File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16408ms, 83.99% of 19535ms total Dropped 782 nodes (cum <= 97.67ms) flat flat% sum% cum cum% 0 0% 0% 19491ms 99.77% __libc_start_call_main 0 0% 0% 19491ms 99.77% __libc_start_main_impl 0 0% 0% 19491ms 99.77% _start 0 0% 0% 19470ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19470ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19470ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19470ms 99.67% main 0 0% 0% 19427ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19427ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19427ms 99.45% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19400ms 99.31% AbstractCellBasedSimulation::Solve 0 0% 0% 14789ms 75.71% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 9347ms 47.85% AbstractCellBasedSimulation::DoCellBirth 4ms 0.02% 0.02% 9241ms 47.30% Cell::ReadyToDivide 4ms 0.02% 0.041% 9167ms 46.93% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.041% 9034ms 46.25% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 10ms 0.051% 0.092% 9020ms 46.17% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.1% 9005ms 46.10% CellCycleModelOdeHandler::SolveOdeToTime 63ms 0.32% 0.42% 8853ms 45.32% AbstractOneStepIvpOdeSolver::InternalSolve 955ms 4.89% 5.31% 7908ms 40.48% RungeKutta4IvpOdeSolver::CalculateNextYValue 2840ms 14.54% 19.85% 6760ms 34.60% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 19.85% 5306ms 27.16% MeshBasedCellPopulation::Update 5ms 0.026% 19.88% 4094ms 20.96% Cylindrical2dMesh::ReMesh 64ms 0.33% 20.20% 3950ms 20.22% AbstractCellProperty::IsType (inline) 359ms 1.84% 22.04% 2602ms 13.32% AbstractCellProperty::IsSame 2ms 0.01% 22.05% 2586ms 13.24% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 22.05% 2259ms 11.56% MutableMesh::ReMesh 0 0% 22.05% 2256ms 11.55% ForwardEulerNumericalMethod::UpdateAllNodePositions 262ms 1.34% 23.39% 2243ms 11.48% std::type_info::operator== (inline) 8ms 0.041% 23.43% 2198ms 11.25% AbstractNumericalMethod::ComputeForcesIncludingDamping 2078ms 10.64% 34.07% 2078ms 10.64% __strcmp_avx2 0 0% 34.07% 2019ms 10.34% AbstractCellPopulation::WriteResultsToFiles 785ms 4.02% 38.09% 1882ms 9.63% std::_Rb_tree::_M_lower_bound (inline) 171ms 0.88% 38.97% 1670ms 8.55% TetrahedralMesh::EdgeIterator::operator++ 77ms 0.39% 39.36% 1370ms 7.01% std::_Rb_tree::find (inline) 2ms 0.01% 39.37% 1163ms 5.95% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.036% 39.41% 1150ms 5.89% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 8ms 0.041% 39.45% 1116ms 5.71% TetrahedralMesh::ImportFromMesher 31ms 0.16% 39.61% 1058ms 5.42% operator new 18ms 0.092% 39.70% 1016ms 5.20% MeshBasedCellPopulation::SpringIterator::operator++ 264ms 1.35% 41.05% 1015ms 5.20% __GI___libc_malloc 11ms 0.056% 41.11% 1003ms 5.13% std::set::insert (inline) 11ms 0.056% 41.16% 991ms 5.07% std::_Rb_tree::_M_insert_unique 26ms 0.13% 41.30% 919ms 4.70% std::__new_allocator::allocate (inline) 0 0% 41.30% 913ms 4.67% std::allocator_traits::allocate (inline) 0 0% 41.30% 903ms 4.62% triangulate 0 0% 41.30% 825ms 4.22% std::set::count (inline) 0 0% 41.30% 824ms 4.22% delaunay 3ms 0.015% 41.31% 824ms 4.22% divconqdelaunay 59ms 0.3% 41.61% 782ms 4.00% std::map::operator[] (partial-inline) 759ms 3.89% 45.50% 759ms 3.89% WntCellCycleOdeSystem::CalculateStoppingEvent 3ms 0.015% 45.51% 754ms 3.86% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 753ms 3.85% 49.37% 753ms 3.85% std::_Rb_tree::_S_right (inline) 8ms 0.041% 49.41% 702ms 3.59% CellPopulationElementWriter::Visit 3ms 0.015% 49.42% 696ms 3.56% AbstractTwoBodyInteractionForce::AddForceContribution 361ms 1.85% 51.27% 668ms 3.42% _int_malloc 14ms 0.072% 51.34% 661ms 3.38% std::less::operator() (inline) 647ms 3.31% 54.66% 647ms 3.31% std::operator< (inline) 223ms 1.14% 55.80% 630ms 3.22% __dynamic_cast 22ms 0.11% 55.91% 619ms 3.17% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 55.91% 619ms 3.17% std::_Rb_tree::lower_bound (inline) 0 0% 55.91% 619ms 3.17% std::map::lower_bound (inline) 22ms 0.11% 56.02% 609ms 3.12% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 56.02% 601ms 3.08% std::_Rb_tree::_M_create_node (inline) 7ms 0.036% 56.06% 590ms 3.02% MeshBasedCellPopulation::AcceptCellWriter 9ms 0.046% 56.10% 589ms 3.02% CellPropertyCollection::GetPropertiesType (inline) 8ms 0.041% 56.15% 583ms 2.98% Element::Element 25ms 0.13% 56.27% 580ms 2.97% std::_Rb_tree::_M_insert_ (inline) 0 0% 56.27% 575ms 2.94% std::_Rb_tree::_M_get_node (inline) 0 0% 56.27% 543ms 2.78% std::map::find (inline) 0 0% 56.27% 536ms 2.74% std::_Rb_tree::_Alloc_node::operator() (inline) 6ms 0.031% 56.30% 523ms 2.68% MutableMesh::ReIndex 3ms 0.015% 56.32% 498ms 2.55% std::ostream::operator<< (inline) 11ms 0.056% 56.38% 496ms 2.54% Cylindrical2dMesh::CorrectNonPeriodicMesh 12ms 0.061% 56.44% 496ms 2.54% Cylindrical2dMesh::ReconstructCylindricalMesh 13ms 0.067% 56.50% 496ms 2.54% Element::RegisterWithNodes (inline) 63ms 0.32% 56.83% 493ms 2.52% std::ostream::_M_insert 2ms 0.01% 56.84% 484ms 2.48% AbstractCellProperty::IsSubType (inline) 6ms 0.031% 56.87% 477ms 2.44% Node::AddElement 123ms 0.63% 57.50% 428ms 2.19% __GI___libc_free 151ms 0.77% 58.27% 401ms 2.05% std::_Rb_tree::_M_get_insert_unique_pos 249ms 1.27% 59.54% 397ms 2.03% AbstractCellMutationState::AbstractCellMutationState 15ms 0.077% 59.62% 391ms 2.00% divconqrecurse 6ms 0.031% 59.65% 388ms 1.99% std::_Rb_tree::erase 2ms 0.01% 59.66% 388ms 1.99% std::set::erase (inline) 12ms 0.061% 59.72% 384ms 1.97% Node::RemoveElement 11ms 0.056% 59.78% 369ms 1.89% std::__new_allocator::deallocate (inline) 97ms 0.5% 60.28% 367ms 1.88% std::_Rb_tree::_M_erase 0 0% 60.28% 367ms 1.88% std::allocator_traits::deallocate (inline) 104ms 0.53% 60.81% 365ms 1.87% mergehulls 28ms 0.14% 60.95% 354ms 1.81% Element::ResetIndex 28ms 0.14% 61.10% 341ms 1.75% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.0051% 61.10% 339ms 1.74% std::_Vector_base::_M_allocate (inline) 0 0% 61.10% 333ms 1.70% std::_Rb_tree::_M_drop_node (inline) 1ms 0.0051% 61.11% 322ms 1.65% Cell::GetMutationState 316ms 1.62% 62.72% 316ms 1.62% [libchaste_cell_based.so] 0 0% 62.72% 307ms 1.57% std::_Rb_tree::_M_put_node (inline) 0 0% 62.72% 307ms 1.57% std::set::~set (inline) 2ms 0.01% 62.73% 305ms 1.56% NodeLocationWriter::Visit 258ms 1.32% 64.05% 305ms 1.56% _int_free 2ms 0.01% 64.06% 304ms 1.56% Cell::GetCellProliferativeType 2ms 0.01% 64.07% 299ms 1.53% AbstractCellPopulation::Iterator::operator++ (inline) 41ms 0.21% 64.28% 296ms 1.52% AbstractCellPopulation::Iterator::IsRealCell (inline) 10ms 0.051% 64.34% 295ms 1.51% AbstractCellPopulation::GetLocationIndexUsingCell 137ms 0.7% 65.04% 293ms 1.50% __cxxabiv1::__si_class_type_info::__do_dyncast 3ms 0.015% 65.05% 288ms 1.47% alternateaxes 271ms 1.39% 66.44% 284ms 1.45% vertexmedian 2ms 0.01% 66.45% 281ms 1.44% LegacyCellProliferativeTypesWriter::VisitCell 280ms 1.43% 67.88% 280ms 1.43% std::vector::operator[] (inline) 9ms 0.046% 67.93% 279ms 1.43% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 16ms 0.082% 68.01% 276ms 1.41% std::_Rb_tree::_Rb_tree (partial-inline) 23ms 0.12% 68.13% 274ms 1.40% std::num_put::_M_insert_float 5ms 0.026% 68.15% 260ms 1.33% AbstractCellPopulation::IsCellAttachedToLocationIndex 15ms 0.077% 68.23% 258ms 1.32% std::vector::push_back (inline) 1ms 0.0051% 68.24% 257ms 1.32% AbstractCentreBasedCellPopulation::GetDampingConstant 19ms 0.097% 68.33% 257ms 1.32% AbstractTetrahedralElement::CalculateJacobian 0 0% 68.33% 257ms 1.32% MeshBasedCellPopulation::GetDampingConstant 0 0% 68.33% 247ms 1.26% std::set::set (inline) 104ms 0.53% 68.87% 241ms 1.23% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 100ms 0.51% 69.38% 235ms 1.20% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 72ms 0.37% 69.75% 233ms 1.19% ApcOneHitCellMutationState::ApcOneHitCellMutationState 10ms 0.051% 69.80% 232ms 1.19% std::vector::_M_realloc_insert 10ms 0.051% 69.85% 230ms 1.18% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 17ms 0.087% 69.94% 228ms 1.17% std::_Rb_tree::_M_erase_aux (inline) 24ms 0.12% 70.06% 220ms 1.13% std::_Rb_tree::_M_copy (inline) 4ms 0.02% 70.08% 220ms 1.13% std::__cxx11::collate::do_transform 1ms 0.0051% 70.08% 215ms 1.10% TetrahedralMesh::RefreshJacobianCachedData 3ms 0.015% 70.10% 212ms 1.09% ___vsnprintf 0 0% 70.10% 210ms 1.07% __vsnprintf_internal (inline) 36ms 0.18% 70.28% 209ms 1.07% __printf_buffer 3ms 0.015% 70.30% 208ms 1.06% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 141ms 0.72% 71.02% 197ms 1.01% AbstractElement::GetNodeGlobalIndex 22ms 0.11% 71.13% 197ms 1.01% AbstractTetrahedralElement::RefreshJacobian 15ms 0.077% 71.21% 194ms 0.99% Element::MarkAsDeleted 13ms 0.067% 71.28% 193ms 0.99% AbstractTetrahedralElement::CalculateInverseJacobian 17ms 0.087% 71.36% 191ms 0.98% TetrahedralMesh::Clear 4ms 0.02% 71.38% 189ms 0.97% CellProliferativeTypesWriter::VisitCell 4ms 0.02% 71.41% 188ms 0.96% AbstractTetrahedralElement::AbstractTetrahedralElement 53ms 0.27% 71.68% 188ms 0.96% std::_Rb_tree::_M_clone_node (inline) 0 0% 71.68% 187ms 0.96% OffLatticeSimulation::ApplyBoundaries 130ms 0.67% 72.34% 175ms 0.9% malloc_consolidate 2ms 0.01% 72.35% 166ms 0.85% CellPropertyCollection::HasProperty 0 0% 72.35% 165ms 0.84% Cell::HasCellProperty (inline) 6ms 0.031% 72.38% 164ms 0.84% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 164ms 0.84% 73.22% 164ms 0.84% incircle 163ms 0.83% 74.06% 163ms 0.83% Node::GetIndex 31ms 0.16% 74.22% 163ms 0.83% TetrahedralMesh::EdgesEnd (partial-inline) 114ms 0.58% 74.80% 161ms 0.82% std::_Rb_tree::equal_range (inline) 161ms 0.82% 75.62% 161ms 0.82% std::_Rb_tree_insert_and_rebalance 70ms 0.36% 75.98% 160ms 0.82% AbstractElement::GetNodeLocation 160ms 0.82% 76.80% 160ms 0.82% unlink_chunk 157ms 0.8% 77.60% 157ms 0.8% std::vector::size (inline) 4ms 0.02% 77.62% 154ms 0.79% __printf_fp_l_buffer 0 0% 77.62% 154ms 0.79% __printf_fp_spec (inline) 154ms 0.79% 78.41% 154ms 0.79% std::type_info::name (inline) 153ms 0.78% 79.20% 153ms 0.78% [libchaste_crypt.so] 72ms 0.37% 79.56% 149ms 0.76% __printf_fp_buffer_1 4ms 0.02% 79.59% 148ms 0.76% boost::numeric::ublas::vector_assign (inline) 5ms 0.026% 79.61% 145ms 0.74% MeshBasedCellPopulation::SpringsEnd (inline) 91ms 0.47% 80.08% 140ms 0.72% Cylindrical2dMesh::GetVectorFromAtoB 50ms 0.26% 80.33% 137ms 0.7% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 123ms 0.63% 80.96% 137ms 0.7% vertexsort 0 0% 80.96% 135ms 0.69% AbstractCellBasedSimulation::DoCellRemoval (inline) 50ms 0.26% 81.22% 129ms 0.66% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 2ms 0.01% 81.23% 127ms 0.65% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2ms 0.01% 81.24% 127ms 0.65% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 12ms 0.061% 81.30% 127ms 0.65% boost::numeric::ublas::c_vector::c_vector (inline) 41ms 0.21% 81.51% 124ms 0.63% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 123ms 0.63% 82.14% 123ms 0.63% AbstractCellMutationState::~AbstractCellMutationState 0 0% 82.14% 122ms 0.62% AbstractCellBasedWriter::OpenOutputFileForAppend 85ms 0.44% 82.57% 122ms 0.62% TetrahedralMesh::EdgeIterator::EdgeIterator 6ms 0.031% 82.61% 122ms 0.62% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 1ms 0.0051% 82.61% 119ms 0.61% OutputFileHandler::OpenOutputFile 6ms 0.031% 82.64% 116ms 0.59% Node::~Node 33ms 0.17% 82.81% 114ms 0.58% boost::numeric::ublas::indexing_vector_assign 28ms 0.14% 82.95% 114ms 0.58% std::num_put::_M_insert_int 31ms 0.16% 83.11% 113ms 0.58% std::__ostream_insert 0 0% 83.11% 108ms 0.55% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.0051% 83.12% 106ms 0.54% Cell::SetCellProliferativeType 14ms 0.072% 83.19% 104ms 0.53% boost::detail::shared_count::~shared_count (inline) 0 0% 83.19% 104ms 0.53% boost::shared_ptr::~shared_ptr (inline) 3ms 0.015% 83.20% 104ms 0.53% std::_Rb_tree::_M_emplace_hint_unique 7ms 0.036% 83.24% 104ms 0.53% std::_Rb_tree_const_iterator::operator++ (inline) 101ms 0.52% 83.76% 101ms 0.52% std::_Rb_tree_increment 41ms 0.21% 83.97% 99ms 0.51% boost::shared_ptr::shared_ptr (inline) 5ms 0.026% 83.99% 98ms 0.5% CryptSimulationBoundaryCondition::ImposeBoundaryCondition