Mini Rosetta 3.45

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Mad_Max

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Message 74778 - Posted: 24 Dec 2012, 16:53:30 UTC
Last modified: 24 Dec 2012, 16:54:29 UTC

Many of CDPK_aa_... WUs in addition to gpaphics app and checkpoints problems fails at start with "ERROR: unrecognized atom_type_name COO" error.
Examples (from 3 different computers):

CDPK_aa_PfCDPK4_3IGOA_SAVE_ALL_OUT_IGNORE_THE_REST_69298_33_0

CDPK_aa_CpCDPK1_3UPXA_SAVE_ALL_OUT_IGNORE_THE_REST_69197_36_0

CDPK_aa_CpCDPK1_3IGOA_SAVE_ALL_OUT_IGNORE_THE_REST_69178_250_0

CDPK_aa_TgCDPK1_3UPXA_SAVE_ALL_OUT_IGNORE_THE_REST_69407_139_1
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Message 74785 - Posted: 26 Dec 2012, 1:52:18 UTC

This one failed after 3sec, not for the first time.


CDPK_aa_TgCDPK1_C77Y_3V51A_SAVE_ALL_OUT_IGNORE_THE_REST_69353_111_1

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=501624408


Unpacking zip data: ../../projects/boinc.bakerlab.org_rosetta/minirosetta_database_rev52077.zip
Unpacking WU data ...
Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/input_CDPK_aa_TgCDPK1_C77Y_3V51A_yfsong.zip
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
BOINC:: Worker startup.
Starting watchdog...
Watchdog active.

ERROR: unrecognized atom_type_name Cl
ERROR:: Exit from: src/core/chemical/AtomTypeSet.hh line: 110
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

</stderr_txt>


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Message 74793 - Posted: 27 Dec 2012, 4:55:21 UTC

Another one failed after 4sec.

CDPK_aa_EtCDPK_3K21A_SAVE_ALL_OUT_IGNORE_THE_REST_69215_126_1

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=501637340


Initialization complete.
Setting WU description ...
Unpacking zip data: ../../projects/boinc.bakerlab.org_rosetta/minirosetta_database_rev52077.zip
Unpacking WU data ...
Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/input_CDPK_aa_EtCDPK_3K21A_yfsong.zip
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
BOINC:: Worker startup.
Starting watchdog...
Watchdog active.

ERROR: unrecognized atom_type_name COO
ERROR:: Exit from: src/core/chemical/AtomTypeSet.hh line: 110
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

</stderr_txt>

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m_vw

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Message 74821 - Posted: 2 Jan 2013, 9:07:13 UTC

I just deleted 3 units that where restarting everytime I rebooted my pc....
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Profile [VENETO] boboviz

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Message 74833 - Posted: 3 Jan 2013, 13:10:35 UTC

I hope these problems will be fixed with a new version.
And, please, test it LARGELY on Ralph, before putting them on Rosetta!
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Message 74836 - Posted: 4 Jan 2013, 6:53:02 UTC

These buggy tasks are back, giving validate errors.

lr_ab_bench_3pu6A_SAVE_ALL_OUT_IGNORE_THE_REST_58289_526_0

# cpu_run_time_pref: 21600
======================================================
DONE :: 1 starting structures 1201 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
BOINC :: WS_max 0

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

</stderr_txt>
]]>

Validate state Invalid

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Message 74863 - Posted: 8 Jan 2013, 6:59:31 UTC

Had two of these fail after about 30min, with same type of error.


TOR_aa_hybrid_

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=504112775

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=504097935

# cpu_run_time_pref: 21600
SIGSEGV: segmentation violation
Stack trace (15 frames):
[0xafed447]
[0xf778b400]
[0xa9ef725]
[0xaa5e0b0]
[0x88f5846]
[0x88feb1d]
[0x866dce3]
[0x97b619f]
[0x97bde49]
[0x9979352]
[0x99d8ed5]
[0x99d6705]
[0x80547cc]
[0xb07d7e8]
[0x8048131]

Exiting...

</stderr_txt>
]]>

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Mad_Max

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Message 74872 - Posted: 9 Jan 2013, 19:12:49 UTC

In all TOR_aa_hybrid_ WUs graphics app (or screesaver app) not working too.
Same as on CDPK_aa_ and endo_aa_ WUs.
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Profile [VENETO] boboviz

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Message 74878 - Posted: 10 Jan 2013, 15:59:28 UTC - in response to Message 74872.  

In all TOR_aa_hybrid_ WUs graphics app (or screesaver app) not working too.


Same here!
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Profile [VENETO] boboviz

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Message 74894 - Posted: 15 Jan 2013, 10:38:02 UTC - in response to Message 74872.  

In all TOR_aa_hybrid_ WUs graphics app (or screesaver app) not working too.
Same as on CDPK_aa_ and endo_aa_ WUs.


Same on CDPK_ab_hybrid_ wus (and problems with checkpoint)

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Profile [VENETO] boboviz

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Message 74897 - Posted: 15 Jan 2013, 17:08:13 UTC

Errors on 556368688 and 556368687

ERROR: unrecognized atom_type_name S
ERROR:: Exit from: C:Usersboincsrcrosetta_sourcesrccore/chemical/AtomTypeSet.hh line: 110
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish
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Profile Greg_BE
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Message 74901 - Posted: 15 Jan 2013, 22:20:32 UTC - in response to Message 74897.  

Errors on 556368688 and 556368687

ERROR: unrecognized atom_type_name S
ERROR:: Exit from: C:Usersboincsrcrosetta_sourcesrccore/chemical/AtomTypeSet.hh line: 110
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish



Same here on all 3 tasks of this type
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frederick corse

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Message 74903 - Posted: 16 Jan 2013, 0:04:35 UTC
Last modified: 16 Jan 2013, 0:05:10 UTC

HELLO I GOT SOME CDPK_ab_hybrid__35575.3mwua.rm-1-101_001
CDPk.ab.hybrid_35577.3mwua.rm-1-101-001
CDPK.ab.hybrid/.3557.3mwua.rm-1-121-0271

they fail at startup same failures as the others . Got another one CDPK_ab_hybrid_35584.3mwua.1245 it ran successful with 2 decoys
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TJ

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Message 74904 - Posted: 16 Jan 2013, 0:08:13 UTC

Indeed all the CDPK_ab_hybrid's I got today are all error out, computation error.
When hitting the "Show graphics" button, a black window appears and disappears immediately again.


Greetings,
TJ.
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Message 74906 - Posted: 16 Jan 2013, 5:30:59 UTC

This failed after 3sec.

CDPK_ab_hybrid_35577.3MWUA.1219_0049_SAVE_ALL_OUT_IGNORE_THE_REST_71159_107_1

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=505597218


Setting WU description ...
Unpacking zip data: ../../projects/boinc.bakerlab.org_rosetta/minirosetta_database_rev52077.zip
Unpacking WU data ...
Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/input_CDPK_ab_hybrid_35577.3MWUA.1219_0049_yfsong.zip
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
BOINC:: Worker startup.
Starting watchdog...
Watchdog active.

ERROR: unrecognized atom_type_name F
ERROR:: Exit from: src/core/chemical/AtomTypeSet.hh line: 110
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

</stderr_txt>
]]>

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frederick corse

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Message 74932 - Posted: 19 Jan 2013, 6:12:41 UTC

Hello



I got 10 rb_01_18_36313_68791 three of them started up and they failed with

error:atom tree:torsion_angle_dof_id_angle range error for message
_
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Message 74975 - Posted: 25 Jan 2013, 7:23:48 UTC

This failed big time after over 10hrs running, this is just some of it the error goes on for pages please fix/check these tasks before releasing them.

rant// I for one am going to abort all of these i get from now on, not going to waste cpu time on them. //end.

thanks.

hyb_ba_bench_02_3slkB_SAVE_ALL_OUT_IGNORE_THE_REST_72022_836_0

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=507038971

Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
BOINC:: Worker startup.
Starting watchdog...
Watchdog active.
# cpu_run_time_pref: 21600
BOINC:: CPU time: 36267.6s, 14400s + 21600s[2013- 1-25 17:59: 7:] :: BOINC
WARNING! cannot get file size for default.out.gz: could not open file.
Output exists: default.out.gz Size: -1
InternalDecoyCount: 0 (GZ)
-----
0
-----
Stream information inconsistent.
Writing W_0000001
======================================================
DONE :: 1 starting structures 36267.6 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================
called boinc_finish
*** glibc detected *** ../../projects/boinc.bakerlab.org_rosetta/minirosetta_3.45_x86_64-pc-linux-gnu: double free or corruption (out): 0xcbd00018 ***
======= Backtrace: =========

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Profile [VENETO] boboviz

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Message 74978 - Posted: 25 Jan 2013, 14:29:24 UTC - in response to Message 74975.  
Last modified: 25 Jan 2013, 15:16:09 UTC

hyb_ba_bench_02_3slkB_SAVE_ALL_OUT_IGNORE_THE_REST_72022_836_0


hyb_ba_ wus are nightmares!
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Profile [VENETO] boboviz

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Message 74979 - Posted: 25 Jan 2013, 15:16:52 UTC

558342604

ERROR: unrecognized atom_type_name S
ERROR:: Exit from: C:Usersboincsrcrosetta_sourcesrccore/chemical/AtomTypeSet.hh line: 110
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish
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Profile dcdc

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Message 74989 - Posted: 26 Jan 2013, 20:00:17 UTC
Last modified: 26 Jan 2013, 20:00:54 UTC

Hi All

Has everyone seen the post by David Kim requesting debug information regarding the apparent nVidia bug here?:

https://boinc.bakerlab.org/rosetta/forum_thread.php?id=6177&nowrap=true#74982

Danny
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Message boards : Number crunching : Mini Rosetta 3.45



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