File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16640ms, 85.18% of 19535ms total Dropped 783 nodes (cum <= 97.67ms) flat flat% sum% cum cum% 0 0% 0% 19485ms 99.74% __libc_start_call_main 0 0% 0% 19485ms 99.74% __libc_start_main_impl 0 0% 0% 19485ms 99.74% _start 0 0% 0% 19462ms 99.63% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19462ms 99.63% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19462ms 99.63% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19462ms 99.63% main 0 0% 0% 19421ms 99.42% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19421ms 99.42% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19421ms 99.42% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19394ms 99.28% AbstractCellBasedSimulation::Solve 0 0% 0% 14806ms 75.79% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.015% 0.015% 9342ms 47.82% AbstractCellBasedSimulation::DoCellBirth 6ms 0.031% 0.046% 9225ms 47.22% Cell::ReadyToDivide 12ms 0.061% 0.11% 9123ms 46.70% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.01% 0.12% 8968ms 45.91% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 11ms 0.056% 0.17% 8963ms 45.88% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.18% 8947ms 45.80% CellCycleModelOdeHandler::SolveOdeToTime 56ms 0.29% 0.47% 8785ms 44.97% AbstractOneStepIvpOdeSolver::InternalSolve 960ms 4.91% 5.39% 7906ms 40.47% RungeKutta4IvpOdeSolver::CalculateNextYValue 2776ms 14.21% 19.60% 6753ms 34.57% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 19.60% 5345ms 27.36% MeshBasedCellPopulation::Update 3ms 0.015% 19.61% 4100ms 20.99% Cylindrical2dMesh::ReMesh 61ms 0.31% 19.92% 4034ms 20.65% AbstractCellProperty::IsType (inline) 392ms 2.01% 21.93% 2601ms 13.31% AbstractCellProperty::IsSame 1ms 0.0051% 21.93% 2560ms 13.10% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 21.93% 2257ms 11.55% MutableMesh::ReMesh 214ms 1.10% 23.03% 2209ms 11.31% std::type_info::operator== (inline) 0 0% 23.03% 2204ms 11.28% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.026% 23.06% 2140ms 10.95% AbstractNumericalMethod::ComputeForcesIncludingDamping 2093ms 10.71% 33.77% 2093ms 10.71% __strcmp_avx2 0 0% 33.77% 2024ms 10.36% AbstractCellPopulation::WriteResultsToFiles 803ms 4.11% 37.88% 1903ms 9.74% std::_Rb_tree::_M_lower_bound (inline) 183ms 0.94% 38.82% 1701ms 8.71% TetrahedralMesh::EdgeIterator::operator++ 85ms 0.44% 39.25% 1430ms 7.32% std::_Rb_tree::find (inline) 1ms 0.0051% 39.26% 1202ms 6.15% MeshBasedCellPopulation::UpdateNodePairs 14ms 0.072% 39.33% 1169ms 5.98% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 11ms 0.056% 39.39% 1134ms 5.80% TetrahedralMesh::ImportFromMesher 15ms 0.077% 39.46% 1070ms 5.48% std::set::insert (inline) 16ms 0.082% 39.54% 1055ms 5.40% std::_Rb_tree::_M_insert_unique 19ms 0.097% 39.64% 1048ms 5.36% MeshBasedCellPopulation::SpringIterator::operator++ 40ms 0.2% 39.85% 1042ms 5.33% operator new 245ms 1.25% 41.10% 980ms 5.02% __GI___libc_malloc 23ms 0.12% 41.22% 903ms 4.62% std::__new_allocator::allocate (inline) 0 0% 41.22% 901ms 4.61% triangulate 0 0% 41.22% 897ms 4.59% std::allocator_traits::allocate (inline) 0 0% 41.22% 859ms 4.40% std::set::count (inline) 0 0% 41.22% 840ms 4.30% delaunay 3ms 0.015% 41.23% 840ms 4.30% divconqdelaunay 2ms 0.01% 41.24% 757ms 3.88% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 731ms 3.74% 44.99% 731ms 3.74% std::_Rb_tree::_S_right (inline) 53ms 0.27% 45.26% 729ms 3.73% std::map::operator[] (partial-inline) 724ms 3.71% 48.96% 724ms 3.71% WntCellCycleOdeSystem::CalculateStoppingEvent 23ms 0.12% 49.08% 677ms 3.47% std::less::operator() (inline) 7ms 0.036% 49.12% 665ms 3.40% CellPopulationElementWriter::Visit 1ms 0.0051% 49.12% 656ms 3.36% AbstractTwoBodyInteractionForce::AddForceContribution 654ms 3.35% 52.47% 654ms 3.35% std::operator< (inline) 362ms 1.85% 54.32% 640ms 3.28% _int_malloc 38ms 0.19% 54.52% 634ms 3.25% std::_Rb_tree::_M_insert_ (inline) 4ms 0.02% 54.54% 625ms 3.20% MeshBasedCellPopulation::AcceptCellWriter 0 0% 54.54% 625ms 3.20% std::_Rb_tree::_M_create_node (inline) 174ms 0.89% 55.43% 624ms 3.19% __dynamic_cast 5ms 0.026% 55.45% 619ms 3.17% Element::Element 9ms 0.046% 55.50% 617ms 3.16% CellPropertyCollection::GetPropertiesType (inline) 0 0% 55.50% 592ms 3.03% std::_Rb_tree::_M_get_node (inline) 0 0% 55.50% 589ms 3.02% std::_Rb_tree::lower_bound (inline) 0 0% 55.50% 589ms 3.02% std::map::lower_bound (inline) 15ms 0.077% 55.58% 581ms 2.97% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 55.58% 572ms 2.93% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 55.58% 567ms 2.90% std::map::find (inline) 40ms 0.2% 55.78% 560ms 2.87% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 16ms 0.082% 55.86% 553ms 2.83% Element::RegisterWithNodes (inline) 8ms 0.041% 55.90% 536ms 2.74% Node::AddElement 4ms 0.02% 55.93% 533ms 2.73% MutableMesh::ReIndex 13ms 0.067% 55.99% 511ms 2.62% Cylindrical2dMesh::ReconstructCylindricalMesh 18ms 0.092% 56.08% 510ms 2.61% Cylindrical2dMesh::CorrectNonPeriodicMesh 4ms 0.02% 56.10% 504ms 2.58% AbstractCellProperty::IsSubType (inline) 0 0% 56.10% 477ms 2.44% std::ostream::operator<< (inline) 73ms 0.37% 56.48% 475ms 2.43% std::ostream::_M_insert 280ms 1.43% 57.91% 433ms 2.22% AbstractCellMutationState::AbstractCellMutationState 124ms 0.63% 58.55% 425ms 2.18% __GI___libc_free 152ms 0.78% 59.32% 405ms 2.07% std::_Rb_tree::_M_get_insert_unique_pos 20ms 0.1% 59.43% 400ms 2.05% divconqrecurse 17ms 0.087% 59.51% 387ms 1.98% Node::RemoveElement 9ms 0.046% 59.56% 383ms 1.96% std::_Rb_tree::erase 1ms 0.0051% 59.56% 382ms 1.96% std::set::erase (inline) 28ms 0.14% 59.71% 372ms 1.90% Element::ResetIndex 372ms 1.90% 61.61% 372ms 1.90% [libchaste_cell_based.so] 19ms 0.097% 61.71% 367ms 1.88% std::__new_allocator::deallocate (inline) 97ms 0.5% 62.21% 365ms 1.87% mergehulls 4ms 0.02% 62.23% 362ms 1.85% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 62.23% 362ms 1.85% std::allocator_traits::deallocate (inline) 93ms 0.48% 62.70% 344ms 1.76% std::_Rb_tree::_M_erase 11ms 0.056% 62.76% 331ms 1.69% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 62.76% 329ms 1.68% std::_Rb_tree::_M_drop_node (inline) 1ms 0.0051% 62.76% 324ms 1.66% Cell::GetMutationState 0 0% 62.76% 322ms 1.65% AbstractCellPopulation::Iterator::operator++ (inline) 1ms 0.0051% 62.77% 322ms 1.65% Cell::GetCellProliferativeType 22ms 0.11% 62.88% 321ms 1.64% std::_Rb_tree::~_Rb_tree (inline) 38ms 0.19% 63.08% 319ms 1.63% AbstractCellPopulation::Iterator::IsRealCell (inline) 6ms 0.031% 63.11% 317ms 1.62% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 1ms 0.0051% 63.11% 317ms 1.62% NodeLocationWriter::Visit 172ms 0.88% 63.99% 314ms 1.61% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 63.99% 305ms 1.56% std::_Vector_base::_M_allocate (inline) 250ms 1.28% 65.27% 299ms 1.53% _int_free 0 0% 65.27% 299ms 1.53% std::set::~set (inline) 0 0% 65.27% 297ms 1.52% std::_Rb_tree::_M_put_node (inline) 286ms 1.46% 66.74% 287ms 1.47% std::vector::operator[] (inline) 3ms 0.015% 66.75% 275ms 1.41% alternateaxes 18ms 0.092% 66.84% 273ms 1.40% std::num_put::_M_insert_float 261ms 1.34% 68.18% 272ms 1.39% vertexmedian 8ms 0.041% 68.22% 261ms 1.34% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 71ms 0.36% 68.58% 260ms 1.33% ApcOneHitCellMutationState::ApcOneHitCellMutationState 22ms 0.11% 68.70% 258ms 1.32% AbstractTetrahedralElement::CalculateJacobian 16ms 0.082% 68.78% 255ms 1.31% std::_Rb_tree::_Rb_tree (partial-inline) 4ms 0.02% 68.80% 251ms 1.28% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 4ms 0.02% 68.82% 241ms 1.23% AbstractCellPopulation::IsCellAttachedToLocationIndex 108ms 0.55% 69.37% 241ms 1.23% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 13ms 0.067% 69.44% 237ms 1.21% std::vector::push_back (inline) 3ms 0.015% 69.45% 233ms 1.19% std::set::set (inline) 89ms 0.46% 69.91% 228ms 1.17% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 0 0% 69.91% 227ms 1.16% OffLatticeSimulation::ApplyBoundaries 12ms 0.061% 69.97% 226ms 1.16% std::__cxx11::collate::do_transform 3ms 0.015% 69.99% 225ms 1.15% CellPropertyCollection::HasProperty 14ms 0.072% 70.06% 223ms 1.14% std::_Rb_tree::_M_erase_aux (inline) 0 0% 70.06% 222ms 1.14% Cell::HasCellProperty (inline) 21ms 0.11% 70.17% 221ms 1.13% Element::MarkAsDeleted 5ms 0.026% 70.19% 220ms 1.13% MeshBasedCellPopulation::GetDampingConstant 2ms 0.01% 70.20% 215ms 1.10% AbstractCentreBasedCellPopulation::GetDampingConstant 1ms 0.0051% 70.21% 211ms 1.08% ___vsnprintf 1ms 0.0051% 70.21% 210ms 1.07% __vsnprintf_internal (inline) 22ms 0.11% 70.33% 207ms 1.06% __printf_buffer 17ms 0.087% 70.41% 207ms 1.06% std::vector::_M_realloc_insert 6ms 0.031% 70.44% 202ms 1.03% AbstractTetrahedralElement::AbstractTetrahedralElement 202ms 1.03% 71.48% 202ms 1.03% [libchaste_crypt.so] 20ms 0.1% 71.58% 202ms 1.03% std::_Rb_tree::_M_copy (inline) 36ms 0.18% 71.76% 196ms 1.00% AbstractTetrahedralElement::RefreshJacobian 0 0% 71.76% 193ms 0.99% TetrahedralMesh::RefreshJacobianCachedData 17ms 0.087% 71.85% 186ms 0.95% TetrahedralMesh::Clear 55ms 0.28% 72.13% 180ms 0.92% std::_Rb_tree::_M_clone_node (inline) 124ms 0.63% 72.77% 179ms 0.92% malloc_consolidate 178ms 0.91% 73.68% 178ms 0.91% incircle 177ms 0.91% 74.58% 177ms 0.91% Node::GetIndex 11ms 0.056% 74.64% 175ms 0.9% AbstractTetrahedralElement::CalculateInverseJacobian 4ms 0.02% 74.66% 175ms 0.9% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 5ms 0.026% 74.69% 175ms 0.9% __printf_fp_l_buffer 0 0% 74.69% 175ms 0.9% __printf_fp_spec (inline) 128ms 0.66% 75.34% 173ms 0.89% AbstractElement::GetNodeGlobalIndex 80ms 0.41% 75.75% 165ms 0.84% __printf_fp_buffer_1 6ms 0.031% 75.78% 158ms 0.81% CellProliferativeTypesWriter::VisitCell 158ms 0.81% 76.59% 158ms 0.81% std::_Rb_tree_insert_and_rebalance 105ms 0.54% 77.13% 156ms 0.8% std::_Rb_tree::equal_range (inline) 48ms 0.25% 77.37% 155ms 0.79% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 93ms 0.48% 77.85% 151ms 0.77% Cylindrical2dMesh::GetVectorFromAtoB 5ms 0.026% 77.88% 151ms 0.77% MeshBasedCellPopulation::SpringsEnd (inline) 140ms 0.72% 78.59% 150ms 0.77% vertexsort 41ms 0.21% 78.80% 148ms 0.76% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 1ms 0.0051% 78.81% 147ms 0.75% boost::numeric::ublas::vector_assign (inline) 147ms 0.75% 79.56% 147ms 0.75% std::type_info::name (inline) 15ms 0.077% 79.64% 139ms 0.71% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 4ms 0.02% 79.66% 139ms 0.71% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 58ms 0.3% 79.95% 137ms 0.7% AbstractElement::GetNodeLocation 9ms 0.046% 80.00% 137ms 0.7% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.0051% 80.01% 136ms 0.7% AbstractCellBasedWriter::OpenOutputFileForAppend 20ms 0.1% 80.11% 135ms 0.69% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 80.11% 134ms 0.69% OutputFileHandler::OpenOutputFile 8ms 0.041% 80.15% 134ms 0.69% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 133ms 0.68% 80.83% 133ms 0.68% unlink_chunk 131ms 0.67% 81.50% 131ms 0.67% std::vector::size (inline) 126ms 0.64% 82.14% 126ms 0.64% std::_Rb_tree_increment 30ms 0.15% 82.30% 124ms 0.63% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 82.30% 123ms 0.63% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 122ms 0.62% 82.92% 122ms 0.62% AbstractCellMutationState::~AbstractCellMutationState 7ms 0.036% 82.96% 122ms 0.62% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.01% 82.97% 121ms 0.62% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 43ms 0.22% 83.19% 121ms 0.62% boost::numeric::ublas::indexing_vector_assign 0 0% 83.19% 119ms 0.61% AbstractCellBasedSimulation::DoCellRemoval (inline) 3ms 0.015% 83.20% 118ms 0.6% Cell::SetCellProliferativeType 78ms 0.4% 83.60% 115ms 0.59% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 1ms 0.0051% 83.61% 112ms 0.57% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 12ms 0.061% 83.67% 109ms 0.56% Node::~Node 37ms 0.19% 83.86% 107ms 0.55% boost::shared_ptr::shared_ptr (inline) 1ms 0.0051% 83.86% 106ms 0.54% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 106ms 0.54% 84.41% 106ms 0.54% TetrahedralMesh::EdgeIterator::operator!= 9ms 0.046% 84.45% 104ms 0.53% boost::detail::shared_count::~shared_count (inline) 0 0% 84.45% 104ms 0.53% boost::shared_ptr::~shared_ptr (inline) 41ms 0.21% 84.66% 103ms 0.53% std::__ostream_insert 101ms 0.52% 85.18% 101ms 0.52% AbstractCellProperty::AbstractCellProperty