File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16260ms, 86.85% of 18721ms total Dropped 743 nodes (cum <= 93.61ms) flat flat% sum% cum cum% 0 0% 0% 18681ms 99.79% __libc_start_call_main 0 0% 0% 18681ms 99.79% __libc_start_main_impl 0 0% 0% 18681ms 99.79% _start 0 0% 0% 18660ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 18660ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 18660ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 18660ms 99.67% main 0 0% 0% 18626ms 99.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 18625ms 99.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 18625ms 99.49% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.0053% 0.0053% 18602ms 99.36% AbstractCellBasedSimulation::Solve 0 0% 0.0053% 14279ms 76.27% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.011% 0.016% 8941ms 47.76% AbstractCellBasedSimulation::DoCellBirth 6ms 0.032% 0.048% 8850ms 47.27% Cell::ReadyToDivide 0 0% 0.048% 8800ms 47.01% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.011% 0.059% 8653ms 46.22% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.043% 0.1% 8645ms 46.18% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 0.1% 8636ms 46.13% CellCycleModelOdeHandler::SolveOdeToTime 68ms 0.36% 0.46% 8460ms 45.19% AbstractOneStepIvpOdeSolver::InternalSolve 809ms 4.32% 4.79% 7571ms 40.44% RungeKutta4IvpOdeSolver::CalculateNextYValue 3470ms 18.54% 23.32% 6503ms 34.74% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0053% 23.33% 5216ms 27.86% MeshBasedCellPopulation::Update 5ms 0.027% 23.35% 3952ms 21.11% Cylindrical2dMesh::ReMesh 384ms 2.05% 25.40% 3165ms 16.91% AbstractCellProperty::IsType (inline) 0 0% 25.40% 2497ms 13.34% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 25.40% 2197ms 11.74% MutableMesh::ReMesh 1ms 0.0053% 25.41% 2169ms 11.59% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.011% 25.42% 2107ms 11.25% AbstractNumericalMethod::ComputeForcesIncludingDamping 892ms 4.76% 30.19% 1838ms 9.82% std::_Rb_tree::_M_lower_bound (inline) 0 0% 30.19% 1822ms 9.73% AbstractCellPopulation::WriteResultsToFiles 173ms 0.92% 31.11% 1788ms 9.55% TetrahedralMesh::EdgeIterator::operator++ 45ms 0.24% 31.35% 1483ms 7.92% std::_Rb_tree::find (inline) 176ms 0.94% 32.29% 1269ms 6.78% AbstractCellProperty::IsSame 0 0% 32.29% 1231ms 6.58% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.021% 32.31% 1164ms 6.22% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 63ms 0.34% 32.65% 1145ms 6.12% operator new 25ms 0.13% 32.78% 1093ms 5.84% std::type_info::operator== (inline) 13ms 0.069% 32.85% 1087ms 5.81% MeshBasedCellPopulation::SpringIterator::operator++ 7ms 0.037% 32.89% 1083ms 5.78% TetrahedralMesh::ImportFromMesher 12ms 0.064% 32.95% 1079ms 5.76% std::set::insert (inline) 1078ms 5.76% 38.71% 1078ms 5.76% __strcmp_evex 405ms 2.16% 40.87% 1069ms 5.71% __GI___libc_malloc 22ms 0.12% 40.99% 1067ms 5.70% std::_Rb_tree::_M_insert_unique 965ms 5.15% 46.15% 965ms 5.15% [libchaste_cell_based.so] 17ms 0.091% 46.24% 957ms 5.11% std::__new_allocator::allocate (inline) 0 0% 46.24% 952ms 5.09% std::allocator_traits::allocate (inline) 0 0% 46.24% 942ms 5.03% std::set::count (inline) 0 0% 46.24% 892ms 4.76% triangulate 0 0% 46.24% 805ms 4.30% delaunay 3ms 0.016% 46.25% 805ms 4.30% divconqdelaunay 10ms 0.053% 46.31% 731ms 3.90% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 46.31% 692ms 3.70% AbstractTwoBodyInteractionForce::AddForceContribution 38ms 0.2% 46.51% 689ms 3.68% std::_Rb_tree::_M_insert_ (inline) 0 0% 46.51% 664ms 3.55% std::_Rb_tree::_M_create_node (inline) 0 0% 46.51% 653ms 3.49% std::_Rb_tree::_M_get_node (inline) 643ms 3.43% 49.94% 643ms 3.43% WntCellCycleOdeSystem::CalculateStoppingEvent 6ms 0.032% 49.98% 635ms 3.39% CellPopulationElementWriter::Visit 20ms 0.11% 50.08% 631ms 3.37% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 167ms 0.89% 50.97% 624ms 3.33% __dynamic_cast 0 0% 50.97% 606ms 3.24% std::_Rb_tree::_Alloc_node::operator() (inline) 56ms 0.3% 51.27% 594ms 3.17% std::map::operator[] (partial-inline) 15ms 0.08% 51.35% 589ms 3.15% MeshBasedCellPopulation::AcceptCellWriter 580ms 3.10% 54.45% 580ms 3.10% std::_Rb_tree::_S_right (inline) 3ms 0.016% 54.47% 574ms 3.07% Element::Element 362ms 1.93% 56.40% 569ms 3.04% _int_malloc 15ms 0.08% 56.48% 564ms 3.01% Element::RegisterWithNodes (inline) 8ms 0.043% 56.52% 551ms 2.94% CellPropertyCollection::GetPropertiesType (inline) 30ms 0.16% 56.69% 544ms 2.91% Node::AddElement 0 0% 56.69% 537ms 2.87% std::map::find (inline) 258ms 1.38% 58.06% 530ms 2.83% AbstractCellMutationState::AbstractCellMutationState 25ms 0.13% 58.20% 527ms 2.82% Cylindrical2dMesh::ReconstructCylindricalMesh 10ms 0.053% 58.25% 501ms 2.68% std::less::operator() (inline) 11ms 0.059% 58.31% 500ms 2.67% AbstractCellPopulation::GetCellUsingLocationIndex 491ms 2.62% 60.93% 491ms 2.62% std::operator< (inline) 8ms 0.043% 60.97% 478ms 2.55% Cylindrical2dMesh::CorrectNonPeriodicMesh 103ms 0.55% 61.52% 477ms 2.55% __GI___libc_free 6ms 0.032% 61.56% 470ms 2.51% MutableMesh::ReIndex 0 0% 61.56% 469ms 2.51% std::_Rb_tree::_M_drop_node (inline) 0 0% 61.56% 443ms 2.37% std::_Rb_tree::lower_bound (inline) 0 0% 61.56% 443ms 2.37% std::map::lower_bound (inline) 2ms 0.011% 61.57% 439ms 2.34% std::ostream::operator<< (inline) 70ms 0.37% 61.94% 434ms 2.32% std::ostream::_M_insert 10ms 0.053% 61.99% 433ms 2.31% std::__new_allocator::deallocate (inline) 2ms 0.011% 62.01% 430ms 2.30% AbstractCellProperty::IsSubType (inline) 0 0% 62.01% 430ms 2.30% std::allocator_traits::deallocate (inline) 59ms 0.32% 62.32% 428ms 2.29% std::_Rb_tree::_M_erase 45ms 0.24% 62.56% 425ms 2.27% std::_Rb_tree::~_Rb_tree (inline) 0 0% 62.56% 405ms 2.16% std::set::~set (inline) 404ms 2.16% 64.72% 404ms 2.16% [libchaste_crypt.so] 16ms 0.085% 64.80% 395ms 2.11% divconqrecurse 313ms 1.67% 66.48% 368ms 1.97% _int_free 0 0% 66.48% 367ms 1.96% std::_Rb_tree::_M_put_node (inline) 12ms 0.064% 66.54% 366ms 1.96% std::_Rb_tree::erase 0 0% 66.54% 366ms 1.96% std::set::erase (inline) 13ms 0.069% 66.61% 365ms 1.95% Node::RemoveElement 99ms 0.53% 67.14% 364ms 1.94% mergehulls 148ms 0.79% 67.93% 356ms 1.90% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 67.93% 334ms 1.78% LegacyCellProliferativeTypesWriter::VisitCell 5ms 0.027% 67.96% 331ms 1.77% Cell::GetMutationState 14ms 0.075% 68.03% 328ms 1.75% Element::ResetIndex 146ms 0.78% 68.81% 316ms 1.69% __cxxabiv1::__si_class_type_info::__do_dyncast 25ms 0.13% 68.94% 310ms 1.66% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 7ms 0.037% 68.98% 303ms 1.62% boost::detail::shared_count::~shared_count (inline) 0 0% 68.98% 303ms 1.62% boost::shared_ptr::~shared_ptr (inline) 1ms 0.0053% 68.99% 300ms 1.60% std::_Vector_base::_M_allocate (inline) 4ms 0.021% 69.01% 296ms 1.58% Cell::GetCellProliferativeType 0 0% 69.01% 289ms 1.54% NodeLocationWriter::Visit 280ms 1.50% 70.50% 282ms 1.51% boost::detail::sp_counted_base::release 0 0% 70.50% 281ms 1.50% AbstractCellPopulation::Iterator::operator++ (inline) 28ms 0.15% 70.65% 280ms 1.50% AbstractCellPopulation::Iterator::IsRealCell (inline) 2ms 0.011% 70.66% 276ms 1.47% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 10ms 0.053% 70.72% 275ms 1.47% AbstractCellPopulation::GetLocationIndexUsingCell 31ms 0.17% 70.88% 268ms 1.43% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 2ms 0.011% 70.89% 264ms 1.41% ApcOneHitCellMutationState::ApcOneHitCellMutationState 4ms 0.021% 70.92% 261ms 1.39% alternateaxes 12ms 0.064% 70.98% 259ms 1.38% std::_Rb_tree::_Rb_tree (partial-inline) 248ms 1.32% 72.30% 256ms 1.37% std::vector::operator[] (inline) 232ms 1.24% 73.54% 255ms 1.36% vertexmedian 6ms 0.032% 73.58% 250ms 1.34% std::vector::push_back (inline) 1ms 0.0053% 73.58% 248ms 1.32% std::set::set (inline) 245ms 1.31% 74.89% 245ms 1.31% [libchaste_mesh.so] 13ms 0.069% 74.96% 240ms 1.28% std::_Rb_tree::_M_erase_aux (inline) 14ms 0.075% 75.03% 239ms 1.28% std::num_put::_M_insert_float 5ms 0.027% 75.06% 236ms 1.26% AbstractCellPopulation::IsCellAttachedToLocationIndex 25ms 0.13% 75.19% 230ms 1.23% std::_Rb_tree::_M_copy (inline) 13ms 0.069% 75.26% 230ms 1.23% std::vector::_M_realloc_insert 0 0% 75.26% 226ms 1.21% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 13ms 0.069% 75.33% 225ms 1.20% AbstractTetrahedralElement::CalculateJacobian 0 0% 75.33% 216ms 1.15% OffLatticeSimulation::ApplyBoundaries 4ms 0.021% 75.35% 212ms 1.13% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 75.35% 210ms 1.12% TetrahedralMesh::RefreshJacobianCachedData 87ms 0.46% 75.82% 199ms 1.06% std::_Rb_tree::_M_clone_node (inline) 8ms 0.043% 75.86% 197ms 1.05% std::__cxx11::collate::do_transform 11ms 0.059% 75.92% 195ms 1.04% Element::MarkAsDeleted 4ms 0.021% 75.94% 192ms 1.03% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.0053% 75.95% 186ms 0.99% ___vsnprintf 0 0% 75.95% 186ms 0.99% __vsnprintf_internal (inline) 4ms 0.021% 75.97% 185ms 0.99% MeshBasedCellPopulation::GetDampingConstant 2ms 0.011% 75.98% 181ms 0.97% AbstractCentreBasedCellPopulation::GetDampingConstant 19ms 0.1% 76.08% 181ms 0.97% __printf_buffer 166ms 0.89% 76.97% 166ms 0.89% std::_Rb_tree_insert_and_rebalance 163ms 0.87% 77.84% 163ms 0.87% std::vector::size (inline) 18ms 0.096% 77.93% 162ms 0.87% AbstractTetrahedralElement::RefreshJacobian 158ms 0.84% 78.78% 158ms 0.84% std::type_info::name (inline) 156ms 0.83% 79.61% 156ms 0.83% incircle 5ms 0.027% 79.64% 156ms 0.83% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 27ms 0.14% 79.78% 155ms 0.83% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 5ms 0.027% 79.81% 147ms 0.79% __printf_fp_l_buffer 0 0% 79.81% 147ms 0.79% __printf_fp_spec (inline) 147ms 0.79% 80.59% 147ms 0.79% std::_Rb_tree::_S_left (inline) 3ms 0.016% 80.61% 144ms 0.77% boost::numeric::ublas::vector_assign (inline) 50ms 0.27% 80.88% 141ms 0.75% AbstractElement::GetNodeGlobalIndex 0 0% 80.88% 141ms 0.75% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 3ms 0.016% 80.89% 141ms 0.75% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 119ms 0.64% 81.53% 141ms 0.75% malloc_consolidate 125ms 0.67% 82.20% 140ms 0.75% vertexsort 138ms 0.74% 82.93% 138ms 0.74% AbstractCellProperty::AbstractCellProperty 0 0% 82.93% 138ms 0.74% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 64ms 0.34% 83.28% 138ms 0.74% __printf_fp_buffer_1 1ms 0.0053% 83.28% 136ms 0.73% TetrahedralMesh::Clear 2ms 0.011% 83.29% 135ms 0.72% AbstractTetrahedralElement::AbstractTetrahedralElement 77ms 0.41% 83.70% 134ms 0.72% Cylindrical2dMesh::GetVectorFromAtoB 1ms 0.0053% 83.71% 133ms 0.71% CellProliferativeTypesWriter::VisitCell 2ms 0.011% 83.72% 132ms 0.71% CellPropertyCollection::HasProperty 0 0% 83.72% 129ms 0.69% Cell::HasCellProperty (inline) 6ms 0.032% 83.75% 129ms 0.69% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 46ms 0.25% 84.00% 128ms 0.68% AbstractElement::GetNodeLocation 20ms 0.11% 84.10% 125ms 0.67% TetrahedralMesh::EdgesEnd 2ms 0.011% 84.11% 124ms 0.66% MeshBasedCellPopulation::SpringsEnd (inline) 6ms 0.032% 84.15% 124ms 0.66% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 84.15% 120ms 0.64% AbstractCellBasedSimulation::DoCellRemoval (inline) 6ms 0.032% 84.18% 117ms 0.62% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 4ms 0.021% 84.20% 117ms 0.62% std::_Rb_tree_const_iterator::operator++ (inline) 6ms 0.032% 84.23% 115ms 0.61% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 59ms 0.32% 84.55% 115ms 0.61% std::_Rb_tree::equal_range (inline) 6ms 0.032% 84.58% 113ms 0.6% Cell::SetCellProliferativeType 112ms 0.6% 85.18% 112ms 0.6% std::_Rb_tree_increment 105ms 0.56% 85.74% 105ms 0.56% [libchaste_ode.so] 0 0% 85.74% 103ms 0.55% std::_Rb_tree::_M_destroy_node (inline) 0 0% 85.74% 103ms 0.55% std::__new_allocator::destroy (inline) 0 0% 85.74% 103ms 0.55% std::allocator_traits::destroy (inline) 36ms 0.19% 85.93% 102ms 0.54% boost::numeric::ublas::indexing_vector_assign 1ms 0.0053% 85.94% 101ms 0.54% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 78ms 0.42% 86.35% 100ms 0.53% TetrahedralMesh::EdgeIterator::EdgeIterator 29ms 0.15% 86.51% 100ms 0.53% std::num_put::_M_insert_int 46ms 0.25% 86.75% 99ms 0.53% std::__ostream_insert 16ms 0.085% 86.84% 97ms 0.52% MeshBasedCellPopulation::SpringIterator::SpringIterator 3ms 0.016% 86.85% 95ms 0.51% std::_Rb_tree::_M_emplace_hint_unique