File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3781ms, 80.57% of 4693ms total Dropped 740 nodes (cum <= 23.46ms) flat flat% sum% cum cum% 0 0% 0% 4502ms 95.93% __libc_start_call_main 0 0% 0% 4502ms 95.93% __libc_start_main_impl 0 0% 0% 4502ms 95.93% _start 0 0% 0% 4484ms 95.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4484ms 95.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4484ms 95.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4484ms 95.55% main 0 0% 0% 4444ms 94.69% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4444ms 94.69% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4444ms 94.69% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4433ms 94.46% AbstractCellBasedSimulation::Solve 0 0% 0% 4123ms 87.85% AbstractCellPopulation::WriteResultsToFiles 16ms 0.34% 0.34% 3915ms 83.42% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.34% 1977ms 42.13% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.021% 0.36% 1688ms 35.97% VertexMeshWriter::MakeVtkMesh 0 0% 0.36% 1236ms 26.34% vtkPolygon::New 2ms 0.043% 0.4% 1235ms 26.32% vtkPolygon::vtkPolygon 6ms 0.13% 0.53% 877ms 18.69% vtkCell::vtkCell 2ms 0.043% 0.58% 767ms 16.34% vtkPoints::New 6ms 0.13% 0.7% 709ms 15.11% vtkPoints::vtkPoints 1ms 0.021% 0.72% 668ms 14.23% VertexMeshWriter::WriteFiles 0 0% 0.72% 653ms 13.91% std::ostream::operator<< (inline) 54ms 1.15% 1.88% 652ms 13.89% std::ostream::_M_insert 36ms 0.77% 2.64% 628ms 13.38% operator new 177ms 3.77% 6.41% 608ms 12.96% __GI___libc_malloc 3ms 0.064% 6.48% 599ms 12.76% vtkQuad::New 8ms 0.17% 6.65% 596ms 12.70% vtkQuad::vtkQuad 2ms 0.043% 6.69% 586ms 12.49% vtkLine::New 0 0% 6.69% 573ms 12.21% vtkStreamingDemandDrivenPipeline::Update 0 0% 6.69% 573ms 12.21% vtkXMLWriterBase::Write 0 0% 6.69% 571ms 12.17% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 6.69% 569ms 12.12% vtkDemandDrivenPipeline::ProcessRequest 11ms 0.23% 6.93% 569ms 12.12% vtkLine::vtkLine 2ms 0.043% 6.97% 568ms 12.10% vtkExecutive::CallAlgorithm 1ms 0.021% 6.99% 567ms 12.08% vtkCompositeDataPipeline::ExecuteData 0 0% 6.99% 567ms 12.08% vtkDemandDrivenPipeline::ExecuteData 1ms 0.021% 7.01% 565ms 12.04% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 7.01% 560ms 11.93% vtkTriangle::New 5ms 0.11% 7.12% 549ms 11.70% vtkTriangle::vtkTriangle 42ms 0.89% 8.01% 528ms 11.25% std::num_put::_M_insert_float 0 0% 8.01% 514ms 10.95% vtkXMLUnstructuredDataWriter::WriteAPiece 1ms 0.021% 8.03% 514ms 10.95% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 128ms 2.73% 10.76% 500ms 10.65% __GI___libc_free 0 0% 10.76% 457ms 9.74% vtkXMLWriter::WriteBinaryData 16ms 0.34% 11.10% 452ms 9.63% vtkPoints::SetDataType 1ms 0.021% 11.12% 450ms 9.59% vtkXMLWriter::WriteBinaryDataInternal 1ms 0.021% 11.14% 449ms 9.57% vtkXMLWriter::WriteBinaryDataBlock 0 0% 11.14% 429ms 9.14% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 10ms 0.21% 11.36% 416ms 8.86% std::__cxx11::collate::do_transform 0 0% 11.36% 392ms 8.35% vtkPolygon::~vtkPolygon 3ms 0.064% 11.42% 389ms 8.29% ___vsnprintf 1ms 0.021% 11.44% 386ms 8.23% __vsnprintf_internal (inline) 66ms 1.41% 12.85% 383ms 8.16% __printf_buffer 228ms 4.86% 17.71% 371ms 7.91% _int_free 241ms 5.14% 22.84% 357ms 7.61% _int_malloc 0 0% 22.84% 334ms 7.12% vtkXMLWriter::WritePointsAppendedData 0 0% 22.84% 331ms 7.05% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 22.84% 326ms 6.95% VtkMeshWriter::WriteFiles 9ms 0.19% 23.03% 315ms 6.71% vtkCell::~vtkCell 0 0% 23.03% 297ms 6.33% OnLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 23.03% 297ms 6.33% PottsBasedCellPopulation::UpdateCellLocations 15ms 0.32% 23.35% 295ms 6.29% __printf_fp_l_buffer 0 0% 23.35% 295ms 6.29% __printf_fp_spec (inline) 35ms 0.75% 24.10% 284ms 6.05% std::__new_allocator::allocate (inline) 3ms 0.064% 24.16% 281ms 5.99% std::__new_allocator::deallocate (inline) 0 0% 24.16% 281ms 5.99% std::allocator_traits::allocate (inline) 0 0% 24.16% 278ms 5.92% std::allocator_traits::deallocate (inline) 116ms 2.47% 26.64% 268ms 5.71% __printf_fp_buffer_1 34ms 0.72% 27.36% 262ms 5.58% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 6ms 0.13% 27.49% 227ms 4.84% vtkBase64OutputStream::Write 0 0% 27.49% 225ms 4.79% vtkXMLWriter::WriteCompressionBlock 20ms 0.43% 27.91% 215ms 4.58% vtkBase64OutputStream::EncodeTriplet 0 0% 27.91% 211ms 4.50% compress2 0 0% 27.91% 211ms 4.50% vtkDataCompressor::Compress 0 0% 27.91% 211ms 4.50% vtkZLibDataCompressor::CompressBuffer 49ms 1.04% 28.96% 210ms 4.47% crc32 0 0% 28.96% 210ms 4.47% deflate 21ms 0.45% 29.41% 210ms 4.47% std::_Rb_tree::_Rb_tree 0 0% 29.41% 210ms 4.47% std::set::set (inline) 5ms 0.11% 29.51% 208ms 4.43% vtkPoints::~vtkPoints 6ms 0.13% 29.64% 184ms 3.92% vtkFloatArray::New 91ms 1.94% 31.58% 181ms 3.86% malloc_consolidate 37ms 0.79% 32.37% 181ms 3.86% std::ostream::write 0 0% 32.37% 176ms 3.75% vtkQuad::~vtkQuad 0 0% 32.37% 175ms 3.73% vtkLine::GetParametricCenter 4ms 0.085% 32.45% 172ms 3.67% std::_Vector_base::_M_deallocate (inline) 0 0% 32.45% 171ms 3.64% NodesOnlyMesh::ConstructNodesWithoutMesh 0 0% 32.45% 169ms 3.60% std::vector::~vector (inline) 0 0% 32.45% 168ms 3.58% VertexMesh::~VertexMesh 0 0% 32.45% 168ms 3.58% tbb::detail::r1::parallel_pipeline 0 0% 32.45% 165ms 3.52% std::_Rb_tree::_M_create_node (inline) 6ms 0.13% 32.58% 161ms 3.43% vtkIdList::AllocateInternal 69ms 1.47% 34.05% 160ms 3.41% std::basic_filebuf::xsputn 0 0% 34.05% 160ms 3.41% vtkTriangle::~vtkTriangle 16ms 0.34% 34.39% 158ms 3.37% std::_Rb_tree::_M_copy (inline) 1ms 0.021% 34.41% 158ms 3.37% vtkFloatArray::vtkFloatArray 0 0% 34.41% 156ms 3.32% clone3 0 0% 34.41% 156ms 3.32% start_thread 0 0% 34.41% 156ms 3.32% std::_Rb_tree::_M_get_node (inline) 153ms 3.26% 37.67% 155ms 3.30% [libz.so.1.3] 36ms 0.77% 38.44% 153ms 3.26% std::_Rb_tree::_M_erase 1ms 0.021% 38.46% 152ms 3.24% vtkTypeFloat64Array::~vtkTypeFloat64Array 2ms 0.043% 38.50% 151ms 3.22% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 4ms 0.085% 38.59% 151ms 3.22% std::_Rb_tree::~_Rb_tree (inline) 0 0% 38.59% 150ms 3.20% std::_Rb_tree::_Alloc_node::operator() (inline) 3ms 0.064% 38.65% 147ms 3.13% VertexMesh::VertexMesh 0 0% 38.65% 146ms 3.11% tbb::detail::r1::reset 3ms 0.064% 38.72% 143ms 3.05% std::_Vector_base::~_Vector_base (inline) 15ms 0.32% 39.04% 143ms 3.05% std::vector::_M_default_append 17ms 0.36% 39.40% 138ms 2.94% std::_Rb_tree::_M_clone_node (inline) 8ms 0.17% 39.57% 135ms 2.88% MutableElement::BuildEdges 0 0% 39.57% 135ms 2.88% NodeLocationWriter::VisitAnyPopulation 0 0% 39.57% 135ms 2.88% VertexMesh::GenerateEdgesFromElements (inline) 64ms 1.36% 40.93% 134ms 2.86% tbb::detail::r1::wait_bounded_queue_monitor 3ms 0.064% 41.00% 133ms 2.83% vtkDataArray::CreateDataArray 0 0% 41.00% 127ms 2.71% std::set::~set (inline) 1ms 0.021% 41.02% 126ms 2.68% std::_Vector_base::_M_allocate (inline) 2ms 0.043% 41.06% 124ms 2.64% CellPropertyCollection::GetPropertiesType (inline) 27ms 0.58% 41.64% 124ms 2.64% vtkObject::vtkObject 1ms 0.021% 41.66% 122ms 2.60% vtkFloatArray::~vtkFloatArray 8ms 0.17% 41.83% 119ms 2.54% vtkTypeFloat64Array::New 117ms 2.49% 44.32% 117ms 2.49% unlink_chunk 55ms 1.17% 45.49% 117ms 2.49% vtkTypeFloat64Array::PrintSelf 1ms 0.021% 45.51% 115ms 2.45% vtkIdList::Allocate 0 0% 45.51% 112ms 2.39% std::_Rb_tree::_M_drop_node (inline) 0 0% 45.51% 110ms 2.34% EdgeHelper::~EdgeHelper (inline) 1ms 0.021% 45.54% 109ms 2.32% EdgeHelper::GetEdgeFromNodes 0 0% 45.54% 109ms 2.32% std::_Rb_tree::_M_put_node (inline) 4ms 0.085% 45.62% 109ms 2.32% vtkDoubleArray::vtkDoubleArray 106ms 2.26% 47.88% 106ms 2.26% __strcmp_avx2 0 0% 47.88% 104ms 2.22% AbstractCellProperty::IsSubType (inline) 24ms 0.51% 48.39% 104ms 2.22% __dynamic_cast 67ms 1.43% 49.82% 102ms 2.17% vtkObjectBase::UnRegisterInternal 4ms 0.085% 49.90% 99ms 2.11% _int_free_maybe_consolidate 4ms 0.085% 49.99% 97ms 2.07% vtkTypeFloat64Array::vtkTypeFloat64Array 47ms 1.00% 50.99% 96ms 2.05% hack_digit 0 0% 50.99% 95ms 2.02% vtkXMLWriter::WritePointDataAppendedData 5ms 0.11% 51.10% 91ms 1.94% std::map::operator[] (partial-inline) 0 0% 51.10% 89ms 1.90% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 7ms 0.15% 51.25% 88ms 1.88% vtkAOSDataArrayTemplate::DataElementChanged 37ms 0.79% 52.03% 84ms 1.79% std::__ostream_insert 1ms 0.021% 52.06% 83ms 1.77% std::operator<< (inline) 0 0% 52.06% 82ms 1.75% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 4ms 0.085% 52.14% 78ms 1.66% vtkDoubleArray::~vtkDoubleArray 0 0% 52.14% 77ms 1.64% Cell::HasCellProperty (inline) 2ms 0.043% 52.18% 77ms 1.64% CellPropertyCollection::HasProperty 21ms 0.45% 52.63% 77ms 1.64% std::_Rb_tree::_M_lower_bound (inline) 2ms 0.043% 52.67% 77ms 1.64% std::vector::push_back (inline) 8ms 0.17% 52.84% 75ms 1.60% AbstractCellPopulation::GetCellUsingLocationIndex 16ms 0.34% 53.19% 75ms 1.60% vtkObject::Modified 2ms 0.043% 53.23% 73ms 1.56% AbstractCellProperty::IsType (inline) 0 0% 53.23% 72ms 1.53% Cell::GetCellProliferativeType 10ms 0.21% 53.44% 70ms 1.49% boost::numeric::ublas::c_vector::c_vector (partial-inline) 68ms 1.45% 54.89% 68ms 1.45% __GI_sched_yield 0 0% 54.89% 68ms 1.45% tcache_get (inline) 68ms 1.45% 56.34% 68ms 1.45% tcache_get_n (inline) 0 0% 56.34% 66ms 1.41% NodesOnlyMesh::SetUpBoxCollection 3ms 0.064% 56.40% 66ms 1.41% vtkIdList::New 2ms 0.043% 56.45% 65ms 1.39% PottsMesh::GetMooreNeighbouringNodeIndices 0 0% 56.45% 62ms 1.32% NodesOnlyMesh::~NodesOnlyMesh 37ms 0.79% 57.23% 62ms 1.32% std::basic_streambuf::xsputn 60ms 1.28% 58.51% 61ms 1.30% __GI___writev 0 0% 58.51% 61ms 1.30% std::__basic_file::xsputn_2 8ms 0.17% 58.68% 60ms 1.28% AbstractCellProperty::IsSame 0 0% 58.68% 60ms 1.28% boost::numeric::ublas::vector_assign (inline) 1ms 0.021% 58.70% 58ms 1.24% VertexMesh::Clear 0 0% 58.70% 58ms 1.24% std::_Rb_tree::lower_bound (inline) 0 0% 58.70% 58ms 1.24% std::map::lower_bound (inline) 31ms 0.66% 59.37% 57ms 1.21% std::_Hashtable::clear 5ms 0.11% 59.47% 57ms 1.21% std::vector::_M_realloc_insert 57ms 1.21% 60.69% 57ms 1.21% vtkTimeStamp::Modified 1ms 0.021% 60.71% 56ms 1.19% std::_Rb_tree::_M_insert_unique 0 0% 60.71% 56ms 1.19% std::set::insert (inline) 55ms 1.17% 61.88% 55ms 1.17% [libstdc++.so.6.0.33] 4ms 0.085% 61.96% 53ms 1.13% vtkSOADataArrayTemplate::FillTypedComponent 10ms 0.21% 62.18% 52ms 1.11% std::type_info::operator== (inline) 33ms 0.7% 62.88% 51ms 1.09% __cxxabiv1::__si_class_type_info::__do_dyncast 49ms 1.04% 63.92% 49ms 1.04% __memcpy_avx_unaligned_erms 1ms 0.021% 63.95% 48ms 1.02% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 48ms 1.02% 64.97% 48ms 1.02% [libvtkCommonCore-9.3.so.9.3] 11ms 0.23% 65.20% 47ms 1.00% std::num_put::_M_insert_int 25ms 0.53% 65.74% 45ms 0.96% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 65.74% 45ms 0.96% DistributedBoxCollection::IsOwned 8ms 0.17% 65.91% 45ms 0.96% std::_Rb_tree::_M_insert_ (inline) 3ms 0.064% 65.97% 45ms 0.96% vtkDataArrayPrivate::DoComputeVectorRange 45ms 0.96% 66.93% 45ms 0.96% vtkObjectBase::vtkObjectBase 45ms 0.96% 67.89% 45ms 0.96% vtkObjectBase::~vtkObjectBase 3ms 0.064% 67.95% 44ms 0.94% DistributedBoxCollection::SetupLocalBoxesHalfOnly 0 0% 67.95% 44ms 0.94% vtkDataArray::ComputeRange 8ms 0.17% 68.12% 44ms 0.94% vtkDataArray::~vtkDataArray 44ms 0.94% 69.06% 44ms 0.94% vtkObject::~vtkObject 0 0% 69.06% 43ms 0.92% DistributedBoxCollection::~DistributedBoxCollection 0 0% 69.06% 43ms 0.92% NodesOnlyMesh::ClearBoxCollection (inline) 11ms 0.23% 69.29% 42ms 0.89% boost::numeric::ublas::indexing_vector_assign 5ms 0.11% 69.40% 42ms 0.89% vtkDataArray::vtkDataArray 0 0% 69.40% 41ms 0.87% vtk::detail::smp::vtkSMPToolsImplForTBB 6ms 0.13% 69.53% 41ms 0.87% vtkAOSDataArrayTemplate::InsertTuple 0 0% 69.53% 39ms 0.83% std::less::operator() (inline) 39ms 0.83% 70.36% 39ms 0.83% std::operator< (inline) 3ms 0.064% 70.42% 39ms 0.83% tbb::detail::r1::cancel_group_execution 2ms 0.043% 70.47% 38ms 0.81% CellProliferativeTypesWriter::GetCellDataForVtkOutput 4ms 0.085% 70.55% 37ms 0.79% VertexMeshWriter::GetNextNode 0 0% 70.55% 37ms 0.79% _dl_init 0 0% 70.55% 37ms 0.79% call_init (inline) 0 0% 70.55% 37ms 0.79% std::_Destroy (inline) 0 0% 70.55% 37ms 0.79% std::_Destroy_aux::__destroy (inline) 12ms 0.26% 70.81% 37ms 0.79% vtkIdList::~vtkIdList 0 0% 70.81% 36ms 0.77% CxxTest::RealWorldDescription::setUp 0 0% 70.81% 36ms 0.77% PMPI_Init_thread 0 0% 70.81% 36ms 0.77% PetscInitialize 0 0% 70.81% 36ms 0.77% PetscSetup::setUpWorld 0 0% 70.81% 36ms 0.77% PetscSetupUtils::CommonSetup 0 0% 70.81% 36ms 0.77% PetscSetupUtils::InitialisePetsc 0 0% 70.81% 36ms 0.77% ompi_mpi_init 1ms 0.021% 70.83% 36ms 0.77% vtk::detail::smp::vtkSMPToolsImpl::For 5ms 0.11% 70.94% 36ms 0.77% vtkAOSDataArrayTemplate::AllocateTuples 0 0% 70.94% 35ms 0.75% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 70.94% 35ms 0.75% _dl_start_user 12ms 0.26% 71.19% 35ms 0.75% vtkAbstractArray::vtkAbstractArray 0 0% 71.19% 34ms 0.72% std::make_unique (inline) 34ms 0.72% 71.92% 34ms 0.72% std::ostream::sentry::sentry 29ms 0.62% 72.53% 34ms 0.72% vtkObject::ObjectFinalize 33ms 0.7% 73.24% 33ms 0.7% boost::numeric::ublas::c_vector::operator() 32ms 0.68% 73.92% 32ms 0.68% [libchaste_cell_based.so] 32ms 0.68% 74.60% 32ms 0.68% __GI___libc_write 32ms 0.68% 75.28% 32ms 0.68% __mpn_divrem 32ms 0.68% 75.96% 32ms 0.68% std::_Rb_tree_increment 0 0% 75.96% 32ms 0.68% std::__basic_file::xsputn 0 0% 75.96% 32ms 0.68% std::basic_filebuf::_M_convert_to_external 0 0% 75.96% 32ms 0.68% std::basic_filebuf::overflow 32ms 0.68% 76.65% 32ms 0.68% vtkObjectBase::Delete 1ms 0.021% 76.67% 31ms 0.66% 0 0% 76.67% 31ms 0.66% PottsBasedCellPopulation::AcceptCellWriter 6ms 0.13% 76.80% 31ms 0.66% vtkSOADataArrayTemplate::GetTupleIndexFromValueIndex 30ms 0.64% 77.43% 30ms 0.64% __memset_avx2_unaligned_erms 0 0% 77.43% 30ms 0.64% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 1ms 0.021% 77.46% 30ms 0.64% std::_Rb_tree_header::_Rb_tree_header (inline) 30ms 0.64% 78.10% 30ms 0.64% std::codecvt::do_always_noconv 0 0% 78.10% 29ms 0.62% Cell::GetCellId 0 0% 78.10% 29ms 0.62% Edge::Edge 0 0% 78.10% 29ms 0.62% Edge::SetNodes (inline) 5ms 0.11% 78.20% 29ms 0.62% Node::~Node 4ms 0.085% 78.29% 29ms 0.62% boost::serialization::singleton::get_instance 29ms 0.62% 78.90% 29ms 0.62% std::_Rb_tree_header::_M_reset (inline) 9ms 0.19% 79.10% 29ms 0.62% std::__new_allocator::construct (inline) 0 0% 79.10% 29ms 0.62% std::allocator_traits::construct (inline) 28ms 0.6% 79.69% 29ms 0.62% vtkDataArray::Modified 0 0% 79.69% 28ms 0.6% Cell::GetMutationState 1ms 0.021% 79.71% 28ms 0.6% std::_Rb_tree::_M_emplace_hint_unique 0 0% 79.71% 27ms 0.58% VtkMeshWriter::MakeVtkMesh 5ms 0.11% 79.82% 27ms 0.58% vtkIdList::vtkIdList 27ms 0.58% 80.40% 27ms 0.58% vtkObject::InvokeEvent 0 0% 80.40% 26ms 0.55% CellIdWriter::GetCellDataForVtkOutput 1ms 0.021% 80.42% 26ms 0.55% Node::SetRadius 0 0% 80.42% 26ms 0.55% PottsMesh::GetVonNeumannNeighbouringNodeIndices 0 0% 80.42% 26ms 0.55% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 0 0% 80.42% 25ms 0.53% Node::ConstructNodeAttributes (inline) 1ms 0.021% 80.44% 25ms 0.53% vtkDataArrayPrivate::DoComputeScalarRange 6ms 0.13% 80.57% 24ms 0.51% _int_free_merge_chunk 0 0% 80.57% 24ms 0.51% orte_init 0 0% 80.57% 24ms 0.51% std::map::~map (inline) 0 0% 80.57% 24ms 0.51% vtkDoubleArray::New