File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 57249ms, 86.85% of 65916ms total Dropped 898 nodes (cum <= 329.58ms) flat flat% sum% cum cum% 0 0% 0% 65859ms 99.91% __libc_start_call_main 0 0% 0% 65859ms 99.91% __libc_start_main_impl 0 0% 0% 65859ms 99.91% _start 0 0% 0% 65841ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 65841ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 65841ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 65841ms 99.89% main 0 0% 0% 65797ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 65797ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 65797ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 65520ms 99.40% AbstractCellBasedSimulation::Solve 0 0% 0% 55146ms 83.66% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 55098ms 83.59% MeshBasedCellPopulation::Update 0 0% 0% 30319ms 46.00% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 30317ms 45.99% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 258ms 0.39% 0.39% 26940ms 40.87% VertexMesh::VertexMesh 0 0% 0.39% 20334ms 30.85% MutableMesh::ReMesh 0 0% 0.39% 16172ms 24.53% tetgen::tetrahedralize 2ms 0.003% 0.39% 16017ms 24.30% tetgen::tetgenmesh::delaunizevertices 11ms 0.017% 0.41% 16010ms 24.29% tetgen::tetgenmesh::incrflipdelaunay 496ms 0.75% 1.16% 14328ms 21.74% tetgen::tetgenmesh::lawson 629ms 0.95% 2.12% 13677ms 20.75% TetrahedralMesh::EdgeIterator::operator++ 39ms 0.059% 2.18% 10476ms 15.89% std::set::insert (inline) 3190ms 4.84% 7.02% 10392ms 15.77% std::_Rb_tree::_M_lower_bound (inline) 355ms 0.54% 7.56% 10071ms 15.28% VertexElement::AddFace 301ms 0.46% 8.01% 10025ms 15.21% std::_Rb_tree::_M_insert_unique 260ms 0.39% 8.41% 9714ms 14.74% std::_Rb_tree::find (inline) 0 0% 8.41% 9118ms 13.83% std::set::count (inline) 125ms 0.19% 8.60% 6894ms 10.46% std::less::operator() (inline) 6839ms 10.38% 18.97% 6839ms 10.38% std::operator< (inline) 6038ms 9.16% 28.13% 6038ms 9.16% std::_Rb_tree_increment 1ms 0.0015% 28.13% 5933ms 9.00% OffLatticeSimulation::UpdateCellLocationsAndTopology 327ms 0.5% 28.63% 5932ms 9.00% std::_Rb_tree::_M_insert_ (inline) 1ms 0.0015% 28.63% 5770ms 8.75% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 28.63% 5749ms 8.72% AbstractNumericalMethod::ComputeForcesIncludingDamping 147ms 0.22% 28.85% 5346ms 8.11% operator new 1228ms 1.86% 30.72% 5135ms 7.79% __GI___libc_malloc 1ms 0.0015% 30.72% 4809ms 7.30% MeshBasedCellPopulation::UpdateNodePairs 8ms 0.012% 30.73% 4783ms 7.26% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 17ms 0.026% 30.76% 4646ms 7.05% MeshBasedCellPopulation::SpringIterator::operator++ 39ms 0.059% 30.81% 4605ms 6.99% std::__new_allocator::allocate (inline) 0 0% 30.81% 4589ms 6.96% std::allocator_traits::allocate (inline) 0 0% 30.81% 4287ms 6.50% AbstractCellPopulation::WriteResultsToFiles 8ms 0.012% 30.83% 4232ms 6.42% std::_Rb_tree::~_Rb_tree (inline) 1547ms 2.35% 33.17% 4223ms 6.41% std::_Rb_tree::_M_erase 6ms 0.0091% 33.18% 4198ms 6.37% std::set_intersection (inline) 261ms 0.4% 33.58% 4192ms 6.36% std::__set_intersection 0 0% 33.58% 4189ms 6.36% std::set::~set (inline) 1306ms 1.98% 35.56% 4054ms 6.15% std::_Rb_tree::_M_get_insert_unique_pos 1115ms 1.69% 37.25% 4053ms 6.15% __GI___libc_free 125ms 0.19% 37.44% 3829ms 5.81% tetgen::tetgenmesh::insphere_sos 0 0% 37.44% 3759ms 5.70% std::_Rb_tree::_M_create_node (inline) 0 0% 37.44% 3723ms 5.65% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 37.44% 3723ms 5.65% std::_Rb_tree::_M_get_node (inline) 149ms 0.23% 37.67% 3707ms 5.62% tetgen::tetgenmesh::flip23 3417ms 5.18% 42.85% 3692ms 5.60% tetgen::insphere 47ms 0.071% 42.92% 3617ms 5.49% Node::AddElement 150ms 0.23% 43.15% 3584ms 5.44% std::__new_allocator::deallocate (inline) 0 0% 43.15% 3569ms 5.41% std::allocator_traits::deallocate (inline) 2538ms 3.85% 47.00% 3511ms 5.33% _int_malloc 194ms 0.29% 47.30% 3494ms 5.30% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.0015% 47.30% 3399ms 5.16% VertexMesh::~VertexMesh 3381ms 5.13% 52.43% 3381ms 5.13% std::_Rb_tree::_S_right (inline) 11ms 0.017% 52.44% 3335ms 5.06% TetrahedralMesh::ImportFromMesher 204ms 0.31% 52.75% 3074ms 4.66% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 4ms 0.0061% 52.76% 2999ms 4.55% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 1390ms 2.11% 54.87% 2934ms 4.45% _int_free 0 0% 54.87% 2881ms 4.37% std::_Rb_tree_iterator::operator++ (inline) 67ms 0.1% 54.97% 2764ms 4.19% MutableElement::AddNode 144ms 0.22% 55.19% 2601ms 3.95% tetgen::tetgenmesh::flip32 180ms 0.27% 55.46% 2391ms 3.63% Node::~Node 163ms 0.25% 55.71% 2211ms 3.35% VertexMesh::Clear 0 0% 55.71% 2127ms 3.23% std::_Rb_tree::_M_drop_node (inline) 0 0% 55.71% 2115ms 3.21% std::_Rb_tree::_M_put_node (inline) 221ms 0.34% 56.04% 2009ms 3.05% tetgen::tetgenmesh::enqueueflipface 1975ms 3.00% 59.04% 1975ms 3.00% std::_Rb_tree_insert_and_rebalance 1896ms 2.88% 61.92% 1896ms 2.88% Node::GetIndex 8ms 0.012% 61.93% 1686ms 2.56% Element::Element 1567ms 2.38% 64.30% 1625ms 2.47% tetgen::orient3d 951ms 1.44% 65.75% 1517ms 2.30% malloc_consolidate 35ms 0.053% 65.80% 1489ms 2.26% std::_Vector_base::_M_deallocate (inline) 0 0% 65.80% 1429ms 2.17% std::vector::~vector (inline) 40ms 0.061% 65.86% 1382ms 2.10% tetgen::tetgenmesh::locate 106ms 0.16% 66.02% 1336ms 2.03% TetrahedralMesh::Clear 6ms 0.0091% 66.03% 1327ms 2.01% Element::RegisterWithNodes (inline) 1ms 0.0015% 66.03% 1322ms 2.01% std::_Vector_base::~_Vector_base (inline) 8ms 0.012% 66.04% 1305ms 1.98% _int_free_maybe_consolidate 72ms 0.11% 66.15% 1298ms 1.97% std::map::operator[] 88ms 0.13% 66.29% 1292ms 1.96% tetgen::tetgenmesh::preciselocate 1194ms 1.81% 68.10% 1194ms 1.81% unlink_chunk 0 0% 68.10% 1139ms 1.73% std::_Rb_tree::lower_bound (inline) 0 0% 68.10% 1139ms 1.73% std::map::lower_bound (inline) 1133ms 1.72% 69.82% 1133ms 1.72% tetgen::tetgenmesh::triface::triface 76ms 0.12% 69.93% 1123ms 1.70% std::vector::_M_realloc_insert 0 0% 69.93% 1031ms 1.56% VoronoiDataWriter::Visit 1025ms 1.56% 71.49% 1025ms 1.56% tetgen::tetgenmesh::oppo 806ms 1.22% 72.71% 1015ms 1.54% AbstractElement::GetNodeGlobalIndex 5ms 0.0076% 72.72% 965ms 1.46% VertexMesh::GenerateVerticesFromElementCircumcentres 154ms 0.23% 72.95% 962ms 1.46% std::vector::push_back (inline) 4ms 0.0061% 72.96% 870ms 1.32% std::_Vector_base::_M_allocate (inline) 801ms 1.22% 74.17% 801ms 1.22% [libchaste_mesh.so] 0 0% 74.17% 799ms 1.21% TetrahedralMesh::RefreshJacobianCachedData 268ms 0.41% 74.58% 768ms 1.17% tetgen::tetgenmesh::sym 0 0% 74.58% 748ms 1.13% AbstractTwoBodyInteractionForce::AddForceContribution 70ms 0.11% 74.69% 746ms 1.13% tetgen::tetgenmesh::enextfnext 11ms 0.017% 74.70% 730ms 1.11% AbstractTetrahedralElement::CalculateInverseJacobian 729ms 1.11% 75.81% 729ms 1.11% tetgen::tetgenmesh::triface::operator= 403ms 0.61% 76.42% 715ms 1.08% tetgen::tetgenmesh::fnextself 315ms 0.48% 76.90% 711ms 1.08% AbstractElement::GetNodeLocation 15ms 0.023% 76.92% 701ms 1.06% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 17ms 0.026% 76.95% 695ms 1.05% AbstractTetrahedralElement::CalculateJacobian 46ms 0.07% 77.02% 676ms 1.03% tetgen::tetgenmesh::queue::push 385ms 0.58% 77.60% 630ms 0.96% tetgen::tetgenmesh::link::add 54ms 0.082% 77.68% 613ms 0.93% tetgen::tetgenmesh::enext2fnext 44ms 0.067% 77.75% 611ms 0.93% __atan2 601ms 0.91% 78.66% 601ms 0.91% Node::rGetLocation 234ms 0.35% 79.02% 592ms 0.9% tetgen::tetgenmesh::bond 18ms 0.027% 79.04% 590ms 0.9% boost::numeric::ublas::vector_assign (inline) 0 0% 79.04% 590ms 0.9% std::set::find (inline) 579ms 0.88% 79.92% 579ms 0.88% std::vector::size (inline) 8ms 0.012% 79.93% 575ms 0.87% boost::numeric::ublas::c_vector::c_vector (inline) 563ms 0.85% 80.79% 563ms 0.85% AbstractElement::IsDeleted 432ms 0.66% 81.44% 557ms 0.85% __ieee754_atan2_fma 528ms 0.8% 82.24% 528ms 0.8% tetgen::tetgenmesh::decode 0 0% 82.24% 515ms 0.78% boost::numeric::ublas::inner_prod (inline) 1ms 0.0015% 82.25% 514ms 0.78% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 45ms 0.068% 82.31% 513ms 0.78% boost::numeric::ublas::vector_scalar_binary::evaluate 35ms 0.053% 82.37% 501ms 0.76% AbstractTetrahedralElement::RefreshJacobian 13ms 0.02% 82.39% 497ms 0.75% Element::CalculateCircumsphere 0 0% 82.39% 475ms 0.72% std::insert_iterator::operator= (inline) 450ms 0.68% 83.07% 450ms 0.68% tetgen::tetgenmesh::org 199ms 0.3% 83.37% 424ms 0.64% AbstractTetrahedralMesh::GetElement 12ms 0.018% 83.39% 423ms 0.64% VertexMesh::CalculateUnitNormalToFaceWithArea 184ms 0.28% 83.67% 414ms 0.63% boost::numeric::ublas::vector_inner_prod::apply (inline) 4ms 0.0061% 83.67% 413ms 0.63% CellPropertyCollection::GetPropertiesType (inline) 0 0% 83.67% 409ms 0.62% std::_Rb_tree::_M_insert_unique_ (inline) 126ms 0.19% 83.87% 402ms 0.61% __dynamic_cast 393ms 0.6% 84.46% 393ms 0.6% tetgen::tetgenmesh::pointmark 392ms 0.59% 85.06% 392ms 0.59% boost::numeric::ublas::c_vector::operator() 0 0% 85.06% 388ms 0.59% VertexMeshWriter::WriteVtkUsingMesh 3ms 0.0046% 85.06% 384ms 0.58% Cell::GetCellId 4ms 0.0061% 85.07% 381ms 0.58% boost::numeric::ublas::c_vector::operator= (inline) 21ms 0.032% 85.10% 378ms 0.57% std::_Rb_tree_iterator::operator-- (inline) 10ms 0.015% 85.11% 369ms 0.56% VertexElement::~VertexElement 103ms 0.16% 85.27% 367ms 0.56% boost::numeric::ublas::indexing_vector_assign 6ms 0.0091% 85.28% 353ms 0.54% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 85.28% 349ms 0.53% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 85.28% 349ms 0.53% tcache_get (inline) 349ms 0.53% 85.81% 349ms 0.53% tcache_get_n (inline) 341ms 0.52% 86.33% 341ms 0.52% tetgen::tetgenmesh::encode 14ms 0.021% 86.35% 336ms 0.51% std::vector::insert (inline) 332ms 0.5% 86.85% 332ms 0.5% std::_Rb_tree_decrement