Minirosetta 3.52

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Profile David E K
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Message 76770 - Posted: 28 May 2014, 19:30:11 UTC

This version includes a couple bug fixes for symmetric modeling. Please report issues/bugs here.
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Killersocke@rosetta

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Message 76816 - Posted: 10 Jun 2014, 1:03:11 UTC
Last modified: 10 Jun 2014, 1:15:57 UTC

since two days iv\'e got same broken WU\'s

they have all the same exit Status:

Exit status -1073741819 (0xffffffffc0000005

Client error Compute error

Task ID 666681305

Task ID 666713879

Task ID 666800013

Task ID 666800018

regards
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Killersocke@rosetta

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Message 76818 - Posted: 10 Jun 2014, 16:42:40 UTC

....
and Today more........

I\'m not happy about this
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svincent

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Message 76819 - Posted: 10 Jun 2014, 17:14:17 UTC

I\'m seeing failures on Linux with tasks named T0763*.

See 666899120

ERROR: HybridizeFoldtreeDynamic: failed to build fold tree from cuts and jumps
ERROR:: Exit from: src/protocols/hybridization/HybridizeFoldtreeDynamic.cc line: 676
SIGSEGV: segmentation violation
Stack trace (20 frames):
[0xbb009c7]

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Message 76821 - Posted: 11 Jun 2014, 2:28:58 UTC

This task erred just now.

http://boinc.bakerlab.org/rosetta/workunit.php?wuid=604963960

T0763_jump_13_70_71_90_hybrid_withlookback_169118_137_0

Watchdog active.
SIGSEGV: segmentation violation
Stack trace (20 frames):
[0xbb009c7]
[0xb7739400]
[0xb3d01ce]
[0xb449439]
[0xa06a109]
[0xa0698a3]
[0xa048b2e]
[0x9823d96]
[0x982475a]
[0x9826b8e]
[0x87aee21]
[0x87e57d9]
[0x9da5fe2]
[0x9da837e]
[0x9f99f2d]
[0xa017d65]
[0xa015595]
[0x8055314]
[0xbb91f88]
[0x8048131]

Exiting...

</stderr_txt>



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Message 76822 - Posted: 11 Jun 2014, 6:03:59 UTC

Had more T0763 fail with this error as well.

ERROR: HybridizeFoldtreeDynamic: failed to build fold tree from cuts and jumps
ERROR:: Exit from: src/protocols/hybridization/HybridizeFoldtreeDynamic.cc line: 676
SIGSEGV: segmentation violation
Stack trace (20 frames):



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achalupka

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Message 76825 - Posted: 11 Jun 2014, 13:47:19 UTC

I have approx 20 completed work units stuck in the uploading state. Not sure if this is an issue specific to Minirosetta 3.52 or a general boinc issue, but none of my other projects are exhibiting this issue. Its been like this for several days.
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Profile [VENETO] boboviz

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Message 76844 - Posted: 16 Jun 2014, 7:13:57 UTC

Crash after few seconds 668119976

ERROR: Warning: can\'t open file hybrid_jumping\\t000_.fasta!
ERROR:: Exit from: ..\\..\\..\\src\\core\\sequence\\util.cc line: 148
# cpu_run_time_pref: 7200

ERROR: Warning: can\'t open file hybrid_jumping\\t000_.fasta!
ERROR:: Exit from: ..\\..\\..\\src\\core\\sequence\\util.cc line: 148

ERROR: Warning: can\'t open file hybrid_jumping\\t000_.fasta!
ERROR:: Exit from: ..\\..\\..\\src\\core\\sequence\\util.cc line: 148
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Dennis

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Message 76845 - Posted: 16 Jun 2014, 11:56:30 UTC

I have 7 jobs with the same error as [VENETO] boboviz
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Message 76847 - Posted: 17 Jun 2014, 6:01:06 UTC

Hi.

I\'ve had a few of these that got validate errors after either a couple of hours or a few minutes.

Tc761_jump_hybrid_1.0_169577_3670_0


ERROR: Warning: can\'t open file hybrid_jumping/t000_.fasta!
ERROR:: Exit from: src/core/sequence/util.cc line: 148

ERROR: Warning: can\'t open file hybrid_jumping/t000_.fasta!
ERROR:: Exit from: src/core/sequence/util.cc line: 148
======================================================
DONE :: 99 starting structures 1201 cpu seconds
This process generated 99 decoys from 99 attempts
======================================================
BOINC :: WS_max 0

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



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sgaboinc

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Message 76857 - Posted: 21 Jun 2014, 15:05:45 UTC - in response to Message 76770.  
Last modified: 21 Jun 2014, 15:07:07 UTC

i\'m trying out the view structure predictions commands as given on
http://boinc.bakerlab.org/rosetta/rah_view_predictions.php

however in stderr.txt
[2014- 6-21 4:23:47:] :: BOINC :: boinc_init()
BOINC:: Setting up shared resources ... ok.
BOINC:: Setting up semaphores ... ok.
semget failure! Cannot create semaphore!
BOINC:: Updating status ... ok.
BOINC:: Registering timer callback... ok.
BOINC:: Worker initialized successfully.
command: /var/lib/boinc/projects/boinc.bakerlab.org_rosetta/minirosetta_3.52_x86_64-pc-linux-gnu -extract -all -s chk_S_00000010_ClassicAbinitio__stage4_kk_1.out
Registering options..
Registered extra options.
Initializing broker options ...
Registered extra options.
Initializing core...
Initializing options.... ok
Options::initialize()
Options::adding_options()
Options::initialize() Check specs.
Options::initialize() End reached
ERROR: Option matching -extract not found in command line top-level context

with the error there is no pdb files created

using this approach as linux hosts currently do not support a screen saver or gui
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Profile [VENETO] boboviz

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Message 76876 - Posted: 25 Jun 2014, 9:19:12 UTC

After 108 minutes, 669716479 returns this error:

Starting work on structure: _00001
# cpu_run_time_pref: 7200
Starting work on structure: _00002
Starting work on structure: _00003
Starting work on structure: _00004
Starting work on structure: _00005
Starting work on structure: _00006
Starting work on structure: _00007
WARNING! attempt to create gzipped file ../../projects/boinc.bakerlab.org_rosetta/benchmark_0014_alex_metric_58c8eb0a169e5c49e1cef5331416f2432f6d8260_ploops_32_input_0002_no_lig_fragments_contact_opt_iteration_1_dbe4269ef4fb4de99e2f824cdcbaf1c6_fold_SAVE_ALL_OUT_170252_3113_0_0 failed.
======================================================
DONE :: 1 starting structures 6499.73 cpu seconds
This process generated 7 decoys from 7 attempts
======================================================
BOINC :: WS_max 5.23985e+008

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

</stderr_txt>
<message>
upload failure: <file_xfer_error>
<file_name>benchmark_0014_alex_metric_58c8eb0a169e5c49e1cef5331416f2432f6d8260_ploops_32_input_0002_no_lig_fragments_contact_opt_iteration_1_dbe4269ef4fb4de99e2f824cdcbaf1c6_fold_SAVE_ALL_OUT_170252_3113_0_0</file_name>
<error_code>-161 (not found)</error_code>
</file_xfer_error>


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Message 76892 - Posted: 27 Jun 2014, 18:24:58 UTC - in response to Message 76857.  

Hi sgaboinc,

See my post here:
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=6358

Tell me if it doesnt work! If it works, I\'ll try get the R@H people to update the rah_view_predictions.php page with these instructions.

i\'m trying out the view structure predictions commands as given on
http://boinc.bakerlab.org/rosetta/rah_view_predictions.php

however in stderr.txt
[2014- 6-21 4:23:47:] :: BOINC :: boinc_init()
BOINC:: Setting up shared resources ... ok.
BOINC:: Setting up semaphores ... ok.
semget failure! Cannot create semaphore!
BOINC:: Updating status ... ok.
BOINC:: Registering timer callback... ok.
BOINC:: Worker initialized successfully.
command: /var/lib/boinc/projects/boinc.bakerlab.org_rosetta/minirosetta_3.52_x86_64-pc-linux-gnu -extract -all -s chk_S_00000010_ClassicAbinitio__stage4_kk_1.out
Registering options..
Registered extra options.
Initializing broker options ...
Registered extra options.
Initializing core...
Initializing options.... ok
Options::initialize()
Options::adding_options()
Options::initialize() Check specs.
Options::initialize() End reached
ERROR: Option matching -extract not found in command line top-level context

with the error there is no pdb files created

using this approach as linux hosts currently do not support a screen saver or gui

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BetelgeuseFive

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Message 76912 - Posted: 29 Jun 2014, 14:22:48 UTC


I have one tasks with the same problems as reported by Killersocke:

Exit status -1073741819 (0xffffffffc0000005)

http://boinc.bakerlab.org/rosetta/result.php?resultid=670799921

Most of the tasks complete without problems however.

Tom
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sgaboinc

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Message 76914 - Posted: 29 Jun 2014, 15:35:58 UTC - in response to Message 76892.  

Hi sgaboinc,

See my post here:
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=6358

Tell me if it doesnt work! If it works, I\'ll try get the R@H people to update the rah_view_predictions.php page with these instructions.




hi krypton,

thanks much for those instructions, i\'m following up in the original thread as it seemed this is some what out of topic of this thread

original thread:
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=6358
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Message 76926 - Posted: 30 Jun 2014, 3:52:45 UTC
Last modified: 30 Jun 2014, 3:53:21 UTC

Hi.

Had these two fail after about 2hrs.30min.


http://boinc.bakerlab.org/rosetta/workunit.php?wuid=608458156

pd1_graftsheet_41limit_1L3E2L3E2L3E3L13H3L3E1L_1-2.P.0_SAVE_ALL_OUT__171170_1_1

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

http://boinc.bakerlab.org/rosetta/workunit.php?wuid=608509726

pd1_graftsheet_41limit_1L4E3L4E3L4E2L15H1L_1-2.P.0_SAVE_ALL_OUT__171149_1_0

# cpu_run_time_pref: 14400
======================================================
DONE :: 1 starting structures 8514.78 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
BOINC :: WS_max 6.80565e+38

BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down cleanly ...
called boinc_finish
terminate called after throwing an instance of \'std::bad_alloc\'
what(): St9bad_alloc

</stderr_txt>

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

# cpu_run_time_pref: 14400
======================================================
DONE :: 1 starting structures 8480.43 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
BOINC :: WS_max 6.80565e+38

BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down cleanly ...
called boinc_finish
terminate called after throwing an instance of \'std::bad_alloc\'
what(): St9bad_alloc

</stderr_txt>


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sgaboinc

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Message 76927 - Posted: 30 Jun 2014, 4:53:35 UTC - in response to Message 76926.  
Last modified: 30 Jun 2014, 4:55:27 UTC


BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down cleanly ...
called boinc_finish
terminate called after throwing an instance of \'std::bad_alloc\'
what(): St9bad_alloc

</stderr_txt>

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

# cpu_run_time_pref: 14400
======================================================
DONE :: 1 starting structures 8480.43 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
BOINC :: WS_max 6.80565e+38

BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down cleanly ...
called boinc_finish
terminate called after throwing an instance of \'std::bad_alloc\'
what(): St9bad_alloc

</stderr_txt>


i\'ve seen a same message, however it seemed the message appeared when the job has completed and i clicked update. it is uncertain if that\'s caused by the click on update (i.e. some scheduler error?)
http://boinc.bakerlab.org/rosetta/result.php?resultid=670699728

apparently cases which i left them alone for automatic transmissions did not show the error. or for those which i clicked update after a while after the job completes

let us know if the boinc client may be involved here
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sgaboinc

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Message 76930 - Posted: 30 Jun 2014, 16:35:06 UTC
Last modified: 30 Jun 2014, 16:46:03 UTC

another case of std::bad_alloc failures

task: pd1_graftsheet_41limit_1L5E2L12H4L8H2L5E1L_1-2.P.0_SAVE_ALL_OUT__171083_4_0
http://boinc.bakerlab.org/rosetta/result.php?resultid=671116399

\"======================================================
DONE :: 21 starting structures 10605.5 cpu seconds
This process generated 21 decoys from 21 attempts
======================================================
BOINC :: WS_max 1.12221e-190

BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down cleanly ...
called boinc_finish
terminate called after throwing an instance of \'std::bad_alloc\'
what(): St9bad_alloc

</stderr_txt>
]]>
\"
aborts occurs at end of job, apparently seemed related to particular tasks
pd1_graftsheet_41limit_1L5E2L12H4L8H2L5E1L*

not sure if it has anything to do with that
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Message 76934 - Posted: 30 Jun 2014, 21:37:36 UTC

Lots of errors in the last days. Wing(wo)man have also errors, very occasionally they get one validated.
Part of error message:

Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x009B7DEB write attempt to address 0x00000000

Engaging BOINC Windows Runtime Debugger...

Hope this will be solved soon.
Greetings,
TJ.
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Profile [VENETO] boboviz

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Message 76947 - Posted: 2 Jul 2014, 13:35:20 UTC
Last modified: 2 Jul 2014, 13:36:13 UTC

Same here, like TJ 671434192

Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x016F7DEB write attempt to address 0x00000000

Engaging BOINC Windows Runtime Debugger...
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