0.55% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 4ms 0.025% 85.45% 88ms 0.55% std::_Rb_tree::_M_emplace_hint_unique 4ms 0.025% 85.48% 85ms 0.53% Cylindrical2dMesh::CreateMirrorNodes 15ms 0.094% 85.57% 81ms 0.51% MeshBasedCellPopulation::SpringIterator::SpringIterator 28ms 0.18% 85.74% 80ms 0.5% Determinant (inline)