File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3759ms, 79.27% of 4742ms total Dropped 671 nodes (cum <= 23.71ms) flat flat% sum% cum cum% 0 0% 0% 4511ms 95.13% __libc_start_call_main 0 0% 0% 4511ms 95.13% __libc_start_main_impl 0 0% 0% 4511ms 95.13% _start 0 0% 0% 4496ms 94.81% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4496ms 94.81% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4496ms 94.81% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4496ms 94.81% main 0 0% 0% 4462ms 94.10% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4462ms 94.10% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4462ms 94.10% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4452ms 93.88% AbstractCellBasedSimulation::Solve 0 0% 0% 4179ms 88.13% AbstractCellPopulation::WriteResultsToFiles 12ms 0.25% 0.25% 3948ms 83.26% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.25% 1938ms 40.87% VertexMeshWriter::WriteVtkUsingMesh 6ms 0.13% 0.38% 1676ms 35.34% VertexMeshWriter::MakeVtkMesh 0 0% 0.38% 1245ms 26.25% vtkPolygon::New 3ms 0.063% 0.44% 1242ms 26.19% vtkPolygon::vtkPolygon 9ms 0.19% 0.63% 878ms 18.52% vtkCell::vtkCell 0 0% 0.63% 760ms 16.03% VertexMeshWriter::WriteFiles 4ms 0.084% 0.72% 756ms 15.94% vtkPoints::New 3ms 0.063% 0.78% 749ms 15.80% std::ostream::operator<< (inline) 57ms 1.20% 1.98% 748ms 15.77% std::ostream::_M_insert 16ms 0.34% 2.32% 707ms 14.91% vtkPoints::vtkPoints 39ms 0.82% 3.14% 652ms 13.75% operator new 189ms 3.99% 7.13% 626ms 13.20% __GI___libc_malloc 60ms 1.27% 8.39% 604ms 12.74% std::num_put::_M_insert_float 1ms 0.021% 8.41% 580ms 12.23% vtkQuad::New 1ms 0.021% 8.44% 579ms 12.21% vtkLine::New 4ms 0.084% 8.52% 576ms 12.15% vtkQuad::vtkQuad 0 0% 8.52% 573ms 12.08% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 8.52% 573ms 12.08% vtkStreamingDemandDrivenPipeline::Update 0 0% 8.52% 573ms 12.08% vtkXMLWriterBase::Write 0 0% 8.52% 571ms 12.04% vtkDemandDrivenPipeline::ProcessRequest 0 0% 8.52% 570ms 12.02% vtkDemandDrivenPipeline::ExecuteData 0 0% 8.52% 569ms 12.00% vtkCompositeDataPipeline::ExecuteData 0 0% 8.52% 569ms 12.00% vtkExecutive::CallAlgorithm 0 0% 8.52% 569ms 12.00% vtkXMLUnstructuredDataWriter::ProcessRequest 12ms 0.25% 8.77% 558ms 11.77% vtkLine::vtkLine 2ms 0.042% 8.81% 523ms 11.03% vtkTriangle::New 0 0% 8.81% 517ms 10.90% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 8.81% 517ms 10.90% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 4ms 0.084% 8.90% 514ms 10.84% vtkTriangle::vtkTriangle 161ms 3.40% 12.29% 481ms 10.14% __GI___libc_free 0 0% 12.29% 466ms 9.83% vtkXMLWriter::WriteBinaryData 0 0% 12.29% 461ms 9.72% vtkXMLWriter::WriteBinaryDataBlock 0 0% 12.29% 461ms 9.72% vtkXMLWriter::WriteBinaryDataInternal 9ms 0.19% 12.48% 453ms 9.55% std::__cxx11::collate::do_transform 1ms 0.021% 12.51% 438ms 9.24% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 4ms 0.084% 12.59% 431ms 9.09% ___vsnprintf 0 0% 12.59% 428ms 9.03% __vsnprintf_internal (inline) 51ms 1.08% 13.67% 421ms 8.88% __printf_buffer 25ms 0.53% 14.19% 414ms 8.73% vtkPoints::SetDataType 1ms 0.021% 14.21% 387ms 8.16% vtkPolygon::~vtkPolygon 245ms 5.17% 19.38% 371ms 7.82% _int_malloc 0 0% 19.38% 352ms 7.42% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 19.38% 347ms 7.32% VtkMeshWriter::WriteFiles 3ms 0.063% 19.44% 335ms 7.06% __printf_fp_spec (inline) 18ms 0.38% 19.82% 332ms 7.00% __printf_fp_l_buffer 0 0% 19.82% 329ms 6.94% vtkXMLWriter::WritePointsAppendedData 192ms 4.05% 23.87% 320ms 6.75% _int_free 4ms 0.084% 23.96% 310ms 6.54% vtkCell::~vtkCell 46ms 0.97% 24.93% 298ms 6.28% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 133ms 2.80% 27.73% 294ms 6.20% __printf_fp_buffer_1 0 0% 27.73% 267ms 5.63% OnLatticeSimulation::UpdateCellLocationsAndTopology 7ms 0.15% 27.88% 267ms 5.63% PottsBasedCellPopulation::UpdateCellLocations 34ms 0.72% 28.60% 264ms 5.57% std::__new_allocator::allocate (inline) 0 0% 28.60% 261ms 5.50% std::allocator_traits::allocate (inline) 4ms 0.084% 28.68% 256ms 5.40% std::__new_allocator::deallocate (inline) 0 0% 28.68% 252ms 5.31% std::allocator_traits::deallocate (inline) 0 0% 28.68% 244ms 5.15% vtkXMLWriter::WriteCompressionBlock 0 0% 28.68% 229ms 4.83% vtkDataCompressor::Compress 0 0% 28.68% 228ms 4.81% compress2 0 0% 28.68% 228ms 4.81% vtkZLibDataCompressor::CompressBuffer 6ms 0.13% 28.81% 227ms 4.79% vtkBase64OutputStream::Write 69ms 1.46% 30.26% 226ms 4.77% crc32 0 0% 30.26% 226ms 4.77% deflate 16ms 0.34% 30.60% 221ms 4.66% vtkBase64OutputStream::EncodeTriplet 0 0% 30.60% 202ms 4.26% tbb::detail::r1::parallel_pipeline 7ms 0.15% 30.75% 199ms 4.20% vtkFloatArray::New 0 0% 30.75% 197ms 4.15% clone3 0 0% 30.75% 197ms 4.15% start_thread 0 0% 30.75% 196ms 4.13% tbb::detail::r1::reset 88ms 1.86% 32.60% 195ms 4.11% tbb::detail::r1::wait_bounded_queue_monitor 4ms 0.084% 32.69% 195ms 4.11% vtkPoints::~vtkPoints 54ms 1.14% 33.83% 183ms 3.86% std::ostream::write 110ms 2.32% 36.15% 176ms 3.71% malloc_consolidate 12ms 0.25% 36.40% 174ms 3.67% vtkIdList::AllocateInternal 2ms 0.042% 36.44% 173ms 3.65% vtkQuad::~vtkQuad 2ms 0.042% 36.48% 171ms 3.61% vtkTriangle::~vtkTriangle 3ms 0.063% 36.55% 167ms 3.52% vtkFloatArray::vtkFloatArray 1ms 0.021% 36.57% 164ms 3.46% VertexMesh::VertexMesh 1ms 0.021% 36.59% 164ms 3.46% vtkLine::GetParametricCenter 1ms 0.021% 36.61% 161ms 3.40% NodeLocationWriter::VisitAnyPopulation 3ms 0.063% 36.67% 161ms 3.40% NodesOnlyMesh::ConstructNodesWithoutMesh 15ms 0.32% 36.99% 160ms 3.37% std::vector::_M_default_append 1ms 0.021% 37.01% 159ms 3.35% std::set::set (inline) 11ms 0.23% 37.24% 158ms 3.33% std::_Rb_tree::_Rb_tree 0 0% 37.24% 158ms 3.33% std::vector::~vector (inline) 3ms 0.063% 37.30% 155ms 3.27% std::_Vector_base::_M_deallocate (inline) 148ms 3.12% 40.43% 151ms 3.18% [libz.so.1.3] 0 0% 40.43% 151ms 3.18% std::_Rb_tree::_M_create_node (inline) 3ms 0.063% 40.49% 150ms 3.16% VertexMesh::GenerateEdgesFromElements (inline) 2ms 0.042% 40.53% 149ms 3.14% vtkTypeFloat64Array::~vtkTypeFloat64Array 44ms 0.93% 41.46% 148ms 3.12% std::_Rb_tree::_M_erase 3ms 0.063% 41.52% 147ms 3.10% MutableElement::BuildEdges 0 0% 41.52% 146ms 3.08% std::_Rb_tree::_M_get_node (inline) 0 0% 41.52% 142ms 2.99% VertexMesh::~VertexMesh 3ms 0.063% 41.59% 142ms 2.99% std::_Rb_tree::~_Rb_tree (inline) 0 0% 41.59% 140ms 2.95% std::_Rb_tree::_Alloc_node::operator() (inline) 5ms 0.11% 41.69% 139ms 2.93% vtkDataArray::CreateDataArray 0 0% 41.69% 135ms 2.85% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 0 0% 41.69% 133ms 2.80% vtkDoubleArray::vtkDoubleArray 7ms 0.15% 41.84% 131ms 2.76% vtkTypeFloat64Array::New 4ms 0.084% 41.92% 130ms 2.74% EdgeHelper::GetEdgeFromNodes 62ms 1.31% 43.23% 129ms 2.72% std::basic_filebuf::xsputn 12ms 0.25% 43.48% 123ms 2.59% std::_Rb_tree::_M_copy (inline) 0 0% 43.48% 123ms 2.59% std::_Vector_base::~_Vector_base (inline) 1ms 0.021% 43.50% 123ms 2.59% vtkIdList::Allocate 0 0% 43.50% 121ms 2.55% std::set::~set (inline) 0 0% 43.50% 115ms 2.43% std::_Vector_base::_M_allocate (inline) 29ms 0.61% 44.12% 113ms 2.38% vtkObject::vtkObject 110ms 2.32% 46.44% 110ms 2.32% __GI_sched_yield 3ms 0.063% 46.50% 108ms 2.28% vtkTypeFloat64Array::vtkTypeFloat64Array 0 0% 46.50% 108ms 2.28% vtkXMLWriter::WritePointDataAppendedData 8ms 0.17% 46.67% 107ms 2.26% std::_Rb_tree::_M_clone_node (inline) 106ms 2.24% 48.90% 106ms 2.24% __strcmp_avx2 2ms 0.042% 48.95% 105ms 2.21% CellPropertyCollection::GetPropertiesType (inline) 5ms 0.11% 49.05% 104ms 2.19% vtkFloatArray::~vtkFloatArray 0 0% 49.05% 102ms 2.15% std::_Rb_tree::_M_drop_node (inline) 0 0% 49.05% 100ms 2.11% EdgeHelper::~EdgeHelper (inline) 44ms 0.93% 49.98% 100ms 2.11% std::__ostream_insert 0 0% 49.98% 99ms 2.09% std::_Rb_tree::_M_put_node (inline) 57ms 1.20% 51.18% 98ms 2.07% hack_digit 49ms 1.03% 52.21% 98ms 2.07% vtkTypeFloat64Array::PrintSelf 0 0% 52.21% 97ms 2.05% std::operator<< (inline) 64ms 1.35% 53.56% 95ms 2.00% std::basic_streambuf::xsputn 1ms 0.021% 53.58% 92ms 1.94% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 53.58% 90ms 1.90% Cell::HasCellProperty (inline) 0 0% 53.58% 90ms 1.90% CellPropertyCollection::HasProperty 0 0% 53.58% 89ms 1.88% AbstractCellProperty::IsSubType (inline) 2ms 0.042% 53.63% 89ms 1.88% std::map::operator[] (partial-inline) 58ms 1.22% 54.85% 89ms 1.88% vtkObjectBase::UnRegisterInternal 18ms 0.38% 55.23% 88ms 1.86% __dynamic_cast 3ms 0.063% 55.29% 86ms 1.81% AbstractCellProperty::IsType (inline) 3ms 0.063% 55.36% 84ms 1.77% _int_free_maybe_consolidate 8ms 0.17% 55.53% 80ms 1.69% vtkAOSDataArrayTemplate::DataElementChanged 79ms 1.67% 57.19% 79ms 1.67% unlink_chunk 24ms 0.51% 57.70% 76ms 1.60% vtkObject::Modified 0 0% 57.70% 75ms 1.58% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 2ms 0.042% 57.74% 72ms 1.52% std::vector::push_back (inline) 19ms 0.4% 58.14% 71ms 1.50% std::_Rb_tree::_M_lower_bound (inline) 3ms 0.063% 58.20% 66ms 1.39% vtkIdList::New 12ms 0.25% 58.46% 65ms 1.37% AbstractCellProperty::IsSame 0 0% 58.46% 65ms 1.37% tcache_get (inline) 65ms 1.37% 59.83% 65ms 1.37% tcache_get_n (inline) 5ms 0.11% 59.93% 64ms 1.35% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.11% 60.04% 64ms 1.35% vtkDoubleArray::~vtkDoubleArray 8ms 0.17% 60.21% 63ms 1.33% std::num_put::_M_insert_int 0 0% 60.21% 62ms 1.31% std::_Rb_tree::_M_insert_unique 0 0% 60.21% 62ms 1.31% std::set::insert (inline) 0 0% 60.21% 60ms 1.27% NodesOnlyMesh::~NodesOnlyMesh 60ms 1.27% 61.47% 60ms 1.27% __memcpy_avx_unaligned_erms 1ms 0.021% 61.49% 58ms 1.22% Cell::GetCellProliferativeType 0 0% 61.49% 58ms 1.22% NodesOnlyMesh::SetUpBoxCollection 0 0% 61.49% 58ms 1.22% std::_Rb_tree::lower_bound (inline) 0 0% 61.49% 58ms 1.22% std::map::lower_bound (inline) 0 0% 61.49% 57ms 1.20% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 2ms 0.042% 61.54% 56ms 1.18% boost::numeric::ublas::c_vector::c_vector (inline) 9ms 0.19% 61.73% 56ms 1.18% vtkDataArray::vtkDataArray 0 0% 61.73% 55ms 1.16% boost::numeric::ublas::vector_assign (inline) 14ms 0.3% 62.02% 53ms 1.12% std::type_info::operator== (inline) 27ms 0.57% 62.59% 51ms 1.08% __cxxabiv1::__si_class_type_info::__do_dyncast 4ms 0.084% 62.67% 51ms 1.08% std::vector::_M_realloc_insert 50ms 1.05% 63.73% 50ms 1.05% std::ostream::sentry::sentry 4ms 0.084% 63.81% 49ms 1.03% std::_Rb_tree::_M_insert_ (inline) 48ms 1.01% 64.82% 48ms 1.01% vtkTimeStamp::Modified 45ms 0.95% 65.77% 46ms 0.97% vtkObjectBase::Delete 8ms 0.17% 65.94% 45ms 0.95% vtkAbstractArray::vtkAbstractArray 0 0% 65.94% 44ms 0.93% PottsMesh::GetMooreNeighbouringNodeIndices 6ms 0.13% 66.07% 44ms 0.93% VertexMeshWriter::GetNextNode 2ms 0.042% 66.11% 44ms 0.93% std::make_unique (inline) 1ms 0.021% 66.13% 42ms 0.89% VertexMesh::Clear 29ms 0.61% 66.74% 41ms 0.86% std::_Hashtable::clear 0 0% 66.74% 40ms 0.84% std::_Destroy (inline) 0 0% 66.74% 40ms 0.84% std::_Destroy_aux::__destroy (inline) 9ms 0.19% 66.93% 40ms 0.84% vtkIdList::~vtkIdList 40ms 0.84% 67.78% 40ms 0.84% vtkObject::~vtkObject 0 0% 67.78% 39ms 0.82% DistributedBoxCollection::~DistributedBoxCollection 0 0% 67.78% 39ms 0.82% NodesOnlyMesh::ClearBoxCollection (inline) 2ms 0.042% 67.82% 39ms 0.82% vtkDoubleArray::New 2ms 0.042% 67.86% 38ms 0.8% DistributedBoxCollection::SetupLocalBoxesHalfOnly 14ms 0.3% 68.16% 38ms 0.8% boost::numeric::ublas::indexing_vector_assign 11ms 0.23% 68.39% 37ms 0.78% vtkSOADataArrayTemplate::FillTypedComponent 4ms 0.084% 68.47% 36ms 0.76% vtkDataArray::~vtkDataArray 35ms 0.74% 69.21% 35ms 0.74% std::_Rb_tree_increment 31ms 0.65% 69.87% 35ms 0.74% std::num_put::do_put 34ms 0.72% 70.58% 34ms 0.72% [libvtkCommonCore-9.3.so.9.3] 34ms 0.72% 71.30% 34ms 0.72% __GI___writev 0 0% 71.30% 34ms 0.72% _dl_init 0 0% 71.30% 34ms 0.72% _dl_start_user 0 0% 71.30% 34ms 0.72% call_init (inline) 34ms 0.72% 72.02% 34ms 0.72% std::codecvt::do_always_noconv 0 0% 72.02% 34ms 0.72% vtkDataArray::ComputeRange 19ms 0.4% 72.42% 33ms 0.7% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 72.42% 33ms 0.7% DistributedBoxCollection::IsOwned 0 0% 72.42% 33ms 0.7% std::__basic_file::xsputn_2 0 0% 72.42% 33ms 0.7% vtk::detail::smp::vtkSMPToolsImplForTBB 0 0% 72.42% 32ms 0.67% Cell::GetCellId 0 0% 72.42% 32ms 0.67% Node::ConstructNodeAttributes (inline) 0 0% 72.42% 32ms 0.67% Node::SetRadius 0 0% 72.42% 32ms 0.67% std::less::operator() (inline) 32ms 0.67% 73.09% 32ms 0.67% std::operator< (inline) 1ms 0.021% 73.11% 31ms 0.65% tbb::detail::r1::cancel_group_execution 1ms 0.021% 73.13% 30ms 0.63% 0 0% 73.13% 30ms 0.63% CxxTest::RealWorldDescription::setUp 0 0% 73.13% 30ms 0.63% PMPI_Init_thread 0 0% 73.13% 30ms 0.63% PetscInitialize 0 0% 73.13% 30ms 0.63% PetscSetup::setUpWorld 0 0% 73.13% 30ms 0.63% PetscSetupUtils::CommonSetup 0 0% 73.13% 30ms 0.63% PetscSetupUtils::InitialisePetsc 0 0% 73.13% 30ms 0.63% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 2ms 0.042% 73.18% 30ms 0.63% boost::serialization::singleton::get_instance 0 0% 73.18% 30ms 0.63% ompi_mpi_init 7ms 0.15% 73.32% 30ms 0.63% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.042% 73.37% 30ms 0.63% std::basic_filebuf::overflow 30ms 0.63% 74.00% 30ms 0.63% vtkObjectBase::~vtkObjectBase 1ms 0.021% 74.02% 29ms 0.61% CellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 74.02% 29ms 0.61% VtkMeshWriter::MakeVtkMesh 2ms 0.042% 74.06% 29ms 0.61% std::unique_ptr::~unique_ptr (inline) 5ms 0.11% 74.17% 29ms 0.61% vtkAOSDataArrayTemplate::InsertTuple 3ms 0.063% 74.23% 28ms 0.59% Node::AddElement 28ms 0.59% 74.82% 28ms 0.59% boost::numeric::ublas::c_vector::operator() 0 0% 74.82% 28ms 0.59% boost::serialization::void_cast_detail::void_caster_primitive::void_caster_primitive (inline) 0 0% 74.82% 28ms 0.59% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.042% 74.86% 28ms 0.59% std::basic_filebuf::_M_convert_to_external 0 0% 74.86% 27ms 0.57% CellIdWriter::GetCellDataForVtkOutput 4ms 0.084% 74.95% 27ms 0.57% __find_specmb (inline) 8ms 0.17% 75.12% 27ms 0.57% _int_free_merge_chunk 0 0% 75.12% 27ms 0.57% boost::serialization::void_cast_detail::void_caster::recursive_register 1ms 0.021% 75.14% 27ms 0.57% std::default_delete::operator() (inline) 27ms 0.57% 75.71% 27ms 0.57% vtkDataArray::Modified 0 0% 75.71% 26ms 0.55% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 26ms 0.55% 76.25% 26ms 0.55% __GI___libc_write 19ms 0.4% 76.66% 26ms 0.55% __printf_buffer_write 0 0% 76.66% 26ms 0.55% std::__basic_file::xsputn 3ms 0.063% 76.72% 26ms 0.55% std::__new_allocator::construct (inline) 0 0% 76.72% 26ms 0.55% std::allocator_traits::construct (inline) 0 0% 76.72% 26ms 0.55% std::basic_filebuf::open 26ms 0.55% 77.27% 26ms 0.55% tcache_put (inline) 26ms 0.55% 77.82% 26ms 0.55% vtkObjectBase::vtkObjectBase 1ms 0.021% 77.84% 25ms 0.53% Edge::Edge 4ms 0.084% 77.92% 25ms 0.53% NodeAttributes::NodeAttributes 0 0% 77.92% 25ms 0.53% PottsMesh::GetVonNeumannNeighbouringNodeIndices 0 0% 77.92% 25ms 0.53% VertexElement::VertexElement 25ms 0.53% 78.45% 25ms 0.53% std::_Rb_tree::_S_right (inline) 3ms 0.063% 78.51% 25ms 0.53% vtk::detail::smp::vtkSMPToolsImpl::For 3ms 0.063% 78.57% 25ms 0.53% vtkDataArrayPrivate::DoComputeVectorRange 0 0% 78.57% 24ms 0.51% Cell::GetMutationState 0 0% 78.57% 24ms 0.51% PottsBasedCellPopulation::AcceptCellWriter 0 0% 78.57% 24ms 0.51% _IO_new_fopen 0 0% 78.57% 24ms 0.51% __fopen_internal (inline) 12ms 0.25% 78.83% 24ms 0.51% boost::serialization::typeid_system::extended_type_info_typeid_0::is_equal 0 0% 78.83% 24ms 0.51% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 3ms 0.063% 78.89% 24ms 0.51% std::_Rb_tree_header::_Rb_tree_header (inline) 0 0% 78.89% 24ms 0.51% std::__basic_file::open 18ms 0.38% 79.27% 24ms 0.51% vtkObject::ObjectFinalize