File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 45153ms, 85.81% of 52617ms total Dropped 850 nodes (cum <= 263.08ms) flat flat% sum% cum cum% 0 0% 0% 52550ms 99.87% __libc_start_call_main 0 0% 0% 52550ms 99.87% __libc_start_main_impl 0 0% 0% 52550ms 99.87% _start 0 0% 0% 52535ms 99.84% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 52535ms 99.84% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 52535ms 99.84% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 52535ms 99.84% main 0 0% 0% 52499ms 99.78% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 52499ms 99.78% CxxTest::TestRunner::runTest (inline) 0 0% 0% 52499ms 99.78% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 52252ms 99.31% AbstractCellBasedSimulation::Solve 0 0% 0% 43831ms 83.30% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 43780ms 83.21% MeshBasedCellPopulation::Update 0 0% 0% 24159ms 45.91% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 24159ms 45.91% MeshBasedCellPopulation::TessellateIfNeeded 180ms 0.34% 0.34% 21728ms 41.29% VertexMesh::VertexMesh 0 0% 0.34% 16022ms 30.45% MutableMesh::ReMesh 0 0% 0.34% 12620ms 23.98% tetgen::tetrahedralize 3ms 0.0057% 0.35% 12479ms 23.72% tetgen::tetgenmesh::delaunizevertices 1ms 0.0019% 0.35% 12474ms 23.71% tetgen::tetgenmesh::incrflipdelaunay 527ms 1.00% 1.35% 11048ms 21.00% tetgen::tetgenmesh::lawson 583ms 1.11% 2.46% 10925ms 20.76% TetrahedralMesh::EdgeIterator::operator++ 35ms 0.067% 2.53% 8666ms 16.47% std::set::insert (inline) 3143ms 5.97% 8.50% 8626ms 16.39% std::_Rb_tree::_M_lower_bound (inline) 332ms 0.63% 9.13% 8577ms 16.30% VertexElement::AddFace 176ms 0.33% 9.46% 8218ms 15.62% std::_Rb_tree::_M_insert_unique 257ms 0.49% 9.95% 8081ms 15.36% std::_Rb_tree::find (partial-inline) 0 0% 9.95% 7513ms 14.28% std::set::count (inline) 109ms 0.21% 10.16% 5320ms 10.11% std::less::operator() (inline) 5270ms 10.02% 20.18% 5271ms 10.02% std::operator< (inline) 289ms 0.55% 20.73% 5041ms 9.58% std::_Rb_tree::_M_insert_ (inline) 0 0% 20.73% 4896ms 9.30% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 20.73% 4787ms 9.10% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0019% 20.73% 4765ms 9.06% AbstractNumericalMethod::ComputeForcesIncludingDamping 200ms 0.38% 21.11% 4252ms 8.08% operator new 4147ms 7.88% 28.99% 4147ms 7.88% std::_Rb_tree_increment 1066ms 2.03% 31.01% 3978ms 7.56% __GI___libc_malloc 2ms 0.0038% 31.02% 3940ms 7.49% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.0057% 31.02% 3913ms 7.44% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 13ms 0.025% 31.05% 3823ms 7.27% MeshBasedCellPopulation::SpringIterator::operator++ 48ms 0.091% 31.14% 3736ms 7.10% std::__new_allocator::allocate (inline) 0 0% 31.14% 3717ms 7.06% std::allocator_traits::allocate (inline) 7ms 0.013% 31.15% 3519ms 6.69% std::_Rb_tree::~_Rb_tree (inline) 109ms 0.21% 31.36% 3513ms 6.68% tetgen::tetgenmesh::insphere_sos 1240ms 2.36% 33.72% 3510ms 6.67% std::_Rb_tree::_M_erase 0 0% 33.72% 3472ms 6.60% std::set::~set (inline) 3098ms 5.89% 39.61% 3386ms 6.44% tetgen::insphere 0 0% 39.61% 3383ms 6.43% AbstractCellPopulation::WriteResultsToFiles 1220ms 2.32% 41.92% 3279ms 6.23% std::_Rb_tree::_M_get_insert_unique_pos 908ms 1.73% 43.65% 3092ms 5.88% __GI___libc_free 0 0% 43.65% 3031ms 5.76% std::_Rb_tree::_M_create_node (inline) 0 0% 43.65% 3004ms 5.71% std::_Rb_tree::_M_get_node (inline) 0 0% 43.65% 2999ms 5.70% std::_Rb_tree::_Alloc_node::operator() (inline) 5ms 0.0095% 43.66% 2873ms 5.46% std::set_intersection (inline) 212ms 0.4% 44.06% 2868ms 5.45% std::__set_intersection 141ms 0.27% 44.33% 2832ms 5.38% std::__new_allocator::deallocate (inline) 0 0% 44.33% 2813ms 5.35% std::allocator_traits::deallocate (inline) 23ms 0.044% 44.37% 2773ms 5.27% Node::AddElement 9ms 0.017% 44.39% 2677ms 5.09% TetrahedralMesh::ImportFromMesher 191ms 0.36% 44.75% 2585ms 4.91% tetgen::tetgenmesh::flip23 1987ms 3.78% 48.53% 2574ms 4.89% _int_malloc 2513ms 4.78% 53.31% 2513ms 4.78% std::_Rb_tree::_S_right (inline) 0 0% 53.31% 2447ms 4.65% VertexMesh::~VertexMesh 219ms 0.42% 53.72% 2341ms 4.45% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 3ms 0.0057% 53.73% 2326ms 4.42% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 175ms 0.33% 54.06% 2289ms 4.35% std::_Rb_tree_const_iterator::operator++ (inline) 1127ms 2.14% 56.20% 2182ms 4.15% _int_free 2ms 0.0038% 56.21% 2134ms 4.06% std::_Rb_tree_iterator::operator++ (inline) 79ms 0.15% 56.36% 2122ms 4.03% MutableElement::AddNode 142ms 0.27% 56.63% 1817ms 3.45% tetgen::tetgenmesh::flip32 1802ms 3.42% 60.05% 1802ms 3.42% std::_Rb_tree_insert_and_rebalance 0 0% 60.05% 1756ms 3.34% std::_Rb_tree::_M_drop_node (inline) 0 0% 60.05% 1743ms 3.31% std::_Rb_tree::_M_put_node (inline) 91ms 0.17% 60.22% 1706ms 3.24% Node::~Node 129ms 0.25% 60.47% 1641ms 3.12% VertexMesh::Clear 5ms 0.0095% 60.48% 1466ms 2.79% Element::Element 1348ms 2.56% 63.04% 1425ms 2.71% tetgen::orient3d 160ms 0.3% 63.34% 1287ms 2.45% tetgen::tetgenmesh::enqueueflipface 1240ms 2.36% 65.70% 1240ms 2.36% Node::GetIndex 26ms 0.049% 65.75% 1211ms 2.30% tetgen::tetgenmesh::locate 101ms 0.19% 65.94% 1134ms 2.16% tetgen::tetgenmesh::preciselocate 4ms 0.0076% 65.95% 1128ms 2.14% Element::RegisterWithNodes (inline) 76ms 0.14% 66.09% 1114ms 2.12% std::map::operator[] 8ms 0.015% 66.11% 1078ms 2.05% std::_Vector_base::_M_deallocate (inline) 642ms 1.22% 67.33% 1056ms 2.01% malloc_consolidate 0 0% 67.33% 1002ms 1.90% std::vector::~vector (inline) 57ms 0.11% 67.44% 987ms 1.88% std::vector::_M_realloc_insert 0 0% 67.44% 975ms 1.85% std::_Rb_tree::lower_bound (inline) 0 0% 67.44% 975ms 1.85% std::map::lower_bound (inline) 93ms 0.18% 67.62% 909ms 1.73% TetrahedralMesh::Clear 7ms 0.013% 67.63% 905ms 1.72% _int_free_maybe_consolidate 1ms 0.0019% 67.63% 891ms 1.69% std::_Vector_base::~_Vector_base (inline) 858ms 1.63% 69.26% 858ms 1.63% tetgen::tetgenmesh::triface::triface 1ms 0.0019% 69.26% 844ms 1.60% VoronoiDataWriter::Visit 8ms 0.015% 69.28% 791ms 1.50% VertexMesh::GenerateVerticesFromElementCircumcentres 101ms 0.19% 69.47% 787ms 1.50% std::vector::push_back (inline) 751ms 1.43% 70.90% 751ms 1.43% unlink_chunk 5ms 0.0095% 70.91% 718ms 1.36% std::_Vector_base::_M_allocate (inline) 3ms 0.0057% 70.91% 705ms 1.34% TetrahedralMesh::RefreshJacobianCachedData 0 0% 70.91% 698ms 1.33% AbstractTwoBodyInteractionForce::AddForceContribution 20ms 0.038% 70.95% 693ms 1.32% boost::numeric::ublas::vector_assign (inline) 692ms 1.32% 72.27% 692ms 1.32% tetgen::tetgenmesh::oppo 366ms 0.7% 72.96% 673ms 1.28% tetgen::tetgenmesh::fnextself 14ms 0.027% 72.99% 665ms 1.26% boost::numeric::ublas::c_vector::c_vector (inline) 18ms 0.034% 73.02% 658ms 1.25% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 5ms 0.0095% 73.03% 657ms 1.25% AbstractTetrahedralElement::CalculateInverseJacobian 9ms 0.017% 73.05% 632ms 1.20% AbstractTetrahedralElement::CalculateJacobian 632ms 1.20% 74.25% 632ms 1.20% tetgen::tetgenmesh::triface::operator= 510ms 0.97% 75.22% 627ms 1.19% AbstractElement::GetNodeGlobalIndex 620ms 1.18% 76.40% 620ms 1.18% [libchaste_mesh.so] 63ms 0.12% 76.52% 610ms 1.16% __atan2 0 0% 76.52% 564ms 1.07% std::set::find (inline) 444ms 0.84% 77.36% 547ms 1.04% __ieee754_atan2_fma 220ms 0.42% 77.78% 530ms 1.01% AbstractElement::GetNodeLocation 335ms 0.64% 78.42% 489ms 0.93% tetgen::tetgenmesh::sym 51ms 0.097% 78.51% 470ms 0.89% AbstractTetrahedralElement::RefreshJacobian 0 0% 78.51% 468ms 0.89% boost::numeric::ublas::inner_prod (inline) 1ms 0.0019% 78.51% 463ms 0.88% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 31ms 0.059% 78.57% 462ms 0.88% boost::numeric::ublas::vector_scalar_binary::evaluate 49ms 0.093% 78.67% 462ms 0.88% tetgen::tetgenmesh::enext2fnext 25ms 0.048% 78.71% 454ms 0.86% Element::CalculateCircumsphere 0 0% 78.71% 443ms 0.84% std::insert_iterator::operator= (inline) 441ms 0.84% 79.55% 441ms 0.84% Node::rGetLocation 117ms 0.22% 79.77% 441ms 0.84% boost::numeric::ublas::indexing_vector_assign 38ms 0.072% 79.85% 440ms 0.84% tetgen::tetgenmesh::enextfnext 7ms 0.013% 79.86% 414ms 0.79% boost::numeric::ublas::c_vector::operator= (inline) 409ms 0.78% 80.64% 409ms 0.78% boost::numeric::ublas::c_vector::operator() 404ms 0.77% 81.41% 404ms 0.77% tetgen::tetgenmesh::org 0 0% 81.41% 379ms 0.72% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 81.41% 378ms 0.72% VertexMeshWriter::WriteVtkUsingMesh 7ms 0.013% 81.42% 376ms 0.71% CellPropertyCollection::GetPropertiesType (inline) 374ms 0.71% 82.13% 374ms 0.71% std::vector::size (inline) 211ms 0.4% 82.53% 370ms 0.7% AbstractTetrahedralMesh::GetElement 20ms 0.038% 82.57% 370ms 0.7% tetgen::tetgenmesh::queue::push 78ms 0.15% 82.72% 367ms 0.7% __dynamic_cast 4ms 0.0076% 82.72% 365ms 0.69% Cell::GetCellId 18ms 0.034% 82.76% 357ms 0.68% std::_Rb_tree_iterator::operator-- (inline) 173ms 0.33% 83.09% 351ms 0.67% boost::numeric::ublas::vector_inner_prod::apply (inline) 257ms 0.49% 83.58% 350ms 0.67% tetgen::tetgenmesh::link::add 232ms 0.44% 84.02% 339ms 0.64% tetgen::tetgenmesh::bond 3ms 0.0057% 84.02% 335ms 0.64% AbstractTetrahedralElement::AbstractTetrahedralElement 17ms 0.032% 84.05% 331ms 0.63% std::vector::insert (inline) 15ms 0.029% 84.08% 323ms 0.61% VertexMesh::CalculateUnitNormalToFaceWithArea 320ms 0.61% 84.69% 320ms 0.61% std::_Rb_tree_decrement 1ms 0.0019% 84.69% 306ms 0.58% AbstractCellProperty::IsSubType (inline) 129ms 0.25% 84.94% 304ms 0.58% Inverse 0 0% 84.94% 303ms 0.58% tcache_get (inline) 303ms 0.58% 85.51% 303ms 0.58% tcache_get_n (inline) 62ms 0.12% 85.63% 295ms 0.56% tetgen::tetgenmesh::queue::pop 36ms 0.068% 85.70% 288ms 0.55% tetgen::insphereadapt 49ms 0.093% 85.79% 278ms 0.53% boost::numeric::ublas::vector_reference::operator() (inline) 11ms 0.021% 85.81% 277ms 0.53% VertexElement::~VertexElement