File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 41384ms, 85.87% of 48194ms total Dropped 878 nodes (cum <= 240.97ms) flat flat% sum% cum cum% 0 0% 0% 48136ms 99.88% __libc_start_call_main 0 0% 0% 48136ms 99.88% __libc_start_main_impl 0 0% 0% 48136ms 99.88% _start 0 0% 0% 48120ms 99.85% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 48120ms 99.85% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 48120ms 99.85% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 48120ms 99.85% main 0 0% 0% 48081ms 99.77% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 48081ms 99.77% CxxTest::TestRunner::runTest (inline) 0 0% 0% 48081ms 99.77% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 47861ms 99.31% AbstractCellBasedSimulation::Solve 0 0% 0% 40887ms 84.84% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 40835ms 84.73% MeshBasedCellPopulation::Update 0 0% 0% 22825ms 47.36% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 22823ms 47.36% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 204ms 0.42% 0.42% 20351ms 42.23% VertexMesh::VertexMesh 0 0% 0.42% 16541ms 34.32% MutableMesh::ReMesh 0 0% 0.42% 13202ms 27.39% tetgen::tetrahedralize 3ms 0.0062% 0.43% 13065ms 27.11% tetgen::tetgenmesh::delaunizevertices 4ms 0.0083% 0.44% 13058ms 27.09% tetgen::tetgenmesh::incrflipdelaunay 547ms 1.13% 1.57% 11591ms 24.05% tetgen::tetgenmesh::lawson 372ms 0.77% 2.34% 8412ms 17.45% VertexElement::AddFace 7ms 0.015% 2.36% 7513ms 15.59% std::set::insert (inline) 91ms 0.19% 2.55% 7060ms 14.65% std::_Rb_tree::_M_insert_unique 5571ms 11.56% 14.11% 5571ms 11.56% std::_Rb_tree_increment 0 0% 14.11% 4436ms 9.20% AbstractCellPopulation::WriteResultsToFiles 270ms 0.56% 14.67% 4205ms 8.73% std::_Rb_tree::_M_insert_ (inline) 157ms 0.33% 14.99% 3790ms 7.86% TetrahedralMesh::EdgeIterator::operator++ 204ms 0.42% 15.42% 3541ms 7.35% operator new 117ms 0.24% 15.66% 3538ms 7.34% tetgen::tetgenmesh::insphere_sos 3ms 0.0062% 15.67% 3460ms 7.18% std::set_intersection (inline) 259ms 0.54% 16.20% 3457ms 7.17% std::__set_intersection 3102ms 6.44% 22.64% 3401ms 7.06% tetgen::insphere 1026ms 2.13% 24.77% 3387ms 7.03% __GI___libc_free 238ms 0.49% 25.26% 3269ms 6.78% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 993ms 2.06% 27.32% 3257ms 6.76% __GI___libc_malloc 50ms 0.1% 27.43% 3248ms 6.74% std::__new_allocator::allocate (inline) 0 0% 27.43% 3224ms 6.69% std::allocator_traits::allocate (inline) 22ms 0.046% 27.47% 3188ms 6.61% Node::AddElement 14ms 0.029% 27.50% 3182ms 6.60% std::_Rb_tree::~_Rb_tree (inline) 1037ms 2.15% 29.65% 3168ms 6.57% std::_Rb_tree::_M_erase 0 0% 29.65% 3137ms 6.51% std::set::~set (inline) 234ms 0.49% 30.14% 3132ms 6.50% std::__new_allocator::deallocate (inline) 0 0% 30.14% 3121ms 6.48% std::allocator_traits::deallocate (inline) 3ms 0.0062% 30.14% 3105ms 6.44% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 914ms 1.90% 32.04% 3060ms 6.35% std::_Rb_tree::_M_get_insert_unique_pos (inline) 3ms 0.0062% 32.05% 3048ms 6.32% std::_Rb_tree_iterator::operator++ (inline) 3015ms 6.26% 38.30% 3015ms 6.26% std::_Rb_tree::_S_right (inline) 143ms 0.3% 38.60% 2759ms 5.72% std::_Rb_tree_const_iterator::operator++ (inline) 226ms 0.47% 39.07% 2742ms 5.69% tetgen::tetgenmesh::flip23 59ms 0.12% 39.19% 2657ms 5.51% MutableElement::AddNode 12ms 0.025% 39.22% 2596ms 5.39% TetrahedralMesh::ImportFromMesher 0 0% 39.22% 2489ms 5.16% VertexMesh::~VertexMesh 1ms 0.0021% 39.22% 2423ms 5.03% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 39.22% 2364ms 4.91% ForwardEulerNumericalMethod::UpdateAllNodePositions 1139ms 2.36% 41.58% 2359ms 4.89% _int_free 1ms 0.0021% 41.58% 2340ms 4.86% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 41.58% 2329ms 4.83% std::_Rb_tree::_M_create_node (inline) 0 0% 41.58% 2311ms 4.80% std::_Rb_tree::_M_get_node (inline) 0 0% 41.58% 2299ms 4.77% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 41.58% 2087ms 4.33% std::_Hashtable::count (inline) 9ms 0.019% 41.60% 2087ms 4.33% std::_Hashtable::find (inline) 0 0% 41.60% 2087ms 4.33% std::unordered_set::count (inline) 176ms 0.37% 41.97% 2018ms 4.19% tetgen::tetgenmesh::flip32 1649ms 3.42% 45.39% 1933ms 4.01% _int_malloc 0 0% 45.39% 1734ms 3.60% MeshBasedCellPopulation::UpdateNodePairs 161ms 0.33% 45.72% 1706ms 3.54% VertexMesh::Clear 1682ms 3.49% 49.21% 1682ms 3.49% std::_Rb_tree_insert_and_rebalance 0 0% 49.21% 1669ms 3.46% std::_Rb_tree::_M_drop_node (inline) 0 0% 49.21% 1657ms 3.44% std::_Rb_tree::_M_put_node (inline) 78ms 0.16% 49.38% 1618ms 3.36% Node::~Node 176ms 0.37% 49.74% 1592ms 3.30% std::_Hashtable::_M_find_before_node (inline) 0 0% 49.74% 1592ms 3.30% std::_Hashtable::_M_find_node (inline) 656ms 1.36% 51.10% 1569ms 3.26% std::_Rb_tree::_M_lower_bound (inline) 4ms 0.0083% 51.11% 1519ms 3.15% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 14ms 0.029% 51.14% 1516ms 3.15% MeshBasedCellPopulation::SpringIterator::operator++ 1399ms 2.90% 54.04% 1480ms 3.07% tetgen::orient3d 206ms 0.43% 54.47% 1393ms 2.89% tetgen::tetgenmesh::enqueueflipface 13ms 0.027% 54.50% 1375ms 2.85% std::__detail::_Hashtable_base::_M_equals (inline) 4ms 0.0083% 54.50% 1350ms 2.80% Element::Element 1314ms 2.73% 57.23% 1314ms 2.73% Node::GetIndex 66ms 0.14% 57.37% 1253ms 2.60% std::map::operator[] 31ms 0.064% 57.43% 1249ms 2.59% tetgen::tetgenmesh::locate 1216ms 2.52% 59.96% 1216ms 2.52% std::__detail::_Hashtable_base::_S_equals (inline) 107ms 0.22% 60.18% 1183ms 2.45% tetgen::tetgenmesh::preciselocate 0 0% 60.18% 1110ms 2.30% std::_Rb_tree::lower_bound (inline) 0 0% 60.18% 1110ms 2.30% std::map::lower_bound (inline) 0 0% 60.18% 1085ms 2.25% VoronoiDataWriter::Visit 20ms 0.041% 60.22% 1054ms 2.19% std::_Vector_base::_M_deallocate (inline) 1040ms 2.16% 62.38% 1040ms 2.16% tetgen::tetgenmesh::triface::triface 615ms 1.28% 63.65% 1036ms 2.15% malloc_consolidate 6ms 0.012% 63.67% 1015ms 2.11% _int_free_maybe_consolidate 2ms 0.0041% 63.67% 1001ms 2.08% Element::RegisterWithNodes (inline) 179ms 0.37% 64.04% 960ms 1.99% TetrahedralMesh::Clear 0 0% 64.04% 925ms 1.92% std::vector::~vector (inline) 0 0% 64.04% 892ms 1.85% std::_Vector_base::~_Vector_base (inline) 64ms 0.13% 64.17% 784ms 1.63% std::vector::_M_realloc_insert 784ms 1.63% 65.80% 784ms 1.63% tetgen::tetgenmesh::triface::operator= 317ms 0.66% 66.46% 766ms 1.59% tetgen::tetgenmesh::fnextself 4ms 0.0083% 66.47% 741ms 1.54% VertexMesh::GenerateVerticesFromElementCircumcentres 1ms 0.0021% 66.47% 715ms 1.48% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 66.47% 704ms 1.46% TetrahedralMesh::RefreshJacobianCachedData 277ms 0.57% 67.04% 694ms 1.44% AbstractElement::GetNodeLocation 19ms 0.039% 67.08% 683ms 1.42% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 12ms 0.025% 67.11% 667ms 1.38% AbstractTetrahedralElement::CalculateInverseJacobian 12ms 0.025% 67.13% 634ms 1.32% AbstractTetrahedralElement::CalculateJacobian 627ms 1.30% 68.43% 627ms 1.30% [libchaste_mesh.so] 18ms 0.037% 68.47% 614ms 1.27% boost::numeric::ublas::vector_assign (inline) 65ms 0.13% 68.61% 611ms 1.27% __atan2 462ms 0.96% 69.56% 610ms 1.27% AbstractElement::GetNodeGlobalIndex 606ms 1.26% 70.82% 606ms 1.26% unlink_chunk 17ms 0.035% 70.86% 595ms 1.23% boost::numeric::ublas::c_vector::c_vector (inline) 95ms 0.2% 71.05% 577ms 1.20% std::vector::push_back (inline) 9ms 0.019% 71.07% 572ms 1.19% std::_Vector_base::_M_allocate (inline) 13ms 0.027% 71.10% 571ms 1.18% Element::CalculateCircumsphere 563ms 1.17% 72.27% 563ms 1.17% tetgen::tetgenmesh::oppo 562ms 1.17% 73.43% 562ms 1.17% Node::rGetLocation 87ms 0.18% 73.61% 551ms 1.14% std::_Rb_tree::find (inline) 0 0% 73.61% 547ms 1.13% std::set::find (inline) 439ms 0.91% 74.53% 546ms 1.13% __ieee754_atan2_fma 546ms 1.13% 75.66% 546ms 1.13% std::vector::size (inline) 7ms 0.015% 75.67% 520ms 1.08% std::_Hashtable::_M_bucket_index (inline) 0 0% 75.67% 513ms 1.06% std::__detail::_Hash_code_base::_M_bucket_index (inline) 513ms 1.06% 76.74% 513ms 1.06% std::__detail::_Mod_range_hashing::operator() (inline) 58ms 0.12% 76.86% 507ms 1.05% tetgen::tetgenmesh::enext2fnext 0 0% 76.86% 494ms 1.03% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 76.86% 494ms 1.03% std::_Hashtable::~_Hashtable (inline) 0 0% 76.86% 494ms 1.03% std::unordered_set::~unordered_set (inline) 39ms 0.081% 76.94% 485ms 1.01% tetgen::tetgenmesh::enextfnext 0 0% 76.94% 483ms 1.00% boost::numeric::ublas::inner_prod (inline) 4ms 0.0083% 76.95% 482ms 1.00% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 76.95% 479ms 0.99% std::insert_iterator::operator= (inline) 25ms 0.052% 77.00% 478ms 0.99% boost::numeric::ublas::vector_scalar_binary::evaluate 293ms 0.61% 77.61% 449ms 0.93% tetgen::tetgenmesh::sym 49ms 0.1% 77.71% 448ms 0.93% AbstractTetrahedralElement::RefreshJacobian 28ms 0.058% 77.77% 445ms 0.92% tetgen::tetgenmesh::queue::push 0 0% 77.77% 443ms 0.92% std::_Hashtable::_M_insert (inline) 22ms 0.046% 77.81% 443ms 0.92% std::_Hashtable::_M_insert_unique_aux (inline) 0 0% 77.81% 443ms 0.92% std::__detail::_Insert_base::insert (inline) 0 0% 77.81% 443ms 0.92% std::unordered_set::insert (inline) 1ms 0.0021% 77.81% 423ms 0.88% std::_Rb_tree::_M_insert_unique_ (inline) 16ms 0.033% 77.85% 421ms 0.87% std::_Hashtable::_M_insert_unique 355ms 0.74% 78.58% 416ms 0.86% tetgen::tetgenmesh::link::add 17ms 0.035% 78.62% 401ms 0.83% VertexMesh::CalculateUnitNormalToFaceWithArea 176ms 0.37% 78.98% 394ms 0.82% boost::numeric::ublas::vector_inner_prod::apply (inline) 388ms 0.81% 79.79% 388ms 0.81% boost::numeric::ublas::c_vector::operator() 112ms 0.23% 80.02% 388ms 0.81% boost::numeric::ublas::indexing_vector_assign 0 0% 80.02% 387ms 0.8% VertexMeshWriter::WriteVtkUsingMesh 5ms 0.01% 80.03% 382ms 0.79% CellPropertyCollection::GetPropertiesType (inline) 370ms 0.77% 80.80% 370ms 0.77% tetgen::tetgenmesh::org 99ms 0.21% 81.01% 369ms 0.77% __dynamic_cast 3ms 0.0062% 81.01% 364ms 0.76% Cell::GetCellId 265ms 0.55% 81.56% 360ms 0.75% tetgen::tetgenmesh::bond 6ms 0.012% 81.57% 353ms 0.73% boost::numeric::ublas::c_vector::operator= (inline) 2ms 0.0041% 81.58% 345ms 0.72% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 81.58% 344ms 0.71% std::__detail::_AllocNode::operator() (inline) 0 0% 81.58% 344ms 0.71% std::__detail::_Hashtable_alloc::_M_allocate_node (inline) 0 0% 81.58% 344ms 0.71% std::__detail::_NodeBuilder::_S_build (inline) 339ms 0.7% 82.28% 339ms 0.7% tetgen::tetgenmesh::pointmark 8ms 0.017% 82.30% 334ms 0.69% std::_Rb_tree_iterator::operator-- (inline) 10ms 0.021% 82.32% 331ms 0.69% std::vector::insert (inline) 18ms 0.037% 82.36% 326ms 0.68% std::_Hashtable::clear (inline) 81ms 0.17% 82.52% 322ms 0.67% tetgen::tetgenmesh::queue::pop 147ms 0.31% 82.83% 320ms 0.66% Inverse 303ms 0.63% 83.46% 303ms 0.63% std::_Rb_tree_decrement 0 0% 83.46% 300ms 0.62% AbstractCellProperty::IsSubType (inline) 35ms 0.073% 83.53% 298ms 0.62% tetgen::insphereadapt 45ms 0.093% 83.62% 294ms 0.61% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 83.62% 289ms 0.6% tcache_get (inline) 289ms 0.6% 84.22% 289ms 0.6% tcache_get_n (inline) 3ms 0.0062% 84.23% 273ms 0.57% VertexMesh::GetVolumeOfElement 7ms 0.015% 84.24% 272ms 0.56% std::__detail::_Hashtable_alloc::_M_deallocate_nodes (inline) 268ms 0.56% 84.80% 268ms 0.56% AbstractElement::IsDeleted 0 0% 84.80% 265ms 0.55% std::__detail::_Hashtable_alloc::_M_deallocate_node (inline) 0 0% 84.80% 265ms 0.55% std::__detail::_Hashtable_alloc::_M_deallocate_node_ptr (inline) 2ms 0.0041% 84.81% 264ms 0.55% VertexMeshWriter::MakeVtkMesh 8ms 0.017% 84.82% 243ms 0.5% VertexElement::~VertexElement 185ms 0.38% 85.21% 242ms 0.5% boost::numeric::ublas::c_matrix::operator() 127ms 0.26% 85.47% 241ms 0.5% Determinant 193ms 0.4% 85.87% 241ms 0.5% tetgen::tetgenmesh::link::deletenode