File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3720ms, 78.63% of 4731ms total Dropped 701 nodes (cum <= 23.66ms) flat flat% sum% cum cum% 0 0% 0% 4546ms 96.09% __libc_start_call_main 0 0% 0% 4546ms 96.09% __libc_start_main_impl 0 0% 0% 4546ms 96.09% _start 0 0% 0% 4527ms 95.69% main 0 0% 0% 4526ms 95.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4526ms 95.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4526ms 95.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4485ms 94.80% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4485ms 94.80% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4485ms 94.80% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4472ms 94.53% AbstractCellBasedSimulation::Solve 0 0% 0% 4164ms 88.02% AbstractCellPopulation::WriteResultsToFiles 12ms 0.25% 0.25% 3938ms 83.24% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.25% 1974ms 41.72% VertexMeshWriter::WriteVtkUsingMesh 0 0% 0.25% 1702ms 35.98% VertexMeshWriter::MakeVtkMesh 1ms 0.021% 0.27% 1247ms 26.36% vtkPolygon::New 2ms 0.042% 0.32% 1243ms 26.27% vtkPolygon::vtkPolygon 7ms 0.15% 0.47% 861ms 18.20% vtkCell::vtkCell 1ms 0.021% 0.49% 737ms 15.58% vtkPoints::New 40ms 0.85% 1.33% 691ms 14.61% operator new 0 0% 1.33% 689ms 14.56% VertexMeshWriter::WriteFiles 11ms 0.23% 1.56% 687ms 14.52% vtkPoints::vtkPoints 49ms 1.04% 2.60% 673ms 14.23% std::ostream::_M_insert 1ms 0.021% 2.62% 672ms 14.20% std::ostream::operator<< (inline) 228ms 4.82% 7.44% 658ms 13.91% __GI___libc_malloc 0 0% 7.44% 577ms 12.20% vtkStreamingDemandDrivenPipeline::Update 0 0% 7.44% 577ms 12.20% vtkXMLWriterBase::Write 0 0% 7.44% 576ms 12.18% vtkDemandDrivenPipeline::ProcessRequest 0 0% 7.44% 575ms 12.15% vtkLine::New 1ms 0.021% 7.46% 573ms 12.11% vtkQuad::New 0 0% 7.46% 572ms 12.09% vtkExecutive::CallAlgorithm 0 0% 7.46% 572ms 12.09% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 7.46% 571ms 12.07% vtkDemandDrivenPipeline::ExecuteData 0 0% 7.46% 571ms 12.07% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 7.46% 570ms 12.05% vtkCompositeDataPipeline::ExecuteData 1ms 0.021% 7.48% 570ms 12.05% vtkQuad::vtkQuad 11ms 0.23% 7.72% 557ms 11.77% vtkLine::vtkLine 49ms 1.04% 8.75% 550ms 11.63% std::num_put::_M_insert_float 2ms 0.042% 8.79% 544ms 11.50% vtkTriangle::New 5ms 0.11% 8.90% 531ms 11.22% vtkTriangle::vtkTriangle 114ms 2.41% 11.31% 516ms 10.91% __GI___libc_free 0 0% 11.31% 515ms 10.89% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 11.31% 515ms 10.89% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 11.31% 463ms 9.79% vtkXMLWriter::WriteBinaryData 0 0% 11.31% 459ms 9.70% vtkXMLWriter::WriteBinaryDataBlock 0 0% 11.31% 459ms 9.70% vtkXMLWriter::WriteBinaryDataInternal 29ms 0.61% 11.92% 445ms 9.41% vtkPoints::SetDataType 0 0% 11.92% 443ms 9.36% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 11ms 0.23% 12.15% 433ms 9.15% std::__cxx11::collate::do_transform 4ms 0.085% 12.24% 412ms 8.71% ___vsnprintf 0 0% 12.24% 409ms 8.65% __vsnprintf_internal (inline) 78ms 1.65% 13.89% 400ms 8.45% __printf_buffer 250ms 5.28% 19.17% 399ms 8.43% _int_free 2ms 0.042% 19.21% 393ms 8.31% vtkPolygon::~vtkPolygon 230ms 4.86% 24.08% 352ms 7.44% _int_malloc 1ms 0.021% 24.10% 348ms 7.36% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 24.10% 342ms 7.23% VtkMeshWriter::WriteFiles 1ms 0.021% 24.12% 332ms 7.02% vtkXMLWriter::WritePointsAppendedData 23ms 0.49% 24.60% 303ms 6.40% __printf_fp_l_buffer 0 0% 24.60% 303ms 6.40% __printf_fp_spec (inline) 5ms 0.11% 24.71% 303ms 6.40% vtkCell::~vtkCell 0 0% 24.71% 300ms 6.34% OnLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.021% 24.73% 300ms 6.34% PottsBasedCellPopulation::UpdateCellLocations 29ms 0.61% 25.34% 280ms 5.92% std::__new_allocator::allocate (inline) 0 0% 25.34% 279ms 5.90% std::allocator_traits::allocate (inline) 1ms 0.021% 25.36% 276ms 5.83% std::__new_allocator::deallocate (inline) 39ms 0.82% 26.19% 276ms 5.83% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 136ms 2.87% 29.06% 272ms 5.75% __printf_fp_buffer_1 0 0% 29.06% 272ms 5.75% std::allocator_traits::deallocate (inline) 0 0% 29.06% 241ms 5.09% vtkXMLWriter::WriteCompressionBlock 0 0% 29.06% 225ms 4.76% compress2 0 0% 29.06% 225ms 4.76% vtkDataCompressor::Compress 0 0% 29.06% 225ms 4.76% vtkZLibDataCompressor::CompressBuffer 46ms 0.97% 30.04% 224ms 4.73% crc32 0 0% 30.04% 224ms 4.73% deflate 3ms 0.063% 30.10% 224ms 4.73% vtkBase64OutputStream::Write 21ms 0.44% 30.54% 216ms 4.57% vtkBase64OutputStream::EncodeTriplet 1ms 0.021% 30.56% 212ms 4.48% std::set::set (inline) 25ms 0.53% 31.09% 210ms 4.44% std::_Rb_tree::_Rb_tree 4ms 0.085% 31.18% 209ms 4.42% vtkPoints::~vtkPoints 115ms 2.43% 33.61% 193ms 4.08% malloc_consolidate 0 0% 33.61% 191ms 4.04% vtkQuad::~vtkQuad 50ms 1.06% 34.66% 185ms 3.91% std::ostream::write 0 0% 34.66% 176ms 3.72% VertexMesh::~VertexMesh 8ms 0.17% 34.83% 174ms 3.68% vtkIdList::AllocateInternal 6ms 0.13% 34.96% 173ms 3.66% vtkFloatArray::New 8ms 0.17% 35.13% 172ms 3.64% std::_Rb_tree::~_Rb_tree (inline) 0 0% 35.13% 171ms 3.61% vtkTriangle::~vtkTriangle 3ms 0.063% 35.19% 170ms 3.59% vtkLine::GetParametricCenter 0 0% 35.19% 169ms 3.57% std::_Rb_tree::_M_create_node (inline) 1ms 0.021% 35.21% 167ms 3.53% NodesOnlyMesh::ConstructNodesWithoutMesh 35ms 0.74% 35.95% 167ms 3.53% std::_Rb_tree::_M_erase 162ms 3.42% 39.38% 164ms 3.47% [libz.so.1.3] 0 0% 39.38% 160ms 3.38% std::_Rb_tree::_M_get_node (inline) 0 0% 39.38% 156ms 3.30% std::_Rb_tree::_Alloc_node::operator() (inline) 14ms 0.3% 39.67% 155ms 3.28% std::_Rb_tree::_M_copy (inline) 2ms 0.042% 39.72% 155ms 3.28% std::_Vector_base::_M_deallocate (inline) 0 0% 39.72% 153ms 3.23% std::vector::~vector (inline) 1ms 0.021% 39.74% 153ms 3.23% tbb::detail::r1::parallel_pipeline 1ms 0.021% 39.76% 150ms 3.17% VertexMesh::VertexMesh 11ms 0.23% 39.99% 150ms 3.17% std::vector::_M_default_append 2ms 0.042% 40.03% 150ms 3.17% vtkTypeFloat64Array::~vtkTypeFloat64Array 0 0% 40.03% 148ms 3.13% clone3 0 0% 40.03% 148ms 3.13% start_thread 1ms 0.021% 40.05% 147ms 3.11% vtkDataArray::CreateDataArray 3ms 0.063% 40.12% 145ms 3.06% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 0 0% 40.12% 144ms 3.04% std::set::~set (inline) 0 0% 40.12% 144ms 3.04% vtkFloatArray::vtkFloatArray 65ms 1.37% 41.49% 141ms 2.98% std::basic_filebuf::xsputn 2ms 0.042% 41.53% 140ms 2.96% VertexMesh::GenerateEdgesFromElements (inline) 6ms 0.13% 41.66% 138ms 2.92% MutableElement::BuildEdges 0 0% 41.66% 138ms 2.92% NodeLocationWriter::VisitAnyPopulation 0 0% 41.66% 138ms 2.92% tbb::detail::r1::reset 7ms 0.15% 41.81% 138ms 2.92% vtkTypeFloat64Array::New 5ms 0.11% 41.92% 135ms 2.85% vtkDoubleArray::vtkDoubleArray 12ms 0.25% 42.17% 133ms 2.81% std::_Rb_tree::_M_clone_node (inline) 58ms 1.23% 43.39% 128ms 2.71% tbb::detail::r1::wait_bounded_queue_monitor 0 0% 43.39% 126ms 2.66% std::_Rb_tree::_M_drop_node (inline) 2ms 0.042% 43.44% 126ms 2.66% std::_Vector_base::~_Vector_base (inline) 0 0% 43.44% 120ms 2.54% EdgeHelper::GetEdgeFromNodes 3ms 0.063% 43.50% 120ms 2.54% vtkFloatArray::~vtkFloatArray 0 0% 43.50% 119ms 2.52% std::_Rb_tree::_M_put_node (inline) 0 0% 43.50% 119ms 2.52% std::_Vector_base::_M_allocate (inline) 4ms 0.085% 43.58% 117ms 2.47% vtkTypeFloat64Array::vtkTypeFloat64Array 0 0% 43.58% 116ms 2.45% EdgeHelper::~EdgeHelper (inline) 1ms 0.021% 43.61% 113ms 2.39% vtkIdList::Allocate 0 0% 43.61% 109ms 2.30% vtkXMLWriter::WritePointDataAppendedData 0 0% 43.61% 107ms 2.26% CellPropertyCollection::GetPropertiesType (inline) 27ms 0.57% 44.18% 107ms 2.26% vtkObject::vtkObject 52ms 1.10% 45.28% 107ms 2.26% vtkTypeFloat64Array::PrintSelf 104ms 2.20% 47.47% 104ms 2.20% __strcmp_avx2 5ms 0.11% 47.58% 101ms 2.13% _int_free_maybe_consolidate 98ms 2.07% 49.65% 98ms 2.07% unlink_chunk 0 0% 49.65% 96ms 2.03% AbstractCellProperty::IsSubType (inline) 27ms 0.57% 50.22% 95ms 2.01% __dynamic_cast 3ms 0.063% 50.29% 93ms 1.97% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 11ms 0.23% 50.52% 92ms 1.94% vtkAOSDataArrayTemplate::DataElementChanged 57ms 1.20% 51.72% 92ms 1.94% vtkObjectBase::UnRegisterInternal 40ms 0.85% 52.57% 91ms 1.92% std::__ostream_insert 0 0% 52.57% 90ms 1.90% Cell::HasCellProperty (inline) 1ms 0.021% 52.59% 89ms 1.88% AbstractCellProperty::IsType (inline) 3ms 0.063% 52.65% 89ms 1.88% CellPropertyCollection::HasProperty 0 0% 52.65% 86ms 1.82% std::operator<< (inline) 6ms 0.13% 52.78% 85ms 1.80% std::map::operator[] (partial-inline) 49ms 1.04% 53.82% 81ms 1.71% hack_digit 6ms 0.13% 53.94% 76ms 1.61% AbstractCellPopulation::GetCellUsingLocationIndex 22ms 0.47% 54.41% 76ms 1.61% std::_Rb_tree::_M_lower_bound (inline) 46ms 0.97% 55.38% 75ms 1.59% std::basic_streambuf::xsputn 19ms 0.4% 55.78% 73ms 1.54% vtkObject::Modified 3ms 0.063% 55.84% 72ms 1.52% std::vector::push_back (inline) 4ms 0.085% 55.93% 71ms 1.50% vtkDoubleArray::~vtkDoubleArray 69ms 1.46% 57.39% 69ms 1.46% __GI_sched_yield 0 0% 57.39% 69ms 1.46% tcache_get (inline) 69ms 1.46% 58.85% 69ms 1.46% tcache_get_n (inline) 0 0% 58.85% 68ms 1.44% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 14ms 0.3% 59.14% 66ms 1.40% AbstractCellProperty::IsSame 0 0% 59.14% 66ms 1.40% Cell::GetCellProliferativeType 3ms 0.063% 59.21% 66ms 1.40% vtkIdList::New 0 0% 59.21% 64ms 1.35% NodesOnlyMesh::SetUpBoxCollection 2ms 0.042% 59.25% 64ms 1.35% PottsMesh::GetMooreNeighbouringNodeIndices 6ms 0.13% 59.37% 62ms 1.31% boost::numeric::ublas::c_vector::c_vector (inline) 2ms 0.042% 59.42% 60ms 1.27% VertexMesh::Clear 59ms 1.25% 60.66% 59ms 1.25% __memcpy_avx_unaligned_erms 36ms 0.76% 61.42% 59ms 1.25% std::_Hashtable::clear 1ms 0.021% 61.45% 55ms 1.16% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 1ms 0.021% 61.47% 55ms 1.16% boost::numeric::ublas::vector_assign (inline) 0 0% 61.47% 53ms 1.12% std::_Rb_tree::lower_bound (inline) 0 0% 61.47% 53ms 1.12% std::map::lower_bound (inline) 53ms 1.12% 62.59% 53ms 1.12% vtkTimeStamp::Modified 13ms 0.27% 62.86% 52ms 1.10% std::type_info::operator== (inline) 0 0% 62.86% 51ms 1.08% NodesOnlyMesh::~NodesOnlyMesh 1ms 0.021% 62.88% 51ms 1.08% std::set::insert (inline) 14ms 0.3% 63.18% 51ms 1.08% vtkDataArray::vtkDataArray 30ms 0.63% 63.81% 50ms 1.06% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.021% 63.83% 50ms 1.06% std::_Rb_tree::_M_insert_unique 6ms 0.13% 63.96% 48ms 1.01% VertexMeshWriter::GetNextNode 11ms 0.23% 64.19% 48ms 1.01% std::num_put::_M_insert_int 3ms 0.063% 64.26% 46ms 0.97% std::vector::_M_realloc_insert 45ms 0.95% 65.21% 45ms 0.95% vtkObject::~vtkObject 43ms 0.91% 66.12% 43ms 0.91% __GI___writev 0 0% 66.12% 43ms 0.91% std::__basic_file::xsputn_2 1ms 0.021% 66.14% 42ms 0.89% DistributedBoxCollection::SetupLocalBoxesHalfOnly 10ms 0.21% 66.35% 42ms 0.89% vtkSOADataArrayTemplate::FillTypedComponent 41ms 0.87% 67.22% 41ms 0.87% [libstdc++.so.6.0.33] 0 0% 67.22% 41ms 0.87% std::less::operator() (inline) 0 0% 67.22% 41ms 0.87% std::make_unique (inline) 41ms 0.87% 68.08% 41ms 0.87% std::operator< (inline) 0 0% 68.08% 40ms 0.85% _dl_init 0 0% 68.08% 40ms 0.85% call_init (inline) 5ms 0.11% 68.19% 40ms 0.85% vtkIdList::~vtkIdList 25ms 0.53% 68.72% 39ms 0.82% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 68.72% 39ms 0.82% DistributedBoxCollection::IsOwned 39ms 0.82% 69.54% 39ms 0.82% std::ostream::sentry::sentry 0 0% 69.54% 39ms 0.82% vtkDoubleArray::New 0 0% 69.54% 38ms 0.8% CxxTest::RealWorldDescription::setUp 0 0% 69.54% 38ms 0.8% PMPI_Init_thread 0 0% 69.54% 38ms 0.8% PetscInitialize 0 0% 69.54% 38ms 0.8% PetscSetup::setUpWorld 0 0% 69.54% 38ms 0.8% PetscSetupUtils::CommonSetup 0 0% 69.54% 38ms 0.8% PetscSetupUtils::InitialisePetsc 0 0% 69.54% 38ms 0.8% ompi_mpi_init 2ms 0.042% 69.58% 38ms 0.8% std::_Rb_tree::_M_insert_ (inline) 0 0% 69.58% 37ms 0.78% _dl_start_user 37ms 0.78% 70.37% 37ms 0.78% vtkObjectBase::~vtkObjectBase 3ms 0.063% 70.43% 36ms 0.76% CellProliferativeTypesWriter::GetCellDataForVtkOutput 9ms 0.19% 70.62% 36ms 0.76% vtkAbstractArray::vtkAbstractArray 0 0% 70.62% 35ms 0.74% DistributedBoxCollection::~DistributedBoxCollection 0 0% 70.62% 35ms 0.74% NodesOnlyMesh::ClearBoxCollection (inline) 35ms 0.74% 71.36% 35ms 0.74% [libvtkCommonCore-9.3.so.9.3] 8ms 0.17% 71.53% 35ms 0.74% boost::numeric::ublas::indexing_vector_assign 3ms 0.063% 71.59% 35ms 0.74% boost::serialization::singleton::get_instance 28ms 0.59% 72.18% 35ms 0.74% vtkObject::ObjectFinalize 0 0% 72.18% 34ms 0.72% vtkDataArray::ComputeRange 13ms 0.27% 72.46% 34ms 0.72% vtkDataArray::~vtkDataArray 0 0% 72.46% 33ms 0.7% 0 0% 72.46% 33ms 0.7% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 0 0% 72.46% 33ms 0.7% std::__basic_file::xsputn 0 0% 72.46% 33ms 0.7% std::basic_filebuf::_M_convert_to_external 0 0% 72.46% 33ms 0.7% std::basic_filebuf::overflow 33ms 0.7% 73.16% 33ms 0.7% std::codecvt::do_always_noconv 31ms 0.66% 73.81% 33ms 0.7% vtkObjectBase::Delete 0 0% 73.81% 32ms 0.68% OutputFileHandler::OpenOutputFile 32ms 0.68% 74.49% 32ms 0.68% __GI___libc_write 4ms 0.085% 74.57% 32ms 0.68% std::__new_allocator::construct (inline) 0 0% 74.57% 32ms 0.68% std::allocator_traits::construct (inline) 0 0% 74.57% 32ms 0.68% std::basic_filebuf::open 0 0% 74.57% 31ms 0.66% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 74.57% 31ms 0.66% PottsBasedCellPopulation::AcceptCellWriter 0 0% 74.57% 31ms 0.66% std::_Destroy (inline) 0 0% 74.57% 31ms 0.66% std::_Destroy_aux::__destroy (inline) 0 0% 74.57% 30ms 0.63% vtk::detail::smp::vtkSMPToolsImplForTBB 5ms 0.11% 74.68% 30ms 0.63% vtkAOSDataArrayTemplate::InsertTuple 3ms 0.063% 74.74% 30ms 0.63% vtkDataArrayPrivate::DoComputeVectorRange 30ms 0.63% 75.38% 30ms 0.63% vtkObjectBase::vtkObjectBase 3ms 0.063% 75.44% 29ms 0.61% Edge::Edge 29ms 0.61% 76.05% 29ms 0.61% __memset_avx2_unaligned_erms 4ms 0.085% 76.14% 29ms 0.61% _int_free_merge_chunk 0 0% 76.14% 29ms 0.61% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 3ms 0.063% 76.20% 29ms 0.61% std::_Rb_tree_header::_Rb_tree_header (inline) 1ms 0.021% 76.22% 28ms 0.59% Cell::GetMutationState 2ms 0.042% 76.26% 28ms 0.59% Node::~Node 0 0% 76.26% 28ms 0.59% std::map::~map (inline) 19ms 0.4% 76.66% 28ms 0.59% std::num_put::do_put 4ms 0.085% 76.75% 28ms 0.59% tbb::detail::r1::cancel_group_execution 0 0% 76.75% 27ms 0.57% std::ostream::flush 0 0% 76.75% 26ms 0.55% VtkMeshWriter::MakeVtkMesh 2ms 0.042% 76.79% 26ms 0.55% std::_Rb_tree::_M_emplace_hint_unique 26ms 0.55% 77.34% 26ms 0.55% std::_Rb_tree_increment 0 0% 77.34% 26ms 0.55% std::basic_filebuf::sync 1ms 0.021% 77.36% 26ms 0.55% std::map::find (inline) 2ms 0.042% 77.40% 26ms 0.55% vtkAOSDataArrayTemplate::AllocateTuples 0 0% 77.40% 25ms 0.53% Cell::GetCellId 0 0% 77.40% 25ms 0.53% Edge::SetNodes (inline) 0 0% 77.40% 25ms 0.53% _IO_new_file_fopen 0 0% 77.40% 25ms 0.53% _IO_new_fopen 0 0% 77.40% 25ms 0.53% __fopen_internal (inline) 2ms 0.042% 77.45% 25ms 0.53% boost::serialization::void_cast_detail::void_caster::recursive_register 0 0% 77.45% 25ms 0.53% boost::serialization::void_cast_detail::void_caster_primitive::void_caster_primitive (inline) 2ms 0.042% 77.49% 25ms 0.53% std::_Rb_tree::find (inline) 0 0% 77.49% 25ms 0.53% std::__basic_file::open 0 0% 77.49% 24ms 0.51% Node::ConstructNodeAttributes (inline) 24ms 0.51% 78.00% 24ms 0.51% Node::GetIndex 0 0% 78.00% 24ms 0.51% Node::SetRadius 0 0% 78.00% 24ms 0.51% __GI__IO_file_open 24ms 0.51% 78.50% 24ms 0.51% std::_Rb_tree_header::_M_reset (inline) 6ms 0.13% 78.63% 24ms 0.51% vtkSOADataArrayTemplate::GetTupleIndexFromValueIndex