File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16644ms, 85.48% of 19471ms total Dropped 777 nodes (cum <= 97.36ms) flat flat% sum% cum cum% 0 0% 0% 19426ms 99.77% __libc_start_call_main 0 0% 0% 19426ms 99.77% __libc_start_main_impl 0 0% 0% 19426ms 99.77% _start 0 0% 0% 19404ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19404ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19404ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19404ms 99.66% main 0 0% 0% 19363ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19363ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19363ms 99.45% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.0051% 0.0051% 19334ms 99.30% AbstractCellBasedSimulation::Solve 0 0% 0.0051% 14793ms 75.97% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0051% 0.01% 9379ms 48.17% AbstractCellBasedSimulation::DoCellBirth 1ms 0.0051% 0.015% 9273ms 47.62% Cell::ReadyToDivide 10ms 0.051% 0.067% 9210ms 47.30% AbstractPhaseBasedCellCycleModel::ReadyToDivide 4ms 0.021% 0.087% 9074ms 46.60% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 12ms 0.062% 0.15% 9064ms 46.55% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 7ms 0.036% 0.18% 9047ms 46.46% CellCycleModelOdeHandler::SolveOdeToTime 66ms 0.34% 0.52% 8870ms 45.55% AbstractOneStepIvpOdeSolver::InternalSolve 1011ms 5.19% 5.72% 7935ms 40.75% RungeKutta4IvpOdeSolver::CalculateNextYValue 2727ms 14.01% 19.72% 6750ms 34.67% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 19.72% 5307ms 27.26% MeshBasedCellPopulation::Update 6ms 0.031% 19.75% 4097ms 21.04% Cylindrical2dMesh::ReMesh 55ms 0.28% 20.03% 4012ms 20.61% AbstractCellProperty::IsType (inline) 352ms 1.81% 21.84% 2595ms 13.33% AbstractCellProperty::IsSame 2ms 0.01% 21.85% 2566ms 13.18% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 21.85% 2245ms 11.53% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 21.85% 2244ms 11.52% MutableMesh::ReMesh 254ms 1.30% 23.16% 2243ms 11.52% std::type_info::operator== (inline) 9ms 0.046% 23.20% 2201ms 11.30% AbstractNumericalMethod::ComputeForcesIncludingDamping 2123ms 10.90% 34.11% 2123ms 10.90% __strcmp_avx2 0 0% 34.11% 1968ms 10.11% AbstractCellPopulation::WriteResultsToFiles 798ms 4.10% 38.21% 1876ms 9.63% std::_Rb_tree::_M_lower_bound (inline) 177ms 0.91% 39.11% 1728ms 8.87% TetrahedralMesh::EdgeIterator::operator++ 60ms 0.31% 39.42% 1383ms 7.10% std::_Rb_tree::find (inline) 0 0% 39.42% 1172ms 6.02% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.026% 39.45% 1151ms 5.91% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 20ms 0.1% 39.55% 1125ms 5.78% TetrahedralMesh::ImportFromMesher 53ms 0.27% 39.82% 1070ms 5.50% operator new 13ms 0.067% 39.89% 1050ms 5.39% MeshBasedCellPopulation::SpringIterator::operator++ 8ms 0.041% 39.93% 1029ms 5.28% std::set::insert (inline) 9ms 0.046% 39.98% 1021ms 5.24% std::_Rb_tree::_M_insert_unique 256ms 1.31% 41.29% 1003ms 5.15% __GI___libc_malloc 40ms 0.21% 41.50% 935ms 4.80% std::__new_allocator::allocate (inline) 0 0% 41.50% 929ms 4.77% std::allocator_traits::allocate (inline) 1ms 0.0051% 41.50% 893ms 4.59% triangulate 0 0% 41.50% 848ms 4.36% std::set::count (inline) 0 0% 41.50% 817ms 4.20% delaunay 0 0% 41.50% 814ms 4.18% divconqdelaunay 3ms 0.015% 41.52% 759ms 3.90% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 1ms 0.0051% 41.52% 739ms 3.80% AbstractTwoBodyInteractionForce::AddForceContribution 726ms 3.73% 45.25% 726ms 3.73% WntCellCycleOdeSystem::CalculateStoppingEvent 8ms 0.041% 45.29% 713ms 3.66% CellPopulationElementWriter::Visit 712ms 3.66% 48.95% 712ms 3.66% std::_Rb_tree::_S_right (inline) 58ms 0.3% 49.25% 710ms 3.65% std::map::operator[] (partial-inline) 217ms 1.11% 50.36% 693ms 3.56% __dynamic_cast 361ms 1.85% 52.22% 659ms 3.38% _int_malloc 25ms 0.13% 52.34% 644ms 3.31% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 12ms 0.062% 52.41% 644ms 3.31% std::less::operator() (inline) 0 0% 52.41% 633ms 3.25% std::_Rb_tree::_M_create_node (inline) 632ms 3.25% 55.65% 632ms 3.25% std::operator< (inline) 23ms 0.12% 55.77% 622ms 3.19% AbstractCellPopulation::GetCellUsingLocationIndex 9ms 0.046% 55.82% 609ms 3.13% CellPropertyCollection::GetPropertiesType (inline) 8ms 0.041% 55.86% 605ms 3.11% MeshBasedCellPopulation::AcceptCellWriter 0 0% 55.86% 604ms 3.10% std::_Rb_tree::_M_get_node (inline) 26ms 0.13% 55.99% 599ms 3.08% std::_Rb_tree::_M_insert_ (inline) 0 0% 55.99% 589ms 3.03% std::_Rb_tree::_Alloc_node::operator() (inline) 9ms 0.046% 56.04% 581ms 2.98% Element::Element 0 0% 56.04% 572ms 2.94% std::_Rb_tree::lower_bound (inline) 0 0% 56.04% 572ms 2.94% std::map::lower_bound (inline) 10ms 0.051% 56.09% 537ms 2.76% MutableMesh::ReIndex 0 0% 56.09% 529ms 2.72% std::map::find (inline) 15ms 0.077% 56.17% 517ms 2.66% Cylindrical2dMesh::CorrectNonPeriodicMesh 15ms 0.077% 56.24% 501ms 2.57% Cylindrical2dMesh::ReconstructCylindricalMesh 1ms 0.0051% 56.25% 493ms 2.53% AbstractCellProperty::IsSubType (inline) 10ms 0.051% 56.30% 483ms 2.48% Element::RegisterWithNodes (inline) 2ms 0.01% 56.31% 479ms 2.46% std::ostream::operator<< (inline) 6ms 0.031% 56.34% 476ms 2.44% Node::AddElement 60ms 0.31% 56.65% 473ms 2.43% std::ostream::_M_insert 308ms 1.58% 58.23% 453ms 2.33% AbstractCellMutationState::AbstractCellMutationState 116ms 0.6% 58.83% 421ms 2.16% __GI___libc_free 179ms 0.92% 59.75% 413ms 2.12% std::_Rb_tree::_M_get_insert_unique_pos 4ms 0.021% 59.77% 410ms 2.11% std::_Rb_tree::erase 1ms 0.0051% 59.77% 410ms 2.11% std::set::erase (inline) 7ms 0.036% 59.81% 402ms 2.06% Node::RemoveElement 16ms 0.082% 59.89% 385ms 1.98% divconqrecurse 116ms 0.6% 60.48% 382ms 1.96% std::_Rb_tree::_M_erase 106ms 0.54% 61.03% 360ms 1.85% mergehulls 34ms 0.17% 61.20% 359ms 1.84% std::_Rb_tree::~_Rb_tree (inline) 22ms 0.11% 61.32% 354ms 1.82% Element::ResetIndex 349ms 1.79% 63.11% 349ms 1.79% [libchaste_cell_based.so] 168ms 0.86% 63.97% 347ms 1.78% __cxxabiv1::__si_class_type_info::__do_dyncast 15ms 0.077% 64.05% 344ms 1.77% std::__new_allocator::deallocate (inline) 0 0% 64.05% 338ms 1.74% std::allocator_traits::deallocate (inline) 14ms 0.072% 64.12% 333ms 1.71% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 64.12% 332ms 1.71% std::set::~set (inline) 2ms 0.01% 64.13% 327ms 1.68% std::_Vector_base::_M_allocate (inline) 4ms 0.021% 64.15% 325ms 1.67% Cell::GetCellProliferativeType 3ms 0.015% 64.17% 324ms 1.66% Cell::GetMutationState 0 0% 64.17% 323ms 1.66% std::_Rb_tree::_M_drop_node (inline) 3ms 0.015% 64.18% 310ms 1.59% alternateaxes 1ms 0.0051% 64.19% 307ms 1.58% LegacyCellProliferativeTypesWriter::VisitCell 297ms 1.53% 65.71% 307ms 1.58% vertexmedian 0 0% 65.71% 304ms 1.56% NodeLocationWriter::Visit 234ms 1.20% 66.91% 303ms 1.56% _int_free 37ms 0.19% 67.10% 287ms 1.47% AbstractCellPopulation::Iterator::IsRealCell (inline) 19ms 0.098% 67.20% 287ms 1.47% std::_Rb_tree::_Rb_tree (partial-inline) 4ms 0.021% 67.22% 285ms 1.46% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 67.22% 285ms 1.46% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 67.22% 274ms 1.41% std::_Rb_tree::_M_put_node (inline) 266ms 1.37% 68.59% 271ms 1.39% std::vector::operator[] (inline) 23ms 0.12% 68.71% 270ms 1.39% std::num_put::_M_insert_float 98ms 0.5% 69.21% 258ms 1.33% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 6ms 0.031% 69.24% 250ms 1.28% AbstractCellPopulation::IsCellAttachedToLocationIndex 12ms 0.062% 69.30% 249ms 1.28% std::_Rb_tree::_M_erase_aux (inline) 64ms 0.33% 69.63% 248ms 1.27% ApcOneHitCellMutationState::ApcOneHitCellMutationState 12ms 0.062% 69.69% 246ms 1.26% std::_Rb_tree::_M_copy (inline) 0 0% 69.69% 243ms 1.25% std::set::set (inline) 16ms 0.082% 69.78% 238ms 1.22% std::vector::push_back (inline) 17ms 0.087% 69.86% 237ms 1.22% AbstractTetrahedralElement::CalculateJacobian 70ms 0.36% 70.22% 230ms 1.18% std::_Rb_tree::_M_clone_node (inline) 89ms 0.46% 70.68% 229ms 1.18% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 4ms 0.021% 70.70% 224ms 1.15% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 3ms 0.015% 70.72% 222ms 1.14% std::__cxx11::collate::do_transform 1ms 0.0051% 70.72% 220ms 1.13% MeshBasedCellPopulation::GetDampingConstant 2ms 0.01% 70.73% 219ms 1.12% AbstractCentreBasedCellPopulation::GetDampingConstant 3ms 0.015% 70.75% 216ms 1.11% ___vsnprintf 15ms 0.077% 70.82% 214ms 1.10% Element::MarkAsDeleted 1ms 0.0051% 70.83% 213ms 1.09% __vsnprintf_internal (inline) 12ms 0.062% 70.89% 213ms 1.09% std::vector::_M_realloc_insert 20ms 0.1% 70.99% 209ms 1.07% __printf_buffer 3ms 0.015% 71.01% 208ms 1.07% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 71.01% 203ms 1.04% TetrahedralMesh::RefreshJacobianCachedData 146ms 0.75% 71.76% 201ms 1.03% AbstractElement::GetNodeGlobalIndex 9ms 0.046% 71.80% 200ms 1.03% AbstractTetrahedralElement::AbstractTetrahedralElement 21ms 0.11% 71.91% 194ms 1% TetrahedralMesh::Clear 0 0% 71.91% 189ms 0.97% OffLatticeSimulation::ApplyBoundaries 3ms 0.015% 71.93% 186ms 0.96% CellProliferativeTypesWriter::VisitCell 10ms 0.051% 71.98% 182ms 0.93% AbstractTetrahedralElement::CalculateInverseJacobian 5ms 0.026% 72.00% 180ms 0.92% __printf_fp_l_buffer 0 0% 72.00% 180ms 0.92% __printf_fp_spec (inline) 129ms 0.66% 72.67% 179ms 0.92% malloc_consolidate 75ms 0.39% 73.05% 174ms 0.89% __printf_fp_buffer_1 19ms 0.098% 73.15% 171ms 0.88% AbstractTetrahedralElement::RefreshJacobian 114ms 0.59% 73.74% 167ms 0.86% std::_Rb_tree::equal_range (inline) 161ms 0.83% 74.56% 161ms 0.83% std::vector::size (inline) 157ms 0.81% 75.37% 157ms 0.81% unlink_chunk 156ms 0.8% 76.17% 156ms 0.8% std::_Rb_tree_insert_and_rebalance 50ms 0.26% 76.43% 152ms 0.78% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 46ms 0.24% 76.66% 152ms 0.78% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 152ms 0.78% 77.44% 152ms 0.78% Node::GetIndex 152ms 0.78% 78.22% 152ms 0.78% [libchaste_crypt.so] 151ms 0.78% 79.00% 151ms 0.78% AbstractCellMutationState::~AbstractCellMutationState 3ms 0.015% 79.01% 151ms 0.78% CellPropertyCollection::HasProperty 149ms 0.77% 79.78% 149ms 0.77% incircle 0 0% 79.78% 146ms 0.75% Cell::HasCellProperty (inline) 59ms 0.3% 80.08% 144ms 0.74% AbstractElement::GetNodeLocation 12ms 0.062% 80.14% 142ms 0.73% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 41ms 0.21% 80.36% 140ms 0.72% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 140ms 0.72% 81.07% 140ms 0.72% std::type_info::name (inline) 7ms 0.036% 81.11% 135ms 0.69% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 4ms 0.021% 81.13% 125ms 0.64% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 81.13% 123ms 0.63% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 20ms 0.1% 81.23% 119ms 0.61% boost::detail::shared_count::~shared_count (inline) 0 0% 81.23% 119ms 0.61% boost::shared_ptr::~shared_ptr (inline) 10ms 0.051% 81.28% 118ms 0.61% std::_Rb_tree_const_iterator::operator++ (inline) 117ms 0.6% 81.89% 117ms 0.6% std::_Rb_tree_increment 116ms 0.6% 82.48% 116ms 0.6% std::_Rb_tree_rebalance_for_erase 115ms 0.59% 83.07% 115ms 0.59% TetrahedralMesh::EdgeIterator::operator!= 25ms 0.13% 83.20% 115ms 0.59% TetrahedralMesh::EdgesEnd 3ms 0.015% 83.22% 113ms 0.58% boost::numeric::ublas::vector_assign (inline) 65ms 0.33% 83.55% 110ms 0.56% Cylindrical2dMesh::GetVectorFromAtoB 31ms 0.16% 83.71% 109ms 0.56% std::__ostream_insert 1ms 0.0051% 83.71% 108ms 0.55% Cell::SetCellProliferativeType 0 0% 83.71% 107ms 0.55% AbstractCellBasedSimulation::DoCellRemoval (inline) 2ms 0.01% 83.72% 106ms 0.54% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 4ms 0.021% 83.75% 105ms 0.54% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 3ms 0.015% 83.76% 105ms 0.54% Node::~Node 103ms 0.53% 84.29% 105ms 0.54% vertexsort 104ms 0.53% 84.82% 104ms 0.53% counterclockwise 78ms 0.4% 85.22% 103ms 0.53% TimeStepper::AdvanceOneTimeStep 28ms 0.14% 85.37% 99ms 0.51% std::num_put::_M_insert_int 16ms 0.082% 85.45% 98ms 0.5% MeshBasedCellPopulation::SpringIterator::SpringIterator 6ms 0.031% 85.48% 98ms 0.5% boost::numeric::ublas::c_vector::c_vector (inline)