File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 4062ms, 82.64% of 4915ms total Dropped 666 nodes (cum <= 24.57ms) flat flat% sum% cum cum% 0 0% 0% 4757ms 96.79% __libc_start_call_main 0 0% 0% 4757ms 96.79% __libc_start_main_impl 0 0% 0% 4757ms 96.79% _start 0 0% 0% 4739ms 96.42% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4739ms 96.42% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4739ms 96.42% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4739ms 96.42% main 0 0% 0% 4705ms 95.73% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4705ms 95.73% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4705ms 95.73% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4695ms 95.52% AbstractCellBasedSimulation::Solve 0 0% 0% 4296ms 87.41% AbstractCellPopulation::WriteResultsToFiles 7ms 0.14% 0.14% 4079ms 82.99% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.14% 2064ms 41.99% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.02% 0.16% 1829ms 37.21% VertexMeshWriter::MakeVtkMesh 0 0% 0.16% 1365ms 27.77% vtkPolygon::New 0 0% 0.16% 1365ms 27.77% vtkPolygon::vtkPolygon 4ms 0.081% 0.24% 990ms 20.14% vtkCell::vtkCell 2ms 0.041% 0.28% 795ms 16.17% vtkPoints::New 38ms 0.77% 1.06% 788ms 16.03% operator new 9ms 0.18% 1.24% 760ms 15.46% vtkPoints::vtkPoints 331ms 6.73% 7.98% 754ms 15.34% __GI___libc_malloc 1ms 0.02% 8.00% 682ms 13.88% VertexMeshWriter::WriteFiles 0 0% 8.00% 626ms 12.74% std::ostream::operator<< (inline) 49ms 1% 8.99% 625ms 12.72% std::ostream::_M_insert 0 0% 8.99% 616ms 12.53% vtkQuad::New 1ms 0.02% 9.01% 614ms 12.49% vtkQuad::vtkQuad 2ms 0.041% 9.05% 601ms 12.23% vtkLine::New 0 0% 9.05% 587ms 11.94% vtkTriangle::New 4ms 0.081% 9.14% 578ms 11.76% vtkTriangle::vtkTriangle 5ms 0.1% 9.24% 574ms 11.68% vtkLine::vtkLine 105ms 2.14% 11.37% 530ms 10.78% __GI___libc_free 46ms 0.94% 12.31% 525ms 10.68% std::num_put::_M_insert_float 0 0% 12.31% 490ms 9.97% vtkStreamingDemandDrivenPipeline::Update 0 0% 12.31% 490ms 9.97% vtkXMLWriterBase::Write 0 0% 12.31% 488ms 9.93% vtkDemandDrivenPipeline::ProcessRequest 1ms 0.02% 12.33% 486ms 9.89% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 12.33% 483ms 9.83% vtkDemandDrivenPipeline::ExecuteData 0 0% 12.33% 482ms 9.81% vtkExecutive::CallAlgorithm 0 0% 12.33% 481ms 9.79% vtkCompositeDataPipeline::ExecuteData 0 0% 12.33% 481ms 9.79% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 12.33% 437ms 8.89% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 12.33% 437ms 8.89% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 31ms 0.63% 12.96% 436ms 8.87% vtkPoints::SetDataType 0 0% 12.96% 424ms 8.63% vtkPolygon::~vtkPolygon 19ms 0.39% 13.35% 423ms 8.61% std::__cxx11::collate::do_transform 275ms 5.60% 18.94% 419ms 8.52% _int_free 61ms 1.24% 20.18% 388ms 7.89% std::__new_allocator::allocate (inline) 0 0% 20.18% 385ms 7.83% std::allocator_traits::allocate (inline) 0 0% 20.18% 385ms 7.83% vtkXMLWriter::WriteBinaryData 1ms 0.02% 20.20% 384ms 7.81% OnLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.061% 20.26% 384ms 7.81% ___vsnprintf 3ms 0.061% 20.33% 383ms 7.79% PottsBasedCellPopulation::UpdateCellLocations 0 0% 20.33% 382ms 7.77% vtkXMLWriter::WriteBinaryDataInternal 0 0% 20.33% 381ms 7.75% __vsnprintf_internal (inline) 0 0% 20.33% 381ms 7.75% vtkXMLWriter::WriteBinaryDataBlock 0 0% 20.33% 374ms 7.61% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 56ms 1.14% 21.46% 371ms 7.55% __printf_buffer 226ms 4.60% 26.06% 361ms 7.34% _int_malloc 43ms 0.87% 26.94% 350ms 7.12% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 3ms 0.061% 27.00% 340ms 6.92% vtkCell::~vtkCell 1ms 0.02% 27.02% 306ms 6.23% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 27.02% 304ms 6.19% VtkMeshWriter::WriteFiles 19ms 0.39% 27.41% 292ms 5.94% std::_Rb_tree::_Rb_tree 5ms 0.1% 27.51% 292ms 5.94% std::__new_allocator::deallocate (inline) 0 0% 27.51% 292ms 5.94% std::set::set (inline) 0 0% 27.51% 289ms 5.88% std::allocator_traits::deallocate (inline) 17ms 0.35% 27.85% 285ms 5.80% vtkObject::vtkObject 0 0% 27.85% 283ms 5.76% std::_Rb_tree::_M_create_node (inline) 0 0% 27.85% 282ms 5.74% vtkXMLWriter::WritePointsAppendedData 1ms 0.02% 27.87% 278ms 5.66% __printf_fp_spec (inline) 9ms 0.18% 28.06% 277ms 5.64% __printf_fp_l_buffer 0 0% 28.06% 257ms 5.23% std::_Rb_tree::_M_get_node (inline) 0 0% 28.06% 256ms 5.21% std::_Rb_tree::_Alloc_node::operator() (inline) 110ms 2.24% 30.30% 248ms 5.05% __printf_fp_buffer_1 27ms 0.55% 30.84% 248ms 5.05% vtkObject::Modified 9ms 0.18% 31.03% 242ms 4.92% std::_Rb_tree::_M_copy (inline) 26ms 0.53% 31.56% 229ms 4.66% std::_Rb_tree::_M_clone_node (inline) 1ms 0.02% 31.58% 223ms 4.54% VertexMesh::~VertexMesh 3ms 0.061% 31.64% 214ms 4.35% vtkPoints::~vtkPoints 0 0% 31.64% 209ms 4.25% vtkFloatArray::New 139ms 2.83% 34.47% 205ms 4.17% malloc_consolidate 205ms 4.17% 38.64% 205ms 4.17% vtkTimeStamp::Modified 0 0% 38.64% 202ms 4.11% vtkXMLWriter::WriteCompressionBlock 0 0% 38.64% 201ms 4.09% vtkQuad::~vtkQuad 0 0% 38.64% 196ms 3.99% vtkFloatArray::vtkFloatArray 0 0% 38.64% 191ms 3.89% std::vector::~vector (inline) 0 0% 38.64% 189ms 3.85% vtkDataCompressor::Compress 154ms 3.13% 41.77% 189ms 3.85% vtkObjectBase::UnRegisterInternal 4ms 0.081% 41.85% 187ms 3.80% vtkBase64OutputStream::Write 1ms 0.02% 41.87% 186ms 3.78% compress2 0 0% 41.87% 186ms 3.78% vtkZLibDataCompressor::CompressBuffer 43ms 0.87% 42.75% 184ms 3.74% crc32 0 0% 42.75% 184ms 3.74% deflate 20ms 0.41% 43.15% 183ms 3.72% vtkBase64OutputStream::EncodeTriplet 9ms 0.18% 43.34% 181ms 3.68% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.02% 43.36% 180ms 3.66% vtkIdList::AllocateInternal 47ms 0.96% 44.31% 179ms 3.64% std::_Rb_tree::_M_erase 0 0% 44.31% 177ms 3.60% vtkTriangle::~vtkTriangle 3ms 0.061% 44.37% 176ms 3.58% std::_Vector_base::_M_deallocate (inline) 1ms 0.02% 44.39% 175ms 3.56% VertexMesh::VertexMesh 3ms 0.061% 44.46% 169ms 3.44% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 1ms 0.02% 44.48% 169ms 3.44% NodesOnlyMesh::ConstructNodesWithoutMesh 0 0% 44.48% 167ms 3.40% vtkLine::GetParametricCenter 1ms 0.02% 44.50% 164ms 3.34% vtkTypeFloat64Array::~vtkTypeFloat64Array 0 0% 44.50% 159ms 3.23% VertexMesh::GenerateEdgesFromElements (inline) 1ms 0.02% 44.52% 158ms 3.21% MutableElement::BuildEdges 0 0% 44.52% 154ms 3.13% std::_Vector_base::~_Vector_base (inline) 2ms 0.041% 44.56% 154ms 3.13% vtkDoubleArray::vtkDoubleArray 2ms 0.041% 44.60% 145ms 2.95% EdgeHelper::GetEdgeFromNodes 0 0% 44.60% 142ms 2.89% EdgeHelper::~EdgeHelper (inline) 0 0% 44.60% 141ms 2.87% vtkDataArray::CreateDataArray 33ms 0.67% 45.27% 140ms 2.85% std::ostream::write 0 0% 45.27% 138ms 2.81% std::set::~set (inline) 0 0% 45.27% 135ms 2.75% NodeLocationWriter::VisitAnyPopulation 134ms 2.73% 48.00% 135ms 2.75% [libz.so.1.3] 2ms 0.041% 48.04% 135ms 2.75% vtkTypeFloat64Array::New 0 0% 48.04% 133ms 2.71% vtkIdList::Allocate 0 0% 48.04% 132ms 2.69% std::_Rb_tree::_M_drop_node (inline) 0 0% 48.04% 132ms 2.69% tbb::detail::r1::parallel_pipeline 0 0% 48.04% 131ms 2.67% PottsMesh::GetMooreNeighbouringNodeIndices 2ms 0.041% 48.08% 130ms 2.64% std::_Vector_base::_M_allocate (inline) 123ms 2.50% 50.58% 123ms 2.50% [libvtkCommonCore-9.3.so.9.3] 0 0% 50.58% 123ms 2.50% clone3 0 0% 50.58% 123ms 2.50% start_thread 1ms 0.02% 50.60% 122ms 2.48% vtkTypeFloat64Array::vtkTypeFloat64Array 0 0% 50.60% 116ms 2.36% std::_Rb_tree::_M_put_node (inline) 1ms 0.02% 50.62% 114ms 2.32% tbb::detail::r1::reset 12ms 0.24% 50.86% 110ms 2.24% std::vector::_M_default_append 1ms 0.02% 50.89% 106ms 2.16% CellPropertyCollection::GetPropertiesType (inline) 34ms 0.69% 51.58% 106ms 2.16% std::basic_filebuf::xsputn 71ms 1.44% 53.02% 106ms 2.16% tbb::detail::r1::wait_bounded_queue_monitor 5ms 0.1% 53.12% 102ms 2.08% vtkDataArray::vtkDataArray 100ms 2.03% 55.16% 100ms 2.03% __strcmp_evex 0 0% 55.16% 99ms 2.01% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 98ms 1.99% 57.15% 98ms 1.99% vtkObjectBase::vtkObjectBase 3ms 0.061% 57.21% 96ms 1.95% std::vector::push_back (inline) 2ms 0.041% 57.25% 96ms 1.95% vtkFloatArray::~vtkFloatArray 8ms 0.16% 57.42% 95ms 1.93% vtkAbstractArray::vtkAbstractArray 2ms 0.041% 57.46% 94ms 1.91% _int_free_maybe_consolidate 38ms 0.77% 58.23% 94ms 1.91% vtkAOSDataArrayTemplate::DataElementChanged 1ms 0.02% 58.25% 92ms 1.87% vtkXMLWriter::WritePointDataAppendedData 5ms 0.1% 58.35% 91ms 1.85% CellPropertyCollection::HasProperty 1ms 0.02% 58.37% 89ms 1.81% Cell::HasCellProperty (inline) 0 0% 58.37% 87ms 1.77% AbstractCellProperty::IsSubType (inline) 35ms 0.71% 59.08% 87ms 1.77% hack_digit 2ms 0.041% 59.13% 87ms 1.77% std::operator<< (inline) 25ms 0.51% 59.63% 86ms 1.75% __dynamic_cast 5ms 0.1% 59.74% 86ms 1.75% std::map::operator[] (partial-inline) 25ms 0.51% 60.24% 86ms 1.75% vtkTypeFloat64Array::PrintSelf 33ms 0.67% 60.92% 85ms 1.73% std::__ostream_insert 1ms 0.02% 60.94% 82ms 1.67% AbstractCellProperty::IsType (inline) 2ms 0.041% 60.98% 82ms 1.67% vtkIdList::New 1ms 0.02% 61.00% 81ms 1.65% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 61.00% 79ms 1.61% VertexMesh::Clear 0 0% 61.00% 77ms 1.57% std::_Rb_tree::_M_insert_unique 0 0% 61.00% 77ms 1.57% std::set::insert (inline) 1ms 0.02% 61.02% 72ms 1.46% vtkDoubleArray::~vtkDoubleArray 0 0% 61.02% 70ms 1.42% NodesOnlyMesh::SetUpBoxCollection 2ms 0.041% 61.06% 70ms 1.42% std::vector::_M_realloc_insert 70ms 1.42% 62.48% 70ms 1.42% unlink_chunk 48ms 0.98% 63.46% 67ms 1.36% std::basic_streambuf::xsputn 0 0% 63.46% 66ms 1.34% Cell::GetCellProliferativeType 0 0% 63.46% 64ms 1.30% NodesOnlyMesh::~NodesOnlyMesh 63ms 1.28% 64.74% 63ms 1.28% [libchaste_cell_based.so] 4ms 0.081% 64.82% 63ms 1.28% std::_Rb_tree::_M_insert_ (inline) 9ms 0.18% 65.01% 62ms 1.26% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 65.01% 62ms 1.26% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 12ms 0.24% 65.25% 60ms 1.22% VertexMeshWriter::GetNextNode 0 0% 65.25% 58ms 1.18% std::make_unique (inline) 11ms 0.22% 65.47% 56ms 1.14% AbstractCellProperty::IsSame 0 0% 65.47% 55ms 1.12% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 10ms 0.2% 65.68% 55ms 1.12% std::_Rb_tree::_M_lower_bound (inline) 3ms 0.061% 65.74% 55ms 1.12% vtkDataArray::~vtkDataArray 54ms 1.10% 66.84% 54ms 1.10% [libstdc++.so.6.0.33] 2ms 0.041% 66.88% 54ms 1.10% boost::numeric::ublas::vector_assign (inline) 52ms 1.06% 67.93% 52ms 1.06% vtkObjectBase::RegisterInternal 0 0% 67.93% 51ms 1.04% std::_Destroy (inline) 0 0% 67.93% 51ms 1.04% std::_Destroy_aux::__destroy (inline) 25ms 0.51% 68.44% 50ms 1.02% std::__new_allocator::construct (inline) 0 0% 68.44% 50ms 1.02% std::allocator_traits::construct (inline) 8ms 0.16% 68.61% 49ms 1% vtkIdList::~vtkIdList 2ms 0.041% 68.65% 45ms 0.92% DistributedBoxCollection::SetupLocalBoxesHalfOnly 0 0% 68.65% 45ms 0.92% PottsMesh::GetVonNeumannNeighbouringNodeIndices 5ms 0.1% 68.75% 45ms 0.92% std::type_info::operator== (inline) 0 0% 68.75% 45ms 0.92% vtkDoubleArray::New 0 0% 68.75% 44ms 0.9% std::_Rb_tree::lower_bound (inline) 0 0% 68.75% 44ms 0.9% std::map::lower_bound (inline) 22ms 0.45% 69.20% 43ms 0.87% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 69.20% 43ms 0.87% std::map::~map (inline) 1ms 0.02% 69.22% 42ms 0.85% VertexElement::~VertexElement 0 0% 69.22% 42ms 0.85% boost::detail::shared_count::~shared_count (inline) 0 0% 69.22% 42ms 0.85% boost::shared_ptr::~shared_ptr (inline) 0 0% 69.22% 41ms 0.83% DistributedBoxCollection::~DistributedBoxCollection 0 0% 69.22% 41ms 0.83% NodesOnlyMesh::ClearBoxCollection (inline) 2ms 0.041% 69.26% 41ms 0.83% vtkDataArray::ComputeRange 39ms 0.79% 70.05% 40ms 0.81% boost::detail::sp_counted_base::release 40ms 0.81% 70.86% 40ms 0.81% std::codecvt::do_always_noconv 0 0% 70.86% 40ms 0.81% tcache_get (inline) 40ms 0.81% 71.68% 40ms 0.81% tcache_get_n (inline) 1ms 0.02% 71.70% 39ms 0.79% Edge::Edge 38ms 0.77% 72.47% 38ms 0.77% [libchaste_mesh.so] 0 0% 72.47% 38ms 0.77% _dl_init 0 0% 72.47% 38ms 0.77% call_init (inline) 0 0% 72.47% 37ms 0.75% Edge::SetNodes (inline) 37ms 0.75% 73.22% 37ms 0.75% __memcpy_evex_unaligned_erms 0 0% 73.22% 37ms 0.75% std::_Rb_tree::_M_emplace_hint_unique 8ms 0.16% 73.39% 37ms 0.75% std::num_put::_M_insert_int 1ms 0.02% 73.41% 37ms 0.75% vtkIdList::vtkIdList 1ms 0.02% 73.43% 35ms 0.71% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 35ms 0.71% 74.14% 35ms 0.71% __GI_sched_yield 0 0% 74.14% 35ms 0.71% _dl_start_user 9ms 0.18% 74.32% 34ms 0.69% boost::numeric::ublas::indexing_vector_assign 6ms 0.12% 74.45% 34ms 0.69% vtkAOSDataArrayTemplate::InsertTuple 33ms 0.67% 75.12% 33ms 0.67% __mpn_divrem 0 0% 75.12% 33ms 0.67% vtk::detail::smp::vtkSMPToolsImplForTBB 0 0% 75.12% 32ms 0.65% MutableElement::~MutableElement 31ms 0.63% 75.75% 32ms 0.65% __GI___writev 2ms 0.041% 75.79% 32ms 0.65% __find_specmb (inline) 27ms 0.55% 76.34% 32ms 0.65% std::_Hashtable::clear 0 0% 76.34% 32ms 0.65% std::__basic_file::xsputn_2 0 0% 76.34% 32ms 0.65% std::default_delete::operator() (inline) 0 0% 76.34% 32ms 0.65% std::unique_ptr::~unique_ptr (inline) 3ms 0.061% 76.40% 32ms 0.65% vtkAOSDataArrayTemplate::AllocateTuples 20ms 0.41% 76.81% 32ms 0.65% vtkObject::ObjectFinalize 0 0% 76.81% 31ms 0.63% CxxTest::RealWorldDescription::setUp 1ms 0.02% 76.83% 31ms 0.63% DistributedBoxCollection::IsOwned 0 0% 76.83% 31ms 0.63% PetscInitialize 0 0% 76.83% 31ms 0.63% PetscSetup::setUpWorld 0 0% 76.83% 31ms 0.63% PetscSetupUtils::CommonSetup 0 0% 76.83% 31ms 0.63% PetscSetupUtils::InitialisePetsc 0 0% 76.83% 30ms 0.61% Cell::GetCellId 21ms 0.43% 77.25% 30ms 0.61% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 77.25% 30ms 0.61% Node::AddElement 30ms 0.61% 77.86% 30ms 0.61% Node::GetIndex 0 0% 77.86% 30ms 0.61% PMPI_Init_thread 2ms 0.041% 77.90% 30ms 0.61% boost::serialization::singleton::get_instance 0 0% 77.90% 30ms 0.61% ompi_mpi_init 0 0% 77.90% 30ms 0.61% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 1ms 0.02% 77.92% 30ms 0.61% std::_Rb_tree_header::_Rb_tree_header (inline) 1ms 0.02% 77.95% 29ms 0.59% CellProliferativeTypesWriter::GetCellDataForVtkOutput 2ms 0.041% 77.99% 29ms 0.59% Node::SetRadius 0 0% 77.99% 29ms 0.59% PottsBasedCellPopulation::AcceptCellWriter 29ms 0.59% 78.58% 29ms 0.59% checked_request2size (inline) 29ms 0.59% 79.17% 29ms 0.59% std::_Rb_tree::_S_right (inline) 3ms 0.061% 79.23% 29ms 0.59% tbb::detail::r1::cancel_group_execution 2ms 0.041% 79.27% 29ms 0.59% vtk::detail::smp::vtkSMPToolsImpl::For 2ms 0.041% 79.31% 29ms 0.59% vtkDataArrayPrivate::DoComputeVectorRange 10ms 0.2% 79.51% 29ms 0.59% vtkSOADataArrayTemplate::GetTupleIndexFromValueIndex 0 0% 79.51% 28ms 0.57% Cell::GetMutationState 0 0% 79.51% 28ms 0.57% CellIdWriter::GetCellDataForVtkOutput 0 0% 79.51% 28ms 0.57% Node::GetPoint 1ms 0.02% 79.53% 28ms 0.57% VtkMeshWriter::MakeVtkMesh 0 0% 79.53% 28ms 0.57% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 28ms 0.57% 80.10% 28ms 0.57% std::_Rb_tree_header::_M_reset (inline) 28ms 0.57% 80.67% 28ms 0.57% tcache_put (inline) 0 0% 80.67% 27ms 0.55% Node::ConstructNodeAttributes (inline) 27ms 0.55% 81.22% 27ms 0.55% __strchrnul_evex 0 0% 81.22% 27ms 0.55% std::_Rb_tree::_Auto_node::_Auto_node (inline) 2ms 0.041% 81.26% 27ms 0.55% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.041% 81.30% 26ms 0.53% boost::serialization::void_cast_detail::void_caster::recursive_register 0 0% 81.30% 26ms 0.53% boost::serialization::void_cast_detail::void_caster_primitive::void_caster_primitive (inline) 0 0% 81.30% 26ms 0.53% std::_Rb_tree::_M_construct_node (inline) 0 0% 81.30% 26ms 0.53% std::vector::vector (inline) 16ms 0.33% 81.63% 25ms 0.51% __printf_buffer_write 0 0% 81.63% 25ms 0.51% boost::numeric::ublas::c_vector::assign (inline) 0 0% 81.63% 25ms 0.51% vtkDataSet::GetCellTypes 25ms 0.51% 82.14% 25ms 0.51% vtkObject::~vtkObject 25ms 0.51% 82.64% 25ms 0.51% vtkObjectBase::Delete