File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3751ms, 79.64% of 4710ms total Dropped 762 nodes (cum <= 23.55ms) flat flat% sum% cum cum% 0 0% 0% 4473ms 94.97% __libc_start_call_main 0 0% 0% 4473ms 94.97% __libc_start_main_impl 0 0% 0% 4473ms 94.97% _start 0 0% 0% 4455ms 94.59% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4455ms 94.59% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4455ms 94.59% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4455ms 94.59% main 0 0% 0% 4412ms 93.67% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4412ms 93.67% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4412ms 93.67% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4401ms 93.44% AbstractCellBasedSimulation::Solve 0 0% 0% 4098ms 87.01% AbstractCellPopulation::WriteResultsToFiles 17ms 0.36% 0.36% 3885ms 82.48% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.36% 1979ms 42.02% VertexMeshWriter::WriteVtkUsingMesh 0 0% 0.36% 1702ms 36.14% VertexMeshWriter::MakeVtkMesh 1ms 0.021% 0.38% 1268ms 26.92% vtkPolygon::New 2ms 0.042% 0.42% 1266ms 26.88% vtkPolygon::vtkPolygon 7ms 0.15% 0.57% 889ms 18.87% vtkCell::vtkCell 5ms 0.11% 0.68% 774ms 16.43% vtkPoints::New 18ms 0.38% 1.06% 730ms 15.50% vtkPoints::vtkPoints 1ms 0.021% 1.08% 653ms 13.86% VertexMeshWriter::WriteFiles 30ms 0.64% 1.72% 624ms 13.25% operator new 38ms 0.81% 2.53% 624ms 13.25% std::ostream::_M_insert 1ms 0.021% 2.55% 622ms 13.21% std::ostream::operator<< (inline) 181ms 3.84% 6.39% 604ms 12.82% __GI___libc_malloc 0 0% 6.39% 570ms 12.10% vtkStreamingDemandDrivenPipeline::Update 0 0% 6.39% 570ms 12.10% vtkXMLWriterBase::Write 1ms 0.021% 6.41% 567ms 12.04% vtkDemandDrivenPipeline::ProcessRequest 0 0% 6.41% 564ms 11.97% vtkExecutive::CallAlgorithm 2ms 0.042% 6.45% 564ms 11.97% vtkLine::New 0 0% 6.45% 564ms 11.97% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 6.45% 562ms 11.93% vtkDemandDrivenPipeline::ExecuteData 0 0% 6.45% 561ms 11.91% vtkCompositeDataPipeline::ExecuteData 0 0% 6.45% 561ms 11.91% vtkXMLUnstructuredDataWriter::ProcessRequest 1ms 0.021% 6.48% 551ms 11.70% vtkQuad::New 2ms 0.042% 6.52% 548ms 11.63% vtkQuad::vtkQuad 9ms 0.19% 6.71% 543ms 11.53% vtkLine::vtkLine 2ms 0.042% 6.75% 532ms 11.30% vtkTriangle::New 4ms 0.085% 6.84% 521ms 11.06% vtkTriangle::vtkTriangle 44ms 0.93% 7.77% 520ms 11.04% std::num_put::_M_insert_float 0 0% 7.77% 494ms 10.49% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 7.77% 494ms 10.49% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 121ms 2.57% 10.34% 488ms 10.36% __GI___libc_free 34ms 0.72% 11.06% 465ms 9.87% vtkPoints::SetDataType 0 0% 11.06% 445ms 9.45% vtkXMLWriter::WriteBinaryData 0 0% 11.06% 439ms 9.32% vtkXMLWriter::WriteBinaryDataInternal 0 0% 11.06% 437ms 9.28% vtkXMLWriter::WriteBinaryDataBlock 0 0% 11.06% 419ms 8.90% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 11ms 0.23% 11.30% 405ms 8.60% std::__cxx11::collate::do_transform 4ms 0.085% 11.38% 389ms 8.26% vtkPolygon::~vtkPolygon 4ms 0.085% 11.46% 376ms 7.98% ___vsnprintf 0 0% 11.46% 372ms 7.90% __vsnprintf_internal (inline) 50ms 1.06% 12.53% 368ms 7.81% __printf_buffer 217ms 4.61% 17.13% 363ms 7.71% _int_free 218ms 4.63% 21.76% 356ms 7.56% _int_malloc 0 0% 21.76% 343ms 7.28% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 21.76% 336ms 7.13% VtkMeshWriter::WriteFiles 0 0% 21.76% 321ms 6.82% vtkXMLWriter::WritePointsAppendedData 11ms 0.23% 22.00% 291ms 6.18% __printf_fp_l_buffer 0 0% 22.00% 291ms 6.18% __printf_fp_spec (inline) 0 0% 22.00% 289ms 6.14% OnLatticeSimulation::UpdateCellLocationsAndTopology 4ms 0.085% 22.08% 289ms 6.14% PottsBasedCellPopulation::UpdateCellLocations 5ms 0.11% 22.19% 287ms 6.09% vtkCell::~vtkCell 40ms 0.85% 23.04% 277ms 5.88% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 125ms 2.65% 25.69% 268ms 5.69% __printf_fp_buffer_1 1ms 0.021% 25.71% 264ms 5.61% std::__new_allocator::deallocate (inline) 0 0% 25.71% 262ms 5.56% std::allocator_traits::deallocate (inline) 35ms 0.74% 26.45% 246ms 5.22% std::__new_allocator::allocate (inline) 0 0% 26.45% 243ms 5.16% std::allocator_traits::allocate (inline) 4ms 0.085% 26.54% 228ms 4.84% vtkBase64OutputStream::Write 11ms 0.23% 26.77% 222ms 4.71% vtkBase64OutputStream::EncodeTriplet 0 0% 26.77% 217ms 4.61% vtkXMLWriter::WriteCompressionBlock 1ms 0.021% 26.79% 208ms 4.42% tbb::detail::r1::parallel_pipeline 0 0% 26.79% 207ms 4.39% vtkDataCompressor::Compress 0 0% 26.79% 206ms 4.37% compress2 0 0% 26.79% 206ms 4.37% vtkZLibDataCompressor::CompressBuffer 42ms 0.89% 27.69% 205ms 4.35% crc32 0 0% 27.69% 205ms 4.35% deflate 0 0% 27.69% 201ms 4.27% clone3 0 0% 27.69% 201ms 4.27% start_thread 118ms 2.51% 30.19% 196ms 4.16% malloc_consolidate 37ms 0.79% 30.98% 196ms 4.16% std::ostream::write 3ms 0.064% 31.04% 193ms 4.10% std::set::set (inline) 10ms 0.21% 31.25% 189ms 4.01% std::_Rb_tree::_Rb_tree 4ms 0.085% 31.34% 189ms 4.01% tbb::detail::r1::reset 5ms 0.11% 31.44% 181ms 3.84% vtkIdList::AllocateInternal 4ms 0.085% 31.53% 181ms 3.84% vtkPoints::~vtkPoints 91ms 1.93% 33.46% 179ms 3.80% std::basic_filebuf::xsputn 2ms 0.042% 33.50% 173ms 3.67% std::_Vector_base::_M_deallocate (inline) 7ms 0.15% 33.65% 171ms 3.63% vtkFloatArray::New 1ms 0.021% 33.67% 170ms 3.61% vtkQuad::~vtkQuad 0 0% 33.67% 169ms 3.59% vtkTriangle::~vtkTriangle 0 0% 33.67% 168ms 3.57% VertexMesh::~VertexMesh 72ms 1.53% 35.20% 168ms 3.57% tbb::detail::r1::wait_bounded_queue_monitor 4ms 0.085% 35.29% 167ms 3.55% NodesOnlyMesh::ConstructNodesWithoutMesh 150ms 3.18% 38.47% 155ms 3.29% [libz.so.1.3] 2ms 0.042% 38.51% 152ms 3.23% VertexMesh::VertexMesh 15ms 0.32% 38.83% 151ms 3.21% std::_Rb_tree::_M_copy (inline) 0 0% 38.83% 151ms 3.21% std::_Rb_tree::_M_create_node (inline) 0 0% 38.83% 151ms 3.21% std::vector::~vector (inline) 1ms 0.021% 38.85% 149ms 3.16% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 0 0% 38.85% 148ms 3.14% NodeLocationWriter::VisitAnyPopulation 4ms 0.085% 38.94% 148ms 3.14% vtkFloatArray::vtkFloatArray 5ms 0.11% 39.04% 148ms 3.14% vtkLine::GetParametricCenter 16ms 0.34% 39.38% 145ms 3.08% std::vector::_M_default_append 0 0% 39.38% 143ms 3.04% std::_Rb_tree::_Alloc_node::operator() (inline) 6ms 0.13% 39.51% 143ms 3.04% vtkDataArray::CreateDataArray 0 0% 39.51% 142ms 3.01% std::_Rb_tree::_M_get_node (inline) 38ms 0.81% 40.32% 141ms 2.99% std::_Rb_tree::_M_erase 5ms 0.11% 40.42% 141ms 2.99% std::_Rb_tree::~_Rb_tree (inline) 7ms 0.15% 40.57% 139ms 2.95% MutableElement::BuildEdges 0 0% 40.57% 139ms 2.95% VertexMesh::GenerateEdgesFromElements (inline) 1ms 0.021% 40.59% 137ms 2.91% vtkTypeFloat64Array::~vtkTypeFloat64Array 3ms 0.064% 40.66% 136ms 2.89% vtkDoubleArray::vtkDoubleArray 0 0% 40.66% 133ms 2.82% vtkIdList::Allocate 12ms 0.25% 40.91% 132ms 2.80% std::_Rb_tree::_M_clone_node (inline) 5ms 0.11% 41.02% 131ms 2.78% vtkTypeFloat64Array::New 1ms 0.021% 41.04% 130ms 2.76% std::_Vector_base::~_Vector_base (inline) 23ms 0.49% 41.53% 123ms 2.61% vtkObject::vtkObject 6ms 0.13% 41.66% 120ms 2.55% vtkFloatArray::~vtkFloatArray 0 0% 41.66% 118ms 2.51% std::set::~set (inline) 1ms 0.021% 41.68% 117ms 2.48% EdgeHelper::GetEdgeFromNodes 0 0% 41.68% 113ms 2.40% EdgeHelper::~EdgeHelper (inline) 69ms 1.46% 43.14% 112ms 2.38% vtkObjectBase::UnRegisterInternal 3ms 0.064% 43.21% 107ms 2.27% vtkTypeFloat64Array::vtkTypeFloat64Array 106ms 2.25% 45.46% 106ms 2.25% unlink_chunk 1ms 0.021% 45.48% 104ms 2.21% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.064% 45.54% 104ms 2.21% std::_Vector_base::_M_allocate (inline) 38ms 0.81% 46.35% 103ms 2.19% std::__ostream_insert 0 0% 46.35% 101ms 2.14% std::_Rb_tree::_M_drop_node (inline) 2ms 0.042% 46.39% 99ms 2.10% _int_free_maybe_consolidate 2ms 0.042% 46.43% 99ms 2.10% std::operator<< (inline) 97ms 2.06% 48.49% 97ms 2.06% __strcmp_avx2 24ms 0.51% 49.00% 95ms 2.02% vtkObject::Modified 0 0% 49.00% 95ms 2.02% vtkXMLWriter::WritePointDataAppendedData 94ms 2.00% 51.00% 94ms 2.00% __GI_sched_yield 49ms 1.04% 52.04% 92ms 1.95% vtkTypeFloat64Array::PrintSelf 0 0% 52.04% 91ms 1.93% std::_Rb_tree::_M_put_node (inline) 1ms 0.021% 52.06% 89ms 1.89% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 52.06% 87ms 1.85% AbstractCellProperty::IsSubType (inline) 14ms 0.3% 52.36% 87ms 1.85% __dynamic_cast 39ms 0.83% 53.18% 87ms 1.85% hack_digit 0 0% 53.18% 86ms 1.83% Cell::HasCellProperty (inline) 0 0% 53.18% 86ms 1.83% CellPropertyCollection::HasProperty 6ms 0.13% 53.31% 85ms 1.80% std::map::operator[] (partial-inline) 3ms 0.064% 53.38% 84ms 1.78% vtkDoubleArray::~vtkDoubleArray 0 0% 53.38% 82ms 1.74% AbstractCellProperty::IsType (inline) 23ms 0.49% 53.86% 82ms 1.74% std::_Rb_tree::_M_lower_bound (inline) 6ms 0.13% 53.99% 81ms 1.72% std::vector::push_back (inline) 46ms 0.98% 54.97% 77ms 1.63% std::basic_streambuf::xsputn 0 0% 54.97% 75ms 1.59% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 3ms 0.064% 55.03% 70ms 1.49% vtkIdList::New 1ms 0.021% 55.05% 68ms 1.44% AbstractCellPopulation::GetCellUsingLocationIndex 6ms 0.13% 55.18% 64ms 1.36% vtkDataArray::vtkDataArray 64ms 1.36% 56.54% 64ms 1.36% vtkTimeStamp::Modified 0 0% 56.54% 63ms 1.34% NodesOnlyMesh::SetUpBoxCollection 7ms 0.15% 56.69% 63ms 1.34% vtkAOSDataArrayTemplate::DataElementChanged 0 0% 56.69% 62ms 1.32% PottsMesh::GetMooreNeighbouringNodeIndices 0 0% 56.69% 61ms 1.30% std::_Rb_tree::lower_bound (inline) 0 0% 56.69% 61ms 1.30% std::map::lower_bound (inline) 13ms 0.28% 56.96% 58ms 1.23% AbstractCellProperty::IsSame 0 0% 56.96% 56ms 1.19% Cell::GetCellProliferativeType 56ms 1.19% 58.15% 56ms 1.19% __GI___writev 0 0% 58.15% 56ms 1.19% std::__basic_file::xsputn_2 17ms 0.36% 58.51% 56ms 1.19% vtkAbstractArray::vtkAbstractArray 0 0% 58.51% 55ms 1.17% VertexMesh::Clear 4ms 0.085% 58.60% 55ms 1.17% std::vector::_M_realloc_insert 0 0% 58.60% 55ms 1.17% tcache_get (inline) 55ms 1.17% 59.77% 55ms 1.17% tcache_get_n (inline) 0 0% 59.77% 52ms 1.10% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 25ms 0.53% 60.30% 51ms 1.08% __cxxabiv1::__si_class_type_info::__do_dyncast 6ms 0.13% 60.42% 50ms 1.06% boost::numeric::ublas::c_vector::c_vector (partial-inline) 47ms 1% 61.42% 47ms 1% __memcpy_avx_unaligned_erms 10ms 0.21% 61.63% 47ms 1% vtkSOADataArrayTemplate::FillTypedComponent 26ms 0.55% 62.19% 46ms 0.98% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 62.19% 46ms 0.98% DistributedBoxCollection::IsOwned 9ms 0.19% 62.38% 45ms 0.96% std::type_info::operator== (inline) 44ms 0.93% 63.31% 44ms 0.93% [libvtkCommonCore-9.3.so.9.3] 1ms 0.021% 63.33% 43ms 0.91% std::make_unique (inline) 0 0% 63.33% 43ms 0.91% vtkDoubleArray::New 35ms 0.74% 64.08% 43ms 0.91% vtkObject::ObjectFinalize 0 0% 64.08% 42ms 0.89% NodesOnlyMesh::~NodesOnlyMesh 42ms 0.89% 64.97% 42ms 0.89% [libstdc++.so.6.0.33] 41ms 0.87% 65.84% 42ms 0.89% vtkObject::~vtkObject 40ms 0.85% 66.69% 40ms 0.85% boost::numeric::ublas::c_vector::operator() 0 0% 66.69% 40ms 0.85% boost::numeric::ublas::vector_assign (inline) 19ms 0.4% 67.09% 40ms 0.85% std::_Hashtable::clear 1ms 0.021% 67.11% 40ms 0.85% std::_Rb_tree::_M_insert_unique 0 0% 67.11% 40ms 0.85% std::set::insert (inline) 0 0% 67.11% 39ms 0.83% CxxTest::RealWorldDescription::setUp 0 0% 67.11% 39ms 0.83% PetscInitialize 0 0% 67.11% 39ms 0.83% PetscSetup::setUpWorld 0 0% 67.11% 39ms 0.83% PetscSetupUtils::CommonSetup 0 0% 67.11% 39ms 0.83% PetscSetupUtils::InitialisePetsc 39ms 0.83% 67.94% 39ms 0.83% [libchaste_cell_based.so] 1ms 0.021% 67.96% 39ms 0.83% vtkDataArrayPrivate::DoComputeVectorRange 0 0% 67.96% 38ms 0.81% PMPI_Init_thread 4ms 0.085% 68.05% 38ms 0.81% VertexMeshWriter::GetNextNode 0 0% 68.05% 38ms 0.81% _dl_init 0 0% 68.05% 38ms 0.81% call_init (inline) 0 0% 68.05% 38ms 0.81% ompi_mpi_init 1ms 0.021% 68.07% 38ms 0.81% std::less::operator() (inline) 7ms 0.15% 68.22% 38ms 0.81% std::num_put::_M_insert_int 37ms 0.79% 69.00% 37ms 0.79% std::operator< (inline) 37ms 0.79% 69.79% 37ms 0.79% vtkObjectBase::~vtkObjectBase 0 0% 69.79% 36ms 0.76% _dl_start_user 36ms 0.76% 70.55% 36ms 0.76% std::_Rb_tree_increment 0 0% 70.55% 36ms 0.76% vtkDataArray::ComputeRange 10ms 0.21% 70.76% 36ms 0.76% vtkDataArray::~vtkDataArray 36ms 0.76% 71.53% 36ms 0.76% vtkObjectBase::Delete 0 0% 71.53% 35ms 0.74% Cell::GetCellId 12ms 0.25% 71.78% 35ms 0.74% _int_free_merge_chunk 0 0% 71.78% 34ms 0.72% vtk::detail::smp::vtkSMPToolsImplForTBB 1ms 0.021% 71.80% 33ms 0.7% 33ms 0.7% 72.51% 33ms 0.7% std::ostream::sentry::sentry 4ms 0.085% 72.59% 33ms 0.7% tbb::detail::r1::cancel_group_execution 0 0% 72.59% 32ms 0.68% PottsMesh::GetVonNeumannNeighbouringNodeIndices 4ms 0.085% 72.68% 32ms 0.68% boost::serialization::singleton::get_instance 32ms 0.68% 73.35% 32ms 0.68% std::codecvt::do_always_noconv 4ms 0.085% 73.44% 32ms 0.68% vtkIdList::~vtkIdList 0 0% 73.44% 31ms 0.66% CellIdWriter::GetCellDataForVtkOutput 0 0% 73.44% 31ms 0.66% DistributedBoxCollection::SetupLocalBoxesHalfOnly 3ms 0.064% 73.50% 31ms 0.66% Edge::Edge 31ms 0.66% 74.16% 31ms 0.66% __mpn_divrem 5ms 0.11% 74.27% 31ms 0.66% vtk::detail::smp::vtkSMPToolsImpl::For 6ms 0.13% 74.39% 31ms 0.66% vtkAOSDataArrayTemplate::InsertTuple 6ms 0.13% 74.52% 31ms 0.66% vtkIdList::vtkIdList 0 0% 74.52% 30ms 0.64% DistributedBoxCollection::~DistributedBoxCollection 0 0% 74.52% 30ms 0.64% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 74.52% 29ms 0.62% OutputFileHandler::OpenOutputFile 0 0% 74.52% 29ms 0.62% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 28ms 0.59% 75.12% 28ms 0.59% __GI___libc_write 28ms 0.59% 75.71% 28ms 0.59% __memset_avx2_unaligned_erms 0 0% 75.71% 28ms 0.59% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 1ms 0.021% 75.73% 28ms 0.59% std::_Rb_tree_header::_Rb_tree_header (inline) 0 0% 75.73% 28ms 0.59% std::__basic_file::xsputn 0 0% 75.73% 28ms 0.59% std::basic_filebuf::_M_convert_to_external 0 0% 75.73% 28ms 0.59% std::basic_filebuf::open 0 0% 75.73% 28ms 0.59% std::basic_filebuf::overflow 28ms 0.59% 76.33% 28ms 0.59% vtkObjectBase::vtkObjectBase 0 0% 76.33% 27ms 0.57% VtkMeshWriter::MakeVtkMesh 0 0% 76.33% 27ms 0.57% _IO_new_file_fopen 0 0% 76.33% 27ms 0.57% _IO_new_fopen 0 0% 76.33% 27ms 0.57% __GI__IO_file_open 0 0% 76.33% 27ms 0.57% __fopen_internal (inline) 2ms 0.042% 76.37% 27ms 0.57% std::_Rb_tree::_M_insert_ (inline) 27ms 0.57% 76.94% 27ms 0.57% vtkObjectBase::Register 0 0% 76.94% 26ms 0.55% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 76.94% 26ms 0.55% Edge::SetNodes (inline) 3ms 0.064% 77.01% 26ms 0.55% VertexMeshWriter::GetNextElement 26ms 0.55% 77.56% 26ms 0.55% __libc_open64 0 0% 77.56% 26ms 0.55% std::_Destroy (inline) 1ms 0.021% 77.58% 26ms 0.55% std::_Destroy_aux::__destroy (inline) 3ms 0.064% 77.64% 26ms 0.55% std::_Rb_tree_const_iterator::operator++ (inline) 26ms 0.55% 78.20% 26ms 0.55% std::_Rb_tree_header::_M_reset (inline) 0 0% 78.20% 26ms 0.55% std::__basic_file::open 6ms 0.13% 78.32% 26ms 0.55% std::__new_allocator::construct (inline) 0 0% 78.32% 26ms 0.55% std::allocator_traits::construct (inline) 1ms 0.021% 78.34% 26ms 0.55% vtkDataSet::GetCellTypes 5ms 0.11% 78.45% 25ms 0.53% boost::detail::shared_count::~shared_count (inline) 0 0% 78.45% 25ms 0.53% boost::shared_ptr::~shared_ptr (inline) 0 0% 78.45% 25ms 0.53% orte_init 25ms 0.53% 78.98% 25ms 0.53% std::_Rb_tree::_S_right (inline) 2ms 0.042% 79.02% 24ms 0.51% __find_specmb (inline) 5ms 0.11% 79.13% 24ms 0.51% vtkAOSDataArrayTemplate::AllocateTuples 24ms 0.51% 79.64% 24ms 0.51% vtkDataArray::Modified