Bug reports for 5.96

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Profile m.mitch
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Message 4065 - Posted: 26 May 2008, 8:57:47 UTC

The last couple of work units stalled at 21 seconds. BOINC Manger reported them running but there were no changes to completion times or percentage done.

[urlhttp://ralph.bakerlab.org/workunit.php?wuid=902848]Here\'s a link[/URL].

The box is running Kubuntu 8.04 on a P4.



Click here to join the #1 Aussie Alliance on RALPH
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Message 4070 - Posted: 26 May 2008, 15:42:36 UTC
Last modified: 26 May 2008, 15:44:34 UTC

Had 1 5.96 task fail:

http://ralph.bakerlab.org/result.php?resultid=982220

<core_client_version>5.10.45</core_client_version>
<![CDATA[
<message>
- exit code -1073741819 (0xc0000005)
</message>
<stderr_txt>
# cpu_run_time_pref: 3600
# random seed: 1326558


Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x0093E2D2 write attempt to address 0x0DC57000

Engaging BOINC Windows Runtime Debugger...

... theres alot more of the error message



All of the other 5.96 tasks assigned to that host seem to have completed or are running just fine so far.
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Jipsu

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Message 4074 - Posted: 26 May 2008, 18:48:38 UTC

http://ralph.bakerlab.org/result.php?resultid=983408 failed.

<core_client_version>5.10.45</core_client_version>
<![CDATA[
<message>
- exit code -1073741819 (0xc0000005)
</message>
<stderr_txt>
# cpu_run_time_pref: 3600
# random seed: 1326360


Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x00BF0601 read attempt to address 0x0E109000

Engaging BOINC Windows Runtime Debugger...
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Hans Sveen

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Message 4086 - Posted: 28 May 2008, 9:00:10 UTC
Last modified: 28 May 2008, 9:44:32 UTC

Hello!
Just wanted to report some odd behavior on this work unit WU
It does not show any thing in the \"Searching\", \"Accepted\" or \"Low Energy\" frames when using the \"Show graphics\" button.

Snapshot to graphics: http://hans.snodig.net/bilder/Ralph1.gif


One taken some time later: http://hans.snodig.net/bilder/Ralph2.gif

Sorry for the big pictures, hope shows ok.
It seem to be running well.
Hope this may help in debbugging vers.5.96 if needed!
Host Id
running boinc 5.10.45.

Some editing, fixing links!

Update: Another from the same series twist ring twist angel WU don\'t show this behaviour , the former wu has some kind of internal error, we\'ll see if it finishes!


With regards,


Hans Sveen
Oslo, Norway

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Profile David Emigh
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Message 4093 - Posted: 31 May 2008, 12:28:32 UTC

Compute error at 13 seconds:

file_xfer_error

ERROR:: Unable to determine sequence length from pdb file

BAK1lcj_loop_model_biased_clusterCC00_4096_6_0
RALPH and Rosie sittin' in a tree,
F - O - L - D - I - N - G!
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Odysseus

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Message 4095 - Posted: 1 Jun 2008, 2:25:07 UTC
Last modified: 1 Jun 2008, 2:25:46 UTC

I happened to open Activity Monitor on my dual-G5 Mac (OS v10.4.11) while a task was preëmpted, and it shows rosetta_beta_5.96_powerpc-apple-darwin using slightly over 1% of a CPU—although BOINC Manager (v5.10.45) displays its status as “Waiting to run” (about half done), and other apps, specifically einstein_S5R3 at the moment, show zero CPU usage under the same circumstances. Some kind of ‘thread leak’? FWIW the apps that are running now (at 90+% CPU each) are setiathome-enhanced and astropulse (SETI@home Beta).
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Message 4096 - Posted: 1 Jun 2008, 7:03:42 UTC
Last modified: 1 Jun 2008, 7:08:10 UTC

Hello all,

This task: resultid=1022982 had a error after 18 seconds:
Process exited with code 1 (0x1, -255), ERROR:: Exit from: input_pdb.cc line: 3030
OS: Ubuntu 7.10 x86, Boinc 5.10.45.

Edit: Saw I had the second run, the first run had the same error on W-XP.

Have a nice day,
Path7.
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Profile [AF>Le_Pommier] ninicool
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Message 4097 - Posted: 1 Jun 2008, 21:07:55 UTC

Hello,

This task resultid=1023265 had an error after half an hour.

<message>
process exited with code 193 (0xc1, -63)
</message>
...
Crashed executable name: rosetta_beta_5.96_powerpc-apple-darwin
...

Sorry for this bad news.

Nicole
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Evan

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Message 4098 - Posted: 1 Jun 2008, 22:26:01 UTC

Yes likewise, this one failed after 7 minutes: 1023411

The error message reads:

<core_client_version>5.10.20</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
# cpu_run_time_pref: 3600
# random seed: 1192676
ERROR:: Exit from: .\\refold.cc line: 338
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Message 4101 - Posted: 3 Jun 2008, 12:32:11 UTC

Had this Validate Error on what appears to be an OK Work Unit. Also it had a very good number of Decoys generated.

stderr out

<core_client_version>5.10.21</core_client_version>
<![CDATA[
<stderr_txt>
Graphics are disabled due to configuration...
# cpu_run_time_pref: 21600
# random seed: 1191993
======================================================
DONE :: 1 starting structures 21593.7 cpu seconds
This process generated 1562 decoys from 1562 attempts
0 starting pdbs were skipped
======================================================


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

</stderr_txt>
]]>

Validate state Invalid
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Message 4103 - Posted: 7 Jun 2008, 1:14:50 UTC

http://ralph.bakerlab.org/result.php?resultid=1023179
http://ralph.bakerlab.org/result.php?resultid=1023178
http://ralph.bakerlab.org/result.php?resultid=1023142
http://ralph.bakerlab.org/result.php?resultid=1023124

The above tasks all failed after around 30 - 45 seconds with the following:

<core_client_version>5.10.45</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
# cpu_run_time_pref: 3600
# random seed: 1192707
ERROR:: Exit from: .\\refold.cc line: 338

</stderr_txt>
]]>


http://ralph.bakerlab.org/result.php?resultid=1023221
http://ralph.bakerlab.org/result.php?resultid=1023214

The above two both failed after about 10 seconds.

<core_client_version>5.10.45</core_client_version>
<![CDATA[
<stderr_txt>
# cpu_run_time_pref: 3600
ERROR:: Unable to determine sequence length from pdb file
======================================================
DONE :: 1 starting structures 10 cpu seconds
This process generated 0 decoys from 0 attempts
1 starting pdbs were skipped
======================================================


BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down...

</stderr_txt>
<message>
<file_xfer_error>
<file_name>BAK1lcj_loop_model_biased_clusterCC02_4096_9_1_0</file_name>
<error_code>-161</error_code>
</file_xfer_error>

</message>
]]>

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Message 4113 - Posted: 16 Jun 2008, 20:03:54 UTC

This one failed after 76.64063 seconds:

Task ID 1035762
Name FRA_t423_CASP8_1G3U_11_IGNORE_THE_RESTaggt423_11_t423__t423_7_aa1G3U_7.fasta.template_0003_4216_1_0
Workunit 916914

stderr out

<core_client_version>6.1.0</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
# cpu_run_time_pref: 7200
# random seed: 1183334
ERROR:: Exit from: .\\loop_relax.cc line: 1745

</stderr_txt>

]]>


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Message 4114 - Posted: 17 Jun 2008, 23:31:43 UTC

t405__CASP8_JUMPAB_TYPE2_RES81to192_SAVE_ALL_OUT_BARCODE__4233_54_0:

<core_client_version>6.2.4</core_client_version>
<![CDATA[ - exit code -1073741819 (0xc0000005)
<stderr_txt>
# cpu_run_time_pref: 7200
# random seed: 1181096

Unhandled Exception Detected...
- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x7C911669 read attempt to address 0x00000000
Engaging BOINC Windows Runtime Debugger...

</stderr_txt>
]]>


Peter
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Message 4115 - Posted: 20 Jun 2008, 4:17:02 UTC

All my t419N_autoalign_ WUs are failing with this message:

<core_client_version>5.10.45</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)
</message>
<stderr_txt>
Rosetta@home Macintosh Stack Size checker.
Original size: 8388608.
Maximum size: 0.
RLIM_INFINITY 67104768
# cpu_run_time_pref: 3600
ERROR:: Unable to determine sequence length from pdb file
# random seed: 1178733
ERROR:: Exit from: refold.cc line: 338

</stderr_txt>
]]>
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Dayne

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Message 4116 - Posted: 20 Jun 2008, 4:53:59 UTC

new errors from t419N_autoalign_ WUs.
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Jipsu

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Message 4117 - Posted: 20 Jun 2008, 6:15:06 UTC

Just pick an error you like most http://ralph.bakerlab.org/results.php?hostid=12816

Only two choices though.

<core_client_version>5.10.45</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
# cpu_run_time_pref: 3600
ERROR:: Unable to determine sequence length from pdb file
# random seed: 1178530
ERROR:: Exit from: .\\refold.cc line: 338

</stderr_txt>
]]>

or

<core_client_version>5.10.45</core_client_version>
<![CDATA[
<message>
Maximum disk usage exceeded
</message>
]]>
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Message 4118 - Posted: 20 Jun 2008, 7:36:45 UTC

Same here. All my \'t419N\' WU\'s are failing.
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Message 4119 - Posted: 20 Jun 2008, 10:06:10 UTC - in response to Message 4118.  

Same here. All my \'t419N\' WU\'s are failing.

The same here today. Lot of \"Report to Microsoft\" confirmation windows. With plenty of apparently unrelated reasons: \"Maximum disk usage exceeded + ERROR:: Unable to determine sequence length from pdb file\", \"Unhandled Exception Record, Reason: Breakpoint Encountered (0x80000003) at address 0x7C90120E\", \"Incorrect function. (0x1) - exit code 1 (0x1) + ERROR:: Exit from: .\\refold.cc line: 338\", \"Maximum disk usage exceeded + ERROR:: Exit from: .\\refold.cc line: 338\", etc. Few debugging outputs.

Once I\'ve noticed in the logs \"Aborting task t419N_autoalign_IGNORE_THE_REST_renumbered_4290_6_0: exceeded disk limit: 531.22MB > 476.84MB\" - the disk space isue seems to be my fault, the free disk space went down to approx. my BOINC \"leave xxxx free\" preference. But still the \"Report to Microsoft\" dialogs should not appear.

Peter
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Message 4120 - Posted: 20 Jun 2008, 11:11:25 UTC

Reporting 4 workunits all with the same error:
ERROR:: Unable to determine sequence length from pdb file
# random seed: 1179014
ERROR:: Exit from: .\\refold.cc line: 338

Task ID 1041144
Name t419N_autoalign_IGNORE_THE_REST_renumbered_4373_4_0
Workunit 921753

CPU time 3106.453
stderr out

<core_client_version>6.1.0</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
# cpu_run_time_pref: 7200
ERROR:: Unable to determine sequence length from pdb file
# random seed: 1178115
ERROR:: Exit from: .\\refold.cc line: 338


</stderr_txt>
]]>

Validate state Invalid
Claimed credit 8.34820561908388
Granted credit 0
application version 5.96

---------------

Task ID 1041154
Name t419N_autoalign_IGNORE_THE_REST_renumbered_4283_5_0
Workunit 921763
CPU time 433.9688
stderr out

<core_client_version>6.1.0</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
# cpu_run_time_pref: 7200
ERROR:: Unable to determine sequence length from pdb file
# random seed: 1179014
ERROR:: Exit from: .\\refold.cc line: 338


</stderr_txt>
]]>

Validate state Invalid
Claimed credit 1.16623711180149
Granted credit 0
application version 5.96

---------------

Task ID 1041155
Name t419N_autoalign_IGNORE_THE_REST_renumbered_4284_5_0
Workunit 921764

CPU time 6452.938
stderr out

<core_client_version>6.1.0</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
# cpu_run_time_pref: 7200
ERROR:: Unable to determine sequence length from pdb file
# random seed: 1179004
ERROR:: Exit from: .\\refold.cc line: 338


</stderr_txt>
]]>

Validate state Invalid
Claimed credit 17.3414673491599
Granted credit 0
application version 5.96

---------------

Task ID 1041643
Name t419N_autoalign_IGNORE_THE_REST_renumbered_4372_9_0
Workunit 922252

CPU time 2584.141
stderr out

<core_client_version>6.1.0</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
# cpu_run_time_pref: 7200
ERROR:: Unable to determine sequence length from pdb file
# random seed: 1178120
ERROR:: Exit from: .\\refold.cc line: 338


</stderr_txt>
]]>

Validate state Invalid
Claimed credit 7.19297851625512
Granted credit 0
application version 5.96

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Message 4121 - Posted: 20 Jun 2008, 11:12:49 UTC - in response to Message 4119.  
Last modified: 20 Jun 2008, 11:26:01 UTC

... \"Maximum disk usage exceeded + ERROR:: Exit from: .\\refold.cc line: 338\", etc. Few debugging outputs.

Once I\'ve noticed in the logs \"Aborting task t419N_autoalign_IGNORE_THE_REST_renumbered_4290_6_0: exceeded disk limit: 531.22MB > 476.84MB\" - the disk space isue seems to be my fault, the free disk space went down to approx. my BOINC \"leave xxxx free\" preference. But still the \"Report to Microsoft\" dialogs should not appear.


No wonder, when two Rosetta Beta 5.96 slots dirs\' stdout.txt files, sized 1 GB, contain no idea how many hundred thousands trailing lines in form of
WARNING: refold called with uninit torsions
I still copied your coordinates into misc::, hope that was the right thing to do!
WARNING: refold called with uninit torsions
I still copied your coordinates into misc::, hope that was the right thing to do!
WARNING: refold called with uninit torsions
I still copied your coordinates into misc::, hope that was the right thing to do!
...


And the slots are not being cleaned upon aborting and reporting the task (Win Boinc 6.2.4).

Peter
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