File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 54429ms, 88.02% of 61835ms total Dropped 851 nodes (cum <= 309.18ms) flat flat% sum% cum cum% 0 0% 0% 61778ms 99.91% __libc_start_call_main 0 0% 0% 61778ms 99.91% __libc_start_main_impl 0 0% 0% 61778ms 99.91% _start 0 0% 0% 61762ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 61762ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 61762ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 61762ms 99.88% main 0 0% 0% 61725ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 61725ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 61725ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 61434ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0% 51182ms 82.77% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 51129ms 82.69% MeshBasedCellPopulation::Update 0 0% 0% 29326ms 47.43% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 29326ms 47.43% MeshBasedCellPopulation::TessellateIfNeeded 257ms 0.42% 0.42% 25831ms 41.77% VertexMesh::VertexMesh 1ms 0.0016% 0.42% 17659ms 28.56% MutableMesh::ReMesh 0 0% 0.42% 13176ms 21.31% tetgen::tetrahedralize 0 0% 0.42% 13039ms 21.09% tetgen::tetgenmesh::delaunizevertices 8ms 0.013% 0.43% 13036ms 21.08% tetgen::tetgenmesh::incrflipdelaunay 532ms 0.86% 1.29% 12555ms 20.30% TetrahedralMesh::EdgeIterator::operator++ 514ms 0.83% 2.12% 11608ms 18.77% tetgen::tetgenmesh::lawson 30ms 0.049% 2.17% 10097ms 16.33% std::set::insert (inline) 2921ms 4.72% 6.89% 9936ms 16.07% std::_Rb_tree::_M_lower_bound (inline) 217ms 0.35% 7.25% 9637ms 15.59% std::_Rb_tree::_M_insert_unique 342ms 0.55% 7.80% 9373ms 15.16% VertexElement::AddFace 220ms 0.36% 8.15% 9130ms 14.77% std::_Rb_tree::find (inline) 0 0% 8.15% 8586ms 13.89% std::set::count (inline) 101ms 0.16% 8.32% 6642ms 10.74% std::less::operator() (inline) 6597ms 10.67% 18.99% 6597ms 10.67% std::operator< (inline) 6131ms 9.92% 28.90% 6131ms 9.92% std::_Rb_tree_increment 229ms 0.37% 29.27% 5704ms 9.22% std::_Rb_tree::_M_insert_ (inline) 0 0% 29.27% 5525ms 8.94% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 29.27% 5389ms 8.72% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0016% 29.27% 5358ms 8.66% AbstractNumericalMethod::ComputeForcesIncludingDamping 193ms 0.31% 29.59% 5336ms 8.63% operator new 1124ms 1.82% 31.40% 5068ms 8.20% __GI___libc_malloc 0 0% 31.40% 4587ms 7.42% AbstractCellPopulation::WriteResultsToFiles 44ms 0.071% 31.47% 4539ms 7.34% std::__new_allocator::allocate (inline) 0 0% 31.47% 4515ms 7.30% std::allocator_traits::allocate (inline) 3ms 0.0049% 31.48% 4476ms 7.24% MeshBasedCellPopulation::UpdateNodePairs 8ms 0.013% 31.49% 4447ms 7.19% std::_Rb_tree::~_Rb_tree (inline) 1801ms 2.91% 34.40% 4436ms 7.17% std::_Rb_tree::_M_erase 1ms 0.0016% 34.41% 4431ms 7.17% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 34.41% 4400ms 7.12% std::set::~set (inline) 12ms 0.019% 34.43% 4314ms 6.98% MeshBasedCellPopulation::SpringIterator::operator++ 2ms 0.0032% 34.43% 4015ms 6.49% std::set_intersection (inline) 264ms 0.43% 34.86% 4013ms 6.49% std::__set_intersection 1217ms 1.97% 36.82% 4002ms 6.47% std::_Rb_tree::_M_get_insert_unique_pos 1168ms 1.89% 38.71% 3934ms 6.36% __GI___libc_free 23ms 0.037% 38.75% 3848ms 6.22% Node::AddElement 14ms 0.023% 38.77% 3639ms 5.89% TetrahedralMesh::ImportFromMesher 0 0% 38.77% 3625ms 5.86% std::_Rb_tree::_M_create_node (inline) 0 0% 38.77% 3597ms 5.82% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 38.77% 3580ms 5.79% std::_Rb_tree::_M_get_node (inline) 2635ms 4.26% 43.03% 3560ms 5.76% _int_malloc 130ms 0.21% 43.24% 3551ms 5.74% tetgen::tetgenmesh::insphere_sos 0 0% 43.24% 3540ms 5.72% VertexMesh::~VertexMesh 3529ms 5.71% 48.95% 3529ms 5.71% std::_Rb_tree::_S_right (inline) 107ms 0.17% 49.12% 3462ms 5.60% std::__new_allocator::deallocate (inline) 0 0% 49.12% 3449ms 5.58% std::allocator_traits::deallocate (inline) 3122ms 5.05% 54.17% 3405ms 5.51% tetgen::insphere 260ms 0.42% 54.59% 3363ms 5.44% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 225ms 0.36% 54.96% 3327ms 5.38% std::_Rb_tree_const_iterator::operator++ (inline) 4ms 0.0065% 54.96% 3196ms 5.17% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 3ms 0.0049% 54.97% 3123ms 5.05% std::_Rb_tree_iterator::operator++ (inline) 76ms 0.12% 55.09% 2840ms 4.59% MutableElement::AddNode 1214ms 1.96% 57.06% 2761ms 4.47% _int_free 201ms 0.33% 57.38% 2748ms 4.44% tetgen::tetgenmesh::flip23 155ms 0.25% 57.63% 2578ms 4.17% Node::~Node 183ms 0.3% 57.93% 2327ms 3.76% VertexMesh::Clear 146ms 0.24% 58.16% 1973ms 3.19% tetgen::tetgenmesh::flip32 0 0% 58.16% 1949ms 3.15% std::_Rb_tree::_M_drop_node (inline) 1948ms 3.15% 61.31% 1948ms 3.15% std::_Rb_tree_insert_and_rebalance 0 0% 61.31% 1940ms 3.14% std::_Rb_tree::_M_put_node (inline) 4ms 0.0065% 61.32% 1864ms 3.01% Element::Element 1698ms 2.75% 64.07% 1698ms 2.75% Node::GetIndex 1020ms 1.65% 65.72% 1576ms 2.55% malloc_consolidate 9ms 0.015% 65.73% 1518ms 2.45% std::_Vector_base::_M_deallocate (inline) 9ms 0.015% 65.74% 1511ms 2.44% Element::RegisterWithNodes (inline) 1426ms 2.31% 68.05% 1511ms 2.44% tetgen::orient3d 208ms 0.34% 68.39% 1445ms 2.34% TetrahedralMesh::Clear 0 0% 68.39% 1413ms 2.29% std::vector::~vector (inline) 5ms 0.0081% 68.39% 1337ms 2.16% _int_free_maybe_consolidate 1ms 0.0016% 68.40% 1316ms 2.13% std::_Vector_base::~_Vector_base (inline) 203ms 0.33% 68.72% 1287ms 2.08% tetgen::tetgenmesh::enqueueflipface 59ms 0.095% 68.82% 1277ms 2.07% std::map::operator[] 37ms 0.06% 68.88% 1219ms 1.97% tetgen::tetgenmesh::locate 63ms 0.1% 68.98% 1162ms 1.88% std::vector::_M_realloc_insert 0 0% 68.98% 1160ms 1.88% std::_Rb_tree::lower_bound (inline) 0 0% 68.98% 1160ms 1.88% std::map::lower_bound (inline) 2ms 0.0032% 68.99% 1138ms 1.84% VoronoiDataWriter::Visit 105ms 0.17% 69.16% 1133ms 1.83% tetgen::tetgenmesh::preciselocate 1124ms 1.82% 70.97% 1124ms 1.82% unlink_chunk 6ms 0.0097% 70.98% 1028ms 1.66% VertexMesh::GenerateVerticesFromElementCircumcentres 1007ms 1.63% 72.61% 1007ms 1.63% tetgen::tetgenmesh::triface::triface 124ms 0.2% 72.81% 962ms 1.56% std::vector::push_back (inline) 4ms 0.0065% 72.82% 939ms 1.52% std::_Vector_base::_M_allocate (inline) 437ms 0.71% 73.52% 893ms 1.44% tetgen::tetgenmesh::fnextself 727ms 1.18% 74.70% 892ms 1.44% AbstractElement::GetNodeGlobalIndex 0 0% 74.70% 825ms 1.33% TetrahedralMesh::RefreshJacobianCachedData 4ms 0.0065% 74.71% 745ms 1.20% AbstractTetrahedralElement::CalculateInverseJacobian 282ms 0.46% 75.16% 737ms 1.19% AbstractElement::GetNodeLocation 0 0% 75.16% 731ms 1.18% AbstractTwoBodyInteractionForce::AddForceContribution 724ms 1.17% 76.33% 724ms 1.17% tetgen::tetgenmesh::triface::operator= 12ms 0.019% 76.35% 715ms 1.16% AbstractTetrahedralElement::CalculateJacobian 12ms 0.019% 76.37% 698ms 1.13% boost::numeric::ublas::vector_assign (inline) 684ms 1.11% 77.48% 684ms 1.11% [libchaste_mesh.so] 14ms 0.023% 77.50% 679ms 1.10% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 13ms 0.021% 77.52% 658ms 1.06% boost::numeric::ublas::c_vector::c_vector (inline) 650ms 1.05% 78.57% 650ms 1.05% Node::rGetLocation 41ms 0.066% 78.64% 620ms 1.00% __atan2 457ms 0.74% 79.38% 579ms 0.94% __ieee754_atan2_fma 58ms 0.094% 79.47% 562ms 0.91% tetgen::tetgenmesh::enextfnext 45ms 0.073% 79.55% 551ms 0.89% AbstractTetrahedralElement::RefreshJacobian 551ms 0.89% 80.44% 551ms 0.89% tetgen::tetgenmesh::oppo 42ms 0.068% 80.50% 549ms 0.89% tetgen::tetgenmesh::enext2fnext 538ms 0.87% 81.37% 538ms 0.87% std::vector::size (inline) 0 0% 81.37% 537ms 0.87% std::set::find (inline) 533ms 0.86% 82.24% 533ms 0.86% AbstractElement::IsDeleted 18ms 0.029% 82.27% 519ms 0.84% Element::CalculateCircumsphere 146ms 0.24% 82.50% 474ms 0.77% boost::numeric::ublas::indexing_vector_assign 0 0% 82.50% 471ms 0.76% boost::numeric::ublas::inner_prod (inline) 5ms 0.0081% 82.51% 466ms 0.75% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 25ms 0.04% 82.55% 461ms 0.75% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 82.55% 450ms 0.73% std::insert_iterator::operator= (inline) 21ms 0.034% 82.58% 445ms 0.72% VertexMesh::CalculateUnitNormalToFaceWithArea 29ms 0.047% 82.63% 444ms 0.72% tetgen::tetgenmesh::queue::push 261ms 0.42% 83.05% 418ms 0.68% tetgen::tetgenmesh::sym 353ms 0.57% 83.62% 413ms 0.67% tetgen::tetgenmesh::link::add 7ms 0.011% 83.64% 401ms 0.65% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 83.64% 399ms 0.65% std::_Rb_tree::_M_insert_unique_ (inline) 388ms 0.63% 84.26% 388ms 0.63% boost::numeric::ublas::c_vector::operator() 0 0% 84.26% 387ms 0.63% VertexMeshWriter::WriteVtkUsingMesh 5ms 0.0081% 84.27% 384ms 0.62% CellPropertyCollection::GetPropertiesType (inline) 22ms 0.036% 84.31% 379ms 0.61% std::_Rb_tree_iterator::operator-- (inline) 175ms 0.28% 84.59% 377ms 0.61% boost::numeric::ublas::vector_inner_prod::apply (inline) 204ms 0.33% 84.92% 375ms 0.61% AbstractTetrahedralMesh::GetElement 108ms 0.17% 85.09% 372ms 0.6% __dynamic_cast 3ms 0.0049% 85.10% 367ms 0.59% Cell::GetCellId 362ms 0.59% 85.68% 362ms 0.59% tetgen::tetgenmesh::org 0 0% 85.68% 357ms 0.58% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 85.68% 356ms 0.58% tcache_get (inline) 356ms 0.58% 86.26% 356ms 0.58% tcache_get_n (inline) 15ms 0.024% 86.28% 354ms 0.57% std::vector::insert (inline) 3ms 0.0049% 86.29% 352ms 0.57% AbstractTetrahedralElement::AbstractTetrahedralElement 8ms 0.013% 86.30% 336ms 0.54% VertexElement::~VertexElement 335ms 0.54% 86.84% 335ms 0.54% std::_Rb_tree_decrement 148ms 0.24% 87.08% 332ms 0.54% Inverse 256ms 0.41% 87.50% 325ms 0.53% tetgen::tetgenmesh::bond 325ms 0.53% 88.02% 325ms 0.53% tetgen::tetgenmesh::pointmark