File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16164ms, 85.74% of 18853ms total Dropped 819 nodes (cum <= 94.27ms) flat flat% sum% cum cum% 0 0% 0% 18805ms 99.75% __libc_start_call_main 0 0% 0% 18805ms 99.75% __libc_start_main_impl 0 0% 0% 18805ms 99.75% _start 0 0% 0% 18783ms 99.63% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 18783ms 99.63% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 18783ms 99.63% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 18783ms 99.63% main 0 0% 0% 18750ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 18750ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 18750ms 99.45% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 18725ms 99.32% AbstractCellBasedSimulation::Solve 0 0% 0% 14309ms 75.90% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0053% 0.0053% 8703ms 46.16% AbstractCellBasedSimulation::DoCellBirth 11ms 0.058% 0.064% 8597ms 45.60% Cell::ReadyToDivide 0 0% 0.064% 8540ms 45.30% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0053% 0.069% 8400ms 44.56% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 11ms 0.058% 0.13% 8394ms 44.52% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0053% 0.13% 8378ms 44.44% CellCycleModelOdeHandler::SolveOdeToTime 57ms 0.3% 0.43% 8172ms 43.35% AbstractOneStepIvpOdeSolver::InternalSolve 859ms 4.56% 4.99% 7326ms 38.86% RungeKutta4IvpOdeSolver::CalculateNextYValue 3222ms 17.09% 22.08% 6202ms 32.90% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.011% 22.09% 5465ms 28.99% MeshBasedCellPopulation::Update 2ms 0.011% 22.10% 4177ms 22.16% Cylindrical2dMesh::ReMesh 366ms 1.94% 24.04% 3108ms 16.49% AbstractCellProperty::IsType (inline) 2ms 0.011% 24.05% 2556ms 13.56% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0053% 24.06% 2312ms 12.26% MutableMesh::ReMesh 0 0% 24.06% 2219ms 11.77% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.021% 24.08% 2169ms 11.50% AbstractNumericalMethod::ComputeForcesIncludingDamping 872ms 4.63% 28.71% 1917ms 10.17% std::_Rb_tree::_M_lower_bound (inline) 0 0% 28.71% 1855ms 9.84% AbstractCellPopulation::WriteResultsToFiles 172ms 0.91% 29.62% 1840ms 9.76% TetrahedralMesh::EdgeIterator::operator++ 48ms 0.25% 29.87% 1517ms 8.05% std::_Rb_tree::find (inline) 0 0% 29.87% 1245ms 6.60% MeshBasedCellPopulation::UpdateNodePairs 172ms 0.91% 30.79% 1215ms 6.44% AbstractCellProperty::IsSame 50ms 0.27% 31.05% 1210ms 6.42% operator new 1ms 0.0053% 31.06% 1164ms 6.17% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 7ms 0.037% 31.09% 1160ms 6.15% TetrahedralMesh::ImportFromMesher 447ms 2.37% 33.46% 1144ms 6.07% __GI___libc_malloc 13ms 0.069% 33.53% 1124ms 5.96% MeshBasedCellPopulation::SpringIterator::operator++ 17ms 0.09% 33.62% 1112ms 5.90% std::set::insert (inline) 15ms 0.08% 33.70% 1095ms 5.81% std::_Rb_tree::_M_insert_unique 15ms 0.08% 33.78% 1043ms 5.53% std::type_info::operator== (inline) 1039ms 5.51% 39.29% 1039ms 5.51% __strcmp_evex 23ms 0.12% 39.42% 971ms 5.15% std::__new_allocator::allocate (inline) 0 0% 39.42% 966ms 5.12% std::allocator_traits::allocate (inline) 0 0% 39.42% 961ms 5.10% std::set::count (inline) 932ms 4.94% 44.36% 932ms 4.94% [libchaste_cell_based.so] 2ms 0.011% 44.37% 856ms 4.54% triangulate 0 0% 44.37% 773ms 4.10% delaunay 3ms 0.016% 44.39% 772ms 4.09% divconqdelaunay 11ms 0.058% 44.44% 726ms 3.85% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 711ms 3.77% 48.22% 711ms 3.77% std::_Rb_tree::_S_right (inline) 1ms 0.0053% 48.22% 696ms 3.69% AbstractTwoBodyInteractionForce::AddForceContribution 53ms 0.28% 48.50% 695ms 3.69% std::_Rb_tree::_M_insert_ (inline) 78ms 0.41% 48.92% 669ms 3.55% std::map::operator[] (partial-inline) 0 0% 48.92% 666ms 3.53% std::_Rb_tree::_M_create_node (inline) 9ms 0.048% 48.96% 644ms 3.42% CellPopulationElementWriter::Visit 644ms 3.42% 52.38% 644ms 3.42% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 52.38% 641ms 3.40% std::_Rb_tree::_M_get_node (inline) 21ms 0.11% 52.49% 625ms 3.32% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 168ms 0.89% 53.38% 625ms 3.32% __dynamic_cast 359ms 1.90% 55.29% 602ms 3.19% _int_malloc 0 0% 55.29% 598ms 3.17% std::_Rb_tree::_Alloc_node::operator() (inline) 4ms 0.021% 55.31% 588ms 3.12% CellPropertyCollection::GetPropertiesType (inline) 17ms 0.09% 55.40% 580ms 3.08% AbstractCellPopulation::GetCellUsingLocationIndex 300ms 1.59% 56.99% 576ms 3.06% AbstractCellMutationState::AbstractCellMutationState 4ms 0.021% 57.01% 567ms 3.01% Element::Element 6ms 0.032% 57.04% 563ms 2.99% MeshBasedCellPopulation::AcceptCellWriter 0 0% 57.04% 553ms 2.93% std::map::find (inline) 6ms 0.032% 57.07% 542ms 2.87% Element::RegisterWithNodes (inline) 22ms 0.12% 57.19% 534ms 2.83% Node::AddElement 14ms 0.074% 57.26% 524ms 2.78% std::less::operator() (inline) 119ms 0.63% 57.90% 515ms 2.73% __GI___libc_free 20ms 0.11% 58.00% 512ms 2.72% Cylindrical2dMesh::ReconstructCylindricalMesh 510ms 2.71% 60.71% 510ms 2.71% std::operator< (inline) 5ms 0.027% 60.73% 505ms 2.68% MutableMesh::ReIndex 0 0% 60.73% 491ms 2.60% std::_Rb_tree::lower_bound (inline) 0 0% 60.73% 491ms 2.60% std::map::lower_bound (inline) 6ms 0.032% 60.76% 472ms 2.50% Cylindrical2dMesh::CorrectNonPeriodicMesh 69ms 0.37% 61.13% 454ms 2.41% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.011% 61.14% 453ms 2.40% AbstractCellProperty::IsSubType (inline) 0 0% 61.14% 441ms 2.34% std::_Rb_tree::_M_drop_node (inline) 92ms 0.49% 61.63% 440ms 2.33% std::_Rb_tree::_M_erase 0 0% 61.63% 436ms 2.31% std::set::~set (inline) 0 0% 61.63% 407ms 2.16% std::ostream::operator<< (inline) 40ms 0.21% 61.84% 405ms 2.15% std::ostream::_M_insert 15ms 0.08% 61.92% 401ms 2.13% std::__new_allocator::deallocate (inline) 0 0% 61.92% 399ms 2.12% std::allocator_traits::deallocate (inline) 398ms 2.11% 64.03% 398ms 2.11% [libchaste_crypt.so] 326ms 1.73% 65.76% 394ms 2.09% _int_free 11ms 0.058% 65.82% 388ms 2.06% std::_Rb_tree::erase 14ms 0.074% 65.89% 387ms 2.05% divconqrecurse 156ms 0.83% 66.72% 387ms 2.05% std::_Rb_tree::_M_get_insert_unique_pos 1ms 0.0053% 66.73% 385ms 2.04% std::set::erase (inline) 10ms 0.053% 66.78% 372ms 1.97% Node::RemoveElement 5ms 0.027% 66.81% 369ms 1.96% Cell::GetMutationState 108ms 0.57% 67.38% 361ms 1.91% mergehulls 0 0% 67.38% 347ms 1.84% std::_Rb_tree::_M_put_node (inline) 158ms 0.84% 68.22% 344ms 1.82% __cxxabiv1::__si_class_type_info::__do_dyncast 26ms 0.14% 68.36% 330ms 1.75% Element::ResetIndex 1ms 0.0053% 68.36% 326ms 1.73% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 68.36% 325ms 1.72% std::_Vector_base::_M_allocate (inline) 40ms 0.21% 68.57% 323ms 1.71% AbstractCellPopulation::Iterator::IsRealCell (inline) 22ms 0.12% 68.69% 311ms 1.65% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 1ms 0.0053% 68.69% 309ms 1.64% LegacyCellProliferativeTypesWriter::VisitCell 6ms 0.032% 68.73% 303ms 1.61% boost::detail::shared_count::~shared_count (inline) 0 0% 68.73% 303ms 1.61% boost::shared_ptr::~shared_ptr (inline) 289ms 1.53% 70.26% 292ms 1.55% boost::detail::sp_counted_base::release 1ms 0.0053% 70.26% 291ms 1.54% Cell::GetCellProliferativeType 1ms 0.0053% 70.27% 283ms 1.50% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 14ms 0.074% 70.34% 277ms 1.47% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0053% 70.35% 277ms 1.47% ApcOneHitCellMutationState::ApcOneHitCellMutationState 6ms 0.032% 70.38% 276ms 1.46% NodeLocationWriter::Visit 0 0% 70.38% 273ms 1.45% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 17ms 0.09% 70.47% 265ms 1.41% std::vector::push_back (inline) 35ms 0.19% 70.66% 264ms 1.40% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 0 0% 70.66% 259ms 1.37% TetrahedralMesh::RefreshJacobianCachedData 257ms 1.36% 72.02% 257ms 1.36% [libchaste_mesh.so] 243ms 1.29% 73.31% 255ms 1.35% std::vector::operator[] (inline) 8ms 0.042% 73.35% 254ms 1.35% alternateaxes 9ms 0.048% 73.40% 252ms 1.34% AbstractTetrahedralElement::CalculateJacobian 5ms 0.027% 73.43% 247ms 1.31% AbstractCellPopulation::IsCellAttachedToLocationIndex 21ms 0.11% 73.54% 246ms 1.30% std::_Rb_tree::_M_erase_aux (inline) 8ms 0.042% 73.58% 245ms 1.30% std::_Rb_tree::_Rb_tree (partial-inline) 214ms 1.14% 74.71% 242ms 1.28% vertexmedian 17ms 0.09% 74.81% 240ms 1.27% std::num_put::_M_insert_float 12ms 0.064% 74.87% 236ms 1.25% std::vector::_M_realloc_insert 2ms 0.011% 74.88% 230ms 1.22% MeshBasedCellPopulation::GetDampingConstant 1ms 0.0053% 74.88% 229ms 1.21% std::set::set (inline) 1ms 0.0053% 74.89% 226ms 1.20% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 74.89% 223ms 1.18% OffLatticeSimulation::ApplyBoundaries 3ms 0.016% 74.91% 221ms 1.17% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 6ms 0.032% 74.94% 221ms 1.17% AbstractTetrahedralElement::CalculateInverseJacobian 30ms 0.16% 75.10% 211ms 1.12% std::_Rb_tree::_M_copy (inline) 5ms 0.027% 75.12% 210ms 1.11% Element::MarkAsDeleted 3ms 0.016% 75.14% 207ms 1.10% TetrahedralMesh::Clear 3ms 0.016% 75.16% 196ms 1.04% std::__cxx11::collate::do_transform 1ms 0.0053% 75.16% 187ms 0.99% ___vsnprintf 0 0% 75.16% 186ms 0.99% __vsnprintf_internal (inline) 17ms 0.09% 75.25% 184ms 0.98% __printf_buffer 20ms 0.11% 75.36% 176ms 0.93% AbstractTetrahedralElement::RefreshJacobian 74ms 0.39% 75.75% 175ms 0.93% std::_Rb_tree::_M_clone_node (inline) 9ms 0.048% 75.80% 166ms 0.88% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 163ms 0.86% 76.66% 163ms 0.86% std::vector::size (inline) 67ms 0.36% 77.02% 160ms 0.85% AbstractElement::GetNodeGlobalIndex 133ms 0.71% 77.72% 158ms 0.84% malloc_consolidate 28ms 0.15% 77.87% 154ms 0.82% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 7ms 0.037% 77.91% 151ms 0.8% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.0053% 77.91% 151ms 0.8% __printf_fp_spec (inline) 4ms 0.021% 77.93% 150ms 0.8% __printf_fp_l_buffer 149ms 0.79% 78.72% 149ms 0.79% incircle 149ms 0.79% 79.52% 149ms 0.79% std::_Rb_tree_insert_and_rebalance 4ms 0.021% 79.54% 148ms 0.79% CellPropertyCollection::HasProperty 0 0% 79.54% 145ms 0.77% Cell::HasCellProperty (inline) 61ms 0.32% 79.86% 144ms 0.76% __printf_fp_buffer_1 142ms 0.75% 80.61% 142ms 0.75% AbstractCellProperty::AbstractCellProperty 2ms 0.011% 80.62% 140ms 0.74% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 0 0% 80.62% 139ms 0.74% AbstractCellBasedSimulation::DoCellRemoval (inline) 139ms 0.74% 81.36% 139ms 0.74% std::type_info::name (inline) 0 0% 81.36% 138ms 0.73% CellProliferativeTypesWriter::VisitCell 3ms 0.016% 81.38% 135ms 0.72% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 84ms 0.45% 81.82% 135ms 0.72% std::_Rb_tree::equal_range (inline) 6ms 0.032% 81.85% 129ms 0.68% Cylindrical2dMesh::CreateMirrorNodes 7ms 0.037% 81.89% 129ms 0.68% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 0 0% 81.89% 127ms 0.67% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 44ms 0.23% 82.12% 126ms 0.67% AbstractElement::GetNodeLocation 116ms 0.62% 82.74% 126ms 0.67% vertexsort 2ms 0.011% 82.75% 125ms 0.66% boost::numeric::ublas::vector_assign (inline) 13ms 0.069% 82.82% 123ms 0.65% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 82.82% 119ms 0.63% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 1ms 0.0053% 82.83% 119ms 0.63% Node::~Node 4ms 0.021% 82.85% 116ms 0.62% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 5ms 0.027% 82.87% 114ms 0.6% Cell::SetCellProliferativeType 5ms 0.027% 82.90% 114ms 0.6% boost::numeric::ublas::c_vector::c_vector (inline) 109ms 0.58% 83.48% 109ms 0.58% std::_Rb_tree::_S_left (inline) 2ms 0.011% 83.49% 107ms 0.57% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 56ms 0.3% 83.79% 106ms 0.56% Cylindrical2dMesh::GetVectorFromAtoB 103ms 0.55% 84.33% 103ms 0.55% [libchaste_ode.so] 79ms 0.42% 84.75% 101ms 0.54% TetrahedralMesh::EdgeIterator::EdgeIterator 1ms 0.0053% 84.76% 101ms 0.54% std::vector::_M_default_append 0 0% 84.76% 101ms 0.54% std::vector::resize (inline) 1ms 0.0053% 84.76% 100ms 0.53% std::_Rb_tree::_M_emplace_hint_unique 24ms 0.13% 84.89% 100ms 0.53% std::num_put::_M_insert_int 3ms 0.016% 84.90% 97ms 0.51% MeshBasedCellPopulation::SpringsEnd (inline) 25ms 0.13% 85.04% 97ms 0.51% boost::numeric::ublas::indexing_vector_assign 96ms 0.51% 85.55% 96ms 0.51% Node::GetIndex 36ms 0.19% 85.74% 96ms 0.51% std::__ostream_insert 0 0% 85.74% 95ms 0.5% std::__new_allocator::destroy (inline) 0 0% 85.74% 95ms 0.5% std::allocator_traits::destroy (inline)