File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 12687ms, 84.27% of 15055ms total Dropped 739 nodes (cum <= 75.28ms) flat flat% sum% cum cum% 0 0% 0% 15013ms 99.72% __libc_start_call_main 0 0% 0% 15013ms 99.72% __libc_start_main_impl 0 0% 0% 15013ms 99.72% _start 0 0% 0% 14996ms 99.61% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 14996ms 99.61% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 14996ms 99.61% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 14996ms 99.61% main 0 0% 0% 14953ms 99.32% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 14953ms 99.32% CxxTest::TestRunner::runTest (inline) 0 0% 0% 14953ms 99.32% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 14933ms 99.19% AbstractCellBasedSimulation::Solve 0 0% 0% 11492ms 76.33% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0066% 0.0066% 7372ms 48.97% AbstractCellBasedSimulation::DoCellBirth 6ms 0.04% 0.046% 7308ms 48.54% Cell::ReadyToDivide 3ms 0.02% 0.066% 7224ms 47.98% AbstractPhaseBasedCellCycleModel::ReadyToDivide 6ms 0.04% 0.11% 7118ms 47.28% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.053% 0.16% 7103ms 47.18% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.02% 0.18% 7095ms 47.13% CellCycleModelOdeHandler::SolveOdeToTime 52ms 0.35% 0.52% 6978ms 46.35% AbstractOneStepIvpOdeSolver::InternalSolve 804ms 5.34% 5.87% 6297ms 41.83% RungeKutta4IvpOdeSolver::CalculateNextYValue 1910ms 12.69% 18.55% 5344ms 35.50% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 18.55% 4043ms 26.85% MeshBasedCellPopulation::Update 61ms 0.41% 18.96% 3452ms 22.93% AbstractCellProperty::IsType (inline) 5ms 0.033% 18.99% 3108ms 20.64% Cylindrical2dMesh::ReMesh 398ms 2.64% 21.63% 2353ms 15.63% AbstractCellProperty::IsSame 249ms 1.65% 23.29% 1955ms 12.99% std::type_info::operator== (inline) 1ms 0.0066% 23.29% 1912ms 12.70% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 23.29% 1735ms 11.52% MutableMesh::ReMesh 1708ms 11.35% 34.64% 1708ms 11.35% __strcmp_evex 0 0% 34.64% 1686ms 11.20% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.033% 34.67% 1649ms 10.95% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 34.67% 1525ms 10.13% AbstractCellPopulation::WriteResultsToFiles 643ms 4.27% 38.94% 1372ms 9.11% std::_Rb_tree::_M_lower_bound (inline) 119ms 0.79% 39.73% 1270ms 8.44% TetrahedralMesh::EdgeIterator::operator++ 62ms 0.41% 40.15% 1042ms 6.92% std::_Rb_tree::find (inline) 1ms 0.0066% 40.15% 906ms 6.02% MeshBasedCellPopulation::UpdateNodePairs 8ms 0.053% 40.21% 881ms 5.85% TetrahedralMesh::ImportFromMesher 3ms 0.02% 40.23% 869ms 5.77% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 36ms 0.24% 40.46% 813ms 5.40% operator new 10ms 0.066% 40.53% 778ms 5.17% MeshBasedCellPopulation::SpringIterator::operator++ 190ms 1.26% 41.79% 763ms 5.07% __GI___libc_malloc 5ms 0.033% 41.83% 756ms 5.02% std::set::insert (inline) 14ms 0.093% 41.92% 751ms 4.99% std::_Rb_tree::_M_insert_unique 24ms 0.16% 42.08% 719ms 4.78% std::__new_allocator::allocate (inline) 0 0% 42.08% 718ms 4.77% std::allocator_traits::allocate (inline) 0 0% 42.08% 649ms 4.31% triangulate 0 0% 42.08% 630ms 4.18% std::set::count (inline) 0 0% 42.08% 598ms 3.97% delaunay 3ms 0.02% 42.10% 598ms 3.97% divconqdelaunay 542ms 3.60% 45.70% 543ms 3.61% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 45.70% 541ms 3.59% AbstractTwoBodyInteractionForce::AddForceContribution 45ms 0.3% 46.00% 536ms 3.56% std::map::operator[] (partial-inline) 7ms 0.046% 46.04% 530ms 3.52% CellPopulationElementWriter::Visit 4ms 0.027% 46.07% 514ms 3.41% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 266ms 1.77% 47.84% 502ms 3.33% _int_malloc 477ms 3.17% 51.01% 477ms 3.17% std::_Rb_tree::_S_right (inline) 124ms 0.82% 51.83% 476ms 3.16% __dynamic_cast 15ms 0.1% 51.93% 472ms 3.14% AbstractCellPopulation::GetCellUsingLocationIndex 7ms 0.046% 51.98% 472ms 3.14% std::less::operator() (inline) 465ms 3.09% 55.06% 465ms 3.09% std::operator< (inline) 18ms 0.12% 55.18% 460ms 3.06% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 0 0% 55.18% 460ms 3.06% std::_Rb_tree::_M_create_node (inline) 27ms 0.18% 55.36% 450ms 2.99% std::_Rb_tree::_M_insert_ (inline) 4ms 0.027% 55.39% 447ms 2.97% Element::Element 0 0% 55.39% 444ms 2.95% std::_Rb_tree::_M_get_node (inline) 13ms 0.086% 55.48% 425ms 2.82% Cylindrical2dMesh::ReconstructCylindricalMesh 2ms 0.013% 55.49% 424ms 2.82% CellPropertyCollection::GetPropertiesType (inline) 0 0% 55.49% 423ms 2.81% std::_Rb_tree::lower_bound (inline) 0 0% 55.49% 423ms 2.81% std::map::lower_bound (inline) 0 0% 55.49% 416ms 2.76% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 55.49% 410ms 2.72% std::map::find (inline) 6ms 0.04% 55.53% 402ms 2.67% MeshBasedCellPopulation::AcceptCellWriter 0 0% 55.53% 399ms 2.65% std::ostream::operator<< (inline) 55ms 0.37% 55.90% 398ms 2.64% std::ostream::_M_insert 13ms 0.086% 55.98% 377ms 2.50% Element::RegisterWithNodes (inline) 9ms 0.06% 56.04% 365ms 2.42% Node::AddElement 247ms 1.64% 57.68% 356ms 2.36% AbstractCellMutationState::AbstractCellMutationState 2ms 0.013% 57.70% 353ms 2.34% AbstractCellProperty::IsSubType (inline) 2ms 0.013% 57.71% 345ms 2.29% MutableMesh::ReIndex 105ms 0.7% 58.41% 344ms 2.28% __GI___libc_free 10ms 0.066% 58.47% 326ms 2.17% Cylindrical2dMesh::CorrectNonPeriodicMesh 13ms 0.086% 58.56% 297ms 1.97% std::__new_allocator::deallocate (inline) 0 0% 58.56% 295ms 1.96% std::allocator_traits::deallocate (inline) 112ms 0.74% 59.30% 288ms 1.91% std::_Rb_tree::_M_get_insert_unique_pos 62ms 0.41% 59.71% 287ms 1.91% std::_Rb_tree::_M_erase 1ms 0.0066% 59.72% 275ms 1.83% std::_Vector_base::_M_allocate (inline) 1ms 0.0066% 59.73% 268ms 1.78% NodeLocationWriter::Visit 4ms 0.027% 59.75% 266ms 1.77% std::_Rb_tree::erase 1ms 0.0066% 59.76% 266ms 1.77% std::set::erase (inline) 0 0% 59.76% 265ms 1.76% std::_Rb_tree::_M_drop_node (inline) 9ms 0.06% 59.82% 264ms 1.75% Node::RemoveElement 13ms 0.086% 59.91% 264ms 1.75% divconqrecurse 22ms 0.15% 60.05% 260ms 1.73% std::_Rb_tree::~_Rb_tree (inline) 254ms 1.69% 61.74% 254ms 1.69% [libchaste_cell_based.so] 0 0% 61.74% 247ms 1.64% std::set::~set (inline) 67ms 0.45% 62.19% 244ms 1.62% mergehulls 0 0% 62.19% 241ms 1.60% std::_Rb_tree::_M_put_node (inline) 2ms 0.013% 62.20% 238ms 1.58% Cell::GetMutationState 131ms 0.87% 63.07% 238ms 1.58% __cxxabiv1::__si_class_type_info::__do_dyncast 189ms 1.26% 64.32% 237ms 1.57% _int_free 16ms 0.11% 64.43% 235ms 1.56% std::num_put::_M_insert_float 24ms 0.16% 64.59% 225ms 1.49% Element::ResetIndex 2ms 0.013% 64.60% 224ms 1.49% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.0066% 64.61% 224ms 1.49% alternateaxes 203ms 1.35% 65.96% 221ms 1.47% vertexmedian 9ms 0.06% 66.02% 215ms 1.43% std::_Rb_tree::_Rb_tree (partial-inline) 212ms 1.41% 67.43% 214ms 1.42% std::vector::operator[] (inline) 13ms 0.086% 67.51% 205ms 1.36% AbstractTetrahedralElement::CalculateJacobian 4ms 0.027% 67.54% 205ms 1.36% LegacyCellProliferativeTypesWriter::VisitCell 5ms 0.033% 67.57% 203ms 1.35% Cell::GetCellProliferativeType 1ms 0.0066% 67.58% 199ms 1.32% std::set::set (inline) 1ms 0.0066% 67.59% 198ms 1.32% AbstractCellPopulation::Iterator::operator++ (inline) 9ms 0.06% 67.65% 198ms 1.32% std::vector::push_back (inline) 27ms 0.18% 67.82% 197ms 1.31% AbstractCellPopulation::Iterator::IsRealCell (inline) 81ms 0.54% 68.36% 194ms 1.29% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 5ms 0.033% 68.40% 194ms 1.29% std::__cxx11::collate::do_transform 193ms 1.28% 69.68% 193ms 1.28% std::type_info::name (inline) 42ms 0.28% 69.96% 192ms 1.28% ApcOneHitCellMutationState::ApcOneHitCellMutationState 1ms 0.0066% 69.96% 192ms 1.28% TetrahedralMesh::RefreshJacobianCachedData 5ms 0.033% 70.00% 187ms 1.24% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 5ms 0.033% 70.03% 184ms 1.22% AbstractCellPopulation::IsCellAttachedToLocationIndex 62ms 0.41% 70.44% 184ms 1.22% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 0 0% 70.44% 184ms 1.22% ___vsnprintf 0 0% 70.44% 184ms 1.22% __vsnprintf_internal (inline) 17ms 0.11% 70.55% 183ms 1.22% __printf_buffer 31ms 0.21% 70.76% 183ms 1.22% std::_Rb_tree::_M_copy (inline) 1ms 0.0066% 70.77% 182ms 1.21% MeshBasedCellPopulation::GetDampingConstant 11ms 0.073% 70.84% 182ms 1.21% std::vector::_M_realloc_insert 2ms 0.013% 70.85% 180ms 1.20% AbstractCentreBasedCellPopulation::GetDampingConstant 14ms 0.093% 70.95% 180ms 1.20% std::_Rb_tree::_M_erase_aux (inline) 12ms 0.08% 71.03% 171ms 1.14% AbstractTetrahedralElement::CalculateInverseJacobian 7ms 0.046% 71.07% 170ms 1.13% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 14ms 0.093% 71.17% 165ms 1.10% Element::MarkAsDeleted 10ms 0.066% 71.23% 158ms 1.05% TetrahedralMesh::Clear 4ms 0.027% 71.26% 157ms 1.04% __printf_fp_l_buffer 0 0% 71.26% 157ms 1.04% __printf_fp_spec (inline) 21ms 0.14% 71.40% 155ms 1.03% AbstractTetrahedralElement::RefreshJacobian 6ms 0.04% 71.44% 153ms 1.02% AbstractTetrahedralElement::AbstractTetrahedralElement 111ms 0.74% 72.18% 151ms 1.00% malloc_consolidate 1ms 0.0066% 72.18% 150ms 1% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 51ms 0.34% 72.52% 148ms 0.98% std::_Rb_tree::_M_clone_node (inline) 107ms 0.71% 73.23% 146ms 0.97% AbstractElement::GetNodeGlobalIndex 0 0% 73.23% 144ms 0.96% OffLatticeSimulation::ApplyBoundaries 59ms 0.39% 73.62% 143ms 0.95% __printf_fp_buffer_1 3ms 0.02% 73.64% 137ms 0.91% CellPropertyCollection::HasProperty 0 0% 73.64% 135ms 0.9% Cell::HasCellProperty (inline) 5ms 0.033% 73.68% 135ms 0.9% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 124ms 0.82% 74.50% 124ms 0.82% [libchaste_crypt.so] 58ms 0.39% 74.89% 121ms 0.8% AbstractElement::GetNodeLocation 117ms 0.78% 75.66% 117ms 0.78% Node::GetIndex 116ms 0.77% 76.43% 116ms 0.77% incircle 0 0% 76.43% 114ms 0.76% boost::numeric::ublas::vector_assign (inline) 112ms 0.74% 77.18% 112ms 0.74% AbstractCellMutationState::~AbstractCellMutationState 33ms 0.22% 77.40% 112ms 0.74% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 4ms 0.027% 77.42% 112ms 0.74% CellProliferativeTypesWriter::VisitCell 25ms 0.17% 77.59% 111ms 0.74% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 111ms 0.74% 78.33% 111ms 0.74% std::vector::size (inline) 4ms 0.027% 78.35% 109ms 0.72% MeshBasedCellPopulation::SpringsEnd (inline) 109ms 0.72% 79.08% 109ms 0.72% std::_Rb_tree_insert_and_rebalance 106ms 0.7% 79.78% 106ms 0.7% unlink_chunk 32ms 0.21% 79.99% 104ms 0.69% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 20ms 0.13% 80.13% 101ms 0.67% TetrahedralMesh::EdgesEnd (partial-inline) 93ms 0.62% 80.74% 101ms 0.67% vertexsort 1ms 0.0066% 80.75% 100ms 0.66% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 80.75% 100ms 0.66% OutputFileHandler::OpenOutputFile 0 0% 80.75% 100ms 0.66% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 58ms 0.39% 81.14% 97ms 0.64% Cylindrical2dMesh::GetVectorFromAtoB 12ms 0.08% 81.22% 95ms 0.63% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 7ms 0.046% 81.26% 94ms 0.62% Node::~Node 32ms 0.21% 81.47% 94ms 0.62% boost::numeric::ublas::indexing_vector_assign 8ms 0.053% 81.53% 93ms 0.62% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 81.53% 90ms 0.6% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 61ms 0.41% 81.93% 88ms 0.58% std::_Rb_tree::equal_range (inline) 13ms 0.086% 82.02% 86ms 0.57% MeshBasedCellPopulation::SpringIterator::SpringIterator 1ms 0.0066% 82.03% 85ms 0.56% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 2ms 0.013% 82.04% 84ms 0.56% Cell::SetCellProliferativeType 0 0% 82.04% 83ms 0.55% std::vector::_M_default_append 0 0% 82.04% 83ms 0.55% std::vector::resize (inline) 50ms 0.33% 82.37% 82ms 0.54% TimeStepper::AdvanceOneTimeStep 82ms 0.54% 82.92% 82ms 0.54% std::_Rb_tree_increment 60ms 0.4% 83.31% 81ms 0.54% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 83.31% 79ms 0.52% NodeMap::NodeMap 12ms 0.08% 83.39% 78ms 0.52% boost::detail::shared_count::~shared_count (inline) 0 0% 83.39% 78ms 0.52% boost::shared_ptr::~shared_ptr (inline) 0 0% 83.39% 77ms 0.51% AbstractCellBasedSimulation::DoCellRemoval (inline) 32ms 0.21% 83.61% 77ms 0.51% AbstractTetrahedralMesh::GetElement 3ms 0.02% 83.63% 77ms 0.51% Cylindrical2dMesh::CreateMirrorNodes 1ms 0.0066% 83.63% 77ms 0.51% std::_Rb_tree_const_iterator::operator++ (inline) 77ms 0.51% 84.14% 77ms 0.51% std::_Rb_tree_rebalance_for_erase 19ms 0.13% 84.27% 77ms 0.51% std::__ostream_insert