File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16816ms, 85.54% of 19659ms total Dropped 738 nodes (cum <= 98.30ms) flat flat% sum% cum cum% 0 0% 0% 19616ms 99.78% __libc_start_call_main 0 0% 0% 19616ms 99.78% __libc_start_main_impl 0 0% 0% 19616ms 99.78% _start 0 0% 0% 19599ms 99.69% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19599ms 99.69% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19599ms 99.69% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19599ms 99.69% main 0 0% 0% 19565ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19565ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19565ms 99.52% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.0051% 0.0051% 19539ms 99.39% AbstractCellBasedSimulation::Solve 0 0% 0.0051% 15243ms 77.54% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.015% 0.02% 10153ms 51.65% AbstractCellBasedSimulation::DoCellBirth 9ms 0.046% 0.066% 10061ms 51.18% Cell::ReadyToDivide 5ms 0.025% 0.092% 10006ms 50.90% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.01% 0.1% 9879ms 50.25% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 10ms 0.051% 0.15% 9868ms 50.20% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 0.15% 9850ms 50.10% CellCycleModelOdeHandler::SolveOdeToTime 69ms 0.35% 0.5% 9672ms 49.20% AbstractOneStepIvpOdeSolver::InternalSolve 865ms 4.40% 4.90% 8815ms 44.84% RungeKutta4IvpOdeSolver::CalculateNextYValue 3406ms 17.33% 22.23% 7735ms 39.35% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 22.23% 4979ms 25.33% MeshBasedCellPopulation::Update 145ms 0.74% 22.97% 4339ms 22.07% AbstractCellProperty::IsType (inline) 7ms 0.036% 23.00% 3810ms 19.38% Cylindrical2dMesh::ReMesh 587ms 2.99% 25.99% 3111ms 15.82% AbstractCellProperty::IsSame 445ms 2.26% 28.25% 2524ms 12.84% std::type_info::operator== (inline) 3ms 0.015% 28.27% 2419ms 12.30% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 28.27% 2127ms 10.82% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0051% 28.27% 2096ms 10.66% MutableMesh::ReMesh 6ms 0.031% 28.30% 2091ms 10.64% AbstractNumericalMethod::ComputeForcesIncludingDamping 2076ms 10.56% 38.86% 2076ms 10.56% __strcmp_avx2 0 0% 38.86% 1872ms 9.52% AbstractCellPopulation::WriteResultsToFiles 813ms 4.14% 43.00% 1679ms 8.54% std::_Rb_tree::_M_lower_bound (inline) 177ms 0.9% 43.90% 1651ms 8.40% TetrahedralMesh::EdgeIterator::operator++ 67ms 0.34% 44.24% 1309ms 6.66% std::_Rb_tree::find (inline) 0 0% 44.24% 1141ms 5.80% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.02% 44.26% 1079ms 5.49% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 10ms 0.051% 44.31% 1024ms 5.21% TetrahedralMesh::ImportFromMesher 18ms 0.092% 44.40% 1004ms 5.11% MeshBasedCellPopulation::SpringIterator::operator++ 38ms 0.19% 44.60% 976ms 4.96% operator new 249ms 1.27% 45.86% 929ms 4.73% __GI___libc_malloc 6ms 0.031% 45.89% 921ms 4.68% std::set::insert (inline) 17ms 0.086% 45.98% 915ms 4.65% std::_Rb_tree::_M_insert_unique 36ms 0.18% 46.16% 884ms 4.50% std::__new_allocator::allocate (inline) 0 0% 46.16% 877ms 4.46% std::allocator_traits::allocate (inline) 1ms 0.0051% 46.17% 821ms 4.18% triangulate 0 0% 46.17% 807ms 4.10% std::set::count (inline) 0 0% 46.17% 744ms 3.78% delaunay 2ms 0.01% 46.18% 744ms 3.78% divconqdelaunay 4ms 0.02% 46.20% 737ms 3.75% AbstractTwoBodyInteractionForce::AddForceContribution 3ms 0.015% 46.21% 677ms 3.44% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 666ms 3.39% 49.60% 675ms 3.43% WntCellCycleOdeSystem::CalculateStoppingEvent 2ms 0.01% 49.61% 657ms 3.34% CellPopulationElementWriter::Visit 20ms 0.1% 49.71% 622ms 3.16% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 152ms 0.77% 50.49% 610ms 3.10% __dynamic_cast 338ms 1.72% 52.21% 604ms 3.07% _int_malloc 64ms 0.33% 52.53% 600ms 3.05% std::map::operator[] (partial-inline) 19ms 0.097% 52.63% 580ms 2.95% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 52.63% 579ms 2.95% std::_Rb_tree::_M_create_node (inline) 24ms 0.12% 52.75% 565ms 2.87% std::_Rb_tree::_M_insert_ (inline) 564ms 2.87% 55.62% 564ms 2.87% std::_Rb_tree::_S_right (inline) 19ms 0.097% 55.71% 562ms 2.86% std::less::operator() (inline) 0 0% 55.71% 554ms 2.82% std::_Rb_tree::_M_get_node (inline) 543ms 2.76% 58.48% 543ms 2.76% std::operator< (inline) 7ms 0.036% 58.51% 539ms 2.74% Element::Element 6ms 0.031% 58.54% 534ms 2.72% MeshBasedCellPopulation::AcceptCellWriter 0 0% 58.54% 528ms 2.69% std::_Rb_tree::_Alloc_node::operator() (inline) 367ms 1.87% 60.41% 520ms 2.65% AbstractCellMutationState::AbstractCellMutationState 16ms 0.081% 60.49% 513ms 2.61% Cylindrical2dMesh::ReconstructCylindricalMesh 6ms 0.031% 60.52% 507ms 2.58% CellPropertyCollection::GetPropertiesType (inline) 207ms 1.05% 61.57% 500ms 2.54% __GI___libc_free 0 0% 61.57% 499ms 2.54% std::map::find (inline) 2ms 0.01% 61.59% 488ms 2.48% std::ostream::operator<< (inline) 65ms 0.33% 61.92% 486ms 2.47% std::ostream::_M_insert 6ms 0.031% 61.95% 472ms 2.40% MutableMesh::ReIndex 0 0% 61.95% 461ms 2.34% std::_Rb_tree::lower_bound (inline) 0 0% 61.95% 461ms 2.34% std::map::lower_bound (inline) 6ms 0.031% 61.98% 452ms 2.30% Element::RegisterWithNodes (inline) 2ms 0.01% 61.99% 441ms 2.24% Node::AddElement 22ms 0.11% 62.10% 435ms 2.21% std::__new_allocator::deallocate (inline) 12ms 0.061% 62.16% 431ms 2.19% Node::RemoveElement 11ms 0.056% 62.22% 429ms 2.18% Cylindrical2dMesh::CorrectNonPeriodicMesh 8ms 0.041% 62.26% 429ms 2.18% std::_Rb_tree::erase 0 0% 62.26% 429ms 2.18% std::allocator_traits::deallocate (inline) 1ms 0.0051% 62.26% 429ms 2.18% std::set::erase (inline) 6ms 0.031% 62.29% 423ms 2.15% AbstractCellProperty::IsSubType (inline) 0 0% 62.29% 420ms 2.14% std::_Rb_tree::_M_drop_node (inline) 101ms 0.51% 62.81% 376ms 1.91% std::_Rb_tree::_M_erase 19ms 0.097% 62.90% 370ms 1.88% divconqrecurse 34ms 0.17% 63.08% 365ms 1.86% std::_Rb_tree::~_Rb_tree (inline) 0 0% 63.08% 363ms 1.85% std::_Rb_tree::_M_put_node (inline) 94ms 0.48% 63.55% 348ms 1.77% mergehulls 0 0% 63.55% 334ms 1.70% std::set::~set (inline) 123ms 0.63% 64.18% 333ms 1.69% std::_Rb_tree::_M_get_insert_unique_pos 14ms 0.071% 64.25% 331ms 1.68% Element::ResetIndex 152ms 0.77% 65.02% 325ms 1.65% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.0051% 65.03% 324ms 1.65% std::_Vector_base::_M_allocate (inline) 3ms 0.015% 65.04% 316ms 1.61% NodeLocationWriter::Visit 8ms 0.041% 65.08% 296ms 1.51% Cell::GetMutationState 253ms 1.29% 66.37% 293ms 1.49% _int_free 4ms 0.02% 66.39% 292ms 1.49% LegacyCellProliferativeTypesWriter::VisitCell 288ms 1.46% 67.86% 288ms 1.46% std::type_info::name (inline) 13ms 0.066% 67.92% 286ms 1.45% std::_Rb_tree::_M_erase_aux (inline) 5ms 0.025% 67.95% 282ms 1.43% AbstractCellPopulation::GetLocationIndexUsingCell 8ms 0.041% 67.99% 279ms 1.42% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 21ms 0.11% 68.10% 278ms 1.41% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 68.10% 274ms 1.39% AbstractCellPopulation::Iterator::operator++ (inline) 4ms 0.02% 68.12% 271ms 1.38% Cell::GetCellProliferativeType 17ms 0.086% 68.20% 270ms 1.37% std::num_put::_M_insert_float 25ms 0.13% 68.33% 267ms 1.36% AbstractTetrahedralElement::CalculateJacobian 258ms 1.31% 69.64% 259ms 1.32% std::vector::operator[] (inline) 12ms 0.061% 69.70% 258ms 1.31% std::_Rb_tree::_Rb_tree (partial-inline) 6ms 0.031% 69.73% 254ms 1.29% alternateaxes 233ms 1.19% 70.92% 247ms 1.26% vertexmedian 0 0% 70.92% 239ms 1.22% std::set::set (inline) 12ms 0.061% 70.98% 236ms 1.20% std::vector::push_back (inline) 9ms 0.046% 71.03% 235ms 1.20% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 0 0% 71.03% 231ms 1.18% TetrahedralMesh::RefreshJacobianCachedData 7ms 0.036% 71.06% 228ms 1.16% Element::MarkAsDeleted 1ms 0.0051% 71.07% 226ms 1.15% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2ms 0.01% 71.08% 226ms 1.15% std::__cxx11::collate::do_transform 62ms 0.32% 71.39% 225ms 1.14% ApcOneHitCellMutationState::ApcOneHitCellMutationState 41ms 0.21% 71.60% 224ms 1.14% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 222ms 1.13% 72.73% 222ms 1.13% [libchaste_cell_based.so] 1ms 0.0051% 72.74% 220ms 1.12% ___vsnprintf 0 0% 72.74% 219ms 1.11% __vsnprintf_internal (inline) 18ms 0.092% 72.83% 219ms 1.11% std::vector::_M_realloc_insert 5ms 0.025% 72.85% 218ms 1.11% AbstractCellPopulation::IsCellAttachedToLocationIndex 27ms 0.14% 72.99% 215ms 1.09% __printf_buffer 23ms 0.12% 73.11% 212ms 1.08% std::_Rb_tree::_M_copy (inline) 35ms 0.18% 73.28% 206ms 1.05% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 23ms 0.12% 73.40% 194ms 0.99% AbstractTetrahedralElement::RefreshJacobian 6ms 0.031% 73.43% 193ms 0.98% AbstractTetrahedralElement::CalculateInverseJacobian 52ms 0.26% 73.70% 188ms 0.96% std::_Rb_tree::_M_clone_node (inline) 140ms 0.71% 74.41% 186ms 0.95% AbstractElement::GetNodeGlobalIndex 2ms 0.01% 74.42% 184ms 0.94% MeshBasedCellPopulation::GetDampingConstant 0 0% 74.42% 183ms 0.93% OffLatticeSimulation::ApplyBoundaries 7ms 0.036% 74.45% 182ms 0.93% AbstractTetrahedralElement::AbstractTetrahedralElement 2ms 0.01% 74.46% 181ms 0.92% AbstractCentreBasedCellPopulation::GetDampingConstant 114ms 0.58% 75.04% 164ms 0.83% malloc_consolidate 14ms 0.071% 75.12% 163ms 0.83% TetrahedralMesh::Clear 163ms 0.83% 75.94% 163ms 0.83% std::_Rb_tree_insert_and_rebalance 158ms 0.8% 76.75% 158ms 0.8% incircle 61ms 0.31% 77.06% 153ms 0.78% AbstractElement::GetNodeLocation 2ms 0.01% 77.07% 150ms 0.76% boost::numeric::ublas::vector_assign (inline) 89ms 0.45% 77.52% 150ms 0.76% std::_Rb_tree::equal_range (inline) 5ms 0.025% 77.55% 147ms 0.75% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 4ms 0.02% 77.57% 145ms 0.74% __printf_fp_l_buffer 0 0% 77.57% 145ms 0.74% __printf_fp_spec (inline) 144ms 0.73% 78.30% 144ms 0.73% std::vector::size (inline) 141ms 0.72% 79.02% 141ms 0.72% AbstractCellMutationState::~AbstractCellMutationState 137ms 0.7% 79.71% 137ms 0.7% Node::GetIndex 75ms 0.38% 80.10% 137ms 0.7% __printf_fp_buffer_1 19ms 0.097% 80.19% 137ms 0.7% boost::detail::shared_count::~shared_count (inline) 0 0% 80.19% 137ms 0.7% boost::shared_ptr::~shared_ptr (inline) 31ms 0.16% 80.35% 136ms 0.69% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 7ms 0.036% 80.39% 135ms 0.69% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 39ms 0.2% 80.58% 134ms 0.68% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 26ms 0.13% 80.72% 132ms 0.67% TetrahedralMesh::EdgesEnd 4ms 0.02% 80.74% 130ms 0.66% MeshBasedCellPopulation::SpringsEnd (inline) 129ms 0.66% 81.39% 129ms 0.66% unlink_chunk 24ms 0.12% 81.51% 128ms 0.65% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 127ms 0.65% 82.16% 127ms 0.65% AbstractCellProperty::~AbstractCellProperty 7ms 0.036% 82.20% 124ms 0.63% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.0051% 82.20% 123ms 0.63% CellProliferativeTypesWriter::VisitCell 79ms 0.4% 82.60% 123ms 0.63% Cylindrical2dMesh::GetVectorFromAtoB 1ms 0.0051% 82.61% 120ms 0.61% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 0 0% 82.61% 119ms 0.61% Cell::HasCellProperty (inline) 5ms 0.025% 82.63% 119ms 0.61% CellPropertyCollection::HasProperty 32ms 0.16% 82.80% 118ms 0.6% boost::numeric::ublas::indexing_vector_assign 116ms 0.59% 83.39% 116ms 0.59% AbstractElement::IsDeleted 112ms 0.57% 83.96% 115ms 0.58% boost::detail::sp_counted_base::release 25ms 0.13% 84.08% 115ms 0.58% std::num_put::_M_insert_int 51ms 0.26% 84.34% 114ms 0.58% std::__ostream_insert 0 0% 84.34% 113ms 0.57% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 84.34% 112ms 0.57% OutputFileHandler::OpenOutputFile 106ms 0.54% 84.88% 112ms 0.57% vertexsort 0 0% 84.88% 110ms 0.56% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.0051% 84.89% 107ms 0.54% Cell::SetCellProliferativeType 50ms 0.25% 85.14% 107ms 0.54% boost::shared_ptr::shared_ptr (inline) 75ms 0.38% 85.52% 105ms 0.53% TetrahedralMesh::EdgeIterator::EdgeIterator 3ms 0.015% 85.54% 100ms 0.51% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 85.54% 100ms 0.51% std::vector::_M_default_append 0 0% 85.54% 100ms 0.51% std::vector::resize (inline)