File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3890ms, 78.95% of 4927ms total Dropped 745 nodes (cum <= 24.64ms) flat flat% sum% cum cum% 0 0% 0% 4706ms 95.51% __libc_start_call_main 0 0% 0% 4706ms 95.51% __libc_start_main_impl 0 0% 0% 4706ms 95.51% _start 0 0% 0% 4691ms 95.21% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4691ms 95.21% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4691ms 95.21% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4691ms 95.21% main 0 0% 0% 4649ms 94.36% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4649ms 94.36% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4649ms 94.36% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4638ms 94.13% AbstractCellBasedSimulation::Solve 0 0% 0% 4328ms 87.84% AbstractCellPopulation::WriteResultsToFiles 17ms 0.35% 0.35% 4088ms 82.97% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.35% 1999ms 40.57% VertexMeshWriter::WriteVtkUsingMesh 0 0% 0.35% 1729ms 35.09% VertexMeshWriter::MakeVtkMesh 1ms 0.02% 0.37% 1305ms 26.49% vtkPolygon::New 1ms 0.02% 0.39% 1303ms 26.45% vtkPolygon::vtkPolygon 8ms 0.16% 0.55% 953ms 19.34% vtkCell::vtkCell 0 0% 0.55% 824ms 16.72% vtkPoints::New 2ms 0.041% 0.59% 780ms 15.83% VertexMeshWriter::WriteFiles 5ms 0.1% 0.69% 775ms 15.73% vtkPoints::vtkPoints 52ms 1.06% 1.75% 750ms 15.22% std::ostream::_M_insert 3ms 0.061% 1.81% 750ms 15.22% std::ostream::operator<< (inline) 48ms 0.97% 2.78% 644ms 13.07% operator new 1ms 0.02% 2.80% 644ms 13.07% vtkLine::New 1ms 0.02% 2.82% 644ms 13.07% vtkQuad::New 0 0% 2.82% 642ms 13.03% vtkQuad::vtkQuad 17ms 0.35% 3.17% 624ms 12.66% vtkLine::vtkLine 27ms 0.55% 3.71% 615ms 12.48% std::num_put::_M_insert_float 1ms 0.02% 3.73% 615ms 12.48% vtkTriangle::New 4ms 0.081% 3.82% 609ms 12.36% vtkTriangle::vtkTriangle 172ms 3.49% 7.31% 607ms 12.32% __GI___libc_malloc 0 0% 7.31% 587ms 11.91% vtkStreamingDemandDrivenPipeline::Update 0 0% 7.31% 587ms 11.91% vtkXMLWriterBase::Write 0 0% 7.31% 584ms 11.85% vtkDemandDrivenPipeline::ProcessRequest 0 0% 7.31% 583ms 11.83% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 7.31% 582ms 11.81% vtkExecutive::CallAlgorithm 0 0% 7.31% 581ms 11.79% vtkCompositeDataPipeline::ExecuteData 0 0% 7.31% 581ms 11.79% vtkDemandDrivenPipeline::ExecuteData 0 0% 7.31% 581ms 11.79% vtkXMLUnstructuredDataWriter::ProcessRequest 158ms 3.21% 10.51% 529ms 10.74% __GI___libc_free 0 0% 10.51% 520ms 10.55% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 10.51% 520ms 10.55% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 38ms 0.77% 11.28% 509ms 10.33% vtkPoints::SetDataType 12ms 0.24% 11.53% 496ms 10.07% std::__cxx11::collate::do_transform 8ms 0.16% 11.69% 470ms 9.54% ___vsnprintf 0 0% 11.69% 462ms 9.38% __vsnprintf_internal (inline) 44ms 0.89% 12.58% 450ms 9.13% __printf_buffer 0 0% 12.58% 446ms 9.05% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 2ms 0.041% 12.62% 446ms 9.05% vtkXMLWriter::WriteBinaryData 0 0% 12.62% 439ms 8.91% vtkXMLWriter::WriteBinaryDataInternal 1ms 0.02% 12.64% 438ms 8.89% vtkXMLWriter::WriteBinaryDataBlock 0 0% 12.64% 381ms 7.73% vtkPolygon::~vtkPolygon 224ms 4.55% 17.19% 371ms 7.53% _int_free 1ms 0.02% 17.21% 368ms 7.47% __printf_fp_spec (inline) 15ms 0.3% 17.52% 367ms 7.45% __printf_fp_l_buffer 0 0% 17.52% 360ms 7.31% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 17.52% 358ms 7.27% VtkMeshWriter::WriteFiles 242ms 4.91% 22.43% 356ms 7.23% _int_malloc 172ms 3.49% 25.92% 335ms 6.80% __printf_fp_buffer_1 0 0% 25.92% 329ms 6.68% vtkXMLWriter::WritePointsAppendedData 6ms 0.12% 26.04% 305ms 6.19% vtkCell::~vtkCell 0 0% 26.04% 298ms 6.05% OnLatticeSimulation::UpdateCellLocationsAndTopology 4ms 0.081% 26.12% 298ms 6.05% PottsBasedCellPopulation::UpdateCellLocations 43ms 0.87% 26.99% 293ms 5.95% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 50ms 1.01% 28.01% 292ms 5.93% std::__new_allocator::allocate (inline) 0 0% 28.01% 288ms 5.85% std::allocator_traits::allocate (inline) 7ms 0.14% 28.15% 273ms 5.54% std::__new_allocator::deallocate (inline) 0 0% 28.15% 271ms 5.50% std::allocator_traits::deallocate (inline) 0 0% 28.15% 233ms 4.73% vtkXMLWriter::WriteCompressionBlock 5ms 0.1% 28.25% 221ms 4.49% vtkBase64OutputStream::Write 20ms 0.41% 28.66% 216ms 4.38% vtkBase64OutputStream::EncodeTriplet 0 0% 28.66% 212ms 4.30% compress2 0 0% 28.66% 212ms 4.30% vtkDataCompressor::Compress 0 0% 28.66% 212ms 4.30% vtkZLibDataCompressor::CompressBuffer 64ms 1.30% 29.96% 210ms 4.26% crc32 0 0% 29.96% 210ms 4.26% deflate 3ms 0.061% 30.02% 205ms 4.16% vtkPoints::~vtkPoints 0 0% 30.02% 192ms 3.90% tbb::detail::r1::parallel_pipeline 0 0% 30.02% 186ms 3.78% clone3 0 0% 30.02% 186ms 3.78% start_thread 0 0% 30.02% 185ms 3.75% tbb::detail::r1::reset 80ms 1.62% 31.64% 185ms 3.75% tbb::detail::r1::wait_bounded_queue_monitor 0 0% 31.64% 183ms 3.71% VertexMesh::~VertexMesh 15ms 0.3% 31.95% 183ms 3.71% std::_Rb_tree::_Rb_tree 0 0% 31.95% 183ms 3.71% std::set::set (inline) 54ms 1.10% 33.04% 180ms 3.65% std::ostream::write 3ms 0.061% 33.10% 178ms 3.61% vtkFloatArray::New 103ms 2.09% 35.19% 173ms 3.51% malloc_consolidate 1ms 0.02% 35.21% 170ms 3.45% vtkLine::GetParametricCenter 2ms 0.041% 35.25% 169ms 3.43% NodesOnlyMesh::ConstructNodesWithoutMesh 2ms 0.041% 35.30% 169ms 3.43% std::_Vector_base::_M_deallocate (inline) 6ms 0.12% 35.42% 167ms 3.39% vtkDataArray::CreateDataArray 1ms 0.02% 35.44% 166ms 3.37% vtkQuad::~vtkQuad 0 0% 35.44% 165ms 3.35% std::vector::~vector (inline) 1ms 0.02% 35.46% 163ms 3.31% NodeLocationWriter::VisitAnyPopulation 1ms 0.02% 35.48% 163ms 3.31% VertexMesh::VertexMesh 46ms 0.93% 36.41% 159ms 3.23% std::_Rb_tree::_M_erase 0 0% 36.41% 158ms 3.21% std::_Rb_tree::_M_create_node (inline) 2ms 0.041% 36.45% 157ms 3.19% vtkTriangle::~vtkTriangle 3ms 0.061% 36.51% 157ms 3.19% vtkTypeFloat64Array::~vtkTypeFloat64Array 2ms 0.041% 36.55% 156ms 3.17% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.02% 36.57% 154ms 3.13% vtkFloatArray::vtkFloatArray 5ms 0.1% 36.68% 154ms 3.13% vtkIdList::AllocateInternal 5ms 0.1% 36.78% 154ms 3.13% vtkTypeFloat64Array::New 0 0% 36.78% 153ms 3.11% std::_Rb_tree::_M_get_node (inline) 76ms 1.54% 38.32% 152ms 3.09% std::basic_filebuf::xsputn 14ms 0.28% 38.60% 152ms 3.09% std::vector::_M_default_append 0 0% 38.60% 151ms 3.06% VertexMesh::GenerateEdgesFromElements (inline) 6ms 0.12% 38.73% 149ms 3.02% MutableElement::BuildEdges 0 0% 38.73% 147ms 2.98% std::_Rb_tree::_Alloc_node::operator() (inline) 10ms 0.2% 38.93% 146ms 2.96% std::_Rb_tree::_M_copy (inline) 5ms 0.1% 39.03% 146ms 2.96% vtkDoubleArray::vtkDoubleArray 3ms 0.061% 39.09% 141ms 2.86% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 4ms 0.081% 39.17% 140ms 2.84% vtkFloatArray::~vtkFloatArray 131ms 2.66% 41.83% 137ms 2.78% [libz.so.1.3] 0 0% 41.83% 136ms 2.76% std::_Vector_base::~_Vector_base (inline) 0 0% 41.83% 135ms 2.74% std::_Vector_base::_M_allocate (inline) 0 0% 41.83% 131ms 2.66% EdgeHelper::~EdgeHelper (inline) 4ms 0.081% 41.91% 131ms 2.66% vtkTypeFloat64Array::vtkTypeFloat64Array 13ms 0.26% 42.18% 129ms 2.62% std::_Rb_tree::_M_clone_node (inline) 7ms 0.14% 42.32% 125ms 2.54% EdgeHelper::GetEdgeFromNodes 30ms 0.61% 42.93% 122ms 2.48% vtkObject::vtkObject 0 0% 42.93% 115ms 2.33% vtkXMLWriter::WritePointDataAppendedData 0 0% 42.93% 113ms 2.29% std::set::~set (inline) 50ms 1.01% 43.94% 113ms 2.29% vtkTypeFloat64Array::PrintSelf 47ms 0.95% 44.90% 112ms 2.27% std::__ostream_insert 0 0% 44.90% 108ms 2.19% std::_Rb_tree::_M_drop_node (inline) 106ms 2.15% 47.05% 106ms 2.15% __GI_sched_yield 106ms 2.15% 49.20% 106ms 2.15% __strcmp_avx2 0 0% 49.20% 106ms 2.15% vtkIdList::Allocate 0 0% 49.20% 105ms 2.13% CellPropertyCollection::GetPropertiesType (inline) 0 0% 49.20% 104ms 2.11% std::_Rb_tree::_M_put_node (inline) 0 0% 49.20% 104ms 2.11% std::operator<< (inline) 7ms 0.14% 49.34% 100ms 2.03% std::vector::push_back (inline) 72ms 1.46% 50.80% 100ms 2.03% vtkObjectBase::UnRegisterInternal 6ms 0.12% 50.92% 99ms 2.01% _int_free_maybe_consolidate 4ms 0.081% 51.00% 98ms 1.99% std::map::operator[] (partial-inline) 29ms 0.59% 51.59% 97ms 1.97% vtkObject::Modified 2ms 0.041% 51.63% 94ms 1.91% AbstractCellProperty::IsSubType (inline) 17ms 0.35% 51.98% 93ms 1.89% __dynamic_cast 8ms 0.16% 52.14% 92ms 1.87% vtkDoubleArray::~vtkDoubleArray 0 0% 52.14% 90ms 1.83% Cell::HasCellProperty (inline) 3ms 0.061% 52.20% 90ms 1.83% CellPropertyCollection::HasProperty 0 0% 52.20% 90ms 1.83% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 46ms 0.93% 53.14% 90ms 1.83% hack_digit 90ms 1.83% 54.96% 90ms 1.83% unlink_chunk 2ms 0.041% 55.00% 85ms 1.73% AbstractCellProperty::IsType (inline) 62ms 1.26% 56.26% 85ms 1.73% std::basic_streambuf::xsputn 13ms 0.26% 56.53% 77ms 1.56% vtkAOSDataArrayTemplate::DataElementChanged 25ms 0.51% 57.03% 76ms 1.54% std::_Rb_tree::_M_lower_bound (inline) 8ms 0.16% 57.20% 75ms 1.52% vtkIdList::New 0 0% 57.20% 73ms 1.48% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 10ms 0.2% 57.40% 70ms 1.42% AbstractCellPopulation::GetCellUsingLocationIndex 8ms 0.16% 57.56% 70ms 1.42% std::vector::_M_realloc_insert 13ms 0.26% 57.82% 68ms 1.38% AbstractCellProperty::IsSame 0 0% 57.82% 68ms 1.38% tcache_get (inline) 68ms 1.38% 59.20% 68ms 1.38% tcache_get_n (inline) 67ms 1.36% 60.56% 67ms 1.36% vtkTimeStamp::Modified 0 0% 60.56% 66ms 1.34% NodesOnlyMesh::SetUpBoxCollection 5ms 0.1% 60.67% 66ms 1.34% boost::numeric::ublas::c_vector::c_vector (partial-inline) 0 0% 60.67% 64ms 1.30% Cell::GetCellProliferativeType 15ms 0.3% 60.97% 63ms 1.28% std::num_put::_M_insert_int 0 0% 60.97% 60ms 1.22% std::_Rb_tree::lower_bound (inline) 0 0% 60.97% 60ms 1.22% std::map::lower_bound (inline) 1ms 0.02% 60.99% 59ms 1.20% boost::numeric::ublas::vector_assign (inline) 0 0% 60.99% 56ms 1.14% vtkDataArray::ComputeRange 0 0% 60.99% 55ms 1.12% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 0 0% 60.99% 55ms 1.12% NodesOnlyMesh::~NodesOnlyMesh 17ms 0.35% 61.34% 55ms 1.12% std::type_info::operator== (inline) 30ms 0.61% 61.94% 54ms 1.10% __cxxabiv1::__si_class_type_info::__do_dyncast 10ms 0.2% 62.15% 54ms 1.10% vtkSOADataArrayTemplate::FillTypedComponent 0 0% 62.15% 52ms 1.06% PottsMesh::GetMooreNeighbouringNodeIndices 1ms 0.02% 62.17% 52ms 1.06% VertexMesh::Clear 50ms 1.01% 63.18% 50ms 1.01% __memcpy_avx_unaligned_erms 7ms 0.14% 63.32% 50ms 1.01% vtkDataArray::vtkDataArray 1ms 0.02% 63.34% 48ms 0.97% std::__basic_file::xsputn_2 47ms 0.95% 64.30% 47ms 0.95% __GI___writev 2ms 0.041% 64.34% 47ms 0.95% std::_Rb_tree::_M_insert_unique 0 0% 64.34% 47ms 0.95% std::set::insert (inline) 46ms 0.93% 65.27% 46ms 0.93% [libvtkCommonCore-9.3.so.9.3] 7ms 0.14% 65.42% 45ms 0.91% VertexMeshWriter::GetNextNode 13ms 0.26% 65.68% 44ms 0.89% vtkIdList::~vtkIdList 27ms 0.55% 66.23% 43ms 0.87% std::_Hashtable::clear 0 0% 66.23% 43ms 0.87% std::map::~map (inline) 0 0% 66.23% 43ms 0.87% vtk::detail::smp::vtkSMPToolsImplForTBB 43ms 0.87% 67.10% 43ms 0.87% vtkObject::~vtkObject 13ms 0.26% 67.36% 42ms 0.85% boost::numeric::ublas::indexing_vector_assign 3ms 0.061% 67.42% 42ms 0.85% std::_Rb_tree::_M_insert_ (inline) 1ms 0.02% 67.44% 42ms 0.85% std::make_unique (inline) 41ms 0.83% 68.28% 42ms 0.85% vtkObjectBase::Delete 1ms 0.02% 68.30% 41ms 0.83% DistributedBoxCollection::IsOwned 7ms 0.14% 68.44% 41ms 0.83% vtkAbstractArray::vtkAbstractArray 21ms 0.43% 68.87% 40ms 0.81% DistributedBoxCollection::CalculateContainingBox (inline) 40ms 0.81% 69.68% 40ms 0.81% std::ostream::sentry::sentry 4ms 0.081% 69.76% 40ms 0.81% tbb::detail::r1::cancel_group_execution 5ms 0.1% 69.86% 39ms 0.79% vtkAOSDataArrayTemplate::InsertTuple 0 0% 69.86% 38ms 0.77% CxxTest::RealWorldDescription::setUp 2ms 0.041% 69.90% 38ms 0.77% DistributedBoxCollection::SetupLocalBoxesHalfOnly 0 0% 69.90% 38ms 0.77% PetscInitialize 0 0% 69.90% 38ms 0.77% PetscSetup::setUpWorld 0 0% 69.90% 38ms 0.77% PetscSetupUtils::CommonSetup 0 0% 69.90% 38ms 0.77% PetscSetupUtils::InitialisePetsc 1ms 0.02% 69.92% 38ms 0.77% std::basic_filebuf::_M_convert_to_external 0 0% 69.92% 38ms 0.77% std::basic_filebuf::overflow 0 0% 69.92% 37ms 0.75% DistributedBoxCollection::~DistributedBoxCollection 0 0% 69.92% 37ms 0.75% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 69.92% 37ms 0.75% PMPI_Init_thread 37ms 0.75% 70.67% 37ms 0.75% __GI___libc_write 0 0% 70.67% 37ms 0.75% ompi_mpi_init 0 0% 70.67% 37ms 0.75% std::_Destroy (inline) 0 0% 70.67% 37ms 0.75% std::_Destroy_aux::__destroy (inline) 0 0% 70.67% 37ms 0.75% std::__basic_file::xsputn 4ms 0.081% 70.75% 36ms 0.73% vtkAOSDataArrayTemplate::AllocateTuples 2ms 0.041% 70.79% 35ms 0.71% __find_specmb (inline) 0 0% 70.79% 35ms 0.71% _dl_init 0 0% 70.79% 35ms 0.71% _dl_start_user 0 0% 70.79% 35ms 0.71% call_init (inline) 0 0% 70.79% 34ms 0.69% CellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 70.79% 34ms 0.69% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.041% 70.83% 34ms 0.69% vtk::detail::smp::vtkSMPToolsImpl::For 1ms 0.02% 70.85% 33ms 0.67% Edge::Edge 33ms 0.67% 71.52% 33ms 0.67% [libstdc++.so.6.0.33] 1ms 0.02% 71.54% 32ms 0.65% 0 0% 71.54% 32ms 0.65% Edge::SetNodes (inline) 3ms 0.061% 71.61% 32ms 0.65% PottsMesh::GetVonNeumannNeighbouringNodeIndices 32ms 0.65% 72.25% 32ms 0.65% __strchrnul_avx2 2ms 0.041% 72.30% 32ms 0.65% std::less::operator() (inline) 7ms 0.14% 72.44% 32ms 0.65% vtkDataArrayPrivate::DoComputeVectorRange 7ms 0.14% 72.58% 32ms 0.65% vtkSOADataArrayTemplate::GetTupleIndexFromValueIndex 29ms 0.59% 73.17% 31ms 0.63% std::num_put::do_put 0 0% 73.17% 31ms 0.63% vtkDataArrayPrivate::DoComputeScalarRange 31ms 0.63% 73.80% 31ms 0.63% vtkObjectBase::~vtkObjectBase 30ms 0.61% 74.41% 30ms 0.61% [libchaste_cell_based.so] 14ms 0.28% 74.69% 30ms 0.61% _int_free_merge_chunk 2ms 0.041% 74.73% 30ms 0.61% boost::serialization::singleton::get_instance 30ms 0.61% 75.34% 30ms 0.61% std::operator< (inline) 5ms 0.1% 75.44% 30ms 0.61% vtkDataArray::~vtkDataArray 0 0% 75.44% 29ms 0.59% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 29ms 0.59% 76.03% 29ms 0.59% boost::numeric::ublas::c_vector::operator() 29ms 0.59% 76.62% 29ms 0.59% vtkObjectBase::vtkObjectBase 1ms 0.02% 76.64% 28ms 0.57% VtkMeshWriter::MakeVtkMesh 0 0% 76.64% 28ms 0.57% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 28ms 0.57% 77.21% 28ms 0.57% std::codecvt::do_always_noconv 7ms 0.14% 77.35% 27ms 0.55% std::__new_allocator::construct (inline) 0 0% 77.35% 27ms 0.55% std::allocator_traits::construct (inline) 0 0% 77.35% 27ms 0.55% std::default_delete::operator() (inline) 0 0% 77.35% 27ms 0.55% std::unique_ptr::~unique_ptr (inline) 0 0% 77.35% 27ms 0.55% std::vector::vector (inline) 0 0% 77.35% 27ms 0.55% vtkDoubleArray::New 1ms 0.02% 77.37% 26ms 0.53% Cell::GetMutationState 0 0% 77.37% 26ms 0.53% PottsBasedCellPopulation::AcceptCellWriter 26ms 0.53% 77.90% 26ms 0.53% __memset_avx2_unaligned_erms 0 0% 77.90% 26ms 0.53% orte_init 6ms 0.12% 78.02% 26ms 0.53% std::vector::emplace_back (inline) 26ms 0.53% 78.55% 26ms 0.53% tcache_put (inline) 20ms 0.41% 78.95% 26ms 0.53% vtkObject::ObjectFinalize 0 0% 78.95% 25ms 0.51% std::basic_filebuf::close