File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 58326ms, 87.03% of 67020ms total Dropped 929 nodes (cum <= 335.10ms) flat flat% sum% cum cum% 0 0% 0% 66958ms 99.91% __libc_start_call_main 0 0% 0% 66958ms 99.91% __libc_start_main_impl 0 0% 0% 66958ms 99.91% _start 0 0% 0% 66938ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 66938ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 66938ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 66938ms 99.88% main 0 0% 0% 66893ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 66893ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 66893ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 66591ms 99.36% AbstractCellBasedSimulation::Solve 0 0% 0% 57266ms 85.45% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 57214ms 85.37% MeshBasedCellPopulation::Update 0 0% 0% 32140ms 47.96% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 32139ms 47.95% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 200ms 0.3% 0.3% 28262ms 42.17% VertexMesh::VertexMesh 0 0% 0.3% 20893ms 31.17% MutableMesh::ReMesh 1ms 0.0015% 0.3% 16389ms 24.45% tetgen::tetrahedralize 2ms 0.003% 0.3% 16241ms 24.23% tetgen::tetgenmesh::delaunizevertices 7ms 0.01% 0.31% 16233ms 24.22% tetgen::tetgenmesh::incrflipdelaunay 474ms 0.71% 1.02% 14526ms 21.67% tetgen::tetgenmesh::lawson 631ms 0.94% 1.96% 13005ms 19.40% TetrahedralMesh::EdgeIterator::operator++ 35ms 0.052% 2.01% 11159ms 16.65% std::set::insert (inline) 266ms 0.4% 2.41% 10720ms 16.00% std::_Rb_tree::_M_insert_unique 430ms 0.64% 3.05% 10299ms 15.37% VertexElement::AddFace 3164ms 4.72% 7.77% 9277ms 13.84% std::_Rb_tree::_M_lower_bound (inline) 268ms 0.4% 8.17% 8787ms 13.11% std::_Rb_tree::find (inline) 0 0% 8.17% 8200ms 12.24% std::set::count (inline) 326ms 0.49% 8.66% 6258ms 9.34% std::_Rb_tree::_M_insert_ (inline) 127ms 0.19% 8.85% 6018ms 8.98% std::less::operator() (inline) 5960ms 8.89% 17.74% 5960ms 8.89% std::operator< (inline) 171ms 0.26% 18.00% 5886ms 8.78% operator new 5862ms 8.75% 26.74% 5862ms 8.75% std::_Rb_tree_increment 1152ms 1.72% 28.46% 5654ms 8.44% __GI___libc_malloc 1ms 0.0015% 28.46% 5609ms 8.37% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 28.46% 5465ms 8.15% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0045% 28.47% 5437ms 8.11% AbstractNumericalMethod::ComputeForcesIncludingDamping 39ms 0.058% 28.53% 4949ms 7.38% std::__new_allocator::allocate (inline) 0 0% 28.53% 4930ms 7.36% std::allocator_traits::allocate (inline) 5ms 0.0075% 28.53% 4812ms 7.18% std::set_intersection (inline) 289ms 0.43% 28.97% 4807ms 7.17% std::__set_intersection 10ms 0.015% 28.98% 4653ms 6.94% std::_Rb_tree::~_Rb_tree (inline) 1650ms 2.46% 31.44% 4640ms 6.92% std::_Rb_tree::_M_erase 0 0% 31.44% 4594ms 6.85% std::set::~set (inline) 1ms 0.0015% 31.44% 4569ms 6.82% MeshBasedCellPopulation::UpdateNodePairs 1268ms 1.89% 33.34% 4540ms 6.77% __GI___libc_free 8ms 0.012% 33.35% 4537ms 6.77% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1408ms 2.10% 35.45% 4473ms 6.67% std::_Rb_tree::_M_get_insert_unique_pos 14ms 0.021% 35.47% 4408ms 6.58% MeshBasedCellPopulation::SpringIterator::operator++ 50ms 0.075% 35.54% 4271ms 6.37% Node::AddElement 3022ms 4.51% 40.05% 4096ms 6.11% _int_malloc 0 0% 40.05% 4055ms 6.05% std::_Rb_tree::_M_create_node (inline) 193ms 0.29% 40.34% 4031ms 6.01% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 40.34% 4012ms 5.99% std::_Rb_tree::_M_get_node (inline) 0 0% 40.34% 4010ms 5.98% std::_Rb_tree::_Alloc_node::operator() (inline) 130ms 0.19% 40.54% 3993ms 5.96% std::__new_allocator::deallocate (inline) 0 0% 40.54% 3980ms 5.94% std::allocator_traits::deallocate (inline) 130ms 0.19% 40.73% 3917ms 5.84% tetgen::tetgenmesh::insphere_sos 1ms 0.0015% 40.73% 3915ms 5.84% VertexMesh::~VertexMesh 3464ms 5.17% 45.90% 3770ms 5.63% tetgen::insphere 3611ms 5.39% 51.29% 3611ms 5.39% std::_Rb_tree::_S_right (inline) 10ms 0.015% 51.30% 3595ms 5.36% TetrahedralMesh::ImportFromMesher 0 0% 51.30% 3550ms 5.30% AbstractCellPopulation::WriteResultsToFiles 130ms 0.19% 51.50% 3539ms 5.28% tetgen::tetgenmesh::flip23 1473ms 2.20% 53.69% 3270ms 4.88% _int_free 68ms 0.1% 53.80% 3249ms 4.85% MutableElement::AddNode 211ms 0.31% 54.11% 2683ms 4.00% Node::~Node 145ms 0.22% 54.33% 2648ms 3.95% tetgen::tetgenmesh::flip32 154ms 0.23% 54.56% 2471ms 3.69% VertexMesh::Clear 3ms 0.0045% 54.56% 2391ms 3.57% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 190ms 0.28% 54.84% 2346ms 3.50% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 54.84% 2268ms 3.38% std::_Rb_tree::_M_drop_node (inline) 0 0% 54.84% 2254ms 3.36% std::_Rb_tree::_M_put_node (inline) 3ms 0.0045% 54.85% 2174ms 3.24% std::_Rb_tree_iterator::operator++ (inline) 1985ms 2.96% 57.81% 1985ms 2.96% std::_Rb_tree_insert_and_rebalance 1927ms 2.88% 60.69% 1927ms 2.88% Node::GetIndex 224ms 0.33% 61.02% 1847ms 2.76% tetgen::tetgenmesh::enqueueflipface 6ms 0.009% 61.03% 1835ms 2.74% Element::Element 1286ms 1.92% 62.95% 1785ms 2.66% malloc_consolidate 34ms 0.051% 63.00% 1760ms 2.63% std::_Vector_base::_M_deallocate (inline) 0 0% 63.00% 1645ms 2.45% std::vector::~vector (inline) 1533ms 2.29% 65.29% 1607ms 2.40% tetgen::orient3d 1ms 0.0015% 65.29% 1573ms 2.35% std::_Vector_base::~_Vector_base (inline) 4ms 0.006% 65.29% 1546ms 2.31% _int_free_maybe_consolidate 7ms 0.01% 65.30% 1523ms 2.27% Element::RegisterWithNodes (inline) 83ms 0.12% 65.43% 1367ms 2.04% TetrahedralMesh::Clear 32ms 0.048% 65.48% 1360ms 2.03% tetgen::tetgenmesh::locate 86ms 0.13% 65.60% 1280ms 1.91% tetgen::tetgenmesh::preciselocate 1230ms 1.84% 67.44% 1230ms 1.84% unlink_chunk 54ms 0.081% 67.52% 1207ms 1.80% std::vector::_M_realloc_insert 67ms 0.1% 67.62% 1130ms 1.69% std::map::operator[] 931ms 1.39% 69.01% 1121ms 1.67% AbstractElement::GetNodeGlobalIndex 1081ms 1.61% 70.62% 1081ms 1.61% tetgen::tetgenmesh::triface::triface 4ms 0.006% 70.63% 1076ms 1.61% VertexMesh::GenerateVerticesFromElementCircumcentres 119ms 0.18% 70.81% 985ms 1.47% std::vector::push_back (inline) 0 0% 70.81% 979ms 1.46% std::_Rb_tree::lower_bound (inline) 0 0% 70.81% 979ms 1.46% std::map::lower_bound (inline) 960ms 1.43% 72.24% 960ms 1.43% tetgen::tetgenmesh::oppo 7ms 0.01% 72.25% 925ms 1.38% std::_Vector_base::_M_allocate (inline) 1ms 0.0015% 72.25% 918ms 1.37% VoronoiDataWriter::Visit 0 0% 72.25% 879ms 1.31% TetrahedralMesh::RefreshJacobianCachedData 277ms 0.41% 72.66% 845ms 1.26% tetgen::tetgenmesh::sym 839ms 1.25% 73.92% 839ms 1.25% tetgen::tetgenmesh::triface::operator= 835ms 1.25% 75.16% 835ms 1.25% [libchaste_mesh.so] 12ms 0.018% 75.18% 762ms 1.14% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.0015% 75.18% 730ms 1.09% AbstractTwoBodyInteractionForce::AddForceContribution 332ms 0.5% 75.68% 728ms 1.09% AbstractElement::GetNodeLocation 399ms 0.6% 76.27% 726ms 1.08% tetgen::tetgenmesh::fnextself 723ms 1.08% 77.35% 723ms 1.08% AbstractElement::IsDeleted 11ms 0.016% 77.37% 692ms 1.03% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 39ms 0.058% 77.42% 682ms 1.02% tetgen::tetgenmesh::queue::push 15ms 0.022% 77.45% 666ms 0.99% AbstractTetrahedralElement::CalculateJacobian 59ms 0.088% 77.54% 661ms 0.99% tetgen::tetgenmesh::enextfnext 656ms 0.98% 78.51% 656ms 0.98% Node::rGetLocation 232ms 0.35% 78.86% 646ms 0.96% tetgen::tetgenmesh::bond 381ms 0.57% 79.43% 643ms 0.96% tetgen::tetgenmesh::link::add 39ms 0.058% 79.49% 627ms 0.94% tetgen::tetgenmesh::enext2fnext 19ms 0.028% 79.52% 611ms 0.91% boost::numeric::ublas::vector_assign (inline) 609ms 0.91% 80.42% 609ms 0.91% std::vector::size (inline) 57ms 0.085% 80.51% 601ms 0.9% __atan2 591ms 0.88% 81.39% 591ms 0.88% tetgen::tetgenmesh::decode 7ms 0.01% 81.40% 588ms 0.88% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 81.40% 579ms 0.86% std::set::find (inline) 21ms 0.031% 81.43% 543ms 0.81% Element::CalculateCircumsphere 411ms 0.61% 82.05% 539ms 0.8% __ieee754_atan2_fma 46ms 0.069% 82.11% 504ms 0.75% AbstractTetrahedralElement::RefreshJacobian 492ms 0.73% 82.85% 492ms 0.73% tetgen::tetgenmesh::org 0 0% 82.85% 491ms 0.73% boost::numeric::ublas::inner_prod (inline) 2ms 0.003% 82.85% 486ms 0.73% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 48ms 0.072% 82.92% 484ms 0.72% boost::numeric::ublas::vector_scalar_binary::evaluate 16ms 0.024% 82.95% 456ms 0.68% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 82.95% 455ms 0.68% std::insert_iterator::operator= (inline) 429ms 0.64% 83.59% 429ms 0.64% tetgen::tetgenmesh::pointmark 24ms 0.036% 83.62% 427ms 0.64% std::_Rb_tree_iterator::operator-- (inline) 424ms 0.63% 84.26% 424ms 0.63% boost::numeric::ublas::c_vector::operator() 204ms 0.3% 84.56% 420ms 0.63% AbstractTetrahedralMesh::GetElement 5ms 0.0075% 84.57% 404ms 0.6% Cell::GetCellId 0 0% 84.57% 401ms 0.6% std::_Rb_tree::_M_insert_unique_ (inline) 397ms 0.59% 85.16% 397ms 0.59% tetgen::tetgenmesh::encode 0 0% 85.16% 389ms 0.58% VertexMeshWriter::WriteVtkUsingMesh 0 0% 85.16% 389ms 0.58% boost::numeric::ublas::c_vector::operator= (inline) 3ms 0.0045% 85.16% 387ms 0.58% CellPropertyCollection::GetPropertiesType (inline) 385ms 0.57% 85.74% 385ms 0.57% std::_Rb_tree_decrement 7ms 0.01% 85.75% 382ms 0.57% VertexElement::~VertexElement 168ms 0.25% 86.00% 381ms 0.57% boost::numeric::ublas::vector_inner_prod::apply (inline) 89ms 0.13% 86.13% 379ms 0.57% __dynamic_cast 90ms 0.13% 86.27% 379ms 0.57% boost::numeric::ublas::indexing_vector_assign 16ms 0.024% 86.29% 365ms 0.54% std::vector::insert (inline) 0 0% 86.29% 361ms 0.54% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 2ms 0.003% 86.29% 356ms 0.53% tcache_get (inline) 354ms 0.53% 86.82% 354ms 0.53% tcache_get_n (inline) 138ms 0.21% 87.03% 342ms 0.51% Inverse