File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16573ms, 83.86% of 19762ms total Dropped 753 nodes (cum <= 98.81ms) flat flat% sum% cum cum% 0 0% 0% 19719ms 99.78% __libc_start_call_main 0 0% 0% 19719ms 99.78% __libc_start_main_impl 0 0% 0% 19719ms 99.78% _start 0 0% 0% 19701ms 99.69% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19701ms 99.69% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19701ms 99.69% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19701ms 99.69% main 0 0% 0% 19667ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19667ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19667ms 99.52% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19639ms 99.38% AbstractCellBasedSimulation::Solve 0 0% 0% 15296ms 77.40% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0051% 0.0051% 10102ms 51.12% AbstractCellBasedSimulation::DoCellBirth 7ms 0.035% 0.04% 10005ms 50.63% Cell::ReadyToDivide 6ms 0.03% 0.071% 9944ms 50.32% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.01% 0.081% 9802ms 49.60% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.04% 0.12% 9790ms 49.54% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.13% 9777ms 49.47% CellCycleModelOdeHandler::SolveOdeToTime 82ms 0.41% 0.55% 9631ms 48.73% AbstractOneStepIvpOdeSolver::InternalSolve 883ms 4.47% 5.01% 8781ms 44.43% RungeKutta4IvpOdeSolver::CalculateNextYValue 3628ms 18.36% 23.37% 7711ms 39.02% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.01% 23.38% 5064ms 25.62% MeshBasedCellPopulation::Update 195ms 0.99% 24.37% 4134ms 20.92% AbstractCellProperty::IsType (inline) 4ms 0.02% 24.39% 3942ms 19.95% Cylindrical2dMesh::ReMesh 643ms 3.25% 27.64% 2890ms 14.62% AbstractCellProperty::IsSame 2ms 0.01% 27.65% 2427ms 12.28% OffLatticeSimulation::UpdateCellLocationsAndTopology 444ms 2.25% 29.90% 2247ms 11.37% std::type_info::operator== (inline) 0 0% 29.90% 2139ms 10.82% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0051% 29.91% 2094ms 10.60% MutableMesh::ReMesh 18ms 0.091% 30.00% 2087ms 10.56% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 30.00% 1914ms 9.69% AbstractCellPopulation::WriteResultsToFiles 782ms 3.96% 33.95% 1834ms 9.28% std::_Rb_tree::_M_lower_bound (inline) 1801ms 9.11% 43.07% 1801ms 9.11% __strcmp_avx2 175ms 0.89% 43.95% 1622ms 8.21% TetrahedralMesh::EdgeIterator::operator++ 62ms 0.31% 44.27% 1323ms 6.69% std::_Rb_tree::find (inline) 6ms 0.03% 44.30% 1093ms 5.53% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1ms 0.0051% 44.30% 1083ms 5.48% MeshBasedCellPopulation::UpdateNodePairs 14ms 0.071% 44.37% 1050ms 5.31% TetrahedralMesh::ImportFromMesher 46ms 0.23% 44.61% 1033ms 5.23% operator new 13ms 0.066% 44.67% 1011ms 5.12% std::set::insert (inline) 12ms 0.061% 44.73% 997ms 5.05% std::_Rb_tree::_M_insert_unique 211ms 1.07% 45.80% 980ms 4.96% __GI___libc_malloc 4ms 0.02% 45.82% 959ms 4.85% MeshBasedCellPopulation::SpringIterator::operator++ 36ms 0.18% 46.00% 893ms 4.52% std::__new_allocator::allocate (inline) 0 0% 46.00% 888ms 4.49% std::allocator_traits::allocate (inline) 0 0% 46.00% 781ms 3.95% triangulate 0 0% 46.00% 755ms 3.82% std::set::count (inline) 739ms 3.74% 49.74% 739ms 3.74% std::_Rb_tree::_S_right (inline) 64ms 0.32% 50.07% 715ms 3.62% std::map::operator[] (partial-inline) 3ms 0.015% 50.08% 709ms 3.59% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 50.08% 709ms 3.59% delaunay 5ms 0.025% 50.11% 708ms 3.58% divconqdelaunay 379ms 1.92% 52.02% 674ms 3.41% _int_malloc 1ms 0.0051% 52.03% 668ms 3.38% AbstractTwoBodyInteractionForce::AddForceContribution 6ms 0.03% 52.06% 659ms 3.33% CellPopulationElementWriter::Visit 635ms 3.21% 55.27% 647ms 3.27% WntCellCycleOdeSystem::CalculateStoppingEvent 167ms 0.85% 56.12% 615ms 3.11% __dynamic_cast 25ms 0.13% 56.24% 614ms 3.11% std::_Rb_tree::_M_insert_ (inline) 0 0% 56.24% 595ms 3.01% std::_Rb_tree::_M_create_node (inline) 19ms 0.096% 56.34% 591ms 2.99% std::less::operator() (inline) 0 0% 56.34% 580ms 2.93% std::_Rb_tree::lower_bound (inline) 0 0% 56.34% 580ms 2.93% std::map::lower_bound (inline) 0 0% 56.34% 575ms 2.91% std::_Rb_tree::_M_get_node (inline) 18ms 0.091% 56.43% 572ms 2.89% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 6ms 0.03% 56.46% 572ms 2.89% MeshBasedCellPopulation::AcceptCellWriter 572ms 2.89% 59.36% 572ms 2.89% std::operator< (inline) 0 0% 59.36% 565ms 2.86% std::map::find (inline) 0 0% 59.36% 555ms 2.81% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.01% 59.37% 553ms 2.80% CellPropertyCollection::GetPropertiesType (inline) 14ms 0.071% 59.44% 547ms 2.77% Element::Element 13ms 0.066% 59.50% 537ms 2.72% AbstractCellPopulation::GetCellUsingLocationIndex 17ms 0.086% 59.59% 530ms 2.68% MutableMesh::ReIndex 9ms 0.046% 59.63% 524ms 2.65% Cylindrical2dMesh::CorrectNonPeriodicMesh 0 0% 59.63% 512ms 2.59% std::ostream::operator<< (inline) 72ms 0.36% 60.00% 510ms 2.58% std::ostream::_M_insert 11ms 0.056% 60.05% 496ms 2.51% Element::RegisterWithNodes (inline) 339ms 1.72% 61.77% 483ms 2.44% AbstractCellMutationState::AbstractCellMutationState 8ms 0.04% 61.81% 482ms 2.44% Node::AddElement 12ms 0.061% 61.87% 472ms 2.39% Cylindrical2dMesh::ReconstructCylindricalMesh 1ms 0.0051% 61.88% 446ms 2.26% AbstractCellProperty::IsSubType (inline) 130ms 0.66% 62.53% 409ms 2.07% __GI___libc_free 5ms 0.025% 62.56% 387ms 1.96% std::_Rb_tree::erase 1ms 0.0051% 62.56% 385ms 1.95% std::set::erase (inline) 14ms 0.071% 62.64% 384ms 1.94% Node::RemoveElement 38ms 0.19% 62.83% 372ms 1.88% Element::ResetIndex 129ms 0.65% 63.48% 372ms 1.88% std::_Rb_tree::_M_get_insert_unique_pos 14ms 0.071% 63.55% 365ms 1.85% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 15ms 0.076% 63.63% 350ms 1.77% divconqrecurse 14ms 0.071% 63.70% 340ms 1.72% std::__new_allocator::deallocate (inline) 107ms 0.54% 64.24% 337ms 1.71% std::_Rb_tree::_M_erase 0 0% 64.24% 331ms 1.67% std::allocator_traits::deallocate (inline) 0 0% 64.24% 329ms 1.66% NodeLocationWriter::Visit 99ms 0.5% 64.74% 327ms 1.65% mergehulls 140ms 0.71% 65.45% 325ms 1.64% __cxxabiv1::__si_class_type_info::__do_dyncast 5ms 0.025% 65.47% 318ms 1.61% std::_Vector_base::_M_allocate (inline) 5ms 0.025% 65.50% 310ms 1.57% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0051% 65.50% 305ms 1.54% Cell::GetCellProliferativeType 16ms 0.081% 65.59% 300ms 1.52% std::_Rb_tree::~_Rb_tree (inline) 4ms 0.02% 65.61% 299ms 1.51% Cell::GetMutationState 2ms 0.01% 65.62% 293ms 1.48% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 65.62% 290ms 1.47% std::_Rb_tree::_M_drop_node (inline) 21ms 0.11% 65.72% 289ms 1.46% std::num_put::_M_insert_float 0 0% 65.72% 288ms 1.46% AbstractCellPopulation::Iterator::operator++ (inline) 29ms 0.15% 65.87% 286ms 1.45% AbstractCellPopulation::Iterator::IsRealCell (inline) 236ms 1.19% 67.06% 279ms 1.41% _int_free 275ms 1.39% 68.45% 275ms 1.39% std::type_info::name (inline) 0 0% 68.45% 272ms 1.38% std::set::~set (inline) 0 0% 68.45% 261ms 1.32% std::_Rb_tree::_M_put_node (inline) 8ms 0.04% 68.50% 256ms 1.30% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 19ms 0.096% 68.59% 247ms 1.25% AbstractTetrahedralElement::CalculateJacobian 242ms 1.22% 69.82% 242ms 1.22% [libchaste_cell_based.so] 10ms 0.051% 69.87% 235ms 1.19% AbstractCellPopulation::IsCellAttachedToLocationIndex 2ms 0.01% 69.88% 235ms 1.19% TetrahedralMesh::RefreshJacobianCachedData 13ms 0.066% 69.94% 233ms 1.18% std::vector::push_back (inline) 4ms 0.02% 69.96% 232ms 1.17% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 62ms 0.31% 70.28% 232ms 1.17% ApcOneHitCellMutationState::ApcOneHitCellMutationState 4ms 0.02% 70.30% 229ms 1.16% std::__cxx11::collate::do_transform 1ms 0.0051% 70.30% 226ms 1.14% MeshBasedCellPopulation::GetDampingConstant 1ms 0.0051% 70.31% 225ms 1.14% AbstractCentreBasedCellPopulation::GetDampingConstant 2ms 0.01% 70.32% 221ms 1.12% ___vsnprintf 4ms 0.02% 70.34% 220ms 1.11% alternateaxes 0 0% 70.34% 219ms 1.11% __vsnprintf_internal (inline) 215ms 1.09% 71.42% 217ms 1.10% std::vector::operator[] (inline) 28ms 0.14% 71.57% 216ms 1.09% __printf_buffer 12ms 0.061% 71.63% 216ms 1.09% std::_Rb_tree::_Rb_tree 12ms 0.061% 71.69% 214ms 1.08% std::_Rb_tree::_M_erase_aux (inline) 199ms 1.01% 72.70% 213ms 1.08% vertexmedian 59ms 0.3% 72.99% 212ms 1.07% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 9ms 0.046% 73.04% 212ms 1.07% std::vector::_M_realloc_insert 1ms 0.0051% 73.04% 201ms 1.02% std::set::set (inline) 1ms 0.0051% 73.05% 199ms 1.01% AbstractTetrahedralElement::CalculateInverseJacobian 41ms 0.21% 73.26% 199ms 1.01% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 134ms 0.68% 73.93% 196ms 0.99% AbstractElement::GetNodeGlobalIndex 21ms 0.11% 74.04% 183ms 0.93% std::_Rb_tree::_M_copy (inline) 25ms 0.13% 74.17% 178ms 0.9% AbstractTetrahedralElement::RefreshJacobian 12ms 0.061% 74.23% 178ms 0.9% Element::MarkAsDeleted 0 0% 74.23% 178ms 0.9% OffLatticeSimulation::ApplyBoundaries 123ms 0.62% 74.85% 174ms 0.88% std::_Rb_tree::equal_range (inline) 169ms 0.86% 75.71% 169ms 0.86% Node::GetIndex 169ms 0.86% 76.56% 169ms 0.86% std::_Rb_tree_insert_and_rebalance 1ms 0.0051% 76.57% 167ms 0.85% __printf_fp_spec (inline) 9ms 0.046% 76.61% 166ms 0.84% __printf_fp_l_buffer 106ms 0.54% 77.15% 162ms 0.82% malloc_consolidate 44ms 0.22% 77.37% 161ms 0.81% std::_Rb_tree::_M_clone_node (inline) 1ms 0.0051% 77.38% 160ms 0.81% CellProliferativeTypesWriter::VisitCell 8ms 0.04% 77.42% 158ms 0.8% TetrahedralMesh::Clear 0 0% 77.42% 157ms 0.79% boost::numeric::ublas::vector_assign (inline) 157ms 0.79% 78.21% 157ms 0.79% unlink_chunk 6ms 0.03% 78.24% 154ms 0.78% AbstractTetrahedralElement::AbstractTetrahedralElement 76ms 0.38% 78.63% 153ms 0.77% __printf_fp_buffer_1 13ms 0.066% 78.69% 140ms 0.71% boost::numeric::ublas::c_vector::c_vector (inline) 10ms 0.051% 78.74% 139ms 0.7% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 59ms 0.3% 79.04% 138ms 0.7% AbstractElement::GetNodeLocation 45ms 0.23% 79.27% 137ms 0.69% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 137ms 0.69% 79.96% 137ms 0.69% incircle 137ms 0.69% 80.65% 137ms 0.69% std::vector::size (inline) 86ms 0.44% 81.09% 135ms 0.68% Cylindrical2dMesh::GetVectorFromAtoB 4ms 0.02% 81.11% 133ms 0.67% CellPropertyCollection::HasProperty 0 0% 81.11% 130ms 0.66% Cell::HasCellProperty (inline) 0 0% 81.11% 129ms 0.65% AbstractCellBasedSimulation::DoCellRemoval (inline) 16ms 0.081% 81.19% 126ms 0.64% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 34ms 0.17% 81.36% 126ms 0.64% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.0051% 81.37% 125ms 0.63% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1ms 0.0051% 81.37% 125ms 0.63% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 1ms 0.0051% 81.38% 125ms 0.63% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 41ms 0.21% 81.59% 123ms 0.62% boost::numeric::ublas::indexing_vector_assign 115ms 0.58% 82.17% 120ms 0.61% vertexsort 14ms 0.071% 82.24% 117ms 0.59% boost::detail::shared_count::~shared_count (inline) 0 0% 82.24% 117ms 0.59% boost::shared_ptr::~shared_ptr (inline) 2ms 0.01% 82.25% 113ms 0.57% MeshBasedCellPopulation::SpringsEnd (inline) 30ms 0.15% 82.40% 111ms 0.56% std::num_put::_M_insert_int 110ms 0.56% 82.96% 110ms 0.56% AbstractElement::IsDeleted 4ms 0.02% 82.98% 108ms 0.55% Cell::SetCellProliferativeType 32ms 0.16% 83.14% 103ms 0.52% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 99ms 0.5% 83.64% 100ms 0.51% boost::detail::sp_counted_base::release 44ms 0.22% 83.86% 99ms 0.5% std::__ostream_insert