File: TestRepresentativePottsBasedOnLatticeSimulation Type: cpu Showing nodes accounting for 3845ms, 78.76% of 4882ms total Dropped 744 nodes (cum <= 24.41ms) flat flat% sum% cum cum% 0 0% 0% 4643ms 95.10% __libc_start_call_main 0 0% 0% 4643ms 95.10% __libc_start_main_impl 0 0% 0% 4643ms 95.10% _start 0 0% 0% 4628ms 94.80% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 4628ms 94.80% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 4628ms 94.80% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 4628ms 94.80% main 0 0% 0% 4589ms 94.00% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 4589ms 94.00% CxxTest::TestRunner::runTest (inline) 0 0% 0% 4589ms 94.00% TestRepresentativePottsBasedOnLatticeSimulation::TestPottsMonolayerCellSorting 0 0% 0% 4579ms 93.79% AbstractCellBasedSimulation::Solve 0 0% 0% 4276ms 87.59% AbstractCellPopulation::WriteResultsToFiles 16ms 0.33% 0.33% 4044ms 82.83% PottsBasedCellPopulation::WriteVtkResultsToFile 0 0% 0.33% 1980ms 40.56% VertexMeshWriter::WriteVtkUsingMesh 2ms 0.041% 0.37% 1708ms 34.99% VertexMeshWriter::MakeVtkMesh 0 0% 0.37% 1265ms 25.91% vtkPolygon::New 2ms 0.041% 0.41% 1265ms 25.91% vtkPolygon::vtkPolygon 7ms 0.14% 0.55% 929ms 19.03% vtkCell::vtkCell 3ms 0.061% 0.61% 773ms 15.83% vtkPoints::New 2ms 0.041% 0.66% 764ms 15.65% VertexMeshWriter::WriteFiles 13ms 0.27% 0.92% 736ms 15.08% vtkPoints::vtkPoints 54ms 1.11% 2.03% 734ms 15.03% std::ostream::_M_insert 2ms 0.041% 2.07% 734ms 15.03% std::ostream::operator<< (inline) 43ms 0.88% 2.95% 670ms 13.72% operator new 220ms 4.51% 7.46% 639ms 13.09% __GI___libc_malloc 42ms 0.86% 8.32% 604ms 12.37% std::num_put::_M_insert_float 2ms 0.041% 8.36% 593ms 12.15% vtkQuad::New 5ms 0.1% 8.46% 591ms 12.11% vtkQuad::vtkQuad 2ms 0.041% 8.50% 590ms 12.09% vtkLine::New 0 0% 8.50% 588ms 12.04% vtkTriangle::New 0 0% 8.50% 587ms 12.02% vtkStreamingDemandDrivenPipeline::Update 0 0% 8.50% 587ms 12.02% vtkXMLWriterBase::Write 0 0% 8.50% 583ms 11.94% vtkDemandDrivenPipeline::ProcessRequest 0 0% 8.50% 582ms 11.92% vtkStreamingDemandDrivenPipeline::ProcessRequest 0 0% 8.50% 579ms 11.86% vtkDemandDrivenPipeline::ExecuteData 0 0% 8.50% 578ms 11.84% vtkExecutive::CallAlgorithm 4ms 0.082% 8.58% 577ms 11.82% vtkTriangle::vtkTriangle 0 0% 8.58% 576ms 11.80% vtkCompositeDataPipeline::ExecuteData 11ms 0.23% 8.81% 576ms 11.80% vtkLine::vtkLine 0 0% 8.81% 576ms 11.80% vtkXMLUnstructuredDataWriter::ProcessRequest 0 0% 8.81% 516ms 10.57% vtkXMLUnstructuredDataWriter::WriteAPiece 1ms 0.02% 8.83% 516ms 10.57% vtkXMLUnstructuredGridWriter::WriteAppendedPieceData 144ms 2.95% 11.78% 499ms 10.22% __GI___libc_free 15ms 0.31% 12.09% 469ms 9.61% std::__cxx11::collate::do_transform 0 0% 12.09% 459ms 9.40% vtkXMLWriter::WriteBinaryData 1ms 0.02% 12.11% 455ms 9.32% vtkXMLWriter::WriteBinaryDataBlock 0 0% 12.11% 455ms 9.32% vtkXMLWriter::WriteBinaryDataInternal 33ms 0.68% 12.78% 446ms 9.14% vtkPoints::SetDataType 0 0% 12.78% 437ms 8.95% vtkXMLUnstructuredDataWriter::WriteAppendedPieceData 5ms 0.1% 12.88% 429ms 8.79% ___vsnprintf 0 0% 12.88% 424ms 8.68% __vsnprintf_internal (inline) 54ms 1.11% 13.99% 414ms 8.48% __printf_buffer 1ms 0.02% 14.01% 397ms 8.13% vtkPolygon::~vtkPolygon 0 0% 14.01% 369ms 7.56% AbstractTetrahedralMeshWriter::WriteFilesUsingMesh 0 0% 14.01% 367ms 7.52% VtkMeshWriter::WriteFiles 218ms 4.47% 18.48% 354ms 7.25% _int_free 210ms 4.30% 22.78% 340ms 6.96% _int_malloc 2ms 0.041% 22.82% 331ms 6.78% vtkCell::~vtkCell 1ms 0.02% 22.84% 326ms 6.68% __printf_fp_spec (inline) 16ms 0.33% 23.17% 325ms 6.66% __printf_fp_l_buffer 0 0% 23.17% 325ms 6.66% vtkXMLWriter::WritePointsAppendedData 0 0% 23.17% 296ms 6.06% OnLatticeSimulation::UpdateCellLocationsAndTopology 5ms 0.1% 23.27% 296ms 6.06% PottsBasedCellPopulation::UpdateCellLocations 159ms 3.26% 26.53% 294ms 6.02% __printf_fp_buffer_1 43ms 0.88% 27.41% 287ms 5.88% std::__new_allocator::allocate (inline) 0 0% 27.41% 286ms 5.86% std::allocator_traits::allocate (inline) 38ms 0.78% 28.19% 274ms 5.61% vtkAOSDataArrayTemplate::vtkAOSDataArrayTemplate 3ms 0.061% 28.25% 239ms 4.90% std::__new_allocator::deallocate (inline) 0 0% 28.25% 238ms 4.88% std::allocator_traits::deallocate (inline) 0 0% 28.25% 237ms 4.85% vtkXMLWriter::WriteCompressionBlock 6ms 0.12% 28.37% 231ms 4.73% vtkBase64OutputStream::Write 14ms 0.29% 28.66% 225ms 4.61% vtkBase64OutputStream::EncodeTriplet 0 0% 28.66% 214ms 4.38% compress2 0 0% 28.66% 214ms 4.38% vtkDataCompressor::Compress 0 0% 28.66% 214ms 4.38% vtkZLibDataCompressor::CompressBuffer 1ms 0.02% 28.68% 213ms 4.36% deflate 77ms 1.58% 30.25% 212ms 4.34% crc32 0 0% 30.25% 212ms 4.34% tbb::detail::r1::parallel_pipeline 7ms 0.14% 30.40% 210ms 4.30% vtkPoints::~vtkPoints 0 0% 30.40% 209ms 4.28% std::set::set (inline) 19ms 0.39% 30.79% 208ms 4.26% std::_Rb_tree::_Rb_tree 0 0% 30.79% 205ms 4.20% clone3 0 0% 30.79% 205ms 4.20% start_thread 0 0% 30.79% 202ms 4.14% tbb::detail::r1::reset 76ms 1.56% 32.34% 202ms 4.14% tbb::detail::r1::wait_bounded_queue_monitor 7ms 0.14% 32.49% 193ms 3.95% vtkFloatArray::New 70ms 1.43% 33.92% 185ms 3.79% std::ostream::write 9ms 0.18% 34.10% 180ms 3.69% vtkIdList::AllocateInternal 0 0% 34.10% 174ms 3.56% VertexMesh::~VertexMesh 0 0% 34.10% 172ms 3.52% std::_Rb_tree::_M_create_node (inline) 7ms 0.14% 34.25% 172ms 3.52% std::_Rb_tree::~_Rb_tree (inline) 57ms 1.17% 35.42% 170ms 3.48% std::_Rb_tree::_M_erase 0 0% 35.42% 170ms 3.48% vtkQuad::~vtkQuad 0 0% 35.42% 169ms 3.46% NodeLocationWriter::VisitAnyPopulation 96ms 1.97% 37.38% 165ms 3.38% malloc_consolidate 0 0% 37.38% 164ms 3.36% std::_Rb_tree::_M_get_node (inline) 1ms 0.02% 37.40% 163ms 3.34% vtkTriangle::~vtkTriangle 0 0% 37.40% 160ms 3.28% VertexMesh::VertexMesh 3ms 0.061% 37.46% 158ms 3.24% vtkFloatArray::vtkFloatArray 0 0% 37.46% 157ms 3.22% std::_Rb_tree::_Alloc_node::operator() (inline) 9ms 0.18% 37.65% 155ms 3.17% std::_Rb_tree::_M_copy (inline) 0 0% 37.65% 155ms 3.17% std::vector::~vector (inline) 3ms 0.061% 37.71% 152ms 3.11% NodesOnlyMesh::ConstructNodesWithoutMesh 2ms 0.041% 37.75% 150ms 3.07% vtkLine::GetParametricCenter 0 0% 37.75% 148ms 3.03% VertexMesh::GenerateEdgesFromElements (inline) 5ms 0.1% 37.85% 147ms 3.01% MutableElement::BuildEdges 1ms 0.02% 37.87% 146ms 2.99% vtkTypeFloat64Array::~vtkTypeFloat64Array 4ms 0.082% 37.96% 145ms 2.97% AdhesionPottsUpdateRule::EvaluateHamiltonianContribution 9ms 0.18% 38.14% 144ms 2.95% vtkDataArray::CreateDataArray 64ms 1.31% 39.45% 143ms 2.93% std::basic_filebuf::xsputn 15ms 0.31% 39.76% 141ms 2.89% std::_Rb_tree::_M_clone_node (inline) 3ms 0.061% 39.82% 139ms 2.85% std::_Vector_base::_M_deallocate (inline) 15ms 0.31% 40.13% 135ms 2.77% std::vector::_M_default_append 2ms 0.041% 40.17% 132ms 2.70% vtkFloatArray::~vtkFloatArray 0 0% 40.17% 129ms 2.64% EdgeHelper::~EdgeHelper (inline) 128ms 2.62% 42.79% 128ms 2.62% [libz.so.1.3] 7ms 0.14% 42.93% 128ms 2.62% vtkTypeFloat64Array::New 4ms 0.082% 43.02% 126ms 2.58% EdgeHelper::GetEdgeFromNodes 2ms 0.041% 43.06% 124ms 2.54% std::_Vector_base::_M_allocate (inline) 123ms 2.52% 45.58% 123ms 2.52% __GI_sched_yield 0 0% 45.58% 123ms 2.52% std::set::~set (inline) 38ms 0.78% 46.35% 122ms 2.50% vtkObject::vtkObject 4ms 0.082% 46.44% 120ms 2.46% vtkDoubleArray::vtkDoubleArray 1ms 0.02% 46.46% 117ms 2.40% std::_Vector_base::~_Vector_base (inline) 0 0% 46.46% 113ms 2.31% vtkIdList::Allocate 0 0% 46.46% 110ms 2.25% vtkXMLWriter::WritePointDataAppendedData 108ms 2.21% 48.67% 108ms 2.21% __strcmp_avx2 0 0% 48.67% 107ms 2.19% std::_Rb_tree::_M_drop_node (inline) 3ms 0.061% 48.73% 107ms 2.19% vtkTypeFloat64Array::vtkTypeFloat64Array 0 0% 48.73% 105ms 2.15% Cell::HasCellProperty (inline) 10ms 0.2% 48.93% 105ms 2.15% CellPropertyCollection::HasProperty 0 0% 48.93% 102ms 2.09% std::_Rb_tree::_M_put_node (inline) 1ms 0.02% 48.96% 101ms 2.07% LegacyCellProliferativeTypesWriter::GetCellDataForVtkOutput 39ms 0.8% 49.75% 100ms 2.05% std::__ostream_insert 2ms 0.041% 49.80% 97ms 1.99% std::operator<< (inline) 53ms 1.09% 50.88% 97ms 1.99% vtkObjectBase::UnRegisterInternal 45ms 0.92% 51.80% 97ms 1.99% vtkTypeFloat64Array::PrintSelf 95ms 1.95% 53.75% 95ms 1.95% unlink_chunk 1ms 0.02% 53.77% 90ms 1.84% CellPropertyCollection::GetPropertiesType (inline) 10ms 0.2% 53.97% 90ms 1.84% vtkIdList::New 0 0% 53.97% 89ms 1.82% std::map::operator[] (partial-inline) 5ms 0.1% 54.08% 87ms 1.78% AbstractCellProperty::IsType (inline) 5ms 0.1% 54.18% 81ms 1.66% vtkDoubleArray::~vtkDoubleArray 29ms 0.59% 54.77% 80ms 1.64% std::_Rb_tree::_M_lower_bound (inline) 8ms 0.16% 54.94% 77ms 1.58% vtkAOSDataArrayTemplate::DataElementChanged 0 0% 54.94% 77ms 1.58% vtkXMLUnstructuredDataWriter::WriteCellsAppendedDataWorker 3ms 0.061% 55.00% 76ms 1.56% _int_free_maybe_consolidate 38ms 0.78% 55.78% 75ms 1.54% hack_digit 49ms 1.00% 56.78% 75ms 1.54% std::basic_streambuf::xsputn 1ms 0.02% 56.80% 75ms 1.54% std::vector::push_back (inline) 0 0% 56.80% 72ms 1.47% AbstractCellProperty::IsSubType (inline) 14ms 0.29% 57.09% 72ms 1.47% __dynamic_cast 3ms 0.061% 57.15% 71ms 1.45% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 57.15% 70ms 1.43% tcache_get (inline) 70ms 1.43% 58.58% 70ms 1.43% tcache_get_n (inline) 21ms 0.43% 59.01% 69ms 1.41% vtkObject::Modified 15ms 0.31% 59.32% 64ms 1.31% AbstractCellProperty::IsSame 0 0% 59.32% 61ms 1.25% DifferentialAdhesionPottsUpdateRule::GetCellCellAdhesionEnergy 11ms 0.23% 59.55% 61ms 1.25% std::num_put::_M_insert_int 45ms 0.92% 60.47% 59ms 1.21% std::_Hashtable::clear 0 0% 60.47% 59ms 1.21% std::_Rb_tree::lower_bound (inline) 0 0% 60.47% 59ms 1.21% std::map::lower_bound (inline) 6ms 0.12% 60.59% 57ms 1.17% boost::numeric::ublas::c_vector::c_vector (inline) 6ms 0.12% 60.71% 57ms 1.17% std::vector::_M_realloc_insert 0 0% 60.71% 55ms 1.13% NodesOnlyMesh::~NodesOnlyMesh 0 0% 60.71% 55ms 1.13% PottsMesh::GetMooreNeighbouringNodeIndices 5ms 0.1% 60.82% 55ms 1.13% vtkDataArray::vtkDataArray 0 0% 60.82% 53ms 1.09% std::set::insert (inline) 0 0% 60.82% 52ms 1.07% NodesOnlyMesh::SetUpBoxCollection 0 0% 60.82% 52ms 1.07% boost::numeric::ublas::vector_assign (inline) 1ms 0.02% 60.84% 52ms 1.07% std::_Rb_tree::_M_insert_unique 50ms 1.02% 61.86% 50ms 1.02% [libvtkCommonCore-9.3.so.9.3] 49ms 1.00% 62.86% 49ms 1.00% __memcpy_avx_unaligned_erms 0 0% 62.86% 49ms 1.00% std::map::~map (inline) 14ms 0.29% 63.15% 49ms 1.00% std::type_info::operator== (inline) 19ms 0.39% 63.54% 48ms 0.98% __cxxabiv1::__si_class_type_info::__do_dyncast 7ms 0.14% 63.68% 48ms 0.98% vtkAbstractArray::vtkAbstractArray 6ms 0.12% 63.81% 48ms 0.98% vtkSOADataArrayTemplate::FillTypedComponent 1ms 0.02% 63.83% 46ms 0.94% Cell::GetCellProliferativeType 45ms 0.92% 64.75% 46ms 0.94% __GI___writev 0 0% 64.75% 46ms 0.94% std::__basic_file::xsputn_2 46ms 0.94% 65.69% 46ms 0.94% vtkTimeStamp::Modified 2ms 0.041% 65.73% 45ms 0.92% VertexMesh::Clear 5ms 0.1% 65.83% 44ms 0.9% VertexMeshWriter::GetNextNode 1ms 0.02% 65.85% 44ms 0.9% std::less::operator() (inline) 0 0% 65.85% 44ms 0.9% vtkDataArray::ComputeRange 17ms 0.35% 66.20% 43ms 0.88% boost::numeric::ublas::indexing_vector_assign 0 0% 66.20% 43ms 0.88% std::_Destroy (inline) 1ms 0.02% 66.22% 43ms 0.88% std::_Destroy_aux::__destroy (inline) 43ms 0.88% 67.10% 43ms 0.88% std::operator< (inline) 26ms 0.53% 67.64% 41ms 0.84% DistributedBoxCollection::CalculateContainingBox (inline) 0 0% 67.64% 41ms 0.84% DistributedBoxCollection::IsOwned 5ms 0.1% 67.74% 41ms 0.84% std::_Rb_tree::_M_insert_ (inline) 40ms 0.82% 68.56% 40ms 0.82% vtkObjectBase::~vtkObjectBase 12ms 0.25% 68.80% 39ms 0.8% _int_free_merge_chunk 29ms 0.59% 69.40% 38ms 0.78% vtkObject::ObjectFinalize 37ms 0.76% 70.16% 37ms 0.76% vtkObjectBase::Delete 1ms 0.02% 70.18% 36ms 0.74% vtk::detail::smp::vtkSMPToolsImplForTBB 0 0% 70.18% 35ms 0.72% CxxTest::RealWorldDescription::setUp 0 0% 70.18% 35ms 0.72% PetscSetup::setUpWorld 0 0% 70.18% 35ms 0.72% PetscSetupUtils::CommonSetup 32ms 0.66% 70.83% 35ms 0.72% std::num_put::do_put 35ms 0.72% 71.55% 35ms 0.72% std::ostream::sentry::sentry 9ms 0.18% 71.73% 35ms 0.72% tbb::detail::r1::cancel_group_execution 35ms 0.72% 72.45% 35ms 0.72% vtkObject::~vtkObject 0 0% 72.45% 34ms 0.7% PMPI_Init_thread 0 0% 72.45% 34ms 0.7% PetscInitialize 0 0% 72.45% 34ms 0.7% PetscSetupUtils::InitialisePetsc 0 0% 72.45% 34ms 0.7% _dl_init 0 0% 72.45% 34ms 0.7% _dl_start_user 0 0% 72.45% 34ms 0.7% call_init (inline) 0 0% 72.45% 34ms 0.7% ompi_mpi_init 3ms 0.061% 72.51% 34ms 0.7% vtkAOSDataArrayTemplate::InsertTuple 7ms 0.14% 72.65% 34ms 0.7% vtkIdList::~vtkIdList 0 0% 72.65% 33ms 0.68% Cell::GetCellId 0 0% 72.65% 33ms 0.68% DistributedBoxCollection::~DistributedBoxCollection 0 0% 72.65% 33ms 0.68% NodesOnlyMesh::ClearBoxCollection (inline) 33ms 0.68% 73.33% 33ms 0.68% __GI___libc_write 0 0% 73.33% 33ms 0.68% std::__basic_file::xsputn 0 0% 73.33% 33ms 0.68% std::basic_filebuf::_M_convert_to_external 0 0% 73.33% 33ms 0.68% std::basic_filebuf::overflow 33ms 0.68% 74.01% 33ms 0.68% std::codecvt::do_always_noconv 0 0% 74.01% 32ms 0.66% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 0 0% 74.01% 32ms 0.66% std::_Rb_tree_header::_Rb_tree_header (inline) 0 0% 74.01% 31ms 0.63% CellIdWriter::GetCellDataForVtkOutput 0 0% 74.01% 31ms 0.63% VtkMeshWriter::MakeVtkMesh 6ms 0.12% 74.13% 31ms 0.63% __find_specmb (inline) 1ms 0.02% 74.15% 31ms 0.63% boost::serialization::singleton::get_instance 31ms 0.63% 74.78% 31ms 0.63% std::_Rb_tree_header::_M_reset (inline) 0 0% 74.78% 31ms 0.63% std::make_unique (inline) 0 0% 74.78% 30ms 0.61% boost::serialization::detail::singleton_wrapper::singleton_wrapper (inline) 0 0% 74.78% 30ms 0.61% std::_Rb_tree::_M_emplace_hint_unique 8ms 0.16% 74.95% 30ms 0.61% vtkDataArray::~vtkDataArray 0 0% 74.95% 29ms 0.59% DistributedBoxCollection::SetupLocalBoxesHalfOnly 29ms 0.59% 75.54% 29ms 0.59% __mpn_divrem 29ms 0.59% 76.14% 29ms 0.59% tcache_put (inline) 3ms 0.061% 76.20% 29ms 0.59% vtk::detail::smp::vtkSMPToolsImpl::For 28ms 0.57% 76.77% 28ms 0.57% std::_Rb_tree_increment 0 0% 76.77% 28ms 0.57% std::basic_filebuf::close 0 0% 76.77% 28ms 0.57% std::basic_ofstream::close (inline) 3ms 0.061% 76.83% 28ms 0.57% vtkDataArrayPrivate::DoComputeVectorRange 0 0% 76.83% 27ms 0.55% 0 0% 76.83% 27ms 0.55% std::default_delete::operator() (inline) 0 0% 76.83% 27ms 0.55% std::unique_ptr::~unique_ptr (inline) 26ms 0.53% 77.37% 26ms 0.53% [libchaste_cell_based.so] 0 0% 77.37% 26ms 0.53% boost::serialization::void_cast_detail::void_caster_primitive::void_caster_primitive (inline) 26ms 0.53% 77.90% 26ms 0.53% vtkObjectBase::vtkObjectBase 2ms 0.041% 77.94% 25ms 0.51% VertexMeshWriter::GetNextElement 0 0% 77.94% 25ms 0.51% boost::numeric::ublas::c_vector::assign (inline) 25ms 0.51% 78.45% 25ms 0.51% boost::numeric::ublas::c_vector::operator() 3ms 0.061% 78.51% 25ms 0.51% boost::serialization::void_cast_detail::void_caster::recursive_register 0 0% 78.51% 25ms 0.51% vtkDataArrayPrivate::DoComputeScalarRange 1ms 0.02% 78.53% 25ms 0.51% vtkDoubleArray::New 11ms 0.23% 78.76% 25ms 0.51% vtkIdList::vtkIdList