File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3740ms, 78.90% of 4740ms total Dropped 754 nodes (cum <= 23.70ms) flat flat% sum% cum cum% 0 0% 0% 4527ms 95.51% __libc_start_call_main 0 0% 0% 4527ms 95.51% __libc_start_main_impl 0 0% 0% 4527ms 95.51% _start 0 0% 0% 4508ms 95.11% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4508ms 95.11% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4508ms 95.11% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4508ms 95.11% main 0 0% 0% 4467ms 94.24% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4467ms 94.24% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4467ms 94.24% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4456ms 94.01% AbstractCellBasedSimulation::Solve 0 0% 0% 4149ms 87.53% AbstractCellPopulation::WriteResultsToFiles 12ms 0.25% 0.25% 3932ms 82.95% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.25% 1996ms 42.11% VertexMeshWriter::WriteVtkUsingMesh 2ms 0.042% 0.3% 1715ms 36.18% VertexMeshWriter::MakeVtkMesh 0 0% 0.3% 1281ms 27.03% vtkPolygon::New 3ms 0.063% 0.36% 1278ms 26.96% vtkPolygon::vtkPolygon 6ms 0.13% 0.49% 888ms 18.73% vtkCell::vtkCell 2ms 0.042% 0.53% 761ms 16.05% vtkPoints::New 9ms 0.19% 0.72% 718ms 15.15% vtkPoints::vtkPoints 0 0% 0.72% 668ms 14.09% VertexMeshWriter::WriteFiles 35ms 0.74% 1.46% 661ms 13.95% operator new 57ms 1.20% 2.66% 653ms 13.78% std::ostream::_M_insert 0 0% 2.66% 652ms 13.76% std::ostream::operator<< (inline) 199ms 4.20% 6.86% 638ms 13.46% __GI___libc_malloc 2ms 0.042% 6.90% 600ms 12.66% vtkLine::New 8ms 0.17% 7.07% 578ms 12.19% vtkLine::vtkLine 1ms 0.021% 7.09% 574ms 12.11% vtkQuad::New 3ms 0.063% 7.15% 572ms 12.07% vtkTriangle::New 4ms 0.084% 7.24% 570ms 12.03% vtkQuad::vtkQuad 0 0% 7.24% 563ms 11.88% vtkStreamingDemandDrivenPipeline::Update 0 0% 7.24% 563ms 11.88% vtkXMLWriterBase::Write 1ms 0.021% 7.26% 560ms 11.81% vtkDemandDrivenPipeline::ProcessRequest 4ms 0.084% 7.34% 558ms 11.77% vtkTriangle::vtkTriangle 0 0% 7.34% 557ms 11.75% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 7.34% 555ms 11.71% vtkCompositeDataPipeline::ExecuteData 0 0% 7.34% 555ms 11.71% vtkDemandDrivenPipeline::ExecuteData 0 0% 7.34% 555ms 11.71% vtkExecutive::CallAlgorithm 0 0% 7.34% 554ms 11.69% vtkXMLUnstructuredDataWriter::ProcessRequest 36ms 0.76% 8.10% 524ms 11.05% std::num_put::_M_insert_float 108ms 2.28% 10.38% 497ms 10.49% __GI___libc_free 0 0% 10.38% 488ms 10.30% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 10.38% 488ms 10.30% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 18ms 0.38% 10.76% 438ms 9.24% vtkPoints::SetDataType 9ms 0.19% 10.95% 434ms 9.16% std::__cxx11::collate::do_transform 0 0% 10.95% 432ms 9.11% vtkXMLWriter::WriteBinaryData 1ms 0.021% 10.97% 427ms 9.01% vtkXMLWriter::WriteBinaryDataBlock 0 0% 10.97% 427ms 9.01% vtkXMLWriter::WriteBinaryDataInternal 3ms 0.063% 11.03% 412ms 8.69% ___vsnprintf 0 0% 11.03% 412ms 8.69% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 11.03% 409ms 8.63% __vsnprintf_internal (inline) 62ms 1.31% 12.34% 404ms 8.52% __printf_buffer 222ms 4.68% 17.03% 383ms 8.08% _int_free 1ms 0.021% 17.05% 381ms 8.04% vtkPolygon::~vtkPolygon 246ms 5.19% 22.24% 365ms 7.70% _int_malloc 0 0% 22.24% 336ms 7.09% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 22.24% 333ms 7.03% VtkMeshWriter::WriteFiles 12ms 0.25% 22.49% 319ms 6.73% __printf_fp_l_buffer 0 0% 22.49% 319ms 6.73% __printf_fp_spec (inline) 0 0% 22.49% 310ms 6.54% vtkXMLWriter::WritePointsAppendedData 0 0% 22.49% 302ms 6.37% OnLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.063% 22.55% 302ms 6.37% PottsBasedCellPopulation::UpdateCellLocations 128ms 2.70% 25.25% 296ms 6.24% __printf_fp_buffer_1 41ms 0.86% 26.12% 283ms 5.97% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 3ms 0.063% 26.18% 282ms 5.95% vtkCell::~vtkCell 0 0% 26.18% 269ms 5.68% std::__new_allocator::deallocate (inline) 0 0% 26.18% 267ms 5.63% std::allocator_traits::deallocate (inline) 39ms 0.82% 27.00% 264ms 5.57% std::__new_allocator::allocate (inline) 0 0% 27.00% 263ms 5.55% std::allocator_traits::allocate (inline) 0 0% 27.00% 223ms 4.70% vtkXMLWriter::WriteCompressionBlock 0 0% 27.00% 212ms 4.47% compress2 0 0% 27.00% 212ms 4.47% vtkDataCompressor::Compress 0 0% 27.00% 212ms 4.47% vtkZLibDataCompressor::CompressBuffer 52ms 1.10% 28.10% 211ms 4.45% crc32 0 0% 28.10% 211ms 4.45% deflate 9ms 0.19% 28.29% 207ms 4.37% vtkFloatArray::New 3ms 0.063% 28.35% 204ms 4.30% vtkBase64OutputStream::Write 14ms 0.3% 28.65% 198ms 4.18% vtkBase64OutputStream::EncodeTriplet 2ms 0.042% 28.69% 195ms 4.11% std::set::set (inline) 3ms 0.063% 28.76% 194ms 4.09% vtkPoints::~vtkPoints 16ms 0.34% 29.09% 192ms 4.05% std::_Rb_tree::_Rb_tree 107ms 2.26% 31.35% 187ms 3.95% malloc_consolidate 0 0% 31.35% 177ms 3.73% clone3 0 0% 31.35% 177ms 3.73% start_thread 3ms 0.063% 31.41% 177ms 3.73% tbb::detail::r1::parallel_pipeline 3ms 0.063% 31.48% 171ms 3.61% NodesOnlyMesh::ConstructNodesWithoutMesh 2ms 0.042% 31.52% 171ms 3.61% tbb::detail::r1::reset 1ms 0.021% 31.54% 171ms 3.61% vtkQuad::~vtkQuad 0 0% 31.54% 170ms 3.59% VertexMesh::~VertexMesh 1ms 0.021% 31.56% 167ms 3.52% vtkTriangle::~vtkTriangle 78ms 1.65% 33.21% 166ms 3.50% tbb::detail::r1::wait_bounded_queue_monitor 47ms 0.99% 34.20% 165ms 3.48% std::_Rb_tree::_M_erase 2ms 0.042% 34.24% 165ms 3.48% vtkIdList::AllocateInternal 2ms 0.042% 34.28% 164ms 3.46% vtkFloatArray::vtkFloatArray 5ms 0.11% 34.39% 161ms 3.40% std::_Rb_tree::~_Rb_tree (inline) 28ms 0.59% 34.98% 158ms 3.33% std::ostream::write 5ms 0.11% 35.08% 157ms 3.31% vtkDataArray::CreateDataArray 1ms 0.021% 35.11% 156ms 3.29% std::_Vector_base::_M_deallocate (inline) 0 0% 35.11% 156ms 3.29% std::vector::~vector (inline) 1ms 0.021% 35.13% 155ms 3.27% VertexMesh::VertexMesh 0 0% 35.13% 151ms 3.19% std::_Rb_tree::_M_create_node (inline) 145ms 3.06% 38.19% 150ms 3.16% [libz.so.1.3] 4ms 0.084% 38.27% 146ms 3.08% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 5ms 0.11% 38.38% 146ms 3.08% MutableElement::BuildEdges 0 0% 38.38% 146ms 3.08% VertexMesh::GenerateEdgesFromElements (inline) 16ms 0.34% 38.71% 146ms 3.08% std::_Rb_tree::_M_copy (inline) 0 0% 38.71% 141ms 2.97% vtkTypeFloat64Array::~vtkTypeFloat64Array 0 0% 38.71% 140ms 2.95% std::_Rb_tree::_M_get_node (inline) 63ms 1.33% 40.04% 140ms 2.95% std::basic_filebuf::xsputn 1ms 0.021% 40.06% 140ms 2.95% vtkLine::GetParametricCenter 0 0% 40.06% 139ms 2.93% NodeLocationWriter::VisitAnyPopulation 6ms 0.13% 40.19% 137ms 2.89% std::vector::_M_default_append 0 0% 40.19% 136ms 2.87% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 40.19% 131ms 2.76% std::set::~set (inline) 10ms 0.21% 40.40% 130ms 2.74% vtkTypeFloat64Array::New 5ms 0.11% 40.51% 128ms 2.70% vtkDoubleArray::vtkDoubleArray 1ms 0.021% 40.53% 126ms 2.66% std::_Vector_base::~_Vector_base (inline) 18ms 0.38% 40.91% 122ms 2.57% std::_Rb_tree::_M_clone_node (inline) 0 0% 40.91% 122ms 2.57% std::_Vector_base::_M_allocate (inline) 3ms 0.063% 40.97% 121ms 2.55% EdgeHelper::GetEdgeFromNodes 0 0% 40.97% 119ms 2.51% EdgeHelper::~EdgeHelper (inline) 5ms 0.11% 41.08% 118ms 2.49% vtkFloatArray::~vtkFloatArray 0 0% 41.08% 115ms 2.43% std::_Rb_tree::_M_drop_node (inline) 0 0% 41.08% 114ms 2.41% CellPropertyCollection::GetPropertiesType (inline) 0 0% 41.08% 112ms 2.36% std::_Rb_tree::_M_put_node (inline) 8ms 0.17% 41.24% 108ms 2.28% _int_free_maybe_consolidate 0 0% 41.24% 108ms 2.28% vtkIdList::Allocate 51ms 1.08% 42.32% 106ms 2.24% hack_digit 3ms 0.063% 42.38% 105ms 2.22% vtkTypeFloat64Array::vtkTypeFloat64Array 54ms 1.14% 43.52% 104ms 2.19% vtkTypeFloat64Array::PrintSelf 103ms 2.17% 45.70% 103ms 2.17% __strcmp_avx2 102ms 2.15% 47.85% 102ms 2.15% unlink_chunk 28ms 0.59% 48.44% 100ms 2.11% vtkObject::vtkObject 0 0% 48.44% 99ms 2.09% vtkXMLWriter::WritePointDataAppendedData 1ms 0.021% 48.46% 98ms 2.07% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 1ms 0.021% 48.48% 98ms 2.07% std::map::operator[] (partial-inline) 0 0% 48.48% 92ms 1.94% AbstractCellProperty::IsSubType (inline) 0 0% 48.48% 92ms 1.94% Cell::HasCellProperty (inline) 3ms 0.063% 48.54% 92ms 1.94% CellPropertyCollection::HasProperty 26ms 0.55% 49.09% 92ms 1.94% __dynamic_cast 30ms 0.63% 49.73% 90ms 1.90% std::__ostream_insert 5ms 0.11% 49.83% 90ms 1.90% std::operator<< (inline) 2ms 0.042% 49.87% 89ms 1.88% AbstractCellProperty::IsType (inline) 89ms 1.88% 51.75% 89ms 1.88% __GI_sched_yield 55ms 1.16% 52.91% 86ms 1.81% vtkObjectBase::UnRegisterInternal 50ms 1.05% 53.97% 84ms 1.77% std::basic_streambuf::xsputn 9ms 0.19% 54.16% 83ms 1.75% vtkAOSDataArrayTemplate::DataElementChanged 24ms 0.51% 54.66% 81ms 1.71% std::_Rb_tree::_M_lower_bound (inline) 20ms 0.42% 55.08% 78ms 1.65% vtkObject::Modified 6ms 0.13% 55.21% 77ms 1.62% vtkIdList::New 7ms 0.15% 55.36% 73ms 1.54% vtkDoubleArray::~vtkDoubleArray 1ms 0.021% 55.38% 72ms 1.52% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 2ms 0.042% 55.42% 71ms 1.50% AbstractCellPopulation::GetCellUsingLocationIndex 2ms 0.042% 55.46% 71ms 1.50% std::vector::push_back (inline) 0 0% 55.46% 69ms 1.46% NodesOnlyMesh::SetUpBoxCollection 37ms 0.78% 56.24% 66ms 1.39% std::_Hashtable::clear 13ms 0.27% 56.52% 65ms 1.37% AbstractCellProperty::IsSame 0 0% 56.52% 65ms 1.37% tcache_get (inline) 65ms 1.37% 57.89% 65ms 1.37% tcache_get_n (inline) 0 0% 57.89% 64ms 1.35% std::_Rb_tree::lower_bound (inline) 0 0% 57.89% 64ms 1.35% std::map::lower_bound (inline) 5ms 0.11% 58.00% 64ms 1.35% vtkDataArray::vtkDataArray 0 0% 58.00% 63ms 1.33% PottsMesh::GetMooreNeighbouringNodeIndices 1ms 0.021% 58.02% 61ms 1.29% Cell::GetCellProliferativeType 0 0% 58.02% 59ms 1.24% NodesOnlyMesh::~NodesOnlyMesh 1ms 0.021% 58.04% 57ms 1.20% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 3ms 0.063% 58.10% 57ms 1.20% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.021% 58.12% 56ms 1.18% std::_Rb_tree::_M_insert_unique 0 0% 58.12% 56ms 1.18% std::set::insert (inline) 16ms 0.34% 58.46% 56ms 1.18% vtkAbstractArray::vtkAbstractArray 56ms 1.18% 59.64% 56ms 1.18% vtkTimeStamp::Modified 0 0% 59.64% 54ms 1.14% boost::numeric::ublas::vector_assign (inline) 52ms 1.10% 60.74% 52ms 1.10% [libvtkCommonCore-9.3.so.9.3] 13ms 0.27% 61.01% 52ms 1.10% std::num_put::_M_insert_int 5ms 0.11% 61.12% 52ms 1.10% std::type_info::operator== (inline) 0 0% 61.12% 51ms 1.08% VertexMesh::Clear 50ms 1.05% 62.17% 50ms 1.05% __GI___writev 50ms 1.05% 63.23% 50ms 1.05% __memcpy_avx_unaligned_erms 0 0% 63.23% 50ms 1.05% std::__basic_file::xsputn_2 0 0% 63.23% 50ms 1.05% std::vector::_M_realloc_insert 5ms 0.11% 63.33% 48ms 1.01% std::_Rb_tree::_M_insert_ (inline) 5ms 0.11% 63.44% 46ms 0.97% VertexMeshWriter::GetNextNode 1ms 0.021% 63.46% 45ms 0.95% DistributedBoxCollection::IsOwned 28ms 0.59% 64.05% 45ms 0.95% __cxxabiv1::__si_class_type_info::__do_dyncast 44ms 0.93% 64.98% 45ms 0.95% vtkObjectBase::Delete 29ms 0.61% 65.59% 44ms 0.93% DistributedBoxCollection::CalculateContainingBox (inline) 44ms 0.93% 66.52% 44ms 0.93% vtkObjectBase::~vtkObjectBase 0 0% 66.52% 43ms 0.91% _dl_init 0 0% 66.52% 43ms 0.91% call_init (inline) 13ms 0.27% 66.79% 42ms 0.89% _int_free_merge_chunk 0 0% 66.79% 40ms 0.84% DistributedBoxCollection::~DistributedBoxCollection 0 0% 66.79% 40ms 0.84% NodesOnlyMesh::ClearBoxCollection (inline) 14ms 0.3% 67.09% 40ms 0.84% boost::numeric::ublas::indexing_vector_assign 1ms 0.021% 67.11% 40ms 0.84% std::basic_filebuf::overflow 1ms 0.021% 67.13% 40ms 0.84% vtkDoubleArray::New 6ms 0.13% 67.26% 40ms 0.84% vtkSOADataArrayTemplate::FillTypedComponent 39ms 0.82% 68.08% 39ms 0.82% __GI___libc_write 1ms 0.021% 68.10% 39ms 0.82% std::__basic_file::xsputn 0 0% 68.10% 39ms 0.82% std::basic_filebuf::_M_convert_to_external 1ms 0.021% 68.12% 39ms 0.82% std::less::operator() (inline) 38ms 0.8% 68.92% 38ms 0.8% std::operator< (inline) 0 0% 68.92% 37ms 0.78% CxxTest::RealWorldDescription::setUp 0 0% 68.92% 37ms 0.78% PetscInitialize 0 0% 68.92% 37ms 0.78% PetscSetup::setUpWorld 0 0% 68.92% 37ms 0.78% PetscSetupUtils::CommonSetup 0 0% 68.92% 37ms 0.78% PetscSetupUtils::InitialisePetsc 2ms 0.042% 68.97% 36ms 0.76% DistributedBoxCollection::SetupLocalBoxesHalfOnly 0 0% 68.97% 36ms 0.76% PMPI_Init_thread 36ms 0.76% 69.73% 36ms 0.76% __memset_avx2_unaligned_erms 36ms 0.76% 70.49% 36ms 0.76% __mpn_divrem 0 0% 70.49% 36ms 0.76% _dl_start_user 0 0% 70.49% 36ms 0.76% ompi_mpi_init 0 0% 70.49% 36ms 0.76% vtkDataArray::ComputeRange 34ms 0.72% 71.20% 34ms 0.72% vtkObject::~vtkObject 33ms 0.7% 71.90% 33ms 0.7% [libstdc++.so.6.0.33] 0 0% 71.90% 33ms 0.7% std::_Rb_tree::_M_emplace_hint_unique 0 0% 71.90% 32ms 0.68% Cell::GetMutationState 32ms 0.68% 72.57% 32ms 0.68% Node::GetIndex 0 0% 72.57% 32ms 0.68% std::_Destroy (inline) 0 0% 72.57% 32ms 0.68% std::_Destroy_aux::__destroy (inline) 32ms 0.68% 73.25% 32ms 0.68% std::ostream::sentry::sentry 5ms 0.11% 73.35% 32ms 0.68% vtkAOSDataArrayTemplate::AllocateTuples 2ms 0.042% 73.40% 31ms 0.65% 0 0% 73.40% 31ms 0.65% Cell::GetCellId 0 0% 73.40% 31ms 0.65% CellProliferativeTypesWriter::GetCellDataForVtkOutput 4ms 0.084% 73.48% 31ms 0.65% boost::serialization::singleton::get_instance 5ms 0.11% 73.59% 31ms 0.65% vtkIdList::~vtkIdList 25ms 0.53% 74.11% 31ms 0.65% vtkObject::ObjectFinalize 1ms 0.021% 74.14% 30ms 0.63% VtkMeshWriter::MakeVtkMesh 0 0% 74.14% 30ms 0.63% std::make_unique (inline) 0 0% 74.14% 30ms 0.63% std::map::~map (inline) 0 0% 74.14% 29ms 0.61% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 2ms 0.042% 74.18% 29ms 0.61% std::_Rb_tree_header::_Rb_tree_header (inline) 29ms 0.61% 74.79% 29ms 0.61% std::_Rb_tree_increment 0 0% 74.79% 28ms 0.59% PottsMesh::GetVonNeumannNeighbouringNodeIndices 0 0% 74.79% 28ms 0.59% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 10ms 0.21% 75.00% 28ms 0.59% vtkDataArray::~vtkDataArray 0 0% 75.00% 27ms 0.57% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 75.00% 27ms 0.57% CellIdWriter::GetCellDataForVtkOutput 21ms 0.44% 75.44% 27ms 0.57% _int_free_create_chunk (inline) 27ms 0.57% 76.01% 27ms 0.57% std::_Rb_tree_header::_M_reset (inline) 27ms 0.57% 76.58% 27ms 0.57% std::codecvt::do_always_noconv 6ms 0.13% 76.71% 27ms 0.57% vtkAOSDataArrayTemplate::InsertTuple 3ms 0.063% 76.77% 27ms 0.57% vtkSOADataArrayTemplate::GetTupleIndexFromValueIndex 0 0% 76.77% 26ms 0.55% std::default_delete::operator() (inline) 0 0% 76.77% 26ms 0.55% std::unique_ptr::~unique_ptr (inline) 0 0% 76.77% 26ms 0.55% vtk::detail::smp::vtkSMPToolsImplForTBB 26ms 0.55% 77.32% 26ms 0.55% vtkBase64Utilities::EncodeTriplet 3ms 0.063% 77.38% 26ms 0.55% vtkDataArrayPrivate::DoComputeVectorRange 1ms 0.021% 77.41% 26ms 0.55% vtkDataSet::GetCellTypes 0 0% 77.41% 26ms 0.55% vtkUnstructuredGrid::GetDistinctCellTypesArray 0 0% 77.41% 25ms 0.53% PottsBasedCellPopulation::AcceptCellWriter 25ms 0.53% 77.93% 25ms 0.53% [libchaste_cell_based.so] 25ms 0.53% 78.46% 25ms 0.53% std::_Rb_tree_insert_and_rebalance 10ms 0.21% 78.67% 25ms 0.53% std::__new_allocator::construct (inline) 0 0% 78.67% 25ms 0.53% std::allocator_traits::construct (inline) 0 0% 78.67% 25ms 0.53% std::ostream::flush 6ms 0.13% 78.80% 25ms 0.53% std::vector::emplace_back (inline) 0 0% 78.80% 24ms 0.51% std::basic_filebuf::sync 0 0% 78.80% 24ms 0.51% std::vector::vector (inline) 5ms 0.11% 78.90% 24ms 0.51% tbb::detail::r1::cancel_group_execution