File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3806ms, 80.81% of 4710ms total Dropped 718 nodes (cum <= 23.55ms) flat flat% sum% cum cum% 0 0% 0% 4500ms 95.54% __libc_start_call_main 0 0% 0% 4500ms 95.54% __libc_start_main_impl 0 0% 0% 4500ms 95.54% _start 0 0% 0% 4482ms 95.16% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4482ms 95.16% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4482ms 95.16% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4482ms 95.16% main 0 0% 0% 4444ms 94.35% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4444ms 94.35% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4444ms 94.35% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4432ms 94.10% AbstractCellBasedSimulation::Solve 0 0% 0% 4141ms 87.92% AbstractCellPopulation::WriteResultsToFiles 13ms 0.28% 0.28% 3925ms 83.33% PottsBasedCellPopulation::WriteVtkResultsToFile 1ms 0.021% 0.3% 1980ms 42.04% VertexMeshWriter::WriteVtkUsingMesh 3ms 0.064% 0.36% 1711ms 36.33% VertexMeshWriter::MakeVtkMesh 1ms 0.021% 0.38% 1268ms 26.92% vtkPolygon::New 1ms 0.021% 0.4% 1266ms 26.88% vtkPolygon::vtkPolygon 8ms 0.17% 0.57% 909ms 19.30% vtkCell::vtkCell 5ms 0.11% 0.68% 780ms 16.56% vtkPoints::New 17ms 0.36% 1.04% 727ms 15.44% vtkPoints::vtkPoints 1ms 0.021% 1.06% 700ms 14.86% VertexMeshWriter::WriteFiles 32ms 0.68% 1.74% 661ms 14.03% operator new 1ms 0.021% 1.76% 655ms 13.91% std::ostream::operator<< (inline) 43ms 0.91% 2.68% 653ms 13.86% std::ostream::_M_insert 187ms 3.97% 6.65% 643ms 13.65% __GI___libc_malloc 3ms 0.064% 6.71% 609ms 12.93% vtkQuad::New 5ms 0.11% 6.82% 604ms 12.82% vtkQuad::vtkQuad 0 0% 6.82% 590ms 12.53% vtkLine::New 11ms 0.23% 7.05% 575ms 12.21% vtkLine::vtkLine 0 0% 7.05% 549ms 11.66% vtkStreamingDemandDrivenPipeline::Update 0 0% 7.05% 549ms 11.66% vtkXMLWriterBase::Write 0 0% 7.05% 548ms 11.63% vtkTriangle::New 0 0% 7.05% 547ms 11.61% vtkDemandDrivenPipeline::ProcessRequest 0 0% 7.05% 547ms 11.61% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 7.05% 545ms 11.57% vtkDemandDrivenPipeline::ExecuteData 0 0% 7.05% 544ms 11.55% vtkExecutive::CallAlgorithm 0 0% 7.05% 543ms 11.53% vtkCompositeDataPipeline::ExecuteData 0 0% 7.05% 543ms 11.53% vtkXMLUnstructuredDataWriter::ProcessRequest 3ms 0.064% 7.11% 541ms 11.49% vtkTriangle::vtkTriangle 45ms 0.96% 8.07% 540ms 11.46% std::num_put::_M_insert_float 0 0% 8.07% 481ms 10.21% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 8.07% 481ms 10.21% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 103ms 2.19% 10.25% 474ms 10.06% __GI___libc_free 26ms 0.55% 10.81% 453ms 9.62% vtkPoints::SetDataType 0 0% 10.81% 433ms 9.19% vtkXMLWriter::WriteBinaryData 0 0% 10.81% 433ms 9.19% vtkXMLWriter::WriteBinaryDataBlock 0 0% 10.81% 433ms 9.19% vtkXMLWriter::WriteBinaryDataInternal 16ms 0.34% 11.15% 428ms 9.09% std::__cxx11::collate::do_transform 0 0% 11.15% 413ms 8.77% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 2ms 0.042% 11.19% 390ms 8.28% ___vsnprintf 1ms 0.021% 11.21% 388ms 8.24% __vsnprintf_internal (inline) 52ms 1.10% 12.31% 381ms 8.09% __printf_buffer 2ms 0.042% 12.36% 381ms 8.09% vtkPolygon::~vtkPolygon 257ms 5.46% 17.81% 373ms 7.92% _int_malloc 227ms 4.82% 22.63% 366ms 7.77% _int_free 0 0% 22.63% 332ms 7.05% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 22.63% 330ms 7.01% VtkMeshWriter::WriteFiles 0 0% 22.63% 315ms 6.69% vtkXMLWriter::WritePointsAppendedData 45ms 0.96% 23.59% 310ms 6.58% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 9ms 0.19% 23.78% 307ms 6.52% __printf_fp_l_buffer 0 0% 23.78% 307ms 6.52% __printf_fp_spec (inline) 3ms 0.064% 23.84% 295ms 6.26% vtkCell::~vtkCell 135ms 2.87% 26.71% 284ms 6.03% __printf_fp_buffer_1 0 0% 26.71% 283ms 6.01% OnLatticeSimulation::UpdateCellLocationsAndTopology 6ms 0.13% 26.84% 283ms 6.01% PottsBasedCellPopulation::UpdateCellLocations 32ms 0.68% 27.52% 277ms 5.88% std::__new_allocator::allocate (inline) 0 0% 27.52% 275ms 5.84% std::allocator_traits::allocate (inline) 5ms 0.11% 27.62% 254ms 5.39% std::__new_allocator::deallocate (inline) 0 0% 27.62% 254ms 5.39% std::allocator_traits::deallocate (inline) 0 0% 27.62% 232ms 4.93% vtkXMLWriter::WriteCompressionBlock 0 0% 27.62% 218ms 4.63% compress2 0 0% 27.62% 218ms 4.63% vtkDataCompressor::Compress 0 0% 27.62% 218ms 4.63% vtkZLibDataCompressor::CompressBuffer 47ms 1% 28.62% 217ms 4.61% crc32 0 0% 28.62% 217ms 4.61% deflate 4ms 0.085% 28.70% 207ms 4.39% vtkBase64OutputStream::Write 17ms 0.36% 29.07% 201ms 4.27% vtkBase64OutputStream::EncodeTriplet 5ms 0.11% 29.17% 194ms 4.12% vtkPoints::~vtkPoints 8ms 0.17% 29.34% 188ms 3.99% vtkFloatArray::New 1ms 0.021% 29.36% 184ms 3.91% tbb::detail::r1::parallel_pipeline 1ms 0.021% 29.38% 180ms 3.82% std::set::set (inline) 13ms 0.28% 29.66% 179ms 3.80% std::_Rb_tree::_Rb_tree 1ms 0.021% 29.68% 177ms 3.76% vtkLine::GetParametricCenter 0 0% 29.68% 176ms 3.74% clone3 0 0% 29.68% 176ms 3.74% start_thread 3ms 0.064% 29.75% 175ms 3.72% vtkIdList::AllocateInternal 94ms 2.00% 31.74% 174ms 3.69% malloc_consolidate 46ms 0.98% 32.72% 170ms 3.61% std::ostream::write 2ms 0.042% 32.76% 165ms 3.50% vtkQuad::~vtkQuad 1ms 0.021% 32.78% 163ms 3.46% tbb::detail::r1::reset 2ms 0.042% 32.82% 162ms 3.44% NodesOnlyMesh::ConstructNodesWithoutMesh 1ms 0.021% 32.85% 161ms 3.42% vtkDataArray::CreateDataArray 0 0% 32.85% 161ms 3.42% vtkFloatArray::vtkFloatArray 11ms 0.23% 33.08% 160ms 3.40% std::vector::_M_default_append 158ms 3.35% 36.43% 159ms 3.38% [libz.so.1.3] 1ms 0.021% 36.45% 158ms 3.35% vtkTypeFloat64Array::~vtkTypeFloat64Array 0 0% 36.45% 154ms 3.27% VertexMesh::~VertexMesh 0 0% 36.45% 153ms 3.25% std::_Rb_tree::_M_create_node (inline) 70ms 1.49% 37.94% 153ms 3.25% tbb::detail::r1::wait_bounded_queue_monitor 10ms 0.21% 38.15% 153ms 3.25% vtkTypeFloat64Array::New 33ms 0.7% 38.85% 152ms 3.23% std::_Rb_tree::_M_erase 2ms 0.042% 38.90% 151ms 3.21% vtkDoubleArray::vtkDoubleArray 0 0% 38.90% 150ms 3.18% VertexMesh::VertexMesh 2ms 0.042% 38.94% 150ms 3.18% vtkTriangle::~vtkTriangle 23ms 0.49% 39.43% 149ms 3.16% std::_Rb_tree::_M_copy (inline) 3ms 0.064% 39.49% 148ms 3.14% std::_Vector_base::_M_deallocate (inline) 0 0% 39.49% 147ms 3.12% std::_Rb_tree::_M_get_node (inline) 1ms 0.021% 39.51% 146ms 3.10% std::_Rb_tree::~_Rb_tree (inline) 56ms 1.19% 40.70% 145ms 3.08% std::basic_filebuf::xsputn 0 0% 40.70% 141ms 2.99% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 40.70% 141ms 2.99% std::vector::~vector (inline) 0 0% 40.70% 140ms 2.97% VertexMesh::GenerateEdgesFromElements (inline) 5ms 0.11% 40.81% 139ms 2.95% MutableElement::BuildEdges 1ms 0.021% 40.83% 137ms 2.91% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 0 0% 40.83% 133ms 2.82% NodeLocationWriter::VisitAnyPopulation 31ms 0.66% 41.49% 132ms 2.80% vtkObject::vtkObject 2ms 0.042% 41.53% 130ms 2.76% std::_Vector_base::_M_allocate (inline) 3ms 0.064% 41.59% 127ms 2.70% vtkTypeFloat64Array::vtkTypeFloat64Array 0 0% 41.59% 123ms 2.61% std::set::~set (inline) 1ms 0.021% 41.61% 122ms 2.59% CellPropertyCollection::GetPropertiesType (inline) 15ms 0.32% 41.93% 121ms 2.57% std::_Rb_tree::_M_clone_node (inline) 0 0% 41.93% 120ms 2.55% vtkIdList::Allocate 2ms 0.042% 41.97% 118ms 2.51% EdgeHelper::GetEdgeFromNodes 45ms 0.96% 42.93% 118ms 2.51% std::__ostream_insert 0 0% 42.93% 116ms 2.46% std::_Rb_tree::_M_drop_node (inline) 1ms 0.021% 42.95% 114ms 2.42% std::operator<< (inline) 0 0% 42.95% 111ms 2.36% EdgeHelper::~EdgeHelper (inline) 0 0% 42.95% 111ms 2.36% std::_Vector_base::~_Vector_base (inline) 0 0% 42.95% 109ms 2.31% std::_Rb_tree::_M_put_node (inline) 108ms 2.29% 45.24% 108ms 2.29% __strcmp_avx2 54ms 1.15% 46.39% 108ms 2.29% vtkTypeFloat64Array::PrintSelf 1ms 0.021% 46.41% 107ms 2.27% AbstractCellProperty::IsSubType (inline) 27ms 0.57% 46.99% 106ms 2.25% __dynamic_cast 47ms 1% 47.98% 100ms 2.12% hack_digit 1ms 0.021% 48.00% 98ms 2.08% std::map::operator[] (partial-inline) 1ms 0.021% 48.03% 98ms 2.08% vtkXMLWriter::WritePointDataAppendedData 0 0% 48.03% 96ms 2.04% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 96ms 2.04% 50.06% 96ms 2.04% unlink_chunk 6ms 0.13% 50.19% 94ms 2.00% _int_free_maybe_consolidate 3ms 0.064% 50.25% 93ms 1.97% vtkFloatArray::~vtkFloatArray 29ms 0.62% 50.87% 91ms 1.93% std::_Rb_tree::_M_lower_bound (inline) 5ms 0.11% 50.98% 85ms 1.80% CellPropertyCollection::HasProperty 9ms 0.19% 51.17% 85ms 1.80% vtkAOSDataArrayTemplate::DataElementChanged 84ms 1.78% 52.95% 84ms 1.78% __GI_sched_yield 0 0% 52.95% 83ms 1.76% Cell::HasCellProperty (inline) 48ms 1.02% 53.97% 83ms 1.76% vtkObjectBase::UnRegisterInternal 19ms 0.4% 54.37% 82ms 1.74% vtkObject::Modified 4ms 0.085% 54.46% 81ms 1.72% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.021% 54.48% 77ms 1.63% AbstractCellProperty::IsType (inline) 49ms 1.04% 55.52% 75ms 1.59% std::basic_streambuf::xsputn 0 0% 55.52% 75ms 1.59% tcache_get (inline) 75ms 1.59% 57.11% 75ms 1.59% tcache_get_n (inline) 3ms 0.064% 57.18% 74ms 1.57% std::vector::push_back (inline) 1ms 0.021% 57.20% 73ms 1.55% vtkIdList::New 0 0% 57.20% 67ms 1.42% std::_Rb_tree::lower_bound (inline) 0 0% 57.20% 67ms 1.42% std::map::lower_bound (inline) 1ms 0.021% 57.22% 66ms 1.40% vtkDoubleArray::~vtkDoubleArray 1ms 0.021% 57.24% 65ms 1.38% Cell::GetCellProliferativeType 0 0% 57.24% 65ms 1.38% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 3ms 0.064% 57.30% 63ms 1.34% boost::numeric::ublas::c_vector::c_vector (inline) 7ms 0.15% 57.45% 62ms 1.32% AbstractCellProperty::IsSame 4ms 0.085% 57.54% 60ms 1.27% vtkDataArray::vtkDataArray 0 0% 57.54% 59ms 1.25% NodesOnlyMesh::SetUpBoxCollection 0 0% 57.54% 58ms 1.23% boost::numeric::ublas::vector_assign (inline) 37ms 0.79% 58.32% 58ms 1.23% std::_Hashtable::clear 58ms 1.23% 59.55% 58ms 1.23% vtkTimeStamp::Modified 30ms 0.64% 60.19% 56ms 1.19% __cxxabiv1::__si_class_type_info::__do_dyncast 14ms 0.3% 60.49% 56ms 1.19% vtkAbstractArray::vtkAbstractArray 0 0% 60.49% 55ms 1.17% NodesOnlyMesh::~NodesOnlyMesh 14ms 0.3% 60.79% 55ms 1.17% std::type_info::operator== (inline) 1ms 0.021% 60.81% 54ms 1.15% std::_Rb_tree::_M_insert_unique 0 0% 60.81% 54ms 1.15% std::set::insert (inline) 53ms 1.13% 61.93% 53ms 1.13% __memcpy_avx_unaligned_erms 0 0% 61.93% 52ms 1.10% PottsMesh::GetMooreNeighbouringNodeIndices 5ms 0.11% 62.04% 48ms 1.02% VertexMeshWriter::GetNextNode 10ms 0.21% 62.25% 48ms 1.02% vtkDataArray::~vtkDataArray 16ms 0.34% 62.59% 47ms 1% boost::numeric::ublas::indexing_vector_assign 0 0% 62.59% 46ms 0.98% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 46ms 0.98% 63.57% 46ms 0.98% __GI___writev 0 0% 63.57% 46ms 0.98% std::__basic_file::xsputn_2 4ms 0.085% 63.65% 46ms 0.98% std::vector::_M_realloc_insert 4ms 0.085% 63.74% 45ms 0.96% std::num_put::_M_insert_int 44ms 0.93% 64.67% 44ms 0.93% [libstdc++.so.6.0.33] 12ms 0.25% 64.93% 44ms 0.93% vtkIdList::~vtkIdList 44ms 0.93% 65.86% 44ms 0.93% vtkObjectBase::~vtkObjectBase 4ms 0.085% 65.94% 44ms 0.93% vtkSOADataArrayTemplate::FillTypedComponent 2ms 0.042% 65.99% 43ms 0.91% VertexMesh::Clear 43ms 0.91% 66.90% 43ms 0.91% std::codecvt::do_always_noconv 43ms 0.91% 67.81% 43ms 0.91% std::ostream::sentry::sentry 0 0% 67.81% 43ms 0.91% vtkDataArray::ComputeRange 27ms 0.57% 68.39% 42ms 0.89% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 68.39% 42ms 0.89% DistributedBoxCollection::IsOwned 6ms 0.13% 68.51% 42ms 0.89% std::_Rb_tree::_M_insert_ (inline) 1ms 0.021% 68.54% 41ms 0.87% DistributedBoxCollection::SetupLocalBoxesHalfOnly 2ms 0.042% 68.58% 40ms 0.85% std::less::operator() (inline) 39ms 0.83% 69.41% 39ms 0.83% __mpn_divrem 4ms 0.085% 69.49% 39ms 0.83% vtkDoubleArray::New 39ms 0.83% 70.32% 39ms 0.83% vtkObject::~vtkObject 38ms 0.81% 71.13% 38ms 0.81% std::operator< (inline) 36ms 0.76% 71.89% 38ms 0.81% vtkObjectBase::Delete 0 0% 71.89% 37ms 0.79% _dl_init 0 0% 71.89% 37ms 0.79% call_init (inline) 1ms 0.021% 71.91% 36ms 0.76% VtkMeshWriter::MakeVtkMesh 36ms 0.76% 72.68% 36ms 0.76% [libvtkCommonCore-9.3.so.9.3] 36ms 0.76% 73.44% 36ms 0.76% __GI___libc_write 0 0% 73.44% 36ms 0.76% std::__basic_file::xsputn 0 0% 73.44% 36ms 0.76% std::basic_filebuf::_M_convert_to_external 0 0% 73.44% 36ms 0.76% std::basic_filebuf::overflow 35ms 0.74% 74.18% 35ms 0.74% boost::numeric::ublas::c_vector::operator() 0 0% 74.18% 35ms 0.74% std::_Destroy (inline) 0 0% 74.18% 35ms 0.74% std::_Destroy_aux::__destroy (inline) 0 0% 74.18% 35ms 0.74% vtkDataArrayPrivate::DoComputeVectorRange 35ms 0.74% 74.93% 35ms 0.74% vtkObjectBase::vtkObjectBase 0 0% 74.93% 34ms 0.72% CxxTest::RealWorldDescription::setUp 0 0% 74.93% 34ms 0.72% PetscInitialize 0 0% 74.93% 34ms 0.72% PetscSetup::setUpWorld 0 0% 74.93% 34ms 0.72% PetscSetupUtils::CommonSetup 0 0% 74.93% 34ms 0.72% PetscSetupUtils::InitialisePetsc 0 0% 74.93% 34ms 0.72% _dl_start_user 31ms 0.66% 75.58% 34ms 0.72% vtkObject::ObjectFinalize 0 0% 75.58% 33ms 0.7% Cell::GetCellId 0 0% 75.58% 33ms 0.7% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 75.58% 33ms 0.7% PMPI_Init_thread 0 0% 75.58% 33ms 0.7% ompi_mpi_init 0 0% 75.58% 32ms 0.68% DistributedBoxCollection::~DistributedBoxCollection 2ms 0.042% 75.63% 32ms 0.68% boost::serialization::singleton::get_instance 0 0% 75.63% 32ms 0.68% std::make_unique (inline) 0 0% 75.63% 32ms 0.68% vtk::detail::smp::vtkSMPToolsImplForTBB 5ms 0.11% 75.73% 32ms 0.68% vtkAOSDataArrayTemplate::AllocateTuples 0 0% 75.73% 31ms 0.66% Cell::GetMutationState 1ms 0.021% 75.75% 31ms 0.66% CellProliferativeTypesWriter::GetCellDataForVtkOutput 14ms 0.3% 76.05% 31ms 0.66% _int_free_merge_chunk 5ms 0.11% 76.16% 31ms 0.66% vtk::detail::smp::vtkSMPToolsImpl::For 0 0% 76.16% 30ms 0.64% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 1ms 0.021% 76.18% 30ms 0.64% std::_Rb_tree::_M_emplace_hint_unique 10ms 0.21% 76.39% 30ms 0.64% vtkIdList::vtkIdList 2ms 0.042% 76.43% 29ms 0.62% 0 0% 76.43% 29ms 0.62% CellIdWriter::GetCellDataForVtkOutput 29ms 0.62% 77.05% 29ms 0.62% Node::GetIndex 0 0% 77.05% 29ms 0.62% boost::numeric::ublas::c_vector::assign (inline) 4ms 0.085% 77.13% 28ms 0.59% tbb::detail::r1::cancel_group_execution 0 0% 77.13% 28ms 0.59% vtkXMLUnstructuredDataWriter::WriteHeader 27ms 0.57% 77.71% 27ms 0.57% std::_Rb_tree::_S_right (inline) 24ms 0.51% 78.22% 27ms 0.57% std::num_put::do_put 2ms 0.042% 78.26% 27ms 0.57% vtkAOSDataArrayTemplate::InsertTuple 27ms 0.57% 78.83% 27ms 0.57% vtkDataArray::Modified 0 0% 78.83% 27ms 0.57% vtkSOADataArrayTemplate::GetTupleIndexFromValueIndex 0 0% 78.83% 26ms 0.55% _IO_new_file_fopen 0 0% 78.83% 26ms 0.55% _IO_new_fopen 0 0% 78.83% 26ms 0.55% __GI__IO_file_open 0 0% 78.83% 26ms 0.55% __fopen_internal (inline) 26ms 0.55% 79.38% 26ms 0.55% __libc_open64 26ms 0.55% 79.94% 26ms 0.55% __memset_avx2_unaligned_erms 0 0% 79.94% 26ms 0.55% std::__basic_file::open 1ms 0.021% 79.96% 26ms 0.55% std::__new_allocator::construct (inline) 0 0% 79.96% 26ms 0.55% std::allocator_traits::construct (inline) 0 0% 79.96% 26ms 0.55% std::basic_filebuf::open 0 0% 79.96% 26ms 0.55% std::basic_filebuf::sync 0 0% 79.96% 26ms 0.55% std::ostream::flush 4ms 0.085% 80.04% 25ms 0.53% Node::GetPoint 1ms 0.021% 80.06% 25ms 0.53% OutputFileHandler::OpenOutputFile 2ms 0.042% 80.11% 25ms 0.53% VertexElement::VertexElement 1ms 0.021% 80.13% 25ms 0.53% std::_Rb_tree::find (inline) 0 0% 80.13% 25ms 0.53% std::map::find (inline) 1ms 0.021% 80.15% 25ms 0.53% std::unique_ptr::~unique_ptr (inline) 4ms 0.085% 80.23% 25ms 0.53% std::vector::emplace_back (inline) 0 0% 80.23% 25ms 0.53% std::vector::vector (inline) 2ms 0.042% 80.28% 24ms 0.51% AbstractTetrahedralMeshWriter::GetNextNode 1ms 0.021% 80.30% 24ms 0.51% boost::serialization::void_cast_detail::void_caster::recursive_register 0 0% 80.30% 24ms 0.51% boost::serialization::void_cast_detail::void_caster_primitive::void_caster_primitive (inline) 24ms 0.51% 80.81% 24ms 0.51% operator delete 0 0% 80.81% 24ms 0.51% std::default_delete::operator() (inline)