File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 50039ms, 86.96% of 57541ms total Dropped 877 nodes (cum <= 287.70ms) flat flat% sum% cum cum% 0 0% 0% 57466ms 99.87% __libc_start_call_main 0 0% 0% 57466ms 99.87% __libc_start_main_impl 0 0% 0% 57466ms 99.87% _start 0 0% 0% 57450ms 99.84% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 57450ms 99.84% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 57450ms 99.84% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 57450ms 99.84% main 0 0% 0% 57412ms 99.78% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 57412ms 99.78% CxxTest::TestRunner::runTest (inline) 0 0% 0% 57412ms 99.78% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 57161ms 99.34% AbstractCellBasedSimulation::Solve 0 0% 0% 48511ms 84.31% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 48460ms 84.22% MeshBasedCellPopulation::Update 0 0% 0% 27795ms 48.30% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 27795ms 48.30% MeshBasedCellPopulation::TessellateIfNeeded 216ms 0.38% 0.38% 24522ms 42.62% VertexMesh::VertexMesh 0 0% 0.38% 16929ms 29.42% MutableMesh::ReMesh 0 0% 0.38% 12783ms 22.22% tetgen::tetrahedralize 1ms 0.0017% 0.38% 12645ms 21.98% tetgen::tetgenmesh::delaunizevertices 7ms 0.012% 0.39% 12642ms 21.97% tetgen::tetgenmesh::incrflipdelaunay 561ms 0.97% 1.36% 11520ms 20.02% TetrahedralMesh::EdgeIterator::operator++ 548ms 0.95% 2.32% 11235ms 19.53% tetgen::tetgenmesh::lawson 29ms 0.05% 2.37% 9928ms 17.25% std::set::insert (inline) 222ms 0.39% 2.75% 9422ms 16.37% std::_Rb_tree::_M_insert_unique 411ms 0.71% 3.47% 9112ms 15.84% VertexElement::AddFace 3145ms 5.47% 8.93% 8683ms 15.09% std::_Rb_tree::_M_lower_bound (inline) 226ms 0.39% 9.33% 8119ms 14.11% std::_Rb_tree::find (inline) 0 0% 9.33% 7523ms 13.07% std::set::count (inline) 266ms 0.46% 9.79% 5636ms 9.79% std::_Rb_tree::_M_insert_ (inline) 125ms 0.22% 10.01% 5343ms 9.29% std::less::operator() (inline) 5274ms 9.17% 19.17% 5274ms 9.17% std::operator< (inline) 0 0% 19.17% 5251ms 9.13% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 19.17% 5121ms 8.90% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0017% 19.17% 5096ms 8.86% AbstractNumericalMethod::ComputeForcesIncludingDamping 204ms 0.35% 19.53% 5062ms 8.80% operator new 1089ms 1.89% 21.42% 4779ms 8.31% __GI___libc_malloc 4690ms 8.15% 29.57% 4690ms 8.15% std::_Rb_tree_increment 46ms 0.08% 29.65% 4384ms 7.62% std::__new_allocator::allocate (inline) 0 0% 29.65% 4355ms 7.57% std::allocator_traits::allocate (inline) 14ms 0.024% 29.67% 4131ms 7.18% std::_Rb_tree::~_Rb_tree (inline) 1608ms 2.79% 32.47% 4116ms 7.15% std::_Rb_tree::_M_erase 4ms 0.007% 32.48% 4098ms 7.12% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 32.48% 4090ms 7.11% std::set::~set (inline) 1ms 0.0017% 32.48% 4074ms 7.08% MeshBasedCellPopulation::UpdateNodePairs 17ms 0.03% 32.51% 3943ms 6.85% MeshBasedCellPopulation::SpringIterator::operator++ 1210ms 2.10% 34.61% 3884ms 6.75% std::_Rb_tree::_M_get_insert_unique_pos 3ms 0.0052% 34.62% 3760ms 6.53% std::set_intersection (inline) 1162ms 2.02% 36.63% 3757ms 6.53% __GI___libc_free 247ms 0.43% 37.06% 3757ms 6.53% std::__set_intersection 34ms 0.059% 37.12% 3686ms 6.41% Node::AddElement 0 0% 37.12% 3525ms 6.13% std::_Rb_tree::_M_create_node (inline) 0 0% 37.12% 3499ms 6.08% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 37.12% 3484ms 6.05% std::_Rb_tree::_M_get_node (inline) 115ms 0.2% 37.32% 3443ms 5.98% tetgen::tetgenmesh::insphere_sos 9ms 0.016% 37.34% 3368ms 5.85% TetrahedralMesh::ImportFromMesher 2465ms 4.28% 41.62% 3354ms 5.83% _int_malloc 3006ms 5.22% 46.85% 3304ms 5.74% tetgen::insphere 0 0% 46.85% 3292ms 5.72% VertexMesh::~VertexMesh 0 0% 46.85% 3253ms 5.65% AbstractCellPopulation::WriteResultsToFiles 3249ms 5.65% 52.49% 3249ms 5.65% std::_Rb_tree::_S_right (inline) 125ms 0.22% 52.71% 3221ms 5.60% std::__new_allocator::deallocate (inline) 0 0% 52.71% 3203ms 5.57% std::allocator_traits::deallocate (inline) 162ms 0.28% 52.99% 3030ms 5.27% std::_Rb_tree_const_iterator::operator++ (inline) 82ms 0.14% 53.13% 2895ms 5.03% MutableElement::AddNode 217ms 0.38% 53.51% 2875ms 5.00% tetgen::tetgenmesh::flip23 1181ms 2.05% 55.56% 2592ms 4.50% _int_free 165ms 0.29% 55.85% 2403ms 4.18% Node::~Node 184ms 0.32% 56.17% 2213ms 3.85% VertexMesh::Clear 3ms 0.0052% 56.18% 2146ms 3.73% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 207ms 0.36% 56.54% 2111ms 3.67% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1943ms 3.38% 59.91% 1943ms 3.38% std::_Rb_tree_insert_and_rebalance 1ms 0.0017% 59.91% 1917ms 3.33% std::_Rb_tree_iterator::operator++ (inline) 0 0% 59.91% 1852ms 3.22% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.91% 1843ms 3.20% std::_Rb_tree::_M_put_node (inline) 171ms 0.3% 60.21% 1807ms 3.14% tetgen::tetgenmesh::flip32 4ms 0.007% 60.22% 1632ms 2.84% Element::Element 1475ms 2.56% 62.78% 1475ms 2.56% Node::GetIndex 224ms 0.39% 63.17% 1451ms 2.52% TetrahedralMesh::Clear 172ms 0.3% 63.47% 1443ms 2.51% tetgen::tetgenmesh::enqueueflipface 914ms 1.59% 65.06% 1385ms 2.41% malloc_consolidate 1305ms 2.27% 67.33% 1383ms 2.40% tetgen::orient3d 15ms 0.026% 67.35% 1374ms 2.39% std::_Vector_base::_M_deallocate (inline) 5ms 0.0087% 67.36% 1314ms 2.28% Element::RegisterWithNodes (inline) 0 0% 67.36% 1269ms 2.21% std::vector::~vector (inline) 1ms 0.0017% 67.36% 1193ms 2.07% std::_Vector_base::~_Vector_base (inline) 35ms 0.061% 67.42% 1191ms 2.07% tetgen::tetgenmesh::locate 3ms 0.0052% 67.43% 1154ms 2.01% _int_free_maybe_consolidate 61ms 0.11% 67.53% 1115ms 1.94% std::vector::_M_realloc_insert 96ms 0.17% 67.70% 1107ms 1.92% tetgen::tetgenmesh::preciselocate 64ms 0.11% 67.81% 1076ms 1.87% std::map::operator[] 1073ms 1.86% 69.68% 1073ms 1.86% unlink_chunk 0 0% 69.68% 953ms 1.66% std::_Rb_tree::lower_bound (inline) 0 0% 69.68% 953ms 1.66% std::map::lower_bound (inline) 4ms 0.007% 69.68% 909ms 1.58% VertexMesh::GenerateVerticesFromElementCircumcentres 883ms 1.53% 71.22% 883ms 1.53% tetgen::tetgenmesh::triface::triface 0 0% 71.22% 876ms 1.52% VoronoiDataWriter::Visit 102ms 0.18% 71.40% 876ms 1.52% std::vector::push_back (inline) 4ms 0.007% 71.40% 875ms 1.52% std::_Vector_base::_M_allocate (inline) 717ms 1.25% 72.65% 849ms 1.48% AbstractElement::GetNodeGlobalIndex 2ms 0.0035% 72.65% 840ms 1.46% AbstractTwoBodyInteractionForce::AddForceContribution 793ms 1.38% 74.03% 793ms 1.38% tetgen::tetgenmesh::oppo 18ms 0.031% 74.06% 790ms 1.37% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 1ms 0.0017% 74.06% 757ms 1.32% TetrahedralMesh::RefreshJacobianCachedData 8ms 0.014% 74.08% 689ms 1.20% AbstractTetrahedralElement::CalculateInverseJacobian 19ms 0.033% 74.11% 659ms 1.15% boost::numeric::ublas::vector_assign (inline) 654ms 1.14% 75.25% 654ms 1.14% [libchaste_mesh.so] 8ms 0.014% 75.26% 646ms 1.12% AbstractTetrahedralElement::CalculateJacobian 6ms 0.01% 75.27% 638ms 1.11% boost::numeric::ublas::c_vector::c_vector (inline) 337ms 0.59% 75.86% 630ms 1.09% tetgen::tetgenmesh::fnextself 56ms 0.097% 75.95% 600ms 1.04% __atan2 591ms 1.03% 76.98% 591ms 1.03% tetgen::tetgenmesh::triface::operator= 0 0% 76.98% 590ms 1.03% std::set::find (inline) 232ms 0.4% 77.38% 581ms 1.01% AbstractElement::GetNodeLocation 548ms 0.95% 78.34% 548ms 0.95% AbstractElement::IsDeleted 404ms 0.7% 79.04% 544ms 0.95% __ieee754_atan2_fma 521ms 0.91% 79.94% 521ms 0.91% Node::rGetLocation 5ms 0.0087% 79.95% 508ms 0.88% Cell::GetCellId 0 0% 79.95% 504ms 0.88% std::insert_iterator::operator= (inline) 7ms 0.012% 79.97% 494ms 0.86% CellPropertyCollection::GetPropertiesType (inline) 0 0% 79.97% 491ms 0.85% boost::numeric::ublas::inner_prod (inline) 2ms 0.0035% 79.97% 489ms 0.85% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 36ms 0.063% 80.03% 487ms 0.85% boost::numeric::ublas::vector_scalar_binary::evaluate 32ms 0.056% 80.09% 473ms 0.82% AbstractTetrahedralElement::RefreshJacobian 17ms 0.03% 80.12% 473ms 0.82% Element::CalculateCircumsphere 120ms 0.21% 80.33% 471ms 0.82% __dynamic_cast 330ms 0.57% 80.90% 471ms 0.82% tetgen::tetgenmesh::sym 463ms 0.8% 81.70% 463ms 0.8% std::vector::size (inline) 2ms 0.0035% 81.71% 457ms 0.79% std::_Rb_tree::_M_insert_unique_ (inline) 58ms 0.1% 81.81% 452ms 0.79% tetgen::tetgenmesh::enextfnext 42ms 0.073% 81.88% 430ms 0.75% tetgen::tetgenmesh::enext2fnext 419ms 0.73% 82.61% 419ms 0.73% boost::numeric::ublas::c_vector::operator() 2ms 0.0035% 82.61% 413ms 0.72% AbstractCellProperty::IsSubType (inline) 3ms 0.0052% 82.62% 413ms 0.72% boost::numeric::ublas::c_vector::operator= (inline) 291ms 0.51% 83.12% 407ms 0.71% tetgen::tetgenmesh::bond 114ms 0.2% 83.32% 406ms 0.71% boost::numeric::ublas::indexing_vector_assign 10ms 0.017% 83.34% 401ms 0.7% VertexMesh::CalculateUnitNormalToFaceWithArea 218ms 0.38% 83.72% 399ms 0.69% AbstractTetrahedralMesh::GetElement 27ms 0.047% 83.76% 396ms 0.69% tetgen::tetgenmesh::queue::push 164ms 0.29% 84.05% 395ms 0.69% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 84.05% 388ms 0.67% VertexMeshWriter::WriteVtkUsingMesh 20ms 0.035% 84.08% 375ms 0.65% std::_Rb_tree_iterator::operator-- (inline) 272ms 0.47% 84.56% 367ms 0.64% tetgen::tetgenmesh::link::add 11ms 0.019% 84.58% 360ms 0.63% std::vector::insert (inline) 335ms 0.58% 85.16% 335ms 0.58% std::_Rb_tree_decrement 4ms 0.007% 85.17% 327ms 0.57% VertexElement::~VertexElement 0 0% 85.17% 319ms 0.55% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 318ms 0.55% 85.72% 318ms 0.55% tetgen::tetgenmesh::org 3ms 0.0052% 85.72% 317ms 0.55% AbstractTetrahedralElement::AbstractTetrahedralElement 50ms 0.087% 85.81% 316ms 0.55% boost::numeric::ublas::vector_reference::operator() (inline) 137ms 0.24% 86.05% 312ms 0.54% Inverse 40ms 0.07% 86.12% 298ms 0.52% tetgen::insphereadapt 196ms 0.34% 86.46% 290ms 0.5% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 86.46% 290ms 0.5% tcache_get (inline) 290ms 0.5% 86.96% 290ms 0.5% tcache_get_n (inline)