File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3728ms, 80.03% of 4658ms total Dropped 724 nodes (cum <= 23.29ms) flat flat% sum% cum cum% 0 0% 0% 4478ms 96.14% __libc_start_call_main 0 0% 0% 4478ms 96.14% __libc_start_main_impl 0 0% 0% 4478ms 96.14% _start 0 0% 0% 4460ms 95.75% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4460ms 95.75% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4460ms 95.75% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4460ms 95.75% main 0 0% 0% 4420ms 94.89% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4420ms 94.89% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4420ms 94.89% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4408ms 94.63% AbstractCellBasedSimulation::Solve 0 0% 0% 4111ms 88.26% AbstractCellPopulation::WriteResultsToFiles 16ms 0.34% 0.34% 3901ms 83.75% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.34% 1975ms 42.40% VertexMeshWriter::WriteVtkUsingMesh 0 0% 0.34% 1701ms 36.52% VertexMeshWriter::MakeVtkMesh 0 0% 0.34% 1284ms 27.57% vtkPolygon::New 3ms 0.064% 0.41% 1283ms 27.54% vtkPolygon::vtkPolygon 2ms 0.043% 0.45% 912ms 19.58% vtkCell::vtkCell 3ms 0.064% 0.52% 784ms 16.83% vtkPoints::New 13ms 0.28% 0.79% 743ms 15.95% vtkPoints::vtkPoints 39ms 0.84% 1.63% 666ms 14.30% operator new 1ms 0.021% 1.65% 665ms 14.28% VertexMeshWriter::WriteFiles 187ms 4.01% 5.67% 632ms 13.57% __GI___libc_malloc 50ms 1.07% 6.74% 628ms 13.48% std::ostream::_M_insert 1ms 0.021% 6.76% 626ms 13.44% std::ostream::operator<< (inline) 4ms 0.086% 6.85% 600ms 12.88% vtkQuad::New 1ms 0.021% 6.87% 593ms 12.73% vtkQuad::vtkQuad 0 0% 6.87% 562ms 12.07% vtkStreamingDemandDrivenPipeline::Update 0 0% 6.87% 562ms 12.07% vtkXMLWriterBase::Write 0 0% 6.87% 560ms 12.02% vtkDemandDrivenPipeline::ProcessRequest 0 0% 6.87% 559ms 12.00% vtkStreamingDemandDrivenPipeline::ProcessRequest 1ms 0.021% 6.89% 557ms 11.96% vtkDemandDrivenPipeline::ExecuteData 1ms 0.021% 6.91% 556ms 11.94% vtkTriangle::New 0 0% 6.91% 555ms 11.91% vtkCompositeDataPipeline::ExecuteData 0 0% 6.91% 555ms 11.91% vtkExecutive::CallAlgorithm 0 0% 6.91% 554ms 11.89% vtkXMLUnstructuredDataWriter::ProcessRequest 2ms 0.043% 6.96% 549ms 11.79% vtkLine::New 5ms 0.11% 7.06% 546ms 11.72% vtkTriangle::vtkTriangle 11ms 0.24% 7.30% 533ms 11.44% vtkLine::vtkLine 35ms 0.75% 8.05% 510ms 10.95% std::num_put::_M_insert_float 36ms 0.77% 8.82% 504ms 10.82% vtkPoints::SetDataType 0 0% 8.82% 499ms 10.71% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 8.82% 499ms 10.71% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 109ms 2.34% 11.16% 478ms 10.26% __GI___libc_free 0 0% 11.16% 453ms 9.73% vtkXMLWriter::WriteBinaryData 1ms 0.021% 11.19% 450ms 9.66% vtkXMLWriter::WriteBinaryDataInternal 0 0% 11.19% 449ms 9.64% vtkXMLWriter::WriteBinaryDataBlock 0 0% 11.19% 430ms 9.23% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 12ms 0.26% 11.44% 409ms 8.78% std::__cxx11::collate::do_transform 3ms 0.064% 11.51% 384ms 8.24% ___vsnprintf 1ms 0.021% 11.53% 381ms 8.18% __vsnprintf_internal (inline) 62ms 1.33% 12.86% 374ms 8.03% __printf_buffer 0 0% 12.86% 370ms 7.94% vtkPolygon::~vtkPolygon 250ms 5.37% 18.23% 368ms 7.90% _int_free 220ms 4.72% 22.95% 363ms 7.79% _int_malloc 0 0% 22.95% 331ms 7.11% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 22.95% 329ms 7.06% VtkMeshWriter::WriteFiles 0 0% 22.95% 326ms 7.00% vtkXMLWriter::WritePointsAppendedData 0 0% 22.95% 295ms 6.33% OnLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.064% 23.01% 295ms 6.33% PottsBasedCellPopulation::UpdateCellLocations 3ms 0.064% 23.08% 294ms 6.31% vtkCell::~vtkCell 10ms 0.21% 23.29% 292ms 6.27% __printf_fp_l_buffer 0 0% 23.29% 292ms 6.27% __printf_fp_spec (inline) 41ms 0.88% 24.17% 290ms 6.23% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 42ms 0.9% 25.08% 284ms 6.10% std::__new_allocator::allocate (inline) 0 0% 25.08% 280ms 6.01% std::allocator_traits::allocate (inline) 133ms 2.86% 27.93% 267ms 5.73% __printf_fp_buffer_1 3ms 0.064% 27.99% 265ms 5.69% std::__new_allocator::deallocate (inline) 0 0% 27.99% 262ms 5.62% std::allocator_traits::deallocate (inline) 0 0% 27.99% 230ms 4.94% vtkXMLWriter::WriteCompressionBlock 4ms 0.086% 28.08% 224ms 4.81% vtkBase64OutputStream::Write 15ms 0.32% 28.40% 217ms 4.66% vtkBase64OutputStream::EncodeTriplet 0 0% 28.40% 216ms 4.64% compress2 0 0% 28.40% 216ms 4.64% vtkDataCompressor::Compress 0 0% 28.40% 216ms 4.64% vtkZLibDataCompressor::CompressBuffer 49ms 1.05% 29.45% 215ms 4.62% crc32 0 0% 29.45% 215ms 4.62% deflate 3ms 0.064% 29.52% 193ms 4.14% vtkPoints::~vtkPoints 13ms 0.28% 29.80% 190ms 4.08% std::_Rb_tree::_Rb_tree 0 0% 29.80% 190ms 4.08% std::set::set (inline) 113ms 2.43% 32.22% 187ms 4.01% malloc_consolidate 3ms 0.064% 32.29% 185ms 3.97% vtkDataArray::CreateDataArray 9ms 0.19% 32.48% 183ms 3.93% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.064% 32.55% 179ms 3.84% NodesOnlyMesh::ConstructNodesWithoutMesh 39ms 0.84% 33.38% 179ms 3.84% std::_Rb_tree::_M_erase 5ms 0.11% 33.49% 179ms 3.84% vtkIdList::AllocateInternal 48ms 1.03% 34.52% 173ms 3.71% std::ostream::write 0 0% 34.52% 172ms 3.69% std::_Rb_tree::_M_create_node (inline) 2ms 0.043% 34.56% 172ms 3.69% vtkQuad::~vtkQuad 10ms 0.21% 34.78% 172ms 3.69% vtkTypeFloat64Array::New 2ms 0.043% 34.82% 169ms 3.63% vtkLine::GetParametricCenter 1ms 0.021% 34.84% 168ms 3.61% vtkTriangle::~vtkTriangle 5ms 0.11% 34.95% 165ms 3.54% vtkFloatArray::New 0 0% 34.95% 159ms 3.41% std::_Rb_tree::_M_get_node (inline) 0 0% 34.95% 158ms 3.39% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 34.95% 156ms 3.35% VertexMesh::~VertexMesh 13ms 0.28% 35.23% 156ms 3.35% std::_Rb_tree::_M_copy (inline) 2ms 0.043% 35.27% 156ms 3.35% vtkTypeFloat64Array::~vtkTypeFloat64Array 151ms 3.24% 38.51% 155ms 3.33% [libz.so.1.3] 5ms 0.11% 38.62% 155ms 3.33% vtkDoubleArray::vtkDoubleArray 56ms 1.20% 39.82% 153ms 3.28% std::basic_filebuf::xsputn 0 0% 39.82% 151ms 3.24% VertexMesh::VertexMesh 10ms 0.21% 40.04% 149ms 3.20% std::vector::_M_default_append 1ms 0.021% 40.06% 149ms 3.20% tbb::detail::r1::parallel_pipeline 0 0% 40.06% 148ms 3.18% std::set::~set (inline) 0 0% 40.06% 148ms 3.18% std::vector::~vector (inline) 0 0% 40.06% 146ms 3.13% clone3 0 0% 40.06% 146ms 3.13% start_thread 1ms 0.021% 40.08% 145ms 3.11% VertexMesh::GenerateEdgesFromElements (inline) 7ms 0.15% 40.23% 144ms 3.09% MutableElement::BuildEdges 2ms 0.043% 40.27% 144ms 3.09% vtkFloatArray::vtkFloatArray 1ms 0.021% 40.30% 143ms 3.07% NodeLocationWriter::VisitAnyPopulation 4ms 0.086% 40.38% 143ms 3.07% vtkTypeFloat64Array::vtkTypeFloat64Array 8ms 0.17% 40.55% 139ms 2.98% std::_Vector_base::_M_deallocate (inline) 3ms 0.064% 40.62% 138ms 2.96% tbb::detail::r1::reset 0 0% 40.62% 137ms 2.94% std::_Rb_tree::_M_drop_node (inline) 9ms 0.19% 40.81% 136ms 2.92% std::_Rb_tree::_M_clone_node (inline) 0 0% 40.81% 131ms 2.81% vtkIdList::Allocate 0 0% 40.81% 130ms 2.79% std::_Rb_tree::_M_put_node (inline) 5ms 0.11% 40.92% 128ms 2.75% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 2ms 0.043% 40.96% 122ms 2.62% vtkFloatArray::~vtkFloatArray 49ms 1.05% 42.01% 121ms 2.60% tbb::detail::r1::wait_bounded_queue_monitor 2ms 0.043% 42.06% 120ms 2.58% EdgeHelper::GetEdgeFromNodes 0 0% 42.06% 120ms 2.58% std::_Vector_base::_M_allocate (inline) 0 0% 42.06% 115ms 2.47% EdgeHelper::~EdgeHelper (inline) 1ms 0.021% 42.08% 114ms 2.45% CellPropertyCollection::GetPropertiesType (inline) 31ms 0.67% 42.74% 110ms 2.36% vtkObject::vtkObject 1ms 0.021% 42.77% 107ms 2.30% std::_Vector_base::~_Vector_base (inline) 34ms 0.73% 43.50% 105ms 2.25% std::__ostream_insert 0 0% 43.50% 103ms 2.21% vtkXMLWriter::WritePointDataAppendedData 102ms 2.19% 45.68% 102ms 2.19% __strcmp_avx2 3ms 0.064% 45.75% 102ms 2.19% std::operator<< (inline) 99ms 2.13% 47.87% 99ms 2.13% unlink_chunk 0 0% 47.87% 94ms 2.02% AbstractCellProperty::IsSubType (inline) 18ms 0.39% 48.26% 93ms 2.00% __dynamic_cast 0 0% 48.26% 90ms 1.93% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 1ms 0.021% 48.28% 89ms 1.91% CellPropertyCollection::HasProperty 5ms 0.11% 48.39% 89ms 1.91% std::map::operator[] (partial-inline) 0 0% 48.39% 88ms 1.89% Cell::HasCellProperty (inline) 41ms 0.88% 49.27% 88ms 1.89% vtkTypeFloat64Array::PrintSelf 40ms 0.86% 50.13% 86ms 1.85% hack_digit 9ms 0.19% 50.32% 86ms 1.85% vtkAOSDataArrayTemplate::DataElementChanged 6ms 0.13% 50.45% 84ms 1.80% vtkIdList::New 3ms 0.064% 50.52% 83ms 1.78% AbstractCellProperty::IsType (inline) 4ms 0.086% 50.60% 82ms 1.76% _int_free_maybe_consolidate 50ms 1.07% 51.67% 81ms 1.74% vtkObjectBase::UnRegisterInternal 45ms 0.97% 52.64% 76ms 1.63% std::basic_streambuf::xsputn 22ms 0.47% 53.11% 76ms 1.63% vtkObject::Modified 2ms 0.043% 53.16% 74ms 1.59% std::vector::push_back (inline) 0 0% 53.16% 72ms 1.55% NodesOnlyMesh::SetUpBoxCollection 23ms 0.49% 53.65% 72ms 1.55% std::_Rb_tree::_M_lower_bound (inline) 0 0% 53.65% 72ms 1.55% tcache_get (inline) 72ms 1.55% 55.20% 72ms 1.55% tcache_get_n (inline) 71ms 1.52% 56.72% 71ms 1.52% __GI_sched_yield 0 0% 56.72% 68ms 1.46% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 0 0% 56.72% 67ms 1.44% PottsMesh::GetMooreNeighbouringNodeIndices 1ms 0.021% 56.74% 66ms 1.42% Cell::GetCellProliferativeType 0 0% 56.74% 64ms 1.37% NodesOnlyMesh::~NodesOnlyMesh 5ms 0.11% 56.85% 62ms 1.33% vtkDoubleArray::~vtkDoubleArray 15ms 0.32% 57.17% 60ms 1.29% AbstractCellProperty::IsSame 0 0% 57.17% 58ms 1.25% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 5ms 0.11% 57.28% 58ms 1.25% boost::numeric::ublas::c_vector::c_vector (inline) 4ms 0.086% 57.36% 58ms 1.25% vtkDataArray::vtkDataArray 31ms 0.67% 58.03% 57ms 1.22% std::_Hashtable::clear 3ms 0.064% 58.09% 56ms 1.20% std::vector::_M_realloc_insert 29ms 0.62% 58.72% 53ms 1.14% __cxxabiv1::__si_class_type_info::__do_dyncast 19ms 0.41% 59.12% 53ms 1.14% vtkAbstractArray::vtkAbstractArray 52ms 1.12% 60.24% 52ms 1.12% [libstdc++.so.6.0.33] 2ms 0.043% 60.28% 52ms 1.12% std::__basic_file::xsputn_2 0 0% 60.28% 51ms 1.09% AbstractCellPopulation::GetCellUsingLocationIndex 51ms 1.09% 61.38% 51ms 1.09% [libvtkCommonCore-9.3.so.9.3] 3ms 0.064% 61.44% 51ms 1.09% std::_Rb_tree::_M_insert_unique 0 0% 61.44% 51ms 1.09% std::set::insert (inline) 19ms 0.41% 61.85% 51ms 1.09% vtkDataArray::~vtkDataArray 51ms 1.09% 62.95% 51ms 1.09% vtkTimeStamp::Modified 50ms 1.07% 64.02% 50ms 1.07% __GI___writev 0 0% 64.02% 49ms 1.05% boost::numeric::ublas::vector_assign (inline) 0 0% 64.02% 49ms 1.05% std::_Rb_tree::lower_bound (inline) 0 0% 64.02% 49ms 1.05% std::map::lower_bound (inline) 8ms 0.17% 64.19% 49ms 1.05% vtkSOADataArrayTemplate::FillTypedComponent 8ms 0.17% 64.36% 47ms 1.01% VertexMeshWriter::GetNextNode 0 0% 64.36% 45ms 0.97% std::_Destroy (inline) 0 0% 64.36% 45ms 0.97% std::_Destroy_aux::__destroy (inline) 45ms 0.97% 65.33% 45ms 0.97% std::codecvt::do_always_noconv 2ms 0.043% 65.37% 45ms 0.97% std::num_put::_M_insert_int 9ms 0.19% 65.56% 45ms 0.97% std::type_info::operator== (inline) 3ms 0.064% 65.63% 43ms 0.92% DistributedBoxCollection::SetupLocalBoxesHalfOnly 43ms 0.92% 66.55% 43ms 0.92% __memcpy_avx_unaligned_erms 1ms 0.021% 66.57% 41ms 0.88% VertexMesh::Clear 41ms 0.88% 67.45% 41ms 0.88% vtkObjectBase::Delete 0 0% 67.45% 40ms 0.86% DistributedBoxCollection::~DistributedBoxCollection 0 0% 67.45% 40ms 0.86% NodesOnlyMesh::ClearBoxCollection (inline) 40ms 0.86% 68.31% 40ms 0.86% std::ostream::sentry::sentry 40ms 0.86% 69.17% 40ms 0.86% vtkObject::~vtkObject 5ms 0.11% 69.28% 39ms 0.84% std::_Rb_tree::_M_insert_ (inline) 38ms 0.82% 70.09% 38ms 0.82% __memset_avx2_unaligned_erms 1ms 0.021% 70.12% 38ms 0.82% std::make_unique (inline) 0 0% 70.12% 38ms 0.82% vtkDataArray::ComputeRange 0 0% 70.12% 37ms 0.79% CxxTest::RealWorldDescription::setUp 0 0% 70.12% 37ms 0.79% PetscSetup::setUpWorld 0 0% 70.12% 37ms 0.79% PetscSetupUtils::CommonSetup 0 0% 70.12% 36ms 0.77% PMPI_Init_thread 0 0% 70.12% 36ms 0.77% PetscInitialize 0 0% 70.12% 36ms 0.77% PetscSetupUtils::InitialisePetsc 0 0% 70.12% 36ms 0.77% _dl_init 0 0% 70.12% 36ms 0.77% call_init (inline) 0 0% 70.12% 36ms 0.77% ompi_mpi_init 36ms 0.77% 70.89% 36ms 0.77% vtkObjectBase::~vtkObjectBase 0 0% 70.89% 35ms 0.75% Cell::GetCellId 1ms 0.021% 70.91% 35ms 0.75% DistributedBoxCollection::IsOwned 3ms 0.064% 70.97% 35ms 0.75% std::_Rb_tree::_M_emplace_hint_unique 0 0% 70.97% 35ms 0.75% std::less::operator() (inline) 0 0% 70.97% 35ms 0.75% std::map::~map (inline) 35ms 0.75% 71.73% 35ms 0.75% std::operator< (inline) 20ms 0.43% 72.16% 34ms 0.73% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 72.16% 34ms 0.73% _dl_start_user 0 0% 72.16% 33ms 0.71% CellIdWriter::GetCellDataForVtkOutput 0 0% 72.16% 33ms 0.71% CellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 72.16% 33ms 0.71% std::basic_filebuf::open 2ms 0.043% 72.20% 32ms 0.69% 0 0% 72.20% 32ms 0.69% _IO_new_fopen 0 0% 72.20% 32ms 0.69% __fopen_internal (inline) 5ms 0.11% 72.31% 32ms 0.69% vtkDataArrayPrivate::DoComputeVectorRange 5ms 0.11% 72.41% 32ms 0.69% vtkIdList::~vtkIdList 0 0% 72.41% 31ms 0.67% _IO_new_file_fopen 0 0% 72.41% 31ms 0.67% __GI__IO_file_open 0 0% 72.41% 31ms 0.67% std::__basic_file::open 0 0% 72.41% 31ms 0.67% vtk::detail::smp::vtkSMPToolsImplForTBB 24ms 0.52% 72.93% 31ms 0.67% vtkObject::ObjectFinalize 30ms 0.64% 73.57% 30ms 0.64% __libc_open64 13ms 0.28% 73.85% 30ms 0.64% std::__new_allocator::construct (inline) 0 0% 73.85% 30ms 0.64% std::allocator_traits::construct (inline) 0 0% 73.85% 29ms 0.62% Node::ConstructNodeAttributes (inline) 0 0% 73.85% 29ms 0.62% Node::SetRadius 3ms 0.064% 73.92% 29ms 0.62% Node::~Node 0 0% 73.92% 29ms 0.62% OutputFileHandler::OpenOutputFile 2ms 0.043% 73.96% 29ms 0.62% PottsMesh::GetVonNeumannNeighbouringNodeIndices 29ms 0.62% 74.58% 29ms 0.62% boost::numeric::ublas::c_vector::operator() 8ms 0.17% 74.75% 29ms 0.62% boost::numeric::ublas::indexing_vector_assign 29ms 0.62% 75.38% 29ms 0.62% vtkBase64Utilities::EncodeTriplet 0 0% 75.38% 29ms 0.62% vtkDoubleArray::New 28ms 0.6% 75.98% 28ms 0.6% std::_Rb_tree_increment 0 0% 75.98% 28ms 0.6% std::default_delete::operator() (inline) 22ms 0.47% 76.45% 28ms 0.6% std::num_put::do_put 0 0% 76.45% 28ms 0.6% std::unique_ptr::~unique_ptr (inline) 3ms 0.064% 76.51% 28ms 0.6% tbb::detail::r1::cancel_group_execution 28ms 0.6% 77.11% 28ms 0.6% vtkDataArray::Modified 27ms 0.58% 77.69% 27ms 0.58% __mpn_divrem 2ms 0.043% 77.74% 27ms 0.58% boost::serialization::singleton::get_instance 4ms 0.086% 77.82% 27ms 0.58% vtkAOSDataArrayTemplate::InsertTuple 27ms 0.58% 78.40% 27ms 0.58% vtkObjectBase::vtkObjectBase 0 0% 78.40% 26ms 0.56% Cell::GetMutationState 1ms 0.021% 78.42% 26ms 0.56% Edge::Edge 3ms 0.064% 78.49% 26ms 0.56% NodeAttributes::NodeAttributes 1ms 0.021% 78.51% 26ms 0.56% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 26ms 0.56% 79.07% 26ms 0.56% vtkAOSDataArrayTemplate::SetTuple 0 0% 79.07% 25ms 0.54% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 1ms 0.021% 79.09% 25ms 0.54% std::basic_filebuf::_M_convert_to_external 0 0% 79.09% 25ms 0.54% std::basic_filebuf::overflow 0 0% 79.09% 24ms 0.52% Edge::SetNodes (inline) 0 0% 79.09% 24ms 0.52% NodesOnlyMesh::Clear (inline) 1ms 0.021% 79.11% 24ms 0.52% PottsBasedCellPopulation::AcceptCellWriter 24ms 0.52% 79.63% 24ms 0.52% __GI___libc_write 5ms 0.11% 79.73% 24ms 0.52% _int_free_merge_chunk 1ms 0.021% 79.76% 24ms 0.52% std::_Rb_tree::find (inline) 0 0% 79.76% 24ms 0.52% std::__basic_file::xsputn 0 0% 79.76% 24ms 0.52% std::basic_ofstream::basic_ofstream (inline) 0 0% 79.76% 24ms 0.52% std::basic_ofstream::open (inline) 0 0% 79.76% 24ms 0.52% std::map::find (inline) 2ms 0.043% 79.80% 24ms 0.52% vtkAOSDataArrayTemplate::AllocateTuples 0 0% 79.80% 24ms 0.52% vtkDataSet::GetCellTypes 11ms 0.24% 80.03% 24ms 0.52% vtkIdList::vtkIdList