File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 17275ms, 85.04% of 20315ms total Dropped 815 nodes (cum <= 101.58ms) flat flat% sum% cum cum% 0 0% 0% 20269ms 99.77% __libc_start_call_main 0 0% 0% 20269ms 99.77% __libc_start_main_impl 0 0% 0% 20269ms 99.77% _start 0 0% 0% 20250ms 99.68% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20250ms 99.68% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20250ms 99.68% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20250ms 99.68% main 0 0% 0% 20207ms 99.47% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20207ms 99.47% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20207ms 99.47% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.0049% 0.0049% 20180ms 99.34% AbstractCellBasedSimulation::Solve 1ms 0.0049% 0.0098% 15608ms 76.83% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0098% 0.02% 10196ms 50.19% AbstractCellBasedSimulation::DoCellBirth 1ms 0.0049% 0.025% 10096ms 49.70% Cell::ReadyToDivide 3ms 0.015% 0.039% 10029ms 49.37% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.0098% 0.049% 9889ms 48.68% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 16ms 0.079% 0.13% 9878ms 48.62% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.0098% 0.14% 9861ms 48.54% CellCycleModelOdeHandler::SolveOdeToTime 81ms 0.4% 0.54% 9690ms 47.70% AbstractOneStepIvpOdeSolver::InternalSolve 841ms 4.14% 4.68% 8880ms 43.71% RungeKutta4IvpOdeSolver::CalculateNextYValue 3701ms 18.22% 22.89% 7845ms 38.62% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0049% 22.90% 5290ms 26.04% MeshBasedCellPopulation::Update 167ms 0.82% 23.72% 4158ms 20.47% AbstractCellProperty::IsType (inline) 5ms 0.025% 23.75% 4102ms 20.19% Cylindrical2dMesh::ReMesh 591ms 2.91% 26.66% 2929ms 14.42% AbstractCellProperty::IsSame 0 0% 26.66% 2548ms 12.54% OffLatticeSimulation::UpdateCellLocationsAndTopology 432ms 2.13% 28.78% 2338ms 11.51% std::type_info::operator== (inline) 1ms 0.0049% 28.79% 2248ms 11.07% MutableMesh::ReMesh 1ms 0.0049% 28.79% 2231ms 10.98% ForwardEulerNumericalMethod::UpdateAllNodePositions 22ms 0.11% 28.90% 2186ms 10.76% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 28.90% 2012ms 9.90% AbstractCellPopulation::WriteResultsToFiles 1888ms 9.29% 38.19% 1888ms 9.29% __strcmp_avx2 793ms 3.90% 42.10% 1877ms 9.24% std::_Rb_tree::_M_lower_bound (inline) 158ms 0.78% 42.87% 1750ms 8.61% TetrahedralMesh::EdgeIterator::operator++ 67ms 0.33% 43.20% 1466ms 7.22% std::_Rb_tree::find (inline) 0 0% 43.20% 1155ms 5.69% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.025% 43.23% 1140ms 5.61% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 21ms 0.1% 43.33% 1124ms 5.53% TetrahedralMesh::ImportFromMesher 36ms 0.18% 43.51% 1063ms 5.23% operator new 18ms 0.089% 43.60% 1052ms 5.18% MeshBasedCellPopulation::SpringIterator::operator++ 231ms 1.14% 44.74% 1018ms 5.01% __GI___libc_malloc 12ms 0.059% 44.79% 968ms 4.76% std::set::insert (inline) 23ms 0.11% 44.91% 955ms 4.70% std::_Rb_tree::_M_insert_unique 48ms 0.24% 45.14% 921ms 4.53% std::__new_allocator::allocate (inline) 0 0% 45.14% 918ms 4.52% std::allocator_traits::allocate (inline) 0 0% 45.14% 888ms 4.37% std::set::count (inline) 0 0% 45.14% 828ms 4.08% triangulate 1ms 0.0049% 45.15% 745ms 3.67% delaunay 2ms 0.0098% 45.16% 744ms 3.66% divconqdelaunay 0 0% 45.16% 741ms 3.65% AbstractTwoBodyInteractionForce::AddForceContribution 385ms 1.90% 47.05% 707ms 3.48% _int_malloc 6ms 0.03% 47.08% 702ms 3.46% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 698ms 3.44% 50.52% 698ms 3.44% std::_Rb_tree::_S_right (inline) 6ms 0.03% 50.55% 694ms 3.42% CellPopulationElementWriter::Visit 207ms 1.02% 51.57% 666ms 3.28% __dynamic_cast 20ms 0.098% 51.67% 655ms 3.22% std::less::operator() (inline) 49ms 0.24% 51.91% 649ms 3.19% std::map::operator[] (partial-inline) 635ms 3.13% 55.03% 635ms 3.13% std::operator< (inline) 31ms 0.15% 55.19% 632ms 3.11% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 25ms 0.12% 55.31% 605ms 2.98% std::_Rb_tree::_M_insert_ (inline) 591ms 2.91% 58.22% 602ms 2.96% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 58.22% 592ms 2.91% std::_Rb_tree::_M_create_node (inline) 0 0% 58.22% 574ms 2.83% std::map::find (inline) 4ms 0.02% 58.24% 562ms 2.77% CellPropertyCollection::GetPropertiesType (inline) 18ms 0.089% 58.33% 556ms 2.74% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 58.33% 556ms 2.74% std::_Rb_tree::_M_get_node (inline) 4ms 0.02% 58.35% 554ms 2.73% MeshBasedCellPopulation::AcceptCellWriter 0 0% 58.35% 537ms 2.64% std::_Rb_tree::_Alloc_node::operator() (inline) 5ms 0.025% 58.37% 525ms 2.58% MutableMesh::ReIndex 1ms 0.0049% 58.38% 517ms 2.54% std::ostream::operator<< (inline) 63ms 0.31% 58.69% 516ms 2.54% std::ostream::_M_insert 2ms 0.0098% 58.70% 512ms 2.52% Element::Element 0 0% 58.70% 508ms 2.50% std::_Rb_tree::lower_bound (inline) 0 0% 58.70% 508ms 2.50% std::map::lower_bound (inline) 12ms 0.059% 58.75% 505ms 2.49% Cylindrical2dMesh::ReconstructCylindricalMesh 4ms 0.02% 58.77% 485ms 2.39% AbstractCellProperty::IsSubType (inline) 9ms 0.044% 58.82% 478ms 2.35% Cylindrical2dMesh::CorrectNonPeriodicMesh 316ms 1.56% 60.37% 466ms 2.29% AbstractCellMutationState::AbstractCellMutationState 9ms 0.044% 60.42% 453ms 2.23% Element::RegisterWithNodes (inline) 8ms 0.039% 60.46% 444ms 2.19% Node::AddElement 165ms 0.81% 61.27% 436ms 2.15% __GI___libc_free 15ms 0.074% 61.34% 384ms 1.89% divconqrecurse 11ms 0.054% 61.40% 374ms 1.84% std::_Rb_tree::erase 1ms 0.0049% 61.40% 373ms 1.84% std::set::erase (inline) 12ms 0.059% 61.46% 370ms 1.82% Node::RemoveElement 5ms 0.025% 61.49% 367ms 1.81% std::_Vector_base::_M_allocate (inline) 102ms 0.5% 61.99% 361ms 1.78% mergehulls 120ms 0.59% 62.58% 358ms 1.76% std::_Rb_tree::_M_erase 5ms 0.025% 62.60% 348ms 1.71% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 15ms 0.074% 62.68% 347ms 1.71% std::__new_allocator::deallocate (inline) 0 0% 62.68% 337ms 1.66% std::allocator_traits::deallocate (inline) 1ms 0.0049% 62.68% 331ms 1.63% NodeLocationWriter::Visit 25ms 0.12% 62.81% 329ms 1.62% Element::ResetIndex 5ms 0.025% 62.83% 328ms 1.61% Cell::GetMutationState 119ms 0.59% 63.42% 327ms 1.61% std::_Rb_tree::_M_get_insert_unique_pos 156ms 0.77% 64.18% 322ms 1.59% __cxxabiv1::__si_class_type_info::__do_dyncast 20ms 0.098% 64.28% 322ms 1.59% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.0049% 64.29% 305ms 1.50% AbstractCellPopulation::Iterator::operator++ (inline) 4ms 0.02% 64.31% 304ms 1.50% AbstractCellPopulation::GetLocationIndexUsingCell 302ms 1.49% 65.79% 302ms 1.49% std::type_info::name (inline) 39ms 0.19% 65.99% 301ms 1.48% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 65.99% 301ms 1.48% std::_Rb_tree::_M_drop_node (inline) 27ms 0.13% 66.12% 297ms 1.46% std::num_put::_M_insert_float 0 0% 66.12% 288ms 1.42% std::set::~set (inline) 3ms 0.015% 66.13% 283ms 1.39% LegacyCellProliferativeTypesWriter::VisitCell 4ms 0.02% 66.15% 277ms 1.36% Cell::GetCellProliferativeType 10ms 0.049% 66.20% 277ms 1.36% std::vector::push_back (inline) 17ms 0.084% 66.29% 276ms 1.36% std::_Rb_tree::_Rb_tree (partial-inline) 11ms 0.054% 66.34% 272ms 1.34% AbstractTetrahedralElement::CalculateJacobian 0 0% 66.34% 271ms 1.33% TetrahedralMesh::RefreshJacobianCachedData 217ms 1.07% 67.41% 270ms 1.33% _int_free 0 0% 67.41% 266ms 1.31% std::_Rb_tree::_M_put_node (inline) 22ms 0.11% 67.52% 264ms 1.30% std::vector::_M_realloc_insert 259ms 1.27% 68.79% 262ms 1.29% std::vector::operator[] (inline) 1ms 0.0049% 68.80% 256ms 1.26% std::set::set (inline) 24ms 0.12% 68.91% 241ms 1.19% std::_Rb_tree::_M_copy (inline) 7ms 0.034% 68.95% 236ms 1.16% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 4ms 0.02% 68.97% 235ms 1.16% std::__cxx11::collate::do_transform 7ms 0.034% 69.00% 234ms 1.15% AbstractCellPopulation::IsCellAttachedToLocationIndex 4ms 0.02% 69.02% 230ms 1.13% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 9ms 0.044% 69.07% 230ms 1.13% AbstractTetrahedralElement::CalculateInverseJacobian 230ms 1.13% 70.20% 230ms 1.13% [libchaste_cell_based.so] 5ms 0.025% 70.22% 229ms 1.13% alternateaxes 23ms 0.11% 70.34% 227ms 1.12% AbstractTetrahedralElement::RefreshJacobian 34ms 0.17% 70.50% 227ms 1.12% TetrahedralMesh::Clear 10ms 0.049% 70.55% 224ms 1.10% ___vsnprintf 52ms 0.26% 70.81% 223ms 1.10% ApcOneHitCellMutationState::ApcOneHitCellMutationState 216ms 1.06% 71.87% 222ms 1.09% vertexmedian 12ms 0.059% 71.93% 220ms 1.08% std::_Rb_tree::_M_erase_aux (inline) 73ms 0.36% 72.29% 215ms 1.06% std::_Rb_tree::_M_clone_node (inline) 0 0% 72.29% 214ms 1.05% __vsnprintf_internal (inline) 21ms 0.1% 72.39% 212ms 1.04% __printf_buffer 1ms 0.0049% 72.40% 209ms 1.03% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 72.40% 209ms 1.03% MeshBasedCellPopulation::GetDampingConstant 204ms 1.00% 73.40% 204ms 1.00% std::_Rb_tree_insert_and_rebalance 43ms 0.21% 73.62% 202ms 0.99% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 17ms 0.084% 73.70% 201ms 0.99% Element::MarkAsDeleted 151ms 0.74% 74.44% 200ms 0.98% malloc_consolidate 66ms 0.32% 74.77% 199ms 0.98% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 0 0% 74.77% 195ms 0.96% OffLatticeSimulation::ApplyBoundaries 151ms 0.74% 75.51% 191ms 0.94% AbstractElement::GetNodeGlobalIndex 82ms 0.4% 75.91% 185ms 0.91% AbstractElement::GetNodeLocation 180ms 0.89% 76.80% 180ms 0.89% Node::GetIndex 8ms 0.039% 76.84% 178ms 0.88% __printf_fp_l_buffer 0 0% 76.84% 178ms 0.88% __printf_fp_spec (inline) 86ms 0.42% 77.26% 162ms 0.8% __printf_fp_buffer_1 2ms 0.0098% 77.27% 159ms 0.78% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.0049% 77.28% 159ms 0.78% CellProliferativeTypesWriter::VisitCell 154ms 0.76% 78.04% 154ms 0.76% incircle 8ms 0.039% 78.08% 153ms 0.75% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 3ms 0.015% 78.09% 152ms 0.75% CellPropertyCollection::HasProperty 0 0% 78.09% 151ms 0.74% Cell::HasCellProperty (inline) 98ms 0.48% 78.57% 151ms 0.74% std::_Rb_tree::equal_range (inline) 151ms 0.74% 79.32% 151ms 0.74% unlink_chunk 1ms 0.0049% 79.32% 148ms 0.73% boost::numeric::ublas::vector_assign (inline) 43ms 0.21% 79.53% 140ms 0.69% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 12ms 0.059% 79.59% 136ms 0.67% boost::numeric::ublas::c_vector::c_vector (inline) 9ms 0.044% 79.64% 136ms 0.67% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 86ms 0.42% 80.06% 135ms 0.66% Cylindrical2dMesh::GetVectorFromAtoB 2ms 0.0098% 80.07% 135ms 0.66% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 134ms 0.66% 80.73% 134ms 0.66% AbstractElement::IsDeleted 37ms 0.18% 80.91% 134ms 0.66% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 0 0% 80.91% 132ms 0.65% AbstractCellBasedWriter::OpenOutputFileForAppend 12ms 0.059% 80.97% 130ms 0.64% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 0 0% 80.97% 130ms 0.64% OutputFileHandler::OpenOutputFile 127ms 0.63% 81.59% 128ms 0.63% std::vector::size (inline) 35ms 0.17% 81.77% 126ms 0.62% boost::numeric::ublas::indexing_vector_assign 12ms 0.059% 81.83% 124ms 0.61% Node::~Node 31ms 0.15% 81.98% 122ms 0.6% TetrahedralMesh::EdgesEnd 0 0% 81.98% 120ms 0.59% AbstractCellBasedSimulation::DoCellRemoval (inline) 109ms 0.54% 82.52% 120ms 0.59% vertexsort 3ms 0.015% 82.53% 116ms 0.57% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 30ms 0.15% 82.68% 116ms 0.57% std::num_put::_M_insert_int 0 0% 82.68% 115ms 0.57% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 2ms 0.0098% 82.69% 114ms 0.56% Cell::SetCellProliferativeType 113ms 0.56% 83.24% 113ms 0.56% AbstractCellMutationState::~AbstractCellMutationState 3ms 0.015% 83.26% 113ms 0.56% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 83.26% 110ms 0.54% std::vector::resize (inline) 41ms 0.2% 83.46% 109ms 0.54% std::__ostream_insert 1ms 0.0049% 83.47% 109ms 0.54% std::vector::_M_default_append 108ms 0.53% 84.00% 108ms 0.53% boost::shared_ptr::operator-> (inline) 107ms 0.53% 84.52% 107ms 0.53% AbstractCellProperty::~AbstractCellProperty 1ms 0.0049% 84.53% 104ms 0.51% NodeMap::NodeMap 1ms 0.0049% 84.53% 102ms 0.5% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 102ms 0.5% 85.04% 102ms 0.5% counterclockwise