File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3747ms, 79.96% of 4686ms total Dropped 698 nodes (cum <= 23.43ms) flat flat% sum% cum cum% 0 0% 0% 4497ms 95.97% __libc_start_call_main 0 0% 0% 4497ms 95.97% __libc_start_main_impl 0 0% 0% 4497ms 95.97% _start 0 0% 0% 4479ms 95.58% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4479ms 95.58% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4479ms 95.58% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4479ms 95.58% main 0 0% 0% 4441ms 94.77% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4441ms 94.77% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4441ms 94.77% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4430ms 94.54% AbstractCellBasedSimulation::Solve 0 0% 0% 4122ms 87.96% AbstractCellPopulation::WriteResultsToFiles 22ms 0.47% 0.47% 3913ms 83.50% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.47% 1985ms 42.36% VertexMeshWriter::WriteVtkUsingMesh 0 0% 0.47% 1701ms 36.30% VertexMeshWriter::MakeVtkMesh 0 0% 0.47% 1232ms 26.29% vtkPolygon::New 3ms 0.064% 0.53% 1231ms 26.27% vtkPolygon::vtkPolygon 6ms 0.13% 0.66% 859ms 18.33% vtkCell::vtkCell 4ms 0.085% 0.75% 742ms 15.83% vtkPoints::New 10ms 0.21% 0.96% 692ms 14.77% vtkPoints::vtkPoints 2ms 0.043% 1.00% 659ms 14.06% VertexMeshWriter::WriteFiles 0 0% 1.00% 630ms 13.44% std::ostream::operator<< (inline) 43ms 0.92% 1.92% 627ms 13.38% operator new 53ms 1.13% 3.05% 625ms 13.34% std::ostream::_M_insert 191ms 4.08% 7.13% 597ms 12.74% __GI___libc_malloc 0 0% 7.13% 573ms 12.23% vtkStreamingDemandDrivenPipeline::Update 0 0% 7.13% 573ms 12.23% vtkXMLWriterBase::Write 0 0% 7.13% 570ms 12.16% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 7.13% 569ms 12.14% vtkExecutive::CallAlgorithm 0 0% 7.13% 568ms 12.12% vtkDemandDrivenPipeline::ProcessRequest 0 0% 7.13% 566ms 12.08% vtkCompositeDataPipeline::ExecuteData 0 0% 7.13% 566ms 12.08% vtkDemandDrivenPipeline::ExecuteData 0 0% 7.13% 566ms 12.08% vtkXMLUnstructuredDataWriter::ProcessRequest 2ms 0.043% 7.17% 549ms 11.72% vtkLine::New 17ms 0.36% 7.53% 532ms 11.35% vtkLine::vtkLine 1ms 0.021% 7.55% 530ms 11.31% vtkQuad::New 0 0% 7.55% 527ms 11.25% vtkTriangle::New 1ms 0.021% 7.58% 523ms 11.16% vtkQuad::vtkQuad 9ms 0.19% 7.77% 519ms 11.08% vtkTriangle::vtkTriangle 49ms 1.05% 8.81% 515ms 10.99% std::num_put::_M_insert_float 0 0% 8.81% 513ms 10.95% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 8.81% 513ms 10.95% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 102ms 2.18% 10.99% 471ms 10.05% __GI___libc_free 0 0% 10.99% 460ms 9.82% vtkXMLWriter::WriteBinaryData 1ms 0.021% 11.01% 456ms 9.73% vtkXMLWriter::WriteBinaryDataBlock 0 0% 11.01% 456ms 9.73% vtkXMLWriter::WriteBinaryDataInternal 33ms 0.7% 11.72% 432ms 9.22% vtkPoints::SetDataType 0 0% 11.72% 430ms 9.18% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 1ms 0.021% 11.74% 412ms 8.79% vtkPolygon::~vtkPolygon 9ms 0.19% 11.93% 406ms 8.66% std::__cxx11::collate::do_transform 2ms 0.043% 11.97% 374ms 7.98% ___vsnprintf 2ms 0.043% 12.01% 372ms 7.94% __vsnprintf_internal (inline) 219ms 4.67% 16.69% 368ms 7.85% _int_free 63ms 1.34% 18.03% 365ms 7.79% __printf_buffer 210ms 4.48% 22.51% 333ms 7.11% _int_malloc 0 0% 22.51% 332ms 7.08% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 22.51% 329ms 7.02% VtkMeshWriter::WriteFiles 0 0% 22.51% 325ms 6.94% vtkXMLWriter::WritePointsAppendedData 6ms 0.13% 22.64% 319ms 6.81% vtkCell::~vtkCell 0 0% 22.64% 301ms 6.42% OnLatticeSimulation::UpdateCellLocationsAndTopology 6ms 0.13% 22.77% 301ms 6.42% PottsBasedCellPopulation::UpdateCellLocations 42ms 0.9% 23.67% 291ms 6.21% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 10ms 0.21% 23.88% 274ms 5.85% __printf_fp_l_buffer 0 0% 23.88% 274ms 5.85% __printf_fp_spec (inline) 40ms 0.85% 24.73% 269ms 5.74% std::__new_allocator::allocate (inline) 6ms 0.13% 24.86% 269ms 5.74% std::__new_allocator::deallocate (inline) 0 0% 24.86% 268ms 5.72% std::allocator_traits::allocate (inline) 0 0% 24.86% 268ms 5.72% std::allocator_traits::deallocate (inline) 123ms 2.62% 27.49% 252ms 5.38% __printf_fp_buffer_1 6ms 0.13% 27.61% 239ms 5.10% vtkBase64OutputStream::Write 13ms 0.28% 27.89% 227ms 4.84% vtkBase64OutputStream::EncodeTriplet 0 0% 27.89% 222ms 4.74% vtkXMLWriter::WriteCompressionBlock 5ms 0.11% 28.00% 217ms 4.63% vtkPoints::~vtkPoints 1ms 0.021% 28.02% 210ms 4.48% compress2 0 0% 28.02% 210ms 4.48% vtkDataCompressor::Compress 0 0% 28.02% 210ms 4.48% vtkZLibDataCompressor::CompressBuffer 46ms 0.98% 29.00% 208ms 4.44% crc32 0 0% 29.00% 208ms 4.44% deflate 16ms 0.34% 29.34% 204ms 4.35% std::_Rb_tree::_Rb_tree 0 0% 29.34% 204ms 4.35% std::set::set (inline) 2ms 0.043% 29.39% 203ms 4.33% vtkQuad::~vtkQuad 48ms 1.02% 30.41% 201ms 4.29% std::ostream::write 132ms 2.82% 33.23% 197ms 4.20% malloc_consolidate 11ms 0.23% 33.46% 180ms 3.84% vtkFloatArray::New 2ms 0.043% 33.50% 176ms 3.76% vtkLine::GetParametricCenter 2ms 0.043% 33.55% 169ms 3.61% NodesOnlyMesh::ConstructNodesWithoutMesh 0 0% 33.55% 169ms 3.61% std::_Rb_tree::_M_create_node (inline) 0 0% 33.55% 168ms 3.59% VertexMesh::~VertexMesh 5ms 0.11% 33.65% 168ms 3.59% vtkDataArray::CreateDataArray 5ms 0.11% 33.76% 168ms 3.59% vtkIdList::AllocateInternal 39ms 0.83% 34.59% 167ms 3.56% std::_Rb_tree::_M_erase 0 0% 34.59% 165ms 3.52% std::vector::~vector (inline) 5ms 0.11% 34.70% 165ms 3.52% vtkTriangle::~vtkTriangle 2ms 0.043% 34.74% 162ms 3.46% std::_Rb_tree::~_Rb_tree (inline) 0 0% 34.74% 161ms 3.44% tbb::detail::r1::parallel_pipeline 4ms 0.085% 34.83% 160ms 3.41% vtkTypeFloat64Array::~vtkTypeFloat64Array 0 0% 34.83% 159ms 3.39% std::_Rb_tree::_M_get_node (inline) 8ms 0.17% 35.00% 158ms 3.37% vtkTypeFloat64Array::New 156ms 3.33% 38.33% 157ms 3.35% [libz.so.1.3] 18ms 0.38% 38.71% 157ms 3.35% std::_Rb_tree::_M_copy (inline) 6ms 0.13% 38.84% 155ms 3.31% std::_Vector_base::_M_deallocate (inline) 0 0% 38.84% 154ms 3.29% clone3 0 0% 38.84% 154ms 3.29% start_thread 0 0% 38.84% 154ms 3.29% std::_Rb_tree::_Alloc_node::operator() (inline) 5ms 0.11% 38.95% 150ms 3.20% vtkDoubleArray::vtkDoubleArray 3ms 0.064% 39.01% 150ms 3.20% vtkFloatArray::vtkFloatArray 66ms 1.41% 40.42% 149ms 3.18% std::basic_filebuf::xsputn 2ms 0.043% 40.46% 147ms 3.14% VertexMesh::VertexMesh 1ms 0.021% 40.48% 139ms 2.97% tbb::detail::r1::reset 1ms 0.021% 40.50% 137ms 2.92% NodeLocationWriter::VisitAnyPopulation 12ms 0.26% 40.76% 137ms 2.92% std::vector::_M_default_append 6ms 0.13% 40.89% 135ms 2.88% MutableElement::BuildEdges 0 0% 40.89% 135ms 2.88% VertexMesh::GenerateEdgesFromElements (inline) 2ms 0.043% 40.93% 131ms 2.80% vtkTypeFloat64Array::vtkTypeFloat64Array 1ms 0.021% 40.95% 130ms 2.77% std::_Vector_base::~_Vector_base (inline) 64ms 1.37% 42.32% 130ms 2.77% tbb::detail::r1::wait_bounded_queue_monitor 34ms 0.73% 43.04% 130ms 2.77% vtkObject::vtkObject 14ms 0.3% 43.34% 128ms 2.73% std::_Rb_tree::_M_clone_node (inline) 1ms 0.021% 43.36% 128ms 2.73% vtkIdList::Allocate 1ms 0.021% 43.38% 127ms 2.71% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 0 0% 43.38% 127ms 2.71% std::set::~set (inline) 0 0% 43.38% 124ms 2.65% std::_Rb_tree::_M_drop_node (inline) 0 0% 43.38% 122ms 2.60% EdgeHelper::~EdgeHelper (inline) 0 0% 43.38% 119ms 2.54% std::_Rb_tree::_M_put_node (inline) 2ms 0.043% 43.43% 116ms 2.48% EdgeHelper::GetEdgeFromNodes 115ms 2.45% 45.88% 115ms 2.45% __strcmp_avx2 1ms 0.021% 45.90% 110ms 2.35% CellPropertyCollection::GetPropertiesType (inline) 0 0% 45.90% 108ms 2.30% std::_Vector_base::_M_allocate (inline) 53ms 1.13% 47.03% 106ms 2.26% vtkTypeFloat64Array::PrintSelf 0 0% 47.03% 102ms 2.18% vtkXMLWriter::WritePointDataAppendedData 1ms 0.021% 47.06% 98ms 2.09% AbstractCellProperty::IsSubType (inline) 5ms 0.11% 47.16% 98ms 2.09% _int_free_maybe_consolidate 0 0% 47.16% 98ms 2.09% vtkFloatArray::~vtkFloatArray 22ms 0.47% 47.63% 97ms 2.07% __dynamic_cast 2ms 0.043% 47.67% 93ms 1.98% AbstractCellProperty::IsType (inline) 0 0% 47.67% 90ms 1.92% Cell::HasCellProperty (inline) 1ms 0.021% 47.70% 90ms 1.92% CellPropertyCollection::HasProperty 1ms 0.021% 47.72% 89ms 1.90% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 5ms 0.11% 47.82% 89ms 1.90% std::map::operator[] (partial-inline) 27ms 0.58% 48.40% 87ms 1.86% std::__ostream_insert 2ms 0.043% 48.44% 87ms 1.86% std::operator<< (inline) 44ms 0.94% 49.38% 87ms 1.86% vtkObjectBase::UnRegisterInternal 86ms 1.84% 51.22% 86ms 1.84% unlink_chunk 0 0% 51.22% 82ms 1.75% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 41ms 0.87% 52.09% 79ms 1.69% hack_digit 0 0% 52.09% 76ms 1.62% PottsMesh::GetMooreNeighbouringNodeIndices 21ms 0.45% 52.54% 76ms 1.62% vtkObject::Modified 20ms 0.43% 52.97% 75ms 1.60% std::_Rb_tree::_M_lower_bound (inline) 42ms 0.9% 53.86% 73ms 1.56% std::basic_streambuf::xsputn 2ms 0.043% 53.91% 71ms 1.52% Cell::GetCellProliferativeType 0 0% 53.91% 70ms 1.49% tcache_get (inline) 70ms 1.49% 55.40% 70ms 1.49% tcache_get_n (inline) 1ms 0.021% 55.42% 69ms 1.47% std::vector::push_back (inline) 5ms 0.11% 55.53% 68ms 1.45% AbstractCellProperty::IsSame 2ms 0.043% 55.57% 67ms 1.43% vtkIdList::New 0 0% 55.57% 66ms 1.41% NodesOnlyMesh::SetUpBoxCollection 66ms 1.41% 56.98% 66ms 1.41% __GI_sched_yield 10ms 0.21% 57.19% 66ms 1.41% vtkAOSDataArrayTemplate::DataElementChanged 2ms 0.043% 57.23% 64ms 1.37% AbstractCellPopulation::GetCellUsingLocationIndex 12ms 0.26% 57.49% 63ms 1.34% std::type_info::operator== (inline) 5ms 0.11% 57.60% 63ms 1.34% vtkDoubleArray::~vtkDoubleArray 6ms 0.13% 57.73% 61ms 1.30% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.021% 57.75% 61ms 1.30% vtkDataArray::vtkDataArray 0 0% 57.75% 60ms 1.28% NodesOnlyMesh::~NodesOnlyMesh 2ms 0.043% 57.79% 59ms 1.26% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 22ms 0.47% 58.26% 59ms 1.26% vtkAbstractArray::vtkAbstractArray 0 0% 58.26% 58ms 1.24% std::set::insert (inline) 26ms 0.55% 58.81% 57ms 1.22% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.043% 58.86% 57ms 1.22% std::_Rb_tree::_M_insert_unique 0 0% 58.86% 57ms 1.22% std::_Rb_tree::lower_bound (inline) 0 0% 58.86% 57ms 1.22% std::map::lower_bound (inline) 0 0% 58.86% 55ms 1.17% boost::numeric::ublas::vector_assign (inline) 53ms 1.13% 59.99% 53ms 1.13% [libvtkCommonCore-9.3.so.9.3] 53ms 1.13% 61.12% 53ms 1.13% __GI___writev 0 0% 61.12% 53ms 1.13% std::__basic_file::xsputn_2 16ms 0.34% 61.46% 53ms 1.13% vtkDataArray::~vtkDataArray 51ms 1.09% 62.55% 51ms 1.09% vtkTimeStamp::Modified 50ms 1.07% 63.62% 50ms 1.07% __memcpy_avx_unaligned_erms 21ms 0.45% 64.06% 49ms 1.05% std::_Hashtable::clear 5ms 0.11% 64.17% 48ms 1.02% std::_Rb_tree::_M_insert_ (inline) 5ms 0.11% 64.28% 47ms 1.00% std::vector::_M_realloc_insert 1ms 0.021% 64.30% 46ms 0.98% VertexMesh::Clear 46ms 0.98% 65.28% 46ms 0.98% std::ostream::sentry::sentry 1ms 0.021% 65.30% 45ms 0.96% DistributedBoxCollection::IsOwned 2ms 0.043% 65.34% 45ms 0.96% DistributedBoxCollection::SetupLocalBoxesHalfOnly 7ms 0.15% 65.49% 44ms 0.94% vtkSOADataArrayTemplate::FillTypedComponent 27ms 0.58% 66.07% 43ms 0.92% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 66.07% 43ms 0.92% DistributedBoxCollection::~DistributedBoxCollection 0 0% 66.07% 43ms 0.92% NodesOnlyMesh::ClearBoxCollection (inline) 11ms 0.23% 66.30% 43ms 0.92% std::num_put::_M_insert_int 34ms 0.73% 67.03% 43ms 0.92% vtkObject::ObjectFinalize 0 0% 67.03% 42ms 0.9% vtkDataArray::ComputeRange 42ms 0.9% 67.93% 42ms 0.9% vtkObject::~vtkObject 7ms 0.15% 68.08% 40ms 0.85% boost::numeric::ublas::indexing_vector_assign 0 0% 68.08% 40ms 0.85% std::_Destroy (inline) 0 0% 68.08% 40ms 0.85% std::_Destroy_aux::__destroy (inline) 0 0% 68.08% 39ms 0.83% _dl_init 0 0% 68.08% 39ms 0.83% call_init (inline) 5ms 0.11% 68.18% 39ms 0.83% vtkDataArrayPrivate::DoComputeVectorRange 39ms 0.83% 69.01% 39ms 0.83% vtkObjectBase::vtkObjectBase 37ms 0.79% 69.80% 37ms 0.79% __memset_avx2_unaligned_erms 37ms 0.79% 70.59% 37ms 0.79% vtkDataArray::Modified 4ms 0.085% 70.68% 36ms 0.77% VertexMeshWriter::GetNextNode 9ms 0.19% 70.87% 36ms 0.77% vtkAOSDataArrayTemplate::InsertTuple 36ms 0.77% 71.64% 36ms 0.77% vtkObjectBase::Delete 1ms 0.021% 71.66% 35ms 0.75% CellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 71.66% 35ms 0.75% CxxTest::RealWorldDescription::setUp 0 0% 71.66% 35ms 0.75% PMPI_Init_thread 0 0% 71.66% 35ms 0.75% PetscInitialize 0 0% 71.66% 35ms 0.75% PetscSetup::setUpWorld 0 0% 71.66% 35ms 0.75% PetscSetupUtils::CommonSetup 0 0% 71.66% 35ms 0.75% PetscSetupUtils::InitialisePetsc 0 0% 71.66% 35ms 0.75% _dl_start_user 0 0% 71.66% 35ms 0.75% ompi_mpi_init 0 0% 71.66% 35ms 0.75% std::less::operator() (inline) 0 0% 71.66% 35ms 0.75% std::map::~map (inline) 35ms 0.75% 72.41% 35ms 0.75% std::operator< (inline) 0 0% 72.41% 35ms 0.75% vtk::detail::smp::vtkSMPToolsImplForTBB 11ms 0.23% 72.64% 34ms 0.73% _int_free_merge_chunk 11ms 0.23% 72.88% 34ms 0.73% vtkIdList::~vtkIdList 4ms 0.085% 72.96% 33ms 0.7% 33ms 0.7% 73.67% 33ms 0.7% Node::GetIndex 33ms 0.7% 74.37% 33ms 0.7% boost::numeric::ublas::c_vector::operator() 9ms 0.19% 74.56% 33ms 0.7% vtk::detail::smp::vtkSMPToolsImpl::For 0 0% 74.56% 32ms 0.68% Cell::GetCellId 10ms 0.21% 74.78% 32ms 0.68% std::__new_allocator::construct (inline) 0 0% 74.78% 32ms 0.68% std::allocator_traits::construct (inline) 0 0% 74.78% 32ms 0.68% vtkDataArrayPrivate::DoComputeScalarRange 6ms 0.13% 74.90% 32ms 0.68% vtkIdList::vtkIdList 0 0% 74.90% 31ms 0.66% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 74.90% 31ms 0.66% PottsBasedCellPopulation::AcceptCellWriter 31ms 0.66% 75.57% 31ms 0.66% std::codecvt::do_always_noconv 1ms 0.021% 75.59% 31ms 0.66% tbb::detail::r1::cancel_group_execution 2ms 0.043% 75.63% 30ms 0.64% std::make_unique (inline) 4ms 0.085% 75.71% 30ms 0.64% vtkAOSDataArrayTemplate::AllocateTuples 30ms 0.64% 76.36% 30ms 0.64% vtkObjectBase::~vtkObjectBase 0 0% 76.36% 29ms 0.62% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 1ms 0.021% 76.38% 29ms 0.62% std::_Rb_tree_header::_Rb_tree_header (inline) 1ms 0.021% 76.40% 29ms 0.62% vtkDoubleArray::New 0 0% 76.40% 28ms 0.6% CellIdWriter::GetCellDataForVtkOutput 1ms 0.021% 76.42% 28ms 0.6% std::basic_filebuf::overflow 4ms 0.085% 76.50% 27ms 0.58% Node::AddElement 0 0% 76.50% 27ms 0.58% VertexMeshWriter::GetNextElement 0 0% 76.50% 27ms 0.58% std::_Rb_tree::_M_emplace_hint_unique 27ms 0.58% 77.08% 27ms 0.58% std::_Rb_tree_header::_M_reset (inline) 0 0% 77.08% 27ms 0.58% std::basic_filebuf::_M_convert_to_external 26ms 0.55% 77.64% 26ms 0.55% __GI___libc_write 0 0% 77.64% 26ms 0.55% std::__basic_file::xsputn 6ms 0.13% 77.76% 26ms 0.55% vtkSOADataArrayTemplate::GetTupleIndexFromValueIndex 0 0% 77.76% 25ms 0.53% PottsMesh::GetVonNeumannNeighbouringNodeIndices 1ms 0.021% 77.78% 25ms 0.53% VtkMeshWriter::MakeVtkMesh 25ms 0.53% 78.32% 25ms 0.53% [libstdc++.so.6.0.33] 25ms 0.53% 78.85% 25ms 0.53% __mpn_divrem 3ms 0.064% 78.92% 25ms 0.53% boost::serialization::singleton::get_instance 25ms 0.53% 79.45% 25ms 0.53% std::_Rb_tree::_S_right (inline) 24ms 0.51% 79.96% 24ms 0.51% vtkAOSDataArrayTemplate::SetTuple