File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3699ms, 79.81% of 4635ms total Dropped 740 nodes (cum <= 23.18ms) flat flat% sum% cum cum% 0 0% 0% 4399ms 94.91% __libc_start_call_main 0 0% 0% 4399ms 94.91% __libc_start_main_impl 0 0% 0% 4399ms 94.91% _start 0 0% 0% 4383ms 94.56% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4383ms 94.56% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4383ms 94.56% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4383ms 94.56% main 0 0% 0% 4347ms 93.79% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4347ms 93.79% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4347ms 93.79% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4345ms 93.74% AbstractCellBasedSimulation::Solve 0 0% 0% 4161ms 89.77% AbstractCellPopulation::WriteResultsToFiles 17ms 0.37% 0.37% 3924ms 84.66% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.37% 1978ms 42.68% VertexMeshWriter::WriteVtkUsingMesh 2ms 0.043% 0.41% 1703ms 36.74% VertexMeshWriter::MakeVtkMesh 1ms 0.022% 0.43% 1239ms 26.73% vtkPolygon::New 1ms 0.022% 0.45% 1236ms 26.67% vtkPolygon::vtkPolygon 11ms 0.24% 0.69% 858ms 18.51% vtkCell::vtkCell 3ms 0.065% 0.76% 761ms 16.42% VertexMeshWriter::WriteFiles 40ms 0.86% 1.62% 745ms 16.07% std::ostream::_M_insert 1ms 0.022% 1.64% 744ms 16.05% std::ostream::operator<< (inline) 2ms 0.043% 1.68% 737ms 15.90% vtkPoints::New 9ms 0.19% 1.88% 698ms 15.06% vtkPoints::vtkPoints 42ms 0.91% 2.78% 625ms 13.48% std::num_put::_M_insert_float 2ms 0.043% 2.83% 612ms 13.20% vtkQuad::New 4ms 0.086% 2.91% 604ms 13.03% vtkQuad::vtkQuad 33ms 0.71% 3.62% 579ms 12.49% operator new 0 0% 3.62% 579ms 12.49% vtkDemandDrivenPipeline::ProcessRequest 0 0% 3.62% 579ms 12.49% vtkStreamingDemandDrivenPipeline::Update 0 0% 3.62% 579ms 12.49% vtkXMLWriterBase::Write 0 0% 3.62% 574ms 12.38% vtkDemandDrivenPipeline::ExecuteData 0 0% 3.62% 574ms 12.38% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 3.62% 573ms 12.36% vtkCompositeDataPipeline::ExecuteData 0 0% 3.62% 573ms 12.36% vtkExecutive::CallAlgorithm 0 0% 3.62% 572ms 12.34% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 3.62% 566ms 12.21% vtkLine::New 177ms 3.82% 7.44% 559ms 12.06% __GI___libc_malloc 7ms 0.15% 7.59% 551ms 11.89% vtkLine::vtkLine 0 0% 7.59% 513ms 11.07% vtkTriangle::New 0 0% 7.59% 512ms 11.05% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 7.59% 512ms 11.05% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 7ms 0.15% 7.75% 507ms 10.94% vtkTriangle::vtkTriangle 10ms 0.22% 7.96% 487ms 10.51% std::__cxx11::collate::do_transform 1ms 0.022% 7.98% 465ms 10.03% vtkXMLWriter::WriteBinaryData 6ms 0.13% 8.11% 463ms 9.99% ___vsnprintf 25ms 0.54% 8.65% 461ms 9.95% vtkPoints::SetDataType 0 0% 8.65% 459ms 9.90% vtkXMLWriter::WriteBinaryDataBlock 0 0% 8.65% 459ms 9.90% vtkXMLWriter::WriteBinaryDataInternal 0 0% 8.65% 457ms 9.86% __vsnprintf_internal (inline) 141ms 3.04% 11.69% 454ms 9.80% __GI___libc_free 57ms 1.23% 12.92% 448ms 9.67% __printf_buffer 0 0% 12.92% 432ms 9.32% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 0 0% 12.92% 407ms 8.78% vtkPolygon::~vtkPolygon 22ms 0.47% 13.40% 351ms 7.57% __printf_fp_l_buffer 0 0% 13.40% 351ms 7.57% __printf_fp_spec (inline) 1ms 0.022% 13.42% 346ms 7.46% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 13.42% 345ms 7.44% VtkMeshWriter::WriteFiles 215ms 4.64% 18.06% 326ms 7.03% _int_malloc 6ms 0.13% 18.19% 323ms 6.97% vtkCell::~vtkCell 0 0% 18.19% 323ms 6.97% vtkXMLWriter::WritePointsAppendedData 161ms 3.47% 21.66% 318ms 6.86% __printf_fp_buffer_1 190ms 4.10% 25.76% 313ms 6.75% _int_free 48ms 1.04% 26.80% 286ms 6.17% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 0 0% 26.80% 246ms 5.31% vtkXMLWriter::WriteCompressionBlock 0 0% 26.80% 235ms 5.07% vtkDataCompressor::Compress 0 0% 26.80% 233ms 5.03% compress2 0 0% 26.80% 233ms 5.03% vtkZLibDataCompressor::CompressBuffer 1ms 0.022% 26.82% 230ms 4.96% deflate 68ms 1.47% 28.28% 229ms 4.94% crc32 2ms 0.043% 28.33% 215ms 4.64% vtkBase64OutputStream::Write 13ms 0.28% 28.61% 213ms 4.60% vtkBase64OutputStream::EncodeTriplet 0 0% 28.61% 207ms 4.47% tbb::detail::r1::parallel_pipeline 9ms 0.19% 28.80% 205ms 4.42% vtkPoints::~vtkPoints 0 0% 28.80% 200ms 4.31% clone3 0 0% 28.80% 200ms 4.31% start_thread 0 0% 28.80% 200ms 4.31% tbb::detail::r1::reset 69ms 1.49% 30.29% 199ms 4.29% tbb::detail::r1::wait_bounded_queue_monitor 2ms 0.043% 30.33% 194ms 4.19% std::__new_allocator::deallocate (inline) 0 0% 30.33% 188ms 4.06% std::allocator_traits::deallocate (inline) 1ms 0.022% 30.36% 184ms 3.97% vtkQuad::~vtkQuad 55ms 1.19% 31.54% 182ms 3.93% std::ostream::write 9ms 0.19% 31.74% 181ms 3.91% std::__new_allocator::allocate (inline) 0 0% 31.74% 180ms 3.88% std::allocator_traits::allocate (inline) 0 0% 31.74% 178ms 3.84% VertexMesh::~VertexMesh 8ms 0.17% 31.91% 178ms 3.84% vtkIdList::AllocateInternal 0 0% 31.91% 176ms 3.80% OnLatticeSimulation::UpdateCellLocationsAndTopology 21ms 0.45% 32.36% 176ms 3.80% PottsBasedCellPopulation::UpdateCellLocations 3ms 0.065% 32.43% 164ms 3.54% vtkLine::GetParametricCenter 106ms 2.29% 34.71% 163ms 3.52% malloc_consolidate 6ms 0.13% 34.84% 162ms 3.50% vtkDataArray::CreateDataArray 0 0% 34.84% 161ms 3.47% NodeLocationWriter::VisitAnyPopulation 5ms 0.11% 34.95% 161ms 3.47% vtkDoubleArray::vtkDoubleArray 1ms 0.022% 34.97% 160ms 3.45% std::vector::~vector (inline) 5ms 0.11% 35.08% 159ms 3.43% std::_Vector_base::_M_deallocate (inline) 12ms 0.26% 35.34% 158ms 3.41% vtkFloatArray::New 0 0% 35.34% 157ms 3.39% VertexMesh::VertexMesh 149ms 3.21% 38.55% 152ms 3.28% [libz.so.1.3] 3ms 0.065% 38.62% 151ms 3.26% vtkTriangle::~vtkTriangle 67ms 1.45% 40.06% 150ms 3.24% std::basic_filebuf::xsputn 10ms 0.22% 40.28% 148ms 3.19% MutableElement::BuildEdges 0 0% 40.28% 148ms 3.19% VertexMesh::GenerateEdgesFromElements (inline) 1ms 0.022% 40.30% 146ms 3.15% vtkTypeFloat64Array::New 1ms 0.022% 40.32% 144ms 3.11% vtkTypeFloat64Array::~vtkTypeFloat64Array 23ms 0.5% 40.82% 135ms 2.91% std::vector::_M_default_append 5ms 0.11% 40.93% 135ms 2.91% vtkFloatArray::~vtkFloatArray 0 0% 40.93% 135ms 2.91% vtkTypeFloat64Array::vtkTypeFloat64Array 1ms 0.022% 40.95% 131ms 2.83% NodesOnlyMesh::ConstructNodesWithoutMesh 5ms 0.11% 41.06% 130ms 2.80% vtkFloatArray::vtkFloatArray 128ms 2.76% 43.82% 128ms 2.76% __GI_sched_yield 0 0% 43.82% 125ms 2.70% std::_Vector_base::~_Vector_base (inline) 71ms 1.53% 45.35% 124ms 2.68% vtkTypeFloat64Array::PrintSelf 0 0% 45.35% 123ms 2.65% EdgeHelper::~EdgeHelper (inline) 123ms 2.65% 48.00% 123ms 2.65% __strcmp_avx2 1ms 0.022% 48.03% 122ms 2.63% EdgeHelper::GetEdgeFromNodes 1ms 0.022% 48.05% 120ms 2.59% std::_Vector_base::_M_allocate (inline) 3ms 0.065% 48.11% 118ms 2.55% vtkIdList::Allocate 14ms 0.3% 48.41% 116ms 2.50% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 31ms 0.67% 49.08% 108ms 2.33% vtkObject::vtkObject 1ms 0.022% 49.10% 108ms 2.33% vtkXMLWriter::WritePointDataAppendedData 0 0% 49.10% 106ms 2.29% CellPropertyCollection::GetPropertiesType (inline) 43ms 0.93% 50.03% 103ms 2.22% std::__ostream_insert 5ms 0.11% 50.14% 101ms 2.18% std::operator<< (inline) 17ms 0.37% 50.51% 97ms 2.09% vtkAOSDataArrayTemplate::DataElementChanged 1ms 0.022% 50.53% 94ms 2.03% AbstractCellProperty::IsSubType (inline) 0 0% 50.53% 94ms 2.03% Cell::HasCellProperty (inline) 1ms 0.022% 50.55% 94ms 2.03% CellPropertyCollection::HasProperty 1ms 0.022% 50.57% 93ms 2.01% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 22ms 0.47% 51.05% 93ms 2.01% __dynamic_cast 75ms 1.62% 52.66% 93ms 2.01% std::basic_streambuf::xsputn 0 0% 52.66% 90ms 1.94% AbstractCellProperty::IsType (inline) 1ms 0.022% 52.69% 89ms 1.92% std::map::operator[] (partial-inline) 53ms 1.14% 53.83% 86ms 1.86% hack_digit 5ms 0.11% 53.94% 86ms 1.86% std::_Rb_tree::~_Rb_tree (inline) 64ms 1.38% 55.32% 86ms 1.86% vtkObjectBase::UnRegisterInternal 4ms 0.086% 55.40% 85ms 1.83% _int_free_maybe_consolidate 2ms 0.043% 55.45% 83ms 1.79% std::vector::push_back (inline) 83ms 1.79% 57.24% 83ms 1.79% unlink_chunk 40ms 0.86% 58.10% 81ms 1.75% std::_Rb_tree::_M_erase 1ms 0.022% 58.12% 80ms 1.73% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 19ms 0.41% 58.53% 73ms 1.57% std::_Rb_tree::_M_lower_bound (inline) 5ms 0.11% 58.64% 73ms 1.57% vtkDoubleArray::~vtkDoubleArray 5ms 0.11% 58.75% 71ms 1.53% boost::numeric::ublas::c_vector::c_vector (partial-inline) 19ms 0.41% 59.16% 71ms 1.53% vtkObject::Modified 2ms 0.043% 59.20% 68ms 1.47% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 59.20% 66ms 1.42% Cell::GetCellProliferativeType 0 0% 59.20% 66ms 1.42% boost::numeric::ublas::vector_assign (inline) 7ms 0.15% 59.35% 66ms 1.42% vtkDataArray::vtkDataArray 0 0% 59.35% 64ms 1.38% std::_Rb_tree::_M_create_node (inline) 5ms 0.11% 59.46% 64ms 1.38% std::vector::_M_realloc_insert 3ms 0.065% 59.53% 64ms 1.38% vtkIdList::New 8ms 0.17% 59.70% 63ms 1.36% AbstractCellProperty::IsSame 0 0% 59.70% 61ms 1.32% std::_Rb_tree::_M_get_node (inline) 0 0% 59.70% 56ms 1.21% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 0 0% 59.70% 56ms 1.21% std::_Rb_tree::lower_bound (inline) 0 0% 59.70% 56ms 1.21% std::map::lower_bound (inline) 0 0% 59.70% 55ms 1.19% NodesOnlyMesh::SetUpBoxCollection 0 0% 59.70% 55ms 1.19% VertexMesh::Clear 55ms 1.19% 60.88% 55ms 1.19% [libvtkCommonCore-9.3.so.9.3] 55ms 1.19% 62.07% 55ms 1.19% std::ostream::sentry::sentry 14ms 0.3% 62.37% 55ms 1.19% std::type_info::operator== (inline) 0 0% 62.37% 55ms 1.19% tcache_get (inline) 55ms 1.19% 63.56% 55ms 1.19% tcache_get_n (inline) 12ms 0.26% 63.82% 55ms 1.19% vtkAbstractArray::vtkAbstractArray 53ms 1.14% 64.96% 53ms 1.14% __memcpy_avx_unaligned_erms 0 0% 64.96% 52ms 1.12% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 64.96% 52ms 1.12% std::set::~set (inline) 52ms 1.12% 66.08% 52ms 1.12% vtkTimeStamp::Modified 16ms 0.35% 66.43% 50ms 1.08% boost::numeric::ublas::indexing_vector_assign 1ms 0.022% 66.45% 50ms 1.08% std::_Rb_tree::_Rb_tree 8ms 0.17% 66.62% 50ms 1.08% std::num_put::_M_insert_int 0 0% 66.62% 50ms 1.08% std::set::set (inline) 46ms 0.99% 67.62% 47ms 1.01% vtkObjectBase::Delete 25ms 0.54% 68.16% 46ms 0.99% std::_Hashtable::clear 1ms 0.022% 68.18% 46ms 0.99% std::__basic_file::xsputn_2 8ms 0.17% 68.35% 46ms 0.99% vtkSOADataArrayTemplate::FillTypedComponent 45ms 0.97% 69.32% 45ms 0.97% __GI___writev 0 0% 69.32% 44ms 0.95% NodesOnlyMesh::~NodesOnlyMesh 0 0% 69.32% 44ms 0.95% std::_Rb_tree::_M_insert_unique 0 0% 69.32% 44ms 0.95% std::set::insert (inline) 8ms 0.17% 69.49% 44ms 0.95% vtkIdList::~vtkIdList 16ms 0.35% 69.84% 43ms 0.93% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 69.84% 41ms 0.88% std::_Destroy (inline) 0 0% 69.84% 41ms 0.88% std::_Destroy_aux::__destroy (inline) 40ms 0.86% 70.70% 41ms 0.88% vtkObject::~vtkObject 0 0% 70.70% 40ms 0.86% std::_Rb_tree::_M_drop_node (inline) 8ms 0.17% 70.87% 38ms 0.82% VertexMeshWriter::GetNextNode 5ms 0.11% 70.98% 38ms 0.82% vtkDataArray::~vtkDataArray 37ms 0.8% 71.78% 37ms 0.8% std::codecvt::do_always_noconv 0 0% 71.78% 37ms 0.8% std::less::operator() (inline) 37ms 0.8% 72.58% 37ms 0.8% std::operator< (inline) 37ms 0.8% 73.38% 37ms 0.8% vtkObjectBase::~vtkObjectBase 5ms 0.11% 73.48% 36ms 0.78% __find_specmb (inline) 0 0% 73.48% 36ms 0.78% _dl_init 0 0% 73.48% 36ms 0.78% _dl_start_user 0 0% 73.48% 36ms 0.78% call_init (inline) 7ms 0.15% 73.64% 36ms 0.78% std::_Rb_tree::_M_insert_ (inline) 3ms 0.065% 73.70% 36ms 0.78% vtkDoubleArray::New 8ms 0.17% 73.87% 35ms 0.76% std::_Rb_tree::_M_copy (inline) 1ms 0.022% 73.89% 35ms 0.76% std::unique_ptr::~unique_ptr (inline) 1ms 0.022% 73.92% 34ms 0.73% boost::serialization::singleton::get_instance 0 0% 73.92% 34ms 0.73% std::_Rb_tree::_M_put_node (inline) 0 0% 73.92% 34ms 0.73% std::map::~map (inline) 0 0% 73.92% 33ms 0.71% DistributedBoxCollection::~DistributedBoxCollection 0 0% 73.92% 33ms 0.71% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 73.92% 33ms 0.71% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 7ms 0.15% 74.07% 33ms 0.71% vtkAOSDataArrayTemplate::InsertTuple 0 0% 74.07% 33ms 0.71% vtkDataArray::ComputeRange 0 0% 74.07% 32ms 0.69% CxxTest::RealWorldDescription::setUp 0 0% 74.07% 32ms 0.69% PMPI_Init_thread 0 0% 74.07% 32ms 0.69% PetscInitialize 0 0% 74.07% 32ms 0.69% PetscSetup::setUpWorld 0 0% 74.07% 32ms 0.69% PetscSetupUtils::CommonSetup 0 0% 74.07% 32ms 0.69% PetscSetupUtils::InitialisePetsc 0 0% 74.07% 32ms 0.69% ompi_mpi_init 0 0% 74.07% 32ms 0.69% std::_Rb_tree::_M_emplace_hint_unique (inline) 6ms 0.13% 74.20% 32ms 0.69% tbb::detail::r1::cancel_group_execution 0 0% 74.20% 32ms 0.69% vtk::detail::smp::vtkSMPToolsImplForTBB 31ms 0.67% 74.87% 31ms 0.67% __strchrnul_avx2 1ms 0.022% 74.89% 31ms 0.67% std::default_delete::operator() (inline) 0 0% 74.89% 30ms 0.65% std::make_unique (inline) 30ms 0.65% 75.53% 30ms 0.65% vtkObjectBase::vtkObjectBase 2ms 0.043% 75.58% 29ms 0.63% 0 0% 75.58% 29ms 0.63% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 75.58% 29ms 0.63% CellProliferativeTypesWriter::GetCellDataForVtkOutput 1ms 0.022% 75.60% 29ms 0.63% DistributedBoxCollection::SetupLocalBoxesHalfOnly 0 0% 75.60% 29ms 0.63% Node::ConstructNodeAttributes (inline) 0 0% 75.60% 29ms 0.63% Node::SetRadius 29ms 0.63% 76.22% 29ms 0.63% __GI___libc_write 0 0% 76.22% 29ms 0.63% boost::numeric::ublas::c_vector::assign (inline) 0 0% 76.22% 29ms 0.63% std::__basic_file::xsputn 0 0% 76.22% 29ms 0.63% std::basic_filebuf::_M_convert_to_external 0 0% 76.22% 29ms 0.63% std::basic_filebuf::overflow 0 0% 76.22% 28ms 0.6% Cell::GetCellId 1ms 0.022% 76.25% 28ms 0.6% DistributedBoxCollection::IsOwned 0 0% 76.25% 28ms 0.6% Edge::Edge 1ms 0.022% 76.27% 28ms 0.6% VertexElement::~VertexElement 4ms 0.086% 76.35% 28ms 0.6% vtkAOSDataArrayTemplate::AllocateTuples 11ms 0.24% 76.59% 27ms 0.58% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 76.59% 27ms 0.58% Edge::SetNodes (inline) 0 0% 76.59% 27ms 0.58% OutputFileHandler::OpenOutputFile 0 0% 76.59% 27ms 0.58% PottsBasedCellPopulation::AcceptCellWriter 11ms 0.24% 76.83% 27ms 0.58% _int_free_merge_chunk 27ms 0.58% 77.41% 27ms 0.58% boost::numeric::ublas::c_vector::operator() 2ms 0.043% 77.45% 27ms 0.58% std::_Rb_tree::_M_clone_node (inline) 26ms 0.56% 78.02% 26ms 0.56% [libchaste_cell_based.so] 24ms 0.52% 78.53% 26ms 0.56% std::num_put::do_put 0 0% 78.53% 25ms 0.54% CellIdWriter::GetCellDataForVtkOutput 2ms 0.043% 78.58% 25ms 0.54% boost::serialization::void_cast_detail::void_caster::recursive_register 0 0% 78.58% 25ms 0.54% boost::serialization::void_cast_detail::void_caster_primitive::void_caster_primitive (inline) 3ms 0.065% 78.64% 25ms 0.54% vtkDataArrayPrivate::DoComputeVectorRange 25ms 0.54% 79.18% 25ms 0.54% vtkObjectBase::UnRegister 0 0% 79.18% 24ms 0.52% Cell::GetMutationState 1ms 0.022% 79.20% 24ms 0.52% VtkMeshWriter::MakeVtkMesh 1ms 0.022% 79.22% 24ms 0.52% _IO_new_file_fopen 0 0% 79.22% 24ms 0.52% _IO_new_fopen 0 0% 79.22% 24ms 0.52% __fopen_internal (inline) 24ms 0.52% 79.74% 24ms 0.52% __memset_avx2_unaligned_erms 0 0% 79.74% 24ms 0.52% std::basic_filebuf::open 3ms 0.065% 79.81% 24ms 0.52% vtkSOADataArrayTemplate::GetTupleIndexFromValueIndex