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.p...@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_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 -- 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
