File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 56599ms, 86.80% of 65208ms total Dropped 834 nodes (cum <= 326.04ms) flat flat% sum% cum cum% 0 0% 0% 65169ms 99.94% __libc_start_call_main 0 0% 0% 65169ms 99.94% __libc_start_main_impl 0 0% 0% 65169ms 99.94% _start 0 0% 0% 65155ms 99.92% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 65155ms 99.92% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 65155ms 99.92% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 65155ms 99.92% main 0 0% 0% 65121ms 99.87% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 65121ms 99.87% CxxTest::TestRunner::runTest (inline) 0 0% 0% 65121ms 99.87% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 64873ms 99.49% AbstractCellBasedSimulation::Solve 0 0% 0% 55732ms 85.47% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 55664ms 85.36% MeshBasedCellPopulation::Update 0 0% 0% 34492ms 52.90% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 34491ms 52.89% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 353ms 0.54% 0.54% 30511ms 46.79% VertexMesh::VertexMesh 0 0% 0.54% 17115ms 26.25% MutableMesh::ReMesh 581ms 0.89% 1.43% 12646ms 19.39% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.43% 12634ms 19.37% tetgen::tetrahedralize 30ms 0.046% 1.48% 12531ms 19.22% std::set::insert (inline) 1ms 0.0015% 1.48% 12478ms 19.14% tetgen::tetgenmesh::delaunizevertices 13ms 0.02% 1.50% 12475ms 19.13% tetgen::tetgenmesh::incrflipdelaunay 174ms 0.27% 1.77% 12007ms 18.41% std::_Rb_tree::_M_insert_unique 630ms 0.97% 2.73% 11074ms 16.98% tetgen::tetgenmesh::lawson 411ms 0.63% 3.36% 10957ms 16.80% VertexElement::AddFace 2809ms 4.31% 7.67% 8956ms 13.73% std::_Rb_tree::_M_lower_bound (inline) 253ms 0.39% 8.06% 8566ms 13.14% std::_Rb_tree::find (inline) 217ms 0.33% 8.39% 8433ms 12.93% operator new 2963ms 4.54% 12.94% 8116ms 12.45% __GI___libc_malloc 0 0% 12.94% 8090ms 12.41% std::set::count (inline) 322ms 0.49% 13.43% 7995ms 12.26% std::_Rb_tree::_M_insert_ (inline) 63ms 0.097% 13.53% 7027ms 10.78% std::__new_allocator::allocate (inline) 0 0% 13.53% 7001ms 10.74% std::allocator_traits::allocate (inline) 5950ms 9.12% 22.65% 5950ms 9.12% std::_Rb_tree_increment 0 0% 22.65% 5693ms 8.73% std::_Rb_tree::_M_create_node (inline) 0 0% 22.65% 5662ms 8.68% std::_Rb_tree::_M_get_node (inline) 0 0% 22.65% 5658ms 8.68% std::_Rb_tree::_Alloc_node::operator() (inline) 1ms 0.0015% 22.65% 5625ms 8.63% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0015% 22.65% 5499ms 8.43% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0046% 22.66% 5470ms 8.39% AbstractNumericalMethod::ComputeForcesIncludingDamping 343ms 0.53% 23.18% 5340ms 8.19% std::__set_intersection 0 0% 23.18% 5340ms 8.19% std::set_intersection (inline) 1074ms 1.65% 24.83% 5331ms 8.18% __GI___libc_free 5193ms 7.96% 32.80% 5193ms 7.96% std::operator< (inline) 20ms 0.031% 32.83% 5142ms 7.89% std::less::operator() (inline) 3550ms 5.44% 38.27% 4721ms 7.24% _int_malloc 21ms 0.032% 38.30% 4609ms 7.07% Node::AddElement 235ms 0.36% 38.66% 4490ms 6.89% std::_Rb_tree_const_iterator::operator++ (inline) 86ms 0.13% 38.79% 4479ms 6.87% std::__new_allocator::deallocate (inline) 0 0% 38.79% 4466ms 6.85% std::allocator_traits::deallocate (inline) 7ms 0.011% 38.81% 4407ms 6.76% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 38.81% 4387ms 6.73% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.011% 38.82% 4373ms 6.71% std::_Rb_tree::~_Rb_tree (inline) 1196ms 1.83% 40.65% 4351ms 6.67% std::_Rb_tree::_M_erase 0 0% 40.65% 4318ms 6.62% std::set::~set (inline) 17ms 0.026% 40.68% 4241ms 6.50% MeshBasedCellPopulation::SpringIterator::operator++ 2001ms 3.07% 43.74% 4190ms 6.43% _int_free 4188ms 6.42% 50.17% 4188ms 6.42% std::_Rb_tree::_S_right (inline) 1194ms 1.83% 52.00% 4164ms 6.39% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 52.00% 4013ms 6.15% VertexMesh::~VertexMesh 12ms 0.018% 52.02% 3564ms 5.47% TetrahedralMesh::ImportFromMesher 60ms 0.092% 52.11% 3554ms 5.45% MutableElement::AddNode 0 0% 52.11% 3342ms 5.13% AbstractCellPopulation::WriteResultsToFiles 108ms 0.17% 52.27% 2966ms 4.55% tetgen::tetgenmesh::insphere_sos 249ms 0.38% 52.66% 2840ms 4.36% tetgen::tetgenmesh::flip23 2608ms 4.00% 56.66% 2834ms 4.35% tetgen::insphere 0 0% 56.66% 2550ms 3.91% std::_Rb_tree::_M_drop_node (inline) 0 0% 56.66% 2518ms 3.86% std::_Rb_tree::_M_put_node (inline) 55ms 0.084% 56.74% 2372ms 3.64% VertexMesh::Clear 4ms 0.0061% 56.75% 2267ms 3.48% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 51ms 0.078% 56.82% 2261ms 3.47% Node::~Node 60ms 0.092% 56.92% 2176ms 3.34% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 194ms 0.3% 57.21% 2128ms 3.26% std::_Rb_tree_iterator::operator++ (inline) 2082ms 3.19% 60.41% 2082ms 3.19% std::_Rb_tree_insert_and_rebalance 4ms 0.0061% 60.41% 2027ms 3.11% Element::Element 1444ms 2.21% 62.63% 2018ms 3.09% malloc_consolidate 14ms 0.021% 62.65% 1962ms 3.01% std::_Vector_base::_M_deallocate (inline) 1957ms 3.00% 65.65% 1957ms 3.00% [libchaste_mesh.so] 174ms 0.27% 65.92% 1925ms 2.95% tetgen::tetgenmesh::flip32 0 0% 65.92% 1796ms 2.75% std::vector::~vector (inline) 2ms 0.0031% 65.92% 1773ms 2.72% std::_Vector_base::~_Vector_base (inline) 13ms 0.02% 65.94% 1745ms 2.68% _int_free_maybe_consolidate 4ms 0.0061% 65.95% 1656ms 2.54% Element::RegisterWithNodes (inline) 1607ms 2.46% 68.41% 1607ms 2.46% Node::GetIndex 1458ms 2.24% 70.65% 1528ms 2.34% tetgen::orient3d 53ms 0.081% 70.73% 1481ms 2.27% std::vector::_M_realloc_insert 5ms 0.0077% 70.74% 1469ms 2.25% VertexMesh::GenerateVerticesFromElementCircumcentres 172ms 0.26% 71.00% 1455ms 2.23% tetgen::tetgenmesh::enqueueflipface 1397ms 2.14% 73.14% 1397ms 2.14% unlink_chunk 4ms 0.0061% 73.15% 1343ms 2.06% std::_Vector_base::_M_allocate (inline) 76ms 0.12% 73.26% 1156ms 1.77% std::vector::push_back (inline) 27ms 0.041% 73.31% 1155ms 1.77% tetgen::tetgenmesh::locate 100ms 0.15% 73.46% 1086ms 1.67% tetgen::tetgenmesh::preciselocate 58ms 0.089% 73.55% 1071ms 1.64% TetrahedralMesh::Clear 71ms 0.11% 73.66% 1065ms 1.63% std::map::operator[] 810ms 1.24% 74.90% 1028ms 1.58% AbstractElement::GetNodeGlobalIndex 0 0% 74.90% 920ms 1.41% std::_Rb_tree::lower_bound (inline) 0 0% 74.90% 920ms 1.41% std::map::lower_bound (inline) 530ms 0.81% 75.71% 899ms 1.38% tetgen::tetgenmesh::sym 1ms 0.0015% 75.71% 889ms 1.36% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.0015% 75.71% 851ms 1.31% VoronoiDataWriter::Visit 190ms 0.29% 76.01% 849ms 1.30% boost::numeric::ublas::vector_assign (inline) 1ms 0.0015% 76.01% 835ms 1.28% AbstractTwoBodyInteractionForce::AddForceContribution 7ms 0.011% 76.02% 830ms 1.27% boost::numeric::ublas::c_vector::c_vector (inline) 826ms 1.27% 77.28% 826ms 1.27% Node::rGetLocation 19ms 0.029% 77.31% 785ms 1.20% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 422ms 0.65% 77.96% 778ms 1.19% AbstractElement::GetNodeLocation 16ms 0.025% 77.99% 770ms 1.18% Element::CalculateCircumsphere 4ms 0.0061% 77.99% 745ms 1.14% AbstractTetrahedralElement::CalculateInverseJacobian 11ms 0.017% 78.01% 735ms 1.13% AbstractTetrahedralElement::CalculateJacobian 719ms 1.10% 79.11% 719ms 1.10% AbstractElement::IsDeleted 578ms 0.89% 80.00% 578ms 0.89% tetgen::tetgenmesh::oppo 47ms 0.072% 80.07% 577ms 0.88% __atan2 58ms 0.089% 80.16% 562ms 0.86% AbstractTetrahedralElement::RefreshJacobian 537ms 0.82% 80.98% 537ms 0.82% tetgen::tetgenmesh::triface::triface 470ms 0.72% 81.70% 527ms 0.81% __ieee754_atan2_fma 526ms 0.81% 82.51% 526ms 0.81% std::vector::size (inline) 0 0% 82.51% 507ms 0.78% std::insert_iterator::operator= (inline) 392ms 0.6% 83.11% 494ms 0.76% tetgen::tetgenmesh::fnextself 6ms 0.0092% 83.12% 486ms 0.75% CellPropertyCollection::GetPropertiesType (inline) 0 0% 83.12% 471ms 0.72% std::set::find (inline) 0 0% 83.12% 470ms 0.72% std::_Rb_tree::_M_insert_unique_ (inline) 18ms 0.028% 83.15% 470ms 0.72% std::vector::insert (inline) 1ms 0.0015% 83.15% 464ms 0.71% Cell::GetCellId 54ms 0.083% 83.23% 459ms 0.7% tetgen::tetgenmesh::enextfnext 31ms 0.048% 83.28% 451ms 0.69% tetgen::tetgenmesh::enext2fnext 103ms 0.16% 83.44% 431ms 0.66% std::_Rb_tree_iterator::operator-- (inline) 84ms 0.13% 83.57% 429ms 0.66% boost::numeric::ublas::indexing_vector_assign 22ms 0.034% 83.60% 420ms 0.64% tetgen::tetgenmesh::queue::push 97ms 0.15% 83.75% 411ms 0.63% tetgen::tetgenmesh::queue::pop 0 0% 83.75% 400ms 0.61% VertexMeshWriter::WriteVtkUsingMesh 0 0% 83.75% 398ms 0.61% boost::numeric::ublas::inner_prod (inline) 25ms 0.038% 83.79% 397ms 0.61% VertexMesh::CalculateUnitNormalToFaceWithArea 17ms 0.026% 83.81% 395ms 0.61% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 83.81% 395ms 0.61% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 296ms 0.45% 84.27% 385ms 0.59% tetgen::tetgenmesh::link::add 207ms 0.32% 84.58% 383ms 0.59% tetgen::tetgenmesh::bond 0 0% 84.58% 381ms 0.58% tcache_get (inline) 381ms 0.58% 85.17% 381ms 0.58% tcache_get_n (inline) 112ms 0.17% 85.34% 377ms 0.58% __dynamic_cast 0 0% 85.34% 368ms 0.56% AbstractTetrahedralElement::AbstractTetrahedralElement 135ms 0.21% 85.55% 366ms 0.56% boost::numeric::ublas::vector_inner_prod::apply (inline) 4ms 0.0061% 85.55% 354ms 0.54% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 85.55% 342ms 0.52% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 5ms 0.0077% 85.56% 333ms 0.51% AbstractCellProperty::IsSubType (inline) 6ms 0.0092% 85.57% 333ms 0.51% VertexElement::~VertexElement 332ms 0.51% 86.08% 332ms 0.51% boost::numeric::ublas::c_vector::operator() 330ms 0.51% 86.59% 330ms 0.51% tetgen::tetgenmesh::decode 138ms 0.21% 86.80% 327ms 0.5% AbstractTetrahedralMesh::GetElement