File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 47457ms, 86.73% of 54718ms total Dropped 824 nodes (cum <= 273.59ms) flat flat% sum% cum cum% 0 0% 0% 54668ms 99.91% __libc_start_call_main 0 0% 0% 54668ms 99.91% __libc_start_main_impl 0 0% 0% 54668ms 99.91% _start 0 0% 0% 54655ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 54655ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 54655ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 54655ms 99.88% main 0 0% 0% 54616ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 54616ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 54616ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 54401ms 99.42% AbstractCellBasedSimulation::Solve 0 0% 0% 46928ms 85.76% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 46891ms 85.70% MeshBasedCellPopulation::Update 0 0% 0% 27181ms 49.67% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 27181ms 49.67% MeshBasedCellPopulation::TessellateIfNeeded 187ms 0.34% 0.34% 23731ms 43.37% VertexMesh::VertexMesh 0 0% 0.34% 16313ms 29.81% MutableMesh::ReMesh 0 0% 0.34% 12166ms 22.23% tetgen::tetrahedralize 3ms 0.0055% 0.35% 12046ms 22.01% tetgen::tetgenmesh::delaunizevertices 10ms 0.018% 0.37% 12039ms 22.00% tetgen::tetgenmesh::incrflipdelaunay 390ms 0.71% 1.08% 10712ms 19.58% tetgen::tetgenmesh::lawson 520ms 0.95% 2.03% 10543ms 19.27% TetrahedralMesh::EdgeIterator::operator++ 35ms 0.064% 2.09% 9480ms 17.33% std::set::insert (inline) 219ms 0.4% 2.49% 9121ms 16.67% std::_Rb_tree::_M_insert_unique 389ms 0.71% 3.20% 8264ms 15.10% VertexElement::AddFace 2507ms 4.58% 7.79% 7341ms 13.42% std::_Rb_tree::_M_lower_bound (inline) 193ms 0.35% 8.14% 6847ms 12.51% std::_Rb_tree::find (inline) 0 0% 8.14% 6427ms 11.75% std::set::count (inline) 251ms 0.46% 8.60% 5439ms 9.94% std::_Rb_tree::_M_insert_ (inline) 132ms 0.24% 8.84% 5259ms 9.61% operator new 999ms 1.83% 10.66% 5066ms 9.26% __GI___libc_malloc 5066ms 9.26% 19.92% 5066ms 9.26% std::_Rb_tree_increment 85ms 0.16% 20.08% 4729ms 8.64% std::less::operator() (inline) 4697ms 8.58% 28.66% 4697ms 8.58% std::operator< (inline) 0 0% 28.66% 4514ms 8.25% OffLatticeSimulation::UpdateCellLocationsAndTopology 38ms 0.069% 28.73% 4403ms 8.05% std::__new_allocator::allocate (inline) 1ms 0.0018% 28.73% 4393ms 8.03% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 28.73% 4393ms 8.03% std::allocator_traits::allocate (inline) 2ms 0.0037% 28.74% 4376ms 8.00% AbstractNumericalMethod::ComputeForcesIncludingDamping 5ms 0.0091% 28.75% 4237ms 7.74% std::set_intersection (inline) 236ms 0.43% 29.18% 4232ms 7.73% std::__set_intersection 45ms 0.082% 29.26% 3951ms 7.22% Node::AddElement 5ms 0.0091% 29.27% 3900ms 7.13% std::_Rb_tree::~_Rb_tree (inline) 1466ms 2.68% 31.95% 3893ms 7.11% std::_Rb_tree::_M_erase 0 0% 31.95% 3839ms 7.02% std::set::~set (inline) 2806ms 5.13% 37.08% 3785ms 6.92% _int_malloc 1084ms 1.98% 39.06% 3744ms 6.84% __GI___libc_free 1ms 0.0018% 39.06% 3695ms 6.75% MeshBasedCellPopulation::UpdateNodePairs 1063ms 1.94% 41.00% 3691ms 6.75% std::_Rb_tree::_M_get_insert_unique_pos 6ms 0.011% 41.01% 3640ms 6.65% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 165ms 0.3% 41.31% 3601ms 6.58% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 41.31% 3594ms 6.57% std::_Rb_tree::_M_create_node (inline) 12ms 0.022% 41.34% 3567ms 6.52% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 41.34% 3567ms 6.52% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 41.34% 3556ms 6.50% std::_Rb_tree::_M_get_node (inline) 0 0% 41.34% 3468ms 6.34% VertexMesh::~VertexMesh 4ms 0.0073% 41.34% 3383ms 6.18% TetrahedralMesh::ImportFromMesher 98ms 0.18% 41.52% 3254ms 5.95% std::__new_allocator::deallocate (inline) 0 0% 41.52% 3243ms 5.93% std::allocator_traits::deallocate (inline) 3195ms 5.84% 47.36% 3195ms 5.84% std::_Rb_tree::_S_right (inline) 91ms 0.17% 47.53% 2950ms 5.39% tetgen::tetgenmesh::insphere_sos 57ms 0.1% 47.63% 2917ms 5.33% MutableElement::AddNode 2641ms 4.83% 52.46% 2847ms 5.20% tetgen::insphere 0 0% 52.46% 2827ms 5.17% AbstractCellPopulation::WriteResultsToFiles 104ms 0.19% 52.65% 2702ms 4.94% tetgen::tetgenmesh::flip23 1105ms 2.02% 54.67% 2656ms 4.85% _int_free 187ms 0.34% 55.01% 2461ms 4.50% Node::~Node 168ms 0.31% 55.32% 2215ms 4.05% VertexMesh::Clear 107ms 0.2% 55.51% 2014ms 3.68% tetgen::tetgenmesh::flip32 1ms 0.0018% 55.51% 1875ms 3.43% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 155ms 0.28% 55.80% 1846ms 3.37% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 55.80% 1768ms 3.23% std::_Rb_tree::_M_drop_node (inline) 0 0% 55.80% 1759ms 3.21% std::_Rb_tree::_M_put_node (inline) 4ms 0.0073% 55.80% 1745ms 3.19% Element::Element 0 0% 55.80% 1707ms 3.12% std::_Rb_tree_iterator::operator++ (inline) 1696ms 3.10% 58.90% 1696ms 3.10% Node::GetIndex 1681ms 3.07% 61.98% 1681ms 3.07% std::_Rb_tree_insert_and_rebalance 1075ms 1.96% 63.94% 1544ms 2.82% malloc_consolidate 16ms 0.029% 63.97% 1500ms 2.74% std::_Vector_base::_M_deallocate (inline) 196ms 0.36% 64.33% 1500ms 2.74% tetgen::tetgenmesh::enqueueflipface 3ms 0.0055% 64.33% 1448ms 2.65% Element::RegisterWithNodes (inline) 0 0% 64.33% 1425ms 2.60% std::vector::~vector (inline) 0 0% 64.33% 1367ms 2.50% std::_Vector_base::~_Vector_base (inline) 7ms 0.013% 64.35% 1331ms 2.43% _int_free_maybe_consolidate 1220ms 2.23% 66.58% 1280ms 2.34% tetgen::orient3d 79ms 0.14% 66.72% 1275ms 2.33% TetrahedralMesh::Clear 1172ms 2.14% 68.86% 1172ms 2.14% unlink_chunk 27ms 0.049% 68.91% 1102ms 2.01% tetgen::tetgenmesh::locate 894ms 1.63% 70.55% 1081ms 1.98% AbstractElement::GetNodeGlobalIndex 81ms 0.15% 70.69% 1040ms 1.90% tetgen::tetgenmesh::preciselocate 43ms 0.079% 70.77% 1033ms 1.89% std::vector::_M_realloc_insert 38ms 0.069% 70.84% 956ms 1.75% std::map::operator[] 4ms 0.0073% 70.85% 910ms 1.66% VertexMesh::GenerateVerticesFromElementCircumcentres 120ms 0.22% 71.07% 875ms 1.60% std::vector::push_back (inline) 0 0% 71.07% 849ms 1.55% std::_Rb_tree::lower_bound (inline) 0 0% 71.07% 849ms 1.55% std::map::lower_bound (inline) 7ms 0.013% 71.08% 844ms 1.54% std::_Vector_base::_M_allocate (inline) 832ms 1.52% 72.60% 832ms 1.52% tetgen::tetgenmesh::oppo 0 0% 72.60% 751ms 1.37% VoronoiDataWriter::Visit 745ms 1.36% 73.96% 745ms 1.36% tetgen::tetgenmesh::triface::triface 0 0% 73.96% 739ms 1.35% TetrahedralMesh::RefreshJacobianCachedData 317ms 0.58% 74.54% 681ms 1.24% AbstractElement::GetNodeLocation 631ms 1.15% 75.70% 631ms 1.15% AbstractElement::IsDeleted 7ms 0.013% 75.71% 629ms 1.15% AbstractTetrahedralElement::CalculateInverseJacobian 13ms 0.024% 75.73% 623ms 1.14% AbstractTetrahedralElement::CalculateJacobian 592ms 1.08% 76.81% 592ms 1.08% [libchaste_mesh.so] 1ms 0.0018% 76.82% 591ms 1.08% AbstractTwoBodyInteractionForce::AddForceContribution 590ms 1.08% 77.89% 590ms 1.08% Node::rGetLocation 564ms 1.03% 78.92% 564ms 1.03% std::vector::size (inline) 16ms 0.029% 78.95% 561ms 1.03% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 207ms 0.38% 79.33% 560ms 1.02% tetgen::tetgenmesh::sym 42ms 0.077% 79.41% 520ms 0.95% __atan2 200ms 0.37% 79.77% 518ms 0.95% tetgen::tetgenmesh::bond 499ms 0.91% 80.69% 499ms 0.91% tetgen::tetgenmesh::triface::operator= 37ms 0.068% 80.75% 488ms 0.89% AbstractTetrahedralElement::RefreshJacobian 10ms 0.018% 80.77% 478ms 0.87% boost::numeric::ublas::c_vector::c_vector (inline) 27ms 0.049% 80.82% 476ms 0.87% tetgen::tetgenmesh::queue::push 353ms 0.65% 81.47% 471ms 0.86% __ieee754_atan2_fma 277ms 0.51% 81.97% 471ms 0.86% tetgen::tetgenmesh::fnextself 9ms 0.016% 81.99% 467ms 0.85% boost::numeric::ublas::vector_assign (inline) 61ms 0.11% 82.10% 466ms 0.85% tetgen::tetgenmesh::enext2fnext 276ms 0.5% 82.61% 449ms 0.82% tetgen::tetgenmesh::link::add 20ms 0.037% 82.64% 446ms 0.82% Element::CalculateCircumsphere 0 0% 82.64% 421ms 0.77% boost::numeric::ublas::inner_prod (inline) 33ms 0.06% 82.70% 419ms 0.77% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 82.70% 419ms 0.77% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 82.70% 418ms 0.76% std::set::find (inline) 47ms 0.086% 82.79% 416ms 0.76% tetgen::tetgenmesh::enextfnext 376ms 0.69% 83.48% 376ms 0.69% tetgen::tetgenmesh::decode 0 0% 83.48% 371ms 0.68% std::insert_iterator::operator= (inline) 13ms 0.024% 83.50% 363ms 0.66% VertexMesh::CalculateUnitNormalToFaceWithArea 351ms 0.64% 84.14% 351ms 0.64% tetgen::tetgenmesh::org 138ms 0.25% 84.39% 342ms 0.63% boost::numeric::ublas::vector_inner_prod::apply (inline) 147ms 0.27% 84.66% 338ms 0.62% AbstractTetrahedralMesh::GetElement 3ms 0.0055% 84.67% 327ms 0.6% VertexElement::~VertexElement 0 0% 84.67% 323ms 0.59% std::_Rb_tree::_M_insert_unique_ (inline) 322ms 0.59% 85.26% 322ms 0.59% boost::numeric::ublas::c_vector::operator() 0 0% 85.26% 321ms 0.59% VertexMeshWriter::WriteVtkUsingMesh 16ms 0.029% 85.28% 320ms 0.58% std::_Rb_tree_iterator::operator-- (inline) 6ms 0.011% 85.30% 311ms 0.57% CellPropertyCollection::GetPropertiesType (inline) 306ms 0.56% 85.85% 306ms 0.56% tetgen::tetgenmesh::encode 0 0% 85.85% 305ms 0.56% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 85.85% 305ms 0.56% boost::numeric::ublas::c_vector::operator= (inline) 4ms 0.0073% 85.86% 301ms 0.55% Cell::GetCellId 77ms 0.14% 86.00% 300ms 0.55% __dynamic_cast 18ms 0.033% 86.04% 300ms 0.55% std::vector::insert (inline) 4ms 0.0073% 86.04% 294ms 0.54% AbstractTetrahedralElement::AbstractTetrahedralElement 291ms 0.53% 86.57% 291ms 0.53% std::_Rb_tree_decrement 79ms 0.14% 86.72% 290ms 0.53% boost::numeric::ublas::indexing_vector_assign 6ms 0.011% 86.73% 276ms 0.5% VertexMesh::GetVolumeOfElement