File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3941ms, 78.65% of 5011ms total Dropped 757 nodes (cum <= 25.05ms) flat flat% sum% cum cum% 0 0% 0% 4763ms 95.05% __libc_start_call_main 0 0% 0% 4763ms 95.05% __libc_start_main_impl 0 0% 0% 4763ms 95.05% _start 0 0% 0% 4746ms 94.71% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4746ms 94.71% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4746ms 94.71% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4746ms 94.71% main 0 0% 0% 4707ms 93.93% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4707ms 93.93% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4707ms 93.93% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4697ms 93.73% AbstractCellBasedSimulation::Solve 0 0% 0% 4369ms 87.19% AbstractCellPopulation::WriteResultsToFiles 14ms 0.28% 0.28% 4123ms 82.28% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.28% 1999ms 39.89% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.02% 0.3% 1727ms 34.46% VertexMeshWriter::MakeVtkMesh 0 0% 0.3% 1281ms 25.56% vtkPolygon::New 2ms 0.04% 0.34% 1279ms 25.52% vtkPolygon::vtkPolygon 7ms 0.14% 0.48% 915ms 18.26% vtkCell::vtkCell 3ms 0.06% 0.54% 790ms 15.77% vtkPoints::New 0 0% 0.54% 780ms 15.57% VertexMeshWriter::WriteFiles 3ms 0.06% 0.6% 749ms 14.95% std::ostream::operator<< (inline) 7ms 0.14% 0.74% 748ms 14.93% vtkPoints::vtkPoints 53ms 1.06% 1.80% 746ms 14.89% std::ostream::_M_insert 42ms 0.84% 2.63% 643ms 12.83% operator new 1ms 0.02% 2.65% 627ms 12.51% vtkQuad::New 6ms 0.12% 2.77% 620ms 12.37% vtkQuad::vtkQuad 198ms 3.95% 6.73% 608ms 12.13% __GI___libc_malloc 46ms 0.92% 7.64% 601ms 11.99% std::num_put::_M_insert_float 0 0% 7.64% 586ms 11.69% vtkStreamingDemandDrivenPipeline::Update 0 0% 7.64% 586ms 11.69% vtkXMLWriterBase::Write 0 0% 7.64% 583ms 11.63% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 7.64% 582ms 11.61% vtkDemandDrivenPipeline::ProcessRequest 1ms 0.02% 7.66% 582ms 11.61% vtkLine::New 0 0% 7.66% 581ms 11.59% vtkDemandDrivenPipeline::ExecuteData 0 0% 7.66% 580ms 11.57% vtkExecutive::CallAlgorithm 0 0% 7.66% 579ms 11.55% vtkCompositeDataPipeline::ExecuteData 0 0% 7.66% 579ms 11.55% vtkXMLUnstructuredDataWriter::ProcessRequest 11ms 0.22% 7.88% 568ms 11.34% vtkLine::vtkLine 0 0% 7.88% 568ms 11.34% vtkTriangle::New 4ms 0.08% 7.96% 559ms 11.16% vtkTriangle::vtkTriangle 151ms 3.01% 10.98% 531ms 10.60% __GI___libc_free 0 0% 10.98% 522ms 10.42% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 10.98% 522ms 10.42% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 36ms 0.72% 11.69% 464ms 9.26% vtkPoints::SetDataType 0 0% 11.69% 463ms 9.24% vtkXMLWriter::WriteBinaryData 14ms 0.28% 11.97% 458ms 9.14% std::__cxx11::collate::do_transform 1ms 0.02% 11.99% 457ms 9.12% vtkXMLWriter::WriteBinaryDataInternal 0 0% 11.99% 456ms 9.10% vtkXMLWriter::WriteBinaryDataBlock 0 0% 11.99% 449ms 8.96% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 3ms 0.06% 12.05% 432ms 8.62% ___vsnprintf 0 0% 12.05% 429ms 8.56% __vsnprintf_internal (inline) 57ms 1.14% 13.19% 419ms 8.36% __printf_buffer 1ms 0.02% 13.21% 384ms 7.66% vtkPolygon::~vtkPolygon 211ms 4.21% 17.42% 379ms 7.56% _int_free 0 0% 17.42% 369ms 7.36% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 17.42% 366ms 7.30% VtkMeshWriter::WriteFiles 238ms 4.75% 22.17% 359ms 7.16% _int_malloc 56ms 1.12% 23.29% 339ms 6.77% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 0 0% 23.29% 336ms 6.71% vtkXMLWriter::WritePointsAppendedData 2ms 0.04% 23.33% 331ms 6.61% __printf_fp_spec (inline) 12ms 0.24% 23.57% 329ms 6.57% __printf_fp_l_buffer 0 0% 23.57% 322ms 6.43% OnLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.06% 23.63% 322ms 6.43% PottsBasedCellPopulation::UpdateCellLocations 137ms 2.73% 26.36% 310ms 6.19% __printf_fp_buffer_1 7ms 0.14% 26.50% 300ms 5.99% vtkCell::~vtkCell 4ms 0.08% 26.58% 292ms 5.83% std::__new_allocator::deallocate (inline) 0 0% 26.58% 287ms 5.73% std::allocator_traits::deallocate (inline) 46ms 0.92% 27.50% 266ms 5.31% std::__new_allocator::allocate (inline) 0 0% 27.50% 264ms 5.27% std::allocator_traits::allocate (inline) 0 0% 27.50% 249ms 4.97% vtkXMLWriter::WriteCompressionBlock 0 0% 27.50% 237ms 4.73% vtkDataCompressor::Compress 1ms 0.02% 27.52% 234ms 4.67% vtkZLibDataCompressor::CompressBuffer 0 0% 27.52% 233ms 4.65% compress2 63ms 1.26% 28.78% 230ms 4.59% crc32 0 0% 28.78% 230ms 4.59% deflate 0 0% 28.78% 215ms 4.29% tbb::detail::r1::parallel_pipeline 9ms 0.18% 28.96% 214ms 4.27% vtkBase64OutputStream::Write 2ms 0.04% 29.00% 212ms 4.23% vtkFloatArray::New 0 0% 29.00% 209ms 4.17% clone3 0 0% 29.00% 209ms 4.17% start_thread 0 0% 29.00% 207ms 4.13% tbb::detail::r1::reset 71ms 1.42% 30.41% 207ms 4.13% tbb::detail::r1::wait_bounded_queue_monitor 24ms 0.48% 30.89% 205ms 4.09% vtkBase64OutputStream::EncodeTriplet 2ms 0.04% 30.93% 199ms 3.97% std::set::set (inline) 0 0% 30.93% 198ms 3.95% VertexMesh::~VertexMesh 20ms 0.4% 31.33% 197ms 3.93% std::_Rb_tree::_Rb_tree 0 0% 31.33% 194ms 3.87% vtkPoints::~vtkPoints 127ms 2.53% 33.87% 193ms 3.85% malloc_consolidate 3ms 0.06% 33.93% 187ms 3.73% vtkFloatArray::vtkFloatArray 3ms 0.06% 33.99% 176ms 3.51% vtkIdList::AllocateInternal 3ms 0.06% 34.05% 175ms 3.49% std::_Vector_base::_M_deallocate (inline) 49ms 0.98% 35.02% 169ms 3.37% std::_Rb_tree::_M_erase 2ms 0.04% 35.06% 169ms 3.37% vtkQuad::~vtkQuad 47ms 0.94% 36.00% 165ms 3.29% std::ostream::write 0 0% 36.00% 165ms 3.29% std::vector::~vector (inline) 2ms 0.04% 36.04% 162ms 3.23% NodesOnlyMesh::ConstructNodesWithoutMesh 2ms 0.04% 36.08% 162ms 3.23% std::_Rb_tree::~_Rb_tree (inline) 0 0% 36.08% 161ms 3.21% VertexMesh::VertexMesh 0 0% 36.08% 158ms 3.15% std::_Rb_tree::_M_create_node (inline) 1ms 0.02% 36.10% 157ms 3.13% NodeLocationWriter::VisitAnyPopulation 1ms 0.02% 36.12% 156ms 3.11% vtkTypeFloat64Array::~vtkTypeFloat64Array 148ms 2.95% 39.07% 154ms 3.07% [libz.so.1.3] 4ms 0.08% 39.15% 154ms 3.07% vtkDataArray::CreateDataArray 4ms 0.08% 39.23% 153ms 3.05% vtkDoubleArray::vtkDoubleArray 0 0% 39.23% 153ms 3.05% vtkTriangle::~vtkTriangle 2ms 0.04% 39.27% 152ms 3.03% vtkLine::GetParametricCenter 4ms 0.08% 39.35% 148ms 2.95% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 0 0% 39.35% 148ms 2.95% EdgeHelper::~EdgeHelper (inline) 0 0% 39.35% 146ms 2.91% std::_Rb_tree::_M_get_node (inline) 20ms 0.4% 39.75% 145ms 2.89% std::vector::_M_default_append 1ms 0.02% 39.77% 145ms 2.89% vtkTypeFloat64Array::New 13ms 0.26% 40.03% 144ms 2.87% std::_Rb_tree::_M_copy (inline) 0 0% 40.03% 142ms 2.83% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 40.03% 139ms 2.77% VertexMesh::GenerateEdgesFromElements (inline) 7ms 0.14% 40.17% 138ms 2.75% MutableElement::BuildEdges 2ms 0.04% 40.21% 137ms 2.73% std::_Vector_base::~_Vector_base (inline) 133ms 2.65% 42.87% 133ms 2.65% __GI_sched_yield 4ms 0.08% 42.95% 133ms 2.65% vtkTypeFloat64Array::vtkTypeFloat64Array 57ms 1.14% 44.08% 131ms 2.61% std::basic_filebuf::xsputn 24ms 0.48% 44.56% 128ms 2.55% vtkObject::vtkObject 16ms 0.32% 44.88% 125ms 2.49% std::_Rb_tree::_M_clone_node (inline) 121ms 2.41% 47.30% 121ms 2.41% __strcmp_avx2 1ms 0.02% 47.32% 119ms 2.37% std::_Vector_base::_M_allocate (inline) 1ms 0.02% 47.34% 118ms 2.35% EdgeHelper::GetEdgeFromNodes 4ms 0.08% 47.42% 118ms 2.35% vtkFloatArray::~vtkFloatArray 0 0% 47.42% 116ms 2.31% std::_Rb_tree::_M_drop_node (inline) 0 0% 47.42% 115ms 2.29% std::_Rb_tree::_M_put_node (inline) 0 0% 47.42% 113ms 2.26% CellPropertyCollection::GetPropertiesType (inline) 0 0% 47.42% 113ms 2.26% vtkIdList::Allocate 0 0% 47.42% 113ms 2.26% vtkXMLWriter::WritePointDataAppendedData 8ms 0.16% 47.58% 111ms 2.22% _int_free_maybe_consolidate 0 0% 47.58% 109ms 2.18% std::set::~set (inline) 2ms 0.04% 47.62% 99ms 1.98% AbstractCellProperty::IsSubType (inline) 1ms 0.02% 47.64% 99ms 1.98% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 2ms 0.04% 47.68% 99ms 1.98% std::operator<< (inline) 52ms 1.04% 48.71% 99ms 1.98% vtkTypeFloat64Array::PrintSelf 22ms 0.44% 49.15% 97ms 1.94% __dynamic_cast 53ms 1.06% 50.21% 97ms 1.94% hack_digit 42ms 0.84% 51.05% 97ms 1.94% std::__ostream_insert 0 0% 51.05% 93ms 1.86% Cell::HasCellProperty (inline) 5ms 0.1% 51.15% 93ms 1.86% CellPropertyCollection::HasProperty 1ms 0.02% 51.17% 92ms 1.84% AbstractCellProperty::IsType (inline) 61ms 1.22% 52.38% 91ms 1.82% vtkObjectBase::UnRegisterInternal 89ms 1.78% 54.16% 89ms 1.78% unlink_chunk 25ms 0.5% 54.66% 85ms 1.70% vtkObject::Modified 62ms 1.24% 55.90% 84ms 1.68% std::basic_streambuf::xsputn 1ms 0.02% 55.92% 81ms 1.62% std::vector::push_back (inline) 1ms 0.02% 55.94% 76ms 1.52% std::map::operator[] (partial-inline) 10ms 0.2% 56.14% 76ms 1.52% vtkAOSDataArrayTemplate::DataElementChanged 5ms 0.1% 56.24% 76ms 1.52% vtkIdList::New 1ms 0.02% 56.26% 74ms 1.48% vtkDoubleArray::~vtkDoubleArray 9ms 0.18% 56.44% 72ms 1.44% AbstractCellProperty::IsSame 1ms 0.02% 56.46% 70ms 1.40% Cell::GetCellProliferativeType 1ms 0.02% 56.48% 69ms 1.38% PottsMesh::GetMooreNeighbouringNodeIndices 2ms 0.04% 56.52% 69ms 1.38% std::vector::_M_realloc_insert 0 0% 56.52% 69ms 1.38% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 20ms 0.4% 56.91% 66ms 1.32% std::num_put::_M_insert_int 16ms 0.32% 57.23% 63ms 1.26% std::type_info::operator== (inline) 0 0% 57.23% 61ms 1.22% NodesOnlyMesh::~NodesOnlyMesh 7ms 0.14% 57.37% 61ms 1.22% boost::numeric::ublas::c_vector::c_vector (inline) 60ms 1.20% 58.57% 60ms 1.20% __memcpy_avx_unaligned_erms 6ms 0.12% 58.69% 60ms 1.20% vtkDataArray::vtkDataArray 0 0% 58.69% 58ms 1.16% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 0 0% 58.69% 57ms 1.14% std::_Rb_tree::_M_insert_unique 0 0% 58.69% 57ms 1.14% std::set::insert (inline) 57ms 1.14% 59.83% 57ms 1.14% vtkTimeStamp::Modified 0 0% 59.83% 55ms 1.10% boost::numeric::ublas::vector_assign (inline) 0 0% 59.83% 54ms 1.08% NodesOnlyMesh::SetUpBoxCollection 18ms 0.36% 60.19% 53ms 1.06% std::_Rb_tree::_M_lower_bound (inline) 0 0% 60.19% 53ms 1.06% std::map::~map (inline) 0 0% 60.19% 52ms 1.04% DistributedBoxCollection::IsOwned 36ms 0.72% 60.91% 52ms 1.04% std::_Hashtable::clear 11ms 0.22% 61.13% 52ms 1.04% vtkAbstractArray::vtkAbstractArray 33ms 0.66% 61.78% 50ms 1% DistributedBoxCollection::CalculateContainingBox (inline) 5ms 0.1% 61.88% 50ms 1% VertexMesh::Clear 50ms 1% 62.88% 50ms 1% [libvtkCommonCore-9.3.so.9.3] 0 0% 62.88% 50ms 1% tcache_get (inline) 50ms 1% 63.88% 50ms 1% tcache_get_n (inline) 0 0% 63.88% 49ms 0.98% vtkDataArray::ComputeRange 6ms 0.12% 64.00% 48ms 0.96% AbstractCellPopulation::GetCellUsingLocationIndex 21ms 0.42% 64.42% 48ms 0.96% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.02% 64.44% 47ms 0.94% std::__basic_file::xsputn_2 46ms 0.92% 65.36% 46ms 0.92% __GI___writev 46ms 0.92% 66.27% 46ms 0.92% std::ostream::sentry::sentry 3ms 0.06% 66.33% 44ms 0.88% vtkSOADataArrayTemplate::FillTypedComponent 4ms 0.08% 66.41% 43ms 0.86% VertexMeshWriter::GetNextNode 15ms 0.3% 66.71% 43ms 0.86% _int_free_merge_chunk 5ms 0.1% 66.81% 43ms 0.86% std::_Rb_tree::_M_insert_ (inline) 0 0% 66.81% 43ms 0.86% std::_Rb_tree::lower_bound (inline) 0 0% 66.81% 43ms 0.86% std::make_unique (inline) 0 0% 66.81% 43ms 0.86% std::map::lower_bound (inline) 8ms 0.16% 66.97% 43ms 0.86% vtkAOSDataArrayTemplate::InsertTuple 0 0% 66.97% 41ms 0.82% vtk::detail::smp::vtkSMPToolsImplForTBB 8ms 0.16% 67.13% 41ms 0.82% vtkDataArray::~vtkDataArray 3ms 0.06% 67.19% 41ms 0.82% vtkDoubleArray::New 41ms 0.82% 68.01% 41ms 0.82% vtkObjectBase::~vtkObjectBase 4ms 0.08% 68.09% 40ms 0.8% tbb::detail::r1::cancel_group_execution 39ms 0.78% 68.87% 40ms 0.8% vtkObjectBase::Delete 0 0% 68.87% 39ms 0.78% _dl_init 0 0% 68.87% 39ms 0.78% _dl_start_user 11ms 0.22% 69.09% 39ms 0.78% boost::numeric::ublas::indexing_vector_assign 0 0% 69.09% 39ms 0.78% call_init (inline) 38ms 0.76% 69.85% 38ms 0.76% Node::GetIndex 0 0% 69.85% 37ms 0.74% DistributedBoxCollection::~DistributedBoxCollection 0 0% 69.85% 37ms 0.74% NodesOnlyMesh::ClearBoxCollection (inline) 9ms 0.18% 70.03% 37ms 0.74% vtkIdList::~vtkIdList 0 0% 70.03% 35ms 0.7% VtkMeshWriter::MakeVtkMesh 4ms 0.08% 70.11% 35ms 0.7% vtkDataArrayPrivate::DoComputeVectorRange 35ms 0.7% 70.80% 35ms 0.7% vtkObject::~vtkObject 0 0% 70.80% 34ms 0.68% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 70.80% 34ms 0.68% CxxTest::RealWorldDescription::setUp 0 0% 70.80% 34ms 0.68% PetscInitialize 0 0% 70.80% 34ms 0.68% PetscSetup::setUpWorld 0 0% 70.80% 34ms 0.68% PetscSetupUtils::CommonSetup 0 0% 70.80% 34ms 0.68% PetscSetupUtils::InitialisePetsc 2ms 0.04% 70.84% 33ms 0.66% DistributedBoxCollection::SetupLocalBoxesHalfOnly 0 0% 70.84% 33ms 0.66% PMPI_Init_thread 5ms 0.1% 70.94% 33ms 0.66% VertexMeshWriter::GetNextElement 0 0% 70.94% 33ms 0.66% ompi_mpi_init 0 0% 70.94% 33ms 0.66% std::basic_filebuf::open 0 0% 70.94% 32ms 0.64% PottsBasedCellPopulation::AcceptCellWriter 5ms 0.1% 71.04% 32ms 0.64% boost::serialization::singleton::get_instance 0 0% 71.04% 32ms 0.64% std::_Destroy (inline) 0 0% 71.04% 32ms 0.64% std::_Destroy_aux::__destroy (inline) 0 0% 71.04% 32ms 0.64% std::_Rb_tree::_M_emplace_hint_unique 0 0% 71.04% 32ms 0.64% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 2ms 0.04% 71.08% 32ms 0.64% std::_Rb_tree_header::_Rb_tree_header (inline) 2ms 0.04% 71.12% 32ms 0.64% vtk::detail::smp::vtkSMPToolsImpl::For 32ms 0.64% 71.76% 32ms 0.64% vtkObjectBase::vtkObjectBase 1ms 0.02% 71.78% 31ms 0.62% PottsMesh::GetVonNeumannNeighbouringNodeIndices 0 0% 71.78% 31ms 0.62% _IO_new_fopen 0 0% 71.78% 31ms 0.62% __fopen_internal (inline) 0 0% 71.78% 30ms 0.6% Cell::GetMutationState 30ms 0.6% 72.38% 30ms 0.6% Node::GetNumContainingElements 30ms 0.6% 72.98% 30ms 0.6% __mpn_divrem 0 0% 72.98% 30ms 0.6% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 0 0% 72.98% 29ms 0.58% 0 0% 72.98% 29ms 0.58% CellProliferativeTypesWriter::GetCellDataForVtkOutput 4ms 0.08% 73.06% 29ms 0.58% Node::GetPoint 0 0% 73.06% 29ms 0.58% _IO_new_file_fopen 0 0% 73.06% 29ms 0.58% __GI__IO_file_open 29ms 0.58% 73.64% 29ms 0.58% __GI___libc_write 5ms 0.1% 73.74% 29ms 0.58% __find_specmb (inline) 29ms 0.58% 74.32% 29ms 0.58% std::_Rb_tree_header::_M_reset (inline) 0 0% 74.32% 29ms 0.58% std::__basic_file::open 0 0% 74.32% 29ms 0.58% std::__basic_file::xsputn 0 0% 74.32% 29ms 0.58% std::basic_filebuf::_M_convert_to_external 0 0% 74.32% 29ms 0.58% std::basic_filebuf::overflow 24ms 0.48% 74.80% 29ms 0.58% std::num_put::do_put 0 0% 74.80% 28ms 0.56% Edge::Edge 0 0% 74.80% 28ms 0.56% Edge::SetNodes (inline) 2ms 0.04% 74.84% 28ms 0.56% Node::ConstructNodeAttributes (inline) 0 0% 74.84% 28ms 0.56% Node::SetRadius 28ms 0.56% 75.39% 28ms 0.56% __libc_open64 1ms 0.02% 75.41% 28ms 0.56% vtkDataArrayPrivate::DoComputeScalarRange 9ms 0.18% 75.59% 28ms 0.56% vtkIdList::vtkIdList 27ms 0.54% 76.13% 27ms 0.54% [libchaste_cell_based.so] 27ms 0.54% 76.67% 27ms 0.54% boost::numeric::ublas::c_vector::operator() 27ms 0.54% 77.21% 27ms 0.54% std::codecvt::do_always_noconv 0 0% 77.21% 27ms 0.54% std::less::operator() (inline) 27ms 0.54% 77.75% 27ms 0.54% std::operator< (inline) 26ms 0.52% 78.27% 26ms 0.52% std::_Rb_tree_increment 0 0% 78.27% 26ms 0.52% std::basic_filebuf::close 0 0% 78.27% 26ms 0.52% std::vector::vector (partial-inline) 19ms 0.38% 78.65% 26ms 0.52% vtkObject::ObjectFinalize