File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 44987ms, 85.78% of 52446ms total Dropped 862 nodes (cum <= 262.23ms) flat flat% sum% cum cum% 0 0% 0% 52388ms 99.89% __libc_start_call_main 0 0% 0% 52388ms 99.89% __libc_start_main_impl 0 0% 0% 52388ms 99.89% _start 0 0% 0% 52374ms 99.86% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 52374ms 99.86% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 52374ms 99.86% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 52374ms 99.86% main 0 0% 0% 52338ms 99.79% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 52338ms 99.79% CxxTest::TestRunner::runTest (inline) 0 0% 0% 52338ms 99.79% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 52084ms 99.31% AbstractCellBasedSimulation::Solve 0 0% 0% 43893ms 83.69% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 43846ms 83.60% MeshBasedCellPopulation::Update 0 0% 0% 23781ms 45.34% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 23780ms 45.34% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 164ms 0.31% 0.31% 21332ms 40.67% VertexMesh::VertexMesh 0 0% 0.31% 16594ms 31.64% MutableMesh::ReMesh 0 0% 0.31% 13229ms 25.22% tetgen::tetrahedralize 2ms 0.0038% 0.32% 13096ms 24.97% tetgen::tetgenmesh::delaunizevertices 7ms 0.013% 0.33% 13089ms 24.96% tetgen::tetgenmesh::incrflipdelaunay 486ms 0.93% 1.26% 11627ms 22.17% tetgen::tetgenmesh::lawson 560ms 1.07% 2.32% 10511ms 20.04% TetrahedralMesh::EdgeIterator::operator++ 29ms 0.055% 2.38% 8793ms 16.77% std::set::insert (inline) 284ms 0.54% 2.92% 8481ms 16.17% VertexElement::AddFace 210ms 0.4% 3.32% 8292ms 15.81% std::_Rb_tree::_M_insert_unique 2957ms 5.64% 8.96% 8199ms 15.63% std::_Rb_tree::_M_lower_bound (inline) 249ms 0.47% 9.43% 7691ms 14.66% std::_Rb_tree::find (inline) 0 0% 9.43% 7161ms 13.65% std::set::count (inline) 125ms 0.24% 9.67% 5167ms 9.85% std::less::operator() (inline) 5102ms 9.73% 19.40% 5102ms 9.73% std::operator< (inline) 289ms 0.55% 19.95% 5019ms 9.57% std::_Rb_tree::_M_insert_ (inline) 0 0% 19.95% 4754ms 9.06% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 19.95% 4652ms 8.87% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0038% 19.96% 4627ms 8.82% AbstractNumericalMethod::ComputeForcesIncludingDamping 214ms 0.41% 20.36% 4151ms 7.91% operator new 4000ms 7.63% 27.99% 4000ms 7.63% std::_Rb_tree_increment 1096ms 2.09% 30.08% 3859ms 7.36% __GI___libc_malloc 2ms 0.0038% 30.08% 3805ms 7.26% MeshBasedCellPopulation::UpdateNodePairs 8ms 0.015% 30.10% 3775ms 7.20% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 34ms 0.065% 30.16% 3679ms 7.01% std::__new_allocator::allocate (inline) 13ms 0.025% 30.19% 3674ms 7.01% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 30.19% 3656ms 6.97% std::allocator_traits::allocate (inline) 113ms 0.22% 30.40% 3497ms 6.67% tetgen::tetgenmesh::insphere_sos 4ms 0.0076% 30.41% 3495ms 6.66% std::_Rb_tree::~_Rb_tree (inline) 1301ms 2.48% 32.89% 3491ms 6.66% std::_Rb_tree::_M_erase 0 0% 32.89% 3457ms 6.59% std::set::~set (inline) 3084ms 5.88% 38.77% 3371ms 6.43% tetgen::insphere 1246ms 2.38% 41.15% 3365ms 6.42% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 41.15% 3301ms 6.29% AbstractCellPopulation::WriteResultsToFiles 895ms 1.71% 42.86% 3031ms 5.78% __GI___libc_free 0 0% 42.86% 3005ms 5.73% std::_Rb_tree::_M_create_node (inline) 0 0% 42.86% 2975ms 5.67% std::_Rb_tree::_M_get_node (inline) 0 0% 42.86% 2972ms 5.67% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.0038% 42.86% 2964ms 5.65% std::set_intersection (inline) 245ms 0.47% 43.33% 2962ms 5.65% std::__set_intersection 216ms 0.41% 43.74% 2833ms 5.40% tetgen::tetgenmesh::flip23 107ms 0.2% 43.94% 2756ms 5.25% std::__new_allocator::deallocate (inline) 0 0% 43.94% 2750ms 5.24% std::allocator_traits::deallocate (inline) 24ms 0.046% 43.99% 2655ms 5.06% Node::AddElement 25ms 0.048% 44.04% 2642ms 5.04% TetrahedralMesh::ImportFromMesher 0 0% 44.04% 2471ms 4.71% VertexMesh::~VertexMesh 1884ms 3.59% 47.63% 2459ms 4.69% _int_malloc 2349ms 4.48% 52.11% 2349ms 4.48% std::_Rb_tree::_S_right (inline) 216ms 0.41% 52.52% 2272ms 4.33% std::_Rb_tree_const_iterator::operator++ (inline) 202ms 0.39% 52.90% 2238ms 4.27% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 5ms 0.0095% 52.91% 2233ms 4.26% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 1100ms 2.10% 55.01% 2128ms 4.06% _int_free 0 0% 55.01% 2041ms 3.89% std::_Rb_tree_iterator::operator++ (inline) 67ms 0.13% 55.14% 2037ms 3.88% MutableElement::AddNode 195ms 0.37% 55.51% 1991ms 3.80% tetgen::tetgenmesh::flip32 1810ms 3.45% 58.96% 1810ms 3.45% std::_Rb_tree_insert_and_rebalance 101ms 0.19% 59.15% 1758ms 3.35% Node::~Node 0 0% 59.15% 1729ms 3.30% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.15% 1719ms 3.28% std::_Rb_tree::_M_put_node (inline) 120ms 0.23% 59.38% 1703ms 3.25% VertexMesh::Clear 1458ms 2.78% 62.16% 1551ms 2.96% tetgen::orient3d 2ms 0.0038% 62.17% 1420ms 2.71% Element::Element 199ms 0.38% 62.55% 1372ms 2.62% tetgen::tetgenmesh::enqueueflipface 27ms 0.051% 62.60% 1226ms 2.34% tetgen::tetgenmesh::locate 96ms 0.18% 62.78% 1152ms 2.20% tetgen::tetgenmesh::preciselocate 1101ms 2.10% 64.88% 1101ms 2.10% Node::GetIndex 1099ms 2.10% 66.98% 1099ms 2.10% tetgen::tetgenmesh::triface::triface 5ms 0.0095% 66.99% 1075ms 2.05% Element::RegisterWithNodes (inline) 13ms 0.025% 67.01% 1044ms 1.99% std::_Vector_base::_M_deallocate (inline) 65ms 0.12% 67.13% 1033ms 1.97% std::map::operator[] 0 0% 67.13% 976ms 1.86% std::vector::~vector (inline) 604ms 1.15% 68.29% 969ms 1.85% malloc_consolidate 101ms 0.19% 68.48% 941ms 1.79% TetrahedralMesh::Clear 60ms 0.11% 68.59% 938ms 1.79% std::vector::_M_realloc_insert 0 0% 68.59% 897ms 1.71% std::_Rb_tree::lower_bound (inline) 0 0% 68.59% 897ms 1.71% std::map::lower_bound (inline) 1ms 0.0019% 68.59% 859ms 1.64% std::_Vector_base::~_Vector_base (inline) 1ms 0.0019% 68.60% 855ms 1.63% VoronoiDataWriter::Visit 10ms 0.019% 68.62% 847ms 1.61% _int_free_maybe_consolidate 329ms 0.63% 69.24% 836ms 1.59% tetgen::tetgenmesh::fnextself 101ms 0.19% 69.44% 745ms 1.42% std::vector::push_back (inline) 9ms 0.017% 69.45% 720ms 1.37% VertexMesh::GenerateVerticesFromElementCircumcentres 711ms 1.36% 70.81% 711ms 1.36% unlink_chunk 0 0% 70.81% 707ms 1.35% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 70.81% 702ms 1.34% TetrahedralMesh::RefreshJacobianCachedData 701ms 1.34% 72.14% 701ms 1.34% tetgen::tetgenmesh::triface::operator= 10ms 0.019% 72.16% 685ms 1.31% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 4ms 0.0076% 72.17% 685ms 1.31% std::_Vector_base::_M_allocate (inline) 495ms 0.94% 73.12% 676ms 1.29% AbstractElement::GetNodeGlobalIndex 11ms 0.021% 73.14% 659ms 1.26% AbstractTetrahedralElement::CalculateInverseJacobian 654ms 1.25% 74.38% 654ms 1.25% [libchaste_mesh.so] 16ms 0.031% 74.41% 651ms 1.24% boost::numeric::ublas::vector_assign (inline) 26ms 0.05% 74.46% 648ms 1.24% boost::numeric::ublas::c_vector::c_vector (inline) 22ms 0.042% 74.51% 621ms 1.18% AbstractTetrahedralElement::CalculateJacobian 35ms 0.067% 74.57% 581ms 1.11% __atan2 47ms 0.09% 74.66% 571ms 1.09% tetgen::tetgenmesh::enextfnext 559ms 1.07% 75.73% 559ms 1.07% tetgen::tetgenmesh::oppo 426ms 0.81% 76.54% 546ms 1.04% __ieee754_atan2_fma 0 0% 76.54% 528ms 1.01% std::set::find (inline) 207ms 0.39% 76.93% 520ms 0.99% AbstractElement::GetNodeLocation 30ms 0.057% 76.99% 515ms 0.98% tetgen::tetgenmesh::queue::push 0 0% 76.99% 514ms 0.98% boost::numeric::ublas::inner_prod (inline) 8ms 0.015% 77.01% 511ms 0.97% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 34ms 0.065% 77.07% 503ms 0.96% boost::numeric::ublas::vector_scalar_binary::evaluate 45ms 0.086% 77.16% 499ms 0.95% tetgen::tetgenmesh::enext2fnext 0 0% 77.16% 490ms 0.93% std::insert_iterator::operator= (inline) 418ms 0.8% 77.95% 482ms 0.92% tetgen::tetgenmesh::link::add 304ms 0.58% 78.53% 448ms 0.85% tetgen::tetgenmesh::sym 440ms 0.84% 79.37% 440ms 0.84% std::vector::size (inline) 0 0% 79.37% 436ms 0.83% std::_Rb_tree::_M_insert_unique_ (inline) 113ms 0.22% 79.59% 428ms 0.82% boost::numeric::ublas::indexing_vector_assign 39ms 0.074% 79.66% 427ms 0.81% AbstractTetrahedralElement::RefreshJacobian 418ms 0.8% 80.46% 418ms 0.8% Node::rGetLocation 14ms 0.027% 80.49% 407ms 0.78% Element::CalculateCircumsphere 220ms 0.42% 80.91% 404ms 0.77% AbstractTetrahedralMesh::GetElement 403ms 0.77% 81.67% 403ms 0.77% boost::numeric::ublas::c_vector::operator() 165ms 0.31% 81.99% 398ms 0.76% boost::numeric::ublas::vector_inner_prod::apply (inline) 3ms 0.0057% 81.99% 393ms 0.75% CellPropertyCollection::GetPropertiesType (inline) 88ms 0.17% 82.16% 390ms 0.74% __dynamic_cast 19ms 0.036% 82.20% 382ms 0.73% std::_Rb_tree_iterator::operator-- (inline) 0 0% 82.20% 378ms 0.72% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.0019% 82.20% 368ms 0.7% Cell::GetCellId 20ms 0.038% 82.24% 368ms 0.7% VertexMesh::CalculateUnitNormalToFaceWithArea 4ms 0.0076% 82.25% 360ms 0.69% boost::numeric::ublas::c_vector::operator= (inline) 3ms 0.0057% 82.25% 344ms 0.66% AbstractTetrahedralElement::AbstractTetrahedralElement 344ms 0.66% 82.91% 344ms 0.66% std::_Rb_tree_decrement 340ms 0.65% 83.56% 340ms 0.65% tetgen::tetgenmesh::org 247ms 0.47% 84.03% 339ms 0.65% tetgen::tetgenmesh::bond 80ms 0.15% 84.18% 333ms 0.63% tetgen::tetgenmesh::queue::pop 55ms 0.1% 84.28% 327ms 0.62% boost::numeric::ublas::vector_reference::operator() (inline) 144ms 0.27% 84.56% 319ms 0.61% Inverse 6ms 0.011% 84.57% 315ms 0.6% VertexElement::~VertexElement 10ms 0.019% 84.59% 315ms 0.6% std::vector::insert (inline) 2ms 0.0038% 84.59% 314ms 0.6% AbstractCellProperty::IsSubType (inline) 302ms 0.58% 85.17% 302ms 0.58% tetgen::tetgenmesh::pointmark 34ms 0.065% 85.23% 286ms 0.55% tetgen::insphereadapt 2ms 0.0038% 85.24% 285ms 0.54% tcache_get (inline) 283ms 0.54% 85.78% 283ms 0.54% tcache_get_n (inline)