[gmx-users] >60% slowdown with GPU / verlet and sd integrator

Szilárd Páll szilard.pall at cbr.su.se
Thu Jan 17 05:03:13 CET 2013 

Hi,

Just to note for the users who might read this: the report is valid, some
non-thread-parallel code is the reason and we hope to have a fix for 4.6.0.

For updates, follow the issue #1211.

Cheers,

--
Szilárd


On Wed, Jan 16, 2013 at 4:45 PM, Berk Hess <gmx3 at hotmail.com> wrote:

>
> The issue I'm referring to is about a factor of 2 in update and
> constraints, but here it's much more.
> I just found out that the SD update is not OpenMP threaded (and I even
> noted in the code why this is).
> I reopened the issue and will find a solution.
>
> Cheers.
>
> Berk
>
> ----------------------------------------
> > Date: Wed, 16 Jan 2013 16:20:32 +0100
> > Subject: Re: [gmx-users] >60% slowdown with GPU / verlet and sd
> integrator
> > From: mark.j.abraham at gmail.com
> > To: gmx-users at gromacs.org
> >
> > We should probably note this effect on the wiki somewhere?
> >
> > Mark
> >
> > On Wed, Jan 16, 2013 at 3:44 PM, Berk Hess <gmx3 at hotmail.com> wrote:
> >
> > >
> > > Hi,
> > >
> > > Unfortunately this is not a bug, but a feature!
> > > We made the non-bondeds so fast on the GPU that integration and
> > > constraints take more time.
> > > The sd1 integrator is almost as fast as the md integrator, but slightly
> > > less accurate.
> > > In most cases that's a good solution.
> > >
> > > I closed the redmine issue:
> > > http://redmine.gromacs.org/issues/1121
> > >
> > > Cheers,
> > >
> > > Berk
> > >
> > > ----------------------------------------
> > > > Date: Wed, 16 Jan 2013 17:26:18 +0300
> > > > Subject: Re: [gmx-users] >60% slowdown with GPU / verlet and sd
> > > integrator
> > > > From: jmsstarlight at gmail.com
> > > > To: gmx-users at gromacs.org
> > > >
> > > > Hi all!
> > > >
> > > > I've also done some calculations with the SD integraator used as the
> > > > thermostat ( without t_coupl ) with the system of 65k atoms I
> obtained
> > > > 10ns\day performance on gtc 670 and 4th core i5.
> > > > I haventrun any simulations with MD integrator yet so It should test
> it.
> > > >
> > > > James
> > > >
> > > > 2013/1/15 Szilárd Páll <szilard.pall at cbr.su.se>:
> > > > > 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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