File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16563ms, 84.41% of 19622ms total Dropped 780 nodes (cum <= 98.11ms) flat flat% sum% cum cum% 0 0% 0% 19577ms 99.77% __libc_start_call_main 0 0% 0% 19577ms 99.77% __libc_start_main_impl 0 0% 0% 19577ms 99.77% _start 0 0% 0% 19557ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19557ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19557ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19557ms 99.67% main 0 0% 0% 19521ms 99.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19521ms 99.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19521ms 99.49% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19495ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0% 15099ms 76.95% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 9922ms 50.57% AbstractCellBasedSimulation::DoCellBirth 5ms 0.025% 0.025% 9828ms 50.09% Cell::ReadyToDivide 5ms 0.025% 0.051% 9756ms 49.72% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.051% 9631ms 49.08% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 14ms 0.071% 0.12% 9624ms 49.05% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 5ms 0.025% 0.15% 9609ms 48.97% CellCycleModelOdeHandler::SolveOdeToTime 84ms 0.43% 0.58% 9445ms 48.13% AbstractOneStepIvpOdeSolver::InternalSolve 865ms 4.41% 4.98% 8550ms 43.57% RungeKutta4IvpOdeSolver::CalculateNextYValue 3489ms 17.78% 22.77% 7460ms 38.02% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 22.77% 5064ms 25.81% MeshBasedCellPopulation::Update 83ms 0.42% 23.19% 4019ms 20.48% AbstractCellProperty::IsType (inline) 5ms 0.025% 23.21% 3938ms 20.07% Cylindrical2dMesh::ReMesh 575ms 2.93% 26.14% 2780ms 14.17% AbstractCellProperty::IsSame 0 0% 26.14% 2424ms 12.35% OffLatticeSimulation::UpdateCellLocationsAndTopology 418ms 2.13% 28.27% 2205ms 11.24% std::type_info::operator== (inline) 0 0% 28.27% 2137ms 10.89% MutableMesh::ReMesh 1ms 0.0051% 28.28% 2106ms 10.73% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.051% 28.33% 2061ms 10.50% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 28.33% 1966ms 10.02% AbstractCellPopulation::WriteResultsToFiles 706ms 3.60% 31.93% 1726ms 8.80% std::_Rb_tree::_M_lower_bound (inline) 1706ms 8.69% 40.62% 1706ms 8.69% __strcmp_avx2 134ms 0.68% 41.31% 1584ms 8.07% TetrahedralMesh::EdgeIterator::operator++ 61ms 0.31% 41.62% 1264ms 6.44% std::_Rb_tree::find (inline) 5ms 0.025% 41.64% 1105ms 5.63% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 41.64% 1086ms 5.53% MeshBasedCellPopulation::UpdateNodePairs 9ms 0.046% 41.69% 1059ms 5.40% TetrahedralMesh::ImportFromMesher 13ms 0.066% 41.75% 1048ms 5.34% std::set::insert (inline) 8ms 0.041% 41.79% 1035ms 5.27% std::_Rb_tree::_M_insert_unique 45ms 0.23% 42.02% 1029ms 5.24% operator new 230ms 1.17% 43.20% 970ms 4.94% __GI___libc_malloc 14ms 0.071% 43.27% 956ms 4.87% MeshBasedCellPopulation::SpringIterator::operator++ 41ms 0.21% 43.48% 915ms 4.66% std::__new_allocator::allocate (inline) 0 0% 43.48% 908ms 4.63% std::allocator_traits::allocate (inline) 3ms 0.015% 43.49% 847ms 4.32% triangulate 0 0% 43.49% 751ms 3.83% delaunay 1ms 0.0051% 43.50% 750ms 3.82% divconqdelaunay 9ms 0.046% 43.54% 744ms 3.79% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 43.54% 736ms 3.75% std::set::count (inline) 685ms 3.49% 47.03% 691ms 3.52% WntCellCycleOdeSystem::CalculateStoppingEvent 5ms 0.025% 47.06% 682ms 3.48% CellPopulationElementWriter::Visit 62ms 0.32% 47.38% 681ms 3.47% std::map::operator[] (partial-inline) 662ms 3.37% 50.75% 662ms 3.37% std::_Rb_tree::_S_right (inline) 362ms 1.84% 52.59% 653ms 3.33% _int_malloc 0 0% 52.59% 643ms 3.28% AbstractTwoBodyInteractionForce::AddForceContribution 17ms 0.087% 52.68% 635ms 3.24% std::less::operator() (inline) 32ms 0.16% 52.84% 630ms 3.21% std::_Rb_tree::_M_insert_ (inline) 618ms 3.15% 55.99% 618ms 3.15% std::operator< (inline) 0 0% 55.99% 601ms 3.06% std::_Rb_tree::_M_create_node (inline) 21ms 0.11% 56.10% 585ms 2.98% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 56.10% 581ms 2.96% std::_Rb_tree::_M_get_node (inline) 4ms 0.02% 56.12% 577ms 2.94% MeshBasedCellPopulation::AcceptCellWriter 179ms 0.91% 57.03% 577ms 2.94% __dynamic_cast 3ms 0.015% 57.05% 564ms 2.87% Element::Element 9ms 0.046% 57.09% 560ms 2.85% CellPropertyCollection::GetPropertiesType (inline) 0 0% 57.09% 555ms 2.83% std::_Rb_tree::_Alloc_node::operator() (inline) 28ms 0.14% 57.24% 539ms 2.75% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 0 0% 57.24% 538ms 2.74% std::_Rb_tree::lower_bound (inline) 0 0% 57.24% 538ms 2.74% std::map::lower_bound (inline) 0 0% 57.24% 519ms 2.64% std::map::find (inline) 15ms 0.076% 57.31% 513ms 2.61% Cylindrical2dMesh::CorrectNonPeriodicMesh 58ms 0.3% 57.61% 510ms 2.60% std::ostream::_M_insert 0 0% 57.61% 510ms 2.60% std::ostream::operator<< (inline) 7ms 0.036% 57.64% 508ms 2.59% MutableMesh::ReIndex 8ms 0.041% 57.69% 493ms 2.51% Element::RegisterWithNodes (inline) 345ms 1.76% 59.44% 490ms 2.50% AbstractCellMutationState::AbstractCellMutationState 12ms 0.061% 59.50% 490ms 2.50% Cylindrical2dMesh::ReconstructCylindricalMesh 8ms 0.041% 59.55% 485ms 2.47% Node::AddElement 1ms 0.0051% 59.55% 451ms 2.30% AbstractCellProperty::IsSubType (inline) 137ms 0.7% 60.25% 422ms 2.15% __GI___libc_free 147ms 0.75% 61.00% 398ms 2.03% std::_Rb_tree::_M_get_insert_unique_pos 4ms 0.02% 61.02% 390ms 1.99% std::set::erase (inline) 8ms 0.041% 61.06% 389ms 1.98% std::_Rb_tree::erase 10ms 0.051% 61.11% 387ms 1.97% Node::RemoveElement 15ms 0.076% 61.19% 366ms 1.87% std::__new_allocator::deallocate (inline) 0 0% 61.19% 361ms 1.84% std::allocator_traits::deallocate (inline) 102ms 0.52% 61.71% 351ms 1.79% std::_Rb_tree::_M_erase 345ms 1.76% 63.46% 345ms 1.76% std::type_info::name (inline) 22ms 0.11% 63.58% 341ms 1.74% Element::ResetIndex 3ms 0.015% 63.59% 330ms 1.68% std::_Vector_base::_M_allocate (inline) 7ms 0.036% 63.63% 328ms 1.67% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 63.63% 327ms 1.67% std::_Rb_tree::_M_drop_node (inline) 15ms 0.076% 63.70% 324ms 1.65% divconqrecurse 25ms 0.13% 63.83% 323ms 1.65% std::_Rb_tree::~_Rb_tree (inline) 4ms 0.02% 63.85% 313ms 1.60% NodeLocationWriter::Visit 3ms 0.015% 63.87% 305ms 1.55% LegacyCellProliferativeTypesWriter::VisitCell 88ms 0.45% 64.32% 305ms 1.55% mergehulls 7ms 0.036% 64.35% 302ms 1.54% AbstractCellPopulation::GetLocationIndexUsingCell 4ms 0.02% 64.37% 302ms 1.54% Cell::GetMutationState 4ms 0.02% 64.39% 299ms 1.52% Cell::GetCellProliferativeType 134ms 0.68% 65.07% 294ms 1.50% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 65.07% 290ms 1.48% std::set::~set (inline) 0 0% 65.07% 288ms 1.47% std::_Rb_tree::_M_put_node (inline) 233ms 1.19% 66.26% 285ms 1.45% _int_free 1ms 0.0051% 66.27% 281ms 1.43% AbstractCellPopulation::Iterator::operator++ (inline) 280ms 1.43% 67.69% 280ms 1.43% std::vector::operator[] (inline) 4ms 0.02% 67.71% 277ms 1.41% alternateaxes 28ms 0.14% 67.86% 273ms 1.39% AbstractCellPopulation::Iterator::IsRealCell (inline) 20ms 0.1% 67.96% 272ms 1.39% std::num_put::_M_insert_float 258ms 1.31% 69.27% 272ms 1.39% vertexmedian 17ms 0.087% 69.36% 267ms 1.36% AbstractTetrahedralElement::CalculateJacobian 9ms 0.046% 69.41% 256ms 1.30% std::vector::push_back (inline) 21ms 0.11% 69.51% 250ms 1.27% std::_Rb_tree::_Rb_tree (partial-inline) 11ms 0.056% 69.57% 249ms 1.27% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 77ms 0.39% 69.96% 243ms 1.24% ApcOneHitCellMutationState::ApcOneHitCellMutationState 11ms 0.056% 70.02% 243ms 1.24% std::_Rb_tree::_M_erase_aux (inline) 17ms 0.087% 70.10% 235ms 1.20% std::vector::_M_realloc_insert 8ms 0.041% 70.15% 234ms 1.19% AbstractCellPopulation::IsCellAttachedToLocationIndex 1ms 0.0051% 70.15% 232ms 1.18% std::set::set (inline) 0 0% 70.15% 229ms 1.17% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 33ms 0.17% 70.32% 228ms 1.16% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 0 0% 70.32% 218ms 1.11% std::__cxx11::collate::do_transform 1ms 0.0051% 70.32% 214ms 1.09% MeshBasedCellPopulation::GetDampingConstant 2ms 0.01% 70.33% 213ms 1.09% ___vsnprintf 1ms 0.0051% 70.34% 212ms 1.08% AbstractCentreBasedCellPopulation::GetDampingConstant 13ms 0.066% 70.41% 212ms 1.08% Element::MarkAsDeleted 0 0% 70.41% 211ms 1.08% __vsnprintf_internal (inline) 162ms 0.83% 71.23% 208ms 1.06% AbstractElement::GetNodeGlobalIndex 0 0% 71.23% 206ms 1.05% TetrahedralMesh::RefreshJacobianCachedData 29ms 0.15% 71.38% 206ms 1.05% __printf_buffer 19ms 0.097% 71.48% 202ms 1.03% std::_Rb_tree::_M_copy (inline) 28ms 0.14% 71.62% 199ms 1.01% AbstractTetrahedralElement::RefreshJacobian 44ms 0.22% 71.84% 198ms 1.01% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 198ms 1.01% 72.85% 198ms 1.01% [libchaste_cell_based.so] 0 0% 72.85% 191ms 0.97% OffLatticeSimulation::ApplyBoundaries 5ms 0.025% 72.88% 189ms 0.96% AbstractTetrahedralElement::AbstractTetrahedralElement 184ms 0.94% 73.82% 184ms 0.94% std::_Rb_tree_insert_and_rebalance 56ms 0.29% 74.10% 181ms 0.92% std::_Rb_tree::_M_clone_node (inline) 5ms 0.025% 74.13% 177ms 0.9% AbstractTetrahedralElement::CalculateInverseJacobian 6ms 0.031% 74.16% 172ms 0.88% CellPropertyCollection::HasProperty 170ms 0.87% 75.02% 170ms 0.87% Node::GetIndex 131ms 0.67% 75.69% 169ms 0.86% malloc_consolidate 2ms 0.01% 75.70% 163ms 0.83% CellProliferativeTypesWriter::VisitCell 4ms 0.02% 75.72% 163ms 0.83% __printf_fp_l_buffer 0 0% 75.72% 163ms 0.83% __printf_fp_spec (inline) 0 0% 75.72% 162ms 0.83% Cell::HasCellProperty (inline) 66ms 0.34% 76.06% 159ms 0.81% AbstractElement::GetNodeLocation 6ms 0.031% 76.09% 158ms 0.81% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 29ms 0.15% 76.24% 157ms 0.8% TetrahedralMesh::EdgesEnd (partial-inline) 74ms 0.38% 76.61% 157ms 0.8% __printf_fp_buffer_1 11ms 0.056% 76.67% 151ms 0.77% TetrahedralMesh::Clear 1ms 0.0051% 76.67% 151ms 0.77% boost::numeric::ublas::vector_assign (inline) 7ms 0.036% 76.71% 148ms 0.75% MeshBasedCellPopulation::SpringsEnd (inline) 107ms 0.55% 77.26% 144ms 0.73% std::_Rb_tree::equal_range (inline) 134ms 0.68% 77.94% 143ms 0.73% vertexsort 141ms 0.72% 78.66% 141ms 0.72% unlink_chunk 12ms 0.061% 78.72% 140ms 0.71% boost::numeric::ublas::c_vector::c_vector (inline) 139ms 0.71% 79.43% 139ms 0.71% AbstractCellMutationState::~AbstractCellMutationState 45ms 0.23% 79.66% 136ms 0.69% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 6ms 0.031% 79.69% 131ms 0.67% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 128ms 0.65% 80.34% 128ms 0.65% std::vector::size (inline) 39ms 0.2% 80.54% 126ms 0.64% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 26ms 0.13% 80.67% 124ms 0.63% std::num_put::_M_insert_int 75ms 0.38% 81.05% 123ms 0.63% Cylindrical2dMesh::GetVectorFromAtoB 37ms 0.19% 81.24% 122ms 0.62% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 35ms 0.18% 81.42% 121ms 0.62% boost::numeric::ublas::indexing_vector_assign 119ms 0.61% 82.03% 119ms 0.61% incircle 0 0% 82.03% 116ms 0.59% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 37ms 0.19% 82.21% 114ms 0.58% std::__ostream_insert 13ms 0.066% 82.28% 113ms 0.58% std::_Rb_tree_const_iterator::operator++ (inline) 112ms 0.57% 82.85% 112ms 0.57% std::_Rb_tree_increment 0 0% 82.85% 111ms 0.57% AbstractCellBasedSimulation::DoCellRemoval (inline) 111ms 0.57% 83.42% 111ms 0.57% AbstractCellProperty::~AbstractCellProperty 0 0% 83.42% 106ms 0.54% AbstractCellBasedWriter::OpenOutputFileForAppend 16ms 0.082% 83.50% 106ms 0.54% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 83.50% 105ms 0.54% OutputFileHandler::OpenOutputFile 77ms 0.39% 83.89% 104ms 0.53% TetrahedralMesh::EdgeIterator::EdgeIterator 1ms 0.0051% 83.90% 103ms 0.52% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 101ms 0.51% 84.41% 101ms 0.51% [libchaste_mesh.so]