File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 54735ms, 87.44% of 62598ms total Dropped 841 nodes (cum <= 312.99ms) flat flat% sum% cum cum% 0 0% 0% 62540ms 99.91% __libc_start_call_main 0 0% 0% 62540ms 99.91% __libc_start_main_impl 0 0% 0% 62540ms 99.91% _start 0 0% 0% 62523ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 62523ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 62523ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 62523ms 99.88% main 0 0% 0% 62492ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 62492ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 62492ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 62226ms 99.41% AbstractCellBasedSimulation::Solve 0 0% 0% 51482ms 82.24% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 51430ms 82.16% MeshBasedCellPopulation::Update 1ms 0.0016% 0.0016% 29820ms 47.64% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0.0016% 29820ms 47.64% MeshBasedCellPopulation::TessellateIfNeeded 195ms 0.31% 0.31% 26152ms 41.78% VertexMesh::VertexMesh 0 0% 0.31% 17309ms 27.65% MutableMesh::ReMesh 561ms 0.9% 1.21% 13033ms 20.82% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.21% 12654ms 20.21% tetgen::tetrahedralize 2ms 0.0032% 1.21% 12519ms 20.00% tetgen::tetgenmesh::delaunizevertices 8ms 0.013% 1.23% 12513ms 19.99% tetgen::tetgenmesh::incrflipdelaunay 589ms 0.94% 2.17% 11089ms 17.71% tetgen::tetgenmesh::lawson 21ms 0.034% 2.20% 10412ms 16.63% std::set::insert (inline) 3108ms 4.97% 7.16% 10295ms 16.45% std::_Rb_tree::_M_lower_bound (inline) 182ms 0.29% 7.46% 9904ms 15.82% std::_Rb_tree::_M_insert_unique 254ms 0.41% 7.86% 9512ms 15.20% std::_Rb_tree::find (inline) 402ms 0.64% 8.50% 9407ms 15.03% VertexElement::AddFace 0 0% 8.50% 8945ms 14.29% std::set::count (inline) 122ms 0.19% 8.70% 6770ms 10.82% std::less::operator() (inline) 6707ms 10.71% 19.41% 6707ms 10.71% std::operator< (inline) 6545ms 10.46% 29.87% 6545ms 10.46% std::_Rb_tree_increment 259ms 0.41% 30.28% 5910ms 9.44% std::_Rb_tree::_M_insert_ (inline) 0 0% 30.28% 5671ms 9.06% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 30.28% 5539ms 8.85% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.0064% 30.29% 5513ms 8.81% AbstractNumericalMethod::ComputeForcesIncludingDamping 234ms 0.37% 30.66% 5428ms 8.67% operator new 1078ms 1.72% 32.38% 5141ms 8.21% __GI___libc_malloc 0 0% 32.38% 4937ms 7.89% AbstractCellPopulation::WriteResultsToFiles 2ms 0.0032% 32.39% 4626ms 7.39% MeshBasedCellPopulation::UpdateNodePairs 42ms 0.067% 32.45% 4597ms 7.34% std::__new_allocator::allocate (inline) 7ms 0.011% 32.47% 4588ms 7.33% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 32.47% 4580ms 7.32% std::allocator_traits::allocate (inline) 19ms 0.03% 32.50% 4475ms 7.15% MeshBasedCellPopulation::SpringIterator::operator++ 6ms 0.0096% 32.51% 4412ms 7.05% std::_Rb_tree::~_Rb_tree (inline) 1840ms 2.94% 35.45% 4405ms 7.04% std::_Rb_tree::_M_erase 0 0% 35.45% 4358ms 6.96% std::set::~set (inline) 1214ms 1.94% 37.38% 4128ms 6.59% std::_Rb_tree::_M_get_insert_unique_pos 35ms 0.056% 37.44% 4109ms 6.56% Node::AddElement 5ms 0.008% 37.45% 4056ms 6.48% std::set_intersection (inline) 272ms 0.43% 37.88% 4051ms 6.47% std::__set_intersection 1104ms 1.76% 39.65% 3858ms 6.16% __GI___libc_free 3799ms 6.07% 45.72% 3799ms 6.07% std::_Rb_tree::_S_right (inline) 6ms 0.0096% 45.73% 3792ms 6.06% TetrahedralMesh::ImportFromMesher 226ms 0.36% 46.09% 3740ms 5.97% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 46.09% 3727ms 5.95% std::_Rb_tree::_M_create_node (inline) 2697ms 4.31% 50.39% 3703ms 5.92% _int_malloc 0 0% 50.39% 3701ms 5.91% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 50.39% 3697ms 5.91% VertexMesh::~VertexMesh 0 0% 50.39% 3678ms 5.88% std::_Rb_tree::_M_get_node (inline) 0 0% 50.39% 3526ms 5.63% std::_Rb_tree_iterator::operator++ (inline) 5ms 0.008% 50.40% 3495ms 5.58% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 101ms 0.16% 50.56% 3452ms 5.51% tetgen::tetgenmesh::insphere_sos 137ms 0.22% 50.78% 3367ms 5.38% std::__new_allocator::deallocate (inline) 0 0% 50.78% 3347ms 5.35% std::allocator_traits::deallocate (inline) 3052ms 4.88% 55.66% 3325ms 5.31% tetgen::insphere 172ms 0.27% 55.93% 3288ms 5.25% std::_Rb_tree_const_iterator::operator++ (inline) 64ms 0.1% 56.04% 2951ms 4.71% MutableElement::AddNode 1109ms 1.77% 57.81% 2748ms 4.39% _int_free 191ms 0.31% 58.11% 2693ms 4.30% tetgen::tetgenmesh::flip23 195ms 0.31% 58.42% 2643ms 4.22% Node::~Node 204ms 0.33% 58.75% 2406ms 3.84% VertexMesh::Clear 2057ms 3.29% 62.04% 2057ms 3.29% std::_Rb_tree_insert_and_rebalance 5ms 0.008% 62.04% 1957ms 3.13% Element::Element 0 0% 62.04% 1818ms 2.90% std::_Rb_tree::_M_drop_node (inline) 0 0% 62.04% 1808ms 2.89% std::_Rb_tree::_M_put_node (inline) 166ms 0.27% 62.31% 1803ms 2.88% tetgen::tetgenmesh::flip32 1725ms 2.76% 65.06% 1725ms 2.76% Node::GetIndex 1034ms 1.65% 66.72% 1638ms 2.62% malloc_consolidate 4ms 0.0064% 66.72% 1614ms 2.58% Element::RegisterWithNodes (inline) 15ms 0.024% 66.75% 1554ms 2.48% std::_Vector_base::_M_deallocate (inline) 0 0% 66.75% 1485ms 2.37% std::vector::~vector (inline) 227ms 0.36% 67.11% 1478ms 2.36% TetrahedralMesh::Clear 1355ms 2.16% 69.27% 1447ms 2.31% tetgen::orient3d 9ms 0.014% 69.29% 1408ms 2.25% _int_free_maybe_consolidate 1ms 0.0016% 69.29% 1401ms 2.24% std::_Vector_base::~_Vector_base (inline) 51ms 0.081% 69.37% 1286ms 2.05% std::map::operator[] 172ms 0.27% 69.65% 1278ms 2.04% tetgen::tetgenmesh::enqueueflipface 1244ms 1.99% 71.63% 1244ms 1.99% unlink_chunk 32ms 0.051% 71.68% 1208ms 1.93% tetgen::tetgenmesh::locate 0 0% 71.68% 1183ms 1.89% VoronoiDataWriter::Visit 0 0% 71.68% 1182ms 1.89% std::_Rb_tree::lower_bound (inline) 0 0% 71.68% 1182ms 1.89% std::map::lower_bound (inline) 108ms 0.17% 71.86% 1129ms 1.80% tetgen::tetgenmesh::preciselocate 4ms 0.0064% 71.86% 1080ms 1.73% VertexMesh::GenerateVerticesFromElementCircumcentres 59ms 0.094% 71.96% 1078ms 1.72% std::vector::_M_realloc_insert 768ms 1.23% 73.18% 940ms 1.50% AbstractElement::GetNodeGlobalIndex 8ms 0.013% 73.20% 910ms 1.45% std::_Vector_base::_M_allocate (inline) 121ms 0.19% 73.39% 904ms 1.44% std::vector::push_back (inline) 2ms 0.0032% 73.39% 840ms 1.34% TetrahedralMesh::RefreshJacobianCachedData 825ms 1.32% 74.71% 825ms 1.32% tetgen::tetgenmesh::triface::triface 306ms 0.49% 75.20% 776ms 1.24% AbstractElement::GetNodeLocation 6ms 0.0096% 75.21% 743ms 1.19% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.0016% 75.21% 727ms 1.16% AbstractTwoBodyInteractionForce::AddForceContribution 398ms 0.64% 75.85% 706ms 1.13% tetgen::tetgenmesh::fnextself 9ms 0.014% 75.86% 700ms 1.12% AbstractTetrahedralElement::CalculateJacobian 15ms 0.024% 75.89% 700ms 1.12% boost::numeric::ublas::vector_assign (inline) 692ms 1.11% 76.99% 692ms 1.11% [libchaste_mesh.so] 688ms 1.10% 78.09% 688ms 1.10% Node::rGetLocation 17ms 0.027% 78.12% 671ms 1.07% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 10ms 0.016% 78.13% 662ms 1.06% boost::numeric::ublas::c_vector::c_vector (inline) 637ms 1.02% 79.15% 637ms 1.02% tetgen::tetgenmesh::triface::operator= 620ms 0.99% 80.14% 620ms 0.99% tetgen::tetgenmesh::oppo 48ms 0.077% 80.22% 616ms 0.98% __atan2 585ms 0.93% 81.15% 585ms 0.93% AbstractElement::IsDeleted 19ms 0.03% 81.18% 575ms 0.92% Element::CalculateCircumsphere 452ms 0.72% 81.91% 568ms 0.91% __ieee754_atan2_fma 0 0% 81.91% 559ms 0.89% std::set::find (inline) 32ms 0.051% 81.96% 548ms 0.88% AbstractTetrahedralElement::RefreshJacobian 543ms 0.87% 82.82% 543ms 0.87% std::vector::size (inline) 0 0% 82.82% 501ms 0.8% std::insert_iterator::operator= (inline) 49ms 0.078% 82.90% 483ms 0.77% tetgen::tetgenmesh::enext2fnext 333ms 0.53% 83.43% 463ms 0.74% tetgen::tetgenmesh::sym 0 0% 83.43% 461ms 0.74% boost::numeric::ublas::inner_prod (inline) 0 0% 83.43% 459ms 0.73% std::_Rb_tree::_M_insert_unique_ (inline) 5ms 0.008% 83.44% 458ms 0.73% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 50ms 0.08% 83.52% 458ms 0.73% tetgen::tetgenmesh::enextfnext 23ms 0.037% 83.56% 453ms 0.72% boost::numeric::ublas::vector_scalar_binary::evaluate 127ms 0.2% 83.76% 435ms 0.69% boost::numeric::ublas::indexing_vector_assign 4ms 0.0064% 83.77% 422ms 0.67% boost::numeric::ublas::c_vector::operator= (inline) 4ms 0.0064% 83.77% 411ms 0.66% CellPropertyCollection::GetPropertiesType (inline) 117ms 0.19% 83.96% 402ms 0.64% __dynamic_cast 14ms 0.022% 83.98% 398ms 0.64% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 83.98% 397ms 0.63% VertexMeshWriter::WriteVtkUsingMesh 2ms 0.0032% 83.99% 381ms 0.61% Cell::GetCellId 199ms 0.32% 84.30% 375ms 0.6% AbstractTetrahedralMesh::GetElement 373ms 0.6% 84.90% 373ms 0.6% tetgen::tetgenmesh::org 372ms 0.59% 85.49% 372ms 0.59% boost::numeric::ublas::c_vector::operator() 172ms 0.27% 85.77% 371ms 0.59% boost::numeric::ublas::vector_inner_prod::apply (inline) 31ms 0.05% 85.82% 358ms 0.57% tetgen::tetgenmesh::queue::push 256ms 0.41% 86.23% 353ms 0.56% tetgen::tetgenmesh::bond 31ms 0.05% 86.28% 352ms 0.56% std::_Rb_tree_iterator::operator-- (inline) 0 0% 86.28% 347ms 0.55% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 3ms 0.0048% 86.28% 337ms 0.54% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.0016% 86.28% 330ms 0.53% AbstractCellProperty::IsSubType (inline) 158ms 0.25% 86.54% 328ms 0.52% Inverse 4ms 0.0064% 86.54% 326ms 0.52% VertexElement::~VertexElement 0 0% 86.54% 325ms 0.52% tcache_get (inline) 325ms 0.52% 87.06% 325ms 0.52% tcache_get_n (inline) 13ms 0.021% 87.08% 324ms 0.52% std::vector::insert (inline) 223ms 0.36% 87.44% 324ms 0.52% tetgen::tetgenmesh::link::add