File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3267ms, 81.07% of 4030ms total Dropped 653 nodes (cum <= 20.15ms) flat flat% sum% cum cum% 0 0% 0% 3893ms 96.60% __libc_start_call_main 0 0% 0% 3893ms 96.60% __libc_start_main_impl 0 0% 0% 3893ms 96.60% _start 0 0% 0% 3877ms 96.20% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 3877ms 96.20% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 3877ms 96.20% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 3877ms 96.20% main 0 0% 0% 3847ms 95.46% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 3846ms 95.43% CxxTest::TestRunner::runTest (inline) 0 0% 0% 3846ms 95.43% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 3837ms 95.21% AbstractCellBasedSimulation::Solve 0 0% 0% 3588ms 89.03% AbstractCellPopulation::WriteResultsToFiles 4ms 0.099% 0.099% 3401ms 84.39% PottsBasedCellPopulation::WriteVtkResultsToFile 1ms 0.025% 0.12% 1776ms 44.07% VertexMeshWriter::WriteVtkUsingMesh 0 0% 0.12% 1590ms 39.45% VertexMeshWriter::MakeVtkMesh 0 0% 0.12% 1173ms 29.11% vtkPolygon::New 0 0% 0.12% 1173ms 29.11% vtkPolygon::vtkPolygon 7ms 0.17% 0.3% 856ms 21.24% vtkCell::vtkCell 2ms 0.05% 0.35% 661ms 16.40% vtkPoints::New 34ms 0.84% 1.19% 643ms 15.96% operator new 4ms 0.099% 1.29% 640ms 15.88% vtkPoints::vtkPoints 279ms 6.92% 8.21% 607ms 15.06% __GI___libc_malloc 3ms 0.074% 8.29% 581ms 14.42% VertexMeshWriter::WriteFiles 0 0% 8.29% 553ms 13.72% std::ostream::operator<< (inline) 40ms 0.99% 9.28% 552ms 13.70% std::ostream::_M_insert 2ms 0.05% 9.33% 540ms 13.40% vtkLine::New 1ms 0.025% 9.35% 526ms 13.05% vtkQuad::New 0 0% 9.35% 524ms 13.00% vtkQuad::vtkQuad 2ms 0.05% 9.40% 517ms 12.83% vtkLine::vtkLine 0 0% 9.40% 506ms 12.56% vtkTriangle::New 0 0% 9.40% 498ms 12.36% vtkTriangle::vtkTriangle 38ms 0.94% 10.35% 458ms 11.36% std::num_put::_M_insert_float 63ms 1.56% 11.91% 444ms 11.02% __GI___libc_free 0 0% 11.91% 389ms 9.65% vtkStreamingDemandDrivenPipeline::Update 0 0% 11.91% 389ms 9.65% vtkXMLWriterBase::Write 0 0% 11.91% 386ms 9.58% vtkDemandDrivenPipeline::ProcessRequest 0 0% 11.91% 386ms 9.58% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 11.91% 384ms 9.53% vtkCompositeDataPipeline::ExecuteData 0 0% 11.91% 384ms 9.53% vtkDemandDrivenPipeline::ExecuteData 0 0% 11.91% 384ms 9.53% vtkExecutive::CallAlgorithm 0 0% 11.91% 384ms 9.53% vtkXMLUnstructuredDataWriter::ProcessRequest 12ms 0.3% 12.21% 382ms 9.48% vtkPoints::SetDataType 246ms 6.10% 18.31% 379ms 9.40% _int_free 1ms 0.025% 18.34% 377ms 9.35% vtkPolygon::~vtkPolygon 9ms 0.22% 18.56% 366ms 9.08% std::__cxx11::collate::do_transform 0 0% 18.56% 347ms 8.61% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 18.56% 347ms 8.61% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 18.56% 345ms 8.56% ___vsnprintf 1ms 0.025% 18.59% 345ms 8.56% __vsnprintf_internal (inline) 36ms 0.89% 19.48% 338ms 8.39% __printf_buffer 0 0% 19.48% 316ms 7.84% vtkXMLWriter::WriteBinaryData 0 0% 19.48% 316ms 7.84% vtkXMLWriter::WriteBinaryDataBlock 0 0% 19.48% 316ms 7.84% vtkXMLWriter::WriteBinaryDataInternal 0 0% 19.48% 301ms 7.47% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 39ms 0.97% 20.45% 295ms 7.32% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 19ms 0.47% 20.92% 292ms 7.25% std::__new_allocator::allocate (inline) 0 0% 20.92% 292ms 7.25% std::allocator_traits::allocate (inline) 159ms 3.95% 24.86% 277ms 6.87% _int_malloc 2ms 0.05% 24.91% 275ms 6.82% vtkCell::~vtkCell 1ms 0.025% 24.94% 271ms 6.72% __printf_fp_spec (inline) 15ms 0.37% 25.31% 271ms 6.72% vtkObject::vtkObject 9ms 0.22% 25.53% 270ms 6.70% __printf_fp_l_buffer 113ms 2.80% 28.34% 250ms 6.20% __printf_fp_buffer_1 0 0% 28.34% 247ms 6.13% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 28.34% 242ms 6.00% VtkMeshWriter::WriteFiles 0 0% 28.34% 240ms 5.96% OnLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.025% 28.36% 240ms 5.96% PottsBasedCellPopulation::UpdateCellLocations 23ms 0.57% 28.93% 238ms 5.91% vtkObject::Modified 0 0% 28.93% 230ms 5.71% vtkXMLWriter::WritePointsAppendedData 2ms 0.05% 28.98% 220ms 5.46% std::__new_allocator::deallocate (inline) 0 0% 28.98% 220ms 5.46% std::allocator_traits::deallocate (inline) 200ms 4.96% 33.95% 200ms 4.96% vtkTimeStamp::Modified 1ms 0.025% 33.97% 191ms 4.74% std::set::set (inline) 4ms 0.099% 34.07% 190ms 4.71% std::_Rb_tree::_Rb_tree 0 0% 34.07% 186ms 4.62% std::_Rb_tree::_M_create_node (inline) 0 0% 34.07% 183ms 4.54% std::_Rb_tree::_M_get_node (inline) 1ms 0.025% 34.09% 168ms 4.17% vtkPoints::~vtkPoints 1ms 0.025% 34.12% 167ms 4.14% vtkQuad::~vtkQuad 14ms 0.35% 34.47% 166ms 4.12% std::_Rb_tree::_M_copy (inline) 0 0% 34.47% 166ms 4.12% vtkXMLWriter::WriteCompressionBlock 115ms 2.85% 37.32% 165ms 4.09% malloc_consolidate 0 0% 37.32% 164ms 4.07% std::_Rb_tree::_Alloc_node::operator() (inline) 5ms 0.12% 37.44% 163ms 4.04% vtkIdList::AllocateInternal 2ms 0.05% 37.49% 160ms 3.97% vtkDoubleArray::vtkDoubleArray 5ms 0.12% 37.62% 157ms 3.90% vtkBase64OutputStream::Write 0 0% 37.62% 154ms 3.82% compress2 0 0% 37.62% 154ms 3.82% deflate 0 0% 37.62% 154ms 3.82% vtkDataCompressor::Compress 3ms 0.074% 37.69% 154ms 3.82% vtkFloatArray::New 0 0% 37.69% 154ms 3.82% vtkZLibDataCompressor::CompressBuffer 35ms 0.87% 38.56% 153ms 3.80% crc32 24ms 0.6% 39.16% 152ms 3.77% std::_Rb_tree::_M_clone_node (inline) 16ms 0.4% 39.55% 151ms 3.75% vtkBase64OutputStream::EncodeTriplet 2ms 0.05% 39.60% 148ms 3.67% vtkTriangle::~vtkTriangle 2ms 0.05% 39.65% 146ms 3.62% vtkDataArray::CreateDataArray 0 0% 39.65% 144ms 3.57% vtkLine::GetParametricCenter 121ms 3.00% 42.66% 144ms 3.57% vtkObjectBase::UnRegisterInternal 1ms 0.025% 42.68% 141ms 3.50% vtkTypeFloat64Array::New 1ms 0.025% 42.70% 140ms 3.47% vtkFloatArray::vtkFloatArray 1ms 0.025% 42.73% 139ms 3.45% VertexMesh::VertexMesh 0 0% 42.73% 137ms 3.40% VertexMesh::~VertexMesh 3ms 0.074% 42.80% 135ms 3.35% MutableElement::BuildEdges 0 0% 42.80% 135ms 3.35% VertexMesh::GenerateEdgesFromElements (inline) 0 0% 42.80% 134ms 3.33% vtkTypeFloat64Array::~vtkTypeFloat64Array 0 0% 42.80% 131ms 3.25% std::vector::~vector (inline) 1ms 0.025% 42.83% 131ms 3.25% vtkTypeFloat64Array::vtkTypeFloat64Array 0 0% 42.83% 128ms 3.18% NodesOnlyMesh::ConstructNodesWithoutMesh 5ms 0.12% 42.95% 127ms 3.15% std::_Rb_tree::~_Rb_tree (inline) 21ms 0.52% 43.47% 126ms 3.13% std::_Rb_tree::_M_erase 0 0% 43.47% 126ms 3.13% std::_Vector_base::_M_deallocate (inline) 1ms 0.025% 43.50% 118ms 2.93% NodeLocationWriter::VisitAnyPopulation 2ms 0.05% 43.55% 117ms 2.90% EdgeHelper::GetEdgeFromNodes 0 0% 43.55% 116ms 2.88% std::set::~set (inline) 0 0% 43.55% 114ms 2.83% tbb::detail::r1::parallel_pipeline 113ms 2.80% 46.35% 113ms 2.80% [libvtkCommonCore-9.3.so.9.3] 107ms 2.66% 49.01% 112ms 2.78% [libz.so.1.3] 3ms 0.074% 49.08% 111ms 2.75% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 27ms 0.67% 49.75% 111ms 2.75% std::ostream::write 1ms 0.025% 49.78% 110ms 2.73% std::_Vector_base::_M_allocate (inline) 0 0% 49.78% 110ms 2.73% vtkIdList::Allocate 0 0% 49.78% 108ms 2.68% clone3 0 0% 49.78% 108ms 2.68% start_thread 0 0% 49.78% 105ms 2.61% std::_Rb_tree::_M_drop_node (inline) 1ms 0.025% 49.80% 105ms 2.61% std::_Vector_base::~_Vector_base (inline) 105ms 2.61% 52.41% 105ms 2.61% vtkObjectBase::vtkObjectBase 103ms 2.56% 54.96% 103ms 2.56% __strcmp_evex 2ms 0.05% 55.01% 102ms 2.53% std::vector::push_back (inline) 1ms 0.025% 55.04% 98ms 2.43% tbb::detail::r1::reset 1ms 0.025% 55.06% 95ms 2.36% vtkIdList::New 0 0% 55.06% 94ms 2.33% EdgeHelper::~EdgeHelper (inline) 0 0% 55.06% 94ms 2.33% std::_Rb_tree::_M_put_node (inline) 5ms 0.12% 55.19% 93ms 2.31% std::vector::_M_default_append 0 0% 55.19% 91ms 2.26% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 1ms 0.025% 55.21% 90ms 2.23% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.099% 55.31% 88ms 2.18% vtkDataArray::vtkDataArray 43ms 1.07% 56.38% 87ms 2.16% std::basic_filebuf::xsputn 55ms 1.36% 57.74% 87ms 2.16% tbb::detail::r1::wait_bounded_queue_monitor 0 0% 57.74% 86ms 2.13% Cell::HasCellProperty (inline) 2ms 0.05% 57.79% 85ms 2.11% AbstractCellProperty::IsType (inline) 2ms 0.05% 57.84% 85ms 2.11% CellPropertyCollection::HasProperty 2ms 0.05% 57.89% 84ms 2.08% vtkAbstractArray::vtkAbstractArray 5ms 0.12% 58.01% 83ms 2.06% _int_free_maybe_consolidate 28ms 0.69% 58.71% 82ms 2.03% hack_digit 36ms 0.89% 59.60% 82ms 2.03% std::__ostream_insert 2ms 0.05% 59.65% 80ms 1.99% std::operator<< (inline) 3ms 0.074% 59.73% 79ms 1.96% AbstractCellProperty::IsSubType (inline) 3ms 0.074% 59.80% 77ms 1.91% vtkFloatArray::~vtkFloatArray 27ms 0.67% 60.47% 76ms 1.89% vtkAOSDataArrayTemplate::DataElementChanged 14ms 0.35% 60.82% 74ms 1.84% __dynamic_cast 28ms 0.69% 61.51% 74ms 1.84% vtkTypeFloat64Array::PrintSelf 0 0% 61.51% 72ms 1.79% PottsMesh::GetMooreNeighbouringNodeIndices 46ms 1.14% 62.66% 70ms 1.74% std::basic_streambuf::xsputn 0 0% 62.66% 70ms 1.74% vtkXMLWriter::WritePointDataAppendedData 3ms 0.074% 62.73% 69ms 1.71% std::map::operator[] (partial-inline) 2ms 0.05% 62.78% 68ms 1.69% std::vector::_M_realloc_insert 1ms 0.025% 62.80% 63ms 1.56% vtkDoubleArray::~vtkDoubleArray 62ms 1.54% 64.34% 62ms 1.54% unlink_chunk 2ms 0.05% 64.39% 59ms 1.46% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.099% 64.49% 59ms 1.46% AbstractCellProperty::IsSame 57ms 1.41% 65.91% 57ms 1.41% [libchaste_cell_based.so] 3ms 0.074% 65.98% 55ms 1.36% std::type_info::operator== (inline) 0 0% 65.98% 54ms 1.34% NodesOnlyMesh::SetUpBoxCollection 1ms 0.025% 66.00% 50ms 1.24% Cell::GetCellProliferativeType 50ms 1.24% 67.25% 50ms 1.24% [libstdc++.so.6.0.33] 0 0% 67.25% 50ms 1.24% std::_Rb_tree::_M_insert_unique 0 0% 67.25% 50ms 1.24% std::set::insert (inline) 1ms 0.025% 67.27% 50ms 1.24% vtkIdList::vtkIdList 0 0% 67.27% 48ms 1.19% std::make_unique (inline) 3ms 0.074% 67.34% 46ms 1.14% std::_Rb_tree::_M_insert_ (inline) 12ms 0.3% 67.64% 45ms 1.12% std::_Rb_tree::_M_lower_bound (inline) 0 0% 67.64% 44ms 1.09% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 1ms 0.025% 67.67% 43ms 1.07% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 0 0% 67.67% 43ms 1.07% DistributedBoxCollection::SetupLocalBoxesHalfOnly 0 0% 67.67% 43ms 1.07% VertexMesh::Clear 7ms 0.17% 67.84% 43ms 1.07% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 67.84% 42ms 1.04% NodesOnlyMesh::~NodesOnlyMesh 8ms 0.2% 68.04% 42ms 1.04% VertexMeshWriter::GetNextNode 41ms 1.02% 69.06% 41ms 1.02% __mpn_divrem 0 0% 69.06% 40ms 0.99% vtkDoubleArray::New 14ms 0.35% 69.40% 39ms 0.97% std::num_put::_M_insert_int 16ms 0.4% 69.80% 38ms 0.94% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 69.80% 37ms 0.92% std::_Destroy (inline) 0 0% 69.80% 37ms 0.92% std::_Destroy_aux::__destroy (inline) 2ms 0.05% 69.85% 37ms 0.92% std::__new_allocator::construct (inline) 0 0% 69.85% 37ms 0.92% std::allocator_traits::construct (inline) 5ms 0.12% 69.98% 37ms 0.92% vtkDataArray::~vtkDataArray 37ms 0.92% 70.89% 37ms 0.92% vtkObjectBase::RegisterInternal 35ms 0.87% 71.76% 35ms 0.87% __memcpy_avx512_unaligned_erms 0 0% 71.76% 35ms 0.87% boost::numeric::ublas::vector_assign (inline) 0 0% 71.76% 33ms 0.82% _dl_init 0 0% 71.76% 33ms 0.82% boost::detail::shared_count::~shared_count (inline) 0 0% 71.76% 33ms 0.82% boost::shared_ptr::~shared_ptr (inline) 0 0% 71.76% 33ms 0.82% call_init (inline) 1ms 0.025% 71.79% 33ms 0.82% std::_Rb_tree::_M_emplace_hint_unique 0 0% 71.79% 33ms 0.82% std::_Rb_tree::lower_bound (inline) 0 0% 71.79% 33ms 0.82% std::map::lower_bound (inline) 33ms 0.82% 72.61% 33ms 0.82% tcache_put (inline) 32ms 0.79% 73.40% 32ms 0.79% __GI_sched_yield 30ms 0.74% 74.14% 31ms 0.77% boost::detail::sp_counted_base::release 0 0% 74.14% 30ms 0.74% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 74.14% 30ms 0.74% Cell::GetCellId 0 0% 74.14% 30ms 0.74% Edge::Edge 0 0% 74.14% 30ms 0.74% Edge::SetNodes (inline) 0 0% 74.14% 29ms 0.72% DistributedBoxCollection::~DistributedBoxCollection 0 0% 74.14% 29ms 0.72% NodesOnlyMesh::ClearBoxCollection (inline) 22ms 0.55% 74.69% 29ms 0.72% __printf_buffer_write 0 0% 74.69% 29ms 0.72% _dl_start_user 29ms 0.72% 75.41% 29ms 0.72% checked_request2size (inline) 0 0% 75.41% 29ms 0.72% vtk::detail::smp::vtkSMPToolsImplForTBB 29ms 0.72% 76.13% 29ms 0.72% vtkObjectBase::Delete 4ms 0.099% 76.23% 28ms 0.69% boost::serialization::singleton::get_instance 28ms 0.69% 76.92% 28ms 0.69% std::codecvt::do_always_noconv 2ms 0.05% 76.97% 28ms 0.69% vtkIdList::~vtkIdList 1ms 0.025% 77.00% 27ms 0.67% CellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 77.00% 27ms 0.67% tbb::detail::r1::cancel_group_execution 4ms 0.099% 77.10% 27ms 0.67% vtkSOADataArrayTemplate::FillTypedComponent 0 0% 77.10% 26ms 0.65% CellIdWriter::GetCellDataForVtkOutput 0 0% 77.10% 26ms 0.65% CxxTest::RealWorldDescription::setUp 0 0% 77.10% 26ms 0.65% PMPI_Init_thread 0 0% 77.10% 26ms 0.65% PetscInitialize 0 0% 77.10% 26ms 0.65% PetscSetup::setUpWorld 0 0% 77.10% 26ms 0.65% PetscSetupUtils::CommonSetup 0 0% 77.10% 26ms 0.65% PetscSetupUtils::InitialisePetsc 0 0% 77.10% 26ms 0.65% PottsBasedCellPopulation::AcceptCellWriter 0 0% 77.10% 26ms 0.65% ompi_mpi_init 0 0% 77.10% 26ms 0.65% std::default_delete::operator() (inline) 0 0% 77.10% 26ms 0.65% std::unique_ptr::~unique_ptr (inline) 3ms 0.074% 77.17% 26ms 0.65% vtkAOSDataArrayTemplate::InsertTuple 0 0% 77.17% 26ms 0.65% vtkDataArray::ComputeRange 3ms 0.074% 77.25% 26ms 0.65% vtkDataArrayPrivate::DoComputeVectorRange 1ms 0.025% 77.27% 25ms 0.62% 1ms 0.025% 77.30% 25ms 0.62% PottsMesh::GetVonNeumannNeighbouringNodeIndices 25ms 0.62% 77.92% 25ms 0.62% [libchaste_mesh.so] 7ms 0.17% 78.09% 25ms 0.62% boost::numeric::ublas::indexing_vector_assign 0 0% 78.09% 25ms 0.62% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 0 0% 78.09% 25ms 0.62% tcache_get (inline) 25ms 0.62% 78.71% 25ms 0.62% tcache_get_n (inline) 0 0% 78.71% 24ms 0.6% Cell::GetMutationState 1ms 0.025% 78.73% 24ms 0.6% VtkMeshWriter::MakeVtkMesh 16ms 0.4% 79.13% 24ms 0.6% std::_Hashtable::clear 0 0% 79.13% 24ms 0.6% std::basic_filebuf::open 2ms 0.05% 79.18% 23ms 0.57% Node::SetRadius 2ms 0.05% 79.23% 23ms 0.57% boost::serialization::void_cast_detail::void_caster::recursive_register 0 0% 79.23% 23ms 0.57% boost::serialization::void_cast_detail::void_caster_primitive::void_caster_primitive (inline) 0 0% 79.23% 23ms 0.57% std::less::operator() (inline) 23ms 0.57% 79.80% 23ms 0.57% std::operator< (inline) 22ms 0.55% 80.35% 23ms 0.57% vtkObject::~vtkObject 1ms 0.025% 80.37% 22ms 0.55% MutableElement::MutableElement 0 0% 80.37% 22ms 0.55% VertexElement::VertexElement 0 0% 80.37% 22ms 0.55% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1ms 0.025% 80.40% 22ms 0.55% std::vector::emplace_back (inline) 2ms 0.05% 80.45% 22ms 0.55% vtk::detail::smp::vtkSMPToolsImpl::For 0 0% 80.45% 21ms 0.52% Node::AddElement 0 0% 80.45% 21ms 0.52% Node::ConstructNodeAttributes (inline) 0 0% 80.45% 21ms 0.52% Node::GetPoint 4ms 0.099% 80.55% 21ms 0.52% __find_specmb (inline) 21ms 0.52% 81.07% 21ms 0.52% boost::numeric::ublas::c_vector::operator()