File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 62266ms, 86.82% of 71719ms total Dropped 925 nodes (cum <= 358.60ms) flat flat% sum% cum cum% 0 0% 0% 71657ms 99.91% __libc_start_call_main 0 0% 0% 71657ms 99.91% __libc_start_main_impl 0 0% 0% 71657ms 99.91% _start 0 0% 0% 71639ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 71639ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 71639ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 71639ms 99.89% main 0 0% 0% 71597ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 71597ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 71597ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 71300ms 99.42% AbstractCellBasedSimulation::Solve 0 0% 0% 61525ms 85.79% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 61472ms 85.71% MeshBasedCellPopulation::Update 0 0% 0% 36255ms 50.55% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 36250ms 50.54% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 292ms 0.41% 0.41% 31623ms 44.09% VertexMesh::VertexMesh 0 0% 0.41% 20844ms 29.06% MutableMesh::ReMesh 0 0% 0.41% 15947ms 22.24% tetgen::tetrahedralize 2ms 0.0028% 0.41% 15787ms 22.01% tetgen::tetgenmesh::delaunizevertices 13ms 0.018% 0.43% 15779ms 22.00% tetgen::tetgenmesh::incrflipdelaunay 556ms 0.78% 1.20% 14061ms 19.61% tetgen::tetgenmesh::lawson 592ms 0.83% 2.03% 13837ms 19.29% TetrahedralMesh::EdgeIterator::operator++ 32ms 0.045% 2.07% 12037ms 16.78% std::set::insert (inline) 242ms 0.34% 2.41% 11598ms 16.17% std::_Rb_tree::_M_insert_unique 478ms 0.67% 3.08% 10818ms 15.08% VertexElement::AddFace 3172ms 4.42% 7.50% 9661ms 13.47% std::_Rb_tree::_M_lower_bound (inline) 298ms 0.42% 7.92% 9100ms 12.69% std::_Rb_tree::find (inline) 0 0% 7.92% 8551ms 11.92% std::set::count (inline) 6974ms 9.72% 17.64% 6974ms 9.72% std::_Rb_tree_increment 308ms 0.43% 18.07% 6823ms 9.51% std::_Rb_tree::_M_insert_ (inline) 172ms 0.24% 18.31% 6594ms 9.19% operator new 105ms 0.15% 18.46% 6339ms 8.84% std::less::operator() (inline) 1178ms 1.64% 20.10% 6319ms 8.81% __GI___libc_malloc 6296ms 8.78% 28.88% 6296ms 8.78% std::operator< (inline) 0 0% 28.88% 5924ms 8.26% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.0042% 28.88% 5923ms 8.26% std::set_intersection (inline) 336ms 0.47% 29.35% 5920ms 8.25% std::__set_intersection 0 0% 29.35% 5774ms 8.05% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0042% 29.35% 5746ms 8.01% AbstractNumericalMethod::ComputeForcesIncludingDamping 30ms 0.042% 29.40% 5373ms 7.49% std::__new_allocator::allocate (inline) 0 0% 29.40% 5348ms 7.46% std::allocator_traits::allocate (inline) 197ms 0.27% 29.67% 5106ms 7.12% std::_Rb_tree_const_iterator::operator++ (inline) 13ms 0.018% 29.69% 4969ms 6.93% std::_Rb_tree::~_Rb_tree (inline) 1853ms 2.58% 32.27% 4952ms 6.90% std::_Rb_tree::_M_erase 1390ms 1.94% 34.21% 4919ms 6.86% __GI___libc_free 0 0% 34.21% 4918ms 6.86% std::set::~set (inline) 36ms 0.05% 34.26% 4901ms 6.83% Node::AddElement 1ms 0.0014% 34.26% 4815ms 6.71% MeshBasedCellPopulation::UpdateNodePairs 1383ms 1.93% 36.19% 4803ms 6.70% std::_Rb_tree::_M_get_insert_unique_pos 2ms 0.0028% 36.19% 4798ms 6.69% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 3501ms 4.88% 41.07% 4794ms 6.68% _int_malloc 1ms 0.0014% 41.08% 4657ms 6.49% VertexMesh::~VertexMesh 14ms 0.02% 41.10% 4653ms 6.49% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 41.10% 4389ms 6.12% std::_Rb_tree::_M_create_node (inline) 132ms 0.18% 41.28% 4368ms 6.09% std::__new_allocator::deallocate (inline) 0 0% 41.28% 4356ms 6.07% std::allocator_traits::deallocate (inline) 0 0% 41.28% 4354ms 6.07% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 41.28% 4341ms 6.05% std::_Rb_tree::_M_get_node (inline) 4163ms 5.80% 47.08% 4163ms 5.80% std::_Rb_tree::_S_right (inline) 11ms 0.015% 47.10% 3866ms 5.39% TetrahedralMesh::ImportFromMesher 124ms 0.17% 47.27% 3829ms 5.34% tetgen::tetgenmesh::insphere_sos 55ms 0.077% 47.35% 3725ms 5.19% MutableElement::AddNode 3402ms 4.74% 52.09% 3694ms 5.15% tetgen::insphere 0 0% 52.09% 3633ms 5.07% AbstractCellPopulation::WriteResultsToFiles 1337ms 1.86% 53.96% 3523ms 4.91% _int_free 108ms 0.15% 54.11% 3431ms 4.78% tetgen::tetgenmesh::flip23 198ms 0.28% 54.38% 3021ms 4.21% Node::~Node 208ms 0.29% 54.67% 2813ms 3.92% VertexMesh::Clear 127ms 0.18% 54.85% 2533ms 3.53% tetgen::tetgenmesh::flip32 4ms 0.0056% 54.86% 2433ms 3.39% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 2369ms 3.30% 58.16% 2369ms 3.30% Node::GetIndex 203ms 0.28% 58.44% 2364ms 3.30% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 58.44% 2234ms 3.11% std::_Rb_tree::_M_drop_node (inline) 1527ms 2.13% 60.57% 2231ms 3.11% malloc_consolidate 2227ms 3.11% 63.68% 2227ms 3.11% std::_Rb_tree_insert_and_rebalance 0 0% 63.68% 2222ms 3.10% std::_Rb_tree::_M_put_node (inline) 1ms 0.0014% 63.68% 2193ms 3.06% std::_Rb_tree_iterator::operator++ (inline) 28ms 0.039% 63.72% 2162ms 3.01% std::_Vector_base::_M_deallocate (inline) 0 0% 63.72% 2048ms 2.86% std::vector::~vector (inline) 8ms 0.011% 63.73% 2005ms 2.80% Element::Element 1ms 0.0014% 63.73% 1996ms 2.78% std::_Vector_base::~_Vector_base (inline) 238ms 0.33% 64.06% 1965ms 2.74% tetgen::tetgenmesh::enqueueflipface 10ms 0.014% 64.08% 1946ms 2.71% _int_free_maybe_consolidate 3ms 0.0042% 64.08% 1656ms 2.31% Element::RegisterWithNodes (inline) 1538ms 2.14% 66.22% 1620ms 2.26% tetgen::orient3d 1619ms 2.26% 68.48% 1619ms 2.26% unlink_chunk 42ms 0.059% 68.54% 1405ms 1.96% tetgen::tetgenmesh::locate 64ms 0.089% 68.63% 1390ms 1.94% TetrahedralMesh::Clear 8ms 0.011% 68.64% 1387ms 1.93% VertexMesh::GenerateVerticesFromElementCircumcentres 1173ms 1.64% 70.28% 1375ms 1.92% AbstractElement::GetNodeGlobalIndex 99ms 0.14% 70.41% 1313ms 1.83% tetgen::tetgenmesh::preciselocate 81ms 0.11% 70.53% 1244ms 1.73% std::map::operator[] 59ms 0.082% 70.61% 1207ms 1.68% std::vector::_M_realloc_insert 1088ms 1.52% 72.13% 1088ms 1.52% tetgen::tetgenmesh::oppo 0 0% 72.13% 1074ms 1.50% std::_Rb_tree::lower_bound (inline) 0 0% 72.13% 1074ms 1.50% std::map::lower_bound (inline) 5ms 0.007% 72.13% 1012ms 1.41% std::_Vector_base::_M_allocate (inline) 0 0% 72.13% 1007ms 1.40% TetrahedralMesh::RefreshJacobianCachedData 133ms 0.19% 72.32% 994ms 1.39% std::vector::push_back (inline) 977ms 1.36% 73.68% 977ms 1.36% AbstractElement::IsDeleted 958ms 1.34% 75.02% 958ms 1.34% tetgen::tetgenmesh::triface::triface 0 0% 75.02% 953ms 1.33% VoronoiDataWriter::Visit 448ms 0.62% 75.64% 934ms 1.30% AbstractElement::GetNodeLocation 873ms 1.22% 76.86% 873ms 1.22% Node::rGetLocation 8ms 0.011% 76.87% 831ms 1.16% AbstractTetrahedralElement::CalculateInverseJacobian 802ms 1.12% 77.99% 802ms 1.12% [libchaste_mesh.so] 310ms 0.43% 78.42% 794ms 1.11% tetgen::tetgenmesh::sym 16ms 0.022% 78.44% 770ms 1.07% AbstractTetrahedralElement::CalculateJacobian 2ms 0.0028% 78.45% 757ms 1.06% AbstractTwoBodyInteractionForce::AddForceContribution 723ms 1.01% 79.45% 723ms 1.01% tetgen::tetgenmesh::triface::operator= 19ms 0.026% 79.48% 717ms 1% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 708ms 0.99% 80.47% 708ms 0.99% std::vector::size (inline) 397ms 0.55% 81.02% 666ms 0.93% tetgen::tetgenmesh::fnextself 52ms 0.073% 81.09% 664ms 0.93% __atan2 12ms 0.017% 81.11% 640ms 0.89% Element::CalculateCircumsphere 40ms 0.056% 81.17% 631ms 0.88% tetgen::tetgenmesh::queue::push 11ms 0.015% 81.18% 628ms 0.88% boost::numeric::ublas::vector_assign (inline) 5ms 0.007% 81.19% 622ms 0.87% boost::numeric::ublas::c_vector::c_vector (inline) 226ms 0.32% 81.50% 611ms 0.85% tetgen::tetgenmesh::bond 475ms 0.66% 82.17% 610ms 0.85% __ieee754_atan2_fma 34ms 0.047% 82.21% 602ms 0.84% AbstractTetrahedralElement::RefreshJacobian 365ms 0.51% 82.72% 591ms 0.82% tetgen::tetgenmesh::link::add 56ms 0.078% 82.80% 586ms 0.82% tetgen::tetgenmesh::enext2fnext 55ms 0.077% 82.88% 584ms 0.81% tetgen::tetgenmesh::enextfnext 0 0% 82.88% 547ms 0.76% std::set::find (inline) 512ms 0.71% 83.59% 512ms 0.71% tetgen::tetgenmesh::decode 0 0% 83.59% 510ms 0.71% boost::numeric::ublas::inner_prod (inline) 2ms 0.0028% 83.59% 508ms 0.71% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 48ms 0.067% 83.66% 506ms 0.71% boost::numeric::ublas::vector_scalar_binary::evaluate 480ms 0.67% 84.33% 480ms 0.67% tetgen::tetgenmesh::org 0 0% 84.33% 465ms 0.65% std::insert_iterator::operator= (inline) 17ms 0.024% 84.35% 457ms 0.64% VertexMesh::CalculateUnitNormalToFaceWithArea 20ms 0.028% 84.38% 433ms 0.6% std::_Rb_tree_iterator::operator-- (inline) 0 0% 84.38% 419ms 0.58% VertexMeshWriter::WriteVtkUsingMesh 0 0% 84.38% 414ms 0.58% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 6ms 0.0084% 84.39% 411ms 0.57% boost::numeric::ublas::c_vector::operator= (inline) 7ms 0.0098% 84.40% 410ms 0.57% CellPropertyCollection::GetPropertiesType (inline) 182ms 0.25% 84.65% 403ms 0.56% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 84.65% 403ms 0.56% std::_Rb_tree::_M_insert_unique_ (inline) 7ms 0.0098% 84.66% 402ms 0.56% Cell::GetCellId 185ms 0.26% 84.92% 395ms 0.55% AbstractTetrahedralMesh::GetElement 100ms 0.14% 85.06% 393ms 0.55% __dynamic_cast 109ms 0.15% 85.21% 383ms 0.53% boost::numeric::ublas::indexing_vector_assign 381ms 0.53% 85.74% 381ms 0.53% boost::numeric::ublas::c_vector::operator() 381ms 0.53% 86.27% 381ms 0.53% std::_Rb_tree_decrement 19ms 0.026% 86.30% 375ms 0.52% std::vector::insert (inline) 5ms 0.007% 86.31% 373ms 0.52% VertexElement::~VertexElement 367ms 0.51% 86.82% 367ms 0.51% tetgen::tetgenmesh::encode