File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 64613ms, 86.03% of 75108ms total Dropped 874 nodes (cum <= 375.54ms) flat flat% sum% cum cum% 0 0% 0% 75054ms 99.93% __libc_start_call_main 0 0% 0% 75054ms 99.93% __libc_start_main_impl 0 0% 0% 75054ms 99.93% _start 0 0% 0% 75036ms 99.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 75036ms 99.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 75036ms 99.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 75036ms 99.90% main 0 0% 0% 74998ms 99.85% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 74998ms 99.85% CxxTest::TestRunner::runTest (inline) 0 0% 0% 74998ms 99.85% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 74749ms 99.52% AbstractCellBasedSimulation::Solve 0 0% 0% 62755ms 83.55% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 62692ms 83.47% MeshBasedCellPopulation::Update 0 0% 0% 41092ms 54.71% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 41091ms 54.71% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 353ms 0.47% 0.47% 36289ms 48.32% VertexMesh::VertexMesh 0 0% 0.47% 16609ms 22.11% MutableMesh::ReMesh 543ms 0.72% 1.19% 15844ms 21.09% TetrahedralMesh::EdgeIterator::operator++ 56ms 0.075% 1.27% 14196ms 18.90% std::set::insert (inline) 166ms 0.22% 1.49% 13598ms 18.10% std::_Rb_tree::_M_insert_unique 4203ms 5.60% 7.08% 12195ms 16.24% std::_Rb_tree::_M_lower_bound (inline) 430ms 0.57% 7.66% 12112ms 16.13% VertexElement::AddFace 201ms 0.27% 7.92% 11526ms 15.35% std::_Rb_tree::find (inline) 0 0% 7.92% 11251ms 14.98% tetgen::tetrahedralize 3ms 0.004% 7.93% 11143ms 14.84% tetgen::tetgenmesh::delaunizevertices 4ms 0.0053% 7.93% 11139ms 14.83% tetgen::tetgenmesh::incrflipdelaunay 0 0% 7.93% 11004ms 14.65% std::set::count (inline) 468ms 0.62% 8.56% 9818ms 13.07% tetgen::tetgenmesh::lawson 232ms 0.31% 8.87% 9747ms 12.98% operator new 2992ms 3.98% 12.85% 9452ms 12.58% __GI___libc_malloc 325ms 0.43% 13.28% 9084ms 12.09% std::_Rb_tree::_M_insert_ (inline) 8921ms 11.88% 25.16% 8921ms 11.88% std::_Rb_tree_increment 62ms 0.083% 25.24% 8092ms 10.77% std::__new_allocator::allocate (inline) 0 0% 25.24% 8076ms 10.75% std::allocator_traits::allocate (inline) 1ms 0.0013% 25.24% 7030ms 9.36% std::set_intersection (inline) 494ms 0.66% 25.90% 7029ms 9.36% std::__set_intersection 93ms 0.12% 26.03% 6987ms 9.30% std::less::operator() (inline) 6952ms 9.26% 35.28% 6952ms 9.26% std::operator< (inline) 0 0% 35.28% 6653ms 8.86% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 35.28% 6540ms 8.71% std::_Rb_tree::_M_create_node (inline) 0 0% 35.28% 6496ms 8.65% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 35.28% 6492ms 8.64% std::_Rb_tree::_M_get_node (inline) 1ms 0.0013% 35.28% 6459ms 8.60% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0013% 35.28% 6439ms 8.57% AbstractNumericalMethod::ComputeForcesIncludingDamping 1057ms 1.41% 36.69% 6118ms 8.15% __GI___libc_free 4612ms 6.14% 42.83% 5990ms 7.98% _int_malloc 281ms 0.37% 43.21% 5855ms 7.80% std::_Rb_tree_const_iterator::operator++ (inline) 78ms 0.1% 43.31% 5572ms 7.42% Node::AddElement 1ms 0.0013% 43.31% 5339ms 7.11% MeshBasedCellPopulation::UpdateNodePairs 10ms 0.013% 43.32% 5332ms 7.10% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 83ms 0.11% 43.43% 5263ms 7.01% std::__new_allocator::deallocate (inline) 0 0% 43.43% 5250ms 6.99% std::allocator_traits::deallocate (inline) 17ms 0.023% 43.46% 5188ms 6.91% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 43.46% 5152ms 6.86% AbstractCellPopulation::WriteResultsToFiles 15ms 0.02% 43.48% 5139ms 6.84% std::_Rb_tree::~_Rb_tree (inline) 1546ms 2.06% 45.54% 5114ms 6.81% std::_Rb_tree::_M_erase 0 0% 45.54% 5069ms 6.75% std::set::~set (inline) 2169ms 2.89% 48.42% 5032ms 6.70% _int_free 0 0% 48.42% 4843ms 6.45% VertexMesh::~VertexMesh 1447ms 1.93% 50.35% 4713ms 6.27% std::_Rb_tree::_M_get_insert_unique_pos 4696ms 6.25% 56.60% 4696ms 6.25% std::_Rb_tree::_S_right (inline) 1ms 0.0013% 56.60% 4265ms 5.68% TetrahedralMesh::ImportFromMesher 47ms 0.063% 56.67% 3999ms 5.32% MutableElement::AddNode 317ms 0.42% 57.09% 3961ms 5.27% std::_Rb_tree_iterator::operator++ (inline) 2ms 0.0027% 57.09% 3931ms 5.23% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 4ms 0.0053% 57.10% 3701ms 4.93% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 89ms 0.12% 57.21% 3004ms 4.00% tetgen::tetgenmesh::insphere_sos 2667ms 3.55% 60.77% 2884ms 3.84% tetgen::insphere 0 0% 60.77% 2869ms 3.82% std::_Rb_tree::_M_drop_node (inline) 0 0% 60.77% 2834ms 3.77% std::_Rb_tree::_M_put_node (inline) 26ms 0.035% 60.80% 2811ms 3.74% Node::~Node 3ms 0.004% 60.80% 2766ms 3.68% VertexMesh::Clear 1848ms 2.46% 63.26% 2581ms 3.44% malloc_consolidate 6ms 0.008% 63.27% 2579ms 3.43% Element::Element 34ms 0.045% 63.32% 2450ms 3.26% std::_Vector_base::_M_deallocate (inline) 251ms 0.33% 63.65% 2385ms 3.18% tetgen::tetgenmesh::flip23 2373ms 3.16% 66.81% 2373ms 3.16% std::_Rb_tree_insert_and_rebalance 0 0% 66.81% 2300ms 3.06% std::vector::~vector (inline) 3ms 0.004% 66.82% 2257ms 3.01% std::_Vector_base::~_Vector_base (inline) 10ms 0.013% 66.83% 2238ms 2.98% _int_free_maybe_consolidate 7ms 0.0093% 66.84% 2190ms 2.92% Element::RegisterWithNodes (inline) 2082ms 2.77% 69.61% 2082ms 2.77% [libchaste_mesh.so] 1889ms 2.52% 72.13% 1889ms 2.52% Node::GetIndex 5ms 0.0067% 72.13% 1730ms 2.30% VertexMesh::GenerateVerticesFromElementCircumcentres 49ms 0.065% 72.20% 1694ms 2.26% std::vector::_M_realloc_insert 1619ms 2.16% 74.35% 1619ms 2.16% unlink_chunk 208ms 0.28% 74.63% 1599ms 2.13% tetgen::tetgenmesh::flip32 3ms 0.004% 74.63% 1587ms 2.11% std::_Vector_base::_M_allocate (inline) 1526ms 2.03% 76.67% 1576ms 2.10% tetgen::orient3d 73ms 0.097% 76.76% 1442ms 1.92% std::map::operator[] 68ms 0.091% 76.85% 1320ms 1.76% std::vector::push_back (inline) 0 0% 76.85% 1267ms 1.69% std::_Rb_tree::lower_bound (inline) 0 0% 76.85% 1267ms 1.69% std::map::lower_bound (inline) 0 0% 76.85% 1210ms 1.61% VoronoiDataWriter::Visit 1196ms 1.59% 78.45% 1196ms 1.59% Node::rGetLocation 13ms 0.017% 78.46% 1193ms 1.59% TetrahedralMesh::Clear 858ms 1.14% 79.61% 1192ms 1.59% AbstractElement::GetNodeGlobalIndex 23ms 0.031% 79.64% 1117ms 1.49% tetgen::tetgenmesh::locate 210ms 0.28% 79.92% 1080ms 1.44% tetgen::tetgenmesh::enqueueflipface 90ms 0.12% 80.04% 1071ms 1.43% tetgen::tetgenmesh::preciselocate 1ms 0.0013% 80.04% 1069ms 1.42% TetrahedralMesh::RefreshJacobianCachedData 542ms 0.72% 80.76% 989ms 1.32% AbstractElement::GetNodeLocation 7ms 0.0093% 80.77% 889ms 1.18% Element::CalculateCircumsphere 5ms 0.0067% 80.77% 863ms 1.15% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.0013% 80.78% 810ms 1.08% AbstractTwoBodyInteractionForce::AddForceContribution 10ms 0.013% 80.79% 800ms 1.07% AbstractTetrahedralElement::CalculateJacobian 7ms 0.0093% 80.80% 782ms 1.04% boost::numeric::ublas::c_vector::c_vector (inline) 5ms 0.0067% 80.80% 782ms 1.04% boost::numeric::ublas::vector_assign (inline) 13ms 0.017% 80.82% 761ms 1.01% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 667ms 0.89% 81.71% 667ms 0.89% std::vector::size (inline) 46ms 0.061% 81.77% 651ms 0.87% AbstractTetrahedralElement::RefreshJacobian 373ms 0.5% 82.27% 613ms 0.82% tetgen::tetgenmesh::sym 0 0% 82.27% 586ms 0.78% std::insert_iterator::operator= (inline) 576ms 0.77% 83.04% 576ms 0.77% AbstractElement::IsDeleted 564ms 0.75% 83.79% 564ms 0.75% tetgen::tetgenmesh::oppo 45ms 0.06% 83.85% 551ms 0.73% __atan2 0 0% 83.85% 516ms 0.69% std::set::find (inline) 0 0% 83.85% 514ms 0.68% std::_Rb_tree::_M_insert_unique_ (inline) 452ms 0.6% 84.45% 499ms 0.66% __ieee754_atan2_fma 7ms 0.0093% 84.46% 495ms 0.66% std::vector::insert (inline) 51ms 0.068% 84.52% 471ms 0.63% std::_Rb_tree_iterator::operator-- (inline) 0 0% 84.52% 456ms 0.61% Cell::GetCellId 9ms 0.012% 84.54% 451ms 0.6% CellPropertyCollection::GetPropertiesType (inline) 22ms 0.029% 84.57% 448ms 0.6% VertexMesh::CalculateUnitNormalToFaceWithArea 142ms 0.19% 84.76% 437ms 0.58% _int_free_merge_chunk 0 0% 84.76% 408ms 0.54% boost::numeric::ublas::inner_prod (inline) 32ms 0.043% 84.80% 407ms 0.54% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 84.80% 407ms 0.54% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 389ms 0.52% 85.32% 389ms 0.52% std::_Rb_tree_decrement 1ms 0.0013% 85.32% 386ms 0.51% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 85.32% 385ms 0.51% VertexMeshWriter::WriteVtkUsingMesh 155ms 0.21% 85.52% 379ms 0.5% Inverse 0 0% 85.52% 378ms 0.5% tcache_get (inline) 378ms 0.5% 86.03% 378ms 0.5% tcache_get_n (inline)