File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3770ms, 79.02% of 4771ms total Dropped 699 nodes (cum <= 23.86ms) flat flat% sum% cum cum% 0 0% 0% 4521ms 94.76% __libc_start_call_main 0 0% 0% 4521ms 94.76% __libc_start_main_impl 0 0% 0% 4521ms 94.76% _start 0 0% 0% 4506ms 94.45% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4506ms 94.45% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4506ms 94.45% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4506ms 94.45% main 0 0% 0% 4468ms 93.65% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4468ms 93.65% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4468ms 93.65% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4458ms 93.44% AbstractCellBasedSimulation::Solve 0 0% 0% 4184ms 87.70% AbstractCellPopulation::WriteResultsToFiles 16ms 0.34% 0.34% 3950ms 82.79% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.34% 1950ms 40.87% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.021% 0.36% 1680ms 35.21% VertexMeshWriter::MakeVtkMesh 1ms 0.021% 0.38% 1238ms 25.95% vtkPolygon::New 2ms 0.042% 0.42% 1236ms 25.91% vtkPolygon::vtkPolygon 8ms 0.17% 0.59% 895ms 18.76% vtkCell::vtkCell 3ms 0.063% 0.65% 768ms 16.10% vtkPoints::New 0 0% 0.65% 757ms 15.87% VertexMeshWriter::WriteFiles 57ms 1.19% 1.84% 731ms 15.32% std::ostream::_M_insert 1ms 0.021% 1.87% 731ms 15.32% std::ostream::operator<< (inline) 11ms 0.23% 2.10% 716ms 15.01% vtkPoints::vtkPoints 46ms 0.96% 3.06% 627ms 13.14% operator new 39ms 0.82% 3.88% 595ms 12.47% std::num_put::_M_insert_float 2ms 0.042% 3.92% 592ms 12.41% vtkQuad::New 202ms 4.23% 8.15% 591ms 12.39% __GI___libc_malloc 3ms 0.063% 8.22% 588ms 12.32% vtkQuad::vtkQuad 3ms 0.063% 8.28% 576ms 12.07% vtkTriangle::New 0 0% 8.28% 572ms 11.99% vtkStreamingDemandDrivenPipeline::Update 0 0% 8.28% 572ms 11.99% vtkXMLWriterBase::Write 0 0% 8.28% 571ms 11.97% vtkDemandDrivenPipeline::ProcessRequest 0 0% 8.28% 571ms 11.97% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 8.28% 569ms 11.93% vtkDemandDrivenPipeline::ExecuteData 0 0% 8.28% 568ms 11.91% vtkCompositeDataPipeline::ExecuteData 0 0% 8.28% 567ms 11.88% vtkExecutive::CallAlgorithm 0 0% 8.28% 567ms 11.88% vtkXMLUnstructuredDataWriter::ProcessRequest 10ms 0.21% 8.49% 561ms 11.76% vtkTriangle::vtkTriangle 0 0% 8.49% 558ms 11.70% vtkLine::New 12ms 0.25% 8.74% 540ms 11.32% vtkLine::vtkLine 174ms 3.65% 12.39% 512ms 10.73% __GI___libc_free 0 0% 12.39% 511ms 10.71% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 12.39% 511ms 10.71% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 19ms 0.4% 12.79% 477ms 10.00% vtkPoints::SetDataType 0 0% 12.79% 475ms 9.96% vtkXMLWriter::WriteBinaryData 1ms 0.021% 12.81% 467ms 9.79% vtkXMLWriter::WriteBinaryDataInternal 9ms 0.19% 13.00% 465ms 9.75% std::__cxx11::collate::do_transform 1ms 0.021% 13.02% 465ms 9.75% vtkXMLWriter::WriteBinaryDataBlock 5ms 0.1% 13.12% 441ms 9.24% ___vsnprintf 0 0% 13.12% 438ms 9.18% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 13.12% 436ms 9.14% __vsnprintf_internal (inline) 49ms 1.03% 14.15% 432ms 9.05% __printf_buffer 3ms 0.063% 14.21% 392ms 8.22% vtkPolygon::~vtkPolygon 3ms 0.063% 14.27% 360ms 7.55% __printf_fp_spec (inline) 21ms 0.44% 14.71% 357ms 7.48% __printf_fp_l_buffer 1ms 0.021% 14.73% 348ms 7.29% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 14.73% 343ms 7.19% VtkMeshWriter::WriteFiles 215ms 4.51% 19.24% 337ms 7.06% _int_free 0 0% 19.24% 331ms 6.94% vtkXMLWriter::WritePointsAppendedData 217ms 4.55% 23.79% 324ms 6.79% _int_malloc 151ms 3.16% 26.95% 321ms 6.73% __printf_fp_buffer_1 7ms 0.15% 27.10% 320ms 6.71% vtkCell::~vtkCell 41ms 0.86% 27.96% 269ms 5.64% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 0 0% 27.96% 266ms 5.58% OnLatticeSimulation::UpdateCellLocationsAndTopology 5ms 0.1% 28.07% 266ms 5.58% PottsBasedCellPopulation::UpdateCellLocations 26ms 0.54% 28.61% 262ms 5.49% std::__new_allocator::allocate (inline) 0 0% 28.61% 262ms 5.49% std::allocator_traits::allocate (inline) 6ms 0.13% 28.74% 253ms 5.30% std::__new_allocator::deallocate (inline) 0 0% 28.74% 249ms 5.22% std::allocator_traits::deallocate (inline) 0 0% 28.74% 247ms 5.18% vtkXMLWriter::WriteCompressionBlock 0 0% 28.74% 239ms 5.01% vtkDataCompressor::Compress 0 0% 28.74% 238ms 4.99% compress2 74ms 1.55% 30.29% 238ms 4.99% crc32 0 0% 30.29% 238ms 4.99% deflate 0 0% 30.29% 238ms 4.99% vtkZLibDataCompressor::CompressBuffer 0 0% 30.29% 219ms 4.59% tbb::detail::r1::parallel_pipeline 5ms 0.1% 30.39% 218ms 4.57% vtkBase64OutputStream::Write 0 0% 30.39% 216ms 4.53% clone3 0 0% 30.39% 216ms 4.53% start_thread 1ms 0.021% 30.41% 214ms 4.49% tbb::detail::r1::reset 83ms 1.74% 32.15% 213ms 4.46% tbb::detail::r1::wait_bounded_queue_monitor 21ms 0.44% 32.59% 213ms 4.46% vtkBase64OutputStream::EncodeTriplet 2ms 0.042% 32.63% 212ms 4.44% vtkPoints::~vtkPoints 49ms 1.03% 33.66% 178ms 3.73% std::ostream::write 0 0% 33.66% 170ms 3.56% vtkLine::GetParametricCenter 11ms 0.23% 33.89% 169ms 3.54% vtkIdList::AllocateInternal 0 0% 33.89% 164ms 3.44% vtkQuad::~vtkQuad 2ms 0.042% 33.93% 161ms 3.37% NodesOnlyMesh::ConstructNodesWithoutMesh 8ms 0.17% 34.10% 161ms 3.37% vtkFloatArray::New 2ms 0.042% 34.14% 158ms 3.31% NodeLocationWriter::VisitAnyPopulation 34ms 0.71% 34.86% 157ms 3.29% std::_Rb_tree::_M_erase 90ms 1.89% 36.74% 154ms 3.23% malloc_consolidate 16ms 0.34% 37.08% 154ms 3.23% std::_Rb_tree::_Rb_tree 0 0% 37.08% 154ms 3.23% std::set::set (inline) 4ms 0.084% 37.16% 154ms 3.23% vtkDataArray::CreateDataArray 2ms 0.042% 37.20% 153ms 3.21% vtkTriangle::~vtkTriangle 6ms 0.13% 37.33% 152ms 3.19% std::_Rb_tree::~_Rb_tree (inline) 75ms 1.57% 38.90% 152ms 3.19% std::basic_filebuf::xsputn 1ms 0.021% 38.92% 151ms 3.16% vtkTypeFloat64Array::~vtkTypeFloat64Array 0 0% 38.92% 150ms 3.14% std::_Rb_tree::_M_create_node (inline) 0 0% 38.92% 149ms 3.12% VertexMesh::VertexMesh 145ms 3.04% 41.96% 149ms 3.12% [libz.so.1.3] 0 0% 41.96% 143ms 3.00% std::_Rb_tree::_M_get_node (inline) 4ms 0.084% 42.05% 143ms 3.00% std::_Vector_base::_M_deallocate (inline) 0 0% 42.05% 141ms 2.96% VertexMesh::~VertexMesh 0 0% 42.05% 141ms 2.96% std::_Rb_tree::_Alloc_node::operator() (inline) 5ms 0.1% 42.15% 140ms 2.93% vtkFloatArray::~vtkFloatArray 1ms 0.021% 42.17% 139ms 2.91% VertexMesh::GenerateEdgesFromElements (inline) 10ms 0.21% 42.38% 139ms 2.91% vtkTypeFloat64Array::New 7ms 0.15% 42.53% 138ms 2.89% MutableElement::BuildEdges 0 0% 42.53% 137ms 2.87% std::vector::~vector (inline) 2ms 0.042% 42.57% 135ms 2.83% vtkDoubleArray::vtkDoubleArray 1ms 0.021% 42.59% 135ms 2.83% vtkFloatArray::vtkFloatArray 16ms 0.34% 42.93% 134ms 2.81% std::vector::_M_default_append 0 0% 42.93% 128ms 2.68% std::set::~set (inline) 0 0% 42.93% 127ms 2.66% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 127ms 2.66% 45.59% 127ms 2.66% __GI_sched_yield 14ms 0.29% 45.88% 123ms 2.58% std::_Rb_tree::_M_copy (inline) 1ms 0.021% 45.90% 120ms 2.52% vtkTypeFloat64Array::vtkTypeFloat64Array 0 0% 45.90% 119ms 2.49% std::_Vector_base::_M_allocate (inline) 33ms 0.69% 46.59% 118ms 2.47% vtkObject::vtkObject 0 0% 46.59% 115ms 2.41% std::_Rb_tree::_M_drop_node (inline) 2ms 0.042% 46.64% 111ms 2.33% EdgeHelper::GetEdgeFromNodes 1ms 0.021% 46.66% 110ms 2.31% CellPropertyCollection::GetPropertiesType (inline) 0 0% 46.66% 110ms 2.31% std::_Rb_tree::_M_put_node (inline) 62ms 1.30% 47.96% 109ms 2.28% hack_digit 1ms 0.021% 47.98% 109ms 2.28% std::_Vector_base::~_Vector_base (inline) 8ms 0.17% 48.15% 107ms 2.24% std::_Rb_tree::_M_clone_node (inline) 1ms 0.021% 48.17% 106ms 2.22% vtkXMLWriter::WritePointDataAppendedData 0 0% 48.17% 100ms 2.10% vtkIdList::Allocate 0 0% 48.17% 99ms 2.08% EdgeHelper::~EdgeHelper (inline) 43ms 0.9% 49.07% 99ms 2.08% std::__ostream_insert 0 0% 49.07% 98ms 2.05% std::operator<< (inline) 97ms 2.03% 51.10% 97ms 2.03% __strcmp_avx2 0 0% 51.10% 95ms 1.99% AbstractCellProperty::IsSubType (inline) 1ms 0.021% 51.12% 95ms 1.99% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 20ms 0.42% 51.54% 95ms 1.99% __dynamic_cast 63ms 1.32% 52.86% 86ms 1.80% std::basic_streambuf::xsputn 1ms 0.021% 52.88% 86ms 1.80% std::map::operator[] (partial-inline) 29ms 0.61% 53.49% 86ms 1.80% vtkObject::Modified 39ms 0.82% 54.31% 86ms 1.80% vtkTypeFloat64Array::PrintSelf 8ms 0.17% 54.47% 83ms 1.74% vtkAOSDataArrayTemplate::DataElementChanged 54ms 1.13% 55.61% 83ms 1.74% vtkObjectBase::UnRegisterInternal 23ms 0.48% 56.09% 81ms 1.70% std::_Rb_tree::_M_lower_bound (inline) 3ms 0.063% 56.15% 81ms 1.70% std::vector::push_back (inline) 4ms 0.084% 56.24% 77ms 1.61% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.084% 56.32% 76ms 1.59% _int_free_maybe_consolidate 4ms 0.084% 56.40% 75ms 1.57% AbstractCellProperty::IsType (inline) 75ms 1.57% 57.98% 75ms 1.57% unlink_chunk 5ms 0.1% 58.08% 75ms 1.57% vtkDoubleArray::~vtkDoubleArray 0 0% 58.08% 73ms 1.53% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 0 0% 58.08% 72ms 1.51% Cell::HasCellProperty (inline) 2ms 0.042% 58.12% 71ms 1.49% CellPropertyCollection::HasProperty 12ms 0.25% 58.37% 71ms 1.49% vtkDataArray::vtkDataArray 2ms 0.042% 58.42% 69ms 1.45% vtkIdList::New 0 0% 58.42% 66ms 1.38% Cell::GetCellProliferativeType 10ms 0.21% 58.63% 63ms 1.32% std::num_put::_M_insert_int 1ms 0.021% 58.65% 61ms 1.28% std::_Rb_tree::_M_insert_unique 0 0% 58.65% 61ms 1.28% std::set::insert (inline) 60ms 1.26% 59.90% 60ms 1.26% [libvtkCommonCore-9.3.so.9.3] 5ms 0.1% 60.01% 60ms 1.26% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 60.01% 59ms 1.24% NodesOnlyMesh::SetUpBoxCollection 0 0% 60.01% 59ms 1.24% NodesOnlyMesh::~NodesOnlyMesh 0 0% 60.01% 59ms 1.24% std::_Rb_tree::lower_bound (inline) 0 0% 60.01% 59ms 1.24% std::map::lower_bound (inline) 33ms 0.69% 60.70% 58ms 1.22% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.042% 60.74% 58ms 1.22% std::vector::_M_realloc_insert 0 0% 60.74% 56ms 1.17% tcache_get (inline) 56ms 1.17% 61.92% 56ms 1.17% tcache_get_n (inline) 15ms 0.31% 62.23% 56ms 1.17% vtkAbstractArray::vtkAbstractArray 56ms 1.17% 63.40% 56ms 1.17% vtkTimeStamp::Modified 1ms 0.021% 63.42% 54ms 1.13% boost::numeric::ublas::vector_assign (inline) 6ms 0.13% 63.55% 53ms 1.11% vtkSOADataArrayTemplate::FillTypedComponent 4ms 0.084% 63.63% 52ms 1.09% std::_Rb_tree::_M_insert_ (inline) 6ms 0.13% 63.76% 50ms 1.05% AbstractCellProperty::IsSame 0 0% 63.76% 49ms 1.03% DistributedBoxCollection::IsOwned 49ms 1.03% 64.79% 49ms 1.03% __memcpy_avx_unaligned_erms 0 0% 64.79% 48ms 1.01% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 30ms 0.63% 65.42% 48ms 1.01% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 65.42% 48ms 1.01% PottsMesh::GetMooreNeighbouringNodeIndices 8ms 0.17% 65.58% 46ms 0.96% VertexMeshWriter::GetNextNode 46ms 0.96% 66.55% 46ms 0.96% __GI___writev 0 0% 66.55% 46ms 0.96% std::__basic_file::xsputn_2 5ms 0.1% 66.65% 44ms 0.92% std::type_info::operator== (inline) 11ms 0.23% 66.88% 43ms 0.9% vtkIdList::~vtkIdList 43ms 0.9% 67.78% 43ms 0.9% vtkObject::~vtkObject 0 0% 67.78% 42ms 0.88% VertexMesh::Clear 26ms 0.54% 68.33% 41ms 0.86% std::_Hashtable::clear 0 0% 68.33% 40ms 0.84% std::_Destroy (inline) 0 0% 68.33% 40ms 0.84% std::_Destroy_aux::__destroy (inline) 2ms 0.042% 68.37% 40ms 0.84% std::basic_filebuf::open 40ms 0.84% 69.21% 40ms 0.84% vtkObjectBase::~vtkObjectBase 0 0% 69.21% 39ms 0.82% DistributedBoxCollection::SetupLocalBoxesHalfOnly 7ms 0.15% 69.36% 38ms 0.8% vtkDataArray::~vtkDataArray 0 0% 69.36% 37ms 0.78% Cell::GetMutationState 11ms 0.23% 69.59% 36ms 0.75% boost::numeric::ublas::indexing_vector_assign 0 0% 69.59% 35ms 0.73% CxxTest::RealWorldDescription::setUp 0 0% 69.59% 35ms 0.73% PetscSetup::setUpWorld 0 0% 69.59% 35ms 0.73% PetscSetupUtils::CommonSetup 35ms 0.73% 70.32% 35ms 0.73% std::_Rb_tree_increment 35ms 0.73% 71.05% 35ms 0.73% std::ostream::sentry::sentry 0 0% 71.05% 34ms 0.71% PMPI_Init_thread 0 0% 71.05% 34ms 0.71% PetscInitialize 0 0% 71.05% 34ms 0.71% PetscSetupUtils::InitialisePetsc 0 0% 71.05% 34ms 0.71% _dl_init 0 0% 71.05% 34ms 0.71% _dl_start_user 0 0% 71.05% 34ms 0.71% call_init (inline) 0 0% 71.05% 34ms 0.71% ompi_mpi_init 0 0% 71.05% 34ms 0.71% std::less::operator() (inline) 34ms 0.71% 71.77% 34ms 0.71% std::operator< (inline) 33ms 0.69% 72.46% 34ms 0.71% vtkObjectBase::Delete 0 0% 72.46% 33ms 0.69% DistributedBoxCollection::~DistributedBoxCollection 0 0% 72.46% 33ms 0.69% NodesOnlyMesh::ClearBoxCollection (inline) 2ms 0.042% 72.50% 33ms 0.69% std::basic_filebuf::overflow 0 0% 72.50% 32ms 0.67% OutputFileHandler::OpenOutputFile 13ms 0.27% 72.77% 31ms 0.65% _int_free_merge_chunk 0 0% 72.77% 31ms 0.65% std::basic_filebuf::_M_convert_to_external 31ms 0.65% 73.42% 31ms 0.65% std::codecvt::do_always_noconv 1ms 0.021% 73.44% 31ms 0.65% std::make_unique (inline) 12ms 0.25% 73.70% 31ms 0.65% vtkIdList::vtkIdList 0 0% 73.70% 30ms 0.63% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 2ms 0.042% 73.74% 30ms 0.63% CellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 73.74% 30ms 0.63% _IO_new_file_fopen 0 0% 73.74% 30ms 0.63% _IO_new_fopen 1ms 0.021% 73.76% 30ms 0.63% __GI__IO_file_open 30ms 0.63% 74.39% 30ms 0.63% __GI___libc_write 0 0% 74.39% 30ms 0.63% __fopen_internal (inline) 30ms 0.63% 75.02% 30ms 0.63% boost::numeric::ublas::c_vector::operator() 0 0% 75.02% 30ms 0.63% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 1ms 0.021% 75.04% 30ms 0.63% boost::serialization::singleton::get_instance 0 0% 75.04% 30ms 0.63% std::__basic_file::open 0 0% 75.04% 30ms 0.63% std::__basic_file::xsputn 0 0% 75.04% 30ms 0.63% std::unique_ptr::~unique_ptr (inline) 29ms 0.61% 75.64% 29ms 0.61% __libc_open64 29ms 0.61% 76.25% 29ms 0.61% std::_Rb_tree::_S_right (inline) 0 0% 76.25% 29ms 0.61% std::basic_ofstream::basic_ofstream (inline) 0 0% 76.25% 29ms 0.61% std::basic_ofstream::open (inline) 0 0% 76.25% 28ms 0.59% PottsBasedCellPopulation::AcceptCellWriter 1ms 0.021% 76.27% 28ms 0.59% VtkMeshWriter::MakeVtkMesh 28ms 0.59% 76.86% 28ms 0.59% [libchaste_cell_based.so] 28ms 0.59% 77.45% 28ms 0.59% __mpn_divrem 4ms 0.084% 77.53% 28ms 0.59% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 77.53% 28ms 0.59% std::default_delete::operator() (inline) 0 0% 77.53% 27ms 0.57% vtk::detail::smp::vtkSMPToolsImplForTBB 2ms 0.042% 77.57% 26ms 0.54% 0 0% 77.57% 26ms 0.54% NodesOnlyMesh::Clear (inline) 2ms 0.042% 77.61% 26ms 0.54% VertexMeshWriter::GetNextElement 1ms 0.021% 77.64% 26ms 0.54% std::_Rb_tree::_M_emplace_hint_unique 5ms 0.1% 77.74% 26ms 0.54% std::__new_allocator::construct (inline) 0 0% 77.74% 26ms 0.54% std::allocator_traits::construct (inline) 26ms 0.54% 78.29% 26ms 0.54% vtkObjectBase::vtkObjectBase 3ms 0.063% 78.35% 25ms 0.52% Node::AddElement 0 0% 78.35% 25ms 0.52% Node::GetPoint 3ms 0.063% 78.41% 25ms 0.52% tbb::detail::r1::cancel_group_execution 0 0% 78.41% 25ms 0.52% vtkDataArray::ComputeRange 0 0% 78.41% 25ms 0.52% vtkDoubleArray::New 2ms 0.042% 78.45% 24ms 0.5% Edge::Edge 0 0% 78.45% 24ms 0.5% boost::serialization::void_cast_detail::void_caster_primitive::void_caster_primitive (inline) 0 0% 78.45% 24ms 0.5% std::map::~map (inline) 23ms 0.48% 78.94% 24ms 0.5% std::num_put::do_put 4ms 0.084% 79.02% 24ms 0.5% vtkAOSDataArrayTemplate::AllocateTuples