File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 51001ms, 87.09% of 58562ms total Dropped 845 nodes (cum <= 292.81ms) flat flat% sum% cum cum% 0 0% 0% 58504ms 99.90% __libc_start_call_main 0 0% 0% 58504ms 99.90% __libc_start_main_impl 0 0% 0% 58504ms 99.90% _start 0 0% 0% 58490ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 58490ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 58490ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 58490ms 99.88% main 0 0% 0% 58451ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 58451ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 58451ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 58180ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0% 49352ms 84.27% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 49316ms 84.21% MeshBasedCellPopulation::Update 0 0% 0% 28492ms 48.65% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 28492ms 48.65% MeshBasedCellPopulation::TessellateIfNeeded 231ms 0.39% 0.39% 25152ms 42.95% VertexMesh::VertexMesh 0 0% 0.39% 16988ms 29.01% MutableMesh::ReMesh 0 0% 0.39% 12638ms 21.58% tetgen::tetrahedralize 2ms 0.0034% 0.4% 12495ms 21.34% tetgen::tetgenmesh::delaunizevertices 13ms 0.022% 0.42% 12490ms 21.33% tetgen::tetgenmesh::incrflipdelaunay 580ms 0.99% 1.41% 11810ms 20.17% TetrahedralMesh::EdgeIterator::operator++ 549ms 0.94% 2.35% 11054ms 18.88% tetgen::tetgenmesh::lawson 37ms 0.063% 2.41% 10292ms 17.57% std::set::insert (inline) 213ms 0.36% 2.77% 9717ms 16.59% std::_Rb_tree::_M_insert_unique 388ms 0.66% 3.44% 9462ms 16.16% VertexElement::AddFace 3033ms 5.18% 8.62% 8735ms 14.92% std::_Rb_tree::_M_lower_bound (inline) 274ms 0.47% 9.08% 8263ms 14.11% std::_Rb_tree::find (inline) 0 0% 9.08% 7700ms 13.15% std::set::count (inline) 283ms 0.48% 9.57% 5910ms 10.09% std::_Rb_tree::_M_insert_ (inline) 108ms 0.18% 9.75% 5563ms 9.50% std::less::operator() (inline) 5512ms 9.41% 19.16% 5512ms 9.41% std::operator< (inline) 0 0% 19.16% 5202ms 8.88% OffLatticeSimulation::UpdateCellLocationsAndTopology 188ms 0.32% 19.49% 5170ms 8.83% operator new 1ms 0.0017% 19.49% 5067ms 8.65% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.01% 19.50% 5043ms 8.61% AbstractNumericalMethod::ComputeForcesIncludingDamping 1134ms 1.94% 21.43% 4910ms 8.38% __GI___libc_malloc 4887ms 8.35% 29.78% 4887ms 8.35% std::_Rb_tree_increment 48ms 0.082% 29.86% 4449ms 7.60% std::__new_allocator::allocate (inline) 0 0% 29.86% 4420ms 7.55% std::allocator_traits::allocate (inline) 6ms 0.01% 29.87% 4391ms 7.50% std::_Rb_tree::~_Rb_tree (inline) 1620ms 2.77% 32.64% 4383ms 7.48% std::_Rb_tree::_M_erase 0 0% 32.64% 4321ms 7.38% std::set::~set (inline) 0 0% 32.64% 4178ms 7.13% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.012% 32.65% 4169ms 7.12% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 9ms 0.015% 32.66% 4041ms 6.90% MeshBasedCellPopulation::SpringIterator::operator++ 1242ms 2.12% 34.79% 3983ms 6.80% std::_Rb_tree::_M_get_insert_unique_pos 1264ms 2.16% 36.94% 3889ms 6.64% __GI___libc_free 2ms 0.0034% 36.95% 3836ms 6.55% std::set_intersection (inline) 264ms 0.45% 37.40% 3834ms 6.55% std::__set_intersection 27ms 0.046% 37.44% 3754ms 6.41% Node::AddElement 0 0% 37.44% 3614ms 6.17% std::_Rb_tree::_M_create_node (inline) 0 0% 37.44% 3576ms 6.11% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 37.44% 3564ms 6.09% std::_Rb_tree::_M_get_node (inline) 105ms 0.18% 37.62% 3544ms 6.05% tetgen::tetgenmesh::insphere_sos 4ms 0.0068% 37.63% 3517ms 6.01% TetrahedralMesh::ImportFromMesher 0 0% 37.63% 3478ms 5.94% AbstractCellPopulation::WriteResultsToFiles 132ms 0.23% 37.86% 3470ms 5.93% std::__new_allocator::deallocate (inline) 0 0% 37.86% 3451ms 5.89% std::allocator_traits::deallocate (inline) 2534ms 4.33% 42.18% 3443ms 5.88% _int_malloc 3111ms 5.31% 47.49% 3428ms 5.85% tetgen::insphere 0 0% 47.49% 3372ms 5.76% VertexMesh::~VertexMesh 3296ms 5.63% 53.12% 3296ms 5.63% std::_Rb_tree::_S_right (inline) 165ms 0.28% 53.40% 3049ms 5.21% std::_Rb_tree_const_iterator::operator++ (inline) 91ms 0.16% 53.56% 2911ms 4.97% MutableElement::AddNode 197ms 0.34% 53.90% 2677ms 4.57% tetgen::tetgenmesh::flip23 1222ms 2.09% 55.98% 2623ms 4.48% _int_free 197ms 0.34% 56.32% 2513ms 4.29% Node::~Node 1ms 0.0017% 56.32% 2312ms 3.95% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 202ms 0.34% 56.67% 2308ms 3.94% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 194ms 0.33% 57.00% 2249ms 3.84% VertexMesh::Clear 2124ms 3.63% 60.62% 2124ms 3.63% std::_Rb_tree_insert_and_rebalance 0 0% 60.62% 2120ms 3.62% std::_Rb_tree_iterator::operator++ (inline) 0 0% 60.62% 2042ms 3.49% std::_Rb_tree::_M_drop_node (inline) 0 0% 60.62% 2035ms 3.47% std::_Rb_tree::_M_put_node (inline) 142ms 0.24% 60.87% 1795ms 3.07% tetgen::tetgenmesh::flip32 6ms 0.01% 60.88% 1710ms 2.92% Element::Element 1540ms 2.63% 63.51% 1540ms 2.63% Node::GetIndex 217ms 0.37% 63.88% 1465ms 2.50% TetrahedralMesh::Clear 21ms 0.036% 63.91% 1437ms 2.45% std::_Vector_base::_M_deallocate (inline) 923ms 1.58% 65.49% 1391ms 2.38% malloc_consolidate 8ms 0.014% 65.50% 1390ms 2.37% Element::RegisterWithNodes (inline) 184ms 0.31% 65.82% 1332ms 2.27% tetgen::tetgenmesh::enqueueflipface 1244ms 2.12% 67.94% 1328ms 2.27% tetgen::orient3d 0 0% 67.94% 1312ms 2.24% std::vector::~vector (inline) 2ms 0.0034% 67.95% 1240ms 2.12% std::_Vector_base::~_Vector_base (inline) 7ms 0.012% 67.96% 1193ms 2.04% _int_free_maybe_consolidate 47ms 0.08% 68.04% 1167ms 1.99% tetgen::tetgenmesh::locate 49ms 0.084% 68.12% 1111ms 1.90% std::vector::_M_realloc_insert 87ms 0.15% 68.27% 1070ms 1.83% tetgen::tetgenmesh::preciselocate 1060ms 1.81% 70.08% 1060ms 1.81% unlink_chunk 59ms 0.1% 70.18% 1053ms 1.80% std::map::operator[] 827ms 1.41% 71.59% 990ms 1.69% AbstractElement::GetNodeGlobalIndex 6ms 0.01% 71.60% 934ms 1.59% VertexMesh::GenerateVerticesFromElementCircumcentres 0 0% 71.60% 929ms 1.59% VoronoiDataWriter::Visit 925ms 1.58% 73.18% 925ms 1.58% tetgen::tetgenmesh::triface::triface 0 0% 73.18% 918ms 1.57% std::_Rb_tree::lower_bound (inline) 0 0% 73.18% 918ms 1.57% std::map::lower_bound (inline) 109ms 0.19% 73.37% 869ms 1.48% std::vector::push_back (inline) 5ms 0.0085% 73.38% 861ms 1.47% std::_Vector_base::_M_allocate (inline) 1ms 0.0017% 73.38% 815ms 1.39% TetrahedralMesh::RefreshJacobianCachedData 10ms 0.017% 73.40% 729ms 1.24% AbstractTetrahedralElement::CalculateInverseJacobian 381ms 0.65% 74.05% 715ms 1.22% tetgen::tetgenmesh::fnextself 1ms 0.0017% 74.05% 708ms 1.21% AbstractTwoBodyInteractionForce::AddForceContribution 703ms 1.20% 75.25% 703ms 1.20% tetgen::tetgenmesh::oppo 675ms 1.15% 76.40% 675ms 1.15% [libchaste_mesh.so] 12ms 0.02% 76.42% 672ms 1.15% boost::numeric::ublas::vector_assign (inline) 14ms 0.024% 76.45% 661ms 1.13% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 15ms 0.026% 76.47% 656ms 1.12% AbstractTetrahedralElement::CalculateJacobian 11ms 0.019% 76.49% 642ms 1.10% boost::numeric::ublas::c_vector::c_vector (inline) 284ms 0.48% 76.97% 614ms 1.05% AbstractElement::GetNodeLocation 60ms 0.1% 77.08% 593ms 1.01% __atan2 570ms 0.97% 78.05% 570ms 0.97% tetgen::tetgenmesh::triface::operator= 0 0% 78.05% 560ms 0.96% std::set::find (inline) 0 0% 78.05% 557ms 0.95% std::insert_iterator::operator= (inline) 534ms 0.91% 78.96% 534ms 0.91% Node::rGetLocation 429ms 0.73% 79.70% 533ms 0.91% __ieee754_atan2_fma 517ms 0.88% 80.58% 517ms 0.88% std::vector::size (inline) 0 0% 80.58% 511ms 0.87% std::_Rb_tree::_M_insert_unique_ (inline) 500ms 0.85% 81.43% 500ms 0.85% AbstractElement::IsDeleted 15ms 0.026% 81.46% 487ms 0.83% Element::CalculateCircumsphere 0 0% 81.46% 487ms 0.83% boost::numeric::ublas::inner_prod (inline) 3ms 0.0051% 81.46% 487ms 0.83% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 38ms 0.065% 81.53% 484ms 0.83% boost::numeric::ublas::vector_scalar_binary::evaluate 50ms 0.085% 81.61% 479ms 0.82% tetgen::tetgenmesh::enext2fnext 43ms 0.073% 81.69% 473ms 0.81% tetgen::tetgenmesh::enextfnext 38ms 0.065% 81.75% 472ms 0.81% AbstractTetrahedralElement::RefreshJacobian 288ms 0.49% 82.24% 430ms 0.73% tetgen::tetgenmesh::sym 18ms 0.031% 82.27% 423ms 0.72% VertexMesh::CalculateUnitNormalToFaceWithArea 126ms 0.22% 82.49% 419ms 0.72% boost::numeric::ublas::indexing_vector_assign 18ms 0.031% 82.52% 409ms 0.7% std::_Rb_tree_iterator::operator-- (inline) 224ms 0.38% 82.90% 403ms 0.69% AbstractTetrahedralMesh::GetElement 0 0% 82.90% 389ms 0.66% VertexMeshWriter::WriteVtkUsingMesh 389ms 0.66% 83.57% 389ms 0.66% boost::numeric::ublas::c_vector::operator() 177ms 0.3% 83.87% 383ms 0.65% boost::numeric::ublas::vector_inner_prod::apply (inline) 71ms 0.12% 83.99% 380ms 0.65% __dynamic_cast 16ms 0.027% 84.02% 380ms 0.65% std::vector::insert (inline) 3ms 0.0051% 84.02% 379ms 0.65% boost::numeric::ublas::c_vector::operator= (inline) 25ms 0.043% 84.06% 379ms 0.65% tetgen::tetgenmesh::queue::push 3ms 0.0051% 84.07% 375ms 0.64% CellPropertyCollection::GetPropertiesType (inline) 372ms 0.64% 84.71% 372ms 0.64% std::_Rb_tree_decrement 2ms 0.0034% 84.71% 353ms 0.6% Cell::GetCellId 256ms 0.44% 85.15% 350ms 0.6% tetgen::tetgenmesh::link::add 252ms 0.43% 85.58% 344ms 0.59% tetgen::tetgenmesh::bond 5ms 0.0085% 85.58% 339ms 0.58% VertexElement::~VertexElement 142ms 0.24% 85.83% 329ms 0.56% Inverse 325ms 0.55% 86.38% 325ms 0.55% tetgen::tetgenmesh::org 44ms 0.075% 86.46% 317ms 0.54% tetgen::insphereadapt 0 0% 86.46% 316ms 0.54% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 4ms 0.0068% 86.46% 312ms 0.53% AbstractTetrahedralElement::AbstractTetrahedralElement 4ms 0.0068% 86.47% 306ms 0.52% VertexMesh::GetVolumeOfElement 1ms 0.0017% 86.47% 296ms 0.51% AbstractCellProperty::IsSubType (inline) 0 0% 86.47% 295ms 0.5% tcache_get (inline) 295ms 0.5% 86.98% 295ms 0.5% tcache_get_n (inline) 66ms 0.11% 87.09% 294ms 0.5% tetgen::tetgenmesh::queue::pop