File: Test2dVertexBasedSimulationWithFreeBoundary Type: cpu Showing nodes accounting for 60366ms, 85.25% of 70810ms total Dropped 887 nodes (cum <= 354.05ms) flat flat% sum% cum cum% 0 0% 0% 68617ms 96.90% __libc_start_call_main 0 0% 0% 68617ms 96.90% __libc_start_main_impl 0 0% 0% 68617ms 96.90% _start 0 0% 0% 68601ms 96.88% main 0 0% 0% 68559ms 96.82% Test2DVertexSimulationWithFreeBoundary::Test2DFreeBoundaryVertexSimulationForProfiling 2ms 0.0028% 0.0028% 67027ms 94.66% AbstractCellBasedSimulation::Solve 1ms 0.0014% 0.0042% 31409ms 44.36% AbstractCellPopulation::WriteResultsToFiles 13ms 0.018% 0.023% 23876ms 33.72% VertexBasedCellPopulation::WriteVtkResultsToFile 64ms 0.09% 0.11% 23565ms 33.28% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1ms 0.0014% 0.11% 20745ms 29.30% VertexMeshWriter::WriteVtkUsingMesh 97ms 0.14% 0.25% 20170ms 28.48% OffLatticeSimulation::UpdateCellLocationsAndTopology 14ms 0.02% 0.27% 19604ms 27.69% ForwardEulerNumericalMethod::UpdateAllNodePositions 82ms 0.12% 0.39% 19320ms 27.28% AbstractNumericalMethod::ComputeForcesIncludingDamping 38ms 0.054% 0.44% 16314ms 23.04% VertexMeshWriter::MakeVtkMesh 816ms 1.15% 1.59% 14869ms 21.00% FarhadifarForce::AddForceContribution 0 0% 1.59% 14305ms 20.20% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 1.59% 13480ms 19.04% VertexBasedCellPopulation::Update 1ms 0.0014% 1.59% 13437ms 18.98% MutableVertexMesh::ReMesh 5ms 0.0071% 1.60% 11618ms 16.41% vtkPolygon::New 13ms 0.018% 1.62% 11601ms 16.38% vtkPolygon::vtkPolygon 438ms 0.62% 2.24% 8511ms 12.02% MutableVertexMesh::CheckForIntersections 42ms 0.059% 2.30% 8007ms 11.31% vtkCell::vtkCell 501ms 0.71% 3.01% 7123ms 10.06% operator new 29ms 0.041% 3.05% 7038ms 9.94% vtkPoints::New 2087ms 2.95% 5.99% 6720ms 9.49% __GI___libc_malloc 121ms 0.17% 6.16% 6585ms 9.30% vtkPoints::vtkPoints 627ms 0.89% 7.05% 6187ms 8.74% VertexMesh::GetVectorFromAtoB 387ms 0.55% 7.60% 5747ms 8.12% FarhadifarForce::GetLineTensionParameter 10ms 0.014% 7.61% 5614ms 7.93% vtkQuad::New 35ms 0.049% 7.66% 5592ms 7.90% vtkQuad::vtkQuad 1593ms 2.25% 9.91% 5248ms 7.41% __GI___libc_free 18ms 0.025% 9.94% 5114ms 7.22% vtkLine::New 12ms 0.017% 9.95% 5031ms 7.10% vtkTriangle::New 90ms 0.13% 10.08% 4991ms 7.05% vtkLine::vtkLine 80ms 0.11% 10.19% 4984ms 7.04% vtkTriangle::vtkTriangle 1279ms 1.81% 12.00% 4755ms 6.72% __dynamic_cast 955ms 1.35% 13.35% 4413ms 6.23% VertexMesh::ElementIncludesPoint 1ms 0.0014% 13.35% 4317ms 6.10% vtkXMLWriterBase::Write 0 0% 13.35% 4314ms 6.09% vtkStreamingDemandDrivenPipeline::Update 1ms 0.0014% 13.35% 4296ms 6.07% vtkDemandDrivenPipeline::ProcessRequest 4ms 0.0056% 13.36% 4276ms 6.04% vtkStreamingDemandDrivenPipeline::ProcessRequest 1ms 0.0014% 13.36% 4269ms 6.03% vtkExecutive::CallAlgorithm 1ms 0.0014% 13.36% 4263ms 6.02% vtkDemandDrivenPipeline::ExecuteData 0 0% 13.36% 4258ms 6.01% vtkCompositeDataPipeline::ExecuteData 1ms 0.0014% 13.36% 4253ms 6.01% vtkXMLUnstructuredDataWriter::ProcessRequest 289ms 0.41% 13.77% 4225ms 5.97% vtkPoints::SetDataType 132ms 0.19% 13.95% 4223ms 5.96% VertexBasedCellPopulation::GetDampingConstant 21ms 0.03% 13.98% 4092ms 5.78% vtkPolygon::~vtkPolygon 890ms 1.26% 15.24% 3795ms 5.36% std::_Rb_tree::_M_erase 2371ms 3.35% 18.59% 3632ms 5.13% boost::numeric::ublas::indexing_vector_assign 3095ms 4.37% 22.96% 3617ms 5.11% _int_free 378ms 0.53% 23.49% 3519ms 4.97% std::ostream::_M_insert 1ms 0.0014% 23.50% 3519ms 4.97% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 23.50% 3518ms 4.97% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 1999ms 2.82% 26.32% 3296ms 4.65% _int_malloc 8ms 0.011% 26.33% 3217ms 4.54% MutableVertexMesh::RemoveDeletedNodesAndElements 98ms 0.14% 26.47% 3186ms 4.50% vtkCell::~vtkCell 182ms 0.26% 26.73% 3142ms 4.44% Cell::GetMutationState 454ms 0.64% 27.37% 3000ms 4.24% VertexMesh::GetNextEdgeGradientOfElementAtNode 2995ms 4.23% 31.60% 2995ms 4.23% __memcpy_avx_unaligned_erms 0 0% 31.60% 2982ms 4.21% vtkXMLWriter::WriteBinaryData 4ms 0.0056% 31.60% 2957ms 4.18% vtkXMLWriter::WriteBinaryDataInternal 1ms 0.0014% 31.60% 2950ms 4.17% vtkXMLWriter::WriteBinaryDataBlock 55ms 0.078% 31.68% 2877ms 4.06% vtkBase64OutputStream::Write 458ms 0.65% 32.33% 2807ms 3.96% AbstractMesh::GetVectorFromAtoB 2802ms 3.96% 36.28% 2802ms 3.96% __strcmp_avx2 18ms 0.025% 36.31% 2795ms 3.95% NodeLocationWriter::VisitAnyPopulation 225ms 0.32% 36.63% 2783ms 3.93% vtkBase64OutputStream::EncodeTriplet 1180ms 1.67% 38.29% 2538ms 3.58% std::_Rb_tree::_M_copy 349ms 0.49% 38.79% 2519ms 3.56% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 1316ms 1.86% 40.65% 2430ms 3.43% __cxxabiv1::__si_class_type_info::__do_dyncast 130ms 0.18% 40.83% 2425ms 3.42% std::num_put::_M_insert_float 22ms 0.031% 40.86% 2406ms 3.40% MutableVertexMesh::RemoveDeletedNodes 620ms 0.88% 41.74% 2338ms 3.30% std::ostream::write 1068ms 1.51% 43.24% 2318ms 3.27% AbstractMesh::GetDistanceBetweenNodes 46ms 0.065% 43.31% 2304ms 3.25% EdgeHelper::RemoveDeletedEdges 0 0% 43.31% 2271ms 3.21% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 14ms 0.02% 43.33% 2251ms 3.18% tbb::detail::r1::parallel_pipeline 101ms 0.14% 43.47% 2229ms 3.15% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 43.47% 2159ms 3.05% clone3 0 0% 43.47% 2159ms 3.05% start_thread 626ms 0.88% 44.36% 2114ms 2.99% EdgeHelper::UpdateEdgesMapKey 7ms 0.0099% 44.37% 2064ms 2.91% tbb::detail::r1::reset 62ms 0.088% 44.45% 2060ms 2.91% vtkPoints::~vtkPoints 35ms 0.049% 44.50% 2005ms 2.83% std::__cxx11::collate::do_transform 946ms 1.34% 45.84% 1988ms 2.81% tbb::detail::r1::wait_bounded_queue_monitor 251ms 0.35% 46.19% 1982ms 2.80% AbstractCellPopulation::GetCellUsingLocationIndex 81ms 0.11% 46.31% 1952ms 2.76% Cell::GetCellProliferativeType 130ms 0.18% 46.49% 1933ms 2.73% MutableElement::ResetIndex 13ms 0.018% 46.51% 1917ms 2.71% ___vsnprintf 4ms 0.0056% 46.51% 1904ms 2.69% __vsnprintf_internal (inline) 175ms 0.25% 46.76% 1889ms 2.67% __printf_buffer 21ms 0.03% 46.79% 1878ms 2.65% VertexBasedCellPopulation::AcceptCellWriter 61ms 0.086% 46.88% 1869ms 2.64% vtkIdList::AllocateInternal 1862ms 2.63% 49.51% 1862ms 2.63% boost::numeric::ublas::same_impl_ex 34ms 0.048% 49.56% 1826ms 2.58% vtkQuad::~vtkQuad 110ms 0.16% 49.71% 1791ms 2.53% CellPopulationElementWriter::Visit 8ms 0.011% 49.72% 1779ms 2.51% vtkTriangle::~vtkTriangle 378ms 0.53% 50.26% 1701ms 2.40% std::__set_intersection 12ms 0.017% 50.27% 1686ms 2.38% vtkLine::GetParametricCenter 42ms 0.059% 50.33% 1653ms 2.33% __printf_fp_l_buffer 0 0% 50.33% 1653ms 2.33% __printf_fp_spec (inline) 11ms 0.016% 50.35% 1596ms 2.25% vtkTypeFloat64Array::~vtkTypeFloat64Array 563ms 0.8% 51.14% 1576ms 2.23% __printf_fp_buffer_1 54ms 0.076% 51.22% 1547ms 2.18% vtkFloatArray::New 647ms 0.91% 52.13% 1540ms 2.17% std::basic_filebuf::xsputn 0 0% 52.13% 1527ms 2.16% VoronoiVertexMeshGenerator::GenerateVoronoiMesh 0 0% 52.13% 1527ms 2.16% VoronoiVertexMeshGenerator::VoronoiVertexMeshGenerator 1073ms 1.52% 53.65% 1519ms 2.15% VoronoiVertexMeshGenerator::CreateVoronoiTessellation 42ms 0.059% 53.71% 1468ms 2.07% vtkDataArray::CreateDataArray 36ms 0.051% 53.76% 1335ms 1.89% vtkFloatArray::vtkFloatArray 79ms 0.11% 53.87% 1333ms 1.88% vtkTypeFloat64Array::New 6ms 0.0085% 53.88% 1309ms 1.85% LegacyCellProliferativeTypesWriter::VisitCell 1300ms 1.84% 55.71% 1300ms 1.84% std::map::operator[] 1284ms 1.81% 57.53% 1284ms 1.81% boost::numeric::ublas::vector_norm_2::apply 38ms 0.054% 57.58% 1257ms 1.78% vtkDoubleArray::vtkDoubleArray 0 0% 57.58% 1255ms 1.77% vtkXMLWriter::WritePointsAppendedData 17ms 0.024% 57.60% 1237ms 1.75% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 818ms 1.16% 58.76% 1237ms 1.75% std::_Rb_tree::erase 1232ms 1.74% 60.50% 1232ms 1.74% boost::numeric::ublas::c_vector::operator() 0 0% 60.50% 1229ms 1.74% tcache_get (inline) 1229ms 1.74% 62.24% 1229ms 1.74% tcache_get_n (inline) 1ms 0.0014% 62.24% 1228ms 1.73% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 52ms 0.073% 62.31% 1213ms 1.71% Cell::GetCellData 26ms 0.037% 62.35% 1171ms 1.65% vtkFloatArray::~vtkFloatArray 295ms 0.42% 62.76% 1163ms 1.64% vtkObject::vtkObject 109ms 0.15% 62.92% 1136ms 1.60% boost::numeric::ublas::vector_assign 22ms 0.031% 62.95% 1115ms 1.57% AbstractTargetAreaModifier::UpdateTargetAreas 40ms 0.056% 63.01% 1112ms 1.57% vtkTypeFloat64Array::vtkTypeFloat64Array 39ms 0.055% 63.06% 1091ms 1.54% TargetAreaLinearGrowthModifier::UpdateTargetAreaOfCell 276ms 0.39% 63.45% 1078ms 1.52% std::vector::_M_default_append 1041ms 1.47% 64.92% 1041ms 1.47% __GI_sched_yield 484ms 0.68% 65.60% 1012ms 1.43% vtkTypeFloat64Array::PrintSelf 0 0% 65.60% 1008ms 1.42% vtkXMLWriter::WriteCellDataAppendedData 378ms 0.53% 66.14% 916ms 1.29% AbstractCellProperty::IsSame 304ms 0.43% 66.57% 910ms 1.29% AbstractElement::GetNodeLocation 595ms 0.84% 67.41% 909ms 1.28% vtkObjectBase::UnRegisterInternal 80ms 0.11% 67.52% 878ms 1.24% CellPropertyCollection::HasProperty 85ms 0.12% 67.64% 822ms 1.16% vtkAOSDataArrayTemplate::DataElementChanged 160ms 0.23% 67.87% 801ms 1.13% VertexMesh::GetAreaGradientOfElementAtNode 83ms 0.12% 67.98% 799ms 1.13% vtkDoubleArray::~vtkDoubleArray 239ms 0.34% 68.32% 792ms 1.12% vtkObject::Modified 287ms 0.41% 68.73% 776ms 1.10% hack_digit 116ms 0.16% 68.89% 746ms 1.05% VertexMesh::GetVolumeOfElement 745ms 1.05% 69.94% 745ms 1.05% std::_Rb_tree_increment 2ms 0.0028% 69.94% 737ms 1.04% vtkIdList::Allocate 130ms 0.18% 70.13% 733ms 1.04% std::_Rb_tree::_Rb_tree 726ms 1.03% 71.15% 726ms 1.03% tcache_put (inline) 57ms 0.08% 71.23% 722ms 1.02% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 680ms 0.96% 72.19% 680ms 0.96% [libchaste_cell_based.so] 430ms 0.61% 72.80% 680ms 0.96% std::basic_streambuf::xsputn 600ms 0.85% 73.65% 670ms 0.95% malloc_consolidate 625ms 0.88% 74.53% 625ms 0.88% [libchaste_mesh.so] 15ms 0.021% 74.55% 608ms 0.86% Node::RemoveElement 20ms 0.028% 74.58% 603ms 0.85% VertexMesh::GetSurfaceAreaOfElement 388ms 0.55% 75.13% 602ms 0.85% boost::numeric::ublas::detail::equals 173ms 0.24% 75.37% 599ms 0.85% std::__ostream_insert 75ms 0.11% 75.48% 587ms 0.83% vtkDataArray::vtkDataArray 29ms 0.041% 75.52% 573ms 0.81% MutableVertexMesh::CheckForSwapsFromShortEdges 1ms 0.0014% 75.52% 561ms 0.79% std::__basic_file::xsputn_2 230ms 0.32% 75.85% 560ms 0.79% AbstractCellPopulation::GetLocationIndexUsingCell 556ms 0.79% 76.63% 558ms 0.79% __GI___writev 67ms 0.095% 76.73% 547ms 0.77% AbstractCellBasedSimulation::DoCellBirth 284ms 0.4% 77.13% 539ms 0.76% std::_Hashtable::clear 94ms 0.13% 77.26% 524ms 0.74% std::num_put::_M_insert_int 523ms 0.74% 78.00% 523ms 0.74% [libstdc++.so.6.0.33] 520ms 0.73% 78.73% 520ms 0.73% [libvtkCommonCore-9.3.so.9.3] 519ms 0.73% 79.47% 519ms 0.73% Node::GetIndex 515ms 0.73% 80.19% 515ms 0.73% vtkTimeStamp::Modified 140ms 0.2% 80.39% 507ms 0.72% vtkAbstractArray::vtkAbstractArray 37ms 0.052% 80.44% 483ms 0.68% vtkIdList::New 93ms 0.13% 80.57% 468ms 0.66% vtkSOADataArrayTemplate::FillTypedComponent 3ms 0.0042% 80.58% 467ms 0.66% CellProliferativeTypesWriter::VisitCell 454ms 0.64% 81.22% 462ms 0.65% vtkObjectBase::Delete 451ms 0.64% 81.86% 451ms 0.64% Node::rGetLocation 98ms 0.14% 82.00% 440ms 0.62% vtkDataArray::~vtkDataArray 5ms 0.0071% 82.00% 430ms 0.61% std::basic_filebuf::overflow 239ms 0.34% 82.34% 426ms 0.6% CellPropertyCollection::AddProperty 3ms 0.0042% 82.34% 425ms 0.6% std::basic_filebuf::_M_convert_to_external 5ms 0.0071% 82.35% 421ms 0.59% std::__basic_file::xsputn 413ms 0.58% 82.93% 415ms 0.59% __GI___libc_write 407ms 0.57% 83.51% 407ms 0.57% std::_Rb_tree_insert_and_rebalance 403ms 0.57% 84.08% 405ms 0.57% vtkObject::~vtkObject 1ms 0.0014% 84.08% 394ms 0.56% vtkDataArray::ComputeRange 67ms 0.095% 84.17% 392ms 0.55% vtkIdList::~vtkIdList 388ms 0.55% 84.72% 388ms 0.55% std::ostream::sentry::sentry 14ms 0.02% 84.74% 387ms 0.55% CellProliferativeTypesWriter::GetCellDataForVtkOutput 360ms 0.51% 85.25% 360ms 0.51% __mpn_divrem