File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3046ms, 80.24% of 3796ms total Dropped 687 nodes (cum <= 18.98ms) flat flat% sum% cum cum% 0 0% 0% 3620ms 95.36% __libc_start_call_main 0 0% 0% 3620ms 95.36% __libc_start_main_impl 0 0% 0% 3620ms 95.36% _start 0 0% 0% 3605ms 94.97% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 3605ms 94.97% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 3605ms 94.97% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 3605ms 94.97% main 0 0% 0% 3566ms 93.94% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 3566ms 93.94% CxxTest::TestRunner::runTest (inline) 0 0% 0% 3566ms 93.94% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 3557ms 93.70% AbstractCellBasedSimulation::Solve 0 0% 0% 3283ms 86.49% AbstractCellPopulation::WriteResultsToFiles 10ms 0.26% 0.26% 3124ms 82.30% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.26% 1553ms 40.91% VertexMeshWriter::WriteVtkUsingMesh 0 0% 0.26% 1340ms 35.30% VertexMeshWriter::MakeVtkMesh 0 0% 0.26% 992ms 26.13% vtkPolygon::New 3ms 0.079% 0.34% 991ms 26.11% vtkPolygon::vtkPolygon 5ms 0.13% 0.47% 713ms 18.78% vtkCell::vtkCell 3ms 0.079% 0.55% 619ms 16.31% vtkPoints::New 9ms 0.24% 0.79% 577ms 15.20% vtkPoints::vtkPoints 0 0% 0.79% 548ms 14.44% VertexMeshWriter::WriteFiles 41ms 1.08% 1.87% 505ms 13.30% std::ostream::_M_insert 0 0% 1.87% 502ms 13.22% std::ostream::operator<< (inline) 25ms 0.66% 2.53% 497ms 13.09% operator new 2ms 0.053% 2.58% 483ms 12.72% vtkLine::New 152ms 4.00% 6.59% 478ms 12.59% __GI___libc_malloc 13ms 0.34% 6.93% 474ms 12.49% vtkLine::vtkLine 0 0% 6.93% 447ms 11.78% vtkQuad::New 1ms 0.026% 6.95% 445ms 11.72% vtkQuad::vtkQuad 0 0% 6.95% 445ms 11.72% vtkStreamingDemandDrivenPipeline::Update 0 0% 6.95% 445ms 11.72% vtkXMLWriterBase::Write 0 0% 6.95% 444ms 11.70% vtkDemandDrivenPipeline::ProcessRequest 0 0% 6.95% 444ms 11.70% vtkTriangle::New 0 0% 6.95% 442ms 11.64% vtkDemandDrivenPipeline::ExecuteData 0 0% 6.95% 442ms 11.64% vtkStreamingDemandDrivenPipeline::ProcessRequest 4ms 0.11% 7.06% 441ms 11.62% vtkTriangle::vtkTriangle 0 0% 7.06% 440ms 11.59% vtkCompositeDataPipeline::ExecuteData 0 0% 7.06% 439ms 11.56% vtkExecutive::CallAlgorithm 0 0% 7.06% 439ms 11.56% vtkXMLUnstructuredDataWriter::ProcessRequest 26ms 0.68% 7.74% 409ms 10.77% std::num_put::_M_insert_float 0 0% 7.74% 392ms 10.33% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 7.74% 392ms 10.33% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 108ms 2.85% 10.59% 377ms 9.93% __GI___libc_free 27ms 0.71% 11.30% 358ms 9.43% vtkPoints::SetDataType 0 0% 11.30% 349ms 9.19% vtkXMLWriter::WriteBinaryData 0 0% 11.30% 346ms 9.11% vtkXMLWriter::WriteBinaryDataInternal 0 0% 11.30% 345ms 9.09% vtkXMLWriter::WriteBinaryDataBlock 0 0% 11.30% 341ms 8.98% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 9ms 0.24% 11.54% 337ms 8.88% std::__cxx11::collate::do_transform 4ms 0.11% 11.64% 317ms 8.35% ___vsnprintf 0 0% 11.64% 313ms 8.25% __vsnprintf_internal (inline) 43ms 1.13% 12.78% 312ms 8.22% __printf_buffer 0 0% 12.78% 307ms 8.09% vtkPolygon::~vtkPolygon 196ms 5.16% 17.94% 279ms 7.35% _int_malloc 0 0% 17.94% 272ms 7.17% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 17.94% 269ms 7.09% VtkMeshWriter::WriteFiles 149ms 3.93% 21.87% 267ms 7.03% _int_free 0 0% 21.87% 264ms 6.95% vtkXMLWriter::WritePointsAppendedData 0 0% 21.87% 260ms 6.85% OnLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.053% 21.92% 260ms 6.85% PottsBasedCellPopulation::UpdateCellLocations 2ms 0.053% 21.97% 252ms 6.64% vtkCell::~vtkCell 5ms 0.13% 22.10% 244ms 6.43% __printf_fp_l_buffer 0 0% 22.10% 244ms 6.43% __printf_fp_spec (inline) 63ms 1.66% 23.76% 241ms 6.35% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 104ms 2.74% 26.50% 226ms 5.95% __printf_fp_buffer_1 32ms 0.84% 27.34% 222ms 5.85% std::__new_allocator::allocate (inline) 0 0% 27.34% 221ms 5.82% std::allocator_traits::allocate (inline) 1ms 0.026% 27.37% 204ms 5.37% std::__new_allocator::deallocate (inline) 0 0% 27.37% 203ms 5.35% std::allocator_traits::deallocate (inline) 0 0% 27.37% 179ms 4.72% vtkXMLWriter::WriteCompressionBlock 0 0% 27.37% 175ms 4.61% std::set::set (inline) 17ms 0.45% 27.82% 174ms 4.58% std::_Rb_tree::_Rb_tree 0 0% 27.82% 171ms 4.50% compress2 0 0% 27.82% 171ms 4.50% vtkDataCompressor::Compress 0 0% 27.82% 171ms 4.50% vtkZLibDataCompressor::CompressBuffer 0 0% 27.82% 170ms 4.48% deflate 5ms 0.13% 27.95% 170ms 4.48% vtkBase64OutputStream::Write 33ms 0.87% 28.82% 169ms 4.45% crc32 2ms 0.053% 28.87% 167ms 4.40% vtkPoints::~vtkPoints 14ms 0.37% 29.24% 162ms 4.27% vtkBase64OutputStream::EncodeTriplet 3ms 0.079% 29.32% 156ms 4.11% vtkFloatArray::New 0 0% 29.32% 148ms 3.90% VertexMesh::~VertexMesh 0 0% 29.32% 148ms 3.90% tbb::detail::r1::parallel_pipeline 0 0% 29.32% 146ms 3.85% clone3 0 0% 29.32% 146ms 3.85% start_thread 76ms 2.00% 31.32% 141ms 3.71% malloc_consolidate 1ms 0.026% 31.35% 141ms 3.71% vtkTriangle::~vtkTriangle 1ms 0.026% 31.38% 139ms 3.66% tbb::detail::r1::reset 36ms 0.95% 32.32% 138ms 3.64% std::ostream::write 2ms 0.053% 32.38% 138ms 3.64% vtkFloatArray::vtkFloatArray 0 0% 32.38% 136ms 3.58% std::vector::~vector (inline) 4ms 0.11% 32.48% 136ms 3.58% vtkIdList::AllocateInternal 42ms 1.11% 33.59% 134ms 3.53% std::_Rb_tree::_M_erase 4ms 0.11% 33.69% 132ms 3.48% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.026% 33.72% 132ms 3.48% vtkTypeFloat64Array::~vtkTypeFloat64Array 2ms 0.053% 33.77% 130ms 3.42% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 53ms 1.40% 35.17% 130ms 3.42% tbb::detail::r1::wait_bounded_queue_monitor 123ms 3.24% 38.41% 129ms 3.40% [libz.so.1.3] 0 0% 38.41% 129ms 3.40% std::_Rb_tree::_M_create_node (inline) 0 0% 38.41% 129ms 3.40% vtkLine::GetParametricCenter 0 0% 38.41% 128ms 3.37% vtkQuad::~vtkQuad 1ms 0.026% 38.44% 125ms 3.29% NodesOnlyMesh::ConstructNodesWithoutMesh 17ms 0.45% 38.88% 125ms 3.29% std::_Rb_tree::_M_copy (inline) 3ms 0.079% 38.96% 125ms 3.29% vtkDataArray::CreateDataArray 2ms 0.053% 39.01% 122ms 3.21% VertexMesh::VertexMesh 0 0% 39.01% 122ms 3.21% std::_Rb_tree::_M_get_node (inline) 7ms 0.18% 39.20% 121ms 3.19% vtkTypeFloat64Array::New 0 0% 39.20% 120ms 3.16% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.053% 39.25% 119ms 3.13% std::_Vector_base::_M_deallocate (inline) 46ms 1.21% 40.46% 117ms 3.08% std::basic_filebuf::xsputn 5ms 0.13% 40.60% 112ms 2.95% MutableElement::BuildEdges 0 0% 40.60% 112ms 2.95% VertexMesh::GenerateEdgesFromElements (inline) 2ms 0.053% 40.65% 108ms 2.85% vtkDoubleArray::vtkDoubleArray 0 0% 40.65% 105ms 2.77% NodeLocationWriter::VisitAnyPopulation 0 0% 40.65% 105ms 2.77% std::_Vector_base::~_Vector_base (inline) 10ms 0.26% 40.91% 104ms 2.74% std::_Rb_tree::_M_clone_node (inline) 0 0% 40.91% 102ms 2.69% EdgeHelper::~EdgeHelper (inline) 2ms 0.053% 40.96% 102ms 2.69% vtkTypeFloat64Array::vtkTypeFloat64Array 0 0% 40.96% 101ms 2.66% std::set::~set (inline) 4ms 0.11% 41.07% 101ms 2.66% std::vector::_M_default_append 1ms 0.026% 41.10% 100ms 2.63% std::_Vector_base::_M_allocate (inline) 3ms 0.079% 41.17% 94ms 2.48% EdgeHelper::GetEdgeFromNodes 91ms 2.40% 43.57% 91ms 2.40% __strcmp_evex 0 0% 43.57% 91ms 2.40% vtkIdList::Allocate 45ms 1.19% 44.76% 91ms 2.40% vtkTypeFloat64Array::PrintSelf 23ms 0.61% 45.36% 89ms 2.34% vtkObject::vtkObject 0 0% 45.36% 88ms 2.32% CellPropertyCollection::GetPropertiesType (inline) 0 0% 45.36% 88ms 2.32% std::_Rb_tree::_M_drop_node (inline) 1ms 0.026% 45.39% 88ms 2.32% vtkFloatArray::~vtkFloatArray 1ms 0.026% 45.42% 87ms 2.29% AbstractCellProperty::IsType (inline) 0 0% 45.42% 86ms 2.27% std::_Rb_tree::_M_put_node (inline) 1ms 0.026% 45.44% 84ms 2.21% AbstractCellProperty::IsSubType (inline) 1ms 0.026% 45.47% 84ms 2.21% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 28ms 0.74% 46.21% 84ms 2.21% __dynamic_cast 0 0% 46.21% 83ms 2.19% Cell::HasCellProperty (inline) 2ms 0.053% 46.26% 83ms 2.19% CellPropertyCollection::HasProperty 45ms 1.19% 47.44% 82ms 2.16% hack_digit 6ms 0.16% 47.60% 80ms 2.11% _int_free_maybe_consolidate 55ms 1.45% 49.05% 80ms 2.11% vtkObjectBase::UnRegisterInternal 79ms 2.08% 51.13% 79ms 2.08% unlink_chunk 24ms 0.63% 51.77% 79ms 2.08% vtkAOSDataArrayTemplate::DataElementChanged 0 0% 51.77% 77ms 2.03% vtkXMLWriter::WritePointDataAppendedData 75ms 1.98% 53.74% 75ms 1.98% __GI_sched_yield 15ms 0.4% 54.14% 73ms 1.92% vtkObject::Modified 11ms 0.29% 54.43% 69ms 1.82% AbstractCellProperty::IsSame 8ms 0.21% 54.64% 67ms 1.77% boost::numeric::ublas::c_vector::c_vector (partial-inline) 2ms 0.053% 54.69% 62ms 1.63% std::operator<< (inline) 3ms 0.079% 54.77% 62ms 1.63% std::vector::push_back (inline) 3ms 0.079% 54.85% 60ms 1.58% vtkDoubleArray::~vtkDoubleArray 37ms 0.97% 55.82% 59ms 1.55% std::_Hashtable::clear 26ms 0.68% 56.51% 59ms 1.55% std::__ostream_insert 2ms 0.053% 56.56% 59ms 1.55% std::map::operator[] (partial-inline) 11ms 0.29% 56.85% 58ms 1.53% std::type_info::operator== (inline) 0 0% 56.85% 57ms 1.50% boost::numeric::ublas::vector_assign (inline) 2ms 0.053% 56.90% 57ms 1.50% vtkIdList::New 2ms 0.053% 56.95% 55ms 1.45% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.026% 56.98% 55ms 1.45% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 55ms 1.45% 58.43% 55ms 1.45% vtkTimeStamp::Modified 1ms 0.026% 58.46% 54ms 1.42% Cell::GetCellProliferativeType 0 0% 58.46% 53ms 1.40% PottsMesh::GetMooreNeighbouringNodeIndices 7ms 0.18% 58.64% 53ms 1.40% vtkDataArray::vtkDataArray 0 0% 58.64% 51ms 1.34% NodesOnlyMesh::SetUpBoxCollection 6ms 0.16% 58.80% 50ms 1.32% VertexMeshWriter::GetNextNode 0 0% 58.80% 49ms 1.29% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 13ms 0.34% 59.14% 47ms 1.24% std::_Rb_tree::_M_lower_bound (inline) 0 0% 59.14% 46ms 1.21% VertexMesh::Clear 0 0% 59.14% 45ms 1.19% NodesOnlyMesh::~NodesOnlyMesh 45ms 1.19% 60.33% 45ms 1.19% __GI___writev 27ms 0.71% 61.04% 45ms 1.19% std::basic_streambuf::xsputn 19ms 0.5% 61.54% 44ms 1.16% boost::numeric::ublas::indexing_vector_assign 0 0% 61.54% 44ms 1.16% std::__basic_file::xsputn_2 16ms 0.42% 61.96% 44ms 1.16% vtkAbstractArray::vtkAbstractArray 1ms 0.026% 61.99% 42ms 1.11% std::_Rb_tree::_M_insert_unique 0 0% 61.99% 42ms 1.11% std::set::insert (inline) 4ms 0.11% 62.09% 42ms 1.11% std::vector::_M_realloc_insert 41ms 1.08% 63.17% 41ms 1.08% __memcpy_avx512_unaligned_erms 0 0% 63.17% 41ms 1.08% tcache_get (inline) 41ms 1.08% 64.25% 41ms 1.08% tcache_get_n (inline) 0 0% 64.25% 40ms 1.05% std::_Rb_tree::lower_bound (inline) 0 0% 64.25% 40ms 1.05% std::map::lower_bound (inline) 1ms 0.026% 64.28% 38ms 1.00% DistributedBoxCollection::IsOwned 23ms 0.61% 64.88% 38ms 1.00% __cxxabiv1::__si_class_type_info::__do_dyncast 7ms 0.18% 65.07% 37ms 0.97% vtkSOADataArrayTemplate::FillTypedComponent 0 0% 65.07% 36ms 0.95% CxxTest::RealWorldDescription::setUp 22ms 0.58% 65.65% 36ms 0.95% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 65.65% 36ms 0.95% PetscSetup::setUpWorld 0 0% 65.65% 36ms 0.95% PetscSetupUtils::CommonSetup 1ms 0.026% 65.67% 35ms 0.92% 0 0% 65.67% 35ms 0.92% PMPI_Init_thread 0 0% 65.67% 35ms 0.92% PetscInitialize 0 0% 65.67% 35ms 0.92% PetscSetupUtils::InitialisePetsc 0 0% 65.67% 35ms 0.92% _dl_init 0 0% 65.67% 35ms 0.92% call_init (inline) 0 0% 65.67% 35ms 0.92% ompi_mpi_init 3ms 0.079% 65.75% 34ms 0.9% DistributedBoxCollection::SetupLocalBoxesHalfOnly 34ms 0.9% 66.65% 34ms 0.9% [libvtkCommonCore-9.3.so.9.3] 0 0% 66.65% 33ms 0.87% std::_Destroy (inline) 0 0% 66.65% 33ms 0.87% std::_Destroy_aux::__destroy (inline) 5ms 0.13% 66.78% 33ms 0.87% std::num_put::_M_insert_int 1ms 0.026% 66.81% 32ms 0.84% std::_Rb_tree::_M_insert_ (inline) 0 0% 66.81% 32ms 0.84% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 0 0% 66.81% 32ms 0.84% std::_Rb_tree_header::_Rb_tree_header (inline) 0 0% 66.81% 32ms 0.84% std::make_unique (inline) 0 0% 66.81% 31ms 0.82% DistributedBoxCollection::~DistributedBoxCollection 0 0% 66.81% 31ms 0.82% NodesOnlyMesh::ClearBoxCollection (inline) 6ms 0.16% 66.97% 31ms 0.82% _int_free_merge_chunk 0 0% 66.97% 31ms 0.82% std::map::~map (inline) 2ms 0.053% 67.02% 30ms 0.79% Node::GetPoint 0 0% 67.02% 30ms 0.79% VtkMeshWriter::MakeVtkMesh 0 0% 67.02% 30ms 0.79% _dl_start_user 0 0% 67.02% 30ms 0.79% vtkDataArray::ComputeRange 6ms 0.16% 67.18% 30ms 0.79% vtkDataArray::~vtkDataArray 29ms 0.76% 67.94% 29ms 0.76% std::_Rb_tree_header::_M_reset (inline) 5ms 0.13% 68.07% 29ms 0.76% vtkDataArrayPrivate::DoComputeVectorRange 0 0% 68.07% 28ms 0.74% boost::numeric::ublas::c_vector::assign (inline) 0 0% 68.07% 27ms 0.71% OutputFileHandler::OpenOutputFile 27ms 0.71% 68.78% 27ms 0.71% [libstdc++.so.6.0.33] 27ms 0.71% 69.49% 27ms 0.71% __memset_avx512_unaligned_erms 27ms 0.71% 70.21% 27ms 0.71% std::codecvt::do_always_noconv 0 0% 70.21% 27ms 0.71% vtk::detail::smp::vtkSMPToolsImplForTBB 6ms 0.16% 70.36% 27ms 0.71% vtkAOSDataArrayTemplate::InsertTuple 0 0% 70.36% 26ms 0.68% std::basic_filebuf::open 0 0% 70.36% 26ms 0.68% std::basic_filebuf::overflow 3ms 0.079% 70.44% 26ms 0.68% tbb::detail::r1::cancel_group_execution 26ms 0.68% 71.13% 26ms 0.68% vtkObjectBase::Delete 0 0% 71.13% 25ms 0.66% Cell::GetCellId 0 0% 71.13% 25ms 0.66% _IO_new_file_fopen 0 0% 71.13% 25ms 0.66% _IO_new_fopen 5ms 0.13% 71.26% 25ms 0.66% __find_specmb (inline) 0 0% 71.26% 25ms 0.66% __fopen_internal (inline) 25ms 0.66% 71.92% 25ms 0.66% __mpn_divrem 21ms 0.55% 72.47% 25ms 0.66% _int_free_create_chunk (inline) 0 0% 72.47% 25ms 0.66% std::__basic_file::open 7ms 0.18% 72.66% 25ms 0.66% std::__new_allocator::construct (inline) 0 0% 72.66% 25ms 0.66% std::allocator_traits::construct (inline) 1ms 0.026% 72.68% 25ms 0.66% std::basic_filebuf::_M_convert_to_external 22ms 0.58% 73.26% 25ms 0.66% vtkObject::ObjectFinalize 25ms 0.66% 73.92% 25ms 0.66% vtkObjectBase::~vtkObjectBase 0 0% 73.92% 24ms 0.63% CellIdWriter::GetCellDataForVtkOutput 2ms 0.053% 73.97% 24ms 0.63% CellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 73.97% 24ms 0.63% __GI__IO_file_open 24ms 0.63% 74.60% 24ms 0.63% __GI___libc_write 24ms 0.63% 75.24% 24ms 0.63% boost::numeric::ublas::c_vector::operator() 0 0% 75.24% 24ms 0.63% std::__basic_file::xsputn 0 0% 75.24% 24ms 0.63% std::less::operator() (inline) 23ms 0.61% 75.84% 24ms 0.63% std::num_put::do_put 24ms 0.63% 76.48% 24ms 0.63% std::operator< (inline) 3ms 0.079% 76.55% 24ms 0.63% vtkIdList::~vtkIdList 24ms 0.63% 77.19% 24ms 0.63% vtkObject::~vtkObject 23ms 0.61% 77.79% 23ms 0.61% __libc_open64 1ms 0.026% 77.82% 23ms 0.61% boost::serialization::singleton::get_instance 5ms 0.13% 77.95% 23ms 0.61% vtkIdList::vtkIdList 0 0% 77.95% 22ms 0.58% Edge::Edge 0 0% 77.95% 22ms 0.58% orte_init 22ms 0.58% 78.53% 22ms 0.58% std::ostream::sentry::sentry 0 0% 78.53% 22ms 0.58% std::vector::vector (partial-inline) 5ms 0.13% 78.66% 21ms 0.55% AbstractTetrahedralMeshWriter::GetNextNode 0 0% 78.66% 21ms 0.55% Edge::SetNodes (inline) 0 0% 78.66% 21ms 0.55% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 4ms 0.11% 78.77% 21ms 0.55% vtk::detail::smp::vtkSMPToolsImpl::For 2ms 0.053% 78.82% 21ms 0.55% vtkAOSDataArrayTemplate::AllocateTuples 0 0% 78.82% 20ms 0.53% PottsMesh::GetVonNeumannNeighbouringNodeIndices 20ms 0.53% 79.35% 20ms 0.53% __strchrnul_evex 0 0% 79.35% 20ms 0.53% std::default_delete::operator() (inline) 0 0% 79.35% 20ms 0.53% std::unique_ptr::~unique_ptr (inline) 20ms 0.53% 79.87% 20ms 0.53% vtkObjectBase::vtkObjectBase 9ms 0.24% 80.11% 19ms 0.5% vtkAbstractArray::~vtkAbstractArray 5ms 0.13% 80.24% 19ms 0.5% vtkSOADataArrayTemplate::GetTupleIndexFromValueIndex 0 0% 80.24% 19ms 0.5% vtkXMLUnstructuredDataWriter::WriteHeader