File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 55786ms, 87.74% of 63583ms total Dropped 857 nodes (cum <= 317.92ms) flat flat% sum% cum cum% 0 0% 0% 63515ms 99.89% __libc_start_call_main 0 0% 0% 63515ms 99.89% __libc_start_main_impl 0 0% 0% 63515ms 99.89% _start 0 0% 0% 63499ms 99.87% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 63499ms 99.87% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 63499ms 99.87% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 63499ms 99.87% main 0 0% 0% 63461ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 63461ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 63461ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 63196ms 99.39% AbstractCellBasedSimulation::Solve 0 0% 0% 52511ms 82.59% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 52460ms 82.51% MeshBasedCellPopulation::Update 0 0% 0% 30971ms 48.71% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 30969ms 48.71% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 238ms 0.37% 0.37% 27219ms 42.81% VertexMesh::VertexMesh 0 0% 0.37% 17246ms 27.12% MutableMesh::ReMesh 569ms 0.89% 1.27% 12997ms 20.44% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.27% 12725ms 20.01% tetgen::tetrahedralize 3ms 0.0047% 1.27% 12581ms 19.79% tetgen::tetgenmesh::delaunizevertices 6ms 0.0094% 1.28% 12576ms 19.78% tetgen::tetgenmesh::incrflipdelaunay 536ms 0.84% 2.13% 11213ms 17.64% tetgen::tetgenmesh::lawson 21ms 0.033% 2.16% 10623ms 16.71% std::set::insert (inline) 183ms 0.29% 2.45% 10085ms 15.86% std::_Rb_tree::_M_insert_unique 3060ms 4.81% 7.26% 10044ms 15.80% std::_Rb_tree::_M_lower_bound (inline) 409ms 0.64% 7.90% 9610ms 15.11% VertexElement::AddFace 233ms 0.37% 8.27% 9338ms 14.69% std::_Rb_tree::find (inline) 0 0% 8.27% 8794ms 13.83% std::set::count (inline) 6729ms 10.58% 18.85% 6729ms 10.58% std::_Rb_tree_increment 120ms 0.19% 19.04% 6665ms 10.48% std::less::operator() (inline) 6608ms 10.39% 29.43% 6608ms 10.39% std::operator< (inline) 280ms 0.44% 29.87% 5922ms 9.31% std::_Rb_tree::_M_insert_ (inline) 1ms 0.0016% 29.88% 5750ms 9.04% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 29.88% 5590ms 8.79% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0031% 29.88% 5561ms 8.75% AbstractNumericalMethod::ComputeForcesIncludingDamping 179ms 0.28% 30.16% 5330ms 8.38% operator new 1092ms 1.72% 31.88% 5073ms 7.98% __GI___libc_malloc 0 0% 31.88% 4780ms 7.52% AbstractCellPopulation::WriteResultsToFiles 15ms 0.024% 31.90% 4694ms 7.38% std::_Rb_tree::~_Rb_tree (inline) 1881ms 2.96% 34.86% 4677ms 7.36% std::_Rb_tree::_M_erase 0 0% 34.86% 4629ms 7.28% std::set::~set (inline) 5ms 0.0079% 34.87% 4606ms 7.24% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1ms 0.0016% 34.87% 4592ms 7.22% MeshBasedCellPopulation::UpdateNodePairs 50ms 0.079% 34.95% 4548ms 7.15% std::__new_allocator::allocate (inline) 0 0% 34.95% 4525ms 7.12% std::allocator_traits::allocate (inline) 2ms 0.0031% 34.95% 4518ms 7.11% std::set_intersection (inline) 244ms 0.38% 35.33% 4516ms 7.10% std::__set_intersection 16ms 0.025% 35.36% 4432ms 6.97% MeshBasedCellPopulation::SpringIterator::operator++ 1261ms 1.98% 37.34% 4351ms 6.84% std::_Rb_tree::_M_get_insert_unique_pos 38ms 0.06% 37.40% 4224ms 6.64% Node::AddElement 1281ms 2.01% 39.42% 4088ms 6.43% __GI___libc_free 3910ms 6.15% 45.57% 3910ms 6.15% std::_Rb_tree::_S_right (inline) 0 0% 45.57% 3778ms 5.94% VertexMesh::~VertexMesh 189ms 0.3% 45.86% 3732ms 5.87% std::_Rb_tree_const_iterator::operator++ (inline) 13ms 0.02% 45.88% 3668ms 5.77% TetrahedralMesh::ImportFromMesher 0 0% 45.88% 3644ms 5.73% std::_Rb_tree::_M_create_node (inline) 110ms 0.17% 46.06% 3640ms 5.72% tetgen::tetgenmesh::insphere_sos 0 0% 46.06% 3604ms 5.67% std::_Rb_tree::_Alloc_node::operator() (inline) 2565ms 4.03% 50.09% 3599ms 5.66% _int_malloc 0 0% 50.09% 3597ms 5.66% std::_Rb_tree::_M_get_node (inline) 148ms 0.23% 50.32% 3590ms 5.65% std::__new_allocator::deallocate (inline) 0 0% 50.32% 3565ms 5.61% std::allocator_traits::deallocate (inline) 251ms 0.39% 50.72% 3540ms 5.57% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 3239ms 5.09% 55.81% 3520ms 5.54% tetgen::insphere 6ms 0.0094% 55.82% 3350ms 5.27% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 1ms 0.0016% 55.82% 3311ms 5.21% std::_Rb_tree_iterator::operator++ (inline) 87ms 0.14% 55.96% 3237ms 5.09% MutableElement::AddNode 1206ms 1.90% 57.86% 2806ms 4.41% _int_free 193ms 0.3% 58.16% 2722ms 4.28% Node::~Node 190ms 0.3% 58.46% 2603ms 4.09% tetgen::tetgenmesh::flip23 232ms 0.36% 58.83% 2480ms 3.90% VertexMesh::Clear 2139ms 3.36% 62.19% 2139ms 3.36% std::_Rb_tree_insert_and_rebalance 0 0% 62.19% 2007ms 3.16% std::_Rb_tree::_M_drop_node (inline) 0 0% 62.19% 1994ms 3.14% std::_Rb_tree::_M_put_node (inline) 1811ms 2.85% 65.04% 1811ms 2.85% Node::GetIndex 4ms 0.0063% 65.04% 1804ms 2.84% Element::Element 142ms 0.22% 65.27% 1781ms 2.80% tetgen::tetgenmesh::flip32 1066ms 1.68% 66.94% 1616ms 2.54% malloc_consolidate 13ms 0.02% 66.96% 1584ms 2.49% std::_Vector_base::_M_deallocate (inline) 217ms 0.34% 67.31% 1505ms 2.37% TetrahedralMesh::Clear 7ms 0.011% 67.32% 1486ms 2.34% Element::RegisterWithNodes (inline) 0 0% 67.32% 1479ms 2.33% std::vector::~vector (inline) 1ms 0.0016% 67.32% 1419ms 2.23% std::_Vector_base::~_Vector_base (inline) 2ms 0.0031% 67.32% 1379ms 2.17% _int_free_maybe_consolidate 1268ms 1.99% 69.32% 1358ms 2.14% tetgen::orient3d 213ms 0.33% 69.65% 1288ms 2.03% tetgen::tetgenmesh::enqueueflipface 74ms 0.12% 69.77% 1252ms 1.97% std::map::operator[] 1214ms 1.91% 71.68% 1214ms 1.91% unlink_chunk 50ms 0.079% 71.76% 1179ms 1.85% tetgen::tetgenmesh::locate 2ms 0.0031% 71.76% 1172ms 1.84% VoronoiDataWriter::Visit 60ms 0.094% 71.85% 1107ms 1.74% std::vector::_M_realloc_insert 0 0% 71.85% 1094ms 1.72% std::_Rb_tree::lower_bound (inline) 0 0% 71.85% 1094ms 1.72% std::map::lower_bound (inline) 96ms 0.15% 72.00% 1075ms 1.69% tetgen::tetgenmesh::preciselocate 2ms 0.0031% 72.01% 1070ms 1.68% VertexMesh::GenerateVerticesFromElementCircumcentres 803ms 1.26% 73.27% 950ms 1.49% AbstractElement::GetNodeGlobalIndex 9ms 0.014% 73.28% 937ms 1.47% std::_Vector_base::_M_allocate (inline) 111ms 0.17% 73.46% 896ms 1.41% std::vector::push_back (inline) 837ms 1.32% 74.77% 837ms 1.32% tetgen::tetgenmesh::triface::triface 1ms 0.0016% 74.78% 827ms 1.30% TetrahedralMesh::RefreshJacobianCachedData 3ms 0.0047% 74.78% 750ms 1.18% AbstractTwoBodyInteractionForce::AddForceContribution 6ms 0.0094% 74.79% 732ms 1.15% AbstractTetrahedralElement::CalculateInverseJacobian 18ms 0.028% 74.82% 719ms 1.13% boost::numeric::ublas::vector_assign (inline) 393ms 0.62% 75.44% 705ms 1.11% tetgen::tetgenmesh::fnextself 275ms 0.43% 75.87% 697ms 1.10% AbstractElement::GetNodeLocation 16ms 0.025% 75.89% 696ms 1.09% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 17ms 0.027% 75.92% 686ms 1.08% boost::numeric::ublas::c_vector::c_vector (inline) 686ms 1.08% 77.00% 686ms 1.08% tetgen::tetgenmesh::oppo 670ms 1.05% 78.05% 670ms 1.05% Node::rGetLocation 12ms 0.019% 78.07% 666ms 1.05% AbstractTetrahedralElement::CalculateJacobian 628ms 0.99% 79.06% 628ms 0.99% AbstractElement::IsDeleted 624ms 0.98% 80.04% 624ms 0.98% [libchaste_mesh.so] 37ms 0.058% 80.10% 621ms 0.98% __atan2 594ms 0.93% 81.03% 594ms 0.93% tetgen::tetgenmesh::triface::operator= 474ms 0.75% 81.78% 584ms 0.92% __ieee754_atan2_fma 18ms 0.028% 81.81% 575ms 0.9% Element::CalculateCircumsphere 0 0% 81.81% 553ms 0.87% std::insert_iterator::operator= (inline) 543ms 0.85% 82.66% 543ms 0.85% std::vector::size (inline) 0 0% 82.66% 540ms 0.85% std::set::find (inline) 4ms 0.0063% 82.67% 506ms 0.8% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.0016% 82.67% 497ms 0.78% std::_Rb_tree::_M_insert_unique_ (inline) 41ms 0.064% 82.73% 490ms 0.77% AbstractTetrahedralElement::RefreshJacobian 0 0% 82.73% 471ms 0.74% boost::numeric::ublas::inner_prod (inline) 5ms 0.0079% 82.74% 470ms 0.74% Cell::GetCellId 5ms 0.0079% 82.75% 469ms 0.74% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 42ms 0.066% 82.82% 469ms 0.74% tetgen::tetgenmesh::enextfnext 31ms 0.049% 82.86% 464ms 0.73% boost::numeric::ublas::vector_scalar_binary::evaluate 13ms 0.02% 82.89% 450ms 0.71% VertexMesh::CalculateUnitNormalToFaceWithArea 28ms 0.044% 82.93% 447ms 0.7% tetgen::tetgenmesh::enext2fnext 123ms 0.19% 83.12% 438ms 0.69% boost::numeric::ublas::indexing_vector_assign 5ms 0.0079% 83.13% 424ms 0.67% AbstractCellProperty::IsSubType (inline) 424ms 0.67% 83.80% 424ms 0.67% boost::numeric::ublas::c_vector::operator() 91ms 0.14% 83.94% 421ms 0.66% __dynamic_cast 272ms 0.43% 84.37% 420ms 0.66% tetgen::tetgenmesh::sym 8ms 0.013% 84.38% 404ms 0.64% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 84.38% 400ms 0.63% VertexMeshWriter::WriteVtkUsingMesh 216ms 0.34% 84.72% 390ms 0.61% AbstractTetrahedralMesh::GetElement 182ms 0.29% 85.01% 383ms 0.6% boost::numeric::ublas::vector_inner_prod::apply (inline) 29ms 0.046% 85.05% 376ms 0.59% std::_Rb_tree_iterator::operator-- (inline) 0 0% 85.05% 368ms 0.58% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 27ms 0.042% 85.10% 363ms 0.57% tetgen::tetgenmesh::queue::push 250ms 0.39% 85.49% 353ms 0.56% tetgen::tetgenmesh::bond 349ms 0.55% 86.04% 349ms 0.55% tetgen::tetgenmesh::org 13ms 0.02% 86.06% 345ms 0.54% std::vector::insert (inline) 1ms 0.0016% 86.06% 343ms 0.54% tcache_get (inline) 342ms 0.54% 86.60% 342ms 0.54% tcache_get_n (inline) 138ms 0.22% 86.81% 338ms 0.53% Inverse 338ms 0.53% 87.35% 338ms 0.53% std::_Rb_tree_decrement 3ms 0.0047% 87.35% 335ms 0.53% VertexElement::~VertexElement 239ms 0.38% 87.73% 334ms 0.53% tetgen::tetgenmesh::link::add 7ms 0.011% 87.74% 321ms 0.5% VertexMesh::GetVolumeOfElement