File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 65023ms, 86.98% of 74760ms total Dropped 892 nodes (cum <= 373.80ms) flat flat% sum% cum cum% 0 0% 0% 74696ms 99.91% __libc_start_call_main 0 0% 0% 74696ms 99.91% __libc_start_main_impl 0 0% 0% 74696ms 99.91% _start 0 0% 0% 74679ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 74679ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 74679ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 74679ms 99.89% main 0 0% 0% 74632ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 74632ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 74632ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 74330ms 99.42% AbstractCellBasedSimulation::Solve 0 0% 0% 64555ms 86.35% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 64510ms 86.29% MeshBasedCellPopulation::Update 0 0% 0% 38531ms 51.54% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 38530ms 51.54% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 305ms 0.41% 0.41% 33835ms 45.26% VertexMesh::VertexMesh 0 0% 0.41% 21542ms 28.81% MutableMesh::ReMesh 0 0% 0.41% 16516ms 22.09% tetgen::tetrahedralize 1ms 0.0013% 0.41% 16358ms 21.88% tetgen::tetgenmesh::delaunizevertices 8ms 0.011% 0.42% 16353ms 21.87% tetgen::tetgenmesh::incrflipdelaunay 541ms 0.72% 1.14% 14682ms 19.64% tetgen::tetgenmesh::lawson 600ms 0.8% 1.95% 14208ms 19.00% TetrahedralMesh::EdgeIterator::operator++ 29ms 0.039% 1.99% 12401ms 16.59% std::set::insert (inline) 285ms 0.38% 2.37% 11980ms 16.02% std::_Rb_tree::_M_insert_unique 510ms 0.68% 3.05% 11480ms 15.36% VertexElement::AddFace 3235ms 4.33% 7.38% 10010ms 13.39% std::_Rb_tree::_M_lower_bound (inline) 252ms 0.34% 7.71% 9309ms 12.45% std::_Rb_tree::find (inline) 0 0% 7.71% 8738ms 11.69% std::set::count (inline) 7585ms 10.15% 17.86% 7585ms 10.15% std::_Rb_tree_increment 311ms 0.42% 18.27% 6936ms 9.28% std::_Rb_tree::_M_insert_ (inline) 165ms 0.22% 18.50% 6819ms 9.12% operator new 1ms 0.0013% 18.50% 6585ms 8.81% std::set_intersection (inline) 381ms 0.51% 19.01% 6584ms 8.81% std::__set_intersection 1229ms 1.64% 20.65% 6560ms 8.77% __GI___libc_malloc 108ms 0.14% 20.79% 6525ms 8.73% std::less::operator() (inline) 6482ms 8.67% 29.46% 6482ms 8.67% std::operator< (inline) 2ms 0.0027% 29.47% 5978ms 8.00% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 29.47% 5820ms 7.78% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0013% 29.47% 5792ms 7.75% AbstractNumericalMethod::ComputeForcesIncludingDamping 202ms 0.27% 29.74% 5699ms 7.62% std::_Rb_tree_const_iterator::operator++ (inline) 42ms 0.056% 29.80% 5568ms 7.45% std::__new_allocator::allocate (inline) 0 0% 29.80% 5546ms 7.42% std::allocator_traits::allocate (inline) 48ms 0.064% 29.86% 5364ms 7.17% Node::AddElement 1323ms 1.77% 31.63% 5119ms 6.85% __GI___libc_free 7ms 0.0094% 31.64% 5041ms 6.74% std::_Rb_tree::~_Rb_tree (inline) 1834ms 2.45% 34.09% 5030ms 6.73% std::_Rb_tree::_M_erase 1392ms 1.86% 35.95% 5027ms 6.72% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 35.95% 4975ms 6.65% std::set::~set (inline) 3624ms 4.85% 40.80% 4946ms 6.62% _int_malloc 1ms 0.0013% 40.80% 4857ms 6.50% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.0054% 40.81% 4855ms 6.49% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1ms 0.0013% 40.81% 4733ms 6.33% VertexMesh::~VertexMesh 3ms 0.004% 40.81% 4673ms 6.25% MeshBasedCellPopulation::SpringIterator::operator++ 139ms 0.19% 41.00% 4497ms 6.02% std::__new_allocator::deallocate (inline) 0 0% 41.00% 4477ms 5.99% std::_Rb_tree::_M_create_node (inline) 0 0% 41.00% 4477ms 5.99% std::allocator_traits::deallocate (inline) 4445ms 5.95% 46.94% 4445ms 5.95% std::_Rb_tree::_S_right (inline) 0 0% 46.94% 4439ms 5.94% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 46.94% 4411ms 5.90% std::_Rb_tree::_M_get_node (inline) 78ms 0.1% 47.05% 4184ms 5.60% MutableElement::AddNode 138ms 0.18% 47.23% 3973ms 5.31% tetgen::tetgenmesh::insphere_sos 14ms 0.019% 47.25% 3935ms 5.26% TetrahedralMesh::ImportFromMesher 3549ms 4.75% 52.00% 3816ms 5.10% tetgen::insphere 1512ms 2.02% 54.02% 3792ms 5.07% _int_free 0 0% 54.02% 3595ms 4.81% AbstractCellPopulation::WriteResultsToFiles 152ms 0.2% 54.23% 3590ms 4.80% tetgen::tetgenmesh::flip23 226ms 0.3% 54.53% 3056ms 4.09% Node::~Node 166ms 0.22% 54.75% 2849ms 3.81% VertexMesh::Clear 2847ms 3.81% 58.56% 2847ms 3.81% Node::GetIndex 132ms 0.18% 58.73% 2518ms 3.37% tetgen::tetgenmesh::flip32 4ms 0.0054% 58.74% 2395ms 3.20% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 187ms 0.25% 58.99% 2390ms 3.20% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1678ms 2.24% 61.23% 2311ms 3.09% malloc_consolidate 0 0% 61.23% 2308ms 3.09% std::_Rb_tree::_M_drop_node (inline) 0 0% 61.23% 2298ms 3.07% std::_Rb_tree::_M_put_node (inline) 2280ms 3.05% 64.28% 2280ms 3.05% std::_Rb_tree_insert_and_rebalance 1ms 0.0013% 64.29% 2232ms 2.99% std::_Rb_tree_iterator::operator++ (inline) 37ms 0.049% 64.34% 2215ms 2.96% std::_Vector_base::_M_deallocate (inline) 0 0% 64.34% 2099ms 2.81% std::vector::~vector (inline) 4ms 0.0054% 64.34% 2085ms 2.79% Element::Element 1ms 0.0013% 64.34% 2049ms 2.74% std::_Vector_base::~_Vector_base (inline) 6ms 0.008% 64.35% 2007ms 2.68% _int_free_maybe_consolidate 227ms 0.3% 64.65% 1836ms 2.46% tetgen::tetgenmesh::enqueueflipface 6ms 0.008% 64.66% 1722ms 2.30% Element::RegisterWithNodes (inline) 1609ms 2.15% 66.81% 1609ms 2.15% unlink_chunk 1475ms 1.97% 68.79% 1564ms 2.09% tetgen::orient3d 1303ms 1.74% 70.53% 1535ms 2.05% AbstractElement::GetNodeGlobalIndex 9ms 0.012% 70.54% 1437ms 1.92% VertexMesh::GenerateVerticesFromElementCircumcentres 58ms 0.078% 70.62% 1392ms 1.86% TetrahedralMesh::Clear 53ms 0.071% 70.69% 1359ms 1.82% tetgen::tetgenmesh::locate 51ms 0.068% 70.76% 1345ms 1.80% std::vector::_M_realloc_insert 56ms 0.075% 70.83% 1286ms 1.72% std::map::operator[] 68ms 0.091% 70.92% 1255ms 1.68% tetgen::tetgenmesh::preciselocate 6ms 0.008% 70.93% 1141ms 1.53% std::_Vector_base::_M_allocate (inline) 0 0% 70.93% 1133ms 1.52% std::_Rb_tree::lower_bound (inline) 0 0% 70.93% 1133ms 1.52% std::map::lower_bound (inline) 1093ms 1.46% 72.39% 1093ms 1.46% tetgen::tetgenmesh::triface::triface 103ms 0.14% 72.53% 1084ms 1.45% std::vector::push_back (inline) 0 0% 72.53% 1055ms 1.41% TetrahedralMesh::RefreshJacobianCachedData 1020ms 1.36% 73.90% 1020ms 1.36% AbstractElement::IsDeleted 994ms 1.33% 75.23% 994ms 1.33% tetgen::tetgenmesh::oppo 0 0% 75.23% 956ms 1.28% VoronoiDataWriter::Visit 925ms 1.24% 76.46% 925ms 1.24% Node::rGetLocation 448ms 0.6% 77.06% 910ms 1.22% AbstractElement::GetNodeLocation 11ms 0.015% 77.08% 872ms 1.17% AbstractTetrahedralElement::CalculateInverseJacobian 312ms 0.42% 77.49% 834ms 1.12% tetgen::tetgenmesh::sym 20ms 0.027% 77.52% 814ms 1.09% AbstractTetrahedralElement::CalculateJacobian 814ms 1.09% 78.61% 814ms 1.09% tetgen::tetgenmesh::triface::operator= 804ms 1.08% 79.69% 804ms 1.08% [libchaste_mesh.so] 731ms 0.98% 80.66% 731ms 0.98% std::vector::size (inline) 3ms 0.004% 80.67% 729ms 0.98% AbstractTwoBodyInteractionForce::AddForceContribution 17ms 0.023% 80.69% 680ms 0.91% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 19ms 0.025% 80.72% 661ms 0.88% Element::CalculateCircumsphere 387ms 0.52% 81.23% 644ms 0.86% tetgen::tetgenmesh::fnextself 67ms 0.09% 81.32% 635ms 0.85% tetgen::tetgenmesh::enext2fnext 51ms 0.068% 81.39% 626ms 0.84% __atan2 56ms 0.075% 81.47% 619ms 0.83% tetgen::tetgenmesh::queue::push 12ms 0.016% 81.48% 599ms 0.8% boost::numeric::ublas::c_vector::c_vector (inline) 42ms 0.056% 81.54% 591ms 0.79% AbstractTetrahedralElement::RefreshJacobian 230ms 0.31% 81.85% 591ms 0.79% tetgen::tetgenmesh::bond 14ms 0.019% 81.86% 590ms 0.79% boost::numeric::ublas::vector_assign (inline) 457ms 0.61% 82.48% 569ms 0.76% __ieee754_atan2_fma 0 0% 82.48% 566ms 0.76% std::set::find (inline) 363ms 0.49% 82.96% 563ms 0.75% tetgen::tetgenmesh::link::add 65ms 0.087% 83.05% 556ms 0.74% tetgen::tetgenmesh::enextfnext 551ms 0.74% 83.79% 551ms 0.74% tetgen::tetgenmesh::decode 0 0% 83.79% 515ms 0.69% boost::numeric::ublas::inner_prod (inline) 1ms 0.0013% 83.79% 512ms 0.68% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 41ms 0.055% 83.84% 511ms 0.68% boost::numeric::ublas::vector_scalar_binary::evaluate 482ms 0.64% 84.49% 482ms 0.64% tetgen::tetgenmesh::org 482ms 0.64% 85.13% 482ms 0.64% tetgen::tetgenmesh::pointmark 0 0% 85.13% 457ms 0.61% std::insert_iterator::operator= (inline) 241ms 0.32% 85.45% 455ms 0.61% AbstractTetrahedralMesh::GetElement 23ms 0.031% 85.48% 453ms 0.61% VertexMesh::CalculateUnitNormalToFaceWithArea 19ms 0.025% 85.51% 435ms 0.58% std::_Rb_tree_iterator::operator-- (inline) 9ms 0.012% 85.52% 426ms 0.57% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 85.52% 425ms 0.57% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 94ms 0.13% 85.65% 423ms 0.57% tetgen::tetgenmesh::queue::pop 186ms 0.25% 85.90% 415ms 0.56% boost::numeric::ublas::vector_inner_prod::apply (inline) 8ms 0.011% 85.91% 410ms 0.55% VertexElement::~VertexElement 397ms 0.53% 86.44% 397ms 0.53% std::_Rb_tree_decrement 22ms 0.029% 86.47% 397ms 0.53% std::vector::insert (inline) 0 0% 86.47% 396ms 0.53% VertexMeshWriter::WriteVtkUsingMesh 0 0% 86.47% 391ms 0.52% std::_Rb_tree::_M_insert_unique_ (inline) 380ms 0.51% 86.98% 380ms 0.51% boost::numeric::ublas::c_vector::operator()