File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 58323ms, 87.59% of 66587ms total Dropped 908 nodes (cum <= 332.94ms) flat flat% sum% cum cum% 0 0% 0% 66515ms 99.89% __libc_start_call_main 0 0% 0% 66515ms 99.89% __libc_start_main_impl 0 0% 0% 66515ms 99.89% _start 0 0% 0% 66498ms 99.87% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 66498ms 99.87% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 66498ms 99.87% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 66498ms 99.87% main 0 0% 0% 66460ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 66460ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 66460ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 66184ms 99.39% AbstractCellBasedSimulation::Solve 0 0% 0% 55184ms 82.88% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 55124ms 82.78% MeshBasedCellPopulation::Update 0 0% 0% 32513ms 48.83% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 32513ms 48.83% MeshBasedCellPopulation::TessellateIfNeeded 207ms 0.31% 0.31% 28138ms 42.26% VertexMesh::VertexMesh 0 0% 0.31% 18269ms 27.44% MutableMesh::ReMesh 543ms 0.82% 1.13% 13333ms 20.02% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.13% 12944ms 19.44% tetgen::tetrahedralize 1ms 0.0015% 1.13% 12805ms 19.23% tetgen::tetgenmesh::delaunizevertices 6ms 0.009% 1.14% 12801ms 19.22% tetgen::tetgenmesh::incrflipdelaunay 25ms 0.038% 1.17% 11395ms 17.11% std::set::insert (inline) 562ms 0.84% 2.02% 11391ms 17.11% tetgen::tetgenmesh::lawson 208ms 0.31% 2.33% 10905ms 16.38% std::_Rb_tree::_M_insert_unique 3131ms 4.70% 7.03% 10382ms 15.59% std::_Rb_tree::_M_lower_bound (inline) 398ms 0.6% 7.63% 9740ms 14.63% VertexElement::AddFace 244ms 0.37% 8.00% 9578ms 14.38% std::_Rb_tree::find (inline) 0 0% 8.00% 9038ms 13.57% std::set::count (inline) 7156ms 10.75% 18.74% 7156ms 10.75% std::_Rb_tree_increment 122ms 0.18% 18.93% 6817ms 10.24% std::less::operator() (inline) 6754ms 10.14% 29.07% 6754ms 10.14% std::operator< (inline) 271ms 0.41% 29.48% 6306ms 9.47% std::_Rb_tree::_M_insert_ (inline) 221ms 0.33% 29.81% 6009ms 9.02% operator new 0 0% 29.81% 5841ms 8.77% OffLatticeSimulation::UpdateCellLocationsAndTopology 1094ms 1.64% 31.45% 5729ms 8.60% __GI___libc_malloc 0 0% 31.45% 5682ms 8.53% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.006% 31.46% 5661ms 8.50% AbstractNumericalMethod::ComputeForcesIncludingDamping 47ms 0.071% 31.53% 5022ms 7.54% std::__new_allocator::allocate (inline) 0 0% 31.53% 5004ms 7.51% std::allocator_traits::allocate (inline) 0 0% 31.53% 4991ms 7.50% AbstractCellPopulation::WriteResultsToFiles 17ms 0.026% 31.55% 4950ms 7.43% Node::AddElement 5ms 0.0075% 31.56% 4910ms 7.37% std::_Rb_tree::~_Rb_tree (inline) 2141ms 3.22% 34.78% 4904ms 7.36% std::_Rb_tree::_M_erase 0 0% 34.78% 4838ms 7.27% std::set::~set (inline) 2ms 0.003% 34.78% 4707ms 7.07% MeshBasedCellPopulation::UpdateNodePairs 1285ms 1.93% 36.71% 4705ms 7.07% std::_Rb_tree::_M_get_insert_unique_pos 2ms 0.003% 36.71% 4697ms 7.05% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 4ms 0.006% 36.72% 4659ms 7.00% std::set_intersection (inline) 310ms 0.47% 37.18% 4655ms 6.99% std::__set_intersection 15ms 0.023% 37.21% 4546ms 6.83% MeshBasedCellPopulation::SpringIterator::operator++ 4437ms 6.66% 43.87% 4437ms 6.66% std::_Rb_tree::_S_right (inline) 0 0% 43.87% 4411ms 6.62% VertexMesh::~VertexMesh 8ms 0.012% 43.88% 4395ms 6.60% TetrahedralMesh::ImportFromMesher 1222ms 1.84% 45.72% 4281ms 6.43% __GI___libc_free 3169ms 4.76% 50.48% 4273ms 6.42% _int_malloc 0 0% 50.48% 4035ms 6.06% std::_Rb_tree::_M_create_node (inline) 0 0% 50.48% 4001ms 6.01% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 50.48% 3998ms 6.00% std::_Rb_tree::_M_get_node (inline) 165ms 0.25% 50.72% 3877ms 5.82% std::_Rb_tree_const_iterator::operator++ (inline) 229ms 0.34% 51.07% 3752ms 5.63% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 115ms 0.17% 51.24% 3703ms 5.56% std::__new_allocator::deallocate (inline) 0 0% 51.24% 3684ms 5.53% std::allocator_traits::deallocate (inline) 6ms 0.009% 51.25% 3554ms 5.34% std::_Rb_tree_iterator::operator++ (inline) 76ms 0.11% 51.36% 3541ms 5.32% MutableElement::AddNode 116ms 0.17% 51.54% 3518ms 5.28% tetgen::tetgenmesh::insphere_sos 2ms 0.003% 51.54% 3490ms 5.24% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 3100ms 4.66% 56.20% 3392ms 5.09% tetgen::insphere 205ms 0.31% 56.51% 3115ms 4.68% Node::~Node 1143ms 1.72% 58.22% 3057ms 4.59% _int_free 248ms 0.37% 58.59% 2847ms 4.28% VertexMesh::Clear 199ms 0.3% 58.89% 2759ms 4.14% tetgen::tetgenmesh::flip23 4ms 0.006% 58.90% 2264ms 3.40% Element::Element 2143ms 3.22% 62.12% 2143ms 3.22% std::_Rb_tree_insert_and_rebalance 1263ms 1.90% 64.01% 1942ms 2.92% malloc_consolidate 1926ms 2.89% 66.91% 1926ms 2.89% Node::GetIndex 2ms 0.003% 66.91% 1909ms 2.87% Element::RegisterWithNodes (inline) 0 0% 66.91% 1864ms 2.80% std::_Rb_tree::_M_drop_node (inline) 26ms 0.039% 66.95% 1856ms 2.79% std::_Vector_base::_M_deallocate (inline) 189ms 0.28% 67.23% 1855ms 2.79% tetgen::tetgenmesh::flip32 0 0% 67.23% 1854ms 2.78% std::_Rb_tree::_M_put_node (inline) 0 0% 67.23% 1755ms 2.64% std::vector::~vector (inline) 0 0% 67.23% 1686ms 2.53% std::_Vector_base::~_Vector_base (inline) 248ms 0.37% 67.60% 1683ms 2.53% TetrahedralMesh::Clear 2ms 0.003% 67.61% 1660ms 2.49% _int_free_maybe_consolidate 1338ms 2.01% 69.62% 1405ms 2.11% tetgen::orient3d 1391ms 2.09% 71.71% 1391ms 2.09% unlink_chunk 62ms 0.093% 71.80% 1343ms 2.02% std::map::operator[] 174ms 0.26% 72.06% 1298ms 1.95% tetgen::tetgenmesh::enqueueflipface 0 0% 72.06% 1232ms 1.85% VoronoiDataWriter::Visit 0 0% 72.06% 1219ms 1.83% std::_Rb_tree::lower_bound (inline) 0 0% 72.06% 1219ms 1.83% std::map::lower_bound (inline) 31ms 0.047% 72.11% 1211ms 1.82% tetgen::tetgenmesh::locate 62ms 0.093% 72.20% 1202ms 1.81% std::vector::_M_realloc_insert 5ms 0.0075% 72.21% 1167ms 1.75% VertexMesh::GenerateVerticesFromElementCircumcentres 105ms 0.16% 72.37% 1120ms 1.68% tetgen::tetgenmesh::preciselocate 888ms 1.33% 73.70% 1023ms 1.54% AbstractElement::GetNodeGlobalIndex 7ms 0.011% 73.71% 1013ms 1.52% std::_Vector_base::_M_allocate (inline) 125ms 0.19% 73.90% 996ms 1.50% std::vector::push_back (inline) 1ms 0.0015% 73.90% 899ms 1.35% TetrahedralMesh::RefreshJacobianCachedData 864ms 1.30% 75.20% 864ms 1.30% tetgen::tetgenmesh::triface::triface 353ms 0.53% 75.73% 836ms 1.26% AbstractElement::GetNodeLocation 775ms 1.16% 76.89% 775ms 1.16% Node::rGetLocation 7ms 0.011% 76.90% 774ms 1.16% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.003% 76.90% 749ms 1.12% AbstractTwoBodyInteractionForce::AddForceContribution 17ms 0.026% 76.93% 732ms 1.10% AbstractTetrahedralElement::CalculateJacobian 18ms 0.027% 76.96% 687ms 1.03% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 684ms 1.03% 77.98% 684ms 1.03% tetgen::tetgenmesh::triface::operator= 679ms 1.02% 79.00% 679ms 1.02% tetgen::tetgenmesh::oppo 675ms 1.01% 80.02% 675ms 1.01% AbstractElement::IsDeleted 21ms 0.032% 80.05% 667ms 1.00% boost::numeric::ublas::vector_assign (inline) 402ms 0.6% 80.65% 663ms 1% tetgen::tetgenmesh::fnextself 11ms 0.017% 80.67% 638ms 0.96% boost::numeric::ublas::c_vector::c_vector (inline) 43ms 0.065% 80.73% 629ms 0.94% __atan2 22ms 0.033% 80.77% 627ms 0.94% Element::CalculateCircumsphere 613ms 0.92% 81.69% 613ms 0.92% [libchaste_mesh.so] 472ms 0.71% 82.40% 585ms 0.88% __ieee754_atan2_fma 30ms 0.045% 82.44% 556ms 0.83% AbstractTetrahedralElement::RefreshJacobian 0 0% 82.44% 535ms 0.8% std::set::find (inline) 524ms 0.79% 83.23% 524ms 0.79% std::vector::size (inline) 0 0% 83.23% 488ms 0.73% boost::numeric::ublas::inner_prod (inline) 8ms 0.012% 83.24% 486ms 0.73% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 83.24% 481ms 0.72% std::insert_iterator::operator= (inline) 39ms 0.059% 83.30% 478ms 0.72% boost::numeric::ublas::vector_scalar_binary::evaluate 51ms 0.077% 83.38% 472ms 0.71% tetgen::tetgenmesh::enextfnext 0 0% 83.38% 436ms 0.65% std::_Rb_tree::_M_insert_unique_ (inline) 14ms 0.021% 83.40% 435ms 0.65% VertexMesh::CalculateUnitNormalToFaceWithArea 47ms 0.071% 83.47% 434ms 0.65% tetgen::tetgenmesh::enext2fnext 27ms 0.041% 83.51% 421ms 0.63% std::_Rb_tree_iterator::operator-- (inline) 116ms 0.17% 83.68% 420ms 0.63% boost::numeric::ublas::indexing_vector_assign 4ms 0.006% 83.69% 419ms 0.63% CellPropertyCollection::GetPropertiesType (inline) 25ms 0.038% 83.73% 414ms 0.62% tetgen::tetgenmesh::queue::push 0 0% 83.73% 398ms 0.6% VertexMeshWriter::WriteVtkUsingMesh 4ms 0.006% 83.73% 396ms 0.59% Cell::GetCellId 105ms 0.16% 83.89% 391ms 0.59% __dynamic_cast 2ms 0.003% 83.89% 391ms 0.59% boost::numeric::ublas::c_vector::operator= (inline) 263ms 0.39% 84.29% 387ms 0.58% tetgen::tetgenmesh::link::add 171ms 0.26% 84.54% 385ms 0.58% boost::numeric::ublas::vector_inner_prod::apply (inline) 384ms 0.58% 85.12% 384ms 0.58% boost::numeric::ublas::c_vector::operator() 381ms 0.57% 85.69% 381ms 0.57% std::_Rb_tree_decrement 205ms 0.31% 86.00% 380ms 0.57% AbstractTetrahedralMesh::GetElement 0 0% 86.00% 379ms 0.57% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 259ms 0.39% 86.39% 379ms 0.57% tetgen::tetgenmesh::sym 377ms 0.57% 86.96% 377ms 0.57% tetgen::tetgenmesh::org 264ms 0.4% 87.35% 372ms 0.56% tetgen::tetgenmesh::bond 5ms 0.0075% 87.36% 369ms 0.55% VertexElement::~VertexElement 11ms 0.017% 87.38% 358ms 0.54% std::vector::insert (inline) 4ms 0.006% 87.38% 351ms 0.53% AbstractTetrahedralElement::AbstractTetrahedralElement 4ms 0.006% 87.39% 337ms 0.51% AbstractCellProperty::IsSubType (inline) 134ms 0.2% 87.59% 336ms 0.5% Inverse