Minirosetta v1.32 bug thread

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Profile David E K
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Message 54936 - Posted: 5 Aug 2008, 23:38:40 UTC

Please post bugs/issues with minirosetta v1.32 here.
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toribio

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Message 54950 - Posted: 6 Aug 2008, 8:34:39 UTC

I\'m sorry if this is irrelevant to the version and not the servers, but, since the new version came out, I have been unable to receive and WUs, and none of my settings ever changed. Once gain I apologize if this is just the servers and not the version. Just a coincidence.
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Message 54971 - Posted: 7 Aug 2008, 3:41:46 UTC

This WU died on startup:
http://boinc.bakerlab.org/rosetta/workunit.php?wuid=165026170

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Message 54972 - Posted: 7 Aug 2008, 4:42:33 UTC
Last modified: 7 Aug 2008, 4:46:48 UTC

The task below just failed on my machine. This is the first mini rosetta work unit to get processed since the new release and the error seems to be similar to the errors that I was repeatedly getting on version 1.28.

http://boinc.bakerlab.org/rosetta/result.php?resultid=182934444

BTW, version 5.98 WUs have been running successfully.
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Message 54982 - Posted: 7 Aug 2008, 15:48:49 UTC

Task reported too late to validate ?????

Here are two tasks submitted by a new machine I just brought up. It\'s a slightly older 2.34 GLIBC machine using 5.8.16 for a client (All the newer ones want GLIBC 2.4+)

The task was obtained, crunched and submitted the next day without any abort or error indicated in the STDOUT.. But with 0.00 credit ??? (The machine is only crunching Rosetta at this point).

What is up with this ?? ... Could it be the machine ?? This is the first time I have seen this one... (and ... yes, the clocks are synchronized by NTP, so TOD should not be an issue)

http://boinc.bakerlab.org/rosetta/result.php?resultid=182943687

stderr out

<core_client_version>5.8.16</core_client_version>
<![CDATA[
<stderr_txt>
# cpu_run_time_pref: 43200
======================================================
DONE :: 1 starting structures 43113 cpu seconds
This process generated 84 decoys from 84 attempts
======================================================

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

</stderr_txt>
]]>

Validate state Task was reported too late to validate
Claimed credit 155.951746654641
Granted credit 0
application version 1.32

http://boinc.bakerlab.org/rosetta/result.php?resultid=182943208

stderr out

<core_client_version>5.8.16</core_client_version>
<![CDATA[
<stderr_txt>
# cpu_run_time_pref: 43200
======================================================
DONE :: 1 starting structures 42875.1 cpu seconds
This process generated 123 decoys from 123 attempts
======================================================

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

</stderr_txt>
]]>

Validate state Task was reported too late to validate
Claimed credit 155.091236560251
Granted credit 0
application version 1.32



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Profile Jim

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Message 54986 - Posted: 7 Aug 2008, 18:48:03 UTC - in response to Message 54936.  

Please post bugs/issues with minirosetta v1.32 here.


Had the first one I got fail.
ERROR: Cannot find file \'minirosetta_database\\chemical/residue_type_sets/centroid/CSD_ATOM_TYPE_SET fa_standard\'
ERROR:: Exit from: ..\\..\\src\\core\\chemical\\residue_io.cc line: 132
called boinc_finish

It is WU ID 165103113

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Message 54988 - Posted: 7 Aug 2008, 21:05:11 UTC - in response to Message 54982.  

Task reported too late to validate ?????

Here are two tasks submitted by a new machine I just brought up. It\'s a slightly older 2.34 GLIBC machine using 5.8.16 for a client (All the newer ones want GLIBC 2.4+)

The task was obtained, crunched and submitted the next day without any abort or error indicated in the STDOUT.. But with 0.00 credit ??? (The machine is only crunching Rosetta at this point).

What is up with this ?? ... Could it be the machine ?? This is the first time I have seen this one... (and ... yes, the clocks are synchronized by NTP, so TOD should not be an issue)

http://boinc.bakerlab.org/rosetta/result.php?resultid=182943687

stderr out

<core_client_version>5.8.16</core_client_version>
<![CDATA[
<stderr_txt>
# cpu_run_time_pref: 43200
======================================================
DONE :: 1 starting structures 43113 cpu seconds
This process generated 84 decoys from 84 attempts
======================================================

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

</stderr_txt>
]]>

Validate state Task was reported too late to validate
Claimed credit 155.951746654641
Granted credit 0
application version 1.32

http://boinc.bakerlab.org/rosetta/result.php?resultid=182943208

stderr out

<core_client_version>5.8.16</core_client_version>
<![CDATA[
<stderr_txt>
# cpu_run_time_pref: 43200
======================================================
DONE :: 1 starting structures 42875.1 cpu seconds
This process generated 123 decoys from 123 attempts
======================================================

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

</stderr_txt>
]]>

Validate state Task was reported too late to validate
Claimed credit 155.091236560251
Granted credit 0
application version 1.32




found the problem for this one.... copied directory from another cruncher and forgot to dump the client_state.... my bad...

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Profile David E K
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Message 54990 - Posted: 7 Aug 2008, 22:41:33 UTC - in response to Message 54986.  

Please post bugs/issues with minirosetta v1.32 here.


Had the first one I got fail.
ERROR: Cannot find file \'minirosetta_database\\chemical/residue_type_sets/centroid/CSD_ATOM_TYPE_SET fa_standard\'
ERROR:: Exit from: ..\\..\\src\\core\\chemical\\residue_io.cc line: 132
called boinc_finish

It is WU ID 165103113



You can ignore these quick failures. They are old jobs that are getting reissued due to errors or past deadlines. These old jobs will fail because they use an incompatible database. There shouldn\'t be too many of these so please just ignore them.
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Message 55002 - Posted: 8 Aug 2008, 18:31:46 UTC

are there no new 1.32 work units?
i only got 2 so far and the rest are all 5.98
last download of 1.32 was the 6th if the report date is the 16th?
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Message 55013 - Posted: 10 Aug 2008, 5:17:04 UTC

Hey David, thanks for clearing that up for us, I was about to say \"Is there some files missing from the Database?\"

Anyhow, just out of curiosity, I checked the Projects folder on all my machines, and it appears that the Mini-Rosetta rev 1.28 executable is gone but the old Database, \"minirosetta_database_rev23035\" is still there. The new 23513 is there as well. Will there be any more use for the 23035 that went with 1.28? Or is it safe to delete it?

Thanks, keep up the good work guys!

P.S. When is/does CASP8 wrap up?
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Message 55020 - Posted: 10 Aug 2008, 14:13:42 UTC
Last modified: 10 Aug 2008, 14:25:25 UTC

now using boinc mgr 6.2.16 and had to restart the project as folders and files from the old 5.10.45 were not being picked up including tasks.

The errors I post here are from a new batch of work:

http://boinc.bakerlab.org/rosetta/result.php?resultid=183864069
http://boinc.bakerlab.org/rosetta/result.php?resultid=183864068
http://boinc.bakerlab.org/rosetta/result.php?resultid=183862855
http://boinc.bakerlab.org/rosetta/result.php?resultid=183862854

there are many more errors from various 1.32 tasks that would take to much time to post, but the error message is more or less the same....

<core_client_version>6.2.16</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>

ERROR: in::file::zip minirosetta_database_rev23035.zip does not exist!
ERROR:: Exit from: ..\\..\\src\\apps\\public\\boinc\\minirosetta.cc line: 105
called boinc_finish
</stderr_txt>


here is another random sample from over a total of 30+ failed work units between 5.98 and 1.32

http://boinc.bakerlab.org/rosetta/result.php?resultid=183857588
core_client_version>6.2.16</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
ERROR: Option file open failed for: 062408_bblum_abrelax_flags

</stderr_txt>
]]>

0 secs run time
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Message 55050 - Posted: 12 Aug 2008, 6:22:00 UTC - in response to Message 54990.  


You can ignore these quick failures. They are old jobs that are getting reissued due to errors or past deadlines. These old jobs will fail because they use an incompatible database. There shouldn\'t be too many of these so please just ignore them.

What\'s up with this task?

Task ID 184003550
ERROR: Cannot find file \'minirosetta_database\\chemical/residue_type_sets/fa_standard/CSD_ATOM_TYPE_SET fa_standard\'
ERROR:: Exit from: ..\\..\\src\\core\\chemical\\residue_io.cc line: 132
called boinc_finish

Outcome Client error
Client state Compute error
Exit status 1 (0x1)
Validate state Invalid
Yet the wing man has completed it good as gold.
Is this normal?
Speedy
Have a crunching good day!!
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Message 55075 - Posted: 14 Aug 2008, 0:32:25 UTC

I had 3 that wouldn\'t run, and it crashed my boinc. I don\'t have a log since when it closed it erased it. I have no more work units left to be processed.
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Profile David E K
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Message 55078 - Posted: 14 Aug 2008, 4:27:31 UTC - in response to Message 55050.  


You can ignore these quick failures. They are old jobs that are getting reissued due to errors or past deadlines. These old jobs will fail because they use an incompatible database. There shouldn\'t be too many of these so please just ignore them.

What\'s up with this task?

Task ID 184003550
ERROR: Cannot find file \'minirosetta_database\\chemical/residue_type_sets/fa_standard/CSD_ATOM_TYPE_SET fa_standard\'
ERROR:: Exit from: ..\\..\\src\\core\\chemical\\residue_io.cc line: 132
called boinc_finish

Outcome Client error
Client state Compute error
Exit status 1 (0x1)
Validate state Invalid
Yet the wing man has completed it good as gold.
Is this normal?
Speedy



The success was from version 1.28. 1.32 versions will fail for these older tasks , few of which are still lingering around.
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Message 55085 - Posted: 14 Aug 2008, 20:41:25 UTC
Last modified: 14 Aug 2008, 20:42:00 UTC

Here\'s another Rosetta Mini unhandled exception error. I got quite a lot of these from 1.28, and this is the only one I have got from ver 1.32 so far. It\'s always on just the one computer, and always from the Rosetta Mini\'s. I\'ve never gotten one of these errors ever from 5.82 or 5.98 on any system. Here\'s a link to the failed WU:

184522226
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Message 55090 - Posted: 15 Aug 2008, 20:53:37 UTC

Another one bites the dust: 184906376

What causes this access violation?? And again, it only happens with the Mini\'s, not Beta.
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eaglezero

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Message 55094 - Posted: 16 Aug 2008, 6:11:38 UTC

Every morning for the last week, I find the computer frozen, and the mini rosetta on the task bar. I have detached from the project, to see what happens with the other projects.. just for info.

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Max DesGeorges

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Message 55125 - Posted: 17 Aug 2008, 9:22:30 UTC - in response to Message 55094.  

When I close the graphics window, Vista tell me that there is an error with \"minirosetta_graphics_1.30_windows_intelx86...\". Even so the WU still running normally.

Windows Vista 32, BOINC 6.3.8.
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Message 55141 - Posted: 17 Aug 2008, 18:18:53 UTC - in response to Message 55094.  

Every morning for the last week, I find the computer frozen, and the mini rosetta on the task bar. I have detached from the project, to see what happens with the other projects.. just for info.



I am having this same issue.
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Message 55155 - Posted: 18 Aug 2008, 11:20:54 UTC

This was a strange one. 185494746
The library was activated and an email was sent off. The work unit stopped responding. Boinc had to be shut down and restarted at which point the unit went to 100% and reported.

The stderr txt showed \'needs psipred_ss2 to run filters\'
access violation

Despite this it was reported to be a success


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