File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16475ms, 84.92% of 19401ms total Dropped 773 nodes (cum <= 97ms) flat flat% sum% cum cum% 0 0% 0% 19361ms 99.79% __libc_start_call_main 0 0% 0% 19361ms 99.79% __libc_start_main_impl 0 0% 0% 19361ms 99.79% _start 0 0% 0% 19342ms 99.70% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19342ms 99.70% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19342ms 99.70% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19342ms 99.70% main 0 0% 0% 19306ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19306ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19306ms 99.51% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.0052% 0.0052% 19283ms 99.39% AbstractCellBasedSimulation::Solve 1ms 0.0052% 0.01% 14126ms 72.81% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.01% 8480ms 43.71% AbstractCellBasedSimulation::DoCellBirth 12ms 0.062% 0.072% 8381ms 43.20% Cell::ReadyToDivide 7ms 0.036% 0.11% 8291ms 42.73% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0052% 0.11% 8130ms 41.91% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 17ms 0.088% 0.2% 8124ms 41.87% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.21% 8103ms 41.77% CellCycleModelOdeHandler::SolveOdeToTime 61ms 0.31% 0.53% 7916ms 40.80% AbstractOneStepIvpOdeSolver::InternalSolve 854ms 4.40% 4.93% 7098ms 36.59% RungeKutta4IvpOdeSolver::CalculateNextYValue 2923ms 15.07% 19.99% 6035ms 31.11% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 19.99% 5518ms 28.44% MeshBasedCellPopulation::Update 9ms 0.046% 20.04% 4327ms 22.30% Cylindrical2dMesh::ReMesh 259ms 1.33% 21.38% 3287ms 16.94% AbstractCellProperty::IsType (inline) 0 0% 21.38% 2818ms 14.53% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0052% 21.38% 2561ms 13.20% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.01% 21.39% 2537ms 13.08% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 21.39% 2429ms 12.52% MutableMesh::ReMesh 0 0% 21.39% 2331ms 12.01% AbstractCellPopulation::WriteResultsToFiles 746ms 3.85% 25.24% 1838ms 9.47% std::_Rb_tree::_M_lower_bound (inline) 160ms 0.82% 26.06% 1730ms 8.92% TetrahedralMesh::EdgeIterator::operator++ 291ms 1.50% 27.56% 1529ms 7.88% AbstractCellProperty::IsSame 56ms 0.29% 27.85% 1386ms 7.14% std::_Rb_tree::find (inline) 63ms 0.32% 28.17% 1347ms 6.94% operator new 20ms 0.1% 28.28% 1342ms 6.92% TetrahedralMesh::ImportFromMesher 485ms 2.50% 30.78% 1260ms 6.49% __GI___libc_malloc 168ms 0.87% 31.64% 1238ms 6.38% std::type_info::operator== (inline) 0 0% 31.64% 1148ms 5.92% MeshBasedCellPopulation::UpdateNodePairs 1138ms 5.87% 37.51% 1138ms 5.87% __strcmp_evex 8ms 0.041% 37.55% 1124ms 5.79% std::set::insert (inline) 3ms 0.015% 37.57% 1118ms 5.76% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 20ms 0.1% 37.67% 1116ms 5.75% std::_Rb_tree::_M_insert_unique 28ms 0.14% 37.81% 1095ms 5.64% std::__new_allocator::allocate (inline) 0 0% 37.81% 1091ms 5.62% std::allocator_traits::allocate (inline) 8ms 0.041% 37.85% 1039ms 5.36% MeshBasedCellPopulation::SpringIterator::operator++ 2ms 0.01% 37.86% 972ms 5.01% AbstractTwoBodyInteractionForce::AddForceContribution 13ms 0.067% 37.93% 913ms 4.71% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 37.93% 891ms 4.59% std::set::count (inline) 29ms 0.15% 38.08% 887ms 4.57% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 9ms 0.046% 38.13% 877ms 4.52% CellPopulationElementWriter::Visit 277ms 1.43% 39.55% 846ms 4.36% __dynamic_cast 832ms 4.29% 43.84% 832ms 4.29% [libchaste_cell_based.so] 14ms 0.072% 43.92% 795ms 4.10% CellPropertyCollection::GetPropertiesType (inline) 0 0% 43.92% 780ms 4.02% std::_Rb_tree::_M_create_node (inline) 0 0% 43.92% 762ms 3.93% std::_Rb_tree::_M_get_node (inline) 5ms 0.026% 43.94% 749ms 3.86% triangulate 75ms 0.39% 44.33% 742ms 3.82% std::map::operator[] (partial-inline) 14ms 0.072% 44.40% 738ms 3.80% MeshBasedCellPopulation::AcceptCellWriter 36ms 0.19% 44.59% 735ms 3.79% std::_Rb_tree::_M_insert_ (inline) 0 0% 44.59% 693ms 3.57% std::_Rb_tree::_Alloc_node::operator() (inline) 376ms 1.94% 46.52% 684ms 3.53% _int_malloc 0 0% 46.52% 662ms 3.41% delaunay 1ms 0.0052% 46.53% 660ms 3.40% divconqdelaunay 645ms 3.32% 49.85% 645ms 3.32% std::_Rb_tree::_S_right (inline) 641ms 3.30% 53.16% 641ms 3.30% WntCellCycleOdeSystem::CalculateStoppingEvent 16ms 0.082% 53.24% 636ms 3.28% AbstractCellPopulation::GetCellUsingLocationIndex 143ms 0.74% 53.98% 592ms 3.05% __GI___libc_free 11ms 0.057% 54.03% 592ms 3.05% std::less::operator() (inline) 5ms 0.026% 54.06% 589ms 3.04% Element::Element 581ms 2.99% 57.05% 581ms 2.99% std::operator< (inline) 6ms 0.031% 57.08% 574ms 2.96% AbstractCellProperty::IsSubType (inline) 9ms 0.046% 57.13% 573ms 2.95% Element::RegisterWithNodes (inline) 1ms 0.0052% 57.14% 571ms 2.94% std::ostream::operator<< (inline) 87ms 0.45% 57.58% 566ms 2.92% std::ostream::_M_insert 12ms 0.062% 57.65% 556ms 2.87% Node::AddElement 0 0% 57.65% 541ms 2.79% std::_Rb_tree::lower_bound (inline) 0 0% 57.65% 541ms 2.79% std::map::lower_bound (inline) 16ms 0.082% 57.73% 529ms 2.73% Cylindrical2dMesh::ReconstructCylindricalMesh 111ms 0.57% 58.30% 505ms 2.60% std::_Rb_tree::_M_erase 14ms 0.072% 58.37% 502ms 2.59% MutableMesh::ReIndex 49ms 0.25% 58.63% 502ms 2.59% std::_Rb_tree::~_Rb_tree (inline) 492ms 2.54% 61.16% 492ms 2.54% [libchaste_crypt.so] 0 0% 61.16% 492ms 2.54% std::map::find (inline) 0 0% 61.16% 480ms 2.47% std::set::~set (inline) 222ms 1.14% 62.31% 478ms 2.46% AbstractCellMutationState::AbstractCellMutationState 0 0% 62.31% 460ms 2.37% std::_Rb_tree::_M_drop_node (inline) 2ms 0.01% 62.32% 454ms 2.34% Cell::GetMutationState 201ms 1.04% 63.35% 446ms 2.30% __cxxabiv1::__si_class_type_info::__do_dyncast 378ms 1.95% 65.30% 439ms 2.26% _int_free 13ms 0.067% 65.37% 417ms 2.15% std::__new_allocator::deallocate (inline) 0 0% 65.37% 408ms 2.10% std::allocator_traits::deallocate (inline) 13ms 0.067% 65.43% 407ms 2.10% Cylindrical2dMesh::CorrectNonPeriodicMesh 3ms 0.015% 65.45% 404ms 2.08% Cell::GetCellProliferativeType 6ms 0.031% 65.48% 397ms 2.05% std::_Rb_tree::erase 1ms 0.0052% 65.49% 394ms 2.03% std::set::erase (inline) 6ms 0.031% 65.52% 387ms 1.99% Node::RemoveElement 5ms 0.026% 65.54% 362ms 1.87% LegacyCellProliferativeTypesWriter::VisitCell 130ms 0.67% 66.21% 361ms 1.86% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 66.21% 353ms 1.82% std::_Rb_tree::_M_put_node (inline) 20ms 0.1% 66.32% 346ms 1.78% TetrahedralMesh::Clear 18ms 0.093% 66.41% 343ms 1.77% divconqrecurse 0 0% 66.41% 341ms 1.76% MeshBasedCellPopulation::GetDampingConstant 2ms 0.01% 66.42% 339ms 1.75% AbstractCentreBasedCellPopulation::GetDampingConstant 1ms 0.0052% 66.42% 330ms 1.70% std::_Vector_base::_M_allocate (inline) 87ms 0.45% 66.87% 315ms 1.62% mergehulls 0 0% 66.87% 310ms 1.60% NodeLocationWriter::Visit 22ms 0.11% 66.99% 308ms 1.59% Element::ResetIndex 1ms 0.0052% 66.99% 306ms 1.58% TetrahedralMesh::RefreshJacobianCachedData 5ms 0.026% 67.02% 301ms 1.55% AbstractCellPopulation::IsCellAttachedToLocationIndex 13ms 0.067% 67.08% 295ms 1.52% std::_Rb_tree::_Rb_tree 25ms 0.13% 67.21% 290ms 1.49% std::num_put::_M_insert_float 2ms 0.01% 67.22% 290ms 1.49% std::set::set (inline) 12ms 0.062% 67.29% 283ms 1.46% boost::detail::shared_count::~shared_count (inline) 0 0% 67.29% 283ms 1.46% boost::shared_ptr::~shared_ptr (inline) 23ms 0.12% 67.40% 274ms 1.41% AbstractTetrahedralElement::CalculateJacobian 1ms 0.0052% 67.41% 267ms 1.38% AbstractCellPopulation::Iterator::operator++ (inline) 26ms 0.13% 67.54% 266ms 1.37% AbstractCellPopulation::Iterator::IsRealCell (inline) 23ms 0.12% 67.66% 266ms 1.37% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 35ms 0.18% 67.84% 266ms 1.37% std::_Rb_tree::_M_copy (inline) 259ms 1.33% 69.18% 264ms 1.36% boost::detail::sp_counted_base::release 13ms 0.067% 69.24% 261ms 1.35% AbstractCellPopulation::GetLocationIndexUsingCell 17ms 0.088% 69.33% 258ms 1.33% std::vector::push_back (inline) 6ms 0.031% 69.36% 246ms 1.27% AbstractTetrahedralElement::CalculateInverseJacobian 16ms 0.082% 69.44% 242ms 1.25% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 1ms 0.0052% 69.45% 241ms 1.24% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 11ms 0.057% 69.51% 241ms 1.24% std::_Rb_tree::_M_erase_aux (inline) 20ms 0.1% 69.61% 234ms 1.21% Element::MarkAsDeleted 1ms 0.0052% 69.61% 233ms 1.20% CellProliferativeTypesWriter::VisitCell 8ms 0.041% 69.66% 231ms 1.19% std::vector::_M_realloc_insert 3ms 0.015% 69.67% 230ms 1.19% ApcOneHitCellMutationState::ApcOneHitCellMutationState 230ms 1.19% 70.86% 230ms 1.19% [libchaste_mesh.so] 4ms 0.021% 70.88% 225ms 1.16% std::__cxx11::collate::do_transform 1ms 0.0052% 70.88% 223ms 1.15% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 91ms 0.47% 71.35% 222ms 1.14% std::_Rb_tree::_M_clone_node (inline) 210ms 1.08% 72.43% 213ms 1.10% std::vector::operator[] (inline) 0 0% 72.43% 208ms 1.07% ___vsnprintf 2ms 0.01% 72.44% 208ms 1.07% __vsnprintf_internal (inline) 2ms 0.01% 72.46% 201ms 1.04% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 6ms 0.031% 72.49% 200ms 1.03% alternateaxes 24ms 0.12% 72.61% 199ms 1.03% AbstractTetrahedralElement::RefreshJacobian 19ms 0.098% 72.71% 199ms 1.03% __printf_buffer 1ms 0.0052% 72.71% 198ms 1.02% Cylindrical2dMesh::CreateMirrorNodes 3ms 0.015% 72.73% 196ms 1.01% Node::~Node 176ms 0.91% 73.64% 193ms 0.99% vertexmedian 6ms 0.031% 73.67% 185ms 0.95% CellPropertyCollection::HasProperty 0 0% 73.67% 181ms 0.93% Cell::HasCellProperty (inline) 12ms 0.062% 73.73% 176ms 0.91% std::_Rb_tree_const_iterator::operator++ (inline) 137ms 0.71% 74.43% 175ms 0.9% malloc_consolidate 170ms 0.88% 75.31% 170ms 0.88% std::_Rb_tree::_S_left (inline) 0 0% 75.31% 169ms 0.87% OffLatticeSimulation::ApplyBoundaries 2ms 0.01% 75.32% 167ms 0.86% boost::numeric::ublas::vector_assign (inline) 53ms 0.27% 75.59% 166ms 0.86% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 1ms 0.0052% 75.60% 163ms 0.84% __printf_fp_spec (inline) 5ms 0.026% 75.62% 162ms 0.84% __printf_fp_l_buffer 162ms 0.84% 76.46% 162ms 0.84% std::type_info::name (inline) 100ms 0.52% 76.98% 161ms 0.83% AbstractElement::GetNodeLocation 2ms 0.01% 76.99% 161ms 0.83% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 157ms 0.81% 77.79% 157ms 0.81% unlink_chunk 8ms 0.041% 77.84% 155ms 0.8% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 154ms 0.79% 78.63% 154ms 0.79% incircle 10ms 0.052% 78.68% 153ms 0.79% boost::numeric::ublas::c_vector::c_vector (inline) 153ms 0.79% 79.47% 153ms 0.79% std::_Rb_tree_increment 152ms 0.78% 80.25% 152ms 0.78% std::_Rb_tree_insert_and_rebalance 70ms 0.36% 80.61% 151ms 0.78% __printf_fp_buffer_1 86ms 0.44% 81.06% 150ms 0.77% std::_Rb_tree::equal_range (inline) 3ms 0.015% 81.07% 147ms 0.76% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 31ms 0.16% 81.23% 142ms 0.73% std::num_put::_M_insert_int 141ms 0.73% 81.96% 141ms 0.73% AbstractCellProperty::AbstractCellProperty 0 0% 81.96% 137ms 0.71% AbstractTetrahedralElement::AbstractTetrahedralElement 59ms 0.3% 82.26% 132ms 0.68% Cylindrical2dMesh::GetVectorFromAtoB 1ms 0.0052% 82.27% 131ms 0.68% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 69ms 0.36% 82.62% 128ms 0.66% std::__ostream_insert 3ms 0.015% 82.64% 126ms 0.65% std::_Rb_tree::_M_emplace_hint_unique 0 0% 82.64% 125ms 0.64% AbstractCellBasedSimulation::DoCellRemoval (inline) 4ms 0.021% 82.66% 123ms 0.63% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 32ms 0.16% 82.83% 123ms 0.63% boost::numeric::ublas::indexing_vector_assign 3ms 0.015% 82.84% 121ms 0.62% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 74ms 0.38% 83.22% 119ms 0.61% AbstractElement::GetNodeGlobalIndex 6ms 0.031% 83.25% 118ms 0.61% MeshBasedCellPopulation::SpringsEnd (inline) 6ms 0.031% 83.28% 117ms 0.6% Cell::SetCellProliferativeType 93ms 0.48% 83.76% 108ms 0.56% vertexsort 0 0% 83.76% 107ms 0.55% std::_Rb_tree::_M_destroy_node (inline) 0 0% 83.76% 107ms 0.55% std::__new_allocator::destroy (inline) 0 0% 83.76% 107ms 0.55% std::allocator_traits::destroy (inline) 15ms 0.077% 83.84% 105ms 0.54% TetrahedralMesh::EdgesEnd 1ms 0.0052% 83.85% 104ms 0.54% std::vector::_M_default_append 0 0% 83.85% 104ms 0.54% std::vector::resize (inline) 104ms 0.54% 84.38% 104ms 0.54% std::vector::size (inline) 103ms 0.53% 84.91% 103ms 0.53% Node::GetIndex 0 0% 84.91% 102ms 0.53% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.0052% 84.92% 102ms 0.53% OutputFileHandler::OpenOutputFile