File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 51810ms, 85.90% of 60313ms total Dropped 854 nodes (cum <= 301.56ms) flat flat% sum% cum cum% 0 0% 0% 60260ms 99.91% __libc_start_call_main 0 0% 0% 60260ms 99.91% __libc_start_main_impl 0 0% 0% 60260ms 99.91% _start 0 0% 0% 60244ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 60244ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 60244ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 60244ms 99.89% main 0 0% 0% 60203ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 60203ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 60203ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 59932ms 99.37% AbstractCellBasedSimulation::Solve 0 0% 0% 50970ms 84.51% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 50924ms 84.43% MeshBasedCellPopulation::Update 0 0% 0% 27267ms 45.21% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 27266ms 45.21% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 210ms 0.35% 0.35% 24674ms 40.91% VertexMesh::VertexMesh 0 0% 0.35% 19679ms 32.63% MutableMesh::ReMesh 0 0% 0.35% 16045ms 26.60% tetgen::tetrahedralize 7ms 0.012% 0.36% 15895ms 26.35% tetgen::tetgenmesh::delaunizevertices 14ms 0.023% 0.38% 15885ms 26.34% tetgen::tetgenmesh::incrflipdelaunay 569ms 0.94% 1.33% 14124ms 23.42% tetgen::tetgenmesh::lawson 629ms 1.04% 2.37% 12180ms 20.19% TetrahedralMesh::EdgeIterator::operator++ 35ms 0.058% 2.43% 9764ms 16.19% std::set::insert (inline) 362ms 0.6% 3.03% 9559ms 15.85% VertexElement::AddFace 258ms 0.43% 3.46% 9287ms 15.40% std::_Rb_tree::_M_insert_unique 3171ms 5.26% 8.71% 8987ms 14.90% std::_Rb_tree::_M_lower_bound (inline) 263ms 0.44% 9.15% 8531ms 14.14% std::_Rb_tree::find (inline) 0 0% 9.15% 7947ms 13.18% std::set::count (inline) 130ms 0.22% 9.36% 5766ms 9.56% std::less::operator() (inline) 5711ms 9.47% 18.83% 5711ms 9.47% std::operator< (inline) 317ms 0.53% 19.36% 5450ms 9.04% std::_Rb_tree::_M_insert_ (inline) 0 0% 19.36% 5366ms 8.90% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.0033% 19.36% 5236ms 8.68% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.005% 19.37% 5213ms 8.64% AbstractNumericalMethod::ComputeForcesIncludingDamping 4862ms 8.06% 27.43% 4862ms 8.06% std::_Rb_tree_increment 181ms 0.3% 27.73% 4763ms 7.90% operator new 1156ms 1.92% 29.65% 4492ms 7.45% __GI___libc_malloc 1ms 0.0017% 29.65% 4350ms 7.21% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.0099% 29.66% 4333ms 7.18% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 6ms 0.0099% 29.67% 4189ms 6.95% MeshBasedCellPopulation::SpringIterator::operator++ 27ms 0.045% 29.71% 4142ms 6.87% std::__new_allocator::allocate (inline) 0 0% 29.71% 4113ms 6.82% std::allocator_traits::allocate (inline) 6ms 0.0099% 29.72% 3886ms 6.44% std::_Rb_tree::~_Rb_tree (inline) 1282ms 2.13% 31.85% 3874ms 6.42% std::_Rb_tree::_M_erase 1341ms 2.22% 34.07% 3845ms 6.38% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 34.07% 3837ms 6.36% std::set::~set (inline) 113ms 0.19% 34.26% 3833ms 6.36% tetgen::tetgenmesh::insphere_sos 2ms 0.0033% 34.26% 3826ms 6.34% std::set_intersection (inline) 255ms 0.42% 34.68% 3824ms 6.34% std::__set_intersection 3435ms 5.70% 40.38% 3710ms 6.15% tetgen::insphere 1084ms 1.80% 42.18% 3561ms 5.90% __GI___libc_free 134ms 0.22% 42.40% 3461ms 5.74% tetgen::tetgenmesh::flip23 0 0% 42.40% 3439ms 5.70% AbstractCellPopulation::WriteResultsToFiles 0 0% 42.40% 3387ms 5.62% std::_Rb_tree::_M_create_node (inline) 0 0% 42.40% 3368ms 5.58% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 42.40% 3359ms 5.57% std::_Rb_tree::_M_get_node (inline) 138ms 0.23% 42.63% 3183ms 5.28% std::__new_allocator::deallocate (inline) 0 0% 42.63% 3168ms 5.25% std::allocator_traits::deallocate (inline) 221ms 0.37% 42.99% 3085ms 5.11% std::_Rb_tree_const_iterator::operator++ (inline) 38ms 0.063% 43.06% 2989ms 4.96% Node::AddElement 2148ms 3.56% 46.62% 2979ms 4.94% _int_malloc 10ms 0.017% 46.64% 2890ms 4.79% TetrahedralMesh::ImportFromMesher 2770ms 4.59% 51.23% 2770ms 4.59% std::_Rb_tree::_S_right (inline) 0 0% 51.23% 2610ms 4.33% VertexMesh::~VertexMesh 139ms 0.23% 51.46% 2489ms 4.13% tetgen::tetgenmesh::flip32 1288ms 2.14% 53.59% 2472ms 4.10% _int_free 54ms 0.09% 53.68% 2345ms 3.89% MutableElement::AddNode 5ms 0.0083% 53.69% 2336ms 3.87% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 187ms 0.31% 54.00% 2320ms 3.85% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 3ms 0.005% 54.01% 2146ms 3.56% std::_Rb_tree_iterator::operator++ (inline) 0 0% 54.01% 2045ms 3.39% std::_Rb_tree::_M_drop_node (inline) 0 0% 54.01% 2024ms 3.36% std::_Rb_tree::_M_put_node (inline) 138ms 0.23% 54.24% 1980ms 3.28% Node::~Node 214ms 0.35% 54.59% 1907ms 3.16% tetgen::tetgenmesh::enqueueflipface 1808ms 3.00% 57.59% 1808ms 3.00% std::_Rb_tree_insert_and_rebalance 118ms 0.2% 57.78% 1735ms 2.88% VertexMesh::Clear 1573ms 2.61% 60.39% 1655ms 2.74% tetgen::orient3d 1467ms 2.43% 62.82% 1467ms 2.43% Node::GetIndex 33ms 0.055% 62.88% 1421ms 2.36% tetgen::tetgenmesh::locate 4ms 0.0066% 62.89% 1388ms 2.30% Element::Element 87ms 0.14% 63.03% 1339ms 2.22% tetgen::tetgenmesh::preciselocate 70ms 0.12% 63.15% 1246ms 2.07% TetrahedralMesh::Clear 24ms 0.04% 63.19% 1168ms 1.94% std::_Vector_base::_M_deallocate (inline) 762ms 1.26% 64.45% 1139ms 1.89% malloc_consolidate 1126ms 1.87% 66.32% 1126ms 1.87% tetgen::tetgenmesh::oppo 0 0% 66.32% 1095ms 1.82% std::vector::~vector (inline) 4ms 0.0066% 66.32% 1071ms 1.78% Element::RegisterWithNodes (inline) 81ms 0.13% 66.46% 1067ms 1.77% std::map::operator[] 1042ms 1.73% 68.18% 1042ms 1.73% tetgen::tetgenmesh::triface::triface 56ms 0.093% 68.28% 1021ms 1.69% std::vector::_M_realloc_insert 0 0% 68.28% 1001ms 1.66% std::_Vector_base::~_Vector_base (inline) 8ms 0.013% 68.29% 957ms 1.59% _int_free_maybe_consolidate 940ms 1.56% 69.85% 940ms 1.56% unlink_chunk 0 0% 69.85% 922ms 1.53% std::_Rb_tree::lower_bound (inline) 0 0% 69.85% 922ms 1.53% std::map::lower_bound (inline) 723ms 1.20% 71.05% 899ms 1.49% AbstractElement::GetNodeGlobalIndex 0 0% 71.05% 865ms 1.43% VoronoiDataWriter::Visit 92ms 0.15% 71.20% 821ms 1.36% std::vector::push_back (inline) 817ms 1.35% 72.55% 817ms 1.35% [libchaste_mesh.so] 773ms 1.28% 73.84% 773ms 1.28% tetgen::tetgenmesh::triface::operator= 4ms 0.0066% 73.84% 771ms 1.28% VertexMesh::GenerateVerticesFromElementCircumcentres 273ms 0.45% 74.30% 764ms 1.27% tetgen::tetgenmesh::sym 9ms 0.015% 74.31% 763ms 1.27% std::_Vector_base::_M_allocate (inline) 0 0% 74.31% 723ms 1.20% TetrahedralMesh::RefreshJacobianCachedData 0 0% 74.31% 712ms 1.18% AbstractTwoBodyInteractionForce::AddForceContribution 15ms 0.025% 74.34% 687ms 1.14% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 9ms 0.015% 74.35% 666ms 1.10% AbstractTetrahedralElement::CalculateInverseJacobian 367ms 0.61% 74.96% 639ms 1.06% tetgen::tetgenmesh::fnextself 14ms 0.023% 74.98% 622ms 1.03% boost::numeric::ublas::vector_assign (inline) 37ms 0.061% 75.04% 620ms 1.03% tetgen::tetgenmesh::queue::push 40ms 0.066% 75.11% 617ms 1.02% __atan2 10ms 0.017% 75.13% 597ms 0.99% boost::numeric::ublas::c_vector::c_vector (inline) 339ms 0.56% 75.69% 583ms 0.97% tetgen::tetgenmesh::link::add 222ms 0.37% 76.06% 581ms 0.96% tetgen::tetgenmesh::bond 0 0% 76.06% 580ms 0.96% std::set::find (inline) 64ms 0.11% 76.16% 577ms 0.96% tetgen::tetgenmesh::enext2fnext 11ms 0.018% 76.18% 576ms 0.96% AbstractTetrahedralElement::CalculateJacobian 431ms 0.71% 76.90% 566ms 0.94% __ieee754_atan2_fma 54ms 0.09% 76.99% 547ms 0.91% tetgen::tetgenmesh::enextfnext 0 0% 76.99% 537ms 0.89% boost::numeric::ublas::inner_prod (inline) 3ms 0.005% 76.99% 535ms 0.89% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 44ms 0.073% 77.06% 532ms 0.88% boost::numeric::ublas::vector_scalar_binary::evaluate 527ms 0.87% 77.94% 527ms 0.87% tetgen::tetgenmesh::decode 521ms 0.86% 78.80% 521ms 0.86% Node::rGetLocation 0 0% 78.80% 513ms 0.85% std::insert_iterator::operator= (inline) 498ms 0.83% 79.63% 498ms 0.83% std::vector::size (inline) 226ms 0.37% 80.00% 495ms 0.82% AbstractElement::GetNodeLocation 464ms 0.77% 80.77% 464ms 0.77% AbstractElement::IsDeleted 23ms 0.038% 80.81% 454ms 0.75% std::_Rb_tree_iterator::operator-- (inline) 48ms 0.08% 80.89% 442ms 0.73% AbstractTetrahedralElement::RefreshJacobian 0 0% 80.89% 440ms 0.73% std::_Rb_tree::_M_insert_unique_ (inline) 424ms 0.7% 81.59% 424ms 0.7% tetgen::tetgenmesh::org 196ms 0.32% 81.92% 421ms 0.7% boost::numeric::ublas::vector_inner_prod::apply (inline) 414ms 0.69% 82.60% 414ms 0.69% boost::numeric::ublas::c_vector::operator() 8ms 0.013% 82.62% 412ms 0.68% boost::numeric::ublas::c_vector::operator= (inline) 170ms 0.28% 82.90% 394ms 0.65% AbstractTetrahedralMesh::GetElement 393ms 0.65% 83.55% 393ms 0.65% std::_Rb_tree_decrement 8ms 0.013% 83.56% 392ms 0.65% Element::CalculateCircumsphere 107ms 0.18% 83.74% 392ms 0.65% __dynamic_cast 0 0% 83.74% 383ms 0.64% VertexMeshWriter::WriteVtkUsingMesh 2ms 0.0033% 83.74% 380ms 0.63% CellPropertyCollection::GetPropertiesType (inline) 2ms 0.0033% 83.75% 376ms 0.62% Cell::GetCellId 88ms 0.15% 83.89% 368ms 0.61% boost::numeric::ublas::indexing_vector_assign 19ms 0.032% 83.92% 367ms 0.61% VertexMesh::CalculateUnitNormalToFaceWithArea 354ms 0.59% 84.51% 354ms 0.59% tetgen::tetgenmesh::pointmark 344ms 0.57% 85.08% 344ms 0.57% tetgen::tetgenmesh::encode 121ms 0.2% 85.28% 331ms 0.55% Inverse 12ms 0.02% 85.30% 328ms 0.54% VertexElement::~VertexElement 317ms 0.53% 85.83% 317ms 0.53% tetgen::tetgenmesh::face::face 3ms 0.005% 85.83% 316ms 0.52% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 85.83% 316ms 0.52% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 1ms 0.0017% 85.83% 313ms 0.52% AbstractCellProperty::IsSubType (inline) 11ms 0.018% 85.85% 313ms 0.52% std::vector::insert (inline) 30ms 0.05% 85.90% 307ms 0.51% boost::numeric::ublas::vector_reference::operator() (inline)