[gmx-users] using dual CPU's
pbuscemi at q.com
pbuscemi at q.com
Mon Dec 17 21:14:11 CET 2018
Thank you again, "I'll be back".... when I sort all this out.
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 Szilárd Páll
Sent: Monday, December 17, 2018 1:16 PM
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Subject: Re: [gmx-users] using dual CPU's
On Thu, Dec 13, 2018 at 8:39 PM p buscemi <pbuscemi at q.com> wrote:
> 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.
>
Yes.
> 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.
>
The AMD Threadrippers are tricky and the 32-core version is an even unusual beast than the 16-core one. Additionally, there can be CPU-GPU communication issues that might required the latest firmware updates (and even than with some boards systems this aspect is not optimal).
You should definitely avoid single runs that span across more than 8 cores as performance with such wide ranks will not be great on the CPU side.
However in throughput mode with GPUs, e.g. using e.g. 4-way multi-runs (or with DD) a 16 C Threadripper should match the performance of 12 Skylake cores.
> Paul
>
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> 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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