File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3794ms, 79.82% of 4753ms total Dropped 757 nodes (cum <= 23.77ms) flat flat% sum% cum cum% 0 0% 0% 4552ms 95.77% __libc_start_call_main 0 0% 0% 4552ms 95.77% __libc_start_main_impl 0 0% 0% 4552ms 95.77% _start 0 0% 0% 4532ms 95.35% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4532ms 95.35% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4532ms 95.35% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4532ms 95.35% main 0 0% 0% 4493ms 94.53% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4493ms 94.53% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4493ms 94.53% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4482ms 94.30% AbstractCellBasedSimulation::Solve 0 0% 0% 4161ms 87.54% AbstractCellPopulation::WriteResultsToFiles 12ms 0.25% 0.25% 3944ms 82.98% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.25% 1980ms 41.66% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.021% 0.27% 1702ms 35.81% VertexMeshWriter::MakeVtkMesh 1ms 0.021% 0.29% 1257ms 26.45% vtkPolygon::New 1ms 0.021% 0.32% 1256ms 26.43% vtkPolygon::vtkPolygon 4ms 0.084% 0.4% 892ms 18.77% vtkCell::vtkCell 2ms 0.042% 0.44% 766ms 16.12% vtkPoints::New 10ms 0.21% 0.65% 722ms 15.19% vtkPoints::vtkPoints 2ms 0.042% 0.69% 680ms 14.31% VertexMeshWriter::WriteFiles 30ms 0.63% 1.33% 658ms 13.84% operator new 57ms 1.20% 2.52% 648ms 13.63% std::ostream::_M_insert 0 0% 2.52% 645ms 13.57% std::ostream::operator<< (inline) 174ms 3.66% 6.19% 632ms 13.30% __GI___libc_malloc 1ms 0.021% 6.21% 590ms 12.41% vtkQuad::New 5ms 0.11% 6.31% 586ms 12.33% vtkQuad::vtkQuad 0 0% 6.31% 580ms 12.20% vtkStreamingDemandDrivenPipeline::Update 0 0% 6.31% 580ms 12.20% vtkXMLWriterBase::Write 0 0% 6.31% 577ms 12.14% vtkDemandDrivenPipeline::ProcessRequest 0 0% 6.31% 576ms 12.12% vtkStreamingDemandDrivenPipeline::ProcessRequest 1ms 0.021% 6.33% 574ms 12.08% vtkExecutive::CallAlgorithm 1ms 0.021% 6.35% 572ms 12.03% vtkDemandDrivenPipeline::ExecuteData 0 0% 6.35% 571ms 12.01% vtkCompositeDataPipeline::ExecuteData 0 0% 6.35% 571ms 12.01% vtkXMLUnstructuredDataWriter::ProcessRequest 2ms 0.042% 6.40% 568ms 11.95% vtkLine::New 1ms 0.021% 6.42% 552ms 11.61% vtkTriangle::New 8ms 0.17% 6.59% 549ms 11.55% vtkLine::vtkLine 7ms 0.15% 6.73% 541ms 11.38% vtkTriangle::vtkTriangle 41ms 0.86% 7.60% 525ms 11.05% std::num_put::_M_insert_float 0 0% 7.60% 513ms 10.79% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 7.60% 513ms 10.79% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 112ms 2.36% 9.95% 458ms 9.64% __GI___libc_free 0 0% 9.95% 454ms 9.55% vtkXMLWriter::WriteBinaryData 32ms 0.67% 10.62% 453ms 9.53% vtkPoints::SetDataType 0 0% 10.62% 450ms 9.47% vtkXMLWriter::WriteBinaryDataBlock 0 0% 10.62% 450ms 9.47% vtkXMLWriter::WriteBinaryDataInternal 0 0% 10.62% 440ms 9.26% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 11ms 0.23% 10.86% 416ms 8.75% std::__cxx11::collate::do_transform 0 0% 10.86% 396ms 8.33% vtkPolygon::~vtkPolygon 1ms 0.021% 10.88% 386ms 8.12% ___vsnprintf 0 0% 10.88% 385ms 8.10% __vsnprintf_internal (inline) 66ms 1.39% 12.27% 379ms 7.97% __printf_buffer 247ms 5.20% 17.46% 374ms 7.87% _int_malloc 0 0% 17.46% 346ms 7.28% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 17.46% 343ms 7.22% VtkMeshWriter::WriteFiles 208ms 4.38% 21.84% 342ms 7.20% _int_free 0 0% 21.84% 335ms 7.05% vtkXMLWriter::WritePointsAppendedData 47ms 0.99% 22.83% 316ms 6.65% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 0 0% 22.83% 315ms 6.63% OnLatticeSimulation::UpdateCellLocationsAndTopology 9ms 0.19% 23.02% 315ms 6.63% PottsBasedCellPopulation::UpdateCellLocations 4ms 0.084% 23.10% 314ms 6.61% vtkCell::~vtkCell 16ms 0.34% 23.44% 290ms 6.10% __printf_fp_l_buffer 0 0% 23.44% 290ms 6.10% __printf_fp_spec (inline) 38ms 0.8% 24.24% 277ms 5.83% std::__new_allocator::allocate (inline) 0 0% 24.24% 277ms 5.83% std::allocator_traits::allocate (inline) 126ms 2.65% 26.89% 264ms 5.55% __printf_fp_buffer_1 3ms 0.063% 26.95% 252ms 5.30% std::__new_allocator::deallocate (inline) 0 0% 26.95% 251ms 5.28% std::allocator_traits::deallocate (inline) 0 0% 26.95% 235ms 4.94% vtkXMLWriter::WriteCompressionBlock 0 0% 26.95% 227ms 4.78% vtkDataCompressor::Compress 0 0% 26.95% 226ms 4.75% compress2 0 0% 26.95% 226ms 4.75% vtkZLibDataCompressor::CompressBuffer 44ms 0.93% 27.88% 223ms 4.69% crc32 0 0% 27.88% 223ms 4.69% deflate 4ms 0.084% 27.96% 212ms 4.46% vtkBase64OutputStream::Write 0 0% 27.96% 205ms 4.31% std::set::set (inline) 15ms 0.32% 28.28% 205ms 4.31% vtkBase64OutputStream::EncodeTriplet 18ms 0.38% 28.66% 203ms 4.27% std::_Rb_tree::_Rb_tree 7ms 0.15% 28.80% 203ms 4.27% vtkPoints::~vtkPoints 11ms 0.23% 29.03% 197ms 4.14% vtkFloatArray::New 109ms 2.29% 31.33% 179ms 3.77% malloc_consolidate 5ms 0.11% 31.43% 177ms 3.72% vtkDataArray::CreateDataArray 40ms 0.84% 32.27% 172ms 3.62% std::ostream::write 165ms 3.47% 35.75% 171ms 3.60% [libz.so.1.3] 0 0% 35.75% 171ms 3.60% std::_Rb_tree::_M_create_node (inline) 2ms 0.042% 35.79% 171ms 3.60% tbb::detail::r1::parallel_pipeline 0 0% 35.79% 171ms 3.60% vtkQuad::~vtkQuad 0 0% 35.79% 169ms 3.56% VertexMesh::~VertexMesh 0 0% 35.79% 168ms 3.53% NodesOnlyMesh::ConstructNodesWithoutMesh 0 0% 35.79% 167ms 3.51% vtkLine::GetParametricCenter 2ms 0.042% 35.83% 167ms 3.51% vtkTriangle::~vtkTriangle 7ms 0.15% 35.98% 166ms 3.49% vtkTypeFloat64Array::New 0 0% 35.98% 165ms 3.47% clone3 0 0% 35.98% 165ms 3.47% start_thread 6ms 0.13% 36.10% 164ms 3.45% std::_Rb_tree::~_Rb_tree (inline) 40ms 0.84% 36.95% 163ms 3.43% std::_Rb_tree::_M_erase 2ms 0.042% 36.99% 163ms 3.43% vtkDoubleArray::vtkDoubleArray 6ms 0.13% 37.11% 163ms 3.43% vtkFloatArray::vtkFloatArray 3ms 0.063% 37.18% 163ms 3.43% vtkIdList::AllocateInternal 15ms 0.32% 37.49% 158ms 3.32% std::_Rb_tree::_M_copy (inline) 77ms 1.62% 39.11% 158ms 3.32% std::basic_filebuf::xsputn 2ms 0.042% 39.15% 157ms 3.30% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 0 0% 39.15% 153ms 3.22% tbb::detail::r1::reset 1ms 0.021% 39.18% 153ms 3.22% vtkTypeFloat64Array::~vtkTypeFloat64Array 2ms 0.042% 39.22% 152ms 3.20% VertexMesh::VertexMesh 0 0% 39.22% 151ms 3.18% std::_Rb_tree::_M_get_node (inline) 0 0% 39.22% 151ms 3.18% std::vector::~vector (inline) 0 0% 39.22% 149ms 3.13% std::_Rb_tree::_Alloc_node::operator() (inline) 14ms 0.29% 39.51% 147ms 3.09% std::vector::_M_default_append 67ms 1.41% 40.92% 146ms 3.07% tbb::detail::r1::wait_bounded_queue_monitor 6ms 0.13% 41.05% 141ms 2.97% MutableElement::BuildEdges 0 0% 41.05% 141ms 2.97% VertexMesh::GenerateEdgesFromElements (inline) 4ms 0.084% 41.13% 138ms 2.90% std::_Vector_base::_M_deallocate (inline) 30ms 0.63% 41.76% 138ms 2.90% vtkObject::vtkObject 0 0% 41.76% 137ms 2.88% NodeLocationWriter::VisitAnyPopulation 12ms 0.25% 42.02% 135ms 2.84% std::_Rb_tree::_M_clone_node (inline) 2ms 0.042% 42.06% 135ms 2.84% vtkTypeFloat64Array::vtkTypeFloat64Array 0 0% 42.06% 128ms 2.69% std::set::~set (inline) 0 0% 42.06% 126ms 2.65% std::_Vector_base::_M_allocate (inline) 0 0% 42.06% 119ms 2.50% EdgeHelper::~EdgeHelper (inline) 0 0% 42.06% 119ms 2.50% std::_Rb_tree::_M_drop_node (inline) 0 0% 42.06% 117ms 2.46% std::_Rb_tree::_M_put_node (inline) 2ms 0.042% 42.10% 116ms 2.44% EdgeHelper::GetEdgeFromNodes 0 0% 42.10% 116ms 2.44% std::_Vector_base::~_Vector_base (inline) 0 0% 42.10% 115ms 2.42% vtkIdList::Allocate 56ms 1.18% 43.28% 104ms 2.19% hack_digit 0 0% 43.28% 103ms 2.17% vtkXMLWriter::WritePointDataAppendedData 0 0% 43.28% 101ms 2.12% CellPropertyCollection::GetPropertiesType (inline) 101ms 2.12% 45.40% 101ms 2.12% __strcmp_avx2 54ms 1.14% 46.54% 101ms 2.12% vtkTypeFloat64Array::PrintSelf 4ms 0.084% 46.62% 100ms 2.10% std::map::operator[] (partial-inline) 5ms 0.11% 46.73% 99ms 2.08% vtkFloatArray::~vtkFloatArray 31ms 0.65% 47.38% 96ms 2.02% vtkObject::Modified 1ms 0.021% 47.40% 95ms 2.00% CellPropertyCollection::HasProperty 29ms 0.61% 48.01% 95ms 2.00% std::__ostream_insert 0 0% 48.01% 94ms 1.98% Cell::HasCellProperty (inline) 94ms 1.98% 49.99% 94ms 1.98% unlink_chunk 10ms 0.21% 50.20% 93ms 1.96% _int_free_maybe_consolidate 1ms 0.021% 50.22% 93ms 1.96% std::operator<< (inline) 0 0% 50.22% 92ms 1.94% AbstractCellProperty::IsSubType (inline) 23ms 0.48% 50.70% 92ms 1.94% __dynamic_cast 2ms 0.042% 50.75% 91ms 1.91% AbstractCellProperty::IsType (inline) 52ms 1.09% 51.84% 90ms 1.89% vtkObjectBase::UnRegisterInternal 3ms 0.063% 51.90% 87ms 1.83% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 51.90% 87ms 1.83% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 30ms 0.63% 52.54% 84ms 1.77% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.021% 52.56% 81ms 1.70% vtkIdList::New 3ms 0.063% 52.62% 77ms 1.62% std::vector::push_back (inline) 75ms 1.58% 54.20% 75ms 1.58% __GI_sched_yield 5ms 0.11% 54.30% 75ms 1.58% vtkDoubleArray::~vtkDoubleArray 0 0% 54.30% 71ms 1.49% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 17ms 0.36% 54.66% 70ms 1.47% AbstractCellProperty::IsSame 42ms 0.88% 55.54% 67ms 1.41% std::basic_streambuf::xsputn 0 0% 55.54% 65ms 1.37% NodesOnlyMesh::SetUpBoxCollection 4ms 0.084% 55.63% 64ms 1.35% boost::numeric::ublas::c_vector::c_vector (partial-inline) 7ms 0.15% 55.78% 64ms 1.35% vtkAOSDataArrayTemplate::DataElementChanged 0 0% 55.78% 63ms 1.33% tcache_get (inline) 63ms 1.33% 57.10% 63ms 1.33% tcache_get_n (inline) 0 0% 57.10% 62ms 1.30% std::_Rb_tree::lower_bound (inline) 0 0% 57.10% 62ms 1.30% std::map::lower_bound (inline) 0 0% 57.10% 61ms 1.28% Cell::GetCellProliferativeType 0 0% 57.10% 60ms 1.26% PottsMesh::GetMooreNeighbouringNodeIndices 0 0% 57.10% 59ms 1.24% boost::numeric::ublas::vector_assign (inline) 6ms 0.13% 57.23% 59ms 1.24% std::vector::_M_realloc_insert 0 0% 57.23% 58ms 1.22% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 0 0% 57.23% 58ms 1.22% NodesOnlyMesh::~NodesOnlyMesh 58ms 1.22% 58.45% 58ms 1.22% vtkTimeStamp::Modified 55ms 1.16% 59.60% 55ms 1.16% [libvtkCommonCore-9.3.so.9.3] 3ms 0.063% 59.67% 55ms 1.16% vtkDataArray::vtkDataArray 15ms 0.32% 59.98% 53ms 1.12% std::type_info::operator== (inline) 52ms 1.09% 61.08% 52ms 1.09% [libstdc++.so.6.0.33] 0 0% 61.08% 52ms 1.09% std::set::insert (inline) 2ms 0.042% 61.12% 51ms 1.07% std::_Rb_tree::_M_insert_unique 8ms 0.17% 61.29% 50ms 1.05% vtkAbstractArray::vtkAbstractArray 2ms 0.042% 61.33% 49ms 1.03% VertexMesh::Clear 10ms 0.21% 61.54% 49ms 1.03% boost::numeric::ublas::indexing_vector_assign 6ms 0.13% 61.67% 48ms 1.01% vtkDataArray::~vtkDataArray 11ms 0.23% 61.90% 48ms 1.01% vtkIdList::~vtkIdList 6ms 0.13% 62.02% 46ms 0.97% VertexMeshWriter::GetNextNode 26ms 0.55% 62.57% 46ms 0.97% std::_Hashtable::clear 45ms 0.95% 63.52% 45ms 0.95% vtkObjectBase::~vtkObjectBase 21ms 0.44% 63.96% 44ms 0.93% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 63.96% 44ms 0.93% vtkDataArray::ComputeRange 2ms 0.042% 64.00% 44ms 0.93% vtkDoubleArray::New 9ms 0.19% 64.19% 44ms 0.93% vtkSOADataArrayTemplate::FillTypedComponent 30ms 0.63% 64.82% 43ms 0.9% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 64.82% 43ms 0.9% DistributedBoxCollection::IsOwned 1ms 0.021% 64.84% 43ms 0.9% DistributedBoxCollection::SetupLocalBoxesHalfOnly 40ms 0.84% 65.68% 43ms 0.9% vtkObjectBase::Delete 42ms 0.88% 66.57% 42ms 0.88% __memcpy_avx_unaligned_erms 0 0% 66.57% 42ms 0.88% std::__basic_file::xsputn_2 41ms 0.86% 67.43% 41ms 0.86% __GI___writev 7ms 0.15% 67.58% 41ms 0.86% vtkDataArrayPrivate::DoComputeVectorRange 4ms 0.084% 67.66% 40ms 0.84% std::_Rb_tree::_M_insert_ (inline) 6ms 0.13% 67.79% 40ms 0.84% std::num_put::_M_insert_int 0 0% 67.79% 39ms 0.82% _dl_init 0 0% 67.79% 39ms 0.82% call_init (inline) 0 0% 67.79% 39ms 0.82% std::_Destroy (inline) 0 0% 67.79% 39ms 0.82% std::_Destroy_aux::__destroy (inline) 39ms 0.82% 68.61% 39ms 0.82% std::codecvt::do_always_noconv 34ms 0.72% 69.32% 38ms 0.8% vtkObject::ObjectFinalize 37ms 0.78% 70.10% 37ms 0.78% vtkObject::~vtkObject 0 0% 70.10% 36ms 0.76% _dl_start_user 0 0% 70.10% 36ms 0.76% std::map::~map (inline) 0 0% 70.10% 35ms 0.74% CxxTest::RealWorldDescription::setUp 0 0% 70.10% 35ms 0.74% DistributedBoxCollection::~DistributedBoxCollection 0 0% 70.10% 35ms 0.74% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 70.10% 35ms 0.74% PetscSetup::setUpWorld 0 0% 70.10% 35ms 0.74% PetscSetupUtils::CommonSetup 35ms 0.74% 70.84% 35ms 0.74% __GI___libc_write 35ms 0.74% 71.58% 35ms 0.74% std::_Rb_tree_increment 1ms 0.021% 71.60% 35ms 0.74% std::__basic_file::xsputn 17ms 0.36% 71.95% 35ms 0.74% std::__new_allocator::construct (inline) 0 0% 71.95% 35ms 0.74% std::allocator_traits::construct (inline) 0 0% 71.95% 35ms 0.74% std::basic_filebuf::_M_convert_to_external 0 0% 71.95% 35ms 0.74% std::basic_filebuf::overflow 0 0% 71.95% 35ms 0.74% vtk::detail::smp::vtkSMPToolsImplForTBB 0 0% 71.95% 34ms 0.72% PMPI_Init_thread 0 0% 71.95% 34ms 0.72% PetscInitialize 0 0% 71.95% 34ms 0.72% PetscSetupUtils::InitialisePetsc 34ms 0.72% 72.67% 34ms 0.72% __mpn_divrem 0 0% 72.67% 34ms 0.72% ompi_mpi_init 1ms 0.021% 72.69% 34ms 0.72% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.042% 72.73% 34ms 0.72% tbb::detail::r1::cancel_group_execution 2ms 0.042% 72.78% 34ms 0.72% vtkAOSDataArrayTemplate::InsertTuple 16ms 0.34% 73.11% 34ms 0.72% vtkIdList::vtkIdList 1ms 0.021% 73.13% 33ms 0.69% std::less::operator() (inline) 2ms 0.042% 73.17% 32ms 0.67% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 73.17% 32ms 0.67% PottsMesh::GetVonNeumannNeighbouringNodeIndices 32ms 0.67% 73.85% 32ms 0.67% [libchaste_cell_based.so] 32ms 0.67% 74.52% 32ms 0.67% std::operator< (inline) 32ms 0.67% 75.19% 32ms 0.67% std::ostream::sentry::sentry 6ms 0.13% 75.32% 32ms 0.67% vtk::detail::smp::vtkSMPToolsImpl::For 32ms 0.67% 75.99% 32ms 0.67% vtkObjectBase::vtkObjectBase 0 0% 75.99% 31ms 0.65% std::make_unique (inline) 30ms 0.63% 76.63% 30ms 0.63% checked_request2size (inline) 2ms 0.042% 76.67% 29ms 0.61% 0 0% 76.67% 29ms 0.61% CellProliferativeTypesWriter::GetCellDataForVtkOutput 2ms 0.042% 76.71% 29ms 0.61% VertexMeshWriter::GetNextElement 5ms 0.11% 76.81% 29ms 0.61% _int_free_merge_chunk 25ms 0.53% 77.34% 29ms 0.61% std::num_put::do_put 1ms 0.021% 77.36% 28ms 0.59% Node::GetPoint 0 0% 77.36% 28ms 0.59% PottsBasedCellPopulation::AcceptCellWriter 3ms 0.063% 77.42% 28ms 0.59% boost::serialization::singleton::get_instance 8ms 0.17% 77.59% 28ms 0.59% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 77.59% 27ms 0.57% VtkMeshWriter::MakeVtkMesh 0 0% 77.59% 27ms 0.57% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 2ms 0.042% 77.64% 27ms 0.57% std::_Rb_tree_header::_Rb_tree_header (inline) 1ms 0.021% 77.66% 26ms 0.55% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 3ms 0.063% 77.72% 26ms 0.55% std::vector::emplace_back (inline) 3ms 0.063% 77.78% 25ms 0.53% VertexElement::~VertexElement 25ms 0.53% 78.31% 25ms 0.53% boost::numeric::ublas::same_impl_ex 0 0% 78.31% 25ms 0.53% std::basic_filebuf::open 0 0% 78.31% 24ms 0.5% Cell::GetCellId 0 0% 78.31% 24ms 0.5% Cell::GetMutationState 24ms 0.5% 78.81% 24ms 0.5% Node::GetIndex 0 0% 78.81% 24ms 0.5% OutputFileHandler::OpenOutputFile 0 0% 78.81% 24ms 0.5% _IO_new_file_fopen 0 0% 78.81% 24ms 0.5% _IO_new_fopen 0 0% 78.81% 24ms 0.5% __fopen_internal (inline) 0 0% 78.81% 24ms 0.5% boost::numeric::ublas::c_vector::assign (inline) 24ms 0.5% 79.32% 24ms 0.5% boost::numeric::ublas::c_vector::operator() 24ms 0.5% 79.82% 24ms 0.5% std::_Rb_tree::_S_right (inline) 0 0% 79.82% 24ms 0.5% std::__basic_file::open 0 0% 79.82% 24ms 0.5% std::default_delete::operator() (inline) 0 0% 79.82% 24ms 0.5% std::unique_ptr::~unique_ptr (inline) 0 0% 79.82% 24ms 0.5% vtkDataArrayPrivate::DoComputeScalarRange 0 0% 79.82% 24ms 0.5% vtkXMLUnstructuredDataWriter::WriteHeader