File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3887ms, 79.96% of 4861ms total Dropped 731 nodes (cum <= 24.30ms) flat flat% sum% cum cum% 0 0% 0% 4600ms 94.63% __libc_start_call_main 0 0% 0% 4600ms 94.63% __libc_start_main_impl 0 0% 0% 4600ms 94.63% _start 0 0% 0% 4585ms 94.32% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4585ms 94.32% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4585ms 94.32% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4585ms 94.32% main 0 0% 0% 4545ms 93.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4545ms 93.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4545ms 93.50% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4535ms 93.29% AbstractCellBasedSimulation::Solve 0 0% 0% 4268ms 87.80% AbstractCellPopulation::WriteResultsToFiles 13ms 0.27% 0.27% 4036ms 83.03% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.27% 1987ms 40.88% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.021% 0.29% 1719ms 35.36% VertexMeshWriter::MakeVtkMesh 0 0% 0.29% 1274ms 26.21% vtkPolygon::New 0 0% 0.29% 1270ms 26.13% vtkPolygon::vtkPolygon 4ms 0.082% 0.37% 916ms 18.84% vtkCell::vtkCell 4ms 0.082% 0.45% 780ms 16.05% vtkPoints::New 1ms 0.021% 0.47% 767ms 15.78% VertexMeshWriter::WriteFiles 2ms 0.041% 0.51% 764ms 15.72% std::ostream::operator<< (inline) 53ms 1.09% 1.60% 761ms 15.66% std::ostream::_M_insert 15ms 0.31% 1.91% 729ms 15.00% vtkPoints::vtkPoints 33ms 0.68% 2.59% 671ms 13.80% operator new 216ms 4.44% 7.04% 636ms 13.08% __GI___libc_malloc 54ms 1.11% 8.15% 624ms 12.84% std::num_put::_M_insert_float 3ms 0.062% 8.21% 615ms 12.65% vtkLine::New 13ms 0.27% 8.48% 595ms 12.24% vtkLine::vtkLine 3ms 0.062% 8.54% 592ms 12.18% vtkQuad::New 2ms 0.041% 8.58% 588ms 12.10% vtkQuad::vtkQuad 0 0% 8.58% 573ms 11.79% vtkStreamingDemandDrivenPipeline::Update 0 0% 8.58% 573ms 11.79% vtkXMLWriterBase::Write 0 0% 8.58% 571ms 11.75% vtkDemandDrivenPipeline::ProcessRequest 0 0% 8.58% 568ms 11.68% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 8.58% 567ms 11.66% vtkDemandDrivenPipeline::ExecuteData 0 0% 8.58% 567ms 11.66% vtkExecutive::CallAlgorithm 0 0% 8.58% 565ms 11.62% vtkCompositeDataPipeline::ExecuteData 0 0% 8.58% 565ms 11.62% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 8.58% 558ms 11.48% vtkTriangle::New 12ms 0.25% 8.83% 551ms 11.34% vtkTriangle::vtkTriangle 164ms 3.37% 12.20% 525ms 10.80% __GI___libc_free 0 0% 12.20% 510ms 10.49% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 12.20% 510ms 10.49% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 11ms 0.23% 12.43% 491ms 10.10% std::__cxx11::collate::do_transform 4ms 0.082% 12.51% 465ms 9.57% ___vsnprintf 0 0% 12.51% 461ms 9.48% __vsnprintf_internal (inline) 21ms 0.43% 12.94% 459ms 9.44% vtkPoints::SetDataType 64ms 1.32% 14.26% 458ms 9.42% __printf_buffer 1ms 0.021% 14.28% 453ms 9.32% vtkXMLWriter::WriteBinaryData 1ms 0.021% 14.30% 444ms 9.13% vtkXMLWriter::WriteBinaryDataInternal 0 0% 14.30% 441ms 9.07% vtkXMLWriter::WriteBinaryDataBlock 0 0% 14.30% 431ms 8.87% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 3ms 0.062% 14.36% 399ms 8.21% vtkPolygon::~vtkPolygon 2ms 0.041% 14.40% 362ms 7.45% __printf_fp_spec (inline) 241ms 4.96% 19.36% 361ms 7.43% _int_free 251ms 5.16% 24.52% 361ms 7.43% _int_malloc 18ms 0.37% 24.89% 360ms 7.41% __printf_fp_l_buffer 0 0% 24.89% 347ms 7.14% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 24.89% 346ms 7.12% VtkMeshWriter::WriteFiles 177ms 3.64% 28.53% 329ms 6.77% __printf_fp_buffer_1 0 0% 28.53% 328ms 6.75% vtkXMLWriter::WritePointsAppendedData 8ms 0.16% 28.70% 303ms 6.23% vtkCell::~vtkCell 38ms 0.78% 29.48% 280ms 5.76% std::__new_allocator::allocate (inline) 0 0% 29.48% 280ms 5.76% std::allocator_traits::allocate (inline) 45ms 0.93% 30.41% 280ms 5.76% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 2ms 0.041% 30.45% 273ms 5.62% std::__new_allocator::deallocate (inline) 0 0% 30.45% 269ms 5.53% std::allocator_traits::deallocate (inline) 0 0% 30.45% 262ms 5.39% OnLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.041% 30.49% 261ms 5.37% PottsBasedCellPopulation::UpdateCellLocations 0 0% 30.49% 231ms 4.75% tbb::detail::r1::parallel_pipeline 0 0% 30.49% 229ms 4.71% vtkXMLWriter::WriteCompressionBlock 0 0% 30.49% 222ms 4.57% clone3 0 0% 30.49% 222ms 4.57% start_thread 89ms 1.83% 32.32% 222ms 4.57% tbb::detail::r1::wait_bounded_queue_monitor 0 0% 32.32% 221ms 4.55% tbb::detail::r1::reset 1ms 0.021% 32.34% 218ms 4.48% vtkDataCompressor::Compress 6ms 0.12% 32.46% 217ms 4.46% vtkBase64OutputStream::Write 0 0% 32.46% 216ms 4.44% compress2 0 0% 32.46% 216ms 4.44% vtkZLibDataCompressor::CompressBuffer 54ms 1.11% 33.57% 213ms 4.38% crc32 0 0% 33.57% 213ms 4.38% deflate 19ms 0.39% 33.96% 211ms 4.34% vtkBase64OutputStream::EncodeTriplet 4ms 0.082% 34.05% 205ms 4.22% vtkPoints::~vtkPoints 3ms 0.062% 34.11% 184ms 3.79% std::set::set (inline) 3ms 0.062% 34.17% 182ms 3.74% vtkFloatArray::New 10ms 0.21% 34.38% 181ms 3.72% std::_Rb_tree::_Rb_tree 47ms 0.97% 35.34% 180ms 3.70% std::_Rb_tree::_M_erase 55ms 1.13% 36.47% 179ms 3.68% std::ostream::write 4ms 0.082% 36.56% 177ms 3.64% std::_Rb_tree::~_Rb_tree (inline) 0 0% 36.56% 172ms 3.54% std::_Rb_tree::_M_create_node (inline) 5ms 0.1% 36.66% 171ms 3.52% NodesOnlyMesh::ConstructNodesWithoutMesh 11ms 0.23% 36.89% 167ms 3.44% std::vector::_M_default_append 1ms 0.021% 36.91% 165ms 3.39% vtkQuad::~vtkQuad 0 0% 36.91% 164ms 3.37% VertexMesh::~VertexMesh 4ms 0.082% 36.99% 163ms 3.35% vtkTriangle::~vtkTriangle 99ms 2.04% 39.02% 160ms 3.29% malloc_consolidate 1ms 0.021% 39.05% 160ms 3.29% vtkLine::GetParametricCenter 1ms 0.021% 39.07% 159ms 3.27% vtkTypeFloat64Array::~vtkTypeFloat64Array 0 0% 39.07% 158ms 3.25% std::_Rb_tree::_M_get_node (inline) 12ms 0.25% 39.31% 156ms 3.21% vtkIdList::AllocateInternal 2ms 0.041% 39.35% 155ms 3.19% NodeLocationWriter::VisitAnyPopulation 1ms 0.021% 39.37% 155ms 3.19% vtkFloatArray::vtkFloatArray 15ms 0.31% 39.68% 152ms 3.13% std::_Rb_tree::_M_copy (inline) 147ms 3.02% 42.71% 150ms 3.09% [libz.so.1.3] 0 0% 42.71% 150ms 3.09% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 42.71% 150ms 3.09% std::_Vector_base::_M_deallocate (inline) 0 0% 42.71% 147ms 3.02% VertexMesh::VertexMesh 0 0% 42.71% 147ms 3.02% std::set::~set (inline) 0 0% 42.71% 145ms 2.98% std::vector::~vector (inline) 58ms 1.19% 43.90% 141ms 2.90% std::basic_filebuf::xsputn 2ms 0.041% 43.94% 141ms 2.90% vtkFloatArray::~vtkFloatArray 0 0% 43.94% 137ms 2.82% VertexMesh::GenerateEdgesFromElements (inline) 1ms 0.021% 43.96% 135ms 2.78% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.082% 44.04% 135ms 2.78% MutableElement::BuildEdges 2ms 0.041% 44.09% 134ms 2.76% vtkDataArray::CreateDataArray 131ms 2.69% 46.78% 131ms 2.69% __GI_sched_yield 18ms 0.37% 47.15% 131ms 2.69% std::_Rb_tree::_M_clone_node (inline) 2ms 0.041% 47.19% 128ms 2.63% vtkDoubleArray::vtkDoubleArray 0 0% 47.19% 126ms 2.59% std::_Rb_tree::_M_drop_node (inline) 4ms 0.082% 47.27% 124ms 2.55% vtkTypeFloat64Array::New 0 0% 47.27% 122ms 2.51% std::_Vector_base::_M_allocate (inline) 26ms 0.53% 47.81% 121ms 2.49% __dynamic_cast 0 0% 47.81% 120ms 2.47% AbstractCellProperty::IsSubType (inline) 0 0% 47.81% 119ms 2.45% std::_Rb_tree::_M_put_node (inline) 4ms 0.082% 47.89% 115ms 2.37% EdgeHelper::GetEdgeFromNodes 0 0% 47.89% 114ms 2.35% EdgeHelper::~EdgeHelper (inline) 0 0% 47.89% 110ms 2.26% std::_Vector_base::~_Vector_base (inline) 3ms 0.062% 47.95% 108ms 2.22% vtkTypeFloat64Array::vtkTypeFloat64Array 25ms 0.51% 48.47% 106ms 2.18% vtkObject::vtkObject 0 0% 48.47% 103ms 2.12% vtkIdList::Allocate 0 0% 48.47% 103ms 2.12% vtkXMLWriter::WritePointDataAppendedData 1ms 0.021% 48.49% 99ms 2.04% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 4ms 0.082% 48.57% 97ms 2.00% std::map::operator[] (partial-inline) 60ms 1.23% 49.80% 95ms 1.95% vtkObjectBase::UnRegisterInternal 3ms 0.062% 49.87% 94ms 1.93% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 38ms 0.78% 50.65% 92ms 1.89% std::__ostream_insert 7ms 0.14% 50.79% 92ms 1.89% vtkDoubleArray::~vtkDoubleArray 54ms 1.11% 51.90% 92ms 1.89% vtkTypeFloat64Array::PrintSelf 87ms 1.79% 53.69% 87ms 1.79% __strcmp_avx2 44ms 0.91% 54.60% 86ms 1.77% hack_digit 66ms 1.36% 55.96% 86ms 1.77% std::basic_streambuf::xsputn 0 0% 55.96% 86ms 1.77% std::operator<< (inline) 12ms 0.25% 56.20% 86ms 1.77% vtkAOSDataArrayTemplate::DataElementChanged 3ms 0.062% 56.26% 85ms 1.75% vtkIdList::New 39ms 0.8% 57.07% 80ms 1.65% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.041% 57.11% 79ms 1.63% _int_free_maybe_consolidate 0 0% 57.11% 77ms 1.58% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 76ms 1.56% 58.67% 76ms 1.56% unlink_chunk 22ms 0.45% 59.12% 76ms 1.56% vtkObject::Modified 2ms 0.041% 59.16% 74ms 1.52% Cell::GetCellProliferativeType 0 0% 59.16% 66ms 1.36% PottsMesh::GetMooreNeighbouringNodeIndices 7ms 0.14% 59.31% 66ms 1.36% boost::numeric::ublas::c_vector::c_vector (partial-inline) 3ms 0.062% 59.37% 66ms 1.36% std::vector::push_back (inline) 0 0% 59.37% 64ms 1.32% NodesOnlyMesh::SetUpBoxCollection 19ms 0.39% 59.76% 63ms 1.30% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.021% 59.78% 63ms 1.30% std::set::insert (inline) 2ms 0.041% 59.82% 62ms 1.28% std::_Rb_tree::_M_insert_unique 5ms 0.1% 59.93% 61ms 1.25% AbstractCellPopulation::GetCellUsingLocationIndex 9ms 0.19% 60.11% 61ms 1.25% std::num_put::_M_insert_int 0 0% 60.11% 60ms 1.23% boost::numeric::ublas::vector_assign (inline) 8ms 0.16% 60.28% 55ms 1.13% vtkSOADataArrayTemplate::FillTypedComponent 54ms 1.11% 61.39% 54ms 1.11% vtkTimeStamp::Modified 0 0% 61.39% 53ms 1.09% NodesOnlyMesh::~NodesOnlyMesh 0 0% 61.39% 52ms 1.07% tcache_get (inline) 52ms 1.07% 62.46% 52ms 1.07% tcache_get_n (inline) 11ms 0.23% 62.68% 52ms 1.07% vtkDataArray::vtkDataArray 1ms 0.021% 62.70% 50ms 1.03% VertexMesh::Clear 1ms 0.021% 62.72% 50ms 1.03% std::__basic_file::xsputn_2 7ms 0.14% 62.87% 49ms 1.01% std::_Rb_tree::_M_insert_ (inline) 0 0% 62.87% 49ms 1.01% std::_Rb_tree::lower_bound (inline) 0 0% 62.87% 49ms 1.01% std::map::lower_bound (inline) 48ms 0.99% 63.86% 48ms 0.99% __GI___writev 7ms 0.14% 64.00% 47ms 0.97% VertexMeshWriter::GetNextNode 4ms 0.082% 64.08% 46ms 0.95% std::vector::_M_realloc_insert 0 0% 64.08% 46ms 0.95% vtkDataArray::ComputeRange 46ms 0.95% 65.03% 46ms 0.95% vtkObject::~vtkObject 45ms 0.93% 65.95% 45ms 0.93% __memcpy_avx_unaligned_erms 32ms 0.66% 66.61% 44ms 0.91% std::_Hashtable::clear 0 0% 66.61% 43ms 0.88% Cell::HasCellProperty (inline) 6ms 0.12% 66.74% 43ms 0.88% CellPropertyCollection::HasProperty 2ms 0.041% 66.78% 43ms 0.88% std::_Rb_tree::_M_emplace_hint_unique 43ms 0.88% 67.66% 43ms 0.88% std::ostream::sentry::sentry 42ms 0.86% 68.52% 42ms 0.86% [libvtkCommonCore-9.3.so.9.3] 14ms 0.29% 68.81% 42ms 0.86% boost::numeric::ublas::indexing_vector_assign 0 0% 68.81% 42ms 0.86% std::_Destroy (inline) 2ms 0.041% 68.85% 42ms 0.86% std::_Destroy_aux::__destroy (inline) 41ms 0.84% 69.70% 41ms 0.84% vtkObjectBase::Delete 1ms 0.021% 69.72% 40ms 0.82% DistributedBoxCollection::SetupLocalBoxesHalfOnly 9ms 0.19% 69.90% 40ms 0.82% vtkAbstractArray::vtkAbstractArray 0 0% 69.90% 39ms 0.8% _dl_init 0 0% 69.90% 39ms 0.8% _dl_start_user 0 0% 69.90% 39ms 0.8% call_init (inline) 4ms 0.082% 69.99% 39ms 0.8% vtkIdList::~vtkIdList 39ms 0.8% 70.79% 39ms 0.8% vtkObjectBase::~vtkObjectBase 0 0% 70.79% 38ms 0.78% Cell::GetCellId 5ms 0.1% 70.89% 38ms 0.78% vtkDataArray::~vtkDataArray 0 0% 70.89% 37ms 0.76% Cell::GetMutationState 0 0% 70.89% 36ms 0.74% CxxTest::RealWorldDescription::setUp 0 0% 70.89% 36ms 0.74% PMPI_Init_thread 0 0% 70.89% 36ms 0.74% PetscInitialize 0 0% 70.89% 36ms 0.74% PetscSetup::setUpWorld 0 0% 70.89% 36ms 0.74% PetscSetupUtils::CommonSetup 0 0% 70.89% 36ms 0.74% PetscSetupUtils::InitialisePetsc 0 0% 70.89% 36ms 0.74% ompi_mpi_init 0 0% 70.89% 35ms 0.72% CellIdWriter::GetCellDataForVtkOutput 2ms 0.041% 70.93% 35ms 0.72% CellProliferativeTypesWriter::GetCellDataForVtkOutput 35ms 0.72% 71.65% 35ms 0.72% std::_Rb_tree_increment 2ms 0.041% 71.69% 34ms 0.7% 16ms 0.33% 72.02% 34ms 0.7% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 72.02% 34ms 0.7% DistributedBoxCollection::IsOwned 0 0% 72.02% 34ms 0.7% Node::ConstructNodeAttributes (inline) 0 0% 72.02% 34ms 0.7% Node::SetRadius 0 0% 72.02% 34ms 0.7% vtkDoubleArray::New 1ms 0.021% 72.04% 33ms 0.68% std::__basic_file::xsputn 0 0% 72.04% 33ms 0.68% std::basic_filebuf::_M_convert_to_external 0 0% 72.04% 33ms 0.68% std::basic_filebuf::overflow 33ms 0.68% 72.72% 33ms 0.68% std::codecvt::do_always_noconv 0 0% 72.72% 33ms 0.68% vtk::detail::smp::vtkSMPToolsImplForTBB 6ms 0.12% 72.85% 33ms 0.68% vtkAOSDataArrayTemplate::InsertTuple 33ms 0.68% 73.52% 33ms 0.68% vtkObjectBase::vtkObjectBase 0 0% 73.52% 32ms 0.66% DistributedBoxCollection::~DistributedBoxCollection 0 0% 73.52% 32ms 0.66% NodesOnlyMesh::ClearBoxCollection (inline) 32ms 0.66% 74.18% 32ms 0.66% __GI___libc_write 4ms 0.082% 74.26% 32ms 0.66% boost::serialization::singleton::get_instance 2ms 0.041% 74.31% 32ms 0.66% tbb::detail::r1::cancel_group_execution 3ms 0.062% 74.37% 32ms 0.66% vtkDataArrayPrivate::DoComputeVectorRange 0 0% 74.37% 30ms 0.62% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 30ms 0.62% 74.98% 30ms 0.62% [libstdc++.so.6.0.33] 0 0% 74.98% 30ms 0.62% std::map::~map (inline) 2ms 0.041% 75.03% 29ms 0.6% __find_specmb (inline) 10ms 0.21% 75.23% 29ms 0.6% std::__new_allocator::construct (inline) 0 0% 75.23% 29ms 0.6% std::allocator_traits::construct (inline) 1ms 0.021% 75.25% 28ms 0.58% VtkMeshWriter::MakeVtkMesh 0 0% 75.25% 28ms 0.58% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 1ms 0.021% 75.27% 28ms 0.58% std::less::operator() (inline) 24ms 0.49% 75.77% 28ms 0.58% std::num_put::do_put 5ms 0.1% 75.87% 28ms 0.58% vtkAOSDataArrayTemplate::AllocateTuples 19ms 0.39% 76.26% 28ms 0.58% vtkObject::ObjectFinalize 0 0% 76.26% 27ms 0.56% PottsMesh::GetVonNeumannNeighbouringNodeIndices 27ms 0.56% 76.82% 27ms 0.56% __mpn_divrem 27ms 0.56% 77.37% 27ms 0.56% std::operator< (inline) 5ms 0.1% 77.47% 27ms 0.56% vtk::detail::smp::vtkSMPToolsImpl::For 12ms 0.25% 77.72% 26ms 0.53% _int_free_merge_chunk 1ms 0.021% 77.74% 26ms 0.53% std::make_unique (inline) 5ms 0.1% 77.84% 26ms 0.53% vtkIdList::vtkIdList 3ms 0.062% 77.91% 25ms 0.51% Node::GetPoint 25ms 0.51% 78.42% 25ms 0.51% __strchrnul_avx2 25ms 0.51% 78.93% 25ms 0.51% boost::numeric::ublas::c_vector::operator() 25ms 0.51% 79.45% 25ms 0.51% operator delete 0 0% 79.45% 25ms 0.51% orte_init 25ms 0.51% 79.96% 25ms 0.51% vtkDataArray::Modified