File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3785ms, 80.72% of 4689ms total Dropped 748 nodes (cum <= 23.45ms) flat flat% sum% cum cum% 0 0% 0% 4473ms 95.39% __libc_start_call_main 0 0% 0% 4473ms 95.39% __libc_start_main_impl 0 0% 0% 4473ms 95.39% _start 0 0% 0% 4455ms 95.01% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4455ms 95.01% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4455ms 95.01% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4455ms 95.01% main 0 0% 0% 4415ms 94.16% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4415ms 94.16% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4415ms 94.16% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4403ms 93.90% AbstractCellBasedSimulation::Solve 0 0% 0% 4110ms 87.65% AbstractCellPopulation::WriteResultsToFiles 16ms 0.34% 0.34% 3893ms 83.02% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.34% 1978ms 42.18% VertexMeshWriter::WriteVtkUsingMesh 0 0% 0.34% 1703ms 36.32% VertexMeshWriter::MakeVtkMesh 0 0% 0.34% 1281ms 27.32% vtkPolygon::New 2ms 0.043% 0.38% 1280ms 27.30% vtkPolygon::vtkPolygon 4ms 0.085% 0.47% 875ms 18.66% vtkCell::vtkCell 2ms 0.043% 0.51% 737ms 15.72% vtkPoints::New 8ms 0.17% 0.68% 701ms 14.95% vtkPoints::vtkPoints 6ms 0.13% 0.81% 671ms 14.31% VertexMeshWriter::WriteFiles 29ms 0.62% 1.43% 664ms 14.16% operator new 190ms 4.05% 5.48% 654ms 13.95% __GI___libc_malloc 3ms 0.064% 5.54% 630ms 13.44% std::ostream::operator<< (inline) 51ms 1.09% 6.63% 626ms 13.35% std::ostream::_M_insert 0 0% 6.63% 586ms 12.50% vtkLine::New 12ms 0.26% 6.89% 572ms 12.20% vtkLine::vtkLine 2ms 0.043% 6.93% 565ms 12.05% vtkQuad::New 4ms 0.085% 7.02% 560ms 11.94% vtkQuad::vtkQuad 0 0% 7.02% 560ms 11.94% vtkStreamingDemandDrivenPipeline::Update 0 0% 7.02% 560ms 11.94% vtkXMLWriterBase::Write 0 0% 7.02% 558ms 11.90% vtkDemandDrivenPipeline::ProcessRequest 0 0% 7.02% 556ms 11.86% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 7.02% 554ms 11.81% vtkDemandDrivenPipeline::ExecuteData 1ms 0.021% 7.04% 554ms 11.81% vtkExecutive::CallAlgorithm 0 0% 7.04% 553ms 11.79% vtkCompositeDataPipeline::ExecuteData 0 0% 7.04% 552ms 11.77% vtkXMLUnstructuredDataWriter::ProcessRequest 2ms 0.043% 7.08% 538ms 11.47% vtkTriangle::New 3ms 0.064% 7.14% 527ms 11.24% vtkTriangle::vtkTriangle 43ms 0.92% 8.06% 516ms 11.00% std::num_put::_M_insert_float 0 0% 8.06% 492ms 10.49% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 8.06% 492ms 10.49% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 116ms 2.47% 10.54% 470ms 10.02% __GI___libc_free 0 0% 10.54% 446ms 9.51% vtkXMLWriter::WriteBinaryData 30ms 0.64% 11.18% 442ms 9.43% vtkPoints::SetDataType 0 0% 11.18% 442ms 9.43% vtkXMLWriter::WriteBinaryDataBlock 0 0% 11.18% 442ms 9.43% vtkXMLWriter::WriteBinaryDataInternal 0 0% 11.18% 415ms 8.85% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 15ms 0.32% 11.49% 413ms 8.81% std::__cxx11::collate::do_transform 263ms 5.61% 17.10% 393ms 8.38% _int_malloc 0 0% 17.10% 383ms 8.17% ___vsnprintf 0 0% 17.10% 383ms 8.17% __vsnprintf_internal (inline) 55ms 1.17% 18.28% 379ms 8.08% __printf_buffer 0 0% 18.28% 374ms 7.98% vtkPolygon::~vtkPolygon 207ms 4.41% 22.69% 349ms 7.44% _int_free 0 0% 22.69% 341ms 7.27% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 22.69% 337ms 7.19% VtkMeshWriter::WriteFiles 0 0% 22.69% 321ms 6.85% vtkXMLWriter::WritePointsAppendedData 12ms 0.26% 22.95% 305ms 6.50% __printf_fp_l_buffer 0 0% 22.95% 305ms 6.50% __printf_fp_spec (inline) 4ms 0.085% 23.03% 299ms 6.38% vtkCell::~vtkCell 0 0% 23.03% 286ms 6.10% OnLatticeSimulation::UpdateCellLocationsAndTopology 4ms 0.085% 23.12% 286ms 6.10% PottsBasedCellPopulation::UpdateCellLocations 127ms 2.71% 25.83% 283ms 6.04% __printf_fp_buffer_1 51ms 1.09% 26.91% 264ms 5.63% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 30ms 0.64% 27.55% 243ms 5.18% std::__new_allocator::allocate (inline) 0 0% 27.55% 242ms 5.16% std::allocator_traits::allocate (inline) 3ms 0.064% 27.62% 241ms 5.14% std::__new_allocator::deallocate (inline) 0 0% 27.62% 237ms 5.05% std::allocator_traits::deallocate (inline) 0 0% 27.62% 224ms 4.78% vtkXMLWriter::WriteCompressionBlock 6ms 0.13% 27.75% 222ms 4.73% vtkBase64OutputStream::Write 0 0% 27.75% 213ms 4.54% compress2 45ms 0.96% 28.71% 213ms 4.54% crc32 0 0% 28.71% 213ms 4.54% deflate 0 0% 28.71% 213ms 4.54% vtkDataCompressor::Compress 0 0% 28.71% 213ms 4.54% vtkZLibDataCompressor::CompressBuffer 15ms 0.32% 29.03% 211ms 4.50% vtkBase64OutputStream::EncodeTriplet 7ms 0.15% 29.17% 206ms 4.39% vtkIdList::AllocateInternal 4ms 0.085% 29.26% 201ms 4.29% vtkPoints::~vtkPoints 0 0% 29.26% 190ms 4.05% tbb::detail::r1::parallel_pipeline 0 0% 29.26% 182ms 3.88% clone3 0 0% 29.26% 182ms 3.88% start_thread 6ms 0.13% 29.39% 182ms 3.88% vtkFloatArray::New 103ms 2.20% 31.58% 181ms 3.86% malloc_consolidate 34ms 0.73% 32.31% 177ms 3.77% std::ostream::write 2ms 0.043% 32.35% 174ms 3.71% tbb::detail::r1::reset 0 0% 32.35% 170ms 3.63% vtkQuad::~vtkQuad 0 0% 32.35% 167ms 3.56% NodesOnlyMesh::ConstructNodesWithoutMesh 68ms 1.45% 33.80% 166ms 3.54% tbb::detail::r1::wait_bounded_queue_monitor 77ms 1.64% 35.44% 164ms 3.50% std::basic_filebuf::xsputn 1ms 0.021% 35.47% 161ms 3.43% vtkTriangle::~vtkTriangle 0 0% 35.47% 158ms 3.37% vtkLine::GetParametricCenter 1ms 0.021% 35.49% 156ms 3.33% VertexMesh::VertexMesh 151ms 3.22% 38.71% 156ms 3.33% [libz.so.1.3] 0 0% 38.71% 154ms 3.28% VertexMesh::~VertexMesh 1ms 0.021% 38.73% 154ms 3.28% std::set::set (inline) 9ms 0.19% 38.92% 153ms 3.26% std::_Rb_tree::_Rb_tree 3ms 0.064% 38.98% 152ms 3.24% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 4ms 0.085% 39.07% 152ms 3.24% vtkFloatArray::vtkFloatArray 2ms 0.043% 39.11% 151ms 3.22% vtkTypeFloat64Array::~vtkTypeFloat64Array 0 0% 39.11% 150ms 3.20% std::_Rb_tree::_M_create_node (inline) 42ms 0.9% 40.01% 148ms 3.16% std::_Rb_tree::_M_erase 0 0% 40.01% 146ms 3.11% NodeLocationWriter::VisitAnyPopulation 0 0% 40.01% 144ms 3.07% std::_Rb_tree::_M_get_node (inline) 2ms 0.043% 40.05% 142ms 3.03% std::_Vector_base::_M_deallocate (inline) 0 0% 40.05% 141ms 3.01% VertexMesh::GenerateEdgesFromElements (inline) 7ms 0.15% 40.20% 140ms 2.99% MutableElement::BuildEdges 1ms 0.021% 40.22% 140ms 2.99% std::vector::~vector (inline) 2ms 0.043% 40.26% 139ms 2.96% std::_Rb_tree::~_Rb_tree (inline) 0 0% 40.26% 135ms 2.88% vtkIdList::Allocate 2ms 0.043% 40.31% 132ms 2.82% vtkDataArray::CreateDataArray 0 0% 40.31% 131ms 2.79% std::_Rb_tree::_Alloc_node::operator() (inline) 12ms 0.26% 40.56% 130ms 2.77% std::vector::_M_default_append 0 0% 40.56% 127ms 2.71% vtkFloatArray::~vtkFloatArray 25ms 0.53% 41.10% 124ms 2.64% vtkObject::vtkObject 5ms 0.11% 41.20% 121ms 2.58% vtkTypeFloat64Array::New 3ms 0.064% 41.27% 118ms 2.52% vtkDoubleArray::vtkDoubleArray 0 0% 41.27% 116ms 2.47% EdgeHelper::GetEdgeFromNodes 11ms 0.23% 41.50% 115ms 2.45% std::_Rb_tree::_M_copy (inline) 0 0% 41.50% 113ms 2.41% EdgeHelper::~EdgeHelper (inline) 0 0% 41.50% 113ms 2.41% std::_Vector_base::~_Vector_base (inline) 0 0% 41.50% 112ms 2.39% std::set::~set (inline) 2ms 0.043% 41.54% 108ms 2.30% std::operator<< (inline) 39ms 0.83% 42.38% 107ms 2.28% std::__ostream_insert 1ms 0.021% 42.40% 106ms 2.26% CellPropertyCollection::GetPropertiesType (inline) 106ms 2.26% 44.66% 106ms 2.26% unlink_chunk 3ms 0.064% 44.72% 105ms 2.24% std::map::operator[] (partial-inline) 52ms 1.11% 45.83% 102ms 2.18% vtkTypeFloat64Array::PrintSelf 10ms 0.21% 46.04% 101ms 2.15% std::_Rb_tree::_M_clone_node (inline) 0 0% 46.04% 101ms 2.15% std::_Rb_tree::_M_drop_node (inline) 47ms 1.00% 47.05% 99ms 2.11% hack_digit 1ms 0.021% 47.07% 99ms 2.11% std::_Vector_base::_M_allocate (inline) 98ms 2.09% 49.16% 98ms 2.09% __strcmp_avx2 0 0% 49.16% 97ms 2.07% AbstractCellProperty::IsSubType (inline) 97ms 2.07% 51.23% 97ms 2.07% __GI_sched_yield 0 0% 51.23% 97ms 2.07% std::_Rb_tree::_M_put_node (inline) 26ms 0.55% 51.78% 96ms 2.05% __dynamic_cast 3ms 0.064% 51.84% 96ms 2.05% vtkTypeFloat64Array::vtkTypeFloat64Array 9ms 0.19% 52.04% 94ms 2.00% _int_free_maybe_consolidate 1ms 0.021% 52.06% 93ms 1.98% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 60ms 1.28% 53.34% 93ms 1.98% vtkObjectBase::UnRegisterInternal 0 0% 53.34% 93ms 1.98% vtkXMLWriter::WritePointDataAppendedData 4ms 0.085% 53.42% 85ms 1.81% CellPropertyCollection::HasProperty 1ms 0.021% 53.44% 84ms 1.79% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 53.44% 84ms 1.79% Cell::HasCellProperty (inline) 8ms 0.17% 53.61% 84ms 1.79% boost::numeric::ublas::c_vector::c_vector (partial-inline) 12ms 0.26% 53.87% 84ms 1.79% vtkIdList::New 30ms 0.64% 54.51% 83ms 1.77% std::_Rb_tree::_M_lower_bound (inline) 20ms 0.43% 54.94% 83ms 1.77% vtkObject::Modified 0 0% 54.94% 81ms 1.73% AbstractCellProperty::IsType (inline) 50ms 1.07% 56.00% 81ms 1.73% std::basic_streambuf::xsputn 8ms 0.17% 56.17% 76ms 1.62% vtkDoubleArray::~vtkDoubleArray 0 0% 56.17% 75ms 1.60% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 1ms 0.021% 56.20% 74ms 1.58% boost::numeric::ublas::vector_assign (inline) 0 0% 56.20% 70ms 1.49% std::_Rb_tree::lower_bound (inline) 0 0% 56.20% 70ms 1.49% std::map::lower_bound (inline) 3ms 0.064% 56.26% 67ms 1.43% vtkAOSDataArrayTemplate::DataElementChanged 0 0% 56.26% 66ms 1.41% tcache_get (inline) 66ms 1.41% 57.67% 66ms 1.41% tcache_get_n (inline) 11ms 0.23% 57.90% 65ms 1.39% AbstractCellProperty::IsSame 0 0% 57.90% 62ms 1.32% NodesOnlyMesh::SetUpBoxCollection 62ms 1.32% 59.22% 62ms 1.32% vtkTimeStamp::Modified 1ms 0.021% 59.25% 60ms 1.28% std::set::insert (inline) 1ms 0.021% 59.27% 59ms 1.26% std::_Rb_tree::_M_insert_unique 1ms 0.021% 59.29% 55ms 1.17% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 14ms 0.3% 59.59% 55ms 1.17% boost::numeric::ublas::indexing_vector_assign 2ms 0.043% 59.63% 55ms 1.17% std::vector::push_back (inline) 1ms 0.021% 59.65% 55ms 1.17% vtkDataArray::vtkDataArray 16ms 0.34% 59.99% 55ms 1.17% vtkSOADataArrayTemplate::FillTypedComponent 0 0% 59.99% 54ms 1.15% Cell::GetCellProliferativeType 54ms 1.15% 61.14% 54ms 1.15% __GI___writev 0 0% 61.14% 54ms 1.15% std::__basic_file::xsputn_2 15ms 0.32% 61.46% 54ms 1.15% std::type_info::operator== (inline) 14ms 0.3% 61.76% 54ms 1.15% vtkAbstractArray::vtkAbstractArray 24ms 0.51% 62.27% 52ms 1.11% std::_Hashtable::clear 0 0% 62.27% 51ms 1.09% NodesOnlyMesh::~NodesOnlyMesh 49ms 1.04% 63.32% 49ms 1.04% __memcpy_avx_unaligned_erms 16ms 0.34% 63.66% 49ms 1.04% vtkDataArray::~vtkDataArray 47ms 1.00% 64.66% 47ms 1.00% [libvtkCommonCore-9.3.so.9.3] 3ms 0.064% 64.73% 46ms 0.98% std::_Rb_tree::_M_insert_ (inline) 32ms 0.68% 65.41% 45ms 0.96% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 65.41% 45ms 0.96% DistributedBoxCollection::IsOwned 28ms 0.6% 66.01% 45ms 0.96% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.043% 66.05% 45ms 0.96% std::vector::_M_realloc_insert 0 0% 66.05% 43ms 0.92% PottsMesh::GetMooreNeighbouringNodeIndices 8ms 0.17% 66.22% 42ms 0.9% VertexMeshWriter::GetNextNode 42ms 0.9% 67.11% 42ms 0.9% vtkObject::~vtkObject 2ms 0.043% 67.16% 41ms 0.87% VertexMesh::Clear 40ms 0.85% 68.01% 40ms 0.85% [libstdc++.so.6.0.33] 38ms 0.81% 68.82% 38ms 0.81% boost::numeric::ublas::c_vector::operator() 37ms 0.79% 69.61% 37ms 0.79% vtkObjectBase::Delete 0 0% 69.61% 36ms 0.77% CxxTest::RealWorldDescription::setUp 0 0% 69.61% 36ms 0.77% PMPI_Init_thread 0 0% 69.61% 36ms 0.77% PetscInitialize 0 0% 69.61% 36ms 0.77% PetscSetup::setUpWorld 0 0% 69.61% 36ms 0.77% PetscSetupUtils::CommonSetup 0 0% 69.61% 36ms 0.77% PetscSetupUtils::InitialisePetsc 36ms 0.77% 70.38% 36ms 0.77% __memset_avx2_unaligned_erms 9ms 0.19% 70.57% 36ms 0.77% _int_free_merge_chunk 0 0% 70.57% 36ms 0.77% ompi_mpi_init 7ms 0.15% 70.72% 36ms 0.77% std::num_put::_M_insert_int 0 0% 70.72% 36ms 0.77% vtkDataArray::ComputeRange 6ms 0.13% 70.85% 36ms 0.77% vtkIdList::~vtkIdList 36ms 0.77% 71.61% 36ms 0.77% vtkObjectBase::vtkObjectBase 1ms 0.021% 71.64% 35ms 0.75% Cell::GetCellId 0 0% 71.64% 35ms 0.75% _dl_init 0 0% 71.64% 35ms 0.75% call_init (inline) 0 0% 71.64% 35ms 0.75% std::basic_filebuf::open 0 0% 71.64% 35ms 0.75% std::make_unique (inline) 0 0% 71.64% 35ms 0.75% vtkDoubleArray::New 0 0% 71.64% 34ms 0.73% _dl_start_user 0 0% 71.64% 34ms 0.73% std::_Destroy (inline) 0 0% 71.64% 34ms 0.73% std::_Destroy_aux::__destroy (inline) 34ms 0.73% 72.36% 34ms 0.73% std::_Rb_tree::_S_right (inline) 3ms 0.064% 72.42% 34ms 0.73% vtkDataArrayPrivate::DoComputeVectorRange 5ms 0.11% 72.53% 33ms 0.7% 32ms 0.68% 73.21% 33ms 0.7% __GI___libc_write 33ms 0.7% 73.92% 33ms 0.7% std::codecvt::do_always_noconv 28ms 0.6% 74.51% 33ms 0.7% vtkObject::ObjectFinalize 0 0% 74.51% 32ms 0.68% CellIdWriter::GetCellDataForVtkOutput 32ms 0.68% 75.20% 32ms 0.68% __mpn_divrem 1ms 0.021% 75.22% 32ms 0.68% std::_Rb_tree::_M_emplace_hint_unique 0 0% 75.22% 32ms 0.68% std::__basic_file::xsputn 0 0% 75.22% 32ms 0.68% std::basic_filebuf::_M_convert_to_external 0 0% 75.22% 32ms 0.68% std::basic_filebuf::overflow 0 0% 75.22% 31ms 0.66% _IO_new_file_fopen 0 0% 75.22% 31ms 0.66% _IO_new_fopen 0 0% 75.22% 31ms 0.66% __GI__IO_file_open 0 0% 75.22% 31ms 0.66% __fopen_internal (inline) 0 0% 75.22% 31ms 0.66% boost::numeric::ublas::c_vector::assign (inline) 31ms 0.66% 75.88% 31ms 0.66% std::ostream::sentry::sentry 30ms 0.64% 76.52% 30ms 0.64% __libc_open64 0 0% 76.52% 30ms 0.64% std::__basic_file::open 0 0% 76.52% 29ms 0.62% Cell::GetMutationState 0 0% 76.52% 29ms 0.62% DistributedBoxCollection::~DistributedBoxCollection 0 0% 76.52% 29ms 0.62% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 76.52% 29ms 0.62% OutputFileHandler::OpenOutputFile 29ms 0.62% 77.14% 29ms 0.62% [libchaste_cell_based.so] 3ms 0.064% 77.20% 29ms 0.62% boost::serialization::singleton::get_instance 2ms 0.043% 77.24% 29ms 0.62% tbb::detail::r1::cancel_group_execution 0 0% 77.24% 29ms 0.62% vtk::detail::smp::vtkSMPToolsImplForTBB 2ms 0.043% 77.29% 29ms 0.62% vtkAOSDataArrayTemplate::AllocateTuples 4ms 0.085% 77.37% 29ms 0.62% vtkAOSDataArrayTemplate::InsertTuple 29ms 0.62% 77.99% 29ms 0.62% vtkObjectBase::~vtkObjectBase 4ms 0.085% 78.08% 28ms 0.6% DistributedBoxCollection::SetupLocalBoxesHalfOnly 0 0% 78.08% 28ms 0.6% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 0 0% 78.08% 28ms 0.6% std::_Rb_tree_header::_Rb_tree_header (inline) 0 0% 78.08% 27ms 0.58% VtkMeshWriter::MakeVtkMesh 27ms 0.58% 78.65% 27ms 0.58% std::_Rb_tree_header::_M_reset (inline) 0 0% 78.65% 27ms 0.58% std::less::operator() (inline) 0 0% 78.65% 27ms 0.58% std::map::~map (inline) 27ms 0.58% 79.23% 27ms 0.58% std::operator< (inline) 2ms 0.043% 79.27% 27ms 0.58% vtkSOADataArrayTemplate::GetTupleIndexFromValueIndex 1ms 0.021% 79.29% 26ms 0.55% CellProliferativeTypesWriter::GetCellDataForVtkOutput 3ms 0.064% 79.36% 26ms 0.55% Node::GetPoint 3ms 0.064% 79.42% 26ms 0.55% PottsMesh::GetVonNeumannNeighbouringNodeIndices 0 0% 79.42% 26ms 0.55% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 26ms 0.55% 79.97% 26ms 0.55% std::_Rb_tree_increment 0 0% 79.97% 25ms 0.53% Node::AddElement 1ms 0.021% 80.00% 25ms 0.53% orte_init 3ms 0.064% 80.06% 25ms 0.53% vtk::detail::smp::vtkSMPToolsImpl::For 0 0% 80.06% 25ms 0.53% vtkXMLUnstructuredDataWriter::WriteHeader 0 0% 80.06% 24ms 0.51% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 80.06% 24ms 0.51% Edge::Edge 0 0% 80.06% 24ms 0.51% Edge::SetNodes (inline) 1ms 0.021% 80.08% 24ms 0.51% Node::ConstructNodeAttributes (inline) 24ms 0.51% 80.59% 24ms 0.51% Node::GetIndex 0 0% 80.59% 24ms 0.51% Node::SetRadius 6ms 0.13% 80.72% 24ms 0.51% std::_Rb_tree_const_iterator::operator++ (inline)