File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16663ms, 85.29% of 19536ms total Dropped 780 nodes (cum <= 97.68ms) flat flat% sum% cum cum% 0 0% 0% 19491ms 99.77% __libc_start_call_main 0 0% 0% 19491ms 99.77% __libc_start_main_impl 0 0% 0% 19491ms 99.77% _start 0 0% 0% 19469ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19469ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19469ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19469ms 99.66% main 0 0% 0% 19426ms 99.44% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19426ms 99.44% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19426ms 99.44% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19400ms 99.30% AbstractCellBasedSimulation::Solve 1ms 0.0051% 0.0051% 14854ms 76.03% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.01% 0.015% 9383ms 48.03% AbstractCellBasedSimulation::DoCellBirth 8ms 0.041% 0.056% 9276ms 47.48% Cell::ReadyToDivide 6ms 0.031% 0.087% 9204ms 47.11% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0051% 0.092% 9075ms 46.45% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 16ms 0.082% 0.17% 9068ms 46.42% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.015% 0.19% 9047ms 46.31% CellCycleModelOdeHandler::SolveOdeToTime 61ms 0.31% 0.5% 8871ms 45.41% AbstractOneStepIvpOdeSolver::InternalSolve 1018ms 5.21% 5.71% 7953ms 40.71% RungeKutta4IvpOdeSolver::CalculateNextYValue 2750ms 14.08% 19.79% 6739ms 34.50% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 19.79% 5365ms 27.46% MeshBasedCellPopulation::Update 2ms 0.01% 19.80% 4168ms 21.33% Cylindrical2dMesh::ReMesh 59ms 0.3% 20.10% 3993ms 20.44% AbstractCellProperty::IsType (inline) 394ms 2.02% 22.12% 2616ms 13.39% AbstractCellProperty::IsSame 0 0% 22.12% 2593ms 13.27% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 22.12% 2266ms 11.60% MutableMesh::ReMesh 0 0% 22.12% 2235ms 11.44% ForwardEulerNumericalMethod::UpdateAllNodePositions 283ms 1.45% 23.57% 2222ms 11.37% std::type_info::operator== (inline) 10ms 0.051% 23.62% 2177ms 11.14% AbstractNumericalMethod::ComputeForcesIncludingDamping 2019ms 10.33% 33.95% 2019ms 10.33% __strcmp_avx2 1ms 0.0051% 33.96% 1950ms 9.98% AbstractCellPopulation::WriteResultsToFiles 784ms 4.01% 37.97% 1850ms 9.47% std::_Rb_tree::_M_lower_bound (inline) 157ms 0.8% 38.77% 1669ms 8.54% TetrahedralMesh::EdgeIterator::operator++ 70ms 0.36% 39.13% 1378ms 7.05% std::_Rb_tree::find (inline) 0 0% 39.13% 1150ms 5.89% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.031% 39.16% 1147ms 5.87% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 9ms 0.046% 39.21% 1145ms 5.86% TetrahedralMesh::ImportFromMesher 32ms 0.16% 39.37% 1093ms 5.59% operator new 246ms 1.26% 40.63% 1052ms 5.38% __GI___libc_malloc 7ms 0.036% 40.67% 1034ms 5.29% std::set::insert (inline) 11ms 0.056% 40.72% 1027ms 5.26% std::_Rb_tree::_M_insert_unique 14ms 0.072% 40.80% 1021ms 5.23% MeshBasedCellPopulation::SpringIterator::operator++ 53ms 0.27% 41.07% 965ms 4.94% std::__new_allocator::allocate (inline) 0 0% 41.07% 962ms 4.92% std::allocator_traits::allocate (inline) 2ms 0.01% 41.08% 896ms 4.59% triangulate 0 0% 41.08% 831ms 4.25% delaunay 3ms 0.015% 41.09% 829ms 4.24% divconqdelaunay 0 0% 41.09% 829ms 4.24% std::set::count (inline) 5ms 0.026% 41.12% 748ms 3.83% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 742ms 3.80% 44.92% 742ms 3.80% WntCellCycleOdeSystem::CalculateStoppingEvent 64ms 0.33% 45.24% 726ms 3.72% std::map::operator[] (partial-inline) 414ms 2.12% 47.36% 721ms 3.69% _int_malloc 712ms 3.64% 51.01% 712ms 3.64% std::_Rb_tree::_S_right (inline) 3ms 0.015% 51.02% 708ms 3.62% AbstractTwoBodyInteractionForce::AddForceContribution 1ms 0.0051% 51.03% 672ms 3.44% CellPopulationElementWriter::Visit 0 0% 51.03% 665ms 3.40% std::_Rb_tree::_M_create_node (inline) 186ms 0.95% 51.98% 636ms 3.26% __dynamic_cast 0 0% 51.98% 633ms 3.24% std::_Rb_tree::_M_get_node (inline) 30ms 0.15% 52.13% 630ms 3.22% std::_Rb_tree::_M_insert_ (inline) 12ms 0.061% 52.20% 626ms 3.20% std::less::operator() (inline) 614ms 3.14% 55.34% 614ms 3.14% std::operator< (inline) 21ms 0.11% 55.45% 610ms 3.12% AbstractCellPopulation::GetCellUsingLocationIndex 12ms 0.061% 55.51% 607ms 3.11% CellPropertyCollection::GetPropertiesType (inline) 0 0% 55.51% 601ms 3.08% std::_Rb_tree::_Alloc_node::operator() (inline) 5ms 0.026% 55.53% 598ms 3.06% MeshBasedCellPopulation::AcceptCellWriter 27ms 0.14% 55.67% 597ms 3.06% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 9ms 0.046% 55.72% 593ms 3.04% Element::Element 0 0% 55.72% 557ms 2.85% std::_Rb_tree::lower_bound (inline) 0 0% 55.72% 557ms 2.85% std::map::lower_bound (inline) 17ms 0.087% 55.80% 554ms 2.84% Cylindrical2dMesh::CorrectNonPeriodicMesh 7ms 0.036% 55.84% 549ms 2.81% MutableMesh::ReIndex 0 0% 55.84% 542ms 2.77% std::map::find (inline) 7ms 0.036% 55.88% 505ms 2.58% Element::RegisterWithNodes (inline) 4ms 0.02% 55.90% 500ms 2.56% Node::AddElement 3ms 0.015% 55.91% 482ms 2.47% std::ostream::operator<< (inline) 1ms 0.0051% 55.92% 481ms 2.46% AbstractCellProperty::IsSubType (inline) 63ms 0.32% 56.24% 476ms 2.44% std::ostream::_M_insert 12ms 0.061% 56.30% 474ms 2.43% Cylindrical2dMesh::ReconstructCylindricalMesh 285ms 1.46% 57.76% 421ms 2.15% AbstractCellMutationState::AbstractCellMutationState 130ms 0.67% 58.43% 416ms 2.13% __GI___libc_free 124ms 0.63% 59.06% 391ms 2.00% std::_Rb_tree::_M_erase 156ms 0.8% 59.86% 386ms 1.98% std::_Rb_tree::_M_get_insert_unique_pos 20ms 0.1% 59.96% 379ms 1.94% Node::RemoveElement 2ms 0.01% 59.97% 375ms 1.92% std::set::erase (inline) 8ms 0.041% 60.01% 373ms 1.91% std::_Rb_tree::erase 18ms 0.092% 60.10% 368ms 1.88% divconqrecurse 32ms 0.16% 60.27% 367ms 1.88% Element::ResetIndex 31ms 0.16% 60.43% 364ms 1.86% std::_Rb_tree::~_Rb_tree (inline) 17ms 0.087% 60.51% 355ms 1.82% std::__new_allocator::deallocate (inline) 0 0% 60.51% 350ms 1.79% std::allocator_traits::deallocate (inline) 100ms 0.51% 61.03% 346ms 1.77% mergehulls 11ms 0.056% 61.08% 336ms 1.72% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 61.08% 336ms 1.72% std::set::~set (inline) 4ms 0.02% 61.10% 329ms 1.68% Cell::GetMutationState 0 0% 61.10% 329ms 1.68% std::_Vector_base::_M_allocate (inline) 190ms 0.97% 62.08% 328ms 1.68% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.0051% 62.08% 323ms 1.65% AbstractCellPopulation::Iterator::operator++ (inline) 9ms 0.046% 62.13% 321ms 1.64% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 62.13% 319ms 1.63% std::_Rb_tree::_M_drop_node (inline) 41ms 0.21% 62.34% 318ms 1.63% AbstractCellPopulation::Iterator::IsRealCell 314ms 1.61% 63.94% 314ms 1.61% [libchaste_cell_based.so] 2ms 0.01% 63.95% 312ms 1.60% Cell::GetCellProliferativeType 2ms 0.01% 63.96% 310ms 1.59% NodeLocationWriter::Visit 6ms 0.031% 63.99% 309ms 1.58% LegacyCellProliferativeTypesWriter::VisitCell 7ms 0.036% 64.03% 309ms 1.58% alternateaxes 282ms 1.44% 65.47% 301ms 1.54% vertexmedian 246ms 1.26% 66.73% 282ms 1.44% _int_free 0 0% 66.73% 280ms 1.43% std::_Rb_tree::_M_put_node (inline) 14ms 0.072% 66.80% 275ms 1.41% std::num_put::_M_insert_float 13ms 0.067% 66.87% 274ms 1.40% std::_Rb_tree::_Rb_tree (partial-inline) 265ms 1.36% 68.23% 267ms 1.37% std::vector::operator[] (inline) 15ms 0.077% 68.30% 266ms 1.36% std::vector::push_back (inline) 7ms 0.036% 68.34% 261ms 1.34% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 15ms 0.077% 68.42% 258ms 1.32% AbstractTetrahedralElement::CalculateJacobian 64ms 0.33% 68.74% 246ms 1.26% ApcOneHitCellMutationState::ApcOneHitCellMutationState 1ms 0.0051% 68.75% 244ms 1.25% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2ms 0.01% 68.76% 243ms 1.24% std::set::set (inline) 102ms 0.52% 69.28% 242ms 1.24% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 15ms 0.077% 69.36% 242ms 1.24% std::vector::_M_realloc_insert 8ms 0.041% 69.40% 240ms 1.23% AbstractCellPopulation::IsCellAttachedToLocationIndex 6ms 0.031% 69.43% 239ms 1.22% std::__cxx11::collate::do_transform 101ms 0.52% 69.95% 233ms 1.19% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 24ms 0.12% 70.07% 232ms 1.19% std::_Rb_tree::_M_copy (inline) 1ms 0.0051% 70.08% 230ms 1.18% MeshBasedCellPopulation::GetDampingConstant 2ms 0.01% 70.09% 229ms 1.17% AbstractCentreBasedCellPopulation::GetDampingConstant 4ms 0.02% 70.11% 227ms 1.16% ___vsnprintf 0 0% 70.11% 224ms 1.15% OffLatticeSimulation::ApplyBoundaries 14ms 0.072% 70.18% 224ms 1.15% std::_Rb_tree::_M_erase_aux (inline) 0 0% 70.18% 223ms 1.14% __vsnprintf_internal (inline) 25ms 0.13% 70.31% 220ms 1.13% __printf_buffer 158ms 0.81% 71.11% 207ms 1.06% AbstractElement::GetNodeGlobalIndex 48ms 0.25% 71.36% 206ms 1.05% std::_Rb_tree::_M_clone_node (inline) 0 0% 71.36% 198ms 1.01% TetrahedralMesh::RefreshJacobianCachedData 8ms 0.041% 71.40% 194ms 0.99% AbstractTetrahedralElement::AbstractTetrahedralElement 15ms 0.077% 71.48% 194ms 0.99% Element::MarkAsDeleted 10ms 0.051% 71.53% 189ms 0.97% __printf_fp_l_buffer 0 0% 71.53% 189ms 0.97% __printf_fp_spec (inline) 22ms 0.11% 71.64% 186ms 0.95% AbstractTetrahedralElement::RefreshJacobian 12ms 0.061% 71.70% 185ms 0.95% TetrahedralMesh::Clear 2ms 0.01% 71.71% 177ms 0.91% CellProliferativeTypesWriter::VisitCell 10ms 0.051% 71.76% 176ms 0.9% AbstractTetrahedralElement::CalculateInverseJacobian 174ms 0.89% 72.66% 174ms 0.89% std::_Rb_tree_insert_and_rebalance 85ms 0.44% 73.09% 171ms 0.88% __printf_fp_buffer_1 166ms 0.85% 73.94% 166ms 0.85% incircle 123ms 0.63% 74.57% 165ms 0.84% malloc_consolidate 158ms 0.81% 75.38% 158ms 0.81% unlink_chunk 5ms 0.026% 75.40% 153ms 0.78% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 152ms 0.78% 76.18% 152ms 0.78% Node::GetIndex 3ms 0.015% 76.20% 151ms 0.77% CellPropertyCollection::HasProperty 2ms 0.01% 76.21% 149ms 0.76% boost::numeric::ublas::vector_assign (inline) 101ms 0.52% 76.73% 148ms 0.76% std::_Rb_tree::equal_range (inline) 147ms 0.75% 77.48% 147ms 0.75% AbstractCellMutationState::~AbstractCellMutationState 51ms 0.26% 77.74% 146ms 0.75% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 0 0% 77.74% 146ms 0.75% Cell::HasCellProperty (inline) 74ms 0.38% 78.12% 145ms 0.74% AbstractElement::GetNodeLocation 145ms 0.74% 78.86% 145ms 0.74% [libchaste_crypt.so] 134ms 0.69% 79.55% 144ms 0.74% vertexsort 38ms 0.19% 79.74% 143ms 0.73% TetrahedralMesh::EdgesEnd 143ms 0.73% 80.47% 143ms 0.73% std::type_info::name (inline) 48ms 0.25% 80.72% 142ms 0.73% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 49ms 0.25% 80.97% 139ms 0.71% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 139ms 0.71% 81.68% 139ms 0.71% std::vector::size (inline) 16ms 0.082% 81.76% 138ms 0.71% boost::numeric::ublas::c_vector::c_vector (inline) 3ms 0.015% 81.78% 132ms 0.68% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 9ms 0.046% 81.82% 126ms 0.64% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 81.82% 124ms 0.63% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 66ms 0.34% 82.16% 121ms 0.62% Cylindrical2dMesh::GetVectorFromAtoB 5ms 0.026% 82.19% 121ms 0.62% Node::~Node 6ms 0.031% 82.22% 119ms 0.61% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 118ms 0.6% 82.82% 118ms 0.6% std::_Rb_tree_increment 117ms 0.6% 83.42% 117ms 0.6% AbstractElement::IsDeleted 30ms 0.15% 83.57% 117ms 0.6% boost::numeric::ublas::indexing_vector_assign 4ms 0.02% 83.59% 114ms 0.58% std::_Rb_tree_const_iterator::operator++ (inline) 9ms 0.046% 83.64% 112ms 0.57% boost::detail::shared_count::~shared_count (inline) 0 0% 83.64% 112ms 0.57% boost::shared_ptr::~shared_ptr (inline) 109ms 0.56% 84.20% 109ms 0.56% TetrahedralMesh::EdgeIterator::operator!= 3ms 0.015% 84.21% 105ms 0.54% std::_Rb_tree::_M_emplace_hint_unique 0 0% 84.21% 104ms 0.53% AbstractCellBasedSimulation::DoCellRemoval (inline) 16ms 0.082% 84.30% 103ms 0.53% std::num_put::_M_insert_int 102ms 0.52% 84.82% 102ms 0.52% std::_Rb_tree_rebalance_for_erase 31ms 0.16% 84.98% 102ms 0.52% std::__ostream_insert 54ms 0.28% 85.25% 101ms 0.52% boost::shared_ptr::shared_ptr (inline) 1ms 0.0051% 85.26% 100ms 0.51% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 7ms 0.036% 85.29% 100ms 0.51% Cylindrical2dMesh::CreateMirrorNodes