File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 51664ms, 87.34% of 59155ms total Dropped 857 nodes (cum <= 295.77ms) flat flat% sum% cum cum% 0 0% 0% 59099ms 99.91% __libc_start_call_main 0 0% 0% 59099ms 99.91% __libc_start_main_impl 0 0% 0% 59099ms 99.91% _start 0 0% 0% 59085ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 59085ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 59085ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 59085ms 99.88% main 0 0% 0% 59053ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 59053ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 59053ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 58801ms 99.40% AbstractCellBasedSimulation::Solve 0 0% 0% 48396ms 81.81% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 48349ms 81.73% MeshBasedCellPopulation::Update 0 0% 0% 27433ms 46.37% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 27433ms 46.37% MeshBasedCellPopulation::TessellateIfNeeded 185ms 0.31% 0.31% 24253ms 41.00% VertexMesh::VertexMesh 0 0% 0.31% 16836ms 28.46% MutableMesh::ReMesh 0 0% 0.31% 12802ms 21.64% tetgen::tetrahedralize 3ms 0.0051% 0.32% 12663ms 21.41% tetgen::tetgenmesh::delaunizevertices 4ms 0.0068% 0.32% 12658ms 21.40% tetgen::tetgenmesh::incrflipdelaunay 560ms 0.95% 1.27% 12463ms 21.07% TetrahedralMesh::EdgeIterator::operator++ 565ms 0.96% 2.23% 11303ms 19.11% tetgen::tetgenmesh::lawson 3117ms 5.27% 7.50% 10167ms 17.19% std::_Rb_tree::_M_lower_bound (inline) 34ms 0.057% 7.55% 9564ms 16.17% std::set::insert (inline) 217ms 0.37% 7.92% 9416ms 15.92% std::_Rb_tree::find (inline) 351ms 0.59% 8.51% 9108ms 15.40% VertexElement::AddFace 239ms 0.4% 8.92% 9075ms 15.34% std::_Rb_tree::_M_insert_unique 0 0% 8.92% 8828ms 14.92% std::set::count (inline) 119ms 0.2% 9.12% 6672ms 11.28% std::less::operator() (inline) 6594ms 11.15% 20.27% 6594ms 11.15% std::operator< (inline) 5966ms 10.09% 30.35% 5966ms 10.09% std::_Rb_tree_increment 0 0% 30.35% 5479ms 9.26% OffLatticeSimulation::UpdateCellLocationsAndTopology 251ms 0.42% 30.78% 5360ms 9.06% std::_Rb_tree::_M_insert_ (inline) 0 0% 30.78% 5346ms 9.04% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0017% 30.78% 5312ms 8.98% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 30.78% 4794ms 8.10% AbstractCellPopulation::WriteResultsToFiles 187ms 0.32% 31.09% 4766ms 8.06% operator new 1026ms 1.73% 32.83% 4509ms 7.62% __GI___libc_malloc 0 0% 32.83% 4405ms 7.45% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.0068% 32.83% 4379ms 7.40% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 17ms 0.029% 32.86% 4261ms 7.20% MeshBasedCellPopulation::SpringIterator::operator++ 39ms 0.066% 32.93% 4075ms 6.89% std::__new_allocator::allocate (inline) 0 0% 32.93% 4056ms 6.86% std::allocator_traits::allocate (inline) 9ms 0.015% 32.94% 4049ms 6.84% std::_Rb_tree::~_Rb_tree (inline) 1575ms 2.66% 35.61% 4038ms 6.83% std::_Rb_tree::_M_erase 0 0% 35.61% 4002ms 6.77% std::set::~set (inline) 1190ms 2.01% 37.62% 3790ms 6.41% std::_Rb_tree::_M_get_insert_unique_pos 258ms 0.44% 38.05% 3651ms 6.17% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1005ms 1.70% 39.75% 3584ms 6.06% __GI___libc_free 3ms 0.0051% 39.76% 3468ms 5.86% std::set_intersection (inline) 226ms 0.38% 40.14% 3465ms 5.86% std::__set_intersection 123ms 0.21% 40.35% 3434ms 5.81% tetgen::tetgenmesh::insphere_sos 4ms 0.0068% 40.35% 3417ms 5.78% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 40.35% 3409ms 5.76% std::_Rb_tree_iterator::operator++ (inline) 30ms 0.051% 40.41% 3400ms 5.75% Node::AddElement 3323ms 5.62% 46.02% 3323ms 5.62% std::_Rb_tree::_S_right (inline) 3011ms 5.09% 51.11% 3304ms 5.59% tetgen::insphere 0 0% 51.11% 3251ms 5.50% std::_Rb_tree::_M_create_node (inline) 9ms 0.015% 51.13% 3245ms 5.49% TetrahedralMesh::ImportFromMesher 132ms 0.22% 51.35% 3236ms 5.47% std::__new_allocator::deallocate (inline) 0 0% 51.35% 3221ms 5.45% std::_Rb_tree::_M_get_node (inline) 0 0% 51.35% 3218ms 5.44% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 51.35% 3216ms 5.44% std::allocator_traits::deallocate (inline) 0 0% 51.35% 3200ms 5.41% VertexMesh::~VertexMesh 2330ms 3.94% 55.29% 3101ms 5.24% _int_malloc 160ms 0.27% 55.56% 2814ms 4.76% std::_Rb_tree_const_iterator::operator++ (inline) 191ms 0.32% 55.88% 2748ms 4.65% tetgen::tetgenmesh::flip23 1159ms 1.96% 57.84% 2578ms 4.36% _int_free 70ms 0.12% 57.96% 2355ms 3.98% MutableElement::AddNode 115ms 0.19% 58.16% 2233ms 3.77% Node::~Node 170ms 0.29% 58.44% 2106ms 3.56% VertexMesh::Clear 1949ms 3.29% 61.74% 1949ms 3.29% std::_Rb_tree_insert_and_rebalance 142ms 0.24% 61.98% 1934ms 3.27% tetgen::tetgenmesh::flip32 0 0% 61.98% 1874ms 3.17% std::_Rb_tree::_M_drop_node (inline) 0 0% 61.98% 1867ms 3.16% std::_Rb_tree::_M_put_node (inline) 5ms 0.0085% 61.99% 1810ms 3.06% Element::Element 1636ms 2.77% 64.75% 1636ms 2.77% Node::GetIndex 4ms 0.0068% 64.76% 1483ms 2.51% Element::RegisterWithNodes (inline) 851ms 1.44% 66.20% 1388ms 2.35% malloc_consolidate 14ms 0.024% 66.22% 1363ms 2.30% std::_Vector_base::_M_deallocate (inline) 188ms 0.32% 66.54% 1347ms 2.28% tetgen::tetgenmesh::enqueueflipface 1265ms 2.14% 68.68% 1335ms 2.26% tetgen::orient3d 0 0% 68.68% 1312ms 2.22% std::vector::~vector (inline) 58ms 0.098% 68.78% 1281ms 2.17% std::map::operator[] 7ms 0.012% 68.79% 1204ms 2.04% _int_free_maybe_consolidate 0 0% 68.79% 1192ms 2.02% std::_Vector_base::~_Vector_base (inline) 0 0% 68.79% 1161ms 1.96% std::_Rb_tree::lower_bound (inline) 0 0% 68.79% 1161ms 1.96% std::map::lower_bound (inline) 40ms 0.068% 68.85% 1147ms 1.94% tetgen::tetgenmesh::locate 0 0% 68.85% 1143ms 1.93% VoronoiDataWriter::Visit 151ms 0.26% 69.11% 1139ms 1.93% TetrahedralMesh::Clear 89ms 0.15% 69.26% 1064ms 1.80% tetgen::tetgenmesh::preciselocate 42ms 0.071% 69.33% 1046ms 1.77% std::vector::_M_realloc_insert 985ms 1.67% 71.00% 985ms 1.67% unlink_chunk 979ms 1.65% 72.65% 979ms 1.65% tetgen::tetgenmesh::triface::triface 5ms 0.0085% 72.66% 953ms 1.61% VertexMesh::GenerateVerticesFromElementCircumcentres 106ms 0.18% 72.84% 864ms 1.46% std::vector::push_back (inline) 6ms 0.01% 72.85% 841ms 1.42% std::_Vector_base::_M_allocate (inline) 424ms 0.72% 73.57% 831ms 1.40% tetgen::tetgenmesh::fnextself 0 0% 73.57% 769ms 1.30% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.0034% 73.57% 739ms 1.25% AbstractTwoBodyInteractionForce::AddForceContribution 715ms 1.21% 74.78% 715ms 1.21% tetgen::tetgenmesh::oppo 8ms 0.014% 74.79% 705ms 1.19% AbstractTetrahedralElement::CalculateInverseJacobian 20ms 0.034% 74.83% 703ms 1.19% boost::numeric::ublas::vector_assign (inline) 14ms 0.024% 74.85% 690ms 1.17% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 540ms 0.91% 75.76% 667ms 1.13% AbstractElement::GetNodeGlobalIndex 13ms 0.022% 75.78% 655ms 1.11% AbstractTetrahedralElement::CalculateJacobian 14ms 0.024% 75.81% 655ms 1.11% boost::numeric::ublas::c_vector::c_vector (inline) 647ms 1.09% 76.90% 647ms 1.09% [libchaste_mesh.so] 252ms 0.43% 77.33% 640ms 1.08% AbstractElement::GetNodeLocation 51ms 0.086% 77.41% 604ms 1.02% __atan2 0 0% 77.41% 583ms 0.99% std::set::find (inline) 575ms 0.97% 78.39% 575ms 0.97% tetgen::tetgenmesh::triface::operator= 571ms 0.97% 79.35% 571ms 0.97% Node::rGetLocation 447ms 0.76% 80.11% 552ms 0.93% __ieee754_atan2_fma 45ms 0.076% 80.18% 540ms 0.91% tetgen::tetgenmesh::enextfnext 53ms 0.09% 80.27% 517ms 0.87% tetgen::tetgenmesh::enext2fnext 19ms 0.032% 80.30% 506ms 0.86% Element::CalculateCircumsphere 50ms 0.085% 80.39% 495ms 0.84% AbstractTetrahedralElement::RefreshJacobian 0 0% 80.39% 480ms 0.81% std::insert_iterator::operator= (inline) 0 0% 80.39% 476ms 0.8% boost::numeric::ublas::inner_prod (inline) 7ms 0.012% 80.40% 474ms 0.8% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 28ms 0.047% 80.45% 467ms 0.79% boost::numeric::ublas::vector_scalar_binary::evaluate 133ms 0.22% 80.67% 462ms 0.78% boost::numeric::ublas::indexing_vector_assign 286ms 0.48% 81.16% 444ms 0.75% tetgen::tetgenmesh::sym 443ms 0.75% 81.91% 443ms 0.75% std::vector::size (inline) 15ms 0.025% 81.93% 425ms 0.72% tetgen::tetgenmesh::queue::push 0 0% 81.93% 423ms 0.72% std::_Rb_tree::_M_insert_unique_ (inline) 417ms 0.7% 82.64% 417ms 0.7% boost::numeric::ublas::c_vector::operator() 22ms 0.037% 82.67% 416ms 0.7% VertexMesh::CalculateUnitNormalToFaceWithArea 8ms 0.014% 82.69% 410ms 0.69% boost::numeric::ublas::c_vector::operator= (inline) 317ms 0.54% 83.22% 407ms 0.69% tetgen::tetgenmesh::link::add 5ms 0.0085% 83.23% 397ms 0.67% CellPropertyCollection::GetPropertiesType (inline) 211ms 0.36% 83.59% 395ms 0.67% AbstractTetrahedralMesh::GetElement 88ms 0.15% 83.74% 393ms 0.66% __dynamic_cast 172ms 0.29% 84.03% 393ms 0.66% boost::numeric::ublas::vector_inner_prod::apply (inline) 17ms 0.029% 84.06% 384ms 0.65% std::_Rb_tree_iterator::operator-- (inline) 0 0% 84.06% 380ms 0.64% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.0017% 84.06% 373ms 0.63% Cell::GetCellId 357ms 0.6% 84.66% 357ms 0.6% tetgen::tetgenmesh::org 355ms 0.6% 85.26% 355ms 0.6% AbstractElement::IsDeleted 257ms 0.43% 85.70% 350ms 0.59% tetgen::tetgenmesh::bond 0 0% 85.70% 349ms 0.59% tcache_get (inline) 349ms 0.59% 86.29% 349ms 0.59% tcache_get_n (inline) 346ms 0.58% 86.87% 346ms 0.58% std::_Rb_tree_decrement 73ms 0.12% 86.99% 331ms 0.56% tetgen::tetgenmesh::queue::pop 1ms 0.0017% 87.00% 326ms 0.55% AbstractCellProperty::IsSubType (inline) 7ms 0.012% 87.01% 325ms 0.55% AbstractTetrahedralElement::AbstractTetrahedralElement 127ms 0.21% 87.22% 318ms 0.54% Inverse 4ms 0.0068% 87.23% 314ms 0.53% VertexElement::~VertexElement 0 0% 87.23% 312ms 0.53% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 13ms 0.022% 87.25% 308ms 0.52% std::vector::insert (inline) 51ms 0.086% 87.34% 304ms 0.51% boost::numeric::ublas::vector_reference::operator() (inline)