Project: 2671 (Run 27, Clone 85, Gen 40) what happened here?
Posted: Mon Jun 01, 2009 2:02 am
What happened here??? Any way of recovering/restoring it?
log:
log:
Code: Select all
[20:15:02]
[20:15:02] *------------------------------*
[20:15:02] Folding@Home Gromacs SMP Core
[20:15:02] Version 2.07 (Sun Apr 19 14:51:09 PDT 2009)
[20:15:02]
[20:15:02] Preparing to commence simulation
[20:15:02] - Ensuring status. Please wait.
[20:15:03] Called DecompressByteArray: compressed_data_size=4824526 data_size=24062605, decompressed_data_size=24062605 diff=0
[20:15:03] - Digital signature verified
[20:15:03]
[20:15:03] Project: 2671 (Run 27, Clone 85, Gen 40)
[20:15:03]
[20:15:03] Assembly optimizations on if available.
[20:15:03] Entering M.D.
[20:15:09] Using Gromacs checkpoints
[20:15:12]
[20:15:13] Entering M.D.
[20:15:19] Using Gromacs checkpoints
NNODES=4, MYRANK=1, HOSTNAME=computenode
NNODES=4, MYRANK=2, HOSTNAME=computenode
NNODES=4, MYRANK=0, HOSTNAME=computenode
NNODES=4, MYRANK=3, HOSTNAME=computenode
NODEID=0 argc=23
NODEID=1 argc=23
NODEID=2 argc=23
NODEID=3 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)
Note: tpx file_version 48, software version 64
Reading checkpoint file work/wudata_00.cpt generated: Sun May 31 16:12:37 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 1D domain decomposition 1 x 1 x 4
starting mdrun '22911 system in water'
10250001 steps, 20500.0 ps (continuing from step 10135010, 20270.0 ps).
[20:15:22] data_00.log
[20:15:22] Verified work/wudata_00.trr
[20:15:22] Verified work/wudata_00.xtc
[20:15:22] Verified work/wudata_00.edr
[20:15:22] Completed 135009 out of 250000 steps (54%)
[20:24:03] Completed 137500 out of 250000 steps (55%)
[20:32:45] Completed 140000 out of 250000 steps (56%)
[20:41:26] Completed 142500 out of 250000 steps (57%)
[20:50:07] Completed 145000 out of 250000 steps (58%)
[20:58:49] Completed 147500 out of 250000 steps (59%)
[21:07:31] Completed 150000 out of 250000 steps (60%)
[21:16:12] Completed 152500 out of 250000 steps (61%)
[21:24:56] Completed 155000 out of 250000 steps (62%)
[21:33:39] Completed 157500 out of 250000 steps (63%)
[21:42:22] Completed 160000 out of 250000 steps (64%)
[21:51:06] Completed 162500 out of 250000 steps (65%)
[21:59:49] Completed 165000 out of 250000 steps (66%)
[22:08:32] Completed 167500 out of 250000 steps (67%)
[22:17:15] Completed 170000 out of 250000 steps (68%)
[22:25:58] Completed 172500 out of 250000 steps (69%)
[22:34:42] Completed 175000 out of 250000 steps (70%)
[22:43:24] Completed 177500 out of 250000 steps (71%)
[22:52:09] Completed 180000 out of 250000 steps (72%)
[23:00:53] Completed 182500 out of 250000 steps (73%)
[23:09:36] Completed 185000 out of 250000 steps (74%)
[23:18:23] Completed 187500 out of 250000 steps (75%)
[23:27:09] Completed 190000 out of 250000 steps (76%)
[23:35:55] Completed 192500 out of 250000 steps (77%)
[23:44:42] Completed 195000 out of 250000 steps (78%)
[23:53:28] Completed 197500 out of 250000 steps (79%)
[00:02:15] Completed 200000 out of 250000 steps (80%)
[00:11:00] Completed 202500 out of 250000 steps (81%)
[00:19:43] Completed 205000 out of 250000 steps (82%)
[00:28:28] Completed 207500 out of 250000 steps (83%)
[00:37:14] Completed 210000 out of 250000 steps (84%)
[00:45:59] Completed 212500 out of 250000 steps (85%)
[00:54:44] Completed 215000 out of 250000 steps (86%)
[01:03:30] Completed 217500 out of 250000 steps (87%)
[01:12:17] Completed 220000 out of 250000 steps (88%)
DD cell 0 0 2: Neighboring cells do not have atoms: 19890 19892 19894 19888
-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090307
Source code file: domdec_con.c, line: 680
Fatal error:
DD cell 0 0 2 could only obtain 166 of the 170 atoms that are connected via constraints from the neighboring cells. This probably means your constraint lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or lincs-order or use the -rcon option of mdrun.
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
[cli_2]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2
[01:17:10]
[01:17:10] Folding@home Core Shutdown: INTERRUPTED
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 102) - process 0
[cli_1]: 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
[01:17:14] CoreStatus = FF (255)
[01:17:14] Sending work to server
[01:17:14] Project: 2671 (Run 27, Clone 85, Gen 40)
[01:17:14] - Error: Could not get length of results file work/wuresults_00.dat
[01:17:14] - Error: Could not read unit 00 file. Removing from queue.
[01:17:14] Trying to send all finished work units
[01:17:14] + No unsent completed units remaining.
[01:17:14] + Closed connections
[01:17:14] + Paused after finishing unit
[01:17:14] Press Enter to continue, Ctrl-C to exit...