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_buel...@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 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
