File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 12526ms, 84.64% of 14799ms total Dropped 745 nodes (cum <= 74ms) flat flat% sum% cum cum% 0 0% 0% 14759ms 99.73% __libc_start_call_main 0 0% 0% 14759ms 99.73% __libc_start_main_impl 0 0% 0% 14759ms 99.73% _start 0 0% 0% 14743ms 99.62% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 14743ms 99.62% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 14743ms 99.62% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 14743ms 99.62% main 0 0% 0% 14708ms 99.39% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 14708ms 99.39% CxxTest::TestRunner::runTest (inline) 0 0% 0% 14708ms 99.39% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 14687ms 99.24% AbstractCellBasedSimulation::Solve 1ms 0.0068% 0.0068% 11285ms 76.26% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.014% 0.02% 7192ms 48.60% AbstractCellBasedSimulation::DoCellBirth 2ms 0.014% 0.034% 7133ms 48.20% Cell::ReadyToDivide 1ms 0.0068% 0.041% 7064ms 47.73% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0068% 0.047% 6952ms 46.98% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 7ms 0.047% 0.095% 6946ms 46.94% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.02% 0.11% 6934ms 46.85% CellCycleModelOdeHandler::SolveOdeToTime 55ms 0.37% 0.49% 6806ms 45.99% AbstractOneStepIvpOdeSolver::InternalSolve 828ms 5.59% 6.08% 6093ms 41.17% RungeKutta4IvpOdeSolver::CalculateNextYValue 1939ms 13.10% 19.18% 5128ms 34.65% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 19.18% 4000ms 27.03% MeshBasedCellPopulation::Update 51ms 0.34% 19.53% 3204ms 21.65% AbstractCellProperty::IsType (inline) 2ms 0.014% 19.54% 3074ms 20.77% Cylindrical2dMesh::ReMesh 262ms 1.77% 21.31% 2106ms 14.23% AbstractCellProperty::IsSame 0 0% 21.31% 1858ms 12.55% OffLatticeSimulation::UpdateCellLocationsAndTopology 177ms 1.20% 22.51% 1844ms 12.46% std::type_info::operator== (inline) 1763ms 11.91% 34.42% 1763ms 11.91% __strcmp_evex 0 0% 34.42% 1750ms 11.83% MutableMesh::ReMesh 0 0% 34.42% 1623ms 10.97% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.027% 34.45% 1598ms 10.80% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 34.45% 1540ms 10.41% AbstractCellPopulation::WriteResultsToFiles 663ms 4.48% 38.93% 1375ms 9.29% std::_Rb_tree::_M_lower_bound (inline) 131ms 0.89% 39.81% 1297ms 8.76% TetrahedralMesh::EdgeIterator::operator++ 52ms 0.35% 40.16% 1052ms 7.11% std::_Rb_tree::find (inline) 0 0% 40.16% 903ms 6.10% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.014% 40.18% 882ms 5.96% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 13ms 0.088% 40.27% 852ms 5.76% TetrahedralMesh::ImportFromMesher 32ms 0.22% 40.48% 811ms 5.48% operator new 8ms 0.054% 40.54% 801ms 5.41% MeshBasedCellPopulation::SpringIterator::operator++ 186ms 1.26% 41.79% 766ms 5.18% __GI___libc_malloc 10ms 0.068% 41.86% 750ms 5.07% std::set::insert (inline) 7ms 0.047% 41.91% 740ms 5.00% std::_Rb_tree::_M_insert_unique 19ms 0.13% 42.04% 706ms 4.77% std::__new_allocator::allocate (inline) 0 0% 42.04% 704ms 4.76% std::allocator_traits::allocate (inline) 1ms 0.0068% 42.04% 679ms 4.59% triangulate 0 0% 42.04% 650ms 4.39% std::set::count (inline) 0 0% 42.04% 614ms 4.15% delaunay 5ms 0.034% 42.08% 614ms 4.15% divconqdelaunay 571ms 3.86% 45.94% 571ms 3.86% WntCellCycleOdeSystem::CalculateStoppingEvent 3ms 0.02% 45.96% 554ms 3.74% CellPopulationElementWriter::Visit 4ms 0.027% 45.98% 553ms 3.74% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 272ms 1.84% 47.82% 519ms 3.51% _int_malloc 42ms 0.28% 48.10% 500ms 3.38% std::map::operator[] (partial-inline) 2ms 0.014% 48.12% 499ms 3.37% AbstractTwoBodyInteractionForce::AddForceContribution 155ms 1.05% 49.17% 493ms 3.33% __dynamic_cast 14ms 0.095% 49.26% 464ms 3.14% std::less::operator() (inline) 7ms 0.047% 49.31% 461ms 3.12% CellPropertyCollection::GetPropertiesType (inline) 0 0% 49.31% 461ms 3.12% std::_Rb_tree::_M_create_node (inline) 458ms 3.09% 52.40% 458ms 3.09% std::_Rb_tree::_S_right (inline) 5ms 0.034% 52.44% 456ms 3.08% MeshBasedCellPopulation::AcceptCellWriter 450ms 3.04% 55.48% 450ms 3.04% std::operator< (inline) 15ms 0.1% 55.58% 444ms 3.00% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 55.58% 439ms 2.97% std::_Rb_tree::_M_get_node (inline) 29ms 0.2% 55.77% 438ms 2.96% std::_Rb_tree::_M_insert_ (inline) 27ms 0.18% 55.96% 431ms 2.91% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 0 0% 55.96% 416ms 2.81% std::_Rb_tree::_Alloc_node::operator() (inline) 6ms 0.041% 56.00% 410ms 2.77% Element::Element 0 0% 56.00% 398ms 2.69% std::map::find (inline) 9ms 0.061% 56.06% 394ms 2.66% Cylindrical2dMesh::ReconstructCylindricalMesh 1ms 0.0068% 56.06% 394ms 2.66% std::ostream::operator<< (inline) 2ms 0.014% 56.08% 390ms 2.64% AbstractCellProperty::IsSubType (inline) 62ms 0.42% 56.50% 390ms 2.64% std::ostream::_M_insert 0 0% 56.50% 385ms 2.60% std::_Rb_tree::lower_bound (inline) 0 0% 56.50% 385ms 2.60% std::map::lower_bound (inline) 6ms 0.041% 56.54% 368ms 2.49% MutableMesh::ReIndex 9ms 0.061% 56.60% 367ms 2.48% Element::RegisterWithNodes (inline) 7ms 0.047% 56.65% 357ms 2.41% Node::AddElement 216ms 1.46% 58.11% 342ms 2.31% AbstractCellMutationState::AbstractCellMutationState 103ms 0.7% 58.80% 331ms 2.24% __GI___libc_free 9ms 0.061% 58.86% 317ms 2.14% Cylindrical2dMesh::CorrectNonPeriodicMesh 13ms 0.088% 58.95% 300ms 2.03% Node::RemoveElement 1ms 0.0068% 58.96% 300ms 2.03% std::set::erase (inline) 9ms 0.061% 59.02% 299ms 2.02% std::_Rb_tree::erase 81ms 0.55% 59.56% 298ms 2.01% std::_Rb_tree::_M_erase 18ms 0.12% 59.69% 296ms 2.00% divconqrecurse 122ms 0.82% 60.51% 295ms 1.99% std::_Rb_tree::_M_get_insert_unique_pos 13ms 0.088% 60.60% 286ms 1.93% std::__new_allocator::deallocate (inline) 0 0% 60.60% 285ms 1.93% std::allocator_traits::deallocate (inline) 0 0% 60.60% 282ms 1.91% std::_Rb_tree::_M_drop_node (inline) 16ms 0.11% 60.71% 276ms 1.86% std::_Rb_tree::~_Rb_tree (inline) 80ms 0.54% 61.25% 271ms 1.83% mergehulls 267ms 1.80% 63.05% 267ms 1.80% [libchaste_cell_based.so] 1ms 0.0068% 63.06% 266ms 1.80% std::_Vector_base::_M_allocate (inline) 0 0% 63.06% 258ms 1.74% std::set::~set (inline) 4ms 0.027% 63.09% 255ms 1.72% Cell::GetCellProliferativeType 2ms 0.014% 63.10% 252ms 1.70% LegacyCellProliferativeTypesWriter::VisitCell 117ms 0.79% 63.89% 249ms 1.68% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 63.89% 246ms 1.66% std::_Rb_tree::_M_put_node (inline) 6ms 0.041% 63.93% 245ms 1.66% Cell::GetMutationState 17ms 0.11% 64.04% 234ms 1.58% Element::ResetIndex 4ms 0.027% 64.07% 232ms 1.57% NodeLocationWriter::Visit 13ms 0.088% 64.16% 230ms 1.55% std::_Rb_tree::_Rb_tree (partial-inline) 184ms 1.24% 65.40% 228ms 1.54% _int_free 7ms 0.047% 65.45% 220ms 1.49% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.014% 65.46% 213ms 1.44% std::set::set (inline) 206ms 1.39% 66.86% 211ms 1.43% std::vector::operator[] (inline) 2ms 0.014% 66.87% 205ms 1.39% alternateaxes 16ms 0.11% 66.98% 205ms 1.39% std::num_put::_M_insert_float 185ms 1.25% 68.23% 202ms 1.36% vertexmedian 17ms 0.11% 68.34% 200ms 1.35% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 68.34% 200ms 1.35% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 68.34% 199ms 1.34% TetrahedralMesh::RefreshJacobianCachedData 85ms 0.57% 68.92% 198ms 1.34% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 78ms 0.53% 69.44% 194ms 1.31% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 29ms 0.2% 69.64% 191ms 1.29% std::_Rb_tree::_M_copy (inline) 7ms 0.047% 69.69% 187ms 1.26% AbstractCellPopulation::IsCellAttachedToLocationIndex 10ms 0.068% 69.75% 186ms 1.26% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 16ms 0.11% 69.86% 186ms 1.26% AbstractTetrahedralElement::CalculateJacobian 43ms 0.29% 70.15% 185ms 1.25% ApcOneHitCellMutationState::ApcOneHitCellMutationState 7ms 0.047% 70.20% 185ms 1.25% std::_Rb_tree::_M_erase_aux (inline) 6ms 0.041% 70.24% 184ms 1.24% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 11ms 0.074% 70.32% 180ms 1.22% std::vector::push_back (inline) 13ms 0.088% 70.40% 179ms 1.21% Element::MarkAsDeleted 6ms 0.041% 70.44% 175ms 1.18% AbstractTetrahedralElement::CalculateInverseJacobian 11ms 0.074% 70.52% 171ms 1.16% TetrahedralMesh::Clear 1ms 0.0068% 70.53% 170ms 1.15% std::__cxx11::collate::do_transform 1ms 0.0068% 70.53% 165ms 1.11% ___vsnprintf 1ms 0.0068% 70.54% 164ms 1.11% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 70.54% 164ms 1.11% __vsnprintf_internal (inline) 9ms 0.061% 70.60% 164ms 1.11% std::vector::_M_realloc_insert 15ms 0.1% 70.70% 162ms 1.09% __printf_buffer 124ms 0.84% 71.54% 157ms 1.06% AbstractElement::GetNodeGlobalIndex 38ms 0.26% 71.80% 156ms 1.05% std::_Rb_tree::_M_clone_node (inline) 3ms 0.02% 71.82% 152ms 1.03% MeshBasedCellPopulation::GetDampingConstant 0 0% 71.82% 149ms 1.01% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 71.82% 146ms 0.99% OffLatticeSimulation::ApplyBoundaries 101ms 0.68% 72.50% 145ms 0.98% malloc_consolidate 12ms 0.081% 72.58% 144ms 0.97% AbstractTetrahedralElement::RefreshJacobian 2ms 0.014% 72.59% 141ms 0.95% __printf_fp_l_buffer 0 0% 72.59% 141ms 0.95% __printf_fp_spec (inline) 0 0% 72.59% 139ms 0.94% Cell::HasCellProperty (inline) 8ms 0.054% 72.65% 139ms 0.94% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 4ms 0.027% 72.67% 138ms 0.93% CellPropertyCollection::HasProperty 60ms 0.41% 73.08% 137ms 0.93% __printf_fp_buffer_1 130ms 0.88% 73.96% 130ms 0.88% [libchaste_crypt.so] 28ms 0.19% 74.15% 123ms 0.83% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 2ms 0.014% 74.16% 123ms 0.83% CellProliferativeTypesWriter::VisitCell 1ms 0.0068% 74.17% 122ms 0.82% AbstractTetrahedralElement::AbstractTetrahedralElement 36ms 0.24% 74.41% 122ms 0.82% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 122ms 0.82% 75.23% 122ms 0.82% unlink_chunk 120ms 0.81% 76.05% 120ms 0.81% std::_Rb_tree_insert_and_rebalance 5ms 0.034% 76.08% 113ms 0.76% MeshBasedCellPopulation::SpringsEnd (inline) 67ms 0.45% 76.53% 111ms 0.75% std::_Rb_tree::equal_range (inline) 47ms 0.32% 76.85% 110ms 0.74% AbstractElement::GetNodeLocation 110ms 0.74% 77.59% 110ms 0.74% incircle 1ms 0.0068% 77.60% 109ms 0.74% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 67ms 0.45% 78.05% 108ms 0.73% Cylindrical2dMesh::GetVectorFromAtoB 3ms 0.02% 78.07% 106ms 0.72% boost::numeric::ublas::vector_assign (inline) 5ms 0.034% 78.11% 105ms 0.71% Node::~Node 3ms 0.02% 78.13% 105ms 0.71% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 20ms 0.14% 78.26% 104ms 0.7% TetrahedralMesh::EdgesEnd (partial-inline) 93ms 0.63% 78.89% 104ms 0.7% vertexsort 102ms 0.69% 79.58% 102ms 0.69% AbstractCellMutationState::~AbstractCellMutationState 100ms 0.68% 80.26% 100ms 0.68% std::type_info::name (inline) 0 0% 80.26% 96ms 0.65% AbstractCellBasedWriter::OpenOutputFileForAppend 12ms 0.081% 80.34% 96ms 0.65% boost::detail::shared_count::~shared_count (inline) 0 0% 80.34% 96ms 0.65% boost::shared_ptr::~shared_ptr (inline) 1ms 0.0068% 80.34% 95ms 0.64% OutputFileHandler::OpenOutputFile 93ms 0.63% 80.97% 94ms 0.64% std::vector::size (inline) 0 0% 80.97% 93ms 0.63% Cell::SetCellProliferativeType 24ms 0.16% 81.13% 93ms 0.63% std::num_put::_M_insert_int 89ms 0.6% 81.74% 89ms 0.6% Node::GetIndex 0 0% 81.74% 88ms 0.59% AbstractCellBasedSimulation::DoCellRemoval (inline) 26ms 0.18% 81.91% 88ms 0.59% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 2ms 0.014% 81.92% 87ms 0.59% boost::numeric::ublas::c_vector::c_vector (inline) 2ms 0.014% 81.94% 85ms 0.57% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 10ms 0.068% 82.01% 83ms 0.56% MeshBasedCellPopulation::SpringIterator::SpringIterator 31ms 0.21% 82.22% 83ms 0.56% boost::numeric::ublas::indexing_vector_assign 3ms 0.02% 82.24% 79ms 0.53% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 54ms 0.36% 82.60% 78ms 0.53% TetrahedralMesh::EdgeIterator::EdgeIterator 78ms 0.53% 83.13% 78ms 0.53% boost::shared_ptr::operator-> (inline) 75ms 0.51% 83.63% 77ms 0.52% boost::detail::sp_counted_base::release 0 0% 83.63% 76ms 0.51% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 75ms 0.51% 84.14% 75ms 0.51% counterclockwise 74ms 0.5% 84.64% 74ms 0.5% TetrahedralMesh::EdgeIterator::operator!= (partial-inline)