File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 2417ms, 81.57% of 2963ms total Dropped 597 nodes (cum <= 14.81ms) flat flat% sum% cum cum% 0 0% 0% 2824ms 95.31% __libc_start_call_main 0 0% 0% 2824ms 95.31% __libc_start_main_impl 0 0% 0% 2824ms 95.31% _start 0 0% 0% 2811ms 94.87% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 2811ms 94.87% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 2811ms 94.87% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 2811ms 94.87% main 0 0% 0% 2777ms 93.72% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 2777ms 93.72% CxxTest::TestRunner::runTest (inline) 0 0% 0% 2777ms 93.72% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 2769ms 93.45% AbstractCellBasedSimulation::Solve 0 0% 0% 2602ms 87.82% AbstractCellPopulation::WriteResultsToFiles 12ms 0.4% 0.4% 2478ms 83.63% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.4% 1330ms 44.89% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.034% 0.44% 1168ms 39.42% VertexMeshWriter::MakeVtkMesh 0 0% 0.44% 829ms 27.98% vtkPolygon::New 0 0% 0.44% 829ms 27.98% vtkPolygon::vtkPolygon 0 0% 0.44% 620ms 20.92% vtkCell::vtkCell 1ms 0.034% 0.47% 504ms 17.01% vtkPoints::New 2ms 0.067% 0.54% 481ms 16.23% vtkPoints::vtkPoints 28ms 0.94% 1.48% 462ms 15.59% operator new 201ms 6.78% 8.27% 433ms 14.61% __GI___libc_malloc 0 0% 8.27% 394ms 13.30% vtkLine::New 0 0% 8.27% 393ms 13.26% VertexMeshWriter::WriteFiles 0 0% 8.27% 389ms 13.13% vtkQuad::New 0 0% 8.27% 389ms 13.13% vtkQuad::vtkQuad 3ms 0.1% 8.37% 384ms 12.96% vtkLine::vtkLine 31ms 1.05% 9.42% 382ms 12.89% std::ostream::_M_insert 1ms 0.034% 9.45% 382ms 12.89% std::ostream::operator<< (inline) 0 0% 9.45% 367ms 12.39% vtkTriangle::New 2ms 0.067% 9.52% 364ms 12.28% vtkTriangle::vtkTriangle 50ms 1.69% 11.20% 348ms 11.74% __GI___libc_free 0 0% 11.20% 312ms 10.53% vtkDemandDrivenPipeline::ProcessRequest 0 0% 11.20% 312ms 10.53% vtkStreamingDemandDrivenPipeline::Update 0 0% 11.20% 312ms 10.53% vtkXMLWriterBase::Write 0 0% 11.20% 308ms 10.39% vtkCompositeDataPipeline::ExecuteData 0 0% 11.20% 308ms 10.39% vtkExecutive::CallAlgorithm 0 0% 11.20% 308ms 10.39% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 11.20% 307ms 10.36% vtkDemandDrivenPipeline::ExecuteData 0 0% 11.20% 307ms 10.36% vtkPolygon::~vtkPolygon 0 0% 11.20% 307ms 10.36% vtkXMLUnstructuredDataWriter::ProcessRequest 25ms 0.84% 12.05% 304ms 10.26% std::num_put::_M_insert_float 219ms 7.39% 19.44% 296ms 9.99% _int_free 8ms 0.27% 19.71% 279ms 9.42% vtkPoints::SetDataType 0 0% 19.71% 271ms 9.15% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 19.71% 271ms 9.15% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 19.71% 245ms 8.27% vtkXMLWriter::WriteBinaryData 1ms 0.034% 19.74% 242ms 8.17% vtkCell::~vtkCell 0 0% 19.74% 242ms 8.17% vtkXMLWriter::WriteBinaryDataBlock 0 0% 19.74% 242ms 8.17% vtkXMLWriter::WriteBinaryDataInternal 7ms 0.24% 19.98% 237ms 8.00% std::__cxx11::collate::do_transform 27ms 0.91% 20.89% 229ms 7.73% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 0 0% 20.89% 229ms 7.73% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 2ms 0.067% 20.96% 223ms 7.53% ___vsnprintf 0 0% 20.96% 221ms 7.46% __vsnprintf_internal (inline) 38ms 1.28% 22.24% 219ms 7.39% __printf_buffer 11ms 0.37% 22.61% 207ms 6.99% std::__new_allocator::allocate (inline) 0 0% 22.61% 207ms 6.99% std::allocator_traits::allocate (inline) 126ms 4.25% 26.86% 192ms 6.48% _int_malloc 0 0% 26.86% 192ms 6.48% vtkXMLWriter::WritePointsAppendedData 0 0% 26.86% 184ms 6.21% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 26.86% 183ms 6.18% VtkMeshWriter::WriteFiles 6ms 0.2% 27.07% 170ms 5.74% __printf_fp_l_buffer 0 0% 27.07% 170ms 5.74% __printf_fp_spec (inline) 0 0% 27.07% 165ms 5.57% OnLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.034% 27.10% 165ms 5.57% PottsBasedCellPopulation::UpdateCellLocations 10ms 0.34% 27.44% 165ms 5.57% vtkObject::vtkObject 63ms 2.13% 29.56% 161ms 5.43% __printf_fp_buffer_1 0 0% 29.56% 158ms 5.33% vtkQuad::~vtkQuad 0 0% 29.56% 156ms 5.26% std::__new_allocator::deallocate (inline) 0 0% 29.56% 156ms 5.26% std::allocator_traits::deallocate (inline) 123ms 4.15% 33.72% 146ms 4.93% vtkObjectBase::UnRegisterInternal 10ms 0.34% 34.05% 144ms 4.86% vtkObject::Modified 1ms 0.034% 34.09% 136ms 4.59% vtkPoints::~vtkPoints 0 0% 34.09% 134ms 4.52% vtkFloatArray::New 3ms 0.1% 34.19% 132ms 4.45% vtkBase64OutputStream::Write 132ms 4.45% 38.64% 132ms 4.45% vtkTimeStamp::Modified 0 0% 38.64% 126ms 4.25% std::_Rb_tree::_M_create_node (inline) 15ms 0.51% 39.15% 124ms 4.18% vtkBase64OutputStream::EncodeTriplet 1ms 0.034% 39.18% 123ms 4.15% tbb::detail::r1::parallel_pipeline 0 0% 39.18% 123ms 4.15% vtkFloatArray::vtkFloatArray 0 0% 39.18% 122ms 4.12% std::_Rb_tree::_M_get_node (inline) 0 0% 39.18% 116ms 3.91% vtkTriangle::~vtkTriangle 0 0% 39.18% 114ms 3.85% clone3 0 0% 39.18% 114ms 3.85% start_thread 1ms 0.034% 39.22% 113ms 3.81% std::set::set (inline) 4ms 0.13% 39.35% 111ms 3.75% std::_Rb_tree::_Rb_tree 0 0% 39.35% 110ms 3.71% vtkXMLWriter::WriteCompressionBlock 0 0% 39.35% 109ms 3.68% compress2 9ms 0.3% 39.66% 109ms 3.68% std::_Rb_tree::~_Rb_tree (inline) 0 0% 39.66% 109ms 3.68% vtkDataArray::CreateDataArray 0 0% 39.66% 109ms 3.68% vtkDataCompressor::Compress 0 0% 39.66% 109ms 3.68% vtkZLibDataCompressor::CompressBuffer 13ms 0.44% 40.09% 108ms 3.64% crc32 0 0% 40.09% 108ms 3.64% deflate 2ms 0.067% 40.16% 108ms 3.64% tbb::detail::r1::reset 3ms 0.1% 40.26% 108ms 3.64% vtkDoubleArray::vtkDoubleArray 1ms 0.034% 40.30% 108ms 3.64% vtkLine::GetParametricCenter 1ms 0.034% 40.33% 106ms 3.58% vtkTypeFloat64Array::New 67ms 2.26% 42.59% 104ms 3.51% malloc_consolidate 0 0% 42.59% 104ms 3.51% vtkTypeFloat64Array::~vtkTypeFloat64Array 12ms 0.4% 43.00% 103ms 3.48% std::_Rb_tree::_M_erase 0 0% 43.00% 102ms 3.44% std::_Rb_tree::_Alloc_node::operator() (inline) 3ms 0.1% 43.10% 101ms 3.41% vtkIdList::AllocateInternal 0 0% 43.10% 100ms 3.37% VertexMesh::VertexMesh 44ms 1.48% 44.58% 100ms 3.37% tbb::detail::r1::wait_bounded_queue_monitor 6ms 0.2% 44.79% 99ms 3.34% std::_Rb_tree::_M_copy (inline) 0 0% 44.79% 98ms 3.31% VertexMesh::~VertexMesh 0 0% 44.79% 98ms 3.31% std::set::~set (inline) 1ms 0.034% 44.82% 97ms 3.27% NodesOnlyMesh::ConstructNodesWithoutMesh 0 0% 44.82% 97ms 3.27% std::vector::~vector (inline) 0 0% 44.82% 94ms 3.17% VertexMesh::GenerateEdgesFromElements (inline) 32ms 1.08% 45.90% 94ms 3.17% std::ostream::write 0 0% 45.90% 94ms 3.17% vtkTypeFloat64Array::vtkTypeFloat64Array 3ms 0.1% 46.00% 93ms 3.14% MutableElement::BuildEdges 10ms 0.34% 46.34% 93ms 3.14% std::_Rb_tree::_M_clone_node (inline) 89ms 3.00% 49.34% 92ms 3.10% [libz.so.1.3] 0 0% 49.34% 91ms 3.07% std::_Rb_tree::_M_drop_node (inline) 2ms 0.067% 49.41% 89ms 3.00% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 0 0% 49.41% 85ms 2.87% std::_Vector_base::_M_allocate (inline) 81ms 2.73% 52.14% 81ms 2.73% vtkObjectBase::vtkObjectBase 0 0% 52.14% 80ms 2.70% EdgeHelper::GetEdgeFromNodes 0 0% 52.14% 79ms 2.67% NodeLocationWriter::VisitAnyPopulation 0 0% 52.14% 79ms 2.67% std::_Rb_tree::_M_put_node (inline) 0 0% 52.14% 77ms 2.60% std::_Vector_base::_M_deallocate (inline) 7ms 0.24% 52.38% 74ms 2.50% std::vector::_M_default_append 35ms 1.18% 53.56% 69ms 2.33% hack_digit 1ms 0.034% 53.59% 69ms 2.33% std::_Vector_base::~_Vector_base (inline) 0 0% 53.59% 69ms 2.33% vtkIdList::Allocate 0 0% 53.59% 68ms 2.29% EdgeHelper::~EdgeHelper (inline) 27ms 0.91% 54.51% 66ms 2.23% std::basic_filebuf::xsputn 3ms 0.1% 54.61% 66ms 2.23% std::map::operator[] (partial-inline) 0 0% 54.61% 65ms 2.19% CellPropertyCollection::GetPropertiesType (inline) 0 0% 54.61% 59ms 1.99% std::vector::push_back (inline) 57ms 1.92% 56.53% 57ms 1.92% __GI_sched_yield 0 0% 56.53% 55ms 1.86% AbstractCellProperty::IsSubType (inline) 16ms 0.54% 57.07% 55ms 1.86% __dynamic_cast 2ms 0.067% 57.14% 54ms 1.82% _int_free_maybe_consolidate 2ms 0.067% 57.21% 54ms 1.82% vtkFloatArray::~vtkFloatArray 0 0% 57.21% 54ms 1.82% vtkIdList::New 4ms 0.13% 57.34% 53ms 1.79% AbstractCellPopulation::GetCellUsingLocationIndex 6ms 0.2% 57.54% 53ms 1.79% vtkAOSDataArrayTemplate::DataElementChanged 2ms 0.067% 57.61% 51ms 1.72% vtkDoubleArray::~vtkDoubleArray 0 0% 57.61% 50ms 1.69% Cell::HasCellProperty (inline) 3ms 0.1% 57.71% 49ms 1.65% CellPropertyCollection::HasProperty 0 0% 57.71% 47ms 1.59% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 47ms 1.59% 59.30% 47ms 1.59% __strcmp_evex 2ms 0.067% 59.37% 47ms 1.59% vtkDataArray::vtkDataArray 2ms 0.067% 59.43% 45ms 1.52% vtkAbstractArray::vtkAbstractArray 33ms 1.11% 60.55% 44ms 1.48% std::basic_streambuf::xsputn 44ms 1.48% 62.03% 44ms 1.48% unlink_chunk 0 0% 62.03% 43ms 1.45% NodesOnlyMesh::SetUpBoxCollection 22ms 0.74% 62.77% 43ms 1.45% vtkTypeFloat64Array::PrintSelf 0 0% 62.77% 42ms 1.42% Cell::GetCellProliferativeType 0 0% 62.77% 42ms 1.42% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 2ms 0.067% 62.84% 41ms 1.38% AbstractCellProperty::IsType (inline) 1ms 0.034% 62.88% 41ms 1.38% std::vector::_M_realloc_insert 6ms 0.2% 63.08% 39ms 1.32% std::__ostream_insert 1ms 0.034% 63.11% 39ms 1.32% std::operator<< (inline) 0 0% 63.11% 38ms 1.28% std::_Rb_tree::_M_emplace_hint_unique 8ms 0.27% 63.38% 37ms 1.25% std::num_put::_M_insert_int 0 0% 63.38% 37ms 1.25% vtkXMLWriter::WritePointDataAppendedData 0 0% 63.38% 36ms 1.21% PottsMesh::GetMooreNeighbouringNodeIndices 1ms 0.034% 63.42% 35ms 1.18% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 34ms 1.15% 64.56% 34ms 1.15% [libvtkCommonCore-9.3.so.9.3] 1ms 0.034% 64.60% 34ms 1.15% std::_Rb_tree::_M_insert_unique 0 0% 64.60% 34ms 1.15% std::set::insert (inline) 0 0% 64.60% 33ms 1.11% CxxTest::RealWorldDescription::setUp 0 0% 64.60% 33ms 1.11% PetscInitialize 0 0% 64.60% 33ms 1.11% PetscSetup::setUpWorld 0 0% 64.60% 33ms 1.11% PetscSetupUtils::CommonSetup 0 0% 64.60% 33ms 1.11% PetscSetupUtils::InitialisePetsc 6ms 0.2% 64.80% 33ms 1.11% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 64.80% 32ms 1.08% PMPI_Init_thread 0 0% 64.80% 32ms 1.08% ompi_mpi_init 10ms 0.34% 65.14% 32ms 1.08% std::_Rb_tree::_M_lower_bound (inline) 4ms 0.13% 65.27% 32ms 1.08% vtkDataArray::~vtkDataArray 0 0% 65.27% 31ms 1.05% NodesOnlyMesh::~NodesOnlyMesh 20ms 0.67% 65.95% 31ms 1.05% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 65.95% 31ms 1.05% _dl_init 0 0% 65.95% 31ms 1.05% call_init (inline) 0 0% 65.95% 30ms 1.01% VertexMesh::Clear 0 0% 65.95% 30ms 1.01% std::_Destroy (inline) 1ms 0.034% 65.98% 30ms 1.01% std::_Destroy_aux::__destroy (inline) 0 0% 65.98% 30ms 1.01% tcache_get (inline) 30ms 1.01% 66.99% 30ms 1.01% tcache_get_n (inline) 4ms 0.13% 67.13% 29ms 0.98% AbstractCellProperty::IsSame 1ms 0.034% 67.16% 28ms 0.94% 0 0% 67.16% 28ms 0.94% CellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 67.16% 28ms 0.94% boost::numeric::ublas::vector_assign (inline) 18ms 0.61% 67.77% 28ms 0.94% std::_Hashtable::clear 27ms 0.91% 68.68% 27ms 0.91% [libstdc++.so.6.0.33] 8ms 0.27% 68.95% 27ms 0.91% std::_Rb_tree::_M_insert_ (inline) 0 0% 68.95% 26ms 0.88% DistributedBoxCollection::SetupLocalBoxesHalfOnly 7ms 0.24% 69.19% 26ms 0.88% VertexMeshWriter::GetNextNode 26ms 0.88% 70.06% 26ms 0.88% __GI___writev 26ms 0.88% 70.94% 26ms 0.88% __memcpy_avx512_unaligned_erms 0 0% 70.94% 26ms 0.88% std::__basic_file::xsputn_2 5ms 0.17% 71.11% 26ms 0.88% vtkIdList::~vtkIdList 25ms 0.84% 71.95% 25ms 0.84% __mpn_divrem 0 0% 71.95% 25ms 0.84% _dl_start_user 0 0% 71.95% 25ms 0.84% boost::detail::shared_count::~shared_count (inline) 7ms 0.24% 72.19% 25ms 0.84% boost::numeric::ublas::indexing_vector_assign 0 0% 72.19% 25ms 0.84% boost::shared_ptr::~shared_ptr (inline) 0 0% 72.19% 25ms 0.84% std::_Rb_tree::lower_bound (inline) 0 0% 72.19% 25ms 0.84% std::map::lower_bound (inline) 4ms 0.13% 72.33% 25ms 0.84% std::type_info::operator== (inline) 23ms 0.78% 73.10% 24ms 0.81% boost::detail::sp_counted_base::release 0 0% 73.10% 24ms 0.81% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 73.10% 24ms 0.81% vtkDataArray::ComputeRange 0 0% 73.10% 24ms 0.81% vtkDoubleArray::New 3ms 0.1% 73.20% 24ms 0.81% vtkIdList::vtkIdList 0 0% 73.20% 23ms 0.78% DistributedBoxCollection::~DistributedBoxCollection 0 0% 73.20% 23ms 0.78% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 73.20% 23ms 0.78% VtkMeshWriter::MakeVtkMesh 4ms 0.13% 73.34% 23ms 0.78% std::__new_allocator::construct (inline) 0 0% 73.34% 23ms 0.78% std::allocator_traits::construct (inline) 0 0% 73.34% 22ms 0.74% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 0 0% 73.34% 22ms 0.74% boost::serialization::singleton::get_instance 5ms 0.17% 73.51% 22ms 0.74% vtkAOSDataArrayTemplate::InsertTuple 1ms 0.034% 73.54% 22ms 0.74% vtkDataArrayPrivate::DoComputeVectorRange 17ms 0.57% 74.11% 22ms 0.74% vtkObject::ObjectFinalize 22ms 0.74% 74.86% 22ms 0.74% vtkObjectBase::RegisterInternal 14ms 0.47% 75.33% 21ms 0.71% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 75.33% 21ms 0.71% DistributedBoxCollection::IsOwned 0 0% 75.33% 21ms 0.71% orte_init 0 0% 75.33% 20ms 0.67% Cell::GetCellId 1ms 0.034% 75.36% 20ms 0.67% PottsMesh::GetVonNeumannNeighbouringNodeIndices 0 0% 75.36% 20ms 0.67% std::basic_filebuf::open 0 0% 75.36% 20ms 0.67% std::make_unique (inline) 0 0% 75.36% 19ms 0.64% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 75.36% 19ms 0.64% _IO_new_fopen 0 0% 75.36% 19ms 0.64% __fopen_internal (inline) 0 0% 75.36% 19ms 0.64% std::__basic_file::open 0 0% 75.36% 19ms 0.64% std::default_delete::operator() (inline) 0 0% 75.36% 19ms 0.64% std::less::operator() (inline) 19ms 0.64% 76.00% 19ms 0.64% std::operator< (inline) 0 0% 76.00% 19ms 0.64% std::unique_ptr::~unique_ptr (inline) 1ms 0.034% 76.04% 19ms 0.64% vtkPoints::Modified 0 0% 76.04% 18ms 0.61% PottsBasedCellPopulation::AcceptCellWriter 0 0% 76.04% 18ms 0.61% _IO_new_file_fopen 0 0% 76.04% 18ms 0.61% __GI__IO_file_open 18ms 0.61% 76.65% 18ms 0.61% __libc_open64 18ms 0.61% 77.25% 18ms 0.61% std::_Rb_tree_increment 16ms 0.54% 77.79% 18ms 0.61% std::num_put::do_put 0 0% 77.79% 18ms 0.61% vtk::detail::smp::vtkSMPToolsImplForTBB 18ms 0.61% 78.40% 18ms 0.61% vtkObject::~vtkObject 0 0% 78.40% 17ms 0.57% CellIdWriter::GetCellDataForVtkOutput 17ms 0.57% 78.97% 17ms 0.57% [libchaste_cell_based.so] 17ms 0.57% 79.55% 17ms 0.57% boost::numeric::ublas::c_vector::operator() 8ms 0.27% 79.82% 17ms 0.57% std::_Rb_tree_const_iterator::operator++ (inline) 15ms 0.51% 80.32% 17ms 0.57% vtkObjectBase::Delete 16ms 0.54% 80.86% 16ms 0.54% std::ostream::sentry::sentry 1ms 0.034% 80.90% 16ms 0.54% std::vector::emplace_back (inline) 0 0% 80.90% 16ms 0.54% tbb::detail::r1::cancel_group_execution 2ms 0.067% 80.97% 16ms 0.54% vtk::detail::smp::vtkSMPToolsImpl::For 0 0% 80.97% 15ms 0.51% Edge::Edge 0 0% 80.97% 15ms 0.51% Edge::SetNodes (inline) 0 0% 80.97% 15ms 0.51% boost::serialization::void_cast_detail::void_caster::recursive_register 0 0% 80.97% 15ms 0.51% boost::serialization::void_cast_detail::void_caster_primitive::void_caster_primitive (inline) 1ms 0.034% 81.00% 15ms 0.51% hwloc_linux_get_tid_last_cpu_location 0 0% 81.00% 15ms 0.51% hwloc_topology_load 15ms 0.51% 81.51% 15ms 0.51% syscall 0 0% 81.51% 15ms 0.51% vtkDataArrayPrivate::DoComputeScalarRange 2ms 0.067% 81.57% 15ms 0.51% vtkSOADataArrayTemplate::FillTypedComponent