File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 11054ms, 86.24% of 12817ms total Dropped 708 nodes (cum <= 64.08ms) flat flat% sum% cum cum% 0 0% 0% 12784ms 99.74% __libc_start_call_main 0 0% 0% 12784ms 99.74% __libc_start_main_impl 0 0% 0% 12784ms 99.74% _start 0 0% 0% 12769ms 99.63% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 12769ms 99.63% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 12769ms 99.63% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 12769ms 99.63% main 0 0% 0% 12734ms 99.35% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 12734ms 99.35% CxxTest::TestRunner::runTest (inline) 0 0% 0% 12734ms 99.35% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 12717ms 99.22% AbstractCellBasedSimulation::Solve 1ms 0.0078% 0.0078% 9783ms 76.33% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0078% 0.016% 6285ms 49.04% AbstractCellBasedSimulation::DoCellBirth 1ms 0.0078% 0.023% 6215ms 48.49% Cell::ReadyToDivide 3ms 0.023% 0.047% 6173ms 48.16% AbstractPhaseBasedCellCycleModel::ReadyToDivide 4ms 0.031% 0.078% 6088ms 47.50% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 7ms 0.055% 0.13% 6078ms 47.42% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0078% 0.14% 6070ms 47.36% CellCycleModelOdeHandler::SolveOdeToTime 46ms 0.36% 0.5% 5963ms 46.52% AbstractOneStepIvpOdeSolver::InternalSolve 707ms 5.52% 6.02% 5381ms 41.98% RungeKutta4IvpOdeSolver::CalculateNextYValue 2327ms 18.16% 24.17% 4504ms 35.14% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 24.17% 3427ms 26.74% MeshBasedCellPopulation::Update 1ms 0.0078% 24.18% 2642ms 20.61% Cylindrical2dMesh::ReMesh 45ms 0.35% 24.53% 2169ms 16.92% AbstractCellProperty::IsType (inline) 0 0% 24.53% 1639ms 12.79% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 24.53% 1478ms 11.53% MutableMesh::ReMesh 0 0% 24.53% 1400ms 10.92% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0078% 24.54% 1362ms 10.63% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 24.54% 1292ms 10.08% AbstractCellPopulation::WriteResultsToFiles 214ms 1.67% 26.21% 1220ms 9.52% AbstractCellProperty::IsSame 106ms 0.83% 27.03% 1094ms 8.54% TetrahedralMesh::EdgeIterator::operator++ 525ms 4.10% 31.13% 1087ms 8.48% std::_Rb_tree::_M_lower_bound (inline) 218ms 1.70% 32.83% 1006ms 7.85% std::type_info::operator== (inline) 897ms 7.00% 39.83% 897ms 7.00% __strcmp_evex 35ms 0.27% 40.10% 838ms 6.54% std::_Rb_tree::find (inline) 29ms 0.23% 40.33% 772ms 6.02% operator new 1ms 0.0078% 40.34% 759ms 5.92% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.016% 40.35% 745ms 5.81% TetrahedralMesh::ImportFromMesher 278ms 2.17% 42.52% 738ms 5.76% __GI___libc_malloc 2ms 0.016% 42.54% 724ms 5.65% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 12ms 0.094% 42.63% 701ms 5.47% std::set::insert (inline) 13ms 0.1% 42.73% 689ms 5.38% std::_Rb_tree::_M_insert_unique 22ms 0.17% 42.90% 688ms 5.37% std::__new_allocator::allocate (inline) 0 0% 42.90% 682ms 5.32% std::allocator_traits::allocate (inline) 4ms 0.031% 42.94% 677ms 5.28% MeshBasedCellPopulation::SpringIterator::operator++ 1ms 0.0078% 42.94% 573ms 4.47% triangulate 0 0% 42.94% 542ms 4.23% std::set::count (inline) 0 0% 42.94% 527ms 4.11% delaunay 1ms 0.0078% 42.95% 526ms 4.10% divconqdelaunay 12ms 0.094% 43.04% 479ms 3.74% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 3ms 0.023% 43.07% 445ms 3.47% CellPopulationElementWriter::Visit 1ms 0.0078% 43.08% 441ms 3.44% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 43.08% 435ms 3.39% std::_Rb_tree::_M_create_node (inline) 430ms 3.35% 46.43% 434ms 3.39% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 46.43% 427ms 3.33% std::_Rb_tree::_M_get_node (inline) 31ms 0.24% 46.67% 418ms 3.26% std::_Rb_tree::_M_insert_ (inline) 0 0% 46.67% 402ms 3.14% std::_Rb_tree::_Alloc_node::operator() (inline) 13ms 0.1% 46.77% 401ms 3.13% AbstractCellPopulation::GetCellUsingLocationIndex 220ms 1.72% 48.49% 401ms 3.13% _int_malloc 12ms 0.094% 48.58% 394ms 3.07% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 8ms 0.062% 48.65% 391ms 3.05% std::less::operator() (inline) 42ms 0.33% 48.97% 391ms 3.05% std::map::operator[] (partial-inline) 383ms 2.99% 51.96% 383ms 2.99% std::operator< (inline) 4ms 0.031% 51.99% 372ms 2.90% MutableMesh::ReIndex 370ms 2.89% 54.88% 370ms 2.89% std::_Rb_tree::_S_right (inline) 87ms 0.68% 55.56% 364ms 2.84% __GI___libc_free 7ms 0.055% 55.61% 360ms 2.81% MeshBasedCellPopulation::AcceptCellWriter 6ms 0.047% 55.66% 358ms 2.79% Element::Element 15ms 0.12% 55.78% 351ms 2.74% Cylindrical2dMesh::ReconstructCylindricalMesh 89ms 0.69% 56.47% 338ms 2.64% __dynamic_cast 5ms 0.039% 56.51% 330ms 2.57% Element::RegisterWithNodes (inline) 206ms 1.61% 58.12% 323ms 2.52% AbstractCellMutationState::AbstractCellMutationState 7ms 0.055% 58.17% 321ms 2.50% Node::AddElement 3ms 0.023% 58.20% 315ms 2.46% CellPropertyCollection::GetPropertiesType (inline) 45ms 0.35% 58.55% 314ms 2.45% std::_Rb_tree::~_Rb_tree (inline) 0 0% 58.55% 298ms 2.33% std::_Rb_tree::lower_bound (inline) 0 0% 58.55% 298ms 2.33% std::map::lower_bound (inline) 54ms 0.42% 58.97% 297ms 2.32% std::_Rb_tree::_M_erase 0 0% 58.97% 294ms 2.29% std::set::~set (inline) 0 0% 58.97% 292ms 2.28% std::_Rb_tree::_M_drop_node (inline) 0 0% 58.97% 291ms 2.27% std::map::find (inline) 27ms 0.21% 59.18% 282ms 2.20% std::ostream::_M_insert 0 0% 59.18% 282ms 2.20% std::ostream::operator<< (inline) 1ms 0.0078% 59.19% 280ms 2.18% std::set::erase (inline) 8ms 0.062% 59.25% 279ms 2.18% Node::RemoveElement 3ms 0.023% 59.27% 279ms 2.18% std::_Rb_tree::erase 259ms 2.02% 61.29% 277ms 2.16% _int_free 6ms 0.047% 61.34% 264ms 2.06% Cylindrical2dMesh::CorrectNonPeriodicMesh 4ms 0.031% 61.37% 263ms 2.05% std::__new_allocator::deallocate (inline) 98ms 0.76% 62.14% 258ms 2.01% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 62.14% 255ms 1.99% std::_Vector_base::_M_allocate (inline) 0 0% 62.14% 255ms 1.99% std::allocator_traits::deallocate (inline) 2ms 0.016% 62.15% 250ms 1.95% AbstractCellProperty::IsSubType (inline) 7ms 0.055% 62.21% 239ms 1.86% divconqrecurse 4ms 0.031% 62.24% 238ms 1.86% boost::detail::shared_count::~shared_count (inline) 0 0% 62.24% 238ms 1.86% boost::shared_ptr::~shared_ptr (inline) 229ms 1.79% 64.02% 233ms 1.82% std::vector::operator[] (inline) 228ms 1.78% 65.80% 231ms 1.80% boost::detail::sp_counted_base::release 12ms 0.094% 65.90% 229ms 1.79% Element::ResetIndex 47ms 0.37% 66.26% 229ms 1.79% mergehulls 15ms 0.12% 66.38% 225ms 1.76% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 66.38% 213ms 1.66% std::_Rb_tree::_M_put_node (inline) 1ms 0.0078% 66.39% 207ms 1.62% std::set::set (inline) 9ms 0.07% 66.46% 206ms 1.61% std::vector::push_back (inline) 1ms 0.0078% 66.47% 203ms 1.58% LegacyCellProliferativeTypesWriter::VisitCell 106ms 0.83% 67.29% 202ms 1.58% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.0078% 67.30% 197ms 1.54% AbstractCellPopulation::Iterator::operator++ (inline) 16ms 0.12% 67.43% 197ms 1.54% std::_Rb_tree::_M_copy (inline) 16ms 0.12% 67.55% 195ms 1.52% AbstractCellPopulation::Iterator::IsRealCell (inline) 191ms 1.49% 69.04% 191ms 1.49% [libchaste_cell_based.so] 7ms 0.055% 69.10% 189ms 1.47% std::vector::_M_realloc_insert 0 0% 69.10% 188ms 1.47% NodeLocationWriter::Visit 0 0% 69.10% 185ms 1.44% Cell::GetMutationState 4ms 0.031% 69.13% 183ms 1.43% AbstractCellPopulation::IsCellAttachedToLocationIndex 78ms 0.61% 69.74% 180ms 1.40% std::_Rb_tree::_M_clone_node (inline) 5ms 0.039% 69.77% 179ms 1.40% AbstractCellPopulation::GetLocationIndexUsingCell 60ms 0.47% 70.24% 179ms 1.40% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 16ms 0.12% 70.37% 170ms 1.33% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 7ms 0.055% 70.42% 169ms 1.32% std::num_put::_M_insert_float 1ms 0.0078% 70.43% 168ms 1.31% alternateaxes 13ms 0.1% 70.53% 167ms 1.30% std::_Rb_tree::_M_erase_aux (inline) 1ms 0.0078% 70.54% 165ms 1.29% Cell::GetCellProliferativeType 154ms 1.20% 71.74% 165ms 1.29% vertexmedian 14ms 0.11% 71.85% 164ms 1.28% AbstractTetrahedralElement::CalculateJacobian 60ms 0.47% 72.32% 162ms 1.26% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 50ms 0.39% 72.71% 158ms 1.23% ApcOneHitCellMutationState::ApcOneHitCellMutationState 6ms 0.047% 72.75% 156ms 1.22% Element::MarkAsDeleted 2ms 0.016% 72.77% 155ms 1.21% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 72.77% 153ms 1.19% OffLatticeSimulation::ApplyBoundaries 4ms 0.031% 72.80% 150ms 1.17% std::__cxx11::collate::do_transform 0 0% 72.80% 149ms 1.16% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.0078% 72.81% 146ms 1.14% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 72.81% 144ms 1.12% ___vsnprintf 21ms 0.16% 72.97% 144ms 1.12% __printf_buffer 0 0% 72.97% 144ms 1.12% __vsnprintf_internal (inline) 5ms 0.039% 73.01% 143ms 1.12% TetrahedralMesh::Clear 0 0% 73.01% 131ms 1.02% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 73.01% 131ms 1.02% MeshBasedCellPopulation::GetDampingConstant 3ms 0.023% 73.04% 130ms 1.01% AbstractTetrahedralElement::CalculateInverseJacobian 97ms 0.76% 73.79% 125ms 0.98% malloc_consolidate 1ms 0.0078% 73.80% 119ms 0.93% CellPropertyCollection::HasProperty 4ms 0.031% 73.83% 117ms 0.91% __printf_fp_l_buffer 0 0% 73.83% 117ms 0.91% __printf_fp_spec (inline) 117ms 0.91% 74.74% 117ms 0.91% incircle 0 0% 74.74% 115ms 0.9% Cell::HasCellProperty (inline) 15ms 0.12% 74.86% 113ms 0.88% AbstractTetrahedralElement::RefreshJacobian 52ms 0.41% 75.27% 112ms 0.87% __printf_fp_buffer_1 1ms 0.0078% 75.28% 112ms 0.87% boost::numeric::ublas::vector_assign (inline) 112ms 0.87% 76.15% 112ms 0.87% std::vector::size (inline) 76ms 0.59% 76.74% 110ms 0.86% AbstractElement::GetNodeGlobalIndex 62ms 0.48% 77.23% 110ms 0.86% std::_Rb_tree::equal_range (inline) 103ms 0.8% 78.03% 108ms 0.84% vertexsort 5ms 0.039% 78.07% 107ms 0.83% AbstractTetrahedralElement::AbstractTetrahedralElement 37ms 0.29% 78.36% 107ms 0.83% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 31ms 0.24% 78.60% 105ms 0.82% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 3ms 0.023% 78.62% 104ms 0.81% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 103ms 0.8% 79.43% 103ms 0.8% AbstractCellProperty::~AbstractCellProperty 103ms 0.8% 80.23% 103ms 0.8% [libchaste_crypt.so] 101ms 0.79% 81.02% 101ms 0.79% std::_Rb_tree_insert_and_rebalance 15ms 0.12% 81.13% 99ms 0.77% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 5ms 0.039% 81.17% 99ms 0.77% boost::numeric::ublas::c_vector::c_vector (inline) 15ms 0.12% 81.29% 93ms 0.73% TetrahedralMesh::EdgesEnd (partial-inline) 11ms 0.086% 81.38% 90ms 0.7% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 86ms 0.67% 82.05% 86ms 0.67% AbstractCellMutationState::~AbstractCellMutationState 2ms 0.016% 82.06% 86ms 0.67% CellProliferativeTypesWriter::VisitCell 43ms 0.34% 82.40% 84ms 0.66% Cylindrical2dMesh::GetVectorFromAtoB 3ms 0.023% 82.42% 83ms 0.65% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 22ms 0.17% 82.59% 83ms 0.65% boost::numeric::ublas::indexing_vector_assign 1ms 0.0078% 82.60% 82ms 0.64% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 0 0% 82.60% 80ms 0.62% std::__new_allocator::destroy (inline) 0 0% 82.60% 80ms 0.62% std::allocator_traits::destroy (inline) 0 0% 82.60% 79ms 0.62% std::_Rb_tree::_M_destroy_node (inline) 0 0% 82.60% 78ms 0.61% AbstractCellBasedWriter::OpenOutputFileForAppend 6ms 0.047% 82.65% 77ms 0.6% MeshBasedCellPopulation::SpringsEnd (inline) 50ms 0.39% 83.04% 76ms 0.59% AbstractElement::GetNodeLocation 0 0% 83.04% 76ms 0.59% OutputFileHandler::OpenOutputFile 14ms 0.11% 83.15% 76ms 0.59% std::_Rb_tree_const_iterator::operator++ (inline) 49ms 0.38% 83.53% 74ms 0.58% TetrahedralMesh::EdgeIterator::EdgeIterator 73ms 0.57% 84.10% 73ms 0.57% unlink_chunk 48ms 0.37% 84.47% 72ms 0.56% TimeStepper::AdvanceOneTimeStep 2ms 0.016% 84.49% 71ms 0.55% Cell::SetCellProliferativeType 0 0% 84.49% 70ms 0.55% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 84.49% 70ms 0.55% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.0078% 84.50% 70ms 0.55% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 84.50% 70ms 0.55% Node::~Node 70ms 0.55% 85.04% 70ms 0.55% [libchaste_mesh.so] 70ms 0.55% 85.59% 70ms 0.55% std::_Rb_tree_rebalance_for_erase 69ms 0.54% 86.13% 69ms 0.54% std::_Rb_tree_increment 13ms 0.1% 86.23% 69ms 0.54% std::num_put::_M_insert_int 2ms 0.016% 86.24% 67ms 0.52% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath