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Project: 2671 (Run 49, Clone 67, Gen 13) - LINCS WARNING

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Project: 2671 (Run 49, Clone 67, Gen 13) - LINCS WARNING

Posted: Tue May 05, 2009 8:22 am
by bollix47

Code: Select all

[08:17:28] Folding@Home Gromacs SMP Core
[08:17:28] Version 2.07 (Sun Apr 19 14:51:09 PDT 2009)
[08:17:28] 
[08:17:28] Preparing to commence simulation
[08:17:28] - Ensuring status. Please wait.
[08:17:37] - Looking at optimizations...
[08:17:37] - Working with standard loops on this execution.
[08:17:37] - Files status OK
[08:17:38] - Expanded 4836004 -> 24036661 (decompressed 497.0 percent)
[08:17:38] Called DecompressByteArray: compressed_data_size=4836004 data_size=24036661, decompressed_data_size=24036661 diff=0
[08:17:39] - Digital signature verified
[08:17:39] 
[08:17:39] Project: 2671 (Run 49, Clone 67, Gen 13)
[08:17:39] 
[08:17:39] Entering M.D.
[08:17:45] Using Gromacs checkpoints
NNODES=8, MYRANK=0, HOSTNAME=Endeavour
NNODES=8, MYRANK=3, HOSTNAME=Endeavour
NNODES=8, MYRANK=1, HOSTNAME=Endeavour
NNODES=8, MYRANK=5, HOSTNAME=Endeavour
NNODES=8, MYRANK=7, HOSTNAME=Endeavour
NNODES=8, MYRANK=2, HOSTNAME=Endeavour
NNODES=8, MYRANK=4, HOSTNAME=Endeavour
NNODES=8, MYRANK=6, HOSTNAME=Endeavour
NODEID=0 argc=23
NODEID=1 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_03.tpr, VERSION 3.3.99_development_20070618 (single precision)
NODEID=6 argc=23
NODEID=4 argc=23
NODEID=5 argc=23
NODEID=2 argc=23
NODEID=3 argc=23
NODEID=7 argc=23
Note: tpx file_version 48, software version 64

Reading checkpoint file work/wudata_03.cpt generated: Tue May  5 02:27:30 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 '22866 system in water'
3500000 steps,   7000.0 ps (continuing from step 3250010,   6500.0 ps).
[08:17:47] Resuming from checkpoint
[08:17:47] Verified work/wudata_03.log
[08:17:47] Verified work/wudata_03.trr
[08:17:47] Verified work/wudata_03.xtc
[08:17:47] Verified work/wudata_03.edr
[08:17:47] Completed 10 out of 250000 steps  (0%)

Step 3250042, time 6500.08 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.005049, max 0.153571 (between atoms 12377 and 12379)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  12377  12379   90.0    0.1090   0.1257      0.1090
  12380  12382   90.0    0.1090   0.1243      0.1090

Step 3250043, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001567, max 0.062674 (between atoms 12377 and 12379)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  12377  12379   90.0    0.1257   0.1158      0.1090

Step 3250044, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.004545, max 0.145226 (between atoms 12377 and 12379)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  12377  12379   90.0    0.1158   0.1248      0.1090
  12380  12382   90.0    0.1089   0.1217      0.1090

Step 3250045, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 3.120422, max 111.609711 (between atoms 12377 and 12379)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  12380  12381   90.0    0.1110   0.9189      0.1090
Warning: 1-4 interaction between 12382 and 12384 at distance 27.450 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 3250046, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 38.075437, max 1283.494141 (between atoms 14123 and 14125)

Step 3250046, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 95.171961, max 3921.419434 (between atoms 12380 and 12381)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  12377  12379   90.0   12.2745  10.6873      0.1090
  12380  12381   90.0    0.9189 427.5437      0.1090
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  14123  14124   90.0    0.1090   2.6297      0.1090
  14123  14126   90.0    0.1090   2.4497      0.1090
Warning: 1-4 interaction between 14119 and 14125 at distance 160.427 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 3250047, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 4605097220767744.000000 (between atoms 14123 and 14125)

Step 3250047, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 398105870336.000000 (between atoms 21729 and 21730)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  21755  21756   90.0    0.1090 841.8890      0.1090
  21755  21757   90.1    0.1090 15891.9805      0.1090
  21758  21760   90.0    0.1090   0.3193      0.1090
  21731  21732   90.0    0.1090 1948560768.0000      0.1090
  21731  21733   90.0    0.1090 19351518.0000      0.1090

Step 3250047, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 129.047577 (between atoms 13523 and 13524)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  13521  13522   90.0    0.1010   0.6434      0.1010
  13523  13524   90.0    2.3020  14.1752      0.1090
  13525  13526   90.0    0.1090   0.6757      0.1090
  12383  12385   90.0    0.1010   1.6799      0.1010
  12374  12375   90.0    0.1090   0.2099      0.1090

t = 6500.094 ps: Water molecule starting at atom 29074 can not be settled.
Check for bad contacts and/or reduce the timestep.
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  12539  12540   90.0    0.1090 6934143.5000      0.1090
  12541  12542   90.0    0.1090 351.9119      0.1090
  12541  12543   91.8    0.1090 523.1652      0.1090
  12541  12544   90.0    0.1090 522.4516      0.1090
  12545  12546   90.0    0.1090 672605568.0000      0.1090
  12545  12547   90.0    0.1090 670442240.0000      0.1090
   8093   8096   90.0    0.1090   0.2780      0.1090
   8097   8098   91.3    0.1090 708.4280      0.1090
   8100   8101   98.1    0.1090  55.9082      0.1090
   8100   8102   90.0    0.1090   3.1610      0.1090
   8100   8103   90.0    0.1090   5.8512      0.1090
  12504  12505   90.3    0.1090 2888.2185      0.1090
   8087   8088   90.0    0.1010   0.1248      0.1010
   8119   8121   92.5    0.1090 332.4854      0.1090
   8119   8122  122.5    0.1090   5.1981      0.1090
  12497  12498   90.0    0.1010 4367650914304.0000      0.1010
  12499  12500   90.0    0.1090 219119091712.0000      0.1090
  12501  12502   90.0    0.1090   8.7054      0.1090
  12501  12503   90.0    0.1090 198.0699      0.1090

Step 3250047, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 1610.863821, max 98658.015625 (between atoms 14146 and 14147)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  14133  14134   90.0    0.1090 8697.7539      0.1090
  14133  14135   90.1    0.1090 10984.3486      0.1090
  14144  14145   91.7    0.1010 1087.5610      0.1010
  14182  14183   90.0    0.1010 812602.8125      0.1010
  14184  14185   90.0    0.1090 1103690203136.0000      0.1090
  14192  14193   90.0    0.1090 290097.7188      0.1090
  14192  14194   90.0    0.1090 191953.4531      0.1090
  14192  14195   90.0    0.1090 289900.7188      0.1090
  12506  12507   90.1    0.1090 6482.4897      0.1090
  14123  14125   90.0  140.0099 501955579346944.0000      0.1090
  14136  14137   90.0    0.1090 55939944448.0000      0.1090
  12450  12451   90.0    0.1090 3561.5610      0.1090
  12452  12453  130.4    0.1090   7.8651      0.1090
  12452  12454   97.9    0.1090  97.9999      0.1090
  14086  14087   90.0    0.1090   0.1270      0.1090

t = 6500.094 ps: Water molecule starting at atom 139786 can not be settled.
Check for bad contacts and/or reduce the timestep.
[08:18:28] ***** Got an Activate signal (2)
[08:18:28] Killing all core threads

Folding@Home Client Shutdown.
Produced the above a couple of times after which I deleted queue.dat and the work files and the client moved on to a different project.

Re: Project: 2671 (Run 49, Clone 67, Gen 13) - LINCS WARNING

Posted: Tue May 05, 2009 11:56 am
by susato
No data in the db for this one -- but the previous generation of this SMP unit was returned at 2009-04-23 00:08:18, nearly two weeks ago.
Neighboring clones have continued right on.

I've marked it bad.

Re: Project: 2671 (Run 49, Clone 67, Gen 13) - LINCS WARNING

Posted: Tue May 05, 2009 5:26 pm
by bollix47
Thanks but it still seems to be around. :?

Code: Select all

[15:34:12] Connecting to http://assign.stanford.edu:8080/
[15:34:13] Posted data.
[15:34:13] Initial: 43AB; - Successful: assigned to (171.67.108.24).
[15:34:13] + News From Folding@Home: Welcome to Folding@Home
[15:34:13] Loaded queue successfully.
[15:34:13] Connecting to http://171.67.108.24:8080/
[15:34:19] Posted data.
[15:34:19] Initial: 0000; - Receiving payload (expected size: 4836516)
[15:34:29] - Downloaded at ~472 kB/s
[15:34:29] - Averaged speed for that direction ~498 kB/s
[15:34:29] + Received work.
[15:34:29] Trying to send all finished work units
[15:34:29] + No unsent completed units remaining.
[15:34:29] + Closed connections
[15:34:29] 
[15:34:29] + Processing work unit
[15:34:29] Core required: FahCore_a2.exe
[15:34:29] Core found.
[15:34:29] Working on queue slot 02 [May 5 15:34:29 UTC]
[15:34:29] + Working ...
[15:34:29] - Calling './mpiexec -np 8 -host 127.0.0.1 ./FahCore_a2.exe -dir work/ -suffix 02 -checkpoint 30 -verbose -lifeline 25833 -version 624'

[15:34:29] 
[15:34:29] *------------------------------*
[15:34:29] Folding@Home Gromacs SMP Core
[15:34:29] Version 2.07 (Sun Apr 19 14:51:09 PDT 2009)
[15:34:29] 
[15:34:29] Preparing to commence simulation
[15:34:29] - Ensuring status. Please wait.
[15:34:30] Called DecompressByteArray: compressed_data_size=4836004 data_size=24036661, decompressed_data_size=24036661 diff=0
[15:34:30] - Digital signature verified
[15:34:30] 
[15:34:30] Project: 2671 (Run 49, Clone 67, Gen 13)
[15:34:30] 
[15:34:30] Assembly optimizations on if available.
[15:34:30] Entering M.D.
[15:34:40] Run 49, Clone 67, Gen 13)
[15:34:40] 
[15:34:40] Entering M.D.
NNODES=8, MYRANK=0, HOSTNAME=Endeavour
NNODES=8, MYRANK=1, HOSTNAME=Endeavour
NNODES=8, MYRANK=3, HOSTNAME=Endeavour
NNODES=8, MYRANK=4, HOSTNAME=Endeavour
NNODES=8, MYRANK=5, HOSTNAME=Endeavour
NNODES=8, MYRANK=6, HOSTNAME=Endeavour
NNODES=8, MYRANK=7, HOSTNAME=Endeavour
NNODES=8, MYRANK=2, HOSTNAME=Endeavour
NODEID=0 argc=20
NODEID=1 argc=20
NODEID=2 argc=20
NODEID=4 argc=20
NODEID=6 argc=20
NODEID=5 argc=20
                         :-)  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  (-:

NODEID=3 argc=20
NODEID=7 argc=20
Reading file work/wudata_02.tpr, VERSION 3.3.99_development_20070618 (single precision)
Note: tpx file_version 48, software version 64

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 '22866 system in water'
3500000 steps,   7000.0 ps (continuing from step 3250000,   6500.0 ps).
[15:34:48] Completed 0 out of 250000 steps  (0%)

Step 3250042, time 6500.08 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.004808, max 0.154546 (between atoms 12377 and 12379)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  12377  12379   90.0    0.1090   0.1258      0.1090
  12380  12382   90.0    0.1090   0.1244      0.1090

Step 3250043, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001489, max 0.062999 (between atoms 12377 and 12379)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  12377  12379   90.0    0.1258   0.1159      0.1090

Step 3250044, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.004329, max 0.146000 (between atoms 12377 and 12379)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 3250045, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 2.996161, max 113.326942 (between atoms 12377 and 12379)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  12377  12378   90.0    0.1102   0.5213      0.1090
  12377  12379   90.0    0.1249  12.4616      0.1090
  12380  12381   90.0    0.1110   0.9337      0.1090
Warning: 1-4 interaction between 12376 and 12379 at distance 32.109 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 3250046, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 88.818836, max 3851.093506 (between atoms 12380 and 12381)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 3250046, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 9.897773, max 517.926086 (between atoms 14123 and 14125)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  14123  14124   90.0    0.1090   0.7516      0.1090
  14123  14125   90.0    0.1090  56.5629      0.1090
  14123  14126   90.0    0.1090   0.3724      0.1090
  12377  12378   90.0    0.5213   3.2089      0.1090
  14123  14125   90.0    0.1090  56.5629      0.1090
  14123  14124   90.0    0.1090   0.7516      0.1090
  14123  14126   90.0    0.1090   0.3724      0.1090
Warning: 1-4 interaction between 14122 and 14125 at distance 75.983 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 3250047, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 865.466553 (between atoms 14188 and 14190)

Step 3250047, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 86221.539062 (between atoms 21833 and 21835)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  21773  21774   90.0    0.1090  10.8989      0.1090

Step 3250047, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 921306656669696.000000 (between atoms 12377 and 12379)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  12334  12336   90.1    0.1090 7452.5278      0.1090
  11995  11997   90.0    0.1090   0.1450      0.1090
  12377  12378   90.0    3.2089 38983996276736.0000      0.1090
  12383  12385   90.0    0.1010   1.5828      0.1010
  12383  12386   90.0    0.1011   1.9451      0.1010
  12287  12288   90.0    0.1010   0.1514      0.1010

t = 6500.094 ps: Water molecule starting at atom 56263 can not be settled.
Check for bad contacts and/or reduce the timestep.
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  11995  11997   90.0    0.1090   0.1450      0.1090
  14188  14189  142.3    0.1090   4.0102      0.1090
  14188  14190  109.0    0.1090  94.4449      0.1090
  12287  12288   90.0    0.1010   0.1514      0.1010
Warning: 1-4 interaction between 14182 and 14188 at distance 8.929 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

Re: Project: 2671 (Run 49, Clone 67, Gen 13) - LINCS WARNING

Posted: Tue May 05, 2009 5:43 pm
by bruce
bollix47 wrote:Thanks but it still seems to be around. :?
Yes, it often takes some time for the "bad WU report" to clear the WUs out of circulation.

Re: Project: 2671 (Run 49, Clone 67, Gen 13) - LINCS WARNING

Posted: Thu May 07, 2009 6:24 pm
by GTron
This "bad WU" visited my little folding garden this morning, with a different error message after only 22 seconds:

Code: Select all

[10:27:45] Connecting to http://assign.stanford.edu:8080/
[10:27:45] Posted data.
[10:27:45] Initial: 43AB; - Successful: assigned to (171.67.108.24).
[10:27:45] + News From Folding@Home: Welcome to Folding@Home
[10:27:45] Loaded queue successfully.
[10:27:45] Connecting to http://171.67.108.24:8080/
[10:27:51] Posted data.
[10:27:51] Initial: 0000; - Receiving payload (expected size: 4836516)
[10:28:00] - Downloaded at ~524 kB/s
[10:28:00] - Averaged speed for that direction ~497 kB/s
[10:28:00] + Received work.
[10:28:00] Trying to send all finished work units
[10:28:00] + No unsent completed units remaining.
[10:28:00] + Closed connections
[10:28:00] 
[10:28:00] + Processing work unit
[10:28:00] Core required: FahCore_a2.exe
[10:28:00] Core found.
[10:28:00] Working on Unit 01 [May 7 10:28:00]
[10:28:00] + Working ...
[10:28:00] - Calling './mpiexec -np 4 -host 127.0.0.1 ./FahCore_a2.exe -dir work/ -suffix 01 -checkpoint 20 -verbose -lifeline 6402 -version 602'

[10:28:00] 
[10:28:00] *------------------------------*
[10:28:00] Folding@Home Gromacs SMP Core
[10:28:00] Version 2.07 (Sun Apr 19 14:51:09 PDT 2009)
[10:28:00] 
[10:28:00] Preparing to commence simulation
[10:28:00] - Ensuring status. Please wait.
[10:28:01] Called DecompressByteArray: compressed_data_size=4836004 data_size=24036661, decompressed_data_size=24036661 diff=0
[10:28:01] - Digital signature verified
[10:28:01] 
[10:28:01] Project: 2671 (Run 49, Clone 67, Gen 13)
[10:28:01] 
[10:28:01] Assembly optimizations on if available.
[10:28:01] Entering M.D.
[10:28:10] Run 49, Clone 67, Gen 13)
[10:28:10] 
[10:28:10] Entering M.D.
[10:28:32] CoreStatus = FF (255)
[10:28:32] Client-core communications error: ERROR 0xff
[10:28:32] Deleting current work unit & continuing...
[14:33:28] ***** Got a SIGTERM signal (15)
[14:33:28] Killing all core threads
As the log shows, it did not successfully delete the WU and continue -- it hung with one of the cores continuing to run.
I manually killed the client and core (core required a -9), deleted queue, unitinfo, and work, and am now folding a new WU.
Greg

Re: Project: 2671 (Run 49, Clone 67, Gen 13) - LINCS WARNING

Posted: Fri May 08, 2009 2:30 pm
by GTron
This WU was served to the same Linux SMP folder 2 more times this morning and quickly resulted in the same core status 255 and client-core communication error 0xff. Unlike my previous post, this time the client was able to "delete and continue" (aided perhaps by the cleaned queue and work folder?) automatically and it only lost a couple of minutes of time. FAHlog follows FWIW at this point.
Greg

Code: Select all

[03:21:03] Connecting to http://assign.stanford.edu:8080/
[03:21:03] Posted data.
[03:21:03] Initial: 43AB; - Successful: assigned to (171.67.108.24).
[03:21:03] + News From Folding@Home: Welcome to Folding@Home
[03:21:03] Loaded queue successfully.
[03:21:03] Connecting to http://171.67.108.24:8080/
[03:21:09] Posted data.
[03:21:09] Initial: 0000; - Receiving payload (expected size: 4836516)
[03:21:19] - Downloaded at ~472 kB/s
[03:21:19] - Averaged speed for that direction ~498 kB/s
[03:21:19] + Received work.
[03:21:19] Trying to send all finished work units
[03:21:19] + No unsent completed units remaining.
[03:21:19] + Closed connections
[03:21:19] 
[03:21:19] + Processing work unit
[03:21:19] Core required: FahCore_a2.exe
[03:21:19] Core found.
[03:21:19] Working on Unit 02 [May 8 03:21:19]
[03:21:19] + Working ...
[03:21:19] - Calling './mpiexec -np 4 -host 127.0.0.1 ./FahCore_a2.exe -dir work/ -suffix 02 -checkpoint 20 -verbose -lifeline 6175 -version 602'

[03:21:19] 
[03:21:19] *------------------------------*
[03:21:19] Folding@Home Gromacs SMP Core
[03:21:19] Version 2.07 (Sun Apr 19 14:51:09 PDT 2009)
[03:21:19] 
[03:21:19] Preparing to commence simulation
[03:21:19] - Ensuring status. Please wait.
[03:21:20] Called DecompressByteArray: compressed_data_size=4836004 data_size=24036661, decompressed_data_size=24036661 diff=0
[03:21:20] - Digital signature verified
[03:21:20] 
[03:21:20] Project: 2671 (Run 49, Clone 67, Gen 13)
[03:21:20] 
[03:21:20] Assembly optimizations on if available.
[03:21:20] Entering M.D.
[03:21:29] Run 49, Clone 67, Gen 13)
[03:21:29] 
[03:21:29] Entering M.D.
[03:21:38] Completed 0 out of 250000 steps  (0%)
[03:21:51] CoreStatus = FF (255)
[03:21:51] Client-core communications error: ERROR 0xff
[03:21:51] Deleting current work unit & continuing...
[03:22:05] - Warning: Could not delete all work unit files (2): Core file absent
[03:22:05] Trying to send all finished work units
[03:22:05] + No unsent completed units remaining.
[03:22:05] - Preparing to get new work unit...
[03:22:05] + Attempting to get work packet
[03:22:05] - Will indicate memory of 1536 MB
[03:22:05] - Connecting to assignment server
[03:22:05] Connecting to http://assign.stanford.edu:8080/
[03:22:05] Posted data.
[03:22:05] Initial: 43AB; - Successful: assigned to (171.67.108.24).
[03:22:05] + News From Folding@Home: Welcome to Folding@Home
[03:22:05] Loaded queue successfully.
[03:22:05] Connecting to http://171.67.108.24:8080/
[03:22:11] Posted data.
[03:22:11] Initial: 0000; - Receiving payload (expected size: 4836516)
[03:22:20] - Downloaded at ~524 kB/s
[03:22:20] - Averaged speed for that direction ~507 kB/s
[03:22:20] + Received work.
[03:22:20] + Closed connections
[03:22:25] 
[03:22:25] + Processing work unit
[03:22:25] Core required: FahCore_a2.exe
[03:22:25] Core found.
[03:22:25] Working on Unit 03 [May 8 03:22:25]
[03:22:25] + Working ...
[03:22:25] - Calling './mpiexec -np 4 -host 127.0.0.1 ./FahCore_a2.exe -dir work/ -suffix 03 -checkpoint 20 -verbose -lifeline 6175 -version 602'

[03:22:25] 
[03:22:25] *------------------------------*
[03:22:25] Folding@Home Gromacs SMP Core
[03:22:25] Version 2.07 (Sun Apr 19 14:51:09 PDT 2009)
[03:22:25] 
[03:22:25] Preparing to commence simulation
[03:22:25] - Ensuring status. Please wait.
[03:22:34] - Looking at optimizations...
[03:22:34] - Working with standard loops on this execution.
[03:22:34] - Files status OK
[03:22:35] - Expanded 4836004 -> 24036661 (decompressed 497.0 percent)
[03:22:35] Called DecompressByteArray: compressed_data_size=4836004 data_size=24036661, decompressed_data_size=24036661 diff=0
[03:22:35] - Digital signature verified
[03:22:35] 
[03:22:35] Project: 2671 (Run 49, Clone 67, Gen 13)
[03:22:35] 
[03:22:35] Entering M.D.
[03:22:44] Completed 0 out of 250000 steps  (0%)
[03:22:53] 
[03:22:53] Folding@home Core Shutdown: INTERRUPTED
[03:22:57] CoreStatus = FF (255)
[03:22:57] Client-core communications error: ERROR 0xff
[03:22:57] Deleting current work unit & continuing...
[03:23:02] - Warning: Could not delete all work unit files (3): Core file absent
[03:23:02] Trying to send all finished work units
[03:23:02] + No unsent completed units remaining.
[03:23:02] - Preparing to get new work unit...
[03:23:02] + Attempting to get work packet
[03:23:02] - Will indicate memory of 1536 MB
[03:23:02] - Connecting to assignment server
[03:23:02] Connecting to http://assign.stanford.edu:8080/
[03:23:02] Posted data.
[03:23:02] Initial: 43AB; - Successful: assigned to (171.67.108.24).
[03:23:02] + News From Folding@Home: Welcome to Folding@Home
[03:23:02] Loaded queue successfully.
[03:23:02] Connecting to http://171.67.108.24:8080/
[03:23:02] Posted data.
[03:23:02] Initial: 0000; - Error: Bad packet type from server, expected work assignment
[03:23:03] - Attempt #1  to get work failed, and no other work to do.
             Waiting before retry.
[03:23:16] + Attempting to get work packet
[03:23:16] - Will indicate memory of 1536 MB
[03:23:16] - Connecting to assignment server
[03:23:16] Connecting to http://assign.stanford.edu:8080/
[03:23:16] Posted data.
[03:23:16] Initial: 43AB; - Successful: assigned to (171.67.108.24).
[03:23:16] + News From Folding@Home: Welcome to Folding@Home
[03:23:17] Loaded queue successfully.
[03:23:17] Connecting to http://171.67.108.24:8080/
[03:23:23] Posted data.
[03:23:23] Initial: 0000; - Receiving payload (expected size: 4843866)
[03:23:33] - Downloaded at ~473 kB/s
[03:23:33] - Averaged speed for that direction ~498 kB/s
[03:23:33] + Received work.
[03:23:33] + Closed connections
[03:23:38] 
[03:23:38] + Processing work unit
[03:23:38] Core required: FahCore_a2.exe
[03:23:38] Core found.
[03:23:38] Working on Unit 04 [May 8 03:23:38]
[03:23:38] + Working ...
[03:23:38] - Calling './mpiexec -np 4 -host 127.0.0.1 ./FahCore_a2.exe -dir work/ -suffix 04 -checkpoint 20 -verbose -lifeline 6175 -version 602'

[03:23:39] 
[03:23:39] *------------------------------*
[03:23:39] Folding@Home Gromacs SMP Core
[03:23:39] Version 2.07 (Sun Apr 19 14:51:09 PDT 2009)
[03:23:39] 
[03:23:39] Preparing to commence simulation
[03:23:39] - Ensuring status. Please wait.
[03:23:40] Called DecompressByteArray: compressed_data_size=4843354 data_size=24024181, decompressed_data_size=24024181 diff=0
[03:23:40] - Digital signature verified
[03:23:40] 
[03:23:40] Project: 2671 (Run 47, Clone 95, Gen 24)
[03:23:40] 
[03:23:40] Assembly optimizations on if available.
[03:23:40] Entering M.D.
[03:23:49] Run 47, Clone 95, Gen 24)
[03:23:49] 
[03:23:49] Entering M.D.
[03:30:43] pleted 2500 out of 250000 steps  (1%)

Re: Project: 2671 (Run 49, Clone 67, Gen 13) - LINCS WARNING

Posted: Sun May 10, 2009 2:36 am
by sick willie
This about the 6th time, on the same machine, with this result:

Code: Select all

23:54:06] 
[23:54:06] Project: 2671 (Run 49, Clone 67, Gen 13)
[23:54:06] 
[23:54:06] Assembly optimizations on if available.
[23:54:06] Entering M.D.
[23:54:14] Completed 0 out of 250000 steps  (0%)
[23:54:25] CoreStatus = FF (255)
[23:54:25] Client-core communications error: ERROR 0xff
[23:54:25] Deleting current work unit & continuing...
This is a stable folding machine. Please quit sending me this WU. :( I've lost about 36 hours folding time on this machine this week.

Re: Project: 2671 (Run 49, Clone 67, Gen 13) - LINCS WARNING

Posted: Sun May 10, 2009 10:56 pm
by sick willie
I've gotten this WU twice more since I posted this last night. :(

I delete it, do another WU, and then it's back to this one again.

Re: Project: 2671 (Run 49, Clone 67, Gen 13) - LINCS WARNING

Posted: Tue May 12, 2009 12:40 am
by sick willie
Is there anyone who can do anything about it, reading these posts? I deleted this WU this morning, downloaded a different one, came home this evening, and was back to this one. Roughly another 6 hours lost today. The same machine has been given this WU ten times. With the same result.

Re: Project: 2671 (Run 49, Clone 67, Gen 13) - LINCS WARNING

Posted: Tue May 12, 2009 2:50 am
by bruce
Your forum Mods can report the WU bad, but that has already been done.

I suggest that you change the MachineID of that client. That often helps.

2671 (Run 49, Clone 67, Gen 13) LINCS WARNING

Posted: Tue May 12, 2009 2:50 pm
by road-runner

Code: Select all

[14:07:35] Project: 2671 (Run 49, Clone 67, Gen 13)
[14:07:35] 
[14:07:35] Entering M.D.
[14:07:41] Using Gromacs checkpoints
NNODES=8, MYRANK=0, HOSTNAME=i7-computer-room
NNODES=8, MYRANK=2, HOSTNAME=i7-computer-room
NNODES=8, MYRANK=3, HOSTNAME=i7-computer-room
NNODES=8, MYRANK=5, HOSTNAME=i7-computer-room
NNODES=8, MYRANK=6, HOSTNAME=i7-computer-room
NNODES=8, MYRANK=7, HOSTNAME=i7-computer-room
NNODES=8, MYRANK=4, HOSTNAME=i7-computer-room
NODEID=2 argc=23
NODEID=3 argc=23
NNODES=8, MYRANK=1, HOSTNAME=i7-computer-room
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_03.tpr, VERSION 3.3.99_development_20070618 (single precision)
NODEID=6 argc=23
NODEID=7 argc=23
NODEID=1 argc=23
NODEID=4 argc=23
NODEID=5 argc=23
Note: tpx file_version 48, software version 64

Reading checkpoint file work/wudata_03.cpt generated: Sun May 10 12:09:45 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 '22866 system in water'
3500000 steps,   7000.0 ps (continuing from step 3250010,   6500.0 ps).
[14:07:44] Resuming from checkpoint
[14:07:44] Verified work/wudata_03.log
[14:07:44] Verified work/wudata_03.trr
[14:07:44] Verified work/wudata_03.xtc
[14:07:44] Verified work/wudata_03.edr
[14:07:45] Completed 10 out of 250000 steps  (0%)

Step 3250042, time 6500.08 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.005147, max 0.153813 (between atoms 12377 and 12379)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  12380  12382   90.0    0.1090   0.1243      0.1090
  12377  12379   90.0    0.1090   0.1258      0.1090

Step 3250043, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001596, max 0.062728 (between atoms 12377 and 12379)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 3250044, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.004634, max 0.145431 (between atoms 12377 and 12379)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 3250045, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 3.163745, max 111.267876 (between atoms 12377 and 12379)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  12380  12381   90.0    0.1110   0.9184      0.1090
  12377  12379   90.0    0.1249  12.2372      0.1090
Warning: 1-4 interaction between 12382 and 12384 at distance 27.405 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 3250046, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 97.013122, max 3927.294434 (between atoms 12380 and 12381)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  12377  12378   90.0    0.5107   3.1636      0.1090

Step 3250046, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 28.588696, max 1278.121338 (between atoms 14123 and 14125)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  14123  14124   90.0    0.1090   2.6711      0.1090
  14123  14125   90.0    0.1090 139.4242      0.1090
  14123  14126   90.0    0.1090   2.4982      0.1090
Warning: 1-4 interaction between 14122 and 14125 at distance 159.665 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 3250047, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max inf (between atoms 12545 and 12546)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  13436  13437   90.0    0.1090 88506837745270784.0000      0.1090
   8091   8092   90.0    0.1090   0.6913      0.1090
   8093   8094   90.1    0.1090 2206.7832      0.1090
   8093   8095   90.0    0.1090 214230.7031      0.1090

Step 3250047, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 3592659456.000000 (between atoms 21729 and 21730)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  21755  21757   91.1    0.1090 1038.9829      0.1090
  21766  21767   90.0    0.1010 6325004.0000      0.1010
  21729  21730   90.0    0.1090 391599872.0000      0.1090
  21731  21732   90.0    0.1090 655.0540      0.1090
  21731  21733  103.6    0.1090  92.5673      0.1090
   8093   8096   90.2    0.1090 2252.7615      0.1090
  12545  12546   90.0    0.1090      inf      0.1090
  12545  12547   90.0    0.1090      inf      0.1090
  12545  12548   90.0    0.1090      inf      0.1090
  12157  12159   90.0    0.1090 811939034455605248.0000      0.1090
  12160  12161   90.0    0.1090 337122116501504.0000      0.1090
  12163  12164   90.0    0.1090      inf      0.1090
  12169  12170   90.0    0.1090      inf      0.1090
  12536  12537   90.0    0.1090 12469709804677365760.0000      0.1090
  12536  12538   90.0    0.1090 12347545266738429952.0000      0.1090
   8097   8098   90.0    0.1090      inf      0.1090
   8097   8099   90.0    0.1090      inf      0.1090
   8106   8107   90.0    0.1010 208028544868024320.0000      0.1010
   8113   8114   90.0    0.1090 484044051209781248.0000      0.1090
  13445  13447   90.0    0.1090 869791141199872.0000      0.1090
  14167  14168   90.0    0.1090      inf      0.1090
  14167  14169   90.0    0.1090      inf      0.1090
  14123  14124   90.0    2.6711      inf      0.1090
  14123  14125   90.0  139.4242      inf      0.1090
  14123  14126   90.0    2.4982      inf      0.1090
  12371  12372   90.0    0.1090      inf      0.1090
  12371  12373   90.0    0.1090      inf      0.1090
  14061  14062   90.0    0.1080      inf      0.1080
  14063  14064  127.2    0.1080  17.6614      0.1080
  14186  14187   90.0    0.1090 14345243545198133248.0000      0.1090
  14157  14158   90.0    0.1090      inf      0.1090
  14157  14159   90.0    0.1090      inf      0.1090
  14157  14160   90.0    0.1090      inf      0.1090
  21721  21722   90.0    0.1080 807793806899412992.0000      0.1080
  14048  14049   90.0    0.1090 14879293574217728.0000      0.1090
  14086  14087   90.0    0.1090      inf      0.1090
  12448  12449   90.0    0.1010      inf      0.1010
   6492   6493   90.0    0.1010      inf      0.1010
   6492   6494   90.0    0.1010      inf      0.1010
  14020  14021   90.0    0.1090      inf      0.1090
  14092  14093   90.0    0.1080 19736.9160      0.1080
  12439  12441   90.0    0.1090   0.3957      0.1090
  12442  12443   90.0    0.1010      inf      0.1010
  12442  12444   90.0    0.1010      inf      0.1010
  12442  12445   90.0    0.1010      inf      0.1010
  14022  14023   90.0    0.1090 3554371.2500      0.1090
[14:07:35] Project: 2671 (Run 49, Clone 67, Gen 13)
[14:07:35] 
[14:07:35] Entering M.D.
[14:07:41] Using Gromacs checkpoints
NNODES=8, MYRANK=0, HOSTNAME=i7-computer-room
NNODES=8, MYRANK=2, HOSTNAME=i7-computer-room
NNODES=8, MYRANK=3, HOSTNAME=i7-computer-room
NNODES=8, MYRANK=5, HOSTNAME=i7-computer-room
NNODES=8, MYRANK=6, HOSTNAME=i7-computer-room
NNODES=8, MYRANK=7, HOSTNAME=i7-computer-room
NNODES=8, MYRANK=4, HOSTNAME=i7-computer-room
NODEID=2 argc=23
NODEID=3 argc=23
NNODES=8, MYRANK=1, HOSTNAME=i7-computer-room
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_03.tpr, VERSION 3.3.99_development_20070618 (single precision)
NODEID=6 argc=23
NODEID=7 argc=23
NODEID=1 argc=23
NODEID=4 argc=23
NODEID=5 argc=23
Note: tpx file_version 48, software version 64

Reading checkpoint file work/wudata_03.cpt generated: Sun May 10 12:09:45 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 '22866 system in water'
3500000 steps,   7000.0 ps (continuing from step 3250010,   6500.0 ps).
[14:07:44] Resuming from checkpoint
[14:07:44] Verified work/wudata_03.log
[14:07:44] Verified work/wudata_03.trr
[14:07:44] Verified work/wudata_03.xtc
[14:07:44] Verified work/wudata_03.edr
[14:07:45] Completed 10 out of 250000 steps  (0%)

Step 3250042, time 6500.08 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.005147, max 0.153813 (between atoms 12377 and 12379)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  12380  12382   90.0    0.1090   0.1243      0.1090
  12377  12379   90.0    0.1090   0.1258      0.1090

Step 3250043, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001596, max 0.062728 (between atoms 12377 and 12379)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 3250044, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.004634, max 0.145431 (between atoms 12377 and 12379)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 3250045, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 3.163745, max 111.267876 (between atoms 12377 and 12379)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  12380  12381   90.0    0.1110   0.9184      0.1090
  12377  12379   90.0    0.1249  12.2372      0.1090
Warning: 1-4 interaction between 12382 and 12384 at distance 27.405 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 3250046, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 97.013122, max 3927.294434 (between atoms 12380 and 12381)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  12377  12378   90.0    0.5107   3.1636      0.1090

Step 3250046, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 28.588696, max 1278.121338 (between atoms 14123 and 14125)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  14123  14124   90.0    0.1090   2.6711      0.1090
  14123  14125   90.0    0.1090 139.4242      0.1090
  14123  14126   90.0    0.1090   2.4982      0.1090
Warning: 1-4 interaction between 14122 and 14125 at distance 159.665 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 3250047, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max inf (between atoms 12545 and 12546)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  13436  13437   90.0    0.1090 88506837745270784.0000      0.1090
   8091   8092   90.0    0.1090   0.6913      0.1090
   8093   8094   90.1    0.1090 2206.7832      0.1090
   8093   8095   90.0    0.1090 214230.7031      0.1090

Step 3250047, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 3592659456.000000 (between atoms 21729 and 21730)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  21755  21757   91.1    0.1090 1038.9829      0.1090
  21766  21767   90.0    0.1010 6325004.0000      0.1010
  21729  21730   90.0    0.1090 391599872.0000      0.1090
  21731  21732   90.0    0.1090 655.0540      0.1090
  21731  21733  103.6    0.1090  92.5673      0.1090
   8093   8096   90.2    0.1090 2252.7615      0.1090
  12545  12546   90.0    0.1090      inf      0.1090
  12545  12547   90.0    0.1090      inf      0.1090
  12545  12548   90.0    0.1090      inf      0.1090
  12157  12159   90.0    0.1090 811939034455605248.0000      0.1090
  12160  12161   90.0    0.1090 337122116501504.0000      0.1090
  12163  12164   90.0    0.1090      inf      0.1090
  12169  12170   90.0    0.1090      inf      0.1090
  12536  12537   90.0    0.1090 12469709804677365760.0000      0.1090
  12536  12538   90.0    0.1090 12347545266738429952.0000      0.1090
   8097   8098   90.0    0.1090      inf      0.1090
   8097   8099   90.0    0.1090      inf      0.1090
   8106   8107   90.0    0.1010 208028544868024320.0000      0.1010
   8113   8114   90.0    0.1090 484044051209781248.0000      0.1090
  13445  13447   90.0    0.1090 869791141199872.0000      0.1090
  14167  14168   90.0    0.1090      inf      0.1090
  14167  14169   90.0    0.1090      inf      0.1090
  14123  14124   90.0    2.6711      inf      0.1090
  14123  14125   90.0  139.4242      inf      0.1090
  14123  14126   90.0    2.4982      inf      0.1090
  12371  12372   90.0    0.1090      inf      0.1090
  12371  12373   90.0    0.1090      inf      0.1090
  14061  14062   90.0    0.1080      inf      0.1080
  14063  14064  127.2    0.1080  17.6614      0.1080
  14186  14187   90.0    0.1090 14345243545198133248.0000      0.1090
  14157  14158   90.0    0.1090      inf      0.1090
  14157  14159   90.0    0.1090      inf      0.1090
  14157  14160   90.0    0.1090      inf      0.1090
  21721  21722   90.0    0.1080 807793806899412992.0000      0.1080
  14048  14049   90.0    0.1090 14879293574217728.0000      0.1090
  14086  14087   90.0    0.1090      inf      0.1090
  12448  12449   90.0    0.1010      inf      0.1010
   6492   6493   90.0    0.1010      inf      0.1010
   6492   6494   90.0    0.1010      inf      0.1010
  14020  14021   90.0    0.1090      inf      0.1090
  14092  14093   90.0    0.1080 19736.9160      0.1080
  12439  12441   90.0    0.1090   0.3957      0.1090
  12442  12443   90.0    0.1010      inf      0.1010
  12442  12444   90.0    0.1010      inf      0.1010
  12442  12445   90.0    0.1010      inf      0.1010
  14022  14023   90.0    0.1090 3554371.2500      0.1090

Step 3250047, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max inf (between atoms 12331 and 12332)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  12331  12332   90.0    0.1090      inf      0.1090
  12331  12333   90.0    0.1090      inf      0.1090
  12383  12385   90.0    0.1010   1.6627      0.1010
  12383  12386   90.0    0.1011   2.0980      0.1010
  13525  13526   90.0    0.1090   0.6698      0.1090
  13535  13536   90.0    0.1010   4.7499      0.1010
  12342  12343   90.0    0.1010      inf      0.1010
  21721  21722   90.0    0.1080 807793806899412992.0000      0.1080

t = 6500.094 ps: Water molecule starting at atom 61585 can not be settled.
Check for bad contacts and/or reduce the timestep.



Step 3250047, time 6500.09 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max inf (between atoms 12331 and 12332)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  12331  12332   90.0    0.1090      inf      0.1090
  12331  12333   90.0    0.1090      inf      0.1090
  12383  12385   90.0    0.1010   1.6627      0.1010
  12383  12386   90.0    0.1011   2.0980      0.1010
  13525  13526   90.0    0.1090   0.6698      0.1090
  13535  13536   90.0    0.1010   4.7499      0.1010
  12342  12343   90.0    0.1010      inf      0.1010
  21721  21722   90.0    0.1080 807793806899412992.0000      0.1080

t = 6500.094 ps: Water molecule starting at atom 61585 can not be settled.
Check for bad contacts and/or reduce the timestep.

Re: 2671 (Run 49, Clone 67, Gen 13) LINCS WARNING

Posted: Tue May 12, 2009 2:56 pm
by bollix47
viewtopic.php?f=19&t=9842

Edit by Mod: Threads merged
-b

Re: Project: 2671 (Run 49, Clone 67, Gen 13) - LINCS WARNING

Posted: Wed May 13, 2009 1:37 am
by kasson
I stopped this one manually, so it shouldn't get assigned again.
All times are UTC
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