(on an otherwise stable h/w)
Code: Select all
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 12 08:16:53 UTC]
# Linux SMP Console Edition ###################################################
###############################################################################
Folding@Home Client Version 6.23 Beta R1
http://folding.stanford.edu
###############################################################################
###############################################################################
Launch directory: /fah/clients/fah
Executable: ./fah6
Arguments: -oneunit -verbosity 9 -smp 8 -forceasm
Warning:
By using the -forceasm flag, you are overriding
safeguards in the program. If you did not intend to
do this, please restart the program without -forceasm.
If work units are not completing fully (and particularly
if your machine is overclocked), then please discontinue
use of the flag.
[08:16:53] - Ask before connecting: No
[08:16:53] - User name: tear (Team 100259)
[08:16:53] - User ID: F50131C3A5301BE
[08:16:53] - Machine ID: 14
[08:16:53]
[08:16:54] Loaded queue successfully.
[08:16:54] - Preparing to get new work unit...
[08:16:54] - Autosending finished units... [January 12 08:16:54 UTC]
[08:16:54] + Attempting to get work packet
[08:16:54] Trying to send all finished work units
[08:16:54] + No unsent completed units remaining.
[08:16:54] - Will indicate memory of 2012 MB
[08:16:54] - Autosend completed
[08:16:54] - Connecting to assignment server
[08:16:54] Connecting to http://assign.stanford.edu:8080/
[08:16:54] Posted data.
[08:16:54] Initial: 43AB; - Successful: assigned to (171.67.108.24).
[08:16:54] + News From Folding@Home: Welcome to Folding@Home
[08:16:54] Loaded queue successfully.
[08:16:54] Connecting to http://171.67.108.24:8080/
[08:17:01] Posted data.
[08:17:01] Initial: 0000; - Receiving payload (expected size: 4830666)
[08:17:04] - Downloaded at ~1572 kB/s
[08:17:04] - Averaged speed for that direction ~1374 kB/s
[08:17:04] + Received work.
[08:17:04] + Closed connections
[08:17:04]
[08:17:04] + Processing work unit
[08:17:04] Core required: FahCore_a2.exe
[08:17:04] Core found.
[08:17:04] Working on queue slot 04 [January 12 08:17:04 UTC]
[08:17:04] + Working ...
[08:17:04] - Calling './mpiexec -np 8 -host 127.0.0.1 ./FahCore_a2.exe -dir work/ -suffix 04 -nocpulock -checkpoint 15 -forceasm -verbose -lifeline 8826 -version 623'
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
Warning: Ignoring unknown arg
[08:17:04]
[08:17:04] *------------------------------*
[08:17:04] Folding@Home Gromacs SMP Core
[08:17:04] Version 2.01 (Wed Aug 13 13:11:25 PDT 2008)
[08:17:04]
[08:17:04] Preparing to commence simulation
[08:17:04] - Ensuring status. Please wait.
[08:17:14] - Assembly optimizations manually forced on.
[08:17:14] - Not checking prior termination.
[08:17:15] - Expanded 4830154 -> 24044301 (decompressed 497.7 percent)
[08:17:15] Called DecompressByteArray: compressed_data_size=4830154 data_size=24044301, decompressed_data_size=24044301 diff=0
[08:17:15] - Digital signature verified
[08:17:15]
[08:17:15] Project: 2671 (Run 23, Clone 6, Gen 58)
[08:17:15]
[08:17:15] Assembly optimizations on if available.
[08:17:15] Entering M.D.
NNODES=8, MYRANK=0, HOSTNAME=carnage
NNODES=8, MYRANK=3, HOSTNAME=carnage
NNODES=8, MYRANK=1, HOSTNAME=carnage
NNODES=8, MYRANK=5, HOSTNAME=carnage
NNODES=8, MYRANK=7, HOSTNAME=carnage
NNODES=8, MYRANK=6, HOSTNAME=carnage
NNODES=8, MYRANK=4, HOSTNAME=carnage
NNODES=8, MYRANK=2, HOSTNAME=carnage
NODEID=4 argc=19
NODEID=5 argc=19
NODEID=0 argc=19
NODEID=1 argc=19
NODEID=6 argc=19
NODEID=7 argc=19
NODEID=2 argc=19
NODEID=3 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_04.tpr, VERSION 3.3.99_development_20070618 (single precision)
Note: tpx file_version 48, software version 56
Making 3D domain decomposition 2 x 2 x 2
starting mdrun '22911 system in water'
250000 steps, 500.0 ps.
[08:22:24] Completed 2500 out of 250000 steps (1%)
[08:26:14] Completed 5000 out of 250000 steps (2%)
[08:30:04] Completed 7500 out of 250000 steps (3%)
Writing checkpoint, step 14509000 at Mon Jan 12 01:32:23 2009
[08:33:55] Completed 10000 out of 250000 steps (4%)
[08:37:46] Completed 12500 out of 250000 steps (5%)
[08:41:36] Completed 15000 out of 250000 steps (6%)
[08:45:27] Completed 17500 out of 250000 steps (7%)
Writing checkpoint, step 14518760 at Mon Jan 12 01:47:23 2009
[08:49:17] Completed 20000 out of 250000 steps (8%)
[08:53:08] Completed 22500 out of 250000 steps (9%)
[08:56:58] Completed 25000 out of 250000 steps (10%)
[09:00:47] Completed 27500 out of 250000 steps (11%)
Writing checkpoint, step 14528540 at Mon Jan 12 02:02:24 2009
[09:04:38] Completed 30000 out of 250000 steps (12%)
[09:08:28] Completed 32500 out of 250000 steps (13%)
[09:12:19] Completed 35000 out of 250000 steps (14%)
[09:16:09] Completed 37500 out of 250000 steps (15%)
Writing checkpoint, step 14538300 at Mon Jan 12 02:17:23 2009
[09:20:00] Completed 40000 out of 250000 steps (16%)
[09:23:52] Completed 42500 out of 250000 steps (17%)
[09:27:41] Completed 45000 out of 250000 steps (18%)
[09:31:31] Completed 47500 out of 250000 steps (19%)
Writing checkpoint, step 14548070 at Mon Jan 12 02:32:23 2009
[09:35:22] Completed 50000 out of 250000 steps (20%)
[09:39:12] Completed 52500 out of 250000 steps (21%)
[09:43:00] Completed 55000 out of 250000 steps (22%)
[09:46:49] Completed 57500 out of 250000 steps (23%)
Writing checkpoint, step 14557870 at Mon Jan 12 02:47:23 2009
[09:50:38] Completed 60000 out of 250000 steps (24%)
[09:54:28] Completed 62500 out of 250000 steps (25%)
[09:58:18] Completed 65000 out of 250000 steps (26%)
[10:02:08] Completed 67500 out of 250000 steps (27%)
Writing checkpoint, step 14567660 at Mon Jan 12 03:02:23 2009
[10:05:57] Completed 70000 out of 250000 steps (28%)
[10:09:47] Completed 72500 out of 250000 steps (29%)
[10:13:37] Completed 75000 out of 250000 steps (30%)
Writing checkpoint, step 14577430 at Mon Jan 12 03:17:23 2009
[10:17:30] Completed 77500 out of 250000 steps (31%)
[10:21:20] Completed 80000 out of 250000 steps (32%)
[10:25:12] Completed 82500 out of 250000 steps (33%)
[10:29:03] Completed 85000 out of 250000 steps (34%)
Writing checkpoint, step 14587150 at Mon Jan 12 03:32:23 2009
[10:32:56] Completed 87500 out of 250000 steps (35%)
[10:36:48] Completed 90000 out of 250000 steps (36%)
[10:40:41] Completed 92500 out of 250000 steps (37%)
[10:44:33] Completed 95000 out of 250000 steps (38%)
Writing checkpoint, step 14596820 at Mon Jan 12 03:47:23 2009
[10:48:27] Completed 97500 out of 250000 steps (39%)
[10:52:23] Completed 100000 out of 250000 steps (40%)
[10:56:17] Completed 102500 out of 250000 steps (41%)
[11:00:13] Completed 105000 out of 250000 steps (42%)
Writing checkpoint, step 14606380 at Mon Jan 12 04:02:23 2009
[11:04:08] Completed 107500 out of 250000 steps (43%)
[11:08:03] Completed 110000 out of 250000 steps (44%)
[11:11:59] Completed 112500 out of 250000 steps (45%)
[11:16:06] Completed 115000 out of 250000 steps (46%)
Writing checkpoint, step 14615810 at Mon Jan 12 04:17:23 2009
[11:20:02] Completed 117500 out of 250000 steps (47%)
[11:23:57] Completed 120000 out of 250000 steps (48%)
[11:27:53] Completed 122500 out of 250000 steps (49%)
[11:31:49] Completed 125000 out of 250000 steps (50%)
Writing checkpoint, step 14625370 at Mon Jan 12 04:32:23 2009
[11:35:44] Completed 127500 out of 250000 steps (51%)
[11:39:40] Completed 130000 out of 250000 steps (52%)
[11:43:34] Completed 132500 out of 250000 steps (53%)
Writing checkpoint, step 14634920 at Mon Jan 12 04:47:23 2009
[11:47:31] Completed 135000 out of 250000 steps (54%)
[11:51:26] Completed 137500 out of 250000 steps (55%)
[11:55:22] Completed 140000 out of 250000 steps (56%)
[11:59:18] Completed 142500 out of 250000 steps (57%)
Writing checkpoint, step 14644460 at Mon Jan 12 05:02:23 2009
[12:03:15] Completed 145000 out of 250000 steps (58%)
[12:07:12] Completed 147500 out of 250000 steps (59%)
[12:11:08] Completed 150000 out of 250000 steps (60%)
[12:15:04] Completed 152500 out of 250000 steps (61%)
Writing checkpoint, step 14653970 at Mon Jan 12 05:17:23 2009
[12:19:00] Completed 155000 out of 250000 steps (62%)
[12:22:57] Completed 157500 out of 250000 steps (63%)
[12:26:53] Completed 160000 out of 250000 steps (64%)
[12:30:50] Completed 162500 out of 250000 steps (65%)
Writing checkpoint, step 14663490 at Mon Jan 12 05:32:23 2009
[12:34:46] Completed 165000 out of 250000 steps (66%)
[12:38:41] Completed 167500 out of 250000 steps (67%)
[12:42:35] Completed 170000 out of 250000 steps (68%)
[12:46:30] Completed 172500 out of 250000 steps (69%)
Writing checkpoint, step 14673070 at Mon Jan 12 05:47:23 2009
[12:50:26] Completed 175000 out of 250000 steps (70%)
[12:54:21] Completed 177500 out of 250000 steps (71%)
[12:58:16] Completed 180000 out of 250000 steps (72%)
[13:02:11] Completed 182500 out of 250000 steps (73%)
Writing checkpoint, step 14682630 at Mon Jan 12 06:02:23 2009
[13:06:04] Completed 185000 out of 250000 steps (74%)
[13:09:58] Completed 187500 out of 250000 steps (75%)
[13:13:52] Completed 190000 out of 250000 steps (76%)
Writing checkpoint, step 14692260 at Mon Jan 12 06:17:23 2009
[13:17:46] Completed 192500 out of 250000 steps (77%)
[13:21:40] Completed 195000 out of 250000 steps (78%)
[13:25:33] Completed 197500 out of 250000 steps (79%)
[13:29:26] Completed 200000 out of 250000 steps (80%)
Writing checkpoint, step 14701900 at Mon Jan 12 06:32:23 2009
[13:33:19] Completed 202500 out of 250000 steps (81%)
[13:37:13] Completed 205000 out of 250000 steps (82%)
[13:41:06] Completed 207500 out of 250000 steps (83%)
[13:44:58] Completed 210000 out of 250000 steps (84%)
Writing checkpoint, step 14711550 at Mon Jan 12 06:47:23 2009
[13:48:52] Completed 212500 out of 250000 steps (85%)
[13:52:46] Completed 215000 out of 250000 steps (86%)
[13:56:39] Completed 217500 out of 250000 steps (87%)
[14:00:32] Completed 220000 out of 250000 steps (88%)
Writing checkpoint, step 14721210 at Mon Jan 12 07:02:23 2009
[14:04:23] Completed 222500 out of 250000 steps (89%)
[14:08:14] Completed 225000 out of 250000 steps (90%)
[14:12:06] Completed 227500 out of 250000 steps (91%)
[14:15:58] Completed 230000 out of 250000 steps (92%)
[14:16:52] - Autosending finished units... [January 12 14:16:52 UTC]
[14:16:52] Trying to send all finished work units
[14:16:52] + No unsent completed units remaining.
[14:16:52] - Autosend completed
Writing checkpoint, step 14730910 at Mon Jan 12 07:17:23 2009
[14:19:50] Completed 232500 out of 250000 steps (93%)
Step 14734376, time 29468.8 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.007249, max 0.271232 (between atoms 14745 and 14747)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
14745 14747 90.0 0.1090 0.1386 0.1090
Step 14734377, time 29468.8 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.119343, max 4.144156 (between atoms 14745 and 14747)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
14742 14743 90.0 0.1090 0.1850 0.1090
14745 14747 90.0 0.1386 0.5607 0.1090
Step 14734378, time 29468.8 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 7.324972, max 246.545578 (between atoms 14739 and 14741)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
14742 14743 133.9 0.1850 13.0156 0.1090
14745 14747 90.0 0.5607 0.1521 0.1090
Warning: 1-4 interaction between 14734 and 14741 at distance 44.168 which is larger than the 1-4 table size 2.200 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Step 14734379, time 29468.8 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 32676477003324.074219, max 852624089808896.000000 (between atoms 7063 and 7064)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
14820 14821 90.0 0.1090 217936576512.0000 0.1090
7656 7657 90.0 0.1090 24039.5059 0.1090
7638 7639 90.0 0.1010 40742.9180 0.1010
7638 7640 90.1 0.1010 3672.6196 0.1010
6993 6994 90.0 0.1090 5.3214 0.1090
7529 7530 90.0 0.1080 528370434048.0000 0.1080
14788 14789 90.0 0.1010 67.8477 0.1010
7045 7046 90.0 0.1090 370782994432.0000 0.1090
7045 7047 90.0 0.1090 1130086656.0000 0.1090
14726 14728 90.0 0.1090 11369362.0000 0.1090
14827 14828 90.0 0.1010 14538203201536.0000 0.1010
14831 14833 90.0 0.1090 665244.8750 0.1090
14843 14844 90.0 0.1080 3.7781 0.1080
14769 14770 90.0 0.1010 2833770.2500 0.1010
14847 14848 90.0 0.1010 34466246656.0000 0.1010
14849 14850 90.0 0.1090 46028852.0000 0.1090
14876 14877 90.0 0.1080 33527195648.0000 0.1080
14758 14759 90.0 0.1090 423150144.0000 0.1090
14758 14760 90.0 0.1090 74143391744.0000 0.1090
7037 7038 90.0 0.1090 1.1305 0.1090
7042 7044 90.0 0.1090 10012879.0000 0.1090
7061 7062 90.0 0.1090 4.4972 0.1090
7063 7064 90.0 0.1090 92936020688896.0000 0.1090
7063 7065 90.0 0.1090 77487316926464.0000 0.1090
7071 7072 90.0 0.1010 575116.3750 0.1010
14732 14733 90.0 0.1010 12317161472.0000 0.1010
14739 14741 90.0 26.9825 1593.8702 0.1090
14742 14744 90.0 1.9449 34274791129088.0000 0.1090
14745 14747 90.0 0.1521 0.3578 0.1090
14895 14896 90.6 0.0960 991.0515 0.0960
14724 14725 90.0 0.1090 6540954112.0000 0.1090
14897 14898 146.0 0.1080 6.9648 0.1080
14884 14885 90.0 0.1090 1.8465 0.1090
14890 14891 90.0 0.1080 2238406.5000 0.1080
t = 29468.760 ps: Water molecule starting at atom 46129 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
Step 14734380:
The charge group starting at atom 14818 moved than the distance allowed by the domain decomposition (1.200000) in direction Z
distance out of cell -205.282318
Old coordinates: 5.845 1.266 10.021
New coordinates: -59.207 3.587 -197.859
Old cell boundaries in direction Z: 7.514 15.000
New cell boundaries in direction Z: 7.423 15.000
-------------------------------------------------------
Program mdrun, VERSION 3.3.99_development_200800503
Source code file: domdec.c, line: 2644
Fatal error:
A charge group move too far between two domain decomposition steps
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
Error on node 5, will try to stop all the nodes
Halting parallel program mdrun on CPU 5 out of 8
gcq#0: Thanx for Using GROMACS - Have a Nice Day
[cli_5]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5
[14:22:45]
[14:22:45] Folding@home Core Shutdown: INTERRUPTED
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 102) - process 0
[cli_1]: aborting job:
Fatal error in MPI_Sendrecv: Error message texts are not available
[cli_3]: aborting job:
Fatal error in MPI_Sendrecv: Error message texts are not available
[cli_4]: aborting job:
Fatal error in MPI_Sendrecv: Error message texts are not available
[0]0:Return code = 102
[0]1:Return code = 1
[0]2:Return code = 0, signaled with Quit
[0]3:Return code = 1
[0]4:Return code = 1
[0]5:Return code = 255
[0]6:Return code = 0, signaled with Quit
[0]7:Return code = 0, signaled with Quit
[14:22:53] CoreStatus = FF (255)
[14:22:53] Sending work to server
[14:22:53] Project: 2671 (Run 23, Clone 6, Gen 58)
[14:22:53] - Error: Could not get length of results file work/wuresults_04.dat
[14:22:53] - Error: Could not read unit 04 file. Removing from queue.
[14:22:53] Trying to send all finished work units
[14:22:53] + No unsent completed units remaining.
[14:22:53] + -oneunit flag given and have now finished a unit. Exiting.- Preparing to get new work unit...
[14:22:53] + Attempting to get work packet
[14:22:53] ***** Got a SIGTERM signal (15)
[14:22:53] - Will indicate memory of 2012 MB
[14:22:53] Killing all core threads
[14:22:53] - Connecting to assignment server
Folding@Home Client Shutdown.
[14:22:53] Connecting to http://assign.stanford.edu:8080/In case of questions you know where to find me.
Cheers,
tear