File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 53324ms, 86.47% of 61668ms total Dropped 923 nodes (cum <= 308.34ms) flat flat% sum% cum cum% 0 0% 0% 61600ms 99.89% __libc_start_call_main 0 0% 0% 61600ms 99.89% __libc_start_main_impl 0 0% 0% 61600ms 99.89% _start 0 0% 0% 61580ms 99.86% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 61580ms 99.86% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 61580ms 99.86% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 61580ms 99.86% main 0 0% 0% 61533ms 99.78% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 61533ms 99.78% CxxTest::TestRunner::runTest (inline) 0 0% 0% 61533ms 99.78% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 61253ms 99.33% AbstractCellBasedSimulation::Solve 0 0% 0% 52131ms 84.53% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 52082ms 84.46% MeshBasedCellPopulation::Update 0 0% 0% 28152ms 45.65% MeshBasedCellPopulation::TessellateIfNeeded 1ms 0.0016% 0.0016% 28151ms 45.65% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 189ms 0.31% 0.31% 25125ms 40.74% VertexMesh::VertexMesh 0 0% 0.31% 19907ms 32.28% MutableMesh::ReMesh 1ms 0.0016% 0.31% 16105ms 26.12% tetgen::tetrahedralize 5ms 0.0081% 0.32% 15941ms 25.85% tetgen::tetgenmesh::delaunizevertices 12ms 0.019% 0.34% 15929ms 25.83% tetgen::tetgenmesh::incrflipdelaunay 485ms 0.79% 1.12% 14266ms 23.13% tetgen::tetgenmesh::lawson 600ms 0.97% 2.10% 12271ms 19.90% TetrahedralMesh::EdgeIterator::operator++ 30ms 0.049% 2.15% 9772ms 15.85% std::set::insert (inline) 367ms 0.6% 2.74% 9704ms 15.74% VertexElement::AddFace 247ms 0.4% 3.14% 9322ms 15.12% std::_Rb_tree::_M_insert_unique 3235ms 5.25% 8.39% 9216ms 14.94% std::_Rb_tree::_M_lower_bound (inline) 209ms 0.34% 8.73% 8679ms 14.07% std::_Rb_tree::find (inline) 0 0% 8.73% 8093ms 13.12% std::set::count (inline) 133ms 0.22% 8.94% 5852ms 9.49% std::less::operator() (inline) 5809ms 9.42% 18.36% 5809ms 9.42% std::operator< (inline) 298ms 0.48% 18.84% 5542ms 8.99% std::_Rb_tree::_M_insert_ (inline) 0 0% 18.84% 5397ms 8.75% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 18.84% 5259ms 8.53% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0016% 18.85% 5237ms 8.49% AbstractNumericalMethod::ComputeForcesIncludingDamping 4981ms 8.08% 26.92% 4981ms 8.08% std::_Rb_tree_increment 180ms 0.29% 27.22% 4908ms 7.96% operator new 1172ms 1.90% 29.12% 4652ms 7.54% __GI___libc_malloc 0 0% 29.12% 4413ms 7.16% MeshBasedCellPopulation::UpdateNodePairs 9ms 0.015% 29.13% 4335ms 7.03% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 42ms 0.068% 29.20% 4276ms 6.93% std::__new_allocator::allocate (inline) 14ms 0.023% 29.22% 4260ms 6.91% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 29.22% 4255ms 6.90% std::allocator_traits::allocate (inline) 13ms 0.021% 29.24% 4110ms 6.66% std::_Rb_tree::~_Rb_tree (inline) 1433ms 2.32% 31.57% 4094ms 6.64% std::_Rb_tree::_M_erase 0 0% 31.57% 4063ms 6.59% std::set::~set (inline) 122ms 0.2% 31.76% 3858ms 6.26% tetgen::tetgenmesh::insphere_sos 6ms 0.0097% 31.77% 3851ms 6.24% std::set_intersection (inline) 262ms 0.42% 32.20% 3845ms 6.24% std::__set_intersection 1324ms 2.15% 34.35% 3803ms 6.17% std::_Rb_tree::_M_get_insert_unique_pos 1044ms 1.69% 36.04% 3786ms 6.14% __GI___libc_free 3448ms 5.59% 41.63% 3727ms 6.04% tetgen::insphere 0 0% 41.63% 3555ms 5.76% AbstractCellPopulation::WriteResultsToFiles 132ms 0.21% 41.84% 3459ms 5.61% tetgen::tetgenmesh::flip23 0 0% 41.84% 3456ms 5.60% std::_Rb_tree::_M_create_node (inline) 0 0% 41.84% 3422ms 5.55% std::_Rb_tree::_M_get_node (inline) 0 0% 41.84% 3416ms 5.54% std::_Rb_tree::_Alloc_node::operator() (inline) 131ms 0.21% 42.06% 3393ms 5.50% std::__new_allocator::deallocate (inline) 0 0% 42.06% 3384ms 5.49% std::allocator_traits::deallocate (inline) 212ms 0.34% 42.40% 3112ms 5.05% std::_Rb_tree_const_iterator::operator++ (inline) 29ms 0.047% 42.45% 3098ms 5.02% Node::AddElement 2235ms 3.62% 46.07% 3098ms 5.02% _int_malloc 0 0% 46.07% 3046ms 4.94% VertexMesh::~VertexMesh 9ms 0.015% 46.09% 3035ms 4.92% TetrahedralMesh::ImportFromMesher 2860ms 4.64% 50.72% 2860ms 4.64% std::_Rb_tree::_S_right (inline) 1397ms 2.27% 52.99% 2741ms 4.44% _int_free 132ms 0.21% 53.20% 2578ms 4.18% tetgen::tetgenmesh::flip32 71ms 0.12% 53.32% 2445ms 3.96% MutableElement::AddNode 1ms 0.0016% 53.32% 2397ms 3.89% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 191ms 0.31% 53.63% 2384ms 3.87% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 153ms 0.25% 53.88% 2237ms 3.63% Node::~Node 1ms 0.0016% 53.88% 2204ms 3.57% std::_Rb_tree_iterator::operator++ (inline) 0 0% 53.88% 2084ms 3.38% std::_Rb_tree::_M_drop_node (inline) 0 0% 53.88% 2074ms 3.36% std::_Rb_tree::_M_put_node (inline) 153ms 0.25% 54.13% 2012ms 3.26% VertexMesh::Clear 1898ms 3.08% 57.20% 1898ms 3.08% std::_Rb_tree_insert_and_rebalance 211ms 0.34% 57.55% 1842ms 2.99% tetgen::tetgenmesh::enqueueflipface 1488ms 2.41% 59.96% 1579ms 2.56% tetgen::orient3d 1564ms 2.54% 62.50% 1564ms 2.54% Node::GetIndex 5ms 0.0081% 62.50% 1455ms 2.36% Element::Element 29ms 0.047% 62.55% 1359ms 2.20% tetgen::tetgenmesh::locate 31ms 0.05% 62.60% 1341ms 2.17% std::_Vector_base::_M_deallocate (inline) 870ms 1.41% 64.01% 1315ms 2.13% malloc_consolidate 83ms 0.13% 64.15% 1285ms 2.08% TetrahedralMesh::Clear 84ms 0.14% 64.28% 1277ms 2.07% tetgen::tetgenmesh::preciselocate 0 0% 64.28% 1264ms 2.05% std::vector::~vector (inline) 0 0% 64.28% 1172ms 1.90% std::_Vector_base::~_Vector_base (inline) 5ms 0.0081% 64.29% 1127ms 1.83% Element::RegisterWithNodes (inline) 7ms 0.011% 64.30% 1122ms 1.82% _int_free_maybe_consolidate 68ms 0.11% 64.41% 1095ms 1.78% std::vector::_M_realloc_insert 1087ms 1.76% 66.18% 1087ms 1.76% tetgen::tetgenmesh::triface::triface 70ms 0.11% 66.29% 1069ms 1.73% std::map::operator[] 1052ms 1.71% 67.99% 1052ms 1.71% tetgen::tetgenmesh::oppo 780ms 1.26% 69.26% 1009ms 1.64% AbstractElement::GetNodeGlobalIndex 993ms 1.61% 70.87% 993ms 1.61% unlink_chunk 0 0% 70.87% 919ms 1.49% std::_Rb_tree::lower_bound (inline) 0 0% 70.87% 919ms 1.49% std::map::lower_bound (inline) 0 0% 70.87% 917ms 1.49% VoronoiDataWriter::Visit 103ms 0.17% 71.04% 883ms 1.43% std::vector::push_back (inline) 2ms 0.0032% 71.04% 853ms 1.38% VertexMesh::GenerateVerticesFromElementCircumcentres 4ms 0.0065% 71.05% 837ms 1.36% std::_Vector_base::_M_allocate (inline) 795ms 1.29% 72.34% 795ms 1.29% [libchaste_mesh.so] 310ms 0.5% 72.84% 788ms 1.28% tetgen::tetgenmesh::sym 0 0% 72.84% 750ms 1.22% TetrahedralMesh::RefreshJacobianCachedData 0 0% 72.84% 733ms 1.19% AbstractTwoBodyInteractionForce::AddForceContribution 728ms 1.18% 74.02% 728ms 1.18% tetgen::tetgenmesh::triface::operator= 17ms 0.028% 74.05% 697ms 1.13% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 7ms 0.011% 74.06% 684ms 1.11% AbstractTetrahedralElement::CalculateInverseJacobian 14ms 0.023% 74.08% 624ms 1.01% AbstractTetrahedralElement::CalculateJacobian 40ms 0.065% 74.15% 624ms 1.01% tetgen::tetgenmesh::queue::push 223ms 0.36% 74.51% 621ms 1.01% tetgen::tetgenmesh::bond 20ms 0.032% 74.54% 616ms 1% boost::numeric::ublas::vector_assign (inline) 11ms 0.018% 74.56% 602ms 0.98% boost::numeric::ublas::c_vector::c_vector (inline) 341ms 0.55% 75.11% 602ms 0.98% tetgen::tetgenmesh::fnextself 36ms 0.058% 75.17% 598ms 0.97% __atan2 412ms 0.67% 75.84% 584ms 0.95% tetgen::tetgenmesh::link::add 59ms 0.096% 75.93% 581ms 0.94% tetgen::tetgenmesh::enext2fnext 0 0% 75.93% 580ms 0.94% std::set::find (inline) 54ms 0.088% 76.02% 578ms 0.94% tetgen::tetgenmesh::enextfnext 572ms 0.93% 76.95% 572ms 0.93% Node::rGetLocation 562ms 0.91% 77.86% 562ms 0.91% std::vector::size (inline) 426ms 0.69% 78.55% 555ms 0.9% __ieee754_atan2_fma 0 0% 78.55% 542ms 0.88% boost::numeric::ublas::inner_prod (inline) 1ms 0.0016% 78.55% 539ms 0.87% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 54ms 0.088% 78.64% 538ms 0.87% boost::numeric::ublas::vector_scalar_binary::evaluate 217ms 0.35% 78.99% 534ms 0.87% AbstractElement::GetNodeLocation 507ms 0.82% 79.81% 507ms 0.82% tetgen::tetgenmesh::org 500ms 0.81% 80.62% 500ms 0.81% AbstractElement::IsDeleted 489ms 0.79% 81.42% 489ms 0.79% tetgen::tetgenmesh::decode 0 0% 81.42% 481ms 0.78% std::insert_iterator::operator= (inline) 54ms 0.088% 81.50% 445ms 0.72% AbstractTetrahedralElement::RefreshJacobian 18ms 0.029% 81.53% 439ms 0.71% Element::CalculateCircumsphere 6ms 0.0097% 81.54% 436ms 0.71% boost::numeric::ublas::c_vector::operator= (inline) 25ms 0.041% 81.58% 433ms 0.7% std::_Rb_tree_iterator::operator-- (inline) 0 0% 81.58% 417ms 0.68% std::_Rb_tree::_M_insert_unique_ (inline) 3ms 0.0049% 81.59% 416ms 0.67% CellPropertyCollection::GetPropertiesType (inline) 108ms 0.18% 81.76% 414ms 0.67% __dynamic_cast 15ms 0.024% 81.79% 409ms 0.66% VertexMesh::CalculateUnitNormalToFaceWithArea 5ms 0.0081% 81.80% 406ms 0.66% Cell::GetCellId 192ms 0.31% 82.11% 405ms 0.66% boost::numeric::ublas::vector_inner_prod::apply (inline) 200ms 0.32% 82.43% 400ms 0.65% AbstractTetrahedralMesh::GetElement 390ms 0.63% 83.06% 390ms 0.63% tetgen::tetgenmesh::pointmark 0 0% 83.06% 386ms 0.63% VertexMeshWriter::WriteVtkUsingMesh 384ms 0.62% 83.69% 384ms 0.62% boost::numeric::ublas::c_vector::operator() 382ms 0.62% 84.31% 382ms 0.62% tetgen::tetgenmesh::encode 378ms 0.61% 84.92% 378ms 0.61% std::_Rb_tree_decrement 104ms 0.17% 85.09% 377ms 0.61% boost::numeric::ublas::indexing_vector_assign 2ms 0.0032% 85.09% 351ms 0.57% AbstractCellProperty::IsSubType (inline) 0 0% 85.09% 349ms 0.57% tcache_get (inline) 349ms 0.57% 85.66% 349ms 0.57% tcache_get_n (inline) 6ms 0.0097% 85.67% 346ms 0.56% VertexElement::~VertexElement 11ms 0.018% 85.68% 336ms 0.54% std::vector::insert (inline) 333ms 0.54% 86.22% 333ms 0.54% tetgen::tetgenmesh::face::face 51ms 0.083% 86.31% 332ms 0.54% tetgen::tetgenmesh::queue::pop 4ms 0.0065% 86.31% 324ms 0.53% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 86.31% 314ms 0.51% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 96ms 0.16% 86.47% 310ms 0.5% Inverse