File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3931ms, 80.64% of 4875ms total Dropped 772 nodes (cum <= 24.38ms) flat flat% sum% cum cum% 0 0% 0% 4693ms 96.27% __libc_start_call_main 0 0% 0% 4693ms 96.27% __libc_start_main_impl 0 0% 0% 4693ms 96.27% _start 0 0% 0% 4675ms 95.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4675ms 95.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4675ms 95.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4675ms 95.90% main 0 0% 0% 4639ms 95.16% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4639ms 95.16% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4639ms 95.16% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4627ms 94.91% AbstractCellBasedSimulation::Solve 0 0% 0% 4255ms 87.28% AbstractCellPopulation::WriteResultsToFiles 6ms 0.12% 0.12% 4038ms 82.83% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.12% 1986ms 40.74% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.021% 0.14% 1703ms 34.93% VertexMeshWriter::MakeVtkMesh 1ms 0.021% 0.16% 1279ms 26.24% vtkPolygon::New 1ms 0.021% 0.18% 1278ms 26.22% vtkPolygon::vtkPolygon 6ms 0.12% 0.31% 911ms 18.69% vtkCell::vtkCell 2ms 0.041% 0.35% 761ms 15.61% vtkPoints::New 8ms 0.16% 0.51% 716ms 14.69% vtkPoints::vtkPoints 1ms 0.021% 0.53% 684ms 14.03% VertexMeshWriter::WriteFiles 38ms 0.78% 1.31% 658ms 13.50% operator new 207ms 4.25% 5.56% 630ms 12.92% __GI___libc_malloc 55ms 1.13% 6.69% 627ms 12.86% std::ostream::_M_insert 1ms 0.021% 6.71% 626ms 12.84% std::ostream::operator<< (inline) 1ms 0.021% 6.73% 599ms 12.29% vtkLine::New 4ms 0.082% 6.81% 597ms 12.25% vtkTriangle::New 0 0% 6.81% 594ms 12.18% vtkStreamingDemandDrivenPipeline::Update 0 0% 6.81% 594ms 12.18% vtkXMLWriterBase::Write 0 0% 6.81% 592ms 12.14% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 6.81% 591ms 12.12% vtkDemandDrivenPipeline::ProcessRequest 2ms 0.041% 6.85% 591ms 12.12% vtkQuad::New 1ms 0.021% 6.87% 589ms 12.08% vtkDemandDrivenPipeline::ExecuteData 0 0% 6.87% 588ms 12.06% vtkCompositeDataPipeline::ExecuteData 0 0% 6.87% 587ms 12.04% vtkExecutive::CallAlgorithm 4ms 0.082% 6.95% 586ms 12.02% vtkQuad::vtkQuad 11ms 0.23% 7.18% 585ms 12.00% vtkLine::vtkLine 0 0% 7.18% 584ms 11.98% vtkXMLUnstructuredDataWriter::ProcessRequest 11ms 0.23% 7.41% 582ms 11.94% vtkTriangle::vtkTriangle 0 0% 7.41% 518ms 10.63% vtkXMLUnstructuredDataWriter::WriteAPiece 1ms 0.021% 7.43% 518ms 10.63% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 114ms 2.34% 9.76% 508ms 10.42% __GI___libc_free 41ms 0.84% 10.61% 500ms 10.26% std::num_put::_M_insert_float 32ms 0.66% 11.26% 466ms 9.56% vtkPoints::SetDataType 0 0% 11.26% 454ms 9.31% vtkXMLWriter::WriteBinaryData 0 0% 11.26% 449ms 9.21% vtkXMLWriter::WriteBinaryDataBlock 0 0% 11.26% 449ms 9.21% vtkXMLWriter::WriteBinaryDataInternal 0 0% 11.26% 436ms 8.94% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 226ms 4.64% 15.90% 390ms 8.00% _int_free 11ms 0.23% 16.12% 387ms 7.94% std::__cxx11::collate::do_transform 1ms 0.021% 16.14% 381ms 7.82% vtkPolygon::~vtkPolygon 1ms 0.021% 16.16% 365ms 7.49% ___vsnprintf 1ms 0.021% 16.18% 364ms 7.47% __vsnprintf_internal (inline) 0 0% 16.18% 360ms 7.38% OnLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.021% 16.21% 360ms 7.38% PottsBasedCellPopulation::UpdateCellLocations 0 0% 16.21% 359ms 7.36% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 60ms 1.23% 17.44% 356ms 7.30% __printf_buffer 0 0% 17.44% 353ms 7.24% VtkMeshWriter::WriteFiles 228ms 4.68% 22.11% 353ms 7.24% _int_malloc 0 0% 22.11% 326ms 6.69% vtkXMLWriter::WritePointsAppendedData 59ms 1.21% 23.32% 306ms 6.28% std::__new_allocator::allocate (inline) 0 0% 23.32% 305ms 6.26% std::allocator_traits::allocate (inline) 42ms 0.86% 24.18% 299ms 6.13% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 6ms 0.12% 24.31% 291ms 5.97% vtkCell::~vtkCell 6ms 0.12% 24.43% 286ms 5.87% std::__new_allocator::deallocate (inline) 0 0% 24.43% 284ms 5.83% std::allocator_traits::deallocate (inline) 13ms 0.27% 24.70% 274ms 5.62% __printf_fp_l_buffer 0 0% 24.70% 274ms 5.62% __printf_fp_spec (inline) 1ms 0.021% 24.72% 257ms 5.27% std::set::set (inline) 32ms 0.66% 25.37% 256ms 5.25% std::_Rb_tree::_Rb_tree 99ms 2.03% 27.41% 251ms 5.15% __printf_fp_buffer_1 0 0% 27.41% 236ms 4.84% vtkXMLWriter::WriteCompressionBlock 4ms 0.082% 27.49% 225ms 4.62% vtkBase64OutputStream::Write 0 0% 27.49% 220ms 4.51% compress2 0 0% 27.49% 220ms 4.51% vtkDataCompressor::Compress 0 0% 27.49% 220ms 4.51% vtkZLibDataCompressor::CompressBuffer 44ms 0.9% 28.39% 217ms 4.45% crc32 0 0% 28.39% 217ms 4.45% deflate 16ms 0.33% 28.72% 216ms 4.43% vtkBase64OutputStream::EncodeTriplet 1ms 0.021% 28.74% 206ms 4.23% VertexMesh::~VertexMesh 113ms 2.32% 31.06% 199ms 4.08% malloc_consolidate 50ms 1.03% 32.08% 186ms 3.82% std::ostream::write 7ms 0.14% 32.23% 186ms 3.82% vtkPoints::~vtkPoints 0 0% 32.23% 185ms 3.79% std::_Rb_tree::_M_create_node (inline) 10ms 0.21% 32.43% 184ms 3.77% vtkFloatArray::New 0 0% 32.43% 181ms 3.71% std::vector::~vector (inline) 12ms 0.25% 32.68% 179ms 3.67% std::_Rb_tree::_M_copy (inline) 0 0% 32.68% 177ms 3.63% std::_Rb_tree::_Alloc_node::operator() (inline) 7ms 0.14% 32.82% 177ms 3.63% std::_Vector_base::_M_deallocate (inline) 3ms 0.062% 32.88% 176ms 3.61% NodesOnlyMesh::ConstructNodesWithoutMesh 51ms 1.05% 33.93% 176ms 3.61% std::_Rb_tree::_M_erase 4ms 0.082% 34.01% 174ms 3.57% std::_Rb_tree::~_Rb_tree (inline) 0 0% 34.01% 173ms 3.55% std::_Rb_tree::_M_get_node (inline) 72ms 1.48% 35.49% 171ms 3.51% std::basic_filebuf::xsputn 23ms 0.47% 35.96% 166ms 3.41% std::vector::_M_default_append 2ms 0.041% 36.00% 165ms 3.38% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 1ms 0.021% 36.02% 165ms 3.38% vtkQuad::~vtkQuad 2ms 0.041% 36.06% 164ms 3.36% vtkTriangle::~vtkTriangle 1ms 0.021% 36.08% 163ms 3.34% vtkDataArray::CreateDataArray 159ms 3.26% 39.34% 162ms 3.32% [libz.so.1.3] 14ms 0.29% 39.63% 162ms 3.32% std::_Rb_tree::_M_clone_node (inline) 1ms 0.021% 39.65% 160ms 3.28% VertexMesh::VertexMesh 5ms 0.1% 39.75% 160ms 3.28% vtkIdList::AllocateInternal 1ms 0.021% 39.77% 157ms 3.22% vtkLine::GetParametricCenter 2ms 0.041% 39.82% 155ms 3.18% vtkTypeFloat64Array::New 4ms 0.082% 39.90% 154ms 3.16% vtkDoubleArray::vtkDoubleArray 3ms 0.062% 39.96% 153ms 3.14% tbb::detail::r1::parallel_pipeline 4ms 0.082% 40.04% 153ms 3.14% vtkFloatArray::vtkFloatArray 0 0% 40.04% 146ms 2.99% EdgeHelper::~EdgeHelper (inline) 0 0% 40.04% 146ms 2.99% clone3 0 0% 40.04% 146ms 2.99% start_thread 1ms 0.021% 40.06% 145ms 2.97% std::_Vector_base::~_Vector_base (inline) 9ms 0.18% 40.25% 143ms 2.93% MutableElement::BuildEdges 0 0% 40.25% 143ms 2.93% VertexMesh::GenerateEdgesFromElements (inline) 0 0% 40.25% 143ms 2.93% vtkTypeFloat64Array::~vtkTypeFloat64Array 0 0% 40.25% 137ms 2.81% NodeLocationWriter::VisitAnyPopulation 5ms 0.1% 40.35% 137ms 2.81% vtkTypeFloat64Array::vtkTypeFloat64Array 1ms 0.021% 40.37% 136ms 2.79% tbb::detail::r1::reset 0 0% 40.37% 132ms 2.71% std::_Vector_base::_M_allocate (inline) 0 0% 40.37% 129ms 2.65% std::set::~set (inline) 0 0% 40.37% 123ms 2.52% vtkIdList::Allocate 0 0% 40.37% 121ms 2.48% std::_Rb_tree::_M_drop_node (inline) 41ms 0.84% 41.21% 121ms 2.48% tbb::detail::r1::wait_bounded_queue_monitor 38ms 0.78% 41.99% 116ms 2.38% std::__ostream_insert 17ms 0.35% 42.34% 116ms 2.38% vtkObject::vtkObject 4ms 0.082% 42.42% 115ms 2.36% EdgeHelper::GetEdgeFromNodes 0 0% 42.42% 114ms 2.34% std::_Rb_tree::_M_put_node (inline) 0 0% 42.42% 112ms 2.30% Cell::HasCellProperty (inline) 1ms 0.021% 42.44% 112ms 2.30% CellPropertyCollection::HasProperty 0 0% 42.44% 112ms 2.30% std::operator<< (inline) 111ms 2.28% 44.72% 111ms 2.28% __strcmp_avx2 0 0% 44.72% 110ms 2.26% vtkXMLWriter::WritePointDataAppendedData 3ms 0.062% 44.78% 109ms 2.24% vtkFloatArray::~vtkFloatArray 0 0% 44.78% 108ms 2.22% CellPropertyCollection::GetPropertiesType (inline) 8ms 0.16% 44.94% 107ms 2.19% _int_free_maybe_consolidate 107ms 2.19% 47.14% 107ms 2.19% unlink_chunk 0 0% 47.14% 106ms 2.17% AbstractCellProperty::IsType (inline) 48ms 0.98% 48.12% 103ms 2.11% hack_digit 1ms 0.021% 48.14% 99ms 2.03% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 10ms 0.21% 48.35% 94ms 1.93% vtkIdList::New 1ms 0.021% 48.37% 91ms 1.87% AbstractCellProperty::IsSubType (inline) 25ms 0.51% 48.88% 91ms 1.87% __dynamic_cast 5ms 0.1% 48.98% 91ms 1.87% std::map::operator[] (partial-inline) 26ms 0.53% 49.52% 87ms 1.78% std::_Rb_tree::_M_lower_bound (inline) 2ms 0.041% 49.56% 87ms 1.78% std::vector::push_back (inline) 43ms 0.88% 50.44% 84ms 1.72% vtkTypeFloat64Array::PrintSelf 0 0% 50.44% 81ms 1.66% PottsMesh::GetMooreNeighbouringNodeIndices 81ms 1.66% 52.10% 81ms 1.66% __GI_sched_yield 50ms 1.03% 53.13% 81ms 1.66% std::basic_streambuf::xsputn 7ms 0.14% 53.27% 80ms 1.64% vtkAOSDataArrayTemplate::DataElementChanged 27ms 0.55% 53.83% 78ms 1.60% vtkObject::Modified 49ms 1.01% 54.83% 78ms 1.60% vtkObjectBase::UnRegisterInternal 0 0% 54.83% 78ms 1.60% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 6ms 0.12% 54.95% 74ms 1.52% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 54.95% 73ms 1.50% NodesOnlyMesh::SetUpBoxCollection 18ms 0.37% 55.32% 72ms 1.48% AbstractCellProperty::IsSame 0 0% 55.32% 71ms 1.46% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 0 0% 55.32% 70ms 1.44% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.021% 55.34% 68ms 1.39% boost::numeric::ublas::vector_assign (inline) 0 0% 55.34% 67ms 1.37% Cell::GetCellProliferativeType 31ms 0.64% 55.98% 64ms 1.31% std::_Hashtable::clear 0 0% 55.98% 64ms 1.31% tcache_get (inline) 64ms 1.31% 57.29% 64ms 1.31% tcache_get_n (inline) 63ms 1.29% 58.58% 63ms 1.29% __GI___writev 0 0% 58.58% 62ms 1.27% std::_Rb_tree::lower_bound (inline) 0 0% 58.58% 62ms 1.27% std::__basic_file::xsputn_2 0 0% 58.58% 62ms 1.27% std::map::lower_bound (inline) 5ms 0.1% 58.69% 62ms 1.27% std::vector::_M_realloc_insert 0 0% 58.69% 61ms 1.25% NodesOnlyMesh::~NodesOnlyMesh 4ms 0.082% 58.77% 61ms 1.25% vtkDoubleArray::~vtkDoubleArray 4ms 0.082% 58.85% 60ms 1.23% vtkDataArray::vtkDataArray 1ms 0.021% 58.87% 59ms 1.21% VertexMesh::Clear 12ms 0.25% 59.12% 54ms 1.11% std::type_info::operator== (inline) 16ms 0.33% 59.45% 53ms 1.09% vtkAbstractArray::vtkAbstractArray 4ms 0.082% 59.53% 52ms 1.07% VertexMeshWriter::GetNextNode 18ms 0.37% 59.90% 51ms 1.05% boost::numeric::ublas::indexing_vector_assign 12ms 0.25% 60.14% 51ms 1.05% vtkSOADataArrayTemplate::FillTypedComponent 0 0% 60.14% 50ms 1.03% std::_Rb_tree::_M_insert_unique 0 0% 60.14% 50ms 1.03% std::set::insert (inline) 49ms 1.01% 61.15% 49ms 1.01% vtkTimeStamp::Modified 47ms 0.96% 62.11% 47ms 0.96% __memset_avx2_unaligned_erms 46ms 0.94% 63.06% 46ms 0.94% [libvtkCommonCore-9.3.so.9.3] 46ms 0.94% 64.00% 46ms 0.94% __memcpy_avx_unaligned_erms 0 0% 64.00% 46ms 0.94% std::map::~map (inline) 46ms 0.94% 64.94% 46ms 0.94% vtkObject::~vtkObject 2ms 0.041% 64.98% 45ms 0.92% DistributedBoxCollection::SetupLocalBoxesHalfOnly 0 0% 64.98% 45ms 0.92% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 45ms 0.92% 65.91% 45ms 0.92% std::_Rb_tree_header::_M_reset (inline) 0 0% 65.91% 45ms 0.92% std::_Rb_tree_header::_Rb_tree_header (inline) 0 0% 65.91% 45ms 0.92% vtkDataArray::ComputeRange 12ms 0.25% 66.15% 45ms 0.92% vtkDataArray::~vtkDataArray 8ms 0.16% 66.32% 45ms 0.92% vtkIdList::~vtkIdList 7ms 0.14% 66.46% 44ms 0.9% std::num_put::_M_insert_int 23ms 0.47% 66.93% 43ms 0.88% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.041% 66.97% 42ms 0.86% DistributedBoxCollection::IsOwned 0 0% 66.97% 42ms 0.86% PottsMesh::GetVonNeumannNeighbouringNodeIndices 0 0% 66.97% 42ms 0.86% std::_Destroy (inline) 0 0% 66.97% 42ms 0.86% std::_Destroy_aux::__destroy (inline) 28ms 0.57% 67.55% 40ms 0.82% DistributedBoxCollection::CalculateContainingBox (inline) 40ms 0.82% 68.37% 40ms 0.82% Node::GetIndex 10ms 0.21% 68.57% 40ms 0.82% _int_free_merge_chunk 0 0% 68.57% 40ms 0.82% std::less::operator() (inline) 40ms 0.82% 69.39% 40ms 0.82% std::operator< (inline) 37ms 0.76% 70.15% 38ms 0.78% vtkObjectBase::Delete 38ms 0.78% 70.93% 38ms 0.78% vtkObjectBase::vtkObjectBase 0 0% 70.93% 37ms 0.76% DistributedBoxCollection::~DistributedBoxCollection 0 0% 70.93% 37ms 0.76% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 70.93% 37ms 0.76% _dl_init 0 0% 70.93% 37ms 0.76% call_init (inline) 37ms 0.76% 71.69% 37ms 0.76% std::codecvt::do_always_noconv 0 0% 71.69% 36ms 0.74% _dl_start_user 1ms 0.021% 71.71% 36ms 0.74% vtkDoubleArray::New 11ms 0.23% 71.94% 36ms 0.74% vtkIdList::vtkIdList 2ms 0.041% 71.98% 34ms 0.7% std::_Rb_tree::_M_insert_ (inline) 8ms 0.16% 72.14% 34ms 0.7% std::__new_allocator::construct (inline) 0 0% 72.14% 34ms 0.7% std::allocator_traits::construct (inline) 6ms 0.12% 72.27% 34ms 0.7% vtkDataArrayPrivate::DoComputeVectorRange 0 0% 72.27% 32ms 0.66% CxxTest::RealWorldDescription::setUp 0 0% 72.27% 32ms 0.66% PetscInitialize 0 0% 72.27% 32ms 0.66% PetscSetup::setUpWorld 0 0% 72.27% 32ms 0.66% PetscSetupUtils::CommonSetup 0 0% 72.27% 32ms 0.66% PetscSetupUtils::InitialisePetsc 32ms 0.66% 72.92% 32ms 0.66% __mpn_divrem 32ms 0.66% 73.58% 32ms 0.66% std::ostream::sentry::sentry 0 0% 73.58% 32ms 0.66% vtkXMLUnstructuredDataWriter::WriteHeader 0 0% 73.58% 31ms 0.64% Cell::GetMutationState 0 0% 73.58% 31ms 0.64% CellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 73.58% 31ms 0.64% PMPI_Init_thread 31ms 0.64% 74.22% 31ms 0.64% [libstdc++.so.6.0.33] 0 0% 74.22% 31ms 0.64% ompi_mpi_init 1ms 0.021% 74.24% 31ms 0.64% vtk::detail::smp::vtkSMPToolsImplForTBB 5ms 0.1% 74.34% 31ms 0.64% vtkAOSDataArrayTemplate::InsertTuple 31ms 0.64% 74.97% 31ms 0.64% vtkObjectBase::~vtkObjectBase 3ms 0.062% 75.04% 30ms 0.62% boost::serialization::singleton::get_instance 0 0% 75.04% 30ms 0.62% std::basic_filebuf::open 0 0% 75.04% 30ms 0.62% std::make_unique (inline) 0 0% 75.04% 29ms 0.59% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 1ms 0.021% 75.06% 29ms 0.59% Node::GetPoint 28ms 0.57% 75.63% 29ms 0.59% __GI___libc_write 29ms 0.59% 76.23% 29ms 0.59% std::_Rb_tree::_S_right (inline) 0 0% 76.23% 29ms 0.59% std::__basic_file::xsputn 0 0% 76.23% 29ms 0.59% std::basic_filebuf::_M_convert_to_external 0 0% 76.23% 29ms 0.59% std::basic_filebuf::overflow 23ms 0.47% 76.70% 29ms 0.59% vtkObject::ObjectFinalize 0 0% 76.70% 29ms 0.59% vtkXMLUnstructuredGridWriter::WriteAppendedPiece 1ms 0.021% 76.72% 28ms 0.57% 0 0% 76.72% 28ms 0.57% PottsBasedCellPopulation::AcceptCellWriter 0 0% 76.72% 28ms 0.57% _IO_new_file_fopen 0 0% 76.72% 28ms 0.57% _IO_new_fopen 0 0% 76.72% 28ms 0.57% __GI__IO_file_open 0 0% 76.72% 28ms 0.57% __fopen_internal (inline) 28ms 0.57% 77.29% 28ms 0.57% __libc_open64 28ms 0.57% 77.87% 28ms 0.57% std::_Rb_tree_increment 0 0% 77.87% 28ms 0.57% std::__basic_file::open 1ms 0.021% 77.89% 28ms 0.57% vtk::detail::smp::vtkSMPToolsImpl::For 21ms 0.43% 78.32% 27ms 0.55% _int_free_create_chunk (inline) 27ms 0.55% 78.87% 27ms 0.55% boost::numeric::ublas::c_vector::operator() 2ms 0.041% 78.91% 27ms 0.55% tbb::detail::r1::cancel_group_execution 27ms 0.55% 79.47% 27ms 0.55% vtkAOSDataArrayTemplate::SetTuple 0 0% 79.47% 27ms 0.55% vtkDataArrayPrivate::DoComputeScalarRange 27ms 0.55% 80.02% 27ms 0.55% vtkObject::InvokeEvent 0 0% 80.02% 26ms 0.53% VertexElement::~VertexElement 0 0% 80.02% 26ms 0.53% boost::numeric::ublas::c_vector::assign (inline) 0 0% 80.02% 26ms 0.53% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 7ms 0.14% 80.16% 26ms 0.53% std::_Rb_tree_const_iterator::operator++ (inline) 23ms 0.47% 80.64% 26ms 0.53% std::num_put::do_put 0 0% 80.64% 25ms 0.51% std::_Rb_tree::find (inline) 0 0% 80.64% 25ms 0.51% std::default_delete::operator() (inline) 0 0% 80.64% 25ms 0.51% std::map::find (inline) 0 0% 80.64% 25ms 0.51% std::unique_ptr::~unique_ptr (inline)