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CraniuMod

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Message 63463 - Posted: 26 Sep 2009, 21:41:46 UTC - in response to Message 63440.  
Last modified: 26 Sep 2009, 22:05:05 UTC

Will keep an eye out for this from hereon out. Has not happened on Rosetta before.
281082606
Name 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0
Workunit 256342237
Created 15 Sep 2009 20:41:03 UTC
Sent 15 Sep 2009 20:53:55 UTC
Received 23 Sep 2009 20:09:18 UTC
Server state Over
Outcome Client error
Client state Aborted by user
Exit status -197 (0xffffff3b)
Computer ID 926185
Report deadline 25 Sep 2009 20:53:55 UTC
CPU time 19541.34
stderr out
<core_client_version>6.6.36</core_client_version>
<![CDATA[
<message>
aborted by user
</message>
]]>
Validate state Invalid
Claimed credit 78.92439165502
Granted credit 0
application version 1.97



Did you abort this task or what happened? 5.5 hrs is not really a long run.



Client was reporting this as running for 38 hrs. I did abort.
Went back to client log and found the below

9/23/2009 4:07:32 PM rosetta@home task 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0 resumed by user
9/23/2009 4:07:33 PM rosetta@home Restarting task 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0 using minirosetta version 197
9/23/2009 4:08:15 PM rosetta@home Task 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0 exited with zero status but no \'finished\' file
9/23/2009 4:08:15 PM rosetta@home If this happens repeatedly you may need to reset the project.
9/23/2009 4:08:15 PM rosetta@home Restarting task 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0 using minirosetta version 197
9/23/2009 4:08:23 PM rosetta@home task 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0 aborted by user
9/23/2009 4:08:24 PM World Community Grid Resuming task faah8210_ZINC04849622_xmdEq_2R5P1c_01_0 using faah version 607
9/23/2009 4:08:38 PM rosetta@home update requested by user
9/23/2009 4:08:44 PM rosetta@home Sending scheduler request: Requested by user.
9/23/2009 4:08:44 PM rosetta@home Reporting 2 completed tasks, not requesting new tasks
9/23/2009 4:08:48 PM rosetta@home Scheduler request completed
9/23/2009 4:08:48 PM rosetta@home [error] garbage_collect(); still have active task for acked result 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0; state 5
9/23/2009 4:08:49 PM rosetta@home Computation for task 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0 finished
9/23/2009 4:08:49 PM rosetta@home Output file 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0_0 for task 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0 absent
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Message 63472 - Posted: 27 Sep 2009, 5:43:57 UTC - in response to Message 63463.  
Last modified: 27 Sep 2009, 5:54:19 UTC

9/23/2009 4:07:32 PM rosetta@home task 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0 resumed by user
9/23/2009 4:07:33 PM rosetta@home Restarting task 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0 using minirosetta version 197
9/23/2009 4:08:15 PM rosetta@home Task 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0 exited with zero status but no \'finished\' file
9/23/2009 4:08:15 PM rosetta@home If this happens repeatedly you may need to reset the project.
9/23/2009 4:08:15 PM rosetta@home Restarting task 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0 using minirosetta version 197
9/23/2009 4:08:23 PM rosetta@home task 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0 aborted by user
9/23/2009 4:08:24 PM World Community Grid Resuming task faah8210_ZINC04849622_xmdEq_2R5P1c_01_0 using faah version 607
9/23/2009 4:08:38 PM rosetta@home update requested by user
9/23/2009 4:08:44 PM rosetta@home Sending scheduler request: Requested by user.
9/23/2009 4:08:44 PM rosetta@home Reporting 2 completed tasks, not requesting new tasks
9/23/2009 4:08:48 PM rosetta@home Scheduler request completed
9/23/2009 4:08:48 PM rosetta@home [error] garbage_collect(); still have active task for acked result 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0; state 5
9/23/2009 4:08:49 PM rosetta@home Computation for task 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0 finished
9/23/2009 4:08:49 PM rosetta@home Output file 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0_0 for task 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0 absent


Looks to me like 1.97 is subject to a new variant of the lockfile problem, but at least a little more information appears to be reported for the new variant.

You may need to reboot or restart BOINC in order to clear away the remnants of the lockfile problem, if it\'s affecting any workunits that try to use the same slot later.

Also, I\'d consider the possibility that 1.97 and faah 6.07 have some kind of conflict in how they handle zinc.
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Message 63558 - Posted: 2 Oct 2009, 6:16:58 UTC

This one took 7hrs, 33min to do ( 1 model ) on a 3ghz rig, dam!

frb_0_8__rnd2_aln_list_mike_chosen_bestaln.alns.homolog_csts_oct09_hb_t303__IGNORE_THE_REST_1FEZA_8_15003_15

http://boinc.bakerlab.org/rosetta/workunit.php?wuid=259645046

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CraniuMod

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Message 63570 - Posted: 2 Oct 2009, 16:59:52 UTC - in response to Message 63472.  

9/23/2009 4:07:32 PM rosetta@home task 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0 resumed by user
9/23/2009 4:07:33 PM rosetta@home Restarting task 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0 using minirosetta version 197
9/23/2009 4:08:15 PM rosetta@home Task 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0 exited with zero status but no \'finished\' file
9/23/2009 4:08:15 PM rosetta@home If this happens repeatedly you may need to reset the project.
9/23/2009 4:08:15 PM rosetta@home Restarting task 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0 using minirosetta version 197
9/23/2009 4:08:23 PM rosetta@home task 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0 aborted by user
9/23/2009 4:08:24 PM World Community Grid Resuming task faah8210_ZINC04849622_xmdEq_2R5P1c_01_0 using faah version 607
9/23/2009 4:08:38 PM rosetta@home update requested by user
9/23/2009 4:08:44 PM rosetta@home Sending scheduler request: Requested by user.
9/23/2009 4:08:44 PM rosetta@home Reporting 2 completed tasks, not requesting new tasks
9/23/2009 4:08:48 PM rosetta@home Scheduler request completed
9/23/2009 4:08:48 PM rosetta@home [error] garbage_collect(); still have active task for acked result 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0; state 5
9/23/2009 4:08:49 PM rosetta@home Computation for task 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0 finished
9/23/2009 4:08:49 PM rosetta@home Output file 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0_0 for task 1fv5A_ZNMP_ABRELAX_tetraR_IGNORE_THE_REST_ZINC_METALLOPROTEIN-1fv5A-_14711_576_0 absent


Looks to me like 1.97 is subject to a new variant of the lockfile problem, but at least a little more information appears to be reported for the new variant.

You may need to reboot or restart BOINC in order to clear away the remnants of the lockfile problem, if it\'s affecting any workunits that try to use the same slot later.

Also, I\'d consider the possibility that 1.97 and faah 6.07 have some kind of conflict in how they handle zinc.


Did as suggested and all appears to be well although I haven\'t seen a zinc go through. Thanks.
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Message 63574 - Posted: 2 Oct 2009, 22:29:43 UTC

Another pig of a task, this one on my quad took 8hrs, 2min for 1 model.

frb_0_8__rnd2_aln_list_mike_chosen_bestaln.alns.homolog_csts_oct09_hb_t305__IGNORE_THE_REST_1LARA_6_15004_15_0

http://boinc.bakerlab.org/rosetta/workunit.php?wuid=259645182

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clayton1966

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Message 63654 - Posted: 13 Oct 2009, 6:17:52 UTC

This is the first task I have ever aborted but after over 12 hours aqnd only 3% finish I figured something was stuck. Here are the log messages I could find regarding this particular task.

10/12/2009 11:03:57 AM rosetta@home Starting task histone_loopbuild_run1_14925_57751_1 using minirosetta version 197
10/12/2009 11:13:34 PM rosetta@home task histone_loopbuild_run1_14925_57751_1 aborted by user
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Message 63670 - Posted: 13 Oct 2009, 19:26:38 UTC

Hi

This WU \"Rossmann2X3_036_15149_10247\" probably have stopped at 30,250% while the CPU time proceded. After pause-resume it finished elapsing app. 9 hours. In report 7870 sec is the CPU time.

http://boinc.bakerlab.org/rosetta/result.php?resultid=287006963
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Message 64445 - Posted: 12 Dec 2009, 6:25:53 UTC

This was done on my quad, on a 4hr run time pref it showed 6hr, 50min boinc time.

Biggest i\'ve had in a while.

broker_idealclose_kic10_hb_t328__IGNORE_THE_REST_16455_612_0

http://boinc.bakerlab.org/rosetta/workunit.php?wuid=277137434

======================================================
DONE :: 2 starting structures 24608.2 cpu seconds
This process generated 2 decoys from 2 attempts
======================================================

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Message 65291 - Posted: 12 Feb 2010, 2:59:07 UTC

My runtime is 4hrs this ran just over 8hrs on a 3Ghz intel.

t365__boinc_filtered_loopbuild_threading_cst_all_tex_IGNORE_THE_REST_16902_9991_0

http://boinc.bakerlab.org/rosetta/workunit.php?wuid=289111193
=========================================================================================
Watchdog active.
# cpu_run_time_pref: 14400
Continuing computation from checkpoint: chk_S_1WB9A_12_0001_FastRelax__chk1_fa ... success!
Continuing computation from checkpoint: chk_S_1WB9A_12_0001_FastRelax__chk2_fa ... success!
Continuing computation from checkpoint: chk_S_1WB9A_12_0001_FastRelax__chk3_fa ... success!
Continuing computation from checkpoint: chk_S_1WB9A_12_0001_FastRelax__chk4_fa ... success!
BOINC:: CPU time: 29194s, 14400s + 14400s[2010- 2-12 13:38:58:] :: BOINC
WARNING! cannot get file size for default.out.gz: could not open file.
Output exists: default.out.gz Size: -1
InternalDecoyCount: 0 (GZ)
-----
0
-----
Stream information inconsistent.
Writing W_0000001
======================================================
DONE :: 1 starting structures 29194 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
called boinc_finish
SIGSEGV: segmentation violation

</stderr_txt>

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Message 65443 - Posted: 2 Mar 2010, 1:52:37 UTC

This ran over my 4hr time set as you can see, on an intel 2.9Ghz.

t323__boinc_filtered_loopbuild_threading_cst_lb_tex_IGNORE_THE_REST_16900_6289_0

http://boinc.bakerlab.org/rosetta/workunit.php?wuid=292851592

InternalDecoyCount: 0
======================================================
DONE :: 1 starting structures 28890.9 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
called boinc_finish

Just over 8hrs.

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Message 65493 - Posted: 9 Mar 2010, 10:21:46 UTC - in response to Message 65443.  

This one took a long time.
placestub_1zvy_1zma_ppk_ProteinInterfaceDesign_28Feb2010_18489_296_0
http://boinc.bakerlab.org/rosetta/result.php?resultid=322582319

CPU time: 15685.67
preferred time: 2h
application version: 2.05
OS: WinXP 64
BOINC Manager: 6.10.36
CPU: phenom II 945 (3GHz)

DONE :: 2 starting structures 15685.5 cpu seconds
This process generated 2 decoys from 2 attempts

now, what surprised me the most:
claimed credit: 92.63
granted credit: 0.38
Did something go wrong during validation or during crunching ?
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Message 65498 - Posted: 10 Mar 2010, 3:14:45 UTC
Last modified: 10 Mar 2010, 3:15:17 UTC

This took double my run time, on my 2.9 intel.

373AA_boinc_slac373_loopbuild_threading_firas_IGNORE_THE_REST_18610_7623_0

http://boinc.bakerlab.org/rosetta/workunit.php?wuid=294620614


BOINC:: CPU time: 29305.1s, 14400s + 14400s[2010- 3-10 13:26:16:] :: BOINC
InternalDecoyCount: 0
======================================================
DONE :: 1 starting structures 29305.1 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
called boinc_finish
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Message 65527 - Posted: 12 Mar 2010, 3:21:07 UTC

Here\'s another long one, this was on my intel quad.

aqp9__boinc_aqp9_run02_blast_yfsong_loopbuild_threading_cst_relax_yfsong_IGNORE_THE_REST_18418_2895_1

http://boinc.bakerlab.org/rosetta/workunit.php?wuid=294212467

BOINC:: CPU time: 28906.1s, 14400s + 14400s[2010- 3-12 14: 7:17:] :: BOINC
InternalDecoyCount: 0
======================================================
DONE :: 1 starting structures 28906.1 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
called boinc_finish

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Message 65571 - Posted: 17 Mar 2010, 3:08:55 UTC
Last modified: 17 Mar 2010, 3:09:32 UTC

This took 8hrs, 2min on my 3ghz intel.

aqp9__boinc_aqp9_fast_run01_yfsong_loopbuild_threading_cst_relax_superfast_yfsong_IGNORE_THE_REST_18658_1421_0

http://boinc.bakerlab.org/rosetta/workunit.php?wuid=296064742

# cpu_run_time_pref: 14400
Continuing computation from checkpoint: chk_S_2B6OA_15_0001_Remodel__loop_1_0_0_S ... success!
BOINC:: CPU time: 28914.7s, 14400s + 14400s[2010- 3-17 13:39:17:] :: BOINC
InternalDecoyCount: 0
======================================================
DONE :: 1 starting structures 28914.7 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
called boinc_finish
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Message 65639 - Posted: 25 Mar 2010, 18:31:33 UTC

Does anyone look at long running models anymore? I have been seeing two to three per week.

-Matt

Win 7 64 bit

v2FcInnerW_1dAl_3fk8_ProteinInterfaceDesign_15Mar2010_18672_235_0

http://boinc.bakerlab.org/rosetta/result.php?resultid=326997251

<core_client_version>6.10.18</core_client_version>

======================================================
DONE :: 2 starting structures 20222.2 cpu seconds
This process generated 2 decoys from 2 attempts
======================================================

Validate state Valid
Claimed credit 115.549211591099
Granted credit 0.467169393634457
application version 2.05
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Trotador

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Message 65662 - Posted: 28 Mar 2010, 14:51:07 UTC

Not sure if they all fall within this category
regards



Task ID 327672671
Name v2FcInnerW_1dAl_1UCH_ProteinInterfaceDesign_15Mar2010_18672_216_0

======================================================
DONE :: 2 starting structures 25768.5 cpu seconds
This process generated 17 decoys from 17 attempts
======================================================
called boinc_finish

</stderr_txt>
]]>

Validate state Valid
Claimed credit 179.886682155965
Granted credit 13.8316680387615
application version 2.05

Task ID 327464846
Name v2FcInnerW_1dAl_2r39_ProteinInterfaceDesign_15Mar2010_18672_188_0



======================================================
DONE :: 49 starting structures 10799 cpu seconds
This process generated 49 decoys from 49 attempts
======================================================

BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down cleanly ...
called boinc_finish

</stderr_txt>
]]>

Validate state Valid
Claimed credit 75.3815505458785
Granted credit 9.5733070767376
application version 2.05


Task ID 326922282
Name placestub_alt_denovo_1zvy_3d6j_ProteinInterfaceDesign_21Mar2010_18705_75_0
Workunit 298345588

======================================================
DONE :: 2 starting structures 13226.9 cpu seconds
This process generated 2 decoys from 2 attempts
======================================================

BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down cleanly ...
called boinc_finish

</stderr_txt>
]]>

Validate state Valid
Claimed credit 78.282098375707
Granted credit 0.513724378027017
application version 2.05


Task ID 326825643
Name placestub_alt_denovo_1zvy_2vg9_ProteinInterfaceDesign_21Mar2010_18705_50_0
Workunit 298255310

======================================================
DONE :: 7 starting structures 11606 cpu seconds
This process generated 7 decoys from 7 attempts
======================================================

BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down cleanly ...
called boinc_finish

</stderr_txt>
]]>

Validate state Valid
Claimed credit 68.6891373975153
Granted credit 1.04329606606261
application version 2.05


Task ID 326822780
Name v2FcInnerW_1dAl_2iwx_ProteinInterfaceDesign_15Mar2010_18672_122_0
Workunit 298252600

======================================================
DONE :: 1 starting structures 25789.3 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
called boinc_finish

</stderr_txt>
]]>

Validate state Valid
Claimed credit 152.642238209485
Granted credit 0.732511919011592
application version 2.05

Task ID 326401609
Name v2FcInnerW_1dAl_1YRV_ProteinInterfaceDesign_15Mar2010_18672_115_0
Workunit 297855809

======================================================
DONE :: 36 starting structures 11274.3 cpu seconds
This process generated 36 decoys from 36 attempts
======================================================

BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down cleanly ...
called boinc_finish

</stderr_txt>
]]>

Validate state Valid
Claimed credit 66.961941133408
Granted credit 9.51201988583631
application version 2.05
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Sid Celery

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Message 65664 - Posted: 28 Mar 2010, 15:20:36 UTC

Another long-running model on this task type running on W7 64bit

v2FcInnerW_1dAl_3HMH_ProteinInterfaceDesign_15Mar2010_18672_208_0
<core_client_version>6.10.36</core_client_version>
[...]
# cpu_run_time_pref: 28800
BOINC:: CPU time: 43407.1s, 14400s + 28800s[2010- 3-27 4:52:24:] :: BOINC
InternalDecoyCount: 46
======================================================
DONE :: 2 starting structures 43407.1 cpu seconds
This process generated 46 decoys from 46 attempts
======================================================
called boinc_finish
[...]
Claimed credit 186.641773268041
Granted credit 11.7636703830492
application version 2.05

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Mad_Max

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Message 65731 - Posted: 12 Apr 2010, 18:09:46 UTC

453AA_boinc_slac453_loopbuild_threading_firas_IGNORE_THE_REST_19484_6668_0
1 model took about ~4 hours of CPU time(3 Ghrz Athlon II X2 250), and client starts second model, ignoring Target CPU Time = 2 hours
Result - task killed by Watchdog at 6 hours from start(2+4), ~2 hours of CPU time lost (time spend on second model)
I met this error already many times before with the tasks of this type (* boinc * loopbuild_threading *). So now I abort them if I see them in the queue. But it was missed and got the same error.
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Message 66225 - Posted: 19 May 2010, 15:36:52 UTC

(Report format copied from above - seems to make sense)

A long-running model on this task, running on a 32-bit Vista laptop:

rhoA15May2010_1lb1_2j49_ProteinInterfaceDesign_15May2010_20686_35_0
<core_client_version>6.10.43</core_client_version>
[...]
# cpu_run_time_pref: 21600
BOINC:: CPU time: 36425.4s, 14400s + 21600s[2010- 5-19 11:49:16:] :: BOINC
InternalDecoyCount: 1206
======================================================
DONE :: 2 starting structures 36425.4 cpu seconds
This process generated 1206 decoys from 1206 attempts
======================================================
called boinc_finish
[...]
Claimed credit 98.1363273365197
Granted credit 81.0898045070925
application version 2.14


What gets me about this is that 1205 decoys seemed to run within my 6 hour runtime, then the last decoy had to get shut-down by the watchdog after exceeding 4 hours. Was I just unlucky? The credit award was still reasonable.
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Tackleway

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Joined: 3 May 10
Posts: 3
Credit: 11,886
RAC: 0
Message 66226 - Posted: 19 May 2010, 17:22:09 UTC

Thoroughly un impressed. Task implied 3...hrs to complete runs for 6.5hrs
claims 84.511 credits then is granted 6.83 credits.
this is not good VFM I will not be processing further tasks that look like

rhoA15May2010_1lb1_1rw1_ProteinInterfaceDesign_15May2010_20686_107_0

339844150 310311035 19 May 2010 5:56:27 UTC 19 May 2010 17:02:41 UTC Over Success Done 21,938.98 84.51 6.83
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