File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 4010ms, 81.08% of 4946ms total Dropped 753 nodes (cum <= 24.73ms) flat flat% sum% cum cum% 0 0% 0% 4745ms 95.94% __libc_start_call_main 0 0% 0% 4745ms 95.94% __libc_start_main_impl 0 0% 0% 4745ms 95.94% _start 0 0% 0% 4726ms 95.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4726ms 95.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4726ms 95.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4726ms 95.55% main 0 0% 0% 4682ms 94.66% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4682ms 94.66% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4681ms 94.64% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4670ms 94.42% AbstractCellBasedSimulation::Solve 1ms 0.02% 0.02% 4284ms 86.62% AbstractCellPopulation::WriteResultsToFiles 18ms 0.36% 0.38% 4073ms 82.35% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.38% 2013ms 40.70% VertexMeshWriter::WriteVtkUsingMesh 0 0% 0.38% 1727ms 34.92% VertexMeshWriter::MakeVtkMesh 0 0% 0.38% 1230ms 24.87% vtkPolygon::New 2ms 0.04% 0.42% 1230ms 24.87% vtkPolygon::vtkPolygon 7ms 0.14% 0.57% 887ms 17.93% vtkCell::vtkCell 3ms 0.061% 0.63% 761ms 15.39% vtkPoints::New 9ms 0.18% 0.81% 716ms 14.48% vtkPoints::vtkPoints 2ms 0.04% 0.85% 691ms 13.97% VertexMeshWriter::WriteFiles 36ms 0.73% 1.58% 651ms 13.16% operator new 61ms 1.23% 2.81% 623ms 12.60% std::ostream::_M_insert 0 0% 2.81% 622ms 12.58% std::ostream::operator<< (inline) 186ms 3.76% 6.57% 617ms 12.47% __GI___libc_malloc 0 0% 6.57% 584ms 11.81% vtkStreamingDemandDrivenPipeline::Update 0 0% 6.57% 584ms 11.81% vtkXMLWriterBase::Write 0 0% 6.57% 580ms 11.73% vtkDemandDrivenPipeline::ProcessRequest 0 0% 6.57% 578ms 11.69% vtkExecutive::CallAlgorithm 0 0% 6.57% 578ms 11.69% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 6.57% 578ms 11.69% vtkTriangle::New 0 0% 6.57% 574ms 11.61% vtkDemandDrivenPipeline::ExecuteData 0 0% 6.57% 573ms 11.59% vtkCompositeDataPipeline::ExecuteData 1ms 0.02% 6.59% 573ms 11.59% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 6.59% 572ms 11.56% vtkQuad::New 1ms 0.02% 6.61% 572ms 11.56% vtkQuad::vtkQuad 10ms 0.2% 6.81% 572ms 11.56% vtkTriangle::vtkTriangle 1ms 0.02% 6.83% 571ms 11.54% vtkLine::New 14ms 0.28% 7.12% 554ms 11.20% vtkLine::vtkLine 145ms 2.93% 10.05% 552ms 11.16% __GI___libc_free 0 0% 10.05% 521ms 10.53% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 10.05% 521ms 10.53% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 38ms 0.77% 10.82% 490ms 9.91% std::num_put::_M_insert_float 26ms 0.53% 11.34% 466ms 9.42% vtkPoints::SetDataType 0 0% 11.34% 464ms 9.38% vtkXMLWriter::WriteBinaryData 0 0% 11.34% 458ms 9.26% vtkXMLWriter::WriteBinaryDataInternal 0 0% 11.34% 457ms 9.24% vtkXMLWriter::WriteBinaryDataBlock 0 0% 11.34% 455ms 9.20% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 6ms 0.12% 11.46% 434ms 8.77% vtkPolygon::~vtkPolygon 236ms 4.77% 16.24% 401ms 8.11% _int_free 16ms 0.32% 16.56% 385ms 7.78% std::__cxx11::collate::do_transform 0 0% 16.56% 378ms 7.64% OnLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.061% 16.62% 376ms 7.60% PottsBasedCellPopulation::UpdateCellLocations 1ms 0.02% 16.64% 364ms 7.36% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 241ms 4.87% 21.51% 364ms 7.36% _int_malloc 0 0% 21.51% 361ms 7.30% VtkMeshWriter::WriteFiles 5ms 0.1% 21.61% 359ms 7.26% ___vsnprintf 1ms 0.02% 21.63% 355ms 7.18% __vsnprintf_internal (inline) 54ms 1.09% 22.73% 348ms 7.04% __printf_buffer 1ms 0.02% 22.75% 346ms 7.00% vtkXMLWriter::WritePointsAppendedData 11ms 0.22% 22.97% 338ms 6.83% vtkCell::~vtkCell 70ms 1.42% 24.38% 302ms 6.11% std::__new_allocator::allocate (inline) 6ms 0.12% 24.50% 300ms 6.07% std::__new_allocator::deallocate (inline) 0 0% 24.50% 299ms 6.05% std::allocator_traits::allocate (inline) 0 0% 24.50% 299ms 6.05% std::allocator_traits::deallocate (inline) 45ms 0.91% 25.41% 288ms 5.82% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 17ms 0.34% 25.76% 271ms 5.48% __printf_fp_l_buffer 0 0% 25.76% 271ms 5.48% __printf_fp_spec (inline) 121ms 2.45% 28.20% 251ms 5.07% __printf_fp_buffer_1 0 0% 28.20% 242ms 4.89% vtkXMLWriter::WriteCompressionBlock 2ms 0.04% 28.25% 235ms 4.75% std::set::set (inline) 28ms 0.57% 28.81% 233ms 4.71% std::_Rb_tree::_Rb_tree 0 0% 28.81% 224ms 4.53% vtkDataCompressor::Compress 2ms 0.04% 28.85% 222ms 4.49% compress2 7ms 0.14% 28.99% 222ms 4.49% vtkPoints::~vtkPoints 0 0% 28.99% 222ms 4.49% vtkZLibDataCompressor::CompressBuffer 40ms 0.81% 29.80% 220ms 4.45% crc32 0 0% 29.80% 220ms 4.45% deflate 4ms 0.081% 29.88% 220ms 4.45% vtkBase64OutputStream::Write 0 0% 29.88% 212ms 4.29% VertexMesh::~VertexMesh 14ms 0.28% 30.17% 212ms 4.29% vtkBase64OutputStream::EncodeTriplet 126ms 2.55% 32.71% 206ms 4.16% malloc_consolidate 0 0% 32.71% 192ms 3.88% vtkQuad::~vtkQuad 60ms 1.21% 33.93% 191ms 3.86% std::_Rb_tree::_M_erase 4ms 0.081% 34.01% 191ms 3.86% std::_Rb_tree::~_Rb_tree (inline) 0 0% 34.01% 189ms 3.82% std::_Rb_tree::_M_create_node (inline) 0 0% 34.01% 189ms 3.82% std::vector::~vector (inline) 11ms 0.22% 34.23% 187ms 3.78% std::_Vector_base::_M_deallocate (inline) 88ms 1.78% 36.01% 186ms 3.76% std::basic_filebuf::xsputn 6ms 0.12% 36.13% 186ms 3.76% vtkLine::GetParametricCenter 36ms 0.73% 36.86% 184ms 3.72% std::ostream::write 2ms 0.04% 36.90% 182ms 3.68% vtkTriangle::~vtkTriangle 6ms 0.12% 37.02% 181ms 3.66% vtkFloatArray::New 0 0% 37.02% 173ms 3.50% std::_Rb_tree::_M_get_node (inline) 1ms 0.02% 37.04% 172ms 3.48% NodesOnlyMesh::ConstructNodesWithoutMesh 167ms 3.38% 40.42% 171ms 3.46% [libz.so.1.3] 12ms 0.24% 40.66% 171ms 3.46% std::_Rb_tree::_M_copy (inline) 0 0% 40.66% 170ms 3.44% std::_Rb_tree::_Alloc_node::operator() (inline) 4ms 0.081% 40.74% 167ms 3.38% vtkIdList::AllocateInternal 4ms 0.081% 40.82% 165ms 3.34% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 0 0% 40.82% 163ms 3.30% clone3 0 0% 40.82% 163ms 3.30% start_thread 1ms 0.02% 40.84% 163ms 3.30% tbb::detail::r1::parallel_pipeline 4ms 0.081% 40.92% 162ms 3.28% VertexMesh::VertexMesh 3ms 0.061% 40.98% 159ms 3.21% vtkTypeFloat64Array::~vtkTypeFloat64Array 11ms 0.22% 41.21% 158ms 3.19% std::_Rb_tree::_M_clone_node (inline) 0 0% 41.21% 154ms 3.11% tbb::detail::r1::reset 0 0% 41.21% 154ms 3.11% vtkFloatArray::vtkFloatArray 1ms 0.02% 41.23% 153ms 3.09% std::_Vector_base::~_Vector_base (inline) 0 0% 41.23% 151ms 3.05% std::set::~set (inline) 12ms 0.24% 41.47% 150ms 3.03% std::vector::_M_default_append 52ms 1.05% 42.52% 148ms 2.99% tbb::detail::r1::wait_bounded_queue_monitor 0 0% 42.52% 147ms 2.97% EdgeHelper::~EdgeHelper (inline) 0 0% 42.52% 147ms 2.97% NodeLocationWriter::VisitAnyPopulation 2ms 0.04% 42.56% 143ms 2.89% vtkDataArray::CreateDataArray 7ms 0.14% 42.70% 135ms 2.73% MutableElement::BuildEdges 0 0% 42.70% 135ms 2.73% VertexMesh::GenerateEdgesFromElements (inline) 5ms 0.1% 42.80% 135ms 2.73% vtkTypeFloat64Array::New 3ms 0.061% 42.86% 132ms 2.67% vtkDoubleArray::vtkDoubleArray 0 0% 42.86% 127ms 2.57% std::_Rb_tree::_M_drop_node (inline) 1ms 0.02% 42.88% 127ms 2.57% std::_Vector_base::_M_allocate (inline) 0 0% 42.88% 123ms 2.49% std::_Rb_tree::_M_put_node (inline) 0 0% 42.88% 121ms 2.45% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.061% 42.94% 120ms 2.43% EdgeHelper::GetEdgeFromNodes 117ms 2.37% 45.31% 117ms 2.37% __strcmp_avx2 7ms 0.14% 45.45% 117ms 2.37% vtkTypeFloat64Array::vtkTypeFloat64Array 2ms 0.04% 45.49% 116ms 2.35% vtkFloatArray::~vtkFloatArray 2ms 0.04% 45.53% 115ms 2.33% _int_free_maybe_consolidate 0 0% 45.53% 115ms 2.33% vtkIdList::Allocate 0 0% 45.53% 112ms 2.26% AbstractCellProperty::IsSubType (inline) 33ms 0.67% 46.20% 112ms 2.26% __dynamic_cast 0 0% 46.20% 109ms 2.20% vtkXMLWriter::WritePointDataAppendedData 38ms 0.77% 46.97% 106ms 2.14% std::__ostream_insert 4ms 0.081% 47.05% 106ms 2.14% std::operator<< (inline) 26ms 0.53% 47.57% 105ms 2.12% vtkObject::vtkObject 104ms 2.10% 49.68% 104ms 2.10% unlink_chunk 2ms 0.04% 49.72% 103ms 2.08% AbstractCellProperty::IsType (inline) 64ms 1.29% 51.01% 103ms 2.08% vtkObjectBase::UnRegisterInternal 2ms 0.04% 51.05% 100ms 2.02% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 41ms 0.83% 51.88% 98ms 1.98% vtkTypeFloat64Array::PrintSelf 97ms 1.96% 53.84% 97ms 1.96% __GI_sched_yield 0 0% 53.84% 96ms 1.94% Cell::HasCellProperty (inline) 1ms 0.02% 53.86% 96ms 1.94% CellPropertyCollection::HasProperty 1ms 0.02% 53.88% 91ms 1.84% PottsMesh::GetMooreNeighbouringNodeIndices 1ms 0.02% 53.90% 85ms 1.72% std::map::operator[] (partial-inline) 42ms 0.85% 54.75% 82ms 1.66% hack_digit 6ms 0.12% 54.87% 81ms 1.64% vtkDoubleArray::~vtkDoubleArray 3ms 0.061% 54.93% 78ms 1.58% vtkAOSDataArrayTemplate::DataElementChanged 27ms 0.55% 55.48% 75ms 1.52% std::_Rb_tree::_M_lower_bound (inline) 16ms 0.32% 55.80% 73ms 1.48% vtkObject::Modified 8ms 0.16% 55.96% 70ms 1.42% boost::numeric::ublas::c_vector::c_vector (partial-inline) 8ms 0.16% 56.13% 69ms 1.40% vtkIdList::New 0 0% 56.13% 68ms 1.37% NodesOnlyMesh::~NodesOnlyMesh 41ms 0.83% 56.96% 68ms 1.37% std::basic_streambuf::xsputn 0 0% 56.96% 67ms 1.35% NodesOnlyMesh::SetUpBoxCollection 16ms 0.32% 57.28% 65ms 1.31% AbstractCellProperty::IsSame 0 0% 57.28% 64ms 1.29% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 1ms 0.02% 57.30% 64ms 1.29% VertexMesh::Clear 0 0% 57.30% 63ms 1.27% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 11ms 0.22% 57.52% 60ms 1.21% VertexMeshWriter::GetNextNode 0 0% 57.52% 60ms 1.21% boost::numeric::ublas::vector_assign (inline) 1ms 0.02% 57.54% 60ms 1.21% std::vector::push_back (inline) 0 0% 57.54% 60ms 1.21% tcache_get (inline) 60ms 1.21% 58.75% 60ms 1.21% tcache_get_n (inline) 2ms 0.04% 58.79% 59ms 1.19% AbstractCellPopulation::GetCellUsingLocationIndex 58ms 1.17% 59.97% 58ms 1.17% __GI___writev 0 0% 59.97% 58ms 1.17% std::__basic_file::xsputn_2 0 0% 59.97% 56ms 1.13% Cell::GetCellProliferativeType 5ms 0.1% 60.07% 56ms 1.13% vtkDataArray::vtkDataArray 1ms 0.02% 60.09% 55ms 1.11% std::_Rb_tree::_M_insert_unique 0 0% 60.09% 55ms 1.11% std::set::insert (inline) 0 0% 60.09% 53ms 1.07% std::_Rb_tree::lower_bound (inline) 0 0% 60.09% 53ms 1.07% std::map::lower_bound (inline) 23ms 0.47% 60.55% 52ms 1.05% __cxxabiv1::__si_class_type_info::__do_dyncast 52ms 1.05% 61.61% 52ms 1.05% vtkTimeStamp::Modified 25ms 0.51% 62.11% 51ms 1.03% std::_Hashtable::clear 11ms 0.22% 62.33% 51ms 1.03% vtkAbstractArray::vtkAbstractArray 50ms 1.01% 63.34% 50ms 1.01% __memcpy_avx_unaligned_erms 2ms 0.04% 63.38% 49ms 0.99% DistributedBoxCollection::IsOwned 10ms 0.2% 63.59% 49ms 0.99% std::num_put::_M_insert_int 12ms 0.24% 63.83% 49ms 0.99% std::type_info::operator== (inline) 48ms 0.97% 64.80% 48ms 0.97% [libvtkCommonCore-9.3.so.9.3] 10ms 0.2% 65.00% 48ms 0.97% boost::numeric::ublas::indexing_vector_assign 29ms 0.59% 65.59% 47ms 0.95% DistributedBoxCollection::CalculateContainingBox (inline) 2ms 0.04% 65.63% 46ms 0.93% std::vector::_M_realloc_insert 45ms 0.91% 66.54% 45ms 0.91% vtkObjectBase::Delete 10ms 0.2% 66.74% 45ms 0.91% vtkSOADataArrayTemplate::FillTypedComponent 0 0% 66.74% 44ms 0.89% Cell::GetCellId 5ms 0.1% 66.84% 42ms 0.85% Node::~Node 0 0% 66.84% 41ms 0.83% DistributedBoxCollection::~DistributedBoxCollection 0 0% 66.84% 41ms 0.83% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 66.84% 41ms 0.83% _dl_init 0 0% 66.84% 41ms 0.83% call_init (inline) 0 0% 66.84% 41ms 0.83% std::basic_filebuf::open 0 0% 66.84% 41ms 0.83% vtkDataArray::ComputeRange 40ms 0.81% 67.65% 40ms 0.81% [libstdc++.so.6.0.33] 40ms 0.81% 68.46% 40ms 0.81% std::codecvt::do_always_noconv 0 0% 68.46% 40ms 0.81% std::map::~map (inline) 0 0% 68.46% 39ms 0.79% CxxTest::RealWorldDescription::setUp 0 0% 68.46% 39ms 0.79% PetscInitialize 0 0% 68.46% 39ms 0.79% PetscSetup::setUpWorld 0 0% 68.46% 39ms 0.79% PetscSetupUtils::CommonSetup 0 0% 68.46% 39ms 0.79% PetscSetupUtils::InitialisePetsc 0 0% 68.46% 39ms 0.79% std::_Destroy (inline) 0 0% 68.46% 39ms 0.79% std::_Destroy_aux::__destroy (inline) 0 0% 68.46% 38ms 0.77% PMPI_Init_thread 0 0% 68.46% 38ms 0.77% _dl_start_user 0 0% 68.46% 38ms 0.77% ompi_mpi_init 0 0% 68.46% 38ms 0.77% std::__basic_file::open 32ms 0.65% 69.11% 38ms 0.77% vtkObject::ObjectFinalize 37ms 0.75% 69.85% 38ms 0.77% vtkObject::~vtkObject 0 0% 69.85% 37ms 0.75% CellIdWriter::GetCellDataForVtkOutput 0 0% 69.85% 37ms 0.75% _IO_new_file_fopen 0 0% 69.85% 37ms 0.75% _IO_new_fopen 0 0% 69.85% 37ms 0.75% __GI__IO_file_open 0 0% 69.85% 37ms 0.75% __fopen_internal (inline) 37ms 0.75% 70.60% 37ms 0.75% __libc_open64 1ms 0.02% 70.62% 37ms 0.75% std::less::operator() (inline) 8ms 0.16% 70.78% 37ms 0.75% vtkDataArray::~vtkDataArray 5ms 0.1% 70.89% 37ms 0.75% vtkIdList::~vtkIdList 1ms 0.02% 70.91% 36ms 0.73% 0 0% 70.91% 36ms 0.73% Cell::GetMutationState 36ms 0.73% 71.63% 36ms 0.73% Node::GetIndex 36ms 0.73% 72.36% 36ms 0.73% std::operator< (inline) 36ms 0.73% 73.09% 36ms 0.73% vtkObjectBase::~vtkObjectBase 0 0% 73.09% 35ms 0.71% boost::numeric::ublas::c_vector::assign (inline) 0 0% 73.09% 34ms 0.69% PottsMesh::GetVonNeumannNeighbouringNodeIndices 0 0% 73.09% 34ms 0.69% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 2ms 0.04% 73.13% 34ms 0.69% std::_Rb_tree_header::_Rb_tree_header (inline) 1ms 0.02% 73.15% 34ms 0.69% vtkDoubleArray::New 6ms 0.12% 73.27% 33ms 0.67% vtkAOSDataArrayTemplate::InsertTuple 32ms 0.65% 73.92% 32ms 0.65% boost::numeric::ublas::c_vector::operator() 32ms 0.65% 74.57% 32ms 0.65% std::_Rb_tree_header::_M_reset (inline) 32ms 0.65% 75.21% 32ms 0.65% std::ostream::sentry::sentry 2ms 0.04% 75.25% 32ms 0.65% vtkDataArrayPrivate::DoComputeVectorRange 9ms 0.18% 75.43% 31ms 0.63% _int_free_merge_chunk 1ms 0.02% 75.45% 31ms 0.63% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.061% 75.52% 31ms 0.63% std::_Rb_tree::_M_insert_ (inline) 30ms 0.61% 76.12% 30ms 0.61% std::_Rb_tree_increment 0 0% 76.12% 30ms 0.61% std::make_unique (inline) 30ms 0.61% 76.73% 30ms 0.61% vtkDataArray::Modified 0 0% 76.73% 29ms 0.59% DistributedBoxCollection::SetupLocalBoxesHalfOnly 0 0% 76.73% 29ms 0.59% Node::AddElement 29ms 0.59% 77.32% 29ms 0.59% Node::GetNumContainingElements 0 0% 77.32% 29ms 0.59% VtkMeshWriter::MakeVtkMesh 2ms 0.04% 77.36% 29ms 0.59% boost::serialization::singleton::get_instance 0 0% 77.36% 28ms 0.57% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 13ms 0.26% 77.62% 28ms 0.57% std::__new_allocator::construct (inline) 0 0% 77.62% 28ms 0.57% std::allocator_traits::construct (inline) 0 0% 77.62% 27ms 0.55% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 77.62% 27ms 0.55% NodesOnlyMesh::Clear (inline) 1ms 0.02% 77.64% 27ms 0.55% VertexMeshWriter::GetNextElement 27ms 0.55% 78.18% 27ms 0.55% __GI___libc_write 27ms 0.55% 78.73% 27ms 0.55% __memset_avx2_unaligned_erms 27ms 0.55% 79.28% 27ms 0.55% std::_Rb_tree::_S_right (inline) 0 0% 79.28% 27ms 0.55% std::__basic_file::xsputn 0 0% 79.28% 27ms 0.55% std::basic_filebuf::_M_convert_to_external 0 0% 79.28% 27ms 0.55% std::basic_filebuf::overflow 4ms 0.081% 79.36% 27ms 0.55% vtk::detail::smp::vtkSMPToolsImpl::For 27ms 0.55% 79.90% 27ms 0.55% vtkObject::InvokeEvent 27ms 0.55% 80.45% 27ms 0.55% vtkObjectBase::vtkObjectBase 0 0% 80.45% 26ms 0.53% PottsBasedCellPopulation::AcceptCellWriter 26ms 0.53% 80.97% 26ms 0.53% __mpn_divrem 0 0% 80.97% 26ms 0.53% vtk::detail::smp::vtkSMPToolsImplForTBB 0 0% 80.97% 26ms 0.53% vtkDataArrayPrivate::DoComputeScalarRange 5ms 0.1% 81.08% 25ms 0.51% AbstractMesh::CalculateBoundingBox 0 0% 81.08% 25ms 0.51% OutputFileHandler::OpenOutputFile