File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 59087ms, 87.05% of 67878ms total Dropped 870 nodes (cum <= 339.39ms) flat flat% sum% cum cum% 0 0% 0% 67823ms 99.92% __libc_start_call_main 0 0% 0% 67823ms 99.92% __libc_start_main_impl 0 0% 0% 67823ms 99.92% _start 0 0% 0% 67805ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 67805ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 67805ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 67805ms 99.89% main 0 0% 0% 67763ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 67763ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 67763ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 67475ms 99.41% AbstractCellBasedSimulation::Solve 0 0% 0% 56890ms 83.81% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 56838ms 83.74% MeshBasedCellPopulation::Update 0 0% 0% 31678ms 46.67% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 31678ms 46.67% MeshBasedCellPopulation::TessellateIfNeeded 232ms 0.34% 0.34% 28081ms 41.37% VertexMesh::VertexMesh 0 0% 0.34% 20612ms 30.37% MutableMesh::ReMesh 1ms 0.0015% 0.34% 16263ms 23.96% tetgen::tetrahedralize 0 0% 0.34% 16106ms 23.73% tetgen::tetgenmesh::delaunizevertices 15ms 0.022% 0.37% 16097ms 23.71% tetgen::tetgenmesh::incrflipdelaunay 534ms 0.79% 1.15% 14412ms 21.23% tetgen::tetgenmesh::lawson 624ms 0.92% 2.07% 13963ms 20.57% TetrahedralMesh::EdgeIterator::operator++ 24ms 0.035% 2.11% 10704ms 15.77% std::set::insert (inline) 3214ms 4.73% 6.84% 10539ms 15.53% std::_Rb_tree::_M_lower_bound (inline) 388ms 0.57% 7.41% 10359ms 15.26% VertexElement::AddFace 239ms 0.35% 7.77% 10252ms 15.10% std::_Rb_tree::_M_insert_unique 283ms 0.42% 8.18% 9810ms 14.45% std::_Rb_tree::find (inline) 0 0% 8.18% 9203ms 13.56% std::set::count (inline) 114ms 0.17% 8.35% 6933ms 10.21% std::less::operator() (inline) 6881ms 10.14% 18.49% 6881ms 10.14% std::operator< (inline) 6276ms 9.25% 27.73% 6276ms 9.25% std::_Rb_tree_increment 0 0% 27.73% 6081ms 8.96% OffLatticeSimulation::UpdateCellLocationsAndTopology 345ms 0.51% 28.24% 6063ms 8.93% std::_Rb_tree::_M_insert_ (inline) 1ms 0.0015% 28.24% 5917ms 8.72% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.0059% 28.25% 5890ms 8.68% AbstractNumericalMethod::ComputeForcesIncludingDamping 211ms 0.31% 28.56% 5589ms 8.23% operator new 1182ms 1.74% 30.30% 5279ms 7.78% __GI___libc_malloc 4ms 0.0059% 30.31% 4923ms 7.25% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 3ms 0.0044% 30.31% 4921ms 7.25% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.01% 30.32% 4754ms 7.00% MeshBasedCellPopulation::SpringIterator::operator++ 36ms 0.053% 30.38% 4751ms 7.00% std::__new_allocator::allocate (inline) 0 0% 30.38% 4734ms 6.97% std::allocator_traits::allocate (inline) 5ms 0.0074% 30.38% 4462ms 6.57% std::_Rb_tree::~_Rb_tree (inline) 1645ms 2.42% 32.81% 4451ms 6.56% std::_Rb_tree::_M_erase 5ms 0.0074% 32.81% 4422ms 6.51% std::set_intersection (inline) 275ms 0.41% 33.22% 4417ms 6.51% std::__set_intersection 0 0% 33.22% 4405ms 6.49% std::set::~set (inline) 0 0% 33.22% 4349ms 6.41% AbstractCellPopulation::WriteResultsToFiles 1227ms 1.81% 35.03% 4319ms 6.36% __GI___libc_free 1359ms 2.00% 37.03% 4218ms 6.21% std::_Rb_tree::_M_get_insert_unique_pos 103ms 0.15% 37.18% 3885ms 5.72% tetgen::tetgenmesh::insphere_sos 49ms 0.072% 37.25% 3868ms 5.70% Node::AddElement 0 0% 37.25% 3841ms 5.66% std::_Rb_tree::_M_create_node (inline) 0 0% 37.25% 3812ms 5.62% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 37.25% 3796ms 5.59% std::_Rb_tree::_M_get_node (inline) 3462ms 5.10% 42.35% 3763ms 5.54% tetgen::insphere 134ms 0.2% 42.55% 3762ms 5.54% std::__new_allocator::deallocate (inline) 0 0% 42.55% 3745ms 5.52% std::allocator_traits::deallocate (inline) 2669ms 3.93% 46.48% 3697ms 5.45% _int_malloc 192ms 0.28% 46.76% 3670ms 5.41% std::_Rb_tree_const_iterator::operator++ (inline) 3648ms 5.37% 52.14% 3648ms 5.37% std::_Rb_tree::_S_right (inline) 1ms 0.0015% 52.14% 3624ms 5.34% VertexMesh::~VertexMesh 7ms 0.01% 52.15% 3504ms 5.16% TetrahedralMesh::ImportFromMesher 132ms 0.19% 52.35% 3422ms 5.04% tetgen::tetgenmesh::flip23 193ms 0.28% 52.63% 3114ms 4.59% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1374ms 2.02% 54.65% 3088ms 4.55% _int_free 1ms 0.0015% 54.66% 3029ms 4.46% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 74ms 0.11% 54.76% 2999ms 4.42% MutableElement::AddNode 1ms 0.0015% 54.77% 2937ms 4.33% std::_Rb_tree_iterator::operator++ (inline) 126ms 0.19% 54.95% 2638ms 3.89% tetgen::tetgenmesh::flip32 168ms 0.25% 55.20% 2479ms 3.65% Node::~Node 178ms 0.26% 55.46% 2292ms 3.38% VertexMesh::Clear 0 0% 55.46% 2143ms 3.16% std::_Rb_tree::_M_drop_node (inline) 0 0% 55.46% 2130ms 3.14% std::_Rb_tree::_M_put_node (inline) 2116ms 3.12% 58.58% 2116ms 3.12% Node::GetIndex 1996ms 2.94% 61.52% 1996ms 2.94% std::_Rb_tree_insert_and_rebalance 236ms 0.35% 61.87% 1897ms 2.79% tetgen::tetgenmesh::enqueueflipface 10ms 0.015% 61.88% 1759ms 2.59% Element::Element 1078ms 1.59% 63.47% 1669ms 2.46% malloc_consolidate 26ms 0.038% 63.51% 1641ms 2.42% std::_Vector_base::_M_deallocate (inline) 0 0% 63.51% 1564ms 2.30% std::vector::~vector (inline) 1442ms 2.12% 65.63% 1533ms 2.26% tetgen::orient3d 3ms 0.0044% 65.64% 1485ms 2.19% std::_Vector_base::~_Vector_base (inline) 9ms 0.013% 65.65% 1437ms 2.12% _int_free_maybe_consolidate 99ms 0.15% 65.80% 1421ms 2.09% TetrahedralMesh::Clear 9ms 0.013% 65.81% 1380ms 2.03% Element::RegisterWithNodes (inline) 77ms 0.11% 65.92% 1378ms 2.03% std::map::operator[] 36ms 0.053% 65.98% 1358ms 2.00% tetgen::tetgenmesh::locate 74ms 0.11% 66.08% 1273ms 1.88% tetgen::tetgenmesh::preciselocate 1241ms 1.83% 67.91% 1241ms 1.83% unlink_chunk 0 0% 67.91% 1221ms 1.80% std::_Rb_tree::lower_bound (inline) 0 0% 67.91% 1221ms 1.80% std::map::lower_bound (inline) 64ms 0.094% 68.01% 1172ms 1.73% std::vector::_M_realloc_insert 887ms 1.31% 69.31% 1098ms 1.62% AbstractElement::GetNodeGlobalIndex 1082ms 1.59% 70.91% 1082ms 1.59% tetgen::tetgenmesh::oppo 5ms 0.0074% 70.92% 1056ms 1.56% VertexMesh::GenerateVerticesFromElementCircumcentres 1ms 0.0015% 70.92% 1056ms 1.56% VoronoiDataWriter::Visit 162ms 0.24% 71.16% 996ms 1.47% std::vector::push_back (inline) 955ms 1.41% 72.56% 955ms 1.41% tetgen::tetgenmesh::triface::triface 1ms 0.0015% 72.56% 939ms 1.38% std::_Vector_base::_M_allocate (inline) 0 0% 72.56% 825ms 1.22% TetrahedralMesh::RefreshJacobianCachedData 811ms 1.19% 73.76% 811ms 1.19% [libchaste_mesh.so] 319ms 0.47% 74.23% 800ms 1.18% tetgen::tetgenmesh::sym 779ms 1.15% 75.38% 779ms 1.15% tetgen::tetgenmesh::triface::operator= 1ms 0.0015% 75.38% 752ms 1.11% AbstractTwoBodyInteractionForce::AddForceContribution 7ms 0.01% 75.39% 747ms 1.10% AbstractTetrahedralElement::CalculateInverseJacobian 14ms 0.021% 75.41% 709ms 1.04% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 708ms 1.04% 76.45% 708ms 1.04% Node::rGetLocation 307ms 0.45% 76.90% 697ms 1.03% AbstractElement::GetNodeLocation 15ms 0.022% 76.93% 673ms 0.99% AbstractTetrahedralElement::CalculateJacobian 63ms 0.093% 77.02% 658ms 0.97% __atan2 34ms 0.05% 77.07% 644ms 0.95% tetgen::tetgenmesh::queue::push 394ms 0.58% 77.65% 637ms 0.94% tetgen::tetgenmesh::fnextself 635ms 0.94% 78.59% 635ms 0.94% AbstractElement::IsDeleted 247ms 0.36% 78.95% 631ms 0.93% tetgen::tetgenmesh::bond 15ms 0.022% 78.97% 624ms 0.92% boost::numeric::ublas::vector_assign (inline) 617ms 0.91% 79.88% 617ms 0.91% std::vector::size (inline) 380ms 0.56% 80.44% 610ms 0.9% tetgen::tetgenmesh::link::add 0 0% 80.44% 601ms 0.89% std::set::find (inline) 59ms 0.087% 80.53% 596ms 0.88% tetgen::tetgenmesh::enext2fnext 461ms 0.68% 81.21% 589ms 0.87% __ieee754_atan2_fma 8ms 0.012% 81.22% 584ms 0.86% boost::numeric::ublas::c_vector::c_vector (inline) 70ms 0.1% 81.32% 578ms 0.85% tetgen::tetgenmesh::enextfnext 545ms 0.8% 82.12% 545ms 0.8% tetgen::tetgenmesh::org 26ms 0.038% 82.16% 532ms 0.78% Element::CalculateCircumsphere 504ms 0.74% 82.90% 504ms 0.74% tetgen::tetgenmesh::decode 0 0% 82.90% 500ms 0.74% boost::numeric::ublas::inner_prod (inline) 46ms 0.068% 82.97% 498ms 0.73% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 82.97% 498ms 0.73% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 82.97% 497ms 0.73% std::insert_iterator::operator= (inline) 481ms 0.71% 83.68% 481ms 0.71% tetgen::tetgenmesh::pointmark 40ms 0.059% 83.74% 479ms 0.71% AbstractTetrahedralElement::RefreshJacobian 21ms 0.031% 83.77% 444ms 0.65% VertexMesh::CalculateUnitNormalToFaceWithArea 191ms 0.28% 84.05% 436ms 0.64% AbstractTetrahedralMesh::GetElement 6ms 0.0088% 84.06% 427ms 0.63% CellPropertyCollection::GetPropertiesType (inline) 0 0% 84.06% 425ms 0.63% std::_Rb_tree::_M_insert_unique_ (inline) 111ms 0.16% 84.22% 415ms 0.61% __dynamic_cast 2ms 0.0029% 84.23% 403ms 0.59% Cell::GetCellId 28ms 0.041% 84.27% 403ms 0.59% std::_Rb_tree_iterator::operator-- (inline) 0 0% 84.27% 396ms 0.58% VertexMeshWriter::WriteVtkUsingMesh 119ms 0.18% 84.44% 396ms 0.58% boost::numeric::ublas::indexing_vector_assign 0 0% 84.44% 390ms 0.57% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 166ms 0.24% 84.69% 387ms 0.57% boost::numeric::ublas::vector_inner_prod::apply (inline) 131ms 0.19% 84.88% 376ms 0.55% Inverse 5ms 0.0074% 84.89% 376ms 0.55% boost::numeric::ublas::c_vector::operator= (inline) 375ms 0.55% 85.44% 375ms 0.55% boost::numeric::ublas::c_vector::operator() 4ms 0.0059% 85.45% 368ms 0.54% AbstractTetrahedralElement::AbstractTetrahedralElement 18ms 0.027% 85.47% 363ms 0.53% std::vector::insert (inline) 9ms 0.013% 85.49% 362ms 0.53% VertexElement::~VertexElement 361ms 0.53% 86.02% 361ms 0.53% tetgen::tetgenmesh::encode 351ms 0.52% 86.54% 351ms 0.52% std::_Rb_tree_decrement 1ms 0.0015% 86.54% 347ms 0.51% tcache_get (inline) 346ms 0.51% 87.05% 346ms 0.51% tcache_get_n (inline) 1ms 0.0015% 87.05% 341ms 0.5% AbstractCellProperty::IsSubType (inline)