File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3916ms, 78.98% of 4958ms total Dropped 770 nodes (cum <= 24.79ms) flat flat% sum% cum cum% 0 0% 0% 4708ms 94.96% __libc_start_call_main 0 0% 0% 4708ms 94.96% __libc_start_main_impl 0 0% 0% 4708ms 94.96% _start 0 0% 0% 4691ms 94.61% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4691ms 94.61% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4691ms 94.61% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4691ms 94.61% main 0 0% 0% 4650ms 93.79% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4650ms 93.79% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4650ms 93.79% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4640ms 93.59% AbstractCellBasedSimulation::Solve 2ms 0.04% 0.04% 4325ms 87.23% AbstractCellPopulation::WriteResultsToFiles 11ms 0.22% 0.26% 4092ms 82.53% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.26% 1984ms 40.02% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.02% 0.28% 1705ms 34.39% VertexMeshWriter::MakeVtkMesh 1ms 0.02% 0.3% 1279ms 25.80% vtkPolygon::New 1ms 0.02% 0.32% 1278ms 25.78% vtkPolygon::vtkPolygon 5ms 0.1% 0.42% 926ms 18.68% vtkCell::vtkCell 0 0% 0.42% 784ms 15.81% VertexMeshWriter::WriteFiles 2ms 0.04% 0.46% 774ms 15.61% vtkPoints::New 2ms 0.04% 0.5% 744ms 15.01% std::ostream::operator<< (inline) 47ms 0.95% 1.45% 741ms 14.95% std::ostream::_M_insert 13ms 0.26% 1.71% 724ms 14.60% vtkPoints::vtkPoints 46ms 0.93% 2.64% 702ms 14.16% operator new 211ms 4.26% 6.90% 660ms 13.31% __GI___libc_malloc 4ms 0.081% 6.98% 627ms 12.65% vtkLine::New 41ms 0.83% 7.81% 622ms 12.55% std::num_put::_M_insert_float 0 0% 7.81% 609ms 12.28% vtkQuad::New 3ms 0.061% 7.87% 606ms 12.22% vtkQuad::vtkQuad 10ms 0.2% 8.07% 604ms 12.18% vtkLine::vtkLine 0 0% 8.07% 599ms 12.08% vtkXMLWriterBase::Write 0 0% 8.07% 598ms 12.06% vtkStreamingDemandDrivenPipeline::Update 0 0% 8.07% 597ms 12.04% vtkDemandDrivenPipeline::ProcessRequest 1ms 0.02% 8.09% 594ms 11.98% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 8.09% 592ms 11.94% vtkDemandDrivenPipeline::ExecuteData 0 0% 8.09% 591ms 11.92% vtkCompositeDataPipeline::ExecuteData 0 0% 8.09% 591ms 11.92% vtkExecutive::CallAlgorithm 0 0% 8.09% 591ms 11.92% vtkXMLUnstructuredDataWriter::ProcessRequest 1ms 0.02% 8.11% 586ms 11.82% vtkTriangle::New 4ms 0.081% 8.19% 577ms 11.64% vtkTriangle::vtkTriangle 161ms 3.25% 11.44% 542ms 10.93% __GI___libc_free 0 0% 11.44% 512ms 10.33% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 11.44% 512ms 10.33% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 9ms 0.18% 11.62% 487ms 9.82% std::__cxx11::collate::do_transform 25ms 0.5% 12.12% 467ms 9.42% vtkPoints::SetDataType 7ms 0.14% 12.26% 458ms 9.24% ___vsnprintf 2ms 0.04% 12.30% 457ms 9.22% vtkXMLWriter::WriteBinaryData 1ms 0.02% 12.32% 452ms 9.12% __vsnprintf_internal (inline) 0 0% 12.32% 445ms 8.98% vtkXMLWriter::WriteBinaryDataInternal 69ms 1.39% 13.72% 443ms 8.94% __printf_buffer 0 0% 13.72% 442ms 8.91% vtkXMLWriter::WriteBinaryDataBlock 0 0% 13.72% 433ms 8.73% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 241ms 4.86% 18.58% 381ms 7.68% _int_free 0 0% 18.58% 380ms 7.66% vtkPolygon::~vtkPolygon 265ms 5.34% 23.92% 379ms 7.64% _int_malloc 1ms 0.02% 23.94% 365ms 7.36% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 2ms 0.04% 23.98% 364ms 7.34% VtkMeshWriter::WriteFiles 1ms 0.02% 24.00% 331ms 6.68% __printf_fp_spec (inline) 17ms 0.34% 24.34% 330ms 6.66% __printf_fp_l_buffer 1ms 0.02% 24.36% 316ms 6.37% vtkXMLWriter::WritePointsAppendedData 0 0% 24.36% 309ms 6.23% OnLatticeSimulation::UpdateCellLocationsAndTopology 4ms 0.081% 24.45% 309ms 6.23% PottsBasedCellPopulation::UpdateCellLocations 140ms 2.82% 27.27% 299ms 6.03% __printf_fp_buffer_1 39ms 0.79% 28.06% 297ms 5.99% std::__new_allocator::allocate (inline) 0 0% 28.06% 295ms 5.95% std::allocator_traits::allocate (inline) 2ms 0.04% 28.10% 289ms 5.83% vtkCell::~vtkCell 5ms 0.1% 28.20% 282ms 5.69% std::__new_allocator::deallocate (inline) 0 0% 28.20% 278ms 5.61% std::allocator_traits::deallocate (inline) 47ms 0.95% 29.14% 273ms 5.51% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 0 0% 29.14% 237ms 4.78% vtkXMLWriter::WriteCompressionBlock 0 0% 29.14% 228ms 4.60% vtkDataCompressor::Compress 0 0% 29.14% 227ms 4.58% compress2 0 0% 29.14% 227ms 4.58% vtkZLibDataCompressor::CompressBuffer 1ms 0.02% 29.16% 225ms 4.54% deflate 63ms 1.27% 30.44% 223ms 4.50% crc32 0 0% 30.44% 217ms 4.38% tbb::detail::r1::parallel_pipeline 0 0% 30.44% 211ms 4.26% clone3 0 0% 30.44% 211ms 4.26% start_thread 0 0% 30.44% 210ms 4.24% tbb::detail::r1::reset 87ms 1.75% 32.19% 209ms 4.22% tbb::detail::r1::wait_bounded_queue_monitor 3ms 0.061% 32.25% 207ms 4.18% vtkBase64OutputStream::Write 17ms 0.34% 32.59% 204ms 4.11% vtkBase64OutputStream::EncodeTriplet 4ms 0.081% 32.67% 200ms 4.03% vtkPoints::~vtkPoints 1ms 0.02% 32.69% 198ms 3.99% std::set::set (inline) 18ms 0.36% 33.06% 196ms 3.95% std::_Rb_tree::_Rb_tree 10ms 0.2% 33.26% 194ms 3.91% std::_Rb_tree::~_Rb_tree (inline) 64ms 1.29% 34.55% 190ms 3.83% std::_Rb_tree::_M_erase 0 0% 34.55% 184ms 3.71% VertexMesh::~VertexMesh 6ms 0.12% 34.67% 178ms 3.59% vtkIdList::AllocateInternal 2ms 0.04% 34.71% 177ms 3.57% vtkFloatArray::New 4ms 0.081% 34.79% 176ms 3.55% NodesOnlyMesh::ConstructNodesWithoutMesh 51ms 1.03% 35.82% 176ms 3.55% std::ostream::write 0 0% 35.82% 174ms 3.51% std::_Rb_tree::_M_create_node (inline) 100ms 2.02% 37.84% 171ms 3.45% malloc_consolidate 17ms 0.34% 38.18% 169ms 3.41% std::vector::_M_default_append 0 0% 38.18% 169ms 3.41% vtkQuad::~vtkQuad 0 0% 38.18% 168ms 3.39% std::_Rb_tree::_M_get_node (inline) 0 0% 38.18% 168ms 3.39% vtkTriangle::~vtkTriangle 2ms 0.04% 38.22% 167ms 3.37% std::_Vector_base::_M_deallocate (inline) 0 0% 38.22% 165ms 3.33% VertexMesh::VertexMesh 0 0% 38.22% 162ms 3.27% NodeLocationWriter::VisitAnyPopulation 0 0% 38.22% 159ms 3.21% std::vector::~vector (inline) 1ms 0.02% 38.24% 157ms 3.17% vtkLine::GetParametricCenter 6ms 0.12% 38.36% 155ms 3.13% MutableElement::BuildEdges 0 0% 38.36% 155ms 3.13% VertexMesh::GenerateEdgesFromElements (inline) 0 0% 38.36% 155ms 3.13% std::_Rb_tree::_Alloc_node::operator() (inline) 3ms 0.061% 38.42% 152ms 3.07% vtkTypeFloat64Array::~vtkTypeFloat64Array 147ms 2.96% 41.39% 151ms 3.05% [libz.so.1.3] 2ms 0.04% 41.43% 146ms 2.94% vtkFloatArray::vtkFloatArray 4ms 0.081% 41.51% 145ms 2.92% vtkDataArray::CreateDataArray 13ms 0.26% 41.77% 142ms 2.86% std::_Rb_tree::_M_copy (inline) 59ms 1.19% 42.96% 142ms 2.86% std::basic_filebuf::xsputn 0 0% 42.96% 139ms 2.80% std::set::~set (inline) 0 0% 42.96% 137ms 2.76% EdgeHelper::~EdgeHelper (inline) 5ms 0.1% 43.06% 135ms 2.72% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 5ms 0.1% 43.16% 133ms 2.68% vtkTypeFloat64Array::New 2ms 0.04% 43.20% 132ms 2.66% EdgeHelper::GetEdgeFromNodes 0 0% 43.20% 131ms 2.64% std::_Vector_base::~_Vector_base (inline) 2ms 0.04% 43.24% 130ms 2.62% vtkDoubleArray::vtkDoubleArray 1ms 0.02% 43.26% 128ms 2.58% std::_Vector_base::_M_allocate (inline) 10ms 0.2% 43.47% 127ms 2.56% std::_Rb_tree::_M_clone_node (inline) 12ms 0.24% 43.71% 125ms 2.52% vtkFloatArray::~vtkFloatArray 123ms 2.48% 46.19% 123ms 2.48% __GI_sched_yield 0 0% 46.19% 120ms 2.42% std::_Rb_tree::_M_drop_node (inline) 31ms 0.63% 46.81% 118ms 2.38% vtkObject::vtkObject 1ms 0.02% 46.83% 117ms 2.36% vtkIdList::Allocate 2ms 0.04% 46.87% 115ms 2.32% vtkXMLWriter::WritePointDataAppendedData 0 0% 46.87% 113ms 2.28% std::_Rb_tree::_M_put_node (inline) 3ms 0.061% 46.93% 110ms 2.22% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.061% 46.99% 110ms 2.22% vtkTypeFloat64Array::vtkTypeFloat64Array 4ms 0.081% 47.08% 107ms 2.16% std::map::operator[] (partial-inline) 106ms 2.14% 49.21% 106ms 2.14% __strcmp_avx2 8ms 0.16% 49.37% 97ms 1.96% _int_free_maybe_consolidate 47ms 0.95% 50.32% 97ms 1.96% std::__ostream_insert 97ms 1.96% 52.28% 97ms 1.96% unlink_chunk 1ms 0.02% 52.30% 95ms 1.92% std::operator<< (inline) 1ms 0.02% 52.32% 92ms 1.86% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 2ms 0.04% 52.36% 91ms 1.84% AbstractCellProperty::IsSubType (inline) 5ms 0.1% 52.46% 91ms 1.84% vtkIdList::New 43ms 0.87% 53.33% 89ms 1.80% vtkTypeFloat64Array::PrintSelf 24ms 0.48% 53.81% 88ms 1.77% __dynamic_cast 68ms 1.37% 55.18% 87ms 1.75% std::basic_streambuf::xsputn 44ms 0.89% 56.07% 78ms 1.57% hack_digit 22ms 0.44% 56.51% 78ms 1.57% vtkObject::Modified 44ms 0.89% 57.40% 78ms 1.57% vtkObjectBase::UnRegisterInternal 4ms 0.081% 57.48% 76ms 1.53% vtkDoubleArray::~vtkDoubleArray 11ms 0.22% 57.70% 75ms 1.51% vtkAOSDataArrayTemplate::DataElementChanged 0 0% 57.70% 75ms 1.51% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 0 0% 57.70% 74ms 1.49% NodesOnlyMesh::SetUpBoxCollection 1ms 0.02% 57.72% 72ms 1.45% std::vector::push_back (inline) 2ms 0.04% 57.77% 71ms 1.43% AbstractCellPopulation::GetCellUsingLocationIndex 20ms 0.4% 58.17% 71ms 1.43% std::_Rb_tree::_M_lower_bound (inline) 0 0% 58.17% 67ms 1.35% AbstractCellProperty::IsType (inline) 0 0% 58.17% 66ms 1.33% Cell::HasCellProperty (inline) 1ms 0.02% 58.19% 66ms 1.33% CellPropertyCollection::HasProperty 5ms 0.1% 58.29% 64ms 1.29% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 58.29% 62ms 1.25% tcache_get (inline) 62ms 1.25% 59.54% 62ms 1.25% tcache_get_n (inline) 0 0% 59.54% 59ms 1.19% PottsMesh::GetMooreNeighbouringNodeIndices 0 0% 59.54% 58ms 1.17% boost::numeric::ublas::vector_assign (inline) 0 0% 59.54% 57ms 1.15% Cell::GetCellProliferativeType 0 0% 59.54% 57ms 1.15% NodesOnlyMesh::~NodesOnlyMesh 0 0% 59.54% 57ms 1.15% std::_Rb_tree::_M_insert_unique 0 0% 59.54% 57ms 1.15% std::set::insert (inline) 11ms 0.22% 59.76% 57ms 1.15% vtkSOADataArrayTemplate::FillTypedComponent 8ms 0.16% 59.92% 56ms 1.13% AbstractCellProperty::IsSame 0 0% 59.92% 55ms 1.11% std::map::~map (inline) 6ms 0.12% 60.04% 54ms 1.09% VertexMeshWriter::GetNextNode 0 0% 60.04% 53ms 1.07% std::_Rb_tree::lower_bound (inline) 0 0% 60.04% 53ms 1.07% std::map::lower_bound (inline) 53ms 1.07% 61.11% 53ms 1.07% vtkTimeStamp::Modified 3ms 0.061% 61.17% 51ms 1.03% vtkDataArray::vtkDataArray 4ms 0.081% 61.25% 50ms 1.01% std::_Rb_tree::_M_insert_ (inline) 4ms 0.081% 61.34% 50ms 1.01% std::vector::_M_realloc_insert 0 0% 61.34% 49ms 0.99% std::_Rb_tree::_M_emplace_hint_unique 10ms 0.2% 61.54% 48ms 0.97% std::type_info::operator== (inline) 10ms 0.2% 61.74% 48ms 0.97% vtkAbstractArray::vtkAbstractArray 47ms 0.95% 62.69% 47ms 0.95% __GI___writev 27ms 0.54% 63.23% 47ms 0.95% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 63.23% 47ms 0.95% std::__basic_file::xsputn_2 17ms 0.34% 63.57% 47ms 0.95% std::num_put::_M_insert_int 0 0% 63.57% 46ms 0.93% VertexMesh::Clear 0 0% 63.57% 43ms 0.87% DistributedBoxCollection::~DistributedBoxCollection 0 0% 63.57% 43ms 0.87% NodesOnlyMesh::ClearBoxCollection (inline) 43ms 0.87% 64.44% 43ms 0.87% __memcpy_avx_unaligned_erms 43ms 0.87% 65.31% 43ms 0.87% std::ostream::sentry::sentry 3ms 0.061% 65.37% 41ms 0.83% DistributedBoxCollection::SetupLocalBoxesHalfOnly 1ms 0.02% 65.39% 41ms 0.83% std::basic_filebuf::overflow 0 0% 65.39% 40ms 0.81% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 40ms 0.81% 66.20% 40ms 0.81% [libvtkCommonCore-9.3.so.9.3] 40ms 0.81% 67.00% 40ms 0.81% __GI___libc_write 11ms 0.22% 67.22% 40ms 0.81% boost::numeric::ublas::indexing_vector_assign 0 0% 67.22% 40ms 0.81% std::__basic_file::xsputn 0 0% 67.22% 40ms 0.81% std::basic_filebuf::_M_convert_to_external 40ms 0.81% 68.03% 40ms 0.81% vtkObject::~vtkObject 1ms 0.02% 68.05% 39ms 0.79% DistributedBoxCollection::IsOwned 0 0% 68.05% 39ms 0.79% _dl_init 0 0% 68.05% 39ms 0.79% _dl_start_user 0 0% 68.05% 39ms 0.79% call_init (inline) 0 0% 68.05% 39ms 0.79% std::_Destroy (inline) 0 0% 68.05% 39ms 0.79% std::_Destroy_aux::__destroy (inline) 29ms 0.58% 68.64% 39ms 0.79% std::_Hashtable::clear 0 0% 68.64% 39ms 0.79% std::basic_filebuf::open 0 0% 68.64% 39ms 0.79% vtkDataArray::ComputeRange 8ms 0.16% 68.80% 39ms 0.79% vtkDataArray::~vtkDataArray 27ms 0.54% 69.34% 38ms 0.77% DistributedBoxCollection::CalculateContainingBox (inline) 2ms 0.04% 69.38% 38ms 0.77% __find_specmb (inline) 0 0% 69.38% 37ms 0.75% CxxTest::RealWorldDescription::setUp 0 0% 69.38% 37ms 0.75% PMPI_Init_thread 0 0% 69.38% 37ms 0.75% PetscInitialize 0 0% 69.38% 37ms 0.75% PetscSetup::setUpWorld 0 0% 69.38% 37ms 0.75% PetscSetupUtils::CommonSetup 0 0% 69.38% 37ms 0.75% PetscSetupUtils::InitialisePetsc 0 0% 69.38% 37ms 0.75% _IO_new_file_fopen 0 0% 69.38% 37ms 0.75% _IO_new_fopen 0 0% 69.38% 37ms 0.75% __GI__IO_file_open 0 0% 69.38% 37ms 0.75% __fopen_internal (inline) 37ms 0.75% 70.13% 37ms 0.75% __libc_open64 0 0% 70.13% 37ms 0.75% ompi_mpi_init 0 0% 70.13% 37ms 0.75% std::__basic_file::open 1ms 0.02% 70.15% 37ms 0.75% std::make_unique (inline) 0 0% 70.15% 36ms 0.73% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 1ms 0.02% 70.17% 36ms 0.73% std::_Rb_tree_header::_Rb_tree_header (inline) 36ms 0.73% 70.90% 36ms 0.73% std::codecvt::do_always_noconv 0 0% 70.90% 36ms 0.73% std::less::operator() (inline) 36ms 0.73% 71.62% 36ms 0.73% std::operator< (inline) 35ms 0.71% 72.33% 35ms 0.71% __strchrnul_avx2 35ms 0.71% 73.03% 35ms 0.71% vtkObjectBase::~vtkObjectBase 34ms 0.69% 73.72% 34ms 0.69% std::_Rb_tree_header::_M_reset (inline) 34ms 0.69% 74.41% 34ms 0.69% std::_Rb_tree_insert_and_rebalance 2ms 0.04% 74.45% 34ms 0.69% vtkDoubleArray::New 34ms 0.69% 75.13% 34ms 0.69% vtkObjectBase::Delete 33ms 0.67% 75.80% 33ms 0.67% vtkObjectBase::vtkObjectBase 2ms 0.04% 75.84% 32ms 0.65% 0 0% 75.84% 32ms 0.65% OutputFileHandler::OpenOutputFile 3ms 0.061% 75.90% 32ms 0.65% boost::serialization::singleton::get_instance 3ms 0.061% 75.96% 32ms 0.65% vtkIdList::~vtkIdList 0 0% 75.96% 31ms 0.63% Cell::GetCellId 31ms 0.63% 76.58% 31ms 0.63% std::_Rb_tree_increment 0 0% 76.58% 31ms 0.63% vtk::detail::smp::vtkSMPToolsImplForTBB 31ms 0.63% 77.21% 31ms 0.63% vtkDataArray::Modified 0 0% 77.21% 30ms 0.61% CellIdWriter::GetCellDataForVtkOutput 10ms 0.2% 77.41% 30ms 0.61% _int_free_merge_chunk 0 0% 77.41% 30ms 0.61% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 0 0% 77.41% 29ms 0.58% Cell::GetMutationState 5ms 0.1% 77.51% 29ms 0.58% std::__new_allocator::construct (inline) 0 0% 77.51% 29ms 0.58% std::allocator_traits::construct (inline) 1ms 0.02% 77.53% 29ms 0.58% std::basic_filebuf::sync 0 0% 77.53% 29ms 0.58% std::ostream::flush 1ms 0.02% 77.55% 29ms 0.58% tbb::detail::r1::cancel_group_execution 23ms 0.46% 78.02% 29ms 0.58% vtkObject::ObjectFinalize 1ms 0.02% 78.04% 28ms 0.56% VertexMeshWriter::GetNextElement 0 0% 78.04% 27ms 0.54% std::_Rb_tree::_Auto_node::_M_insert (inline) 2ms 0.04% 78.08% 27ms 0.54% std::_Rb_tree::_M_insert_node (inline) 0 0% 78.08% 27ms 0.54% vtkXMLUnstructuredDataWriter::WriteHeader 2ms 0.04% 78.12% 26ms 0.52% CellProliferativeTypesWriter::GetCellDataForVtkOutput 1ms 0.02% 78.14% 26ms 0.52% Node::ConstructNodeAttributes (inline) 2ms 0.04% 78.18% 26ms 0.52% Node::GetPoint 0 0% 78.18% 26ms 0.52% Node::SetRadius 1ms 0.02% 78.20% 26ms 0.52% vtkDataArrayPrivate::DoComputeVectorRange 5ms 0.1% 78.30% 26ms 0.52% vtkIdList::vtkIdList 2ms 0.04% 78.34% 25ms 0.5% Edge::Edge 1ms 0.02% 78.36% 25ms 0.5% PottsMesh::GetVonNeumannNeighbouringNodeIndices 17ms 0.34% 78.70% 25ms 0.5% __printf_buffer_write 0 0% 78.70% 25ms 0.5% boost::numeric::ublas::c_vector::assign (inline) 0 0% 78.70% 25ms 0.5% orte_init 10ms 0.2% 78.90% 25ms 0.5% std::_Rb_tree_const_iterator::operator++ (inline) 4ms 0.081% 78.98% 25ms 0.5% vtkAOSDataArrayTemplate::InsertTuple