minirosetta 1.13 bug thread

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James
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Message 3918 - Posted: 17 Apr 2008, 17:29:47 UTC
Last modified: 17 Apr 2008, 17:30:02 UTC

Version 1.13 of minirosetta is released, please post bugs in this thread.

After talking with the BOINC developers, we have a brand-new version of the BOINC API and a new version of the minirosetta application for everyone to try. I\'m especially hopeful that the problems on the Linux platform will be fixed, our local tests on Linux have completed successfully.

It\'s critical for CASP8 that we have minirosetta up and running, so thank you all for your help and comments.
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Path7

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Message 3919 - Posted: 17 Apr 2008, 23:50:58 UTC

Thanks, the Minirosetta 1.13 has successfully run on my Linux-box (Ubuntu 7.10 x86) and ended valid.
Thanks again for your efforts.

Path7.
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James
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Message 3921 - Posted: 18 Apr 2008, 0:13:30 UTC - in response to Message 3919.  

Thanks, the Minirosetta 1.13 has successfully run on my Linux-box (Ubuntu 7.10 x86) and ended valid.
Thanks again for your efforts.

Path7.


Hi Path7,

I was very excited to get your workunit back. You\'re totally correct, this application seems to be running properly on Linux machines. Thanks for your help!
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Evan

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Message 3922 - Posted: 18 Apr 2008, 9:39:12 UTC

I have had trouble with these two:

919139 and 91907

using windows xp and Boinc 5.10.20
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Evan

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Message 3923 - Posted: 18 Apr 2008, 11:57:18 UTC

and this one 900773
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Message 3924 - Posted: 18 Apr 2008, 14:47:58 UTC

FYI this 1a19A_BOINC_ABINITIO_IGNORE_THE_REST-S25-9-S3-3--1a19A-_3508_214_0
has a peak memory usage of 558MB on WinXP so far (10hrs in to 24hr run time).
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Message 3925 - Posted: 18 Apr 2008, 21:09:01 UTC

Juhuu!
My first minirosetta without error just arrived on your servers. As you can see here most other ones have errored out.
I hope I will get soon some more than my 2 tasks per day, the limit that the older minis have put my puter to ;)
Gruesse vom Saenger

For questions about Boinc look in the BOINC-Wiki
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Message 3926 - Posted: 18 Apr 2008, 22:54:56 UTC - in response to Message 3924.  

FYI this 1a19A_BOINC_ABINITIO_IGNORE_THE_REST-S25-9-S3-3--1a19A-_3508_214_0
has a peak memory usage of 558MB on WinXP so far (10hrs in to 24hr run time).

...after 17hrs, peak is 786MB, 26million page faults on a machine with 2.5GB for 2 processes.
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Message 3927 - Posted: 19 Apr 2008, 4:13:35 UTC

Yes minirosetta 1.13 is now finally working ok, no errors, much better than 1.10, 1.11 and 1.12.

People with Windows machine have been lapping up the extra work that we Linux users have not been able to get to work.
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Path7

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Message 3928 - Posted: 19 Apr 2008, 7:16:53 UTC

Hello Dev\'s & Tench\'s,
Running Windows XP & Boinc 5.10.45 I had two times a Validate error:

<core_client_version>5.10.45</core_client_version>
<![CDATA[
<stderr_txt>
WARNING: Override of option -out:nstruct sets a different value
can not open 1-mer fragment library file: none
# cpu_run_time_pref: 7200

Task ID: 920921 & 921439
Another cruncher had the same error before on the second WU I mention.

Have I good day,
Path7.
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Message 3929 - Posted: 19 Apr 2008, 11:36:31 UTC

Working fine of my Fedora 7 x86 box. I\'m about to add it to the x64 box.
Kathryn :o)
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Message 3931 - Posted: 20 Apr 2008, 18:09:00 UTC
Last modified: 20 Apr 2008, 18:10:53 UTC

mini_abinitio-1vie_-test_2008-2-6_3310_22_0 and mini_abinitio-1vie_-test_2008-2-6_3310_18_0

<core_client_version>5.10.45</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>

ERROR: Cannot open file 1vie.pdb
ERROR:: Exit from: ..\\..\\src\\core\\io\\pdb\\pose_io.cc line: 157
called boinc_finish

</stderr_txt>
]]>



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Message 3936 - Posted: 20 Apr 2008, 21:42:33 UTC

Running Windows XP Home SP2... task ran for almost 6 seconds before crashing - it could not find the output file:

Task ID 922185
Name mini_abinitio-1vie_-test_2008-2-6_3310_17_0
Workunit 820813
Server state Over
Outcome Client error
Client state Compute error
Exit status 1 (0x1)
CPU time 5.953125
stderr out
<core_client_version>6.1.0</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>

ERROR: Cannot open file 1vie.pdb
ERROR:: Exit from: ..\\..\\src\\core\\io\\pdb\\pose_io.cc line: 157

called boinc_finish

</stderr_txt>
]]>

Validate state Invalid
Claimed credit 0.0171578784915296
Granted credit 0
application version 1.13

4/20/2008 4:21:47 PM Output file mini_abinitio-1vie_-test_2008-2-6_3310_17_0_0 for task mini_abinitio-1vie_-test_2008-2-6_3310_17_0 absent



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Message 3937 - Posted: 21 Apr 2008, 3:48:44 UTC

Result
Host

<core_client_version>5.10.21</core_client_version>
<![CDATA[
<stderr_txt>
WARNING: Override of option -out:nstruct sets a different value
can not open 1-mer fragment library file: none
# cpu_run_time_pref: 7200
======================================================
DONE :: 1 starting structures 302.263 cpu seconds
This process generated 0 decoys from 0 attempts
======================================================

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

</stderr_txt>
]]>


I\'ll have to grep my logs to see what happened.
Kathryn :o)
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Message 3938 - Posted: 21 Apr 2008, 4:47:25 UTC

Got this error on Linux machine

<core_client_version>5.10.21</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)
</message>
<stderr_txt>

ERROR: Cannot open file 1vie.pdb
ERROR:: Exit from: src/core/io/pdb/pose_io.cc line: 157
called boinc_finish

</stderr_txt>

See this WU

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Message 3940 - Posted: 21 Apr 2008, 14:13:20 UTC
Last modified: 21 Apr 2008, 14:13:47 UTC

This one mini_abinitio-1bk2_-test_2008-2-6_3310_73_0 shows peak memory of 867MB! It\'s 17hrs in to a 24hr runtime preference on WinXP.

Memory does not seem to be growing without bounds (i.e. no memory leak), just seems to use a lot, then free it again at various times as it runs.
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Klimax

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Message 3941 - Posted: 21 Apr 2008, 16:30:12 UTC

WU failed.
Incorrect function.

WU

Full text:
<core_client_version>5.10.18</core_client_version>
<![CDATA[
<message>
Nesprávná funkce. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>

ERROR: Cannot open file 1vie.pdb
ERROR:: Exit from: ..\\..\\src\\core\\io\\pdb\\pose_io.cc line: 157
called boinc_finish

</stderr_txt>
]]>
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Message 3942 - Posted: 21 Apr 2008, 20:23:56 UTC
Last modified: 21 Apr 2008, 20:25:57 UTC

Had to install security patches and reboot WinXP. Ended BOINC normally, installed the fixes, rebooted, restarted BOINC. Both mini 1.13 WUs that were running fine ended upon the restart.

WU1
WU2

Both say one decoy was completed. No signs of watchdog causing them to end. I could see that perhaps they ended upon restart due to insufficient time to complete another model... but then why didn\'t it reach the same conclusion when model 1 completed back before I rebooted??

If you are curious, here are the messages from BOINC Manger upon restart

4/21/2008 1:29:56 PM|ralph@home|Restarting task mini_abinitio-1bk2_-test_2008-2-6_3310_73_0 using minirosetta version 113
4/21/2008 1:29:56 PM|ralph@home|Restarting task mini_abinitio-1bkrA-test_2008-2-6_3310_73_0 using minirosetta version 113
4/21/2008 1:30:51 PM|ralph@home|Computation for task mini_abinitio-1bk2_-test_2008-2-6_3310_73_0 finished
4/21/2008 1:30:51 PM|ralph@home|Starting mini_abinitio-1tif_-test_2008-2-6_3310_72_0
4/21/2008 1:30:51 PM|ralph@home|Starting task mini_abinitio-1tif_-test_2008-2-6_3310_72_0 using minirosetta version 113
4/21/2008 1:30:58 PM|ralph@home|Computation for task mini_abinitio-1bkrA-test_2008-2-6_3310_73_0 finished

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Message 3943 - Posted: 21 Apr 2008, 21:16:36 UTC

Running Linux, Boinc 5.10.45 this WU failed.

mini_abinitio-1vie_-test_2008-2-6_3310_79_0
process exited with code 1 (0x1, -255)
ERROR: Cannot open file 1vie.pdb
ERROR:: Exit from: src/core/io/pdb/pose_io.cc line: 157
called boinc_finish

Have a nice day,
Path7.
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Thomas Leibold

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Message 3944 - Posted: 22 Apr 2008, 6:48:23 UTC - in response to Message 3943.  

Running Linux, Boinc 5.10.45 this WU failed.

Same error here: Workunit 826331
<core_client_version>5.10.45</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)
</message>
<stderr_txt>

ERROR: Cannot open file 1vie.pdb
ERROR:: Exit from: src/core/io/pdb/pose_io.cc line: 157
called boinc_finish

</stderr_txt>
]]>

However there is clearly progress since most minirosetta 1.13 are now succeeding on my two Ralph Linux servers.

Are those minirosetta workunits supposed to have graphics ? The \"Show Graphics\" button stays grayed out.
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