[gmx-users] using dual CPU's
pbuscemi at q.com
pbuscemi at q.com
Thu Dec 13 22:31:27 CET 2018
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-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of p buscemi
Sent: Thursday, December 13, 2018 1:38 PM
To: gmx-users at gromacs.org
Cc: gmx-users at 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-v1.5.3-420ce003@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 <ckutzne at gwdg.de> wrote:
> Hi,
>
> > On 13. Dec 2018, at 01:11, paul buscemi <pbuscemi at 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 <ckutzne at gwdg.de> wrote:
> > > Hi Paul,
> > > > On 12. Dec 2018, at 15:36, pbuscemi at 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
> > > >
> > > >
> > > >
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