File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 59183ms, 86.50% of 68423ms total Dropped 869 nodes (cum <= 342.12ms) flat flat% sum% cum cum% 0 0% 0% 68371ms 99.92% __libc_start_call_main 0 0% 0% 68371ms 99.92% __libc_start_main_impl 0 0% 0% 68371ms 99.92% _start 0 0% 0% 68352ms 99.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 68352ms 99.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 68352ms 99.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 68352ms 99.90% main 0 0% 0% 68317ms 99.85% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 68317ms 99.85% CxxTest::TestRunner::runTest (inline) 0 0% 0% 68317ms 99.85% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 68076ms 99.49% AbstractCellBasedSimulation::Solve 0 0% 0% 56233ms 82.18% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 56162ms 82.08% MeshBasedCellPopulation::Update 0 0% 0% 35105ms 51.31% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 35104ms 51.30% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 262ms 0.38% 0.38% 31444ms 45.96% VertexMesh::VertexMesh 0 0% 0.38% 16172ms 23.64% MutableMesh::ReMesh 502ms 0.73% 1.12% 15142ms 22.13% TetrahedralMesh::EdgeIterator::operator++ 43ms 0.063% 1.18% 13030ms 19.04% std::set::insert (inline) 154ms 0.23% 1.40% 12383ms 18.10% std::_Rb_tree::_M_insert_unique 4208ms 6.15% 7.55% 11927ms 17.43% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.0015% 7.56% 11432ms 16.71% tetgen::tetrahedralize 311ms 0.45% 8.01% 11428ms 16.70% VertexElement::AddFace 2ms 0.0029% 8.01% 11323ms 16.55% tetgen::tetgenmesh::delaunizevertices 6ms 0.0088% 8.02% 11321ms 16.55% tetgen::tetgenmesh::incrflipdelaunay 179ms 0.26% 8.28% 11228ms 16.41% std::_Rb_tree::find (inline) 0 0% 8.28% 10650ms 15.56% std::set::count (inline) 504ms 0.74% 9.02% 9984ms 14.59% tetgen::tetgenmesh::lawson 258ms 0.38% 9.40% 8526ms 12.46% operator new 323ms 0.47% 9.87% 8364ms 12.22% std::_Rb_tree::_M_insert_ (inline) 2866ms 4.19% 14.06% 8201ms 11.99% __GI___libc_malloc 7316ms 10.69% 24.75% 7316ms 10.69% std::_Rb_tree_increment 93ms 0.14% 24.89% 7296ms 10.66% std::__new_allocator::allocate (inline) 0 0% 24.89% 7272ms 10.63% std::allocator_traits::allocate (inline) 6718ms 9.82% 34.70% 6718ms 9.82% std::operator< (inline) 76ms 0.11% 34.82% 6715ms 9.81% std::less::operator() (inline) 0 0% 34.82% 6497ms 9.50% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 34.82% 6315ms 9.23% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.0073% 34.82% 6302ms 9.21% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 34.82% 5929ms 8.67% std::_Rb_tree::_M_create_node (inline) 0 0% 34.82% 5886ms 8.60% std::_Rb_tree::_M_get_node (inline) 0 0% 34.82% 5885ms 8.60% std::_Rb_tree::_Alloc_node::operator() (inline) 4ms 0.0058% 34.83% 5218ms 7.63% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1ms 0.0015% 34.83% 5208ms 7.61% MeshBasedCellPopulation::UpdateNodePairs 918ms 1.34% 36.17% 5194ms 7.59% __GI___libc_free 0 0% 36.17% 5178ms 7.57% AbstractCellPopulation::WriteResultsToFiles 1ms 0.0015% 36.17% 5170ms 7.56% std::set_intersection (inline) 329ms 0.48% 36.65% 5169ms 7.55% std::__set_intersection 21ms 0.031% 36.69% 5056ms 7.39% MeshBasedCellPopulation::SpringIterator::operator++ 3794ms 5.54% 42.23% 4897ms 7.16% _int_malloc 19ms 0.028% 42.26% 4669ms 6.82% std::_Rb_tree::~_Rb_tree (inline) 1395ms 2.04% 44.30% 4640ms 6.78% std::_Rb_tree::_M_erase 0 0% 44.30% 4630ms 6.77% std::set::~set (inline) 65ms 0.095% 44.39% 4519ms 6.60% Node::AddElement 69ms 0.1% 44.49% 4456ms 6.51% std::__new_allocator::deallocate (inline) 0 0% 44.49% 4442ms 6.49% std::allocator_traits::deallocate (inline) 1375ms 2.01% 46.50% 4264ms 6.23% std::_Rb_tree::_M_get_insert_unique_pos 2120ms 3.10% 49.60% 4261ms 6.23% _int_free 295ms 0.43% 50.03% 4228ms 6.18% std::_Rb_tree_const_iterator::operator++ (inline) 4046ms 5.91% 55.94% 4046ms 5.91% std::_Rb_tree::_S_right (inline) 308ms 0.45% 56.39% 3985ms 5.82% std::_Rb_tree_iterator::operator++ (inline) 3ms 0.0044% 56.40% 3972ms 5.81% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 3ms 0.0044% 56.40% 3775ms 5.52% TetrahedralMesh::ImportFromMesher 5ms 0.0073% 56.41% 3743ms 5.47% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 56.41% 3691ms 5.39% VertexMesh::~VertexMesh 54ms 0.079% 56.49% 3291ms 4.81% MutableElement::AddNode 86ms 0.13% 56.62% 3153ms 4.61% tetgen::tetgenmesh::insphere_sos 2807ms 4.10% 60.72% 3043ms 4.45% tetgen::insphere 0 0% 60.72% 2676ms 3.91% std::_Rb_tree::_M_drop_node (inline) 0 0% 60.72% 2642ms 3.86% std::_Rb_tree::_M_put_node (inline) 220ms 0.32% 61.04% 2411ms 3.52% tetgen::tetgenmesh::flip23 51ms 0.075% 61.11% 2395ms 3.50% Node::~Node 2ms 0.0029% 61.12% 2265ms 3.31% VertexMesh::Clear 2248ms 3.29% 64.40% 2248ms 3.29% std::_Rb_tree_insert_and_rebalance 6ms 0.0088% 64.41% 2166ms 3.17% Element::Element 2073ms 3.03% 67.44% 2073ms 3.03% [libchaste_mesh.so] 1215ms 1.78% 69.22% 1887ms 2.76% malloc_consolidate 21ms 0.031% 69.25% 1821ms 2.66% std::_Vector_base::_M_deallocate (inline) 7ms 0.01% 69.26% 1805ms 2.64% Element::RegisterWithNodes (inline) 0 0% 69.26% 1647ms 2.41% std::vector::~vector (inline) 59ms 0.086% 69.34% 1597ms 2.33% std::vector::_M_realloc_insert 2ms 0.0029% 69.35% 1594ms 2.33% std::_Vector_base::~_Vector_base (inline) 6ms 0.0088% 69.36% 1574ms 2.30% _int_free_maybe_consolidate 1517ms 2.22% 71.57% 1570ms 2.29% tetgen::orient3d 207ms 0.3% 71.87% 1537ms 2.25% tetgen::tetgenmesh::flip32 1432ms 2.09% 73.97% 1432ms 2.09% Node::GetIndex 91ms 0.13% 74.10% 1425ms 2.08% std::map::operator[] 2ms 0.0029% 74.10% 1388ms 2.03% std::_Vector_base::_M_allocate (inline) 1305ms 1.91% 76.01% 1305ms 1.91% unlink_chunk 0 0% 76.01% 1240ms 1.81% std::_Rb_tree::lower_bound (inline) 0 0% 76.01% 1240ms 1.81% std::map::lower_bound (inline) 60ms 0.088% 76.10% 1235ms 1.80% std::vector::push_back (inline) 6ms 0.0088% 76.11% 1233ms 1.80% VertexMesh::GenerateVerticesFromElementCircumcentres 1ms 0.0015% 76.11% 1186ms 1.73% VoronoiDataWriter::Visit 234ms 0.34% 76.45% 1155ms 1.69% tetgen::tetgenmesh::enqueueflipface 22ms 0.032% 76.48% 1149ms 1.68% TetrahedralMesh::Clear 34ms 0.05% 76.53% 1130ms 1.65% tetgen::tetgenmesh::locate 78ms 0.11% 76.65% 1063ms 1.55% tetgen::tetgenmesh::preciselocate 664ms 0.97% 77.62% 1027ms 1.50% AbstractElement::GetNodeGlobalIndex 0 0% 77.62% 939ms 1.37% TetrahedralMesh::RefreshJacobianCachedData 904ms 1.32% 78.94% 904ms 1.32% Node::rGetLocation 6ms 0.0088% 78.95% 816ms 1.19% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.0015% 78.95% 815ms 1.19% AbstractTwoBodyInteractionForce::AddForceContribution 11ms 0.016% 78.96% 777ms 1.14% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 5ms 0.0073% 78.97% 737ms 1.08% boost::numeric::ublas::vector_assign (inline) 8ms 0.012% 78.98% 713ms 1.04% boost::numeric::ublas::c_vector::c_vector (inline) 10ms 0.015% 79.00% 688ms 1.01% AbstractTetrahedralElement::CalculateJacobian 331ms 0.48% 79.48% 676ms 0.99% AbstractElement::GetNodeLocation 13ms 0.019% 79.50% 626ms 0.91% Element::CalculateCircumsphere 0 0% 79.50% 624ms 0.91% std::insert_iterator::operator= (inline) 370ms 0.54% 80.04% 605ms 0.88% tetgen::tetgenmesh::sym 602ms 0.88% 80.92% 602ms 0.88% std::vector::size (inline) 36ms 0.053% 80.97% 597ms 0.87% __atan2 0 0% 80.97% 576ms 0.84% std::set::find (inline) 563ms 0.82% 81.80% 563ms 0.82% tetgen::tetgenmesh::oppo 0 0% 81.80% 562ms 0.82% std::_Rb_tree::_M_insert_unique_ (inline) 509ms 0.74% 82.54% 554ms 0.81% __ieee754_atan2_fma 135ms 0.2% 82.74% 539ms 0.79% std::_Rb_tree_iterator::operator-- (inline) 39ms 0.057% 82.80% 524ms 0.77% AbstractTetrahedralElement::RefreshJacobian 14ms 0.02% 82.82% 469ms 0.69% std::vector::insert (inline) 3ms 0.0044% 82.82% 465ms 0.68% Cell::GetCellId 6ms 0.0088% 82.83% 454ms 0.66% CellPropertyCollection::GetPropertiesType (inline) 449ms 0.66% 83.49% 449ms 0.66% AbstractElement::IsDeleted 16ms 0.023% 83.51% 416ms 0.61% VertexMesh::CalculateUnitNormalToFaceWithArea 158ms 0.23% 83.74% 409ms 0.6% Inverse 0 0% 83.74% 395ms 0.58% VertexMeshWriter::WriteVtkUsingMesh 393ms 0.57% 84.31% 393ms 0.57% boost::numeric::ublas::c_vector::operator() 0 0% 84.31% 384ms 0.56% boost::numeric::ublas::inner_prod (inline) 25ms 0.037% 84.35% 382ms 0.56% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 84.35% 382ms 0.56% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 145ms 0.21% 84.56% 378ms 0.55% _int_free_merge_chunk 54ms 0.079% 84.64% 377ms 0.55% tetgen::tetgenmesh::queue::push 373ms 0.55% 85.19% 373ms 0.55% std::_Rb_tree_decrement 1ms 0.0015% 85.19% 361ms 0.53% tcache_get (inline) 360ms 0.53% 85.71% 360ms 0.53% tcache_get_n (inline) 122ms 0.18% 85.89% 358ms 0.52% __dynamic_cast 4ms 0.0058% 85.90% 355ms 0.52% AbstractTetrahedralElement::AbstractTetrahedralElement 290ms 0.42% 86.32% 349ms 0.51% tetgen::tetgenmesh::fnextself 119ms 0.17% 86.50% 343ms 0.5% boost::numeric::ublas::vector_inner_prod::apply (inline)