File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 4128ms, 80.48% of 5129ms total Dropped 779 nodes (cum <= 25.64ms) flat flat% sum% cum cum% 0 0% 0% 4943ms 96.37% __libc_start_call_main 0 0% 0% 4943ms 96.37% __libc_start_main_impl 0 0% 0% 4943ms 96.37% _start 0 0% 0% 4924ms 96.00% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4924ms 96.00% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4924ms 96.00% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4924ms 96.00% main 0 0% 0% 4882ms 95.18% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4882ms 95.18% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4882ms 95.18% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4870ms 94.95% AbstractCellBasedSimulation::Solve 0 0% 0% 4433ms 86.43% AbstractCellPopulation::WriteResultsToFiles 15ms 0.29% 0.29% 4215ms 82.18% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.29% 2035ms 39.68% VertexMeshWriter::WriteVtkUsingMesh 4ms 0.078% 0.37% 1738ms 33.89% VertexMeshWriter::MakeVtkMesh 1ms 0.019% 0.39% 1256ms 24.49% vtkPolygon::New 1ms 0.019% 0.41% 1254ms 24.45% vtkPolygon::vtkPolygon 5ms 0.097% 0.51% 875ms 17.06% vtkCell::vtkCell 4ms 0.078% 0.58% 745ms 14.53% vtkPoints::New 0 0% 0.58% 707ms 13.78% VertexMeshWriter::WriteFiles 9ms 0.18% 0.76% 689ms 13.43% vtkPoints::vtkPoints 47ms 0.92% 1.68% 659ms 12.85% std::ostream::_M_insert 2ms 0.039% 1.72% 657ms 12.81% std::ostream::operator<< (inline) 35ms 0.68% 2.40% 654ms 12.75% operator new 203ms 3.96% 6.36% 637ms 12.42% __GI___libc_malloc 0 0% 6.36% 615ms 11.99% vtkStreamingDemandDrivenPipeline::Update 0 0% 6.36% 615ms 11.99% vtkXMLWriterBase::Write 0 0% 6.36% 613ms 11.95% vtkDemandDrivenPipeline::ProcessRequest 0 0% 6.36% 606ms 11.82% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 6.36% 605ms 11.80% vtkDemandDrivenPipeline::ExecuteData 1ms 0.019% 6.38% 605ms 11.80% vtkQuad::New 0 0% 6.38% 604ms 11.78% vtkExecutive::CallAlgorithm 0 0% 6.38% 603ms 11.76% vtkCompositeDataPipeline::ExecuteData 7ms 0.14% 6.51% 603ms 11.76% vtkQuad::vtkQuad 1ms 0.019% 6.53% 602ms 11.74% vtkXMLUnstructuredDataWriter::ProcessRequest 2ms 0.039% 6.57% 579ms 11.29% vtkLine::New 130ms 2.53% 9.11% 572ms 11.15% __GI___libc_free 11ms 0.21% 9.32% 558ms 10.88% vtkLine::vtkLine 1ms 0.019% 9.34% 554ms 10.80% vtkTriangle::New 4ms 0.078% 9.42% 543ms 10.59% vtkTriangle::vtkTriangle 37ms 0.72% 10.14% 534ms 10.41% std::num_put::_M_insert_float 0 0% 10.14% 534ms 10.41% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 10.14% 534ms 10.41% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 10.14% 474ms 9.24% vtkXMLWriter::WriteBinaryData 0 0% 10.14% 471ms 9.18% vtkXMLWriter::WriteBinaryDataBlock 0 0% 10.14% 471ms 9.18% vtkXMLWriter::WriteBinaryDataInternal 0 0% 10.14% 464ms 9.05% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 236ms 4.60% 14.74% 440ms 8.58% _int_free 8ms 0.16% 14.90% 433ms 8.44% std::__cxx11::collate::do_transform 25ms 0.49% 15.38% 431ms 8.40% vtkPoints::SetDataType 0 0% 15.38% 424ms 8.27% OnLatticeSimulation::UpdateCellLocationsAndTopology 5ms 0.097% 15.48% 424ms 8.27% PottsBasedCellPopulation::UpdateCellLocations 1ms 0.019% 15.50% 413ms 8.05% vtkPolygon::~vtkPolygon 2ms 0.039% 15.54% 410ms 7.99% ___vsnprintf 0 0% 15.54% 409ms 7.97% __vsnprintf_internal (inline) 62ms 1.21% 16.75% 402ms 7.84% __printf_buffer 0 0% 16.75% 381ms 7.43% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 16.75% 381ms 7.43% VtkMeshWriter::WriteFiles 250ms 4.87% 21.62% 369ms 7.19% _int_malloc 0 0% 21.62% 355ms 6.92% vtkXMLWriter::WritePointsAppendedData 1ms 0.019% 21.64% 344ms 6.71% std::__new_allocator::deallocate (inline) 0 0% 21.64% 344ms 6.71% std::allocator_traits::deallocate (inline) 5ms 0.097% 21.74% 331ms 6.45% vtkCell::~vtkCell 92ms 1.79% 23.53% 328ms 6.40% std::__new_allocator::allocate (inline) 0 0% 23.53% 326ms 6.36% std::allocator_traits::allocate (inline) 12ms 0.23% 23.77% 310ms 6.04% __printf_fp_l_buffer 0 0% 23.77% 310ms 6.04% __printf_fp_spec (inline) 1ms 0.019% 23.79% 299ms 5.83% std::set::set (inline) 25ms 0.49% 24.27% 298ms 5.81% std::_Rb_tree::_Rb_tree 40ms 0.78% 25.05% 287ms 5.60% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 124ms 2.42% 27.47% 278ms 5.42% __printf_fp_buffer_1 0 0% 27.47% 260ms 5.07% VertexMesh::~VertexMesh 0 0% 27.47% 247ms 4.82% vtkXMLWriter::WriteCompressionBlock 142ms 2.77% 30.24% 233ms 4.54% malloc_consolidate 8ms 0.16% 30.40% 232ms 4.52% std::_Vector_base::_M_deallocate (inline) 5ms 0.097% 30.49% 232ms 4.52% vtkBase64OutputStream::Write 0 0% 30.49% 231ms 4.50% compress2 0 0% 30.49% 231ms 4.50% vtkDataCompressor::Compress 0 0% 30.49% 231ms 4.50% vtkZLibDataCompressor::CompressBuffer 54ms 1.05% 31.55% 228ms 4.45% crc32 0 0% 31.55% 228ms 4.45% deflate 0 0% 31.55% 227ms 4.43% std::_Rb_tree::_M_create_node (inline) 13ms 0.25% 31.80% 226ms 4.41% vtkBase64OutputStream::EncodeTriplet 6ms 0.12% 31.92% 222ms 4.33% vtkPoints::~vtkPoints 9ms 0.18% 32.09% 219ms 4.27% std::_Rb_tree::_M_copy (inline) 0 0% 32.09% 219ms 4.27% std::vector::~vector (inline) 0 0% 32.09% 212ms 4.13% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 32.09% 208ms 4.06% std::_Rb_tree::_M_get_node (inline) 27ms 0.53% 32.62% 206ms 4.02% std::_Rb_tree::_M_clone_node (inline) 46ms 0.9% 33.52% 203ms 3.96% std::ostream::write 1ms 0.019% 33.53% 199ms 3.88% std::_Vector_base::~_Vector_base (inline) 64ms 1.25% 34.78% 192ms 3.74% std::_Rb_tree::_M_erase 5ms 0.097% 34.88% 188ms 3.67% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.019% 34.90% 185ms 3.61% vtkLine::GetParametricCenter 0 0% 34.90% 184ms 3.59% vtkQuad::~vtkQuad 0 0% 34.90% 182ms 3.55% EdgeHelper::~EdgeHelper (inline) 2ms 0.039% 34.94% 181ms 3.53% vtkTriangle::~vtkTriangle 71ms 1.38% 36.32% 179ms 3.49% std::basic_filebuf::xsputn 5ms 0.097% 36.42% 178ms 3.47% vtkFloatArray::New 3ms 0.058% 36.48% 177ms 3.45% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 2ms 0.039% 36.52% 175ms 3.41% VertexMesh::VertexMesh 1ms 0.019% 36.54% 168ms 3.28% NodesOnlyMesh::ConstructNodesWithoutMesh 5ms 0.097% 36.63% 167ms 3.26% vtkIdList::AllocateInternal 163ms 3.18% 39.81% 165ms 3.22% [libz.so.1.3] 2ms 0.039% 39.85% 162ms 3.16% vtkTypeFloat64Array::~vtkTypeFloat64Array 2ms 0.039% 39.89% 157ms 3.06% tbb::detail::r1::parallel_pipeline 2ms 0.039% 39.93% 157ms 3.06% vtkFloatArray::vtkFloatArray 0 0% 39.93% 151ms 2.94% VertexMesh::GenerateEdgesFromElements (inline) 9ms 0.18% 40.11% 150ms 2.92% MutableElement::BuildEdges 9ms 0.18% 40.28% 150ms 2.92% _int_free_maybe_consolidate 0 0% 40.28% 148ms 2.89% clone3 0 0% 40.28% 148ms 2.89% start_thread 2ms 0.039% 40.32% 148ms 2.89% vtkDataArray::CreateDataArray 13ms 0.25% 40.57% 146ms 2.85% std::vector::_M_default_append 0 0% 40.57% 144ms 2.81% NodeLocationWriter::VisitAnyPopulation 2ms 0.039% 40.61% 139ms 2.71% tbb::detail::r1::reset 10ms 0.19% 40.81% 138ms 2.69% vtkTypeFloat64Array::New 2ms 0.039% 40.85% 135ms 2.63% vtkDoubleArray::vtkDoubleArray 57ms 1.11% 41.96% 133ms 2.59% tbb::detail::r1::wait_bounded_queue_monitor 0 0% 41.96% 129ms 2.52% std::set::~set (inline) 0 0% 41.96% 126ms 2.46% std::_Rb_tree::_M_drop_node (inline) 0 0% 41.96% 123ms 2.40% PottsMesh::GetMooreNeighbouringNodeIndices 61ms 1.19% 43.15% 123ms 2.40% vtkTypeFloat64Array::PrintSelf 4ms 0.078% 43.22% 121ms 2.36% EdgeHelper::GetEdgeFromNodes 3ms 0.058% 43.28% 120ms 2.34% CellPropertyCollection::GetPropertiesType (inline) 0 0% 43.28% 120ms 2.34% std::_Rb_tree::_M_put_node (inline) 1ms 0.019% 43.30% 119ms 2.32% std::_Vector_base::_M_allocate (inline) 116ms 2.26% 45.56% 116ms 2.26% __strcmp_avx2 3ms 0.058% 45.62% 115ms 2.24% vtkTypeFloat64Array::vtkTypeFloat64Array 23ms 0.45% 46.07% 113ms 2.20% vtkObject::vtkObject 111ms 2.16% 48.24% 111ms 2.16% unlink_chunk 1ms 0.019% 48.26% 111ms 2.16% vtkIdList::Allocate 0 0% 48.26% 109ms 2.13% vtkXMLWriter::WritePointDataAppendedData 0 0% 48.26% 108ms 2.11% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 1ms 0.019% 48.27% 106ms 2.07% vtkFloatArray::~vtkFloatArray 46ms 0.9% 49.17% 99ms 1.93% hack_digit 0 0% 49.17% 98ms 1.91% AbstractCellProperty::IsSubType (inline) 2ms 0.039% 49.21% 97ms 1.89% CellPropertyCollection::HasProperty 26ms 0.51% 49.72% 97ms 1.89% __dynamic_cast 0 0% 49.72% 96ms 1.87% Cell::HasCellProperty (inline) 50ms 0.97% 50.69% 95ms 1.85% vtkObjectBase::UnRegisterInternal 2ms 0.039% 50.73% 93ms 1.81% AbstractCellProperty::IsType (inline) 26ms 0.51% 51.24% 90ms 1.75% std::__ostream_insert 1ms 0.019% 51.26% 83ms 1.62% std::map::operator[] (partial-inline) 1ms 0.019% 51.28% 83ms 1.62% std::operator<< (inline) 4ms 0.078% 51.36% 82ms 1.60% vtkIdList::New 1ms 0.019% 51.37% 79ms 1.54% VertexMesh::Clear 18ms 0.35% 51.73% 76ms 1.48% vtkObject::Modified 2ms 0.039% 51.76% 75ms 1.46% NodesOnlyMesh::~NodesOnlyMesh 6ms 0.12% 51.88% 75ms 1.46% vtkDoubleArray::~vtkDoubleArray 3ms 0.058% 51.94% 74ms 1.44% std::vector::push_back (inline) 13ms 0.25% 52.19% 74ms 1.44% vtkAOSDataArrayTemplate::DataElementChanged 73ms 1.42% 53.62% 73ms 1.42% __GI_sched_yield 15ms 0.29% 53.91% 73ms 1.42% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.019% 53.93% 69ms 1.35% std::__basic_file::xsputn_2 0 0% 53.93% 68ms 1.33% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 67ms 1.31% 55.23% 67ms 1.31% __GI___writev 3ms 0.058% 55.29% 65ms 1.27% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 55.29% 65ms 1.27% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 2ms 0.039% 55.33% 64ms 1.25% std::_Rb_tree::_M_insert_unique 0 0% 55.33% 64ms 1.25% std::set::insert (inline) 9ms 0.18% 55.51% 63ms 1.23% AbstractCellProperty::IsSame 0 0% 55.51% 63ms 1.23% NodesOnlyMesh::SetUpBoxCollection 35ms 0.68% 56.19% 61ms 1.19% std::_Hashtable::clear 7ms 0.14% 56.33% 61ms 1.19% std::vector::_M_realloc_insert 33ms 0.64% 56.97% 60ms 1.17% std::basic_streambuf::xsputn 0 0% 56.97% 60ms 1.17% tcache_get (inline) 60ms 1.17% 58.14% 60ms 1.17% tcache_get_n (inline) 1ms 0.019% 58.16% 59ms 1.15% Cell::GetCellProliferativeType 59ms 1.15% 59.31% 59ms 1.15% Node::GetIndex 0 0% 59.31% 59ms 1.15% std::map::~map (inline) 3ms 0.058% 59.37% 57ms 1.11% vtkDataArray::vtkDataArray 3ms 0.058% 59.43% 56ms 1.09% VertexMeshWriter::GetNextNode 56ms 1.09% 60.52% 56ms 1.09% vtkTimeStamp::Modified 1ms 0.019% 60.54% 54ms 1.05% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.019% 60.56% 54ms 1.05% boost::numeric::ublas::vector_assign (inline) 0 0% 60.56% 54ms 1.05% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 1ms 0.019% 60.58% 54ms 1.05% std::_Rb_tree_header::_Rb_tree_header (inline) 12ms 0.23% 60.81% 54ms 1.05% std::type_info::operator== (inline) 53ms 1.03% 61.84% 53ms 1.03% [libvtkCommonCore-9.3.so.9.3] 0 0% 61.84% 53ms 1.03% std::_Rb_tree::lower_bound (inline) 53ms 1.03% 62.88% 53ms 1.03% std::_Rb_tree_header::_M_reset (inline) 0 0% 62.88% 53ms 1.03% std::map::lower_bound (inline) 0 0% 62.88% 51ms 0.99% PottsMesh::GetVonNeumannNeighbouringNodeIndices 12ms 0.23% 63.11% 50ms 0.97% vtkAbstractArray::vtkAbstractArray 26ms 0.51% 63.62% 47ms 0.92% __cxxabiv1::__si_class_type_info::__do_dyncast 9ms 0.18% 63.79% 47ms 0.92% std::num_put::_M_insert_int 46ms 0.9% 64.69% 47ms 0.92% vtkObject::~vtkObject 1ms 0.019% 64.71% 45ms 0.88% vtkDataArray::ComputeRange 36ms 0.7% 65.41% 45ms 0.88% vtkObject::ObjectFinalize 0 0% 65.41% 44ms 0.86% VtkMeshWriter::MakeVtkMesh 44ms 0.86% 66.27% 44ms 0.86% __memcpy_avx_unaligned_erms 44ms 0.86% 67.13% 44ms 0.86% vtkObjectBase::~vtkObjectBase 0 0% 67.13% 43ms 0.84% DistributedBoxCollection::IsOwned 0 0% 67.13% 43ms 0.84% DistributedBoxCollection::~DistributedBoxCollection 0 0% 67.13% 43ms 0.84% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 67.13% 43ms 0.84% VertexMeshWriter::GetNextElement 6ms 0.12% 67.25% 43ms 0.84% std::_Rb_tree::_M_insert_ (inline) 16ms 0.31% 67.56% 43ms 0.84% vtkDataArray::~vtkDataArray 9ms 0.18% 67.73% 43ms 0.84% vtkSOADataArrayTemplate::FillTypedComponent 23ms 0.45% 68.18% 42ms 0.82% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 68.18% 42ms 0.82% _dl_init 14ms 0.27% 68.45% 42ms 0.82% boost::numeric::ublas::indexing_vector_assign 0 0% 68.45% 42ms 0.82% call_init (inline) 42ms 0.82% 69.27% 42ms 0.82% std::ostream::sentry::sentry 5ms 0.097% 69.37% 42ms 0.82% vtkIdList::~vtkIdList 41ms 0.8% 70.17% 41ms 0.8% [libstdc++.so.6.0.33] 0 0% 70.17% 40ms 0.78% _IO_new_fopen 0 0% 70.17% 40ms 0.78% __fopen_internal (inline) 0 0% 70.17% 40ms 0.78% std::basic_filebuf::open 0 0% 70.17% 39ms 0.76% std::__basic_file::open 39ms 0.76% 70.93% 39ms 0.76% std::codecvt::do_always_noconv 7ms 0.14% 71.07% 38ms 0.74% Node::~Node 1ms 0.019% 71.09% 38ms 0.74% _IO_new_file_fopen 0 0% 71.09% 38ms 0.74% _dl_start_user 10ms 0.19% 71.28% 38ms 0.74% _int_free_merge_chunk 0 0% 71.28% 38ms 0.74% std::less::operator() (inline) 38ms 0.74% 72.02% 38ms 0.74% std::operator< (inline) 37ms 0.72% 72.74% 38ms 0.74% vtkObjectBase::Delete 0 0% 72.74% 37ms 0.72% Cell::GetMutationState 0 0% 72.74% 37ms 0.72% CxxTest::RealWorldDescription::setUp 0 0% 72.74% 37ms 0.72% PetscInitialize 0 0% 72.74% 37ms 0.72% PetscSetup::setUpWorld 0 0% 72.74% 37ms 0.72% PetscSetupUtils::CommonSetup 0 0% 72.74% 37ms 0.72% PetscSetupUtils::InitialisePetsc 0 0% 72.74% 37ms 0.72% __GI__IO_file_open 37ms 0.72% 73.46% 37ms 0.72% __libc_open64 1ms 0.019% 73.48% 37ms 0.72% std::make_unique (inline) 3ms 0.058% 73.54% 37ms 0.72% vtkDoubleArray::New 0 0% 73.54% 36ms 0.7% Cell::GetCellId 0 0% 73.54% 36ms 0.7% PMPI_Init_thread 0 0% 73.54% 36ms 0.7% ompi_mpi_init 35ms 0.68% 74.22% 35ms 0.68% __mpn_divrem 0 0% 74.22% 35ms 0.68% vtk::detail::smp::vtkSMPToolsImplForTBB 0 0% 74.22% 34ms 0.66% CellIdWriter::GetCellDataForVtkOutput 3ms 0.058% 74.28% 33ms 0.64% boost::serialization::singleton::get_instance 6ms 0.12% 74.40% 33ms 0.64% tbb::detail::r1::cancel_group_execution 10ms 0.19% 74.60% 33ms 0.64% vtkIdList::vtkIdList 32ms 0.62% 75.22% 32ms 0.62% __GI___libc_write 0 0% 75.22% 32ms 0.62% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 1ms 0.019% 75.24% 32ms 0.62% std::basic_filebuf::_M_convert_to_external 0 0% 75.24% 32ms 0.62% std::basic_filebuf::overflow 1ms 0.019% 75.26% 32ms 0.62% vtkDataArrayPrivate::DoComputeVectorRange 1ms 0.019% 75.28% 31ms 0.6% Node::AddElement 0 0% 75.28% 31ms 0.6% VertexElement::~VertexElement 31ms 0.6% 75.88% 31ms 0.6% std::_Rb_tree::_S_right (inline) 0 0% 75.88% 31ms 0.6% std::__basic_file::xsputn 5ms 0.097% 75.98% 31ms 0.6% vtkAOSDataArrayTemplate::AllocateTuples 4ms 0.078% 76.06% 30ms 0.58% 0 0% 76.06% 30ms 0.58% NodesOnlyMesh::Clear (inline) 30ms 0.58% 76.64% 30ms 0.58% __memset_avx2_unaligned_erms 16ms 0.31% 76.95% 30ms 0.58% std::__new_allocator::construct (inline) 0 0% 76.95% 30ms 0.58% std::allocator_traits::construct (inline) 30ms 0.58% 77.54% 30ms 0.58% vtkObjectBase::vtkObjectBase 1ms 0.019% 77.56% 29ms 0.57% DistributedBoxCollection::SetupLocalBoxesHalfOnly 0 0% 77.56% 29ms 0.57% std::_Destroy (inline) 0 0% 77.56% 29ms 0.57% std::_Destroy_aux::__destroy (inline) 2ms 0.039% 77.60% 29ms 0.57% std::_Rb_tree::_M_emplace_hint_unique 5ms 0.097% 77.70% 29ms 0.57% vtkAOSDataArrayTemplate::InsertTuple 5ms 0.097% 77.79% 27ms 0.53% AbstractTetrahedralMeshWriter::GetNextNode 3ms 0.058% 77.85% 27ms 0.53% Edge::Edge 0 0% 77.85% 27ms 0.53% OutputFileHandler::OpenOutputFile 27ms 0.53% 78.38% 27ms 0.53% [libchaste_cell_based.so] 20ms 0.39% 78.77% 27ms 0.53% _int_free_create_chunk (inline) 24ms 0.47% 79.24% 27ms 0.53% std::num_put::do_put 27ms 0.53% 79.76% 27ms 0.53% vtkAOSDataArrayTemplate::SetTuple 0 0% 79.76% 27ms 0.53% vtkDataArrayPrivate::DoComputeScalarRange 3ms 0.058% 79.82% 26ms 0.51% Node::GetPoint 4ms 0.078% 79.90% 26ms 0.51% vtk::detail::smp::vtkSMPToolsImpl::For 26ms 0.51% 80.41% 26ms 0.51% vtkDataArray::Modified 3ms 0.058% 80.46% 26ms 0.51% vtkSOADataArrayTemplate::GetTupleIndexFromValueIndex 1ms 0.019% 80.48% 26ms 0.51% vtkXMLUnstructuredDataWriter::WriteHeader