File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3650ms, 77.87% of 4687ms total Dropped 761 nodes (cum <= 23.43ms) flat flat% sum% cum cum% 0 0% 0% 4451ms 94.96% __libc_start_call_main 0 0% 0% 4451ms 94.96% __libc_start_main_impl 0 0% 0% 4451ms 94.96% _start 0 0% 0% 4436ms 94.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4436ms 94.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4436ms 94.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4436ms 94.64% main 0 0% 0% 4396ms 93.79% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4396ms 93.79% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4396ms 93.79% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4393ms 93.73% AbstractCellBasedSimulation::Solve 0 0% 0% 4191ms 89.42% AbstractCellPopulation::WriteResultsToFiles 19ms 0.41% 0.41% 3958ms 84.45% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.41% 1963ms 41.88% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.021% 0.43% 1691ms 36.08% VertexMeshWriter::MakeVtkMesh 0 0% 0.43% 1271ms 27.12% vtkPolygon::New 1ms 0.021% 0.45% 1269ms 27.07% vtkPolygon::vtkPolygon 5ms 0.11% 0.55% 927ms 19.78% vtkCell::vtkCell 0 0% 0.55% 792ms 16.90% VertexMeshWriter::WriteFiles 1ms 0.021% 0.58% 791ms 16.88% vtkPoints::New 58ms 1.24% 1.81% 763ms 16.28% std::ostream::_M_insert 2ms 0.043% 1.86% 761ms 16.24% std::ostream::operator<< (inline) 13ms 0.28% 2.13% 746ms 15.92% vtkPoints::vtkPoints 42ms 0.9% 3.03% 626ms 13.36% std::num_put::_M_insert_float 41ms 0.87% 3.90% 614ms 13.10% operator new 1ms 0.021% 3.93% 613ms 13.08% vtkLine::New 6ms 0.13% 4.05% 590ms 12.59% vtkLine::vtkLine 183ms 3.90% 7.96% 579ms 12.35% __GI___libc_malloc 2ms 0.043% 8.00% 578ms 12.33% vtkQuad::New 5ms 0.11% 8.11% 575ms 12.27% vtkQuad::vtkQuad 0 0% 8.11% 572ms 12.20% vtkStreamingDemandDrivenPipeline::Update 0 0% 8.11% 572ms 12.20% vtkXMLWriterBase::Write 0 0% 8.11% 568ms 12.12% vtkDemandDrivenPipeline::ProcessRequest 0 0% 8.11% 566ms 12.08% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 8.11% 564ms 12.03% vtkExecutive::CallAlgorithm 0 0% 8.11% 563ms 12.01% vtkCompositeDataPipeline::ExecuteData 0 0% 8.11% 563ms 12.01% vtkDemandDrivenPipeline::ExecuteData 0 0% 8.11% 563ms 12.01% vtkXMLUnstructuredDataWriter::ProcessRequest 1ms 0.021% 8.13% 557ms 11.88% vtkTriangle::New 2ms 0.043% 8.17% 543ms 11.59% vtkTriangle::vtkTriangle 0 0% 8.17% 509ms 10.86% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 8.17% 509ms 10.86% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 11ms 0.23% 8.41% 498ms 10.63% std::__cxx11::collate::do_transform 34ms 0.73% 9.13% 482ms 10.28% vtkPoints::SetDataType 5ms 0.11% 9.24% 475ms 10.13% ___vsnprintf 0 0% 9.24% 470ms 10.03% __vsnprintf_internal (inline) 150ms 3.20% 12.44% 466ms 9.94% __GI___libc_free 67ms 1.43% 13.87% 459ms 9.79% __printf_buffer 0 0% 13.87% 446ms 9.52% vtkXMLWriter::WriteBinaryData 0 0% 13.87% 442ms 9.43% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 1ms 0.021% 13.89% 437ms 9.32% vtkXMLWriter::WriteBinaryDataBlock 0 0% 13.89% 437ms 9.32% vtkXMLWriter::WriteBinaryDataInternal 2ms 0.043% 13.93% 372ms 7.94% vtkPolygon::~vtkPolygon 1ms 0.021% 13.95% 365ms 7.79% __printf_fp_spec (inline) 14ms 0.3% 14.25% 364ms 7.77% __printf_fp_l_buffer 3ms 0.064% 14.32% 360ms 7.68% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 14.32% 355ms 7.57% VtkMeshWriter::WriteFiles 222ms 4.74% 19.05% 352ms 7.51% _int_malloc 0 0% 19.05% 332ms 7.08% vtkXMLWriter::WritePointsAppendedData 156ms 3.33% 22.38% 331ms 7.06% __printf_fp_buffer_1 185ms 3.95% 26.33% 315ms 6.72% _int_free 2ms 0.043% 26.37% 300ms 6.40% vtkCell::~vtkCell 42ms 0.9% 27.27% 276ms 5.89% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 0 0% 27.27% 235ms 5.01% vtkXMLWriter::WriteCompressionBlock 0 0% 27.27% 229ms 4.89% vtkDataCompressor::Compress 0 0% 27.27% 227ms 4.84% compress2 0 0% 27.27% 227ms 4.84% vtkZLibDataCompressor::CompressBuffer 64ms 1.37% 28.63% 225ms 4.80% crc32 0 0% 28.63% 225ms 4.80% deflate 0 0% 28.63% 209ms 4.46% tbb::detail::r1::parallel_pipeline 10ms 0.21% 28.85% 208ms 4.44% std::__new_allocator::allocate (inline) 0 0% 28.85% 207ms 4.42% std::allocator_traits::allocate (inline) 3ms 0.064% 28.91% 203ms 4.33% vtkBase64OutputStream::Write 5ms 0.11% 29.02% 202ms 4.31% std::__new_allocator::deallocate (inline) 0 0% 29.02% 200ms 4.27% std::allocator_traits::deallocate (inline) 17ms 0.36% 29.38% 200ms 4.27% vtkBase64OutputStream::EncodeTriplet 0 0% 29.38% 199ms 4.25% clone3 1ms 0.021% 29.40% 199ms 4.25% start_thread 0 0% 29.40% 197ms 4.20% tbb::detail::r1::reset 5ms 0.11% 29.51% 196ms 4.18% vtkPoints::~vtkPoints 81ms 1.73% 31.24% 195ms 4.16% tbb::detail::r1::wait_bounded_queue_monitor 0 0% 31.24% 192ms 4.10% OnLatticeSimulation::UpdateCellLocationsAndTopology 14ms 0.3% 31.53% 192ms 4.10% PottsBasedCellPopulation::UpdateCellLocations 10ms 0.21% 31.75% 182ms 3.88% vtkFloatArray::New 1ms 0.021% 31.77% 181ms 3.86% VertexMesh::~VertexMesh 1ms 0.021% 31.79% 180ms 3.84% vtkQuad::~vtkQuad 119ms 2.54% 34.33% 171ms 3.65% malloc_consolidate 8ms 0.17% 34.50% 170ms 3.63% vtkIdList::AllocateInternal 51ms 1.09% 35.59% 162ms 3.46% std::ostream::write 2ms 0.043% 35.63% 158ms 3.37% NodeLocationWriter::VisitAnyPopulation 0 0% 35.63% 156ms 3.33% VertexMesh::VertexMesh 5ms 0.11% 35.74% 154ms 3.29% vtkFloatArray::vtkFloatArray 147ms 3.14% 38.87% 153ms 3.26% [libz.so.1.3] 0 0% 38.87% 151ms 3.22% std::vector::~vector (inline) 0 0% 38.87% 150ms 3.20% vtkLine::GetParametricCenter 0 0% 38.87% 149ms 3.18% VertexMesh::GenerateEdgesFromElements (inline) 1ms 0.021% 38.89% 149ms 3.18% std::_Vector_base::_M_deallocate (inline) 6ms 0.13% 39.02% 149ms 3.18% vtkFloatArray::~vtkFloatArray 8ms 0.17% 39.19% 148ms 3.16% MutableElement::BuildEdges 5ms 0.11% 39.30% 147ms 3.14% vtkDataArray::CreateDataArray 1ms 0.021% 39.32% 147ms 3.14% vtkTypeFloat64Array::~vtkTypeFloat64Array 0 0% 39.32% 143ms 3.05% vtkTriangle::~vtkTriangle 9ms 0.19% 39.51% 141ms 3.01% std::vector::_M_default_append 1ms 0.021% 39.53% 139ms 2.97% std::_Vector_base::_M_allocate (inline) 6ms 0.13% 39.66% 135ms 2.88% vtkTypeFloat64Array::New 0 0% 39.66% 128ms 2.73% vtkDoubleArray::vtkDoubleArray 23ms 0.49% 40.15% 127ms 2.71% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 0 0% 40.15% 127ms 2.71% EdgeHelper::~EdgeHelper (inline) 65ms 1.39% 41.54% 127ms 2.71% std::basic_filebuf::xsputn 0 0% 41.54% 126ms 2.69% NodesOnlyMesh::ConstructNodesWithoutMesh 2ms 0.043% 41.58% 125ms 2.67% EdgeHelper::GetEdgeFromNodes 2ms 0.043% 41.63% 119ms 2.54% std::_Vector_base::~_Vector_base (inline) 32ms 0.68% 42.31% 117ms 2.50% vtkObject::vtkObject 7ms 0.15% 42.46% 116ms 2.47% std::_Rb_tree::~_Rb_tree (inline) 4ms 0.085% 42.54% 115ms 2.45% vtkTypeFloat64Array::vtkTypeFloat64Array 0 0% 42.54% 114ms 2.43% vtkIdList::Allocate 113ms 2.41% 44.95% 113ms 2.41% __GI_sched_yield 111ms 2.37% 47.32% 111ms 2.37% __strcmp_avx2 50ms 1.07% 48.39% 109ms 2.33% std::_Rb_tree::_M_erase 0 0% 48.39% 109ms 2.33% vtkXMLWriter::WritePointDataAppendedData 1ms 0.021% 48.41% 108ms 2.30% CellPropertyCollection::GetPropertiesType (inline) 49ms 1.05% 49.46% 103ms 2.20% hack_digit 2ms 0.043% 49.50% 98ms 2.09% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 61ms 1.30% 50.80% 98ms 2.09% vtkObjectBase::UnRegisterInternal 12ms 0.26% 51.06% 97ms 2.07% vtkAOSDataArrayTemplate::DataElementChanged 33ms 0.7% 51.76% 96ms 2.05% std::__ostream_insert 1ms 0.021% 51.78% 93ms 1.98% std::operator<< (inline) 0 0% 51.78% 92ms 1.96% AbstractCellProperty::IsSubType (inline) 20ms 0.43% 52.21% 92ms 1.96% __dynamic_cast 42ms 0.9% 53.10% 88ms 1.88% vtkTypeFloat64Array::PrintSelf 63ms 1.34% 54.45% 87ms 1.86% std::basic_streambuf::xsputn 2ms 0.043% 54.49% 85ms 1.81% std::vector::push_back (inline) 1ms 0.021% 54.51% 82ms 1.75% AbstractCellProperty::IsType (inline) 0 0% 54.51% 82ms 1.75% Cell::HasCellProperty (inline) 1ms 0.021% 54.53% 82ms 1.75% CellPropertyCollection::HasProperty 18ms 0.38% 54.92% 80ms 1.71% vtkObject::Modified 79ms 1.69% 56.60% 79ms 1.69% unlink_chunk 2ms 0.043% 56.65% 78ms 1.66% _int_free_maybe_consolidate 5ms 0.11% 56.75% 77ms 1.64% vtkIdList::New 4ms 0.085% 56.84% 74ms 1.58% vtkDoubleArray::~vtkDoubleArray 8ms 0.17% 57.01% 71ms 1.51% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.085% 57.09% 71ms 1.51% std::map::operator[] (partial-inline) 4ms 0.085% 57.18% 70ms 1.49% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 57.18% 69ms 1.47% std::_Rb_tree::_M_create_node (inline) 0 0% 57.18% 68ms 1.45% std::_Rb_tree::_M_get_node (inline) 0 0% 57.18% 68ms 1.45% std::set::~set (inline) 23ms 0.49% 57.67% 67ms 1.43% std::_Rb_tree::_M_lower_bound (inline) 10ms 0.21% 57.88% 66ms 1.41% AbstractCellProperty::IsSame 2ms 0.043% 57.93% 66ms 1.41% std::set::set (inline) 0 0% 57.93% 65ms 1.39% boost::numeric::ublas::vector_assign (inline) 0 0% 57.93% 64ms 1.37% NodesOnlyMesh::SetUpBoxCollection 1ms 0.021% 57.95% 63ms 1.34% std::_Rb_tree::_Rb_tree 0 0% 57.95% 63ms 1.34% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 2ms 0.043% 57.99% 62ms 1.32% Cell::GetCellProliferativeType 7ms 0.15% 58.14% 62ms 1.32% std::vector::_M_realloc_insert 0 0% 58.14% 59ms 1.26% std::_Rb_tree::_Alloc_node::operator() (inline) 1ms 0.021% 58.16% 58ms 1.24% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 58ms 1.24% 59.40% 58ms 1.24% vtkTimeStamp::Modified 57ms 1.22% 60.61% 57ms 1.22% __memcpy_avx_unaligned_erms 5ms 0.11% 60.72% 57ms 1.22% vtkDataArray::vtkDataArray 12ms 0.26% 60.98% 56ms 1.19% std::type_info::operator== (inline) 0 0% 60.98% 55ms 1.17% std::_Rb_tree::_M_drop_node (inline) 7ms 0.15% 61.13% 55ms 1.17% vtkSOADataArrayTemplate::FillTypedComponent 15ms 0.32% 61.45% 54ms 1.15% std::num_put::_M_insert_int 0 0% 61.45% 53ms 1.13% NodesOnlyMesh::~NodesOnlyMesh 1ms 0.021% 61.47% 53ms 1.13% VertexMesh::Clear 0 0% 61.47% 52ms 1.11% std::_Rb_tree::_M_put_node (inline) 27ms 0.58% 62.04% 51ms 1.09% __cxxabiv1::__si_class_type_info::__do_dyncast 15ms 0.32% 62.36% 51ms 1.09% vtkAbstractArray::vtkAbstractArray 0 0% 62.36% 48ms 1.02% std::_Rb_tree::_M_insert_unique 0 0% 62.36% 48ms 1.02% std::map::~map (inline) 0 0% 62.36% 48ms 1.02% std::set::insert (inline) 0 0% 62.36% 46ms 0.98% std::_Rb_tree::lower_bound (inline) 0 0% 62.36% 46ms 0.98% std::map::lower_bound (inline) 25ms 0.53% 62.90% 45ms 0.96% std::_Hashtable::clear 11ms 0.23% 63.13% 44ms 0.94% boost::numeric::ublas::indexing_vector_assign 0 0% 63.13% 44ms 0.94% std::_Destroy (inline) 0 0% 63.13% 44ms 0.94% std::_Destroy_aux::__destroy (inline) 3ms 0.064% 63.20% 44ms 0.94% std::_Rb_tree::_M_copy (inline) 0 0% 63.20% 44ms 0.94% vtkDataArray::ComputeRange 0 0% 63.20% 43ms 0.92% std::__basic_file::xsputn_2 42ms 0.9% 64.09% 42ms 0.9% __GI___writev 42ms 0.9% 64.99% 42ms 0.9% vtkObjectBase::Delete 3ms 0.064% 65.05% 41ms 0.87% DistributedBoxCollection::SetupLocalBoxesHalfOnly 41ms 0.87% 65.93% 41ms 0.87% [libvtkCommonCore-9.3.so.9.3] 16ms 0.34% 66.27% 41ms 0.87% _int_free_merge_chunk 10ms 0.21% 66.48% 41ms 0.87% std::_Rb_tree::_M_clone_node (inline) 41ms 0.87% 67.36% 41ms 0.87% std::ostream::sentry::sentry 41ms 0.87% 68.23% 41ms 0.87% vtkObject::~vtkObject 0 0% 68.23% 40ms 0.85% DistributedBoxCollection::~DistributedBoxCollection 0 0% 68.23% 40ms 0.85% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 68.23% 40ms 0.85% std::make_unique (inline) 0 0% 68.23% 40ms 0.85% tcache_get (inline) 40ms 0.85% 69.08% 40ms 0.85% tcache_get_n (inline) 6ms 0.13% 69.21% 39ms 0.83% VertexMeshWriter::GetNextNode 4ms 0.085% 69.30% 39ms 0.83% std::_Rb_tree::_M_insert_ (inline) 0 0% 69.30% 37ms 0.79% _dl_init 0 0% 69.30% 37ms 0.79% _dl_start_user 0 0% 69.30% 37ms 0.79% call_init (inline) 37ms 0.79% 70.09% 37ms 0.79% vtkObjectBase::~vtkObjectBase 0 0% 70.09% 36ms 0.77% CxxTest::RealWorldDescription::setUp 0 0% 70.09% 36ms 0.77% PetscInitialize 0 0% 70.09% 36ms 0.77% PetscSetup::setUpWorld 0 0% 70.09% 36ms 0.77% PetscSetupUtils::CommonSetup 0 0% 70.09% 36ms 0.77% PetscSetupUtils::InitialisePetsc 7ms 0.15% 70.24% 36ms 0.77% vtkDataArray::~vtkDataArray 3ms 0.064% 70.30% 36ms 0.77% vtkIdList::~vtkIdList 0 0% 70.30% 35ms 0.75% PMPI_Init_thread 0 0% 70.30% 35ms 0.75% ompi_mpi_init 2ms 0.043% 70.34% 35ms 0.75% tbb::detail::r1::cancel_group_execution 0 0% 70.34% 35ms 0.75% vtk::detail::smp::vtkSMPToolsImplForTBB 0 0% 70.34% 34ms 0.73% Cell::GetMutationState 34ms 0.73% 71.07% 34ms 0.73% __mpn_divrem 4ms 0.085% 71.15% 34ms 0.73% std::less::operator() (inline) 33ms 0.7% 71.86% 34ms 0.73% vtkObject::ObjectFinalize 1ms 0.021% 71.88% 33ms 0.7% std::__basic_file::xsputn 0 0% 71.88% 33ms 0.7% std::basic_filebuf::_M_convert_to_external 0 0% 71.88% 33ms 0.7% std::basic_filebuf::open 0 0% 71.88% 33ms 0.7% std::basic_filebuf::overflow 33ms 0.7% 72.58% 33ms 0.7% vtkObjectBase::vtkObjectBase 0 0% 72.58% 32ms 0.68% Node::ConstructNodeAttributes (inline) 0 0% 72.58% 32ms 0.68% Node::SetRadius 0 0% 72.58% 32ms 0.68% VtkMeshWriter::MakeVtkMesh 32ms 0.68% 73.27% 32ms 0.68% __GI___libc_write 1ms 0.021% 73.29% 32ms 0.68% std::unique_ptr::~unique_ptr (inline) 0 0% 73.29% 31ms 0.66% std::vector::vector (partial-inline) 0 0% 73.29% 30ms 0.64% _IO_new_file_fopen 0 0% 73.29% 30ms 0.64% _IO_new_fopen 0 0% 73.29% 30ms 0.64% __GI__IO_file_open 0 0% 73.29% 30ms 0.64% __fopen_internal (inline) 30ms 0.64% 73.93% 30ms 0.64% __libc_open64 1ms 0.021% 73.95% 30ms 0.64% std::default_delete::operator() (inline) 30ms 0.64% 74.59% 30ms 0.64% std::operator< (inline) 3ms 0.064% 74.65% 30ms 0.64% vtkDataArrayPrivate::DoComputeVectorRange 1ms 0.021% 74.67% 29ms 0.62% CellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 74.67% 29ms 0.62% std::__basic_file::open 1ms 0.021% 74.70% 28ms 0.6% 0 0% 74.70% 28ms 0.6% Cell::GetCellId 5ms 0.11% 74.80% 28ms 0.6% NodeAttributes::NodeAttributes 3ms 0.064% 74.87% 28ms 0.6% VertexMeshWriter::GetNextElement 0 0% 74.87% 28ms 0.6% std::_Vector_base::_Vector_base (inline) 4ms 0.085% 74.95% 28ms 0.6% vtkAOSDataArrayTemplate::InsertTuple 28ms 0.6% 75.55% 28ms 0.6% vtkDataArray::Modified 1ms 0.021% 75.57% 27ms 0.58% Edge::Edge 27ms 0.58% 76.15% 27ms 0.58% [libstdc++.so.6.0.33] 1ms 0.021% 76.17% 27ms 0.58% boost::serialization::singleton::get_instance 6ms 0.13% 76.30% 27ms 0.58% vtkIdList::vtkIdList 0 0% 76.30% 26ms 0.55% CellIdWriter::GetCellDataForVtkOutput 0 0% 76.30% 26ms 0.55% Edge::SetNodes (inline) 0 0% 76.30% 26ms 0.55% OutputFileHandler::OpenOutputFile 26ms 0.55% 76.85% 26ms 0.55% __memset_avx2_unaligned_erms 0 0% 76.85% 26ms 0.55% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 1ms 0.021% 76.87% 26ms 0.55% std::_Vector_base::_M_create_storage (inline) 17ms 0.36% 77.23% 26ms 0.55% std::num_put::do_put 2ms 0.043% 77.28% 26ms 0.55% vtkDoubleArray::New 1ms 0.021% 77.30% 25ms 0.53% BoundaryNodeWriter::VisitAnyPopulation 25ms 0.53% 77.83% 25ms 0.53% Node::GetIndex 1ms 0.021% 77.85% 25ms 0.53% std::vector::emplace_back (inline) 1ms 0.021% 77.87% 25ms 0.53% vtk::detail::smp::vtkSMPToolsImpl::For