Carsten, A possible issue...
I compiled gmx 18.3 with gcc-5 ( CUDA 9 seems to run normally ) Should recompile with gcc-6.4 ? Paul -----Original Message----- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of p buscemi Sent: Thursday, December 13, 2018 1:38 PM To: gmx-us...@gromacs.org Cc: gmx-us...@gromacs.org Subject: Re: [gmx-users] using dual CPU's Carsten thanks for the suggestion. Is it necessary to use the MPI version for gromacs when using multdir? - now have the single node version loaded. I'm hammering out the first 2080ti with the 32 core AMD. results are not stellar. slower than an intel 17-7000 But I'll beat on it some more before throwing in the hammer. Paul Sent from Mailspring (https://link.getmailspring.com/link/1544729553.local-d6faf123-7363-v1.5.3-420ce...@getmailspring.com/0?redirect=https%3A%2F%2Fgetmailspring.com%2F&recipient=Z214LXVzZXJzQGdyb21hY3Mub3Jn), the best free email app for work On Dec 13 2018, at 4:33 am, Kutzner, Carsten <ckut...@gwdg.de> wrote: > Hi, > > > On 13. Dec 2018, at 01:11, paul buscemi <pbusc...@q.com> wrote: > > Carsten,THanks for the response. > > my mistake - it was the GTX 980 from fig 3. … I was recalling from > > memory….. I assume that similar > There we measured a 19 percent performance increase for the 80k atom system. > > > results would be achieved with the 1060’s > If you want to run a small system very fast, it is probably better to > put in one strong GPU instead of two weaker ones. What you could do > with your two 1060, though, is to maximize your aggregate performance > by running two (or even 4) simulations at the same time using the > -multidir argument to mdrun. For the science, probably several independent > trajectories are needed anyway. > > > > No I did not reset , > I would at least use the -resethway mdrun command line switch, this > way your measured performances will be more reliable also for shorter runs. > > Carsten > > my results were a compilation of 4-5 runs each under slightly different > > conditions on two computers. All with the same outcome - that is ugh!. Mark > > had asked for the log outputs indicating some useful conclusions could be > > drawn from them. > > Paul > > > On Dec 12, 2018, at 9:02 AM, Kutzner, Carsten <ckut...@gwdg.de> wrote: > > > Hi Paul, > > > > On 12. Dec 2018, at 15:36, pbusc...@q.com wrote: > > > > Dear users ( one more try ) > > > > I am trying to use 2 GPU cards to improve modeling speed. The > > > > computer described in the log files is used to iron out models and am > > > > using to learn how to use two GPU cards before purchasing two new RTX > > > > 2080 ti's. The CPU is a 8 core 16 thread AMD and the GPU's are two GTX > > > > 1060; there are 50000 atoms in the model Using ntpmi and ntomp settings > > > > of 1: 16, auto ( 4:4) and 2: 8 ( and any other combination factoring to > > > > 16) the rating for ns/day are approx. 12-16 and for any other setting > > > > ~6-8 i.e adding a card cuts efficiency by half. The average load > > > > imbalance is less than 3.4% for the multicard setup . > > > > I am not at this point trying to maximize efficiency, but only > > > > to show some improvement going from one to two cards. According > > > > to a 2015 paper form the Gromacs group “ Best bang for your > > > > buck: GPU nodes for GROMACS biomolecular simulations “ I should > > > > expect maybe (at best ) 50% improvement for 90k atoms ( with 2x > > > > GTX 970 ) > > > We did not benchmark GTX 970 in that publication. > > > > > > But from Table 6 you can see that we also had quite a few cases > > > with out 80k benchmark where going from 1 to 2 GPUs, simulation > > > speed did not increase much: E.g. for the > > > E5-2670v2 going from one to 2 GTX 980 GPUs led to an increase of 10 > > > percent. > > > > > > Did you use counter resetting for the benchnarks? > > > Carsten > > > > > > > What bothers me in my initial attempts is that my simulations became > > > > slower by adding the second GPU - it is frustrating to say the least. > > > > It's like swimming backwards. > > > > I know am missing - as a minimum - the correct setup for mdrun > > > > and suggestions would be welcome The output from the last section of > > > > the log files is included below. > > > > =========================== ntpmi 1 ntomp:16 > > > > ============================== <====== ############### ==> <==== > > > > A V E R A G E S ====> <== ############### ======> > > > > > > > > Statistics over 29301 steps using 294 frames Energies (kJ/mol) > > > > Angle G96Angle Proper Dih. Improper Dih. LJ-14 > > > > 9.17533e+05 2.27874e+04 6.64128e+04 2.31214e+02 8.34971e+04 > > > > Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. > > > > -2.84567e+07 -1.43385e+05 -2.04658e+03 1.33320e+07 1.59914e+05 > > > > Position Rest. Potential Kinetic En. Total Energy Temperature > > > > 7.79893e+01 -1.40196e+07 1.88467e+05 -1.38312e+07 3.00376e+02 > > > > Pres. DC (bar) Pressure (bar) Constr. rmsd > > > > -2.88685e+00 3.75436e+01 0.00000e+00 > > > > > > > > Total Virial (kJ/mol) > > > > 5.27555e+04 -4.87626e+02 1.86144e+02 > > > > -4.87648e+02 4.04479e+04 -1.91959e+02 > > > > 1.86177e+02 -1.91957e+02 5.45671e+04 > > > > > > > > Pressure (bar) > > > > 2.22202e+01 1.27887e+00 -4.71738e-01 > > > > 1.27893e+00 6.48135e+01 5.12638e-01 > > > > -4.71830e-01 5.12632e-01 2.55971e+01 > > > > > > > > T-PDMS T-VMOS > > > > 2.99822e+02 3.32834e+02 > > > > > > > > > > > > M E G A - F L O P S A C C O U N T I N G NB=Group-cutoff > > > > nonbonded kernels NxN=N-by-N cluster Verlet kernels > > > > RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table > > > > W3=SPC/TIP3p W4=TIP4p (single or pairs) V&F=Potential and force > > > > V=Potential only F=Force only > > > > > > > > Computing: M-Number M-Flops % Flops > > > > ---------------------------------------------------------------- > > > > ------------- Pair Search distance check 2349.753264 21147.779 > > > > 0.0 NxN Ewald Elec. + LJ [F] 1771584.591744 116924583.055 96.6 > > > > NxN Ewald Elec. + LJ [V&F] 17953.091840 1920980.827 1.6 > > > > 1,4 nonbonded interactions 5278.575150 475071.763 0.4 Shift-X > > > > 22.173480 133.041 0.0 Angles 4178.908620 702056.648 0.6 Propers > > > > 879.909030 201499.168 0.2 Impropers 5.274180 1097.029 0.0 Pos. > > > > Restr. 42.193440 2109.672 0.0 Virial 22.186710 399.361 0.0 > > > > Update 2209.881420 68506.324 0.1 Stop-CM 22.248900 222.489 0.0 > > > > Calc-Ekin 44.346960 1197.368 0.0 Lincs 4414.639320 264878.359 > > > > 0.2 Lincs-Mat 100297.229760 401188.919 0.3 Constraint-V > > > > 8829.127980 70633.024 0.1 Constraint-Vir 22.147020 531.528 0.0 > > > > ---------------------------------------------------------------- > > > > ------------- > > > > Total 121056236.355 100.0 > > > > ---------------------------------------------------------------- > > > > ------------- R E A L C Y C L E A N D T I M E A C C O U N T I N > > > > G On 1 MPI rank, each using 16 OpenMP threads > > > > > > > > Computing: Num Num Call Wall time Giga-Cycles Ranks Threads > > > > Count (s) total sum % > > > > ---------------------------------------------------------------- > > > > ------------- Neighbor search 1 16 294 2.191 129.485 1.0 Launch > > > > GPU ops. 1 16 58602 4.257 251.544 2.0 Force 1 16 29301 23.769 > > > > 1404.510 11.3 Wait PME GPU gather 1 16 29301 33.740 1993.695 > > > > 16.0 Reduce GPU PME F 1 16 29301 7.244 428.079 3.4 Wait GPU NB > > > > local 1 16 29301 60.054 3548.612 28.5 NB X/F buffer ops. 1 16 > > > > 58308 9.823 580.459 4.7 Write traj. 1 16 7 0.119 7.048 0.1 > > > > Update 1 16 58602 11.089 655.275 5.3 Constraints 1 16 58602 > > > > 40.378 2385.992 19.2 Rest 17.743 1048.462 8.4 > > > > ---------------------------------------------------------------- > > > > ------------- > > > > Total 210.408 12433.160 100.0 > > > > ---------------------------------------------------------------- > > > > ------------- > > > > > > > > Core t (s) Wall t (s) (%) > > > > Time: 3366.529 210.408 1600.0 > > > > (ns/day) (hour/ns) > > > > Performance: 12.032 1.995 > > > > Finished mdrun on rank 0 Mon Dec 10 17:17:04 2018 > > > > > > > > > > > > =========================== ntpmi and ntomp auto ( 4:4 ) > > > > ======================================= > > > > > > > > <====== ############### ==> > > > > <==== A V E R A G E S ====> > > > > <== ############### ======> > > > > > > > > Statistics over 3301 steps using 34 frames Energies (kJ/mol) > > > > Angle G96Angle Proper Dih. Improper Dih. LJ-14 > > > > 9.20586e+05 1.95534e+04 6.56058e+04 2.21093e+02 8.56673e+04 > > > > Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. > > > > -2.84553e+07 -1.44595e+05 -2.04658e+03 1.34518e+07 4.26167e+04 > > > > Position Rest. Potential Kinetic En. Total Energy Temperature > > > > 3.83653e+01 -1.40159e+07 1.90353e+05 -1.38255e+07 3.03381e+02 > > > > Pres. DC (bar) Pressure (bar) Constr. rmsd > > > > -2.88685e+00 2.72913e+02 0.00000e+00 > > > > > > > > Total Virial (kJ/mol) > > > > -5.05948e+04 -3.29107e+03 4.84786e+02 > > > > -3.29135e+03 -3.42006e+04 -3.32392e+03 > > > > 4.84606e+02 -3.32403e+03 -2.06849e+04 > > > > > > > > Pressure (bar) > > > > 3.09713e+02 8.98192e+00 -1.19828e+00 > > > > 8.98270e+00 2.73248e+02 8.99543e+00 > > > > -1.19778e+00 8.99573e+00 2.35776e+02 > > > > > > > > T-PDMS T-VMOS > > > > 2.98623e+02 5.82467e+02 > > > > > > > > > > > > P P - P M E L O A D B A L A N C I N G > > > > NOTE: The PP/PME load balancing was limited by the maximum > > > > allowed grid scaling, you might not have reached a good load balance. > > > > > > > > PP/PME load balancing changed the cut-off and PME settings: > > > > particle-particle PME > > > > rcoulomb rlist grid spacing 1/beta initial 1.000 nm 1.000 nm 160 > > > > 160 128 0.156 nm 0.320 nm final 1.628 nm 1.628 nm 96 96 80 0.260 > > > > nm 0.521 nm cost-ratio 4.31 0.23 (note that these numbers > > > > concern only part of the total PP and PME load) > > > > > > > > > > > > M E G A - F L O P S A C C O U N T I N G NB=Group-cutoff > > > > nonbonded kernels NxN=N-by-N cluster Verlet kernels > > > > RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table > > > > W3=SPC/TIP3p W4=TIP4p (single or pairs) V&F=Potential and force > > > > V=Potential only F=Force only > > > > > > > > Computing: M-Number M-Flops % Flops > > > > ---------------------------------------------------------------- > > > > ------------- Pair Search distance check 285.793872 2572.145 0.0 > > > > NxN Ewald Elec. + LJ [F] 367351.034688 24245168.289 92.1 NxN > > > > Ewald Elec. + LJ [V&F] 3841.181056 411006.373 1.6 > > > > 1,4 nonbonded interactions 594.675150 53520.763 0.2 Calc Weights > > > > 746.884260 26887.833 0.1 Spread Q Bspline 15933.530880 31867.062 > > > > 0.1 Gather F Bspline 15933.530880 95601.185 0.4 3D-FFT > > > > 154983.295306 1239866.362 4.7 Solve PME 40.079616 2565.095 0.0 > > > > Reset In Box 2.564280 7.693 0.0 CG-CoM 2.639700 7.919 0.0 Angles > > > > 470.788620 79092.488 0.3 Propers 99.129030 22700.548 0.1 > > > > Impropers 0.594180 123.589 0.0 Pos. Restr. 4.753440 237.672 0.0 > > > > Virial 2.570400 46.267 0.0 Update 248.961420 7717.804 0.0 > > > > Stop-CM 2.639700 26.397 0.0 Calc-Ekin 5.128560 138.471 0.0 Lincs > > > > 557.713246 33462.795 0.1 Lincs-Mat 12624.363456 50497.454 0.2 > > > > Constraint-V 1115.257670 8922.061 0.0 Constraint-Vir 2.871389 > > > > 68.913 0.0 > > > > ---------------------------------------------------------------- > > > > ------------- > > > > Total 26312105.181 100.0 > > > > ---------------------------------------------------------------- > > > > ------------- > > > > > > > > > > > > D O M A I N D E C O M P O S I T I O N S T A T I S T I C S av. > > > > #atoms communicated per step for force: 2 x 16748.9 av. #atoms > > > > communicated per step for LINCS: 2 x 9361.6 > > > > > > > > > > > > Dynamic load balancing report: > > > > DLB was off during the run due to low measured imbalance. > > > > Average load imbalance: 3.4%. > > > > The balanceable part of the MD step is 46%, load imbalance is computed > > > > from this. > > > > Part of the total run time spent waiting due to load imbalance: 1.6%. > > > > > > > > > > > > R E A L C Y C L E A N D T I M E A C C O U N T I N G On 4 MPI > > > > ranks, each using 4 OpenMP threads > > > > Computing: Num Num Call Wall time Giga-Cycles Ranks Threads > > > > Count (s) total sum % > > > > ---------------------------------------------------------------- > > > > ------------- Domain decomp. 4 4 34 0.457 26.976 1.0 DD comm. > > > > load 4 4 2 0.000 0.008 0.0 Neighbor search 4 4 34 0.138 8.160 > > > > 0.3 Launch GPU ops. 4 4 6602 0.441 26.070 0.9 Comm. coord. 4 4 > > > > 3267 0.577 34.081 1.2 Force 4 4 3301 2.298 135.761 4.9 Wait + > > > > Comm. F 4 4 3301 0.276 16.330 0.6 PME mesh 4 4 3301 25.822 > > > > 1525.817 54.8 Wait GPU NB nonloc. 4 4 3301 0.132 7.819 0.3 Wait > > > > GPU NB local 4 4 3301 0.012 0.724 0.0 NB X/F buffer ops. 4 4 > > > > 13136 0.471 27.822 1.0 Write traj. 4 4 2 0.014 0.839 0.0 Update > > > > 4 4 6602 1.006 59.442 2.1 Constraints 4 4 6602 6.926 409.290 > > > > 14.7 Comm. energies 4 4 34 0.009 0.524 0.0 Rest 8.548 505.108 > > > > 18.1 > > > > ---------------------------------------------------------------- > > > > ------------- > > > > Total 47.127 2784.772 100.0 > > > > ---------------------------------------------------------------- > > > > ------------- Breakdown of PME mesh computation > > > > ---------------------------------------------------------------- > > > > ------------- PME redist. X/F 4 4 6602 2.538 149.998 5.4 PME > > > > spread 4 4 3301 6.055 357.770 12.8 PME gather 4 4 3301 3.432 > > > > 202.814 7.3 PME 3D-FFT 4 4 6602 10.559 623.925 22.4 PME 3D-FFT > > > > Comm. 4 4 6602 2.691 158.993 5.7 PME solve Elec 4 4 3301 0.521 > > > > 30.805 1.1 > > > > ---------------------------------------------------------------- > > > > ------------- > > > > > > > > Core t (s) Wall t (s) (%) > > > > Time: 754.033 47.127 1600.0 > > > > (ns/day) (hour/ns) > > > > Performance: 6.052 3.966 > > > > Finished mdrun on rank 0 Mon Dec 10 17:10:34 2018 > > > > > > > > > > > > =========================================== ntmpi 2: ntomp 8 > > > > ============================================== > > > > <====== ############### ==> > > > > <==== A V E R A G E S ====> > > > > <== ############### ======> > > > > > > > > Statistics over 11201 steps using 113 frames Energies (kJ/mol) > > > > Angle G96Angle Proper Dih. Improper Dih. LJ-14 > > > > 9.16403e+05 2.12953e+04 6.61725e+04 2.26296e+02 8.35215e+04 > > > > Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. > > > > -2.84508e+07 -1.43740e+05 -2.04658e+03 1.34647e+07 2.76232e+04 > > > > Position Rest. Potential Kinetic En. Total Energy Temperature > > > > 5.93627e+01 -1.40166e+07 1.88847e+05 -1.38277e+07 3.00981e+02 > > > > Pres. DC (bar) Pressure (bar) Constr. rmsd > > > > -2.88685e+00 8.53077e+01 0.00000e+00 > > > > > > > > Total Virial (kJ/mol) > > > > 3.15233e+04 -6.80636e+02 9.80007e+01 > > > > -6.81075e+02 2.45640e+04 -1.40642e+03 > > > > 9.81033e+01 -1.40643e+03 4.02877e+04 > > > > > > > > Pressure (bar) > > > > 8.11163e+01 1.87348e+00 -2.03329e-01 > > > > 1.87469e+00 1.09211e+02 3.83468e+00 > > > > -2.03613e-01 3.83470e+00 6.55961e+01 > > > > > > > > T-PDMS T-VMOS > > > > 2.99551e+02 3.84895e+02 > > > > > > > > > > > > P P - P M E L O A D B A L A N C I N G > > > > NOTE: The PP/PME load balancing was limited by the maximum > > > > allowed grid scaling, you might not have reached a good load balance. > > > > > > > > PP/PME load balancing changed the cut-off and PME settings: > > > > particle-particle PME > > > > rcoulomb rlist grid spacing 1/beta initial 1.000 nm 1.000 nm 160 > > > > 160 128 0.156 nm 0.320 nm final 1.628 nm 1.628 nm 96 96 80 0.260 > > > > nm 0.521 nm cost-ratio 4.31 0.23 (note that these numbers > > > > concern only part of the total PP and PME load) > > > > > > > > > > > > M E G A - F L O P S A C C O U N T I N G NB=Group-cutoff > > > > nonbonded kernels NxN=N-by-N cluster Verlet kernels > > > > RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table > > > > W3=SPC/TIP3p W4=TIP4p (single or pairs) V&F=Potential and force > > > > V=Potential only F=Force only > > > > > > > > Computing: M-Number M-Flops % Flops > > > > ---------------------------------------------------------------- > > > > ------------- Pair Search distance check 1057.319360 9515.874 > > > > 0.0 NxN Ewald Elec. + LJ [F] 1410325.411968 93081477.190 93.9 > > > > NxN Ewald Elec. + LJ [V&F] 14378.367616 1538485.335 1.6 > > > > 1,4 nonbonded interactions 2017.860150 181607.413 0.2 Calc > > > > Weights 2534.338260 91236.177 0.1 Spread Q Bspline 54065.882880 > > > > 108131.766 0.1 Gather F Bspline 54065.882880 324395.297 0.3 > > > > 3D-FFT 383450.341906 3067602.735 3.1 Solve PME 113.199616 > > > > 7244.775 0.0 Reset In Box 8.522460 25.567 0.0 CG-CoM 8.597880 > > > > 25.794 0.0 Angles 1597.486620 268377.752 0.3 Propers 336.366030 > > > > 77027.821 0.1 Impropers 2.016180 419.365 0.0 Pos. Restr. > > > > 16.129440 806.472 0.0 Virial 8.532630 153.587 0.0 Update > > > > 844.779420 26188.162 0.0 Stop-CM 8.597880 85.979 0.0 Calc-Ekin > > > > 17.044920 460.213 0.0 Lincs 1753.732822 105223.969 0.1 Lincs-Mat > > > > 39788.083512 159152.334 0.2 Constraint-V 3507.309174 28058.473 > > > > 0.0 Constraint-Vir 8.845375 212.289 0.0 > > > > ---------------------------------------------------------------- > > > > ------------- > > > > Total 99075914.342 100.0 > > > > ---------------------------------------------------------------- > > > > ------------- > > > > > > > > > > > > D O M A I N D E C O M P O S I T I O N S T A T I S T I C S av. > > > > #atoms communicated per step for force: 2 x 6810.8 av. #atoms > > > > communicated per step for LINCS: 2 x 3029.3 > > > > > > > > > > > > Dynamic load balancing report: > > > > DLB was off during the run due to low measured imbalance. > > > > Average load imbalance: 0.8%. > > > > The balanceable part of the MD step is 46%, load imbalance is computed > > > > from this. > > > > Part of the total run time spent waiting due to load imbalance: 0.4%. > > > > > > > > > > > > R E A L C Y C L E A N D T I M E A C C O U N T I N G On 2 MPI > > > > ranks, each using 8 OpenMP threads > > > > Computing: Num Num Call Wall time Giga-Cycles Ranks Threads > > > > Count (s) total sum % > > > > ---------------------------------------------------------------- > > > > ------------- Domain decomp. 2 8 113 1.532 90.505 1.4 DD comm. > > > > load 2 8 4 0.000 0.027 0.0 Neighbor search 2 8 113 0.442 26.107 > > > > 0.4 Launch GPU ops. 2 8 22402 1.230 72.668 1.1 Comm. coord. 2 8 > > > > 11088 0.894 52.844 0.8 Force 2 8 11201 8.166 482.534 7.5 Wait + > > > > Comm. F 2 8 11201 0.672 39.720 0.6 PME mesh 2 8 11201 61.637 > > > > 3642.183 56.6 Wait GPU NB nonloc. 2 8 11201 0.342 20.205 0.3 > > > > Wait GPU NB local 2 8 11201 0.031 1.847 0.0 NB X/F buffer ops. 2 > > > > 8 44578 1.793 105.947 1.6 Write traj. 2 8 4 0.040 2.386 0.0 > > > > Update 2 8 22402 4.148 245.121 3.8 Constraints 2 8 22402 19.207 > > > > 1134.940 17.6 Comm. energies 2 8 113 0.006 0.354 0.0 Rest 8.801 > > > > 520.065 8.1 > > > > ---------------------------------------------------------------- > > > > ------------- > > > > Total 108.942 6437.452 100.0 > > > > ---------------------------------------------------------------- > > > > ------------- Breakdown of PME mesh computation > > > > ---------------------------------------------------------------- > > > > ------------- PME redist. X/F 2 8 22402 4.992 294.991 4.6 PME > > > > spread 2 8 11201 16.979 1003.299 15.6 PME gather 2 8 11201 > > > > 11.687 690.563 10.7 PME 3D-FFT 2 8 22402 21.648 1279.195 19.9 > > > > PME 3D-FFT Comm. 2 8 22402 4.985 294.567 4.6 PME solve Elec 2 8 > > > > 11201 1.241 73.332 1.1 > > > > ---------------------------------------------------------------- > > > > ------------- > > > > > > > > Core t (s) Wall t (s) (%) > > > > Time: 1743.073 108.942 1600.0 > > > > (ns/day) (hour/ns) > > > > Performance: 8.883 2.702 > > > > Finished mdrun on rank 0 Mon Dec 10 17:01:45 2018 > > > > > > > > > > > > > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > * Can't post? 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