Minirosetta 2.14

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Message 5147 - Posted: 24 May 2010, 22:18:15 UTC

Posts for this series of work units were being posted under thread "Minirosetta 2.12" so I thought I would create one for the current series of work units.

On WU 1831281
Had this error

ERROR: Cannot open patchdock file: 1fAc_2odh.patchdock
ERROR:: Exit from: src/protocols/ProteinInterfaceDesign/read_patchdock.cc line: 101
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

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Message 5149 - Posted: 27 May 2010, 8:34:10 UTC

Had this WU 1834847 that reached 86.402% completion sometime between 6 and 7 hours run time, it was still at 86.402% after 19 hours 21 minutes so I aborted it.
If I have read the slot directory right then it did 167 checkpoints but just did not progress.

My preferences are set for 6 hours so the WU should of timed out for taking so long, if it still had not finished the first decoy then the WU has a problem.
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Message 5150 - Posted: 28 May 2010, 0:46:36 UTC

ERROR: ERROR: FragmentIO: could not open file myoglobin.frag9.rosetta.tab
ERROR:: Exit from: ..\..\src\core\fragment\FragmentIO.cc line: 258
BOINC:: Error reading and gzipping output datafile: default.out

On This WU

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Message 5151 - Posted: 28 May 2010, 5:59:45 UTC - in response to Message 5150.  

parvalbumin_redo_targets_CONTROL_BOINC_abrelax.score12.fastrelax.v1_SAVE_ALL_OUT_14803_2_1
http://ralph.bakerlab.org/workunit.php?wuid=1631447

This unit crashed in similiar fashion at both hosts crunching it.

http://ralph.bakerlab.org/result.php?resultid=1848472


2010-05-28 07:30:03 ralph@home Output file parvalbumin_redo_targets_CONTROL_BOINC_abrelax.score12.fastrelax.v1_SAVE_ALL_OUT_14803_2_1_0 for task parvalbumin_redo_targets_CONTROL_BOINC_abrelax.score12.fastrelax.v1_SAVE_ALL_OUT_14803_2_1 absent
# cpu_run_time_pref: 28800
======================================================
DONE :: 50 starting structures 28554.5 cpu seconds
This process generated 50 decoys from 50 attempts
======================================================

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

</stderr_txt>
<message>
<file_xfer_error>
<file_name>parvalbumin_redo_targets_CONTROL_BOINC_abrelax.score12.fastrelax.v1_SAVE_ALL_OUT_14803_2_1_0</file_name>
<error_code>-161</error_code>
</file_xfer_error>

</message>
]]>
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Message 5152 - Posted: 28 May 2010, 20:54:18 UTC - in response to Message 5151.  

1849542


ERROR: Unable to open weights. Neither ./pcs.weight1.patch nor minirosetta_database\scoring/weights/pcs.weight1.patch.wts_patchexist
ERROR:: Exit from: ..\..\src\core\scoring\ScoreFunction.cc line: 262
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish
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Message 5153 - Posted: 29 May 2010, 0:34:50 UTC - in response to Message 5152.  

1849542


ERROR: Unable to open weights. Neither ./pcs.weight1.patch nor minirosetta_database\scoring/weights/pcs.weight1.patch.wts_patchexist
ERROR:: Exit from: ..\..\src\core\scoring\ScoreFunction.cc line: 262
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish



Same error on 3 work units
1849128
1849129
1849130

Also had a file transfer error (XFER ERROR)
on 1848730

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Message 5154 - Posted: 30 May 2010, 2:01:41 UTC - in response to Message 5153.  
Last modified: 30 May 2010, 2:02:45 UTC

[quote]1849542


ERROR: Unable to open weights. Neither ./pcs.weight1.patch nor minirosetta_database\scoring/weights/pcs.weight1.patch.wts_patchexist
ERROR:: Exit from: ..\..\src\core\scoring\ScoreFunction.cc line: 262
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish


Here is another with the same error
1849490
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Message 5155 - Posted: 5 Jun 2010, 7:06:43 UTC

Completed successfully and validated, but with an odd error message:

ERROR: ERROR: Residue not supported by Placement coordinate constraint machinery
ERROR:: Exit from: ..\..\src\protocols\ProteinInterfaceDesign\movers\PlaceUtils.cc line: 281
called boinc_finish

http://ralph.bakerlab.org/result.php?resultid=1851904

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Message 5157 - Posted: 6 Jun 2010, 16:52:24 UTC - in response to Message 5155.  

Same here:
1851619
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Message 5159 - Posted: 19 Jul 2010, 20:39:10 UTC

No work, no debug.... :-)
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Message 5160 - Posted: 21 Jul 2010, 18:36:39 UTC - in response to Message 5159.  

No work, no debug.... :-)


oh, well....thank you!!
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Message 5164 - Posted: 6 Sep 2010, 8:27:59 UTC

Another batch of this series and another batch of computation errors!
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Message 5165 - Posted: 6 Sep 2010, 16:14:23 UTC
Last modified: 6 Sep 2010, 16:14:58 UTC

SAXS-rescore-1eovA__14879_15

Mon Sep 6 12:03:24 2010 ralph@home Output file SAXS-rescore-1eovA__14879_15_0_0 for task SAXS-rescore-1eovA__14879_15_0 absent

======================================================
DONE :: 1 starting structures 12857.1 cpu seconds
This process generated 6 decoys from 6 attempts
======================================================

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

</stderr_txt>
<message>
<file_xfer_error>
<file_name>SAXS-rescore-1eovA__14879_15_0_0</file_name>
<error_code>-161</error_code>
</file_xfer_error>
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Message 5166 - Posted: 6 Sep 2010, 17:39:42 UTC

SAXS-rescore-1ks9A__14879_6_1

The same error as Snagletooth.
ma 06 sep 2010 17:07:49 CEST	ralph@home	Output file SAXS-rescore-1ks9A__14879_6_1_0 for task SAXS-rescore-1ks9A__14879_6_1 absent

stderr out:
======================================================
DONE ::     1 starting structures  13314.1 cpu seconds
This process generated      9 decoys from       9 attempts
======================================================

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

</stderr_txt>
<message>
<file_xfer_error>
  <file_name>SAXS-rescore-1ks9A__14879_6_1_0</file_name>
  <error_code>-161</error_code>
</file_xfer_error>


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Message 5167 - Posted: 6 Sep 2010, 20:31:34 UTC - in response to Message 5166.  
Last modified: 6 Sep 2010, 20:39:16 UTC

No luck here either on those "SAXS-rescore".
For 13 tasks crunched so far on two machines (1 windows, 1 linux), all 13 got "computation error".
<message>
<file_xfer_error>
  <file_name>SAXS-rescore-1tf4B__14879_16_0_0</file_name>
  <error_code>-161</error_code>
</file_xfer_error>

</message>


For Your Information.

EDIT

I just saw one WU finish on win7, got to 100% and then this:
2010-09-06 22:37:57	ralph@home	Output file SAXS-rescore-1mgtA__14879_16_0_0 for task SAXS-rescore-1mgtA__14879_16_0 absent

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Message 5168 - Posted: 6 Sep 2010, 20:39:20 UTC - in response to Message 5167.  

Same here 1906579
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Message 5169 - Posted: 7 Sep 2010, 6:26:05 UTC

Another one here
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Message 5171 - Posted: 7 Sep 2010, 7:58:12 UTC

SAXS-rescore-1qfjC__14882_5_0

stderr out:
ERROR: ERROR: Unable to open silent_input file: 'default.out'
ERROR:: Exit from: src/core/io/silent/SilentFileData.cc line: 86
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish
Watchdog active.


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Message 5172 - Posted: 7 Sep 2010, 8:55:50 UTC

Compute error in WU: SAXS-rescore-1eudA__14881_3_1 with the following error:

ERROR: Option file open failed for: 1eudA-linker_sampler_protocol-saxs-1.0.flags
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Message 5173 - Posted: 7 Sep 2010, 11:56:19 UTC
Last modified: 7 Sep 2010, 12:04:49 UTC

All SAXS tasks erroed out
<file_xfer_error>
  <file_name>SAXS-rescore-1gcyA__14879_3_0_0</file_name>
  <error_code>-161</error_code>
</file_xfer_error>
after finishing wu's (cca 42 000 s).
XP 32bit SAXS-rescore-1bi5A__14879_2_1, SAXS-rescore-1mgtA__14879_12_0
XP 64bit SAXS-rescore-1gcyA__14879_3_0, SAXS-rescore-1d5rA__14879_7_1, SAXS-rescore-1dzfA__14879_15_1

No credit granted.
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