File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 59238ms, 87.11% of 68000ms total Dropped 878 nodes (cum <= 340ms) flat flat% sum% cum cum% 0 0% 0% 67932ms 99.90% __libc_start_call_main 0 0% 0% 67932ms 99.90% __libc_start_main_impl 0 0% 0% 67932ms 99.90% _start 0 0% 0% 67916ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 67916ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 67916ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 67916ms 99.88% main 0 0% 0% 67882ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 67882ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 67882ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 67624ms 99.45% AbstractCellBasedSimulation::Solve 0 0% 0% 56783ms 83.50% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 56732ms 83.43% MeshBasedCellPopulation::Update 0 0% 0% 34176ms 50.26% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 34175ms 50.26% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 255ms 0.38% 0.38% 29674ms 43.64% VertexMesh::VertexMesh 1ms 0.0015% 0.38% 18195ms 26.76% MutableMesh::ReMesh 545ms 0.8% 1.18% 13429ms 19.75% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.18% 13239ms 19.47% tetgen::tetrahedralize 4ms 0.0059% 1.18% 13100ms 19.26% tetgen::tetgenmesh::delaunizevertices 9ms 0.013% 1.20% 13093ms 19.25% tetgen::tetgenmesh::incrflipdelaunay 561ms 0.83% 2.02% 11637ms 17.11% tetgen::tetgenmesh::lawson 28ms 0.041% 2.06% 11481ms 16.88% std::set::insert (inline) 226ms 0.33% 2.40% 11026ms 16.21% std::_Rb_tree::_M_insert_unique 451ms 0.66% 3.06% 10250ms 15.07% VertexElement::AddFace 2953ms 4.34% 7.40% 10237ms 15.05% std::_Rb_tree::_M_lower_bound (inline) 215ms 0.32% 7.72% 9330ms 13.72% std::_Rb_tree::find (inline) 0 0% 7.72% 8772ms 12.90% std::set::count (inline) 7439ms 10.94% 18.66% 7439ms 10.94% std::_Rb_tree_increment 112ms 0.16% 18.82% 6803ms 10.00% std::less::operator() (inline) 6753ms 9.93% 28.75% 6753ms 9.93% std::operator< (inline) 269ms 0.4% 29.15% 6351ms 9.34% std::_Rb_tree::_M_insert_ (inline) 233ms 0.34% 29.49% 6031ms 8.87% operator new 0 0% 29.49% 5809ms 8.54% OffLatticeSimulation::UpdateCellLocationsAndTopology 986ms 1.45% 30.94% 5725ms 8.42% __GI___libc_malloc 0 0% 30.94% 5643ms 8.30% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0029% 30.94% 5607ms 8.25% AbstractNumericalMethod::ComputeForcesIncludingDamping 5ms 0.0074% 30.95% 5182ms 7.62% std::set_intersection (inline) 319ms 0.47% 31.42% 5177ms 7.61% std::__set_intersection 10ms 0.015% 31.44% 5003ms 7.36% std::_Rb_tree::~_Rb_tree (inline) 2100ms 3.09% 34.52% 4989ms 7.34% std::_Rb_tree::_M_erase 51ms 0.075% 34.60% 4965ms 7.30% std::__new_allocator::allocate (inline) 0 0% 34.60% 4942ms 7.27% std::allocator_traits::allocate (inline) 0 0% 34.60% 4931ms 7.25% std::set::~set (inline) 0 0% 34.60% 4867ms 7.16% AbstractCellPopulation::WriteResultsToFiles 42ms 0.062% 34.66% 4843ms 7.12% Node::AddElement 1296ms 1.91% 36.57% 4723ms 6.95% std::_Rb_tree::_M_get_insert_unique_pos 1ms 0.0015% 36.57% 4712ms 6.93% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.0044% 36.57% 4667ms 6.86% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1272ms 1.87% 38.44% 4538ms 6.67% __GI___libc_free 12ms 0.018% 38.46% 4537ms 6.67% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 38.46% 4525ms 6.65% VertexMesh::~VertexMesh 4399ms 6.47% 44.93% 4399ms 6.47% std::_Rb_tree::_S_right (inline) 3205ms 4.71% 49.64% 4398ms 6.47% _int_malloc 213ms 0.31% 49.96% 4380ms 6.44% std::_Rb_tree_const_iterator::operator++ (inline) 161ms 0.24% 50.19% 3978ms 5.85% std::__new_allocator::deallocate (inline) 0 0% 50.19% 3967ms 5.83% std::_Rb_tree::_M_create_node (inline) 0 0% 50.19% 3961ms 5.83% std::allocator_traits::deallocate (inline) 10ms 0.015% 50.21% 3953ms 5.81% TetrahedralMesh::ImportFromMesher 0 0% 50.21% 3925ms 5.77% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 50.21% 3917ms 5.76% std::_Rb_tree::_M_get_node (inline) 68ms 0.1% 50.31% 3657ms 5.38% MutableElement::AddNode 239ms 0.35% 50.66% 3595ms 5.29% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 126ms 0.19% 50.84% 3520ms 5.18% tetgen::tetgenmesh::insphere_sos 6ms 0.0088% 50.85% 3398ms 5.00% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 3095ms 4.55% 55.40% 3385ms 4.98% tetgen::insphere 2ms 0.0029% 55.41% 3370ms 4.96% std::_Rb_tree_iterator::operator++ (inline) 1240ms 1.82% 57.23% 3264ms 4.80% _int_free 210ms 0.31% 57.54% 3057ms 4.50% Node::~Node 243ms 0.36% 57.90% 2879ms 4.23% VertexMesh::Clear 201ms 0.3% 58.19% 2733ms 4.02% tetgen::tetgenmesh::flip23 2261ms 3.33% 61.52% 2261ms 3.33% std::_Rb_tree_insert_and_rebalance 2108ms 3.10% 64.62% 2108ms 3.10% Node::GetIndex 155ms 0.23% 64.85% 2043ms 3.00% tetgen::tetgenmesh::flip32 0 0% 64.85% 2036ms 2.99% std::_Rb_tree::_M_drop_node (inline) 0 0% 64.85% 2025ms 2.98% std::_Rb_tree::_M_put_node (inline) 1386ms 2.04% 66.88% 2010ms 2.96% malloc_consolidate 6ms 0.0088% 66.89% 1989ms 2.93% Element::Element 15ms 0.022% 66.91% 1951ms 2.87% std::_Vector_base::_M_deallocate (inline) 0 0% 66.91% 1810ms 2.66% std::vector::~vector (inline) 2ms 0.0029% 66.92% 1760ms 2.59% std::_Vector_base::~_Vector_base (inline) 12ms 0.018% 66.94% 1757ms 2.58% _int_free_maybe_consolidate 6ms 0.0088% 66.94% 1671ms 2.46% Element::RegisterWithNodes (inline) 225ms 0.33% 67.27% 1553ms 2.28% TetrahedralMesh::Clear 1434ms 2.11% 69.38% 1434ms 2.11% unlink_chunk 72ms 0.11% 69.49% 1411ms 2.08% std::map::operator[] 1309ms 1.93% 71.41% 1401ms 2.06% tetgen::orient3d 204ms 0.3% 71.71% 1357ms 2.00% tetgen::tetgenmesh::enqueueflipface 3ms 0.0044% 71.72% 1280ms 1.88% VertexMesh::GenerateVerticesFromElementCircumcentres 0 0% 71.72% 1256ms 1.85% std::_Rb_tree::lower_bound (inline) 0 0% 71.72% 1256ms 1.85% std::map::lower_bound (inline) 53ms 0.078% 71.80% 1245ms 1.83% std::vector::_M_realloc_insert 33ms 0.049% 71.85% 1242ms 1.83% tetgen::tetgenmesh::locate 0 0% 71.85% 1211ms 1.78% VoronoiDataWriter::Visit 97ms 0.14% 71.99% 1167ms 1.72% tetgen::tetgenmesh::preciselocate 994ms 1.46% 73.45% 1150ms 1.69% AbstractElement::GetNodeGlobalIndex 1035ms 1.52% 74.97% 1035ms 1.52% tetgen::tetgenmesh::triface::triface 133ms 0.2% 75.17% 1034ms 1.52% std::vector::push_back (inline) 7ms 0.01% 75.18% 1032ms 1.52% std::_Vector_base::_M_allocate (inline) 1ms 0.0015% 75.18% 978ms 1.44% TetrahedralMesh::RefreshJacobianCachedData 393ms 0.58% 75.76% 899ms 1.32% AbstractElement::GetNodeLocation 878ms 1.29% 77.05% 878ms 1.29% Node::rGetLocation 868ms 1.28% 78.33% 868ms 1.28% tetgen::tetgenmesh::triface::operator= 10ms 0.015% 78.34% 847ms 1.25% AbstractTetrahedralElement::CalculateInverseJacobian 329ms 0.48% 78.82% 829ms 1.22% tetgen::tetgenmesh::fnextself 780ms 1.15% 79.97% 780ms 1.15% AbstractElement::IsDeleted 13ms 0.019% 79.99% 769ms 1.13% AbstractTetrahedralElement::CalculateJacobian 0 0% 79.99% 735ms 1.08% AbstractTwoBodyInteractionForce::AddForceContribution 16ms 0.024% 80.01% 689ms 1.01% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 19ms 0.028% 80.04% 637ms 0.94% Element::CalculateCircumsphere 629ms 0.92% 80.97% 629ms 0.92% [libchaste_mesh.so] 9ms 0.013% 80.98% 623ms 0.92% boost::numeric::ublas::c_vector::c_vector (inline) 38ms 0.056% 81.04% 622ms 0.91% __atan2 18ms 0.026% 81.06% 620ms 0.91% boost::numeric::ublas::vector_assign (inline) 40ms 0.059% 81.12% 595ms 0.88% AbstractTetrahedralElement::RefreshJacobian 464ms 0.68% 81.80% 584ms 0.86% __ieee754_atan2_fma 560ms 0.82% 82.63% 560ms 0.82% tetgen::tetgenmesh::oppo 0 0% 82.63% 556ms 0.82% std::set::find (inline) 53ms 0.078% 82.70% 551ms 0.81% tetgen::tetgenmesh::enext2fnext 548ms 0.81% 83.51% 548ms 0.81% std::vector::size (inline) 79ms 0.12% 83.63% 536ms 0.79% tetgen::tetgenmesh::enextfnext 29ms 0.043% 83.67% 484ms 0.71% tetgen::tetgenmesh::queue::push 0 0% 83.67% 483ms 0.71% boost::numeric::ublas::inner_prod (inline) 5ms 0.0074% 83.68% 481ms 0.71% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 24ms 0.035% 83.71% 476ms 0.7% boost::numeric::ublas::vector_scalar_binary::evaluate 27ms 0.04% 83.75% 456ms 0.67% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 83.75% 450ms 0.66% std::insert_iterator::operator= (inline) 384ms 0.56% 84.32% 450ms 0.66% tetgen::tetgenmesh::link::add 307ms 0.45% 84.77% 446ms 0.66% tetgen::tetgenmesh::sym 23ms 0.034% 84.80% 424ms 0.62% std::_Rb_tree_iterator::operator-- (inline) 0 0% 84.80% 420ms 0.62% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 241ms 0.35% 85.16% 411ms 0.6% AbstractTetrahedralMesh::GetElement 0 0% 85.16% 402ms 0.59% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 85.16% 400ms 0.59% VertexMeshWriter::WriteVtkUsingMesh 5ms 0.0074% 85.16% 396ms 0.58% CellPropertyCollection::GetPropertiesType (inline) 188ms 0.28% 85.44% 396ms 0.58% boost::numeric::ublas::vector_inner_prod::apply (inline) 393ms 0.58% 86.02% 393ms 0.58% boost::numeric::ublas::c_vector::operator() 97ms 0.14% 86.16% 389ms 0.57% boost::numeric::ublas::indexing_vector_assign 379ms 0.56% 86.72% 379ms 0.56% std::_Rb_tree_decrement 3ms 0.0044% 86.72% 377ms 0.55% Cell::GetCellId 78ms 0.11% 86.84% 376ms 0.55% __dynamic_cast 9ms 0.013% 86.85% 363ms 0.53% std::vector::insert (inline) 11ms 0.016% 86.87% 359ms 0.53% VertexElement::~VertexElement 8ms 0.012% 86.88% 355ms 0.52% boost::numeric::ublas::c_vector::operator= (inline) 161ms 0.24% 87.11% 341ms 0.5% Inverse