File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 4071ms, 79.70% of 5108ms total Dropped 774 nodes (cum <= 25.54ms) flat flat% sum% cum cum% 0 0% 0% 4863ms 95.20% __libc_start_call_main 0 0% 0% 4863ms 95.20% __libc_start_main_impl 0 0% 0% 4863ms 95.20% _start 0 0% 0% 4846ms 94.87% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4846ms 94.87% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4846ms 94.87% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4846ms 94.87% main 0 0% 0% 4807ms 94.11% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4807ms 94.11% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4807ms 94.11% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4795ms 93.87% AbstractCellBasedSimulation::Solve 0 0% 0% 4467ms 87.45% AbstractCellPopulation::WriteResultsToFiles 16ms 0.31% 0.31% 4219ms 82.60% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.31% 2014ms 39.43% VertexMeshWriter::WriteVtkUsingMesh 0 0% 0.31% 1724ms 33.75% VertexMeshWriter::MakeVtkMesh 0 0% 0.31% 1251ms 24.49% vtkPolygon::New 1ms 0.02% 0.33% 1251ms 24.49% vtkPolygon::vtkPolygon 8ms 0.16% 0.49% 888ms 17.38% vtkCell::vtkCell 1ms 0.02% 0.51% 826ms 16.17% VertexMeshWriter::WriteFiles 2ms 0.039% 0.55% 773ms 15.13% vtkPoints::New 47ms 0.92% 1.47% 762ms 14.92% std::ostream::_M_insert 1ms 0.02% 1.49% 760ms 14.88% std::ostream::operator<< (inline) 17ms 0.33% 1.82% 731ms 14.31% vtkPoints::vtkPoints 46ms 0.9% 2.72% 633ms 12.39% operator new 37ms 0.72% 3.45% 613ms 12.00% std::num_put::_M_insert_float 0 0% 3.45% 613ms 12.00% vtkStreamingDemandDrivenPipeline::Update 0 0% 3.45% 613ms 12.00% vtkXMLWriterBase::Write 0 0% 3.45% 611ms 11.96% vtkDemandDrivenPipeline::ProcessRequest 0 0% 3.45% 608ms 11.90% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 3.45% 605ms 11.84% vtkCompositeDataPipeline::ExecuteData 0 0% 3.45% 605ms 11.84% vtkExecutive::CallAlgorithm 0 0% 3.45% 604ms 11.82% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 3.45% 603ms 11.81% vtkDemandDrivenPipeline::ExecuteData 191ms 3.74% 7.18% 600ms 11.75% __GI___libc_malloc 0 0% 7.18% 589ms 11.53% vtkLine::New 6ms 0.12% 7.30% 571ms 11.18% vtkLine::vtkLine 0 0% 7.30% 569ms 11.14% vtkTriangle::New 7ms 0.14% 7.44% 561ms 10.98% vtkTriangle::vtkTriangle 1ms 0.02% 7.46% 553ms 10.83% vtkQuad::New 7ms 0.14% 7.60% 549ms 10.75% vtkQuad::vtkQuad 0 0% 7.60% 531ms 10.40% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 7.60% 531ms 10.40% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 175ms 3.43% 11.02% 521ms 10.20% __GI___libc_free 12ms 0.23% 11.26% 497ms 9.73% std::__cxx11::collate::do_transform 29ms 0.57% 11.82% 471ms 9.22% vtkPoints::SetDataType 0 0% 11.82% 469ms 9.18% vtkXMLWriter::WriteBinaryData 6ms 0.12% 11.94% 467ms 9.14% ___vsnprintf 1ms 0.02% 11.96% 462ms 9.04% vtkXMLWriter::WriteBinaryDataInternal 0 0% 11.96% 461ms 9.03% __vsnprintf_internal (inline) 0 0% 11.96% 461ms 9.03% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 11.96% 461ms 9.03% vtkXMLWriter::WriteBinaryDataBlock 69ms 1.35% 13.31% 452ms 8.85% __printf_buffer 2ms 0.039% 13.35% 420ms 8.22% vtkPolygon::~vtkPolygon 1ms 0.02% 13.37% 377ms 7.38% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 13.37% 375ms 7.34% VtkMeshWriter::WriteFiles 200ms 3.92% 17.29% 346ms 6.77% _int_free 2ms 0.039% 17.33% 342ms 6.70% __printf_fp_spec (inline) 0 0% 17.33% 342ms 6.70% vtkXMLWriter::WritePointsAppendedData 19ms 0.37% 17.70% 340ms 6.66% __printf_fp_l_buffer 218ms 4.27% 21.97% 338ms 6.62% _int_malloc 5ms 0.098% 22.06% 324ms 6.34% vtkCell::~vtkCell 0 0% 22.06% 320ms 6.26% OnLatticeSimulation::UpdateCellLocationsAndTopology 7ms 0.14% 22.20% 320ms 6.26% PottsBasedCellPopulation::UpdateCellLocations 157ms 3.07% 25.27% 305ms 5.97% __printf_fp_buffer_1 48ms 0.94% 26.21% 274ms 5.36% std::__new_allocator::allocate (inline) 6ms 0.12% 26.33% 274ms 5.36% std::__new_allocator::deallocate (inline) 49ms 0.96% 27.29% 274ms 5.36% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 0 0% 27.29% 273ms 5.34% std::allocator_traits::allocate (inline) 0 0% 27.29% 270ms 5.29% std::allocator_traits::deallocate (inline) 0 0% 27.29% 249ms 4.87% vtkXMLWriter::WriteCompressionBlock 0 0% 27.29% 236ms 4.62% vtkDataCompressor::Compress 0 0% 27.29% 233ms 4.56% compress2 0 0% 27.29% 233ms 4.56% vtkZLibDataCompressor::CompressBuffer 59ms 1.16% 28.45% 231ms 4.52% crc32 0 0% 28.45% 231ms 4.52% deflate 7ms 0.14% 28.58% 224ms 4.39% vtkPoints::~vtkPoints 6ms 0.12% 28.70% 216ms 4.23% vtkBase64OutputStream::Write 0 0% 28.70% 213ms 4.17% std::set::set (inline) 20ms 0.39% 29.09% 212ms 4.15% std::_Rb_tree::_Rb_tree 20ms 0.39% 29.48% 210ms 4.11% vtkBase64OutputStream::EncodeTriplet 0 0% 29.48% 205ms 4.01% clone3 0 0% 29.48% 205ms 4.01% start_thread 0 0% 29.48% 205ms 4.01% tbb::detail::r1::parallel_pipeline 0 0% 29.48% 200ms 3.92% VertexMesh::~VertexMesh 1ms 0.02% 29.50% 199ms 3.90% tbb::detail::r1::reset 85ms 1.66% 31.17% 196ms 3.84% tbb::detail::r1::wait_bounded_queue_monitor 1ms 0.02% 31.19% 194ms 3.80% vtkQuad::~vtkQuad 2ms 0.039% 31.23% 186ms 3.64% vtkTriangle::~vtkTriangle 114ms 2.23% 33.46% 183ms 3.58% malloc_consolidate 3ms 0.059% 33.52% 178ms 3.48% NodesOnlyMesh::ConstructNodesWithoutMesh 45ms 0.88% 34.40% 176ms 3.45% std::ostream::write 6ms 0.12% 34.51% 175ms 3.43% std::_Vector_base::_M_deallocate (inline) 67ms 1.31% 35.83% 174ms 3.41% std::_Rb_tree::_M_erase 3ms 0.059% 35.88% 170ms 3.33% vtkTypeFloat64Array::~vtkTypeFloat64Array 5ms 0.098% 35.98% 169ms 3.31% vtkFloatArray::New 0 0% 35.98% 169ms 3.31% vtkLine::GetParametricCenter 0 0% 35.98% 168ms 3.29% VertexMesh::VertexMesh 161ms 3.15% 39.13% 167ms 3.27% [libz.so.1.3] 4ms 0.078% 39.21% 167ms 3.27% std::_Rb_tree::~_Rb_tree (inline) 0 0% 39.21% 167ms 3.27% std::vector::~vector (inline) 4ms 0.078% 39.29% 165ms 3.23% vtkIdList::AllocateInternal 0 0% 39.29% 156ms 3.05% std::_Rb_tree::_M_create_node (inline) 7ms 0.14% 39.43% 154ms 3.01% vtkFloatArray::~vtkFloatArray 0 0% 39.43% 152ms 2.98% NodeLocationWriter::VisitAnyPopulation 11ms 0.22% 39.64% 152ms 2.98% std::_Rb_tree::_M_copy (inline) 0 0% 39.64% 151ms 2.96% std::_Rb_tree::_Alloc_node::operator() (inline) 63ms 1.23% 40.88% 150ms 2.94% std::basic_filebuf::xsputn 17ms 0.33% 41.21% 149ms 2.92% std::vector::_M_default_append 3ms 0.059% 41.27% 148ms 2.90% MutableElement::BuildEdges 0 0% 41.27% 148ms 2.90% VertexMesh::GenerateEdgesFromElements (inline) 2ms 0.039% 41.31% 147ms 2.88% vtkFloatArray::vtkFloatArray 8ms 0.16% 41.46% 146ms 2.86% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 0 0% 41.46% 145ms 2.84% std::_Rb_tree::_M_get_node (inline) 2ms 0.039% 41.50% 143ms 2.80% vtkDataArray::CreateDataArray 22ms 0.43% 41.93% 139ms 2.72% std::_Rb_tree::_M_clone_node (inline) 0 0% 41.93% 137ms 2.68% EdgeHelper::~EdgeHelper (inline) 0 0% 41.93% 136ms 2.66% std::_Vector_base::~_Vector_base (inline) 0 0% 41.93% 128ms 2.51% std::_Vector_base::_M_allocate (inline) 6ms 0.12% 42.05% 128ms 2.51% vtkTypeFloat64Array::New 0 0% 42.05% 126ms 2.47% EdgeHelper::GetEdgeFromNodes 2ms 0.039% 42.09% 126ms 2.47% vtkDoubleArray::vtkDoubleArray 0 0% 42.09% 118ms 2.31% vtkXMLWriter::WritePointDataAppendedData 1ms 0.02% 42.11% 116ms 2.27% vtkIdList::Allocate 0 0% 42.11% 114ms 2.23% CellPropertyCollection::GetPropertiesType (inline) 113ms 2.21% 44.32% 113ms 2.21% __strcmp_avx2 0 0% 44.32% 111ms 2.17% std::set::~set (inline) 26ms 0.51% 44.83% 111ms 2.17% vtkObject::vtkObject 110ms 2.15% 46.99% 110ms 2.15% __GI_sched_yield 18ms 0.35% 47.34% 108ms 2.11% vtkAOSDataArrayTemplate::DataElementChanged 5ms 0.098% 47.44% 105ms 2.06% vtkTypeFloat64Array::vtkTypeFloat64Array 0 0% 47.44% 104ms 2.04% std::_Rb_tree::_M_drop_node (inline) 0 0% 47.44% 101ms 1.98% std::_Rb_tree::_M_put_node (inline) 0 0% 47.44% 100ms 1.96% AbstractCellProperty::IsSubType (inline) 22ms 0.43% 47.87% 100ms 1.96% __dynamic_cast 43ms 0.84% 48.71% 98ms 1.92% std::__ostream_insert 54ms 1.06% 49.77% 97ms 1.90% vtkObjectBase::UnRegisterInternal 65ms 1.27% 51.04% 96ms 1.88% std::basic_streambuf::xsputn 1ms 0.02% 51.06% 96ms 1.88% std::operator<< (inline) 6ms 0.12% 51.17% 94ms 1.84% _int_free_maybe_consolidate 44ms 0.86% 52.04% 94ms 1.84% vtkTypeFloat64Array::PrintSelf 1ms 0.02% 52.06% 93ms 1.82% Cell::HasCellProperty (inline) 3ms 0.059% 52.11% 93ms 1.82% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 51ms 1% 53.11% 93ms 1.82% hack_digit 11ms 0.22% 53.33% 92ms 1.80% CellPropertyCollection::HasProperty 34ms 0.67% 53.99% 89ms 1.74% vtkObject::Modified 2ms 0.039% 54.03% 87ms 1.70% std::vector::push_back (inline) 2ms 0.039% 54.07% 86ms 1.68% std::map::operator[] (partial-inline) 5ms 0.098% 54.17% 86ms 1.68% vtkDoubleArray::~vtkDoubleArray 5ms 0.098% 54.27% 85ms 1.66% AbstractCellProperty::IsType (inline) 30ms 0.59% 54.86% 83ms 1.62% std::_Rb_tree::_M_lower_bound (inline) 82ms 1.61% 56.46% 82ms 1.61% unlink_chunk 15ms 0.29% 56.75% 78ms 1.53% std::num_put::_M_insert_int 0 0% 56.75% 73ms 1.43% NodesOnlyMesh::~NodesOnlyMesh 6ms 0.12% 56.87% 72ms 1.41% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 56.87% 67ms 1.31% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 0 0% 56.87% 67ms 1.31% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 0 0% 56.87% 66ms 1.29% NodesOnlyMesh::SetUpBoxCollection 0 0% 56.87% 66ms 1.29% tcache_get (inline) 66ms 1.29% 58.16% 66ms 1.29% tcache_get_n (inline) 11ms 0.22% 58.38% 65ms 1.27% VertexMeshWriter::GetNextNode 0 0% 58.38% 65ms 1.27% boost::numeric::ublas::vector_assign (inline) 15ms 0.29% 58.67% 64ms 1.25% AbstractCellProperty::IsSame 0 0% 58.67% 64ms 1.25% PottsMesh::GetMooreNeighbouringNodeIndices 7ms 0.14% 58.81% 64ms 1.25% std::vector::_M_realloc_insert 3ms 0.059% 58.87% 64ms 1.25% vtkIdList::New 0 0% 58.87% 63ms 1.23% VertexMesh::Clear 0 0% 58.87% 62ms 1.21% std::set::insert (inline) 3ms 0.059% 58.93% 60ms 1.17% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.02% 58.95% 60ms 1.17% std::_Rb_tree::_M_insert_unique 7ms 0.14% 59.08% 59ms 1.16% vtkDataArray::vtkDataArray 0 0% 59.08% 58ms 1.14% Cell::GetCellProliferativeType 0 0% 59.08% 56ms 1.10% std::map::~map (inline) 0 0% 59.08% 55ms 1.08% std::_Rb_tree::lower_bound (inline) 0 0% 59.08% 55ms 1.08% std::map::lower_bound (inline) 54ms 1.06% 60.14% 54ms 1.06% vtkTimeStamp::Modified 53ms 1.04% 61.18% 53ms 1.04% __GI___writev 0 0% 61.18% 53ms 1.04% std::__basic_file::xsputn_2 33ms 0.65% 61.82% 52ms 1.02% std::_Hashtable::clear 51ms 1% 62.82% 51ms 1% __memcpy_avx_unaligned_erms 50ms 0.98% 63.80% 50ms 0.98% [libvtkCommonCore-9.3.so.9.3] 26ms 0.51% 64.31% 50ms 0.98% __cxxabiv1::__si_class_type_info::__do_dyncast 10ms 0.2% 64.51% 49ms 0.96% boost::numeric::ublas::indexing_vector_assign 8ms 0.16% 64.66% 49ms 0.96% std::_Rb_tree::_M_insert_ (inline) 9ms 0.18% 64.84% 49ms 0.96% std::type_info::operator== (inline) 10ms 0.2% 65.04% 49ms 0.96% vtkAbstractArray::vtkAbstractArray 23ms 0.45% 65.49% 46ms 0.9% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 65.49% 46ms 0.9% DistributedBoxCollection::IsOwned 0 0% 65.49% 46ms 0.9% vtkDataArray::ComputeRange 0 0% 65.49% 45ms 0.88% VertexMeshWriter::GetNextElement 14ms 0.27% 65.76% 45ms 0.88% vtkDataArray::~vtkDataArray 45ms 0.88% 66.64% 45ms 0.88% vtkObjectBase::Delete 2ms 0.039% 66.68% 44ms 0.86% std::less::operator() (inline) 44ms 0.86% 67.54% 44ms 0.86% vtkObjectBase::~vtkObjectBase 0 0% 67.54% 43ms 0.84% DistributedBoxCollection::~DistributedBoxCollection 0 0% 67.54% 43ms 0.84% NodesOnlyMesh::ClearBoxCollection (inline) 42ms 0.82% 68.36% 42ms 0.82% std::operator< (inline) 7ms 0.14% 68.50% 42ms 0.82% vtkIdList::~vtkIdList 0 0% 68.50% 41ms 0.8% DistributedBoxCollection::SetupLocalBoxesHalfOnly 0 0% 68.50% 41ms 0.8% _dl_init 0 0% 68.50% 41ms 0.8% call_init (inline) 5ms 0.098% 68.60% 41ms 0.8% vtkSOADataArrayTemplate::FillTypedComponent 0 0% 68.60% 40ms 0.78% _dl_start_user 0 0% 68.60% 40ms 0.78% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 1ms 0.02% 68.62% 40ms 0.78% std::_Rb_tree_header::_Rb_tree_header (inline) 36ms 0.7% 69.32% 40ms 0.78% vtkObject::ObjectFinalize 15ms 0.29% 69.62% 39ms 0.76% _int_free_merge_chunk 0 0% 69.62% 39ms 0.76% vtk::detail::smp::vtkSMPToolsImplForTBB 0 0% 69.62% 38ms 0.74% std::_Destroy (inline) 0 0% 69.62% 38ms 0.74% std::_Destroy_aux::__destroy (inline) 38ms 0.74% 70.36% 38ms 0.74% std::_Rb_tree_header::_M_reset (inline) 38ms 0.74% 71.10% 38ms 0.74% std::ostream::sentry::sentry 37ms 0.72% 71.83% 37ms 0.72% boost::numeric::ublas::c_vector::operator() 5ms 0.098% 71.93% 37ms 0.72% boost::serialization::singleton::get_instance 5ms 0.098% 72.02% 37ms 0.72% vtkAOSDataArrayTemplate::InsertTuple 0 0% 72.02% 36ms 0.7% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 36ms 0.7% 72.73% 36ms 0.7% __GI___libc_write 0 0% 72.73% 36ms 0.7% std::__basic_file::xsputn 0 0% 72.73% 36ms 0.7% std::basic_filebuf::_M_convert_to_external 0 0% 72.73% 36ms 0.7% std::basic_filebuf::overflow 0 0% 72.73% 35ms 0.69% CxxTest::RealWorldDescription::setUp 0 0% 72.73% 35ms 0.69% PetscInitialize 0 0% 72.73% 35ms 0.69% PetscSetup::setUpWorld 0 0% 72.73% 35ms 0.69% PetscSetupUtils::CommonSetup 0 0% 72.73% 35ms 0.69% PetscSetupUtils::InitialisePetsc 5ms 0.098% 72.83% 35ms 0.69% tbb::detail::r1::cancel_group_execution 0 0% 72.83% 34ms 0.67% PMPI_Init_thread 0 0% 72.83% 34ms 0.67% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 0 0% 72.83% 34ms 0.67% ompi_mpi_init 34ms 0.67% 73.49% 34ms 0.67% std::codecvt::do_always_noconv 0 0% 73.49% 34ms 0.67% std::make_unique (inline) 0 0% 73.49% 33ms 0.65% Cell::GetCellId 33ms 0.65% 74.14% 33ms 0.65% Node::GetIndex 0 0% 74.14% 33ms 0.65% PottsBasedCellPopulation::AcceptCellWriter 0 0% 74.14% 33ms 0.65% boost::numeric::ublas::c_vector::assign (inline) 0 0% 74.14% 33ms 0.65% std::basic_filebuf::open 1ms 0.02% 74.16% 33ms 0.65% vtkDoubleArray::New 33ms 0.65% 74.80% 33ms 0.65% vtkObject::~vtkObject 3ms 0.059% 74.86% 32ms 0.63% __find_specmb (inline) 4ms 0.078% 74.94% 32ms 0.63% vtkDataArrayPrivate::DoComputeVectorRange 1ms 0.02% 74.96% 31ms 0.61% 4ms 0.078% 75.04% 31ms 0.61% Node::GetPoint 0 0% 75.04% 31ms 0.61% OutputFileHandler::OpenOutputFile 9ms 0.18% 75.22% 31ms 0.61% std::__new_allocator::construct (inline) 0 0% 75.22% 31ms 0.61% std::allocator_traits::construct (inline) 0 0% 75.22% 30ms 0.59% NodesOnlyMesh::Clear (inline) 30ms 0.59% 75.80% 30ms 0.59% [libstdc++.so.6.0.33] 1ms 0.02% 75.82% 30ms 0.59% _IO_new_fopen 0 0% 75.82% 30ms 0.59% std::__basic_file::open 4ms 0.078% 75.90% 30ms 0.59% vtk::detail::smp::vtkSMPToolsImpl::For 0 0% 75.90% 29ms 0.57% Cell::GetMutationState 0 0% 75.90% 29ms 0.57% CellIdWriter::GetCellDataForVtkOutput 0 0% 75.90% 29ms 0.57% __fopen_internal (inline) 1ms 0.02% 75.92% 29ms 0.57% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.02% 75.94% 29ms 0.57% std::_Rb_tree::find (inline) 0 0% 75.94% 29ms 0.57% std::map::find (inline) 25ms 0.49% 76.43% 29ms 0.57% std::num_put::do_put 0 0% 76.43% 28ms 0.55% _IO_new_file_fopen 28ms 0.55% 76.98% 28ms 0.55% __mpn_divrem 1ms 0.02% 77.00% 28ms 0.55% boost::serialization::void_cast_detail::void_caster::recursive_register 0 0% 77.00% 28ms 0.55% boost::serialization::void_cast_detail::void_caster_primitive::void_caster_primitive (inline) 28ms 0.55% 77.55% 28ms 0.55% std::_Rb_tree_increment 0 0% 77.55% 28ms 0.55% std::unique_ptr::~unique_ptr (inline) 28ms 0.55% 78.09% 28ms 0.55% vtkObjectBase::vtkObjectBase 0 0% 78.09% 27ms 0.53% __GI__IO_file_open 27ms 0.53% 78.62% 27ms 0.53% __libc_open64 27ms 0.53% 79.15% 27ms 0.53% __strchrnul_avx2 0 0% 79.15% 27ms 0.53% std::default_delete::operator() (inline) 0 0% 79.15% 27ms 0.53% vtkXMLUnstructuredDataWriter::WriteHeader 1ms 0.02% 79.17% 26ms 0.51% CellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 79.17% 26ms 0.51% VertexMesh::VertexElementIterator::operator++ (inline) 1ms 0.02% 79.19% 26ms 0.51% VtkMeshWriter::MakeVtkMesh 26ms 0.51% 79.70% 26ms 0.51% std::_Rb_tree_insert_and_rebalance 0 0% 79.70% 26ms 0.51% std::vector::vector (inline)