| | | | | | | 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.7.0.0:0x4023cc | _INTERNAL53d1705a::nbnxn_kernel_cpu(PairlistSet const&, Nbnx... | kerneldispatch.cpp:265 | 0 | 0 | runtime | parallel | 52 | 19.134 | 10.0 E3 | 0.878 | 0.876 | 4.59 | 1.048 | 1.016 |
| libgromacs_mpi.so.7.0.0:0xb9323d | gmx_pme_do(gmx_pme_t*, gmx::ArrayRef<gmx::BasicVector<float>... | pme.cpp:1296 | 0 | 0 | runtime | parallel | 52 | 6.081 | 10.0 E3 | 0.878 | 0.860 | 14.4 | 1.169 | 1.016 |
| libgromacs_mpi.so.7.0.0:0xa5e02a | gmx::constrain_lincs(bool, t_inputrec const&, long, gmx::Lin... | lincs.cpp:2483 | 0 | 0 | runtime | parallel | 52 | 4.079 | 10.0 E3 | 1.817 | 1.757 | 44.5 | 1.803 | 1.034 |
| libgromacs_mpi.so.7.0.0:0xbb9106 | spread_on_grid(gmx_pme_t const*, PmeAtomComm*, pmegrids_t co... | pme_spread.cpp:936 | 0 | 0 | runtime | parallel | 52 | 3.345 | 10.0 E3 | 0.581 | 0.579 | 17.4 | 1.210 | 1.011 |
| libgromacs_mpi.so.7.0.0:0xb7e26b | _INTERNAL01945b58::calcBondedForces(InteractionDefinitions c... | listed_forces.cpp:385 | 0 | 0 | runtime | parallel | 52 | 2.542 | 10.0 E3 | 0.632 | 0.630 | 24.9 | 1.331 | 1.012 |
| libgromacs_mpi.so.7.0.0:0xb933ca | gmx_pme_do(gmx_pme_t*, gmx::ArrayRef<gmx::BasicVector<float>... | pme.cpp:1401 | 0 | 0 | runtime | parallel | 52 | 2.530 | 10.0 E3 | 0.494 | 0.493 | 19.5 | 1.243 | 1.009 |
| libgromacs_mpi.so.7.0.0:0xbb9237 | spread_on_grid(gmx_pme_t const*, PmeAtomComm*, pmegrids_t co... | pme_spread.cpp:1010 | 0 | 0 | runtime | parallel | 52 | 1.880 | 10.0 E3 | 0.328 | 0.326 | 17.4 | 1.211 | 1.006 |
| libgromacs_mpi.so.7.0.0:0x3cc0cf | _INTERNALa817b2b7::nbnxn_atomdata_add_nbat_f_to_f_reduce(nbn... | atomdata.cpp:1188 | 0 | 0 | runtime | parallel | 52 | 1.071 | 10.0 E3 | 0.321 | 0.319 | 30.0 | 1.428 | 1.006 |
| libgromacs_mpi.so.7.0.0:0x4ec415 | PairlistSet::constructPairlists(gmx::InteractionLocality, Nb... | pairlist.cpp:3958 | 0 | 0 | runtime | parallel | 52 | 0.854 | 126 | 83.2 E-3 | 83.2 E-3 | 9.74 | 1.108 | 1.002 |
| libgromacs_mpi.so.7.0.0:0xa2da39 | L__ZN3gmx11Constraints4Impl5applyEbblifNS_19ArrayRefWithPadd... | constr.cpp:587 | 0 | 0 | runtime | parallel | 52 | 0.795 | 10.0 E3 | 0.207 | 0.205 | 26.0 | 1.352 | 1.004 |
| libgromacs_mpi.so.7.0.0:0xbb901a | spread_on_grid(gmx_pme_t const*, PmeAtomComm*, pmegrids_t co... | pme_spread.cpp:910 | 0 | 0 | runtime | parallel | 52 | 0.659 | 10.0 E3 | 0.130 | 0.128 | 19.7 | 1.245 | 1.002 |
| libgromacs_mpi.so.7.0.0:0x5b12ff | void _INTERNALd056bbd4::gmx::(anonymous namespace)::reduceTh... | threaded_force_buffer.cpp:170 | 0 | 0 | runtime | parallel | 52 | 0.393 | 10.0 E3 | 94.9 E-3 | 93.3 E-3 | 24.1 | 1.318 | 1.002 |
| libgromacs_mpi.so.7.0.0:0xa9c691 | gmx::Update::Impl::update_coords(t_inputrec const&, long, in... | update.cpp:1687 | 0 | 0 | runtime | parallel | 52 | 0.386 | 10.0 E3 | 78.0 E-3 | 76.3 E-3 | 20.2 | 1.253 | 1.001 |
| libgromacs_mpi.so.7.0.0:0x3ca092 | nbnxn_atomdata_copy_x_to_nbat_x(Nbnxm::GridSet const&, gmx::... | atomdata.cpp:993 | 0 | 0 | runtime | parallel | 52 | 0.383 | 9.88 E3 | 0.194 | 0.193 | 50.7 | 2.027 | 1.004 |
| libgromacs_mpi.so.7.0.0:0x545b84 | dd_make_local_constraints(gmx_domdec_t*, int, gmx_mtop_t con... | domdec_constraints.cpp:458 | 0 | 0 | runtime | parallel | 52 | 0.379 | 127 | 0.340 | 0.339 | 89.5 | 9.510 | 1.006 |
| libgromacs_mpi.so.7.0.0:0x507a32 | PairlistSet::dispatchPruneKernel(nbnxn_atomdata_t const*, gm... | prunekerneldispatch.cpp:68 | 0 | 0 | runtime | parallel | 52 | 0.316 | 876 | 31.4 E-3 | 31.3 E-3 | 9.95 | 1.111 | 1.001 |
| libgromacs_mpi.so.7.0.0:0xaa7c55 | gmx::Update::Impl::finish_update(t_inputrec const&, bool, in... | update.cpp:1637 | 0 | 0 | runtime | parallel | 52 | 0.277 | 10.0 E3 | 70.3 E-3 | 68.7 E-3 | 25.4 | 1.340 | 1.001 |
| libgromacs_mpi.so.7.0.0:0x3cba50 | reduceForces(nbnxn_atomdata_t*, gmx::AtomLocality, Nbnxm::Gr... | atomdata.cpp:1262 | 0 | 0 | runtime | parallel | 52 | 0.196 | 10.0 E3 | 56.6 E-3 | 54.9 E-3 | 28.9 | 1.407 | 1.001 |
| libgromacs_mpi.so.7.0.0:0xba14df | unwrap_periodic_pmegrid(gmx_pme_t*, float*) | pme_grid.cpp:529 | 0 | 0 | runtime | parallel | 52 | 0.131 | 10.0 E3 | 39.3 E-3 | 37.7 E-3 | 29.9 | 1.427 | 1.001 |
| libgromacs_mpi.so.7.0.0:0x559a70 | _INTERNAL80d859f8::make_local_bondeds_excls(gmx_domdec_t con... | localtopology.cpp:845 | 0 | 0 | runtime | parallel | 52 | 0.127 | 127 | 49.5 E-3 | 49.4 E-3 | 39.0 | 1.638 | 1.001 |
| libgromacs_mpi.so.7.0.0:0xa8fa93 | _INTERNALc6865387::setupForceOutputs(ForceHelperBuffers*, gm... | sim_util.cpp:473 | 0 | 0 | runtime | parallel | 52 | 0.114 | 10.0 E3 | 30.2 E-3 | 28.7 E-3 | 26.5 | 1.360 | 1.001 |
| libgromacs_mpi.so.7.0.0:0xba1bd3 | unwrap_periodic_pmegrid(gmx_pme_t*, float*) | pme_grid.cpp:512 | 0 | 0 | runtime | parallel | 52 | 98.9 E-3 | 10.0 E3 | 42.5 E-3 | 40.7 E-3 | 43.0 | 1.754 | 1.001 |
| libgromacs_mpi.so.7.0.0:0xa6a207 | _INTERNAL727fa8dd::calc_ke_part_normal(gmx::ArrayRef<gmx::Ba... | md_support.cpp:113 | 0 | 0 | runtime | parallel | 52 | 70.6 E-3 | 2.00 E3 | 9.49 E-3 | 9.13 E-3 | 13.4 | 1.155 | 1.000 |
| libgromacs_mpi.so.7.0.0:0x4fb785 | _INTERNALb293ce76::rebalanceSimpleLists(gmx::ArrayRef<NbnxnP... | pairlist.cpp:3681 | 0 | 0 | runtime | parallel | 52 | 47.9 E-3 | 126 | 12.0 E-3 | 11.9 E-3 | 25.0 | 1.334 | 1.000 |
| libgromacs_mpi.so.7.0.0:0x3f7570 | Nbnxm::Grid::setCellIndices(int, int, Nbnxm::GridSetData*, g... | grid.cpp:1481 | 0 | 0 | runtime | parallel | 52 | 47.3 E-3 | 127 | 19.5 E-3 | 19.5 E-3 | 41.2 | 1.700 | 1.000 |
| libgromacs_mpi.so.7.0.0:0xa91bce | _INTERNALc6865387::postProcessForces(t_commrec const*, long,... | sim_util.cpp:149 | 0 | 0 | runtime | parallel | 52 | 32.0 E-3 | 1.00 E3 | 11.2 E-3 | 11.1 E-3 | 35.2 | 1.542 | 1.000 |
| libgromacs_mpi.so.7.0.0:0xb7f3aa | setup_bonded_threading(bonded_threading_t*, int, bool, Inter... | manage_threading.cpp:396 | 0 | 0 | runtime | parallel | 52 | 28.4 E-3 | 127 | 5.43 E-3 | 5.41 E-3 | 19.1 | 1.236 | 1.000 |
| libgromacs_mpi.so.7.0.0:0xa25577 | calc_vir(int, float const (*) [3], float const (*) [3], floa... | calcvir.cpp:109 | 0 | 0 | runtime | parallel | 52 | 27.1 E-3 | 1.00 E3 | 5.45 E-3 | 5.27 E-3 | 20.1 | 1.252 | 1.000 |
| libgromacs_mpi.so.7.0.0:0xa6b8f9 | atoms2md(gmx_mtop_t const&, t_inputrec const&, int, gmx::Arr... | mdatoms.cpp:327 | 0 | 0 | runtime | parallel | 52 | 23.0 E-3 | 127 | 8.02 E-3 | 8.00 E-3 | 34.8 | 1.534 | 1.000 |
| libgromacs_mpi.so.7.0.0:0xa8ffaa | _INTERNALc6865387::setupForceOutputs(ForceHelperBuffers*, gm... | sim_util.cpp:473 | 0 | 0 | runtime | parallel | 52 | 15.2 E-3 | 1.00 E3 | 3.84 E-3 | 3.67 E-3 | 25.2 | 1.337 | 1.000 |
| libgromacs_mpi.so.7.0.0:0xc2b2f7 | _INTERNAL27725562::set_affinity(t_commrec const*, int, int, ... | threadaffinity.cpp:314 | 0 | 0 | runtime | parallel | 52 | 12.8 E-3 | 1.00 | 4.40 E-3 | 4.40 E-3 | 34.3 | 1.522 | 1.000 |
| libgromacs_mpi.so.7.0.0:0xa63afe | _INTERNAL1bba7552::gmx::lincs_thread_setup(_INTERNAL1bba7552... | lincs.cpp:1636 | 0 | 0 | runtime | parallel | 52 | 11.8 E-3 | 127 | 2.71 E-3 | 2.68 E-3 | 22.9 | 1.298 | 1.000 |
| libgromacs_mpi.so.7.0.0:0xbc4fd4 | fft5d_plan_3d(int, int, int, int*, int, t_complex**, t_compl... | fft5d.cpp:643 | 0 | 0 | runtime | parallel | 52 | 10.5 E-3 | 6.00 | 2.03 E-3 | 2.03 E-3 | 19.4 | 1.240 | 1.000 |
| libgromacs_mpi.so.7.0.0:0xa65e91 | gmx::set_lincs(InteractionDefinitions const&, int, gmx::Arra... | lincs.cpp:2196 | 0 | 0 | runtime | parallel | 52 | 9.51 E-3 | 127 | 2.59 E-3 | 2.56 E-3 | 27.2 | 1.374 | 1.000 |
| libgromacs_mpi.so.7.0.0:0xa62cbc | _INTERNAL1bba7552::gmx::set_lincs_matrix(_INTERNAL1bba7552::... | lincs.cpp:1347 | 0 | 0 | runtime | parallel | 52 | 9.28 E-3 | 127 | 3.31 E-3 | 3.20 E-3 | 35.6 | 1.554 | 1.000 |
| libgromacs_mpi.so.7.0.0:0x3fed69 | Nbnxm::GridSet::putOnGrid(float const (*) [3], int, float co... | gridset.cpp:212 | 0 | 0 | runtime | parallel | 52 | 7.62 E-3 | 127 | 2.82 E-3 | 2.78 E-3 | 37.0 | 1.587 | 1.000 |
| libgromacs_mpi.so.7.0.0:0x571470 | dd_redistribute_cg(_IO_FILE*, long, gmx_domdec_t*, int*, t_s... | redistribute.cpp:624 | 0 | 0 | runtime | parallel | 52 | 6.37 E-3 | 126 | 898 E-6 | 875 E-6 | 14.1 | 1.164 | 1.000 |
| libgromacs_mpi.so.7.0.0:0xa63f49 | _INTERNAL1bba7552::gmx::lincs_thread_setup(_INTERNAL1bba7552... | lincs.cpp:1695 | 0 | 0 | runtime | parallel | 52 | 6.00 E-3 | 127 | 1.39 E-3 | 1.37 E-3 | 23.2 | 1.301 | 1.000 |
| libgromacs_mpi.so.7.0.0:0xab42d2 | calc_vcm_grp(t_mdatoms const&, gmx::ArrayRef<gmx::BasicVecto... | vcm.cpp:170 | 0 | 0 | runtime | parallel | 52 | 2.32 E-3 | 102 | 924 E-6 | 852 E-6 | 39.9 | 1.663 | 1.000 |
| libgromacs_mpi.so.7.0.0:0xab8048 | _INTERNALa73835ba::do_stopcm_grp(t_mdatoms const&, gmx::Arra... | vcm.cpp:374 | 0 | 0 | runtime | parallel | 52 | 2.00 E-3 | 102 | 783 E-6 | 707 E-6 | 39.1 | 1.642 | 1.000 |
| libgromacs_mpi.so.7.0.0:0x5b7a4e | gmx::ThreadedForceBuffer<float [4]>::ThreadedForceBuffer(int... | threaded_force_buffer.cpp:230 | 0 | 0 | runtime | parallel | 52 | 60.5 E-6 | 1.00 | 24.4 E-6 | 24.2 E-6 | 40.2 | 1.673 | 1.000 |
| libgromacs_mpi.so.7.0.0:0xbb8866 | pme_init_all_work(pme_solve_work_t**, int, int) | pme_solve.cpp:144 | 0 | 0 | runtime | parallel | 52 | 37.3 E-6 | 1.00 | 17.2 E-6 | 17.0 E-6 | 46.1 | 1.855 | 1.000 |
| libgromacs_mpi.so.7.0.0:0xb96ee1 | PmeAtomComm::PmeAtomComm(int, int, int, int, bool) | pme.cpp:325 | 0 | 0 | runtime | parallel | 52 | 16.2 E-6 | 1.00 | 2.19 E-6 | 1.97 E-6 | 13.5 | 1.156 | 1.000 |
| libgromacs_mpi.so.7.0.0:0x59b0d1 | gmx_ekindata_t::gmx_ekindata_t(int, float, int) | group.cpp:66 | 0 | 0 | runtime | parallel | 52 | 7.22 E-6 | 1.00 | 2.05 E-6 | 1.83 E-6 | 28.3 | 1.396 | 1.000 |
