File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16681ms, 85.50% of 19509ms total Dropped 786 nodes (cum <= 97.55ms) flat flat% sum% cum cum% 0 0% 0% 19462ms 99.76% __libc_start_call_main 0 0% 0% 19462ms 99.76% __libc_start_main_impl 0 0% 0% 19462ms 99.76% _start 0 0% 0% 19440ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19440ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19440ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19440ms 99.65% main 0 0% 0% 19398ms 99.43% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19398ms 99.43% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19398ms 99.43% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19371ms 99.29% AbstractCellBasedSimulation::Solve 1ms 0.0051% 0.0051% 14786ms 75.79% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.01% 0.015% 9303ms 47.69% AbstractCellBasedSimulation::DoCellBirth 2ms 0.01% 0.026% 9203ms 47.17% Cell::ReadyToDivide 6ms 0.031% 0.056% 9131ms 46.80% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0051% 0.062% 9006ms 46.16% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 24ms 0.12% 0.18% 8997ms 46.12% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 7ms 0.036% 0.22% 8965ms 45.95% CellCycleModelOdeHandler::SolveOdeToTime 57ms 0.29% 0.51% 8787ms 45.04% AbstractOneStepIvpOdeSolver::InternalSolve 1003ms 5.14% 5.65% 7804ms 40.00% RungeKutta4IvpOdeSolver::CalculateNextYValue 2776ms 14.23% 19.88% 6627ms 33.97% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0051% 19.89% 5369ms 27.52% MeshBasedCellPopulation::Update 6ms 0.031% 19.92% 4175ms 21.40% Cylindrical2dMesh::ReMesh 64ms 0.33% 20.25% 3858ms 19.78% AbstractCellProperty::IsType (inline) 0 0% 20.25% 2585ms 13.25% OffLatticeSimulation::UpdateCellLocationsAndTopology 338ms 1.73% 21.98% 2454ms 12.58% AbstractCellProperty::IsSame 2ms 0.01% 21.99% 2304ms 11.81% MutableMesh::ReMesh 2ms 0.01% 22.00% 2273ms 11.65% ForwardEulerNumericalMethod::UpdateAllNodePositions 14ms 0.072% 22.07% 2217ms 11.36% AbstractNumericalMethod::ComputeForcesIncludingDamping 217ms 1.11% 23.18% 2116ms 10.85% std::type_info::operator== (inline) 0 0% 23.18% 1994ms 10.22% AbstractCellPopulation::WriteResultsToFiles 1992ms 10.21% 33.39% 1992ms 10.21% __strcmp_avx2 792ms 4.06% 37.45% 1864ms 9.55% std::_Rb_tree::_M_lower_bound (inline) 148ms 0.76% 38.21% 1691ms 8.67% TetrahedralMesh::EdgeIterator::operator++ 76ms 0.39% 38.60% 1386ms 7.10% std::_Rb_tree::find (inline) 1ms 0.0051% 38.61% 1161ms 5.95% MeshBasedCellPopulation::UpdateNodePairs 10ms 0.051% 38.66% 1158ms 5.94% TetrahedralMesh::ImportFromMesher 8ms 0.041% 38.70% 1145ms 5.87% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 12ms 0.062% 38.76% 1032ms 5.29% MeshBasedCellPopulation::SpringIterator::operator++ 34ms 0.17% 38.94% 1013ms 5.19% operator new 7ms 0.036% 38.97% 972ms 4.98% std::set::insert (inline) 229ms 1.17% 40.15% 965ms 4.95% __GI___libc_malloc 22ms 0.11% 40.26% 965ms 4.95% std::_Rb_tree::_M_insert_unique 33ms 0.17% 40.43% 900ms 4.61% std::__new_allocator::allocate (inline) 0 0% 40.43% 898ms 4.60% std::allocator_traits::allocate (inline) 1ms 0.0051% 40.43% 878ms 4.50% triangulate 0 0% 40.43% 856ms 4.39% std::set::count (inline) 0 0% 40.43% 794ms 4.07% delaunay 6ms 0.031% 40.46% 794ms 4.07% divconqdelaunay 777ms 3.98% 44.45% 777ms 3.98% WntCellCycleOdeSystem::CalculateStoppingEvent 60ms 0.31% 44.75% 735ms 3.77% std::map::operator[] (partial-inline) 6ms 0.031% 44.78% 730ms 3.74% CellPopulationElementWriter::Visit 3ms 0.015% 44.80% 728ms 3.73% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 725ms 3.72% 48.52% 725ms 3.72% std::_Rb_tree::_S_right (inline) 3ms 0.015% 48.53% 723ms 3.71% AbstractTwoBodyInteractionForce::AddForceContribution 362ms 1.86% 50.39% 659ms 3.38% _int_malloc 221ms 1.13% 51.52% 654ms 3.35% __dynamic_cast 16ms 0.082% 51.60% 620ms 3.18% std::less::operator() (inline) 30ms 0.15% 51.76% 619ms 3.17% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 21ms 0.11% 51.86% 605ms 3.10% AbstractCellPopulation::GetCellUsingLocationIndex 604ms 3.10% 54.96% 604ms 3.10% std::operator< (inline) 12ms 0.062% 55.02% 602ms 3.09% CellPropertyCollection::GetPropertiesType (inline) 0 0% 55.02% 581ms 2.98% std::_Rb_tree::lower_bound (inline) 0 0% 55.02% 581ms 2.98% std::map::lower_bound (inline) 0 0% 55.02% 578ms 2.96% std::_Rb_tree::_M_create_node (inline) 8ms 0.041% 55.06% 575ms 2.95% MeshBasedCellPopulation::AcceptCellWriter 34ms 0.17% 55.24% 572ms 2.93% std::_Rb_tree::_M_insert_ (inline) 0 0% 55.24% 555ms 2.84% std::_Rb_tree::_M_get_node (inline) 11ms 0.056% 55.29% 546ms 2.80% Element::Element 9ms 0.046% 55.34% 535ms 2.74% MutableMesh::ReIndex 0 0% 55.34% 526ms 2.70% std::map::find (inline) 0 0% 55.34% 521ms 2.67% std::_Rb_tree::_Alloc_node::operator() (inline) 1ms 0.0051% 55.34% 503ms 2.58% std::ostream::operator<< (inline) 171ms 0.88% 56.22% 501ms 2.57% __GI___libc_free 73ms 0.37% 56.59% 499ms 2.56% std::ostream::_M_insert 11ms 0.056% 56.65% 498ms 2.55% Cylindrical2dMesh::ReconstructCylindricalMesh 3ms 0.015% 56.67% 489ms 2.51% AbstractCellProperty::IsSubType (inline) 16ms 0.082% 56.75% 483ms 2.48% Cylindrical2dMesh::CorrectNonPeriodicMesh 9ms 0.046% 56.79% 482ms 2.47% Element::RegisterWithNodes (inline) 7ms 0.036% 56.83% 471ms 2.41% Node::AddElement 286ms 1.47% 58.30% 439ms 2.25% AbstractCellMutationState::AbstractCellMutationState 11ms 0.056% 58.35% 407ms 2.09% std::__new_allocator::deallocate (inline) 0 0% 58.35% 397ms 2.03% std::allocator_traits::deallocate (inline) 15ms 0.077% 58.43% 395ms 2.02% divconqrecurse 17ms 0.087% 58.52% 388ms 1.99% Node::RemoveElement 110ms 0.56% 59.08% 383ms 1.96% std::_Rb_tree::_M_erase 8ms 0.041% 59.12% 380ms 1.95% std::_Rb_tree::erase 2ms 0.01% 59.13% 380ms 1.95% std::set::erase (inline) 144ms 0.74% 59.87% 371ms 1.90% std::_Rb_tree::_M_get_insert_unique_pos 103ms 0.53% 60.40% 364ms 1.87% mergehulls 29ms 0.15% 60.55% 355ms 1.82% std::_Rb_tree::~_Rb_tree (inline) 25ms 0.13% 60.67% 353ms 1.81% Element::ResetIndex 0 0% 60.67% 353ms 1.81% std::_Rb_tree::_M_drop_node (inline) 2ms 0.01% 60.68% 345ms 1.77% std::_Vector_base::_M_allocate (inline) 5ms 0.026% 60.71% 334ms 1.71% Cell::GetMutationState 0 0% 60.71% 334ms 1.71% std::set::~set (inline) 329ms 1.69% 62.40% 329ms 1.69% [libchaste_cell_based.so] 270ms 1.38% 63.78% 327ms 1.68% _int_free 0 0% 63.78% 321ms 1.65% std::_Rb_tree::_M_put_node (inline) 3ms 0.015% 63.80% 307ms 1.57% Cell::GetCellProliferativeType 8ms 0.041% 63.84% 305ms 1.56% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 150ms 0.77% 64.61% 301ms 1.54% __cxxabiv1::__si_class_type_info::__do_dyncast 22ms 0.11% 64.72% 299ms 1.53% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 64.72% 297ms 1.52% NodeLocationWriter::Visit 2ms 0.01% 64.73% 287ms 1.47% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 64.73% 281ms 1.44% AbstractCellPopulation::Iterator::operator++ (inline) 11ms 0.056% 64.79% 280ms 1.44% AbstractCellPopulation::GetLocationIndexUsingCell 32ms 0.16% 64.95% 280ms 1.44% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.0051% 64.95% 275ms 1.41% alternateaxes 13ms 0.067% 65.02% 275ms 1.41% std::vector::push_back (inline) 250ms 1.28% 66.30% 274ms 1.40% vertexmedian 10ms 0.051% 66.35% 272ms 1.39% AbstractCellPopulation::IsCellAttachedToLocationIndex 109ms 0.56% 66.91% 271ms 1.39% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 2ms 0.01% 66.92% 267ms 1.37% std::set::set (inline) 16ms 0.082% 67.00% 264ms 1.35% std::num_put::_M_insert_float 18ms 0.092% 67.10% 255ms 1.31% std::vector::_M_realloc_insert 252ms 1.29% 68.39% 254ms 1.30% std::vector::operator[] (inline) 0 0% 68.39% 242ms 1.24% TetrahedralMesh::RefreshJacobianCachedData 13ms 0.067% 68.46% 240ms 1.23% AbstractTetrahedralElement::CalculateJacobian 8ms 0.041% 68.50% 240ms 1.23% std::_Rb_tree::_M_erase_aux (inline) 1ms 0.0051% 68.50% 239ms 1.23% MeshBasedCellPopulation::GetDampingConstant 5ms 0.026% 68.53% 238ms 1.22% AbstractCentreBasedCellPopulation::GetDampingConstant 24ms 0.12% 68.65% 233ms 1.19% std::_Rb_tree::_M_copy (inline) 9ms 0.046% 68.70% 230ms 1.18% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 19ms 0.097% 68.79% 230ms 1.18% TetrahedralMesh::Clear 89ms 0.46% 69.25% 225ms 1.15% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 5ms 0.026% 69.28% 224ms 1.15% std::__cxx11::collate::do_transform 55ms 0.28% 69.56% 221ms 1.13% ApcOneHitCellMutationState::ApcOneHitCellMutationState 157ms 0.8% 70.36% 213ms 1.09% AbstractElement::GetNodeGlobalIndex 3ms 0.015% 70.38% 211ms 1.08% ___vsnprintf 10ms 0.051% 70.43% 209ms 1.07% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.0051% 70.43% 208ms 1.07% __vsnprintf_internal (inline) 4ms 0.021% 70.45% 207ms 1.06% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 22ms 0.11% 70.57% 207ms 1.06% Element::MarkAsDeleted 20ms 0.1% 70.67% 204ms 1.05% __printf_buffer 71ms 0.36% 71.03% 200ms 1.03% std::_Rb_tree::_M_clone_node (inline) 0 0% 71.03% 197ms 1.01% OffLatticeSimulation::ApplyBoundaries 33ms 0.17% 71.20% 189ms 0.97% AbstractTetrahedralElement::RefreshJacobian 3ms 0.015% 71.22% 179ms 0.92% CellProliferativeTypesWriter::VisitCell 7ms 0.036% 71.25% 179ms 0.92% __printf_fp_l_buffer 0 0% 71.25% 179ms 0.92% __printf_fp_spec (inline) 130ms 0.67% 71.92% 178ms 0.91% malloc_consolidate 7ms 0.036% 71.96% 173ms 0.89% AbstractTetrahedralElement::AbstractTetrahedralElement 170ms 0.87% 72.83% 170ms 0.87% [libchaste_crypt.so] 69ms 0.35% 73.18% 169ms 0.87% __printf_fp_buffer_1 162ms 0.83% 74.01% 162ms 0.83% incircle 162ms 0.83% 74.84% 162ms 0.83% std::_Rb_tree_insert_and_rebalance 160ms 0.82% 75.66% 160ms 0.82% std::type_info::name (inline) 160ms 0.82% 76.48% 160ms 0.82% std::vector::size (inline) 5ms 0.026% 76.51% 158ms 0.81% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 153ms 0.78% 77.29% 153ms 0.78% Node::GetIndex 2ms 0.01% 77.30% 152ms 0.78% CellPropertyCollection::HasProperty 151ms 0.77% 78.08% 151ms 0.77% unlink_chunk 45ms 0.23% 78.31% 150ms 0.77% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 0 0% 78.31% 150ms 0.77% Cell::HasCellProperty (inline) 2ms 0.01% 78.32% 150ms 0.77% boost::numeric::ublas::vector_assign (inline) 5ms 0.026% 78.34% 147ms 0.75% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 91ms 0.47% 78.81% 142ms 0.73% std::_Rb_tree::equal_range (inline) 41ms 0.21% 79.02% 141ms 0.72% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 5ms 0.026% 79.05% 140ms 0.72% MeshBasedCellPopulation::SpringsEnd (inline) 138ms 0.71% 79.75% 138ms 0.71% AbstractCellMutationState::~AbstractCellMutationState 58ms 0.3% 80.05% 138ms 0.71% AbstractElement::GetNodeLocation 83ms 0.43% 80.48% 135ms 0.69% Cylindrical2dMesh::GetVectorFromAtoB 56ms 0.29% 80.76% 134ms 0.69% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 12ms 0.062% 80.82% 131ms 0.67% boost::numeric::ublas::c_vector::c_vector (inline) 36ms 0.18% 81.01% 129ms 0.66% std::__ostream_insert 14ms 0.072% 81.08% 126ms 0.65% boost::detail::shared_count::~shared_count (inline) 0 0% 81.08% 126ms 0.65% boost::shared_ptr::~shared_ptr (inline) 11ms 0.056% 81.14% 125ms 0.64% Node::~Node 25ms 0.13% 81.27% 125ms 0.64% TetrahedralMesh::EdgesEnd 11ms 0.056% 81.32% 125ms 0.64% std::_Rb_tree_const_iterator::operator++ (inline) 122ms 0.63% 81.95% 122ms 0.63% std::_Rb_tree_increment 3ms 0.015% 81.96% 117ms 0.6% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 31ms 0.16% 82.12% 115ms 0.59% boost::numeric::ublas::indexing_vector_assign 0 0% 82.12% 112ms 0.57% AbstractCellBasedSimulation::DoCellRemoval (inline) 17ms 0.087% 82.21% 112ms 0.57% std::num_put::_M_insert_int 0 0% 82.21% 110ms 0.56% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 110ms 0.56% 82.77% 110ms 0.56% TetrahedralMesh::EdgeIterator::operator!= 50ms 0.26% 83.03% 110ms 0.56% std::basic_filebuf::xsputn 101ms 0.52% 83.55% 110ms 0.56% vertexsort 9ms 0.046% 83.59% 107ms 0.55% MeshBasedCellPopulation::SpringIterator::SpringIterator 82ms 0.42% 84.01% 103ms 0.53% TimeStepper::AdvanceOneTimeStep 1ms 0.0051% 84.02% 103ms 0.53% std::operator<< (inline) 0 0% 84.02% 102ms 0.52% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1ms 0.0051% 84.02% 100ms 0.51% std::vector::_M_default_append 0 0% 84.02% 100ms 0.51% std::vector::resize (inline) 93ms 0.48% 84.50% 99ms 0.51% boost::detail::sp_counted_base::release 98ms 0.5% 85.00% 98ms 0.5% [libchaste_mesh.so] 98ms 0.5% 85.50% 98ms 0.5% counterclockwise