File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 17314ms, 84.15% of 20576ms total Dropped 805 nodes (cum <= 102.88ms) flat flat% sum% cum cum% 0 0% 0% 20527ms 99.76% __libc_start_call_main 0 0% 0% 20527ms 99.76% __libc_start_main_impl 0 0% 0% 20527ms 99.76% _start 0 0% 0% 20507ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20507ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20507ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20507ms 99.66% main 0 0% 0% 20465ms 99.46% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20465ms 99.46% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20465ms 99.46% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 20437ms 99.32% AbstractCellBasedSimulation::Solve 0 0% 0% 15768ms 76.63% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 10125ms 49.21% AbstractCellBasedSimulation::DoCellBirth 7ms 0.034% 0.034% 10036ms 48.78% Cell::ReadyToDivide 6ms 0.029% 0.063% 9917ms 48.20% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.063% 9777ms 47.52% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 17ms 0.083% 0.15% 9768ms 47.47% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.0097% 0.16% 9747ms 47.37% CellCycleModelOdeHandler::SolveOdeToTime 74ms 0.36% 0.52% 9537ms 46.35% AbstractOneStepIvpOdeSolver::InternalSolve 853ms 4.15% 4.66% 8675ms 42.16% RungeKutta4IvpOdeSolver::CalculateNextYValue 3653ms 17.75% 22.41% 7600ms 36.94% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 22.41% 5506ms 26.76% MeshBasedCellPopulation::Update 5ms 0.024% 22.44% 4303ms 20.91% Cylindrical2dMesh::ReMesh 92ms 0.45% 22.89% 4012ms 19.50% AbstractCellProperty::IsType (inline) 609ms 2.96% 25.85% 2776ms 13.49% AbstractCellProperty::IsSame 1ms 0.0049% 25.85% 2580ms 12.54% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0049% 25.86% 2443ms 11.87% MutableMesh::ReMesh 1ms 0.0049% 25.86% 2286ms 11.11% ForwardEulerNumericalMethod::UpdateAllNodePositions 13ms 0.063% 25.92% 2238ms 10.88% AbstractNumericalMethod::ComputeForcesIncludingDamping 488ms 2.37% 28.30% 2167ms 10.53% std::type_info::operator== (inline) 0 0% 28.30% 2084ms 10.13% AbstractCellPopulation::WriteResultsToFiles 797ms 3.87% 32.17% 1840ms 8.94% std::_Rb_tree::_M_lower_bound (inline) 139ms 0.68% 32.84% 1671ms 8.12% TetrahedralMesh::EdgeIterator::operator++ 1639ms 7.97% 40.81% 1639ms 7.97% __strcmp_avx2 75ms 0.36% 41.17% 1385ms 6.73% std::_Rb_tree::find (inline) 10ms 0.049% 41.22% 1274ms 6.19% TetrahedralMesh::ImportFromMesher 1ms 0.0049% 41.23% 1162ms 5.65% MeshBasedCellPopulation::UpdateNodePairs 48ms 0.23% 41.46% 1132ms 5.50% operator new 7ms 0.034% 41.49% 1107ms 5.38% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 244ms 1.19% 42.68% 1068ms 5.19% __GI___libc_malloc 10ms 0.049% 42.73% 1028ms 5.00% MeshBasedCellPopulation::SpringIterator::operator++ 41ms 0.2% 42.93% 1004ms 4.88% std::__new_allocator::allocate (inline) 0 0% 42.93% 996ms 4.84% std::allocator_traits::allocate (inline) 11ms 0.053% 42.98% 985ms 4.79% std::set::insert (inline) 9ms 0.044% 43.03% 973ms 4.73% std::_Rb_tree::_M_insert_unique 0 0% 43.03% 882ms 4.29% std::set::count (inline) 2ms 0.0097% 43.04% 821ms 3.99% triangulate 5ms 0.024% 43.06% 769ms 3.74% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 396ms 1.92% 44.98% 734ms 3.57% _int_malloc 0 0% 44.98% 733ms 3.56% delaunay 3ms 0.015% 45.00% 732ms 3.56% divconqdelaunay 2ms 0.0097% 45.01% 729ms 3.54% AbstractTwoBodyInteractionForce::AddForceContribution 10ms 0.049% 45.06% 724ms 3.52% CellPopulationElementWriter::Visit 52ms 0.25% 45.31% 718ms 3.49% std::map::operator[] (partial-inline) 232ms 1.13% 46.44% 680ms 3.30% __dynamic_cast 13ms 0.063% 46.50% 675ms 3.28% CellPropertyCollection::GetPropertiesType (inline) 663ms 3.22% 49.72% 673ms 3.27% WntCellCycleOdeSystem::CalculateStoppingEvent 20ms 0.097% 49.82% 662ms 3.22% std::less::operator() (inline) 37ms 0.18% 50.00% 654ms 3.18% std::_Rb_tree::_M_insert_ (inline) 0 0% 50.00% 649ms 3.15% std::_Rb_tree::_M_create_node (inline) 642ms 3.12% 53.12% 642ms 3.12% std::operator< (inline) 641ms 3.12% 56.24% 641ms 3.12% std::_Rb_tree::_S_right (inline) 36ms 0.17% 56.41% 637ms 3.10% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 2ms 0.0097% 56.42% 631ms 3.07% MeshBasedCellPopulation::AcceptCellWriter 0 0% 56.42% 620ms 3.01% std::_Rb_tree::_M_get_node (inline) 22ms 0.11% 56.53% 600ms 2.92% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 56.53% 578ms 2.81% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 56.53% 567ms 2.76% std::_Rb_tree::lower_bound (inline) 0 0% 56.53% 567ms 2.76% std::map::lower_bound (inline) 5ms 0.024% 56.55% 552ms 2.68% Element::Element 2ms 0.0097% 56.56% 530ms 2.58% AbstractCellProperty::IsSubType (inline) 10ms 0.049% 56.61% 526ms 2.56% MutableMesh::ReIndex 2ms 0.0097% 56.62% 507ms 2.46% std::ostream::operator<< (inline) 193ms 0.94% 57.56% 505ms 2.45% __GI___libc_free 70ms 0.34% 57.90% 505ms 2.45% std::ostream::_M_insert 10ms 0.049% 57.95% 504ms 2.45% Element::RegisterWithNodes (inline) 0 0% 57.95% 496ms 2.41% std::map::find (inline) 6ms 0.029% 57.98% 492ms 2.39% Node::AddElement 334ms 1.62% 59.60% 476ms 2.31% AbstractCellMutationState::AbstractCellMutationState 7ms 0.034% 59.63% 467ms 2.27% Cylindrical2dMesh::ReconstructCylindricalMesh 10ms 0.049% 59.68% 455ms 2.21% Cylindrical2dMesh::CorrectNonPeriodicMesh 137ms 0.67% 60.35% 443ms 2.15% std::_Rb_tree::_M_erase 27ms 0.13% 60.48% 415ms 2.02% std::_Rb_tree::~_Rb_tree (inline) 6ms 0.029% 60.51% 395ms 1.92% Cell::GetMutationState 0 0% 60.51% 386ms 1.88% std::set::~set (inline) 11ms 0.053% 60.56% 383ms 1.86% std::_Rb_tree::erase 1ms 0.0049% 60.57% 382ms 1.86% std::set::erase (inline) 5ms 0.024% 60.59% 381ms 1.85% std::_Vector_base::_M_allocate (inline) 62ms 0.3% 60.89% 380ms 1.85% TetrahedralMesh::Clear 24ms 0.12% 61.01% 378ms 1.84% divconqrecurse 13ms 0.063% 61.07% 374ms 1.82% std::__new_allocator::deallocate (inline) 4ms 0.019% 61.09% 372ms 1.81% Node::RemoveElement 0 0% 61.09% 368ms 1.79% std::allocator_traits::deallocate (inline) 172ms 0.84% 61.93% 350ms 1.70% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 61.93% 348ms 1.69% std::_Rb_tree::_M_drop_node (inline) 105ms 0.51% 62.44% 341ms 1.66% mergehulls 36ms 0.17% 62.61% 337ms 1.64% Element::ResetIndex 3ms 0.015% 62.63% 330ms 1.60% Cell::GetCellProliferativeType 1ms 0.0049% 62.63% 322ms 1.56% TetrahedralMesh::RefreshJacobianCachedData 10ms 0.049% 62.68% 318ms 1.55% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 62.68% 317ms 1.54% NodeLocationWriter::Visit 253ms 1.23% 63.91% 311ms 1.51% _int_free 119ms 0.58% 64.49% 311ms 1.51% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 64.49% 307ms 1.49% std::_Rb_tree::_M_put_node (inline) 31ms 0.15% 64.64% 307ms 1.49% std::_Rb_tree::_Rb_tree 307ms 1.49% 66.13% 307ms 1.49% std::type_info::name (inline) 7ms 0.034% 66.16% 305ms 1.48% LegacyCellProliferativeTypesWriter::VisitCell 3ms 0.015% 66.18% 304ms 1.48% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0049% 66.18% 296ms 1.44% MeshBasedCellPopulation::GetDampingConstant 1ms 0.0049% 66.19% 295ms 1.43% AbstractCentreBasedCellPopulation::GetDampingConstant 2ms 0.0097% 66.20% 290ms 1.41% std::set::set (inline) 1ms 0.0049% 66.20% 288ms 1.40% AbstractCellPopulation::Iterator::operator++ (inline) 46ms 0.22% 66.43% 286ms 1.39% AbstractCellPopulation::Iterator::IsRealCell (inline) 20ms 0.097% 66.52% 277ms 1.35% AbstractTetrahedralElement::CalculateJacobian 18ms 0.087% 66.61% 277ms 1.35% std::num_put::_M_insert_float 9ms 0.044% 66.66% 276ms 1.34% AbstractCellPopulation::IsCellAttachedToLocationIndex 272ms 1.32% 67.98% 273ms 1.33% std::vector::operator[] (inline) 16ms 0.078% 68.06% 272ms 1.32% AbstractTetrahedralElement::CalculateInverseJacobian 10ms 0.049% 68.10% 252ms 1.22% std::vector::push_back (inline) 32ms 0.16% 68.26% 245ms 1.19% std::_Rb_tree::_M_copy (inline) 15ms 0.073% 68.33% 232ms 1.13% std::_Rb_tree::_M_erase_aux (inline) 10ms 0.049% 68.38% 230ms 1.12% std::vector::_M_realloc_insert 57ms 0.28% 68.66% 229ms 1.11% ApcOneHitCellMutationState::ApcOneHitCellMutationState 1ms 0.0049% 68.66% 220ms 1.07% alternateaxes 219ms 1.06% 69.73% 219ms 1.06% [libchaste_cell_based.so] 7ms 0.034% 69.76% 218ms 1.06% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 161ms 0.78% 70.54% 218ms 1.06% malloc_consolidate 205ms 1% 71.54% 218ms 1.06% vertexmedian 25ms 0.12% 71.66% 216ms 1.05% AbstractTetrahedralElement::RefreshJacobian 45ms 0.22% 71.88% 215ms 1.04% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 10ms 0.049% 71.93% 215ms 1.04% Node::~Node 6ms 0.029% 71.96% 213ms 1.04% std::__cxx11::collate::do_transform 63ms 0.31% 72.26% 211ms 1.03% std::_Rb_tree::_M_clone_node (inline) 36ms 0.17% 72.44% 210ms 1.02% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 4ms 0.019% 72.46% 208ms 1.01% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.0049% 72.46% 205ms 1% ___vsnprintf 0 0% 72.46% 204ms 0.99% __vsnprintf_internal (inline) 203ms 0.99% 73.45% 203ms 0.99% std::_Rb_tree_insert_and_rebalance 24ms 0.12% 73.57% 202ms 0.98% __printf_buffer 13ms 0.063% 73.63% 200ms 0.97% Element::MarkAsDeleted 0 0% 73.63% 192ms 0.93% OffLatticeSimulation::ApplyBoundaries 3ms 0.015% 73.64% 190ms 0.92% CellProliferativeTypesWriter::VisitCell 1ms 0.0049% 73.65% 189ms 0.92% CellPropertyCollection::HasProperty 0 0% 73.65% 186ms 0.9% Cell::HasCellProperty (inline) 138ms 0.67% 74.32% 182ms 0.88% AbstractElement::GetNodeGlobalIndex 174ms 0.85% 75.17% 174ms 0.85% unlink_chunk 89ms 0.43% 75.60% 170ms 0.83% AbstractElement::GetNodeLocation 5ms 0.024% 75.62% 168ms 0.82% __printf_fp_l_buffer 0 0% 75.62% 168ms 0.82% __printf_fp_spec (inline) 10ms 0.049% 75.67% 158ms 0.77% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 4ms 0.019% 75.69% 157ms 0.76% AbstractTetrahedralElement::AbstractTetrahedralElement 157ms 0.76% 76.45% 157ms 0.76% Node::GetIndex 82ms 0.4% 76.85% 155ms 0.75% __printf_fp_buffer_1 3ms 0.015% 76.87% 151ms 0.73% boost::numeric::ublas::vector_assign (inline) 151ms 0.73% 77.60% 151ms 0.73% incircle 94ms 0.46% 78.06% 147ms 0.71% std::_Rb_tree::equal_range (inline) 12ms 0.058% 78.12% 143ms 0.69% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 30ms 0.15% 78.26% 142ms 0.69% TetrahedralMesh::EdgesEnd 142ms 0.69% 78.95% 142ms 0.69% std::vector::size (inline) 139ms 0.68% 79.63% 139ms 0.68% std::_Rb_tree_increment 0 0% 79.63% 135ms 0.66% AbstractCellBasedSimulation::DoCellRemoval (inline) 8ms 0.039% 79.67% 133ms 0.65% std::_Rb_tree_const_iterator::operator++ (inline) 50ms 0.24% 79.91% 132ms 0.64% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 44ms 0.21% 80.12% 132ms 0.64% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 2ms 0.0097% 80.13% 131ms 0.64% MeshBasedCellPopulation::SpringsEnd (inline) 1ms 0.0049% 80.14% 131ms 0.64% std::vector::_M_default_append 0 0% 80.14% 131ms 0.64% std::vector::resize (inline) 0 0% 80.14% 128ms 0.62% AbstractCellBasedWriter::OpenOutputFileForAppend 128ms 0.62% 80.76% 128ms 0.62% AbstractCellProperty::~AbstractCellProperty 2ms 0.0097% 80.77% 128ms 0.62% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 80.77% 127ms 0.62% OutputFileHandler::OpenOutputFile 72ms 0.35% 81.12% 126ms 0.61% Cylindrical2dMesh::GetVectorFromAtoB 9ms 0.044% 81.16% 125ms 0.61% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 81.16% 123ms 0.6% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 114ms 0.55% 81.72% 123ms 0.6% vertexsort 119ms 0.58% 82.29% 119ms 0.58% AbstractCellMutationState::~AbstractCellMutationState 9ms 0.044% 82.34% 119ms 0.58% Cylindrical2dMesh::CreateMirrorNodes 0 0% 82.34% 119ms 0.58% NodeMap::NodeMap 56ms 0.27% 82.61% 117ms 0.57% std::_Vector_base::_M_deallocate (inline) 26ms 0.13% 82.74% 115ms 0.56% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 113ms 0.55% 83.29% 113ms 0.55% AbstractElement::IsDeleted 11ms 0.053% 83.34% 113ms 0.55% boost::detail::shared_count::~shared_count (inline) 0 0% 83.34% 113ms 0.55% boost::shared_ptr::~shared_ptr (inline) 33ms 0.16% 83.50% 110ms 0.53% boost::numeric::ublas::indexing_vector_assign 40ms 0.19% 83.69% 110ms 0.53% std::__ostream_insert 0 0% 83.69% 107ms 0.52% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 67ms 0.33% 84.02% 104ms 0.51% TetrahedralMesh::EdgeIterator::EdgeIterator 24ms 0.12% 84.14% 104ms 0.51% std::num_put::_M_insert_int 2ms 0.0097% 84.15% 103ms 0.5% Cell::SetCellProliferativeType