Code: Select all
[06:44:17] Completed 217500 out of 250000 steps (87%)
[06:51:15] Completed 220000 out of 250000 steps (88%)
[06:58:13] Completed 222500 out of 250000 steps (89%)
[07:04:24] - Autosending finished units... [February 18 07:04:24 UTC]
[07:04:24] Trying to send all finished work units
[07:04:24] + No unsent completed units remaining.
[07:04:24] - Autosend completed
[07:05:12] Completed 225000 out of 250000 steps (90%)
Step 24975377, time 49950.8 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.363684, max 16.850767 (between atoms 14741 and 14743)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
14741 14743 90.0 0.1091 1.9457 0.1090
Warning: 1-4 interaction between 14739 and 14743 at distance 3.865 which is larger than the 1-4 table size 2.200 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Step 24975378, time 49950.8 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 9879595556853.123047, max 612950150742016.000000 (between atoms 14741 and 14743)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
7650 7651 90.0 0.1010 2049676935168.0000 0.1010
7636 7638 90.0 0.1010 153184.7812 0.1010
7636 7639 90.0 0.1010 151421.9531 0.1010
7640 7641 103.9 0.1090 23.3808 0.1090
7642 7644 90.0 0.1090 554774429696.0000 0.1090
7671 7672 90.0 0.1090 64381.2852 0.1090
7673 7676 90.0 0.1090 1094262.0000 0.1090
14872 14873 90.0 0.1080 86.7748 0.1080
7652 7653 90.0 0.1090 0.6394 0.1090
14858 14859 90.0 0.1010 34740494336.0000 0.1010
14862 14864 90.0 0.1090 1.1101 0.1090
14874 14875 90.0 0.1080 9325786431488.0000 0.1080
14845 14846 90.0 0.1090 17509.5215 0.1090
14880 14881 90.0 0.1090 0.5167 0.1090
14888 14889 90.0 0.1080 68263.2578 0.1080
14741 14742 90.0 0.1079 9906506694656.0000 0.1090
14741 14743 90.0 1.9457 66811567538176.0000 0.1090
14658 14659 90.0 0.1090 12212251.0000 0.1090
14658 14660 90.0 0.1090 19180.3887 0.1090
14658 14661 90.0 0.1090 18741.8633 0.1090
14662 14663 90.0 0.1090 10825.4648 0.1090
14662 14664 90.1 0.1090 11067.6689 0.1090
14662 14665 90.0 0.1090 320484.0312 0.1090
14653 14654 90.0 0.1090 0.5339 0.1090
14653 14655 167.4 0.1090 5.6493 0.1090
14656 14657 90.0 0.1090 65738436.0000 0.1090
14718 14719 90.0 0.1010 0.2622 0.1010
14720 14721 90.0 0.1090 80657.0469 0.1090
14722 14723 90.0 0.1090 434619328.0000 0.1090
14722 14724 90.0 0.1090 26715846.0000 0.1090
14722 14725 90.0 0.1090 25111434.0000 0.1090
14754 14756 90.0 0.1090 12763.4619 0.1090
14765 14766 90.0 0.1010 2.1860 0.1010
14891 14892 90.0 0.0960 1553242.0000 0.0960
14738 14740 90.0 0.1058 184446795776.0000 0.1090
7059 7060 90.0 0.1090 12552460.0000 0.1090
14670 14671 134.4 0.1090 20.2211 0.1090
14672 14673 137.6 0.1090 10.3482 0.1090
14672 14674 115.2 0.1090 18.0190 0.1090
14757 14758 90.0 0.1090 0.2438 0.1090
7035 7036 90.0 0.1090 22946.8535 0.1090
7037 7039 90.0 0.1090 0.1528 0.1090
7040 7041 90.0 0.1090 3791454.7500 0.1090
7040 7042 90.0 0.1090 18666204.0000 0.1090
t = 49950.758 ps: Water molecule starting at atom 103084 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
[07:06:16]
[07:06:16] Folding@home Core Shutdown: INTERRUPTED
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 102) - process 0
[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 = 0, signaled with Quit
[07:06:21] CoreStatus = 66 (102)
[07:06:21] + Shutdown requested by user. Exiting.***** Got a SIGTERM signal (15)
[07:06:21] Killing all core threads
Folding@Home Client Shutdown.
bollix@challenger:~/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.
4 cores detected
--- Opening Log file [February 18 10:00:19 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 -verbosity 9
[10:00:19] - Ask before connecting: No
[10:00:19] - User name: bollix47 (Team 39340)
[10:00:19] - User ID: 629DB96A76D95BCF
[10:00:19] - Machine ID: 1
[10:00:19]
[10:00:19] Loaded queue successfully.
[10:00:19] - Autosending finished units... [February 18 10:00:19 UTC]
[10:00:19] Trying to send all finished work units
[10:00:19] + No unsent completed units remaining.
[10:00:19] - Autosend completed
[10:00:19]
[10:00:19] + Processing work unit
[10:00:19] At least 4 processors must be requested.Core required: FahCore_a2.exe
[10:00:19] Core found.
[10:00:19] Working on queue slot 05 [February 18 10:00:19 UTC]
[10:00:19] + Working ...
[10:00:19] - Calling './mpiexec -np 4 -host 127.0.0.1 ./FahCore_a2.exe -dir work/ -suffix 05 -priority 96 -checkpoint 30 -verbose -lifeline 19017 -version 624'
[10:00:19]
[10:00:19] *------------------------------*
[10:00:19] Folding@Home Gromacs SMP Core
[10:00:19] Version 2.04 (Thu Jan 29 16:43:57 PST 2009)
[10:00:19]
[10:00:19] Preparing to commence simulation
[10:00:19] - Ensuring status. Please wait.
[10:00:20] Called DecompressByteArray: compressed_data_size=4845248 data_size=24001501, decompressed_data_size=24001501 diff=0
[10:00:20] - Digital signature verified
[10:00:20]
[10:00:20] Project: 2674 (Run 0, Clone 97, Gen 99)
[10:00:20]
[10:00:20] Assembly optimizations on if available.
[10:00:20] Entering M.D.
[10:00:26] Will resume from checkpoint file
[10:00:30] ng M.D.
[10:00:36] Will resume from checkpoint file
NNODES=4, MYRANK=0, HOSTNAME=challenger
NNODES=4, MYRANK=2, HOSTNAME=challenger
NNODES=4, MYRANK=3, HOSTNAME=challenger
NNODES=4, MYRANK=1, HOSTNAME=challenger
NODEID=0 argc=20
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 4.0.3_pre (-:
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_05.tpr, VERSION 3.3.99_development_20070618 (single precision)
NODEID=2 argc=20
NODEID=3 argc=20
NODEID=1 argc=20
Note: tpx file_version 48, software version 58
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'
25000000 steps, 50000.0 ps (continuing from step 24750000, 49500.0 ps).
[10:00:38] data_05.log
[10:00:38] Verified work/wudata_05.trr
[10:00:39] Verified work/wudata_05.xtc
[10:00:39] Verified work/wudata_05.edr
[10:00:39] Completed 225010 out of 250000 steps (90%)
[10:08:21] Completed 227500 out of 250000 steps (91%)
[10:16:04] Completed 230000 out of 250000 steps (92%)
[10:24:00] Completed 232500 out of 250000 steps (93%)
[07:06:21] + Shutdown requested by user. Exiting.***** Got a SIGTERM signal (15)
[07:06:21] Killing all core threads
It wasn't requested by me! Guessing it was the client???
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
It did not explode.
Running on a Q6600 @ stock using ubuntu 8.04 with an 8800GT running in wine. The gpu client had no problems.
As can be seen from the log a restart carried on from the checkpoint without incident(so far).
