File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3817ms, 80.41% of 4747ms total Dropped 675 nodes (cum <= 23.73ms) flat flat% sum% cum cum% 0 0% 0% 4529ms 95.41% __libc_start_call_main 0 0% 0% 4529ms 95.41% __libc_start_main_impl 0 0% 0% 4529ms 95.41% _start 0 0% 0% 4513ms 95.07% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4513ms 95.07% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4513ms 95.07% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4513ms 95.07% main 0 0% 0% 4475ms 94.27% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4475ms 94.27% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4475ms 94.27% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4464ms 94.04% AbstractCellBasedSimulation::Solve 1ms 0.021% 0.021% 4183ms 88.12% AbstractCellPopulation::WriteResultsToFiles 17ms 0.36% 0.38% 3954ms 83.29% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.38% 1942ms 40.91% VertexMeshWriter::WriteVtkUsingMesh 4ms 0.084% 0.46% 1675ms 35.29% VertexMeshWriter::MakeVtkMesh 0 0% 0.46% 1233ms 25.97% vtkPolygon::New 1ms 0.021% 0.48% 1233ms 25.97% vtkPolygon::vtkPolygon 4ms 0.084% 0.57% 882ms 18.58% vtkCell::vtkCell 1ms 0.021% 0.59% 760ms 16.01% VertexMeshWriter::WriteFiles 4ms 0.084% 0.67% 754ms 15.88% vtkPoints::New 55ms 1.16% 1.83% 743ms 15.65% std::ostream::_M_insert 1ms 0.021% 1.85% 742ms 15.63% std::ostream::operator<< (inline) 9ms 0.19% 2.04% 709ms 14.94% vtkPoints::vtkPoints 48ms 1.01% 3.05% 669ms 14.09% operator new 200ms 4.21% 7.27% 630ms 13.27% __GI___libc_malloc 46ms 0.97% 8.24% 606ms 12.77% std::num_put::_M_insert_float 0 0% 8.24% 579ms 12.20% vtkLine::New 1ms 0.021% 8.26% 572ms 12.05% vtkQuad::New 0 0% 8.26% 571ms 12.03% vtkStreamingDemandDrivenPipeline::Update 0 0% 8.26% 571ms 12.03% vtkXMLWriterBase::Write 0 0% 8.26% 570ms 12.01% vtkDemandDrivenPipeline::ProcessRequest 0 0% 8.26% 570ms 12.01% vtkQuad::vtkQuad 0 0% 8.26% 566ms 11.92% vtkDemandDrivenPipeline::ExecuteData 0 0% 8.26% 566ms 11.92% vtkExecutive::CallAlgorithm 0 0% 8.26% 566ms 11.92% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 8.26% 565ms 11.90% vtkCompositeDataPipeline::ExecuteData 0 0% 8.26% 564ms 11.88% vtkXMLUnstructuredDataWriter::ProcessRequest 12ms 0.25% 8.51% 560ms 11.80% vtkLine::vtkLine 0 0% 8.51% 533ms 11.23% vtkTriangle::New 6ms 0.13% 8.64% 528ms 11.12% vtkTriangle::vtkTriangle 0 0% 8.64% 506ms 10.66% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 8.64% 506ms 10.66% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 139ms 2.93% 11.57% 496ms 10.45% __GI___libc_free 10ms 0.21% 11.78% 463ms 9.75% std::__cxx11::collate::do_transform 0 0% 11.78% 451ms 9.50% vtkXMLWriter::WriteBinaryData 0 0% 11.78% 448ms 9.44% vtkXMLWriter::WriteBinaryDataBlock 0 0% 11.78% 448ms 9.44% vtkXMLWriter::WriteBinaryDataInternal 3ms 0.063% 11.84% 436ms 9.18% ___vsnprintf 0 0% 11.84% 433ms 9.12% __vsnprintf_internal (inline) 0 0% 11.84% 432ms 9.10% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 46ms 0.97% 12.81% 429ms 9.04% __printf_buffer 21ms 0.44% 13.25% 423ms 8.91% vtkPoints::SetDataType 0 0% 13.25% 378ms 7.96% vtkPolygon::~vtkPolygon 260ms 5.48% 18.73% 366ms 7.71% _int_malloc 230ms 4.85% 23.57% 356ms 7.50% _int_free 0 0% 23.57% 349ms 7.35% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 23.57% 348ms 7.33% VtkMeshWriter::WriteFiles 3ms 0.063% 23.64% 333ms 7.01% __printf_fp_spec (inline) 14ms 0.29% 23.93% 330ms 6.95% __printf_fp_l_buffer 0 0% 23.93% 323ms 6.80% vtkXMLWriter::WritePointsAppendedData 4ms 0.084% 24.02% 312ms 6.57% vtkCell::~vtkCell 152ms 3.20% 27.22% 304ms 6.40% __printf_fp_buffer_1 32ms 0.67% 27.89% 302ms 6.36% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 31ms 0.65% 28.54% 286ms 6.02% std::__new_allocator::allocate (inline) 0 0% 28.54% 286ms 6.02% std::allocator_traits::allocate (inline) 0 0% 28.54% 275ms 5.79% OnLatticeSimulation::UpdateCellLocationsAndTopology 4ms 0.084% 28.63% 275ms 5.79% PottsBasedCellPopulation::UpdateCellLocations 0 0% 28.63% 235ms 4.95% vtkXMLWriter::WriteCompressionBlock 4ms 0.084% 28.71% 233ms 4.91% std::__new_allocator::deallocate (inline) 0 0% 28.71% 232ms 4.89% std::allocator_traits::deallocate (inline) 0 0% 28.71% 227ms 4.78% vtkDataCompressor::Compress 0 0% 28.71% 226ms 4.76% compress2 79ms 1.66% 30.38% 226ms 4.76% crc32 0 0% 30.38% 226ms 4.76% deflate 0 0% 30.38% 226ms 4.76% vtkZLibDataCompressor::CompressBuffer 2ms 0.042% 30.42% 216ms 4.55% vtkBase64OutputStream::Write 11ms 0.23% 30.65% 215ms 4.53% vtkPoints::~vtkPoints 18ms 0.38% 31.03% 214ms 4.51% vtkBase64OutputStream::EncodeTriplet 10ms 0.21% 31.24% 200ms 4.21% vtkFloatArray::New 0 0% 31.24% 192ms 4.04% tbb::detail::r1::parallel_pipeline 0 0% 31.24% 184ms 3.88% clone3 0 0% 31.24% 184ms 3.88% start_thread 0 0% 31.24% 183ms 3.86% tbb::detail::r1::reset 55ms 1.16% 32.40% 182ms 3.83% std::ostream::write 87ms 1.83% 34.23% 182ms 3.83% tbb::detail::r1::wait_bounded_queue_monitor 1ms 0.021% 34.25% 179ms 3.77% std::set::set (inline) 10ms 0.21% 34.46% 178ms 3.75% std::_Rb_tree::_Rb_tree 1ms 0.021% 34.48% 172ms 3.62% vtkTypeFloat64Array::~vtkTypeFloat64Array 4ms 0.084% 34.57% 170ms 3.58% vtkFloatArray::vtkFloatArray 0 0% 34.57% 169ms 3.56% std::_Rb_tree::_M_create_node (inline) 1ms 0.021% 34.59% 168ms 3.54% vtkTriangle::~vtkTriangle 3ms 0.063% 34.65% 163ms 3.43% NodesOnlyMesh::ConstructNodesWithoutMesh 2ms 0.042% 34.70% 161ms 3.39% NodeLocationWriter::VisitAnyPopulation 108ms 2.28% 36.97% 161ms 3.39% malloc_consolidate 0 0% 36.97% 161ms 3.39% vtkLine::GetParametricCenter 0 0% 36.97% 160ms 3.37% std::_Rb_tree::_M_get_node (inline) 0 0% 36.97% 159ms 3.35% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 36.97% 159ms 3.35% vtkQuad::~vtkQuad 5ms 0.11% 37.08% 154ms 3.24% vtkIdList::AllocateInternal 6ms 0.13% 37.20% 152ms 3.20% vtkDataArray::CreateDataArray 2ms 0.042% 37.24% 151ms 3.18% VertexMesh::VertexMesh 0 0% 37.24% 149ms 3.14% VertexMesh::~VertexMesh 43ms 0.91% 38.15% 147ms 3.10% std::_Rb_tree::_M_erase 12ms 0.25% 38.40% 147ms 3.10% std::vector::_M_default_append 0 0% 38.40% 147ms 3.10% std::vector::~vector (inline) 3ms 0.063% 38.47% 145ms 3.05% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.042% 38.51% 141ms 2.97% std::_Vector_base::_M_deallocate (inline) 8ms 0.17% 38.68% 140ms 2.95% vtkTypeFloat64Array::New 1ms 0.021% 38.70% 139ms 2.93% VertexMesh::GenerateEdgesFromElements (inline) 66ms 1.39% 40.09% 138ms 2.91% std::basic_filebuf::xsputn 4ms 0.084% 40.17% 137ms 2.89% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 5ms 0.11% 40.28% 137ms 2.89% MutableElement::BuildEdges 134ms 2.82% 43.10% 137ms 2.89% [libz.so.1.3] 11ms 0.23% 43.33% 137ms 2.89% std::_Rb_tree::_M_copy (inline) 2ms 0.042% 43.37% 135ms 2.84% vtkDoubleArray::vtkDoubleArray 1ms 0.021% 43.40% 127ms 2.68% std::_Vector_base::_M_allocate (inline) 11ms 0.23% 43.63% 121ms 2.55% std::_Rb_tree::_M_clone_node (inline) 32ms 0.67% 44.30% 121ms 2.55% vtkObject::vtkObject 120ms 2.53% 46.83% 120ms 2.53% __strcmp_avx2 0 0% 46.83% 120ms 2.53% std::set::~set (inline) 1ms 0.021% 46.85% 115ms 2.42% EdgeHelper::GetEdgeFromNodes 3ms 0.063% 46.91% 115ms 2.42% vtkTypeFloat64Array::vtkTypeFloat64Array 46ms 0.97% 47.88% 112ms 2.36% std::__ostream_insert 60ms 1.26% 49.15% 110ms 2.32% vtkTypeFloat64Array::PrintSelf 0 0% 49.15% 109ms 2.30% std::_Vector_base::~_Vector_base (inline) 1ms 0.021% 49.17% 108ms 2.28% vtkIdList::Allocate 1ms 0.021% 49.19% 107ms 2.25% vtkXMLWriter::WritePointDataAppendedData 4ms 0.084% 49.27% 106ms 2.23% vtkFloatArray::~vtkFloatArray 0 0% 49.27% 104ms 2.19% EdgeHelper::~EdgeHelper (inline) 0 0% 49.27% 102ms 2.15% std::_Rb_tree::_M_drop_node (inline) 0 0% 49.27% 101ms 2.13% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.021% 49.29% 101ms 2.13% std::operator<< (inline) 4ms 0.084% 49.38% 99ms 2.09% AbstractCellProperty::IsType (inline) 2ms 0.042% 49.42% 99ms 2.09% CellPropertyCollection::HasProperty 0 0% 49.42% 98ms 2.06% Cell::HasCellProperty (inline) 97ms 2.04% 51.46% 97ms 2.04% __GI_sched_yield 54ms 1.14% 52.60% 96ms 2.02% hack_digit 14ms 0.29% 52.90% 96ms 2.02% vtkAOSDataArrayTemplate::DataElementChanged 1ms 0.021% 52.92% 94ms 1.98% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 70ms 1.47% 54.39% 94ms 1.98% std::basic_streambuf::xsputn 0 0% 54.39% 93ms 1.96% std::_Rb_tree::_M_put_node (inline) 3ms 0.063% 54.46% 87ms 1.83% std::map::operator[] (partial-inline) 21ms 0.44% 54.90% 86ms 1.81% vtkObject::Modified 6ms 0.13% 55.02% 85ms 1.79% _int_free_maybe_consolidate 1ms 0.021% 55.05% 84ms 1.77% AbstractCellProperty::IsSubType (inline) 4ms 0.084% 55.13% 84ms 1.77% std::vector::push_back (inline) 16ms 0.34% 55.47% 83ms 1.75% __dynamic_cast 56ms 1.18% 56.65% 82ms 1.73% vtkObjectBase::UnRegisterInternal 14ms 0.29% 56.94% 76ms 1.60% AbstractCellProperty::IsSame 24ms 0.51% 57.45% 75ms 1.58% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.021% 57.47% 73ms 1.54% std::set::insert (inline) 0 0% 57.47% 73ms 1.54% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 2ms 0.042% 57.51% 72ms 1.52% std::_Rb_tree::_M_insert_unique 71ms 1.50% 59.01% 71ms 1.50% unlink_chunk 1ms 0.021% 59.03% 70ms 1.47% vtkIdList::New 2ms 0.042% 59.07% 64ms 1.35% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.11% 59.17% 64ms 1.35% boost::numeric::ublas::c_vector::c_vector (partial-inline) 64ms 1.35% 60.52% 64ms 1.35% std::ostream::sentry::sentry 64ms 1.35% 61.87% 64ms 1.35% vtkTimeStamp::Modified 2ms 0.042% 61.91% 63ms 1.33% vtkDoubleArray::~vtkDoubleArray 0 0% 61.91% 62ms 1.31% boost::numeric::ublas::vector_assign (inline) 10ms 0.21% 62.12% 62ms 1.31% std::type_info::operator== (inline) 0 0% 62.12% 61ms 1.29% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 0 0% 62.12% 61ms 1.29% NodesOnlyMesh::SetUpBoxCollection 4ms 0.084% 62.21% 61ms 1.29% std::vector::_M_realloc_insert 0 0% 62.21% 60ms 1.26% NodesOnlyMesh::~NodesOnlyMesh 5ms 0.11% 62.31% 58ms 1.22% std::_Rb_tree::_M_insert_ (inline) 0 0% 62.31% 57ms 1.20% PottsMesh::GetMooreNeighbouringNodeIndices 28ms 0.59% 62.90% 56ms 1.18% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 62.90% 55ms 1.16% std::_Rb_tree::lower_bound (inline) 0 0% 62.90% 55ms 1.16% std::map::lower_bound (inline) 1ms 0.021% 62.92% 55ms 1.16% tcache_get (inline) 54ms 1.14% 64.06% 54ms 1.14% tcache_get_n (inline) 6ms 0.13% 64.19% 52ms 1.10% std::num_put::_M_insert_int 7ms 0.15% 64.34% 51ms 1.07% vtkDataArray::vtkDataArray 0 0% 64.34% 49ms 1.03% Cell::GetCellProliferativeType 48ms 1.01% 65.35% 48ms 1.01% [libvtkCommonCore-9.3.so.9.3] 6ms 0.13% 65.47% 47ms 0.99% VertexMeshWriter::GetNextNode 46ms 0.97% 66.44% 46ms 0.97% __memcpy_avx_unaligned_erms 18ms 0.38% 66.82% 46ms 0.97% boost::numeric::ublas::indexing_vector_assign 1ms 0.021% 66.84% 45ms 0.95% VertexMesh::Clear 0 0% 66.84% 45ms 0.95% std::_Destroy (inline) 1ms 0.021% 66.86% 45ms 0.95% std::_Destroy_aux::__destroy (inline) 26ms 0.55% 67.41% 45ms 0.95% std::_Hashtable::clear 2ms 0.042% 67.45% 45ms 0.95% std::__basic_file::xsputn_2 5ms 0.11% 67.56% 45ms 0.95% vtkDataArray::~vtkDataArray 13ms 0.27% 67.83% 44ms 0.93% vtkAbstractArray::vtkAbstractArray 1ms 0.021% 67.85% 43ms 0.91% vtkDoubleArray::New 0 0% 67.85% 42ms 0.88% NodesOnlyMesh::ClearBoxCollection (inline) 42ms 0.88% 68.74% 42ms 0.88% __GI___writev 0 0% 68.74% 41ms 0.86% DistributedBoxCollection::SetupLocalBoxesHalfOnly 0 0% 68.74% 41ms 0.86% DistributedBoxCollection::~DistributedBoxCollection 0 0% 68.74% 40ms 0.84% vtkDataArray::ComputeRange 23ms 0.48% 69.22% 38ms 0.8% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 69.22% 38ms 0.8% DistributedBoxCollection::IsOwned 14ms 0.29% 69.52% 37ms 0.78% _int_free_merge_chunk 3ms 0.063% 69.58% 36ms 0.76% __find_specmb (inline) 6ms 0.13% 69.71% 36ms 0.76% vtkAOSDataArrayTemplate::InsertTuple 0 0% 69.71% 35ms 0.74% Cell::GetCellId 0 0% 69.71% 35ms 0.74% _dl_init 0 0% 69.71% 35ms 0.74% call_init (inline) 0 0% 69.71% 35ms 0.74% vtk::detail::smp::vtkSMPToolsImplForTBB 35ms 0.74% 70.44% 35ms 0.74% vtkObject::~vtkObject 5ms 0.11% 70.55% 35ms 0.74% vtkSOADataArrayTemplate::FillTypedComponent 0 0% 70.55% 34ms 0.72% CxxTest::RealWorldDescription::setUp 0 0% 70.55% 34ms 0.72% PetscInitialize 0 0% 70.55% 34ms 0.72% PetscSetup::setUpWorld 0 0% 70.55% 34ms 0.72% PetscSetupUtils::CommonSetup 0 0% 70.55% 34ms 0.72% PetscSetupUtils::InitialisePetsc 0 0% 70.55% 34ms 0.72% _dl_start_user 0 0% 70.55% 34ms 0.72% std::make_unique (inline) 6ms 0.13% 70.68% 34ms 0.72% vtkIdList::~vtkIdList 0 0% 70.68% 33ms 0.7% PMPI_Init_thread 33ms 0.7% 71.37% 33ms 0.7% __strchrnul_avx2 0 0% 71.37% 33ms 0.7% ompi_mpi_init 1ms 0.021% 71.39% 33ms 0.7% tbb::detail::r1::cancel_group_execution 1ms 0.021% 71.41% 32ms 0.67% boost::serialization::singleton::get_instance 0 0% 71.41% 32ms 0.67% std::basic_filebuf::open 1ms 0.021% 71.43% 32ms 0.67% std::less::operator() (inline) 0 0% 71.43% 31ms 0.65% CellIdWriter::GetCellDataForVtkOutput 0 0% 71.43% 31ms 0.65% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 1ms 0.021% 71.46% 31ms 0.65% std::_Rb_tree_header::_Rb_tree_header (inline) 31ms 0.65% 72.11% 31ms 0.65% std::operator< (inline) 0 0% 72.11% 31ms 0.65% std::unique_ptr::~unique_ptr (inline) 3ms 0.063% 72.17% 31ms 0.65% vtkDataArrayPrivate::DoComputeVectorRange 30ms 0.63% 72.80% 30ms 0.63% __memset_avx2_unaligned_erms 30ms 0.63% 73.44% 30ms 0.63% boost::numeric::ublas::c_vector::operator() 0 0% 73.44% 30ms 0.63% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 7ms 0.15% 73.58% 30ms 0.63% std::__new_allocator::construct (inline) 0 0% 73.58% 30ms 0.63% std::allocator_traits::construct (inline) 1ms 0.021% 73.60% 30ms 0.63% std::default_delete::operator() (inline) 6ms 0.13% 73.73% 30ms 0.63% vtkAOSDataArrayTemplate::AllocateTuples 0 0% 73.73% 29ms 0.61% Cell::GetMutationState 0 0% 73.73% 29ms 0.61% VtkMeshWriter::MakeVtkMesh 0 0% 73.73% 29ms 0.61% _IO_new_file_fopen 0 0% 73.73% 29ms 0.61% _IO_new_fopen 0 0% 73.73% 29ms 0.61% __GI__IO_file_open 0 0% 73.73% 29ms 0.61% __fopen_internal (inline) 29ms 0.61% 74.34% 29ms 0.61% __libc_open64 26ms 0.55% 74.89% 29ms 0.61% __printf_buffer_write 2ms 0.042% 74.93% 29ms 0.61% std::_Rb_tree::_M_emplace_hint_unique 29ms 0.61% 75.54% 29ms 0.61% std::_Rb_tree_header::_M_reset (inline) 0 0% 75.54% 29ms 0.61% std::__basic_file::open 23ms 0.48% 76.03% 29ms 0.61% std::num_put::do_put 29ms 0.61% 76.64% 29ms 0.61% vtkObjectBase::vtkObjectBase 1ms 0.021% 76.66% 28ms 0.59% 28ms 0.59% 77.25% 28ms 0.59% [libstdc++.so.6.0.33] 28ms 0.59% 77.84% 28ms 0.59% std::_Rb_tree::_S_right (inline) 27ms 0.57% 78.41% 28ms 0.59% vtkObjectBase::Delete 0 0% 78.41% 27ms 0.57% Edge::Edge 0 0% 78.41% 27ms 0.57% Edge::SetNodes (inline) 27ms 0.57% 78.98% 27ms 0.57% std::codecvt::do_always_noconv 27ms 0.57% 79.54% 27ms 0.57% vtkObjectBase::~vtkObjectBase 0 0% 79.54% 26ms 0.55% CellProliferativeTypesWriter::GetCellDataForVtkOutput 1ms 0.021% 79.57% 26ms 0.55% Node::SetRadius 26ms 0.55% 80.11% 26ms 0.55% std::_Rb_tree_increment 7ms 0.15% 80.26% 26ms 0.55% vtk::detail::smp::vtkSMPToolsImpl::For 0 0% 80.26% 25ms 0.53% Node::ConstructNodeAttributes (inline) 2ms 0.042% 80.30% 25ms 0.53% Node::GetPoint 0 0% 80.30% 25ms 0.53% std::map::~map (inline) 3ms 0.063% 80.37% 24ms 0.51% boost::serialization::void_cast_detail::void_caster::recursive_register 0 0% 80.37% 24ms 0.51% boost::serialization::void_cast_detail::void_caster_primitive::void_caster_primitive (inline) 2ms 0.042% 80.41% 24ms 0.51% vtkSOADataArrayTemplate::GetTupleIndexFromValueIndex