File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 48636ms, 86.66% of 56121ms total Dropped 834 nodes (cum <= 280.61ms) flat flat% sum% cum cum% 0 0% 0% 56060ms 99.89% __libc_start_call_main 0 0% 0% 56060ms 99.89% __libc_start_main_impl 0 0% 0% 56060ms 99.89% _start 0 0% 0% 56044ms 99.86% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 56044ms 99.86% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 56044ms 99.86% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 56044ms 99.86% main 0 0% 0% 56005ms 99.79% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 56005ms 99.79% CxxTest::TestRunner::runTest (inline) 0 0% 0% 56005ms 99.79% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 55757ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0% 47293ms 84.27% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 47239ms 84.17% MeshBasedCellPopulation::Update 0 0% 0% 26572ms 47.35% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 26572ms 47.35% MeshBasedCellPopulation::TessellateIfNeeded 180ms 0.32% 0.32% 23593ms 42.04% VertexMesh::VertexMesh 0 0% 0.32% 16964ms 30.23% MutableMesh::ReMesh 0 0% 0.32% 12743ms 22.71% tetgen::tetrahedralize 2ms 0.0036% 0.32% 12605ms 22.46% tetgen::tetgenmesh::delaunizevertices 10ms 0.018% 0.34% 12597ms 22.45% tetgen::tetgenmesh::incrflipdelaunay 586ms 1.04% 1.39% 11316ms 20.16% TetrahedralMesh::EdgeIterator::operator++ 537ms 0.96% 2.34% 11169ms 19.90% tetgen::tetgenmesh::lawson 23ms 0.041% 2.38% 9753ms 17.38% std::set::insert (inline) 176ms 0.31% 2.70% 9259ms 16.50% std::_Rb_tree::_M_insert_unique 385ms 0.69% 3.38% 8905ms 15.87% VertexElement::AddFace 3000ms 5.35% 8.73% 8529ms 15.20% std::_Rb_tree::_M_lower_bound (inline) 224ms 0.4% 9.13% 8036ms 14.32% std::_Rb_tree::find (inline) 0 0% 9.13% 7489ms 13.34% std::set::count (inline) 245ms 0.44% 9.57% 5496ms 9.79% std::_Rb_tree::_M_insert_ (inline) 116ms 0.21% 9.77% 5402ms 9.63% std::less::operator() (inline) 5334ms 9.50% 19.28% 5334ms 9.50% std::operator< (inline) 1ms 0.0018% 19.28% 5035ms 8.97% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 19.28% 4917ms 8.76% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 19.28% 4894ms 8.72% AbstractNumericalMethod::ComputeForcesIncludingDamping 200ms 0.36% 19.63% 4875ms 8.69% operator new 1040ms 1.85% 21.49% 4613ms 8.22% __GI___libc_malloc 4478ms 7.98% 29.47% 4478ms 7.98% std::_Rb_tree_increment 53ms 0.094% 29.56% 4221ms 7.52% std::__new_allocator::allocate (inline) 0 0% 29.56% 4206ms 7.49% std::allocator_traits::allocate (inline) 1ms 0.0018% 29.56% 4066ms 7.25% MeshBasedCellPopulation::UpdateNodePairs 9ms 0.016% 29.58% 4034ms 7.19% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.0053% 29.58% 4029ms 7.18% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1516ms 2.70% 32.29% 4024ms 7.17% std::_Rb_tree::_M_erase 0 0% 32.29% 3989ms 7.11% std::set::~set (inline) 12ms 0.021% 32.31% 3930ms 7.00% MeshBasedCellPopulation::SpringIterator::operator++ 1285ms 2.29% 34.60% 3905ms 6.96% std::_Rb_tree::_M_get_insert_unique_pos 36ms 0.064% 34.66% 3577ms 6.37% Node::AddElement 1059ms 1.89% 36.55% 3558ms 6.34% __GI___libc_free 4ms 0.0071% 36.55% 3516ms 6.27% std::set_intersection (inline) 219ms 0.39% 36.95% 3512ms 6.26% std::__set_intersection 98ms 0.17% 37.12% 3477ms 6.20% tetgen::tetgenmesh::insphere_sos 0 0% 37.12% 3436ms 6.12% std::_Rb_tree::_M_create_node (inline) 2ms 0.0036% 37.12% 3433ms 6.12% TetrahedralMesh::ImportFromMesher 0 0% 37.12% 3406ms 6.07% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 37.12% 3397ms 6.05% std::_Rb_tree::_M_get_node (inline) 3065ms 5.46% 42.58% 3363ms 5.99% tetgen::insphere 0 0% 42.58% 3267ms 5.82% AbstractCellPopulation::WriteResultsToFiles 2478ms 4.42% 47.00% 3203ms 5.71% _int_malloc 115ms 0.2% 47.21% 3124ms 5.57% std::__new_allocator::deallocate (inline) 0 0% 47.21% 3109ms 5.54% std::allocator_traits::deallocate (inline) 3101ms 5.53% 52.73% 3101ms 5.53% std::_Rb_tree::_S_right (inline) 0 0% 52.73% 2994ms 5.33% VertexMesh::~VertexMesh 171ms 0.3% 53.04% 2823ms 5.03% std::_Rb_tree_const_iterator::operator++ (inline) 202ms 0.36% 53.40% 2741ms 4.88% tetgen::tetgenmesh::flip23 81ms 0.14% 53.54% 2719ms 4.84% MutableElement::AddNode 1205ms 2.15% 55.69% 2496ms 4.45% _int_free 144ms 0.26% 55.94% 2241ms 3.99% Node::~Node 2ms 0.0036% 55.95% 2167ms 3.86% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 221ms 0.39% 56.34% 2134ms 3.80% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 194ms 0.35% 56.69% 2012ms 3.59% VertexMesh::Clear 0 0% 56.69% 1925ms 3.43% std::_Rb_tree_iterator::operator++ (inline) 1919ms 3.42% 60.11% 1919ms 3.42% std::_Rb_tree_insert_and_rebalance 0 0% 60.11% 1855ms 3.31% std::_Rb_tree::_M_drop_node (inline) 0 0% 60.11% 1844ms 3.29% std::_Rb_tree::_M_put_node (inline) 4ms 0.0071% 60.11% 1708ms 3.04% Element::Element 154ms 0.27% 60.39% 1705ms 3.04% tetgen::tetgenmesh::flip32 1330ms 2.37% 62.76% 1428ms 2.54% tetgen::orient3d 204ms 0.36% 63.12% 1388ms 2.47% TetrahedralMesh::Clear 6ms 0.011% 63.13% 1383ms 2.46% Element::RegisterWithNodes (inline) 213ms 0.38% 63.51% 1328ms 2.37% tetgen::tetgenmesh::enqueueflipface 1310ms 2.33% 65.85% 1310ms 2.33% Node::GetIndex 27ms 0.048% 65.89% 1292ms 2.30% std::_Vector_base::_M_deallocate (inline) 819ms 1.46% 67.35% 1261ms 2.25% malloc_consolidate 30ms 0.053% 67.41% 1191ms 2.12% tetgen::tetgenmesh::locate 1ms 0.0018% 67.41% 1177ms 2.10% std::vector::~vector (inline) 102ms 0.18% 67.59% 1122ms 2.00% tetgen::tetgenmesh::preciselocate 1ms 0.0018% 67.59% 1100ms 1.96% std::_Vector_base::~_Vector_base (inline) 65ms 0.12% 67.71% 1088ms 1.94% std::vector::_M_realloc_insert 5ms 0.0089% 67.72% 1081ms 1.93% _int_free_maybe_consolidate 59ms 0.11% 67.82% 1019ms 1.82% std::map::operator[] 940ms 1.67% 69.50% 940ms 1.67% unlink_chunk 0 0% 69.50% 896ms 1.60% std::_Rb_tree::lower_bound (inline) 0 0% 69.50% 896ms 1.60% std::map::lower_bound (inline) 0 0% 69.50% 864ms 1.54% VoronoiDataWriter::Visit 4ms 0.0071% 69.50% 858ms 1.53% VertexMesh::GenerateVerticesFromElementCircumcentres 106ms 0.19% 69.69% 856ms 1.53% std::vector::push_back (inline) 847ms 1.51% 71.20% 847ms 1.51% tetgen::tetgenmesh::triface::triface 699ms 1.25% 72.45% 827ms 1.47% AbstractElement::GetNodeGlobalIndex 3ms 0.0053% 72.45% 812ms 1.45% std::_Vector_base::_M_allocate (inline) 1ms 0.0018% 72.45% 767ms 1.37% TetrahedralMesh::RefreshJacobianCachedData 0 0% 72.45% 707ms 1.26% AbstractTwoBodyInteractionForce::AddForceContribution 2ms 0.0036% 72.46% 690ms 1.23% AbstractTetrahedralElement::CalculateInverseJacobian 7ms 0.012% 72.47% 670ms 1.19% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 670ms 1.19% 73.66% 670ms 1.19% tetgen::tetgenmesh::triface::operator= 339ms 0.6% 74.27% 667ms 1.19% tetgen::tetgenmesh::fnextself 666ms 1.19% 75.45% 666ms 1.19% tetgen::tetgenmesh::oppo 13ms 0.023% 75.48% 655ms 1.17% AbstractTetrahedralElement::CalculateJacobian 643ms 1.15% 76.62% 643ms 1.15% [libchaste_mesh.so] 14ms 0.025% 76.65% 639ms 1.14% boost::numeric::ublas::vector_assign (inline) 15ms 0.027% 76.68% 627ms 1.12% boost::numeric::ublas::c_vector::c_vector (inline) 43ms 0.077% 76.75% 567ms 1.01% __atan2 251ms 0.45% 77.20% 549ms 0.98% AbstractElement::GetNodeLocation 0 0% 77.20% 546ms 0.97% std::set::find (inline) 409ms 0.73% 77.93% 524ms 0.93% __ieee754_atan2_fma 0 0% 77.93% 500ms 0.89% std::insert_iterator::operator= (inline) 0 0% 77.93% 493ms 0.88% boost::numeric::ublas::inner_prod (inline) 1ms 0.0018% 77.93% 490ms 0.87% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 24ms 0.043% 77.97% 489ms 0.87% boost::numeric::ublas::vector_scalar_binary::evaluate 483ms 0.86% 78.83% 483ms 0.86% Node::rGetLocation 51ms 0.091% 78.92% 466ms 0.83% tetgen::tetgenmesh::enext2fnext 31ms 0.055% 78.98% 462ms 0.82% Element::CalculateCircumsphere 51ms 0.091% 79.07% 458ms 0.82% AbstractTetrahedralElement::RefreshJacobian 46ms 0.082% 79.15% 454ms 0.81% tetgen::tetgenmesh::enextfnext 443ms 0.79% 79.94% 443ms 0.79% AbstractElement::IsDeleted 0 0% 79.94% 441ms 0.79% std::_Rb_tree::_M_insert_unique_ (inline) 436ms 0.78% 80.72% 436ms 0.78% std::vector::size (inline) 23ms 0.041% 80.76% 431ms 0.77% tetgen::tetgenmesh::queue::push 257ms 0.46% 81.22% 426ms 0.76% AbstractTetrahedralMesh::GetElement 289ms 0.51% 81.73% 415ms 0.74% tetgen::tetgenmesh::sym 20ms 0.036% 81.77% 410ms 0.73% std::_Rb_tree_iterator::operator-- (inline) 287ms 0.51% 82.28% 405ms 0.72% tetgen::tetgenmesh::link::add 118ms 0.21% 82.49% 404ms 0.72% boost::numeric::ublas::indexing_vector_assign 21ms 0.037% 82.53% 397ms 0.71% VertexMesh::CalculateUnitNormalToFaceWithArea 196ms 0.35% 82.88% 396ms 0.71% boost::numeric::ublas::vector_inner_prod::apply (inline) 8ms 0.014% 82.89% 391ms 0.7% CellPropertyCollection::GetPropertiesType (inline) 0 0% 82.89% 391ms 0.7% VertexMeshWriter::WriteVtkUsingMesh 5ms 0.0089% 82.90% 385ms 0.69% Cell::GetCellId 101ms 0.18% 83.08% 384ms 0.68% __dynamic_cast 375ms 0.67% 83.75% 375ms 0.67% boost::numeric::ublas::c_vector::operator() 373ms 0.66% 84.41% 373ms 0.66% tetgen::tetgenmesh::org 370ms 0.66% 85.07% 370ms 0.66% std::_Rb_tree_decrement 278ms 0.5% 85.57% 364ms 0.65% tetgen::tetgenmesh::bond 5ms 0.0089% 85.58% 362ms 0.65% boost::numeric::ublas::c_vector::operator= (inline) 11ms 0.02% 85.60% 361ms 0.64% std::vector::insert (inline) 3ms 0.0053% 85.60% 333ms 0.59% AbstractCellProperty::IsSubType (inline) 5ms 0.0089% 85.61% 324ms 0.58% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 85.61% 320ms 0.57% tcache_get (inline) 320ms 0.57% 86.18% 320ms 0.57% tcache_get_n (inline) 0 0% 86.18% 307ms 0.55% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 126ms 0.22% 86.40% 303ms 0.54% Inverse 29ms 0.052% 86.46% 298ms 0.53% tetgen::insphereadapt 7ms 0.012% 86.47% 297ms 0.53% VertexElement::~VertexElement 58ms 0.1% 86.57% 288ms 0.51% tetgen::tetgenmesh::queue::pop 51ms 0.091% 86.66% 282ms 0.5% boost::numeric::ublas::vector_reference::operator() (inline)