File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16699ms, 83.25% of 20060ms total Dropped 796 nodes (cum <= 100.30ms) flat flat% sum% cum cum% 0 0% 0% 20012ms 99.76% __libc_start_call_main 0 0% 0% 20012ms 99.76% __libc_start_main_impl 0 0% 0% 20012ms 99.76% _start 0 0% 0% 19991ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19991ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19991ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19991ms 99.66% main 0 0% 0% 19952ms 99.46% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19952ms 99.46% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19952ms 99.46% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19926ms 99.33% AbstractCellBasedSimulation::Solve 1ms 0.005% 0.005% 15385ms 76.69% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.01% 0.015% 10023ms 49.97% AbstractCellBasedSimulation::DoCellBirth 10ms 0.05% 0.065% 9927ms 49.49% Cell::ReadyToDivide 3ms 0.015% 0.08% 9832ms 49.01% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.005% 0.085% 9690ms 48.31% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 9ms 0.045% 0.13% 9675ms 48.23% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.14% 9663ms 48.17% CellCycleModelOdeHandler::SolveOdeToTime 67ms 0.33% 0.47% 9466ms 47.19% AbstractOneStepIvpOdeSolver::InternalSolve 850ms 4.24% 4.71% 8660ms 43.17% RungeKutta4IvpOdeSolver::CalculateNextYValue 3557ms 17.73% 22.44% 7612ms 37.95% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.005% 22.45% 5246ms 26.15% MeshBasedCellPopulation::Update 94ms 0.47% 22.92% 4132ms 20.60% AbstractCellProperty::IsType (inline) 5ms 0.025% 22.94% 4062ms 20.25% Cylindrical2dMesh::ReMesh 621ms 3.10% 26.04% 2909ms 14.50% AbstractCellProperty::IsSame 0 0% 26.04% 2495ms 12.44% OffLatticeSimulation::UpdateCellLocationsAndTopology 430ms 2.14% 28.18% 2288ms 11.41% std::type_info::operator== (inline) 0 0% 28.18% 2279ms 11.36% MutableMesh::ReMesh 0 0% 28.18% 2185ms 10.89% ForwardEulerNumericalMethod::UpdateAllNodePositions 11ms 0.055% 28.24% 2132ms 10.63% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 28.24% 2040ms 10.17% AbstractCellPopulation::WriteResultsToFiles 801ms 3.99% 32.23% 1860ms 9.27% std::_Rb_tree::_M_lower_bound (inline) 1749ms 8.72% 40.95% 1749ms 8.72% __strcmp_avx2 143ms 0.71% 41.66% 1726ms 8.60% TetrahedralMesh::EdgeIterator::operator++ 76ms 0.38% 42.04% 1401ms 6.98% std::_Rb_tree::find (inline) 0 0% 42.04% 1149ms 5.73% MeshBasedCellPopulation::UpdateNodePairs 15ms 0.075% 42.11% 1146ms 5.71% TetrahedralMesh::ImportFromMesher 4ms 0.02% 42.13% 1112ms 5.54% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 46ms 0.23% 42.36% 1046ms 5.21% operator new 12ms 0.06% 42.42% 1029ms 5.13% MeshBasedCellPopulation::SpringIterator::operator++ 229ms 1.14% 43.56% 988ms 4.93% __GI___libc_malloc 9ms 0.045% 43.61% 983ms 4.90% std::set::insert (inline) 23ms 0.11% 43.72% 974ms 4.86% std::_Rb_tree::_M_insert_unique 38ms 0.19% 43.91% 932ms 4.65% std::__new_allocator::allocate (inline) 0 0% 43.91% 927ms 4.62% std::allocator_traits::allocate (inline) 0 0% 43.91% 871ms 4.34% std::set::count (inline) 1ms 0.005% 43.92% 830ms 4.14% triangulate 3ms 0.015% 43.93% 733ms 3.65% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 1ms 0.005% 43.94% 730ms 3.64% delaunay 1ms 0.005% 43.94% 729ms 3.63% divconqdelaunay 4ms 0.02% 43.96% 689ms 3.43% AbstractTwoBodyInteractionForce::AddForceContribution 5ms 0.025% 43.99% 687ms 3.42% CellPopulationElementWriter::Visit 55ms 0.27% 44.26% 687ms 3.42% std::map::operator[] (partial-inline) 389ms 1.94% 46.20% 674ms 3.36% _int_malloc 661ms 3.30% 49.50% 661ms 3.30% std::_Rb_tree::_S_right (inline) 14ms 0.07% 49.57% 657ms 3.28% std::less::operator() (inline) 643ms 3.21% 52.77% 643ms 3.21% std::operator< (inline) 239ms 1.19% 53.96% 633ms 3.16% __dynamic_cast 613ms 3.06% 57.02% 629ms 3.14% WntCellCycleOdeSystem::CalculateStoppingEvent 7ms 0.035% 57.05% 627ms 3.13% CellPropertyCollection::GetPropertiesType (inline) 29ms 0.14% 57.20% 607ms 3.03% std::_Rb_tree::_M_insert_ (inline) 22ms 0.11% 57.31% 605ms 3.02% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 57.31% 602ms 3.00% std::_Rb_tree::_M_create_node (inline) 0 0% 57.31% 586ms 2.92% std::_Rb_tree::_M_get_node (inline) 2ms 0.01% 57.32% 579ms 2.89% MeshBasedCellPopulation::AcceptCellWriter 28ms 0.14% 57.46% 578ms 2.88% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 7ms 0.035% 57.49% 565ms 2.82% Element::Element 0 0% 57.49% 551ms 2.75% std::_Rb_tree::lower_bound (inline) 0 0% 57.49% 551ms 2.75% std::map::lower_bound (inline) 0 0% 57.49% 548ms 2.73% std::_Rb_tree::_Alloc_node::operator() (inline) 78ms 0.39% 57.88% 537ms 2.68% std::ostream::_M_insert 0 0% 57.88% 537ms 2.68% std::ostream::operator<< (inline) 9ms 0.045% 57.93% 521ms 2.60% Cylindrical2dMesh::ReconstructCylindricalMesh 0 0% 57.93% 517ms 2.58% std::map::find (inline) 2ms 0.01% 57.94% 503ms 2.51% AbstractCellProperty::IsSubType (inline) 8ms 0.04% 57.98% 503ms 2.51% MutableMesh::ReIndex 9ms 0.045% 58.02% 470ms 2.34% Element::RegisterWithNodes (inline) 313ms 1.56% 59.58% 461ms 2.30% AbstractCellMutationState::AbstractCellMutationState 164ms 0.82% 60.40% 460ms 2.29% __GI___libc_free 11ms 0.055% 60.45% 451ms 2.25% Node::AddElement 9ms 0.045% 60.50% 446ms 2.22% Cylindrical2dMesh::CorrectNonPeriodicMesh 1ms 0.005% 60.50% 405ms 2.02% std::set::erase (inline) 13ms 0.065% 60.57% 404ms 2.01% std::_Rb_tree::erase 14ms 0.07% 60.64% 392ms 1.95% divconqrecurse 10ms 0.05% 60.69% 386ms 1.92% Node::RemoveElement 116ms 0.58% 61.27% 377ms 1.88% std::_Rb_tree::_M_erase 13ms 0.065% 61.33% 372ms 1.85% std::__new_allocator::deallocate (inline) 105ms 0.52% 61.85% 371ms 1.85% mergehulls 0 0% 61.85% 371ms 1.85% std::allocator_traits::deallocate (inline) 363ms 1.81% 63.66% 363ms 1.81% std::type_info::name (inline) 23ms 0.11% 63.78% 358ms 1.78% std::_Rb_tree::~_Rb_tree (inline) 127ms 0.63% 64.41% 344ms 1.71% std::_Rb_tree::_M_get_insert_unique_pos 3ms 0.015% 64.43% 344ms 1.71% std::_Vector_base::_M_allocate (inline) 0 0% 64.43% 340ms 1.69% Cell::GetMutationState 1ms 0.005% 64.43% 337ms 1.68% NodeLocationWriter::Visit 30ms 0.15% 64.58% 332ms 1.66% Element::ResetIndex 0 0% 64.58% 327ms 1.63% std::_Rb_tree::_M_drop_node (inline) 0 0% 64.58% 324ms 1.62% std::set::~set (inline) 5ms 0.025% 64.61% 319ms 1.59% Cell::GetCellProliferativeType 7ms 0.035% 64.64% 312ms 1.56% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 141ms 0.7% 65.34% 296ms 1.48% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 65.34% 296ms 1.48% std::_Rb_tree::_M_put_node (inline) 234ms 1.17% 66.51% 293ms 1.46% _int_free 20ms 0.1% 66.61% 291ms 1.45% std::num_put::_M_insert_float 2ms 0.01% 66.62% 283ms 1.41% AbstractCellPopulation::Iterator::operator++ (inline) 3ms 0.015% 66.64% 282ms 1.41% AbstractCellPopulation::GetLocationIndexUsingCell 24ms 0.12% 66.75% 282ms 1.41% AbstractTetrahedralElement::CalculateJacobian 2ms 0.01% 66.76% 281ms 1.40% LegacyCellProliferativeTypesWriter::VisitCell 39ms 0.19% 66.96% 279ms 1.39% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 66.96% 278ms 1.39% TetrahedralMesh::RefreshJacobianCachedData 16ms 0.08% 67.04% 276ms 1.38% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 67.04% 255ms 1.27% MeshBasedCellPopulation::GetDampingConstant 1ms 0.005% 67.04% 253ms 1.26% std::set::set (inline) 251ms 1.25% 68.30% 253ms 1.26% std::vector::operator[] (inline) 1ms 0.005% 68.30% 252ms 1.26% AbstractCentreBasedCellPopulation::GetDampingConstant 15ms 0.075% 68.37% 242ms 1.21% std::_Rb_tree::_M_erase_aux (inline) 1ms 0.005% 68.38% 240ms 1.20% alternateaxes 23ms 0.11% 68.49% 239ms 1.19% TetrahedralMesh::Clear 219ms 1.09% 69.59% 239ms 1.19% vertexmedian 12ms 0.06% 69.65% 238ms 1.19% std::vector::push_back (inline) 6ms 0.03% 69.68% 235ms 1.17% AbstractCellPopulation::IsCellAttachedToLocationIndex 1ms 0.005% 69.68% 234ms 1.17% std::__cxx11::collate::do_transform 46ms 0.23% 69.91% 230ms 1.15% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 23ms 0.11% 70.02% 229ms 1.14% std::_Rb_tree::_M_copy (inline) 9ms 0.045% 70.07% 228ms 1.14% AbstractTetrahedralElement::CalculateInverseJacobian 227ms 1.13% 71.20% 227ms 1.13% [libchaste_cell_based.so] 62ms 0.31% 71.51% 225ms 1.12% ApcOneHitCellMutationState::ApcOneHitCellMutationState 1ms 0.005% 71.52% 225ms 1.12% ___vsnprintf 0 0% 71.52% 224ms 1.12% __vsnprintf_internal (inline) 13ms 0.065% 71.58% 220ms 1.10% __printf_buffer 3ms 0.015% 71.60% 215ms 1.07% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 19ms 0.095% 71.69% 215ms 1.07% AbstractTetrahedralElement::RefreshJacobian 15ms 0.075% 71.76% 215ms 1.07% std::vector::_M_realloc_insert 13ms 0.065% 71.83% 213ms 1.06% Element::MarkAsDeleted 5ms 0.025% 71.85% 204ms 1.02% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 62ms 0.31% 72.16% 202ms 1.01% std::_Rb_tree::_M_clone_node (inline) 8ms 0.04% 72.20% 199ms 0.99% AbstractTetrahedralElement::AbstractTetrahedralElement 39ms 0.19% 72.40% 194ms 0.97% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 8ms 0.04% 72.44% 193ms 0.96% __printf_fp_l_buffer 0 0% 72.44% 193ms 0.96% __printf_fp_spec (inline) 4ms 0.02% 72.46% 190ms 0.95% CellPropertyCollection::HasProperty 0 0% 72.46% 190ms 0.95% OffLatticeSimulation::ApplyBoundaries 186ms 0.93% 73.38% 186ms 0.93% std::_Rb_tree_insert_and_rebalance 2ms 0.01% 73.39% 185ms 0.92% CellProliferativeTypesWriter::VisitCell 0 0% 73.39% 183ms 0.91% Cell::HasCellProperty (inline) 68ms 0.34% 73.73% 179ms 0.89% AbstractElement::GetNodeLocation 76ms 0.38% 74.11% 178ms 0.89% __printf_fp_buffer_1 122ms 0.61% 74.72% 175ms 0.87% malloc_consolidate 144ms 0.72% 75.44% 172ms 0.86% AbstractElement::GetNodeGlobalIndex 172ms 0.86% 76.30% 172ms 0.86% Node::GetIndex 167ms 0.83% 77.13% 167ms 0.83% incircle 160ms 0.8% 77.93% 160ms 0.8% unlink_chunk 101ms 0.5% 78.43% 157ms 0.78% std::_Rb_tree::equal_range (inline) 7ms 0.035% 78.46% 145ms 0.72% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 5ms 0.025% 78.49% 143ms 0.71% boost::numeric::ublas::vector_assign (inline) 34ms 0.17% 78.66% 136ms 0.68% TetrahedralMesh::EdgesEnd 51ms 0.25% 78.91% 135ms 0.67% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 11ms 0.055% 78.97% 133ms 0.66% Node::~Node 1ms 0.005% 78.97% 133ms 0.66% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 133ms 0.66% 79.64% 133ms 0.66% std::vector::size (inline) 4ms 0.02% 79.66% 129ms 0.64% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 128ms 0.64% 80.29% 128ms 0.64% std::_Rb_tree_increment 50ms 0.25% 80.54% 125ms 0.62% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 16ms 0.08% 80.62% 124ms 0.62% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 80.62% 122ms 0.61% AbstractCellBasedWriter::OpenOutputFileForAppend 7ms 0.035% 80.66% 122ms 0.61% std::_Rb_tree_const_iterator::operator++ (inline) 9ms 0.045% 80.70% 121ms 0.6% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 80.70% 121ms 0.6% OutputFileHandler::OpenOutputFile 1ms 0.005% 80.71% 118ms 0.59% Cell::SetCellProliferativeType 0 0% 80.71% 114ms 0.57% AbstractCellBasedSimulation::DoCellRemoval (inline) 2ms 0.01% 80.72% 112ms 0.56% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 51ms 0.25% 80.97% 112ms 0.56% std::__ostream_insert 109ms 0.54% 81.52% 109ms 0.54% AbstractCellMutationState::~AbstractCellMutationState 35ms 0.17% 81.69% 109ms 0.54% boost::numeric::ublas::indexing_vector_assign 108ms 0.54% 82.23% 108ms 0.54% AbstractElement::IsDeleted 0 0% 82.23% 104ms 0.52% std::vector::vector (inline) 102ms 0.51% 82.74% 102ms 0.51% AbstractCellProperty::~AbstractCellProperty 102ms 0.51% 83.25% 102ms 0.51% std::_Rb_tree_rebalance_for_erase