File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 58373ms, 87.91% of 66403ms total Dropped 888 nodes (cum <= 332.01ms) flat flat% sum% cum cum% 0 0% 0% 66354ms 99.93% __libc_start_call_main 0 0% 0% 66354ms 99.93% __libc_start_main_impl 0 0% 0% 66354ms 99.93% _start 0 0% 0% 66339ms 99.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 66339ms 99.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 66339ms 99.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 66339ms 99.90% main 0 0% 0% 66300ms 99.84% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 66300ms 99.84% CxxTest::TestRunner::runTest (inline) 0 0% 0% 66300ms 99.84% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 66009ms 99.41% AbstractCellBasedSimulation::Solve 0 0% 0% 55155ms 83.06% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 55099ms 82.98% MeshBasedCellPopulation::Update 0 0% 0% 32829ms 49.44% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 32829ms 49.44% MeshBasedCellPopulation::TessellateIfNeeded 263ms 0.4% 0.4% 28507ms 42.93% VertexMesh::VertexMesh 0 0% 0.4% 17907ms 26.97% MutableMesh::ReMesh 535ms 0.81% 1.20% 13387ms 20.16% TetrahedralMesh::EdgeIterator::operator++ 1ms 0.0015% 1.20% 12987ms 19.56% tetgen::tetrahedralize 0 0% 1.20% 12852ms 19.35% tetgen::tetgenmesh::delaunizevertices 7ms 0.011% 1.21% 12851ms 19.35% tetgen::tetgenmesh::incrflipdelaunay 529ms 0.8% 2.01% 11384ms 17.14% tetgen::tetgenmesh::lawson 28ms 0.042% 2.05% 11176ms 16.83% std::set::insert (inline) 238ms 0.36% 2.41% 10652ms 16.04% std::_Rb_tree::_M_insert_unique 3077ms 4.63% 7.04% 10326ms 15.55% std::_Rb_tree::_M_lower_bound (inline) 419ms 0.63% 7.68% 9849ms 14.83% VertexElement::AddFace 242ms 0.36% 8.04% 9508ms 14.32% std::_Rb_tree::find (inline) 0 0% 8.04% 8984ms 13.53% std::set::count (inline) 7013ms 10.56% 18.60% 7013ms 10.56% std::_Rb_tree_increment 119ms 0.18% 18.78% 6854ms 10.32% std::less::operator() (inline) 6785ms 10.22% 29.00% 6785ms 10.22% std::operator< (inline) 280ms 0.42% 29.42% 6193ms 9.33% std::_Rb_tree::_M_insert_ (inline) 211ms 0.32% 29.74% 5949ms 8.96% operator new 1ms 0.0015% 29.74% 5807ms 8.75% OffLatticeSimulation::UpdateCellLocationsAndTopology 1141ms 1.72% 31.46% 5676ms 8.55% __GI___libc_malloc 0 0% 31.46% 5655ms 8.52% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.0075% 31.47% 5631ms 8.48% AbstractNumericalMethod::ComputeForcesIncludingDamping 50ms 0.075% 31.54% 4919ms 7.41% std::__new_allocator::allocate (inline) 0 0% 31.54% 4902ms 7.38% std::allocator_traits::allocate (inline) 0 0% 31.54% 4893ms 7.37% AbstractCellPopulation::WriteResultsToFiles 5ms 0.0075% 31.55% 4860ms 7.32% std::_Rb_tree::~_Rb_tree (inline) 2038ms 3.07% 34.62% 4854ms 7.31% std::_Rb_tree::_M_erase 0 0% 34.62% 4793ms 7.22% std::set::~set (inline) 2ms 0.003% 34.62% 4702ms 7.08% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.009% 34.63% 4677ms 7.04% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 4ms 0.006% 34.64% 4639ms 6.99% std::set_intersection (inline) 264ms 0.4% 35.03% 4635ms 6.98% std::__set_intersection 34ms 0.051% 35.08% 4584ms 6.90% Node::AddElement 1245ms 1.87% 36.96% 4554ms 6.86% std::_Rb_tree::_M_get_insert_unique_pos 8ms 0.012% 36.97% 4536ms 6.83% MeshBasedCellPopulation::SpringIterator::operator++ 1301ms 1.96% 38.93% 4426ms 6.67% __GI___libc_free 0 0% 38.93% 4368ms 6.58% VertexMesh::~VertexMesh 4269ms 6.43% 45.36% 4269ms 6.43% std::_Rb_tree::_S_right (inline) 2984ms 4.49% 49.85% 4159ms 6.26% _int_malloc 10ms 0.015% 49.87% 3986ms 6.00% TetrahedralMesh::ImportFromMesher 0 0% 49.87% 3936ms 5.93% std::_Rb_tree::_M_create_node (inline) 0 0% 49.87% 3895ms 5.87% std::_Rb_tree::_M_get_node (inline) 0 0% 49.87% 3891ms 5.86% std::_Rb_tree::_Alloc_node::operator() (inline) 156ms 0.23% 50.10% 3862ms 5.82% std::_Rb_tree_const_iterator::operator++ (inline) 137ms 0.21% 50.31% 3814ms 5.74% std::__new_allocator::deallocate (inline) 0 0% 50.31% 3794ms 5.71% std::allocator_traits::deallocate (inline) 259ms 0.39% 50.70% 3631ms 5.47% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 101ms 0.15% 50.85% 3572ms 5.38% tetgen::tetgenmesh::insphere_sos 90ms 0.14% 50.99% 3475ms 5.23% MutableElement::AddNode 3158ms 4.76% 55.74% 3457ms 5.21% tetgen::insphere 5ms 0.0075% 55.75% 3443ms 5.19% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 3ms 0.0045% 55.76% 3400ms 5.12% std::_Rb_tree_iterator::operator++ (inline) 1152ms 1.73% 57.49% 3123ms 4.70% _int_free 196ms 0.3% 57.79% 2986ms 4.50% Node::~Node 208ms 0.31% 58.10% 2772ms 4.17% tetgen::tetgenmesh::flip23 252ms 0.38% 58.48% 2766ms 4.17% VertexMesh::Clear 2121ms 3.19% 61.67% 2121ms 3.19% std::_Rb_tree_insert_and_rebalance 1335ms 2.01% 63.68% 1989ms 3.00% malloc_consolidate 2ms 0.003% 63.69% 1974ms 2.97% Element::Element 0 0% 63.69% 1953ms 2.94% std::_Rb_tree::_M_drop_node (inline) 1940ms 2.92% 66.61% 1940ms 2.92% Node::GetIndex 0 0% 66.61% 1933ms 2.91% std::_Rb_tree::_M_put_node (inline) 22ms 0.033% 66.64% 1883ms 2.84% std::_Vector_base::_M_deallocate (inline) 144ms 0.22% 66.86% 1833ms 2.76% tetgen::tetgenmesh::flip32 0 0% 66.86% 1750ms 2.64% std::vector::~vector (inline) 7ms 0.011% 66.87% 1716ms 2.58% _int_free_maybe_consolidate 1ms 0.0015% 66.87% 1700ms 2.56% std::_Vector_base::~_Vector_base (inline) 3ms 0.0045% 66.87% 1644ms 2.48% Element::RegisterWithNodes (inline) 232ms 0.35% 67.22% 1608ms 2.42% TetrahedralMesh::Clear 1451ms 2.19% 69.41% 1451ms 2.19% unlink_chunk 1304ms 1.96% 71.37% 1385ms 2.09% tetgen::orient3d 64ms 0.096% 71.47% 1358ms 2.05% std::map::operator[] 185ms 0.28% 71.75% 1325ms 2.00% tetgen::tetgenmesh::enqueueflipface 6ms 0.009% 71.76% 1247ms 1.88% VertexMesh::GenerateVerticesFromElementCircumcentres 88ms 0.13% 71.89% 1245ms 1.87% std::vector::_M_realloc_insert 47ms 0.071% 71.96% 1243ms 1.87% tetgen::tetgenmesh::locate 0 0% 71.96% 1212ms 1.83% std::_Rb_tree::lower_bound (inline) 0 0% 71.96% 1212ms 1.83% std::map::lower_bound (inline) 1ms 0.0015% 71.96% 1188ms 1.79% VoronoiDataWriter::Visit 92ms 0.14% 72.10% 1140ms 1.72% tetgen::tetgenmesh::preciselocate 124ms 0.19% 72.29% 1026ms 1.55% std::vector::push_back (inline) 1ms 0.0015% 72.29% 1008ms 1.52% std::_Vector_base::_M_allocate (inline) 851ms 1.28% 73.57% 988ms 1.49% AbstractElement::GetNodeGlobalIndex 944ms 1.42% 74.99% 944ms 1.42% tetgen::tetgenmesh::triface::triface 3ms 0.0045% 75.00% 903ms 1.36% TetrahedralMesh::RefreshJacobianCachedData 346ms 0.52% 75.52% 849ms 1.28% AbstractElement::GetNodeLocation 798ms 1.20% 76.72% 798ms 1.20% Node::rGetLocation 6ms 0.009% 76.73% 786ms 1.18% AbstractTetrahedralElement::CalculateInverseJacobian 374ms 0.56% 77.29% 741ms 1.12% tetgen::tetgenmesh::fnextself 1ms 0.0015% 77.29% 739ms 1.11% AbstractTwoBodyInteractionForce::AddForceContribution 12ms 0.018% 77.31% 738ms 1.11% AbstractTetrahedralElement::CalculateJacobian 728ms 1.10% 78.41% 728ms 1.10% AbstractElement::IsDeleted 19ms 0.029% 78.43% 685ms 1.03% boost::numeric::ublas::vector_assign (inline) 683ms 1.03% 79.46% 683ms 1.03% tetgen::tetgenmesh::triface::operator= 9ms 0.014% 79.48% 679ms 1.02% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 674ms 1.02% 80.49% 674ms 1.02% tetgen::tetgenmesh::oppo 9ms 0.014% 80.51% 641ms 0.97% boost::numeric::ublas::c_vector::c_vector (inline) 637ms 0.96% 81.46% 637ms 0.96% [libchaste_mesh.so] 57ms 0.086% 81.55% 634ms 0.95% __atan2 20ms 0.03% 81.58% 631ms 0.95% Element::CalculateCircumsphere 466ms 0.7% 82.28% 576ms 0.87% __ieee754_atan2_fma 41ms 0.062% 82.34% 569ms 0.86% AbstractTetrahedralElement::RefreshJacobian 564ms 0.85% 83.19% 564ms 0.85% std::vector::size (inline) 0 0% 83.19% 521ms 0.78% std::set::find (inline) 0 0% 83.19% 520ms 0.78% std::insert_iterator::operator= (inline) 0 0% 83.19% 473ms 0.71% std::_Rb_tree::_M_insert_unique_ (inline) 38ms 0.057% 83.25% 473ms 0.71% tetgen::tetgenmesh::enextfnext 42ms 0.063% 83.31% 469ms 0.71% tetgen::tetgenmesh::enext2fnext 22ms 0.033% 83.35% 467ms 0.7% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 83.35% 467ms 0.7% boost::numeric::ublas::inner_prod (inline) 4ms 0.006% 83.35% 463ms 0.7% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 29ms 0.044% 83.40% 459ms 0.69% boost::numeric::ublas::vector_scalar_binary::evaluate 307ms 0.46% 83.86% 456ms 0.69% tetgen::tetgenmesh::sym 117ms 0.18% 84.04% 440ms 0.66% boost::numeric::ublas::indexing_vector_assign 411ms 0.62% 84.65% 411ms 0.62% tetgen::tetgenmesh::org 229ms 0.34% 85.00% 410ms 0.62% AbstractTetrahedralMesh::GetElement 0 0% 85.00% 400ms 0.6% VertexMeshWriter::WriteVtkUsingMesh 100ms 0.15% 85.15% 395ms 0.59% __dynamic_cast 30ms 0.045% 85.19% 391ms 0.59% tetgen::tetgenmesh::queue::push 390ms 0.59% 85.78% 390ms 0.59% boost::numeric::ublas::c_vector::operator() 2ms 0.003% 85.79% 389ms 0.59% CellPropertyCollection::GetPropertiesType (inline) 0 0% 85.79% 388ms 0.58% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 24ms 0.036% 85.82% 387ms 0.58% std::_Rb_tree_iterator::operator-- (inline) 165ms 0.25% 86.07% 378ms 0.57% boost::numeric::ublas::vector_inner_prod::apply (inline) 2ms 0.003% 86.07% 375ms 0.56% Cell::GetCellId 16ms 0.024% 86.10% 370ms 0.56% std::vector::insert (inline) 261ms 0.39% 86.49% 369ms 0.56% tetgen::tetgenmesh::bond 4ms 0.006% 86.50% 366ms 0.55% boost::numeric::ublas::c_vector::operator= (inline) 254ms 0.38% 86.88% 359ms 0.54% tetgen::tetgenmesh::link::add 339ms 0.51% 87.39% 339ms 0.51% std::_Rb_tree_decrement 0 0% 87.39% 339ms 0.51% tcache_get (inline) 339ms 0.51% 87.90% 339ms 0.51% tcache_get_n (inline) 5ms 0.0075% 87.91% 337ms 0.51% VertexMesh::GetVolumeOfElement