File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3800ms, 80.10% of 4744ms total Dropped 767 nodes (cum <= 23.72ms) flat flat% sum% cum cum% 0 0% 0% 4554ms 95.99% __libc_start_call_main 0 0% 0% 4554ms 95.99% __libc_start_main_impl 0 0% 0% 4554ms 95.99% _start 0 0% 0% 4537ms 95.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4537ms 95.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4537ms 95.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4537ms 95.64% main 0 0% 0% 4497ms 94.79% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4497ms 94.79% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4497ms 94.79% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4486ms 94.56% AbstractCellBasedSimulation::Solve 0 0% 0% 4181ms 88.13% AbstractCellPopulation::WriteResultsToFiles 12ms 0.25% 0.25% 3966ms 83.60% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.25% 1999ms 42.14% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.021% 0.27% 1727ms 36.40% VertexMeshWriter::MakeVtkMesh 0 0% 0.27% 1294ms 27.28% vtkPolygon::New 2ms 0.042% 0.32% 1293ms 27.26% vtkPolygon::vtkPolygon 4ms 0.084% 0.4% 915ms 19.29% vtkCell::vtkCell 4ms 0.084% 0.48% 795ms 16.76% vtkPoints::New 19ms 0.4% 0.89% 748ms 15.77% vtkPoints::vtkPoints 38ms 0.8% 1.69% 703ms 14.82% operator new 0 0% 1.69% 683ms 14.40% VertexMeshWriter::WriteFiles 223ms 4.70% 6.39% 676ms 14.25% __GI___libc_malloc 0 0% 6.39% 655ms 13.81% vtkLine::New 64ms 1.35% 7.74% 646ms 13.62% std::ostream::_M_insert 1ms 0.021% 7.76% 646ms 13.62% std::ostream::operator<< (inline) 11ms 0.23% 7.99% 634ms 13.36% vtkLine::vtkLine 2ms 0.042% 8.03% 602ms 12.69% vtkQuad::New 3ms 0.063% 8.09% 599ms 12.63% vtkQuad::vtkQuad 2ms 0.042% 8.14% 588ms 12.39% vtkTriangle::New 5ms 0.11% 8.24% 577ms 12.16% vtkTriangle::vtkTriangle 0 0% 8.24% 573ms 12.08% vtkStreamingDemandDrivenPipeline::Update 0 0% 8.24% 573ms 12.08% vtkXMLWriterBase::Write 0 0% 8.24% 571ms 12.04% vtkDemandDrivenPipeline::ProcessRequest 0 0% 8.24% 570ms 12.02% vtkCompositeDataPipeline::ExecuteData 0 0% 8.24% 570ms 12.02% vtkDemandDrivenPipeline::ExecuteData 0 0% 8.24% 570ms 12.02% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 8.24% 569ms 11.99% vtkExecutive::CallAlgorithm 0 0% 8.24% 569ms 11.99% vtkXMLUnstructuredDataWriter::ProcessRequest 47ms 0.99% 9.23% 522ms 11.00% std::num_put::_M_insert_float 0 0% 9.23% 506ms 10.67% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 9.23% 506ms 10.67% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 127ms 2.68% 11.91% 493ms 10.39% __GI___libc_free 26ms 0.55% 12.46% 445ms 9.38% vtkPoints::SetDataType 0 0% 12.46% 445ms 9.38% vtkXMLWriter::WriteBinaryData 0 0% 12.46% 435ms 9.17% vtkXMLWriter::WriteBinaryDataBlock 0 0% 12.46% 435ms 9.17% vtkXMLWriter::WriteBinaryDataInternal 0 0% 12.46% 434ms 9.15% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 23ms 0.48% 12.94% 417ms 8.79% std::__cxx11::collate::do_transform 260ms 5.48% 18.42% 386ms 8.14% _int_malloc 0 0% 18.42% 381ms 8.03% vtkPolygon::~vtkPolygon 3ms 0.063% 18.49% 374ms 7.88% ___vsnprintf 0 0% 18.49% 371ms 7.82% __vsnprintf_internal (inline) 220ms 4.64% 23.12% 363ms 7.65% _int_free 49ms 1.03% 24.16% 362ms 7.63% __printf_buffer 1ms 0.021% 24.18% 355ms 7.48% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 24.18% 353ms 7.44% VtkMeshWriter::WriteFiles 0 0% 24.18% 333ms 7.02% vtkXMLWriter::WritePointsAppendedData 46ms 0.97% 25.15% 329ms 6.94% std::__new_allocator::allocate (inline) 0 0% 25.15% 327ms 6.89% std::allocator_traits::allocate (inline) 4ms 0.084% 25.23% 300ms 6.32% vtkCell::~vtkCell 33ms 0.7% 25.93% 297ms 6.26% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 0 0% 25.93% 295ms 6.22% OnLatticeSimulation::UpdateCellLocationsAndTopology 7ms 0.15% 26.08% 295ms 6.22% PottsBasedCellPopulation::UpdateCellLocations 11ms 0.23% 26.31% 288ms 6.07% __printf_fp_l_buffer 0 0% 26.31% 288ms 6.07% __printf_fp_spec (inline) 125ms 2.63% 28.94% 265ms 5.59% __printf_fp_buffer_1 1ms 0.021% 28.96% 264ms 5.56% std::__new_allocator::deallocate (inline) 0 0% 28.96% 261ms 5.50% std::allocator_traits::deallocate (inline) 0 0% 28.96% 226ms 4.76% vtkXMLWriter::WriteCompressionBlock 1ms 0.021% 28.98% 222ms 4.68% vtkBase64OutputStream::Write 15ms 0.32% 29.30% 218ms 4.60% vtkBase64OutputStream::EncodeTriplet 3ms 0.063% 29.36% 210ms 4.43% vtkFloatArray::New 0 0% 29.36% 209ms 4.41% compress2 0 0% 29.36% 209ms 4.41% vtkDataCompressor::Compress 0 0% 29.36% 209ms 4.41% vtkZLibDataCompressor::CompressBuffer 43ms 0.91% 30.27% 208ms 4.38% crc32 0 0% 30.27% 208ms 4.38% deflate 7ms 0.15% 30.42% 203ms 4.28% vtkPoints::~vtkPoints 20ms 0.42% 30.84% 188ms 3.96% std::_Rb_tree::_Rb_tree 0 0% 30.84% 188ms 3.96% std::set::set (inline) 48ms 1.01% 31.85% 187ms 3.94% std::ostream::write 9ms 0.19% 32.04% 185ms 3.90% std::_Rb_tree::~_Rb_tree (inline) 5ms 0.11% 32.15% 184ms 3.88% vtkFloatArray::vtkFloatArray 14ms 0.3% 32.44% 182ms 3.84% std::vector::_M_default_append 45ms 0.95% 33.39% 179ms 3.77% std::_Rb_tree::_M_erase 0 0% 33.39% 176ms 3.71% std::_Rb_tree::_M_create_node (inline) 0 0% 33.39% 175ms 3.69% vtkTriangle::~vtkTriangle 0 0% 33.39% 172ms 3.63% std::_Rb_tree::_M_get_node (inline) 2ms 0.042% 33.43% 168ms 3.54% NodesOnlyMesh::ConstructNodesWithoutMesh 1ms 0.021% 33.45% 165ms 3.48% vtkQuad::~vtkQuad 1ms 0.021% 33.47% 162ms 3.41% VertexMesh::VertexMesh 100ms 2.11% 35.58% 162ms 3.41% malloc_consolidate 1ms 0.021% 35.60% 161ms 3.39% tbb::detail::r1::parallel_pipeline 0 0% 35.60% 160ms 3.37% VertexMesh::~VertexMesh 5ms 0.11% 35.71% 160ms 3.37% vtkIdList::AllocateInternal 0 0% 35.71% 155ms 3.27% clone3 0 0% 35.71% 155ms 3.27% start_thread 0 0% 35.71% 155ms 3.27% std::_Vector_base::_M_allocate (inline) 0 0% 35.71% 155ms 3.27% vtkTypeFloat64Array::~vtkTypeFloat64Array 151ms 3.18% 38.89% 154ms 3.25% [libz.so.1.3] 0 0% 38.89% 153ms 3.23% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 38.89% 152ms 3.20% std::vector::~vector (inline) 2ms 0.042% 38.93% 152ms 3.20% vtkLine::GetParametricCenter 69ms 1.45% 40.39% 149ms 3.14% std::basic_filebuf::xsputn 1ms 0.021% 40.41% 149ms 3.14% tbb::detail::r1::reset 0 0% 40.41% 148ms 3.12% std::set::~set (inline) 13ms 0.27% 40.68% 147ms 3.10% std::_Rb_tree::_M_copy (inline) 2ms 0.042% 40.73% 143ms 3.01% MutableElement::BuildEdges 0 0% 40.73% 143ms 3.01% NodeLocationWriter::VisitAnyPopulation 0 0% 40.73% 143ms 3.01% VertexMesh::GenerateEdgesFromElements (inline) 64ms 1.35% 42.07% 140ms 2.95% tbb::detail::r1::wait_bounded_queue_monitor 1ms 0.021% 42.10% 139ms 2.93% std::_Vector_base::_M_deallocate (inline) 4ms 0.084% 42.18% 136ms 2.87% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 0 0% 42.18% 132ms 2.78% std::_Rb_tree::_M_drop_node (inline) 9ms 0.19% 42.37% 131ms 2.76% std::_Rb_tree::_M_clone_node (inline) 3ms 0.063% 42.43% 128ms 2.70% EdgeHelper::GetEdgeFromNodes 7ms 0.15% 42.58% 126ms 2.66% vtkFloatArray::~vtkFloatArray 0 0% 42.58% 123ms 2.59% std::_Rb_tree::_M_put_node (inline) 0 0% 42.58% 121ms 2.55% EdgeHelper::~EdgeHelper (inline) 2ms 0.042% 42.62% 121ms 2.55% vtkDoubleArray::vtkDoubleArray 59ms 1.24% 43.87% 121ms 2.55% vtkTypeFloat64Array::PrintSelf 3ms 0.063% 43.93% 118ms 2.49% vtkDataArray::CreateDataArray 117ms 2.47% 46.40% 117ms 2.47% __strcmp_avx2 0 0% 46.40% 114ms 2.40% std::_Vector_base::~_Vector_base (inline) 3ms 0.063% 46.46% 110ms 2.32% vtkTypeFloat64Array::New 0 0% 46.46% 109ms 2.30% vtkIdList::Allocate 62ms 1.31% 47.77% 109ms 2.30% vtkObjectBase::UnRegisterInternal 0 0% 47.77% 108ms 2.28% CellPropertyCollection::GetPropertiesType (inline) 16ms 0.34% 48.10% 106ms 2.23% vtkObject::vtkObject 0 0% 48.10% 101ms 2.13% vtkXMLWriter::WritePointDataAppendedData 45ms 0.95% 49.05% 96ms 2.02% hack_digit 1ms 0.021% 49.07% 95ms 2.00% AbstractCellProperty::IsSubType (inline) 2ms 0.042% 49.11% 95ms 2.00% std::map::operator[] (partial-inline) 1ms 0.021% 49.14% 94ms 1.98% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 21ms 0.44% 49.58% 94ms 1.98% __dynamic_cast 94ms 1.98% 51.56% 94ms 1.98% unlink_chunk 1ms 0.021% 51.58% 94ms 1.98% vtkTypeFloat64Array::vtkTypeFloat64Array 2ms 0.042% 51.62% 89ms 1.88% std::operator<< (inline) 28ms 0.59% 52.21% 89ms 1.88% vtkObject::Modified 34ms 0.72% 52.93% 88ms 1.85% std::__ostream_insert 1ms 0.021% 52.95% 87ms 1.83% AbstractCellProperty::IsType (inline) 5ms 0.11% 53.06% 84ms 1.77% _int_free_maybe_consolidate 0 0% 53.06% 83ms 1.75% Cell::HasCellProperty (inline) 1ms 0.021% 53.08% 82ms 1.73% CellPropertyCollection::HasProperty 5ms 0.11% 53.18% 81ms 1.71% vtkAOSDataArrayTemplate::DataElementChanged 76ms 1.60% 54.78% 76ms 1.60% __GI_sched_yield 2ms 0.042% 54.83% 74ms 1.56% vtkDoubleArray::~vtkDoubleArray 18ms 0.38% 55.21% 72ms 1.52% std::_Rb_tree::_M_lower_bound (inline) 46ms 0.97% 56.18% 72ms 1.52% std::basic_streambuf::xsputn 0 0% 56.18% 68ms 1.43% PottsMesh::GetMooreNeighbouringNodeIndices 0 0% 56.18% 68ms 1.43% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 5ms 0.11% 56.28% 67ms 1.41% AbstractCellPopulation::GetCellUsingLocationIndex 11ms 0.23% 56.51% 66ms 1.39% AbstractCellProperty::IsSame 0 0% 56.51% 65ms 1.37% Cell::GetCellProliferativeType 2ms 0.042% 56.56% 64ms 1.35% std::_Rb_tree::_M_insert_unique 0 0% 56.56% 64ms 1.35% std::set::insert (inline) 1ms 0.021% 56.58% 64ms 1.35% vtkIdList::New 4ms 0.084% 56.66% 63ms 1.33% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 56.66% 62ms 1.31% NodesOnlyMesh::SetUpBoxCollection 29ms 0.61% 57.27% 61ms 1.29% std::_Hashtable::clear 1ms 0.021% 57.29% 61ms 1.29% std::vector::push_back (inline) 0 0% 57.29% 61ms 1.29% tcache_get (inline) 61ms 1.29% 58.58% 61ms 1.29% tcache_get_n (inline) 0 0% 58.58% 58ms 1.22% NodesOnlyMesh::~NodesOnlyMesh 2ms 0.042% 58.62% 58ms 1.22% boost::numeric::ublas::vector_assign (inline) 57ms 1.20% 59.82% 57ms 1.20% vtkTimeStamp::Modified 11ms 0.23% 60.05% 55ms 1.16% std::type_info::operator== (inline) 0 0% 60.05% 53ms 1.12% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 0 0% 60.05% 53ms 1.12% std::_Rb_tree::lower_bound (inline) 0 0% 60.05% 53ms 1.12% std::map::lower_bound (inline) 28ms 0.59% 60.65% 51ms 1.08% __cxxabiv1::__si_class_type_info::__do_dyncast 7ms 0.15% 60.79% 49ms 1.03% VertexMeshWriter::GetNextNode 4ms 0.084% 60.88% 49ms 1.03% vtkDataArray::vtkDataArray 11ms 0.23% 61.11% 47ms 0.99% vtkSOADataArrayTemplate::FillTypedComponent 0 0% 61.11% 46ms 0.97% std::_Destroy (inline) 0 0% 61.11% 46ms 0.97% std::_Destroy_aux::__destroy (inline) 0 0% 61.11% 46ms 0.97% vtkDataArray::ComputeRange 45ms 0.95% 62.06% 45ms 0.95% [libstdc++.so.6.0.33] 4ms 0.084% 62.14% 45ms 0.95% std::vector::_M_realloc_insert 13ms 0.27% 62.42% 45ms 0.95% vtkAbstractArray::vtkAbstractArray 35ms 0.74% 63.15% 45ms 0.95% vtkObject::ObjectFinalize 43ms 0.91% 64.06% 43ms 0.91% __GI___writev 0 0% 64.06% 43ms 0.91% std::__basic_file::xsputn_2 3ms 0.063% 64.12% 42ms 0.89% std::_Rb_tree::_M_insert_ (inline) 41ms 0.86% 64.99% 41ms 0.86% [libvtkCommonCore-9.3.so.9.3] 12ms 0.25% 65.24% 41ms 0.86% boost::numeric::ublas::indexing_vector_assign 9ms 0.19% 65.43% 41ms 0.86% std::num_put::_M_insert_int 41ms 0.86% 66.29% 41ms 0.86% vtkObjectBase::~vtkObjectBase 40ms 0.84% 67.14% 40ms 0.84% __memset_avx2_unaligned_erms 0 0% 67.14% 40ms 0.84% std::_Rb_tree::_M_emplace_hint_unique 39ms 0.82% 67.96% 40ms 0.84% vtkObjectBase::Delete 2ms 0.042% 68.00% 39ms 0.82% VertexMesh::Clear 39ms 0.82% 68.82% 39ms 0.82% __mpn_divrem 10ms 0.21% 69.03% 39ms 0.82% vtkDataArray::~vtkDataArray 3ms 0.063% 69.10% 39ms 0.82% vtkDataArrayPrivate::DoComputeVectorRange 21ms 0.44% 69.54% 38ms 0.8% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 69.54% 38ms 0.8% DistributedBoxCollection::IsOwned 0 0% 69.54% 38ms 0.8% DistributedBoxCollection::~DistributedBoxCollection 0 0% 69.54% 38ms 0.8% NodesOnlyMesh::ClearBoxCollection (inline) 38ms 0.8% 70.34% 38ms 0.8% __memcpy_avx_unaligned_erms 0 0% 70.34% 38ms 0.8% _dl_init 0 0% 70.34% 38ms 0.8% call_init (inline) 5ms 0.11% 70.45% 38ms 0.8% vtkIdList::~vtkIdList 0 0% 70.45% 37ms 0.78% CxxTest::RealWorldDescription::setUp 0 0% 70.45% 37ms 0.78% PMPI_Init_thread 0 0% 70.45% 37ms 0.78% PetscInitialize 0 0% 70.45% 37ms 0.78% PetscSetup::setUpWorld 0 0% 70.45% 37ms 0.78% PetscSetupUtils::CommonSetup 0 0% 70.45% 37ms 0.78% PetscSetupUtils::InitialisePetsc 0 0% 70.45% 37ms 0.78% ompi_mpi_init 37ms 0.78% 71.23% 37ms 0.78% std::codecvt::do_always_noconv 1ms 0.021% 71.25% 37ms 0.78% std::less::operator() (inline) 0 0% 71.25% 37ms 0.78% std::map::~map (inline) 36ms 0.76% 72.01% 36ms 0.76% boost::numeric::ublas::c_vector::operator() 36ms 0.76% 72.77% 36ms 0.76% std::operator< (inline) 0 0% 72.77% 36ms 0.76% vtkDoubleArray::New 0 0% 72.77% 35ms 0.74% _dl_start_user 8ms 0.17% 72.93% 35ms 0.74% _int_free_merge_chunk 0 0% 72.93% 34ms 0.72% Cell::GetCellId 34ms 0.72% 73.65% 34ms 0.72% vtkObjectBase::vtkObjectBase 0 0% 73.65% 33ms 0.7% DistributedBoxCollection::SetupLocalBoxesHalfOnly 3ms 0.063% 73.71% 32ms 0.67% 0 0% 73.71% 32ms 0.67% CellIdWriter::GetCellDataForVtkOutput 1ms 0.021% 73.74% 32ms 0.67% std::basic_filebuf::overflow 0 0% 73.74% 32ms 0.67% std::make_unique (inline) 32ms 0.67% 74.41% 32ms 0.67% std::ostream::sentry::sentry 3ms 0.063% 74.47% 32ms 0.67% vtkAOSDataArrayTemplate::AllocateTuples 2ms 0.042% 74.52% 31ms 0.65% Node::AddElement 0 0% 74.52% 31ms 0.65% VtkMeshWriter::MakeVtkMesh 31ms 0.65% 75.17% 31ms 0.65% __GI___libc_write 3ms 0.063% 75.23% 31ms 0.65% boost::serialization::singleton::get_instance 31ms 0.65% 75.89% 31ms 0.65% std::_Rb_tree::_S_right (inline) 0 0% 75.89% 31ms 0.65% std::__basic_file::xsputn 0 0% 75.89% 31ms 0.65% std::basic_filebuf::_M_convert_to_external 0 0% 75.89% 31ms 0.65% vtk::detail::smp::vtkSMPToolsImplForTBB 31ms 0.65% 76.54% 31ms 0.65% vtkObject::~vtkObject 1ms 0.021% 76.56% 29ms 0.61% Node::ConstructNodeAttributes (inline) 0 0% 76.56% 29ms 0.61% Node::SetRadius 29ms 0.61% 77.17% 29ms 0.61% [libchaste_cell_based.so] 1ms 0.021% 77.19% 29ms 0.61% tbb::detail::r1::cancel_group_execution 6ms 0.13% 77.32% 29ms 0.61% vtkSOADataArrayTemplate::GetTupleIndexFromValueIndex 2ms 0.042% 77.36% 28ms 0.59% PottsMesh::GetVonNeumannNeighbouringNodeIndices 28ms 0.59% 77.95% 28ms 0.59% std::_Rb_tree_increment 3ms 0.063% 78.01% 28ms 0.59% vtkAOSDataArrayTemplate::InsertTuple 0 0% 78.01% 27ms 0.57% OutputFileHandler::OpenOutputFile 0 0% 78.01% 27ms 0.57% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 27ms 0.57% 78.58% 27ms 0.57% tcache_put (inline) 0 0% 78.58% 26ms 0.55% __GI___get_nprocs 0 0% 78.58% 26ms 0.55% read_sysfs_file 0 0% 78.58% 26ms 0.55% std::default_delete::operator() (inline) 0 0% 78.58% 26ms 0.55% std::thread::hardware_concurrency 0 0% 78.58% 26ms 0.55% std::unique_ptr::~unique_ptr (inline) 0 0% 78.58% 25ms 0.53% boost::numeric::ublas::c_vector::assign (inline) 6ms 0.13% 78.71% 25ms 0.53% vtk::detail::smp::vtkSMPToolsImpl::For 0 0% 78.71% 25ms 0.53% vtkDataArrayPrivate::DoComputeScalarRange 0 0% 78.71% 24ms 0.51% CellProliferativeTypesWriter::GetCellDataForVtkOutput 2ms 0.042% 78.75% 24ms 0.51% VertexMeshWriter::GetNextElement 17ms 0.36% 79.11% 24ms 0.51% _int_free_create_chunk (inline) 0 0% 79.11% 24ms 0.51% orte_init 21ms 0.44% 79.55% 24ms 0.51% std::num_put::do_put 24ms 0.51% 80.06% 24ms 0.51% vtkDataArray::Modified 2ms 0.042% 80.10% 24ms 0.51% vtkDataSet::GetCellTypes