File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3955ms, 78.99% of 5007ms total Dropped 731 nodes (cum <= 25.04ms) flat flat% sum% cum cum% 0 0% 0% 4780ms 95.47% __libc_start_call_main 0 0% 0% 4780ms 95.47% __libc_start_main_impl 0 0% 0% 4780ms 95.47% _start 0 0% 0% 4763ms 95.13% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4763ms 95.13% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4763ms 95.13% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4763ms 95.13% main 0 0% 0% 4727ms 94.41% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4727ms 94.41% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4727ms 94.41% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4716ms 94.19% AbstractCellBasedSimulation::Solve 0 0% 0% 4394ms 87.76% AbstractCellPopulation::WriteResultsToFiles 16ms 0.32% 0.32% 4147ms 82.82% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.32% 2034ms 40.62% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.02% 0.34% 1758ms 35.11% VertexMeshWriter::MakeVtkMesh 0 0% 0.34% 1351ms 26.98% vtkPolygon::New 1ms 0.02% 0.36% 1350ms 26.96% vtkPolygon::vtkPolygon 9ms 0.18% 0.54% 974ms 19.45% vtkCell::vtkCell 3ms 0.06% 0.6% 823ms 16.44% vtkPoints::New 1ms 0.02% 0.62% 796ms 15.90% VertexMeshWriter::WriteFiles 15ms 0.3% 0.92% 776ms 15.50% vtkPoints::vtkPoints 2ms 0.04% 0.96% 762ms 15.22% std::ostream::operator<< (inline) 43ms 0.86% 1.82% 760ms 15.18% std::ostream::_M_insert 43ms 0.86% 2.68% 694ms 13.86% operator new 218ms 4.35% 7.03% 658ms 13.14% __GI___libc_malloc 52ms 1.04% 8.07% 643ms 12.84% std::num_put::_M_insert_float 1ms 0.02% 8.09% 643ms 12.84% vtkQuad::New 3ms 0.06% 8.15% 639ms 12.76% vtkQuad::vtkQuad 1ms 0.02% 8.17% 622ms 12.42% vtkTriangle::New 6ms 0.12% 8.29% 616ms 12.30% vtkTriangle::vtkTriangle 0 0% 8.29% 608ms 12.14% vtkLine::New 0 0% 8.29% 600ms 11.98% vtkStreamingDemandDrivenPipeline::Update 0 0% 8.29% 600ms 11.98% vtkXMLWriterBase::Write 0 0% 8.29% 599ms 11.96% vtkDemandDrivenPipeline::ProcessRequest 0 0% 8.29% 597ms 11.92% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 8.29% 596ms 11.90% vtkDemandDrivenPipeline::ExecuteData 0 0% 8.29% 595ms 11.88% vtkCompositeDataPipeline::ExecuteData 0 0% 8.29% 595ms 11.88% vtkExecutive::CallAlgorithm 0 0% 8.29% 595ms 11.88% vtkXMLUnstructuredDataWriter::ProcessRequest 8ms 0.16% 8.45% 589ms 11.76% vtkLine::vtkLine 0 0% 8.45% 537ms 10.72% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 8.45% 537ms 10.72% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 168ms 3.36% 11.80% 500ms 9.99% __GI___libc_free 24ms 0.48% 12.28% 498ms 9.95% vtkPoints::SetDataType 11ms 0.22% 12.50% 487ms 9.73% std::__cxx11::collate::do_transform 0 0% 12.50% 487ms 9.73% vtkXMLWriter::WriteBinaryData 0 0% 12.50% 480ms 9.59% vtkXMLWriter::WriteBinaryDataBlock 0 0% 12.50% 480ms 9.59% vtkXMLWriter::WriteBinaryDataInternal 5ms 0.1% 12.60% 461ms 9.21% ___vsnprintf 0 0% 12.60% 456ms 9.11% __vsnprintf_internal (inline) 0 0% 12.60% 455ms 9.09% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 62ms 1.24% 13.84% 449ms 8.97% __printf_buffer 0 0% 13.84% 374ms 7.47% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 268ms 5.35% 19.19% 373ms 7.45% _int_malloc 0 0% 19.19% 370ms 7.39% VtkMeshWriter::WriteFiles 3ms 0.06% 19.25% 363ms 7.25% __printf_fp_spec (inline) 1ms 0.02% 19.27% 361ms 7.21% vtkPolygon::~vtkPolygon 22ms 0.44% 19.71% 360ms 7.19% __printf_fp_l_buffer 0 0% 19.71% 344ms 6.87% vtkXMLWriter::WritePointsAppendedData 181ms 3.61% 23.33% 330ms 6.59% __printf_fp_buffer_1 210ms 4.19% 27.52% 330ms 6.59% _int_free 48ms 0.96% 28.48% 324ms 6.47% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 40ms 0.8% 29.28% 314ms 6.27% std::__new_allocator::allocate (inline) 0 0% 29.28% 312ms 6.23% OnLatticeSimulation::UpdateCellLocationsAndTopology 6ms 0.12% 29.40% 312ms 6.23% PottsBasedCellPopulation::UpdateCellLocations 0 0% 29.40% 312ms 6.23% std::allocator_traits::allocate (inline) 9ms 0.18% 29.58% 278ms 5.55% vtkCell::~vtkCell 0 0% 29.58% 252ms 5.03% vtkXMLWriter::WriteCompressionBlock 2ms 0.04% 29.62% 251ms 5.01% std::__new_allocator::deallocate (inline) 0 0% 29.62% 251ms 5.01% std::allocator_traits::deallocate (inline) 0 0% 29.62% 240ms 4.79% vtkDataCompressor::Compress 0 0% 29.62% 239ms 4.77% compress2 0 0% 29.62% 239ms 4.77% vtkZLibDataCompressor::CompressBuffer 1ms 0.02% 29.64% 233ms 4.65% deflate 61ms 1.22% 30.86% 232ms 4.63% crc32 11ms 0.22% 31.08% 224ms 4.47% vtkBase64OutputStream::Write 1ms 0.02% 31.10% 215ms 4.29% std::set::set (inline) 15ms 0.3% 31.40% 213ms 4.25% vtkBase64OutputStream::EncodeTriplet 21ms 0.42% 31.82% 212ms 4.23% std::_Rb_tree::_Rb_tree 0 0% 31.82% 195ms 3.89% tbb::detail::r1::parallel_pipeline 7ms 0.14% 31.96% 191ms 3.81% vtkFloatArray::New 0 0% 31.96% 190ms 3.79% clone3 0 0% 31.96% 190ms 3.79% start_thread 0 0% 31.96% 189ms 3.77% tbb::detail::r1::reset 87ms 1.74% 33.69% 189ms 3.77% tbb::detail::r1::wait_bounded_queue_monitor 6ms 0.12% 33.81% 189ms 3.77% vtkPoints::~vtkPoints 0 0% 33.81% 188ms 3.75% std::_Rb_tree::_M_create_node (inline) 62ms 1.24% 35.05% 185ms 3.69% std::ostream::write 4ms 0.08% 35.13% 185ms 3.69% vtkIdList::AllocateInternal 1ms 0.02% 35.15% 181ms 3.61% NodeLocationWriter::VisitAnyPopulation 0 0% 35.15% 177ms 3.54% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 35.15% 176ms 3.52% VertexMesh::~VertexMesh 0 0% 35.15% 175ms 3.50% std::_Rb_tree::_M_get_node (inline) 8ms 0.16% 35.31% 172ms 3.44% std::_Rb_tree::~_Rb_tree (inline) 56ms 1.12% 36.43% 170ms 3.40% std::_Rb_tree::_M_erase 2ms 0.04% 36.47% 168ms 3.36% vtkFloatArray::vtkFloatArray 13ms 0.26% 36.73% 164ms 3.28% std::_Rb_tree::_M_copy (inline) 11ms 0.22% 36.95% 163ms 3.26% std::vector::_M_default_append 3ms 0.06% 37.01% 163ms 3.26% vtkQuad::~vtkQuad 155ms 3.10% 40.10% 161ms 3.22% [libz.so.1.3] 4ms 0.08% 40.18% 161ms 3.22% vtkDataArray::CreateDataArray 2ms 0.04% 40.22% 160ms 3.20% vtkLine::GetParametricCenter 0 0% 40.22% 159ms 3.18% std::vector::~vector (inline) 3ms 0.06% 40.28% 159ms 3.18% vtkDoubleArray::vtkDoubleArray 107ms 2.14% 42.42% 158ms 3.16% malloc_consolidate 1ms 0.02% 42.44% 156ms 3.12% VertexMesh::VertexMesh 4ms 0.08% 42.52% 154ms 3.08% NodesOnlyMesh::ConstructNodesWithoutMesh 11ms 0.22% 42.74% 154ms 3.08% vtkFloatArray::~vtkFloatArray 4ms 0.08% 42.82% 150ms 3.00% std::_Vector_base::_M_deallocate (inline) 8ms 0.16% 42.98% 150ms 3.00% vtkTypeFloat64Array::New 71ms 1.42% 44.40% 148ms 2.96% std::basic_filebuf::xsputn 2ms 0.04% 44.44% 147ms 2.94% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 6ms 0.12% 44.56% 147ms 2.94% std::_Rb_tree::_M_clone_node (inline) 2ms 0.04% 44.60% 147ms 2.94% vtkTypeFloat64Array::~vtkTypeFloat64Array 2ms 0.04% 44.64% 143ms 2.86% vtkTriangle::~vtkTriangle 4ms 0.08% 44.72% 137ms 2.74% MutableElement::BuildEdges 0 0% 44.72% 137ms 2.74% VertexMesh::GenerateEdgesFromElements (inline) 0 0% 44.72% 137ms 2.74% std::_Vector_base::_M_allocate (inline) 4ms 0.08% 44.80% 133ms 2.66% vtkTypeFloat64Array::vtkTypeFloat64Array 0 0% 44.80% 127ms 2.54% std::set::~set (inline) 0 0% 44.80% 125ms 2.50% EdgeHelper::~EdgeHelper (inline) 56ms 1.12% 45.92% 121ms 2.42% std::__ostream_insert 1ms 0.02% 45.94% 118ms 2.36% std::_Vector_base::~_Vector_base (inline) 0 0% 45.94% 118ms 2.36% std::operator<< (inline) 32ms 0.64% 46.57% 118ms 2.36% vtkObject::vtkObject 1ms 0.02% 46.59% 117ms 2.34% EdgeHelper::GetEdgeFromNodes 1ms 0.02% 46.61% 113ms 2.26% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.02% 46.63% 112ms 2.24% vtkIdList::Allocate 0 0% 46.63% 109ms 2.18% std::_Rb_tree::_M_drop_node (inline) 0 0% 46.63% 108ms 2.16% vtkXMLWriter::WritePointDataAppendedData 0 0% 46.63% 105ms 2.10% std::_Rb_tree::_M_put_node (inline) 58ms 1.16% 47.79% 105ms 2.10% vtkTypeFloat64Array::PrintSelf 98ms 1.96% 49.75% 98ms 1.96% __GI_sched_yield 96ms 1.92% 51.67% 96ms 1.92% __strcmp_avx2 0 0% 51.67% 94ms 1.88% AbstractCellProperty::IsSubType (inline) 20ms 0.4% 52.07% 94ms 1.88% __dynamic_cast 67ms 1.34% 53.41% 94ms 1.88% std::basic_streambuf::xsputn 0 0% 53.41% 91ms 1.82% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 4ms 0.08% 53.49% 91ms 1.82% std::map::operator[] (partial-inline) 64ms 1.28% 54.76% 85ms 1.70% vtkObjectBase::UnRegisterInternal 28ms 0.56% 55.32% 84ms 1.68% vtkObject::Modified 6ms 0.12% 55.44% 81ms 1.62% _int_free_maybe_consolidate 9ms 0.18% 55.62% 81ms 1.62% vtkAOSDataArrayTemplate::DataElementChanged 5ms 0.1% 55.72% 81ms 1.62% vtkIdList::New 8ms 0.16% 55.88% 79ms 1.58% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 55.88% 79ms 1.58% Cell::HasCellProperty (inline) 4ms 0.08% 55.96% 79ms 1.58% CellPropertyCollection::HasProperty 0 0% 55.96% 79ms 1.58% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 46ms 0.92% 56.88% 78ms 1.56% hack_digit 5ms 0.1% 56.98% 75ms 1.50% vtkDoubleArray::~vtkDoubleArray 2ms 0.04% 57.02% 74ms 1.48% std::vector::push_back (inline) 4ms 0.08% 57.10% 72ms 1.44% AbstractCellProperty::IsType (inline) 7ms 0.14% 57.24% 71ms 1.42% vtkDataArray::vtkDataArray 69ms 1.38% 58.62% 69ms 1.38% unlink_chunk 24ms 0.48% 59.10% 67ms 1.34% std::_Rb_tree::_M_lower_bound (inline) 0 0% 59.10% 64ms 1.28% PottsMesh::GetMooreNeighbouringNodeIndices 18ms 0.36% 59.46% 64ms 1.28% vtkAbstractArray::vtkAbstractArray 14ms 0.28% 59.74% 64ms 1.28% vtkSOADataArrayTemplate::FillTypedComponent 0 0% 59.74% 63ms 1.26% NodesOnlyMesh::~NodesOnlyMesh 2ms 0.04% 59.78% 63ms 1.26% std::_Rb_tree::_M_insert_unique 0 0% 59.78% 63ms 1.26% std::set::insert (inline) 0 0% 59.78% 58ms 1.16% std::_Rb_tree::lower_bound (inline) 0 0% 59.78% 58ms 1.16% std::map::lower_bound (inline) 5ms 0.1% 59.88% 58ms 1.16% std::vector::_M_realloc_insert 1ms 0.02% 59.90% 56ms 1.12% boost::numeric::ublas::c_vector::c_vector (inline) 10ms 0.2% 60.10% 56ms 1.12% std::num_put::_M_insert_int 26ms 0.52% 60.62% 55ms 1.10% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.04% 60.66% 54ms 1.08% boost::numeric::ublas::vector_assign (inline) 0 0% 60.66% 54ms 1.08% tcache_get (inline) 54ms 1.08% 61.73% 54ms 1.08% tcache_get_n (inline) 54ms 1.08% 62.81% 54ms 1.08% vtkTimeStamp::Modified 0 0% 62.81% 53ms 1.06% NodesOnlyMesh::SetUpBoxCollection 53ms 1.06% 63.87% 53ms 1.06% __memcpy_avx_unaligned_erms 0 0% 63.87% 52ms 1.04% Cell::GetCellProliferativeType 0 0% 63.87% 51ms 1.02% VertexMesh::Clear 0 0% 63.87% 48ms 0.96% std::_Destroy (inline) 0 0% 63.87% 48ms 0.96% std::_Destroy_aux::__destroy (inline) 31ms 0.62% 64.49% 48ms 0.96% std::_Hashtable::clear 1ms 0.02% 64.51% 47ms 0.94% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 10ms 0.2% 64.71% 46ms 0.92% AbstractCellProperty::IsSame 46ms 0.92% 65.63% 46ms 0.92% __GI___writev 0 0% 65.63% 46ms 0.92% std::__basic_file::xsputn_2 0 0% 65.63% 46ms 0.92% std::map::~map (inline) 45ms 0.9% 66.53% 46ms 0.92% vtkObjectBase::Delete 4ms 0.08% 66.61% 44ms 0.88% std::_Rb_tree::_M_insert_ (inline) 8ms 0.16% 66.77% 43ms 0.86% VertexMeshWriter::GetNextNode 43ms 0.86% 67.63% 43ms 0.86% __GI___libc_write 15ms 0.3% 67.92% 43ms 0.86% boost::numeric::ublas::indexing_vector_assign 0 0% 67.92% 43ms 0.86% std::__basic_file::xsputn 0 0% 67.92% 43ms 0.86% std::basic_filebuf::_M_convert_to_external 0 0% 67.92% 43ms 0.86% std::basic_filebuf::overflow 9ms 0.18% 68.10% 42ms 0.84% vtkDataArray::~vtkDataArray 0 0% 68.10% 40ms 0.8% DistributedBoxCollection::~DistributedBoxCollection 0 0% 68.10% 40ms 0.8% NodesOnlyMesh::ClearBoxCollection (inline) 0 0% 68.10% 39ms 0.78% std::make_unique (inline) 1ms 0.02% 68.12% 39ms 0.78% vtkDoubleArray::New 39ms 0.78% 68.90% 39ms 0.78% vtkObject::~vtkObject 38ms 0.76% 69.66% 38ms 0.76% [libstdc++.so.6.0.33] 38ms 0.76% 70.42% 38ms 0.76% [libvtkCommonCore-9.3.so.9.3] 0 0% 70.42% 38ms 0.76% std::basic_filebuf::open 21ms 0.42% 70.84% 37ms 0.74% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 70.84% 37ms 0.74% DistributedBoxCollection::IsOwned 0 0% 70.84% 37ms 0.74% _dl_init 0 0% 70.84% 37ms 0.74% _dl_start_user 0 0% 70.84% 37ms 0.74% call_init (inline) 0 0% 70.84% 36ms 0.72% Cell::GetMutationState 36ms 0.72% 71.56% 36ms 0.72% std::_Rb_tree_increment 8ms 0.16% 71.72% 36ms 0.72% std::type_info::operator== (inline) 0 0% 71.72% 36ms 0.72% vtkDataArray::ComputeRange 1ms 0.02% 71.74% 35ms 0.7% PottsMesh::GetVonNeumannNeighbouringNodeIndices 2ms 0.04% 71.78% 35ms 0.7% boost::serialization::singleton::get_instance 0 0% 71.78% 35ms 0.7% std::__basic_file::open 35ms 0.7% 72.48% 35ms 0.7% std::ostream::sentry::sentry 7ms 0.14% 72.62% 34ms 0.68% vtkIdList::~vtkIdList 34ms 0.68% 73.30% 34ms 0.68% vtkObjectBase::~vtkObjectBase 0 0% 73.30% 33ms 0.66% _IO_new_fopen 0 0% 73.30% 33ms 0.66% __fopen_internal (inline) 8ms 0.16% 73.46% 33ms 0.66% vtkAOSDataArrayTemplate::InsertTuple 0 0% 73.46% 32ms 0.64% Cell::GetCellId 0 0% 73.46% 32ms 0.64% CxxTest::RealWorldDescription::setUp 0 0% 73.46% 32ms 0.64% PMPI_Init_thread 0 0% 73.46% 32ms 0.64% PetscInitialize 0 0% 73.46% 32ms 0.64% PetscSetup::setUpWorld 0 0% 73.46% 32ms 0.64% PetscSetupUtils::CommonSetup 0 0% 73.46% 32ms 0.64% PetscSetupUtils::InitialisePetsc 0 0% 73.46% 32ms 0.64% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 0 0% 73.46% 32ms 0.64% ompi_mpi_init 3ms 0.06% 73.52% 31ms 0.62% Node::AddElement 1ms 0.02% 73.54% 31ms 0.62% VtkMeshWriter::MakeVtkMesh 0 0% 73.54% 31ms 0.62% _IO_new_file_fopen 0 0% 73.54% 31ms 0.62% __GI__IO_file_open 31ms 0.62% 74.16% 31ms 0.62% __libc_open64 31ms 0.62% 74.78% 31ms 0.62% std::codecvt::do_always_noconv 0 0% 74.78% 30ms 0.6% CellIdWriter::GetCellDataForVtkOutput 6ms 0.12% 74.90% 30ms 0.6% std::_Rb_tree_const_iterator::operator++ (inline) 22ms 0.44% 75.33% 29ms 0.58% __printf_buffer_write 1ms 0.02% 75.35% 29ms 0.58% std::_Rb_tree::_M_emplace_hint_unique 0 0% 75.35% 29ms 0.58% std::ostream::flush 1ms 0.02% 75.37% 29ms 0.58% std::unique_ptr::~unique_ptr (inline) 5ms 0.1% 75.47% 29ms 0.58% tbb::detail::r1::cancel_group_execution 0 0% 75.47% 28ms 0.56% DistributedBoxCollection::SetupLocalBoxesHalfOnly 2ms 0.04% 75.51% 28ms 0.56% Edge::Edge 1ms 0.02% 75.53% 28ms 0.56% VertexMeshWriter::GetNextElement 9ms 0.18% 75.71% 28ms 0.56% _int_free_merge_chunk 0 0% 75.71% 28ms 0.56% std::basic_filebuf::sync 0 0% 75.71% 28ms 0.56% std::default_delete::operator() (inline) 0 0% 75.71% 28ms 0.56% vtk::detail::smp::vtkSMPToolsImplForTBB 28ms 0.56% 76.27% 28ms 0.56% vtkDataArray::Modified 0 0% 76.27% 27ms 0.54% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 1ms 0.02% 76.29% 27ms 0.54% std::_Rb_tree_header::_Rb_tree_header (inline) 0 0% 76.29% 27ms 0.54% std::less::operator() (inline) 20ms 0.4% 76.69% 27ms 0.54% std::num_put::do_put 27ms 0.54% 77.23% 27ms 0.54% std::operator< (inline) 27ms 0.54% 77.77% 27ms 0.54% vtkObjectBase::vtkObjectBase 1ms 0.02% 77.79% 26ms 0.52% 0 0% 77.79% 26ms 0.52% Edge::SetNodes (inline) 7ms 0.14% 77.93% 26ms 0.52% Node::GetPoint 0 0% 77.93% 26ms 0.52% OutputFileHandler::OpenOutputFile 26ms 0.52% 78.45% 26ms 0.52% [libchaste_cell_based.so] 0 0% 78.45% 26ms 0.52% boost::numeric::ublas::c_vector::assign (inline) 26ms 0.52% 78.97% 26ms 0.52% boost::numeric::ublas::c_vector::operator() 1ms 0.02% 78.99% 26ms 0.52% vtkDataArrayPrivate::DoComputeVectorRange