| | | | | | | requested parallelism | walltime sum (s) | nb instances | any sync average per thread time (s) | any wait average per thread time (s) | parallelism overhead (%) | local speedup if perfectly balanced | global speedup if perfectly balanced |
|---|
| start addr | function name | source location | level | ancestor thread num | invoker | parallel or teams | 1x52 | 1x52 | 1x52 | 1x52 | 1x52 | 1x52 | 1x52 | 1x52 |
|---|
| libgromacs_mpi.so.7:0x62d1dc | _INTERNALce49b591::nbnxn_kernel_cpu(PairlistSet const&, Nbnx... | kerneldispatch.cpp:265 | 0 | 0 | runtime | parallel | 52 | 20.050 | 10.0 E3 | 1.520 | 1.519 | 7.58 | 1.082 | 1.024 |
| libgromacs_mpi.so.7:0xd1382e | gmx_pme_do(gmx_pme_t*, gmx::ArrayRef<gmx::BasicVector<float>... | pme.cpp:1296 | 0 | 0 | runtime | parallel | 52 | 11.001 | 10.0 E3 | 2.982 | 2.970 | 27.1 | 1.372 | 1.048 |
| libgromacs_mpi.so.7:0xc05577 | gmx::constrain_lincs(bool, t_inputrec const&, long, gmx::Lin... | lincs.cpp:2483 | 0 | 0 | runtime | parallel | 52 | 6.746 | 10.0 E3 | 5.234 | 5.195 | 77.6 | 4.460 | 1.088 |
| libgromacs_mpi.so.7:0xd35286 | spread_on_grid(gmx_pme_t const*, PmeAtomComm*, pmegrids_t co... | pme_spread.cpp:936 | 0 | 0 | runtime | parallel | 52 | 4.126 | 10.0 E3 | 1.132 | 1.131 | 27.4 | 1.378 | 1.018 |
| libgromacs_mpi.so.7:0xd139bb | gmx_pme_do(gmx_pme_t*, gmx::ArrayRef<gmx::BasicVector<float>... | pme.cpp:1401 | 0 | 0 | runtime | parallel | 52 | 2.661 | 10.0 E3 | 0.931 | 0.930 | 35.0 | 1.538 | 1.015 |
| libgromacs_mpi.so.7:0xd353ae | spread_on_grid(gmx_pme_t const*, PmeAtomComm*, pmegrids_t co... | pme_spread.cpp:1010 | 0 | 0 | runtime | parallel | 52 | 2.086 | 10.0 E3 | 0.566 | 0.565 | 27.2 | 1.373 | 1.009 |
| libgromacs_mpi.so.7:0xd023db | _INTERNAL115a3b1f::calcBondedForces(InteractionDefinitions c... | listed_forces.cpp:385 | 0 | 0 | runtime | parallel | 52 | 1.772 | 10.0 E3 | 0.322 | 0.321 | 18.2 | 1.223 | 1.005 |
| libgromacs_mpi.so.7:0x5fb2ff | _INTERNAL95fec573::nbnxn_atomdata_add_nbat_f_to_f_reduce(nbn... | atomdata.cpp:1188 | 0 | 0 | runtime | parallel | 52 | 1.403 | 10.0 E3 | 0.399 | 0.397 | 28.4 | 1.397 | 1.006 |
| libgromacs_mpi.so.7:0xd351ad | spread_on_grid(gmx_pme_t const*, PmeAtomComm*, pmegrids_t co... | pme_spread.cpp:910 | 0 | 0 | runtime | parallel | 52 | 1.228 | 10.0 E3 | 0.229 | 0.228 | 18.6 | 1.229 | 1.004 |
| libgromacs_mpi.so.7:0xd40124 | fft5d_plan_3d(int, int, int, ompi_communicator_t**, int, t_c... | fft5d.cpp:643 | 0 | 0 | runtime | parallel | 52 | 1.215 | 6.00 | 55.9 E-3 | 55.9 E-3 | 4.60 | 1.048 | 1.001 |
| libgromacs_mpi.so.7:0x5f9118 | nbnxn_atomdata_copy_x_to_nbat_x(Nbnxm::GridSet const&, gmx::... | atomdata.cpp:993 | 0 | 0 | runtime | parallel | 52 | 0.974 | 9.88 E3 | 0.460 | 0.459 | 47.3 | 1.897 | 1.007 |
| libgromacs_mpi.so.7:0xbda44d | L__ZN3gmx11Constraints4Impl5applyEbblifNS_19ArrayRefWithPadd... | constr.cpp:587 | 0 | 0 | runtime | parallel | 52 | 0.934 | 10.0 E3 | 0.296 | 0.295 | 31.7 | 1.464 | 1.005 |
| libgromacs_mpi.so.7:0x7d1bff | void _INTERNALd56b7fc3::gmx::(anonymous namespace)::reduceTh... | threaded_force_buffer.cpp:170 | 0 | 0 | runtime | parallel | 52 | 0.720 | 10.0 E3 | 0.339 | 0.338 | 47.1 | 1.891 | 1.005 |
| libgromacs_mpi.so.7:0xc4dddb | gmx::Update::Impl::finish_update(t_inputrec const&, bool, in... | update.cpp:1637 | 0 | 0 | runtime | parallel | 52 | 0.612 | 10.0 E3 | 0.198 | 0.197 | 32.4 | 1.479 | 1.003 |
| libgromacs_mpi.so.7:0xc41858 | gmx::Update::Impl::update_coords(t_inputrec const&, long, in... | update.cpp:1687 | 0 | 0 | runtime | parallel | 52 | 0.560 | 10.0 E3 | 0.194 | 0.193 | 34.6 | 1.530 | 1.003 |
| libgromacs_mpi.so.7:0x71e829 | PairlistSet::constructPairlists(gmx::InteractionLocality, Nb... | pairlist.cpp:3958 | 0 | 0 | runtime | parallel | 52 | 0.487 | 126 | 48.9 E-3 | 48.8 E-3 | 10.0 | 1.112 | 1.001 |
| libgromacs_mpi.so.7:0x5fad00 | reduceForces(nbnxn_atomdata_t*, gmx::AtomLocality, Nbnxm::Gr... | atomdata.cpp:1262 | 0 | 0 | runtime | parallel | 52 | 0.383 | 10.0 E3 | 0.164 | 0.163 | 42.8 | 1.749 | 1.003 |
| libgromacs_mpi.so.7:0xc3686b | _INTERNAL14e05f89::setupForceOutputs(ForceHelperBuffers*, gm... | sim_util.cpp:473 | 0 | 0 | runtime | parallel | 52 | 0.379 | 10.0 E3 | 0.158 | 0.157 | 41.7 | 1.714 | 1.002 |
| libgromacs_mpi.so.7:0x73631f | PairlistSet::dispatchPruneKernel(nbnxn_atomdata_t const*, gm... | prunekerneldispatch.cpp:68 | 0 | 0 | runtime | parallel | 52 | 0.365 | 876 | 29.5 E-3 | 29.4 E-3 | 8.08 | 1.088 | 1.000 |
| libgromacs_mpi.so.7:0xd2055f | unwrap_periodic_pmegrid(gmx_pme_t*, float*) | pme_grid.cpp:529 | 0 | 0 | runtime | parallel | 52 | 0.342 | 10.0 E3 | 0.160 | 0.159 | 46.8 | 1.881 | 1.002 |
| libgromacs_mpi.so.7:0xd20c53 | unwrap_periodic_pmegrid(gmx_pme_t*, float*) | pme_grid.cpp:512 | 0 | 0 | runtime | parallel | 52 | 0.339 | 10.0 E3 | 0.161 | 0.160 | 47.5 | 1.903 | 1.002 |
| libgromacs_mpi.so.7:0x76f2c4 | dd_make_local_constraints(gmx_domdec_t*, int, gmx_mtop_t con... | domdec_constraints.cpp:458 | 0 | 0 | runtime | parallel | 52 | 0.290 | 127 | 0.271 | 0.271 | 93.5 | 15.309 | 1.004 |
| libgromacs_mpi.so.7:0x7811a5 | _INTERNALd64f4cfb::make_local_bondeds_excls(gmx_domdec_t con... | localtopology.cpp:845 | 0 | 0 | runtime | parallel | 52 | 94.6 E-3 | 127 | 33.5 E-3 | 33.5 E-3 | 35.5 | 1.550 | 1.001 |
| libgromacs_mpi.so.7:0xc0fdf7 | _INTERNAL7742301e::calc_ke_part_normal(gmx::ArrayRef<gmx::Ba... | md_support.cpp:113 | 0 | 0 | runtime | parallel | 52 | 91.7 E-3 | 2.00 E3 | 31.9 E-3 | 31.7 E-3 | 34.8 | 1.535 | 1.000 |
| libgromacs_mpi.so.7:0xd031ea | setup_bonded_threading(bonded_threading_t*, int, bool, Inter... | manage_threading.cpp:396 | 0 | 0 | runtime | parallel | 52 | 75.3 E-3 | 127 | 7.33 E-3 | 7.28 E-3 | 9.74 | 1.108 | 1.000 |
| libgromacs_mpi.so.7:0xbd4038 | calc_vir(int, float const (*) [3], float const (*) [3], floa... | calcvir.cpp:109 | 0 | 0 | runtime | parallel | 52 | 45.3 E-3 | 1.00 E3 | 15.9 E-3 | 15.9 E-3 | 35.2 | 1.543 | 1.000 |
| libgromacs_mpi.so.7:0xc358ac | _INTERNAL14e05f89::postProcessForces(t_commrec const*, long,... | sim_util.cpp:149 | 0 | 0 | runtime | parallel | 52 | 43.2 E-3 | 1.00 E3 | 16.8 E-3 | 16.7 E-3 | 38.9 | 1.637 | 1.000 |
| libgromacs_mpi.so.7:0xc36ac8 | _INTERNAL14e05f89::setupForceOutputs(ForceHelperBuffers*, gm... | sim_util.cpp:473 | 0 | 0 | runtime | parallel | 52 | 41.8 E-3 | 1.00 E3 | 16.6 E-3 | 16.5 E-3 | 39.8 | 1.660 | 1.000 |
| libgromacs_mpi.so.7:0x62428d | Nbnxm::Grid::setCellIndices(int, int, Nbnxm::GridSetData*, g... | grid.cpp:1481 | 0 | 0 | runtime | parallel | 52 | 40.6 E-3 | 127 | 17.4 E-3 | 17.4 E-3 | 42.9 | 1.750 | 1.000 |
| libgromacs_mpi.so.7:0x72c31e | _INTERNALb629d8fd::rebalanceSimpleLists(gmx::ArrayRef<NbnxnP... | pairlist.cpp:3681 | 0 | 0 | runtime | parallel | 52 | 34.4 E-3 | 126 | 10.4 E-3 | 10.4 E-3 | 30.3 | 1.435 | 1.000 |
| libgromacs_mpi.so.7:0xc11419 | atoms2md(gmx_mtop_t const&, t_inputrec const&, int, gmx::Arr... | mdatoms.cpp:327 | 0 | 0 | runtime | parallel | 52 | 22.8 E-3 | 127 | 5.98 E-3 | 5.97 E-3 | 26.2 | 1.356 | 1.000 |
| libgromacs_mpi.so.7:0xc0cb70 | gmx::set_lincs(InteractionDefinitions const&, int, gmx::Arra... | lincs.cpp:2196 | 0 | 0 | runtime | parallel | 52 | 15.2 E-3 | 127 | 3.16 E-3 | 3.14 E-3 | 20.8 | 1.263 | 1.000 |
| libgromacs_mpi.so.7:0xc09f40 | _INTERNAL661916bb::gmx::set_lincs_matrix(_INTERNAL661916bb::... | lincs.cpp:1347 | 0 | 0 | runtime | parallel | 52 | 13.9 E-3 | 127 | 7.78 E-3 | 7.71 E-3 | 56.1 | 2.279 | 1.000 |
| libgromacs_mpi.so.7:0xc0aad1 | _INTERNAL661916bb::gmx::lincs_thread_setup(_INTERNAL661916bb... | lincs.cpp:1636 | 0 | 0 | runtime | parallel | 52 | 13.3 E-3 | 127 | 2.79 E-3 | 2.77 E-3 | 20.9 | 1.264 | 1.000 |
| libgromacs_mpi.so.7:0x798c52 | dd_redistribute_cg(_IO_FILE*, long, gmx_domdec_t*, int*, t_s... | redistribute.cpp:624 | 0 | 0 | runtime | parallel | 52 | 8.59 E-3 | 126 | 2.19 E-3 | 2.18 E-3 | 25.5 | 1.343 | 1.000 |
| libgromacs_mpi.so.7:0x62a5ae | Nbnxm::GridSet::putOnGrid(float const (*) [3], int, float co... | gridset.cpp:212 | 0 | 0 | runtime | parallel | 52 | 7.36 E-3 | 127 | 2.66 E-3 | 2.65 E-3 | 36.2 | 1.568 | 1.000 |
| libgromacs_mpi.so.7:0xc5ba48 | _INTERNAL30ba3db8::do_stopcm_grp(t_mdatoms const&, gmx::Arra... | vcm.cpp:374 | 0 | 0 | runtime | parallel | 52 | 6.85 E-3 | 102 | 4.67 E-3 | 4.63 E-3 | 68.2 | 3.141 | 1.000 |
| libgromacs_mpi.so.7:0xc57b12 | calc_vcm_grp(t_mdatoms const&, gmx::ArrayRef<gmx::BasicVecto... | vcm.cpp:170 | 0 | 0 | runtime | parallel | 52 | 6.70 E-3 | 102 | 4.64 E-3 | 4.60 E-3 | 69.2 | 3.247 | 1.000 |
| libgromacs_mpi.so.7:0xc0af66 | _INTERNAL661916bb::gmx::lincs_thread_setup(_INTERNAL661916bb... | lincs.cpp:1695 | 0 | 0 | runtime | parallel | 52 | 5.95 E-3 | 127 | 2.32 E-3 | 2.31 E-3 | 39.0 | 1.641 | 1.000 |
| libgromacs_mpi.so.7:0xda0ea6 | gmx_set_thread_affinity(gmx::MDLogger const&, t_commrec cons... | threadaffinity.cpp:314 | 0 | 0 | runtime | parallel | 52 | 3.87 E-3 | 1.00 | 156 E-6 | 142 E-6 | 4.04 | 1.042 | 1.000 |
| libgromacs_mpi.so.7:0xd34a76 | pme_init_all_work(pme_solve_work_t**, int, int) | pme_solve.cpp:144 | 0 | 0 | runtime | parallel | 52 | 93.9 E-6 | 1.00 | 58.0 E-6 | 57.9 E-6 | 61.7 | 2.612 | 1.000 |
| libgromacs_mpi.so.7:0x7d743b | gmx::ThreadedForceBuffer<float [4]>::ThreadedForceBuffer(int... | threaded_force_buffer.cpp:230 | 0 | 0 | runtime | parallel | 52 | 73.6 E-6 | 1.00 | 25.6 E-6 | 25.5 E-6 | 34.9 | 1.535 | 1.000 |
| libgromacs_mpi.so.7:0xd174ff | PmeAtomComm::PmeAtomComm(ompi_communicator_t*, int, int, int... | pme.cpp:325 | 0 | 0 | runtime | parallel | 52 | 43.2 E-6 | 1.00 | 19.5 E-6 | 19.3 E-6 | 45.3 | 1.827 | 1.000 |
| libgromacs_mpi.so.7:0x7bd2f9 | gmx_ekindata_t::gmx_ekindata_t(int, float, int) | group.cpp:66 | 0 | 0 | runtime | parallel | 52 | 34.6 E-6 | 1.00 | 15.9 E-6 | 15.8 E-6 | 46.0 | 1.850 | 1.000 |
