Minirosetta 3.59

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Message 78420 - Posted: 7 Jul 2015, 20:13:23 UTC - in response to Message 78387.  

Please report which BOINC version is installed and which host you are making yout observations on.
BOINC 7.4.42 on Windows 8.1/64(4core i3/8GB of RAM).

Task ID 742059437 and Task ID 742059580.

After restarting BOINC 3 or 4 times and shutdown and restart my laptop half a couple times since yesterday, right now both WUs are currently continuing working again, but I have the feeling that they will stop and do the same thing all over again in a while...

Ralf





The first task looks to be completed, the second failed with:

[2015- 7- 3 19:15: 0:] :: BOINC:: Initializing ... ok.
Can\'t acquire lockfile - exiting
FILE_LOCK::unlock(): close failed.: No error
[2015- 7- 3 19:15:42:] :: BOINC:: Initializing ... ok.
Can\'t acquire lockfile - exiting


not sure what is causing this. maybe someone else could chime in.

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Murasaki
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Message 78421 - Posted: 7 Jul 2015, 22:44:26 UTC - in response to Message 78420.  

Please report which BOINC version is installed and which host you are making yout observations on.
BOINC 7.4.42 on Windows 8.1/64(4core i3/8GB of RAM).

Task ID 742059437 and Task ID 742059580.

After restarting BOINC 3 or 4 times and shutdown and restart my laptop half a couple times since yesterday, right now both WUs are currently continuing working again, but I have the feeling that they will stop and do the same thing all over again in a while...

Ralf





The first task looks to be completed, the second failed with:

[2015- 7- 3 19:15: 0:] :: BOINC:: Initializing ... ok.
Can\'t acquire lockfile - exiting
FILE_LOCK::unlock(): close failed.: No error
[2015- 7- 3 19:15:42:] :: BOINC:: Initializing ... ok.
Can\'t acquire lockfile - exiting


not sure what is causing this. maybe someone else could chime in.




Here is some advice I found on an archive copy of the BOINC wiki:

This Message means that the BOINC Client Software has tried to acquire the \"Lock File\" but was unable to obtain an exclusive access to this file. This can occur for the following reasons:


  • A previous copy of the BOINC Client Software is still running, or
  • The BOINC Client Software did not exit cleanly and the \"Lock File\" is still present and is marked as \"read only\".


The cure for this is to make sure that no copy of the BOINC Manager and BOINC Daemon is running, and then to delete the \"Lock File\".

You may have to change the permissions on the file to remove it. Restarting your computer after removing the \"Lock File\" will allow the BOINC Client Software to create a new copy of the \"Lock File\".

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Alexander

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Message 78446 - Posted: 14 Jul 2015, 22:47:04 UTC

On Ubuntu Linux kernel update to 4.2RC kernel (latest testing version) causes all Rosetta tasks (currently running and new ones) to fail with \"Compute error\". Reverting to current stable 3.19 kernel version (officially provided by Ubuntu repositories) appears to fix it. I encountered no similar behavior from other projects I run.
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P . P . L .

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Message 78511 - Posted: 28 Jul 2015, 1:53:46 UTC
Last modified: 28 Jul 2015, 1:58:09 UTC

Getting a lot of errors on these tasks.

Edit // I\'ve taken the rig that started getting all these errors since it got new work this morning off rosetta.


C3C3P213xtal_3fuy_3nz2_004017_0005_0001.pdb_150726UN_15_07_09_24_22_globalDocking_2_SAVE_ALL_OUT_276123_35_0



<core_client_version>7.2.42</core_client_version>
<![CDATA[
<message>
process exited with code 193 (0xc1, -63)


SIGSEGV: segmentation violation
Stack trace (14 frames):
[0xccc64cf]
[0xf7736410]
[0xcce9213]
[0xcce2ade]
[0xcce47ec]
[0xccebcd4]
[0xccec12a]
[0xccd3229]
[0xccd33c9]
[0xccd0144]
[0xccd107d]
[0x80534f9]
[0xcd5e0d8]
[0x8048131]

Exiting...

</stderr_txt>
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Sid Celery

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Message 78534 - Posted: 3 Aug 2015, 2:10:36 UTC
Last modified: 3 Aug 2015, 2:14:46 UTC

Compute error on this task:

jr6mer_rd2_0182__fold_SAVE_ALL_OUT_276187_1934_0

ERROR: Assertion failure: runtime_assert( ( begin + size - 1 ) <= pose.total_residue() );
ERROR:: Exit from: ..\\..\\..\\src\\protocols\\simple_moves\\FragmentMover.cc line: 301
std::cerr: Exception was thrown:


[ERROR] EXCN_utility_exit has been thrown from: ..\\..\\..\\src\\protocols\\simple_moves\\FragmentMover.cc line: 301
ERROR: Assertion failure: runtime_assert( ( begin + size - 1 ) <= pose.total_residue() );


Also:
jr3_0019__fold_SAVE_ALL_OUT_276302_72_0

Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
Setting up folding (abrelax) ...
ERROR:: Exit from: ..\\..\\..\\src\\core\\scoring\\dssp\\PairingsList.cc line: 85
std::cerr: Exception was thrown:


[ERROR] EXCN_utility_exit has been thrown from: ..\\..\\..\\src\\core\\scoring\\dssp\\PairingsList.cc line: 85

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svincent

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Message 78545 - Posted: 6 Aug 2015, 17:29:23 UTC

FFD__5strand14helixWYY_filteredloops_321_0001_dock_PD1CancerImmunotherapy_15_08_07_40_34_globalDocking_4_SAVE_ALL_OUT_277259_19

crashed immediately on Linux (nothing useful in stderr): it also crashed on a Windows machine
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P . P . L .

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Message 78551 - Posted: 6 Aug 2015, 21:44:18 UTC - in response to Message 78545.  

FFD__5strand14helixWYY_filteredloops_321_0001_dock_PD1CancerImmunotherapy_15_08_07_40_34_globalDocking_4_SAVE_ALL_OUT_277259_19

crashed immediately on Linux (nothing useful in stderr): it also crashed on a Windows machine


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

I,ve had a few of those error as well.

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natteruw

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Message 78553 - Posted: 7 Aug 2015, 1:01:26 UTC - in response to Message 78511.  

Hi P.P.L.,

Just to check, did your edit indicate that the errors were somehow resolved?
I submitted those C3C3P2123xtal_ jobs and most of them seem to have worked...

Looking forward to your response,
natteruw



Getting a lot of errors on these tasks.

Edit // I\'ve taken the rig that started getting all these errors since it got new work this morning off rosetta.


C3C3P213xtal_3fuy_3nz2_004017_0005_0001.pdb_150726UN_15_07_09_24_22_globalDocking_2_SAVE_ALL_OUT_276123_35_0



<core_client_version>7.2.42</core_client_version>
<![CDATA[
<message>
process exited with code 193 (0xc1, -63)


SIGSEGV: segmentation violation
Stack trace (14 frames):
[0xccc64cf]
[0xf7736410]
[0xcce9213]
[0xcce2ade]
[0xcce47ec]
[0xccebcd4]
[0xccec12a]
[0xccd3229]
[0xccd33c9]
[0xccd0144]
[0xccd107d]
[0x80534f9]
[0xcd5e0d8]
[0x8048131]

Exiting...

</stderr_txt>

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P . P . L .

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Message 78554 - Posted: 7 Aug 2015, 5:03:45 UTC
Last modified: 7 Aug 2015, 5:09:59 UTC

Hi natteruw.

The problem was that there was a bad kernel update that seemed to cause those errors, a few days later they put out a fix for whatever the problem was.

I\'ve put that rig back on Rosetta and it\'s still going fine now, it was only the one AMD rig for some reason, my other Intel rigs didn\'t have any problems.

Thanks for asking. :)
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Sid Celery

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Message 78571 - Posted: 12 Aug 2015, 12:48:45 UTC

Two validate errors in quick succession. One with a very obvious problem, the other without one I can spot:

FFD__5strand14helixWYR_filteredloops_243_0001_dock_PD1CancerImmunotherapy_15_08_07_40_27_localDocking_9_SAVE_ALL_OUT_277200_4_1
util.cc line: 131

ERROR: Attempting to auto-detect interface partner chains, however the pose contains no jumps.
ERROR:: Exit from: ..\\..\\..\\src\\protocols\\docking\\util.cc line: 131

ERROR: Attempting to auto-detect interface partner chains, however the pose contains no jumps.
ERROR:: Exit from: ..\\..\\..\\src\\protocols\\docking\\util.cc line: 131

ERROR: Attempting to auto-detect interface partner chains, however the pose contains no jumps.
ERROR:: Exit from: ..\\..\\..\\src\\protocols\\docking\\util.cc line: 131

...& repeat...


HH7SRPEG_SiliCar9_F6A_relax_SAVE_ALL_OUT_277610_16_1
======================================================
DONE :: 99 starting structures 1201 cpu seconds
This process generated 99 decoys from 99 attempts
======================================================
BOINC :: WS_max 2.19148e+008

Not sure if that last line is an error of sorts
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Message boards : Number crunching : Minirosetta 3.59



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