File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3779ms, 80.30% of 4706ms total Dropped 784 nodes (cum <= 23.53ms) flat flat% sum% cum cum% 0 0% 0% 4516ms 95.96% __libc_start_call_main 0 0% 0% 4516ms 95.96% __libc_start_main_impl 0 0% 0% 4516ms 95.96% _start 0 0% 0% 4496ms 95.54% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4496ms 95.54% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4496ms 95.54% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4496ms 95.54% main 0 0% 0% 4452ms 94.60% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4452ms 94.60% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4452ms 94.60% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 1ms 0.021% 0.021% 4441ms 94.37% AbstractCellBasedSimulation::Solve 0 0% 0.021% 4138ms 87.93% AbstractCellPopulation::WriteResultsToFiles 9ms 0.19% 0.21% 3918ms 83.26% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.21% 1973ms 41.93% VertexMeshWriter::WriteVtkUsingMesh 0 0% 0.21% 1697ms 36.06% VertexMeshWriter::MakeVtkMesh 0 0% 0.21% 1246ms 26.48% vtkPolygon::New 2ms 0.042% 0.25% 1246ms 26.48% vtkPolygon::vtkPolygon 7ms 0.15% 0.4% 902ms 19.17% vtkCell::vtkCell 2ms 0.042% 0.45% 771ms 16.38% vtkPoints::New 10ms 0.21% 0.66% 723ms 15.36% vtkPoints::vtkPoints 1ms 0.021% 0.68% 689ms 14.64% VertexMeshWriter::WriteFiles 34ms 0.72% 1.40% 652ms 13.85% operator new 2ms 0.042% 1.44% 650ms 13.81% std::ostream::operator<< (inline) 60ms 1.27% 2.72% 647ms 13.75% std::ostream::_M_insert 2ms 0.042% 2.76% 629ms 13.37% vtkLine::New 1ms 0.021% 2.78% 625ms 13.28% vtkQuad::New 0 0% 2.78% 621ms 13.20% vtkQuad::vtkQuad 186ms 3.95% 6.74% 617ms 13.11% __GI___libc_malloc 9ms 0.19% 6.93% 611ms 12.98% vtkLine::vtkLine 0 0% 6.93% 567ms 12.05% vtkStreamingDemandDrivenPipeline::Update 0 0% 6.93% 567ms 12.05% vtkXMLWriterBase::Write 0 0% 6.93% 564ms 11.98% vtkDemandDrivenPipeline::ProcessRequest 0 0% 6.93% 561ms 11.92% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 6.93% 560ms 11.90% vtkDemandDrivenPipeline::ExecuteData 0 0% 6.93% 559ms 11.88% vtkExecutive::CallAlgorithm 0 0% 6.93% 556ms 11.81% vtkCompositeDataPipeline::ExecuteData 0 0% 6.93% 556ms 11.81% vtkXMLUnstructuredDataWriter::ProcessRequest 2ms 0.042% 6.97% 555ms 11.79% vtkTriangle::New 2ms 0.042% 7.01% 540ms 11.47% vtkTriangle::vtkTriangle 38ms 0.81% 7.82% 522ms 11.09% std::num_put::_M_insert_float 0 0% 7.82% 493ms 10.48% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 7.82% 493ms 10.48% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 98ms 2.08% 9.90% 488ms 10.37% __GI___libc_free 25ms 0.53% 10.43% 457ms 9.71% vtkPoints::SetDataType 0 0% 10.43% 448ms 9.52% vtkXMLWriter::WriteBinaryData 0 0% 10.43% 445ms 9.46% vtkXMLWriter::WriteBinaryDataBlock 0 0% 10.43% 445ms 9.46% vtkXMLWriter::WriteBinaryDataInternal 16ms 0.34% 10.77% 425ms 9.03% std::__cxx11::collate::do_transform 0 0% 10.77% 417ms 8.86% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 2ms 0.042% 10.82% 407ms 8.65% vtkPolygon::~vtkPolygon 2ms 0.042% 10.86% 393ms 8.35% ___vsnprintf 0 0% 10.86% 391ms 8.31% __vsnprintf_internal (inline) 238ms 5.06% 15.92% 386ms 8.20% _int_free 56ms 1.19% 17.11% 376ms 7.99% __printf_buffer 257ms 5.46% 22.57% 366ms 7.78% _int_malloc 0 0% 22.57% 339ms 7.20% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 22.57% 337ms 7.16% VtkMeshWriter::WriteFiles 8ms 0.17% 22.74% 329ms 6.99% vtkCell::~vtkCell 0 0% 22.74% 317ms 6.74% vtkXMLWriter::WritePointsAppendedData 16ms 0.34% 23.08% 300ms 6.37% __printf_fp_l_buffer 0 0% 23.08% 300ms 6.37% __printf_fp_spec (inline) 0 0% 23.08% 287ms 6.10% OnLatticeSimulation::UpdateCellLocationsAndTopology 5ms 0.11% 23.18% 287ms 6.10% PottsBasedCellPopulation::UpdateCellLocations 6ms 0.13% 23.31% 278ms 5.91% std::__new_allocator::deallocate (inline) 0 0% 23.31% 274ms 5.82% std::allocator_traits::deallocate (inline) 118ms 2.51% 25.82% 273ms 5.80% __printf_fp_buffer_1 31ms 0.66% 26.48% 266ms 5.65% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 27ms 0.57% 27.05% 252ms 5.35% std::__new_allocator::allocate (inline) 0 0% 27.05% 252ms 5.35% std::allocator_traits::allocate (inline) 0 0% 27.05% 227ms 4.82% vtkXMLWriter::WriteCompressionBlock 3ms 0.064% 27.11% 223ms 4.74% vtkBase64OutputStream::Write 8ms 0.17% 27.28% 222ms 4.72% vtkPoints::~vtkPoints 0 0% 27.28% 219ms 4.65% compress2 21ms 0.45% 27.73% 219ms 4.65% vtkBase64OutputStream::EncodeTriplet 0 0% 27.73% 219ms 4.65% vtkDataCompressor::Compress 0 0% 27.73% 219ms 4.65% vtkZLibDataCompressor::CompressBuffer 67ms 1.42% 29.15% 218ms 4.63% crc32 0 0% 29.15% 218ms 4.63% deflate 7ms 0.15% 29.30% 190ms 4.04% vtkFloatArray::New 2ms 0.042% 29.35% 183ms 3.89% vtkTriangle::~vtkTriangle 47ms 1% 30.34% 181ms 3.85% std::ostream::write 1ms 0.021% 30.37% 177ms 3.76% std::_Vector_base::_M_deallocate (inline) 115ms 2.44% 32.81% 176ms 3.74% malloc_consolidate 1ms 0.021% 32.83% 174ms 3.70% vtkLine::GetParametricCenter 1ms 0.021% 32.85% 172ms 3.65% std::set::set (inline) 20ms 0.42% 33.28% 171ms 3.63% std::_Rb_tree::_Rb_tree 1ms 0.021% 33.30% 168ms 3.57% vtkQuad::~vtkQuad 4ms 0.085% 33.38% 164ms 3.48% VertexMesh::VertexMesh 73ms 1.55% 34.93% 164ms 3.48% std::basic_filebuf::xsputn 12ms 0.25% 35.19% 163ms 3.46% std::vector::_M_default_append 3ms 0.064% 35.25% 162ms 3.44% NodesOnlyMesh::ConstructNodesWithoutMesh 0 0% 35.25% 162ms 3.44% std::vector::~vector (inline) 8ms 0.17% 35.42% 162ms 3.44% vtkIdList::AllocateInternal 0 0% 35.42% 160ms 3.40% VertexMesh::~VertexMesh 0 0% 35.42% 160ms 3.40% vtkTypeFloat64Array::~vtkTypeFloat64Array 1ms 0.021% 35.44% 158ms 3.36% vtkFloatArray::vtkFloatArray 0 0% 35.44% 154ms 3.27% clone3 0 0% 35.44% 154ms 3.27% start_thread 1ms 0.021% 35.47% 154ms 3.27% tbb::detail::r1::parallel_pipeline 3ms 0.064% 35.53% 147ms 3.12% MutableElement::BuildEdges 0 0% 35.53% 147ms 3.12% VertexMesh::GenerateEdgesFromElements (inline) 1ms 0.021% 35.55% 145ms 3.08% NodeLocationWriter::VisitAnyPopulation 0 0% 35.55% 145ms 3.08% tbb::detail::r1::reset 0 0% 35.55% 141ms 3.00% std::_Rb_tree::_M_create_node (inline) 135ms 2.87% 38.42% 139ms 2.95% [libz.so.1.3] 38ms 0.81% 39.23% 139ms 2.95% std::_Rb_tree::_M_erase 3ms 0.064% 39.29% 137ms 2.91% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.021% 39.31% 135ms 2.87% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 0 0% 39.31% 135ms 2.87% std::_Rb_tree::_M_get_node (inline) 3ms 0.064% 39.38% 134ms 2.85% vtkDataArray::CreateDataArray 0 0% 39.38% 132ms 2.80% std::_Vector_base::~_Vector_base (inline) 63ms 1.34% 40.71% 131ms 2.78% tbb::detail::r1::wait_bounded_queue_monitor 1ms 0.021% 40.74% 128ms 2.72% EdgeHelper::GetEdgeFromNodes 17ms 0.36% 41.10% 125ms 2.66% std::_Rb_tree::_M_copy (inline) 0 0% 41.10% 124ms 2.63% std::_Rb_tree::_Alloc_node::operator() (inline) 10ms 0.21% 41.31% 122ms 2.59% vtkTypeFloat64Array::New 1ms 0.021% 41.33% 120ms 2.55% CellPropertyCollection::GetPropertiesType (inline) 119ms 2.53% 43.86% 119ms 2.53% __strcmp_avx2 1ms 0.021% 43.88% 118ms 2.51% std::_Vector_base::_M_allocate (inline) 0 0% 43.88% 118ms 2.51% std::set::~set (inline) 3ms 0.064% 43.94% 118ms 2.51% vtkFloatArray::~vtkFloatArray 0 0% 43.94% 114ms 2.42% EdgeHelper::~EdgeHelper (inline) 5ms 0.11% 44.05% 114ms 2.42% vtkDoubleArray::vtkDoubleArray 1ms 0.021% 44.07% 106ms 2.25% AbstractCellProperty::IsSubType (inline) 56ms 1.19% 45.26% 106ms 2.25% vtkTypeFloat64Array::PrintSelf 26ms 0.55% 45.81% 104ms 2.21% __dynamic_cast 11ms 0.23% 46.05% 104ms 2.21% std::_Rb_tree::_M_clone_node (inline) 0 0% 46.05% 102ms 2.17% Cell::HasCellProperty (inline) 2ms 0.042% 46.09% 102ms 2.17% CellPropertyCollection::HasProperty 6ms 0.13% 46.22% 101ms 2.15% std::map::operator[] (partial-inline) 0 0% 46.22% 101ms 2.15% vtkIdList::Allocate 0 0% 46.22% 100ms 2.12% std::_Rb_tree::_M_drop_node (inline) 40ms 0.85% 47.07% 100ms 2.12% std::__ostream_insert 0 0% 47.07% 100ms 2.12% std::operator<< (inline) 0 0% 47.07% 100ms 2.12% vtkXMLWriter::WritePointDataAppendedData 18ms 0.38% 47.45% 99ms 2.10% vtkObject::vtkObject 56ms 1.19% 48.64% 98ms 2.08% hack_digit 0 0% 48.64% 98ms 2.08% std::_Rb_tree::_M_put_node (inline) 2ms 0.042% 48.68% 98ms 2.08% vtkTypeFloat64Array::vtkTypeFloat64Array 2ms 0.042% 48.73% 97ms 2.06% AbstractCellProperty::IsType (inline) 3ms 0.064% 48.79% 95ms 2.02% _int_free_maybe_consolidate 0 0% 48.79% 94ms 2.00% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 57ms 1.21% 50.00% 94ms 2.00% vtkObjectBase::UnRegisterInternal 5ms 0.11% 50.11% 88ms 1.87% vtkAOSDataArrayTemplate::DataElementChanged 30ms 0.64% 50.74% 88ms 1.87% vtkObject::Modified 30ms 0.64% 51.38% 84ms 1.78% std::_Rb_tree::_M_lower_bound (inline) 81ms 1.72% 53.10% 81ms 1.72% unlink_chunk 21ms 0.45% 53.55% 79ms 1.68% AbstractCellProperty::IsSame 2ms 0.042% 53.59% 76ms 1.61% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 1ms 0.021% 53.61% 75ms 1.59% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 3ms 0.064% 53.68% 74ms 1.57% vtkIdList::New 7ms 0.15% 53.82% 71ms 1.51% boost::numeric::ublas::c_vector::c_vector (inline) 67ms 1.42% 55.25% 67ms 1.42% __GI_sched_yield 50ms 1.06% 56.31% 67ms 1.42% std::basic_streambuf::xsputn 1ms 0.021% 56.33% 66ms 1.40% std::vector::push_back (inline) 9ms 0.19% 56.52% 66ms 1.40% vtkDoubleArray::~vtkDoubleArray 0 0% 56.52% 65ms 1.38% std::_Rb_tree::lower_bound (inline) 0 0% 56.52% 65ms 1.38% std::map::lower_bound (inline) 1ms 0.021% 56.54% 64ms 1.36% boost::numeric::ublas::vector_assign (inline) 1ms 0.021% 56.57% 63ms 1.34% Cell::GetCellProliferativeType 4ms 0.085% 56.65% 62ms 1.32% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 56.65% 61ms 1.30% NodesOnlyMesh::SetUpBoxCollection 0 0% 56.65% 61ms 1.30% tcache_get (inline) 61ms 1.30% 57.95% 61ms 1.30% tcache_get_n (inline) 60ms 1.27% 59.22% 60ms 1.27% __GI___writev 1ms 0.021% 59.24% 59ms 1.25% PottsMesh::GetMooreNeighbouringNodeIndices 0 0% 59.24% 59ms 1.25% std::__basic_file::xsputn_2 17ms 0.36% 59.60% 58ms 1.23% std::type_info::operator== (inline) 4ms 0.085% 59.69% 57ms 1.21% vtkDataArray::vtkDataArray 55ms 1.17% 60.86% 55ms 1.17% [libstdc++.so.6.0.33] 55ms 1.17% 62.03% 55ms 1.17% [libvtkCommonCore-9.3.so.9.3] 28ms 0.59% 62.62% 54ms 1.15% __cxxabiv1::__si_class_type_info::__do_dyncast 28ms 0.59% 63.22% 54ms 1.15% std::_Hashtable::clear 6ms 0.13% 63.34% 54ms 1.15% std::vector::_M_realloc_insert 54ms 1.15% 64.49% 54ms 1.15% vtkTimeStamp::Modified 16ms 0.34% 64.83% 52ms 1.10% vtkAbstractArray::vtkAbstractArray 0 0% 64.83% 51ms 1.08% NodesOnlyMesh::~NodesOnlyMesh 1ms 0.021% 64.85% 49ms 1.04% std::_Rb_tree::_M_insert_unique 0 0% 64.85% 49ms 1.04% std::set::insert (inline) 13ms 0.28% 65.13% 48ms 1.02% boost::numeric::ublas::indexing_vector_assign 2ms 0.042% 65.17% 46ms 0.98% VertexMesh::Clear 43ms 0.91% 66.09% 44ms 0.93% vtkObject::~vtkObject 0 0% 66.09% 43ms 0.91% _dl_init 0 0% 66.09% 43ms 0.91% call_init (inline) 0 0% 66.09% 43ms 0.91% std::_Destroy (inline) 0 0% 66.09% 43ms 0.91% std::_Destroy_aux::__destroy (inline) 27ms 0.57% 66.66% 41ms 0.87% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 66.66% 41ms 0.87% DistributedBoxCollection::IsOwned 2ms 0.042% 66.70% 40ms 0.85% 0 0% 66.70% 40ms 0.85% CxxTest::RealWorldDescription::setUp 0 0% 66.70% 40ms 0.85% PMPI_Init_thread 0 0% 66.70% 40ms 0.85% PetscInitialize 0 0% 66.70% 40ms 0.85% PetscSetup::setUpWorld 0 0% 66.70% 40ms 0.85% PetscSetupUtils::CommonSetup 0 0% 66.70% 40ms 0.85% PetscSetupUtils::InitialisePetsc 0 0% 66.70% 40ms 0.85% ompi_mpi_init 6ms 0.13% 66.83% 40ms 0.85% vtkDataArray::~vtkDataArray 6ms 0.13% 66.96% 40ms 0.85% vtkSOADataArrayTemplate::FillTypedComponent 11ms 0.23% 67.19% 39ms 0.83% VertexMeshWriter::GetNextNode 0 0% 67.19% 39ms 0.83% std::less::operator() (inline) 39ms 0.83% 68.02% 39ms 0.83% std::operator< (inline) 6ms 0.13% 68.15% 39ms 0.83% vtkIdList::~vtkIdList 0 0% 68.15% 37ms 0.79% DistributedBoxCollection::~DistributedBoxCollection 0 0% 68.15% 37ms 0.79% NodesOnlyMesh::ClearBoxCollection (inline) 34ms 0.72% 68.87% 37ms 0.79% vtkObject::ObjectFinalize 0 0% 68.87% 36ms 0.76% OutputFileHandler::OpenOutputFile 36ms 0.76% 69.63% 36ms 0.76% __memcpy_avx_unaligned_erms 0 0% 69.63% 36ms 0.76% _dl_start_user 0 0% 69.63% 36ms 0.76% std::_Rb_tree::_M_insert_ (inline) 3ms 0.064% 69.70% 36ms 0.76% std::num_put::_M_insert_int 1ms 0.021% 69.72% 36ms 0.76% vtkDataArray::ComputeRange 0 0% 69.72% 35ms 0.74% Cell::GetMutationState 5ms 0.11% 69.83% 35ms 0.74% vtkDataArrayPrivate::DoComputeVectorRange 35ms 0.74% 70.57% 35ms 0.74% vtkObjectBase::Delete 1ms 0.021% 70.59% 34ms 0.72% std::make_unique (inline) 33ms 0.7% 71.29% 33ms 0.7% __memset_avx2_unaligned_erms 1ms 0.021% 71.31% 33ms 0.7% std::__basic_file::xsputn 0 0% 71.31% 33ms 0.7% std::basic_filebuf::_M_convert_to_external 0 0% 71.31% 33ms 0.7% std::basic_filebuf::overflow 33ms 0.7% 72.01% 33ms 0.7% vtkObjectBase::~vtkObjectBase 32ms 0.68% 72.69% 32ms 0.68% __GI___libc_write 32ms 0.68% 73.37% 32ms 0.68% std::codecvt::do_always_noconv 0 0% 73.37% 31ms 0.66% Cell::GetCellId 2ms 0.042% 73.42% 31ms 0.66% DistributedBoxCollection::SetupLocalBoxesHalfOnly 1ms 0.021% 73.44% 31ms 0.66% VtkMeshWriter::MakeVtkMesh 31ms 0.66% 74.10% 31ms 0.66% std::_Rb_tree_increment 1ms 0.021% 74.12% 31ms 0.66% std::basic_filebuf::open 0 0% 74.12% 30ms 0.64% CellIdWriter::GetCellDataForVtkOutput 1ms 0.021% 74.14% 30ms 0.64% std::_Rb_tree::_M_emplace_hint_unique 0 0% 74.14% 30ms 0.64% std::default_delete::operator() (inline) 27ms 0.57% 74.71% 30ms 0.64% std::num_put::do_put 30ms 0.64% 75.35% 30ms 0.64% std::ostream::sentry::sentry 0 0% 75.35% 30ms 0.64% std::unique_ptr::~unique_ptr (inline) 0 0% 75.35% 29ms 0.62% boost::serialization::singleton::get_instance 1ms 0.021% 75.37% 28ms 0.59% CellProliferativeTypesWriter::GetCellDataForVtkOutput 28ms 0.59% 75.97% 28ms 0.59% __mpn_divrem 28ms 0.59% 76.56% 28ms 0.59% tcache_put (inline) 28ms 0.59% 77.16% 28ms 0.59% vtkAOSDataArrayTemplate::SetTuple 10ms 0.21% 77.37% 27ms 0.57% _int_free_merge_chunk 0 0% 77.37% 27ms 0.57% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 1ms 0.021% 77.39% 27ms 0.57% vtkDoubleArray::New 27ms 0.57% 77.96% 27ms 0.57% vtkObjectBase::vtkObjectBase 0 0% 77.96% 26ms 0.55% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 1ms 0.021% 77.99% 26ms 0.55% PottsMesh::GetVonNeumannNeighbouringNodeIndices 0 0% 77.99% 26ms 0.55% _IO_new_file_fopen 0 0% 77.99% 26ms 0.55% _IO_new_fopen 0 0% 77.99% 26ms 0.55% __GI__IO_file_open 0 0% 77.99% 26ms 0.55% __fopen_internal (inline) 25ms 0.53% 78.52% 26ms 0.55% __libc_open64 0 0% 78.52% 26ms 0.55% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 1ms 0.021% 78.54% 26ms 0.55% std::_Rb_tree_header::_Rb_tree_header (inline) 0 0% 78.54% 26ms 0.55% std::__basic_file::open 0 0% 78.54% 25ms 0.53% PottsBasedCellPopulation::AcceptCellWriter 25ms 0.53% 79.07% 25ms 0.53% [libchaste_cell_based.so] 25ms 0.53% 79.60% 25ms 0.53% boost::numeric::ublas::c_vector::operator() 1ms 0.021% 79.62% 25ms 0.53% vtkDataSet::GetCellTypes 0 0% 79.62% 24ms 0.51% Edge::~Edge (inline) 6ms 0.13% 79.75% 24ms 0.51% std::_Rb_tree_const_iterator::operator++ (inline) 24ms 0.51% 80.26% 24ms 0.51% std::_Rb_tree_header::_M_reset (inline) 2ms 0.042% 80.30% 24ms 0.51% tbb::detail::r1::cancel_group_execution 0 0% 80.30% 24ms 0.51% vtk::detail::smp::vtkSMPToolsImplForTBB 0 0% 80.30% 24ms 0.51% vtkXMLUnstructuredDataWriter::WriteHeader