1)
Code: Select all
[21:57:17] Project: 2671 (Run 28, Clone 18, Gen 76)
[21:57:17]
[21:57:17] Assembly optimizations on if available.
[21:57:17] Entering M.D.
[21:57:27] Run 28, Clone 18, Gen 76)
[21:57:27]
[21:57:27] Entering M.D.
NNODES=4, MYRANK=0, HOSTNAME=adak-Rocketfish
NNODES=4, MYRANK=1, HOSTNAME=adak-Rocketfish
NNODES=4, MYRANK=2, HOSTNAME=adak-Rocketfish
NODEID=0 argc=19
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 3.3.99_development_200800503 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
:-) mdrun (-:
Reading file work/wudata_03.tpr, VERSION 3.3.99_development_20070618 (single precision)
NODEID=1 argc=19
NNODES=4, MYRANK=3, HOSTNAME=adak-Rocketfish
NODEID=2 argc=19
NODEID=3 argc=19
Note: tpx file_version 48, software version 56
Making 1D domain decomposition 1 x 1 x 4
starting mdrun '22911 system in water'
250000 steps, 500.0 ps.
[22:19:22] Completed 5008 out of 250000 steps (2%)
Writing checkpoint, step 19006910 at Wed Jan 28 14:27:36 2009
[22:30:12] Completed 7508 out of 250000 steps (3%)
[22:41:01] Completed 10008 out of 250000 steps (4%)
[22:51:48] Completed 12508 out of 250000 steps (5%)
Writing checkpoint, step 19013850 at Wed Jan 28 14:57:35 2009
[23:02:36] Completed 15008 out of 250000 steps (6%)
[23:13:24] Completed 17508 out of 250000 steps (7%)
[23:24:17] Completed 20008 out of 250000 steps (8%)
Writing checkpoint, step 19020780 at Wed Jan 28 15:27:37 2009
[23:35:03] Completed 22508 out of 250000 steps (9%)
[23:45:50] Completed 25008 out of 250000 steps (10%)
[23:56:40] Completed 27508 out of 250000 steps (11%)
Writing checkpoint, step 19027720 at Wed Jan 28 15:57:35 2009
[00:07:33] Completed 30008 out of 250000 steps (12%)
[00:18:24] Completed 32508 out of 250000 steps (13%)
Writing checkpoint, step 19034630 at Wed Jan 28 16:27:35 2009
[00:29:13] Completed 35008 out of 250000 steps (14%)
[00:40:05] Completed 37508 out of 250000 steps (15%)
[00:50:59] Completed 40008 out of 250000 steps (16%)
Writing checkpoint, step 19041540 at Wed Jan 28 16:57:36 2009
[01:01:47] Completed 42508 out of 250000 steps (17%)
[01:10:20] Completed 45008 out of 250000 steps (18%)
[01:18:33] Completed 47508 out of 250000 steps (19%)
Writing checkpoint, step 19049960 at Wed Jan 28 17:27:37 2009
[01:27:50] Completed 50008 out of 250000 steps (20%)
[01:38:37] Completed 52508 out of 250000 steps (21%)
[01:44:56] - Autosending finished units...
[01:44:56] Trying to send all finished work units
[01:44:56] + No unsent completed units remaining.
[01:44:56] - Autosend completed
[01:49:26] Completed 55008 out of 250000 steps (22%)
Writing checkpoint, step 19056900 at Wed Jan 28 17:57:37 2009
[02:00:14] Completed 57508 out of 250000 steps (23%)
[02:10:59] Completed 60008 out of 250000 steps (24%)
[02:21:47] Completed 62508 out of 250000 steps (25%)
Writing checkpoint, step 19063850 at Wed Jan 28 18:27:35 2009
[02:32:35] Completed 65008 out of 250000 steps (26%)
[02:43:25] Completed 67508 out of 250000 steps (27%)
[02:54:10] Completed 70008 out of 250000 steps (28%)
Writing checkpoint, step 19070800 at Wed Jan 28 18:57:36 2009
[03:04:58] Completed 72508 out of 250000 steps (29%)
[03:15:48] Completed 75008 out of 250000 steps (30%)
[03:26:37] Completed 77508 out of 250000 steps (31%)
Writing checkpoint, step 19077740 at Wed Jan 28 19:27:36 2009
[03:37:24] Completed 80008 out of 250000 steps (32%)
[03:48:09] Completed 82508 out of 250000 steps (33%)
Writing checkpoint, step 19084700 at Wed Jan 28 19:57:36 2009
[03:58:57] Completed 85008 out of 250000 steps (34%)
[04:09:45] Completed 87508 out of 250000 steps (35%)
[04:20:31] Completed 90008 out of 250000 steps (36%)
Writing checkpoint, step 19091650 at Wed Jan 28 20:27:36 2009
[04:31:18] Completed 92508 out of 250000 steps (37%)
[04:42:06] Completed 95008 out of 250000 steps (38%)
[04:52:54] Completed 97508 out of 250000 steps (39%)
Writing checkpoint, step 19098600 at Wed Jan 28 20:57:36 2009
[05:03:42] Completed 100008 out of 250000 steps (40%)
[05:14:31] Completed 102508 out of 250000 steps (41%)
[05:25:19] Completed 105008 out of 250000 steps (42%)
Writing checkpoint, step 19105530 at Wed Jan 28 21:27:34 2009
[05:36:07] Completed 107508 out of 250000 steps (43%)
[05:46:56] Completed 110008 out of 250000 steps (44%)
Writing checkpoint, step 19112490 at Wed Jan 28 21:57:36 2009
[05:57:42] Completed 112508 out of 250000 steps (45%)
[06:08:31] Completed 115008 out of 250000 steps (46%)
[06:19:17] Completed 117508 out of 250000 steps (47%)
Writing checkpoint, step 19119430 at Wed Jan 28 22:27:35 2009
[06:30:06] Completed 120008 out of 250000 steps (48%)
[06:40:52] Completed 122508 out of 250000 steps (49%)
[06:51:43] Completed 125008 out of 250000 steps (50%)
Writing checkpoint, step 19126370 at Wed Jan 28 22:57:36 2009
[07:02:30] Completed 127508 out of 250000 steps (51%)
[07:13:16] Completed 130008 out of 250000 steps (52%)
[07:24:04] Completed 132508 out of 250000 steps (53%)
Writing checkpoint, step 19133320 at Wed Jan 28 23:27:35 2009
[07:34:53] Completed 135008 out of 250000 steps (54%)
[07:44:56] - Autosending finished units...
[07:44:56] Trying to send all finished work units
[07:44:56] + No unsent completed units remaining.
[07:44:56] - Autosend completed
[07:45:42] Completed 137508 out of 250000 steps (55%)
[07:56:30] Completed 140008 out of 250000 steps (56%)
Writing checkpoint, step 19140260 at Wed Jan 28 23:57:35 2009
[08:07:19] Completed 142508 out of 250000 steps (57%)
[08:18:07] Completed 145008 out of 250000 steps (58%)
Writing checkpoint, step 19147200 at Thu Jan 29 00:27:36 2009
[08:28:56] Completed 147508 out of 250000 steps (59%)
[08:39:47] Completed 150008 out of 250000 steps (60%)
[08:50:35] Completed 152508 out of 250000 steps (61%)
Writing checkpoint, step 19154120 at Thu Jan 29 00:57:35 2009
[09:01:25] Completed 155008 out of 250000 steps (62%)
[09:12:13] Completed 157508 out of 250000 steps (63%)
[09:23:00] Completed 160008 out of 250000 steps (64%)
Writing checkpoint, step 19161070 at Thu Jan 29 01:27:35 2009
[09:33:47] Completed 162508 out of 250000 steps (65%)
[09:44:34] Completed 165008 out of 250000 steps (66%)
[09:55:25] Completed 167508 out of 250000 steps (67%)
Writing checkpoint, step 19168010 at Thu Jan 29 01:57:35 2009
[10:06:11] Completed 170008 out of 250000 steps (68%)
[10:16:58] Completed 172508 out of 250000 steps (69%)
Writing checkpoint, step 19174970 at Thu Jan 29 02:27:36 2009
[10:27:47] Completed 175008 out of 250000 steps (70%)
[10:38:35] Completed 177508 out of 250000 steps (71%)
[10:49:24] Completed 180008 out of 250000 steps (72%)
Writing checkpoint, step 19181900 at Thu Jan 29 02:57:35 2009
[11:00:12] Completed 182508 out of 250000 steps (73%)
[11:10:58] Completed 185008 out of 250000 steps (74%)
[11:21:47] Completed 187508 out of 250000 steps (75%)
Writing checkpoint, step 19188850 at Thu Jan 29 03:27:35 2009
[11:32:34] Completed 190008 out of 250000 steps (76%)
[11:43:23] Completed 192508 out of 250000 steps (77%)
[11:54:11] Completed 195008 out of 250000 steps (78%)
Writing checkpoint, step 19195800 at Thu Jan 29 03:57:35 2009
[12:04:57] Completed 197508 out of 250000 steps (79%)
[12:15:46] Completed 200008 out of 250000 steps (80%)
[12:26:34] Completed 202508 out of 250000 steps (81%)
Writing checkpoint, step 19202740 at Thu Jan 29 04:27:34 2009
[12:37:20] Completed 205008 out of 250000 steps (82%)
[12:48:09] Completed 207508 out of 250000 steps (83%)
Writing checkpoint, step 19209680 at Thu Jan 29 04:57:34 2009
[12:59:00] Completed 210008 out of 250000 steps (84%)
[13:09:48] Completed 212508 out of 250000 steps (85%)
[13:20:41] Completed 215008 out of 250000 steps (86%)
Writing checkpoint, step 19216600 at Thu Jan 29 05:27:36 2009
[13:31:31] Completed 217508 out of 250000 steps (87%)
[13:42:19] Completed 220008 out of 250000 steps (88%)
[13:44:56] - Autosending finished units...
[13:44:56] Trying to send all finished work units
[13:44:56] + No unsent completed units remaining.
[13:44:56] - Autosend completed
[13:52:54] Completed 222508 out of 250000 steps (89%)
Writing checkpoint, step 19223800 at Thu Jan 29 05:57:36 2009
[14:02:01] Completed 225008 out of 250000 steps (90%)
[14:12:55] Completed 227508 out of 250000 steps (91%)
[14:24:31] Completed 230008 out of 250000 steps (92%)
Writing checkpoint, step 19230670 at Thu Jan 29 06:27:35 2009
[14:36:07] Completed 232508 out of 250000 steps (93%)
[14:47:45] Completed 235008 out of 250000 steps (94%)
Writing checkpoint, step 19237130 at Thu Jan 29 06:57:36 2009
[14:59:22] Completed 237508 out of 250000 steps (95%)
[15:10:23] Completed 240008 out of 250000 steps (96%)
[15:19:30] Completed 242508 out of 250000 steps (97%)
Writing checkpoint, step 19244720 at Thu Jan 29 07:27:34 2009
[15:28:37] Completed 245008 out of 250000 steps (98%)
[15:37:43] Completed 247508 out of 250000 steps (99%)
Writing checkpoint, step 19250002 at Thu Jan 29 07:46:48 2009
Writing final coordinates.
Average load imbalance: 8.1 %
Part of the total run time spent waiting due to load imbalance: 4.6 %
Steps where the load balancing was limited by -rdd, -rcon and/or -dds: Z 0 %
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 64155.000 64155.000 100.0
17h49:15
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 55.923 8.514 0.673 35.642
gcq#0: Thanx for Using GROMACS - Have a Nice Day
[15:47:49]
[15:47:49] Finished Work Unit:
[15:47:49] - Reading up to 21207600 from "work/wudata_03.trr": Read 21207600
[15:47:49] trr file hash check passed.
[15:47:49] - Reading up to 27181640 from "work/wudata_03.xtc": Read 27181640
[15:47:49] xtc file hash check passed.
[15:47:49] edr file hash check passed.
[15:47:49] logfile size: 178254
[15:47:49] Leaving Run
[15:47:53] - Writing 48775318 bytes of core data to disk...
[15:47:54] ... Done.
[15:48:01] - Shutting down core
[19:44:56] - Autosending finished units...
[19:44:56] Trying to send all finished work units
[19:44:56] + No unsent completed units remaining.
[19:44:56] - Autosend completed
[01:44:56] - Autosending finished units...
[01:44:56] Trying to send all finished work units
[01:44:56] + No unsent completed units remaining.
[01:44:56] - Autosend completed
[07:44:56] - Autosending finished units...
[07:44:56] Trying to send all finished work units
[07:44:56] + No unsent completed units remaining.
[07:44:56] - Autosend completed
[13:44:56] - Autosending finished units...
[13:44:56] Trying to send all finished work units
[13:44:56] + No unsent completed units remaining.
[13:44:56] - Autosend completed
[15:46:39] ***** Got an Activate signal (2)
[15:46:39] Killing all core threads
Folding@Home Client Shutdown.
adak@adak-Rocketfish:~/fah1/FAH6.02-Linux$ ./fah6 -smp -verbosity 9
Note: Please read the license agreement (fah6 -license). Further
use of this software requires that you have read and accepted this agreement.
8 cores detected
--- Opening Log file [January 30 15:46:48]
# SMP Client ##################################################################
###############################################################################
Folding@Home Client Version 6.02
http://folding.stanford.edu
###############################################################################
###############################################################################
Launch directory: /home/adak/fah1/FAH6.02-Linux
Executable: ./fah6
Arguments: -smp -verbosity 9
[15:46:48] - Ask before connecting: No
[15:46:48] - User name: Adak (Team 32)
[15:46:48] - User ID: 112417230D27B962
[15:46:48] - Machine ID: 1
[15:46:48]
[15:46:48] Loaded queue successfully.
[15:46:48] - Autosending finished units...
[15:46:48] Trying to send all finished work units
[15:46:48] + No unsent completed units remaining.
[15:46:48] - Autosend completed
[15:46:48]
[15:46:48] + Processing work unit
[15:46:48] Core required: FahCore_a2.exe
[15:46:48] Core found.
[15:46:48] Working on Unit 03 [January 30 15:46:48]
[15:46:48] + Working ...
[15:46:48] - Calling './mpiexec -np 4 -host 127.0.0.1 ./FahCore_a2.exe -dir work/ -suffix 03 -checkpoint 30 -verbose -lifeline 29851 -version 602'
[15:46:48]
[15:46:48] *------------------------------*
[15:46:48] Folding@Home Gromacs SMP Core
[15:46:48] Version 2.01 (Wed Aug 13 13:11:25 PDT 2008)
[15:46:48]
[15:46:48] Preparing to commence simulation
[15:46:48] - Ensuring status. Please wait.
[15:46:58] - Looking at optimizations...
[15:46:58] - Working with standard loops on this execution.
[15:46:58] - Files status OK
[15:46:58] Need version 202
[15:46:58] Error: Work unit read from disk is invalid
[15:46:59] - Expanded 4827761 -> 24064221 (decompressed 498.4 percent)
[15:46:59] Called DecompressByteArray: compressed_data_size=4827761 data_size=24064221, decompressed_data_size=24064221 diff=0
[15:46:59] - Digital signature verified
Code: Select all
[21:23:18] Preparing to commence simulation
[21:23:18] - Ensuring status. Please wait.
[21:23:19] Called DecompressByteArray: compressed_data_size=4835644 data_size=24041281, decompressed_data_size=24041281 diff=0
[21:23:19] - Digital signature verified
[21:23:19]
[21:23:19] Project: 2671 (Run 15, Clone 3, Gen 75)
[21:23:19]
[21:23:19] Assembly optimizations on if available.
[21:23:19] Entering M.D.
[21:23:28] (Run 15, Clone 3, Gen 75)
[21:23:28]
[21:23:28] Entering M.D.
NNODES=4, MYRANK=0, HOSTNAME=adak-Rocketfish
NNODES=4, MYRANK=1, HOSTNAME=adak-Rocketfish
NNODES=4, MYRANK=2, HOSTNAME=adak-Rocketfish
NNODES=4, MYRANK=3, HOSTNAME=adak-Rocketfish
NODEID=0 argc=19
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 3.3.99_development_200800503 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
:-) mdrun (-:
Reading file work/wudata_02.tpr, VERSION 3.3.99_development_20070618 (single precision)
NODEID=1 argc=19
NODEID=2 argc=19
NODEID=3 argc=19
Note: tpx file_version 48, software version 56
Making 1D domain decomposition 1 x 1 x 4
starting mdrun '22884 system in water'
250000 steps, 500.0 ps.
[21:40:12] Completed 5008 out of 250000 steps (2%)
[21:48:27] Completed 7508 out of 250000 steps (3%)
Writing checkpoint, step 18759080 at Wed Jan 28 13:53:37 2009
[21:56:43] Completed 10008 out of 250000 steps (4%)
[22:07:15] Completed 12508 out of 250000 steps (5%)
[22:18:05] Completed 15008 out of 250000 steps (6%)
Writing checkpoint, step 18766290 at Wed Jan 28 14:23:37 2009
[22:28:53] Completed 17508 out of 250000 steps (7%)
[22:39:47] Completed 20008 out of 250000 steps (8%)
[22:50:33] Completed 22508 out of 250000 steps (9%)
Writing checkpoint, step 18773210 at Wed Jan 28 14:53:37 2009
[23:01:27] Completed 25008 out of 250000 steps (10%)
[23:12:18] Completed 27508 out of 250000 steps (11%)
[23:23:07] Completed 30008 out of 250000 steps (12%)
Writing checkpoint, step 18780130 at Wed Jan 28 15:23:38 2009
[23:34:00] Completed 32508 out of 250000 steps (13%)
[23:44:53] Completed 35008 out of 250000 steps (14%)
Writing checkpoint, step 18787030 at Wed Jan 28 15:53:38 2009
[23:55:42] Completed 37508 out of 250000 steps (15%)
[00:06:32] Completed 40008 out of 250000 steps (16%)
[00:17:22] Completed 42508 out of 250000 steps (17%)
Writing checkpoint, step 18793950 at Wed Jan 28 16:23:36 2009
[00:28:11] Completed 45008 out of 250000 steps (18%)
[00:39:00] Completed 47508 out of 250000 steps (19%)
[00:49:49] Completed 50008 out of 250000 steps (20%)
Writing checkpoint, step 18800890 at Wed Jan 28 16:53:37 2009
[01:00:37] Completed 52508 out of 250000 steps (21%)
[01:09:27] Completed 55008 out of 250000 steps (22%)
[01:17:42] Completed 57508 out of 250000 steps (23%)
Writing checkpoint, step 18809300 at Wed Jan 28 17:23:38 2009
[01:26:41] Completed 60008 out of 250000 steps (24%)
[01:37:26] Completed 62508 out of 250000 steps (25%)
[01:45:39] - Autosending finished units...
[01:45:39] Trying to send all finished work units
[01:45:39] + No unsent completed units remaining.
[01:45:39] - Autosend completed
[01:48:14] Completed 65008 out of 250000 steps (26%)
Writing checkpoint, step 18816260 at Wed Jan 28 17:53:37 2009
[01:59:01] Completed 67508 out of 250000 steps (27%)
[02:09:45] Completed 70008 out of 250000 steps (28%)
[02:20:32] Completed 72508 out of 250000 steps (29%)
Writing checkpoint, step 18823230 at Wed Jan 28 18:23:38 2009
[02:31:19] Completed 75008 out of 250000 steps (30%)
[02:42:04] Completed 77508 out of 250000 steps (31%)
[02:52:51] Completed 80008 out of 250000 steps (32%)
Writing checkpoint, step 18830190 at Wed Jan 28 18:53:37 2009
[03:03:35] Completed 82508 out of 250000 steps (33%)
[03:14:21] Completed 85008 out of 250000 steps (34%)
Writing checkpoint, step 18837160 at Wed Jan 28 19:23:38 2009
[03:25:09] Completed 87508 out of 250000 steps (35%)
[03:35:54] Completed 90008 out of 250000 steps (36%)
[03:46:39] Completed 92508 out of 250000 steps (37%)
Writing checkpoint, step 18844130 at Wed Jan 28 19:53:36 2009
[03:57:23] Completed 95008 out of 250000 steps (38%)
[04:08:15] Completed 97508 out of 250000 steps (39%)
[04:19:03] Completed 100008 out of 250000 steps (40%)
Writing checkpoint, step 18851070 at Wed Jan 28 20:23:37 2009
[04:29:49] Completed 102508 out of 250000 steps (41%)
[04:40:38] Completed 105008 out of 250000 steps (42%)
[04:51:25] Completed 107508 out of 250000 steps (43%)
Writing checkpoint, step 18858020 at Wed Jan 28 20:53:38 2009
[05:02:16] Completed 110008 out of 250000 steps (44%)
[05:13:02] Completed 112508 out of 250000 steps (45%)
Writing checkpoint, step 18864960 at Wed Jan 28 21:23:36 2009
[05:23:49] Completed 115008 out of 250000 steps (46%)
[05:34:36] Completed 117508 out of 250000 steps (47%)
[05:45:21] Completed 120008 out of 250000 steps (48%)
Writing checkpoint, step 18871930 at Wed Jan 28 21:53:38 2009
[05:56:09] Completed 122508 out of 250000 steps (49%)
[06:06:55] Completed 125008 out of 250000 steps (50%)
[06:17:42] Completed 127508 out of 250000 steps (51%)
Writing checkpoint, step 18878880 at Wed Jan 28 22:23:38 2009
[06:28:30] Completed 130008 out of 250000 steps (52%)
[06:39:17] Completed 132508 out of 250000 steps (53%)
[06:50:04] Completed 135008 out of 250000 steps (54%)
Writing checkpoint, step 18885840 at Wed Jan 28 22:53:39 2009
[07:00:52] Completed 137508 out of 250000 steps (55%)
[07:11:38] Completed 140008 out of 250000 steps (56%)
[07:22:24] Completed 142508 out of 250000 steps (57%)
Writing checkpoint, step 18892790 at Wed Jan 28 23:23:36 2009
[07:33:07] Completed 145008 out of 250000 steps (58%)
[07:43:53] Completed 147508 out of 250000 steps (59%)
[07:45:39] - Autosending finished units...
[07:45:39] Trying to send all finished work units
[07:45:39] + No unsent completed units remaining.
[07:45:39] - Autosend completed
Writing checkpoint, step 18899760 at Wed Jan 28 23:53:36 2009
[07:54:41] Completed 150008 out of 250000 steps (60%)
[08:05:31] Completed 152508 out of 250000 steps (61%)
[08:16:17] Completed 155008 out of 250000 steps (62%)
Writing checkpoint, step 18906700 at Thu Jan 29 00:23:36 2009
[08:27:04] Completed 157508 out of 250000 steps (63%)
[08:37:50] Completed 160008 out of 250000 steps (64%)
[08:48:36] Completed 162508 out of 250000 steps (65%)
Writing checkpoint, step 18913680 at Thu Jan 29 00:53:38 2009
[08:59:20] Completed 165008 out of 250000 steps (66%)
[09:10:07] Completed 167508 out of 250000 steps (67%)
[09:20:52] Completed 170008 out of 250000 steps (68%)
Writing checkpoint, step 18920650 at Thu Jan 29 01:23:37 2009
[09:31:37] Completed 172508 out of 250000 steps (69%)
[09:42:26] Completed 175008 out of 250000 steps (70%)
[09:53:12] Completed 177508 out of 250000 steps (71%)
Writing checkpoint, step 18927610 at Thu Jan 29 01:53:39 2009
[10:03:59] Completed 180008 out of 250000 steps (72%)
[10:14:45] Completed 182508 out of 250000 steps (73%)
Writing checkpoint, step 18934580 at Thu Jan 29 02:23:37 2009
[10:25:29] Completed 185008 out of 250000 steps (74%)
[10:36:12] Completed 187508 out of 250000 steps (75%)
[10:47:00] Completed 190008 out of 250000 steps (76%)
Writing checkpoint, step 18941540 at Thu Jan 29 02:53:37 2009
[10:57:48] Completed 192508 out of 250000 steps (77%)
[11:08:37] Completed 195008 out of 250000 steps (78%)
[11:19:26] Completed 197508 out of 250000 steps (79%)
Writing checkpoint, step 18948480 at Thu Jan 29 03:23:38 2009
[11:30:14] Completed 200008 out of 250000 steps (80%)
[11:41:03] Completed 202508 out of 250000 steps (81%)
[11:51:52] Completed 205008 out of 250000 steps (82%)
Writing checkpoint, step 18955420 at Thu Jan 29 03:53:38 2009
[12:02:39] Completed 207508 out of 250000 steps (83%)
[12:13:27] Completed 210008 out of 250000 steps (84%)
Writing checkpoint, step 18962370 at Thu Jan 29 04:23:38 2009
[12:24:14] Completed 212508 out of 250000 steps (85%)
[12:35:05] Completed 215008 out of 250000 steps (86%)
[12:45:52] Completed 217508 out of 250000 steps (87%)
Writing checkpoint, step 18969310 at Thu Jan 29 04:53:38 2009
[12:56:38] Completed 220008 out of 250000 steps (88%)
[13:07:26] Completed 222508 out of 250000 steps (89%)
[13:18:12] Completed 225008 out of 250000 steps (90%)
Writing checkpoint, step 18976270 at Thu Jan 29 05:23:37 2009
[13:28:57] Completed 227508 out of 250000 steps (91%)
[13:39:44] Completed 230008 out of 250000 steps (92%)
[13:45:39] - Autosending finished units...
[13:45:39] Trying to send all finished work units
[13:45:39] + No unsent completed units remaining.
[13:45:39] - Autosend completed
[13:50:34] Completed 232508 out of 250000 steps (93%)
Writing checkpoint, step 18983300 at Thu Jan 29 05:53:37 2009
[13:59:51] Completed 235008 out of 250000 steps (94%)
[14:10:10] Completed 237508 out of 250000 steps (95%)
[14:21:46] Completed 240008 out of 250000 steps (96%)
Writing checkpoint, step 18990410 at Thu Jan 29 06:23:37 2009
[14:33:22] Completed 242508 out of 250000 steps (97%)
[14:44:55] Completed 245008 out of 250000 steps (98%)
Writing checkpoint, step 18996880 at Thu Jan 29 06:53:39 2009
[14:56:33] Completed 247508 out of 250000 steps (99%)
Writing checkpoint, step 19000002 at Thu Jan 29 07:08:08 2009
Writing final coordinates.
Average load imbalance: 8.0 %
Part of the total run time spent waiting due to load imbalance: 4.6 %
Steps where the load balancing was limited by -rdd, -rcon and/or -dds: Z 0 %
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 63873.000 63873.000 100.0
17h44:33
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 55.772 8.544 0.676 35.485
gcq#0: Thanx for Using GROMACS - Have a Nice Day
[15:09:09]
[15:09:09] Finished Work Unit:
[15:09:09] - Reading up to 21187728 from "work/wudata_02.trr": Read 21187728
[15:09:09] trr file hash check passed.
[15:09:09] - Reading up to 27149116 from "work/wudata_02.xtc": Read 27149116
[15:09:09] xtc file hash check passed.
[15:09:09] edr file hash check passed.
[15:09:09] logfile size: 178254
[15:09:09] Leaving Run
[15:09:10] - Writing 48722922 bytes of core data to disk...
[15:09:10] ... Done.
[15:09:17] - Shutting down core
[19:45:39] - Autosending finished units...
[19:45:39] Trying to send all finished work units
[19:45:39] + No unsent completed units remaining.
[19:45:39] - Autosend completed
[01:45:39] - Autosending finished units...
[01:45:39] Trying to send all finished work units
[01:45:39] + No unsent completed units remaining.
[01:45:39] - Autosend completed
[07:45:39] - Autosending finished units...
[07:45:39] Trying to send all finished work units
[07:45:39] + No unsent completed units remaining.
[07:45:39] - Autosend completed
[13:45:39] - Autosending finished units...
[13:45:39] Trying to send all finished work units
[13:45:39] + No unsent completed units remaining.
[13:45:39] - Autosend completed
Code: Select all
[01:23:09] Preparing to commence simulation
[01:23:09] - Ensuring status. Please wait.
[01:23:10] Called DecompressByteArray: compressed_data_size=4822646 data_size=24058077, decompressed_data_size=24058077 diff=0
[01:23:10] - Digital signature verified
[01:23:10]
[01:23:10] Project: 2671 (Run 38, Clone 3, Gen 76)
[01:23:10]
[01:23:10] Assembly optimizations on if available.
[01:23:10] Entering M.D.
[01:23:20] (Run 38, Clone 3, Gen 76)
[01:23:20]
[01:23:20] Entering M.D.
NNODES=4, MYRANK=0, HOSTNAME=adak-Rocketfish
NNODES=4, MYRANK=3, HOSTNAME=adak-Rocketfish
NNODES=4, MYRANK=1, HOSTNAME=adak-Rocketfish
NNODES=4, MYRANK=2, HOSTNAME=adak-Rocketfish
NODEID=0 argc=19
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 3.3.99_development_200800503 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
:-) mdrun (-:
Reading file work/wudata_07.tpr, VERSION 3.3.99_development_20070618 (single precision)
NODEID=1 argc=19
NODEID=3 argc=19
NODEID=2 argc=19
Note: tpx file_version 48, software version 56
Making 1D domain decomposition 1 x 1 x 4
starting mdrun '22908 system in water'
250000 steps, 500.0 ps.
[01:45:18] Completed 5008 out of 250000 steps (2%)
[01:46:23] - Autosending finished units...
[01:46:23] Trying to send all finished work units
[01:46:23] + No unsent completed units remaining.
[01:46:23] - Autosend completed
Writing checkpoint, step 19006890 at Wed Jan 28 17:53:29 2009
[01:56:11] Completed 7508 out of 250000 steps (3%)
[02:07:08] Completed 10008 out of 250000 steps (4%)
[02:18:04] Completed 12508 out of 250000 steps (5%)
Writing checkpoint, step 19013750 at Wed Jan 28 18:23:29 2009
[02:28:56] Completed 15008 out of 250000 steps (6%)
[02:39:53] Completed 17508 out of 250000 steps (7%)
[02:50:47] Completed 20008 out of 250000 steps (8%)
Writing checkpoint, step 19020630 at Wed Jan 28 18:53:30 2009
[03:01:42] Completed 22508 out of 250000 steps (9%)
[03:12:37] Completed 25008 out of 250000 steps (10%)
[03:23:30] Completed 27508 out of 250000 steps (11%)
Writing checkpoint, step 19027510 at Wed Jan 28 19:23:31 2009
[03:34:26] Completed 30008 out of 250000 steps (12%)
[03:45:23] Completed 32508 out of 250000 steps (13%)
Writing checkpoint, step 19034360 at Wed Jan 28 19:53:30 2009
[03:56:19] Completed 35008 out of 250000 steps (14%)
[04:07:13] Completed 37508 out of 250000 steps (15%)
[04:18:09] Completed 40008 out of 250000 steps (16%)
Writing checkpoint, step 19041230 at Wed Jan 28 20:23:29 2009
[04:29:07] Completed 42508 out of 250000 steps (17%)
[04:40:01] Completed 45008 out of 250000 steps (18%)
[04:50:54] Completed 47508 out of 250000 steps (19%)
Writing checkpoint, step 19048100 at Wed Jan 28 20:53:29 2009
[05:01:49] Completed 50008 out of 250000 steps (20%)
[05:12:42] Completed 52508 out of 250000 steps (21%)
Writing checkpoint, step 19054980 at Wed Jan 28 21:23:29 2009
[05:23:37] Completed 55008 out of 250000 steps (22%)
[05:34:33] Completed 57508 out of 250000 steps (23%)
[05:45:29] Completed 60008 out of 250000 steps (24%)
Writing checkpoint, step 19061840 at Wed Jan 28 21:53:30 2009
[05:56:26] Completed 62508 out of 250000 steps (25%)
[06:07:19] Completed 65008 out of 250000 steps (26%)
[06:18:12] Completed 67508 out of 250000 steps (27%)
Writing checkpoint, step 19068720 at Wed Jan 28 22:23:29 2009
[06:29:08] Completed 70008 out of 250000 steps (28%)
[06:40:02] Completed 72508 out of 250000 steps (29%)
[06:50:56] Completed 75008 out of 250000 steps (30%)
Writing checkpoint, step 19075590 at Wed Jan 28 22:53:29 2009
[07:01:50] Completed 77508 out of 250000 steps (31%)
[07:12:46] Completed 80008 out of 250000 steps (32%)
Writing checkpoint, step 19082480 at Wed Jan 28 23:23:30 2009
[07:23:38] Completed 82508 out of 250000 steps (33%)
[07:34:33] Completed 85008 out of 250000 steps (34%)
[07:45:29] Completed 87508 out of 250000 steps (35%)
[07:46:23] - Autosending finished units...
[07:46:23] Trying to send all finished work units
[07:46:23] + No unsent completed units remaining.
[07:46:23] - Autosend completed
Writing checkpoint, step 19089350 at Wed Jan 28 23:53:29 2009
[07:56:21] Completed 90008 out of 250000 steps (36%)
[08:07:15] Completed 92508 out of 250000 steps (37%)
[08:18:09] Completed 95008 out of 250000 steps (38%)
Writing checkpoint, step 19096240 at Thu Jan 29 00:23:29 2009
[08:29:01] Completed 97508 out of 250000 steps (39%)
[08:39:56] Completed 100008 out of 250000 steps (40%)
[08:50:49] Completed 102508 out of 250000 steps (41%)
Writing checkpoint, step 19103120 at Thu Jan 29 00:53:30 2009
[09:01:45] Completed 105008 out of 250000 steps (42%)
[09:12:41] Completed 107508 out of 250000 steps (43%)
Writing checkpoint, step 19109970 at Thu Jan 29 01:23:30 2009
[09:23:41] Completed 110008 out of 250000 steps (44%)
[09:34:35] Completed 112508 out of 250000 steps (45%)
[09:45:30] Completed 115008 out of 250000 steps (46%)
Writing checkpoint, step 19116840 at Thu Jan 29 01:53:29 2009
[09:56:23] Completed 117508 out of 250000 steps (47%)
[10:07:16] Completed 120008 out of 250000 steps (48%)
[10:18:16] Completed 122508 out of 250000 steps (49%)
Writing checkpoint, step 19123700 at Thu Jan 29 02:23:30 2009
[10:29:14] Completed 125008 out of 250000 steps (50%)
[10:40:12] Completed 127508 out of 250000 steps (51%)
[10:51:05] Completed 130008 out of 250000 steps (52%)
Writing checkpoint, step 19130560 at Thu Jan 29 02:53:29 2009
[11:01:58] Completed 132508 out of 250000 steps (53%)
[11:12:51] Completed 135008 out of 250000 steps (54%)
Writing checkpoint, step 19137450 at Thu Jan 29 03:23:29 2009
[11:23:46] Completed 137508 out of 250000 steps (55%)
[11:34:39] Completed 140008 out of 250000 steps (56%)
[11:45:33] Completed 142508 out of 250000 steps (57%)
Writing checkpoint, step 19144330 at Thu Jan 29 03:53:30 2009
[11:56:27] Completed 145008 out of 250000 steps (58%)
[12:07:20] Completed 147508 out of 250000 steps (59%)
[12:18:15] Completed 150008 out of 250000 steps (60%)
Writing checkpoint, step 19151210 at Thu Jan 29 04:23:29 2009
[12:29:11] Completed 152508 out of 250000 steps (61%)
[12:40:04] Completed 155008 out of 250000 steps (62%)
[12:50:58] Completed 157508 out of 250000 steps (63%)
Writing checkpoint, step 19158090 at Thu Jan 29 04:53:29 2009
[13:01:51] Completed 160008 out of 250000 steps (64%)
[13:12:45] Completed 162508 out of 250000 steps (65%)
Writing checkpoint, step 19164970 at Thu Jan 29 05:23:30 2009
[13:23:41] Completed 165008 out of 250000 steps (66%)
[13:34:35] Completed 167508 out of 250000 steps (67%)
[13:45:25] Completed 170008 out of 250000 steps (68%)
[13:46:23] - Autosending finished units...
[13:46:23] Trying to send all finished work units
[13:46:23] + No unsent completed units remaining.
[13:46:23] - Autosend completed
Writing checkpoint, step 19171930 at Thu Jan 29 05:53:28 2009
[13:55:36] Completed 172508 out of 250000 steps (69%)
[14:04:51] Completed 175008 out of 250000 steps (70%)
[14:16:33] Completed 177508 out of 250000 steps (71%)
Writing checkpoint, step 19178990 at Thu Jan 29 06:23:30 2009
[14:28:18] Completed 180008 out of 250000 steps (72%)
[14:40:04] Completed 182508 out of 250000 steps (73%)
[14:51:46] Completed 185008 out of 250000 steps (74%)
Writing checkpoint, step 19185380 at Thu Jan 29 06:53:29 2009
[15:03:30] Completed 187508 out of 250000 steps (75%)
[15:13:42] Completed 190008 out of 250000 steps (76%)
[15:22:53] Completed 192508 out of 250000 steps (77%)
Writing checkpoint, step 19192680 at Thu Jan 29 07:23:30 2009
[15:32:00] Completed 195008 out of 250000 steps (78%)
[15:41:10] Completed 197508 out of 250000 steps (79%)
[15:49:05] Completed 200008 out of 250000 steps (80%)
Writing checkpoint, step 19201880 at Thu Jan 29 07:53:29 2009
[15:54:58] Completed 202508 out of 250000 steps (81%)
[16:00:51] Completed 205008 out of 250000 steps (82%)
[16:06:44] Completed 207508 out of 250000 steps (83%)
[16:12:36] Completed 210008 out of 250000 steps (84%)
[16:18:29] Completed 212508 out of 250000 steps (85%)
Writing checkpoint, step 19214630 at Thu Jan 29 08:23:28 2009
[16:24:22] Completed 215008 out of 250000 steps (86%)
[16:30:14] Completed 217508 out of 250000 steps (87%)
[16:36:07] Completed 220008 out of 250000 steps (88%)
[16:41:59] Completed 222508 out of 250000 steps (89%)
[16:47:52] Completed 225008 out of 250000 steps (90%)
Writing checkpoint, step 19227400 at Thu Jan 29 08:53:29 2009
[16:53:44] Completed 227508 out of 250000 steps (91%)
[16:59:37] Completed 230008 out of 250000 steps (92%)
[17:05:29] Completed 232508 out of 250000 steps (93%)
[17:11:21] Completed 235008 out of 250000 steps (94%)
[17:17:14] Completed 237508 out of 250000 steps (95%)
[17:23:06] Completed 240008 out of 250000 steps (96%)
Writing checkpoint, step 19240170 at Thu Jan 29 09:23:29 2009
[17:28:59] Completed 242508 out of 250000 steps (97%)
[17:34:51] Completed 245008 out of 250000 steps (98%)
[17:40:43] Completed 247508 out of 250000 steps (99%)
Writing checkpoint, step 19250002 at Thu Jan 29 09:46:35 2009
Writing final coordinates.
Average load imbalance: 6.7 %
Part of the total run time spent waiting due to load imbalance: 4.0 %
Steps where the load balancing was limited by -rdd, -rcon and/or -dds: Z 0 %
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 58988.000 58988.000 100.0
16h23:08
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 61.038 9.264 0.732 32.771
gcq#0: Thanx for Using GROMACS - Have a Nice Day
[17:47:36]
[17:47:36] Finished Work Unit:
[17:47:36] - Reading up to 21201120 from "work/wudata_07.trr": Read 21201120
[17:47:37] trr file hash check passed.
[17:47:37] - Reading up to 27171720 from "work/wudata_07.xtc": Read 27171720
[17:47:37] xtc file hash check passed.
[17:47:37] edr file hash check passed.
[17:47:37] logfile size: 178065
[17:47:37] Leaving Run
[17:47:42] - Writing 48756569 bytes of core data to disk...
[17:47:42] ... Done.
[17:47:48] - Shutting down core
[19:46:23] - Autosending finished units...
[19:46:23] Trying to send all finished work units
[19:46:23] + No unsent completed units remaining.
[19:46:23] - Autosend completed
[01:46:23] - Autosending finished units...
[01:46:23] Trying to send all finished work units
[01:46:23] + No unsent completed units remaining.
[01:46:23] - Autosend completed
[07:46:23] - Autosending finished units...
[07:46:23] Trying to send all finished work units
[07:46:23] + No unsent completed units remaining.
[07:46:23] - Autosend completed
[13:46:23] - Autosending finished units...
[13:46:23] Trying to send all finished work units
[13:46:23] + No unsent completed units remaining.
[13:46:23] - Autosend completed