File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 2546ms, 82.05% of 3103ms total Dropped 610 nodes (cum <= 15.52ms) flat flat% sum% cum cum% 0 0% 0% 2933ms 94.52% __libc_start_call_main 0 0% 0% 2933ms 94.52% __libc_start_main_impl 0 0% 0% 2933ms 94.52% _start 0 0% 0% 2921ms 94.13% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 2921ms 94.13% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 2921ms 94.13% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 2921ms 94.13% main 0 0% 0% 2888ms 93.07% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 2888ms 93.07% CxxTest::TestRunner::runTest (inline) 0 0% 0% 2888ms 93.07% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 2880ms 92.81% AbstractCellBasedSimulation::Solve 0 0% 0% 2639ms 85.05% AbstractCellPopulation::WriteResultsToFiles 8ms 0.26% 0.26% 2519ms 81.18% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.26% 1311ms 42.25% VertexMeshWriter::WriteVtkUsingMesh 2ms 0.064% 0.32% 1149ms 37.03% VertexMeshWriter::MakeVtkMesh 0 0% 0.32% 834ms 26.88% vtkPolygon::New 0 0% 0.32% 833ms 26.84% vtkPolygon::vtkPolygon 1ms 0.032% 0.35% 635ms 20.46% vtkCell::vtkCell 1ms 0.032% 0.39% 516ms 16.63% vtkPoints::New 3ms 0.097% 0.48% 495ms 15.95% vtkPoints::vtkPoints 20ms 0.64% 1.13% 447ms 14.41% operator new 218ms 7.03% 8.15% 434ms 13.99% __GI___libc_malloc 1ms 0.032% 8.19% 407ms 13.12% VertexMeshWriter::WriteFiles 0 0% 8.19% 397ms 12.79% vtkLine::New 1ms 0.032% 8.22% 395ms 12.73% vtkQuad::New 1ms 0.032% 8.25% 394ms 12.70% vtkQuad::vtkQuad 4ms 0.13% 8.38% 384ms 12.38% vtkLine::vtkLine 25ms 0.81% 9.18% 373ms 12.02% std::ostream::_M_insert 1ms 0.032% 9.22% 373ms 12.02% std::ostream::operator<< (inline) 1ms 0.032% 9.25% 367ms 11.83% vtkTriangle::New 2ms 0.064% 9.31% 360ms 11.60% vtkTriangle::vtkTriangle 53ms 1.71% 11.02% 350ms 11.28% __GI___libc_free 0 0% 11.02% 320ms 10.31% vtkStreamingDemandDrivenPipeline::Update 0 0% 11.02% 320ms 10.31% vtkXMLWriterBase::Write 0 0% 11.02% 319ms 10.28% vtkDemandDrivenPipeline::ProcessRequest 0 0% 11.02% 318ms 10.25% vtkExecutive::CallAlgorithm 0 0% 11.02% 317ms 10.22% vtkCompositeDataPipeline::ExecuteData 0 0% 11.02% 317ms 10.22% vtkDemandDrivenPipeline::ExecuteData 0 0% 11.02% 317ms 10.22% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 11.02% 317ms 10.22% vtkXMLUnstructuredDataWriter::ProcessRequest 18ms 0.58% 11.60% 306ms 9.86% std::num_put::_M_insert_float 11ms 0.35% 11.96% 300ms 9.67% vtkPoints::SetDataType 201ms 6.48% 18.43% 293ms 9.44% _int_free 1ms 0.032% 18.47% 283ms 9.12% vtkPolygon::~vtkPolygon 0 0% 18.47% 272ms 8.77% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 18.47% 272ms 8.77% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 6ms 0.19% 18.66% 260ms 8.38% std::__cxx11::collate::do_transform 3ms 0.097% 18.76% 250ms 8.06% ___vsnprintf 0 0% 18.76% 249ms 8.02% __vsnprintf_internal (inline) 40ms 1.29% 20.05% 244ms 7.86% __printf_buffer 0 0% 20.05% 244ms 7.86% vtkXMLWriter::WriteBinaryData 0 0% 20.05% 242ms 7.80% vtkXMLWriter::WriteBinaryDataBlock 0 0% 20.05% 242ms 7.80% vtkXMLWriter::WriteBinaryDataInternal 0 0% 20.05% 237ms 7.64% OnLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 20.05% 237ms 7.64% PottsBasedCellPopulation::UpdateCellLocations 0 0% 20.05% 227ms 7.32% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 35ms 1.13% 21.17% 224ms 7.22% std::__new_allocator::allocate (inline) 0 0% 21.17% 222ms 7.15% std::allocator_traits::allocate (inline) 42ms 1.35% 22.53% 218ms 7.03% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 0 0% 22.53% 216ms 6.96% vtkCell::~vtkCell 1ms 0.032% 22.56% 188ms 6.06% __printf_fp_spec (inline) 2ms 0.064% 22.62% 188ms 6.06% std::__new_allocator::deallocate (inline) 6ms 0.19% 22.82% 187ms 6.03% __printf_fp_l_buffer 0 0% 22.82% 187ms 6.03% std::allocator_traits::deallocate (inline) 103ms 3.32% 26.14% 186ms 5.99% _int_malloc 0 0% 26.14% 181ms 5.83% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 26.14% 180ms 5.80% vtkXMLWriter::WritePointsAppendedData 0 0% 26.14% 178ms 5.74% VtkMeshWriter::WriteFiles 78ms 2.51% 28.65% 178ms 5.74% __printf_fp_buffer_1 22ms 0.71% 29.36% 167ms 5.38% std::_Rb_tree::_Rb_tree 0 0% 29.36% 167ms 5.38% std::set::set (inline) 6ms 0.19% 29.55% 167ms 5.38% vtkObject::vtkObject 13ms 0.42% 29.97% 164ms 5.29% vtkObject::Modified 149ms 4.80% 34.77% 149ms 4.80% vtkTimeStamp::Modified 0 0% 34.77% 147ms 4.74% tbb::detail::r1::parallel_pipeline 0 0% 34.77% 145ms 4.67% std::_Rb_tree::_M_create_node (inline) 0 0% 34.77% 144ms 4.64% clone3 0 0% 34.77% 144ms 4.64% start_thread 0 0% 34.77% 141ms 4.54% tbb::detail::r1::reset 3ms 0.097% 34.87% 136ms 4.38% vtkFloatArray::New 0 0% 34.87% 135ms 4.35% vtkPoints::~vtkPoints 0 0% 34.87% 134ms 4.32% std::_Rb_tree::_M_get_node (inline) 0 0% 34.87% 133ms 4.29% std::_Rb_tree::_Alloc_node::operator() (inline) 106ms 3.42% 38.29% 133ms 4.29% vtkObjectBase::UnRegisterInternal 81ms 2.61% 40.90% 132ms 4.25% tbb::detail::r1::wait_bounded_queue_monitor 0 0% 40.90% 128ms 4.13% VertexMesh::~VertexMesh 79ms 2.55% 43.44% 128ms 4.13% malloc_consolidate 1ms 0.032% 43.47% 127ms 4.09% vtkBase64OutputStream::Write 1ms 0.032% 43.51% 127ms 4.09% vtkQuad::~vtkQuad 18ms 0.58% 44.09% 126ms 4.06% vtkBase64OutputStream::EncodeTriplet 9ms 0.29% 44.38% 124ms 4.00% std::_Rb_tree::_M_copy (inline) 4ms 0.13% 44.51% 123ms 3.96% std::_Rb_tree::~_Rb_tree (inline) 0 0% 44.51% 123ms 3.96% vtkFloatArray::vtkFloatArray 22ms 0.71% 45.21% 122ms 3.93% std::_Rb_tree::_M_erase 1ms 0.032% 45.25% 122ms 3.93% vtkLine::GetParametricCenter 0 0% 45.25% 116ms 3.74% vtkXMLWriter::WriteCompressionBlock 16ms 0.52% 45.76% 115ms 3.71% std::_Rb_tree::_M_clone_node (inline) 0 0% 45.76% 111ms 3.58% std::vector::~vector (inline) 0 0% 45.76% 109ms 3.51% compress2 0 0% 45.76% 109ms 3.51% vtkDataCompressor::Compress 0 0% 45.76% 109ms 3.51% vtkTriangle::~vtkTriangle 0 0% 45.76% 109ms 3.51% vtkZLibDataCompressor::CompressBuffer 25ms 0.81% 46.57% 108ms 3.48% crc32 0 0% 46.57% 108ms 3.48% deflate 5ms 0.16% 46.73% 107ms 3.45% vtkIdList::AllocateInternal 0 0% 46.73% 106ms 3.42% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 0 0% 46.73% 105ms 3.38% NodesOnlyMesh::ConstructNodesWithoutMesh 1ms 0.032% 46.76% 104ms 3.35% vtkTypeFloat64Array::~vtkTypeFloat64Array 0 0% 46.76% 103ms 3.32% std::set::~set (inline) 0 0% 46.76% 102ms 3.29% VertexMesh::VertexMesh 2ms 0.064% 46.83% 102ms 3.29% std::_Vector_base::_M_deallocate (inline) 0 0% 46.83% 97ms 3.13% std::_Rb_tree::_M_drop_node (inline) 29ms 0.93% 47.76% 97ms 3.13% std::ostream::write 2ms 0.064% 47.82% 97ms 3.13% vtkDoubleArray::vtkDoubleArray 2ms 0.064% 47.89% 95ms 3.06% VertexMesh::GenerateEdgesFromElements (inline) 2ms 0.064% 47.95% 93ms 3.00% MutableElement::BuildEdges 0 0% 47.95% 91ms 2.93% vtkDataArray::CreateDataArray 1ms 0.032% 47.99% 89ms 2.87% std::_Vector_base::~_Vector_base (inline) 0 0% 47.99% 89ms 2.87% vtkTypeFloat64Array::New 0 0% 47.99% 88ms 2.84% std::_Vector_base::_M_allocate (inline) 0 0% 47.99% 87ms 2.80% EdgeHelper::~EdgeHelper (inline) 0 0% 47.99% 87ms 2.80% std::_Rb_tree::_M_put_node (inline) 0 0% 47.99% 81ms 2.61% vtkTypeFloat64Array::vtkTypeFloat64Array 1ms 0.032% 48.02% 79ms 2.55% EdgeHelper::GetEdgeFromNodes 77ms 2.48% 50.50% 79ms 2.55% [libz.so.1.3] 0 0% 50.50% 78ms 2.51% NodeLocationWriter::VisitAnyPopulation 42ms 1.35% 51.85% 78ms 2.51% std::basic_filebuf::xsputn 8ms 0.26% 52.11% 78ms 2.51% std::vector::_M_default_append 0 0% 52.11% 77ms 2.48% vtkIdList::Allocate 0 0% 52.11% 70ms 2.26% PottsMesh::GetMooreNeighbouringNodeIndices 0 0% 52.11% 70ms 2.26% vtkFloatArray::~vtkFloatArray 3ms 0.097% 52.21% 66ms 2.13% _int_free_maybe_consolidate 66ms 2.13% 54.33% 66ms 2.13% vtkObjectBase::vtkObjectBase 63ms 2.03% 56.36% 63ms 2.03% unlink_chunk 9ms 0.29% 56.65% 62ms 2.00% vtkDataArray::vtkDataArray 1ms 0.032% 56.69% 61ms 1.97% CellPropertyCollection::GetPropertiesType (inline) 26ms 0.84% 57.52% 61ms 1.97% hack_digit 0 0% 57.52% 60ms 1.93% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 22ms 0.71% 58.23% 58ms 1.87% vtkTypeFloat64Array::PrintSelf 1ms 0.032% 58.27% 57ms 1.84% std::vector::push_back (inline) 1ms 0.032% 58.30% 57ms 1.84% vtkIdList::New 0 0% 58.30% 53ms 1.71% Cell::HasCellProperty (inline) 3ms 0.097% 58.40% 53ms 1.71% CellPropertyCollection::HasProperty 3ms 0.097% 58.49% 53ms 1.71% vtkAbstractArray::vtkAbstractArray 1ms 0.032% 58.52% 53ms 1.71% vtkDoubleArray::~vtkDoubleArray 52ms 1.68% 60.20% 52ms 1.68% __GI_sched_yield 52ms 1.68% 61.88% 52ms 1.68% __strcmp_evex 17ms 0.55% 62.42% 52ms 1.68% vtkAOSDataArrayTemplate::DataElementChanged 2ms 0.064% 62.49% 48ms 1.55% std::_Rb_tree::_M_insert_unique 0 0% 62.49% 48ms 1.55% std::set::insert (inline) 0 0% 62.49% 46ms 1.48% AbstractCellProperty::IsSubType (inline) 7ms 0.23% 62.71% 46ms 1.48% __dynamic_cast 7ms 0.23% 62.94% 46ms 1.48% std::__ostream_insert 1ms 0.032% 62.97% 46ms 1.48% std::operator<< (inline) 0 0% 62.97% 46ms 1.48% vtkXMLWriter::WritePointDataAppendedData 2ms 0.064% 63.04% 45ms 1.45% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 63.04% 45ms 1.45% AbstractCellProperty::IsType (inline) 0 0% 63.04% 44ms 1.42% NodesOnlyMesh::SetUpBoxCollection 0 0% 63.04% 44ms 1.42% std::map::operator[] (partial-inline) 0 0% 63.04% 44ms 1.42% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 7ms 0.23% 63.26% 43ms 1.39% boost::numeric::ublas::c_vector::c_vector (partial-inline) 5ms 0.16% 63.42% 43ms 1.39% std::vector::_M_realloc_insert 0 0% 63.42% 41ms 1.32% VertexMesh::Clear 6ms 0.19% 63.62% 41ms 1.32% std::_Rb_tree::_M_insert_ (inline) 0 0% 63.62% 39ms 1.26% Cell::GetCellProliferativeType 4ms 0.13% 63.74% 39ms 1.26% vtkDataArray::~vtkDataArray 3ms 0.097% 63.84% 38ms 1.22% VertexMeshWriter::GetNextNode 34ms 1.10% 64.94% 38ms 1.22% std::basic_streambuf::xsputn 37ms 1.19% 66.13% 37ms 1.19% [libvtkCommonCore-9.3.so.9.3] 9ms 0.29% 66.42% 36ms 1.16% AbstractCellProperty::IsSame 0 0% 66.42% 36ms 1.16% NodesOnlyMesh::~NodesOnlyMesh 0 0% 66.42% 34ms 1.10% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 1ms 0.032% 66.45% 34ms 1.10% boost::numeric::ublas::vector_assign (inline) 5ms 0.16% 66.61% 33ms 1.06% vtkIdList::~vtkIdList 6ms 0.19% 66.81% 31ms 1% std::num_put::_M_insert_int 10ms 0.32% 67.13% 30ms 0.97% std::_Rb_tree::_M_lower_bound (inline) 0 0% 67.13% 29ms 0.93% CxxTest::RealWorldDescription::setUp 0 0% 67.13% 29ms 0.93% PMPI_Init_thread 0 0% 67.13% 29ms 0.93% PetscInitialize 0 0% 67.13% 29ms 0.93% PetscSetup::setUpWorld 0 0% 67.13% 29ms 0.93% PetscSetupUtils::CommonSetup 0 0% 67.13% 29ms 0.93% PetscSetupUtils::InitialisePetsc 0 0% 67.13% 29ms 0.93% PottsMesh::GetVonNeumannNeighbouringNodeIndices 29ms 0.93% 68.06% 29ms 0.93% __mpn_divrem 0 0% 68.06% 29ms 0.93% ompi_mpi_init 1ms 0.032% 68.10% 29ms 0.93% std::basic_filebuf::_M_convert_to_external 0 0% 68.10% 29ms 0.93% std::basic_filebuf::overflow 0 0% 68.10% 29ms 0.93% std::make_unique (inline) 28ms 0.9% 69.00% 28ms 0.9% __GI___libc_write 0 0% 69.00% 28ms 0.9% std::_Destroy (inline) 0 0% 69.00% 28ms 0.9% std::_Destroy_aux::__destroy (inline) 0 0% 69.00% 28ms 0.9% std::__basic_file::xsputn 28ms 0.9% 69.90% 28ms 0.9% vtkObjectBase::RegisterInternal 0 0% 69.90% 27ms 0.87% _dl_init 0 0% 69.90% 27ms 0.87% call_init (inline) 13ms 0.42% 70.32% 27ms 0.87% std::__new_allocator::construct (inline) 0 0% 70.32% 27ms 0.87% std::allocator_traits::construct (inline) 3ms 0.097% 70.42% 27ms 0.87% std::type_info::operator== (inline) 0 0% 70.42% 26ms 0.84% 3ms 0.097% 70.51% 26ms 0.84% Node::GetPoint 18ms 0.58% 71.09% 26ms 0.84% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 71.09% 26ms 0.84% _dl_start_user 12ms 0.39% 71.48% 26ms 0.84% std::_Hashtable::clear 2ms 0.064% 71.54% 25ms 0.81% DistributedBoxCollection::SetupLocalBoxesHalfOnly 25ms 0.81% 72.35% 25ms 0.81% __GI___writev 0 0% 72.35% 25ms 0.81% std::__basic_file::xsputn_2 2ms 0.064% 72.41% 24ms 0.77% DistributedBoxCollection::IsOwned 24ms 0.77% 73.19% 24ms 0.77% [libstdc++.so.6.0.33] 0 0% 73.19% 24ms 0.77% boost::detail::shared_count::~shared_count (inline) 23ms 0.74% 73.93% 24ms 0.77% boost::detail::sp_counted_base::release 0 0% 73.93% 24ms 0.77% boost::shared_ptr::~shared_ptr (inline) 0 0% 73.93% 24ms 0.77% std::_Rb_tree::_M_emplace_hint_unique 0 0% 73.93% 24ms 0.77% vtkDataArray::ComputeRange 0 0% 73.93% 24ms 0.77% vtkIdList::vtkIdList 0 0% 73.93% 23ms 0.74% vtkXMLUnstructuredDataWriter::WriteHeader 15ms 0.48% 74.41% 22ms 0.71% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 74.41% 22ms 0.71% DistributedBoxCollection::~DistributedBoxCollection 0 0% 74.41% 22ms 0.71% NodesOnlyMesh::ClearBoxCollection (inline) 9ms 0.29% 74.70% 22ms 0.71% boost::numeric::ublas::indexing_vector_assign 4ms 0.13% 74.83% 22ms 0.71% boost::serialization::singleton::get_instance 0 0% 74.83% 22ms 0.71% std::basic_filebuf::open 1ms 0.032% 74.86% 22ms 0.71% std::ostream::flush 2ms 0.064% 74.93% 22ms 0.71% vtkSOADataArrayTemplate::FillTypedComponent 0 0% 74.93% 21ms 0.68% orte_init 0 0% 74.93% 21ms 0.68% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 2ms 0.064% 74.99% 21ms 0.68% std::_Rb_tree_header::_Rb_tree_header (inline) 0 0% 74.99% 21ms 0.68% std::basic_filebuf::sync 16ms 0.52% 75.51% 21ms 0.68% std::num_put::do_put 0 0% 75.51% 21ms 0.68% tcache_get (inline) 21ms 0.68% 76.18% 21ms 0.68% tcache_get_n (inline) 16ms 0.52% 76.70% 21ms 0.68% vtkObject::ObjectFinalize 20ms 0.64% 77.34% 20ms 0.64% [libchaste_cell_based.so] 0 0% 77.34% 20ms 0.64% _IO_new_file_fopen 0 0% 77.34% 20ms 0.64% _IO_new_fopen 0 0% 77.34% 20ms 0.64% __GI__IO_file_open 0 0% 77.34% 20ms 0.64% __fopen_internal (inline) 20ms 0.64% 77.99% 20ms 0.64% __libc_open64 0 0% 77.99% 20ms 0.64% std::_Rb_tree::lower_bound (inline) 0 0% 77.99% 20ms 0.64% std::map::lower_bound (inline) 0 0% 77.99% 20ms 0.64% std::map::~map (inline) 0 0% 77.99% 20ms 0.64% vtkDoubleArray::New 12ms 0.39% 78.38% 19ms 0.61% _int_free_merge_chunk 19ms 0.61% 78.99% 19ms 0.61% std::_Rb_tree_header::_M_reset (inline) 0 0% 78.99% 19ms 0.61% std::__basic_file::open 4ms 0.13% 79.12% 19ms 0.61% vtkAOSDataArrayTemplate::InsertTuple 0 0% 79.12% 18ms 0.58% CellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 79.12% 18ms 0.58% Node::ConstructNodeAttributes (inline) 0 0% 79.12% 18ms 0.58% Node::SetRadius 0 0% 79.12% 18ms 0.58% OutputFileHandler::OpenOutputFile 18ms 0.58% 79.70% 18ms 0.58% __memcpy_avx512_unaligned_erms 2ms 0.064% 79.76% 18ms 0.58% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 0 0% 79.76% 18ms 0.58% std::default_delete::operator() (inline) 0 0% 79.76% 18ms 0.58% std::unique_ptr::~unique_ptr (inline) 0 0% 79.76% 18ms 0.58% vtkXMLUnstructuredGridWriter::WriteAppendedPiece 0 0% 79.76% 17ms 0.55% Cell::GetCellId 17ms 0.55% 80.31% 17ms 0.55% std::_Rb_tree_increment 17ms 0.55% 80.86% 17ms 0.55% std::ostream::sentry::sentry 0 0% 80.86% 17ms 0.55% std::vector::emplace_back (inline) 0 0% 80.86% 17ms 0.55% std::vector::vector (inline) 3ms 0.097% 80.95% 17ms 0.55% vtk::detail::smp::vtkSMPToolsImpl::For 0 0% 80.95% 17ms 0.55% vtk::detail::smp::vtkSMPToolsImplForTBB 0 0% 80.95% 16ms 0.52% CellIdWriter::GetCellDataForVtkOutput 0 0% 80.95% 16ms 0.52% Edge::Edge 0 0% 80.95% 16ms 0.52% Edge::SetNodes (inline) 16ms 0.52% 81.47% 16ms 0.52% __memset_avx512_unaligned_erms 0 0% 81.47% 16ms 0.52% boost::numeric::ublas::c_vector::assign (inline) 16ms 0.52% 81.99% 16ms 0.52% operator delete 2ms 0.064% 82.05% 16ms 0.52% vtkDataArrayPrivate::DoComputeVectorRange