[gmx-users] >60% slowdown with GPU / verlet and sd integrator
Szilárd Páll
szilard.pall at cbr.su.se
Tue Jan 15 19:35:22 CET 2013
Hi Floris,
Great feedback, this needs to be looked into. Could you please file a bug
report, preferably with a tpr (and/or all inputs) as well as log files.
Thanks,
--
Szilárd
On Tue, Jan 15, 2013 at 3:50 AM, Floris Buelens <floris_buelens at yahoo.com>wrote:
> Hi,
>
>
> I'm seeing MD simulation running a lot slower with the sd integrator than
> with md - ca. 10 vs. 30 ns/day for my 47000 atom system. I found no
> documented indication that this should be the case.
> Timings and logs pasted in below - wall time seems to be accumulating up
> in Update and Rest, adding up to >60% of total. The effect is still there
> without GPU, ca. 40% slowdown when switching from group to Verlet with the
> SD integrator
> System: Xeon E5-1620, 1x GTX 680, gromacs
> 4.6-beta3-dev-20130107-e66851a-unknown, GCC 4.4.6 and 4.7.0
>
> I didn't file a bug report yet as I don't have much variety of testing
> conditions available right now, I hope someone else has a moment to try to
> reproduce?
>
> Timings:
>
> cpu (ns/day)
> sd / verlet: 6
> sd / group: 10
> md / verlet: 9.2
> md / group: 11.4
>
> gpu (ns/day)
> sd / verlet: 11
> md / verlet: 29.8
>
>
>
> **************MD integrator, GPU / verlet
>
> 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 1244.988096 11204.893 0.1
> NxN QSTab Elec. + VdW [F] 194846.615488 7988711.235 91.9
> NxN QSTab Elec. + VdW [V&F] 2009.923008 118585.457 1.4
> 1,4 nonbonded interactions 31.616322 2845.469 0.0
> Calc Weights 703.010574 25308.381 0.3
> Spread Q Bspline 14997.558912 29995.118 0.3
> Gather F Bspline 14997.558912 89985.353 1.0
> 3D-FFT 47658.567884 381268.543 4.4
> Solve PME 20.580896 1317.177 0.0
> Shift-X 9.418458 56.511 0.0
> Angles 21.879375 3675.735 0.0
> Propers 48.599718 11129.335 0.1
> Virial 23.498403 422.971 0.0
> Stop-CM 2.436616 24.366 0.0
> Calc-Ekin 93.809716 2532.862 0.0
> Lincs 12.147284 728.837 0.0
> Lincs-Mat 131.328750 525.315 0.0
> Constraint-V 246.633614 1973.069 0.0
> Constraint-Vir 23.486379 563.673 0.0
> Settle 74.129451 23943.813 0.3
>
> -----------------------------------------------------------------------------
> Total 8694798.114 100.0
>
> -----------------------------------------------------------------------------
>
>
> 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
>
> Computing: Nodes Th. Count Wall t (s) G-Cycles %
>
> -----------------------------------------------------------------------------
> Neighbor search 1 8 201 0.944 27.206 3.3
> Launch GPU ops. 1 8 5001 0.371 10.690 1.3
> Force 1 8 5001 2.185 62.987 7.7
> PME mesh 1 8 5001 15.033 433.441 52.9
> Wait GPU local 1 8 5001 1.551 44.719 5.5
> NB X/F buffer ops. 1 8 9801 0.538 15.499 1.9
> Write traj. 1 8 2 0.725 20.912 2.6
> Update 1 8 5001 2.318 66.826 8.2
> Constraints 1 8 5001 2.898 83.551 10.2
> Rest 1 1.832 52.828 6.5
>
> -----------------------------------------------------------------------------
> Total 1 28.394 818.659 100.0
>
> -----------------------------------------------------------------------------
>
> -----------------------------------------------------------------------------
> PME spread/gather 1 8 10002 8.745 252.144 30.8
> PME 3D-FFT 1 8 10002 5.392 155.458 19.0
> PME solve 1 8 5001 0.869 25.069 3.1
>
> -----------------------------------------------------------------------------
>
> GPU timings
>
> -----------------------------------------------------------------------------
> Computing: Count Wall t (s) ms/step %
>
> -----------------------------------------------------------------------------
> Pair list H2D 201 0.080 0.397 0.4
> X / q H2D 5001 0.698 0.140 3.7
> Nonbonded F kernel 4400 14.856 3.376 79.1
> Nonbonded F+ene k. 400 1.667 4.167 8.9
> Nonbonded F+prune k. 100 0.441 4.407 2.3
> Nonbonded F+ene+prune k. 101 0.535 5.300 2.9
> F D2H 5001 0.501 0.100 2.7
>
> -----------------------------------------------------------------------------
> Total 18.778 3.755 100.0
>
> -----------------------------------------------------------------------------
>
> Force evaluation time GPU/CPU: 3.755 ms/3.443 ms = 1.091
> For optimal performance this ratio should be close to 1!
>
>
> Core t (s) Wall t (s) (%)
> Time: 221.730 28.394 780.9
> (ns/day) (hour/ns)
> Performance: 30.435 0.789
>
>
>
>
> *****************SD integrator, GPU / verlet
>
> 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 1254.604928 11291.444 0.1
> NxN QSTab Elec. + VdW [F] 197273.059584 8088195.443 91.6
> NxN QSTab Elec. + VdW [V&F] 2010.150784 118598.896 1.3
> 1,4 nonbonded interactions 31.616322 2845.469 0.0
> Calc Weights 703.010574 25308.381 0.3
> Spread Q Bspline 14997.558912 29995.118 0.3
> Gather F Bspline 14997.558912 89985.353 1.0
> 3D-FFT 47473.892284 379791.138 4.3
> Solve PME 20.488896 1311.289 0.0
> Shift-X 9.418458 56.511 0.0
> Angles 21.879375 3675.735 0.0
> Propers 48.599718 11129.335 0.1
> Virial 23.498403 422.971 0.0
> Update 234.336858 7264.443 0.1
> Stop-CM 2.436616 24.366 0.0
> Calc-Ekin 93.809716 2532.862 0.0
> Lincs 24.289712 1457.383 0.0
> Lincs-Mat 262.605000 1050.420 0.0
> Constraint-V 246.633614 1973.069 0.0
> Constraint-Vir 23.486379 563.673 0.0
> Settle 148.229268 47878.054 0.5
>
> -----------------------------------------------------------------------------
> Total 8825351.354 100.0
>
> -----------------------------------------------------------------------------
>
>
> 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
>
> Computing: Nodes Th. Count Wall t (s) G-Cycles %
>
> -----------------------------------------------------------------------------
> Neighbor search 1 8 201 0.945 27.212 1.2
> Launch GPU ops. 1 8 5001 0.384 11.069 0.5
> Force 1 8 5001 2.180 62.791 2.7
> PME mesh 1 8 5001 15.029 432.967 18.5
> Wait GPU local 1 8 5001 3.327 95.844 4.1
> NB X/F buffer ops. 1 8 9801 0.542 15.628 0.7
> Write traj. 1 8 2 0.749 21.582 0.9
> Update 1 8 5001 28.044 807.908 34.5
> Constraints 1 8 10002 5.562 160.243 6.8
> Rest 1 24.488 705.458 30.1
>
> -----------------------------------------------------------------------------
> Total 1 81.250 2340.701 100.0
>
> -----------------------------------------------------------------------------
>
> -----------------------------------------------------------------------------
> PME spread/gather 1 8 10002 8.769 252.615 10.8
> PME 3D-FFT 1 8 10002 5.367 154.630 6.6
> PME solve 1 8 5001 0.865 24.910 1.1
>
> -----------------------------------------------------------------------------
>
> GPU timings
>
> -----------------------------------------------------------------------------
> Computing: Count Wall t (s) ms/step %
>
> -----------------------------------------------------------------------------
> Pair list H2D 201 0.080 0.398 0.4
> X / q H2D 5001 0.699 0.140 3.4
> Nonbonded F kernel 4400 16.271 3.698 79.6
> Nonbonded F+ene k. 400 1.827 4.568 8.9
> Nonbonded F+prune k. 100 0.482 4.816 2.4
> Nonbonded F+ene+prune k. 101 0.584 5.787 2.9
> F D2H 5001 0.505 0.101 2.5
>
> -----------------------------------------------------------------------------
> Total 20.448 4.089 100.0
>
> -----------------------------------------------------------------------------
>
> Force evaluation time GPU/CPU: 4.089 ms/3.441 ms = 1.188
> For optimal performance this ratio should be close to 1!
>
> Core t (s) Wall t (s) (%)
> Time: 643.440 81.250 791.9
> (ns/day) (hour/ns)
> Performance: 10.636 2.256
> --
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