File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3953ms, 78.01% of 5067ms total Dropped 752 nodes (cum <= 25.34ms) flat flat% sum% cum cum% 0 0% 0% 4834ms 95.40% __libc_start_call_main 0 0% 0% 4834ms 95.40% __libc_start_main_impl 0 0% 0% 4834ms 95.40% _start 0 0% 0% 4818ms 95.09% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4818ms 95.09% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4818ms 95.09% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4818ms 95.09% main 0 0% 0% 4777ms 94.28% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4777ms 94.28% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4777ms 94.28% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4765ms 94.04% AbstractCellBasedSimulation::Solve 1ms 0.02% 0.02% 4408ms 86.99% AbstractCellPopulation::WriteResultsToFiles 22ms 0.43% 0.45% 4155ms 82.00% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.45% 1978ms 39.04% VertexMeshWriter::WriteVtkUsingMesh 4ms 0.079% 0.53% 1711ms 33.77% VertexMeshWriter::MakeVtkMesh 1ms 0.02% 0.55% 1271ms 25.08% vtkPolygon::New 0 0% 0.55% 1269ms 25.04% vtkPolygon::vtkPolygon 7ms 0.14% 0.69% 894ms 17.64% vtkCell::vtkCell 0 0% 0.69% 796ms 15.71% VertexMeshWriter::WriteFiles 6ms 0.12% 0.81% 761ms 15.02% vtkPoints::New 58ms 1.14% 1.95% 757ms 14.94% std::ostream::_M_insert 1ms 0.02% 1.97% 757ms 14.94% std::ostream::operator<< (inline) 15ms 0.3% 2.27% 725ms 14.31% vtkPoints::vtkPoints 49ms 0.97% 3.24% 687ms 13.56% operator new 217ms 4.28% 7.52% 645ms 12.73% __GI___libc_malloc 42ms 0.83% 8.35% 610ms 12.04% std::num_put::_M_insert_float 1ms 0.02% 8.37% 603ms 11.90% vtkQuad::New 1ms 0.02% 8.39% 601ms 11.86% vtkQuad::vtkQuad 0 0% 8.39% 597ms 11.78% vtkLine::New 2ms 0.039% 8.43% 578ms 11.41% vtkTriangle::New 0 0% 8.43% 576ms 11.37% vtkStreamingDemandDrivenPipeline::Update 0 0% 8.43% 576ms 11.37% vtkXMLWriterBase::Write 8ms 0.16% 8.58% 575ms 11.35% vtkLine::vtkLine 0 0% 8.58% 574ms 11.33% vtkExecutive::CallAlgorithm 0 0% 8.58% 574ms 11.33% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 8.58% 573ms 11.31% vtkDemandDrivenPipeline::ProcessRequest 0 0% 8.58% 571ms 11.27% vtkDemandDrivenPipeline::ExecuteData 186ms 3.67% 12.26% 570ms 11.25% __GI___libc_free 0 0% 12.26% 570ms 11.25% vtkCompositeDataPipeline::ExecuteData 0 0% 12.26% 570ms 11.25% vtkXMLUnstructuredDataWriter::ProcessRequest 3ms 0.059% 12.31% 560ms 11.05% vtkTriangle::vtkTriangle 0 0% 12.31% 500ms 9.87% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 12.31% 500ms 9.87% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 7ms 0.14% 12.45% 483ms 9.53% std::__cxx11::collate::do_transform 4ms 0.079% 12.53% 461ms 9.10% ___vsnprintf 0 0% 12.53% 457ms 9.02% __vsnprintf_internal (inline) 65ms 1.28% 13.81% 451ms 8.90% __printf_buffer 0 0% 13.81% 441ms 8.70% vtkXMLWriter::WriteBinaryData 0 0% 13.81% 438ms 8.64% vtkXMLWriter::WriteBinaryDataInternal 1ms 0.02% 13.83% 436ms 8.60% vtkXMLWriter::WriteBinaryDataBlock 32ms 0.63% 14.47% 432ms 8.53% vtkPoints::SetDataType 0 0% 14.47% 430ms 8.49% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 216ms 4.26% 18.73% 382ms 7.54% _int_free 1ms 0.02% 18.75% 382ms 7.54% vtkPolygon::~vtkPolygon 249ms 4.91% 23.66% 369ms 7.28% _int_malloc 0 0% 23.66% 367ms 7.24% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 23.66% 365ms 7.20% VtkMeshWriter::WriteFiles 2ms 0.039% 23.70% 354ms 6.99% __printf_fp_spec (inline) 22ms 0.43% 24.14% 352ms 6.95% __printf_fp_l_buffer 0 0% 24.14% 347ms 6.85% OnLatticeSimulation::UpdateCellLocationsAndTopology 5ms 0.099% 24.24% 347ms 6.85% PottsBasedCellPopulation::UpdateCellLocations 0 0% 24.24% 319ms 6.30% vtkXMLWriter::WritePointsAppendedData 144ms 2.84% 27.08% 308ms 6.08% __printf_fp_buffer_1 2ms 0.039% 27.12% 305ms 6.02% std::__new_allocator::deallocate (inline) 0 0% 27.12% 302ms 5.96% std::allocator_traits::deallocate (inline) 50ms 0.99% 28.10% 301ms 5.94% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 3ms 0.059% 28.16% 298ms 5.88% vtkCell::~vtkCell 51ms 1.01% 29.17% 294ms 5.80% std::__new_allocator::allocate (inline) 0 0% 29.17% 293ms 5.78% std::allocator_traits::allocate (inline) 0 0% 29.17% 239ms 4.72% std::set::set (inline) 16ms 0.32% 29.48% 238ms 4.70% std::_Rb_tree::_Rb_tree 0 0% 29.48% 236ms 4.66% vtkXMLWriter::WriteCompressionBlock 0 0% 29.48% 221ms 4.36% VertexMesh::~VertexMesh 1ms 0.02% 29.50% 220ms 4.34% compress2 0 0% 29.50% 220ms 4.34% vtkDataCompressor::Compress 0 0% 29.50% 220ms 4.34% vtkZLibDataCompressor::CompressBuffer 62ms 1.22% 30.73% 218ms 4.30% crc32 0 0% 30.73% 218ms 4.30% deflate 142ms 2.80% 33.53% 213ms 4.20% malloc_consolidate 7ms 0.14% 33.67% 208ms 4.10% vtkBase64OutputStream::Write 3ms 0.059% 33.73% 206ms 4.07% vtkFloatArray::New 13ms 0.26% 33.98% 201ms 3.97% vtkBase64OutputStream::EncodeTriplet 10ms 0.2% 34.18% 197ms 3.89% vtkPoints::~vtkPoints 0 0% 34.18% 196ms 3.87% tbb::detail::r1::parallel_pipeline 0 0% 34.18% 194ms 3.83% clone3 0 0% 34.18% 194ms 3.83% start_thread 0 0% 34.18% 192ms 3.79% tbb::detail::r1::reset 0 0% 34.18% 191ms 3.77% std::vector::~vector (inline) 91ms 1.80% 35.98% 187ms 3.69% tbb::detail::r1::wait_bounded_queue_monitor 0 0% 35.98% 186ms 3.67% std::_Rb_tree::_M_create_node (inline) 1ms 0.02% 36.00% 182ms 3.59% std::_Vector_base::_M_deallocate (inline) 4ms 0.079% 36.08% 180ms 3.55% vtkFloatArray::vtkFloatArray 52ms 1.03% 37.10% 179ms 3.53% std::_Rb_tree::_M_erase 7ms 0.14% 37.24% 178ms 3.51% vtkIdList::AllocateInternal 0 0% 37.24% 176ms 3.47% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.039% 37.28% 172ms 3.39% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.039% 37.32% 170ms 3.36% NodesOnlyMesh::ConstructNodesWithoutMesh 1ms 0.02% 37.34% 169ms 3.34% VertexMesh::VertexMesh 3ms 0.059% 37.40% 169ms 3.34% vtkLine::GetParametricCenter 0 0% 37.40% 167ms 3.30% NodeLocationWriter::VisitAnyPopulation 10ms 0.2% 37.60% 167ms 3.30% std::_Rb_tree::_M_copy (inline) 0 0% 37.60% 167ms 3.30% std::_Rb_tree::_M_get_node (inline) 53ms 1.05% 38.64% 166ms 3.28% std::ostream::write 0 0% 38.64% 163ms 3.22% vtkQuad::~vtkQuad 1ms 0.02% 38.66% 161ms 3.18% std::_Vector_base::~_Vector_base (inline) 0 0% 38.66% 160ms 3.16% EdgeHelper::~EdgeHelper (inline) 0 0% 38.66% 160ms 3.16% vtkTriangle::~vtkTriangle 154ms 3.04% 41.70% 155ms 3.06% [libz.so.1.3] 14ms 0.28% 41.98% 151ms 2.98% std::_Rb_tree::_M_clone_node (inline) 0 0% 41.98% 151ms 2.98% vtkTypeFloat64Array::~vtkTypeFloat64Array 1ms 0.02% 42.00% 150ms 2.96% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 0 0% 42.00% 150ms 2.96% VertexMesh::GenerateEdgesFromElements (inline) 7ms 0.14% 42.14% 149ms 2.94% MutableElement::BuildEdges 14ms 0.28% 42.41% 140ms 2.76% std::vector::_M_default_append 3ms 0.059% 42.47% 137ms 2.70% vtkFloatArray::~vtkFloatArray 58ms 1.14% 43.62% 134ms 2.64% std::basic_filebuf::xsputn 6ms 0.12% 43.73% 133ms 2.62% _int_free_maybe_consolidate 1ms 0.02% 43.75% 132ms 2.61% vtkDataArray::CreateDataArray 4ms 0.079% 43.83% 128ms 2.53% EdgeHelper::GetEdgeFromNodes 2ms 0.039% 43.87% 128ms 2.53% std::_Vector_base::_M_allocate (inline) 3ms 0.059% 43.93% 128ms 2.53% vtkDoubleArray::vtkDoubleArray 3ms 0.059% 43.99% 126ms 2.49% vtkTypeFloat64Array::New 1ms 0.02% 44.01% 124ms 2.45% CellPropertyCollection::GetPropertiesType (inline) 0 0% 44.01% 123ms 2.43% std::_Rb_tree::_M_drop_node (inline) 0 0% 44.01% 121ms 2.39% std::_Rb_tree::_M_put_node (inline) 0 0% 44.01% 118ms 2.33% std::set::~set (inline) 0 0% 44.01% 111ms 2.19% vtkXMLWriter::WritePointDataAppendedData 0 0% 44.01% 108ms 2.13% AbstractCellProperty::IsSubType (inline) 31ms 0.61% 44.62% 108ms 2.13% __dynamic_cast 52ms 1.03% 45.65% 108ms 2.13% vtkTypeFloat64Array::PrintSelf 4ms 0.079% 45.73% 108ms 2.13% vtkTypeFloat64Array::vtkTypeFloat64Array 0 0% 45.73% 106ms 2.09% vtkIdList::Allocate 21ms 0.41% 46.14% 106ms 2.09% vtkObject::vtkObject 44ms 0.87% 47.01% 104ms 2.05% std::__ostream_insert 101ms 1.99% 49.00% 101ms 1.99% __strcmp_avx2 1ms 0.02% 49.02% 98ms 1.93% std::operator<< (inline) 97ms 1.91% 50.94% 97ms 1.91% __GI_sched_yield 2ms 0.039% 50.98% 96ms 1.89% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 95ms 1.87% 52.85% 95ms 1.87% unlink_chunk 3ms 0.059% 52.91% 94ms 1.86% std::map::operator[] (partial-inline) 3ms 0.059% 52.97% 88ms 1.74% vtkIdList::New 6ms 0.12% 53.09% 83ms 1.64% vtkAOSDataArrayTemplate::DataElementChanged 41ms 0.81% 53.90% 82ms 1.62% hack_digit 24ms 0.47% 54.37% 82ms 1.62% std::_Rb_tree::_M_lower_bound (inline) 3ms 0.059% 54.43% 82ms 1.62% vtkDoubleArray::~vtkDoubleArray 48ms 0.95% 55.38% 82ms 1.62% vtkObjectBase::UnRegisterInternal 0 0% 55.38% 79ms 1.56% Cell::HasCellProperty (inline) 2ms 0.039% 55.42% 79ms 1.56% CellPropertyCollection::HasProperty 2ms 0.039% 55.46% 78ms 1.54% AbstractCellProperty::IsType (inline) 32ms 0.63% 56.09% 78ms 1.54% vtkObject::Modified 0 0% 56.09% 75ms 1.48% PottsMesh::GetMooreNeighbouringNodeIndices 55ms 1.09% 57.17% 74ms 1.46% std::basic_streambuf::xsputn 2ms 0.039% 57.21% 73ms 1.44% std::vector::push_back (inline) 5ms 0.099% 57.31% 71ms 1.40% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 57.31% 68ms 1.34% Cell::GetCellProliferativeType 1ms 0.02% 57.33% 68ms 1.34% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 0 0% 57.33% 66ms 1.30% NodesOnlyMesh::SetUpBoxCollection 6ms 0.12% 57.45% 66ms 1.30% boost::numeric::ublas::vector_assign (inline) 0 0% 57.45% 65ms 1.28% NodesOnlyMesh::~NodesOnlyMesh 0 0% 57.45% 65ms 1.28% std::_Rb_tree::_M_insert_unique 0 0% 57.45% 65ms 1.28% std::set::insert (inline) 0 0% 57.45% 62ms 1.22% std::_Rb_tree::lower_bound (inline) 0 0% 57.45% 62ms 1.22% std::map::lower_bound (inline) 2ms 0.039% 57.49% 61ms 1.20% VertexMesh::Clear 14ms 0.28% 57.77% 60ms 1.18% std::num_put::_M_insert_int 11ms 0.22% 57.98% 58ms 1.14% AbstractCellProperty::IsSame 4ms 0.079% 58.06% 58ms 1.14% std::vector::_M_realloc_insert 7ms 0.14% 58.20% 58ms 1.14% vtkDataArray::vtkDataArray 54ms 1.07% 59.27% 54ms 1.07% __GI___writev 0 0% 59.27% 54ms 1.07% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 1ms 0.02% 59.29% 54ms 1.07% std::_Rb_tree_header::_Rb_tree_header (inline) 0 0% 59.29% 54ms 1.07% std::__basic_file::xsputn_2 0 0% 59.29% 54ms 1.07% std::map::~map (inline) 7ms 0.14% 59.42% 54ms 1.07% vtkSOADataArrayTemplate::FillTypedComponent 53ms 1.05% 60.47% 53ms 1.05% std::_Rb_tree_header::_M_reset (inline) 5ms 0.099% 60.57% 52ms 1.03% VertexMeshWriter::GetNextNode 52ms 1.03% 61.59% 52ms 1.03% std::ostream::sentry::sentry 0 0% 61.59% 51ms 1.01% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 31ms 0.61% 62.21% 51ms 1.01% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 62.21% 51ms 1.01% tcache_get (inline) 51ms 1.01% 63.21% 51ms 1.01% tcache_get_n (inline) 1ms 0.02% 63.23% 50ms 0.99% AbstractCellPopulation::GetCellUsingLocationIndex 17ms 0.34% 63.57% 49ms 0.97% vtkAbstractArray::vtkAbstractArray 8ms 0.16% 63.73% 49ms 0.97% vtkIdList::~vtkIdList 11ms 0.22% 63.94% 48ms 0.95% boost::numeric::ublas::indexing_vector_assign 4ms 0.079% 64.02% 48ms 0.95% std::_Rb_tree::_M_insert_ (inline) 0 0% 64.02% 47ms 0.93% DistributedBoxCollection::~DistributedBoxCollection 0 0% 64.02% 47ms 0.93% NodesOnlyMesh::ClearBoxCollection (inline) 10ms 0.2% 64.22% 47ms 0.93% std::type_info::operator== (inline) 30ms 0.59% 64.81% 46ms 0.91% std::_Hashtable::clear 0 0% 64.81% 46ms 0.91% std::less::operator() (inline) 46ms 0.91% 65.72% 46ms 0.91% std::operator< (inline) 45ms 0.89% 66.61% 45ms 0.89% vtkTimeStamp::Modified 1ms 0.02% 66.63% 44ms 0.87% vtkDataArray::ComputeRange 24ms 0.47% 67.10% 42ms 0.83% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 67.10% 42ms 0.83% DistributedBoxCollection::IsOwned 42ms 0.83% 67.93% 42ms 0.83% __GI___libc_write 0 0% 67.93% 42ms 0.83% std::basic_filebuf::_M_convert_to_external 0 0% 67.93% 42ms 0.83% std::basic_filebuf::overflow 41ms 0.81% 68.74% 42ms 0.83% vtkObjectBase::Delete 0 0% 68.74% 41ms 0.81% std::__basic_file::xsputn 40ms 0.79% 69.53% 40ms 0.79% [libvtkCommonCore-9.3.so.9.3] 0 0% 69.53% 39ms 0.77% Cell::GetCellId 39ms 0.77% 70.30% 39ms 0.77% __memcpy_avx_unaligned_erms 0 0% 70.30% 39ms 0.77% _dl_init 0 0% 70.30% 39ms 0.77% _dl_start_user 0 0% 70.30% 39ms 0.77% call_init (inline) 0 0% 70.30% 39ms 0.77% std::basic_filebuf::open 0 0% 70.30% 39ms 0.77% vtkDoubleArray::New 39ms 0.77% 71.07% 39ms 0.77% vtkObject::~vtkObject 8ms 0.16% 71.23% 38ms 0.75% vtkDataArray::~vtkDataArray 0 0% 71.23% 37ms 0.73% _IO_new_file_fopen 0 0% 71.23% 37ms 0.73% _IO_new_fopen 0 0% 71.23% 37ms 0.73% __GI__IO_file_open 0 0% 71.23% 37ms 0.73% __fopen_internal (inline) 0 0% 71.23% 37ms 0.73% std::__basic_file::open 0 0% 71.23% 36ms 0.71% CellIdWriter::GetCellDataForVtkOutput 0 0% 71.23% 36ms 0.71% CxxTest::RealWorldDescription::setUp 0 0% 71.23% 36ms 0.71% OutputFileHandler::OpenOutputFile 0 0% 71.23% 36ms 0.71% PMPI_Init_thread 0 0% 71.23% 36ms 0.71% PetscInitialize 0 0% 71.23% 36ms 0.71% PetscSetup::setUpWorld 0 0% 71.23% 36ms 0.71% PetscSetupUtils::CommonSetup 0 0% 71.23% 36ms 0.71% PetscSetupUtils::InitialisePetsc 0 0% 71.23% 36ms 0.71% ompi_mpi_init 29ms 0.57% 71.80% 36ms 0.71% std::num_put::do_put 35ms 0.69% 72.49% 35ms 0.69% __libc_open64 5ms 0.099% 72.59% 35ms 0.69% boost::serialization::singleton::get_instance 1ms 0.02% 72.61% 34ms 0.67% CellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 72.61% 34ms 0.67% DistributedBoxCollection::SetupLocalBoxesHalfOnly 5ms 0.099% 72.71% 34ms 0.67% Node::GetPoint 0 0% 72.71% 34ms 0.67% std::make_unique (inline) 8ms 0.16% 72.86% 34ms 0.67% vtkAOSDataArrayTemplate::InsertTuple 2ms 0.039% 72.90% 33ms 0.65% 2ms 0.039% 72.94% 33ms 0.65% VtkMeshWriter::MakeVtkMesh 1ms 0.02% 72.96% 32ms 0.63% PottsMesh::GetVonNeumannNeighbouringNodeIndices 0 0% 72.96% 32ms 0.63% boost::numeric::ublas::c_vector::assign (inline) 0 0% 72.96% 32ms 0.63% std::_Destroy (inline) 1ms 0.02% 72.98% 32ms 0.63% std::_Destroy_aux::__destroy (inline) 1ms 0.02% 73.00% 31ms 0.61% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 1ms 0.02% 73.02% 31ms 0.61% vtk::detail::smp::vtkSMPToolsImplForTBB 5ms 0.099% 73.12% 31ms 0.61% vtkDataArrayPrivate::DoComputeVectorRange 0 0% 73.12% 30ms 0.59% Cell::GetMutationState 30ms 0.59% 73.71% 30ms 0.59% __mpn_divrem 13ms 0.26% 73.97% 30ms 0.59% std::__new_allocator::construct (inline) 0 0% 73.97% 30ms 0.59% std::allocator_traits::construct (inline) 0 0% 73.97% 29ms 0.57% Node::AddElement 1ms 0.02% 73.99% 29ms 0.57% VertexMeshWriter::GetNextElement 24ms 0.47% 74.46% 29ms 0.57% __printf_buffer_write 0 0% 74.46% 29ms 0.57% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.02% 74.48% 29ms 0.57% std::ostream::flush 0 0% 74.48% 29ms 0.57% std::vector::vector (inline) 4ms 0.079% 74.56% 29ms 0.57% tbb::detail::r1::cancel_group_execution 2ms 0.039% 74.60% 28ms 0.55% Edge::Edge 28ms 0.55% 75.15% 28ms 0.55% Node::GetIndex 0 0% 75.15% 28ms 0.55% std::basic_ofstream::basic_ofstream (inline) 0 0% 75.15% 28ms 0.55% std::basic_ofstream::open (inline) 27ms 0.53% 75.69% 28ms 0.55% vtkDataArray::Modified 28ms 0.55% 76.24% 28ms 0.55% vtkObjectBase::~vtkObjectBase 1ms 0.02% 76.26% 27ms 0.53% std::basic_filebuf::sync 5ms 0.099% 76.36% 27ms 0.53% vtkAOSDataArrayTemplate::AllocateTuples 8ms 0.16% 76.51% 27ms 0.53% vtkIdList::vtkIdList 24ms 0.47% 76.99% 27ms 0.53% vtkObject::ObjectFinalize 0 0% 76.99% 26ms 0.51% Edge::SetNodes (inline) 26ms 0.51% 77.50% 26ms 0.51% boost::numeric::ublas::c_vector::operator() 0 0% 77.50% 26ms 0.51% std::_Vector_base::_Vector_base (inline) 26ms 0.51% 78.01% 26ms 0.51% vtkObjectBase::vtkObjectBase