File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16914ms, 83.42% of 20276ms total Dropped 769 nodes (cum <= 101.38ms) flat flat% sum% cum cum% 0 0% 0% 20232ms 99.78% __libc_start_call_main 0 0% 0% 20232ms 99.78% __libc_start_main_impl 0 0% 0% 20232ms 99.78% _start 0 0% 0% 20213ms 99.69% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20213ms 99.69% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20213ms 99.69% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20213ms 99.69% main 0 0% 0% 20178ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20178ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20178ms 99.52% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 20151ms 99.38% AbstractCellBasedSimulation::Solve 0 0% 0% 15751ms 77.68% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0049% 0.0049% 10529ms 51.93% AbstractCellBasedSimulation::DoCellBirth 4ms 0.02% 0.025% 10445ms 51.51% Cell::ReadyToDivide 5ms 0.025% 0.049% 10375ms 51.17% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.0099% 0.059% 10249ms 50.55% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 19ms 0.094% 0.15% 10242ms 50.51% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.02% 0.17% 10220ms 50.40% CellCycleModelOdeHandler::SolveOdeToTime 83ms 0.41% 0.58% 10026ms 49.45% AbstractOneStepIvpOdeSolver::InternalSolve 882ms 4.35% 4.93% 9231ms 45.53% RungeKutta4IvpOdeSolver::CalculateNextYValue 3859ms 19.03% 23.96% 8125ms 40.07% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 23.96% 5108ms 25.19% MeshBasedCellPopulation::Update 196ms 0.97% 24.93% 4323ms 21.32% AbstractCellProperty::IsType (inline) 4ms 0.02% 24.95% 3941ms 19.44% Cylindrical2dMesh::ReMesh 535ms 2.64% 27.59% 3079ms 15.19% AbstractCellProperty::IsSame 862ms 4.25% 31.84% 2544ms 12.55% std::type_info::operator== (inline) 1ms 0.0049% 31.85% 2462ms 12.14% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0049% 31.85% 2162ms 10.66% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 31.85% 2119ms 10.45% MutableMesh::ReMesh 5ms 0.025% 31.88% 2117ms 10.44% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 31.88% 1933ms 9.53% AbstractCellPopulation::WriteResultsToFiles 838ms 4.13% 36.01% 1848ms 9.11% std::_Rb_tree::_M_lower_bound (inline) 173ms 0.85% 36.86% 1685ms 8.31% TetrahedralMesh::EdgeIterator::operator++ 1642ms 8.10% 44.96% 1642ms 8.10% __strcmp_avx2 65ms 0.32% 45.28% 1379ms 6.80% std::_Rb_tree::find (inline) 0 0% 45.28% 1126ms 5.55% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.025% 45.30% 1116ms 5.50% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 15ms 0.074% 45.38% 1067ms 5.26% TetrahedralMesh::ImportFromMesher 54ms 0.27% 45.65% 1063ms 5.24% operator new 8ms 0.039% 45.68% 1015ms 5.01% MeshBasedCellPopulation::SpringIterator::operator++ 232ms 1.14% 46.83% 1000ms 4.93% __GI___libc_malloc 10ms 0.049% 46.88% 971ms 4.79% std::set::insert (inline) 13ms 0.064% 46.94% 961ms 4.74% std::_Rb_tree::_M_insert_unique 47ms 0.23% 47.17% 950ms 4.69% std::__new_allocator::allocate (inline) 0 0% 47.17% 941ms 4.64% std::allocator_traits::allocate (inline) 0 0% 47.17% 813ms 4.01% std::set::count (inline) 0 0% 47.17% 789ms 3.89% triangulate 7ms 0.035% 47.21% 722ms 3.56% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 65ms 0.32% 47.53% 702ms 3.46% std::map::operator[] (partial-inline) 4ms 0.02% 47.55% 701ms 3.46% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 47.55% 696ms 3.43% delaunay 3ms 0.015% 47.56% 696ms 3.43% divconqdelaunay 373ms 1.84% 49.40% 676ms 3.33% _int_malloc 8ms 0.039% 49.44% 660ms 3.26% CellPopulationElementWriter::Visit 657ms 3.24% 52.68% 657ms 3.24% std::_Rb_tree::_S_right (inline) 20ms 0.099% 52.78% 625ms 3.08% std::less::operator() (inline) 181ms 0.89% 53.67% 605ms 2.98% __dynamic_cast 605ms 2.98% 56.66% 605ms 2.98% std::operator< (inline) 34ms 0.17% 56.83% 601ms 2.96% std::_Rb_tree::_M_insert_ (inline) 578ms 2.85% 59.68% 587ms 2.90% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 59.68% 586ms 2.89% std::_Rb_tree::_M_create_node (inline) 32ms 0.16% 59.83% 576ms 2.84% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 2ms 0.0099% 59.84% 571ms 2.82% MeshBasedCellPopulation::AcceptCellWriter 0 0% 59.84% 565ms 2.79% std::_Rb_tree::_M_get_node (inline) 0 0% 59.84% 557ms 2.75% std::map::find (inline) 0 0% 59.84% 551ms 2.72% std::_Rb_tree::lower_bound (inline) 0 0% 59.84% 551ms 2.72% std::map::lower_bound (inline) 8ms 0.039% 59.88% 542ms 2.67% CellPropertyCollection::GetPropertiesType (inline) 0 0% 59.88% 527ms 2.60% std::_Rb_tree::_Alloc_node::operator() (inline) 6ms 0.03% 59.91% 521ms 2.57% MutableMesh::ReIndex 16ms 0.079% 59.99% 512ms 2.53% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.025% 60.02% 510ms 2.52% Element::Element 17ms 0.084% 60.10% 501ms 2.47% Cylindrical2dMesh::CorrectNonPeriodicMesh 17ms 0.084% 60.18% 473ms 2.33% Element::RegisterWithNodes (inline) 332ms 1.64% 61.82% 470ms 2.32% AbstractCellMutationState::AbstractCellMutationState 1ms 0.0049% 61.83% 458ms 2.26% std::ostream::operator<< (inline) 65ms 0.32% 62.15% 457ms 2.25% std::ostream::_M_insert 5ms 0.025% 62.17% 455ms 2.24% Cylindrical2dMesh::ReconstructCylindricalMesh 11ms 0.054% 62.23% 451ms 2.22% Node::AddElement 2ms 0.0099% 62.24% 438ms 2.16% AbstractCellProperty::IsSubType (inline) 142ms 0.7% 62.94% 413ms 2.04% __GI___libc_free 3ms 0.015% 62.95% 379ms 1.87% std::_Vector_base::_M_allocate (inline) 124ms 0.61% 63.56% 347ms 1.71% std::_Rb_tree::_M_get_insert_unique_pos 9ms 0.044% 63.61% 344ms 1.70% std::_Rb_tree::erase 10ms 0.049% 63.66% 343ms 1.69% Node::RemoveElement 18ms 0.089% 63.75% 343ms 1.69% divconqrecurse 1ms 0.0049% 63.75% 343ms 1.69% std::set::erase (inline) 21ms 0.1% 63.85% 335ms 1.65% Element::ResetIndex 119ms 0.59% 64.44% 335ms 1.65% std::_Rb_tree::_M_erase 159ms 0.78% 65.22% 330ms 1.63% __cxxabiv1::__si_class_type_info::__do_dyncast 5ms 0.025% 65.25% 324ms 1.60% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 12ms 0.059% 65.31% 323ms 1.59% std::__new_allocator::deallocate (inline) 96ms 0.47% 65.78% 321ms 1.58% mergehulls 0 0% 65.78% 318ms 1.57% std::allocator_traits::deallocate (inline) 28ms 0.14% 65.92% 308ms 1.52% std::_Rb_tree::~_Rb_tree (inline) 4ms 0.02% 65.94% 306ms 1.51% Cell::GetMutationState 6ms 0.03% 65.97% 305ms 1.50% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.0099% 65.98% 299ms 1.47% NodeLocationWriter::Visit 3ms 0.015% 65.99% 287ms 1.42% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 65.99% 284ms 1.40% std::_Rb_tree::_M_drop_node (inline) 10ms 0.049% 66.04% 282ms 1.39% Cell::GetCellProliferativeType 0 0% 66.04% 282ms 1.39% std::set::~set (inline) 278ms 1.37% 67.41% 278ms 1.37% [libchaste_cell_based.so] 276ms 1.36% 68.78% 278ms 1.37% std::vector::operator[] (inline) 36ms 0.18% 68.95% 273ms 1.35% AbstractCellPopulation::Iterator::IsRealCell (inline) 273ms 1.35% 70.30% 273ms 1.35% std::type_info::name (inline) 0 0% 70.30% 271ms 1.34% AbstractCellPopulation::Iterator::operator++ (inline) 208ms 1.03% 71.33% 270ms 1.33% _int_free 8ms 0.039% 71.37% 267ms 1.32% std::vector::push_back (inline) 10ms 0.049% 71.41% 257ms 1.27% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 71.41% 257ms 1.27% std::_Rb_tree::_M_put_node (inline) 25ms 0.12% 71.54% 251ms 1.24% std::num_put::_M_insert_float 16ms 0.079% 71.62% 250ms 1.23% std::vector::_M_realloc_insert 12ms 0.059% 71.68% 247ms 1.22% AbstractTetrahedralElement::CalculateJacobian 9ms 0.044% 71.72% 246ms 1.21% std::_Rb_tree::_Rb_tree (partial-inline) 4ms 0.02% 71.74% 240ms 1.18% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 1ms 0.0049% 71.74% 236ms 1.16% TetrahedralMesh::RefreshJacobianCachedData 45ms 0.22% 71.97% 230ms 1.13% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 3ms 0.015% 71.98% 228ms 1.12% alternateaxes 214ms 1.06% 73.04% 224ms 1.10% vertexmedian 56ms 0.28% 73.31% 223ms 1.10% ApcOneHitCellMutationState::ApcOneHitCellMutationState 14ms 0.069% 73.38% 219ms 1.08% std::_Rb_tree::_M_erase_aux (inline) 1ms 0.0049% 73.39% 217ms 1.07% std::set::set (inline) 22ms 0.11% 73.50% 212ms 1.05% std::_Rb_tree::_M_copy (inline) 6ms 0.03% 73.53% 211ms 1.04% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2ms 0.0099% 73.54% 205ms 1.01% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.0099% 73.55% 201ms 0.99% MeshBasedCellPopulation::GetDampingConstant 27ms 0.13% 73.68% 199ms 0.98% AbstractTetrahedralElement::RefreshJacobian 1ms 0.0049% 73.68% 198ms 0.98% AbstractCentreBasedCellPopulation::GetDampingConstant 136ms 0.67% 74.35% 192ms 0.95% AbstractElement::GetNodeGlobalIndex 70ms 0.35% 74.70% 187ms 0.92% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 0 0% 74.70% 186ms 0.92% OffLatticeSimulation::ApplyBoundaries 54ms 0.27% 74.97% 186ms 0.92% std::_Rb_tree::_M_clone_node (inline) 0 0% 74.97% 186ms 0.92% std::__cxx11::collate::do_transform 13ms 0.064% 75.03% 185ms 0.91% TetrahedralMesh::Clear 123ms 0.61% 75.64% 185ms 0.91% malloc_consolidate 1ms 0.0049% 75.64% 181ms 0.89% ___vsnprintf 0 0% 75.64% 180ms 0.89% __vsnprintf_internal (inline) 179ms 0.88% 76.52% 179ms 0.88% std::_Rb_tree_insert_and_rebalance 28ms 0.14% 76.66% 176ms 0.87% __printf_buffer 170ms 0.84% 77.50% 170ms 0.84% Node::GetIndex 7ms 0.035% 77.54% 160ms 0.79% Element::MarkAsDeleted 2ms 0.0099% 77.54% 159ms 0.78% CellProliferativeTypesWriter::VisitCell 159ms 0.78% 78.33% 159ms 0.78% unlink_chunk 7ms 0.035% 78.36% 156ms 0.77% AbstractTetrahedralElement::AbstractTetrahedralElement 3ms 0.015% 78.38% 156ms 0.77% CellPropertyCollection::HasProperty 59ms 0.29% 78.67% 153ms 0.75% AbstractElement::GetNodeLocation 0 0% 78.67% 152ms 0.75% Cell::HasCellProperty (inline) 152ms 0.75% 79.42% 152ms 0.75% incircle 150ms 0.74% 80.16% 150ms 0.74% std::vector::size (inline) 4ms 0.02% 80.18% 148ms 0.73% boost::numeric::ublas::vector_assign (inline) 5ms 0.025% 80.20% 148ms 0.73% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 7ms 0.035% 80.24% 143ms 0.71% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 7ms 0.035% 80.27% 142ms 0.7% __printf_fp_l_buffer 0 0% 80.27% 142ms 0.7% __printf_fp_spec (inline) 0 0% 80.27% 140ms 0.69% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.0049% 80.28% 135ms 0.67% OutputFileHandler::OpenOutputFile 38ms 0.19% 80.46% 128ms 0.63% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 65ms 0.32% 80.79% 128ms 0.63% __printf_fp_buffer_1 73ms 0.36% 81.15% 126ms 0.62% std::_Rb_tree::equal_range (inline) 76ms 0.37% 81.52% 123ms 0.61% Cylindrical2dMesh::GetVectorFromAtoB 13ms 0.064% 81.58% 121ms 0.6% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 81.58% 120ms 0.59% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 24ms 0.12% 81.70% 119ms 0.59% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 81.70% 118ms 0.58% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 2ms 0.0099% 81.71% 116ms 0.57% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 6ms 0.03% 81.74% 115ms 0.57% MeshBasedCellPopulation::SpringsEnd (inline) 42ms 0.21% 81.95% 114ms 0.56% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 113ms 0.56% 82.51% 113ms 0.56% AbstractElement::IsDeleted 9ms 0.044% 82.55% 113ms 0.56% Node::~Node 33ms 0.16% 82.71% 112ms 0.55% boost::numeric::ublas::indexing_vector_assign 108ms 0.53% 83.25% 112ms 0.55% vertexsort 0 0% 83.25% 111ms 0.55% AbstractCellBasedSimulation::DoCellRemoval (inline) 35ms 0.17% 83.42% 109ms 0.54% std::__ostream_insert 0 0% 83.42% 106ms 0.52% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath