File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3716ms, 78.26% of 4748ms total Dropped 714 nodes (cum <= 23.74ms) flat flat% sum% cum cum% 0 0% 0% 4504ms 94.86% __libc_start_call_main 0 0% 0% 4504ms 94.86% __libc_start_main_impl 0 0% 0% 4504ms 94.86% _start 0 0% 0% 4489ms 94.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4489ms 94.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4489ms 94.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4489ms 94.55% main 0 0% 0% 4457ms 93.87% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4457ms 93.87% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4457ms 93.87% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4446ms 93.64% AbstractCellBasedSimulation::Solve 0 0% 0% 4162ms 87.66% AbstractCellPopulation::WriteResultsToFiles 10ms 0.21% 0.21% 3930ms 82.77% PottsBasedCellPopulation::WriteVtkResultsToFile 1ms 0.021% 0.23% 1948ms 41.03% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.021% 0.25% 1687ms 35.53% VertexMeshWriter::MakeVtkMesh 0 0% 0.25% 1276ms 26.87% vtkPolygon::New 1ms 0.021% 0.27% 1273ms 26.81% vtkPolygon::vtkPolygon 7ms 0.15% 0.42% 923ms 19.44% vtkCell::vtkCell 1ms 0.021% 0.44% 793ms 16.70% vtkPoints::New 44ms 0.93% 1.37% 750ms 15.80% std::ostream::_M_insert 2ms 0.042% 1.41% 750ms 15.80% std::ostream::operator<< (inline) 0 0% 1.41% 746ms 15.71% VertexMeshWriter::WriteFiles 16ms 0.34% 1.75% 746ms 15.71% vtkPoints::vtkPoints 35ms 0.74% 2.49% 661ms 13.92% operator new 211ms 4.44% 6.93% 626ms 13.18% __GI___libc_malloc 46ms 0.97% 7.90% 625ms 13.16% std::num_put::_M_insert_float 0 0% 7.90% 612ms 12.89% vtkQuad::New 3ms 0.063% 7.96% 612ms 12.89% vtkQuad::vtkQuad 3ms 0.063% 8.02% 593ms 12.49% vtkLine::New 7ms 0.15% 8.17% 567ms 11.94% vtkLine::vtkLine 1ms 0.021% 8.19% 565ms 11.90% vtkXMLWriterBase::Write 0 0% 8.19% 564ms 11.88% vtkStreamingDemandDrivenPipeline::Update 0 0% 8.19% 562ms 11.84% vtkDemandDrivenPipeline::ProcessRequest 0 0% 8.19% 559ms 11.77% vtkExecutive::CallAlgorithm 0 0% 8.19% 559ms 11.77% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 8.19% 558ms 11.75% vtkDemandDrivenPipeline::ExecuteData 0 0% 8.19% 557ms 11.73% vtkCompositeDataPipeline::ExecuteData 0 0% 8.19% 557ms 11.73% vtkXMLUnstructuredDataWriter::ProcessRequest 1ms 0.021% 8.21% 552ms 11.63% vtkTriangle::New 5ms 0.11% 8.32% 542ms 11.42% vtkTriangle::vtkTriangle 153ms 3.22% 11.54% 509ms 10.72% __GI___libc_free 0 0% 11.54% 506ms 10.66% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 11.54% 506ms 10.66% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 29ms 0.61% 12.15% 473ms 9.96% vtkPoints::SetDataType 13ms 0.27% 12.43% 465ms 9.79% std::__cxx11::collate::do_transform 1ms 0.021% 12.45% 450ms 9.48% vtkXMLWriter::WriteBinaryData 0 0% 12.45% 439ms 9.25% vtkXMLWriter::WriteBinaryDataInternal 0 0% 12.45% 438ms 9.22% vtkXMLWriter::WriteBinaryDataBlock 5ms 0.11% 12.55% 435ms 9.16% ___vsnprintf 0 0% 12.55% 430ms 9.06% __vsnprintf_internal (inline) 0 0% 12.55% 424ms 8.93% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 51ms 1.07% 13.63% 419ms 8.82% __printf_buffer 0 0% 13.63% 365ms 7.69% vtkPolygon::~vtkPolygon 227ms 4.78% 18.41% 356ms 7.50% _int_free 242ms 5.10% 23.50% 352ms 7.41% _int_malloc 1ms 0.021% 23.53% 350ms 7.37% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 23.53% 347ms 7.31% VtkMeshWriter::WriteFiles 1ms 0.021% 23.55% 346ms 7.29% __printf_fp_spec (inline) 13ms 0.27% 23.82% 345ms 7.27% __printf_fp_l_buffer 0 0% 23.82% 320ms 6.74% vtkXMLWriter::WritePointsAppendedData 159ms 3.35% 27.17% 318ms 6.70% __printf_fp_buffer_1 50ms 1.05% 28.22% 298ms 6.28% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 4ms 0.084% 28.31% 280ms 5.90% vtkCell::~vtkCell 0 0% 28.31% 273ms 5.75% OnLatticeSimulation::UpdateCellLocationsAndTopology 7ms 0.15% 28.45% 273ms 5.75% PottsBasedCellPopulation::UpdateCellLocations 37ms 0.78% 29.23% 266ms 5.60% std::__new_allocator::allocate (inline) 0 0% 29.23% 263ms 5.54% std::allocator_traits::allocate (inline) 5ms 0.11% 29.34% 254ms 5.35% std::__new_allocator::deallocate (inline) 0 0% 29.34% 252ms 5.31% std::allocator_traits::deallocate (inline) 0 0% 29.34% 231ms 4.87% vtkXMLWriter::WriteCompressionBlock 0 0% 29.34% 220ms 4.63% vtkDataCompressor::Compress 0 0% 29.34% 219ms 4.61% compress2 0 0% 29.34% 219ms 4.61% tbb::detail::r1::parallel_pipeline 0 0% 29.34% 219ms 4.61% vtkZLibDataCompressor::CompressBuffer 59ms 1.24% 30.58% 217ms 4.57% crc32 0 0% 30.58% 217ms 4.57% deflate 7ms 0.15% 30.73% 214ms 4.51% vtkBase64OutputStream::Write 0 0% 30.73% 209ms 4.40% clone3 0 0% 30.73% 209ms 4.40% start_thread 0 0% 30.73% 209ms 4.40% tbb::detail::r1::reset 77ms 1.62% 32.35% 209ms 4.40% tbb::detail::r1::wait_bounded_queue_monitor 15ms 0.32% 32.67% 207ms 4.36% vtkBase64OutputStream::EncodeTriplet 11ms 0.23% 32.90% 195ms 4.11% vtkFloatArray::New 5ms 0.11% 33.00% 195ms 4.11% vtkPoints::~vtkPoints 0 0% 33.00% 177ms 3.73% std::set::set (inline) 17ms 0.36% 33.36% 176ms 3.71% std::_Rb_tree::_Rb_tree 52ms 1.10% 34.46% 175ms 3.69% std::ostream::write 3ms 0.063% 34.52% 172ms 3.62% NodeLocationWriter::VisitAnyPopulation 3ms 0.063% 34.58% 167ms 3.52% vtkIdList::AllocateInternal 3ms 0.063% 34.65% 163ms 3.43% vtkFloatArray::vtkFloatArray 3ms 0.063% 34.71% 161ms 3.39% vtkQuad::~vtkQuad 1ms 0.021% 34.73% 159ms 3.35% VertexMesh::VertexMesh 0 0% 34.73% 159ms 3.35% std::_Rb_tree::_M_create_node (inline) 6ms 0.13% 34.86% 156ms 3.29% vtkDataArray::CreateDataArray 1ms 0.021% 34.88% 156ms 3.29% vtkTriangle::~vtkTriangle 84ms 1.77% 36.65% 155ms 3.26% malloc_consolidate 0 0% 36.65% 154ms 3.24% NodesOnlyMesh::ConstructNodesWithoutMesh 0 0% 36.65% 154ms 3.24% std::_Rb_tree::_M_get_node (inline) 0 0% 36.65% 153ms 3.22% VertexMesh::GenerateEdgesFromElements (inline) 6ms 0.13% 36.77% 152ms 3.20% MutableElement::BuildEdges 30ms 0.63% 37.41% 152ms 3.20% std::_Rb_tree::_M_erase 5ms 0.11% 37.51% 152ms 3.20% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.063% 37.57% 150ms 3.16% vtkLine::GetParametricCenter 0 0% 37.57% 148ms 3.12% VertexMesh::~VertexMesh 145ms 3.05% 40.63% 146ms 3.07% [libz.so.1.3] 62ms 1.31% 41.93% 146ms 3.07% std::basic_filebuf::xsputn 1ms 0.021% 41.95% 146ms 3.07% vtkTypeFloat64Array::~vtkTypeFloat64Array 0 0% 41.95% 145ms 3.05% std::_Rb_tree::_Alloc_node::operator() (inline) 6ms 0.13% 42.08% 144ms 3.03% vtkDoubleArray::vtkDoubleArray 6ms 0.13% 42.21% 144ms 3.03% vtkTypeFloat64Array::New 14ms 0.29% 42.50% 141ms 2.97% std::_Rb_tree::_M_copy (inline) 7ms 0.15% 42.65% 141ms 2.97% vtkFloatArray::~vtkFloatArray 3ms 0.063% 42.71% 139ms 2.93% std::_Vector_base::_M_deallocate (inline) 3ms 0.063% 42.78% 136ms 2.86% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 0 0% 42.78% 134ms 2.82% std::set::~set (inline) 13ms 0.27% 43.05% 134ms 2.82% std::vector::_M_default_append 3ms 0.063% 43.11% 131ms 2.76% EdgeHelper::GetEdgeFromNodes 130ms 2.74% 45.85% 130ms 2.74% __GI_sched_yield 0 0% 45.85% 128ms 2.70% std::vector::~vector (inline) 1ms 0.021% 45.87% 125ms 2.63% vtkTypeFloat64Array::vtkTypeFloat64Array 10ms 0.21% 46.08% 123ms 2.59% std::_Rb_tree::_M_clone_node (inline) 0 0% 46.08% 118ms 2.49% std::_Rb_tree::_M_drop_node (inline) 0 0% 46.08% 115ms 2.42% std::_Rb_tree::_M_put_node (inline) 0 0% 46.08% 112ms 2.36% CellPropertyCollection::GetPropertiesType (inline) 112ms 2.36% 48.44% 112ms 2.36% __strcmp_avx2 49ms 1.03% 49.47% 110ms 2.32% std::__ostream_insert 85ms 1.79% 51.26% 110ms 2.32% std::basic_streambuf::xsputn 27ms 0.57% 51.83% 110ms 2.32% vtkObject::vtkObject 0 0% 51.83% 109ms 2.30% std::_Vector_base::_M_allocate (inline) 0 0% 51.83% 109ms 2.30% std::_Vector_base::~_Vector_base (inline) 0 0% 51.83% 105ms 2.21% std::operator<< (inline) 0 0% 51.83% 105ms 2.21% vtkIdList::Allocate 0 0% 51.83% 104ms 2.19% vtkXMLWriter::WritePointDataAppendedData 48ms 1.01% 52.84% 102ms 2.15% vtkTypeFloat64Array::PrintSelf 0 0% 52.84% 98ms 2.06% EdgeHelper::~EdgeHelper (inline) 51ms 1.07% 53.92% 96ms 2.02% hack_digit 2ms 0.042% 53.96% 96ms 2.02% std::map::operator[] (partial-inline) 0 0% 53.96% 91ms 1.92% AbstractCellProperty::IsSubType (inline) 19ms 0.4% 54.36% 91ms 1.92% __dynamic_cast 53ms 1.12% 55.48% 90ms 1.90% vtkObjectBase::UnRegisterInternal 1ms 0.021% 55.50% 89ms 1.87% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 7ms 0.15% 55.64% 87ms 1.83% _int_free_maybe_consolidate 87ms 1.83% 57.48% 87ms 1.83% unlink_chunk 6ms 0.13% 57.60% 84ms 1.77% CellPropertyCollection::HasProperty 0 0% 57.60% 83ms 1.75% Cell::HasCellProperty (inline) 4ms 0.084% 57.69% 81ms 1.71% AbstractCellProperty::IsType (inline) 7ms 0.15% 57.83% 81ms 1.71% vtkAOSDataArrayTemplate::DataElementChanged 1ms 0.021% 57.86% 79ms 1.66% std::vector::push_back (inline) 0 0% 57.86% 79ms 1.66% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 22ms 0.46% 58.32% 78ms 1.64% std::_Rb_tree::_M_lower_bound (inline) 10ms 0.21% 58.53% 73ms 1.54% vtkDataArray::vtkDataArray 4ms 0.084% 58.61% 72ms 1.52% vtkDoubleArray::~vtkDoubleArray 3ms 0.063% 58.68% 71ms 1.50% vtkIdList::New 1ms 0.021% 58.70% 68ms 1.43% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.063% 58.76% 68ms 1.43% boost::numeric::ublas::c_vector::c_vector (partial-inline) 18ms 0.38% 59.14% 68ms 1.43% vtkObject::Modified 10ms 0.21% 59.35% 63ms 1.33% std::num_put::_M_insert_int 0 0% 59.35% 62ms 1.31% boost::numeric::ublas::vector_assign (inline) 19ms 0.4% 59.75% 62ms 1.31% vtkAbstractArray::vtkAbstractArray 11ms 0.23% 59.98% 61ms 1.28% AbstractCellProperty::IsSame 0 0% 59.98% 60ms 1.26% std::_Rb_tree::lower_bound (inline) 0 0% 59.98% 60ms 1.26% std::map::lower_bound (inline) 7ms 0.15% 60.13% 59ms 1.24% std::vector::_M_realloc_insert 0 0% 60.13% 58ms 1.22% tcache_get (inline) 58ms 1.22% 61.35% 58ms 1.22% tcache_get_n (inline) 3ms 0.063% 61.42% 57ms 1.20% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 0 0% 61.42% 56ms 1.18% NodesOnlyMesh::SetUpBoxCollection 1ms 0.021% 61.44% 56ms 1.18% PottsMesh::GetMooreNeighbouringNodeIndices 0 0% 61.44% 54ms 1.14% Cell::GetCellProliferativeType 21ms 0.44% 61.88% 52ms 1.10% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 61.88% 50ms 1.05% VertexMesh::Clear 10ms 0.21% 62.09% 50ms 1.05% std::type_info::operator== (inline) 49ms 1.03% 63.12% 49ms 1.03% __memcpy_avx_unaligned_erms 1ms 0.021% 63.14% 48ms 1.01% std::__basic_file::xsputn_2 48ms 1.01% 64.15% 48ms 1.01% vtkTimeStamp::Modified 47ms 0.99% 65.14% 47ms 0.99% __GI___writev 0 0% 65.14% 47ms 0.99% std::_Rb_tree::_M_insert_unique 0 0% 65.14% 47ms 0.99% std::set::insert (inline) 22ms 0.46% 65.61% 46ms 0.97% boost::numeric::ublas::indexing_vector_assign 7ms 0.15% 65.75% 45ms 0.95% vtkIdList::~vtkIdList 43ms 0.91% 66.66% 44ms 0.93% vtkObjectBase::Delete 28ms 0.59% 67.25% 42ms 0.88% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 67.25% 42ms 0.88% DistributedBoxCollection::IsOwned 0 0% 67.25% 42ms 0.88% NodesOnlyMesh::~NodesOnlyMesh 4ms 0.084% 67.33% 42ms 0.88% std::_Rb_tree::_M_insert_ (inline) 0 0% 67.33% 42ms 0.88% vtkDataArray::ComputeRange 26ms 0.55% 67.88% 41ms 0.86% std::_Hashtable::clear 40ms 0.84% 68.72% 40ms 0.84% [libvtkCommonCore-9.3.so.9.3] 0 0% 68.72% 40ms 0.84% std::less::operator() (inline) 40ms 0.84% 69.57% 40ms 0.84% std::operator< (inline) 6ms 0.13% 69.69% 40ms 0.84% vtkDataArray::~vtkDataArray 39ms 0.82% 70.51% 39ms 0.82% std::ostream::sentry::sentry 7ms 0.15% 70.66% 39ms 0.82% vtkSOADataArrayTemplate::FillTypedComponent 9ms 0.19% 70.85% 38ms 0.8% VertexMeshWriter::GetNextNode 0 0% 70.85% 37ms 0.78% DistributedBoxCollection::SetupLocalBoxesHalfOnly 0 0% 70.85% 37ms 0.78% std::make_unique (inline) 36ms 0.76% 71.61% 36ms 0.76% std::codecvt::do_always_noconv 0 0% 71.61% 36ms 0.76% vtk::detail::smp::vtkSMPToolsImplForTBB 2ms 0.042% 71.65% 36ms 0.76% vtkDoubleArray::New 36ms 0.76% 72.41% 36ms 0.76% vtkObjectBase::~vtkObjectBase 0 0% 72.41% 35ms 0.74% _dl_init 0 0% 72.41% 35ms 0.74% _dl_start_user 0 0% 72.41% 35ms 0.74% call_init (inline) 5ms 0.11% 72.51% 35ms 0.74% vtkAOSDataArrayTemplate::InsertTuple 0 0% 72.51% 34ms 0.72% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.021% 72.54% 34ms 0.72% tbb::detail::r1::cancel_group_execution 32ms 0.67% 73.21% 33ms 0.7% __GI___libc_write 1ms 0.021% 73.23% 33ms 0.7% std::basic_filebuf::overflow 3ms 0.063% 73.29% 33ms 0.7% vtkDataArrayPrivate::DoComputeVectorRange 0 0% 73.29% 32ms 0.67% Cell::GetCellId 1ms 0.021% 73.32% 32ms 0.67% Cell::GetMutationState 0 0% 73.32% 32ms 0.67% std::__basic_file::xsputn 0 0% 73.32% 32ms 0.67% std::basic_filebuf::_M_convert_to_external 32ms 0.67% 73.99% 32ms 0.67% vtkObject::~vtkObject 3ms 0.063% 74.05% 31ms 0.65% boost::serialization::singleton::get_instance 3ms 0.063% 74.12% 31ms 0.65% vtk::detail::smp::vtkSMPToolsImpl::For 30ms 0.63% 74.75% 31ms 0.65% vtkDataArray::Modified 28ms 0.59% 75.34% 31ms 0.65% vtkObject::ObjectFinalize 0 0% 75.34% 30ms 0.63% CellIdWriter::GetCellDataForVtkOutput 2ms 0.042% 75.38% 29ms 0.61% CellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 75.38% 29ms 0.61% Edge::Edge 0 0% 75.38% 29ms 0.61% Edge::SetNodes (inline) 29ms 0.61% 75.99% 29ms 0.61% __mpn_divrem 11ms 0.23% 76.22% 29ms 0.61% _int_free_merge_chunk 29ms 0.61% 76.83% 29ms 0.61% boost::numeric::ublas::c_vector::operator() 0 0% 76.83% 29ms 0.61% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 0 0% 76.83% 28ms 0.59% CxxTest::RealWorldDescription::setUp 0 0% 76.83% 28ms 0.59% PMPI_Init_thread 0 0% 76.83% 28ms 0.59% PetscInitialize 0 0% 76.83% 28ms 0.59% PetscSetup::setUpWorld 0 0% 76.83% 28ms 0.59% PetscSetupUtils::CommonSetup 0 0% 76.83% 28ms 0.59% PetscSetupUtils::InitialisePetsc 0 0% 76.83% 28ms 0.59% boost::numeric::ublas::c_vector::assign (inline) 0 0% 76.83% 28ms 0.59% ompi_mpi_init 1ms 0.021% 76.85% 27ms 0.57% VtkMeshWriter::MakeVtkMesh 26ms 0.55% 77.40% 26ms 0.55% [libstdc++.so.6.0.33] 26ms 0.55% 77.95% 26ms 0.55% vtkObjectBase::vtkObjectBase 1ms 0.021% 77.97% 25ms 0.53% 0 0% 77.97% 25ms 0.53% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 2ms 0.042% 78.01% 25ms 0.53% boost::serialization::void_cast_detail::void_caster::recursive_register 0 0% 78.01% 25ms 0.53% boost::serialization::void_cast_detail::void_caster_primitive::void_caster_primitive (inline) 0 0% 78.01% 25ms 0.53% std::_Destroy (inline) 0 0% 78.01% 25ms 0.53% std::_Destroy_aux::__destroy (inline) 4ms 0.084% 78.10% 24ms 0.51% Node::~Node 0 0% 78.10% 24ms 0.51% PottsBasedCellPopulation::AcceptCellWriter 1ms 0.021% 78.12% 24ms 0.51% PottsMesh::GetVonNeumannNeighbouringNodeIndices 7ms 0.15% 78.26% 24ms 0.51% vtkAOSDataArrayTemplate::AllocateTuples