File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3001ms, 78.97% of 3800ms total Dropped 668 nodes (cum <= 19ms) flat flat% sum% cum cum% 0 0% 0% 3627ms 95.45% __libc_start_call_main 0 0% 0% 3627ms 95.45% __libc_start_main_impl 0 0% 0% 3627ms 95.45% _start 0 0% 0% 3612ms 95.05% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 3612ms 95.05% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 3612ms 95.05% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 3612ms 95.05% main 0 0% 0% 3573ms 94.03% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 3573ms 94.03% CxxTest::TestRunner::runTest (inline) 0 0% 0% 3573ms 94.03% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 3564ms 93.79% AbstractCellBasedSimulation::Solve 0 0% 0% 3300ms 86.84% AbstractCellPopulation::WriteResultsToFiles 7ms 0.18% 0.18% 3134ms 82.47% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.18% 1602ms 42.16% VertexMeshWriter::WriteVtkUsingMesh 2ms 0.053% 0.24% 1383ms 36.39% VertexMeshWriter::MakeVtkMesh 1ms 0.026% 0.26% 1020ms 26.84% vtkPolygon::New 1ms 0.026% 0.29% 1019ms 26.82% vtkPolygon::vtkPolygon 3ms 0.079% 0.37% 694ms 18.26% vtkCell::vtkCell 7ms 0.18% 0.55% 583ms 15.34% vtkPoints::New 7ms 0.18% 0.74% 532ms 14.00% vtkPoints::vtkPoints 0 0% 0.74% 523ms 13.76% VertexMeshWriter::WriteFiles 1ms 0.026% 0.76% 507ms 13.34% std::ostream::operator<< (inline) 38ms 1.00% 1.76% 506ms 13.32% std::ostream::_M_insert 21ms 0.55% 2.32% 492ms 12.95% operator new 138ms 3.63% 5.95% 483ms 12.71% __GI___libc_malloc 2ms 0.053% 6.00% 476ms 12.53% vtkQuad::New 2ms 0.053% 6.05% 472ms 12.42% vtkQuad::vtkQuad 0 0% 6.05% 462ms 12.16% vtkLine::New 1ms 0.026% 6.08% 456ms 12.00% vtkTriangle::New 5ms 0.13% 6.21% 450ms 11.84% vtkTriangle::vtkTriangle 0 0% 6.21% 449ms 11.82% vtkStreamingDemandDrivenPipeline::Update 0 0% 6.21% 449ms 11.82% vtkXMLWriterBase::Write 0 0% 6.21% 448ms 11.79% vtkDemandDrivenPipeline::ProcessRequest 7ms 0.18% 6.39% 447ms 11.76% vtkLine::vtkLine 0 0% 6.39% 445ms 11.71% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 6.39% 444ms 11.68% vtkDemandDrivenPipeline::ExecuteData 0 0% 6.39% 443ms 11.66% vtkCompositeDataPipeline::ExecuteData 0 0% 6.39% 442ms 11.63% vtkExecutive::CallAlgorithm 0 0% 6.39% 441ms 11.61% vtkXMLUnstructuredDataWriter::ProcessRequest 42ms 1.11% 7.50% 409ms 10.76% std::num_put::_M_insert_float 0 0% 7.50% 393ms 10.34% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 7.50% 393ms 10.34% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 96ms 2.53% 10.03% 391ms 10.29% __GI___libc_free 0 0% 10.03% 359ms 9.45% vtkXMLWriter::WriteBinaryData 0 0% 10.03% 353ms 9.29% vtkXMLWriter::WriteBinaryDataBlock 0 0% 10.03% 353ms 9.29% vtkXMLWriter::WriteBinaryDataInternal 17ms 0.45% 10.47% 351ms 9.24% vtkPoints::SetDataType 0 0% 10.47% 326ms 8.58% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 1ms 0.026% 10.50% 323ms 8.50% vtkPolygon::~vtkPolygon 4ms 0.11% 10.61% 305ms 8.03% std::__cxx11::collate::do_transform 182ms 4.79% 15.39% 298ms 7.84% _int_malloc 173ms 4.55% 19.95% 294ms 7.74% _int_free 1ms 0.026% 19.97% 292ms 7.68% ___vsnprintf 2ms 0.053% 20.03% 292ms 7.68% __vsnprintf_internal (inline) 45ms 1.18% 21.21% 287ms 7.55% __printf_buffer 0 0% 21.21% 277ms 7.29% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 21.21% 275ms 7.24% VtkMeshWriter::WriteFiles 0 0% 21.21% 259ms 6.82% vtkXMLWriter::WritePointsAppendedData 0 0% 21.21% 256ms 6.74% OnLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.026% 21.24% 256ms 6.74% PottsBasedCellPopulation::UpdateCellLocations 5ms 0.13% 21.37% 256ms 6.74% vtkCell::~vtkCell 1ms 0.026% 21.39% 229ms 6.03% std::__new_allocator::deallocate (inline) 0 0% 21.39% 225ms 5.92% std::allocator_traits::deallocate (inline) 12ms 0.32% 21.71% 219ms 5.76% __printf_fp_l_buffer 0 0% 21.71% 219ms 5.76% __printf_fp_spec (inline) 36ms 0.95% 22.66% 213ms 5.61% std::__new_allocator::allocate (inline) 0 0% 22.66% 212ms 5.58% std::allocator_traits::allocate (inline) 90ms 2.37% 25.03% 199ms 5.24% __printf_fp_buffer_1 41ms 1.08% 26.11% 197ms 5.18% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 4ms 0.11% 26.21% 185ms 4.87% vtkBase64OutputStream::Write 21ms 0.55% 26.76% 178ms 4.68% vtkBase64OutputStream::EncodeTriplet 0 0% 26.76% 176ms 4.63% vtkXMLWriter::WriteCompressionBlock 21ms 0.55% 27.32% 175ms 4.61% std::_Rb_tree::_Rb_tree 0 0% 27.32% 175ms 4.61% std::set::set (inline) 6ms 0.16% 27.47% 169ms 4.45% vtkPoints::~vtkPoints 98ms 2.58% 30.05% 167ms 4.39% malloc_consolidate 0 0% 30.05% 166ms 4.37% compress2 0 0% 30.05% 166ms 4.37% vtkDataCompressor::Compress 0 0% 30.05% 166ms 4.37% vtkZLibDataCompressor::CompressBuffer 39ms 1.03% 31.08% 165ms 4.34% crc32 0 0% 31.08% 165ms 4.34% deflate 0 0% 31.08% 150ms 3.95% tbb::detail::r1::parallel_pipeline 1ms 0.026% 31.11% 148ms 3.89% std::vector::~vector (inline) 0 0% 31.11% 146ms 3.84% VertexMesh::~VertexMesh 0 0% 31.11% 144ms 3.79% std::_Rb_tree::_M_create_node (inline) 0 0% 31.11% 142ms 3.74% clone3 0 0% 31.11% 142ms 3.74% start_thread 1ms 0.026% 31.13% 142ms 3.74% vtkQuad::~vtkQuad 34ms 0.89% 32.03% 140ms 3.68% std::ostream::write 2ms 0.053% 32.08% 139ms 3.66% vtkIdList::AllocateInternal 2ms 0.053% 32.13% 138ms 3.63% std::_Vector_base::_M_deallocate (inline) 0 0% 32.13% 136ms 3.58% std::_Rb_tree::_M_get_node (inline) 0 0% 32.13% 135ms 3.55% tbb::detail::r1::reset 0 0% 32.13% 132ms 3.47% std::_Rb_tree::_Alloc_node::operator() (inline) 9ms 0.24% 32.37% 130ms 3.42% std::_Rb_tree::_M_copy (inline) 51ms 1.34% 33.71% 130ms 3.42% tbb::detail::r1::wait_bounded_queue_monitor 1ms 0.026% 33.74% 130ms 3.42% vtkTriangle::~vtkTriangle 2ms 0.053% 33.79% 130ms 3.42% vtkTypeFloat64Array::~vtkTypeFloat64Array 1ms 0.026% 33.82% 129ms 3.39% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 0 0% 33.82% 128ms 3.37% NodesOnlyMesh::ConstructNodesWithoutMesh 9ms 0.24% 34.05% 128ms 3.37% vtkFloatArray::New 6ms 0.16% 34.21% 125ms 3.29% std::_Rb_tree::~_Rb_tree (inline) 57ms 1.50% 35.71% 124ms 3.26% std::basic_filebuf::xsputn 1ms 0.026% 35.74% 124ms 3.26% vtkLine::GetParametricCenter 28ms 0.74% 36.47% 122ms 3.21% std::_Rb_tree::_M_erase 120ms 3.16% 39.63% 121ms 3.18% [libz.so.1.3] 0 0% 39.63% 120ms 3.16% VertexMesh::VertexMesh 0 0% 39.63% 119ms 3.13% std::_Vector_base::~_Vector_base (inline) 10ms 0.26% 39.89% 115ms 3.03% std::_Rb_tree::_M_clone_node (inline) 0 0% 39.89% 109ms 2.87% VertexMesh::GenerateEdgesFromElements (inline) 1ms 0.026% 39.92% 108ms 2.84% MutableElement::BuildEdges 0 0% 39.92% 108ms 2.84% vtkDataArray::CreateDataArray 1ms 0.026% 39.95% 108ms 2.84% vtkFloatArray::~vtkFloatArray 0 0% 39.95% 107ms 2.82% NodeLocationWriter::VisitAnyPopulation 45ms 1.18% 41.13% 107ms 2.82% vtkTypeFloat64Array::PrintSelf 0 0% 41.13% 106ms 2.79% std::set::~set (inline) 1ms 0.026% 41.16% 105ms 2.76% vtkFloatArray::vtkFloatArray 1ms 0.026% 41.18% 103ms 2.71% vtkIdList::Allocate 19ms 0.5% 41.68% 102ms 2.68% vtkObject::vtkObject 8ms 0.21% 41.89% 101ms 2.66% vtkTypeFloat64Array::New 0 0% 41.89% 99ms 2.61% EdgeHelper::~EdgeHelper (inline) 1ms 0.026% 41.92% 95ms 2.50% EdgeHelper::GetEdgeFromNodes 94ms 2.47% 44.39% 94ms 2.47% __strcmp_evex 0 0% 44.39% 93ms 2.45% std::_Rb_tree::_M_drop_node (inline) 1ms 0.026% 44.42% 93ms 2.45% vtkDoubleArray::vtkDoubleArray 0 0% 44.42% 91ms 2.39% CellPropertyCollection::GetPropertiesType (inline) 5ms 0.13% 44.55% 91ms 2.39% std::vector::_M_default_append 0 0% 44.55% 89ms 2.34% std::_Rb_tree::_M_put_node (inline) 22ms 0.58% 45.13% 89ms 2.34% vtkAOSDataArrayTemplate::DataElementChanged 1ms 0.026% 45.16% 84ms 2.21% AbstractCellProperty::IsSubType (inline) 20ms 0.53% 45.68% 84ms 2.21% __dynamic_cast 4ms 0.11% 45.79% 83ms 2.18% _int_free_maybe_consolidate 83ms 2.18% 47.97% 83ms 2.18% unlink_chunk 2ms 0.053% 48.03% 83ms 2.18% vtkTypeFloat64Array::vtkTypeFloat64Array 13ms 0.34% 48.37% 82ms 2.16% vtkObject::Modified 80ms 2.11% 50.47% 80ms 2.11% __GI_sched_yield 3ms 0.079% 50.55% 79ms 2.08% std::_Vector_base::_M_allocate (inline) 0 0% 50.55% 78ms 2.05% Cell::HasCellProperty (inline) 4ms 0.11% 50.66% 78ms 2.05% CellPropertyCollection::HasProperty 26ms 0.68% 51.34% 75ms 1.97% hack_digit 2ms 0.053% 51.39% 74ms 1.95% AbstractCellProperty::IsType (inline) 2ms 0.053% 51.45% 74ms 1.95% std::map::operator[] (partial-inline) 0 0% 51.45% 73ms 1.92% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 42ms 1.11% 52.55% 70ms 1.84% std::_Hashtable::clear 21ms 0.55% 53.11% 70ms 1.84% std::__ostream_insert 42ms 1.11% 54.21% 70ms 1.84% vtkObjectBase::UnRegisterInternal 3ms 0.079% 54.29% 69ms 1.82% vtkIdList::New 68ms 1.79% 56.08% 68ms 1.79% vtkTimeStamp::Modified 0 0% 56.08% 66ms 1.74% vtkXMLWriter::WritePointDataAppendedData 0 0% 56.08% 65ms 1.71% PottsMesh::GetMooreNeighbouringNodeIndices 1ms 0.026% 56.11% 65ms 1.71% std::operator<< (inline) 0 0% 56.11% 65ms 1.71% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 44ms 1.16% 57.26% 63ms 1.66% std::basic_streambuf::xsputn 4ms 0.11% 57.37% 63ms 1.66% vtkDoubleArray::~vtkDoubleArray 6ms 0.16% 57.53% 61ms 1.61% std::vector::push_back (inline) 3ms 0.079% 57.61% 59ms 1.55% boost::numeric::ublas::c_vector::c_vector (partial-inline) 9ms 0.24% 57.84% 56ms 1.47% AbstractCellProperty::IsSame 0 0% 57.84% 56ms 1.47% boost::numeric::ublas::vector_assign (inline) 1ms 0.026% 57.87% 55ms 1.45% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 57.87% 54ms 1.42% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 15ms 0.39% 58.26% 54ms 1.42% std::_Rb_tree::_M_lower_bound (inline) 0 0% 58.26% 50ms 1.32% Cell::GetCellProliferativeType 1ms 0.026% 58.29% 47ms 1.24% VertexMesh::Clear 47ms 1.24% 59.53% 47ms 1.24% __GI___writev 14ms 0.37% 59.89% 47ms 1.24% std::type_info::operator== (inline) 0 0% 59.89% 46ms 1.21% std::__basic_file::xsputn_2 3ms 0.079% 59.97% 46ms 1.21% vtkDataArray::vtkDataArray 16ms 0.42% 60.39% 45ms 1.18% boost::numeric::ublas::indexing_vector_assign 0 0% 60.39% 45ms 1.18% std::_Rb_tree::lower_bound (inline) 0 0% 60.39% 45ms 1.18% std::map::lower_bound (inline) 10ms 0.26% 60.66% 44ms 1.16% vtkIdList::~vtkIdList 0 0% 60.66% 43ms 1.13% NodesOnlyMesh::SetUpBoxCollection 3ms 0.079% 60.74% 43ms 1.13% std::vector::_M_realloc_insert 11ms 0.29% 61.03% 41ms 1.08% vtkAbstractArray::vtkAbstractArray 0 0% 61.03% 40ms 1.05% NodesOnlyMesh::~NodesOnlyMesh 0 0% 61.03% 40ms 1.05% std::_Rb_tree::_M_insert_unique 9ms 0.24% 61.26% 40ms 1.05% std::num_put::_M_insert_int 0 0% 61.26% 40ms 1.05% std::set::insert (inline) 0 0% 61.26% 40ms 1.05% tcache_get (inline) 40ms 1.05% 62.32% 40ms 1.05% tcache_get_n (inline) 24ms 0.63% 62.95% 38ms 1.00% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 62.95% 38ms 1.00% DistributedBoxCollection::IsOwned 38ms 1.00% 63.95% 38ms 1.00% __memcpy_avx512_unaligned_erms 13ms 0.34% 64.29% 38ms 1.00% vtkDataArray::~vtkDataArray 8ms 0.21% 64.50% 37ms 0.97% vtkSOADataArrayTemplate::FillTypedComponent 0 0% 64.50% 35ms 0.92% CxxTest::RealWorldDescription::setUp 0 0% 64.50% 35ms 0.92% PetscInitialize 0 0% 64.50% 35ms 0.92% PetscSetup::setUpWorld 0 0% 64.50% 35ms 0.92% PetscSetupUtils::CommonSetup 0 0% 64.50% 35ms 0.92% PetscSetupUtils::InitialisePetsc 35ms 0.92% 65.42% 35ms 0.92% [libstdc++.so.6.0.33] 0 0% 65.42% 35ms 0.92% _dl_init 0 0% 65.42% 35ms 0.92% call_init (inline) 0 0% 65.42% 34ms 0.89% PMPI_Init_thread 34ms 0.89% 66.32% 34ms 0.89% [libvtkCommonCore-9.3.so.9.3] 18ms 0.47% 66.79% 34ms 0.89% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 66.79% 34ms 0.89% ompi_mpi_init 0 0% 66.79% 34ms 0.89% std::_Destroy (inline) 0 0% 66.79% 34ms 0.89% std::_Destroy_aux::__destroy (inline) 33ms 0.87% 67.66% 34ms 0.89% vtkObjectBase::Delete 33ms 0.87% 68.53% 33ms 0.87% __memset_avx512_unaligned_erms 33ms 0.87% 69.39% 33ms 0.87% __mpn_divrem 0 0% 69.39% 32ms 0.84% 4ms 0.11% 69.50% 32ms 0.84% VertexMeshWriter::GetNextNode 32ms 0.84% 70.34% 32ms 0.84% vtkObject::~vtkObject 0 0% 70.34% 31ms 0.82% _dl_start_user 31ms 0.82% 71.16% 31ms 0.82% std::ostream::sentry::sentry 0 0% 71.16% 30ms 0.79% DistributedBoxCollection::~DistributedBoxCollection 0 0% 71.16% 30ms 0.79% NodesOnlyMesh::ClearBoxCollection (inline) 1ms 0.026% 71.18% 30ms 0.79% std::_Rb_tree::_M_insert_ (inline) 30ms 0.79% 71.97% 30ms 0.79% vtkObjectBase::vtkObjectBase 3ms 0.079% 72.05% 29ms 0.76% vtkAOSDataArrayTemplate::AllocateTuples 29ms 0.76% 72.82% 29ms 0.76% vtkObjectBase::~vtkObjectBase 0 0% 72.82% 28ms 0.74% std::less::operator() (inline) 28ms 0.74% 73.55% 28ms 0.74% std::operator< (inline) 0 0% 73.55% 28ms 0.74% vtkDataArray::ComputeRange 2ms 0.053% 73.61% 27ms 0.71% std::_Rb_tree::_M_emplace_hint_unique 0 0% 73.61% 27ms 0.71% std::make_unique (inline) 0 0% 73.61% 27ms 0.71% vtk::detail::smp::vtkSMPToolsImplForTBB 21ms 0.55% 74.16% 27ms 0.71% vtkObject::ObjectFinalize 26ms 0.68% 74.84% 26ms 0.68% __GI___libc_write 9ms 0.24% 75.08% 26ms 0.68% _int_free_merge_chunk 0 0% 75.08% 26ms 0.68% boost::numeric::ublas::c_vector::assign (inline) 0 0% 75.08% 26ms 0.68% std::__basic_file::xsputn 0 0% 75.08% 26ms 0.68% std::basic_filebuf::_M_convert_to_external 0 0% 75.08% 26ms 0.68% std::basic_filebuf::overflow 2ms 0.053% 75.13% 26ms 0.68% tbb::detail::r1::cancel_group_execution 8ms 0.21% 75.34% 26ms 0.68% vtkSOADataArrayTemplate::GetTupleIndexFromValueIndex 0 0% 75.34% 25ms 0.66% Cell::GetCellId 1ms 0.026% 75.37% 25ms 0.66% VtkMeshWriter::MakeVtkMesh 25ms 0.66% 76.03% 25ms 0.66% boost::numeric::ublas::c_vector::operator() 6ms 0.16% 76.18% 25ms 0.66% vtkAOSDataArrayTemplate::InsertTuple 10ms 0.26% 76.45% 25ms 0.66% vtkIdList::vtkIdList 0 0% 76.45% 24ms 0.63% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 0 0% 76.45% 24ms 0.63% std::_Rb_tree_header::_Rb_tree_header (inline) 0 0% 76.45% 23ms 0.61% CellIdWriter::GetCellDataForVtkOutput 1ms 0.026% 76.47% 23ms 0.61% PottsMesh::GetVonNeumannNeighbouringNodeIndices 1ms 0.026% 76.50% 23ms 0.61% boost::serialization::singleton::get_instance 23ms 0.61% 77.11% 23ms 0.61% std::_Rb_tree_header::_M_reset (inline) 1ms 0.026% 77.13% 22ms 0.58% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 0 0% 77.13% 22ms 0.58% orte_init 0 0% 77.13% 22ms 0.58% std::basic_filebuf::open 1ms 0.026% 77.16% 21ms 0.55% CellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 77.16% 21ms 0.55% VertexElement::~VertexElement 4ms 0.11% 77.26% 21ms 0.55% __find_specmb (inline) 1ms 0.026% 77.29% 21ms 0.55% std::basic_filebuf::sync 21ms 0.55% 77.84% 21ms 0.55% std::codecvt::do_always_noconv 0 0% 77.84% 21ms 0.55% std::default_delete::operator() (inline) 0 0% 77.84% 21ms 0.55% std::ostream::flush 0 0% 77.84% 21ms 0.55% std::unique_ptr::~unique_ptr (inline) 0 0% 77.84% 21ms 0.55% vtkXMLUnstructuredDataWriter::WriteHeader 0 0% 77.84% 20ms 0.53% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 77.84% 20ms 0.53% Cell::GetMutationState 2ms 0.053% 77.89% 20ms 0.53% DistributedBoxCollection::SetupLocalBoxesHalfOnly 0 0% 77.89% 20ms 0.53% OutputFileHandler::OpenOutputFile 0 0% 77.89% 20ms 0.53% PottsBasedCellPopulation::AcceptCellWriter 0 0% 77.89% 20ms 0.53% _IO_new_file_fopen 0 0% 77.89% 20ms 0.53% _IO_new_fopen 0 0% 77.89% 20ms 0.53% __fopen_internal (inline) 0 0% 77.89% 20ms 0.53% vtk::detail::smp::vtkSMPToolsImpl::For 0 0% 77.89% 20ms 0.53% vtkDataArrayPrivate::DoComputeScalarRange 1ms 0.026% 77.92% 19ms 0.5% Edge::Edge 0 0% 77.92% 19ms 0.5% Node::AddElement 19ms 0.5% 78.42% 19ms 0.5% Node::GetIndex 0 0% 78.42% 19ms 0.5% __GI__IO_file_open 19ms 0.5% 78.92% 19ms 0.5% __libc_open64 0 0% 78.92% 19ms 0.5% std::__basic_file::open 0 0% 78.92% 19ms 0.5% std::map::~map (inline) 2ms 0.053% 78.97% 19ms 0.5% vtkDataArrayPrivate::DoComputeVectorRange 0 0% 78.97% 19ms 0.5% vtkXMLUnstructuredGridWriter::WriteAppendedPiece