File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3785ms, 79.63% of 4753ms total Dropped 691 nodes (cum <= 23.77ms) flat flat% sum% cum cum% 0 0% 0% 4495ms 94.57% __libc_start_call_main 0 0% 0% 4495ms 94.57% __libc_start_main_impl 0 0% 0% 4495ms 94.57% _start 0 0% 0% 4478ms 94.21% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4478ms 94.21% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4478ms 94.21% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4478ms 94.21% main 0 0% 0% 4445ms 93.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4445ms 93.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4445ms 93.52% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4433ms 93.27% AbstractCellBasedSimulation::Solve 0 0% 0% 4159ms 87.50% AbstractCellPopulation::WriteResultsToFiles 20ms 0.42% 0.42% 3923ms 82.54% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.42% 1949ms 41.01% VertexMeshWriter::WriteVtkUsingMesh 3ms 0.063% 0.48% 1686ms 35.47% VertexMeshWriter::MakeVtkMesh 2ms 0.042% 0.53% 1246ms 26.22% vtkPolygon::New 4ms 0.084% 0.61% 1242ms 26.13% vtkPolygon::vtkPolygon 4ms 0.084% 0.69% 890ms 18.73% vtkCell::vtkCell 2ms 0.042% 0.74% 763ms 16.05% vtkPoints::New 1ms 0.021% 0.76% 743ms 15.63% VertexMeshWriter::WriteFiles 11ms 0.23% 0.99% 726ms 15.27% vtkPoints::vtkPoints 2ms 0.042% 1.03% 701ms 14.75% std::ostream::operator<< (inline) 34ms 0.72% 1.75% 700ms 14.73% std::ostream::_M_insert 44ms 0.93% 2.67% 671ms 14.12% operator new 189ms 3.98% 6.65% 643ms 13.53% __GI___libc_malloc 2ms 0.042% 6.69% 617ms 12.98% vtkQuad::New 4ms 0.084% 6.77% 611ms 12.86% vtkQuad::vtkQuad 1ms 0.021% 6.80% 597ms 12.56% vtkLine::New 48ms 1.01% 7.81% 594ms 12.50% std::num_put::_M_insert_float 11ms 0.23% 8.04% 579ms 12.18% vtkLine::vtkLine 1ms 0.021% 8.06% 563ms 11.85% vtkExecutive::CallAlgorithm 0 0% 8.06% 563ms 11.85% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 8.06% 563ms 11.85% vtkStreamingDemandDrivenPipeline::Update 0 0% 8.06% 563ms 11.85% vtkXMLWriterBase::Write 0 0% 8.06% 562ms 11.82% vtkCompositeDataPipeline::ExecuteData 0 0% 8.06% 562ms 11.82% vtkDemandDrivenPipeline::ExecuteData 0 0% 8.06% 562ms 11.82% vtkDemandDrivenPipeline::ProcessRequest 0 0% 8.06% 562ms 11.82% vtkXMLUnstructuredDataWriter::ProcessRequest 1ms 0.021% 8.08% 517ms 10.88% vtkTriangle::New 13ms 0.27% 8.35% 513ms 10.79% vtkTriangle::vtkTriangle 0 0% 8.35% 507ms 10.67% vtkXMLUnstructuredDataWriter::WriteAPiece 0 0% 8.35% 507ms 10.67% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 140ms 2.95% 11.30% 488ms 10.27% __GI___libc_free 41ms 0.86% 12.16% 468ms 9.85% vtkPoints::SetDataType 0 0% 12.16% 455ms 9.57% vtkXMLWriter::WriteBinaryData 0 0% 12.16% 446ms 9.38% vtkXMLWriter::WriteBinaryDataInternal 0 0% 12.16% 444ms 9.34% vtkXMLWriter::WriteBinaryDataBlock 10ms 0.21% 12.37% 437ms 9.19% std::__cxx11::collate::do_transform 0 0% 12.37% 421ms 8.86% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 10ms 0.21% 12.58% 414ms 8.71% ___vsnprintf 1ms 0.021% 12.60% 405ms 8.52% __vsnprintf_internal (inline) 0 0% 12.60% 395ms 8.31% vtkPolygon::~vtkPolygon 51ms 1.07% 13.68% 393ms 8.27% __printf_buffer 259ms 5.45% 19.12% 381ms 8.02% _int_malloc 0 0% 19.12% 350ms 7.36% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 19.12% 348ms 7.32% VtkMeshWriter::WriteFiles 221ms 4.65% 23.77% 348ms 7.32% _int_free 2ms 0.042% 23.82% 314ms 6.61% vtkCell::~vtkCell 0 0% 23.82% 314ms 6.61% vtkXMLWriter::WritePointsAppendedData 2ms 0.042% 23.86% 303ms 6.37% __printf_fp_spec (inline) 13ms 0.27% 24.13% 301ms 6.33% __printf_fp_l_buffer 49ms 1.03% 25.16% 291ms 6.12% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 35ms 0.74% 25.90% 286ms 6.02% std::__new_allocator::allocate (inline) 0 0% 25.90% 283ms 5.95% std::allocator_traits::allocate (inline) 148ms 3.11% 29.01% 278ms 5.85% __printf_fp_buffer_1 0 0% 29.01% 266ms 5.60% OnLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.063% 29.08% 266ms 5.60% PottsBasedCellPopulation::UpdateCellLocations 5ms 0.11% 29.18% 251ms 5.28% std::__new_allocator::deallocate (inline) 0 0% 29.18% 248ms 5.22% std::allocator_traits::deallocate (inline) 0 0% 29.18% 235ms 4.94% vtkXMLWriter::WriteCompressionBlock 0 0% 29.18% 225ms 4.73% tbb::detail::r1::parallel_pipeline 7ms 0.15% 29.33% 225ms 4.73% vtkPoints::~vtkPoints 0 0% 29.33% 220ms 4.63% clone3 0 0% 29.33% 220ms 4.63% start_thread 0 0% 29.33% 217ms 4.57% vtkDataCompressor::Compress 1ms 0.021% 29.35% 216ms 4.54% vtkZLibDataCompressor::CompressBuffer 0 0% 29.35% 215ms 4.52% compress2 0 0% 29.35% 215ms 4.52% tbb::detail::r1::reset 7ms 0.15% 29.50% 215ms 4.52% vtkBase64OutputStream::Write 61ms 1.28% 30.78% 212ms 4.46% crc32 0 0% 30.78% 212ms 4.46% deflate 90ms 1.89% 32.67% 209ms 4.40% tbb::detail::r1::wait_bounded_queue_monitor 20ms 0.42% 33.09% 208ms 4.38% vtkBase64OutputStream::EncodeTriplet 0 0% 33.09% 180ms 3.79% vtkQuad::~vtkQuad 0 0% 33.09% 173ms 3.64% std::_Rb_tree::_M_create_node (inline) 3ms 0.063% 33.16% 173ms 3.64% vtkFloatArray::New 63ms 1.33% 34.48% 172ms 3.62% std::ostream::write 2ms 0.042% 34.53% 171ms 3.60% vtkTriangle::~vtkTriangle 0 0% 34.53% 170ms 3.58% std::_Rb_tree::_M_get_node (inline) 96ms 2.02% 36.55% 166ms 3.49% malloc_consolidate 15ms 0.32% 36.86% 166ms 3.49% std::_Rb_tree::_Rb_tree 0 0% 36.86% 166ms 3.49% std::set::set (inline) 1ms 0.021% 36.88% 165ms 3.47% vtkLine::GetParametricCenter 1ms 0.021% 36.90% 163ms 3.43% NodesOnlyMesh::ConstructNodesWithoutMesh 1ms 0.021% 36.92% 162ms 3.41% NodeLocationWriter::VisitAnyPopulation 0 0% 36.92% 160ms 3.37% vtkTypeFloat64Array::~vtkTypeFloat64Array 48ms 1.01% 37.93% 157ms 3.30% std::_Rb_tree::_M_erase 2ms 0.042% 37.98% 155ms 3.26% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.063% 38.04% 155ms 3.26% vtkFloatArray::vtkFloatArray 0 0% 38.04% 153ms 3.22% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.042% 38.08% 153ms 3.22% vtkIdList::AllocateInternal 0 0% 38.08% 151ms 3.18% std::_Vector_base::_M_deallocate (inline) 2ms 0.042% 38.12% 147ms 3.09% vtkDataArray::CreateDataArray 9ms 0.19% 38.31% 145ms 3.05% std::vector::_M_default_append 5ms 0.11% 38.42% 145ms 3.05% vtkDoubleArray::vtkDoubleArray 0 0% 38.42% 144ms 3.03% VertexMesh::~VertexMesh 136ms 2.86% 41.28% 142ms 2.99% [libz.so.1.3] 0 0% 41.28% 141ms 2.97% VertexMesh::VertexMesh 0 0% 41.28% 141ms 2.97% std::vector::~vector (inline) 2ms 0.042% 41.32% 139ms 2.92% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 63ms 1.33% 42.65% 138ms 2.90% std::basic_filebuf::xsputn 2ms 0.042% 42.69% 135ms 2.84% vtkTypeFloat64Array::New 5ms 0.11% 42.79% 134ms 2.82% vtkFloatArray::~vtkFloatArray 15ms 0.32% 43.11% 133ms 2.80% std::_Rb_tree::_M_copy (inline) 7ms 0.15% 43.26% 132ms 2.78% MutableElement::BuildEdges 0 0% 43.26% 132ms 2.78% VertexMesh::GenerateEdgesFromElements (inline) 0 0% 43.26% 131ms 2.76% std::set::~set (inline) 53ms 1.12% 44.37% 130ms 2.74% std::__ostream_insert 0 0% 44.37% 122ms 2.57% std::operator<< (inline) 118ms 2.48% 46.85% 118ms 2.48% __GI_sched_yield 0 0% 46.85% 118ms 2.48% vtkIdList::Allocate 26ms 0.55% 47.40% 118ms 2.48% vtkObject::vtkObject 3ms 0.063% 47.46% 118ms 2.48% vtkTypeFloat64Array::vtkTypeFloat64Array 6ms 0.13% 47.59% 117ms 2.46% std::_Rb_tree::_M_clone_node (inline) 3ms 0.063% 47.65% 116ms 2.44% EdgeHelper::GetEdgeFromNodes 0 0% 47.65% 113ms 2.38% std::_Vector_base::_M_allocate (inline) 1ms 0.021% 47.68% 110ms 2.31% CellPropertyCollection::GetPropertiesType (inline) 0 0% 47.68% 110ms 2.31% std::_Vector_base::~_Vector_base (inline) 0 0% 47.68% 106ms 2.23% vtkXMLWriter::WritePointDataAppendedData 2ms 0.042% 47.72% 103ms 2.17% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 0 0% 47.72% 102ms 2.15% EdgeHelper::~EdgeHelper (inline) 102ms 2.15% 49.86% 102ms 2.15% __strcmp_avx2 0 0% 49.86% 99ms 2.08% std::_Rb_tree::_M_drop_node (inline) 2ms 0.042% 49.91% 97ms 2.04% AbstractCellProperty::IsSubType (inline) 0 0% 49.91% 97ms 2.04% std::_Rb_tree::_M_put_node (inline) 45ms 0.95% 50.85% 97ms 2.04% vtkTypeFloat64Array::PrintSelf 17ms 0.36% 51.21% 94ms 1.98% __dynamic_cast 76ms 1.60% 52.81% 93ms 1.96% std::basic_streambuf::xsputn 1ms 0.021% 52.83% 91ms 1.91% std::map::operator[] (partial-inline) 88ms 1.85% 54.68% 88ms 1.85% unlink_chunk 0 0% 54.68% 87ms 1.83% Cell::HasCellProperty (inline) 6ms 0.13% 54.81% 87ms 1.83% CellPropertyCollection::HasProperty 3ms 0.063% 54.87% 86ms 1.81% AbstractCellProperty::IsType (inline) 11ms 0.23% 55.10% 86ms 1.81% vtkAOSDataArrayTemplate::DataElementChanged 0 0% 55.10% 85ms 1.79% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 3ms 0.063% 55.17% 84ms 1.77% vtkIdList::New 4ms 0.084% 55.25% 81ms 1.70% _int_free_maybe_consolidate 56ms 1.18% 56.43% 81ms 1.70% vtkObjectBase::UnRegisterInternal 43ms 0.9% 57.33% 79ms 1.66% hack_digit 1ms 0.021% 57.35% 79ms 1.66% vtkDoubleArray::~vtkDoubleArray 25ms 0.53% 57.88% 73ms 1.54% vtkObject::Modified 28ms 0.59% 58.47% 72ms 1.51% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.021% 58.49% 68ms 1.43% Cell::GetCellProliferativeType 1ms 0.021% 58.51% 68ms 1.43% std::vector::push_back (inline) 1ms 0.021% 58.53% 68ms 1.43% tcache_get (inline) 67ms 1.41% 59.94% 67ms 1.41% tcache_get_n (inline) 0 0% 59.94% 65ms 1.37% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 9ms 0.19% 60.13% 62ms 1.30% AbstractCellProperty::IsSame 0 0% 60.13% 60ms 1.26% NodesOnlyMesh::SetUpBoxCollection 5ms 0.11% 60.24% 60ms 1.26% boost::numeric::ublas::c_vector::c_vector (partial-inline) 35ms 0.74% 60.97% 56ms 1.18% std::_Hashtable::clear 1ms 0.021% 60.99% 56ms 1.18% std::set::insert (inline) 0 0% 60.99% 55ms 1.16% boost::numeric::ublas::vector_assign (inline) 0 0% 60.99% 55ms 1.16% std::_Rb_tree::_M_insert_unique 55ms 1.16% 62.15% 55ms 1.16% std::ostream::sentry::sentry 3ms 0.063% 62.21% 54ms 1.14% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 62.21% 54ms 1.14% PottsMesh::GetMooreNeighbouringNodeIndices 0 0% 62.21% 54ms 1.14% std::_Rb_tree::lower_bound (inline) 0 0% 62.21% 54ms 1.14% std::map::lower_bound (inline) 32ms 0.67% 62.89% 53ms 1.12% __cxxabiv1::__si_class_type_info::__do_dyncast 13ms 0.27% 63.16% 53ms 1.12% std::type_info::operator== (inline) 1ms 0.021% 63.18% 50ms 1.05% NodesOnlyMesh::~NodesOnlyMesh 3ms 0.063% 63.24% 50ms 1.05% std::vector::_M_realloc_insert 4ms 0.084% 63.33% 49ms 1.03% std::_Rb_tree::_M_insert_ (inline) 10ms 0.21% 63.54% 48ms 1.01% vtkSOADataArrayTemplate::FillTypedComponent 4ms 0.084% 63.62% 47ms 0.99% vtkDataArray::vtkDataArray 47ms 0.99% 64.61% 47ms 0.99% vtkTimeStamp::Modified 46ms 0.97% 65.58% 46ms 0.97% __memcpy_avx_unaligned_erms 2ms 0.042% 65.62% 43ms 0.9% VertexMesh::Clear 18ms 0.38% 66.00% 43ms 0.9% boost::numeric::ublas::indexing_vector_assign 9ms 0.19% 66.19% 43ms 0.9% vtkAbstractArray::vtkAbstractArray 0 0% 66.19% 43ms 0.9% vtkDataArray::ComputeRange 1ms 0.021% 66.21% 43ms 0.9% vtkDoubleArray::New 7ms 0.15% 66.36% 41ms 0.86% VertexMeshWriter::GetNextNode 0 0% 66.36% 41ms 0.86% std::_Destroy (inline) 0 0% 66.36% 41ms 0.86% std::_Destroy_aux::__destroy (inline) 9ms 0.19% 66.55% 41ms 0.86% std::num_put::_M_insert_int 6ms 0.13% 66.67% 41ms 0.86% vtkDataArray::~vtkDataArray 41ms 0.86% 67.54% 41ms 0.86% vtkObjectBase::~vtkObjectBase 40ms 0.84% 68.38% 40ms 0.84% __GI___writev 0 0% 68.38% 40ms 0.84% std::__basic_file::xsputn_2 40ms 0.84% 69.22% 40ms 0.84% vtkObject::~vtkObject 3ms 0.063% 69.28% 39ms 0.82% DistributedBoxCollection::SetupLocalBoxesHalfOnly 39ms 0.82% 70.10% 39ms 0.82% vtkObjectBase::Delete 38ms 0.8% 70.90% 38ms 0.8% __GI___libc_write 0 0% 70.90% 38ms 0.8% _dl_init 0 0% 70.90% 38ms 0.8% _dl_start_user 0 0% 70.90% 38ms 0.8% call_init (inline) 0 0% 70.90% 38ms 0.8% std::__basic_file::xsputn 0 0% 70.90% 38ms 0.8% std::basic_filebuf::_M_convert_to_external 0 0% 70.90% 38ms 0.8% std::basic_filebuf::overflow 0 0% 70.90% 36ms 0.76% DistributedBoxCollection::~DistributedBoxCollection 0 0% 70.90% 36ms 0.76% NodesOnlyMesh::ClearBoxCollection (inline) 36ms 0.76% 71.66% 36ms 0.76% [libvtkCommonCore-9.3.so.9.3] 0 0% 71.66% 36ms 0.76% std::_Rb_tree::_M_emplace_hint_unique 35ms 0.74% 72.40% 35ms 0.74% std::codecvt::do_always_noconv 8ms 0.17% 72.56% 35ms 0.74% vtkAOSDataArrayTemplate::InsertTuple 0 0% 72.56% 34ms 0.72% VtkMeshWriter::MakeVtkMesh 3ms 0.063% 72.63% 34ms 0.72% tbb::detail::r1::cancel_group_execution 15ms 0.32% 72.94% 33ms 0.69% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 72.94% 33ms 0.69% DistributedBoxCollection::IsOwned 1ms 0.021% 72.96% 33ms 0.69% std::make_unique (inline) 0 0% 72.96% 33ms 0.69% vtk::detail::smp::vtkSMPToolsImplForTBB 3ms 0.063% 73.03% 32ms 0.67% __find_specmb (inline) 13ms 0.27% 73.30% 32ms 0.67% _int_free_merge_chunk 2ms 0.042% 73.34% 31ms 0.65% std::less::operator() (inline) 7ms 0.15% 73.49% 31ms 0.65% vtkIdList::~vtkIdList 0 0% 73.49% 30ms 0.63% Cell::GetMutationState 0 0% 73.49% 30ms 0.63% CxxTest::RealWorldDescription::setUp 0 0% 73.49% 30ms 0.63% PMPI_Init_thread 0 0% 73.49% 30ms 0.63% PetscInitialize 0 0% 73.49% 30ms 0.63% PetscSetup::setUpWorld 0 0% 73.49% 30ms 0.63% PetscSetupUtils::CommonSetup 0 0% 73.49% 30ms 0.63% PetscSetupUtils::InitialisePetsc 0 0% 73.49% 30ms 0.63% PottsMesh::GetVonNeumannNeighbouringNodeIndices 0 0% 73.49% 30ms 0.63% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 2ms 0.042% 73.53% 30ms 0.63% boost::serialization::singleton::get_instance 0 0% 73.53% 30ms 0.63% ompi_mpi_init 1ms 0.021% 73.55% 30ms 0.63% std::basic_filebuf::sync 0 0% 73.55% 30ms 0.63% std::ostream::flush 4ms 0.084% 73.64% 30ms 0.63% vtkDataArrayPrivate::DoComputeVectorRange 30ms 0.63% 74.27% 30ms 0.63% vtkObjectBase::vtkObjectBase 0 0% 74.27% 29ms 0.61% boost::numeric::ublas::c_vector::assign (inline) 29ms 0.61% 74.88% 29ms 0.61% std::operator< (inline) 4ms 0.084% 74.96% 29ms 0.61% vtkAOSDataArrayTemplate::AllocateTuples 28ms 0.59% 75.55% 28ms 0.59% [libchaste_cell_based.so] 28ms 0.59% 76.14% 28ms 0.59% __memset_avx2_unaligned_erms 28ms 0.59% 76.73% 28ms 0.59% __strchrnul_avx2 1ms 0.021% 76.75% 27ms 0.57% 0 0% 76.75% 27ms 0.57% Cell::GetCellId 5ms 0.11% 76.86% 27ms 0.57% CellProliferativeTypesWriter::GetCellDataForVtkOutput 1ms 0.021% 76.88% 27ms 0.57% Node::SetRadius 0 0% 76.88% 27ms 0.57% OutputFileHandler::OpenOutputFile 27ms 0.57% 77.45% 27ms 0.57% __mpn_divrem 21ms 0.44% 77.89% 27ms 0.57% std::num_put::do_put 0 0% 77.89% 26ms 0.55% AbstractCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 77.89% 26ms 0.55% Node::ConstructNodeAttributes (inline) 26ms 0.55% 78.43% 26ms 0.55% std::_Rb_tree_increment 3ms 0.063% 78.50% 26ms 0.55% vtk::detail::smp::vtkSMPToolsImpl::For 1ms 0.021% 78.52% 26ms 0.55% vtkDataArrayPrivate::DoComputeScalarRange 1ms 0.021% 78.54% 25ms 0.53% std::unique_ptr::~unique_ptr (inline) 4ms 0.084% 78.62% 25ms 0.53% vtkSOADataArrayTemplate::GetTupleIndexFromValueIndex 24ms 0.5% 79.13% 24ms 0.5% boost::numeric::ublas::c_vector::operator() 0 0% 79.13% 24ms 0.5% std::default_delete::operator() (inline) 0 0% 79.13% 24ms 0.5% std::map::~map (inline) 24ms 0.5% 79.63% 24ms 0.5% vtkDataArray::Modified