File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 44342ms, 86.43% of 51305ms total Dropped 799 nodes (cum <= 256.52ms) flat flat% sum% cum cum% 0 0% 0% 51254ms 99.90% __libc_start_call_main 0 0% 0% 51254ms 99.90% __libc_start_main_impl 0 0% 0% 51254ms 99.90% _start 0 0% 0% 51240ms 99.87% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 51240ms 99.87% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 51240ms 99.87% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 51240ms 99.87% main 0 0% 0% 51204ms 99.80% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 51204ms 99.80% CxxTest::TestRunner::runTest (inline) 0 0% 0% 51204ms 99.80% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 50986ms 99.38% AbstractCellBasedSimulation::Solve 0 0% 0% 43738ms 85.25% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 43699ms 85.17% MeshBasedCellPopulation::Update 0 0% 0% 24311ms 47.39% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 24311ms 47.39% MeshBasedCellPopulation::TessellateIfNeeded 158ms 0.31% 0.31% 21270ms 41.46% VertexMesh::VertexMesh 0 0% 0.31% 16131ms 31.44% MutableMesh::ReMesh 0 0% 0.31% 12514ms 24.39% tetgen::tetrahedralize 1ms 0.0019% 0.31% 12399ms 24.17% tetgen::tetgenmesh::delaunizevertices 6ms 0.012% 0.32% 12395ms 24.16% tetgen::tetgenmesh::incrflipdelaunay 405ms 0.79% 1.11% 11142ms 21.72% tetgen::tetgenmesh::lawson 443ms 0.86% 1.97% 9884ms 19.27% TetrahedralMesh::EdgeIterator::operator++ 28ms 0.055% 2.03% 8494ms 16.56% std::set::insert (inline) 190ms 0.37% 2.40% 8140ms 15.87% std::_Rb_tree::_M_insert_unique 322ms 0.63% 3.03% 7945ms 15.49% VertexElement::AddFace 2505ms 4.88% 7.91% 7067ms 13.77% std::_Rb_tree::_M_lower_bound (inline) 216ms 0.42% 8.33% 6677ms 13.01% std::_Rb_tree::find (inline) 0 0% 8.33% 6214ms 12.11% std::set::count (inline) 273ms 0.53% 8.86% 4896ms 9.54% std::_Rb_tree::_M_insert_ (inline) 91ms 0.18% 9.04% 4494ms 8.76% std::less::operator() (inline) 4457ms 8.69% 17.73% 4457ms 8.69% std::operator< (inline) 142ms 0.28% 18.00% 4448ms 8.67% operator new 4349ms 8.48% 26.48% 4349ms 8.48% std::_Rb_tree_increment 0 0% 26.48% 4332ms 8.44% OffLatticeSimulation::UpdateCellLocationsAndTopology 975ms 1.90% 28.38% 4249ms 8.28% __GI___libc_malloc 0 0% 28.38% 4219ms 8.22% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 28.38% 4201ms 8.19% AbstractNumericalMethod::ComputeForcesIncludingDamping 28ms 0.055% 28.44% 3799ms 7.40% std::__new_allocator::allocate (inline) 0 0% 28.44% 3780ms 7.37% std::allocator_traits::allocate (inline) 2ms 0.0039% 28.44% 3763ms 7.33% std::_Rb_tree::~_Rb_tree (inline) 1333ms 2.60% 31.04% 3757ms 7.32% std::_Rb_tree::_M_erase 0 0% 31.04% 3717ms 7.24% std::set::~set (inline) 1ms 0.0019% 31.04% 3551ms 6.92% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.0078% 31.05% 3514ms 6.85% std::set_intersection (inline) 227ms 0.44% 31.49% 3510ms 6.84% std::__set_intersection 4ms 0.0078% 31.50% 3503ms 6.83% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1058ms 2.06% 33.56% 3474ms 6.77% __GI___libc_free 15ms 0.029% 33.59% 3429ms 6.68% MeshBasedCellPopulation::SpringIterator::operator++ 1049ms 2.04% 35.63% 3267ms 6.37% std::_Rb_tree::_M_get_insert_unique_pos 36ms 0.07% 35.70% 3110ms 6.06% Node::AddElement 0 0% 35.70% 3103ms 6.05% std::_Rb_tree::_M_create_node (inline) 0 0% 35.70% 3077ms 6.00% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 35.70% 3070ms 5.98% std::_Rb_tree::_M_get_node (inline) 0 0% 35.70% 3061ms 5.97% VertexMesh::~VertexMesh 95ms 0.19% 35.89% 3010ms 5.87% std::__new_allocator::deallocate (inline) 2203ms 4.29% 40.18% 3004ms 5.86% _int_malloc 0 0% 40.18% 2996ms 5.84% std::allocator_traits::deallocate (inline) 7ms 0.014% 40.20% 2937ms 5.72% TetrahedralMesh::ImportFromMesher 79ms 0.15% 40.35% 2936ms 5.72% tetgen::tetgenmesh::insphere_sos 153ms 0.3% 40.65% 2914ms 5.68% std::_Rb_tree_const_iterator::operator++ (inline) 2626ms 5.12% 45.77% 2844ms 5.54% tetgen::insphere 0 0% 45.77% 2787ms 5.43% AbstractCellPopulation::WriteResultsToFiles 2718ms 5.30% 51.07% 2718ms 5.30% std::_Rb_tree::_S_right (inline) 109ms 0.21% 51.28% 2691ms 5.25% tetgen::tetgenmesh::flip23 1098ms 2.14% 53.42% 2412ms 4.70% _int_free 46ms 0.09% 53.51% 2351ms 4.58% MutableElement::AddNode 168ms 0.33% 53.83% 2254ms 4.39% Node::~Node 150ms 0.29% 54.13% 2030ms 3.96% VertexMesh::Clear 98ms 0.19% 54.32% 1996ms 3.89% tetgen::tetgenmesh::flip32 0 0% 54.32% 1875ms 3.65% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 160ms 0.31% 54.63% 1832ms 3.57% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 54.63% 1789ms 3.49% std::_Rb_tree::_M_drop_node (inline) 0 0% 54.63% 1777ms 3.46% std::_Rb_tree::_M_put_node (inline) 1ms 0.0019% 54.63% 1687ms 3.29% std::_Rb_tree_iterator::operator++ (inline) 1597ms 3.11% 57.74% 1597ms 3.11% std::_Rb_tree_insert_and_rebalance 168ms 0.33% 58.07% 1459ms 2.84% tetgen::tetgenmesh::enqueueflipface 5ms 0.0097% 58.08% 1424ms 2.78% Element::Element 1376ms 2.68% 60.76% 1376ms 2.68% Node::GetIndex 1209ms 2.36% 63.12% 1279ms 2.49% tetgen::orient3d 898ms 1.75% 64.87% 1270ms 2.48% malloc_consolidate 26ms 0.051% 64.92% 1245ms 2.43% std::_Vector_base::_M_deallocate (inline) 67ms 0.13% 65.05% 1223ms 2.38% TetrahedralMesh::Clear 0 0% 65.05% 1201ms 2.34% std::vector::~vector (inline) 4ms 0.0078% 65.06% 1142ms 2.23% Element::RegisterWithNodes (inline) 0 0% 65.06% 1134ms 2.21% std::_Vector_base::~_Vector_base (inline) 6ms 0.012% 65.07% 1094ms 2.13% _int_free_maybe_consolidate 31ms 0.06% 65.13% 1047ms 2.04% tetgen::tetgenmesh::locate 57ms 0.11% 65.24% 972ms 1.89% tetgen::tetgenmesh::preciselocate 946ms 1.84% 67.09% 946ms 1.84% unlink_chunk 735ms 1.43% 68.52% 893ms 1.74% AbstractElement::GetNodeGlobalIndex 50ms 0.097% 68.62% 874ms 1.70% std::map::operator[] 45ms 0.088% 68.70% 873ms 1.70% std::vector::_M_realloc_insert 800ms 1.56% 70.26% 800ms 1.56% tetgen::tetgenmesh::triface::triface 780ms 1.52% 71.78% 780ms 1.52% tetgen::tetgenmesh::oppo 3ms 0.0058% 71.79% 777ms 1.51% VertexMesh::GenerateVerticesFromElementCircumcentres 0 0% 71.79% 764ms 1.49% std::_Rb_tree::lower_bound (inline) 0 0% 71.79% 764ms 1.49% std::map::lower_bound (inline) 109ms 0.21% 72.00% 727ms 1.42% std::vector::push_back (inline) 0 0% 72.00% 714ms 1.39% VoronoiDataWriter::Visit 4ms 0.0078% 72.01% 714ms 1.39% std::_Vector_base::_M_allocate (inline) 0 0% 72.01% 659ms 1.28% TetrahedralMesh::RefreshJacobianCachedData 646ms 1.26% 73.27% 646ms 1.26% [libchaste_mesh.so] 244ms 0.48% 73.75% 601ms 1.17% tetgen::tetgenmesh::sym 592ms 1.15% 74.90% 592ms 1.15% tetgen::tetgenmesh::triface::operator= 585ms 1.14% 76.04% 585ms 1.14% AbstractElement::IsDeleted 4ms 0.0078% 76.05% 568ms 1.11% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 76.05% 547ms 1.07% AbstractTwoBodyInteractionForce::AddForceContribution 326ms 0.64% 76.68% 546ms 1.06% tetgen::tetgenmesh::fnextself 12ms 0.023% 76.71% 532ms 1.04% AbstractTetrahedralElement::CalculateJacobian 247ms 0.48% 77.19% 525ms 1.02% AbstractElement::GetNodeLocation 9ms 0.018% 77.20% 522ms 1.02% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 12ms 0.023% 77.23% 518ms 1.01% boost::numeric::ublas::vector_assign (inline) 28ms 0.055% 77.28% 500ms 0.97% __atan2 5ms 0.0097% 77.29% 499ms 0.97% boost::numeric::ublas::c_vector::c_vector (inline) 491ms 0.96% 78.25% 491ms 0.96% Node::rGetLocation 491ms 0.96% 79.21% 491ms 0.96% std::vector::size (inline) 43ms 0.084% 79.29% 489ms 0.95% tetgen::tetgenmesh::enext2fnext 185ms 0.36% 79.65% 486ms 0.95% tetgen::tetgenmesh::bond 25ms 0.049% 79.70% 476ms 0.93% tetgen::tetgenmesh::queue::push 368ms 0.72% 80.42% 466ms 0.91% __ieee754_atan2_fma 0 0% 80.42% 461ms 0.9% std::set::find (inline) 32ms 0.062% 80.48% 454ms 0.88% tetgen::tetgenmesh::enextfnext 261ms 0.51% 80.99% 451ms 0.88% tetgen::tetgenmesh::link::add 415ms 0.81% 81.80% 415ms 0.81% tetgen::tetgenmesh::pointmark 407ms 0.79% 82.59% 407ms 0.79% tetgen::tetgenmesh::org 31ms 0.06% 82.65% 398ms 0.78% AbstractTetrahedralElement::RefreshJacobian 0 0% 82.65% 394ms 0.77% boost::numeric::ublas::inner_prod (inline) 2ms 0.0039% 82.65% 391ms 0.76% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 19ms 0.037% 82.69% 390ms 0.76% Element::CalculateCircumsphere 25ms 0.049% 82.74% 389ms 0.76% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 82.74% 372ms 0.73% std::insert_iterator::operator= (inline) 173ms 0.34% 83.08% 368ms 0.72% AbstractTetrahedralMesh::GetElement 365ms 0.71% 83.79% 365ms 0.71% tetgen::tetgenmesh::decode 12ms 0.023% 83.81% 339ms 0.66% VertexMesh::CalculateUnitNormalToFaceWithArea 2ms 0.0039% 83.82% 324ms 0.63% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.0058% 83.82% 322ms 0.63% VertexElement::~VertexElement 84ms 0.16% 83.99% 322ms 0.63% boost::numeric::ublas::indexing_vector_assign 15ms 0.029% 84.02% 322ms 0.63% std::_Rb_tree_iterator::operator-- (inline) 74ms 0.14% 84.16% 320ms 0.62% __dynamic_cast 3ms 0.0058% 84.17% 319ms 0.62% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 84.17% 318ms 0.62% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 84.17% 316ms 0.62% VertexMeshWriter::WriteVtkUsingMesh 314ms 0.61% 84.78% 314ms 0.61% boost::numeric::ublas::c_vector::operator() 2ms 0.0039% 84.78% 311ms 0.61% Cell::GetCellId 125ms 0.24% 85.02% 309ms 0.6% boost::numeric::ublas::vector_inner_prod::apply (inline) 289ms 0.56% 85.59% 289ms 0.56% tetgen::tetgenmesh::encode 0 0% 85.59% 286ms 0.56% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 282ms 0.55% 86.14% 282ms 0.55% std::_Rb_tree_decrement 13ms 0.025% 86.16% 279ms 0.54% std::vector::insert (inline) 4ms 0.0078% 86.17% 276ms 0.54% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.0019% 86.17% 272ms 0.53% AbstractCellProperty::IsSubType (inline) 2ms 0.0039% 86.18% 272ms 0.53% Element::~Element 0 0% 86.18% 270ms 0.53% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 90ms 0.18% 86.35% 260ms 0.51% Inverse 36ms 0.07% 86.42% 258ms 0.5% boost::numeric::ublas::vector_reference::operator() (inline) 3ms 0.0058% 86.43% 257ms 0.5% VertexMesh::GetVolumeOfElement