File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 56879ms, 87.84% of 64756ms total Dropped 855 nodes (cum <= 323.78ms) flat flat% sum% cum cum% 1ms 0.0015% 0.0015% 64694ms 99.90% _start 0 0% 0.0015% 64693ms 99.90% __libc_start_call_main 0 0% 0.0015% 64693ms 99.90% __libc_start_main_impl 0 0% 0.0015% 64677ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0.0015% 64677ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0.0015% 64677ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0.0015% 64677ms 99.88% main 0 0% 0.0015% 64640ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0.0015% 64640ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0.0015% 64640ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0.0015% 64374ms 99.41% AbstractCellBasedSimulation::Solve 0 0% 0.0015% 53999ms 83.39% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0015% 53951ms 83.31% MeshBasedCellPopulation::Update 0 0% 0.0015% 31872ms 49.22% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0.0015% 31872ms 49.22% MeshBasedCellPopulation::TessellateIfNeeded 216ms 0.33% 0.34% 27802ms 42.93% VertexMesh::VertexMesh 0 0% 0.34% 17842ms 27.55% MutableMesh::ReMesh 0 0% 0.34% 13147ms 20.30% tetgen::tetrahedralize 3ms 0.0046% 0.34% 13019ms 20.10% tetgen::tetgenmesh::delaunizevertices 9ms 0.014% 0.35% 13012ms 20.09% tetgen::tetgenmesh::incrflipdelaunay 578ms 0.89% 1.25% 12975ms 20.04% TetrahedralMesh::EdgeIterator::operator++ 575ms 0.89% 2.13% 11624ms 17.95% tetgen::tetgenmesh::lawson 25ms 0.039% 2.17% 10710ms 16.54% std::set::insert (inline) 194ms 0.3% 2.47% 10217ms 15.78% std::_Rb_tree::_M_insert_unique 2941ms 4.54% 7.01% 10027ms 15.48% std::_Rb_tree::_M_lower_bound (inline) 384ms 0.59% 7.61% 9491ms 14.66% VertexElement::AddFace 229ms 0.35% 7.96% 9152ms 14.13% std::_Rb_tree::find (inline) 0 0% 7.96% 8636ms 13.34% std::set::count (inline) 6833ms 10.55% 18.51% 6833ms 10.55% std::_Rb_tree_increment 114ms 0.18% 18.69% 6677ms 10.31% std::less::operator() (inline) 6635ms 10.25% 28.93% 6635ms 10.25% std::operator< (inline) 256ms 0.4% 29.33% 5912ms 9.13% std::_Rb_tree::_M_insert_ (inline) 0 0% 29.33% 5636ms 8.70% OffLatticeSimulation::UpdateCellLocationsAndTopology 199ms 0.31% 29.64% 5586ms 8.63% operator new 1ms 0.0015% 29.64% 5490ms 8.48% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0031% 29.64% 5463ms 8.44% AbstractNumericalMethod::ComputeForcesIncludingDamping 997ms 1.54% 31.18% 5319ms 8.21% __GI___libc_malloc 1ms 0.0015% 31.18% 4762ms 7.35% std::set_intersection (inline) 295ms 0.46% 31.64% 4761ms 7.35% std::__set_intersection 11ms 0.017% 31.66% 4686ms 7.24% std::_Rb_tree::~_Rb_tree (inline) 1942ms 3.00% 34.65% 4674ms 7.22% std::_Rb_tree::_M_erase 0 0% 34.65% 4625ms 7.14% std::set::~set (inline) 40ms 0.062% 34.72% 4601ms 7.11% std::__new_allocator::allocate (inline) 0 0% 34.72% 4599ms 7.10% AbstractCellPopulation::WriteResultsToFiles 0 0% 34.72% 4588ms 7.09% std::allocator_traits::allocate (inline) 2ms 0.0031% 34.72% 4563ms 7.05% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.0046% 34.72% 4523ms 6.98% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1249ms 1.93% 36.65% 4435ms 6.85% std::_Rb_tree::_M_get_insert_unique_pos 20ms 0.031% 36.68% 4385ms 6.77% MeshBasedCellPopulation::SpringIterator::operator++ 22ms 0.034% 36.72% 4283ms 6.61% Node::AddElement 1249ms 1.93% 38.65% 4223ms 6.52% __GI___libc_free 0 0% 38.65% 4101ms 6.33% VertexMesh::~VertexMesh 4091ms 6.32% 44.96% 4091ms 6.32% std::_Rb_tree::_S_right (inline) 2914ms 4.50% 49.46% 3995ms 6.17% _int_malloc 206ms 0.32% 49.78% 3979ms 6.14% std::_Rb_tree_const_iterator::operator++ (inline) 5ms 0.0077% 49.79% 3795ms 5.86% TetrahedralMesh::ImportFromMesher 116ms 0.18% 49.97% 3687ms 5.69% std::__new_allocator::deallocate (inline) 0 0% 49.97% 3679ms 5.68% std::_Rb_tree::_M_create_node (inline) 0 0% 49.97% 3669ms 5.67% std::allocator_traits::deallocate (inline) 0 0% 49.97% 3649ms 5.63% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 49.97% 3634ms 5.61% std::_Rb_tree::_M_get_node (inline) 98ms 0.15% 50.12% 3512ms 5.42% tetgen::tetgenmesh::insphere_sos 3098ms 4.78% 54.90% 3403ms 5.26% tetgen::insphere 239ms 0.37% 55.27% 3369ms 5.20% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 78ms 0.12% 55.39% 3214ms 4.96% MutableElement::AddNode 5ms 0.0077% 55.40% 3190ms 4.93% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 55.40% 3150ms 4.86% std::_Rb_tree_iterator::operator++ (inline) 1148ms 1.77% 57.17% 2973ms 4.59% _int_free 214ms 0.33% 57.51% 2829ms 4.37% Node::~Node 190ms 0.29% 57.80% 2705ms 4.18% tetgen::tetgenmesh::flip23 232ms 0.36% 58.16% 2611ms 4.03% VertexMesh::Clear 2102ms 3.25% 61.40% 2102ms 3.25% std::_Rb_tree_insert_and_rebalance 165ms 0.25% 61.66% 2053ms 3.17% tetgen::tetgenmesh::flip32 0 0% 61.66% 1932ms 2.98% std::_Rb_tree::_M_drop_node (inline) 0 0% 61.66% 1918ms 2.96% std::_Rb_tree::_M_put_node (inline) 4ms 0.0062% 61.66% 1894ms 2.92% Element::Element 1226ms 1.89% 63.56% 1870ms 2.89% malloc_consolidate 1843ms 2.85% 66.40% 1843ms 2.85% Node::GetIndex 18ms 0.028% 66.43% 1769ms 2.73% std::_Vector_base::_M_deallocate (inline) 0 0% 66.43% 1647ms 2.54% std::vector::~vector (inline) 3ms 0.0046% 66.44% 1592ms 2.46% _int_free_maybe_consolidate 1ms 0.0015% 66.44% 1590ms 2.46% std::_Vector_base::~_Vector_base (inline) 1ms 0.0015% 66.44% 1551ms 2.40% Element::RegisterWithNodes (inline) 233ms 0.36% 66.80% 1521ms 2.35% TetrahedralMesh::Clear 1360ms 2.10% 68.90% 1429ms 2.21% tetgen::orient3d 1382ms 2.13% 71.03% 1382ms 2.13% unlink_chunk 187ms 0.29% 71.32% 1363ms 2.10% tetgen::tetgenmesh::enqueueflipface 54ms 0.083% 71.40% 1362ms 2.10% std::map::operator[] 0 0% 71.40% 1234ms 1.91% std::_Rb_tree::lower_bound (inline) 0 0% 71.40% 1234ms 1.91% std::map::lower_bound (inline) 5ms 0.0077% 71.41% 1193ms 1.84% VertexMesh::GenerateVerticesFromElementCircumcentres 25ms 0.039% 71.45% 1182ms 1.83% tetgen::tetgenmesh::locate 56ms 0.086% 71.54% 1164ms 1.80% std::vector::_M_realloc_insert 0 0% 71.54% 1151ms 1.78% VoronoiDataWriter::Visit 97ms 0.15% 71.69% 1111ms 1.72% tetgen::tetgenmesh::preciselocate 1024ms 1.58% 73.27% 1024ms 1.58% tetgen::tetgenmesh::triface::triface 845ms 1.30% 74.57% 1001ms 1.55% AbstractElement::GetNodeGlobalIndex 125ms 0.19% 74.77% 963ms 1.49% std::vector::push_back (inline) 6ms 0.0093% 74.78% 960ms 1.48% std::_Vector_base::_M_allocate (inline) 4ms 0.0062% 74.78% 880ms 1.36% TetrahedralMesh::RefreshJacobianCachedData 805ms 1.24% 76.03% 805ms 1.24% tetgen::tetgenmesh::triface::operator= 319ms 0.49% 76.52% 773ms 1.19% tetgen::tetgenmesh::fnextself 10ms 0.015% 76.53% 771ms 1.19% AbstractTetrahedralElement::CalculateInverseJacobian 754ms 1.16% 77.70% 754ms 1.16% Node::rGetLocation 334ms 0.52% 78.21% 753ms 1.16% AbstractElement::GetNodeLocation 16ms 0.025% 78.24% 744ms 1.15% AbstractTetrahedralElement::CalculateJacobian 0 0% 78.24% 728ms 1.12% AbstractTwoBodyInteractionForce::AddForceContribution 19ms 0.029% 78.27% 689ms 1.06% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 664ms 1.03% 79.29% 664ms 1.03% [libchaste_mesh.so] 52ms 0.08% 79.37% 645ms 1% __atan2 18ms 0.028% 79.40% 638ms 0.99% boost::numeric::ublas::vector_assign (inline) 8ms 0.012% 79.41% 630ms 0.97% boost::numeric::ublas::c_vector::c_vector (inline) 624ms 0.96% 80.38% 624ms 0.96% AbstractElement::IsDeleted 463ms 0.71% 81.09% 593ms 0.92% __ieee754_atan2_fma 23ms 0.036% 81.13% 586ms 0.9% Element::CalculateCircumsphere 48ms 0.074% 81.20% 553ms 0.85% AbstractTetrahedralElement::RefreshJacobian 551ms 0.85% 82.05% 551ms 0.85% tetgen::tetgenmesh::oppo 49ms 0.076% 82.13% 517ms 0.8% tetgen::tetgenmesh::enextfnext 513ms 0.79% 82.92% 513ms 0.79% std::vector::size (inline) 0 0% 82.92% 511ms 0.79% std::set::find (inline) 0 0% 82.92% 507ms 0.78% std::insert_iterator::operator= (inline) 0 0% 82.92% 489ms 0.76% boost::numeric::ublas::inner_prod (inline) 31ms 0.048% 82.97% 488ms 0.75% tetgen::tetgenmesh::queue::push 44ms 0.068% 83.04% 487ms 0.75% tetgen::tetgenmesh::enext2fnext 4ms 0.0062% 83.04% 486ms 0.75% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 41ms 0.063% 83.11% 482ms 0.74% boost::numeric::ublas::vector_scalar_binary::evaluate 389ms 0.6% 83.71% 456ms 0.7% tetgen::tetgenmesh::link::add 294ms 0.45% 84.16% 447ms 0.69% tetgen::tetgenmesh::sym 0 0% 84.16% 445ms 0.69% std::_Rb_tree::_M_insert_unique_ (inline) 23ms 0.036% 84.20% 433ms 0.67% VertexMesh::CalculateUnitNormalToFaceWithArea 221ms 0.34% 84.54% 424ms 0.65% AbstractTetrahedralMesh::GetElement 0 0% 84.54% 399ms 0.62% VertexMeshWriter::WriteVtkUsingMesh 97ms 0.15% 84.69% 394ms 0.61% boost::numeric::ublas::indexing_vector_assign 157ms 0.24% 84.93% 393ms 0.61% boost::numeric::ublas::vector_inner_prod::apply (inline) 389ms 0.6% 85.53% 389ms 0.6% boost::numeric::ublas::c_vector::operator() 379ms 0.59% 86.12% 379ms 0.59% tetgen::tetgenmesh::org 3ms 0.0046% 86.12% 378ms 0.58% CellPropertyCollection::GetPropertiesType (inline) 19ms 0.029% 86.15% 376ms 0.58% std::_Rb_tree_iterator::operator-- (inline) 91ms 0.14% 86.29% 371ms 0.57% __dynamic_cast 0 0% 86.29% 368ms 0.57% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 6ms 0.0093% 86.30% 368ms 0.57% boost::numeric::ublas::c_vector::operator= (inline) 5ms 0.0077% 86.31% 359ms 0.55% Cell::GetCellId 357ms 0.55% 86.86% 357ms 0.55% tetgen::tetgenmesh::pointmark 12ms 0.019% 86.88% 349ms 0.54% std::vector::insert (inline) 269ms 0.42% 87.29% 348ms 0.54% tetgen::tetgenmesh::bond 344ms 0.53% 87.82% 344ms 0.53% std::_Rb_tree_decrement 5ms 0.0077% 87.83% 339ms 0.52% AbstractTetrahedralElement::AbstractTetrahedralElement 3ms 0.0046% 87.84% 327ms 0.5% VertexElement::~VertexElement