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Minirosetta 3.48

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Message boards : Number crunching : Minirosetta 3.48

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David E K Profile
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Joined: Jul 1 05
Posts: 942
ID: 14
Credit: 2,303,046
RAC: 485
Message 76117 - Posted 10 Oct 2013 23:39:29 UTC

Minirosetta has been updated to version 3.48. This update includes a number of bug fixes in our hybridize protocol, a new rotamer based centroid fragment sampling protocol, and also an improved energy function. Please post issues/bugs here.

Killersocke@rosetta

Joined: Nov 13 06
Posts: 20
ID: 129065
Credit: 652,476
RAC: 1,935
Message 76141 - Posted 21 Oct 2013 23:22:32 UTC

Calculation Error in File
21.10.2013 20:54:56 | rosetta@home | Output file endo_ae__Soc368.015_SAVE_ALL_OUT_IGNORE_THE_REST_95920_691_0_0 for task endo_ae__Soc368.015_SAVE_ALL_OUT_IGNORE_THE_REST_95920_691_0 absent

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[VENETO] boboviz Profile

Joined: Dec 1 05
Posts: 545
ID: 25524
Credit: 1,510,213
RAC: 1,277
Message 76151 - Posted 25 Oct 2013 19:06:30 UTC

Now "endo_ac" screensaver is ok!! :-)
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[VENETO] boboviz Profile

Joined: Dec 1 05
Posts: 545
ID: 25524
Credit: 1,510,213
RAC: 1,277
Message 76172 - Posted 6 Nov 2013 8:36:20 UTC

This new version seems to be very stable.
News about scientific side of the app? Run ok?
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Greg_BE Profile
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Joined: May 30 06
Posts: 4835
ID: 85645
Credit: 2,948,921
RAC: 243
Message 76200 - Posted 21 Nov 2013 3:03:24 UTC

Task ID 616996009
Name r769_nohelix1_1LW-6HA-3LX-11HA-2LX_0016_0319_0044_0001_1221_fold_SAVE_ALL_OUT_104983_5591_0

http://boinc.bakerlab.org/result.php?resultid=616996009


This task died before it had a chance to start.

<core_client_version>7.2.28</core_client_version>
<![CDATA[
<message>
Maximum elapsed time exceeded
</message>

No firewall messages as the partition for all Boinc programs is excluded.
So something is buggy in the software.

Tom Zolotor Profile

Joined: Apr 28 11
Posts: 11
ID: 417981
Credit: 229,688
RAC: 0
Message 76210 - Posted 23 Nov 2013 17:25:35 UTC

Rosetta keeps stopping doing work every few seconds. Plz, fix this since the update.

Tom Zolotor
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dcdc Profile

Joined: Nov 3 05
Posts: 1596
ID: 8948
Credit: 33,801,861
RAC: 17,327
Message 76211 - Posted 23 Nov 2013 17:40:00 UTC - in response to Message ID 76210.

Rosetta keeps stopping doing work every few seconds. Plz, fix this since the update.

Tom Zolotor

Are you sure the problem started when Rosetta was updated at the start of October?

Do you have BOINC set to do work when the computer is in use, or have you unchecked "leave applications in memory when suspended"?

I doubt it's a BOINC issue, but 7.2.28 is the stable version so you could try updating to that too.

D
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Sid Celery

Joined: Feb 11 08
Posts: 796
ID: 241409
Credit: 9,545,746
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Message 76291 - Posted 16 Dec 2013 0:41:52 UTC

I don't usually post complaints about credit scores, but this particular one seems different to others:

31_input_0001_no_lig_fragments_fold_SAVE_ALL_OUT_108256_3302_0

======================================================
DONE :: 1 starting structures 28555.7 cpu seconds
This process generated 24 decoys from 24 attempts
======================================================

This part's fine, but another one comes up later:

======================================================
DONE :: 1 starting structures 28237 cpu seconds
This process generated 1 decoys from 1 attempts
======================================================

Then

Validate state Valid
Claimed credit 180.538587796693
Granted credit 6.80219874455716
application version 3.48

It seems to have only awarded for the later 1 decoy and not for the earlier 24 decoys.

I can't say if there was some interruption in the job run, but it starts initialising "2013-12-11 9:23:19" and then second time around "2013-12-15 5:51: 9".

I did return from a few days away to find my system had hung and needing a reboot, but don't get why it seemed to report fully the first time round, then run and report a second time. Any ideas?
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cnick6

Joined: May 30 06
Posts: 24
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Credit: 4,992,991
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Message 76300 - Posted 19 Dec 2013 19:10:00 UTC

Crash dump with this result: http://boinc.bakerlab.org/rosetta/result.php?resultid=624166808
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[VENETO] boboviz Profile

Joined: Dec 1 05
Posts: 545
ID: 25524
Credit: 1,510,213
RAC: 1,277
Message 76318 - Posted 1 Jan 2014 9:49:18 UTC

627055893
This wu restart every 20/30 seconds and, at the end, this error:

ERROR: Cannot open PDB file "y042.pdb.gz"
ERROR:: Exit from: ..\..\..\src\core\import_pose\import_pose.cc line: 218
[2013-12-31 18:35:12:] :: BOINC:: Initializing ... ok.
[2013-12-31 18:35:12:] :: BOINC :: boinc_init()
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cnick6

Joined: May 30 06
Posts: 24
ID: 85398
Credit: 4,992,991
RAC: 5,962
Message 76375 - Posted 21 Jan 2014 22:21:27 UTC

Another crash:

http://boinc.bakerlab.org/result.php?resultid=631776446

Do you guys care about these? I'm seeing a few assertions with my results as well...
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[VENETO] boboviz Profile

Joined: Dec 1 05
Posts: 545
ID: 25524
Credit: 1,510,213
RAC: 1,277
Message 76423 - Posted 12 Feb 2014 20:47:04 UTC

638287613
638287644

Loaded options.... ok
Processed options.... ok
Initializing random generators... ok
Initialization complete.
Setting WU description ...
Unpacking zip data: ../../projects/boinc.bakerlab.org_rosetta/minirosetta_database_b14204d.zip
Unpacking WU data ...
Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/input_V1_dock4_S_00001_0000895_0_0001.AB_DkTx_part1.model3.re_chain_060_yfsong.zip
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
BOINC:: Worker startup.
Starting watchdog...
Watchdog active.
error - tag names do not match! (Possibly due to unclosed tag.) stage2 != ddg_score
# cpu_run_time_pref: 7200

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P . P . L .
Avatar

Joined: Aug 20 06
Posts: 581
ID: 105843
Credit: 4,864,105
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Message 76427 - Posted 14 Feb 2014 6:34:36 UTC

Getting a lot of these tasks erring out with the same error.

V1_dock4_S_00001_0000525_0_0001.AB_DkTx_part1.model2.re_chain_180_SAVE_ALL_OUT_IGNORE_THE_REST_138660_2_1


error - tag names do not match! (Possibly due to unclosed tag.) stage2 != ddg_score

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svincent

Joined: Dec 30 05
Posts: 202
ID: 44923
Credit: 4,102,500
RAC: 5,735
Message 76435 - Posted 16 Feb 2014 17:53:46 UTC

Task 638918818 (ActCys_native_1iu8_idealize_y008_010_141286_3_0) failed

Watchdog active.
Starting work on structure: _00001

ERROR: [ERROR] invalid kill type for kill_hairpins. ANTI or PARA, is required.
ERROR:: Exit from: src/core/scoring/SS_Killhairpins_Info.cc line: 379
std::cerr: Exception was thrown:


[ERROR] EXCN_utility_exit has been thrown from: src/core/scoring/SS_Killhairpins_Info.cc line: 379
ERROR: [ERROR] invalid kill type for kill_hairpins. ANTI or PARA, is required.


</stderr_txt>
]]>

Jesse Viviano

Joined: Jan 14 10
Posts: 39
ID: 366696
Credit: 447,858
RAC: 912
Message 76500 - Posted 2 Mar 2014 3:25:07 UTC

Work unit 583729340 crashed on both computers it ran on including mine. It was running Minirosetta 3.48 on both computers.

Message boards : Number crunching : Minirosetta 3.48


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