Project: 2671 (Run 25, Clone 84, Gen 22)
Posted: Wed May 06, 2009 9:14 pm
I think this one may be bad, it exited on its on. I tried restarting it and this is what I got...
Code: Select all
[12:15:21] Project: 2671 (Run - Digital signature verified
[12:15:21]
[12:15:21] Project: 2671 (Run 25, Clone 84, Gen 22)
[12:15:21]
[12:15:21] Entering M.D.
[12:15:31] lone 84, Gen 22)
[12:15:31]
[12:15:31] Entering M.D.
NNODES=8, MYRANK=0, HOSTNAME=i7-living-room
NNODES=8, MYRANK=1, HOSTNAME=i7-living-room
NNODES=8, MYRANK=5, HOSTNAME=i7-living-room
NNODES=8, MYRANK=2, HOSTNAME=i7-living-room
NNODES=8, MYRANK=3, HOSTNAME=i7-living-room
NNODES=8, MYRANK=4, HOSTNAME=i7-living-room
NNODES=8, MYRANK=7, HOSTNAME=i7-living-room
NNODES=8, MYRANK=6, HOSTNAME=i7-living-room
NODEID=0 argc=20
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 4.0.99_development_20090307 (-:
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_00.tpr, VERSION 3.3.99_development_20070618 (single precision)
NODEID=1 argc=20
NODEID=2 argc=20
NODEID=3 argc=20
NODEID=4 argc=20
NODEID=6 argc=20
NODEID=7 argc=20
NODEID=5 argc=20
Note: tpx file_version 48, software version 64
NOTE: The tpr file used for this simulation is in an old format, for less memory usage and possibly more performance create a new tpr file with an up to date version of grompp
Making 3D domain decomposition 2 x 2 x 2
starting mdrun '22911 system in water'
5750000 steps, 11500.0 ps (continuing from step 5500000, 11000.0 ps).
[12:21:25] pleted 2500 out of 250000 steps (1%)
[12:27:12] Completed 5000 out of 250000 steps (2%)
[12:32:57] Completed 7500 out of 250000 steps (3%)
[12:38:42] Completed 10000 out of 250000 steps (4%)
[12:44:27] Completed 12500 out of 250000 steps (5%)
[12:50:14] Completed 15000 out of 250000 steps (6%)
[12:56:00] Completed 17500 out of 250000 steps (7%)
[13:01:45] Completed 20000 out of 250000 steps (8%)
[13:07:31] Completed 22500 out of 250000 steps (9%)
[13:13:16] Completed 25000 out of 250000 steps (10%)
[13:19:03] Completed 27500 out of 250000 steps (11%)
[13:24:49] Completed 30000 out of 250000 steps (12%)
[13:30:34] Completed 32500 out of 250000 steps (13%)
[13:36:19] Completed 35000 out of 250000 steps (14%)
[13:42:05] Completed 37500 out of 250000 steps (15%)
[13:47:52] Completed 40000 out of 250000 steps (16%)
[13:53:36] Completed 42500 out of 250000 steps (17%)
[13:59:22] Completed 45000 out of 250000 steps (18%)
[14:05:08] Completed 47500 out of 250000 steps (19%)
[14:10:54] Completed 50000 out of 250000 steps (20%)
[14:16:40] Completed 52500 out of 250000 steps (21%)
[14:22:26] Completed 55000 out of 250000 steps (22%)
[14:28:11] Completed 57500 out of 250000 steps (23%)
[14:33:55] Completed 60000 out of 250000 steps (24%)
[14:39:40] Completed 62500 out of 250000 steps (25%)
[14:45:25] Completed 65000 out of 250000 steps (26%)
[14:51:10] Completed 67500 out of 250000 steps (27%)
[14:56:54] Completed 70000 out of 250000 steps (28%)
[15:02:38] Completed 72500 out of 250000 steps (29%)
[15:08:25] Completed 75000 out of 250000 steps (30%)
[15:14:08] Completed 77500 out of 250000 steps (31%)
[15:19:53] Completed 80000 out of 250000 steps (32%)
[15:25:40] Completed 82500 out of 250000 steps (33%)
[15:31:25] Completed 85000 out of 250000 steps (34%)
[15:37:09] Completed 87500 out of 250000 steps (35%)
[15:42:54] Completed 90000 out of 250000 steps (36%)
[15:48:39] Completed 92500 out of 250000 steps (37%)
[15:54:26] Completed 95000 out of 250000 steps (38%)
[16:00:10] Completed 97500 out of 250000 steps (39%)
[16:05:55] Completed 100000 out of 250000 steps (40%)
[16:11:41] Completed 102500 out of 250000 steps (41%)
[16:17:28] Completed 105000 out of 250000 steps (42%)
[16:23:13] Completed 107500 out of 250000 steps (43%)
[16:28:59] Completed 110000 out of 250000 steps (44%)
[16:34:46] Completed 112500 out of 250000 steps (45%)
[16:40:31] Completed 115000 out of 250000 steps (46%)
[16:46:15] Completed 117500 out of 250000 steps (47%)
[16:52:02] Completed 120000 out of 250000 steps (48%)
[16:57:47] Completed 122500 out of 250000 steps (49%)
[17:03:32] Completed 125000 out of 250000 steps (50%)
[17:09:17] Completed 127500 out of 250000 steps (51%)
[17:15:02] Completed 130000 out of 250000 steps (52%)
[17:20:47] Completed 132500 out of 250000 steps (53%)
[17:26:32] Completed 135000 out of 250000 steps (54%)
[17:32:17] Completed 137500 out of 250000 steps (55%)
[17:38:02] Completed 140000 out of 250000 steps (56%)
[17:43:48] Completed 142500 out of 250000 steps (57%)
[17:49:35] Completed 145000 out of 250000 steps (58%)
[17:55:21] Completed 147500 out of 250000 steps (59%)
[18:01:07] Completed 150000 out of 250000 steps (60%)
[18:06:52] Completed 152500 out of 250000 steps (61%)
[18:12:39] Completed 155000 out of 250000 steps (62%)
[18:18:26] Completed 157500 out of 250000 steps (63%)
[18:24:11] Completed 160000 out of 250000 steps (64%)
[18:29:58] Completed 162500 out of 250000 steps (65%)
[18:35:42] Completed 165000 out of 250000 steps (66%)
Step 5665692, time 11331.4 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.042102, max 1.538039 (between atoms 7642 and 7643)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
7638 7640 90.0 0.1010 0.2102 0.1010
7642 7643 90.0 0.1090 0.2766 0.1090
Step 5665693, time 11331.4 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 1.869559, max 67.743530 (between atoms 7644 and 7646)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
Warning: 1-4 interaction between 7638 and 7646 at distance 7.350 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 5665694, time 11331.4 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.920940, max 38.578472 (between atoms 7642 and 7643)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
7644 7645 90.0 0.1085 0.3899 0.1090
7644 7646 90.0 7.4930 1.6358 0.1090
Step 5665695, time 11331.4 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 11116.456630, max 351894.375000 (between atoms 7642 and 7643)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
7638 7639 90.0 0.0967 0.1067 0.1010
7642 7643 90.0 4.3141 38356.5938 0.1090
7644 7645 90.0 0.3899 0.2089 0.1090
7644 7646 90.0 1.6358 13.0063 0.1090
14914 14915 90.0 0.1010 35369.8438 0.1010
[18:37:18]
[18:37:18] Folding@home Core Shutdown: INTERRUPTED
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 102) - process 0
Folding@Home Client Shutdown.
david@i7-living-room:~/folding1/FAH1$ ./fah6 -smp 8 -local
Note: Please read the license agreement (fah6 -license). Further
use of this software requires that you have read and accepted this agreement.
Using local directory for work files
8 cores detected
--- Opening Log file [May 6 19:49:50 UTC]
# Linux SMP Console Edition ###################################################
###############################################################################
Folding@Home Client Version 6.24beta
http://folding.stanford.edu
###############################################################################
###############################################################################
Launch directory: /home/david/folding1/FAH1
Executable: ./fah6
Arguments: -smp 8 -local
[19:49:50] - Ask before connecting: No
[19:49:50] - User name: road-runner (Team 36362)
[19:49:50] - User ID: 7DCB20E473C611DC
[19:49:50] - Machine ID: 1
[19:49:50]
[19:49:50] Loaded queue successfully.
[19:49:50]
[19:49:50] + Processing work unit
[19:49:50] Core required: FahCore_a2.exe
[19:49:50] Core found.
[19:49:50] Working on queue slot 00 [May 6 19:49:50 UTC]
[19:49:50] + Working ...
[19:49:50]
[19:49:50] *------------------------------*
[19:49:50] Folding@Home Gromacs SMP Core
[19:49:50] Version 2.07 (Sun Apr 19 14:51:09 PDT 2009)
[19:49:50]
[19:49:50] Preparing to commence simulation
[19:49:50] - Ensuring status. Please wait.
[19:49:51] Called DecompressByteArray: compressed_data_size=4824769 data_size=24052205, decompressed_data_size=24052205 diff=0
[19:49:51] - Digital signature verified
[19:49:51]
[19:49:51] Project: 2671 (Run 25, Clone 84, Gen 22)
[19:49:51]
[19:49:51] Assembly optimizations on if available.
[19:49:51] Entering M.D.
[19:49:57] Using Gromacs checkpoints
[19:50:01]
[19:50:01] Entering M.D.
[19:50:07] Using Gromacs checkpoints
NNODES=8, MYRANK=0, HOSTNAME=i7-living-room
NNODES=8, MYRANK=2, HOSTNAME=i7-living-room
NNODES=8, MYRANK=3, HOSTNAME=i7-living-room
NNODES=8, MYRANK=4, HOSTNAME=i7-living-room
NNODES=8, MYRANK=1, HOSTNAME=i7-living-room
NNODES=8, MYRANK=6, HOSTNAME=i7-living-room
NNODES=8, MYRANK=7, HOSTNAME=i7-living-room
NNODES=8, MYRANK=5, HOSTNAME=i7-living-room
NODEID=4 argc=23
NODEID=6 argc=23
NODEID=5 argc=23
NODEID=7 argc=23
NODEID=2 argc=23
NODEID=3 argc=23
NODEID=0 argc=23
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 4.0.99_development_20090307 (-:
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_00.tpr, VERSION 3.3.99_development_20070618 (single precision)
NODEID=1 argc=23
Note: tpx file_version 48, software version 64
Reading checkpoint file work/wudata_00.cpt generated: Wed May 6 13:35:43 2009
NOTE: The tpr file used for this simulation is in an old format, for less memory usage and possibly more performance create a new tpr file with an up to date version of grompp
Making 3D domain decomposition 2 x 2 x 2
starting mdrun '22911 system in water'
5750000 steps, 11500.0 ps (continuing from step 5665010, 11330.0 ps).
[19:50:10] data_00.log
[19:50:10] Verified work/wudata_00.trr
[19:50:10] Verified work/wudata_00.xtc
[19:50:10] Verified work/wudata_00.edr
[19:50:10] Completed 165010 out of 250000 steps (66%)
[19:55:54] Completed 167500 out of 250000 steps (67%)
[20:01:42] Completed 170000 out of 250000 steps (68%)
[20:07:30] Completed 172500 out of 250000 steps (69%)
[20:13:16] Completed 175000 out of 250000 steps (70%)
[20:19:01] Completed 177500 out of 250000 steps (71%)
[20:24:46] Completed 180000 out of 250000 steps (72%)
[20:30:33] Completed 182500 out of 250000 steps (73%)
Step 5683761, time 11367.5 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000296, max 0.009763 (between atoms 7638 and 7640)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 5683778, time 11367.6 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000502, max 0.019920 (between atoms 7638 and 7639)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 5683780, time 11367.6 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001392, max 0.064136 (between atoms 7638 and 7639)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
7638 7639 90.0 0.1011 0.1075 0.1010
Step 5683857, time 11367.7 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000493, max 0.022313 (between atoms 7638 and 7641)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
7638 7639 90.0 0.1011 0.1012 0.1010
Step 5683863, time 11367.7 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001008, max 0.044871 (between atoms 7638 and 7641)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
7638 7641 90.0 0.1012 0.1055 0.1010
Step 5683902, time 11367.8 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001150, max 0.054322 (between atoms 7638 and 7641)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
7638 7641 90.0 0.1016 0.1065 0.1010
Step 5683910, time 11367.8 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000412, max 0.017413 (between atoms 7638 and 7641)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
7638 7640 90.0 0.1018 0.1018 0.1010
Step 5683911, time 11367.8 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000696, max 0.025978 (between atoms 7638 and 7640)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 5683979, time 11368 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.039493, max 1.926021 (between atoms 7638 and 7639)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 5683980, time 11368 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.053824, max 2.555308 (between atoms 7638 and 7639)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
7638 7639 90.0 0.2955 0.3591 0.1010
Step 5683981, time 11368 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.039919, max 1.894928 (between atoms 7638 and 7639)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 5683982, time 11368 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.050252, max 2.385738 (between atoms 7638 and 7639)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 5683983, time 11368 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.082052, max 3.894845 (between atoms 7638 and 7639)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
7638 7639 90.0 0.3420 0.4944 0.1010
Step 5683984, time 11368 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.049544, max 2.351655 (between atoms 7638 and 7639)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
Step 5683985, time 11368 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.406454, max 19.289139 (between atoms 7638 and 7639)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
7638 7639 90.0 0.3385 2.0492 0.1010
7638 7640 90.0 0.1055 0.1547 0.1010
7638 7641 90.0 0.1028 0.1145 0.1010
t = 11367.971 ps: Water molecule starting at atom 139480 can not be settled.
Check for bad contacts and/or reduce the timestep.
Step 5683986, time 11368 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.079768, max 2.644508 (between atoms 7638 and 7640)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
7638 7639 90.0 2.0492 0.3223 0.1010
7638 7640 90.0 0.1547 0.3681 0.1010
7638 7641 90.0 0.1145 0.2622 0.1010
Step 5683987, time 11368 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 141.295153, max 6707.586914 (between atoms 7638 and 7641)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
7638 7639 111.0 0.3223 4.6103 0.1010
7638 7641 93.0 0.2622 677.5673 0.1010
t = 11367.975 ps: Water molecule starting at atom 139480 can not be settled.
Check for bad contacts and/or reduce the timestep.
Warning: 1-4 interaction between 7639 and 7643 at distance 7.595 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 5683988, time 11368 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms inf, max inf (between atoms 13046 and 13047)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
13046 13047 90.0 0.1080 inf 0.1080
7654 7655 90.0 0.1090 inf 0.1090
7638 7639 108.8 4.6103 42.6962 0.1010
7638 7640 92.4 7.8347 79.3019 0.1010
7671 7672 92.6 0.1090 607.0408 0.1090
13137 13138 90.0 0.1090 inf 0.1090
t = 11367.977 ps: Water molecule starting at atom 33406 can not be settled.
Check for bad contacts and/or reduce the timestep.
[20:33:59]
[20:33:59] Folding@home Core Shutdown: INTERRUPTED
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 102) - process 0
[cli_2]: 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
[0]0:Return code = 102
[0]1:Return code = 0, signaled with Segmentation fault
[0]2:Return code = 1
[0]3:Return code = 1
[0]4:Return code = 0, signaled with Quit
[0]5:Return code = 0, signaled with Segmentation fault
[0]6:Return code = 0, signaled with Quit
[0]7:Return code = 0, signaled with Quit
[20:34:07] CoreStatus = 66 (102)
[20:34:07] + Shutdown requested by user. Exiting.
Folding@Home Client Shutdown.
david@i7-living-room:~/folding1/FAH1$
I dont know...