File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 54079ms, 87.58% of 61747ms total Dropped 852 nodes (cum <= 308.74ms) flat flat% sum% cum cum% 0 0% 0% 61686ms 99.90% __libc_start_call_main 0 0% 0% 61686ms 99.90% __libc_start_main_impl 0 0% 0% 61686ms 99.90% _start 0 0% 0% 61671ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 61671ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 61671ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 61671ms 99.88% main 0 0% 0% 61634ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 61634ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 61634ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 61363ms 99.38% AbstractCellBasedSimulation::Solve 0 0% 0% 50782ms 82.24% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 50728ms 82.15% MeshBasedCellPopulation::Update 0 0% 0% 29231ms 47.34% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 29231ms 47.34% MeshBasedCellPopulation::TessellateIfNeeded 212ms 0.34% 0.34% 25554ms 41.39% VertexMesh::VertexMesh 0 0% 0.34% 17312ms 28.04% MutableMesh::ReMesh 0 0% 0.34% 12766ms 20.67% tetgen::tetrahedralize 547ms 0.89% 1.23% 12744ms 20.64% TetrahedralMesh::EdgeIterator::operator++ 2ms 0.0032% 1.23% 12622ms 20.44% tetgen::tetgenmesh::delaunizevertices 9ms 0.015% 1.25% 12620ms 20.44% tetgen::tetgenmesh::incrflipdelaunay 553ms 0.9% 2.14% 11168ms 18.09% tetgen::tetgenmesh::lawson 29ms 0.047% 2.19% 10331ms 16.73% std::set::insert (inline) 3022ms 4.89% 7.08% 10017ms 16.22% std::_Rb_tree::_M_lower_bound (inline) 210ms 0.34% 7.42% 9803ms 15.88% std::_Rb_tree::_M_insert_unique 376ms 0.61% 8.03% 9268ms 15.01% VertexElement::AddFace 237ms 0.38% 8.42% 9262ms 15.00% std::_Rb_tree::find (inline) 0 0% 8.42% 8692ms 14.08% std::set::count (inline) 116ms 0.19% 8.60% 6621ms 10.72% std::less::operator() (inline) 6566ms 10.63% 19.24% 6566ms 10.63% std::operator< (inline) 6228ms 10.09% 29.32% 6228ms 10.09% std::_Rb_tree_increment 287ms 0.46% 29.79% 5888ms 9.54% std::_Rb_tree::_M_insert_ (inline) 2ms 0.0032% 29.79% 5621ms 9.10% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0016% 29.79% 5486ms 8.88% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.0065% 29.80% 5460ms 8.84% AbstractNumericalMethod::ComputeForcesIncludingDamping 206ms 0.33% 30.13% 5316ms 8.61% operator new 1092ms 1.77% 31.90% 5031ms 8.15% __GI___libc_malloc 0 0% 31.90% 4822ms 7.81% AbstractCellPopulation::WriteResultsToFiles 45ms 0.073% 31.98% 4556ms 7.38% std::__new_allocator::allocate (inline) 0 0% 31.98% 4534ms 7.34% std::allocator_traits::allocate (inline) 1ms 0.0016% 31.98% 4520ms 7.32% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.011% 31.99% 4520ms 7.32% std::_Rb_tree::~_Rb_tree (inline) 1882ms 3.05% 35.04% 4512ms 7.31% std::_Rb_tree::_M_erase 5ms 0.0081% 35.04% 4511ms 7.31% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 35.04% 4463ms 7.23% std::set::~set (inline) 22ms 0.036% 35.08% 4371ms 7.08% MeshBasedCellPopulation::SpringIterator::operator++ 1236ms 2.00% 37.08% 4051ms 6.56% std::_Rb_tree::_M_get_insert_unique_pos 30ms 0.049% 37.13% 3954ms 6.40% Node::AddElement 1124ms 1.82% 38.95% 3872ms 6.27% __GI___libc_free 2ms 0.0032% 38.95% 3842ms 6.22% std::set_intersection (inline) 239ms 0.39% 39.34% 3840ms 6.22% std::__set_intersection 9ms 0.015% 39.36% 3724ms 6.03% TetrahedralMesh::ImportFromMesher 0 0% 39.36% 3713ms 6.01% VertexMesh::~VertexMesh 3705ms 6.00% 45.36% 3705ms 6.00% std::_Rb_tree::_S_right (inline) 252ms 0.41% 45.76% 3659ms 5.93% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 45.76% 3639ms 5.89% std::_Rb_tree::_M_create_node (inline) 0 0% 45.76% 3615ms 5.85% std::_Rb_tree::_M_get_node (inline) 0 0% 45.76% 3606ms 5.84% std::_Rb_tree::_Alloc_node::operator() (inline) 2635ms 4.27% 50.03% 3546ms 5.74% _int_malloc 99ms 0.16% 50.19% 3542ms 5.74% tetgen::tetgenmesh::insphere_sos 3141ms 5.09% 55.28% 3427ms 5.55% tetgen::insphere 2ms 0.0032% 55.28% 3421ms 5.54% std::_Rb_tree_iterator::operator++ (inline) 5ms 0.0081% 55.29% 3413ms 5.53% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 103ms 0.17% 55.46% 3359ms 5.44% std::__new_allocator::deallocate (inline) 0 0% 55.46% 3345ms 5.42% std::allocator_traits::deallocate (inline) 180ms 0.29% 55.75% 3088ms 5.00% std::_Rb_tree_const_iterator::operator++ (inline) 71ms 0.11% 55.86% 2871ms 4.65% MutableElement::AddNode 1192ms 1.93% 57.79% 2746ms 4.45% _int_free 164ms 0.27% 58.06% 2716ms 4.40% Node::~Node 207ms 0.34% 58.39% 2679ms 4.34% tetgen::tetgenmesh::flip23 221ms 0.36% 58.75% 2489ms 4.03% VertexMesh::Clear 2074ms 3.36% 62.11% 2074ms 3.36% std::_Rb_tree_insert_and_rebalance 4ms 0.0065% 62.12% 1934ms 3.13% Element::Element 0 0% 62.12% 1859ms 3.01% std::_Rb_tree::_M_drop_node (inline) 0 0% 62.12% 1846ms 2.99% std::_Rb_tree::_M_put_node (inline) 162ms 0.26% 62.38% 1806ms 2.92% tetgen::tetgenmesh::flip32 1667ms 2.70% 65.08% 1667ms 2.70% Node::GetIndex 4ms 0.0065% 65.09% 1566ms 2.54% Element::RegisterWithNodes (inline) 980ms 1.59% 66.67% 1558ms 2.52% malloc_consolidate 15ms 0.024% 66.70% 1514ms 2.45% std::_Vector_base::_M_deallocate (inline) 203ms 0.33% 67.03% 1457ms 2.36% TetrahedralMesh::Clear 1368ms 2.22% 69.24% 1456ms 2.36% tetgen::orient3d 0 0% 69.24% 1432ms 2.32% std::vector::~vector (inline) 4ms 0.0065% 69.25% 1336ms 2.16% _int_free_maybe_consolidate 0 0% 69.25% 1336ms 2.16% std::_Vector_base::~_Vector_base (inline) 57ms 0.092% 69.34% 1279ms 2.07% std::map::operator[] 176ms 0.29% 69.63% 1256ms 2.03% tetgen::tetgenmesh::enqueueflipface 22ms 0.036% 69.66% 1215ms 1.97% tetgen::tetgenmesh::locate 2ms 0.0032% 69.66% 1158ms 1.88% VoronoiDataWriter::Visit 0 0% 69.66% 1153ms 1.87% std::_Rb_tree::lower_bound (inline) 0 0% 69.66% 1153ms 1.87% std::map::lower_bound (inline) 1144ms 1.85% 71.52% 1144ms 1.85% unlink_chunk 95ms 0.15% 71.67% 1141ms 1.85% tetgen::tetgenmesh::preciselocate 55ms 0.089% 71.76% 1137ms 1.84% std::vector::_M_realloc_insert 5ms 0.0081% 71.77% 1023ms 1.66% VertexMesh::GenerateVerticesFromElementCircumcentres 4ms 0.0065% 71.78% 923ms 1.49% std::_Vector_base::_M_allocate (inline) 108ms 0.17% 71.95% 920ms 1.49% std::vector::push_back (inline) 918ms 1.49% 73.44% 918ms 1.49% tetgen::tetgenmesh::triface::triface 681ms 1.10% 74.54% 810ms 1.31% AbstractElement::GetNodeGlobalIndex 2ms 0.0032% 74.54% 800ms 1.30% TetrahedralMesh::RefreshJacobianCachedData 380ms 0.62% 75.16% 763ms 1.24% tetgen::tetgenmesh::fnextself 1ms 0.0016% 75.16% 746ms 1.21% AbstractTwoBodyInteractionForce::AddForceContribution 12ms 0.019% 75.18% 726ms 1.18% AbstractTetrahedralElement::CalculateJacobian 283ms 0.46% 75.64% 723ms 1.17% AbstractElement::GetNodeLocation 10ms 0.016% 75.65% 719ms 1.16% AbstractTetrahedralElement::CalculateInverseJacobian 16ms 0.026% 75.68% 694ms 1.12% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 691ms 1.12% 76.80% 691ms 1.12% Node::rGetLocation 668ms 1.08% 77.88% 668ms 1.08% tetgen::tetgenmesh::oppo 54ms 0.087% 77.97% 662ms 1.07% __atan2 15ms 0.024% 77.99% 661ms 1.07% boost::numeric::ublas::vector_assign (inline) 643ms 1.04% 79.03% 643ms 1.04% [libchaste_mesh.so] 11ms 0.018% 79.05% 640ms 1.04% boost::numeric::ublas::c_vector::c_vector (inline) 483ms 0.78% 79.83% 607ms 0.98% __ieee754_atan2_fma 0 0% 79.83% 567ms 0.92% std::set::find (inline) 14ms 0.023% 79.86% 557ms 0.9% Element::CalculateCircumsphere 555ms 0.9% 80.76% 555ms 0.9% tetgen::tetgenmesh::triface::operator= 0 0% 80.76% 541ms 0.88% std::insert_iterator::operator= (inline) 41ms 0.066% 80.82% 533ms 0.86% AbstractTetrahedralElement::RefreshJacobian 57ms 0.092% 80.91% 519ms 0.84% tetgen::tetgenmesh::enext2fnext 493ms 0.8% 81.71% 493ms 0.8% AbstractElement::IsDeleted 58ms 0.094% 81.81% 486ms 0.79% tetgen::tetgenmesh::enextfnext 0 0% 81.81% 478ms 0.77% std::_Rb_tree::_M_insert_unique_ (inline) 477ms 0.77% 82.58% 477ms 0.77% std::vector::size (inline) 0 0% 82.58% 456ms 0.74% boost::numeric::ublas::inner_prod (inline) 9ms 0.015% 82.59% 453ms 0.73% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 321ms 0.52% 83.11% 450ms 0.73% tetgen::tetgenmesh::sym 15ms 0.024% 83.14% 444ms 0.72% boost::numeric::ublas::vector_scalar_binary::evaluate 433ms 0.7% 83.84% 433ms 0.7% boost::numeric::ublas::c_vector::operator() 235ms 0.38% 84.22% 422ms 0.68% AbstractTetrahedralMesh::GetElement 6ms 0.0097% 84.23% 409ms 0.66% CellPropertyCollection::GetPropertiesType (inline) 2ms 0.0032% 84.23% 407ms 0.66% Cell::GetCellId 80ms 0.13% 84.36% 406ms 0.66% __dynamic_cast 99ms 0.16% 84.52% 400ms 0.65% boost::numeric::ublas::indexing_vector_assign 190ms 0.31% 84.83% 398ms 0.64% boost::numeric::ublas::vector_inner_prod::apply (inline) 24ms 0.039% 84.87% 396ms 0.64% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 84.87% 393ms 0.64% VertexMeshWriter::WriteVtkUsingMesh 377ms 0.61% 85.48% 377ms 0.61% tetgen::tetgenmesh::org 26ms 0.042% 85.52% 375ms 0.61% tetgen::tetgenmesh::queue::push 14ms 0.023% 85.54% 372ms 0.6% std::_Rb_tree_iterator::operator-- (inline) 2ms 0.0032% 85.55% 364ms 0.59% AbstractTetrahedralElement::AbstractTetrahedralElement 16ms 0.026% 85.57% 352ms 0.57% std::vector::insert (inline) 253ms 0.41% 85.98% 352ms 0.57% tetgen::tetgenmesh::bond 250ms 0.4% 86.39% 347ms 0.56% tetgen::tetgenmesh::link::add 0 0% 86.39% 346ms 0.56% tcache_get (inline) 346ms 0.56% 86.95% 346ms 0.56% tcache_get_n (inline) 8ms 0.013% 86.96% 343ms 0.56% VertexElement::~VertexElement 3ms 0.0049% 86.97% 342ms 0.55% boost::numeric::ublas::c_vector::operator= (inline) 1ms 0.0016% 86.97% 335ms 0.54% AbstractCellProperty::IsSubType (inline) 0 0% 86.97% 334ms 0.54% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 334ms 0.54% 87.51% 334ms 0.54% std::_Rb_tree_decrement 45ms 0.073% 87.58% 310ms 0.5% boost::numeric::ublas::vector_reference::operator() (inline)