Minirosetta v1.34 bug thread

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Odd Braathun

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Message 55865 - Posted: 18 Sep 2008, 17:20:01 UTC

Hi. I am new to this, but today I have the second computation error with
mini 1.34. abinitio_nohomfrag_70_A_1qgvA_4466_19414_1 stopped after 39:32
It also blocked my 'puter for computing other tasks for 6 hours.
I have 1 finished task ready to report, but are not receiving any new jobs.
My first error was task ID 191724559 work unit 175139940. In both cases mini 1.34 asked for permission to enter internet, so I was assuming that the error
was reported back to the project. Last time I reset the project, but now I am
not sure what to do.

Odd

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PsYcHoK9

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Message 55866 - Posted: 18 Sep 2008, 17:26:24 UTC - in response to Message 55865.  
Last modified: 18 Sep 2008, 17:27:13 UTC

Hello!
I have many "Compute error" on Boinc 6.2/6.3, and i cant't understand why.
My Q6600 is prime95-4xcore stable.
https://boinc.bakerlab.org/rosetta/results.php?hostid=896756
This is my computer.
Thank you!

Config:
Q6600-3.2GHz-1,325v
nVidia 8800 GT 512Mb AMP!
4Gbyte RAM DDR2 1066MHz
Asus P5Q Deluxe bios 1402
Windows Vista Ultimate x64
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Odd Braathun

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Message 55867 - Posted: 18 Sep 2008, 17:44:26 UTC

My compute errors are only with Rosetta. Not with ABC, Einstein or Malariacontrol
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Profile Greg_BE
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Message 55873 - Posted: 18 Sep 2008, 21:23:11 UTC - in response to Message 55867.  

when rosetta crashes, it wants to access the internet to report and get information. be sure to give it full access to the internet.
blocking other tasks, not sure what is causing that.
not receiving any new work, not to worry, boinc is trying to understand how rosetta operates on your machine and sometimes it feels there is already enough work from rosetta and your other projects to keep it busy for awhile. when it feels it needs more work for rosetta it will download it. just be sure to report failures here as they happen.

My compute errors are only with Rosetta. Not with ABC, Einstein or Malariacontrol

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funkydude

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Message 55902 - Posted: 20 Sep 2008, 16:58:03 UTC - in response to Message 55873.  
Last modified: 20 Sep 2008, 16:59:38 UTC

when rosetta crashes, it wants to access the internet to report and get information. be sure to give it full access to the internet.
blocking other tasks, not sure what is causing that.
not receiving any new work, not to worry, boinc is trying to understand how rosetta operates on your machine and sometimes it feels there is already enough work from rosetta and your other projects to keep it busy for awhile. when it feels it needs more work for rosetta it will download it. just be sure to report failures here as they happen.

My compute errors are only with Rosetta. Not with ABC, Einstein or Malariacontrol




I've had this pretty frequently, and I've never let it access the internet because my firewall tells me the hostname of the IP is something like "bogusproxyserver.something". Other times it is something like proxy.opendns.com. Could this be related to OpenDNS? I don't plan on allowing it to communicate like that. Although I do use OpenDNS.

EDIT: If it needs access why doesn't it use BOINC? It will pop up for a new individual firewall rule EVERY time as far as I can see, VERY inappropriate for a network.
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Mod.Sense
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Message 55908 - Posted: 20 Sep 2008, 22:46:19 UTC - in response to Message 55902.  

If it needs access why doesn't it use BOINC?


The project uses BOINC to access the internet to report back your results and request more work. But if a task ends abnormally, the exception is caught and the attempts to report the symbol table directly back. This is because the application is now in to the error handling routines. If you don't permit that access, you probably end up with a message that requires a response. The task will then complete and report back with just an error code.

Rosetta Moderator: Mod.Sense
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The_Bad_Penguin
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Message 55913 - Posted: 21 Sep 2008, 2:29:46 UTC

Failed on two computers:

abinitio_nohomfrag_70_A_1qgvA_4466_15862_0

CPU time 2347.503
stderr out <core_client_version>6.2.18</core_client_version>
<![CDATA[
<message>
- exit code -1073741819 (0xc0000005)
</message>
<stderr_txt>


Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x007D3863 read attempt to address 0x00000008

Engaging BOINC Windows Runtime Debugger...



********************


BOINC Windows Runtime Debugger Version 6.3.10



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The_Bad_Penguin
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Message 55914 - Posted: 21 Sep 2008, 2:34:23 UTC

Failed on 2 computers:

abinitio_nohomfrag_70_A_1qgvA_4466_15638_0

CPU time 2475.393
stderr out <core_client_version>6.2.18</core_client_version>
<![CDATA[
<message>
- exit code -1073741819 (0xc0000005)
</message>
<stderr_txt>


Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x007D3863 read attempt to address 0x00000008

Engaging BOINC Windows Runtime Debugger...



********************


BOINC Windows Runtime Debugger Version 6.3.10


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The_Bad_Penguin
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Message 55915 - Posted: 21 Sep 2008, 2:37:38 UTC

Failed on 2 computers:

abinitio_nohomfrag_70_A_1a8oA_4466_15796_0

CPU time 1.185608
stderr out <core_client_version>5.10.13</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>

ERROR: unrecognized aa HOH
ERROR:: Exit from: ....srccoreiopdbfile_data.cc line: 468
called boinc_finish

</stderr_txt>
]]>


Validate state Invalid
Claimed credit 0.00501246821586943
Granted credit 0
application version 1.34

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The_Bad_Penguin
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Message 55916 - Posted: 21 Sep 2008, 2:43:14 UTC

Failed on 2 computers:

abinitio_nohomfrag_70_A_1a8oA_4466_11979_1

CPU time 2.262014
stderr out <core_client_version>6.2.18</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>

ERROR: unrecognized aa HOH
ERROR:: Exit from: ....srccoreiopdbfile_data.cc line: 468
called boinc_finish

</stderr_txt>
]]>


Validate state Invalid
Claimed credit 0.00577404253079493
Granted credit 0
application version 1.34
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The_Bad_Penguin
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Message 55924 - Posted: 21 Sep 2008, 17:56:13 UTC

abinitio_nohomfrag_70_A_1a8oA_4466_10475_0

stderr out <core_client_version>6.2.18</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>

ERROR: unrecognized aa HOH
ERROR:: Exit from: ....srccoreiopdbfile_data.cc line: 468
called boinc_finish

</stderr_txt>
]]>


Validate state Invalid
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Profile rochester new york
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Message 55930 - Posted: 21 Sep 2008, 19:02:43 UTC

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Mike Tyka

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Message 55931 - Posted: 21 Sep 2008, 20:43:10 UTC - in response to Message 55924.  

Thanks for catching this - it appears that a water molecule (residue code HOH)
found it's way into one of our input structures and rosetta didnt know what to do with it. This should be fixed now, i've sent out a new batch of work units
and removed the old ones. THere may well be a few old WUs floating around for while though.

sorry for this glitch and thanks for pointing it out!

Mike


abinitio_nohomfrag_70_A_1a8oA_4466_10475_0

stderr out <core_client_version>6.2.18</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>

ERROR: unrecognized aa HOH
ERROR:: Exit from: ....srccoreiopdbfile_data.cc line: 468
called boinc_finish

</stderr_txt>
]]>


Validate state Invalid


http://beautifulproteins.blogspot.com/
http://www.miketyka.com/
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Mike Tyka

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Message 55933 - Posted: 21 Sep 2008, 22:05:00 UTC - in response to Message 55725.  

This should really be a warning and is not a problem. If your WU failed then the real problem is probably somewhere else, sadly.

Mike :)


Still getting the "needs psipred_ss2 to run filters" messages just like in 1.32...

191557749

What gives with the filters?


http://beautifulproteins.blogspot.com/
http://www.miketyka.com/
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Mike Tyka

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Message 55942 - Posted: 22 Sep 2008, 0:53:57 UTC - in response to Message 55824.  
Last modified: 22 Sep 2008, 0:54:51 UTC

Thanks for posting this, I totally just found the corresponding bug! Well.. there should have been a check for a certain condition (which would presumably lead to crashes on some machines) .. so this didnt get caught during local/RALPH testing.
Will get fixed on the next BOINC update - for now i have removed the faulty jobs.


Mostly smooth crunching here, except for a few bad ones:

abinitio_nohomfrag_70_A_1qgvA_4466_3309
abinitio_nohomfrag_70_A_1qgvA_4466_4935
abinitio_nohomfrag_70_A_1qgvA_4466_7612

abinitio_nohomfrag_70_A_1a8oA_4466_6635

http://beautifulproteins.blogspot.com/
http://www.miketyka.com/
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[AF>france>pas-de-calais]symaski62

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Message 55951 - Posted: 22 Sep 2008, 16:19:59 UTC

https://boinc.bakerlab.org/rosetta/result.php?resultid=193950857

<core_client_version>6.2.18</core_client_version>
<![CDATA[
<stderr_txt>
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
======================================================
DONE ::     1 starting structures  10463.4 cpu seconds
This process generated     12 decoys from      12 attempts
======================================================

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

</stderr_txt>
]]>


moins 5 FPS

Number of frames per second for graphics: not selected

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Profile Greg_BE
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Message 55956 - Posted: 22 Sep 2008, 18:42:48 UTC - in response to Message 55951.  

known issue, read here for information.

https://boinc.bakerlab.org/rosetta/result.php?resultid=193950857

<core_client_version>6.2.18</core_client_version>
<![CDATA[
<stderr_txt>
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
needs psipred_ss2 to run filters
======================================================
DONE ::     1 starting structures  10463.4 cpu seconds
This process generated     12 decoys from      12 attempts
======================================================

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

</stderr_txt>
]]>


moins 5 FPS

Number of frames per second for graphics: not selected

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[AF>france>pas-de-calais]symaski62

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Message 55958 - Posted: 22 Sep 2008, 19:17:07 UTC - in response to Message 55956.  
Last modified: 22 Sep 2008, 19:32:51 UTC

known issue, read here for information.



1ttzA.psipred_ss2.gz <= fichier

pas là ...



22/09/2008 02:25:16|rosetta@home|Finished download of minirosetta_graphics_1.30_windows_intelx86.exe
22/09/2008 02:26:30|rosetta@home|Finished download of minirosetta_1.34_windows_intelx86.exe
22/09/2008 02:29:02|rosetta@home|Finished download of minirosetta_database_rev23513.zip
22/09/2008 02:29:29|rosetta@home|Finished download of 1ttz.pdb.gz
22/09/2008 02:29:56|rosetta@home|Finished download of boinc_aa1ttzA03_05.200_v1_3.gz
22/09/2008 02:30:28|rosetta@home|Finished download of boinc_aa1ttzA09_05.200_v1_3.gz

désole, je suis française

sorry, i am french
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Profile Greg_BE
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Message 55970 - Posted: 23 Sep 2008, 11:42:48 UTC - in response to Message 55958.  

that is a normal download sequence
.gz is a file extension for gzip (www.gzip.org)

known issue, read here for information.



1ttzA.psipred_ss2.gz <= fichier

pas là ...



22/09/2008 02:25:16|rosetta@home|Finished download of minirosetta_graphics_1.30_windows_intelx86.exe
22/09/2008 02:26:30|rosetta@home|Finished download of minirosetta_1.34_windows_intelx86.exe
22/09/2008 02:29:02|rosetta@home|Finished download of minirosetta_database_rev23513.zip
22/09/2008 02:29:29|rosetta@home|Finished download of 1ttz.pdb.gz
22/09/2008 02:29:56|rosetta@home|Finished download of boinc_aa1ttzA03_05.200_v1_3.gz
22/09/2008 02:30:28|rosetta@home|Finished download of boinc_aa1ttzA09_05.200_v1_3.gz

désole, je suis française

sorry, i am french

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Message 55999 - Posted: 24 Sep 2008, 8:18:15 UTC
Last modified: 24 Sep 2008, 8:19:44 UTC

I just got back after 3 weeks away and found one of my machines "stopped" by Rosetta. It Appears to be this wu that crashed for one of the all to frequent usual reasons. It then needed to access the net - I've read earlier in the thread that it does this, I don't think it should - but that is another issue. The thing then is that F-Secure determines that a "changed application wants to do 'net access - should I let it?" and that then hangs BOINC completely until I come back and press okay.

This is AGAIN a problem with Rosetta that I don't see at other projects. You should not stall a machine from all it's other projects because of faults in your application. 8 days crunching lost.

16/09/2008 11:37:35|rosetta@home|Sending scheduler request: To fetch work. Requesting 8640 seconds of work, reporting 1 completed tasks
16/09/2008 11:37:38|uFluids|Finished upload of rect_gen1_boinc5_30_30_80_80_80_80_16.534_4_35000_-50.00000000_50.00000000_2_0
16/09/2008 11:37:41|rosetta@home|Scheduler request succeeded: got 1 new tasks
16/09/2008 11:37:44|rosetta@home|Started download of 1qgv.pdb.gz
16/09/2008 11:37:44|rosetta@home|Started download of boinc_aa1qgvA03_05.200_v1_3.gz
16/09/2008 11:37:45|rosetta@home|Finished download of 1qgv.pdb.gz
16/09/2008 11:37:45|rosetta@home|Started download of boinc_aa1qgvA09_05.200_v1_3.gz
16/09/2008 11:37:54|rosetta@home|Finished download of boinc_aa1qgvA03_05.200_v1_3.gz
16/09/2008 11:38:11|rosetta@home|Finished download of boinc_aa1qgvA09_05.200_v1_3.gz
16/09/2008 11:38:13|rosetta@home|Starting abinitio_nohomfrag_70_A_1qgvA_4466_15189_0
16/09/2008 11:38:13|rosetta@home|Starting task abinitio_nohomfrag_70_A_1qgvA_4466_15189_0 using minirosetta version 134
24/09/2008 09:00:41||Running CPU benchmarks
24/09/2008 09:00:41||Suspending computation - running CPU benchmarks
Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.
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