File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16093ms, 83.81% of 19201ms total Dropped 772 nodes (cum <= 96ms) flat flat% sum% cum cum% 0 0% 0% 19159ms 99.78% __libc_start_call_main 0 0% 0% 19159ms 99.78% __libc_start_main_impl 0 0% 0% 19159ms 99.78% _start 0 0% 0% 19138ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19138ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19138ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19138ms 99.67% main 0 0% 0% 19094ms 99.44% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19094ms 99.44% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19094ms 99.44% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19067ms 99.30% AbstractCellBasedSimulation::Solve 0 0% 0% 14526ms 75.65% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0052% 0.0052% 9137ms 47.59% AbstractCellBasedSimulation::DoCellBirth 4ms 0.021% 0.026% 9031ms 47.03% Cell::ReadyToDivide 7ms 0.036% 0.062% 8937ms 46.54% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0052% 0.068% 8791ms 45.78% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 11ms 0.057% 0.12% 8775ms 45.70% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0052% 0.13% 8763ms 45.64% CellCycleModelOdeHandler::SolveOdeToTime 72ms 0.37% 0.51% 8612ms 44.85% AbstractOneStepIvpOdeSolver::InternalSolve 1017ms 5.30% 5.80% 7659ms 39.89% RungeKutta4IvpOdeSolver::CalculateNextYValue 2766ms 14.41% 20.21% 6456ms 33.62% WntCellCycleOdeSystem::EvaluateYDerivatives 3ms 0.016% 20.22% 5282ms 27.51% MeshBasedCellPopulation::Update 2ms 0.01% 20.23% 4092ms 21.31% Cylindrical2dMesh::ReMesh 60ms 0.31% 20.55% 3704ms 19.29% AbstractCellProperty::IsType (inline) 1ms 0.0052% 20.55% 2523ms 13.14% OffLatticeSimulation::UpdateCellLocationsAndTopology 353ms 1.84% 22.39% 2305ms 12.00% AbstractCellProperty::IsSame 0 0% 22.39% 2261ms 11.78% MutableMesh::ReMesh 1ms 0.0052% 22.39% 2219ms 11.56% ForwardEulerNumericalMethod::UpdateAllNodePositions 12ms 0.062% 22.46% 2164ms 11.27% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 22.46% 2012ms 10.48% AbstractCellPopulation::WriteResultsToFiles 225ms 1.17% 23.63% 1952ms 10.17% std::type_info::operator== (inline) 1821ms 9.48% 33.11% 1821ms 9.48% __strcmp_avx2 758ms 3.95% 37.06% 1817ms 9.46% std::_Rb_tree::_M_lower_bound (inline) 154ms 0.8% 37.86% 1689ms 8.80% TetrahedralMesh::EdgeIterator::operator++ 72ms 0.37% 38.24% 1366ms 7.11% std::_Rb_tree::find (inline) 0 0% 38.24% 1157ms 6.03% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.021% 38.26% 1129ms 5.88% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 5ms 0.026% 38.28% 1122ms 5.84% TetrahedralMesh::ImportFromMesher 54ms 0.28% 38.57% 1062ms 5.53% operator new 10ms 0.052% 38.62% 1031ms 5.37% MeshBasedCellPopulation::SpringIterator::operator++ 7ms 0.036% 38.65% 1005ms 5.23% std::set::insert (inline) 13ms 0.068% 38.72% 998ms 5.20% std::_Rb_tree::_M_insert_unique 232ms 1.21% 39.93% 986ms 5.14% __GI___libc_malloc 40ms 0.21% 40.14% 952ms 4.96% std::__new_allocator::allocate (inline) 0 0% 40.14% 951ms 4.95% std::allocator_traits::allocate (inline) 0 0% 40.14% 894ms 4.66% triangulate 0 0% 40.14% 843ms 4.39% std::set::count (inline) 0 0% 40.14% 806ms 4.20% delaunay 4ms 0.021% 40.16% 806ms 4.20% divconqdelaunay 4ms 0.021% 40.18% 759ms 3.95% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 2ms 0.01% 40.19% 744ms 3.87% AbstractTwoBodyInteractionForce::AddForceContribution 741ms 3.86% 44.05% 741ms 3.86% WntCellCycleOdeSystem::CalculateStoppingEvent 7ms 0.036% 44.09% 710ms 3.70% CellPopulationElementWriter::Visit 62ms 0.32% 44.41% 699ms 3.64% std::map::operator[] (partial-inline) 688ms 3.58% 47.99% 688ms 3.58% std::_Rb_tree::_S_right (inline) 356ms 1.85% 49.85% 656ms 3.42% _int_malloc 30ms 0.16% 50.00% 654ms 3.41% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 14ms 0.073% 50.08% 640ms 3.33% std::less::operator() (inline) 626ms 3.26% 53.34% 626ms 3.26% std::operator< (inline) 0 0% 53.34% 619ms 3.22% std::_Rb_tree::_M_create_node (inline) 19ms 0.099% 53.43% 610ms 3.18% AbstractCellPopulation::GetCellUsingLocationIndex 197ms 1.03% 54.46% 603ms 3.14% __dynamic_cast 2ms 0.01% 54.47% 601ms 3.13% MeshBasedCellPopulation::AcceptCellWriter 0 0% 54.47% 596ms 3.10% std::_Rb_tree::_M_get_node (inline) 28ms 0.15% 54.62% 585ms 3.05% std::_Rb_tree::_M_insert_ (inline) 11ms 0.057% 54.67% 574ms 2.99% Element::Element 0 0% 54.67% 559ms 2.91% std::_Rb_tree::_Alloc_node::operator() (inline) 5ms 0.026% 54.70% 545ms 2.84% CellPropertyCollection::GetPropertiesType (inline) 0 0% 54.70% 539ms 2.81% std::_Rb_tree::lower_bound (inline) 0 0% 54.70% 539ms 2.81% std::map::lower_bound (inline) 7ms 0.036% 54.74% 523ms 2.72% MutableMesh::ReIndex 0 0% 54.74% 520ms 2.71% std::map::find (inline) 13ms 0.068% 54.80% 507ms 2.64% Cylindrical2dMesh::ReconstructCylindricalMesh 15ms 0.078% 54.88% 503ms 2.62% Element::RegisterWithNodes (inline) 13ms 0.068% 54.95% 488ms 2.54% Cylindrical2dMesh::CorrectNonPeriodicMesh 11ms 0.057% 55.01% 488ms 2.54% Node::AddElement 145ms 0.76% 55.76% 485ms 2.53% __GI___libc_free 0 0% 55.76% 453ms 2.36% std::ostream::operator<< (inline) 53ms 0.28% 56.04% 452ms 2.35% std::ostream::_M_insert 3ms 0.016% 56.05% 442ms 2.30% AbstractCellProperty::IsSubType (inline) 285ms 1.48% 57.54% 429ms 2.23% AbstractCellMutationState::AbstractCellMutationState 17ms 0.089% 57.63% 406ms 2.11% std::__new_allocator::deallocate (inline) 14ms 0.073% 57.70% 403ms 2.10% divconqrecurse 0 0% 57.70% 402ms 2.09% std::allocator_traits::deallocate (inline) 163ms 0.85% 58.55% 400ms 2.08% std::_Rb_tree::_M_get_insert_unique_pos 106ms 0.55% 59.10% 392ms 2.04% std::_Rb_tree::_M_erase 1ms 0.0052% 59.11% 381ms 1.98% std::_Rb_tree::erase 2ms 0.01% 59.12% 381ms 1.98% std::set::erase (inline) 105ms 0.55% 59.66% 375ms 1.95% mergehulls 13ms 0.068% 59.73% 374ms 1.95% Node::RemoveElement 0 0% 59.73% 363ms 1.89% std::_Rb_tree::_M_drop_node (inline) 26ms 0.14% 59.87% 362ms 1.89% std::_Rb_tree::~_Rb_tree (inline) 0 0% 59.87% 355ms 1.85% std::_Vector_base::_M_allocate (inline) 342ms 1.78% 61.65% 342ms 1.78% [libchaste_cell_based.so] 287ms 1.49% 63.14% 340ms 1.77% _int_free 30ms 0.16% 63.30% 335ms 1.74% Element::ResetIndex 0 0% 63.30% 334ms 1.74% std::set::~set (inline) 0 0% 63.30% 329ms 1.71% std::_Rb_tree::_M_put_node (inline) 13ms 0.068% 63.37% 326ms 1.70% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 3ms 0.016% 63.38% 313ms 1.63% LegacyCellProliferativeTypesWriter::VisitCell 151ms 0.79% 64.17% 303ms 1.58% __cxxabiv1::__si_class_type_info::__do_dyncast 6ms 0.031% 64.20% 297ms 1.55% Cell::GetMutationState 18ms 0.094% 64.29% 295ms 1.54% std::vector::push_back (inline) 1ms 0.0052% 64.30% 292ms 1.52% AbstractCellPopulation::Iterator::operator++ (inline) 4ms 0.021% 64.32% 292ms 1.52% Cell::GetCellProliferativeType 290ms 1.51% 65.83% 292ms 1.52% std::vector::operator[] (inline) 40ms 0.21% 66.04% 291ms 1.52% AbstractCellPopulation::Iterator::IsRealCell (inline) 20ms 0.1% 66.14% 283ms 1.47% std::_Rb_tree::_Rb_tree (partial-inline) 7ms 0.036% 66.18% 281ms 1.46% AbstractCellPopulation::GetLocationIndexUsingCell 26ms 0.14% 66.31% 278ms 1.45% AbstractTetrahedralElement::CalculateJacobian 1ms 0.0052% 66.32% 277ms 1.44% NodeLocationWriter::Visit 16ms 0.083% 66.40% 269ms 1.40% std::vector::_M_realloc_insert 3ms 0.016% 66.42% 256ms 1.33% std::set::set (inline) 7ms 0.036% 66.45% 255ms 1.33% alternateaxes 6ms 0.031% 66.49% 247ms 1.29% AbstractCellPopulation::IsCellAttachedToLocationIndex 236ms 1.23% 67.72% 247ms 1.29% vertexmedian 90ms 0.47% 68.18% 246ms 1.28% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 104ms 0.54% 68.73% 243ms 1.27% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 25ms 0.13% 68.86% 243ms 1.27% std::_Rb_tree::_M_copy (inline) 18ms 0.094% 68.95% 238ms 1.24% std::num_put::_M_insert_float 7ms 0.036% 68.99% 232ms 1.21% std::_Rb_tree::_M_erase_aux (inline) 0 0% 68.99% 227ms 1.18% TetrahedralMesh::RefreshJacobianCachedData 60ms 0.31% 69.30% 225ms 1.17% ApcOneHitCellMutationState::ApcOneHitCellMutationState 14ms 0.073% 69.37% 223ms 1.16% Element::MarkAsDeleted 29ms 0.15% 69.52% 217ms 1.13% AbstractTetrahedralElement::RefreshJacobian 5ms 0.026% 69.55% 216ms 1.12% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 8ms 0.042% 69.59% 215ms 1.12% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 66ms 0.34% 69.93% 214ms 1.11% std::_Rb_tree::_M_clone_node (inline) 159ms 0.83% 70.76% 210ms 1.09% AbstractElement::GetNodeGlobalIndex 2ms 0.01% 70.77% 202ms 1.05% MeshBasedCellPopulation::GetDampingConstant 6ms 0.031% 70.80% 201ms 1.05% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.01% 70.81% 200ms 1.04% AbstractCentreBasedCellPopulation::GetDampingConstant 12ms 0.062% 70.88% 198ms 1.03% TetrahedralMesh::Clear 8ms 0.042% 70.92% 192ms 1% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 70.92% 192ms 1% std::__cxx11::collate::do_transform 2ms 0.01% 70.93% 188ms 0.98% ___vsnprintf 0 0% 70.93% 186ms 0.97% __vsnprintf_internal (inline) 1ms 0.0052% 70.93% 185ms 0.96% CellPropertyCollection::HasProperty 125ms 0.65% 71.58% 185ms 0.96% malloc_consolidate 0 0% 71.58% 183ms 0.95% Cell::HasCellProperty (inline) 0 0% 71.58% 183ms 0.95% OffLatticeSimulation::ApplyBoundaries 29ms 0.15% 71.74% 183ms 0.95% __printf_buffer 170ms 0.89% 72.62% 170ms 0.89% incircle 165ms 0.86% 73.48% 165ms 0.86% std::_Rb_tree_insert_and_rebalance 4ms 0.021% 73.50% 160ms 0.83% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 57ms 0.3% 73.80% 159ms 0.83% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 64ms 0.33% 74.13% 158ms 0.82% AbstractElement::GetNodeLocation 109ms 0.57% 74.70% 156ms 0.81% std::_Rb_tree::equal_range (inline) 155ms 0.81% 75.51% 155ms 0.81% unlink_chunk 93ms 0.48% 75.99% 154ms 0.8% Cylindrical2dMesh::GetVectorFromAtoB 153ms 0.8% 76.79% 153ms 0.8% [libchaste_crypt.so] 3ms 0.016% 76.80% 149ms 0.78% CellProliferativeTypesWriter::VisitCell 149ms 0.78% 77.58% 149ms 0.78% Node::GetIndex 4ms 0.021% 77.60% 146ms 0.76% boost::numeric::ublas::vector_assign (inline) 4ms 0.021% 77.62% 145ms 0.76% __printf_fp_l_buffer 0 0% 77.62% 145ms 0.76% __printf_fp_spec (inline) 50ms 0.26% 77.88% 139ms 0.72% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 126ms 0.66% 78.54% 138ms 0.72% vertexsort 54ms 0.28% 78.82% 137ms 0.71% __printf_fp_buffer_1 134ms 0.7% 79.52% 134ms 0.7% AbstractCellMutationState::~AbstractCellMutationState 1ms 0.0052% 79.52% 134ms 0.7% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 0 0% 79.52% 130ms 0.68% AbstractCellBasedWriter::OpenOutputFileForAppend 36ms 0.19% 79.71% 130ms 0.68% std::__ostream_insert 130ms 0.68% 80.39% 130ms 0.68% std::vector::size (inline) 48ms 0.25% 80.64% 129ms 0.67% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 9ms 0.047% 80.68% 129ms 0.67% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 80.68% 128ms 0.67% OutputFileHandler::OpenOutputFile 2ms 0.01% 80.69% 127ms 0.66% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 20ms 0.1% 80.80% 124ms 0.65% boost::detail::shared_count::~shared_count (inline) 14ms 0.073% 80.87% 124ms 0.65% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 80.87% 124ms 0.65% boost::shared_ptr::~shared_ptr (inline) 122ms 0.64% 81.51% 122ms 0.64% std::type_info::name (inline) 29ms 0.15% 81.66% 120ms 0.62% boost::numeric::ublas::indexing_vector_assign 7ms 0.036% 81.69% 116ms 0.6% Node::~Node 3ms 0.016% 81.71% 115ms 0.6% Cell::SetCellProliferativeType 5ms 0.026% 81.74% 113ms 0.59% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 81.74% 112ms 0.58% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 111ms 0.58% 82.31% 111ms 0.58% std::_Rb_tree_increment 0 0% 82.31% 107ms 0.56% AbstractCellBasedSimulation::DoCellRemoval (inline) 4ms 0.021% 82.33% 105ms 0.55% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 19ms 0.099% 82.43% 105ms 0.55% std::num_put::_M_insert_int 19ms 0.099% 82.53% 103ms 0.54% MeshBasedCellPopulation::SpringIterator::SpringIterator 1ms 0.0052% 82.54% 102ms 0.53% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 62ms 0.32% 82.86% 102ms 0.53% TimeStepper::AdvanceOneTimeStep 3ms 0.016% 82.88% 100ms 0.52% std::operator<< (inline) 20ms 0.1% 82.98% 99ms 0.52% TetrahedralMesh::EdgesEnd 6ms 0.031% 83.01% 98ms 0.51% std::_Rb_tree::_M_emplace_hint_unique 97ms 0.51% 83.52% 97ms 0.51% AbstractElement::IsDeleted 57ms 0.3% 83.81% 97ms 0.51% boost::numeric::ublas::c_matrix::operator() (partial-inline)