File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 15868ms, 86.01% of 18450ms total Dropped 786 nodes (cum <= 92.25ms) flat flat% sum% cum cum% 0 0% 0% 18412ms 99.79% __libc_start_call_main 0 0% 0% 18412ms 99.79% __libc_start_main_impl 0 0% 0% 18412ms 99.79% _start 0 0% 0% 18393ms 99.69% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 18393ms 99.69% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 18393ms 99.69% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 18393ms 99.69% main 0 0% 0% 18364ms 99.53% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 18364ms 99.53% CxxTest::TestRunner::runTest (inline) 0 0% 0% 18364ms 99.53% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.0054% 0.0054% 18340ms 99.40% AbstractCellBasedSimulation::Solve 0 0% 0.0054% 13595ms 73.69% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0054% 0.011% 8332ms 45.16% AbstractCellBasedSimulation::DoCellBirth 9ms 0.049% 0.06% 8219ms 44.55% Cell::ReadyToDivide 3ms 0.016% 0.076% 8157ms 44.21% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0054% 0.081% 8012ms 43.43% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 7ms 0.038% 0.12% 8004ms 43.38% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.011% 0.13% 7992ms 43.32% CellCycleModelOdeHandler::SolveOdeToTime 61ms 0.33% 0.46% 7813ms 42.35% AbstractOneStepIvpOdeSolver::InternalSolve 895ms 4.85% 5.31% 6964ms 37.75% RungeKutta4IvpOdeSolver::CalculateNextYValue 2985ms 16.18% 21.49% 5883ms 31.89% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.011% 21.50% 5156ms 27.95% MeshBasedCellPopulation::Update 3ms 0.016% 21.52% 3983ms 21.59% Cylindrical2dMesh::ReMesh 238ms 1.29% 22.81% 3030ms 16.42% AbstractCellProperty::IsType (inline) 1ms 0.0054% 22.81% 2701ms 14.64% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 22.81% 2449ms 13.27% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0054% 22.82% 2418ms 13.11% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 22.82% 2216ms 12.01% MutableMesh::ReMesh 1ms 0.0054% 22.82% 2037ms 11.04% AbstractCellPopulation::WriteResultsToFiles 742ms 4.02% 26.85% 1775ms 9.62% std::_Rb_tree::_M_lower_bound (inline) 149ms 0.81% 27.65% 1687ms 9.14% TetrahedralMesh::EdgeIterator::operator++ 71ms 0.38% 28.04% 1390ms 7.53% std::_Rb_tree::find (inline) 249ms 1.35% 29.39% 1367ms 7.41% AbstractCellProperty::IsSame 66ms 0.36% 29.75% 1231ms 6.67% operator new 11ms 0.06% 29.80% 1164ms 6.31% TetrahedralMesh::ImportFromMesher 438ms 2.37% 32.18% 1136ms 6.16% __GI___libc_malloc 0 0% 32.18% 1130ms 6.12% MeshBasedCellPopulation::UpdateNodePairs 8ms 0.043% 32.22% 1119ms 6.07% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 190ms 1.03% 33.25% 1118ms 6.06% std::type_info::operator== (inline) 11ms 0.06% 33.31% 1083ms 5.87% std::set::insert (inline) 12ms 0.065% 33.38% 1072ms 5.81% std::_Rb_tree::_M_insert_unique 32ms 0.17% 33.55% 1064ms 5.77% std::__new_allocator::allocate (inline) 0 0% 33.55% 1057ms 5.73% std::allocator_traits::allocate (inline) 7ms 0.038% 33.59% 1009ms 5.47% MeshBasedCellPopulation::SpringIterator::operator++ 1009ms 5.47% 39.06% 1009ms 5.47% __strcmp_evex 0 0% 39.06% 889ms 4.82% std::set::count (inline) 14ms 0.076% 39.13% 870ms 4.72% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 840ms 4.55% 43.69% 840ms 4.55% [libchaste_cell_based.so] 5ms 0.027% 43.71% 830ms 4.50% AbstractTwoBodyInteractionForce::AddForceContribution 1ms 0.0054% 43.72% 822ms 4.46% triangulate 3ms 0.016% 43.73% 748ms 4.05% CellPopulationElementWriter::Visit 0 0% 43.73% 747ms 4.05% std::_Rb_tree::_M_create_node (inline) 0 0% 43.73% 746ms 4.04% delaunay 2ms 0.011% 43.75% 745ms 4.04% divconqdelaunay 237ms 1.28% 45.03% 736ms 3.99% __dynamic_cast 24ms 0.13% 45.16% 730ms 3.96% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 45.16% 730ms 3.96% std::_Rb_tree::_M_get_node (inline) 12ms 0.065% 45.22% 709ms 3.84% CellPropertyCollection::GetPropertiesType (inline) 81ms 0.44% 45.66% 700ms 3.79% std::map::operator[] (partial-inline) 34ms 0.18% 45.85% 693ms 3.76% std::_Rb_tree::_M_insert_ (inline) 18ms 0.098% 45.95% 689ms 3.73% AbstractCellPopulation::GetCellUsingLocationIndex 8ms 0.043% 45.99% 666ms 3.61% MeshBasedCellPopulation::AcceptCellWriter 0 0% 45.99% 655ms 3.55% std::_Rb_tree::_Alloc_node::operator() (inline) 642ms 3.48% 49.47% 642ms 3.48% std::_Rb_tree::_S_right (inline) 3ms 0.016% 49.49% 603ms 3.27% Element::Element 602ms 3.26% 52.75% 602ms 3.26% WntCellCycleOdeSystem::CalculateStoppingEvent 344ms 1.86% 54.61% 585ms 3.17% _int_malloc 11ms 0.06% 54.67% 571ms 3.09% Element::RegisterWithNodes (inline) 4ms 0.022% 54.69% 559ms 3.03% Node::AddElement 13ms 0.07% 54.76% 549ms 2.98% std::less::operator() (inline) 5ms 0.027% 54.79% 544ms 2.95% AbstractCellProperty::IsSubType (inline) 536ms 2.91% 57.70% 536ms 2.91% std::operator< (inline) 126ms 0.68% 58.38% 532ms 2.88% __GI___libc_free 22ms 0.12% 58.50% 518ms 2.81% Cylindrical2dMesh::ReconstructCylindricalMesh 0 0% 58.50% 505ms 2.74% std::_Rb_tree::_M_drop_node (inline) 60ms 0.33% 58.82% 505ms 2.74% std::_Rb_tree::~_Rb_tree (inline) 0 0% 58.82% 500ms 2.71% std::map::find (inline) 92ms 0.5% 59.32% 499ms 2.70% std::_Rb_tree::_M_erase 0 0% 59.32% 487ms 2.64% std::_Rb_tree::lower_bound (inline) 0 0% 59.32% 487ms 2.64% std::map::lower_bound (inline) 0 0% 59.32% 484ms 2.62% std::set::~set (inline) 5ms 0.027% 59.35% 480ms 2.60% MutableMesh::ReIndex 233ms 1.26% 60.61% 472ms 2.56% AbstractCellMutationState::AbstractCellMutationState 5ms 0.027% 60.64% 459ms 2.49% Cell::GetMutationState 15ms 0.081% 60.72% 459ms 2.49% Cylindrical2dMesh::CorrectNonPeriodicMesh 16ms 0.087% 60.81% 450ms 2.44% std::__new_allocator::deallocate (inline) 0 0% 60.81% 443ms 2.40% std::allocator_traits::deallocate (inline) 1ms 0.0054% 60.81% 427ms 2.31% std::ostream::operator<< (inline) 423ms 2.29% 63.11% 423ms 2.29% [libchaste_crypt.so] 69ms 0.37% 63.48% 419ms 2.27% std::ostream::_M_insert 3ms 0.016% 63.50% 404ms 2.19% std::set::erase (inline) 8ms 0.043% 63.54% 403ms 2.18% std::_Rb_tree::erase 329ms 1.78% 65.32% 393ms 2.13% _int_free 0 0% 65.32% 390ms 2.11% std::_Rb_tree::_M_put_node (inline) 13ms 0.07% 65.39% 386ms 2.09% divconqrecurse 3ms 0.016% 65.41% 385ms 2.09% Node::RemoveElement 150ms 0.81% 66.22% 374ms 2.03% __cxxabiv1::__si_class_type_info::__do_dyncast 124ms 0.67% 66.89% 367ms 1.99% std::_Rb_tree::_M_get_insert_unique_pos 106ms 0.57% 67.47% 361ms 1.96% mergehulls 0 0% 67.47% 356ms 1.93% MeshBasedCellPopulation::GetDampingConstant 1ms 0.0054% 67.47% 354ms 1.92% AbstractCentreBasedCellPopulation::GetDampingConstant 4ms 0.022% 67.50% 341ms 1.85% Cell::GetCellProliferativeType 25ms 0.14% 67.63% 337ms 1.83% Element::ResetIndex 2ms 0.011% 67.64% 329ms 1.78% std::_Vector_base::_M_allocate (inline) 9ms 0.049% 67.69% 311ms 1.69% std::_Rb_tree::_Rb_tree 3ms 0.016% 67.71% 307ms 1.66% std::set::set (inline) 1ms 0.0054% 67.71% 304ms 1.65% LegacyCellProliferativeTypesWriter::VisitCell 8ms 0.043% 67.76% 291ms 1.58% AbstractCellPopulation::IsCellAttachedToLocationIndex 18ms 0.098% 67.85% 290ms 1.57% boost::detail::shared_count::~shared_count (inline) 0 0% 67.85% 290ms 1.57% boost::shared_ptr::~shared_ptr (inline) 28ms 0.15% 68.01% 283ms 1.53% std::_Rb_tree::_M_copy (inline) 18ms 0.098% 68.10% 280ms 1.52% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 258ms 1.40% 69.50% 266ms 1.44% boost::detail::sp_counted_base::release 8ms 0.043% 69.54% 266ms 1.44% std::vector::push_back (inline) 0 0% 69.54% 262ms 1.42% AbstractCellPopulation::Iterator::operator++ (inline) 32ms 0.17% 69.72% 252ms 1.37% AbstractCellPopulation::Iterator::IsRealCell (inline) 105ms 0.57% 70.29% 246ms 1.33% std::_Rb_tree::_M_clone_node (inline) 11ms 0.06% 70.35% 246ms 1.33% std::vector::_M_realloc_insert 1ms 0.0054% 70.35% 242ms 1.31% NodeLocationWriter::Visit 2ms 0.011% 70.36% 239ms 1.30% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 239ms 1.30% 71.66% 239ms 1.30% [libchaste_mesh.so] 17ms 0.092% 71.75% 239ms 1.30% std::_Rb_tree::_M_erase_aux (inline) 7ms 0.038% 71.79% 238ms 1.29% alternateaxes 4ms 0.022% 71.81% 230ms 1.25% AbstractCellPopulation::GetLocationIndexUsingCell 3ms 0.016% 71.83% 230ms 1.25% ApcOneHitCellMutationState::ApcOneHitCellMutationState 216ms 1.17% 73.00% 229ms 1.24% vertexmedian 25ms 0.14% 73.13% 226ms 1.22% Element::MarkAsDeleted 14ms 0.076% 73.21% 220ms 1.19% AbstractTetrahedralElement::CalculateJacobian 1ms 0.0054% 73.21% 220ms 1.19% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 18ms 0.098% 73.31% 213ms 1.15% std::num_put::_M_insert_float 0 0% 73.31% 205ms 1.11% CellProliferativeTypesWriter::VisitCell 3ms 0.016% 73.33% 202ms 1.09% TetrahedralMesh::RefreshJacobianCachedData 8ms 0.043% 73.37% 199ms 1.08% TetrahedralMesh::Clear 14ms 0.076% 73.45% 196ms 1.06% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 188ms 1.02% 74.47% 189ms 1.02% std::vector::operator[] (inline) 7ms 0.038% 74.50% 182ms 0.99% boost::numeric::ublas::vector_assign (inline) 0 0% 74.50% 176ms 0.95% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2ms 0.011% 74.51% 176ms 0.95% std::__cxx11::collate::do_transform 7ms 0.038% 74.55% 175ms 0.95% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.011% 74.56% 169ms 0.92% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 0 0% 74.56% 165ms 0.89% ___vsnprintf 0 0% 74.56% 165ms 0.89% __vsnprintf_internal (inline) 165ms 0.89% 75.46% 165ms 0.89% incircle 19ms 0.1% 75.56% 164ms 0.89% AbstractTetrahedralElement::RefreshJacobian 18ms 0.098% 75.66% 163ms 0.88% __printf_buffer 134ms 0.73% 76.38% 162ms 0.88% malloc_consolidate 161ms 0.87% 77.26% 161ms 0.87% std::_Rb_tree_insert_and_rebalance 4ms 0.022% 77.28% 159ms 0.86% boost::numeric::ublas::c_vector::c_vector (inline) 3ms 0.016% 77.30% 156ms 0.85% AbstractTetrahedralElement::AbstractTetrahedralElement 94ms 0.51% 77.80% 156ms 0.85% std::_Rb_tree::equal_range (inline) 57ms 0.31% 78.11% 152ms 0.82% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 58ms 0.31% 78.43% 152ms 0.82% Cylindrical2dMesh::GetVectorFromAtoB 8ms 0.043% 78.47% 152ms 0.82% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 146ms 0.79% 79.26% 146ms 0.79% std::type_info::name (inline) 145ms 0.79% 80.05% 145ms 0.79% std::_Rb_tree::_S_left (inline) 3ms 0.016% 80.07% 142ms 0.77% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 0 0% 80.07% 139ms 0.75% OffLatticeSimulation::ApplyBoundaries 91ms 0.49% 80.56% 138ms 0.75% AbstractElement::GetNodeGlobalIndex 3ms 0.016% 80.57% 137ms 0.74% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 1ms 0.0054% 80.58% 136ms 0.74% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 1ms 0.0054% 80.59% 135ms 0.73% __printf_fp_l_buffer 0 0% 80.59% 135ms 0.73% __printf_fp_spec (inline) 29ms 0.16% 80.74% 134ms 0.73% boost::numeric::ublas::indexing_vector_assign 7ms 0.038% 80.78% 132ms 0.72% std::_Rb_tree::_M_emplace_hint_unique 58ms 0.31% 81.09% 130ms 0.7% __printf_fp_buffer_1 16ms 0.087% 81.18% 129ms 0.7% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 81.18% 122ms 0.66% Cell::HasCellProperty (inline) 3ms 0.016% 81.20% 122ms 0.66% CellPropertyCollection::HasProperty 73ms 0.4% 81.59% 118ms 0.64% AbstractElement::GetNodeLocation 117ms 0.63% 82.23% 117ms 0.63% std::_Rb_tree_increment 0 0% 82.23% 117ms 0.63% std::__new_allocator::destroy (inline) 0 0% 82.23% 117ms 0.63% std::allocator_traits::destroy (inline) 0 0% 82.23% 116ms 0.63% std::_Rb_tree::_M_destroy_node (inline) 115ms 0.62% 82.85% 115ms 0.62% AbstractCellProperty::AbstractCellProperty 55ms 0.3% 83.15% 113ms 0.61% std::__ostream_insert 111ms 0.6% 83.75% 111ms 0.6% Node::GetIndex 0 0% 83.75% 110ms 0.6% Node::~Node 99ms 0.54% 84.29% 110ms 0.6% vertexsort 7ms 0.038% 84.33% 109ms 0.59% MeshBasedCellPopulation::SpringsEnd (inline) 7ms 0.038% 84.36% 107ms 0.58% Cell::SetCellProliferativeType 5ms 0.027% 84.39% 107ms 0.58% CellLocationIndexWriter::VisitCell 0 0% 84.39% 105ms 0.57% AbstractCellBasedSimulation::DoCellRemoval (inline) 61ms 0.33% 84.72% 105ms 0.57% TimeStepper::AdvanceOneTimeStep 21ms 0.11% 84.83% 104ms 0.56% std::num_put::_M_insert_int 3ms 0.016% 84.85% 99ms 0.54% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 99ms 0.54% 85.39% 99ms 0.54% unlink_chunk 16ms 0.087% 85.47% 98ms 0.53% TetrahedralMesh::EdgesEnd 0 0% 85.47% 96ms 0.52% tcache_get (inline) 96ms 0.52% 85.99% 96ms 0.52% tcache_get_n (inline) 2ms 0.011% 86.01% 94ms 0.51% Cylindrical2dMesh::CreateMirrorNodes