File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3804ms, 78.68% of 4835ms total Dropped 724 nodes (cum <= 24.18ms) flat flat% sum% cum cum% 0 0% 0% 4618ms 95.51% __libc_start_call_main 0 0% 0% 4618ms 95.51% __libc_start_main_impl 0 0% 0% 4618ms 95.51% _start 0 0% 0% 4604ms 95.22% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4604ms 95.22% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4604ms 95.22% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4604ms 95.22% main 0 0% 0% 4568ms 94.48% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4568ms 94.48% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4568ms 94.48% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4558ms 94.27% AbstractCellBasedSimulation::Solve 0 0% 0% 4262ms 88.15% AbstractCellPopulation::WriteResultsToFiles 18ms 0.37% 0.37% 4034ms 83.43% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.37% 1978ms 40.91% VertexMeshWriter::WriteVtkUsingMesh 6ms 0.12% 0.5% 1708ms 35.33% VertexMeshWriter::MakeVtkMesh 0 0% 0.5% 1263ms 26.12% vtkPolygon::New 2ms 0.041% 0.54% 1262ms 26.10% vtkPolygon::vtkPolygon 8ms 0.17% 0.7% 892ms 18.45% vtkCell::vtkCell 1ms 0.021% 0.72% 774ms 16.01% VertexMeshWriter::WriteFiles 55ms 1.14% 1.86% 769ms 15.90% std::ostream::_M_insert 1ms 0.021% 1.88% 768ms 15.88% vtkPoints::New 1ms 0.021% 1.90% 767ms 15.86% std::ostream::operator<< (inline) 11ms 0.23% 2.13% 725ms 14.99% vtkPoints::vtkPoints 43ms 0.89% 3.02% 696ms 14.40% operator new 198ms 4.10% 7.11% 662ms 13.69% __GI___libc_malloc 40ms 0.83% 7.94% 626ms 12.95% std::num_put::_M_insert_float 0 0% 7.94% 615ms 12.72% vtkQuad::New 3ms 0.062% 8.00% 613ms 12.68% vtkQuad::vtkQuad 1ms 0.021% 8.02% 600ms 12.41% vtkLine::New 9ms 0.19% 8.21% 578ms 11.95% vtkLine::vtkLine 0 0% 8.21% 577ms 11.93% vtkStreamingDemandDrivenPipeline::Update 0 0% 8.21% 577ms 11.93% vtkXMLWriterBase::Write 0 0% 8.21% 575ms 11.89% vtkDemandDrivenPipeline::ProcessRequest 0 0% 8.21% 572ms 11.83% vtkExecutive::CallAlgorithm 0 0% 8.21% 571ms 11.81% vtkCompositeDataPipeline::ExecuteData 0 0% 8.21% 571ms 11.81% vtkDemandDrivenPipeline::ExecuteData 0 0% 8.21% 571ms 11.81% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 8.21% 571ms 11.81% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 8.21% 568ms 11.75% vtkTriangle::New 6ms 0.12% 8.34% 566ms 11.71% vtkTriangle::vtkTriangle 0 0% 8.34% 515ms 10.65% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 8.34% 515ms 10.65% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 13ms 0.27% 8.60% 499ms 10.32% std::__cxx11::collate::do_transform 155ms 3.21% 11.81% 494ms 10.22% __GI___libc_free 7ms 0.14% 11.95% 460ms 9.51% ___vsnprintf 25ms 0.52% 12.47% 455ms 9.41% vtkPoints::SetDataType 1ms 0.021% 12.49% 453ms 9.37% __vsnprintf_internal (inline) 0 0% 12.49% 453ms 9.37% vtkXMLWriter::WriteBinaryData 1ms 0.021% 12.51% 448ms 9.27% vtkXMLWriter::WriteBinaryDataInternal 0 0% 12.51% 447ms 9.25% vtkXMLWriter::WriteBinaryDataBlock 51ms 1.05% 13.57% 446ms 9.22% __printf_buffer 0 0% 13.57% 438ms 9.06% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 2ms 0.041% 13.61% 380ms 7.86% vtkPolygon::~vtkPolygon 245ms 5.07% 18.68% 377ms 7.80% _int_malloc 2ms 0.041% 18.72% 364ms 7.53% __printf_fp_spec (inline) 19ms 0.39% 19.11% 362ms 7.49% __printf_fp_l_buffer 1ms 0.021% 19.13% 356ms 7.36% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 19.13% 351ms 7.26% VtkMeshWriter::WriteFiles 206ms 4.26% 23.39% 338ms 6.99% _int_free 0 0% 23.39% 328ms 6.78% vtkXMLWriter::WritePointsAppendedData 162ms 3.35% 26.74% 322ms 6.66% __printf_fp_buffer_1 36ms 0.74% 27.49% 318ms 6.58% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 1ms 0.021% 27.51% 301ms 6.23% vtkCell::~vtkCell 0 0% 27.51% 290ms 6.00% OnLatticeSimulation::UpdateCellLocationsAndTopology 4ms 0.083% 27.59% 290ms 6.00% PottsBasedCellPopulation::UpdateCellLocations 33ms 0.68% 28.27% 286ms 5.92% std::__new_allocator::allocate (inline) 0 0% 28.27% 286ms 5.92% std::allocator_traits::allocate (inline) 4ms 0.083% 28.36% 252ms 5.21% std::__new_allocator::deallocate (inline) 0 0% 28.36% 248ms 5.13% std::allocator_traits::deallocate (inline) 0 0% 28.36% 230ms 4.76% vtkXMLWriter::WriteCompressionBlock 1ms 0.021% 28.38% 222ms 4.59% vtkBase64OutputStream::Write 18ms 0.37% 28.75% 221ms 4.57% vtkBase64OutputStream::EncodeTriplet 7ms 0.14% 28.89% 214ms 4.43% vtkPoints::~vtkPoints 0 0% 28.89% 213ms 4.41% compress2 0 0% 28.89% 213ms 4.41% vtkDataCompressor::Compress 0 0% 28.89% 213ms 4.41% vtkZLibDataCompressor::CompressBuffer 1ms 0.021% 28.91% 212ms 4.38% deflate 64ms 1.32% 30.24% 211ms 4.36% crc32 7ms 0.14% 30.38% 195ms 4.03% vtkFloatArray::New 0 0% 30.38% 189ms 3.91% tbb::detail::r1::parallel_pipeline 64ms 1.32% 31.71% 187ms 3.87% std::ostream::write 4ms 0.083% 31.79% 185ms 3.83% vtkIdList::AllocateInternal 0 0% 31.79% 183ms 3.78% clone3 0 0% 31.79% 183ms 3.78% start_thread 1ms 0.021% 31.81% 183ms 3.78% std::set::set (inline) 24ms 0.5% 32.31% 182ms 3.76% std::_Rb_tree::_Rb_tree 0 0% 32.31% 182ms 3.76% tbb::detail::r1::reset 76ms 1.57% 33.88% 180ms 3.72% tbb::detail::r1::wait_bounded_queue_monitor 2ms 0.041% 33.92% 171ms 3.54% vtkLine::GetParametricCenter 107ms 2.21% 36.13% 170ms 3.52% malloc_consolidate 1ms 0.021% 36.15% 169ms 3.50% vtkFloatArray::vtkFloatArray 0 0% 36.15% 167ms 3.45% VertexMesh::~VertexMesh 55ms 1.14% 37.29% 166ms 3.43% std::_Rb_tree::_M_erase 11ms 0.23% 37.52% 162ms 3.35% std::vector::_M_default_append 1ms 0.021% 37.54% 161ms 3.33% vtkDataArray::CreateDataArray 5ms 0.1% 37.64% 160ms 3.31% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.021% 37.66% 159ms 3.29% vtkQuad::~vtkQuad 0 0% 37.66% 159ms 3.29% vtkTriangle::~vtkTriangle 1ms 0.021% 37.68% 158ms 3.27% NodesOnlyMesh::ConstructNodesWithoutMesh 1ms 0.021% 37.70% 158ms 3.27% vtkTypeFloat64Array::~vtkTypeFloat64Array 0 0% 37.70% 157ms 3.25% NodeLocationWriter::VisitAnyPopulation 6ms 0.12% 37.83% 157ms 3.25% std::_Vector_base::_M_deallocate (inline) 3ms 0.062% 37.89% 156ms 3.23% VertexMesh::VertexMesh 0 0% 37.89% 152ms 3.14% std::_Vector_base::_M_allocate (inline) 0 0% 37.89% 151ms 3.12% std::vector::~vector (inline) 4ms 0.083% 37.97% 151ms 3.12% vtkDoubleArray::vtkDoubleArray 4ms 0.083% 38.06% 151ms 3.12% vtkTypeFloat64Array::New 4ms 0.083% 38.14% 145ms 3.00% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 0 0% 38.14% 142ms 2.94% std::_Rb_tree::_M_create_node (inline) 1ms 0.021% 38.16% 139ms 2.87% VertexMesh::GenerateEdgesFromElements (inline) 6ms 0.12% 38.28% 138ms 2.85% MutableElement::BuildEdges 135ms 2.79% 41.08% 137ms 2.83% [libz.so.1.3] 0 0% 41.08% 134ms 2.77% std::_Rb_tree::_M_get_node (inline) 69ms 1.43% 42.50% 133ms 2.75% std::basic_filebuf::xsputn 0 0% 42.50% 128ms 2.65% std::_Rb_tree::_Alloc_node::operator() (inline) 14ms 0.29% 42.79% 128ms 2.65% std::_Rb_tree::_M_copy (inline) 2ms 0.041% 42.83% 127ms 2.63% vtkTypeFloat64Array::vtkTypeFloat64Array 29ms 0.6% 43.43% 122ms 2.52% vtkObject::vtkObject 0 0% 43.43% 121ms 2.50% EdgeHelper::~EdgeHelper (inline) 0 0% 43.43% 118ms 2.44% std::_Vector_base::~_Vector_base (inline) 0 0% 43.43% 118ms 2.44% vtkIdList::Allocate 0 0% 43.43% 117ms 2.42% std::set::~set (inline) 5ms 0.1% 43.54% 117ms 2.42% vtkFloatArray::~vtkFloatArray 1ms 0.021% 43.56% 111ms 2.30% EdgeHelper::GetEdgeFromNodes 58ms 1.20% 44.76% 110ms 2.28% hack_digit 15ms 0.31% 45.07% 109ms 2.25% std::_Rb_tree::_M_clone_node (inline) 0 0% 45.07% 108ms 2.23% vtkXMLWriter::WritePointDataAppendedData 1ms 0.021% 45.09% 106ms 2.19% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.083% 45.17% 103ms 2.13% std::map::operator[] (partial-inline) 102ms 2.11% 47.28% 102ms 2.11% __GI_sched_yield 0 0% 47.28% 102ms 2.11% std::_Rb_tree::_M_drop_node (inline) 0 0% 47.28% 97ms 2.01% std::_Rb_tree::_M_put_node (inline) 38ms 0.79% 48.07% 96ms 1.99% std::__ostream_insert 3ms 0.062% 48.13% 95ms 1.96% std::operator<< (inline) 94ms 1.94% 50.07% 94ms 1.94% __strcmp_avx2 4ms 0.083% 50.16% 93ms 1.92% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 37ms 0.77% 50.92% 93ms 1.92% vtkTypeFloat64Array::PrintSelf 4ms 0.083% 51.00% 91ms 1.88% std::vector::push_back (inline) 3ms 0.062% 51.07% 88ms 1.82% AbstractCellProperty::IsSubType (inline) 62ms 1.28% 52.35% 88ms 1.82% std::basic_streambuf::xsputn 17ms 0.35% 52.70% 85ms 1.76% __dynamic_cast 84ms 1.74% 54.44% 84ms 1.74% unlink_chunk 4ms 0.083% 54.52% 80ms 1.65% _int_free_maybe_consolidate 0 0% 54.52% 79ms 1.63% AbstractCellProperty::IsType (inline) 0 0% 54.52% 79ms 1.63% tcache_get (inline) 79ms 1.63% 56.15% 79ms 1.63% tcache_get_n (inline) 51ms 1.05% 57.21% 79ms 1.63% vtkObjectBase::UnRegisterInternal 0 0% 57.21% 78ms 1.61% Cell::HasCellProperty (inline) 2ms 0.041% 57.25% 78ms 1.61% CellPropertyCollection::HasProperty 17ms 0.35% 57.60% 77ms 1.59% vtkObject::Modified 5ms 0.1% 57.70% 76ms 1.57% vtkDoubleArray::~vtkDoubleArray 8ms 0.17% 57.87% 75ms 1.55% vtkAOSDataArrayTemplate::DataElementChanged 2ms 0.041% 57.91% 75ms 1.55% vtkIdList::New 25ms 0.52% 58.43% 74ms 1.53% std::_Rb_tree::_M_lower_bound (inline) 3ms 0.062% 58.49% 71ms 1.47% std::vector::_M_realloc_insert 0 0% 58.49% 71ms 1.47% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 1ms 0.021% 58.51% 69ms 1.43% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.062% 58.57% 63ms 1.30% std::_Rb_tree::_M_insert_unique 0 0% 58.57% 63ms 1.30% std::set::insert (inline) 0 0% 58.57% 61ms 1.26% NodesOnlyMesh::~NodesOnlyMesh 0 0% 58.57% 61ms 1.26% std::_Rb_tree::lower_bound (inline) 0 0% 58.57% 61ms 1.26% std::map::lower_bound (inline) 0 0% 58.57% 60ms 1.24% Cell::GetCellProliferativeType 10ms 0.21% 58.78% 60ms 1.24% boost::numeric::ublas::c_vector::c_vector (inline) 60ms 1.24% 60.02% 60ms 1.24% vtkTimeStamp::Modified 11ms 0.23% 60.25% 59ms 1.22% std::num_put::_M_insert_int 0 0% 60.25% 58ms 1.20% NodesOnlyMesh::SetUpBoxCollection 10ms 0.21% 60.46% 57ms 1.18% AbstractCellProperty::IsSame 11ms 0.23% 60.68% 54ms 1.12% vtkDataArray::vtkDataArray 7ms 0.14% 60.83% 54ms 1.12% vtkSOADataArrayTemplate::FillTypedComponent 53ms 1.10% 61.92% 53ms 1.10% std::ostream::sentry::sentry 1ms 0.021% 61.94% 50ms 1.03% PottsMesh::GetMooreNeighbouringNodeIndices 50ms 1.03% 62.98% 50ms 1.03% __memcpy_avx_unaligned_erms 0 0% 62.98% 48ms 0.99% boost::numeric::ublas::vector_assign (inline) 0 0% 62.98% 47ms 0.97% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 11ms 0.23% 63.21% 47ms 0.97% std::type_info::operator== (inline) 4ms 0.083% 63.29% 46ms 0.95% VertexMesh::Clear 30ms 0.62% 63.91% 46ms 0.95% __cxxabiv1::__si_class_type_info::__do_dyncast 37ms 0.77% 64.67% 46ms 0.95% std::_Hashtable::clear 0 0% 64.67% 44ms 0.91% vtkDataArray::ComputeRange 44ms 0.91% 65.58% 44ms 0.91% vtkObject::~vtkObject 43ms 0.89% 66.47% 43ms 0.89% [libvtkCommonCore-9.3.so.9.3] 5ms 0.1% 66.58% 43ms 0.89% std::_Rb_tree::_M_insert_ (inline) 0 0% 66.58% 43ms 0.89% std::map::~map (inline) 41ms 0.85% 67.43% 42ms 0.87% __GI___libc_write 0 0% 67.43% 42ms 0.87% std::__basic_file::xsputn 0 0% 67.43% 42ms 0.87% std::basic_filebuf::_M_convert_to_external 0 0% 67.43% 42ms 0.87% std::basic_filebuf::overflow 20ms 0.41% 67.84% 41ms 0.85% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 67.84% 41ms 0.85% DistributedBoxCollection::IsOwned 0 0% 67.84% 41ms 0.85% std::_Destroy (inline) 0 0% 67.84% 41ms 0.85% std::_Destroy_aux::__destroy (inline) 4ms 0.083% 67.92% 41ms 0.85% vtkAbstractArray::vtkAbstractArray 7ms 0.14% 68.07% 40ms 0.83% VertexMeshWriter::GetNextNode 8ms 0.17% 68.23% 39ms 0.81% vtkDataArray::~vtkDataArray 39ms 0.81% 69.04% 39ms 0.81% vtkObjectBase::vtkObjectBase 11ms 0.23% 69.27% 38ms 0.79% boost::numeric::ublas::indexing_vector_assign 0 0% 69.27% 38ms 0.79% std::_Rb_tree::_M_emplace_hint_unique 31ms 0.64% 69.91% 38ms 0.79% std::num_put::do_put 5ms 0.1% 70.01% 38ms 0.79% tbb::detail::r1::cancel_group_execution 2ms 0.041% 70.05% 37ms 0.77% DistributedBoxCollection::SetupLocalBoxesHalfOnly 0 0% 70.05% 37ms 0.77% vtk::detail::smp::vtkSMPToolsImplForTBB 6ms 0.12% 70.18% 36ms 0.74% vtkAOSDataArrayTemplate::InsertTuple 0 0% 70.18% 35ms 0.72% Cell::GetCellId 0 0% 70.18% 35ms 0.72% std::make_unique (inline) 35ms 0.72% 70.90% 35ms 0.72% tcache_put (inline) 0 0% 70.90% 34ms 0.7% DistributedBoxCollection::~DistributedBoxCollection 0 0% 70.90% 34ms 0.7% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 70.90% 34ms 0.7% _dl_init 0 0% 70.90% 34ms 0.7% _dl_start_user 0 0% 70.90% 34ms 0.7% call_init (inline) 0 0% 70.90% 34ms 0.7% std::__basic_file::xsputn_2 0 0% 70.90% 33ms 0.68% CxxTest::RealWorldDescription::setUp 0 0% 70.90% 33ms 0.68% PetscInitialize 0 0% 70.90% 33ms 0.68% PetscSetup::setUpWorld 0 0% 70.90% 33ms 0.68% PetscSetupUtils::CommonSetup 0 0% 70.90% 33ms 0.68% PetscSetupUtils::InitialisePetsc 33ms 0.68% 71.58% 33ms 0.68% __GI___writev 1ms 0.021% 71.60% 33ms 0.68% std::vector::emplace_back (inline) 0 0% 71.60% 33ms 0.68% vtkDoubleArray::New 0 0% 71.60% 32ms 0.66% CellIdWriter::GetCellDataForVtkOutput 0 0% 71.60% 32ms 0.66% PMPI_Init_thread 32ms 0.66% 72.26% 32ms 0.66% __mpn_divrem 0 0% 72.26% 32ms 0.66% ompi_mpi_init 4ms 0.083% 72.35% 32ms 0.66% vtkDataArrayPrivate::DoComputeVectorRange 0 0% 72.35% 31ms 0.64% PottsMesh::GetVonNeumannNeighbouringNodeIndices 0 0% 72.35% 31ms 0.64% VtkMeshWriter::MakeVtkMesh 0 0% 72.35% 30ms 0.62% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 0 0% 72.35% 30ms 0.62% std::_Rb_tree_header::_Rb_tree_header (inline) 30ms 0.62% 72.97% 30ms 0.62% std::codecvt::do_always_noconv 1ms 0.021% 72.99% 30ms 0.62% std::ostream::flush 4ms 0.083% 73.07% 30ms 0.62% vtkAOSDataArrayTemplate::AllocateTuples 29ms 0.6% 73.67% 30ms 0.62% vtkDataArray::Modified 6ms 0.12% 73.80% 30ms 0.62% vtkIdList::vtkIdList 1ms 0.021% 73.82% 29ms 0.6% 14ms 0.29% 74.11% 29ms 0.6% _int_free_merge_chunk 0 0% 74.11% 29ms 0.6% boost::numeric::ublas::c_vector::assign (inline) 1ms 0.021% 74.13% 29ms 0.6% boost::serialization::singleton::get_instance 0 0% 74.13% 29ms 0.6% std::basic_filebuf::open 5ms 0.1% 74.23% 29ms 0.6% vtk::detail::smp::vtkSMPToolsImpl::For 28ms 0.58% 74.81% 29ms 0.6% vtkObjectBase::Delete 29ms 0.6% 75.41% 29ms 0.6% vtkObjectBase::~vtkObjectBase 1ms 0.021% 75.43% 28ms 0.58% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 28ms 0.58% 76.01% 28ms 0.58% std::_Rb_tree_header::_M_reset (inline) 0 0% 76.01% 28ms 0.58% std::basic_filebuf::sync 1ms 0.021% 76.03% 28ms 0.58% std::less::operator() (inline) 0 0% 76.03% 28ms 0.58% vtkDataArrayPrivate::DoComputeScalarRange 3ms 0.062% 76.09% 28ms 0.58% vtkIdList::~vtkIdList 1ms 0.021% 76.11% 27ms 0.56% CellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 76.11% 27ms 0.56% NodesOnlyMesh::Clear (inline) 27ms 0.56% 76.67% 27ms 0.56% std::_Rb_tree::_S_right (inline) 27ms 0.56% 77.23% 27ms 0.56% std::operator< (inline) 0 0% 77.23% 26ms 0.54% Node::AddElement 2ms 0.041% 77.27% 26ms 0.54% Node::GetPoint 0 0% 77.27% 26ms 0.54% _IO_new_file_fopen 0 0% 77.27% 26ms 0.54% _IO_new_fopen 0 0% 77.27% 26ms 0.54% __GI__IO_file_open 4ms 0.083% 77.35% 26ms 0.54% __find_specmb (inline) 0 0% 77.35% 26ms 0.54% __fopen_internal (inline) 25ms 0.52% 77.87% 26ms 0.54% __libc_open64 0 0% 77.87% 26ms 0.54% std::__basic_file::open 9ms 0.19% 78.06% 26ms 0.54% vtkSOADataArrayTemplate::GetTupleIndexFromValueIndex 1ms 0.021% 78.08% 25ms 0.52% Edge::Edge 0 0% 78.08% 25ms 0.52% OutputFileHandler::OpenOutputFile 25ms 0.52% 78.59% 25ms 0.52% [libchaste_cell_based.so] 0 0% 78.59% 25ms 0.52% boost::serialization::void_cast_detail::void_caster_primitive::void_caster_primitive (inline) 4ms 0.083% 78.68% 25ms 0.52% std::__new_allocator::construct (inline) 0 0% 78.68% 25ms 0.52% std::allocator_traits::construct (inline) 0 0% 78.68% 25ms 0.52% std::default_delete::operator() (inline) 0 0% 78.68% 25ms 0.52% std::unique_ptr::~unique_ptr (inline)