File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 45488ms, 86.02% of 52880ms total Dropped 850 nodes (cum <= 264.40ms) flat flat% sum% cum cum% 0 0% 0% 52817ms 99.88% __libc_start_call_main 0 0% 0% 52817ms 99.88% __libc_start_main_impl 0 0% 0% 52817ms 99.88% _start 0 0% 0% 52803ms 99.85% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 52803ms 99.85% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 52803ms 99.85% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 52803ms 99.85% main 0 0% 0% 52767ms 99.79% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 52766ms 99.78% CxxTest::TestRunner::runTest (inline) 0 0% 0% 52766ms 99.78% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 52523ms 99.32% AbstractCellBasedSimulation::Solve 0 0% 0% 44174ms 83.54% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 44130ms 83.45% MeshBasedCellPopulation::Update 0 0% 0% 24328ms 46.01% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 24328ms 46.01% MeshBasedCellPopulation::TessellateIfNeeded 227ms 0.43% 0.43% 21713ms 41.06% VertexMesh::VertexMesh 0 0% 0.43% 16190ms 30.62% MutableMesh::ReMesh 0 0% 0.43% 12633ms 23.89% tetgen::tetrahedralize 2ms 0.0038% 0.43% 12498ms 23.63% tetgen::tetgenmesh::delaunizevertices 8ms 0.015% 0.45% 12492ms 23.62% tetgen::tetgenmesh::incrflipdelaunay 519ms 0.98% 1.43% 11108ms 21.01% tetgen::tetgenmesh::lawson 550ms 1.04% 2.47% 10887ms 20.59% TetrahedralMesh::EdgeIterator::operator++ 30ms 0.057% 2.53% 8780ms 16.60% std::set::insert (inline) 318ms 0.6% 3.13% 8608ms 16.28% VertexElement::AddFace 2998ms 5.67% 8.80% 8432ms 15.95% std::_Rb_tree::_M_lower_bound (inline) 228ms 0.43% 9.23% 8267ms 15.63% std::_Rb_tree::_M_insert_unique 263ms 0.5% 9.73% 7976ms 15.08% std::_Rb_tree::find (inline) 0 0% 9.73% 7421ms 14.03% std::set::count (inline) 96ms 0.18% 9.91% 5319ms 10.06% std::less::operator() (inline) 5281ms 9.99% 19.89% 5281ms 9.99% std::operator< (inline) 269ms 0.51% 20.40% 5031ms 9.51% std::_Rb_tree::_M_insert_ (inline) 0 0% 20.40% 4879ms 9.23% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 20.40% 4781ms 9.04% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 20.40% 4750ms 8.98% AbstractNumericalMethod::ComputeForcesIncludingDamping 212ms 0.4% 20.80% 4299ms 8.13% operator new 4071ms 7.70% 28.50% 4071ms 7.70% std::_Rb_tree_increment 1071ms 2.03% 30.53% 4017ms 7.60% __GI___libc_malloc 2ms 0.0038% 30.53% 3944ms 7.46% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.0076% 30.54% 3872ms 7.32% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 6ms 0.011% 30.55% 3821ms 7.23% MeshBasedCellPopulation::SpringIterator::operator++ 53ms 0.1% 30.65% 3771ms 7.13% std::__new_allocator::allocate (inline) 0 0% 30.65% 3750ms 7.09% std::allocator_traits::allocate (inline) 3ms 0.0057% 30.66% 3701ms 7.00% std::_Rb_tree::~_Rb_tree (inline) 1359ms 2.57% 33.23% 3694ms 6.99% std::_Rb_tree::_M_erase 0 0% 33.23% 3650ms 6.90% std::set::~set (inline) 123ms 0.23% 33.46% 3514ms 6.65% tetgen::tetgenmesh::insphere_sos 3078ms 5.82% 39.28% 3375ms 6.38% tetgen::insphere 1205ms 2.28% 41.56% 3329ms 6.30% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 41.56% 3328ms 6.29% AbstractCellPopulation::WriteResultsToFiles 935ms 1.77% 43.33% 3246ms 6.14% __GI___libc_free 0 0% 43.33% 3044ms 5.76% std::_Rb_tree::_M_create_node (inline) 0 0% 43.33% 3017ms 5.71% std::_Rb_tree::_M_get_node (inline) 0 0% 43.33% 3016ms 5.70% std::_Rb_tree::_Alloc_node::operator() (inline) 129ms 0.24% 43.57% 2941ms 5.56% std::__new_allocator::deallocate (inline) 4ms 0.0076% 43.58% 2921ms 5.52% std::set_intersection (inline) 192ms 0.36% 43.94% 2917ms 5.52% std::__set_intersection 0 0% 43.94% 2916ms 5.51% std::allocator_traits::deallocate (inline) 13ms 0.025% 43.97% 2826ms 5.34% TetrahedralMesh::ImportFromMesher 25ms 0.047% 44.01% 2742ms 5.19% Node::AddElement 168ms 0.32% 44.33% 2738ms 5.18% tetgen::tetgenmesh::flip23 0 0% 44.33% 2629ms 4.97% VertexMesh::~VertexMesh 1990ms 3.76% 48.09% 2612ms 4.94% _int_malloc 2513ms 4.75% 52.85% 2513ms 4.75% std::_Rb_tree::_S_right (inline) 1179ms 2.23% 55.08% 2306ms 4.36% _int_free 183ms 0.35% 55.42% 2296ms 4.34% std::_Rb_tree_const_iterator::operator++ (inline) 4ms 0.0076% 55.43% 2276ms 4.30% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 208ms 0.39% 55.82% 2267ms 4.29% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 3ms 0.0057% 55.83% 2064ms 3.90% std::_Rb_tree_iterator::operator++ (inline) 80ms 0.15% 55.98% 2048ms 3.87% MutableElement::AddNode 91ms 0.17% 56.15% 1920ms 3.63% Node::~Node 148ms 0.28% 56.43% 1828ms 3.46% tetgen::tetgenmesh::flip32 0 0% 56.43% 1824ms 3.45% std::_Rb_tree::_M_drop_node (inline) 0 0% 56.43% 1814ms 3.43% std::_Rb_tree::_M_put_node (inline) 126ms 0.24% 56.67% 1801ms 3.41% VertexMesh::Clear 1798ms 3.40% 60.07% 1798ms 3.40% std::_Rb_tree_insert_and_rebalance 6ms 0.011% 60.08% 1484ms 2.81% Element::Element 1299ms 2.46% 62.54% 1382ms 2.61% tetgen::orient3d 147ms 0.28% 62.82% 1325ms 2.51% tetgen::tetgenmesh::enqueueflipface 1238ms 2.34% 65.16% 1238ms 2.34% Node::GetIndex 4ms 0.0076% 65.16% 1173ms 2.22% Element::RegisterWithNodes (inline) 38ms 0.072% 65.24% 1164ms 2.20% tetgen::tetgenmesh::locate 9ms 0.017% 65.25% 1111ms 2.10% std::_Vector_base::_M_deallocate (inline) 96ms 0.18% 65.43% 1084ms 2.05% tetgen::tetgenmesh::preciselocate 643ms 1.22% 66.65% 1066ms 2.02% malloc_consolidate 99ms 0.19% 66.84% 1042ms 1.97% TetrahedralMesh::Clear 0 0% 66.84% 1039ms 1.96% std::vector::~vector (inline) 57ms 0.11% 66.95% 1017ms 1.92% std::map::operator[] 64ms 0.12% 67.07% 984ms 1.86% std::vector::_M_realloc_insert 7ms 0.013% 67.08% 924ms 1.75% _int_free_maybe_consolidate 920ms 1.74% 68.82% 920ms 1.74% tetgen::tetgenmesh::triface::triface 0 0% 68.82% 916ms 1.73% std::_Vector_base::~_Vector_base (inline) 0 0% 68.82% 899ms 1.70% std::_Rb_tree::lower_bound (inline) 0 0% 68.82% 899ms 1.70% std::map::lower_bound (inline) 0 0% 68.82% 839ms 1.59% VoronoiDataWriter::Visit 805ms 1.52% 70.34% 805ms 1.52% unlink_chunk 9ms 0.017% 70.36% 782ms 1.48% VertexMesh::GenerateVerticesFromElementCircumcentres 97ms 0.18% 70.54% 768ms 1.45% std::vector::push_back (inline) 746ms 1.41% 71.95% 746ms 1.41% tetgen::tetgenmesh::oppo 4ms 0.0076% 71.96% 737ms 1.39% std::_Vector_base::_M_allocate (inline) 2ms 0.0038% 71.96% 717ms 1.36% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 71.96% 712ms 1.35% TetrahedralMesh::RefreshJacobianCachedData 389ms 0.74% 72.70% 711ms 1.34% tetgen::tetgenmesh::fnextself 19ms 0.036% 72.74% 680ms 1.29% boost::numeric::ublas::vector_assign (inline) 22ms 0.042% 72.78% 670ms 1.27% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 6ms 0.011% 72.79% 668ms 1.26% AbstractTetrahedralElement::CalculateInverseJacobian 17ms 0.032% 72.82% 662ms 1.25% boost::numeric::ublas::c_vector::c_vector (inline) 519ms 0.98% 73.80% 651ms 1.23% AbstractElement::GetNodeGlobalIndex 640ms 1.21% 75.01% 640ms 1.21% [libchaste_mesh.so] 17ms 0.032% 75.05% 615ms 1.16% AbstractTetrahedralElement::CalculateJacobian 56ms 0.11% 75.15% 587ms 1.11% __atan2 0 0% 75.15% 553ms 1.05% std::set::find (inline) 535ms 1.01% 76.16% 535ms 1.01% tetgen::tetgenmesh::triface::operator= 215ms 0.41% 76.57% 531ms 1.00% AbstractElement::GetNodeLocation 436ms 0.82% 77.39% 531ms 1.00% __ieee754_atan2_fma 0 0% 77.39% 518ms 0.98% std::insert_iterator::operator= (inline) 0 0% 77.39% 494ms 0.93% boost::numeric::ublas::inner_prod (inline) 4ms 0.0076% 77.40% 493ms 0.93% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 31ms 0.059% 77.46% 489ms 0.92% boost::numeric::ublas::vector_scalar_binary::evaluate 52ms 0.098% 77.56% 463ms 0.88% tetgen::tetgenmesh::enextfnext 0 0% 77.56% 457ms 0.86% std::_Rb_tree::_M_insert_unique_ (inline) 47ms 0.089% 77.65% 454ms 0.86% tetgen::tetgenmesh::enext2fnext 16ms 0.03% 77.68% 451ms 0.85% Element::CalculateCircumsphere 38ms 0.072% 77.75% 439ms 0.83% AbstractTetrahedralElement::RefreshJacobian 121ms 0.23% 77.98% 434ms 0.82% boost::numeric::ublas::indexing_vector_assign 429ms 0.81% 78.79% 429ms 0.81% std::vector::size (inline) 292ms 0.55% 79.34% 429ms 0.81% tetgen::tetgenmesh::sym 244ms 0.46% 79.80% 421ms 0.8% AbstractTetrahedralMesh::GetElement 419ms 0.79% 80.60% 419ms 0.79% boost::numeric::ublas::c_vector::operator() 405ms 0.77% 81.36% 405ms 0.77% Node::rGetLocation 201ms 0.38% 81.74% 405ms 0.77% boost::numeric::ublas::vector_inner_prod::apply (inline) 5ms 0.0095% 81.75% 389ms 0.74% CellPropertyCollection::GetPropertiesType (inline) 18ms 0.034% 81.79% 380ms 0.72% tetgen::tetgenmesh::queue::push 5ms 0.0095% 81.79% 379ms 0.72% Cell::GetCellId 0 0% 81.79% 375ms 0.71% VertexMeshWriter::WriteVtkUsingMesh 374ms 0.71% 82.50% 374ms 0.71% tetgen::tetgenmesh::org 84ms 0.16% 82.66% 372ms 0.7% __dynamic_cast 7ms 0.013% 82.67% 370ms 0.7% boost::numeric::ublas::c_vector::operator= (inline) 22ms 0.042% 82.72% 362ms 0.68% std::_Rb_tree_iterator::operator-- (inline) 13ms 0.025% 82.74% 359ms 0.68% VertexMesh::CalculateUnitNormalToFaceWithArea 243ms 0.46% 83.20% 357ms 0.68% tetgen::tetgenmesh::link::add 263ms 0.5% 83.70% 354ms 0.67% tetgen::tetgenmesh::bond 22ms 0.042% 83.74% 337ms 0.64% std::vector::insert (inline) 327ms 0.62% 84.36% 327ms 0.62% std::_Rb_tree_decrement 139ms 0.26% 84.62% 309ms 0.58% Inverse 3ms 0.0057% 84.63% 306ms 0.58% AbstractCellProperty::IsSubType (inline) 7ms 0.013% 84.64% 306ms 0.58% VertexElement::~VertexElement 0 0% 84.64% 305ms 0.58% AbstractTetrahedralElement::AbstractTetrahedralElement 49ms 0.093% 84.73% 305ms 0.58% boost::numeric::ublas::vector_reference::operator() (inline) 39ms 0.074% 84.81% 297ms 0.56% tetgen::insphereadapt 1ms 0.0019% 84.81% 296ms 0.56% tcache_get (inline) 295ms 0.56% 85.36% 295ms 0.56% tcache_get_n (inline) 286ms 0.54% 85.91% 286ms 0.54% AbstractElement::IsDeleted 61ms 0.12% 86.02% 274ms 0.52% tetgen::tetgenmesh::queue::pop