Code: Select all
[16:19:57] Project: 2676 (Run 1, Clone 151, Gen 70)
[16:19:57]
[16:19:57] Assembly optimizations on if available.
[16:19:57] Entering M.D.
[16:20:07] Run 1, Clone 151, Gen 70)
[16:20:07]
[16:20:07] Entering M.D.
NNODES=8, MYRANK=0, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=2, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=1, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=3, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=5, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=6, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=7, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=4, HOSTNAME=i7-Upstairs
NODEID=2 argc=20
NODEID=0 argc=20
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 4.0.3_pre (-:
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)
NODEID=1 argc=20
NODEID=3 argc=20
NODEID=6 argc=20
NODEID=7 argc=20
NODEID=4 argc=20
NODEID=5 argc=20
Note: tpx file_version 48, software version 58
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 '23130 system in water'
17750002 steps, 35500.0 ps (continuing from step 17500002, 35000.0 ps).
[16:32:33] Completed 5008 out of 250000 steps (2%)
[16:38:40] Completed 7508 out of 250000 steps (3%)
[16:44:48] Completed 10008 out of 250000 steps (4%)
[16:50:55] Completed 12508 out of 250000 steps (5%)
[16:57:04] Completed 15008 out of 250000 steps (6%)
[17:03:12] Completed 17508 out of 250000 steps (7%)
[17:09:20] Completed 20008 out of 250000 steps (8%)
[17:15:29] Completed 22508 out of 250000 steps (9%)
[17:21:37] Completed 25008 out of 250000 steps (10%)
[17:27:44] Completed 27508 out of 250000 steps (11%)
[17:33:51] Completed 30008 out of 250000 steps (12%)
[17:39:58] Completed 32508 out of 250000 steps (13%)
[17:46:06] Completed 35008 out of 250000 steps (14%)
[17:52:15] Completed 37508 out of 250000 steps (15%)
[17:58:23] Completed 40008 out of 250000 steps (16%)
[18:04:33] Completed 42508 out of 250000 steps (17%)
[18:10:42] Completed 45008 out of 250000 steps (18%)
[18:16:48] Completed 47508 out of 250000 steps (19%)
[18:22:57] Completed 50008 out of 250000 steps (20%)
[18:29:06] Completed 52508 out of 250000 steps (21%)
[18:35:14] Completed 55008 out of 250000 steps (22%)
[18:41:22] Completed 57508 out of 250000 steps (23%)
[18:47:32] Completed 60008 out of 250000 steps (24%)
[18:53:40] Completed 62508 out of 250000 steps (25%)
[18:59:50] Completed 65008 out of 250000 steps (26%)
[19:05:58] Completed 67508 out of 250000 steps (27%)
[19:12:05] Completed 70008 out of 250000 steps (28%)
[19:18:14] Completed 72508 out of 250000 steps (29%)
[19:24:21] Completed 75008 out of 250000 steps (30%)
[19:30:30] Completed 77508 out of 250000 steps (31%)
[19:36:36] Completed 80008 out of 250000 steps (32%)
[19:42:45] Completed 82508 out of 250000 steps (33%)
[19:48:54] Completed 85008 out of 250000 steps (34%)
[19:55:02] Completed 87508 out of 250000 steps (35%)
[20:01:10] Completed 90008 out of 250000 steps (36%)
[20:07:18] Completed 92508 out of 250000 steps (37%)
[20:13:25] Completed 95008 out of 250000 steps (38%)
[20:19:34] Completed 97508 out of 250000 steps (39%)
[20:25:43] Completed 100008 out of 250000 steps (40%)
[20:31:51] Completed 102508 out of 250000 steps (41%)
[cli_6]: aborting job:
Fatal error in MPI_Sendrecv: Error message texts are not available
[cli_7]: aborting job:
Fatal error in MPI_Sendrecv: Error message texts are not available
[0]0:Return code = 0, signaled with Segmentation fault
[0]1:Return code = 0, signaled with Segmentation fault
[0]2:Return code = 0, signaled with Segmentation fault
[0]3:Return code = 0, signaled with Segmentation fault
[0]4:Return code = 0, signaled with Segmentation fault
[0]5:Return code = 0, signaled with Segmentation fault
[0]6:Return code = 1
[0]7:Return code = 1
[20:36:22] CoreStatus = 1 (1)
[20:36:22] Sending work to server
[20:36:22] Project: 2676 (Run 1, Clone 151, Gen 70)
[20:36:22] - Error: Could not get length of results file work/wuresults_04.dat
[20:36:22] - Error: Could not read unit 04 file. Removing from queue.
[20:36:22] - Preparing to get new work unit...
[20:36:22] + Attempting to get work packet
[20:36:22] - Connecting to assignment server
[20:36:23] - Successful: assigned to (171.67.108.24).
[20:36:23] + News From Folding@Home: Welcome to Folding@Home
[20:36:23] Loaded queue successfully.
[20:36:34] + Closed connections
[20:36:39]
[20:36:39] + Processing work unit
[20:36:40] Core required: FahCore_a2.exe
[20:36:40] Core found.
[20:36:40] Working on queue slot 05 [April 3 20:36:40 UTC]
[20:36:40] + Working ...
[20:36:40]
[20:36:40] *------------------------------*
[20:36:40] Folding@Home Gromacs SMP Core
[20:36:40] Version 2.04 (Thu Jan 29 16:43:57 PST 2009)
[20:36:40]
[20:36:40] Preparing to commence simulation
[20:36:40] - Ensuring status. Please wait.
[20:36:49] - Looking at optimizations...
[20:36:49] - Working with standard loops on this execution.
[20:36:49] - Files status OK
[20:36:50] - Expanded 4864663 -> 24067137 (decompressed 494.7 percent)
[20:36:50] Called DecompressByteArray: compressed_data_size=4864663 data_size=24067137, decompressed_data_size=24067137 diff=0
[20:36:50] - Digital signature verified
[20:36:50]
[20:36:50] Project: 2676 (Run 1, Clone 151, Gen 70)
[20:36:50]
[20:36:51] Entering M.D.
NNODES=8, MYRANK=1, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=2, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=3, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=0, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=4, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=5, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=6, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=7, HOSTNAME=i7-Upstairs
NODEID=2 argc=20
NODEID=3 argc=20
NODEID=4 argc=20
NODEID=5 argc=20
NODEID=0 argc=20
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 4.0.3_pre (-:
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_05.tpr, VERSION 3.3.99_development_20070618 (single precision)
NODEID=1 argc=20
NODEID=6 argc=20
NODEID=7 argc=20
Note: tpx file_version 48, software version 58
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 '23130 system in water'
17750002 steps, 35500.0 ps (continuing from step 17500002, 35000.0 ps).
[20:43:08] Completed 2508 out of 250000 steps (1%)
[20:49:15] Completed 5008 out of 250000 steps (2%)
[20:55:23] Completed 7508 out of 250000 steps (3%)
[21:01:30] Completed 10008 out of 250000 steps (4%)
[21:07:39] Completed 12508 out of 250000 steps (5%)
[21:13:46] Completed 15008 out of 250000 steps (6%)
[21:19:55] Completed 17508 out of 250000 steps (7%)
[21:26:03] Completed 20008 out of 250000 steps (8%)
[21:32:10] Completed 22508 out of 250000 steps (9%)
[21:38:17] Completed 25008 out of 250000 steps (10%)
[21:44:24] Completed 27508 out of 250000 steps (11%)
[21:50:33] Completed 30008 out of 250000 steps (12%)
[21:56:38] Completed 32508 out of 250000 steps (13%)
[22:02:46] Completed 35008 out of 250000 steps (14%)
[22:08:53] Completed 37508 out of 250000 steps (15%)
[22:15:01] Completed 40008 out of 250000 steps (16%)
[22:21:10] Completed 42508 out of 250000 steps (17%)
[22:27:18] Completed 45008 out of 250000 steps (18%)
[22:33:23] Completed 47508 out of 250000 steps (19%)
[22:39:31] Completed 50008 out of 250000 steps (20%)
[22:45:39] Completed 52508 out of 250000 steps (21%)
[22:51:46] Completed 55008 out of 250000 steps (22%)
[22:57:52] Completed 57508 out of 250000 steps (23%)
[23:04:01] Completed 60008 out of 250000 steps (24%)
[23:10:09] Completed 62508 out of 250000 steps (25%)
[23:16:15] Completed 65008 out of 250000 steps (26%)
[23:22:23] Completed 67508 out of 250000 steps (27%)
[23:28:30] Completed 70008 out of 250000 steps (28%)
[23:34:37] Completed 72508 out of 250000 steps (29%)
[23:40:44] Completed 75008 out of 250000 steps (30%)
[23:46:52] Completed 77508 out of 250000 steps (31%)
-------------------------------------------------------
Program mdrun, VERSION 4.0.3_pre
Source code file: domdec_top.c, line: 172
Software inconsistency error:
Some interactions seem to be assigned multiple times
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
Error on node 7, will try to stop all the nodes
Halting parallel program mdrun on CPU 7 out of 8
gcq#0: Thanx for Using GROMACS - Have a Nice Day
[cli_7]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 7
[23:51:29]
[23:51:29] Folding@home Core Shutdown: INTERRUPTED
A list of missing interactions:
Angle of 42183 missing -1
exclusions of 250365 missing -4
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 102) - process 0
[cli_1]: aborting job:
Fatal error in MPI_Allreduce: Error message texts are not available
[cli_2]: aborting job:
Fatal error in MPI_Allreduce: Error message texts are not available
[cli_3]: aborting job:
Fatal error in MPI_Allreduce: Error message texts are not available
[cli_5]: aborting job:
Fatal error in MPI_Allreduce: Error message texts are not available
Folding@Home Client Shutdown.
david@i7-Upstairs:~/folding1/FAH1$ ./fah6 -smp 8 -local'
>
>
david@i7-Upstairs:~/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 [April 4 01:10:03 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
[01:10:03] - Ask before connecting: No
[01:10:03] - User name: road-runner (Team 12772)
[01:10:03] - User ID: 96D91915346BDE2
[01:10:03] - Machine ID: 1
[01:10:03]
[01:10:03] Loaded queue successfully.
[01:10:03]
[01:10:03] + Processing work unit
[01:10:03] Core required: FahCore_a2.exe
[01:10:03] Core found.
[01:10:03] Working on queue slot 05 [April 4 01:10:03 UTC]
[01:10:03] + Working ...
[01:10:03]
[01:10:03] *------------------------------*
[01:10:03] Folding@Home Gromacs SMP Core
[01:10:03] Version 2.04 (Thu Jan 29 16:43:57 PST 2009)
[01:10:03]
[01:10:03] Preparing to commence simulation
[01:10:03] - Ensuring status. Please wait.
[01:10:04] Called DecompressByteArray: compressed_data_size=4864663 data_size=24067137, decompressed_data_size=24067137 diff=0
[01:10:04] - Digital signature verified
[01:10:04]
[01:10:04] Project: 2676 (Run 1, Clone 151, Gen 70)
[01:10:04]
[01:10:04] Assembly optimizations on if available.
[01:10:04] Entering M.D.
[01:10:10] Will resume from checkpoint file
[01:10:14] ng M.D.
[01:10:20] Will resume from checkpoint file
NNODES=8, MYRANK=0, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=1, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=2, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=3, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=5, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=6, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=7, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=4, HOSTNAME=i7-Upstairs
NODEID=2 argc=20
NODEID=3 argc=20
NODEID=0 argc=20
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 4.0.3_pre (-:
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 (-:
NODEID=1 argc=20
Reading file work/wudata_05.tpr, VERSION 3.3.99_development_20070618 (single precision)
NODEID=6 argc=20
NODEID=4 argc=20
NODEID=7 argc=20
NODEID=5 argc=20
Note: tpx file_version 48, software version 58
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 '23130 system in water'
17750002 steps, 35500.0 ps (continuing from step 17500002, 35000.0 ps).
-------------------------------------------------------
Program mdrun, VERSION 4.0.3_pre
Source code file: md.c, line: 1107
Fatal error:
Checkpoint error on step 17577520
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun on CPU 0 out of 8
gcq#0: Thanx for Using GROMACS - Have a Nice Day
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
[01:10:22] te: I/O failed dir=0, var=0000000001EE8150, varsize=394668
[01:10:22] fcCheckPointResume: failure in call to fcSaveRestoreState() to restore state.
[0]0:Return code = 255
[0]1:Return code = 0, signaled with Quit
[0]2:Return code = 0, signaled with Quit
[0]3:Return code = 0, signaled with Quit
[0]4:Return code = 0, signaled with Quit
[0]5:Return code = 0, signaled with Quit
[0]6:Return code = 0, signaled with Quit
[0]7:Return code = 0, signaled with Quit
[01:10:30] CoreStatus = FF (255)
[01:10:30] Sending work to server
[01:10:30] Project: 2676 (Run 1, Clone 151, Gen 70)
[01:10:30] - Error: Could not get length of results file work/wuresults_05.dat
[01:10:30] - Error: Could not read unit 05 file. Removing from queue.
[01:10:30] - Preparing to get new work unit...
[01:10:30] + Attempting to get work packet
[01:10:30] - Connecting to assignment server
[01:10:31] - Successful: assigned to (171.67.108.24).
[01:10:31] + News From Folding@Home: Welcome to Folding@Home
[01:10:31] Loaded queue successfully.
[01:10:44] + Closed connections
[01:10:49]
[01:10:49] + Processing work unit
[01:10:49] Core required: FahCore_a2.exe
[01:10:49] Core found.
[01:10:49] Working on queue slot 06 [April 4 01:10:49 UTC]
[01:10:49] + Working ...
[01:10:49]
[01:10:49] *------------------------------*
[01:10:49] Folding@Home Gromacs SMP Core
[01:10:49] Version 2.04 (Thu Jan 29 16:43:57 PST 2009)
[01:10:49]
[01:10:49] Preparing to commence simulation
[01:10:49] - Ensuring status. Please wait.
[01:10:59] - Looking at optimizations...
[01:10:59] - Working with standard loops on this execution.
[01:10:59] - Files status OK
[01:11:00] - Expanded 4864663 -> 24067137 (decompressed 494.7 percent)
[01:11:00] Called DecompressByteArray: compressed_data_size=4864663 data_size=24067137, decompressed_data_size=24067137 diff=0
[01:11:00] - Digital signature verified
[01:11:00]
[01:11:00] Project: 2676 (Run 1, Clone 151, Gen 70)
[01:11:00]
[01:11:00] Entering M.D.
NNODES=8, MYRANK=0, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=1, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=2, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=4, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=5, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=7, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=3, HOSTNAME=i7-Upstairs
NNODES=8, MYRANK=6, HOSTNAME=i7-Upstairs
NODEID=4 argc=20
NODEID=0 argc=20
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 4.0.3_pre (-:
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_06.tpr, VERSION 3.3.99_development_20070618 (single precision)
NODEID=1 argc=20
NODEID=5 argc=20
NODEID=6 argc=20
NODEID=7 argc=20
NODEID=2 argc=20
NODEID=3 argc=20
Note: tpx file_version 48, software version 58
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 '23130 system in water'
17750002 steps, 35500.0 ps (continuing from step 17500002, 35000.0 ps).