File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3830ms, 80.08% of 4783ms total Dropped 707 nodes (cum <= 23.91ms) flat flat% sum% cum cum% 0 0% 0% 4597ms 96.11% __libc_start_call_main 0 0% 0% 4597ms 96.11% __libc_start_main_impl 0 0% 0% 4597ms 96.11% _start 0 0% 0% 4581ms 95.78% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4581ms 95.78% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4581ms 95.78% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4581ms 95.78% main 0 0% 0% 4540ms 94.92% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4540ms 94.92% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4540ms 94.92% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4529ms 94.69% AbstractCellBasedSimulation::Solve 0 0% 0% 4243ms 88.71% AbstractCellPopulation::WriteResultsToFiles 18ms 0.38% 0.38% 4006ms 83.75% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.38% 1965ms 41.08% VertexMeshWriter::WriteVtkUsingMesh 2ms 0.042% 0.42% 1701ms 35.56% VertexMeshWriter::MakeVtkMesh 2ms 0.042% 0.46% 1267ms 26.49% vtkPolygon::New 2ms 0.042% 0.5% 1264ms 26.43% vtkPolygon::vtkPolygon 10ms 0.21% 0.71% 930ms 19.44% vtkCell::vtkCell 4ms 0.084% 0.79% 782ms 16.35% vtkPoints::New 0 0% 0.79% 765ms 15.99% VertexMeshWriter::WriteFiles 4ms 0.084% 0.88% 749ms 15.66% std::ostream::operator<< (inline) 69ms 1.44% 2.32% 748ms 15.64% std::ostream::_M_insert 10ms 0.21% 2.53% 740ms 15.47% vtkPoints::vtkPoints 36ms 0.75% 3.28% 645ms 13.49% operator new 0 0% 3.28% 616ms 12.88% vtkQuad::New 187ms 3.91% 7.19% 614ms 12.84% __GI___libc_malloc 0 0% 7.19% 614ms 12.84% vtkQuad::vtkQuad 2ms 0.042% 7.23% 609ms 12.73% vtkLine::New 0 0% 7.23% 603ms 12.61% vtkTriangle::New 49ms 1.02% 8.26% 597ms 12.48% std::num_put::_M_insert_float 5ms 0.1% 8.36% 597ms 12.48% vtkTriangle::vtkTriangle 7ms 0.15% 8.51% 588ms 12.29% vtkLine::vtkLine 0 0% 8.51% 568ms 11.88% vtkStreamingDemandDrivenPipeline::Update 0 0% 8.51% 568ms 11.88% vtkXMLWriterBase::Write 0 0% 8.51% 566ms 11.83% vtkDemandDrivenPipeline::ProcessRequest 0 0% 8.51% 566ms 11.83% vtkStreamingDemandDrivenPipeline::ProcessRequest 1ms 0.021% 8.53% 565ms 11.81% vtkCompositeDataPipeline::ExecuteData 1ms 0.021% 8.55% 565ms 11.81% vtkExecutive::CallAlgorithm 0 0% 8.55% 564ms 11.79% vtkDemandDrivenPipeline::ExecuteData 0 0% 8.55% 564ms 11.79% vtkXMLUnstructuredDataWriter::ProcessRequest 143ms 2.99% 11.54% 531ms 11.10% __GI___libc_free 0 0% 11.54% 519ms 10.85% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 11.54% 519ms 10.85% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 33ms 0.69% 12.23% 486ms 10.16% vtkPoints::SetDataType 0 0% 12.23% 463ms 9.68% vtkXMLWriter::WriteBinaryData 9ms 0.19% 12.42% 459ms 9.60% std::__cxx11::collate::do_transform 1ms 0.021% 12.44% 455ms 9.51% vtkXMLWriter::WriteBinaryDataInternal 0 0% 12.44% 454ms 9.49% vtkXMLWriter::WriteBinaryDataBlock 0 0% 12.44% 449ms 9.39% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 4ms 0.084% 12.52% 426ms 8.91% ___vsnprintf 0 0% 12.52% 422ms 8.82% __vsnprintf_internal (inline) 56ms 1.17% 13.69% 417ms 8.72% __printf_buffer 0 0% 13.69% 391ms 8.17% vtkPolygon::~vtkPolygon 243ms 5.08% 18.77% 387ms 8.09% _int_free 262ms 5.48% 24.25% 364ms 7.61% _int_malloc 1ms 0.021% 24.27% 351ms 7.34% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 24.27% 348ms 7.28% VtkMeshWriter::WriteFiles 0 0% 24.27% 333ms 6.96% vtkXMLWriter::WritePointsAppendedData 1ms 0.021% 24.29% 330ms 6.90% __printf_fp_spec (inline) 11ms 0.23% 24.52% 329ms 6.88% __printf_fp_l_buffer 5ms 0.1% 24.63% 305ms 6.38% vtkCell::~vtkCell 137ms 2.86% 27.49% 301ms 6.29% __printf_fp_buffer_1 47ms 0.98% 28.48% 293ms 6.13% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 0 0% 28.48% 278ms 5.81% OnLatticeSimulation::UpdateCellLocationsAndTopology 6ms 0.13% 28.60% 278ms 5.81% PottsBasedCellPopulation::UpdateCellLocations 3ms 0.063% 28.66% 266ms 5.56% std::__new_allocator::deallocate (inline) 0 0% 28.66% 264ms 5.52% std::allocator_traits::deallocate (inline) 34ms 0.71% 29.37% 252ms 5.27% std::__new_allocator::allocate (inline) 0 0% 29.37% 252ms 5.27% std::allocator_traits::allocate (inline) 0 0% 29.37% 238ms 4.98% vtkXMLWriter::WriteCompressionBlock 0 0% 29.37% 226ms 4.73% compress2 0 0% 29.37% 226ms 4.73% vtkDataCompressor::Compress 0 0% 29.37% 226ms 4.73% vtkZLibDataCompressor::CompressBuffer 7ms 0.15% 29.52% 224ms 4.68% vtkBase64OutputStream::Write 72ms 1.51% 31.03% 222ms 4.64% crc32 0 0% 31.03% 222ms 4.64% deflate 21ms 0.44% 31.47% 217ms 4.54% vtkBase64OutputStream::EncodeTriplet 5ms 0.1% 31.57% 207ms 4.33% vtkPoints::~vtkPoints 55ms 1.15% 32.72% 182ms 3.81% std::ostream::write 5ms 0.1% 32.82% 181ms 3.78% vtkFloatArray::New 1ms 0.021% 32.85% 175ms 3.66% vtkQuad::~vtkQuad 3ms 0.063% 32.91% 166ms 3.47% NodesOnlyMesh::ConstructNodesWithoutMesh 116ms 2.43% 35.33% 166ms 3.47% malloc_consolidate 0 0% 35.33% 166ms 3.47% std::set::set (inline) 10ms 0.21% 35.54% 165ms 3.45% std::_Rb_tree::_Rb_tree 0 0% 35.54% 165ms 3.45% std::vector::~vector (inline) 7ms 0.15% 35.69% 162ms 3.39% vtkDataArray::CreateDataArray 1ms 0.021% 35.71% 161ms 3.37% VertexMesh::VertexMesh 0 0% 35.71% 161ms 3.37% tbb::detail::r1::parallel_pipeline 2ms 0.042% 35.75% 160ms 3.35% vtkTypeFloat64Array::~vtkTypeFloat64Array 9ms 0.19% 35.94% 158ms 3.30% vtkIdList::AllocateInternal 3ms 0.063% 36.00% 156ms 3.26% vtkTriangle::~vtkTriangle 5ms 0.1% 36.11% 155ms 3.24% std::_Vector_base::_M_deallocate (inline) 0 0% 36.11% 155ms 3.24% vtkLine::GetParametricCenter 3ms 0.063% 36.17% 153ms 3.20% NodeLocationWriter::VisitAnyPopulation 0 0% 36.17% 151ms 3.16% clone3 0 0% 36.17% 151ms 3.16% start_thread 2ms 0.042% 36.21% 151ms 3.16% vtkFloatArray::vtkFloatArray 0 0% 36.21% 150ms 3.14% tbb::detail::r1::reset 7ms 0.15% 36.36% 149ms 3.12% MutableElement::BuildEdges 0 0% 36.36% 149ms 3.12% VertexMesh::GenerateEdgesFromElements (inline) 24ms 0.5% 36.86% 149ms 3.12% std::_Rb_tree::_M_erase 61ms 1.28% 38.14% 149ms 3.12% tbb::detail::r1::wait_bounded_queue_monitor 0 0% 38.14% 148ms 3.09% VertexMesh::~VertexMesh 0 0% 38.14% 148ms 3.09% std::_Rb_tree::_M_create_node (inline) 6ms 0.13% 38.26% 148ms 3.09% std::_Rb_tree::~_Rb_tree (inline) 68ms 1.42% 39.68% 147ms 3.07% std::basic_filebuf::xsputn 2ms 0.042% 39.72% 147ms 3.07% vtkDoubleArray::vtkDoubleArray 5ms 0.1% 39.83% 143ms 2.99% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 7ms 0.15% 39.97% 142ms 2.97% vtkTypeFloat64Array::New 135ms 2.82% 42.80% 138ms 2.89% [libz.so.1.3] 0 0% 42.80% 138ms 2.89% std::_Rb_tree::_M_get_node (inline) 13ms 0.27% 43.07% 138ms 2.89% std::vector::_M_default_append 4ms 0.084% 43.15% 138ms 2.89% vtkFloatArray::~vtkFloatArray 0 0% 43.15% 134ms 2.80% std::set::~set (inline) 0 0% 43.15% 132ms 2.76% std::_Rb_tree::_Alloc_node::operator() (inline) 15ms 0.31% 43.47% 132ms 2.76% std::_Rb_tree::_M_copy (inline) 33ms 0.69% 44.16% 131ms 2.74% vtkObject::vtkObject 3ms 0.063% 44.22% 130ms 2.72% EdgeHelper::GetEdgeFromNodes 0 0% 44.22% 124ms 2.59% std::_Vector_base::~_Vector_base (inline) 2ms 0.042% 44.26% 123ms 2.57% vtkTypeFloat64Array::vtkTypeFloat64Array 49ms 1.02% 45.29% 122ms 2.55% std::__ostream_insert 0 0% 45.29% 121ms 2.53% std::_Rb_tree::_M_drop_node (inline) 2ms 0.042% 45.33% 119ms 2.49% std::operator<< (inline) 1ms 0.021% 45.35% 115ms 2.40% std::_Vector_base::_M_allocate (inline) 16ms 0.33% 45.68% 114ms 2.38% std::_Rb_tree::_M_clone_node (inline) 0 0% 45.68% 114ms 2.38% std::_Rb_tree::_M_put_node (inline) 0 0% 45.68% 114ms 2.38% vtkXMLWriter::WritePointDataAppendedData 0 0% 45.68% 105ms 2.20% EdgeHelper::~EdgeHelper (inline) 105ms 2.20% 47.88% 105ms 2.20% __strcmp_avx2 61ms 1.28% 49.15% 102ms 2.13% hack_digit 1ms 0.021% 49.17% 99ms 2.07% CellPropertyCollection::GetPropertiesType (inline) 28ms 0.59% 49.76% 99ms 2.07% vtkObject::Modified 10ms 0.21% 49.97% 98ms 2.05% _int_free_maybe_consolidate 4ms 0.084% 50.05% 97ms 2.03% std::map::operator[] (partial-inline) 1ms 0.021% 50.07% 97ms 2.03% vtkIdList::Allocate 50ms 1.05% 51.12% 95ms 1.99% vtkTypeFloat64Array::PrintSelf 0 0% 51.12% 92ms 1.92% Cell::HasCellProperty (inline) 6ms 0.13% 51.24% 92ms 1.92% CellPropertyCollection::HasProperty 73ms 1.53% 52.77% 92ms 1.92% std::basic_streambuf::xsputn 0 0% 52.77% 89ms 1.86% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 86ms 1.80% 54.57% 86ms 1.80% __GI_sched_yield 56ms 1.17% 55.74% 86ms 1.80% vtkObjectBase::UnRegisterInternal 1ms 0.021% 55.76% 84ms 1.76% AbstractCellProperty::IsSubType (inline) 16ms 0.33% 56.09% 84ms 1.76% vtkAOSDataArrayTemplate::DataElementChanged 9ms 0.19% 56.28% 84ms 1.76% vtkDoubleArray::~vtkDoubleArray 20ms 0.42% 56.70% 83ms 1.74% __dynamic_cast 1ms 0.021% 56.72% 82ms 1.71% std::vector::push_back (inline) 2ms 0.042% 56.76% 81ms 1.69% AbstractCellProperty::IsType (inline) 3ms 0.063% 56.83% 79ms 1.65% vtkIdList::New 75ms 1.57% 58.39% 75ms 1.57% unlink_chunk 4ms 0.084% 58.48% 71ms 1.48% AbstractCellPopulation::GetCellUsingLocationIndex 19ms 0.4% 58.88% 71ms 1.48% std::_Rb_tree::_M_lower_bound (inline) 69ms 1.44% 60.32% 69ms 1.44% vtkTimeStamp::Modified 0 0% 60.32% 69ms 1.44% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 13ms 0.27% 60.59% 67ms 1.40% AbstractCellProperty::IsSame 0 0% 60.59% 63ms 1.32% NodesOnlyMesh::~NodesOnlyMesh 14ms 0.29% 60.88% 63ms 1.32% std::num_put::_M_insert_int 0 0% 60.88% 62ms 1.30% NodesOnlyMesh::SetUpBoxCollection 0 0% 60.88% 62ms 1.30% tcache_get (inline) 62ms 1.30% 62.18% 62ms 1.30% tcache_get_n (inline) 6ms 0.13% 62.30% 61ms 1.28% vtkDataArray::vtkDataArray 4ms 0.084% 62.39% 59ms 1.23% std::vector::_M_realloc_insert 4ms 0.084% 62.47% 58ms 1.21% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 62.47% 57ms 1.19% std::_Rb_tree::lower_bound (inline) 0 0% 62.47% 57ms 1.19% std::map::lower_bound (inline) 0 0% 62.47% 56ms 1.17% Cell::GetCellProliferativeType 0 0% 62.47% 55ms 1.15% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 0 0% 62.47% 55ms 1.15% std::_Destroy (inline) 0 0% 62.47% 55ms 1.15% std::_Destroy_aux::__destroy (inline) 0 0% 62.47% 54ms 1.13% boost::numeric::ublas::vector_assign (inline) 10ms 0.21% 62.68% 54ms 1.13% std::type_info::operator== (inline) 8ms 0.17% 62.85% 54ms 1.13% vtkAbstractArray::vtkAbstractArray 51ms 1.07% 63.91% 51ms 1.07% [libvtkCommonCore-9.3.so.9.3] 0 0% 63.91% 50ms 1.05% std::__basic_file::xsputn_2 50ms 1.05% 64.96% 50ms 1.05% std::ostream::sentry::sentry 49ms 1.02% 65.98% 49ms 1.02% __GI___writev 49ms 1.02% 67.01% 49ms 1.02% __memcpy_avx_unaligned_erms 0 0% 67.01% 47ms 0.98% DistributedBoxCollection::~DistributedBoxCollection 0 0% 67.01% 47ms 0.98% NodesOnlyMesh::ClearBoxCollection (inline) 1ms 0.021% 67.03% 47ms 0.98% std::_Rb_tree::_M_insert_unique 0 0% 67.03% 47ms 0.98% std::set::insert (inline) 0 0% 67.03% 47ms 0.98% vtkDataArray::ComputeRange 28ms 0.59% 67.61% 46ms 0.96% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 67.61% 46ms 0.96% DistributedBoxCollection::IsOwned 0 0% 67.61% 45ms 0.94% std::make_unique (inline) 15ms 0.31% 67.93% 45ms 0.94% vtkDataArray::~vtkDataArray 17ms 0.36% 68.28% 44ms 0.92% boost::numeric::ublas::indexing_vector_assign 0 0% 68.28% 43ms 0.9% VertexMesh::Clear 40ms 0.84% 69.12% 43ms 0.9% vtkObjectBase::Delete 3ms 0.063% 69.18% 43ms 0.9% vtkSOADataArrayTemplate::FillTypedComponent 0 0% 69.18% 42ms 0.88% PottsMesh::GetMooreNeighbouringNodeIndices 9ms 0.19% 69.37% 42ms 0.88% vtkIdList::~vtkIdList 42ms 0.88% 70.25% 42ms 0.88% vtkObject::~vtkObject 1ms 0.021% 70.27% 41ms 0.86% vtkDoubleArray::New 4ms 0.084% 70.35% 40ms 0.84% DistributedBoxCollection::SetupLocalBoxesHalfOnly 15ms 0.31% 70.67% 39ms 0.82% __cxxabiv1::__si_class_type_info::__do_dyncast 26ms 0.54% 71.21% 39ms 0.82% std::_Hashtable::clear 2ms 0.042% 71.25% 39ms 0.82% std::_Rb_tree::_M_insert_ (inline) 7ms 0.15% 71.40% 39ms 0.82% vtkAOSDataArrayTemplate::InsertTuple 0 0% 71.40% 38ms 0.79% std::unique_ptr::~unique_ptr (inline) 2ms 0.042% 71.44% 37ms 0.77% Cell::GetMutationState 0 0% 71.44% 37ms 0.77% CxxTest::RealWorldDescription::setUp 0 0% 71.44% 37ms 0.77% PMPI_Init_thread 0 0% 71.44% 37ms 0.77% PetscInitialize 0 0% 71.44% 37ms 0.77% PetscSetup::setUpWorld 0 0% 71.44% 37ms 0.77% PetscSetupUtils::CommonSetup 0 0% 71.44% 37ms 0.77% PetscSetupUtils::InitialisePetsc 0 0% 71.44% 37ms 0.77% ompi_mpi_init 0 0% 71.44% 37ms 0.77% std::default_delete::operator() (inline) 2ms 0.042% 71.48% 36ms 0.75% std::_Rb_tree::_M_emplace_hint_unique 0 0% 71.48% 35ms 0.73% _dl_init 0 0% 71.48% 35ms 0.73% _dl_start_user 0 0% 71.48% 35ms 0.73% call_init (inline) 0 0% 71.48% 35ms 0.73% vtk::detail::smp::vtkSMPToolsImplForTBB 2ms 0.042% 71.52% 34ms 0.71% tbb::detail::r1::cancel_group_execution 5ms 0.1% 71.63% 34ms 0.71% vtkDataArrayPrivate::DoComputeVectorRange 3ms 0.063% 71.69% 33ms 0.69% 0 0% 71.69% 33ms 0.69% CellProliferativeTypesWriter::GetCellDataForVtkOutput 1ms 0.021% 71.71% 33ms 0.69% std::less::operator() (inline) 5ms 0.1% 71.82% 33ms 0.69% vtk::detail::smp::vtkSMPToolsImpl::For 32ms 0.67% 72.49% 32ms 0.67% boost::numeric::ublas::c_vector::operator() 32ms 0.67% 73.15% 32ms 0.67% std::operator< (inline) 0 0% 73.15% 31ms 0.65% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 1ms 0.021% 73.18% 31ms 0.65% PottsBasedCellPopulation::AcceptCellWriter 8ms 0.17% 73.34% 31ms 0.65% std::__new_allocator::construct (inline) 0 0% 73.34% 31ms 0.65% std::allocator_traits::construct (inline) 0 0% 73.34% 31ms 0.65% std::basic_filebuf::open 31ms 0.65% 73.99% 31ms 0.65% vtkObjectBase::~vtkObjectBase 1ms 0.021% 74.01% 30ms 0.63% VertexMeshWriter::GetNextNode 3ms 0.063% 74.07% 30ms 0.63% VtkMeshWriter::MakeVtkMesh 5ms 0.1% 74.18% 30ms 0.63% _int_free_merge_chunk 2ms 0.042% 74.22% 30ms 0.63% boost::serialization::singleton::get_instance 1ms 0.021% 74.24% 30ms 0.63% std::__basic_file::xsputn 0 0% 74.24% 30ms 0.63% std::basic_filebuf::_M_convert_to_external 0 0% 74.24% 30ms 0.63% std::basic_filebuf::overflow 0 0% 74.24% 29ms 0.61% Edge::Edge 0 0% 74.24% 29ms 0.61% Edge::SetNodes (inline) 29ms 0.61% 74.85% 29ms 0.61% __GI___libc_write 29ms 0.61% 75.45% 29ms 0.61% std::codecvt::do_always_noconv 1ms 0.021% 75.48% 29ms 0.61% vtkDataArrayPrivate::DoComputeScalarRange 0 0% 75.48% 28ms 0.59% Edge::~Edge (inline) 0 0% 75.48% 28ms 0.59% _IO_new_file_fopen 0 0% 75.48% 28ms 0.59% _IO_new_fopen 0 0% 75.48% 28ms 0.59% __GI__IO_file_open 2ms 0.042% 75.52% 28ms 0.59% __find_specmb (inline) 0 0% 75.52% 28ms 0.59% __fopen_internal (inline) 28ms 0.59% 76.10% 28ms 0.59% __libc_open64 1ms 0.021% 76.12% 28ms 0.59% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 0 0% 76.12% 28ms 0.59% std::__basic_file::open 7ms 0.15% 76.27% 28ms 0.59% vtkIdList::vtkIdList 0 0% 76.27% 27ms 0.56% PottsMesh::GetVonNeumannNeighbouringNodeIndices 26ms 0.54% 76.81% 26ms 0.54% [libchaste_cell_based.so] 26ms 0.54% 77.36% 26ms 0.54% __mpn_divrem 26ms 0.54% 77.90% 26ms 0.54% __strchrnul_avx2 0 0% 77.90% 26ms 0.54% orte_init 18ms 0.38% 78.28% 26ms 0.54% std::num_put::do_put 0 0% 78.28% 25ms 0.52% OutputFileHandler::OpenOutputFile 24ms 0.5% 78.78% 24ms 0.5% __GI___uselocale 14ms 0.29% 79.07% 24ms 0.5% _int_free_create_chunk (inline) 24ms 0.5% 79.57% 24ms 0.5% std::_Rb_tree::_S_right (inline) 24ms 0.5% 80.08% 24ms 0.5% vtkObjectBase::vtkObjectBase