File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 4031ms, 79.85% of 5048ms total Dropped 786 nodes (cum <= 25.24ms) flat flat% sum% cum cum% 0 0% 0% 4849ms 96.06% __libc_start_call_main 0 0% 0% 4849ms 96.06% __libc_start_main_impl 0 0% 0% 4849ms 96.06% _start 0 0% 0% 4829ms 95.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4829ms 95.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4829ms 95.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4829ms 95.66% main 0 0% 0% 4787ms 94.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4787ms 94.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4787ms 94.83% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4775ms 94.59% AbstractCellBasedSimulation::Solve 0 0% 0% 4404ms 87.24% AbstractCellPopulation::WriteResultsToFiles 17ms 0.34% 0.34% 4186ms 82.92% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.34% 2083ms 41.26% VertexMeshWriter::WriteVtkUsingMesh 2ms 0.04% 0.38% 1710ms 33.87% VertexMeshWriter::MakeVtkMesh 1ms 0.02% 0.4% 1239ms 24.54% vtkPolygon::New 1ms 0.02% 0.42% 1237ms 24.50% vtkPolygon::vtkPolygon 7ms 0.14% 0.55% 861ms 17.06% vtkCell::vtkCell 2ms 0.04% 0.59% 731ms 14.48% vtkPoints::New 0 0% 0.59% 709ms 14.05% VertexMeshWriter::WriteFiles 1ms 0.02% 0.61% 698ms 13.83% vtkStreamingDemandDrivenPipeline::Update 0 0% 0.61% 698ms 13.83% vtkXMLWriterBase::Write 12ms 0.24% 0.85% 693ms 13.73% vtkPoints::vtkPoints 0 0% 0.85% 692ms 13.71% vtkDemandDrivenPipeline::ProcessRequest 0 0% 0.85% 684ms 13.55% vtkExecutive::CallAlgorithm 0 0% 0.85% 683ms 13.53% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 0.85% 679ms 13.45% vtkCompositeDataPipeline::ExecuteData 0 0% 0.85% 679ms 13.45% vtkDemandDrivenPipeline::ExecuteData 0 0% 0.85% 679ms 13.45% vtkXMLUnstructuredDataWriter::ProcessRequest 37ms 0.73% 1.58% 667ms 13.21% operator new 62ms 1.23% 2.81% 662ms 13.11% std::ostream::_M_insert 0 0% 2.81% 658ms 13.03% std::ostream::operator<< (inline) 175ms 3.47% 6.28% 643ms 12.74% __GI___libc_malloc 0 0% 6.28% 600ms 11.89% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 6.28% 600ms 11.89% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 1ms 0.02% 6.30% 553ms 10.95% vtkQuad::New 0 0% 6.30% 552ms 10.94% vtkTriangle::New 2ms 0.04% 6.34% 548ms 10.86% vtkQuad::vtkQuad 2ms 0.04% 6.38% 542ms 10.74% vtkLine::New 5ms 0.099% 6.48% 542ms 10.74% vtkTriangle::vtkTriangle 0 0% 6.48% 542ms 10.74% vtkXMLWriter::WriteBinaryData 0 0% 6.48% 538ms 10.66% vtkXMLWriter::WriteBinaryDataBlock 0 0% 6.48% 538ms 10.66% vtkXMLWriter::WriteBinaryDataInternal 127ms 2.52% 8.99% 526ms 10.42% __GI___libc_free 9ms 0.18% 9.17% 526ms 10.42% vtkLine::vtkLine 49ms 0.97% 10.14% 520ms 10.30% std::num_put::_M_insert_float 0 0% 10.14% 503ms 9.96% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 28ms 0.55% 10.70% 437ms 8.66% vtkPoints::SetDataType 15ms 0.3% 10.99% 405ms 8.02% std::__cxx11::collate::do_transform 0 0% 10.99% 402ms 7.96% vtkPolygon::~vtkPolygon 0 0% 10.99% 396ms 7.84% vtkXMLWriter::WritePointsAppendedData 242ms 4.79% 15.79% 394ms 7.81% _int_free 252ms 4.99% 20.78% 383ms 7.59% _int_malloc 0 0% 20.78% 380ms 7.53% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 20.78% 380ms 7.53% VtkMeshWriter::WriteFiles 4ms 0.079% 20.86% 379ms 7.51% ___vsnprintf 1ms 0.02% 20.88% 375ms 7.43% __vsnprintf_internal (inline) 60ms 1.19% 22.07% 367ms 7.27% __printf_buffer 0 0% 22.07% 365ms 7.23% OnLatticeSimulation::UpdateCellLocationsAndTopology 4ms 0.079% 22.15% 365ms 7.23% PottsBasedCellPopulation::UpdateCellLocations 8ms 0.16% 22.31% 307ms 6.08% vtkCell::~vtkCell 5ms 0.099% 22.40% 301ms 5.96% vtkBase64OutputStream::Write 33ms 0.65% 23.06% 291ms 5.76% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 14ms 0.28% 23.34% 291ms 5.76% vtkBase64OutputStream::EncodeTriplet 2ms 0.04% 23.38% 288ms 5.71% std::__new_allocator::deallocate (inline) 0 0% 23.38% 288ms 5.71% std::allocator_traits::deallocate (inline) 15ms 0.3% 23.67% 274ms 5.43% __printf_fp_l_buffer 0 0% 23.67% 274ms 5.43% __printf_fp_spec (inline) 45ms 0.89% 24.56% 270ms 5.35% std::__new_allocator::allocate (inline) 0 0% 24.56% 269ms 5.33% std::allocator_traits::allocate (inline) 66ms 1.31% 25.87% 250ms 4.95% std::ostream::write 100ms 1.98% 27.85% 243ms 4.81% __printf_fp_buffer_1 0 0% 27.85% 242ms 4.79% vtkXMLWriter::WriteCompressionBlock 0 0% 27.85% 233ms 4.62% vtkDataCompressor::Compress 0 0% 27.85% 232ms 4.60% compress2 0 0% 27.85% 232ms 4.60% vtkZLibDataCompressor::CompressBuffer 57ms 1.13% 28.98% 230ms 4.56% crc32 0 0% 28.98% 230ms 4.56% deflate 0 0% 28.98% 214ms 4.24% VertexMesh::~VertexMesh 23ms 0.46% 29.44% 213ms 4.22% std::_Rb_tree::_Rb_tree 0 0% 29.44% 213ms 4.22% std::set::set (inline) 6ms 0.12% 29.56% 203ms 4.02% vtkPoints::~vtkPoints 2ms 0.04% 29.60% 197ms 3.90% vtkQuad::~vtkQuad 119ms 2.36% 31.95% 196ms 3.88% malloc_consolidate 63ms 1.25% 33.20% 193ms 3.82% std::_Rb_tree::_M_erase 2ms 0.04% 33.24% 186ms 3.68% std::_Rb_tree::~_Rb_tree (inline) 5ms 0.099% 33.34% 178ms 3.53% vtkFloatArray::New 5ms 0.099% 33.44% 178ms 3.53% vtkIdList::AllocateInternal 2ms 0.04% 33.48% 175ms 3.47% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 2ms 0.04% 33.52% 173ms 3.43% NodesOnlyMesh::ConstructNodesWithoutMesh 2ms 0.04% 33.56% 172ms 3.41% std::vector::~vector (inline) 7ms 0.14% 33.70% 171ms 3.39% std::_Vector_base::_M_deallocate (inline) 0 0% 33.70% 171ms 3.39% vtkTriangle::~vtkTriangle 81ms 1.60% 35.30% 170ms 3.37% std::basic_filebuf::xsputn 166ms 3.29% 38.59% 169ms 3.35% [libz.so.1.3] 1ms 0.02% 38.61% 165ms 3.27% tbb::detail::r1::parallel_pipeline 0 0% 38.61% 165ms 3.27% vtkLine::GetParametricCenter 0 0% 38.61% 160ms 3.17% clone3 0 0% 38.61% 160ms 3.17% start_thread 0 0% 38.61% 159ms 3.15% std::_Rb_tree::_M_create_node (inline) 3ms 0.059% 38.67% 154ms 3.05% VertexMesh::VertexMesh 5ms 0.099% 38.77% 152ms 3.01% vtkDataArray::CreateDataArray 12ms 0.24% 39.01% 151ms 2.99% std::_Rb_tree::_M_copy (inline) 7ms 0.14% 39.14% 151ms 2.99% vtkDoubleArray::vtkDoubleArray 0 0% 39.14% 150ms 2.97% EdgeHelper::~EdgeHelper (inline) 0 0% 39.14% 150ms 2.97% vtkTypeFloat64Array::~vtkTypeFloat64Array 3ms 0.059% 39.20% 149ms 2.95% vtkFloatArray::vtkFloatArray 4ms 0.079% 39.28% 147ms 2.91% tbb::detail::r1::reset 0 0% 39.28% 145ms 2.87% std::_Vector_base::~_Vector_base (inline) 0 0% 39.28% 144ms 2.85% std::_Rb_tree::_Alloc_node::operator() (inline) 11ms 0.22% 39.50% 144ms 2.85% vtkTypeFloat64Array::New 0 0% 39.50% 141ms 2.79% std::_Rb_tree::_M_get_node (inline) 13ms 0.26% 39.76% 141ms 2.79% std::vector::_M_default_append 74ms 1.47% 41.22% 138ms 2.73% tbb::detail::r1::wait_bounded_queue_monitor 21ms 0.42% 41.64% 134ms 2.65% std::_Rb_tree::_M_clone_node (inline) 0 0% 41.64% 133ms 2.63% NodeLocationWriter::VisitAnyPopulation 0 0% 41.64% 130ms 2.58% VertexMesh::GenerateEdgesFromElements (inline) 2ms 0.04% 41.68% 130ms 2.58% std::_Vector_base::_M_allocate (inline) 0 0% 41.68% 130ms 2.58% std::set::~set (inline) 5ms 0.099% 41.78% 128ms 2.54% MutableElement::BuildEdges 0 0% 41.78% 128ms 2.54% std::_Rb_tree::_M_drop_node (inline) 0 0% 41.78% 124ms 2.46% std::_Rb_tree::_M_put_node (inline) 0 0% 41.78% 122ms 2.42% vtkIdList::Allocate 3ms 0.059% 41.84% 121ms 2.40% vtkTypeFloat64Array::vtkTypeFloat64Array 1ms 0.02% 41.86% 119ms 2.36% vtkFloatArray::~vtkFloatArray 26ms 0.52% 42.37% 112ms 2.22% vtkObject::vtkObject 0 0% 42.37% 111ms 2.20% EdgeHelper::GetEdgeFromNodes 0 0% 42.37% 105ms 2.08% vtkXMLWriter::WritePointDataAppendedData 5ms 0.099% 42.47% 104ms 2.06% _int_free_maybe_consolidate 0 0% 42.47% 103ms 2.04% CellPropertyCollection::GetPropertiesType (inline) 71ms 1.41% 43.88% 103ms 2.04% vtkObjectBase::UnRegisterInternal 100ms 1.98% 45.86% 100ms 1.98% unlink_chunk 34ms 0.67% 46.53% 99ms 1.96% std::__ostream_insert 1ms 0.02% 46.55% 98ms 1.94% std::operator<< (inline) 0 0% 46.55% 95ms 1.88% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 94ms 1.86% 48.42% 94ms 1.86% __strcmp_avx2 0 0% 48.42% 93ms 1.84% Cell::HasCellProperty (inline) 2ms 0.04% 48.45% 93ms 1.84% CellPropertyCollection::HasProperty 0 0% 48.45% 92ms 1.82% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 48.45% 91ms 1.80% AbstractCellProperty::IsSubType (inline) 0 0% 48.45% 91ms 1.80% AbstractCellProperty::IsType (inline) 32ms 0.63% 49.09% 91ms 1.80% __dynamic_cast 2ms 0.04% 49.13% 89ms 1.76% std::map::operator[] (partial-inline) 40ms 0.79% 49.92% 89ms 1.76% vtkTypeFloat64Array::PrintSelf 44ms 0.87% 50.79% 88ms 1.74% hack_digit 88ms 1.74% 52.54% 88ms 1.74% std::ostream::sentry::sentry 4ms 0.079% 52.61% 86ms 1.70% vtkDoubleArray::~vtkDoubleArray 26ms 0.52% 53.13% 81ms 1.60% vtkObject::Modified 5ms 0.099% 53.23% 76ms 1.51% vtkAOSDataArrayTemplate::DataElementChanged 3ms 0.059% 53.29% 73ms 1.45% std::vector::push_back (inline) 5ms 0.099% 53.39% 71ms 1.41% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 53.39% 71ms 1.41% tcache_get (inline) 71ms 1.41% 54.79% 71ms 1.41% tcache_get_n (inline) 7ms 0.14% 54.93% 71ms 1.41% vtkIdList::New 0 0% 54.93% 68ms 1.35% NodesOnlyMesh::SetUpBoxCollection 34ms 0.67% 55.61% 68ms 1.35% std::_Rb_tree::_M_lower_bound (inline) 18ms 0.36% 55.96% 67ms 1.33% AbstractCellProperty::IsSame 0 0% 55.96% 66ms 1.31% NodesOnlyMesh::~NodesOnlyMesh 1ms 0.02% 55.98% 65ms 1.29% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 2ms 0.04% 56.02% 64ms 1.27% VertexMesh::Clear 43ms 0.85% 56.87% 64ms 1.27% std::basic_streambuf::xsputn 63ms 1.25% 58.12% 63ms 1.25% __GI_sched_yield 8ms 0.16% 58.28% 62ms 1.23% VertexMeshWriter::GetNextNode 0 0% 58.28% 61ms 1.21% PottsMesh::GetMooreNeighbouringNodeIndices 5ms 0.099% 58.38% 61ms 1.21% boost::numeric::ublas::c_vector::c_vector (inline) 3ms 0.059% 58.44% 61ms 1.21% std::_Rb_tree::_M_insert_unique 0 0% 58.44% 61ms 1.21% std::set::insert (inline) 13ms 0.26% 58.70% 61ms 1.21% vtkSOADataArrayTemplate::FillTypedComponent 1ms 0.02% 58.72% 59ms 1.17% Cell::GetCellProliferativeType 3ms 0.059% 58.78% 59ms 1.17% vtkDataArray::vtkDataArray 57ms 1.13% 59.90% 57ms 1.13% __GI___writev 0 0% 59.90% 56ms 1.11% std::__basic_file::xsputn_2 0 0% 59.90% 56ms 1.11% std::map::~map (inline) 4ms 0.079% 59.98% 56ms 1.11% std::vector::_M_realloc_insert 0 0% 59.98% 55ms 1.09% std::_Rb_tree::lower_bound (inline) 0 0% 59.98% 55ms 1.09% std::map::lower_bound (inline) 13ms 0.26% 60.24% 55ms 1.09% std::num_put::_M_insert_int 23ms 0.46% 60.70% 55ms 1.09% vtkAbstractArray::vtkAbstractArray 0 0% 60.70% 54ms 1.07% boost::numeric::ublas::vector_assign (inline) 53ms 1.05% 61.75% 53ms 1.05% vtkTimeStamp::Modified 1ms 0.02% 61.77% 52ms 1.03% vtkDoubleArray::New 11ms 0.22% 61.98% 50ms 0.99% vtkDataArray::~vtkDataArray 49ms 0.97% 62.96% 49ms 0.97% [libvtkCommonCore-9.3.so.9.3] 15ms 0.3% 63.25% 49ms 0.97% std::type_info::operator== (inline) 23ms 0.46% 63.71% 47ms 0.93% std::_Hashtable::clear 44ms 0.87% 64.58% 45ms 0.89% vtkObject::~vtkObject 22ms 0.44% 65.02% 43ms 0.85% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 65.02% 43ms 0.85% _dl_init 0 0% 65.02% 43ms 0.85% call_init (inline) 42ms 0.83% 65.85% 42ms 0.83% Node::GetIndex 17ms 0.34% 66.18% 42ms 0.83% boost::numeric::ublas::indexing_vector_assign 3ms 0.059% 66.24% 40ms 0.79% std::_Rb_tree::_M_insert_ (inline) 40ms 0.79% 67.04% 40ms 0.79% vtkObjectBase::~vtkObjectBase 39ms 0.77% 67.81% 39ms 0.77% __GI___libc_write 0 0% 67.81% 39ms 0.77% _dl_start_user 0 0% 67.81% 39ms 0.77% std::__basic_file::xsputn 0 0% 67.81% 39ms 0.77% std::basic_filebuf::_M_convert_to_external 0 0% 67.81% 39ms 0.77% std::basic_filebuf::overflow 9ms 0.18% 67.99% 39ms 0.77% vtkIdList::~vtkIdList 5ms 0.099% 68.09% 38ms 0.75% 0 0% 68.09% 38ms 0.75% CxxTest::RealWorldDescription::setUp 2ms 0.04% 68.13% 38ms 0.75% DistributedBoxCollection::SetupLocalBoxesHalfOnly 0 0% 68.13% 38ms 0.75% PMPI_Init_thread 0 0% 68.13% 38ms 0.75% PetscInitialize 0 0% 68.13% 38ms 0.75% PetscSetup::setUpWorld 0 0% 68.13% 38ms 0.75% PetscSetupUtils::CommonSetup 0 0% 68.13% 38ms 0.75% PetscSetupUtils::InitialisePetsc 38ms 0.75% 68.88% 38ms 0.75% [libchaste_cell_based.so] 38ms 0.75% 69.63% 38ms 0.75% __memcpy_avx_unaligned_erms 0 0% 69.63% 38ms 0.75% ompi_mpi_init 0 0% 69.63% 38ms 0.75% vtkDataArray::ComputeRange 37ms 0.73% 70.36% 38ms 0.75% vtkObjectBase::Delete 1ms 0.02% 70.38% 37ms 0.73% DistributedBoxCollection::~DistributedBoxCollection 0 0% 70.38% 37ms 0.73% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 70.38% 37ms 0.73% PottsMesh::GetVonNeumannNeighbouringNodeIndices 0 0% 70.38% 37ms 0.73% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 2ms 0.04% 70.42% 37ms 0.73% std::_Rb_tree_header::_Rb_tree_header (inline) 1ms 0.02% 70.44% 36ms 0.71% DistributedBoxCollection::IsOwned 36ms 0.71% 71.16% 36ms 0.71% [libstdc++.so.6.0.33] 36ms 0.71% 71.87% 36ms 0.71% boost::numeric::ublas::c_vector::operator() 18ms 0.36% 72.23% 35ms 0.69% DistributedBoxCollection::CalculateContainingBox (inline) 14ms 0.28% 72.50% 35ms 0.69% _int_free_merge_chunk 0 0% 72.50% 35ms 0.69% std::_Destroy (inline) 35ms 0.69% 73.20% 35ms 0.69% std::_Rb_tree_header::_M_reset (inline) 1ms 0.02% 73.22% 34ms 0.67% std::_Destroy_aux::__destroy (inline) 0 0% 73.22% 34ms 0.67% std::make_unique (inline) 0 0% 73.22% 33ms 0.65% VtkMeshWriter::MakeVtkMesh 33ms 0.65% 73.87% 33ms 0.65% std::codecvt::do_always_noconv 0 0% 73.87% 33ms 0.65% vtk::detail::smp::vtkSMPToolsImplForTBB 32ms 0.63% 74.50% 32ms 0.63% Node::GetNumContainingElements 0 0% 74.50% 32ms 0.63% _IO_new_file_fopen 0 0% 74.50% 32ms 0.63% _IO_new_fopen 1ms 0.02% 74.52% 32ms 0.63% __GI__IO_file_open 0 0% 74.52% 32ms 0.63% __fopen_internal (inline) 1ms 0.02% 74.54% 32ms 0.63% std::_Rb_tree::_M_emplace_hint_unique 17ms 0.34% 74.88% 32ms 0.63% std::__new_allocator::construct (inline) 0 0% 74.88% 32ms 0.63% std::allocator_traits::construct (inline) 0 0% 74.88% 31ms 0.61% Cell::GetMutationState 31ms 0.61% 75.50% 31ms 0.61% __libc_open64 1ms 0.02% 75.52% 31ms 0.61% std::basic_filebuf::open 25ms 0.5% 76.01% 31ms 0.61% std::num_put::do_put 24ms 0.48% 76.49% 31ms 0.61% vtkObject::ObjectFinalize 30ms 0.59% 77.08% 30ms 0.59% __mpn_divrem 5ms 0.099% 77.18% 30ms 0.59% boost::serialization::singleton::get_instance 2ms 0.04% 77.22% 30ms 0.59% tbb::detail::r1::cancel_group_execution 2ms 0.04% 77.26% 29ms 0.57% Node::~Node 0 0% 77.26% 29ms 0.57% NodesOnlyMesh::Clear (inline) 0 0% 77.26% 29ms 0.57% OutputFileHandler::OpenOutputFile 0 0% 77.26% 29ms 0.57% VertexElement::~VertexElement 0 0% 77.26% 29ms 0.57% std::__basic_file::open 29ms 0.57% 77.83% 29ms 0.57% vtkObjectBase::vtkObjectBase 0 0% 77.83% 28ms 0.55% CellProliferativeTypesWriter::GetCellDataForVtkOutput 5ms 0.099% 77.93% 28ms 0.55% Node::GetPoint 28ms 0.55% 78.49% 28ms 0.55% __memset_avx2_unaligned_erms 0 0% 78.49% 28ms 0.55% vtkDataArrayPrivate::DoComputeScalarRange 5ms 0.099% 78.59% 28ms 0.55% vtkDataArrayPrivate::DoComputeVectorRange 0 0% 78.59% 27ms 0.53% BoundaryNodeWriter::VisitAnyPopulation 6ms 0.12% 78.70% 27ms 0.53% __find_specmb (inline) 0 0% 78.70% 27ms 0.53% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 0 0% 78.70% 27ms 0.53% orte_init 27ms 0.53% 79.24% 27ms 0.53% vtkAOSDataArrayTemplate::SetTuple 27ms 0.53% 79.77% 27ms 0.53% vtkBase64Utilities::EncodeTriplet 0 0% 79.77% 27ms 0.53% vtkXMLUnstructuredDataWriter::WriteHeader 0 0% 79.77% 26ms 0.52% VertexMeshWriter::GetNextElement 4ms 0.079% 79.85% 26ms 0.52% vtkAOSDataArrayTemplate::InsertTuple