File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3745ms, 79.65% of 4702ms total Dropped 779 nodes (cum <= 23.51ms) flat flat% sum% cum cum% 0 0% 0% 4510ms 95.92% __libc_start_call_main 0 0% 0% 4510ms 95.92% __libc_start_main_impl 0 0% 0% 4510ms 95.92% _start 0 0% 0% 4492ms 95.53% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4492ms 95.53% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4492ms 95.53% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4492ms 95.53% main 0 0% 0% 4453ms 94.70% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4453ms 94.70% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4453ms 94.70% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4441ms 94.45% AbstractCellBasedSimulation::Solve 0 0% 0% 4135ms 87.94% AbstractCellPopulation::WriteResultsToFiles 17ms 0.36% 0.36% 3925ms 83.48% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.36% 1979ms 42.09% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.021% 0.38% 1708ms 36.32% VertexMeshWriter::MakeVtkMesh 0 0% 0.38% 1253ms 26.65% vtkPolygon::New 0 0% 0.38% 1251ms 26.61% vtkPolygon::vtkPolygon 8ms 0.17% 0.55% 895ms 19.03% vtkCell::vtkCell 7ms 0.15% 0.7% 776ms 16.50% vtkPoints::New 11ms 0.23% 0.94% 719ms 15.29% vtkPoints::vtkPoints 1ms 0.021% 0.96% 679ms 14.44% VertexMeshWriter::WriteFiles 47ms 1% 1.96% 633ms 13.46% std::ostream::_M_insert 1ms 0.021% 1.98% 633ms 13.46% std::ostream::operator<< (inline) 38ms 0.81% 2.79% 627ms 13.33% operator new 3ms 0.064% 2.85% 608ms 12.93% vtkLine::New 178ms 3.79% 6.64% 594ms 12.63% __GI___libc_malloc 15ms 0.32% 6.95% 593ms 12.61% vtkLine::vtkLine 3ms 0.064% 7.02% 585ms 12.44% vtkQuad::New 4ms 0.085% 7.10% 580ms 12.34% vtkQuad::vtkQuad 0 0% 7.10% 576ms 12.25% vtkStreamingDemandDrivenPipeline::Update 0 0% 7.10% 576ms 12.25% vtkXMLWriterBase::Write 0 0% 7.10% 573ms 12.19% vtkDemandDrivenPipeline::ProcessRequest 0 0% 7.10% 573ms 12.19% vtkStreamingDemandDrivenPipeline::ProcessRequest 1ms 0.021% 7.12% 572ms 12.17% vtkExecutive::CallAlgorithm 0 0% 7.12% 571ms 12.14% vtkCompositeDataPipeline::ExecuteData 0 0% 7.12% 571ms 12.14% vtkDemandDrivenPipeline::ExecuteData 0 0% 7.12% 570ms 12.12% vtkXMLUnstructuredDataWriter::ProcessRequest 2ms 0.043% 7.17% 560ms 11.91% vtkTriangle::New 4ms 0.085% 7.25% 549ms 11.68% vtkTriangle::vtkTriangle 0 0% 7.25% 510ms 10.85% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 7.25% 510ms 10.85% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 39ms 0.83% 8.08% 506ms 10.76% std::num_put::_M_insert_float 131ms 2.79% 10.87% 491ms 10.44% __GI___libc_free 34ms 0.72% 11.59% 456ms 9.70% vtkPoints::SetDataType 0 0% 11.59% 440ms 9.36% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 11.59% 438ms 9.32% vtkXMLWriter::WriteBinaryData 0 0% 11.59% 433ms 9.21% vtkXMLWriter::WriteBinaryDataBlock 0 0% 11.59% 433ms 9.21% vtkXMLWriter::WriteBinaryDataInternal 0 0% 11.59% 412ms 8.76% vtkPolygon::~vtkPolygon 10ms 0.21% 11.80% 408ms 8.68% std::__cxx11::collate::do_transform 3ms 0.064% 11.87% 387ms 8.23% ___vsnprintf 1ms 0.021% 11.89% 384ms 8.17% __vsnprintf_internal (inline) 57ms 1.21% 13.10% 376ms 8.00% __printf_buffer 215ms 4.57% 17.67% 356ms 7.57% _int_free 226ms 4.81% 22.48% 350ms 7.44% _int_malloc 0 0% 22.48% 343ms 7.29% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 22.48% 340ms 7.23% VtkMeshWriter::WriteFiles 0 0% 22.48% 329ms 7.00% vtkXMLWriter::WritePointsAppendedData 5ms 0.11% 22.59% 324ms 6.89% vtkCell::~vtkCell 0 0% 22.59% 300ms 6.38% OnLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.021% 22.61% 300ms 6.38% PottsBasedCellPopulation::UpdateCellLocations 13ms 0.28% 22.88% 295ms 6.27% __printf_fp_l_buffer 0 0% 22.88% 295ms 6.27% __printf_fp_spec (inline) 40ms 0.85% 23.73% 279ms 5.93% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 125ms 2.66% 26.39% 269ms 5.72% __printf_fp_buffer_1 41ms 0.87% 27.26% 259ms 5.51% std::__new_allocator::allocate (inline) 0 0% 27.26% 256ms 5.44% std::allocator_traits::allocate (inline) 5ms 0.11% 27.37% 252ms 5.36% std::__new_allocator::deallocate (inline) 0 0% 27.37% 248ms 5.27% std::allocator_traits::deallocate (inline) 0 0% 27.37% 229ms 4.87% vtkXMLWriter::WriteCompressionBlock 8ms 0.17% 27.54% 218ms 4.64% vtkPoints::~vtkPoints 0 0% 27.54% 216ms 4.59% compress2 46ms 0.98% 28.52% 216ms 4.59% crc32 0 0% 28.52% 216ms 4.59% deflate 0 0% 28.52% 216ms 4.59% vtkDataCompressor::Compress 0 0% 28.52% 216ms 4.59% vtkZLibDataCompressor::CompressBuffer 1ms 0.021% 28.54% 207ms 4.40% vtkBase64OutputStream::Write 17ms 0.36% 28.90% 203ms 4.32% vtkBase64OutputStream::EncodeTriplet 13ms 0.28% 29.18% 200ms 4.25% std::_Rb_tree::_Rb_tree 0 0% 29.18% 200ms 4.25% std::set::set (inline) 0 0% 29.18% 195ms 4.15% vtkQuad::~vtkQuad 9ms 0.19% 29.37% 186ms 3.96% vtkFloatArray::New 1ms 0.021% 29.39% 182ms 3.87% vtkLine::GetParametricCenter 1ms 0.021% 29.41% 175ms 3.72% NodesOnlyMesh::ConstructNodesWithoutMesh 71ms 1.51% 30.92% 173ms 3.68% std::basic_filebuf::xsputn 45ms 0.96% 31.88% 172ms 3.66% std::ostream::write 1ms 0.021% 31.90% 168ms 3.57% vtkTriangle::~vtkTriangle 0 0% 31.90% 167ms 3.55% tbb::detail::r1::parallel_pipeline 0 0% 31.90% 166ms 3.53% std::_Rb_tree::_M_create_node (inline) 6ms 0.13% 32.03% 165ms 3.51% std::_Rb_tree::~_Rb_tree (inline) 43ms 0.91% 32.94% 164ms 3.49% std::_Rb_tree::_M_erase 5ms 0.11% 33.05% 163ms 3.47% vtkIdList::AllocateInternal 5ms 0.11% 33.16% 161ms 3.42% vtkTypeFloat64Array::~vtkTypeFloat64Array 103ms 2.19% 35.35% 159ms 3.38% malloc_consolidate 0 0% 35.35% 159ms 3.38% std::_Rb_tree::_M_get_node (inline) 10ms 0.21% 35.56% 158ms 3.36% std::_Rb_tree::_M_copy (inline) 0 0% 35.56% 157ms 3.34% clone3 0 0% 35.56% 157ms 3.34% start_thread 3ms 0.064% 35.62% 156ms 3.32% vtkFloatArray::vtkFloatArray 0 0% 35.62% 155ms 3.30% VertexMesh::~VertexMesh 152ms 3.23% 38.86% 155ms 3.30% [libz.so.1.3] 0 0% 38.86% 155ms 3.30% std::_Rb_tree::_Alloc_node::operator() (inline) 1ms 0.021% 38.88% 149ms 3.17% VertexMesh::VertexMesh 0 0% 38.88% 147ms 3.13% std::vector::~vector (inline) 2ms 0.043% 38.92% 147ms 3.13% vtkDataArray::CreateDataArray 5ms 0.11% 39.03% 146ms 3.11% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 14ms 0.3% 39.32% 144ms 3.06% std::_Rb_tree::_M_clone_node (inline) 0 0% 39.32% 143ms 3.04% NodeLocationWriter::VisitAnyPopulation 1ms 0.021% 39.34% 141ms 3.00% tbb::detail::r1::reset 3ms 0.064% 39.41% 140ms 2.98% std::_Vector_base::_M_deallocate (inline) 0 0% 39.41% 138ms 2.93% VertexMesh::GenerateEdgesFromElements (inline) 4ms 0.085% 39.49% 137ms 2.91% MutableElement::BuildEdges 0 0% 39.49% 136ms 2.89% std::set::~set (inline) 5ms 0.11% 39.60% 131ms 2.79% vtkDoubleArray::vtkDoubleArray 9ms 0.19% 39.79% 130ms 2.76% vtkTypeFloat64Array::New 15ms 0.32% 40.11% 129ms 2.74% std::vector::_M_default_append 54ms 1.15% 41.26% 127ms 2.70% tbb::detail::r1::wait_bounded_queue_monitor 22ms 0.47% 41.73% 122ms 2.59% vtkObject::vtkObject 5ms 0.11% 41.83% 121ms 2.57% EdgeHelper::GetEdgeFromNodes 0 0% 41.83% 117ms 2.49% std::_Rb_tree::_M_drop_node (inline) 0 0% 41.83% 114ms 2.42% CellPropertyCollection::GetPropertiesType (inline) 113ms 2.40% 44.24% 113ms 2.40% __strcmp_avx2 0 0% 44.24% 112ms 2.38% EdgeHelper::~EdgeHelper (inline) 1ms 0.021% 44.26% 112ms 2.38% vtkIdList::Allocate 0 0% 44.26% 111ms 2.36% std::_Rb_tree::_M_put_node (inline) 1ms 0.021% 44.28% 110ms 2.34% std::_Vector_base::~_Vector_base (inline) 4ms 0.085% 44.36% 110ms 2.34% vtkFloatArray::~vtkFloatArray 3ms 0.064% 44.43% 107ms 2.28% vtkTypeFloat64Array::vtkTypeFloat64Array 0 0% 44.43% 107ms 2.28% vtkXMLWriter::WritePointDataAppendedData 67ms 1.42% 45.85% 102ms 2.17% vtkObjectBase::UnRegisterInternal 17ms 0.36% 46.21% 101ms 2.15% std::__ostream_insert 1ms 0.021% 46.24% 101ms 2.15% std::operator<< (inline) 2ms 0.043% 46.28% 98ms 2.08% CellPropertyCollection::HasProperty 0 0% 46.28% 97ms 2.06% Cell::HasCellProperty (inline) 0 0% 46.28% 97ms 2.06% std::_Vector_base::_M_allocate (inline) 1ms 0.021% 46.30% 96ms 2.04% AbstractCellProperty::IsSubType (inline) 20ms 0.43% 46.72% 95ms 2.02% __dynamic_cast 46ms 0.98% 47.70% 93ms 1.98% vtkTypeFloat64Array::PrintSelf 3ms 0.064% 47.77% 92ms 1.96% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 40ms 0.85% 48.62% 92ms 1.96% hack_digit 92ms 1.96% 50.57% 92ms 1.96% unlink_chunk 0 0% 50.57% 89ms 1.89% AbstractCellProperty::IsType (inline) 7ms 0.15% 50.72% 89ms 1.89% vtkDoubleArray::~vtkDoubleArray 3ms 0.064% 50.79% 82ms 1.74% std::map::operator[] (partial-inline) 6ms 0.13% 50.91% 82ms 1.74% vtkAOSDataArrayTemplate::DataElementChanged 3ms 0.064% 50.98% 81ms 1.72% _int_free_maybe_consolidate 10ms 0.21% 51.19% 81ms 1.72% boost::numeric::ublas::c_vector::c_vector (inline) 73ms 1.55% 52.74% 73ms 1.55% __GI_sched_yield 13ms 0.28% 53.02% 71ms 1.51% vtkObject::Modified 20ms 0.43% 53.45% 70ms 1.49% std::_Rb_tree::_M_lower_bound (inline) 41ms 0.87% 54.32% 69ms 1.47% std::basic_streambuf::xsputn 0 0% 54.32% 68ms 1.45% boost::numeric::ublas::vector_assign (inline) 12ms 0.26% 54.57% 67ms 1.42% AbstractCellProperty::IsSame 0 0% 54.57% 67ms 1.42% NodesOnlyMesh::SetUpBoxCollection 5ms 0.11% 54.68% 66ms 1.40% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 54.68% 65ms 1.38% std::vector::push_back (inline) 1ms 0.021% 54.70% 64ms 1.36% Cell::GetCellProliferativeType 1ms 0.021% 54.72% 64ms 1.36% PottsMesh::GetMooreNeighbouringNodeIndices 5ms 0.11% 54.83% 63ms 1.34% vtkIdList::New 1ms 0.021% 54.85% 63ms 1.34% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 0 0% 54.85% 61ms 1.30% NodesOnlyMesh::~NodesOnlyMesh 60ms 1.28% 56.13% 60ms 1.28% [libvtkCommonCore-9.3.so.9.3] 0 0% 56.13% 60ms 1.28% tcache_get (inline) 60ms 1.28% 57.40% 60ms 1.28% tcache_get_n (inline) 57ms 1.21% 58.61% 57ms 1.21% std::codecvt::do_always_noconv 0 0% 58.61% 56ms 1.19% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 6ms 0.13% 58.74% 56ms 1.19% vtkDataArray::vtkDataArray 8ms 0.17% 58.91% 55ms 1.17% VertexMeshWriter::GetNextNode 12ms 0.26% 59.17% 55ms 1.17% std::type_info::operator== (inline) 55ms 1.17% 60.34% 55ms 1.17% vtkTimeStamp::Modified 0 0% 60.34% 53ms 1.13% std::_Rb_tree::lower_bound (inline) 0 0% 60.34% 53ms 1.13% std::map::lower_bound (inline) 52ms 1.11% 61.44% 52ms 1.11% __memcpy_avx_unaligned_erms 23ms 0.49% 61.93% 51ms 1.08% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.021% 61.95% 51ms 1.08% std::set::insert (inline) 1ms 0.021% 61.97% 50ms 1.06% std::_Rb_tree::_M_insert_unique 11ms 0.23% 62.21% 50ms 1.06% vtkAbstractArray::vtkAbstractArray 0 0% 62.21% 49ms 1.04% std::_Destroy (inline) 0 0% 62.21% 49ms 1.04% std::_Destroy_aux::__destroy (inline) 24ms 0.51% 62.72% 49ms 1.04% std::_Hashtable::clear 1ms 0.021% 62.74% 49ms 1.04% vtkDataArray::ComputeRange 1ms 0.021% 62.76% 49ms 1.04% vtkDataArrayPrivate::DoComputeVectorRange 11ms 0.23% 62.99% 48ms 1.02% std::num_put::_M_insert_int 2ms 0.043% 63.04% 48ms 1.02% std::vector::_M_realloc_insert 22ms 0.47% 63.50% 47ms 1% boost::numeric::ublas::indexing_vector_assign 46ms 0.98% 64.48% 46ms 0.98% __GI___writev 45ms 0.96% 65.44% 45ms 0.96% [libstdc++.so.6.0.33] 0 0% 65.44% 45ms 0.96% std::__basic_file::xsputn_2 0 0% 65.44% 44ms 0.94% vtk::detail::smp::vtkSMPToolsImplForTBB 5ms 0.11% 65.55% 43ms 0.91% DistributedBoxCollection::SetupLocalBoxesHalfOnly 1ms 0.021% 65.57% 43ms 0.91% VertexMesh::Clear 18ms 0.38% 65.95% 43ms 0.91% vtkDataArray::~vtkDataArray 42ms 0.89% 66.84% 42ms 0.89% vtkObjectBase::vtkObjectBase 10ms 0.21% 67.06% 41ms 0.87% _int_free_merge_chunk 3ms 0.064% 67.12% 41ms 0.87% tbb::detail::r1::cancel_group_execution 0 0% 67.12% 40ms 0.85% DistributedBoxCollection::~DistributedBoxCollection 0 0% 67.12% 40ms 0.85% NodesOnlyMesh::ClearBoxCollection (inline) 39ms 0.83% 67.95% 40ms 0.85% __GI___libc_write 2ms 0.043% 67.99% 39ms 0.83% DistributedBoxCollection::IsOwned 0 0% 67.99% 39ms 0.83% _dl_init 0 0% 67.99% 39ms 0.83% call_init (inline) 0 0% 67.99% 39ms 0.83% std::__basic_file::xsputn 0 0% 67.99% 39ms 0.83% std::basic_filebuf::_M_convert_to_external 0 0% 67.99% 39ms 0.83% std::basic_filebuf::overflow 0 0% 67.99% 39ms 0.83% std::make_unique (inline) 4ms 0.085% 68.08% 39ms 0.83% vtk::detail::smp::vtkSMPToolsImpl::For 3ms 0.064% 68.14% 39ms 0.83% vtkDoubleArray::New 7ms 0.15% 68.29% 39ms 0.83% vtkSOADataArrayTemplate::FillTypedComponent 27ms 0.57% 68.86% 38ms 0.81% std::num_put::do_put 0 0% 68.86% 37ms 0.79% Cell::GetMutationState 25ms 0.53% 69.40% 37ms 0.79% DistributedBoxCollection::CalculateContainingBox (inline) 37ms 0.79% 70.18% 37ms 0.79% vtkObject::~vtkObject 37ms 0.79% 70.97% 37ms 0.79% vtkObjectBase::Delete 0 0% 70.97% 36ms 0.77% vtkAOSDataArrayTemplate::InsertTuple 0 0% 70.97% 35ms 0.74% CxxTest::RealWorldDescription::setUp 0 0% 70.97% 35ms 0.74% PetscInitialize 0 0% 70.97% 35ms 0.74% PetscSetup::setUpWorld 0 0% 70.97% 35ms 0.74% PetscSetupUtils::CommonSetup 0 0% 70.97% 35ms 0.74% PetscSetupUtils::InitialisePetsc 0 0% 70.97% 35ms 0.74% _dl_start_user 4ms 0.085% 71.05% 35ms 0.74% std::_Rb_tree::_M_insert_ (inline) 0 0% 71.05% 35ms 0.74% std::less::operator() (inline) 35ms 0.74% 71.80% 35ms 0.74% std::operator< (inline) 30ms 0.64% 72.44% 35ms 0.74% vtkObject::ObjectFinalize 2ms 0.043% 72.48% 34ms 0.72% 0 0% 72.48% 34ms 0.72% PMPI_Init_thread 0 0% 72.48% 34ms 0.72% ompi_mpi_init 34ms 0.72% 73.20% 34ms 0.72% std::ostream::sentry::sentry 0 0% 73.20% 32ms 0.68% Cell::GetCellId 0 0% 73.20% 32ms 0.68% Node::ConstructNodeAttributes (inline) 0 0% 73.20% 32ms 0.68% Node::SetRadius 31ms 0.66% 73.86% 31ms 0.66% __mpn_divrem 17ms 0.36% 74.22% 31ms 0.66% _int_free_create_chunk (inline) 2ms 0.043% 74.27% 30ms 0.64% CellProliferativeTypesWriter::GetCellDataForVtkOutput 3ms 0.064% 74.33% 30ms 0.64% Node::GetPoint 30ms 0.64% 74.97% 30ms 0.64% __memset_avx2_unaligned_erms 0 0% 74.97% 30ms 0.64% std::map::~map (inline) 4ms 0.085% 75.05% 29ms 0.62% NodeAttributes::NodeAttributes 5ms 0.11% 75.16% 29ms 0.62% boost::serialization::singleton::get_instance 0 0% 75.16% 29ms 0.62% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 0 0% 75.16% 29ms 0.62% std::_Rb_tree_header::_Rb_tree_header (inline) 29ms 0.62% 75.78% 29ms 0.62% std::_Rb_tree_increment 0 0% 75.78% 29ms 0.62% std::basic_filebuf::open 0 0% 75.78% 29ms 0.62% std::default_delete::operator() (inline) 0 0% 75.78% 29ms 0.62% std::unique_ptr::~unique_ptr (inline) 5ms 0.11% 75.88% 29ms 0.62% vtkIdList::~vtkIdList 0 0% 75.88% 28ms 0.6% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 75.88% 28ms 0.6% CellIdWriter::GetCellDataForVtkOutput 0 0% 75.88% 28ms 0.6% PottsBasedCellPopulation::AcceptCellWriter 28ms 0.6% 76.48% 28ms 0.6% std::_Rb_tree_header::_M_reset (inline) 11ms 0.23% 76.71% 28ms 0.6% vtkAbstractArray::~vtkAbstractArray 1ms 0.021% 76.73% 27ms 0.57% std::ostream::flush 27ms 0.57% 77.31% 27ms 0.57% vtkObjectBase::~vtkObjectBase 1ms 0.021% 77.33% 26ms 0.55% Edge::Edge 1ms 0.021% 77.35% 26ms 0.55% PottsMesh::GetVonNeumannNeighbouringNodeIndices 26ms 0.55% 77.90% 26ms 0.55% [libchaste_cell_based.so] 0 0% 77.90% 26ms 0.55% _IO_new_file_fopen 0 0% 77.90% 26ms 0.55% _IO_new_fopen 0 0% 77.90% 26ms 0.55% __GI__IO_file_open 0 0% 77.90% 26ms 0.55% __fopen_internal (inline) 26ms 0.55% 78.46% 26ms 0.55% __libc_open64 0 0% 78.46% 26ms 0.55% boost::numeric::ublas::c_vector::assign (inline) 2ms 0.043% 78.50% 26ms 0.55% std::_Rb_tree::_M_emplace_hint_unique 0 0% 78.50% 26ms 0.55% std::__basic_file::open 0 0% 78.50% 26ms 0.55% std::basic_filebuf::sync 26ms 0.55% 79.05% 26ms 0.55% syscall 0 0% 79.05% 25ms 0.53% Edge::SetNodes (inline) 24ms 0.51% 79.56% 24ms 0.51% boost::numeric::ublas::c_vector::operator() 0 0% 79.56% 24ms 0.51% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 0 0% 79.56% 24ms 0.51% std::basic_filebuf::close 4ms 0.085% 79.65% 24ms 0.51% vtkAOSDataArrayTemplate::AllocateTuples