File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 12739ms, 84.81% of 15021ms total Dropped 754 nodes (cum <= 75.11ms) flat flat% sum% cum cum% 0 0% 0% 14984ms 99.75% __libc_start_call_main 0 0% 0% 14984ms 99.75% __libc_start_main_impl 0 0% 0% 14984ms 99.75% _start 0 0% 0% 14969ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 14969ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 14969ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 14969ms 99.65% main 0 0% 0% 14935ms 99.43% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 14935ms 99.43% CxxTest::TestRunner::runTest (inline) 0 0% 0% 14935ms 99.43% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 14912ms 99.27% AbstractCellBasedSimulation::Solve 0 0% 0% 11395ms 75.86% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0067% 0.0067% 7186ms 47.84% AbstractCellBasedSimulation::DoCellBirth 4ms 0.027% 0.033% 7110ms 47.33% Cell::ReadyToDivide 2ms 0.013% 0.047% 7022ms 46.75% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0067% 0.053% 6913ms 46.02% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 12ms 0.08% 0.13% 6902ms 45.95% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 5ms 0.033% 0.17% 6886ms 45.84% CellCycleModelOdeHandler::SolveOdeToTime 43ms 0.29% 0.45% 6756ms 44.98% AbstractOneStepIvpOdeSolver::InternalSolve 818ms 5.45% 5.90% 6096ms 40.58% RungeKutta4IvpOdeSolver::CalculateNextYValue 2073ms 13.80% 19.70% 5114ms 34.05% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 19.70% 4120ms 27.43% MeshBasedCellPopulation::Update 2ms 0.013% 19.71% 3192ms 21.25% Cylindrical2dMesh::ReMesh 46ms 0.31% 20.02% 3052ms 20.32% AbstractCellProperty::IsType (inline) 0 0% 20.02% 2002ms 13.33% OffLatticeSimulation::UpdateCellLocationsAndTopology 256ms 1.70% 21.72% 1966ms 13.09% AbstractCellProperty::IsSame 1ms 0.0067% 21.73% 1800ms 11.98% MutableMesh::ReMesh 0 0% 21.73% 1756ms 11.69% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.06% 21.79% 1721ms 11.46% AbstractNumericalMethod::ComputeForcesIncludingDamping 158ms 1.05% 22.84% 1710ms 11.38% std::type_info::operator== (inline) 1680ms 11.18% 34.03% 1680ms 11.18% __strcmp_evex 1ms 0.0067% 34.03% 1509ms 10.05% AbstractCellPopulation::WriteResultsToFiles 612ms 4.07% 38.11% 1374ms 9.15% std::_Rb_tree::_M_lower_bound (inline) 119ms 0.79% 38.90% 1261ms 8.39% TetrahedralMesh::EdgeIterator::operator++ 66ms 0.44% 39.34% 1026ms 6.83% std::_Rb_tree::find (inline) 0 0% 39.34% 900ms 5.99% MeshBasedCellPopulation::UpdateNodePairs 10ms 0.067% 39.40% 898ms 5.98% TetrahedralMesh::ImportFromMesher 2ms 0.013% 39.42% 875ms 5.83% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 47ms 0.31% 39.73% 816ms 5.43% operator new 16ms 0.11% 39.84% 804ms 5.35% MeshBasedCellPopulation::SpringIterator::operator++ 195ms 1.30% 41.14% 757ms 5.04% __GI___libc_malloc 8ms 0.053% 41.19% 743ms 4.95% std::set::insert (inline) 11ms 0.073% 41.26% 734ms 4.89% std::_Rb_tree::_M_insert_unique 25ms 0.17% 41.43% 702ms 4.67% std::__new_allocator::allocate (inline) 0 0% 41.43% 698ms 4.65% std::allocator_traits::allocate (inline) 1ms 0.0067% 41.44% 672ms 4.47% triangulate 0 0% 41.44% 640ms 4.26% std::set::count (inline) 0 0% 41.44% 614ms 4.09% delaunay 3ms 0.02% 41.46% 613ms 4.08% divconqdelaunay 2ms 0.013% 41.47% 574ms 3.82% AbstractTwoBodyInteractionForce::AddForceContribution 35ms 0.23% 41.70% 540ms 3.59% std::map::operator[] (partial-inline) 11ms 0.073% 41.77% 537ms 3.57% CellPopulationElementWriter::Visit 529ms 3.52% 45.30% 529ms 3.52% WntCellCycleOdeSystem::CalculateStoppingEvent 2ms 0.013% 45.31% 511ms 3.40% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 19ms 0.13% 45.44% 503ms 3.35% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 142ms 0.95% 46.38% 502ms 3.34% __dynamic_cast 497ms 3.31% 49.69% 497ms 3.31% std::_Rb_tree::_S_right (inline) 18ms 0.12% 49.81% 497ms 3.31% std::less::operator() (inline) 271ms 1.80% 51.61% 482ms 3.21% _int_malloc 479ms 3.19% 54.80% 479ms 3.19% std::operator< (inline) 19ms 0.13% 54.93% 464ms 3.09% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 54.93% 455ms 3.03% std::_Rb_tree::_M_create_node (inline) 31ms 0.21% 55.14% 449ms 2.99% std::_Rb_tree::_M_insert_ (inline) 4ms 0.027% 55.16% 438ms 2.92% CellPropertyCollection::GetPropertiesType (inline) 0 0% 55.16% 435ms 2.90% std::_Rb_tree::_M_get_node (inline) 0 0% 55.16% 432ms 2.88% std::_Rb_tree::lower_bound (inline) 0 0% 55.16% 432ms 2.88% std::map::lower_bound (inline) 7ms 0.047% 55.21% 411ms 2.74% Cylindrical2dMesh::ReconstructCylindricalMesh 0 0% 55.21% 409ms 2.72% std::_Rb_tree::_Alloc_node::operator() (inline) 4ms 0.027% 55.24% 408ms 2.72% Element::Element 6ms 0.04% 55.28% 402ms 2.68% MeshBasedCellPopulation::AcceptCellWriter 1ms 0.0067% 55.28% 389ms 2.59% std::ostream::operator<< (inline) 59ms 0.39% 55.68% 388ms 2.58% std::ostream::_M_insert 0 0% 55.68% 384ms 2.56% std::map::find (inline) 4ms 0.027% 55.70% 367ms 2.44% Element::RegisterWithNodes (inline) 5ms 0.033% 55.74% 361ms 2.40% Node::AddElement 9ms 0.06% 55.80% 359ms 2.39% MutableMesh::ReIndex 133ms 0.89% 56.68% 356ms 2.37% __GI___libc_free 2ms 0.013% 56.69% 350ms 2.33% AbstractCellProperty::IsSubType (inline) 4ms 0.027% 56.72% 342ms 2.28% Cylindrical2dMesh::CorrectNonPeriodicMesh 218ms 1.45% 58.17% 337ms 2.24% AbstractCellMutationState::AbstractCellMutationState 97ms 0.65% 58.82% 317ms 2.11% std::_Rb_tree::_M_erase 23ms 0.15% 58.97% 303ms 2.02% std::_Rb_tree::~_Rb_tree (inline) 10ms 0.067% 59.04% 301ms 2.00% std::__new_allocator::deallocate (inline) 5ms 0.033% 59.07% 300ms 2.00% std::_Rb_tree::erase 1ms 0.0067% 59.08% 299ms 1.99% std::set::erase (inline) 0 0% 59.08% 297ms 1.98% std::allocator_traits::deallocate (inline) 8ms 0.053% 59.13% 292ms 1.94% Node::RemoveElement 13ms 0.087% 59.22% 284ms 1.89% divconqrecurse 0 0% 59.22% 278ms 1.85% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.22% 275ms 1.83% std::set::~set (inline) 98ms 0.65% 59.87% 274ms 1.82% std::_Rb_tree::_M_get_insert_unique_pos 71ms 0.47% 60.34% 266ms 1.77% mergehulls 0 0% 60.34% 263ms 1.75% std::_Vector_base::_M_allocate (inline) 126ms 0.84% 61.18% 256ms 1.70% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 61.18% 251ms 1.67% Cell::GetMutationState 0 0% 61.18% 246ms 1.64% std::_Rb_tree::_M_put_node (inline) 244ms 1.62% 62.81% 244ms 1.62% [libchaste_cell_based.so] 2ms 0.013% 62.82% 242ms 1.61% NodeLocationWriter::Visit 17ms 0.11% 62.93% 235ms 1.56% Element::ResetIndex 230ms 1.53% 64.46% 235ms 1.56% std::vector::operator[] (inline) 22ms 0.15% 64.61% 234ms 1.56% std::vector::push_back (inline) 19ms 0.13% 64.74% 228ms 1.52% std::_Rb_tree::_Rb_tree (partial-inline) 183ms 1.22% 65.95% 223ms 1.48% _int_free 14ms 0.093% 66.05% 222ms 1.48% std::num_put::_M_insert_float 2ms 0.013% 66.06% 220ms 1.46% Cell::GetCellProliferativeType 0 0% 66.06% 215ms 1.43% alternateaxes 201ms 1.34% 67.40% 215ms 1.43% vertexmedian 8ms 0.053% 67.45% 207ms 1.38% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 5ms 0.033% 67.49% 206ms 1.37% AbstractCellPopulation::GetLocationIndexUsingCell 12ms 0.08% 67.57% 206ms 1.37% AbstractTetrahedralElement::CalculateJacobian 2ms 0.013% 67.58% 205ms 1.36% LegacyCellProliferativeTypesWriter::VisitCell 1ms 0.0067% 67.59% 205ms 1.36% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.0067% 67.59% 200ms 1.33% std::set::set (inline) 17ms 0.11% 67.71% 199ms 1.32% std::vector::_M_realloc_insert 1ms 0.0067% 67.71% 198ms 1.32% AbstractCellPopulation::Iterator::operator++ (inline) 30ms 0.2% 67.91% 196ms 1.30% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.0067% 67.92% 196ms 1.30% MeshBasedCellPopulation::GetDampingConstant 1ms 0.0067% 67.92% 195ms 1.30% AbstractCentreBasedCellPopulation::GetDampingConstant 57ms 0.38% 68.30% 193ms 1.28% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 14ms 0.093% 68.40% 189ms 1.26% TetrahedralMesh::Clear 3ms 0.02% 68.42% 187ms 1.24% AbstractTetrahedralElement::CalculateInverseJacobian 22ms 0.15% 68.56% 183ms 1.22% std::_Rb_tree::_M_copy (inline) 11ms 0.073% 68.64% 181ms 1.20% Element::MarkAsDeleted 11ms 0.073% 68.71% 181ms 1.20% std::_Rb_tree::_M_erase_aux (inline) 4ms 0.027% 68.74% 180ms 1.20% AbstractCellPopulation::IsCellAttachedToLocationIndex 55ms 0.37% 69.10% 180ms 1.20% ApcOneHitCellMutationState::ApcOneHitCellMutationState 77ms 0.51% 69.62% 180ms 1.20% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 3ms 0.02% 69.64% 178ms 1.19% std::__cxx11::collate::do_transform 1ms 0.0067% 69.64% 169ms 1.13% ___vsnprintf 1ms 0.0067% 69.65% 168ms 1.12% __vsnprintf_internal (inline) 19ms 0.13% 69.78% 164ms 1.09% __printf_buffer 50ms 0.33% 70.11% 155ms 1.03% std::_Rb_tree::_M_clone_node (inline) 8ms 0.053% 70.16% 153ms 1.02% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 26ms 0.17% 70.33% 146ms 0.97% AbstractTetrahedralElement::RefreshJacobian 0 0% 70.33% 140ms 0.93% Cell::HasCellProperty (inline) 2ms 0.013% 70.35% 140ms 0.93% CellPropertyCollection::HasProperty 105ms 0.7% 71.05% 137ms 0.91% AbstractElement::GetNodeGlobalIndex 1ms 0.0067% 71.05% 136ms 0.91% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 105ms 0.7% 71.75% 136ms 0.91% malloc_consolidate 4ms 0.027% 71.78% 134ms 0.89% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 1ms 0.0067% 71.79% 133ms 0.89% OffLatticeSimulation::ApplyBoundaries 4ms 0.027% 71.81% 130ms 0.87% __printf_fp_l_buffer 0 0% 71.81% 130ms 0.87% __printf_fp_spec (inline) 3ms 0.02% 71.83% 128ms 0.85% AbstractTetrahedralElement::AbstractTetrahedralElement 127ms 0.85% 72.68% 127ms 0.85% AbstractCellMutationState::~AbstractCellMutationState 127ms 0.85% 73.52% 127ms 0.85% incircle 41ms 0.27% 73.80% 126ms 0.84% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 4ms 0.027% 73.82% 125ms 0.83% MeshBasedCellPopulation::SpringsEnd (inline) 2ms 0.013% 73.84% 125ms 0.83% boost::numeric::ublas::vector_assign (inline) 24ms 0.16% 74.00% 124ms 0.83% TetrahedralMesh::EdgesEnd (partial-inline) 61ms 0.41% 74.40% 123ms 0.82% __printf_fp_buffer_1 79ms 0.53% 74.93% 122ms 0.81% std::_Rb_tree::equal_range (inline) 119ms 0.79% 75.72% 119ms 0.79% [libchaste_crypt.so] 30ms 0.2% 75.92% 118ms 0.79% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 118ms 0.79% 76.71% 118ms 0.79% std::_Rb_tree_insert_and_rebalance 118ms 0.79% 77.49% 118ms 0.79% std::vector::size (inline) 11ms 0.073% 77.56% 117ms 0.78% boost::numeric::ublas::c_vector::c_vector (partial-inline) 4ms 0.027% 77.59% 110ms 0.73% CellProliferativeTypesWriter::VisitCell 69ms 0.46% 78.05% 110ms 0.73% Cylindrical2dMesh::GetVectorFromAtoB 109ms 0.73% 78.78% 109ms 0.73% Node::GetIndex 5ms 0.033% 78.81% 109ms 0.73% Node::~Node 49ms 0.33% 79.14% 107ms 0.71% AbstractElement::GetNodeLocation 23ms 0.15% 79.29% 107ms 0.71% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 7ms 0.047% 79.34% 107ms 0.71% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 2ms 0.013% 79.35% 104ms 0.69% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 28ms 0.19% 79.54% 104ms 0.69% boost::numeric::ublas::indexing_vector_assign 98ms 0.65% 80.19% 104ms 0.69% vertexsort 102ms 0.68% 80.87% 102ms 0.68% std::_Rb_tree_increment 1ms 0.0067% 80.87% 100ms 0.67% AbstractCellBasedWriter::OpenOutputFileForAppend 8ms 0.053% 80.93% 98ms 0.65% std::_Rb_tree_const_iterator::operator++ (inline) 98ms 0.65% 81.58% 98ms 0.65% unlink_chunk 1ms 0.0067% 81.59% 97ms 0.65% OutputFileHandler::OpenOutputFile 16ms 0.11% 81.69% 93ms 0.62% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 81.69% 90ms 0.6% Cell::SetCellProliferativeType 0 0% 81.69% 89ms 0.59% AbstractCellBasedSimulation::DoCellRemoval (inline) 63ms 0.42% 82.11% 89ms 0.59% TetrahedralMesh::EdgeIterator::EdgeIterator 8ms 0.053% 82.16% 88ms 0.59% Cylindrical2dMesh::CreateMirrorNodes 11ms 0.073% 82.24% 87ms 0.58% boost::detail::shared_count::~shared_count (inline) 0 0% 82.24% 87ms 0.58% boost::shared_ptr::~shared_ptr (inline) 0 0% 82.24% 85ms 0.57% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 82.24% 84ms 0.56% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 10ms 0.067% 82.30% 84ms 0.56% std::num_put::_M_insert_int 23ms 0.15% 82.46% 83ms 0.55% std::__ostream_insert 82ms 0.55% 83.00% 82ms 0.55% TetrahedralMesh::EdgeIterator::operator!= 81ms 0.54% 83.54% 81ms 0.54% [libchaste_mesh.so] 79ms 0.53% 84.07% 79ms 0.53% std::type_info::name (inline) 77ms 0.51% 84.58% 77ms 0.51% AbstractCellProperty::AbstractCellProperty 34ms 0.23% 84.81% 76ms 0.51% std::basic_filebuf::xsputn