File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3718ms, 78.75% of 4721ms total Dropped 681 nodes (cum <= 23.61ms) flat flat% sum% cum cum% 0 0% 0% 4505ms 95.42% __libc_start_call_main 0 0% 0% 4505ms 95.42% __libc_start_main_impl 0 0% 0% 4505ms 95.42% _start 0 0% 0% 4490ms 95.11% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4490ms 95.11% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4490ms 95.11% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4490ms 95.11% main 0 0% 0% 4454ms 94.34% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4454ms 94.34% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4454ms 94.34% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4442ms 94.09% AbstractCellBasedSimulation::Solve 0 0% 0% 4194ms 88.84% AbstractCellPopulation::WriteResultsToFiles 7ms 0.15% 0.15% 3958ms 83.84% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.15% 1957ms 41.45% VertexMeshWriter::WriteVtkUsingMesh 0 0% 0.15% 1694ms 35.88% VertexMeshWriter::MakeVtkMesh 0 0% 0.15% 1268ms 26.86% vtkPolygon::New 6ms 0.13% 0.28% 1268ms 26.86% vtkPolygon::vtkPolygon 5ms 0.11% 0.38% 919ms 19.47% vtkCell::vtkCell 6ms 0.13% 0.51% 788ms 16.69% vtkPoints::New 1ms 0.021% 0.53% 770ms 16.31% VertexMeshWriter::WriteFiles 0 0% 0.53% 761ms 16.12% std::ostream::operator<< (inline) 62ms 1.31% 1.84% 760ms 16.10% std::ostream::_M_insert 8ms 0.17% 2.01% 746ms 15.80% vtkPoints::vtkPoints 41ms 0.87% 2.88% 646ms 13.68% operator new 201ms 4.26% 7.14% 618ms 13.09% __GI___libc_malloc 42ms 0.89% 8.03% 613ms 12.98% std::num_put::_M_insert_float 2ms 0.042% 8.07% 600ms 12.71% vtkLine::New 3ms 0.064% 8.13% 593ms 12.56% vtkQuad::New 12ms 0.25% 8.39% 588ms 12.45% vtkLine::vtkLine 3ms 0.064% 8.45% 588ms 12.45% vtkQuad::vtkQuad 0 0% 8.45% 572ms 12.12% vtkStreamingDemandDrivenPipeline::Update 0 0% 8.45% 572ms 12.12% vtkXMLWriterBase::Write 1ms 0.021% 8.47% 570ms 12.07% vtkDemandDrivenPipeline::ProcessRequest 0 0% 8.47% 567ms 12.01% vtkExecutive::CallAlgorithm 0 0% 8.47% 566ms 11.99% vtkStreamingDemandDrivenPipeline::ProcessRequest 1ms 0.021% 8.49% 566ms 11.99% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 8.49% 565ms 11.97% vtkCompositeDataPipeline::ExecuteData 0 0% 8.49% 565ms 11.97% vtkDemandDrivenPipeline::ExecuteData 1ms 0.021% 8.52% 532ms 11.27% vtkTriangle::New 9ms 0.19% 8.71% 526ms 11.14% vtkTriangle::vtkTriangle 143ms 3.03% 11.73% 508ms 10.76% __GI___libc_free 0 0% 11.73% 507ms 10.74% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 11.73% 507ms 10.74% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 7ms 0.15% 11.88% 481ms 10.19% std::__cxx11::collate::do_transform 26ms 0.55% 12.43% 481ms 10.19% vtkPoints::SetDataType 6ms 0.13% 12.56% 459ms 9.72% ___vsnprintf 0 0% 12.56% 455ms 9.64% vtkXMLWriter::WriteBinaryData 0 0% 12.56% 453ms 9.60% __vsnprintf_internal (inline) 2ms 0.042% 12.60% 446ms 9.45% vtkXMLWriter::WriteBinaryDataInternal 0 0% 12.60% 444ms 9.40% vtkXMLWriter::WriteBinaryDataBlock 62ms 1.31% 13.92% 443ms 9.38% __printf_buffer 0 0% 13.92% 428ms 9.07% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 13.92% 393ms 8.32% vtkPolygon::~vtkPolygon 237ms 5.02% 18.94% 365ms 7.73% _int_free 1ms 0.021% 18.96% 353ms 7.48% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 241ms 5.10% 24.06% 352ms 7.46% _int_malloc 4ms 0.085% 24.15% 347ms 7.35% __printf_fp_spec (inline) 0 0% 24.15% 346ms 7.33% VtkMeshWriter::WriteFiles 15ms 0.32% 24.47% 343ms 7.27% __printf_fp_l_buffer 0 0% 24.47% 322ms 6.82% vtkXMLWriter::WritePointsAppendedData 4ms 0.085% 24.55% 314ms 6.65% vtkCell::~vtkCell 170ms 3.60% 28.15% 310ms 6.57% __printf_fp_buffer_1 49ms 1.04% 29.19% 299ms 6.33% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 23ms 0.49% 29.68% 265ms 5.61% std::__new_allocator::allocate (inline) 6ms 0.13% 29.80% 264ms 5.59% std::__new_allocator::deallocate (inline) 0 0% 29.80% 263ms 5.57% std::allocator_traits::allocate (inline) 0 0% 29.80% 263ms 5.57% std::allocator_traits::deallocate (inline) 0 0% 29.80% 240ms 5.08% OnLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.021% 29.82% 240ms 5.08% PottsBasedCellPopulation::UpdateCellLocations 1ms 0.021% 29.85% 228ms 4.83% vtkXMLWriter::WriteCompressionBlock 7ms 0.15% 29.99% 223ms 4.72% vtkBase64OutputStream::Write 0 0% 29.99% 218ms 4.62% vtkDataCompressor::Compress 0 0% 29.99% 216ms 4.58% compress2 22ms 0.47% 30.46% 216ms 4.58% vtkBase64OutputStream::EncodeTriplet 0 0% 30.46% 216ms 4.58% vtkZLibDataCompressor::CompressBuffer 56ms 1.19% 31.65% 215ms 4.55% crc32 0 0% 31.65% 215ms 4.55% deflate 3ms 0.064% 31.71% 208ms 4.41% vtkPoints::~vtkPoints 10ms 0.21% 31.92% 194ms 4.11% vtkFloatArray::New 0 0% 31.92% 187ms 3.96% tbb::detail::r1::parallel_pipeline 55ms 1.17% 33.09% 182ms 3.86% std::ostream::write 0 0% 33.09% 181ms 3.83% clone3 0 0% 33.09% 181ms 3.83% start_thread 0 0% 33.09% 177ms 3.75% vtkQuad::~vtkQuad 0 0% 33.09% 176ms 3.73% tbb::detail::r1::reset 0 0% 33.09% 176ms 3.73% vtkTriangle::~vtkTriangle 85ms 1.80% 34.89% 174ms 3.69% tbb::detail::r1::wait_bounded_queue_monitor 8ms 0.17% 35.06% 172ms 3.64% vtkIdList::AllocateInternal 2ms 0.042% 35.10% 169ms 3.58% vtkFloatArray::vtkFloatArray 6ms 0.13% 35.23% 168ms 3.56% vtkTypeFloat64Array::~vtkTypeFloat64Array 100ms 2.12% 37.34% 165ms 3.50% malloc_consolidate 1ms 0.021% 37.36% 160ms 3.39% vtkLine::GetParametricCenter 2ms 0.042% 37.41% 155ms 3.28% NodesOnlyMesh::ConstructNodesWithoutMesh 0 0% 37.41% 155ms 3.28% VertexMesh::VertexMesh 2ms 0.042% 37.45% 154ms 3.26% std::_Vector_base::_M_deallocate (inline) 3ms 0.064% 37.51% 154ms 3.26% vtkDataArray::CreateDataArray 147ms 3.11% 40.63% 150ms 3.18% [libz.so.1.3] 0 0% 40.63% 149ms 3.16% NodeLocationWriter::VisitAnyPopulation 70ms 1.48% 42.11% 147ms 3.11% std::basic_filebuf::xsputn 0 0% 42.11% 145ms 3.07% VertexMesh::GenerateEdgesFromElements (inline) 9ms 0.19% 42.30% 144ms 3.05% MutableElement::BuildEdges 9ms 0.19% 42.49% 144ms 3.05% vtkTypeFloat64Array::New 9ms 0.19% 42.68% 142ms 3.01% std::vector::_M_default_append 0 0% 42.68% 142ms 3.01% std::vector::~vector (inline) 19ms 0.4% 43.08% 141ms 2.99% std::_Rb_tree::_M_erase 1ms 0.021% 43.11% 140ms 2.97% std::set::set (inline) 6ms 0.13% 43.23% 139ms 2.94% std::_Rb_tree::_Rb_tree 2ms 0.042% 43.27% 137ms 2.90% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.042% 43.32% 137ms 2.90% vtkFloatArray::~vtkFloatArray 0 0% 43.32% 136ms 2.88% std::_Vector_base::_M_allocate (inline) 0 0% 43.32% 135ms 2.86% std::_Rb_tree::_M_create_node (inline) 0 0% 43.32% 130ms 2.75% vtkDoubleArray::vtkDoubleArray 0 0% 43.32% 129ms 2.73% VertexMesh::~VertexMesh 0 0% 43.32% 127ms 2.69% std::_Rb_tree::_M_get_node (inline) 2ms 0.042% 43.36% 125ms 2.65% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 0 0% 43.36% 125ms 2.65% std::_Rb_tree::_Alloc_node::operator() (inline) 4ms 0.085% 43.44% 118ms 2.50% vtkTypeFloat64Array::vtkTypeFloat64Array 0 0% 43.44% 117ms 2.48% std::_Rb_tree::_M_drop_node (inline) 0 0% 43.44% 117ms 2.48% std::set::~set (inline) 1ms 0.021% 43.47% 116ms 2.46% std::_Vector_base::~_Vector_base (inline) 2ms 0.042% 43.51% 114ms 2.41% CellPropertyCollection::GetPropertiesType (inline) 2ms 0.042% 43.55% 114ms 2.41% EdgeHelper::GetEdgeFromNodes 15ms 0.32% 43.87% 114ms 2.41% std::_Rb_tree::_M_copy (inline) 26ms 0.55% 44.42% 114ms 2.41% vtkObject::vtkObject 0 0% 44.42% 113ms 2.39% vtkIdList::Allocate 0 0% 44.42% 111ms 2.35% std::_Rb_tree::_M_put_node (inline) 107ms 2.27% 46.69% 107ms 2.27% __strcmp_avx2 0 0% 46.69% 106ms 2.25% vtkXMLWriter::WritePointDataAppendedData 38ms 0.8% 47.49% 105ms 2.22% std::__ostream_insert 46ms 0.97% 48.46% 103ms 2.18% vtkTypeFloat64Array::PrintSelf 5ms 0.11% 48.57% 101ms 2.14% std::operator<< (inline) 0 0% 48.57% 97ms 2.05% EdgeHelper::~EdgeHelper (inline) 9ms 0.19% 48.76% 95ms 2.01% std::_Rb_tree::_M_clone_node (inline) 6ms 0.13% 48.89% 94ms 1.99% vtkAOSDataArrayTemplate::DataElementChanged 2ms 0.042% 48.93% 93ms 1.97% AbstractCellProperty::IsSubType (inline) 64ms 1.36% 50.29% 92ms 1.95% std::basic_streambuf::xsputn 21ms 0.44% 50.73% 91ms 1.93% __dynamic_cast 52ms 1.10% 51.83% 91ms 1.93% vtkObjectBase::UnRegisterInternal 90ms 1.91% 53.74% 90ms 1.91% __GI_sched_yield 7ms 0.15% 53.89% 90ms 1.91% _int_free_maybe_consolidate 3ms 0.064% 53.95% 90ms 1.91% std::vector::push_back (inline) 7ms 0.15% 54.10% 89ms 1.89% vtkDoubleArray::~vtkDoubleArray 0 0% 54.10% 88ms 1.86% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 3ms 0.064% 54.16% 88ms 1.86% std::map::operator[] (partial-inline) 85ms 1.80% 55.96% 85ms 1.80% unlink_chunk 47ms 1% 56.96% 83ms 1.76% hack_digit 0 0% 56.96% 82ms 1.74% Cell::HasCellProperty (inline) 4ms 0.085% 57.04% 82ms 1.74% CellPropertyCollection::HasProperty 4ms 0.085% 57.13% 82ms 1.74% vtkIdList::New 27ms 0.57% 57.70% 78ms 1.65% vtkObject::Modified 0 0% 57.70% 78ms 1.65% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 3ms 0.064% 57.76% 75ms 1.59% AbstractCellProperty::IsType (inline) 7ms 0.15% 57.91% 74ms 1.57% std::vector::_M_realloc_insert 19ms 0.4% 58.31% 73ms 1.55% std::_Rb_tree::_M_lower_bound (inline) 0 0% 58.31% 65ms 1.38% Cell::GetCellProliferativeType 4ms 0.085% 58.40% 65ms 1.38% boost::numeric::ublas::c_vector::c_vector (inline) 3ms 0.064% 58.46% 63ms 1.33% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 58.46% 62ms 1.31% boost::numeric::ublas::vector_assign (inline) 4ms 0.085% 58.55% 62ms 1.31% std::_Rb_tree::_M_insert_unique 18ms 0.38% 58.93% 62ms 1.31% std::num_put::_M_insert_int 0 0% 58.93% 62ms 1.31% std::set::insert (inline) 0 0% 58.93% 61ms 1.29% NodesOnlyMesh::~NodesOnlyMesh 7ms 0.15% 59.08% 60ms 1.27% vtkDataArray::vtkDataArray 0 0% 59.08% 57ms 1.21% std::_Rb_tree::lower_bound (inline) 0 0% 59.08% 57ms 1.21% std::map::lower_bound (inline) 0 0% 59.08% 56ms 1.19% tcache_get (inline) 56ms 1.19% 60.26% 56ms 1.19% tcache_get_n (inline) 0 0% 60.26% 55ms 1.17% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 39ms 0.83% 61.09% 54ms 1.14% std::_Hashtable::clear 9ms 0.19% 61.28% 53ms 1.12% AbstractCellProperty::IsSame 0 0% 61.28% 52ms 1.10% NodesOnlyMesh::SetUpBoxCollection 7ms 0.15% 61.43% 51ms 1.08% vtkSOADataArrayTemplate::FillTypedComponent 50ms 1.06% 62.49% 50ms 1.06% vtkObjectBase::~vtkObjectBase 49ms 1.04% 63.52% 49ms 1.04% [libvtkCommonCore-9.3.so.9.3] 49ms 1.04% 64.56% 49ms 1.04% __memcpy_avx_unaligned_erms 5ms 0.11% 64.67% 49ms 1.04% std::_Rb_tree::_M_insert_ (inline) 49ms 1.04% 65.71% 49ms 1.04% std::ostream::sentry::sentry 49ms 1.04% 66.74% 49ms 1.04% vtkObject::~vtkObject 27ms 0.57% 67.32% 48ms 1.02% __cxxabiv1::__si_class_type_info::__do_dyncast 16ms 0.34% 67.66% 48ms 1.02% vtkAbstractArray::vtkAbstractArray 45ms 0.95% 68.61% 45ms 0.95% __GI___writev 14ms 0.3% 68.90% 45ms 0.95% boost::numeric::ublas::indexing_vector_assign 0 0% 68.90% 45ms 0.95% std::__basic_file::xsputn_2 45ms 0.95% 69.86% 45ms 0.95% vtkTimeStamp::Modified 11ms 0.23% 70.09% 44ms 0.93% std::type_info::operator== (inline) 0 0% 70.09% 44ms 0.93% vtkDataArray::ComputeRange 0 0% 70.09% 42ms 0.89% DistributedBoxCollection::~DistributedBoxCollection 0 0% 70.09% 42ms 0.89% NodesOnlyMesh::ClearBoxCollection (inline) 41ms 0.87% 70.96% 41ms 0.87% boost::numeric::ublas::c_vector::operator() 1ms 0.021% 70.98% 39ms 0.83% DistributedBoxCollection::IsOwned 9ms 0.19% 71.17% 39ms 0.83% vtkIdList::~vtkIdList 22ms 0.47% 71.64% 38ms 0.8% DistributedBoxCollection::CalculateContainingBox (inline) 2ms 0.042% 71.68% 38ms 0.8% PottsMesh::GetMooreNeighbouringNodeIndices 0 0% 71.68% 38ms 0.8% std::_Destroy (inline) 0 0% 71.68% 38ms 0.8% std::_Destroy_aux::__destroy (inline) 0 0% 71.68% 36ms 0.76% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 71.68% 36ms 0.76% std::make_unique (inline) 28ms 0.59% 72.27% 36ms 0.76% vtkObject::ObjectFinalize 1ms 0.021% 72.29% 35ms 0.74% Cell::GetMutationState 0 0% 72.29% 35ms 0.74% PottsBasedCellPopulation::AcceptCellWriter 0 0% 72.29% 35ms 0.74% _dl_init 0 0% 72.29% 35ms 0.74% _dl_start_user 0 0% 72.29% 35ms 0.74% call_init (inline) 0 0% 72.29% 34ms 0.72% CellProliferativeTypesWriter::GetCellDataForVtkOutput 1ms 0.021% 72.32% 34ms 0.72% std::less::operator() (inline) 4ms 0.085% 72.40% 34ms 0.72% vtkDataArray::~vtkDataArray 34ms 0.72% 73.12% 34ms 0.72% vtkObjectBase::Delete 33ms 0.7% 73.82% 33ms 0.7% std::operator< (inline) 1ms 0.021% 73.84% 33ms 0.7% vtkDoubleArray::New 33ms 0.7% 74.54% 33ms 0.7% vtkObjectBase::vtkObjectBase 0 0% 74.54% 32ms 0.68% CxxTest::RealWorldDescription::setUp 1ms 0.021% 74.56% 32ms 0.68% Edge::Edge 0 0% 74.56% 32ms 0.68% PMPI_Init_thread 0 0% 74.56% 32ms 0.68% PetscInitialize 0 0% 74.56% 32ms 0.68% PetscSetup::setUpWorld 0 0% 74.56% 32ms 0.68% PetscSetupUtils::CommonSetup 0 0% 74.56% 32ms 0.68% PetscSetupUtils::InitialisePetsc 0 0% 74.56% 32ms 0.68% VertexMesh::Clear 0 0% 74.56% 32ms 0.68% ompi_mpi_init 32ms 0.68% 75.24% 32ms 0.68% std::codecvt::do_always_noconv 27ms 0.57% 75.81% 32ms 0.68% std::num_put::do_put 0 0% 75.81% 32ms 0.68% vtk::detail::smp::vtkSMPToolsImplForTBB 2ms 0.042% 75.85% 32ms 0.68% vtkAOSDataArrayTemplate::InsertTuple 0 0% 75.85% 31ms 0.66% Edge::SetNodes (inline) 8ms 0.17% 76.02% 31ms 0.66% __find_specmb (inline) 2ms 0.042% 76.06% 31ms 0.66% vtkDataArrayPrivate::DoComputeVectorRange 4ms 0.085% 76.15% 30ms 0.64% VertexMeshWriter::GetNextNode 29ms 0.61% 76.76% 30ms 0.64% vtkDataArray::Modified 1ms 0.021% 76.78% 29ms 0.61% VtkMeshWriter::MakeVtkMesh 4ms 0.085% 76.87% 29ms 0.61% boost::serialization::singleton::get_instance 1ms 0.021% 76.89% 29ms 0.61% std::basic_filebuf::overflow 8ms 0.17% 77.06% 29ms 0.61% vtkIdList::vtkIdList 0 0% 77.06% 28ms 0.59% Cell::GetCellId 1ms 0.021% 77.08% 28ms 0.59% DistributedBoxCollection::SetupLocalBoxesHalfOnly 28ms 0.59% 77.67% 28ms 0.59% __GI___libc_write 0 0% 77.67% 28ms 0.59% std::_Rb_tree::_M_emplace_hint_unique 0 0% 77.67% 28ms 0.59% std::__basic_file::xsputn 0 0% 77.67% 28ms 0.59% std::basic_filebuf::_M_convert_to_external 1ms 0.021% 77.70% 28ms 0.59% std::default_delete::operator() (inline) 0 0% 77.70% 28ms 0.59% std::unique_ptr::~unique_ptr (inline) 1ms 0.021% 77.72% 28ms 0.59% tbb::detail::r1::cancel_group_execution 5ms 0.11% 77.82% 28ms 0.59% vtk::detail::smp::vtkSMPToolsImpl::For 1ms 0.021% 77.84% 27ms 0.57% 9ms 0.19% 78.03% 27ms 0.57% _int_free_merge_chunk 1ms 0.021% 78.06% 27ms 0.57% std::vector::emplace_back (inline) 2ms 0.042% 78.10% 27ms 0.57% vtkAOSDataArrayTemplate::AllocateTuples 0 0% 78.10% 26ms 0.55% Node::ConstructNodeAttributes (inline) 0 0% 78.10% 26ms 0.55% Node::SetRadius 0 0% 78.10% 25ms 0.53% CellIdWriter::GetCellDataForVtkOutput 0 0% 78.10% 25ms 0.53% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 25ms 0.53% 78.63% 25ms 0.53% std::_Rb_tree::_S_right (inline) 6ms 0.13% 78.75% 25ms 0.53% vtkSOADataArrayTemplate::GetTupleIndexFromValueIndex 0 0% 78.75% 24ms 0.51% vtkXMLUnstructuredDataWriter::WriteHeader