File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 2949ms, 78.98% of 3734ms total Dropped 655 nodes (cum <= 18.67ms) flat flat% sum% cum cum% 0 0% 0% 3582ms 95.93% __libc_start_call_main 0 0% 0% 3582ms 95.93% __libc_start_main_impl 0 0% 0% 3582ms 95.93% _start 0 0% 0% 3568ms 95.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 3568ms 95.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 3568ms 95.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 3568ms 95.55% main 0 0% 0% 3530ms 94.54% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 3530ms 94.54% CxxTest::TestRunner::runTest (inline) 0 0% 0% 3530ms 94.54% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 3521ms 94.30% AbstractCellBasedSimulation::Solve 0 0% 0% 3279ms 87.81% AbstractCellPopulation::WriteResultsToFiles 11ms 0.29% 0.29% 3114ms 83.40% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.29% 1601ms 42.88% VertexMeshWriter::WriteVtkUsingMesh 3ms 0.08% 0.37% 1382ms 37.01% VertexMeshWriter::MakeVtkMesh 0 0% 0.37% 1039ms 27.83% vtkPolygon::New 0 0% 0.37% 1039ms 27.83% vtkPolygon::vtkPolygon 2ms 0.054% 0.43% 720ms 19.28% vtkCell::vtkCell 3ms 0.08% 0.51% 620ms 16.60% vtkPoints::New 2ms 0.054% 0.56% 591ms 15.83% vtkPoints::vtkPoints 0 0% 0.56% 526ms 14.09% VertexMeshWriter::WriteFiles 27ms 0.72% 1.29% 510ms 13.66% operator new 45ms 1.21% 2.49% 485ms 12.99% std::ostream::_M_insert 129ms 3.45% 5.95% 484ms 12.96% __GI___libc_malloc 0 0% 5.95% 484ms 12.96% std::ostream::operator<< (inline) 1ms 0.027% 5.97% 477ms 12.77% vtkLine::New 9ms 0.24% 6.21% 463ms 12.40% vtkLine::vtkLine 1ms 0.027% 6.24% 463ms 12.40% vtkTriangle::New 2ms 0.054% 6.29% 457ms 12.24% vtkQuad::New 1ms 0.027% 6.32% 455ms 12.19% vtkTriangle::vtkTriangle 2ms 0.054% 6.37% 452ms 12.10% vtkQuad::vtkQuad 0 0% 6.37% 434ms 11.62% vtkStreamingDemandDrivenPipeline::Update 0 0% 6.37% 434ms 11.62% vtkXMLWriterBase::Write 0 0% 6.37% 433ms 11.60% vtkDemandDrivenPipeline::ProcessRequest 0 0% 6.37% 431ms 11.54% vtkCompositeDataPipeline::ExecuteData 0 0% 6.37% 431ms 11.54% vtkDemandDrivenPipeline::ExecuteData 0 0% 6.37% 431ms 11.54% vtkExecutive::CallAlgorithm 0 0% 6.37% 431ms 11.54% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 6.37% 431ms 11.54% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 6.37% 389ms 10.42% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 6.37% 389ms 10.42% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 93ms 2.49% 8.86% 385ms 10.31% __GI___libc_free 29ms 0.78% 9.64% 382ms 10.23% std::num_put::_M_insert_float 21ms 0.56% 10.20% 380ms 10.18% vtkPoints::SetDataType 0 0% 10.20% 354ms 9.48% vtkXMLWriter::WriteBinaryData 0 0% 10.20% 351ms 9.40% vtkXMLWriter::WriteBinaryDataBlock 0 0% 10.20% 351ms 9.40% vtkXMLWriter::WriteBinaryDataInternal 0 0% 10.20% 323ms 8.65% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 11ms 0.29% 10.50% 310ms 8.30% std::__cxx11::collate::do_transform 0 0% 10.50% 307ms 8.22% vtkPolygon::~vtkPolygon 201ms 5.38% 15.88% 302ms 8.09% _int_malloc 176ms 4.71% 20.59% 288ms 7.71% _int_free 2ms 0.054% 20.65% 283ms 7.58% ___vsnprintf 0 0% 20.65% 281ms 7.53% __vsnprintf_internal (inline) 45ms 1.21% 21.85% 279ms 7.47% __printf_buffer 53ms 1.42% 23.27% 254ms 6.80% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 0 0% 23.27% 253ms 6.78% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 23.27% 251ms 6.72% VtkMeshWriter::WriteFiles 2ms 0.054% 23.33% 247ms 6.61% vtkCell::~vtkCell 0 0% 23.33% 246ms 6.59% vtkXMLWriter::WritePointsAppendedData 0 0% 23.33% 234ms 6.27% OnLatticeSimulation::UpdateCellLocationsAndTopology 5ms 0.13% 23.46% 234ms 6.27% PottsBasedCellPopulation::UpdateCellLocations 31ms 0.83% 24.29% 223ms 5.97% std::__new_allocator::allocate (inline) 0 0% 24.29% 222ms 5.95% std::allocator_traits::allocate (inline) 1ms 0.027% 24.32% 220ms 5.89% std::__new_allocator::deallocate (inline) 0 0% 24.32% 215ms 5.76% std::allocator_traits::deallocate (inline) 1ms 0.027% 24.34% 213ms 5.70% __printf_fp_spec (inline) 11ms 0.29% 24.64% 212ms 5.68% __printf_fp_l_buffer 79ms 2.12% 26.75% 189ms 5.06% __printf_fp_buffer_1 2ms 0.054% 26.81% 183ms 4.90% vtkBase64OutputStream::Write 17ms 0.46% 27.26% 180ms 4.82% vtkBase64OutputStream::EncodeTriplet 0 0% 27.26% 172ms 4.61% vtkXMLWriter::WriteCompressionBlock 0 0% 27.26% 163ms 4.37% vtkDataCompressor::Compress 0 0% 27.26% 162ms 4.34% compress2 0 0% 27.26% 162ms 4.34% deflate 3ms 0.08% 27.34% 162ms 4.34% vtkPoints::~vtkPoints 0 0% 27.34% 162ms 4.34% vtkZLibDataCompressor::CompressBuffer 31ms 0.83% 28.17% 161ms 4.31% crc32 92ms 2.46% 30.64% 160ms 4.28% malloc_consolidate 4ms 0.11% 30.74% 156ms 4.18% vtkFloatArray::New 47ms 1.26% 32.00% 151ms 4.04% std::ostream::write 1ms 0.027% 32.03% 145ms 3.88% std::set::set (inline) 1ms 0.027% 32.06% 145ms 3.88% vtkLine::GetParametricCenter 15ms 0.4% 32.46% 143ms 3.83% std::_Rb_tree::_Rb_tree 0 0% 32.46% 142ms 3.80% NodesOnlyMesh::ConstructNodesWithoutMesh 1ms 0.027% 32.49% 142ms 3.80% vtkFloatArray::vtkFloatArray 3ms 0.08% 32.57% 141ms 3.78% vtkIdList::AllocateInternal 0 0% 32.57% 136ms 3.64% vtkQuad::~vtkQuad 0 0% 32.57% 135ms 3.62% std::_Rb_tree::_M_create_node (inline) 0 0% 32.57% 134ms 3.59% std::vector::~vector (inline) 0 0% 32.57% 131ms 3.51% tbb::detail::r1::parallel_pipeline 0 0% 32.57% 130ms 3.48% std::_Rb_tree::_M_get_node (inline) 0 0% 32.57% 130ms 3.48% std::_Vector_base::_M_deallocate (inline) 125ms 3.35% 35.91% 128ms 3.43% [libz.so.1.3] 54ms 1.45% 37.36% 128ms 3.43% std::basic_filebuf::xsputn 0 0% 37.36% 128ms 3.43% vtkDataArray::CreateDataArray 0 0% 37.36% 126ms 3.37% VertexMesh::~VertexMesh 4ms 0.11% 37.47% 125ms 3.35% std::_Rb_tree::~_Rb_tree (inline) 0 0% 37.47% 124ms 3.32% clone3 0 0% 37.47% 124ms 3.32% start_thread 28ms 0.75% 38.22% 123ms 3.29% std::_Rb_tree::_M_erase 7ms 0.19% 38.40% 123ms 3.29% vtkTypeFloat64Array::New 0 0% 38.40% 121ms 3.24% VertexMesh::VertexMesh 2ms 0.054% 38.46% 119ms 3.19% tbb::detail::r1::reset 7ms 0.19% 38.64% 118ms 3.16% vtkDoubleArray::vtkDoubleArray 3ms 0.08% 38.73% 118ms 3.16% vtkFloatArray::~vtkFloatArray 0 0% 38.73% 118ms 3.16% vtkTriangle::~vtkTriangle 1ms 0.027% 38.75% 115ms 3.08% vtkTypeFloat64Array::~vtkTypeFloat64Array 0 0% 38.75% 114ms 3.05% VertexMesh::GenerateEdgesFromElements (inline) 30ms 0.8% 39.56% 113ms 3.03% vtkObject::vtkObject 5ms 0.13% 39.69% 112ms 3.00% MutableElement::BuildEdges 7ms 0.19% 39.88% 112ms 3.00% std::_Rb_tree::_M_copy (inline) 50ms 1.34% 41.22% 112ms 3.00% tbb::detail::r1::wait_bounded_queue_monitor 0 0% 41.22% 111ms 2.97% std::_Rb_tree::_Alloc_node::operator() (inline) 8ms 0.21% 41.43% 110ms 2.95% std::vector::_M_default_append 3ms 0.08% 41.51% 109ms 2.92% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 2ms 0.054% 41.56% 108ms 2.89% std::_Vector_base::~_Vector_base (inline) 0 0% 41.56% 107ms 2.87% std::set::~set (inline) 0 0% 41.56% 105ms 2.81% NodeLocationWriter::VisitAnyPopulation 0 0% 41.56% 104ms 2.79% vtkIdList::Allocate 10ms 0.27% 41.83% 100ms 2.68% std::_Rb_tree::_M_clone_node (inline) 1ms 0.027% 41.86% 100ms 2.68% vtkTypeFloat64Array::vtkTypeFloat64Array 2ms 0.054% 41.91% 98ms 2.62% EdgeHelper::GetEdgeFromNodes 2ms 0.054% 41.97% 94ms 2.52% std::_Vector_base::_M_allocate (inline) 0 0% 41.97% 93ms 2.49% EdgeHelper::~EdgeHelper (inline) 0 0% 41.97% 91ms 2.44% std::_Rb_tree::_M_drop_node (inline) 26ms 0.7% 42.66% 88ms 2.36% vtkAOSDataArrayTemplate::DataElementChanged 2ms 0.054% 42.72% 86ms 2.30% std::map::operator[] (partial-inline) 0 0% 42.72% 85ms 2.28% std::_Rb_tree::_M_put_node (inline) 40ms 1.07% 43.79% 85ms 2.28% vtkTypeFloat64Array::PrintSelf 21ms 0.56% 44.35% 84ms 2.25% std::__ostream_insert 4ms 0.11% 44.46% 81ms 2.17% _int_free_maybe_consolidate 1ms 0.027% 44.48% 81ms 2.17% std::operator<< (inline) 81ms 2.17% 46.65% 81ms 2.17% unlink_chunk 80ms 2.14% 48.79% 80ms 2.14% __strcmp_evex 44ms 1.18% 49.97% 80ms 2.14% vtkObjectBase::UnRegisterInternal 0 0% 49.97% 77ms 2.06% vtkXMLWriter::WritePointDataAppendedData 1ms 0.027% 50.00% 76ms 2.04% CellPropertyCollection::GetPropertiesType (inline) 0 0% 50.00% 76ms 2.04% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 50.00% 75ms 2.01% Cell::HasCellProperty (inline) 1ms 0.027% 50.03% 75ms 2.01% CellPropertyCollection::HasProperty 1ms 0.027% 50.05% 74ms 1.98% AbstractCellProperty::IsType (inline) 20ms 0.54% 50.59% 74ms 1.98% vtkObject::Modified 45ms 1.21% 51.79% 69ms 1.85% std::_Hashtable::clear 0 0% 51.79% 67ms 1.79% AbstractCellProperty::IsSubType (inline) 16ms 0.43% 52.22% 66ms 1.77% __dynamic_cast 29ms 0.78% 53.00% 65ms 1.74% hack_digit 0 0% 53.00% 64ms 1.71% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 62ms 1.66% 54.66% 62ms 1.66% __GI_sched_yield 18ms 0.48% 55.14% 61ms 1.63% std::_Rb_tree::_M_lower_bound (inline) 40ms 1.07% 56.21% 59ms 1.58% std::basic_streambuf::xsputn 6ms 0.16% 56.37% 58ms 1.55% std::vector::push_back (inline) 5ms 0.13% 56.51% 58ms 1.55% vtkIdList::New 1ms 0.027% 56.53% 57ms 1.53% AbstractCellPopulation::GetCellUsingLocationIndex 8ms 0.21% 56.75% 57ms 1.53% AbstractCellProperty::IsSame 0 0% 56.75% 57ms 1.53% NodesOnlyMesh::SetUpBoxCollection 2ms 0.054% 56.80% 56ms 1.50% vtkDoubleArray::~vtkDoubleArray 5ms 0.13% 56.94% 52ms 1.39% boost::numeric::ublas::c_vector::c_vector (partial-inline) 1ms 0.027% 56.96% 52ms 1.39% vtkDataArray::vtkDataArray 14ms 0.37% 57.34% 50ms 1.34% vtkAbstractArray::vtkAbstractArray 0 0% 57.34% 49ms 1.31% PottsMesh::GetMooreNeighbouringNodeIndices 18ms 0.48% 57.82% 49ms 1.31% std::type_info::operator== (inline) 49ms 1.31% 59.13% 49ms 1.31% vtkTimeStamp::Modified 0 0% 59.13% 47ms 1.26% boost::numeric::ublas::vector_assign (inline) 0 0% 59.13% 47ms 1.26% std::_Rb_tree::lower_bound (inline) 0 0% 59.13% 47ms 1.26% std::map::lower_bound (inline) 0 0% 59.13% 46ms 1.23% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 10ms 0.27% 59.40% 44ms 1.18% std::num_put::_M_insert_int 0 0% 59.40% 44ms 1.18% tcache_get (inline) 44ms 1.18% 60.58% 44ms 1.18% tcache_get_n (inline) 10ms 0.27% 60.85% 42ms 1.12% vtkSOADataArrayTemplate::FillTypedComponent 0 0% 60.85% 41ms 1.10% NodesOnlyMesh::~NodesOnlyMesh 0 0% 60.85% 40ms 1.07% Cell::GetCellProliferativeType 40ms 1.07% 61.92% 40ms 1.07% __memcpy_avx512_unaligned_erms 1ms 0.027% 61.94% 39ms 1.04% std::__basic_file::xsputn_2 38ms 1.02% 62.96% 38ms 1.02% [libvtkCommonCore-9.3.so.9.3] 38ms 1.02% 63.98% 38ms 1.02% __GI___writev 5ms 0.13% 64.11% 38ms 1.02% std::vector::_M_realloc_insert 1ms 0.027% 64.14% 37ms 0.99% std::_Rb_tree::_M_emplace_hint_unique 36ms 0.96% 65.10% 37ms 0.99% vtkObject::~vtkObject 37ms 0.99% 66.10% 37ms 0.99% vtkObjectBase::vtkObjectBase 3ms 0.08% 66.18% 36ms 0.96% std::_Rb_tree::_M_insert_unique 0 0% 66.18% 36ms 0.96% std::set::insert (inline) 30ms 0.8% 66.98% 36ms 0.96% vtkObject::ObjectFinalize 0 0% 66.98% 35ms 0.94% CxxTest::RealWorldDescription::setUp 3ms 0.08% 67.06% 35ms 0.94% DistributedBoxCollection::SetupLocalBoxesHalfOnly 0 0% 67.06% 35ms 0.94% PMPI_Init_thread 0 0% 67.06% 35ms 0.94% PetscInitialize 0 0% 67.06% 35ms 0.94% PetscSetup::setUpWorld 0 0% 67.06% 35ms 0.94% PetscSetupUtils::CommonSetup 0 0% 67.06% 35ms 0.94% PetscSetupUtils::InitialisePetsc 0 0% 67.06% 35ms 0.94% ompi_mpi_init 0 0% 67.06% 35ms 0.94% std::_Destroy (inline) 1ms 0.027% 67.09% 35ms 0.94% std::_Destroy_aux::__destroy (inline) 35ms 0.94% 68.02% 35ms 0.94% std::codecvt::do_always_noconv 3ms 0.08% 68.10% 35ms 0.94% vtkDoubleArray::New 0 0% 68.10% 34ms 0.91% DistributedBoxCollection::~DistributedBoxCollection 0 0% 68.10% 34ms 0.91% NodesOnlyMesh::ClearBoxCollection (inline) 34ms 0.91% 69.01% 34ms 0.91% vtkObjectBase::Delete 0 0% 69.01% 33ms 0.88% VertexMesh::Clear 6ms 0.16% 69.18% 33ms 0.88% boost::numeric::ublas::indexing_vector_assign 6ms 0.16% 69.34% 32ms 0.86% VertexMeshWriter::GetNextNode 32ms 0.86% 70.19% 32ms 0.86% [libstdc++.so.6.0.33] 17ms 0.46% 70.65% 32ms 0.86% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 70.65% 32ms 0.86% _dl_init 0 0% 70.65% 32ms 0.86% call_init (inline) 1ms 0.027% 70.67% 30ms 0.8% DistributedBoxCollection::IsOwned 0 0% 70.67% 30ms 0.8% std::less::operator() (inline) 30ms 0.8% 71.48% 30ms 0.8% std::operator< (inline) 0 0% 71.48% 29ms 0.78% 19ms 0.51% 71.99% 29ms 0.78% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 71.99% 28ms 0.75% _dl_start_user 27ms 0.72% 72.71% 27ms 0.72% __memset_avx512_unaligned_erms 27ms 0.72% 73.43% 27ms 0.72% vtkObjectBase::~vtkObjectBase 26ms 0.7% 74.13% 26ms 0.7% std::ostream::sentry::sentry 3ms 0.08% 74.21% 26ms 0.7% vtkIdList::vtkIdList 0 0% 74.21% 25ms 0.67% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 2ms 0.054% 74.26% 25ms 0.67% boost::serialization::singleton::get_instance 0 0% 74.26% 25ms 0.67% std::default_delete::operator() (inline) 0 0% 74.26% 25ms 0.67% std::unique_ptr::~unique_ptr (inline) 0 0% 74.26% 25ms 0.67% vtk::detail::smp::vtkSMPToolsImplForTBB 0 0% 74.26% 25ms 0.67% vtkDataArray::ComputeRange 25ms 0.67% 74.93% 25ms 0.67% vtkDataArray::Modified 0 0% 74.93% 24ms 0.64% PottsBasedCellPopulation::AcceptCellWriter 24ms 0.64% 75.58% 24ms 0.64% __GI___libc_write 1ms 0.027% 75.60% 24ms 0.64% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 0 0% 75.60% 24ms 0.64% orte_init 0 0% 75.60% 24ms 0.64% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 75.60% 24ms 0.64% std::__basic_file::xsputn 0 0% 75.60% 24ms 0.64% std::basic_filebuf::_M_convert_to_external 0 0% 75.60% 24ms 0.64% std::basic_filebuf::open 0 0% 75.60% 24ms 0.64% std::basic_filebuf::overflow 7ms 0.19% 75.79% 24ms 0.64% vtkIdList::~vtkIdList 0 0% 75.79% 23ms 0.62% std::_Rb_tree::_M_insert_ (inline) 2ms 0.054% 75.84% 23ms 0.62% tbb::detail::r1::cancel_group_execution 0 0% 75.84% 22ms 0.59% Cell::GetCellId 0 0% 75.84% 22ms 0.59% Cell::GetMutationState 0 0% 75.84% 22ms 0.59% VtkMeshWriter::MakeVtkMesh 1ms 0.027% 75.87% 22ms 0.59% vtkAOSDataArrayTemplate::InsertTuple 0 0% 75.87% 21ms 0.56% CellIdWriter::GetCellDataForVtkOutput 1ms 0.027% 75.90% 21ms 0.56% Node::ConstructNodeAttributes (inline) 0 0% 75.90% 21ms 0.56% Node::SetRadius 0 0% 75.90% 21ms 0.56% OutputFileHandler::OpenOutputFile 0 0% 75.90% 21ms 0.56% _IO_new_file_fopen 0 0% 75.90% 21ms 0.56% _IO_new_fopen 0 0% 75.90% 21ms 0.56% __GI__IO_file_open 0 0% 75.90% 21ms 0.56% __fopen_internal (inline) 21ms 0.56% 76.46% 21ms 0.56% __libc_open64 21ms 0.56% 77.02% 21ms 0.56% __mpn_divrem 8ms 0.21% 77.24% 21ms 0.56% _int_free_merge_chunk 0 0% 77.24% 21ms 0.56% std::__basic_file::open 0 0% 77.24% 21ms 0.56% std::make_unique (inline) 17ms 0.46% 77.69% 21ms 0.56% std::num_put::do_put 4ms 0.11% 77.80% 21ms 0.56% vtkDataArray::~vtkDataArray 0 0% 77.80% 20ms 0.54% VertexMeshWriter::GetNextElement 20ms 0.54% 78.33% 20ms 0.54% [libchaste_cell_based.so] 0 0% 78.33% 19ms 0.51% boost::serialization::void_cast_detail::void_caster_primitive::void_caster_primitive (inline) 19ms 0.51% 78.84% 19ms 0.51% std::vector::size (inline) 0 0% 78.84% 19ms 0.51% std::vector::vector (inline) 4ms 0.11% 78.95% 19ms 0.51% vtk::detail::smp::vtkSMPToolsImpl::For 1ms 0.027% 78.98% 19ms 0.51% vtkDataArrayPrivate::DoComputeVectorRange