File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 56429ms, 88.20% of 63977ms total Dropped 866 nodes (cum <= 319.88ms) flat flat% sum% cum cum% 0 0% 0% 63909ms 99.89% __libc_start_call_main 0 0% 0% 63909ms 99.89% __libc_start_main_impl 0 0% 0% 63909ms 99.89% _start 0 0% 0% 63891ms 99.87% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 63891ms 99.87% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 63891ms 99.87% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 63891ms 99.87% main 0 0% 0% 63857ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 63857ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 63857ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 63592ms 99.40% AbstractCellBasedSimulation::Solve 1ms 0.0016% 0.0016% 52604ms 82.22% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0016% 52555ms 82.15% MeshBasedCellPopulation::Update 0 0% 0.0016% 30915ms 48.32% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0.0016% 30915ms 48.32% MeshBasedCellPopulation::TessellateIfNeeded 240ms 0.38% 0.38% 27044ms 42.27% VertexMesh::VertexMesh 0 0% 0.38% 17312ms 27.06% MutableMesh::ReMesh 552ms 0.86% 1.24% 13178ms 20.60% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.24% 12672ms 19.81% tetgen::tetrahedralize 1ms 0.0016% 1.24% 12533ms 19.59% tetgen::tetgenmesh::delaunizevertices 6ms 0.0094% 1.25% 12527ms 19.58% tetgen::tetgenmesh::incrflipdelaunay 550ms 0.86% 2.11% 11172ms 17.46% tetgen::tetgenmesh::lawson 28ms 0.044% 2.15% 10630ms 16.62% std::set::insert (inline) 3109ms 4.86% 7.01% 10274ms 16.06% std::_Rb_tree::_M_lower_bound (inline) 198ms 0.31% 7.32% 10126ms 15.83% std::_Rb_tree::_M_insert_unique 237ms 0.37% 7.69% 9503ms 14.85% std::_Rb_tree::find (inline) 389ms 0.61% 8.30% 9446ms 14.76% VertexElement::AddFace 0 0% 8.30% 8952ms 13.99% std::set::count (inline) 6820ms 10.66% 18.96% 6820ms 10.66% std::_Rb_tree_increment 130ms 0.2% 19.16% 6817ms 10.66% std::less::operator() (inline) 6750ms 10.55% 29.72% 6750ms 10.55% std::operator< (inline) 287ms 0.45% 30.16% 5839ms 9.13% std::_Rb_tree::_M_insert_ (inline) 1ms 0.0016% 30.17% 5788ms 9.05% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 30.17% 5639ms 8.81% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.0094% 30.17% 5616ms 8.78% AbstractNumericalMethod::ComputeForcesIncludingDamping 179ms 0.28% 30.45% 5427ms 8.48% operator new 1057ms 1.65% 32.11% 5176ms 8.09% __GI___libc_malloc 0 0% 32.11% 5051ms 7.90% AbstractCellPopulation::WriteResultsToFiles 2ms 0.0031% 32.11% 4663ms 7.29% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.011% 32.12% 4661ms 7.29% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 8ms 0.013% 32.13% 4599ms 7.19% std::_Rb_tree::~_Rb_tree (inline) 1934ms 3.02% 35.16% 4588ms 7.17% std::_Rb_tree::_M_erase 57ms 0.089% 35.25% 4583ms 7.16% std::__new_allocator::allocate (inline) 0 0% 35.25% 4561ms 7.13% std::allocator_traits::allocate (inline) 0 0% 35.25% 4532ms 7.08% std::set::~set (inline) 15ms 0.023% 35.27% 4495ms 7.03% MeshBasedCellPopulation::SpringIterator::operator++ 1202ms 1.88% 37.15% 4433ms 6.93% std::_Rb_tree::_M_get_insert_unique_pos 7ms 0.011% 37.16% 4276ms 6.68% std::set_intersection (inline) 272ms 0.43% 37.58% 4269ms 6.67% std::__set_intersection 30ms 0.047% 37.63% 4265ms 6.67% Node::AddElement 1191ms 1.86% 39.49% 4180ms 6.53% __GI___libc_free 4049ms 6.33% 45.82% 4049ms 6.33% std::_Rb_tree::_S_right (inline) 0 0% 45.82% 3899ms 6.09% VertexMesh::~VertexMesh 248ms 0.39% 46.21% 3798ms 5.94% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 8ms 0.013% 46.22% 3777ms 5.90% TetrahedralMesh::ImportFromMesher 2769ms 4.33% 50.55% 3755ms 5.87% _int_malloc 0 0% 50.55% 3653ms 5.71% std::_Rb_tree::_M_create_node (inline) 0 0% 50.55% 3621ms 5.66% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 50.55% 3610ms 5.64% std::_Rb_tree::_M_get_node (inline) 127ms 0.2% 50.75% 3573ms 5.58% std::__new_allocator::deallocate (inline) 97ms 0.15% 50.90% 3563ms 5.57% tetgen::tetgenmesh::insphere_sos 0 0% 50.90% 3562ms 5.57% std::_Rb_tree_iterator::operator++ (inline) 0 0% 50.90% 3551ms 5.55% std::allocator_traits::deallocate (inline) 9ms 0.014% 50.91% 3545ms 5.54% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 177ms 0.28% 51.19% 3531ms 5.52% std::_Rb_tree_const_iterator::operator++ (inline) 3143ms 4.91% 56.10% 3446ms 5.39% tetgen::insphere 69ms 0.11% 56.21% 3181ms 4.97% MutableElement::AddNode 1223ms 1.91% 58.12% 2985ms 4.67% _int_free 183ms 0.29% 58.41% 2746ms 4.29% Node::~Node 190ms 0.3% 58.71% 2725ms 4.26% tetgen::tetgenmesh::flip23 220ms 0.34% 59.05% 2513ms 3.93% VertexMesh::Clear 2041ms 3.19% 62.24% 2041ms 3.19% std::_Rb_tree_insert_and_rebalance 0 0% 62.24% 1896ms 2.96% std::_Rb_tree::_M_drop_node (inline) 5ms 0.0078% 62.25% 1883ms 2.94% Element::Element 0 0% 62.25% 1879ms 2.94% std::_Rb_tree::_M_put_node (inline) 1830ms 2.86% 65.11% 1830ms 2.86% Node::GetIndex 168ms 0.26% 65.37% 1803ms 2.82% tetgen::tetgenmesh::flip32 1147ms 1.79% 67.16% 1758ms 2.75% malloc_consolidate 11ms 0.017% 67.18% 1683ms 2.63% std::_Vector_base::_M_deallocate (inline) 0 0% 67.18% 1552ms 2.43% std::vector::~vector (inline) 214ms 0.33% 67.51% 1548ms 2.42% TetrahedralMesh::Clear 5ms 0.0078% 67.52% 1541ms 2.41% Element::RegisterWithNodes (inline) 16ms 0.025% 67.55% 1519ms 2.37% _int_free_maybe_consolidate 0 0% 67.55% 1488ms 2.33% std::_Vector_base::~_Vector_base (inline) 63ms 0.098% 67.65% 1372ms 2.14% std::map::operator[] 1229ms 1.92% 69.57% 1326ms 2.07% tetgen::orient3d 189ms 0.3% 69.86% 1265ms 1.98% tetgen::tetgenmesh::enqueueflipface 3ms 0.0047% 69.87% 1240ms 1.94% VoronoiDataWriter::Visit 0 0% 69.87% 1232ms 1.93% std::_Rb_tree::lower_bound (inline) 0 0% 69.87% 1232ms 1.93% std::map::lower_bound (inline) 1231ms 1.92% 71.79% 1231ms 1.92% unlink_chunk 33ms 0.052% 71.84% 1148ms 1.79% tetgen::tetgenmesh::locate 51ms 0.08% 71.92% 1144ms 1.79% std::vector::_M_realloc_insert 2ms 0.0031% 71.93% 1136ms 1.78% VertexMesh::GenerateVerticesFromElementCircumcentres 105ms 0.16% 72.09% 1075ms 1.68% tetgen::tetgenmesh::preciselocate 141ms 0.22% 72.31% 978ms 1.53% std::vector::push_back (inline) 7ms 0.011% 72.32% 958ms 1.50% std::_Vector_base::_M_allocate (inline) 833ms 1.30% 73.62% 955ms 1.49% AbstractElement::GetNodeGlobalIndex 0 0% 73.62% 842ms 1.32% TetrahedralMesh::RefreshJacobianCachedData 813ms 1.27% 74.89% 813ms 1.27% tetgen::tetgenmesh::triface::triface 449ms 0.7% 75.60% 794ms 1.24% tetgen::tetgenmesh::fnextself 311ms 0.49% 76.08% 752ms 1.18% AbstractElement::GetNodeLocation 1ms 0.0016% 76.08% 742ms 1.16% AbstractTwoBodyInteractionForce::AddForceContribution 4ms 0.0063% 76.09% 740ms 1.16% AbstractTetrahedralElement::CalculateInverseJacobian 734ms 1.15% 77.24% 734ms 1.15% Node::rGetLocation 11ms 0.017% 77.25% 707ms 1.11% AbstractTetrahedralElement::CalculateJacobian 22ms 0.034% 77.29% 695ms 1.09% boost::numeric::ublas::vector_assign (inline) 694ms 1.08% 78.37% 694ms 1.08% [libchaste_mesh.so] 9ms 0.014% 78.39% 681ms 1.06% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 11ms 0.017% 78.40% 665ms 1.04% boost::numeric::ublas::c_vector::c_vector (inline) 649ms 1.01% 79.42% 649ms 1.01% tetgen::tetgenmesh::triface::operator= 639ms 1% 80.42% 639ms 1% tetgen::tetgenmesh::oppo 605ms 0.95% 81.36% 605ms 0.95% AbstractElement::IsDeleted 46ms 0.072% 81.44% 583ms 0.91% __atan2 16ms 0.025% 81.46% 577ms 0.9% Element::CalculateCircumsphere 0 0% 81.46% 547ms 0.85% std::set::find (inline) 440ms 0.69% 82.15% 537ms 0.84% __ieee754_atan2_fma 54ms 0.084% 82.23% 530ms 0.83% tetgen::tetgenmesh::enext2fnext 32ms 0.05% 82.28% 520ms 0.81% AbstractTetrahedralElement::RefreshJacobian 0 0% 82.28% 505ms 0.79% std::insert_iterator::operator= (inline) 39ms 0.061% 82.34% 499ms 0.78% tetgen::tetgenmesh::enextfnext 490ms 0.77% 83.11% 490ms 0.77% std::vector::size (inline) 319ms 0.5% 83.61% 482ms 0.75% tetgen::tetgenmesh::sym 0 0% 83.61% 480ms 0.75% boost::numeric::ublas::inner_prod (inline) 4ms 0.0063% 83.61% 475ms 0.74% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 30ms 0.047% 83.66% 471ms 0.74% boost::numeric::ublas::vector_scalar_binary::evaluate 26ms 0.041% 83.70% 447ms 0.7% std::_Rb_tree_iterator::operator-- (inline) 0 0% 83.70% 444ms 0.69% std::_Rb_tree::_M_insert_unique_ (inline) 133ms 0.21% 83.91% 438ms 0.68% boost::numeric::ublas::indexing_vector_assign 433ms 0.68% 84.59% 433ms 0.68% boost::numeric::ublas::c_vector::operator() 10ms 0.016% 84.60% 428ms 0.67% VertexMesh::CalculateUnitNormalToFaceWithArea 6ms 0.0094% 84.61% 419ms 0.65% CellPropertyCollection::GetPropertiesType (inline) 0 0% 84.61% 401ms 0.63% VertexMeshWriter::WriteVtkUsingMesh 401ms 0.63% 85.24% 401ms 0.63% std::_Rb_tree_decrement 182ms 0.28% 85.52% 393ms 0.61% boost::numeric::ublas::vector_inner_prod::apply (inline) 6ms 0.0094% 85.53% 390ms 0.61% boost::numeric::ublas::c_vector::operator= (inline) 4ms 0.0063% 85.54% 387ms 0.6% Cell::GetCellId 384ms 0.6% 86.14% 384ms 0.6% tetgen::tetgenmesh::org 270ms 0.42% 86.56% 382ms 0.6% tetgen::tetgenmesh::bond 0 0% 86.56% 376ms 0.59% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 98ms 0.15% 86.71% 371ms 0.58% __dynamic_cast 20ms 0.031% 86.75% 365ms 0.57% tetgen::tetgenmesh::queue::push 196ms 0.31% 87.05% 364ms 0.57% AbstractTetrahedralMesh::GetElement 8ms 0.013% 87.06% 344ms 0.54% VertexElement::~VertexElement 255ms 0.4% 87.46% 343ms 0.54% tetgen::tetgenmesh::link::add 0 0% 87.46% 338ms 0.53% AbstractTetrahedralElement::AbstractTetrahedralElement 6ms 0.0094% 87.47% 331ms 0.52% VertexMesh::GetVolumeOfElement 7ms 0.011% 87.48% 329ms 0.51% std::vector::insert (inline) 138ms 0.22% 87.70% 328ms 0.51% Inverse 0 0% 87.70% 322ms 0.5% tcache_get (inline) 322ms 0.5% 88.20% 322ms 0.5% tcache_get_n (inline)