File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16732ms, 84.26% of 19858ms total Dropped 757 nodes (cum <= 99.29ms) flat flat% sum% cum cum% 0 0% 0% 19816ms 99.79% __libc_start_call_main 0 0% 0% 19816ms 99.79% __libc_start_main_impl 0 0% 0% 19816ms 99.79% _start 0 0% 0% 19797ms 99.69% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19797ms 99.69% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19797ms 99.69% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19797ms 99.69% main 0 0% 0% 19762ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19762ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19762ms 99.52% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19735ms 99.38% AbstractCellBasedSimulation::Solve 1ms 0.005% 0.005% 15269ms 76.89% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.005% 0.01% 10076ms 50.74% AbstractCellBasedSimulation::DoCellBirth 3ms 0.015% 0.025% 9986ms 50.29% Cell::ReadyToDivide 3ms 0.015% 0.04% 9933ms 50.02% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.005% 0.045% 9811ms 49.41% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 11ms 0.055% 0.1% 9802ms 49.36% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.005% 0.11% 9789ms 49.29% CellCycleModelOdeHandler::SolveOdeToTime 67ms 0.34% 0.44% 9625ms 48.47% AbstractOneStepIvpOdeSolver::InternalSolve 853ms 4.30% 4.74% 8803ms 44.33% RungeKutta4IvpOdeSolver::CalculateNextYValue 3632ms 18.29% 23.03% 7727ms 38.91% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 23.03% 5087ms 25.62% MeshBasedCellPopulation::Update 204ms 1.03% 24.06% 4152ms 20.91% AbstractCellProperty::IsType (inline) 5ms 0.025% 24.08% 3909ms 19.68% Cylindrical2dMesh::ReMesh 551ms 2.77% 26.86% 2876ms 14.48% AbstractCellProperty::IsSame 0 0% 26.86% 2469ms 12.43% OffLatticeSimulation::UpdateCellLocationsAndTopology 425ms 2.14% 29.00% 2325ms 11.71% std::type_info::operator== (inline) 3ms 0.015% 29.01% 2193ms 11.04% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.05% 29.06% 2157ms 10.86% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 29.06% 2146ms 10.81% MutableMesh::ReMesh 0 0% 29.06% 1995ms 10.05% AbstractCellPopulation::WriteResultsToFiles 1868ms 9.41% 38.47% 1868ms 9.41% __strcmp_avx2 765ms 3.85% 42.32% 1814ms 9.13% std::_Rb_tree::_M_lower_bound (inline) 155ms 0.78% 43.10% 1686ms 8.49% TetrahedralMesh::EdgeIterator::operator++ 73ms 0.37% 43.47% 1366ms 6.88% std::_Rb_tree::find (inline) 0 0% 43.47% 1155ms 5.82% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.025% 43.49% 1108ms 5.58% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 42ms 0.21% 43.71% 1075ms 5.41% operator new 13ms 0.065% 43.77% 1050ms 5.29% TetrahedralMesh::ImportFromMesher 9ms 0.045% 43.82% 1025ms 5.16% MeshBasedCellPopulation::SpringIterator::operator++ 229ms 1.15% 44.97% 1016ms 5.12% __GI___libc_malloc 13ms 0.065% 45.03% 1007ms 5.07% std::set::insert (inline) 15ms 0.076% 45.11% 994ms 5.01% std::_Rb_tree::_M_insert_unique 45ms 0.23% 45.34% 951ms 4.79% std::__new_allocator::allocate (inline) 0 0% 45.34% 945ms 4.76% std::allocator_traits::allocate (inline) 1ms 0.005% 45.34% 838ms 4.22% triangulate 0 0% 45.34% 811ms 4.08% std::set::count (inline) 0 0% 45.34% 764ms 3.85% delaunay 2ms 0.01% 45.35% 761ms 3.83% divconqdelaunay 1ms 0.005% 45.36% 746ms 3.76% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 1ms 0.005% 45.36% 742ms 3.74% AbstractTwoBodyInteractionForce::AddForceContribution 404ms 2.03% 47.40% 724ms 3.65% _int_malloc 6ms 0.03% 47.43% 715ms 3.60% CellPopulationElementWriter::Visit 61ms 0.31% 47.73% 703ms 3.54% std::map::operator[] (partial-inline) 701ms 3.53% 51.26% 701ms 3.53% std::_Rb_tree::_S_right (inline) 624ms 3.14% 54.41% 636ms 3.20% WntCellCycleOdeSystem::CalculateStoppingEvent 13ms 0.065% 54.47% 621ms 3.13% std::less::operator() (inline) 27ms 0.14% 54.61% 616ms 3.10% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 27ms 0.14% 54.74% 609ms 3.07% std::_Rb_tree::_M_insert_ (inline) 608ms 3.06% 57.81% 608ms 3.06% std::operator< (inline) 176ms 0.89% 58.69% 607ms 3.06% __dynamic_cast 2ms 0.01% 58.70% 600ms 3.02% MeshBasedCellPopulation::AcceptCellWriter 0 0% 58.70% 600ms 3.02% std::_Rb_tree::_M_create_node (inline) 0 0% 58.70% 590ms 2.97% std::_Rb_tree::_M_get_node (inline) 27ms 0.14% 58.84% 567ms 2.86% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 58.84% 554ms 2.79% std::_Rb_tree::lower_bound (inline) 0 0% 58.84% 554ms 2.79% std::map::lower_bound (inline) 5ms 0.025% 58.86% 552ms 2.78% Element::Element 0 0% 58.86% 551ms 2.77% std::_Rb_tree::_Alloc_node::operator() (inline) 6ms 0.03% 58.89% 549ms 2.76% CellPropertyCollection::GetPropertiesType (inline) 0 0% 58.89% 549ms 2.76% std::map::find (inline) 9ms 0.045% 58.94% 542ms 2.73% Cylindrical2dMesh::ReconstructCylindricalMesh 10ms 0.05% 58.99% 481ms 2.42% MutableMesh::ReIndex 8ms 0.04% 59.03% 467ms 2.35% Element::RegisterWithNodes (inline) 6ms 0.03% 59.06% 456ms 2.30% Node::AddElement 319ms 1.61% 60.67% 454ms 2.29% AbstractCellMutationState::AbstractCellMutationState 10ms 0.05% 60.72% 448ms 2.26% Cylindrical2dMesh::CorrectNonPeriodicMesh 6ms 0.03% 60.75% 446ms 2.25% AbstractCellProperty::IsSubType (inline) 65ms 0.33% 61.07% 443ms 2.23% std::ostream::_M_insert 0 0% 61.07% 443ms 2.23% std::ostream::operator<< (inline) 158ms 0.8% 61.87% 438ms 2.21% __GI___libc_free 118ms 0.59% 62.46% 388ms 1.95% std::_Rb_tree::_M_erase 27ms 0.14% 62.60% 379ms 1.91% divconqrecurse 151ms 0.76% 63.36% 370ms 1.86% std::_Rb_tree::_M_get_insert_unique_pos 10ms 0.05% 63.41% 361ms 1.82% std::__new_allocator::deallocate (inline) 4ms 0.02% 63.43% 359ms 1.81% std::_Vector_base::_M_allocate (inline) 0 0% 63.43% 358ms 1.80% std::allocator_traits::deallocate (inline) 13ms 0.065% 63.50% 353ms 1.78% std::_Rb_tree::erase 0 0% 63.50% 352ms 1.77% std::set::erase (inline) 7ms 0.035% 63.53% 349ms 1.76% Node::RemoveElement 23ms 0.12% 63.65% 348ms 1.75% std::_Rb_tree::~_Rb_tree (inline) 102ms 0.51% 64.16% 343ms 1.73% mergehulls 0 0% 64.16% 331ms 1.67% std::_Rb_tree::_M_drop_node (inline) 0 0% 64.16% 317ms 1.60% std::set::~set (inline) 1ms 0.005% 64.17% 316ms 1.59% Cell::GetCellProliferativeType 125ms 0.63% 64.80% 316ms 1.59% __cxxabiv1::__si_class_type_info::__do_dyncast 314ms 1.58% 66.38% 314ms 1.58% std::type_info::name (inline) 26ms 0.13% 66.51% 313ms 1.58% Element::ResetIndex 13ms 0.065% 66.57% 310ms 1.56% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 3ms 0.015% 66.59% 298ms 1.50% LegacyCellProliferativeTypesWriter::VisitCell 8ms 0.04% 66.63% 288ms 1.45% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 66.63% 287ms 1.45% std::_Rb_tree::_M_put_node (inline) 235ms 1.18% 67.81% 280ms 1.41% _int_free 6ms 0.03% 67.84% 277ms 1.39% AbstractCellPopulation::GetLocationIndexUsingCell 270ms 1.36% 69.20% 270ms 1.36% std::vector::operator[] (inline) 0 0% 69.20% 268ms 1.35% AbstractCellPopulation::Iterator::operator++ (inline) 38ms 0.19% 69.39% 267ms 1.34% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.005% 69.40% 267ms 1.34% NodeLocationWriter::Visit 16ms 0.081% 69.48% 264ms 1.33% AbstractTetrahedralElement::CalculateJacobian 2ms 0.01% 69.49% 264ms 1.33% Cell::GetMutationState 6ms 0.03% 69.52% 247ms 1.24% alternateaxes 11ms 0.055% 69.57% 245ms 1.23% std::vector::push_back (inline) 21ms 0.11% 69.68% 242ms 1.22% std::_Rb_tree::_Rb_tree 240ms 1.21% 70.89% 240ms 1.21% [libchaste_cell_based.so] 225ms 1.13% 72.02% 238ms 1.20% vertexmedian 1ms 0.005% 72.03% 233ms 1.17% TetrahedralMesh::RefreshJacobianCachedData 89ms 0.45% 72.47% 230ms 1.16% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 17ms 0.086% 72.56% 230ms 1.16% std::num_put::_M_insert_float 1ms 0.005% 72.57% 229ms 1.15% std::set::set (inline) 16ms 0.081% 72.65% 227ms 1.14% std::vector::_M_realloc_insert 62ms 0.31% 72.96% 217ms 1.09% ApcOneHitCellMutationState::ApcOneHitCellMutationState 5ms 0.025% 72.98% 215ms 1.08% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 12ms 0.06% 73.04% 212ms 1.07% std::_Rb_tree::_M_erase_aux (inline) 54ms 0.27% 73.32% 209ms 1.05% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 147ms 0.74% 74.06% 207ms 1.04% malloc_consolidate 6ms 0.03% 74.09% 197ms 0.99% AbstractTetrahedralElement::CalculateInverseJacobian 156ms 0.79% 74.87% 192ms 0.97% AbstractElement::GetNodeGlobalIndex 1ms 0.005% 74.88% 192ms 0.97% CellProliferativeTypesWriter::VisitCell 24ms 0.12% 75.00% 192ms 0.97% std::_Rb_tree::_M_copy (inline) 2ms 0.01% 75.01% 190ms 0.96% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 19ms 0.096% 75.10% 188ms 0.95% AbstractTetrahedralElement::RefreshJacobian 17ms 0.086% 75.19% 186ms 0.94% Element::MarkAsDeleted 2ms 0.01% 75.20% 184ms 0.93% MeshBasedCellPopulation::GetDampingConstant 0 0% 75.20% 182ms 0.92% AbstractCentreBasedCellPopulation::GetDampingConstant 2ms 0.01% 75.21% 180ms 0.91% std::__cxx11::collate::do_transform 2ms 0.01% 75.22% 176ms 0.89% AbstractTetrahedralElement::AbstractTetrahedralElement 174ms 0.88% 76.10% 174ms 0.88% Node::GetIndex 0 0% 76.10% 173ms 0.87% ___vsnprintf 0 0% 76.10% 173ms 0.87% __vsnprintf_internal (inline) 18ms 0.091% 76.19% 172ms 0.87% __printf_buffer 171ms 0.86% 77.05% 171ms 0.86% std::_Rb_tree_insert_and_rebalance 0 0% 77.05% 169ms 0.85% OffLatticeSimulation::ApplyBoundaries 53ms 0.27% 77.31% 167ms 0.84% std::_Rb_tree::_M_clone_node (inline) 165ms 0.83% 78.14% 165ms 0.83% incircle 3ms 0.015% 78.16% 160ms 0.81% CellPropertyCollection::HasProperty 13ms 0.065% 78.23% 160ms 0.81% TetrahedralMesh::Clear 159ms 0.8% 79.03% 159ms 0.8% unlink_chunk 0 0% 79.03% 156ms 0.79% Cell::HasCellProperty (inline) 71ms 0.36% 79.38% 152ms 0.77% AbstractElement::GetNodeLocation 5ms 0.025% 79.41% 141ms 0.71% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 3ms 0.015% 79.42% 140ms 0.71% __printf_fp_l_buffer 0 0% 79.42% 140ms 0.71% __printf_fp_spec (inline) 0 0% 79.42% 139ms 0.7% AbstractCellBasedWriter::OpenOutputFileForAppend 5ms 0.025% 79.45% 138ms 0.69% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 0 0% 79.45% 138ms 0.69% OutputFileHandler::OpenOutputFile 19ms 0.096% 79.54% 138ms 0.69% TetrahedralMesh::EdgesEnd (partial-inline) 3ms 0.015% 79.56% 136ms 0.68% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 79ms 0.4% 79.96% 133ms 0.67% std::_Rb_tree::equal_range (inline) 68ms 0.34% 80.30% 130ms 0.65% __printf_fp_buffer_1 121ms 0.61% 80.91% 129ms 0.65% vertexsort 2ms 0.01% 80.92% 126ms 0.63% boost::numeric::ublas::vector_assign (inline) 126ms 0.63% 81.55% 126ms 0.63% std::vector::size (inline) 124ms 0.62% 82.18% 124ms 0.62% AbstractElement::IsDeleted 40ms 0.2% 82.38% 123ms 0.62% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 14ms 0.071% 82.45% 123ms 0.62% boost::detail::shared_count::~shared_count (inline) 0 0% 82.45% 123ms 0.62% boost::shared_ptr::~shared_ptr (inline) 41ms 0.21% 82.66% 119ms 0.6% std::__ostream_insert 7ms 0.035% 82.69% 118ms 0.59% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 82.69% 117ms 0.59% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 38ms 0.19% 82.88% 117ms 0.59% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 62ms 0.31% 83.20% 116ms 0.58% Cylindrical2dMesh::GetVectorFromAtoB 1ms 0.005% 83.20% 112ms 0.56% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 26ms 0.13% 83.33% 111ms 0.56% std::num_put::_M_insert_int 108ms 0.54% 83.88% 108ms 0.54% boost::detail::sp_counted_base::release 10ms 0.05% 83.93% 108ms 0.54% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 83.93% 105ms 0.53% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 83.93% 104ms 0.52% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2ms 0.01% 83.94% 103ms 0.52% std::operator<< (inline) 64ms 0.32% 84.26% 102ms 0.51% TetrahedralMesh::EdgeIterator::EdgeIterator