File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 60800ms, 86.20% of 70534ms total Dropped 848 nodes (cum <= 352.67ms) flat flat% sum% cum cum% 0 0% 0% 70483ms 99.93% __libc_start_call_main 0 0% 0% 70483ms 99.93% __libc_start_main_impl 0 0% 0% 70483ms 99.93% _start 0 0% 0% 70469ms 99.91% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 70469ms 99.91% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 70469ms 99.91% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 70469ms 99.91% main 0 0% 0% 70433ms 99.86% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 70433ms 99.86% CxxTest::TestRunner::runTest (inline) 1ms 0.0014% 0.0014% 70433ms 99.86% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0.0014% 70179ms 99.50% AbstractCellBasedSimulation::Solve 0 0% 0.0014% 60709ms 86.07% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0014% 60633ms 85.96% MeshBasedCellPopulation::Update 0 0% 0.0014% 38571ms 54.68% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0.0014% 38571ms 54.68% MeshBasedCellPopulation::TessellateIfNeeded 479ms 0.68% 0.68% 33836ms 47.97% VertexMesh::VertexMesh 0 0% 0.68% 17820ms 25.26% MutableMesh::ReMesh 36ms 0.051% 0.73% 13650ms 19.35% std::set::insert (inline) 628ms 0.89% 1.62% 13442ms 19.06% TetrahedralMesh::EdgeIterator::operator++ 186ms 0.26% 1.89% 13134ms 18.62% std::_Rb_tree::_M_insert_unique 0 0% 1.89% 12696ms 18.00% tetgen::tetrahedralize 1ms 0.0014% 1.89% 12531ms 17.77% tetgen::tetgenmesh::delaunizevertices 6ms 0.0085% 1.90% 12520ms 17.75% tetgen::tetgenmesh::incrflipdelaunay 410ms 0.58% 2.48% 11708ms 16.60% VertexElement::AddFace 602ms 0.85% 3.33% 11120ms 15.77% tetgen::tetgenmesh::lawson 2764ms 3.92% 7.25% 9541ms 13.53% std::_Rb_tree::_M_lower_bound (inline) 230ms 0.33% 7.58% 9197ms 13.04% operator new 253ms 0.36% 7.93% 9061ms 12.85% std::_Rb_tree::find (inline) 3032ms 4.30% 12.23% 8861ms 12.56% __GI___libc_malloc 323ms 0.46% 12.69% 8698ms 12.33% std::_Rb_tree::_M_insert_ (inline) 0 0% 12.69% 8584ms 12.17% std::set::count (inline) 65ms 0.092% 12.78% 7635ms 10.82% std::__new_allocator::allocate (inline) 0 0% 12.78% 7582ms 10.75% std::allocator_traits::allocate (inline) 6722ms 9.53% 22.31% 6722ms 9.53% std::_Rb_tree_increment 0 0% 22.31% 6171ms 8.75% std::_Rb_tree::_M_create_node (inline) 1ms 0.0014% 22.31% 6156ms 8.73% std::set_intersection (inline) 377ms 0.53% 22.85% 6155ms 8.73% std::__set_intersection 0 0% 22.85% 6148ms 8.72% std::_Rb_tree::_M_get_node (inline) 0 0% 22.85% 6133ms 8.70% std::_Rb_tree::_Alloc_node::operator() (inline) 1156ms 1.64% 24.49% 6116ms 8.67% __GI___libc_free 1ms 0.0014% 24.49% 5857ms 8.30% OffLatticeSimulation::UpdateCellLocationsAndTopology 5751ms 8.15% 32.64% 5751ms 8.15% std::operator< (inline) 26ms 0.037% 32.68% 5722ms 8.11% std::less::operator() (inline) 1ms 0.0014% 32.68% 5704ms 8.09% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0043% 32.68% 5677ms 8.05% AbstractNumericalMethod::ComputeForcesIncludingDamping 29ms 0.041% 32.73% 5596ms 7.93% Node::AddElement 4113ms 5.83% 38.56% 5371ms 7.61% _int_malloc 226ms 0.32% 38.88% 5213ms 7.39% std::_Rb_tree_const_iterator::operator++ (inline) 96ms 0.14% 39.01% 5118ms 7.26% std::__new_allocator::deallocate (inline) 0 0% 39.01% 5104ms 7.24% std::allocator_traits::deallocate (inline) 2146ms 3.04% 42.06% 4903ms 6.95% _int_free 0 0% 42.06% 4770ms 6.76% VertexMesh::~VertexMesh 4684ms 6.64% 48.70% 4684ms 6.64% std::_Rb_tree::_S_right (inline) 11ms 0.016% 48.71% 4644ms 6.58% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 10ms 0.014% 48.73% 4637ms 6.57% std::_Rb_tree::~_Rb_tree (inline) 1301ms 1.84% 50.57% 4614ms 6.54% std::_Rb_tree::_M_erase 0 0% 50.57% 4594ms 6.51% MeshBasedCellPopulation::UpdateNodePairs 1231ms 1.75% 52.32% 4585ms 6.50% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 52.32% 4568ms 6.48% std::set::~set (inline) 13ms 0.018% 52.34% 4443ms 6.30% MeshBasedCellPopulation::SpringIterator::operator++ 68ms 0.096% 52.43% 4230ms 6.00% MutableElement::AddNode 15ms 0.021% 52.45% 4117ms 5.84% TetrahedralMesh::ImportFromMesher 0 0% 52.45% 3425ms 4.86% AbstractCellPopulation::WriteResultsToFiles 93ms 0.13% 52.58% 2958ms 4.19% tetgen::tetgenmesh::insphere_sos 2633ms 3.73% 56.32% 2849ms 4.04% tetgen::insphere 220ms 0.31% 56.63% 2833ms 4.02% tetgen::tetgenmesh::flip23 51ms 0.072% 56.70% 2666ms 3.78% VertexMesh::Clear 0 0% 56.70% 2657ms 3.77% std::_Rb_tree::_M_drop_node (inline) 0 0% 56.70% 2635ms 3.74% std::_Rb_tree::_M_put_node (inline) 1792ms 2.54% 59.24% 2545ms 3.61% malloc_consolidate 49ms 0.069% 59.31% 2515ms 3.57% Node::~Node 20ms 0.028% 59.34% 2489ms 3.53% std::_Vector_base::_M_deallocate (inline) 4ms 0.0057% 59.35% 2434ms 3.45% Element::Element 2316ms 3.28% 62.63% 2316ms 3.28% std::_Rb_tree_insert_and_rebalance 1ms 0.0014% 62.63% 2275ms 3.23% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 62.63% 2273ms 3.22% std::vector::~vector (inline) 5ms 0.0071% 62.64% 2260ms 3.20% _int_free_maybe_consolidate 1ms 0.0014% 62.64% 2256ms 3.20% std::_Vector_base::~_Vector_base (inline) 58ms 0.082% 62.72% 2223ms 3.15% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 194ms 0.28% 63.00% 2196ms 3.11% std::_Rb_tree_iterator::operator++ (inline) 2079ms 2.95% 65.94% 2079ms 2.95% Node::GetIndex 193ms 0.27% 66.22% 2008ms 2.85% tetgen::tetgenmesh::flip32 3ms 0.0043% 66.22% 2000ms 2.84% Element::RegisterWithNodes (inline) 1965ms 2.79% 69.01% 1965ms 2.79% [libchaste_mesh.so] 3ms 0.0043% 69.01% 1851ms 2.62% VertexMesh::GenerateVerticesFromElementCircumcentres 1666ms 2.36% 71.37% 1666ms 2.36% unlink_chunk 57ms 0.081% 71.45% 1582ms 2.24% std::vector::_M_realloc_insert 153ms 0.22% 71.67% 1473ms 2.09% tetgen::tetgenmesh::enqueueflipface 1ms 0.0014% 71.67% 1435ms 2.03% std::_Vector_base::_M_allocate (inline) 1368ms 1.94% 73.61% 1433ms 2.03% tetgen::orient3d 90ms 0.13% 73.74% 1244ms 1.76% std::vector::push_back (inline) 72ms 0.1% 73.84% 1166ms 1.65% std::map::operator[] 947ms 1.34% 75.19% 1159ms 1.64% AbstractElement::GetNodeGlobalIndex 33ms 0.047% 75.23% 1154ms 1.64% tetgen::tetgenmesh::locate 52ms 0.074% 75.31% 1149ms 1.63% TetrahedralMesh::Clear 1081ms 1.53% 76.84% 1081ms 1.53% Node::rGetLocation 111ms 0.16% 77.00% 1074ms 1.52% tetgen::tetgenmesh::preciselocate 0 0% 77.00% 1003ms 1.42% std::_Rb_tree::lower_bound (inline) 0 0% 77.00% 1003ms 1.42% std::map::lower_bound (inline) 1ms 0.0014% 77.00% 985ms 1.40% TetrahedralMesh::RefreshJacobianCachedData 554ms 0.79% 77.78% 984ms 1.40% AbstractElement::GetNodeLocation 9ms 0.013% 77.80% 964ms 1.37% Element::CalculateCircumsphere 229ms 0.32% 78.12% 925ms 1.31% boost::numeric::ublas::vector_assign (inline) 0 0% 78.12% 921ms 1.31% VoronoiDataWriter::Visit 10ms 0.014% 78.13% 884ms 1.25% boost::numeric::ublas::c_vector::c_vector (inline) 515ms 0.73% 78.86% 864ms 1.22% tetgen::tetgenmesh::sym 16ms 0.023% 78.89% 821ms 1.16% AbstractTetrahedralElement::CalculateJacobian 805ms 1.14% 80.03% 805ms 1.14% AbstractElement::IsDeleted 22ms 0.031% 80.06% 802ms 1.14% AbstractTetrahedralElement::CalculateInverseJacobian 4ms 0.0057% 80.06% 773ms 1.10% AbstractTwoBodyInteractionForce::AddForceContribution 6ms 0.0085% 80.07% 718ms 1.02% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 49ms 0.069% 80.14% 629ms 0.89% AbstractTetrahedralElement::RefreshJacobian 573ms 0.81% 80.96% 573ms 0.81% tetgen::tetgenmesh::oppo 567ms 0.8% 81.76% 567ms 0.8% std::vector::size (inline) 543ms 0.77% 82.53% 543ms 0.77% tetgen::tetgenmesh::triface::triface 37ms 0.052% 82.58% 529ms 0.75% __atan2 0 0% 82.58% 508ms 0.72% std::insert_iterator::operator= (inline) 44ms 0.062% 82.64% 505ms 0.72% tetgen::tetgenmesh::enext2fnext 425ms 0.6% 83.25% 497ms 0.7% tetgen::tetgenmesh::fnextself 33ms 0.047% 83.29% 495ms 0.7% std::vector::insert (inline) 450ms 0.64% 83.93% 486ms 0.69% __ieee754_atan2_fma 0 0% 83.93% 476ms 0.67% std::set::find (inline) 101ms 0.14% 84.07% 474ms 0.67% tetgen::tetgenmesh::queue::pop 54ms 0.077% 84.15% 462ms 0.66% tetgen::tetgenmesh::enextfnext 0 0% 84.15% 461ms 0.65% std::_Rb_tree::_M_insert_unique_ (inline) 22ms 0.031% 84.18% 452ms 0.64% tetgen::tetgenmesh::queue::push 10ms 0.014% 84.20% 439ms 0.62% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.0057% 84.20% 431ms 0.61% AbstractTetrahedralElement::AbstractTetrahedralElement 16ms 0.023% 84.22% 428ms 0.61% VertexMesh::CalculateUnitNormalToFaceWithArea 94ms 0.13% 84.36% 419ms 0.59% boost::numeric::ublas::indexing_vector_assign 49ms 0.069% 84.43% 409ms 0.58% std::_Rb_tree_iterator::operator-- (inline) 290ms 0.41% 84.84% 409ms 0.58% tetgen::tetgenmesh::link::add 2ms 0.0028% 84.84% 405ms 0.57% Cell::GetCellId 0 0% 84.84% 401ms 0.57% VertexMeshWriter::WriteVtkUsingMesh 0 0% 84.84% 398ms 0.56% tcache_get (inline) 398ms 0.56% 85.41% 398ms 0.56% tcache_get_n (inline) 0 0% 85.41% 393ms 0.56% boost::numeric::ublas::inner_prod (inline) 23ms 0.033% 85.44% 392ms 0.56% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 85.44% 392ms 0.56% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 214ms 0.3% 85.74% 390ms 0.55% tetgen::tetgenmesh::bond 0 0% 85.74% 375ms 0.53% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 5ms 0.0071% 85.75% 373ms 0.53% VertexElement::~VertexElement 9ms 0.013% 85.76% 366ms 0.52% boost::numeric::ublas::c_vector::operator= (inline) 309ms 0.44% 86.20% 356ms 0.5% tetgen::tetgenmesh::link::deletenode