File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3758ms, 79.57% of 4723ms total Dropped 770 nodes (cum <= 23.61ms) flat flat% sum% cum cum% 0 0% 0% 4525ms 95.81% __libc_start_call_main 0 0% 0% 4525ms 95.81% __libc_start_main_impl 0 0% 0% 4525ms 95.81% _start 0 0% 0% 4507ms 95.43% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4507ms 95.43% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4507ms 95.43% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4507ms 95.43% main 0 0% 0% 4466ms 94.56% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4466ms 94.56% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4465ms 94.54% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4453ms 94.28% AbstractCellBasedSimulation::Solve 0 0% 0% 4147ms 87.80% AbstractCellPopulation::WriteResultsToFiles 7ms 0.15% 0.15% 3935ms 83.32% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.15% 1973ms 41.77% VertexMeshWriter::WriteVtkUsingMesh 0 0% 0.15% 1701ms 36.02% VertexMeshWriter::MakeVtkMesh 0 0% 0.15% 1249ms 26.45% vtkPolygon::New 3ms 0.064% 0.21% 1248ms 26.42% vtkPolygon::vtkPolygon 4ms 0.085% 0.3% 900ms 19.06% vtkCell::vtkCell 0 0% 0.3% 787ms 16.66% vtkPoints::New 10ms 0.21% 0.51% 741ms 15.69% vtkPoints::vtkPoints 1ms 0.021% 0.53% 690ms 14.61% VertexMeshWriter::WriteFiles 24ms 0.51% 1.04% 669ms 14.16% operator new 226ms 4.79% 5.82% 651ms 13.78% __GI___libc_malloc 58ms 1.23% 7.05% 650ms 13.76% std::ostream::_M_insert 0 0% 7.05% 650ms 13.76% std::ostream::operator<< (inline) 5ms 0.11% 7.16% 596ms 12.62% vtkLine::New 1ms 0.021% 7.18% 580ms 12.28% vtkQuad::New 2ms 0.042% 7.22% 576ms 12.20% vtkQuad::vtkQuad 9ms 0.19% 7.41% 572ms 12.11% vtkLine::vtkLine 1ms 0.021% 7.43% 570ms 12.07% vtkTriangle::New 4ms 0.085% 7.52% 556ms 11.77% vtkTriangle::vtkTriangle 0 0% 7.52% 553ms 11.71% vtkDemandDrivenPipeline::ProcessRequest 0 0% 7.52% 553ms 11.71% vtkStreamingDemandDrivenPipeline::Update 0 0% 7.52% 553ms 11.71% vtkXMLWriterBase::Write 0 0% 7.52% 552ms 11.69% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 7.52% 551ms 11.67% vtkDemandDrivenPipeline::ExecuteData 0 0% 7.52% 550ms 11.65% vtkExecutive::CallAlgorithm 1ms 0.021% 7.54% 549ms 11.62% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 7.54% 548ms 11.60% vtkCompositeDataPipeline::ExecuteData 138ms 2.92% 10.46% 528ms 11.18% __GI___libc_free 43ms 0.91% 11.37% 515ms 10.90% std::num_put::_M_insert_float 0 0% 11.37% 491ms 10.40% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 11.37% 491ms 10.40% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 32ms 0.68% 12.05% 444ms 9.40% vtkPoints::SetDataType 0 0% 12.05% 438ms 9.27% vtkXMLWriter::WriteBinaryData 1ms 0.021% 12.07% 436ms 9.23% vtkXMLWriter::WriteBinaryDataBlock 0 0% 12.07% 436ms 9.23% vtkXMLWriter::WriteBinaryDataInternal 0 0% 12.07% 425ms 9.00% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 11ms 0.23% 12.30% 417ms 8.83% std::__cxx11::collate::do_transform 0 0% 12.30% 402ms 8.51% vtkPolygon::~vtkPolygon 2ms 0.042% 12.34% 400ms 8.47% ___vsnprintf 0 0% 12.34% 399ms 8.45% __vsnprintf_internal (inline) 50ms 1.06% 13.40% 395ms 8.36% __printf_buffer 237ms 5.02% 18.42% 387ms 8.19% _int_free 240ms 5.08% 23.50% 361ms 7.64% _int_malloc 1ms 0.021% 23.52% 332ms 7.03% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 23.52% 331ms 7.01% vtkXMLWriter::WritePointsAppendedData 0 0% 23.52% 327ms 6.92% VtkMeshWriter::WriteFiles 1ms 0.021% 23.54% 325ms 6.88% __printf_fp_spec (inline) 12ms 0.25% 23.80% 324ms 6.86% __printf_fp_l_buffer 3ms 0.064% 23.86% 318ms 6.73% vtkCell::~vtkCell 42ms 0.89% 24.75% 308ms 6.52% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 1ms 0.021% 24.77% 301ms 6.37% OnLatticeSimulation::UpdateCellLocationsAndTopology 8ms 0.17% 24.94% 300ms 6.35% PottsBasedCellPopulation::UpdateCellLocations 131ms 2.77% 27.72% 296ms 6.27% __printf_fp_buffer_1 5ms 0.11% 27.82% 285ms 6.03% std::__new_allocator::deallocate (inline) 42ms 0.89% 28.71% 281ms 5.95% std::__new_allocator::allocate (inline) 0 0% 28.71% 279ms 5.91% std::allocator_traits::allocate (inline) 0 0% 28.71% 279ms 5.91% std::allocator_traits::deallocate (inline) 4ms 0.085% 28.80% 223ms 4.72% vtkBase64OutputStream::Write 9ms 0.19% 28.99% 223ms 4.72% vtkFloatArray::New 0 0% 28.99% 220ms 4.66% vtkXMLWriter::WriteCompressionBlock 23ms 0.49% 29.47% 216ms 4.57% vtkBase64OutputStream::EncodeTriplet 7ms 0.15% 29.62% 209ms 4.43% vtkPoints::~vtkPoints 0 0% 29.62% 208ms 4.40% compress2 0 0% 29.62% 208ms 4.40% vtkDataCompressor::Compress 0 0% 29.62% 208ms 4.40% vtkZLibDataCompressor::CompressBuffer 47ms 1% 30.62% 207ms 4.38% crc32 0 0% 30.62% 207ms 4.38% deflate 23ms 0.49% 31.10% 197ms 4.17% std::_Rb_tree::_Rb_tree 0 0% 31.10% 197ms 4.17% std::set::set (inline) 5ms 0.11% 31.21% 191ms 4.04% vtkFloatArray::vtkFloatArray 0 0% 31.21% 188ms 3.98% vtkQuad::~vtkQuad 2ms 0.042% 31.25% 187ms 3.96% vtkLine::GetParametricCenter 47ms 1% 32.25% 180ms 3.81% std::ostream::write 83ms 1.76% 34.00% 170ms 3.60% std::basic_filebuf::xsputn 2ms 0.042% 34.05% 170ms 3.60% vtkTriangle::~vtkTriangle 96ms 2.03% 36.08% 169ms 3.58% malloc_consolidate 37ms 0.78% 36.86% 169ms 3.58% std::_Rb_tree::_M_erase 4ms 0.085% 36.95% 168ms 3.56% NodesOnlyMesh::ConstructNodesWithoutMesh 13ms 0.28% 37.22% 168ms 3.56% std::vector::_M_default_append 3ms 0.064% 37.29% 167ms 3.54% vtkIdList::AllocateInternal 1ms 0.021% 37.31% 166ms 3.51% tbb::detail::r1::parallel_pipeline 0 0% 37.31% 163ms 3.45% VertexMesh::~VertexMesh 0 0% 37.31% 163ms 3.45% clone3 0 0% 37.31% 163ms 3.45% start_thread 3ms 0.064% 37.37% 163ms 3.45% std::_Rb_tree::~_Rb_tree (inline) 0 0% 37.37% 160ms 3.39% vtkTypeFloat64Array::~vtkTypeFloat64Array 1ms 0.021% 37.39% 156ms 3.30% VertexMesh::VertexMesh 3ms 0.064% 37.46% 155ms 3.28% std::_Vector_base::_M_deallocate (inline) 0 0% 37.46% 153ms 3.24% std::_Rb_tree::_M_create_node (inline) 148ms 3.13% 40.59% 150ms 3.18% [libz.so.1.3] 0 0% 40.59% 149ms 3.15% tbb::detail::r1::reset 0 0% 40.59% 147ms 3.11% std::_Rb_tree::_M_get_node (inline) 9ms 0.19% 40.78% 146ms 3.09% MutableElement::BuildEdges 0 0% 40.78% 146ms 3.09% VertexMesh::GenerateEdgesFromElements (inline) 0 0% 40.78% 145ms 3.07% std::vector::~vector (inline) 11ms 0.23% 41.01% 143ms 3.03% std::_Rb_tree::_M_copy (inline) 0 0% 41.01% 141ms 2.99% NodeLocationWriter::VisitAnyPopulation 3ms 0.064% 41.08% 140ms 2.96% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 0 0% 41.08% 140ms 2.96% std::_Rb_tree::_Alloc_node::operator() (inline) 59ms 1.25% 42.32% 135ms 2.86% tbb::detail::r1::wait_bounded_queue_monitor 1ms 0.021% 42.35% 135ms 2.86% vtkDataArray::CreateDataArray 0 0% 42.35% 134ms 2.84% std::set::~set (inline) 1ms 0.021% 42.37% 133ms 2.82% std::_Vector_base::_M_allocate (inline) 0 0% 42.37% 130ms 2.75% std::_Rb_tree::_M_drop_node (inline) 5ms 0.11% 42.47% 129ms 2.73% vtkTypeFloat64Array::New 0 0% 42.47% 126ms 2.67% std::_Rb_tree::_M_put_node (inline) 11ms 0.23% 42.71% 124ms 2.63% std::_Rb_tree::_M_clone_node (inline) 2ms 0.042% 42.75% 124ms 2.63% vtkDoubleArray::vtkDoubleArray 1ms 0.021% 42.77% 119ms 2.52% EdgeHelper::GetEdgeFromNodes 36ms 0.76% 43.53% 116ms 2.46% std::__ostream_insert 27ms 0.57% 44.10% 116ms 2.46% vtkObject::vtkObject 0 0% 44.10% 115ms 2.43% EdgeHelper::~EdgeHelper (inline) 1ms 0.021% 44.12% 113ms 2.39% std::_Vector_base::~_Vector_base (inline) 1ms 0.021% 44.15% 111ms 2.35% std::operator<< (inline) 7ms 0.15% 44.29% 110ms 2.33% vtkTypeFloat64Array::vtkTypeFloat64Array 48ms 1.02% 45.31% 106ms 2.24% hack_digit 1ms 0.021% 45.33% 102ms 2.16% vtkFloatArray::~vtkFloatArray 101ms 2.14% 47.47% 101ms 2.14% __strcmp_avx2 100ms 2.12% 49.59% 100ms 2.12% unlink_chunk 0 0% 49.59% 100ms 2.12% vtkIdList::Allocate 0 0% 49.59% 99ms 2.10% CellPropertyCollection::GetPropertiesType (inline) 5ms 0.11% 49.69% 98ms 2.07% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 8ms 0.17% 49.86% 97ms 2.05% std::map::operator[] (partial-inline) 61ms 1.29% 51.15% 96ms 2.03% vtkObjectBase::UnRegisterInternal 4ms 0.085% 51.24% 93ms 1.97% std::vector::push_back (inline) 5ms 0.11% 51.34% 91ms 1.93% _int_free_maybe_consolidate 0 0% 51.34% 91ms 1.93% vtkXMLWriter::WritePointDataAppendedData 23ms 0.49% 51.83% 85ms 1.80% __dynamic_cast 0 0% 51.83% 84ms 1.78% AbstractCellProperty::IsSubType (inline) 25ms 0.53% 52.36% 84ms 1.78% vtkObject::Modified 5ms 0.11% 52.47% 83ms 1.76% CellPropertyCollection::HasProperty 0 0% 52.47% 82ms 1.74% Cell::HasCellProperty (inline) 3ms 0.064% 52.53% 79ms 1.67% AbstractCellProperty::IsType (inline) 1ms 0.021% 52.55% 79ms 1.67% vtkDoubleArray::~vtkDoubleArray 78ms 1.65% 54.20% 78ms 1.65% __GI_sched_yield 36ms 0.76% 54.97% 77ms 1.63% vtkTypeFloat64Array::PrintSelf 6ms 0.13% 55.09% 76ms 1.61% AbstractCellPopulation::GetCellUsingLocationIndex 8ms 0.17% 55.26% 73ms 1.55% vtkAOSDataArrayTemplate::DataElementChanged 42ms 0.89% 56.15% 69ms 1.46% std::basic_streambuf::xsputn 18ms 0.38% 56.53% 67ms 1.42% std::_Rb_tree::_M_lower_bound (inline) 2ms 0.042% 56.57% 66ms 1.40% PottsMesh::GetMooreNeighbouringNodeIndices 1ms 0.021% 56.60% 66ms 1.40% boost::numeric::ublas::c_vector::c_vector (inline) 5ms 0.11% 56.70% 66ms 1.40% std::vector::_M_realloc_insert 0 0% 56.70% 65ms 1.38% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 0 0% 56.70% 64ms 1.36% NodesOnlyMesh::SetUpBoxCollection 1ms 0.021% 56.72% 64ms 1.36% boost::numeric::ublas::vector_assign (inline) 3ms 0.064% 56.79% 62ms 1.31% vtkIdList::New 0 0% 56.79% 61ms 1.29% NodesOnlyMesh::~NodesOnlyMesh 0 0% 56.79% 59ms 1.25% Cell::GetCellProliferativeType 6ms 0.13% 56.91% 58ms 1.23% AbstractCellProperty::IsSame 0 0% 56.91% 57ms 1.21% std::_Rb_tree::lower_bound (inline) 0 0% 56.91% 57ms 1.21% std::map::lower_bound (inline) 0 0% 56.91% 56ms 1.19% tcache_get (inline) 56ms 1.19% 58.10% 56ms 1.19% tcache_get_n (inline) 10ms 0.21% 58.31% 56ms 1.19% vtkSOADataArrayTemplate::FillTypedComponent 4ms 0.085% 58.40% 55ms 1.16% vtkDataArray::vtkDataArray 55ms 1.16% 59.56% 55ms 1.16% vtkTimeStamp::Modified 0 0% 59.56% 53ms 1.12% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 27ms 0.57% 60.13% 52ms 1.10% std::_Hashtable::clear 6ms 0.13% 60.26% 52ms 1.10% std::type_info::operator== (inline) 16ms 0.34% 60.60% 51ms 1.08% vtkAbstractArray::vtkAbstractArray 13ms 0.28% 60.87% 49ms 1.04% vtkDataArray::~vtkDataArray 2ms 0.042% 60.91% 48ms 1.02% VertexMesh::Clear 46ms 0.97% 61.89% 47ms 1% __GI___writev 47ms 1% 62.88% 47ms 1% __memcpy_avx_unaligned_erms 47ms 1% 63.88% 47ms 1% std::ostream::sentry::sentry 2ms 0.042% 63.92% 46ms 0.97% std::_Rb_tree::_M_insert_unique 0 0% 63.92% 46ms 0.97% std::__basic_file::xsputn_2 0 0% 63.92% 46ms 0.97% std::set::insert (inline) 0 0% 63.92% 44ms 0.93% std::make_unique (inline) 43ms 0.91% 64.83% 43ms 0.91% __mpn_divrem 10ms 0.21% 65.04% 43ms 0.91% _int_free_merge_chunk 7ms 0.15% 65.19% 43ms 0.91% std::num_put::_M_insert_int 24ms 0.51% 65.70% 42ms 0.89% __cxxabiv1::__si_class_type_info::__do_dyncast 41ms 0.87% 66.57% 41ms 0.87% [libstdc++.so.6.0.33] 0 0% 66.57% 41ms 0.87% _dl_init 0 0% 66.57% 41ms 0.87% call_init (inline) 41ms 0.87% 67.44% 41ms 0.87% std::codecvt::do_always_noconv 41ms 0.87% 68.30% 41ms 0.87% vtkObjectBase::~vtkObjectBase 12ms 0.25% 68.56% 39ms 0.83% boost::numeric::ublas::indexing_vector_assign 0 0% 68.56% 39ms 0.83% vtkDataArray::ComputeRange 0 0% 68.56% 38ms 0.8% CxxTest::RealWorldDescription::setUp 1ms 0.021% 68.58% 38ms 0.8% DistributedBoxCollection::IsOwned 0 0% 68.58% 38ms 0.8% PetscSetup::setUpWorld 0 0% 68.58% 38ms 0.8% PetscSetupUtils::CommonSetup 0 0% 68.58% 38ms 0.8% PetscSetupUtils::InitialisePetsc 38ms 0.8% 69.38% 38ms 0.8% [libvtkCommonCore-9.3.so.9.3] 0 0% 69.38% 37ms 0.78% 0 0% 69.38% 37ms 0.78% DistributedBoxCollection::SetupLocalBoxesHalfOnly 0 0% 69.38% 37ms 0.78% PMPI_Init_thread 0 0% 69.38% 37ms 0.78% PetscInitialize 0 0% 69.38% 37ms 0.78% ompi_mpi_init 0 0% 69.38% 37ms 0.78% std::_Destroy (inline) 0 0% 69.38% 37ms 0.78% std::_Destroy_aux::__destroy (inline) 5ms 0.11% 69.49% 37ms 0.78% vtkAOSDataArrayTemplate::InsertTuple 2ms 0.042% 69.53% 37ms 0.78% vtkIdList::~vtkIdList 37ms 0.78% 70.32% 37ms 0.78% vtkObjectBase::vtkObjectBase 26ms 0.55% 70.87% 36ms 0.76% DistributedBoxCollection::CalculateContainingBox (inline) 4ms 0.085% 70.95% 36ms 0.76% std::_Rb_tree::_M_insert_ (inline) 0 0% 70.95% 36ms 0.76% vtk::detail::smp::vtkSMPToolsImplForTBB 36ms 0.76% 71.71% 36ms 0.76% vtkObject::~vtkObject 0 0% 71.71% 35ms 0.74% _dl_start_user 0 0% 71.71% 35ms 0.74% vtkDoubleArray::New 31ms 0.66% 72.37% 35ms 0.74% vtkObject::ObjectFinalize 0 0% 72.37% 34ms 0.72% DistributedBoxCollection::~DistributedBoxCollection 1ms 0.021% 72.39% 34ms 0.72% Edge::Edge 0 0% 72.39% 34ms 0.72% NodesOnlyMesh::ClearBoxCollection (inline) 33ms 0.7% 73.09% 33ms 0.7% __memset_avx2_unaligned_erms 28ms 0.59% 73.68% 33ms 0.7% _int_free_create_chunk (inline) 6ms 0.13% 73.81% 33ms 0.7% boost::serialization::singleton::get_instance 1ms 0.021% 73.83% 33ms 0.7% std::less::operator() (inline) 6ms 0.13% 73.96% 33ms 0.7% tbb::detail::r1::cancel_group_execution 6ms 0.13% 74.08% 33ms 0.7% vtkDataArrayPrivate::DoComputeVectorRange 0 0% 74.08% 32ms 0.68% Edge::SetNodes (inline) 7ms 0.15% 74.23% 32ms 0.68% VertexMeshWriter::GetNextNode 0 0% 74.23% 32ms 0.68% std::basic_filebuf::open 32ms 0.68% 74.91% 32ms 0.68% std::operator< (inline) 32ms 0.68% 75.59% 32ms 0.68% vtkObjectBase::Delete 0 0% 75.59% 31ms 0.66% PottsMesh::GetVonNeumannNeighbouringNodeIndices 0 0% 75.59% 31ms 0.66% std::_Rb_tree::_M_emplace_hint_unique 0 0% 75.59% 31ms 0.66% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 1ms 0.021% 75.61% 31ms 0.66% std::_Rb_tree_header::_Rb_tree_header (inline) 27ms 0.57% 76.18% 31ms 0.66% std::num_put::do_put 1ms 0.021% 76.20% 30ms 0.64% Node::SetRadius 30ms 0.64% 76.84% 30ms 0.64% std::_Rb_tree_header::_M_reset (inline) 0 0% 76.84% 29ms 0.61% Cell::GetMutationState 1ms 0.021% 76.86% 29ms 0.61% CellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 76.86% 29ms 0.61% Node::ConstructNodeAttributes (inline) 29ms 0.61% 77.47% 29ms 0.61% [libchaste_cell_based.so] 0 0% 77.47% 29ms 0.61% std::map::~map (inline) 3ms 0.064% 77.54% 29ms 0.61% vtk::detail::smp::vtkSMPToolsImpl::For 0 0% 77.54% 28ms 0.59% VtkMeshWriter::MakeVtkMesh 1ms 0.021% 77.56% 28ms 0.59% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 0 0% 77.56% 27ms 0.57% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 77.56% 27ms 0.57% NodesOnlyMesh::Clear (inline) 0 0% 77.56% 27ms 0.57% _IO_new_file_fopen 0 0% 77.56% 27ms 0.57% _IO_new_fopen 0 0% 77.56% 27ms 0.57% __GI__IO_file_open 0 0% 77.56% 27ms 0.57% __fopen_internal (inline) 27ms 0.57% 78.13% 27ms 0.57% __libc_open64 0 0% 78.13% 27ms 0.57% std::default_delete::operator() (inline) 0 0% 78.13% 27ms 0.57% std::unique_ptr::~unique_ptr (inline) 27ms 0.57% 78.70% 27ms 0.57% vtkDataArray::Modified 0 0% 78.70% 26ms 0.55% std::__basic_file::open 4ms 0.085% 78.78% 26ms 0.55% std::__new_allocator::construct (inline) 0 0% 78.78% 26ms 0.55% std::allocator_traits::construct (inline) 2ms 0.042% 78.83% 26ms 0.55% vtkDataSet::GetCellTypes 0 0% 78.83% 25ms 0.53% OutputFileHandler::OpenOutputFile 0 0% 78.83% 25ms 0.53% std::basic_ofstream::basic_ofstream (inline) 3ms 0.064% 78.89% 25ms 0.53% std::vector::emplace_back (inline) 4ms 0.085% 78.98% 25ms 0.53% vtkIdList::vtkIdList 0 0% 78.98% 24ms 0.51% Cell::GetCellId 1ms 0.021% 79.00% 24ms 0.51% NodeAttributes::NodeAttributes 3ms 0.064% 79.06% 24ms 0.51% boost::serialization::void_cast_detail::void_caster::recursive_register 0 0% 79.06% 24ms 0.51% boost::serialization::void_cast_detail::void_caster_primitive::void_caster_primitive (inline) 24ms 0.51% 79.57% 24ms 0.51% std::_Rb_tree_increment