File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 18246ms, 83.78% of 21778ms total Dropped 783 nodes (cum <= 108.89ms) flat flat% sum% cum cum% 0 0% 0% 21731ms 99.78% __libc_start_call_main 0 0% 0% 21731ms 99.78% __libc_start_main_impl 0 0% 0% 21731ms 99.78% _start 0 0% 0% 21711ms 99.69% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 21711ms 99.69% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 21711ms 99.69% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 21711ms 99.69% main 0 0% 0% 21677ms 99.54% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 21677ms 99.54% CxxTest::TestRunner::runTest (inline) 0 0% 0% 21677ms 99.54% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 2ms 0.0092% 0.0092% 21649ms 99.41% AbstractCellBasedSimulation::Solve 0 0% 0.0092% 17260ms 79.25% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0092% 12025ms 55.22% AbstractCellBasedSimulation::DoCellBirth 4ms 0.018% 0.028% 11945ms 54.85% Cell::ReadyToDivide 6ms 0.028% 0.055% 11872ms 54.51% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0046% 0.06% 11744ms 53.93% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.037% 0.096% 11727ms 53.85% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 0.096% 11716ms 53.80% CellCycleModelOdeHandler::SolveOdeToTime 75ms 0.34% 0.44% 11534ms 52.96% AbstractOneStepIvpOdeSolver::InternalSolve 879ms 4.04% 4.48% 10717ms 49.21% RungeKutta4IvpOdeSolver::CalculateNextYValue 4163ms 19.12% 23.59% 9623ms 44.19% WntCellCycleOdeSystem::EvaluateYDerivatives 375ms 1.72% 25.31% 5504ms 25.27% AbstractCellProperty::IsType (inline) 0 0% 25.31% 5110ms 23.46% MeshBasedCellPopulation::Update 4ms 0.018% 25.33% 3920ms 18.00% Cylindrical2dMesh::ReMesh 520ms 2.39% 27.72% 3424ms 15.72% AbstractCellProperty::IsSame 1134ms 5.21% 32.93% 2904ms 13.33% std::type_info::operator== (inline) 1ms 0.0046% 32.93% 2434ms 11.18% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 32.93% 2121ms 9.74% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 32.93% 2109ms 9.68% MutableMesh::ReMesh 14ms 0.064% 33.00% 2064ms 9.48% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 33.00% 1951ms 8.96% AbstractCellPopulation::WriteResultsToFiles 801ms 3.68% 36.67% 1855ms 8.52% std::_Rb_tree::_M_lower_bound (inline) 146ms 0.67% 37.35% 1671ms 7.67% TetrahedralMesh::EdgeIterator::operator++ 1626ms 7.47% 44.81% 1626ms 7.47% __strcmp_avx2 77ms 0.35% 45.16% 1418ms 6.51% std::_Rb_tree::find (inline) 1ms 0.0046% 45.17% 1157ms 5.31% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.028% 45.20% 1111ms 5.10% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 14ms 0.064% 45.26% 1035ms 4.75% TetrahedralMesh::ImportFromMesher 44ms 0.2% 45.46% 1018ms 4.67% operator new 10ms 0.046% 45.51% 1017ms 4.67% MeshBasedCellPopulation::SpringIterator::operator++ 237ms 1.09% 46.60% 964ms 4.43% __GI___libc_malloc 15ms 0.069% 46.67% 942ms 4.33% std::set::insert (inline) 12ms 0.055% 46.72% 927ms 4.26% std::_Rb_tree::_M_insert_unique 38ms 0.17% 46.90% 908ms 4.17% std::__new_allocator::allocate (inline) 0 0% 46.90% 905ms 4.16% std::allocator_traits::allocate (inline) 0 0% 46.90% 886ms 4.07% std::set::count (inline) 679ms 3.12% 50.01% 818ms 3.76% AbstractCellMutationState::AbstractCellMutationState 2ms 0.0092% 50.02% 813ms 3.73% triangulate 5ms 0.023% 50.05% 722ms 3.32% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 50.05% 716ms 3.29% delaunay 1ms 0.0046% 50.05% 715ms 3.28% divconqdelaunay 62ms 0.28% 50.34% 685ms 3.15% std::map::operator[] (partial-inline) 1ms 0.0046% 50.34% 681ms 3.13% AbstractTwoBodyInteractionForce::AddForceContribution 6ms 0.028% 50.37% 680ms 3.12% CellPopulationElementWriter::Visit 657ms 3.02% 53.38% 657ms 3.02% std::_Rb_tree::_S_right (inline) 22ms 0.1% 53.49% 647ms 2.97% std::less::operator() (inline) 373ms 1.71% 55.20% 643ms 2.95% _int_malloc 629ms 2.89% 58.09% 638ms 2.93% WntCellCycleOdeSystem::CalculateStoppingEvent 625ms 2.87% 60.96% 625ms 2.87% std::operator< (inline) 176ms 0.81% 61.76% 602ms 2.76% __dynamic_cast 38ms 0.17% 61.94% 593ms 2.72% std::_Rb_tree::_M_insert_ (inline) 5ms 0.023% 61.96% 584ms 2.68% CellPropertyCollection::GetPropertiesType (inline) 0 0% 61.96% 584ms 2.68% std::_Rb_tree::_M_create_node (inline) 22ms 0.1% 62.06% 583ms 2.68% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.014% 62.08% 574ms 2.64% MeshBasedCellPopulation::AcceptCellWriter 28ms 0.13% 62.20% 567ms 2.60% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 0 0% 62.20% 550ms 2.53% std::_Rb_tree::_M_get_node (inline) 0 0% 62.20% 543ms 2.49% std::_Rb_tree::lower_bound (inline) 0 0% 62.20% 543ms 2.49% std::map::lower_bound (inline) 6ms 0.028% 62.23% 539ms 2.47% Element::Element 184ms 0.84% 63.08% 533ms 2.45% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 0 0% 63.08% 531ms 2.44% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 63.08% 530ms 2.43% std::map::find (inline) 8ms 0.037% 63.11% 524ms 2.41% MutableMesh::ReIndex 14ms 0.064% 63.18% 495ms 2.27% Cylindrical2dMesh::ReconstructCylindricalMesh 9ms 0.041% 63.22% 494ms 2.27% Element::RegisterWithNodes (inline) 13ms 0.06% 63.28% 484ms 2.22% Cylindrical2dMesh::CorrectNonPeriodicMesh 9ms 0.041% 63.32% 478ms 2.19% Node::AddElement 6ms 0.028% 63.35% 475ms 2.18% AbstractCellProperty::IsSubType (inline) 59ms 0.27% 63.62% 473ms 2.17% std::ostream::_M_insert 0 0% 63.62% 473ms 2.17% std::ostream::operator<< (inline) 426ms 1.96% 65.58% 426ms 1.96% std::type_info::name (inline) 146ms 0.67% 66.25% 414ms 1.90% __GI___libc_free 118ms 0.54% 66.79% 381ms 1.75% std::_Rb_tree::_M_erase 72ms 0.33% 67.12% 377ms 1.73% ApcOneHitCellMutationState::ApcOneHitCellMutationState 10ms 0.046% 67.16% 369ms 1.69% std::_Rb_tree::erase 0 0% 67.16% 368ms 1.69% std::set::erase (inline) 8ms 0.037% 67.20% 362ms 1.66% Node::RemoveElement 16ms 0.073% 67.27% 361ms 1.66% divconqrecurse 3ms 0.014% 67.29% 358ms 1.64% std::_Vector_base::_M_allocate (inline) 25ms 0.11% 67.40% 353ms 1.62% std::_Rb_tree::~_Rb_tree (inline) 30ms 0.14% 67.54% 349ms 1.60% Element::ResetIndex 81ms 0.37% 67.91% 343ms 1.57% mergehulls 12ms 0.055% 67.97% 340ms 1.56% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 10ms 0.046% 68.01% 339ms 1.56% std::__new_allocator::deallocate (inline) 1ms 0.0046% 68.02% 337ms 1.55% Cell::GetMutationState 0 0% 68.02% 333ms 1.53% std::allocator_traits::deallocate (inline) 0 0% 68.02% 327ms 1.50% std::set::~set (inline) 130ms 0.6% 68.62% 322ms 1.48% std::_Rb_tree::_M_get_insert_unique_pos 142ms 0.65% 69.27% 315ms 1.45% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 69.27% 315ms 1.45% std::_Rb_tree::_M_drop_node (inline) 4ms 0.018% 69.29% 314ms 1.44% NodeLocationWriter::Visit 7ms 0.032% 69.32% 305ms 1.40% AbstractCellPopulation::GetLocationIndexUsingCell 5ms 0.023% 69.34% 297ms 1.36% Cell::GetCellProliferativeType 1ms 0.0046% 69.35% 294ms 1.35% AbstractCellPopulation::Iterator::operator++ (inline) 1ms 0.0046% 69.35% 293ms 1.35% LegacyCellProliferativeTypesWriter::VisitCell 34ms 0.16% 69.51% 292ms 1.34% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 69.51% 278ms 1.28% std::_Rb_tree::_M_put_node (inline) 15ms 0.069% 69.57% 269ms 1.24% std::num_put::_M_insert_float 216ms 0.99% 70.57% 266ms 1.22% _int_free 15ms 0.069% 70.64% 263ms 1.21% std::_Rb_tree::_Rb_tree (partial-inline) 63ms 0.29% 70.92% 261ms 1.20% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 253ms 1.16% 72.09% 253ms 1.16% [libchaste_cell_based.so] 10ms 0.046% 72.13% 248ms 1.14% std::vector::push_back (inline) 243ms 1.12% 73.25% 247ms 1.13% std::vector::operator[] (inline) 13ms 0.06% 73.31% 245ms 1.12% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.014% 73.32% 244ms 1.12% alternateaxes 15ms 0.069% 73.39% 243ms 1.12% AbstractTetrahedralElement::CalculateJacobian 218ms 1.00% 74.39% 241ms 1.11% vertexmedian 1ms 0.0046% 74.40% 234ms 1.07% std::set::set (inline) 1ms 0.0046% 74.40% 233ms 1.07% TetrahedralMesh::RefreshJacobianCachedData 7ms 0.032% 74.43% 231ms 1.06% AbstractCellPopulation::IsCellAttachedToLocationIndex 17ms 0.078% 74.51% 229ms 1.05% std::vector::_M_realloc_insert 3ms 0.014% 74.52% 225ms 1.03% std::__cxx11::collate::do_transform 2ms 0.0092% 74.53% 224ms 1.03% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 25ms 0.11% 74.65% 220ms 1.01% std::_Rb_tree::_M_copy (inline) 0 0% 74.65% 215ms 0.99% ___vsnprintf 0 0% 74.65% 215ms 0.99% __vsnprintf_internal (inline) 18ms 0.083% 74.73% 211ms 0.97% __printf_buffer 161ms 0.74% 75.47% 210ms 0.96% AbstractElement::GetNodeGlobalIndex 10ms 0.046% 75.52% 198ms 0.91% AbstractTetrahedralElement::CalculateInverseJacobian 5ms 0.023% 75.54% 198ms 0.91% std::_Rb_tree::_M_erase_aux (inline) 0 0% 75.54% 197ms 0.9% OffLatticeSimulation::ApplyBoundaries 59ms 0.27% 75.81% 191ms 0.88% std::_Rb_tree::_M_clone_node (inline) 11ms 0.051% 75.86% 187ms 0.86% Element::MarkAsDeleted 20ms 0.092% 75.95% 184ms 0.84% AbstractTetrahedralElement::RefreshJacobian 1ms 0.0046% 75.96% 182ms 0.84% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 75.96% 182ms 0.84% MeshBasedCellPopulation::GetDampingConstant 137ms 0.63% 76.59% 177ms 0.81% malloc_consolidate 3ms 0.014% 76.60% 174ms 0.8% __printf_fp_l_buffer 0 0% 76.60% 174ms 0.8% __printf_fp_spec (inline) 171ms 0.79% 77.39% 171ms 0.79% std::_Rb_tree_insert_and_rebalance 5ms 0.023% 77.41% 170ms 0.78% AbstractTetrahedralElement::AbstractTetrahedralElement 105ms 0.48% 77.89% 169ms 0.78% std::_Rb_tree::equal_range (inline) 78ms 0.36% 78.25% 164ms 0.75% __printf_fp_buffer_1 94ms 0.43% 78.68% 163ms 0.75% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 2ms 0.0092% 78.69% 160ms 0.73% CellProliferativeTypesWriter::VisitCell 160ms 0.73% 79.42% 160ms 0.73% Node::GetIndex 4ms 0.018% 79.44% 157ms 0.72% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 154ms 0.71% 80.15% 154ms 0.71% incircle 12ms 0.055% 80.20% 150ms 0.69% TetrahedralMesh::Clear 56ms 0.26% 80.46% 148ms 0.68% AbstractElement::GetNodeLocation 3ms 0.014% 80.48% 143ms 0.66% CellPropertyCollection::HasProperty 0 0% 80.48% 141ms 0.65% Cell::HasCellProperty (inline) 2ms 0.0092% 80.48% 140ms 0.64% boost::numeric::ublas::vector_assign (inline) 137ms 0.63% 81.11% 137ms 0.63% std::vector::size (inline) 47ms 0.22% 81.33% 135ms 0.62% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 3ms 0.014% 81.34% 132ms 0.61% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 37ms 0.17% 81.51% 132ms 0.61% TetrahedralMesh::EdgesEnd 13ms 0.06% 81.57% 128ms 0.59% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 128ms 0.59% 82.16% 128ms 0.59% unlink_chunk 74ms 0.34% 82.50% 127ms 0.58% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 82.50% 125ms 0.57% AbstractCellBasedSimulation::DoCellRemoval (inline) 10ms 0.046% 82.55% 120ms 0.55% boost::numeric::ublas::c_vector::c_vector (inline) 3ms 0.014% 82.56% 119ms 0.55% MeshBasedCellPopulation::SpringsEnd (inline) 2ms 0.0092% 82.57% 116ms 0.53% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 115ms 0.53% 83.10% 115ms 0.53% AbstractElement::IsDeleted 1ms 0.0046% 83.10% 115ms 0.53% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 38ms 0.17% 83.28% 110ms 0.51% boost::numeric::ublas::indexing_vector_assign 1ms 0.0046% 83.28% 109ms 0.5% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 109ms 0.5% 83.78% 109ms 0.5% [libchaste_crypt.so]