File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 17059ms, 84.15% of 20273ms total Dropped 818 nodes (cum <= 101.36ms) flat flat% sum% cum cum% 0 0% 0% 20226ms 99.77% __libc_start_call_main 0 0% 0% 20226ms 99.77% __libc_start_main_impl 0 0% 0% 20226ms 99.77% _start 0 0% 0% 20207ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20207ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20207ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20207ms 99.67% main 0 0% 0% 20168ms 99.48% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20168ms 99.48% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20168ms 99.48% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 20140ms 99.34% AbstractCellBasedSimulation::Solve 1ms 0.0049% 0.0049% 15631ms 77.10% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.015% 0.02% 10207ms 50.35% AbstractCellBasedSimulation::DoCellBirth 3ms 0.015% 0.035% 10100ms 49.82% Cell::ReadyToDivide 3ms 0.015% 0.049% 10020ms 49.43% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.015% 0.064% 9882ms 48.74% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 12ms 0.059% 0.12% 9874ms 48.71% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.02% 0.14% 9861ms 48.64% CellCycleModelOdeHandler::SolveOdeToTime 55ms 0.27% 0.41% 9712ms 47.91% AbstractOneStepIvpOdeSolver::InternalSolve 913ms 4.50% 4.92% 8935ms 44.07% RungeKutta4IvpOdeSolver::CalculateNextYValue 3614ms 17.83% 22.74% 7828ms 38.61% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0049% 22.75% 5302ms 26.15% MeshBasedCellPopulation::Update 183ms 0.9% 23.65% 4250ms 20.96% AbstractCellProperty::IsType (inline) 5ms 0.025% 23.68% 4103ms 20.24% Cylindrical2dMesh::ReMesh 641ms 3.16% 26.84% 2978ms 14.69% AbstractCellProperty::IsSame 1ms 0.0049% 26.84% 2516ms 12.41% OffLatticeSimulation::UpdateCellLocationsAndTopology 422ms 2.08% 28.93% 2337ms 11.53% std::type_info::operator== (inline) 1ms 0.0049% 28.93% 2230ms 11.00% MutableMesh::ReMesh 0 0% 28.93% 2200ms 10.85% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.035% 28.96% 2148ms 10.60% AbstractNumericalMethod::ComputeForcesIncludingDamping 2ms 0.0099% 28.97% 1988ms 9.81% AbstractCellPopulation::WriteResultsToFiles 810ms 4.00% 32.97% 1880ms 9.27% std::_Rb_tree::_M_lower_bound (inline) 1851ms 9.13% 42.10% 1851ms 9.13% __strcmp_avx2 183ms 0.9% 43.00% 1709ms 8.43% TetrahedralMesh::EdgeIterator::operator++ 52ms 0.26% 43.26% 1364ms 6.73% std::_Rb_tree::find (inline) 0 0% 43.26% 1160ms 5.72% MeshBasedCellPopulation::UpdateNodePairs 15ms 0.074% 43.33% 1142ms 5.63% TetrahedralMesh::ImportFromMesher 5ms 0.025% 43.36% 1141ms 5.63% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 51ms 0.25% 43.61% 1093ms 5.39% operator new 9ms 0.044% 43.65% 1038ms 5.12% MeshBasedCellPopulation::SpringIterator::operator++ 239ms 1.18% 44.83% 1035ms 5.11% __GI___libc_malloc 14ms 0.069% 44.90% 1005ms 4.96% std::set::insert (inline) 13ms 0.064% 44.97% 991ms 4.89% std::_Rb_tree::_M_insert_unique 36ms 0.18% 45.14% 957ms 4.72% std::__new_allocator::allocate (inline) 0 0% 45.14% 952ms 4.70% std::allocator_traits::allocate (inline) 0 0% 45.14% 838ms 4.13% std::set::count (inline) 0 0% 45.14% 802ms 3.96% triangulate 66ms 0.33% 45.47% 754ms 3.72% std::map::operator[] (partial-inline) 405ms 2.00% 47.47% 727ms 3.59% _int_malloc 0 0% 47.47% 721ms 3.56% delaunay 3ms 0.015% 47.48% 721ms 3.56% divconqdelaunay 3ms 0.015% 47.50% 712ms 3.51% CellPopulationElementWriter::Visit 3ms 0.015% 47.51% 709ms 3.50% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 708ms 3.49% 51.00% 708ms 3.49% std::_Rb_tree::_S_right (inline) 2ms 0.0099% 51.01% 700ms 3.45% AbstractTwoBodyInteractionForce::AddForceContribution 25ms 0.12% 51.14% 645ms 3.18% std::less::operator() (inline) 28ms 0.14% 51.28% 637ms 3.14% std::_Rb_tree::_M_insert_ (inline) 0 0% 51.28% 632ms 3.12% std::_Rb_tree::_M_create_node (inline) 180ms 0.89% 52.16% 628ms 3.10% __dynamic_cast 620ms 3.06% 55.22% 620ms 3.06% std::operator< (inline) 23ms 0.11% 55.33% 610ms 3.01% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 55.33% 601ms 2.96% std::_Rb_tree::lower_bound (inline) 0 0% 55.33% 601ms 2.96% std::map::lower_bound (inline) 0 0% 55.33% 600ms 2.96% std::_Rb_tree::_M_get_node (inline) 22ms 0.11% 55.44% 590ms 2.91% AbstractCellPopulation::GetCellUsingLocationIndex 581ms 2.87% 58.31% 589ms 2.91% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 58.31% 583ms 2.88% std::_Rb_tree::_Alloc_node::operator() (inline) 10ms 0.049% 58.36% 569ms 2.81% MutableMesh::ReIndex 4ms 0.02% 58.38% 566ms 2.79% MeshBasedCellPopulation::AcceptCellWriter 5ms 0.025% 58.40% 560ms 2.76% CellPropertyCollection::GetPropertiesType (inline) 5ms 0.025% 58.43% 537ms 2.65% Element::Element 0 0% 58.43% 524ms 2.58% std::map::find (inline) 10ms 0.049% 58.48% 506ms 2.50% Cylindrical2dMesh::CorrectNonPeriodicMesh 326ms 1.61% 60.08% 488ms 2.41% AbstractCellMutationState::AbstractCellMutationState 9ms 0.044% 60.13% 474ms 2.34% Element::RegisterWithNodes (inline) 170ms 0.84% 60.97% 472ms 2.33% __GI___libc_free 13ms 0.064% 61.03% 468ms 2.31% Node::AddElement 0 0% 61.03% 467ms 2.30% std::ostream::operator<< (inline) 59ms 0.29% 61.32% 466ms 2.30% std::ostream::_M_insert 12ms 0.059% 61.38% 462ms 2.28% Cylindrical2dMesh::ReconstructCylindricalMesh 3ms 0.015% 61.40% 455ms 2.24% AbstractCellProperty::IsSubType (inline) 3ms 0.015% 61.41% 384ms 1.89% std::set::erase (inline) 10ms 0.049% 61.46% 383ms 1.89% std::_Rb_tree::erase 12ms 0.059% 61.52% 378ms 1.86% Node::RemoveElement 18ms 0.089% 61.61% 376ms 1.85% divconqrecurse 26ms 0.13% 61.74% 368ms 1.82% Element::ResetIndex 132ms 0.65% 62.39% 367ms 1.81% std::_Rb_tree::_M_erase 2ms 0.0099% 62.40% 354ms 1.75% std::_Vector_base::_M_allocate (inline) 96ms 0.47% 62.87% 351ms 1.73% mergehulls 8ms 0.039% 62.91% 351ms 1.73% std::__new_allocator::deallocate (inline) 0 0% 62.91% 349ms 1.72% std::allocator_traits::deallocate (inline) 19ms 0.094% 63.00% 347ms 1.71% std::_Rb_tree::~_Rb_tree (inline) 111ms 0.55% 63.55% 341ms 1.68% std::_Rb_tree::_M_get_insert_unique_pos 11ms 0.054% 63.61% 340ms 1.68% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 158ms 0.78% 64.39% 338ms 1.67% __cxxabiv1::__si_class_type_info::__do_dyncast 313ms 1.54% 65.93% 313ms 1.54% std::type_info::name (inline) 0 0% 65.93% 307ms 1.51% std::set::~set (inline) 0 0% 65.93% 305ms 1.50% std::_Rb_tree::_M_drop_node (inline) 4ms 0.02% 65.95% 304ms 1.50% NodeLocationWriter::Visit 3ms 0.015% 65.96% 303ms 1.49% Cell::GetCellProliferativeType 244ms 1.20% 67.17% 302ms 1.49% _int_free 3ms 0.015% 67.18% 299ms 1.47% LegacyCellProliferativeTypesWriter::VisitCell 4ms 0.02% 67.20% 298ms 1.47% Cell::GetMutationState 40ms 0.2% 67.40% 295ms 1.46% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.0049% 67.40% 294ms 1.45% AbstractCellPopulation::Iterator::operator++ (inline) 17ms 0.084% 67.49% 285ms 1.41% std::_Rb_tree::_Rb_tree (partial-inline) 22ms 0.11% 67.60% 280ms 1.38% AbstractTetrahedralElement::CalculateJacobian 279ms 1.38% 68.97% 279ms 1.38% [libchaste_cell_based.so] 3ms 0.015% 68.99% 278ms 1.37% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 68.99% 275ms 1.36% std::_Rb_tree::_M_put_node (inline) 10ms 0.049% 69.04% 275ms 1.36% std::vector::push_back (inline) 8ms 0.039% 69.08% 270ms 1.33% AbstractCellPopulation::IsCellAttachedToLocationIndex 20ms 0.099% 69.18% 259ms 1.28% std::num_put::_M_insert_float 1ms 0.0049% 69.18% 258ms 1.27% std::set::set (inline) 22ms 0.11% 69.29% 257ms 1.27% std::vector::_M_realloc_insert 1ms 0.0049% 69.29% 253ms 1.25% TetrahedralMesh::RefreshJacobianCachedData 8ms 0.039% 69.33% 244ms 1.20% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 35ms 0.17% 69.51% 243ms 1.20% TetrahedralMesh::Clear 233ms 1.15% 70.66% 236ms 1.16% std::vector::operator[] (inline) 3ms 0.015% 70.67% 232ms 1.14% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 5ms 0.025% 70.70% 232ms 1.14% alternateaxes 211ms 1.04% 71.74% 227ms 1.12% vertexmedian 23ms 0.11% 71.85% 225ms 1.11% std::_Rb_tree::_M_copy (inline) 53ms 0.26% 72.11% 222ms 1.10% ApcOneHitCellMutationState::ApcOneHitCellMutationState 15ms 0.074% 72.18% 221ms 1.09% std::_Rb_tree::_M_erase_aux (inline) 41ms 0.2% 72.39% 218ms 1.08% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 2ms 0.0099% 72.40% 215ms 1.06% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 72.40% 215ms 1.06% MeshBasedCellPopulation::GetDampingConstant 10ms 0.049% 72.45% 211ms 1.04% AbstractTetrahedralElement::CalculateInverseJacobian 24ms 0.12% 72.56% 210ms 1.04% AbstractTetrahedralElement::RefreshJacobian 2ms 0.0099% 72.57% 206ms 1.02% std::__cxx11::collate::do_transform 63ms 0.31% 72.89% 204ms 1.01% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 0 0% 72.89% 200ms 0.99% ___vsnprintf 0 0% 72.89% 200ms 0.99% __vsnprintf_internal (inline) 21ms 0.1% 72.99% 197ms 0.97% __printf_buffer 63ms 0.31% 73.30% 197ms 0.97% std::_Rb_tree::_M_clone_node (inline) 143ms 0.71% 74.00% 193ms 0.95% malloc_consolidate 14ms 0.069% 74.07% 187ms 0.92% Element::MarkAsDeleted 0 0% 74.07% 185ms 0.91% OffLatticeSimulation::ApplyBoundaries 2ms 0.0099% 74.08% 176ms 0.87% AbstractTetrahedralElement::AbstractTetrahedralElement 175ms 0.86% 74.95% 175ms 0.86% std::_Rb_tree_insert_and_rebalance 174ms 0.86% 75.81% 174ms 0.86% unlink_chunk 129ms 0.64% 76.44% 173ms 0.85% AbstractElement::GetNodeGlobalIndex 7ms 0.035% 76.48% 169ms 0.83% CellPropertyCollection::HasProperty 61ms 0.3% 76.78% 167ms 0.82% AbstractElement::GetNodeLocation 165ms 0.81% 77.59% 165ms 0.81% Node::GetIndex 0 0% 77.59% 162ms 0.8% Cell::HasCellProperty (inline) 1ms 0.0049% 77.60% 162ms 0.8% __printf_fp_spec (inline) 0 0% 77.60% 161ms 0.79% CellProliferativeTypesWriter::VisitCell 8ms 0.039% 77.64% 161ms 0.79% __printf_fp_l_buffer 100ms 0.49% 78.13% 158ms 0.78% std::_Rb_tree::equal_range (inline) 6ms 0.03% 78.16% 157ms 0.77% boost::numeric::ublas::vector_assign (inline) 6ms 0.03% 78.19% 155ms 0.76% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 73ms 0.36% 78.55% 149ms 0.73% __printf_fp_buffer_1 16ms 0.079% 78.63% 144ms 0.71% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 13ms 0.064% 78.69% 144ms 0.71% boost::numeric::ublas::c_vector::c_vector (inline) 144ms 0.71% 79.40% 144ms 0.71% std::vector::size (inline) 82ms 0.4% 79.81% 142ms 0.7% Cylindrical2dMesh::GetVectorFromAtoB 142ms 0.7% 80.51% 142ms 0.7% incircle 39ms 0.19% 80.70% 137ms 0.68% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 51ms 0.25% 80.95% 134ms 0.66% std::__ostream_insert 15ms 0.074% 81.02% 132ms 0.65% Node::~Node 1ms 0.0049% 81.03% 129ms 0.64% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 28ms 0.14% 81.17% 128ms 0.63% TetrahedralMesh::EdgesEnd 42ms 0.21% 81.37% 125ms 0.62% boost::numeric::ublas::indexing_vector_assign 7ms 0.035% 81.41% 122ms 0.6% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 33ms 0.16% 81.57% 120ms 0.59% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 3ms 0.015% 81.59% 119ms 0.59% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 81.59% 118ms 0.58% AbstractCellBasedSimulation::DoCellRemoval (inline) 117ms 0.58% 82.16% 117ms 0.58% boost::shared_ptr::operator-> (inline) 4ms 0.02% 82.18% 115ms 0.57% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 32ms 0.16% 82.34% 113ms 0.56% std::num_put::_M_insert_int 112ms 0.55% 82.89% 112ms 0.55% AbstractCellProperty::~AbstractCellProperty 2ms 0.0099% 82.90% 110ms 0.54% std::vector::resize (inline) 2ms 0.0099% 82.91% 108ms 0.53% std::vector::_M_default_append 0 0% 82.91% 105ms 0.52% AbstractCellBasedWriter::OpenOutputFileForAppend 105ms 0.52% 83.43% 105ms 0.52% AbstractCellMutationState::~AbstractCellMutationState 4ms 0.02% 83.45% 105ms 0.52% Cell::SetCellProliferativeType 4ms 0.02% 83.47% 105ms 0.52% std::operator<< (inline) 4ms 0.02% 83.49% 104ms 0.51% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 30ms 0.15% 83.64% 104ms 0.51% std::_Vector_base::_M_deallocate (inline) 0 0% 83.64% 103ms 0.51% OutputFileHandler::OpenOutputFile 103ms 0.51% 84.15% 103ms 0.51% counterclockwise