Project: 2675 (Run 3, Clone 13, Gen 159) CoreStatus = 66

[BrokenWolf]

Had a system get this Wu and it barely starts and come up with an error message about Water molecule starting @ atom # cannot be settled.

Code: Select all

[17:46:17]
[17:46:17] *------------------------------*
[17:46:17] Folding@Home Gromacs SMP Core
[17:46:17] Version 2.08 (Mon May 18 14:47:42 PDT 2009)
[17:46:17]
[17:46:17] Preparing to commence simulation
[17:46:17] - Ensuring status. Please wait.
[17:46:27] - Looking at optimizations...
[17:46:27] - Working with standard loops on this execution.
[17:46:27] - Files status OK
[17:46:29] - Expanded 4842739 -> 23994061 (decompressed 495.4 percent)
[17:46:29] Called DecompressByteArray: compressed_data_size=4842739 data_size=23994061, decompressed_data_size=23994061 diff=0
[17:46:29] - Digital signature verified
[17:46:29]
[17:46:29] Project: 2675 (Run 3, Clone 13, Gen 159)
[17:46:29]
[17:46:29] Entering M.D.
NNODES=4, MYRANK=1, HOSTNAME=rhel4bw11.lab1.com
NNODES=4, MYRANK=0, HOSTNAME=rhel4bw11.lab1.com
NNODES=4, MYRANK=3, HOSTNAME=rhel4bw11.lab1.com
NNODES=4, MYRANK=2, HOSTNAME=rhel4bw11.lab1.com
NODEID=0 argc=22
                         :-)  G  R  O  M  A  C  S  (-:

                   Groningen Machine for Chemical Simulation

                 :-)  VERSION 4.0.99_development_20090425  (-:


      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=22
Reading file work/wudata_07.tpr, VERSION 3.3.99_development_20070618 (single precision)
NODEID=3 argc=22
NODEID=2 argc=22
Note: tpx file_version 48, software version 65

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 '22878 system in water'
40000004 steps,  80000.0 ps (continuing from step 39750004,  79500.0 ps).

t = 79500.012 ps: Water molecule starting at atom 132199 can not be settled.
Check for bad contacts and/or reduce the timestep.

t = 79500.012 ps: Water molecule starting at atom 60856 can not be settled.
Check for bad contacts and/or reduce the timestep.
[17:46:40] Completed 0 out of 250000 steps  (0%)
[17:46:40]
[17:46:40] Folding@home Core Shutdown: INTERRUPTED
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 102) - process 0
[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 = 0, signaled with Segmentation fault
[0]3:Return code = 1
[17:46:44] CoreStatus = 66 (102)
[17:46:44] + Shutdown requested by user. Exiting.***** Got a SIGTERM signal (15)[17:46:44] Killing all core threads

B

[parkut]

Project: 2675 (Run 3, Clone 13, Gen 159) CoreStatus = 66 (102)

This WU fails immediately and repeatedly. I have deleted queue.dat and
the contents of the work folder.

model name : Intel(R) Core(TM)2 Quad CPU Q9300 @ 2.50GHz
cpu MHz : 2508.431
cache size : 3072 KB
Memory: 1.96 GB physical, 1.94 GB virtual
...
Client Version 6.24R3

Code: Select all

[12:23:08] Preparing to commence simulation
[12:23:08] - Ensuring status. Please wait.
[12:23:09] Called DecompressByteArray: compressed_data_size=4842739 data_size=23994061, decompressed_data_size=23994061 diff=0
[12:23:09] - Digital signature verified
[12:23:09] 
[12:23:09] Project: 2675 (Run 3, Clone 13, Gen 159)
[12:23:09] 
[12:23:09] Assembly optimizations on if available.
[12:23:09] Entering M.D.
[12:23:19] Run 3, Clone 13, Gen 159)
[12:23:19] 
[12:23:19] Entering M.D.
[12:23:27] lding@home Core Shutdown: INTERRUPTED
[12:23:31] CoreStatus = 66 (102)
[12:23:31] + Shutdown requested by user. Exiting.***** Got a SIGTERM signal (15)
[12:23:31] Killing all core threads

Folding@Home Client Shutdown.



Making 1D domain decomposition 1 x 1 x 4
starting mdrun '22878 system in water'
40000004 steps,  80000.0 ps (continuing from step 39750004,  79500.0 ps).

t = 79500.012 ps: Water molecule starting at atom 60856 can not be settled.
Check for bad contacts and/or reduce the timestep.

t = 79500.012 ps: Water molecule starting at atom 132199 can not be settled.
Check for bad contacts and/or reduce the timestep.
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 102) - process 0
[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 = 0, signaled with Segmentation fault
[0]3:Return code = 1