File: Test2dVertexBasedSimulationWithFreeBoundary Type: cpu Showing nodes accounting for 42702ms, 87.07% of 49042ms total Dropped 1149 nodes (cum <= 245.21ms) flat flat% sum% cum cum% 0 0% 0% 47212ms 96.27% __libc_start_call_main 0 0% 0% 47212ms 96.27% __libc_start_main_impl 0 0% 0% 47212ms 96.27% _start 0 0% 0% 47198ms 96.24% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 47198ms 96.24% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 47198ms 96.24% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 47198ms 96.24% main 0 0% 0% 47161ms 96.16% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 47161ms 96.16% CxxTest::TestRunner::runTest (inline) 0 0% 0% 47161ms 96.16% Test2DVertexSimulationWithFreeBoundary::Test2DFreeBoundaryVertexSimulationForProfiling 3ms 0.0061% 0.0061% 45501ms 92.78% AbstractCellBasedSimulation::Solve 8ms 0.016% 0.022% 20205ms 41.20% OffLatticeSimulation::UpdateCellLocationsAndTopology 6ms 0.012% 0.035% 19559ms 39.88% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.018% 0.053% 19185ms 39.12% AbstractNumericalMethod::ComputeForcesIncludingDamping 159ms 0.32% 0.38% 14907ms 30.40% FarhadifarForce::AddForceContribution 1ms 0.002% 0.38% 13520ms 27.57% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.38% 12557ms 25.60% VertexBasedCellPopulation::Update 0 0% 0.38% 12513ms 25.51% MutableVertexMesh::ReMesh 0 0% 0.38% 10861ms 22.15% AbstractCellPopulation::WriteResultsToFiles 217ms 0.44% 0.82% 7651ms 15.60% MutableVertexMesh::CheckForIntersections 287ms 0.59% 1.41% 6784ms 13.83% boost::numeric::ublas::c_vector::c_vector (partial-inline) 151ms 0.31% 1.71% 6050ms 12.34% FarhadifarForce::GetLineTensionParameter 184ms 0.38% 2.09% 5953ms 12.14% boost::numeric::ublas::vector_assign (inline) 401ms 0.82% 2.91% 5731ms 11.69% VertexMesh::GetVectorFromAtoB 67ms 0.14% 3.04% 5501ms 11.22% CellPropertyCollection::GetPropertiesType (inline) 0 0% 3.04% 4982ms 10.16% VertexBasedCellPopulation::WriteVtkResultsToFile 1407ms 2.87% 5.91% 4803ms 9.79% boost::numeric::ublas::indexing_vector_assign 14ms 0.029% 5.94% 4781ms 9.75% VertexBasedCellPopulation::WriteCellVtkResultsToFile 34ms 0.069% 6.01% 4503ms 9.18% AbstractCellProperty::IsSubType (inline) 1047ms 2.13% 8.15% 4464ms 9.10% __dynamic_cast 24ms 0.049% 8.20% 4095ms 8.35% VertexBasedCellPopulation::GetDampingConstant 597ms 1.22% 9.41% 4012ms 8.18% std::_Rb_tree::_M_erase 603ms 1.23% 10.64% 3958ms 8.07% VertexMesh::ElementIncludesPoint 388ms 0.79% 11.43% 3914ms 7.98% std::__new_allocator::allocate (inline) 0 0% 11.43% 3840ms 7.83% std::_Rb_tree::_M_create_node (inline) 0 0% 11.43% 3796ms 7.74% std::allocator_traits::allocate (inline) 337ms 0.69% 12.12% 3679ms 7.50% operator new 0 0% 12.12% 3591ms 7.32% std::_Rb_tree::_M_get_node (inline) 145ms 0.3% 12.42% 3570ms 7.28% std::_Rb_tree::~_Rb_tree (inline) 0 0% 12.42% 3503ms 7.14% std::_Rb_tree::_M_drop_node (inline) 0 0% 12.42% 3413ms 6.96% std::set::~set (inline) 147ms 0.3% 12.72% 3387ms 6.91% std::__new_allocator::deallocate (inline) 0 0% 12.72% 3374ms 6.88% std::allocator_traits::deallocate (inline) 0 0% 12.72% 3332ms 6.79% std::_Rb_tree::_M_put_node (inline) 0 0% 12.72% 3321ms 6.77% std::_Rb_tree::_Alloc_node::operator() (inline) 1267ms 2.58% 15.30% 3267ms 6.66% __GI___libc_malloc 36ms 0.073% 15.37% 3114ms 6.35% Cell::GetMutationState 1222ms 2.49% 17.86% 3099ms 6.32% __GI___libc_free 389ms 0.79% 18.66% 3055ms 6.23% AbstractMesh::GetVectorFromAtoB 9ms 0.018% 18.68% 3040ms 6.20% MutableVertexMesh::RemoveDeletedNodesAndElements 222ms 0.45% 19.13% 2871ms 5.85% std::map::operator[] (partial-inline) 62ms 0.13% 19.25% 2833ms 5.78% std::_Rb_tree::_Rb_tree (partial-inline) 144ms 0.29% 19.55% 2797ms 5.70% VertexMesh::GetNextEdgeGradientOfElementAtNode 15ms 0.031% 19.58% 2687ms 5.48% std::set::set (inline) 2653ms 5.41% 24.99% 2653ms 5.41% __strcmp_avx2 313ms 0.64% 25.63% 2637ms 5.38% std::_Rb_tree::_M_copy (inline) 148ms 0.3% 25.93% 2455ms 5.01% boost::numeric::ublas::c_vector::operator= (inline) 11ms 0.022% 25.95% 2429ms 4.95% MutableVertexMesh::RemoveDeletedNodes 1149ms 2.34% 28.29% 2391ms 4.88% __cxxabiv1::__si_class_type_info::__do_dyncast 24ms 0.049% 28.34% 2348ms 4.79% EdgeHelper::RemoveDeletedEdges 0 0% 28.34% 2334ms 4.76% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 28.34% 2334ms 4.76% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 2199ms 4.48% 32.83% 2199ms 4.48% __memcpy_avx_unaligned_erms 11ms 0.022% 32.85% 2187ms 4.46% EdgeHelper::UpdateEdgesMapKey 233ms 0.48% 33.32% 2170ms 4.42% std::_Rb_tree::_M_clone_node (inline) 584ms 1.19% 34.52% 2169ms 4.42% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 71ms 0.14% 34.66% 2160ms 4.40% std::__copy_move::__copy_m (inline) 0 0% 34.66% 2160ms 4.40% std::__copy_move_a (inline) 0 0% 34.66% 2160ms 4.40% std::__copy_move_a1 (inline) 0 0% 34.66% 2160ms 4.40% std::__copy_move_a2 (inline) 0 0% 34.66% 2160ms 4.40% std::copy (inline) 11ms 0.022% 34.68% 2117ms 4.32% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 34.68% 2104ms 4.29% std::set::insert (inline) 1003ms 2.05% 36.73% 2095ms 4.27% std::_Rb_tree::_M_lower_bound (inline) 0 0% 36.73% 2027ms 4.13% VertexMeshWriter::WriteVtkUsingMesh 2013ms 4.10% 40.83% 2013ms 4.10% boost::numeric::ublas::same_impl_ex 1943ms 3.96% 44.79% 1943ms 3.96% boost::numeric::ublas::c_vector::operator() 0 0% 44.79% 1914ms 3.90% boost::numeric::ublas::norm_2 (inline) 80ms 0.16% 44.96% 1893ms 3.86% AbstractCellPopulation::GetCellUsingLocationIndex 1522ms 3.10% 48.06% 1888ms 3.85% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1747ms 3.56% 51.62% 1873ms 3.82% _int_free 9ms 0.018% 51.64% 1863ms 3.80% Cell::GetCellProliferativeType 81ms 0.17% 51.81% 1852ms 3.78% MutableElement::ResetIndex 3ms 0.0061% 51.81% 1836ms 3.74% tbb::detail::r1::parallel_pipeline 24ms 0.049% 51.86% 1831ms 3.73% std::set_intersection (inline) 119ms 0.24% 52.10% 1807ms 3.68% std::__set_intersection 198ms 0.4% 52.51% 1805ms 3.68% std::_Rb_tree::_M_insert_ (inline) 0 0% 52.51% 1795ms 3.66% clone3 0 0% 52.51% 1795ms 3.66% start_thread 0 0% 52.51% 1795ms 3.66% std::_Rb_tree::lower_bound (inline) 0 0% 52.51% 1795ms 3.66% std::map::lower_bound (inline) 18ms 0.037% 52.54% 1788ms 3.65% VertexBasedCellPopulation::AcceptCellWriter 2ms 0.0041% 52.55% 1784ms 3.64% tbb::detail::r1::reset 736ms 1.50% 54.05% 1722ms 3.51% tbb::detail::r1::wait_bounded_queue_monitor 0 0% 54.05% 1656ms 3.38% VoronoiVertexMeshGenerator::GenerateVoronoiMesh 0 0% 54.05% 1656ms 3.38% VoronoiVertexMeshGenerator::VoronoiVertexMeshGenerator 12ms 0.024% 54.07% 1651ms 3.37% CellPopulationElementWriter::Visit 864ms 1.76% 55.84% 1649ms 3.36% VoronoiVertexMeshGenerator::CreateVoronoiTessellation 0 0% 55.84% 1497ms 3.05% vtkStreamingDemandDrivenPipeline::Update 0 0% 55.84% 1497ms 3.05% vtkXMLWriterBase::Write 0 0% 55.84% 1472ms 3.00% vtkDemandDrivenPipeline::ProcessRequest 2ms 0.0041% 55.84% 1461ms 2.98% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 55.84% 1445ms 2.95% vtkDemandDrivenPipeline::ExecuteData 0 0% 55.84% 1444ms 2.94% vtkExecutive::CallAlgorithm 0 0% 55.84% 1437ms 2.93% vtkCompositeDataPipeline::ExecuteData 0 0% 55.84% 1436ms 2.93% vtkXMLUnstructuredDataWriter::ProcessRequest 157ms 0.32% 56.16% 1383ms 2.82% boost::numeric::ublas::vector_binary::size (inline) 0 0% 56.16% 1363ms 2.78% std::insert_iterator::operator= (inline) 1028ms 2.10% 58.26% 1362ms 2.78% _int_malloc 7ms 0.014% 58.27% 1327ms 2.71% NodeLocationWriter::VisitAnyPopulation 0 0% 58.27% 1264ms 2.58% AbstractCellBasedWriter::WriteDoubleAndSpace (inline) 0 0% 58.27% 1208ms 2.46% boost::numeric::ublas::c_vector::assign (inline) 2ms 0.0041% 58.27% 1200ms 2.45% std::_Rb_tree::_M_insert_unique_ (inline) 2ms 0.0041% 58.28% 1195ms 2.44% LegacyCellProliferativeTypesWriter::VisitCell 19ms 0.039% 58.32% 1193ms 2.43% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 21ms 0.043% 58.36% 1168ms 2.38% std::_Rb_tree::erase 26ms 0.053% 58.41% 1131ms 2.31% AbstractCellProperty::IsType (inline) 12ms 0.024% 58.44% 1112ms 2.27% Cell::GetCellData 26ms 0.053% 58.49% 1093ms 2.23% CellPropertyCollection::HasProperty 4ms 0.0082% 58.50% 1088ms 2.22% AbstractCellBasedWriter::WriteDouble (inline) 0 0% 58.50% 1079ms 2.20% Cell::HasCellProperty (inline) 0 0% 58.50% 1002ms 2.04% boost::numeric::ublas::c_vector::operator-= (inline) 968ms 1.97% 60.47% 968ms 1.97% __GI_sched_yield 174ms 0.35% 60.83% 933ms 1.90% std::_Rb_tree_const_iterator::operator++ (inline) 914ms 1.86% 62.69% 914ms 1.86% std::_Rb_tree::_S_right (inline) 4ms 0.0082% 62.70% 907ms 1.85% std::_Rb_tree::_M_insert_unique (inline) 8ms 0.016% 62.72% 900ms 1.84% AbstractTargetAreaModifier::UpdateTargetAreas 1ms 0.002% 62.72% 883ms 1.80% TargetAreaLinearGrowthModifier::UpdateTargetAreaOfCell 7ms 0.014% 62.73% 876ms 1.79% AbstractCellPopulation::Iterator::operator++ (inline) 835ms 1.70% 64.43% 868ms 1.77% std::from_chars 232ms 0.47% 64.91% 868ms 1.77% std::ostream::_M_insert 57ms 0.12% 65.02% 866ms 1.77% AbstractCellPopulation::Iterator::IsRealCell (inline) 3ms 0.0061% 65.03% 861ms 1.76% std::ostream::operator<< (inline) 194ms 0.4% 65.43% 850ms 1.73% AbstractElement::GetNodeLocation 13ms 0.027% 65.45% 834ms 1.70% std::_Rb_tree::_M_emplace_hint_unique 134ms 0.27% 65.73% 816ms 1.66% AbstractCellProperty::IsSame 0 0% 65.73% 816ms 1.66% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 143ms 0.29% 66.02% 775ms 1.58% VertexMesh::GetAreaGradientOfElementAtNode 171ms 0.35% 66.37% 769ms 1.57% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 66.37% 759ms 1.55% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 66.37% 759ms 1.55% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 57ms 0.12% 66.48% 743ms 1.52% boost::numeric::ublas::vector_reference::operator() (inline) 66ms 0.13% 66.62% 740ms 1.51% VertexMesh::GetVolumeOfElement 423ms 0.86% 67.48% 740ms 1.51% std::_Rb_tree::equal_range (inline) 14ms 0.029% 67.51% 710ms 1.45% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 67.51% 710ms 1.45% boost::numeric::ublas::vector_binary::operator() (inline) 703ms 1.43% 68.94% 703ms 1.43% std::_Rb_tree_increment 227ms 0.46% 69.40% 703ms 1.43% std::basic_filebuf::xsputn 144ms 0.29% 69.70% 682ms 1.39% std::type_info::operator== (inline) 230ms 0.47% 70.17% 639ms 1.30% std::__ostream_insert 1ms 0.002% 70.17% 610ms 1.24% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 70.17% 589ms 1.20% std::_Rb_tree::clear (inline) 10ms 0.02% 70.19% 580ms 1.18% AbstractCellBasedSimulation::DoCellBirth 580ms 1.18% 71.37% 580ms 1.18% Node::rGetLocation 0 0% 71.37% 579ms 1.18% tcache_get (inline) 579ms 1.18% 72.55% 579ms 1.18% tcache_get_n (inline) 0 0% 72.55% 572ms 1.17% std::map::clear (inline) 19ms 0.039% 72.59% 563ms 1.15% Node::RemoveElement 35ms 0.071% 72.66% 559ms 1.14% MutableVertexMesh::CheckForSwapsFromShortEdges 37ms 0.075% 72.74% 556ms 1.13% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 555ms 1.13% 73.87% 555ms 1.13% [libchaste_mesh.so] 8ms 0.016% 73.89% 547ms 1.12% std::set::erase (inline) 12ms 0.024% 73.91% 546ms 1.11% AbstractCellPopulation::GetLocationIndexUsingCell 11ms 0.022% 73.93% 532ms 1.08% VertexMesh::GetSurfaceAreaOfElement 0 0% 73.93% 519ms 1.06% std::_Rb_tree::_Auto_node::_Auto_node (inline) 23ms 0.047% 73.98% 518ms 1.06% std::less::operator() (inline) 134ms 0.27% 74.25% 518ms 1.06% std::num_put::_M_insert_int 104ms 0.21% 74.46% 513ms 1.05% boost::detail::shared_count::~shared_count (inline) 0 0% 74.46% 513ms 1.05% boost::shared_ptr::~shared_ptr (inline) 6ms 0.012% 74.48% 510ms 1.04% boost::numeric::ublas::detail::expression_type_check (inline) 58ms 0.12% 74.60% 501ms 1.02% CellPropertyCollection::AddProperty 45ms 0.092% 74.69% 498ms 1.02% boost::numeric::ublas::detail::equals 410ms 0.84% 75.52% 495ms 1.01% std::operator< (inline) 490ms 1% 76.52% 490ms 1% Node::GetIndex 487ms 0.99% 77.52% 487ms 0.99% [libchaste_cell_based.so] 13ms 0.027% 77.54% 475ms 0.97% std::operator<< (partial-inline) 1ms 0.002% 77.54% 472ms 0.96% CellProliferativeTypesWriter::VisitCell 2ms 0.0041% 77.55% 442ms 0.9% vtkXMLWriter::WriteCellDataAppendedData 0 0% 77.55% 420ms 0.86% boost::numeric::ublas::norm_inf (inline) 145ms 0.3% 77.84% 420ms 0.86% boost::numeric::ublas::vector_norm_inf::apply (inline) 47ms 0.096% 77.94% 420ms 0.86% std::ostream::write 4ms 0.0082% 77.95% 417ms 0.85% CellProliferativeTypesWriter::GetCellDataForVtkOutput 39ms 0.08% 78.03% 408ms 0.83% std::_Rb_tree::_M_erase_aux (inline) 404ms 0.82% 78.85% 404ms 0.82% std::_Rb_tree_insert_and_rebalance 124ms 0.25% 79.10% 400ms 0.82% boost::shared_ptr::shared_ptr (inline) 0 0% 79.10% 395ms 0.81% boost::numeric::ublas::c_vector::assign_temporary (inline) 0 0% 79.10% 395ms 0.81% boost::numeric::ublas::c_vector::swap (inline) 29ms 0.059% 79.16% 395ms 0.81% std::swap_ranges (inline) 390ms 0.8% 79.96% 392ms 0.8% boost::detail::sp_counted_base::release 49ms 0.1% 80.06% 384ms 0.78% MutableElement::GetNodeLocalIndex 0 0% 80.06% 382ms 0.78% AbstractCellBasedSimulation::DoCellRemoval (inline) 374ms 0.76% 80.82% 375ms 0.76% __GI___writev 1ms 0.002% 80.82% 375ms 0.76% std::__basic_file::xsputn_2 5ms 0.01% 80.83% 372ms 0.76% VertexMeshWriter::MakeVtkMesh 371ms 0.76% 81.59% 371ms 0.76% std::vector::size (inline) 6ms 0.012% 81.60% 368ms 0.75% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 81.60% 366ms 0.75% std::iter_swap (inline) 366ms 0.75% 82.35% 366ms 0.75% std::swap (inline) 0 0% 82.35% 356ms 0.73% vtkDataArray::ComputeRange 0 0% 82.35% 344ms 0.7% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 82.35% 342ms 0.7% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 82.35% 339ms 0.69% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 82.35% 339ms 0.69% OutputFileHandler::OpenOutputFile 44ms 0.09% 82.44% 331ms 0.67% std::_Rb_tree::find (inline) 2ms 0.0041% 82.44% 327ms 0.67% std::basic_filebuf::open 3ms 0.0061% 82.45% 327ms 0.67% std::basic_filebuf::overflow 5ms 0.01% 82.46% 324ms 0.66% std::basic_filebuf::_M_convert_to_external 3ms 0.0061% 82.46% 319ms 0.65% std::__basic_file::xsputn 312ms 0.64% 83.10% 315ms 0.64% __GI___libc_write 1ms 0.002% 83.10% 299ms 0.61% vtkXMLUnstructuredDataWriter::WriteHeader 90ms 0.18% 83.29% 295ms 0.6% Edge::GetMapIndex 44ms 0.09% 83.38% 295ms 0.6% tbb::detail::r1::cancel_group_execution 1ms 0.002% 83.38% 288ms 0.59% vtk::detail::smp::vtkSMPToolsImplForTBB 12ms 0.024% 83.40% 281ms 0.57% MutableElement::RegisterWithEdges (inline) 41ms 0.084% 83.49% 280ms 0.57% std::__new_allocator::construct (inline) 0 0% 83.49% 280ms 0.57% std::allocator_traits::construct (inline) 267ms 0.54% 84.03% 276ms 0.56% boost::detail::shared_count::shared_count (inline) 269ms 0.55% 84.58% 269ms 0.55% operator delete 0 0% 84.58% 269ms 0.55% vtkDataArrayPrivate::DoComputeScalarRange 13ms 0.027% 84.61% 265ms 0.54% Edge::AddElement 264ms 0.54% 85.14% 264ms 0.54% AbstractElement::IsDeleted 4ms 0.0082% 85.15% 264ms 0.54% vtkXMLWriter::WriteBinaryData 0 0% 85.15% 262ms 0.53% vtkXMLUnstructuredGridWriter::WriteAppendedPiece 9ms 0.018% 85.17% 257ms 0.52% MutableElement::RegisterWithNodes (inline) 4ms 0.0082% 85.18% 256ms 0.52% AbstractMesh::NodeIterator::operator++ (inline) 158ms 0.32% 85.50% 255ms 0.52% std::_Rb_tree::_M_get_insert_hint_unique_pos 254ms 0.52% 86.02% 254ms 0.52% [libstdc++.so.6.0.33] 30ms 0.061% 86.08% 254ms 0.52% std::_Rb_tree::_M_upper_bound (inline) 176ms 0.36% 86.44% 253ms 0.52% std::basic_streambuf::xsputn 51ms 0.1% 86.54% 251ms 0.51% vtkDataArrayPrivate::DoComputeVectorRange 0 0% 86.54% 249ms 0.51% std::_Rb_tree::_M_construct_node (inline) 13ms 0.027% 86.57% 248ms 0.51% AbstractMesh::NodeIterator::IsAllowedNode (inline) 247ms 0.5% 87.07% 247ms 0.5% Node::IsDeleted