File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 11637ms, 88.33% of 13174ms total Dropped 651 nodes (cum <= 65.87ms) flat flat% sum% cum cum% 0 0% 0% 13145ms 99.78% __libc_start_call_main 0 0% 0% 13145ms 99.78% __libc_start_main_impl 0 0% 0% 13145ms 99.78% _start 0 0% 0% 13127ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 13127ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 13127ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 13127ms 99.64% main 0 0% 0% 13099ms 99.43% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 13099ms 99.43% CxxTest::TestRunner::runTest (inline) 0 0% 0% 13099ms 99.43% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 13081ms 99.29% AbstractCellBasedSimulation::Solve 0 0% 0% 10001ms 75.91% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0076% 0.0076% 6123ms 46.48% AbstractCellBasedSimulation::DoCellBirth 6ms 0.046% 0.053% 6053ms 45.95% Cell::ReadyToDivide 1ms 0.0076% 0.061% 6016ms 45.67% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0076% 0.068% 5904ms 44.82% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 5ms 0.038% 0.11% 5899ms 44.78% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0076% 0.11% 5892ms 44.72% CellCycleModelOdeHandler::SolveOdeToTime 40ms 0.3% 0.42% 5770ms 43.80% AbstractOneStepIvpOdeSolver::InternalSolve 531ms 4.03% 4.45% 5164ms 39.20% RungeKutta4IvpOdeSolver::CalculateNextYValue 2249ms 17.07% 21.52% 4441ms 33.71% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 21.52% 3789ms 28.76% MeshBasedCellPopulation::Update 2ms 0.015% 21.53% 2896ms 21.98% Cylindrical2dMesh::ReMesh 198ms 1.50% 23.04% 2271ms 17.24% AbstractCellProperty::IsType (inline) 1ms 0.0076% 23.05% 1762ms 13.37% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 23.05% 1596ms 12.11% MutableMesh::ReMesh 1ms 0.0076% 23.05% 1526ms 11.58% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0076% 23.06% 1503ms 11.41% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 23.06% 1312ms 9.96% AbstractCellPopulation::WriteResultsToFiles 138ms 1.05% 24.11% 1304ms 9.90% TetrahedralMesh::EdgeIterator::operator++ 587ms 4.46% 28.56% 1304ms 9.90% std::_Rb_tree::_M_lower_bound (inline) 31ms 0.24% 28.80% 1028ms 7.80% std::_Rb_tree::find (inline) 115ms 0.87% 29.67% 886ms 6.73% AbstractCellProperty::IsSame 42ms 0.32% 29.99% 881ms 6.69% operator new 1ms 0.0076% 30.00% 866ms 6.57% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.0076% 30.01% 864ms 6.56% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 246ms 1.87% 31.87% 830ms 6.30% __GI___libc_malloc 9ms 0.068% 31.94% 784ms 5.95% std::set::insert (inline) 6ms 0.046% 31.99% 779ms 5.91% TetrahedralMesh::ImportFromMesher 13ms 0.099% 32.09% 774ms 5.88% std::_Rb_tree::_M_insert_unique 18ms 0.14% 32.22% 773ms 5.87% std::__new_allocator::allocate (inline) 14ms 0.11% 32.33% 771ms 5.85% std::type_info::operator== (inline) 9ms 0.068% 32.40% 770ms 5.84% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 32.40% 765ms 5.81% std::allocator_traits::allocate (inline) 735ms 5.58% 37.98% 735ms 5.58% __strcmp_evex 701ms 5.32% 43.30% 701ms 5.32% [libchaste_cell_based.so] 0 0% 43.30% 655ms 4.97% std::set::count (inline) 0 0% 43.30% 628ms 4.77% triangulate 0 0% 43.30% 575ms 4.36% delaunay 2ms 0.015% 43.31% 575ms 4.36% divconqdelaunay 297ms 2.25% 45.57% 499ms 3.79% _int_malloc 6ms 0.046% 45.61% 489ms 3.71% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 45.61% 488ms 3.70% std::_Rb_tree::_M_create_node (inline) 16ms 0.12% 45.73% 485ms 3.68% std::_Rb_tree::_M_insert_ (inline) 0 0% 45.73% 480ms 3.64% std::_Rb_tree::_M_get_node (inline) 480ms 3.64% 49.38% 480ms 3.64% std::_Rb_tree::_S_right (inline) 4ms 0.03% 49.41% 473ms 3.59% CellPopulationElementWriter::Visit 36ms 0.27% 49.68% 447ms 3.39% std::map::operator[] (partial-inline) 1ms 0.0076% 49.69% 442ms 3.36% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 49.69% 438ms 3.32% std::_Rb_tree::_Alloc_node::operator() (inline) 432ms 3.28% 52.97% 432ms 3.28% WntCellCycleOdeSystem::CalculateStoppingEvent 4ms 0.03% 53.00% 409ms 3.10% Element::Element 5ms 0.038% 53.04% 404ms 3.07% AbstractCellPopulation::GetCellUsingLocationIndex 7ms 0.053% 53.09% 402ms 3.05% Element::RegisterWithNodes (inline) 128ms 0.97% 54.06% 397ms 3.01% __dynamic_cast 24ms 0.18% 54.24% 396ms 3.01% Cylindrical2dMesh::ReconstructCylindricalMesh 11ms 0.083% 54.33% 393ms 2.98% Node::AddElement 7ms 0.053% 54.38% 388ms 2.95% CellPropertyCollection::GetPropertiesType (inline) 190ms 1.44% 55.82% 382ms 2.90% AbstractCellMutationState::AbstractCellMutationState 13ms 0.099% 55.92% 382ms 2.90% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 13ms 0.099% 56.02% 374ms 2.84% std::less::operator() (inline) 12ms 0.091% 56.11% 372ms 2.82% MeshBasedCellPopulation::AcceptCellWriter 3ms 0.023% 56.13% 371ms 2.82% MutableMesh::ReIndex 84ms 0.64% 56.77% 371ms 2.82% __GI___libc_free 0 0% 56.77% 371ms 2.82% std::map::find (inline) 361ms 2.74% 59.51% 361ms 2.74% std::operator< (inline) 0 0% 59.51% 338ms 2.57% std::_Rb_tree::lower_bound (inline) 0 0% 59.51% 338ms 2.57% std::map::lower_bound (inline) 0 0% 59.51% 334ms 2.54% std::_Rb_tree::_M_drop_node (inline) 40ms 0.3% 59.81% 332ms 2.52% std::_Rb_tree::~_Rb_tree (inline) 61ms 0.46% 60.28% 322ms 2.44% std::_Rb_tree::_M_erase 3ms 0.023% 60.30% 322ms 2.44% std::__new_allocator::deallocate (inline) 0 0% 60.30% 315ms 2.39% std::allocator_traits::deallocate (inline) 1ms 0.0076% 60.31% 315ms 2.39% std::ostream::operator<< (inline) 33ms 0.25% 60.56% 309ms 2.35% std::ostream::_M_insert 0 0% 60.56% 308ms 2.34% std::set::~set (inline) 304ms 2.31% 62.87% 304ms 2.31% [libchaste_crypt.so] 2ms 0.015% 62.88% 303ms 2.30% AbstractCellProperty::IsSubType (inline) 7ms 0.053% 62.93% 296ms 2.25% Cylindrical2dMesh::CorrectNonPeriodicMesh 5ms 0.038% 62.97% 296ms 2.25% std::_Rb_tree::erase 0 0% 62.97% 296ms 2.25% std::set::erase (inline) 10ms 0.076% 63.05% 287ms 2.18% divconqrecurse 8ms 0.061% 63.11% 286ms 2.17% Node::RemoveElement 242ms 1.84% 64.95% 286ms 2.17% _int_free 0 0% 64.95% 285ms 2.16% std::_Vector_base::_M_allocate (inline) 124ms 0.94% 65.89% 277ms 2.10% std::_Rb_tree::_M_get_insert_unique_pos 72ms 0.55% 66.43% 267ms 2.03% mergehulls 0 0% 66.43% 264ms 2.00% std::_Rb_tree::_M_put_node (inline) 16ms 0.12% 66.56% 251ms 1.91% Element::ResetIndex 2ms 0.015% 66.57% 236ms 1.79% Cell::GetMutationState 8ms 0.061% 66.63% 220ms 1.67% boost::detail::shared_count::~shared_count (inline) 0 0% 66.63% 220ms 1.67% boost::shared_ptr::~shared_ptr (inline) 0 0% 66.63% 213ms 1.62% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 1ms 0.0076% 66.64% 210ms 1.59% NodeLocationWriter::Visit 204ms 1.55% 68.19% 205ms 1.56% boost::detail::sp_counted_base::release 4ms 0.03% 68.22% 205ms 1.56% std::vector::push_back (inline) 9ms 0.068% 68.29% 200ms 1.52% std::_Rb_tree::_Rb_tree (partial-inline) 5ms 0.038% 68.32% 199ms 1.51% AbstractCellPopulation::IsCellAttachedToLocationIndex 18ms 0.14% 68.46% 198ms 1.50% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 68.46% 198ms 1.50% AbstractCellPopulation::Iterator::operator++ (inline) 3ms 0.023% 68.48% 197ms 1.50% std::vector::_M_realloc_insert 3ms 0.023% 68.51% 196ms 1.49% alternateaxes 2ms 0.015% 68.52% 195ms 1.48% Cell::GetCellProliferativeType 89ms 0.68% 69.20% 195ms 1.48% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.015% 69.21% 195ms 1.48% std::set::set (inline) 6ms 0.046% 69.26% 194ms 1.47% std::num_put::_M_insert_float 3ms 0.023% 69.28% 193ms 1.47% LegacyCellProliferativeTypesWriter::VisitCell 182ms 1.38% 70.66% 193ms 1.47% vertexmedian 7ms 0.053% 70.72% 187ms 1.42% std::_Rb_tree::_M_erase_aux (inline) 1ms 0.0076% 70.72% 184ms 1.40% ApcOneHitCellMutationState::ApcOneHitCellMutationState 9ms 0.068% 70.79% 183ms 1.39% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 180ms 1.37% 72.16% 180ms 1.37% std::vector::operator[] (inline) 8ms 0.061% 72.22% 177ms 1.34% AbstractTetrahedralElement::CalculateJacobian 18ms 0.14% 72.35% 174ms 1.32% std::_Rb_tree::_M_copy (inline) 173ms 1.31% 73.67% 173ms 1.31% [libchaste_mesh.so] 0 0% 73.67% 172ms 1.31% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.015% 73.68% 172ms 1.31% std::__cxx11::collate::do_transform 0 0% 73.68% 168ms 1.28% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 1ms 0.0076% 73.69% 165ms 1.25% ___vsnprintf 1ms 0.0076% 73.70% 164ms 1.24% __vsnprintf_internal (inline) 19ms 0.14% 73.84% 162ms 1.23% __printf_buffer 3ms 0.023% 73.87% 157ms 1.19% AbstractCellPopulation::GetLocationIndexUsingCell 111ms 0.84% 74.71% 155ms 1.18% malloc_consolidate 66ms 0.5% 75.21% 155ms 1.18% std::_Rb_tree::_M_clone_node (inline) 25ms 0.19% 75.40% 154ms 1.17% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 5ms 0.038% 75.44% 152ms 1.15% AbstractTetrahedralElement::CalculateInverseJacobian 4ms 0.03% 75.47% 151ms 1.15% Element::MarkAsDeleted 36ms 0.27% 75.74% 149ms 1.13% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 1ms 0.0076% 75.75% 143ms 1.09% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 75.75% 143ms 1.09% MeshBasedCellPopulation::GetDampingConstant 4ms 0.03% 75.78% 142ms 1.08% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 75.78% 142ms 1.08% OffLatticeSimulation::ApplyBoundaries 39ms 0.3% 76.07% 135ms 1.02% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 1ms 0.0076% 76.08% 132ms 1.00% __printf_fp_spec (inline) 18ms 0.14% 76.22% 131ms 0.99% AbstractTetrahedralElement::RefreshJacobian 1ms 0.0076% 76.23% 131ms 0.99% __printf_fp_l_buffer 130ms 0.99% 77.21% 130ms 0.99% std::_Rb_tree_insert_and_rebalance 55ms 0.42% 77.63% 126ms 0.96% __printf_fp_buffer_1 121ms 0.92% 78.55% 121ms 0.92% incircle 22ms 0.17% 78.72% 115ms 0.87% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 2ms 0.015% 78.73% 113ms 0.86% TetrahedralMesh::Clear 1ms 0.0076% 78.74% 107ms 0.81% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 54ms 0.41% 79.15% 107ms 0.81% std::_Rb_tree::equal_range (inline) 3ms 0.023% 79.17% 104ms 0.79% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 6ms 0.046% 79.22% 103ms 0.78% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 1ms 0.0076% 79.22% 102ms 0.77% AbstractTetrahedralElement::AbstractTetrahedralElement 100ms 0.76% 79.98% 100ms 0.76% AbstractCellProperty::AbstractCellProperty 36ms 0.27% 80.26% 97ms 0.74% AbstractElement::GetNodeLocation 95ms 0.72% 80.98% 95ms 0.72% std::type_info::name (inline) 2ms 0.015% 80.99% 92ms 0.7% CellProliferativeTypesWriter::VisitCell 41ms 0.31% 81.30% 91ms 0.69% AbstractElement::GetNodeGlobalIndex 7ms 0.053% 81.36% 90ms 0.68% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 81.36% 89ms 0.68% AbstractCellBasedSimulation::DoCellRemoval (inline) 79ms 0.6% 81.96% 89ms 0.68% vertexsort 86ms 0.65% 82.61% 86ms 0.65% std::vector::size (inline) 86ms 0.65% 83.26% 86ms 0.65% unlink_chunk 5ms 0.038% 83.30% 85ms 0.65% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2ms 0.015% 83.32% 82ms 0.62% Cell::SetCellProliferativeType 2ms 0.015% 83.33% 81ms 0.61% boost::numeric::ublas::vector_assign (inline) 1ms 0.0076% 83.34% 79ms 0.6% std::_Rb_tree_const_iterator::operator++ (inline) 79ms 0.6% 83.94% 79ms 0.6% std::_Rb_tree_increment 0 0% 83.94% 77ms 0.58% CellPropertyCollection::HasProperty 77ms 0.58% 84.52% 77ms 0.58% std::_Rb_tree::_S_left (inline) 0 0% 84.52% 76ms 0.58% Cell::HasCellProperty (inline) 76ms 0.58% 85.10% 76ms 0.58% Node::GetIndex 44ms 0.33% 85.43% 76ms 0.58% TimeStepper::AdvanceOneTimeStep 0 0% 85.43% 76ms 0.58% tcache_get (inline) 76ms 0.58% 86.01% 76ms 0.58% tcache_get_n (inline) 5ms 0.038% 86.05% 73ms 0.55% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 5ms 0.038% 86.09% 73ms 0.55% Cylindrical2dMesh::CreateMirrorNodes 1ms 0.0076% 86.09% 73ms 0.55% std::_Rb_tree::_M_emplace_hint_unique 11ms 0.083% 86.18% 72ms 0.55% TetrahedralMesh::EdgesEnd 1ms 0.0076% 86.18% 71ms 0.54% Node::~Node 71ms 0.54% 86.72% 71ms 0.54% [libchaste_ode.so] 71ms 0.54% 87.26% 71ms 0.54% std::_Rb_tree_rebalance_for_erase 42ms 0.32% 87.58% 70ms 0.53% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 87.58% 70ms 0.53% std::_Rb_tree::_M_destroy_node (inline) 0 0% 87.58% 70ms 0.53% std::__new_allocator::destroy (inline) 0 0% 87.58% 70ms 0.53% std::allocator_traits::destroy (inline) 2ms 0.015% 87.60% 69ms 0.52% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 6ms 0.046% 87.64% 66ms 0.5% MeshBasedCellPopulation::SpringIterator::SpringIterator 66ms 0.5% 88.14% 66ms 0.5% counterclockwise 25ms 0.19% 88.33% 66ms 0.5% std::__ostream_insert