File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3724ms, 78.40% of 4750ms total Dropped 761 nodes (cum <= 23.75ms) flat flat% sum% cum cum% 0 0% 0% 4533ms 95.43% __libc_start_call_main 0 0% 0% 4533ms 95.43% __libc_start_main_impl 0 0% 0% 4533ms 95.43% _start 0 0% 0% 4514ms 95.03% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4514ms 95.03% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4514ms 95.03% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4514ms 95.03% main 0 0% 0% 4470ms 94.11% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4469ms 94.08% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4469ms 94.08% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4458ms 93.85% AbstractCellBasedSimulation::Solve 0 0% 0% 4157ms 87.52% AbstractCellPopulation::WriteResultsToFiles 12ms 0.25% 0.25% 3942ms 82.99% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.25% 1981ms 41.71% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.021% 0.27% 1704ms 35.87% VertexMeshWriter::MakeVtkMesh 0 0% 0.27% 1280ms 26.95% vtkPolygon::New 0 0% 0.27% 1278ms 26.91% vtkPolygon::vtkPolygon 3ms 0.063% 0.34% 889ms 18.72% vtkCell::vtkCell 3ms 0.063% 0.4% 763ms 16.06% vtkPoints::New 11ms 0.23% 0.63% 715ms 15.05% vtkPoints::vtkPoints 1ms 0.021% 0.65% 693ms 14.59% VertexMeshWriter::WriteFiles 22ms 0.46% 1.12% 663ms 13.96% operator new 213ms 4.48% 5.60% 654ms 13.77% __GI___libc_malloc 2ms 0.042% 5.64% 643ms 13.54% std::ostream::operator<< (inline) 53ms 1.12% 6.76% 639ms 13.45% std::ostream::_M_insert 1ms 0.021% 6.78% 620ms 13.05% vtkTriangle::New 4ms 0.084% 6.86% 608ms 12.80% vtkQuad::New 4ms 0.084% 6.95% 603ms 12.69% vtkQuad::vtkQuad 5ms 0.11% 7.05% 603ms 12.69% vtkTriangle::vtkTriangle 1ms 0.021% 7.07% 578ms 12.17% vtkLine::New 0 0% 7.07% 570ms 12.00% vtkStreamingDemandDrivenPipeline::Update 0 0% 7.07% 570ms 12.00% vtkXMLWriterBase::Write 0 0% 7.07% 567ms 11.94% vtkDemandDrivenPipeline::ProcessRequest 0 0% 7.07% 566ms 11.92% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 7.07% 565ms 11.89% vtkExecutive::CallAlgorithm 0 0% 7.07% 564ms 11.87% vtkCompositeDataPipeline::ExecuteData 0 0% 7.07% 564ms 11.87% vtkDemandDrivenPipeline::ExecuteData 2ms 0.042% 7.12% 564ms 11.87% vtkXMLUnstructuredDataWriter::ProcessRequest 11ms 0.23% 7.35% 561ms 11.81% vtkLine::vtkLine 130ms 2.74% 10.08% 514ms 10.82% __GI___libc_free 41ms 0.86% 10.95% 514ms 10.82% std::num_put::_M_insert_float 0 0% 10.95% 505ms 10.63% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 10.95% 505ms 10.63% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 0 0% 10.95% 462ms 9.73% vtkXMLWriter::WriteBinaryData 0 0% 10.95% 455ms 9.58% vtkXMLWriter::WriteBinaryDataInternal 0 0% 10.95% 454ms 9.56% vtkXMLWriter::WriteBinaryDataBlock 28ms 0.59% 11.54% 438ms 9.22% vtkPoints::SetDataType 0 0% 11.54% 427ms 8.99% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 15ms 0.32% 11.85% 418ms 8.80% std::__cxx11::collate::do_transform 2ms 0.042% 11.89% 391ms 8.23% ___vsnprintf 0 0% 11.89% 389ms 8.19% __vsnprintf_internal (inline) 235ms 4.95% 16.84% 382ms 8.04% _int_free 54ms 1.14% 17.98% 379ms 7.98% __printf_buffer 266ms 5.60% 23.58% 375ms 7.89% _int_malloc 3ms 0.063% 23.64% 374ms 7.87% vtkPolygon::~vtkPolygon 1ms 0.021% 23.66% 339ms 7.14% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 23.66% 337ms 7.09% VtkMeshWriter::WriteFiles 0 0% 23.66% 329ms 6.93% vtkXMLWriter::WritePointsAppendedData 5ms 0.11% 23.77% 310ms 6.53% vtkCell::~vtkCell 13ms 0.27% 24.04% 299ms 6.29% __printf_fp_l_buffer 0 0% 24.04% 299ms 6.29% __printf_fp_spec (inline) 0 0% 24.04% 297ms 6.25% OnLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.042% 24.08% 297ms 6.25% PottsBasedCellPopulation::UpdateCellLocations 48ms 1.01% 25.09% 290ms 6.11% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 53ms 1.12% 26.21% 286ms 6.02% std::__new_allocator::allocate (inline) 0 0% 26.21% 285ms 6.00% std::allocator_traits::allocate (inline) 133ms 2.80% 29.01% 270ms 5.68% __printf_fp_buffer_1 4ms 0.084% 29.09% 268ms 5.64% std::__new_allocator::deallocate (inline) 0 0% 29.09% 268ms 5.64% std::allocator_traits::deallocate (inline) 0 0% 29.09% 234ms 4.93% vtkXMLWriter::WriteCompressionBlock 0 0% 29.09% 227ms 4.78% vtkDataCompressor::Compress 0 0% 29.09% 226ms 4.76% compress2 0 0% 29.09% 226ms 4.76% vtkZLibDataCompressor::CompressBuffer 51ms 1.07% 30.17% 222ms 4.67% crc32 0 0% 30.17% 222ms 4.67% deflate 3ms 0.063% 30.23% 220ms 4.63% vtkBase64OutputStream::Write 17ms 0.36% 30.59% 214ms 4.51% vtkBase64OutputStream::EncodeTriplet 7ms 0.15% 30.74% 207ms 4.36% vtkPoints::~vtkPoints 20ms 0.42% 31.16% 196ms 4.13% std::_Rb_tree::_Rb_tree 0 0% 31.16% 195ms 4.11% std::set::set (inline) 3ms 0.063% 31.22% 185ms 3.89% tbb::detail::r1::parallel_pipeline 3ms 0.063% 31.28% 184ms 3.87% vtkFloatArray::New 0 0% 31.28% 180ms 3.79% clone3 0 0% 31.28% 180ms 3.79% start_thread 47ms 0.99% 32.27% 179ms 3.77% std::ostream::write 0 0% 32.27% 177ms 3.73% std::_Rb_tree::_M_create_node (inline) 105ms 2.21% 34.48% 173ms 3.64% malloc_consolidate 0 0% 34.48% 173ms 3.64% std::_Rb_tree::_M_get_node (inline) 0 0% 34.48% 169ms 3.56% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 34.48% 169ms 3.56% std::vector::~vector (inline) 0 0% 34.48% 167ms 3.52% tbb::detail::r1::reset 1ms 0.021% 34.51% 167ms 3.52% vtkQuad::~vtkQuad 8ms 0.17% 34.67% 166ms 3.49% vtkIdList::AllocateInternal 2ms 0.042% 34.72% 165ms 3.47% NodesOnlyMesh::ConstructNodesWithoutMesh 82ms 1.73% 36.44% 165ms 3.47% std::basic_filebuf::xsputn 0 0% 36.44% 160ms 3.37% VertexMesh::~VertexMesh 155ms 3.26% 39.71% 160ms 3.37% [libz.so.1.3] 7ms 0.15% 39.85% 160ms 3.37% std::_Rb_tree::~_Rb_tree (inline) 33ms 0.69% 40.55% 159ms 3.35% std::_Rb_tree::_M_erase 81ms 1.71% 42.25% 157ms 3.31% tbb::detail::r1::wait_bounded_queue_monitor 3ms 0.063% 42.32% 157ms 3.31% vtkFloatArray::vtkFloatArray 0 0% 42.32% 156ms 3.28% VertexMesh::VertexMesh 1ms 0.021% 42.34% 155ms 3.26% vtkLine::GetParametricCenter 13ms 0.27% 42.61% 153ms 3.22% std::_Rb_tree::_M_copy (inline) 4ms 0.084% 42.69% 152ms 3.20% vtkTypeFloat64Array::~vtkTypeFloat64Array 3ms 0.063% 42.76% 151ms 3.18% std::_Vector_base::_M_deallocate (inline) 6ms 0.13% 42.88% 149ms 3.14% vtkDataArray::CreateDataArray 0 0% 42.88% 148ms 3.12% vtkTriangle::~vtkTriangle 14ms 0.29% 43.18% 145ms 3.05% std::vector::_M_default_append 12ms 0.25% 43.43% 141ms 2.97% MutableElement::BuildEdges 0 0% 43.43% 141ms 2.97% VertexMesh::GenerateEdgesFromElements (inline) 0 0% 43.43% 141ms 2.97% std::set::~set (inline) 3ms 0.063% 43.49% 141ms 2.97% vtkFloatArray::~vtkFloatArray 5ms 0.11% 43.60% 139ms 2.93% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 3ms 0.063% 43.66% 138ms 2.91% std::_Rb_tree::_M_clone_node (inline) 3ms 0.063% 43.73% 138ms 2.91% vtkDoubleArray::vtkDoubleArray 8ms 0.17% 43.89% 136ms 2.86% vtkTypeFloat64Array::New 0 0% 43.89% 133ms 2.80% NodeLocationWriter::VisitAnyPopulation 1ms 0.021% 43.92% 128ms 2.69% std::_Vector_base::~_Vector_base (inline) 0 0% 43.92% 125ms 2.63% std::_Rb_tree::_M_drop_node (inline) 0 0% 43.92% 120ms 2.53% std::_Rb_tree::_M_put_node (inline) 0 0% 43.92% 118ms 2.48% EdgeHelper::GetEdgeFromNodes 118ms 2.48% 46.40% 118ms 2.48% __strcmp_avx2 3ms 0.063% 46.46% 118ms 2.48% vtkTypeFloat64Array::vtkTypeFloat64Array 1ms 0.021% 46.48% 112ms 2.36% std::_Vector_base::_M_allocate (inline) 0 0% 46.48% 111ms 2.34% EdgeHelper::~EdgeHelper (inline) 2ms 0.042% 46.53% 108ms 2.27% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.021% 46.55% 108ms 2.27% vtkIdList::Allocate 62ms 1.31% 47.85% 108ms 2.27% vtkTypeFloat64Array::PrintSelf 31ms 0.65% 48.51% 103ms 2.17% std::__ostream_insert 4ms 0.084% 48.59% 101ms 2.13% std::operator<< (inline) 34ms 0.72% 49.31% 101ms 2.13% vtkObject::vtkObject 0 0% 49.31% 98ms 2.06% vtkXMLWriter::WritePointDataAppendedData 1ms 0.021% 49.33% 96ms 2.02% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 5ms 0.11% 49.43% 96ms 2.02% _int_free_maybe_consolidate 1ms 0.021% 49.45% 95ms 2.00% AbstractCellProperty::IsSubType (inline) 51ms 1.07% 50.53% 94ms 1.98% hack_digit 15ms 0.32% 50.84% 93ms 1.96% __dynamic_cast 90ms 1.89% 52.74% 90ms 1.89% unlink_chunk 1ms 0.021% 52.76% 87ms 1.83% AbstractCellProperty::IsType (inline) 5ms 0.11% 52.86% 85ms 1.79% vtkAOSDataArrayTemplate::DataElementChanged 5ms 0.11% 52.97% 84ms 1.77% std::map::operator[] (partial-inline) 0 0% 52.97% 83ms 1.75% Cell::HasCellProperty (inline) 3ms 0.063% 53.03% 82ms 1.73% CellPropertyCollection::HasProperty 5ms 0.11% 53.14% 79ms 1.66% vtkIdList::New 35ms 0.74% 53.87% 78ms 1.64% vtkObjectBase::UnRegisterInternal 1ms 0.021% 53.89% 78ms 1.64% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 75ms 1.58% 55.47% 75ms 1.58% __GI_sched_yield 27ms 0.57% 56.04% 75ms 1.58% std::_Rb_tree::_M_lower_bound (inline) 4ms 0.084% 56.13% 75ms 1.58% vtkDoubleArray::~vtkDoubleArray 39ms 0.82% 56.95% 72ms 1.52% std::basic_streambuf::xsputn 1ms 0.021% 56.97% 67ms 1.41% Cell::GetCellProliferativeType 15ms 0.32% 57.28% 66ms 1.39% AbstractCellProperty::IsSame 3ms 0.063% 57.35% 66ms 1.39% boost::numeric::ublas::c_vector::c_vector (partial-inline) 1ms 0.021% 57.37% 66ms 1.39% std::vector::push_back (inline) 15ms 0.32% 57.68% 66ms 1.39% vtkObject::Modified 2ms 0.042% 57.73% 64ms 1.35% boost::numeric::ublas::vector_assign (inline) 0 0% 57.73% 63ms 1.33% NodesOnlyMesh::SetUpBoxCollection 6ms 0.13% 57.85% 62ms 1.31% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 57.85% 62ms 1.31% tcache_get (inline) 62ms 1.31% 59.16% 62ms 1.31% tcache_get_n (inline) 0 0% 59.16% 61ms 1.28% NodesOnlyMesh::~NodesOnlyMesh 33ms 0.69% 59.85% 61ms 1.28% std::_Hashtable::clear 1ms 0.021% 59.87% 60ms 1.26% std::_Rb_tree::_M_insert_unique 0 0% 59.87% 60ms 1.26% std::set::insert (inline) 0 0% 59.87% 57ms 1.20% PottsMesh::GetMooreNeighbouringNodeIndices 1ms 0.021% 59.89% 56ms 1.18% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 54ms 1.14% 61.03% 54ms 1.14% __GI___writev 0 0% 61.03% 54ms 1.14% std::_Rb_tree::lower_bound (inline) 0 0% 61.03% 54ms 1.14% std::map::lower_bound (inline) 0 0% 61.03% 53ms 1.12% std::__basic_file::xsputn_2 11ms 0.23% 61.26% 53ms 1.12% vtkSOADataArrayTemplate::FillTypedComponent 22ms 0.46% 61.73% 51ms 1.07% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 61.73% 51ms 1.07% std::_Destroy (inline) 0 0% 61.73% 51ms 1.07% std::_Destroy_aux::__destroy (inline) 17ms 0.36% 62.08% 51ms 1.07% std::type_info::operator== (inline) 7ms 0.15% 62.23% 51ms 1.07% vtkDataArray::vtkDataArray 11ms 0.23% 62.46% 50ms 1.05% std::num_put::_M_insert_int 1ms 0.021% 62.48% 49ms 1.03% VertexMesh::Clear 49ms 1.03% 63.52% 49ms 1.03% [libstdc++.so.6.0.33] 49ms 1.03% 64.55% 49ms 1.03% __memcpy_avx_unaligned_erms 49ms 1.03% 65.58% 49ms 1.03% vtkTimeStamp::Modified 0 0% 65.58% 46ms 0.97% DistributedBoxCollection::~DistributedBoxCollection 0 0% 65.58% 46ms 0.97% NodesOnlyMesh::ClearBoxCollection (inline) 5ms 0.11% 65.68% 46ms 0.97% VertexMeshWriter::GetNextNode 10ms 0.21% 65.89% 46ms 0.97% vtkDataArray::~vtkDataArray 3ms 0.063% 65.96% 43ms 0.91% std::vector::_M_realloc_insert 14ms 0.29% 66.25% 43ms 0.91% vtkAbstractArray::vtkAbstractArray 42ms 0.88% 67.14% 42ms 0.88% [libvtkCommonCore-9.3.so.9.3] 13ms 0.27% 67.41% 42ms 0.88% boost::numeric::ublas::indexing_vector_assign 3ms 0.063% 67.47% 41ms 0.86% std::_Rb_tree::_M_insert_ (inline) 31ms 0.65% 68.13% 41ms 0.86% vtkObject::ObjectFinalize 0 0% 68.13% 40ms 0.84% CxxTest::RealWorldDescription::setUp 0 0% 68.13% 40ms 0.84% PMPI_Init_thread 0 0% 68.13% 40ms 0.84% PetscInitialize 0 0% 68.13% 40ms 0.84% PetscSetup::setUpWorld 0 0% 68.13% 40ms 0.84% PetscSetupUtils::CommonSetup 0 0% 68.13% 40ms 0.84% PetscSetupUtils::InitialisePetsc 0 0% 68.13% 40ms 0.84% _dl_init 0 0% 68.13% 40ms 0.84% call_init (inline) 0 0% 68.13% 40ms 0.84% ompi_mpi_init 39ms 0.82% 68.95% 40ms 0.84% vtkObject::~vtkObject 2ms 0.042% 68.99% 39ms 0.82% DistributedBoxCollection::SetupLocalBoxesHalfOnly 38ms 0.8% 69.79% 38ms 0.8% __memset_avx2_unaligned_erms 0 0% 69.79% 38ms 0.8% std::less::operator() (inline) 38ms 0.8% 70.59% 38ms 0.8% std::operator< (inline) 2ms 0.042% 70.63% 37ms 0.78% 2ms 0.042% 70.67% 37ms 0.78% CellProliferativeTypesWriter::GetCellDataForVtkOutput 25ms 0.53% 71.20% 37ms 0.78% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 71.20% 37ms 0.78% DistributedBoxCollection::IsOwned 0 0% 71.20% 37ms 0.78% _dl_start_user 11ms 0.23% 71.43% 37ms 0.78% _int_free_merge_chunk 1ms 0.021% 71.45% 36ms 0.76% PottsMesh::GetVonNeumannNeighbouringNodeIndices 0 0% 71.45% 36ms 0.76% std::make_unique (inline) 0 0% 71.45% 36ms 0.76% vtkDataArray::ComputeRange 2ms 0.042% 71.49% 35ms 0.74% vtkDoubleArray::New 4ms 0.084% 71.58% 34ms 0.72% vtkAOSDataArrayTemplate::AllocateTuples 4ms 0.084% 71.66% 34ms 0.72% vtkDataArrayPrivate::DoComputeVectorRange 34ms 0.72% 72.38% 34ms 0.72% vtkObjectBase::Delete 33ms 0.69% 73.07% 33ms 0.69% std::ostream::sentry::sentry 10ms 0.21% 73.28% 33ms 0.69% vtkAOSDataArrayTemplate::InsertTuple 33ms 0.69% 73.98% 33ms 0.69% vtkObjectBase::~vtkObjectBase 2ms 0.042% 74.02% 32ms 0.67% std::basic_filebuf::overflow 0 0% 74.02% 32ms 0.67% std::unique_ptr::~unique_ptr (inline) 6ms 0.13% 74.15% 32ms 0.67% vtkIdList::~vtkIdList 0 0% 74.15% 31ms 0.65% Cell::GetMutationState 1ms 0.021% 74.17% 31ms 0.65% VtkMeshWriter::MakeVtkMesh 0 0% 74.17% 31ms 0.65% std::default_delete::operator() (inline) 1ms 0.021% 74.19% 30ms 0.63% std::basic_filebuf::_M_convert_to_external 30ms 0.63% 74.82% 30ms 0.63% std::codecvt::do_always_noconv 0 0% 74.82% 30ms 0.63% vtk::detail::smp::vtkSMPToolsImplForTBB 5ms 0.11% 74.93% 30ms 0.63% vtkSOADataArrayTemplate::GetTupleIndexFromValueIndex 1ms 0.021% 74.95% 29ms 0.61% std::__basic_file::xsputn 1ms 0.021% 74.97% 28ms 0.59% Node::AddElement 28ms 0.59% 75.56% 28ms 0.59% __GI___libc_write 5ms 0.11% 75.66% 28ms 0.59% boost::serialization::singleton::get_instance 0 0% 75.66% 28ms 0.59% vtkXMLUnstructuredDataWriter::WriteHeader 27ms 0.57% 76.23% 27ms 0.57% __mpn_divrem 27ms 0.57% 76.80% 27ms 0.57% boost::numeric::ublas::c_vector::operator() 20ms 0.42% 77.22% 27ms 0.57% std::num_put::do_put 0 0% 77.22% 26ms 0.55% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 77.22% 26ms 0.55% OutputFileHandler::OpenOutputFile 4ms 0.084% 77.31% 26ms 0.55% std::__new_allocator::construct (inline) 0 0% 77.31% 26ms 0.55% std::allocator_traits::construct (inline) 1ms 0.021% 77.33% 26ms 0.55% tbb::detail::r1::cancel_group_execution 26ms 0.55% 77.87% 26ms 0.55% vtkObjectBase::vtkObjectBase 0 0% 77.87% 25ms 0.53% PottsBasedCellPopulation::AcceptCellWriter 0 0% 77.87% 25ms 0.53% boost::numeric::ublas::c_vector::assign (inline) 0 0% 77.87% 25ms 0.53% orte_init 4ms 0.084% 77.96% 25ms 0.53% std::_Rb_tree::_M_emplace_hint_unique 0 0% 77.96% 25ms 0.53% std::basic_filebuf::open 3ms 0.063% 78.02% 25ms 0.53% vtkIdList::vtkIdList 0 0% 78.02% 24ms 0.51% BoundaryNodeWriter::VisitAnyPopulation 0 0% 78.02% 24ms 0.51% Cell::GetCellId 0 0% 78.02% 24ms 0.51% Edge::~Edge (inline) 17ms 0.36% 78.38% 24ms 0.51% _int_free_create_chunk (inline) 1ms 0.021% 78.40% 24ms 0.51% std::ostream::flush