File: Test2dVertexBasedSimulationWithFreeBoundary Type: cpu Showing nodes accounting for 61315ms, 84.24% of 72789ms total Dropped 949 nodes (cum <= 363.94ms) flat flat% sum% cum cum% 0 0% 0% 70526ms 96.89% __libc_start_call_main 0 0% 0% 70526ms 96.89% __libc_start_main_impl 0 0% 0% 70526ms 96.89% _start 0 0% 0% 70509ms 96.87% main 0 0% 0% 70466ms 96.81% Test2DVertexSimulationWithFreeBoundary::Test2DFreeBoundaryVertexSimulationForProfiling 1ms 0.0014% 0.0014% 68877ms 94.63% AbstractCellBasedSimulation::Solve 1ms 0.0014% 0.0027% 32499ms 44.65% AbstractCellPopulation::WriteResultsToFiles 19ms 0.026% 0.029% 24790ms 34.06% VertexBasedCellPopulation::WriteVtkResultsToFile 82ms 0.11% 0.14% 24503ms 33.66% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1ms 0.0014% 0.14% 21620ms 29.70% VertexMeshWriter::WriteVtkUsingMesh 173ms 0.24% 0.38% 20704ms 28.44% OffLatticeSimulation::UpdateCellLocationsAndTopology 18ms 0.025% 0.41% 19977ms 27.45% ForwardEulerNumericalMethod::UpdateAllNodePositions 89ms 0.12% 0.53% 19647ms 26.99% AbstractNumericalMethod::ComputeForcesIncludingDamping 59ms 0.081% 0.61% 17111ms 23.51% VertexMeshWriter::MakeVtkMesh 732ms 1.01% 1.61% 14936ms 20.52% FarhadifarForce::AddForceContribution 0 0% 1.61% 14619ms 20.08% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0027% 1.62% 13632ms 18.73% VertexBasedCellPopulation::Update 1ms 0.0014% 1.62% 13585ms 18.66% MutableVertexMesh::ReMesh 7ms 0.0096% 1.63% 12186ms 16.74% vtkPolygon::New 16ms 0.022% 1.65% 12169ms 16.72% vtkPolygon::vtkPolygon 417ms 0.57% 2.22% 8234ms 11.31% MutableVertexMesh::CheckForIntersections 58ms 0.08% 2.30% 8150ms 11.20% vtkCell::vtkCell 521ms 0.72% 3.02% 7605ms 10.45% operator new 2016ms 2.77% 5.79% 7218ms 9.92% __GI___libc_malloc 24ms 0.033% 5.82% 7138ms 9.81% vtkPoints::New 110ms 0.15% 5.97% 6688ms 9.19% vtkPoints::vtkPoints 643ms 0.88% 6.86% 6062ms 8.33% VertexMesh::GetVectorFromAtoB 8ms 0.011% 6.87% 5911ms 8.12% vtkQuad::New 43ms 0.059% 6.93% 5883ms 8.08% vtkQuad::vtkQuad 359ms 0.49% 7.42% 5642ms 7.75% FarhadifarForce::GetLineTensionParameter 18ms 0.025% 7.44% 5360ms 7.36% vtkLine::New 1720ms 2.36% 9.81% 5247ms 7.21% __GI___libc_free 17ms 0.023% 9.83% 5236ms 7.19% vtkTriangle::New 91ms 0.13% 9.95% 5235ms 7.19% vtkLine::vtkLine 55ms 0.076% 10.03% 5181ms 7.12% vtkTriangle::vtkTriangle 1337ms 1.84% 11.87% 4704ms 6.46% __dynamic_cast 104ms 0.14% 12.01% 4484ms 6.16% VertexBasedCellPopulation::GetDampingConstant 314ms 0.43% 12.44% 4403ms 6.05% vtkPoints::SetDataType 1ms 0.0014% 12.44% 4355ms 5.98% vtkXMLWriterBase::Write 1ms 0.0014% 12.44% 4354ms 5.98% vtkStreamingDemandDrivenPipeline::Update 1ms 0.0014% 12.45% 4335ms 5.96% vtkDemandDrivenPipeline::ProcessRequest 1ms 0.0014% 12.45% 4321ms 5.94% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 12.45% 4304ms 5.91% vtkDemandDrivenPipeline::ExecuteData 0 0% 12.45% 4300ms 5.91% vtkExecutive::CallAlgorithm 0 0% 12.45% 4293ms 5.90% vtkCompositeDataPipeline::ExecuteData 2ms 0.0027% 12.45% 4289ms 5.89% vtkXMLUnstructuredDataWriter::ProcessRequest 44ms 0.06% 12.51% 4263ms 5.86% vtkPolygon::~vtkPolygon 931ms 1.28% 13.79% 4252ms 5.84% VertexMesh::ElementIncludesPoint 936ms 1.29% 15.08% 3803ms 5.22% std::_Rb_tree::_M_erase 2221ms 3.05% 18.13% 3733ms 5.13% _int_malloc 2435ms 3.35% 21.47% 3701ms 5.08% boost::numeric::ublas::indexing_vector_assign 0 0% 21.47% 3571ms 4.91% vtkXMLUnstructuredDataWriter::WriteAPiece 1ms 0.0014% 21.47% 3571ms 4.91% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 2964ms 4.07% 25.55% 3482ms 4.78% _int_free 7ms 0.0096% 25.55% 3471ms 4.77% MutableVertexMesh::RemoveDeletedNodesAndElements 352ms 0.48% 26.04% 3458ms 4.75% std::ostream::_M_insert 146ms 0.2% 26.24% 3368ms 4.63% vtkCell::~vtkCell 203ms 0.28% 26.52% 3177ms 4.36% Cell::GetMutationState 444ms 0.61% 27.13% 2926ms 4.02% VertexMesh::GetNextEdgeGradientOfElementAtNode 2ms 0.0027% 27.13% 2907ms 3.99% vtkXMLWriter::WriteBinaryData 2881ms 3.96% 31.09% 2881ms 3.96% __memcpy_avx_unaligned_erms 2ms 0.0027% 31.09% 2874ms 3.95% vtkXMLWriter::WriteBinaryDataInternal 1ms 0.0014% 31.09% 2865ms 3.94% vtkXMLWriter::WriteBinaryDataBlock 460ms 0.63% 31.72% 2805ms 3.85% AbstractMesh::GetVectorFromAtoB 14ms 0.019% 31.74% 2781ms 3.82% NodeLocationWriter::VisitAnyPopulation 49ms 0.067% 31.81% 2777ms 3.82% vtkBase64OutputStream::Write 1374ms 1.89% 33.70% 2753ms 3.78% std::_Rb_tree::_M_copy 2712ms 3.73% 37.42% 2712ms 3.73% __strcmp_avx2 235ms 0.32% 37.75% 2691ms 3.70% vtkBase64OutputStream::EncodeTriplet 325ms 0.45% 38.19% 2646ms 3.64% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 1ms 0.0014% 38.20% 2450ms 3.37% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 116ms 0.16% 38.35% 2381ms 3.27% std::num_put::_M_insert_float 1092ms 1.50% 39.85% 2377ms 3.27% AbstractMesh::GetDistanceBetweenNodes 14ms 0.019% 39.87% 2375ms 3.26% MutableVertexMesh::RemoveDeletedNodes 276ms 0.38% 40.25% 2346ms 3.22% AbstractCellPopulation::GetCellUsingLocationIndex 1279ms 1.76% 42.01% 2340ms 3.21% __cxxabiv1::__si_class_type_info::__do_dyncast 18ms 0.025% 42.04% 2325ms 3.19% tbb::detail::r1::parallel_pipeline 32ms 0.044% 42.08% 2299ms 3.16% EdgeHelper::RemoveDeletedEdges 98ms 0.13% 42.21% 2273ms 3.12% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 608ms 0.84% 43.05% 2252ms 3.09% std::ostream::write 156ms 0.21% 43.26% 2232ms 3.07% MutableElement::ResetIndex 0 0% 43.26% 2226ms 3.06% clone3 1ms 0.0014% 43.26% 2226ms 3.06% start_thread 69ms 0.095% 43.36% 2199ms 3.02% vtkIdList::AllocateInternal 61ms 0.084% 43.44% 2166ms 2.98% vtkPoints::~vtkPoints 681ms 0.94% 44.38% 2154ms 2.96% EdgeHelper::UpdateEdgesMapKey 14ms 0.019% 44.40% 2090ms 2.87% tbb::detail::r1::reset 37ms 0.051% 44.45% 1976ms 2.71% std::__cxx11::collate::do_transform 944ms 1.30% 45.75% 1968ms 2.70% tbb::detail::r1::wait_bounded_queue_monitor 15ms 0.021% 45.77% 1901ms 2.61% ___vsnprintf 30ms 0.041% 45.81% 1900ms 2.61% vtkQuad::~vtkQuad 3ms 0.0041% 45.81% 1886ms 2.59% __vsnprintf_internal (inline) 80ms 0.11% 45.92% 1884ms 2.59% Cell::GetCellProliferativeType 24ms 0.033% 45.95% 1882ms 2.59% VertexBasedCellPopulation::AcceptCellWriter 177ms 0.24% 46.20% 1861ms 2.56% __printf_buffer 1842ms 2.53% 48.73% 1842ms 2.53% boost::numeric::ublas::same_impl_ex 16ms 0.022% 48.75% 1800ms 2.47% vtkTriangle::~vtkTriangle 94ms 0.13% 48.88% 1776ms 2.44% CellPopulationElementWriter::Visit 8ms 0.011% 48.89% 1742ms 2.39% vtkLine::GetParametricCenter 15ms 0.021% 48.91% 1682ms 2.31% vtkTypeFloat64Array::~vtkTypeFloat64Array 46ms 0.063% 48.97% 1606ms 2.21% __printf_fp_l_buffer 0 0% 48.97% 1606ms 2.21% __printf_fp_spec (inline) 0 0% 48.97% 1585ms 2.18% VoronoiVertexMeshGenerator::GenerateVoronoiMesh 0 0% 48.97% 1585ms 2.18% VoronoiVertexMeshGenerator::VoronoiVertexMeshGenerator 1096ms 1.51% 50.48% 1579ms 2.17% VoronoiVertexMeshGenerator::CreateVoronoiTessellation 332ms 0.46% 50.94% 1570ms 2.16% std::__set_intersection 40ms 0.055% 50.99% 1547ms 2.13% vtkFloatArray::New 1078ms 1.48% 52.47% 1530ms 2.10% std::_Rb_tree::erase 655ms 0.9% 53.37% 1523ms 2.09% std::basic_filebuf::xsputn 570ms 0.78% 54.16% 1519ms 2.09% __printf_fp_buffer_1 33ms 0.045% 54.20% 1488ms 2.04% vtkDataArray::CreateDataArray 1479ms 2.03% 56.23% 1479ms 2.03% std::map::operator[] 33ms 0.045% 56.28% 1360ms 1.87% vtkDoubleArray::vtkDoubleArray 58ms 0.08% 56.36% 1360ms 1.87% vtkTypeFloat64Array::New 0 0% 56.36% 1356ms 1.86% tcache_get (inline) 1356ms 1.86% 58.22% 1356ms 1.86% tcache_get_n (inline) 29ms 0.04% 58.26% 1333ms 1.83% vtkFloatArray::vtkFloatArray 13ms 0.018% 58.28% 1306ms 1.79% LegacyCellProliferativeTypesWriter::VisitCell 28ms 0.038% 58.32% 1275ms 1.75% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 94ms 0.13% 58.45% 1270ms 1.74% Cell::GetCellData 1249ms 1.72% 60.16% 1249ms 1.72% boost::numeric::ublas::vector_norm_2::apply 2ms 0.0027% 60.16% 1241ms 1.70% vtkXMLWriter::WriteCellDataAppendedData 282ms 0.39% 60.55% 1219ms 1.67% vtkObject::vtkObject 40ms 0.055% 60.61% 1196ms 1.64% vtkFloatArray::~vtkFloatArray 0 0% 60.61% 1190ms 1.63% vtkXMLWriter::WritePointsAppendedData 257ms 0.35% 60.96% 1183ms 1.63% std::vector::_M_default_append 129ms 0.18% 61.14% 1181ms 1.62% boost::numeric::ublas::vector_assign 1166ms 1.60% 62.74% 1166ms 1.60% boost::numeric::ublas::c_vector::operator() 33ms 0.045% 62.78% 1147ms 1.58% vtkTypeFloat64Array::vtkTypeFloat64Array 1ms 0.0014% 62.79% 1095ms 1.50% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 499ms 0.69% 63.47% 1074ms 1.48% vtkTypeFloat64Array::PrintSelf 18ms 0.025% 63.50% 1036ms 1.42% AbstractTargetAreaModifier::UpdateTargetAreas 1018ms 1.40% 64.89% 1018ms 1.40% __GI_sched_yield 28ms 0.038% 64.93% 1016ms 1.40% TargetAreaLinearGrowthModifier::UpdateTargetAreaOfCell 339ms 0.47% 65.40% 997ms 1.37% AbstractElement::GetNodeLocation 214ms 0.29% 65.69% 939ms 1.29% VertexMesh::GetAreaGradientOfElementAtNode 373ms 0.51% 66.21% 896ms 1.23% AbstractCellProperty::IsSame 272ms 0.37% 66.58% 869ms 1.19% vtkObject::Modified 571ms 0.78% 67.36% 869ms 1.19% vtkObjectBase::UnRegisterInternal 864ms 1.19% 68.55% 864ms 1.19% tcache_put (inline) 62ms 0.085% 68.64% 852ms 1.17% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 158ms 0.22% 68.85% 851ms 1.17% std::_Rb_tree::_Rb_tree 88ms 0.12% 68.97% 846ms 1.16% vtkAOSDataArrayTemplate::DataElementChanged 76ms 0.1% 69.08% 829ms 1.14% CellPropertyCollection::HasProperty 138ms 0.19% 69.27% 781ms 1.07% VertexMesh::GetVolumeOfElement 5ms 0.0069% 69.27% 777ms 1.07% vtkIdList::Allocate 63ms 0.087% 69.36% 766ms 1.05% vtkDoubleArray::~vtkDoubleArray 750ms 1.03% 70.39% 750ms 1.03% std::_Rb_tree_increment 23ms 0.032% 70.42% 736ms 1.01% Node::RemoveElement 42ms 0.058% 70.48% 731ms 1.00% MutableVertexMesh::CheckForSwapsFromShortEdges 654ms 0.9% 71.38% 731ms 1.00% malloc_consolidate 292ms 0.4% 71.78% 708ms 0.97% hack_digit 88ms 0.12% 71.90% 682ms 0.94% AbstractCellBasedSimulation::DoCellBirth 682ms 0.94% 72.84% 682ms 0.94% [libchaste_cell_based.so] 397ms 0.55% 73.38% 677ms 0.93% std::basic_streambuf::xsputn 214ms 0.29% 73.68% 656ms 0.9% std::__ostream_insert 285ms 0.39% 74.07% 643ms 0.88% AbstractCellPopulation::GetLocationIndexUsingCell 641ms 0.88% 74.95% 641ms 0.88% [libchaste_mesh.so] 423ms 0.58% 75.53% 632ms 0.87% boost::numeric::ublas::detail::equals 47ms 0.065% 75.60% 610ms 0.84% vtkDataArray::vtkDataArray 585ms 0.8% 76.40% 585ms 0.8% vtkTimeStamp::Modified 16ms 0.022% 76.42% 580ms 0.8% VertexMesh::GetSurfaceAreaOfElement 176ms 0.24% 76.66% 557ms 0.77% vtkAbstractArray::vtkAbstractArray 257ms 0.35% 77.02% 548ms 0.75% std::_Hashtable::clear 539ms 0.74% 77.76% 539ms 0.74% Node::GetIndex 0 0% 77.76% 537ms 0.74% std::__basic_file::xsputn_2 536ms 0.74% 78.49% 536ms 0.74% [libstdc++.so.6.0.33] 535ms 0.74% 79.23% 536ms 0.74% __GI___writev 29ms 0.04% 79.27% 523ms 0.72% vtkIdList::New 87ms 0.12% 79.39% 517ms 0.71% vtkDataArray::~vtkDataArray 80ms 0.11% 79.50% 516ms 0.71% std::num_put::_M_insert_int 0 0% 79.50% 497ms 0.68% vtkDataArray::ComputeRange 2ms 0.0027% 79.50% 486ms 0.67% CellProliferativeTypesWriter::VisitCell 476ms 0.65% 80.15% 476ms 0.65% Node::rGetLocation 470ms 0.65% 80.80% 470ms 0.65% [libvtkCommonCore-9.3.so.9.3] 460ms 0.63% 81.43% 463ms 0.64% vtkObjectBase::Delete 71ms 0.098% 81.53% 445ms 0.61% vtkSOADataArrayTemplate::FillTypedComponent 432ms 0.59% 82.12% 436ms 0.6% vtkObject::~vtkObject 4ms 0.0055% 82.13% 417ms 0.57% vtkDataArrayPrivate::DoComputeScalarRange 3ms 0.0041% 82.13% 415ms 0.57% std::basic_filebuf::overflow 4ms 0.0055% 82.14% 412ms 0.57% std::basic_filebuf::_M_convert_to_external 226ms 0.31% 82.45% 408ms 0.56% CellPropertyCollection::AddProperty 1ms 0.0014% 82.45% 408ms 0.56% std::__basic_file::xsputn 403ms 0.55% 83.00% 407ms 0.56% __GI___libc_write 405ms 0.56% 83.56% 405ms 0.56% std::ostream::sentry::sentry 0 0% 83.56% 404ms 0.56% vtk::detail::smp::vtkSMPToolsImplForTBB 40ms 0.055% 83.61% 400ms 0.55% tbb::detail::r1::cancel_group_execution 69ms 0.095% 83.71% 387ms 0.53% vtkIdList::~vtkIdList 384ms 0.53% 84.24% 384ms 0.53% std::_Rb_tree_insert_and_rebalance