File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16581ms, 84.77% of 19559ms total Dropped 753 nodes (cum <= 97.80ms) flat flat% sum% cum cum% 0 0% 0% 19515ms 99.78% __libc_start_call_main 0 0% 0% 19515ms 99.78% __libc_start_main_impl 0 0% 0% 19515ms 99.78% _start 0 0% 0% 19497ms 99.68% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19497ms 99.68% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19497ms 99.68% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19497ms 99.68% main 0 0% 0% 19459ms 99.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19459ms 99.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19459ms 99.49% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19432ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0% 15213ms 77.78% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0051% 0.0051% 10182ms 52.06% AbstractCellBasedSimulation::DoCellBirth 2ms 0.01% 0.015% 10116ms 51.72% Cell::ReadyToDivide 4ms 0.02% 0.036% 10057ms 51.42% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0051% 0.041% 9942ms 50.83% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 20ms 0.1% 0.14% 9934ms 50.79% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0051% 0.15% 9913ms 50.68% CellCycleModelOdeHandler::SolveOdeToTime 79ms 0.4% 0.55% 9745ms 49.82% AbstractOneStepIvpOdeSolver::InternalSolve 945ms 4.83% 5.38% 8894ms 45.47% RungeKutta4IvpOdeSolver::CalculateNextYValue 3651ms 18.67% 24.05% 7748ms 39.61% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0051% 24.06% 4918ms 25.14% MeshBasedCellPopulation::Update 168ms 0.86% 24.91% 4134ms 21.14% AbstractCellProperty::IsType (inline) 3ms 0.015% 24.93% 3775ms 19.30% Cylindrical2dMesh::ReMesh 506ms 2.59% 27.52% 2859ms 14.62% AbstractCellProperty::IsSame 0 0% 27.52% 2357ms 12.05% OffLatticeSimulation::UpdateCellLocationsAndTopology 410ms 2.10% 29.61% 2353ms 12.03% std::type_info::operator== (inline) 0 0% 29.61% 2091ms 10.69% MutableMesh::ReMesh 1ms 0.0051% 29.62% 2072ms 10.59% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.031% 29.65% 2017ms 10.31% AbstractNumericalMethod::ComputeForcesIncludingDamping 1913ms 9.78% 39.43% 1913ms 9.78% __strcmp_avx2 0 0% 39.43% 1859ms 9.50% AbstractCellPopulation::WriteResultsToFiles 799ms 4.09% 43.51% 1640ms 8.38% std::_Rb_tree::_M_lower_bound (inline) 164ms 0.84% 44.35% 1639ms 8.38% TetrahedralMesh::EdgeIterator::operator++ 65ms 0.33% 44.69% 1273ms 6.51% std::_Rb_tree::find (inline) 0 0% 44.69% 1115ms 5.70% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.036% 44.72% 1100ms 5.62% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 11ms 0.056% 44.78% 1018ms 5.20% TetrahedralMesh::ImportFromMesher 18ms 0.092% 44.87% 1007ms 5.15% MeshBasedCellPopulation::SpringIterator::operator++ 9ms 0.046% 44.92% 999ms 5.11% std::set::insert (inline) 40ms 0.2% 45.12% 994ms 5.08% operator new 23ms 0.12% 45.24% 990ms 5.06% std::_Rb_tree::_M_insert_unique 237ms 1.21% 46.45% 932ms 4.77% __GI___libc_malloc 32ms 0.16% 46.61% 913ms 4.67% std::__new_allocator::allocate (inline) 0 0% 46.61% 906ms 4.63% std::allocator_traits::allocate (inline) 0 0% 46.61% 808ms 4.13% std::set::count (inline) 0 0% 46.61% 802ms 4.10% triangulate 0 0% 46.61% 721ms 3.69% delaunay 3ms 0.015% 46.63% 721ms 3.69% divconqdelaunay 3ms 0.015% 46.64% 675ms 3.45% AbstractTwoBodyInteractionForce::AddForceContribution 7ms 0.036% 46.68% 666ms 3.41% CellPopulationElementWriter::Visit 5ms 0.026% 46.70% 662ms 3.38% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 638ms 3.26% 49.97% 655ms 3.35% WntCellCycleOdeSystem::CalculateStoppingEvent 25ms 0.13% 50.09% 623ms 3.19% std::_Rb_tree::_M_insert_ (inline) 344ms 1.76% 51.85% 618ms 3.16% _int_malloc 0 0% 51.85% 612ms 3.13% std::_Rb_tree::_M_create_node (inline) 137ms 0.7% 52.55% 609ms 3.11% __dynamic_cast 15ms 0.077% 52.63% 595ms 3.04% std::less::operator() (inline) 49ms 0.25% 52.88% 582ms 2.98% std::map::operator[] (partial-inline) 0 0% 52.88% 580ms 2.97% std::_Rb_tree::_M_get_node (inline) 580ms 2.97% 55.85% 580ms 2.97% std::operator< (inline) 0 0% 55.85% 576ms 2.94% std::_Rb_tree::_Alloc_node::operator() (inline) 32ms 0.16% 56.01% 560ms 2.86% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 5ms 0.026% 56.04% 542ms 2.77% Element::Element 3ms 0.015% 56.05% 536ms 2.74% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.015% 56.07% 533ms 2.73% MeshBasedCellPopulation::AcceptCellWriter 519ms 2.65% 58.72% 519ms 2.65% std::_Rb_tree::_S_right (inline) 357ms 1.83% 60.55% 516ms 2.64% AbstractCellMutationState::AbstractCellMutationState 21ms 0.11% 60.65% 499ms 2.55% AbstractCellPopulation::GetCellUsingLocationIndex 15ms 0.077% 60.73% 496ms 2.54% Element::RegisterWithNodes (inline) 67ms 0.34% 61.07% 491ms 2.51% std::ostream::_M_insert 0 0% 61.07% 491ms 2.51% std::ostream::operator<< (inline) 8ms 0.041% 61.11% 480ms 2.45% Node::AddElement 4ms 0.02% 61.13% 473ms 2.42% MutableMesh::ReIndex 13ms 0.066% 61.20% 468ms 2.39% Cylindrical2dMesh::CorrectNonPeriodicMesh 0 0% 61.20% 465ms 2.38% std::_Rb_tree::lower_bound (inline) 0 0% 61.20% 465ms 2.38% std::map::lower_bound (inline) 0 0% 61.20% 462ms 2.36% std::map::find (inline) 19ms 0.097% 61.30% 437ms 2.23% Cylindrical2dMesh::ReconstructCylindricalMesh 3ms 0.015% 61.31% 423ms 2.16% AbstractCellProperty::IsSubType (inline) 152ms 0.78% 62.09% 415ms 2.12% __GI___libc_free 24ms 0.12% 62.21% 383ms 1.96% divconqrecurse 14ms 0.072% 62.28% 362ms 1.85% std::__new_allocator::deallocate (inline) 179ms 0.92% 63.20% 359ms 1.84% __cxxabiv1::__si_class_type_info::__do_dyncast 125ms 0.64% 63.84% 356ms 1.82% mergehulls 0 0% 63.84% 356ms 1.82% std::allocator_traits::deallocate (inline) 137ms 0.7% 64.54% 345ms 1.76% std::_Rb_tree::_M_get_insert_unique_pos 88ms 0.45% 64.99% 337ms 1.72% std::_Rb_tree::_M_erase 0 0% 64.99% 326ms 1.67% std::_Vector_base::_M_allocate (inline) 4ms 0.02% 65.01% 326ms 1.67% std::set::erase (inline) 14ms 0.072% 65.08% 324ms 1.66% Node::RemoveElement 1ms 0.0051% 65.09% 323ms 1.65% std::_Rb_tree::erase 0 0% 65.09% 322ms 1.65% std::_Rb_tree::_M_drop_node (inline) 16ms 0.082% 65.17% 315ms 1.61% Element::ResetIndex 2ms 0.01% 65.18% 313ms 1.60% NodeLocationWriter::Visit 20ms 0.1% 65.28% 309ms 1.58% std::_Rb_tree::~_Rb_tree (inline) 13ms 0.066% 65.35% 296ms 1.51% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 294ms 1.50% 66.85% 294ms 1.50% std::type_info::name (inline) 1ms 0.0051% 66.85% 284ms 1.45% Cell::GetCellProliferativeType 3ms 0.015% 66.87% 283ms 1.45% Cell::GetMutationState 0 0% 66.87% 282ms 1.44% std::set::~set (inline) 14ms 0.072% 66.94% 278ms 1.42% std::num_put::_M_insert_float 0 0% 66.94% 276ms 1.41% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 66.94% 275ms 1.41% std::_Rb_tree::_M_put_node (inline) 3ms 0.015% 66.96% 274ms 1.40% AbstractCellPopulation::GetLocationIndexUsingCell 25ms 0.13% 67.08% 270ms 1.38% AbstractTetrahedralElement::CalculateJacobian 269ms 1.38% 68.46% 269ms 1.38% [libchaste_cell_based.so] 215ms 1.10% 69.56% 263ms 1.34% _int_free 9ms 0.046% 69.60% 260ms 1.33% std::_Rb_tree::_Rb_tree (partial-inline) 55ms 0.28% 69.89% 250ms 1.28% ApcOneHitCellMutationState::ApcOneHitCellMutationState 0 0% 69.89% 246ms 1.26% TetrahedralMesh::RefreshJacobianCachedData 0 0% 69.89% 243ms 1.24% AbstractCellPopulation::Iterator::operator++ (inline) 242ms 1.24% 71.12% 243ms 1.24% std::vector::operator[] (inline) 23ms 0.12% 71.24% 240ms 1.23% AbstractCellPopulation::Iterator::IsRealCell (inline) 3ms 0.015% 71.26% 235ms 1.20% std::set::set (inline) 14ms 0.072% 71.33% 233ms 1.19% std::vector::push_back (inline) 3ms 0.015% 71.34% 226ms 1.16% std::__cxx11::collate::do_transform 6ms 0.031% 71.37% 224ms 1.15% AbstractCellPopulation::IsCellAttachedToLocationIndex 26ms 0.13% 71.51% 221ms 1.13% std::_Rb_tree::_M_copy (inline) 68ms 0.35% 71.85% 215ms 1.10% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 6ms 0.031% 71.89% 214ms 1.09% AbstractTetrahedralElement::CalculateInverseJacobian 14ms 0.072% 71.96% 213ms 1.09% std::_Rb_tree::_M_erase_aux (inline) 9ms 0.046% 72.00% 213ms 1.09% std::vector::_M_realloc_insert 6ms 0.031% 72.03% 212ms 1.08% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 5ms 0.026% 72.06% 212ms 1.08% ___vsnprintf 39ms 0.2% 72.26% 210ms 1.07% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 0 0% 72.26% 207ms 1.06% __vsnprintf_internal (inline) 3ms 0.015% 72.27% 205ms 1.05% alternateaxes 19ms 0.097% 72.37% 203ms 1.04% __printf_buffer 193ms 0.99% 73.36% 201ms 1.03% vertexmedian 26ms 0.13% 73.49% 198ms 1.01% AbstractTetrahedralElement::RefreshJacobian 140ms 0.72% 74.21% 194ms 0.99% malloc_consolidate 47ms 0.24% 74.45% 193ms 0.99% std::_Rb_tree::_M_clone_node (inline) 3ms 0.015% 74.46% 191ms 0.98% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 184ms 0.94% 75.40% 184ms 0.94% std::_Rb_tree_insert_and_rebalance 0 0% 75.40% 183ms 0.94% OffLatticeSimulation::ApplyBoundaries 129ms 0.66% 76.06% 176ms 0.9% AbstractElement::GetNodeGlobalIndex 5ms 0.026% 76.09% 169ms 0.86% AbstractTetrahedralElement::AbstractTetrahedralElement 14ms 0.072% 76.16% 169ms 0.86% TetrahedralMesh::Clear 12ms 0.061% 76.22% 166ms 0.85% Element::MarkAsDeleted 1ms 0.0051% 76.23% 165ms 0.84% __printf_fp_spec (inline) 4ms 0.02% 76.25% 165ms 0.84% boost::numeric::ublas::vector_assign (inline) 8ms 0.041% 76.29% 164ms 0.84% __printf_fp_l_buffer 2ms 0.01% 76.30% 159ms 0.81% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 76.30% 159ms 0.81% MeshBasedCellPopulation::GetDampingConstant 9ms 0.046% 76.34% 159ms 0.81% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 3ms 0.015% 76.36% 156ms 0.8% CellProliferativeTypesWriter::VisitCell 152ms 0.78% 77.14% 152ms 0.78% incircle 70ms 0.36% 77.49% 151ms 0.77% AbstractElement::GetNodeLocation 8ms 0.041% 77.53% 150ms 0.77% boost::numeric::ublas::c_vector::c_vector (inline) 75ms 0.38% 77.92% 149ms 0.76% __printf_fp_buffer_1 141ms 0.72% 78.64% 141ms 0.72% Node::GetIndex 5ms 0.026% 78.66% 135ms 0.69% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 49ms 0.25% 78.92% 133ms 0.68% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 33ms 0.17% 79.08% 133ms 0.68% TetrahedralMesh::EdgesEnd (partial-inline) 133ms 0.68% 79.76% 133ms 0.68% std::vector::size (inline) 43ms 0.22% 79.98% 132ms 0.67% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 22ms 0.11% 80.10% 131ms 0.67% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 129ms 0.66% 80.76% 129ms 0.66% unlink_chunk 2ms 0.01% 80.77% 128ms 0.65% CellPropertyCollection::HasProperty 65ms 0.33% 81.10% 127ms 0.65% Cylindrical2dMesh::GetVectorFromAtoB 34ms 0.17% 81.27% 127ms 0.65% boost::numeric::ublas::indexing_vector_assign 6ms 0.031% 81.30% 126ms 0.64% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 81.30% 125ms 0.64% Cell::HasCellProperty (inline) 114ms 0.58% 81.89% 121ms 0.62% vertexsort 117ms 0.6% 82.48% 117ms 0.6% std::_Rb_tree_increment 68ms 0.35% 82.83% 113ms 0.58% std::_Rb_tree::equal_range (inline) 0 0% 82.83% 112ms 0.57% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.0051% 82.84% 111ms 0.57% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 8ms 0.041% 82.88% 111ms 0.57% std::_Rb_tree_const_iterator::operator++ (inline) 12ms 0.061% 82.94% 107ms 0.55% boost::detail::shared_count::~shared_count (inline) 0 0% 82.94% 107ms 0.55% boost::shared_ptr::~shared_ptr (inline) 1ms 0.0051% 82.94% 106ms 0.54% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 0 0% 82.94% 104ms 0.53% AbstractCellBasedWriter::OpenOutputFileForAppend 103ms 0.53% 83.47% 103ms 0.53% AbstractCellProperty::~AbstractCellProperty 4ms 0.02% 83.49% 102ms 0.52% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 66ms 0.34% 83.83% 101ms 0.52% TetrahedralMesh::EdgeIterator::EdgeIterator 0 0% 83.83% 100ms 0.51% OutputFileHandler::OpenOutputFile 16ms 0.082% 83.91% 100ms 0.51% std::num_put::_M_insert_int 64ms 0.33% 84.24% 99ms 0.51% AbstractTetrahedralMesh::GetElement 7ms 0.036% 84.27% 98ms 0.5% Node::~Node 98ms 0.5% 84.77% 98ms 0.5% [libchaste_mesh.so]