File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 17262ms, 84.74% of 20371ms total Dropped 817 nodes (cum <= 101.86ms) flat flat% sum% cum cum% 0 0% 0% 20320ms 99.75% __libc_start_call_main 0 0% 0% 20320ms 99.75% __libc_start_main_impl 0 0% 0% 20320ms 99.75% _start 0 0% 0% 20297ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20297ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20297ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20297ms 99.64% main 0 0% 0% 20256ms 99.44% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20256ms 99.44% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20256ms 99.44% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 20229ms 99.30% AbstractCellBasedSimulation::Solve 0 0% 0% 15374ms 75.47% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.015% 0.015% 9617ms 47.21% AbstractCellBasedSimulation::DoCellBirth 6ms 0.029% 0.044% 9517ms 46.72% Cell::ReadyToDivide 6ms 0.029% 0.074% 9397ms 46.13% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.015% 0.088% 9248ms 45.40% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 21ms 0.1% 0.19% 9239ms 45.35% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0049% 0.2% 9215ms 45.24% CellCycleModelOdeHandler::SolveOdeToTime 70ms 0.34% 0.54% 9019ms 44.27% AbstractOneStepIvpOdeSolver::InternalSolve 1053ms 5.17% 5.71% 8134ms 39.93% RungeKutta4IvpOdeSolver::CalculateNextYValue 2852ms 14.00% 19.71% 6886ms 33.80% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.0098% 19.72% 5651ms 27.74% MeshBasedCellPopulation::Update 8ms 0.039% 19.76% 4413ms 21.66% Cylindrical2dMesh::ReMesh 71ms 0.35% 20.11% 4101ms 20.13% AbstractCellProperty::IsType (inline) 448ms 2.20% 22.31% 2652ms 13.02% AbstractCellProperty::IsSame 0 0% 22.31% 2626ms 12.89% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.0098% 22.32% 2458ms 12.07% MutableMesh::ReMesh 0 0% 22.32% 2345ms 11.51% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.034% 22.35% 2291ms 11.25% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0049% 22.36% 2218ms 10.89% AbstractCellPopulation::WriteResultsToFiles 278ms 1.36% 23.72% 2204ms 10.82% std::type_info::operator== (inline) 2059ms 10.11% 33.83% 2059ms 10.11% __strcmp_avx2 805ms 3.95% 37.78% 1850ms 9.08% std::_Rb_tree::_M_lower_bound (inline) 171ms 0.84% 38.62% 1724ms 8.46% TetrahedralMesh::EdgeIterator::operator++ 60ms 0.29% 38.91% 1374ms 6.74% std::_Rb_tree::find (inline) 11ms 0.054% 38.97% 1234ms 6.06% TetrahedralMesh::ImportFromMesher 0 0% 38.97% 1188ms 5.83% MeshBasedCellPopulation::UpdateNodePairs 36ms 0.18% 39.14% 1169ms 5.74% operator new 5ms 0.025% 39.17% 1139ms 5.59% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 244ms 1.20% 40.37% 1116ms 5.48% __GI___libc_malloc 14ms 0.069% 40.43% 1047ms 5.14% MeshBasedCellPopulation::SpringIterator::operator++ 15ms 0.074% 40.51% 1039ms 5.10% std::set::insert (inline) 18ms 0.088% 40.60% 1024ms 5.03% std::_Rb_tree::_M_insert_unique 51ms 0.25% 40.85% 1012ms 4.97% std::__new_allocator::allocate (inline) 0 0% 40.85% 1006ms 4.94% std::allocator_traits::allocate (inline) 1ms 0.0049% 40.85% 867ms 4.26% triangulate 0 0% 40.85% 839ms 4.12% std::set::count (inline) 3ms 0.015% 40.87% 830ms 4.07% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 40.87% 803ms 3.94% delaunay 3ms 0.015% 40.88% 801ms 3.93% divconqdelaunay 444ms 2.18% 43.06% 771ms 3.78% _int_malloc 12ms 0.059% 43.12% 753ms 3.70% CellPopulationElementWriter::Visit 2ms 0.0098% 43.13% 751ms 3.69% AbstractTwoBodyInteractionForce::AddForceContribution 19ms 0.093% 43.22% 744ms 3.65% CellPropertyCollection::GetPropertiesType (inline) 61ms 0.3% 43.52% 736ms 3.61% std::map::operator[] (partial-inline) 724ms 3.55% 47.08% 724ms 3.55% WntCellCycleOdeSystem::CalculateStoppingEvent 263ms 1.29% 48.37% 701ms 3.44% __dynamic_cast 701ms 3.44% 51.81% 701ms 3.44% std::_Rb_tree::_S_right (inline) 0 0% 51.81% 684ms 3.36% std::_Rb_tree::_M_create_node (inline) 33ms 0.16% 51.97% 670ms 3.29% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 7ms 0.034% 52.01% 670ms 3.29% MeshBasedCellPopulation::AcceptCellWriter 30ms 0.15% 52.15% 662ms 3.25% std::less::operator() (inline) 21ms 0.1% 52.26% 654ms 3.21% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 52.26% 648ms 3.18% std::_Rb_tree::_M_get_node (inline) 632ms 3.10% 55.36% 632ms 3.10% std::operator< (inline) 0 0% 55.36% 606ms 2.97% std::_Rb_tree::_Alloc_node::operator() (inline) 27ms 0.13% 55.49% 593ms 2.91% std::_Rb_tree::_M_insert_ (inline) 10ms 0.049% 55.54% 573ms 2.81% MutableMesh::ReIndex 0 0% 55.54% 559ms 2.74% std::_Rb_tree::lower_bound (inline) 0 0% 55.54% 559ms 2.74% std::map::lower_bound (inline) 2ms 0.0098% 55.55% 546ms 2.68% AbstractCellProperty::IsSubType (inline) 6ms 0.029% 55.58% 538ms 2.64% Element::Element 176ms 0.86% 56.44% 535ms 2.63% __GI___libc_free 0 0% 56.44% 532ms 2.61% std::map::find (inline) 12ms 0.059% 56.50% 492ms 2.42% Cylindrical2dMesh::CorrectNonPeriodicMesh 10ms 0.049% 56.55% 491ms 2.41% Element::RegisterWithNodes (inline) 14ms 0.069% 56.62% 490ms 2.41% Cylindrical2dMesh::ReconstructCylindricalMesh 1ms 0.0049% 56.62% 490ms 2.41% std::ostream::operator<< (inline) 56ms 0.27% 56.90% 487ms 2.39% std::ostream::_M_insert 332ms 1.63% 58.53% 484ms 2.38% AbstractCellMutationState::AbstractCellMutationState 10ms 0.049% 58.58% 484ms 2.38% Node::AddElement 138ms 0.68% 59.26% 446ms 2.19% std::_Rb_tree::_M_erase 156ms 0.77% 60.02% 413ms 2.03% std::_Rb_tree::_M_get_insert_unique_pos 17ms 0.083% 60.11% 409ms 2.01% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.0098% 60.11% 391ms 1.92% Cell::GetMutationState 0 0% 60.11% 389ms 1.91% std::set::~set (inline) 11ms 0.054% 60.17% 384ms 1.89% std::_Rb_tree::erase 3ms 0.015% 60.18% 384ms 1.89% std::set::erase (inline) 5ms 0.025% 60.21% 383ms 1.88% Cell::GetCellProliferativeType 18ms 0.088% 60.30% 383ms 1.88% std::__new_allocator::deallocate (inline) 14ms 0.069% 60.37% 379ms 1.86% Node::RemoveElement 22ms 0.11% 60.47% 379ms 1.86% divconqrecurse 0 0% 60.47% 378ms 1.86% std::allocator_traits::deallocate (inline) 374ms 1.84% 62.31% 374ms 1.84% [libchaste_cell_based.so] 0 0% 62.31% 367ms 1.80% std::_Rb_tree::_M_drop_node (inline) 1ms 0.0049% 62.31% 359ms 1.76% std::_Vector_base::_M_allocate (inline) 273ms 1.34% 63.65% 358ms 1.76% _int_free 106ms 0.52% 64.17% 354ms 1.74% mergehulls 28ms 0.14% 64.31% 348ms 1.71% Element::ResetIndex 31ms 0.15% 64.46% 345ms 1.69% TetrahedralMesh::Clear 19ms 0.093% 64.56% 336ms 1.65% std::_Rb_tree::_Rb_tree (partial-inline) 2ms 0.0098% 64.57% 327ms 1.61% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 64.57% 323ms 1.59% std::_Rb_tree::_M_put_node (inline) 5ms 0.025% 64.59% 320ms 1.57% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 147ms 0.72% 65.31% 320ms 1.57% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.0049% 65.32% 311ms 1.53% TetrahedralMesh::RefreshJacobianCachedData 0 0% 65.32% 305ms 1.50% std::set::set (inline) 0 0% 65.32% 294ms 1.44% MeshBasedCellPopulation::GetDampingConstant 2ms 0.0098% 65.33% 293ms 1.44% AbstractCentreBasedCellPopulation::GetDampingConstant 18ms 0.088% 65.42% 285ms 1.40% AbstractTetrahedralElement::CalculateJacobian 3ms 0.015% 65.43% 283ms 1.39% NodeLocationWriter::Visit 29ms 0.14% 65.57% 282ms 1.38% std::_Rb_tree::_M_copy (inline) 277ms 1.36% 66.93% 278ms 1.36% std::vector::operator[] (inline) 11ms 0.054% 66.99% 277ms 1.36% AbstractCellPopulation::IsCellAttachedToLocationIndex 1ms 0.0049% 66.99% 273ms 1.34% AbstractCellPopulation::Iterator::operator++ (inline) 47ms 0.23% 67.22% 271ms 1.33% AbstractCellPopulation::Iterator::IsRealCell (inline) 20ms 0.098% 67.32% 271ms 1.33% AbstractTetrahedralElement::CalculateInverseJacobian 4ms 0.02% 67.34% 262ms 1.29% alternateaxes 67ms 0.33% 67.67% 259ms 1.27% ApcOneHitCellMutationState::ApcOneHitCellMutationState 245ms 1.20% 68.87% 258ms 1.27% vertexmedian 89ms 0.44% 69.31% 256ms 1.26% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 13ms 0.064% 69.37% 254ms 1.25% std::vector::push_back (inline) 6ms 0.029% 69.40% 248ms 1.22% AbstractCellPopulation::GetLocationIndexUsingCell 71ms 0.35% 69.75% 248ms 1.22% std::_Rb_tree::_M_clone_node (inline) 16ms 0.079% 69.83% 248ms 1.22% std::num_put::_M_insert_float 86ms 0.42% 70.25% 244ms 1.20% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 10ms 0.049% 70.30% 235ms 1.15% std::_Rb_tree::_M_erase_aux (inline) 16ms 0.079% 70.38% 233ms 1.14% std::vector::_M_realloc_insert 40ms 0.2% 70.58% 230ms 1.13% AbstractTetrahedralElement::RefreshJacobian 1ms 0.0049% 70.58% 230ms 1.13% CellProliferativeTypesWriter::VisitCell 1ms 0.0049% 70.59% 221ms 1.08% CellPropertyCollection::HasProperty 0 0% 70.59% 220ms 1.08% Cell::HasCellProperty (inline) 11ms 0.054% 70.64% 211ms 1.04% Node::~Node 14ms 0.069% 70.71% 208ms 1.02% Element::MarkAsDeleted 161ms 0.79% 71.50% 206ms 1.01% malloc_consolidate 5ms 0.025% 71.52% 203ms 1% std::__cxx11::collate::do_transform 5ms 0.025% 71.55% 196ms 0.96% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 192ms 0.94% 72.49% 192ms 0.94% [libchaste_crypt.so] 3ms 0.015% 72.51% 188ms 0.92% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.0049% 72.51% 184ms 0.9% ___vsnprintf 17ms 0.083% 72.59% 183ms 0.9% __printf_buffer 0 0% 72.59% 183ms 0.9% __vsnprintf_internal (inline) 180ms 0.88% 73.48% 180ms 0.88% unlink_chunk 5ms 0.025% 73.50% 171ms 0.84% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 73.50% 170ms 0.83% OffLatticeSimulation::ApplyBoundaries 57ms 0.28% 73.78% 168ms 0.82% AbstractElement::GetNodeLocation 0 0% 73.78% 167ms 0.82% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 73.78% 164ms 0.81% OutputFileHandler::OpenOutputFile 8ms 0.039% 73.82% 164ms 0.81% std::_Rb_tree_const_iterator::operator++ (inline) 159ms 0.78% 74.60% 159ms 0.78% Node::GetIndex 3ms 0.015% 74.62% 158ms 0.78% __printf_fp_l_buffer 0 0% 74.62% 158ms 0.78% __printf_fp_spec (inline) 5ms 0.025% 74.64% 157ms 0.77% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 156ms 0.77% 75.41% 156ms 0.77% incircle 155ms 0.76% 76.17% 155ms 0.76% std::_Rb_tree_insert_and_rebalance 71ms 0.35% 76.52% 153ms 0.75% __printf_fp_buffer_1 150ms 0.74% 77.25% 150ms 0.74% std::_Rb_tree_increment 100ms 0.49% 77.74% 149ms 0.73% AbstractElement::GetNodeGlobalIndex 5ms 0.025% 77.77% 149ms 0.73% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 47ms 0.23% 78.00% 148ms 0.73% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 95ms 0.47% 78.46% 147ms 0.72% std::_Rb_tree::equal_range (inline) 137ms 0.67% 79.14% 145ms 0.71% vertexsort 144ms 0.71% 79.84% 144ms 0.71% std::vector::size (inline) 1ms 0.0049% 79.85% 142ms 0.7% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 5ms 0.025% 79.87% 141ms 0.69% boost::numeric::ublas::vector_assign (inline) 6ms 0.029% 79.90% 140ms 0.69% MeshBasedCellPopulation::SpringsEnd (inline) 140ms 0.69% 80.59% 140ms 0.69% std::type_info::name (inline) 18ms 0.088% 80.68% 137ms 0.67% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 3ms 0.015% 80.69% 137ms 0.67% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 43ms 0.21% 80.90% 136ms 0.67% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 28ms 0.14% 81.04% 133ms 0.65% std::num_put::_M_insert_int 22ms 0.11% 81.15% 131ms 0.64% TetrahedralMesh::EdgesEnd 22ms 0.11% 81.26% 127ms 0.62% boost::detail::shared_count::~shared_count (inline) 0 0% 81.26% 127ms 0.62% boost::shared_ptr::~shared_ptr (inline) 126ms 0.62% 81.88% 126ms 0.62% boost::shared_ptr::operator-> (inline) 3ms 0.015% 81.89% 125ms 0.61% Cylindrical2dMesh::CreateMirrorNodes 85ms 0.42% 82.31% 121ms 0.59% Cylindrical2dMesh::GetVectorFromAtoB 10ms 0.049% 82.36% 121ms 0.59% boost::numeric::ublas::c_vector::c_vector (inline) 4ms 0.02% 82.38% 116ms 0.57% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.0049% 82.38% 109ms 0.54% Cell::SetCellProliferativeType 106ms 0.52% 82.90% 106ms 0.52% [libchaste_mesh.so] 32ms 0.16% 83.06% 106ms 0.52% boost::numeric::ublas::indexing_vector_assign 104ms 0.51% 83.57% 104ms 0.51% AbstractCellMutationState::~AbstractCellMutationState 0 0% 83.57% 103ms 0.51% AbstractCellBasedSimulation::DoCellRemoval (inline) 103ms 0.51% 84.08% 103ms 0.51% AbstractElement::IsDeleted 55ms 0.27% 84.35% 103ms 0.51% AbstractTetrahedralMesh::GetElement 11ms 0.054% 84.40% 103ms 0.51% MeshBasedCellPopulation::SpringIterator::SpringIterator 69ms 0.34% 84.74% 103ms 0.51% TetrahedralMesh::EdgeIterator::EdgeIterator