Project 6904 (Run2, Clone 47, Gen 48)
Posted: Sun Feb 26, 2012 2:54 pm
Successfully completed a number of WU on this system, and haven't seen this error before.
step 12090705: Water molecule starting at atom 1191683 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Code: Select all
[20:43:00] *------------------------------*
[20:43:00] Folding@Home Gromacs SMP Core
[20:43:00] Version 2.27 (Thu Feb 10 09:46:40 PST 2011)
[20:43:00]
[20:43:00] Preparing to commence simulation
[20:43:00] - Looking at optimizations...
[20:43:00] - Created dyn
[20:43:00] - Files status OK
[20:43:05] - Expanded 57218887 -> 71843392 (decompressed 50.4 percent)
[20:43:05] Called DecompressByteArray: compressed_data_size=57218887 data_size=71843392, decompressed_data_size=71843392 diff=0
[20:43:05] - Digital signature verified
[20:43:05]
[20:43:05] Project: 6904 (Run 2, Clone 47, Gen 48)
[20:43:05]
[20:43:05] Assembly optimizations on if available.
[20:43:05] Entering M.D.
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 4.5.3 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
:-) Gromacs (-:
Reading file work/wudata_08.tpr, VERSION 4.5.4-dev-20110530-cc815 (single precision)
[20:43:13] Mapping NT from 32 to 32
Starting 32 threads
Making 2D domain decomposition 8 x 4 x 1
starting mdrun 'Overlay'
12250000 steps, 49000.0 ps (continuing from step 12000000, 48000.0 ps).
[20:43:18] Completed 0 out of 250000 steps (0%)
[21:12:52] Completed 2500 out of 250000 steps (1%)
[21:42:36] Completed 5000 out of 250000 steps (2%)
[22:12:22] Completed 7500 out of 250000 steps (3%)
[22:41:41] Completed 10000 out of 250000 steps (4%)
[23:11:02] Completed 12500 out of 250000 steps (5%)
[23:40:26] Completed 15000 out of 250000 steps (6%)
[00:11:24] Completed 17500 out of 250000 steps (7%)
[00:41:35] Completed 20000 out of 250000 steps (8%)
[01:13:18] Completed 22500 out of 250000 steps (9%)
[01:44:57] Completed 25000 out of 250000 steps (10%)
[02:18:00] Completed 27500 out of 250000 steps (11%)
[02:49:32] Completed 30000 out of 250000 steps (12%)
[03:18:57] Completed 32500 out of 250000 steps (13%)
[03:48:19] Completed 35000 out of 250000 steps (14%)
[04:17:43] Completed 37500 out of 250000 steps (15%)
[04:47:10] Completed 40000 out of 250000 steps (16%)
[05:16:32] Completed 42500 out of 250000 steps (17%)
[05:45:56] Completed 45000 out of 250000 steps (18%)
[06:15:18] Completed 47500 out of 250000 steps (19%)
[06:44:44] Completed 50000 out of 250000 steps (20%)
[07:14:11] Completed 52500 out of 250000 steps (21%)
[07:43:37] Completed 55000 out of 250000 steps (22%)
[08:13:05] Completed 57500 out of 250000 steps (23%)
[08:42:19] Completed 60000 out of 250000 steps (24%)
[09:11:34] Completed 62500 out of 250000 steps (25%)
[09:40:58] Completed 65000 out of 250000 steps (26%)
[10:10:23] Completed 67500 out of 250000 steps (27%)
[10:39:43] Completed 70000 out of 250000 steps (28%)
[11:09:08] Completed 72500 out of 250000 steps (29%)
[11:38:32] Completed 75000 out of 250000 steps (30%)
[12:07:57] Completed 77500 out of 250000 steps (31%)
[12:37:26] Completed 80000 out of 250000 steps (32%)
[13:06:49] Completed 82500 out of 250000 steps (33%)
[13:36:16] Completed 85000 out of 250000 steps (34%)
[14:05:42] Completed 87500 out of 250000 steps (35%)
[14:35:08] Completed 90000 out of 250000 steps (36%)
step 12090705: Water molecule starting at atom 1191683 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
-------------------------------------------------------
Program Gromacs, VERSION 4.5.3
Source code file: /vspm58/VM/fah-converted/mnt/fah_windows_build/LinuxBuilds/gromacs-4.5.3/src/mdlib/pme.c, line: 534
Fatal error:
1 particles communicated to PME node 20 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
[14:43:26] mdrun returned 255
[14:43:26] Going to send back what have done -- stepsTotalG=250000
[14:43:26] Work fraction=132.2970 steps=250000.
[14:43:30] logfile size=81435 infoLength=81435 edr=25 trr=1
[14:43:30] logfile size: 81435 info=81435 bed=25 hdr=1
[14:43:30] - Writing 81973 bytes of core data to disk...
[14:43:30] Done: 81461 -> 11235 (compressed to 13.7 percent)
[14:43:30] ... Done.
[14:45:19]
[14:45:19] Folding@home Core Shutdown: UNSTABLE_MACHINE
[14:45:19] CoreStatus = 7A (122)
[14:45:19] Sending work to server
[14:45:19] Project: 6904 (Run 2, Clone 47, Gen 48)