Ci-dessous, les différences entre deux révisions de la page.
ressources:ressources:hoomd [2019/07/12 17:43] equemene créée |
ressources:ressources:hoomd [2019/07/12 17:50] equemene [Exemple d'utilisation] |
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La sortie exécutée sur une machine équipée d'une GTX 780 (une carte relativement ancienne) est : | La sortie exécutée sur une machine équipée d'une GTX 780 (une carte relativement ancienne) est : | ||
<code> | <code> | ||
+ | HOOMD-blue 2.6.0 CUDA (9.1) DOUBLE HPMC_MIXED SSE SSE2 | ||
+ | Compiled: 07/12/2019 | ||
+ | Copyright (c) 2009-2019 The Regents of the University of Michigan. | ||
+ | ----- | ||
+ | You are using HOOMD-blue. Please cite the following: | ||
+ | * J A Anderson, C D Lorenz, and A Travesset. "General purpose molecular dynamics | ||
+ | simulations fully implemented on graphics processing units", Journal of | ||
+ | Computational Physics 227 (2008) 5342--5359 | ||
+ | * J Glaser, T D Nguyen, J A Anderson, P Liu, F Spiga, J A Millan, D C Morse, and | ||
+ | S C Glotzer. "Strong scaling of general-purpose molecular dynamics simulations | ||
+ | on GPUs", Computer Physics Communications 192 (2015) 97--107 | ||
+ | ----- | ||
+ | notice(2): Notice: GPU id 1 is not available for computation because it's compute capability is not high enough | ||
+ | notice(2): This build of hoomd was compiled for a minimum capability of of 3.5 but the GPU is only 3.0 | ||
+ | HOOMD-blue is running on the following GPU(s): | ||
+ | [0] GeForce GTX 780 12 SM_3.5 @ 0.901 GHz, 3022 MiB DRAM | ||
+ | bmark.py:016 | system = init.read_gsd(filename=os.path.join(d,'init.gsd')) | ||
+ | notice(2): Group "all" created containing 1428364 particles | ||
+ | bmark.py:018 | harmonic = md.bond.harmonic(name="tether") | ||
+ | bmark.py:019 | harmonic.bond_coeff.set('tether', k=4., r0=0.) | ||
+ | bmark.py:021 | nl = md.nlist.cell() | ||
+ | bmark.py:022 | dpd = md.pair.dpd(nlist = nl, r_cut=1.0, kT=1., seed=1) | ||
+ | ----- | ||
+ | You are using DPD. Please cite the following: | ||
+ | * C L Phillips, J A Anderson, and S C Glotzer. "Pseudo-random number generation | ||
+ | for Brownian Dynamics and Dissipative Particle Dynamics simulations on GPU | ||
+ | devices", Journal of Computational Physics 230 (2011) 7191--7201 | ||
+ | ----- | ||
+ | bmark.py:024 | dpd.pair_coeff.set(system.particles.types, system.particles.types, A=A, gamma= 1.0) | ||
+ | bmark.py:025 | dpd.pair_coeff.set('glycerol', 'polymer', A=2*A, gamma= 1.0) | ||
+ | bmark.py:026 | dpd.pair_coeff.set('hydroxyl', 'polymer', A=2*A, gamma= 1.0) | ||
+ | bmark.py:027 | dpd.pair_coeff.set('hydroxyl', 'core', A=2*A, gamma= 1.0) | ||
+ | bmark.py:028 | dpd.pair_coeff.set('hydroxyl', 'glycerol', A=A/2., gamma= 1.0) | ||
+ | bmark.py:029 | dpd.pair_coeff.set('hydroxyl', 'hydroxyl', A=A/2., gamma= 1.0) | ||
+ | bmark.py:030 | md.integrate.mode_standard(dt=0.01) | ||
+ | bmark.py:031 | md.integrate.nve(group=group.all()) | ||
+ | bmark.py:031 | md.integrate.nve(group=group.all()) | ||
+ | bmark.py:033 | nl.reset_exclusions(exclusions = ['bond', 'body']) | ||
+ | notice(2): -- Neighborlist exclusion statistics -- : | ||
+ | notice(2): Particles with 0 exclusions : 1000000 | ||
+ | notice(2): Particles with 1 exclusions : 10432 | ||
+ | notice(2): Particles with 2 exclusions : 417280 | ||
+ | notice(2): Particles with 16 exclusions : 652 | ||
+ | notice(2): Neighbors included by diameter : no | ||
+ | notice(2): Neighbors excluded when in the same body: no | ||
+ | bmark.py:034 | nl.set_params(r_buff=0.35, check_period=2) | ||
+ | bmark.py:038 | run(10000) | ||
+ | ** starting run ** | ||
+ | Time 00:00:12 | Step 20087 / 30000 | TPS 8.6576 | ETA 00:19:05 | ||
+ | Time 00:00:22 | Step 20208 / 30000 | TPS 11.9515 | ETA 00:13:39 | ||
+ | Time 00:00:32 | Step 20340 / 30000 | TPS 13.1698 | ETA 00:12:13 | ||
+ | Time 00:00:42 | Step 20461 / 30000 | TPS 12.0668 | ETA 00:13:10 | ||
+ | Time 00:00:52 | Step 20584 / 30000 | TPS 12.2681 | ETA 00:12:47 | ||
+ | Time 00:01:02 | Step 20705 / 30000 | TPS 12.0506 | ETA 00:12:51 | ||
+ | Time 00:01:12 | Step 20821 / 30000 | TPS 11.5262 | ETA 00:13:16 | ||
+ | Time 00:01:22 | Step 20933 / 30000 | TPS 11.0785 | ETA 00:13:38 | ||
+ | Time 00:01:32 | Step 21057 / 30000 | TPS 12.3853 | ETA 00:12:02 | ||
+ | Time 00:01:42 | Step 21182 / 30000 | TPS 12.4549 | ETA 00:11:47 | ||
+ | Time 00:01:52 | Step 21305 / 30000 | TPS 12.1527 | ETA 00:11:55 | ||
+ | Time 00:02:03 | Step 21433 / 30000 | TPS 12.6534 | ETA 00:11:17 | ||
+ | Time 00:02:13 | Step 21557 / 30000 | TPS 12.3448 | ETA 00:11:23 | ||
+ | Time 00:02:23 | Step 21675 / 30000 | TPS 11.6808 | ETA 00:11:52 | ||
+ | Time 00:02:33 | Step 21795 / 30000 | TPS 11.8401 | ETA 00:11:32 | ||
+ | Time 00:02:43 | Step 21913 / 30000 | TPS 11.6582 | ETA 00:11:33 | ||
+ | Time 00:02:53 | Step 22036 / 30000 | TPS 12.2585 | ETA 00:10:49 | ||
+ | Time 00:03:03 | Step 22159 / 30000 | TPS 12.1688 | ETA 00:10:44 | ||
+ | Time 00:03:13 | Step 22273 / 30000 | TPS 11.3407 | ETA 00:11:21 | ||
+ | Time 00:03:23 | Step 22382 / 30000 | TPS 10.7981 | ETA 00:11:45 | ||
+ | Time 00:03:33 | Step 22490 / 30000 | TPS 10.7574 | ETA 00:11:38 | ||
+ | Time 00:03:43 | Step 22595 / 30000 | TPS 10.4942 | ETA 00:11:45 | ||
+ | Time 00:03:53 | Step 22704 / 30000 | TPS 10.7573 | ETA 00:11:18 | ||
+ | Time 00:04:04 | Step 22813 / 30000 | TPS 10.7357 | ETA 00:11:09 | ||
+ | Time 00:04:14 | Step 22925 / 30000 | TPS 11.0336 | ETA 00:10:41 | ||
+ | Time 00:04:24 | Step 23037 / 30000 | TPS 11.0566 | ETA 00:10:29 | ||
+ | Time 00:04:34 | Step 23149 / 30000 | TPS 11.0623 | ETA 00:10:19 | ||
+ | Time 00:04:44 | Step 23263 / 30000 | TPS 11.389 | ETA 00:09:51 | ||
+ | Time 00:04:54 | Step 23374 / 30000 | TPS 11.0891 | ETA 00:09:57 | ||
+ | Time 00:05:04 | Step 23484 / 30000 | TPS 10.95 | ETA 00:09:55 | ||
+ | Time 00:05:14 | Step 23599 / 30000 | TPS 11.4622 | ETA 00:09:18 | ||
+ | Time 00:05:24 | Step 23711 / 30000 | TPS 11.1758 | ETA 00:09:22 | ||
+ | Time 00:05:34 | Step 23836 / 30000 | TPS 12.4148 | ETA 00:08:16 | ||
+ | Time 00:05:44 | Step 23978 / 30000 | TPS 14.0757 | ETA 00:07:07 | ||
+ | Time 00:05:54 | Step 24118 / 30000 | TPS 13.9819 | ETA 00:07:00 | ||
+ | Time 00:06:04 | Step 24259 / 30000 | TPS 14.0758 | ETA 00:06:47 | ||
+ | Time 00:06:14 | Step 24401 / 30000 | TPS 14.1366 | ETA 00:06:36 | ||
+ | Time 00:06:24 | Step 24545 / 30000 | TPS 14.2167 | ETA 00:06:23 | ||
+ | Time 00:06:35 | Step 24687 / 30000 | TPS 14.0931 | ETA 00:06:16 | ||
+ | Time 00:06:45 | Step 24829 / 30000 | TPS 14.0411 | ETA 00:06:08 | ||
+ | Time 00:06:55 | Step 24969 / 30000 | TPS 13.9563 | ETA 00:06:00 | ||
+ | Time 00:07:05 | Step 25112 / 30000 | TPS 14.2127 | ETA 00:05:43 | ||
+ | Time 00:07:15 | Step 25250 / 30000 | TPS 13.6839 | ETA 00:05:47 | ||
+ | Time 00:07:25 | Step 25389 / 30000 | TPS 13.8633 | ETA 00:05:32 | ||
+ | Time 00:07:35 | Step 25528 / 30000 | TPS 13.8195 | ETA 00:05:23 | ||
+ | Time 00:07:45 | Step 25671 / 30000 | TPS 14.2016 | ETA 00:05:04 | ||
+ | Time 00:07:55 | Step 25811 / 30000 | TPS 13.9533 | ETA 00:05:00 | ||
+ | Time 00:08:05 | Step 25954 / 30000 | TPS 14.2758 | ETA 00:04:43 | ||
+ | Time 00:08:15 | Step 26095 / 30000 | TPS 13.9971 | ETA 00:04:38 | ||
+ | Time 00:08:25 | Step 26238 / 30000 | TPS 14.1391 | ETA 00:04:26 | ||
+ | Time 00:08:35 | Step 26379 / 30000 | TPS 14.0259 | ETA 00:04:18 | ||
+ | Time 00:08:45 | Step 26522 / 30000 | TPS 14.2178 | ETA 00:04:04 | ||
+ | Time 00:08:55 | Step 26660 / 30000 | TPS 13.7057 | ETA 00:04:03 | ||
+ | Time 00:09:05 | Step 26804 / 30000 | TPS 14.3207 | ETA 00:03:43 | ||
+ | Time 00:09:15 | Step 26946 / 30000 | TPS 14.1341 | ETA 00:03:36 | ||
+ | Time 00:09:26 | Step 27085 / 30000 | TPS 13.8153 | ETA 00:03:30 | ||
+ | Time 00:09:36 | Step 27227 / 30000 | TPS 14.1656 | ETA 00:03:15 | ||
+ | Time 00:09:46 | Step 27366 / 30000 | TPS 13.7888 | ETA 00:03:11 | ||
+ | Time 00:09:56 | Step 27507 / 30000 | TPS 14.0391 | ETA 00:02:57 | ||
+ | Time 00:10:06 | Step 27648 / 30000 | TPS 13.9304 | ETA 00:02:48 | ||
+ | Time 00:10:16 | Step 27791 / 30000 | TPS 14.2767 | ETA 00:02:34 | ||
+ | Time 00:10:26 | Step 27928 / 30000 | TPS 13.6466 | ETA 00:02:31 | ||
+ | Time 00:10:36 | Step 28070 / 30000 | TPS 14.1904 | ETA 00:02:16 | ||
+ | Time 00:10:46 | Step 28210 / 30000 | TPS 13.9845 | ETA 00:02:07 | ||
+ | Time 00:10:56 | Step 28353 / 30000 | TPS 14.1502 | ETA 00:01:56 | ||
+ | Time 00:11:06 | Step 28494 / 30000 | TPS 14.0047 | ETA 00:01:47 | ||
+ | Time 00:11:16 | Step 28635 / 30000 | TPS 14.0597 | ETA 00:01:37 | ||
+ | Time 00:11:26 | Step 28773 / 30000 | TPS 13.7972 | ETA 00:01:28 | ||
+ | Time 00:11:36 | Step 28914 / 30000 | TPS 14.0043 | ETA 00:01:17 | ||
+ | Time 00:11:46 | Step 29055 / 30000 | TPS 14.0696 | ETA 00:01:07 | ||
+ | Time 00:11:56 | Step 29195 / 30000 | TPS 13.8935 | ETA 00:00:57 | ||
+ | Time 00:12:06 | Step 29336 / 30000 | TPS 13.9687 | ETA 00:00:47 | ||
+ | Time 00:12:16 | Step 29476 / 30000 | TPS 13.9598 | ETA 00:00:37 | ||
+ | Time 00:12:26 | Step 29618 / 30000 | TPS 14.049 | ETA 00:00:27 | ||
+ | Time 00:12:37 | Step 29757 / 30000 | TPS 13.7718 | ETA 00:00:17 | ||
+ | Time 00:12:47 | Step 29901 / 30000 | TPS 14.297 | ETA 00:00:06 | ||
+ | Time 00:12:54 | Step 30000 / 30000 | TPS 13.9359 | ETA 00:00:00 | ||
+ | Average TPS: 12.9538 | ||
+ | --------- | ||
+ | -- Neighborlist stats: | ||
+ | 2599 normal updates / 34 forced updates / 0 dangerous updates | ||
+ | n_neigh_min: 8 / n_neigh_max: 36 / n_neigh_avg: 21.2323 | ||
+ | shortest rebuild period: 3 | ||
+ | -- Cell list stats: | ||
+ | Dimension: 64, 64, 64 | ||
+ | n_min : 1 / n_max: 14 / n_avg: 5.44878 | ||
+ | ** run complete ** | ||
+ | benchmark.py:035 | hoomd.run(steps, limit_hours=limit_hours); | ||
+ | ** starting run ** | ||
+ | Time 00:13:04 | Step 30137 / 80000 | TPS 13.6623 | ETA 01:00:49 | ||
+ | notice(2): Ending run at time step 30278 as 0.00555556 hours have passed | ||
+ | Time 00:13:14 | Step 30278 / 80000 | TPS 14.0483 | ETA 00:58:59 | ||
+ | Average TPS: 13.8553 | ||
+ | --------- | ||
+ | -- Neighborlist stats: | ||
+ | 75 normal updates / 1 forced updates / 0 dangerous updates | ||
+ | n_neigh_min: 8 / n_neigh_max: 36 / n_neigh_avg: 21.2208 | ||
+ | shortest rebuild period: 3 | ||
+ | -- Cell list stats: | ||
+ | Dimension: 64, 64, 64 | ||
+ | n_min : 1 / n_max: 14 / n_avg: 5.44878 | ||
+ | ** run complete ** | ||
+ | benchmark.py:035 | hoomd.run(steps, limit_hours=limit_hours); | ||
+ | ** starting run ** | ||
+ | Time 00:13:24 | Step 30417 / 80278 | TPS 13.8014 | ETA 01:00:12 | ||
+ | notice(2): Ending run at time step 30558 as 0.00555556 hours have passed | ||
+ | Time 00:13:34 | Step 30558 / 80278 | TPS 14.113 | ETA 00:58:42 | ||
+ | Average TPS: 13.9566 | ||
+ | --------- | ||
+ | -- Neighborlist stats: | ||
+ | 73 normal updates / 2 forced updates / 0 dangerous updates | ||
+ | n_neigh_min: 9 / n_neigh_max: 35 / n_neigh_avg: 21.2263 | ||
+ | shortest rebuild period: 3 | ||
+ | -- Cell list stats: | ||
+ | Dimension: 64, 64, 64 | ||
+ | n_min : 0 / n_max: 14 / n_avg: 5.44878 | ||
+ | ** run complete ** | ||
+ | benchmark.py:035 | hoomd.run(steps, limit_hours=limit_hours); | ||
+ | ** starting run ** | ||
+ | Time 00:13:44 | Step 30698 / 80558 | TPS 13.9234 | ETA 00:59:41 | ||
+ | notice(2): Ending run at time step 30837 as 0.00555556 hours have passed | ||
+ | Time 00:13:54 | Step 30837 / 80558 | TPS 13.8157 | ETA 00:59:58 | ||
+ | Average TPS: 13.8695 | ||
+ | --------- | ||
+ | -- Neighborlist stats: | ||
+ | 74 normal updates / 2 forced updates / 0 dangerous updates | ||
+ | n_neigh_min: 8 / n_neigh_max: 35 / n_neigh_avg: 21.2222 | ||
+ | shortest rebuild period: 3 | ||
+ | -- Cell list stats: | ||
+ | Dimension: 64, 64, 64 | ||
+ | n_min : 0 / n_max: 14 / n_avg: 5.44878 | ||
+ | ** run complete ** | ||
+ | benchmark.py:035 | hoomd.run(steps, limit_hours=limit_hours); | ||
+ | ** starting run ** | ||
+ | Time 00:14:04 | Step 30975 / 80837 | TPS 13.6708 | ETA 01:00:47 | ||
+ | notice(2): Ending run at time step 31119 as 0.00555556 hours have passed | ||
+ | Time 00:14:14 | Step 31119 / 80837 | TPS 14.4202 | ETA 00:57:27 | ||
+ | Average TPS: 14.0435 | ||
+ | --------- | ||
+ | -- Neighborlist stats: | ||
+ | 72 normal updates / 2 forced updates / 0 dangerous updates | ||
+ | n_neigh_min: 9 / n_neigh_max: 36 / n_neigh_avg: 21.2511 | ||
+ | shortest rebuild period: 3 | ||
+ | -- Cell list stats: | ||
+ | Dimension: 64, 64, 64 | ||
+ | n_min : 1 / n_max: 13 / n_avg: 5.44878 | ||
+ | ** run complete ** | ||
+ | Hours to complete 10e6 steps: 199.39225245711478 | ||
+ | bmark.py:049 | meta.dump_metadata(filename = workspace+"/metadata.json", user = {'mps': ptps, 'tps': tps}); | ||
</code> | </code> | ||
+ | |||
+ |