File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 9945ms, 78.28% of 12705ms total Dropped 841 nodes (cum <= 63.52ms) flat flat% sum% cum cum% 0 0% 0% 12665ms 99.69% __libc_start_call_main 0 0% 0% 12665ms 99.69% __libc_start_main_impl 0 0% 0% 12665ms 99.69% _start 0 0% 0% 12648ms 99.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 12648ms 99.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 12648ms 99.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 12648ms 99.55% main 0 0% 0% 12605ms 99.21% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 12605ms 99.21% CxxTest::TestRunner::runTest (inline) 0 0% 0% 12605ms 99.21% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.0079% 0.0079% 12584ms 99.05% AbstractCellBasedSimulation::Solve 0 0% 0.0079% 9145ms 71.98% AbstractCellBasedSimulation::UpdateCellPopulation 6ms 0.047% 0.055% 4979ms 39.19% AbstractCellBasedSimulation::DoCellBirth 20ms 0.16% 0.21% 4876ms 38.38% Cell::ReadyToDivide 10ms 0.079% 0.29% 4798ms 37.76% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.0079% 0.3% 4649ms 36.59% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 11ms 0.087% 0.39% 4635ms 36.48% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.031% 0.42% 4621ms 36.37% CellCycleModelOdeHandler::SolveOdeToTime 4ms 0.031% 0.45% 4481ms 35.27% CvodeAdaptor::Solve 55ms 0.43% 0.88% 4095ms 32.23% CVode 0 0% 0.88% 4066ms 32.00% MeshBasedCellPopulation::Update 38ms 0.3% 1.18% 3676ms 28.93% CVodeFree 0 0% 1.18% 3111ms 24.49% Cylindrical2dMesh::ReMesh 142ms 1.12% 2.30% 2866ms 22.56% cvRescale 3ms 0.024% 2.32% 2572ms 20.24% SUNNonlinSolSolve 46ms 0.36% 2.68% 2569ms 20.22% SUNNonlinSolSolve_Newton 46ms 0.36% 3.05% 2467ms 19.42% cvNlsInit 2ms 0.016% 3.06% 1873ms 14.74% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0079% 3.07% 1778ms 13.99% MutableMesh::ReMesh 1ms 0.0079% 3.08% 1622ms 12.77% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.063% 3.14% 1581ms 12.44% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 3.14% 1561ms 12.29% AbstractCellPopulation::WriteResultsToFiles 16ms 0.13% 3.27% 1466ms 11.54% cvLsSetup 686ms 5.40% 8.67% 1367ms 10.76% std::_Rb_tree::_M_lower_bound (inline) 138ms 1.09% 9.75% 1341ms 10.55% TetrahedralMesh::EdgeIterator::operator++ 9ms 0.071% 9.82% 1070ms 8.42% cvLsDQJtimes 62ms 0.49% 10.31% 1068ms 8.41% std::_Rb_tree::find (inline) 1ms 0.0079% 10.32% 930ms 7.32% MeshBasedCellPopulation::UpdateNodePairs 12ms 0.094% 10.41% 918ms 7.23% TetrahedralMesh::ImportFromMesher 3ms 0.024% 10.44% 888ms 6.99% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1ms 0.0079% 10.44% 819ms 6.45% MeshBasedCellPopulation::SpringIterator::operator++ 42ms 0.33% 10.78% 818ms 6.44% operator new 213ms 1.68% 12.45% 793ms 6.24% __GI___libc_malloc 11ms 0.087% 12.54% 781ms 6.15% std::set::insert (inline) 9ms 0.071% 12.61% 770ms 6.06% std::_Rb_tree::_M_insert_unique 25ms 0.2% 12.81% 720ms 5.67% std::__new_allocator::allocate (inline) 0 0% 12.81% 716ms 5.64% std::allocator_traits::allocate (inline) 0 0% 12.81% 662ms 5.21% std::set::count (inline) 1ms 0.0079% 12.81% 645ms 5.08% triangulate 1ms 0.0079% 12.82% 578ms 4.55% delaunay 2ms 0.016% 12.84% 577ms 4.54% divconqdelaunay 3ms 0.024% 12.86% 557ms 4.38% CellPopulationElementWriter::Visit 0 0% 12.86% 541ms 4.26% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 29ms 0.23% 13.09% 528ms 4.16% cvLsSolve 160ms 1.26% 14.35% 510ms 4.01% __dynamic_cast 289ms 2.27% 16.62% 503ms 3.96% _int_malloc 3ms 0.024% 16.65% 498ms 3.92% CellPropertyCollection::GetPropertiesType (inline) 60ms 0.47% 17.12% 494ms 3.89% std::map::operator[] (partial-inline) 144ms 1.13% 18.25% 482ms 3.79% cvRestore 27ms 0.21% 18.47% 481ms 3.79% std::_Rb_tree::_M_insert_ (inline) 480ms 3.78% 22.24% 480ms 3.78% N_VBufUnpack_Serial 0 0% 22.24% 478ms 3.76% std::_Rb_tree::_M_create_node (inline) 12ms 0.094% 22.34% 474ms 3.73% std::less::operator() (inline) 1ms 0.0079% 22.35% 463ms 3.64% AbstractTwoBodyInteractionForce::AddForceContribution 462ms 3.64% 25.98% 462ms 3.64% std::operator< (inline) 0 0% 25.98% 454ms 3.57% std::_Rb_tree::_M_get_node (inline) 146ms 1.15% 27.13% 443ms 3.49% __GI___libc_free 24ms 0.19% 27.32% 442ms 3.48% N_VWrmsNorm 7ms 0.055% 27.38% 441ms 3.47% Element::Element 0 0% 27.38% 439ms 3.46% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.016% 27.39% 436ms 3.43% MeshBasedCellPopulation::AcceptCellWriter 432ms 3.40% 30.79% 432ms 3.40% std::_Rb_tree::_S_right (inline) 8ms 0.063% 30.85% 429ms 3.38% SUNLinSolSolve 89ms 0.7% 31.55% 421ms 3.31% N_VLinearSum_Serial 27ms 0.21% 31.77% 421ms 3.31% SUNLinSolSolve_Dense 13ms 0.1% 31.87% 420ms 3.31% Cylindrical2dMesh::ReconstructCylindricalMesh 106ms 0.83% 32.70% 418ms 3.29% N_VWrmsNorm_Serial 10ms 0.079% 32.78% 410ms 3.23% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.0079% 32.79% 407ms 3.20% AbstractCellProperty::IsSubType (inline) 19ms 0.15% 32.94% 404ms 3.18% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 0 0% 32.94% 402ms 3.16% std::map::find (inline) 6ms 0.047% 32.99% 381ms 3.00% Element::RegisterWithNodes (inline) 1ms 0.0079% 32.99% 381ms 3.00% cvLsDQJac 0 0% 32.99% 381ms 3.00% std::_Rb_tree::lower_bound (inline) 0 0% 32.99% 381ms 3.00% std::map::lower_bound (inline) 47ms 0.37% 33.36% 378ms 2.98% cvLsDenseDQJac 1ms 0.0079% 33.37% 377ms 2.97% SUNLinSolSetup 13ms 0.1% 33.48% 377ms 2.97% SUNMatScaleAddI 8ms 0.063% 33.54% 376ms 2.96% SUNLinSolSetup_Dense 11ms 0.087% 33.62% 372ms 2.93% Node::AddElement 364ms 2.87% 36.49% 364ms 2.87% SUNMatScaleAddI_Dense 35ms 0.28% 36.77% 361ms 2.84% N_VLinearSum 0 0% 36.77% 358ms 2.82% std::ostream::operator<< (inline) 61ms 0.48% 37.25% 357ms 2.81% std::ostream::_M_insert 356ms 2.80% 40.05% 356ms 2.80% SUNDlsMat_denseGETRF 349ms 2.75% 42.79% 349ms 2.75% __strcmp_evex 6ms 0.047% 42.84% 344ms 2.71% MutableMesh::ReIndex 343ms 2.70% 45.54% 343ms 2.70% SUNDlsMat_denseGETRS 21ms 0.17% 45.71% 338ms 2.66% CvodeRhsAdaptor 6ms 0.047% 45.75% 324ms 2.55% Cylindrical2dMesh::CorrectNonPeriodicMesh 4ms 0.031% 45.79% 303ms 2.38% CvodeAdaptor::SetupCvode 239ms 1.88% 47.67% 295ms 2.32% _int_free 8ms 0.063% 47.73% 294ms 2.31% std::__new_allocator::deallocate (inline) 0 0% 47.73% 292ms 2.30% std::allocator_traits::deallocate (inline) 123ms 0.97% 48.70% 291ms 2.29% WntCellCycleOdeSystem::EvaluateYDerivatives 75ms 0.59% 49.29% 291ms 2.29% std::_Rb_tree::_M_erase 4ms 0.031% 49.32% 284ms 2.24% std::_Rb_tree::erase 1ms 0.0079% 49.33% 284ms 2.24% std::set::erase (inline) 12ms 0.094% 49.42% 283ms 2.23% divconqrecurse 1ms 0.0079% 49.43% 281ms 2.21% AbstractCellProperty::IsType (inline) 105ms 0.83% 50.26% 280ms 2.20% std::_Rb_tree::_M_get_insert_unique_pos 279ms 2.20% 52.45% 279ms 2.20% N_VWSqrSumLocal_Serial 10ms 0.079% 52.53% 279ms 2.20% Node::RemoveElement 0 0% 52.53% 266ms 2.09% std::_Rb_tree::_M_drop_node (inline) 15ms 0.12% 52.65% 266ms 2.09% std::_Rb_tree::~_Rb_tree (inline) 0 0% 52.65% 262ms 2.06% std::_Vector_base::_M_allocate (inline) 80ms 0.63% 53.28% 261ms 2.05% mergehulls 4ms 0.031% 53.31% 260ms 2.05% SUNMatCopy 241ms 1.90% 55.21% 256ms 2.01% SUNMatCopy_Dense 2ms 0.016% 55.22% 253ms 1.99% Cell::GetMutationState 0 0% 55.22% 252ms 1.98% Cell::GetCellProliferativeType 0 0% 55.22% 247ms 1.94% std::set::~set (inline) 5ms 0.039% 55.26% 245ms 1.93% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.016% 55.28% 243ms 1.91% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 55.28% 242ms 1.90% AbstractCellPopulation::Iterator::operator++ (inline) 35ms 0.28% 55.55% 240ms 1.89% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 55.55% 235ms 1.85% std::_Rb_tree::_M_put_node (inline) 114ms 0.9% 56.45% 232ms 1.83% __cxxabiv1::__si_class_type_info::__do_dyncast 10ms 0.079% 56.53% 226ms 1.78% std::_Rb_tree::_Rb_tree (partial-inline) 17ms 0.13% 56.66% 217ms 1.71% std::vector::push_back (inline) 13ms 0.1% 56.77% 216ms 1.70% Element::ResetIndex 2ms 0.016% 56.78% 210ms 1.65% NodeLocationWriter::Visit 45ms 0.35% 57.13% 207ms 1.63% AbstractCellProperty::IsSame 29ms 0.23% 57.36% 205ms 1.61% N_VScale 13ms 0.1% 57.47% 203ms 1.60% AbstractCellPopulation::IsCellAttachedToLocationIndex 6ms 0.047% 57.51% 201ms 1.58% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 0 0% 57.51% 200ms 1.57% std::set::set (inline) 47ms 0.37% 57.88% 195ms 1.53% N_VScale_Serial 13ms 0.1% 57.99% 190ms 1.50% std::num_put::_M_insert_float 8ms 0.063% 58.05% 190ms 1.50% std::vector::_M_realloc_insert 0 0% 58.05% 189ms 1.49% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.0079% 58.06% 186ms 1.46% alternateaxes 10ms 0.079% 58.13% 185ms 1.46% std::_Rb_tree::_M_erase_aux (inline) 171ms 1.35% 59.48% 185ms 1.46% vertexmedian 24ms 0.19% 59.67% 184ms 1.45% std::_Rb_tree::_M_copy (inline) 2ms 0.016% 59.69% 182ms 1.43% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 21ms 0.17% 59.85% 182ms 1.43% TetrahedralMesh::Clear 8ms 0.063% 59.91% 181ms 1.42% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 9ms 0.071% 59.98% 179ms 1.41% AbstractTetrahedralElement::CalculateJacobian 18ms 0.14% 60.13% 178ms 1.40% cvEwtSet 5ms 0.039% 60.17% 166ms 1.31% Element::MarkAsDeleted 4ms 0.031% 60.20% 164ms 1.29% std::__cxx11::collate::do_transform 24ms 0.19% 60.39% 162ms 1.28% std::type_info::operator== (inline) 8ms 0.063% 60.45% 158ms 1.24% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.0079% 60.46% 156ms 1.23% ___vsnprintf 1ms 0.0079% 60.46% 155ms 1.22% __vsnprintf_internal (inline) 1ms 0.0079% 60.47% 154ms 1.21% OffLatticeSimulation::ApplyBoundaries 43ms 0.34% 60.81% 154ms 1.21% std::_Rb_tree::_M_clone_node (inline) 23ms 0.18% 60.99% 152ms 1.20% __printf_buffer 1ms 0.0079% 61.00% 151ms 1.19% MeshBasedCellPopulation::GetDampingConstant 4ms 0.031% 61.03% 149ms 1.17% AbstractCentreBasedCellPopulation::GetDampingConstant 19ms 0.15% 61.18% 142ms 1.12% AbstractTetrahedralElement::RefreshJacobian 7ms 0.055% 61.24% 137ms 1.08% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.0079% 61.24% 134ms 1.05% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 11ms 0.087% 61.33% 130ms 1.02% CVodeSetLinearSolver 10ms 0.079% 61.41% 130ms 1.02% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 26ms 0.2% 61.61% 125ms 0.98% __printf_fp_l_buffer 0 0% 61.61% 125ms 0.98% __printf_fp_spec (inline) 1ms 0.0079% 61.62% 124ms 0.98% CellPropertyCollection::HasProperty 5ms 0.039% 61.66% 123ms 0.97% CellProliferativeTypesWriter::VisitCell 123ms 0.97% 62.63% 123ms 0.97% std::_Rb_tree_insert_and_rebalance 84ms 0.66% 63.29% 122ms 0.96% malloc_consolidate 121ms 0.95% 64.24% 121ms 0.95% unlink_chunk 0 0% 64.24% 120ms 0.94% Cell::HasCellProperty (inline) 8ms 0.063% 64.31% 120ms 0.94% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 13ms 0.1% 64.41% 117ms 0.92% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.0079% 64.42% 117ms 0.92% boost::numeric::ublas::vector_assign (inline) 86ms 0.68% 65.09% 116ms 0.91% AbstractElement::GetNodeGlobalIndex 116ms 0.91% 66.01% 116ms 0.91% Node::GetIndex 116ms 0.91% 66.92% 116ms 0.91% incircle 74ms 0.58% 67.50% 113ms 0.89% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 67.50% 112ms 0.88% AbstractCellBasedWriter::OpenOutputFileForAppend 25ms 0.2% 67.70% 111ms 0.87% N_VScaleAddMulti 10ms 0.079% 67.78% 111ms 0.87% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 67.78% 109ms 0.86% OutputFileHandler::OpenOutputFile 109ms 0.86% 68.63% 109ms 0.86% std::vector::size (inline) 1ms 0.0079% 68.64% 107ms 0.84% Cell::SetCellProliferativeType 39ms 0.31% 68.95% 105ms 0.83% AbstractElement::GetNodeLocation 4ms 0.031% 68.98% 101ms 0.79% Node::~Node 94ms 0.74% 69.72% 101ms 0.79% vertexsort 10ms 0.079% 69.80% 99ms 0.78% boost::detail::shared_count::~shared_count (inline) 0 0% 69.80% 99ms 0.78% boost::shared_ptr::~shared_ptr (inline) 72ms 0.57% 70.37% 99ms 0.78% std::_Rb_tree::equal_range (inline) 0 0% 70.37% 98ms 0.77% AbstractCellBasedSimulation::DoCellRemoval (inline) 10ms 0.079% 70.44% 98ms 0.77% SUNRpowerR 67ms 0.53% 70.97% 97ms 0.76% TetrahedralMesh::EdgeIterator::EdgeIterator 4ms 0.031% 71.00% 95ms 0.75% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 10ms 0.079% 71.08% 94ms 0.74% N_VCloneEmpty_Serial 3ms 0.024% 71.11% 93ms 0.73% MeshBasedCellPopulation::SpringsEnd (inline) 93ms 0.73% 71.84% 93ms 0.73% std::_Rb_tree_increment 6ms 0.047% 71.89% 91ms 0.72% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 71.89% 90ms 0.71% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 42ms 0.33% 72.22% 89ms 0.7% AbstractTetrahedralMesh::GetElement 41ms 0.32% 72.54% 89ms 0.7% __printf_fp_buffer_1 88ms 0.69% 73.23% 88ms 0.69% [libchaste_mesh.so] 12ms 0.094% 73.33% 88ms 0.69% __pow 25ms 0.2% 73.52% 88ms 0.69% boost::numeric::ublas::indexing_vector_assign 4ms 0.031% 73.55% 84ms 0.66% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 79ms 0.62% 74.18% 84ms 0.66% boost::detail::sp_counted_base::release 25ms 0.2% 74.37% 78ms 0.61% std::__ostream_insert 15ms 0.12% 74.49% 78ms 0.61% std::num_put::_M_insert_int 0 0% 74.49% 78ms 0.61% std::vector::_M_default_append 0 0% 74.49% 78ms 0.61% std::vector::resize (inline) 77ms 0.61% 75.10% 77ms 0.61% Node::rGetLocation 8ms 0.063% 75.16% 76ms 0.6% __ieee754_pow_fma 6ms 0.047% 75.21% 72ms 0.57% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 75.21% 72ms 0.57% tcache_get (inline) 72ms 0.57% 75.77% 72ms 0.57% tcache_get_n (inline) 0 0% 75.77% 71ms 0.56% NodeMap::NodeMap 4ms 0.031% 75.80% 70ms 0.55% Cylindrical2dMesh::CreateMirrorNodes 70ms 0.55% 76.36% 70ms 0.55% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 3ms 0.024% 76.38% 69ms 0.54% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 5ms 0.039% 76.42% 69ms 0.54% TetrahedralMesh::EdgeIterator::GetNodeA 52ms 0.41% 76.83% 68ms 0.54% boost::numeric::ublas::c_matrix::operator() 68ms 0.54% 77.36% 68ms 0.54% std::_Rb_tree_rebalance_for_erase 66ms 0.52% 77.88% 66ms 0.52% [libchaste_cell_based.so] 11ms 0.087% 77.97% 66ms 0.52% std::_Vector_base::_M_deallocate (inline) 5ms 0.039% 78.01% 65ms 0.51% N_VMake_Serial 33ms 0.26% 78.27% 65ms 0.51% boost::shared_ptr::shared_ptr (inline) 1ms 0.0079% 78.28% 65ms 0.51% std::operator<< (inline)