File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3737ms, 80.04% of 4669ms total Dropped 722 nodes (cum <= 23.34ms) flat flat% sum% cum cum% 0 0% 0% 4441ms 95.12% __libc_start_call_main 0 0% 0% 4441ms 95.12% __libc_start_main_impl 0 0% 0% 4441ms 95.12% _start 0 0% 0% 4426ms 94.80% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4426ms 94.80% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4426ms 94.80% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4426ms 94.80% main 0 0% 0% 4393ms 94.09% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4393ms 94.09% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4393ms 94.09% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4383ms 93.87% AbstractCellBasedSimulation::Solve 0 0% 0% 4133ms 88.52% AbstractCellPopulation::WriteResultsToFiles 10ms 0.21% 0.21% 3907ms 83.68% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.21% 1947ms 41.70% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.021% 0.24% 1691ms 36.22% VertexMeshWriter::MakeVtkMesh 0 0% 0.24% 1232ms 26.39% vtkPolygon::New 2ms 0.043% 0.28% 1232ms 26.39% vtkPolygon::vtkPolygon 7ms 0.15% 0.43% 856ms 18.33% vtkCell::vtkCell 67ms 1.43% 1.86% 761ms 16.30% std::ostream::_M_insert 0 0% 1.86% 758ms 16.23% std::ostream::operator<< (inline) 0 0% 1.86% 749ms 16.04% VertexMeshWriter::WriteFiles 4ms 0.086% 1.95% 733ms 15.70% vtkPoints::New 14ms 0.3% 2.25% 691ms 14.80% vtkPoints::vtkPoints 45ms 0.96% 3.21% 676ms 14.48% operator new 206ms 4.41% 7.62% 645ms 13.81% __GI___libc_malloc 40ms 0.86% 8.48% 629ms 13.47% std::num_put::_M_insert_float 0 0% 8.48% 583ms 12.49% vtkQuad::New 4ms 0.086% 8.57% 580ms 12.42% vtkQuad::vtkQuad 1ms 0.021% 8.59% 559ms 11.97% vtkLine::New 0 0% 8.59% 549ms 11.76% vtkXMLWriterBase::Write 0 0% 8.59% 548ms 11.74% vtkCompositeDataPipeline::ExecuteData 0 0% 8.59% 548ms 11.74% vtkDemandDrivenPipeline::ExecuteData 0 0% 8.59% 548ms 11.74% vtkDemandDrivenPipeline::ProcessRequest 0 0% 8.59% 548ms 11.74% vtkExecutive::CallAlgorithm 0 0% 8.59% 548ms 11.74% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 8.59% 548ms 11.74% vtkStreamingDemandDrivenPipeline::Update 0 0% 8.59% 548ms 11.74% vtkXMLUnstructuredDataWriter::ProcessRequest 11ms 0.24% 8.82% 539ms 11.54% vtkLine::vtkLine 0 0% 8.82% 522ms 11.18% vtkTriangle::New 5ms 0.11% 8.93% 514ms 11.01% vtkTriangle::vtkTriangle 0 0% 8.93% 497ms 10.64% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 8.93% 497ms 10.64% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 12ms 0.26% 9.19% 496ms 10.62% std::__cxx11::collate::do_transform 139ms 2.98% 12.17% 493ms 10.56% __GI___libc_free 7ms 0.15% 12.32% 458ms 9.81% ___vsnprintf 0 0% 12.32% 451ms 9.66% __vsnprintf_internal (inline) 52ms 1.11% 13.43% 443ms 9.49% __printf_buffer 18ms 0.39% 13.81% 440ms 9.42% vtkPoints::SetDataType 1ms 0.021% 13.84% 436ms 9.34% vtkXMLWriter::WriteBinaryData 0 0% 13.84% 431ms 9.23% vtkXMLWriter::WriteBinaryDataInternal 0 0% 13.84% 430ms 9.21% vtkXMLWriter::WriteBinaryDataBlock 1ms 0.021% 13.86% 423ms 9.06% vtkPolygon::~vtkPolygon 0 0% 13.86% 422ms 9.04% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 251ms 5.38% 19.23% 377ms 8.07% _int_malloc 18ms 0.39% 19.62% 352ms 7.54% __printf_fp_l_buffer 0 0% 19.62% 352ms 7.54% __printf_fp_spec (inline) 209ms 4.48% 24.10% 352ms 7.54% _int_free 0 0% 24.10% 333ms 7.13% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 24.10% 332ms 7.11% VtkMeshWriter::WriteFiles 4ms 0.086% 24.18% 330ms 7.07% vtkCell::~vtkCell 165ms 3.53% 27.71% 323ms 6.92% __printf_fp_buffer_1 0 0% 27.71% 314ms 6.73% vtkXMLWriter::WritePointsAppendedData 37ms 0.79% 28.51% 262ms 5.61% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 24ms 0.51% 29.02% 252ms 5.40% std::__new_allocator::allocate (inline) 0 0% 29.02% 250ms 5.35% std::allocator_traits::allocate (inline) 0 0% 29.02% 246ms 5.27% OnLatticeSimulation::UpdateCellLocationsAndTopology 6ms 0.13% 29.15% 246ms 5.27% PottsBasedCellPopulation::UpdateCellLocations 0 0% 29.15% 239ms 5.12% std::__new_allocator::deallocate (inline) 0 0% 29.15% 239ms 5.12% std::allocator_traits::deallocate (inline) 0 0% 29.15% 231ms 4.95% vtkXMLWriter::WriteCompressionBlock 0 0% 29.15% 222ms 4.75% vtkDataCompressor::Compress 1ms 0.021% 29.17% 222ms 4.75% vtkZLibDataCompressor::CompressBuffer 0 0% 29.17% 221ms 4.73% compress2 75ms 1.61% 30.78% 218ms 4.67% crc32 0 0% 30.78% 218ms 4.67% deflate 0 0% 30.78% 211ms 4.52% vtkQuad::~vtkQuad 0 0% 30.78% 202ms 4.33% tbb::detail::r1::parallel_pipeline 5ms 0.11% 30.88% 202ms 4.33% vtkPoints::~vtkPoints 6ms 0.13% 31.01% 200ms 4.28% vtkBase64OutputStream::Write 0 0% 31.01% 194ms 4.16% clone3 0 0% 31.01% 194ms 4.16% start_thread 27ms 0.58% 31.59% 194ms 4.16% vtkBase64OutputStream::EncodeTriplet 0 0% 31.59% 191ms 4.09% tbb::detail::r1::reset 78ms 1.67% 33.26% 189ms 4.05% tbb::detail::r1::wait_bounded_queue_monitor 111ms 2.38% 35.64% 188ms 4.03% malloc_consolidate 2ms 0.043% 35.68% 188ms 4.03% vtkIdList::AllocateInternal 4ms 0.086% 35.77% 186ms 3.98% vtkTriangle::~vtkTriangle 3ms 0.064% 35.83% 169ms 3.62% vtkLine::GetParametricCenter 5ms 0.11% 35.94% 164ms 3.51% NodesOnlyMesh::ConstructNodesWithoutMesh 10ms 0.21% 36.15% 160ms 3.43% vtkFloatArray::New 2ms 0.043% 36.20% 155ms 3.32% NodeLocationWriter::VisitAnyPopulation 3ms 0.064% 36.26% 150ms 3.21% std::_Vector_base::_M_deallocate (inline) 46ms 0.99% 37.25% 149ms 3.19% std::ostream::write 2ms 0.043% 37.29% 149ms 3.19% vtkTypeFloat64Array::~vtkTypeFloat64Array 1ms 0.021% 37.31% 148ms 3.17% std::vector::~vector (inline) 5ms 0.11% 37.42% 147ms 3.15% vtkDataArray::CreateDataArray 0 0% 37.42% 145ms 3.11% VertexMesh::~VertexMesh 3ms 0.064% 37.48% 141ms 3.02% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.021% 37.50% 139ms 2.98% VertexMesh::VertexMesh 31ms 0.66% 38.17% 139ms 2.98% std::_Rb_tree::_M_erase 12ms 0.26% 38.42% 139ms 2.98% std::vector::_M_default_append 132ms 2.83% 41.25% 138ms 2.96% [libz.so.1.3] 0 0% 41.25% 138ms 2.96% std::_Rb_tree::_M_create_node (inline) 1ms 0.021% 41.27% 138ms 2.96% std::set::set (inline) 0 0% 41.27% 136ms 2.91% std::_Rb_tree::_M_get_node (inline) 7ms 0.15% 41.42% 136ms 2.91% std::_Rb_tree::_Rb_tree 1ms 0.021% 41.44% 136ms 2.91% vtkIdList::Allocate 0 0% 41.44% 134ms 2.87% VertexMesh::GenerateEdgesFromElements (inline) 6ms 0.13% 41.57% 134ms 2.87% vtkFloatArray::~vtkFloatArray 0 0% 41.57% 133ms 2.85% vtkFloatArray::vtkFloatArray 38ms 0.81% 42.39% 133ms 2.85% vtkObject::vtkObject 4ms 0.086% 42.47% 132ms 2.83% MutableElement::BuildEdges 8ms 0.17% 42.64% 132ms 2.83% vtkTypeFloat64Array::New 0 0% 42.64% 130ms 2.78% std::set::~set (inline) 2ms 0.043% 42.69% 130ms 2.78% vtkDoubleArray::vtkDoubleArray 2ms 0.043% 42.73% 129ms 2.76% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 0 0% 42.73% 124ms 2.66% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 42.73% 124ms 2.66% std::_Vector_base::~_Vector_base (inline) 45ms 0.96% 43.69% 122ms 2.61% std::basic_filebuf::xsputn 1ms 0.021% 43.71% 117ms 2.51% EdgeHelper::GetEdgeFromNodes 10ms 0.21% 43.93% 115ms 2.46% std::_Rb_tree::_M_copy (inline) 0 0% 43.93% 114ms 2.44% std::_Vector_base::_M_allocate (inline) 112ms 2.40% 46.33% 112ms 2.40% __GI_sched_yield 2ms 0.043% 46.37% 111ms 2.38% vtkTypeFloat64Array::vtkTypeFloat64Array 0 0% 46.37% 107ms 2.29% vtkXMLWriter::WritePointDataAppendedData 0 0% 46.37% 105ms 2.25% CellPropertyCollection::GetPropertiesType (inline) 102ms 2.18% 48.55% 102ms 2.18% __strcmp_avx2 9ms 0.19% 48.75% 102ms 2.18% std::_Rb_tree::_M_clone_node (inline) 100ms 2.14% 50.89% 100ms 2.14% unlink_chunk 0 0% 50.89% 98ms 2.10% std::_Rb_tree::_M_drop_node (inline) 3ms 0.064% 50.95% 96ms 2.06% AbstractCellProperty::IsSubType (inline) 56ms 1.20% 52.15% 95ms 2.03% hack_digit 48ms 1.03% 53.18% 95ms 2.03% vtkTypeFloat64Array::PrintSelf 0 0% 53.18% 94ms 2.01% EdgeHelper::~EdgeHelper (inline) 49ms 1.05% 54.23% 94ms 2.01% vtkObjectBase::UnRegisterInternal 20ms 0.43% 54.66% 93ms 1.99% __dynamic_cast 7ms 0.15% 54.81% 93ms 1.99% _int_free_maybe_consolidate 0 0% 54.81% 92ms 1.97% std::_Rb_tree::_M_put_node (inline) 3ms 0.064% 54.87% 89ms 1.91% std::map::operator[] (partial-inline) 1ms 0.021% 54.89% 88ms 1.88% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 9ms 0.19% 55.09% 83ms 1.78% AbstractCellProperty::IsType (inline) 37ms 0.79% 55.88% 83ms 1.78% std::__ostream_insert 4ms 0.086% 55.96% 81ms 1.73% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 55.96% 80ms 1.71% Cell::HasCellProperty (inline) 3ms 0.064% 56.03% 80ms 1.71% CellPropertyCollection::HasProperty 1ms 0.021% 56.05% 80ms 1.71% std::operator<< (inline) 4ms 0.086% 56.14% 80ms 1.71% vtkDoubleArray::~vtkDoubleArray 26ms 0.56% 56.69% 79ms 1.69% std::_Rb_tree::_M_lower_bound (inline) 10ms 0.21% 56.91% 78ms 1.67% vtkAOSDataArrayTemplate::DataElementChanged 25ms 0.54% 57.44% 76ms 1.63% vtkObject::Modified 48ms 1.03% 58.47% 73ms 1.56% std::basic_streambuf::xsputn 0 0% 58.47% 72ms 1.54% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 3ms 0.064% 58.54% 71ms 1.52% std::vector::push_back (inline) 3ms 0.064% 58.60% 70ms 1.50% vtkIdList::New 0 0% 58.60% 63ms 1.35% Cell::GetCellProliferativeType 0 0% 58.60% 63ms 1.35% NodesOnlyMesh::SetUpBoxCollection 7ms 0.15% 58.75% 60ms 1.29% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 58.75% 59ms 1.26% std::_Rb_tree::lower_bound (inline) 0 0% 58.75% 59ms 1.26% std::map::lower_bound (inline) 0 0% 58.75% 58ms 1.24% std::set::insert (inline) 1ms 0.021% 58.77% 57ms 1.22% std::_Rb_tree::_M_insert_unique 11ms 0.24% 59.01% 53ms 1.14% AbstractCellProperty::IsSame 0 0% 59.01% 53ms 1.14% boost::numeric::ublas::vector_assign (inline) 1ms 0.021% 59.03% 51ms 1.09% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 1ms 0.021% 59.05% 51ms 1.09% VertexMesh::Clear 51ms 1.09% 60.14% 51ms 1.09% vtkObject::~vtkObject 6ms 0.13% 60.27% 51ms 1.09% vtkSOADataArrayTemplate::FillTypedComponent 4ms 0.086% 60.36% 50ms 1.07% std::vector::_M_realloc_insert 0 0% 60.36% 50ms 1.07% tcache_get (inline) 50ms 1.07% 61.43% 50ms 1.07% tcache_get_n (inline) 49ms 1.05% 62.48% 49ms 1.05% __memcpy_avx_unaligned_erms 3ms 0.064% 62.54% 49ms 1.05% vtkDataArray::vtkDataArray 49ms 1.05% 63.59% 49ms 1.05% vtkTimeStamp::Modified 24ms 0.51% 64.10% 48ms 1.03% __cxxabiv1::__si_class_type_info::__do_dyncast 45ms 0.96% 65.07% 46ms 0.99% __GI___writev 26ms 0.56% 65.62% 46ms 0.99% std::_Hashtable::clear 0 0% 65.62% 46ms 0.99% std::__basic_file::xsputn_2 6ms 0.13% 65.75% 46ms 0.99% vtkIdList::~vtkIdList 2ms 0.043% 65.80% 45ms 0.96% vtkAbstractArray::vtkAbstractArray 1ms 0.021% 65.82% 45ms 0.96% vtkDataArray::ComputeRange 8ms 0.17% 65.99% 45ms 0.96% vtkDataArray::~vtkDataArray 2ms 0.043% 66.03% 44ms 0.94% DistributedBoxCollection::SetupLocalBoxesHalfOnly 8ms 0.17% 66.20% 44ms 0.94% std::num_put::_M_insert_int 42ms 0.9% 67.10% 42ms 0.9% [libvtkCommonCore-9.3.so.9.3] 13ms 0.28% 67.38% 42ms 0.9% std::type_info::operator== (inline) 5ms 0.11% 67.49% 41ms 0.88% std::_Rb_tree::_M_insert_ (inline) 41ms 0.88% 68.37% 41ms 0.88% std::ostream::sentry::sentry 41ms 0.88% 69.24% 41ms 0.88% vtkObjectBase::Delete 18ms 0.39% 69.63% 40ms 0.86% boost::numeric::ublas::indexing_vector_assign 0 0% 69.63% 39ms 0.84% NodesOnlyMesh::~NodesOnlyMesh 8ms 0.17% 69.80% 39ms 0.84% _int_free_merge_chunk 39ms 0.84% 70.64% 39ms 0.84% vtkObjectBase::vtkObjectBase 6ms 0.13% 70.76% 38ms 0.81% vtkAOSDataArrayTemplate::InsertTuple 5ms 0.11% 70.87% 37ms 0.79% __find_specmb (inline) 32ms 0.69% 71.56% 37ms 0.79% vtkObject::ObjectFinalize 0 0% 71.56% 36ms 0.77% vtkDoubleArray::New 0 0% 71.56% 35ms 0.75% _dl_init 0 0% 71.56% 35ms 0.75% call_init (inline) 34ms 0.73% 72.29% 34ms 0.73% __mpn_divrem 0 0% 72.29% 34ms 0.73% _dl_start_user 1ms 0.021% 72.31% 34ms 0.73% std::less::operator() (inline) 0 0% 72.31% 34ms 0.73% std::make_unique (inline) 3ms 0.064% 72.37% 34ms 0.73% vtkDataArrayPrivate::DoComputeVectorRange 22ms 0.47% 72.84% 33ms 0.71% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 72.84% 33ms 0.71% DistributedBoxCollection::IsOwned 0 0% 72.84% 33ms 0.71% PottsMesh::GetMooreNeighbouringNodeIndices 33ms 0.71% 73.55% 33ms 0.71% std::operator< (inline) 0 0% 73.55% 33ms 0.71% vtk::detail::smp::vtkSMPToolsImplForTBB 3ms 0.064% 73.61% 32ms 0.69% vtk::detail::smp::vtkSMPToolsImpl::For 0 0% 73.61% 31ms 0.66% Cell::GetMutationState 4ms 0.086% 73.70% 31ms 0.66% VertexMeshWriter::GetNextNode 31ms 0.66% 74.36% 31ms 0.66% std::codecvt::do_always_noconv 2ms 0.043% 74.41% 31ms 0.66% tbb::detail::r1::cancel_group_execution 31ms 0.66% 75.07% 31ms 0.66% vtkObjectBase::~vtkObjectBase 5ms 0.11% 75.18% 30ms 0.64% Node::GetPoint 30ms 0.64% 75.82% 30ms 0.64% __strchrnul_avx2 0 0% 75.82% 29ms 0.62% Cell::GetCellId 0 0% 75.82% 29ms 0.62% CxxTest::RealWorldDescription::setUp 0 0% 75.82% 29ms 0.62% DistributedBoxCollection::~DistributedBoxCollection 0 0% 75.82% 29ms 0.62% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 75.82% 29ms 0.62% PMPI_Init_thread 0 0% 75.82% 29ms 0.62% PetscInitialize 0 0% 75.82% 29ms 0.62% PetscSetup::setUpWorld 0 0% 75.82% 29ms 0.62% PetscSetupUtils::CommonSetup 0 0% 75.82% 29ms 0.62% PetscSetupUtils::InitialisePetsc 20ms 0.43% 76.25% 29ms 0.62% _int_free_create_chunk (inline) 0 0% 76.25% 29ms 0.62% ompi_mpi_init 0 0% 76.25% 29ms 0.62% std::_Destroy (inline) 0 0% 76.25% 29ms 0.62% std::_Destroy_aux::__destroy (inline) 1ms 0.021% 76.27% 29ms 0.62% std::basic_filebuf::overflow 0 0% 76.27% 28ms 0.6% CellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 76.27% 28ms 0.6% Node::ConstructNodeAttributes (inline) 0 0% 76.27% 28ms 0.6% Node::SetRadius 28ms 0.6% 76.87% 28ms 0.6% __memset_avx2_unaligned_erms 2ms 0.043% 76.91% 28ms 0.6% boost::serialization::singleton::get_instance 1ms 0.021% 76.93% 28ms 0.6% std::basic_filebuf::_M_convert_to_external 27ms 0.58% 77.51% 27ms 0.58% __GI___libc_write 0 0% 77.51% 27ms 0.58% std::_Rb_tree::_M_emplace_hint_unique 0 0% 77.51% 27ms 0.58% std::__basic_file::xsputn 0 0% 77.51% 27ms 0.58% vtkAOSDataArrayTemplate::AllocateTuples 6ms 0.13% 77.64% 27ms 0.58% vtkSOADataArrayTemplate::GetTupleIndexFromValueIndex 2ms 0.043% 77.68% 26ms 0.56% 0 0% 77.68% 26ms 0.56% CellIdWriter::GetCellDataForVtkOutput 1ms 0.021% 77.70% 26ms 0.56% Edge::Edge 1ms 0.021% 77.73% 26ms 0.56% VtkMeshWriter::MakeVtkMesh 26ms 0.56% 78.28% 26ms 0.56% __GI___uselocale 0 0% 78.28% 26ms 0.56% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 26ms 0.56% 78.84% 26ms 0.56% std::_Rb_tree_increment 0 0% 78.84% 25ms 0.54% Edge::SetNodes (inline) 25ms 0.54% 79.37% 25ms 0.54% [libchaste_cell_based.so] 1ms 0.021% 79.40% 25ms 0.54% boost::serialization::void_cast_detail::void_caster::recursive_register 0 0% 79.40% 25ms 0.54% boost::serialization::void_cast_detail::void_caster_primitive::void_caster_primitive (inline) 8ms 0.17% 79.57% 25ms 0.54% std::_Rb_tree_const_iterator::operator++ (inline) 22ms 0.47% 80.04% 25ms 0.54% std::num_put::do_put 0 0% 80.04% 24ms 0.51% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 80.04% 24ms 0.51% boost::numeric::ublas::c_vector::assign (inline) 0 0% 80.04% 24ms 0.51% vtkDataArrayPrivate::DoComputeScalarRange