File: Test2dVertexBasedSimulationWithFreeBoundary Type: cpu Showing nodes accounting for 60628ms, 84.69% of 71590ms total Dropped 943 nodes (cum <= 357.95ms) flat flat% sum% cum cum% 0 0% 0% 68621ms 95.85% __libc_start_call_main 0 0% 0% 68621ms 95.85% __libc_start_main_impl 0 0% 0% 68621ms 95.85% _start 0 0% 0% 68606ms 95.83% main 0 0% 0% 68567ms 95.78% Test2DVertexSimulationWithFreeBoundary::Test2DFreeBoundaryVertexSimulationForProfiling 1ms 0.0014% 0.0014% 66826ms 93.35% AbstractCellBasedSimulation::Solve 1ms 0.0014% 0.0028% 31769ms 44.38% AbstractCellPopulation::WriteResultsToFiles 9ms 0.013% 0.015% 24302ms 33.95% VertexBasedCellPopulation::WriteVtkResultsToFile 77ms 0.11% 0.12% 24082ms 33.64% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1ms 0.0014% 0.12% 21300ms 29.75% VertexMeshWriter::WriteVtkUsingMesh 134ms 0.19% 0.31% 20305ms 28.36% OffLatticeSimulation::UpdateCellLocationsAndTopology 30ms 0.042% 0.35% 19580ms 27.35% ForwardEulerNumericalMethod::UpdateAllNodePositions 84ms 0.12% 0.47% 19275ms 26.92% AbstractNumericalMethod::ComputeForcesIncludingDamping 45ms 0.063% 0.53% 16510ms 23.06% VertexMeshWriter::MakeVtkMesh 674ms 0.94% 1.48% 14820ms 20.70% FarhadifarForce::AddForceContribution 1ms 0.0014% 1.48% 13720ms 19.16% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 1.48% 12792ms 17.87% VertexBasedCellPopulation::Update 0 0% 1.48% 12760ms 17.82% MutableVertexMesh::ReMesh 2ms 0.0028% 1.48% 11925ms 16.66% vtkPolygon::New 13ms 0.018% 1.50% 11918ms 16.65% vtkPolygon::vtkPolygon 41ms 0.057% 1.55% 8187ms 11.44% vtkCell::vtkCell 536ms 0.75% 2.30% 7752ms 10.83% operator new 423ms 0.59% 2.89% 7692ms 10.74% MutableVertexMesh::CheckForIntersections 2228ms 3.11% 6.01% 7285ms 10.18% __GI___libc_malloc 33ms 0.046% 6.05% 7143ms 9.98% vtkPoints::New 103ms 0.14% 6.20% 6747ms 9.42% vtkPoints::vtkPoints 391ms 0.55% 6.74% 5993ms 8.37% FarhadifarForce::GetLineTensionParameter 630ms 0.88% 7.62% 5694ms 7.95% VertexMesh::GetVectorFromAtoB 6ms 0.0084% 7.63% 5660ms 7.91% vtkQuad::New 36ms 0.05% 7.68% 5639ms 7.88% vtkQuad::vtkQuad 2187ms 3.05% 10.74% 5581ms 7.80% __GI___libc_free 7ms 0.0098% 10.75% 5407ms 7.55% vtkLine::New 95ms 0.13% 10.88% 5260ms 7.35% vtkLine::vtkLine 7ms 0.0098% 10.89% 5086ms 7.10% vtkTriangle::New 70ms 0.098% 10.99% 5031ms 7.03% vtkTriangle::vtkTriangle 1094ms 1.53% 12.51% 4725ms 6.60% __dynamic_cast 0 0% 12.51% 4670ms 6.52% vtkXMLWriterBase::Write 0 0% 12.51% 4668ms 6.52% vtkStreamingDemandDrivenPipeline::Update 1ms 0.0014% 12.52% 4644ms 6.49% vtkDemandDrivenPipeline::ProcessRequest 0 0% 12.52% 4636ms 6.48% vtkStreamingDemandDrivenPipeline::ProcessRequest 2ms 0.0028% 12.52% 4621ms 6.45% vtkExecutive::CallAlgorithm 0 0% 12.52% 4616ms 6.45% vtkDemandDrivenPipeline::ExecuteData 0 0% 12.52% 4604ms 6.43% vtkCompositeDataPipeline::ExecuteData 1ms 0.0014% 12.52% 4601ms 6.43% vtkXMLUnstructuredDataWriter::ProcessRequest 241ms 0.34% 12.86% 4465ms 6.24% vtkPoints::SetDataType 98ms 0.14% 12.99% 4227ms 5.90% VertexBasedCellPopulation::GetDampingConstant 35ms 0.049% 13.04% 4021ms 5.62% vtkPolygon::~vtkPolygon 866ms 1.21% 14.25% 4004ms 5.59% VertexMesh::ElementIncludesPoint 829ms 1.16% 15.41% 3836ms 5.36% std::_Rb_tree::_M_erase 0 0% 15.41% 3835ms 5.36% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 15.41% 3835ms 5.36% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 2452ms 3.43% 18.84% 3777ms 5.28% boost::numeric::ublas::indexing_vector_assign 2165ms 3.02% 21.86% 3644ms 5.09% _int_malloc 337ms 0.47% 22.33% 3432ms 4.79% std::ostream::_M_insert 2947ms 4.12% 26.45% 3382ms 4.72% _int_free 9ms 0.013% 26.46% 3343ms 4.67% MutableVertexMesh::RemoveDeletedNodesAndElements 235ms 0.33% 26.79% 3245ms 4.53% Cell::GetMutationState 4ms 0.0056% 26.79% 3143ms 4.39% vtkXMLWriter::WriteBinaryData 2ms 0.0028% 26.80% 3099ms 4.33% vtkXMLWriter::WriteBinaryDataInternal 137ms 0.19% 26.99% 3097ms 4.33% vtkCell::~vtkCell 1ms 0.0014% 26.99% 3092ms 4.32% vtkXMLWriter::WriteBinaryDataBlock 531ms 0.74% 27.73% 3057ms 4.27% AbstractMesh::GetVectorFromAtoB 3ms 0.0042% 27.73% 3037ms 4.24% tbb::detail::r1::parallel_pipeline 67ms 0.094% 27.83% 3014ms 4.21% vtkBase64OutputStream::Write 2980ms 4.16% 31.99% 2980ms 4.16% __strcmp_avx2 274ms 0.38% 32.37% 2944ms 4.11% vtkBase64OutputStream::EncodeTriplet 0 0% 32.37% 2934ms 4.10% clone3 0 0% 32.37% 2934ms 4.10% start_thread 2ms 0.0028% 32.38% 2915ms 4.07% tbb::detail::r1::reset 1271ms 1.78% 34.15% 2897ms 4.05% tbb::detail::r1::wait_bounded_queue_monitor 30ms 0.042% 34.19% 2777ms 3.88% NodeLocationWriter::VisitAnyPopulation 443ms 0.62% 34.81% 2745ms 3.83% VertexMesh::GetNextEdgeGradientOfElementAtNode 1208ms 1.69% 36.50% 2720ms 3.80% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.0014% 36.50% 2538ms 3.55% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 1079ms 1.51% 38.01% 2506ms 3.50% std::_Rb_tree::_M_copy 399ms 0.56% 38.57% 2496ms 3.49% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 804ms 1.12% 39.69% 2443ms 3.41% std::ostream::write 145ms 0.2% 39.89% 2378ms 3.32% std::num_put::_M_insert_float 2343ms 3.27% 43.16% 2343ms 3.27% __memcpy_avx_unaligned_erms 14ms 0.02% 43.18% 2251ms 3.14% MutableVertexMesh::RemoveDeletedNodes 91ms 0.13% 43.31% 2197ms 3.07% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 27ms 0.038% 43.35% 2175ms 3.04% EdgeHelper::RemoveDeletedEdges 152ms 0.21% 43.56% 2172ms 3.03% MutableElement::ResetIndex 948ms 1.32% 44.88% 2090ms 2.92% AbstractMesh::GetDistanceBetweenNodes 226ms 0.32% 45.20% 2086ms 2.91% AbstractCellPopulation::GetCellUsingLocationIndex 30ms 0.042% 45.24% 2059ms 2.88% vtkIdList::AllocateInternal 658ms 0.92% 46.16% 2032ms 2.84% EdgeHelper::UpdateEdgesMapKey 61ms 0.085% 46.25% 1984ms 2.77% vtkPoints::~vtkPoints 38ms 0.053% 46.30% 1961ms 2.74% std::__cxx11::collate::do_transform 1945ms 2.72% 49.02% 1945ms 2.72% boost::numeric::ublas::same_impl_ex 102ms 0.14% 49.16% 1913ms 2.67% Cell::GetCellProliferativeType 8ms 0.011% 49.17% 1878ms 2.62% ___vsnprintf 0 0% 49.17% 1870ms 2.61% __vsnprintf_internal (inline) 21ms 0.029% 49.20% 1837ms 2.57% VertexBasedCellPopulation::AcceptCellWriter 442ms 0.62% 49.82% 1836ms 2.56% std::__set_intersection 180ms 0.25% 50.07% 1825ms 2.55% __printf_buffer 23ms 0.032% 50.10% 1824ms 2.55% vtkTriangle::~vtkTriangle 26ms 0.036% 50.14% 1766ms 2.47% vtkQuad::~vtkQuad 0 0% 50.14% 1736ms 2.42% VoronoiVertexMeshGenerator::GenerateVoronoiMesh 0 0% 50.14% 1736ms 2.42% VoronoiVertexMeshGenerator::VoronoiVertexMeshGenerator 1028ms 1.44% 51.57% 1728ms 2.41% VoronoiVertexMeshGenerator::CreateVoronoiTessellation 9ms 0.013% 51.59% 1681ms 2.35% vtkLine::GetParametricCenter 91ms 0.13% 51.71% 1650ms 2.30% CellPopulationElementWriter::Visit 1604ms 2.24% 53.95% 1604ms 2.24% __GI_sched_yield 6ms 0.0084% 53.96% 1565ms 2.19% __printf_fp_spec (inline) 49ms 0.068% 54.03% 1559ms 2.18% __printf_fp_l_buffer 7ms 0.0098% 54.04% 1520ms 2.12% vtkTypeFloat64Array::~vtkTypeFloat64Array 40ms 0.056% 54.10% 1506ms 2.10% vtkDataArray::CreateDataArray 46ms 0.064% 54.16% 1489ms 2.08% vtkFloatArray::New 614ms 0.86% 55.02% 1456ms 2.03% __printf_fp_buffer_1 1070ms 1.49% 56.51% 1454ms 2.03% std::_Rb_tree::erase 1410ms 1.97% 58.48% 1410ms 1.97% std::map::operator[] 599ms 0.84% 59.32% 1407ms 1.97% std::basic_filebuf::xsputn 52ms 0.073% 59.39% 1368ms 1.91% vtkTypeFloat64Array::New 39ms 0.054% 59.45% 1353ms 1.89% vtkFloatArray::~vtkFloatArray 0 0% 59.45% 1308ms 1.83% vtkXMLWriter::WritePointsAppendedData 0 0% 59.45% 1300ms 1.82% tcache_get (inline) 1300ms 1.82% 61.26% 1300ms 1.82% tcache_get_n (inline) 29ms 0.041% 61.30% 1291ms 1.80% vtkDoubleArray::vtkDoubleArray 3ms 0.0042% 61.31% 1276ms 1.78% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 93ms 0.13% 61.44% 1265ms 1.77% Cell::GetCellData 19ms 0.027% 61.46% 1254ms 1.75% vtkFloatArray::vtkFloatArray 9ms 0.013% 61.48% 1247ms 1.74% LegacyCellProliferativeTypesWriter::VisitCell 4ms 0.0056% 61.48% 1216ms 1.70% vtkXMLWriter::WriteCellDataAppendedData 28ms 0.039% 61.52% 1153ms 1.61% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 30ms 0.042% 61.56% 1132ms 1.58% vtkTypeFloat64Array::vtkTypeFloat64Array 252ms 0.35% 61.91% 1118ms 1.56% std::vector::_M_default_append 227ms 0.32% 62.23% 1115ms 1.56% vtkObject::vtkObject 160ms 0.22% 62.45% 1114ms 1.56% boost::numeric::ublas::vector_assign 1093ms 1.53% 63.98% 1093ms 1.53% boost::numeric::ublas::c_vector::operator() 1091ms 1.52% 65.50% 1091ms 1.52% boost::numeric::ublas::vector_norm_2::apply 19ms 0.027% 65.53% 1009ms 1.41% AbstractTargetAreaModifier::UpdateTargetAreas 36ms 0.05% 65.58% 990ms 1.38% TargetAreaLinearGrowthModifier::UpdateTargetAreaOfCell 460ms 0.64% 66.22% 927ms 1.29% vtkTypeFloat64Array::PrintSelf 326ms 0.46% 66.68% 919ms 1.28% AbstractElement::GetNodeLocation 124ms 0.17% 66.85% 898ms 1.25% vtkAOSDataArrayTemplate::DataElementChanged 338ms 0.47% 67.33% 843ms 1.18% AbstractCellProperty::IsSame 9ms 0.013% 67.34% 840ms 1.17% vtkIdList::Allocate 525ms 0.73% 68.07% 838ms 1.17% vtkObjectBase::UnRegisterInternal 272ms 0.38% 68.45% 830ms 1.16% vtkObject::Modified 219ms 0.31% 68.76% 812ms 1.13% VertexMesh::GetAreaGradientOfElementAtNode 780ms 1.09% 69.85% 780ms 1.09% std::_Rb_tree_increment 110ms 0.15% 70.00% 772ms 1.08% VertexMesh::GetVolumeOfElement 704ms 0.98% 70.98% 749ms 1.05% malloc_consolidate 132ms 0.18% 71.17% 744ms 1.04% std::_Rb_tree::_Rb_tree 736ms 1.03% 72.20% 736ms 1.03% tcache_put (inline) 517ms 0.72% 72.92% 732ms 1.02% std::basic_streambuf::xsputn 26ms 0.036% 72.95% 728ms 1.02% Node::RemoveElement 54ms 0.075% 73.03% 724ms 1.01% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 85ms 0.12% 73.15% 722ms 1.01% CellPropertyCollection::HasProperty 64ms 0.089% 73.24% 701ms 0.98% vtkDoubleArray::~vtkDoubleArray 265ms 0.37% 73.61% 679ms 0.95% std::__ostream_insert 664ms 0.93% 74.54% 664ms 0.93% Node::rGetLocation 269ms 0.38% 74.91% 631ms 0.88% hack_digit 37ms 0.052% 74.96% 630ms 0.88% MutableVertexMesh::CheckForSwapsFromShortEdges 249ms 0.35% 75.31% 574ms 0.8% AbstractCellPopulation::GetLocationIndexUsingCell 50ms 0.07% 75.38% 569ms 0.79% AbstractCellBasedSimulation::DoCellBirth 74ms 0.1% 75.48% 566ms 0.79% vtkDataArray::vtkDataArray 543ms 0.76% 76.24% 543ms 0.76% [libchaste_mesh.so] 118ms 0.16% 76.41% 542ms 0.76% std::num_put::_M_insert_int 530ms 0.74% 77.15% 530ms 0.74% [libchaste_cell_based.so] 1ms 0.0014% 77.15% 524ms 0.73% std::__basic_file::xsputn_2 522ms 0.73% 77.88% 523ms 0.73% __GI___writev 520ms 0.73% 78.60% 520ms 0.73% vtkTimeStamp::Modified 28ms 0.039% 78.64% 516ms 0.72% vtkIdList::New 294ms 0.41% 79.05% 510ms 0.71% boost::numeric::ublas::detail::equals 501ms 0.7% 79.75% 506ms 0.71% vtkObjectBase::Delete 2ms 0.0028% 79.76% 497ms 0.69% vtkDataArray::ComputeRange 8ms 0.011% 79.77% 488ms 0.68% VertexMesh::GetSurfaceAreaOfElement 134ms 0.19% 79.96% 485ms 0.68% vtkAbstractArray::vtkAbstractArray 7ms 0.0098% 79.97% 483ms 0.67% CellProliferativeTypesWriter::VisitCell 284ms 0.4% 80.36% 478ms 0.67% CellPropertyCollection::AddProperty 295ms 0.41% 80.77% 469ms 0.66% std::_Hashtable::clear 466ms 0.65% 81.42% 466ms 0.65% Node::GetIndex 456ms 0.64% 82.06% 456ms 0.64% std::ostream::sentry::sentry 450ms 0.63% 82.69% 450ms 0.63% [libvtkCommonCore-9.3.so.9.3] 23ms 0.032% 82.72% 431ms 0.6% CellProliferativeTypesWriter::GetCellDataForVtkOutput 94ms 0.13% 82.85% 431ms 0.6% vtkDataArray::~vtkDataArray 5ms 0.007% 82.86% 409ms 0.57% std::basic_filebuf::overflow 4ms 0.0056% 82.87% 403ms 0.56% std::basic_filebuf::_M_convert_to_external 2ms 0.0028% 82.87% 399ms 0.56% std::__basic_file::xsputn 34ms 0.047% 82.92% 399ms 0.56% tbb::detail::r1::cancel_group_execution 1ms 0.0014% 82.92% 396ms 0.55% vtk::detail::smp::vtkSMPToolsImplForTBB 393ms 0.55% 83.47% 395ms 0.55% __GI___libc_write 58ms 0.081% 83.55% 388ms 0.54% vtkSOADataArrayTemplate::FillTypedComponent 381ms 0.53% 84.08% 381ms 0.53% std::_Rb_tree_insert_and_rebalance 71ms 0.099% 84.18% 377ms 0.53% vtkIdList::~vtkIdList 5ms 0.007% 84.19% 365ms 0.51% vtkDataArrayPrivate::DoComputeScalarRange 359ms 0.5% 84.69% 360ms 0.5% vtkObject::~vtkObject