File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 11487ms, 85.44% of 13445ms total Dropped 717 nodes (cum <= 67.22ms) flat flat% sum% cum cum% 0 0% 0% 13410ms 99.74% __libc_start_call_main 0 0% 0% 13410ms 99.74% __libc_start_main_impl 0 0% 0% 13410ms 99.74% _start 0 0% 0% 13394ms 99.62% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 13394ms 99.62% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 13394ms 99.62% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 13394ms 99.62% main 0 0% 0% 13354ms 99.32% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 13354ms 99.32% CxxTest::TestRunner::runTest (inline) 0 0% 0% 13354ms 99.32% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.0074% 0.0074% 13335ms 99.18% AbstractCellBasedSimulation::Solve 0 0% 0.0074% 10163ms 75.59% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0074% 6282ms 46.72% AbstractCellBasedSimulation::DoCellBirth 4ms 0.03% 0.037% 6202ms 46.13% Cell::ReadyToDivide 2ms 0.015% 0.052% 6155ms 45.78% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0074% 0.06% 6076ms 45.19% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 5ms 0.037% 0.097% 6072ms 45.16% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 0.097% 6066ms 45.12% CellCycleModelOdeHandler::SolveOdeToTime 31ms 0.23% 0.33% 5939ms 44.17% AbstractOneStepIvpOdeSolver::InternalSolve 532ms 3.96% 4.28% 5338ms 39.70% RungeKutta4IvpOdeSolver::CalculateNextYValue 2322ms 17.27% 21.55% 4614ms 34.32% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 21.55% 3796ms 28.23% MeshBasedCellPopulation::Update 1ms 0.0074% 21.56% 2897ms 21.55% Cylindrical2dMesh::ReMesh 199ms 1.48% 23.04% 2400ms 17.85% AbstractCellProperty::IsType (inline) 0 0% 23.04% 1820ms 13.54% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0074% 23.05% 1587ms 11.80% MutableMesh::ReMesh 0 0% 23.05% 1583ms 11.77% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 23.05% 1561ms 11.61% AbstractNumericalMethod::ComputeForcesIncludingDamping 629ms 4.68% 27.73% 1349ms 10.03% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.0074% 27.74% 1347ms 10.02% AbstractCellPopulation::WriteResultsToFiles 112ms 0.83% 28.57% 1307ms 9.72% TetrahedralMesh::EdgeIterator::operator++ 37ms 0.28% 28.84% 1064ms 7.91% std::_Rb_tree::find (inline) 110ms 0.82% 29.66% 992ms 7.38% AbstractCellProperty::IsSame 12ms 0.089% 29.75% 882ms 6.56% std::type_info::operator== (inline) 0 0% 29.75% 867ms 6.45% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.0074% 29.76% 867ms 6.45% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 33ms 0.25% 30.00% 828ms 6.16% operator new 818ms 6.08% 36.09% 818ms 6.08% __strcmp_evex 238ms 1.77% 37.86% 789ms 5.87% __GI___libc_malloc 4ms 0.03% 37.89% 779ms 5.79% TetrahedralMesh::ImportFromMesher 8ms 0.06% 37.95% 773ms 5.75% std::set::insert (inline) 13ms 0.097% 38.04% 769ms 5.72% MeshBasedCellPopulation::SpringIterator::operator++ 10ms 0.074% 38.12% 765ms 5.69% std::_Rb_tree::_M_insert_unique 18ms 0.13% 38.25% 717ms 5.33% std::__new_allocator::allocate (inline) 0 0% 38.25% 716ms 5.33% std::allocator_traits::allocate (inline) 701ms 5.21% 43.47% 701ms 5.21% [libchaste_cell_based.so] 0 0% 43.47% 674ms 5.01% std::set::count (inline) 1ms 0.0074% 43.47% 625ms 4.65% triangulate 0 0% 43.47% 562ms 4.18% delaunay 3ms 0.022% 43.50% 562ms 4.18% divconqdelaunay 6ms 0.045% 43.54% 522ms 3.88% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 2ms 0.015% 43.56% 490ms 3.64% AbstractTwoBodyInteractionForce::AddForceContribution 306ms 2.28% 45.83% 486ms 3.61% _int_malloc 480ms 3.57% 49.40% 480ms 3.57% std::_Rb_tree::_S_right (inline) 32ms 0.24% 49.64% 468ms 3.48% std::_Rb_tree::_M_insert_ (inline) 0 0% 49.64% 466ms 3.47% std::_Rb_tree::_M_create_node (inline) 31ms 0.23% 49.87% 460ms 3.42% std::map::operator[] (partial-inline) 0 0% 49.87% 459ms 3.41% std::_Rb_tree::_M_get_node (inline) 2ms 0.015% 49.88% 457ms 3.40% CellPopulationElementWriter::Visit 442ms 3.29% 53.17% 442ms 3.29% WntCellCycleOdeSystem::CalculateStoppingEvent 16ms 0.12% 53.29% 432ms 3.21% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 27ms 0.2% 53.49% 427ms 3.18% Cylindrical2dMesh::ReconstructCylindricalMesh 5ms 0.037% 53.53% 417ms 3.10% MeshBasedCellPopulation::AcceptCellWriter 218ms 1.62% 55.15% 410ms 3.05% AbstractCellMutationState::AbstractCellMutationState 0 0% 55.15% 404ms 3.00% std::_Rb_tree::_Alloc_node::operator() (inline) 118ms 0.88% 56.03% 402ms 2.99% __dynamic_cast 6ms 0.045% 56.07% 392ms 2.92% Element::Element 9ms 0.067% 56.14% 390ms 2.90% AbstractCellPopulation::GetCellUsingLocationIndex 6ms 0.045% 56.18% 388ms 2.89% Element::RegisterWithNodes (inline) 0 0% 56.18% 385ms 2.86% std::map::find (inline) 12ms 0.089% 56.27% 383ms 2.85% Node::AddElement 5ms 0.037% 56.31% 370ms 2.75% CellPropertyCollection::GetPropertiesType (inline) 10ms 0.074% 56.39% 366ms 2.72% std::less::operator() (inline) 3ms 0.022% 56.41% 358ms 2.66% MutableMesh::ReIndex 356ms 2.65% 59.06% 356ms 2.65% std::operator< (inline) 80ms 0.6% 59.65% 353ms 2.63% __GI___libc_free 0 0% 59.65% 342ms 2.54% std::_Rb_tree::lower_bound (inline) 0 0% 59.65% 342ms 2.54% std::map::lower_bound (inline) 1ms 0.0074% 59.66% 323ms 2.40% std::ostream::operator<< (inline) 34ms 0.25% 59.91% 320ms 2.38% std::ostream::_M_insert 5ms 0.037% 59.95% 308ms 2.29% divconqrecurse 4ms 0.03% 59.98% 305ms 2.27% Cylindrical2dMesh::CorrectNonPeriodicMesh 4ms 0.03% 60.01% 305ms 2.27% std::_Rb_tree::erase 4ms 0.03% 60.04% 304ms 2.26% AbstractCellProperty::IsSubType (inline) 0 0% 60.04% 303ms 2.25% std::set::erase (inline) 300ms 2.23% 62.27% 300ms 2.23% [libchaste_crypt.so] 0 0% 62.27% 300ms 2.23% std::_Rb_tree::_M_drop_node (inline) 82ms 0.61% 62.88% 297ms 2.21% mergehulls 5ms 0.037% 62.92% 296ms 2.20% Node::RemoveElement 8ms 0.06% 62.98% 290ms 2.16% std::__new_allocator::deallocate (inline) 0 0% 62.98% 289ms 2.15% std::allocator_traits::deallocate (inline) 118ms 0.88% 63.85% 287ms 2.13% std::_Rb_tree::_M_get_insert_unique_pos 37ms 0.28% 64.13% 281ms 2.09% std::_Rb_tree::~_Rb_tree (inline) 49ms 0.36% 64.49% 278ms 2.07% std::_Rb_tree::_M_erase 226ms 1.68% 66.17% 269ms 2.00% _int_free 0 0% 66.17% 268ms 1.99% std::set::~set (inline) 1ms 0.0074% 66.18% 258ms 1.92% std::_Vector_base::_M_allocate (inline) 13ms 0.097% 66.28% 249ms 1.85% Element::ResetIndex 0 0% 66.28% 235ms 1.75% std::_Rb_tree::_M_put_node (inline) 3ms 0.022% 66.30% 229ms 1.70% Cell::GetMutationState 7ms 0.052% 66.35% 229ms 1.70% boost::detail::shared_count::~shared_count (inline) 0 0% 66.35% 229ms 1.70% boost::shared_ptr::~shared_ptr (inline) 1ms 0.0074% 66.36% 228ms 1.70% LegacyCellProliferativeTypesWriter::VisitCell 13ms 0.097% 66.46% 221ms 1.64% std::vector::push_back (inline) 2ms 0.015% 66.47% 217ms 1.61% AbstractCellPopulation::Iterator::operator++ (inline) 213ms 1.58% 68.06% 216ms 1.61% boost::detail::sp_counted_base::release 27ms 0.2% 68.26% 215ms 1.60% AbstractCellPopulation::Iterator::IsRealCell (inline) 12ms 0.089% 68.35% 214ms 1.59% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 68.35% 206ms 1.53% ApcOneHitCellMutationState::ApcOneHitCellMutationState 1ms 0.0074% 68.35% 205ms 1.52% NodeLocationWriter::Visit 9ms 0.067% 68.42% 202ms 1.50% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 1ms 0.0074% 68.43% 199ms 1.48% std::set::set (inline) 4ms 0.03% 68.46% 199ms 1.48% std::vector::_M_realloc_insert 105ms 0.78% 69.24% 197ms 1.47% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.0074% 69.25% 194ms 1.44% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 0 0% 69.25% 193ms 1.44% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 185ms 1.38% 70.62% 192ms 1.43% std::vector::operator[] (inline) 24ms 0.18% 70.80% 190ms 1.41% std::_Rb_tree::_M_copy (inline) 1ms 0.0074% 70.81% 185ms 1.38% AbstractCellPopulation::IsCellAttachedToLocationIndex 20ms 0.15% 70.96% 185ms 1.38% std::num_put::_M_insert_float 2ms 0.015% 70.97% 184ms 1.37% Cell::GetCellProliferativeType 10ms 0.074% 71.04% 184ms 1.37% std::_Rb_tree::_M_erase_aux (inline) 25ms 0.19% 71.23% 171ms 1.27% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 12ms 0.089% 71.32% 167ms 1.24% AbstractCellPopulation::GetLocationIndexUsingCell 4ms 0.03% 71.35% 166ms 1.23% AbstractTetrahedralElement::CalculateJacobian 6ms 0.045% 71.39% 164ms 1.22% Element::MarkAsDeleted 0 0% 71.39% 162ms 1.20% TetrahedralMesh::RefreshJacobianCachedData 76ms 0.57% 71.96% 162ms 1.20% std::_Rb_tree::_M_clone_node (inline) 0 0% 71.96% 159ms 1.18% alternateaxes 145ms 1.08% 73.04% 158ms 1.18% vertexmedian 2ms 0.015% 73.05% 156ms 1.16% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 155ms 1.15% 74.21% 155ms 1.15% [libchaste_mesh.so] 0 0% 74.21% 154ms 1.15% OffLatticeSimulation::ApplyBoundaries 4ms 0.03% 74.24% 150ms 1.12% std::__cxx11::collate::do_transform 4ms 0.03% 74.27% 145ms 1.08% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.0074% 74.27% 142ms 1.06% ___vsnprintf 0 0% 74.27% 141ms 1.05% __vsnprintf_internal (inline) 34ms 0.25% 74.53% 140ms 1.04% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 15ms 0.11% 74.64% 139ms 1.03% __printf_buffer 136ms 1.01% 75.65% 136ms 1.01% incircle 1ms 0.0074% 75.66% 135ms 1.00% MeshBasedCellPopulation::GetDampingConstant 1ms 0.0074% 75.66% 134ms 1% AbstractCentreBasedCellPopulation::GetDampingConstant 36ms 0.27% 75.93% 131ms 0.97% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 103ms 0.77% 76.70% 127ms 0.94% malloc_consolidate 121ms 0.9% 77.60% 121ms 0.9% std::_Rb_tree_insert_and_rebalance 30ms 0.22% 77.82% 120ms 0.89% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 0 0% 77.82% 120ms 0.89% CellPropertyCollection::HasProperty 69ms 0.51% 78.33% 120ms 0.89% std::_Rb_tree::equal_range (inline) 0 0% 78.33% 119ms 0.89% Cell::HasCellProperty (inline) 17ms 0.13% 78.46% 115ms 0.86% AbstractTetrahedralElement::RefreshJacobian 1ms 0.0074% 78.47% 114ms 0.85% TetrahedralMesh::Clear 1ms 0.0074% 78.48% 113ms 0.84% __printf_fp_l_buffer 0 0% 78.48% 113ms 0.84% __printf_fp_spec (inline) 1ms 0.0074% 78.48% 113ms 0.84% boost::numeric::ublas::vector_assign (inline) 111ms 0.83% 79.31% 111ms 0.83% AbstractCellProperty::AbstractCellProperty 6ms 0.045% 79.35% 111ms 0.83% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 0 0% 79.35% 109ms 0.81% CellProliferativeTypesWriter::VisitCell 45ms 0.33% 79.69% 108ms 0.8% __printf_fp_buffer_1 107ms 0.8% 80.48% 107ms 0.8% std::vector::size (inline) 3ms 0.022% 80.51% 103ms 0.77% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 103ms 0.77% 81.27% 103ms 0.77% std::type_info::name (inline) 43ms 0.32% 81.59% 101ms 0.75% AbstractElement::GetNodeGlobalIndex 4ms 0.03% 81.62% 98ms 0.73% boost::numeric::ublas::c_vector::c_vector (partial-inline) 4ms 0.03% 81.65% 95ms 0.71% AbstractTetrahedralElement::AbstractTetrahedralElement 94ms 0.7% 82.35% 94ms 0.7% std::_Rb_tree::_S_left (inline) 21ms 0.16% 82.51% 93ms 0.69% boost::numeric::ublas::indexing_vector_assign 80ms 0.6% 83.10% 90ms 0.67% vertexsort 32ms 0.24% 83.34% 89ms 0.66% AbstractElement::GetNodeLocation 7ms 0.052% 83.39% 87ms 0.65% std::_Rb_tree::_M_emplace_hint_unique 50ms 0.37% 83.76% 86ms 0.64% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 83.76% 84ms 0.62% AbstractCellBasedSimulation::DoCellRemoval (inline) 6ms 0.045% 83.81% 81ms 0.6% MeshBasedCellPopulation::SpringsEnd (inline) 5ms 0.037% 83.85% 81ms 0.6% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 8ms 0.06% 83.90% 80ms 0.6% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 16ms 0.12% 84.02% 79ms 0.59% TetrahedralMesh::EdgesEnd (partial-inline) 31ms 0.23% 84.25% 79ms 0.59% std::num_put::_M_insert_int 77ms 0.57% 84.83% 77ms 0.57% Node::GetIndex 0 0% 84.83% 77ms 0.57% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 0 0% 84.83% 75ms 0.56% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 84.83% 75ms 0.56% OutputFileHandler::OpenOutputFile 6ms 0.045% 84.87% 74ms 0.55% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 72ms 0.54% 85.41% 72ms 0.54% counterclockwise 4ms 0.03% 85.44% 68ms 0.51% std::_Rb_tree_const_iterator::operator++ (inline)