Project: 2671 (Run 39, Clone 95, Gen 38) LINCS WARNING
Posted: Thu May 28, 2009 10:34 am
FYI
This WU died as indicated in the following log. It appears to carry on okay after a restart.
This WU died as indicated in the following log. It appears to carry on okay after a restart.
Code: Select all
[06:34:31] Completed 152500 out of 250000 steps (61%)
[06:38:55] Completed 155000 out of 250000 steps (62%)
[06:43:22] Completed 157500 out of 250000 steps (63%)
Step 9657860, time 19315.7 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.040056, max 1.179423 (between atoms 723 and 725)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
723 725 90.0 0.1090 0.2376 0.1090
726 727 90.0 0.1010 0.2059 0.1010
Step 9657861, time 19315.7 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 775.789356, max 21975.304688 (between atoms 723 and 725)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
[06:44:00]
[06:44:00] Folding@home Core Shutdown: INTERRUPTED
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 102) - process 0
[07:28:22] - Autosending finished units... [May 28 07:28:22 UTC]
[07:28:22] Trying to send all finished work units
[07:28:22] + No unsent completed units remaining.
[07:28:22] - Autosend completed
[10:22:25] ***** Got an Activate signal (2)
[10:22:25] Killing all core threads
Folding@Home Client Shutdown.
bollix@XXXXXXX:~/fah/smp$ ./fah6
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 [May 28 10:22:59 UTC]
# Linux SMP Console Edition ###################################################
###############################################################################
Folding@Home Client Version 6.24beta
http://folding.stanford.edu
###############################################################################
###############################################################################
Launch directory: /home/bollix/fah/smp
Executable: ./fah6
Arguments: -smp 8 -verbosity 9
[10:22:59] - Ask before connecting: No
[10:22:59] - User name: bollix47 (Team 39340)
[10:22:59] - User ID: XXXXXXXXXXXXXXXX
[10:22:59] - Machine ID: 1
[10:22:59]
[10:23:00] Loaded queue successfully.
[10:23:00] - Autosending finished units... [May 28 10:23:00 UTC]
[10:23:00] Trying to send all finished work units
[10:23:00] + No unsent completed units remaining.
[10:23:00] - Autosend completed
[10:23:00]
[10:23:00] + Processing work unit
[10:23:00] Core required: FahCore_a2.exe
[10:23:00] Core found.
[10:23:00] Working on queue slot 09 [May 28 10:23:00 UTC]
[10:23:00] + Working ...
[10:23:00] - Calling './mpiexec -np 8 -host 127.0.0.1 ./FahCore_a2.exe -dir work/ -suffix 09 -checkpoint 30 -verbose -lifeline 31185 -version 624'
[10:23:00]
[10:23:00] *------------------------------*
[10:23:00] Folding@Home Gromacs SMP Core
[10:23:00] Version 2.07 (Sun Apr 19 14:51:09 PDT 2009)
[10:23:00]
[10:23:00] Preparing to commence simulation
[10:23:00] - Ensuring status. Please wait.
[10:23:01] Called DecompressByteArray: compressed_data_size=4825702 data_size=24048925, decompressed_data_size=24048925 diff=0
[10:23:01] - Digital signature verified
[10:23:01]
[10:23:01] Project: 2671 (Run - Digital signature verAssembly optimizations on if available.
[10:23:01] Entering Entering M.D.
[10:23:07] Using Gromacs checkpoints
[10:23:10] M.D.
[10:23:16] Using Gromacs checkpoints
NNODES=8, MYRANK=0, HOSTNAME=XXXXXX
NNODES=8, MYRANK=4, HOSTNAME=XXXXXX
NNODES=8, MYRANK=1, HOSTNAME=XXXXXX
NNODES=8, MYRANK=2, HOSTNAME=XXXXXX
NNODES=8, MYRANK=3, HOSTNAME=XXXXXX
NNODES=8, MYRANK=5, HOSTNAME=XXXXXX
NNODES=8, MYRANK=7, HOSTNAME=XXXXXX
NNODES=8, MYRANK=6, HOSTNAME=XXXXXX
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_09.tpr, VERSION 3.3.99_development_20070618 (single precision)
NODEID=1 argc=23
NODEID=4 argc=23
NODEID=5 argc=23
NODEID=6 argc=23
NODEID=7 argc=23
Note: tpx file_version 48, software version 64
Reading checkpoint file work/wudata_09.cpt generated: Thu May 28 02:43:22 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 '22908 system in water'
9750001 steps, 19500.0 ps (continuing from step 9657510, 19315.0 ps).
[10:23:19] d work/wudata_09.log
[10:23:20] Verified work/wudata_09.trr
[10:23:20] Verified work/wudata_09.xtc
[10:23:20] Verified work/wudata_09.edr
[10:23:20] Completed 157509 out of 250000 steps (63%)
[10:27:45] Completed 160000 out of 250000 steps (64%)
