File: Test2dVertexBasedSimulationWithFreeBoundary Type: cpu Showing nodes accounting for 60112ms, 86.17% of 69760ms total Dropped 896 nodes (cum <= 348.80ms) flat flat% sum% cum cum% 0 0% 0% 67714ms 97.07% __libc_start_call_main 0 0% 0% 67714ms 97.07% __libc_start_main_impl 0 0% 0% 67714ms 97.07% _start 0 0% 0% 67697ms 97.04% main 0 0% 0% 67667ms 97.00% Test2DVertexSimulationWithFreeBoundary::Test2DFreeBoundaryVertexSimulationForProfiling 0 0% 0% 66443ms 95.25% AbstractCellBasedSimulation::Solve 1ms 0.0014% 0.0014% 31571ms 45.26% AbstractCellPopulation::WriteResultsToFiles 17ms 0.024% 0.026% 24175ms 34.65% VertexBasedCellPopulation::WriteVtkResultsToFile 132ms 0.19% 0.22% 23971ms 34.36% VertexBasedCellPopulation::WriteCellVtkResultsToFile 0 0% 0.22% 20955ms 30.04% VertexMeshWriter::WriteVtkUsingMesh 118ms 0.17% 0.38% 20760ms 29.76% OffLatticeSimulation::UpdateCellLocationsAndTopology 23ms 0.033% 0.42% 20080ms 28.78% ForwardEulerNumericalMethod::UpdateAllNodePositions 68ms 0.097% 0.51% 19773ms 28.34% AbstractNumericalMethod::ComputeForcesIncludingDamping 37ms 0.053% 0.57% 17273ms 24.76% VertexMeshWriter::MakeVtkMesh 612ms 0.88% 1.44% 15219ms 21.82% FarhadifarForce::AddForceContribution 0 0% 1.44% 12949ms 18.56% AbstractCellBasedSimulation::UpdateCellPopulation 6ms 0.0086% 1.45% 12352ms 17.71% vtkPolygon::New 4ms 0.0057% 1.46% 12335ms 17.68% vtkPolygon::vtkPolygon 1ms 0.0014% 1.46% 11992ms 17.19% VertexBasedCellPopulation::Update 0 0% 1.46% 11950ms 17.13% MutableVertexMesh::ReMesh 44ms 0.063% 1.52% 9169ms 13.14% vtkCell::vtkCell 542ms 0.78% 2.30% 8204ms 11.76% operator new 2701ms 3.87% 6.17% 7490ms 10.74% __GI___libc_malloc 12ms 0.017% 6.19% 7326ms 10.50% vtkPoints::New 387ms 0.55% 6.74% 7047ms 10.10% MutableVertexMesh::CheckForIntersections 74ms 0.11% 6.85% 7035ms 10.08% vtkPoints::vtkPoints 222ms 0.32% 7.17% 6922ms 9.92% FarhadifarForce::GetLineTensionParameter 1118ms 1.60% 8.77% 6078ms 8.71% __GI___libc_free 1ms 0.0014% 8.77% 5967ms 8.55% vtkQuad::New 19ms 0.027% 8.80% 5959ms 8.54% vtkQuad::vtkQuad 12ms 0.017% 8.82% 5417ms 7.77% vtkLine::New 4ms 0.0057% 8.82% 5414ms 7.76% vtkTriangle::New 34ms 0.049% 8.87% 5367ms 7.69% vtkTriangle::vtkTriangle 27ms 0.039% 8.91% 5279ms 7.57% vtkLine::vtkLine 417ms 0.6% 9.51% 5262ms 7.54% VertexMesh::GetVectorFromAtoB 4353ms 6.24% 15.75% 4892ms 7.01% _int_free 18ms 0.026% 15.77% 4534ms 6.50% vtkPolygon::~vtkPolygon 267ms 0.38% 16.16% 4360ms 6.25% VertexBasedCellPopulation::GetDampingConstant 743ms 1.07% 17.22% 4352ms 6.24% std::_Rb_tree::_M_erase 180ms 0.26% 17.48% 4202ms 6.02% vtkPoints::SetDataType 1098ms 1.57% 19.05% 4162ms 5.97% __dynamic_cast 2791ms 4.00% 23.05% 3928ms 5.63% _int_malloc 632ms 0.91% 23.96% 3712ms 5.32% VertexMesh::ElementIncludesPoint 42ms 0.06% 24.02% 3583ms 5.14% vtkCell::~vtkCell 0 0% 24.02% 3578ms 5.13% vtkXMLWriterBase::Write 0 0% 24.02% 3577ms 5.13% vtkStreamingDemandDrivenPipeline::Update 2ms 0.0029% 24.02% 3556ms 5.10% vtkDemandDrivenPipeline::ProcessRequest 1ms 0.0014% 24.03% 3541ms 5.08% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 24.03% 3526ms 5.05% vtkDemandDrivenPipeline::ExecuteData 0 0% 24.03% 3523ms 5.05% vtkExecutive::CallAlgorithm 0 0% 24.03% 3515ms 5.04% vtkCompositeDataPipeline::ExecuteData 0 0% 24.03% 3507ms 5.03% vtkXMLUnstructuredDataWriter::ProcessRequest 435ms 0.62% 24.65% 3197ms 4.58% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 85ms 0.12% 24.77% 3194ms 4.58% Cell::GetMutationState 1738ms 2.49% 27.26% 3157ms 4.53% boost::numeric::ublas::indexing_vector_assign 6ms 0.0086% 27.27% 3110ms 4.46% MutableVertexMesh::RemoveDeletedNodesAndElements 1117ms 1.60% 28.87% 2996ms 4.29% std::_Rb_tree::_M_copy 276ms 0.4% 29.27% 2996ms 4.29% std::ostream::_M_insert 0 0% 29.27% 2993ms 4.29% vtkXMLUnstructuredDataWriter::WriteAPiece 1ms 0.0014% 29.27% 2993ms 4.29% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 232ms 0.33% 29.60% 2883ms 4.13% vtkObject::vtkObject 280ms 0.4% 30.00% 2520ms 3.61% vtkObject::Modified 227ms 0.33% 30.33% 2516ms 3.61% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 1ms 0.0014% 30.33% 2502ms 3.59% vtkXMLWriter::WriteBinaryData 17ms 0.024% 30.35% 2483ms 3.56% NodeLocationWriter::VisitAnyPopulation 0 0% 30.35% 2482ms 3.56% vtkXMLWriter::WriteBinaryDataInternal 1ms 0.0014% 30.36% 2480ms 3.56% vtkXMLWriter::WriteBinaryDataBlock 85ms 0.12% 30.48% 2456ms 3.52% vtkBase64OutputStream::Write 252ms 0.36% 30.84% 2447ms 3.51% AbstractCellPopulation::GetCellUsingLocationIndex 377ms 0.54% 31.38% 2426ms 3.48% std::__set_intersection 2425ms 3.48% 34.86% 2425ms 3.48% __memcpy_evex_unaligned_erms 306ms 0.44% 35.29% 2419ms 3.47% VertexMesh::GetNextEdgeGradientOfElementAtNode 416ms 0.6% 35.89% 2404ms 3.45% AbstractMesh::GetVectorFromAtoB 220ms 0.32% 36.21% 2336ms 3.35% vtkBase64OutputStream::EncodeTriplet 25ms 0.036% 36.24% 2279ms 3.27% MutableVertexMesh::RemoveDeletedNodes 30ms 0.043% 36.28% 2253ms 3.23% vtkPoints::~vtkPoints 65ms 0.093% 36.38% 2215ms 3.18% EdgeHelper::RemoveDeletedEdges 2184ms 3.13% 39.51% 2184ms 3.13% __strcmp_evex 1071ms 1.54% 41.04% 2165ms 3.10% __cxxabiv1::__si_class_type_info::__do_dyncast 138ms 0.2% 41.24% 2148ms 3.08% std::num_put::_M_insert_float 2124ms 3.04% 44.29% 2124ms 3.04% vtkTimeStamp::Modified 7ms 0.01% 44.30% 2096ms 3.00% tbb::detail::r1::parallel_pipeline 82ms 0.12% 44.41% 2086ms 2.99% Cell::GetCellProliferativeType 699ms 1.00% 45.42% 2072ms 2.97% EdgeHelper::UpdateEdgesMapKey 0 0% 45.42% 2013ms 2.89% clone3 0 0% 45.42% 2013ms 2.89% start_thread 10ms 0.014% 45.43% 2009ms 2.88% vtkQuad::~vtkQuad 43ms 0.062% 45.49% 1999ms 2.87% VertexBasedCellPopulation::AcceptCellWriter 1678ms 2.41% 47.90% 1991ms 2.85% vtkObjectBase::UnRegisterInternal 1979ms 2.84% 50.73% 1979ms 2.84% boost::numeric::ublas::same_impl_ex 105ms 0.15% 50.88% 1965ms 2.82% MutableElement::ResetIndex 0 0% 50.88% 1932ms 2.77% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 10ms 0.014% 50.90% 1923ms 2.76% tbb::detail::r1::reset 6ms 0.0086% 50.91% 1904ms 2.73% vtkTriangle::~vtkTriangle 787ms 1.13% 52.04% 1876ms 2.69% AbstractMesh::GetDistanceBetweenNodes 48ms 0.069% 52.10% 1797ms 2.58% std::__cxx11::collate::do_transform 13ms 0.019% 52.12% 1790ms 2.57% vtkLine::GetParametricCenter 1134ms 1.63% 53.75% 1782ms 2.55% tbb::detail::r1::wait_bounded_queue_monitor 142ms 0.2% 53.95% 1751ms 2.51% CellPopulationElementWriter::Visit 7ms 0.01% 53.96% 1749ms 2.51% vtkTypeFloat64Array::~vtkTypeFloat64Array 493ms 0.71% 54.67% 1747ms 2.50% std::ostream::write 34ms 0.049% 54.72% 1715ms 2.46% vtkIdList::AllocateInternal 14ms 0.02% 54.74% 1698ms 2.43% vtkFloatArray::New 9ms 0.013% 54.75% 1696ms 2.43% ___vsnprintf 2ms 0.0029% 54.75% 1687ms 2.42% __vsnprintf_internal (inline) 138ms 0.2% 54.95% 1663ms 2.38% __printf_buffer 21ms 0.03% 54.98% 1636ms 2.35% vtkDataArray::CreateDataArray 14ms 0.02% 55.00% 1629ms 2.34% vtkDoubleArray::vtkDoubleArray 11ms 0.016% 55.02% 1600ms 2.29% vtkFloatArray::vtkFloatArray 20ms 0.029% 55.05% 1568ms 2.25% vtkTypeFloat64Array::New 1533ms 2.20% 57.24% 1533ms 2.20% [libchaste_cell_based.so] 1497ms 2.15% 59.39% 1497ms 2.15% [libchaste_mesh.so] 1440ms 2.06% 61.45% 1441ms 2.07% std::map::operator[] 13ms 0.019% 61.47% 1434ms 2.06% vtkTypeFloat64Array::vtkTypeFloat64Array 1ms 0.0014% 61.47% 1423ms 2.04% __printf_fp_spec (inline) 35ms 0.05% 61.52% 1422ms 2.04% __printf_fp_l_buffer 467ms 0.67% 62.19% 1351ms 1.94% __printf_fp_buffer_1 14ms 0.02% 62.21% 1335ms 1.91% LegacyCellProliferativeTypesWriter::VisitCell 16ms 0.023% 62.24% 1323ms 1.90% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 1274ms 1.83% 64.06% 1274ms 1.83% boost::numeric::ublas::c_vector::operator() 70ms 0.1% 64.16% 1230ms 1.76% Cell::GetCellData 0 0% 64.16% 1220ms 1.75% VoronoiVertexMeshGenerator::GenerateVoronoiMesh 0 0% 64.16% 1220ms 1.75% VoronoiVertexMeshGenerator::VoronoiVertexMeshGenerator 544ms 0.78% 64.94% 1213ms 1.74% VoronoiVertexMeshGenerator::CreateVoronoiTessellation 1194ms 1.71% 66.65% 1194ms 1.71% [libvtkCommonCore-9.3.so.9.3] 30ms 0.043% 66.70% 1148ms 1.65% AbstractTargetAreaModifier::UpdateTargetAreas 617ms 0.88% 67.58% 1132ms 1.62% std::_Rb_tree::erase 31ms 0.044% 67.63% 1118ms 1.60% TargetAreaLinearGrowthModifier::UpdateTargetAreaOfCell 436ms 0.62% 68.25% 1076ms 1.54% std::basic_filebuf::xsputn 0 0% 68.25% 1052ms 1.51% vtkXMLWriter::WritePointsAppendedData 0 0% 68.25% 1033ms 1.48% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 1026ms 1.47% 69.72% 1026ms 1.47% vtkObjectBase::vtkObjectBase 107ms 0.15% 69.88% 1022ms 1.47% boost::numeric::ublas::vector_assign 32ms 0.046% 69.92% 988ms 1.42% vtkFloatArray::~vtkFloatArray 42ms 0.06% 69.98% 964ms 1.38% vtkDataArray::vtkDataArray 334ms 0.48% 70.46% 949ms 1.36% vtkAOSDataArrayTemplate::DataElementChanged 2ms 0.0029% 70.46% 933ms 1.34% vtkIdList::Allocate 144ms 0.21% 70.67% 927ms 1.33% std::_Rb_tree::_Rb_tree 45ms 0.065% 70.73% 911ms 1.31% vtkAbstractArray::vtkAbstractArray 279ms 0.4% 71.13% 893ms 1.28% AbstractElement::GetNodeLocation 0 0% 71.13% 867ms 1.24% vtkXMLWriter::WriteCellDataAppendedData 861ms 1.23% 72.37% 861ms 1.23% boost::numeric::ublas::vector_norm_2::apply 139ms 0.2% 72.57% 823ms 1.18% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 21ms 0.03% 72.60% 790ms 1.13% vtkDoubleArray::~vtkDoubleArray 51ms 0.073% 72.67% 781ms 1.12% CellPropertyCollection::HasProperty 147ms 0.21% 72.88% 759ms 1.09% VertexMesh::GetAreaGradientOfElementAtNode 757ms 1.09% 73.97% 757ms 1.09% [libstdc++.so.6.0.33] 703ms 1.01% 74.97% 745ms 1.07% malloc_consolidate 323ms 0.46% 75.44% 717ms 1.03% vtkTypeFloat64Array::PrintSelf 264ms 0.38% 75.82% 711ms 1.02% hack_digit 11ms 0.016% 75.83% 700ms 1.00% vtkIdList::New 246ms 0.35% 76.18% 674ms 0.97% AbstractCellProperty::IsSame 671ms 0.96% 77.15% 671ms 0.96% std::_Rb_tree_increment 339ms 0.49% 77.63% 652ms 0.93% CellPropertyCollection::AddProperty 38ms 0.054% 77.69% 652ms 0.93% MutableVertexMesh::CheckForSwapsFromShortEdges 626ms 0.9% 78.58% 626ms 0.9% __GI_sched_yield 206ms 0.3% 78.88% 620ms 0.89% std::vector::_M_default_append 0 0% 78.88% 618ms 0.89% tcache_get (inline) 618ms 0.89% 79.76% 618ms 0.89% tcache_get_n (inline) 614ms 0.88% 80.65% 615ms 0.88% boost::detail::sp_counted_base::release 610ms 0.87% 81.52% 610ms 0.87% tcache_put (inline) 127ms 0.18% 81.70% 592ms 0.85% AbstractCellBasedSimulation::DoCellBirth 399ms 0.57% 82.27% 582ms 0.83% std::basic_streambuf::xsputn 76ms 0.11% 82.38% 569ms 0.82% VertexMesh::GetVolumeOfElement 16ms 0.023% 82.41% 554ms 0.79% Node::RemoveElement 51ms 0.073% 82.48% 522ms 0.75% vtkDataArray::~vtkDataArray 5ms 0.0072% 82.49% 520ms 0.75% CellProliferativeTypesWriter::VisitCell 160ms 0.23% 82.72% 511ms 0.73% AbstractCellPopulation::GetLocationIndexUsingCell 174ms 0.25% 82.96% 502ms 0.72% std::__ostream_insert 328ms 0.47% 83.43% 498ms 0.71% boost::numeric::ublas::detail::equals 27ms 0.039% 83.47% 490ms 0.7% VertexMesh::GetSurfaceAreaOfElement 466ms 0.67% 84.14% 471ms 0.68% vtkObjectBase::RegisterInternal 27ms 0.039% 84.18% 465ms 0.67% vtkIdList::vtkIdList 37ms 0.053% 84.23% 462ms 0.66% Edge::AddElement 7ms 0.01% 84.24% 440ms 0.63% CellProliferativeTypesWriter::GetCellDataForVtkOutput 116ms 0.17% 84.41% 434ms 0.62% std::num_put::_M_insert_int 410ms 0.59% 85.00% 417ms 0.6% CellPropertyCollection::GetProperty 391ms 0.56% 85.56% 391ms 0.56% Node::GetIndex 1ms 0.0014% 85.56% 377ms 0.54% vtkDataArray::ComputeRange 30ms 0.043% 85.60% 371ms 0.53% vtkIdList::~vtkIdList 354ms 0.51% 86.11% 354ms 0.51% std::_Rb_tree_insert_and_rebalance 42ms 0.06% 86.17% 354ms 0.51% tbb::detail::r1::cancel_group_execution 0 0% 86.17% 353ms 0.51% vtk::detail::smp::vtkSMPToolsImplForTBB