[06:10:49] *------------------------------*
[06:10:49] Folding@Home Gromacs SMP Core
[06:10:49] Version 2.10 (Sun Aug 30 03:43:28 CEST 2009)
[06:10:49]
[06:10:49] Preparing to commence simulation
[06:10:49] - Ensuring status. Please wait.
[06:10:49] Files status OK
[06:10:50] - Expanded 4835226 -> 24044373 (decompressed 497.2 percent)
[06:10:50] Called DecompressByteArray: compressed_data_size=4835226 data_size=24044373, decompressed_data_size=24044373 diff=0
[06:10:51] - Digital signature verified
[06:10:51]
[06:10:51] Project: 2671 (Run 59, Clone 80, Gen 122)
[06:10:51]
[06:10:51] Assembly optimizations on if available.
[06:10:51] Entering M.D.
[06:11:00] un 59, Clone 80, Gen 122)
[06:11:00]
[06:11:00] Entering M.D.
NNODES=4, MYRANK=1, HOSTNAME=fold55
NNODES=4, MYRANK=0, HOSTNAME=fold55
NODEID=0 argc=20
NNODES=4, MYRANK=3, HOSTNAME=fold55
NODEID=1 argc=20
NNODES=4, MYRANK=2, HOSTNAME=fold55
NODEID=2 argc=20
NODEID=3 argc=20
Reading file work/wudata_00.tpr, VERSION 3.3.99_development_20070618 (single precision)
Note: tpx file_version 48, software version 68
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 1D domain decomposition 1 x 1 x 4
starting mdrun '22887 system in water'
30750000 steps, 61500.0 ps (continuing from step 30500000, 61000.0 ps).
t = 61000.003 ps: Water molecule starting at atom 39907 can not be settled.
Check for bad contacts and/or reduce the timestep.
[06:11:10] Completed 0 out of 250000 steps (0%)
t = 61000.005 ps: Water molecule starting at atom 137968 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 61000.007 ps: Water molecule starting at atom 39907 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 61000.009 ps: Water molecule starting at atom 137968 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 61000.011 ps: Water molecule starting at atom 38731 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 61000.013 ps: Water molecule starting at atom 137968 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 61000.015 ps: Water molecule starting at atom 38731 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 61000.017 ps: Water molecule starting at atom 137968 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 61000.019 ps: Water molecule starting at atom 38731 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 61000.021 ps: Water molecule starting at atom 137968 can not be settled.
Check for bad contacts and/or reduce the timestep.
Step 30500010:
The charge group starting at atom 38731 moved than the distance allowed by the domain decomposition (1.200000) in direction Z
distance out of cell 175.460800
Old coordinates: 9.513 0.233 11.192
New coordinates: -73.201 151.582 186.917
Old cell boundaries in direction Z: 7.500 11.250
New cell boundaries in direction Z: 7.395 11.456
-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090605
Source code file: domdec.c, line: 4038
Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated
For more information and tips for trouble shooting please check the GROMACS Wiki at
http://wiki.gromacs.org/index.php/Errors
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
Error on node 2, will try to stop all the nodes
Halting parallel program mdrun on CPU 2 out of 4
gcq#0: Thanx for Using GROMACS - Have a Nice Day
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2
[06:11:12]
[06:11:12] Folding@home Core Shutdown: INTERRUPTED
application called MPI_Abort(MPI_COMM_WORLD, 102) - process 0
[06:24:51] ***** Got an Activate signal (2)
[06:24:51] Killing all core threads
Folding@Home Client Shutdown.
I deleted the work folder and queue.dat and received a different unit, but when it finished I ended up with this again. When someone is back at work can they please kill this one?
Working on queue slot 02 [November 15 15:25:37 UTC]
[15:25:37] + Working ...
[15:25:37]
[15:25:37] *------------------------------*
[15:25:37] Folding@Home Gromacs SMP Core
[15:25:37] Version 2.10 (Sun Aug 30 03:43:28 CEST 2009)
[15:25:37]
[15:25:37] Preparing to commence simulation
[15:25:37] - Ensuring status. Please wait.
[15:25:47] - Assembly optimizations manually forced on.
[15:25:47] - Not checking prior termination.
[15:25:48] - Expanded 4835226 -> 24044373 (decompressed 497.2 percent)
[15:25:48] Called DecompressByteArray: compressed_data_size=4835226 data_size=24044373, decompressed_data_size=24044373 diff=0
[15:25:48] - Digital signature verified
[15:25:48]
[15:25:48] Project: 2671 (Run 59, Clone 80, Gen 122)
[15:25:48]
[15:25:48] Assembly optimizations on if available.
[15:25:48] Entering M.D.
[15:25:57] Completed 0 out of 250000 steps (0%)
[15:25:58]
[15:25:58] Folding@home Core Shutdown: INTERRUPTED
[15:26:02] CoreStatus = 66 (102)
[15:26:02] + Shutdown requested by user. Exiting.
Folding@Home Client Shutdown.
I have the same problem with project 2671 running in a quad core SMP linux (VM).
Right after the beginning of processing, this occurs. I deleted the queue.dat + work folder, and the next project running was 2662. with 2662 I have no problems
I had this issue with 2671 already more than once
Please fix it, because it totally blocks my 24h folding machine... And I do not have daily access to it, in order to repair it.
One of my dedicated folders got this WU Friday. Restarting can produce a message saying deleting and continuing but really just hangs. When flushing this WU, it gets a new WU but upon completion gets this one again -- still.
A second dedicated folder started this process this afternoon.
I hope Stanford can kill this WU server side soon!
Two of my three dedicated folders still are battling this bad WU. It also doesn't have the decency to die gracefully -- had to kill the hung processes and flush it 4 times today so far.
06:09:39]
[06:09:39] *------------------------------*
[06:09:39] Folding@Home Gromacs SMP Core
[06:09:39] Version 2.10 (Sun Aug 30 03:43:28 CEST 2009)
[06:09:39]
[06:09:39] Preparing to commence simulation
[06:09:39] - Ensuring status. Please wait.
[06:09:40] Called DecompressByteArray: compressed_data_size=4835226 data_size=24044373, decompressed_data_size=24044373 diff=0
[06:09:40] - Digital signature verified
[06:09:40]
[06:09:40] Project: 2671 (Run 59, Clone 80, Gen 122)
[06:09:40]
[06:09:40] Assembly optimizations on if available.
[06:09:40] Entering M.D.
[06:09:50] un 59, Clone 80, Gen 122)
[06:09:50]
[06:09:50] Entering M.D.
[06:10:03] CoreStatus = FF (255)
[06:10:03] Sending work to server
[06:10:03] Project: 2671 (Run 59, Clone 80, Gen 122)
[06:10:03] - Error: Could not get length of results file work/wuresults_04.dat
[06:10:03] - Error: Could not read unit 04 file. Removing from queue.
Please post a log. The server can't transmit this work unit to you because the data files are no longer there.
It is possible that there are stale files on your client, but you might double-check that you're running the WU you think you are.
