File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 2965ms, 79.75% of 3718ms total Dropped 638 nodes (cum <= 18.59ms) flat flat% sum% cum cum% 0 0% 0% 3543ms 95.29% __libc_start_call_main 0 0% 0% 3543ms 95.29% __libc_start_main_impl 0 0% 0% 3543ms 95.29% _start 0 0% 0% 3529ms 94.92% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 3529ms 94.92% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 3529ms 94.92% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 3529ms 94.92% main 0 0% 0% 3493ms 93.95% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 3493ms 93.95% CxxTest::TestRunner::runTest (inline) 0 0% 0% 3493ms 93.95% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 3484ms 93.71% AbstractCellBasedSimulation::Solve 0 0% 0% 3250ms 87.41% AbstractCellPopulation::WriteResultsToFiles 12ms 0.32% 0.32% 3083ms 82.92% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.32% 1572ms 42.28% VertexMeshWriter::WriteVtkUsingMesh 0 0% 0.32% 1352ms 36.36% VertexMeshWriter::MakeVtkMesh 0 0% 0.32% 995ms 26.76% vtkPolygon::New 1ms 0.027% 0.35% 995ms 26.76% vtkPolygon::vtkPolygon 6ms 0.16% 0.51% 696ms 18.72% vtkCell::vtkCell 2ms 0.054% 0.56% 592ms 15.92% vtkPoints::New 5ms 0.13% 0.7% 562ms 15.12% vtkPoints::vtkPoints 1ms 0.027% 0.73% 529ms 14.23% VertexMeshWriter::WriteFiles 49ms 1.32% 2.04% 507ms 13.64% std::ostream::_M_insert 0 0% 2.04% 506ms 13.61% std::ostream::operator<< (inline) 29ms 0.78% 2.82% 470ms 12.64% operator new 2ms 0.054% 2.88% 464ms 12.48% vtkLine::New 142ms 3.82% 6.70% 450ms 12.10% __GI___libc_malloc 0 0% 6.70% 449ms 12.08% vtkXMLWriterBase::Write 0 0% 6.70% 448ms 12.05% vtkStreamingDemandDrivenPipeline::Update 12ms 0.32% 7.02% 447ms 12.02% vtkLine::vtkLine 0 0% 7.02% 447ms 12.02% vtkQuad::New 1ms 0.027% 7.05% 446ms 12.00% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 7.05% 445ms 11.97% vtkDemandDrivenPipeline::ProcessRequest 1ms 0.027% 7.07% 444ms 11.94% vtkExecutive::CallAlgorithm 2ms 0.054% 7.13% 444ms 11.94% vtkQuad::vtkQuad 0 0% 7.13% 443ms 11.92% vtkCompositeDataPipeline::ExecuteData 0 0% 7.13% 443ms 11.92% vtkDemandDrivenPipeline::ExecuteData 0 0% 7.13% 443ms 11.92% vtkXMLUnstructuredDataWriter::ProcessRequest 1ms 0.027% 7.15% 427ms 11.48% vtkTriangle::New 3ms 0.081% 7.24% 420ms 11.30% vtkTriangle::vtkTriangle 93ms 2.50% 9.74% 400ms 10.76% __GI___libc_free 0 0% 9.74% 400ms 10.76% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 9.74% 400ms 10.76% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 28ms 0.75% 10.49% 397ms 10.68% std::num_put::_M_insert_float 0 0% 10.49% 359ms 9.66% vtkXMLWriter::WriteBinaryData 0 0% 10.49% 353ms 9.49% vtkXMLWriter::WriteBinaryDataBlock 0 0% 10.49% 353ms 9.49% vtkXMLWriter::WriteBinaryDataInternal 19ms 0.51% 11.00% 341ms 9.17% vtkPoints::SetDataType 0 0% 11.00% 331ms 8.90% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 1ms 0.027% 11.03% 329ms 8.85% vtkPolygon::~vtkPolygon 4ms 0.11% 11.14% 327ms 8.80% std::__cxx11::collate::do_transform 3ms 0.081% 11.22% 309ms 8.31% ___vsnprintf 0 0% 11.22% 306ms 8.23% __vsnprintf_internal (inline) 176ms 4.73% 15.95% 304ms 8.18% _int_free 38ms 1.02% 16.97% 301ms 8.10% __printf_buffer 186ms 5.00% 21.97% 271ms 7.29% _int_malloc 1ms 0.027% 22.00% 262ms 7.05% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 22.00% 260ms 6.99% VtkMeshWriter::WriteFiles 0 0% 22.00% 253ms 6.80% vtkXMLWriter::WritePointsAppendedData 6ms 0.16% 22.16% 247ms 6.64% __printf_fp_l_buffer 0 0% 22.16% 247ms 6.64% __printf_fp_spec (inline) 4ms 0.11% 22.27% 242ms 6.51% vtkCell::~vtkCell 56ms 1.51% 23.78% 227ms 6.11% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 0 0% 23.78% 226ms 6.08% OnLatticeSimulation::UpdateCellLocationsAndTopology 5ms 0.13% 23.91% 226ms 6.08% PottsBasedCellPopulation::UpdateCellLocations 105ms 2.82% 26.73% 225ms 6.05% __printf_fp_buffer_1 26ms 0.7% 27.43% 204ms 5.49% std::__new_allocator::allocate (inline) 0 0% 27.43% 202ms 5.43% std::allocator_traits::allocate (inline) 2ms 0.054% 27.49% 200ms 5.38% std::__new_allocator::deallocate (inline) 0 0% 27.49% 198ms 5.33% std::allocator_traits::deallocate (inline) 0 0% 27.49% 180ms 4.84% vtkXMLWriter::WriteCompressionBlock 5ms 0.13% 27.62% 175ms 4.71% vtkBase64OutputStream::Write 0 0% 27.62% 172ms 4.63% compress2 0 0% 27.62% 172ms 4.63% vtkDataCompressor::Compress 6ms 0.16% 27.78% 172ms 4.63% vtkPoints::~vtkPoints 0 0% 27.78% 172ms 4.63% vtkZLibDataCompressor::CompressBuffer 1ms 0.027% 27.81% 171ms 4.60% deflate 21ms 0.56% 28.38% 170ms 4.57% crc32 12ms 0.32% 28.70% 167ms 4.49% vtkBase64OutputStream::EncodeTriplet 5ms 0.13% 28.83% 155ms 4.17% vtkFloatArray::New 1ms 0.027% 28.86% 155ms 4.17% vtkTriangle::~vtkTriangle 3ms 0.081% 28.94% 152ms 4.09% tbb::detail::r1::parallel_pipeline 1ms 0.027% 28.97% 149ms 4.01% std::set::set (inline) 0 0% 28.97% 148ms 3.98% clone3 0 0% 28.97% 148ms 3.98% start_thread 9ms 0.24% 29.21% 148ms 3.98% std::_Rb_tree::_Rb_tree 0 0% 29.21% 142ms 3.82% vtkQuad::~vtkQuad 92ms 2.47% 31.68% 141ms 3.79% malloc_consolidate 40ms 1.08% 32.76% 141ms 3.79% std::ostream::write 138ms 3.71% 36.47% 140ms 3.77% [libz.so.1.3] 4ms 0.11% 36.58% 135ms 3.63% vtkFloatArray::vtkFloatArray 0 0% 36.58% 134ms 3.60% NodesOnlyMesh::ConstructNodesWithoutMesh 0 0% 36.58% 132ms 3.55% std::_Rb_tree::_M_create_node (inline) 0 0% 36.58% 132ms 3.55% std::vector::~vector (inline) 3ms 0.081% 36.66% 132ms 3.55% tbb::detail::r1::reset 0 0% 36.66% 132ms 3.55% vtkLine::GetParametricCenter 0 0% 36.66% 131ms 3.52% vtkTypeFloat64Array::~vtkTypeFloat64Array 0 0% 36.66% 129ms 3.47% VertexMesh::~VertexMesh 7ms 0.19% 36.85% 129ms 3.47% vtkIdList::AllocateInternal 3ms 0.081% 36.93% 127ms 3.42% std::_Vector_base::_M_deallocate (inline) 17ms 0.46% 37.39% 124ms 3.34% std::_Rb_tree::_M_copy (inline) 0 0% 37.39% 124ms 3.34% std::_Rb_tree::_M_get_node (inline) 50ms 1.34% 38.73% 122ms 3.28% tbb::detail::r1::wait_bounded_queue_monitor 1ms 0.027% 38.76% 120ms 3.23% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 7ms 0.19% 38.95% 118ms 3.17% std::_Rb_tree::~_Rb_tree (inline) 0 0% 38.95% 117ms 3.15% std::_Rb_tree::_Alloc_node::operator() (inline) 55ms 1.48% 40.42% 116ms 3.12% std::basic_filebuf::xsputn 0 0% 40.42% 113ms 3.04% VertexMesh::VertexMesh 27ms 0.73% 41.15% 112ms 3.01% std::_Rb_tree::_M_erase 6ms 0.16% 41.31% 108ms 2.90% MutableElement::BuildEdges 0 0% 41.31% 108ms 2.90% VertexMesh::GenerateEdgesFromElements (inline) 0 0% 41.31% 108ms 2.90% std::_Vector_base::~_Vector_base (inline) 0 0% 41.31% 107ms 2.88% NodeLocationWriter::VisitAnyPopulation 7ms 0.19% 41.50% 102ms 2.74% std::_Rb_tree::_M_clone_node (inline) 0 0% 41.50% 101ms 2.72% vtkDataArray::CreateDataArray 2ms 0.054% 41.55% 100ms 2.69% vtkDoubleArray::vtkDoubleArray 0 0% 41.55% 99ms 2.66% std::set::~set (inline) 2ms 0.054% 41.61% 99ms 2.66% vtkFloatArray::~vtkFloatArray 24ms 0.65% 42.25% 99ms 2.66% vtkObject::vtkObject 6ms 0.16% 42.42% 97ms 2.61% vtkTypeFloat64Array::New 9ms 0.24% 42.66% 96ms 2.58% std::vector::_M_default_append 1ms 0.027% 42.68% 93ms 2.50% EdgeHelper::GetEdgeFromNodes 41ms 1.10% 43.79% 93ms 2.50% vtkTypeFloat64Array::PrintSelf 0 0% 43.79% 90ms 2.42% EdgeHelper::~EdgeHelper (inline) 43ms 1.16% 44.94% 87ms 2.34% hack_digit 0 0% 44.94% 86ms 2.31% vtkIdList::Allocate 21ms 0.56% 45.51% 85ms 2.29% vtkObject::Modified 83ms 2.23% 47.74% 83ms 2.23% __strcmp_evex 2ms 0.054% 47.79% 83ms 2.23% vtkTypeFloat64Array::vtkTypeFloat64Array 3ms 0.081% 47.88% 80ms 2.15% CellPropertyCollection::HasProperty 0 0% 47.88% 79ms 2.12% Cell::HasCellProperty (inline) 0 0% 47.88% 78ms 2.10% std::_Vector_base::_M_allocate (inline) 51ms 1.37% 49.25% 78ms 2.10% vtkObjectBase::UnRegisterInternal 0 0% 49.25% 78ms 2.10% vtkXMLWriter::WritePointDataAppendedData 3ms 0.081% 49.33% 77ms 2.07% AbstractCellProperty::IsType (inline) 3ms 0.081% 49.41% 77ms 2.07% _int_free_maybe_consolidate 0 0% 49.41% 77ms 2.07% std::_Rb_tree::_M_drop_node (inline) 1ms 0.027% 49.44% 77ms 2.07% std::map::operator[] (partial-inline) 23ms 0.62% 50.05% 77ms 2.07% vtkAOSDataArrayTemplate::DataElementChanged 2ms 0.054% 50.11% 75ms 2.02% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 50.11% 74ms 1.99% std::_Rb_tree::_M_put_node (inline) 0 0% 50.11% 73ms 1.96% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.081% 50.19% 72ms 1.94% vtkDoubleArray::~vtkDoubleArray 71ms 1.91% 52.10% 71ms 1.91% __GI_sched_yield 30ms 0.81% 52.90% 68ms 1.83% std::__ostream_insert 0 0% 52.90% 67ms 1.80% std::operator<< (inline) 0 0% 52.90% 67ms 1.80% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 1ms 0.027% 52.93% 65ms 1.75% AbstractCellProperty::IsSubType (inline) 14ms 0.38% 53.31% 64ms 1.72% __dynamic_cast 64ms 1.72% 55.03% 64ms 1.72% unlink_chunk 17ms 0.46% 55.49% 62ms 1.67% std::_Rb_tree::_M_lower_bound (inline) 62ms 1.67% 57.15% 62ms 1.67% vtkTimeStamp::Modified 37ms 1% 58.15% 61ms 1.64% std::_Hashtable::clear 4ms 0.11% 58.26% 57ms 1.53% AbstractCellPopulation::GetCellUsingLocationIndex 7ms 0.19% 58.45% 55ms 1.48% AbstractCellProperty::IsSame 0 0% 58.45% 54ms 1.45% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 1ms 0.027% 58.47% 52ms 1.40% vtkIdList::New 2ms 0.054% 58.53% 51ms 1.37% std::vector::push_back (inline) 12ms 0.32% 58.85% 48ms 1.29% std::type_info::operator== (inline) 7ms 0.19% 59.04% 47ms 1.26% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 59.04% 45ms 1.21% std::_Rb_tree::lower_bound (inline) 0 0% 59.04% 45ms 1.21% std::map::lower_bound (inline) 2ms 0.054% 59.09% 45ms 1.21% vtkDataArray::vtkDataArray 0 0% 59.09% 44ms 1.18% NodesOnlyMesh::SetUpBoxCollection 2ms 0.054% 59.14% 43ms 1.16% PottsMesh::GetMooreNeighbouringNodeIndices 26ms 0.7% 59.84% 43ms 1.16% std::basic_streambuf::xsputn 0 0% 59.84% 42ms 1.13% Cell::GetCellProliferativeType 2ms 0.054% 59.90% 42ms 1.13% VertexMeshWriter::GetNextNode 12ms 0.32% 60.22% 42ms 1.13% vtkAbstractArray::vtkAbstractArray 0 0% 60.22% 39ms 1.05% VertexMesh::Clear 0 0% 60.22% 38ms 1.02% NodesOnlyMesh::~NodesOnlyMesh 0 0% 60.22% 38ms 1.02% boost::numeric::ublas::vector_assign (inline) 37ms 1% 61.22% 37ms 1% [libvtkCommonCore-9.3.so.9.3] 9ms 0.24% 61.46% 37ms 1% std::num_put::_M_insert_int 5ms 0.13% 61.59% 37ms 1% vtkDataArray::~vtkDataArray 36ms 0.97% 62.56% 36ms 0.97% __memcpy_avx512_unaligned_erms 20ms 0.54% 63.10% 34ms 0.91% __cxxabiv1::__si_class_type_info::__do_dyncast 12ms 0.32% 63.42% 34ms 0.91% _int_free_merge_chunk 2ms 0.054% 63.47% 34ms 0.91% std::_Rb_tree::_M_insert_unique 0 0% 63.47% 34ms 0.91% std::set::insert (inline) 33ms 0.89% 64.36% 34ms 0.91% vtkObject::~vtkObject 33ms 0.89% 65.25% 33ms 0.89% std::codecvt::do_always_noconv 6ms 0.16% 65.41% 33ms 0.89% std::vector::_M_realloc_insert 33ms 0.89% 66.30% 33ms 0.89% vtkObjectBase::Delete 0 0% 66.30% 32ms 0.86% CxxTest::RealWorldDescription::setUp 1ms 0.027% 66.33% 32ms 0.86% DistributedBoxCollection::IsOwned 0 0% 66.33% 32ms 0.86% PetscInitialize 0 0% 66.33% 32ms 0.86% PetscSetup::setUpWorld 0 0% 66.33% 32ms 0.86% PetscSetupUtils::CommonSetup 0 0% 66.33% 32ms 0.86% PetscSetupUtils::InitialisePetsc 0 0% 66.33% 32ms 0.86% std::less::operator() (inline) 32ms 0.86% 67.19% 32ms 0.86% std::operator< (inline) 0 0% 67.19% 32ms 0.86% tcache_get (inline) 32ms 0.86% 68.05% 32ms 0.86% tcache_get_n (inline) 12ms 0.32% 68.37% 31ms 0.83% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 68.37% 31ms 0.83% PMPI_Init_thread 0 0% 68.37% 31ms 0.83% ompi_mpi_init 2ms 0.054% 68.42% 31ms 0.83% std::_Rb_tree::_M_emplace_hint_unique 0 0% 68.42% 31ms 0.83% vtkDataArray::ComputeRange 5ms 0.13% 68.56% 31ms 0.83% vtkSOADataArrayTemplate::FillTypedComponent 30ms 0.81% 69.37% 30ms 0.81% [libstdc++.so.6.0.33] 3ms 0.081% 69.45% 29ms 0.78% 0 0% 69.45% 29ms 0.78% DistributedBoxCollection::~DistributedBoxCollection 0 0% 69.45% 29ms 0.78% NodesOnlyMesh::ClearBoxCollection (inline) 29ms 0.78% 70.23% 29ms 0.78% __memset_avx512_unaligned_erms 0 0% 70.23% 29ms 0.78% _dl_init 0 0% 70.23% 29ms 0.78% call_init (inline) 28ms 0.75% 70.98% 28ms 0.75% __GI___writev 0 0% 70.98% 28ms 0.75% std::_Destroy (inline) 0 0% 70.98% 28ms 0.75% std::_Destroy_aux::__destroy (inline) 28ms 0.75% 71.73% 28ms 0.75% std::_Rb_tree_increment 0 0% 71.73% 28ms 0.75% std::__basic_file::xsputn_2 28ms 0.75% 72.49% 28ms 0.75% std::ostream::sentry::sentry 0 0% 72.49% 28ms 0.75% vtk::detail::smp::vtkSMPToolsImplForTBB 0 0% 72.49% 27ms 0.73% _dl_start_user 27ms 0.73% 73.21% 27ms 0.73% boost::numeric::ublas::c_vector::operator() 4ms 0.11% 73.32% 27ms 0.73% vtkDataArrayPrivate::DoComputeVectorRange 24ms 0.65% 73.96% 27ms 0.73% vtkObject::ObjectFinalize 27ms 0.73% 74.69% 27ms 0.73% vtkObjectBase::~vtkObjectBase 1ms 0.027% 74.72% 26ms 0.7% PottsMesh::GetVonNeumannNeighbouringNodeIndices 26ms 0.7% 75.42% 26ms 0.7% __GI___libc_write 26ms 0.7% 76.12% 26ms 0.7% __mpn_divrem 10ms 0.27% 76.39% 26ms 0.7% boost::numeric::ublas::indexing_vector_assign 3ms 0.081% 76.47% 26ms 0.7% std::_Rb_tree::_M_insert_ (inline) 0 0% 76.47% 26ms 0.7% std::__basic_file::xsputn 0 0% 76.47% 26ms 0.7% std::basic_filebuf::_M_convert_to_external 0 0% 76.47% 26ms 0.7% std::basic_filebuf::overflow 2ms 0.054% 76.52% 26ms 0.7% tbb::detail::r1::cancel_group_execution 3ms 0.081% 76.60% 26ms 0.7% vtkAOSDataArrayTemplate::InsertTuple 1ms 0.027% 76.63% 26ms 0.7% vtkDoubleArray::New 1ms 0.027% 76.65% 25ms 0.67% DistributedBoxCollection::SetupLocalBoxesHalfOnly 3ms 0.081% 76.73% 25ms 0.67% vtkIdList::~vtkIdList 1ms 0.027% 76.76% 24ms 0.65% Cell::GetCellId 2ms 0.054% 76.82% 24ms 0.65% CellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 76.82% 24ms 0.65% orte_init 1ms 0.027% 76.84% 24ms 0.65% std::make_unique (inline) 4ms 0.11% 76.95% 24ms 0.65% vtk::detail::smp::vtkSMPToolsImpl::For 3ms 0.081% 77.03% 24ms 0.65% vtkAOSDataArrayTemplate::AllocateTuples 9ms 0.24% 77.27% 24ms 0.65% vtkIdList::vtkIdList 15ms 0.4% 77.68% 22ms 0.59% _int_free_create_chunk (inline) 1ms 0.027% 77.70% 22ms 0.59% boost::serialization::singleton::get_instance 1ms 0.027% 77.73% 22ms 0.59% std::ostream::flush 1ms 0.027% 77.76% 21ms 0.56% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 4ms 0.11% 77.86% 21ms 0.56% std::_Rb_tree_const_iterator::operator++ (inline) 21ms 0.56% 78.43% 21ms 0.56% vtkObjectBase::vtkObjectBase 3ms 0.081% 78.51% 21ms 0.56% vtkSOADataArrayTemplate::GetTupleIndexFromValueIndex 0 0% 78.51% 20ms 0.54% CellIdWriter::GetCellDataForVtkOutput 20ms 0.54% 79.05% 20ms 0.54% [libchaste_cell_based.so] 18ms 0.48% 79.53% 20ms 0.54% std::num_put::do_put 0 0% 79.53% 20ms 0.54% vtkDataArrayPrivate::DoComputeScalarRange 0 0% 79.53% 19ms 0.51% Cell::GetMutationState 0 0% 79.53% 19ms 0.51% Edge::Edge 1ms 0.027% 79.56% 19ms 0.51% Node::ConstructNodeAttributes (inline) 0 0% 79.56% 19ms 0.51% Node::SetRadius 7ms 0.19% 79.75% 19ms 0.51% std::__new_allocator::construct (inline) 0 0% 79.75% 19ms 0.51% std::allocator_traits::construct (inline) 0 0% 79.75% 19ms 0.51% std::basic_filebuf::close 0 0% 79.75% 19ms 0.51% std::basic_filebuf::sync 0 0% 79.75% 19ms 0.51% std::map::~map (inline) 0 0% 79.75% 19ms 0.51% vtkXMLUnstructuredDataWriter::WriteHeader