File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 13793ms, 86.23% of 15996ms total Dropped 747 nodes (cum <= 79.98ms) flat flat% sum% cum cum% 0 0% 0% 15958ms 99.76% __libc_start_call_main 0 0% 0% 15958ms 99.76% __libc_start_main_impl 0 0% 0% 15958ms 99.76% _start 0 0% 0% 15939ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 15939ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 15939ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 15939ms 99.64% main 0 0% 0% 15906ms 99.44% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 15906ms 99.44% CxxTest::TestRunner::runTest (inline) 0 0% 0% 15906ms 99.44% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 15884ms 99.30% AbstractCellBasedSimulation::Solve 0 0% 0% 12082ms 75.53% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 7448ms 46.56% AbstractCellBasedSimulation::DoCellBirth 7ms 0.044% 0.044% 7350ms 45.95% Cell::ReadyToDivide 1ms 0.0063% 0.05% 7294ms 45.60% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0063% 0.056% 7179ms 44.88% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 5ms 0.031% 0.088% 7175ms 44.85% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.013% 0.1% 7159ms 44.75% CellCycleModelOdeHandler::SolveOdeToTime 37ms 0.23% 0.33% 6994ms 43.72% AbstractOneStepIvpOdeSolver::InternalSolve 694ms 4.34% 4.67% 6255ms 39.10% RungeKutta4IvpOdeSolver::CalculateNextYValue 2947ms 18.42% 23.09% 5343ms 33.40% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0063% 23.10% 4539ms 28.38% MeshBasedCellPopulation::Update 1ms 0.0063% 23.11% 3433ms 21.46% Cylindrical2dMesh::ReMesh 258ms 1.61% 24.72% 2514ms 15.72% AbstractCellProperty::IsType (inline) 1ms 0.0063% 24.72% 2187ms 13.67% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0063% 24.73% 1911ms 11.95% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 24.73% 1893ms 11.83% MutableMesh::ReMesh 2ms 0.013% 24.74% 1868ms 11.68% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0063% 24.75% 1608ms 10.05% AbstractCellPopulation::WriteResultsToFiles 711ms 4.44% 29.19% 1577ms 9.86% std::_Rb_tree::_M_lower_bound (inline) 124ms 0.78% 29.97% 1527ms 9.55% TetrahedralMesh::EdgeIterator::operator++ 46ms 0.29% 30.26% 1231ms 7.70% std::_Rb_tree::find (inline) 0 0% 30.26% 1069ms 6.68% MeshBasedCellPopulation::UpdateNodePairs 38ms 0.24% 30.50% 1030ms 6.44% operator new 3ms 0.019% 30.51% 1016ms 6.35% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 340ms 2.13% 32.64% 985ms 6.16% __GI___libc_malloc 15ms 0.094% 32.73% 948ms 5.93% MeshBasedCellPopulation::SpringIterator::operator++ 139ms 0.87% 33.60% 942ms 5.89% AbstractCellProperty::IsSame 4ms 0.025% 33.63% 935ms 5.85% TetrahedralMesh::ImportFromMesher 13ms 0.081% 33.71% 924ms 5.78% std::set::insert (inline) 11ms 0.069% 33.78% 911ms 5.70% std::_Rb_tree::_M_insert_unique 22ms 0.14% 33.91% 872ms 5.45% std::__new_allocator::allocate (inline) 0 0% 33.91% 871ms 5.45% std::allocator_traits::allocate (inline) 811ms 5.07% 38.98% 811ms 5.07% __strcmp_evex 19ms 0.12% 39.10% 803ms 5.02% std::type_info::operator== (inline) 802ms 5.01% 44.12% 802ms 5.01% [libchaste_cell_based.so] 0 0% 44.12% 766ms 4.79% std::set::count (inline) 2ms 0.013% 44.13% 736ms 4.60% triangulate 1ms 0.0063% 44.14% 651ms 4.07% delaunay 3ms 0.019% 44.15% 650ms 4.06% divconqdelaunay 11ms 0.069% 44.22% 634ms 3.96% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 1ms 0.0063% 44.23% 595ms 3.72% AbstractTwoBodyInteractionForce::AddForceContribution 10ms 0.063% 44.29% 580ms 3.63% CellPopulationElementWriter::Visit 0 0% 44.29% 575ms 3.59% std::_Rb_tree::_M_create_node (inline) 40ms 0.25% 44.54% 569ms 3.56% std::_Rb_tree::_M_insert_ (inline) 0 0% 44.54% 559ms 3.49% std::_Rb_tree::_M_get_node (inline) 351ms 2.19% 46.74% 557ms 3.48% _int_malloc 556ms 3.48% 50.21% 556ms 3.48% WntCellCycleOdeSystem::CalculateStoppingEvent 553ms 3.46% 53.67% 553ms 3.46% std::_Rb_tree::_S_right (inline) 49ms 0.31% 53.98% 553ms 3.46% std::map::operator[] (partial-inline) 0 0% 53.98% 530ms 3.31% std::_Rb_tree::_Alloc_node::operator() (inline) 23ms 0.14% 54.12% 524ms 3.28% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 15ms 0.094% 54.21% 510ms 3.19% AbstractCellPopulation::GetCellUsingLocationIndex 9ms 0.056% 54.27% 507ms 3.17% CellPropertyCollection::GetPropertiesType (inline) 143ms 0.89% 55.16% 504ms 3.15% __dynamic_cast 7ms 0.044% 55.21% 495ms 3.09% MeshBasedCellPopulation::AcceptCellWriter 24ms 0.15% 55.36% 464ms 2.90% Cylindrical2dMesh::ReconstructCylindricalMesh 2ms 0.013% 55.37% 464ms 2.90% Element::Element 0 0% 55.37% 463ms 2.89% std::map::find (inline) 15ms 0.094% 55.46% 446ms 2.79% std::less::operator() (inline) 81ms 0.51% 55.97% 442ms 2.76% __GI___libc_free 8ms 0.05% 56.02% 441ms 2.76% Element::RegisterWithNodes (inline) 207ms 1.29% 57.31% 431ms 2.69% AbstractCellMutationState::AbstractCellMutationState 21ms 0.13% 57.45% 431ms 2.69% Node::AddElement 0 0% 57.45% 431ms 2.69% std::_Rb_tree::lower_bound (inline) 0 0% 57.45% 431ms 2.69% std::map::lower_bound (inline) 431ms 2.69% 60.14% 431ms 2.69% std::operator< (inline) 5ms 0.031% 60.17% 395ms 2.47% Cylindrical2dMesh::CorrectNonPeriodicMesh 5ms 0.031% 60.20% 393ms 2.46% AbstractCellProperty::IsSubType (inline) 3ms 0.019% 60.22% 392ms 2.45% MutableMesh::ReIndex 8ms 0.05% 60.27% 386ms 2.41% std::__new_allocator::deallocate (inline) 0 0% 60.27% 383ms 2.39% std::_Rb_tree::_M_drop_node (inline) 379ms 2.37% 62.64% 379ms 2.37% [libchaste_crypt.so] 0 0% 62.64% 376ms 2.35% std::allocator_traits::deallocate (inline) 2ms 0.013% 62.65% 368ms 2.30% std::ostream::operator<< (inline) 50ms 0.31% 62.97% 364ms 2.28% std::ostream::_M_insert 43ms 0.27% 63.23% 358ms 2.24% std::_Rb_tree::~_Rb_tree (inline) 67ms 0.42% 63.65% 356ms 2.23% std::_Rb_tree::_M_erase 289ms 1.81% 65.46% 352ms 2.20% _int_free 7ms 0.044% 65.50% 339ms 2.12% std::_Rb_tree::erase 0 0% 65.50% 338ms 2.11% std::set::erase (inline) 0 0% 65.50% 336ms 2.10% std::set::~set (inline) 8ms 0.05% 65.55% 331ms 2.07% Node::RemoveElement 138ms 0.86% 66.42% 331ms 2.07% std::_Rb_tree::_M_get_insert_unique_pos 7ms 0.044% 66.46% 325ms 2.03% divconqrecurse 1ms 0.0063% 66.47% 321ms 2.01% Cell::GetMutationState 1ms 0.0063% 66.47% 313ms 1.96% std::_Vector_base::_M_allocate (inline) 79ms 0.49% 66.97% 311ms 1.94% mergehulls 0 0% 66.97% 310ms 1.94% std::_Rb_tree::_M_put_node (inline) 2ms 0.013% 66.98% 271ms 1.69% LegacyCellProliferativeTypesWriter::VisitCell 12ms 0.075% 67.05% 264ms 1.65% boost::detail::shared_count::~shared_count (inline) 0 0% 67.05% 264ms 1.65% boost::shared_ptr::~shared_ptr (inline) 1ms 0.0063% 67.06% 253ms 1.58% AbstractCellPopulation::Iterator::operator++ (inline) 21ms 0.13% 67.19% 251ms 1.57% AbstractCellPopulation::Iterator::IsRealCell (inline) 9ms 0.056% 67.25% 250ms 1.56% Element::ResetIndex 89ms 0.56% 67.80% 250ms 1.56% __cxxabiv1::__si_class_type_info::__do_dyncast 245ms 1.53% 69.34% 247ms 1.54% boost::detail::sp_counted_base::release 21ms 0.13% 69.47% 244ms 1.53% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 14ms 0.088% 69.55% 243ms 1.52% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 69.55% 241ms 1.51% NodeLocationWriter::Visit 8ms 0.05% 69.60% 241ms 1.51% std::vector::push_back (inline) 2ms 0.013% 69.62% 230ms 1.44% Cell::GetCellProliferativeType 2ms 0.013% 69.63% 230ms 1.44% std::set::set (inline) 5ms 0.031% 69.66% 229ms 1.43% AbstractCellPopulation::IsCellAttachedToLocationIndex 4ms 0.025% 69.69% 229ms 1.43% std::_Rb_tree::_M_erase_aux (inline) 7ms 0.044% 69.73% 226ms 1.41% std::vector::_M_realloc_insert 220ms 1.38% 71.11% 220ms 1.38% [libchaste_mesh.so] 0 0% 71.11% 216ms 1.35% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 1ms 0.0063% 71.11% 215ms 1.34% ApcOneHitCellMutationState::ApcOneHitCellMutationState 4ms 0.025% 71.14% 215ms 1.34% alternateaxes 206ms 1.29% 72.42% 215ms 1.34% std::vector::operator[] (inline) 12ms 0.075% 72.50% 214ms 1.34% AbstractCellPopulation::GetLocationIndexUsingCell 9ms 0.056% 72.56% 211ms 1.32% std::num_put::_M_insert_float 17ms 0.11% 72.66% 208ms 1.30% std::_Rb_tree::_M_copy (inline) 186ms 1.16% 73.82% 208ms 1.30% vertexmedian 8ms 0.05% 73.87% 202ms 1.26% AbstractTetrahedralElement::CalculateJacobian 0 0% 73.87% 201ms 1.26% TetrahedralMesh::RefreshJacobianCachedData 29ms 0.18% 74.06% 197ms 1.23% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 4ms 0.025% 74.08% 193ms 1.21% Element::MarkAsDeleted 0 0% 74.08% 189ms 1.18% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 2ms 0.013% 74.09% 187ms 1.17% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2ms 0.013% 74.11% 187ms 1.17% AbstractTetrahedralElement::CalculateInverseJacobian 4ms 0.025% 74.13% 185ms 1.16% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 74.13% 185ms 1.16% MeshBasedCellPopulation::GetDampingConstant 71ms 0.44% 74.57% 185ms 1.16% std::_Rb_tree::_M_clone_node (inline) 0 0% 74.57% 178ms 1.11% OffLatticeSimulation::ApplyBoundaries 5ms 0.031% 74.61% 176ms 1.10% std::__cxx11::collate::do_transform 1ms 0.0063% 74.61% 165ms 1.03% ___vsnprintf 19ms 0.12% 74.73% 164ms 1.03% __printf_buffer 0 0% 74.73% 164ms 1.03% __vsnprintf_internal (inline) 124ms 0.78% 75.51% 157ms 0.98% malloc_consolidate 12ms 0.075% 75.58% 150ms 0.94% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 21ms 0.13% 75.71% 148ms 0.93% AbstractTetrahedralElement::RefreshJacobian 38ms 0.24% 75.95% 148ms 0.93% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 64ms 0.4% 76.35% 145ms 0.91% AbstractElement::GetNodeGlobalIndex 144ms 0.9% 77.25% 144ms 0.9% std::vector::size (inline) 28ms 0.18% 77.43% 141ms 0.88% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 6ms 0.038% 77.46% 134ms 0.84% __printf_fp_l_buffer 0 0% 77.46% 134ms 0.84% __printf_fp_spec (inline) 16ms 0.1% 77.56% 133ms 0.83% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 1ms 0.0063% 77.57% 129ms 0.81% TetrahedralMesh::Clear 55ms 0.34% 77.91% 126ms 0.79% __printf_fp_buffer_1 123ms 0.77% 78.68% 123ms 0.77% incircle 1ms 0.0063% 78.69% 121ms 0.76% boost::numeric::ublas::vector_assign (inline) 3ms 0.019% 78.71% 118ms 0.74% CellPropertyCollection::HasProperty 117ms 0.73% 79.44% 117ms 0.73% AbstractCellProperty::AbstractCellProperty 2ms 0.013% 79.45% 117ms 0.73% AbstractTetrahedralElement::AbstractTetrahedralElement 117ms 0.73% 80.18% 117ms 0.73% std::_Rb_tree::_S_left (inline) 117ms 0.73% 80.91% 117ms 0.73% std::_Rb_tree_insert_and_rebalance 116ms 0.73% 81.64% 116ms 0.73% std::type_info::name (inline) 0 0% 81.64% 115ms 0.72% Cell::HasCellProperty (inline) 2ms 0.013% 81.65% 115ms 0.72% MeshBasedCellPopulation::SpringsEnd (inline) 18ms 0.11% 81.76% 115ms 0.72% TetrahedralMesh::EdgesEnd (partial-inline) 39ms 0.24% 82.01% 114ms 0.71% AbstractElement::GetNodeLocation 1ms 0.0063% 82.01% 114ms 0.71% CellProliferativeTypesWriter::VisitCell 1ms 0.0063% 82.02% 112ms 0.7% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 68ms 0.43% 82.45% 111ms 0.69% std::_Rb_tree::equal_range (inline) 10ms 0.063% 82.51% 106ms 0.66% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 102ms 0.64% 83.15% 102ms 0.64% Node::GetIndex 96ms 0.6% 83.75% 101ms 0.63% vertexsort 63ms 0.39% 84.14% 100ms 0.63% Cylindrical2dMesh::GetVectorFromAtoB 100ms 0.63% 84.76% 100ms 0.63% counterclockwise 0 0% 84.76% 95ms 0.59% AbstractCellBasedSimulation::DoCellRemoval (inline) 5ms 0.031% 84.80% 93ms 0.58% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.0063% 84.80% 92ms 0.58% Cell::SetCellProliferativeType 6ms 0.038% 84.84% 92ms 0.58% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 4ms 0.025% 84.86% 88ms 0.55% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 12ms 0.075% 84.94% 87ms 0.54% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 84.94% 87ms 0.54% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.013% 84.95% 86ms 0.54% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 32ms 0.2% 85.15% 86ms 0.54% std::__ostream_insert 3ms 0.019% 85.17% 83ms 0.52% Cylindrical2dMesh::CreateMirrorNodes 83ms 0.52% 85.69% 83ms 0.52% std::_Rb_tree_rebalance_for_erase 64ms 0.4% 86.09% 82ms 0.51% TetrahedralMesh::EdgeIterator::EdgeIterator 0 0% 86.09% 82ms 0.51% std::vector::resize (inline) 1ms 0.0063% 86.10% 81ms 0.51% std::vector::_M_default_append 21ms 0.13% 86.23% 80ms 0.5% std::num_put::_M_insert_int