File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 49079ms, 86.51% of 56731ms total Dropped 870 nodes (cum <= 283.65ms) flat flat% sum% cum cum% 0 0% 0% 56678ms 99.91% __libc_start_call_main 0 0% 0% 56678ms 99.91% __libc_start_main_impl 0 0% 0% 56678ms 99.91% _start 0 0% 0% 56663ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 56663ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 56663ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 56663ms 99.88% main 0 0% 0% 56625ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 56625ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 56624ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 56370ms 99.36% AbstractCellBasedSimulation::Solve 0 0% 0% 47610ms 83.92% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 47561ms 83.84% MeshBasedCellPopulation::Update 0 0% 0% 26815ms 47.27% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 26815ms 47.27% MeshBasedCellPopulation::TessellateIfNeeded 187ms 0.33% 0.33% 23734ms 41.84% VertexMesh::VertexMesh 0 0% 0.33% 16993ms 29.95% MutableMesh::ReMesh 0 0% 0.33% 12825ms 22.61% tetgen::tetrahedralize 3ms 0.0053% 0.33% 12695ms 22.38% tetgen::tetgenmesh::delaunizevertices 12ms 0.021% 0.36% 12686ms 22.36% tetgen::tetgenmesh::incrflipdelaunay 578ms 1.02% 1.37% 11378ms 20.06% TetrahedralMesh::EdgeIterator::operator++ 556ms 0.98% 2.35% 11264ms 19.86% tetgen::tetgenmesh::lawson 40ms 0.071% 2.43% 9599ms 16.92% std::set::insert (inline) 223ms 0.39% 2.82% 9099ms 16.04% std::_Rb_tree::_M_insert_unique 390ms 0.69% 3.51% 8926ms 15.73% VertexElement::AddFace 2975ms 5.24% 8.75% 8549ms 15.07% std::_Rb_tree::_M_lower_bound (inline) 237ms 0.42% 9.17% 8000ms 14.10% std::_Rb_tree::find (inline) 0 0% 9.17% 7432ms 13.10% std::set::count (inline) 288ms 0.51% 9.68% 5464ms 9.63% std::_Rb_tree::_M_insert_ (inline) 101ms 0.18% 9.85% 5399ms 9.52% std::less::operator() (inline) 5348ms 9.43% 19.28% 5348ms 9.43% std::operator< (inline) 0 0% 19.28% 5114ms 9.01% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 19.28% 4999ms 8.81% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0035% 19.28% 4974ms 8.77% AbstractNumericalMethod::ComputeForcesIncludingDamping 217ms 0.38% 19.67% 4896ms 8.63% operator new 4714ms 8.31% 27.98% 4714ms 8.31% std::_Rb_tree_increment 1060ms 1.87% 29.84% 4574ms 8.06% __GI___libc_malloc 56ms 0.099% 29.94% 4240ms 7.47% std::__new_allocator::allocate (inline) 0 0% 29.94% 4218ms 7.44% std::allocator_traits::allocate (inline) 10ms 0.018% 29.96% 4120ms 7.26% std::_Rb_tree::~_Rb_tree (inline) 1561ms 2.75% 32.71% 4104ms 7.23% std::_Rb_tree::_M_erase 0 0% 32.71% 4087ms 7.20% MeshBasedCellPopulation::UpdateNodePairs 0 0% 32.71% 4077ms 7.19% std::set::~set (inline) 2ms 0.0035% 32.72% 4074ms 7.18% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 14ms 0.025% 32.74% 3956ms 6.97% MeshBasedCellPopulation::SpringIterator::operator++ 1210ms 2.13% 34.87% 3727ms 6.57% std::_Rb_tree::_M_get_insert_unique_pos 1138ms 2.01% 36.88% 3614ms 6.37% __GI___libc_free 5ms 0.0088% 36.89% 3585ms 6.32% std::set_intersection (inline) 245ms 0.43% 37.32% 3580ms 6.31% std::__set_intersection 0 0% 37.32% 3508ms 6.18% AbstractCellPopulation::WriteResultsToFiles 118ms 0.21% 37.53% 3497ms 6.16% tetgen::tetgenmesh::insphere_sos 0 0% 37.53% 3442ms 6.07% std::_Rb_tree::_M_create_node (inline) 0 0% 37.53% 3408ms 6.01% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 37.53% 3400ms 5.99% std::_Rb_tree::_M_get_node (inline) 9ms 0.016% 37.54% 3366ms 5.93% TetrahedralMesh::ImportFromMesher 3070ms 5.41% 42.96% 3364ms 5.93% tetgen::insphere 18ms 0.032% 42.99% 3321ms 5.85% Node::AddElement 116ms 0.2% 43.19% 3228ms 5.69% std::__new_allocator::deallocate (inline) 0 0% 43.19% 3211ms 5.66% std::allocator_traits::deallocate (inline) 2383ms 4.20% 47.39% 3193ms 5.63% _int_malloc 0 0% 47.39% 3104ms 5.47% VertexMesh::~VertexMesh 3020ms 5.32% 52.72% 3020ms 5.32% std::_Rb_tree::_S_right (inline) 224ms 0.39% 53.11% 2883ms 5.08% std::_Rb_tree_const_iterator::operator++ (inline) 215ms 0.38% 53.49% 2756ms 4.86% tetgen::tetgenmesh::flip23 79ms 0.14% 53.63% 2563ms 4.52% MutableElement::AddNode 1203ms 2.12% 55.75% 2472ms 4.36% _int_free 202ms 0.36% 56.11% 2371ms 4.18% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 2ms 0.0035% 56.11% 2349ms 4.14% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 175ms 0.31% 56.42% 2349ms 4.14% Node::~Node 2ms 0.0035% 56.42% 2180ms 3.84% std::_Rb_tree_iterator::operator++ (inline) 193ms 0.34% 56.76% 2113ms 3.72% VertexMesh::Clear 0 0% 56.76% 1922ms 3.39% std::_Rb_tree::_M_drop_node (inline) 0 0% 56.76% 1916ms 3.38% std::_Rb_tree::_M_put_node (inline) 1842ms 3.25% 60.01% 1842ms 3.25% std::_Rb_tree_insert_and_rebalance 135ms 0.24% 60.25% 1824ms 3.22% tetgen::tetgenmesh::flip32 3ms 0.0053% 60.25% 1579ms 2.78% Element::Element 1315ms 2.32% 62.57% 1415ms 2.49% tetgen::orient3d 200ms 0.35% 62.92% 1402ms 2.47% TetrahedralMesh::Clear 165ms 0.29% 63.21% 1365ms 2.41% tetgen::tetgenmesh::enqueueflipface 16ms 0.028% 63.24% 1310ms 2.31% std::_Vector_base::_M_deallocate (inline) 1298ms 2.29% 65.53% 1298ms 2.29% Node::GetIndex 801ms 1.41% 66.94% 1277ms 2.25% malloc_consolidate 8ms 0.014% 66.95% 1254ms 2.21% Element::RegisterWithNodes (inline) 0 0% 66.95% 1203ms 2.12% std::vector::~vector (inline) 42ms 0.074% 67.03% 1196ms 2.11% tetgen::tetgenmesh::locate 2ms 0.0035% 67.03% 1112ms 1.96% std::_Vector_base::~_Vector_base (inline) 111ms 0.2% 67.23% 1097ms 1.93% tetgen::tetgenmesh::preciselocate 50ms 0.088% 67.32% 1091ms 1.92% std::vector::_M_realloc_insert 5ms 0.0088% 67.32% 1077ms 1.90% _int_free_maybe_consolidate 60ms 0.11% 67.43% 1076ms 1.90% std::map::operator[] 1020ms 1.80% 69.23% 1020ms 1.80% unlink_chunk 0 0% 69.23% 959ms 1.69% std::_Rb_tree::lower_bound (inline) 0 0% 69.23% 959ms 1.69% std::map::lower_bound (inline) 0 0% 69.23% 926ms 1.63% VoronoiDataWriter::Visit 111ms 0.2% 69.42% 886ms 1.56% std::vector::push_back (inline) 4ms 0.0071% 69.43% 864ms 1.52% VertexMesh::GenerateVerticesFromElementCircumcentres 676ms 1.19% 70.62% 825ms 1.45% AbstractElement::GetNodeGlobalIndex 5ms 0.0088% 70.63% 823ms 1.45% std::_Vector_base::_M_allocate (inline) 794ms 1.40% 72.03% 794ms 1.40% tetgen::tetgenmesh::triface::triface 0 0% 72.03% 775ms 1.37% TetrahedralMesh::RefreshJacobianCachedData 477ms 0.84% 72.87% 758ms 1.34% tetgen::tetgenmesh::fnextself 1ms 0.0018% 72.87% 738ms 1.30% AbstractTwoBodyInteractionForce::AddForceContribution 16ms 0.028% 72.90% 700ms 1.23% boost::numeric::ublas::vector_assign (inline) 10ms 0.018% 72.92% 696ms 1.23% AbstractTetrahedralElement::CalculateInverseJacobian 7ms 0.012% 72.93% 694ms 1.22% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 691ms 1.22% 74.15% 691ms 1.22% tetgen::tetgenmesh::oppo 13ms 0.023% 74.17% 672ms 1.18% AbstractTetrahedralElement::CalculateJacobian 17ms 0.03% 74.20% 669ms 1.18% boost::numeric::ublas::c_vector::c_vector (inline) 642ms 1.13% 75.33% 642ms 1.13% [libchaste_mesh.so] 48ms 0.085% 75.42% 600ms 1.06% __atan2 257ms 0.45% 75.87% 588ms 1.04% AbstractElement::GetNodeLocation 0 0% 75.87% 565ms 1% std::set::find (inline) 38ms 0.067% 75.94% 558ms 0.98% tetgen::tetgenmesh::queue::push 554ms 0.98% 76.92% 554ms 0.98% tetgen::tetgenmesh::triface::operator= 434ms 0.77% 77.68% 552ms 0.97% __ieee754_atan2_fma 414ms 0.73% 78.41% 516ms 0.91% tetgen::tetgenmesh::link::add 512ms 0.9% 79.31% 512ms 0.9% AbstractElement::IsDeleted 0 0% 79.31% 511ms 0.9% boost::numeric::ublas::inner_prod (inline) 4ms 0.0071% 79.32% 509ms 0.9% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 29ms 0.051% 79.37% 505ms 0.89% boost::numeric::ublas::vector_scalar_binary::evaluate 63ms 0.11% 79.48% 498ms 0.88% tetgen::tetgenmesh::enextfnext 40ms 0.071% 79.55% 488ms 0.86% tetgen::tetgenmesh::enext2fnext 0 0% 79.55% 487ms 0.86% std::insert_iterator::operator= (inline) 483ms 0.85% 80.40% 483ms 0.85% std::vector::size (inline) 53ms 0.093% 80.50% 482ms 0.85% AbstractTetrahedralElement::RefreshJacobian 20ms 0.035% 80.53% 469ms 0.83% Element::CalculateCircumsphere 467ms 0.82% 81.36% 467ms 0.82% Node::rGetLocation 456ms 0.8% 82.16% 456ms 0.8% boost::numeric::ublas::c_vector::operator() 2ms 0.0035% 82.16% 450ms 0.79% boost::numeric::ublas::c_vector::operator= (inline) 112ms 0.2% 82.36% 449ms 0.79% boost::numeric::ublas::indexing_vector_assign 1ms 0.0018% 82.36% 439ms 0.77% std::_Rb_tree::_M_insert_unique_ (inline) 174ms 0.31% 82.67% 405ms 0.71% boost::numeric::ublas::vector_inner_prod::apply (inline) 14ms 0.025% 82.69% 402ms 0.71% std::_Rb_tree_iterator::operator-- (inline) 1ms 0.0018% 82.70% 398ms 0.7% CellPropertyCollection::GetPropertiesType (inline) 0 0% 82.70% 394ms 0.69% VertexMeshWriter::WriteVtkUsingMesh 260ms 0.46% 83.15% 392ms 0.69% tetgen::tetgenmesh::sym 239ms 0.42% 83.58% 388ms 0.68% AbstractTetrahedralMesh::GetElement 19ms 0.033% 83.61% 384ms 0.68% VertexMesh::CalculateUnitNormalToFaceWithArea 88ms 0.16% 83.76% 381ms 0.67% __dynamic_cast 2ms 0.0035% 83.77% 378ms 0.67% Cell::GetCellId 365ms 0.64% 84.41% 365ms 0.64% std::_Rb_tree_decrement 349ms 0.62% 85.03% 349ms 0.62% tetgen::tetgenmesh::org 15ms 0.026% 85.05% 344ms 0.61% std::vector::insert (inline) 241ms 0.42% 85.48% 344ms 0.61% tetgen::tetgenmesh::bond 58ms 0.1% 85.58% 337ms 0.59% boost::numeric::ublas::vector_reference::operator() (inline) 11ms 0.019% 85.60% 324ms 0.57% VertexElement::~VertexElement 3ms 0.0053% 85.60% 323ms 0.57% AbstractTetrahedralElement::AbstractTetrahedralElement 6ms 0.011% 85.61% 322ms 0.57% AbstractCellProperty::IsSubType (inline) 0 0% 85.61% 300ms 0.53% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 129ms 0.23% 85.84% 298ms 0.53% Inverse 25ms 0.044% 85.89% 294ms 0.52% tetgen::insphereadapt 0 0% 85.89% 290ms 0.51% tcache_get (inline) 290ms 0.51% 86.40% 290ms 0.51% tcache_get_n (inline) 65ms 0.11% 86.51% 284ms 0.5% tetgen::tetgenmesh::queue::pop