File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 59394ms, 87.93% of 67545ms total Dropped 859 nodes (cum <= 337.73ms) flat flat% sum% cum cum% 0 0% 0% 67476ms 99.90% __libc_start_call_main 0 0% 0% 67476ms 99.90% __libc_start_main_impl 0 0% 0% 67476ms 99.90% _start 0 0% 0% 67461ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 67461ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 67461ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 67461ms 99.88% main 0 0% 0% 67426ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 67426ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 67426ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 67147ms 99.41% AbstractCellBasedSimulation::Solve 0 0% 0% 56342ms 83.41% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 56292ms 83.34% MeshBasedCellPopulation::Update 0 0% 0% 34327ms 50.82% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 34327ms 50.82% MeshBasedCellPopulation::TessellateIfNeeded 257ms 0.38% 0.38% 29848ms 44.19% VertexMesh::VertexMesh 0 0% 0.38% 17518ms 25.94% MutableMesh::ReMesh 553ms 0.82% 1.20% 13657ms 20.22% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.20% 12643ms 18.72% tetgen::tetrahedralize 2ms 0.003% 1.20% 12499ms 18.50% tetgen::tetgenmesh::delaunizevertices 5ms 0.0074% 1.21% 12495ms 18.50% tetgen::tetgenmesh::incrflipdelaunay 27ms 0.04% 1.25% 11425ms 16.91% std::set::insert (inline) 611ms 0.9% 2.15% 11091ms 16.42% tetgen::tetgenmesh::lawson 224ms 0.33% 2.49% 10900ms 16.14% std::_Rb_tree::_M_insert_unique 3005ms 4.45% 6.93% 10410ms 15.41% std::_Rb_tree::_M_lower_bound (inline) 431ms 0.64% 7.57% 10148ms 15.02% VertexElement::AddFace 246ms 0.36% 7.94% 9636ms 14.27% std::_Rb_tree::find (inline) 0 0% 7.94% 9081ms 13.44% std::set::count (inline) 7453ms 11.03% 18.97% 7453ms 11.03% std::_Rb_tree_increment 127ms 0.19% 19.16% 7025ms 10.40% std::less::operator() (inline) 6964ms 10.31% 29.47% 6964ms 10.31% std::operator< (inline) 244ms 0.36% 29.83% 6383ms 9.45% std::_Rb_tree::_M_insert_ (inline) 204ms 0.3% 30.13% 6353ms 9.41% operator new 1184ms 1.75% 31.89% 6080ms 9.00% __GI___libc_malloc 1ms 0.0015% 31.89% 5886ms 8.71% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 31.89% 5725ms 8.48% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.01% 31.90% 5701ms 8.44% AbstractNumericalMethod::ComputeForcesIncludingDamping 43ms 0.064% 31.96% 5223ms 7.73% std::__new_allocator::allocate (inline) 0 0% 31.96% 5205ms 7.71% std::allocator_traits::allocate (inline) 1ms 0.0015% 31.96% 5159ms 7.64% std::set_intersection (inline) 250ms 0.37% 32.33% 5158ms 7.64% std::__set_intersection 8ms 0.012% 32.34% 4985ms 7.38% std::_Rb_tree::~_Rb_tree (inline) 2051ms 3.04% 35.38% 4976ms 7.37% std::_Rb_tree::_M_erase 0 0% 35.38% 4910ms 7.27% std::set::~set (inline) 1ms 0.0015% 35.38% 4790ms 7.09% MeshBasedCellPopulation::UpdateNodePairs 0 0% 35.38% 4773ms 7.07% AbstractCellPopulation::WriteResultsToFiles 6ms 0.0089% 35.39% 4758ms 7.04% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1349ms 2.00% 37.39% 4707ms 6.97% __GI___libc_free 32ms 0.047% 37.44% 4673ms 6.92% Node::AddElement 1219ms 1.80% 39.24% 4643ms 6.87% std::_Rb_tree::_M_get_insert_unique_pos 9ms 0.013% 39.25% 4614ms 6.83% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 39.25% 4518ms 6.69% VertexMesh::~VertexMesh 170ms 0.25% 39.51% 4401ms 6.52% std::_Rb_tree_const_iterator::operator++ (inline) 3137ms 4.64% 44.15% 4384ms 6.49% _int_malloc 4371ms 6.47% 50.62% 4371ms 6.47% std::_Rb_tree::_S_right (inline) 0 0% 50.62% 4163ms 6.16% std::_Rb_tree::_M_create_node (inline) 0 0% 50.62% 4123ms 6.10% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 50.62% 4102ms 6.07% std::_Rb_tree::_M_get_node (inline) 131ms 0.19% 50.82% 4073ms 6.03% std::__new_allocator::deallocate (inline) 0 0% 50.82% 4052ms 6.00% std::allocator_traits::deallocate (inline) 20ms 0.03% 50.84% 3942ms 5.84% TetrahedralMesh::ImportFromMesher 79ms 0.12% 50.96% 3611ms 5.35% MutableElement::AddNode 247ms 0.37% 51.33% 3537ms 5.24% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 124ms 0.18% 51.51% 3467ms 5.13% tetgen::tetgenmesh::insphere_sos 1304ms 1.93% 53.44% 3354ms 4.97% _int_free 6ms 0.0089% 53.45% 3342ms 4.95% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 3036ms 4.49% 57.95% 3327ms 4.93% tetgen::insphere 0 0% 57.95% 3317ms 4.91% std::_Rb_tree_iterator::operator++ (inline) 206ms 0.3% 58.25% 3023ms 4.48% Node::~Node 248ms 0.37% 58.62% 2858ms 4.23% VertexMesh::Clear 180ms 0.27% 58.88% 2651ms 3.92% tetgen::tetgenmesh::flip23 2109ms 3.12% 62.01% 2109ms 3.12% std::_Rb_tree_insert_and_rebalance 1407ms 2.08% 64.09% 2068ms 3.06% malloc_consolidate 0 0% 64.09% 2055ms 3.04% std::_Rb_tree::_M_drop_node (inline) 0 0% 64.09% 2043ms 3.02% std::_Rb_tree::_M_put_node (inline) 26ms 0.038% 64.13% 2035ms 3.01% std::_Vector_base::_M_deallocate (inline) 2013ms 2.98% 67.11% 2013ms 2.98% Node::GetIndex 3ms 0.0044% 67.11% 1983ms 2.94% Element::Element 0 0% 67.11% 1856ms 2.75% std::vector::~vector (inline) 4ms 0.0059% 67.12% 1820ms 2.69% std::_Vector_base::~_Vector_base (inline) 151ms 0.22% 67.34% 1796ms 2.66% tetgen::tetgenmesh::flip32 7ms 0.01% 67.35% 1787ms 2.65% _int_free_maybe_consolidate 9ms 0.013% 67.37% 1644ms 2.43% Element::RegisterWithNodes (inline) 228ms 0.34% 67.70% 1554ms 2.30% TetrahedralMesh::Clear 1521ms 2.25% 69.95% 1521ms 2.25% unlink_chunk 1312ms 1.94% 71.90% 1408ms 2.08% tetgen::orient3d 4ms 0.0059% 71.90% 1345ms 1.99% VertexMesh::GenerateVerticesFromElementCircumcentres 54ms 0.08% 71.98% 1338ms 1.98% std::map::operator[] 51ms 0.076% 72.06% 1327ms 1.96% std::vector::_M_realloc_insert 150ms 0.22% 72.28% 1251ms 1.85% tetgen::tetgenmesh::enqueueflipface 0 0% 72.28% 1211ms 1.79% std::_Rb_tree::lower_bound (inline) 0 0% 72.28% 1211ms 1.79% std::map::lower_bound (inline) 42ms 0.062% 72.34% 1193ms 1.77% tetgen::tetgenmesh::locate 2ms 0.003% 72.35% 1171ms 1.73% VoronoiDataWriter::Visit 8ms 0.012% 72.36% 1111ms 1.64% std::_Vector_base::_M_allocate (inline) 977ms 1.45% 73.80% 1100ms 1.63% AbstractElement::GetNodeGlobalIndex 109ms 0.16% 73.97% 1091ms 1.62% tetgen::tetgenmesh::preciselocate 127ms 0.19% 74.15% 1073ms 1.59% std::vector::push_back (inline) 972ms 1.44% 75.59% 972ms 1.44% tetgen::tetgenmesh::triface::triface 1ms 0.0015% 75.59% 915ms 1.35% TetrahedralMesh::RefreshJacobianCachedData 358ms 0.53% 76.12% 872ms 1.29% AbstractElement::GetNodeLocation 841ms 1.25% 77.37% 841ms 1.25% Node::rGetLocation 4ms 0.0059% 77.38% 779ms 1.15% AbstractTetrahedralElement::CalculateInverseJacobian 774ms 1.15% 78.52% 774ms 1.15% AbstractElement::IsDeleted 21ms 0.031% 78.55% 740ms 1.10% AbstractTetrahedralElement::CalculateJacobian 1ms 0.0015% 78.55% 725ms 1.07% AbstractTwoBodyInteractionForce::AddForceContribution 707ms 1.05% 79.60% 707ms 1.05% tetgen::tetgenmesh::oppo 19ms 0.028% 79.63% 706ms 1.05% boost::numeric::ublas::vector_assign (inline) 367ms 0.54% 80.17% 679ms 1.01% tetgen::tetgenmesh::fnextself 12ms 0.018% 80.19% 666ms 0.99% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 8ms 0.012% 80.20% 651ms 0.96% boost::numeric::ublas::c_vector::c_vector (inline) 69ms 0.1% 80.30% 642ms 0.95% __atan2 15ms 0.022% 80.33% 633ms 0.94% Element::CalculateCircumsphere 632ms 0.94% 81.26% 632ms 0.94% [libchaste_mesh.so] 45ms 0.067% 81.33% 586ms 0.87% AbstractTetrahedralElement::RefreshJacobian 475ms 0.7% 82.03% 573ms 0.85% __ieee754_atan2_fma 0 0% 82.03% 549ms 0.81% std::set::find (inline) 540ms 0.8% 82.83% 540ms 0.8% tetgen::tetgenmesh::triface::operator= 0 0% 82.83% 527ms 0.78% std::insert_iterator::operator= (inline) 517ms 0.77% 83.60% 517ms 0.77% std::vector::size (inline) 0 0% 83.60% 478ms 0.71% tcache_get (inline) 478ms 0.71% 84.30% 478ms 0.71% tcache_get_n (inline) 0 0% 84.30% 468ms 0.69% std::_Rb_tree::_M_insert_unique_ (inline) 37ms 0.055% 84.36% 467ms 0.69% tetgen::tetgenmesh::enext2fnext 118ms 0.17% 84.53% 459ms 0.68% boost::numeric::ublas::indexing_vector_assign 0 0% 84.53% 459ms 0.68% boost::numeric::ublas::inner_prod (inline) 6ms 0.0089% 84.54% 456ms 0.68% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 29ms 0.043% 84.59% 450ms 0.67% boost::numeric::ublas::vector_scalar_binary::evaluate 21ms 0.031% 84.62% 440ms 0.65% VertexMesh::CalculateUnitNormalToFaceWithArea 21ms 0.031% 84.65% 434ms 0.64% std::_Rb_tree_iterator::operator-- (inline) 37ms 0.055% 84.70% 428ms 0.63% tetgen::tetgenmesh::enextfnext 281ms 0.42% 85.12% 419ms 0.62% tetgen::tetgenmesh::sym 232ms 0.34% 85.46% 413ms 0.61% AbstractTetrahedralMesh::GetElement 0 0% 85.46% 413ms 0.61% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 20ms 0.03% 85.49% 412ms 0.61% std::vector::insert (inline) 8ms 0.012% 85.50% 410ms 0.61% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 85.50% 409ms 0.61% VertexMeshWriter::WriteVtkUsingMesh 401ms 0.59% 86.10% 401ms 0.59% boost::numeric::ublas::c_vector::operator() 7ms 0.01% 86.11% 389ms 0.58% CellPropertyCollection::GetPropertiesType (inline) 26ms 0.038% 86.15% 389ms 0.58% tetgen::tetgenmesh::queue::push 388ms 0.57% 86.72% 388ms 0.57% std::_Rb_tree_decrement 279ms 0.41% 87.13% 384ms 0.57% tetgen::tetgenmesh::bond 97ms 0.14% 87.28% 379ms 0.56% __dynamic_cast 2ms 0.003% 87.28% 369ms 0.55% Cell::GetCellId 162ms 0.24% 87.52% 369ms 0.55% boost::numeric::ublas::vector_inner_prod::apply (inline) 269ms 0.4% 87.92% 359ms 0.53% tetgen::tetgenmesh::link::add 10ms 0.015% 87.93% 345ms 0.51% VertexElement::~VertexElement