normal Slow mdruns with gromacs 2018.1

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11 months 3 weeks ago #7584 by nanogod
Slow mdruns with gromacs 2018.1 was created by nanogod
Hi,

anyone else noticed that performance slows significantly down with cuda 9.1 and gromacs 2018.1? I dont know from which version since i jumped from gromacs 2016 and cuda 8.

Best regards
Morten

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11 months 3 weeks ago #7585 by nanogod
Replied by nanogod on topic Slow mdruns with gromacs 2018.1
Before update md.log

On 1 MPI rank, each using 12 OpenMP threads

Computing: Num Num Call Wall time Giga-Cycles
Ranks Threads Count (s) total sum %
Neighbor search 1 12 15001 20.363 830.191 9.4
Launch GPU ops. 1 12 300001 13.433 547.687 6.2
Force 1 12 300001 14.810 603.804 6.8
Wait GPU local 1 12 300001 68.948 2811.045 31.8
NB X/F buffer ops. 1 12 585001 15.172 618.568 7.0
Write traj. 1 12 39 0.212 8.642 0.1
Update 1 12 300001 47.775 1947.824 22.0
Constraints 1 12 300001 11.899 485.122 5.5
Rest 24.429 995.973 11.3
Total 217.041 8848.857 100.0

GPU timings
Computing: Count Wall t (s) ms/step %
Pair list H2D 15001 1.581 0.105 1.8
X / q H2D 300001 17.238 0.057 19.4
Nonbonded F kernel 285000 53.969 0.189 60.8
Nonbonded F+prune k. 12000 2.783 0.232 3.1
Nonbonded F+ene+prune k. 3001 0.890 0.297 1.0
F D2H 300001 12.268 0.041 13.8
Total 88.729 0.296 100.0

Average per-step force GPU/CPU evaluation time ratio: 0.296 ms/0.049 ms = 5.991

Core t (s) Wall t (s) (%)
Time: 2604.493 217.041 1200.0
(ns/day) (hour/ns)
Performance: 3582.743 0.007
Finished mdrun on rank 0 Sun Mar 18 07:26:17 2018

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11 months 3 weeks ago - 11 months 3 weeks ago #7586 by nanogod
Replied by nanogod on topic Slow mdruns with gromacs 2018.1
After update



Computing: M-Number M-Flops % Flops
Pair Search distance check 113111.867628 1018006.809 1.1
NxN RF Elec. + LJ [F] 49815.906048 2490795.302 2.8
NxN RF Elec. + LJ [V&F] 503.095984 38235.295 0.0
NxN LJ [F] 1887833.749440 84952518.725 94.3
NxN LJ [V&F] 19075.148672 1239884.664 1.4
NxN RF Electrostatics [F] 72.985920 2262.564 0.0
NxN RF Electrostatics [V&F] 0.742000 26.712 0.0
Shift-X 556.777116 3340.663 0.0
Bonds 278.400928 16425.655 0.0
Angles 777.602592 130637.235 0.1
Propers 297.600992 68150.627 0.1
Impropers 96.000320 19968.067 0.0
Virial 557.452161 10034.139 0.0
Stop-CM 111.422232 1114.222 0.0
Calc-Ekin 1113.554232 30065.964 0.0
Lincs 604.806048 36288.363 0.0
Lincs-Mat 9446.494464 37785.978 0.0
Constraint-V 1209.608064 9676.865 0.0
Constraint-Vir 30.242016 725.808 0.0
Total 90105943.656 100.0


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 12 OpenMP threads

Computing: Num Num Call Wall time Giga-Cycles
Ranks Threads Count (s) total sum %
Neighbor search 1 12 15001 52.342 2134.340 9.8
Force 1 12 300001 400.974 16350.539 75.2
NB X/F buffer ops. 1 12 585001 44.190 1801.930 8.3
Write traj. 1 12 39 0.197 8.014 0.0
Update 1 12 300001 11.249 458.707 2.1
Constraints 1 12 300001 19.712 803.810 3.7
Rest 4.732 192.953 0.9
Total 533.396 21750.293 100.0

Core t (s) Wall t (s) (%)
Time: 6400.751 533.396 1200.0
(ns/day) (hour/ns)
Performance: 1457.834 0.016
Finished mdrun on rank 0 Sun Mar 25 09:01:56 2018
Last edit: 11 months 3 weeks ago by nanogod. Reason: explanation added

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11 months 3 weeks ago #7588 by nanogod
Replied by nanogod on topic Slow mdruns with gromacs 2018.1
Just a short update. I installed gromacs 2016.5 and i got an 100% performance improvement compared to gromacs 2018.1. Cuda is not the issue. Anyone has an idea what is wrong? 2018. is supposed to be a big performance improvement for a system like mine (12 cores + 1 GTX1080)

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11 months 3 weeks ago #7589 by peterkroon
Replied by peterkroon on topic Slow mdruns with gromacs 2018.1
Hi Morten,

which mdp settings do you use? If you're not already try using the new-rf parameters from cgmartini.nl/index.php/force-field-parameters/input-parameters . Beyond that I'd refer you to the Gromacs userlist. They'll want at the very least your mdp settings, a log file and a description of your system.

I don't think anybody in the lab runs a lot of things with 2018(.1) yet. We tend to try and finish projects using the same Gromacs version.

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