File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 17211ms, 84.60% of 20345ms total Dropped 808 nodes (cum <= 101.72ms) flat flat% sum% cum cum% 0 0% 0% 20296ms 99.76% __libc_start_call_main 0 0% 0% 20296ms 99.76% __libc_start_main_impl 0 0% 0% 20296ms 99.76% _start 0 0% 0% 20276ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20276ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20276ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20276ms 99.66% main 0 0% 0% 20234ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20234ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20234ms 99.45% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 20205ms 99.31% AbstractCellBasedSimulation::Solve 0 0% 0% 15558ms 76.47% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0049% 0.0049% 10065ms 49.47% AbstractCellBasedSimulation::DoCellBirth 16ms 0.079% 0.084% 9970ms 49.00% Cell::ReadyToDivide 4ms 0.02% 0.1% 9848ms 48.41% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.1% 9685ms 47.60% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 19ms 0.093% 0.2% 9672ms 47.54% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.015% 0.21% 9653ms 47.45% CellCycleModelOdeHandler::SolveOdeToTime 73ms 0.36% 0.57% 9454ms 46.47% AbstractOneStepIvpOdeSolver::InternalSolve 891ms 4.38% 4.95% 8636ms 42.45% RungeKutta4IvpOdeSolver::CalculateNextYValue 3603ms 17.71% 22.66% 7514ms 36.93% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.0098% 22.67% 5383ms 26.46% MeshBasedCellPopulation::Update 7ms 0.034% 22.70% 4188ms 20.58% Cylindrical2dMesh::ReMesh 76ms 0.37% 23.08% 3996ms 19.64% AbstractCellProperty::IsType (inline) 566ms 2.78% 25.86% 2801ms 13.77% AbstractCellProperty::IsSame 0 0% 25.86% 2526ms 12.42% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 25.86% 2350ms 11.55% MutableMesh::ReMesh 416ms 2.04% 27.90% 2235ms 10.99% std::type_info::operator== (inline) 1ms 0.0049% 27.91% 2222ms 10.92% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.049% 27.96% 2177ms 10.70% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0049% 27.96% 2109ms 10.37% AbstractCellPopulation::WriteResultsToFiles 830ms 4.08% 32.04% 1847ms 9.08% std::_Rb_tree::_M_lower_bound (inline) 1768ms 8.69% 40.73% 1768ms 8.69% __strcmp_avx2 156ms 0.77% 41.50% 1725ms 8.48% TetrahedralMesh::EdgeIterator::operator++ 61ms 0.3% 41.80% 1377ms 6.77% std::_Rb_tree::find (inline) 10ms 0.049% 41.85% 1191ms 5.85% TetrahedralMesh::ImportFromMesher 0 0% 41.85% 1145ms 5.63% MeshBasedCellPopulation::UpdateNodePairs 8ms 0.039% 41.89% 1136ms 5.58% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 46ms 0.23% 42.11% 1078ms 5.30% operator new 7ms 0.034% 42.15% 1033ms 5.08% MeshBasedCellPopulation::SpringIterator::operator++ 229ms 1.13% 43.27% 1022ms 5.02% __GI___libc_malloc 12ms 0.059% 43.33% 1017ms 5.00% std::set::insert (inline) 15ms 0.074% 43.41% 1003ms 4.93% std::_Rb_tree::_M_insert_unique 44ms 0.22% 43.62% 946ms 4.65% std::__new_allocator::allocate (inline) 0 0% 43.62% 943ms 4.64% std::allocator_traits::allocate (inline) 0 0% 43.62% 864ms 4.25% std::set::count (inline) 3ms 0.015% 43.64% 816ms 4.01% triangulate 4ms 0.02% 43.66% 787ms 3.87% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 43.66% 740ms 3.64% delaunay 0 0% 43.66% 740ms 3.64% divconqdelaunay 1ms 0.0049% 43.66% 725ms 3.56% AbstractTwoBodyInteractionForce::AddForceContribution 15ms 0.074% 43.74% 710ms 3.49% CellPopulationElementWriter::Visit 49ms 0.24% 43.98% 709ms 3.48% std::map::operator[] (partial-inline) 373ms 1.83% 45.81% 700ms 3.44% _int_malloc 234ms 1.15% 46.96% 684ms 3.36% __dynamic_cast 14ms 0.069% 47.03% 671ms 3.30% CellPropertyCollection::GetPropertiesType (inline) 15ms 0.074% 47.10% 664ms 3.26% std::less::operator() (inline) 663ms 3.26% 50.36% 663ms 3.26% std::_Rb_tree::_S_right (inline) 647ms 3.18% 53.54% 662ms 3.25% WntCellCycleOdeSystem::CalculateStoppingEvent 649ms 3.19% 56.73% 649ms 3.19% std::operator< (inline) 3ms 0.015% 56.75% 642ms 3.16% MeshBasedCellPopulation::AcceptCellWriter 32ms 0.16% 56.90% 638ms 3.14% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 27ms 0.13% 57.04% 629ms 3.09% std::_Rb_tree::_M_insert_ (inline) 0 0% 57.04% 621ms 3.05% std::_Rb_tree::_M_create_node (inline) 0 0% 57.04% 597ms 2.93% std::_Rb_tree::_M_get_node (inline) 0 0% 57.04% 570ms 2.80% std::_Rb_tree::lower_bound (inline) 0 0% 57.04% 570ms 2.80% std::map::lower_bound (inline) 17ms 0.084% 57.12% 568ms 2.79% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 57.12% 557ms 2.74% std::_Rb_tree::_Alloc_node::operator() (inline) 3ms 0.015% 57.13% 543ms 2.67% Element::Element 2ms 0.0098% 57.14% 540ms 2.65% AbstractCellProperty::IsSubType (inline) 12ms 0.059% 57.20% 533ms 2.62% Cylindrical2dMesh::ReconstructCylindricalMesh 0 0% 57.20% 511ms 2.51% std::map::find (inline) 6ms 0.029% 57.23% 501ms 2.46% MutableMesh::ReIndex 2ms 0.0098% 57.24% 498ms 2.45% std::ostream::operator<< (inline) 67ms 0.33% 57.57% 495ms 2.43% std::ostream::_M_insert 335ms 1.65% 59.22% 492ms 2.42% AbstractCellMutationState::AbstractCellMutationState 10ms 0.049% 59.27% 484ms 2.38% Element::RegisterWithNodes (inline) 171ms 0.84% 60.11% 475ms 2.33% __GI___libc_free 14ms 0.069% 60.18% 467ms 2.30% Cylindrical2dMesh::CorrectNonPeriodicMesh 9ms 0.044% 60.22% 466ms 2.29% Node::AddElement 139ms 0.68% 60.90% 413ms 2.03% std::_Rb_tree::_M_erase 5ms 0.025% 60.93% 399ms 1.96% std::_Rb_tree::erase 0 0% 60.93% 396ms 1.95% std::set::erase (inline) 5ms 0.025% 60.95% 383ms 1.88% Node::RemoveElement 17ms 0.084% 61.04% 370ms 1.82% std::_Rb_tree::~_Rb_tree (inline) 16ms 0.079% 61.12% 367ms 1.80% std::__new_allocator::deallocate (inline) 18ms 0.088% 61.20% 360ms 1.77% divconqrecurse 130ms 0.64% 61.84% 360ms 1.77% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 61.84% 359ms 1.76% std::allocator_traits::deallocate (inline) 5ms 0.025% 61.87% 349ms 1.72% Cell::GetCellProliferativeType 1ms 0.0049% 61.87% 347ms 1.71% std::_Vector_base::_M_allocate (inline) 2ms 0.0098% 61.88% 344ms 1.69% Cell::GetMutationState 0 0% 61.88% 337ms 1.66% std::set::~set (inline) 89ms 0.44% 62.32% 336ms 1.65% mergehulls 168ms 0.83% 63.15% 335ms 1.65% __cxxabiv1::__si_class_type_info::__do_dyncast 332ms 1.63% 64.78% 332ms 1.63% std::type_info::name (inline) 0 0% 64.78% 328ms 1.61% std::_Rb_tree::_M_drop_node (inline) 27ms 0.13% 64.91% 319ms 1.57% Element::ResetIndex 8ms 0.039% 64.95% 311ms 1.53% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 5ms 0.025% 64.97% 305ms 1.50% LegacyCellProliferativeTypesWriter::VisitCell 237ms 1.16% 66.14% 304ms 1.49% _int_free 21ms 0.1% 66.24% 303ms 1.49% AbstractTetrahedralElement::CalculateJacobian 0 0% 66.24% 303ms 1.49% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.0049% 66.25% 302ms 1.48% NodeLocationWriter::Visit 0 0% 66.25% 294ms 1.45% std::_Rb_tree::_M_put_node (inline) 43ms 0.21% 66.46% 290ms 1.43% TetrahedralMesh::Clear 269ms 1.32% 67.78% 271ms 1.33% std::vector::operator[] (inline) 1ms 0.0049% 67.79% 270ms 1.33% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0049% 67.79% 269ms 1.32% AbstractCellPopulation::Iterator::operator++ (inline) 40ms 0.2% 67.99% 267ms 1.31% AbstractCellPopulation::Iterator::IsRealCell (inline) 3ms 0.015% 68.00% 266ms 1.31% alternateaxes 12ms 0.059% 68.06% 266ms 1.31% std::num_put::_M_insert_float 20ms 0.098% 68.16% 265ms 1.30% std::_Rb_tree::_Rb_tree 11ms 0.054% 68.21% 263ms 1.29% std::vector::push_back (inline) 241ms 1.18% 69.40% 261ms 1.28% vertexmedian 18ms 0.088% 69.49% 260ms 1.28% std::_Rb_tree::_M_erase_aux (inline) 14ms 0.069% 69.56% 258ms 1.27% AbstractCellPopulation::IsCellAttachedToLocationIndex 9ms 0.044% 69.60% 258ms 1.27% AbstractTetrahedralElement::CalculateInverseJacobian 11ms 0.054% 69.65% 249ms 1.22% std::vector::_M_realloc_insert 3ms 0.015% 69.67% 246ms 1.21% std::set::set (inline) 1ms 0.0049% 69.67% 244ms 1.20% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 69.67% 244ms 1.20% MeshBasedCellPopulation::GetDampingConstant 31ms 0.15% 69.83% 235ms 1.16% AbstractTetrahedralElement::RefreshJacobian 36ms 0.18% 70.00% 232ms 1.14% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 50ms 0.25% 70.25% 228ms 1.12% ApcOneHitCellMutationState::ApcOneHitCellMutationState 2ms 0.0098% 70.26% 219ms 1.08% std::__cxx11::collate::do_transform 24ms 0.12% 70.38% 218ms 1.07% std::_Rb_tree::_M_copy (inline) 10ms 0.049% 70.43% 216ms 1.06% Element::MarkAsDeleted 2ms 0.0098% 70.43% 212ms 1.04% ___vsnprintf 7ms 0.034% 70.47% 210ms 1.03% CellPropertyCollection::HasProperty 0 0% 70.47% 210ms 1.03% __vsnprintf_internal (inline) 0 0% 70.47% 208ms 1.02% Cell::HasCellProperty (inline) 20ms 0.098% 70.57% 208ms 1.02% __printf_buffer 155ms 0.76% 71.33% 206ms 1.01% AbstractElement::GetNodeGlobalIndex 48ms 0.24% 71.57% 203ms 1% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 3ms 0.015% 71.58% 201ms 0.99% CellProliferativeTypesWriter::VisitCell 3ms 0.015% 71.59% 199ms 0.98% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 135ms 0.66% 72.26% 194ms 0.95% malloc_consolidate 64ms 0.31% 72.57% 193ms 0.95% std::_Rb_tree::_M_clone_node (inline) 5ms 0.025% 72.60% 191ms 0.94% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 189ms 0.93% 73.53% 189ms 0.93% unlink_chunk 1ms 0.0049% 73.53% 186ms 0.91% OffLatticeSimulation::ApplyBoundaries 185ms 0.91% 74.44% 185ms 0.91% [libchaste_cell_based.so] 78ms 0.38% 74.82% 181ms 0.89% AbstractElement::GetNodeLocation 180ms 0.88% 75.71% 180ms 0.88% std::_Rb_tree_insert_and_rebalance 3ms 0.015% 75.72% 171ms 0.84% __printf_fp_l_buffer 0 0% 75.72% 171ms 0.84% __printf_fp_spec (inline) 7ms 0.034% 75.76% 167ms 0.82% AbstractTetrahedralElement::AbstractTetrahedralElement 76ms 0.37% 76.13% 164ms 0.81% __printf_fp_buffer_1 163ms 0.8% 76.93% 163ms 0.8% Node::GetIndex 9ms 0.044% 76.98% 162ms 0.8% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 11ms 0.054% 77.03% 159ms 0.78% Node::~Node 159ms 0.78% 77.81% 159ms 0.78% incircle 0 0% 77.81% 157ms 0.77% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 88ms 0.43% 78.25% 149ms 0.73% Cylindrical2dMesh::GetVectorFromAtoB 144ms 0.71% 78.95% 144ms 0.71% std::vector::size (inline) 95ms 0.47% 79.42% 143ms 0.7% std::_Rb_tree::equal_range (inline) 0 0% 79.42% 139ms 0.68% Cell::SetCellProliferativeType 1ms 0.0049% 79.42% 139ms 0.68% boost::numeric::ublas::vector_assign (inline) 0 0% 79.42% 136ms 0.67% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 79.42% 136ms 0.67% OutputFileHandler::OpenOutputFile 11ms 0.054% 79.48% 133ms 0.65% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 123ms 0.6% 80.08% 123ms 0.6% AbstractCellProperty::~AbstractCellProperty 40ms 0.2% 80.28% 123ms 0.6% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 122ms 0.6% 80.88% 122ms 0.6% std::_Rb_tree_rebalance_for_erase 0 0% 80.88% 121ms 0.59% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 10ms 0.049% 80.93% 121ms 0.59% boost::numeric::ublas::c_vector::c_vector (inline) 27ms 0.13% 81.06% 118ms 0.58% std::num_put::_M_insert_int 44ms 0.22% 81.28% 116ms 0.57% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 33ms 0.16% 81.44% 115ms 0.57% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 48ms 0.24% 81.68% 115ms 0.57% std::__ostream_insert 37ms 0.18% 81.86% 114ms 0.56% boost::numeric::ublas::indexing_vector_assign 112ms 0.55% 82.41% 112ms 0.55% AbstractElement::IsDeleted 1ms 0.0049% 82.41% 110ms 0.54% AbstractCellBasedSimulation::DoCellRemoval (inline) 3ms 0.015% 82.43% 109ms 0.54% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 12ms 0.059% 82.49% 107ms 0.53% std::_Rb_tree_const_iterator::operator++ (inline) 19ms 0.093% 82.58% 105ms 0.52% TetrahedralMesh::EdgesEnd 105ms 0.52% 83.10% 105ms 0.52% std::_Rb_tree_increment 104ms 0.51% 83.61% 104ms 0.51% AbstractCellMutationState::~AbstractCellMutationState 0 0% 83.61% 104ms 0.51% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 98ms 0.48% 84.09% 104ms 0.51% vertexsort 103ms 0.51% 84.60% 103ms 0.51% boost::shared_ptr::operator-> (inline)