File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 47218ms, 86.52% of 54574ms total Dropped 869 nodes (cum <= 272.87ms) flat flat% sum% cum cum% 0 0% 0% 54499ms 99.86% __libc_start_call_main 0 0% 0% 54499ms 99.86% __libc_start_main_impl 0 0% 0% 54499ms 99.86% _start 0 0% 0% 54486ms 99.84% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 54486ms 99.84% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 54486ms 99.84% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 54486ms 99.84% main 0 0% 0% 54447ms 99.77% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 54447ms 99.77% CxxTest::TestRunner::runTest (inline) 0 0% 0% 54447ms 99.77% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 54214ms 99.34% AbstractCellBasedSimulation::Solve 0 0% 0% 46716ms 85.60% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 46687ms 85.55% MeshBasedCellPopulation::Update 0 0% 0% 27220ms 49.88% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 27219ms 49.88% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 170ms 0.31% 0.31% 23661ms 43.36% VertexMesh::VertexMesh 0 0% 0.31% 16123ms 29.54% MutableMesh::ReMesh 0 0% 0.31% 12300ms 22.54% tetgen::tetrahedralize 2ms 0.0037% 0.32% 12180ms 22.32% tetgen::tetgenmesh::delaunizevertices 3ms 0.0055% 0.32% 12178ms 22.31% tetgen::tetgenmesh::incrflipdelaunay 426ms 0.78% 1.10% 10926ms 20.02% tetgen::tetgenmesh::lawson 460ms 0.84% 1.94% 10557ms 19.34% TetrahedralMesh::EdgeIterator::operator++ 20ms 0.037% 1.98% 9248ms 16.95% std::set::insert (inline) 195ms 0.36% 2.34% 8885ms 16.28% std::_Rb_tree::_M_insert_unique 343ms 0.63% 2.97% 8313ms 15.23% VertexElement::AddFace 2451ms 4.49% 7.46% 7256ms 13.30% std::_Rb_tree::_M_lower_bound (inline) 241ms 0.44% 7.90% 6922ms 12.68% std::_Rb_tree::find (inline) 0 0% 7.90% 6471ms 11.86% std::set::count (inline) 251ms 0.46% 8.36% 5229ms 9.58% std::_Rb_tree::_M_insert_ (inline) 5159ms 9.45% 17.81% 5159ms 9.45% std::_Rb_tree_increment 133ms 0.24% 18.06% 4965ms 9.10% operator new 1001ms 1.83% 19.89% 4777ms 8.75% __GI___libc_malloc 106ms 0.19% 20.08% 4761ms 8.72% std::less::operator() (inline) 4725ms 8.66% 28.74% 4725ms 8.66% std::operator< (inline) 0 0% 28.74% 4522ms 8.29% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 28.74% 4395ms 8.05% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0018% 28.74% 4377ms 8.02% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0018% 28.75% 4336ms 7.95% std::set_intersection (inline) 236ms 0.43% 29.18% 4335ms 7.94% std::__set_intersection 30ms 0.055% 29.23% 4153ms 7.61% std::__new_allocator::allocate (inline) 0 0% 29.23% 4143ms 7.59% std::allocator_traits::allocate (inline) 3ms 0.0055% 29.24% 4015ms 7.36% std::_Rb_tree::~_Rb_tree (inline) 1546ms 2.83% 32.07% 4009ms 7.35% std::_Rb_tree::_M_erase 0 0% 32.07% 3968ms 7.27% std::set::~set (inline) 1133ms 2.08% 34.15% 3810ms 6.98% __GI___libc_free 29ms 0.053% 34.20% 3703ms 6.79% Node::AddElement 165ms 0.3% 34.50% 3694ms 6.77% std::_Rb_tree_const_iterator::operator++ (inline) 1056ms 1.93% 36.44% 3686ms 6.75% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 36.44% 3662ms 6.71% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.0055% 36.44% 3654ms 6.70% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 36.44% 3589ms 6.58% VertexMesh::~VertexMesh 12ms 0.022% 36.47% 3515ms 6.44% MeshBasedCellPopulation::SpringIterator::operator++ 2601ms 4.77% 41.23% 3511ms 6.43% _int_malloc 0 0% 41.23% 3416ms 6.26% std::_Rb_tree::_M_create_node (inline) 0 0% 41.23% 3390ms 6.21% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 41.23% 3372ms 6.18% std::_Rb_tree::_M_get_node (inline) 100ms 0.18% 41.42% 3321ms 6.09% std::__new_allocator::deallocate (inline) 0 0% 41.42% 3306ms 6.06% std::allocator_traits::deallocate (inline) 3143ms 5.76% 47.17% 3143ms 5.76% std::_Rb_tree::_S_right (inline) 7ms 0.013% 47.19% 3091ms 5.66% TetrahedralMesh::ImportFromMesher 95ms 0.17% 47.36% 2998ms 5.49% tetgen::tetgenmesh::insphere_sos 2671ms 4.89% 52.26% 2892ms 5.30% tetgen::insphere 47ms 0.086% 52.34% 2820ms 5.17% MutableElement::AddNode 0 0% 52.34% 2819ms 5.17% AbstractCellPopulation::WriteResultsToFiles 113ms 0.21% 52.55% 2708ms 4.96% tetgen::tetgenmesh::flip23 1080ms 1.98% 54.53% 2674ms 4.90% _int_free 195ms 0.36% 54.89% 2536ms 4.65% Node::~Node 160ms 0.29% 55.18% 2297ms 4.21% VertexMesh::Clear 96ms 0.18% 55.35% 1915ms 3.51% tetgen::tetgenmesh::flip32 5ms 0.0092% 55.36% 1881ms 3.45% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 135ms 0.25% 55.61% 1839ms 3.37% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 55.61% 1793ms 3.29% std::_Rb_tree::_M_drop_node (inline) 0 0% 55.61% 1789ms 3.28% std::_Rb_tree::_M_put_node (inline) 3ms 0.0055% 55.62% 1721ms 3.15% std::_Rb_tree_iterator::operator++ (inline) 1685ms 3.09% 58.70% 1685ms 3.09% Node::GetIndex 1645ms 3.01% 61.72% 1645ms 3.01% std::_Rb_tree_insert_and_rebalance 1124ms 2.06% 63.78% 1587ms 2.91% malloc_consolidate 189ms 0.35% 64.12% 1544ms 2.83% tetgen::tetgenmesh::enqueueflipface 24ms 0.044% 64.17% 1541ms 2.82% std::_Vector_base::_M_deallocate (inline) 4ms 0.0073% 64.18% 1500ms 2.75% Element::Element 0 0% 64.18% 1468ms 2.69% std::vector::~vector (inline) 1ms 0.0018% 64.18% 1406ms 2.58% std::_Vector_base::~_Vector_base (inline) 8ms 0.015% 64.19% 1376ms 2.52% _int_free_maybe_consolidate 62ms 0.11% 64.31% 1274ms 2.33% TetrahedralMesh::Clear 0 0% 64.31% 1250ms 2.29% Element::RegisterWithNodes (inline) 1159ms 2.12% 66.43% 1220ms 2.24% tetgen::orient3d 1139ms 2.09% 68.52% 1139ms 2.09% unlink_chunk 916ms 1.68% 70.19% 1097ms 2.01% AbstractElement::GetNodeGlobalIndex 29ms 0.053% 70.25% 1007ms 1.85% tetgen::tetgenmesh::locate 3ms 0.0055% 70.25% 946ms 1.73% VertexMesh::GenerateVerticesFromElementCircumcentres 35ms 0.064% 70.32% 943ms 1.73% std::vector::_M_realloc_insert 65ms 0.12% 70.44% 943ms 1.73% tetgen::tetgenmesh::preciselocate 871ms 1.60% 72.03% 871ms 1.60% tetgen::tetgenmesh::oppo 52ms 0.095% 72.13% 850ms 1.56% std::map::operator[] 106ms 0.19% 72.32% 786ms 1.44% std::vector::push_back (inline) 7ms 0.013% 72.33% 778ms 1.43% std::_Vector_base::_M_allocate (inline) 767ms 1.41% 73.74% 767ms 1.41% tetgen::tetgenmesh::triface::triface 0 0% 73.74% 741ms 1.36% VoronoiDataWriter::Visit 0 0% 73.74% 730ms 1.34% std::_Rb_tree::lower_bound (inline) 0 0% 73.74% 730ms 1.34% std::map::lower_bound (inline) 0 0% 73.74% 709ms 1.30% TetrahedralMesh::RefreshJacobianCachedData 682ms 1.25% 74.99% 682ms 1.25% AbstractElement::IsDeleted 236ms 0.43% 75.42% 629ms 1.15% tetgen::tetgenmesh::sym 300ms 0.55% 75.97% 623ms 1.14% AbstractElement::GetNodeLocation 8ms 0.015% 75.99% 617ms 1.13% AbstractTetrahedralElement::CalculateInverseJacobian 587ms 1.08% 77.06% 587ms 1.08% Node::rGetLocation 0 0% 77.06% 582ms 1.07% AbstractTwoBodyInteractionForce::AddForceContribution 579ms 1.06% 78.12% 579ms 1.06% [libchaste_mesh.so] 565ms 1.04% 79.16% 565ms 1.04% std::vector::size (inline) 9ms 0.016% 79.18% 561ms 1.03% AbstractTetrahedralElement::CalculateJacobian 11ms 0.02% 79.20% 548ms 1.00% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 547ms 1.00% 80.20% 547ms 1.00% tetgen::tetgenmesh::triface::operator= 28ms 0.051% 80.25% 490ms 0.9% tetgen::tetgenmesh::queue::push 52ms 0.095% 80.34% 470ms 0.86% __atan2 13ms 0.024% 80.37% 469ms 0.86% boost::numeric::ublas::vector_assign (inline) 16ms 0.029% 80.40% 467ms 0.86% boost::numeric::ublas::c_vector::c_vector (inline) 293ms 0.54% 80.93% 462ms 0.85% tetgen::tetgenmesh::link::add 11ms 0.02% 80.95% 461ms 0.84% Element::CalculateCircumsphere 38ms 0.07% 81.02% 459ms 0.84% tetgen::tetgenmesh::enext2fnext 274ms 0.5% 81.53% 457ms 0.84% tetgen::tetgenmesh::fnextself 0 0% 81.53% 448ms 0.82% std::set::find (inline) 46ms 0.084% 81.61% 432ms 0.79% AbstractTetrahedralElement::RefreshJacobian 176ms 0.32% 81.93% 432ms 0.79% tetgen::tetgenmesh::bond 45ms 0.082% 82.02% 423ms 0.78% tetgen::tetgenmesh::enextfnext 422ms 0.77% 82.79% 422ms 0.77% tetgen::tetgenmesh::decode 335ms 0.61% 83.40% 415ms 0.76% __ieee754_atan2_fma 0 0% 83.40% 397ms 0.73% boost::numeric::ublas::inner_prod (inline) 37ms 0.068% 83.47% 392ms 0.72% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 83.47% 392ms 0.72% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 83.47% 391ms 0.72% std::insert_iterator::operator= (inline) 15ms 0.027% 83.50% 357ms 0.65% VertexMesh::CalculateUnitNormalToFaceWithArea 166ms 0.3% 83.80% 349ms 0.64% AbstractTetrahedralMesh::GetElement 0 0% 83.80% 337ms 0.62% std::_Rb_tree::_M_insert_unique_ (inline) 9ms 0.016% 83.82% 329ms 0.6% VertexElement::~VertexElement 13ms 0.024% 83.84% 324ms 0.59% std::_Rb_tree_iterator::operator-- (inline) 0 0% 83.84% 319ms 0.58% VertexMeshWriter::WriteVtkUsingMesh 0 0% 83.84% 316ms 0.58% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 4ms 0.0073% 83.85% 314ms 0.58% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.0018% 83.85% 314ms 0.58% boost::numeric::ublas::c_vector::operator= (inline) 313ms 0.57% 84.42% 313ms 0.57% tetgen::tetgenmesh::org 2ms 0.0037% 84.43% 309ms 0.57% Cell::GetCellId 122ms 0.22% 84.65% 309ms 0.57% boost::numeric::ublas::vector_inner_prod::apply (inline) 79ms 0.14% 84.80% 308ms 0.56% __dynamic_cast 3ms 0.0055% 84.80% 290ms 0.53% Element::~Element 289ms 0.53% 85.33% 289ms 0.53% std::_Rb_tree_decrement 2ms 0.0037% 85.34% 288ms 0.53% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 288ms 0.53% 85.86% 288ms 0.53% boost::numeric::ublas::c_vector::operator() 10ms 0.018% 85.88% 284ms 0.52% std::vector::insert (inline) 67ms 0.12% 86.00% 282ms 0.52% boost::numeric::ublas::indexing_vector_assign 282ms 0.52% 86.52% 282ms 0.52% tetgen::tetgenmesh::pointmark