File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 15819ms, 86.86% of 18213ms total Dropped 774 nodes (cum <= 91.06ms) flat flat% sum% cum cum% 0 0% 0% 18167ms 99.75% __libc_start_call_main 0 0% 0% 18167ms 99.75% __libc_start_main_impl 0 0% 0% 18167ms 99.75% _start 0 0% 0% 18145ms 99.63% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 18145ms 99.63% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 18145ms 99.63% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 18145ms 99.63% main 0 0% 0% 18111ms 99.44% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 18111ms 99.44% CxxTest::TestRunner::runTest (inline) 0 0% 0% 18111ms 99.44% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.0055% 0.0055% 18087ms 99.31% AbstractCellBasedSimulation::Solve 0 0% 0.0055% 13860ms 76.10% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0055% 8556ms 46.98% AbstractCellBasedSimulation::DoCellBirth 18ms 0.099% 0.1% 8438ms 46.33% Cell::ReadyToDivide 2ms 0.011% 0.12% 8362ms 45.91% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0055% 0.12% 8200ms 45.02% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 9ms 0.049% 0.17% 8193ms 44.98% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.011% 0.18% 8179ms 44.91% CellCycleModelOdeHandler::SolveOdeToTime 45ms 0.25% 0.43% 7995ms 43.90% AbstractOneStepIvpOdeSolver::InternalSolve 815ms 4.47% 4.90% 7130ms 39.15% RungeKutta4IvpOdeSolver::CalculateNextYValue 3376ms 18.54% 23.44% 6038ms 33.15% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 23.44% 5179ms 28.44% MeshBasedCellPopulation::Update 2ms 0.011% 23.45% 3955ms 21.72% Cylindrical2dMesh::ReMesh 285ms 1.56% 25.02% 2805ms 15.40% AbstractCellProperty::IsType (inline) 0 0% 25.02% 2413ms 13.25% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 25.02% 2222ms 12.20% MutableMesh::ReMesh 0 0% 25.02% 2097ms 11.51% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.011% 25.03% 2045ms 11.23% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 25.03% 1806ms 9.92% AbstractCellPopulation::WriteResultsToFiles 914ms 5.02% 30.04% 1797ms 9.87% std::_Rb_tree::_M_lower_bound (inline) 156ms 0.86% 30.90% 1713ms 9.41% TetrahedralMesh::EdgeIterator::operator++ 50ms 0.27% 31.18% 1447ms 7.94% std::_Rb_tree::find (inline) 56ms 0.31% 31.48% 1243ms 6.82% operator new 0 0% 31.48% 1187ms 6.52% MeshBasedCellPopulation::UpdateNodePairs 464ms 2.55% 34.03% 1168ms 6.41% __GI___libc_malloc 3ms 0.016% 34.05% 1115ms 6.12% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 4ms 0.022% 34.07% 1095ms 6.01% TetrahedralMesh::ImportFromMesher 18ms 0.099% 34.17% 1084ms 5.95% std::set::insert (inline) 19ms 0.1% 34.27% 1066ms 5.85% std::_Rb_tree::_M_insert_unique 18ms 0.099% 34.37% 1049ms 5.76% MeshBasedCellPopulation::SpringIterator::operator++ 19ms 0.1% 34.48% 1030ms 5.66% std::__new_allocator::allocate (inline) 0 0% 34.48% 1024ms 5.62% std::allocator_traits::allocate (inline) 157ms 0.86% 35.34% 996ms 5.47% AbstractCellProperty::IsSame 925ms 5.08% 40.42% 925ms 5.08% [libchaste_cell_based.so] 0 0% 40.42% 894ms 4.91% std::set::count (inline) 0 0% 40.42% 889ms 4.88% triangulate 29ms 0.16% 40.58% 839ms 4.61% std::type_info::operator== (inline) 1ms 0.0055% 40.58% 809ms 4.44% delaunay 4ms 0.022% 40.60% 807ms 4.43% divconqdelaunay 797ms 4.38% 44.98% 797ms 4.38% __strcmp_evex 11ms 0.06% 45.04% 719ms 3.95% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 45.04% 705ms 3.87% std::_Rb_tree::_M_create_node (inline) 61ms 0.33% 45.37% 699ms 3.84% std::_Rb_tree::_M_insert_ (inline) 0 0% 45.37% 692ms 3.80% std::_Rb_tree::_M_get_node (inline) 684ms 3.76% 49.13% 684ms 3.76% WntCellCycleOdeSystem::CalculateStoppingEvent 9ms 0.049% 49.18% 637ms 3.50% CellPopulationElementWriter::Visit 0 0% 49.18% 637ms 3.50% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.011% 49.19% 615ms 3.38% AbstractTwoBodyInteractionForce::AddForceContribution 52ms 0.29% 49.48% 592ms 3.25% std::map::operator[] (partial-inline) 347ms 1.91% 51.38% 584ms 3.21% _int_malloc 568ms 3.12% 54.50% 568ms 3.12% std::_Rb_tree::_S_right (inline) 12ms 0.066% 54.57% 565ms 3.10% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.027% 54.59% 561ms 3.08% CellPropertyCollection::GetPropertiesType (inline) 8ms 0.044% 54.64% 559ms 3.07% MeshBasedCellPopulation::AcceptCellWriter 148ms 0.81% 55.45% 559ms 3.07% __dynamic_cast 6ms 0.033% 55.48% 555ms 3.05% Element::Element 0 0% 55.48% 548ms 3.01% std::map::find (inline) 19ms 0.1% 55.59% 542ms 2.98% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 6ms 0.033% 55.62% 538ms 2.95% Element::RegisterWithNodes (inline) 29ms 0.16% 55.78% 528ms 2.90% Node::AddElement 250ms 1.37% 57.15% 492ms 2.70% AbstractCellMutationState::AbstractCellMutationState 21ms 0.12% 57.27% 492ms 2.70% Cylindrical2dMesh::ReconstructCylindricalMesh 116ms 0.64% 57.90% 483ms 2.65% __GI___libc_free 14ms 0.077% 57.98% 470ms 2.58% std::less::operator() (inline) 5ms 0.027% 58.01% 463ms 2.54% Cylindrical2dMesh::CorrectNonPeriodicMesh 3ms 0.016% 58.02% 460ms 2.53% MutableMesh::ReIndex 456ms 2.50% 60.53% 456ms 2.50% std::operator< (inline) 0 0% 60.53% 441ms 2.42% std::_Rb_tree::lower_bound (inline) 0 0% 60.53% 441ms 2.42% std::map::lower_bound (inline) 63ms 0.35% 60.87% 436ms 2.39% std::ostream::_M_insert 0 0% 60.87% 436ms 2.39% std::ostream::operator<< (inline) 0 0% 60.87% 430ms 2.36% std::_Rb_tree::_M_drop_node (inline) 4ms 0.022% 60.90% 429ms 2.36% AbstractCellProperty::IsSubType (inline) 59ms 0.32% 61.22% 420ms 2.31% std::_Rb_tree::~_Rb_tree (inline) 418ms 2.30% 63.52% 418ms 2.30% [libchaste_crypt.so] 0 0% 63.52% 407ms 2.23% std::set::~set (inline) 12ms 0.066% 63.58% 400ms 2.20% divconqrecurse 59ms 0.32% 63.90% 391ms 2.15% std::_Rb_tree::_M_erase 10ms 0.055% 63.96% 383ms 2.10% std::__new_allocator::deallocate (inline) 0 0% 63.96% 379ms 2.08% std::allocator_traits::deallocate (inline) 119ms 0.65% 64.61% 377ms 2.07% mergehulls 292ms 1.60% 66.22% 361ms 1.98% _int_free 10ms 0.055% 66.27% 360ms 1.98% std::_Rb_tree::erase 0 0% 66.27% 360ms 1.98% std::set::erase (inline) 7ms 0.038% 66.31% 358ms 1.97% Node::RemoveElement 140ms 0.77% 67.08% 348ms 1.91% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 67.08% 332ms 1.82% std::_Vector_base::_M_allocate (inline) 2ms 0.011% 67.09% 320ms 1.76% Cell::GetMutationState 12ms 0.066% 67.16% 316ms 1.74% boost::detail::shared_count::~shared_count (inline) 0 0% 67.16% 316ms 1.74% boost::shared_ptr::~shared_ptr (inline) 0 0% 67.16% 314ms 1.72% std::_Rb_tree::_M_put_node (inline) 3ms 0.016% 67.17% 312ms 1.71% Cell::GetCellProliferativeType 15ms 0.082% 67.25% 311ms 1.71% Element::ResetIndex 137ms 0.75% 68.01% 307ms 1.69% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.0055% 68.01% 304ms 1.67% AbstractCellPopulation::Iterator::operator++ (inline) 20ms 0.11% 68.12% 300ms 1.65% AbstractCellPopulation::Iterator::IsRealCell (inline) 23ms 0.13% 68.25% 300ms 1.65% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 1ms 0.0055% 68.25% 299ms 1.64% LegacyCellProliferativeTypesWriter::VisitCell 292ms 1.60% 69.86% 298ms 1.64% boost::detail::sp_counted_base::release 0 0% 69.86% 283ms 1.55% NodeLocationWriter::Visit 8ms 0.044% 69.90% 280ms 1.54% std::_Rb_tree::_Rb_tree (partial-inline) 8ms 0.044% 69.94% 278ms 1.53% alternateaxes 239ms 1.31% 71.26% 270ms 1.48% vertexmedian 10ms 0.055% 71.31% 269ms 1.48% AbstractCellPopulation::GetLocationIndexUsingCell 258ms 1.42% 72.73% 269ms 1.48% std::vector::operator[] (inline) 5ms 0.027% 72.76% 268ms 1.47% std::set::set (inline) 35ms 0.19% 72.95% 267ms 1.47% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 0 0% 72.95% 263ms 1.44% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 5ms 0.027% 72.98% 260ms 1.43% std::vector::push_back (inline) 22ms 0.12% 73.10% 256ms 1.41% std::_Rb_tree::_M_copy (inline) 11ms 0.06% 73.16% 247ms 1.36% std::num_put::_M_insert_float 1ms 0.0055% 73.16% 246ms 1.35% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 15ms 0.082% 73.24% 244ms 1.34% std::_Rb_tree::_M_erase_aux (inline) 7ms 0.038% 73.28% 243ms 1.33% std::vector::_M_realloc_insert 2ms 0.011% 73.29% 239ms 1.31% ApcOneHitCellMutationState::ApcOneHitCellMutationState 5ms 0.027% 73.32% 233ms 1.28% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.0055% 73.33% 233ms 1.28% MeshBasedCellPopulation::GetDampingConstant 3ms 0.016% 73.34% 230ms 1.26% AbstractCentreBasedCellPopulation::GetDampingConstant 89ms 0.49% 73.83% 227ms 1.25% std::_Rb_tree::_M_clone_node (inline) 0 0% 73.83% 224ms 1.23% TetrahedralMesh::RefreshJacobianCachedData 5ms 0.027% 73.86% 222ms 1.22% AbstractCellPopulation::IsCellAttachedToLocationIndex 215ms 1.18% 75.04% 215ms 1.18% [libchaste_mesh.so] 0 0% 75.04% 214ms 1.17% OffLatticeSimulation::ApplyBoundaries 10ms 0.055% 75.09% 211ms 1.16% AbstractTetrahedralElement::CalculateJacobian 8ms 0.044% 75.14% 211ms 1.16% std::__cxx11::collate::do_transform 4ms 0.022% 75.16% 205ms 1.13% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.0055% 75.17% 197ms 1.08% ___vsnprintf 23ms 0.13% 75.29% 197ms 1.08% __printf_buffer 0 0% 75.29% 196ms 1.08% __vsnprintf_internal (inline) 7ms 0.038% 75.33% 190ms 1.04% Element::MarkAsDeleted 39ms 0.21% 75.54% 172ms 0.94% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 125ms 0.69% 76.23% 162ms 0.89% malloc_consolidate 0 0% 76.23% 161ms 0.88% TetrahedralMesh::Clear 38ms 0.21% 76.44% 159ms 0.87% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 6ms 0.033% 76.47% 159ms 0.87% __printf_fp_l_buffer 0 0% 76.47% 159ms 0.87% __printf_fp_spec (inline) 2ms 0.011% 76.48% 155ms 0.85% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 151ms 0.83% 77.31% 151ms 0.83% incircle 0 0% 77.31% 149ms 0.82% CellProliferativeTypesWriter::VisitCell 19ms 0.1% 77.42% 148ms 0.81% AbstractTetrahedralElement::RefreshJacobian 148ms 0.81% 78.23% 148ms 0.81% std::vector::size (inline) 18ms 0.099% 78.33% 147ms 0.81% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 60ms 0.33% 78.66% 146ms 0.8% __printf_fp_buffer_1 146ms 0.8% 79.46% 146ms 0.8% std::_Rb_tree_insert_and_rebalance 2ms 0.011% 79.47% 145ms 0.8% CellPropertyCollection::HasProperty 0 0% 79.47% 143ms 0.79% Cell::HasCellProperty (inline) 4ms 0.022% 79.49% 143ms 0.79% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 21ms 0.12% 79.61% 139ms 0.76% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 79.61% 133ms 0.73% boost::numeric::ublas::vector_assign (inline) 3ms 0.016% 79.62% 132ms 0.72% MeshBasedCellPopulation::SpringsEnd (inline) 5ms 0.027% 79.65% 128ms 0.7% AbstractTetrahedralElement::AbstractTetrahedralElement 46ms 0.25% 79.90% 127ms 0.7% AbstractElement::GetNodeGlobalIndex 126ms 0.69% 80.60% 126ms 0.69% AbstractCellProperty::AbstractCellProperty 0 0% 80.60% 125ms 0.69% AbstractCellBasedSimulation::DoCellRemoval (inline) 7ms 0.038% 80.63% 124ms 0.68% Cell::SetCellProliferativeType 124ms 0.68% 81.32% 124ms 0.68% std::_Rb_tree::_S_left (inline) 7ms 0.038% 81.35% 120ms 0.66% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 118ms 0.65% 82.00% 118ms 0.65% std::type_info::name (inline) 0 0% 82.00% 117ms 0.64% std::__new_allocator::destroy (inline) 0 0% 82.00% 117ms 0.64% std::allocator_traits::destroy (inline) 0 0% 82.00% 116ms 0.64% std::_Rb_tree::_M_destroy_node (inline) 105ms 0.58% 82.58% 116ms 0.64% vertexsort 2ms 0.011% 82.59% 115ms 0.63% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 45ms 0.25% 82.84% 113ms 0.62% AbstractElement::GetNodeLocation 56ms 0.31% 83.14% 113ms 0.62% std::_Rb_tree::equal_range (inline) 3ms 0.016% 83.16% 109ms 0.6% boost::numeric::ublas::c_vector::c_vector (inline) 84ms 0.46% 83.62% 106ms 0.58% TetrahedralMesh::EdgeIterator::EdgeIterator 23ms 0.13% 83.75% 105ms 0.58% MeshBasedCellPopulation::SpringIterator::SpringIterator 7ms 0.038% 83.79% 105ms 0.58% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 20ms 0.11% 83.90% 105ms 0.58% std::num_put::_M_insert_int 3ms 0.016% 83.91% 103ms 0.57% Cylindrical2dMesh::CreateMirrorNodes 40ms 0.22% 84.13% 103ms 0.57% std::__ostream_insert 101ms 0.55% 84.69% 101ms 0.55% [libchaste_ode.so] 100ms 0.55% 85.24% 100ms 0.55% std::_Rb_tree_increment 8ms 0.044% 85.28% 99ms 0.54% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 61ms 0.33% 85.61% 99ms 0.54% Cylindrical2dMesh::GetVectorFromAtoB 4ms 0.022% 85.64% 99ms 0.54% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.011% 85.65% 98ms 0.54% std::_Rb_tree_const_iterator::operator++ (inline) 5ms 0.027% 85.68% 94ms 0.52% CellPropertyCollection::AddProperty 94ms 0.52% 86.19% 94ms 0.52% unlink_chunk 28ms 0.15% 86.34% 92ms 0.51% boost::numeric::ublas::indexing_vector_assign 92ms 0.51% 86.85% 92ms 0.51% counterclockwise 1ms 0.0055% 86.86% 92ms 0.51% std::vector::resize (inline)