File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 55462ms, 85.71% of 64708ms total Dropped 864 nodes (cum <= 323.54ms) flat flat% sum% cum cum% 0 0% 0% 64649ms 99.91% __libc_start_call_main 0 0% 0% 64649ms 99.91% __libc_start_main_impl 0 0% 0% 64649ms 99.91% _start 0 0% 0% 64632ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 64632ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 64632ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 64632ms 99.88% main 0 0% 0% 64590ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 64590ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 64590ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 64293ms 99.36% AbstractCellBasedSimulation::Solve 0 0% 0% 55107ms 85.16% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 55053ms 85.08% MeshBasedCellPopulation::Update 0 0% 0% 30362ms 46.92% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 30362ms 46.92% MeshBasedCellPopulation::TessellateIfNeeded 228ms 0.35% 0.35% 26599ms 41.11% VertexMesh::VertexMesh 0 0% 0.35% 20548ms 31.75% MutableMesh::ReMesh 0 0% 0.35% 16181ms 25.01% tetgen::tetrahedralize 0 0% 0.35% 16032ms 24.78% tetgen::tetgenmesh::delaunizevertices 7ms 0.011% 0.36% 16025ms 24.77% tetgen::tetgenmesh::incrflipdelaunay 477ms 0.74% 1.10% 14321ms 22.13% tetgen::tetgenmesh::lawson 585ms 0.9% 2.00% 12508ms 19.33% TetrahedralMesh::EdgeIterator::operator++ 22ms 0.034% 2.04% 10736ms 16.59% std::set::insert (inline) 295ms 0.46% 2.49% 10274ms 15.88% std::_Rb_tree::_M_insert_unique 370ms 0.57% 3.07% 10074ms 15.57% VertexElement::AddFace 3147ms 4.86% 7.93% 9149ms 14.14% std::_Rb_tree::_M_lower_bound (inline) 251ms 0.39% 8.32% 8564ms 13.23% std::_Rb_tree::find (inline) 0 0% 8.32% 7962ms 12.30% std::set::count (inline) 350ms 0.54% 8.86% 6164ms 9.53% std::_Rb_tree::_M_insert_ (inline) 125ms 0.19% 9.05% 5850ms 9.04% std::less::operator() (inline) 5779ms 8.93% 17.98% 5779ms 8.93% std::operator< (inline) 185ms 0.29% 18.27% 5639ms 8.71% operator new 0 0% 18.27% 5510ms 8.52% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0015% 18.27% 5382ms 8.32% ForwardEulerNumericalMethod::UpdateAllNodePositions 1246ms 1.93% 20.20% 5381ms 8.32% __GI___libc_malloc 2ms 0.0031% 20.20% 5348ms 8.26% AbstractNumericalMethod::ComputeForcesIncludingDamping 5319ms 8.22% 28.42% 5319ms 8.22% std::_Rb_tree_increment 38ms 0.059% 28.48% 4802ms 7.42% std::__new_allocator::allocate (inline) 0 0% 28.48% 4780ms 7.39% std::allocator_traits::allocate (inline) 13ms 0.02% 28.50% 4528ms 7.00% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.0015% 28.50% 4518ms 6.98% MeshBasedCellPopulation::UpdateNodePairs 1612ms 2.49% 30.99% 4514ms 6.98% std::_Rb_tree::_M_erase 0 0% 30.99% 4482ms 6.93% std::set::~set (inline) 3ms 0.0046% 30.99% 4437ms 6.86% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 15ms 0.023% 31.02% 4353ms 6.73% MeshBasedCellPopulation::SpringIterator::operator++ 1207ms 1.87% 32.88% 4333ms 6.70% __GI___libc_free 2ms 0.0031% 32.89% 4193ms 6.48% std::set_intersection (inline) 266ms 0.41% 33.30% 4191ms 6.48% std::__set_intersection 1334ms 2.06% 35.36% 4110ms 6.35% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 35.36% 3931ms 6.07% std::_Rb_tree::_M_create_node (inline) 125ms 0.19% 35.55% 3930ms 6.07% tetgen::tetgenmesh::insphere_sos 0 0% 35.55% 3906ms 6.04% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 35.55% 3899ms 6.03% std::_Rb_tree::_M_get_node (inline) 0 0% 35.55% 3797ms 5.87% VertexMesh::~VertexMesh 47ms 0.073% 35.62% 3796ms 5.87% Node::AddElement 128ms 0.2% 35.82% 3795ms 5.86% std::__new_allocator::deallocate (inline) 3504ms 5.42% 41.24% 3792ms 5.86% tetgen::insphere 0 0% 41.24% 3778ms 5.84% std::allocator_traits::deallocate (inline) 2786ms 4.31% 45.54% 3759ms 5.81% _int_malloc 147ms 0.23% 45.77% 3566ms 5.51% tetgen::tetgenmesh::flip23 0 0% 45.77% 3516ms 5.43% AbstractCellPopulation::WriteResultsToFiles 6ms 0.0093% 45.78% 3510ms 5.42% TetrahedralMesh::ImportFromMesher 172ms 0.27% 46.05% 3452ms 5.33% std::_Rb_tree_const_iterator::operator++ (inline) 3330ms 5.15% 51.19% 3330ms 5.15% std::_Rb_tree::_S_right (inline) 1399ms 2.16% 53.35% 3123ms 4.83% _int_free 74ms 0.11% 53.47% 2855ms 4.41% MutableElement::AddNode 176ms 0.27% 53.74% 2637ms 4.08% Node::~Node 135ms 0.21% 53.95% 2612ms 4.04% tetgen::tetgenmesh::flip32 158ms 0.24% 54.19% 2432ms 3.76% VertexMesh::Clear 2ms 0.0031% 54.20% 2380ms 3.68% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 190ms 0.29% 54.49% 2354ms 3.64% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 54.49% 2173ms 3.36% std::_Rb_tree_iterator::operator++ (inline) 0 0% 54.49% 2165ms 3.35% std::_Rb_tree::_M_drop_node (inline) 0 0% 54.49% 2152ms 3.33% std::_Rb_tree::_M_put_node (inline) 1964ms 3.04% 57.52% 1964ms 3.04% std::_Rb_tree_insert_and_rebalance 227ms 0.35% 57.88% 1860ms 2.87% tetgen::tetgenmesh::enqueueflipface 5ms 0.0077% 57.88% 1805ms 2.79% Element::Element 1178ms 1.82% 59.70% 1691ms 2.61% malloc_consolidate 31ms 0.048% 59.75% 1657ms 2.56% std::_Vector_base::_M_deallocate (inline) 1655ms 2.56% 62.31% 1655ms 2.56% Node::GetIndex 1520ms 2.35% 64.66% 1604ms 2.48% tetgen::orient3d 0 0% 64.66% 1590ms 2.46% std::vector::~vector (inline) 0 0% 64.66% 1503ms 2.32% std::_Vector_base::~_Vector_base (inline) 9ms 0.014% 64.67% 1476ms 2.28% _int_free_maybe_consolidate 6ms 0.0093% 64.68% 1431ms 2.21% Element::RegisterWithNodes (inline) 42ms 0.065% 64.75% 1419ms 2.19% tetgen::tetgenmesh::locate 93ms 0.14% 64.89% 1359ms 2.10% TetrahedralMesh::Clear 78ms 0.12% 65.01% 1313ms 2.03% tetgen::tetgenmesh::preciselocate 1274ms 1.97% 66.98% 1274ms 1.97% tetgen::tetgenmesh::triface::triface 949ms 1.47% 68.45% 1193ms 1.84% AbstractElement::GetNodeGlobalIndex 1191ms 1.84% 70.29% 1191ms 1.84% unlink_chunk 79ms 0.12% 70.41% 1170ms 1.81% std::map::operator[] 58ms 0.09% 70.50% 1108ms 1.71% std::vector::_M_realloc_insert 0 0% 70.50% 1013ms 1.57% std::_Rb_tree::lower_bound (inline) 0 0% 70.50% 1013ms 1.57% std::map::lower_bound (inline) 996ms 1.54% 72.04% 996ms 1.54% tetgen::tetgenmesh::oppo 2ms 0.0031% 72.04% 987ms 1.53% VertexMesh::GenerateVerticesFromElementCircumcentres 1ms 0.0015% 72.04% 893ms 1.38% VoronoiDataWriter::Visit 110ms 0.17% 72.21% 893ms 1.38% std::vector::push_back (inline) 9ms 0.014% 72.23% 890ms 1.38% std::_Vector_base::_M_allocate (inline) 0 0% 72.23% 827ms 1.28% TetrahedralMesh::RefreshJacobianCachedData 799ms 1.23% 73.46% 799ms 1.23% [libchaste_mesh.so] 790ms 1.22% 74.68% 790ms 1.22% tetgen::tetgenmesh::triface::operator= 279ms 0.43% 75.11% 749ms 1.16% tetgen::tetgenmesh::sym 9ms 0.014% 75.13% 738ms 1.14% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 75.13% 738ms 1.14% AbstractTwoBodyInteractionForce::AddForceContribution 302ms 0.47% 75.59% 726ms 1.12% AbstractElement::GetNodeLocation 18ms 0.028% 75.62% 706ms 1.09% AbstractTetrahedralElement::CalculateJacobian 16ms 0.025% 75.65% 694ms 1.07% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 389ms 0.6% 76.25% 659ms 1.02% tetgen::tetgenmesh::fnextself 658ms 1.02% 77.26% 658ms 1.02% Node::rGetLocation 655ms 1.01% 78.28% 655ms 1.01% std::vector::size (inline) 46ms 0.071% 78.35% 652ms 1.01% __atan2 60ms 0.093% 78.44% 626ms 0.97% tetgen::tetgenmesh::enextfnext 625ms 0.97% 79.41% 625ms 0.97% AbstractElement::IsDeleted 53ms 0.082% 79.49% 616ms 0.95% tetgen::tetgenmesh::enext2fnext 468ms 0.72% 80.21% 600ms 0.93% __ieee754_atan2_fma 0 0% 80.21% 600ms 0.93% std::set::find (inline) 10ms 0.015% 80.23% 585ms 0.9% boost::numeric::ublas::vector_assign (inline) 44ms 0.068% 80.29% 581ms 0.9% tetgen::tetgenmesh::queue::push 10ms 0.015% 80.31% 566ms 0.87% boost::numeric::ublas::c_vector::c_vector (inline) 325ms 0.5% 80.81% 537ms 0.83% tetgen::tetgenmesh::link::add 537ms 0.83% 81.64% 537ms 0.83% tetgen::tetgenmesh::org 43ms 0.066% 81.71% 532ms 0.82% AbstractTetrahedralElement::RefreshJacobian 0 0% 81.71% 510ms 0.79% boost::numeric::ublas::inner_prod (inline) 2ms 0.0031% 81.71% 504ms 0.78% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 36ms 0.056% 81.77% 502ms 0.78% boost::numeric::ublas::vector_scalar_binary::evaluate 19ms 0.029% 81.80% 501ms 0.77% Element::CalculateCircumsphere 0 0% 81.80% 500ms 0.77% std::insert_iterator::operator= (inline) 248ms 0.38% 82.18% 494ms 0.76% tetgen::tetgenmesh::bond 489ms 0.76% 82.94% 489ms 0.76% tetgen::tetgenmesh::decode 257ms 0.4% 83.33% 456ms 0.7% AbstractTetrahedralMesh::GetElement 66ms 0.1% 83.43% 437ms 0.68% tetgen::tetgenmesh::queue::pop 1ms 0.0015% 83.44% 436ms 0.67% std::_Rb_tree::_M_insert_unique_ (inline) 25ms 0.039% 83.47% 429ms 0.66% std::_Rb_tree_iterator::operator-- (inline) 15ms 0.023% 83.50% 412ms 0.64% VertexMesh::CalculateUnitNormalToFaceWithArea 159ms 0.25% 83.74% 407ms 0.63% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 83.74% 397ms 0.61% VertexMeshWriter::WriteVtkUsingMesh 6ms 0.0093% 83.75% 388ms 0.6% VertexElement::~VertexElement 5ms 0.0077% 83.76% 381ms 0.59% CellPropertyCollection::GetPropertiesType (inline) 375ms 0.58% 84.34% 375ms 0.58% std::_Rb_tree_decrement 374ms 0.58% 84.92% 374ms 0.58% boost::numeric::ublas::c_vector::operator() 3ms 0.0046% 84.92% 370ms 0.57% AbstractTetrahedralElement::AbstractTetrahedralElement 2ms 0.0031% 84.93% 361ms 0.56% Cell::GetCellId 194ms 0.3% 85.23% 361ms 0.56% tetgen::tetgenmesh::link::deletenode 82ms 0.13% 85.35% 357ms 0.55% boost::numeric::ublas::indexing_vector_assign 21ms 0.032% 85.39% 354ms 0.55% std::vector::insert (inline) 92ms 0.14% 85.53% 347ms 0.54% __dynamic_cast 0 0% 85.53% 340ms 0.53% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 6ms 0.0093% 85.54% 338ms 0.52% boost::numeric::ublas::c_vector::operator= (inline) 113ms 0.17% 85.71% 333ms 0.51% Inverse