File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 58515ms, 87.46% of 66903ms total Dropped 881 nodes (cum <= 334.51ms) flat flat% sum% cum cum% 0 0% 0% 66833ms 99.90% __libc_start_call_main 0 0% 0% 66833ms 99.90% __libc_start_main_impl 0 0% 0% 66833ms 99.90% _start 0 0% 0% 66813ms 99.87% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 66813ms 99.87% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 66813ms 99.87% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 66813ms 99.87% main 0 0% 0% 66773ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 66773ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 66773ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 66491ms 99.38% AbstractCellBasedSimulation::Solve 0 0% 0% 56012ms 83.72% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 55969ms 83.66% MeshBasedCellPopulation::Update 0 0% 0% 31245ms 46.70% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 31245ms 46.70% MeshBasedCellPopulation::TessellateIfNeeded 211ms 0.32% 0.32% 27757ms 41.49% VertexMesh::VertexMesh 0 0% 0.32% 20197ms 30.19% MutableMesh::ReMesh 0 0% 0.32% 15908ms 23.78% tetgen::tetrahedralize 3ms 0.0045% 0.32% 15739ms 23.53% tetgen::tetgenmesh::delaunizevertices 6ms 0.009% 0.33% 15733ms 23.52% tetgen::tetgenmesh::incrflipdelaunay 516ms 0.77% 1.10% 14064ms 21.02% tetgen::tetgenmesh::lawson 614ms 0.92% 2.02% 13923ms 20.81% TetrahedralMesh::EdgeIterator::operator++ 23ms 0.034% 2.05% 10731ms 16.04% std::set::insert (inline) 3239ms 4.84% 6.89% 10566ms 15.79% std::_Rb_tree::_M_lower_bound (inline) 279ms 0.42% 7.31% 10315ms 15.42% std::_Rb_tree::_M_insert_unique 417ms 0.62% 7.93% 10156ms 15.18% VertexElement::AddFace 253ms 0.38% 8.31% 9836ms 14.70% std::_Rb_tree::find (inline) 0 0% 8.31% 9257ms 13.84% std::set::count (inline) 127ms 0.19% 8.50% 7036ms 10.52% std::less::operator() (inline) 6987ms 10.44% 18.95% 6987ms 10.44% std::operator< (inline) 6239ms 9.33% 28.27% 6239ms 9.33% std::_Rb_tree_increment 0 0% 28.27% 6009ms 8.98% OffLatticeSimulation::UpdateCellLocationsAndTopology 324ms 0.48% 28.76% 5980ms 8.94% std::_Rb_tree::_M_insert_ (inline) 2ms 0.003% 28.76% 5853ms 8.75% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.009% 28.77% 5826ms 8.71% AbstractNumericalMethod::ComputeForcesIncludingDamping 167ms 0.25% 29.02% 5477ms 8.19% operator new 1157ms 1.73% 30.75% 5231ms 7.82% __GI___libc_malloc 2ms 0.003% 30.75% 4889ms 7.31% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.0075% 30.76% 4867ms 7.27% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 25ms 0.037% 30.79% 4719ms 7.05% MeshBasedCellPopulation::SpringIterator::operator++ 43ms 0.064% 30.86% 4678ms 6.99% std::__new_allocator::allocate (inline) 0 0% 30.86% 4650ms 6.95% std::allocator_traits::allocate (inline) 7ms 0.01% 30.87% 4388ms 6.56% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.0045% 30.87% 4379ms 6.55% std::set_intersection (inline) 1638ms 2.45% 33.32% 4377ms 6.54% std::_Rb_tree::_M_erase 259ms 0.39% 33.71% 4376ms 6.54% std::__set_intersection 0 0% 33.71% 4348ms 6.50% std::set::~set (inline) 0 0% 33.71% 4312ms 6.45% AbstractCellPopulation::WriteResultsToFiles 1301ms 1.94% 35.65% 4293ms 6.42% std::_Rb_tree::_M_get_insert_unique_pos 1126ms 1.68% 37.34% 4153ms 6.21% __GI___libc_free 95ms 0.14% 37.48% 3907ms 5.84% tetgen::tetgenmesh::insphere_sos 46ms 0.069% 37.55% 3865ms 5.78% Node::AddElement 3515ms 5.25% 42.80% 3795ms 5.67% tetgen::insphere 0 0% 42.80% 3752ms 5.61% std::_Rb_tree::_M_create_node (inline) 0 0% 42.80% 3716ms 5.55% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 42.80% 3710ms 5.55% std::_Rb_tree::_M_get_node (inline) 187ms 0.28% 43.08% 3678ms 5.50% std::_Rb_tree_const_iterator::operator++ (inline) 3630ms 5.43% 48.51% 3630ms 5.43% std::_Rb_tree::_S_right (inline) 2572ms 3.84% 52.35% 3626ms 5.42% _int_malloc 128ms 0.19% 52.54% 3592ms 5.37% std::__new_allocator::deallocate (inline) 0 0% 52.54% 3572ms 5.34% std::allocator_traits::deallocate (inline) 0 0% 52.54% 3511ms 5.25% VertexMesh::~VertexMesh 14ms 0.021% 52.56% 3441ms 5.14% TetrahedralMesh::ImportFromMesher 122ms 0.18% 52.75% 3406ms 5.09% tetgen::tetgenmesh::flip23 219ms 0.33% 53.07% 3099ms 4.63% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1385ms 2.07% 55.14% 3024ms 4.52% _int_free 5ms 0.0075% 55.15% 3011ms 4.50% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 60ms 0.09% 55.24% 2920ms 4.36% MutableElement::AddNode 1ms 0.0015% 55.24% 2897ms 4.33% std::_Rb_tree_iterator::operator++ (inline) 139ms 0.21% 55.45% 2595ms 3.88% tetgen::tetgenmesh::flip32 169ms 0.25% 55.70% 2476ms 3.70% Node::~Node 167ms 0.25% 55.95% 2278ms 3.40% VertexMesh::Clear 0 0% 55.95% 2093ms 3.13% std::_Rb_tree::_M_drop_node (inline) 0 0% 55.95% 2083ms 3.11% std::_Rb_tree::_M_put_node (inline) 2020ms 3.02% 58.97% 2020ms 3.02% std::_Rb_tree_insert_and_rebalance 1953ms 2.92% 61.89% 1953ms 2.92% Node::GetIndex 218ms 0.33% 62.22% 1937ms 2.90% tetgen::tetgenmesh::enqueueflipface 5ms 0.0075% 62.22% 1757ms 2.63% Element::Element 1013ms 1.51% 63.74% 1629ms 2.43% malloc_consolidate 1506ms 2.25% 65.99% 1596ms 2.39% tetgen::orient3d 26ms 0.039% 66.03% 1515ms 2.26% std::_Vector_base::_M_deallocate (inline) 0 0% 66.03% 1448ms 2.16% std::vector::~vector (inline) 5ms 0.0075% 66.03% 1421ms 2.12% Element::RegisterWithNodes (inline) 37ms 0.055% 66.09% 1394ms 2.08% tetgen::tetgenmesh::locate 9ms 0.013% 66.10% 1381ms 2.06% _int_free_maybe_consolidate 104ms 0.16% 66.26% 1364ms 2.04% TetrahedralMesh::Clear 2ms 0.003% 66.26% 1364ms 2.04% std::_Vector_base::~_Vector_base (inline) 62ms 0.093% 66.35% 1319ms 1.97% std::map::operator[] 92ms 0.14% 66.49% 1309ms 1.96% tetgen::tetgenmesh::preciselocate 1270ms 1.90% 68.39% 1270ms 1.90% unlink_chunk 0 0% 68.39% 1179ms 1.76% std::_Rb_tree::lower_bound (inline) 0 0% 68.39% 1179ms 1.76% std::map::lower_bound (inline) 61ms 0.091% 68.48% 1153ms 1.72% std::vector::_M_realloc_insert 859ms 1.28% 69.77% 1045ms 1.56% AbstractElement::GetNodeGlobalIndex 1ms 0.0015% 69.77% 1041ms 1.56% VoronoiDataWriter::Visit 7ms 0.01% 69.78% 1035ms 1.55% VertexMesh::GenerateVerticesFromElementCircumcentres 1035ms 1.55% 71.32% 1035ms 1.55% tetgen::tetgenmesh::oppo 158ms 0.24% 71.56% 985ms 1.47% std::vector::push_back (inline) 4ms 0.006% 71.57% 944ms 1.41% std::_Vector_base::_M_allocate (inline) 940ms 1.41% 72.97% 940ms 1.41% tetgen::tetgenmesh::triface::triface 0 0% 72.97% 822ms 1.23% TetrahedralMesh::RefreshJacobianCachedData 800ms 1.20% 74.17% 800ms 1.20% [libchaste_mesh.so] 1ms 0.0015% 74.17% 748ms 1.12% AbstractTwoBodyInteractionForce::AddForceContribution 13ms 0.019% 74.19% 743ms 1.11% AbstractTetrahedralElement::CalculateInverseJacobian 283ms 0.42% 74.61% 727ms 1.09% tetgen::tetgenmesh::sym 9ms 0.013% 74.62% 701ms 1.05% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 302ms 0.45% 75.08% 689ms 1.03% AbstractElement::GetNodeLocation 16ms 0.024% 75.10% 679ms 1.01% AbstractTetrahedralElement::CalculateJacobian 675ms 1.01% 76.11% 675ms 1.01% Node::rGetLocation 671ms 1.00% 77.11% 671ms 1.00% tetgen::tetgenmesh::triface::operator= 36ms 0.054% 77.17% 666ms 1% tetgen::tetgenmesh::queue::push 245ms 0.37% 77.53% 653ms 0.98% tetgen::tetgenmesh::bond 382ms 0.57% 78.10% 647ms 0.97% tetgen::tetgenmesh::fnextself 64ms 0.096% 78.20% 645ms 0.96% __atan2 383ms 0.57% 78.77% 630ms 0.94% tetgen::tetgenmesh::link::add 629ms 0.94% 79.71% 629ms 0.94% AbstractElement::IsDeleted 18ms 0.027% 79.74% 624ms 0.93% boost::numeric::ublas::vector_assign (inline) 14ms 0.021% 79.76% 610ms 0.91% boost::numeric::ublas::c_vector::c_vector (inline) 51ms 0.076% 79.83% 581ms 0.87% tetgen::tetgenmesh::enext2fnext 448ms 0.67% 80.50% 575ms 0.86% __ieee754_atan2_fma 0 0% 80.50% 572ms 0.85% std::set::find (inline) 59ms 0.088% 80.59% 562ms 0.84% tetgen::tetgenmesh::enextfnext 539ms 0.81% 81.40% 539ms 0.81% std::vector::size (inline) 0 0% 81.40% 519ms 0.78% boost::numeric::ublas::inner_prod (inline) 22ms 0.033% 81.43% 517ms 0.77% Element::CalculateCircumsphere 44ms 0.066% 81.50% 515ms 0.77% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 81.50% 515ms 0.77% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 34ms 0.051% 81.55% 494ms 0.74% AbstractTetrahedralElement::RefreshJacobian 464ms 0.69% 82.24% 464ms 0.69% tetgen::tetgenmesh::decode 464ms 0.69% 82.93% 464ms 0.69% tetgen::tetgenmesh::pointmark 19ms 0.028% 82.96% 458ms 0.68% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 82.96% 456ms 0.68% std::insert_iterator::operator= (inline) 432ms 0.65% 83.61% 432ms 0.65% tetgen::tetgenmesh::org 26ms 0.039% 83.65% 431ms 0.64% std::_Rb_tree_iterator::operator-- (inline) 4ms 0.006% 83.65% 423ms 0.63% boost::numeric::ublas::c_vector::operator= (inline) 412ms 0.62% 84.27% 412ms 0.62% boost::numeric::ublas::c_vector::operator() 168ms 0.25% 84.52% 412ms 0.62% boost::numeric::ublas::vector_inner_prod::apply (inline) 2ms 0.003% 84.52% 408ms 0.61% CellPropertyCollection::GetPropertiesType (inline) 211ms 0.32% 84.84% 403ms 0.6% AbstractTetrahedralMesh::GetElement 5ms 0.0075% 84.85% 397ms 0.59% Cell::GetCellId 394ms 0.59% 85.44% 394ms 0.59% tetgen::tetgenmesh::encode 0 0% 85.44% 391ms 0.58% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 85.44% 390ms 0.58% tcache_get (inline) 390ms 0.58% 86.02% 390ms 0.58% tcache_get_n (inline) 107ms 0.16% 86.18% 389ms 0.58% __dynamic_cast 0 0% 86.18% 386ms 0.58% VertexMeshWriter::WriteVtkUsingMesh 383ms 0.57% 86.75% 383ms 0.57% std::_Rb_tree_decrement 106ms 0.16% 86.91% 375ms 0.56% boost::numeric::ublas::indexing_vector_assign 0 0% 86.91% 366ms 0.55% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 20ms 0.03% 86.94% 359ms 0.54% std::vector::insert (inline) 7ms 0.01% 86.95% 355ms 0.53% VertexElement::~VertexElement 341ms 0.51% 87.46% 341ms 0.51% tetgen::tetgenmesh::face::face 2ms 0.003% 87.46% 336ms 0.5% AbstractCellProperty::IsSubType (inline)