File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 58856ms, 86.75% of 67843ms total Dropped 882 nodes (cum <= 339.21ms) flat flat% sum% cum cum% 0 0% 0% 67786ms 99.92% __libc_start_call_main 0 0% 0% 67786ms 99.92% __libc_start_main_impl 0 0% 0% 67786ms 99.92% _start 0 0% 0% 67769ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 67769ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 67769ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 67769ms 99.89% main 0 0% 0% 67729ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 67729ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 67728ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 67436ms 99.40% AbstractCellBasedSimulation::Solve 0 0% 0% 58021ms 85.52% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 57974ms 85.45% MeshBasedCellPopulation::Update 0 0% 0% 33199ms 48.94% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 33199ms 48.94% MeshBasedCellPopulation::TessellateIfNeeded 199ms 0.29% 0.29% 28895ms 42.59% VertexMesh::VertexMesh 0 0% 0.29% 20557ms 30.30% MutableMesh::ReMesh 0 0% 0.29% 15845ms 23.36% tetgen::tetrahedralize 0 0% 0.29% 15682ms 23.12% tetgen::tetgenmesh::delaunizevertices 9ms 0.013% 0.31% 15675ms 23.10% tetgen::tetgenmesh::incrflipdelaunay 508ms 0.75% 1.06% 14055ms 20.72% tetgen::tetgenmesh::lawson 599ms 0.88% 1.94% 13071ms 19.27% TetrahedralMesh::EdgeIterator::operator++ 27ms 0.04% 1.98% 11237ms 16.56% std::set::insert (inline) 214ms 0.32% 2.29% 10806ms 15.93% std::_Rb_tree::_M_insert_unique 405ms 0.6% 2.89% 10391ms 15.32% VertexElement::AddFace 3244ms 4.78% 7.67% 9288ms 13.69% std::_Rb_tree::_M_lower_bound (inline) 277ms 0.41% 8.08% 8824ms 13.01% std::_Rb_tree::find (inline) 0 0% 8.08% 8262ms 12.18% std::set::count (inline) 330ms 0.49% 8.57% 6547ms 9.65% std::_Rb_tree::_M_insert_ (inline) 6241ms 9.20% 17.77% 6241ms 9.20% std::_Rb_tree_increment 159ms 0.23% 18.00% 6204ms 9.14% operator new 1286ms 1.90% 19.90% 5966ms 8.79% __GI___libc_malloc 91ms 0.13% 20.03% 5939ms 8.75% std::less::operator() (inline) 5915ms 8.72% 28.75% 5915ms 8.72% std::operator< (inline) 0 0% 28.75% 5704ms 8.41% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 28.75% 5558ms 8.19% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.01% 28.76% 5533ms 8.16% AbstractNumericalMethod::ComputeForcesIncludingDamping 23ms 0.034% 28.79% 5149ms 7.59% std::__new_allocator::allocate (inline) 2ms 0.0029% 28.80% 5144ms 7.58% std::set_intersection (inline) 322ms 0.47% 29.27% 5142ms 7.58% std::__set_intersection 0 0% 29.27% 5124ms 7.55% std::allocator_traits::allocate (inline) 1358ms 2.00% 31.27% 4911ms 7.24% __GI___libc_free 13ms 0.019% 31.29% 4806ms 7.08% std::_Rb_tree::~_Rb_tree (inline) 1729ms 2.55% 33.84% 4790ms 7.06% std::_Rb_tree::_M_erase 0 0% 33.84% 4752ms 7.00% std::set::~set (inline) 0 0% 33.84% 4594ms 6.77% MeshBasedCellPopulation::UpdateNodePairs 11ms 0.016% 33.86% 4566ms 6.73% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 12ms 0.018% 33.87% 4442ms 6.55% MeshBasedCellPopulation::SpringIterator::operator++ 1ms 0.0015% 33.88% 4338ms 6.39% VertexMesh::~VertexMesh 171ms 0.25% 34.13% 4331ms 6.38% std::_Rb_tree_const_iterator::operator++ (inline) 1298ms 1.91% 36.04% 4314ms 6.36% std::_Rb_tree::_M_get_insert_unique_pos 3113ms 4.59% 40.63% 4306ms 6.35% _int_malloc 57ms 0.084% 40.71% 4272ms 6.30% Node::AddElement 132ms 0.19% 40.91% 4201ms 6.19% std::__new_allocator::deallocate (inline) 0 0% 40.91% 4194ms 6.18% std::_Rb_tree::_M_create_node (inline) 0 0% 40.91% 4181ms 6.16% std::allocator_traits::deallocate (inline) 0 0% 40.91% 4168ms 6.14% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 40.91% 4143ms 6.11% std::_Rb_tree::_M_get_node (inline) 120ms 0.18% 41.08% 3838ms 5.66% tetgen::tetgenmesh::insphere_sos 10ms 0.015% 41.10% 3800ms 5.60% TetrahedralMesh::ImportFromMesher 3418ms 5.04% 46.14% 3707ms 5.46% tetgen::insphere 3600ms 5.31% 51.44% 3600ms 5.31% std::_Rb_tree::_S_right (inline) 1483ms 2.19% 53.63% 3552ms 5.24% _int_free 0 0% 53.63% 3538ms 5.21% AbstractCellPopulation::WriteResultsToFiles 121ms 0.18% 53.81% 3494ms 5.15% tetgen::tetgenmesh::flip23 68ms 0.1% 53.91% 3232ms 4.76% MutableElement::AddNode 147ms 0.22% 54.12% 2831ms 4.17% Node::~Node 182ms 0.27% 54.39% 2763ms 4.07% VertexMesh::Clear 137ms 0.2% 54.60% 2573ms 3.79% tetgen::tetgenmesh::flip32 183ms 0.27% 54.86% 2379ms 3.51% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1ms 0.0015% 54.87% 2377ms 3.50% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 54.87% 2309ms 3.40% std::_Rb_tree::_M_drop_node (inline) 0 0% 54.87% 2303ms 3.39% std::_Rb_tree::_M_put_node (inline) 2ms 0.0029% 54.87% 2218ms 3.27% std::_Rb_tree_iterator::operator++ (inline) 2118ms 3.12% 57.99% 2118ms 3.12% std::_Rb_tree_insert_and_rebalance 232ms 0.34% 58.33% 1966ms 2.90% tetgen::tetgenmesh::enqueueflipface 1368ms 2.02% 60.35% 1947ms 2.87% malloc_consolidate 1910ms 2.82% 63.16% 1910ms 2.82% Node::GetIndex 25ms 0.037% 63.20% 1903ms 2.81% std::_Vector_base::_M_deallocate (inline) 2ms 0.0029% 63.20% 1890ms 2.79% Element::Element 0 0% 63.20% 1822ms 2.69% std::vector::~vector (inline) 1ms 0.0015% 63.21% 1730ms 2.55% std::_Vector_base::~_Vector_base (inline) 8ms 0.012% 63.22% 1674ms 2.47% _int_free_maybe_consolidate 1475ms 2.17% 65.39% 1558ms 2.30% tetgen::orient3d 4ms 0.0059% 65.40% 1517ms 2.24% Element::RegisterWithNodes (inline) 82ms 0.12% 65.52% 1473ms 2.17% TetrahedralMesh::Clear 1410ms 2.08% 67.60% 1410ms 2.08% unlink_chunk 47ms 0.069% 67.67% 1315ms 1.94% tetgen::tetgenmesh::locate 1031ms 1.52% 69.19% 1249ms 1.84% AbstractElement::GetNodeGlobalIndex 80ms 0.12% 69.30% 1224ms 1.80% tetgen::tetgenmesh::preciselocate 69ms 0.1% 69.41% 1210ms 1.78% std::vector::_M_realloc_insert 5ms 0.0074% 69.41% 1192ms 1.76% VertexMesh::GenerateVerticesFromElementCircumcentres 62ms 0.091% 69.50% 1085ms 1.60% std::map::operator[] 1049ms 1.55% 71.05% 1049ms 1.55% tetgen::tetgenmesh::oppo 141ms 0.21% 71.26% 1036ms 1.53% std::vector::push_back (inline) 6ms 0.0088% 71.27% 987ms 1.45% std::_Vector_base::_M_allocate (inline) 986ms 1.45% 72.72% 986ms 1.45% tetgen::tetgenmesh::triface::triface 0 0% 72.72% 954ms 1.41% std::_Rb_tree::lower_bound (inline) 0 0% 72.72% 954ms 1.41% std::map::lower_bound (inline) 0 0% 72.72% 912ms 1.34% VoronoiDataWriter::Visit 1ms 0.0015% 72.72% 889ms 1.31% TetrahedralMesh::RefreshJacobianCachedData 813ms 1.20% 73.92% 813ms 1.20% [libchaste_mesh.so] 297ms 0.44% 74.36% 805ms 1.19% tetgen::tetgenmesh::sym 346ms 0.51% 74.87% 792ms 1.17% AbstractElement::GetNodeLocation 2ms 0.0029% 74.87% 781ms 1.15% AbstractTwoBodyInteractionForce::AddForceContribution 7ms 0.01% 74.88% 772ms 1.14% AbstractTetrahedralElement::CalculateInverseJacobian 13ms 0.019% 74.90% 747ms 1.10% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 744ms 1.10% 76.00% 744ms 1.10% AbstractElement::IsDeleted 19ms 0.028% 76.03% 740ms 1.09% AbstractTetrahedralElement::CalculateJacobian 717ms 1.06% 77.08% 717ms 1.06% tetgen::tetgenmesh::triface::operator= 713ms 1.05% 78.13% 713ms 1.05% Node::rGetLocation 34ms 0.05% 78.18% 663ms 0.98% tetgen::tetgenmesh::queue::push 653ms 0.96% 79.15% 653ms 0.96% std::vector::size (inline) 382ms 0.56% 79.71% 629ms 0.93% tetgen::tetgenmesh::link::add 383ms 0.56% 80.27% 619ms 0.91% tetgen::tetgenmesh::fnextself 11ms 0.016% 80.29% 601ms 0.89% boost::numeric::ublas::c_vector::c_vector (inline) 60ms 0.088% 80.38% 601ms 0.89% tetgen::tetgenmesh::enext2fnext 211ms 0.31% 80.69% 589ms 0.87% tetgen::tetgenmesh::bond 12ms 0.018% 80.71% 586ms 0.86% boost::numeric::ublas::vector_assign (inline) 46ms 0.068% 80.77% 582ms 0.86% __atan2 20ms 0.029% 80.80% 558ms 0.82% Element::CalculateCircumsphere 0 0% 80.80% 558ms 0.82% std::set::find (inline) 66ms 0.097% 80.90% 557ms 0.82% tetgen::tetgenmesh::enextfnext 45ms 0.066% 80.97% 546ms 0.8% AbstractTetrahedralElement::RefreshJacobian 414ms 0.61% 81.58% 535ms 0.79% __ieee754_atan2_fma 526ms 0.78% 82.35% 526ms 0.78% tetgen::tetgenmesh::decode 0 0% 82.35% 515ms 0.76% boost::numeric::ublas::inner_prod (inline) 1ms 0.0015% 82.35% 513ms 0.76% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 42ms 0.062% 82.42% 512ms 0.75% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 82.42% 467ms 0.69% std::insert_iterator::operator= (inline) 4ms 0.0059% 82.42% 461ms 0.68% CellPropertyCollection::GetPropertiesType (inline) 440ms 0.65% 83.07% 440ms 0.65% tetgen::tetgenmesh::org 1ms 0.0015% 83.07% 433ms 0.64% Cell::GetCellId 203ms 0.3% 83.37% 429ms 0.63% AbstractTetrahedralMesh::GetElement 8ms 0.012% 83.38% 424ms 0.62% VertexElement::~VertexElement 33ms 0.049% 83.43% 420ms 0.62% std::_Rb_tree_iterator::operator-- (inline) 118ms 0.17% 83.61% 415ms 0.61% __dynamic_cast 194ms 0.29% 83.89% 413ms 0.61% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 83.89% 401ms 0.59% std::_Rb_tree::_M_insert_unique_ (inline) 20ms 0.029% 83.92% 398ms 0.59% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 83.92% 391ms 0.58% VertexMeshWriter::WriteVtkUsingMesh 386ms 0.57% 84.49% 386ms 0.57% boost::numeric::ublas::c_vector::operator() 12ms 0.018% 84.51% 381ms 0.56% boost::numeric::ublas::c_vector::operator= (inline) 4ms 0.0059% 84.51% 370ms 0.55% AbstractTetrahedralElement::AbstractTetrahedralElement 370ms 0.55% 85.06% 370ms 0.55% std::_Rb_tree_decrement 365ms 0.54% 85.60% 365ms 0.54% tetgen::tetgenmesh::encode 83ms 0.12% 85.72% 364ms 0.54% boost::numeric::ublas::indexing_vector_assign 354ms 0.52% 86.24% 354ms 0.52% tetgen::tetgenmesh::face::face 3ms 0.0044% 86.25% 349ms 0.51% AbstractCellProperty::IsSubType (inline) 0 0% 86.25% 346ms 0.51% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 344ms 0.51% 86.75% 344ms 0.51% tetgen::tetgenmesh::pointmark