File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3307ms, 80.99% of 4083ms total Dropped 674 nodes (cum <= 20.41ms) flat flat% sum% cum cum% 0 0% 0% 3934ms 96.35% __libc_start_main_impl 0 0% 0% 3934ms 96.35% _start 0 0% 0% 3933ms 96.33% __libc_start_call_main 0 0% 0% 3918ms 95.96% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 3918ms 95.96% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 3918ms 95.96% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 3918ms 95.96% main 0 0% 0% 3887ms 95.20% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 3887ms 95.20% CxxTest::TestRunner::runTest (inline) 0 0% 0% 3887ms 95.20% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 3877ms 94.95% AbstractCellBasedSimulation::Solve 0 0% 0% 3569ms 87.41% AbstractCellPopulation::WriteResultsToFiles 7ms 0.17% 0.17% 3396ms 83.17% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.17% 1789ms 43.82% VertexMeshWriter::WriteVtkUsingMesh 0 0% 0.17% 1591ms 38.97% VertexMeshWriter::MakeVtkMesh 0 0% 0.17% 1203ms 29.46% vtkPolygon::New 0 0% 0.17% 1203ms 29.46% vtkPolygon::vtkPolygon 2ms 0.049% 0.22% 905ms 22.17% vtkCell::vtkCell 2ms 0.049% 0.27% 706ms 17.29% vtkPoints::New 4ms 0.098% 0.37% 674ms 16.51% vtkPoints::vtkPoints 40ms 0.98% 1.35% 625ms 15.31% operator new 280ms 6.86% 8.20% 583ms 14.28% __GI___libc_malloc 0 0% 8.20% 579ms 14.18% vtkQuad::New 1ms 0.024% 8.23% 576ms 14.11% vtkQuad::vtkQuad 39ms 0.96% 9.18% 569ms 13.94% std::ostream::_M_insert 0 0% 9.18% 569ms 13.94% std::ostream::operator<< (inline) 1ms 0.024% 9.21% 568ms 13.91% VertexMeshWriter::WriteFiles 1ms 0.024% 9.23% 568ms 13.91% vtkLine::New 2ms 0.049% 9.28% 548ms 13.42% vtkLine::vtkLine 0 0% 9.28% 525ms 12.86% vtkTriangle::New 3ms 0.073% 9.36% 516ms 12.64% vtkTriangle::vtkTriangle 40ms 0.98% 10.34% 472ms 11.56% std::num_put::_M_insert_float 16ms 0.39% 10.73% 414ms 10.14% vtkPoints::SetDataType 77ms 1.89% 12.61% 396ms 9.70% __GI___libc_free 0 0% 12.61% 394ms 9.65% vtkStreamingDemandDrivenPipeline::Update 0 0% 12.61% 394ms 9.65% vtkXMLWriterBase::Write 0 0% 12.61% 392ms 9.60% vtkDemandDrivenPipeline::ProcessRequest 17ms 0.42% 13.03% 390ms 9.55% std::__cxx11::collate::do_transform 0 0% 13.03% 390ms 9.55% vtkDemandDrivenPipeline::ExecuteData 0 0% 13.03% 390ms 9.55% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 13.03% 389ms 9.53% vtkCompositeDataPipeline::ExecuteData 0 0% 13.03% 389ms 9.53% vtkExecutive::CallAlgorithm 0 0% 13.03% 389ms 9.53% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 13.03% 366ms 8.96% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 13.03% 366ms 8.96% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 1ms 0.024% 13.05% 354ms 8.67% ___vsnprintf 0 0% 13.05% 354ms 8.67% __vsnprintf_internal (inline) 0 0% 13.05% 351ms 8.60% vtkPolygon::~vtkPolygon 45ms 1.10% 14.16% 347ms 8.50% __printf_buffer 0 0% 14.16% 336ms 8.23% vtkXMLWriter::WriteBinaryData 0 0% 14.16% 334ms 8.18% vtkXMLWriter::WriteBinaryDataInternal 0 0% 14.16% 333ms 8.16% vtkXMLWriter::WriteBinaryDataBlock 58ms 1.42% 15.58% 332ms 8.13% std::__new_allocator::allocate (inline) 0 0% 15.58% 331ms 8.11% std::allocator_traits::allocate (inline) 208ms 5.09% 20.67% 315ms 7.71% _int_free 36ms 0.88% 21.55% 306ms 7.49% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 0 0% 21.55% 306ms 7.49% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 21.55% 301ms 7.37% OnLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 21.55% 301ms 7.37% PottsBasedCellPopulation::UpdateCellLocations 22ms 0.54% 22.09% 281ms 6.88% vtkObject::vtkObject 1ms 0.024% 22.12% 278ms 6.81% vtkCell::~vtkCell 8ms 0.2% 22.31% 270ms 6.61% __printf_fp_l_buffer 0 0% 22.31% 270ms 6.61% __printf_fp_spec (inline) 164ms 4.02% 26.33% 262ms 6.42% _int_malloc 110ms 2.69% 29.02% 252ms 6.17% __printf_fp_buffer_1 2ms 0.049% 29.07% 248ms 6.07% std::set::set (inline) 13ms 0.32% 29.39% 245ms 6.00% std::_Rb_tree::_Rb_tree 0 0% 29.39% 242ms 5.93% std::_Rb_tree::_M_create_node (inline) 0 0% 29.39% 238ms 5.83% vtkXMLWriter::WritePointsAppendedData 25ms 0.61% 30.00% 236ms 5.78% vtkObject::Modified 0 0% 30.00% 227ms 5.56% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 30.00% 226ms 5.54% VtkMeshWriter::WriteFiles 0 0% 30.00% 222ms 5.44% std::_Rb_tree::_M_get_node (inline) 10ms 0.24% 30.25% 212ms 5.19% std::_Rb_tree::_M_copy (inline) 4ms 0.098% 30.35% 211ms 5.17% std::__new_allocator::deallocate (inline) 0 0% 30.35% 210ms 5.14% std::_Rb_tree::_Alloc_node::operator() (inline) 209ms 5.12% 35.46% 209ms 5.12% vtkTimeStamp::Modified 0 0% 35.46% 208ms 5.09% std::allocator_traits::deallocate (inline) 29ms 0.71% 36.17% 201ms 4.92% std::_Rb_tree::_M_clone_node (inline) 150ms 3.67% 39.85% 189ms 4.63% vtkObjectBase::UnRegisterInternal 6ms 0.15% 40.00% 171ms 4.19% vtkBase64OutputStream::Write 0 0% 40.00% 164ms 4.02% vtkDoubleArray::vtkDoubleArray 0 0% 40.00% 164ms 4.02% vtkQuad::~vtkQuad 0 0% 40.00% 163ms 3.99% vtkXMLWriter::WriteCompressionBlock 18ms 0.44% 40.44% 161ms 3.94% vtkBase64OutputStream::EncodeTriplet 0 0% 40.44% 161ms 3.94% vtkFloatArray::New 3ms 0.073% 40.51% 160ms 3.92% vtkPoints::~vtkPoints 0 0% 40.51% 159ms 3.89% compress2 35ms 0.86% 41.37% 159ms 3.89% crc32 0 0% 41.37% 159ms 3.89% deflate 0 0% 41.37% 159ms 3.89% vtkDataCompressor::Compress 0 0% 41.37% 159ms 3.89% vtkZLibDataCompressor::CompressBuffer 0 0% 41.37% 157ms 3.85% vtkTriangle::~vtkTriangle 2ms 0.049% 41.42% 155ms 3.80% vtkDataArray::CreateDataArray 99ms 2.42% 43.84% 152ms 3.72% malloc_consolidate 4ms 0.098% 43.94% 147ms 3.60% vtkFloatArray::vtkFloatArray 1ms 0.024% 43.96% 146ms 3.58% vtkTypeFloat64Array::New 0 0% 43.96% 144ms 3.53% VertexMesh::~VertexMesh 4ms 0.098% 44.06% 142ms 3.48% NodesOnlyMesh::ConstructNodesWithoutMesh 0 0% 44.06% 142ms 3.48% vtkLine::GetParametricCenter 0 0% 44.06% 141ms 3.45% PottsMesh::GetMooreNeighbouringNodeIndices 0 0% 44.06% 137ms 3.36% VertexMesh::VertexMesh 0 0% 44.06% 136ms 3.33% vtkIdList::AllocateInternal 7ms 0.17% 44.23% 134ms 3.28% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.024% 44.26% 134ms 3.28% vtkTypeFloat64Array::vtkTypeFloat64Array 28ms 0.69% 44.94% 133ms 3.26% std::_Rb_tree::_M_erase 0 0% 44.94% 126ms 3.09% std::vector::~vector (inline) 0 0% 44.94% 126ms 3.09% tbb::detail::r1::parallel_pipeline 4ms 0.098% 45.04% 124ms 3.04% MutableElement::BuildEdges 0 0% 45.04% 124ms 3.04% VertexMesh::GenerateEdgesFromElements (inline) 38ms 0.93% 45.97% 123ms 3.01% std::ostream::write 0 0% 45.97% 123ms 3.01% vtkTypeFloat64Array::~vtkTypeFloat64Array 0 0% 45.97% 122ms 2.99% clone3 0 0% 45.97% 122ms 2.99% start_thread 113ms 2.77% 48.74% 118ms 2.89% [libz.so.1.3] 2ms 0.049% 48.79% 117ms 2.87% NodeLocationWriter::VisitAnyPopulation 1ms 0.024% 48.81% 116ms 2.84% std::_Vector_base::_M_deallocate (inline) 0 0% 48.81% 114ms 2.79% std::set::~set (inline) 0 0% 48.81% 113ms 2.77% tbb::detail::r1::reset 110ms 2.69% 51.51% 110ms 2.69% [libvtkCommonCore-9.3.so.9.3] 1ms 0.024% 51.53% 109ms 2.67% std::_Vector_base::_M_allocate (inline) 0 0% 51.53% 105ms 2.57% EdgeHelper::~EdgeHelper (inline) 0 0% 51.53% 105ms 2.57% std::_Rb_tree::_M_drop_node (inline) 61ms 1.49% 53.02% 103ms 2.52% tbb::detail::r1::wait_bounded_queue_monitor 3ms 0.073% 53.10% 102ms 2.50% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 1ms 0.024% 53.12% 102ms 2.50% EdgeHelper::GetEdgeFromNodes 9ms 0.22% 53.34% 101ms 2.47% std::vector::_M_default_append 0 0% 53.34% 100ms 2.45% std::_Vector_base::~_Vector_base (inline) 41ms 1.00% 54.35% 98ms 2.40% hack_digit 97ms 2.38% 56.72% 97ms 2.38% vtkObjectBase::vtkObjectBase 0 0% 56.72% 95ms 2.33% vtkIdList::Allocate 0 0% 56.72% 93ms 2.28% std::_Rb_tree::_M_put_node (inline) 1ms 0.024% 56.75% 93ms 2.28% vtkFloatArray::~vtkFloatArray 0 0% 56.75% 90ms 2.20% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 56.75% 89ms 2.18% vtkIdList::New 88ms 2.16% 58.90% 88ms 2.16% __strcmp_evex 27ms 0.66% 59.56% 87ms 2.13% std::basic_filebuf::xsputn 0 0% 59.56% 86ms 2.11% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.098% 59.66% 86ms 2.11% vtkDataArray::vtkDataArray 0 0% 59.66% 82ms 2.01% Cell::HasCellProperty (inline) 2ms 0.049% 59.71% 82ms 2.01% CellPropertyCollection::HasProperty 5ms 0.12% 59.83% 82ms 2.01% vtkAbstractArray::vtkAbstractArray 3ms 0.073% 59.91% 80ms 1.96% _int_free_maybe_consolidate 1ms 0.024% 59.93% 79ms 1.93% AbstractCellProperty::IsType (inline) 25ms 0.61% 60.54% 78ms 1.91% vtkAOSDataArrayTemplate::DataElementChanged 2ms 0.049% 60.59% 76ms 1.86% std::vector::push_back (inline) 20ms 0.49% 61.08% 71ms 1.74% __dynamic_cast 32ms 0.78% 61.87% 71ms 1.74% vtkTypeFloat64Array::PrintSelf 0 0% 61.87% 70ms 1.71% AbstractCellProperty::IsSubType (inline) 2ms 0.049% 61.92% 68ms 1.67% std::map::operator[] (partial-inline) 0 0% 61.92% 68ms 1.67% vtkXMLWriter::WritePointDataAppendedData 66ms 1.62% 63.53% 66ms 1.62% unlink_chunk 2ms 0.049% 63.58% 65ms 1.59% AbstractCellPopulation::GetCellUsingLocationIndex 10ms 0.24% 63.83% 60ms 1.47% AbstractCellProperty::IsSame 0 0% 63.83% 59ms 1.45% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 0 0% 63.83% 58ms 1.42% NodesOnlyMesh::SetUpBoxCollection 42ms 1.03% 64.85% 57ms 1.40% std::basic_streambuf::xsputn 0 0% 64.85% 53ms 1.30% std::_Rb_tree::_M_insert_unique 2ms 0.049% 64.90% 53ms 1.30% std::operator<< (inline) 0 0% 64.90% 53ms 1.30% std::set::insert (inline) 3ms 0.073% 64.98% 52ms 1.27% std::vector::_M_realloc_insert 1ms 0.024% 65.00% 52ms 1.27% vtkDoubleArray::~vtkDoubleArray 0 0% 65.00% 51ms 1.25% Cell::GetCellProliferativeType 20ms 0.49% 65.49% 51ms 1.25% std::__ostream_insert 5ms 0.12% 65.61% 50ms 1.22% std::type_info::operator== (inline) 3ms 0.073% 65.69% 49ms 1.20% boost::numeric::ublas::c_vector::c_vector (partial-inline) 46ms 1.13% 66.81% 46ms 1.13% vtkObjectBase::RegisterInternal 3ms 0.073% 66.89% 45ms 1.10% std::_Rb_tree::_M_insert_ (inline) 0 0% 66.89% 45ms 1.10% vtkDataArray::~vtkDataArray 0 0% 66.89% 44ms 1.08% boost::numeric::ublas::vector_assign (inline) 1ms 0.024% 66.91% 44ms 1.08% vtkIdList::vtkIdList 5ms 0.12% 67.03% 43ms 1.05% VertexMeshWriter::GetNextNode 18ms 0.44% 67.47% 42ms 1.03% std::__new_allocator::construct (inline) 0 0% 67.47% 42ms 1.03% std::allocator_traits::construct (inline) 7ms 0.17% 67.65% 42ms 1.03% std::num_put::_M_insert_int 0 0% 67.65% 41ms 1.00% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 40ms 0.98% 68.63% 40ms 0.98% __memcpy_avx512_unaligned_erms 0 0% 68.63% 39ms 0.96% VertexMesh::Clear 39ms 0.96% 69.58% 39ms 0.96% [libchaste_cell_based.so] 0 0% 69.58% 39ms 0.96% std::_Rb_tree::_M_emplace_hint_unique 0 0% 69.58% 39ms 0.96% vtkDoubleArray::New 38ms 0.93% 70.51% 38ms 0.93% __GI_sched_yield 38ms 0.93% 71.44% 38ms 0.93% __mpn_divrem 8ms 0.2% 71.64% 37ms 0.91% std::_Rb_tree::_M_lower_bound (inline) 0 0% 71.64% 36ms 0.88% NodesOnlyMesh::~NodesOnlyMesh 14ms 0.34% 71.98% 36ms 0.88% __cxxabiv1::__si_class_type_info::__do_dyncast 28ms 0.69% 72.67% 36ms 0.88% std::_Hashtable::clear 35ms 0.86% 73.52% 35ms 0.86% [libstdc++.so.6.0.33] 11ms 0.27% 73.79% 35ms 0.86% boost::numeric::ublas::indexing_vector_assign 0 0% 73.79% 34ms 0.83% std::_Destroy (inline) 1ms 0.024% 73.82% 34ms 0.83% std::_Destroy_aux::__destroy (inline) 34ms 0.83% 74.65% 34ms 0.83% std::codecvt::do_always_noconv 0 0% 74.65% 33ms 0.81% std::make_unique (inline) 0 0% 74.65% 32ms 0.78% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 74.65% 31ms 0.76% Cell::GetCellId 1ms 0.024% 74.68% 31ms 0.76% DistributedBoxCollection::SetupLocalBoxesHalfOnly 19ms 0.47% 75.14% 31ms 0.76% vtkObject::ObjectFinalize 1ms 0.024% 75.17% 29ms 0.71% CellIdWriter::GetCellDataForVtkOutput 2ms 0.049% 75.21% 29ms 0.71% boost::detail::shared_count::~shared_count (inline) 0 0% 75.21% 29ms 0.71% boost::shared_ptr::~shared_ptr (inline) 0 0% 75.21% 29ms 0.71% call_init (inline) 3ms 0.073% 75.29% 29ms 0.71% vtkDataArrayPrivate::DoComputeVectorRange 1ms 0.024% 75.31% 28ms 0.69% 0 0% 75.31% 28ms 0.69% CxxTest::RealWorldDescription::setUp 0 0% 75.31% 28ms 0.69% PMPI_Init_thread 0 0% 75.31% 28ms 0.69% PetscInitialize 0 0% 75.31% 28ms 0.69% PetscSetup::setUpWorld 0 0% 75.31% 28ms 0.69% PetscSetupUtils::CommonSetup 0 0% 75.31% 28ms 0.69% PetscSetupUtils::InitialisePetsc 0 0% 75.31% 28ms 0.69% _dl_init 0 0% 75.31% 28ms 0.69% ompi_mpi_init 0 0% 75.31% 28ms 0.69% tcache_get (inline) 28ms 0.69% 76.00% 28ms 0.69% tcache_get_n (inline) 2ms 0.049% 76.05% 28ms 0.69% vtkIdList::~vtkIdList 0 0% 76.05% 27ms 0.66% _dl_start_user 0 0% 76.05% 27ms 0.66% std::_Rb_tree::lower_bound (inline) 0 0% 76.05% 27ms 0.66% std::map::lower_bound (inline) 5ms 0.12% 76.17% 27ms 0.66% tbb::detail::r1::cancel_group_execution 0 0% 76.17% 27ms 0.66% vtkDataArray::ComputeRange 26ms 0.64% 76.81% 26ms 0.64% __GI___writev 24ms 0.59% 77.39% 26ms 0.64% boost::detail::sp_counted_base::release 0 0% 77.39% 26ms 0.64% std::__basic_file::xsputn_2 6ms 0.15% 77.54% 26ms 0.64% vtk::detail::smp::vtkSMPToolsImpl::For 3ms 0.073% 77.61% 26ms 0.64% vtkAOSDataArrayTemplate::InsertTuple 0 0% 77.61% 25ms 0.61% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 14ms 0.34% 77.96% 25ms 0.61% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 77.96% 25ms 0.61% DistributedBoxCollection::IsOwned 1ms 0.024% 77.98% 25ms 0.61% PottsMesh::GetVonNeumannNeighbouringNodeIndices 25ms 0.61% 78.59% 25ms 0.61% boost::numeric::ublas::c_vector::operator() 0 0% 78.59% 25ms 0.61% vtk::detail::smp::vtkSMPToolsImplForTBB 1ms 0.024% 78.62% 24ms 0.59% Node::AddElement 0 0% 78.62% 24ms 0.59% Node::ConstructNodeAttributes (inline) 0 0% 78.62% 24ms 0.59% Node::SetRadius 24ms 0.59% 79.21% 24ms 0.59% [libchaste_mesh.so] 14ms 0.34% 79.55% 24ms 0.59% __printf_buffer_write 4ms 0.098% 79.65% 24ms 0.59% boost::serialization::singleton::get_instance 0 0% 79.65% 24ms 0.59% std::unique_ptr::~unique_ptr (inline) 1ms 0.024% 79.67% 23ms 0.56% Cell::GetMutationState 4ms 0.098% 79.77% 23ms 0.56% __find_specmb (inline) 0 0% 79.77% 23ms 0.56% std::default_delete::operator() (inline) 1ms 0.024% 79.79% 23ms 0.56% std::vector::emplace_back (inline) 23ms 0.56% 80.36% 23ms 0.56% vtkObject::~vtkObject 0 0% 80.36% 22ms 0.54% DistributedBoxCollection::~DistributedBoxCollection 0 0% 80.36% 22ms 0.54% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 80.36% 22ms 0.54% PottsBasedCellPopulation::AcceptCellWriter 1ms 0.024% 80.38% 22ms 0.54% VertexMeshWriter::GetNextElement 1ms 0.024% 80.41% 22ms 0.54% orte_init 22ms 0.54% 80.95% 22ms 0.54% std::ostream::sentry::sentry 0 0% 80.95% 21ms 0.51% VertexElement::VertexElement 1ms 0.024% 80.97% 21ms 0.51% VtkMeshWriter::MakeVtkMesh 0 0% 80.97% 21ms 0.51% boost::numeric::ublas::c_vector::assign (inline) 1ms 0.024% 80.99% 21ms 0.51% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline)