File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16771ms, 84.94% of 19745ms total Dropped 764 nodes (cum <= 98.72ms) flat flat% sum% cum cum% 0 0% 0% 19700ms 99.77% __libc_start_call_main 0 0% 0% 19700ms 99.77% __libc_start_main_impl 0 0% 0% 19700ms 99.77% _start 0 0% 0% 19681ms 99.68% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19681ms 99.68% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19681ms 99.68% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19681ms 99.68% main 0 0% 0% 19646ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19646ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19646ms 99.50% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19619ms 99.36% AbstractCellBasedSimulation::Solve 0 0% 0% 15273ms 77.35% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 10148ms 51.40% AbstractCellBasedSimulation::DoCellBirth 3ms 0.015% 0.015% 10065ms 50.97% Cell::ReadyToDivide 2ms 0.01% 0.025% 10007ms 50.68% AbstractPhaseBasedCellCycleModel::ReadyToDivide 4ms 0.02% 0.046% 9868ms 49.98% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 14ms 0.071% 0.12% 9856ms 49.92% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 0.12% 9841ms 49.84% CellCycleModelOdeHandler::SolveOdeToTime 80ms 0.41% 0.52% 9684ms 49.05% AbstractOneStepIvpOdeSolver::InternalSolve 877ms 4.44% 4.96% 8843ms 44.79% RungeKutta4IvpOdeSolver::CalculateNextYValue 3371ms 17.07% 22.04% 7737ms 39.18% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0051% 22.04% 5017ms 25.41% MeshBasedCellPopulation::Update 198ms 1.00% 23.04% 4375ms 22.16% AbstractCellProperty::IsType (inline) 3ms 0.015% 23.06% 3912ms 19.81% Cylindrical2dMesh::ReMesh 614ms 3.11% 26.17% 3159ms 16.00% AbstractCellProperty::IsSame 385ms 1.95% 28.12% 2545ms 12.89% std::type_info::operator== (inline) 0 0% 28.12% 2445ms 12.38% OffLatticeSimulation::UpdateCellLocationsAndTopology 2140ms 10.84% 38.96% 2140ms 10.84% __strcmp_avx2 0 0% 38.96% 2112ms 10.70% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 38.96% 2095ms 10.61% MutableMesh::ReMesh 7ms 0.035% 38.99% 2064ms 10.45% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 38.99% 1896ms 9.60% AbstractCellPopulation::WriteResultsToFiles 744ms 3.77% 42.76% 1780ms 9.01% std::_Rb_tree::_M_lower_bound (inline) 135ms 0.68% 43.44% 1621ms 8.21% TetrahedralMesh::EdgeIterator::operator++ 56ms 0.28% 43.73% 1279ms 6.48% std::_Rb_tree::find (inline) 6ms 0.03% 43.76% 1097ms 5.56% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 43.76% 1083ms 5.48% MeshBasedCellPopulation::UpdateNodePairs 56ms 0.28% 44.04% 1052ms 5.33% operator new 12ms 0.061% 44.10% 1032ms 5.23% TetrahedralMesh::ImportFromMesher 10ms 0.051% 44.15% 1019ms 5.16% std::set::insert (inline) 15ms 0.076% 44.23% 1009ms 5.11% std::_Rb_tree::_M_insert_unique 247ms 1.25% 45.48% 986ms 4.99% __GI___libc_malloc 9ms 0.046% 45.53% 977ms 4.95% MeshBasedCellPopulation::SpringIterator::operator++ 41ms 0.21% 45.73% 927ms 4.69% std::__new_allocator::allocate (inline) 0 0% 45.73% 921ms 4.66% std::allocator_traits::allocate (inline) 0 0% 45.73% 782ms 3.96% triangulate 0 0% 45.73% 759ms 3.84% std::set::count (inline) 4ms 0.02% 45.75% 722ms 3.66% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 717ms 3.63% 49.38% 717ms 3.63% std::_Rb_tree::_S_right (inline) 64ms 0.32% 49.71% 707ms 3.58% std::map::operator[] (partial-inline) 0 0% 49.71% 691ms 3.50% delaunay 2ms 0.01% 49.72% 691ms 3.50% divconqdelaunay 379ms 1.92% 51.64% 677ms 3.43% _int_malloc 1ms 0.0051% 51.64% 669ms 3.39% AbstractTwoBodyInteractionForce::AddForceContribution 655ms 3.32% 54.96% 664ms 3.36% WntCellCycleOdeSystem::CalculateStoppingEvent 3ms 0.015% 54.98% 646ms 3.27% CellPopulationElementWriter::Visit 0 0% 54.98% 613ms 3.10% std::_Rb_tree::_M_create_node (inline) 170ms 0.86% 55.84% 611ms 3.09% __dynamic_cast 22ms 0.11% 55.95% 609ms 3.08% std::_Rb_tree::_M_insert_ (inline) 26ms 0.13% 56.08% 606ms 3.07% std::less::operator() (inline) 1ms 0.0051% 56.09% 588ms 2.98% MeshBasedCellPopulation::AcceptCellWriter 0 0% 56.09% 583ms 2.95% std::_Rb_tree::_M_get_node (inline) 580ms 2.94% 59.02% 580ms 2.94% std::operator< (inline) 6ms 0.03% 59.05% 579ms 2.93% CellPropertyCollection::GetPropertiesType (inline) 0 0% 59.05% 561ms 2.84% std::_Rb_tree::lower_bound (inline) 0 0% 59.05% 561ms 2.84% std::map::lower_bound (inline) 0 0% 59.05% 559ms 2.83% std::_Rb_tree::_Alloc_node::operator() (inline) 23ms 0.12% 59.17% 555ms 2.81% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 13ms 0.066% 59.24% 552ms 2.80% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.015% 59.25% 549ms 2.78% Element::Element 8ms 0.041% 59.29% 546ms 2.77% MutableMesh::ReIndex 0 0% 59.29% 518ms 2.62% std::map::find (inline) 0 0% 59.29% 497ms 2.52% std::ostream::operator<< (inline) 77ms 0.39% 59.68% 496ms 2.51% std::ostream::_M_insert 12ms 0.061% 59.74% 493ms 2.50% Cylindrical2dMesh::CorrectNonPeriodicMesh 13ms 0.066% 59.81% 478ms 2.42% Cylindrical2dMesh::ReconstructCylindricalMesh 12ms 0.061% 59.87% 467ms 2.37% Element::RegisterWithNodes (inline) 320ms 1.62% 61.49% 465ms 2.36% AbstractCellMutationState::AbstractCellMutationState 2ms 0.01% 61.50% 458ms 2.32% AbstractCellProperty::IsSubType (inline) 4ms 0.02% 61.52% 455ms 2.30% Node::AddElement 128ms 0.65% 62.17% 397ms 2.01% __GI___libc_free 9ms 0.046% 62.21% 387ms 1.96% std::_Rb_tree::erase 1ms 0.0051% 62.22% 387ms 1.96% std::set::erase (inline) 139ms 0.7% 62.92% 385ms 1.95% std::_Rb_tree::_M_get_insert_unique_pos 5ms 0.025% 62.95% 382ms 1.93% Node::RemoveElement 35ms 0.18% 63.12% 354ms 1.79% Element::ResetIndex 121ms 0.61% 63.74% 343ms 1.74% std::_Rb_tree::_M_erase 4ms 0.02% 63.76% 342ms 1.73% std::_Vector_base::_M_allocate (inline) 15ms 0.076% 63.83% 340ms 1.72% divconqrecurse 12ms 0.061% 63.89% 339ms 1.72% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 8ms 0.041% 63.94% 322ms 1.63% AbstractCellPopulation::GetLocationIndexUsingCell 149ms 0.75% 64.69% 319ms 1.62% __cxxabiv1::__si_class_type_info::__do_dyncast 5ms 0.025% 64.72% 314ms 1.59% Cell::GetCellProliferativeType 3ms 0.015% 64.73% 314ms 1.59% NodeLocationWriter::Visit 100ms 0.51% 65.24% 314ms 1.59% mergehulls 20ms 0.1% 65.34% 311ms 1.58% std::_Rb_tree::~_Rb_tree (inline) 6ms 0.03% 65.37% 302ms 1.53% LegacyCellProliferativeTypesWriter::VisitCell 14ms 0.071% 65.44% 300ms 1.52% std::__new_allocator::deallocate (inline) 1ms 0.0051% 65.44% 299ms 1.51% Cell::GetMutationState 0 0% 65.44% 292ms 1.48% std::allocator_traits::deallocate (inline) 17ms 0.086% 65.53% 287ms 1.45% AbstractTetrahedralElement::CalculateJacobian 287ms 1.45% 66.98% 287ms 1.45% std::type_info::name (inline) 281ms 1.42% 68.41% 281ms 1.42% std::vector::operator[] (inline) 0 0% 68.41% 278ms 1.41% std::set::~set (inline) 32ms 0.16% 68.57% 277ms 1.40% AbstractCellPopulation::Iterator::IsRealCell 0 0% 68.57% 275ms 1.39% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 68.57% 275ms 1.39% std::_Rb_tree::_M_drop_node (inline) 20ms 0.1% 68.67% 272ms 1.38% std::num_put::_M_insert_float 200ms 1.01% 69.68% 267ms 1.35% _int_free 0 0% 69.68% 252ms 1.28% TetrahedralMesh::RefreshJacobianCachedData 15ms 0.076% 69.76% 245ms 1.24% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 69.76% 241ms 1.22% std::_Rb_tree::_M_put_node (inline) 7ms 0.035% 69.79% 240ms 1.22% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 239ms 1.21% 71.01% 239ms 1.21% [libchaste_cell_based.so] 77ms 0.39% 71.40% 238ms 1.21% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 1ms 0.0051% 71.40% 231ms 1.17% alternateaxes 14ms 0.071% 71.47% 231ms 1.17% std::_Rb_tree::_M_erase_aux (inline) 7ms 0.035% 71.51% 230ms 1.16% AbstractCellPopulation::IsCellAttachedToLocationIndex 215ms 1.09% 72.60% 230ms 1.16% vertexmedian 10ms 0.051% 72.65% 228ms 1.15% std::vector::push_back (inline) 4ms 0.02% 72.67% 226ms 1.14% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.0051% 72.67% 223ms 1.13% std::set::set (inline) 29ms 0.15% 72.82% 217ms 1.10% AbstractTetrahedralElement::RefreshJacobian 1ms 0.0051% 72.82% 215ms 1.09% OffLatticeSimulation::ApplyBoundaries 4ms 0.02% 72.84% 214ms 1.08% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.0051% 72.85% 213ms 1.08% std::__cxx11::collate::do_transform 11ms 0.056% 72.90% 212ms 1.07% std::vector::_M_realloc_insert 151ms 0.76% 73.67% 206ms 1.04% AbstractElement::GetNodeGlobalIndex 50ms 0.25% 73.92% 206ms 1.04% ApcOneHitCellMutationState::ApcOneHitCellMutationState 0 0% 73.92% 205ms 1.04% ___vsnprintf 0 0% 73.92% 205ms 1.04% __vsnprintf_internal (inline) 24ms 0.12% 74.04% 205ms 1.04% std::_Rb_tree::_M_copy (inline) 1ms 0.0051% 74.05% 204ms 1.03% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 74.05% 204ms 1.03% MeshBasedCellPopulation::GetDampingConstant 148ms 0.75% 74.80% 201ms 1.02% malloc_consolidate 30ms 0.15% 74.95% 200ms 1.01% __printf_buffer 9ms 0.046% 75.00% 189ms 0.96% Element::MarkAsDeleted 35ms 0.18% 75.17% 182ms 0.92% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 20ms 0.1% 75.27% 180ms 0.91% TetrahedralMesh::Clear 179ms 0.91% 76.18% 179ms 0.91% Node::GetIndex 8ms 0.041% 76.22% 176ms 0.89% AbstractTetrahedralElement::AbstractTetrahedralElement 49ms 0.25% 76.47% 176ms 0.89% std::_Rb_tree::_M_clone_node (inline) 171ms 0.87% 77.34% 171ms 0.87% std::_Rb_tree_insert_and_rebalance 79ms 0.4% 77.74% 170ms 0.86% AbstractElement::GetNodeLocation 3ms 0.015% 77.75% 165ms 0.84% CellProliferativeTypesWriter::VisitCell 13ms 0.066% 77.82% 158ms 0.8% __printf_fp_l_buffer 0 0% 77.82% 158ms 0.8% __printf_fp_spec (inline) 106ms 0.54% 78.35% 153ms 0.77% std::_Rb_tree::equal_range (inline) 150ms 0.76% 79.11% 150ms 0.76% unlink_chunk 4ms 0.02% 79.13% 149ms 0.75% boost::numeric::ublas::vector_assign (inline) 8ms 0.041% 79.17% 140ms 0.71% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 140ms 0.71% 79.88% 140ms 0.71% incircle 68ms 0.34% 80.23% 138ms 0.7% __printf_fp_buffer_1 137ms 0.69% 80.92% 137ms 0.69% std::vector::size (inline) 4ms 0.02% 80.94% 131ms 0.66% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 3ms 0.015% 80.96% 130ms 0.66% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 5ms 0.025% 80.98% 128ms 0.65% CellPropertyCollection::HasProperty 7ms 0.035% 81.02% 128ms 0.65% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 81.02% 127ms 0.64% Cell::HasCellProperty (inline) 48ms 0.24% 81.26% 124ms 0.63% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 30ms 0.15% 81.41% 122ms 0.62% TetrahedralMesh::EdgesEnd 120ms 0.61% 82.02% 120ms 0.61% AbstractElement::IsDeleted 42ms 0.21% 82.23% 117ms 0.59% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 77ms 0.39% 82.62% 115ms 0.58% Cylindrical2dMesh::GetVectorFromAtoB 13ms 0.066% 82.69% 114ms 0.58% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 108ms 0.55% 83.24% 114ms 0.58% vertexsort 3ms 0.015% 83.25% 113ms 0.57% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 35ms 0.18% 83.43% 112ms 0.57% boost::numeric::ublas::indexing_vector_assign 2ms 0.01% 83.44% 109ms 0.55% Cell::SetCellProliferativeType 14ms 0.071% 83.51% 106ms 0.54% boost::detail::shared_count::~shared_count (inline) 0 0% 83.51% 106ms 0.54% boost::shared_ptr::~shared_ptr (inline) 51ms 0.26% 83.77% 106ms 0.54% std::__ostream_insert 0 0% 83.77% 105ms 0.53% AbstractCellBasedSimulation::DoCellRemoval (inline) 5ms 0.025% 83.79% 103ms 0.52% MeshBasedCellPopulation::SpringsEnd (inline) 10ms 0.051% 83.84% 103ms 0.52% std::_Rb_tree_const_iterator::operator++ (inline) 103ms 0.52% 84.37% 103ms 0.52% std::_Rb_tree_increment 1ms 0.0051% 84.37% 101ms 0.51% AbstractTetrahedralMesh::ElementIterator::operator++ (inline) 3ms 0.015% 84.39% 101ms 0.51% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 0 0% 84.39% 100ms 0.51% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 10ms 0.051% 84.44% 99ms 0.5% Node::~Node 99ms 0.5% 84.94% 99ms 0.5% std::_Rb_tree_rebalance_for_erase