File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 45519ms, 85.99% of 52938ms total Dropped 857 nodes (cum <= 264.69ms) flat flat% sum% cum cum% 0 0% 0% 52876ms 99.88% __libc_start_call_main 0 0% 0% 52876ms 99.88% __libc_start_main_impl 0 0% 0% 52876ms 99.88% _start 0 0% 0% 52862ms 99.86% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 52862ms 99.86% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 52862ms 99.86% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 52862ms 99.86% main 0 0% 0% 52823ms 99.78% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 52823ms 99.78% CxxTest::TestRunner::runTest (inline) 0 0% 0% 52823ms 99.78% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 52575ms 99.31% AbstractCellBasedSimulation::Solve 0 0% 0% 44254ms 83.60% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 44208ms 83.51% MeshBasedCellPopulation::Update 0 0% 0% 24268ms 45.84% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 24268ms 45.84% MeshBasedCellPopulation::TessellateIfNeeded 205ms 0.39% 0.39% 21696ms 40.98% VertexMesh::VertexMesh 0 0% 0.39% 16352ms 30.89% MutableMesh::ReMesh 0 0% 0.39% 12872ms 24.32% tetgen::tetrahedralize 1ms 0.0019% 0.39% 12732ms 24.05% tetgen::tetgenmesh::delaunizevertices 8ms 0.015% 0.4% 12729ms 24.05% tetgen::tetgenmesh::incrflipdelaunay 529ms 1% 1.40% 11401ms 21.54% tetgen::tetgenmesh::lawson 551ms 1.04% 2.44% 10782ms 20.37% TetrahedralMesh::EdgeIterator::operator++ 35ms 0.066% 2.51% 9016ms 17.03% std::set::insert (inline) 313ms 0.59% 3.10% 8706ms 16.45% VertexElement::AddFace 221ms 0.42% 3.52% 8485ms 16.03% std::_Rb_tree::_M_insert_unique 3088ms 5.83% 9.35% 8483ms 16.02% std::_Rb_tree::_M_lower_bound (inline) 232ms 0.44% 9.79% 8012ms 15.13% std::_Rb_tree::find (inline) 0 0% 9.79% 7451ms 14.07% std::set::count (inline) 115ms 0.22% 10.01% 5341ms 10.09% std::less::operator() (inline) 5293ms 10.00% 20.01% 5293ms 10.00% std::operator< (inline) 265ms 0.5% 20.51% 5257ms 9.93% std::_Rb_tree::_M_insert_ (inline) 0 0% 20.51% 4873ms 9.21% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 20.51% 4764ms 9.00% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 20.51% 4733ms 8.94% AbstractNumericalMethod::ComputeForcesIncludingDamping 193ms 0.36% 20.87% 4428ms 8.36% operator new 1181ms 2.23% 23.10% 4157ms 7.85% __GI___libc_malloc 3922ms 7.41% 30.51% 3922ms 7.41% std::_Rb_tree_increment 0 0% 30.51% 3918ms 7.40% MeshBasedCellPopulation::UpdateNodePairs 29ms 0.055% 30.57% 3888ms 7.34% std::__new_allocator::allocate (inline) 0 0% 30.57% 3869ms 7.31% std::allocator_traits::allocate (inline) 4ms 0.0076% 30.57% 3861ms 7.29% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 9ms 0.017% 30.59% 3799ms 7.18% MeshBasedCellPopulation::SpringIterator::operator++ 9ms 0.017% 30.61% 3643ms 6.88% std::_Rb_tree::~_Rb_tree (inline) 1231ms 2.33% 32.93% 3632ms 6.86% std::_Rb_tree::_M_erase 0 0% 32.93% 3590ms 6.78% std::set::~set (inline) 122ms 0.23% 33.16% 3518ms 6.65% tetgen::tetgenmesh::insphere_sos 3112ms 5.88% 39.04% 3381ms 6.39% tetgen::insphere 1194ms 2.26% 41.30% 3348ms 6.32% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 41.30% 3310ms 6.25% AbstractCellPopulation::WriteResultsToFiles 929ms 1.75% 43.05% 3222ms 6.09% __GI___libc_free 0 0% 43.05% 3222ms 6.09% std::_Rb_tree::_M_create_node (inline) 0 0% 43.05% 3193ms 6.03% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 43.05% 3191ms 6.03% std::_Rb_tree::_M_get_node (inline) 145ms 0.27% 43.33% 3011ms 5.69% std::__new_allocator::deallocate (inline) 0 0% 43.33% 2984ms 5.64% std::allocator_traits::deallocate (inline) 3ms 0.0057% 43.33% 2913ms 5.50% std::set_intersection (inline) 241ms 0.46% 43.79% 2910ms 5.50% std::__set_intersection 195ms 0.37% 44.16% 2865ms 5.41% tetgen::tetgenmesh::flip23 27ms 0.051% 44.21% 2823ms 5.33% Node::AddElement 29ms 0.055% 44.26% 2741ms 5.18% TetrahedralMesh::ImportFromMesher 2023ms 3.82% 48.08% 2635ms 4.98% _int_malloc 0 0% 48.08% 2587ms 4.89% VertexMesh::~VertexMesh 2455ms 4.64% 52.72% 2455ms 4.64% std::_Rb_tree::_S_right (inline) 1198ms 2.26% 54.98% 2292ms 4.33% _int_free 3ms 0.0057% 54.99% 2258ms 4.27% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 221ms 0.42% 55.41% 2247ms 4.24% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 220ms 0.42% 55.82% 2225ms 4.20% std::_Rb_tree_const_iterator::operator++ (inline) 76ms 0.14% 55.97% 2110ms 3.99% MutableElement::AddNode 1ms 0.0019% 55.97% 2036ms 3.85% std::_Rb_tree_iterator::operator++ (inline) 0 0% 55.97% 1887ms 3.56% std::_Rb_tree::_M_drop_node (inline) 0 0% 55.97% 1879ms 3.55% std::_Rb_tree::_M_put_node (inline) 161ms 0.3% 56.27% 1864ms 3.52% tetgen::tetgenmesh::flip32 1849ms 3.49% 59.76% 1849ms 3.49% std::_Rb_tree_insert_and_rebalance 98ms 0.19% 59.95% 1816ms 3.43% Node::~Node 132ms 0.25% 60.20% 1753ms 3.31% VertexMesh::Clear 3ms 0.0057% 60.20% 1504ms 2.84% Element::Element 1294ms 2.44% 62.65% 1387ms 2.62% tetgen::orient3d 211ms 0.4% 63.05% 1363ms 2.57% tetgen::tetgenmesh::enqueueflipface 3ms 0.0057% 63.05% 1158ms 2.19% Element::RegisterWithNodes (inline) 1151ms 2.17% 65.23% 1151ms 2.17% Node::GetIndex 14ms 0.026% 65.25% 1119ms 2.11% std::_Vector_base::_M_deallocate (inline) 41ms 0.077% 65.33% 1104ms 2.09% tetgen::tetgenmesh::locate 0 0% 65.33% 1087ms 2.05% std::vector::~vector (inline) 662ms 1.25% 66.58% 1064ms 2.01% malloc_consolidate 74ms 0.14% 66.72% 1040ms 1.96% std::map::operator[] 97ms 0.18% 66.90% 1016ms 1.92% tetgen::tetgenmesh::preciselocate 1ms 0.0019% 66.91% 940ms 1.78% std::_Vector_base::~_Vector_base (inline) 91ms 0.17% 67.08% 938ms 1.77% TetrahedralMesh::Clear 63ms 0.12% 67.20% 927ms 1.75% std::vector::_M_realloc_insert 10ms 0.019% 67.22% 918ms 1.73% _int_free_maybe_consolidate 908ms 1.72% 68.93% 908ms 1.72% tetgen::tetgenmesh::triface::triface 0 0% 68.93% 902ms 1.70% std::_Rb_tree::lower_bound (inline) 0 0% 68.93% 902ms 1.70% std::map::lower_bound (inline) 483ms 0.91% 69.84% 878ms 1.66% tetgen::tetgenmesh::fnextself 0 0% 69.84% 845ms 1.60% VoronoiDataWriter::Visit 773ms 1.46% 71.30% 773ms 1.46% unlink_chunk 118ms 0.22% 71.53% 772ms 1.46% std::vector::push_back (inline) 5ms 0.0094% 71.54% 761ms 1.44% VertexMesh::GenerateVerticesFromElementCircumcentres 1ms 0.0019% 71.54% 726ms 1.37% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.0019% 71.54% 722ms 1.36% AbstractTwoBodyInteractionForce::AddForceContribution 18ms 0.034% 71.57% 717ms 1.35% boost::numeric::ublas::vector_assign (inline) 19ms 0.036% 71.61% 687ms 1.30% boost::numeric::ublas::c_vector::c_vector (inline) 685ms 1.29% 72.90% 685ms 1.29% [libchaste_mesh.so] 5ms 0.0094% 72.91% 683ms 1.29% std::_Vector_base::_M_allocate (inline) 7ms 0.013% 72.93% 678ms 1.28% AbstractTetrahedralElement::CalculateInverseJacobian 675ms 1.28% 74.20% 675ms 1.28% tetgen::tetgenmesh::oppo 7ms 0.013% 74.22% 674ms 1.27% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 14ms 0.026% 74.24% 657ms 1.24% AbstractTetrahedralElement::CalculateJacobian 499ms 0.94% 75.18% 607ms 1.15% AbstractElement::GetNodeGlobalIndex 607ms 1.15% 76.33% 607ms 1.15% tetgen::tetgenmesh::triface::operator= 53ms 0.1% 76.43% 592ms 1.12% tetgen::tetgenmesh::enextfnext 44ms 0.083% 76.51% 578ms 1.09% __atan2 234ms 0.44% 76.96% 558ms 1.05% AbstractElement::GetNodeLocation 0 0% 76.96% 557ms 1.05% std::set::find (inline) 422ms 0.8% 77.75% 534ms 1.01% __ieee754_atan2_fma 0 0% 77.75% 511ms 0.97% std::insert_iterator::operator= (inline) 37ms 0.07% 77.82% 498ms 0.94% tetgen::tetgenmesh::enext2fnext 49ms 0.093% 77.92% 484ms 0.91% AbstractTetrahedralElement::RefreshJacobian 122ms 0.23% 78.15% 471ms 0.89% boost::numeric::ublas::indexing_vector_assign 0 0% 78.15% 466ms 0.88% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 78.15% 462ms 0.87% boost::numeric::ublas::inner_prod (inline) 6ms 0.011% 78.16% 458ms 0.87% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 20ms 0.038% 78.20% 452ms 0.85% boost::numeric::ublas::vector_scalar_binary::evaluate 309ms 0.58% 78.78% 439ms 0.83% tetgen::tetgenmesh::sym 33ms 0.062% 78.84% 433ms 0.82% tetgen::tetgenmesh::queue::push 1ms 0.0019% 78.84% 431ms 0.81% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.0057% 78.85% 426ms 0.8% boost::numeric::ublas::c_vector::operator= (inline) 22ms 0.042% 78.89% 421ms 0.8% Element::CalculateCircumsphere 419ms 0.79% 79.68% 419ms 0.79% boost::numeric::ublas::c_vector::operator() 1ms 0.0019% 79.68% 414ms 0.78% Cell::GetCellId 95ms 0.18% 79.86% 411ms 0.78% __dynamic_cast 399ms 0.75% 80.62% 399ms 0.75% Node::rGetLocation 278ms 0.53% 81.14% 399ms 0.75% tetgen::tetgenmesh::link::add 20ms 0.038% 81.18% 396ms 0.75% std::_Rb_tree_iterator::operator-- (inline) 386ms 0.73% 81.91% 386ms 0.73% std::vector::size (inline) 0 0% 81.91% 382ms 0.72% VertexMeshWriter::WriteVtkUsingMesh 197ms 0.37% 82.28% 378ms 0.71% AbstractTetrahedralMesh::GetElement 169ms 0.32% 82.60% 376ms 0.71% boost::numeric::ublas::vector_inner_prod::apply (inline) 12ms 0.023% 82.62% 369ms 0.7% VertexMesh::CalculateUnitNormalToFaceWithArea 354ms 0.67% 83.29% 354ms 0.67% std::_Rb_tree_decrement 3ms 0.0057% 83.30% 351ms 0.66% AbstractCellProperty::IsSubType (inline) 351ms 0.66% 83.96% 351ms 0.66% tetgen::tetgenmesh::org 4ms 0.0076% 83.97% 343ms 0.65% AbstractTetrahedralElement::AbstractTetrahedralElement 259ms 0.49% 84.46% 334ms 0.63% tetgen::tetgenmesh::bond 3ms 0.0057% 84.46% 324ms 0.61% VertexElement::~VertexElement 61ms 0.12% 84.58% 324ms 0.61% boost::numeric::ublas::vector_reference::operator() (inline) 126ms 0.24% 84.82% 313ms 0.59% Inverse 0 0% 84.82% 308ms 0.58% tcache_get (inline) 308ms 0.58% 85.40% 308ms 0.58% tcache_get_n (inline) 62ms 0.12% 85.52% 307ms 0.58% tetgen::tetgenmesh::queue::pop 11ms 0.021% 85.54% 298ms 0.56% std::vector::insert (inline) 36ms 0.068% 85.60% 269ms 0.51% tetgen::insphereadapt 202ms 0.38% 85.99% 267ms 0.5% boost::numeric::ublas::c_matrix::operator()