Project: 2669 (Run 12, Clone 44, Gen 124) LINCS WARNING

[DaveHand]

Twice now at 94% this wu has failed.

Making 1D domain decomposition 1 x 1 x 4
starting mdrun '22866 system'
31250000 steps, 62500.0 ps (continuing from step 31235010, 62470.0 ps).
[18:46:48] d work/wudata_07.log
[18:46:49] Verified work/wudata_07.trr
[18:46:49] Verified work/wudata_07.xtc
[18:46:49] Verified work/wudata_07.edr
[18:46:50] Completed 235010 out of 250000 steps (94%)

Step 31236434, time 62472.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.124374, max 5.465165 (between atoms 20005 and 20006)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length

Step 31236435, time 62472.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.062209, max 3.842220 (between atoms 20002 and 20003)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
20002 20003 90.0 0.6978 0.5278 0.1090

Step 31236436, time 62472.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 45.559172, max 2814.585449 (between atoms 20002 and 20003)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
20002 20004 90.0 0.1115 4.7740 0.1090

t = 62472.875 ps: Water molecule starting at atom 60397 can not be settled.
Check for bad contacts and/or reduce the timestep.
Warning: 1-4 interaction between 19997 and 20002 at distance 5.822 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 31236437, time 62472.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 636622077952.000000 (between atoms 21133 and 21135)

Step 31236437, time 62472.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.154821, max 8.821330 (between atoms 6466 and 6467)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
6466 6467 90.0 0.1090 1.0705 0.1090
6479 6480 90.0 0.1080 0.8345 0.1080
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
21161 21162 90.0 0.1090 1.9718 0.1090
20005 20006 90.0 0.6111 0.3823 0.1010
20005 20007 90.0 0.1011 0.3460 0.1010
20005 20008 90.0 0.1011 0.4262 0.1010
21163 21164 101.8 0.1090 47.3720 0.1090
21163 21165 90.0 0.1090 73.4817 0.1090
21147 21148 90.0 0.1090 225848.0312 0.1090
21147 21149 90.0 0.1090 212697.8906 0.1090
21152 21153 90.0 0.1010 1663.3772 0.1010
21152 21154 90.0 0.1010 848.9731 0.1010
6479 6480 90.0 0.1080 0.8345 0.1080
6470 6471 90.0 0.1080 70136.0938 0.1080

t = 62472.877 ps: Water molecule starting at atom 59638 can not be settled.
Check for bad contacts and/or reduce the timestep.
6472 6473 90.0 0.1080 4559.6069 0.1080
6475 6476 90.0 0.0960 645.7097 0.0960
21128 21129 90.0 0.1090 118.9781 0.1090
21130 21131 90.0 0.1090 2670.5117 0.1090
21130 21132 90.2 0.1090 123.4505 0.1090
21133 21134 90.0 0.1090 12225088512.0000 0.1090
21137 21138 90.0 0.1090 7604626432.0000 0.1090
21137 21139 90.0 0.1090 8026430464.0000 0.1090
15715 15716 90.0 0.1090 4.3492 0.1090
15715 15717 90.0 0.1090 0.5782 0.1090
15715 15718 90.0 0.1090 0.5895 0.1090
6477 6478 90.0 0.1080 1.6446 0.1080
21789 21790 90.0 0.1090 0.1408 0.1090
21814 21815 171.9 0.1090 1.5111 0.1090
21814 21816 90.0 0.1090 5.5830 0.1090
21814 21817 90.0 0.1090 64.0841 0.1090
20163 20165 90.0 0.1090 10723.6064 0.1090
20163 20166 90.0 0.1090 664047.9375 0.1090

t = 62472.877 ps: Water molecule starting at atom 87673 can not be settled.
Check for bad contacts and/or reduce the timestep.
[18:57:20]
[18:57:20] Folding@home Core Shutdown: INTERRUPTED
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 102) - process 0

EDIT - Though it seems to have done it on a different step.
Log from the first time it crashed

Step 31236955, time 62473.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 1.474197, max 83.613762 (between atoms 20005 and 20008)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
20002 20004 90.0 0.1089 3.6668 0.1090
20005 20006 90.0 0.1010 0.3304 0.1010
Warning: 1-4 interaction between 20000 and 20004 at distance 3.737 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 31236956, time 62473.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 2149.082828, max 80586.414062 (between atoms 20005 and 20006)
bonds that rotated more than 90 degrees:
atom 1 atom 2 angle previous, current, constraint length
19799 19800 97.8 0.1080 46.9695 0.1080
20005 20006 90.0 0.3304 8139.3291 0.1010
20005 20007 90.0 0.1938 5974.4175 0.1010
[15:46:44]
[15:46:44] 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 Quit
[0]2:Return code = 0, signaled with Segmentation fault
[0]3:Return code = 0, signaled with Segmentation fault
[15:46:48] CoreStatus = 66 (102)
[15:46:48] + Shutdown requested by user. Exiting.
Folding@Home Client Shutdown.

Should I just dump it and get working on the next one?

[DaveHand]

Dropped the -forceasm flag and reduced my cpu frequency from 1.67 to 1GHz (intel T7200) and tried again. Bizarrely it has reached 95%.

Hope my lappy isn't starting to fade......

Using ubuntu 8.04

[bruce]

Apparently the lower clock rate fixed it.

Hi DaveHand (team 46590),
Your WU (P2669 R12 C44 G124) was added to the stats database on 2009-05-06 20:12:54 for 1920 points of credit.

[DaveHand]

Yup, it did finish ok.

It's just a little unusual as I run the machine under-clocked anyways and it has as yet never skipped a beat. I know the vents are all free from dust as I thoroughly cleaned the fans etc recently.

Ho hum..

Cheers.