Bug Reports for Minirosetta version 1.34

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James Thompson
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Message 4193 - Posted: 7 Sep 2008, 21:55:33 UTC

Please post issues/bugs relating to minirosetta version 1.34 here. Version 1.34 is an attempt to fix several issues from the 1.33 release.

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Jipsu

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Message 4194 - Posted: 8 Sep 2008, 9:12:19 UTC
Last modified: 8 Sep 2008, 9:13:39 UTC

<core_client_version>5.10.45</core_client_version>
<![CDATA[
<stderr_txt>
**********************************************************************
Rosetta is going too long. Watchdog is ending the run!
CPU time: 11060.8 seconds. Greater than 3X preferred time: 3600 seconds
**********************************************************************
called boinc_finish

ERROR: unknown atom_name: ASN
ERROR:: Exit from: src/core/chemical/ResidueType.hh line: 928
called boinc_finish

</stderr_txt>
]]>

http://ralph.bakerlab.org/result.php?resultid=1082964



<core_client_version>5.10.45</core_client_version>
<![CDATA[
<stderr_txt>
**********************************************************************
Rosetta is going too long. Watchdog is ending the run!
CPU time: 14322.2 seconds. Greater than 3X preferred time: 3600 seconds
**********************************************************************
called boinc_finish

</stderr_txt>
]]>

http://ralph.bakerlab.org/result.php?resultid=1083365

Both computers are running linux btw. :)
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Profile Conan
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Message 4195 - Posted: 8 Sep 2008, 12:34:42 UTC

I too have a WU that is at 98% after 8 hours 20 min with 9 min still to go.
Not stuck but as my preferences are set to 6 hours this one is going too long.
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Message 4196 - Posted: 9 Sep 2008, 11:37:45 UTC - in response to Message 4195.  

I too have a WU that is at 98% after 8 hours 20 min with 9 min still to go.
Not stuck but as my preferences are set to 6 hours this one is going too long.


It finally finished after 9.7 hours on a 6 hours preference.
See WU
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James
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Message 4197 - Posted: 10 Sep 2008, 8:50:07 UTC

Based on these test, we\'ve identified an issue with on of our protocols taking an unacceptable amount of time to produce a single model, especially for larger proteins. In the next release of the minirosetta application, we\'re going to put an upper limit on the number of cycles that this protocol can execute so that your workunit time limits aren\'t exceeded in the future.

Thanks for crunching! I\'m going to try and write up something tomorrow about the new scientific improvements we\'re testing with this latest version of minirosetta.
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James
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Message 4198 - Posted: 10 Sep 2008, 8:52:12 UTC
Last modified: 10 Sep 2008, 22:19:56 UTC

Based on these tests, we\'ve identified an issue with on of our protocols taking an unacceptable amount of time to produce a single model, especially for larger proteins. In the next release of the minirosetta application, we\'re going to put an upper limit on the number of cycles that this protocol can execute so that your workunit time limits aren\'t exceeded in the future.

Thanks for crunching! I\'m going to try and write up something tomorrow about the new scientific improvements we\'re testing with this latest version of minirosetta.
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Tonno

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Message 4199 - Posted: 10 Sep 2008, 9:29:48 UTC - in response to Message 4198.  

This WU ended after 1 second:

<core_client_version>6.2.18</core_client_version>
<![CDATA[
<message>
Funzione non corretta. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>

ERROR: unrecognized aa HOH
ERROR:: Exit from: ..\\..\\src\\core\\io\\pdb\\file_data.cc line: 468
called boinc_finish

</stderr_txt>
]]>


I\'m going to try and write up something tomorrow about the new scientific improvements we\'re testing with this latest version of minirosetta.

Thanks, we are always happy to now about scientific improvements. :)
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Pepo
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Message 4200 - Posted: 11 Sep 2008, 9:31:42 UTC

Similarly like mentioned in the Bug Reports for Minirosetta version 1.33 thread, my task fa_dis7-t313_-2008-9-4_4786_8_1 prematurely exited, after 5 sec runtime (Linux host, stock BCC 6.2.4):

<core_client_version>6.2.4</core_client_version>
process exited with code 1 (0x1, -255)

ERROR: Cannot open file /work/tex/projects/cm/benchmark/targets/t313_/native/T0313.pdb
ERROR:: Exit from: src/core/io/pdb/pose_io.cc line: 161
called boinc_finish


James Thompson mentioned that 1.34 should fix this error, apparently it did not (or it was not exactly the same error).

My wingman processed this WU with minirosetta 1.33 and failed with \"Maximum CPU time exceeded\", the result was reported just yesterday. As this WU is already older, actually from before this note \"...I sent out a batch with options for minirosetta version 1.32 rather than version 1.33. The offending workunits have been removed from the queue...\", I wonder whether the WU was left on the system by accident and survived the deletion.

Peter
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Message 4201 - Posted: 11 Sep 2008, 9:52:33 UTC

This didn\'t cause a failure, but it was unusual:

<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
======================================================
DONE :: 1 starting structures 3254.23 cpu seconds
This process generated 3 decoys from 3 attempts
======================================================

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

</stderr_txt>
]]>

==Mike
Don't believe everything you think.
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Message 4203 - Posted: 17 Sep 2008, 12:06:56 UTC

hombench_mtyka_ralph_test1_foldcst_simple_t303___4839_2_0 prematurely exited, after 200 sec runtime (Windows XP host, own modified BCC 6.3.8):

Incorrect function. (0x1) - exit code 1 (0x1)
WARNING: Override of option -out:file:silent sets a different value

ERROR: unknown atom_name: PRO H
ERROR:: Exit from: c:\\cygwin\\home\\boinc\\boinc_build\\minirosetta\\minirosetta_1.34\\mini\\src\\core/chemical/ResidueType.hh line: 928
called boinc_finish


Peter
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Message 4204 - Posted: 22 Sep 2008, 4:17:27 UTC - in response to Message 4203.  

I got the same warning, but it finished normally:

<core_client_version>6.2.18</core_client_version>
<![CDATA[
<stderr_txt>
WARNING: Override of option -out:file:silent sets a different value
WARNING: Override of option -out:file:silent sets a different value
======================================================
DONE :: 1 starting structures 3817.05 cpu seconds
This process generated 6 decoys from 6 attempts
======================================================

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

</stderr_txt>
]]>

==Mike
Don't believe everything you think.
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Message 4205 - Posted: 22 Sep 2008, 12:01:45 UTC

I recieved a similar error message, on this WU

CPU time 20248.67
stderr out

<core_client_version>5.10.21</core_client_version>
<![CDATA[
<stderr_txt>
WARNING: Override of option -out:file:silent sets a different value
WARNING: Override of option -out:file:silent sets a different value
# cpu_run_time_pref: 21600
======================================================
DONE :: 1 starting structures 20248.2 cpu seconds
This process generated 6 decoys from 6 attempts
======================================================

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

</stderr_txt>
<message>
<file_xfer_error>
<file_name>hombench_mtyka_looprelax_test_full_2_looprelax_t326__IGNORE_THE_REST_1S1MA_7_4951_1_0_0</file_name>
<error_code>-161</error_code>
</file_xfer_error>
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Path7

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Message 4207 - Posted: 23 Sep 2008, 21:45:17 UTC

Hello all,

I had a long running WU:
hombench_mtyka_looprelax_test_full_2_looprelax_t326__IGNORE_THE_REST_1HFJA_15_4951_1_0

After 5 hours of Processor Time I switched my computer off. Switching it on let the WU start at about 1 hour.

Runtime: 26778.01 seconds (7.4 hours), preferred runtime: 7200 seconds (2 hours).

Message:Rosetta is going too long. Watchdog is ending the run!
CPU time: 26776 seconds. Greater than 3X preferred time: 7200 seconds

Surprisingly the outcome is Success and 80 credits were granted.

Have a nice day,
Path7.
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Message 4208 - Posted: 24 Sep 2008, 2:03:12 UTC

hombench_mtyka_looprelax_test_full_2_looprelax_t326__IGNORE_THE_REST_1Q7RA_4_4951_1_0 using minirosetta version 134
has been running 16hrs, and still only on model 2. I have a 24hr runtime preference, but this is way too long for 2 models.
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Evan

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Message 4209 - Posted: 24 Sep 2008, 12:33:37 UTC

compute error with this one
http://ralph.bakerlab.org/result.php?resultid=1098367
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Message 4210 - Posted: 24 Sep 2008, 21:22:31 UTC

\'Client error\' failure on WU 1098636

<core_client_version>6.2.18</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
Loops::add_loop error -- bad loop definition
begin/cut/end: 134/133/0
ERROR:: Exit from: ..\\..\\src\\protocols\\loops\\LoopClass.cc line: 169
called boinc_finish

</stderr_txt>
]]>

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Message 4211 - Posted: 24 Sep 2008, 21:44:14 UTC

And again on WU 1098676
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Evan

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Message 4212 - Posted: 24 Sep 2008, 22:21:38 UTC

compute failures for
1099605 (also failed on 2nd computer)
1099603
1099596
973721
1098390
1098367 (passed on 2nd computer)
1098343
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Message 4213 - Posted: 25 Sep 2008, 12:09:16 UTC

A few more \'Computation Errors\'

1098726
1098736
1098770
1098778
1098779
1098780
1098781
1098797
1098798
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Pieface

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Message 4214 - Posted: 25 Sep 2008, 13:27:10 UTC

This one died with an Access Violation:

1098475

core_client_version>6.2.18</core_client_version>
<![CDATA[
<message>
- exit code -1073741819 (0xc0000005)
</message>
<stderr_txt>
# cpu_run_time_pref: 86400
# cpu_run_time_pref: 86400
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